eLife Episode 45: Ant Undertakers and the Human Cell Atlas
In this episode, we hear about disease control in insects, placental development, post-traumatic stress disorder, the mission to create a human cell atlas and how crickets amplify their song...
In this episode
00:37 - Ant Infection Control
Ant Infection Control
with Chris Pull, Royal Holloway
This winter, we’ve seen very high levels of respiratory infections that have caused severe outbreaks when they’ve spread around care homes and hospitals in the UK. Transmission tends to occur in these environments because individuals are cared for at high density; and the way institutions control infections under these circumstances is by using strict policies that isolate and even exclude cases. That’s us humans, but there are other classes of animals that also live in high density and they’ve developed ingenious infection control strategies of their own. Speaking with Chris Smith, Chris Pull explains how he's been looking at what ants do…
Chris Pull - We know that social insects, so that's ants, bees, wasps, and termites have evolved collective disease defences to try and control epidemics in their colonies. But a lot of the work so far has looked at how they prevent infections. So, for example, they groom one another and they use anti-microbial disinfectants to prevent individuals which come into contact with pathogens from actually contracting an infection. But what we wanted to know is how they actually prevent successful infections from spreading. So in cases where these sort of first line defences fail to prevent disease what can a colony do to prevent the infection spreading into others.
Chris Smith - How do they know that they have an outbreak situation in the first place?
Chris Pull - So what we've been able to show through our research using chemical analyses, is that they can actually smell when another individual is sick. So we've shown that sick individuals when they have an infection and when you also inject them with an immune elicitor to increase cuticular hydrocarbons this attracts the attention of ants in the colony and triggers a response.
Chris Smith - So this is like "ant B.O." isn't it, these cuticular hydrocarbons that they can sniff on each other?
Chris Pull - Yes exactly. So they use them typically to tell if you're a member of the colony or not but we've been able to show now that they actually also change them in response to infection and that can actually tell others who's sick.
Chris Smith - So what is the situation when they pick up this chemical trace or chemical signature of diseases there. How do they respond?
Chris Pull - It's quite interesting. They, sort of, have this multi-component behaviour. So we were looking at infections in pupa and the pupae are these sort of developmental stage in between a larvae and an adult and they're going through metamorphosis and they're encased in these silk cocoons. What we found is that upon detecting an infection the ants will actually break open this silk cocoon and then they start biting the infected pupa and then they spray poison which is made up of formic acid and acetic acid from a gland at the end of their abdomen. And this ensures that the fungus or the pathogen grown inside the infected brood can't grow anymore. So, the acids actually seem to kill this fungus which is inside the body of the pupa and it seems like they do this because the poison itself can't actually penetrate into the body of the pupa unless the cocoon is removed and unless they make these holes in the body of the pupa itself
Chris Smith - And can you demonstrate that this really does mitigate or curtail the spread? So in other words, if you abolish this behaviour it would be curtains for the colony.
Chris Pull - Yes. So we've actually been able to show by mimicking a situation where they failed to detect and destroy these infections, so we simply kept ants with an infectious pupa. Forty percent of these small groups of ants actually contracted the infection and became infectious themselves. And you can imagine that in a full colony set up that can very quickly lead to a sort of huge mass break out of this disease, but by performing these behaviours we actually saw that there was zero disease transmission.
Chris Smith - Do other social insects that have similar problems deal with it the same way or do they have a different strategy?
Chris Pull - So we do see different strategies. So in honeybees, because they live in these hives and they forage on the wing, what they can do is to simply take disease brood out of the nest fly away a few hundred metres and just drop it somewhere in the vegetation because they forage on plants and they forage for wide distances around the colony. The chances that they encounter that infectious corpse are really low. The termites on the other hand, what they do is actually eat their dead so they are living encased in these sort of pieces of wood which are rotting away and for them it's hard to remove things from the wood because they really live inside it. So what they tend to do is to actually eat their diseased individuals but at the end of the day, they all use more or less a similar strategy so they're all trying to detect very early these infections and even remove, or to destroy, or to eat them before they have the chance to become infectious.
Chris Smith - That's quite an undertaking strategy isn't it, actually eating you're dead? But how do you think this evolved in the first place? Because it's quite a complicated behaviour isn't it? Involves the ability to do chemical detection and recognition and then to have evolved a strategy that is itself successful in mitigating the threat.
Chris Pull - Yeah so we think that these behaviours have evolved because a social insect colony is like a superorganism, so they behave and they reproduce like a single organism in itself, and in a way, they're very similar then to a multicellular body like a frog or a human being. And in the same way when a human has an infected cell in its body you have this immune reaction to remove that infected cell and we see then common processes in multicellular organisms and these sort of super organismal insect societies and we think that common evolutionary processes were at play during the evolution of both multicellular organisms and superorganisms, and been able to basically detect and remove elements which might harm the entire organism in itself were necessary, sort of, prerequisites or at least were necessary to evolve in order to ensure that, like, you have the survival of the whole over its parts.
06:22 - Crickets make leaf amplifiers
Crickets make leaf amplifiers
with Natasha Mhatre, University of Toronto
Tree crickets amplify the sounds of their mating calls by cutting a hole into the centre of a leaf and using it as an acoustic baffle, as Chris Smith hears from Natasha Mhatre...
Natasha - So these creatures are called tree crickets, they're about a centimetre in length. They're really beautiful. I mean most of us see crickets from the pet store which look kind of brown and a bit cockroach-like tree crickets are really pretty. They have translucent wings, have long antennae, they're small green things and there's tree cricket species more or less all over the world. The ones that we're working on come from India. All tree crickets do this really amazing thing which is that they sing to attract mates. They put up their wings which are resonant, rub them together, set them into vibration and produce really beautiful tonal sounds. That's what you can hear most summer nights. These sounds are heard by the females who can use them to identify males of their own species from other males and find the males. These tree crickets also do this amazing other thing which is that they make an aid that helps them be louder than they would be on their own.
Chris - Really what do they do?
Natasha - They make a thing called a baffle. A baffle is, for a tree cricket, very simply a hole cut in a leaf that they sing from, so they place their wings directly against this hole and seeing from inside it. And this makes them louder.
Chris - Is that a bit like, you see people walking around in the old days on Hollywood sets with a megaphone which was basically a cone with the end chopped off and they shout into it. Is it sort of doing something similar they're creating an amplifier from a leaf to make themselves louder?
Natasha - It's a bit similar. So I'll try and explain the physics as simply as I can. So if you can imagine the wings as a board that's vibrating back and forth. Every time the board moves forward it produces high pressure in front of it. And behind it, it produces low pressure and this is essentially what sound is, it's changes in pressure. What will happen is that the high pressure and the low pressure will meet at the edge of the board and when they meet with each other they'll cancel each other out. This is something we call acousic short-circuiting. Now the smaller the board is, the more of the sound that's produced is short circuited. If you can somehow prevent these two high pressure and the low pressure from meeting each other than you can prevent acoustic short-circuiting. And the more you can do this the more loud the sound will be. And that's essentially what's happening when a cricket puts itself in the hole in a leaf. What happens is that the front face of the wing is effectively acoustically separated from the back face of the wing and they end up being louder.
Chris - And how does the cricket find the leaf and the hole in the first place?
Natasha - There's a big secret in that. So one of the things that we did was to see whether there are different baffle designs. So basically, you know, what are the different sizes of leaves that are available to the cricket? What are the different sizes of holes they can make? Where do they put the hole? And it turned out if you model this you find that some baffles perform a lot better than others and the baffle that performs the best is made with the largest leaf, with a hole that's exactly the size of the wings and placed dead centre in the leaf.
Chris - Right, so next question then, given that that's the optimal solution, what proportion of the crickets actually opt for that? In other words are they actively pursuing that solution or do they arrive at that sometimes by chance?
Natasha - Well it depends on the situation. But when we did an experiment in which we gave 19 crickets the choice between a small leaf which wouldn't make such a good baffle, and a large leaf which would make a great baffle, 15 crickets made a baffle and every single one of them made a baffle in the large leaf. They made a baffle in the large leaf, with the optimally sized hole and they got pretty close to the centre so all of the Crickets seemed to know how to make an optimal baffle.
Chris - Now given that crickets sing at night, they're therefore able to work out the size of a leaf, discriminate between leaves that are bigger and smaller, and then having worked out the size of the leaf and made a choice, they're then working out where the middle is. How on earth are they doing that?
Natasha - That's, yeah, they are doing that. We have no idea. There may be different ways in which they're doing this. One is to walk along the edge of the leaf. The other is to use these really beautiful long antennae that they have to touch the edges of the leaf to see if the edges are further away on one leaf than another one, and you know, sort of using them to centre themselves in the middle of the leaf. But to be honest the answer is we don't know how they're doing it yet.
Chris - And now that you've done these experiments and you can actually make the measurements, the sounds they're producing. How much louder is the baffled cricket compared with a non-baffled cricket. In other words what sort of advantage, a sonic advantage, do they gain through doing this?
Natasha - So between a cricket that singing on its own and one in an optimal baffle there's a four times change. So a cricket that's in an optimal baffle will be four times as loud as a cricket that's on its own.
Chris - This completely changes our view of insects doesn't it? Because we mostly think of insects as sort of dumb automatons with a brain that's, sort of, hardwired to process inputs and generate outputs. But here you've got very simple organisms, they're making a sequence of decisions informed by their own measurements in order to achieve an outcome and that's really quite striking!
Natasha - Absolutely. It has been a long-held view that invertebrates are stereotyped, and vertebrates, mammals, birds, etc. are extremely clever and we've been having to change this view. I mean I think one of the first things that really jolted this was when they found that octopuses can make tools, they were making all sorts of tools. Now if you think about it a little bit an octopus is a mollusc. It's the same as a snail. So really, we can't hold on to this idea anymore that invertebrates are simpler animals, they're just different from us and we're absolutely going to have to look very closely at how insects behave in order to be able to appreciate what's going on that's not immediately apparent on the surface.
13:34 - An animal model of pre-eclampsia
An animal model of pre-eclampsia
with Katie Bezold Lamm, Massachusetts Institute of Technology (MIT)
Every year millions of women fall pregnant; but up to 10% of them can develop the condition pre-eclampsia, which is associated with dangerously high blood pressure that can be life-threatening if it’s not managed promptly and appropriately. And although doctors are very good at doing that, we’re still not entirely sure why the condition occurs in the first place; which makes predicting and preventing it that much more difficult. Now, speaking with Chris Smith, MIT scientist Katie Bezold Lamm explains how she has found a way to produce a very similar manifestation in mice, which might give us new clues as to what’s going on…
Katie - The placenta is a specialised organ that only occurs during pregnancy. It's created by the developing baby. It's the site of communication between mom and baby and the site of gas and nutrient exchange for the developing baby.
Chris - How does it actually form?
Katie - So the placenta is formed by invasive cells from the developing fetus that invade into the maternal uterus. These cells locate maternal spiral arteries and replace the underlining endothelium, widening these arteries to increase the amount of blood flow to the placenta, effectively increasing the amount of available nutrients and oxygen for the placenta to deliver to the baby. However, in a certain subset of pregnancies, this invasion of specialised cells called trophoblasts does not occur quite as effectively as it should. The spiral arteries aren't properly remodelled so the amount of blood flow available is drastically decreased. And since these spiral arteries are thinner or the diameter is reduced the mother is at risk for developing high blood pressure in pregnancy which can lead to pre-eclampsia. Additionally, since there is a reduction in the amount of blood flow available the baby is at risk for developing intrauterine growth restriction where the baby is then small for its gestational age.
Chris - It's quite common this isn't it, pre-eclampsia? But do we actually know what causes it?
Katie - Absolutely, pre-eclampsia is very common. But while it is generally understood that pre-eclampsia arises due to shallowly invading trophoblast cells we don't actually know what regulates invasion of these cells and what goes wrong to cause pre-eclampsia. And so we sought to determine the mechanisms that regulate trophoblast invasion. And so we decided to study the inverted formin-2 protein which is responsible for generating invasive structures in cells.
Chris - So what actually is this protein? Where does it come from and how does it act on a cell?
Katie - So inverted formin-2 is actually found in a wide variety of different cell types but what its primary role is in the cell is to maintain the actin's cytoskeleton. It has a unique ability to depolymerise actin filaments. This is important in invasion because cells need to be able to form actin rich protrusions that allow cells to invade.
Chris - Right, so you've got this protein is made in these trophoblast cells that are doing the invading into the maternal arteries and they're expressing heavily this protein which can remodel the skeleton inside the cell which will warp the cells making them change shape and bend and twist and so on. So is your hypothesis then, that this protein is in some way linked to the ability to invade and if it wasn't being expressed correctly or in the right amounts, that might be why invasion fails or doesn't progress far enough down the artery, and that's what causes pre-eclampsia?
Katie - Yes. Our hypothesis was that inverted formin-2 (INF2) is necessary for trophoblast invasion and that loss of inverted formin-2 would reduce spiral artery invasion and lead to pre-eclampsia. So to test this hypothesis we used a culture method of extravillous trophoblasts, in which we've knocked down inverted formin-2 and saw that these cells had a reduced capability of invasion.
Chris - What about in vivo though because it's one thing to do this in a dish it's a very different effect in vivo?
Katie - That's actually a really good question. So to understand the role of inverted formin-2 in vivo, we turned to a knockout mouse model. When we studied the pregnancies of these knockout mice we found that the pregnant mice displayed new-onset high blood pressure late in pregnancy and that it wasn't until they delivered the pups and their placentas that blood pressure returned to normal. Additionally, we looked at the spiral artery remodelling in these INF2 knockout mice and found that there was a significant reduction in the number of spiral arteries in these knockout mice, suggesting that spiral artery remodeling in these mice is reduced. The pups in these INF2 knockout mice were significantly smaller than the wild-type counterparts.
Chris - So basically what you've managed to create is a very, very close mimic of what we see in human pre-eclampsia, because you've got animals that develop high tension, they have intrauterine growth retardation, and all of the other negative consequences go away after the animals give birth which, which is a very strong mimic for what we see in the human condition?
Katie - Yeah, it is a really interesting phenotype that does recapitulate several aspects of pre-eclampsia and intrauterine growth restriction. I do think we are a bit far from thinking about potentially treating preeclampsia but this would provide an interesting method for screening people at increased risk for developing pre-eclampsia.
19:18 - Post Traumatic Stress Disorder
Post Traumatic Stress Disorder
with Pearl Chiu & Brooks King Casas, Virginia Tech
People with Post-traumatic stress disorder, or PTSD, experience harrowing flashbacks to frightening events and encounters from their past. Usually, these are triggered by some sort of reminder of what happened to them originally, and patients are also more alert to potential threats than the average person. But what has changed in the brain to make them respond like this? Speaking with Chris Smith, Virginia Tech researchers Pearl Chiu and Brooks King Casas explain how they’ve been trying to find out…
Pearl - Post-traumatic stress disorder, PTSD, is a debilitating psychiatric illness that often occurs after someone's experienced a dangerous or threatening event and people with PTSD tend to overreact to unexpected reminders of the events and are often hyper-vigilant for danger. And so what we've done here is take new findings, from computational neuroscience, from computer science, from statistics, to try to fit models to understand what might be happening in PTSD.
Chris - So in essence which bits of the brain are miswiring or misfiring in order to provoke the changes in behaviour you see in someone who's manifesting PTSD?
Pearl - Yeah that's exactly right.
Chris - And Brooks, how did you actually do that?
Brooks - So we recruited 75 veterans who had served in Iraq and Afghanistan and we brought them into the lab and placed them into a fMRI scanner. While we were monitoring the blood flow in their brain we had them play a gambling task in which they were trying to evaluate and make decisions between two different options one of which was better than the other
Chris - So, Pearl, why does a gambling task actually help to shed light in this instance?
Pearl - Previous data suggests that PTSD may be a disorder of disrupted learning. So one of the symptoms of PTSD is hyper-vigilance when you encounter something unexpected. People with PTSD tend to overreact, and a gambling task in the learning context lets us evaluate what parts of learning, what parts of the brain may be disrupted. The way we're able to quantify surprise in the context of a behavioural paradigm is people with and without PTSD are choosing between two stimuli or two ambiguous pictures and trying to learn which one is better and then you see the outcome. And we can infer what your expectations were by how surprised you are by the outcome.
Chris - I get it; so essentially you put them in the scanner, you give them a gambling task, and they learn if I do this I win if I don't do that I lose. Then you, what, flip the odds so that then the losing one they don't expect to win they're surprised?
Brooks - Every so often they'll get something that they're not expecting. In those cases, we're studying how the brain is responding to those unexpected events. Here in our task, we were trying to figure out whether it's how the brain is responding to those surprises that might be different in PTSD, or whether it's how folks are attending to information once they get that surprise.
Chris - And Pearl, do you see a difference, so in the people who have PTSD. Does the brain get more surprised more readily than in people who don't?
Pearl - So the people with PTSD show an equal amount of surprise as people without PTSD. But it's how much attention they're paying to the surprise that's different
Chris - And how are you quantifying that?
Pearl - So that's what our computational model lets us determine. We have different components of the model that measure how responsive a participant is to surprise, how responsive they are to reward or loss, and how much attention they're paying to the surprise. And in our analyses, we show that it's particularly the attention to surprise that's different in the veterans with PTSD. So everyone shows the same brain response to surprise itself, but it's how much attention you pay to the surprise that extends into choices in the future.
Chris - Do you think that that difference was there before they got PTSD and that's why they're prone to getting PTSD or did they develop that as a response to having got PTSD?
Brooks- Certainly within this study, we can't examine that prospectively, but it is potentially the case that those who are more predisposed to developing these symptoms of hyper-vigilance might be the ones who are starting off with a predisposition to have this attention modulated learning process.
Chris - And Pearl, what are the consequences then of them paying more attention in this way the brain generates a surprise signal, it's generic, everyone has it but then downstream of that you then end up with, in some people some areas of the brain responding a bit too much.
Pearl - So one of the potential consequences is that this contributes to learning difficulties that lead people with PTSD to overestimate the likelihood of negative outcomes into the future which then contributes to a hyper-vigilant response.
Chris - So does this mean that if a person gets surprised and they then become highly vigilant? Does this transfer to things other than the thing they find traumatic? So will they for instance, if you present them with, I don't know the sequence of cards to remember and you surprise them, will they remember those card sequences much better than someone who doesn't have PTSD?
Brooks - That's a good question. We don't know the answer to that, but it could be the case. A negative outcome, a negative event triggers this increase in attention that changes their focus so that they're learning about really any information that's temporally close to that unexpected negative event. So although we didn't test for that in this experiment it certainly could generalize to other information that they're seeing in that same context.
Chris - And Pearl does this shed any light on how we can help people with PTSD?
Pearl - This work absolutely does contribute to how we might treat or understand PTSD in the future. One of our perspectives is that using these computational models that tease out processes, allow us to characterise mental illnesses like PTSD in the ways that you might characterise some kind of physical conditions. For example, in the case of hypertension, salt, stress, or smoking they all contribute to hypertension. But depending on which contributes the most we might have very, very different treatment strategies. So similarly for PTSD, or post-traumatic stress disorder. Knowing what contributes in a particular case may help us devise different treatment strategies.
25:58 - Human Cell Atlas
Human Cell Atlas
with Sarah Teichman, Sanger Institute
One of the largest biological endeavours of recent years was the human genome project that mapped and sequenced all 3 billion of the genetic letters in our DNA code. Now scientists are embarking on an even more ambitious initiative. Speaking with Chris Smith, the Sanger Institute's Sarah Teichman...
Sarah - We're setting out the goal of mapping all cells in the human body, through an international effort that involves cell biologists genomics experts computational biologists and the medical community to collaborate on creating an atlas of the human body at the level of individual cells.
Chris - I'm gobsmacked, Sarah, this doesn't exist already. I mean, cell biology has a history going back hundreds of years. So why are we only doing this now?
Sarah - So it's really thanks to high resolution and high throughput technologies that have been evolving over the past five to ten years that we can now see cells in terms of their entire genome's transcriptomes at the level of tens and hundreds of thousands of cells at a time. And so what I'm talking about in a nutshell is the resolution revolution in genomics. This coupled with also spatial methods that are microscopy based to map cells in their two and three-dimensional context has meant that we can now grab hold of cells at a completely different level.
Chris - It's almost like multi-dimensional then this atlas, in the sense that yes, you can say "that's what a liver cell looks like," but one can zoom inside the liver cell and say "and this is what it's transcribing. That's these are the proteins it's making."
Sarah - That's right. So you're basically describing the entire molecular fingerprint of that cell rather than the morphology of the cell the way we've been doing with conventional microscopy methods.
Chris - Sounds like a huge undertaking though because it's not as simple as just saying "I'm going to take a snapshot of an adult now," because obviously, cells go through phases during the day, they go through phases during the week, an immune cell can turn from one type of cell to a completely different type of cell as it matures for example, and we'll start life as an egg which then turns into all these different cell types so, how were you going to do this?
Sarah - That's a great question, and it really gets the bottom of asking what is a cell type or what is a cell state. And as you mentioned there are, sort of, developmental dynamics so the human cell atlas will encompass human development, and also at different ages in the human lifespan. Although in the short term the aim is to build a first reference initially so this is a project that we envision will run for five to ten-year term.
Chris - I was going to say it does sound like it's going to be an extremely long term undertaking. It's huge, and potentially bigger than the human genome project because you're going into all these different dimensions?
Sarah - That's right. It's also more complex at the level of the samples. So basically acquiring tissues from different organs in the body and as you said different developmental stages. That sample acquisition part is certainly more complex than the Human Genome Project.
Chris - I suppose is some of the challenges that had to be surmounted for the Human Genome Project, 13 years ago when it finished. Before that, obviously, when it was running they must be informing or helping with this because marshaling massive amounts of data was a big challenge then and it helped to actually change the world in the way that we process data so you must be to build on some of that?
Sarah - Yes. I mean the human genome project is certainly a template for collaborative efforts in biology and for building a resource. And it's also as you're saying, the data challenge is similar, although I'd say we're in a new era of big data and biology now where we really are talking serious big data. It's not just a software engineering and database challenge, it also becomes a data mining and statistical and computational challenge, with sort of very sophisticated machine learning and artificial intelligence methods that we're developing to make sense of the data and to mine the data and to get the biological knowledge out of it.
Chris - This is a quite provocative question which I want to put to you because I think there'll be people listening to this who will think "well that sounds wonderful but I don't understand why it matters" why does having this cell atlas that tells us what's where in the body but in many dimensions at many levels what's going on in those cells how they're changing and so why does this help us do science better.
Sarah - To me there is a sort of curiosity argument, we want to know what's inside our body and how it works. But there is also a very clear relevance for medicine in the sense of new diagnostics that can be developed based on markers and molecular patterns that we find in the healthy reference body immediately it provides a template for saying okay what are the cell states that we need to probe that are indicators of disease tumour mapping learning about cancer cell states essentially having the healthy reference atlas is a very obvious kind of framework for the tumour biology. So there's the basic curiosity about ourselves. But there's also medical applications.
Chris - And just in case anyone isn't completely across how massive this undertaking is, put some numbers on it for us. How many cell types? How many different ways of looking at those cell types are you going to have to go across? I mean what's the scale of this project?
Sarah - Well we don't really know how many cell types there are, conventional estimates on Wikipedia and so on say there are 200-300 cell types but we're seeing thousands essentially now with these high-resolution technologies. There are 37 trillion cells, probably, in the human body and we're not going to sequence all of them but by sampling in a strategic way from different tissues in the body, we hope to learn about the vast majority of the cell space that's out there. My estimate is that we will sequence billions of cells and we will discover thousands of cell states over the next five years or so.