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Breaking Science: Frozen clones, friendly bacteria, Dalmations...

Updated Friday 7th November 2008

How to remove carbon dioxide from the atmosphere, clone a frozen mouse, and harness the elusive power of vitamins.

The team learns about a new technique for removing carbon dioxide from the atmosphere, the protein linked to alcohol tolerance, a method for cloning frozen mice, the awkward truth about the power of vitamins, and the friendly bacteria that could save lives.

Plus, in 'Stuff and Non-Science', do your nails and hair keep growing after you die?


Copyright Naked Scientists


Chris Smith: Hello, welcome to the Naked Scientists: Up All Night, which is produced in association with the Open University. I’m Chris Smith. In this week’s show, a breakthrough that might enable us to bring woolly mammoths back from the dead.

Kat Arney: Now, so far, the only clones that have been created have been made by cells taken from living donors, but now Teruhiko Wakayama and his colleagues in Japan have done what was almost unthinkable, they’ve managed to clone a mouse that has been in the deep freeze for 16 years. And this is pretty impressive, because normally when you freeze something, tiny ice crystals form inside the cells, this causes damage to the DNA, it means that they can’t really be successfully cloned.

Chris Smith: So how did they do it? Well Kat Arney will be explaining later. When we’ll also be finding out how researchers have come up with a rock solid way, they say, to lock away CO2 and combat the greenhouse affect.

Peter Kelemen: Well, our calculations, which admittedly are very optimistic, seem to indicate that one could pick up on the order of four billion tons of CO2 per year per cubic kilometre of rock that is involved in their reaction.

Chris Smith: And that’s compared with 30 billion tons of CO2 that we’re producing every year globally – that’s on the way. As is the answer to another growing problem which is do your nails really continue growing after you die? Find out shortly on this week’s Naked Scientists: Up All Night.

First, let’s take a look at some of this week’s top science news stories from around the world, and with a selection of the juiciest findings, here’s our own science PI, Kat Arney. Now Kat, first off, I hear scientists are bringing frozen mice back from the dead.

Kat Arney: Yes, this is an absolutely fantastic story, and since the cloning of Dolly the sheep in the 1990s, researchers have been able to produce cloned mammals. And you make these by removing the genetic material, that’s the DNA, from the egg cell, and then you put in the DNA from a donor cell. Now, so far, the only clones that have been created have been made by cells taken from living donors, but now Teruhiko Wakayama and his colleagues in Japan have done what was almost unthinkable, they’ve managed to clone a mouse that has been in the deep freeze for 16 years. And this is pretty impressive, because normally when you freeze something, especially when you freeze a whole animal, tiny ice crystals form inside the cells, this causes damage to the DNA, it means that they can’t really be successfully cloned.

Chris Smith: So how have they managed to get round the problem and make it work?

Kat Arney: Well, they’ve used a slight variation of their normal technique. It means that you don’t really need to keep the whole nucleus of the cell, that’s where the DNA’s stored, you don’t need to keep all of that intact, but the main thing is that they used brain cells. Now brain cells are really interesting because they’ve got very high sugar content, they’ve got quite a lot of strange molecules in them, and the researchers think that this helped to protect the DNA while it was being frozen. And then they took the nuclei, the DNA from these frozen brain cells, put them in to empty egg cells and grew these up. And they didn’t straight away make them into embryos into new mice, they made them into something called embryonic stem cells, which are the very early cells that we get when babies first start to grow, and then they turned them into embryos and put them into mice. And they found that they were getting a success rate about 39 per cent using these frozen brain cells, and that’s pretty much comparable to healthy fresh tissue.

Chris Smith: It’s also very high, isn’t it? Do you think the spin-offs for this could be things like bringing extinct animals back from the dead? Because I’m thinking in the last 10 years or so we’ve seen mammoths being defrozen from the ice in Siberia, that kind of thing. Could we use this technology that way?

Kat Arney: Absolutely, I mean that’s been, what’s been really on the media speculation this week is could we see woolly mammoths roaming the Earth again. And it is possible. I mean of course these mice they’ve been frozen in a domestic freezer at minus 20 degrees for 16 years. When you’re talking mammoths, they’ve been frozen much, much colder than that for a much, much longer time, so we still don’t really know how good their DNA would be. But certainly the development of this technique, it’s certainly hopeful, and if anything it may be useful for bringing back mammals that have recently gone extinct. So if we have frozen samples of tissue that aren’t that old, it certainly is hopeful.

Chris Smith: And that’s certainly the case because there are various frozen zoo initiatives around the world these days that do seek to preserve animals that way. Kat, let’s move onto another interesting thing that’s emerged this week, which is a way of using effectively fire to fight fire. Here scientists are talking about giving someone a dose of bacteria to stop them getting an infection paradoxically.

Kat Arney: Yes, we hear a lot in the news about these friendly bacteria, you get them in those little yoghurt drinks, and I personally think they’re revolting but some people like them, and they’re meant to help your digestion, and the idea is you put good bacteria, friendly bacteria into your body and they out compete the nasty bacteria and help to keep you healthy.

Now researchers in Sweden have shown that sloshing around solutions of these so called friendly bacteria, bacteria called Lactobacillus plantarum 299, it could actually help to cut down on the infections that cause pneumonia in patients in intensive care who are on ventilators. And these infections are caused by nasty bacteria in the mouth or throat, they get inhaled into the lungs, and it can be a killer because it’s really hard to spot the symptoms early because these people are usually quite sick anyway.

And writing in the journal Critical Care this week, the scientists, and they’re led by a guy called Bengt Klarin, they compared the benefits of swabbing the mouths of people on ventilators with either a solution of an antiseptic called chlorhexidine or a solution of these friendly bacteria, and they found that the bacteria were just as effective as the antiseptic.

Chris Smith: So are they suggesting then that anyone who goes into critical care should have these bacteria added to their body because this might reduce the infection?

Kat Arney: Well the key experiment here was that they were just swabbing the mouth. You don’t have to drink them. You don’t have to put them into someone. You just have to kind of swab or wash around their mouth. And they think it’s because these friendly bacteria, like I mentioned earlier, are out competing the nasty bacteria. And what’s quite good about bacteria, as well, is these friendly bacteria will cling to stuff, as bacteria do, they’ll stay inside the mouth. They don’t have the unpleasant side effects that some of these antiseptics do like discolouring the teeth, irritating the tissues and that kind of thing. So it’s potentially quite a long lasting, kind and just as effective treatment as using antiseptics.

Chris Smith: Well, let’s hope so because infections acquired in hospital are a major problem, and also we’ve got rising levels of antibiotic resistance, so we want to try and cut down the levels of antibiotic use in hospital. But moving from antibiotics to vitamins now, there’s been a long, long controversy over whether vitamins are or aren’t good at stopping certain diseases, including cancer, so what are the numbers look like on this now?

Kat Arney: Well, there’s been a mixed week for vitamins this week, and one group of scientists has found that folic acid, that’s a vitamin along with vitamins B6 and B12, has no impact on cancer risk in women in the study who were at high risk of heart disease. But another study has found that vitamin B3 could actually help to reduce the memory loss associated with Alzheimer’s disease – well at the moment at least if you’re a mouse.

And now the first study, the cancer study, was published in the Journal of the American Medical Association. And the researchers were carrying out a clinical trial over more than seven years, involving more than 5,400 middle aged women who’d already got heart disease or were at high risk, and they were testing whether folic acid and these vitamins B6 and B12 could actually reduce the risk of cancer in these women.

And the reasoning was that some studies have found a reduction in risk but actually the evidence is quite patchy and we’re not really sure. But when they looked at this whole study, they found that there was basically no difference in the number of women developing cancer who had taken the supplements, compared with those who had taken a placebo. So, well, the good news is they don’t do you any harm, unlike some other studies, but they don’t particularly do you any good either.

Chris Smith: But I think this is going to leave people very confused because it wasn’t that long ago that we had a big meta-analysis, an analysis of lots of lots of studies all added together, that showed that in fact some of these vitamins increase your risk of cancer. So people are getting a message one day saying vitamins are good for you, another day saying vitamins are bad for you, I don’t think we can blame them for being confused.

Kat Arney: Yes, the key thing is there are a lot of studies that come out about vitamins, and obviously there’s quite a big industry trying to push vitamins because there’s money in it, but the key thing is that really if you want to reduce your risk of cancer, the very best way to do that is to eat your fruit and veg – that’s where all these really complicated biological molecules are that do you good. You can’t really replicate that with supplements. And that’s what these studies are showing.

But one interesting study that came out this week that is maybe positive for a vitamin supplement is this study about Alzheimer’s disease, and this is from researchers at the University of California. And they’ve been studying mice that have been genetically engineered to develop Alzheimer’s. And they’ve found that the vitamin B3 could actually reduce the levels of a protein called phosphorylated tau. And this is what builds up in nerve cells. It causes all these kind of tangles that lead to Alzheimer’s disease.

And they’re actually now carrying out a clinical trial of vitamin B3 in humans, because so far it’s only been done in mice, and if there is a certain rational reason why we should use a certain vitamin supplements for certain diseases then that could be very positive. But, as I said, for overall general good health and reduction in cancer risk and things like that, you just want your fruit and veg.

Chris Smith: So the moral of that story is eat your greens or you’re not having anything from the sweet trolley. Now to finish off this week Kat, what are dogs telling doctors and scientists about stones that can form in different bits of the body?

Kat Arney: Well, the dogs themselves are going ruff ruff ruff ruff ruff. What their DNA is telling us is that we’ve potentially found an interesting gene that’s involved in the formation of bladder stones in Dalmatians and in kidney stones and things like that and gout in humans, and this is according to scientists at the School of Veterinary Medicine at the University of California. Now bladder and kidney stones are particularly painful infliction caused by the production of uric acid in the urine, and only humans, great apes like gorillas and, unusually, Dalmatian dogs are the only types of dogs that get these. They produce high levels of uric acid in their wee, basically, and in humans this uric acid causes kidney stones, it can cause high blood pressure and it can cause that famous Victorian disease, gout, while in Dalmatians it leads to bladder stones which often have to have surgery to get rid of them.

And writing in the journal PLoS Genetics, the researchers studied DNA and urine samples from hundreds of Dalmatians, as well crosses between Pointers and Dalmatians, and they tracked down the gene that’s responsible for producing these exceptional high levels of uric acid. Now it’s got a very catchy name, yes, it’s called SLC2A9, but it’s also found in humans. Now not only could this discovery really pave the way for research into the causes of kidney stones and gout in humans, but it also now provides dog breeders with the knowledge to breed out this harmful gene from their dogs, and you could cross Dalmatians for example to the Dalmatian-Pointer crosses that were bred in the 70s, and these dogs will be genetically identical to Dalmatians but won’t have the risk of the bladder stones.

Chris Smith: Do you honestly think that people are going to go as far as to genotype, genetically test dogs to see if they actually are not going to get a disease? Because the whole point of selective breeding has led to dogs which are genetically completely screwed up, and they have all kinds of horrible diseases, but that’s been because we’ve bred them that way.

Kat Arney: Well dog breeding is a very big business, and in fact the researchers who’ve done this work are now actually offering genetic testing for Dalmatian breeders – that’s for their dogs, not for the actual owners. But they’re offering that from December onwards, and you can find out more on the web at www.vgl.ucdavis.edu. But bear in mind they are based in California, so Dalmatian breeders of the UK, you know, it might not be so applicable for you. But it’s big business and people are really trying to breed out these harmful diseases from dogs, so you can keep the best strains about them, the spottiness and the friendliness, but try and breed out things like kidney stones.

Chris Smith: And I think we’d probably all agree that some dog owners could use a genetic test themselves. Thank you Kat. That was Kat Arney with a round up of some of this weeks top science news stories. And if you’d like to follow up on any of those items, the details are all on the Open University’s website which is at open2.net/nakedscientist.

In just a moment we’ll be finding out how researchers have tracked down a molecule in the brain that makes some people prone to alcoholism. But first to another way of dealing with the CO2 that we’re pumping out into the atmosphere by burning fossil fuels. Scientists at Columbia University have found a way to soak up the CO2 using a rock found in the Earth’s mantle known as peridotite which contains a key mineral known as olivine. Here’s Peter Kelemen.

Peter Kelemen: Well, overall, what we’d like to do is to help get carbon dioxide out of the atmosphere. As you know, human input to the atmosphere is very large and increasing. It’s roughly 30 billion tons per year right now, and that’s causing the concentration of CO2 in the atmosphere to increase every year. And for a number of reasons, one being climate warming but also increasing the acidity of the oceans, scientists are almost in universal agreement that raising the concentration of atmospheric CO2 beyond where it is now is very, very dangerous for the planet.

Chris Smith: Sure, it’s easy to say that but what is the solution that you’re trying to work on in order to try and overcome the problem.

Peter Kelemen: Right, so the solution that we’re focused on in particular is taking CO2 out of the air and turning it into solid carbonate minerals.

Chris Smith: And what minerals are you talking about here?

Peter Kelemen: Well, in particular, what people have proposed before us is that the mineral, olivine, which is the primary constituent of the Earth’s mantle, is particularly good for sucking up CO2 from the air and making it into a solid mineral because it has the most magnesium and calcium per kilogramme or per cubic metre of any common rock type on Earth.

Chris Smith: And what’s the reaction that occurs between the CO2 and the olivine in order to lock away CO2 as a solid?

Peter Kelemen: Well, the simplest way to think of it is that olivine is a magnesium silicate, and so when you add carbon dioxide to that, you make a carbonate mineral, magnesite, which is magnesium plus CO2, and then the excess silica is precipitated as quartz.

Chris Smith: And this is presumably the same reaction that happens naturally when you get big changes in carbon dioxide in our planet’s history, where mountains have grown up, like the Himalayas, for example, they expose lots of these minerals and this brings down carbon dioxide and that would have cooled the planet in the past, which is why you presumably think this will work.

Peter Kelemen: Well, that’s right. This is something that occurs all the time by a weathering of these rocks. Normally the mantle is 6 to 40 kilometres below the surface and deeper. So plate tectonics, collision of tectonic plates brings these rocks to the surface, and they’re very, very far from equilibrium with the atmosphere. So pretty much, no matter what the CO2 concentration in the atmosphere is, there’s always this reaction going on at some rate.

Chris Smith: The thing is though it’s one thing for plate tectonics to do this. They tend to do that though over a million year timescale. We need a solution to the CO2 problem now. So how do you propose to get this to work on that sort of timescale?

Peter Kelemen: Well, what we’ve found is that the reaction is so strongly favoured to occur, that it will happen spontaneously and give off heat. And so if you can initially heat rocks so that the reaction rate is over a million times what the natural rate is in nature, the heat that’s given off by this reaction is sufficient to maintain high temperatures. So then you can pump surface temperature carbon dioxide into the rocks but have the reaction going on at 185°C where it’s much, much faster, a million times faster than in weathering on the surface.

Chris Smith: Are these rock types and these minerals, the olivines that you’d need to do this, readily accessible? Because I know you said they’re in the mantle, that’s a long way down, so would there be areas on Earth where you could do this but nowhere else, or could you do this pretty much anywhere?

Peter Kelemen: Well, what you do is you take advantage of mountain belts where plate tectonics, as I said before, has thrust these rocks from the rift deep interior up to the surface, and they’re not everywhere but they’re on every continent, and so, for example, in the United States that would be along the West Coast mostly in California and Oregon. The really, really big deposits of the world are in the Balkans, in Saudi Arabia, the United Arab Emirates and Oman, and then in big Western Pacific islands, Papua New Guinea and New Caledonia.

Chris Smith: So how much CO2 do you think, assuming that we went down this road, how much CO2 could we lock away with this strategy and is it a reasonable amount that is therefore worth pursuing?

Peter Kelemen: Well, our calculations, which admittedly are very optimistic, seem to indicate that one could take up on the order of four billion tons of CO2 per year per cubic kilometre of rock that is involved in the reaction. And, famously, Sir Richard Branson set up a large cash prize to anybody who could capture and store a billion tons per year. So this process, at least from an optimistic perspective, looks like it’s definitely in the ballpark for things that could make a significant difference.

Chris Smith: So you’ll be applying to Richard Branson for the prize presumably.

Peter Kelemen: No, no, I’m quite sure that Richard Branson wants to see more than a short paper in a journal.

Chris Smith: But just to sort of finish this off, are there any environmental impacts of doing what you’re suggesting, because it’s one thing to say we can make this reaction happen, we can lock away CO2 but what are the possible negatives?

Peter Kelemen: Well, you know, first of all I would say they are probably pretty small because the natural process, which I’ve studied mostly in the Sultanate of Oman, is something that the local people actually take advantage of, for various reasons. That’s the good news. On the other hand, if you’re involving cubic kilometres of rock in a reaction that changes the rock volume quite a bit, there’s going to be uplift of the land surface, there’s going to be cracking, and that’s just something that people who are interested in this process, let’s say the Government of Oman for example, are going have to decide whether the trade-offs, in terms of changing the landscape, are worth it to them or not.

Chris Smith: It’s ironic isn’t it that the countries that have a lot of the oil that’s causing the problem are also potentially sitting on the solution. That was Peter Kelemen from the University of Columbia, who, with his colleague Jürg Matter, has worked out how we can use a natural mineral to soak up CO2. That work’s published this week in the journal PNAS.

Now to another problem of excess, but not CO2 this time, alcohol. Alcoholism is a serious problem, and in the UK as many as one person in every 20 could be affected, and one key behaviour that precedes full blown alcohol addiction is tolerance, where the brain adapts to the presence of alcohol. Previously, no one knew what was responsible for this adaptation process, but now scientists at the University of Massachusetts have found that part of a pore, called the BK channel, which regulates the activity of nerve cells, seems to be critical for the process occurring. The part of the channel that they’ve focused on is called the beta 4 subunit, and by switching off the gene that makes it, the researchers have been able to make nerve cells that become alcohol tolerant much more quickly. Here’s Gilles Martin.

Gilles Martin: The question we tried to answer revolves around the notion of alcohol tolerance. People who are addicted to alcohol, well, first, you know, they will typically show dependence and there is craving. What we’re really focused on is really what will appear very early on is called tolerance. Tolerance can be generally described as the loss of efficacy of alcohol over time. It means that although alcohol is still in your system, the alcohol affect will disappear. So this is really what tolerance is all about.

Chris Smith: And you’re saying there is some kind of brain mechanism by which it’s not the alcohol leaving the body, it’s the brain changing the way it’s working to overcome the effect of the alcohol being present.

Gilles Martin: Exactly, and what is really interesting is that people who show tolerance are actually more likely to become addicted to alcohol.

Chris Smith: And how have you tried to get to the bottom of what’s going on here?

Gilles Martin: What we did was to use an animal model. So we used mice that do not express the protein that we’re interested in. It’s called the beta 4 protein. So this protein is part of a much larger protein complex. And this complex is found in the membrane of neurons. And what this large protein complex does is it regulates excitability of neurons, the way the neurons really communicate with each other. We use a technique that is called electrorheology. When we expose this protein, this iron channel that is called the BK channel to alcohol, then its activity is going to increase. Now, if we do this exact same experiment, but we remove this beta 4 subunit that I was talking about, then we see initially the same response, the activity of the channel is going to increase, but very rapidly after a couple of minutes we can see that the activity goes back down to control level.

Chris Smith: So this is effectively tolerance kicking in isn’t it? Do you know what’s actually happening in the proteins so that when the alcohol is present and this subunit is not there, it makes it recover much more quickly? I guess that’s the key thing to answer isn’t it?

Gilles Martin: Yes, and we have the beginning of an answer. When the beta 4 subunit is expressed, it appears to really alter the interaction between this iron channel that we’ve studied and other signals into the cell.

Chris Smith: So putting all that together, does this mean then the people who have a tendency towards alcoholism could perhaps be deficient in this protein, perhaps they have less of this beta subunit in their own brains, or is it just too early for you to know that?

Gilles Martin: We don’t know yet, but we have the idea that actually not only you’re right, you know, that the amount of beta 4 subunit might be different in the population of alcoholics, but we are thinking about another possibility. And we believe that in the population of alcoholics this beta 4 subunit may have mutations that would prevent the beta 4 from maybe interacting with the other protein forming the iron channels.

Chris Smith: And I know that you’re saying that this is obviously speculation but, thinking therapeutically for a minute, if that’s the case that suggests that putting that subunit into more cells could be a way or a novel way to treat people who do have a problem with alcohol.

Gilles Martin: Well, it could be but I think you know if we think in terms of therapy or at least something that could help, the way I see it is that if we are indeed right that there might be mutations of this beta 4 subunit, then we could possibly develop maybe a kind of screening test that would enable people to really determine whether they are at risk or not, or if they have a predisposition to develop alcohol addiction.

Chris Smith: So perhaps in future your insurance company might want to know how much beta 4 subunit there is in your brain before they’ll insure you. That was Gilles Martin from the University of Massachusetts, and you can find that work published in this week’s PNAS.

This is the Naked Scientists: Up All Night with me Chris Smith, and time now for this week’s Stuff and Non-Science, where we massacre myths and bash bad science, and last seen hanging around a morgue, although thankfully very much alive and kicking, was Diana O’Carroll.

Diana O’Carroll: On this week’s Stuff and Non-Science it’s all about dead bodies. Yes, some would have you believe that hair and nails grow after death but this is probably not true. So here’s Alison Cluroe with the real truth.

Alison Cluroe: Yes, the idea that hair and nails can grow postmortem is in fact a myth. They do not grow at all after death when there is no further cell division. What people are actually seeing when they think that nails or hair have grown is actually retraction and drying of the tissues from around the nail bed and from around the cuticle, the retraction and drying of the scalps skin, and this gives an illusion of lengthening of the nails and lengthening of the hair, but in fact there is no hair growth. I think one of the reasons that some of these myths have come about are that there are anecdotal stories out of history suggesting that bodies that have been exhumed have shown growths of hair all over the body or extra growths of hair over the face or indeed change of colour of hair. I think that these are most likely to be related to fungal growth that’s been misinterpreted, fungal growth causing a change in the colour of hair or indeed giving the impression of actual hair growth.

Diana O’Carroll: Alison Cluroe, she’s a forensic pathologist at Addenbrooke’s Hospital in Cambridge. It turns out it’s not so much to do with nails growing as everything else shrinking. If you’ve got a science myth then let us know by emailing diana@thenakedscientists.com.

Chris Smith: So no need to worry too much about your postmortem manicure. Thank you Diana, that’s Diana O’Carroll with this week’s Stuff and Non-Science.

Well, that’s it for this time. We’re back next week with another round up of the latest findings from the world of science.

The Naked Scientists: Up All Night is produced in association with the Open University and you can follow up on any of the items included in the programme via the OU’s website, that’s at open2.net/nakedscientist. Alternatively, you can also get there by following the links from the BBC Radio Five Live Up All Night website.

Production this week was by Diana O’Carroll from thenakedscientist.com and I’m Chris Smith, until next time goodbye!

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Mark Hirst explains the impact of the news about cloning frozen mice: There's a mammoth in my freezer.


These are the sources used by the team in making the show:

In the news

'Production of healthy cloned mice from bodies frozen at -20°C for 16 years'
by Sayaka Wakayama, et al
Published online

'Use of the probiotic Lactobacillus plantarum 299 to reduce pathogenic bacteria in the oropharynx of intubated patients: a randomised controlled open pilot study'
by Bengt Klarin, Göran Molin, Bengt Jeppsson and Anders Larsson
in Critical Care

'Gene Cause Hyperuricosuria and Hyperuricemia in the Dog‘
by Bannasch D, et al. (2008) Mutations
in PLoS Genet 4(11)

'Effect of Combined Folic Acid, Vitamin B6, and Vitamin B12 on Cancer Risk in Women: A Randomized Trial' by Shumin M. Zhang, MD, ScD; Nancy R. Cook, ScD; Christine M. Albert, MD, MPH; J. Michael Gaziano, MD, MPH; Julie E. Buring, ScD; JoAnn E. Manson, MD, DrPH JAMA.

'Folate Deficiency Induces In Vitro and Mouse Brain Region-Specific Downregulation of Leucine Carboxyl Methyltransferase-1 and Protein Phosphatase 2A B Subunit Expression That Correlate with Enhanced Tau Phosphorylation'
by Jean-Marie Sontag, et al


Sequestering carbon dioxide in rocks with Peter Kelemen “In situ carbonation of peridotite for CO2 storage,” by Peter B. Kelemen and Jürg Matter in PNAS

The protein responsible for alcohol tolerance with Gilles Martin “Identification of a BK channel auxiliary protein controlling molecular and behavioral tolerance to alcohol,” by Gilles Martin, Linzy Hendrickson, Krista Penta, Ryan Friesen, Andrezj Pietrzykowski, Andrew Tapper, Steven Treistman in PNAS


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