Tardigrades and the Ten Commandments

20 December 2019
Presented by Chris Smith.

TARDIGRADE.jpg

A tardigrade

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What accounts for the bomb-proof biology of the tardigrade? How do ants avoid traffic jams? Why thou shalt not abuse statistics in 2020, do badgers transmit bovine TB to cows, and is mental illness on the rise among early-career scientists?

In this episode

A tardigrade

00:34 - How tardigrades defend DNA from radiation

What makes this microscopic animals biologically bomb-proof?

How tardigrades defend DNA from radiation
Jim Kadonaga, UCSD

They’re only about half a millimetre long, and they resemble a scrawny maggot with claws, but these animals are biologically bombproof: they can be frozen to -272 Celsius; you can remove 99% of the water they contain; boil them in alcohol; put them under pressure six times greater than the ocean floor; zap them with cosmic rays and expose them to the void of space for 10 days… and they don’t die! These microscopic marvels are “tardigrades”. And, as he explains to Chris Smith, a suitably intrigued Jim Kadonaga set about discovering the basis of at least part of this story: how these creatures protect their DNA from lethal doses of radiation...

Jim - The reason we got into this project as I was reading Chemical and Engineering News and I read a fascinating article on tardigrades. They described a protein that made cells more resistant to x rays. And I looked at that protein and I thought well this looks like a protein that's related to chromatin which is a subject that we work on. I kind of filed that away in the back of my mind. A couple of months later a student Carolyn Chavez expressed an interest in working in my lab and so I suggested her that she try out that project. And so that's how we got started on it.

Chris - When you say that the protein that you saw in the magazine was very similar to the structure of chromatic.

Jim - In what way was similar chromatin as the natural form of DNA in our cells. DNA is a long molecular chain and it gets wound around these protein spores in a form that's called chromatin. And so I've worked on chromatin for 30 years. And when I looked at the actual components of the protein I thought, "this protein looks like it's going to bind to chromatin!" Of course it was just an idea, but that's what we first tested.

Chris - And your idea is that it binds because the DNA - for want of a better analogy - looks a bit like a hand, and the protein looks like a glove, and one would fit "hand in glove" with the other, which is why you think that they would stick together? 

Jim - Something like that. They had complementary properties.

Chris - So what was the project you embarked upon?

Jim - This project actually had four phases. And the first phase was testing whether or not this protein - called Dsup - binds the chromatin. And in fact it did bind to chromatin.

Chris - So you literally mix the two up together in a tube and ask "does one stick to the other?"

Jim - That's pretty much what we did. And we actually did it like a couple of different ways to show that they bind to each other, just to make we're absolutely sure that we were correct about that.

Chris - And when you look in the tardigrades themselves, do you find this Dsup protein glued onto chromatin in the same way that it appears to be gluing onto the chromatin in your experiments?

Jim - Our experiments were done all biochemically. So these are all done in the test tube. So we actually never looked in the tardigrades themselves, but that's something of a presumption at this point. But the fact that it binds in the test tube very well, we're pretty confident that that's how it binds in the organism. The next phase was that this Dsup protein was found in one tardigrade, but people had looked at a second tardigrade and said it's not there. So that kind of made Dsup seem uninteresting and unimportant if it's present in one tardigrade, but not another. But what we did find was that actually that second tardigrade also did have a Dsup protein.

Chris - Oh, so it had been missed!

Jim - It was missed.  The second tardigrade had a protein that kind of looked like Dsup, but people didn't think that was really Dsup. We confirmed that that second Dsup protein really is Dsup by doing the same experiments that we did with the first one and got the same results.

Chris - So you've basically got the smoking gun at the scene of the crime. Now you can prove this protein walks the walk and it talks the talk. You've got a protein that looks right; it binds the way you think it does; it's found in other tardidegrades which share this behaviour of being very resistant organisms. So that's looking pretty promising. What did you do next?

Jim - Now phase 3 was we asked the question how does this protein make cells resistant to X-rays? Tardigrades themselves of course live on Earth. And so they don't normally get exposed to high levels of X-rays, but they are still resistant to high levels of X-rays. And so then we realised that X-rays, when they strike water molecules, they generate highly reactive molecules called hydroxide radicals, and these hydroxide radicals degrade the DNA. So what we ended up doing was testing whether or not this Dsup protein protects DNA from hydroxide radicals. And, in fact, yes it does. Somewhat remarkably Dsup protects DNA from hydroxide radicals. So we kind of solved the mystery of how Dsup protects tardigrades from X-ray radiation.

Chris - And of course X-ray radiation is not the only reason why you would end up with hydroxide radicals inside cells; other things, like hydrogen peroxide, would lead to that as well wouldn't it? So this is a general defense mechanism against oxidative stress then isn't it?

Jim - Exactly. That's correct. And the Dsup protein serves to protect tardigrades from hydroxide radicals that are formed, especially when they're in this kind of dried dormant state.

Chris - And do you know how the Dsup protein does that protection?

Jim - It goes back to the Phase 1 of our project, that it protects it by binding to the chromatin. After it binds a chromatin, the rest of the protein appears to be unstructured. And so kind of like a cloud, that protects the chromatin from the hydroxide radical molecules.

Chris - So the hydroxyls would jump on to the Dsup protein and do things to these fairly amorphous chunks of the protein rather than unleashing their energy on the DNA?

Jim - That's it!

Chris - And you're saying that the tardigrades do this because they have to exist in particularly fierce environments. Do they therefore turn this stuff on, and apply it to their DNA only when they need it? Because, obviously, if they've got something like a giant protein stuck on to their DNA, it's going to get in the way of other important proteins that need to interact with the DNA - things like these chemicals called transcription factors, that turn genes on and off, and also the enzymes that read the DNA signature - this would be in the way wouldn't it?

Jim - It is kind of an interesting question, and that's in fact one of the things that we're investigating now - how can tardigrades protect DNA yet allow everything else on their DNA to still happen correctly? We don't know the answer, but that's probably going to be very interesting.

Chris - Now, when this paper came out in eLife, you got quite a bit of attention didn't you?

Jim - Yes we sure did!

Chris - Did you go to "overnight celebrity status"?!

Jim - Well I know about that, but it did impress my relatives!

Ants

07:14 - How ants avoid traffic jams

Why does insect congestion not lead to a hold-up, like it does for humans?

How ants avoid traffic jams
Laure-Anne Poissonnier, University of Toulouse

The incredible thing about ants is that, despite running along congested roads and paths like we do, they never seem to get stuck in traffic jams. And, as she explains to Chris Smith, Laure-Anne Poissonnier, who’s at the University of Toulouse, wanted to know why…

Laure-Anne - I've observed social insects - bees and ants - since I was little. I always find it fascinating how they can be so organised because they don't have any signs, traffic lights or any police officers telling them what to do. When you see ants in the wild, you never observe a traffic jam. Yeah. We're wondering if that was really the case, and we wanted to test that.

Chris - And how much - before you did this very comprehensive study - how much did we know about ant traffic?

Laure-Anne - Actually, there was really little data. It's very time consuming to do these kinds of experiments and counting ants on a trail takes a lot of time.

Chris - Because it's fair to say that, apart from us humans, there are not many other species - maybe termites - that travel in both directions on roads?

Laure-Anne - Yeah, exactly. We share with ants and termites the fact that we live in one place and we get our food in another place and then we bring it back home.

Chris - But unlike us, where, given my experience of my commute, I don't know what yours is like in Toulouse, but mine's turning into a nightmare on a daily basis, ants don't seem to have this problem. You, you add more and more ants to the equation and they just seem to find a way and carry on moving.

Laure-Anne - Hmm. There are definitely way better than we are. They do get slowed down a little bit when there is a lot of ants, but that's a very limited effect compared to what we can observe with pedestrian traffic or, or cars. And one of the reason is because they have a hard body so they can bump into each other and it doesn't hurt them, contrary it to a car or us for example, we don't want to bump into each other. So we slow down and we avoid each other. So we lose time, and ants don't have to do that. And some other reason is that they can regain their maximum speed very quickly while for a car for example, you have to accelerate again and it takes some time to go back to the maximum speed and ants do that in one or two steps. They compensate for the time they have lost. When ants see another ant's coming from the opposite direction. They will stop and interact with this ant because they can, get information they can check if it's not an invader or another ant coming to attack them. So they do a, they touch antennae and they smell for example, if it does find some nice food there. And when there is a lot of ants, they shorten those interactions. So they do it way quicker and also accelerate between each interaction to regain the time they've lost. And the last thing when they see that there is a lot of ants already on the trail, they stop going there, which is what we should probably do. When we see that there's already a lot of cars, if we go, which is going to create a traffic jam which should just Wait rather than go there.

Chris - How did you observe this?

Laure-Anne - We used different colony sizes with really small density all the way across to very high densities. So just leaving the ants in their little nests in the lab, we linked the nests to a platform where we're giving them food, so we use the sugar water because those ants - we used Argentine ants and they really like sugar - they had to cross a bridge to go there and what we did is that we used colonies from 400 ants to the maximum group we had was 25,600 ants. And also we varied the width of the bridge to make them more crowded

Chris - And what you were counting them on and off the bridge so you knew roughly what the traffic flow was?

Laure-Anne - Exactly. I counted the ants crossing the bridge.

Chris - Did you have electronic help? Because that sounds like a nightmare when there's 25,000 ants. How on earth did you keep track of them?

Laure-Anne - That was a tedious work. The number of ants that are crossing the bridge I counted that by hand. So I had basically a help available software. So I was clicking every time an ant was crossing and it was recording the time and the direction of the ant. And then we we use image analysis to know how many ants were on the beach. So that was done by the computer.

Chris - Can you express any of these relationships mathematically? So are there now ways in which you can say you can model this effectively and show why it's good for ants and why it's not good for humans and therefore what we might be able to do to improve how humans get around?

Laure-Anne - There's a lot of difference between ants and humans, but we can compare things. For example, what is usually used to study the flow is to link the density. So the number of individuals or ants on a surface with the speed. So usually at the beginnings a flow increases with density because at the beginning there is not many individuals. So the flow is low, but they all, they can all go fast. And then after a while, when there is a lot of individuals, they all slow each other down. And so the flow decreases at very high density. So it gives a sort of a bell curve.

Chris - Given that it is Christmas time, am I allowed to try a cracker joke on you?

Laure-Anne - Please go ahead!

Chris - How do you tell the difference between a male and a female ant?

Laure-Anne - Oh they're all females. I just ruined the joke!

Chris - Well, not necessarily. The answer is you drop it in water. If it's male, it floats: "boy ant".

Laure-Anne - Ha ha! And do you know why ants never get sick?

Chris - It's gotta be something like "antibiotics" or "antibodies" or something. Is it?

Laure-Anne - Yeah - they have a lot of antibodies!

A badger

12:57 - Bovine TB: spread from badgers to cows?

Whole genome sequencing reveals how M. bovis moves

Bovine TB: spread from badgers to cows?
Rowland Kao, University of Edinburgh

Bovine TB; this disease of cattle is caused by Mycobacterium bovis, a close relative of human TB. And because of the threat to human health, the livestock industry operates under a regimen of regular testing and strict controls. But bovine TB is also found in badgers. So do the cows give it to the badgers; or do the badgers give it to the cows? Or are both true? To get to the bottom of this, and speaking with Chris Smith, Edinburgh’s Rowland Kao has been conducting a very comprehensive genome screening programme to track how the disease spreads…

Rowland - What we know is that there's a lot of controversy regarding the control of the disease, whether you should control it in cattle, in badgers, or in both. And the fundamental question of that is essentially how often does one of those species infect the other, and vice versa. And what we were aiming to do is to try to get at that precise question,

Chris - Because, of course, what we don't know is whether it's one way traffic or two way traffic. Do the Badgers give it to the cows, or the cows give it to the badgers, or does it go round in one giant whirlpool?

Rowland - Absolutely I mean we have lots of indirect evidence to show that each species is important in the transmission process. But what we've not been able to do until now is to get any idea of just how much is going on in both directions.

Chris - So how did you solve it?

Rowland - A few years ago working with some colleagues in Northern Ireland, we did a relatively small study looking at the bacteria which causes bovine tuberculosis. So this bacterium, called Mycobacterium bovis, is very closely related to human TB, but is more specifically oriented around cattle. Now, what we did, was we took what's called the whole genome sequence of these bacteria - so essentially you take the entire genetic code - and, by tracing changes in the genetic code - essentially how is the bacteria evolving from individual to individual - you can get quite a good idea of who is infecting whom.

Chris - How does this solve the problem though? Because, obviously, if I can match a sequence in a badger with some cows, how do I know that the badger gave it to the cows, or the cows gave it to the badger? I just know that they're infected with a genetically extremely similar strain.

Rowland - Absolutely, and people are probably familiar with DNA fingerprinting, which tells you whether or not two individuals are closely-related to each other, or where a genetic sample might come from a person. Now that technology is now relatively established, but only gives you a very vague idea. Whole genome sequencing does the same thing only it's much more precise. And what we can use is mathematical and statistical models to analyse relationships to track the bacteria as it evolves from individual to individual, herd to herd, badger group to badger group and determine the rate at which it's most likely that each one transmits to the other.

Chris - And where did you get the raw data from and how were those data collected?

Rowland - So we were really fortunate that we had contacts with a group of scientists who work in a place called Winchester Park, in Gloucestershire, and they've been studying badgers there since the 1970s; they regularly trap badgers, sample them for bacteria, and then release them again. We also have similar information from the cattle every single time they test them. So we have a nice comprehensive dataset looking at how the bacteria evolves in both populations,

Chris - And what does it show? 

Rowland - We have on the order of about 100 samples from both populations. And what they show is the vast majority are very very similar to each other. And it appears to be that there's more diversity existing in the Badger population.

Chris - And would that suggest then that the badges are the main host and that they're injecting certain strains into the cows. Or, is there evidence for a feedback loop so the cows have it for a while, they give some back to the badgers, the Badgers then recirculate, amplify, maybe ditch some strains, amplify others. What does the dynamic now look like?

Rowland - There's a field of study called phylodynamics, where what people aim to do is try to integrate different sources of information - not just the genetic data, but the information you have about the populations - to try to understand exactly those kinds of questions. And for this particular population what those analyses show us is that, on the whole, transmission of the disease within each species appears to be greater than the transmission between species. But we do get some transmission in both, and the badgers are giving it more to the cattle.

Chris - Because at the moment people are saying this apparent relationship is grounds for various culling manoeuvers and things like that. If you then consider culling in your model, would that make a difference?

Rowland - I'm sure it would. I mean one thing about the Winchester Park area in particular in this timeframe is there was no official culling going on. So it's a relatively undisturbed badger population. Now, if you were to cull them, what you might expect to see, the spatial relationships - so essentially if I took two samples one from a badger on one from a cow - I'm asking the question how closely related are they. Does their distance from each other geographically tell us something about that we'd expect those relationships to change because they change they would also change the outcome of the what we think the transmission rates are. So I think if I were to ask what the important message to get from this is, in this area it shows that badgers are important. What it allows us to do, if we can so studies in other areas, is to refine the way we consider the control of both populations. Because, obviously, the disease in cattle for farmers is extremely important. It's hugely debilitating to the farm To have this going on. At the same time. badger welfare and badger conservation is important. So if we can tailor the way we do the control, identify areas where badgers are important and where they are not, that helps us to do the most scientifically sensible approach to controlling the disease.

Statistics and graphs

Ten statistical commandments
Tamar Makin, UCL

How do you make a statistician shudder? The answer is to read a few neuroscience papers, where the abuse of statistics appears to be rampant in some quarters and was enough to motivate eLife editor and UCL neuroscientist Tamar Makin to draw up 10 “thou shalt not” commandments; as she explains to Chris Smith, her manuscript turned into one of the most popular eLife papers yet…

Tamar - I was in the Annual Society for Neuroscience meeting, and I was interested in a poster showing how they can use this really cool new technique called optogenetics to change the way the brain is organised. What they do is they measure the neuronal responses in a given brain area. Then they manipulate the brain area with this technique and then they record the neurons again. To quantify the differences, they first identify the neurons that are most responsive in a certain way and they go back to the same neurones after this manipulation. And, lo and behold, they find that the neurons that were originally found to be very selective are now responding much less; whereas the neurons that didn't really respond are now relatively more responsive. So they thought they have a really fascinating example of changing how the brain responds and how it is organised. But, in fact, what they found is that if you pre-select your neurons or your samples based on a specific characteristic, this characteristic is going to be expressed less if you repeat the measurement. So basically with optogenetic, they found a very simple statistical artifact.

Chris - Basically they had to use optogenetics to discover regression to the mean!

Tamar - Exactly!

Chris - Now, tell us a bit about you Tamar, and how you come to be doing this.

Tamar - I'm a neuroscientist. I'm also an editor in eLife and I go through a lot of manuscripts both for my own education. And as part of my role, I go through many papers with my lab as part of my students' interest and training in our weekly journal club. You know, we see these problems that are just recurrent and repeated and it can get very frustrating, especially when there's a potential clinical impact to how the discovery is being interpreted. And we were, you know, going over a particularly bad paper in a particularly good journal one day at journal club. And I got so exasperated, I said, okay, let's make a list of 10 most simple rules that everyone needs to follow when they're writing a manuscript. And we came up with this, we call it the 10 commandments, thou shall not. And I was surprised to see how useful it was for my students so that whenever we would go over a paper in journal club, we would go over this list of 10 they shall not, and see if they've been violated. And seeing how well this was taken by my group, I thought, you know, maybe other people would also find it useful. What motivated me most is the idea that we can be constructive about it so we don't just have to tell people what not to do. We could also tell them what to.

Chris - Is there also a sort of deeper rooted issue here which is that it's a bit of a blind leading blind situation because what we've got are reviewers on some of these papers who are equally likely to make the same mistakes that the people writing the papers are making because no one's saying anyone setting out to deceive here, rather they're just making statistical mistakes because they haven't been taught how to do statistics because at the end of the day, stats is a very specialised thing that you need a statistician to help with?

Tamar - Absolutely. I think at the end of the day, this is certainly the responsibility of the authors, but the utmost final responsibility is for the community. Do we accept evidence that has been misinterpreted? Do we accept evidence that hasn't been carefully interrogated statistically.

Chris - if we know why we're in this position, we know how to fix it, don't we? So this is two questions really rolled into one, why is it happening and therefore what do we have to do so that the next generation of neuroscientists who send you papers don't make you go 'tch'?

Tamar - I think, for the average student, statistics is kind of dull. Even if they do take comprehensive statistical lessons, this information is bound to evaporate. So I think the question for us is how do we maintain this standard of statistical interpretation is a lively discussion. And when we were writing this manuscript, we wanted to launch a discussion and a conversation. And I think here social media potentially offers an existing tool to try and maintain these conversations.

Chris - So it really comes down to still stats has an image problem, doesn't it? I mean this happened to me when, when I was at medical school, I remember someone declared, not epidemiology, but "epidemi-holiday" lectures and they just took the week off! Surely that's the issue, isn't it? If we can make the subject have a better image, then more people will get into it. Teach it better and then this problem will go away.

Tamar - Yes, absolutely. But we should also insist on a higher standard of how science is carried and how science is interpreted, because at the end of the day, what's the point of pouring so much money and training and effort? If we are able to correctly infer or interpret what the results are actually saying. I think every student, every PI, every community really needs to insist that this basic training and understanding of what the results are, it needs to be maintained at a higher level.

Mental health

24:27 - Mental health in science

Are scientists suffering more mental illness?

Mental health in science
Liesl Krause, Purdue University

eLife recently launched a new collection focusing on the question of mental illness. It’s curated by Elsa Loissel and it asks how can the scientific community support researchers with mental health issues. The problem appears to be worsening, but why? Speaking with Chris Smith, Liesl Krause is a graduate student at Purdue University; she’s been very active in this space; she volunteers with the initiative PhD Balance, and pursues research on relationships between supervisors and PhD students…

Liesl - I had some mental health struggles when I entered my Masters programme, and I saw that there were a lot of other graduate students out there who were struggling, and I thought, 'if there are other people out there struggling with this, and we don't really talk about it, there has to be some sort of research that we can use to show other academics this is important and something that we should be looking and talking more about.'

Chris - Do you think this is a phenomenon that's becoming more common; or do you think it's something that people are just feeling a bit more comfortable talking about: it's always been there but we're just talking about it more...?

Liesl - I think it's a bit of both. There's been a lot of great work to kind of do the hashtag and the stigma movement, which is where people post on social media about their own mental health struggles so that you understand that everyone has a mental health struggle: it's not just behind closed doors anymore, and you can still succeed with that. And then there is a lot more resources out there that allow people who might otherwise not have been able to enter graduate school due to their mental illnesses to now enter into those spaces. So I think it's a combination of the two.

Chris - And when you talk to people, what sorts of mental health issues are they having?

Liesl - Primarily in graduate schools, we see a lot of depression; we see a lot of anxiety. Those are the two most common

Chris - Are they more common in that particular group than if you say took age-matched individuals who are not at graduate school?

Liesl - There have been studies that have shown that graduate students actually experience mental illness at about twice the rate that the otherwise general public do. And that general populace that they're being compared to are people who have graduate degrees and college degrees. So it's something very specific about being in graduate school that kind of leads to these sorts of mental illnesses.

Chris - And what do you think is triggering that?

Liesl - I don't think that anyone truly knows the answer yet, but I do think that part of it is due to some of the academic culture. A lot of advisers and faculty say 'well, this is what I had to do when I was a graduate student. I made it through. So you should be able to do that too.' And they're not empathetic to the fact that some of their graduate students might be in different stages of life than them; they might have different physical and mental capabilities that have them working different hours; and they have other stressors in their life. Graduate school has become a little bit more stressful recently. There's a lot more issues surrounding stipends and how those stipends are actually able to be a livable wage. When you break it down to an hourly wage, we actually get paid less than minimum wage. The stipend hasn't really increased in several years. So you might be getting the same stipend that you were getting, you know, when your adviser was in graduate school.

Chris - And in your own studies, what are you actually doing, and what's actually emerging What are you finding?

Liesl - I use something called skin conductivity to look at emotions. So skin conductivity is, when you sweat on your hands, it raises the skin conductivity. And that's actually happening even as we're speaking right now, or if you're driving in your car, you're having minute changes. So what I do is I have two participants hooked up, and then I look at how often those skin conductivity peaks happen in correlation with each other. What we're anticipating - and what we're starting to see - is that, when you have emotional or empathetic spikes happening at the same time, there's a better mental wellness there in that partnership and the partners are closer. And so I think that empathy between advisers and advisees is something that's really important, because the better your relationship is the better you guys can kind of get along.

Chris - How do you know it's just empathy though? Because, for instance, if a supervisor and supervisee have a row, arguably the skin conductivity is going to go up because they're going to sweat. That wouldn't be necessarily a beneficial interaction. It could be quite an aggressive one.

Liesl - Oh it definitely could be. And that's something that I plan on looking at later on down the line. But it's when if, in that situation, the student was having some sort of major emotional response but the adviser was having no emotional response, it's not a great sign. That kind of tells you that something's wrong with that adviser.

Chris - Ah, so it's the reactivity and the responsiveness on the part of the adviser. It's the fact they're reactive to each other showing that there's a strong relationship. But if they sat there and stonewalled the student, that's arguably going to make the person feel worse not better?

Liesl - Exactly. And something that we do over at PhD Balance is we ask people to share their stories. And part of what we've been learning from people sharing their stories is that they feel isolated in their graduate programmes. Because it is a really isolating thing to be put in a situation where, you know, you're really stressed out and your adviser doesn't seem to care about it.

Chris - And what this is going to translate into is, you think, more 'teaching the teachers to teach' type courses more focused on these are the danger signs: This is what to look out for. This is how to be a good supervisor?

Liesl - Yeah. That's definitely where this is going. Is some sort of how to mentor how to teach. At Purdue, we're actually starting this programme where, in our faculty, members will be coming in and for the first year they won't be asked to teach any classes. Instead they'll be taught how to teach classes and we also are starting programmes where it's called 'First Aid for mental health'. So faculty will be able to have some quick tips in how to assess students right in their office rather than having to send them to our psychological services, which are overburdened.

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