In this episode of the eLife podcast we hear about midnight snacking, X-ray imaging of fossils, hummingbirds, monkeys gambling and axolotls regenerating...
In this episode
00:32 - Food for Thought
Food for Thought
with Dawn Loh, UCLA
午夜的盛宴将会是一个概念familiar to many youngsters but, increasingly, older kids - including some in their 30s, 40s and 50s - are embracing lifestyles that lead to sleep deprivation and eating at what could be regarded as "all the wrong times" including late into the night. Often this is to meet deadlines or cram in work around family life and other obligations. But it could be having a detrimental effect on your memory, by throwing the body clock off kilter in your hippocampus, the part of the brain where memories are first made. Chris Smith spoke to Dawn Loh...
Dawn - We took two groups of mice. We put one of them under fairly normal housing conditions and allowed them to eat when they should be active. In the second group of mice, we gave them food during what should’ve been their sleep time and then we tested their ability to learn and remember after being housed in these two conditions.
Chris - Now, these mice that you are feeding, the mouse equivalent to the midnight feast to, were they being woken up for that? In other words, were you depriving them of sleep and upsetting them in other ways?
Dawn - In this study, we used some automated feeders so we didn’t have to disturb the mice. So we didn’t have to go into the cage and wake them up and give them food. But it is true that the mice had to stay up during a time that they would not normally want to stay up to eat their food. And they actually adapted to that within about 6 days. What happened to their sleep was that although the sleep in the first few days was disturbed, the sleep caught up later on so that they no longer was sleep deprived when you considered them over a 24-hour cycle.
Chris - What sorts of measurements were you making on the mice when you did this to them?
Dawn - Well, we were able to test them at two different times of day with the same test. So with one group of mice, we tested them at what should have been their normal week time when they should perform very well on the test that we called ‘novel object recognition test’. So this is a test where we give them two identical objects and we train them to recognise them. The next day, we replace one of those objects and a normal mouse would spend more time with the new object, the novel object. That’s how we would know that the mouse remembers the old object. What happened to our two groups of mice was that while the aligned mice, the mice who were eating during their normal time performed this test remarkably well, spending most of their time with the new object, the novel object. The misaligned mice who were eating during their sleep time spend significantly less time with the new object and in fact, they didn’t pass the criteria for this novel object recognition test at all.
Chris - This would suggest that something is impaired in their ability to form memories.
Dawn - That’s right. We suspect some of these problems may be arising in the hippocampus and this suspicion is borne by previous evidence from another lab showing that the clock in the hippocampus may actually shift according to when you eat. So we specifically looked at a hippocampal dependent learning and memory test where we train a mouse to recognise a specific context with a fearful stimulus. Again in this case, the misaligned mice were unable to remember the context. So they had a hippocampal-specific loss of memory.
Chris - How do you account for this? What do you think is going on? Is this just sleep deprivation? It would argue not if they're making up the sleep. So, what underlies this?
Dawn - We think that perhaps the clock in the hippocampus is changing the state of the hippocampus. The clock that I'm referring to is this endogenous set of genes that we have that causes a feedback loop that autocompletes within the day. This little clock is in each and every one of our cells. We know that the cells in the hippocampus express this clock and it’s a rhythmic clock, and it drives certain types of physiology in the hippocampus. What we think is going on in these misaligned mice is that the master clock which is driven by light, it’s in a different part of the brain called the suprachiasmatic nucleus. It’s ticking along and following the light/dark cycle. There are certain other clocks in the rest of the body that might be more prone to being entrained or being driven by food so some of these clocks in the body include the liver and quite surprisingly, the hippocampus, so some of these other clocks are starting up at a different time compared to the master pace maker in the brain. What we think we’ve done in these misaligned mice is set up this internal desynchronization between some metabolic parameters and other brain function.
Chris - So in other words, the hippocampus is effectively optimised to operate at the wrong time of day in these mice.
Dawn - That’s right. That’s what we think is happening.
Chris - If you were then to test the mice at the time when the hippocampus was more optimally operating, would they perform better?
黎明,但当我们执行这些测试those tests at the opposite time of day, we found that the mice were still not performing well on the test.
Chris - So, how do you explain that then?
Dawn - We don’t have a very good explanation for that at present. We think that perhaps the internal desynchronization has led to some changes in the hippocampus that are long lasting.
Chris - If you move your misaligned mice so that you start to feed them at the right time again, do they go back to normal?
Dawn - That is an experiment that we have yet to do and would definitely be part of our next study. Whether this is a long term chronic effect or whether the mice can recover.
06:08 - Beneath the surface
Beneath the surface
with Thomas van de Kamp, Karlsruhe Institute of Technology
Fossils are a valuable insight into the evolutionary past, although the quality of their preservation can be highly variable. But focusing chiefly on the specimens that look nice means we might have overlooked a valuable source of material to study. Thomas van de Kamp, from the Karlsruhe Institute of Technology wondered whether a synchrotron X-ray beam could enable him and his team to see inside what are called mineralised specimens of insects, which are often dismissed as being of much lower scientific value. The results, from a fossil collection that hadn't seen the light of day since the 1940s, are impressive...
Thomas - Our groups worked quite a lot on the fossil insects also before but until then we scanned amber specimens. So it’s like inclusions in fossil tree resin where you can see the insects from the exterior quite nicely. But these insects were mineralised fossils. Three-dimensional insect that looked much worse than these nice looking amber fossils from the exterior and there were x-ray methods we employ here. We wanted to have a look inside. We wanted to create virtual three-dimensional images and cut virtually through their fossils to see if there is something inside.
Chris - In other words, in these insect specimens, the tissues have been almost replaced with the minerals, making them effectively into a stone replica of the insect as it once was.
Thomas - Yes, this is true. So parts of the exoskeleton of the original insects were replaced by minerals and parts were replaced by air-filled spaces. While most of the soft tissue parts were replaced by minerals.
Chris - How big were the insects we’re talking about?
Thomas - They’re mediocre in size. So, our beetles, we scanned 8 specimens. All of them were around 3 millimetres in length and 2 millimetres in width and in height.
Chris - Thomas, how did you do this? How did you image these tiny, effectively grains of stone to work out what the anatomy was?
Thomas - So first, start with a more or less standard micro CT setup at a synchrotron light source so we’re producing intense x-rays. We place our objects inside a sample holder on a rotary stage. Then we radiate the specimen with x-rays and during the scan, we rotate the sample for 180 degrees. During the rotation, we acquire a few thousand, I think, 3,000 images in this case, of the specimen. After the scan, we reconstruct a three-dimensional volume from the 3,000 projections we took.
Chris - What do you compare them to? Do you have any beetles that have not been mineralised in order to ask how do they hold up to the same interrogation and so you can work out whether there's any effect of the mineralisation on the actual imaging you were able to achieve?
Thomas - Yes. What we did for this study was we compared the extinct species with close related species that still is alive nowadays in Europe. So we have roughly 30 million Europe beetle and we compared it with our existing beetle species using the same tomographic setup.
Chris - Does this turn out to be a valid way to study these fossils?
Thomas - Yeah, definitely. What we also did is we scanned two specimens of the existing species - one that was fixed in ethanol where we could see all the organs in the more or less natural state and then with the dried museum specimen. We really can conclude that the preservation of the fossilised specimen is better than the preservation of the air dried specimen with respect to the soft tissues. So from this comparison, we can conclude that the fossilisation had to be very fast because an air dried specimen from the museum is really degraded so you cannot see much of their soft tissue anymore while in the fossil, you can see some glands, the genitals, almost like in the alcohol fixed specimen.
Chris - Does the fact that you’ve solved this for this particular species of beetle, does this mean you can now extrapolate this technique to other species? It means you can unlock a lot more fossil information – not just about these beetles, but many other types of fossilised insect which could perhaps be lurking in collections of specimen museums totally unobserved and unstudied because people thought that there was a limit to the data they're going to get from them.
Thomas - Yeah, that's exactly what we wanted to show with this study because now, we really see that there are thousands of neglected fossils inside museum collections. You can see that on this collection, we investigated was more or less dormant in the museum of Brazil for over 70 years. The exterior shape was studied in 1944 the last time and with our fast setup, we are able to screen them in a very short time, so effectively, we need 16 seconds for a scan, 3 minutes if we include all the coping. So let’s say, 3 minutes per scan. So you can imagine, we can really image a lot of samples from the collections in a short time to get a better idea about evolutionary history of insects.
11:16 - Up in the air
Up in the air
with Doug Altshuler, University of British Columbia
The ability of an animal to manoeuvre is fundamental to its survival and is the product of millions of years of evolution. So it's surprising then that we haven't really got a way to quantify manoeuverability and that's largely because it's extremely hard to study in an objective and consistent way. But the University of British Columbia's Doug Altshuler and his colleagues have now managed to do this for the first time by spending literally years painstakingly recording birds in a
special flight chamber and using a computer to extract the relevant flight metrics...
Doug - These experiments were done with the Anna’s hummingbirds which is a North American hummingbird on the west coast of Canada and the United States. We would capture them, get them used to the chambers, and then that was really all we had to do. The chamber was relatively large for a hummingbird – 5 feet by 5 feet by 10 feet. If we put a feeder and some bird seeds in there, they would take to it quite readily. If we put two birds in there, they would often compete with each other.
Chris - But how did you watch them? Did you have cameras that were filming and then you were able to go and analyse that footage and how did you challenge them in order to see what manoeuvres they could or couldn’t do, and how fast?
Doug - We didn’t challenge them to make specific manoeuvres. Instead, we just let them do the manoeuvres that they showed us. The only challenge that we occasionally employed was having a competitor. But it turns out that the competitor didn’t really change their manoeuvrability that much. The way we measure manoeuvrability is by using automated tracking system. This was composed of 4 cameras that were filming the chamber simultaneously and the way the system works is that it films the chamber so we can see the birds moving around. It also has an image of the background. What our computers do is that they scan through those images and they look for changes, which is to say when the bird is moving relative to the background with no bird. The other thing the computer does is not only find the birds but it also figures out what direction they're pointing. This is all done semi-automatically. That means that up to 200 times a second, we’re getting data on where the bird is in the chamber and the way the bird is oriented. That turned out to be a very rich dataset that yielded us literally millions of points for this study.
Chris - Is there now sort of an SI unit of manoeuvrability that you can come up with because of this study? You can say, “Aha, now we have a way of actually objectively quantifying manoeuvrability.”
Doug - We have found actually that there is no SI unit of manoeuvrability. The reason is because the natural manoeuvres the bird show us were complex, but we did have to measure this somehow. What we finally came up with was actually a suite of measures of manoeuvrability. These were very fundamental things. We defined a measure of manoeuvrability for example that is the maximum acceleration that a bird shows in the horizontal plane. We also came up with another one which was the maximum acceleration that the bird gives us in a vertical dimension. We also came up with some other manoeuvres that were specifically related to turns such as the minimum radius that a bird gives during an arcing turn or the maximum centripetal acceleration that a bird gives during an arcing turn. So we have a suite of different manoeuvrability measures that we could then compare between individuals.
Chris - If you take those measures and relate them to other features of the birds such as muscle mass, such as wing area, do you see relationships emerging now? That means that you can actually begin to make predictions about other animals or you can take those measurements and parameters from other animals, and make predictions about their potential for manoeuvrability.
Doug - So our initial question is, is manoeuvrability more determined by muscle capacity or wing and body morphology. And so, once we had these suite of manoeuvres, we could then test that. What we found was that the majority of the manoeuvres that we defined were more explained by muscle capacity than they were by wing morphology. Really only, a very small number of manoeuvres were related to wing morphology over those manoeuvres were heavily related to wing morphology.
克里斯,所以简单来说,基本上可以实现nything you want to achieve if you’ve got enough power to do it. So it’s pretty similar to politics in the modern era.
Doug - That’s a good way to think about it actually! I think that it also shows us the efficiency with which one can execute a manoeuvre is probably very much influenced by your morphology. But the thing about manoeuvres is they're very brief. We’re often doing them for things that are important such as running away from something or running towards something in the case of humans. Similarly for the birds, I think manoeuvrabilities were so short that they don’t really care much about the efficiency of the manoeuvres. Instead, they can use this high muscle capacity to power their way through even an otherwise inefficient manoeuvre.
Decisions, decisions
with Veit Stuphorn, Johns Hopkins University
Making decisions is something we do continuously throughout the day. But what's going on neurologically while this is happening? There are two theories: one says that we weigh up all of the possible options, pick the best one and then make a motor plan to achieve the desired outcome. In contrast, the other theory posits that the decision is part of the motor process itself and that different neuronal assemblages representing the possible outcomes compete
with each other until one wins out and becomes the decision we make. Unfortunately, there's data supporting both theories! And they can't both be right. But what no one had done before was to test both theories at the same time, to see what the real pecking order is. And this is what Veit Stuphorn set out to do...
Veit - So what we tried to do is set up an experiment in which information that would allow you to make a selection based on the outcomes and the selection of a motor process is available simultaneously. The idea that we had is so that we then can see whether there's one kind of selection process that leads the other. We used these macaque monkeys. We trained them to do the following - so they looked into a computer screen and on the computer screen, there were images basically. These images indicated to the animals both possible amounts that they could get at two different ones, and the probability for each of the two amounts. So basically there were gambles. For each trial in the experiment, there were two different gambles and from trial to trial, the monkey couldn’t really predict which pair of gambles hewould have to make a decision between.
Chris - So, he’s choosing whether he wants to take a big risk and have a big reward or a smaller risk and a degree of certainty. So you're stressing the system but in a different way each time so it’s not just a pre-planned motor action each time.
Veit - That’s right. So this is sort of the option part and the action part is basically, we could record to which part of the screen the monkey was looking. By looking at either one or the other of these visual targets, the monkey indicated which one he wanted. He presented this, let’s say, the same pair of gambles, we presented in different positions on the screen so that the monkey had to make different eye movements to indicate the same choice. In that way, across many different trials, we could differentiate between activity in the brain that was related to the motor response that the monkey chose or the option that he chose.
Chris - Which one seems to hold the key to what the monkey’s ultimate choice is?
Veit - So, the main finding in our study was that these neurons indicated both the options that he selected and the action that he chose, but there was a sequence between them. So early in the trial, the neuron showed us which of the two options the monkey preferred, which one he would choose – independent of the eye movement he made on that particular trial. And then sometime later, that activity changed and started to show the eye movement – the action that the monkey had to do in order to indicate this choice. So this first showed the selection of an option and then a little bit later – about 100 milliseconds later – selection of particular eye movement.
Chris - Which population of nerve cells was it specifically that you were recording from to get this data?
Veit——所以我们记录在一个叫做the supplementary eye field. It’s an area in the middle frontal part of the primate brain and humans have also such an area. It has been known for a long time that it’s somehow responsible or involved in the control of eye movements. That’s why we chose it because we had selected eye movements as the type of movement of the monkey to do in order to indicate his choice.
Chris - That’s a visual stimulus though. So, what would’ve happened say, they had to feel something? It wouldn’t obviously involve those same pre-motor areas but on supplementary motor areas corresponding to visual movements because they… or would it? I mean, would they do it with their eyes closed and still perform the same way?
Veit - Yes, whether or not the supplementary eye field specifically would be involved in some other form of decision making that’s strictly speaking, unclear because that experiment hasn’t been done and actually should be tested. The immediate neighbouring regions to the supplementary eye field are other regions that are involved in the control of arm movements or for example in humans, they are known to involve in speech – control of the tongue, and the lips and support. There's an entire map of all the different parts of the body in this region and you can think of a particular region that we recorded as the subpart related to the control of eye movements. And so, you could imagine that we would have found very similar findings if we had recorded in this neighbouring region. But let’s say, train the animal to indicate his choice by making an arm movement which is going to the left or to the right and pressing a particular button to indicate his choice.
Chris - Where does this lead us then? How does this leave the field now? We started this interview with, there are two models. One of them is based on sizing things up first. The other is basically, you keep all these things in parallel in your head at once and then make a decision. Where do we now stand based on what you found?
Veit——我们搁浅船受浪摇摆est a different model in our paper. According to our new model, every decision that you make really involves two different steps. One step would be to select the option and another step is to select the action that is most likely to bring that option about. So the idea would be that two different parts of the brain are responsible for the first selection step and another network would be responsible for the selection of the action.
世界,回到过去
Going back in time
with Elly Tanaka, Technishe University
Neural stem cells in injured axolotls behave like embryonic cells. This enigma of neuroscience has stood for decades; Elly Tanaka has been taking a genetics approach to try to get to the bottom of why this happens...
Elly - We’re trying to understand why the salamander can regenerate these very complex body parts like the limb and the tail. Remarkably, within the tail a fully functional spinal cord can be regenerated after we amputate a piece of the tail off. So, they have some cells as we have stem cells in the nervous system but signals that get made after the amputated tail promote these stem cells to build a new spinal cord and that’s what we’re starting to study now.
Chris - Why does the same thing not happen in us though? We’ve got stem cells too. Why don’t I grow a new spinal cord if I injure it?
Elly - Many people think that there are differences in the immune system and the immune reaction. The study that we have done in this case indicates that the neural stem cells in a salamander can go back in time and become like a stem cell that you find in a very early developing embryo. And so, our hypothesis is that in humans, this kind of what we call de-differentiation or the ability of adult cell to become an embryonic-like cell again doesn’t happen.
Chris - So something stops the cells un-specialising which is what enables them, endows them with the ability to almost think they're back creating an embryo again and regrow a structure from scratch.
Elly - Right.
克里斯-现在他们怎么知道尾巴届“多大”ey’ve got to make is, given that when they were growing in an embryo, they may be in order of magnitude or more smaller than ultimately the adult thing that they turn into?
Elly - That’s a very interesting question. We’re working on that now in the lab. It seems that the cells surrounding the spinal cord might give the instruction as to where along the body you are then there's some kind of system for saying how much you have to grow. But in terms of this issue about size, the embryo is tiny and then an adult x level is huge. It seems that when a spinal cord regenerates, you turn on a subset of these embryonic genes and this allows the existing spinal cord to just extend itself using mechanisms that stimulate stem cells to divide in a specific orientation so that you extend the two rather than making a big round mass of cells.
Chris - Yes, that was going to be my follow up point which is also, it’s got to know again, which direction it wants to grow in and only grow in that direction. So, how do you think that’s achieved?
Elly - When you amputate the spinal cord, the tip cells, they start to make healers that basically fill out into the open space. We believe that kind of initial orientation is probably very important in orienting a process called planar cell polarity that tells the two which direction is kind of the backend, so in which direction to grow. Then the cells in the spinal cord then start dividing in that direction. So they orient their division apparatus so that both daughters end up pointing in the direction that the spinal cord should grow.
Chris - They inherit a direction of recovery from the original injury which polarises the cells. They know what direction they have to grow in and at the same time there are signals coming in laterally. In other words, from the side, from other tissues which gives them a clue as to how far down the body they are so they roughly know how many divisions to go through in a longitudinal direction to rebuild the tail.
艾莉——是的。这之间的横向交流the surrounding tissue and spinal cord, there are some general experiments that indicate that that’s happening but there's very little known about that process.
Chris - But how do you know that the changes that you're seeing in these gene expression profiles are upstream of the developmental and regenerative outcome and they're not merely a bystander effect that they are actually orchestrating this process? Have you tried manipulating the levels of those genes and then demonstrating that there is a different regenerative outcome when you do that which proves they're necessary and sufficient to have that outcome?
艾莉——是的。That’s one of the important things of the study. We deregulated this pathway called planar cell polarity which cause the stem cells to divide in the wrong orientations. By doing that, we blocked the spinal cord from growing out. When you do that actually, the cells, they don’t expand enough and they start turning into neurons too early.
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