Nature [周日, 15 9月 2019]
Author: calibre
Date: 2019-09-15T14:29:55.253000+00:00
Description: 本期文章: Take action to stop the Amazon burning Set citation data free Look out for potential bias in chemical data sets Tackle the epidemic, not the opioids Zip-lining owls reveal what really scares their prey The crop that’s gobbling up a vast Brazilian ecosystem How a cheap mineral could make a better battery — and help the planet ‘Extreme inbreeding’ revealed by massive human-genome survey The mystery of the missing mountain snow A peculiar atom shakes up assumptions of nuclear structure A dog’s breed is a window onto its brain Lost Moon craft, e-cigarette deaths and Iran’s nuclear activity D

[周日, 15 9月 2019]

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This Week

- Take action to stop the Amazon burning [10 September 2019]

Editorial • The planet’s largest rainforest is on fire. Brazil and the world must halt the destruction before it’s too late.

- Set citation data free [11 September 2019]

Editorial • Respondents to a Nature poll want to make their own decisions about how to interpret citation metrics. That requires data to be freely accessible.

- Look out for potential bias in chemical data sets [11 September 2019]

Editorial • Materials science has embraced machine learning. As with other disciplines, researchers must be alert to the risks of biased data.

- Tackle the epidemic, not the opioids [09 September 2019]

World View • Unless attention turns to what leads to addiction and overdose, treatment will always be out of date, says Judith Feinberg.

- Zip-lining owls reveal what really scares their prey [02 September 2019]

Research Highlight • The light of a full moon gives white barn owls a deadly glow.

- The crop that’s gobbling up a vast Brazilian ecosystem [03 September 2019]

Research Highlight • But all is not lost: targeted soya-bean planting could help to preserve the country’s species-rich savanna.

- How a cheap mineral could make a better battery — and help the planet [06 September 2019]

Research Highlight • Calcium could replace lithium in batteries that store solar and wind power.

- ‘Extreme inbreeding’ revealed by massive human-genome survey [06 September 2019]

Research Highlight • Analysis suggests that roughly one in 3,600 people studied were born to closely related parents.

- The mystery of the missing mountain snow [04 September 2019]

Research Highlight • Global data sets don’t accurately capture the size of mountain snowpack, a crucial water resource.

- A peculiar atom shakes up assumptions of nuclear structure [06 September 2019]

Research Highlight • Lopsided potassium isotope survives longer than predicted by theory.

- A dog’s breed is a window onto its brain [02 September 2019]

Research Highlight • Brain anatomy reflects the activities — such as hunting — for which a breed is known.

- Lost Moon craft, e-cigarette deaths and Iran’s nuclear activity [11 September 2019]

Seven Days • The week in science: 6–12 September 2019.

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EDITORIAL

10 September 2019

Take action to stop the Amazon burning

The planet’s largest rainforest is on fire. Brazil and the world must halt the destruction before it’s too late.

Environmental protesters in Rio de Janeiro, Brazil. The attention of world leaders on the Amazon is welcome, but their response is “a drop in the bucket”.Credit: Bruna Prado/Getty

Less than a decade ago, Brazil was an environmental leader. Its government had elevated forest conservation and sustainable development to national policy and then, with the help of satellite imagery, it had cracked down on illegal deforestation across the world’s largest tropical rainforest. Deforestation in the Amazon plummeted even as agricultural production — the biggest driver of forest loss — increased. Now, that progress is going up in smoke.

Data from Brazil’s National Institute for Space Research (INPE) showing a sharp uptick in the number of fires in the Amazon this year triggered headlines around the globe. Landowners use fire to clear forest illegally to make way for crops and cattle grazing, but Brazil’s populist president, Jair Bolsonaro, has effectively fanned the flames with his anti-environmentalist agenda since taking office in January. Scientists who live and work in the region were not surprised at what is happening, but INPE’s report sparked concerns in world capitals just as leaders of the G7 group of countries with the world’s biggest economies gathered for their annual summit in Biarritz, France.

Neither extinguishing the flames nor solving the underlying problem of deforestation will be easy. It doesn’t help that Bolsonaro is among those world leaders questioning whether an environmental agenda can deliver long-promised economic benefits. His development-at-any-cost policies hark back to an earlier era in which deforestation was treated as a measure of progress.

He has railed against regulation, cut the budget of Brazil’s environmental enforcement agency and advocated mining on lands belonging to Indigenous people. When news of the fires spread, Bolsonaro accused environmental groups of setting blazes to make him look bad. When G7 leaders pledged emergency funding to help put the fires out, he called it colonialism.

More efforts needed

The attention of world leaders on the Amazon is welcome, but their response is insufficient to deal with the scale of the crisis. The G7’s offer of US$22 million, initially rebuffed by Bolsonaro, seemed rushed. This sum would hardly fight the fires, let alone address the underlying problems. In the words of the former UN climate-secretariat chief Christiana Figueres, it was “a drop in the bucket”. On 6 September, at a forest-conservation summit convened by Brazil, seven Amazon countries pledged to work together — but provided few details on what they would actually do.

Paradoxically, there is already a large pot of money dedicated to tropical-forest conservation in Brazil. This is the Amazon Fund, established by Brazil in 2008 to attract international donations for conservation efforts. Since the fund’s inception, Norway has invested the lion’s share of the almost $1.3-billion total, while Germany has contributed another $68 million and Brazil’s national oil company, Petrobras of Rio de Janeiro, nearly $8 million. The funds have been used to pay for everything from research and land-use planning to law enforcement. But these investments were contingent on the government curbing deforestation, and both Germany and Norway have now suspended payments.

This decision is unlikely to change unless there is a shift in the Bolsonaro government’s priorities, but European Union countries could have some extra leverage. The EU has negotiated a trade agreement with several South American states, including Brazil. France and Ireland have threatened to refuse to ratify the deal — limiting Brazil’s exports of beef and soya to the EU — unless Bolsonaro changes his approach to the Amazon. Brazil’s agri-businesses are concerned about these developments. That gives them an opportunity to persuade Bolsonaro to re-engage with Europe over the Amazon if not doing so means that the interests of the country’s agricultural producers are on the line.

Fifteen years ago, many people assumed that the Brazilian government had little control or influence over illegal deforestation in the Amazon. We now know that is not true. Between 2004 and 2012, Brazil was able to curb deforestation by more than 80% while almost eliminating industrial-scale land-clearing.

The Amazon rainforest is a reservoir of biodiversity and carbon, which is locked up in trees and soils. Clearing and burning the forest to make way for agriculture destroys the former and sends the latter into the atmosphere, contributing to global warming. Brazil rightly claims sovereignty over its territory, but the forest is a global good, just as the soya beans and beef produced by farmers and ranchers there are global commodities. The responsibility for what happens on Brazil’s turf extends well beyond its borders.

Nature 573, 163 (2019)

doi: 10.1038/d41586-019-02615-3

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02615-3

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EDITORIAL

11 September 2019

Set citation data free

Respondents to a Nature poll want to make their own decisions about how to interpret citation metrics. That requires data to be freely accessible.

For many papers, citation data are locked inside proprietary databases.Credit: iLexx/Getty

Whenever scientists are ranked and rewarded by metrics, such as citations, some are tempted to grab a little extra credit where they can. As we report this week, the publisher Elsevier has been investigating cases in which reviewers have repeatedly asked authors of papers to cite the reviewers’ own work.

This is not an isolated incident. Last month, we reported that some 250 highly cited scientists had amassed more than half of their citations from their own work or that of co-authors — much more than the usual proportion for their field or career stage (see Nature 572, 578–579; 2019).

Such examples should not come as a surprise, because the gaming of measurement systems is well known. In economics it is called Goodhart’s law, named after the economist Charles Goodhart, who described the concept. It was refined by the anthropologist Marilyn Strathern, and states that when a measure becomes a target, it ceases to be a good measure.

One obvious answer is for institutions and funders to just stop using citation-based metrics as a proxy for importance or quality when assessing researchers. “Stop the damn bean-counting!” one reader exclaimed in response to an online poll in Nature last month, in which we asked what — if anything — needed to be done to curb excessive self-citation. Metrics-based analysis can certainly reveal useful insights about research. But any assessment procedure that rewards scientists according to citation-based metrics alone seems designed to invite game-playing.

It can also be argued that, all things considered, excessive self-citation is a minor problem and therefore doesn’t need a particular response. Of the more than 5,000 readers who answered Nature’s poll, 10% said nothing needed to be done. “Let active researchers draw their own conclusions about self-citing researchers, and allow reputation to build naturally,” one respondent wrote.

However, most poll respondents felt that citation-based indicators are useful, but that they should be deployed in more nuanced and open ways. The most popular responses to the poll were that citation-based indicators should be tweaked to exclude self-citations, or that self-citation rates should be reported alongside other metrics (see ‘The numbers game’). On the whole, respondents wanted to be able to judge for themselves when self-citations might be appropriate, and when not; to be able to compare self-citation across fields; and more.

But this is where there is a real problem, because for many papers citation data are locked inside proprietary databases. Since 2000, more and more publishers have been depositing information about research-paper references with an organization called Crossref, the non-profit agency that registers digital object identifiers (DOIs), the strings of characters that identify papers on the web. But not all publishers allow their reference lists to be made open for anyone to download and analyse — only 59% of the almost 48 million articles deposited with Crossref currently have open references.

There is, however, a solution. Two years ago, the Initiative for Open Citations (I4OC) was established for the purpose of promoting open scholarly citation data. As of 1 September, more than 1,000 publishers were members, including Sage Publishing, Taylor and Francis, Wiley and Springer Nature — which joined last year. Publishers still to join I4OC include the American Chemical Society, Elsevier — the largest not to do so — and the IEEE.

Last January, I4OC co-founder David Shotton at the Oxford e-Research Centre, University of Oxford, UK, urged all research publishers to join the initiative (see Nature 553, 129; 2018). They should. Excessive self-citation cannot be eliminated, but free access to citation data for everyone — researchers and non-researchers — will help to illuminate some darker corners. Without more journals coming on board, these necessary efforts to analyse self-citation data will remain incomplete.

Nature 573, 163-164 (2019)

doi: 10.1038/d41586-019-02669-3

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02669-3

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EDITORIAL

11 September 2019

Look out for potential bias in chemical data sets

Materials science has embraced machine learning. As with other disciplines, researchers must be alert to the risks of biased data.

There might be disadvantages to using tried and trusted methods.Credit: Science Photo Library

Like most research fields, materials science has embraced ‘big data’, including machine-learning models and techniques. These are being used to predict new materials and properties, and devise routes to existing drugs and chemicals.

But machine learning requires training data, such as those on reagents, conditions and starting materials. These are usually gleaned from the literature, and are human-generated. The choice of reagents that researchers use could come, for example, from experience or from previously published work. It might be based on a recommendation passed from supervisor to graduate student, or simply on how easy reagents are to find or buy. But that subjectivity becomes a potential problem for the accuracy of machine-learning models, as research published this week in Nature shows.

Joshua Schrier at Fordham University in New York City, Alexander Norquist and Sorelle Friedler at Haverford College in Pennsylvania and their colleagues looked at materials called amine-templated vanadium borates. These were chosen because success and failure are easily defined in their synthesis — simply by whether or not crystals form. The researchers compiled a data set of several hundred synthetic conditions that are used to make vanadium borates. They then trained a machine-learning model on this data set to predict the success or failure of reactions. The team found that a model trained on a human-generated data set was less successful in predicting the success or failure of a reaction than one trained on a data set with randomly generated reaction conditions (X. Jia et al. Nature 573, 251–255; 2019).

In some sense, this should be no surprise. It is now well known that when machine-learning techniques are used to pick out patterns in aggregated data, biases in those data can be amplified. For example, facial-recognition algorithms trained mostly on white faces are less able to distinguish between the faces of people of other ethnicities, thereby introducing bias that could lead to entrenched inequality.

Does the existence of bias matter to chemistry and materials science? When the goal of a research project is to find new materials, it could be argued that it’s irrelevant which reagents are used as long as they work.

But there are potential drawbacks to relying on ‘tried and trusted’ methods. A prevalence of favourite protocols — even an unintentional one — in a training data set could hinder the success of machine-learning models that are used to predict materials. Or, as this study reveals, more efficient ways to make existing ones.

No one would argue that the consequences of biased chemical data are as serious as those of biases in facial-recognition software, but they share a similar origin. Researchers should be alert to the potential for bias in their chemical data sets, before it gets baked into a machine.

Nature 573, 164 (2019)

doi: 10.1038/d41586-019-02670-w

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02670-w

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WORLD VIEW

09 September 2019

Tackle the epidemic, not the opioids

Unless attention turns to what leads to addiction and overdose, treatment will always be out of date, says Judith Feinberg.

Judith Feinberg

Judith Feinberg is a professor of behavioural medicine, psychiatry and infectious diseases at West Virginia University in Morgantown.

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Of the estimated 70,000 deaths from drug overdose in the United States in 2017 — the most recent year for which finalized figures are available — more than two-thirds were caused by opioids, including prescription pain relievers, fentanyl and its analogues, and heroin. Since 2000, the US Congress has passed several bills to address this opioid epidemic, starting with the DATA 2000 legislation that allows more physicians to prescribe buprenorphine, an opioid derivative used to treat opioid addiction. Other initiatives have focused on expanding treatment options and strategies for pain control, as well as slowing the flow of illicit opioids from overseas. Two years ago next month, US President Donald Trump declared opioid addition a public-health emergency. Last year, federal research funding to control opioid misuse and manage pain reached US$1.1 billion.

All of these efforts have specifically targeted opioids. And that is part of the problem.

Historically, substance misuse has come in waves, with a new drug supplanting the previous one: the ‘heroin chic’ of the 1990s followed the ‘crack babies’ of the 1980s. By the time federal programmes target a specific drug, the issue is being attacked where it was, not where it is. Funding should be targeted to substance misuse, not to the drug du jour.

The current opioid epidemic is a symptom of the fraying of the socio-economic fabric of the rural United States. The epidemic arose in the 1990s in areas that had experienced economic decline, a brain drain and population loss over decades. Many factors combined to create a monstrous situation in which small towns were flooded with prescription opioids: the preponderance of injury-prone hard labour jobs, requirements that physicians routinely ask patients about pain, aggressive marketing by the pharmaceutical industry, greed and extensive job losses from the collapse of key rural industries such as coal mining.

By the time Congress moved to address the opioid epidemic, the pattern of drug use had started to shift. Once, those using multiple drugs combined opioids with alcohol and other drugs, such as anti-anxiety agents that act on the central nervous system. Where I work in central Appalachia (West Virginia, southern Ohio, eastern Kentucky and northeastern Tennessee), opioids are being rapidly supplanted or exacerbated by cheap, readily available, high-potency methamphetamine. When opioids are used, they are being increasingly combined with stimulants such as cocaine — which, like methamphetamine, is thought to help to counteract the depressant effect of opioids.

Federal grants come tagged for combating opioids and cannot be repurposed to deal with the rising incidence of methamphetamine misuse. The narrow focus on opioids means we cannot keep up with the drug du jour cycle: we will just keep playing whack-a-mole.

Curbing opioid addiction needs more than new drugs

Similar short-sightedness has kept us from addressing syndemics — epidemics that accompany the use of injection drugs. Although there has been some (but not enough) funding to slow the spread of HIV and hepatitis C among people who inject drugs, little attention has been paid to other potential conditions, such as endocarditis, a life-threatening infection of the heart. Injection-drug users are particularly susceptible, because needles puncturing unclean skin or delivering drugs prepared with unclean paraphernalia introduce bacteria directly into the bloodstream. West Virginia University’s flagship hospital in Morgantown now has a dedicated ward for these patients, some of whom require intensive care and heart surgery. In 2018, the hospital admitted 373 people for endocarditis (it was the primary diagnosis for 73 of these), with total costs exceeding $37 million; there were no signs of this trend slowing in the first half of 2019. This pattern is seen throughout the United States, yet the US Centers for Disease Control and Prevention has not made endocarditis a reportable illness, so does not track its incidence.

Even more neglected are efforts to understand why the rural United States is vulnerable. Why is attention focused on this drug or that drug, when the real question is why is there a raging epidemic of addiction?

In Kermit, West Virginia, a coalfield town with about 400 inhabitants, a local family-run pharmacy received 9 million pain pills in 2 years. The collapse of the coal industry in central Appalachia made the region particularly vulnerable. McDowell County, on West Virginia’s southern border, had a population of 100,000 in 1970, when coal was king. It now has 19,000 residents and a boarded-up Walmart store. Donations of used clothing, shoes and hotel-size toiletries sit on tables for the taking at the entrance to the county health department. Local officials tell me that half of the county’s children are in foster care. Life expectancy is falling, and the primary causes of death among rural middle-aged white men are overdose, suicide and liver disease. Our interviews with people who inject drugs in southern West Virginia reveal hopelessness, boredom and despair. Opioids ease the pain from years of crawling through mine tunnels and the harshness of everyday life. Perhaps the pertinent question isn’t why people turned to opioids, but why didn’t even more people take that path?

Without an effort to rebuild the social and economic fabric of rural communities, addiction will persist. That’s where the real problem lies, and as yet there are no serious attempts to address it. Our current approach to drug misuse means that we will always be playing catch-up and leaving vulnerable people behind.

Nature 573, 165 (2019)

doi: 10.1038/d41586-019-02671-9

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02671-9

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White barn owls, although relatively visible in the dark of night, are highly effective hunters thanks to the way light reflects off their feathers. Credit: Rolf Nussbaumer/NPL

Evolution

02 September 2019

Zip-lining owls reveal what really scares their prey

The light of a full moon gives white barn owls a deadly glow.

Taxidermied owls that barrelled down zip lines have helped scientists to understand how moonlight shaped the evolution of nocturnal animals.

The barn owl (Tyto alba) hunts at night, and ranges in colour from white to brownish-red. Alexandre Roulin at the University of Lausanne in Switzerland and his colleagues harnessed 20 years’ worth of observations of barn owls in Switzerland to track how plumage colouration and the phase of the Moon affect the owls’ hunting.

The team found that as the Moon brightened each month, red owls’ hunting success dipped, as did the amount of food — mostly voles — the owls supplied to their chicks. But white owls remained good providers all month long, and hunted best under a full moon.

To understand this variation, the researchers attached taxidermied owls to a zip line and flew the decoys at voles under artificial moonlight. Under ‘full moon’ conditions, the light that reflected off white owls’ plumage caused voles to freeze for an average of 5 seconds longer than did light bouncing off red owls, giving white owls a better chance of capturing their prey.

Nature Ecol. Evol. (2019)

- Evolution

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02605-5

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Neat rows of soya beans grow in the Cerrado, a Brazilian region where about half of soya farms have cleared more land than is legally allowed. Credit: Asuyoshi Chiba/AFP/Getty

Conservation biology

03 September 2019

The crop that’s gobbling up a vast Brazilian ecosystem

But all is not lost: targeted soya-bean planting could help to preserve the country’s species-rich savanna.

Soya-bean farming has destroyed enormous chunks of one of South America’s largest savannas — but an analysis of satellite data offers hope for this hotspot of biodiversity.

Brazil’s Cerrado is a vast tropical savanna covering some 200 million hectares, and is both a vital ecosystem and the nation’s breadbasket. Lisa Rausch at the University of Wisconsin–Madison and her colleagues combined imagery from multiple satellites to show that soya-bean fields replaced 22% of the native vegetation that was cleared in the Cerrado between 2003 and 2014. The data indicate that soya farms are five times more likely to contain illegally cleared land than are other types of property.

The researchers also identified roughly 23 million hectares of the Cerrado that have already been cleared of native vegetation and are suitable for growing soya beans. Policies that nudge soya farmers towards such surplus land could preserve the remaining native plants, the team says.

Conserv. Lett. (2019)

- Conservation biology

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02606-4

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Batteries in Ontario, California, store renewable energy for release when demand is high. The price of such systems could fall thanks to the development of an electrolyte for calcium-based batteries. Credit: Patrick T. Fallon/Bloomberg via Getty

Energy

06 September 2019

How a cheap mineral could make a better battery — and help the planet

Calcium could replace lithium in batteries that store solar and wind power.

A newly synthesized chemical could pave the way for the manufacture of calcium-based batteries, which might be safer and cheaper than today’s lithium-based models.

The lithium-ion batteries in mobile phones and other electronic devices have numerous drawbacks: they sometimes catch fire, and they depend on increasingly scarce and toxic substances such as lithium and cobalt.

Batteries with anodes made of calcium — a more abundant substance — might be more sustainable and safer than batteries with lithium anodes. But researchers working on calcium batteries have lacked a suitable electrolyte, the medium through which electrical charge flows inside a battery.

Zhirong Zhao-Karger at the Helmholtz Institute Ulm in Germany and her colleagues reacted a calcium compound with a fluorine-containing compound to create a new type of calcium salt. The resulting material conducted electricity more effectively than any calcium-based electrolyte yet reported. It also efficiently conducted ions at a higher voltage than other calcium-based electrolytes.

Calcium-based batteries could be used in industrial-scale systems to store wind and solar energy.

Energ. Environ. Sci. (2019)

- Energy

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02634-0

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According to Greek legend, the goddess Hera (right) had children with her brother Zeus (centre), providing a mythological example of extreme inbreeding. Credit: Kunsthistorisches Museum, Vienna/Bridgeman Images

Genomics

06 September 2019

‘Extreme inbreeding’ revealed by massive human-genome survey

Analysis suggests that roughly one in 3,600 people studied were born to closely related parents.

Genomic analysis has provided a new way of investigating a tricky topic: the prevalence of extreme inbreeding in humans.

Cultural and religious taboos around inbreeding make its frequency difficult to assess. Rather than relying on surveys, Loic Yengo and his colleagues at the University of Queensland in Brisbane, Australia, examined roughly 450,000 human genomes from a British biomedical database. By looking at thousands of single points in the genome, the researchers were able to identify any long stretches of DNA that were identical on both chromosomes in a pair, which are separately inherited from a person’s father and mother. These stretches indicate that the parents were closely related.

The researchers found that the genomes of one in 3,652 people born in the United Kingdom between 1938 and 1967 show extreme inbreeding, with the two sets of chromosomes sharing more than 10% of their DNA. This indicates unions between full siblings, a parent and a child, a grandparent and a grandchild, or other relatives with similar degrees of relatedness.

People whose genomes showed extreme inbreeding tended to be shorter, less muscular and have weaker cognitive abilities than average.

Nature Commun. (2019)

- Genomics

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02633-1

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Snow coats the Cascade Range in the United States. Modelling suggests that snowpack in the Cascades and other mountains has been underestimated. Credit: Ding Ying Xu/Alamy

Climate sciences

04 September 2019

The mystery of the missing mountain snow

Global data sets don’t accurately capture the size of mountain snowpack, a crucial water resource.

Scientists could be seriously underestimating the amount of snow stored atop mountains — an important source of water for people around the world.

Mountain snowpack is notoriously hard to calculate because satellites can’t measure snow depth. Melissa Wrzesien at the University of North Carolina in Chapel Hill and her colleagues studied four global data sets that quantify mountain snowpacks. The four data sets agree reasonably well with each other — but they do not agree with high-resolution simulations of snow across several North American mountain ranges, such as the Cascades.

The simulations suggest that 40–66% more snow is frozen in those mountains than scientists had realized. If that pattern holds true globally, then the data sets could be missing as much as 1,500 cubic kilometres of mountain snowpack.

If melted, that snow would supply an amount of water equivalent to 4% of that carried by the world’s rivers.

Water Resour. Res. (2019)

- Climate sciences

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02643-z

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Atomic nuclei (artist’s impression) contain both protons and neutrons. A newly reported isotope offers the hope of testing fundamental principles of nuclear structure. Credit: Mark Garlick/SPL

Atomic and molecular physics

06 September 2019

A peculiar atom shakes up assumptions of nuclear structure

Lopsided potassium isotope survives longer than predicted by theory.

Physicists have found an exotic variant of potassium that is much longer-lived than predicted — hinting at the existence of other more-extreme atoms that stretch the known limits of nuclear structure.

Isotopes are alternative forms of a single chemical element, each with the same number of protons but differing numbers of neutrons. If an isotope has too few neutrons, the nucleus can no longer hold itself together. Such an isotope is said to be ‘beyond the proton dripline’.

Daria Kostyleva at the GSI Helmholtz Centre for Heavy Ion Research in Darmstadt, Germany, and her colleagues formed a beam of argon atoms. The atoms exchanged protons and neutrons, creating potassium-31, which has 12 neutrons and 19 protons. It is four neutrons beyond the dripline — meaning that it is four neutrons short of being stable.

The team’s analysis showed that the half-life of potassium-31 is about five trillionths of a second, much longer than predicted for an isotope so far beyond the dripline. It might be possible to detect atoms that are as many as seven neutrons beyond the dripline, which could help researchers to test fundamental predictions of quantum physics, the authors write.

Phys. Rev. Lett. (2019)

- Atomic and molecular physics

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02655-9

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The Labrador Retriever (left) is known for its enthusiasm for fetching objects, whereas the Maltese (right) is sought for companionship. These characteristic roles are reflected in the breeds’ brain structures. Left: Ger Mai/Pixabay. Right: Seifen Blase/Pixabay

Neuroscience

02 September 2019

A dog’s breed is a window onto its brain

Brain anatomy reflects the activities — such as hunting — for which a breed is known.

For thousands of years, humans have bred dogs for traits such as slender bodies and sheep-herding abilities. Now it turns out that breeders have also shaped canines’ brains.

When Erin Hecht at Harvard University in Cambridge, Massachusetts, and her colleagues studied brain scans from 62 dogs across 33 breeds, they found that brain structures varied markedly between breeds. These differences did not relate solely to the dogs’ brain or body sizes, nor to their skull shapes; instead, particular variations were associated with specific activities, such as hunting by scent, or guarding.

The team also examined the brain areas that varied the most across breeds. That analysis identified six brain networks — each composed of multiple regions of the brain — that the researchers suspect are involved in tasks from social bonding to movement.

Variations in these brain networks were linked to specific breed characteristics: for example, brain regions involved in movement and navigation were bigger in dogs bred for coursing, such as Greyhounds, than in dogs bred for companionship, such as the Maltese.

J. Neurosci. (2019)

- Neuroscience

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02610-8

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SEVEN DAYS

11 September 2019

Lost Moon craft, e-cigarette deaths and Iran’s nuclear activity

The week in science: 6–12 September 2019.

SPACE

India loses contact with Moon craft India’s space agency lost contact with its Moon lander during the final few minutes of the craft’s descent early on 7 September, Indian time. The mission was the country’s first attempt to place a craft on the Moon. Mission control at the Indian Space Research Organization tweeted that the descent had gone as planned until the lander, called Vikram, reached 2.1 kilometres above the lunar surface. “Subsequently, communication from Lander to the ground stations was lost,” the tweet said. The Chandrayaan-2 orbiter later located Vikram using its cameras. Efforts to establish contact with the lander continue, said the agency’s chair, Kailasavadivoo Sivan.

The Indian space agency’s tracking and command centre, which lost contact with its Moon lander on 7 September.Credit: Jagadeesh NV/EPA-EFE/Shutterstock

POLITICS

Nuclear activity Iran is preparing to ramp up centrifuge development for uranium enrichment. The move tests a deal made in 2015 in which Iran agreed to curb its nuclear activities in exchange for the lifting of economic sanctions. When the United States pulled out of the deal, known as the Joint Comprehensive Plan of Action, last year, Iran expected Europe to restore its international trade and help it circumvent a US embargo. But a France-led initiative has failed to deliver, Iran’s nuclear chief Ali Akbar Salehi said in a press conference in Tehran with Cornel Feruta, acting head of the International Atomic Energy Agency (IAEA). Iran has said it will continue to allow the IAEA to inspect its nuclear facilities. The IAEA board of governors is meeting in Vienna to decide next steps.

PEOPLE

Science minister The UK science minister, Jo Johnson, resigned from his post and as a Member of Parliament on 5 September — citing conflicts between what he thinks is best for the country and his family ties. Jo Johnson is the younger brother of Conservative Prime Minister Boris Johnson, who has said that the United Kingdom will leave the European Union by a 31 October deadline, even if there is no deal in place to regulate its future relations with the bloc. A no-deal Brexit is widely predicted to be detrimental to science. Jo Johnson, who campaigned for the United Kingdom to stay in the EU in 2016, first held the science minister post from 2015 to 2018, and was well liked by researchers, who have praised his understanding of the sector. He was reappointed in July.

Mayoral race Cédric Villani, a mathematician and member of the French parliament, is to run for election as mayor of Paris. Villani has represented President Emmanuel Macron’s ruling party, La République en Marche! (LREM), in France’s National Assembly since 2017. He will stand as an independent candidate, having missed out on LREM’s nomination. In a speech on 4 September, Villani said that he had spent his research career solving complex problems, and that he entered politics to try to bring more scientific knowledge into government. Ecology would be at the heart of his plans to improve the lives of Paris’s citizens, said Villani, who won the coveted Fields Medal for mathematics in 2010. Mayoral elections will be held next March.

Data pioneer Donald Lindberg, who oversaw the creation of the biomedical database PubMed, died on 17 August, aged 85. Lindberg was the director of the US National Library of Medicine (NLM) — the world’s largest biomedical library — for more than 30 years. As director, he digitized the library’s holdings and established systems for providing biomedical-research articles, clinical-trial results, genomic data and other medical information to researchers, doctors and patients around the world. The library’s online tools, including PubMed and ClinicalTrials.gov, have become staples of biomedical research. Lindberg, who originally trained as a pathologist, left a faculty position at the University of Missouri in Columbia to become NLM director in 1984. He retired from the library in March 2015, but continued to serve as its director emeritus.

EVENTS

Catastrophic storm Hurricane Dorian made landfall in the Bahamas on 1 September as a category-5 storm, devastating the islands and matching or breaking weather records. The storm tied for the second-strongest hurricane to make landfall — as judged by wind speed — ever recorded in the Atlantic. It also intensified at an unprecedented rate for a storm this strong, increasing its peak wind speed from 240 to 298 kilometres per hour in 9 hours. The hurricane (pictured) pounded the Bahamas for 40 hours, severely damaging or destroying about 45% of the homes on 2 of the nation’s northernmost islands with 300-kilometre-per-hour winds and a 5-metre storm surge. As of 10 September, at least 50 people had died in the Bahamas. After thrashing the island nation, Dorian crawled north along the US east coast, spawning tornadoes and floods, before making landfall in North Carolina as a category-1 hurricane on 6 September.

Credit: NOAA/Planetpix/Alamy

Epstein fallout Joichi Ito, the director of the Massachusetts Institute of Technology (MIT) Media Lab in Cambridge, resigned on 7 September because of his interactions with sex offender and alleged sex trafficker Jeffrey Epstein. The same day, MIT president Rafael Reif said that he had asked the university’s general counsel to hire an outside law firm to conduct “an immediate, thorough and independent” investigation of MIT’s dealings with Epstein, a financier who died in August. Reif cited “deeply disturbing allegations” published by The New Yorker, which reported on 6 September that Media Lab staff had concealed donations from Epstein. Nature was unable to reach Ito for comment; last month, he publicly apologized for accepting money from Epstein’s foundations for the lab and for technology investment funds that he runs.

RESEARCH

Baffling illness A lung illness linked to e-cigarette use has killed 5 people and potentially affected 450 others in 33 US states and one territory, said the Centers for Disease Control and Prevention on 6 September. The symptoms include nausea, fever and difficulty breathing, and cases began surfacing earlier this year. Public-health officials haven’t been able to identify a specific device, product or substance common to all cases, but they suspect that an inhaled chemical is responsible. In a study of ill teenagers and young adults in Wisconsin, published on 6 September in the New England Journal of Medicine, 84% reported vaping substances containing tetrahydrocannabinol — the main psychoactive chemical responsible for marijuana’s ‘high’ — although others reported using only nicotine products (J. E. Layden et al. N. Engl. J. Med. http://doi.org/c99f; 2019).

AWARDS

Breakthrough prizes The Event Horizon Telescope team has been awarded one of this year’s US$3-million Breakthrough prizes for taking the first direct image of a black hole and its event horizon. The picture, unveiled in April, shows the supermassive black hole at the centre of the galaxy Messier 87. The prize will be shared equally between the collaboration’s 347 members, and will be awarded in a ceremony at NASA’s Ames Research Center in Mountain View, California, on 3 November, along with four Breakthrough prizes in the life sciences and one in mathematics. Russian–Israeli billionaire Yuri Milner launched the Breakthrough prizes in 2012; the awards are now sponsored by him and other Internet entrepreneurs, including Facebook chief Mark Zuckerberg and Google’s Sergey Brin.

TREND WATCH

A study of people in Germany suggests that they have a reasonably good grasp of the science surrounding climate change, but occasionally overestimate — or underestimate — their understanding. Psychologists showed 8 scientific statements about climate change to a group of 509 citizens, and asked them whether the statements were true or false. Participants were then asked how certain they were that their answer was correct, on a scale from mere guesswork (50%) to absolute certainty (100%). Most of the participants correctly identified true statements, and were fairly confident that their judgements were correct. But people weren’t as good at identifying statements that were false, despite being just as confident in their answers. For comparison, the study team asked 207 German climate-change researchers to verify the same set of statements. On average, the scientists responded with both greater accuracy and more confidence in their knowledge than citizens. The study team was keen to base the research in Germany, where the social justice of pricing carbon emissions from cars and buildings has generated heated debate.

Source: H. Fischer et al. Nature Clim. Change http://doi.org/dbbn (2019).

Nature 573, 168-169 (2019)

doi: 10.1038/d41586-019-02672-8

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02672-8

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News in Focus

- Daring scientists extract ice from Earth’s highest tropical glacier [04 September 2019]

News • Researchers race to retrieve ice amid protests by local residents.

- First hint that body’s ‘biological age’ can be reversed [05 September 2019]

News • In a small trial, drugs seemed to rejuvenate the body’s ‘epigenetic clock’, which tracks a person’s biological age.

- Elsevier investigates hundreds of peer reviewers for manipulating citations [10 September 2019]

News • The publisher is scrutinizing researchers who might be inappropriately using the review process to promote their own work.

- South Korea’s ‘Nobel prize project’ rocked by tough year [10 September 2019]

News • Researchers fear for the future of the Institute for Basic Science, which has faced accusations of misconduct and a sizeable budget cut.

- Lost Denisovan bone reveals surprisingly human-like finger [05 September 2019]

News • Photos of missing fossil show these ancient hominins had slimmer digits than their Neanderthal relatives.

- Exclusive: Behind the front lines of the Ebola wars [11 September 2019]

News Feature • How the World Health Organization is battling bullets, politics and a deadly virus in the Democratic Republic of the Congo.

- How to banish manels and manferences from scientific meetings [10 September 2019]

News Feature • A Nature analysis finds that several fields of science are moving away from male-dominated conferences and panels — but it’s easy to slip back into old habits.

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NEWS

04 September 2019

Daring scientists extract ice from Earth’s highest tropical glacier

Researchers race to retrieve ice amid protests by local residents.

Barbara Fraser

Barbara Fraser is a freelance journalist in Lima.

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Mount Huascarán in Peru is home to Earth’s highest tropical glacier.Credit: Carlos Viola/Getty

An expedition to drill ice cores from Earth’s highest remaining tropical glacier — on Mount Huascarán in Peru — was cut short last month after a protest by local residents forced researchers to abandon their mountain camp.

The protestors accused the team of being a front for a mining company, a claim that the scientists, led by glaciologist Lonnie Thompson of Ohio State University in Columbus, deny.

Despite the conflict, the researchers managed to extract four ice cores before being evacuated by helicopter. These samples could reveal new details about changes in atmospheric greenhouse-gas levels, temperature and land use in the Andes Mountains and the adjacent Amazon basin over the past 20,000 years. The climate record preserved in the cores could also strengthen predictions about the effects of glacial melting, which has put communities downstream at risk of water shortages and catastrophic landslides.

The team’s expedition began in early July with the goal of sampling ice from two sites on Mount Huascarán, Peru’s tallest mountain. Even before Thompson’s team was forced to leave the mountain, he saw the trip as a “salvage mission”. That’s because Mount Huascarán’s ice is thawing rapidly, a process that is releasing trapped air bubbles that glaciologists use to reconstruct the past climate.

The project is personal for 71-year-old Thompson, who began studying glaciers in Peru in 1974 and has seen them shrink steadily since then. He compares his trips to dwindling glaciers to visiting a loved one with terminal cancer. “I can monitor and document the rate of retreat,” he says, “but unfortunately cannot stop its demise.”

The researchers plan to use analytical techniques that were not available in 1993, the last time Thompson extracted a full-length ice core from the glacier. These include examining embedded pollen, sooty black-carbon particles and bacteria for clues to how the Amazon’s extreme biodiversity has evolved since the last ice age.

Scientists drilled through glacial ice until they reached bedrock. Credit: Vladimir Mikhalenko

On previous trips to the area, Thompson extracted cores at lower altitudes than those he targeted during the latest trip. But the surface area of Peru’s glaciers has shrunk by about 40% since the 1970s, and the tops of many glaciers no longer stay frozen year-round. Meltwater trickling down through the thawing ice is blurring the boundaries between layers. Thompson hopes to get a clearer climate record from the Huascarán cores.

His team is also studying the topography and thickness of glaciers across the Cordillera Blanca, the section of the Andes Mountains that includes Mount Huascarán, seeking ways to calculate how much water they store and predict their risk of collapse. As the climate warms, ice blocks could break off and plunge into meltwater lakes, sending water, mud and rock cascading through towns along the Santa River in the valley.

Icy reception

The scientists started drilling on Mount Huascarán in mid-July. It took them a week to extract two cores in a col — or saddle between two peaks — at about 6,000 metres above sea level. One sample measured 165 metres long; the other, 168 metres. The team then spent three days drilling a pair of shorter cores on the mountain’s south peak at 6,768 metres above sea level.

Rumours that the scientists were actually a front for a foreign mining company began circulating on about 1 August. Social-media posts urged local leaders to demand that the researchers leave the mountain. The non-Peruvian members of the team were evacuated by helicopter on 5 August, leaving behind most of their ice cores.

The ice cores from Mount Huascarán could reveal new details about temperature changes in in the Andes Mountains and the adjacent Amazon basin since the last ice age.Credit: Vladimir Mikhalenko

On 11 August, Thompson’s team and representatives of Peru’s National Institute for Research on Glaciers and Mountain Ecosystems (INAIGEM) in Huaraz met with protestors from the town of Musho, who gave them three days to bring the ice cores and equipment down from the mountain.

That task fell to Wilmer Sánchez Rodríguez, a project member from Peru and an intern at the American Climber Science Program in Eldora, Colorado, and local climbers whom the researchers had hired as porters. On 13 August, they returned to the project’s staging area, an alpine hut, to begin retrieving 471 metres of cored ice from the col in one-metre chunks. A government helicopter carried the last shipment of ice off the mountain on 18 August.

“Glaciers are political,” says Mark Carey, an environmental historian at the University of Oregon in Eugene who has studied the relationship between people and ice in the Cordillera Blanca. The Huascarán expedition was not the first in the region to be caught up in conflicts related to water scarcity, political manoeuvring and residents’ reverence for the mountains.

In 2016, people living near Carhuaz, Peru, destroyed an early-warning system for glacier outburst floods. The system had been installed in 2012, after an outburst flood in 2010 from a lake stopped just short of the town. But a subsequent drought exacerbated tensions over water rights. The people who attacked the network of microphones and cameras designed to detect ice falling into the lake blamed the equipment for keeping clouds at bay.

Lingering suspicions

Local residents’ concerns about the expedition to Mount Huascarán are probably rooted in a number of factors. These include a desire to protect the mountain and reinforce territorial and water rights, fears about the effects of mining, and discontent over the distribution of revenue from the Huascarán National Park and tourism, says Benjamin Orlove, an anthropologist at Columbia University in New York City who studies Andean communities in Peru.

Scientists extracted 471 metres of cored ice from Mount Huascarán.Credit: Ohio State University

He says that the people who destroyed the early-warning system near Carhuaz and those who protested against the ice-core drilling may also have felt that they did not benefit from the projects, even though both were designed to provide data that could help local people deal with the effects of melting glaciers.

To head off future conflicts, Gisella Orjeda Fernández, executive president of INAIGEM, is developing an outreach programme for communities in the Cordillera Blanca. Its goal will be to explain what scientists are studying in the mountains — and how such analyses could contribute to policies that benefit communities that depend on glacial meltwater.

The recent conflict was not the first time Thompson has faced sceptical local residents. Tribal leaders forced him to descend Jaya Peak in New Guinea in 2010, and in 1997 residents of Sajama, Bolivia, required that he donate to their library, hire local porters and participate in a ritual that involved sacrificing an alpaca before he could drill on Mount Sajama.

Thompson sees a positive side to communities’ protectiveness towards their peaks. “Glaciers are sacred places,” he says. “If every mountain had a village that was trying to protect it, we wouldn’t have the environmental problems we have today.”

Nature 573, 171-172 (2019)

doi: 10.1038/d41586-019-02566-9

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02566-9

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NEWS

05 September 2019

First hint that body’s ‘biological age’ can be reversed

In a small trial, drugs seemed to rejuvenate the body’s ‘epigenetic clock’, which tracks a person’s biological age.

Alison Abbott

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A person’s biological age, measured by the epigenetic clock, can lag behind or exceed their chronological ageCredit: Patrick McDermott/Getty

A small clinical study in California has suggested for the first time that it might be possible to reverse the body’s epigenetic clock, which measures a person’s biological age.

For one year, nine healthy volunteers took a cocktail of three common drugs — growth hormone and two diabetes medications — and on average shed 2.5 years of their biological ages, measured by analysing marks on a person’s genomes. The participants’ immune systems also showed signs of rejuvenation.

The results were a surprise even to the trial organizers — but researchers caution that the findings are preliminary because the trial was small and did not include a control arm.

Biomarkers and ageing: The clock-watcher

“I’d expected to see slowing down of the clock, but not a reversal,” says geneticist Steve Horvath at the University of California, Los Angeles, who conducted the epigenetic analysis. “That felt kind of futuristic.” The findings were published on 5 September in Aging Cell[1].

“It may be that there is an effect,” says cell biologist Wolfgang Wagner at the University of Aachen in Germany. “But the results are not rock solid because the study is very small and not well controlled.”

Marks of life

The epigenetic clock relies on the body’s epigenome, which comprises chemical modifications, such as methyl groups, that tag DNA. The pattern of these tags changes during the course of life, and tracks a person’s biological age, which can lag behind or exceed chronological age.

Scientists construct epigenetic clocks by selecting sets of DNA-methylation sites across the genome. In the past few years, Horvath — a pioneer in epigenetic-clock research — has developed some of the most accurate ones.

The latest trial was designed mainly to test whether growth hormone could be used safely in humans to restore tissue in the thymus gland. The gland, which is in the chest between the lungs and the breastbone, is crucial for efficient immune function. White blood cells are produced in bone marrow and then mature inside the thymus, where they become specialized T cells that help the body to fight infections and cancers. But the gland starts to shrink after puberty and increasingly becomes clogged with fat.

Evidence from animal and some human studies shows that growth hormone stimulates regeneration of the thymus. But this hormone can also promote diabetes, so the trial included two widely used anti-diabetic drugs, dehydroepiandrosterone (DHEA) and metformin, in the treatment cocktail.

Epigenetics: The sins of the father

The Thymus Regeneration, Immunorestoration and Insulin Mitigation (TRIIM) trial tested 9 white men between 51 and 65 years of age. It was led by immunologist Gregory Fahy, the chief scientific officer and co-founder of Intervene Immune in Los Angeles, and was approved by the US Food and Drug Administration in May 2015. It began a few months later at Stanford Medical Center in Palo Alto, California.

Fahy’s fascination with the thymus goes back to 1986, when he read a study in which scientists transplanted growth-hormone-secreting cells into rats, apparently rejuvenating their immune systems. He was surprised that no one seemed to have followed up on the result with a clinical trial. A decade later, at age 46, he treated himself for a month with growth hormone and DHEA, and found some regeneration of his own thymus.

In the TRIIM trial, the scientists took blood samples from participants during the treatment period. Tests showed that blood-cell count was rejuvenated in each of the participants. The researchers also used magnetic resonance imaging (MRI) to determine the composition of the thymus at the start and end of the study. They found that in seven participants, accumulated fat had been replaced with regenerated thymus tissue.

Rewinding the clock

Checking the effect of the drugs on the participants’ epigenetic clocks was an afterthought. The clinical study had finished when Fahy approached Horvath to conduct an analysis.

Horvath used four different epigenetic clocks to assess each patient’s biological age, and he found significant reversal for each trial participant in all of the tests. “This told me that the biological effect of the treatment was robust,” he says. What’s more, the effect persisted in the six participants who provided a final blood sample six months after stopping the trial, he says.

There’s no limit to longevity, says study that revives human lifespan debate

“Because we could follow the changes within each individual, and because the effect was so very strong in each of them, I am optimistic,” says Horvath.

Researchers are already testing metformin for its potential to protect against common age-related diseases, such as cancer and heart disease. Fahy says that the three drugs in the cocktail might contribute separately to the effect on biological ageing through unique mechanisms. Intervene Immune is planning a larger study that will include people of different age groups and ethnicities, and women.

Regenerating the thymus could be useful in people who have underactive immune systems, including older people, he says. Pneumonia and other infectious diseases are a major cause of death in people older than 70.

Cancer immunologist Sam Palmer at the Heriot-Watt University in Edinburgh says that it is exciting to see the expansion of immune cells in the blood. This “has huge implications not just for infectious disease but also for cancer and ageing in general”.

Nature 573, 173 (2019)

doi: 10.1038/d41586-019-02638-w

References

1. 1.

Fahy, G. M. et al. Aging Cell https://doi.org/10.1111/acel.13028 (2019).

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02638-w

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NEWS

10 September 2019

Elsevier investigates hundreds of peer reviewers for manipulating citations

The publisher is scrutinizing researchers who might be inappropriately using the review process to promote their own work.

Dalmeet Singh Chawla

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The Dutch publisher Elsevier is investigating hundreds of researchers whom it suspects of deliberately manipulating the peer-review process to boost their own citation numbers.

Hundreds of extreme self-citing scientists revealed in new database

The publisher is looking into the possibility that some peer reviewers are encouraging the authors of work under review to cite the reviewers’ own research in exchange for positive reviews — a frowned-on practice broadly termed coercive citation.

Elsevier’s probe has also revealed that several of these reviewers seem to be engaging in other questionable publishing practices in studies that they have themselves authored. The Elsevier analysts who uncovered the activity told Nature that they “discovered clear evidence of peer-review manipulation” and of academics publishing the same studies more than once. Elsevier said that their investigations will lead to some of these studies being retracted.

But it said it won’t be necessary to retract any studies found to be affected by coercive citation because the authors aren’t responsible for the problem, and citation manipulation doesn’t affect the research.

Data detectives

The suspicious activity was uncovered by Elsevier analytics experts Jeroen Baas and Catriona Fennell. The pair, based in Amsterdam, looked at the peer-review activity of almost 55,000 academics who review for Elsevier journals, in a bid to find how often these researchers’ work is cited by the papers they review. The study, which hasn’t yet been peer reviewed, was posted on the SSRN repository for social-science research on 6 September.

That analysis was prompted by a case at the Elsevier journal Geoderma. In 2017, Artemi Cerdà resigned from the journal’s editorial board after being accused of using his power to boost his own citation count and that of the journals he edited. (Cerdà, a soil scientist at the University of Valencia in Spain has denied accusations of citation manipulation; the publishing arm of the European Geosciences Union, where Cerdà also did editorial work, and Elsevier investigated the accusations and both concluded that he had manipulated citations). Elsevier has since amended its editor guidelines, editor contracts and reviewer guidelines to warn against the practice.

Fennell and Baas’s study found that, in most cases, reviewers’ own studies are not cited in work that they have assessed. Around 98.5% of the reviewers in the study’s sample are cited in fewer than 10% of the papers they reviewed.

But a small minority of reviewers — less than 1% of the nearly 55,000 examined — consistently seem to have their own work referenced in studies they have reviewed.

The science that’s never been cited

Because reviewers and authors tend to work in the same field, some overlap in citations is expected. But consistently seeing a reviewer’s work referenced in work they have assessed can be suspicious and could indicate instances of coercive citation. The practice is widely known to occur, but its extent is unknown, partly because the data underlying peer review usually remain confidential.

Elsevier is now approaching journal editors to ask whether the references in question are relevant. Fennell says that the company has completed its investigation into the most suspicious cases, but is still interrogating less-serious ones.

Limited options

“Something needs to be done,” about citation manipulation, says Jonathan Wren, a bioinformatician at the Oklahoma Medical Research Foundation in Oklahoma City who is an associate editor for the journal Bioinformatics. Earlier this year, Bioinformatics banned a referee from reviewing for the journal after an investigation found that the researcher, whom Wren declined to name, had requested an average of 35 additional citations per review, 90% of which were for papers they had co-authored[1].

Wren is currently writing an algorithm that would automatically flag unusual patterns in papers — including excessive citations to one particular author. “If we start policing it after it gets published,” he says, “then what do you do with the extra references?”

One idea that Elsevier is considering is the retraction of individual references in studies, a move that would be unprecedented. Another option, Fennell says, might be to issue corrections. “We’re still working out the best way forward,” she says.

Nature 573, 174 (2019)

doi: 10.1038/d41586-019-02639-9

References

1. 1.

Wren, J. D., Valencia, A. & Kelso, J. Bioinformatics https://doi.org/10.1093/bioinformatics/btz071 (2019).

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02639-9

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NEWS

10 September 2019

- Correction 11 September 2019

South Korea’s ‘Nobel prize project’ rocked by tough year

Researchers fear for the future of the Institute for Basic Science, which has faced accusations of misconduct and a sizeable budget cut.

Mark Zastrow

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President of the Institute for Basic Science Kim Doochul. His term ends this month. Credit: IBS

Update: South Korea's science ministry announced on 10 September that the Institute for Basic Science would be reorganized, following government investigations into the institute's research centres.

It’s been a tumultuous year for the prestigious Institute for Basic Science in South Korea — a collection of research centres that was founded in 2011 and designed to win the country its first science Nobel prize. Modelled on the Max Planck Society in Germany and RIKEN in Japan, the institute’s mission is to foster blue-skies basic science in a country traditionally more focused on applied research. But over the past 12 months, it has faced government investigations and calls for reform, following accusations of nepotism and financial mismanagement — as well as a sizeable cut to its research budget.

The Institute for Basic Science (IBS) is now seeking a new leader: the current president Doochul Kim’s term ends later this month. But many IBS researchers say his replacement, whoever it is, will face a considerable challenge to turn around the organization’s fortunes. Many researchers argue that the allegations against the institute — and the media's response — have been overblown. Still, they worry that the events of the past year might have a lasting impact and make it difficult for the organization to properly function.

“The basic philosophy of the IBS was to give full freedom for the researchers to carry out whatever they want to do,” says Narry Kim, director of the IBS Center for RNA Research. Leading scientists from South Korea and abroad were recruited to start the IBS centres, and were promised autonomy to run them along with roughly 10 billion won (US$8.4 million) a year. But some centre directors worry that proposals for reform, made in wake of the turmoil could erode their autonomy, which they argue would undermine the organization’s original mission.

Many researchers say that IBS has helped to globalize South Korea’s research. The scale and resources of IBS centres help to forge collaborations with international researchers, says Philip Kim, a condensed matter physicist at Harvard University in Cambridge, Massachusetts. “That’s one of the best things that IBS has done for Korean research,” he says.

Tough year

The institute’s recent troubles started in October, when lawmakers from the ruling liberal Democratic Party grilled Doochul Kim during annual parliamentary hearings. They criticized a project to construct a heavy ion particle accelerator in Daejeon for being over budget and behind schedule. The Rare Isotope Science Project consumes about one-third of IBS’s budget. Doochul Kim told Nature that one of the project’s ion sources has been delayed by a year, but that this is a minor setback for a large-scale project.

Following the hearings, the government announced in November that it was auditing 4 of IBS’s 30 centres. And a week later, it confirmed that IBS’s research budget would be cut by 7%, from 254 billion to 236.3 billion won. The cut, which came into effect this year, left centres with an average budget of a little over 6 billion won, says Doochul Kim.

The organization came under further scrutiny when several South Korean broadcasters reported in June that according to audit results, at least two centres had misspent research funds. Media reports also called out multiple centres for questionable hiring procedures, including candidates being reviewed by acquaintances. The media coverage was followed by another government audit — this time of 24 of the 30 IBS centres. The investigation was due to finish last month. The science ministry has not yet released its findings, and the negative media coverage of the organization has continued.

Doochul Kim told Nature that most of the allegations against IBS reported in the media amount to administrative errors rather than nefarious wrongdoing. He thinks that the audits are politically motivated, and criticizes the way some preliminary results have been leaked to the press.

Since its inception, IBS has had critics who think the institute swallows up too much of the nation’s basic research budget. It’s the institute’s “original sin”, says So Young Kim, a science and technology political scientist at KAIST. The institute is also associated with the country's main conservative party which founded it. When the Democratic Party to power in 2017, it was more interested in spreading resources to many researchers, says So Young Kim. “It's a very different philosophy."

When president Moon Jae-in campaigned for election in 2017, his party promised to double the country’s researcher-led grants for basic research. The science ministry says it is on track to meet that goal by 2020.

Doochul Kim says his biggest regret as IBS president is not adapting to the political environment and failing to persuade more politicians to support the institute’s vision.

The shifting political mood has already impacted IBS's vision, laments Doochul Kim. IBS centres were originally granted a ten-year term, with a review for extension in their eighth year. The founding group of centres will come up for review from next year—and it seems likely that only some will be extended, says Kim.

Yannis Semertzidis, director of the IBS Center for Axion and Precision Physics Research at KAIST in Daejeon, suspects that falling budgets are also partly to blame for a decision to put his request to purchase a high-temperature superconducting magnet on hold. Such equipment is crucial for the centre's search for the axion — a theorized particle that could be a component of dark matter. The magnet would give his group a significant advantage over its competition, the Axion Dark Matter Experiment at the University of Washington in Seattle.

But a spokesperson for IBS says the project was reviewed in two evaluations and both found that the project lacked proper feasibility to continue.

Growing pains

Narry Kim, who leads an IBS centre that she says was audited in July, notes that the behaviours that have been criticized might have arisen because of confusion about the rules — rather than anything more nefarious — and that this is an expected “growing pain” for an innovative style of research organization. IBS was designed to break the mould of other public institutions and universities in South Korea by giving centre directors freedom and larger-scale funding to pursue high-risk, high-reward projects that could win Nobel prizes. South Korea has never won a scientific Nobel, and IBS is frequently referred to as the nation’s “Nobel prize project”.

But IBS’s flexibility has sometimes led to ambiguity, Kim says. For instance, ten IBS centres, including hers, are administered by host universities and so are subject to both university and IBS regulations, which sometimes conflict or lead to confusion.

Doochul Kim accepts that some features of IBS need to change to protect centres from being involved in further scandals. He says that he has proposed redefining the institute’s core principle of autonomy so that centre heads would no longer have direct authority to hire tenure-track research fellows, and avoid accusations of nepotism. IBS directors are allowed to do this, but the public can be quick to anger at any hint of nepotism. He also proposed changes to IBS’ administrative structure. For instance, the institute currently has administrative staff at each research centre, but he wants the five IBS centres at KAIST to share a centralized office that would be more powerful and relieve directors of some of their administrative burdens, such as approving all purchasing decisions, no matter how small.

But the proposals undermine IBS’s original goal of having centre directors make decisions about how they are run, says Semertzidis. IBS management should strengthen internal auditing to root out actual misconduct, but not interfere with the decision-making of directors, he argues.

With Kim’s term almost over, it will be up to his successor to follow-through on his proposals. A committee formed by the IBS board of trustees announced on 5 September a shortlist of three South Korean physicists. The nation’s science minister will nominate one person, subject to the approval of Moon Jae-in.

One bit of good news for the institute is a funding boost for 2020, according to the science ministry’s proposed budget, announced earlier this month. Although this will be for construction of future facilities and not for research centres, an IBS official told Nature.

Semertzidis says the new leader will need time to work out the path forward for IBS. He hopes they will defend IBS’ original goals and establish a better relationship with the government than the current IBS administration. “It’s easy to damage IBS,” he says.

Nature 573, 174-175 (2019)

doi: 10.1038/d41586-019-02363-4

Updates & Corrections

- Correction 11 September 2019: An earlier version of this story gave the wrong affiliation for Philip Kim.

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02363-4

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NEWS

05 September 2019

- Correction 06 September 2019

Lost Denisovan bone reveals surprisingly human-like finger

Photos of missing fossil show these ancient hominins had slimmer digits than their Neanderthal relatives.

Ewen Callaway

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Bones belonging to ancient hominins have been discovered in the Denisova Cave in Siberia’s Altai mountains.Credit: Eddie Gerald/Alamy

A new analysis of a finger bone used to study the Denisovans — a group of ancient humans identified in 2010 — offers clues to a decade-long mystery surrounding one the most important hominin fossils ever found.

The study describes the tip of a right-hand little finger, which was separated from the rest of the finger bone after it was excavated 11 years ago. A digital reconstruction of the complete finger bone, or phalanx, reveals that the Denisovans’ fingers were much more similar to those of modern humans than expected.

“I’m happy that we could get something out,” says Eva-Maria Geigl, a palaeogeneticist at the Institute Jacques Monod in Paris, who co-led the study. “So far there was nothing, as if the phalanx was lost.”

Mum’s a Neanderthal, Dad’s a Denisovan: First discovery of an ancient-human hybrid

Her team sequenced DNA from the missing fragment to show that it matched the rest of the fingertip bone, and used photographs to reunite the two pieces digitally. The work was published on 4 September in Science Advances[1].

“It’s not going to revolutionize our knowledge of Denisovan morphology, but it adds a little piece,” says Bence Viola, a palaeoanthropologist at the University of Toronto in Canada who was part of the team.

Denisovan discovery

The mystery surrounding the lost piece began in a remote valley at the foot of the Altai Mountains in southern Siberia, where Russian archaeologists excavating the Denisova Cave uncovered a finger bone belonging to a group of ancient humans in 2008. Anatoly Derevianko, who is an archaeologist at the Russian Academy of Sciences Institute of Archeology and Ethnography in Novosibirsk and was leading the dig, decided to divide the bone and send the pieces to two labs to see whether DNA could be extracted from either half.

One of the fragments went to Svante Pääbo, an evolutionary geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. His team sequenced its DNA and discovered that the bone belonged to a lineage distinct from modern humans and from Neanderthals. In January 2010, Pääbo and several of his colleagues flew to Novosibirsk.

Use ancient remains more wisely

That’s when Derevianko told Pääbo’s team that he had divided the bone in two and sent the other half to Edward Rubin, a geneticist then at Lawrence Berkeley National Laboratory (LBNL) in California, whose team had been competing with Pääbo’s to sequence Neanderthal DNA.

“We freaked out a bit,” remembers Viola, who joined Pääbo on the trip. “We had no idea there was this second part.”

Worried about getting scooped, Pääbo and his team raced to report their discovery. They published the fossil’s mitochondrial genome — a short stretch of maternally inherited DNA — in March 2010[2]. Several months later, they went on to reveal the first complete nuclear genome of a Denisovan[3]. The studies showed that Denisovans were a group of extinct hominins that were more closely related to Neanderthals than to modern humans, and that they lived in the Siberian cave — and probably across Asia — more than 30,000 years ago.

The whereabouts of the missing bone fragment are still unclear.Credit: Eva-Maria Geigl

The 2010 finding transformed the cave into one of the world’s most important archaeological sites. Researchers have since found more ancient-human bones in the cave, including the stunning discovery of a first-generation hybrid, which had a Neanderthal mother and Denisovan father.

But Viola — who has analysed nearly every Denisovan fossil from the cave — says he never forgot about the second finger-bone fragment. “I’ve been wondering the whole time what the other half would have looked like,” he says. “All I knew is that it was in Berkeley.”

Revisiting old bones

According to Geigl, Rubin, who left the LBNL in 2016 for industry and could not be reached for comment, sent his half of the fossil to her lab in 2010. Pääbo’s team had already published the fossil’s mitochondrial genome. But Geigl hoped to obtain nuclear DNA from the fossil, which could indicate much more about the hominin’s relationship to humans and Neanderthals.

Move over, DNA: ancient proteins are starting to reveal humanity’s history

Initial efforts to extract DNA from the bone failed, so Geigl’s team worked on developing other methods. But after Pääbo's team published the Denisovan nuclear genome, Rubin asked Geigl to return the fossil. She returned the fragment in 2011, but was able to sample its DNA and take detailed photographs first.

Geigl sat on the data for years, but in 2016, she decided to publish them, at the suggestion of Pääbo. Her team sequenced the mitochondrial genome and discovered — unsurprisingly — that it exactly matched the sequence Pääbo’s team had published in 2010. But a digital reconstruction of the complete finger bone held a surprise: the bone was slim, and more like the fingers of modern humans than the stout digits of Neanderthals, even though Denisovans are more closely related to Neanderthals. The few other Denisovan remains that have been discovered, including large molar teeth, tend not to resemble those of modern humans.

“Given the limited skeletal remains definitively associated with Denisovans, this is an important discovery,” says Tracy Kivell, a palaeoanthropologist at the University of Kent, UK, who was not involved in the study. The slender shape of the Denisovan finger also suggests that Neanderthals’ burlier fingers might have evolved as a result of strenuous use of their hands, she adds.

Although the story of the missing fragment has become clearer, its current whereabouts are still unknown. According to Derevianko, Rubin sent the sample to the ancient-DNA lab of Eske Willerslev at the University of Copenhagen and the Natural History Museum of Denmark in 2011 or 2012. Willerslev did not respond to requests for comment by Nature’s news team.

Pääbo and his team had to grind up a portion of their piece of the bone to produce a high-quality genome sequence and returned the rest to Derevianko, but Geigl is unsure if the half she analysed is gone. “It’s like a Sherlock Holmes story,” she says.

Nature 573, 175-176 (2019)

doi: 10.1038/d41586-019-02647-9

Updates & Corrections

- Correction 06 September 2019: An earlier version of this story stated that Svante Pääbo and his team had to grind up their piece of the bone to produce a high-quality genome sequence. They ground up a sample of the inner parts and returned the rest to Anatoly Derevianko.

References

1. 1.

Bennett, E. A. et al. Sci. Adv. 5, eaaw3950 (2019).

2. 2.

Krause, J. et al. Nature 464, 894–897 (2010).

3. 3.

Reich, D. et al. Nature 468, 1053–1060 (2010).

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02647-9

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NEWS FEATURE

11 September 2019

Exclusive: Behind the front lines of the Ebola wars

How the World Health Organization is battling bullets, politics and a deadly virus in the Democratic Republic of the Congo.

Amy Maxmen

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Health workers in a war-weary region are confronted with Ebola, a deadly virus that has claimed more than 2,000 lives. Credit: John Wessels for Nature

This story was supported by the Pulitzer Center on Crisis Reporting.

Tedros Adhanom Ghebreyesus concentrates on a map of a long-forsaken war zone in the northeastern provinces of the Democratic Republic of the Congo (DRC). Ebola is gaining ground here, and Tedros, the director-general of the World Health Organization (WHO), needs to stop it. He huddles in a dim corner of a mess hall with his officers on the front lines. Their fingers dance across the map as they point to areas occupied by militia, and explain how their teams struggle to circulate through these parts with vaccines and thermometers, key tools for limiting Ebola’s transmission.

As darkness falls, more WHO staff file into the hall at the United Nations compound in Butembo, a volatile city in North Kivu province. The din of their conversations rises as a buffet of stewed meat, fried fish and plantains gets cold and some boxed wine grows warm. Eventually, Tedros, as he prefers to be called, ends the meeting with his top aides and announces that it’s time to eat.

He settles into a chair at a table of young Ebola responders — mainly Congolese public-health specialists and physicians — and falls silent. It was June, and Tedros was facing pressure from all directions. The outbreak had already grown to be the second largest in history. And despite having a new Ebola vaccine and drugs to treat the disease, the death rate was soaring at 67% because the therapies weren’t reaching everyone in need. Armed groups weren’t the WHO’s only challenge. Many residents just didn’t accept that Ebola responders were there to help. A deep-seated scepticism of outsiders comes from more than a century of conflict, exploitation and political corruption in the region. And wars over the past 25 years have destroyed any semblance of a reliable, regulated health system. “The outbreak of Ebola is a symptom,” Tedros explains. “The root cause is political instability.”

This explanation doesn’t satisfy health-policy analysts who observe the escalating outbreak — which has killed more than 2,000 people — and question the WHO’s ability to contain it. Their criticism comes just as the organization is asking governments and philanthropists to give millions more dollars for the response. The WHO has more Ebola responders on the ground than any other international organization because ongoing violence keeps many others at bay. The responders have faced death threats and stones, bullets and grenades.

Tedros had come to Butembo to hear about obstacles, and to speak to leaders around the city about calming tensions so that his teams could work without harm. As he eats with the responders, he grows defensive on their behalf. “They are working day and night,” he says. “Other groups come and stay for a few hours; they run when they hear one bullet fired.” He rests a hand on the shoulder of an epidemiologist sitting beside him. Her colleague, Richard Mouzoko, was shot dead at a hospital in Butembo two months earlier. “She’s taking the same risk Richard took,” Tedros says. “We are doing this to save lives.”

Violence and mistrust

In the morning, Tedros heads into the luminous forests on the outskirts of Butembo in a convoy of black armoured jeeps. In the town of Katwa, the vehicles pull over at an Ebola treatment centre that came under fire a few months earlier. Snipers from the DRC army now guard its entrance. Tedros strides rapidly through the wards and poses for a flurry of photographs with his team wearing WHO tactical vests. “I am very proud,” he tells the workers. “Even when I’m not around, I am thinking of you.”

WHO director-general Tedros Adhanom Ghebreyesus (in white shirt) in Katwa.Credit: John Wessels for Nature

In a flash, he is back in the motorcade, rushing to a runway where a helicopter awaits. Ibrahima Socé Fall, the official leading the WHO’s Ebola response on the ground, sees Tedros off. I stay behind with Fall, to see what it means to battle one of the most deadly pathogens known to humankind in a city tortured by war.

We slide into an armoured vehicle and head north to the city of Beni on an unpaved highway that slices through tall grass and lush, tropical trees. This strip of land is controlled by grass-roots militia groups known as the Mai-Mai, so the vehicle moves at a steady clip behind a pickup truck carrying soldiers in the back. When the sky opens with heavy rain, they pull faded winter parkas over their heads.

On the drive, Fall talks about the toll of violence. A surge of killings, arson and gang rapes has traumatized communities. Around 1,900 civilians have been massacred in North and South Kivu in the past three years and another 3,300 people have been abducted, according to the Congo research group, a non-profit investigative project at New York University (see ‘Conflict and contagion’). Parents mourn for children who have been stolen and forced to serve as soldiers. “The people here are very stressed,” Fall says. He notes that clashes a week earlier, in the Ebola-stricken province of Ituri, killed 160 people and sent 300,000 fleeing for their lives. It hardly made the news. “The people here don’t believe that anyone cares for them, even their own government, so it’s very hard to convince them that we are here to help,” he says.

Source: Congo Research Group

The roots of mistrust run deep. The east has been embroiled in wars that began in 1996, after the genocide in Rwanda spilled into the DRC. At least eight other African countries were soon involved in what became known as Africa’s World War. By 2007, an estimated five million people had died from violence, disease and malnutrition as systems crumbled. Although the wars have technically ended, around 130 armed groups now occupy the east.

It was into this tinder-box that Ebola spilled over from an animal reservoir, most likely bats or apes, into humans. On 1 August 2018, a patient’s blood sample collected near Beni tested positive for Ebola. Oly Ilunga Kalenga, the DRC minister of health at the time, declared that the virus had arrived in northeastern DRC for the first time. “From day one,” says Ilunga, “I warned everyone that this would be a very bad outbreak because of conflict.”

Within a week, the Ministry of Health, the WHO and aid groups began establishing Ebola treatment centres. Health workers carted high-tech coolers filled with frozen Ebola vaccines into the rainforest, and epidemiologists from the WHO’s emergency-operations division arrived to investigate the spread of the disease. They were trying to learn how each individual got infected, and to search for anyone those individuals touched while sick. Health workers monitor these contacts for signs of Ebola, such as vomiting and fever, for 21 days — the incubation period of the virus. If they suspect an infection, they test and isolate people before it spreads. This cornerstone of the Ebola response, called contact tracing, is the key to stopping the virus’s transmission.

In a country with a strong, centralized network of doctors and public-health workers, contact tracing is manageable. But after decades of political instability, eastern DRC has no such system, and conflict makes it impossible to create one quickly. Between September and November last year, an armed group infamous for hacking civilians to death with machetes, the Allied Democratic Forces (ADF), slayed an estimated 55 civilians in and around Beni, and kidnapped dozens. Amid one attack, a rocket-propelled grenade hit the Okapi Hotel, where Ebola responders from the WHO were staying. It failed to explode, sparing their lives.

After each attack, front-line responders pulled back for their safety and the disease spread unfettered, with a surge of people dying from Ebola in the weeks following violence (see ‘Violence spreads’). Marta Lado, an infectious-disease physician at an Ebola centre in Beni, explains: “We start thinking we’ve got it under control, and then an attack happens and for three or four days, we can’t go into the community because it’s not safe, and the contacts disappear.”

Source: WHO

By December, the outbreak had already become the world’s second-worst. Then things went from bad to worse. The president at the time, Joseph Kabila, barred more than one million people in Beni and Butembo — strongholds of opposition parties — from voting in the upcoming election. He blamed it on Ebola and the security situation, but many DRC citizens saw this as a thinly veiled attempt to retain power after an 18-year stranglehold on the presidency.

Volatile demonstrations erupted across the country. An Ebola centre was looted during one protest in Beni, but the real damage to the Ebola response was the politicization of the outbreak. The voting ban seemed to confirm rumours that this terrifying disease was a tool designed to disenfranchise the opposition and make money. After all, many Ebola responders came from the capital, Kinshasa, and from other countries. They stayed in comparatively upscale accommodations, and hadn’t cared about suffering in the region before. Some residents believed that these foreigners were importing Ebola to kill them, similar to the ADF, which arose seemingly out of nowhere and with international ties. As a doctor from Beni explained to me, “People think this is just another thing brought from outside to kill.”

A police officer stands guard outside a clinic in Katwa.Credit: John Wessels for Nature

Mistrust grew in January after the election, which was widely considered a sham. Kabila handed the presidency to a candidate who would later allow him to share power. On the night of 24 February, assailants burnt down parts of an Ebola treatment centre in Katwa. Three days later, they set another centre and its vehicles ablaze in Butembo. Immobile patients watched in fear from their hospital beds. Four people with Ebola fled into the forest. This attack coincided with the centre’s busiest hour, as daytime staff handed over to the evening shift. “They were such violent attacks. And they were planned,” says Trish Newport, an Ebola programme manager at the aid group Médecins Sans Frontières (MSF, also known as Doctors Without Borders). Fearing for their safety, MSF evacuated staff from Butembo and Katwa, and the WHO and the DRC Ministry of Health together filled the vacuum.

By early March, these groups had rebuilt facilities. But a week later, assailants ambushed one of the centres again, killing a police officer on duty. Tedros arrived at the bullet-pocked clinic later that afternoon to check on his staff. He announced that rather than running away, his legions would double down. Then, in April, Mouzoko was shot dead at another hospital in Butembo.

Tedros’s eyes well up with tears when he speaks of Mouzoko and his four children, now fatherless in Cameroon. Tedros flew from Geneva, Switzerland, to Butembo again just after the murder. “When I got there I couldn’t speak,” he recalls. “The staff were scared but at the same time, they told me they won’t be intimidated.” He made a decision: “We can show our respect to him by finishing Ebola.”

Tedros has put the WHO in the spotlight in the DRC. Throughout this year, the WHO has had around 700 of its staff in the cities and towns where Ebola is spreading. In contrast, the US Centers for Disease Control and Prevention (CDC) has had only about a dozen epidemiologists in the country, and they are not in the hot zone. Other aid groups that were at the forefront of the world’s largest Ebola crisis — in West Africa from 2014 to 2016 — such as MSF and the Red Cross, are helping, but in lesser numbers than the WHO.

Health workers in Aloya try to convince a mother to send her child to an Ebola treatment centre.Credit: John Wessels for Nature

Another difference in the current outbreak is that the WHO’s Ebola responders are almost all African — from the DRC, Guinea, Senegal and other French-speaking nations. Fall says it’s a sign of Africa’s growing ability to fight outbreaks on the continent. And he feels a personal sense of commitment: “I’m an African, and when I see my own people suffering, it is like my family is suffering and I have to do something.”

Yet by June, the WHO had conceded that it needed help from sister UN agencies that handle other aspects of humanitarian crises. The head of the UN peacekeeping mission in the DRC, David Gressly, stepped in as emergency Ebola coordinator. Some 3,000 UN troops had already been deployed to areas around Butembo and Beni, and Gressly tasked them with making the region secure for the Ebola response.

Tedros returned again that month to check on the transition with Gressly, and to depoliticize the outbreak by winning the support of key figures in the country. This included meeting the head of the DRC alliance of traditional authorities — a system of leadership that pre-dates colonization — and the head of the leading opposition party. “They all need to have the same position” on Ebola, he explained.

Although Tedros’s background is in science — he is an epidemiologist by training — it’s his years as a politician that surface as he navigates the complexities of DRC politics. He served his home country of Ethiopia as minister of health, and then as the minister of foreign affairs from 2012 to 2016. When the previous head of the WHO, Margaret Chan, announced she would be stepping down, Tedros campaigned for the position with support from former US president Jimmy Carter, among others. In July 2017, he became the first African to run the WHO. He pauses to think about what that means to Africans, then says, “When I visit, they understand that I understand their situation.”

A delicate operation

One hot June afternoon, a 52-year-old woman, Kyamwatsi Muswagha, returns from hours spent walking through the town of Aloya. She is one of hundreds of locals rapidly enlisted to do contact tracing, and she was searching for two dozen people who had been close to Ebola-infected individuals. That day in Aloya alone, these locals were supposed to monitor 1,500 people. Across North Kivu and Ituri, the daily number of contacts to trace was around 20,000.

Muswagha hands a stack of papers to a WHO epidemiologist who is already surrounded by piles of paper on a picnic table. Each sheet lists a contact’s name and checkboxes for fever, diarrhoea and other Ebola symptoms. When someone’s symptoms persist for a couple of days, Ebola responders investigate. But when I asked how the data in these stacks of paper are collated and analysed, I never got a clear answer. And Muswagha concedes that she misses some information. Some families hide; others say they’re fine, hoping she’ll go away. And the contacts on the list are only a fraction of those who might be infected. As of May, fewer than half of the individuals diagnosed with Ebola had been on a contact list. That meant that they weren’t offered Ebola vaccines and weren’t being monitored.

Across a clearing from the picnic table is a dusty, concrete building that is Aloya’s main health facility. In one of seven dank rooms, a woman draped in shadow holds her seven-year old daughter, who has hives and a high fever. A physician and epidemiologist, Dorine Ngono, explains that the woman refuses to let health workers take her child to the Ebola centre an hour away. On a mattress in another room lies a woman who delivered a stillborn baby a few days earlier. Stillbirths are a symptom of Ebola, so the responders want to test both her and the infant for the virus. The woman is distraught, however, and won’t reveal where she has buried her baby. Ngono has shed her WHO vest, and beads of sweat pool near her hairline. “People need to trust me, so I’m removing all things that could appear as a barrier,” she says.

Soldiers patrol Butembo, a northeastern city in the DRC racked by conflict and Ebola.Credit: John Wessels for Nature

When Ebola first hit a year ago, responders directed people who felt feverish to well-equipped Ebola centres. But they soon realized that many people weren’t going. As of May, roughly one-third of those with Ebola had died outside of the centres (O. Ilunga Kalenga et al. N. Engl. J. Med. 381, 373–383; 2019). And of those who did go, the WHO estimated that an average of around six days passed between the onset of symptoms and check-in. In the intervening time, the sick visited their pastors, healers, pharmacists and local health workers long before they travelled to specialized Ebola units. And responders found that these facilities were becoming sources of new infections.

So rather than ignore medicine shops and clinics like the one in Aloya, the WHO decided to prepare them for the deadly virus. So far, Ebola responders have identified more than 1,000 such facilities in North Kivu, and they say they’re offering Ebola vaccines to the people working there. But 156 health workers have been infected in this outbreak, suggesting that something has gone awry. Bringing the clinics up to speed is labour-intensive, says Marie-Roseline Darnycka Bélizaire, a WHO field coordinator in Butembo. “You should see some of these places,” she says. “The floor is earth; the walls are old, decayed wood; some have no running water and the ceiling is so low you can’t stand up. And the main room with patients is about the size of one of our bathrooms.”

Ngono says that she and other outside specialists cannot just take the reins from local health workers, either. “We have to train them and let them do the work,” she says, “and give them a bonus in their salaries to do it.”

Criticism amid chaos

Ngono eventually convinces the woman who had given birth to have her blood tested. She is negative. That’s a good sign, as is the rising rate of people getting vaccinated in Beni. But good news always seems to be followed by bad. In July, two local Ebola responders were killed by their neighbours, who allegedly envied them for finding employment in the response. The following week, a woman with Ebola travelled to Uganda to sell fish, vomiting along the way. And an evangelical pastor with Ebola took a two-day bus ride from Beni to Goma, a city of two million with an international airport. From there, the virus could feasibly hitch a ride to Dubai, Belgium or Beijing.

The risk of the epidemic spreading internationally was growing larger every day, along with a chorus of analysts and researchers who criticized Tedros for not declaring the outbreak a ‘public-health emergency of international concern’, or PHEIC. Some observers worried that the WHO was repeating mistakes from the West African outbreak. Back then, critics had accused the organization of ignoring signs of an escalating crisis, and initially shirking its responsibility to assist Sierra Leone, Liberia and Guinea — countries where the infrastructures are too weak to handle the outbreak without help. An independent audit of the WHO’s actions in 2015 concluded that without significant change, the agency would no longer be considered the pre-eminent guardian of global public health.

Ebola responders disinfect a home in Aloya in which three people have died.Credit: John Wessels for Nature

Such opinions matter because the WHO is kept afloat by donations from governments and philanthropists, who must be convinced of the value of their investments. In response to the charges, in 2016, the WHO created an emergency operations programme that included a contingency fund of a proposed US$100 million to be tapped quickly in a crisis. When Tedros took office, he promised to strengthen the operation’s capacity. The number of WHO emergency responders in Africa has more than doubled from 100 in 2016 to more than 250 in 2019.

Money from the contingency fund allowed the WHO to deploy epidemiologists and supplies to eastern DRC as soon as the Ebola outbreak started. And Tedros has consistently called the situation an emergency — even though he and his advisers delayed calling it a PHEIC, worrying that this could backfire if countries responded by closing borders. “Whether or not you label it a PHEIC does not matter for us,” says Newport at MSF. “What matters is that the WHO has been present and is working hard in one of the most complex emergencies we’ve seen in a long time.”

But by July, the WHO had burnt through its contingency fund, forcing it to scale back support in other disasters around the world, such as a surge of childhood HIV in Pakistan. Come August, only $8.7 million was left in the pot, and donors weren’t giving enough additional money. For the first half of 2019, they had given the WHO less than half of the $98 million it requested for the Ebola response. And the agency estimates that the response for the second half of the year will cost nearly $300 million. On 17 July, Tedros sounded the alarm, declaring the outbreak a PHEIC.

Suddenly, the media was all over the epidemic. But with renewed attention comes added scrutiny. Some officials and researchers bemoan a lack of epidemiological information — the type of data collected in piles of paper on the picnic table in Aloya. Either they don’t exist or the WHO isn’t sharing them, suggests Jennifer Nuzzo, an epidemiologist at Johns Hopkins University in Baltimore, Maryland. Intelligence on how many contacts aren’t being monitored daily, or on how many health workers refuse vaccines, could help scientists to pinpoint gaps in the response. Nuzzo says she understands the WHO needs the money, “but we need to make sure we’re not trying to fill a bucket with a hole in it”.

In May, an independent committee published a different set of concerns about the WHO’s emergency response. The group called the operation impressive, but expressed concern over public-health messaging. The committee had spoken with community leaders in Butembo, for example, who said that Ebola is spread by dirty hands when, in fact, it passes through the bodily fluids of infected people. The report also said the WHO was overstretched, and suggested that armed guards around Ebola centres and vaccine stations could intimidate communities.

Tedros acknowledges gaps in his agency’s response, but notes that the WHO and the DRC government had rapidly contained an Ebola outbreak just before this one in western DRC, a more stable region of the country. “We’re trying to do better,” he says, “but we also need to protect our responders from ambushes — we’ve already lost seven.” Another 60 have been injured in targeted attacks just this year.

And Tedros is trying to respond to complaints from people in the DRC, too. Chief among their issues is what they see as neglect for other pressing health problems, such as measles, malaria and malnutrition. So now, the WHO, the DRC Ministry of Health and aid groups are providing more general health care, to show that they want to help. “When I visit, people ask me why I care about Ebola alone when they have other killers,” says Tedros, “and I am embarrassed that the answer to that question is that the international community is only concerned if something can cross the border.”

Fragile states

Back in June, on a warm evening filled with birdsong in Beni, medical anthropologist Julienne Anoko sits by a pool at the Okapi Hotel. A silhouette of a sniper’s nest on the roof is the only reminder that the city is under siege. Anoko was staying here last November, when bullets blasted through the plaster of her room. She will sleep in the same room tonight, but she seems relaxed, having just returned from several days spent deep in the forest.

Anoko is renowned for such missions. In 2014, she calmed tensions in Guinea by introducing a ceremony for burying Ebola-infected corpses that appeased mourners and infectious-disease specialists alike. As soon as the DRC outbreak began, the WHO flew her to North Kivu, asking her to lead a team of 40 other social scientists. Their goal is to change the behaviour of communities so that people will permit invasive measures, such as Ebola responders dressed in white space suits dousing belongings with chlorine solution.

On Anoko’s most recent trip, she had ridden motorcycles through the jungle with a handful of other Ebola responders. At one town known to have housed several people with Ebola, a community refused to allow the group to enter. “I tried to talk with the mothers, but they just stared at me,” Anoko says. As people gathered to watch, she asked a boy for his name. He sassily said he was Lionel Messi, the Argentinian football star. So she told him to call her Cristiano Ronaldo, and then challenged him to arm-wrestle her for the World Cup. “So we wrestled,” she says, “and everyone was watching and laughing.” Anoko returned the next day with a football as a gift. And then the community agreed to let in health workers with vaccines.

Tedros greets colleagues in Butembo with what has become the unofficial salutation for Ebola responders.Credit: John Wessels for Nature

“People are so afraid. They don’t know if we might be terrorists who want to kill them,” she says. “So we just show them that we are human — mothers, fathers, sisters, brothers — we explain why we want to help.” These conversations work, she says; they only take time. And when armed groups ambush, people run for their lives. “It’s like Sisyphus,” says Anoko, lifting her arms. “You are pushing this boulder and when you think you’re at the top, there’s an attack and the rock rolls down again.”

In July and August, armed groups killed and abducted more DRC civilians. In response, residents of Beni held a protest directed at UN troops and the authorities who had failed to protect them. The responders stayed indoors that day. As of 7 September, Ebola had infected roughly 3,080 people, killed 2,060 and spread 700 kilometres to the war-weary province of South Kivu, bordering Burundi and Rwanda.

A prospect that terrifies specialists on pandemics is that the outbreak in eastern DRC represents a type of complex emergency that no health agency will ever be able to extinguish rapidly. Ebola and other deadly pathogens will keep spilling over from animals into humans, and the ever-increasing mobility of people will help infections spread. It’s no coincidence that the world’s two largest Ebola outbreaks have exploded in densely populated regions of countries with ineffective health systems, extreme poverty and a history of exploitative colonization and conflict.

Chikwe Ihekweazu, the director of Nigeria’s Centre for Disease Control, reflects on Ebola responders who have been stationed at the epicentre of the outbreak for months. “I know how hard my colleagues in the field are working — 18-hour days, losing track of the weekend,” he says. “In some ways, they are paying for all of us ignoring the situation in this part of the continent for many years.”

This outbreak will eventually end, but it could cost tens of thousands of lives and billions of dollars. When Tedros took the helm at the WHO, the top of his agenda was not emergency response, but universal health care — delivering basics such as antibiotics, vaccines and a network of labs to identify infections. Curbing Ebola should be straightforward with political stability and a robust health system, Tedros says. But in their absence, a cycle of tragic, multimillion-dollar health disasters will continue to flourish in the DRC, Yemen and other fractured regions of the globe. “As long as places are this vulnerable, this will keep happening,” he says. “We will fix Ebola — and it will come back tomorrow.”

Nature 573, 178-183 (2019)

doi: 10.1038/d41586-019-02673-7

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NEWS FEATURE

10 September 2019

How to banish manels and manferences from scientific meetings

A Nature analysis finds that several fields of science are moving away from male-dominated conferences and panels — but it’s easy to slip back into old habits.

Holly Else

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Nancy Amato didn’t want to go to Las Vegas. In 2015, it was the chosen venue for one of the main events in her field — the International Conference on Robotics and Automation (ICRA). But she and other women involved in organizing it felt that the city, famed for its strip clubs, was unsuitable. Among the first achievements of the organizing committee — which that year was all-female — was moving the conference to Seattle in Washington.

The committee had even bigger ambitions for the male-skewed meeting. “Often, people say there aren’t any women speaking because there aren’t any out there, so we thought, ‘Let’s show them a tonne of women and that might change things’,” she says.

Hear reporter Holly Else talk more about ‘manferences’.

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Keen for attendees to focus on the agenda of the event, rather than on the gender of its coordinators, Amato and the committee set out to create the best possible version of the conference. They came up with new features to foster greater diversity and inclusion, including an advice forum for PhD students and a careers fair. They invited roughly an equal number of male and female speakers, in contrast to the 100% male line-up of the 2014 meeting. The event also broke records for submissions and attendance, and sold out of space for exhibitors and sponsors for the first time in its history. “Overall, it was a success on any measure,” she says.

“But if you look at the follow-on years, it doesn’t seem like it has changed the story on diversity much,” says Amato, a computer scientist at the University of Illinois at Urbana–Champaign. Over the years, ICRA has slipped in and out of being a ‘manference’ — a conference heavily dominated by male speakers.

Source: ICRA

It’s a common problem for scientific fields. A new analysis by Nature suggests that meetings are able to correct a pronounced gender bias at the podium, but that it takes persistent and constant effort to banish the manference.

Our investigation looked at the line-up of invited speakers at key meetings in five disciplines — neuroscience, artificial intelligence (AI), chemistry, geology and microbiology — over the past nine years. Four of the five fields seem to have made progress in diversifying the speakers at their key meetings, and in all five fields the ratio of women to men among invited speakers exceeded the overall ratio of senior women in those fields. Those with farthest to go have made the biggest gains: at the 11 machine-learning and AI meetings Nature examined, for example, the proportion of female speakers increased from 7% in 2011 to 38% in 2019. Neuroscience, geology and microbiology also show positive trends. But chemists are struggling to move the needle on diversity; across 13 chemistry conferences in the Nature analysis, the proportion of women among invited speakers rose by just one percentage point.

Good intentions are not enough, say some conference organizers. Instead, firm gender quotas or policies that compel diversity seem to reap the most success. And the effort must be repeated every year. “The conferences that are doing well should see that as a first step to asking themselves what they can do next,” says Anne Churchland, a systems neuroscientist at Cold Spring Harbor Laboratory in New York.

Panel police

The manference and its sibling — the ‘manel’, or male-only panel — have yet to reach the pages of dictionaries but first took off as hashtags on social media in the early 2010s. In 2012, microbiologist Jonathan Eisen began using his blog to flag male-dominated meetings in his field. The same year, Churchland started posting details of potential female speakers online, in a bid to highlight overlooked women in neuroscience. The list now features more than 600 female systems neuroscientists. And in 2015, Finnish political scientist Saara Särmä set up a Tumblr site to post photographs and screenshots of manels under the tagline: ‘Congrats, you have an all male panel!’ The site has since documented more than 2,000 manels. Several researchers have publicly stated that they will turn down invitations to appear at conferences at which the schedule is male-dominated. These efforts have blossomed into an ecosystem of blogs, Tumblr and Twitter accounts documenting manferences and manels. (Organizers of several of the meetings investigated by Nature started trying to increase diversity before this social-media buzz.)

There is more at stake than just the accolade of being asked to speak. The administrator of the Australia-based Twitter account @ManelWatchAU, a biomedical scientist who wishes to remain anonymous for fear of retaliation, says that passing over women for speaking engagements harms their careers. “In grant applications, you have to explain how you have a national or international profile. If women are not invited to talk at these events, they don’t have that.”

To assess the extent of manferences across five disciplines, Nature selected at least nine influential meetings in each community and recorded, as far as possible, the presumed gender of all invited speakers — those hand-picked by conference organizers, rather than scientists who put themselves forward to give talks or present posters (Nature did not ask about non-binary people in the analysis). Adding together the number of male and female invited speakers across each field’s meetings reveals some trends, despite the small sample size (see ‘A changing balance’). In neuroscience, the proportion of female speakers almost doubled, rising from 24% in 2011 to 42% in 2019. Microbiology has shown similar improvement, with the proportion of female invited speakers increasing from 28% to 40% across the same time period. Geology has seen more rapid progress, but from a lower starting position: women took the podium for 38% of invited talks in 2019, up from 13% in 2011. And in AI, the needle moved 31 percentage points from a lowly 7% in 2011. Not every discipline saw an increase, however: across 8 years of 13 chemistry events, female representation has remained below 24%.

But these trends mask sometimes dramatic swings in the number of female speakers, depending on which conference and year is under scrutiny (see full data at Supplementary information). For example, in 2013, more than 40% of invited speakers at the Japanese Neuroscience Society’s annual meeting were women. But in 2016, they were all men, despite a diversity and inclusion committee having been established in 2005. Meanwhile, in AI, the International Conference on Learning Representations has gone from an all-male line-up to a 50:50 split over the past four years.

To estimate the overall proportion of female researchers in each field, and the proportion of female senior authors — those who might be invited to speak at conferences most often — Nature examined data on the gender of authors of research papers, approximated using gender-analysis software by informaticians Vincent Larivière, at the University of Montreal in Canada, and Cassidy Sugimoto at Indiana University Bloomington. Others have used different methods with similar results: the website BiasWatchNeuro estimates the underlying proportion of senior women in various neuroscience disciplines by looking at the gender balance among those securing grants from the US National Institutes of Health or, where available, conference attendance records.

Some researchers are disappointed not to see a more consistent upward trend for the meetings in their fields. Churchland says that the number of female speakers is an indicator of the extent to which organizers have reached out beyond the usual invitees. “If the line-up is all-male, you know the conference organizers invited their friends from grad school and did not put much effort in to create the best programme,” she says.

Angeline Pendergrass, an atmospheric scientist at the US National Center for Atmospheric Research in Boulder, Colorado, was pleasantly surprised at the changes in the geosciences. “It’s better than I expected. I’m not mentally tallying this up when I’m at a meeting, but some of these are getting close to 50%.” She thinks that heightened awareness of the importance of diversity in science has probably played a part in the trend.

Such sea changes in science are having an impact on conferences. Raia Hadsell, a machine-learning researcher who has helped to organize several of the conferences analysed by Nature, says that the drive for diversity has coincided with increased public scrutiny of AI and a rash of headlines about bias in algorithms themselves. But conferences influence each other, too, says Hadsell, who works at the Google-owned AI company DeepMind in London. For example, when the Neural Information Processing Systems conference introduced a code of conduct to improve inclusivity in 2018, several others followed suit, and most events now offer child care.

Hadsell says Nature’s data suggest that the efforts made in AI over the past decade have led to real change. “It wasn’t just a blip; we aren’t going to go back,” she says. But Nature’s data on robotics meetings show that gains are not always steady. After the 2015 ICRA meeting, which Amato and colleagues worked hard to balance, the invited speaker line-up ricocheted back to more than 80% male. Only in 2017 did the ratio come close to parity again.

This informal approach is giving some positive results in AI, but it has not always had the desired effect in chemistry. Frustrated by the lack of progress, several chemists say they are now considering installing more formal policies — or even quotas — for conferences they organize.

At the International Union of Pure and Applied Chemistry (IUPAC), which endorses a large number of conferences and which has held an annual world congress for almost 50 years, organizers must report the anticipated speaker line-up for plenary sessions and keynote talks. The hope is to raise awareness by specifying the male-to-female ratio. Chemist and IUPAC secretary-general Richard Hartshorn, at the University of Canterbury in Christchurch, New Zealand, says that alarm bells ring if the reported proportion of female speakers falls below 30%. “There is no official policy on this; possibly there should be, and this is something that I will look at. Regrettably, I have still had to intercede on rather too many occasions,” he says.

Source: IUPAC

Finding women to fill these slots can be tricky, says chemist Varinder Aggarwal at the University of Bristol, UK, who runs the Bristol Synthesis Meeting. “We are fishing in a smaller pool; the people we target are heavily in demand. Women are pulled in all directions because we want them on committees, as speakers and on interview panels,” he says. Having seen Nature’s data, he suggests that tougher action is needed. “There needs to be a stronger policy about it. But what is the right number?” he asks.

Plenty of conference organizers still dodge this question, and have no formal policy on gender balance. The scientist behind @ManelWatchAU says that a perceived lack of women in a field is no excuse for skewed slots: “Even in fields where the percentage of women is low, there are more excellent women speakers than the number of speaking slots.” In June she posted a series of tweets calling out the skewed gender balance at a series of events organized by Nature Research (Nature Research is part of Springer Nature, which publishes Nature). Nature’s editor-in-chief, Magdalena Skipper, who is also chief editorial adviser for Nature Research, says that Nature Conferences is in the process of formalizing a code of conduct for meeting organizers. “We want to foster diversity at our conferences and other events, focusing on gender diversity but also recognizing that there are many axes of diversity,” she says.

Many scientists would welcome a code of conduct holding organizers accountable. Heather Carson, a PhD student at the University of Sheffield, UK, was disappointed on attending a theoretical-chemistry event for early-career scientists this year to find only men talking about their work. It is easy for conference organizers to say they are trying, but until there are consequences, she says, they won’t go out of their comfort zone to find female speakers. “In theoretical chemistry, we are not being heard,” she adds. Spurred by her experience, Carson is now planning to organize her own event for female junior researchers.

Programme of improvement

Even meetings that have made strides in gender balancing find it is all too easy to slip into skewed territory. In 2016, BiasWatchNeuro highlighted the computational neuroscience meeting Cosyne as a poster child for diversity. Cosyne had reversed years of male-skewed programmes by requiring a 50:50 gender split among invited speakers. At its 2019 event in Lisbon, it complied with the rule, and included seven male and six female invited speakers. But the story was different for the individuals who gave the 30 or so contributed talks, and who were chosen from a pool of applications rather than being invited by the committee. Cosyne’s informal target is to give around 30% of the slots to women.

Source: Cosyne

An unexpected dip in the number of women giving contributed talks — from 45% in 2018 to 23% this year — meant that women were at the low end of the expected range given the number of applications they made. For Stephanie Palmer, a theoretical neuroscientist who joined the conference’s committee in 2017, this year’s event was the most stressful of her career. Angry attendees turned to Twitter to call out the meeting’s lack of diversity using the hashtag #Brosyne. Palmer says she felt responsible and upset. With a background in the heavily male-skewed discipline of theoretical physics, she knows what it is like to encounter bias. “You care about people not having that same uphill battle,” she says. For the 2020 conference, organizers are trialling blind reviews of proposals to make sure that the selection process for posters and contributed talks isn’t biased.

The Cosyne example shows that quotas can add complications. Amato says she is hesitant to mandate gender quotas because the body that oversees ICRA — the IEEE Robotics and Automation Society in New Jersey — already has requirements for geographical diversity at its events. “In Asia, it is hard to find the senior women, and you don’t want the same people speaking all the time.” Indeed, the 2015 meeting achieved gender parity only because it did away with the geographical requirement, she says.

As far as forms of diversity go, ethnicity and race, country of origin and language are important, yet are harder to monitor than gender, says DeepMind’s Hadsell, who is conscious of the broad impact of machine learning. “The owners of this technology have to be global, and that means having representation at conferences,” she adds. Efforts to broaden diversity at the International Conference on Learning Representations, for instance, mean that the 2020 event will be held in Ethiopia for the first time.

Several high-profile figures have taken a stand to ensure that meetings strike a good balance. In June, Francis Collins, the head of the US National Institutes of Health, vowed to decline speaking invitations at events that did not have sufficient speaker diversity. Jeremy Farrar, head of London-based biomedical charity Wellcome, quickly followed suit, and Skipper pledged not to chair all-male panels.

Those actions go some way towards changing the status quo, but many scientists still feel they have a battle ahead. “People have a very mistaken idea that once you take gender or race into account you are lowering the quality,” says Yael Niv, a neuroscientist at Princeton University in New Jersey and a member of BiasWatchNeuro. “That is completely false and demonstrably false, but that’s the zeitgeist.”

Even for meetings that have achieved equality by inviting women to speak, Pendergrass says there is a more important task to remember: listen to what they have to say.

Nature 573, 184-186 (2019)

doi: 10.1038/d41586-019-02658-6

Richard Van Noorden and Emiliano Rodríguez Mega assisted with data analysis.

Supplementary Information

1. Full data and methodology

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02658-6

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Comment

- What’s next for Registered Reports? [10 September 2019]

Comment • Reviewing and accepting study plans before results are known can counter perverse incentives. Chris Chambers sets out three ways to improve the approach.

- Keep quantum computing global and open [11 September 2019]

Comment • The race to cash in is draining universities of talent, fracturing the field and closing off avenues of enquiry, warn Jacob D. Biamonte, Pavel Dorozhkin and Igor Zacharov.

- Danger and strangers: the trouble with face value [09 September 2019]

Books & Arts • Malcolm Gladwell’s latest tome probes mutual misunderstanding and violations of trust. Tim Radford weighs up its riches.

- The enlightenment of age [10 September 2019]

Books & Arts • Toren Finkel lauds two books outlining very different ways of achieving a longer ‘healthspan’ — through pharmacology or integrative care.

- India’s journey to the red planet [11 September 2019]

Books & Arts • Subhra Priyadarshini lauds a film on the country’s first interplanetary craft, the Mars Orbiter Mission.

- Scientists — make time for contemplation [10 September 2019]

Correspondence •

- South African system tracks SDG research [10 September 2019]

Correspondence •

- Colombia short on political will to protect pollinators [10 September 2019]

Correspondence •

- Bioethicists clarify mitochondrial-therapy ban [10 September 2019]

Correspondence •

- Not a first: identifying hominin fossils from their proteins [10 September 2019]

Correspondence •

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COMMENT

10 September 2019

What’s next for Registered Reports?

Reviewing and accepting study plans before results are known can counter perverse incentives. Chris Chambers sets out three ways to improve the approach.

Chris Chambers

Chris Chambers is a professor of cognitive neuroscience at Cardiff University, UK.

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What part of a research study — hypotheses, methods, results, or discussion — should remain beyond a scientist’s control? The answer, of course, is the results: the part that matters most for publishing in prestigious journals and advancing careers. This paradox means that the careful scepticism required to avoid massaging data or skewing analysis is pitted against the drive to identify eye-catching outcomes. Unbiased, negative and complicated findings lose out to cherry-picked highlights that can bring prominent articles, grant funding, promotion and esteem.

The ‘results paradox’ is a chief cause of unreliable science. Negative, or null, results go unpublished, leading other researchers into unwittingly redundant studies. Ambiguous or otherwise ‘unattractive’ results are airbrushed (consciously or not) into publishable false positives, spurring follow-up research and theories that are bound to collapse.

Clearly, we need to change how we evaluate and publish research. For the past six years, I have championed Registered Reports (RRs), a type of research article that is radically different from conventional papers. The 30 or so journals that were early adopters have together published some 200 RRs, and more than 200 journals are now accepting submissions in this format (see ‘Rapid rise’). When it launched in 2017, Nature Human Behaviour became the first of the Nature journals to join this group. In July, it published its first two such reports[1]. With RRs on the rise, now is a good time to take stock of their potential and limitations.

Source: C. Chambers

How do they work?

The Registered Report format splits conventional peer review in half. First, authors write an explanation of how they will probe an important question. This ‘Stage 1’ manuscript includes an overview of the background literature, preliminary work, theory, hypotheses and proposed methods, including the study procedures and analysis plan. Before researchers do the studies, peer reviewers assess the value and validity of the research question, the rationale of the hypotheses and the rigour of the proposed methods. They might reject the Stage 1 manuscript, accept it or accept it pending revisions to the study design and rationale. This ‘in-principle acceptance’ means that the research will be published whatever the outcome, as long as the authors adhere closely to their protocol and interpret the results according to the evidence.

Animal registries aim to reduce bias

After the Stage 1 manuscript is accepted, the authors formally preregister it in a recognized repository such as the Open Science Framework, either publicly or under a temporary embargo. They then collect and analyse data and submit a completed ‘Stage 2’ manuscript that includes results and a discussion. They are free to conduct further exploratory analyses, provided these are clearly identified as post hoc — having been done after planned analyses were completed. The Stage 2 submission is sent back to the original reviewers, who cannot question the study rationale or design now that the results are known. Whether the results are judged by reviewers to be new, groundbreaking or exciting is irrelevant to acceptance. At the journal Cortex, where I serve as an editor, the acceptance rate for Stage 1 RRs that enter in-depth review is about 90%: more than double that of conventional articles. The publication rate at Stage 2 is currently 100%, with no withdrawals by authors.

This assured acceptance means that authors are free to present results as they are, without having to shoehorn them into a clean, compelling narrative. And the outcome is striking. An analysis this year[2] suggests that RRs are more likely to report null findings than are conventional articles: 66% of RRs for replication studies did not support initial hypotheses; for RRs of novel studies, the figure was 55%. Estimates for conventional papers range from 5 to 20%[2]. It is possible that researchers opt for this format when they think that null findings are likely. Nonetheless, these disparities suggest that RRs are a powerful way to counter publication bias (see ‘A brief history of Registered Reports’). And the research community cares: preliminary evidence finds that RRs are cited at levels that are comparable to or slighter higher than those for conventional articles[3].

A brief history of Registered Reports

The potential of protocol registration to prevent publication bias and increase rigour has been recognized for decades in clinical-trials research. A format similar to Registered Reports (RRs) was also piloted at the now-defunct European Journal for Parapsychology in the 1970s to help ensure publication of negative results.

In 1997, The Lancet launched an article type similar to Stage 1 of RRs, which reviewed protocols of proposed research. Almost 150 were published before the article type was discontinued in 2015, ostensibly because other outlets served the same purpose^6.

I began lobbying the editorial board of Cortex to consider RRs almost as soon as I joined as an editor. It gave the green light in November 2012, and by March 2013 it had adopted the full RR format. At around the same time, a separate group launched a variant focusing on replications at Perspectives on Psychological Science^7. The same year, psychologists Brian Nosek and Daniël Lakens announced that a special issue of Social Psychology would use the format to publish replications of important results^8.

From 2014, more journals in neuroscience and psychology began adopting and publishing RRs, and the format has now expanded across the life and social sciences. No specialized physical-science journals yet offer them.

Some multidisciplinary journals — including Royal Society Open Science — have launched the format across all subjects in science, technology, engineering and mathematics. I hope RRs will become an option in all mainstream life- and social-science journals within ten years.

One of the most striking characteristics of RRs is that reviewers can help authors to improve the protocol or rationale while it is still possible to make changes. I have overseen numerous cases in which reviewers have intervened to prevent a serious flaw in a study design — adding crucial controls, ensuring the sample size is sufficient or explaining why the hypotheses or planned statistical analyses cannot really answer the research question. Even when a proposed design is sound, the review process often adds clarity and focus. In my experience, the reviewers find the process rewarding. One comment from a reviewer is typical of the informal feedback I receive: “If the authors can incorporate many of the suggestions from all of us reviewers, they will have a far better study than what they originally planned, which is really valuable and exciting.”

Real and imagined concerns

As RRs have grown, I have come to spend as much time advocating, optimizing and getting feedback on the format as I do on my own research. I chair the Registered Reports committee supported by the Center for Open Science, and serve as a Registered Reports editor at BMJ Open Science, Collabra: Psychology, the European Journal of Neuroscience, NeuroImage, PLoS Biology and Royal Society Open Science.

I am often asked whether all research publications should be RRs. No! Work that is purely exploratory and not driven by a hypothesis is usually not suitable for the format. For example, an RR might be a poor fit for the discovery of a new disease mechanism or potential drug molecule without a clear set of predictions. Often, the same goes for work to develop new experimental methods. RRs are not designed to supplant publications that announce this kind of research; they are intended only to strengthen the rigour and transparency of studies that test hypotheses.

Another common question is whether RRs are suitable for sequential experiments in which the results of one study determine the design of the next. In principle, yes: many journals now offer ‘incremental registrations’ in which authors can re-enter Stage 1 review after the results are in, and then add protocols for one or more further studies.

In practice, authors rarely take up this option, probably because of the time associated with multiple rounds of Stage 1 review. More common is for authors to perform a series of experiments and report these in the Stage 1 manuscript. These can then be used to design one or more extra experiments to ‘seal the deal’. The final article describes all of the experiments and is badged as an RR. Another option is for authors to preregister multiple experiments at the beginning, as in one recent study. Over eight experiments, it asked whether light in the range typically used in optogenetics studies can influence neuronal physiology in mice[4].

Reboot undergraduate courses for reproducibility

There are also times when hypothesis-driven research itself is not suitable for RRs. Studies seeking to capture the effects of unpredictable events (such as solar flares, flash floods, mass violence or stroke-induced brain injury) must start collecting data as soon as is feasible. They cannot wait two to four months for a Stage 1 manuscript to complete peer review. (Ideally, researchers would still take a few minutes to self-register their protocol in a recognized repository.) Similarly, undergraduate students who must finish a summer project in a short time might not be able to wait for reviewer feedback, although some teaching programmes have had success by dividing up research-project design and execution in creative ways (see, for example, K. Button Nature 561, 287; 2018).

By contrast, RRs have distinct advantages for longer-term students. The in-principle acceptance at Stage 1 allows them to list a publication much sooner than they could for a conventional manuscript, and with more certainty. There is emerging evidence that RRs are popular with early-career researchers. For example, at Cortex, 78% of RR first authors (n = 82) are PhD students or postdocs, compared with 67% in a control sample (n = 57) of conventional articles.

Although RRs require researchers to wait for review before starting experiments, I suspect that the time to publication probably declines overall. A conventional article might be rejected on the basis of results or because of methodological problems that can no longer be fixed, leaving authors to submit their work to journal after journal, or to perform extra experiments. Over the past six years, dozens of authors have told me —and written publicly — that they appreciate the more-predictable timeline of RRs (see, for example, go.nature.com/2kwnjuj).

Decreased flexibility is an oft-expressed concern over the format. One early critic said it would “put science in chains”. The fear is that peer-reviewed preregistration dampens the creativity and serendipity that could come from free-wheeling data exploration. But preregistration imposes no such limit: it merely requires that exploratory analyses are labelled transparently as post hoc and do not dominate conclusions.

Exploration is alive and well. Stage 2 submissions almost always include further analyses. The difference is that researchers cannot fool themselves or their readers by presenting only the most interesting analyses or imply that these were intended from the outset. RRs are a plan, not a prison.

A related misgiving is that researchers will find themselves locked into a suboptimal protocol once experiments begin. In my experience, the opposite is more likely: reviewers can prevent researchers from running less-informative experiments. And reviewers of Stage 2 manuscripts generally understand reasonable changes. It is not flexibility that is lost, but the ability to airbrush both reasonable and questionable changes out of the picture.

Moving forward

RRs are not a panacea — the format needs constant refinement. It currently sits rather awkwardly between the old world of scientific publishing and the new. Innovations over the next few years should make this format even more powerful, and stimulate wider reforms.

Transparency. When RRs first launched, some journals published Stage 2 manuscripts but not those for Stage 1, making it impossible for readers to see whether the completed protocol matched the planned one. In 2018, the Center for Open Science launched a simple tool that places submitted Stage 1 manuscripts in a public registry (see go.nature.com/2kb5s7v). This is now used by many journals, including Cortex and Animal Behavior and Cognition. The publisher Wiley has opted to publish accepted protocols. And venues such as F1000Research offer the option to post Stage 1 articles before peer review, with reviews and revisions made public as they become available. A badging system shows that the Stage 2 article adhered to the criteria and can be labelled as a RR.

Standardization. Improving the standardization of submitted protocols promises to improve computational reproducibility. Currently, submitted manuscripts are often prepared in word-processing software and contain insufficient methodological detail or linking between predictions and analyses. The next generation of RRs — ‘Registered Reports 2.0’ — is likely to be template-based and could integrate tools such as Code Ocean (see https://codeocean.com/researchers). This would ensure that analyses are immutable within a stable, self-contained software environment. With standardized metadata and badging, RRs will become useful for systematic reviews and meta-analyses.

Efficiency. The review process can be extended even further back in the research life cycle. Under the emerging RR grant model, reviewers award funding and signal in-principle acceptance of a research publication simultaneously or in rapid succession. The Children’s Tumor Foundation and PLoS ONE have pioneered such a partnership (see go.nature.com/2kpjzat), as have Cancer Research UK and the journal Nicotine & Tobacco Research[5]. More are in the works.

The lesson of RRs speaks to all areas of science reform. Instead of forcing quality to compete with success, partner them up. Instead of pitting what is best for the individual against what is best for all, create a model that benefits everyone — the scientist, their community and the taxpayer — and the rest will come naturally.

Nature 573, 187-189 (2019)

doi: 10.1038/d41586-019-02674-6

References

1. 1.

Nature Hum. Behav. 3, 763 (2019).

2. 2.

Allen, C. & Mehler, D. M. A. PLoS Biol 17, e3000246 (2019).

3. 3.

Hummer, L. T., Singleton Thorn, F., Nosek, B. A. & Errington, T. M. Preprint at OSF Preprints https://doi.org/10.31219/osf.io/5y8w7 (2017).

4. 4.

Ouares, K. A., Beurrier, C., Canepari, M., Laverne, G. & Kuczewski, N. Eur. J. Neurosci. 49, 6–26 (2019).

5. 5.

Munafò, M. R. Nicotine Tob. Res. 19, 773 (2017).

6. 6.

The Editors of The Lancet. Lancet 386, 2456–2457 (2015–16).

7. 7.

Simons, D. J., Holcombe, A. O. & Spellman, B. A. Persp. Psychol. Sci. 9, 552–555 (2014).

8. 8.

Nosek, B. A. & Lakens, D. Soc. Psychol. 44, 59–60 (2013).

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COMMENT

11 September 2019

Keep quantum computing global and open

The race to cash in is draining universities of talent, fracturing the field and closing off avenues of enquiry, warn Jacob D. Biamonte, Pavel Dorozhkin and Igor Zacharov.

Jacob D. Biamonte,

Jacob D. Biamonte is associate professor and head of laboratory at the Deep Quantum Laboratory, Skolkovo Institute of Science and Technology, Moscow, Russia.

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Pavel Dorozhkin &

Pavel Dorozhkin is deputy director of the industrial programmes department at the Deep Quantum Laboratory, Skolkovo Institute of Science and Technology, Moscow, Russia.

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Igor Zacharov

Igor Zacharov is a senior research scientist at the Deep Quantum Laboratory, Skolkovo Institute of Science and Technology, Moscow, Russia.

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A researcher works on a device for cooling the quantum enhanced processor developed by D-Wave Systems in Burnaby, Canada. Credit: D-Wave Systems

In just a few years, the field of quantum computing has moved swiftly from an academic backwater to a subject of vast public and private interest. The ultimate goal of a ‘universal’ quantum computer — capable of performing any calculation while correcting for noise, faults and disruptions — remains decades away. But billions of dollars are being ploughed into commercializing the first fruits[1].

The US technology company IBM and Canadian firm D-Wave Systems are already selling access to quantum-enhanced calculators. Google, Microsoft and Intel plan to do so in three to five years. These early devices should perform certain tasks faster than a conventional computer. They are, however, less versatile and less powerful than a universal quantum computer, and are still subject to errors and noise. Areas such as machine learning and optimization could benefit — if technical challenges can be overcome[2],[3].

But the race to cash in is fracturing the field. Companies are rushing to build large teams of researchers, draining universities of talent[4],[5]. Hundreds of start-ups are patenting the products of publicly funded research, closing off avenues of enquiry.

Quantum computers put blockchain security at risk

Public funding for quantum computing is also booming. But it is uneven and skewed towards hardware. North American institutions dominate, and drive the field in directions that suit them. They focus on superconductor technologies, for example. Researchers lacking huge labs and infrastructure find it hard to compete. Geopolitical walls are also rising as national security and commercial interests heat up.

All of this is happening at a crucial time. Moore’s law — which states that the number of transistors in integrated microchip circuits doubles about every two years — is stalling. And machine learning is opening its doors to entirely new industries. We cannot wait decades for ‘quantum advantage’: the point at which a quantum processor solves a problem impossible for any existing classical computer to solve. This contrasts with other fields, such as biotechnology, in which the revolutionary technique of CRISPR gene editing emerged 20 years after the field seemed to have peaked in the 1990s.

We appeal to academic and industrial scientists to develop quantum applications in an open scientific spirit. Basic research must not be done in isolation or steered by political agendas. These huge investments and the devices stemming from them should serve all of humankind, like science itself.

Global quantum state

Most of the concepts underpinning quantum computers have come from publicly funded research. Now that quantum computing is potentially valuable, many governments are ramping up support.

A handful of nations — the United States, the United Kingdom, Japan, Sweden, Singapore, Canada and China — are leading the way. Each committed between US$100 million and $300 million per year to quantum computing research in 2017; the United Kingdom’s total public and private investment since 2014 now exceeds $1 billion. In 2018, the United States and the European Union both launched billion-dollar behemoths: the five-year US National Quantum Initiative and the ten-year EU Quantum Technologies Flagship programme. China aims to open the world’s largest quantum-research laboratory in 2020 at a cost of $10 billion.

First quantum computers need smart software

Other countries are following suit. India and South Korea each intend to invest tens of millions of US dollars per year. And Russia includes quantum technology in its top-ten list of national technological initiatives. A number of leading centres are being formed there to coordinate private and government research and development. Large projects should receive up to $300 million in the first phase.

But many of the results flowing from all this investment are being hived off. Corporate interests and a cooling of the international political climate are making it harder for scientists to collaborate and share knowledge[6],[7]. Closing off areas leads to pointless replication and time wasted pursuing dead ends.

For example, quantum computing’s implications for national security were highlighted in a 2019 report by the US National Academy of Sciences[8], sponsored by the Office of the Director of National Intelligence. Scientists funded by the US Department of Energy now face a ban on collaborating with researchers from some 30 countries, including China and Russia[6].

Such shadows are affecting our research at Moscow’s Skolkovo Institute of Science and Technology — an English-speaking advanced research university that was established in 2011 in partnership with the Massachusetts Institute of Technology in Cambridge. We chose to work at Skoltech because of its international, world-class and collaborative atmosphere. Take our origins: J.D.B. is American, P.D. is Russian and I.Z. is a Dutch citizen of Russian descent. Although our close collaborators continue to interact with us, old research agreements between Russia and the EU are fizzling out, with no discussion of renewal. Partnerships between participants in the EU quantum flagship and scientists in the United States, Russia or China now require special negotiations.

Research gaps

Quantum technology risks becoming another ‘Moonshot’ race in which the winner takes all. North America has built up an insurmountable lead in quantum hardware. Companies such as Google in California and D-Wave in Canada still grant access to their machines without borders in mind — but only through the cloud. No one expects to touch the processors.

European politicians fear they have missed the technology boat. The region has only one large computer-hardware manufacturer (France-based Atos/Bull) with a quantum-technology programme. The EU quantum flagship promotes the development of hardware similar to that being created in the United States, and is investigating some approaches not being widely explored by US efforts. But the EU Commission failed to allocate much funding to quantum applications or algorithm research in the first round — a major omission, in our view. Those behind the flagship effort have indicated that they will invest more in quantum software in subsequent funding rounds.

Commercialize quantum technologies in five years

Many researchers hope that companies will fill the applications gap. But businesses have little interest in addressing the basic theory of quantum information processing, and they often operate in isolation. This means that the proliferation of start-ups and commercialization of quantum software at this early stage could hinder the development of theoretical methods and quantum software tools.

Outdated conventions and assumptions are also holding back the field. The range of applications for quantum-enhanced technology is limited and has not been mapped out. Even known uses, such as the benefits for machine learning, are poorly understood. The devices might not deliver anticipated improvements. Textbook algorithms (such as Shor’s quantum factoring algorithm or Grover’s search algorithm) seem not to work on non-ideal machines without error correction. Can programmers write better codes that can work on realistic devices subject to noise?

What next?

Academic researchers must map out the space of quantum-computing concepts and applications more fully. This is a fruitful moment for solving difficult problems that industry and start-ups will not be able to address. How far can these devices be pushed in the presence of noise? Will some developments stall, causing investment to dry up?

Governments should direct more funding to quantum software. Experimentalists are happy to pitch for large sums of money to build a quantum processor that might lead to a Nobel prize. Quantum programmers should similarly state their grand challenges confidently. Sponsors, too, need to understand that this is a long game that requires diverse approaches. Even when the hardware scales up, we might still be unsure what to do with it.

Industry, particularly start-up firms, should work more closely with universities. Companies could fund small theory projects and invest in developing the fundamentals of the field.

And international collaborations should be protected. Governments should work harder to keep science agreements intact despite political disagreements. Scientists and funders must respect the fact that research is truly global, international and open. Researchers relocate all over the globe. There are many random factors behind the jobs we end up with. It is not in anyone’s interests to cut off relationships just because one person crosses a border.

Mid-sized quantum processors will appear soon (although they will still be noisy). Will the quantum software be ready? Or will companies kick themselves for failing to invest in the algorithms and ideas that will drive the devices?

Nature 573, 190-191 (2019)

doi: 10.1038/d41586-019-02675-5

References

1. 1.

Preskill, J. Quantum 2, 79 (2018).

2. 2.

Kandala, A. et al. Nature 549, 242–246 (2017).

3. 3.

Biamonte, J. et al. Nature 549, 195–202 (2017).

4. 4.

Leddy, C. MIT News (23 January 2019); available at https://go.nature.com/2jaitpi

5. 5.

Metz, C. The New York Times (21 October 2018); available at https://go.nature.com/2kyhtkv

6. 6.

Mervis, J. & Cho, A. Science https://doi.org/10.1126/science.aaw9541 (2019).

7. 7.

Giles, M. MIT Technol. Rev. (3 January 2019); available at https://go.nature.com/2kys6qv

8. 8.

National Academies of Sciences, Engineering, and Medicine. Quantum Computing: Progress and Prospects (National Academies Press, 2019).

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BOOKS AND ARTS

09 September 2019

Danger and strangers: the trouble with face value

Malcolm Gladwell’s latest tome probes mutual misunderstanding and violations of trust. Tim Radford weighs up its riches.

Tim Radford

Tim Radford is a former science editor of The Guardian, and author of The Consolations of Physics.

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Traffic stops can become dangerous when strangers misunderstand each other.Credit: Gabe Souza/Getty

Talking to Strangers: What We Should Know about the People We Don’t Know Malcolm Gladwell Little, Brown (2019)

People, like books, can be difficult to read. Assumed ‘universal’ grammars of demeanour and facial expression seem not to translate across all cultures. Even within communities, there are individuals who react differently — who might, for instance, look most honest when they are not.

Talking to Strangers, Canadian journalist Malcolm Gladwell’s latest book, is a rich, detailed study of the mutual misunderstanding and violations of trust that can occur when we lack the tools to make sense of strangers. As in The Tipping Point (2000) and other books, he tests his thesis with topical case studies in areas from diplomacy to espionage, summoning evidence from psychologists, anthropologists, criminologists and economists.

Human behaviour: Guns and roses

The core of Talking to Strangers is an exploration of relatively new thinking about human interaction. For instance, the psychologist Tim Levine proposes that because liars are relatively rare, it’s simplest for people to believe each other. Gladwell examines Charles Darwin’s proposition that facial expressions — such as those signalling fear, disgust, hate — are evolutionary signals with universal significance. Psychologist Jennifer Fugate has pinpointed 43 facial-muscle movements that signal emotion. Deciphering them, however, is not always straightforward.

“To assume the best about another is the trait that has created modern society,” Gladwell writes. But we often fail to read others correctly. Gladwell demonstrates how this can lead to catastrophe.

In 1938, British Prime Minister Neville Chamberlain flew to Germany to meet Adolf Hitler, who was threatening war in Europe. Chamberlain’s aim was to exact from Hitler a promise of ‘peace for our time’. Later, Chamberlain wrote to his sister: “I got the impression that here was a man who could be relied upon when he had given his word.” In Gladwell’s thesis, meeting Hitler face to face was Chamberlain’s first mistake: “The people who were right about Hitler were those who knew the least about him personally.” In 1939, the Second World War began.

Chamberlain seemed to see in Hitler what he wanted to see. And as Gladwell points out, “the same puzzling pattern crops up everywhere”.

War and peace and summer camp

It is evident in a tragedy the book turns to repeatedly. In 2015, in Prairie View, Texas, state trooper Brian Encinia stopped driver Sandra Bland, an African American woman, for what may or may not have been a petty traffic offence. There was no suggestion of any crime. In a transcript of the encounter, she admits to being irritated. Gladwell concludes that her manner fitted Encinia’s idea of how a potential criminal might behave. Emotions escalated. An argument about a cigarette ended with a drawn taser, and a forcible arrest.

Bland was charged with felony assault. Three days later, she was found hanged in a police cell. Encinia was fired for violating the Texas state trooper manual, and ultimately forbidden from working in law enforcement. “Prejudice and incompetence go a long way toward explaining social dysfunction in the United States,” writes Gladwell, with considerable understatement.

The courts, he shows, are rife with misjudgements sparked by close encounters. A study by economist Sendhil Mullainathan and his colleagues looked at 554,689 bail hearings conducted by judges in New York City between 2008 and 2013. Of the more than 400,000 people released, over 40% either failed to appear at their subsequent trials, or were arrested for another crime. Mullainathan applied a machine-learning program to the raw data available to the judges; indifferent to the gaze of the accused, the computer made decisions on whom to detain or release that would have resulted in 25% fewer crimes (J. Kleinberg et al. Q. J. Econ. 133, 237–293; 2018).

Even intelligence agencies can be hotbeds of gullibility and bias, Gladwell reveals in two true spy stories. In 1987, Cuban-born Florentino Aspillaga defected from a posting in Eastern Europe, walking into the US embassy in Vienna. He delivered a bombshell, claiming that almost the entire roster of CIA spies in Cuba were double agents working for Havana. It was true: they had video-recorded the US agency’s activities for a decade.

Even on home soil, agents have missed evidence. In 1996, an operative in the US Defense Intelligence Agency (DIA) — Ana Belén Montes, known as “the Queen of Cuba” for her specialist knowledge — was suspected of being a double agent. A counter-intelligence officer, reviewing her file, decided that she had passed the test: “This woman is gonna be the next Director of Intelligence for DIA. She’s just fabulous.” She was arrested in 2001.

Psychology: Improbable heroes

She was not even a particularly accomplished spy, Gladwell notes. Her secret codes from Havana were in her purse, her shortwave radio in a shoebox in her cupboard. “The issue with spies is not that there is something brilliant about them,” Gladwell writes. “It is that there is something wrong with us.” Further crisply told case studies amplify his argument, from a bleak account of ‘enhanced interrogation’ techniques used to extract dubious confessions from al-Qaeda operative Khalid Sheikh Mohammed, to readings of coded facial expression in the US television series Friends.

In addition, Gladwell discusses a bias towards default-to-truth. This is beautifully explicated in the case of the more than US$50-billion fraud by financier Bernard Madoff, made public in 2008. (Madoff is currently serving a 150-year sentence.) People repressed suspicions about the schemer because they trusted the regulatory system. Few believed fund manager Harry Markopolos, who identified the fraud around 2000 and repeatedly reported it to the Securities and Exchange Commission. However, as Gladwell points out, if we had too low a trust threshold, we’d never commit to anything and would forever be suspicious. But that is just part of Gladwell’s story.

He explores, for instance, the sociological concept of coupling: how aspects of place can affect the outcome of close encounters and related decisions. A 1988 study, for instance, showed how the removal of carbon monoxide from the public gas supply in England and Wales led to a steep decline in the number of people taking their own lives between 1963 and 1975 (R. V. Clarke and P. Mayhew Crime Justice 10, 79–116; 1988). And US criminologists have found that for better overall crime prevention, police patrols should focus on urban crime hotspots (D. Weisburd Criminol. Public Policy 17, 5–25; 2018).

These findings, Gladwell asserts, have relevance for the tragic outcome of the incident in Texas. He does note that African American drivers are more likely to be stopped than white ones. But he persuades us to reconsider the episode as a misunderstanding between an over-zealous traffic cop in the wrong place and a motorist who should never have been stopped. It remains hard, however, to imagine that it would have ended so badly had Bland been white. Ultimately, Gladwell delivers analysis, but not much in the way of answers.

In close encounters with those we don’t know, Gladwell recommends “restraint and humility”. His examples of what happens without that have immediate and obvious political resonance. Perhaps wisely, he declines to make the connection. “Those occasions when our trusting nature is violated are tragic,” Gladwell writes. “But the alternative — to abandon trust as a defense against predation and deception — is worse.”

Nature 573, 192-193 (2019)

doi: 10.1038/d41586-019-02666-6

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BOOKS AND ARTS

10 September 2019

The enlightenment of age

Toren Finkel lauds two books outlining very different ways of achieving a longer ‘healthspan’ — through pharmacology or integrative care.

Toren Finkel

Toren Finkel holds the Beckwith Chair in Translational Medicine and is director of the Aging Institute at the University of Pittsburgh and the University of Pittsburgh Medical Center in Pennsylvania.

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Staying active into old age can extend health.Credit:Barbara Alper/Getty

Lifespan: Why We Age — and Why We Don’t Have To David A. Sinclair and Matthew D. LaPlante Atria (2019)

Elderhood: Redefining Ageing, Transforming Medicine, Reimagining Life Louise Aronson Bloomsbury (2019)

This year, people over 65 began to outnumber those under 5 for the first time in history. Like climate change, the ageing of humanity is indisputable. Yet the implications of that, and remedies for it, are subject to considerable debate. Now, two books with very different perspectives seek to address how to prepare for this ‘grey tsunami’.

Lifespan, by geneticist David Sinclair and journalist Matthew LaPlante, provides a vision of a not-too-distant future in which living beyond 120 will be commonplace. Physician Louise Aronson’s Elderhood focuses, by contrast, on the often bewildering and sometimes dehumanizing landscape of current geriatric care. Both books wrestle with the complexities of the coming demographic shift. Countries such as the United States — already devoting more than one-third of its health-care dollars to people over 65 — will have to come to terms with an iller, older population. But their solutions are distinct. For Sinclair and LaPlante, the answer lies in understanding and leveraging why we age; for Aronson, in re-evaluating and re-orienting how we view and treat older people.

Age as disease

Lifespan is entertaining and fast-paced — a whirlwind tour of the recent past and a near future that will see 90 become the new 70. In a succession of colourfully titled chapters (‘The demented pianist’, ‘A better pill to swallow’), Sinclair and LaPlante weave a masterful narrative of how we arrived at this crucial inflection point. Among the historical figures evoked are a sixteenth-century Venetian proponent of caloric restriction, Luigi Cornaro, and the twentieth-century ‘father of information theory’, Claude Shannon.

Ageing more gracefully

The authors detail how we might alter the trajectory of human ageing by extrapolating from Sinclair’s own research on key signalling molecules such as NAD+ and the proteins called sirtuins, which alter the lifespans of yeast, certain worms and mice. They predict the emergence of drugs that will modulate these and other molecules known to be involved in longevity pathways, or destroy harmful senescent cells that accumulate as we age and help to fuel disease. Sinclair and LaPlante claim that some of these drugs might already be here. The effects of the widely prescribed diabetes drug metformin and the immune modulator rapamycin, for instance, seem to mimic beneficial strategies — the equivalent of (respectively) exercising more and eating less, in pill form.

Defining ageing as a disease is central to their approach. If we treat age medically, as we do heart disease or cancer, they argue, innovative therapies will emerge more rapidly. That mirrors the increasingly popular ‘geroscience hypothesis’, which posits that therapies targeting the fundamental biology of ageing will help to slow or prevent chronic diseases that plague older people, such as type 2 diabetes and dementia. Sinclair’s argument, based on decades in the lab, is that there is no immutable biological tenet that limits how long, or how well, we can live.

Sinclair and LaPlante examine the economics of extending lives on a crowded, resource-limited planet, and the ethics of tinkering with the supposed natural order. But they also speculate on some inadvertent, potentially positive effects. Knowing you were going to meet your great-great-grandchildren, for instance, might make you a more accountable steward of the present. If many generations lived and worked together, we might all become more empathetic — as Sinclair puts it, “more human”. At a time of political, economic and environmental uncertainty, that could be ever more important.

Extending the healthspan

If Lifespan is a lively sprint into the future of ageing, Elderhood is a contemplative walk in its here and now. Since the early 1990s, Aronson has worked as a geriatrician at the University of California, San Francisco. Her exquisitely written book mixes vignettes about her patients (remarkably, she still makes house calls) with lessons learnt from caring for her elderly parents and insights from her own experience of ageing.

Many of her stories reveal cracks in the US health-care system. We learn, for instance, about Neeta, a frail patient with mild dementia who breaks her hip. After surgery, Neeta is transferred to a less-than-stellar care home where she becomes agitated, is sedated, develops bedsores and spirals into hospice care. We also learn of Aronson’s personal frustrations. In one instance, when physicians in a busy accident and emergency department were too distracted, she had to perform a rectal examination on her own father to demonstrate that he was bleeding internally.

Essential stage

Meshed with these very human tales are a wealth of social, cultural and historical perspectives. At the start of the book, Aronson tells of an encounter with Guy Micco, a physician teaching at the University of California, Berkeley. Micco asked a class to write down associations with the word ‘old’: concepts such as weak and frail predominated. The word ‘elder’, by contrast, elicited terms including respect, experience and knowledge. To Aronson, part of the problem is that we adhere to a utilitarian, late-nineteenth-century concept of the body as a machine. Viewed through that industrial lens, being ‘old’ is no longer the apex of life experience. It is a loss of function and, by extension, of intrinsic worth.

Longevity examined: an ancient Greek’s very modern views on ageing

Aronson sees life as a three-act drama: childhood, adulthood and elderhood, the latter subdivided into senior, old, elderly and aged. Each act builds on the one before, and is essential. Aronson notes that emphasizing only the vicissitudes of elderhood is like saying that youth is defined by acne. In fact, in old age we might know ourselves better than ever and obtain more overall life satisfaction. Aronson conceives of anti-ageing not as Sinclair and LaPlante see it — as a bid to medically ‘cure’ the condition — but as battling the many “discriminatory beliefs and policies” affecting the elderly. In her view, the very idea of ‘curing’ ageing is ageist; such a concept is not invoked for any other life stage.

Indeed, in Aronson’s eyes, the worst offender might be the medical system itself. She sees it as failing both patient and physician. It lacks nuance on subtle but important differences in life phases, and focuses on “diseases and organs rather than people and lives”. For instance, she notes that many over-the-counter medicines are not tested on older people, adding risk to prescribing them. She advocates a new paradigm: a re-balancing act in which technology has a role but the focus returns to care. Unlike the high-tech, algorithmic march of modern medicine, her idea of truly ‘personalized medicine’ incorporates the patient’s past experiences and current expectations. This integrative, humanistic model of geriatrics is rare. One can only hope its practices are adopted swiftly.

What are we to conclude? Is ageing a disease that can be eradicated by science, or the natural third act of life, threatened by over-medicalization? Viewpoints will undoubtedly be as variable as experience and temperament. There might be some wisdom in simply following an adage attributed to seventeeth-century philosopher Francis Bacon: “old age is always 15 years older than I am”.

Nature 573, 193-194 (2019)

doi: 10.1038/d41586-019-02667-5

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BOOKS AND ARTS

11 September 2019

India’s journey to the red planet

Subhra Priyadarshini lauds a film on the country’s first interplanetary craft, the Mars Orbiter Mission.

Subhra Priyadarshini

Subhra Priyadarshini is chief editor of Nature India.

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Vidya Balan plays Tara Shinde, project director for India’s Mars Orbiter Mission, in Mission Mangal.Credit: Sterling Media

Mission Mangal Director: Jagan Shakti Cape of Good Films/Hope/Fox Star Studios (2019)

In 2013, India reached for Mars. Its first interplanetary mission, dubbed Mangalyaan (officially the Mars Orbiter Mission, or MOM), launched a probe carrying five instruments to study aspects of the red planet, from its mineral composition to potential signs of past life. Now, a fictional treatment on film by first-time director Jagan Shakti celebrates the scientists who got MOM off the ground.

Released on 15 August — India’s independence day — Mission Mangal fictionalizes the tense months from approval to launch, a race to lift off when Mars would be closest to Earth. It is very much a homage to the Indian Space Research Organisation (ISRO) and the country’s technological prowess, and as such stirs up national pride. But the film is also successful scientific storytelling, performed by a glittering cast.

Five millennia of Indian science

Science communication can be notoriously tricky, treading a line between oversimplification of concepts and overuse of jargon. Mission Mangal avoids the latter, but some sections have been accused of dumbing down highly technical ideas. One scene drew widespread criticism at the trailer’s launch in July. MOM project director Tara Shinde (played by the supremely talented Vidya Balan) is shown making puris, deep-fried rounds of Indian bread. After she turns the stove off to save gas, the oil remains on the boil for some time. She then realizes that a similar technique would allow ‘smart’ space vehicles to stay in orbit: the fuel could be switched off to make use of Earth’s gravitational pull. As I watched this supposedly divisive scene, a woman sitting beside me nodded approvingly. The principle of economy in space had hit home.

It’s a key point: judicious use of resources is an ISRO speciality. The organization boasts the world’s cheapest solutions for space missions. They range from the compact Small Satellite Launch Vehicle to space-saving satellites such as the Microsat, which weighs about 100 kilograms and can latch on to any space mission as a co-payload. Mission Mangal emphasizes how stripped-back ISRO labs and tight budgets encourage innovation.

Frugal efficiency

After MOM launched, Prime Minister Narendra Modi commented that at just 4.5 billion rupees (US$74 million), it cost less than Alfonso Cuarón’s 2013 film Gravity. In fact, starting with physicist Vikram Sarabhai and aerospace engineer Satish Dhawan in the 1960s and 1970s, Indian scientists paving the way to a national space programme have practised ‘frugal efficiency’.

Mission Mangal is framed by an apparent setback. This is the moment in 2010 when a test of ISRO’s Geosynchronous Satellite Launch Vehicle was aborted just over a minute after lift-off, after scientists detected snapped communication connectors. The film recounts how lead scientists Shinde and Rakesh Dhawan (Akshay Kumar) plan a relaunch, but are politely shunted to ISRO’s unglamorous, underfunded Mars section.

Science and the rise of nationalism in India

Here, they begin to work their magic as they pull together and train their team. NASA, inevitably, is a recurrent theme. The Indian-born, NASA-trained scientist Rupert Desai (Dalip Tahil) helms ISRO’s prestigious Moon mission, Chandrayaan. The young Eka Gandhi (Sonakshi Sinha) wants to use ISRO as a stepping stone to the US space agency. There are glimpses, too, of the personal lives of scientists beyond lab and launch site, breaking down tedious stereotypes in the process. One scene shows the mission’s female scientists dressed in bright saris — just as they were in a memorable 2014 photo showcasing ISRO’s womanpower.

The technological jockeying for position common among space-faring nations is also captured. Mission Mangal alludes to a cartoon published in The New York Times in 2014, of a turbaned man leading a cow knocking at the door of a building marked ‘Elite Space Club’. It was widely criticized as racist, and the paper apologized. Three years later, after India launched a record 104 satellites on one craft, The Times of India published a cartoon showing India inside the club as other countries seek entry.

Built by bicycle

The coming decade is set to see some of India’s major space ambitions take wing. The Department of Space got an 11% budget hike for 2019–20, and ISRO is set to launch its first crewed mission, Gaganyaan, before the 75th anniversary of India’s independence, in 2022. And, in a fitting 50th-anniversary tribute to Apollo 11, India’s second mission to the Moon, Chandrayaan-2, set a course for the uncharted lunar south pole in July. As Nature went to press, the Vikram lander was due to touch down on 7 September.

Amid vast global challenges and the emergence of space-flight entrepreneurs, India’s space innovation continues apace. Mission Mangal’s focus on the dedicated, visionary researchers behind ISRO’s Mars mission reminds us how doing science that is of use to society demands an inner fire.

Nature 573, 194-195 (2019)

doi: 10.1038/d41586-019-02668-4

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CORRESPONDENCE

10 September 2019

Scientists — make time for contemplation

Stephen Webster

Imperial College, London, UK.

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Behind the satisfying hum of scientific progress, we hear the drumbeat of scientists pushing and shoving. Concerns surface constantly about research integrity, reproducibility and pressure to publish. We need to draw on the history of science and kindle the benefits of three contemplative but immensely practical ideals: reticence, intimacy and innocence.

To be reticent is to reflect on the significance of our work. Pausing can make for better science. Describing the 16-year delay in publishing his book on insectivorous plants, Darwin wrote that “…a man after a long interval can criticize his own work, almost as well as if it were that of another person”. The advice remains good today: consider the alarms over human-genome editing.

The precept of intimacy lifts our research beyond the collection of measurements and data. Think of the gifted cytogeneticist Barbara McClintock, whose biography was entitled A Feeling for the Organism. Or the evolutionary theorist Lynn Margulis, who instinctively navigated the complex biological systems of Massachusetts’ Sippewissett marshes (see D. Sagan (ed.) Lynn Margulis: The Life and Legacy of a Scientific Rebel; Chelsea Green Publishing, 2012).

Scientific innocence means that ideas — not money or fame — take centre stage. We are modest, open to fresh perspectives and new approaches. We take time for exploratory discussions and to listen. Let the conversation begin.

Nature 573, 196 (2019)

doi: 10.1038/d41586-019-02693-3

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CORRESPONDENCE

10 September 2019

South African system tracks SDG research

Willem Fourie,

University of Pretoria, South Africa.

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Isak van der Walt,

University of Pretoria, South Africa.

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Hannes Strydom &

University of Pretoria, South Africa.

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Christopher Marais

University of Pretoria, South Africa.

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South Africa is developing a coding system to track research progress towards the United Nations’ Sustainable Development Goals (SDGs; see I. Capua and E. Giovannini Nature 572, 178; 2019). Known as the South African SDG Hub, this national facility is hosted by the University of Pretoria (sasdghub.org). We invite other institutions, particularly those in Africa, to join us in unlocking the impact of research related to the development goals.

With the support of the national Department of Science and Innovation, the South African SDG Hub collects, classifies and disseminates publicly available peer-reviewed research from South Africa that stands to contribute to any of the topics covered by the goals’ 169 targets.

The hub’s first iteration, in 2017, was compiled manually, but it is now being automated. We are currently completing an SDG text classifier.

Nature 573, 196 (2019)

doi: 10.1038/d41586-019-02678-2

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CORRESPONDENCE

10 September 2019

Colombia short on political will to protect pollinators

Sofía López-Cubillos,

University of Queensland, Brisbane, Australia.

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Felipe Suárez-Castro,

University of Queensland, Brisbane, Australia.

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Eve McDonald-Madden,

University of Queensland, Brisbane, Australia.

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Duan Biggs,

Griffith University, Nathan, Australia.

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Guiomar Nates-Parra,

National University of Colombia, Bogotá, Colombia.

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Catalina Gutierrez-Chacón &

Wildlife Conservation Society, Cali, Colombia.

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Rebecca K. Runting

University of Melbourne, Parkville, Australia.

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Colombia faces substantial challenges associated with high deforestation rates and rapid sociopolitical transition in the wake of the 2016 peace agreement. We urge the government to avoid solutions that could be at odds with its international commitment to safeguard pollinators (see go.nature.com/2uzxyc1).

For example, Colombia plans to reintroduce large-scale application of glyphosate to destroy illegal coca fields — despite the damage that the herbicide causes to honeybees (E. V. S. Motta et al. Proc. Natl Acad. Sci. USA 115, 10305–10310; 2018) and a previous nationwide ban on its use. This trade-off is unacceptable. Alternative measures must be taken to combat illicit coca production, such as those laid out in the Colombian Pollination Initiative (see go.nature.com/2uuycrc).

Over one-third of Colombia’s beehives collapsed in 2014–17 owing to excessive use of agrochemicals. Proposed legislation for pesticide-free zones is pending in its Congress. However, deforestation will continue to destroy pollinator habitat — even though Colombia’s 2019 Development Plan aims to cut the rate of deforestation by 2022 to 30% of that in 2018. The amount of rainforest lost each year by 2022 will still exceed that in 2017 (see D. Armenteras and T. Defler Nature 569, 487; 2019).

Policies that create sustainable livelihoods without harming pollinating insects stand to strengthen Colombia’s economy and so can help to counter illicit activities such as coca production.

Nature 573, 196 (2019)

doi: 10.1038/d41586-019-02680-8

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CORRESPONDENCE

10 September 2019

Bioethicists clarify mitochondrial-therapy ban

Amy Gutmann &

University of Pennsylvania, USA.

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Jonathan D. Moreno

University of Pennsylvania, USA.

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We wish to clarify two points raised by Eric Topol in his review of our book Everybody Wants to Go to Heaven but Nobody Wants to Die (Nature 572, 308–309; 2019).

First, mitochondrial-replacement therapy is still banned by the US Food and Drug Administration, and we say nothing to the contrary. In the book, we note that “in 2016, committees in both the United States and the United Kingdom gave cautious green lights for mitochondrial replacement therapy” — not that any US regulatory agency had done so. The reports we cite were produced by the US National Academies and the Nuffield Council on Bioethics in the United Kingdom, where the Human Fertilisation and Embryology Authority regulates applications of the therapy.

Second, we do not argue that we have witnessed a complete collapse in the practice of medical paternalism. Rather, we document the many ways in which bioethics and popular American culture have challenged the prevalent view of half a century ago that ‘doctor knows best’. The national conversation on bioethics can help to ensure that the voices of patients are increasingly heard.

Nature 573, 196 (2019)

doi: 10.1038/d41586-019-02679-1

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CORRESPONDENCE

10 September 2019

Not a first: identifying hominin fossils from their proteins

Enrique G. Olivares

University of Granada, Spain.

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You claim that the identification of a 160,000-year-old Denisovan jawbone from its proteins alone is a first for palaeoproteomics (Nature 570, 433–436; 2019). This is not entirely true.

Jerold Lowenstein pioneered the detection and identification of proteins by immunological methods in fossils of hominins (a 0.5-million-year-old Homo erectus and a 1.9-million-year-old Australopithecus robustus) and other animal species (J. M. Lowenstein Phil. Trans. R. Soc. Lond. B 292, 143–149 (1981); see also C. Borja et al. Am. J. Phys. Anthropol. 103, 433–441; 1997).

Those immunological techniques relied on protein-binding information and so were less precise than mass spectrometry, which can directly provide the amino-acid sequence of fossil proteins such as collagen from the Denisovan mandible. Nevertheless, they were an important milestone in the history of molecular methods used to identify hominin fossils.

Nature 573, 196 (2019)

doi: 10.1038/d41586-019-02692-4

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Technology

- Animal registries aim to reduce bias [09 September 2019]

Technology Feature • Some advocates are betting that documenting experimental plans online will improve animal research, but uptake has been slow.

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TECHNOLOGY FEATURE

09 September 2019

Animal registries aim to reduce bias

Some advocates are betting that documenting experimental plans online will improve animal research, but uptake has been slow.

Monya Baker

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Each year, researchers use millions of mice and rats in experiments from which results either never get published or are of poor quality.Credit: fotografixx/Getty

Millions of mice and rats are used in research each year. But one-third to one-half of animal experiments are never published, and of those that are, many are too poorly conducted to be reliable. Advocates for better animal research and reproducibility are promoting a strategy established in other fields to counter publication bias, improve investigations and increase transparency: study registries.

Registries ask researchers to detail their hypotheses, experimental strategy and analytical plans before studies begin. The intention is to prevent teams from simply cherry-picking significant or desirable findings and to supply the scientific community with a way of learning about experiments that would otherwise go unpublished.

The best-known registry, clinicaltrials.gov, has logged more than 300,000 human clinical trials since it launched in 2000, amid outrage over drug companies burying unfavourable clinical-trial results. Regulatory authorities around the world now require registration for drugs and devices approved for market, and medical journals require it for publication.

The Open Science Framework is an example of a voluntary registration system. Researchers, mainly psychologists and social scientists, input or ‘preregister’ research plans before starting a project, which they can keep private, or ‘embargoed’, for up to four years. More than 30,500 preregistrations have been entered since 2012, but few of these involve animals.

What’s next for Registered Reports?

The first registry specifically set up for animal studies, preclinicaltrials.eu, was launched in April 2018. Registry co-founder Mira van der Naald and her colleagues at the University Medical Center Utrecht in the Netherlands were carrying out systematic reviews in cardiac regenerative medicine, and found themselves frustrated by the consistently poor quality of preclinical evidence. They felt a dedicated registry would help, and were surprised that none existed. “We thought, ‘Hey, let’s just start it. We’re not getting anywhere just talking about it’.”

Unknown to them, Germany’s centre for the protection of laboratory animals, Bf3R in Berlin, had taken on a similar project. Animalstudyregistry.org launched in January. Together, the two registries have only a few dozen entries.

The registries use templates specifically designed for animal experiments, with fields for species as well as several experimental design parameters described in a set of reporting guidelines known as Animal Research: Reporting of In Vivo Experiments, or ARRIVE. (In 2017, M.B. served on a working group to update these guidelines, which ask authors to state whether they have preregistered their experiment.) Curators at both registries review entries and can ask for more detail. Registration is open to researchers worldwide.

A tough sell

Malcolm Macleod, a stroke researcher at the University of Edinburgh, UK, who has documented research quality and bias in preclinical work, says that for journal editors and peer reviewers, registration can boost a study’s credibility. “Registries and preregistration are pretty essential in terms of being able to demonstrate the rigour with which the research was done, and to reassure research users that you answered the questions that you set out to answer,” he says.

Open framework tackles backwards science

But convincing researchers to use animal-study registries could prove to be a tough sell, he says. “We are going to ask a group of researchers who have not had any experience with this at all to suddenly change what they do.” Researchers are used to communicating their work as a final manuscript that describes experiments and findings as if everything went to plan, notes physiologist Kieron Rooney, a registry advocate at the University of Sydney, Australia. “You don’t see any battle scars of my project, where I had to change direction.”

Scientists largely agree that registration would yield communal advantages by reducing cherry-picking, publication bias and duplication, says Daniel Strech, a bioethicist at Charité Medical University in Berlin who studies animal researchers’ attitudes to study registration. But they also worry about individual disadvantages such as increased administrative burden, the possibility of having their ideas stolen and being targeted by animal-rights activists (S. Wieschowski et al. PLoS Biol. 14, e2000391; 2016). “They think, on average, animal registries will have no impact on efficiencies,” Strech says.

Researchers who have submitted protocols to their animal-ethics committees or funding agencies can simply paste relevant portions into the registry, upload supporting files (animalstudyregistry.org) or provide URLs (preclinicaltrials.eu). Finalized registrations are time-stamped, but researchers can add annotations to explain deviations from the plan, or to flag that further experiments have been done. The registries also provide secure embargo periods.

Steps towards transparency in research publishing

Still unclear, however, is which types of study should be registered. Bf3R head Gilbert Schönfelder encourages researchers to log any study requiring approval from an institute’s ethical advisory board. This helps to advance the ethical aim that any experiment using animals should increase the overall level of knowledge. Bioethicist Jonathan Kimmelman at McGill University in Montreal, Canada, counters that the push should be for researchers doing preclinical trials — highly structured studies that serve as the basis for deciding whether to test a drug in people.

To Macleod, the optimal registration process would target confirmatory studies that set out to test (rather than generate) hypotheses and require no more than half an hour to complete, even if that means omitting some details. If researchers documented half a dozen items including the hypothesis, experimental intervention, primary outcome and how it will be measured, and statistical parameters, “you deal with 95% of the problems that arise”. It would also increase the number of entries for those studies in which registration is most advantageous, he says. “If people get 90% of the benefits for ten minutes, I think that would be much more likely to happen than getting 100% of the benefits for two hours.”

Also worth logging are animal housing and handling details, says Adrian Smith, secretary of Norecopa, an organization in Oslo that aims to improve and reduce the use of animals in research. Isolating mice or picking them up by the tail can strongly impact certain types of study, he notes. “It is unthinkable to try and solve the reproducibility crisis without also attending to these ‘non-mathematical’ factors.”

Broad participation and fully described experiments are key, says Deborah Zarin, who from 2005 to 2018 directed clinicaltrials.gov. Yet it could prove difficult to get researchers to provide sufficient detail in their registrations to really know whether they are cherry-picking results, she warns. Also, the fewer researchers who participate in a registry, the less valuable it will be for helping others to identify collaborators, or to know whether anyone else has tried to address similar questions. And separate, uncoordinated registries will make searching for particular kinds of study inefficient, further undermining their use.

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Even incomplete registries could promote “good researcher hygiene” that would improve individual studies, says Kimmelman. Still, the availability of a registry is just one piece of the puzzle, says Manoj Lalu, an anaesthesiologist at Ottawa Hospital Research Institute, who is working to improve translational research. Many researchers do not understand why techniques to reduce bias are necessary or how they should be implemented. This means that even if they do register a study, they might do so inaccurately. Thus, registries must be combined with educational resources, he says.
Incentives are also essential, adds Roberta Scherer, who studies clinical-trial methodology at Johns Hopkins Bloomberg School of Public Health in Baltimore, Maryland. “If researchers go to the site, they may become educated, but they have to get there first.” Funders, journals and institutions will have to require or reward registration for it to become common practice, she predicts.

Rooney says that a better strategy would be to show that registries can benefit researchers by helping them to find collaborators or determine whether and how to repeat studies other researchers have tried. “We have to say we want this not because we want to make science difficult, but because we want to fix some issues,” he says. “Give it a few years, and it just becomes part of the process.”

Nature 573, 297-298 (2019)

doi: 10.1038/d41586-019-02676-4

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Careers

- Developing cancer drugs from African plants [23 August 2019]

Career Q&A • Mansurah Abdulazeez discusses how her visionary plant research could help in the fight against cancer.

- Make science PhDs more than just a training path for academia [28 August 2019]

Career Column • Science PhD programmes cater almost exclusively to students bound for academia, but they don’t have to, says Sarah Anderson.

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CAREER Q&A

23 August 2019

Developing cancer drugs from African plants

Mansurah Abdulazeez discusses how her visionary plant research could help in the fight against cancer.

Abdullahi Tsanni

Abdullahi Tsanni is a freelance science journalist based in Abuja, Nigeria.

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Molecular biologist Mansurah Abdulazeez recruits African plants in the fight against cancer. Credit: Mansurah Abdulazeez

Mansurah Abdulazeez is a molecular biologist at the Center for Biotechnology Research, Bayero University Kano, Nigeria. Her research aims to identify potent anticancer agents in African plants. Last November, the government of Spain awarded her their Science by Women Fellowship. And in June, she won a Nigerian National Research Grant of 31 million naira (US $86,000) from the Tertiary Education Trust Fund. Nature asked Abdulazeez about her life and research.

What can you tell us about your scientific background?

Growing up, I always enjoyed science. I originally wanted to become a medical doctor, but I ended up studying biochemistry during my undergraduate studies at Ahmadu Bello University in Zaria, Nigeria. I got my master’s degree, and then my PhD there, studying antihypertensive and anticancer activities of African plants. I was also a visiting scholar at Chiang Mai University in Thailand for six months as part of my PhD research.

Careers toolkit: An early career researcher’s guide to the working world of science, from Nature Careers.

What does your research focus on?

My research is aimed at identifying potent, safe and effective anticancer agents from Nigerian plants. We have screened and confirmed the cytotoxic activities of extracts of the drumstick (Moringa oleifera) and soursop (Annona muricata) trees as well as the native Nigerian shrub Peristrophe bicalyculata on cervical carcinoma and fetal lung carcinoma cell lines. We also studied what anticancer mechanisms these plants exhibit. We found that these plants act in the body through a variety of mechanisms — there is no single mode of action for all plants[1].

Why is the study of African plants important for cancer research?

It is well documented[2] that these plants have an enormous, largely unstudied anticancer potential. Research into herbs such as Guiera senegalensis, which is used by traditional African healers and known as ‘Sabara’ by locals, has led to the discovery of several anticancer drugs. In my view, this demonstrates how the study of African plants can result in the development of valuable drugs.

What is your advice to young African women who want to pursue science?

Participate in local and international conferences that are relevant to your fields of study, so as to keep yourself updated on cutting-edge research tools, methodologies and funding opportunities. Always ask for support from senior colleagues — and family members — whenever you need it. Remain focused, tenacious and hard working.

Nature 573, 300 (2019)

doi: 10.1038/d41586-019-02564-x

This interview has been edited for length and clarity.

References

1. 1.

Mansurah, A. A. et al. Rom. Biotechnol. Lett. 18, 7995–8006 (2013).

2. 2.

Kuete, V. & Efferth, T. Biomed. Res. Int. 2015, 914813 (2015).

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CAREER COLUMN

28 August 2019

Make science PhDs more than just a training path for academia

Science PhD programmes cater almost exclusively to students bound for academia, but they don’t have to, says Sarah Anderson.

Sarah Anderson

Sarah Anderson is a PhD candidate in the chemistry department at Northwestern University in Evanston, Illinois.

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My committee member looked up from the document in his hand, which detailed my ideas for my research proposal. He cleared his throat: “You know, when you apply for faculty positions…” he began. I gave a quick, impulsive nod in response, but thought to myself, “That’s never going to happen.”

I’m a PhD candidate in chemistry with no intention of pursuing a career in academia, and I’m certainly not alone: out of 81 students in my programme, only 40% plan to go into academia. A more comprehensive survey of 5,700 science doctoral students worldwide, conducted in 2017, found that 75% of respondents wanted to work in academia after graduation, although a significant portion of those reported equivalent interest in the industry sector, suggesting indecision[1]. Clearly, the desire to pursue academia is not universal among PhD students. Furthermore, tenure-track job openings are a rare find: a study of job availability carried out in 2014 concluded that only 13% of PhD graduates can attain academic positions in the United States[2].

Despite the lack of exclusive interest in academic careers and the low demand for professors, PhD programmes are designed to accommodate students with their sights set on academia. This fact is evident in the requirements that PhD students must meet to earn their doctoral degree, as well as the events hosted and sponsored by science departments.

Research is of course at the heart of a PhD, and assessment of productivity through a qualifying exam and thesis defence is needed to bestow a doctorate. But the goal of an original research proposal, such as the one my committee member was holding, isn’t to evaluate progress, but rather to serve as practice for developing exploratory project ideas and securing funding for them — skills most relevant to future professors.

This agenda isn’t hidden: the reminder that a great proposal could be used later in faculty applications was dangled in front of my colleagues and me as a largely inapplicable and therefore ineffective incentive to put in the work.

Also, the majority of events hosted by science departments — seminars given by professors, lunches with professors, panels of professors — are of greatest value to students taking an academic route.

Collection: Young scientists

There are typically more opportunities for non-academic professional development outside of a candidate’s department of study, such as science-journalism and business-certification courses. But a lack of department promotion and sponsorship of these programmes means that students are often either unaware of their existence or feel discouraged from participating.

Research proposals are one example in which PhD programme requirements could be better tailored to the career goals of each individual student. Those interested in science communication shouldn’t waste their time producing a proposal for research they’re not interested in performing. They could instead write a piece on their research targeted at a non-expert audience, for example. Similarly, those planning to enter industry could pitch a new product, and those aiming to become lecturers could participate in and report on a teaching internship. Choosing a career track with corresponding requirements could become as standard as selecting an inorganic, organic, physical or biological chemistry track.

The events hosted and sponsored by science departments are an area in which graduate school could become more inclusive and beneficial to students pursuing careers beyond academia. There are many professionals in industry and non-conventional fields who could occupy some slots on the department calendar. Furthermore, by promoting external programmes aimed at non-academic-career preparation, science departments could ensure that students are aware of such opportunities and display public support for their participation.

To successfully implement these changes, we must first subvert the assumption on which PhD programmes seem to be built: that their participants plan to pursue academia. This mindset is in part a consequence of PhD programmes being crafted by professors who used their own career trajectory as a template.

But I suspect it’s also a product of the unfortunate reality that PhD advisers simply do not view non-academic careers with the same degree of admiration. The fact that multiple people have written articles on how to break the apparently devastating news to your adviser that you aren’t following in their footsteps speaks volumes. If academia can’t appreciate the inherent value of professions beyond ‘research professor’, then maybe it can at least recognize the benefits it gains from having PhD-trained scientists in roles outside academia.

For example, science communicators create crucial dialogue between scientists and the public, helping to establish a wider audience for researchers’ work and prevent misinterpretation of findings. Those in the field of science policy help to inform important regulations that affect national agencies funding academic research. High-school science teachers, lecturers and lab instructors are training the next generation of graduate students who will work in university labs. Hopefully, the PhD programmes that these students experience help them to feel validated in and prepared for whatever career path they choose.

Nature 573, 299-300 (2019)

doi: 10.1038/d41586-019-02586-5

This is an article from the Nature Careers Community, a place for Nature readers to share their professional experiences and advice. Guest posts are encouraged. You can get in touch with the editor at naturecareerseditor@nature.com.

References

1. 1.

Woolston, C. Nature 550, 549–552 (2017).

2. 2.

Larson, R. C., Ghaffarzadegan, N. & Xue, Y. Syst. Res. Behav. Sci. 31, 745–750 (2014).

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Futures

- Hello, Hello [11 September 2019]

Futures • Time for a civilized conversation.

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FUTURES

11 September 2019

Hello, Hello

Time for a civilized conversation.

Jeff Hecht

Jeff Hecht writes about lasers, dinosaurs and other science and technology. His latest book is Lasers, Death Rays, and the Long, Strange Quest for the Ultimate Weapon.

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Illustration by Jacey

Begin transmission directed to third planet.

Hello, Hello. We are messengers bringing you greetings from the Galaxy, and are we are pleased to welcome you to the ranks of its intelligent civilizations.

We came as quickly as possible after we learnt you had reached this level, but delay is unavoidable in a Universe where the speed of light is finite and civilizations are separated by many light years. Our automated systems monitor all planets capable of developing intelligent civilizations, but their messages travel at light speed, so the news that you had crossed the threshold of civilization took 237 of your years to reach the nearest Galactic Civilization Response Centre.

Read more science fiction from Nature Futures

We messengers have finite mass and finite energy, so we travel much slower than light. It took 5,422 of your years to get here, and our trip left us with so much inertia that we cannot land on your planet and share a cup of your tea. You would probably find us rather boring, anyway, because we messengers are mechanical agents of civilized life, chosen because we can survive travel through interstellar space, unlike intelligent life.

We know you wait impatiently for visitors from other planets. That is normal. Living beings lose patience once they evolve intelligence. Intelligence gives you curiosity, so you look up at the sky and wonder what is out there. You invent telescopes and discover the Galaxy is full of stars, and once you find those stars have planets, you decide that other intelligent beings like yourselves must live there. Then you wonder why none of them have come to solve your problems, and you decide the reason must be that you are the most advanced civilization in the Galaxy. We must inform you that this is a fallacy. To become a highly advanced civilization, you must accept that, like all natural life, your capabilities are limited. Only machines and dormant forms of microbial life can survive in space for the thousands of years needed to travel between stars.

When a civilization is young, intelligent beings imagine that their technology can do anything. You crossed great oceans. You flew to the Moon you can see in your sky. You sent robots to other planets in your planetary system. You invented science fiction, and when you calculated how long it would take you to get to the stars, you decided to invent a drive to travel faster than light. We know it will never work, but you don’t want to know that.

We know that young technological civilizations burn through large amounts of the natural resources present on their home planet. You dig up ancient organic wastes and turn them into short-lived plastic talismans that you put into indigestible bags made of other plastics. That is a bad idea. At peak burn rate, you feel so wealthy you can afford anything, so you fight wars and build mansions and empires. That is an even worse idea.

You think your civilization is uniquely sane and rational. All young technological civilizations do that, and they all are wrong. Maybe you have learnt that by now. Technology can run out of control, like a nuclear chain reaction. You call that comparison a simile, but it is also a symbol. The nuclear chain reactions of war cannot totally destroy an entire planet, but they can exterminate advanced life, so evolution can start again and make new mistakes.

We know that you are still living somewhere on your planet because our automated systems have told us that you are hiding. We have been trying to contact you since we entered your system. We have information to share that may help you, but we need you to contact us for us to send it to you. Please contact us.

Discover the inspiration behind this story in Jeff’s blog post

We know that it is hard for civilizations that have discovered the wonders of technology to accept that both their technologies and their lives have inherent limitations no matter how rich they are. However, nature is like that. Advanced civilizations must learn to live within the limits of natural energy and the resources of their planetary systems, or they will stop being advanced civilizations. They must stop burning old organic wastes to power aeroplanes and automobiles and learn to live sustainably.

Some advanced civilizations carefully limit their consumption and technology to preserve their resources and their civilization. Others go back to living in caves and chasing their breakfasts with stone hand axes. The citizens of the Galaxy accept the lifestyle choices of formerly advanced civilizations who learnt that survival requires sustainability.

All intelligent civilizations are entitled to their privacy, but the Galaxy is full of other civilizations who would like to hear from you. Please listen to us so you can learn how to say hello to the Galaxy. Please tell us who you are, where you are and what you are doing. We transmit on many radio channels and listen for your signals on many other radio channels. We have been roaming this part of the Galaxy for over a hundred thousand of your years. Please talk to us. Even we boring mechanical agents of civilized life can get bored.

Begin silent interval. When silent interval is complete, repeat in next language.

Hallo, Hallo …

Nature 573, 302 (2019)

doi: 10.1038/d41586-019-02677-3

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02677-3

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Research

Electrochemical reactions drive morphing of materials [11 September 2019]

News & Views • Silicon anodes in lithium batteries expand during discharge, causing failure. This expansion has been used constructively in a material whose architecture controllably and reversibly changes to alter its function.

A mechanism for touch [21 August 2019]

News & Views • Piezo proteins mediate the sense of touch. A near-complete structure of one such protein has been obtained, and the mechanism for converting mechanical signals into electrical ones has been probed in another.

Elusive cranium of early hominin found [28 August 2019]

News & Views • A 3.8-million-year-old hominin fossil reveals what the cranium of the oldest known Australopithecus species looked like, casting doubt on assumptions about how these ancient relatives of humans evolved.

One tick closer to a nuclear clock [11 September 2019]

News & Views • Clocks that are based on the nucleus of a single thorium atom could be more precise than existing timekeepers. Such clocks have not yet been realized, but two experiments provide keys steps towards this goal.

Strategies for combating online hate [21 August 2019]

News & Views • An analysis of the dynamics of online hate groups on social-media platforms reveals why current methods to ban hate content are ineffective, and provides the basis for four potential strategies to combat online hate.

A 3.8-million-year-old hominin cranium from Woranso-Mille, Ethiopia [28 August 2019]

Article • Two related studies describe a newly discovered cranium of Australopithecus anamensis, the environment in which this hominin would have lived approximately 3.8 million years ago and how it is related to Australopithecus afarensis.

Age and context of mid-Pliocene hominin cranium from Woranso-Mille, Ethiopia [28 August 2019]

Article • Two related studies describe a newly discovered cranium of Australopithecus anamensis, the environment in which this hominin would have lived approximately 3.8 million years ago and how it is related to Australopithecus afarensis.

Structure and mechanogating of the mammalian tactile channel PIEZO2 [21 August 2019]

Article • The cryo-electron microscopy structure of mouse PIEZO2 is determined and compared to that of PIEZO1, providing insights into the potential gating mechanisms of these mechanosensitive ion channels.

Force-induced conformational changes in PIEZO1 [21 August 2019]

Article • Cryo-electron microscopy and high-speed atomic force microscopy reveal that PIEZO1 can reversibly deform its shape towards a planar structure, which may explain how the PIEZO1 channel is gated in response to mechanical stimulation.

Inflation of 430-parsec bipolar radio bubbles in the Galactic Centre by an energetic event [11 September 2019]

Letter • Radio observations show a bipolar bubble structure of size 140 parsecs by 430 parsecs both above and below the Galactic Centre.

X-ray pumping of the 229Th nuclear clock isomer [11 September 2019]

Letter • Excitation to the second excited state of 229Th is used to populate the metastable state 229mTh, enabling accurate determination of the isomer’s energy, half-life and excitation linewidth.

Energy of the 229Th nuclear clock transition [11 September 2019]

Letter • The transition energy of the first excited state of 229Th to the ground state is determined through the measurement of internal conversion electrons to correspond to a wavelength of 149.7 ± 3.1 nanometres.

Position and momentum mapping of vibrations in graphene nanostructures [12 August 2019]

Letter • Investigation of a free-standing graphene monolayer using a technique based on transmission electron microscopy allows identification of atomic vibrations characteristic of the bulk or the edge of the sample.

Anthropogenic biases in chemical reaction data hinder exploratory inorganic synthesis [11 September 2019]

Letter • Human scientists make unrepresentative chemical reagent and reaction condition choices, and machine-learning algorithms trained on human-selected experiments are less capable of successfully predicting reaction outcomes than those trained on randomly generated experiments.

Mediterranean winter rainfall in phase with African monsoons during the past 1.36 million years [02 September 2019]

Letter • Comparisons between past regional drivers of precipitation extremes found time series data from Lake Ohrid and modern climate models of the Mediterranean may help to reduce simulation uncertainties in predictions of the Mediterranean climate.

Hidden resilience and adaptive dynamics of the global online hate ecology [21 August 2019]

Letter • The dynamics of interactions between hate-orientated networks on different online platforms is characterized, and a mathematical model predicts that policing on one online platform can make matters worse and generate ‘darker’ parts of the Internet.

An actin-based viscoplastic lock ensures progressive body-axis elongation [28 August 2019]

Letter • Molecular analysis and mathematical modelling are combined to identify a network of factors that account for viscoplastic deformation in elongation of Caenorhabditis elegans during embryonic development.

Maternal vitamin C regulates reprogramming of DNA methylation and germline development [04 September 2019]

Letter • The effect of vitamin C deprivation on mouse germline development is analysed, revealing that maternal vitamin C is required for proper DNA demethylation and the development of fetal oocytes, whereas the lack of vitamin C during pregnancy leads to reduced female fecundity in the offspring.

Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut [04 September 2019]

Letter • The re-seeding of antibiotic-resistant persister subpopulations of Salmonella enterica into the gut lumen favours the transfer of resistance plasmids to gut-resident enterobacteria, showing that even small reservoirs of persister bacteria facilitate the spread of antibiotic resistance.

The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape [04 September 2019]

Letter • H3K36me2 targets DNMT3A to intergenic regions and this process, together with H3K36me3-mediated recruitment of DNMT3B, has a key role in establishing and maintaining genomic DNA methylation landscapes.

Structures of influenza A virus RNA polymerase offer insight into viral genome replication [04 September 2019]

Letter • Structures of RNA polymerase of human and avian influenza A viruses reveal that the interface of the RNA polymerase dimer is required to initiate viral RNA synthesis in viral genome replication.

Structure and mechanism of mitochondrial proton-translocating transhydrogenase [28 August 2019]

Letter • The structure of a mammalian proton-translocating transhydrogenase in various conformations is solved by cryo-electron microscopy, and a mechanism for the coupling process within the enzyme is proposed.

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NEWS AND VIEWS

11 September 2019

Electrochemical reactions drive morphing of materials

Silicon anodes in lithium batteries expand during discharge, causing failure. This expansion has been used constructively in a material whose architecture controllably and reversibly changes to alter its function.

Seung-Yeol Jeon &

Seung-Yeol Jeon is in the Department of Mechanical Engineering and the Hopkins Extreme Materials Institute, Johns Hopkins University, Baltimore, Maryland 21218, USA.

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Sung Hoon Kang

Sung Hoon Kang is in the Department of Mechanical Engineering and the Hopkins Extreme Materials Institute, Johns Hopkins University, Baltimore, Maryland 21218, USA.

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If pressure is applied to a block of rubber, it flattens, but reverts to its original form once the pressure is removed — the shape transformation is said to be volatile. But if the same pressure is applied to Play-Doh, the new shape persists even without the pressure. Such a difference is due to inherent dissimilarities in each material’s properties, rather than in the nature of the shape produced, and it has not been possible to turn the volatility of a material’s shape changes on or off on demand. Writing in Nature, Xia et al.[1] report a type of ‘architected’ material for which the shape-transformation volatility can be modulated by controlling an applied charge and the geometry of substructures in the material, using electrochemical reactions that occur in batteries.

Read the paper: Electrochemically reconfigurable architected materials

Architected materials are a new class of material in which desirable properties are achieved through careful arrangement of substructural elements, such as beams and plates[2]. Many researchers are attempting to engineer normal (non-architected) materials to produce architected materials that have the exceptional characteristics of natural materials made from other compounds or elements, or that exhibit unusual properties not found in nature. Architected materials can have very different properties from those of their analogous non-architected materials.

Many studies on architected materials have sought to develop ‘smart’ materials that change their shape, and therefore their function, by responding to stimuli such as temperature, humidity or magnetic fields — similar to the capabilities of the robots in the Transformers films. The buckling of railway tracks in hot weather has inspired a strategy for inducing large shape and property changes: similar buckling of constrained substructures in materials has been triggered by applying mechanical loads[3] or by controlled swelling caused by the absorption of a solvent[4].

However, previously reported approaches for generating buckling-induced shape changes involve a finite number of shape configurations (usually two), and cannot switch the shape-transformation volatility of a material. That is, either an external stimulus must be maintained to retain the new shapes (as in the rubber-block example), or else the architected materials do not recover their original form when the external stimulus is removed (as with Play-Doh).

Xia and colleagues overcome this issue by using a new approach to induce shape transformations. They began by fabricating a cage-like 3D lattice (Fig. 1a) from a polymer using a 3D printer, then coated the lattice sequentially with a nickel layer and a silicon layer. Silicon is used as an anode material in lithium-ion batteries, which discharge by moving lithium ions from their cathode to the anode. Silicon anodes expand by about 300% when fully loaded with lithium[5], and the authors used this electrochemical transformation as an external stimulus to trigger buckling in their architected material. Xia and colleagues’ approach builds on previously reported work[6] in which honeycomb-like silicon structures were observed to buckle on loading with lithium ions.

Figure 1 | Structural reconfiguration of a material through electrochemical reactions. a, Xia et al.[1] report an ‘architected’ material whose microscopic structure consists of a 3D cage-like lattice, which has an outer coating of silicon. When lithium ions are loaded into the silicon through electrochemical reactions, the silicon expands, causing the lattice to buckle. The buckling is reversible, and the extent of buckling depends on the amount of lithium trapped in the silicon. b, The buckling can be precisely controlled to produce changes in the shape of the architected material. Scale bars: 15 micrometres. Micrographs reproduced from ref. 1.

The authors observed that the silicon-coated lattice undergoes shape transformations on discharging that can be reversed by recharging, and vice versa. Unlike architected materials based on soft materials, this shape change can be continuously modulated by electricity, and the new shape is maintained when discharging and/or charging is stopped — that is, the shape transformation is non-volatile. Moreover, Xia et al. carried out a numerical analysis to show that their approach can be used to switch the architected material between volatile and non-volatile shape-transformation states. They did not demonstrate such switching experimentally, but they did show that volatile and non-volatile states can be produced individually.

The researchers could control where in the lattice buckling occurred, thus enabling complex shape changes to be produced (Fig. 1b; see also Fig. 4h and Figs 6d–k of the paper[1]). These complex changes were engineered by introducing precisely positioned imperfections into the lattice, to provide a slight bias that caused buckling to occur in a particular direction. Such imperfections would generally be undesirable in other contexts.

Atomic-scale hardening mechanisms apply on larger scales in ‘architected’ materials

One of the current limitations of Xia and colleagues’ work is that it takes a long time to make a tiny amount of the architected material — we estimate that it would take about a day to produce 1 cubic millimetre of material, although the exact timing will vary depending on the printing conditions and the geometries of the material involved. A new 3D-printing approach known as volumetric additive manufacturing[7] might help to accelerate and scale up the process, but it currently has limited spatial resolution and works with only a small range of materials.

Xia and colleagues’ findings have a variety of potential applications. For example, in micrometre-scale robots, which have limited room for components, the use of materials that can change shape to perform multiple functions would be most helpful. The technology might also find uses in autonomous micro-devices that perform desired functions by changing shape in response to stimuli such as changes in ion concentration, or in devices known as microactuators[8] that ‘snap’[9] between two configurations in response to electrical signals or electrochemical stimuli.

The study also demonstrates a means of releasing the stress that builds up in silicon anodes of lithium batteries as they change volume during discharge, to prevent failure of the anodes — which is one of the key challenges in the development of next-generation silicon–lithium batteries. Moreover, the work opens up opportunities for controlling the propagation of high-frequency vibrations (known as phonons) using electricity, which might enable the development of potentially useful microelectromechanical systems.

Future research into electrochemically reconfigurable materials could benefit from the use of computational methods, such as machine learning, to optimize the topology of architected materials and the shapes produced for different applications. Such methods might increase the lifetime and/or the number of possible lithium loading–unloading cycles of architected materials by decreasing the strains required to induce buckling. They might also reduce the time taken for materials to respond to an electrochemical stimulus (currently 5 to 10 minutes), by increasing the surface area at which electrochemical reactions can occur, for example by using hierarchical substructures.

Finally, if the material systems that are compatible with this approach can be expanded, it would open the way for sensors and smart actuators to be used in many other applications, including medical devices. Given that our bodies contain various ion-containing, water-based fluids, it might be possible to devise micro-devices that sense physiological variables without external power, or to make smart implants that adapt to local conditions by modulating their shapes.

Nature 573, 198-199 (2019)

doi: 10.1038/d41586-019-02663-9

References

1. 1.

Xia, X. et al. Nature 573, 205–213 (2019).

2. 2.

Jung, G. S. & Buehler M. J. Nature 565, 303–304 (2019).

3. 3.

Mullin, T., Deschanel, S., Bertoldi, K. & Boyce, M. C. Phys. Rev. Lett. 99, 084301 (2007).

4. 4.

Kang, S. H. et al. Adv. Mater. 25, 3380–3385 (2013).

5. 5.

McDowell, M. T., Lee, S. W., Nix, W. D. & Cui, Y. Adv. Mater. 25, 4966–4985 (2013).

6. 6.

Baggetto, L., Danilov, D. & Notten, P. H. L. Adv. Mater. 23, 1563–1566 (2011).

7. 7.

Kelly, B. E. et al. Science 363, 1075–1079 (2019).

8. 8.

Jiang, Y., Korpas, L. M., & Raney, J. R. Nature Commun. 10, 128 (2019).

9. 9.

Shan, S. et al. Adv. Mater. 27, 4296–4301 (2015).

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02663-9

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NEWS AND VIEWS

21 August 2019

A mechanism for touch

Piezo proteins mediate the sense of touch. A near-complete structure of one such protein has been obtained, and the mechanism for converting mechanical signals into electrical ones has been probed in another.

Edwin W. McCleskey

Edwin W. McCleskey is in the Science Program of the Chan Zuckerberg Initiative, Redwood City, California 94002, USA.

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Our bodies can sense a wide array of mechanical stimuli: our sense of touch can distinguish between a soft breeze floating over the skin and a painful pinch, and other systems can detect the stretch of a muscle or even blood pressure. Our ability to sense these things requires an applied force to be turned into an electrical signal in the tiny endings of sensory neuronal cells that suffuse different tissues. Two related proteins, the Piezo1 and Piezo2 ion channels, mediate many of the mechanically stimulated processes in animals, by allowing positive ions to flow across the surface membrane of cells in response to force applied to the membrane[1]. Such mechano-electric transduction is mediated by Piezo2 in sensory neurons and by Piezo1 in non-neuronal cells that respond to forces such as shear and osmotic force[2]. Writing in Nature, Wang et al.[3] report a remarkable, almost complete structure of Piezo2, and Lin et al.[4] describe experiments that test how transduction occurs in Piezo1.

Piezo ion channels assemble from three identical Piezo proteins, each containing more than 2,500 amino-acid residues[5]. Solving such large structures — finding the location of each atom — is a great technical challenge. Nevertheless, studies in the past couple of years have described partial structures of Piezo1 at near-atomic resolution[6]–[8].

Read the paper: Structure and mechanogating of the mammalian tactile channel PIEZO2

Wang and colleagues now take things further with their near-atomic-resolution structure of Piezo2, resolving each of its 38 transmembrane helices. This is yet another achievement of the ‘resolution revolution’ in single-particle cryo-electron microscopy (cryo-EM)[9]. Cryo-EM obtains molecular structures by analysing thousands of images of individual protein molecules that have been frozen randomly throughout a thin layer of non-crystalline ice. It has proved particularly powerful for solving the structures of large membrane proteins, such as ion channels, that do not readily form the crystals required for X-ray crystallography.

A model of the target protein is often required as a template for cryo-EM analysis. Wang et al. used the previously reported structures of Piezo1 as the model for Piezo2. The resulting enormous structure of Piezo2 can therefore be viewed as the culmination of multi-year efforts from multiple labs.

These efforts have revealed that Piezo channels have four key features, which have been given helpfully descriptive names: the propeller, the cap, the pore and the nano-bowl (sometimes also called the dome). The propeller has three blades, one from each of the constituent proteins, equally spaced around the centre and each casting an arc roughly 200 ångströms in length. Each blade contains 36 α-helices, which have the correct lengths to fit across a lipid bilayer, and the correct hydrophobicity to be embedded in one. The string of helices therefore probably weaves back and forth across the membrane. Together, the three spring-like blades define an area of membrane of about 600 square nanometres — a sound arrangement for a sensor of membrane stretch (Fig. 1a).

Figure 1 | The structure of Piezo ion channels and their response to forces. Wang et al.[3] report the near-complete structure of Piezo2, a membrane ion channel that converts mechanical stimuli into electrical signals. Viewed from above or below the membrane, the trimeric channel looks like a three-bladed propeller and defines an extensive membrane area of about 600 square nanometres — in line with the idea that it responds to stretching of the membrane. b, Lin et al.[4] report that the bowl-like shape of the Piezo1 channel, viewed here from the side, creates a dimple in the surrounding membrane. The protein and dimple flatten reversibly when a force (not shown) of the size that could cause the channel’s pore to open is applied to Piezo1, perpendicular to the membrane.

The cap is a large, extracellular domain that sits outside the pore, similar to the caps that have been implicated in the gating of other trimeric ion channels[10]. The pore region is composed of six α-helices (two from each protein), and it has the internal surface charge expected of channels that allow the passage of positive ions rather than negative ones[6]. The pores of Piezo1 and Piezo2 are both clamped shut in the solved structures, with one constriction site in Piezo1 and two in Piezo2.

So, what is the transduction mechanism by which force opens the pore? There are two general ways in which a membrane protein might detect an external force: it could simply sense the stretch of the lipid membrane itself, or it might be pulled or pushed by other proteins that are attached to it in the regions either side of the membrane (the extracellular matrix or the cytoplasm). Both types of Piezo channel have a curved geometry, like a bowl open to the outside of the cell, and this unusual shape suggests a simple mechanism for force transduction[8]: if the curve of the protein causes local distortion of the membrane, then a lateral stretch could flatten both the membrane and the protein. If this flattening of the protein structure is somehow linked to the gates that open the channel’s pore, no accessory proteins would be needed for transduction.

Read the paper: Force-induced conformational changes in PIEZO1

Lin et al. tested this proposal in two ways. First, they studied Piezo1 channels in lipid vesicles. This was crucial because previously reported Piezo structures were obtained in aggregates of detergents (detergent micelles), rather than in lipids, so it has been uncertain how Piezos sit within, and interact with, lipid bilayers. The authors found that Piezo1 does indeed distort the vesicle membrane (Fig. 1b), clearly puckering the vesicles into non-spherical shapes. In the second test, the authors applied force to the Piezo channel using the probe of an atomic force microscope (AFM), and found that the bowl underwent reversible flattening at biologically relevant pressures.

It should be noted that the AFM applies force perpendicular to the membrane, rather than laterally through it, but the experiment still demonstrates the springiness of the bowl at appropriate forces — a crucial requirement of the proposal. However, the experiment does not address whether biological stimuli directly stretch cell membranes or act through an accessory protein (akin to the action of the AFM probe). Also not addressed is how flattening of the bowl would open the pore. The extracellular cap might be important for pore opening because, as Wang et al. show[3], mutations that eliminate most of it render the channel insensitive to membrane deformation. However, there are many ways to explain the loss of function of a protein when a large part of it is deleted.

Force-activated ion channels in close-up

Further effort is now required to verify which transduction mechanism — membrane stretch or protein–protein interaction — operates in cells. The first task is to solve the atomic structure of both Piezo channels isolated in artificial lipid membranes, rather than in detergent micelles. Ideally, this would be achieved using lipid vesicles that have been frozen under different osmotic conditions. Osmotic forces will stretch the membrane and, according to the membrane-stretch model, should bias Piezo towards different gating states. Such states might be detectable using cryo-EM or by measuring ion flux through the pores, thereby demonstrating that Piezo can open without aid from other proteins. The two Piezo channels might behave differently in such experiments.

The protein–protein interaction model could be explored further by electron tomography, a method that can distinguish between and locate different types of membrane protein in nerve cells and identify cytoplasmic proteins with which they interact[11]. The observation of force transduction in real time will also be essential. The activity of ion channels, and conformational changes in them, have been measured simultaneously in real time in live cells[12]. This would be a powerful assay for detecting whether protein–protein interactions affect Piezo transduction, and for investigating how channel flattening might link to gates in the pore. Each of these lines of research presents formidable technical challenges. Nevertheless, such high-risk research seems worth the effort, because our sense of touch is so fundamental to our sense of being.

Nature 573, 199-200 (2019)

doi: 10.1038/d41586-019-02454-2

References

1. 1.

Coste, B. et al. Nature 483, 176–181 (2012).

2. 2.

Murthy, S. E., Dubin, A. E. & Patapoutian, A. Nature Rev. Mol. Cell Biol. 18, 771–783 (2017).

3. 3.

Wang, L. et al. Nature 573, 225–229 (2019).

4. 4.

Lin, Y.-C. et al. Nature 573, 230–234 (2019).

5. 5.

Ge, J. et al. Nature 527, 64–69 (2015).

6. 6.

Saotome, K. et al. Nature 554, 481–486 (2018).

7. 7.

Zhao, Q. et al. Nature 554, 487–492 (2018).

8. 8.

Guo, Y. R. & MacKinnon, R. eLife 6, e33660 (2017).

9. 9.

Cheng, Y. Cell 161, 450–457 (2015).

10. 10.

Mansoor, S. E. et al. Nature 538, 66–71 (2016).

11. 11.

Chen, X. et al. J. Neurosci. 31, 6329–6338 (2011).

12. 12.

Sasmal, D. K. & Lu, H. P. J. Am. Chem. Soc. 136, 12998–3005 (2014).

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NEWS AND VIEWS

28 August 2019

Elusive cranium of early hominin found

A 3.8-million-year-old hominin fossil reveals what the cranium of the oldest known Australopithecus species looked like, casting doubt on assumptions about how these ancient relatives of humans evolved.

Fred Spoor

Fred Spoor is at the Centre for Human Evolution Research, Natural History Museum, London SW7 5BD, UK, in the Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, and in the Department of Anthropology, University College London, UK.

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Human evolution often captures the imagination, not least because some of our extinct hominin relatives are personified by well-preserved fossils with catchy nicknames. For example, a partial skeleton of Australopithecus afarensis is named Lucy, and an Australopithecus africanus cranium (the skull without its lower jaw) is called Mrs Ples. However, the oldest known species that is unambiguously part of the human evolutionary tree[1], Australopithecus anamensis, has mainly languished away from the limelight because of its small and not particularly glamorous fossil record. Until now, A. anamensis was known only from partial upper and lower jaw bones, isolated teeth, a small part of the braincase and a few limb bones. These specimens were found in Kenya and Ethiopia and are between 4.2 million and 3.9 million years old[2].

Read the paper: A 3.8-million-year-old hominin cranium from Woranso-Mille, Ethiopia

Writing in Nature, Haile-Selassie et al.[3] and Saylor et al.[4] report the discovery of a mostly complete 3.8-million-year-old cranium found in the Woranso-Mille area of Ethiopia. The fossil is of an adult, probably male, and was identified as A. anamensis mainly on the basis of the characteristics of its jaw and canine teeth. This cranium looks set to become another celebrated icon of human evolution.

A complete skull is not essential for a good understanding of the morphology of an extinct species. For example, A. afarensis had already been well documented from a large collection of fragmentary remains when the first skull from an adult of this species was found[5]. However, the newly discovered cranium of A. anamensis, casually named MRD after its collection number, MRD-VP-1/1, provides a wealth of information about A. anamensis by revealing for the first time what its full face and braincase looked like (Fig. 1).

Figure 1 | The skull of the hominin species Australopithecus anamensis. Haile-Selassie et al.[3] and Saylor et al.[4] report the discovery and dating of a 3.8-million-year-old cranium (grey) of A. anamensis, found in Ethiopia (collection number MRD-VP-1/1). Surface reconstructions (yellow) of fossils representing the only previously known parts of the skull region of this species are superimposed on the cranium. These 4.2-million-year-old fossils from Kenya[2] are an upper jaw bone (collection number KNM-KP29283) and a lower jaw and ear bone (KNM-KP29281). The projecting cheekbones (blue arrow) create an apparent facial similarity to a 2.5-million-year-old specimen of the hominin Paranthropus aethiopicus[8]; however, the authors propose that this feature evolved independently in Paranthropus and A. anamensis. Both the Kenyan and Ethiopian fossils of A. anamensis are characterized, among other features, by protruding jaws (red arrow) and a small earhole (black arrow). Scale bar, 1 centimetre. The Kenyan fossils are presented at 97% of their original size to match the cranium size.

MRD offers insight into the shape of hominin skulls at an early stage of the better understood part of human evolution, from about 4.2 million years ago to the present. The new information will help scientists to determine which skull features are primitive (ancestral) and which are derived (evolved — that is, different from the corresponding feature in an ancestor); this, in turn, will affect inferences about the evolutionary relationships between species. The discovery will also trigger a re-evaluation of the sparse hominin fossil record from before 4.2 million years ago. Whether previously discovered fossils assigned to species of Ardipithecus, Orrorin and Sahelanthropus are all indeed part of the human evolutionary tree or are extinct apes is controversial[1],[6]. MRD provides information that will advance this debate.

By comparing A. anamensis with other species, and including their new evidence, the authors generated evolutionary family trees in which A. anamensis was consistently placed as the most ancestral of all Australopithecus species and later hominins. This result confirms previous findings[6], and reflects the fact that the cranium shows predominantly primitive features — including some in parts never documented before in A. anamensis fossils. MRD has a distinctly protruding face (Fig. 1) and a notably long and narrow braincase. The latter feature is remarkably similar in this respect to that of the 7-million-year-old cranium of Sahelanthropus[7], and these two species both had a small brain. The new fossil has several features that are assumed by the authors to be derived rather than primitive. Most striking is the forward projection of the cheek bones, which creates a facial appearance reminiscent of much younger Paranthropus hominin species, particularly the 2.5-million-year-old Paranthropus aethiopicus[8]. The authors conclude that this facial characteristic evolved independently in A. anamensis and later species, but the resemblance might inspire alternative interpretations.

Read the paper: Age and context of mid-Pliocene hominin cranium from Woranso-Mille, Ethiopia

On the basis of previous comparisons in which only information about jaws and teeth was available for A. anamensis, it has been widely accepted that A. anamensis and A. afarensis were successively part of a single evolving lineage through time, and were represented in the fossil record, respectively, from 4.2 million to 3.9 million years ago, and from 3.8 million to 3.0 million years ago[2],[9]. Thus, it has been argued that A. anamensis and A. afarensis should be considered a single evolutionary species[9].

The MRD cranium now increases the number of A. anamensis features that can be compared with those of the other species to explore this issue further, and the authors present evidence that is not consistent with the two species being part of a single evolving lineage. First, they identify a number of features that are derived in A. anamensis but are primitive in A. afarensis. Second, with the shape of MRD as a basis, the authors conclude that a 3.9-million-year-old frontal bone (part of the forehead) from Ethiopia represents A. afarensis rather than A. anamensis. This attribution, along with the discovery of the 3.8-million-year-old MRD cranium of A. anamensis (dating evidence reported by Saylor et al.), provides a revised timeframe indicating that A. anamensis existed from at least 4.2 million to 3.8 million years ago, and A. afarensis from at least 3.9 million to 3.0 million years ago — so the temporal overlap between the two species was at least 100,000 years.

The model of a single, evolving lineage is certainly challenged by this new evidence, but more aspects will need to be considered. The isolated frontal bone attributed to A. afarensis might instead belong to Kenyanthropus platyops or Australopithecus deyiremeda, other broadly contemporary hominin species from eastern Africa[10]. Moreover, little is known about the face of early A. afarensis[2],[9], and in particular, whether it showed more similarities to the face of the MRD cranium than does the face of later A. afarensis.

Small-brained and big-mouthed

One way in which Haile-Selassie and colleagues’ analysis of the fossil specimen stands out is in their use of wide-ranging digital reconstruction that corrects distortions of the fossil’s shape, and estimates missing parts. These digital methods are readily available and offer unique opportunities for research. However, many more shapes can be morphed and matched this way than would be possible with conventional methods, and care is needed to generate only the most realistic options. It is therefore essential that any digital reconstruction is carried out with detailed, first-hand knowledge of the original fossil, including how it is preserved and distorted.

This point is particularly relevant with respect to the forward-projecting cheekbones of the newly discovered fossil. After reconstruction, this area looks smoothed, with hardly any sign of the original bone surface. One prominent aspect of MRD where the reconstruction could be improved is the front of the upper jaw. Here, digital processing resulted in a less accurate idea of what the characteristic, strongly projecting subnasal area would have looked like before the fossil was broken.

MRD is a great addition to the fossil record of human evolution. Its discovery will substantially affect our thinking on the origin of the genus Australopithecus specifically, and on the evolutionary family tree of early hominins more broadly. This work demonstrates the importance that a single fossil can have in palaeontology, something we should remember when we get puzzled looks and sighs from our colleagues in the experimental biosciences regarding excitement about a sample size of n = 1.

Nature 573, 200-202 (2019)

doi: 10.1038/d41586-019-02520-9

References

1. 1.

Wood, B. & Harrison, T. Nature 470, 347–352 (2011).

2. 2.

Kimbel, W. H. in Handbook of Paleoanthropology: Vol III: Phylogeny of Hominids (eds Henke, W. & Tattersall, I.) 2071–2105 (Springer, 2015).

3. 3.

Haile-Selassie, Y., Melillo, S. M., Vazzana, A., Benazzi, S. & Ryan T. M. Nature 573, 214–219 (2019).

4. 4.

Saylor, B. Z. et al. Nature 573, 220–224 (2019).

5. 5.

Kimbel, W. H., Johanson, D. C. & Rak, Y. Nature 368, 449–451 (1994).

6. 6.

Mongle, C. S., Strait, D. S. & Grine, F. E. J. Hum. Evol. 131, 28–39 (2019).

7. 7.

Zollikofer, C. P. et al. Nature 434, 755–759 (2005).

8. 8.

Walker, A., Leakey, R. E., Harris, J. M. & Brown, F. H. Nature 322, 517–522 (1986).

9. 9.

Kimbel, W. H. et al. J. Hum. Evol. 51, 134–152 (2006).

10. 10.

Spoor, F. Nature 521, 432–433 (2015).

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02520-9

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NEWS AND VIEWS

11 September 2019

One tick closer to a nuclear clock

Clocks that are based on the nucleus of a single thorium atom could be more precise than existing timekeepers. Such clocks have not yet been realized, but two experiments provide keys steps towards this goal.

Jason T. Burke

Jason T. Burke is in the Nuclear and Particle Physics Group, Nuclear and Chemical Sciences Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA.

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Atomic clocks are currently the gold standard of timekeeping. These devices measure time on the basis of transitions between two states of an atom. In two papers in Nature, Masuda et al.[1] and Seiferle et al.[2] report progress towards a clock that instead uses transitions between two states of an atomic nucleus. Such a nuclear clock could outperform existing atomic timekeepers, and have applications in both fundamental and applied physics.

Read the paper: X-ray pumping of the 229Th nuclear clock isomer

Humans have been trying to measure the passage of time for thousands of years. From the sundial, to the hourglass, to the pocket watch, we have continually tried to improve our ability to quantify and standardize time. In the early 1900s, scientists struggled to define time consistently, and put forth various standards to help synchronize humanity. What was missing was a natural reference point that could be used, regardless of its location on Earth. We needed to define what a second truly meant: something fundamental that remains accurate and precise across all space, for all millennia.

Scientists realized that the properties of atomic transitions are independent of location in space or time. This recognition led to the idea of using a known transition between two atomic states as a means to define time. If a standardized second could be defined as a specific and agreed-on number of atomic transitions, time could be quantified. Researchers set out to do this in the 1930s, and by the end of the 1940s the world had its first atomic clock[3].

Read the paper: Energy of the 229Th nuclear clock transition

Over the past 70 years, atomic clocks have been continually improved and currently have a precision[4] of about 1 part in 10^18. But what if we could do better than these devices? What if we could make a clock that was 100,000 times smaller, was less susceptible to its environment and possibly had a precision of 1 part in 10^19? An atomic nucleus, which is about 100,000 times smaller than an atom, could provide such a device[5].

Since 2003, researchers around the world have been trying to make a nuclear clock using the nucleus of a thorium-229 atom[6]. This nucleus, unlike all others that are known, has an excited state (called an isomeric state) that is only a few electronvolts (eV) in energy above its ground state[7]. As a result, the transition between these two states is accessible using specialized lasers. The problem is that the exact energy of the isomeric state is currently unknown. Masuda et al. and Seiferle et al. have made progress towards understanding the exact character of the thorium-229 isomeric transition, by carrying out experiments that extend previous work[7].

In Masuda and colleagues’ experiment, a high-intensity X-ray beam was passed through a pair of silicon crystals that narrowed the energy range of the X-rays to 0.1 eV. These X-rays were then used to irradiate a thorium-229 nucleus that was in the ground state (Fig. 1). The nucleus transitioned to a second excited state that has an energy much higher than that of the isomeric state. The narrow X-ray energy range allowed the authors to determine the exact energy of this second excited state: 29.19 keV. Finally, the nucleus decayed directly to the isomeric state. The approach of Masuda et al. could enable this state to be produced more efficiently than was previously possible.

Figure 1 | Low-energy states and transitions of the thorium-229 nucleus. Masuda et al.[1] report a technique to produce nuclei of thorium-229 atoms in an excited state called an isomeric state. The authors irradiated a thorium-229 nucleus in the ground state with X-rays, which caused the nucleus to transition to a second excited state that has an energy of 29.19 keV (eV; electronvolts). The nucleus then decayed to the isomeric state. Seiferle et al.[2] observed a process known as internal conversion, in which a thorium-229 nucleus in the isomeric state decayed to the ground state and the neutral atom emitted an electron. By studying the energy of emitted electrons, the authors estimated the energy of the isomeric state to be about 8.28 eV. These two studies could lead to ultraprecise clocks that are based on thorium-229 nuclei.

In Seiferle and colleagues’ experiment, a beam of thorium-229 ions was generated from the natural decay of uranium-233 ions. About 2% of the thorium ions were in the isomeric state. These ions were then neutralized to allow them to decay to the ground state through a process called internal conversion. In this process, a nuclear decay that would typically produce a γ-ray instead causes the neutral atom to emit an electron (Fig. 1). However, internal conversion is complicated, because the electron can originate from many different energy levels in the neutral atom.

Elusive transition spotted in thorium

To observe the ejected electrons from internal conversion, Seiferle and co-workers used a magnetic field to bend the trajectory of these particles towards an electron detector. They applied an electric field to the electrons until the voltage associated with this field was large enough to stop the electrons. The final voltage was equal to the initial energy of the electrons. Seiferle et al. then used a theoretical model to interpret the electron energy spectrum, which is the first energy spectrum observed from the decay products of the isomeric state. Their analysis indicated that the energy of the isomeric state is 8.28 ± 0.17 eV.

Although the ultimate and groundbreaking goal of directly observing the thorium-229 isomeric transition remains elusive, substantial progress continues to be made. The results of Masuda et al. and Seiferle et al. are key steps forward. Hopefully, the observation is not too far off, as teams of scientists race to make the world’s first nuclear clock, which would offer unprecedented precision. This finding would enable a whole host of experiments and discoveries in the decades to follow. For instance, a nuclear clock could have applications in dark-matter research[8] and in the observation of possible variations in the fundamental constants of physics[9].

Nature 573, 202-203 (2019)

doi: 10.1038/d41586-019-02664-8

References

1. 1.

Masuda, T. et al. Nature 573, 238–242 (2019).

2. 2.

Seiferle, B. et al. Nature 573, 243–246 (2019).

3. 3.

Lyons, H. Instruments 22, 133–135 (1949).

4. 4.

Brewer, S. M. et al. Phys. Rev. Lett. 123, 033201 (2019).

5. 5.

Campbell, C. J. et al. Phys. Rev. Lett. 108, 120802 (2012).

6. 6.

Peik, E. & Tamm, C. Europhys. Lett. 61, 181–186 (2003).

7. 7.

Beck, B. R. et al. Phys. Rev. Lett. 98, 142501 (2007).

8. 8.

Derevianko, A. & Pospelov, M. Nature Phys. 10, 933–936 (2014).

9. 9.

Flambaum, V. V. Phys. Rev. Lett. 97, 092502 (2006).

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02664-8

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NEWS AND VIEWS

21 August 2019

Strategies for combating online hate

An analysis of the dynamics of online hate groups on social-media platforms reveals why current methods to ban hate content are ineffective, and provides the basis for four potential strategies to combat online hate.

Noemi Derzsy

Noemi Derzsy is in the Data Science and AI Research Organization, AT&T Labs, New York, New York 10007, USA.

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How does the online hate ecosystem persist on social-media platforms, and what measures can be taken to effectively reduce its presence? Writing in Nature, Johnson et al.[1] address these questions in a captivating report on the behaviour of online hate communities that reside on multiple social-media platforms. The authors shed light on the structure and dynamics of online hate groups and, informed by the results, propose four policies to reduce hate content on online social media.

Read the paper: Hidden resilience and adaptive dynamics of the global online hate ecology

We live in an age of high social interconnectedness, whereby opinions shared in one geographical region do not remain spatially localized, but can spread rapidly around the globe thanks to online social media. The high speed of such diffusion poses problems for those policing hate speech, and creates opportunities for nefarious organizations to share their messages and expand their recruiting efforts globally. When the policing of social media is inefficient, the online ecosystem can become a powerful radicalizing instrument[2]. Understanding the mechanisms that govern hate-community dynamics is thus crucial to proposing effective measures to combat such organizations in this online battleground.

Johnson et al. examined the dynamics of hate clusters on two social-media platforms, Facebook and VKontakte, over a period of a few months. Clusters were defined as online pages or groups that organized individuals who shared similar views, interests or declared purposes, into communities. These pages and groups on social-media platforms contain links to other clusters with similar content that users can join. Through these links, the authors established the network connections between clusters, and could track how members of one cluster also joined other clusters. Two clusters (groups or pages) were considered connected if they contained links to one another. The authors’ approach had the advantage of not requiring individual-level information about users who are members of clusters.

Johnson et al. show that online hate groups are organized in highly resilient clusters. The users in these clusters are not geographically localized, but are globally interconnected by ‘highways’ that facilitate the spread of online hate across different countries, continents and languages. When these clusters are attacked — for example, when hate groups are removed by social-media platform administrators (Fig. 1) — the clusters rapidly rewire and repair themselves, and strong bonds are made between clusters, formed by users shared between them, analogous to covalent chemical bonds. In some cases, two or more small clusters can even merge to form a large cluster, in a process the authors liken to the fusion of two atomic nuclei. Using their mathematical model, the authors demonstrated that banning hate content on a single platform aggravates online hate ecosystems and promotes the creation of clusters that are not detectable by platform policing (which the authors call ‘dark pools’), where hate content can thrive unchecked.

Figure 1 | Facebook moderators removing hate-related content. Johnson et al.[1] examined the dynamics of online hate groups on Facebook and another social-media platform, VKontakte, and used their results to propose four policies to tackle online hate.Credit: Gordon Welters/NYT/Redux/eyevine

Online social-media platforms are challenging to regulate, and policymakers have struggled to suggest practicable ways of reducing hate online. Efforts to ban and remove hate-related content have proved ineffective[3],[4]. Over the past few years, the incidence of reports of hate speech online has been rising[5], indicating that the battle against the diffusion of hateful content is being lost, an unsettling direction for the well-being and safety of our society. Furthermore, exposure to and engagement with online hate on social media has been suggested to promote offline aggression[6], with some perpetrators of violent hate crimes reported to have engaged with such content[7].

Previous studies (for example, ref. 8) have considered hate groups as individual networks, or considered the interconnected clusters together as one global network. In their fresh approach, Johnson and colleagues studied the interconnected structure of a community of hate clusters as a ‘network of networks’[9]–[11], in which clusters are networks that are interconnected by highways. Moreover, they propose four policies for effective intervention that are informed by the mechanisms their study revealed govern the structure and dynamics of the online-hate ecosystem.

Currently, social-media companies must decide which content to ban, but often have to contend with overwhelming volumes of content and various legal and regulatory constraints in different countries. Johnson and co-workers’ four recommended interventions — policies 1 to 4 — take into account the legal considerations associated with banning groups and individual users. Notably, each of the authors’ suggested policies could be implemented independently by individual platforms without the need for sharing sensitive information between them, which in most cases is not legally allowed without explicit user consent.

In policy 1, the authors propose banning relatively small hate clusters, rather than removing the largest online hate cluster. This policy leverages the authors’ finding that the size distribution of online hate clusters follows a power-law trend, such that most clusters are small and only very few are large. Banning the largest hate cluster would be predicted to lead to the formation of a new large cluster from the myriad small ones. By contrast, small clusters are highly abundant — meaning that they are relatively easy to locate — and eliminating them prevents the emergence of other large clusters.

Degrees of control

Banning whole groups of users, regardless of the size of the groups, can result in outrage in the hate community and allegations against social-media platforms that rights to free speech are being suppressed[12]. To avoid that, policy 2 instead recommends banning a small number of users selected at random from online hate clusters. This random-targeting approach does not require users to be spatially located or the use of sensitive user-profile information (which cannot be applied to target specific users), thus avoiding potential violations of privacy regulations. However, the effectiveness of this approach depends heavily on the structure of the social network, because the topological characteristics of networks strongly shape their resilience to random failures or targeted attacks.

Policy 3 leverages the finding that clusters self-organize from an initially disordered group of users; it recommends that platform administrators promote the organization of clusters of anti-hate users, which could serve as a ‘human immune system’ to fight and counteract hate clusters. Policy 4 exploits the fact that many hate groups online have opposing views. The policy suggests that the platform administrators introduce an artificial group of users to encourage interactions between hate clusters that have opposing views, with a view to the hate clusters subsequently battling out their differences among themselves. The authors’ modelling demonstrated that such battles would effectively remove large hate clusters that have opposing views. Once put into action, policies 3 and 4 would require little direct intervention by the platform administrators; however, setting opposing clusters against each other would require meticulous engineering.

The authors recommend caution in assessing the advantages and disadvantages of adopting each policy, because the feasibility of implementing a policy will rely on available computational and human resources, and legal privacy constraints. Moreover, any decisions about whether to implement one policy over another must be made on the basis of empirical analysis and data obtained by closely monitoring these clusters.

Over the years, it has become apparent that effective solutions to dealing with online hate and the legal and privacy issues that arise from online social-media platforms cannot arise solely from individual industry segments, but instead will require a combined effort from technology companies, policymakers and researchers. Johnson and colleagues’ study provides valuable insights, and their proposed policies can serve as a guideline for future efforts.

Nature 573, 203-204 (2019)

doi: 10.1038/d41586-019-02447-1

Noemi Derzsy contributed to this article in her personal capacity; the views expressed are her own and do not necessarily represent the views of AT&T.

References

1. 1.

Johnson, N. F. et al. Nature 573, 261–265 (2019).

2. 2.

Hernandez, D. & Olson, P. Wall Street J. (5 July 2019); available at go.nature.com/2oxoqdw

3. 3.

Wakefield, J. BBC News (15 March 2019); available at go.nature.com/2kabi2p

4. 4.

O’Brien, S. A. CNN Business (28 February 2019); available at go.nature.com/31c2nny

5. 5.

BBC News (17 March 2018); available at go.nature.com/2h04gci

6. 6.

SELMA (23 April 2019); available at go.nature.com/2ygkhs1

7. 7.

Benner, K. & Spencer, H. New York Times (27 June 2019).

8. 8.

Mathew, B., Dutt, R., Goyal, P. & Mukherjee, A. Proc. 10th ACM Conf. Web Sci. 173–182 (2019).

9. 9.

Havlin, S., Kenett, D. Y., Bashan, A., Gao, J. & Stanley, H. E. Eur. Phys. J. Spec. Top. 223, 2087–2106 (2014).

10. 10.

Palla, G., Barabasi, A. L. & Vicsek, T. Nature 446, 664–667 (2007).

11. 11.

Jarrett, T. C., Ashton, D. J., Fricker, M. & Johnson, N. F. Phys. Rev. E 74, 026116 (2006).

12. 12.

Coaston, J. Vox (14 May 2019).

This article was downloaded by calibre from https://www.nature.com/articles/d41586-019-02447-1

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- Article

- Published: 28 August 2019

A 3.8-million-year-old hominin cranium from Woranso-Mille, Ethiopia

- Yohannes Haile-Selassie[1] na1,
- Stephanie M. Melillo[2] na1,
- Antonino Vazzana[3],
- Stefano Benazzi[3] &
- Timothy M. Ryan[4]

Naturevolume 573, pages214–219 (2019) | Download Citation

Subjects

- Evolution

- Palaeontology

Abstract

The cranial morphology of the earliest known hominins in the genus Australopithecus remains unclear. The oldest species in this genus (Australopithecus anamensis, specimens of which have been dated to 4.2–3.9 million years ago) is known primarily from jaws and teeth, whereas younger species (dated to 3.5–2.0 million years ago) are typically represented by multiple skulls. Here we describe a nearly complete hominin cranium from Woranso-Mille (Ethiopia) that we date to 3.8 million years ago. We assign this cranium to A. anamensis on the basis of the taxonomically and phylogenetically informative morphology of the canine, maxilla and temporal bone. This specimen thus provides the first glimpse of the entire craniofacial morphology of the earliest known members of the genus Australopithecus. We further demonstrate that A. anamensis and Australopithecus afarensis differ more than previously recognized and that these two species overlapped for at least 100,000 years—contradicting the widely accepted hypothesis of anagenesis.

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Fig. 1: The MRD-VP-1/1 cranium.

Fig. 2: Comparisons of upper canine morphology.

Fig. 3: Structure of the face and neurocranium.

Data availability

The data that support the findings of this study that were not included in the Supplementary Information are available from the corresponding authors upon reasonable request.

References

1.

Brunet, M. et al. Australopithecus bahrelghazali, une nouvelle espèce d’Hominidé ancien de la région de Koro Toro (Tchad). C. R. Acad. Sci. IIA 322, 907–913 (1996).

- Google Scholar

2.

Brunet, M. et al. New material of the earliest hominid from the Upper Miocene of Chad. Nature 434, 752–755 (2005).

- ADS
- CAS
- Article
- Google Scholar

3.

Brunet, M. et al. A new hominid from the Upper Miocene of Chad, Central Africa. Nature 418, 145–151 (2002).

- ADS
- CAS
- Article
- Google Scholar

4.

Haile-Selassie, Y. Late Miocene hominids from the Middle Awash, Ethiopia. Nature 412, 178–181 (2001).

- ADS
- CAS
- Article
- Google Scholar

5.

Haile-Selassie, Y. et al. New species from Ethiopia further expands Middle Pliocene hominin diversity. Nature 521, 483–488 (2015).

- ADS
- CAS
- Article
- Google Scholar

6.

Haile-Selassie, Y. et al. A new hominin foot from Ethiopia shows multiple Pliocene bipedal adaptations. Nature 483, 565–569 (2012).

- ADS
- CAS
- Article
- Google Scholar

7.

Leakey, M. G., Feibel, C. S., McDougall, I. & Walker, A. New four-million-year-old hominid species from Kanapoi and Allia Bay, Kenya. Nature 376, 565–571 (1995).

- ADS
- CAS
- Article
- Google Scholar

8.

Leakey, M. G., Feibel, C. S., McDougall, I., Ward, C. & Walker, A. New specimens and confirmation of an early age for Australopithecus anamensis. Nature 393, 62–66 (1998).

- ADS
- CAS
- Article
- Google Scholar

9.

Leakey, M. G. et al. New hominin genus from eastern Africa shows diverse middle Pliocene lineages. Nature 410, 433–440 (2001).

- ADS
- CAS
- Article
- Google Scholar

10.

Senut, B. et al. First hominid from the Miocene (Lukeino formation, Kenya). C. R. Acad. Sci. IIA 332, 137–144 (2001).

- Google Scholar

11.

White, T. D., Suwa, G. & Asfaw, B. Australopithecus ramidus, a new species of early hominid from Aramis, Ethiopia. Nature 371, 306–312 (1994).

- ADS
- CAS
- Article
- Google Scholar

12.

White, T. D. et al. Ardipithecus ramidus and the paleobiology of early hominids. Science 326, 64–86 (2009).

- ADS
- Article
- Google Scholar

13.

Wood, B. & K Boyle, E. Hominin taxic diversity: fact or fantasy? Am. J. Phys. Anthropol. 159, 37–78 (2016).

- Article

- Google Scholar

14.

Haile-Selassie, Y., Melillo, S. M. & Su, D. F. The Pliocene hominin diversity conundrum: do more fossils mean less clarity? Proc. Natl Acad. Sci. USA 113, 6364–6371 (2016).

- CAS
- Article
- Google Scholar

15.

Haile-Selassie, Y. et al. Dentognathic remains of Australopithecus afarensis from Nefuraytu (Woranso-Mille, Ethiopia): comparative description, geology, and paleoecological context. J. Hum. Evol. 100, 35–53 (2016).

- Article

- Google Scholar

16.

Haile-Selassie, Y. Phylogeny of early Australopithecus: new fossil evidence from the Woranso-Mille (central Afar, Ethiopia). Phil. Trans. R. Soc. Lond. B 365, 3323–3331 (2010).

- Article

- Google Scholar

17.

Haile-Selassie, Y., Saylor, B. Z., Deino, A., Alene, M. & Latimer, B. M. New hominid fossils from Woranso-Mille (Central Afar, Ethiopia) and taxonomy of early Australopithecus. Am. J. Phys. Anthropol. 141, 406–417 (2010).

- PubMed

- Google Scholar

18.

Saylor, B. Z. et al. Age and context of new mid-Pliocene hominin cranium from Woranso-Mille, Ethiopia. Nature https://doi.org/10.1038/s41586-019-1514-7 (2019).

19.

Ward, C. V., Leakey, M. G. & Walker, A. Morphology of Australopithecus anamensis from Kanapoi and Allia Bay, Kenya. J. Hum. Evol. 41, 255–368 (2001).

- CAS
- Article
- Google Scholar

20.

Ward, C. V., Manthi, F. K. & Plavcan, J. M. New fossils of Australopithecus anamensis from Kanapoi, West Turkana, Kenya (2003–2008). J. Hum. Evol. 65, 501–524 (2013).

- CAS
- Article
- Google Scholar

21.

Ward, C. V., Plavcan, J. M. & Manthi, F. K. New fossils of Australopithecus anamensis from Kanapoi, West Turkana, Kenya (2012–2015). J. Hum. Evol. https://doi.org/10.1016/j.jhevol.2017.07.008 (2017).

22.

Manthi, F. K., Plavcan, J. M. & Ward, C. V. New hominin fossils from Kanapoi, Kenya, and the mosaic evolution of canine teeth in early hominins. S. Afr. J. Sci. 108, 724 (2012).

- Article

- Google Scholar

23.

Suwa, G. et al. Paleobiological implications of the Ardipithecus ramidus dentition. Science 326, 69–99 (2009).

- ADS
- Article
- Google Scholar

24.

Haile-Selassie, Y., Suwa, G. & White, T. D. Late Miocene teeth from Middle Awash, Ethiopia, and early hominid dental evolution. Science 303, 1503–1505 (2004).

- ADS
- CAS
- Article
- Google Scholar

25.

White, T. D. et al. Asa Issie, Aramis and the origin of Australopithecus. Nature 440, 883–889 (2006).

- ADS
- CAS
- Article
- Google Scholar

26.

Suwa, G. et al. The Ardipithecus ramidus skull and its implications for hominid origins. Science 326, 68–68e7 (2009).

- ADS
- Article
- Google Scholar

27.

Kimbel, W. H., Rak, Y. & Johanson, D. C. The Skull of Australopithecus afarensis (Oxford Univ. Press, 2004).

28.

Guy, F. et al. Morphological affinities of the Sahelanthropus tchadensis (Late Miocene hominid from Chad) cranium. Proc. Natl Acad. Sci. USA 102, 18836–18841 (2005).

- ADS
- CAS
- Article
- Google Scholar

29.

Rak, Y. The Australopithecine Face (Academic, 1983).

30.

Kimbel, W. H. & Rak, Y. Australopithecus sediba and the emergence of Homo: Questionable evidence from the cranium of the juvenile holotype MH 1. J. Hum. Evol. 107, 94–106 (2017).

- Article

- Google Scholar

31.

Kimbel, W. H., White, T. D. & Johanson, D. C. Cranial morphology of Australopithecus afarensis: a comparative study based on a composite reconstruction of the adult skull. Am. J. Phys. Anthropol. 64, 337–388 (1984).

- CAS
- Article
- Google Scholar

32.

Kimbel, W. H. & Rak, Y. The cranial base of Australopithecus afarensis: new insights from the female skull. Phil. Trans. R. Soc. Lond. B 365, 3365–3376 (2010).

- Article

- Google Scholar

33.

Strait, D. S. & Grine, F. E. Inferring hominoid and early hominid phylogeny using craniodental characters: the role of fossil taxa. J. Hum. Evol. 47, 399–452 (2004).

- Article

- Google Scholar

34.

Dembo, M., Matzke, N. J., Mooers, A. Ø. & Collard, M. Bayesian analysis of a morphological supermatrix sheds light on controversial fossil hominin relationships. Proc. R. Soc. Lond. B 282, 20150943 (2015).

- Article

- Google Scholar

35.

Kimbel, W. H. et al. Was Australopithecus anamensis ancestral to A. afarensis? A case of anagenesis in the hominin fossil record. J. Hum. Evol. 51, 134–152 (2006).

- Article

- Google Scholar

36.

Asfaw, B. The Belohdelie frontal: new evidence of early hominid cranial morphology from the Afar of Ethiopia. J. Hum. Evol. 16, 611–624 (1987).

- Article

- Google Scholar

37.

Renne, P. R. et al. Chronostratigraphy of Mio-Pliocene Sagantole Formation, Middle Awash Valley, Afar rift, Ethiopia. Bull. Geol. Soc. Am. 111, 869–885 (1999).

- CAS
- Article
- Google Scholar

38.

Kimbel, W. H., Johanson, D. C. & Rak, Y. The first skull and other new discoveries of Australopithecus afarensis at Hadar, Ethiopia. Nature 368, 449–451 (1994).

- ADS
- CAS
- Article
- Google Scholar

39.

Ward, C. V. Taxonomic affinity of the Pliocene hominin fossils from Fejej, Ethiopia. J. Hum. Evol. 73, 98–102 (2014).

- Article

- Google Scholar

40.

Fleagle, J. G., Rasmussen, D. T., Yirga, S., Bown, T. M. & Grine, F. E. New hominid fossils from Fejej, Southern Ethiopia. J. Hum. Evol. 21, 145–152 (1991).

- Article

- Google Scholar

41.

Kappelman, J. et al. Age of Australopithecus afarensis from Fejej, Ethiopia. J. Hum. Evol. 30, 139–146 (1996).

- Article

- Google Scholar

42.

Kimbel, W. H., Johanson, D. C. & Coppens, Y. Pliocene hominid cranial remains from the Hadar Formation, Ethiopia. Am. J. Phys. Anthropol. 57, 453–499 (1982).

- Article

- Google Scholar

43.

Wood, B. Koobi Fora Research Project: Hominid Cranial Remains Vol. 4 (Clarendon, 1991).

44.

Lockwood, C. A. & Tobias, P. V. A large male hominin cranium from Sterkfontein, South Africa, and the status of Australopithecus africanus. J. Hum. Evol. 36, 637–685 (1999).

- CAS
- Article
- Google Scholar

45.

Zollikofer, C. P. et al. Virtual cranial reconstruction of Sahelanthropus tchadensis. Nature 434, 755–759 (2005).

- ADS
- CAS
- Article
- Google Scholar

46.

Martin, R. & Knussman, R. Anthropologie: Handbuch der vergleichenden Biologie des Menschen Vol. 1 (Gustav Fischer, 1988).

47.

Benazzi, S., Gruppioni, G., Strait, D. S. & Hublin, J.-J. Technical note: virtual reconstruction of KNM-ER 1813 Homo habilis cranium. Am. J. Phys. Anthropol. 153, 154–160 (2014).

- Article

- Google Scholar

48.

Besl, P. J. & McKay, N. D. A method for registration of 3-D shapes. IEEE Trans. Pattern Anal. Mach. Intell. 14, 239–256 (1992).

- Article

- Google Scholar

49.

Zhang, Z. Iterative point matching for registration of free-form curves and surfaces. Int. J. Comput. Vis. 13, 119–152 (1994).

- Article

- Google Scholar

50.

Bookstein, F. L. Morphometric Tools for Landmark Data: Geometry and Biology (Cambridge Univ. Press, 1997).

Download references

Acknowledgements

We thank the Authority for Research and Conservation of Cultural Heritage (ARCCH) for permission to conduct field and laboratory work; the Afar people of Woranso-Mille and the Mille District administration for their hospitality; the project’s fieldwork crew members for their tireless support of field activities; The National Museum of Kenya, National Museum of Tanzania, Ditsong Museum and the Evolutionary Studies Institute of South Africa for access to original hominin specimens in their care; Max Planck Institute for Evolutionary Anthropology for access to comparative hominin computed tomography scan data; T. White, G. Suwa and B. Asfaw for access to the original A. ramidus material and for providing images and unpublished measurements; M. Brunet and F. Guy for images and unpublished measurements of S. tchadensis; W. H. Kimbel for informative discussions and for access to a surface model of the A.L. 444-2 cranium; D. Lieberman (the Peabody Museum (Harvard)), R. Beutel (Phyletisches Museum Jena), C. Funk (Museum für Naturkunde), M. Tocheri (National Museum of Natural History (Smithsonian)), U. Olbrich-Schwarz (the Max Planck Institute for Evolutionary Anthropology) for the use of computed tomography scans of extant apes; A. Girmaye, M. Endalamaw, Y. Assefa, T. Getachew, S. Melaku and G. Tekle of ARCCH for access to the fossil collections housed in the Paleoanthropology Laboratory in Addis Ababa; T. Stecko from the Penn State Center for Quantitative Imaging for assistance with computed tomography scanning; and N. Meisel and D. N. Kaweesa (Made By Design Lab (Pennsylvania State University)) for assistance in 3D printing. This research was supported by grants from the US National Science Foundation (BCS-1124705, BCS-1124713, BCS-1124716, BCS-1125157 and BCS-1125345) and The Cleveland Museum of Natural History. Y.H.-S. was also supported by W. J. and L. Hlavin, T. and K. Leiden, and E. Lincoln. S.B. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC-724046-SUCCESS; http://www.erc-success.eu). S.M.M. was supported by the Max Planck Institute for Evolutionary Anthropology, Department of Human Evolution.

Author information

Author notes

1. These authors contributed equally: Yohannes Haile-Selassie, Stephanie M. Melillo

Affiliations

1. Department of Physical Anthropology, Cleveland Museum of Natural History, Cleveland, OH, USA

- Yohannes Haile-Selassie

2. Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

- Stephanie M. Melillo

3. Department of Cultural Heritage, University of Bologna, Ravenna, Italy

- Antonino Vazzana

- & Stefano Benazzi

4. Department of Anthropology, Pennsylvania State University, University Park, PA, USA

- Timothy M. Ryan

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Contributions

Y.H.-S. and S.M.M. conducted fieldwork and collected data. T.M.R. scanned the specimen using computed tomography. T.M.R., S.B. and A.V. performed the three-dimensional reconstruction with contributions from Y.H.-S. and S.M.M. Y.H.-S. and S.M.M. performed the comparative analysis. S.M.M. and Y.H.-S. wrote the paper with contributions from T.M.R., S.B. and A.V.

Corresponding authors

Correspondence to Yohannes Haile-Selassie or Stephanie M. Melillo.

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Peer review information Nature thanks Craig S. Feibel, John W. Kappelman and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Fig. 1 MRD-VP-1/1 digital reconstructions.

Digitally reconstructed cranium and comparison of three alternative reconstructions. a–f, The reconstructed cranium MRD- Sts 5 is shown in anterior view (a), posterior view (b), superior view (c), left (d) and right (e) lateral views and inferior view (f). Additional images illustrate minor differences in reconstructed zygomatic arches. g, MRD-Sts 5. h, MRD-A.L. 444-2. i, MRD-WT 17000. j, MRD-Sts 5 with edges superimposed to the three different restored versions: MRD-Sts 5 (blue lines); MRD-A.L. 444-2 (green lines) and MRD-WT 17000 (red lines). Scale bars, 2 cm.

Extended Data Fig. 2 Basic steps involved in repositioning and reconstructing the MRD face.

a, Midsagittal planes computed for the original neurocranium (ivory) and facial portion (red). b, The original facial portion is rotated to align the midsagittal plane of the face with the midsagittal plane of the neurocranium, then the former is moved along the midsagittal plane to establish contact with the latter. c, The left supra-orbital bone was mirrored and aligned to the original MRD right side. d, The complete right side was mirrored and aligned to the left side. e, f, Anterior (e) and inferior (f) views of the original left maxillary dental arcade and part of the palate superimposed to the mirrored copy of the right hemiface. g, h, Frontal (g) and basal (h) view of the right dental arcade reconstructed by mirroring the left dental arcade (except for the right M^3). Mirrored portions are shown in green. Scale bar, 4 cm. See Methods for details.

Extended Data Fig. 3 MRD symmetrization using a reflected relabelling procedure and neurocranium reconstruction.

a, The template with landmarks (red), non-osteometric homologous landmarks (blue), curve semilandmarks (light blue) and surface semilandmarks (yellow) was digitized on the MRD cranium. b, The template configuration with names of landmarks and curves numbers (Supplementary Note 2). c, Basal view of the template digitized on the MRD cranium. d, The template digitized on the mirrored cranium. e, Symmetric configuration of the (semi)landmarks and warped surface. f, Basal view of the final result for MRD-sym. g, Basal view of the left zygomatic process, the right mastoid process and other parts of the basicranium reconstructed by mirroring the original counterparts (integrated parts are shown in green). h, Basal view, final result after integrating the mirrored counterparts. Scale bars, 2 cm. See Methods for details.

Extended Data Fig. 4 Integration of missing parts using Sts 5.

a, Template built on the cranium of A. africanus (Sts 5). Templates with landmarks (red), curve semilandmarks (light blue) and surface semilandmarks (yellow) were digitized on Sts 5. b, Template configuration with names of landmarks and curves numbers (labels are related to Supplementary Note 3). c, The same set of (semi)landmarks on the MRD-sym cranium. d, TPS interpolation of the Sts 5 cranium, warped to MRD-sym (blue and grey, respectively). e–h, MRD-sym with the integrated missing parts (blue) isolated from the resulting warped surfaces obtained by the deformation of Sts 5 (shown here as an example) in anterior (e), left lateral (f), inferior (g) and superior (h) views. Scale bar, 4 cm.

Extended Data Fig. 5 Integration of missing parts using A.L. 444-2 and KNM-WT 17000.

a, e, Templates with landmarks (red), curve semilandmarks (light blue) and surface semilandmarks (yellow) digitized on A.L. 444-2 (a) and KNM-WT 17000 (e) crania. b, f, The configurations of (semi)landmarks with names of landmarks and curves numbers digitized on A.L. 444-2 (b) and KNM-WT 17000 (f) crania (labels are related to Supplementary Notes 4, 5). c, g, Sets of (semi)landmarks on the MRD-sym cranium. d, h, TPS interpolation of the A.L. 444-2 (green) and KMN-WT 17000 (red) crania warped to MRD-sym (grey). Scale bar, 4 cm.

Extended Data Fig. 6 Canine orientation in MRD and KNM-KP 29283.

The method for measuring the implantation angle of the upper canine is shown in a, b. a, The internal alveolar plane was established by best-fitting a plane (outlined in blue) to three landmarks between left P^3 and P^4, between right P^3 and P^4 and between left M^1 and M^2. b, Landmarks were placed at the root tip and at the occlusal-most incursion along the distal enamel line. Upper canine implantation was measured in lateral view as the two-dimensional angle (θ) between a line connecting the canine landmarks and the axis of the alveolar plane. c, d, Upper canine implantation in the fossil specimens. c, A. anamensis paratype maxilla KNM-KP 29283. d, MRD. Of the other two A. anamensis maxillae currently known, one (KNM-KP 58579) is qualitatively similar to KNM-KP 29283 and the other (ARA-VP-14/1) is more inclined. Scale bar, 1 cm. The scale bar applies to images in c and d. e, The magnitude of difference in canine implantation angle between MRD and KNM-KP 29283 (12.5°, red dashed line) is shown in the context of expected conspecific differences. The expectation distributions were constructed using a permutation approach, for which the measurements from two individuals were randomly drawn (without replacement) from a comparative sample and the difference in orientation angle was computed. This procedure was repeated 500 times, separately for comparative species P. troglodytes and G. gorilla (Supplementary Note 6.2).

Extended Data Fig. 7 Maxillary arcade shape.

Maxillae in occlusal view of select A. afarensis and A. anamensis specimens and MRD (original, as preserved). The canine and postcanine teeth form a nearly straight line in A. anamensis and MRD. By contrast, the canine tends to be slightly medially offset relative to the postcanine row in many A. afarensis specimens. The position of the canine is indicated by the black asterisk. Scale bar, 1 cm.

Extended Data Fig. 8 Comparison of crania in lateral view.

Red lines and arrows show the inclination of the frontal and the presence of a post-toral sulcus, respectively. Blue lines show the orientation of the mid and lower face, with an broken line indicating a segmented facial profile[27]. The green arrow marks the anterior projection of the zygomatic tubercle (relative to the anterior zygomatic root). Scale bar, 2 cm.

Extended Data Fig. 9 Comparison of crania in posterior view.

The transverse contour of the cranial base is convex in African apes, whereas A. afarensis shows an angular transition between the nuchal region and the greatly expanded mastoids (red dashed lines). In this regard, A. afarensis anticipates the morphology of robust australopiths, but A. africanus is less derived. MRD shows the primitive convex contour of the base, even though the mastoids are expanded. MRD is also primitive with regard to the great length of the nuchal plane (black arrows). However, it is similar to A. afarensis in the configuration of the compound temporal–nuchal crest (white dashed lines), the bare area (blue hatched triangle), and the overall ‘bell-shaped’ posterior outline (that is, the parietal walls are slightly convergent superiorly and the greatest width occurs basally across the enlarged mastoids).

Extended Data Fig. 10 Results of phylogenetic analyses.

a, Cladogram resulting from the character matrix of ref. [27], with the addition of MRD and previously described A. anamensis specimens (combined as a single OTU, K-combined). Parsimony analysis returned a single most-parsimonious tree (l = 196, C = 0.71, R = 0.70). b, Cladogram resulting from the character matrix of ref. [33] (and references therein) with the addition of the combined MRD–A. anamensis OTU (S&G-combined). This analysis returned a single most-parsimonious tree (l = 429, C = 0.47, R = 0.66) with identical topology. The position of the combined MRD–A. anamensis OTU reinforces accepted relationships and is consistent with geochronology. c–g, Cladograms resulting from analyses in which MRD is treated as a separate OTU (that is, an OTU bearing observations primarily for cranial characters, but very few dental characters and no mandibular characters.) c, d, Equally parsimonious cladograms from the K-separate analysis (l = 196, C = 0.71, R = 0.68). e–g, Equally parsimonious cladograms from the S&G-separate analysis (l = 430, C = 0.47, R = 0.66). The ‘pre-2004 A. anamensis’ OTU in e–g bears observations primarily on dentognathic characters. Character scores for MRD are provided in Supplementary Table  1, sheets 1 and 2. Regardless of whether cranial or dentognathic characters are considered, the phylogenetic placement of MRD and the previously known A. anamensis sample remains stable relative to other hominins. h, i, Cladograms from the K-combined and S&G-combined analyses (as in a and b), with apomorphies added to the cladograms to illustrate the implied pattern of evolutionary change. The character states reconstructed at nodes A and B provide the reference for identifying A. anamensis and A. afarensis apomorphies, which are shown here as rectangles containing their abbreviated character labels. Characters in red, orange, gold and green describe similar morphology and appear in both previously published studies27,33. See Supplementary Note 9 and Supplementary Table  1.

Supplementary information

Supplementary Information

This file contains Supplementary Notes 1-10 and Supplementary Tables S6.1, S9.1, S9.2 and S9.3.

Reporting Summary

Supplementary Table

This file contains Supplementary Table 1: MRD character scores.

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- Received

09 April 2019

- Accepted

01 August 2019

- Published

28 August 2019

- Issue Date

12 September 2019

- DOI
https://doi.org/10.1038/s41586-019-1513-8

Further reading

- Elusive cranium of early hominin found

- Fred Spoor

Nature (2019)

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- Published: 28 August 2019

Age and context of mid-Pliocene hominin cranium from Woranso-Mille, Ethiopia

Beverly Z. Saylor[1],
Luis Gibert[2],
Alan Deino[3],
Mulugeta Alene[4],
Naomi E. Levin[5],
Stephanie M. Melillo[6],
Mark D. Peaple[7],
Sarah J. Feakins[7],
Benjamin Bourel[8],
Doris Barboni[8],
Alice Novello[8],
Florence Sylvestre[8],
Stanley A. Mertzman[9] &
Yohannes Haile-Selassie[10]

Naturevolume 573, pages220–224 (2019) | Download Citation

Subjects

- Ecology

- Palaeontology

Abstract

A fossil hominin cranium was discovered in mid-Pliocene deltaic strata in the Godaya Valley of the northwestern Woranso-Mille study area in Ethiopia. Here we show that analyses of chemically correlated volcanic layers and the palaeomagnetic stratigraphy, combined with Bayesian modelling of dated tuffs, yield an age range of 3.804 ± 0.013 to 3.777 ± 0.014 million years old (mean ± 1σ) for the deltaic strata and the fossils that they contain. We also document deposits of a perennial lake beneath the deltaic sequence. Mammalian fossils associated with the cranium represent taxa that were widespread at the time and data from botanical remains indicate that the vegetation in the lake and delta catchment was predominantly dry shrubland with varying proportions of grassland, wetland and riparian forest. In addition, we report high rates of sediment accumulation and depositional features that are typical of a steep topographic relief and differ from younger Woranso-Mille fossil localities, reflecting the influence of active rift processes on the palaeolandscape.

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Fig. 1: Stratigraphic setting of the fossil cranium.

Fig. 2: Lake, delta and tuffaceous strata below and above the level where the hominin cranium was found.

Data availability

Any data supporting the findings of this study that are not included in the paper and Supplementary Information are available from the corresponding author upon reasonable request.

Code availability

A data analysis version of the 40Ar/39Ar dating software is available at no cost from A.D. (adeino@bgc.org). The Bayesian age–stratigraphic analysis model is available at https://github.com/brenhinkeller.

References

1.

Deino, A. L. et al. 40Ar/39Ar dating, paleomagnetism, and tephrochemistry of Pliocene strata of the hominid-bearing Woranso-Mille area, west-central Afar Rift, Ethiopia. J. Hum. Evol. 58, 111–126 (2010).

- Article

- Google Scholar

2.

Haile-Selassie, Y. et al. An early Australopithecus afarensis postcranium from Woranso-Mille, Ethiopia. Proc. Natl Acad. Sci. USA 107, 12121–12126 (2010).

- ADS
- CAS
- Article
- Google Scholar

3.

Haile-Selassie, Y. et al. A new hominin foot from Ethiopia shows multiple Pliocene bipedal adaptations. Nature 483, 565–569 (2012).

- ADS
- CAS
- Article
- Google Scholar

4.

Haile-Selassie, Y. et al. New species from Ethiopia further expands Middle Pliocene hominin diversity. Nature 521, 483–488 (2015).

- ADS
- CAS
- Article
- Google Scholar

5.

Haile-Selassie, Y. et al. Dentognathic remains of Australopithecus afarensis from Nefuraytu (Woranso-Mille, Ethiopia): comparative description, geology, and paleoecological context. J. Hum. Evol. 100, 35–53 (2016).

- Article

- Google Scholar

6.

Haile-Selassie, Y., Saylor, B. Z., Deino, A., Alene, M. & Latimer, B. M. New hominid fossils from Woranso-Mille (Central Afar, Ethiopia) and taxonomy of early Australopithecus. Am. J. Phys. Anthropol. 141, 406–417 (2010).

- PubMed

- Google Scholar

7.

Haile-Selassie, Y. et al. A 3.8-million-year-old hominin cranium from Woranso-Mille, Ethiopia. Nature https://doi.org/10.1038/s41586-019-1513-8 (2019).

8.

Taieb, M., Johanson, D. C., Coppens, Y. & Aronson, J. L. Geological and palaeontological background of Hadar hominid site, Afar, Ethiopia. Nature 260, 289–293 (1976).

- ADS
- CAS
- Article
- Google Scholar

9.

Campisano, C. J. & Feibel, C. S. in The Geology of Early Humans in the Horn of Africa Vol. 446 (eds Quade, J. &Wynn, J.) 179–201 (Geological Society of America, 2008).

10.

Wynn, J. G. et al. in The Geology of Early Humans in the Horn of Africa Vol. 446 (eds Quade, J. & Wynn, J.) 87–118 (Geological Society of America, 2008).

11.

Renne, P. R., WoldeGabriel, G., Hart, W. K., Heiken, G. & White, T. D. Chronostratigraphy of the Miocene–Pliocene Sagantole Formation, Middle Awash Valley, Afar rift, Ethiopia. Geol. Soc. Am. Bull. 111, 869–885 (1999).

- ADS
- CAS
- Article
- Google Scholar

12.

White, T. D. et al. Asa Issie, Aramis and the origin of Australopithecus. Nature 440, 883–889 (2006).

- ADS
- CAS
- Article
- Google Scholar

13.

Quade, J. et al. in The Geology of Early Humans in the Horn of Africa Vol. 446 (eds Quade, J. & Wynn, J.) 1–31 (Geological Society of America, 2008).

14.

Asfaw, B. The Belohdelie frontal: new evidence of early hominid cranial morphology from the Afar of Ethiopia. J. Hum. Evol. 16, 611–624 (1987).

- Article

- Google Scholar

15.

White, T. D. et al. New discoveries of Australopithecus at Maka in Ethiopia. Nature 366, 261–265 (1993).

- ADS
- CAS
- Article
- Google Scholar

16.

Leakey, M. G., Feibel, C. S., McDougall, I. & Walker, A. New four-million-year-old hominid species from Kanapoi and Allia Bay, Kenya. Nature 376, 565–571 (1995).

- ADS
- CAS
- Article
- Google Scholar

17.

Leakey, M. G., Feibel, C. S., McDougall, I., Ward, C. & Walker, A. New specimens and confirmation of an early age for Australopithecus anamensis. Nature 393, 62–66 (1998).

- ADS
- CAS
- Article
- Google Scholar

18.

Deino, A. in Paleontology and Geology of Laetoli: Human Evolution in Context Vol. 1 (ed. Harrison, T.) 77–97 (Springer, 2011).

19.

Fleagle, J. G., Rasmussen, D. T., Yirga, S., Bown, T. M. & Grine, F. E. New hominid fossils from Fejej, southern Ethiopia. J. Hum. Evol. 21, 145–152 (1991).

- Article

- Google Scholar

20.

Kappelman, J. et al. Age of Australopithecus afarensis from Fejej, Ethiopia. J. Hum. Evol. 30, 139–146 (1996).

- Article

- Google Scholar

21.

Alene, M. et al. Geochemistry of Woranso-Mille Pliocene basalts from west-central Afar, Ethiopia: implications for mantle source characteristics and rift evolution. Lithos 282–283, 187–200 (2017).

- ADS
- Article
- Google Scholar

22.

Saylor, B. Z. et al. Tephrostratigraphy of the Waki-Mille area of the Woranso-Mille paleoanthropological research project, Afar, Ethiopia. J. Hum. Evol. 93, 25–45 (2016).

- Article

- Google Scholar

23.

Walter, R. C. & Aronson, J. L. Age and source of the Sidi Hakoma Tuff, Hadar Formation, Ethiopia. J. Hum. Evol. 25, 229–240 (1993).

- Article

- Google Scholar

24.

Lourens, L., Hilgen, F., Laskar, J. & Wilson, D. S. in A Geological Time Scale (eds Gradstein, F. M. et al.) 409–440 (Cambridge Univ. Press, 2004).

25.

Saylor, B. Z. et al. in The Postcranial Anatomy of Australopithecus afarensis (eds Haile-Selassie, Y. & Su, D.) 13–23 (Springer, 2016).

26.

Middleton, G. V. & Hampton, M. A. in Marine Sediment Transport and Environmental Management Ch. 11 (eds Stanley, D. J. & Swift, P.) 197–218 (Wiley, 1976).

27.

Elliot, T. in Sedimentary Environments and Facies (ed. Reading, H. G.) 113–154 (Blackwell Scientific, 1986).

28.

Prospero, J. M. et al. Environmental characterization of global sources of atmospheric soil dust identified with the NIMBUS 7 Total Ozone Mapping Spectrometer (TOMS) absorbing aerosol product. Rev. Geophys. 40, 1002 (2002).

- ADS
- Article
- Google Scholar

29.

Liddy, H. M., Feakins, S. J. & Tierney, J. E. Cooling and drying in northeast Africa across the Pliocene. Earth Planet. Sci. Lett. 449, 430–438 (2016).

- ADS
- CAS
- Article
- Google Scholar

30.

Bonnefille, R. Cenozoic vegetation, climate changes and hominid evolution in tropical Africa. Global Planet. Change 72, 390–411 (2010).

- ADS
- Article
- Google Scholar

31.

Winters, Y. D., Lowenstein, T. K. & Timofeeff, M. N. Identification of carotenoids in ancient salt from Death Valley, Saline Valley, and Searles Lake, California, using laser Raman spectroscopy. Astrobiology 13, 1065–1080 (2013).

- ADS
- CAS
- Article
- Google Scholar

32.

Stab, M. et al. Modes of rifting in magma-rich settings: tsectono-magmatic evolution of Central Afar. Tectonics 35, 2–38 (2016).

- ADS
- Article
- Google Scholar

33.

Friis, I., Demissew, S. & van Breugel, P. Atlas of the Potential Vegetation of Ethiopia (The Royal Danish Academy of Sciences and Letters, 2010).

34.

Lahitte, P., Gillot, P. Y. & Courtillot, V. Silicic central volcanoes as precursors to rift propagation: the Afar case. Earth Planet. Sci. Lett. 207, 103–116 (2003).

- ADS
- CAS
- Article
- Google Scholar

35.

Prentice, I. C., Guiot, J., Huntley, B., Jolly, D., & Cheddadi, R. Reconstructing biomes from palaeoecological data: a general method and its application to European pollen data at 0 and 6 ka. Clim. Dyn. 12, 185–194 (1996).

- Article

- Google Scholar

36.

Mertzman, S. A. K–Ar results from the southern Oregon-northern California Cascade range. Or. Geol. 62, 99–122 (2000).

- Google Scholar

37.

Niespolo, E. M., Rutte, D., Deino, A. L. & Renne, P. R. Intercalibration and age of the Alder Creek sanidine 40Ar/39Ar standard. Quat. Geochronol. 39, 205–213 (2017).

- Article

- Google Scholar

38.

Lee, J.-Y. A redetermination of the isotopic abundances of atmospheric Ar. Geochim. Cosmochim. Acta 70, 4507–4512 (2006).

- ADS
- CAS
- Article
- Google Scholar

39.

Min, K. W., Mundil, R., Renne, P. R. & Ludwig, K. R. A test for systematic errors in 40Ar/39Ar-geochronology through comparison with U/Pb analysis of a 1.1-Ga rhyolite. Geochim. Cosmochim. Acta 64, 73–98 (2000).

- ADS
- CAS
- Article
- Google Scholar

40.

Lee, H. et al. Comparison of three methods for the methylation of aliphatic and aromatic compounds. Rapid Commun. Mass Spectrom. 31, 1633–1640 (2017).

- ADS
- CAS
- Article
- Google Scholar

41.

Bonnefille, R., Vincens, A. & Buchet, A. Palynology, stratigraphy and palaeoenvironment of a Pliocene hominid site (2.9–3.3 M.Y.) at Hadar, Ethiopia. Palaeogeogr. Palaeoclimatol. Palaeoecol. 60, 249–281 (1987).

- Article

- Google Scholar

42.

Bonnefille, R., Potts, R., Chalié, F., Jolly, D. & Peyron, O. High-resolution vegetation and climate change associated with Pliocene Australopithecus afarensis. Proc. Natl Acad. Sci. USA 101, 12125–12129 (2004).

- ADS
- CAS
- Article
- Google Scholar

43.

Strömberg, C. A. E. The Origin and Spread of Grass-Dominated Ecosystems during the Tertiary of North America and How It Relates to the Evolution of Hypsodonty in Equids. PhD Thesis, Univ. California Berkeley (2003).

44.

Deino, A. L. et al. Chronostratigraphic model of a high-resolution drill core record of the past million years from the Koora Basin, south Kenya Rift: overcoming the difficulties of variable sedimentation rate and hiatuses. Quat. Sci. Rev. 215, 213–231 (2019).

- ADS
- Article
- Google Scholar

45.

Miall, A.D. The Geology of Fluvial Deposits: Sedimentary Facies, Basin Analysis and Petroleum Geology (Springer, 1996).

46.

DiMaggio, E. N. et al. Late Pliocene fossiliferous sedimentary record and the environmental context of early Homo from Afar, Ethiopia. Science 347, 1355–1359 (2015).

- ADS
- CAS
- Article
- Google Scholar

47.

Kirschvink, J. L. The least-squares line and plane and the analysis of palaeomagnetic data. Geophys. J. Int. 62, 699–718 (1980).

- ADS
- Article
- Google Scholar

48.

Sournia, A. Diatomées planctoniques du Canal de Mozambique et de l’Île de la Réunion (ORSTOM, 1968).

49.

Foged, N. Some Littoral Diatoms from the Coast of Tanzania (Biblioteca Phycologia, 1975).

50.

Ryan, W. B. F. et al. Global multi-resolution topography synthesis. Geochem. Geophys. Geosyst. 10, Q03014 (2009).

- ADS
- Article
- Google Scholar

Download references

Acknowledgements

We thank the Authority for Research and Conservation of Cultural Heritage for permission to conduct field and laboratory work, the Afar people of Woranso-Millle for their hospitality, and the project’s fieldwork crew members for their tireless support of field activities; M. Atkins and I. Van Orman for assistance with the preparation of tephrochemical samples and J. Fournelle for assistance with their analysis. This research was supported by grants from the Spanish Government CGL2016-79458-P, Catalan Government 2017-SGR 824, the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 659596 and the US National Science Foundation (1124705, 1124716, 1125157, 1125345, 1322017).

Author information

Affiliations

1. Department of Earth, Environmental and Planetary Sciences, Case Western Reserve University, Cleveland, OH, USA

- Beverly Z. Saylor

2. Departament de Mineralogia, Petrologia i Geologia Aplicada Facultat de Ciències de la Terra, Universitat de Barcelona, Barcelona, Spain

- Luis Gibert

3. Berkeley Geochronology Center, Berkeley, CA, USA

- Alan Deino

4. School of Earth Sciences, Addis Ababa University, Addis Ababa, Ethiopia

- Mulugeta Alene

5. Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA

- Naomi E. Levin

6. Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

- Stephanie M. Melillo

7. Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA

- Mark D. Peaple

- & Sarah J. Feakins

8. Aix-Marseille University, CNRS, IRD, INRA, Collège de France, CEREGE, Aix-en-Provence, France

- Benjamin Bourel
- , Doris Barboni
- , Alice Novello
- & Florence Sylvestre

9. Department of Earth and Environment, Franklin and Marshall College, Lancaster, PA, USA

- Stanley A. Mertzman

10. Cleveland Museum of Natural History, Cleveland, OH, USA

- Yohannes Haile-Selassie

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Contributions

B.Z.S., L.G., M.A., A.D., N.E.L., S.M.M., M.D.P. and Y.H.-S. conducted field research. M.A. collected basalt samples and S.A.M. analysed the samples for major and trace element concentrations. B.Z.S. collected and analysed tuff samples for major and minor element abundances in glass. A.D. collected and analysed tuff samples for 40Ar/39Ar dating. L.G. collected sediment samples and analysed their palaeomagnetic polarity. N.E.L. and M.D.P. collected sediment samples for analysis of botanical remains. S.M.M. contributed to the collection and analysis of mammalian fossils. M.D.P. and S.J.F. analysed and interpreted leaf wax isotopes. B.B. and D.B. separated and identified pollen. A.N. and F.S. separated and identified phytolith and diatom components. Y.H.-S. collected and analysed the mammalian fossils and directed the field station. B.Z.S. took the lead in writing the paper with contributions from all co-authors.

Corresponding author

Correspondence to Yohannes Haile-Selassie.

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Peer review information Nature thanks Craig S. Feibel, John W. Kappelman and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Fig. 1 Field photographs.

a, Location of the horizon of the MRD-VP-1 fossil relative to features on the Miro Dora plateau (capped by Am-Ado basalts) and the higher Guda plateau (background). b, Coarse sand matrix on MRD-VP-1/1. Additional matrix types, which are not shown, included very hard fine sand and soft silty clay. c, Lehaysule Gera hill (section S2); image shows the position of geochemically identified tuffs (Mille tuff sequence and associated basaltic tuffs, and Araskimiro tuff) and the dated T9 tuff (WM12/LHG-6) above dark deltaic siltstone and lacustrine claystone. A lower dated tuff (WM18/LHG-1) near the bottom of the claystone exposure is not discernable. d, The hill of section S5; image shows the position of the deltaic sequence relative to the geochemically identified Mille tuff and associated basaltic tuff sequence and T9 tuff. e, Large-scale cross-bedded sandstone at MRD-VP-1. Arrows show foreset dip directions, indicating the flow toward the southeast (right arrow) and toward the south-southwest (left arrow). f, Upward-coarsening delta lobe(s) along the Am-Ado Plateau (S3) with Mille tuff sequence and Am-Ado basalt above and between.

Extended Data Fig. 2 Tephrochemical data and age–depth models.

a, Bivariate plots of oxide abundances in volcanic glass normalized for differences in water content (Supplementary Table 2). Symbol colours and shapes are as in Fig. 1 with closed, smaller symbols indicating newly reported analyses of individual glass shards from samples from the study area, differentiated by symbol border colour and size. Open symbols indicate previously published[22] sample means with 1σ variation for named tuffs near the Waki-Mille confluence, specifically: Kilaytoli tuff (WM-KSD-3, n = 19, 11 high iron and 8 low iron), Mesgid Dora tuff (MSD-08-5, n = 12), Araskimiro tuff (MSD-08-3R, n = 12 and WM-MD5 P, n = 10, duplicate samples from same location), bimodal tuff (WMC-08-3, n = 16, n = 10, duplicate analyses of same sample), Mille tuff sequence (ARI-08-3, n = 16, ARI-08-4, n = 11, two chemically similar, vertically adjacent tuffs in the sequence). The Mille tuff sequence, the rhyolitic component of the basaltic and rhyolitic ‘bimodal tuff’ and their correlates are distinguished from other pumice tuffs in the area by their low CaO abundances. The Araskimiro tuff and its correlates are distinguished from chemically similar pumice tuffs in the area, including the Mesgid Dora tuff, by position above the Mille tuff/basaltic tuff sequence and below the Waki tuff, which is present below the Mesgid Dora tuff in a drainage approximately 300 m to the east of S2 (Fig. 1d). b, Bayesian age–stratigraphic model[44] for n = 3 tuffs at S2, including the lowermost dated tuff (WM18/LHG-1), the T9 tuff (WM12/LHG-6) and the bottom of the Mille tuff sequence (around 2 m below LLG-12-10, which is chemically similar to the Mille/basaltic tuff sequence), and a similar model correlating these horizons to S6.

Extended Data Fig. 3 Detailed stratigraphic sections with positions of samples that were investigated and analysed for leaf wax, pollen and phytolith content.

All sections are in centimetres except for MRD18-03. Names of sections are listed at the top of each column and equivalent section names reported in Fig. 2 are listed in parentheses. The number associated with each sample identifier is listed next to the dot that indicates the stratigraphic position of samples. If sample numbers are equivalent stratigraphically to other samples, this is noted in parentheses. Tuff numbering is included on the left of each column. Dashed lines provide ties between stratigraphic and lithologic equivalent horizons for non-tuffaceous units. The tuff numbering scheme also indicates tie points. Facies classification abbreviations are from a previously published study[45]. F, S and G indicate grain size (clay or silt size, sand size and gravel size, respectively) and the descriptors m, h, l, p and t describe the primary bedding as massive, horizontal, laminated, planar and trough, respectively. Listed latitudes and longitudes are in reference to the WGS-84 datum and indicate the position of the base of the section unless otherwise noted. The stratigraphic positions for samples WM18-MRD-210, -413, -414, -416 (section S4) and WM18-LHG-258 (section S2) can be found in Fig. 2.

Extended Data Fig. 4 Incremental heating release spectra from single-grain 40Ar/39Ar analyses.

The x axis of each subplot is the cumulative percentage release of 39Ar during the course of the experiment. ‘Int. Age’ is the ‘integrated’ or total-gas age, obtained by isotopically summing the individual steps weighted by the inverse variance, with the error calculated as the modified standard error at 1σ (standard error of the weighted mean multiplied by the square root of the MSWD when MSWD > 1). The apparent age plateau—defined as a sequence of at least three or more consecutive steps representing at least half of the total 39Ar release, and for which analytical error alone is sufficient to explain the observed age dispersion at a probability of 95%—is calculated as the mean age weighted by the inverse variance, with the error shown as the 1σ modified standard error. Neither the integrated age nor plateau age incorporated the error in J at this stage in the data reduction; this systematic error is included in the final weighted-mean age calculated from the isochron results. Results for sample WM12/LHG-6 indicated n = 10 plateaus identified out of a total of n = 13 single-crystal incremental heating experiments; for sample WM18/LHG-1, n = 8 plateaus were found in n = 8 heating experiments.

Extended Data Fig. 5 Inverse-isochron correlation plots of plateau steps from incremental heating experiments.

Plots show isotope correlation diagrams for 36Ar/40Ar and 39Ar/40Ar ratios Each grain is plotted separately. The age is obtained from the x-axis intercept and is shown with a 1σ modified standard error. ‘40Ar/39Ar Int.’ refers to the ‘trapped’ non-radiogenic 40Ar/36Ar ratio derived from the y-axis intercept of the isochron. ‘P’ refers to the probability that the observed scatter can be explained by analytical errors alone; a value below 0.05 indicates that analytical errors are insufficient to explain the magnitude of the dispersion (that is, geological scatter is present). ‘n’ indicates the included number of analyses.

Extended Data Fig. 6 Age-probability density plot of ages derived from isochron analyses.

a, Mean Ca/K atomic ratio of individual grains estimated from 37Ar/39Ar measurements. b, Rank-order plot of single-crystal isochron results with 1σ analytical uncertainty. c, The vertical scale is the relative likelihood of a given age occurring in the sample. The weighted-mean ages of the population are shown, the 1σ error includes the error in J, the neutron-fluence parameter. The MSWD and number of included analyses are included after the mean age. Values in purple were omitted from analyses based on distance from the median age, with the cut-off level of 2.0 normalized median absolute deviations[46]. For sample WM12/LHG-6, eight out of ten isochron results are included in the weighted mean; for sample WM18/LHG-1, six out of eight results are included.

Extended Data Fig. 7 Palaeomagnetic results.

a, Magnetostratigraphy for sections S6, S4 and S2 with results expressed as the angle to expected normal direction (Δ). The reverse–normal–reverse polarity sequence in S6 is correlated with the GPTS[24] on the basis of dated and geochemically identified tuffs in S2. White circles are mean directions of specimens (black), open circles are ambiguous specimen directions. vf, very fine sand; m, medium sand; C, coarse sand. b, Stereoplots and orthogonal demagnetization diagrams for a reverse (MRD-19a) and a normal (MRD-22b) sample. dec, declination; inc, inclination; int, intensity; NRM, natural remanent magnetization. The plots show the stepwise demagnetization process and the characteristic remanent magnetization directions (red lines) calculated using a principal component analysis[47]. In the stereonet plots (left), open circles show negative inclinations and solid dots show positive inclinations. In the orthogonal plots (right), solid dots indicate declination values and empty circles inclination values. Intensity units are in 10 A m−1. mad, maximum angle deviation. c, Stereographic projection, referred to magnetic North of characteristic remanent magnetization directions for specimens collected at S6, S4 and S2.Circles indicate individual specimens. The plot shows the associated normal and reversed mean directions (squares) of the specimens, as determined by Fisher statistics, and the position of the present field (triangle). Only those samples showing non-ambiguous directions are plotted. In total, 48 specimens show reverse polarity and 10 samples show normal polarity.

Extended Data Fig. 8 Pollen diagrams for sample WM18-MRD-210 and diatom diagram for WM18-LHG-248.

a, Relative abundances of pollen taxa (percentage) in WM18-MRD-210 calculated using the total number of pollen grains and fern spores. The asterisk indicate ‘-type’. Numbers in brackets refer to the number of pollen grains. b, Relative abundance of arboreal pollen (AP; trees and shrubs), non-arboreal pollen (NAP; herbs and forbs) and non-classified habitus (NC) in WM18-MRD-210. Numbers in brackets refer to the number of pollen grains. aqua., aquatic. c, Distribution of diatoms in WN18-LGH 248 according their ecological affinity: coastal–marine (yellow) versus brackish lacustrine (blue) environments. Among the species with coastal–marine affinities, Coscinodiscus lineatus and Coscinodiscus excentricus are typically observed in the Indian Ocean and Mozambique Channel48,49. Numbers in brackets refer to the number of diatom samples.

Extended Data Fig. 9 Examples of fossil pollen grains (sample WM18-MRD-210) and biogenic silica remains (sample WM18-LHG-248).

a–d, Pollen grains. a, Aerva-type javanica. b, Euclea. c, Acacia. d, Tribulus. e–g, Phytolith bodies. e, A spherical/globular psilate body, probably an indicator of dicot tree/shrub taxa. f, g, Two unidentified phytolith remains. h, A sponge spicule. i–l, Diatom frustules. i, Cyclotella meneghiniana. j, Actinoptychus splendens. k, Denticula valida. l, Cyclotella stylorum. Scale bars, 10 μm.

Extended Data Fig. 10 Shaded relief map of west central Afar.

Volcanic and sedimentary strata of the Sullu Adu Range (including the Guda Plateau) are sub-horizontal, 4 Myr old and younger, and stratigraphically above Oligocene and Miocene basalts and rhyolites that are tilted to the east-northeast, indicating periods of extension[32] before approximately 4 Myr ago. Nearby areas with well-studied exposures13,32 of these Oligocene and Miocene formations are labelled in bold. Areas with lake deposits10,13 in the lower Hadar or upper Sagantole formations are labelled in italics. The base map is from http://www.geomapapp.org using the global multi-resolution topography synthesis[50].

Supplementary information

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About this article

- Received

10 April 2019

- Accepted

26 July 2019

- Published

28 August 2019

- Issue Date

12 September 2019

- DOI
https://doi.org/10.1038/s41586-019-1514-7

Further reading

- A 3.8-million-year-old hominin cranium from Woranso-Mille, Ethiopia

- Yohannes Haile-Selassie
- , Stephanie M. Melillo
- , Antonino Vazzana
- , Stefano Benazzi
- & Timothy M. Ryan

Nature (2019)

- Elusive cranium of early hominin found

- Fred Spoor

Nature (2019)

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- Article

- Published: 21 August 2019

Structure and mechanogating of the mammalian tactile channel PIEZO2

Li Wang[1] na1,
Heng Zhou[2] na1,
Mingmin Zhang1,3 na1,
Wenhao Liu1,3 na1,
Tuan Deng[1],
Qiancheng Zhao[1],
Yiran Li[1],
Jianlin Lei[2],
Xueming Li[2] &
Bailong Xiao1,3

Naturevolume 573, pages225–229 (2019) | Download Citation

Subjects

- Cryoelectron microscopy

- Ion channels in the nervous system

Abstract

PIEZO2 is a mechanosensitive cation channel that has a key role in sensing touch, tactile pain, breathing and blood pressure. Here we describe the cryo-electron microscopy structure of mouse PIEZO2, which is a three-bladed, propeller-like trimer that comprises 114 transmembrane helices (38 per protomer). Transmembrane helices 1–36 (TM1–36) are folded into nine tandem units of four transmembrane helices each to form the unusual non-planar blades. The three blades are collectively curved into a nano-dome of 28-nm diameter and 10-nm depth, with an extracellular cap-like structure embedded in the centre and a 9-nm-long intracellular beam connecting to the central pore. TM38 and the C-terminal domain are surrounded by the anchor domain and TM37, and enclose the central pore with both transmembrane and cytoplasmic constriction sites. Structural comparison between PIEZO2 and its homologue PIEZO1 reveals that the transmembrane constriction site might act as a transmembrane gate that is controlled by the cap domain. Together, our studies provide insights into the structure and mechanogating mechanism of Piezo channels.

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Fig. 1: The homotrimeric structure of PIEZO2.

Fig. 2: The 38-transmembrane-helix topological organization.

Fig. 3: The ion-conducting pore.

Fig. 4: Coordinated displacement of the cap domain and the transmembrane gate.

Data availability

The structural coordinates of mouse PIEZO2 have been deposited in the PDB under the accession 6KG7. The cryo-EM map was deposited into the Electron Microscopy Data Bank (EMDB) under the accession 9975.

References

1.

Coste, B. et al. Piezo1 and Piezo2 are essential components of distinct mechanically activated cation channels. Science 330, 55–60 (2010).

- ADS
- CAS
- Article
- Google Scholar

2.

Coste, B. et al. Piezo proteins are pore-forming subunits of mechanically activated channels. Nature 483, 176–181 (2012).

- ADS
- CAS
- Article
- Google Scholar

3.

Woo, S. H. et al. Piezo2 is required for Merkel-cell mechanotransduction. Nature 509, 622–626 (2014).

- ADS
- CAS
- Article
- Google Scholar

4.

Ranade, S. S. et al. Piezo2 is the major transducer of mechanical forces for touch sensation in mice. Nature 516, 121–125 (2014).

- ADS
- CAS
- Article
- Google Scholar

5.

Chesler, A. T. et al. The role of PIEZO2 in human mechanosensation. N. Engl. J. Med. 375, 1355–1364 (2016).

- CAS
- Article
- Google Scholar

6.

Murthy, S. E., Dubin, A. E. & Patapoutian, A. Piezos thrive under pressure: mechanically activated ion channels in health and disease. Nat. Rev. Mol. Cell Biol. 18, 771–783 (2017).

- CAS
- Article
- Google Scholar

7.

Szczot, M. et al. PIEZO2 mediates injury-induced tactile pain in mice and humans. Sci. Transl. Med. 10, eaat9892 (2018).

- Article

- Google Scholar

8.

Murthy, S. E. et al. The mechanosensitive ion channel Piezo2 mediates sensitivity to mechanical pain in mice. Sci. Transl. Med. 10, eaat9897 (2018).

- Article

- Google Scholar

9.

Woo, S. H. et al. Piezo2 is the principal mechanotransduction channel for proprioception. Nat. Neurosci. 18, 1756–1762 (2015).

- CAS
- Article
- Google Scholar

10.

Zhang, M., Wang, Y., Geng, J., Zhou, S. & Xiao, B. Mechanically activated Piezo channels mediate touch and suppress acute mechanical pain response in mice. Cell Rep. 26, 1419–1431 (2019).

- CAS
- Article
- Google Scholar

11.

Nonomura, K. et al. Piezo2 senses airway stretch and mediates lung inflation-induced apnoea. Nature 541, 176–181 (2017).

- ADS
- CAS
- Article
- Google Scholar

12.

Zeng, W. Z. et al. PIEZOs mediate neuronal sensing of blood pressure and the baroreceptor reflex. Science 362, 464–467 (2018).

- ADS
- CAS
- Article
- Google Scholar

13.

Coste, B. et al. Gain-of-function mutations in the mechanically activated ion channel PIEZO2 cause a subtype of distal arthrogryposis. Proc. Natl Acad. Sci. USA 110, 4667–4672 (2013).

- ADS
- CAS
- Article
- Google Scholar

14.

McMillin, M. J. et al. Mutations in PIEZO2 cause Gordon syndrome, Marden-Walker syndrome, and distal arthrogryposis type 5. Am. J. Hum. Genet. 94, 734–744 (2014).

- CAS
- Article
- Google Scholar

15.

Ge, J. et al. Architecture of the mammalian mechanosensitive Piezo1 channel. Nature 527, 64–69 (2015).

- ADS
- CAS
- Article
- Google Scholar

16.

Zhao, Q. et al. Structure and mechanogating mechanism of the Piezo1 channel. Nature 554, 487–492 (2018).

- ADS
- CAS
- Article
- Google Scholar

17.

Zhao, Q., Zhou, H., Li, X. & Xiao, B. The mechanosensitive Piezo1 channel: a three-bladed propeller-like structure and a lever-like mechanogating mechanism. FEBS J. 286, 2461–2470 (2019).

- CAS
- Article
- Google Scholar

18.

Guo, Y. R. & MacKinnon, R. Structure-based membrane dome mechanism for Piezo mechanosensitivity. eLife 6, e33660 (2017).

- Article

- Google Scholar

19.

Saotome, K. et al. Structure of the mechanically activated ion channel Piezo1. Nature 554, 481–486 (2018).

- ADS
- CAS
- Article
- Google Scholar

20.

von Heijne, G. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J. Mol. Biol. 225, 487–494 (1992).

- Article

- Google Scholar

21.

Bavi, N. et al. The role of MscL amphipathic N terminus indicates a blueprint for bilayer-mediated gating of mechanosensitive channels. Nat. Commun. 7, 11984 (2016).

- ADS
- CAS
- Article
- Google Scholar

22.

Zhao, Q. et al. Ion permeation and mechanotransduction mechanisms of mechanosensitive Piezo channels. Neuron 89, 1248–1263 (2016).

- CAS
- Article
- Google Scholar

23.

Wu, J. et al. Inactivation of mechanically activated Piezo1 ion channels is determined by the C-terminal extracellular domain and the inner pore helix. Cell Rep. 21, 2357–2366 (2017).

- CAS
- Article
- Google Scholar

24.

Wang, Y. et al. A lever-like transduction pathway for long-distance chemical- and mechano-gating of the mechanosensitive Piezo1 channel. Nat. Commun. 9, 1300 (2018).

- ADS
- Article
- Google Scholar

25.

Haselwandter, C. A. & MacKinnon, R. Piezo’s membrane footprint and its contribution to mechanosensitivity. eLife 7, e41968 (2018).

- Article

- Google Scholar

26.

Perozo, E., Cortes, D. M., Sompornpisut, P., Kloda, A. & Martinac, B. Open channel structure of MscL and the gating mechanism of mechanosensitive channels. Nature 418, 942–948 (2002).

- ADS
- CAS
- Article
- Google Scholar

27.

Chiang, C. S., Anishkin, A. & Sukharev, S. Gating of the large mechanosensitive channel in situ: estimation of the spatial scale of the transition from channel population responses. Biophys. J. 86, 2846–2861 (2004).

- ADS
- CAS
- Article
- Google Scholar

28.

Chang, G., Spencer, R. H., Lee, A. T., Barclay, M. T. & Rees, D. C. Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel. Science 282, 2220–2226 (1998).

- ADS
- CAS
- Article
- Google Scholar

29.

Lewis, A. H. & Grandl, J. Mechanical sensitivity of Piezo1 ion channels can be tuned by cellular membrane tension. eLife 4, e12088 (2015).

- Article

- Google Scholar

30.

Cox, C. D. et al. Removal of the mechanoprotective influence of the cytoskeleton reveals PIEZO1 is gated by bilayer tension. Nat. Commun. 7, 10366 (2016).

- ADS
- CAS
- Article
- Google Scholar

31.

Coste, B. et al. Piezo1 ion channel pore properties are dictated by C-terminal region. Nat. Commun. 6, 7223 (2015).

- ADS
- Article
- Google Scholar

32.

Lukacs, V. et al. Impaired PIEZO1 function in patients with a novel autosomal recessive congenital lymphatic dysplasia. Nat. Commun. 6, 8329 (2015).

- ADS
- CAS
- Article
- Google Scholar

33.

Lü, W., Du, J., Goehring, A. & Gouaux, E. Cryo-EM structures of the triheteromeric NMDA receptor and its allosteric modulation. Science 355, eaal3729 (2017).

- Article

- Google Scholar

34.

Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).

- CAS
- Article
- Google Scholar

35.

Mindell, J. A. & Grigorieff, N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334–347 (2003).

- Article

- Google Scholar

36.

Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).

- Article

- Google Scholar

37.

Zhang, K. Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016).

- ADS
- CAS
- Article
- Google Scholar

38.

Pettersen, E. F. et al. UCSF Chimera–a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

- CAS
- Article
- Google Scholar

39.

Scheres, S. H. & Chen, S. Prevention of overfitting in cryo-EM structure determination. Nat. Methods 9, 853–854 (2012).

- CAS
- Article
- Google Scholar

40.

Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003).

- CAS
- Article
- Google Scholar

41.

Kucukelbir, A., Sigworth, F. J. & Tagare, H. D. Quantifying the local resolution of cryo-EM density maps. Nat. Methods 11, 63–65 (2014).

- CAS
- Article
- Google Scholar

42.

Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).

- CAS
- Article
- Google Scholar

43.

Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).

- CAS
- Article
- Google Scholar

44.

Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010).

- CAS
- Article
- Google Scholar

45.

Zhang, T., Chi, S., Jiang, F., Zhao, Q. & Xiao, B. A protein interaction mechanism for suppressing the mechanosensitive Piezo channels. Nat. Commun. 8, 1797 (2017).

- ADS
- Article
- Google Scholar

46.

Moroni, M., Servin-Vences, M. R., Fleischer, R., Sánchez-Carranza, O. & Lewin, G. R. Voltage gating of mechanosensitive PIEZO channels. Nat. Commun. 9, 1096 (2018).

- ADS
- Article
- Google Scholar

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Acknowledgements

We thank A. Patapoutian for sharing the mouse Piezo2 cDNA and the Tsinghua University Branch of the China National Center for Protein Sciences (Beijing) for providing cryo-EM facility support. This work was supported by grant numbers 2016YFA0500402, 31825014, 31630090 and 2015CB910102 to B.X. and 31570730, 2016YFA0501102 and 2016YFA0501902 to X.L., from either the National Key R&D Program of China or the National Natural Science Foundation of China.

Author information

Author notes

1. These authors contributed equally: Li Wang, Heng Zhou, Mingmin Zhang, Wenhao Liu

Affiliations

1. State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China

- Li Wang
- , Mingmin Zhang
- , Wenhao Liu
- , Tuan Deng
- , Qiancheng Zhao
- , Yiran Li
- & Bailong Xiao

2. MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China

- Heng Zhou
- , Jianlin Lei
- & Xueming Li

3. Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing, China

- Mingmin Zhang
- , Wenhao Liu
- & Bailong Xiao

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Contributions

L.W. carried out protein purification, electron microscopy sample preparation and data collection; H.Z. performed electron microscopy sample preparation, data collection, image processing and model building; M.Z. did electrophysiology; W.L. did electrophysiology and plasmid preparation; T.D. did mutagenesis; Q.Z. cloned the expression vector and helped with initial testing of expression; Y.L. helped with experiments; L.L. assisted in collection of electron microscopy data; X.L. supervised collection and analysis of electron microscopy data; B.X. conceived and directed the study, analysed the structure, made the figures and wrote the manuscript with help from all other authors.

Corresponding authors

Correspondence to Xueming Li or Bailong Xiao.

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Peer review information Nature thanks Boris Martinac, Edwin McCleskey and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Fig. 1 Optimization of the purification of recombinant PIEZO2 proteins.

a, Schematic of the PIEZO2-pp-GST-IRES-GFP expression construct driven by the cytomegalovirus (CMV) promoter. b, Representative traces of inward currents at −80 mV evoked by a series of mechanically probing steps in 1-μm increments in whole-cell configuration in PIEZO1-KO-HEK cells transfected with the indicated constructs. The number of cells recorded is shown in c. P2, PIEZO2.c, d, Scatter plots of the maximal poking-induced currents (Imax) (c) and the inactivation τ (d). Data are mean ± s.e.m. and the number of recorded cells is labelled. Two-tailed unpaired Student’s t-test; P = 0.2347 (c) and P = 0.5826 (d). e, Western blotting of cell lysates derived from HEK293T cells transfected with the indicated constructs. The anti-GST antibody detected the PIEZO1-GST and PIEZO2-GST proteins, and the anti-β-actin antibody detected β-actin for a loading control. m indicates a mouse-derived protein. f, Representative traces of gel filtration of purified PIEZO1 or PIEZO2 proteins using the detergent C_12E_10. UV, ultraviolet. g, A representative trace of gel filtration of the purified full-length PIEZO2 with the GST affinity tag cleaved, in the detergent GDN. h, Coomassie blue staining showing the purified PIEZO2 proteins separated on an 8% SDS–PAGE gel. i, Representative negative-staining electron microscopy images of PIEZO2 purified in either C_12E_10 or GDN. The experiments in e–i were independently repeated at least three times with similar results.

Extended Data Fig. 2 Determination of the cryo-EM structure of PIEZO2.

a, Representative cryo-electron micrograph of PIEZO2 solubilized in the detergent GDN. b, Power spectrum of the micrograph in a, with the 3.0 Å frequency indicated. c, Gold-standard Fourier shell correlation (FSC) curves of the indicated density maps. Reported resolutions were based on the FSC = 0.143 criterium. d, Representative 2D class averages of PIEZO2 particles, showing the three-bladed, propeller-like top view and a bowl-like side view. e–h, Top, local-resolution maps of the indicated densities. Bottom, Euler angle distribution of particles that were used in the final 3D reconstruction; the height of the cylinder is proportional to the number of particles for that view.

Extended Data Fig. 3 Flowchart of electron-microscopy data processing.

Details of data processing are described in the ‘Imaging processing’ section of the Methods.

Extended Data Fig. 4 Local electron-microscopy density of the indicated domains of PIEZO2.

The helices are shown in cartoon representation with side chains as sticks. The cryo-EM density is shown as grey mesh. Clearly resolved residues with bulky side chains—for example, phenylalanine, tryptophan, tyrosine, proline and histidine—are labelled. The three pore-lining inner helices are shown in both side and top views to highlight the side-chain density of F2754, which forms a transmembrane gate, and E2757, which controls ion-permeation properties. The N-acetylglucosamine (NAG) groups that were modelled onto residues N769, N1030, N1037 and N2642 are labelled.

Extended Data Fig. 5 The structure of PIEZO2 and the THU organization.

a, A protomer structure of PIEZO2 is presented in a format in which its transmembrane helices roughly adopt a planar configuration. The extracellular loops and intracellular membrane-parallel helices are shown in surface electrostatic potential. Notably, except THU1, which has a short N terminus of seven residues, each of the other eight THUs is preceded by a membrane-parallel helix, which connects perpendicularly to the first transmembrane helices. These intracellular membrane-parallel helices (including TM5pre-α, TM9pre-α, TM13pre-α, TM17pre-α, TM21pre-α, TM25pre-α, TM29pre-α, claspα1–α2 and anchorα3) collectively form an intracellular helical layer with the hydrophobic side facing the membrane side. The enlarged view of the EL7–8, EL11–12, EL15–16, EL19–20 and EL23–24 illustrates the flattened arrangement that is formed by these extracellular loops leaning against each other, except that EL19–20 sits on top of EL23–24. Such an organization might help to stabilize the blade and facilitate conformational propagation from the distal blade to the central region. b, THU5 is used as a typical example to show the organization pattern of the left-handed bundle of four transmembrane helices and the preceding membrane-parallel helix. c, Overlay of THU2 and THU4–THU7 (colour-coded as in a), showing the similar folding pattern. d, Intertwined interaction of the distal beam domain, THU7 and the clasp domain. The residues involved in forming polar interactions are shown in yellow. THU7 is shown in surface representation. The distal part of the beam is apparently kinked at the position of S1466 and buried within a space enclosed by the intracellular side of THU7 and the second and third α-helices of the clasp (claspα2–α3). The clasp domain is composed of two long membrane-parallel helices (claspα1–α2) to form an L-shaped helical structure, and a short helix (claspα3) that is positioned underneath the kink position of the beam. The beam and clasp domains are intertwined together with hydrogen-bond interactions between D1457 and R1702, S1466 and R1717, and R1467 and E1701 for stabilization. The 280 unresolved residues (1728–1947) that link the claspα3 and TM29pre-α1–α2 helices (indicated by the red dashed line) might provide additional interactions and regulation at the distal end of the beam. e, Bottom view of the trimeric central region comprising the beam, the CTD and the latch domain. Two subunits are presented in surface electrostatic potential, and the other subunit is shown in ribbon representation. The proximal end of the beam directly contacts the hairpin-like CTD positioned on top, and connects to the perpendicularly crossed latch domain through 42 unresolved residues (1513–1556). f, Ribbon diagram showing positively charged (blue) and negatively charged (red) residues that contribute to the negative surface potential of the latch domain and positive surface potential of the beam and CTD (as shown in e). The C-terminal section of the latch domain is rich in negatively charged and polar residues (1572-ETDSEE-1577) and is sandwiched in between the beam and the CTD with clusters of positively charged residues (R1500, R1504, K1507 and K1512 in the beam and K2815, R2818 and K2820 in the C-terminal tail). Y1568 in the latch domain points towards the putative intracellular exit of the central pore and forms hydrogen bonds with E2811, which contributes to the cytosolic constriction neck. g, Ribbon diagram showing the intertwined polar interactions of the indicated structural domains. The long membrane-parallel anchorα3 sits right on top of the CTD-hairpin plane and connects to the outer helix through a lysine-rich anchor–outer-helix linker (2456-KRYPQPRGQKKKK-2468), which forms interactions with the polar-residue-rich anchorα2–α3 turn (2426-TDTTT-2430), the glutamate-rich region of the CTDα1–α2-turn (2789-ETGELELEED-2798) and the N-terminal section of the latch domain. Several pairs of hydrogen bonds, including D2427–K2465, T2428–E2796 and T2429–E2797, might help to facilitate the intertwined interactions. The corresponding anchor–outer-helix linker in PIEZO1 is critical for mediating regulation by the sarco/endoplasmic reticulum Ca2+-ATPase (SERCA), which binds to both PIEZO1 and PIEZO2.

Extended Data Fig. 6 The central ion-conducting pore and lateral portals of PIEZO2.

a, Ribbon diagram showing the pore module (comprising the outer helix, cap, inner helix and CTD) together with the anchor, latch and beam domains. The central solvent-accessible pathway is marked with a dotted mesh (purple, green and red) generated by the program HOLE (pore radius: red, <1 Å; green, <2 Å; purple, >2 Å). The extracellular vestibule (EV), membrane vestibule and intracellular vestibule are labelled. b, Pore radius along the central axis of the ion-conduction pathway of PIEZO2. The residues that form constriction sites are labelled. c, Representative traces of poking-evoked whole-cell currents in PIEZO1-KO-HEK cells transfected with the indicated constructs. Traces were recorded in an intracellular solution containing 149 mM caesium methanesulfonate and 1 mM CsCl, and an extracellular solution containing 50 mM calcium gluconate and 0.5 mM CaCl_2. Currents were elicited from −30 to +30 mV with a change of 10 mV at every step. The red trace represents the current elicited at 0 mV. The number of recorded cells is shown in e. d, Linear regression fit of average I–V relationships of whole-cell currents of the indicated constructs recorded under the conditions described in c. The liquid junction potential of 7.1 mV was subtracted. The number of recorded cells is shown in e. e, Scatter plots of PCa/PCs of the indicated constructs. Data are mean ± s.e.m. and the number of cells tested is labelled. One-way ANOVA: P (PIEZO1 versus PIEZO2) = 0.8323 (not significant; NS); ****P (PIEZO2 versus PIEZO2(E2757A)) < 0.0001. f, Scatter plots of PCa/PCs of the indicated constructs. Data are mean ± s.e.m. and the number of cells tested is labelled. Two-tailed unpaired Student’s t-test: P (PIEZO1 versus PIEZO1(E2537A)) = 0.4353 (NS); P (PIEZO2 versus PIEZO2(E2811A)) = 0.5566 (NS). g, Representative stretch-evoked single-channel current traces recorded at the indicated holding voltages in PIEZO1-KO-HEK cells transfected with constructs expressing either PIEZO2 (seven cells recorded with currents) or PIEZO2(E2757A) (seven cells recorded with currents). h, Histogram analysis of the single-channel conductance from current traces recorded at −140 mV. i, Linear plots of the I–V relationships of the indicated constructs. j, Scatter plots of the slope of the single-channel conductance of the indicated constructs. Data are mean ± s.e.m. and the number of cells tested is labelled. Two-tailed unpaired Student’s t-test: ****P (PIEZO2 versus PIEZO2-E2757A) < 0.0001. k, Surface electrostatic potential representation of the inner helix–CTD-enclosed central pore of PIEZO2 and PIEZO1, showing the hydrophobic transmembrane pore, intracellular fenestration site and the lateral negative surface potential that is contributed by the indicated negatively charged residues (which determine the properties of the pore). Notably, PIEZO1 has apparent membrane-facing cavities (indicated by the green dashed line) between two inner helices. l, m, Surface electrostatic potential representations of the inner helix–CTD-enclosed central pore together with the surrounding anchor, beam and latch domains, showing the intracellular fenestration sites and lateral portals in either a side-view (l) or top-view (m) section at the position indicated by the arrow in panel l. The fenestrations and lateral portals are outlined with yellow dashed lines.

Extended Data Fig. 7 Structural comparison between PIEZO1 and PIEZO2.

a, b, Side (a) or top (b) overlay view of PIEZO2 (salmon), PIEZO1 (PDB: 6B3R) (cyan), PIEZO1 (PDB: 5Z10) (green) and PIEZO1 (PDB: 6BPZ) (purple). c, An enlarged view of the cap and blade regions zoomed in at the capα1–α2 position. Red arrows indicate the shifted positions of PIEZO1 relative to PIEZO2. The clockwise twist and upward displacement of the cap domain is more robust in PIEZO1 (PDB: 6B3R) and PIEZO1 (PDB: 6BZ) than in PIEZO1 (PDB: 5Z10), whereas the lateral displacement of the distal blade of TM13–TM24 is relatively stronger in PIEZO1 (PDB: 5Z10) than in PIEZO1 (PDB: 6B3R). TM13–TM24 of PIEZO1 (PDB: 6PBZ) were not modelled. d, Pore radius along the inner helix–CTD central axis of the ion-permeation pore of the indicated PIEZO2 and PIEZO1 structures. The residues that form constriction sites are labelled. Notably, the transmembrane gates of all three PIEZO1 structures determined in different detergents including GDN (PDB: 6B3R), digitonin (PDB: 6BPZ) and C_12E_10 (PDB: 5Z10) have dilated transmembrane gates relative to that of PIEZO2 determined in GDN. Furthermore, dilation of the transmembrane gate of PIEZO1 is closely correlated with the displacement of the cap among the three PIEZO1 structures (a–d). For example, compared to PIEZO1 (PDB: 5Z10), PIEZO1 (PDB: 6B3R) and PIEZO1 (PDB: 6BPZ) show relatively stronger displacement of the cap domain (for example, the capα1–α2 region) (c) and concurrent larger expansion of the upper transmembrane gate of L2469 (d). Given that PIEZO2 is much less responsive to stretch stimulation, we speculate that surface tension generated during cryo-EM sample preparation might lead to opening of the transmembrane pore of PIEZO1, but not PIEZO2. e–g, Western blotting of the biotinylated or whole-cell lysate samples derived from HEK293T cells transfected with the indicated constructs using the indicated antibodies. The PIEZO2 antibody in f was raised against the peptide corresponding to residues 2662–2674 in the cap domain of mouse PIEZO2, and could not recognize the PIEZO2(Δcap) protein (data not shown). Thus, the anti-Flag antibody was used to detect the PIEZO2-mRuby2-Flag and PIEZO2(Δcap)-mRuby2-Flag proteins in g. The anti-β-actin antibody detected β-actin for a loading control. The experiment was independently repeated twice or three times with similar results.

Extended Data Fig. 8 Structural comparison between PIEZO1 (PDB: 6B3R) and PIEZO2.

a, c, d, g, Top views of the superimposed PIEZO2 (salmon) and PIEZO1 (PDB: 6B3R) (cyan) structures zoomed in at either capα1–α2 (a), the PIEZO2(L2743) residue (c), the PIEZO2 (F2754) residue (d) or the cytosolic constriction site of PIEZO2(M2767/P2810/E2811) (g). The boxed regions at the centre of a, c and d are presented in enlarged views in Fig. 4a–c, respectively. Arrows indicate the displacement direction of PIEZO1 relative to PIEZO2; red arrows show the displacement of the cap or the blade domains, whereas purple arrows show the displacement of the side chain of the indicated residues. For example, TM16 of PIEZO1 has a lateral displacement of about 12 Å relative to that of PIEZO2 (a). b, e, Side views of the superimposed PIEZO2 (salmon) and PIEZO1 (PDB: 6B3R) (cyan) trimers (b) or monomers (e). Red arrows indicate the displacement direction of PIEZO1 relative to PIEZO2. The blue and red dashed lines in e indicate the flatness of the curved transmembrane region of the blade. f, The upward displacement associated with the beam, CTD, anchor and outer helix might contribute to the upward displacement of the cytosolic constriction neck, the transmembrane gate and the inner helix.

Extended Data Fig. 9 Mapping disease-causing mutations in human PIEZO1 and PIEZO2 onto the mouse PIEZO2 structure.

The dots in different colours represent the disease-causing residues labelled in the protein sequence shown in Supplementary Fig. 2.

Extended Data Table 1 Cryo-EM data collection, refinement and validation statistics

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Supplementary information

Supplementary Information

This file contains Supplementary Figs. 1, 2 and Supplementary Table 1.

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About this article

- Received

26 March 2019

- Accepted

22 July 2019

- Published

21 August 2019

- Issue Date

12 September 2019

- DOI
https://doi.org/10.1038/s41586-019-1505-8

Further reading

- Piezo1 mechanosensitive channels: what are they and why are they important

- Pietro Ridone
- , Massimo Vassalli
- & Boris Martinac

Biophysical Reviews (2019)

- A mechanism for touch

- Edwin W. McCleskey

Nature (2019)

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A mechanism for touch

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- Article

- Published: 21 August 2019

Force-induced conformational changes in PIEZO1

- Yi-Chih Lin1,2 na1,
- Yusong R. Guo[3] na1,
- Atsushi Miyagi1,2,
- Jesper Levring[3],
- Roderick MacKinnon[3] &
- Simon Scheuring1,2

Naturevolume 573, pages230–234 (2019) | Download Citation

Subjects

- Atomic force microscopy
- Ion transport
- Molecular conformation

Abstract

PIEZO1 is a mechanosensitive channel that converts applied force into electrical signals. Partial molecular structures show that PIEZO1 is a bowl-shaped trimer with extended arms. Here we use cryo-electron microscopy to show that PIEZO1 adopts different degrees of curvature in lipid vesicles of different sizes. We also use high-speed atomic force microscopy to analyse the deformability of PIEZO1 under force in membranes on a mica surface, and show that PIEZO1 can be flattened reversibly into the membrane plane. By approximating the absolute force applied, we estimate a range of values for the mechanical spring constant of PIEZO1. Both methods of microscopy demonstrate that PIEZO1 can deform its shape towards a planar structure. This deformation could explain how lateral membrane tension can be converted into a conformation-dependent change in free energy to gate the PIEZO1 channel in response to mechanical perturbations.

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Fig. 1: Proposed activation mechanisms of PIEZO1.

Fig. 2: Reconstitutions of PIEZO1 in vesicles exhibit various orientations in cryo-EM micrographs.

Fig. 3: PIEZO1 channels become flatter in large vesicles.

Fig. 4: HS-AFM experiments of PIEZO1.

Fig. 5: Mechanical response of PIEZO1 to applied force.

Data availability

Any data relating to the findings presented in this Article are available from the corresponding authors upon reasonable request.

References

1.

Coste, B. et al. Piezo1 and Piezo2 are essential components of distinct mechanically activated cation channels. Science 330, 55–60 (2010).

- ADS
- CAS
- Article
- Google Scholar

2.

Coste, B. et al. Piezo proteins are pore-forming subunits of mechanically activated channels. Nature 483, 176–181 (2012).

- ADS
- CAS
- Article
- Google Scholar

3.

Wu, J., Lewis, A. H. & Grandl, J. Touch, tension, and transduction – the function and regulation of Piezo ion channels. Trends Biochem. Sci. 42, 57–71 (2017).

- Article

- Google Scholar

4.

Li, J. et al. Piezo1 integration of vascular architecture with physiological force. Nature 515, 279–282 (2014).

- ADS
- CAS
- Article
- Google Scholar

5.

Ranade, S. S. et al. Piezo1, a mechanically activated ion channel, is required for vascular development in mice. Proc. Natl Acad. Sci. USA 111, 10347–10352 (2014).

- ADS
- CAS
- Article
- Google Scholar

6.

Retailleau, K. et al. Piezo1 in smooth muscle cells is involved in hypertension-dependent arterial remodeling. Cell Reports 13, 1161–1171 (2015).

- CAS
- Article
- Google Scholar

7.

Cahalan, S. M. et al. Piezo1 links mechanical forces to red blood cell volume. eLife 4, (2015).

8.

Wang, S. et al. Endothelial cation channel PIEZO1 controls blood pressure by mediating flow-induced ATP release. J. Clin. Invest. 126, 4527–4536 (2016).

- Article

- Google Scholar

9.

Rode, B. et al. Piezo1 channels sense whole body physical activity to reset cardiovascular homeostasis and enhance performance. Nat. Commun. 8, 350 (2017).

- ADS
- Article
- Google Scholar

10.

Ranade, S. S. et al. Piezo2 is the major transducer of mechanical forces for touch sensation in mice. Nature 516, 121–125 (2014).

- ADS
- CAS
- Article
- Google Scholar

11.

Woo, S. H. et al. Piezo2 is the principal mechanotransduction channel for proprioception. Nat. Neurosci. 18, 1756–1762 (2015).

- CAS
- Article
- Google Scholar

12.

Demolombe, S., Duprat, F., Honoré, E. & Patel, A. Slower Piezo1 inactivation in dehydrated hereditary stomatocytosis (xerocytosis). Biophys. J. 105, 833–834 (2013).

- ADS
- CAS
- Article
- Google Scholar

13.

Andolfo, I. et al. Novel Gardos channel mutations linked to dehydrated hereditary stomatocytosis (xerocytosis). Am. J. Hematol. 90, 921–926 (2015).

- CAS
- Article
- Google Scholar

14.

Fotiou, E. et al. Novel mutations in PIEZO1 cause an autosomal recessive generalized lymphatic dysplasia with non-immune hydrops fetalis. Nat. Commun. 6, 8085 (2015).

- ADS
- Article
- Google Scholar

15.

Coste, B. et al. Gain-of-function mutations in the mechanically activated ion channel PIEZO2 cause a subtype of distal arthrogryposis. Proc. Natl Acad. Sci. USA 110, 4667–4672 (2013).

- ADS
- CAS
- Article
- Google Scholar

16.

Guo, Y. R. & MacKinnon, R. Structure-based membrane dome mechanism for Piezo mechanosensitivity. eLife 6, e33660 (2017).

- Article

- Google Scholar

17.

Saotome, K. et al. Structure of the mechanically activated ion channel Piezo1. Nature 554, 481–486 (2018).

- ADS
- CAS
- Article
- Google Scholar

18.

Zhao, Q. et al. Structure and mechanogating mechanism of the Piezo1 channel. Nature 554, 487–492 (2018).

- ADS
- CAS
- Article
- Google Scholar

19.

Wu, J., Goyal, R. & Grandl, J. Localized force application reveals mechanically sensitive domains of Piezo1. Nat. Commun. 7, 12939 (2016).

- ADS
- CAS
- Article
- Google Scholar

20.

Wang, Y. et al. A lever-like transduction pathway for long-distance chemical- and mechano-gating of the mechanosensitive Piezo1 channel. Nat. Commun. 9, 1300 (2018).

- ADS
- Article
- Google Scholar

21.

Lewis, A. H. & Grandl, J. Mechanical sensitivity of Piezo1 ion channels can be tuned by cellular membrane tension. eLife 4, e12088 (2015

- Article

- Google Scholar

22.

Cox, C. D. et al. Removal of the mechanoprotective influence of the cytoskeleton reveals PIEZO1 is gated by bilayer tension. Nat. Commun. 7, 10366 (2016).

- ADS
- CAS
- Article
- Google Scholar

23.

Árnadóttir, J. & Chalfie, M. Eukaryotic mechanosensitive channels. Annu. Rev. Biophys. 39, 111–137 (2010).

- Article

- Google Scholar

24.

Brohawn, S. G., Su, Z. & MacKinnon, R. Mechanosensitivity is mediated directly by the lipid membrane in TRAAK and TREK1 K+ channels. Proc. Natl Acad. Sci. USA 111, 3614–3619 (2014).

- ADS
- CAS
- Article
- Google Scholar

25.

Brohawn, S. G., Campbell, E. B. & MacKinnon, R. Physical mechanism for gating and mechanosensitivity of the human TRAAK K+ channel. Nature 516, 126–130 (2014).

- ADS
- CAS
- Article
- Google Scholar

26.

Moe, P. & Blount, P. Assessment of potential stimuli for mechano-dependent gating of MscL: effects of pressure, tension, and lipid headgroups. Biochemistry 44, 12239–12244 (2005).

- CAS
- Article
- Google Scholar

27.

Zhang, W. et al. Ankyrin repeats convey force to gate the NOMPC mechanotransduction channel. Cell 162, 1391–1403 (2015).

- CAS
- Article
- Google Scholar

28.

Jin, P. et al. Electron cryo-microscopy structure of the mechanotransduction channel NOMPC. Nature 547, 118–122 (2017).

- ADS
- CAS
- Article
- Google Scholar

29.

Gaub, B. M. & Müller, D. J. Mechanical stimulation of Piezo1 receptors depends on extracellular matrix proteins and directionality of force. Nano Lett. 17, 2064–2072 (2017).

- ADS
- CAS
- Article
- Google Scholar

30.

Hamill, O. P. & McBride, D. W., Jr. Induced membrane hypo/hyper-mechanosensitivity: a limitation of patch-clamp recording. Annu. Rev. Physiol. 59, 621–631 (1997).

- CAS
- Article
- Google Scholar

31.

Suchyna, T. M., Markin, V. S. & Sachs, F. Biophysics and structure of the patch and the gigaseal. Biophys. J. 97, 738–747 (2009).

- ADS
- CAS
- Article
- Google Scholar

32.

Moroni, M., Servin-Vences, M. R., Fleischer, R., Sánchez-Carranza, O. & Lewin, G. R. Voltage gating of mechanosensitive PIEZO channels. Nat. Commun. 9, 1096 (2018).

- ADS
- Article
- Google Scholar

33.

Lacroix, J. J., Botello-Smith, W. M. & Luo, Y. Probing the gating mechanism of the mechanosensitive channel Piezo1 with the small molecule Yoda1. Nat. Commun. 9, 2029 (2018).

- ADS
- Article
- Google Scholar

34.

Ando, T., Uchihashi, T. & Scheuring, S. Filming biomolecular processes by high-speed atomic force microscopy. Chem. Rev. 114, 3120–3188 (2014).

- CAS
- Article
- Google Scholar

35.

Miyagi, A. & Scheuring, S. Automated force controller for amplitude modulation atomic force microscopy. Rev. Sci. Instrum. 87, 053705 (2016).

- Article

- Google Scholar

36.

Helfrich, W. Elastic properties of lipid bilayers: theory and possible experiments. Z. Naturforsch. C 28, 693–703 (1973).

- CAS
- Article
- Google Scholar

37.

Legleiter, J., Park, M., Cusick, B. & Kowalewski, T. Scanning probe acceleration microscopy (SPAM) in fluids: mapping mechanical properties of surfaces at the nanoscale. Proc. Natl Acad. Sci. USA 103, 4813–4818 (2006).

- ADS
- CAS
- Article
- Google Scholar

38.

Kiracofe, D. et al. VEDA: Virtual Environment for Dynamic AFM, https://nanohub.org/resources/veda (2012).

39.

Guzman, H. V., Garcia, P. D. & Garcia, R. Dynamic force microscopy simulator (dForce): A tool for planning and understanding tapping and bimodal AFM experiments. Beilstein J. Nanotechnol. 6, 369–379 (2015).

- CAS
- Article
- Google Scholar

40.

García, R. & San Paulo, A. Attractive and repulsive tip-sample interaction regimes in tapping-mode atomic force microscopy. Phys. Rev. B 60, 4961–4967 (1999).

- ADS
- Article
- Google Scholar

41.

Weisstein, E. W. Spherical Cap, from MathWorld–a Wolfram web resource. http://mathworld.wolfram.com/SphericalCap.html.

42.

Haselwandter, C. A. & MacKinnon, R. Piezo’s membrane footprint and its contribution to mechanosensitivity. eLife 7, e41968 (2018).

- Article

- Google Scholar

43.

Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005).

- Article

- Google Scholar

44.

Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).

- CAS
- Article
- Google Scholar

45.

Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).

- Article

- Google Scholar

46.

Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).

- CAS
- Article
- Google Scholar

47.

Kimanius, D., Forsberg, B. O., Scheres, S. H. & Lindahl, E. Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. eLife 5, e18722 (2016).

- Article

- Google Scholar

Download references

Acknowledgements

We thank M. Ebrahim and J. Sotiris at the Evelyn Gruss Lipper Cryo-EM Resource Center of Rockefeller University for assistance with cryo-EM data collection. Y.R.G. is a Howard Hughes Medical Institute Fellow of the Damon Runyon Cancer Research Foundation (DRG 2317-18). R.M. is an investigator in the Howard Hughes Medical Institute.

Author information

Author notes

1. These authors contributed equally: Yi-Chih Lin, Yusong R. Guo

Affiliations

1. Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA

- Yi-Chih Lin
- , Atsushi Miyagi
- & Simon Scheuring

2. Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA

- Yi-Chih Lin
- , Atsushi Miyagi
- & Simon Scheuring

3. Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, TheRockefeller University, New York, NY, USA

- Yusong R. Guo
- , Jesper Levring
- & Roderick MacKinnon

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Contributions

Y.-C.L., Y.R.G., R.M. and S.S. designed the study; Y.R.G. and J.L. purified and reconstituted the protein. Y.R.G. performed cryo-EM measurements. Y.-C.L. and A.M. performed HS-AFM experiments. Y.-C.L., Y.R.G., R.M. and S.S. analysed the data. Y.-C.L., Y.R.G., R.M. and S.S. wrote the paper.

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Correspondence to Roderick MacKinnon or Simon Scheuring.

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Peer review information Nature thanks Ardem Patapoutian, Victor Shahin and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Fig. 1 Architecture and topology of the mechanosensitive channel PIEZO1.

a, Top, bottom and side views of PIEZO1 (PDB 6B3R) in cartoon representation (top) and embedded in the micelle density map (EMD-7042), contoured at 6σ. CTD, C-terminal domain. b, Top, topology of PIEZO1 shown rainbow-coloured (with N terminus in blue and C terminus in red), except for the structurally unsolved TM1–TM12 regions (shown in grey). Helices are represented as cylinders, loops as solid lines and unresolved regions as dotted lines. Bottom, top view of transmembrane helices, labelled as in the topology. Red squares outline four-transmembrane units that constitute the arm. TM21–TM24 are at the ‘elbow’ of the arm. The hypothetical position of the unresolved units TM1–TM4, TM5–TM8 and TM9–TM12 are indicated (dashed outline).

Extended Data Fig. 2 Image processing procedure to determine the Rc of side-view PIEZO1 channels, and the intrinsic Rc of the vesicles in which they are embedded.

a, The input 2D-averaged image of one side of the vesicle (here the PIEZO1 occupied side). b, Edge detection output using the Canny method. c, Edge detection output overlaid with the selection polygon. d, Edges in the selected polygon region annotated with numbers in different colours for easier identification. e, f, Measured (blue circle) and fitted (red dotted line) circles of the edges corresponding to the outer (e) and inner (f) boundaries of the vesicle membrane. Centre coordinates, the radius and its 95% confidence interval are shown. The unit of all values is in pixels. g, Fitted circles (red dashed lines) overlaid onto the edge detection output. Radii with the confidence interval of outer and inner boundaries are shown in units of nm. h, Fitted circles (red dashed lines) overlaid onto the input 2D-averaged image.

Extended Data Fig. 3 Estimation of Fts in HS-AFM at various Aratio, on the basis of experimental tip motion analysis and numerical simulation.

a, b, Average tip motions observed at different Aratio in buffer solution during HS-AFM imaging on mica (a) and a supported lipid bilayer (1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC):DOPS, 4:1) (b). c, d, Forces caused by the elastic response of the cantilever (top), the hydrodynamic damping with the medium (middle) and the total force that governs the tip motion (bottom). e, f, Sum of the drive force and tip-sample interaction force. g, h, Reconstructed Fts trajectories during a single oscillation cycle, based on the point-mass model (equation (7), equation (8), Methods). i, Comparison between peak forces obtained from reconstructed Fts trajectories on mica (blue dashed line) and membrane (red dashed line), and peak forces simulated using different surface stiffness using VEDA[38] (dashed lines and grey shadowed area). The VEDA simulation is performed by using the amplitude-modulation-approach curve tool with the following settings: discrete approach steps within a defined z-range, acoustic excitation, Afree = 2 nm, Hertz contact model (Etip = 130 GPa, νtip = 0.3, νsample = 0.5, ν is the Poisson’s ratio) with a tip radius of 1 nm, and other HS-AFM experimental parameters (for example, k, Q and ω_0). j, Comparison between average forces obtained from reconstructed Fts trajectories on mica (blue dashed line) and membrane (red dashed line) and values calculated through equation (1) (thick black dashed line). k, Comparison between peak forces obtained from experimental Fts trajectories on membrane at different Afree values. Using second-order polynomial fitting, the peak force reconstructed in the condition of Afree = 1.5 nm can be well-described by y = −688.7x^2 + 633.4x + 55 (black dashed line) with R^2 = 0.99. This fitting allows us to estimate the upper bound of force (peak force) applied to PIEZO1 channels at any given Aratio. Tip trajectories are representative of ≥5 independent experiments using ≥3 different HS-AFM cantilevers.

Extended Data Fig. 4 Classification of PIEZO1 channels using cross-correlation analysis on characteristic dimensions measured upon force application.

a, b, Cross-correlation density maps of smallest halo radius (Rmin) at low applied force versus largest halo radius (Rmax) at highest applied force (a) and of smallest halo radius (Rmin) versus maximum central height (Hmax) at lowest applied force (b). Along the diagonal direction of the cross-correlation density maps, the molecules separate into two peaks. This suggests the existence of two subtypes of PIEZO1 with different sizes in HS-AFM force-sweep movies. Therefore, we assigned the molecules in the peaks as type-1 (about 70%, white dashed circle) and type-2 (about 30%, yellow dashed circle) PIEZO1, respectively. The same molecules populate in the same subtype according to all analysed criteria. The total number of analysed PIEZO1 particles is 143, from 11 HS-AFM movies acquired on ≥5 different samples, days and HS-AFM tips.

Extended Data Fig. 5 Mechanical response of type-2 PIEZO1 to applied force.

a, HS-AFM image at \(\left\langle {F}_{{\rm{HS-AFM}}}\right\rangle \) of about 52 pN, of type-2 PIEZO1 viewed from the extracellular face. b, Height section profile (top) and radial height profile (bottom) of the topography displayed in a. c, Dimensional analysis of single type-2 PIEZO1 particle in a force-sweep HS-AFM experiment. Similar to the type-1 PIEZO1 (as reported in the main text), each single molecule (left) is 360-fold-symmetry averaged (centre) and a kymograph (right) across the centre profile (dashed line in 360-fold image) is calculated. The kymograph highlights the halo expansion (dashed line) as a function of force. Bottom, force as function of frame acquisition or time during the force-sweep HS-AFM movie acquisition. The yellow coloured area corresponds to the image acquisition of the particle shown (left). d, Normalized probability density maps of halo radius (R) as a function of force. Type-2 PIEZO1 also shows structural reversibility. The total number of analysed type-2 PIEZO1 particles is 43, from 11 HS-AFM movies acquired on ≥5 different samples, days and HS-AFM tips.

Extended Data Fig. 6 PIEZO1 has an exceptional low 2D density of transmembrane helices.

Transmembrane-helix 2D-density analysis for channels and transporters of known 3D structure. The transmembrane-helix density is estimated by the total number of transmembrane helices divided by the occupied membrane area of each known structure. A total of 201 channels and transporters structures have been analysed. A general trend seems to be that the channels are somewhat less densely packed than transporters, which is possibly a signature of the existence of a protein-free pore region. The PIEZO1 structure is an outlier: it is of exceptional size and has an exceptionally low density of transmembrane helices, (less than 0.2 of a helix per square nanometre. This unique feature might be a signature, and prerequisite for PIEZO1 mechanosensing.

Supplementary information

Supplementary Information

This file contains a Supplementary Discussion.

Reporting Summary

Video 1

HS-AFM force-sweep video of the extracellular face of Piezo1 channels undergoing reversible conformational changes under force application. The top right molecule is the molecule shown in the middle panel in Fig. 4c. The bottom graph displays the calculated <FHS-AFM> during video acquisition. The HS-AFM video was recorded at 187 nm x 187 nm image size (280 x 280 pixels) and 1.0 s per frame.

Video 2

HS-AFM force-sweep video of Piezo1 channels exposed to a reverse force cycle. The bottom graph displays the calculated <FHS-AFM> (red), Aset/Afree ratio (blue) and the Z-piezo displacement (green) as a function of frame acquisition or time during the force-sweep HS-AFM video acquisition shown in Fig. 5a. The HS-AFM video was recorded at 350 nm x 350 nm image size (350 x 350 pixels) and 1.0 s per frame.

Video 3

Example of lateral expansion analysis of a single Piezo1 particle shown in Fig. 5b. The single molecule (left) is 360-fold symmetry averaged (middle) and a kymograph (right) across the center of the Piezo1 calculated (dashed line in 360-fold image). The kymograph highlights the outer radius (halo) expansion as a function of force application.

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About this article

- Received

14 November 2018

- Accepted

25 July 2019

- Published

21 August 2019

- Issue Date

12 September 2019

- DOI
https://doi.org/10.1038/s41586-019-1499-2

Further reading

- A mechanism for touch

- Edwin W. McCleskey

Nature (2019)

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- Letter

- Published: 11 September 2019

Inflation of 430-parsec bipolar radio bubbles in the Galactic Centre by an energetic event

I. Heywood1,2,3,
F. Camilo[3],
W. D. Cotton3,4,
F. Yusef-Zadeh[5],
T. D. Abbott[3],
R. M. Adam[3],
M. A. Aldera[6],
E. F. Bauermeister[3],
R. S. Booth[7],
A. G. Botha[3],
D. H. Botha[8],
L. R. S. Brederode3,17 nAff17,
Z. B. Brits[3],
S. J. Buchner[3],
J. P. Burger[3],
J. M. Chalmers[3],
T. Cheetham[3],
D. de Villiers[9],
M. A. Dikgale-Mahlakoana[3],
L. J. du Toit[8],
S. W. P. Esterhuyse[3],
B. L. Fanaroff[3],
A. R. Foley[3],
D. J. Fourie[3],
R. R. G. Gamatham[3],
S. Goedhart[3],
S. Gounden[3],
M. J. Hlakola[3],
C. J. Hoek[3],
A. Hokwana[3],
D. M. Horn[3],
J. M. G. Horrell[10],
B. Hugo2,3,
A. R. Isaacson[3],
J. L. Jonas2,3,
J. D. B. L. Jordaan3,8,
A. F. Joubert[3],
G. I. G. Józsa2,3,
R. P. M. Julie[3],
F. B. Kapp[3],
J. S. Kenyon[2],
P. P. A. Kotzé[3],
H. Kriel[3],
T. W. Kusel[3],
R. Lehmensiek8,11,
D. Liebenberg[3],
A. Loots[12],
R. T. Lord[3],
B. M. Lunsky[3],
P. S. Macfarlane[3],
L. G. Magnus[3],
C. M. Magozore[3],
O. Mahgoub[3],
J. P. L. Main[3],
J. A. Malan[3],
R. D. Malgas[3],
J. R. Manley[3],
M. D. J. Maree[3],
B. Merry[3],
R. Millenaar[3],
N. Mnyandu[3],
I. P. T. Moeng[3],
T. E. Monama[3],
M. C. Mphego[3],
W. S. New[3],
B. Ngcebetsha2,3,
N. Oozeer3,13,
A. J. Otto[3],
S. S. Passmoor[3],
A. A. Patel[3],
A. Peens-Hough[3],
S. J. Perkins[3],
S. M. Ratcliffe[3],
R. Renil[3],
A. Rust[3],
S. Salie[3],
L. C. Schwardt[3],
M. Serylak3,14,
R. Siebrits[3],
S. K. Sirothia2,3,
O. M. Smirnov2,3,
L. Sofeya[3],
P. S. Swart[3],
C. Tasse2,15,
D. T. Taylor[3],
I. P. Theron2,8,
K. Thorat2,3,
A. J. Tiplady[3],
S. Tshongweni[3],
T. J. van Balla[3],
A. van der Byl[3],
C. van der Merwe[3],
C. L. van Dyk[16],
R. Van Rooyen[3],
V. Van Tonder[3],
R. Van Wyk[3],
B. H. Wallace[3],
M. G. Welz[3] &
L. P. Williams[3]

Naturevolume 573, pages235–237 (2019) | Download Citation

Subjects

- Astronomy and astrophysics

Abstract

The Galactic Centre contains a supermassive black hole with a mass of four million Suns[1] within an environment that differs markedly from that of the Galactic disk. Although the black hole is essentially quiescent in the broader context of active galactic nuclei, X-ray observations have provided evidence for energetic outbursts from its surroundings[2]. Also, although the levels of star formation in the Galactic Centre have been approximately constant over the past few hundred million years, there is evidence of increased short-duration bursts[3], strongly influenced by the interaction of the black hole with the enhanced gas density present within the ring-like central molecular zone[4] at Galactic longitude |l| < 0.7 degrees and latitude |b| < 0.2 degrees. The inner 200-parsec region is characterized by large amounts of warm molecular gas[5], a high cosmic-ray ionization rate[6], unusual gas chemistry, enhanced synchrotron emission7,8, and a multitude of radio-emitting magnetized filaments[9], the origin of which has not been established. Here we report radio imaging that reveals a bipolar bubble structure, with an overall span of 1 degree by 3 degrees (140 parsecs × 430 parsecs), extending above and below the Galactic plane and apparently associated with the Galactic Centre. The structure is edge-brightened and bounded, with symmetry implying creation by an energetic event in the Galactic Centre. We estimate the age of the bubbles to be a few million years, with a total energy of 7 × 10^52 ergs. We postulate that the progenitor event was a major contributor to the increased cosmic-ray density in the Galactic Centre, and is in turn the principal source of the relativistic particles required to power the synchrotron emission of the radio filaments within and in the vicinity of the bubble cavities.

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Fig. 1: Radio emission from the Galactic Centre bubbles.

Fig. 2: Major features of the Galactic Centre radio bubbles.

Data availability

The data that support the findings of this study are available from a corresponding author upon reasonable request.

References

1.

Gillessen, S. et al. An update on monitoring stellar orbits in the Galactic Center. Astrophys. J. 837, 30 (2017).

- ADS
- Article
- Google Scholar

2.

Ponti, G., Terrier, R., Goldwurm, A., Belanger, G. & Trap, G. Discovery of a superluminal Fe K echo at the Galactic Center: the glorious past of Sgr A* preserved by molecular clouds. Astrophys. J. 714, 732–747 (2010).

- ADS
- CAS
- Article
- Google Scholar

3.

Genzel, R., Eisenhauer, F. & Gillessen, S. The Galactic Center massive black hole and nuclear star cluster. Rev. Mod. Phys. 82, 3121–3195 (2010).

- ADS
- CAS
- Article
- Google Scholar

4.

Sormani, M. C. et al. A theoretical explanation for the Central Molecular Zone asymmetry. Mon. Not. R. Astron. Soc. 475, 2383–2402 (2018).

- ADS
- CAS
- Article
- Google Scholar

5.

Huettemeister, S., Wilson, T. L., Bania, T. M. & Martin-Pintado, J. Kinetic temperatures in Galactic Center molecular clouds. Astron. Astrophys. 280, 255–267 (1993).

- ADS
- CAS
- Google Scholar

6.

Oka, T., Geballe, T. R., Goto, M., Usuda, T. & McCall, B. J. Hot and diffuse clouds near the Galactic Center probed by metastable H+
3. Astrophys. J. 632, 882–893 (2005).

- ADS
- CAS
- Article
- Google Scholar

7.

Sofue, Y. & Handa, T. A radio lobe over the Galactic Centre. Nature 310, 568–569 (1984).

- ADS
- Article
- Google Scholar

8.

Law, C. J. A multiwavelength view of a mass outflow from the Galactic Centre. Astrophys. J. 708, 474–484 (2010).

- ADS
- CAS
- Article
- Google Scholar

9.

Yusef-Zadeh, F., Morris, M. & Chance, D. Large, highly organized radio structures near the Galactic Centre. Nature 310, 557–561 (1984).

- ADS
- Article
- Google Scholar

10.

Camilo, F. et al. Revival of the magnetar PSR J1622–4950: observations with MeerKAT, Parkes, XMM-Newton, Swift, Chandra, and NuSTAR. Astrophys. J. 856, 180 (2018).

- ADS
- Article
- Google Scholar

11.

Law, C. J., Backer, D., Yusef-Zadeh, F. & Maddalena, R. Radio recombination lines toward the Galactic Center Lobe. Astrophys. J. 695, 1070–1081 (2009).

- ADS
- CAS
- Article
- Google Scholar

12.

Wardle, M. & Yusef-Zadeh, F. On the origin of the central 1″ hole in the stellar disk of Sgr A* and the Fermi gamma-ray bubbles. Astrophys. J. 787, L14 (2014).

- ADS
- Article
- Google Scholar

13.

Su, M., Slatyer, T. R. & Finkbeiner, D. P. Giant gamma-ray bubbles from Fermi-LAT: Active Galactic Nucleus activity or bipolar Galactic wind? Astrophys. J. 724, 1044–1082 (2010).

- ADS
- Article
- Google Scholar

14.

Carretti, E. et al. Giant magnetized outflows from the centre of the Milky Way. Nature 493, 66–69 (2013).

- ADS
- Article
- Google Scholar

15.

Yang, H.-Y. K., Ruszkowski, M. & Zweibel, E. The Fermi bubbles: gamma-ray, microwave, and polarization signatures of leptonic AGN jets. Mon. Not. R. Astron. Soc. 436, 2734–2746 (2013).

- ADS
- Article
- Google Scholar

16.

Crocker, R. M. & Aharonian, F. Fermi bubbles: giant, multibillion-year-old reservoirs of Galactic Center cosmic rays. Phys. Rev. Lett. 106, 101102 (2011).

- ADS
- Article
- Google Scholar

17.

Nakashima, S. et al. Discovery of the recombining plasma in the south of the Galactic Center: a relic of the past Galactic Center activity? Astrophys. J. 773, 20 (2013).

- ADS
- Article
- Google Scholar

18.

Ponti, G. et al. An X-ray chimney extending hundreds of parsecs above and below the Galactic Centre. Nature 567, 347–350 (2019).

- ADS
- CAS
- Article
- Google Scholar

19.

Le Petit, F. et al. Physical conditions in the central molecular zone inferred by H_3
+. Astron. Astrophys. 585, A105 (2016).

- Article

- Google Scholar

20.

Everett, J. E., Schiller, Q. G. & Zweibel, E. G. Synchrotron constraints on a hybrid cosmic-ray and thermally driven Galactic wind. Astrophys. J. 711, 13–24 (2010).

- ADS
- Article
- Google Scholar

21.

Blasi, P. Cosmic ray acceleration in supernova remnants. In Cosmic Rays for Particle and Astroparticle Physics (eds Giani, S., Leroy, C. & Rancoita, P. G.) 493–506 (World Scientific, 2011).

22.

Yusef-Zadeh, F., Hewitt, J. W. & Cotton, W. A. 20 centimeter survey of the Galactic Center region. I. Detection of numerous linear filaments. Astrophys. J. Suppl. Ser. 155, 421–550 (2004).

- ADS
- Article
- Google Scholar

23.

LaRosa, T. N., Nord, M. E., Lazio, T. J. W. & Kassim, N. E. New nonthermal filaments at the Galactic Center: are they tracing a globally ordered magnetic field? Astrophys. J. 607, 302–308 (2004).

- ADS
- Article
- Google Scholar

24.

Gray, A. D., Nicholls, J., Ekers, R. D. & Cram, L. E. Multifrequency radio studies of G359.1–00.2. Astrophys. J. 448, 164–178 (1995).

- ADS
- Article
- Google Scholar

25.

Morris, M. What are the radio filaments near the Galactic Center? In Unsolved Problems of the Milky Way (eds Blitz, L. & Teuben, P.) 247–261 (Proc. IAU Symp. 169, Kluwer, 1996).

26.

Linden, T., Hooper, D. & Yusef-Zadeh, F. Dark matter and synchrotron emission from Galactic Center radio filaments. Astrophys. J. 741, 95 (2011).

- ADS
- Article
- Google Scholar

27.

Crocker, R. M., Bicknell, G. V., Taylor, A. M. & Carretti, E. A unified model of the Fermi bubbles, microwave haze, and polarized radio lobes: reverse shocks in the Galactic Center’s giant outflow. Astrophys. J. 808, 107 (2015).

- ADS
- Article
- Google Scholar

28.

Di Teodoro, E. M. et al. Blowing in the Milky Way wind: neutral hydrogen clouds tracing the Galactic nuclear outflow. Astrophys. J. 855, 33 (2018).

- ADS
- Article
- Google Scholar

29.

Offringa, A. et al. WSCLEAN: an implementation of a fast, generic wide-field imager for radio astronomy. Mon. Not. R. Astron. Soc. 444, 606–619 (2014).

- ADS
- Article
- Google Scholar

30.

Offringa, A. & Smirnov, O. M. An optimized algorithm for multi-scale wideband deconvolution of radio astronomical images. Mon. Not. R. Astron. Soc. 471, 301–316 (2017).

- ADS
- Article
- Google Scholar

31.

Kenyon, J. S., Smirnov, O. M., Grobler, T. L. & Perkins, S. J. CUBICAL – fast radio interferometric calibration suite exploiting complex optimization. Mon. Not. R. Astron. Soc. 478, 2399–2415 (2018).

- ADS
- Article
- Google Scholar

32.

Parker, Q. A. et al. The Macquarie/AAO/Strasbourg Hα planetary nebula catalogue: MASH. Mon. Not. R. Astron. Soc. 373, 79–94 (2006).

- ADS
- CAS
- Article
- Google Scholar

33.

Siódmiak, N. & Tylenda, R. An analysis of the observed radio emission from planetary nebulae. Astron. Astrophys. 373, 1032–1042 (2001).

- ADS
- Article
- Google Scholar

34.

Yusef-Zadeh, F. et al. Interacting cosmic rays with molecular clouds: a Bremsstrahlung origin of diffuse high-energy emission from the inner 2° × 1° of the Galactic Center. Astrophys. J. 762, 33 (2013).

- ADS
- Article
- Google Scholar

35.

LaRosa, T. N. et al. Evidence of a weak Galactic Center magnetic field from diffuse low-frequency nonthermal radio emission. Astrophys. J. 626, L23–L27 (2005).

- ADS
- CAS
- Article
- Google Scholar

36.

Condon, J. J. & Ransom, S. M. Essential Radio Astronomy 183 (Princeton Univ. Press, 2016).

37.

Indriolo, N. et al. Herschel survey of Galactic OH+, H_2O+, and H_3O+: probing the molecular hydrogen fraction and cosmic-ray ionization rate. Astrophys. J. 800, 40 (2015).

- ADS
- Article
- Google Scholar

38.

Webber, W. R. A new estimate of the local interstellar energy density and ionization rate of Galactic cosmic rays. Astrophys. J. 506, 329–334 (1998).

- ADS
- CAS
- Article
- Google Scholar

Download references

Acknowledgements

The MeerKAT telescope is operated by the South African Radio Astronomy Observatory, which is a facility of the National Research Foundation, an agency of the Department of Science and Innovation. We acknowledge use of the Inter-University Institute for Data Intensive Astronomy (IDIA) data intensive research cloud for data processing. IDIA is a South African university partnership involving the University of Cape Town, the University of Pretoria and the University of the Western Cape. This research made use of Montage, which is funded by the US National Science Foundation under grant number ACI-1440620, and was previously funded by the National Aeronautics and Space Administration’s Earth Science Technology Office, Computation Technologies Project, under cooperative agreement number NCC5-626 between NASA and the California Institute of Technology. I.H. acknowledges support from the Oxford Hintze Centre for Astrophysical Surveys, which is funded through generous support from the Hintze Family Charitable Foundation. F.Y.-Z. is partially supported by grant AST-0807400 from the US National Science Foundation.

Author information

Author notes

- L. R. S. Brederode

Present address: SKA Organisation, Jodrell Bank, Macclesfield, UK

Affiliations

Department of Physics, University of Oxford, Oxford, UK

- I. Heywood

Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa

- I. Heywood
- , B. Hugo
- , J. L. Jonas
- , G. I. G. Józsa
- , J. S. Kenyon
- , B. Ngcebetsha
- , S. K. Sirothia
- , O. M. Smirnov
- , C. Tasse
- , I. P. Theron
- & K. Thorat

South African Radio Astronomy Observatory, Cape Town, South Africa

- I. Heywood
- , F. Camilo
- , W. D. Cotton
- , T. D. Abbott
- , R. M. Adam
- , E. F. Bauermeister
- , A. G. Botha
- , L. R. S. Brederode
- , Z. B. Brits
- , S. J. Buchner
- , J. P. Burger
- , J. M. Chalmers
- , T. Cheetham
- , M. A. Dikgale-Mahlakoana
- , S. W. P. Esterhuyse
- , B. L. Fanaroff
- , A. R. Foley
- , D. J. Fourie
- , R. R. G. Gamatham
- , S. Goedhart
- , S. Gounden
- , M. J. Hlakola
- , C. J. Hoek
- , A. Hokwana
- , D. M. Horn
- , B. Hugo
- , A. R. Isaacson
- , J. L. Jonas
- , J. D. B. L. Jordaan
- , A. F. Joubert
- , G. I. G. Józsa
- , R. P. M. Julie
- , F. B. Kapp
- , P. P. A. Kotzé
- , H. Kriel
- , T. W. Kusel
- , D. Liebenberg
- , R. T. Lord
- , B. M. Lunsky
- , P. S. Macfarlane
- , L. G. Magnus
- , C. M. Magozore
- , O. Mahgoub
- , J. P. L. Main
- , J. A. Malan
- , R. D. Malgas
- , J. R. Manley
- , M. D. J. Maree
- , B. Merry
- , R. Millenaar
- , N. Mnyandu
- , I. P. T. Moeng
- , T. E. Monama
- , M. C. Mphego
- , W. S. New
- , B. Ngcebetsha
- , N. Oozeer
- , A. J. Otto
- , S. S. Passmoor
- , A. A. Patel
- , A. Peens-Hough
- , S. J. Perkins
- , S. M. Ratcliffe
- , R. Renil
- , A. Rust
- , S. Salie
- , L. C. Schwardt
- , M. Serylak
- , R. Siebrits
- , S. K. Sirothia
- , O. M. Smirnov
- , L. Sofeya
- , P. S. Swart
- , D. T. Taylor
- , K. Thorat
- , A. J. Tiplady
- , S. Tshongweni
- , T. J. van Balla
- , A. van der Byl
- , C. van der Merwe
- , R. Van Rooyen
- , V. Van Tonder
- , R. Van Wyk
- , B. H. Wallace
- , M. G. Welz
- & L. P. Williams

National Radio Astronomy Observatory, Charlottesville, VA, USA

- W. D. Cotton

CIERA and Department of Physics and Astronomy, Northwestern University, Evanston, IL, USA

- F. Yusef-Zadeh

Tellumat (Pty) Ltd, Retreat, South Africa

- M. A. Aldera

Chalmers University of Technology, Gothenburg, Sweden

- R. S. Booth

EMSS Antennas (Pty) Ltd, Stellenbosch, South Africa

- D. H. Botha
- , L. J. du Toit
- , J. D. B. L. Jordaan
- , R. Lehmensiek
- & I. P. Theron

Department of Electrical and Electronic Engineering, Stellenbosch University, Stellenbosch, South Africa

- D. de Villiers

IDIA, University of Cape Town, Rondebosch, South Africa

- J. M. G. Horrell

Department of Electrical Engineering, Cape Peninsula University of Technology, Bellville, South Africa

- R. Lehmensiek

Presidential Infrastructure Coordinating Commission, Pretoria, South Africa

- A. Loots

African Institute for Mathematical Sciences, Muizenberg, South Africa

- N. Oozeer

Department of Physics and Astronomy, University of the Western Cape, Bellville, South Africa

- M. Serylak

GEPI, CNRS, PSL Research University, Meudon, France

- C. Tasse

Peralex Electronics (Pty) Ltd, Bergvliet, South Africa

- C. L. van Dyk

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Contributions

I.H. and F.C. planned the MeerKAT observations presented here. I.H. performed the calibration and imaging of the observations. I.H. wrote the manuscript together with F.Y.-Z., F.C. and W.D.C. All other authors have contributed to one or more of the planning, design, construction, commissioning or operation of the MeerKAT radio telescope.

Corresponding authors

Correspondence to I. Heywood or F. Camilo.

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Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Peer review information Nature thanks Maria Chernyakova and Roland Crocker for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Fig. 1 Spectral-index map of the region surrounding the southern tip of the radio bubbles.

A single sub-band image at 1,123 MHz from pointing GCXS30 (see Extended Data Table 1), convolved to 30-arcsec resolution and corrected for primary-beam attenuation effects, is shown in greyscale. Overlaid upon this is a map of the spectral index, derived by fitting for this quantity through an image cube formed from five such sub-band images (see Extended Data Table 2). The spectral-index values for features that have a high signal-to-noise ratio detection in each sub-band can be reliably measured using this method, with values as indicated by the colour bar. The mean and 1σ spectral-index values for two such extended regions are marked on the map (in the format \(\bar{\alpha }\) = mean ±1σ) and are consistent with non-thermal synchrotron emission. The spectral indices of the additional compact sources marked A–E are also measured for verification purposes, with the results listed in Extended Data Table 3.

Extended Data Table 1 IDs and pointing centres for the MeerKAT observations

Full size table

Extended Data Table 2 Central frequencies of the eight sub-band images

Full size table

Extended Data Table 3 Additional spectral-index measurements for verification purposes

Full size table

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About this article

- Received

25 March 2019

- Accepted

28 June 2019

- Published

11 September 2019

- Issue Date

12 September 2019

- DOI
https://doi.org/10.1038/s41586-019-1532-5

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- Letter

- Published: 11 September 2019

X-ray pumping of the 229Th nuclear clock isomer

Takahiko Masuda[1],
Akihiro Yoshimi[1],
Akira Fujieda[1],
Hiroyuki Fujimoto[2],
Hiromitsu Haba[3],
Hideaki Hara[1],
Takahiro Hiraki[1],
Hiroyuki Kaino[1],
Yoshitaka Kasamatsu[4],
Shinji Kitao[5],
Kenji Konashi[6],
Yuki Miyamoto[1],
Koichi Okai[1],
Sho Okubo[1],
Noboru Sasao[1],
Makoto Seto[5],
Thorsten Schumm[7],
Yudai Shigekawa[4],
Kenta Suzuki[1],
Simon Stellmer7,10 nAff10,
Kenji Tamasaku[8],
Satoshi Uetake[1],
Makoto Watanabe[6],
Tsukasa Watanabe[2],
Yuki Yasuda[4],
Atsushi Yamaguchi[3],
Yoshitaka Yoda[9],
Takuya Yokokita[3],
Motohiko Yoshimura[1] &
Koji Yoshimura[1]

Naturevolume 573, pages238–242 (2019) | Download Citation

Subjects

- Experimental nuclear physics

- X-rays

Abstract

The metastable first excited state of thorium-229, 229mTh, is just a few electronvolts above the nuclear ground state1,2,3,4 and is accessible by vacuum ultraviolet lasers. The ability to manipulate the 229Th nuclear states with the precision of atomic laser spectroscopy[5] opens up several prospects[6], from studies of fundamental interactions in physics7,8 to applications such as a compact and robust nuclear clock5,9,10. However, direct optical excitation of the isomer and its radiative decay to the ground state have not yet been observed, and several key nuclear structure parameters—such as the exact energies and half-lives of the low-lying nuclear levels of 229Th—remain unknown[11]. Here we present active optical pumping into 229mTh, achieved using narrow-band 29-kiloelectronvolt synchrotron radiation to resonantly excite the second excited state of 229Th, which then decays predominantly into the isomer. We determine the resonance energy with an accuracy of 0.07 electronvolts, measure a half-life of 82.2 picoseconds and an excitation linewidth of 1.70 nanoelectronvolts, and extract the branching ratio of the second excited state into the ground and isomeric state. These measurements allow us to constrain the 229mTh isomer energy by combining them with γ-spectroscopy data collected over the past 40 years.

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Fig. 1: Low-energy nuclear level structure of 229Th.

Fig. 2: Experimental setup and the NRS measurement principle.

Fig. 3: Resonance curves of 229Th.

Fig. 4: Determination of half-life of the second excited state of 229Th.

Fig. 5: Constraining the isomer energy Eis.

References

1.

Beck, B. R. et al. Energy splitting of the ground-state doublet in the nucleus 229Th. Phys. Rev. Lett. 98, 142501 (2007).

- ADS
- CAS
- Article
- Google Scholar

2.

Beck, B. R. et al. Improved Value for the Energy Splitting of the Ground-State Doublet in the Nucleus 229m
Th. Report No. LLNL-PROC-415170 (Lawrence Livermore National Laboratory, 2009).

3.

Kroger, L. A. & Reich, C. W. Features of the low-energy level scheme of 229Th as observed in the α-decay of 233U. Nucl. Phys. A 259, 29–60 (1976).

- ADS
- Article
- Google Scholar

4.

Helmer, R. G. & Reich, C. W. An excited state of 229Th at 3.5 eV. Phys. Rev. C 49, 1845–1858 (1994).

- ADS
- CAS
- Article
- Google Scholar

5.

Peik, E. & Tamm, C. Nuclear laser spectroscopy of the 3.5 eV transition in Th-229. Europhys. Lett. 61, 181–186 (2003).

- ADS
- CAS
- Article
- Google Scholar

6.

Matinyan, S. Lasers as a bridge between atomic and nuclear physics. Phys. Rep. 298, 199–249 (1998).

- ADS
- CAS
- Article
- Google Scholar

7.

Flambaum, V. V. Enhanced effect of temporal variation of the fine structure constant and the strong interaction in 229Th. Phys. Rev. Lett. 97, 092502 (2006).

- ADS
- CAS
- Article
- Google Scholar

8.

Flambaum, V. V. Enhancing the effect of Lorentz invariance and Einstein’s equivalence principle violation in nuclei and atoms. Phys. Rev. Lett. 117, 072501 (2016).

- ADS
- CAS
- Article
- Google Scholar

9.

Campbell, C. J. et al. Single-ion nuclear clock for metrology at the 19th decimal place. Phys. Rev. Lett. 108, 120802 (2012).

- ADS
- CAS
- Article
- Google Scholar

10.

Kazakov, G. A. et al. Performance of a 229Thorium solid-state nuclear clock. New J. Phys. 14, 083019 (2012).

- ADS
- Article
- Google Scholar

11.

Peik, E. & Okhapkin, M. Nuclear clocks based on resonant excitation of γ-transitions. C. R. Phys. 16, 516–523 (2015).

- CAS
- Article
- Google Scholar

12.

von der Wense, L. et al. Direct detection of the 229Th nuclear clock transition. Nature 533, 47–51 (2016).

- ADS
- Article
- Google Scholar

13.

Takano, T. et al. Geopotential measurements with synchronously linked optical lattice clocks. Nat. Photon. 10, 662–666 (2016).

- ADS
- CAS
- Article
- Google Scholar

14.

Hayes, A. C. & Friar, J. L. Sensitivity of nuclear transition frequencies to temporal variation of the fine structure constant or the strong interaction. Phys. Lett. B 650, 229 (2007).

- ADS
- CAS
- Article
- Google Scholar

15.

Berengut, J. C. et al. Proposed experimental method to determine α sensitivity of splitting between ground and 7.6 eV isomeric states in 229Th. Phys. Rev. Lett. 102, 210801 (2009).

- ADS
- CAS
- Article
- Google Scholar

16.

Thielking, J. et al. Laser spectroscopic characterization of the nuclear-clock isomer 229mTh. Nature 556, 321–325 (2018).

- ADS
- CAS
- Article
- Google Scholar

17.

Seiferle, B. et al. Energy of the 229Th nuclear clock transition. Nature https://doi.org/10.1038/s41586-019-1533-4 (2019).

18.

Jeet, J. et al. Results of a direct search using synchrotron radiation for the low-energy 229Th nuclear isomeric transition. Phys. Rev. Lett. 114, 253001 (2015).

- ADS
- Article
- Google Scholar

19.

Yamaguchi, A. et al. Experimental search for the low-energy nuclear transition in 229Th with undulator radiation. New J. Phys. 17, 053053 (2015).

- ADS
- Article
- Google Scholar

20.

Stellmer, S. et al. Attempt to optically excite the nuclear isomer in 229Th. Phys. Rev. A 97, 062506 (2018).

- ADS
- CAS
- Article
- Google Scholar

21.

Browne, E. & Tuli, J. K. Nuclear data sheets for A = 229. Nucl. Data Sheets 11, 2657–2724 (2008).

- ADS
- Article
- Google Scholar

22.

Seto, M. Condensed matter physics using nuclear resonant scattering. J. Phys. Soc. Jpn. 82, 021016 (2013).

- ADS
- Article
- Google Scholar

23.

Yabashi, M. et al. Design of a beamline for the SPring-8 long undulator source 1. Nucl. Instrum. Methods Phys. Res. A 467–468, 678–681 (2001).

- ADS
- Article
- Google Scholar

24.

Krywka, C. et al. Polymer compound refractive lenses for hard X-ray nanofocusing. AIP Conf. Proc. 1764, 020001 (2016).

- Article

- Google Scholar

25.

Masuda, T. et al. Energy response of X-rays under high flux conditions using a thin APD for the energy range of 6–33 keV. Nucl. Instrum. Methods Phys. Res. A 913, 72–77 (2019).

- ADS
- CAS
- Article
- Google Scholar

26.

Masuda, T. et al. Fast X-ray detector system with simultaneous measurement of timing and energy for a single photon. Rev. Sci. Instrum. 88, 063105 (2017).

- ADS
- CAS
- Article
- Google Scholar

27.

Bond, W. L. Precision lattice constant determination. Acta Crystallogr. 13, 814–818 (1960).

- CAS
- Article
- Google Scholar

28.

Raboud, P.-A., Dousse, J.-Cl., Hoszowska, J. & Savoy, I. L
1 to N
5 atomic level widths of thorium and uranium as inferred from measurements of L and M X-ray spectra. Phys. Rev. A 61, 012507 (1999).

- ADS
- Article
- Google Scholar

29.

Firestone, R. B. et al. Table of Isotopes 8th edn (John Wiley & Sons, 1996).

30.

Yoshimi, A. et al. Nuclear resonant scattering experiment with fast time response: photonuclear excitation of 201Hg. Phys. Rev. C 97, 024607 (2018).

- ADS
- CAS
- Article
- Google Scholar

31.

Berger, M. J. et al. NIST Photon Cross Sections Database XCOM: Photon Cross Section Database (version 1.5) http://physics.nist.gov/xcom (National Institute of Standards and Technology, 2010).

32.

Barci, V. et al. Nuclear structure of 229Th from γ-ray spectroscopy study of 233U α-particle decay. Phys. Rev. C 68, 034329 (2003).

- ADS
- Article
- Google Scholar

33.

Tkalya, E. V. et al. Radiative lifetime and energy of the low-energy isomeric level in 229Th. Phys. Rev. C 92, 054324 (2015).

- ADS
- Article
- Google Scholar

34.

Kazakov, G. A. et al. Prospects for measuring the 229Th isomer energy using a metallic magnetic microcalorimeter. Nucl. Instrum. Methods Phys. Res. A 735, 229–239 (2014).

- ADS
- CAS
- Article
- Google Scholar

35.

Seiferle, B., von der Wense, L. & Thirolf, P. G. Lifetime measurement of the 229Th nuclear isomer. Phys. Rev. Lett. 118, 042501 (2017).

- ADS
- Article
- Google Scholar

36.

Cavagnero, G. et al. Measurement repetitions of the Si(220) lattice spacing. Metrologia 41, 56–64 (2004).

- ADS
- CAS
- Article
- Google Scholar

37.

Cavagnero, G. et al. Erratum: measurement repetitions of the Si(220) lattice spacing. Metrologia 41, 445–446 (2004).

- ADS
- CAS
- Article
- Google Scholar

38.

Fujimoto, H. et al. Homogeneity characterization of lattice spacing of silicon single crystals by a self-referenced lattice comparator. Metrologia 48, S55–S61 (2011).

- CAS
- Article
- Google Scholar

39.

Schoedel, R. & Boensch, G. Precise interferometric measurements at single-crystal silicon yielding thermal expansion coefficients from 12 °C to 28 °C and compressibility. Proc. SPIE 4401, 54–62 (2001).

- ADS
- Article
- Google Scholar

40.

Lyon, K. G., Salinger, G. L., Swenson, C. A. & White, G. K. Linear thermal expansion measurements on silicon from 6 to 340 K. J. Appl. Phys. 48, 865–868 (1977).

- ADS
- CAS
- Article
- Google Scholar

41.

Hall, J. J. Electronic effects in the elastic constants of the n-type silicon. Phys. Rev. 161, 756–761 (1967).

- ADS
- CAS
- Article
- Google Scholar

42.

Watanabe, T., Kon, M., Nabeshima, N. & Taniguchi, K. An angle encoder for super-high resolution and super-high accuracy using SelfA. Meas. Sci. Technol. 25, 065002 (2014).

- ADS
- Article
- Google Scholar

43.

Seto, M. et al. Nuclear resonance scattering of synchrotron radiation by 40K. Phys. Rev. Lett. 84, 566–569 (2000).

- ADS
- CAS
- Article
- Google Scholar

44.

Tanabashi, M. et al. Review of Particle Physics. Phys. Rev. D 98, 030001 (2018).

- ADS
- Article
- Google Scholar

45.

Scofield, J. H. Theoretical Photoionization Cross Sections from 1 to 1500 keV. Report No. UCRL-51326 (Lawrence Livermore Laboratory, 1973).

46.

Kibédi, T. et al. Evaluation of theoretical conversion coefficients using BrIcc. Nucl. Instrum. Methods Phys. Res. A 589, 202–229 (2008).

- ADS
- Article
- Google Scholar

Download references

Acknowledgements

The synchrotron radiation experiments were performed at the BL09XU and BL19LXU lines of SPring-8 with the approval of the Japan Synchrotron Radiation Research Institute (JASRI) (proposals 2016B1232, 2017B1335, 2018A1326 and 2018B1436) and RIKEN (proposal number 20180045). We thank all members of the SPring-8 operation and supporting teams. The experiment received support from the KEK Photon Factory (proposal number 2017G085) and the Institute for Materials Research, Tohoku University (18F0014), where indispensable detector tests and target preparation were performed. We especially thank S. Kishimoto for support at KEK, T. Kobayashi for technical assistance at SPring-8 and K. Beeks for discussion during the preparation of the manuscript. This work was supported by JSPS KAKENHI grants JP15H03661, JP17K14291, JP18H01230 and JP18H04353. T.S. and S.S. gratefully acknowledge funding by the EU FET-Open project, grant number 664732 (nuClock). A. Yoshimi and A. Yamaguchi acknowledge the MATSUO foundation and Technology Pioneering Projects in RIKEN, respectively.

Author information

Author notes

- Simon Stellmer

Present address: Physikalisches Institut, Universität Bonn, Bonn, Germany

Affiliations

1. Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan

- Takahiko Masuda
- , Akihiro Yoshimi
- , Akira Fujieda
- , Hideaki Hara
- , Takahiro Hiraki
- , Hiroyuki Kaino
- , Yuki Miyamoto
- , Koichi Okai
- , Sho Okubo
- , Noboru Sasao
- , Kenta Suzuki
- , Satoshi Uetake
- , Motohiko Yoshimura
- & Koji Yoshimura

2. National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan

- Hiroyuki Fujimoto

- & Tsukasa Watanabe

3. RIKEN, Wako, Japan

- Hiromitsu Haba
- , Atsushi Yamaguchi
- & Takuya Yokokita

4. Graduate School of Science, Osaka University, Toyonaka, Japan

- Yoshitaka Kasamatsu
- , Yudai Shigekawa
- & Yuki Yasuda

5. Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori-cho, Japan

- Shinji Kitao

- & Makoto Seto

6. Institute for Materials Research, Tohoku University, Higashiibaraki-gun, Japan

- Kenji Konashi

- & Makoto Watanabe

7. Institute for Atomic and Subatomic Physics, TU Wien, Vienna, Austria

- Thorsten Schumm

- & Simon Stellmer

8. RIKEN SPring-8 Center, Sayo-cho, Japan

- Kenji Tamasaku

9. Japan Synchrotron Radiation Research Institute, Sayo-cho, Japan

- Yoshitaka Yoda

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Contributions

The Okayama University group, S.K., M.S., K.T., A. Yamaguchi and Y. Yoda performed the synchrotron radiation experiments. T.M., A. Yoshimi, T.H., H.K., K.O., S.O., N.S., K.S., K.Y. and S.U. developed the detector system. The Osaka University, Tohoku University and RIKEN groups, together with A. Yoshimi, H.K. and K.Y. prepared the thorium-229 target. T.M., A. Yoshimi, T.H., H.K., N.S., K.S., K.Y., S.S. and T.S. analysed the data. H.F., T.W. and Y. Yoda developed the absolute energy monitor. T.M., A. Yoshimi, K.Y., T.S. and N.S. wrote the manuscript with input from all authors. All authors discussed the results.

Corresponding authors

Correspondence to Noboru Sasao or Koji Yoshimura.

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The authors declare no competing interests.

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Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Peer review information Nature thanks Jason Burke, Feodor Karpeshin and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Fig. 1 Pulse-processing scheme.

a, Timing diagram. Line (A) shows an analogue pulse from a Si-APD chip and line (B) represents the accelerator reference clock. The example shows two pulses with different photon energies within a cycle. b, Block diagram. For each pulse, three parameters are stored for the post-analysis: the timing of the pulse (CFD), the pulse height (ATC) and the TE timing. Preamp, preamplifier; Amp., amplifier; TDC, time-to-digital converter; USB; universal serial bus.

Extended Data Fig. 2 Absolute energy measurement setup.

The X-ray beam is diffracted by a single Si crystal. Two p–i–n (PIN) photodiodes monitor the diffracted beams. The rotary table (black disk) adjusts the angle between the Si crystal and the X-ray beam so that the diffraction condition is satisfied. The two swivel stages adjust the tilt angles between the X-ray beam, the reciprocal lattice vector of the crystal and the rotation axis of the rotary table.

Extended Data Fig. 3 NRS spectrum of 40K.

Temporal profiles measured at incident X-ray energy on resonance (blue histogram) and off resonance (black histogram). Inset, resonance curve (black dots) with a Gaussian fit (blue curve).

Extended Data Fig. 4 Energy spectra of the prompt and NRS events.

a, Energy spectrum of the prompt signal (black line). The coloured lines show various X-ray emission lines convoluted with the Si-APD energy response function: the photoelectric absorption lines listed in Extended Data Table 2 (blue), Compton scattering (magenta) and the Kα and Kβ lines of Cu, Zn and Fe (green). The strengths of these lines are adjusted to give the best fit to the data. The sum of all lines (red) reproduces the data above 7 keV well . b, NRS energy spectrum, obtained by subtracting the off-resonance data from the on-resonance data. The coloured lines are fits of the X-ray emission lines. We note that there is no contribution from Compton scattering or the Cu, Zn and Fe lines. Both experimental datasets are normalized to a 3,600-s run. The error bars represent statistical uncertainty of one standard deviation.

Extended Data Table 1 Estimation of radiative width \({{\boldsymbol{\Gamma }}}_{{\boldsymbol{\gamma }}}^{{\bf{c}}{\bf{r}}}\)

Full size table

Extended Data Table 2 Comparison of energy-averaged line strengths

Full size table

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About this article

- Received

08 February 2019

- Accepted

23 July 2019

- Published

11 September 2019

- Issue Date

12 September 2019

- DOI
https://doi.org/10.1038/s41586-019-1542-3

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- Letter

- Published: 11 September 2019

Energy of the 229Th nuclear clock transition

Benedict Seiferle[1],
Lars von der Wense[1],
Pavlo V. Bilous[2],
Ines Amersdorffer[1],
Christoph Lemell[3],
Florian Libisch[3],
Simon Stellmer[4],
Thorsten Schumm[5],
Christoph E. Düllmann6,7,8,
Adriana Pálffy[2] &
Peter G. Thirolf[1]

Naturevolume 573, pages243–246 (2019) | Download Citation

Subjects

- Experimental nuclear physics

- Optical metrology

Abstract

Owing to its low excitation energy and long radiative lifetime, the first excited isomeric state of thorium-229, 229mTh, can be optically controlled by a laser1,2 and is an ideal candidate for the creation of a nuclear optical clock[3], which is expected to complement and outperform current electronic-shell-based atomic clocks[4]. A nuclear clock will have various applications—such as in relativistic geodesy[5], dark matter research[6] and the observation of potential temporal variations of fundamental constants[7]—but its development has so far been impeded by the imprecise knowledge of the energy of 229mTh. Here we report a direct measurement of the transition energy of this isomeric state to the ground state with an uncertainty of 0.17 electronvolts (one standard deviation) using spectroscopy of the internal conversion electrons emitted in flight during the decay of neutral 229mTh atoms. The energy of the transition between the ground state and the first excited state corresponds to a wavelength of 149.7 ± 3.1 nanometres, which is accessible by laser spectroscopy through high-harmonic generation. Our method combines nuclear and atomic physics measurements to advance precision metrology, and our findings are expected to facilitate the application of high-resolution laser spectroscopy on nuclei and to enable the development of a nuclear optical clock of unprecedented accuracy.

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Fig. 1: Experimental setup used for the determination of the isomeric energy of 229mTh.

Fig. 2: Measured and predicted internal conversion electron spectra.

Data availability

Drawings of the spectrometer are available from the corresponding author on request.

References

1.

Kroger, L. A. & Reich, C. W. Features of the low-energy level scheme of 229Th as observed in the α-decay of 233U. Nucl. Phys. A 259, 29–60 (1976).

- ADS
- Article
- Google Scholar

2.

von der Wense, L. et al. Direct detection of the 229Th nuclear clock transition. Nature 533, 47–51 (2016).

- ADS
- Article
- Google Scholar

3.

Peik, E. & Tamm, C. Nuclear laser spectroscopy of the 3.5 eV transition in 229Th. EPL 61, 181–186 (2003).

- ADS
- CAS
- Article
- Google Scholar

4.

Campbell, C. J. et al. Single-ion nuclear clock for metrology at the 19th decimal place. Phys. Rev. Lett. 108, 120802 (2012).

- ADS
- CAS
- Article
- Google Scholar

5.

Mehlstäubler, T. E. et al. Atomic clocks for geodesy. Rep. Prog. Phys. 81, 064401 (2018).

- ADS
- Article
- Google Scholar

6.

Derevianko, A. & Pospelov, M. Hunting for topological dark matter with atomic clocks. Nat. Phys. 10, 933–936 (2014).

- CAS
- Article
- Google Scholar

7.

Flambaum, V. V. Enhanced effect of temporal variation of the fine structure constant and the strong interaction in 229Th. Phys. Rev. Lett. 97, 092502 (2006).

- ADS
- CAS
- Article
- Google Scholar

8.

Reich, C. W. & Helmer, R. G. Energy separation of the doublet of intrinsic states at the ground state of 229Th. Phys. Rev. Lett. 64, 271–273 (1990).

- ADS
- CAS
- Article
- Google Scholar

9.

Helmer, R. G. & Reich, C. W. An excited state of 229Th at 3.5 eV. Phys. Rev. C 49, 1845–1858 (1994).

- ADS
- CAS
- Article
- Google Scholar

10.

Beck, B. R. et al. Energy splitting of the ground-state doublet in the nucleus 229Th. Phys. Rev. Lett. 98, 142501 (2007).

- ADS
- CAS
- Article
- Google Scholar

11.

Beck, B.R. et al. Improved Value for the Energy Splitting of the Ground-State Doublet in the Nucleus 229m
Th. Report No. LLNL-PROC-415170 (Los Alamos National Laboratory, 2009).

- Google Scholar

12.

Tkalya, E. V. et al. Radiative lifetime and energy of the low-energy isomeric level in 229Th. Phys. Rev. C 92, 054324 (2015).

- ADS
- Article
- Google Scholar

13.

Minkov, N. & Pálffy, A. Reduced transition probabilities for the gamma decay of the 7.8 eV isomer in 229Th. Phys. Rev. Lett. 118, 212501 (2017).

- ADS
- Article
- Google Scholar

14.

Rellergert, W. D. et al. Constraining the evolution of the fundamental constants with a solid-state optical frequency reference based on the 229Th nucleus. Phys. Rev. Lett. 104, 200802 (2010).

- ADS
- Article
- Google Scholar

15.

Karpeshin, F. F. & Trzhaskovskaya, M. B. Impact of the electron environment on the lifetime of the 229Thm low-lying isomer. Phys. Rev. C 76, 054313 (2007).

- ADS
- Article
- Google Scholar

16.

Burke, D. G., Garrett, P. E., Qu, T. & Naumann, R. A. Nuclear structure of 229,231Th studied with the 230,232Th(d, t) reactions. Nucl. Phys. A 809, 129–170 (2008).

- ADS
- Article
- Google Scholar

17.

Raeder, S. et al. Resonance ionization spectroscopy of thorium isotopes – towards a laser spectroscopic identification of the low-lying 7.6 eV isomer of 229Th. J. Phys. At. Mol. Opt. Phys. 44, 165005 (2011).

- ADS
- Article
- Google Scholar

18.

Jeet, J. et al. Results of a direct search using synchrotron radiation for the low-energy 229Th nuclear isomeric transition. Phys. Rev. Lett. 114, 253001 (2015).

- ADS
- Article
- Google Scholar

19.

Yamaguchi, A. et al. Experimental search for the low-energy nuclear transition in 229Th with undulator radiation. New J. Phys. 17, 053053 (2015).

- ADS
- Article
- Google Scholar

20.

Stellmer, S. et al. Attempt to optically excite the nuclear isomer in 229Th. Phys. Rev. A 97, 062506 (2018).

- ADS
- CAS
- Article
- Google Scholar

21.

Borisyuk, P. V. et al. Experimental studies of thorium ion implantation from pulse laser plasma into thin silicon oxide layers. Laser Phys. Lett. 15, 056101 (2018).

- ADS
- Article
- Google Scholar

22.

Stellmer, S. et al. Toward an energy measurement of the internal conversion electron in the deexcitation of the 229Th isomer. Phys. Rev. C 98, 014317 (2018).

- ADS
- CAS
- Article
- Google Scholar

23.

Campbell, C. J., Radnaev, A. G. & Kuzmich, A. Wigner crystals of 229Th for optical excitation of the nuclear isomer. Phys. Rev. Lett. 106, 223001 (2011).

- ADS
- CAS
- Article
- Google Scholar

24.

Kazakov, G. A. et al. Prospects for measuring the 229Th isomer energy using a metallic magnetic microcalorimeter. Nucl. Instrum. Meth. A 735, 229 (2014).

- ADS
- CAS
- Article
- Google Scholar

25.

Bilous, P. V. et al. Internal conversion from excited electronic states of 229Th ions. Phys. Rev. A 95, 032503 (2017).

- ADS
- Article
- Google Scholar

26.

von der Wense, L. et al. A laser excitation scheme for 229mTh. Phys. Rev. Lett. 119, 132503 (2017).

- ADS
- Article
- Google Scholar

27.

Masuda, T. et al. X-ray pumping of the 229Th nuclear clock isomer. Nature https://doi.org/10.1038/s41586-019-1542-3 (2019).

28.

Seiferle, B., v. d. Wense, L. & Thirolf, P. G. Lifetime measurement of the 229Th nuclear isomer. Phys. Rev. Lett. 118, 042501 (2017).

- ADS
- Article
- Google Scholar

29.

Thielking, J. et al. Laser spectroscopic characterization of the nuclear-clock isomer 229mTh. Nature 556, 321–325 (2018).

- ADS
- CAS
- Article
- Google Scholar

30.

Yamakita, Y. et al. A highly sensitive electron spectrometer for crossed-beam collisional ionization: a retarding-type magnetic bottle analyzer and its application to collision-energy resolved Penning ionization electron spectroscopy. Rev. Sci. Instrum. 71, 3042–3049 (2000).

- ADS
- CAS
- Article
- Google Scholar

31.

Seiferle, B. et al. Towards a precise determination of the excitation energy of the Thorium nuclear isomer using a magnetic bottle spectrometer. Preprint at https://arxiv.org/abs/1812.04621 (2018).

32.

Arnau, A. et al. Interaction of slow multicharged ions with solid surfaces. Surf. Sci. Rep. 27, 113 (1997).

- ADS
- CAS
- Article
- Google Scholar

33.

Lias S. G. Ionization energy evaluation. NIST Chemistry WebBook, NIST Standard Reference Database Number 69 (eds Linstrom P. J. & Mallard, W. G.) (National Institute of Standards and Technology, 2005).

34.

van der Wense, L. et al. Determination of the extraction efficiency for 233U source α-recoil ions from the MLL buffer-gas stopping cell. Eur. Phys. J. A 51, 29 (2015).

- ADS
- Article
- Google Scholar

35.

van der Wense, L. On the Direct Detection of 229m
Th (Springer, 2018).

36.

Eberhardt, K. et al. Actinide targets for fundamental research in nuclear physics. AIP Conf. Proc. 1962, 030009 (2018).

- Article

- Google Scholar

37.

Haettner, E. et al. A versatile triple radiofrequency quadrupole system for cooling, mass separation and bunching of exotic nuclei. Nucl. Instrum. Meth. A 880, 138–151 (2018).

- ADS
- CAS
- Article
- Google Scholar

38.

Amersdorffer, I. Charge-exchange of 229(m)Th ions in carbon foils. BSc thesis, Ludwig-Maximilians Univ. (2018).

39.

Eland, J. H. D. Photoelectron Spectroscopy (Elsevier, 1984).

40.

Harada, K., Wada, T. & Tanaka, T. Near-infrared diode laser spectroscopy of the (2, 0) band of the \({A}^{{\rm{2}}}{\Pi }_{{\rm{u}}}-{X}^{2}{\Sigma }_{{\rm{g}}}^{+}\) system of the \({{\rm{N}}}_{2}^{+}\)ion. J. Mol. Spectrosc. 163, 436–442 (1994).

- ADS
- CAS
- Article
- Google Scholar

41.

Gardner, J. L. & Samson, J. A. R. Calibration of electron spectrometers. J. Electron Spectrosc. 8, 469–474 (1976).

- ADS
- CAS
- Article
- Google Scholar

42.

Karpeshin, F. F. & Trzhaskovskaya, M. B. Impact of the ionization of the atomic shell on the lifetime of the 229mTh isomer. Nucl. Phys. A 969, 173 (2018).

- ADS
- CAS
- Article
- Google Scholar

43.

Pálffy, A., Scheid, W. & Harman, Z. Theory of nuclear excitation by electron capture for heavy ions. Phys. Rev. A 73, 012715 (2006).

- ADS
- Article
- Google Scholar

44.

Blaise, J. & Wyart, J.-F. Database of Selected Constants, Energy Levels and Atomic Spectra of Actinides http://web2.lac.u-psud.fr/lac/Database/Tab-energy/Thorium/ (2014).

45.

Jönsson, P. et al. New version: Grasp2k relativistic atomic structure package. Comput. Phys. Commun. 184, 2197–2203 (2013).

- ADS
- Article
- Google Scholar

46.

Bilous, P. V., Minkov, N. & Pálffy, A. Electric quadrupole channel of the 7.8 eV 229Th transition. Phys. Rev. C 97, 044320 (2018).

- ADS
- CAS
- Article
- Google Scholar

47.

Fritzsche, S. The RATIP program for relativistic calculations of atomic transition, ionization and recombination properties. Comput. Phys. Commun. 183, 1525 (2012).

- ADS
- CAS
- Article
- Google Scholar

48.

Burgdörfer, J., Lerner, P. & Meyer, F. W. Above-surface neutralization of highly charged ions: the classical over-the-barrier model. Phys. Rev. A 44, 5674 (1991).

- ADS
- Article
- Google Scholar

49.

Gruber, E. et al. Ultrafast electronic response of graphene to a strong and localized electric field. Nat. Commun. 7, 13948 (2016).

- ADS
- CAS
- Article
- Google Scholar

50.

Perdew, J. P., Burke, K. & Ernzerhof, M. Generalized gradient approximation made simple. Phys. Rev. Lett. 77, 3865–3868 (1996); erratum 78, 1396 (1997).

- ADS
- CAS
- Article
- Google Scholar

51.

Kresse, G. & Furthmüller, J. Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Phys. Rev. B 54, 11169–11186 (1996).

- ADS
- CAS
- Article
- Google Scholar

52.

Kresse, G. & Joubert, D. From ultrasoft pseudopotentials to the projector augmented-wave method. Phys. Rev. B 59, 1758–1774 (1999).

- ADS
- CAS
- Article
- Google Scholar

53.

Behrens, R. G. et al. Th Thorium: General Properties. Spectra. Recoil Reactions. Gmelin Handbook of Inorganic Chemistry (Springer, 1989).

54.

Roy, S. K. Prasad, R. & Chandra, P. Electron correlation and relativistic effects in atomic structure calculations of the thorium atom. J. Chem. Phys. 134, 234302 (2011).

- ADS
- CAS
- Article
- Google Scholar

Download references

Acknowledgements

We acknowledge discussions with D. Habs, J. Weitenberg, M. Laatiaoui, A. Ulrich, W. Plaß and colleagues, J. Crespo, C. Weber, F. Zacherl and K. Beeks and we thank K. Eberhardt, C. Mokry, J. Runke and N. Trautmann for producing the 233U and 234U sources. This work was supported by DFG (Th956/3-2), by the LMU Chair of Medical Physics via the Maier-Leibnitz Laboratory Garching and by the European Union’s Horizon 2020 research and innovation programme under grant agreement number 664732 (nuClock).

Author information

Affiliations

1. Ludwig-Maximilians-University Munich, Garching, Germany

- Benedict Seiferle
- , Lars von der Wense
- , Ines Amersdorffer
- & Peter G. Thirolf

2. Max-Planck-Institut für Kernphysik, Heidelberg, Germany

- Pavlo V. Bilous

- & Adriana Pálffy

3. Institute for Theoretical Physics, TU Wien, Vienna, Austria

- Christoph Lemell

- & Florian Libisch

4. University of Bonn, Bonn, Germany

- Simon Stellmer

5. Atominstitut, TU Wien, Vienna, Austria

- Thorsten Schumm

6. GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt, Germany

- Christoph E. Düllmann

7. Helmholtz Institute Mainz, Mainz, Germany

- Christoph E. Düllmann

8. Johannes Gutenberg University, Mainz, Germany

- Christoph E. Düllmann

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1. Search for Benedict Seiferle in:

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- PubMed •

- Google Scholar

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Contributions

B.S., L.v.d.W. and I.A. performed the experiments. B.S., L.v.d.W., P.V.B., I.A., S.S., C.L., F.L., T.S., C.E.D., A.P. and P.G.T. discussed the experimental results. P.V.B. and A.P. performed the theoretical calculations. The radioactive sources were produced in C.E.D.’s group. C.L. and F.L. performed the DFT calculations. B.S., L.v.d.W. and P.G.T. wrote the manuscript with input from all authors.

Corresponding author

Correspondence to Benedict Seiferle.

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Peer review information Nature thanks Jason Burke, Feodor Karpeshin and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Fig. 1 Sectional view of the focusing and bending electrodes and the collection region.

a, Top view. b, Lateral view. Ions are focused by focusing electrodes (labelled ‘1’, ‘2’, ‘3’ and ‘4’) onto graphene. A large fraction (∼50%) of the ions is neutralized. Secondary electrons, as well as ions that are not neutralized, are deflected by bending electrodes and cannot enter the spectrometer collection region. A grid placed at the entrance of the collection region is used to shield electric radiofrequency and d.c. fields. The collection region is accessible via several ports to allow calibration. For the calibration a gas discharge lamp is used and photoelectrons are generated along the line indicated by the arrow (labelled ‘He I radiation’). An MCP detector is used to monitor the ion and atom extraction.

Extended Data Fig. 2 Sectional view of the magnetic-bottle-type retarding-field electron spectrometer.

The retarding-field voltage is applied to the central grid in the retarding-field unit. The outer grids are kept grounded and the electrodes between them are biased via a voltage divider chain.

Extended Data Fig. 3 Experimental scheme.

a–c, A mixed-ion cloud (containing Th2+ and Th3+ ions) is trapped in a segmented RFQ magnet (blue area). The cloud/bunch (white) is released and injected into the QMS (red area), which serves as an ion guide. The difference in kinetic energy (Th3+ ions are faster than Th2+ ions) leads to a temporal separation of the two charge states. The ion bunches are then neutralized in graphene and continue their flight as atoms (black). The atoms are counted with an MCP detector (MCP II). A time-of-flight spectrum is shown in b (the corresponding measurement is presented in Extended Data Fig. 4b). The neutralization also triggers the internal conversion decay of the 229mTh nuclear isomer. When 229mTh decays inside the collection region of the electron spectrometer, the internal conversion (IC) electron is guided towards MCP I and generates a signal. The time-resolved signal, as well as the time windows that are used to count the internal conversion electrons, are shown in c (a measurement is shown in Extended Data Fig. 4a). cts, number of counts. Dimensions are not to scale.

Extended Data Fig. 4 Internal conversion electron signal.

a, b, Internal conversion electron signal measured with MCP I at two different retarding voltages (a). Th3+ (Th2+) ions generate a signal at t ≈ 80 μs (t ≈ 97 μs) from the release of the ion bunch. 10^5 bunches were recorded for each retarding voltage. The number of counts from neutralized atoms measured with MCP II are shown in b (for 2.25 × 10^6 bunches recorded). We note that the ratio of the Th2+ and Th3+ peaks from a is not reflected in b. This can be explained as follows: in the Th2+ charged state, 229Th and 233U are extracted from the buffer-gas stopping cell at approximately equal rates, whereas the extraction rate in the Th3+ charged state is dominated by 229Th (see ref. [34]). In our setup, thorium cannot be separated from uranium by the time-of-flight method; therefore, it can be expected that only ∼50% of the Th2+ peak in b results from neutralized 229Th2+ ions. By contrast, the internal conversion electron signal results solely from neutralized 229mTh ions.

Extended Data Fig. 5 Comparative measurements.

Comparative measurement of 230Th and 229(m)Th at a blocking voltage of 0 V. For the 229(m)Th (230Th) measurement, 5,000 (>800,000) bunches were recorded. To compare 230Th with 229(m)Th, the number of counts was normalized to the number of extracted atoms measured with MCP II (see Extended Data Fig. 3). Constant background has been subtracted in the 230Th measurement.

Extended Data Fig. 6 Calibration measurements.

Measured (integrated) calibration spectra (red) and their derivatives, shown together with a fitting function (black). For better visualization, data and derivatives are normalized to their respective maxima. The energy scale has been corrected for surface potentials. Measurements were obtained as detailed in ref. [31]. a, Typical argon calibration spectrum used in the measurements (electron kinetic energies of 5.46 eV and 5.28 eV). b, Neon calibration spectrum, showing a clear separation of the two lines (electron kinetic energies of 1.52 eV and 1.43 eV). arb., arbitrary units.

Extended Data Fig. 7 Monitoring of the applied blocking voltages.

a, Time-resolved behaviour of the applied retarding voltages. Retarding voltages between −0.5 V and −3.5 V are applied in steps of −0.1 V. Each retarding voltage is held for 1,000 bunches (about 100 s). Before incrementing the voltage, it is set to 0 V to make the measurement independent from the order in which the voltages are applied. b, Distribution of an exemplary retarding voltage over three days of measurement. The stability is better than 10 mV and limited by temperature fluctuations.

Extended Data Fig. 8 Single-electron orbital energies for thorium.

Single-electron (Kohn–Sham) orbital energies for a thorium atom as a function of the distance from the topmost carbon layer, located at z = 0 Å. Screening of the core by the target’s electrons leads to distance-dependent shifts of the orbital energies. The 6s and 6p states (asymptotic energies of about −40 eV and −20 eV, respectively) remain atomic in graphene, whereas higher orbitals (7s, 6d, 5f) become resonant with the graphene valence bands (overlapping red and green shaded areas, indicating the region of high electron density in the target) at different distances. In the target, a prevalence of states with f characteristic (purple symbols) is observed. EF denotes the Fermi energy.

Extended Data Fig. 9 Summary of internal conversion electron rates.

Bottom, possible values for IP − Ei + Ef, given by the internal conversion selection rules for even (blue) and odd (red) initial electronic states of Th. Initial states are numbered according to their state index (given in Extended Data Table 1). The ionization potential of the Th atom is shown by the black dashed line. The size of the symbols indicates the transition rate from an initial state to a final state. Top, projection of the data shown in the lower panel onto the horizontal axis (energy bin, 0.1 eV).

Extended Data Table 1 Considered excited states in thorium

Full size table

Extended Data Table 2 Uncertainty of the data analysis

Full size table

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- Issue Date

12 September 2019

- DOI
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- Letter

- Published: 12 August 2019

Position and momentum mapping of vibrations in graphene nanostructures

- Ryosuke Senga[1],
- Kazu Suenaga[1],
- Paolo Barone[2],
- Shigeyuki Morishita[3],
- Francesco Mauri4,5 &
- Thomas Pichler[6]

Naturevolume 573, pages247–250 (2019) | Download Citation

Subjects

- Characterization and analytical techniques

- Computational methods

- Mechanical and structural properties and devices

- Transmission electron microscopy

- Two-dimensional materials

Abstract

Propagating atomic vibrational waves—phonons—determine important thermal, mechanical, optoelectronic and transport characteristics of materials. Thus a knowledge of phonon dispersion (that is, the dependence of vibrational energy on momentum) is a key part of our understanding and optimization of a material’s behaviour. However, the phonon dispersion of a free-standing monolayer of a two-dimensional material such as graphene, and its local variations, have remained elusive for the past decade because of the experimental limitations of vibrational spectroscopy. Even though electron energy loss spectroscopy (EELS) in transmission has recently been shown to probe local vibrational charge responses1,2,3,4, such studies are still limited by momentum space integration due to the focused beam geometry; they are also restricted to polar materials such as boron nitride or oxides1,2,3,4, in which huge signals induced by strong dipole moments are present. On the other hand, measurements on graphene performed by inelastic X-ray (neutron) scattering spectroscopy5,6,7 or EELS in reflection8,9 do not have any spatial resolution and require large microcrystals. Here we provide a new pathway to determine phonon dispersions down to the scale of an individual free-standing graphene monolayer by mapping the distinct vibrational modes for a large momentum transfer. The measured scattering intensities are accurately reproduced and interpreted with density functional perturbation theory[10]. Additionally, a nanometre-scale mapping of selected momentum-resolved vibrational modes using graphene nanoribbon structures has enabled us to spatially disentangle bulk, edge and surface vibrations. Our results are a proof-of-principle demonstration of the feasibility of studying local vibrational modes in two-dimensional monolayer materials at the nanometre scale.

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Fig. 1: Momentum-resolved vibrational spectroscopy of graphite and hBN using EELS.

Fig. 2: Total phonon intensity and charge modulation in EELS.

Fig. 3: Momentum mapping of vibrations in a graphene monolayer.

Fig. 4: Position mapping of vibrations in graphene nanoribbons.

Data availability

The datasets generated and/or analysed during the current study are available from the corresponding author on reasonable request.

Code availability

Quantum ESPRESSO is an open-source suite of computational tools available at www.quantum-espresso.org. The PH package was modified to print out the valence-electron density response to ionic displacements. The post-processing code used to simulate the EEL spectra will be included in a next release of the PH package.

References

1.

Krivanek, O. L. et al. Vibrational spectroscopy in the electron microscope. Nature 514, 209–212 (2014).

- ADS
- CAS
- Article
- Google Scholar

2.

Lagos, M. J., Trügler, A., Hohenester, U. & Batson, P. E. Mapping vibrational surface and bulk modes in a single nanocube. Nature 543, 529–532 (2017).

- ADS
- CAS
- Article
- Google Scholar

3.

Hage, F. S. et al. Nanoscale momentum-resolved vibrational spectroscopy. Sci. Adv. 1, eaar7495 (2018).

- ADS
- Article
- Google Scholar

4.

Dwyer, C. et al. Electron-beam mapping of vibrational modes with nanometer spatial resolution. Phys. Rev. Lett. 117, 256101 (2016).

- ADS
- CAS
- Article
- Google Scholar

5.

Maultzsch, J., Reich, S., Thomsen, C., Requardt, H. & Ordejón, P. Phonon dispersion in graphite. Phys. Rev. Lett. 92, 075501 (2004).

- ADS
- CAS
- Article
- Google Scholar

6.

Mohr, M. et al. Phonon dispersion of graphite by inelastic X-ray scattering. Phys. Rev. B 76, 035439 (2007).

- ADS
- Article
- Google Scholar

7.

Nicklow, R., Wakabayashi, N. & Smith, H. G. Lattice dynamics of pyrolytic graphite. Phys. Rev. B 5, 4951–4962 (1972).

- ADS
- Article
- Google Scholar

8.

Vig, S. et al. Measurement of the dynamic charge response of materials using low-energy, momentum-resolved electron energy-loss spectroscopy (M-EELS). SciPost Phys. 3, 026 (2017).

- ADS
- Article
- Google Scholar

9.

Oshima, C., Aizawa, T., Souda, R., Ishizawa, Y. & Sumiyoshi, Y. Surface phonon dispersion curves of graphite (0001) over the entire energy region. Solid State Commun. 65, 1601–1604 (1988).

- ADS
- CAS
- Article
- Google Scholar

10.

Giannozzi, P., De Gironcoli, S., Pavone, P. & Baroni, S. Ab initio calculation of phonon dispersions in semiconductors. Phys. Rev. B 43, 7231–7242 (1991).

- ADS
- CAS
- Article
- Google Scholar

11.

Van Hove, L. Correlations in space and time and Born approximation scattering in systems of interacting particles. Phys. Rev. 95, 249–262 (1954).

- ADS
- MathSciNet
- Article
- Google Scholar

12.

Roth, F., König, A., Fink, J., Büchner, B. & Knupfer, M. Electron energy-loss spectroscopy: a versatile tool for the investigations of plasmonic excitations. J. Electron Spectrosc. Relat. Phenom. 195, 85–95 (2014).

- CAS
- Article
- Google Scholar

13.

Nicholls, R. J. et al. Theory of momentum-resolved phonon spectroscopy in the electron microscope. Phys. Rev. B 99, 094105 (2019).

14.

Vogl, P. Microscopic theory of electron-phonon interaction in insulators or semiconductors. Phys. Rev. B 13, 694–704 (1976).

- ADS
- Article
- Google Scholar

15.

Falter, C., Ludwig, W., Maradudin, A. A., Selmke, M. & Zierau, W. Valence charge density and effective charges within the density-response theory. Phys. Rev. B 32, 6510–6517 (1985).

- ADS
- CAS
- Article
- Google Scholar

16.

Ghosez, P., Michenaud, J.-P. & Gonze, X. Dynamical atomic charges: the case of ABO_3 compounds. Phys. Rev. B 58, 6224–6240 (1998).

- ADS
- CAS
- Article
- Google Scholar

17.

Muller, D. & Silcox, J. Delocalization in inelastic scattering. Ultramicroscopy 59, 195–213 (1995).

- CAS
- Article
- Google Scholar

18.

Hage, F. S., Kepaptsoglou, D. M., Ramasse, Q. M. & Allen, L. J. Phonon spectroscopy at atomic resolution. Phys. Rev. Lett. 122, 016103 (2019).

- ADS
- CAS
- Article
- Google Scholar

19.

Venkatraman, K., Levin, B. D. A., March, K., Rez, P. & Crozier, P. A. Vibrational spectroscopy at atomic resolution with electron impact scattering. Preprint at https://arXiv.org/abs/1812.08895 (2018).

20.

Sohier, T., Gibertini, M., Calandra, M., Mauri, F. & Marzari, N. Breakdown of optical phonons’ splitting in two-dimensional materials. Nano Lett. 17, 3758–3763 (2017).

- ADS
- CAS
- Article
- Google Scholar

21.

Giannozzi, P. et al. QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials. J. Phys. Condens. Matter 21, 395502 (2009).

- Article

- Google Scholar

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Acknowledgements

This work was supported by KAKENHI (17H04797 and 16H06333) and by the European Graphene Flagship Core 2 grant no. 785219. T.P. thanks the FWF for funding (P27769-N20). P.B. and F.M. acknowledge CINECA awards under the ISCRA initiative (grants HP10B3EDF2 and HP10BSZ6LY) for making available high-performance computing resources and support. We thank P. Ayala for fruitful discussions.

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Affiliations

1. Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan

- Ryosuke Senga

- & Kazu Suenaga

2. SPIN-CNR, c/o Università G. D’Annunzio, Chieti, Italy

- Paolo Barone

3. EM Research and Development Department, JEOL Ltd, Akishima, Japan

- Shigeyuki Morishita

4. Dipartimento di Fisica, Università di Roma La Sapienza, Roma, Italy

- Francesco Mauri

5. Graphene Labs, Fondazione Istituto Italiano di Tecnologia, Genova, Italy

- Francesco Mauri

6. Faculty of Physics, University of Vienna, Vienna, Austria

- Thomas Pichler

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Contributions

R.S., S.M., T.P. and K.S. designed the experiments. R.S. performed EELS measurements. R.S. and T.P. analysed data. P.B. and F.M. established the theory and performed ab initio calculations. R.S., T.P., P.B., F.M. and K.S. co-wrote the paper. All authors commented on manuscript.

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Extended data figures and tables

Extended Data Fig. 1 Raw EEL spectra including quasi-elastic lines.

a–d, Series of momentum-resolved EEL spectra along the ΓΜΓΜ (a, c) and ΓΚΜΚΓ (b, d) directions taken from graphite (a, b) and hBN (c, d) flakes.

Extended Data Fig. 2 Line shape analysis of the measured spectra of graphite.

Shown are typical examples of line shape analysis of the EEL spectra of graphite at q = 2.25, 3.25 and 4.00 Å−1 (left, middle and right panels, respectively). Each component (modes LA, LO, TO, LA; purple lines) is fitted with a Voigtian including the fixed experimental broadening factor (30–40 meV). The data points and the fitting lines are shown by black dots and blue lines, respectively.

Extended Data Fig. 3 Phonon dispersion of hBN and graphite along the ΓΚΜΚΓ direction.

a, b, Series of momentum-resolved EEL spectra (left) and simulated spectra (right) along the ΓΚΜΚΓ direction (from top to bottom) for graphite and hBN, respectively. The quasi-elastic lines have been subtracted. (The raw data including the quasi-elastic lines are shown in Extended Data Fig. 1). The spectra are recorded at every 0.25 Å−1 from q = 0 to 5.00 Å−1 in the ΓΜ direction and at the second Γ point of graphite (5.11 Å−1). The spectra at every Γ point (red lines) include the Bragg reflection spots. c–f, Intensity colour maps of graphite (c, e) and hBN (d, f) constructed from the measured EEL spectra (c, d) and from the simulated spectra (e, f) are shown with the simulated phonon dispersion curves (solid lines). The peak positions extracted from the measured spectra by the line shape analysis are indicated by the open triangles in c and d.

Extended Data Fig. 4 Bubble plots of the phonon dispersion of graphite and hBN.

Left column, along the ΓMΓM direction; right column, along the ΓKMKΓ direction. These plots are obtained by line shape analysis of the measured spectra (‘Experiment’; first and third rows) and from the simulation (DFPT; second and fourth rows). The size (cross-section) of each point (the ‘bubble’) corresponds to the intensity, which is normalized by the highest peak at each measured (or calculated) q.

Extended Data Fig. 5 The contribution of out-of-plane modes induced by sample tilting.

Left, middle, right, simulated spectra of hBN at q = 1, 1.75, 2.5 Å−1 respectively along the ΓΚΜΚΓ line: each panel shows the effect of the tilting angle. ZA and ZO modes are gradually activated as the tilting angle increases. Bars indicate the mode-resolved calculated intensities at each phonon frequency that are then broadened with a 25-meV Lorentzian, resulting in the simulated spectra.

Extended Data Fig. 6 q-dependence of effective charges and total intensity for phonon EEL spectra.

Top, the evolution of effective charges in both hBN and graphite as a function of q are shown along the ΓΜΓΜ (left panel) and ΓΚΜΚΓ (right panel) directions. Solid (dashed) lines correspond to the real (imaginary) part of the effective charge. Despite graphite hosting two inequivalent carbon ions (C_1 and C_2), their effective charges are substantially indistinguishable except for very small momenta, where tiny differences only can be seen (inset). Bottom, the total intensity for graphite (black) and hBN (red) as a function of momentum transfer obtained from the experiments (filled circles with dotted lines) and from DFPT calculations (solid lines), evaluated as \(I({\boldsymbol{q}})={\int }_{0}^{{\rm{\infty }}}{\rm{d}}\omega \frac{{{\rm{d}}}^{2}\sigma }{{\rm{d}}\Omega {\rm{d}}\omega }({\boldsymbol{q}},\omega )\). The singular behaviour of the theoretical total intensity observed at Γ points in higher-order Brillouin zones can be ascribed to the 1/ωqν dependence of the differential cross-section, which diverges for LA modes (notice that this diverging behaviour does not appear if the total intensity is evaluated with a low-frequency cut-off ωcut, as shown in Fig. 2a). A renormalized intensity defined as \(I({\boldsymbol{q}})\propto \sum _{\nu }{|\sum _{I}\frac{1}{\sqrt{{M}_{I}}}{{\boldsymbol{Z}}}_{I}({\boldsymbol{q}})\cdot {{\boldsymbol{e}}}_{{\boldsymbol{q}},\nu }^{I}{{\rm{e}}}^{-i{\boldsymbol{q}}\cdot {{\boldsymbol{\tau }}}_{I}}|}^{2}\) is also shown in the bottom panels. This highlights the non-trivial momentum-dependence of EEL intensity that stems from effective charges when the trivial momentum and phonon dependencies 1/q^2 and (1+nqv)/ωqv, respectively, are neglected. A blue line scaling as 1/q^2 (q^2) is also shown as a reference for total (renormalized) intensities.

Extended Data Fig. 7 Phonon EEL spectra of monolayer graphene.

a–d, Series of momentum-resolved EEL spectra along ΓΜΓΜ (a), ΓΚΜΚΓ (b), asymmetric ΓΚ (c) and ΚΚ (d) directions taken from monolayer graphene. The quasi-elastic lines have been subtracted.

Extended Data Fig. 8 Bubble plots for the phonon dispersion of monolayer graphene.

Each vertical pair of panels is labelled at the top by the sample material and the direction: in each of these vertical pairs, the top panel exhibits the plots obtained by line shape analysis of the measured spectra, and the bottom panel presents the plots obtained by simulation (DFPT). The directions are ΓΜΓΜ (top left), ΓΚΜΚΓ (top right), Γ → the third-closest Κ (bottom left) and ΚΚ (bottom right). The plot size (cross-section) corresponds to the intensity, which has been normalized by the highest peak at each measured or calculated q. In the ΓΜΓΜ line, LO modes (170–200 meV) are visible at the second Brillouin zone along with LA modes that show up throughout. In the ΓΚΜΚΓ direction, the TO mode is additionally seen at the second Brillouin zone along the KMK line for both experiment and simulation. In the low-symmetry line (Γ → the third-closest Κ), the TA mode shows up in the latter half of the second Brillouin zone. The dispersion along the ΚΚ direction that cuts across the second Brillouin zone shows the LO mode in the first half and the TO mode in the second half in the simulation, while this asymmetric behaviour is not clearly seen in the experiment. LA and TA modes are also activated weakly at the middle of the ΚΚ line in both experiment and simulation.

Extended Data Fig. 9 Momentum mapping of vibrations in graphite.

Shown are EELS spectra along two different directions: Γ → the third-closest Κ (‘Graphite asymmetric ΓK’; top four panels) and ΚΚ (‘Graphite ΚΚ’; bottom four panels). Within each group of four panels, the top two exhibit the intensity colour map (left) and bubble plots (right) obtained by line shape analysis of the measured spectra (Exp.): the bottom two present intensity colour maps and bubble plots obtained by the simulation (DFPT).

Extended Data Fig. 10 Position mapping of vibrations in monolayer graphene.

a, An STEM image of free-standing graphene; it has two-, three- and four-layer regions as well as a single-layer region (b). c, Typical EEL spectrum at q = 3.5 Å−1 taken from a clean single-layer region where 16 pixels are integrated. The phonon response there consists of two broad peaks: peak A (between 60 and 100 meV), which is related to the LA/ZO mode as well as the edge and sp^3 defect contributions; and peak B (at about 200 meV), which is related to the LO/TO mode. d, e, Corresponding position mappings of vibration modes A and B, respectively (dashed lines show information from b). The integration windows for the mappings are also shown by the light green and light blue stripes in c. f, Intensity profiles of vibration modes A and B along the orange line in a across the two impurity-decorated grain boundaries. The intensity of the LO/TO mode (B) is simply proportional to the layer number (the specimen thickness), while the lower-energy mode (A) clearly shows higher intensity at the edges of two- and four-layer regions. Interestingly, no obvious intensity enhancement can be seen at the edge of the single-layer region. In addition, we found intensity variations of the low-energy mode at grain boundaries, as shown in f, although their interpretation is more complicated because there must be contributions from different momentum transfers derived from domains with different orientations.

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- Received

17 December 2018

- Accepted

03 June 2019

- Published

12 August 2019

- Issue Date

12 September 2019

- DOI
https://doi.org/10.1038/s41586-019-1477-8

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- Letter

- Published: 11 September 2019

Anthropogenic biases in chemical reaction data hinder exploratory inorganic synthesis

Xiwen Jia[1],
Allyson Lynch[1],
Yuheng Huang[1],
Matthew Danielson[1],
Immaculate Lang’at[1],
Alexander Milder[1],
Aaron E. Ruby[1],
Hao Wang[1],
Sorelle A. Friedler[2],
Alexander J. Norquist[1] &
Joshua Schrier1,3

Naturevolume 573, pages251–255 (2019) | Download Citation

Subjects

- Cheminformatics
- Research data
- Scientific data
- Solid-state chemistry
- Chemical synthesis

Abstract

Most chemical experiments are planned by human scientists and therefore are subject to a variety of human cognitive biases[1], heuristics[2] and social influences[3]. These anthropogenic chemical reaction data are widely used to train machine-learning models[4] that are used to predict organic[5] and inorganic6,7 syntheses. However, it is known that societal biases are encoded in datasets and are perpetuated in machine-learning models[8]. Here we identify as-yet-unacknowledged anthropogenic biases in both the reagent choices and reaction conditions of chemical reaction datasets using a combination of data mining and experiments. We find that the amine choices in the reported crystal structures of hydrothermal synthesis of amine-templated metal oxides[9] follow a power-law distribution in which 17% of amine reactants occur in 79% of reported compounds, consistent with distributions in social influence models10,11,12. An analysis of unpublished historical laboratory notebook records shows similarly biased distributions of reaction condition choices. By performing 548 randomly generated experiments, we demonstrate that the popularity of reactants or the choices of reaction conditions are uncorrelated to the success of the reaction. We show that randomly generated experiments better illustrate the range of parameter choices that are compatible with crystal formation. Machine-learning models that we train on a smaller randomized reaction dataset outperform models trained on larger human-selected reaction datasets, demonstrating the importance of identifying and addressing anthropogenic biases in scientific data.

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Fig. 1: Occurrence of amines in structures of reported metal oxide crystals.

Fig. 2: Distribution of the choices of reaction parameters and reaction outcomes.

Fig. 3: Reaction outcomes from randomly generated experiments for popular amines and not-popular (unpopular and absent) amines.

Data availability

The authors declare that all data supporting the findings of this study are available within the article and its supplementary information.

Code availability

The code used for this project is available in the supplementary information files.

References

1.

Tversky, A. & Kahneman, D. Judgment under uncertainty: heuristics and biases. Science 185, 1124–1131 (1974).

- ADS
- CAS
- Article
- Google Scholar

2.

Gigerenzer, G. & Gaissmaier, W. Heuristic decision making. Annu. Rev. Psychol. 62, 451–482 (2011).

- Article

- Google Scholar

3.

Salganik, M. J., Dodds, P. S. & Watts, D. J. Experimental study of inequality and unpredictability in an artificial cultural market. Science 311, 854–856 (2006).

- ADS
- CAS
- Article
- Google Scholar

4.

Henson, A. B., Gromski, P. S. & Cronin, L. Designing algorithms to aid discovery by chemical robots. ACS Cent. Sci. 4, 793–804 (2018).

- CAS
- Article
- Google Scholar

5.

Coley, C. W., Green, W. H. & Jensen, K. F. Machine learning in computer-aided synthesis planning. Acc. Chem. Res. 51, 1281–1289 (2018).

- CAS
- Article
- Google Scholar

6.

Raccuglia, P. et al. Machine-learning-assisted materials discovery using failed experiments. Nature 533, 73–76 (2016).

- ADS
- CAS
- Article
- Google Scholar

7.

Kim, E. et al. Materials synthesis insights from scientific literature via text extraction and machine learning. Chem. Mater. 29, 9436–9444 (2017).

- CAS
- Article
- Google Scholar

8.

Caliskan, A., Bryson, J. J. & Narayanan, A. Semantics derived automatically from language corpora contain human-like biases. Science 356, 183–186 (2017).

- ADS
- CAS
- Article
- Google Scholar

9.

Cheetham, A. K., Férey, G. & Loiseau, T. Open-framework inorganic materials. Angew. Chem. 38, 3268–3292 (1999).

- CAS
- Article
- Google Scholar

10.

Price, D. D. S. A general theory of bibliometric and other cumulative advantage processes. J. Am. Soc. Inf. Sci. 27, 292–306 (1976).

- Article

- Google Scholar

11.

Candia, C., Jara-Figueroa, C., Rodriguez-Sickert, C., Barabási, A.-L. & Hidalgo, C. A. The universal decay of collective memory and attention. Nat. Hum. Behav. 3, 82–91 (2018).

- Article

- Google Scholar

12.

Carroll, H. A., Toumpakari, Z., Johnson, L. & Betts, J. A. The perceived feasibility of methods to reduce publication bias. PLoS One 12, e0186472 (2017).

- Article

- Google Scholar

13.

Fortunato, S. et al. Science of science. Science 359, (2018).

14.

Greenslade, P., Florentine, S. K., Hansen, B. D. & Gell, P. A. Biases encountered in long-term monitoring studies of invertebrates and microflora: Australian examples of protocols, personnel, tools and site location. Environ. Monit. Assess. 188, 491 (2016).

- Article

- Google Scholar

15.

Boobier, S., Osbourn, A. & Mitchell, J. B. O. Can human experts predict solubility better than computers? J. Cheminform. 9, 63 (2017).

- Article

- Google Scholar

16.

Keserű, G. M., Soós, T. & Kappe, C. O. Anthropogenic reaction parameters – the missing link between chemical intuition and the available chemical space. Chem. Soc. Rev. 43, 5387–5399 (2014).

- Article

- Google Scholar

17.

Varela, J. N., Lammoglia Cobo, M. F., Pawar, S. V. & Yadav, V. G. Cheminformatic analysis of antimalarial chemical space illuminates therapeutic mechanisms and offers strategies for therapy development. J. Chem. Inf. Model. 57, 2119–2131 (2017).

- CAS
- Article
- Google Scholar

18.

Zdrazil, B. & Guha, R. The rise and fall of a scaffold: a trend analysis of scaffolds in the medicinal chemistry literature. J. Med. Chem. 61, 4688–4703 (2018).

- CAS
- Article
- Google Scholar

19.

Cleves, A. E. & Jain, A. N. Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery. J. Comput. Aided Mol. Des. 22, 147–159 (2008).

- ADS
- CAS
- Article
- Google Scholar

20.

Jain, A. N. & Cleves, A. E. Does your model weigh the same as a duck? J. Comput. Aided Mol. Des. 26, 57–67 (2012).

- ADS
- Article
- Google Scholar

21.

Brown, D. G. & Boström, J. Analysis of past and present synthetic methodologies on medicinal chemistry: where have all the new reactions gone? J. Med. Chem. 59, 4443–4458 (2016).

- CAS
- Article
- Google Scholar

22.

Brown, D. G., Gagnon, M. M. & Boström, J. Understanding our love affair with p-chlorophenyl: present day implications from historical biases of reagent selection. J. Med. Chem. 58, 2390–2405 (2015).

- CAS
- Article
- Google Scholar

23.

Kirkwood, J., Hargreaves, D., O’Keefe, S. & Wilson, J. Analysis of crystallization data in the Protein Data Bank. Acta Crystallogr. F 71, 1228–1234 (2015).

- CAS
- Article
- Google Scholar

24.

Rijssenbeek, J. T., Rose, D. J., Haushalter, R. C. & Zubieta, J. Novel clusters of transition metals and main group oxides in the alkylamine/oxovanadium/borate system. Angew. Chem. 36, 1008–1010 (1997).

- CAS
- Article
- Google Scholar

25.

Duros, V. et al. Human versus robots in the discovery and crystallization of gigantic polyoxometalates. Angew. Chem. 56, 10815–10820 (2017).

- CAS
- Article
- Google Scholar

26.

Cao, B. et al. How to optimize materials and devices via design of experiments and machine learning: demonstration using organic photovoltaics. ACS Nano 12, 7434–7444 (2018).

- CAS
- Article
- Google Scholar

27.

Kahneman, D. & Klein, G. Conditions for intuitive expertise: a failure to disagree. Am. Psychol. 64, 515–526 (2009).

- Article

- Google Scholar

28.

Evans, D. W. et al. Human preferences for symmetry: subjective experience, cognitive conflict and cortical brain activity. PLoS One 7, e38966 (2012).

- ADS
- CAS
- Article
- Google Scholar

29.

Liu, Z. & Kersten, D. Three-dimensional symmetric shapes are discriminated more efficiently than asymmetric ones. J. Opt. Soc. Am. A 20, 1331–1340 (2003).

- ADS
- Article
- Google Scholar

30.

Falcon, A. Aristotle on causality. The Stanford Encyclopedia of Philosophy Spring 2019 edn (ed. Zalta, E. N.) https://plato.stanford.edu/archives/spr2019/entries/aristotle-causality (Stanford Univ., 2019).

31.

Menard, W. H. & Sharman, G. Scientific uses of random drilling models. Science 190, 337–343 (1975).

- ADS
- Article
- Google Scholar

32.

Menard, W. H. & Sharman, G. Random drilling. Science 192, 206–208 (1976).

- CAS
- Article
- Google Scholar

33.

McNally, A., Prier, C. K. & MacMillan, D. W. C. Discovery of an α-amino C–H arylation reaction using the strategy of accelerated serendipity. Science 334, 1114–1117 (2011).

- ADS
- CAS
- Article
- Google Scholar

34.

Biondo, A. E., Pluchino, A. & Rapisarda, A. The beneficial role of random strategies in social and financial systems. J. Stat. Phys. 151, 607–622 (2013).

- ADS
- MathSciNet
- Article
- Google Scholar

35.

Adler, P. et al. Auditing black-box models for indirect influence. Knowl. Inf. Syst. 54, 95–122 (2018).

- Article

- Google Scholar

36.

Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. The Cambridge Structural Database. Acta Crystallogr. B 72, 171–179 (2016).

- CAS
- Article
- Google Scholar

37.

Landrum, G. RDKit: open-source cheminformatics http://www.rdkit.org (2018).

38.

ChemAxon. JChem cxcalc 5.2.0. http://www.chemaxon.com (2018).

39.

Pedregosa, F. et al. Scikit-learn: machine learning in Python. J. Mach. Learn. Res. 12, 2825–2830 (2011).

- MathSciNet
- MATH
- Google Scholar

40.

Lundberg, S. M. & Lee, S.-I. A unified approach to interpreting model predictions. In 31st Conference on Neural Information Processing Systems (eds Guyon, I. et al.) 4765–4774 (Curran Associates, 2017).

41.

Lundberg, S. M. SHAP. (SHapley Additive exPlanations) https://github.com/slundberg/shap (2019).

42.

Scheidegger, C., Falk, C., Friedler, S., Venkatasubramanian, S. & Nix, T. BlackBoxAuditing https://github.com/algofairness/BlackBoxAuditing (2019).

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Acknowledgements

We thank G. Cattabriga for software engineering support and X. Weng for proofreading the experimental data entries. This project was funded by the National Science Foundation (award no. DMR-1709351). I.L. was partially supported by a Bryn Mawr College LILAC Summer Internship Funding Program. J.S. acknowledges the Henry Dreyfus Teacher-Scholar Award (TH-14-010).

Author information

Affiliations

1. Department of Chemistry, Haverford College, Haverford, PA, USA

- Xiwen Jia
- , Allyson Lynch
- , Yuheng Huang
- , Matthew Danielson
- , Immaculate Lang’at
- , Alexander Milder
- , Aaron E. Ruby
- , Hao Wang
- , Alexander J. Norquist
- & Joshua Schrier

2. Department of Computer Science, Haverford College, Haverford, PA, USA

- Sorelle A. Friedler

3. Department of Chemistry, Fordham University, The Bronx, New York, NY, USA

- Joshua Schrier

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Contributions

J.S. and A.J.N. conceived the project. A.R., H.W., X.J., and A.M. devised and performed the human-selected reactions, supervised by A.J.N. X.J. and A.M. collected historical notebook data, supervised by A.J.N; A.J.N and X.J. extracted the appropriate structures. A.L., I.L. and J.S. determined the amine counts from these structures. J.S. generated the random reactions. O.H., X.J., M.D. and A.M. performed the randomly generated and test set reactions, supervised by A.J.N. Statistical analysis was performed by A.L. and J.S. S.A.F. performed model construction and analysis. S.A.F., J.S. and A.J.N. performed and interpreted the feature influence analysis calculations. J.S., A.J.N and S.A.F. wrote the paper. All authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence to Sorelle A. Friedler or Alexander J. Norquist or Joshua Schrier.

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The authors declare no competing interests.

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Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Peer review information Nature thanks Leroy Cronin, Edward Kim and Hans Conrad Zur Loye for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Fig. 1 Cambridge Structural Database (CSD) search results for templated metals borates.

a, A plot of the number of unique structures for each amine, ordered from the amine with the fewest structures to the most. b, A plot of cumulative probability versus amine proportion. The grey rectangle represents the Pareto split.

Extended Data Fig. 2 Amine price and availability.

a, Amine price versus quantity for the randomized reaction amines. The data are separated by amine popularity (popular, unpopular or absent). Amines used in the test set experiments are also included. b, Amine pricing information for those used in the randomized reactions. The price per gram was calculated assuming amine densities of 1 g ml−1. The data presented in the figures above suggest that there is no systematic difference in amine prices between the popular, unpopular and absent amines. Additionally, the distribution of amine pricing for the test set amines is similar to the other distributions, suggesting a representative sample of amines.

Extended Data Fig. 3 Outcome probabilities for not-popular, unpopular and absent organic amines.

The not-popular set includes the unpopular and absent amines.

Extended Data Fig. 4 Average nearest-neighbour distances in the datasets, and nearest-neighbour choices on model performance.

a, Average distances to the kth nearest neighbour within each training set. b, Average distances from each training set to the kth nearest neighbour within the test set. c, AUC for the kth nearest neighbour classifier for k = 1 to 100.

Extended Data Fig. 5 Comparison of the influence of direct and indirect features.

a, Direct influence values of descriptors in the human reaction test set versus the random reaction test set. b, Indirect influence values of descriptors in the human reaction test set versus the random reaction test set.

Extended Data Table 1 Structure inclusion and exclusion criteria

Full size table

Extended Data Table 2 Matthews correlation coefficient (MCC), accuracy and AUC results for each machine-learning algorithm, trained on either the human-selected or randomly generated reaction data using all features

Full size table

Extended Data Table 3 Feature selection comparison

Full size table

Extended Data Table 4 Comparison of discrepancies between model predictions and reaction outcomes

Full size table

Supplementary information

Supplementary Information

The Supplementary Information document contains two figures and 21 tables, and a manifest describing the content of the electronic supplementary information file below.

Supplementary Data

The Supplementary Information zip file contains all experimental and computational data, and computational codes used for this study. A manifest is contained in the Supplementary Information document file.

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- Received

30 December 2018

- Accepted

10 July 2019

- Published

11 September 2019

- Issue Date

12 September 2019

- DOI
https://doi.org/10.1038/s41586-019-1540-5

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- Letter

- Published: 02 September 2019

Mediterranean winter rainfall in phase with African monsoons during the past 1.36 million years

Bernd Wagner[1] na1,
Hendrik Vogel[2] na1,
Alexander Francke1,3,
Tobias Friedrich[4],
Timme Donders[5],
Jack H. Lacey[6],
Melanie J. Leng6,7,
Eleonora Regattieri8,9,
Laura Sadori[10],
Thomas Wilke[11],
Giovanni Zanchetta[8],
Christian Albrecht[11],
Adele Bertini[12],
Nathalie Combourieu-Nebout[13],
Aleksandra Cvetkoska5,11,
Biagio Giaccio[14],
Andon Grazhdani[15],
Torsten Hauffe[11],
Jens Holtvoeth[16],
Sebastien Joannin[17],
Elena Jovanovska[11],
Janna Just1,18,
Katerina Kouli[19],
Ilias Kousis[20],
Andreas Koutsodendris[20],
Sebastian Krastel[21],
Markus Lagos[22],
Niklas Leicher[1],
Zlatko Levkov[23],
Katja Lindhorst[21],
Alessia Masi[10],
Martin Melles[1],
Anna M. Mercuri[24],
Sebastien Nomade[25],
Norbert Nowaczyk[26],
Konstantinos Panagiotopoulos[1],
Odile Peyron[17],
Jane M. Reed[27],
Leonardo Sagnotti[28],
Gaia Sinopoli[10],
Björn Stelbrink[11],
Roberto Sulpizio29,30,
Axel Timmermann31,32,
Slavica Tofilovska[22],
Paola Torri[24],
Friederike Wagner-Cremer[5],
Thomas Wonik[33] &
Xiaosen Zhang[34]

Naturevolume 573, pages256–260 (2019) | Download Citation

Subjects

- Atmospheric dynamics
- Climate change
- Palaeoclimate

Abstract

Mediterranean climates are characterized by strong seasonal contrasts between dry summers and wet winters. Changes in winter rainfall are critical for regional socioeconomic development, but are difficult to simulate accurately[1] and reconstruct on Quaternary timescales. This is partly because regional hydroclimate records that cover multiple glacial–interglacial cycles2,3 with different orbital geometries, global ice volume and atmospheric greenhouse gas concentrations are scarce. Moreover, the underlying mechanisms of change and their persistence remain unexplored. Here we show that, over the past 1.36 million years, wet winters in the northcentral Mediterranean tend to occur with high contrasts in local, seasonal insolation and a vigorous African summer monsoon. Our proxy time series from Lake Ohrid on the Balkan Peninsula, together with a 784,000-year transient climate model hindcast, suggest that increased sea surface temperatures amplify local cyclone development and refuel North Atlantic low-pressure systems that enter the Mediterranean during phases of low continental ice volume and high concentrations of atmospheric greenhouse gases. A comparison with modern reanalysis data shows that current drivers of the amount of rainfall in the Mediterranean share some similarities to those that drive the reconstructed increases in precipitation. Our data cover multiple insolation maxima and are therefore an important benchmark for testing climate model performance.

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Fig. 1: Chronology and location of the Lake Ohrid DEEP site record.

Fig. 2: Lake Ohrid precipitation indicators and global monsoon records for the past 1.4 Myr.

Fig. 3: Simulated Lake Ohrid precipitation and atmospheric anomaly pattern associated with precipitation maxima.

Data availability

Data are available from the Pangaea database (https://doi.pangaea.de/10.1594/PANGAEA.896848); links to the individual datasets are provided within this dataset. Data used for LOVECLIM are available at https://climatedata.ibs.re.kr/grav/data/loveclim-784k. Additional data are available upon request made to T.F. (tobiasf@hawaii.edu).

Code availability

Model data produced by the LOVECLIM simulations are available through the data centre of the IBS Center for Climate Physics (https://climatedata.ibs.re.kr/grav/data/loveclim-784k).

References

1.

IPCC. Climate Change 2013: The Physical Science Basis (eds Stocker, T. F. et al.) (Cambridge Univ. Press, 2013).

2.

Kutzbach, J. E., Chen, G., Cheng, H., Edwards, R. & Liu, Z. Potential role of winter rainfall in explaining increased moisture in the Mediterranean and Middle East during periods of maximum orbitally-forced insolation seasonality. Clim. Dyn. 42, 1079–1095 (2014).

- Google Scholar

3.

Tzedakis, P. C., Hooghiemstra, H. & Pälike, H. The last 1.35 million years at Tenaghi Philippon, revised chronostratigraphy and long-term vegetation trends. Quat. Sci. Rev. 25, 3416–3430 (2006).

- ADS

- Google Scholar

4.

Hoerling, M. et al. On the increased frequency of Mediterranean drought. J. Clim. 25, 2146–2161 (2012).

- ADS

- Google Scholar

5.

Weisheimer, A. & Palmer, T. N. On the reliability of seasonal climate forecasts. J. R. Soc. Interface 11, 20131162 (2014).

- CAS
- PubMed
- PubMed Central
- Google Scholar

6.

Totz, S., Tziperman, E., Coumou, D., Pfeiffer, K. & Cohen, J. Winter precipitation forecast in the European and Mediterranean regions using cluster analysis. Geophys. Res. Lett. 44, 12,418–12,426 (2017).

- Google Scholar

7.

Milner, A. M. et al. Enhanced seasonality of precipitation in the Mediterranean during the early part of the Last Interglacial. Geology 40, 919–922 (2012).

- ADS

- Google Scholar

8.

Toucanne, S. et al. Tracking rainfall in the northern Mediterranean borderlands during sapropel deposition. Quat. Sci. Rev. 129, 178–195 (2015).

- ADS

- Google Scholar

9.

Stockhecke, M. et al. Millennial to orbital-scale variations of drought intensity in the eastern Mediterranean. Quat. Sci. Rev. 133, 77–95 (2016).

- ADS

- Google Scholar

10.

Roberts, N. et al. Stable isotope records of Late Quaternary climate and hydrology from Mediterranean lakes: the ISOMED synthesis. Quat. Sci. Rev. 27, 2426–2441 (2008).

- ADS

- Google Scholar

11.

Magny, M. et al. North–south palaeohydrological contrasts in the central Mediterranean during the Holocene: tentative synthesis and working hypotheses. Clim. Past 9, 2043–2071 (2013).

- Google Scholar

12.

Emeis, K.-C., Camerlenghi, A., McKenzie, J. A., Rio, D. & Sprovieri, R. The occurrence and significance of Pleistocene and Upper Pliocene sapropels in the Tyrrhenian Sea. Mar. Geol. 100, 155–182 (1991).

- ADS
- CAS
- Google Scholar

13.

Kroon, D. et al. Oxygen isotope and sapropel stratigraphy in the Eastern Mediterranean during the last 3.2 million years. In Proc. Ocean Drilling Program, Scientific Results Vol. 160 (eds Robertson, A. H. F. et al.) 181−190 (1998).

14.

Rossignol-Strick, M. Mediterranean Quaternary sapropels, an immediate response of the African monsoon to variation of insolation. Palaeogeogr. Palaeoclimatol. Palaeoecol. 49, 237–263 (1985).

- Google Scholar

15.

Rohling, E. J., Marino, G. & Grant, K. M. Mediterranean climate and oceanography, and the periodic development of anoxic events (sapropels). Earth Sci. Rev. 143, 62–97 (2015).

- CAS

- Google Scholar

16.

Tzedakis, P. C. Seven ambiguities in the Mediterranean palaeoenvironmental narrative. Quat. Sci. Rev. 26, 2042–2066 (2007).

- ADS

- Google Scholar

17.

Bosmans, J. H. C. et al. Precession and obliquity forcing of the freshwater budget over the Mediterranean. Quat. Sci. Rev. 123, 16–30 (2015).

- ADS

- Google Scholar

18.

Wagner, B. et al. The environmental and evolutionary history of Lake Ohrid (FYROM/Albania): interim results from the SCOPSCO deep drilling project. Biogeosciences 14, 2033–2054 (2017).

- ADS

- Google Scholar

19.

Vogel, H., Wagner, B., Zanchetta, G., Sulpizio, R. & Rosén, P. A paleoclimate record with tephrochronological age control for the last glacial–interglacial cycle from Lake Ohrid, Albania and Macedonia. J. Paleolimnol. 44, 295–310 (2010).

- ADS

- Google Scholar

20.

Francke, A. et al. Sedimentological processes and environmental variability at Lake Ohrid (Macedonia, Albania) between 637 ka and the present. Biogeosciences 13, 1179–1196 (2016).

- ADS
- CAS
- Google Scholar

21.

Forner, A. et al. Extreme droughts affecting Mediterranean tree species’ growth and water-use efficiency: the importance of timing. Tree Physiol. 38, 1127–1137 (2018).

- PubMed

- Google Scholar

22.

Friedrich, T., Timmermann, A., Tigchelaar, M., Elison Timm, O. & Ganopolski, A. Nonlinear climate sensitivity and its implications for future greenhouse warming. Sci. Adv. 2, e1501923 (2016).

- ADS
- PubMed
- PubMed Central
- Google Scholar

23.

Timmermann, A. & Friedrich, T. Late Pleistocene climate drivers of early human migration. Nature 538, 92–95 (2016).

- ADS
- CAS
- PubMed
- Google Scholar

24.

Lisiecki, L. E. & Raymo, M. E. A Pliocene–Pleistocene stack of 57 globally distributed benthic δ^18O records. Paleoceanography 20, PA1003 (2005).

- ADS

- Google Scholar

25.

Cheng, H. et al. The Asian monsoon over the past 640,000 years and ice age terminations. Nature 534, 640–646 (2016).

- ADS
- CAS
- PubMed
- Google Scholar

26.

Konijnendijk, T. Y. M., Ziegler, M. & Lourens, L. J. Chronological constraints on Pleistocene sapropel depositions from high-resolution geochemical records of ODP sites 967 and 968. Newsl. Stratigr. 47, 263–282 (2014).

- Google Scholar

27.

Colleoni, F., Masina, S., Negri, A. & Marzocchi, A. Plio–Pleistocene high–low latitude climate interplay: a Mediterranean point of view. Earth Planet. Sci. Lett. 319–320, 35–44 (2012).

- ADS

- Google Scholar

28.

Martrat, B., Jimenez-Amat, P., Zahn, R. & Grimalt, J. O. Similarities and dissimilarities between the last two deglaciations and interglaciations in the North Atlantic region. Quat. Sci. Rev. 99, 122–134 (2014).

- ADS

- Google Scholar

29.

Trigo, R. M., Osborne, T. J. & Corte-Real, J. M. The North Atlantic Oscillation influence on Europe: climate impacts and associated physical mechanisms. Clim. Res. 20, 9–17 (2002).

- Google Scholar

30.

Laskar, J. et al. A long-term numerical solution for the insolation quantities of the Earth. Astron. Astrophys. 428, 261–285 (2004).

- ADS

- Google Scholar

31.

Popovska, C. & Bonacci, O. Basic data on the hydrology of Lakes Ohrid and Prespa. Hydrol. Processes 21, 658–664 (2007).

- ADS

- Google Scholar

32.

Matzinger, A., Spirkovski, Z., Patceva, S. & Wüest, A. Sensitivity of ancient Lake Ohrid to local anthropogenic impacts and global warming. J. Great Lakes Res. 32, 158–179 (2006).

- Google Scholar

33.

Wagner, B. et al. The SCOPSCO drilling project recovers more than 1.2 million years of history from Lake Ohrid. Sci. Drill. 17, 19–29 (2014).

- Google Scholar

34.

Farmer, V. C. (ed.) The Infrared Spectra of Minerals (Adlard & Son, 1974).

35.

Chukanov, N. V. Infrared Spectra of Mineral Species (Springer, 2014).

36.

Sadori, L. et al. Pollen-based paleoenvironmental and paleoclimatic change at Lake Ohrid (south-eastern Europe) during the past 500 ka. Biogeosciences 13, 1423–1437 (2016).

- ADS
- CAS
- Google Scholar

37.

Beug, H.-J. Leitfaden der Pollenbestimmung für Mitteleuropa und angrenzende Gebiete (Friedrich Pfeil, 2004).

38.

Cheddadi, R. et al. Imprints of glacial refugia in the modern genetic diversity of Pinus sylvestris. Glob. Ecol. Biogeogr. 15, 271–282 (2006).

- Google Scholar

39.

Rossignol-Strick, M. The Holocene climatic optimum and pollen records of sapropel 1 in the Eastern Mediterranean, 9000–6000 BP. Quat. Sci. Rev. 18, 515–530 (1999).

- ADS

- Google Scholar

40.

Langgut, D., Almogi-Labin, A., Bar-Matthews, M. & Weinstein-Evron, M. Vegetation and climate changes in the South Eastern Mediterranean during the Last Glacial–Interglacial cycle (86 ka): new marine pollen record. Quat. Sci. Rev. 30, 3960–3972 (2011).

- ADS

- Google Scholar

41.

Combourieu-Nebout, N. et al. Climate changes in the central Mediterranean and Italian vegetation dynamics since the Pliocene. Rev. Palaeobot. Palynol. 218, 127–147 (2015).

- Google Scholar

42.

Lacey, J. H. et al. Northern Mediterranean climate since the Middle Pleistocene: a 637 ka stable isotope record from Lake Ohrid (Albania/Macedonia). Biogeosciences 13, 1801–1820 (2016).

- ADS
- CAS
- Google Scholar

43.

Just, J. et al. Environmental control on the occurrence of high-coercivity magnetic minerals and formation of iron sulfides in a 640 ka sediment sequence from Lake Ohrid (Balkans). Biogeosciences 13, 2093–2109 (2016).

- ADS
- CAS
- Google Scholar

44.

Leicher, N. et al. First tephrostratigraphic results of the DEEP site record from Lake Ohrid (Macedonia and Albania). Biogeosciences 13, 2151–2178 (2016).

- ADS

- Google Scholar

45.

Kousis, I. et al. Centennial-scale vegetation dynamics and climate variability in SE Europe during Marine Isotope Stage 11 based on a pollen record from Lake Ohrid. Quat. Sci. Rev. 190, 20–38 (2018).

- ADS

- Google Scholar

46.

Francke, A. et al. Sediment residence time reveals Holocene shift from climatic to vegetation control on catchment erosion in the Balkans. Global Planet. Change 177, 186–200 (2019).

- ADS

- Google Scholar

47.

Niespolo, E. M., Rutte, D., Deino, A. L. & Renne, P. R. Intercalibration and age of the Alder Creek sanidine 40Ar/39Ar standard. Quat. Geochronol. 39, 205–213 (2017).

- Google Scholar

48.

Renne, P. R., Balco, G., Ludwig, K. R., Mundil, R. & Min, K. Response to the comment by W. H. Schwarz et al. on “Joint determination of 40K decay constants and 40Ar*/40K for the Fish Canyon sanidine standard, and improved accuracy for 40Ar/39Ar geochronology” by P. R. Renne et al. (2010). Geochim. Cosmochim. Acta 75, 5097–5100 (2011).

- ADS
- CAS
- Google Scholar

49.

Lee, J. Y. et al. A redetermination of the isotopic abundances of atmospheric Ar. Geochim. Cosmochim. Acta 70, 4507–4512 (2006).

- ADS
- CAS
- Google Scholar

50.

Giaccio, B. et al. Revised chronology of the Sulmona lacustrine succession, central Italy. J. Quat. Sci. 28, 545–551 (2013).

- Google Scholar

51.

Giaccio, B. et al. Tephra layers from Holocene lake sediments of the Sulmona Basin, central Italy: implications for volcanic activity in peninsular Italy and tephrostratigraphy in the central Mediterranean area. Quat. Sci. Rev. 28, 2710–2733 (2009).

- ADS

- Google Scholar

52.

Petrosino, P. et al. The Montalbano Jonico marine succession: an archive for distal tephra layers at the early–middle Pleistocene boundary in southern Italy. Quat. Int. 383, 89–103 (2015).

- Google Scholar

53.

Ciaranfi, N. et al. Integrated stratigraphy and astronomical tuning of lower–middle Pleistocene Montalbano Jonico section (Southern Italy). Quat. Int. 219, 109–120 (2010).

- Google Scholar

54.

Massari, F. et al. Interplay between tectonics and glacio-eustasy: Pleistocene succession of the Crotone basin, Calabria (southern Italy). Geol. Soc. Am. Bull. 114, 1183–1209 (2002).

- ADS

- Google Scholar

55.

Capraro, L. et al. Climatic patterns revealed by pollen and oxygen isotope records across the Matuyama–Brunhes boundary in the central Mediterranean (southern Italy). Geol. Soc. Lond. Spec. Publ. 247, 159–182 (2005).

- ADS

- Google Scholar

56.

Capraro, L. et al. Chronology of the lower–middle Pleistocene succession of the south-western part of the Crotone basin (Calabria, southern Italy). Quat. Sci. Rev. 30, 1185–1200 (2011).

- ADS

- Google Scholar

57.

Giaccio, B. et al. Duration and dynamics of the best orbital analogue to the present interglacial. Geology 43, 603–606 (2015).

- ADS

- Google Scholar

58.

Sagnotti, L. et al. Extremely rapid directional change during Matuyama–Brunhes geomagnetic polarity reversal. Geophys. J. Int. 199, 1110–1124 (2014).

- ADS

- Google Scholar

59.

Sagnotti, L. et al. How fast was the Matuyama–Brunhes geomagnetic reversal? A new subcentennial record from the Sulmona basin, central Italy. Geophys. J. Int. 204, 798–812 (2016).

- ADS

- Google Scholar

60.

Simon, Q. et al. Authigenic 10Be/9Be ratio signature of the Matuyama–Brunhes boundary in the Montalbano Jonico marine succession. Earth Planet. Sci. Lett. 460, 255–267 (2017).

- ADS
- CAS
- Google Scholar

61.

Rio, D. et al. Reading Pleistocene eustasy in a tectonically active siliciclastic shelf setting (Crotone peninsula, southern Italy). Geology 24, 743–746 (1996).

- ADS
- CAS
- Google Scholar

62.

Macrì, P., Capraro, L., Ferretti, P. & Scarponi, D. A high-resolution record of the Matuyama–Brunhes transition from the Mediterranean region: the Valle di Manche section (Calabria, Southern Italy). Phys. Earth Planet. Inter. 278, 1–15 (2018).

- ADS

- Google Scholar

63.

Giaccio, B., Hajdas, I., Isaia, R., Deino, A. & Nomade, S. High-precision 14C and 40Ar/39Ar dating of the Campanian Ignimbrite (Y-5) reconciles the time-scales of climatic–cultural processes at 40 ka. Sci. Rep. 7, 45940 (2017).

- ADS
- CAS
- PubMed
- PubMed Central
- Google Scholar

64.

Regattieri, E. et al. A Last Interglacial record of environmental changes from the Sulmona basin (central Italy). Palaeogeogr. Palaeoclimatol. Palaeoecol. 472, 51–66 (2017).

- Google Scholar

65.

Giaccio, B. et al. First integrated tephrochronological record for the last ~190 kyr from the Fucino Quaternary lacustrine succession, central Italy. Quat. Sci. Rev. 158, 211–234 (2017).

- ADS

- Google Scholar

66.

Laurenzi, M. A. & Villa, I. 40Ar/39Ar chronostratigraphy of Vico ignimbrites. Period. Mineral. 56, 285–293 (1987).

- Google Scholar

67.

Karner, D. B., Marra, F. & Renne, P. R. The history of the Monti Sabatini and Alban Hills volcanoes: groundwork for assessing volcanic–tectonic hazards for Rome. J. Volcanol. Geotherm. Res. 107, 185–219 (2001).

- ADS
- CAS
- Google Scholar

68.

Mercer, C. M. & Hodges, K. V. ArAR — a software tool to promote the robust comparison of K–Ar and 40Ar/39Ar dates published using different decay, isotopic, and monitor-age parameters. Chem. Geol. 440, 148–163 (2016).

- ADS
- CAS
- Google Scholar

69.

Blaauw, M. & Christen, J. A. Flexible paleoclimate age–depth models using an autoregressive gamma process. Bayesian Anal. 6, 457–474 (2011).

- MathSciNet
- MATH
- Google Scholar

70.

Grant, K. M. et al. Rapid coupling between ice volume and polar temperature over the past 150,000 years. Nature 491, 744–747 (2012).

- ADS
- CAS
- PubMed
- Google Scholar

71.

Bar-Matthews, M., Ayalon, A., Gilmour, M., Matthews, A. & Hawkesworth, C. J. Sea-land oxygen isotopic relationships from planktonic foraminifera and speleothems in the eastern Mediterranean region and their implication for paleorainfall during interglacial intervals. Geochim. Cosmochim. Acta 67, 3181–3199 (2003).

- ADS
- CAS
- Google Scholar

72.

Goosse, H. et al. Description of the Earth system model of intermediate complexity LOVECLIM version 1.2. Geosci. Model Dev. 3, 603–633 (2010).

- ADS

- Google Scholar

73.

Opsteegh, J. D., Haarsma, R. J., Selten, F. M. & Kattenberg, A. ECBILT: a dynamic alternative to mixed boundary conditions in ocean models. Tellus A Dyn. Meterol. Oceanogr. 50, 348–367 (1998).

- Google Scholar

74.

Goosse, H. & Fichefet, T. Importance of ice–ocean interactions for the global ocean circulation: a model study. J. Geophys. Res. 104, 23337–23355 (1999).

- ADS

- Google Scholar

75.

Brovkin, V., Ganopolski, A. & Svirezhev, Y. A continuous climate–vegetation classification for use in climate–biosphere studies. Ecol. Modell. 101, 251–261 (1997).

- Google Scholar

76.

Timmermann, A. et al. Modeling obliquity and CO_2 effects on Southern Hemisphere climate during the past 408 ka. J. Clim. 27, 1863–1875 (2014).

- ADS

- Google Scholar

77.

Berger, A. Long-term variations of daily insolation and Quaternary climate change. J. Atmos. Sci. 35, 2362–2367 (1978).

- ADS

- Google Scholar

78.

Lüthi, D. et al. High-resolution carbon dioxide concentration record 650,000–800,000 years before present. Nature 453, 379–382 (2008).

- ADS
- PubMed
- Google Scholar

79.

EPICA community members. Eight glacial cycles from an Antarctic ice core. Nature 429, 623–628 (2004).

- Google Scholar

80.

Ganopolski, A. & Calov, R. The role of orbital forcing, carbon dioxide and regolith in 100 kyr glacial cycles. Clim. Past 7, 1415–1425 (2011).

- Google Scholar

81.

Hammer, O. Paleontological Statistics (PAST) version 3.21 reference manual. https://folk.uio.no/ohammer/past/ (2018).

82.

Torrence, C. & Compo, G. P. A practical guide to wavelet analysis. Bull. Am. Meteorol. Soc. 79, 61–78 (1998).

- ADS

- Google Scholar

83.

Wagner, B. et al. The last 40 ka tephrostratigraphic record of Lake Ohrid, Albania and Macedonia: a very distal archive for ash dispersal from Italian volcanoes. J. Volcanol. Geotherm. Res. 177, 71–80 (2008).

- ADS
- CAS
- Google Scholar

84.

Zanchetta, G. et al. Tephrostratigraphy, chronology and climatic events of the Mediterranean basin during the Holocene: an overview. Holocene 21, 33–52 (2011).

- ADS

- Google Scholar

85.

Siani, G., Sulpizio, R., Paterne, M. & Sbrana, A. Tephrostratigraphy study for the last 18,000 14C years in a deep-sea sediment sequence for the South Adriatic. Quat. Sci. Rev. 23, 2485–2500 (2004).

- ADS

- Google Scholar

86.

Albert, P. G. et al. Revisiting the Y-3 tephrostratigraphic marker: a new diagnostic glass geochemistry, age estimate, and details on its climatostratigraphical context. Quat. Sci. Rev. 118, 105–121 (2015).

- ADS

- Google Scholar

87.

Satow, C. et al. A new contribution to the Late Quaternary tephrostratigraphy of the Mediterranean: Aegean Sea core LC21. Quat. Sci. Rev. 117, 96–112 (2015).

- ADS

- Google Scholar

88.

Giaccio, B. et al. Isotopic (Sr–Nd) and major element fingerprinting of distal tephras: an application to the middle–late Pleistocene markers from the Colli Albani volcano, central Italy. Quat. Sci. Rev. 67, 190–206 (2013).

- ADS

- Google Scholar

89.

Petrosino, P., Jicha, B. R., Mazzeo, F. C. & Russo Ermolli, E. A high resolution tephrochronological record of MIS 14–12 in the Southern Apennines (Acerno basin, Italy). J. Volcanol. Geotherm. Res. 274, 34–50 (2014).

- ADS
- CAS
- Google Scholar

90.

Marra, F., Karner, D. B., Freda, C., Gaeta, M. & Renne, P. Large mafic eruptions at Alban Hills Volcanic District (central Italy): chronostratigraphy, petrography and eruptive behavior. J. Volcanol. Geotherm. Res. 179, 217–232 (2009).

- ADS
- CAS
- Google Scholar

91.

Lindhorst, K. et al. Sedimentary and tectonic evolution of Lake Ohrid (Macedonia/Albania). Basin Res. 27, 84–101 (2015).

- ADS

- Google Scholar

92.

Le Bas, M. J., Le Maitre, R. W., Streckeisen, A., Zanettin, B. & IUGS Subcommission on the Systematics of Igneous Rocks. A chemical classification of volcanic rocks based on the total alkali-silica diagram. J. Petrol. 27, 745–750 (1986).

- ADS

- Google Scholar

93.

Melard, G. Algorithm AS 197: a fast algorithm for the exact likelihood of autoregressive-moving average models. Appl. Stat. 33, 104–114 (1984).

- MATH

- Google Scholar

94.

Zanchetta, G. et al. Aligning and synchronization of MIS5 proxy records from Lake Ohrid (FYROM) with independently dated Mediterranean archives: implications for DEEP core chronology. Biogeosciences 13, 2757–2768 (2016).

- ADS

- Google Scholar

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Acknowledgements

The Hydrobiological Institute in Ohrid (S. Trajanovski and G. Kostoski) and the Hydrometeorological Institute in Tirana (M. Sanxhaku and B. Lushaj) provided logistic support for site surveys and the scientific drilling campaign. Drilling was carried out by Drilling, Observation and Sampling of the Earth’s Continental Crust (DOSECC). A. Skinner provided logistic and technical advice before and during the drilling operation. The Scientific Collaboration on Past Speciation Conditions in Lake Ohrid (SCOPSCO) drilling project was funded by the International Continental Scientific Drilling Program (ICDP), the German Ministry of Higher Education and Research, the German Research Foundation, the University of Cologne, the British Geological Survey, the INGV and CNR (both Italy), and the governments of the republics of North Macedonia and Albania. V. Scao collected the V5 tephra, which was 40Ar/39Ar dated with funding from the LEFE ‘INTERMED’ grant (CNRS-INSU) to S.N.

Author information

Author notes

1. These authors contributed equally: Bernd Wagner, Hendrik Vogel.

Affiliations

Institute of Geology and Mineralogy, University of Cologne, Cologne, Germany

- Bernd Wagner
- , Alexander Francke
- , Janna Just
- , Niklas Leicher
- , Martin Melles
- & Konstantinos Panagiotopoulos

Institute of Geological Sciences & Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland

- Hendrik Vogel

School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia

- Alexander Francke

International Pacific Research Center, University of Hawai‘i at Mānoa, Honolulu, HI, USA

- Tobias Friedrich

Palaeoecology, Department of Physical Geography, Utrecht University, Utrecht, The Netherlands

- Timme Donders
- , Aleksandra Cvetkoska
- & Friederike Wagner-Cremer

National Environmental Isotope Facility, British Geological Survey, Nottingham, UK

- Jack H. Lacey

- & Melanie J. Leng

Centre for Environmental Geochemistry, School of Biosciences, University of Nottingham, Nottingham, UK

- Melanie J. Leng

Dipartimento di Scienze della Terra, University of Pisa, Pisa, Italy

- Eleonora Regattieri

- & Giovanni Zanchetta

Institute of Earth Sciences and Earth Resources-Italian National Research Council (IGG-CNR), Pisa, Italy

- Eleonora Regattieri

Dipartimento di Biologia Ambientale, Università di Roma ‘La Sapienza’, Rome, Italy

- Laura Sadori
- , Alessia Masi
- & Gaia Sinopoli

Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany

- Thomas Wilke
- , Christian Albrecht
- , Aleksandra Cvetkoska
- , Torsten Hauffe
- , Elena Jovanovska
- & Björn Stelbrink

Dipartimento di Scienze della Terra, Università di Firenze, Florence, Italy

- Adele Bertini

Institut de Paléontologie Humaine, Muséum National d’Histoire Naturelle, CNRS UMR 7194, Paris, France

- Nathalie Combourieu-Nebout

Istituto di Geologia Ambientale e Geoingegneria – CNR, Rome, Italy

- Biagio Giaccio

Faculty of Geology and Mineralogy, University of Tirana, Tirana, Albania

- Andon Grazhdani

School of Chemistry, University of Bristol, Bristol, UK

- Jens Holtvoeth

Institut des Sciences de l’Evolution de Montpellier, Université de Montpellier, CNRS UMR 5554, Montpellier, France

- Sebastien Joannin

- & Odile Peyron

Fachbereich Geowissenschaften, Universität Bremen, Bremen, Germany

- Janna Just

Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece

- Katerina Kouli

Paleoenvironmental Dynamics Group, Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany

- Ilias Kousis

- & Andreas Koutsodendris

Institute of Geosciences, Christian-Albrechts-Universität zu Kiel, Kiel, Germany

- Sebastian Krastel

- & Katja Lindhorst

Institute of Geosciences and Meteorology, University of Bonn, Bonn, Germany

- Markus Lagos

- & Slavica Tofilovska

Institute of Biology, University Ss Cyril and Methodius, Skopje, North Macedonia

- Zlatko Levkov

Laboratorio di Palinologia e Paleobotanica, Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy

- Anna M. Mercuri

- & Paola Torri

Laboratoire des Sciences du Climat et de l’Environnement, Université Paris-Saclay, CEA/CNRS/UVSQ UMR 8212, Gif-Sur-Yvette, France

- Sebastien Nomade

Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, Potsdam, Germany

- Norbert Nowaczyk

Department of Geography, Geology and Environment, University of Hull, Hull, UK

- Jane M. Reed

Istituto Nazionale di Geofisica e Vulcanologia, Rome, Italy

- Leonardo Sagnotti

Dipartimento di Scienze della Terra e Geoambientali, University of Bari, Bari, Italy

- Roberto Sulpizio

IDPA-CNR, Milan, Italy

- Roberto Sulpizio

Center for Climate Physics, Institute for Basic Science, Busan, South Korea

- Axel Timmermann

Pusan National University, Busan, South Korea

- Axel Timmermann

Leibniz Institute for Applied Geophysics (LIAG), Hannover, Germany

- Thomas Wonik

Institute of Loess Plateau, Shanxi University, Taiyuan, China

- Xiaosen Zhang

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Contributions

B.W. and H.V. designed the study. B.W. initiated and coordinated the SCOPSCO drilling project and drilling campaign. H.V. conceived major scientific ideas for this study. A.F. (sedimentology, chronology), T.F. (LOVECLIM modelling), T.D. (palynology), J.H.L. (isotope geochemistry) and L. Sadori (palynology) contributed and oversaw key datasets used in the study and coordinated the discussion and interpretations of proxy data groups and model results together with F.W.-C., M.J.L., E.R., T. Wilke and G.Z. Specific data were provided by A.B. (pollen, MIS 19–21, MIS 25–28, MIS 42–43), N.C.-N. (pollen, MIS 1–4, MIS 8, MIS 14–15), B.G. (tephrostratigraphy), S.J. (pollen, MIS 1–4, MIS 13–16, MIS 30), J.J. (palaeomagnetic data), K.K. (pollen, MIS 6–8, MIS 10, MIS 16–19, MIS 28–30, MIS 33), I.K. (pollen, MIS 11–12, MIS 15), A.K. (pollen, MIS 11–12, MIS 15), M.L. (trace elements), N.L. (tephrostratigraphy), A.M. (pollen, MIS 5–6, MIS 20–25, MIS 31–32), A.M.M. (pollen, MIS 6, MIS 34), S.N. (tephrochronology), N.N. (palaeomagnetic data), K.P. (pollen, MIS 7–8, MIS 35–43), O.P. (pollen, MIS 1–4, MIS 13–16, MIS 30), L.Sagnotti (palaeomagnetic data), G.S. (pollen, MIS 5–6), R.S. (tephrostratigraphy) and P.T. (pollen, MIS 6, MIS 34). S.K., K.L. and T. Wonik coordinated the seismic survey of Lake Ohrid, the selection of the coring location and the geophysical measurements needed for core correlation. A.G., M.M., J.M.R. and Z.L. contributed to the conception of the work. A.C., J.H., E.J., S.T. and X.Z. provided micropalaeontological and organic geochemistry data, which confirmed that the sediment succession from the DEEP site covers the entire history of Lake Ohrid. A.T. provided model infrastructure and resources. All authors contributed to the discussion and interpretation of the data and provided comments and suggestions to the manuscript.

Corresponding author

Correspondence to Bernd Wagner.

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Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature thanks Simon Blockley, Dirk Verschuren and Zhongshi Zhang for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Fig. 1 Map of Lake Ohrid and its surrounding area.

Geology, topography and bathymetry were compiled from previous studies19,91 and geological maps of Albania and North Macedonia. The lake is located at an altitude of 693 m a.s.l. and has a maximum water depth of 293 m. The water depth at the DEEP drill site is 240 m.

Extended Data Fig. 2 Correlation of tephra layers at the DEEP site with tephra layers from mid-distal records.

a–e, Bi-oxide plots of CaO versus FeOtotal (a), CaO versus Al_2O_3 (b), CaO versus TiO_2 (c), Na_2O versus K_2O (d) and a total alkali versus silica diagram[92] (e) show the correlation of OH-DP-2669 with the tephra layers SC1-35.30/SUL2-1/V5 and the differences to the Parmenide ash. f–j, Bi-oxide plots of CaO versus FeOtotal (f), CaO versus Al_2O_3 (g), CaO versus TiO_2 (h), Na_2O versus K_2O (i) and total alkali versus silica diagram (j) show the correlation of OH-DP-2898 with tephra SUL2-22 and the differences to SUL2-23, SUL2-27, SUL2-31, V4, V3 and the Pitagora ash. Error bars for the data of the Parmenide ash indicate the standard deviation[54]. Tephra ages, geochemical data, tephrostratigraphic discussion and references are provided in Extended Data Tables 1, 2 and the Methods. Source Data

Extended Data Fig. 3 Correlation of tephra layers OH-DP-2669 and V5 based on trace element compositions.

Trace element data of OH-DP-2669 support the correlation with tephra V5a/b[52]. a, Th versus Y. b, Th versus Zr. c, Th versus Nb. d, Th versus La. e, Th versus Ce. f, Th versus Pr. g, Th versus Nd. h, Th versus Gd. i, Th versus Yb. Error bars for the data of OH-DP-2669 represent uncertainties at a 95% confidence interval. ppm, parts per million.

Extended Data Fig. 4 Lake Ohrid LOVECLIM simulation data and sedimentary palaeoclimate and palaeoenvironment proxies.

a, Simulated surface-air temperature (SAT) for the Lake Ohrid grid cell from the LOVECLIM simulation. b, Simulated precipitation amount for the Lake Ohrid grid cell from the LOVECLIM simulation. c, Lake Ohrid TOC concentrations. d, Lake Ohrid δ^13C endogenic calcite in parts per thousand relative to VPDB. e, Lake Ohrid δ^18O endogenic calcite in parts per thousand relative to VPDB. f, Lake Ohrid relative sedimentary quartz content. g, Lake Ohrid K intensities in kilo counts and displayed using a 11-point (pt) running mean. h, Lake Ohrid ratio of Ca/K intensities displayed using a 11-point running mean. i, Lake Ohrid Ca intensities in kilo counts and displayed using a 11-point running mean. j, Lake Ohrid TIC concentrations. k, Percentages of deciduous oak pollen at Lake Ohrid. l, Percentages of arboreal pollen excluding Pinus pollen at Lake Ohrid. Red and white diamonds indicate the position of radiometrically dated tephra layers, blue and white diamonds the position of reversals of Earth’s magnetic field in the Lake Ohrid sediment record. b, d, e, j–l, Data are the same as in Fig. 2. Source Data

Extended Data Fig. 5 Data analysis.

a, b, Continuous wavelet transform on the percentage of TIC (a) and percentage of deciduous oak pollen (DOP; b) from Ohrid DEEP. Yellow, highest power; red, lowest power; grey contour, cone of influence; black contour, 5% significance level[82] against red-noise background corrected for autocorrelation81,93. c, d, Least squares regression (red line) between band pass-filtered 18–25-kyr-old component of percentage of TIC (c) and the percentage of DOP against precession at a 1-kyr resolution (d). Blue lines indicate 95% bootstrapped (n = 1,999) confidence intervals. Significant negative responses to precession are seen in both proxies, with a stronger response in DOP. Partial datasets for the intervals <0.78 Myr ago, <1.2 Myr ago, <1.36 Myr ago indicate persistence of the correlation despite changes in lake ontogeny and global scale changes in boundary conditions. e, f, PLSR using TIC and DOP as predictive variables and LOVECLIM temperature (e) and precipitation (f) simulations as observations demonstrate significant explanatory power by the proxies on the simulation time series, particularly for precipitation. PLSR was performed using SIMCA 14 (Sartorius Stedim Biotech), using 1.4–33-kyr bandpass-filtered data to accommodate for slight age offsets between proxy and simulation data. Source Data

Extended Data Fig. 6 Lake Ohrid precipitation indicators and global monsoon records during MIS 5.

a, Ages of sapropels and humid phases in the eastern Mediterranean based on Soreq Cave speleothem δ^18O data and U/Th chronology[71]. b, Simulated precipitation amount for the Lake Ohrid grid cell from the LOVECLIM simulation. c, Percentage of deciduous oak pollen at Lake Ohrid. d, Lake Ohrid TIC concentrations. e, Chinese Speleostack[25] δ^18O in parts per thousand relative to VPDB. Red and white diamonds indicate the position of radiometrically dated tephra layers in the Lake Ohrid record. The chronology of the MIS 5 interval in the Lake Ohrid DEEP site record is based on a previous study[94]. Source Data

Extended Data Fig. 7 Simulated Lake Ohrid precipitation for full-forcing run and sensitivity simulations.

a, Lake Ohrid precipitation (cm yr−1) for full-forcing simulation (black) and a simulation using only orbital forcing under a warm background climate (red). b, Black line as in a and a simulation using only orbital forcing under a cold background climate (blue). c, Black line as in a and a simulation using full-forcing except for a constant preindustrial Northern Hemisphere (NH) ice sheet. d, Black line as in a and a simulation using full-forcing except for constant preindustrial GHG concentrations. Note that the sensitivity simulations only cover the past 408 kyr (see Methods for details on the sensitivity simulations). Source Data

Extended Data Fig. 8 Mean seasonal cycle of precipitation in the Lake Ohrid grid cell from LOVECLIM model simulation and NOAA reanalysis data.

a, Reconstructed precipitation (cm yr−1) for the Lake Ohrid reanalysis grid cell. Data are based on monthly means. Dashed line indicates two standard deviations above the mean. b, Composite anomalies of 850 hPa geopotential height (m) associated with Lake Ohrid precipitation maxima shown in a and referring to the months shown in c. c, Monthly distribution of precipitation maxima shown in a. d, Mean seasonal cycle of simulated Lake Ohrid precipitation (cm yr−1) for all model years (green) and model years with annual mean precipitation exceeding two standard deviations (magenta). See also Fig. 3a. e, Mean seasonal cycle of Lake Ohrid precipitation (cm yr−1) derived from NOAA reanalysis data (blue) and simulated for the period from 1 kyr ago to present (red). The annual means were removed for better comparison and are provided in the panel. Source Data

Extended Data Table 1 Selected tephra layers from Lake Ohrid and their correlation with tephra layers of other records

Full size table

Extended Data Table 2 Average compositions of OH-DP-2669 and OH-DP-2898 and potential equivalent correlations

Full size table

Source data

Source Data Fig. 1

Source Data Fig. 2

Source Data Fig. 3

Source Data Extended Data Fig. 2

Source Data Extended Data Fig. 4

Source Data Extended Data Fig. 5

Source Data Extended Data Fig. 6

Source Data Extended Data Fig. 7

Source Data Extended Data Fig. 8

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- Received

31 January 2019

- Accepted

28 June 2019

- Published

02 September 2019

- Issue Date

12 September 2019

- DOI
https://doi.org/10.1038/s41586-019-1529-0

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- Letter

- Published: 21 August 2019

Hidden resilience and adaptive dynamics of the global online hate ecology

- N. F. Johnson[1],
- R. Leahy[1],
- N. Johnson Restrepo[1],
- N. Velasquez[2],
- M. Zheng[3],
- P. Manrique[3],
- P. Devkota[4] &
- S. Wuchty[4]

Naturevolume 573, pages261–265 (2019) | Download Citation

Subjects

- Complex networks

- Interdisciplinary studies

Abstract

Online hate and extremist narratives have been linked to abhorrent real-world events, including a current surge in hate crimes1,2,3,4,5,6 and an alarming increase in youth suicides that result from social media vitriol[7]; inciting mass shootings such as the 2019 attack in Christchurch, stabbings and bombings8,9,10,11; recruitment of extremists12,13,14,15,16, including entrapment and sex-trafficking of girls as fighter brides[17]; threats against public figures, including the 2019 verbal attack against an anti-Brexit politician, and hybrid (racist–anti-women–anti-immigrant) hate threats against a US member of the British royal family[18]; and renewed anti-western hate in the 2019 post-ISIS landscape associated with support for Osama Bin Laden’s son and Al Qaeda. Social media platforms seem to be losing the battle against online hate19,20 and urgently need new insights. Here we show that the key to understanding the resilience of online hate lies in its global network-of-network dynamics. Interconnected hate clusters form global ‘hate highways’ that—assisted by collective online adaptations—cross social media platforms, sometimes using ‘back doors’ even after being banned, as well as jumping between countries, continents and languages. Our mathematical model predicts that policing within a single platform (such as Facebook) can make matters worse, and will eventually generate global ‘dark pools’ in which online hate will flourish. We observe the current hate network rapidly rewiring and self-repairing at the micro level when attacked, in a way that mimics the formation of covalent bonds in chemistry. This understanding enables us to propose a policy matrix that can help to defeat online hate, classified by the preferred (or legally allowed) granularity of the intervention and top-down versus bottom-up nature. We provide quantitative assessments for the effects of each intervention. This policy matrix also offers a tool for tackling a broader class of illicit online behaviours21,22 such as financial fraud.

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Fig. 1: Global ecology of online hate clusters.

Fig. 2: Mathematical model showing resilience of hate-cluster ecology.

Fig. 3: Adaptive dynamics of online hate at the microscale.

Fig. 4: Policy matrix from our findings.

Data availability

The dataset is provided as Source Data. The open-source software packages Gephi and R were used to produce the networks in the figures. No custom software was used.

References

1.

The UK Home Affairs Select Committee. Hate Crime: Abuse, Hate and Extremism Online. session 2016–17 HC 609 https://publications.parliament.uk/pa/cm201617/cmselect/cmhaff/609/609.pdf (2017).

2.

Patrisse Cullors. Online Hate Is A Deadly Threat https://edition.cnn.com/2018/11/01/opinions/social-media-hate-speech-cullors/index.html (2017).

3.

Beirich, H., Hankes, K., Piggott, S., Schlatter, E. & Viets, S. The Year in Hate and Extremism https://www.splcenter.org/fighting-hate/intelligence-report/2017/year-hate-and-extremism (2017).

4.

Hohmann, J. Hate Crimes Are a Much Bigger Problem than Even the New FBI Statistics Show https://www.washingtonpost.com/news/powerpost/paloma/daily-202/2018/11/14/daily-202-hate-crimes-are-a-much-bigger-problem-than-even-the-new-fbi-statistics-show/5beba5bd1b326b39290547e2/?utm_term=.e203814306e8 (2018).

5.

Reitman, J. U.S. Law Enforcement Failed to See the Threat of White Nationalism. Now they Don’t Know How to Stop It https://www.nytimes.com/2018/11/03/magazine/FBI-charlottesville-white-nationalism-far-right.html (2018).

6.

Southern Poverty Law Center (SPLC). Extremist Groups https://www.splcenter.org/fighting-hate/extremist-files/groups (2018).

7.

John, A. et al. Self-harm, suicidal behaviours, and cyberbullying in children and younG people: systematic review. J. Med. Internet Res. 20, e129 (2018).

- Article

- Google Scholar

8.

Berman, M. Prosecutors Say Accused Charleston Church Gunman Self-Radicalized Online https://www.washingtonpost.com/news/post-nation/wp/2016/08/22/prosecutors-say-accused-charleston-church-gunman-self-radicalized-online/?utm_term=.4f17303dffd4 (2016).

9.

Pagliery, J. The Suspect in Congressional Shooting Was Bernie Sanders Supporter, Strongly Anti-Trump http://www.cnn.com/2017/06/14/homepage2/james-hodgkinson-profile/index.html (2017).

10.

Yan, H., Simon, D. & Graef, A. Campus Killing: Suspect is a Member of ‘Alt-Reich’ Facebook Group http://www.cnn.com/2017/05/22/us/university-of-maryland-stabbing/index.html (2017).

11.

Amend, A. Analyzing a Terrorist’s Social Media Manifesto: the Pittsburgh Synagogue Shooter’s Posts on Gab https://www.splcenter.org/hatewatch/2018/10/28/analyzing-terrorists-social-media-manifesto-pittsburgh-synagogue-shooters-posts-gab (2018).

12.

Gill, P. & Corner, E. in Terrorism Online: Politics, Law, Technology (eds Jarvis, L. et al.) Ch. 1 (Routledge, 2015).

13.

Gill, P. et al. Terrorist use of the internet by the numbers quantifying behaviors, patterns, and processes. Criminol. Public Pol. 16, 99–117 (2017).

- Google Scholar

14.

Gill, P. Lone Actor Terrorists: A Behavioral Analysis (Routledge, 2015).

15.

Gill, P., Horgan, J. & Deckert, P. Bombing alone: tracing the motivations and antecedent behaviors of lone-actor terrorists. J. Forensic Sci. 59, 425–435 (2014).

- Article

- Google Scholar

16.

Schuurman, B. et al. End of the lone wolf: the typology that should not have been. Stud. Conflict Terrorism 42, 771–778 (2017).

- Article

- Google Scholar

17.

Panin, A. & Smith, L. Russian Students Targeted as Recruits by Islamic State https://www.bbc.co.uk/news/world-europe-33634214 (2015).

18.

Foster, M. The Racist Online Abuse of Meghan Markle Has Put Royal Staff on High Alert https://www.cnn.com/2019/03/07/uk/meghan-kate-social-media-gbr-intl/index.html (2019).

19.

Wakefield, J. Christchurch Shootings: Social Media Races to Stop Attack Footage https://www.bbc.com/news/technology-47583393 (2019).

20.

O’Brien, S. A. Moderating the Internet is Hurting Workers https://www.cnn.com/2019/02/28/tech/facebook-google-content-moderators/index.html (2019).

21.

KrebsOnSecurity. Deleted Facebook Cybercrime Groups Had 300,000 Members https://krebsonsecurity.com/2018/04/deleted-facebook-cybercrime-groups-had-300000-members/ (2019).

22.

Wong, J. C. Anti-Vaxx Mobs: Doctors Face Harassment Campaigns on Facebook https://www.theguardian.com/technology/2019/feb/27/facebook-anti-vaxx-harassment-campaigns-doctors-fight-back (2019).

23.

Martínez, A. G. Want Facebook to Censor Speech? Be Careful What You Wish For https://www.wired.com/story/want-facebook-to-censor-speech-be-careful-what-you-wish-for/ (2018).

24.

Stanley, H. E. Introduction to Phase Transitions and Critical Phenomena (Oxford Univ. Press, 1988).

25.

Hedström, P., Sandell, R. & Stern, C. Meso-level networks and the diffusion of social movements. Am. J. Sociol. 106, 145–172 (2000).

- Article

- Google Scholar

26.

Grinberg, N., Joseph, K., Friedland, L., Swire-Thompson, B. & Lazer, D. Fake news on Twitter during the 2016 U.S. presidential election. Science 363, 374–378 (2019).

- ADS
- CAS
- Article
- Google Scholar

27.

Johnson, N. F. et al. New online ecology of adversarial aggregates: ISIS and beyond. Science 352, 1459–1463 (2016).

- ADS
- CAS
- Article
- Google Scholar

28.

Havlin, S., Kenett, D. Y., Bashan, A., Gao, J. & Stanley, H. E. Vulnerability of network of networks. Eur. Phys. J. Spec. Top. 223, 2087 (2014).

- Article

- Google Scholar

29.

Palla, G., Barabási, A. L. & Vicsek, T. Quantifying social group evolution. Nature 446, 664–667 (2007).

- ADS
- CAS
- Article
- Google Scholar

30.

Jarrett, T. C., Ashton, D. J., Fricker, M. & Johnson, N. F. Interplay between function and structure in complex networks. Phys. Rev. E 74, 026116 (2006).

- ADS
- MathSciNet
- Article
- Google Scholar

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Acknowledgements

N.F.J. is supported by US Air Force (AFOSR) grant FA9550-16-1-0247.

Author information

Affiliations

1. Physics Department, George Washington University, Washington, DC, USA

- N. F. Johnson
- , R. Leahy
- & N. Johnson Restrepo

2. Elliot School of International Affairs, George Washington University, Washington, DC, USA

- N. Velasquez

3. Physics Department, University of Miami, Coral Gables, FL, USA

- M. Zheng

- & P. Manrique

4. Computer Science Department, University of Miami, Coral Gables, FL, USA

- P. Devkota

- & S. Wuchty

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Contributions

All authors contributed to the research design, the analysis and writing the paper.

Corresponding author

Correspondence to N. F. Johnson.

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The authors declare no competing interests.

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Peer review information Nature thanks Paul Gill, Nour Kteily and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Fig. 1 Power laws.

a, b, Power laws for the KKK ecology (a) and the ecology of illicit financial activities (b). Their power-law exponents (α) are similar in a and b, and also consistent with c. c, The results from aggregating data from different thematic subsystems, each of which has a power-law distribution with an exponent (βi) distributed around 2.5. d, Summary of the simulation procedure. N power-law distributions are created with a power-law exponent distributed around 2.5. Power-law exponents were then sampled, followed by a power-law test. e, Distribution of the resulting power-law exponents from this simulation procedure, for different values of the mean number of points in the underlying distributions (mu values). The resulting power law exponents α are centred near 1.7, as observed in a and b.

Extended Data Fig. 2 Cluster loop.

a, Cluster loop from Fig. 2. b, Example of a loop of clusters.

Extended Data Fig. 3 Predicted policy effects.

a, The effects of policy 1, with on average more than 550 widely spaced time steps for τ = 10 and N = 10^4. If the size of an aggregate remains within the range smin to smax for a particular time period τ, that aggregate then fragments. b, The effects of policy 2. Colours represent different intervention starting times (tI) in units of days (vertical grey lines): green tI = 80, red tI = 120, blue tI = 200. Line types represent different percentages of individuals randomly removed (that is, banned) at time tI: dashed line 10%, dotted line 30%, solid line 50%. c, Results for policy 3 of the time to extinction (T) as a function of the initial population partition (N + P = 1,000 fixed, with N being the initial size of the hate population and P being the initial size of the anti-hate population) and the banning rate of the platform, from numerical simulations and also analytic theory. d, Policy 4 shows effect of different allocations of 100 peacekeepers in the hate-cluster versus anti-hate-cluster scenario. nc is the number of clusters of peacekeepers (that is, individuals of type C) that have size sc.

Supplementary information

Supplementary Information

Supplementary Methods, Supplementary Discussion, Supplementary Equations and Supplementary Notes.

Reporting Summary

Source data

Source Data Fig. 1

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About this article

- Received

08 January 2019

- Accepted

24 July 2019

- Published

21 August 2019

- Issue Date

12 September 2019

- DOI
https://doi.org/10.1038/s41586-019-1494-7

Further reading

- Strategies for combating online hate

- Noemi Derzsy

Nature (2019)

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- Noemi Derzsy

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- Letter

- Published: 28 August 2019

An actin-based viscoplastic lock ensures progressive body-axis elongation

Alicia Lardennois[1] na1,
Gabriella Pásti[2] na1,
Teresa Ferraro[1],
Flora Llense[1],
Pierre Mahou[3],
Julien Pontabry2,4,
David Rodriguez[2],
Samantha Kim[2],
Shoichiro Ono[5],
Emmanuel Beaurepaire[3],
Christelle Gally[2] &
Michel Labouesse1,2

Naturevolume 573, pages266–270 (2019) | Download Citation

Subjects

- Biophysics

- Morphogenesis

- A Publisher Correction to this article was published on 06 September 2019

- This article has been updated

Abstract

Body-axis elongation constitutes a key step in animal development, laying out the final form of the entire animal. It relies on the interplay between intrinsic forces generated by molecular motors1,2,3, extrinsic forces exerted by adjacent cells4,5,6,7 and mechanical resistance forces due to tissue elasticity or friction8,9,10. Understanding how mechanical forces influence morphogenesis at the cellular and molecular level remains a challenge[1]. Recent work has outlined how small incremental steps power cell-autonomous epithelial shape changes1,2,3, which suggests the existence of specific mechanisms that stabilize cell shapes and counteract cell elasticity. Beyond the twofold stage, embryonic elongation in Caenorhabditis elegans is dependent on both muscle activity[7] and the epidermis; the tension generated by muscle activity triggers a mechanotransduction pathway in the epidermis that promotes axis elongation[7]. Here we identify a network that stabilizes cell shapes in C. elegans embryos at a stage that involves non-autonomous mechanical interactions between epithelia and contractile cells. We searched for factors genetically or molecularly interacting with the p21-activating kinase homologue PAK-1 and acting in this pathway, thereby identifying the α-spectrin SPC-1. Combined absence of PAK-1 and SPC-1 induced complete axis retraction, owing to defective epidermal actin stress fibre. Modelling predicts that a mechanical viscoplastic deformation process can account for embryo shape stabilization. Molecular analysis suggests that the cellular basis for viscoplasticity originates from progressive shortening of epidermal microfilaments that are induced by muscle contractions relayed by actin-severing proteins and from formin homology 2 domain-containing protein 1 (FHOD-1) formin bundling. Our work thus identifies an essential molecular lock acting in a developmental ratchet-like process.

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Fig. 1: Combined loss of PAK-1 and SPC-1 triggers muscle-dependent embryo retraction.

Fig. 2: Actin-filament abnormalities in spc-1 pak-1 defective embryos.

Fig. 3: Muscle contractions are linked to severing of epidermal actin filaments.

Fig. 4: An actin-remodelling network providing mechanical plasticity ensures embryo elongation.

Data availability

Source Data for Figs. 1d, 2c–f, 3c–e, 4d, e and Extended Data Figs. 1b, d, k, 3b, c, 4c, d, 5d, e, l, 7a, b, 9f, as well as numbers of replicates and P values (where applicable) for all figures are provided in the online version of the paper.

Code availability

All MATLAB scripts used for the present analysis are available upon reasonable request.

Change history

- 06 September 2019

An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

References

1.

Gilmour, D., Rembold, M. & Leptin, M. From morphogen to morphogenesis and back. Nature 541, 311–320 (2017).

- ADS
- CAS
- Article
- Google Scholar

2.

Martin, A. C., Kaschube, M. & Wieschaus, E. F. Pulsed contractions of an actin–myosin network drive apical constriction. Nature 457, 495–499 (2009).

- ADS
- CAS
- Article
- Google Scholar

3.

Rauzi, M., Lenne, P. F. & Lecuit, T. Planar polarized actomyosin contractile flows control epithelial junction remodelling. Nature 468, 1110–1114 (2017).

- ADS
- Article
- Google Scholar

4.

Collinet, C., Rauzi, M., Lenne, P. F. & Lecuit, T. Local and tissue-scale forces drive oriented junction growth during tissue extension. Nat. Cell Biol. 17, 1247–1258 (2015).

- CAS
- Article
- Google Scholar

5.

Desprat, N., Supatto, W., Pouille, P. A., Beaurepaire, E. & Farge, E. Tissue deformation modulates twist expression to determine anterior midgut differentiation in Drosophila embryos. Dev. Cell 15, 470–477 (2008).

- CAS
- Article
- Google Scholar

6.

Lye, C. M. et al. Mechanical coupling between endoderm invagination and axis extension in Drosophila. PLoS Biol. 13, e1002292 (2015).

- Article

- Google Scholar

7.

Zhang, H. et al. A tension-induced mechanotransduction pathway promotes epithelial morphogenesis. Nature 471, 99–103 (2011).

- ADS
- CAS
- Article
- Google Scholar

8.

Behrndt, M. et al. Forces driving epithelial spreading in zebrafish gastrulation. Science 338, 257–260 (2012).

- ADS
- CAS
- Article
- Google Scholar

9.

Dierkes, K., Sumi, A., Solon, J. & Salbreux, G. Spontaneous oscillations of elastic contractile materials with turnover. Phys. Rev. Lett. 113, 148102 (2014).

- ADS
- Article
- Google Scholar

10.

Vuong-Brender, T. T., Ben Amar, M., Pontabry, J. & Labouesse, M. The interplay of stiffness and force anisotropies drives embryo elongation. eLife 6, e23866 (2017).

- Article

- Google Scholar

11.

Munro, E., Nance, J. & Priess, J. R. Cortical flows powered by asymmetrical contraction transport PAR proteins to establish and maintain anterior-posterior polarity in the early C. elegans embryo. Dev. Cell 7, 413–424 (2004).

- CAS
- Article
- Google Scholar

12.

Vuong-Brender, T. T., Yang, X. & Labouesse, M. C. elegans embryonic morphogenesis. Curr. Top. Dev. Biol. 116, 597–616 (2016).

- CAS
- Article
- Google Scholar

13.

Simões, Sde. M., Mainieri, A. & Zallen, J. A. Rho GTPase and Shroom direct planar polarized actomyosin contractility during convergent extension. J. Cell Biol. 204, 575–589 (2014).

- Article

- Google Scholar

14.

Vasquez, C. G., Tworoger, M. & Martin, A. C. Dynamic myosin phosphorylation regulates contractile pulses and tissue integrity during epithelial morphogenesis. J. Cell Biol. 206, 435–450 (2014).

- CAS
- Article
- Google Scholar

15.

Gally, C. et al. Myosin II regulation during C. elegans embryonic elongation: LET-502/ROCK, MRCK-1 and PAK-1, three kinases with different roles. Development 136, 3109–3119 (2009).

- CAS
- Article
- Google Scholar

16.

Vuong-Brender, T. T. K., Suman, S. K. & Labouesse, M. The apical ECM preserves embryonic integrity and distributes mechanical stress during morphogenesis. Development 144, 4336–4349 (2017).

- CAS
- Article
- Google Scholar

17.

Rogalski, T. M., Mullen, G. P., Gilbert, M. M., Williams, B. D. & Moerman, D. G. The UNC-112 gene in Caenorhabditis elegans encodes a novel component of cell-matrix adhesion structures required for integrin localization in the muscle cell membrane. J. Cell Biol. 150, 253–264 (2000).

- CAS
- Article
- Google Scholar

18.

Costa, M., Draper, B. W. & Priess, J. R. The role of actin filaments in patterning the Caenorhabditis elegans cuticle. Dev. Biol. 184, 373–384 (1997).

- CAS
- Article
- Google Scholar

19.

Priess, J. R. & Hirsh, D. I. Caenorhabditis elegans morphogenesis: the role of the cytoskeleton in elongation of the embryo. Dev. Biol. 117, 156–173 (1986).

- CAS
- Article
- Google Scholar

20.

Praitis, V., Ciccone, E. & Austin, J. SMA-1 spectrin has essential roles in epithelial cell sheet morphogenesis in C. elegans. Dev. Biol. 283, 157–170 (2005).

- CAS
- Article
- Google Scholar

21.

McCullough, B. R. et al. Cofilin-linked changes in actin filament flexibility promote severing. Biophys. J. 101, 151–159 (2011).

- ADS
- CAS
- Article
- Google Scholar

22.

Bonakdar, N. et al. Mechanical plasticity of cells. Nat. Mater. 15, 1090–1094 (2016).

- ADS
- CAS
- Article
- Google Scholar

23.

Doubrovinski, K., Swan, M., Polyakov, O. & Wieschaus, E. F. Measurement of cortical elasticity in Drosophila melanogaster embryos using ferrofluids. Proc. Natl Acad. Sci. USA 114, 1051–1056 (2017).

- CAS
- Article
- Google Scholar

24.

Muñoz, J. J. & Albo, S. Physiology-based model of cell viscoelasticity. Phys. Rev. E 88, 012708 (2013).

- ADS
- Article
- Google Scholar

25.

Vanneste, C. A., Pruyne, D. & Mains, P. E. The role of the formin gene fhod-1 in C. elegans embryonic morphogenesis. Worm 2, e25040 (2013).

- Article

- Google Scholar

26.

Schönichen, A. et al. FHOD1 is a combined actin filament capping and bundling factor that selectively associates with actin arcs and stress fibers. J. Cell Sci. 126, 1891–1901 (2013).

- Article

- Google Scholar

27.

Kühn, S. & Geyer, M. Formins as effector proteins of Rho GTPases. Small GTPases 5, e983876 (2014).

- Article

- Google Scholar

28.

Jurmeister, S. et al. MicroRNA-200c represses migration and invasion of breast cancer cells by targeting actin-regulatory proteins FHOD1 and PPM1F. Mol. Cell. Biol. 32, 633–651 (2012).

- CAS
- Article
- Google Scholar

29.

Brenner, S. The genetics of Caenorhabditis elegans. Genetics 77, 71–94 (1974).

- CAS
- PubMed
- PubMed Central
- Google Scholar

30.

Gomes, J. E. et al. Microtubule severing by the katanin complex is activated by PPFR-1-dependent MEI-1 dephosphorylation. J. Cell Biol. 202, 431–439 (2013).

- Article

- Google Scholar

31.

Fromont-Racine, M., Rain, J. C. & Legrain, P. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nat. Genet. 16, 277–282 (1997).

- CAS
- Article
- Google Scholar

32.

Kamath, R. S. et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421, 231–237 (2003).

- ADS
- CAS
- Article
- Google Scholar

33.

Gally, C., Zhang, H. & Labouesse, M. Functional and genetic analysis of VAB-10 spectraplakin in Caenorhabditis elegans. Methods Enzymol. 569, 407–430 (2016).

- CAS
- Article
- Google Scholar

34.

Naganathan, S. R. et al. Morphogenetic degeneracies in the actomyosin cortex. eLife 7, e37677 (2018).

- Article

- Google Scholar

35.

Bosher, J. M. et al. The Caenorhabditis elegans vab-10 spectraplakin isoforms protect the epidermis against internal and external forces. J. Cell Biol. 161, 757–768 (2003).

- CAS
- Article
- Google Scholar

36.

Mi-Mi, L., Votra, S., Kemphues, K., Bretscher, A. & Pruyne, D. Z-line formins promote contractile lattice growth and maintenance in striated muscles of C. elegans. J. Cell Biol. 198, 87–102 (2012).

- Article

- Google Scholar

37.

Gustafsson, M. G. Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J. Microsc. 198, 82–87 (2000).

- CAS
- Article
- Google Scholar

38.

Kner, P., Chhun, B. B., Griffis, E. R., Winoto, L. & Gustafsson, M. G. Super-resolution video microscopy of live cells by structured illumination. Nat. Methods 6, 339–342 (2009).

- CAS
- Article
- Google Scholar

39.

Matthews, I., Ishikawa, T. & Baker, S. The template update problem. IEEE Trans. Pattern Anal. Mach. Intell. 26, 810–815 (2004).

- Article

- Google Scholar

40.

Gonzalez, R. C. & Woods, R. E. Digital Image Processing 3rd edn (Prentice–Hall, 2006).

Download references

Acknowledgements

The authors thank A. Spang, S. Grill, Y. Bellaïche and R. Voituriez for critical comments on the manuscript and M. Gettings for improving the English. We also thank the Caenorhabditis Genetics Center (funded by the NIH Office of Research Infrastructure Programs P40 OD010440) and National BioResource Project at Tokyo Women's Medical University for strains, the IBPS Imaging Facility for advice. This work was supported by the Agence Nationale pour la Recherche, the European Research Council (grant no. 294744), Israel–France Maïmonide exchange program grants, and installation funds from the Centre National de la Recherche Scientifique (CNRS) and University Pierre et Marie Curie (UPMC) to M.L. A.L. was supported by a fellowship from the Fondation pour la Recherche Médicale (FDT201805005501). This work was also made possible by institutional funds from the CNRS, University of Strasbourg and UPMC, the grant ANR-10-LABX-0030-INRT, which is a French State fund managed by the Agence Nationale de la Recherche under the framework programme Investissements d’Avenir labelled ANR-10-IDEX-0002-02 to the IGBMC. The work of P.M. and E.B. was partly supported by the Agence Nationale de la Recherche (contract ANR-11-EQPX-0029 Morphoscope2), the work of S.O. was partly supported by the National Institutes of Health (grant AR048615).

Author information

Author notes

1. These authors contributed equally: Alicia Lardennois, Gabriella Pásti

Affiliations

1. CNRS UMR7622, Institut de Biologie Paris–Seine (IBPS), Sorbonne Université, Paris, France

- Alicia Lardennois
- , Teresa Ferraro
- , Flora Llense
- & Michel Labouesse

2. IGBMC –CNRS UMR 7104, INSERM U964, Development and Stem Cells Department, Université de Strasbourg, Illkirch, France

- Gabriella Pásti
- , Julien Pontabry
- , David Rodriguez
- , Samantha Kim
- , Christelle Gally
- & Michel Labouesse

3. INSERM U1182 – CNRS/ UMR7645, Laboratoire d’Optique et Biosciences, Ecole Polytechnique, Paris, France

- Pierre Mahou

- & Emmanuel Beaurepaire

4. RS2D, Mundolsheim, France

- Julien Pontabry

5. Departments of Pathology and Cell Biology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA

- Shoichiro Ono

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Contributions

M.L. conceived the project. A.L. performed most experiments with initial contributions from G.P. T.F. conceived the modelling, F.L. generated the FHOD-1 variants and the screen reported in Supplementary Table 3, P.M. and E.B. helped with TIRF–SIM imaging, T.F. and J.P. performed image analysis, C.G. shared data from a related screen, S.K. helped with the spc-1(ra409) mini-RNAi screen, D.R. provided technical assistance and S.O. provided the outcrossed gsnl-1 and viln-1 mutants. M.L. wrote the manuscript, and all authors commented and proofread it (except S.K., who was an intern), A.L. assembled figures, T.F. conceived and wrote the supplementary mathematical modelling material and F.L. prepared the Methods section.

Corresponding author

Correspondence to Michel Labouesse.

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Extended data figures and tables

Extended Data Fig. 1 Genes required to maintain embryonic elongation.

a, RNAi screen in a pak-1 mutant identified spc-1 as an enhancer (Supplementary Table 1). b, DIC images and quantification of newly hatched wild-type body length (n = 38 embryos), pak-1(tm403) (n = 32 embryos), spc-1(RNAi) (n = 26 embryos) and spc-1(RNAi) pak-1(tm403) (n = 36 embryos). Scale bars, 25 µm (WT and pak-1), 10 µm (spc-1 and spc-1 pak-1). Data represent mean values ± s.d. Two-sided paired t-test. c, A yeast two-hybrid screen using the PAK-1 N-terminal domain as a bait identified the SPC-1 SH3 domain as a prey (orange background) (Supplementary Table 2). d–j, Loss of the proteins GIT-1 and PIX-1, acting upstream of PAK-1 in the mechanotransduction pathway promoted by muscle contractions, in the absence of spc-1 also triggers a retraction phenotype. d–j, Elongation curves (d) and terminal phenotypes of wild type (n = 12 embryos), pak-1(tm403) (e; n = 11 embryos), git-1(tm1962) (f; n = 10 embryos), pix-1(gk416) (g; n = 10 embryos), spc-1(RNAi) pak-1(tm403) (h; n = 9 embryos), spc-1(RNAi) git-1(tm1962) (i; n = 11 embryos), spc-1(RNAi) pix-1(tm416) (j; n = 8 embryos). Data represent mean ± s.e.m. k–n, Elongation curves (k) and DIC pictures showing the terminal phenotypes of unc-112(RNAi) embryos (l; n = 14) and unc-112(RNAi) pak-1(tm403) (m; n = 8 embryos). n, Terminal phenotype of unc-112(RNAi) spc-1(ra409) obtained by inducing unc-112(RNAi) in the strain ML2436 bearing a rescuing extrachromosomal spc-1::gfp array and looking for embryos having lost the array; we could only obtain a few embryos of the desired phenotype despite numerous repeats (n = 4 embryos), all of which had the phenotype illustrated here, which is similar to that of spc-1(ra409) alone. Data represent mean ± s.e.m. Scale bars in e–j, l–n, 17 µm. *P < 0.05; **P < 0.001; ***P < 0.0001. Source data

Extended Data Fig. 2 PAK-1and SPC-1 colocalize with actin filaments.

a, b, Distribution of PAK-1::mKate (a; n = 20 embryos) and SPC-1::GFP (b; n = 13 embryos) in a late embryo. Enlarged images of PAK-1 and SPC-1 showing a filamentous distribution in the dorsoventral epidermis similar to actin filaments. c, Fluorescence images of PAK-1::mKate (red) and SPC-1::GFP (green) (n = 20 embryos). The panel shows the colocalization image for the most-apical focal planes (top image), and full XZ (green panel) and YZ (red panel) projections. The level of co-localization is high based on Pearson’s correlation coefficient (0.7–0.9, n = 20 embryos). The highest level of colocalization is detected at the apical cortex. d, Fluorescence images of Plin-26::VAB-10(ABD)::mKate (red) and SPC-1::GFP (green) (n = 8 embryos). The panel shows the colocalization image for the most-apical focal planes (top image), and full XZ (green panel) and YZ (red panel) projections. The level of colocalization is high based on Pearson’s correlation coefficient (0.7–0.9, n = 8 embryos). The colocalization is detected almost exclusively at the apical cortex. The gene lin-26 drives expression in the epidermis; VAB-10(ABD) corresponds to the two actin-binding domains (calponin homology) of the protein VAB-10. Scale bar, 10 µm.

Extended Data Fig. 3 Actin-filament continuity and orientation at three elongation stages.

a, d–i, Epidermal actin filaments visualized with the Pdpy-7::LifeAct::GFP reporter construct in wild type (a), pak-1(tm403) (d), spc-1(RNAi) (e), spc-1(RNAi) pak-1(tm403) (f), unc-112(RNAi) (g), fhod-1(tm2363) (h) and fhod-1(tm2363) spc-1(RNAi) (i) at mid-elongation (twofold equivalent) stage. Yellow rectangle, ROI. Scale bar, 10 µm. ROI after binarization (green) and major axis detection (red) (a, top middle, d–i, bottom), based on three steps of image treatment for continuity and orientation analysis (a, right). Actin continuity: distribution of actin segments based on their length (a, bottom middle). b, Quantification of actin-filament continuity; the graph represents the length (in pixels) along the circumferential axis of actin filaments in early, mid and late (corresponding to 1.7-fold, 2-fold and 3-fold equivalent stages in a wild-type embryo, respectively) embryos of wild-type (early n = 12, mid n = 19, late n = 16), pak-1(tm403) (early n = 16, mid n = 21, late n = 16), spc-1(RNAi) (early n = 15, mid n = 21, late n = 20), spc-1(RNAi) pak-1(tm403) (early n = 12, mid n = 17, late n = 26), unc-112(RNAi) (early n = 8, mid n = 13, late n = 12), fhod-1(tm2363) (early n = 12, mid n = 14, late n = 10), fhod-1(tm2363); spc-1(RNAi) (early n = 7, mid n = 11, late n = 8), spc-1(ra409) pak-1(tm403) (mid n = 14, late n = 20) and unc-112(RNAi) ; spc-1(ra409) pak-1(tm403) (early n = 8, mid n = 15, late n = 19) genotypes. c, Actin-filament orientation based on FFT and binarization. Wild-type (early n = 12, mid n = 18, late n = 14), pak-1(tm403) (early n = 16, mid n = 20, late n = 16), spc-1(RNAi) (early n = 14, mid n = 18, late n = 18), spc-1(RNAi) pak-1(tm403) (early n = 12, mid n = 18, late n = 21), unc-112(RNAi) (early n = 8, mid n = 13, late n = 12), fhod-1(tm2363) (early n = 12, mid n = 14, late n = 10), fhod-1(tm2363); spc-1(RNAi) (early n = 7, mid n = 11, late n = 8), spc-1(ra409) pak-1(tm403) (mid n = 14, late n = 19) and unc-112(RNAi) spc-1(ra409) pak-1(tm403) (early n = 8, mid n = 15, late n = 19) genotypes. Note that the characteristics of actin filaments in spc-1(RNAi) pak-1(tm403) embryos differ mostly at the equivalent of the twofold stage when muscles become active. At earlier and later stages, spc-1(RNAi) embryos and spc-1(RNAi) pak-1(tm403) embryos become similar. Each graph represents median values, 25th and 75th percentiles. The whiskers extend to the most extreme data points not considered outliers. Two-sided paired t-test. *P < 0.05; **P < 0.001; ***P < 0.0001; n.s, not significant. Source data

Extended Data Fig. 4 Changes in embryo diameter during elongation.

a, b, Fluorescence micrographs of embryos expressing the Pepid::Lifeact::GFP construct in the epidermis at three elongation stages early, middle and late (corresponding to 1.7-fold, 2-fold and 3-fold equivalent stages in a wild-type embryo, respectively) for wild-type (a) and spc-1(RNAi) pak-1(tm403) embryos (b). Scale bar, 10 µm. The Pepid promoter corresponds to Pdpy-7. The yellow lines correspond to the segments used to measure the dorsoventral width of the V1 seam cell. c, d, Quantification of the average V1 cell circumferential width normalized to the initial width during elongation (c), and of the average dorsoventral circumferential width at the level of the V1 seam cell (d), which was calculated using the measured embryo length and V1 cell width, taking into consideration the conservation of the total embryo volume, in wild-type (early n = 38, mid n = 10, late n = 14), pak-1(tm403) (early n = 26, mid n = 8, late n = 20), spc-1(RNAi) (early n = 24, mid n = 26, late n = 18), spc-1(RNAi) pak-1(tm403) (early n = 22, mid n = 30, late n = 38), unc-112(RNAi) (early n = 8, mid n = 9, late n = 8), and unc-112(RNAi) spc-1(ra409) pak-1(tm403) (early n = 7, mid n = 12, late n = 17) embryos. Error bars, s.e.m. A notable feature of spc-1(RNAi) pak-1(tm403) embryos is that the circumferential dimension of the seam cells decreased much more than that of their dorsoventral cells, which most probably reflects the actin-filament integrity defects combined with a Fseam force largely unchanged. Source data

Extended Data Fig. 5 Bending and severing of actin bundles during muscle contractions.

a, b, Kymographs of the regions boxed in yellow in Fig. 3a, b after spinning-disc time-lapse imaging of epidermal actin filaments (Pdpy-7::LifeAct::GFP reporter) in wild-type (a) and spc-1(RNAi) pak-1(tm403) (b) embryos at mid-elongation (twofold equivalent) stage. Scale bar, 5 µm. c, Principle of the RNAi screen performed to identify proteins mediating actin remodelling; the recipient strain carried a rescuing, but frequently lost, spc-1(+) transgene (green). d, Quantification of L1 hatchling length after downregulation or mutation of the indicated genes; the presence of the spc-1::gfp transgene is denoted +. Control worms fed on L4440 bacteria. e–k, Elongation curves (e) and DIC images showing the terminal phenotypes of pak-1(tm403) (f; n = 11 embryos), gsnl-1(tm2730); pak-1(tm403) (g; n = 9 embryos), viln-1(ok2413); pak-1(tm403) (h; n = 9 embryos), gsnl-1(tm2730); spc-1(RNAi) pak-1(tm403) (i; n = 5 embryos), viln-1(ok2413); spc-1(RNAi) pak-1(tm403) (j; n = 11 embryos) and spc-1(RNAi) pak-1(tm403) (k; n = 9 embryos). Pink box in e, period of muscle activity. Data represent mean ± s.e.m. Scale bar, 25 µm. l, Quantification of the L1 hatchling body length of wild type (n = 65 hatchlings), gsnl-1(tm2730) (n = 52 hatchlings), viln-1(ok2413) (n = 43 hatchlings), viln-1(ok2413); gsnl-1(tm2730) (n = 41 hatchlings), pak-1(tm403) (n = 47 hatchlings), gsnl-1(tm2730); pak-1(tm403) (n = 51 hatchlings), viln-1(ok2413); pak-1(tm403) (n = 70 hatchlings), viln-1(ok2413); gsnl-1(tm2730); pak-1(RNAi) (n = 35), spc-1(RNAi) (n = 27 hatchlings) and viln-1(ok2413); gsnl-1(tm2730); spc-1(RNAi) (n = 41 hatchlings). Data represent mean ± s.d. Two side paired t-test. *P < 0.05; **P < 0.001; ***P < 0.0001; n.s, not significant. Source data

Extended Data Fig. 6 Time-dependent length of a Kelvin–Voigt model in different conditions.

a, A generic Kelvin–Voigt system exposed to a constant force Fepid, and its predicted elongation change for Fseam = 0.85 and four different values of αDV based on the equation \({F}_{epid}={F}_{seam}\;{\alpha }_{DV}\). b, A similar system exposed to two forces, Fepid and an oscillating force Fmuscles, and predicted elongation change using Fepid = 0.85 and Fmuscles with an amplitude equal to 1 and the behaviour depicted in the blue-boxed inset. For simplicity, we will refer to the amplitude of Fmuscles as Fmuscles. As the pulsatile force induces both compression and stretching (see Fig. 1c), its net input on elongation is transient and the system oscillates around the maximal value reached without Fmuscles. In all other panels (except in a), Fmuscles was set as a periodic function with positive and negative steps of duration 6 s modulated by a cosine function, alternating with periods of null value of duration 15 s (b, inset). c, A Kelvin–Voigt system with mechanical plasticity introduced according to equations (1), (4), (6) and (7) in the Supplementary Information, and predicted elongation change using Fepid = 0.85, Fc = 0, Fmuscles = 3 and four distinct values of the plasticity factor β, or using Fepid = 0.85, Fc = 0, β = 0.10 and four distinct values of Fmuscles. d, A Kelvin–Voigt system in which the plasticity is defective (β = 0), and in which there is actin tearing according to equation (7) in the Supplementary Information, inducing a progressive reduction of Fepid, and predicted elongation change with an initial value of Fepid = 0.85, the tearing factor γ = 0.15 and Fmuscles = 3; the inset outlined in blue shows the behaviour of αDV(t) over time. In a–d, the elastic constant of the spring is k = 1, the initial resting length has the value λ(t = 0) = 1, and the viscosity is η = 10. e, Result of the fit for the following genotypes: WT, unc-112(−) alone spc-1(−) alone, spc-1(−) pak-1(−) double, unc-112(−); spc-1(−) pak(−) according to equations (1), (4), (9) to (11) in the Supplementary Information. The values of the parameters are specified in paragraphs 1.5 and 1.6 in the Supplementary Information. The shallow decrease in length for the curve of unc-112(−); spc-1(−) pak-1(−) after 150 min is due to a deformation of the embryos under the effect of unc-112 knockdown but not to retraction, which is why the fit has been evaluated on the first 150 min of the curve.

Extended Data Fig. 7 Comparable retraction phenotypes after the combined loss of SPC-1 and PAK-1 or SPC-1 and FHOD-1.

a, Principle of the retraction screen in a spc-1 mutant that identified fhod-1. b, DIC image of spc-1 deficient embryos after feeding on L4440 control (n = 21 hatchlings) or fhod-1(RNAi) (n = 25 hatchlings) bacteria, and quantification of spc-1(ra409) L1 hatchling body length after feeding. Data represent mean ± s.d. Two-sided paired t-test. c–j, Elongation curves and (d) corresponding DIC images showing the terminal phenotypes at hatching of wild type (d; n = 12 embryos), fhod-1(tm2363) (e; n = 10 embryos), fhod-1(RNAi) (f; n = 10 embryos), pak-1(tm403) (g; n = 11 embryos), fhod-1(RNAi) pak1(tm403) (h; n = 10 embryos), spc-1(RNAi) pak-1(tm403) (i; n = 8 embryos) and fhod-1(tm2363); spc-1(RNAi) (j; n = 9 embryos). Data in c represent mean ± s.e.m. Scale bar, 25 µm. Source data

Extended Data Fig. 8 PAK-1 and FHOD-1 form aggregates in spc-1(RNAi) loss of function.

a, PAK-1::GFP localization in wild-type and spc-1(RNAi) embryos. Yellow box, area enlarged below the panel. Note the punctae in SPC-1 deficient embryos. b, FHOD-1 localization in wild-type and spc-1(RNAi) embryos. Note the aggregates (arrowheads). Note also that FHOD-1::GFP displayed a filamentous organization reminiscent of actin filaments. Scale bar, 10 µm.

Extended Data Fig. 9 Actin displacement ratio.

a–d, Spinning-disc microscopy tracking of actin filaments visualized with a Pdpy-7::Lifeact::GFP marker specifically expressed in the epidermis. Individual displacement tracks of wild-type (a), pak-1(tm403) (b), spc-1(RNAi) (c) and spc-1(RNAi) pak-1(tm403) (d) embryos at a stage equivalent to twofold in a wild-type embryo. Scale bar, 10 µm. e, Typical kymographs of the Lifeact::GFP–labelled actin filaments in wild-type and spc-1(RNAi) pak-1(tm403) embryos from which the tracks in a–d were derived. Time interval between two images is 0.41 s. Yellow dots correspond to landmarks for quantitative analysis. f, Quantification of the displacement duration in (N = number of embryos, n = number of contractions): wild type, N = 11, n = 51; pak-1(tm403), N = 11, n = 26; spc-1(RNAi), N = 11, n = 73; spc-1(RNAi) pak-1(tm403), N = 11, n = 89. Data represent median values, 25th and 75th percentiles. The whiskers extend to the most extreme data points not considered outliers. Two-sided paired t-test. *P < 0.05; **P < 0.001; ***P < 0.0001; n.s., not significant. Source data

Supplementary information

Supplementary Information

This file contains details of Supplementary Mechanical Modelling and Supplementary References.

Reporting Summary

Supplementary Tables

This file contains Supplementary Tables 1-8.

Supplementary Data 1

Results of statistical tests: P-values for all statistical tests (even when not displayed on the figures).

Supplementary Data 2

Number of replicates: Number of analyzed embryos and independent repeats of all experiments.

Video 1

Embryonic elongation and retraction profiles Combined DIC timelapse video. Image acquisition was every 5 minutes in wild-type, pak-1(tm403), spc-1(RNAi), spc-1(RNAi) pak-1(tm403) embryos. Scale Bar, 10 µm.

Video 2

Muscle-dependence of the retraction profile Combined DIC timelapse video of unc-112(RNAi) and unc-112(RNAi); spc-1(RNAi) pak-1(tm403) embryos. Scale Bar,10 µm.

Video 3

Retraction profile of fhod-1; spc-1 defective embryos Combined DIC timelapse videos of spc-1(ra409) and fhod-1(RNAi); spc-1(ra409) embryos. Scale Bar, 10 µm.

Video 4

Epithelial actin displacement in mutants Fluorescence video showing the displacement of actin filaments labelled with Pdpy-7::lifeact::GFP in the epidermis in wild-type, pak-1(tm403),  spc-1(RNAi) and  spc-1(RNAi) pak-1(tm403) embryos. Time interval, 0.41 s. Scale Bar,10 µm.

Source data

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About this article

- Received

16 May 2018

- Accepted

29 July 2019

- Published

28 August 2019

- Issue Date

12 September 2019

- DOI
https://doi.org/10.1038/s41586-019-1509-4

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- Letter

- Published: 04 September 2019

Maternal vitamin C regulates reprogramming of DNA methylation and germline development

Stephanie P. DiTroia1,2,8 nAff8,
Michelle Percharde1,2,3,4,
Marie-Justine Guerquin[5],
Estelle Wall1,2,
Evelyne Collignon[6],
Kevin T. Ebata1,2,
Kathryn Mesh1,2,
Swetha Mahesula[7],
Michalis Agathocleous[7],
Diana J. Laird1,2,
Gabriel Livera[5] &
Miguel Ramalho-Santos1,2,6

Naturevolume 573, pages271–275 (2019) | Download Citation

Subjects

- Epigenetic memory

- Oogenesis

Abstract

Development is often assumed to be hardwired in the genome, but several lines of evidence indicate that it is susceptible to environmental modulation with potential long-term consequences, including in mammals1,2. The embryonic germline is of particular interest because of the potential for intergenerational epigenetic effects. The mammalian germline undergoes extensive DNA demethylation3,4,5,6,7 that occurs in large part by passive dilution of methylation over successive cell divisions, accompanied by active DNA demethylation by TET enzymes3,8,9,10. TET activity has been shown to be modulated by nutrients and metabolites, such as vitamin C11,12,13,14,15. Here we show that maternal vitamin C is required for proper DNA demethylation and the development of female fetal germ cells in a mouse model. Maternal vitamin C deficiency does not affect overall embryonic development but leads to reduced numbers of germ cells, delayed meiosis and reduced fecundity in adult offspring. The transcriptome of germ cells from vitamin-C-deficient embryos is remarkably similar to that of embryos carrying a null mutation in Tet1. Vitamin C deficiency leads to an aberrant DNA methylation profile that includes incomplete demethylation of key regulators of meiosis and transposable elements. These findings reveal that deficiency in vitamin C during gestation partially recapitulates loss of TET1, and provide a potential intergenerational mechanism for adjusting fecundity to environmental conditions.

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Fig. 1: Maternal vitamin C promotes female germ-cell development.

Fig. 2: Gestational vitamin C deficiency has a long-term effect on female fecundity.

Fig. 3: Vitamin C deficiency induces a Tet1−/−-like expression profile in the developing germline.

Fig. 4: Vitamin C deficiency leads to incomplete loss of DNA methylation at meiosis regulators and transposable elements in the embryonic germline.

Code availability

Custom codes used for data analysis were deposited in Github (https://github.com/Santosi/VitC-PGCs) and are also available upon request.

Data availability

RNA-seq, RRBS and CUT&RUN data have been deposited in Gene Expression Omnibus (GEO) under accession number GSE109747.

References

1.

Barker, D. J. P. The developmental origins of adult disease. J. Am. Coll. Nutr. 23, 588S–595S (2004).

- CAS
- Article
- Google Scholar

2.

Boekelheide, K. et al. Predicting later-life outcomes of early-life exposures. Environ. Health Perspect. 120, 1353–1361 (2012).

- Article

- Google Scholar

3.

Seisenberger, S. et al. The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol. Cell 48, 849–862 (2012).

- CAS
- Article
- Google Scholar

4.

Hackett, J. A. et al. Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine. Science 339, 448–452 (2013).

- ADS
- CAS
- Article
- Google Scholar

5.

Gkountela, S. et al. DNA demethylation dynamics in the human prenatal germline. Cell 161, 1425–1436 (2015).

- CAS
- Article
- Google Scholar

6.

Guo, F. et al. The transcriptome and DNA methylome landscapes of human primordial germ cells. Cell 161, 1437–1452 (2015).

- CAS
- Article
- Google Scholar

7.

Tang, W. W. C. et al. A unique gene regulatory network resets the human germline epigenome for development. Cell 161, 1453–1467 (2015).

- CAS
- Article
- Google Scholar

8.

Yamaguchi, S. et al. Tet1 controls meiosis by regulating meiotic gene expression. Nature 492, 443–447 (2012).

- ADS
- CAS
- Article
- Google Scholar

9.

Yamaguchi, S., Shen, L., Liu, Y., Sendler, D. & Zhang, Y. Role of Tet1 in erasure of genomic imprinting. Nature 504, 460–464 (2013).

- ADS
- CAS
- Article
- Google Scholar

10.

Hajkova, P. et al. Chromatin dynamics during epigenetic reprogramming in the mouse germ line. Nature 452, 877–881 (2008).

- ADS
- CAS
- Article
- Google Scholar

11.

Blaschke, K. et al. Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells. Nature 500, 222–226 (2013).

- ADS
- CAS
- Article
- Google Scholar

12.

Carey, B. W., Finley, L. W. S., Cross, J. R., Allis, C. D. & Thompson, C. B. Intracellular α-ketoglutarate maintains the pluripotency of embryonic stem cells. Nature 518, 413–416 (2014).

- ADS
- Article
- Google Scholar

13.

Zhang, Q. et al. Differential regulation of the ten-eleven translocation (TET) family of dioxygenases by O-linked β-N-acetylglucosamine transferase (OGT). J. Biol. Chem. 289, 5986–5996 (2014).

- CAS
- Article
- Google Scholar

14.

Yin, R. et al. Ascorbic acid enhances Tet-mediated 5-methylcytosine oxidation and promotes DNA demethylation in mammals. J. Am. Chem. Soc. 135, 10396–10403 (2013).

- CAS
- Article
- Google Scholar

15.

Wu, H. & Zhang, Y. Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. Genes Dev. 25, 2436–2452 (2011).

- CAS
- Article
- Google Scholar

16.

Maeda, N. et al. Aortic wall damage in mice unable to synthesize ascorbic acid. Proc. Natl Acad. Sci. USA 97, 841–846 (2000).

- ADS
- CAS
- Article
- Google Scholar

17.

Szabó, P. E., Hübner, K., Schöler, H. & Mann, J. R. Allele-specific expression of imprinted genes in mouse migratory primordial germ cells. Mech. Dev. 115, 157–160 (2002).

- Article

- Google Scholar

18.

Hill, P. W. S. et al. Epigenetic reprogramming enables the transition from primordial germ cell to gonocyte. Nature 555, 392–396 (2018).

- ADS
- CAS
- Article
- Google Scholar

19.

Kobayashi, H. et al. High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice. Genome Res. 23, 616–627 (2013).

- CAS
- Article
- Google Scholar

20.

Ohno, R. et al. A replication-dependent passive mechanism modulates DNA demethylation in mouse primordial germ cells. Development 140, 2892–2903 (2013).

- CAS
- Article
- Google Scholar

21.

Ebata, K. T. et al. Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b. Epigenetics Chromatin 10, 36 (2017).

- Article

- Google Scholar

22.

Seki, Y. et al. Cellular dynamics associated with the genome-wide epigenetic reprogramming in migrating primordial germ cells in mice. Development 134, 2627–2638 (2007).

- CAS
- Article
- Google Scholar

23.

Drouin, G., Godin, J.-R. & Pagé, B. The genetics of vitamin C loss in vertebrates. Curr. Genomics 12, 371–378 (2011).

- CAS
- Article
- Google Scholar

24.

Salnikow, K. & Zhitkovich, A. Genetic and epigenetic mechanisms in metal carcinogenesis and cocarcinogenesis: nickel, arsenic, and chromium. Chem. Res. Toxicol. 21, 28–44 (2008).

- Article

- Google Scholar

25.

Ercal, N., Gurer-Orhan, H. & Aykin-Burns, N. Toxic metals and oxidative stress part I: mechanisms involved in metal-induced oxidative damage. Curr. Top. Med. Chem. 1, 529–539 (2001).

- CAS
- Article
- Google Scholar

26.

Cross, C. E., Traber, M., Eiserich, J. & van der Vliet, A. Micronutrient antioxidants and smoking. Br. Med. Bull. 55, 691–704 (1999).

- CAS
- Article
- Google Scholar

27.

Alsharif, N. Z., Lawson, T. & Stohs, S. J. Oxidative stress induced by 2,3,7,8-tetrachlorodibenzo-p-dioxin is mediated by the aryl hydrocarbon (Ah) receptor complex. Toxicology 92, 39–51 (1994).

- CAS
- Article
- Google Scholar

28.

Matsumura, F. On the significance of the role of cellular stress response reactions in the toxic actions of dioxin. Biochem. Pharmacol. 66, 527–540 (2003).

- CAS
- Article
- Google Scholar

29.

Cyr, A. R. & Domann, F. E. The redox basis of epigenetic modifications: from mechanisms to functional consequences. Antioxid. Redox Signal. 15, 551–589 (2011).

- CAS
- Article
- Google Scholar

30.

Kim, H. et al. The analysis of vitamin C concentration in organs of Gulo
−/− mice upon vitamin C withdrawal. Immune Netw. 12, 18–26 (2012).

- Article

- Google Scholar

31.

Franks, L. M. & Payne, J. The influence of age on reproductive capacity in C57BL mice. J. Reprod. Fertil. 21, 563–565 (1970).

- CAS
- Article
- Google Scholar

32.

Agathocleous, M. et al. Ascorbate regulates haematopoietic stem cell function and leukaemogenesis. Nature 549, 476–481 (2017).

- ADS
- Article
- Google Scholar

33.

Guerquin, M.-J. et al. New testicular mechanisms involved in the prevention of fetal meiotic initiation in mice. Dev. Biol. 346, 320–330 (2010).

- CAS
- Article
- Google Scholar

34.

Arora, R. et al. Meiotic onset is reliant on spatial distribution but independent of germ cell number in the mouse ovary. J. Cell Sci. 129, 2493–2499 (2016).

- CAS
- Article
- Google Scholar

35.

Abby, E. et al. Implementation of meiosis prophase I programme requires a conserved retinoid-independent stabilizer of meiotic transcripts. Nat. Commun. 7, 10324 (2016).

- ADS
- CAS
- Article
- Google Scholar

36.

Faire, M. et al. Follicle dynamics and global organization in the intact mouse ovary. Dev. Biol. 403, 69–79 (2015).

- CAS
- Article
- Google Scholar

37.

Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).

- Article

- Google Scholar

38.

Anders, S., Pyl, P. T. & Huber, W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).

- CAS
- Article
- Google Scholar

39.

Huber, W. et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nat. Methods 12, 115–121 (2015).

- CAS
- Article
- Google Scholar

40.

Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

- Article

- Google Scholar

41.

Huang, W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protocols 4, 44–57 (2009).

- CAS
- Article
- Google Scholar

42.

Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).

- ADS
- CAS
- Article
- Google Scholar

43.

Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766–770 (2008).

- ADS
- CAS
- Article
- Google Scholar

44.

Guo, H. et al. Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing. Genome Res. 23, 2126–2135 (2013).

- CAS
- Article
- Google Scholar

45.

Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571–1572 (2011).

- CAS
- Article
- Google Scholar

46.

Hebestreit, K., Dugas, M. & Klein, H.-U. Detection of significantly differentially methylated regions in targeted bisulfite sequencing data. Bioinformatics 29, 1647–1653 (2013).

- CAS
- Article
- Google Scholar

47.

McLean, C. Y. et al. GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol. 28, 495–501 (2010).

- CAS
- Article
- Google Scholar

48.

Wu, H. et al. Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature 473, 389–393 (2011).

- ADS
- CAS
- Article
- Google Scholar

49.

Li, Z. et al. Distinct roles of DNMT1-dependent and DNMT1-independent methylation patterns in the genome of mouse embryonic stem cells. Genome Biol. 16, 115 (2015).

- Article

- Google Scholar

50.

Hainer, S. J., Bošković, A., McCannel, K. N., Rando, O. J. & Fazzio, T. G. Profiling of pluripotency factors in stem cells and early embryos. Cell 177, 1319–1329 (2019).

- CAS
- Article
- Google Scholar

51.

Skene, P. J., Henikoff, J. G. & Henikoff, S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat. Protocols 13, 1006–1019 (2018).

- CAS
- Article
- Google Scholar

52.

Percharde, M., Wong, P. & Ramalho-Santos, M. Global hypertranscription in the mouse embryonic germline. Cell Reports 19, 1987–1996 (2017).

- CAS
- Article
- Google Scholar

53.

Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).

- Article

- Google Scholar

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Acknowledgements

We thank M. Conti, R. Blelloch, P. Rinaudo, M. Lorincz, S. Fisher, L. Selleri and members of the Santos laboratory for input and critical reading of the manuscript. We thank E. Chow and members of the UCSF Center for Advanced Technology for assistance with sequencing; B. Soygur for meiotic spread protocol and reagents; Y. Zhang and L. Shen for technical advice on RRBS. We are grateful to S. Henikoff for providing the pA-MN and yeast tRNA spike-ins, and to S. Henikoff and T. Fazzio for providing technical help with performing CUT&RUN experiments. Flow cytometry data were generated in the UCSF Parnassus Flow Cytometry Core, which is supported by a Diabetes Research Center grant and NIH grant P30 DK063720. S.P.D. was supported by the National Science Foundation Graduate Research Fellowship Program under grant no. 1650113. Any opinions, findings and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. G.L. was partly supported by Institut Universitaire de France. This work was supported by National Institutes of Health (NIH) grants R21ES023297 and R01ES028212 to D.J.L., and NIH grants R01OD012204 and R01GM123556, and a Canada 150 Research Chair to M.R.-S.

Author information

Author notes

- Stephanie P. DiTroia

Present address: Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA

Affiliations

1. Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA

- Stephanie P. DiTroia
- , Michelle Percharde
- , Estelle Wall
- , Kevin T. Ebata
- , Kathryn Mesh
- , Diana J. Laird
- & Miguel Ramalho-Santos

2. Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA

- Stephanie P. DiTroia
- , Michelle Percharde
- , Estelle Wall
- , Kevin T. Ebata
- , Kathryn Mesh
- , Diana J. Laird
- & Miguel Ramalho-Santos

3. MRC London Institute of Medical Sciences (LMS), London, UK

- Michelle Percharde

4. Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK

- Michelle Percharde

5. UMR967 INSERM, CEA/DRF/iRCM/SCSR/LDG, Université Paris Diderot, Sorbonne Paris Cité, Université Paris-Sud, Université Paris-Saclay, Laboratory of Development of the Gonads, Fontenay aux Roses, France

- Marie-Justine Guerquin

- & Gabriel Livera

6. Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada

- Evelyne Collignon

- & Miguel Ramalho-Santos

7. Children’s Research Institute and the Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA

- Swetha Mahesula

- & Michalis Agathocleous

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Contributions

S.P.D. and M.R.-S. conceived the project. S.P.D. designed, performed and analysed most experiments with following exceptions. M.P. performed and analysed CUT&RUN experiments and somatic cell RNA-seq. M.P. collaborated with E.C., S.M. and M.A. to quantify vitamin C levels in embryos. M.-J.G. performed histology, immunohistochemistry and meiosis analysis on E14.5 fetal ovaries and testes under the supervision of G.L. E.W. performed and analysed whole-mount imaging on day 7 ovaries under the supervision of D.J.L. E.C. performed hmC quantifications. K.T.E. and K.M. set up the initial conditions for analysis of the mouse gestational vitamin C deficiency model. M.R.-S. supervised the project. S.P.D. and M.R.-S. wrote the manuscript with feedback from all authors.

Corresponding author

Correspondence to Miguel Ramalho-Santos.

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Extended data figures and tables

Extended Data Fig. 1 Validation of vitamin C depletion and the downregulation of TET1-dependent germline genes in a mouse model of gestational vitamin C deficiency.

a, Expression of vitamin C transporters (SVCT1, SVCT2 and GLUT8, encoded by Slc23a1, Slc23a2 and Glut8, respectively) in developing female (F) germ cells. Data are from Seisenberger et al.[3]. b, Kinetics of vitamin C depletion from the serum of pregnant Gulo−/− mice after withdrawal from their drinking water. Pregnant female mice were removed from vitamin C supplementation at E3.5 and circulating blood serum was tested over the time course indicated. It takes five days of withdrawal for the circulating vitamin C levels to be <25%, and seven days to be essentially undetectable. Line plot connects the average blood serum values of three biological replicates. c, Vitamin C levels measured by mass spectrometry in E13.5 embryonic tissue with and without gestational vitamin C removal. E13.5 female head or liver were normalized by tissue weight. Samples with non-detectable levels of vitamin C were set to zero. n = 5 biological replicates per condition. d, The reduction in E13.5 female germ cells numbers after vitamin C deficiency is confirmed using both Oct4–eGFP and SSEA1 positivity. n = 6 matched biological replicates per condition. e, Gestational vitamin C deficiency does not affect average somatic cell number. n = 13 control and n = 10 vitamin-C-depleted biological replicates. f, Vitamin-C-deficient E13.5 female germ cells express lower levels of key germline genes, as measured by qRT–PCR. n = 3 control and n = 4 vitamin-C-depleted biological replicates. The variability in Stra8 expression in controls as assessed by qRT–PCR at E13.5 is because it is just being induced at this stage; RNA-seq and immunofluorescence data further document the significant reduction in Stra8 RNA and protein levels in vitamin-C-deficient PGCs (Extended Data Fig. 3b, c). g, Expression of select germline genes are induced in a TET1/2-dependent manner after the addition of vitamin to cultured mouse ES cells[11]. Gene expression was measured by qRT–PCR, plotted as mean of technical triplicates. Data are from Blaschke et al.[11]. h, Decreased expression of select germline genes in Tet1−/− E13.5 germ cells as measured by RNA-seq. Data are from Yamaguchi et al.[8], and denote averages of three controls and two Tet1−/− samples. i, Select germline genes induced by vitamin C in cultured ES cells (c) and downregulated in Tet1−/− germ cells (d) are also downregulated in vitamin-C-deficient E13.5 germ cells. Gene expression was measured by RNA-seq. n = 6 biological replicates. j, Gestational vitamin C deficiency does not affect transcription in the somatic cells of E13.5 female gonads as shown by unsupervised clustering of RNA-seq analysis. Clustering performed on n = 6 biological replicates per condition. Data are single values per stage (a), mean values (b, h), mean ± s.e.m. (c, i) or mean ± s.d. (d–g). P values determined by two-tailed t-test with Welch’s correction (c, d, e), two-tailed Student’s t-test (f). Source Data

Extended Data Fig. 2 Analyses of gonad development upon vitamin C deficiency.

a, There is an overall normal induction of key markers of developmental progression of somatic cells of the ovaries between E11.5 and E13.5 in vitamin-C-deficient embryos, as measured by qRT–PCR. E13.5 somatic ovary cells are matched with PGCs in Extended Data Fig. 1f. In this analysis, Foxl2 expression is strongly induced after vitamin C deficiency, but to a slightly lower extent than in control samples. However, no significant changes in Foxl2 were detected by RNA-seq (Fig. 1f) or immunofluorescence (b). Error bars of E13.5 samples depict mean ± s.d. of four biological replicates; E11.5 data are from two biological replicates. b, Sexual differentiation is controlled by a balance between SOX9 (leading to expression of anti-Müllerian hormone (AMH)) in male and FOXL2 in female mice. Expression of FOXL2 in E14 and E18 ovaries (O14 and O18, respectively) does not change after vitamin C depletion as measured by immunohistochemistry. As expected, FOXL2 was not detected in E14 testes (T14). Images are representative of n = 5 control and n = 4 vitamin-C-deficient ovaries, and n = 2 control and n = 3 vitamin-C-deficient testes. c, Expression of AMH in E14 testis does not change after vitamin C depletion as measured by immunohistochemistry. As expected, AMH was not detected in E14 or E18 ovaries. Images are representative of n = 5 control and n = 4 vitamin-C-deficient ovaries, and n = 2 control and n = 3 vitamin-C-deficient testes. d, Gestational vitamin C deficiency does not affect the presence of Leydig cells (3BHSD) in developing testes or the absence of Leydig cells in developing ovaries. Images are representative of n = 5 control and n = 4 vitamin-C-deficient ovaries, and n = 2 control and n = 3 vitamin-C-deficient testes. Source Data

Extended Data Fig. 3 Detailed analyses of meiotic staging in germ cells of E14.5 vitamin-C-deficient ovaries.

a, Representative images of STRA8 and SYCP3 abundance in E14.5 control or vitamin-C-deficient female germ cells. Images are representative of n = 7 STRA8 and n = 8 SYCP3 biologically independent experiments, as indicated in b and d. b, Significant reduction in the percentage of DDX4+ germ cells that are STRA8+ after vitamin C deficiency. c, Stra8 mRNA abundance is significantly reduced at E13.5 as measured by RNA-seq. n = 6 biological replicates. d, There was a non-significant reduction in the average percentage of DDX4+ germ cells that are SYCP3+ in vitamin-C-deficient E14.5 female germ cells compared with controls. e, Abundance of Sycp3 mRNA is significantly reduced at E13.5 as measured by RNA-seq. n = 6 biological replicates. f, Representative haematoxylin and eosin staining of E14.5 embryonic ovaries for data quantified in Fig. 1h. Black arrowheads indicate germ cells at the indicated stage of meiosis. Images are representative of n = 8 biologically independent experiments. g, The percentage of germ cells in meiotic S phase versus post-S phase is significantly higher in vitamin-C-deficient E14.5 female mice, relative to controls. Additional analysis of data from meiosis staging is shown in Fig. 1h. n = 8 biologically independent experiments. h, Representative images of CREST and SYCP1 staining in E18.5 germ cells, as in Fig. 1h. i, Ovarian follicle volume and frequency are not significantly different in P7 female mice deprived of vitamin C in utero (P = 0.206). Ovarian follicles were stained by NOBOX and quantified using whole-mount imaging. n = 6 control and n = 9 vitamin-C-depleted ovaries per condition. Data are mean (c, e), mean ± s.e.m. (b, d) or mean ± s.d. (i). P values determined by two-sided Mann–Whitney U-test (b, d), Wald χ^2 test (c, e, g) or paired two-sided homoscedastic Student’s t-test (i). Source Data

Extended Data Fig. 4 Analyses of the effects of vitamin C deficiency on the development of male germ cells.

a, Unlike the consistent reduction of female germ cells (top), vitamin C (VC) deficiency does not decrease the number of germ cells in E13.5 male gonads (bottom). ns, not significant. The number of biological replicates is indicated. b, The meiotic germ-cell marker SYCP3 was not identified in n = 2 or n = 3 male gonads with or without vitamin C depletion, respectively. n = 6 control and n = 5 vitamin-C-deficient biological replicates. c, The meiotic germ-cell marker STRA8 was not identified in n = 2 or n = 3 male gonads with or without vitamin C depletion, respectively. Female graph includes n = 6 biological replicates. d, Most germ cells in developing testis are proliferative (Ki67+), with a few quiescent (Ki67−) germ cells, and no deviations from this pattern are detected with vitamin C deficiency. Images are representative of n = 2 control and n = 3 vitamin-C-deficient biological replicates. Data are mean ± s.d. (a) or mean ± s.e.m. (b, c). P values determined by two-sided Welch’s t-test (a) or two-tailed Mann–Whitney U-test (b–d). Source Data

Extended Data Fig. 5 Further analyses of RNA-seq data from vitamin-C-deficient E13.5 female germ cells.

a, Table of RNA-seq samples and number of germ cells per sample. Each sample represents germ cells from a single E13.5 female. b, Unsupervised hierarchical clustering of n = 6 biological replicates in each condition documents the overall separation between control and vitamin-C-deficient samples (columns) and relative gene expression (rows). 1CF1 denotes control litter 1, female embryo 1; 4VF2 denotes vitamin-C-deficient litter 4, female embryo 2. c, Scatterplot of differential gene expression in vitamin-C-deficient E13.5 female PGCs of genes differentially expressed in E13.5 Tet1−/− female PGCs[8]. Spearman’s rho statistic is used to estimate a rank-based measure of association. d, Expression of Dnmt and Tet genes in vitamin-C-deficient samples is similar to control samples. n = 6 biological replicates per condition. e, Heat map documenting the consistent expression of Tet and Dnmt genes across the six control and six vitamin-C-deficient samples. f, Expression of other genes belonging to families of enzymes with the potential to be vitamin C-sensitive (such as Kdm genes, collagen hydroxylases (P4h genes), prolyl hydroxylases (Lepre genes), HIF hydroxylases (Egln genes)). Lepre1 is also known as P3h1; Leprel1 is also known as P3h2; Leprel2 is also known as P3h3; and Leprel4 is also known as P3h4. None of these displays differential expression in vitamin-C-deficient female germ cells. n = 6 biological replicates per condition. Data are mean ± s.d. (d, f). Statistical significance assessed by two-tailed Student’s t-test (d, f). n.d., not determined. Source Data

Extended Data Fig. 6 Identification of the window of susceptibility to vitamin C deficiency between E3.5 and E13.5.

a, Pregnant female mice mated in vitamin-C-deficient conditions were either maintained without vitamin C (−VitC) or returned to vitamin-C-containing water at E3.5 (3.5 return). b, Adding back vitamin C from E3.5 to E13.5 tends to rescue the defects in the expression of key germline regulators induced with full vitamin C deficiency. Gene expression was measured by qRT–PCR in E13.5 female germ cells. n = 4 biological replicates. c, The numbers of E13.5 Oct4–eGFP+ germ cells are mostly recovered after the return of vitamin C at E3.5. Data are normalized to the germ-cell count of the control embryos. n = 11–22 biological replicates of each condition as indicated. Data are mean ± s.e.m. (b, c). *P < 0.05; **P < 0.01; two-tailed Student’s t-test (b, c). Source Data

Extended Data Fig. 7 DNA methylation defects in E13.5 vitamin-C-deficient female germ cells.

a, Average methylation of cytosine according to sequence context. Genome-wide CpG methylation is 3–6% regardless of vitamin C supplementation. Methylation of cytosine in a CHG or CHH context (in which H correspond to A, T or C) is below 1%. b, Average methylation according to genomic context in control and vitamin-C-deficient samples. Box plots indicate minimum to maximum measurements of n = 6 biological replicates, with centre line denoting the mean. c, Top, density plot of 460 DMRs with a >5% methylation change reveals an overall increase in the number and magnitude of methylation gains over losses after vitamin C deficiency. Bottom, GREAT analysis of 175 hypomethylated DMRs (hypermethylated DMRs are in Fig. 4b). d, Transposable elements of the LINE1, LTR, ERVK and IAP families that are associated with DMRs show a consistent pattern of hypermethylation after vitamin C deficiency. n = 6 biological replicates. e, Average methylation in control or vitamin-C-deficient samples in different transposable element families across the genome. Data are from uniquely mapped transposable elements annotated by RepeatMasker and captured by RRBS, regardless of the DMR calls, based on 558 elements and 3,180 CpGs (LINE1), 185 elements and 1,065 CpGs (full-length LINE1; >6 kb), 384 elements and 1,724 CpGs (SINE), 568 elements and 2,691 CpGs (ERVK), 226 elements and 1,057 CpGs (ERVK-IAP), 10 elements and 73 CpGs (satellite). The box extends to 25th and 75th percentiles, with centre line indicating the median transposable element methylation across n = 6 biological replicates. Error bars extend to 5th and 95th percentiles. f, hmC quantification by dot blot in E13.5 brain and liver indicate that hmC abundance is higher in brain and reduced with vitamin C depletion. Each group represents three biological replicates (across) and two technical replicates (vertical pairs). g, hmC quantification by ELISA (Active Motif) confirmed a significant decrease of hmC in both E13.5 brain and liver. Quantification was performed using 50 ng of DNA. n = 5 biological replicates. Data are mean ± s.e.m. (d, g). P values were determined by two-tailed Student’s t-tests (d), two-tailed Wilcoxon matched-pairs signed-rank test (e) or two-sided Welch’s t-test (g). Source Data

Extended Data Fig. 8 CUT&RUN analysis of H3K9me2 abundance in E13.5 female gonads.

a, Diagram of CUT&RUN experiments. E13.5 control or vitamin-C-deficient gonads were dissociated and the PGCs and soma were separated by FACS for cryopreservation and CUT&RUN analysis. PGCs and soma from 3–5 independent embryos per condition were subjected to H3K9me2 (K9me2) or control (IgG) CUT&RUN. b, K9me2 enrichment is highest at non- or low-expressed genes. Box plots of average K9me2 coverage at genes in control soma or PGC samples, separated into quartiles from lowest (quartile 1) to highest (quartile 4) expression level in control E13.5 soma. Coverage is calculated from average (K9me2/IgG + 0.001) of n = 4 control and n = 3 vitamin-C-depleted soma replicates, and n = 5 PGC replicates per condition. c, Scatter plots of average K9me2 coverage at genes or transposable element families in control or vitamin-C-deficient E13.5 female soma and PGCs. n = 4 control and n = 3 vitamin-C-depleted soma replicates, and n = 5 PGC replicates per condition. Significantly upregulated (yellow) or downregulated (blue) genes or transposable element families are indicated (log_2-transformed fold change > |1|, FDR < 0.05). d, Increases in soma K9me2 levels are highest at already K9me2-marked genes. Box plot showing K9me2 log_2-transformed fold change after vitamin C depletion in soma in groups of genes ranked according to K9me2 enrichment in control (lowest and highest quartile of K9me2 enrichment, and all genes). n = 4 control and n = 3 vitamin-C-depleted soma replicates, and n = 5 PGC replicates per condition. e, f, Histograms of K9me2 or IgG coverage at selected transposable element families in E13.5 female soma (e) or PGCs (f). n = 4 control and n = 3 vitamin-C-depleted soma replicates, and n = 5 PGC replicates per condition. Box plots in b and d indicate 25th and 75th percentiles, with centre lines marking the median values. Data are mean ± s.e.m. (e, f). P values were determined by two-sided Wilcoxon rank-sum test (b, d) or are the FDR from Limma analysis (c, e, f). See Supplementary Data 5 and Methods for details.

Extended Data Fig. 9 Model for the role of vitamin C in DNA methylation reprogramming and development of the embryonic germline.

Embryonic germline cells require vitamin C for proper DNA demethylation of key regulators of meiosis and transposable elements (TEs). Gestational vitamin C deficiency is compatible with development to term and adulthood, but induces a phenotype akin to a TET1 hypomorph, with incomplete DNA demethylation and downregulation of germline genes, reduced numbers of germ cell, meiosis defects and decreased fecundity. Vitamin C deficiency may also affect other enzymatic reactions in the germline.

Supplementary information

Reporting Summary

Supplementary Data 1

E13.5 germ cell RNA-seq from n = 6 control and Vitamin C-deficient female embryos. Toptable output from DESeq2.

Supplementary Data 2

qRT-PCR primer list

Supplementary data 3

RNA-seq significant genes’ gene ontology. Significant genes defined as padj < 0.05 from Supplementary Data 1.

Supplementary Data 4

Days of Vitamin C depletion per experiment.

Supplementary Data 5

Limma CUT&RUN toptable

Source data

Source Data Fig. 1

Source Data Fig. 2

Source Data Extended Data Fig. 1

Source Data Extended Data Fig. 2

Source Data Extended Data Fig. 3

Source Data Extended Data Fig. 4.

Source Data Extended Data Fig. 5.

Source Data Extended Data Fig. 6.

Source Data Extended Data Fig. 7.

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About this article

- Received

02 February 2018

- Accepted

02 August 2019

- Published

04 September 2019

- Issue Date

12 September 2019

- DOI
https://doi.org/10.1038/s41586-019-1536-1

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- Letter

- Published: 04 September 2019

Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut

Erik Bakkeren[1],
Jana S. Huisman2,3,
Stefan A. Fattinger1,4,
Annika Hausmann[1],
Markus Furter[1],
Adrian Egli5,6,
Emma Slack1,7,
Mikael E. Sellin[4],
Sebastian Bonhoeffer[2],
Roland R. Regoes[2],
Médéric Diard1,8 na1 &
Wolf-Dietrich Hardt[1] na1

Naturevolume 573, pages276–280 (2019) | Download Citation

Subjects

- Antibiotics
- Bacteria
- Bacterial evolution
- Evolution

Abstract

The emergence of antibiotic-resistant bacteria through mutations or the acquisition of genetic material such as resistance plasmids represents a major public health issue1,2. Persisters are subpopulations of bacteria that survive antibiotics by reversibly adapting their physiology3,4,5,6,7,8,9,10, and can promote the emergence of antibiotic-resistant mutants[11]. We investigated whether persisters can also promote the spread of resistance plasmids. In contrast to mutations, the transfer of resistance plasmids requires the co-occurrence of both a donor and a recipient bacterial strain. For our experiments, we chose the facultative intracellular entero-pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) and Escherichia coli, a common member of the microbiota[12]. S. Typhimurium forms persisters that survive antibiotic therapy in several host tissues. Here we show that tissue-associated S. Typhimurium persisters represent long-lived reservoirs of plasmid donors or recipients. The formation of reservoirs of S. Typhimurium persisters requires Salmonella pathogenicity island (SPI)-1 and/or SPI-2 in gut-associated tissues, or SPI-2 at systemic sites. The re-seeding of these persister bacteria into the gut lumen enables the co-occurrence of donors with gut-resident recipients, and thereby favours plasmid transfer between various strains of Enterobacteriaceae. We observe up to 99% transconjugants within two to three days of re-seeding. Mathematical modelling shows that rare re-seeding events may suffice for a high frequency of conjugation. Vaccination reduces the formation of reservoirs of persisters after oral infection with S. Typhimurium, as well as subsequent plasmid transfer. We conclude that—even without selection for plasmid-encoded resistance genes—small reservoirs of pathogen persisters can foster the spread of promiscuous resistance plasmids in the gut.

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Fig. 1: S. Typhimurium persisters associated with gut tissue are a reservoir for conjugative plasmids.

Fig. 2: Persisters at systemic sites are a reservoir for plasmid transfer in the gut.

Fig. 3: Plasmid transfer is initiated by rare re-seeding events from donors and can be prevented by vaccination.

Fig. 4: Tissue-associated persisters promote the transfer of resistance plasmids between different species of Enterobacteriaceae.

Data availability

The genome and plasmid sequence of E. coli ESBL 15 have been deposited in GenBank under accession numbers CP041678–CP041681 (Biosample SAMN12275742). Numerical Source Data for all figures are provided with the paper. Source images are available upon request to the corresponding authors.

Code availability

Code for the stochastic simulation of plasmid-transfer dynamics and parameter estimation from the experimental data are provided with the paper. The R code follows the notation used in the Supplementary Information.

References

1.

Parisi, A. et al. Health outcomes from multidrug-resistant Salmonella infections in high-income countries: a systematic review and meta-analysis. Foodborne Pathog. Dis. 15, 428–436 (2018).

- Article

- Google Scholar

2.

Wright, G. D. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat. Rev. Microbiol. 5, 175–186 (2007).

- CAS
- Article
- Google Scholar

3.

Brauner, A., Fridman, O., Gefen, O. & Balaban, N. Q. Distinguishing between resistance, tolerance and persistence to antibiotic treatment. Nat. Rev. Microbiol. 14, 320–330 (2016).

- CAS
- Article
- Google Scholar

4.

Fridman, O., Goldberg, A., Ronin, I., Shoresh, N. & Balaban, N. Q. Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations. Nature 513, 418–421 (2014).

- ADS
- CAS
- Article
- Google Scholar

5.

Claudi, B. et al. Phenotypic variation of Salmonella in host tissues delays eradication by antimicrobial chemotherapy. Cell 158, 722–733 (2014).

- CAS
- Article
- Google Scholar

6.

Helaine, S. et al. Internalization of Salmonella by macrophages induces formation of nonreplicating persisters. Science 343, 204–208 (2014).

- ADS
- CAS
- Article
- Google Scholar

7.

Kaiser, P. et al. Cecum lymph node dendritic cells harbor slow-growing bacteria phenotypically tolerant to antibiotic treatment. PLoS Biol. 12, e1001793 (2014).

- Article

- Google Scholar

8.

Dolowschiak, T. et al. IFN-γ hinders recovery from mucosal inflammation during antibiotic therapy for Salmonella gut infection. Cell Host Microbe 20, 238–249 (2016).

- CAS
- Article
- Google Scholar

9.

Balaban, N. Q. et al. Definitions and guidelines for research on antibiotic persistence. Nat. Rev. Microbiol. 17, 441–448 (2019).

- CAS
- Article
- Google Scholar

10.

Balaban, N. Q., Merrin, J., Chait, R., Kowalik, L. & Leibler, S. Bacterial persistence as a phenotypic switch. Science 305, 1622–1625 (2004).

- ADS
- CAS
- Article
- Google Scholar

11.

Levin-Reisman, I. et al. Antibiotic tolerance facilitates the evolution of resistance. Science 355, 826–830 (2017).

- ADS
- CAS
- Article
- Google Scholar

12.

Wotzka, S. Y. et al. Microbiota stability in healthy individuals after single-dose lactulose challenge–a randomized controlled study. PLoS ONE 13, e0206214 (2018).

- Article

- Google Scholar

13.

Coque, T. M., Baquero, F. & Canton, R. Increasing prevalence of ESBL-producing Enterobacteriaceae in Europe. Eurosurveillance 13, 19044 (2008).

- Google Scholar

14.

Crump, J. A., Sjölund-Karlsson, M., Gordon, M. A. & Parry, C. M. Epidemiology, clinical presentation, laboratory diagnosis, antimicrobial resistance, and antimicrobial management of invasive Salmonella infections. Clin. Microbiol. Rev. 28, 901–937 (2015).

- CAS
- Article
- Google Scholar

15.

Wilcock, B. P., Armstrong, C. H. & Olander, H. J. The significance of the serotype in the clinical and pathological features of naturally occurring porcine salmonellosis. Can. J. Comp. Med. 40, 80–88 (1976).

- CAS
- PubMed
- PubMed Central
- Google Scholar

16.

Wood, R. L., Pospischil, A. & Rose, R. Distribution of persistent Salmonella typhimurium infection in internal organs of swine. Am. J. Vet. Res. 50, 1015–1021 (1989).

- CAS
- PubMed
- Google Scholar

17.

San Román, B. et al. Relationship between Salmonella infection, shedding and serology in fattening pigs in low–moderate prevalence areas. Zoonoses Public Health 65, 481–489 (2018).

- Article

- Google Scholar

18.

Tenaillon, O., Skurnik, D., Picard, B. & Denamur, E. The population genetics of commensal Escherichia coli. Nat. Rev. Microbiol. 8, 207–217 (2010).

- CAS
- Article
- Google Scholar

19.

Apperloo-Renkema, H. Z., Van der Waaij, B. D. & Van der Waaij, D. Determination of colonization resistance of the digestive tract by biotyping of Enterobacteriaceae. Epidemiol. Infect. 105, 355–361 (1990).

- CAS
- Article
- Google Scholar

20.

Stecher, B. et al. Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae. Proc. Natl Acad. Sci. USA 109, 1269–1274 (2012).

- ADS
- CAS
- Article
- Google Scholar

21.

Diard, M. et al. Inflammation boosts bacteriophage transfer between Salmonella spp. Science 355, 1211–1215 (2017).

- ADS
- CAS
- Article
- Google Scholar

22.

Moor, K. et al. High-avidity IgA protects the intestine by enchaining growing bacteria. Nature 544, 498–502 (2017).

- ADS
- CAS
- Article
- Google Scholar

23.

Monack, D. M., Bouley, D. M. & Falkow, S. Salmonella typhimurium persists within macrophages in the mesenteric lymph nodes of chronically infected Nramp1
+/+ mice and can be reactivated by IFNγ neutralization. J. Exp. Med. 199, 231–241 (2004).

- CAS
- Article
- Google Scholar

24.

Diard, M. et al. Antibiotic treatment selects for cooperative virulence of Salmonella Typhimurium. Curr. Biol. 24, 2000–2005 (2014).

- CAS
- Article
- Google Scholar

25.

Sampei, G. et al. Complete genome sequence of the incompatibility group I1 plasmid R64. Plasmid 64, 92–103 (2010).

- CAS
- Article
- Google Scholar

26.

Hensel, M. et al. Simultaneous identification of bacterial virulence genes by negative selection. Science 269, 400–403 (1995).

- ADS
- CAS
- Article
- Google Scholar

27.

Stapels, D. A. C. et al. Salmonella persisters undermine host immune defenses during antibiotic treatment. Science 362, 1156–1160 (2018).

- ADS
- CAS
- Article
- Google Scholar

28.

Moor, K. et al. Peracetic acid treatment generates potent inactivated oral vaccines from a broad range of culturable bacterial species. Front. Immunol. 7, 34 (2016).

- Article

- Google Scholar

29.

Fauvart, M., De Groote, V. N. & Michiels, J. Role of persister cells in chronic infections: clinical relevance and perspectives on anti-persister therapies. J. Med. Microbiol. 60, 699–709 (2011).

- Article

- Google Scholar

30.

Roberts, M. E. & Stewart, P. S. Modelling protection from antimicrobial agents in biofilms through the formation of persister cells. Microbiology 151, 75–80 (2005).

- CAS
- Article
- Google Scholar

31.

Knodler, L. A. et al. Noncanonical inflammasome activation of caspase-4/caspase-11 mediates epithelial defenses against enteric bacterial pathogens. Cell Host Microbe 16, 249–256 (2014).

- CAS
- Article
- Google Scholar

32.

Sellin, M. E. et al. Epithelium-intrinsic NAIP/NLRC4 inflammasome drives infected enterocyte expulsion to restrict Salmonella replication in the intestinal mucosa. Cell Host Microbe 16, 237–248 (2014).

- CAS
- Article
- Google Scholar

33.

Defraine, V., Fauvart, M. & Michiels, J. Fighting bacterial persistence: current and emerging anti-persister strategies and therapeutics. Drug Resist. Updat. 38, 12–26 (2018).

- Article

- Google Scholar

34.

Grant, A. J. et al. Modelling within-host spatiotemporal dynamics of invasive bacterial disease. PLoS Biol. 6, e74 (2008).

- Article

- Google Scholar

35.

Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640–6645 (2000).

- ADS
- CAS
- Article
- Google Scholar

36.

Sternberg, N. L. & Maurer, R. Bacteriophage-mediated generalized transduction in Escherichia coli and Salmonella typhimurium. Methods Enzymol. 204, 18–43 (1991).

- CAS
- Article
- Google Scholar

37.

Stecher, B. et al. Chronic Salmonella enterica serovar Typhimurium-induced colitis and cholangitis in streptomycin-pretreated Nramp1
+/+ mice. Infect. Immun. 74, 5047–5057 (2006).

- CAS
- Article
- Google Scholar

38.

Barthel, M. et al. Pretreatment of mice with streptomycin provides a Salmonella enterica serovar Typhimurium colitis model that allows analysis of both pathogen and host. Infect. Immun. 71, 2839–2858 (2003).

- CAS
- Article
- Google Scholar

39.

Johansson, M. E. & Hansson, G. C. Preservation of mucus in histological sections, immunostaining of mucins in fixed tissue, and localization of bacteria with FISH. Methods Mol. Biol. 842, 229–235 (2012).

- CAS
- Article
- Google Scholar

40.

Marjoram, P., Molitor, J., Plagnol, V. & Tavare, S. Markov chain Monte Carlo without likelihoods. Proc. Natl Acad. Sci. USA 100, 15324–15328 (2003).

- ADS
- CAS
- Article
- Google Scholar

41.

Zankari, E. et al. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67, 2640–2644 (2012).

- CAS
- Article
- Google Scholar

Download references

Acknowledgements

We thank the members of the Hardt, Slack, Bonhoeffer, Stadler and Ackermann labs for helpful discussion, and the staff at the RCHCI and EPIC animal facilities for their excellent support. This work has been funded, in part, by grants from the Swiss National Science Foundation (SNF; 310030B-173338), the Promedica Foundation, Chur and the Helmut Horten Foundation to W.-D.H., and from the SNF NFP 72 (407240-167121) to W.-D.H., S.B. and A.E. M.D. is funded by an SNF professorship grant (PP00PP_176954), E.B. by a Boehringer Ingelheim Fonds PhD fellowship, and M.E.S. and S.A.F. (in part) by the Swedish Research Council (2015-00635, 2018-02223). R.R.R. is funded by SNF grant number 31003A_179170. E.S. is supported by grant GRS 073/17 from the ‘Microbials’ programme of the Gebert Rüf Foundation and the SNF Bridge Discover Grant 20B2-1 180953.

Author information

Author notes

1. These authors contributed equally: Médéric Diard, Wolf-Dietrich Hardt

Affiliations

1. Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland

- Erik Bakkeren
- , Stefan A. Fattinger
- , Annika Hausmann
- , Markus Furter
- , Emma Slack
- , Médéric Diard
- & Wolf-Dietrich Hardt

2. Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland

- Jana S. Huisman
- , Sebastian Bonhoeffer
- & Roland R. Regoes

3. Swiss Institute of Bioinformatics, Lausanne, Switzerland

- Jana S. Huisman

4. Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

- Stefan A. Fattinger

- & Mikael E. Sellin

5. Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland

- Adrian Egli

6. Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland

- Adrian Egli

7. Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland

- Emma Slack

8. Biozentrum, University of Basel, Basel, Switzerland

- Médéric Diard

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Contributions

E.B. (Figs. 1, 2, 3a, b, e, f, 4, Extended Data Figs. 1–3, 4a–c, e, f, 5–9), S.A.F. (Fig. 1e, Extended Data Fig. 4a–d), A.H. (Fig. 2, Extended Data Figs. 5, 6e, f, 9e), M.F. (Extended Data Fig. 4e–h) and E.S. (Fig. 3e, f, Extended Data Fig. 7b) performed the experiments shown in the indicated figures. J.S.H., S.B. and R.R.R. (Fig. 3c, d, Extended Data Figs. 1b, 6g, 10) performed mathematical modelling shown in the indicated figures. A.E. (Extended Data Fig. 1b) provided E. coli strain Z2115. E.B., M.D. and W.-D.H. designed the experiments. S.A.F., M.F. and M.E.S. designed the microscopy-based experiments and analysis. E.B., M.D. and W.-D.H. conceived the project and wrote the manuscript. All authors read, commented and approved this manuscript.

Corresponding authors

Correspondence to Médéric Diard or Wolf-Dietrich Hardt.

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Peer review information Nature thanks Sophie Helaine and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Fig. 1 Emergence and spread of antibiotic resistance in bacteria using P2 as a model for conjugation.

a, Antibiotic resistance in bacteria can emerge through mutation, or be acquired via horizontal gene transfer. Plasmid transfer is an important driver of the spread of antibiotic resistance. Tolerance increases the abundance of bacteria that survive antibiotic exposure, allowing for a higher probability of the emergence of mutations that lead to resistance[11]. We hypothesize that antibiotic resistance can also spread through the formation of reservoirs of persisters that contain plasmids; here, we hypothesize that the gut mucosa of the host can serve as a reservoir for persisters. The formation of long-term reservoirs, followed by re-seeding of bacteria from this reservoir into a niche occupied by other bacteria (for example, the gut lumen occupied by the microbiota following antibiotic therapy) increases the chance that two different strains interact with each other, leading to plasmid transfer (that is, increased strain co-occurrence). The representation in the bottom right panel is an example of donor persisters boosting co-occurrence. Note that tissue-associated recipient persisters may also increase co-occurrence. b, P2 shares homology with resistance plasmids. An alignment is shown between S. Typhimurium SL1344 P2 (GenBank sequence identifier HE654725.1), S. Typhimurium plasmid R64 (GenBank sequence identifier AP005147.1), and pESBL15 of E. coli Z2115 (strain isolated from a rectal swab of a patient at the University Hospital Basel) using the Artemis comparison tool (https://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act). Red fill indicates high sequence identity (>85% sequence identity), blue fill indicates inversions and no fill indicates no sequence identity. For each plasmid, open reading frames (in each of the six translational frames) are shown by white regions (detected by the Artemis comparison tool). Antibiotic resistances (for example, streptomycin and tetracycline resistances on R64 and CTX-M-1 on pESBL15) are labelled, shown by light-blue directed rectangles (found by a Basic Local Alignment Search Tool (NCBI) search against the ResFinder antibiotic-resistance-gene database[41]). In P2, the locus for insertion of the chloramphenicol-resistance cassette and neutral sequence tags is shown. For each alignment, the percentage of the sequence that aligns to P2 is shown, as well as the average sequence similarity for these regions. c, Model strains for addressing evolution by conjugation in S. Typhimurium. SL1344 contains P2cat (chloramphenicol-resistance cassette (cat) that allows the enumeration of plasmid-bearing strains by selective plating) that can be conjugated to 14028S (kanamycin-resistance cassette (aphT) used for selective plating) to form a transconjugant (CmR and KanR). Transconjugants can then transfer P2cat to additional recipients. d, P2cat transfer kinetics in vitro. P2cat transfer is dependent on the density of donors and recipients. Donor and recipient strains were inoculated into LB (n = 2, 1 experiment) at a 1:1 ratio and selective plating was performed every hour. CFUs per millilitre are reported for each population (donors in blue, recipients in green and transconjugants in red). Solid lines connect medians. The dotted line indicates the detection limit by selective plating. Source data

Extended Data Fig. 2 Antibiotic-resistance profile of key strains.

Antibiotic susceptibility testing was performed in LB in 96-well plates. Six strains (indicated on the figure axes) were tested against seven antibiotics, grown at 37 °C at 120 r.p.m. for 16 h, at which point the OD600 nm was measured. For each antibiotic, the highest concentration used was based on the working concentration in this study. For example, the concentration of antibiotic used for selective plating in the case of streptomycin, kanamycin, ampicillin and chloramphenicol (the highest concentration of chloramphenicol was fivefold-higher than the concentration used for selective plating, because this was already close to the minimum inhibitory concentration), or the concentration of antibiotic used for the gentamicin protection assay. Importantly, a very low minimum inhibitory concentration was observed for antibiotics used in vivo to enrich for persisters (that is, ciprofloxacin and ceftriaxone). The mean of three experiments is presented on a blue–white colour gradient, in which blue indicates a large amount of bacterial growth. This is calculated by subtracting the OD600 nm measured for each sample well from the background generated by the medium. Source data

Extended Data Fig. 3 Controls for conjugation after antibiotic treatment in the oral infection model.

a–c, Faecal bacterial-population sizes and inflammatory status of mice in Fig. 1c, d (comparison of invasive versus non-invasive donors in the oral model). Faecal loads of donors (blue, SmR and CmR), recipients (green, KanR), and transconjugants (red, CmR and KanR) were determined by selective plating on MacConkey agar. Black dotted line indicates detection limits for donors and transconjugants. Green dotted line indicates detection limit for recipients. The detection limit is higher for recipients once transconjugants reach a density of >10^8 CFU per gram of faeces. Before this happens, recipients can be found below the detection limit; the black dotted line should then be considered as the detection limit. Blue lines connect medians of donor populations; red lines connect medians of transconjugant populations. a, Mice infected with invasive S. Typhimurium donors (solid circles; n = 15 singly housed mice from 5 independent experiments). b, Mice infected with non-invasive S. Typhimurium donors (open circles; n = 6 singly housed mice from 2 independent experiments). c, Inflammatory status was determined by lipocalin-2 ELISA. Statistics were performed using a two-tailed Mann–Whitney U-test. NS, not significant (P ≥ 0.05), ****P < 0.0001, comparing mice infected with an invasive donor (solid black circles; n = 15 singly housed mice from 5 independent experiments) to mice infected with a non-invasive donor (open black circles; n = 6 singly housed mice from 2 independent experiments) at each time point. Medians are shown (solid red line for invasive donors; dotted red line for non-invasive donors). Dotted line indicates the detection limit. d, e, Carrying P2cat does not lead to a measurable fitness cost or benefit. d, A ‘locked’ transconjugant (14028S P2aphT ΔoriT (KanR and AmpR), in which conjugation is blocked by removing the origin of transfer) was competed against a recipient (14028S cat (CmR and AmpR)). e, To ensure that removing the origin of transfer did not affect fitness, the locked transconjugant was competed against a transconjugant with a normal P2cat plasmid (that is, mobile transconjugant) (14028S P2cat (CmR and AmpR)). In d, e, both strains were introduced at a 1:1 ratio (total inoculum size about 5 × 10^7 CFU per os) and faeces were monitored daily by selective plating (n = 6 singly housed mice from 2 independent experiments for both experiments). The competitive index is calculated by dividing the population size of one competitor by the other. Lines indicate medians. The dotted line indicates no competitive advantage for either strain. This is consistent with previously published data[20]. These data indicate that it is the plasmid-encoded conjugation efficiency (not the effects of the plasmid on host bacterial fitness) that drives the rise of transconjugants (Fig. 1c). f, g, Plasmid transfer in the oral model does not require an invasive recipient. Invasive donors (SL1344 P2cat (SmR and CmR)) were orally infected into pre-treated mice. After ciprofloxacin treatment, a non-invasive mutant of S. Typhimurium 14028S was used as a recipient (non-invasive 14028S aphT (KanR and AmpR)). n = 5 mice. f, Selective plating determined faecal loads of donors (blue, SmR and CmR), recipients (green, KanR), and transconjugants (red, CmR and KanR). Black dotted line indicates the detection limit for donors and transconjugants. Green dotted line indicates the detection limit for recipients. The detection limit is higher for recipients once transconjugants reach a density of >10^8 CFU per gram of faeces. Before this happens, recipients can be found below the detection limit; the black dotted line should then be considered as the detection limit. Blue lines connect medians of donor populations; red lines connect medians of transconjugant populations. g, Donor populations enumerated after a gentamicin protection assay on caecal tissue of mice shown in f. Median indicated by solid line. Dotted line indicates the detection limit. h, i, Conjugation is required for plasmid transfer after antibiotic treatment. Mice were infected with invasive S. Typhimurium that lacks the origin of transfer in P2cat (SL1344 P2cat ΔoriT (SmR and CmR)) as a donor, and 14028S aphT (KanR and AmpR) as a recipient, after antibiotic treatment. n = 5 mice. h, Selective plating determined the faecal loads of donors (blue, SmR and CmR), recipients (green, KanR) and transconjugants (red, CmR and KanR). Black dotted line indicates the detection limit for donors and transconjugants. Green dotted line indicates detection limit for recipients. The detection limit is higher for recipients once transconjugants reach a density of >10^8 CFU per gram of faeces. Before this happens, recipients can be found below the detection limit; the black dotted line should then be considered as the detection limit. Blue lines connect medians of donor populations; red lines connect medians of transconjugant populations. i, Donor populations enumerated after a gentamicin protection assay on caecal tissue of mice shown in h. Median indicated by solid line. Dotted line indicates the detection limit. Source data

Extended Data Fig. 4 Quantification and localization of S. Typhimurium in the host mucosa after antibiotic treatments in the oral model.

a–d, Mice were orally infected with either an invasive (SL1344 P2cat) (blue solid circles, n = 7 mice) or non-invasive (non-invasive SL1344 P2cat, TTSS-1 negative) (blue open circles, n = 7 mice) donor and treated with antibiotics. Mice were euthanized at day 8 after infection (at which point recipients were normally added), and organs were analysed. Dotted lines indicate the detection limits. a, Faecal populations were monitored daily by selective plating on MacConkey agar. Blue lines connect medians. b, Organ loads were determined by selective plating. c, Population size of donors in the caecal mucosa determined by selective plating after a gentamicin protection assay, or microscopy of tissue sections (same mice for each quantification method). Each data point is the average of 12 sections (10-μm thick). b, c, Statistics were performed using a two-tailed Mann–Whitney U-test. NS, not significant (P ≥ 0.05), *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001, comparing mice infected with invasive or non-invasive donors for each organ. d, Localization of S. Typhimurium detected in the caecal tissue by microscopy, reported as a percentage of bacteria detected in c in either the lamina propria (l.p.) or epithelium (ep.). Bar indicates the median from five mice. e–h, Analysis of reservoirs of persisters in Carnoy-fixed caecal tissue sections. Mice were orally infected with an invasive (SL1344 P2cat, n = 5 mice) donor and treated with antibiotics. Mice were euthanized at day 8 after infection (at which point recipients are normally added) and organs were analysed. Dotted lines indicate the detection limits. e, Faecal populations were monitored daily by selective plating on MacConkey agar. Blue lines connect medians. f, Organ loads were determined by selective plating. Line indicates median. g, A Carnoy fixation was performed on caeca of mice to preserve the mucus structure. Ten-micrometre sections were stained to visualize S. Typhimurium (yellow, anti-LPS O5), actin (green, phalloidin–FITC), the mucus (red, wheat germ agglutinin AF647 conjugate) and nuclei (blue, DAPI). Mu., mucus. Scale bars, 20 μm. White arrows highlight S. Typhimurium (magnified in inset). Representative images shown from two independent experiments. h, Localization of S. Typhimurium detected in the caecal tissue by microscopy, reported as a percentage of bacteria detected each section (12 sections per mouse caecum) in the lamina propria, epithelium, mucus or lumen. Bar indicates the median from five mice. Source data

Extended Data Fig. 5 Determination of reservoirs of tissue-associated persisters after intravenous infection, and subsequent plasmid transfer.

a, An equal mix of five SL1344 P2cat tag strains (SmR and CmR) were intravenously infected into mice (10^3 CFU). Treatments were as described in Fig. 2b (grey circles, 3 intraperitoneal doses of ceftriaxone; n = 8 singly housed mice from 2 independent experiments) or mice were left untreated (black circles; n = 8 singly housed mice from 2 independent experiments). Mice were euthanized on day 5 of the experiment (after the final dose of ceftriaxone was given). The tissue-associated populations in organs were enumerated by selective plating. Detection limit by selective plating is shown as a dotted line. Lines indicate median. b, c, Faecal bacterial population sizes of mice in Fig. 2d, e (comparison of wild-type and SPI-2-negative donors in the intravenous model). Faecal loads of donors (blue, SmR and CmR), recipients (green, KanR) and transconjugants (red, CmR and KanR) were determined by selective plating on MacConkey agar. Black dotted line indicates the detection limits for donors and transconjugants. Green dotted line indicates the detection limit for recipients. The detection limit is higher for recipients once transconjugants reach a density of >10^8 CFU per gram of faeces. Before this happens, recipients can be found below the detection limit; the black dotted line should then be considered as the detection limit. Blue lines connect medians of donor populations; red lines connect medians of transconjugant populations. b, Mice infected with wild-type S. Typhimurium donors (solid circles). c, Mice infected with SPI-2-deficient S. Typhimurium donors (open circles). Source data

Extended Data Fig. 6 Experimental strategy for assessing population dynamics and tag frequencies.

Relates to Fig. 3a–d. a–c, Tags introduced in the oral model. a, Tags coupled to a chloramphenicol-resistance cassette were introduced in P2. qPCR primers are specific to the chloramphenicol-resistance cassette and the specific tag (shown as one-sided arrows). Five tagged donors were pooled and orally infected as a 1:1:1:1:1 mix into mice. b, Relative plasmid-tag proportion detected by qPCR in the initial donor population, the donor population persisting in the caecal mucosa and the transconjugant population is shown for eight mice (three independent inocula). Dotted line indicates the detection limit. Each tag is given a unique colour. c, Scheme illustrating how tags were sorted and recoloured to yield the plots in Fig. 3a, b. Two mice are shown as examples. For the mucosa-associated donor populations (top) and for the faecal transconjugant populations (bottom), tags were sorted according to relative frequency. These tags were re-coloured (darker colour indicates higher frequency) to visualize the trends shown in Fig. 3a, b. These re-ordered tags were used as the experimental data for fitting the mathematical model. d–f, Experimental strategy to assess plasmid-transfer dynamics in the intravenous model. d, Tags coupled to a chloramphenicol-resistance cassette were introduced in P2. qPCR primers are specific to ydgA (a pseudogene flanking the specific tags) and the specific tag (shown as one-sided arrows). Five tagged donors were pooled and intravenously infected as a 1:1:1:1:1 mix into mice. e, Tags from the faecal transconjugant population at day 25 are sorted by abundance. Note that each abundance rank can consist of any tag (ranking and re-colouring scheme in c and raw tag data in f). n = 6 singly housed mice from 2 independent experiments. Dotted line indicates the conservative detection limit by qPCR. This detection limit refers to the most-conservative detection limit of any qPCR run (2.9 × 10−3; that is, tags can appear below this detection limit if the qPCR run yielded a lower detection limit). Line indicates the mean; error bars indicate the s.d. f, Relative plasmid-tag proportion detected by qPCR in the inoculum, the donor population persisting in the internal organs and the transconjugant population in the faeces is shown for six mice (three independent inocula; faeces and organ population data in Fig. 2d). Dotted line indicates the detection limit. Each tag is given a unique colour. g, Representation of key parameters in the mathematical model. Donors form a reservoir of persisters in host tissues. These cells can interact with other bacteria that colonize the gut lumen (that is, recipients), and transfer plasmids. Our mathematical model summarizes these plasmid-transfer dynamics using a few key parameters. Donors re-seed the gut lumen and transfer plasmids at rate η, transconjugants transfer plasmids to recipients (without a plasmid) at rate γ and the turn-over of each bacterial population is given by r − c, in which r is the birth rate and c is the clearance rate. Source data

Extended Data Fig. 7 Faecal bacterial-population sizes and inflammatory status of mice (comparison of vaccinated versus naive mice in the oral model), and validation by mixtures of invasive and non-invasive donors.

Relates to Fig. 3e, f. a, b, Faecal loads of donors (blue, SmR and CmR), recipients (green, KanR), and transconjugants (red, CmR and KanR) were determined by selective plating on MacConkey agar. Barcode analysis of the recipient chromosome tags could not be performed because of technical issues with kanamycin enrichments and subsequent qPCR. Black dotted lines indicate the detection limits for donors and transconjugants. Green dotted line indicates the detection limit for recipients. The detection limit is higher for recipients once transconjugants reach a density of >10^8 CFU per gram of faeces. Before this happens, recipients can be found below the detection limit; the black dotted line should then be considered as the detection limit. Blue lines connect medians of donor populations; red lines connect medians of transconjugant populations. a, Naive mice infected with invasive S. Typhimurium donors (solid circles). b, Vaccinated mice infected with invasive S. Typhimurium donors (open circles with light-grey fill). c, Inflammatory status to determine the success of vaccination was determined by lipocalin-2 ELISA. Statistics were performed using a two-tailed Mann–Whitney U-test. NS, not significant (P ≥ 0.05), *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001, comparing naive mice (black circles, n = 9 singly housed mice from 3 independent experiments) to vaccinated mice (open circles, n = 14 singly housed mice from 4 independent experiments) at each time point. Medians are shown (solid red line for naive mice and dotted red line for vaccinated mice). Dotted line the indicates detection limit. d–g, Experimentally reducing the population size of mucosa-associated persisters by mixing invasive and non-invasive donors reduces plasmid transfer in the oral model. Mice were orally infected with a mixture of invasive (SL1344 P2cat, SmR and CmR) and non-invasive (non-invasive SL1344 P2cat, SmR and CmR) donors at two ratios: 1:10 (n = 6 singly housed mice) or 1:500 (n = 5 singly housed mice). In both cases, an excess of non-invasive donors was used to experimentally reduce the number of cells that can establish a reservoir of persisters in the intestinal mucosa (two independent experiments). S. Typhimurium 14028S aphT (KanR and AmpR) was used as a recipient after antibiotic treatment. d, Donor populations enumerated after a gentamicin protection assay on caecal tissue of mice infected with a 1:10 ratio (blue circles with dark grey fill; line indicates median) or 1:500 ratio (blue circles with light grey fill; line indicates median) of invasive to non-invasive donors. Statistics were performed using a two-tailed Mann–Whitney U-test **P < 0.01. e, Proportion of transconjugants (transconjugant population size divided by the sum of recipients and transconjugants) in the faeces is shown for each day, for mice infected with a 1:10 ratio (black circles with dark grey fill, grey bars indicate median) or a 1:500 ratio (black circles with light grey fill, light grey bars indicate median) of invasive to non-invasive donors. f, g, Faecal loads of donors (blue, SmR and CmR), recipients (green, KanR) and transconjugants (red, CmR and KanR) were determined by selective plating on MacConkey agar. f, Mice infected with a 1:10 ratio of invasive to non-invasive donors. g, Mice infected with a 1:500 ratio of invasive to non-invasive donors. In d–g, the black dotted line indicates the detection limit for donors and transconjugants. Green dotted line indicates the detection limit for recipients. The detection limit is higher for recipients once transconjugants reach a density of >10^8 CFU per gram of faeces. Before this happens, recipients can be found below the detection limit; the black dotted line should then be considered as the detection limit. Source data

Extended Data Fig. 8 Faecal bacterial-population sizes of mice and the role of persistence and conjugation in host tissues if the recipient constitutes the reservoir.

Relates to Fig. 4. a, Faecal loads of donors (blue, SmR and CmR), recipients (green, AmpR), and transconjugants (red, CmR and AmpR) were determined by selective plating on MacConkey agar (same mice as in Fig. 4a, b; S. Typhimurium donor and E. coli recipient in the oral model). Black dotted line indicates the detection limit for donors and transconjugants. Green dotted line indicates the detection limit for recipients. The detection limit is higher for recipients once transconjugants reach a density of >10^8 CFU per gram of faeces. Before this happens, recipients can be found below the detection limit; the black dotted line should then be considered as the detection limit. Blue lines connect medians of donor populations; red lines connect medians of transconjugant populations. b–d, Persistence in host tissues also promotes plasmid transfer if the recipient constitutes the reservoir. Pre-treated mice were orally infected with a S. Typhimurium recipient (SL1344 P2cured aphT, SmR and KanR) and treated with ciprofloxacin and ampicillin as in the oral model (Fig. 1b). On day 8, ampicillin was removed from the drinking water and an E. coli donor was introduced orally (E. coli 8178 P2cat, CmR and AmpR). b, Recipient populations enumerated after a gentamicin protection assay on caecal tissue (n = 5 singly housed mice from 2 independent experiments). Line indicates median. c, Proportion of transconjugants (transconjugant population size divided by sum of recipients and transconjugants) in the faeces is shown for each day. Grey bars indicate median. d, Faecal loads of recipients (green, SmR and KanR), donors (blue, CmR and AmpR), and transconjugants (red, SmR, CmR and KanR) were determined by selective plating on MacConkey agar. In b–d, dotted lines indicate detection limits by selective plating. e, Faecal bacterial-populations sizes of mice in Fig. 4c, d (S. Typhimurium ESBL donor in the oral model). Faecal loads of donors (blue, SmR and AmpR), recipients (green, KanR) and transconjugants (red, KanR and AmpR) were determined by selective plating on MacConkey agar. Black dotted line indicates the detection limit for donors and transconjugants. Green dotted line indicates the detection limit for recipients. The detection limit is higher for recipients once transconjugants reach a density of >10^8 CFU per gram of faeces. Before this happens, recipients can be found below the detection limit; the black dotted line should then be considered as the detection limit. Blue lines connect medians of donor populations; red lines connect medians of transconjugant populations. Source data

Extended Data Fig. 9 Exchanging ampicillin for kanamycin to limit gut-luminal growth of the donor does not affect the overall plasmid-transfer kinetics, and faecal bacteria-population sizes of intravenously infected mice.

Relates to Fig. 4. a–d, Mice were orally infected with SL1344 P2cat (SmR and CmR) as a donor, and 14028S aphT (KanR and AmpR) as a recipient after antibiotic treatment. Mice were either treated with ampicillin in the drinking water until day 15 (normal protocol as in Fig. 1b), day 8 (when the recipient is added) or kanamycin until day 8. a, Donor populations enumerated after a gentamicin protection assay on caecal tissue of mice, in which ampicillin is maintained until day 15 (solid blue circles, n = 15 singly housed mice from 5 independent experiments; data taken from Fig. 1d), ampicillin is removed on day 8 (blue circles with pink fill, n = 3 singly housed mice from 1 experiment) or kanamycin is used until day 8 (blue circles with yellow fill, n = 3 singly housed mice from 1 experiment). Median indicated by solid line. b, Proportion of transconjugants (transconjugant population size divided by the sum of recipients and transconjugants) is shown for the groups receiving ampicillin treatment until day 15 (solid black circles, grey bars indicate median; n = 15 singly housed mice from 5 independent experiments; data taken from Fig. 1c), ampicillin treatment until day 8 (black circles with pink fill, pink bars indicate median; n = 3 singly housed mice from 1 experiment), and kanamycin treatment until day 8 (black circles with yellow fill, yellow bars indicate median; n = 3 singly housed mice from 1 experiment). c, d, Faecal loads of donors (blue, SmR and CmR), recipients (green, KanR) and transconjugants (red, CmR and KanR) were determined by selective plating on MacConkey agar. c, Mice treated until day 8 with ampicillin. d, Mice treated until day 8 with kanamycin. In a–d, the black dotted line indicates the detection limit for donors and transconjugants. Green dotted line indicates the detection limit for recipients. The detection limit is higher for recipients once transconjugants reach a density of >10^8 CFU per gram of faeces. Before this happens, recipients can be found below the detection limit; the black dotted line should then be considered as the detection limit. e, Faecal bacterial-populations sizes of mice in Fig. 4e, f (S. Typhimurium donor and E. coli recipient in the intravenous model). Faecal loads of donors (blue, SmR and AmpR), recipients (green, KanR) and transconjugants (red, KanR and AmpR) were determined by selective plating on MacConkey agar. Black dotted line indicates the detection limit for donors and transconjugants. Green dotted line indicates the detection limit for recipients. The detection limit is higher for recipients once transconjugants reach a density of >10^8 CFU per gram faeces. Before this happens, recipients can be found below the detection limit; the black dotted line should then be considered as the detection limit. Blue lines connect medians of donor populations; red lines connect medians of transconjugant populations. Source data

Extended Data Fig. 10 Increasing growth rate at carrying capacity to model inflammation, or running simulations on a finer parameter grid, does not affect overall simulation trends.

a, b, Simulations were run with identical parameters to Fig. 3c, d, but an increased birth and death rate at carrying capacity to simulate cases in which inflammation is present (Supplementary Information). The trends of the simulations remain the same as in Fig. 3c, d. a, Likelihood of the model as a function of the donor re-seeding (including donor-to-recipient conjugation) rate, and the rate of transconjugant-to-recipient plasmid transfer. All other parameter values are given in the Supplementary Information. The most-likely set of parameters is shown in red (η = 1 × 10−9 events per recipient per day; γ = 3.16 × 10−8 events per recipient per CFU per gram of faeces per day). b, The fraction of simulations with plasmid re-seeding (defined as a final transconjugant population size above 5 × 10^8 CFU per gram of faeces) is shown as a function of η. Here, γ is fixed at its most-likely value of 3.16 × 10−8 events per recipient per CFU per gram of faeces per day. The black vertical dotted line at η = 1 × 10−9 events per recipient per day indicates the estimated most-likely value from a. The red vertical dotted line at η = 1 × 10–11 events per recipient per day indicates a hypothetical 100-fold decrease of η (shown by a red arrow) (as might be caused, for example, by vaccination). c–f, Running simulations on a finer parameter grid does not affect the overall simulation trends. Supplementary Table 4 provides details of the differences between specific simulation results. c, d, Simulations were run on a grid of η = 10−12 to 10−6 and γ = 10−10 to 10−1 with 0.25-log increments, instead of the η = 10−12 to 10−1 and γ = 10−12 to 10−1 with 0.5-log increments used in Fig. 3c, d. e, f, Simulations were run with parameters identical to a, b, but on a grid of η = 10−12 to 10−6 and γ = 10−10 to 10−1 with 0.25-log increments, instead of η = 10−12 to 10−1 and γ = 10−12 to 10−1 with 0.5-log increments. c, e, Likelihood of the model as a function of the donor re-seeding (including donor-to-recipient conjugation) rate, and the rate of transconjugant-to-recipient plasmid transfer. All other parameter values are given in the Supplementary Information. The most-likely set of parameters is shown in red. d, f, The fraction of simulations with plasmid re-seeding (defined as a final transconjugant population size above 5 × 10^8 CFU per gram of faeces) is shown as a function of η. Here γ is fixed at its most likely value. The black vertical dotted line indicates the estimated most-likely value (from c or e). The red vertical dotted line indicates a hypothetical 100-fold decrease of η (shown by a red arrow) (as might be caused, for example, by vaccination). Source data

Supplementary information

Supplementary Information

The PDF file "Supplementary Materials" contains Supplementary Tables 1–4 and Supplementary Discussion A–D. Supplementary Tables 1 and 2 indicate the strains, plasmids and primers used in this study. Supplementary Table 3 contains input parameters and priors used in the stochastic simulations, and Supplementary Table 4 contains parameter estimate for different simulations. Supplementary Discussions A–C provide additional context and relevance for the present study, and Supplementary Discussion D provides a detailed description of the mathematical model.

Reporting Summary

Supplementary Data

This zip file contains R scripts and input data used for running simulations.

Source data

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About this article

- Received

18 October 2018

- Accepted

05 August 2019

- Published

04 September 2019

- Issue Date

12 September 2019

- DOI
https://doi.org/10.1038/s41586-019-1521-8

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- Letter

- Published: 04 September 2019

The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape

Daniel N. Weinberg[1] na1,
Simon Papillon-Cavanagh[2] na1,
Haifen Chen[2],
Yuan Yue[3],
Xiao Chen4,5,
Kartik N. Rajagopalan[6],
Cynthia Horth[2],
John T. McGuire4,5,
Xinjing Xu4,5,
Hamid Nikbakht[2],
Agata E. Lemiesz[1],
Dylan M. Marchione7,8,
Matthew R. Marunde[9],
Matthew J. Meiners[9],
Marcus A. Cheek[9],
Michael-Christopher Keogh[9],
Eric Bareke[2],
Anissa Djedid[2],
Ashot S. Harutyunyan[2],
Nada Jabado2,10,11,
Benjamin A. Garcia7,8,
Haitao Li[3],
C. David Allis[1] na2,
Jacek Majewski[2] na2 &
Chao Lu4,5 na2

Naturevolume 573, pages281–286 (2019) | Download Citation

Subjects

- Chromatin analysis
- Differentiation
- DNA methylation
- Head and neck cancer
- Histone post-translational modifications

Abstract

Enzymes that catalyse CpG methylation in DNA, including the DNA methyltransferases 1 (DNMT1), 3A (DNMT3A) and 3B (DNMT3B), are indispensable for mammalian tissue development and homeostasis1,2,3,4. They are also implicated in human developmental disorders and cancers5,6,7,8, supporting the critical role of DNA methylation in the specification and maintenance of cell fate. Previous studies have suggested that post-translational modifications of histones are involved in specifying patterns of DNA methyltransferase localization and DNA methylation at promoters and actively transcribed gene bodies9,10,11. However, the mechanisms that control the establishment and maintenance of intergenic DNA methylation remain poorly understood. Tatton–Brown–Rahman syndrome (TBRS) is a childhood overgrowth disorder that is defined by germline mutations in DNMT3A. TBRS shares clinical features with Sotos syndrome (which is caused by haploinsufficiency of NSD1, a histone methyltransferase that catalyses the dimethylation of histone H3 at K36 (H3K36me2)8,12,13), which suggests that there is a mechanistic link between these two diseases. Here we report that NSD1-mediated H3K36me2 is required for the recruitment of DNMT3A and maintenance of DNA methylation at intergenic regions. Genome-wide analysis shows that the binding and activity of DNMT3A colocalize with H3K36me2 at non-coding regions of euchromatin. Genetic ablation of Nsd1 and its paralogue Nsd2 in mouse cells results in a redistribution of DNMT3A to H3K36me3-modified gene bodies and a reduction in the methylation of intergenic DNA. Blood samples from patients with Sotos syndrome and NSD1-mutant tumours also exhibit hypomethylation of intergenic DNA. The PWWP domain of DNMT3A shows dual recognition of H3K36me2 and H3K36me3 in vitro, with a higher binding affinity towards H3K36me2 that is abrogated by TBRS-derived missense mutations. Together, our study reveals a trans-chromatin regulatory pathway that connects aberrant intergenic CpG methylation to human neoplastic and developmental overgrowth.

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Fig. 1: Genome-wide colocalization of DNMT3A, CpG methylation and H3K36me2.

Fig. 2: NSD1-mediated H3K36me2 is required for intergenic DNMT3A localization and CpG methylation.

Fig. 3: Preferential recognition of H3K36me2 and H3K36me3 by the PWWP domain of DNMT3A facilitates its localization.

Fig. 4: Impaired intergenic DNMT3A localization and CpG methylation in neoplastic and developmental overgrowth.

Data availability

The WGBS, ChIP–seq and RNA-sequencing data have been deposited in the GEO under accession number GSE118785.

Code availability

The source code for bioinformatic analysis is available on request.

References

1.

Li, E., Bestor, T. H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992).

- CAS
- Article
- Google Scholar

2.

Okano, M., Bell, D. W., Haber, D. A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257 (1999).

- CAS
- Article
- Google Scholar

3.

Wu, H. et al. Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes. Science 329, 444–448 (2010).

- ADS
- CAS
- Article
- Google Scholar

4.

Challen, G. A. et al. Dnmt3a is essential for hematopoietic stem cell differentiation. Nat. Genet. 44, 23–31 (2012).

- CAS
- Article
- Google Scholar

5.

Ley, T. J. et al. DNMT3A mutations in acute myeloid leukemia. N. Engl. J. Med. 363, 2424–2433 (2010).

- CAS
- Article
- Google Scholar

6.

Klein, C. J. et al. Mutations in DNMT1 cause hereditary sensory neuropathy with dementia and hearing loss. Nat. Genet. 43, 595–600 (2011).

- CAS
- Article
- Google Scholar

7.

Xu, G. L. et al. Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature 402, 187–191 (1999).

- ADS
- CAS
- Article
- Google Scholar

8.

Tatton-Brown, K. et al. Mutations in the DNA methyltransferase gene DNMT3A cause an overgrowth syndrome with intellectual disability. Nat. Genet. 46, 385–388 (2014).

- CAS
- Article
- Google Scholar

9.

Ooi, S. K. T. et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714–717 (2007).

- ADS
- CAS
- Article
- Google Scholar

10.

Baubec, T. et al. Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation. Nature 520, 243–247 (2015).

- ADS
- CAS
- Article
- Google Scholar

11.

Morselli, M. et al. In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse. eLife 4, e06205 (2015).

- Article

- Google Scholar

12.

Kurotaki, N. et al. Haploinsufficiency of NSD1 causes Sotos syndrome. Nat. Genet. 30, 365–366 (2002).

- CAS
- Article
- Google Scholar

13.

Rayasam, G. V. et al. NSD1 is essential for early post-implantation development and has a catalytically active SET domain. EMBO J. 22, 3153–3163 (2003).

- CAS
- Article
- Google Scholar

14.

Rao, B., Shibata, Y., Strahl, B. D. & Lieb, J. D. Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide. Mol. Cell. Biol. 25, 9447–9459 (2005).

- CAS
- Article
- Google Scholar

15.

Xiao, T. et al. Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes Dev. 17, 654–663 (2003).

- CAS
- Article
- Google Scholar

16.

Doynova, M. D., Markworth, J. F., Cameron-Smith, D., Vickers, M. H. & O’Sullivan, J. M. Linkages between changes in the 3D organization of the genome and transcription during myotube differentiation in vitro. Skelet. Muscle 7, 5 (2017).

- Article

- Google Scholar

17.

Kuo, A. J. et al. NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming. Mol. Cell 44, 609–620 (2011).

- CAS
- Article
- Google Scholar

18.

Orlando, D. A. et al. Quantitative ChIP-seq normalization reveals global modulation of the epigenome. Cell Rep. 9, 1163–1170 (2014).

- CAS
- Article
- Google Scholar

19.

Dhayalan, A. et al. The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation. J. Biol. Chem. 285, 26114–26120 (2010).

- CAS
- Article
- Google Scholar

20.

Papillon-Cavanagh, S. et al. Impaired H3K36 methylation defines a subset of head and neck squamous cell carcinomas. Nat. Genet. 49, 180–185 (2017).

- CAS
- Article
- Google Scholar

21.

Choufani, S. et al. NSD1 mutations generate a genome-wide DNA methylation signature. Nat. Commun. 6, 10207 (2015).

- ADS
- CAS
- Article
- Google Scholar

22.

Tatton-Brown, K. et al. Mutations in epigenetic regulation genes are a major cause of overgrowth with intellectual disability. Am. J. Hum. Genet. 100, 725–736 (2017).

- CAS
- Article
- Google Scholar

23.

Heyn, P. et al. Gain-of-function DNMT3A mutations cause microcephalic dwarfism and hypermethylation of Polycomb-regulated regions. Nat. Genet. 51, 96–105 (2019).

- CAS
- Article
- Google Scholar

24.

Jeffries, A. R. et al. Growth disrupting mutations in epigenetic regulatory molecules are associated with abnormalities of epigenetic aging. Genome Res. 29, 1057–1066 (2019).

- CAS
- Article
- Google Scholar

25.

Williams, K., Christensen, J. & Helin, K. DNA methylation: TET proteins—guardians of CpG islands? EMBO Rep. 13, 28–35 (2011).

- Article

- Google Scholar

26.

Boulard, M., Edwards, J. R. & Bestor, T. H. FBXL10 protects Polycomb-bound genes from hypermethylation. Nat. Genet. 47, 479–485 (2015).

- CAS
- Article
- Google Scholar

27.

Quintana, R. M. et al. A transposon-based analysis of gene mutations related to skin cancer development. J. Invest. Dermatol. 133, 239–248 (2013).

- CAS
- Article
- Google Scholar

28.

Rinaldi, L. et al. Loss of Dnmt3a and Dnmt3b does not affect epidermal homeostasis but promotes squamous transformation through PPAR-γ. eLife 6, e21697 (2017).

- Article

- Google Scholar

29.

Jaju, R. J. et al. A novel gene, NSD1, is fused to NUP98 in the t(5;11)(q35;p15.5) in de novo childhood acute myeloid leukemia. Blood 98, 1264–1267 (2001).

- CAS
- Article
- Google Scholar

30.

Sendžikaitė, G., Hanna, C. W., Stewart-Morgan, K. R., Ivanova, E. & Kelsey, G. A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and growth retardation in mice. Nat. Commun. 10, 1884 (2019).

- ADS
- Article
- Google Scholar

31.

Sidoli, S., Bhanu, N. V., Karch, K. R., Wang, X. & Garcia, B. A. Complete workflow for analysis of histone post-translational modifications using bottom-up mass spectrometry: from histone extraction to data analysis. J. Vis. Exp. 111, e54112 (2016).

- Google Scholar

32.

Yuan, Z. F. et al. EpiProfile 2.0: a computational platform for processing epi-proteomics mass spectrometry data. J. Proteome Res. 17, 2533–2541 (2018).

- CAS
- Article
- Google Scholar

33.

Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

- CAS
- Article
- Google Scholar

34.

Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

- CAS
- Article
- Google Scholar

35.

Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).

- CAS
- Article
- Google Scholar

36.

Thorvaldsdóttir, H., Robinson, J. T. & Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178–192 (2013).

- Article

- Google Scholar

37.

Killick, R. et al. Optimal detection of changepoints with a linear computation cost. J. Am. Stat. Assoc. 107, 1590–1598 (2012).

- MathSciNet
- CAS
- Article
- Google Scholar

38.

Wambui, G. D. et al. The power of the pruned exact linear time (PELT) test in multiple changepoint detection. Am. J. Theor. Appl. Stat. 4, 581–586 (2015).

- Article

- Google Scholar

39.

Shen, L., Shao, N., Liu, X. & Nestler, E. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics 15, 284 (2014).

- Article

- Google Scholar

40.

Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).

- CAS
- Article
- Google Scholar

41.

Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

- Google Scholar

42.

Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

- Article

- Google Scholar

43.

ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).

- ADS
- Article
- Google Scholar

44.

Hovestadt, V. et al. Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing. Nature 510, 537–541 (2014).

- ADS
- CAS
- Article
- Google Scholar

45.

Berman, B. P. et al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat. Genet. 44, 40–46 (2012).

- CAS
- Article
- Google Scholar

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Acknowledgements

We thank T. Bestor and members of the Lu, Majewski and Allis laboratories for critical reading of the manuscript. This research was supported by US National Institutes of Health (NIH) grants (P01CA196539 to N.J., B.A.G., C.D.A. and J.M.; R00CA212257 to C.L.; T32GM007739 and F30CA224971 to D.N.W.; T32GM008275 to D.M.M.; and R44GM116584 and R44GM117683 to M.-C.K.), the Rockefeller University (C.D.A.) and the Cedars Cancer Foundation (N.J.). The research was funded in part through the NIH/NCI Cancer Center Support Grant P30CA013696 and used the HICCC Flow Cytometry Shared Resource. This work was performed within the context of the I-CHANGE consortium and was supported by funding from Genome Canada, Genome Quebec, the Institute for Cancer Research of the CIHR, McGill University and the Montreal Children’s Hospital Foundation. B.A.G. is funded by a Leukemia and Lymphoma Society Dr. Robert Arceci Scholar Award; H.L. is funded by the National Natural Science Foundation of China (31725014 and 91753203); C.L. is the Giannandrea Family Dale F. Frey Breakthrough Scientist of the Damon Runyon Foundation (DFS-28-18), a Pew-Stewart Scholar for Cancer Research and supported by an AACR Gertrude B. Elion Cancer Research Grant; N.J. is a member of the Penny Cole Laboratory and the recipient of a Chercheur Boursier, Chaire de Recherche Award from the Fond de la Recherche du Québec en Santé; and S.P.-C. and A.S.H. are supported by a studentship and postdoctoral fellowship from the Fond de la Recherche du Québec en Santé, respectively.

Author information

Author notes

1. These authors contributed equally: Daniel N. Weinberg, Simon Papillon-Cavanagh

2. These authors jointly supervised this work: C. David Allis, Jacek Majewski, Chao Lu

Affiliations

1. Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA

- Daniel N. Weinberg
- , Agata E. Lemiesz
- & C. David Allis

2. Department of Human Genetics, McGill University, Montreal, Quebec, Canada

- Simon Papillon-Cavanagh
- , Haifen Chen
- , Cynthia Horth
- , Hamid Nikbakht
- , Eric Bareke
- , Anissa Djedid
- , Ashot S. Harutyunyan
- , Nada Jabado
- & Jacek Majewski

3. MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China

- Yuan Yue

- & Haitao Li

4. Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA

- Xiao Chen
- , John T. McGuire
- , Xinjing Xu
- & Chao Lu

5. Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA

- Xiao Chen
- , John T. McGuire
- , Xinjing Xu
- & Chao Lu

6. Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Irving Medical Center, New York, NY, USA

- Kartik N. Rajagopalan

7. Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

- Dylan M. Marchione

- & Benjamin A. Garcia

8. Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

- Dylan M. Marchione

- & Benjamin A. Garcia

9. EpiCypher Inc, Durham, NC, USA

- Matthew R. Marunde
- , Matthew J. Meiners
- , Marcus A. Cheek
- & Michael-Christopher Keogh

10. Department of Pediatrics, McGill University, Montreal, Quebec, Canada

- Nada Jabado

11. Research Institute of the McGill University Health Center, Montreal, Quebec, Canada

- Nada Jabado

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Contributions

D.N.W., S.P.-C., C.D.A., J.M. and C.L. conceived and designed the experiments. D.N.W., K.N.R., C.H., J.T.M., X.X., A.E.L., D.M.M., A.S.H., N.J., B.A.G. and C.L. performed cell-based experiments and analysed data. S.P.-C., H.C., X.C., H.N., E.B., A.D. and J.M. performed bioinformatic analysis on sequencing-based data. Y.Y., M.R.M., M.J.M., M.A.C., M.-C.K. and H.L. performed in vitro experiments with recombinant proteins and analysed data. H.C. and Y.Y. contributed equally as co-second authors to this manuscript. All authors contributed to the written manuscript.

Corresponding authors

Correspondence to C. David Allis or Jacek Majewski or Chao Lu.

Ethics declarations

Competing interests

EpiCypher (M.R.M., M.J.M., M.A.C. and M.-C.K.) is a commercial developer and supplier of platforms similar to those used in this study: recombinant semi-synthetic modified nucleosomes and the dCypher nucleosome-binding assay.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Peer review information Nature thanks Taiping Chen, Jonathan Licht and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Fig. 1 H3K36me2 and H3K36me3 mark transcriptionally active euchromatin.

a, ChIP–seq normalized reads of H3K36me2 relative to the average percentage of CpG methylation in mouse MSCs for 100-kb non-overlapping bins (n = 25,624). Pearson’s correlation coefficient is indicated. b, Quantification of ChIP–seq normalized reads for averaged CpG methylation, DNMT3A1 and DNMT3B within H3K36me2 and H3K36me3 (n = 591), H3K27me3 (n = 283) or H3K9me3 (n = 545) domains. P values were <2.2 × 10−16 for all pair-wise comparisons, as determined by Wilcoxon’s rank-sum test (two-sided), except for DNMT3B (P = 3.73 × 10−14) between H3K27me3 and H3K9me3 domains. For box plots, the centre lines represent the median, the box limits are the 25th and 75th percentiles, the whiskers are the minimum to maximum values and discrete points represent outliers. c, Quantification of ChIP–seq normalized reads for gene expression, H3K4me1 and H3K27ac within H3K36me2 and H3K36me3 (n = 591), H3K27me3 (n = 283) or H3K9me3 (n = 545) domains. P values were <2.2 × 10−16 for all pair-wise comparisons, as determined by Wilcoxon’s rank-sum test (two-sided), except for gene expression (P = 1.72 × 10−6) between H3K27me3 and H3K9me3 domains. Box plots as in b. d, Three-dimensional genome browser representation of Hi-C chromatin conformation capture data from mouse myoblasts compared to ChIP–seq normalized reads for histone PTMs in mouse MSCs at Chr4: 52.2–99.1 Mb. The levels of CpG methylation (CpGme) are depicted as a heat map (blue, low; white, intermediate; red, high). For H3K36me3 and H3K36me2, data are representative of two independent ChIP–seq experiments; for H3K27me3 and H3K9me3, ChIP–seq was performed once and an independent ChIP was performed in which genomic regions of selective enrichment and depletion were confirmed by qPCR. WGBS was performed once.

Extended Data Fig. 2 Distinct enrichment patterns between H3K36me2 and H3K36me3 at euchromatin.

a, Genome browser representation of ChIP–seq normalized reads for H3K36me3, H3K36me2, DNMT3A1 and DNMT3B in mouse MSCs at Chr8: 75.0–75.1 Mb. The levels of CpG methylation are depicted as a heat map (blue, low; white, intermediate; red, high) and RefSeq genes are annotated at the bottom. For H3K36me3, H3K36me2 and DNMT3A1, data are representative of two independent ChIP–seq experiments; for DNMT3B, ChIP–seq was performed once and an independent ChIP was performed in which genomic regions of selective enrichment and depletion were confirmed by qPCR. WGBS was performed once. b, Ratio of observed-to-expected ChIP–seq reads for H3K36me2 and H3K36me3 in annotated genomic regions. Numbers of expected reads were generated assuming equivalent genomic distribution to input. c, Heat maps representing ChIP–seq signal density for H3K36me2 and H3K36me3 in mouse MSCs across all gene bodies. Genes are ranked by the length of the first intron. Each gene is displayed as a row. d, Averaged ChIP–seq normalized signal across gene bodies stratified by expression quartile, represented as log_2(ChIP signal/input signal) over input for DNMT3A1 (top) and DNMT3B (bottom) in parental MSCs. Sample sizes (which are the same for DNMT3A1 and DNMT3B) are n = 7,524, n = 7,435, n = 6,923 and n = 8,550 for the first, second, third and fourth quartiles, respectively; and n = 35,777 for the average. TES, transcription end site; TSS, transcription start site.

Extended Data Fig. 3 Genome-wide colocalization between H3K36me2 and DNMT3A2 in mouse ES cells.

a, Immunoblots of lysates generated from parental and sgDnmt3a mouse ES cells (termed mESCs in the Extended Data figures) that ectopically express HA-tagged DNMT3A2. Vinculin was used as a loading control. Endogenous expression of the long isoform (DNMT3A1) and the short isoform (DNMT3A2) of DNMT3A is indicated. Data are representative of two independent experiments. b, ChIP–seq normalized reads of HA-tagged DNMT3A2 in sgDnmt3a relative to parental ES cells for 100-kb non-overlapping bins (n = 26,181). Pearson’s correlation coefficient is indicated. c, Genome browser representation of ChIP–seq normalized reads for H3K36me3, H3K36me2, DNMT3A2 and DNMT3B in ES cells at Chr12: 86.6–87.5 Mb. RefSeq genes are annotated at the bottom. The shaded areas indicate H3K36me2-enriched intergenic regions (orange) and H3K36me3-enriched genic regions (green) in parental cells. For H3K36me2 and DNMT3A2, ChIP–seq was performed once and an independent ChIP was performed in which genomic regions of selective enrichment and depletion were confirmed by qPCR. H3K36me3 and DNMT3B ChIP–seq were performed once. d, ChIP–seq normalized reads per 10-kb bin for DNMT3A2 (y axis) and DNMT3B (x axis) in ES cells (n = 246,285). Bins (dots) are colour-coded on the basis of differences between H3K36me3 and H3K36me2 ChIP–seq reads, to show selective enrichment for H3K36me2 (orange) or H3K36me3 (green). e, De novo methylation per bin by DNMT3A2 (brown) or DNMT3B (grey) after reintroduction into Dnmt1, Dnmt3a and Dnmt3b triple-knockout ES cells relative to H3K36me3. To generate bins, 1-kb genomic tiles (n = 2,462,755) were ranked by H3K36me3 enrichment in ES cells and grouped into 1,000 bins, ordered by rank (2,463 tiles per group). The dashed lines indicate H3K36me3 enrichment per bin. Goodness of fit was computed using a quadratic model (red lines). For gel source data, see Supplementary Fig. 1.

Extended Data Fig. 4 Genetic ablation of Nsd1 and Nsd2 in mouse MSCs and Nsd1 in mouse ES cells.

a, Immunoblots of lysates from parental and H3K36-methyltransferase-knockout mouse MSC clonal lines for NSD1, NSD2 and SETD2. Vinculin was used as a loading control. b, Immunoblots of lysates from parental and sgNsd1 mouse ES cells that express HA-tagged DNMT3A. sgNsd1 cells were rescued with ectopic expression of wild-type NSD1 or the C2023A catalytic mutant. Vinculin was used as a loading control. c, Immunoblots of lysates generated from parental, sgSetd2 and sgNsd1/2 MSCs for H3K36me3 and H3K36me2. Total H3 was used as a loading control. d, Ratios of ChIP–seq reads for H3K36me2 and H3K36me3 in mouse MSCs between target chromatin (mouse) and reference spike-in chromatin (Drosophila). Data are representative of two independent experiments. e, Quantitative mass spectrometry measurement of the abundance of histone PTMs in acid-extracted histones derived from the indicated MSC lines. Data are from one experiment. f, Ratios of ChIP–seq reads for H3K36me2 and H3K36me3 in ES cells between target chromatin (mouse) and reference spike-in chromatin (Drosophila). Data are from one experiment. g, Density plots of H3K36me2 levels at intergenic (n = 1,165), exonic (n = 13,601) and intronic (n = 12,364) regions for parental (grey) and sgNsd1/2 (orange) MSCs. P values were determined by Wilcoxon’s rank-sum test (two-sided). h, Density plots of H3K36me2 levels at intergenic (n = 1,165), exonic (n = 13,601) and intronic (n = 12,364) regions for parental (grey) and sgNsd1 (orange) ES cells. P values were determined by Wilcoxon’s rank-sum test (two-sided). The immunoblot experiments in a–c were independently repeated twice with similar results. For gel source data, see Supplementary Fig. 1. Source data

Extended Data Fig. 5 H3K36me2 depletion impairs genomic targeting of DNMT3A and reduces intergenic CpG methylation.

a, Immunoblots of lysates from parental, sgSetd2 and sgNsd1/2 mouse MSCs that ectopically express HA-tagged DNMT3A1 or DNMT3B. β-tubulin was used as a loading control. b, Immunoblots of lysates from sgDnmt3a, parental and sgNsd1 mouse ES cells that ectopically express HA-tagged DNMT3A2 or DNMT3B. Vinculin was used as a loading control. c, Genome browser representation of ChIP–seq normalized reads for H3K36me3, H3K36me2 and DNMT3A1 in parental and sgNsd1/2 MSCs at Chr17: 87.9–88.7 Mb. The levels of CpG methylation (CpGme) are depicted as a heat map (blue, low; white, intermediate; red, high) and RefSeq genes are annotated at the bottom. The shaded area indicates H3K36me2-enriched intergenic region in parental cells. For H3K36me2, H3K36me3 and DNMT3A1 in parental cells, data are representative of two independent ChIP–seq experiments. DNMT3A1 ChIP–seq in sgNsd1/2 cells and WGBS in both lines were performed once. d, Genome browser representation of ChIP–seq normalized reads for H3K36me3, H3K36me2 and DNMT3A2 in parental and sgNsd1 ES cells at Chr17: 87.9-88.7 Mb. The levels of CpG methylation are depicted as a heat map (blue, low; white, intermediate; red, high) and RefSeq genes are annotated at the bottom. The shaded area indicates the H3K36me2-enriched intergenic region in parental cells. For H3K36me2 and DNMT3A2, ChIP–seq was performed once and an independent ChIP was performed in which genomic regions of selective enrichment and depletion were confirmed by qPCR. WGBS and H3K36me3 ChIP–seq were performed once. e, Per cent change in averaged CpG methylation between parental and sgNsd1/2 MSCs relative to changes in ChIP–seq normalized reads of H3K36me2 for 100-kb non-overlapping bins (n = 25,611). Pearson’s correlation coefficient is indicated. f, Per cent change in averaged CpG methylation between parental and sgNsd1 ES cells relative to changes in ChIP–seq normalized reads of H3K36me2 for 100-kb non-overlapping bins (n = 26,044). Pearson’s correlation coefficient is indicated. g, The enrichment (per cent input) of H3K36me2 at various intergenic regions in parental (black) and sgNsd1 (orange) ES cells rescued with ectopic expression of wild-type NSD1 or the C2023A catalytic mutant was measured by ChIP–qPCR. Each data point represents a genomic locus (n = 10 for H3K36me2-enriched regions, n = 4 for H3K36me2-depleted regions). Data are mean ± s.d. P values were determined by one-way ANOVA. The immunoblot experiments in a, b were independently repeated twice with similar results. For gel source data, see Supplementary Fig. 1. Source data

Extended Data Fig. 6 The PWWP domain of DNMT3A preferentially binds to H3K36me2.

a, The dCypher approach for interrogating chromatin readers (Methods). Biotinylated nucleosomes are immobilized on streptavidin donor beads and GST-tagged DNMT3APWWP on glutathione AlphaLISA acceptor beads. Laser excitation of the donor generates singlet oxygen, which diffuses to activate emission from the acceptor. Fluorescence counts are directly proportional to the amount of donor–acceptor complex bridged by the nucleosome-reader interaction. b, Quantification of AlphaLISA counts for isolated GST-tagged DNMT3APWWP interaction, titrated against H3K36-modified nucleosomes. Data are the mean of two replicates. c, ITC titration and fitting curves of human DNMT3APWWP with H3.3(1–42) K36-modified peptides. d, ITC titration and fitting curves of human DNMT3APWWP with H3.1(1–42) K36-modified peptides. Source data

Extended Data Fig. 7 Redistribution of DNMT3A to H3K36me3-marked gene bodies after loss of H3K36me2.

a, Averaged ChIP–seq normalized signal across all gene bodies, represented as log_2(ChIP signal/input signal) for DNMT3A1 (grey, n = 14,959) and DNMT3B (green, n = 14,959) in parental mouse MSCs, and for DNMT3A1 (orange, n = 14,311) in sgNsd1/2 MSCs. b, Quantification of ChIP–seq normalized reads of DNMT3A1 in parental, sgNsd1/2 and triple-knockout (TKO) MSCs at 10-kb non-overlapping bins enriched for H3K36me3 in parental cells (top 20% of bins, n = 54,624). Reads were normalized by read depth. P values were <2.2 × 10−16 for all pair-wise comparisons, as determined by Wilcoxon’s rank-sum test (two-sided). For box plots, the centre lines represent the median, the box limits are the 25th and 75th percentiles, the whiskers are the minimum to maximum values and discrete points represent outliers. c, Genome browser representation of ChIP–seq normalized reads for H3K36me2, H3K36me3 and DNMT3A1 in parental, sgNsd1/2 and triple-knockout MSCs at Chr10: 74.8–77.8 Mb. RefSeq genes are annotated at the bottom. The shaded areas indicate H3K36me3-enriched genic regions in parental cells. For H3K36me2 and H3K36me3, data in parental and sgNsd1/2 cells are representative of two independent ChIP–seq experiments. ChIP–seq in triple-knockout cells for H3K36me2 and H3K36me3 was performed once. For DNMT3A1, data in parental cells are representative of two independent ChIP–seq experiments. ChIP–seq in sgNsd1/2 and triple-knockout cells for DNMT3A1 was performed once. d, Immunoblots of lysates from parental, sgNsd1/2 and triple-knockout MSCs that ectopically express HA-tagged wild-type or D333A-mutant DNMT3A1. β-actin was used as a loading control. Data are representative of two independent experiments. e, Fold enrichment of wild-type or PWWP-mutant (D333A) DNMT3A1 at gene-body versus intergenic regions in parental (black) and sgNsd1/2 (orange) MSCs was measured by ChIP–qPCR. Each data point represents a genomic locus (n = 10). Data are mean ± s.d. P values were determined by one-way ANOVA. For gel source data, see Supplementary Fig. 1. Source data

Extended Data Fig. 8 Assessment of binding affinity between DNMT3B and H3K36me2 in vitro and in cells.

a, Immunoblots of His–MBP-tagged recombinant DNMT3A and DNMT3B PWWP domains. b, Immunoblots of recombinant His–MBP-tagged wild-type DNMT3A and DNMT3B PWWP domains bound to H3K36-modified recombinant nucleosomes following the in vitro pull-down assay. c, ChIP–seq normalized reads per bin for DNMT3A1 (grey) and DNMT3B (blue) in parental mouse MSCs and DNMT3B (red) in sgSetd2 MSCs relative to H3K36me2. To generate bins, 1-kb genomic tiles were ranked by H3K36me2 enrichment in parental MSCs and grouped into 1,000 bins, ordered by rank. The dashed line indicates H3K36me2 enrichment per bin. d, Genome browser representation of ChIP–seq normalized reads for H3K36me2, H3K36me3 and DNMT3B in parental and sgSetd2 MSCs at Chr10: 83.4–84.3 Mb. RefSeq genes are annotated at the bottom. The shaded areas indicate H3K36me2-enriched intergenic regions (orange) and H3K36me3-enriched genic regions (green) in parental cells. For H3K36me2 and H3K36me3, data are representative of two independent ChIP–seq experiments; for DNMT3B, ChIP–seq was performed once and an independent ChIP was performed in which genomic regions of selective enrichment and depletion were confirmed by qPCR. The immunoblot experiments in a, b were independently repeated twice with similar results. For gel source data, see Supplementary Fig. 1.

Extended Data Fig. 9 TBRS-associated mutations in DNMT3A are loss-of-function and result in DNA hypomethylation similar to that observed in Sotos syndrome.

a, Immunoblots of the recombinant His–MBP-tagged DNMT3A PWWP domain containing TBRS-associated mutations. MBP alone was used as a control. b, Immunoblots of soluble or chromatin-associated lysates generated from cells that ectopically express HA-tagged wild-type or mutant (W297del or I310N) DNMT3A. β-tubulin and lamin B1 were used as loading controls for the soluble and chromatin-associated fractions, respectively. c, Immunoblots of lysates from parental mouse MSCs that ectopically express HA-tagged wild-type or TBRS-associated mutant (W297del, I310N or Y365C) DNMT3A. Data are from one experiment. β-tubulin was used as a loading control. d, Immunoblots of nucleosomes bound to HA-tagged wild-type or mutant (W297del, I310N or Y365C) DNMT3A after ChIP with anti-HA-tag antibodies. Total H3 was used as a loading control and to normalize for differences in protein expression and nucleosome pull-down efficiency between samples. e, Genome browser representation of ChIP–seq normalized reads for H3K36me2, wild-type DNMT3A1 and I310N-mutant DNMT3A1 in mouse MSCs at Chr13: 62.2–66.8 Mb. The levels of CpG methylation (CpGme) are depicted as a heat map (blue, low; white, intermediate; red, high) and RefSeq genes are annotated at the bottom. f, ChIP–seq normalized reads of wild-type or PWWP-mutant (I310N) DNMT3A1 relative to that of H3K36me2 for 100-kb non-overlapping bins (wild type: n = 25,694; I310N: n = 25,757). Pearson’s correlation coefficient is indicated. For H3K36me2 and wild-type DNMT3A1, data are representative of two independent ChIP–seq experiments; for I310N-mutant DNMT3A1, ChIP–seq was performed once and an independent ChIP was performed in which genomic regions of selective enrichment and depletion were confirmed by qPCR. WGBS was performed once. g, Unsupervised hierarchical clustering of publicly available Infinium Human Methylation 450K array profiles of blood samples from patients with TBRS, Sotos syndrome and Weaver syndrome and healthy control individuals, based on the top 1,000 most-variable probes. h, Model depicting the changes in chromatin landscape in human developmental overgrowth syndromes (Sotos syndrome and TBRS). In normal development, DNMT3A and DNMT3B act in parallel to methylate CpG dinucleotides at H3K36me2-enriched intergenic and H3K36me3-enriched genic regions, respectively. Haploinsufficiency of NSD1 and depletion of intergenic H3K36me2 levels in Sotos syndrome abrogate PWWP-mediated intergenic recruitment of DNMT3A, which leads to hypomethylation of intergenic DNA and the redistribution of DNMT3A to H3K36me3-enriched gene bodies. Mutations within the PWWP domain of DNMT3A in TBRS impair chromatin occupancy and reduce cellular levels of the protein—thereby also causing hypomethylation of intergenic DNA. The immunoblot experiments in a, c, d were independently repeated twice with similar results. For gel source data, see Supplementary Fig. 1.

Supplementary information

Supplementary Figure 1

Source Gel images (15 display items). One for each figure panel that contains immunoblot analysis, with red box indicating cropped region.

Reporting Summary

Supplementary Table 1

Sanger sequencing verification results for CRISPR-Cas9 gene editing of Setd2, Nsd1, Nsd2, and Dnmt3a in mMSCs and mESCs.

Supplementary Table 2

Primers used for ChIP-qPCR analysis in this study.

Source data

Source Data Fig. 2

Source Data Fig. 3

Source Data Extended Data Fig. 4

Source Data Extended Data Fig. 5

Source Data Extended Data Fig. 6

Source Data Extended Data Fig. 7

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- Received

30 August 2018

- Accepted

06 August 2019

- Published

04 September 2019

- Issue Date

12 September 2019

- DOI
https://doi.org/10.1038/s41586-019-1534-3

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- Letter

- Published: 04 September 2019

Structures of influenza A virus RNA polymerase offer insight into viral genome replication

Haitian Fan[1] na1,
Alexander P. Walker[1] na1,
Loïc Carrique[2] na1,
Jeremy R. Keown[2] na1,
Itziar Serna Martin1,2,6 nAff6,
Dimple Karia[2],
Jane Sharps[1],
Narin Hengrung1,2,7 nAff7,
Els Pardon[3],
Jan Steyaert[4],
Jonathan M. Grimes2,5 na2 &
Ervin Fodor[1] na2

Naturevolume 573, pages287–290 (2019) | Download Citation

Subjects

- Cryoelectron microscopy
- Influenza virus
- Transcription
- X-ray crystallography

Abstract

Influenza A viruses are responsible for seasonal epidemics, and pandemics can arise from the transmission of novel zoonotic influenza A viruses to humans1,2. Influenza A viruses contain a segmented negative-sense RNA genome, which is transcribed and replicated by the viral-RNA-dependent RNA polymerase (FluPolA) composed of PB1, PB2 and PA subunits3,4,5. Although the high-resolution crystal structure of FluPolA of bat influenza A virus has previously been reported[6], there are no complete structures available for human and avian FluPolA. Furthermore, the molecular mechanisms of genomic viral RNA (vRNA) replication—which proceeds through a complementary RNA (cRNA) replicative intermediate, and requires oligomerization of the polymerase7,8,9,10—remain largely unknown. Here, using crystallography and cryo-electron microscopy, we determine the structures of FluPolA from human influenza A/NT/60/1968 (H3N2) and avian influenza A/duck/Fujian/01/2002 (H5N1) viruses at a resolution of 3.0–4.3 Å, in the presence or absence of a cRNA or vRNA template. In solution, FluPolA forms dimers of heterotrimers through the C-terminal domain of the PA subunit, the thumb subdomain of PB1 and the N1 subdomain of PB2. The cryo-electron microscopy structure of monomeric FluPolA bound to the cRNA template reveals a binding site for the 3′ cRNA at the dimer interface. We use a combination of cell-based and in vitro assays to show that the interface of the FluPolA dimer is required for vRNA synthesis during replication of the viral genome. We also show that a nanobody (a single-domain antibody) that interferes with FluPolA dimerization inhibits the synthesis of vRNA and, consequently, inhibits virus replication in infected cells. Our study provides high-resolution structures of medically relevant FluPolA, as well as insights into the replication mechanisms of the viral RNA genome. In addition, our work identifies sites in FluPolA that could be targeted in the development of antiviral drugs.

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Fig. 1: Structures of human H3N2 and avian H5N1 FluPolA.

Fig. 2: Mutations at the interface of the FluPolA dimer inhibit cRNA to vRNA replication.

Fig. 3: Structures of H3N2 FluPolA bound to cRNA promoter.

Fig. 4: Nb8205, which binds FluPolA at the dimer interface, inhibits cRNA to vRNA replication and virus growth.

Data availability

All data are available from the corresponding authors and/or included in the manuscript or Supplementary Information. Atomic coordinates have been deposited in the PDB with accession codes 6QNW (H3N2 FluPolA), 6QPF (H5N1 FluPolA) and 6QPG (H3N2 FluPolA + Nb8205). Cryo-EM density maps have been deposited in the Electron Microscopy Data Bank with accession codes EMD-4661 (monomeric H3N2 FluPolA + cRNA + Nb8205), EMD-4663 and EMD-4664 (dimeric H3N2 FluPolA + cRNA), EMD-4666 (dimeric H3N2 FluPolA + cRNA + Nb8205), EMD-4660 (monomeric FluPolB + cRNA) and EMD-4986 (monomeric H3N2 FluPolA + vRNA + capped RNA) with the corresponding atomic coordinates deposited in the PDB with accession numbers 6QX3, 6QX8, 6QXE, 6QWL and 6RR7, respectively.

References

1.

Taubenberger, J. K. & Kash, J. C. Influenza virus evolution, host adaptation, and pandemic formation. Cell Host Microbe 7, 440–451 (2010).

- CAS
- Article
- Google Scholar

2.

Mostafa, A., Abdelwhab, E. M., Mettenleiter, T. C. & Pleschka, S. Zoonotic potential of influenza A viruses: a comprehensive overview. Viruses 10, 497 (2018).

- Article

- Google Scholar

3.

Pflug, A., Lukarska, M., Resa-Infante, P., Reich, S. & Cusack, S. Structural insights into RNA synthesis by the influenza virus transcription-replication machine. Virus Res. 234, 103–117 (2017).

- CAS
- Article
- Google Scholar

4.

te Velthuis, A. J. & Fodor, E. Influenza virus RNA polymerase: insights into the mechanisms of viral RNA synthesis. Nat. Rev. Microbiol. 14, 479–493 (2016).

- Article

- Google Scholar

5.

Walker, A. P. & Fodor, E. Interplay between influenza virus and the host RNA polymerase II transcriptional machinery. Trends Microbiol. 27, 398–407 (2019).

- CAS
- Article
- Google Scholar

6.

Pflug, A., Guilligay, D., Reich, S. & Cusack, S. Structure of influenza A polymerase bound to the viral RNA promoter. Nature 516, 355–360 (2014).

- ADS
- CAS
- Article
- Google Scholar

7.

Jorba, N., Coloma, R. & Ortín, J. Genetic trans-complementation establishes a new model for influenza virus RNA transcription and replication. PLoS Pathog. 5, e1000462 (2009).

- Article

- Google Scholar

8.

York, A., Hengrung, N., Vreede, F. T., Huiskonen, J. T. & Fodor, E. Isolation and characterization of the positive-sense replicative intermediate of a negative-strand RNA virus. Proc. Natl Acad. Sci. USA 110, E4238–E4245 (2013).

- ADS
- CAS
- Article
- Google Scholar

9.

Jorba, N., Area, E. & Ortín, J. Oligomerization of the influenza virus polymerase complex in vivo. J. Gen. Virol. 89, 520–524 (2008).

- CAS
- Article
- Google Scholar

10.

Moeller, A., Kirchdoerfer, R. N., Potter, C. S., Carragher, B. & Wilson, I. A. Organization of the influenza virus replication machinery. Science 338, 1631–1634 (2012).

- ADS
- CAS
- Article
- Google Scholar

11.

Chang, S. et al. Cryo-EM structure of influenza virus RNA polymerase complex at 4.3 Å resolution. Mol. Cell 57, 925–935 (2015).

- CAS
- Article
- Google Scholar

12.

Hara, K., Schmidt, F. I., Crow, M. & Brownlee, G. G. Amino acid residues in the N-terminal region of the PA subunit of influenza A virus RNA polymerase play a critical role in protein stability, endonuclease activity, cap binding, and virion RNA promoter binding. J. Virol. 80, 7789–7798 (2006).

- CAS
- Article
- Google Scholar

13.

Mänz, B., Brunotte, L., Reuther, P. & Schwemmle, M. Adaptive mutations in NEP compensate for defective H5N1 RNA replication in cultured human cells. Nat. Commun. 3, 802 (2012).

- ADS
- Article
- Google Scholar

14.

Deng, T., Vreede, F. T. & Brownlee, G. G. Different de novo initiation strategies are used by influenza virus RNA polymerase on its cRNA and viral RNA promoters during viral RNA replication. J. Virol. 80, 2337–2348 (2006).

- CAS
- Article
- Google Scholar

15.

Hengrung, N. et al. Crystal structure of the RNA-dependent RNA polymerase from influenza C virus. Nature 527, 114–117 (2015).

- ADS
- CAS
- Article
- Google Scholar

16.

Thierry, E. et al. Influenza polymerase can adopt an alternative configuration involving a radical repacking of PB2 domains. Mol. Cell 61, 125–137 (2016).

- CAS
- Article
- Google Scholar

17.

Serna Martin, I. et al. A mechanism for the activation of the influenza virus transcriptase. Mol. Cell 70, 1101–1110 (2018).

- CAS
- Article
- Google Scholar

18.

Reich, S. et al. Structural insight into cap-snatching and RNA synthesis by influenza polymerase. Nature 516, 361–366 (2014).

- ADS
- CAS
- Article
- Google Scholar

19.

Gerlach, P., Malet, H., Cusack, S. & Reguera, J. Structural insights into bunyavirus replication and its regulation by the vRNA promoter. Cell 161, 1267–1279 (2015).

- CAS
- Article
- Google Scholar

20.

Oymans, J. & Te Velthuis, A. J. W. A mechanism for priming and realignment during influenza A virus replication. J. Virol. 92, e01773-17 (2018).

- CAS
- PubMed
- PubMed Central
- Google Scholar

21.

te Velthuis, A. J., Robb, N. C., Kapanidis, A. N. & Fodor, E. The role of the priming loop in influenza A virus RNA synthesis. Nat. Microbiol. 1, 16029 (2016).

- Article

- Google Scholar

22.

Killip, M. J., Fodor, E. & Randall, R. E. Influenza virus activation of the interferon system. Virus Res. 209, 11–22 (2015).

- CAS
- Article
- Google Scholar

23.

te Velthuis, A. J. W. et al. Mini viral RNAs act as innate immune agonists during influenza virus infection. Nat. Microbiol. 3, 1234–1242 (2018).

- Article

- Google Scholar

24.

Bieniossek, C., Imasaki, T., Takagi, Y. & Berger, I. MultiBac: expanding the research toolbox for multiprotein complexes. Trends Biochem. Sci. 37, 49–57 (2012).

- CAS
- Article
- Google Scholar

25.

Weissmann, F. et al. biGBac enables rapid gene assembly for the expression of large multisubunit protein complexes. Proc. Natl Acad. Sci. USA 113, E2564–E2569 (2016).

- CAS
- Article
- Google Scholar

26.

Pardon, E. et al. A general protocol for the generation of nanobodies for structural biology. Nat. Protocols 9, 674–693 (2014).

- CAS
- Article
- Google Scholar

27.

Walter, T. S. et al. A procedure for setting up high-throughput nanolitre crystallization experiments. Crystallization workflow for initial screening, automated storage, imaging and optimization. Acta Crystallogr. D 61, 651–657 (2005).

- Article

- Google Scholar

28.

Kabsch, W. Xds. Acta Crystallogr. D 66, 125–132 (2010).

- CAS
- Article
- Google Scholar

29.

Tickle, I. J. et al. STARANISO. http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi (2018).

30.

McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).

- CAS
- Article
- Google Scholar

31.

Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).

- CAS
- Article
- Google Scholar

32.

Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).

- Article

- Google Scholar

33.

Smart, O. S. et al. Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER. Acta Crystallogr. D 68, 368–380 (2012).

- CAS
- Article
- Google Scholar

34.

Rasmussen, S. G. et al. Crystal structure of the β_2 adrenergic receptor–Gs protein complex. Nature 477, 549–555 (2011).

- ADS
- CAS
- Article
- Google Scholar

35.

Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).

- CAS
- Article
- Google Scholar

36.

Zhang, K. Gctf: real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016).

- ADS
- CAS
- Article
- Google Scholar

37.

Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).

- CAS
- Article
- Google Scholar

38.

Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

- CAS
- Article
- Google Scholar

39.

Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

- CAS
- Article
- Google Scholar

40.

Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).

- CAS
- Article
- Google Scholar

41.

Davis, I. W. et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35, W375–W383 (2007).

- ADS
- Article
- Google Scholar

42.

Shkumatov, A. V. & Strelkov, S. V. DATASW, a tool for HPLC-SAXS data analysis. Acta Crystallogr. D 71, 1347–1350 (2015).

- CAS
- Article
- Google Scholar

43.

Deng, T., Sharps, J., Fodor, E. & Brownlee, G. G. In vitro assembly of PB2 with a PB1-PA dimer supports a new model of assembly of influenza A virus polymerase subunits into a functional trimeric complex. J. Virol. 79, 8669–8674 (2005).

- CAS
- Article
- Google Scholar

44.

Fodor, E. et al. A single amino acid mutation in the PA subunit of the influenza virus RNA polymerase inhibits endonucleolytic cleavage of capped RNAs. J. Virol. 76, 8989–9001 (2002).

- CAS
- Article
- Google Scholar

45.

Fodor, E. et al. Rescue of influenza A virus from recombinant DNA. J. Virol. 73, 9679–9682 (1999).

- CAS
- PubMed
- PubMed Central
- Google Scholar

46.

Fodor, E. & Smith, M. The PA subunit is required for efficient nuclear accumulation of the PB1 subunit of the influenza A virus RNA polymerase complex. J. Virol. 78, 9144–9153 (2004).

- CAS
- Article
- Google Scholar

47.

Vreede, F. T., Jung, T. E. & Brownlee, G. G. Model suggesting that replication of influenza virus is regulated by stabilization of replicative intermediates. J. Virol. 78, 9568–9572 (2004).

- CAS
- Article
- Google Scholar

48.

Nilsson-Payant, B. E., Sharps, J., Hengrung, N. & Fodor, E. The surface-exposed PA51–72-loop of the influenza A virus polymerase is required for viral genome replication. J. Virol. 92, e00687-18 (2018).

- CAS
- Article
- Google Scholar

49.

Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).

- CAS
- Article
- Google Scholar

50.

Robb, N. C., Smith, M., Vreede, F. T. & Fodor, E. NS2/NEP protein regulates transcription and replication of the influenza virus RNA genome. J. Gen. Virol. 90, 1398–1407 (2009).

- CAS
- Article
- Google Scholar

51.

Reich, S., Guilligay, D. & Cusack, S. An in vitro fluorescence based study of initiation of RNA synthesis by influenza B polymerase. Nucleic Acids Res. 45, 3353–3368 (2017).

- CAS
- PubMed
- PubMed Central
- Google Scholar

52.

Bussey, K. A. et al. PA residues in the 2009 H1N1 pandemic influenza virus enhance avian influenza virus polymerase activity in mammalian cells. J. Virol. 85, 7020–7028 (2011).

- CAS
- Article
- Google Scholar

53.

Hu, J. et al. The PA-gene-mediated lethal dissemination and excessive innate immune response contribute to the high virulence of H5N1 avian influenza virus in mice. J. Virol. 87, 2660–2672 (2013).

- CAS
- Article
- Google Scholar

54.

Ilyushina, N. A. et al. Adaptation of pandemic H1N1 influenza viruses in mice. J. Virol. 84, 8607–8616 (2010).

- CAS
- Article
- Google Scholar

55.

Kamiki, H. et al. A PB1-K577E mutation in H9N2 influenza virus increases polymerase activity and pathogenicity in mice. Viruses 10, 653 (2018).

- CAS
- Article
- Google Scholar

56.

Lee, C. Y. et al. Novel mutations in avian PA in combination with an adaptive mutation in PR8 NP exacerbate the virulence of PR8-derived recombinant influenza A viruses in mice. Vet. Microbiol. 221, 114–121 (2018).

- CAS
- Article
- Google Scholar

57.

Liedmann, S. et al. New virulence determinants contribute to the enhanced immune response and reduced virulence of an influenza A virus A/PR8/34 variant. J. Infect. Dis. 209, 532–541 (2014).

- CAS
- Article
- Google Scholar

58.

Mehle, A., Dugan, V. G., Taubenberger, J. K. & Doudna, J. A. Reassortment and mutation of the avian influenza virus polymerase PA subunit overcome species barriers. J. Virol. 86, 1750–1757 (2012).

- CAS
- Article
- Google Scholar

59.

Neumann, G., Macken, C. A. & Kawaoka, Y. Identification of amino acid changes that may have been critical for the genesis of A(H7N9) influenza viruses. J. Virol. 88, 4877–4896 (2014).

- Article

- Google Scholar

60.

Peng, X. et al. Amino acid substitutions HA A150V, PA A343T, and PB2 E627K increase the virulence of H5N6 influenza virus in mice. Front. Microbiol. 9, 453 (2018).

- Article

- Google Scholar

61.

Slaine, P. D. et al. Adaptive mutations in influenza A/California/07/2009 enhance polymerase activity and infectious virion production. Viruses 10, 272 (2018).

- Article

- Google Scholar

62.

Wu, R. et al. Multiple amino acid substitutions are involved in the adaptation of H9N2 avian influenza virus to mice. Vet. Microbiol. 138, 85–91 (2009).

- CAS
- Article
- Google Scholar

63.

Xu, G. et al. Prevailing PA mutation K356R in avian influenza H9N2 virus increases mammalian replication and pathogenicity. J. Virol. 90, 8105–8114 (2016).

- CAS
- Article
- Google Scholar

64.

Yamaji, R. et al. Mammalian adaptive mutations of the PA protein of highly pathogenic avian H5N1 influenza virus. J. Virol. 89, 4117–4125 (2015).

- CAS
- Article
- Google Scholar

65.

Zhang, Z. et al. Multiple amino acid substitutions involved in enhanced pathogenicity of LPAI H9N2 in mice. Infect. Genet. Evol. 11, 1790–1797 (2011).

- CAS
- Article
- Google Scholar

66.

Zhong, G. et al. Mutations in the PA protein of avian H5N1 influenza viruses affect polymerase activity and mouse virulence. J. Virol. 92, e01557-17 (2018).

- CAS
- PubMed
- PubMed Central
- Google Scholar

67.

Tan, Y. Z. et al. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat. Methods 14, 793–796 (2017).

- CAS
- Article
- Google Scholar

68.

Naydenova, K. & Russo, C. J. Measuring the effects of particle orientation to improve the efficiency of electron cryomicroscopy. Nat. Commun. 8, 629 (2017).

- ADS
- Article
- Google Scholar

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Acknowledgements

We thank G. G. Brownlee and F. Vreede for plasmids; I. Berger for the MultiBac system; S. Cusack for sharing and discussing unpublished data on the 3′ promoter binding site; K. Harlos and T. Walter for assistance with crystallization; K. Dent and D. Clare for cryo-EM assistance; G. G. Brownlee, D. Stuart and A. te Velthuis, as well as members of the Fodor and Grimes laboratories, for helpful comments and discussions; and Instruct-ERIC, part of the European Strategy Forum on Research Infrastructures (ESFRI), Instruct-ULTRA (EU H2020 Grant 731005), and the Research Foundation - Flanders (FWO) for support with nanobody discovery. This work was supported by Medical Research Council (MRC) programme grants MR/K000241/1 and MR/R009945/1 (to E.F.), Wellcome Investigator Award 200835/Z/16/Z (to J.M.G.), MRC Studentships (to A.P.W. and I.S.M.) and Wellcome Studentship 092931/Z/10/Z (to N.H.). We thank Diamond Light source for beamtime (proposals MX10627, MX14744, and MX19946), and for access and support of the cryo-EM facilities at the UK National Electron Bio-Imaging Centre (eBIC) (proposals EM14856 and EM20233), funded by the Wellcome, MRC and BBSRC. Further electron microscopy provision was provided through the OPIC electron microscopy facility, which was funded by a Wellcome JIF award (060208/Z/00/Z) and is supported by a Wellcome equipment grant (093305/Z/10/Z). Computation used the Oxford Biomedical Research Computing (BMRC) facility, a joint development between the Wellcome Centre for Human Genetics and the Big Data Institute, supported by Health Data Research UK and the NIHR Oxford Biomedical Research Centre. Financial support was provided by a Wellcome Trust Core Award (203141/Z/16/Z). The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health. Part of this work was supported by Wellcome administrative support grant 203141/Z/16/Z.

Author information

Author notes

- Itziar Serna Martin

Present address: Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands

- Narin Hengrung

Present address: Francis Crick Institute, London, UK

3. These authors contributed equally: Haitian Fan, Alexander P. Walker, Loïc Carrique, Jeremy R. Keown

4. These authors jointly supervised this work: Jonathan M. Grimes, Ervin Fodor

Affiliations

1. Sir William Dunn School of Pathology, University of Oxford, Oxford, UK

- Haitian Fan
- , Alexander P. Walker
- , Itziar Serna Martin
- , Jane Sharps
- , Narin Hengrung
- & Ervin Fodor

2. Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK

- Loïc Carrique
- , Jeremy R. Keown
- , Itziar Serna Martin
- , Dimple Karia
- , Narin Hengrung
- & Jonathan M. Grimes

3. VIB–VUB Center for Structural Biology, VIB, Brussels, Belgium

- Els Pardon

4. Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium

- Jan Steyaert

5. Diamond Light Source, Didcot, UK

- Jonathan M. Grimes

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Contributions

H.F., A.P.W., L.C., J.R.K., J.M.G. and E.F. conceived and designed the study. H.F., L.C., J.R.K. and N.H. carried out cloning of recombinant baculoviruses and protein purification. H.F. and J.R.K. performed crystallizations, data collection and analysis, model building and refinement. L.C. and J.R.K. collected and processed electron microscopy data, and built and refined models with assistance from D.K. and I.S.M. A.P.W. performed functional assays and analysed data. J. Sharps performed dimerization assays in mammalian cells and E.F. analysed the data. E.P. and J. Steyaert designed and generated Nb8205 and Nb8210, and N.H. performed nanobody expression and purification. J.M.G. and E.F. supervised the structural and functional studies, respectively. H.F., A.P.W., L.C., J.R.K, J.M.G. and E.F. wrote the manuscript, with input from all co-authors.

Corresponding authors

Correspondence to Jonathan M. Grimes or Ervin Fodor.

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The authors declare no competing interests.

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Peer review information Nature thanks Seth Darst, Achilleas Frangakis and Peng Gong for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Fig. 1 Subunit organization of FluPolA heterotrimers.

a, b, Views of the structure of human H3N2 (a) and avian H5N1 (b) FluPolA heterotrimers, coloured according to subunit. c–e, Structures of the human H3N2 FluPolA subunits PA (c), PB1 (d) and PB2 (e), coloured and labelled by domain. f, Domain maps of each of the H3N2 FluPolA subunits. g–i, The 2D Fo − Fc electron density maps of FluPolA dimer interface as shown in Fig. 1c (g, stereo view) and Fig. 1d (h, stereo view), as well as of the complete FluPolA dimer (i), are shown in grey mesh (contoured at 1.5σ, all from the structure model of H3N2 FluPolA).

Extended Data Fig. 2 Effect of mutations at the dimer interface on FluPolA dimerization and activity.

a, SEC-MALS analysis of wild-type and PA(352–356A) mutant H3N2 FluPolA (n = 1 experiment). Smooth lines reflect the relative UV signal of SEC, and dotted lines indicate estimated molecular mass for each frame. Note that monomeric FluPolA heterotrimer has an approximate molecular mass of 255 kDa. b, Effect of PA(352–356A) mutation on FluPolA dimerization in HEK293T cells. Data are mean ± s.e.m. n = 3 independent transfections. One-way ANOVA. P < 0.05 is considered significant. c, Effect of mutations designed to destabilize PB2, and PA loops, at the FluPolA dimer interface on FluPolA activity in a viral RNP reconstitution assay. Data are mean ± s.e.m. n = 3 independent transfections. Two-way ANOVA. P < 0.05 is considered significant. d, e, Effect of PA(352–356A) mutation on in vitro ApG-primer replication by FluPolA on a vRNA (d) and cRNA (e) template. f, Effect of an active-site polymerase mutant (PB1a) on in vitro ApG-primer replication by FluPolA on a cRNA template. Data are mean ± s.e.m. n = 4 independent reactions. g, Omitting UTP from in vitro ApG-primer replication by FluPolA on a cRNA template affects the synthesis of the 15-nucleotide, full-length vRNA but not of the 12-nucleotide, short vRNA, which indicates that the 12-nucleotide product is derived from internal initiation by the ApG dinucleotide at positions 4 and 5 of the cRNA template. The position in the template at which UTP is required is indicated in red. Representative data from n = 2 independent reactions. For gel source data, see Supplementary Fig. 2.

Extended Data Fig. 3 Single-particle cryo-EM analysis of human H3N2 FluPolA bound to cRNA promoter.

a, Representative micrograph of cRNA-bound FluPolA heterotrimer particles embedded in vitreous ice. b, Representative 2D class averages. c, Fourier shell correlation (FSC) curves for 3D reconstruction using gold-standard refinement in RELION, indicating overall map resolution of 4.07 Å and the model-to-map FSC. Curves are shown for phase-randomization, unmasked, masked and phase-randomization-corrected masked maps. d, A 3D reconstruction, locally filtered and coloured according to RELION local resolution. e, Angular distribution of particle projections with the cryo-EM map shown in grey. f, Cryo-EM density of the PA loop 352–356 at the dimer interface. g, Cryo-EM map of cRNA-bound FluPolA dimer refined without symmetry imposed (C_1), which reveals an extra density (green) located next to the 3′ end of the 5′ cRNA close to the template entry channel. h, Close-up views highlighting extra density in the cryo-EM map (dark green) with the 3′ vRNA strand from the superimposed FluPolB structure[51] (PDB 5MSG, light green) inserting into the polymerase active site. Localization of the 3′ vRNA shows that bases are positioned in the extra density, facing the density that corresponds to the 3′ end of the 5′ cRNA. This suggests the presence of a promoter RNA duplex region, as observed in the vRNA-bound FluPolB structure[51]. The extra density is consistent with the presence of a 3′ cRNA in one of the heterotrimers of the cRNA-bound FluPolA dimer, oriented towards the polymerase active site.

Extended Data Fig. 4 The effect of Nb8205 on FluPolA dimerization.

a, SDS–PAGE of purified nanobodies (n = 1 experiment). b, Analytical SEC of FluPolA in complex with nanobodies (n = 4 experiments for Nb8205 and n = 2 experiments or Nb8210, with similar results). c, Effect of nanobodies on FluPolA dimerization in HEK293T cells. Data are mean ± s.e.m. n = 4 independent transfections. One-way ANOVA. P < 0.05 is considered significant. For gel source data, see Supplementary Fig. 2. d, Crystal structure of H3N2 FluPolA in complex with Nb8205. e, Close-up view of FluPolA–Nb8205 interactions. Residues involved in hydrogen-bonding interactions are labelled, and hydrogen bonds are indicated with dashed lines. The complementarity determining regions (CDRs) are coloured individually, and labelled.

Extended Data Fig. 5 Single-particle cryo-EM analysis of monomeric and dimeric cRNA-bound human H3N2 FluPolA heterotrimer in complex with Nb8205.

a, Representative micrograph of cRNA-bound FluPolA in complex with Nb8205, embedded in vitreous ice. b, Representative 2D class averages. c, FSC curves for the 3D reconstruction using gold-standard refinement in RELION, indicating an overall map resolution of 3.79 Å and 4.15 Å for the monomeric and dimeric FluPolA form, respectively, and the model-to-map FSC. Curves are shown for phase-randomization, unmasked, masked and phase-randomization-corrected masked maps. d, f, The 3D reconstructions, locally filtered and coloured according to RELION local resolution, for the dimeric (d) and monomeric (f) form. e, g, Angular distribution of particle projections for the dimeric (e) and monomeric (g) form, with the cryo-EM map shown in grey. h, Dimer of FluPolA heterotrimers bound to cRNA promoter and Nb8205 rigid-body-fitted into the cryo-EM map of dimeric cRNA-bound FluPolA heterotrimer in complex with Nb8205. i, Cryo-EM map of the dimeric cRNA-bound FluPolA heterotrimer in complex with Nb8205, revealing an extra density (green) located next to the 3′ end of the 5′ cRNA (as also observed for the cRNA-bound FluPolA dimer; Extended Data Fig. 3g, h).

Extended Data Fig. 6 Single-particle cryo-EM analysis of cRNA-bound FluPolB.

a, Representative micrograph of cRNA-bound FluPolB heterotrimer particles embedded in vitreous ice. b, Representative 2D class averages. c, A 3D reconstruction, locally filtered and coloured according to RELION local resolution. d, FSC curves for the 3D reconstruction using gold-standard refinement in RELION, indicating an overall map resolution of 4.18 Å and the model-to-map FSC. Curves are shown for the phase-randomization, unmasked, masked, phase-randomization-corrected masked maps. e, Angular distribution of particle projections according to cryoSPARC v.2.5 non-uniform refinement. f, Cryo-EM map of cRNA-bound FluPolB. g, Comparison of the dimerization interface and the 3ʹ cRNA binding site in H3N2 FluPolA (PDB 6QNW and 6QPG). h, 3′ cRNA binding site in FluPolA and FluPolB overlaps with the previously identified 3′ vRNA binding site in the La Crosse orthobunyavirus polymerase[19] (PDB 5AMQ). Sites of 3′ vRNA binding at surface of the polymerase in FluPolB (PDB 4WRT) and in the polymerase active site for FluPolB (PDB 5MSG) are shown for comparison6,51. i, Comparison of the structure of dimeric FluPolA to monomeric FluPolB (PDB 5MSG)[51] reveals a movement of the priming loop that protrudes from the thumb subdomain of PB1 into the polymerase active site. Resolved PB1 residues closest to the tip of the priming loop (residues E638 and M656) move away from the corresponding E637 and M655 residues in FluPolB and the polymerase active site (indicated by the end of the 3′ vRNA) by approximately 7 Å.

Extended Data Fig. 7 Single-particle cryo-EM analysis of human H3N2 FluPolA bound to vRNA promoter.

a, Representative micrograph of vRNA-bound FluPolA heterotrimer particles embedded in vitreous ice. b, Representative 2D class averages. c, FSC curves for 3D reconstruction using gold-standard refinement in RELION, indicating an overall map resolution of 3.01 Å and the model-to-map FSC. Curves are shown for phase-randomization, unmasked, masked and phase-randomization-corrected masked maps. d, A 3D reconstruction, locally filtered and coloured according to RELION local resolution. e, Angular distribution of particle projections with the cryo-EM map shown in grey. f, Cryo-EM map of vRNA-bound FluPolA heterotrimer, revealing the presence of a fully resolved priming loop. g, Close-up views highlighting the stacking of the 3′ vRNA by the priming loop. h, Cartoon of the role of polymerase dimerization in template realignment during replication initiation on a cRNA template. Base-pairing between the 5′ and 3′ cRNAs positions bases 4 and 5 of the 3′ cRNA next to the catalytic aspartates (residues D445 and D446 of PB1) in the active site to enable internal replication initiation by the synthesis of a pppApG dinucleotide. The priming loop stacks the cRNA template through P651 of PB1 (left). Rotation of the thumb subdomain of PB1 and the N1 subdomain of PB2 triggered by polymerase dimerization results in a movement of the priming loop and backtracking of the stacked template (arrows). Backtracking is also facilitated by an interaction of residue R46 of PB2 with the 3′ cRNA, which introduces a ‘kink’ into the template. Backtracking positions bases 1 and 2 of the cRNA template opposite the pppApG dinucleotide that remains coordinated by the catalytic aspartates. The resulting replication complex is ready to extend the pppApG dinucleotide by incorporating the next incoming NTP (right).

Extended Data Fig. 8 Effect of Nb8205 on FluPolA activity, and mapping of host adaptive mutations at the FluPolA dimer interface.

a, b, Effect of Nb8205 on in vitro ApG-primer replication by FluPolA on a vRNA (a) and cRNA (b) template. Data are mean ± s.e.m. n = 3 independent reactions. c, Omitting UTP from in vitro ApG-primer replication by FluPolA on a cRNA template affects the synthesis of the 15-nucleotide, full-length vRNA but not of the 12-nucleotide, short vRNA. The position in the template at which UTP is required is indicated in red. Representative data from n = 2 independent reactions. For gel source data, see Supplementary Fig. 2. d, Crystal structure of H3N2 FluPolA with amino acid residues implicated in avian-to-mammalian host adaptation of influenza A viruses indicated52,53,54,55,56,57,58,59,60,61,62,63,64,65,66.

Extended Data Table 1 Crystallographic data collection and refinement statistics

Full size table

Extended Data Table 2 Cryo-EM data collection, refinement and validation statistics

Full size table

Supplementary information

Supplementary Figures

This file contains Supplementary Figures 1-2. Supplementary Fig. 1 Sequence similarity of FluPol from different influenza virus genera. a-c, Sequence alignment of polymerase subunits PA (a), PB1 (b) and PB2 (c) from A/NT/60/1968 (H3N2), A/duck/Fujian/01/2002 (H5N1), A/bat/Guatemala/060/2010 (H17N10), B/Panama/45/1990, and C/Johannesburg/1/1966. Residues involved in hydrogen bonding interactions at the FluPolA dimer interface are indicated in cyan, residues involved in 3ʹ cRNA promoter binding site are indicated in orange, and residues involved in binding Nb8205 are shown in pink. The figure was prepared with Espript 3.0 (http://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi). Supplementary Fig. 2 Source data (gels). a, Source data for main figures. b, Source data for extended data figures.

Reporting Summary

Video 1

Structure of human H3N2 FluPolA bound to cRNA and Nb8205. This video shows a close-up of the 3′ cRNA binding site.

Video 2

Comparison of monomeric and dimeric FluPolA structures in complex with Nb8205. The video shows that dimerisation induces a movement of a helical bundle formed by the PB1 thumb and PB2 N1 subdomains. Dimerisation leads to the opening of the 3′ cRNA binding site which is incompatible with 3′ cRNA binding.

Video 3

Comparison of the structure of dimeric FluPolA to monomeric FluPolB (PDB: 5MSG). Comparison of the structure of dimeric FluPolA to monomeric FluPolB (PDB: 5MSG).

Video 4

Comparison of the structure of dimeric FluPolA to monomeric vRNA-bound FluPolA. This video shows the movement of the priming loop in the polymerase active site triggered by dimerisation.

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- Received

12 March 2019

- Accepted

07 August 2019

- Published

04 September 2019

- Issue Date

12 September 2019

- DOI
https://doi.org/10.1038/s41586-019-1530-7

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- Letter

- Published: 28 August 2019

Structure and mechanism of mitochondrial proton-translocating transhydrogenase

- Domen Kampjut[1] &

- Leonid A. Sazanov[1]

Naturevolume 573, pages291–295 (2019) | Download Citation

Subjects

- Electron microscopy

- Enzyme mechanisms

Abstract

Proton-translocating transhydrogenase (also known as nicotinamide nucleotide transhydrogenase (NNT)) is found in the plasma membranes of bacteria and the inner mitochondrial membranes of eukaryotes. NNT catalyses the transfer of a hydride between NADH and NADP+, coupled to the translocation of one proton across the membrane. Its main physiological function is the generation of NADPH, which is a substrate in anabolic reactions and a regulator of oxidative status; however, NNT may also fine-tune the Krebs cycle1,2. NNT deficiency causes familial glucocorticoid deficiency in humans and metabolic abnormalities in mice, similar to those observed in type II diabetes3,4. The catalytic mechanism of NNT has been proposed to involve a rotation of around 180° of the entire NADP(H)-binding domain that alternately participates in hydride transfer and proton-channel gating. However, owing to the lack of high-resolution structures of intact NNT, the details of this process remain unclear5,6. Here we present the cryo-electron microscopy structure of intact mammalian NNT in different conformational states. We show how the NADP(H)-binding domain opens the proton channel to the opposite sides of the membrane, and we provide structures of these two states. We also describe the catalytically important interfaces and linkers between the membrane and the soluble domains and their roles in nucleotide exchange. These structures enable us to propose a revised mechanism for a coupling process in NNT that is consistent with a large body of previous biochemical work. Our results are relevant to the development of currently unavailable NNT inhibitors, which may have therapeutic potential in ischaemia reperfusion injury, metabolic syndrome and some cancers7,8,9.

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Fig. 1: Mammalian transhydrogenase.

Fig. 2: NADP(H) binding influences the overall conformation of transhydrogenase.

Fig. 3: The transmembrane dII domain and the proton translocation pathway in the double face-down conformation.

Fig. 4: Attachment of dIII changes the conformation of the proton translocation pathway and opens the NADP(H)-binding pocket.

Fig. 5: The catalytic mechanism of transhydrogenase.

Data availability

Structures of ‘double face-down’ and ‘single face-down’ NADP+ states and apo-NNT have been deposited in the Protein Data Bank with accession numbers 6QTI, 6QUE and 6S59, respectively. The corresponding cryo-EM density maps in have been deposited in the Electron Microscopy Data Bank with accession numbers EMD-4635, EMD-4637 and EMD-10099.

References

1.

Jackson, J. B. A review of the binding-change mechanism for proton-translocating transhydrogenase. Biochim. Biophys. Acta. 1817, 1839–1846 (2012).

- CAS
- Article
- Google Scholar

2.

Sazanov, L. A. & Jackson, J. B. Proton-translocating transhydrogenase and NAD- and NADP-linked isocitrate dehydrogenases operate in a substrate cycle which contributes to fine regulation of the tricarboxylic acid cycle activity in mitochondria. FEBS Lett. 344, 109–116 (1994).

- CAS
- Article
- Google Scholar

3.

Meimaridou, E. et al. Mutations in NNT encoding nicotinamide nucleotide transhydrogenase cause familial glucocorticoid deficiency. Nat. Genet. 44, 740–742 (2012).

- CAS
- Article
- Google Scholar

4.

Toye, A. A. et al. A genetic and physiological study of impaired glucose homeostasis control in C57BL/6J mice. Diabetologia 48, 675–686 (2005).

- CAS
- Article
- Google Scholar

5.

Leung, J. H. et al. Division of labor in transhydrogenase by alternating proton translocation and hydride transfer. Science 347, 178–181 (2015).

- ADS
- CAS
- Article
- Google Scholar

6.

Jackson, J. B., Leung, J. H., Stout, C. D., Schurig-Briccio, L. A. & Gennis, R. B. Review and Hypothesis. New insights into the reaction mechanism of transhydrogenase: Swivelling the dIII component may gate the proton channel. FEBS Lett. 589, 2027–2033 (2015).

- CAS
- Article
- Google Scholar

7.

Li, S. et al. Nicotinamide nucleotide transhydrogenase-mediated redox homeostasis promotes tumor growth and metastasis in gastric cancer. Redox Biol. 18, 246–255 (2018).

- CAS
- Article
- Google Scholar

8.

Santos, L. R. B. et al. NNT reverse mode of operation mediates glucose control of mitochondrial NADPH and glutathione redox state in mouse pancreatic β-cells. Mol. Metab. 6, 535–547 (2017).

- CAS
- Article
- Google Scholar

9.

Nickel, A. G. et al. Reversal of mitochondrial transhydrogenase causes oxidative stress in heart failure. Cell Metab. 22, 472–484 (2015).

- CAS
- Article
- Google Scholar

10.

Prasad, G. S., Sridhar, V., Yamaguchi, M., Hatefi, Y. & Stout, C. D. Crystal structure of transhydrogenase domain III at 1.2 Å resolution. Nat. Struct. Biol. 6, 1126–1131 (1999).

- CAS
- Article
- Google Scholar

11.

Cotton, N. P. J., White, S. A., Peake, S. J., McSweeney, S. & Jackson, J. B. The crystal structure of an asymmetric complex of the two nucleotide binding components of proton-translocating transhydrogenase. Structure 9, 165–176 (2001).

- CAS
- Article
- Google Scholar

12.

Sundaresan, V., Yamaguchi, M., Chartron, J. & Stout, C. D. Conformational change in the NADP(H) binding domain of transhydrogenase defines four states. Biochemistry 42, 12143–12153 (2003).

- CAS
- Article
- Google Scholar

13.

Johansson, T. et al. X-ray structure of domain I of the proton-pumping membrane protein transhydrogenase from Escherichia coli. J. Mol. Biol. 352, 299–312 (2005).

- CAS
- Article
- Google Scholar

14.

Mather, O. C., Singh, A., van Boxel, G. I., White, S. A. & Jackson, J. B. Active-site conformational changes associated with hydride transfer in proton-translocating transhydrogenase. Biochemistry 43, 10952–10964 (2004).

- CAS
- Article
- Google Scholar

15.

Yamaguchi, M., Wakabayashi, S. & Hatefi, Y. Mitochondrial energy-linked nicotinamide nucleotide transhydrogenase: effect of substrates on the sensitivity of the enzyme to trypsin and identification of tryptic cleavage sites. Biochemistry 29, 4136–4143 (1990).

- CAS
- Article
- Google Scholar

16.

Yamaguchi, M. & Hatefi, Y. Mitochondrial nicotinamide nucleotide transhydrogenase: NADPH binding increases and NADP binding decreases the acidity and susceptibility to modification of cysteine-893. Biochemistry 28, 6050–6056 (1989).

- CAS
- Article
- Google Scholar

17.

Padayatti, P. S. et al. Critical role of water molecules in proton translocation by the membrane-bound transhydrogenase. Structure 25, 1111–1119 (2017).

- CAS
- Article
- Google Scholar

18.

Glavas, N. A., Hou, C. & Bragg, P. D. Involvement of histidine-91 of the β subunit in proton translocation by the pyridine nucleotide transhydrogenase of Escherichia coli. Biochemistry 34, 7694–7702 (1995).

- CAS
- Article
- Google Scholar

19.

Venning, J. D., Peake, S. J., Quirk, P. G. & Jackson, J. B. Stopped-flow reaction kinetics of recombinant components of proton-translocating transhydrogenase with physiological nucleotides. J. Biol. Chem. 275, 19490–19497 (2000).

- CAS
- Article
- Google Scholar

20.

Yamaguchi, M. & Hatefi, Y. High cyclic transhydrogenase activity catalyzed by expressed and reconstituted nucleotide-binding domains of Rhodospirillum rubrum transhydrogenase. Biochim. Biophys. Acta 1318, 225–234 (1997).

- CAS
- Article
- Google Scholar

21.

Venning, J. D., Bizouarn, T., Cotton, N. P. J., Quirk, P. G. & Jackson, J. B. Stopped-flow kinetics of hydride transfer between nucleotides by recombinant domains of proton-translocating transhydrogenase. Eur. J. Biochem. 257, 202–209 (1998).

- CAS
- Article
- Google Scholar

22.

Fjellström, O., Johansson, C. & Rydström, J. Structural and catalytic properties of the expressed and purified NAD(H)- and NADP(H)-binding domains of proton-pumping transhydrogenase from Escherichia coli. Biochemistry 36, 11331–11341 (1997).

- Article

- Google Scholar

23.

Bizouarn, T., van Boxel, G. I., Bhakta, T. & Jackson, J. B. Nucleotide binding affinities of the intact proton-translocating transhydrogenase from Escherichia coli. Biochim. Biophys. Acta 1708, 404–410 (2005).

- CAS
- Article
- Google Scholar

24.

Glavas, N. A. & Bragg, P. D. The mechanism of hydride transfer between NADH and 3-acetylpyridine adenine dinucleotide by the pyridine nucleotide transhydrogenase of Escherichia coli. Biochim. Biophys. Acta 1231, 297–303 (1995).

- Article

- Google Scholar

25.

Sazanov, L. A. & Jackson, J. B. Cyclic reactions catalysed by detergent-dispersed and reconstituted transhydrogenase from beef-heart mitochondria; implications for the mechanism of proton translocation. Biochim. Biophys. Acta 1231, 304–312 (1995).

- Article

- Google Scholar

26.

Hutton, M., Day, J. M., Bizouarn, T. & Jackson, J. B. Kinetic resolution of the reaction catalysed by proton-translocating transhydrogenase from Escherichia coli as revealed by experiments with analogues of the nucleotide substrates. Eur. J. Biochem. 219, 1041–1051 (1994).

- CAS
- Article
- Google Scholar

27.

Phelps, D. C. & Hatefi, Y. Interaction of purified nicotinamidenucleotide transhydrogenase with dicyclohexylcarbodiimide. Biochemistry 23, 4475–4480 (1984).

- CAS
- Article
- Google Scholar

28.

Yamaguchi, M. & Hatefi, Y. Energy-transducing nicotinamide nucleotide transhydrogenase. Nucleotide binding properties of the purified enzyme and proteolytic fragments. J. Biol. Chem. 268, 17871–17877 (1993).

- CAS
- PubMed
- Google Scholar

29.

Obiozo, U. M. et al. Substitution of tyrosine 146 in the dI component of proton-translocating transhydrogenase leads to reversible dissociation of the active dimer into inactive monomers. J. Biol. Chem. 282, 36434–36443 (2007).

- CAS
- Article
- Google Scholar

30.

Fjellström, O. et al. Catalytic properties of hybrid complexes of the NAD(H)-binding and NADP(H)-binding domains of the proton-translocating transhydrogenases from Escherichia coli and Rhodospirillum rubrum. Biochemistry 38, 415–422 (1999).

- Article

- Google Scholar

31.

Smith, A. L. Preparation, properties, and conditions for assay of mitochondria: Slaughterhouse material, small-scale. Methods Enzymol. 10, 81–86 (1967).

- CAS
- Article
- Google Scholar

32.

Letts, J. A., Degliesposti, G., Fiedorczuk, K., Skehel, M. & Sazanov, L. A. Purification of ovine respiratory complex I results in a highly active and stable preparation. J. Biol. Chem. 291, 24657–24675 (2016).

- CAS
- Article
- Google Scholar

33.

Scheres, S. H. W. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).

- CAS
- Article
- Google Scholar

34.

Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).

- CAS
- Article
- Google Scholar

35.

Rohou, A. & Grigorieff, N. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).

- Article

- Google Scholar

36.

Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).

- Article

- Google Scholar

37.

Kucukelbir, A., Sigworth, F. J. & Tagare, H. D. Quantifying the local resolution of cryo-EM density maps. Nat. Methods 11, 63–65 (2014).

- CAS
- Article
- Google Scholar

38.

Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N. & Sternberg, M. J. E. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 10, 845–858 (2015).

- CAS
- Article
- Google Scholar

39.

Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).

- CAS
- Article
- Google Scholar

40.

Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).

- CAS
- Article
- Google Scholar

41.

Letts, J. A., Fiedorczuk, K., Degliesposti, G., Skehel, M. & Sazanov L. A. Structures of respiratory supercomplex I+III_2 reveal functional and conformational crosstalk. Mol. Cell (in the press).

42.

Vandock, K. P., Emerson, D. J., McLendon, K. E. & Rassman, A. A. Phospholipid dependence of the reversible, energy-linked, mitochondrial transhydrogenase in Manduca sexta. J. Membr. Biol. 242, 89–94 (2011).

- CAS
- Article
- Google Scholar

43.

Hu, X., Zhang, J. W., Persson, A. & Rydström, J. Characterization of the interaction of NADH with proton pumping E. coli transhydrogenase reconstituted in the absence and in the presence of bacteriorhodopsin. Biochim. Biophys. Acta Bioenerg. 1229, 64–72 (1995).

- Article

- Google Scholar

44.

Tong, R. C. W., Glavas, N. A. & Bragg, P. D. Topological analysis of the pyridine nucleotide transhydrogenase of Escherichia coli using proteolytic enzymes. Biochim. Biophys. Acta 1080, 19–28 (1991).

- CAS
- Article
- Google Scholar

45.

Landau, M. et al. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res. 33, W299–W302 (2005).

- ADS
- CAS
- Article
- Google Scholar

46.

Zhang, L. & Hermans, J. Hydrophilicity of cavities in proteins. Proteins 24, 433-438 (1996).

- CAS
- Article
- Google Scholar

47.

Pravda, L. et al. MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Res. 46, W368–W373 (2018).

- CAS
- Article
- Google Scholar

48.

Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007).

- CAS
- Article
- Google Scholar

49.

Krissinel, E. Crystal contacts as nature’s docking solutions. J. Comput. Chem. 31, 133–143 (2010).

- CAS
- Article
- Google Scholar

50.

Barad, B. A. et al. EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Nat. Methods 12, 943–946 (2015).

- CAS
- Article
- Google Scholar

51.

Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010).

- CAS
- Article
- Google Scholar

52.

Goujon, M. et al. A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res. 38, W695–W699 (2010).

- ADS
- CAS
- Article
- Google Scholar

53.

Larkin, M. A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948 (2007).

- CAS
- Article
- Google Scholar

54.

Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

- CAS
- Article
- Google Scholar

55.

Wu, L. N. Y., Alberta, J. A. & Fisher, R. R. Purification and reconstitution of bovine heart mitochondrial transhydrogenase. Methods Enzymol. 126, 353–360 (1986).

- CAS
- Article
- Google Scholar

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Acknowledgements

We thank R. Thompson, G. Effantin and V.-V. Hodirnau for their assistance with collecting NADP+, NADPH and apo datasets, respectively. Data processing was performed at the IST high-performance computing cluster. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement no. 665385.

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1. Institute of Science and Technology Austria, Klosterneuburg, Austria

- Domen Kampjut

- & Leonid A. Sazanov

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D.K. purified transhydrogenase, prepared cryo-EM grids, acquired and processed EM data, built and analysed the atomic models and wrote the initial draft of the manuscript. L.A.S. designed and supervised the project, acquired funding, analysed data and revised the manuscript.

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Correspondence to Leonid A. Sazanov.

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Peer review information Nature thanks Amandine Marechal and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Fig. 1 Comparison of model transhydrogenases from different species.

a, The domain split and organization of transhydrogenase in the four model species: T. thermophilus, Rhodospirillum rubrum, E. coli and Ovis aries. The dII–dIII linker is conserved in all transhydrogenases, whereas the dI–dII linker and TM1 are limited to NNTs with an α-β polypeptide split (for example, E. coli) and single-polypeptide NNTs (metazoans, including mammals). TM5 is present only in metazoans. b, Residue conservation scores (calculated in Consurf, coloured cyan to magenta from low to high conservation) mapped on the structure of a single monomer of transhydrogenase. The most highly conserved regions are the proton translocation pathway, the nucleotide binding sites and the dI–dIII, dII–dIII and dI–dI interfaces. c, The architecture of mammalian dII. Supernumerary helices TM1 and TM5 are coloured in a darker shade of blue. Residues of the proton transfer pathway are labelled in the helices. The 3_10-helix stretch within TM3 is depicted as a triangular helix. d, Alignment of conserved residues on TM3, TM9, TM13, TM14 and CL7 and CL8 important for proton translocation and reaction coupling in T. thermophilus (Tt), R. rubrum (Rr), E. coli (Ec), O. aries (Oa) and Homo sapiens (Hs). T. thermophilus and a few other species with an NGXGG motif on TM9 have the protonatable histidine on TM3 (α_2H42 in T. thermophilus), whereas most other species that share an HSXXG motif on TM9 have the protonatable histidine on TM9 (βH91 in E. coli and H664 in O. aries).

Extended Data Fig. 2 Purification and biochemical characterization of ovine transhydrogenase.

a, Ovine NNT was purified chromatographically. The last step of purification—size-exclusion chromatography—is shown in two different detergents, FOM and LMNG. b, SDS–PAGE shows the presence of an approximately 110 kDa polypeptide of NNT. The highest purity fractions (which eluted at around 10.5 ml) were pooled and concentrated for cryo-EM sample preparation. c, NNT is highly active and stable when purified in LMNG as shown by undiminished activity over several days when stored at 4 °C. Error bars represent standard deviations based on n = 3 independent measurements. d, Reconstitution of purified NNT into DOPC liposomes shows that the reverse transhydrogenation reaction is tightly coupled to proton transfer, as it is stimulated around tenfold by the proton-gradient uncoupler CCCP and by solubilisation in CHAPS detergent. Error bars represent standard deviations based on n = 3 independent measurements. e, Trypsinolysis of NNT at different pH values in the presence of substrates. The full NNT (110 kDa) and previously identified[15] fragments at 66 and 43 kDa are labelled with asterisks. As the pH decreases from 8 to 6, NADPH-induced proteolysis diminishes relative to that induced by NADP+. At pH 5 trypsin produces different fragments, but stabilization of the intact NNT by NADPH is evident. Trypsinolysis was performed independently three times with similar results. The purification of NNT was repeated independently ten times with similar results as shown in a, b. For gel source data, see Supplementary Fig. 1.

Extended Data Fig. 3 Processing of the NNT–NADP+ dataset.

Thorough classification of particles resulted in six distinct classes with different domain orientations and resolutions. The best-resolution class (double face-down NNT) is almost symmetric with both dIIIs bound in the face-down position, whereas the other five have only one dIII bound in the face-down position, with the other dIII detached and the dI_2 tilted at different angles. Simultaneous tilting of dI_2 and dissociation of dIIIb is probably necessary to permit full dIIIb rotation during the catalytic cycle. Monomers with dIII detached from dII also show little or no density for the dI–dII linker, which suggests that it detaches from dIII to enable dI_2 to open.

Extended Data Fig. 4 Processing of NNT–NADPH and Apo-NNT datasets.

a, NNT bound to NADPH exhibited a large degree of conformational flexibility, which prevented a high-resolution (beyond 8 Å) refinement of any class of particles. Classification into 20 classes revealed that only a small proportion (around 5%) of particles have one dIII bound to dII in the face-down orientation (class C). About another 10% have partially detached dIII (classes A and B). The majority, however, have both dIIIs dissociated from the other domains, leading to a large degree of freedom of movement of dI_2 and of both dIIIs independent of each other (see classes D, E and F). b, Apo-NNT exhibited a single conformational class, similar to the double face-down NNT class in the presence of NADP+.

Extended Data Fig. 5 Examples of cryo-EM density of protein and ligand.

All examples are from the double face-down class in the presence of NADP+, unless otherwise stated. a, Density of the transmembrane helices that line the proton channel (TM3 and TM13). b, Comparison of density of the TM2 between the double face-down and the single face-down (dIII-detached monomer) NADP+ classes, as well as the apo class, which remains in the same conformation upon dII opening while TM9 changes (Extended Data Fig. 6c). c, Beta-sheet density of dI. d, Beta-sheet density of dIII. e, α-helical segment density of dI. f, α-helical segment density of dIII. g, Two phosphatidyl cholines bound in the cavity enclosed by TM1, TM2 and TM6. h, Density of dIIIa–NADP+. i, Density of dIIIb–NADP+. j, Partial NAD+ density in dIa. k, Partial NAD+ density in dIb. The density for lipids and putative NAD+ is discussed in Methods.

Extended Data Fig. 6 Comparison of double face-down and single face-down NNT–NADP+ conformations and apo-NNT.

a, Local resolution and Fourier shell correlation (FSC) curves for the double face-down NNT–NADP+ structure. b, Local resolution and FSC curves for the single face-down NNT–NADP+ structure. c, Local resolution and FSC curves for the apo-NNT structure. d, Overall comparison of double face-down (cyan) and single face-down (green) classes of NNT. An increased dI tilt, dIIIb detachment and dIIb conformation change are visible. e, Comparison of the two monomers in the closed NADP+ class, as viewed from the dimerization interface reveals a tilt of dI_2 and asymmetry in dI-dIIIa/b contacts. f, Overall comparison of double face-down NNT–NADP+ (cyan) and apo-NNT. dII and dIII are in the same conformation and dI_2 is slightly more tilted in apo-NNT. g, Electrostatic surface potential of the proton entry cavities on the matrix (bottom) and IMS sides (top) as well as that of the membrane-facing side (right). h, Hydrophobicity of residues on the surface of dII_2 (coloured white to red from hydrophobic to hydrophilic). Surface-exposed tyrosine and tryptophan residues, which often delineate the surface of the lipid membrane, are highlighted in green and the lipid-binding pocket is circled.

Extended Data Fig. 7 Changes in the proton translocation channel upon dIII detachment and comparison between ovine and T. thermophilus dII.

a, Comparison of T. thermophilus dII (salmon, PDB: 5UNI) and double face-down (dIII attached) ovine dII (cyan, supernumerary TM1 and TM5 in blue). Residues in the N side cavity display markedly different conformations. b, Comparison of T. thermophilus dII (salmon, PDB: 5UNI) and single face-down (dIII-detached monomer) ovine dII (blue). Residues in the N side cavity match more closely as both of these dII structures are detached from dIII. c, Comparison of the TM9 density in the double face-down, single face-down (dIII-detached monomer) and apo dII clearly displaying a H664 flip in the dIII-detached dII. d, Comparison of Dowser-predicted waters in the dIII-attached (cyan) and dIII-detached (green) dII. The dIII-attached structure has two water molecules—one below and one above the N side proton gate—whereas the dIII-detached structure only has one water molecule above the gate, which is consistent with the proposal that the channel is open to the P side when dIII is attached. e, Density for a water molecule coordinated between H664 and S492, consistent with Dowser-predicted water, is beginning to show in our cryo-EM density. f, Proton pathway profile (calculated in Mole 2.5) in dIII-attached dII reveals a diameter constriction between the N side and H664, a hydrophobic stretch between H664 and E806 and a negatively charged P side proton-entry site. g, Proton pathway profile in the dIII-detached dII. Additional constriction appearing between H664 and the P side upon dIII detachment is indicated.

Extended Data Fig. 8 Different conformations of dIII.

a, A homology model of the asymmetric ovine NNT based on the T. thermophilus dI_2dIII heterotrimer structure (PDB: 4J16). Note the putative interacting residues at the dIIIup–dIIIdown interface. The dI–dII linker contacts the loop D of dIII in the face-down conformation. D942 and Y941 from dIII form hydrogen bonds with R544 on the CL2 loop, which stabilizes the dII–dIII interface. Helix 4 and loop D also contribute towards formation of the dI–dIII interface, but Y941 is too far away to interact with dI. b, Comparison of ovine dIII (red) with dIII isolated from R. rubrum (PDB: 1PNO; chain A in blue and chain B in green). Helix 4, loop D and loop E are all more open around the nucleotide in the ovine structure, but the nucleotide is occluded by the interactions from the dII residues (not shown) in the ovine face-down structure. c, Comparison of the NADP(H) binding site in double face-down NNT (left) and apo-NNT (right). Loop E, K999 and R1000 are disordered in apo-NNT and R925 flips into an outward-facing orientation, opening the site to the solvent.

Extended Data Fig. 9 Validation of the mechanism and the reverse transhydrogenation mechanism.

a, Summary of the biochemical evidence and mutagenesis data supporting the proposed mechanism. A full description of mutants in E. coli, R. rubrum and human patients are provided in Supplementary Tables 1–3. b, Our proposal for the reverse reaction. The reverse transhydrogenation reaction consumes NADPH and NAD+ and results in proton pumping, supporting the proton motive force. The driving forces for this reaction are the nucleotide ratios and low proton motive force, which promotes protonation of H664 from the matrix side.

Extended Data Table 1 Cryo-EM data collection, refinement and validation statistics

Full size table

Supplementary information

Supplementary Information

This file contains a Supplementary Discussion and Supplementary Tables 1-3.

Reporting Summary

Supplementary Figure

This file contains gel blot data scans.

Video 1

Anti-phase mechanism of transhydrogenase.

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Author Correction: Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function

Will Bailis1,2 na1,
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Jun Zhao1,3,4,
Juan Carlos Garcia Canaveras5,6,7,
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In this Letter, the ‘Competing interests’ statement should have stated: “R.A.F. is a founder, shareholder and advisor for Rheos Medicines, Inc”. The original Letter has been corrected online.

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Author Correction: Niche stiffness underlies the ageing of central nervous system progenitor cells

Michael Segel1,2,
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In this Letter, the first name of author Staffan Holmqvist was misspelled as ‘Steffan’. In addition, the funding statement in the Acknowledgements section should have mentioned that the work was supported by a Royal Society University Research Fellowship (to K.J.C.). The Letter has been corrected online.

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