E. coli outbreaks, and sniffing the air for DNA
This episode of The Naked Scientists: How scientists are getting to grips with the UK’s E. coli outbreak. Lettuce leaves look like the source, but how? Also, how atomic bomb tests have helped us build a better picture of how much carbon plants can lock away - and the news is both good and bad. And, how scientists near Norwich are sniffing the air… for DNA.
In this episode
01:06 - E. coli outbreak blamed on lettuce leaves
E. coli outbreak blamed on lettuce leaves
Nicholas Brown, Addenbrooke's Hospital
The UK’s Food Standards Agency has said that lettuce leaves are behind an outbreak of E. coli that has left hundreds of people unwell. It has forced some of the UK’s biggest supermarkets to withdraw some sandwiches containing salad leaves. To find out more about the bacteria behind this intestinal infection, I went to meet Nicholas Brown who is a consultant microbiologist at Addenbrooke’s Hospital, Cambridge…
Nick - Over the last few weeks, there have been a number of cases of haemolytic uremic syndrome and also children with bloody diarrhoea presenting in different parts of the country. And this has been picked up through national surveillance, both of cases, clinical cases, diagnosed in hospitals, but also through laboratory surveillance of isolates of shiga toxin producing E. coli. These have been linked together because when they have been analysed genetically, they have been indistinguishable, which suggests that there has been a common source. Though the fact that they are so geographically dispersed makes it difficult to know what that single source is and therefore makes it more difficult to control it.
Chris - It's a form of E. coli, but where will it have come from? Because all of us carry e coli. So what's different about this one and why is it doing what it's doing?
Nick - Absolutely. So E. coli is one of the commonest bugs that we have associated with particularly our gut. It is found in faeces of all humans and animals, and most of us carry it completely innocuously without any problem at all. However, some strains of E. coli carry virulence factors, which can cause more severe disease and a variety of different diseases too. So some strains are associated with urinary tract infections, some strains associated with meningitis in neonates, and others causing gastrointestinal problems. So that shiga toxin producing strains are just one subgroup of E. coli that are particularly virulent and can cause bloody or hemorrhagic colitis and sometimes severe complications such as haemolytic uremic syndrome, particularly in children.
Chris - Where will they come from? What normally carries them?
Nick - They are carried within the gut of mainly animals and therefore most cases are associated with contact with animals or sometimes petting farms situations where we might come into contact with animal faeces and then through the hand-mouth route, faecal-oral spread, then get it into our guts where it can cause disease.
Chris - How's it got into the food chain then? Because the finger is being pointed at some kind of food source for this.
Nick - It would seem likely therefore that there would be some sort of faecal contamination of the raw material, the food at source. And clearly a lot of food stuffs come from farms where there is also animal livestock as well. And so therefore it would likely be a breakdown of basic hygiene at some point in the food manufacturing process, although difficult to say exactly where.
Chris - So it need not be just the meat of an animal. It could be if some salad vegetables have animal faeces on them and those salad leaves or whatever have gone into a sandwich, you could get it from either of those two routes.
Nick - Absolutely, yes. And, that is why it's so important that we wash raw foods that we eat without any further processing, such as salads.
Chris - And how do we manage the cases that we detect?
Nick - Most of the treatment of these cases is what's called supportive. There is no particular antibiotic therapy required or indeed appropriate. And the patient's symptoms are managed as they occur with appropriate fluid resuscitation and most cases of diarrhoea resolve by themselves. With time.
Chris - Anybody particularly vulnerable?
Nick - Young children are particularly more likely to develop the severe complications of shiga toxin producing E. coli, which is hemolytic uremic syndrome, which is a kidney disease sometimes requiring support with dialysis and on occasion support in a paediatric intensive care unit. That's very much the tip of the iceberg with the most severe cases. Majority of people with this infection will not develop that and will simply present with diarrhoeal symptoms.
Chris - So how will public health teams now act on this and how have they been acting on it and what will eventually happen?
Nick - The mainstay of the initial investigation is surveillance, putting together the pieces of the jigsaw puzzle to try and identify what the source is. Most of the outbreaks that we see in this country are associated with contact with farms. However, my understanding is that the current outbreak is not, and the fact that the cases are so geographically dispersed would obviously point against that. So we are looking at a likely common source with something that is distributed across the UK and hence the focus on food. What would happen next with such an investigation is that cases would have a detailed food history taken from them. Clearly this is not a hundred percent reliable because people's memory of what they've eaten two weeks ago is often not accurate. But by piecing together the details that we get from those food histories, sometimes it's possible to develop a hypothesis about what sort of food might be responsible.
07:04 - Plants carbon consumption revealed by atomic bomb tests
Plants carbon consumption revealed by atomic bomb tests
Heather Graven, Imperial College
Plants take up a lot more carbon from the air than we first thought, a new study has shown. But, unfortunately, it’s not all good news: they hang onto it for a lot less long too. Imperial College’s Heather Graven made the discovery by using the high levels of radioactive carbon - also called Carbon-14 - added to the atmosphere by the atomic bomb tests of the 1950s and 60s. By following this radioactive signature out of the air, into plants and back out into the environment, she was able to produce much more accurate figures for the carbon cycle, which will come in very handy when we’re making future predictions about climate change and the impact of greenhouse gas emissions…
Heather - We were studying how quickly plants take up and release carbon, using radiocarbon that was produced by nuclear bomb testing in the 1960s. So radiocarbon is an isotope of carbon and it's naturally occurring, but the bombs produced extra radiocarbon. So we were able to see how quickly plants took up the extra radiocarbon from the air in the 1960s. We found that plants take up carbon more quickly than we thought, but that also means the carbon is stored in plants for a shorter time because it's before it's lost. again, as the plants die or they lose leaves, branches or other materials. Plants are actually more productive than we thought. It also means that the removal of CO2 from the air to store in ecosystems which occurs naturally, but is also of interest for enhancing to reach net zero emissions targets, will actually not store the carbon for as long.
Chris - And how far adrift in our calculations were we, if we take what we thought was going on with the carbon budget before you came along with this research and then you've got your study, what's the disparity?
Heather - Yeah, so what we're looking at is the carbon that plants take in to form their tissues. So it could be wood, leaves, roots, or things like fruit or seeds. There's a lot of different ways that plants can use that carbon. So actually if you go out into the field and look at a particular plant it is hard to track all of that carbon. So previously there haven't been very many measurements like that. So the ones that have been taken were scaled up to come up with an estimate for all the plants on the globe. And so our approach is different in looking at this radiocarbon that was produced by the bomb testing and then seeing how quickly that was taken up. The results of our study suggests that the uptake of carbon into plants and their materials and products is about a third more than what was previously estimated.
Chris - Is that good news or is that bad news, Heather? The fact is the plants are taking up more CO2 than we thought. Does that actually mean that we've got more to play with from a climate change perspective? Or does it throw our sums totally out of the window?
Heather - Well, it's telling us that the carbon is actually cycling through the system more quickly. So the plants are taking in more carbon, but then they're also releasing more carbon. So then actually the carbon that's in the vegetation, in the plants, in their different tissues is actually not going to stay there as long before it comes back out again. So as the plant dies or the leaves or branches fall to the soil, that turnover is happening more quickly than we thought.
Chris - When people therefore say, well I'm going to do some carbon offsetting, I'm going to plant a tree or a million, is that therefore a flawed philosophy? Because not only are they going to release that CO2 more quickly than we first thought, they're also not going to lock it away for any long term period. Full stop.
Heather - So yeah, what we're saying is that the carbon isn't going to be stored for as long. So if the plant is taking up that carbon, then compared to what we thought previously, it's not going to be locked away as long as we thought. So that will likely kind of limit some of the potential of carbon reduction CO2 removal strategies that are trying to lock the carbon away in the ecosystem. And really emphasise that to limit climate change, we need to reduce fossil fuel emissions as quickly as possible.
Chris - Have you plugged your revised numbers into any of the models that are being used by organisations, climate scientists and theorists, planet wide in order to compute where we think the climate's going in the future in order to see how this might affect predictions that we're all working to.
Heather - So if we want to predict what's going to happen in the future, we really have to understand how those processes are taking up and storing the carbon. So from our study, we suggest that the carbon is taking up into the plants more quickly and then cycled more quickly. So we do need to take that into account in these future projections as well as how the carbon uptake in turnover is going to respond to changes in the climate, in future, and other environmental changes that are happening.
13:09 - Immune-suppressing regulatory T cells constantly patrol body
Immune-suppressing regulatory T cells constantly patrol body
Adrian Liston, University of Cambridge
Cambridge scientists have discovered that a type of white blood cell - called a regulatory T cell - constantly moves throughout the body looking for - and suppressing - inflammation and the toxic effects it can have on tissues. The findings - published in the journal Immunity - challenge our understanding of the way that these cells work: previously scientists thought they migrated to an organ and then stayed put. The discovery means we now know how to lay bait to attract them to a site of inflammation - like an asthmatic lung - and then use them to control the condition. Adrian Liston led the team behind the discovery…
Adrian - So we're working on these cells in the immune system that actually shut down the immune system and they shut down inflammation. They start to promote the healing after an infection. We've got some of these cells that are present in our circulation. And then we've also got some of these cells that are present in more or less every organ. So they'll be sitting inside our brain, sitting inside the liver, sitting inside the lung. And what we want to work out is how these cells get there, what they do there, how they're related to each other.
Chris - And I suppose are they all one giant population that just spreads everywhere, like spreading butter across a piece of toast or are they specialised for each of those different domains in the body?
Adrian - Exactly. And for a lot of the immune cells that are present in our body, the ones that are inside organs tend to go into those organs very early in life. They're there before we're born and we'll never get any more of those cells. Now what we found out actually is, for these healing cells, these anti-inflammatory cells that shut down the immune response, these are not specialised per organ. They're not going in during very early developmental life. Instead they're kind of just travelling across our body continuously. They might be going through the blood, they'll pop in, spend a couple of weeks in your brain, they go back into the blood, then they can spend maybe a couple of months in the liver and they're just sort of slowly surveying the whole body, looking for any places where damage could be happening.
Chris - Given that there are millions of these cells and they are tiny, how did you establish that?
Adrian - So one of the things you can do is to take cells from one mouse and we can take the cells that are present in the liver and then we can actually take a gene from jellyfish that makes jellyfish glow green. We can have that present in the cells and then we transfer them into a new mouse. And the interesting thing is that we can then track where those green cells are in the new mouse and we can find that the cells that were in the lung, when you transfer them into a new mouse and you make them green, you can then spot them in the liver or you can spot them in the brain. And this process allows us to track where these cells are over time
Chris - And what's the purpose of that? Why don't they just go somewhere and stay put. There must be a reason why they are on the move like this. And what do you think the implications of this finding are?
Adrian - I think the fact that they move and they travel from organ to organ might be linked to their role as basically the global policemen, they're looking for spots where the immune system is too active, they're looking for spots where there is too much damage and need to shut it down. And that spot changes over time. Sometimes you might have a twisted knee and you've got a really inflamed knee, the muscle is injured and you need to have more cells in there shutting down the inflammation. Another time you've had an infection with a respiratory virus and the immune system has gone in there and done a lot of damage in the process of getting rid of that infection. And afterwards you need to start healing that lung, try to regain that function. So the place where we need these cells is going to be different all the time. And I think having this population that is basically on patrol across the whole body, it allows you to mobilise the forces where you need the most at the point where you need the most. Now from a therapeutic point of view, this is actually great for medicine because now that we know that these cells can move from organ to organ, we've got the potential to directly push them in the place that we want to go to.
Chris - What, you mean like laying bait to pull them in so that you can allure them into an area where you want to drive the inflammation down? Because they'll come in and they'll exert their peacekeeping role.
Adrian - Exactly. Bait's a great way to look at it. Another way you can look at it is giving them the food that they need. So these cells, the anti-inflammatory cells basically constantly need to be fed. They survive on this diet of a protein called interleukin 2. And essentially if you keep on feeding these cells, they thrive and they do their job. But if you starve those cells even for a day or two, then they die off. Now what we can do is if we want to have more of these healing cells in a particular organ, we can simply add a novel drug that we've developed that can produce more of the food for the cells in that particular organ. So we can take a mouse that has got neuroinflammation, they've got inflammatory problems going on in the brain that are really critically damaging their ability to think. And we can give more of this food for the regulatory T cells so that the cells can then expand up in the brain. And if we do that, what we find is that those cells are able to shut down the inflammation and they can also start actively repairing the brain damage. Now ideally we can then move this into the human context because this is what we ultimately want to do. The reason we study disease in mice is so that we can cure disease in humans.
Chris - People often talk about these regulatory T cells in the context of things like asthma as well. So would one possibility with this or one application of this be you inhale some interleukin 2 food for these regulators and pull them into the lungs where they'll damp down that sort of inflammation and they make people's asthma better.
Adrian - I think that's a strong possibility. The food that we're giving them can be applied in an aerosol. We can give it into their lungs. And if we do that, we see more of these cells build up in the lung. Now the regulatory T cells that we're dealing with, they are really quite potent. They are able to express a whole bunch of different medicines essentially, and they can tackle different inflammation and what they sense is the type of inflammation that's going on. And so they might see a situation where the lungs are damaged by an infection and they can heal that way. But also if they see the damage that's going on in asthma or chronic lung disease, they'll turn on different medicines and start the healing process there.
20:10 - Sampling air for DNA can spot disease arrival early
Sampling air for DNA can spot disease arrival early
Mia Berelson, Earlham Institute
Scientists at the Earlham Institute in Norwich have been sampling DNA in the air to monitor the spread of potentially deadly diseases. The machine - which is called Air-seq - detects bacteria, viruses and other microorganisms more quickly and accurately than other techniques. Used near fields, it might mean invasive crop diseases can be picked up much earlier… I’ve been speaking to Mia Berelson who is a PhD student working on the study...
Mia - So at the moment farmers and growers will mainly use fungicides to protect their crops, but these aren't that great for the environment and also resistance is developing against those fungicide applications so they don't work as well as they used to. So the hope is with this new technology Air-seq, we might be able to better understand what diseases are in the air and therefore protect plants.
Chris - It's also indiscriminate, isn't it? I think if you want to protect your plants, you put these chemicals down whether the plants have got a problem yet or not, and therefore it's inherently wasteful.
Mia - Yeah, it can be guided by the environment and maybe what you see, but ideally you would spray before your plants are beginning to be infected. So we're hoping that we can give farmers a bit more knowledge so they are more aware of what is in the air and if it's at high levels.
Chris - And how are you trying to do that?
Mia - That's where Air-seq comes in. So it's sort of a four stage method. We start by collecting DNA out of the air. So people might not be aware of this, but all sorts of DNA is in the air. You have human skin particles, bits of pollen, but also bits of fungal spores which could cause diseases on those plants. So we use what's called an air sampler and all of that stuff that's floating around in the air, all those particles, are trapped onto a filter. And from that filter we can take all of that DNA, break all of the cells open and then we sequence the DNA. So sequencing the DNA means working out the letters that make up the DNA strand. And if you have that sequence of letters you can see what species it came from and it will tell us what is in the air basically.
Chris - How does it actually work in terms of grabbing those particles from the air? Have you got effectively like a vacuum cleaner sucking air through this thing to grab a sample all the time then?
Mia - At the moment we actually only use them for a couple of hours a week. It's collecting 200 litres per minute of air. In two hours you're getting thousands of litres of air or being trapped onto that filter. So yeah, it's behaving sort of like a Hoover and therefore all of the particles get stuck onto the filter as the air is sucked through it.
Chris - And how sensitive is it?
Mia - It's really difficult to know if that's because the fungal species you found was just really far away. So not much of the DNA made into your filter. It's actually quite difficult at the moment because it's such a new technology to say definitively how sensitive it is.
Chris - Because of course it might be that you don't need very much to then start an infestation in a crop with a very virulent or vigorous pathogen. But on the other hand, things that don't spread very well, you might need loads of them. So can you actually quantify with the experiment as well as sensitively finding things, can you also put a number on roughly how much of it there is in the air to give you some insights into that?
Mia - In my lab group, we currently use relative abundance. So how much of something is in the air compared to how much of other things are in the air. You can sort of see how it's changing over time. If you get a sudden like there's loads of oak pollen in the air, then everything else's abundance would be decreased. So it's not necessarily the best way to do it, but it's the way we do it at the moment.
Chris - And beyond protecting plants, which obviously that's a really important goal, we are worried about food security, we're worried about environmental protection and so minimising our use of things that we don't have to use is important. But could you extend this beyond just crops and use it to look for other things, human diseases or things that might impact animals or the, the physical presence of invasive species or of animals for example, that we want to monitor our shores for the arrival of?
Mia - Yeah, I mean it's already been used to look for COVID, for example, in hospitals. But it can also be used for biodiversity monitoring. So you know, you could go to the middle of the Amazon rainforest and get an idea of what animals are in the area without actually having to go and see them. So it's a less invasive monitoring procedure and also it's a lot quicker because you don't have to traipse around a whole forest. You just could put the sampler in a few different locations.
Chris - And presumably drop them off with drones.
Mia - It's not something that I have done but people who are doing airborne sampling have started using some drones. So you can fly them in and pick some stuff up and then fly them back. Yeah, so it allows you to sample way more diverse landscapes.
Chris - The downside is, Mia, that you're doing yourself out of a job. One of the attractions of doing your job was that you did get to go to the Amazon and now you're coming up with reasons not to. That's a bit of a shame.
Mia - Yeah, I have realised that doing a PhD on wheat and crop pathogens actually means I don't get to travel nearly as much as all these other amazing projects that are out there. Because I just go to the farm down the road.
Chris - I'm sure they'll be grateful though, how long before you'll get some results. That means you will be able to tell farmers what's bothering their crops realistically.
Mia - So we've done a preliminary study in a strawberry greenhouse. And that worked really well because the strawberries were being disease scored so I could compare my data to what was actually being seen. But in terms of actually deploying this in a useful way, I think that's still a fair few years down the line. But we are getting there.
25:53 - How do wind turbines work with such thin blades?
How do wind turbines work with such thin blades?
James - Wind turbines and old fashioned windmills are both designed to capture wind energy, but advancements in technology have led to more efficient designs over time. Here to help me answer your question is professor of engineering at the University of Durham, Simon Hogg. Hello Simon.
Simon - Hello. There are two things that really determine the amount of power that a wind turbine is able to extract from the wind. The size of the turbine, so the swept area of the blade, the circle within which the rotor rotates. The bigger that is, the more air the turbine interacts with, the more power you get. And then the other thing is the amount that the air is deflected. I don't recommend you do this, but if you're driving a car down a road and if you put your hand out the window of the car and then if you tilt your hand such that you deflect the air flow downwards, what you feel is a force on your hand pushing it upwards. And that's in effect all a sail or an airfoil does. It's responsible for deflecting the airflow to create lift. And the extent to which it's able to do that depends upon the careful design of the airfoil. So on modern wind turbines, there's an awful lot of engineering design and innovation that goes into the shapes of the airfoils on the blades that are used in order to maximise the amount that they're able to deflect the air. Whereas on older designs of windmills, they are by no means as efficient. If you look at the blades, they're not aerofoils. They can be sails or even wooden structures, much more basic designs and therefore much less efficient.
James - Interesting. And while I've got you, another thing that will always strike you if you look at a wind turbine is the consistent number of blades. It always seems to be three, whereas in a traditional windmill you may see more. Why is that?
Simon - So imagine that we didn't have to worry about unbalanced effects and imagine that you've had a wind turbine with just one blade on it. Quite a large portion of the air will just pass straight past the turbine through the area where the blade is going to rotate at some point in the future, but not deflected at all. So that's not going to be a good aerodynamic design. But the number of blades you need depends upon how fast the blades are going because clearly the faster the blade is sweeping round, the greater proportion of the air that's flowing through the turbine is going to be affected by that blade. And you may not realise it when you look from the ground, but typically the big wind turbines that you see now when you drive around, the blade tips are going round about 200 miles an hour. So they're actually going very fast. And that's why you only see three blades. Look at aircraft propellers there. You often see two blades, one, sometimes three, sometimes four. It's the same reason.
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