Nature Podcast 25 May 2006

Introduction

This is a transcript of the 25 May edition of the weekly Nature Podcast. Audio files for the current show and archive episodes can be accessed from the Nature Podcast index page (http://www.nature.com/nature/podcast), which also contains details on how to subscribe to the Nature Podcast for FREE, and has troubleshooting top-tips. Send us your feedback to mailto:podcast@nature.com

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Derek Thorne: Hello there and welcome to this week's podcast from 25th May edition of Nature. I'm Derek Thorne, standing in for Chris Smith. Coming up in the podcast this week: male sperm cells have something new in store for the egg they fertilise. We'll hear about a close-up picture of HIV and how lobsters that carry a lethal virus are left to a lonely death. But firstly, this week, we're journeying to one of the most dangerous and inhospitable places on Earth, the site of an underwater volcano on the floor of the Pacific Ocean. A group of researchers has been investigating this volcano because it's especially active and, since no one in their right mind would go down there in person, they've been using a remotely operated vehicle to make measurements instead. Talking to Chris Smith, from onboard a ship in the Pacific, was Bob Embley of the Pacific Marine Environmental Laboratory in Newport, Oregon. Nature 441, 494–497 (25 May 2006)

Bob Embley: What we've been able to observe over the last two and a half years is the cycle of an active volcano under about 500 metres in depth and this time we actually observed activity that had never been seen before in the ocean actually, in a submarine volcano; we actually observed erupting lava and red glowing rock. And this volcano has now been active for about two years. This is our third visit to it and every time we come to it, it surprises us by continuing to be active.

Derek Thorne: How did you make your measurements and how were you making these recordings?

Bob Embley: We had a two year programme. We first surveyed the area doing mapping and water column surveys and then we came back the next year with a remotely operated vehicle. This is a vehicle that's hung under the ship on a cable and then has its own thrusters and cameras and you control it as a robot but it's tethered to the ship. So this is the kind of vehicle you have to use in these extreme environments because you don't want to put a person down there in a manned submersible. And so these things can do pretty much everything: they can image them and they can sample them to various types of water samplers. It's like you have a virtual presence on the sea floor.

Derek Thorne: What sort of environment would this craft have been experiencing down on the sea floor?

Bob Embley: We crossed quite a few small rocks. There were rocks being thrown out of the vehicle. There was sulphurous acidic water that came out of it. There was quite a challenging environment but the pilots of the JASON did very well and they were able to observe it and sample it, but keep their distance. And sometimes they had to back off because it became a little bit too violent. It's challenging; we're just starting to learn how to work in these environments on Earth.

Derek Thorne: What about animal life? Was there any evidence of animal life tolerating this harsh environment?

Bob Embley: Well, yes. Actually the only animals that were living there were two species of shrimp and some crabs and very little else because they have to be very quick on their feet, so to speak, to get out of the way. And we think their habitat has shrunken and expanded as the volcano becomes less or more active. But there's lots of material going down this slope. We have no idea what the effect on that is of deeper animals and so forth while one of these is active.

Derek Thorne: So what did you learn from this?

Bob Embley: Well, we're just trying to put the pieces together, but somehow there is a cycle going on here... where we saw... five months ago we were there and there was a cinder cone [?] there. When we came this time the cinder cone was gone and all that was there was a little bit of steam and hot water coming out of the bottom. But then, as we sat there, we saw that it started to have this huge gas expulsion: a lot of gas bubbles came out. And then we started to see evidence of fragmental lava coming out and, as we went back there over the next five days, it got more and more intense and finally settled into a very cyclic pulsing behaviour which we don't yet understand. We've never seen this kind of activity before.

Derek Thorne: That's Bob Embley of the Pacific Marine Environmental Laboratory recounting his daring tales investigating a volcano deep under water.Now, some news on HIV, the virus which causes AIDS. If we are to develop a vaccine for this infection then we need to know in detail what the virus looks like on the outside. Well, we now have a much better idea, thanks to Ken Roux of Florida State University and his team. They've been looking at the so-called envelope spikes which are the protein molecules that protrude outwards from the HIV virus. Nature advance online publication 24 May 2006

Ken Roux: HIV, of course, is the virus that causes AIDS and there's been a tremendous interest in trying to figure out, not only how the virus infects, but also how the immune system protects against viral infection. And, as far as antibodies are concerned, which are one of the main ways the body protects against the virus, the only targets on the virus are the envelope proteins. And what we've done is to first get a reasonably good look at what these envelope proteins look like. We call the envelope spikes. And what this should do is allow immunologists to perhaps develop better vaccines for generating the good immune response that would protect individuals from infection.

Derek Thorne: Just to put it in perspective for a minute, how big are these spikes that you've managed to image?

Ken Roux: The spikes are about 14 nanometres tall and about 10 nanometres in diameter.

Derek Thorne: So they're pretty small. How do you go about physically measuring something like that?

Ken Roux: Well, basically, what we do is use the electron microscope. We freeze the virus and what's called vitreous ice and essentially the ice is frozen so quickly that there are no crystals. So it's like glass. And then we're able to put this into the electron microscope and actually look at the entire virus in its native state without any fixation artefacts or staining artefacts. And, at that point, we're able to actually measure the size of the virus itself and then measure the size of the spikes on the surface.

Derek Thorne: And then, when you come up with a model, how did it change your understanding of the structure of these spikes?

Ken Roux: The typical textbook picture of a spike is that the two portions, GP120, which is the outer portion, and GP41, which is the stalk portion, were similar to the way a child might draw a tree. Essentially the GP120 was the head of the tree and the GP41 was the stalk. What we see is something rather different. The virus spike is much more chunky; there is no stalk in the sense of a thin rod running up. Rather the GP41 is splayed out tripod-like and they have an entirely different way of engaging the membrane as compared to, say, what one would find in influenza.

Derek Thorne: Do you think the fact that you found this difference in the structure of what we anticipated and what you now know is there is actually going to help with people developing novel agents that can target this as a way to block HIV infection?

Ken Roux: Well, we think so. Actually some of our preliminary data which we had presented at meetings a while back captured the attention of several laboratories that are involved in designing virus vaccines and they've incorporated this into some of the new designs. So we're hoping, within a relatively short period of time, there'll be perhaps a new set of synthetic envelope spikes that could be used as vaccine candidates based on this new model.

Derek Thorne: That's Ken Roux of Florida State University on the how the envelope spikes could ultimately be the downfall of HIV. Nature's Podcast, bringing the world of nature to life.

Derek Thorne: Still to come in this Nature Podcast, why spiny lobsters are uncaring crustaceans and how the sperm cells of mice are carrying some unusual instructions. But, firstly, it's time for a round up of some of this week's other major science news. Here's Anna Lacey speaking with Nature's David Cyranoski.

David Cyranoski: Thanks, we have three stories for you this week. The first is about scientific misconduct in China. Scientific misconduct has been a problem in the news lately with a variety of cases, the most widely publicised being that of the cloning expert, Woo-Suk Hwang. And the high publicity of these cases has led to a willingness to believe any accusation of scientific fraud and this is especially a problem in places like China where there aren't good mechanisms in place to judge these allegations of scientific fraud. Nature 441, 392–393 (25 May 2006)

Anna Lacey: But do they not have good reason to be accusing people in the first place?

David Cyranoski: It's very hard to judge actually what the reasons are. Sometimes they do have good reasons, sometimes they don't. But part of the problem is that now you can put up anything you want on the Internet and it stands as an accusation and people start to react to it, the media starts to react to it and it can put people's careers in jeopardy. They believe it's a lot of post-docs or younger researchers but a lot of them are not identified by name; they're identified by some kind of Internet name.

Anna Lacey: But if people are making these accusations on the Internet, why aren't they going through proper channels if they even exist?

David Cyranoski: There are some channels to go through in China but apparently people find them difficult to access, or not very responsive. In one of the cases this week that we've talked about a researcher has said that he couldn't find the contact information to go through the proper investigative committee. So he went to an Internet site instead. But I think there's also a problem in that people don't find that these committees are responsive and that they investigate in a transparent manner.

Anna Lacey: Well, with this in mind, what are people doing to try and protect scientists from this?

David Cyranoski: Well, just last week, over 100 scientists in the US sent a letter to many scientific policy officials in China asking them to take some kind of measures to, not only investigate scientific misconduct allegations, but also to make sure that these allegations are investigated in a way that protects scientists who might have done nothing wrong and were just accused of doing something wrong.

Anna Lacey: Well, now let's move away from scientists working against each other to an example of fusion bringing people together.

David Cyranoski: Yes, there's a Fusion Project going on, several countries working together in the International Thermonuclear Experimental Reaction, the ITER project that's been ongoing. Last year they decided on a site and they're still trying to decide on a design for the reactor. And it's a reactor that's based on a fusion reaction of two light elements and they collide to form a new element in a process which releases a huge amount of energy. The problem is that they have to try to contain this reaction and what they've come up with is magnetic fields that can suspend the plasma in a doughnut-shaped device. Nature 441, 394 (25 May 2006)

Anna Lacey: Okay, so then what's the problem? You've got the fusion happening inside of a magnetic field like a little case. Then what goes wrong?

David Cyranoski: The problem is that the energy is so great that it has discharges at certain points that can damage the device. And this is a $5.5-billion project so many of these parts are very expensive. So what they're trying to do is find a way to dismiss some of this energy and this week Nature Physics has reported a method of siphoning off some of this plasma discharge by introducing static charges into the fields and introducing a kind of chaos into the fields that can dispel some of this energy. But they're expecting some difficulties because seven countries must agree on this design.

Anna Lacey: And, finally this week, the saying good things come to those who wait is particularly apt for a Japanese palaeontologist.

David Cyranoski: Yes, this is a story of patience and determination. Tadashi Suzuki in 1968, when he was a high school student, found a fossil and he was quite sure that it was a plesiosaur but it took 38 years for him to finally get that published and recognised as such. Nature 441, 390 (25 May 2006)

Anna Lacey: So what's taken them so long?

David Cyranoski: There's been a problem with funding and it took seven years for them to unearth and assemble it into the structure. It's a 3-metre long structure. And it was not until 2003 that Tamaki Sato and other researchers came onboard. He had experience in this field and this month it was published in the Journal of Palaeontology.

Anna Lacey: And what was the verdict?

David Cyranoski: The verdict is that it's an 85-million-year-old fossil specimen of a species that is now called Futabasaurus suzukii after its founder. And it's a long-necked turtle-like creature that lived in the seas.

Anna Lacey: And are other palaeontologists likely to have to wait as long if they find a new fossil?

David Cyranoski: Apparently it can be done in about five years but that's assuming that there's a good amount of funding and most palaeontologist probably don't think they have that kind of funding.

Derek Thorne: That was David Cyranoski with some of the major science news stories of the week.You're listening to Nature's Podcast from 25th May edition of the Journal. I'm Derek Thorne. If you'd like to find out more about our featured stories this week you can go to our website at http://www.nature.com/nature and, if you have any comments on this or any of our podcasts, then please send an email to mailto:podcast@nature.com.Inheritance of a trait from one organism to its offspring normally happens via its genes. The trait is coded in the organism's genetic material, or DNA, and this is passed on. But this isn't always how it works. Sometimes inheritance can be epigenetic, meaning it's caused by something other than the genes. As reported in this week's Nature, a group from France has uncovered an interesting epigenetic system in the mouse. They've found that in the tip of the mouse sperm cell there are some microRNA molecules and, when the sperm fertilises an egg cell, these microRNAs cause changes in the resulting embryo. And, what's more, these changes are inherited through further generations. It's clear that these RNA molecules aren't actually changing the genetic material. Instead, it seems they might be affecting how it is used by dictating which bits of DNA are made available and which bits are hidden away. From the University of Nice, here's François Cuzin. Nature 441, 469–474 (25 May 2006)

François Cuzin: What we've discovered is the occurrence in the mouse of an epigenetic modification of expression of a gene without a change in the DNA structure. So it's not a mutation but it's still inherited and the way it is transmited to the next generation involves the transfer of RNA molecules and specifically of microRNAs which are carried to the embryo by the spermatozoan head. And if injected in the normal embryo they induce the same modification.

Derek Thorne: How do these microRNAs actually do that though? What are they doing to the RNA of the gene they're targeting?

François Cuzin: We assume that the RNA in fact induces in a way that we don't know yet, but induces change in the chromatin structure which results in a change of expression.

Derek Thorne: And that change is then inherited into the subsequent daughter cells that those ancestors make?

François Cuzin: Yes, it is transmitted from cell to cell and from one generation to the next. But the next generation, we found again RNA present in the spermatozoon head and the change is transmitted over several generations.

Derek Thorne: And it's inherited into all of the daughter cells produced by that particular zygote?

François Cuzin: It's present in all the daughter cells.

Derek Thorne: What do you think the implications of this are now?

François Cuzin: The fact that sperm mutation occurs in animals is the first observation to do this [unclear] and the transfer of genetic information by RNA molecule associated with sperm cell, we think is likely to be applied because it has been reported over the last few years that there were RNA molecules in human sperm. And several reports have confirmed that finding but no-one has been able to define the function of these RNAs in the human sperm. And the system that we have now in experiment on system in the mouse provides the first hint at what the function of these RNAs could be.

Derek Thorne: François Cuzin of the University of Nice explaining a novel system of inheritance in the mouse.And, finally this week, if you're a Caribbean Spiny Lobster and you're ill, don't expect any sympathy. But, don't worry, it's all for the greater good of the population. A team working in the Florida Keys has been looking at a particular virus that infects the Spiny Lobster and has found that fellow lobsters, or conspecifics, that are not infected, try to avoid those that are. Here's Donald Behringer from Old Dominion University in Norfolk, Virginia. Nature 441, 421 (25 May 2006)

Donald Behringer: In the first study we discovered a virus that infects lobsters, specifically Spiny Lobsters down in the Florida Keys, and it turns out to be the first virus discovered to infect any lobster in the world. And what we discovered beyond that is that it has some really interesting impacts in that the healthy lobsters are actually able to detect and avoid infected conspecifics before those infected conspecifics actually become infectious to other lobsters.

Derek Thorne: Do you know what the giveaway signs are of an infected lobster then?

Donald Behringer: It's not a rapidly progressing virus. In the beginning they really show no outward signs. It takes them anywhere between about 30 to 80 days to show outward signs and that's largely dependent on their size. It progresses much more rapidly in the smaller individuals. But once they do begin to show signs, the signs are that their blood turns a milky white colour; normally it's clear with a grey or an amber tint. And then, along with that, they start to become lethargic; they cease grooming, their movement rates slow down and eventually they don't move at all and then they pass away.

Derek Thorne: So it turns into a scruffy lobster, first of all, but what is it that their conspecifics are able to spot about them that you think gives away the fact that they've got something wrong with them?

Donald Behringer: Lobsters are very chemically sensitive so we theorise that it's some type of a chemical clue that they're either receiving or not receiving from the infected individuals. But it might be a culmination of visual and chemical clues and that's one of the things that we hope to investigate here in the next year or so.

Derek Thorne: So do you know roughly how many lobsters, if you just randomly sample the population, are actually carrying the agent?

Donald Behringer: From our field sampling – and we do this yearly. There are certain suite of sites that we establish as permanent sites that we go back to, to get an idea on whether it's changing in these areas. We also do a larger sampling throughout the Florida Keys each year and the prevalence seems to stay in the range of about 5% to 8%. But those results are from actually looking at them visually and looking for the latter stages of infections. And then, when we actually have gone out and sub-sampled populations in various areas and analysed them using microscopic techniques, histology, it's slightly above that. But we were surprised. We thought when we did the histology that we'd find it much harder than that. But the histology might not be sensitive enough to pick up those really early stage infections.

Derek Thorne: Is it a threat to these lobsters or is it not actually making a major dent in the population?

Donald Behringer: That's troubling too. We often get the question of is this going to be the death knell for the lobster population. But one of the things we're not clear on is how long it's been in the population. What we do know is that the time that we've been aware of it conclusively and actually had an idea that it was a virus, the prevalence again hasn't changed dramatically. So that's one of the things we want to try and figure out. Hopefully if we can figure out regarding whether it's a chemical detection and if that chemical detection is something very specific to the virus, that might give us an indication of knowing whether these two things actually evolved together or not, the behaviour and this virus.

Derek Thorne: Donald Behringer on how Spiny Lobsters are shunning those who are in poor health.Well, that's it for this week. Many thanks for listening but do join us next time when we'll be falling into a deep dreamy sleep and also taking a dip in the Arctic Ocean. And in the meantime, don't forget to check out the Naked Scientist podcast this week when we'll be hearing about the science of sound, making music in a teacup and creating the voice of a castrati, a man with a voice of a choirboy. That's the Naked Scientist podcast which is freely available from http://www.thenakedscientist.com.The Nature Podcast is produced in the Division of Virology at Cambridge University by Anna Lacey, myself, Derek Thorne, and Chris Smith. Advertisement The Nature Podcast is sponsored by Bio-Rad, at the centre of scientific discovery for over 50 years and on the web at http://www.discover.biorad.com.