Class Supplement, Nature Podcast Digest Feb 23 2012

The original script of this podcast: http://www.nature.com/nature/podcast/v482/n7386/nature-2012-02-23.html
The audio file of this podcast: http://www.nature.com/nature/podcast/archive.html


雄を作るＹ染色体は（Ｘ染色体と違い予備がないので）変異を起こした部分が消滅しやすいが、変異を起こす箇所は決まっているのでＹ染色体全体が消滅することはない（雄は消滅しない）。
Jennifer Hughes: Well, it is really just a shell of its former self. It has been evolving separately from the X chromosome for hundreds of millions of years. So the X and the Y used to be identical. They used to be just like every other pair of chromosomes in our genome. They used to undergo recombination with each other and at some point, way back in the ancestor of mammals, the Y got a new role, it became the sex-determining chromosome and that started a cascade of events that suppressed recombination between the X and the Y. When you stop recombining, you lose the ability to repair yourself, so it lost genes, it lost big chunks of DNA and it just started withering away. The Y has only about 30 unique genes while the X chromosome has at least 800 genes, so it's a pretty interesting idea that the Y could be heading towards extinction and perhaps men too.

Geoff Marsh: Right, but some of these older inversion events happened many many millions of years ago and since then there’s some real stability.

Jennifer Hughes: Exactly. That was the interesting thing that we found that the only region that has suffered any gene loss was just in the most recently formed one and the smallest one. If you look back all the other strata, which cover the rest of the chromosome, there's been absolutely no gene loss in either of the human or the rhesus lineages. So that means for hundreds of millions of years, the gene contents within these regions has been unchanged, it's been holding steady. Sure a lot of gene loss happened initially, but what was left after the initial, you know, massacre, you could call it, the genes that are left are here to stay.
Jennifer Hughes: I'm very confident in saying that the Y chromosome is not going anywhere.

微生物の全種類の87％が綿棒1本で採取できる。将来はバクテリア観察ガイドブックや、ある土地のバクテリア生態系の作用のシミュレーションなどが可能に。
Jack Gilbert: Okay, so those samples were basically Q-tips, sterile Q-tips that have no bacterial contamination. So we swabbed your phones, we put those in tubes, we stored them on frozen carbon dioxide, this dry ice and then shipped those directly back to Argonne, that's Argonne National Laboratory just outside Chicago. So they've arrived there already. On Monday morning, when Jarred Marcell, who is the technician who was helping you do the sampling, when he gets back, he's going to take the DNA that was on the bacteria or in the bacteria that were on the swabs that were or used to be on the soles of your shoes or the phone and is going to then use an amplification technique. By that we mean, he's going to take a gene, he's going to sequence that gene and that's going to tell him what organisms, what bacterial species are on your phone and your shoes and we're going to publish that on Facebook, say Tuesday or Wednesday.

Jack Gilbert: Okay. One of the, it sounds may be slightly geeky, but one of my favourite revelations is that we've already encapsulated the largest amount of diversity ever found by any study in just the last year with a number of samples we processed. So we'd actually found 87% of all of the bacterial organisms that have ever been known about or already been found by the study. The next largest study to ever done this, which was the 175 million dollar NIH initiative, the Human Microbiome Project, where they're looking at intestinal bacteria and bacteria on the skin, that's found about 13% of the bacteria that have been found. But what's even more remarkable is 85% of everything we've ever found on the Earthmicrobiome project is completely unidentified, has not been seen, that's quite remarkable.

Jack Gilbert: We have two short-term goals. The first goal is to create a field guide for microbiology, this book which can tell everybody what bacteria are found where and what they do. The other major key thing that we're interested in doing is creating models. These models can be used to encapsulate in a mathematical formula the variety of the bacteria and also more importantly what they're doing. So for example, I can go into a farmer's field and I can characterize the microbial diversity and their functional ability in that soil and then I can derive a model which describes that relationship and then I can in my computer, I can increase the temperature on these bacterial communities in this model and see what happens to them, which might be able to tell me what yield of plants he'll get, what species of plant he should be growing and it's only these long-term explorations of the microbial community, which enable us to actually explore that.

コンピューターサイエンスの祖、アラン・チューリンクﾞは、第二次世界大戦中のドイツ軍の暗号解読で有名だが、データと指示の一本化を考案し、人工知能を通して知性を探ろうとし、インターネットの構想を持っていた。
Geoff Marsh: This week, Nature is celebrating the 100th anniversary of the birth of Alan Turing. To some Turing is the founder of modern computer science. To others, he's known for the Turing test, a test of artificial intelligence, in which a human interrogator tries to distinguish between answers from a machine and from another human. But to many, his name isn't as familiar as perhaps it should be. Charlotte Stoddart has been digging into his life. Her quest took her to Oxford University. Nature 482, 441 (23 February 2012)

Andrew Hodges: Well, as you've been saying, Alan Turing was a very secret and hidden figure until the 1970s when it really came out that he being the most important scientific figure in the breaking of the German ciphers in the II world war. Of course, he was always famous to mathematicians before that, but his place in history of computers was not so well known and it really only began to make sense when people knew that he had had this tremendous role in the II World War which bridged his working logic, pure logic in the 1930s into the emergence of electronic computing as we know it today and in 1945. And the other thing that he was a gay man and this in the 1950s was really a terrible thing, I mean no one wanted to talk about it and certainly didn't want to talk about what happened to him when he was arrested in 1952 and suffered considerably. As a result, and indeed he died in 1954, some two years afterwards and it certainly kept him out of the standard kind of reference to great scientific figures that other people enjoyed.

Andrew Hodges: The absolutely crucial thing that Turing had is different from what anyone else would have had before, was that data and instructions read the same thing, that instructions are a form of data. Every kind a machine building that have gone on before and people like Babbage have thought about great calculating engines, have thought of instructions as being completely different in nature from the material, the numbers on which you're working and the big calculators built in the 1930s which worked on that principle. And what's completely different about Turing's perception is something that you got from within mathematics was to see that if you have, in modern terms, a computer program, a program is just a list of data. Now Turing really, he really let it fly that idea in 1945 and saw that software was going to be the key. The whole point was that you could do anything by just changing instructions and leaving the engineering alone, which is an absolute breakthrough at the time and no one had seen anything like that before.

Charlotte Stoddart: Turing was also interested in machine intelligence wasn't he?

Andrew Hodges: Well, Alan Turing was always most interested in the nature of the mind and in the paper he wrote in 1950, Computing Machinery and Intelligence which actually has an elaborate discussion of what a machine is, it's quite a substantial thing and also about practical techniques one might go into to develop Artificial Intelligence, but what's most famous in all instructs that readers most strongly for his reason and humour indeed is this concept that the Turing test of playing a game, an interrogation game, in which a computer program is pitted against a human respondent and they have to compete to show that they're human. So Turing really wants an objective measure of what you'd mean by intelligence, or thinking. He doesn't want to say a machine is made of silicon chips or whatever and therefore it can't be thinking, which tended to be the philosopher's own say. He wanted something that would give some objective measure.

Andrew Hodges: Well, what's happened with computing that people didn't foresee, I think in the early period is simply how small, cheap, fast they could be, especially cheap and Turing was certainly much more so democratically involved in the computers than most people. He envisaged sense in which people would interact personally with computers in a way that would have seemed very strange in the 1940s, but in his writing about computation, I don't think he envisaged that you'd simply get the tiny scale and size and then very fast speeds that are available now.

体が凍らない魚の持つ不凍タンパク質が出現した時期と気候変動をこの魚の進化と照合した結果、この魚の進化には不凍タンパク質だけでなく寒冷化も関係があることが分かった。
Kerri Smith: Anti-freeze proteins in the bodies of Antarctic fish are a crucial adaptation to life in the deep freeze and they were thought to be a major driving force behind the evolution of these fishes until now. A team from Yale University constructed a family tree of Antarctic fish species and compared it with the appearance of these proteins and changes in climate. It turns out that the proteins alone can't explain the diversity of these fish. Their evolution also has to do with the cooling event that happen, when the proteins had already been around for millions of years. The cooling event meant more ice in the oceans, opening up a new polar habitat. The work appears in Proceedings of the National Academies of Science. Nature 482, 443 (23 February 2012)

健康なヒトでも何百もの遺伝子に突然変異があることが分かっている。大部分は重要とされない遺伝子の異常だが、医療で危険因子特定への応用も考えられる。
Kerri Smith: Even healthy humans carry hundreds of gene mutation that seriously disrupts genes, finds a study published in science. These are called loss of function mutations. A team based near in Cambridge in the UK analyzed almost 200 genomes and found that a typical individual harbours a hundred of these mutations; a fifth of those turn off both copies of a gene. Most mutations occurred in non-essential genes. But in future, the work could help scientists identify which mutations to be wary of in medical screening. Nature 482, 443 (23 February 2012)

早朝に心臓マヒになりやすいのは、体内時計の働きも関係している。体内時計はKif15（心臓機能関連を含む多くの遺伝子の発現を制御するたんぱく質）に左右される。
Mukesh Jain: The cardiovascular system in particular has a number of disease processes that have a predilection to occur during certain times of the day and sudden cardiac death is one of them. The occurrence of heart failure and heart attack is another and these tend to occur in the early morning hours, so in the wee hours of the morning through the first few hours, as were all busy and ready and getting to work, those are peak incidents and so it's been a major curiosity and so our study helps shed insight into this issue because we identified a factor that alters the susceptibility to arrhythmias at least in rodents and number two we linked it to components of the biological clock and showed that this factor's expression changes during the course of the day.

Kerri Smith: And this is a molecule called, Klf15.

Mukesh Jain: Right, Klf15 is the factor. My laboratory and one other group had identified it in the early part of the last decade and it is a transcription factor. So it is a DNA binding protein that regulates the expression of many, many genes and in this case, in the heart, we identified a specific ionic channel and current that it regulates the potassium current specifically.

Kerri Smith: Now what led you to connect it with heart function and you say in your paper you made a serendipitous observation about it.

Mukesh Jain: Right. It was serendipitous in the sense that we noted that animals, when they were kept, our animals that are deficient in Klf15, when they were kept in the normal animal facility, we had observed certain patterns of behaviour and when we brought them up into the laboratory and they would stay there for a few days under constant light condition, so you see the animal facility has day-night conditions where the laboratory is under constant light condition. We noted that there were differences in the expression of certain genes in the heart, so it made us begin to wonder whether day-night may contribute. So, it was a particular way to , you know, to get into the area of circadian biology.


空気感染が可能な鳥インフルエンザウイルスが作成された件について、作成方法の情報取り扱いに慎重論があり情報開示を控える動きがあるが、関係業界の圧力が対抗している。
Richard Van Noorden: The World Health Organization got 22 experts together at the end of last week to kind of hammer out what to do about this flu situation. You'll remember that researchers in two places have created this mutant, transmissible strain of Avian flu by passing it between ferrets, so that it's now transmissible in air, which fortunately, the bird flu virus that's currently still around is not easily transmissible and this caused a great rumpus when they wanted to publish their work in Nature and in Science. And the US government and the US National Science Advisory Board for Biosecurity has said, you got to have a sense of these paper if you publish them because someone could get details of this work, could recreate this transmissible virus perhaps and who knows what could happen.

Richard Van Noorden: Well, the meeting concluded that this kind of research has to happen in the future. It's very, very important and interestingly at the meeting, according to a Nature editorial this week, people realize that current avian viruses already have some of the mutations that were created in this new work. In other words, there's already a kind of substantial risk to humans. So, this new data where they've created this transmissible virus could actually be able to have a lot of value for surveillance, we should check mixed viruses that are out there and see whether they're acquiring some of the mutations that this work has picked up that could make this virus transmissible.

Richard Van Noorden: There were still opposers. So the only guy from the National Science Advisory Board for Biosecurity at the meeting was Paul Keim, he was acting chair and he didn't go along with this recommendation that the paper should be published in full. According to Reuters, they quote a scientist close to this board who said that Paul Keim got the hell beat out of him, it was close meeting dominated by flu people, who have a vested interest in continuing in this kind of work. So this was a source telling Reuters, we don't know who this was. But clearly this wasn't quite a result and there were 22 people there but there was only one from the Security Board.

永久凍土に埋まっていた植物を再生し増やすことに成功。種ではなく種と本体をつなく組織を使用。しかし恐竜で同じことをする研究が実を結ぶことはたぶんなさそう。
Geoff Marsh: Okay so the tables may turn yet. Next up, we've got this story, the resurrection of a very, very old plant.

Richard Van Noorden: This was a plant, wild flower that is more than 30,000 years old. It's been buried in permafrost, well below freezing for more than 30,000 years and scientists have now resurrected this plant. Thanks to some squirrels that very helpfully buried lots of samples in the permafrost.

Geoff Marsh: Sounds a lot like Scrat from Ice Age, doesn't it?

Richard Van Noorden: Yeah, it's very good of them actually. If only they were still around, we could thank them. So this is the first time that we've managed to create viable plant from ancient remains in frost. We've actually tried before and we've actually got seeds from things like sedge and alpine plants and we've never quite managed to get them to germinate, but we actually succeeded this time using a slightly different approach. This is a team led by David Gilichinsky, the Russian Academy of Sciences' Institute of Physical Chemical and Biological Problems and sadly Gilichinsky passed away last week, but not before he's seen the success of his work. So, he and his colleagues, what they did was instead of taking the seeds, they take bits of the placental tissue, which is, it's a bit like the white matter inside papery, it kind of gives rise to and holds to the seeds, it's going to be where the seeds ultimately come from and when they cultivated that tissue, in vitro giving it nutrients that then produced shoots and then they took cuttings, propagated more plants and they've also got fertile seeds from this plant.

Geoff Marsh: So, we were limited by our techniques before. The Jurassic Park fan inside me has to ask are we limited to seeds in this field of resurrection.

Richard Van Noorden: Well, we're kind of actually apparently trying to resurrect the woolly mammoth. This is a project that's supposed to happen, I don't think this is ever going to happen, but some Russian scientists are working on it, but it's much, much more complicated than plants.
Geoff Marsh: Okay and next up a story about a technology that seems like it's straight out of star trek.

手のひらサイズのＤＮＡ解析器。ナノサイズの穴で数珠つなぎにしたＤＮＡの基を伝導率で順に読み取る。来年には使い捨て用を販売する計画もある。
Richard Van Noorden: This is pretty exciting. I don't have in my hand, but I wish I did. This incredible sequencer. It's a DNA sequencer, it's smaller than somebody's palm, and it's just a one use disposable sequence and its going to be selling for less than 900 dollars and this is all technology from a company called Oxford Nanopore which is a UK based company and for the last 5-6 years, it's been working on a cool new way to sequence DNA by threading the DNA through a nanopore and reading off the bases by looking at the change in electrical conductivity one by one in real time. This week, we saw the first sort of data run from these guys and it looks quite promising. The error rate is still quite high, 4% error rate and they've only managed to do small genomes like those of viruses, but obviously got to give them time to improve and they say they're in the second half of this year, they're going to launch their main machine and then they're going to plan to sell this disposable sequence later on, may be next year.
for Biosecurity has said, you got to have a sense of these paper if you publish them because someone could get details of this work, could recreate this transmissible virus perhaps and who knows what could happen.

Richard Van Noorden: Well, the meeting concluded that this kind of research has to happen in the future. It's very, very important and interestingly at the meeting, according to a Nature editorial this week, people realize that current avian viruses already have some of the mutations that were created in this new work. In other words, there's already a kind of substantial risk to humans. So, this new data where they've created this transmissible virus could actually be able to have a lot of value for surveillance, we should check mixed viruses that are out there and see whether they're acquiring some of the mutations that this work has picked up that could make this virus transmissible.

Richard Van Noorden: There were still opposers. So the only guy from the National Science Advisory Board for Biosecurity at the meeting was Paul Keim, he was acting chair and he didn't go along with this recommendation that the paper should be published in full. According to Reuters, they quote a scientist close to this board who said that Paul Keim got the hell beat out of him, it was close meeting dominated by flu people, who have a vested interest in continuing in this kind of work. So this was a source telling Reuters, we don't know who this was. But clearly this wasn't quite a result and there were 22 people there but there was only one from the Security Board.

永久凍土に埋まっていた植物を再生し増やすことに成功。種ではなく種と本体をつなく組織を使用。しかし恐竜で同じことをする研究が実を結ぶことはたぶんなさそう。
Geoff Marsh: Okay so the tables may turn yet. Next up, we've got this story, the resurrection of a very, very old plant.

Richard Van Noorden: This was a plant, wild flower that is more than 30,000 years old. It's been buried in permafrost, well below freezing for more than 30,000 years and scientists have now resurrected this plant. Thanks to some squirrels that very helpfully buried lots of samples in the permafrost.

Geoff Marsh: Sounds a lot like Scrat from Ice Age, doesn't it?

Richard Van Noorden: Yeah, it's very good of them actually. If only they were still around, we could thank them. So this is the first time that we've managed to create viable plant from ancient remains in frost. We've actually tried before and we've actually got seeds from things like sedge and alpine plants and we've never quite managed to get them to germinate, but we actually succeeded this time using a slightly different approach. This is a team led by David Gilichinsky, the Russian Academy of Sciences' Institute of Physical Chemical and Biological Problems and sadly Gilichinsky passed away last week, but not before he's seen the success of his work. So, he and his colleagues, what they did was instead of taking the seeds, they take bits of the placental tissue, which is, it's a bit like the white matter inside papery, it kind of gives rise to and holds to the seeds, it's going to be where the seeds ultimately come from and when they cultivated that tissue, in vitro giving it nutrients that then produced shoots and then they took cuttings, propagated more plants and they've also got fertile seeds from this plant.

Geoff Marsh: So, we were limited by our techniques before. The Jurassic Park fan inside me has to ask are we limited to seeds in this field of resurrection.

Richard Van Noorden: Well, we're kind of actually apparently trying to resurrect the woolly mammoth. This is a project that's supposed to happen, I don't think this is ever going to happen, but some Russian scientists are working on it, but it's much, much more complicated than plants.
Geoff Marsh: Okay and next up a story about a technology that seems like it's straight out of star trek.

手のひらサイズのＤＮＡ解析器。ナノサイズの穴に糸を通して数珠つなぎにしたＤＮＡの基を伝導率で順に読み取る。来年には使い捨て用を販売する計画もある。
Richard Van Noorden: This is pretty exciting. I don't have in my hand, but I wish I did. This incredible sequencer. It's a DNA sequencer, it's smaller than somebody's palm, and it's just a one use disposable sequence and its going to be selling for less than 900 dollars and this is all technology from a company called Oxford Nanopore which is a UK based company and for the last 5-6 years, it's been working on a cool new way to sequence DNA by threading the DNA through a nanopore and reading off the bases by looking at the change in electrical conductivity one by one in real time. This week, we saw the first sort of data run from these guys and it looks quite promising. The error rate is still quite high, 4% error rate and they've only managed to do small genomes like those of viruses, but obviously got to give them time to improve and they say they're in the second half of this year, they're going to launch their main machine and then they're going to plan to sell this disposable sequence later on, may be next year.