Diamond Podcast - Episode 9 Transript
Meera Senthilingam: Welcome to this July edition of the Diamond Light Source podcast with me, Meera Senthilingam. This month we’ve got a special edition, brought to you from the Royal Society Summer Exhibition, which took place at the London Southbank Centre at the start of the month. We’ll be finding out just what the summer science exhibition is all about.
Peter Cotgreave: It’s for any member of the public to come in and directly interact with people who are doing some of the most cutting edge and exciting science in the UK. So it’s not like watching telly, or going to a museum where it’s mediated by a presenter or curator, you get to interact directly with the people who are doing the cutting edge stuff.
Meera Senthilingam: Peter Cotgreave from the Royal Society will be explaining more about the aims of the exhibition later on. And speaking of the scientists doing cutting edge stuff we’ll also be finding out about the science Diamond has been exhibiting there, including how bacteria in our stomachs could help design personalised diets.
Elizabeth Lowe: They can actually monitor the environment of your gut and tell what sugars you’ve eaten and turn on the right enzymes to digest and use those sugars. But not everyone has the same bacteria in their gut so by knowing how the different bacteria work and which bacteria are in your gut we can predict how they will respond to different things you eat.
Meera Senthilingam: So all that insight, plus hydrogen cars, stressed out bacteria and science in extreme conditions coming up in this July edition of the Diamond Light Source podcast. The Royal Society is the UK’s national academy of science and each year they hold a summer exhibition showcasing some of the UK’s cutting edge scientific research. This year however is slightly special as it’s their three hundred and fiftieth anniversary. So the exhibition has been turned into a bit of a festival and took place in London’s Southbank Centre. I spoke to the Royal Society’s Director of Public Relations Peter Cotgreave to find out more.
Peter Cotgreave: Well the great thing about the summer science exhibition it’s for any member of the public to come in and directly interactive with people who are doing some of the most cutting edge and exciting science in the UK. So it’s not like watching telly, or going to a museum where it’s mediated by a presenter or curator you get to interact directly with the people who are doing the cutting edge stuff.
Meera Senthilingam: And what’s special about the fact that’s it’s the Royal Society’s one?
Peter Cotgreave: Well the Royal Society is all about excellence in science so the exhibits here today have been chosen by a committee of the Royal Society really to represent a nice broad spread of what is really really the cutting edge what is really happening in British science that is exciting today.
Meera Senthilingam: Now the exhibition takes place every year usually at the Royal Society base but this year it’s special, it’s at the Southbank Centre so this is all in honour of the 350th anniversary?
Peter Cotgreave: That’s right, it’s the 350th anniversary of the Royal Society and we thought rather than have the exhibition in the society as we always do and we always get thousands of people coming, we’d bring it here to Southbank Centre where tens of thousands of people will just bump into science. They will be here anyway, they don’t think they want to go to a science exhibition but when they come here they love it and we’ve had people coming back actually day after day because they can’t get through it all in one day, it’s been absolutely fantastic.
Meera Senthilingam: Actually, that’s definitely something I’ve picked up on because I come here quite a lot and people have just been in the café and seen that’s something’s going on and come for a stumble.
Peter Cotgreave: That’s exactly right, tens of thousands of people just come here for a meal, or drink, or a meeting, or some other kind of event and this week their bumping into science while they’re here, learning about science and interacting with scientists.
Meera Senthilingam: As well as the new location what else is different or special about this year’s exhibition?
Peter Cotgreave: Well this year’s exhibition is part of a wider festival so we’ve got the exhibition here, its bigger than it normally is we’ll get more people through but also, here in the Royal Festival Hall and the other Southbank Centre venues we’ve got music concerts, performances, conferences all sorts of things going on around the exhibition so there’s a whole ten day long festival of science and art.
Meera Senthilingam: What would you say some of the highlights then have been so the events as well as some of the highlighted stands?
Peter Cotgreave: What has been a real highlight for me is that there have been very artistic performances, the first ever performance of ‘2001 a Space Odyssey’ with a live orchestra playing the music, that was at the beginning of the festival. Mixed with conferences, so a conference for young people called ‘Tomorrows Giants’ about the future leaders in science. All of these things juxtaposed with one another so that everyone whether they’re a little kid or a scientist who’s really into their field or a young scientist who wants to really get into their field can get something out of it. So that I think is what’s been the real highlight of the whole festival for me. They are all trying to engage people so they can get a flavour of what science is like and then maybe when they go away they might want to get more involved, if they’re a child they might want to get more involved in doing science, if they’re an adult they might want to come to some more science events or read some science books or whatever so that’s what we’re hoping to achieve.
Meera Senthilingam: Peter Cotgreave there, the Royal Society’s Director of Public Relations discussing the aims of this year’s bigger exhibition, and as Peter mentioned the exhibition showcases cutting edge science in the UK, an area where Diamond plays a large role. From previous podcasts we’ve learnt about the great variety of science taking place at the synchrotron. So which of these many areas of science were represented at their stand at the exhibition? Here’s Laura Holland from Diamond’s communications team.
Laura Holland: Well on the Diamond stand we’ve got information about what we do, how the machine works, why we generate the light and we’ve also got people who use the light so we’ve got users from Newcastle, Warwick, Imperial, Edinburgh and Nottingham all talking about the science they do using Diamond so why they use it their research and why it’s important.
Meera Senthilingam: Have there been any good demos that they’re all using to explain a bit more about what they do?
Laura Holland: Yes, they’ve all brought some really amazing cool stuff actually. Edinburgh’s got demos talking about pressure so they’ve got vacuum demos, they’ve got marshmallows they’ve got a bed of nails for some reason. The guys from Warwick have had really lovely model made showing the brain and the different areas they’re looking at. We’ve got model proteins, fluffy microbes. We’ve got all sorts of things!
Meera Senthilingam: Is it true at the weekend there’s been a hydrogen car?
Laura Holland: Yes it is. A real hydrogen powered car, definitely yes, they were electrolysing water and using the hydrogen made by that to power their little car along. So they were showing that it is possible now but maybe not practical to carry.
Meera Senthilingam: And how far, did the car move much? Did it go very fast or what was it like in action?
Laura Holland: It was much like any remote controlled powered car so they were showing that it’s a fuel source like any other. So it pootled around the floor and bumped in to things. Yeah it’s a completely normal fuel source so you can use it like any other it’s just storing it is the problem. Its showing it’s a great fuel source just maybe not a very practical one unless they find better ways of storing it.
Meera Senthilingam: Which is what they’re trying to do at Diamond?
Laura Holland: Exactly, so they’re using what they call metal organic frameworks so new chemical compounds they’re trying to make that will store hydrogen in its structure and they can store it at much higher volumes than you can at room temperature and pressure without using a big high pressure vat.
Meera Senthilingam: So there’s a lot going on here, so they are looking into brain activity for particular diseases and proteins and as we just discussed hydrogen storage so what’s the reaction been like from visitors?
Laura Holland: I think visitors have all been really impressed that you can do so many things using a particle physics facility, I don’t think people realise maybe that particle physics had so many applications in the wider world.
Meera Senthilingam: Laura Holland from Diamond’s communication team giving us a taster of what Diamond had to offer at the exhibition.
Meera Senthilingam: You’re listening to the Diamond Light Source podcast and this month we’re giving you Diamond’s highlights from the Royal Society’s exhibition which took place at Southbank Centre at the start of July we’ve had an overview of the types of science showcased by Diamond but now we move in a bit closer and on to a smaller scale. One scientist showcasing her work was Elizabeth Lowe from the University of Newcastle who works with the friendly bacteria in our gut.
Elizabeth Lowe: So we look at sugar usage by gut bacteria so the friendly gut bacteria that live in your gut all the time. We look at how they can use the carbohydrates that you eat in your diet and how they can utilise those for energy.
Meera Senthilingam: So what kind of bacteria do live in your gut?
Elizabeth Lowe: Well there’s a lot there’s actually ten times more bacteria in your gut than cells in the human body. But the one that we work on is bacteroides so there’s quite a lot of different species of bacteroides and they can all respond and use different sugars.
Meera Senthilingam: So what’s important say about looking at the responses of these bacteria to sugars then so they would obviously respond differently to different things in your diet?
Elizabeth Lowe: They can actually monitor the environment of your gut and tell what sugars that you’ve eaten and turn on the right enzymes to digest and use those sugars but not everyone has the same bacteria in their gut so by knowing how the different bacteria work and which bacteria are in your gut we can predict how they will respond to different things you eat.
Meera Senthilingam: So how do you set about actually looking at these bacteria, what do you look in to?
Elizabeth : Okay so we have the genomw sequence of a lot of them and if you look at the different genes in the bacteria they’re sometimes grouped into collections of genes that are all expressed together and might have similar functions. so sometimes in one these groups that we call a locust it has enzymes and also proteins that we think are on the outside of the bacteria and the bacteria use them for binding the proteins and sugars in the environment and bringing them into the cell so it can use them. We identify the proteins from the genome and then we try to make a lot of them and look at what sugars they might bind and also try and grow crystals out of them and take them to Diamond and see if we can solve the structure and see if that tells us anything about how they work.
Meera: So how do you actually look in to them at Diamond then and what are you able to see how they work?
Elizabeth: So using Diamond we can see the actual molecular structure using X-ray crystallography we can see the structure of the protein, we can crystallise them with sugar so we can see actually where the sugars bind, and if the binding of the sugar has any effect on the shape of the protein and what it does when it binds to the protein.
Meera : How clear is the picture then that you get of this activity?
Elizabeth: It depends on the protein but some of the ones that we’ve got here we managed to get really high resolution data for the proteins so we can see at the atomic level exactly where things are binding and exactly what the proteins look like.
Meera: Now you mentioned then that you can then know about the different species of bacteria and know different people have different quantities of each in their stomach so how can you identify for a personalised nutrition in the future knowing what bacteria different people have?
Elizabeth: The projects at the moment called the human microbioium project which they’re sequencing huge amounts of bacteria in certain people to see what bacteria are there but obviously that’s a very early stage because there are so many billions of bacteria it takes a long time and they’re developing ways of sequencing a lot of things at the same time or just sequencing small amounts which enables you to identify a whole bacteria from just a small bit of DNA just to speed everything up but it is a future not a current technology.
Meera Senthilingam: And having looked into the different proteins and the binding so far with your work what have you found?
Elizabeth: Well we found out about different species of the bacteria called bacteroides and how they respond to fructans, which is a type of sugar containing fructose, so there are two different types called inulin and levan and most bacteria grow very well on inulin but we’ve found that one of ours, even though it looks very similar and has nearly exactly the same genes, it doesn’t use inulin at all, but it uses levan. And if you look at it on a broader scale it looks like it should behave exactly the same, but actually at the molecular level it’s really different. And we found that using Diamond to look at the structures.
Meera: So this can then hopefully be applied then to enhance this particular gut bacteria?
Elizabeth: Yes, that’s the plan!
Meera: So could you give an example about how sugars that are known about so far, say, as you’ve mentioned inulin, what, say, uses they’ve had or how they’ve been used to potentially increase someone’s gut bacteria so far?
Elizabeth: Inulin is used in a number of yoghurts and drinks as a prebiotic – there’s probiotics that have other bacteria added in to them but prebiotics often contain sugars which are going to be good bacteria and they are known to use well. Inulin is in a number of these.
Meera: And I imagine this is useful if say, someone has just had a course of antibiotics then in order to reproduce their gut flora.
Elizabeth: Yes, that’s the plan.
Meera: What would you say then the overall aim is of doing this work?
Elizabeth: Understanding what the gut bacteria are mainly, because there is a huge population of bacteria and their effects on human health are widespread and we probably don’t even understand a fraction of how they work. It’s like a whole other organ, so understanding how they respond and molecularly, how they work, is key to human health.
Meera: Elizabeth Lowe from the University of Newcastle. And staying on the topic of gut bacteria I also met Jon Marles-Wright, also from Newcastle, who works with stressed out bacteria.
Jon Marles-Wright: So I work on stress response in bacteria, so this is how bacteria respond to changes in environment on a basic level. So the bacteria we work on live in the soil, so they respond to changes in the soil concentration and respond to changes in the PH of the soil and how they respond to light levels, so how they respond close to the surface of the soil to the UV light from the sun. So these bacteria have a special sense organ, a protein complex that’s inside these bacteria that has sensory modules that respond to different stimuli. So they have modules that respond to different salts, modules that respond to alcohol, strangely, and modules that respond to light. And this particular complex, it then takes these signals and activates a cascade which leads to the expression of over 200 genes.
Meera: So what type of bacteria are these?
Jon: So the particular bacteria we’re working in is Bacillius subtilis which is a soil bacteria, but these complexes are found in hundreds of different bacteria species, ones that live in the sea, ones that live in your gut, and other ones that live in really extreme environments such as the radiation resistant bacteria.
Meera: And this particular complex you’re talking about that responds to is called a stressosome?
Jon: Yes, it’s called a stressosome because it’s a big protein complex that responds to stress.
Meera: What do you know so far then in terms of how this functions for the bacteria to respond to these stresses that you’ve mentioned, such as light or particular chemicals?
Jon: So we know the complex consists of a number of different molecules that respond to stress and other molecules that signal the stress, and we know its structure, we know it has these sensory domains and we know it has these signalling domains, it’s actually how these things fit together.
Meera: How do you set about looking into this?
Jon: We’ve used Diamond Light Source to look into the individual components of this structure. We’ve got the X-ray crystal structure. We’ve also used cryo-electron microscopy, which looks at larger complexes and we’ve been able to fit the data we’ve got together to build an atomic model of these complexes.
Meera: So can you visualise what’s going on or is it more a theoretical idea of what’s going on and what it looks like?
Jon: So what we have is a static view of the molecule in this state before it senses stress. So we have a view of the resting complex before stress. What we want to do it take the research we’ve got and look at how it changes in response to different stresses.
Meera: So what have you managed to find out so far then, how does it respond to particular stresses?
Jon: So what we have so far, this is mostly biochemical evidence, that it responds more like a dimmer switch than an on/off switch, so it responds to different levels of stresses, by activating a different level of response.
Meera: Why do you think it does this, and how is it actually all controlled, to tame, or kind of control these responses?
Jon: So what we think is happening, because the responses are very big responses, there are over 200 genes transcribed because of its action, if you’ve got a small level of stress you don’t want to subscribe huge amounts of these different genes, but with a large level of stress you want a proportionally larger response. So that’s why we think it’s tuned like a switch.
Meera: And how crucial would you say this is then to the survival of the bacteria?
Jon: So in the soil bacteria we study, without this complex they basically can’t survive in the wild. In the other bacteria we can only speculate that it’s very important for changes in the lifestyle, so one of the bacteria is anerobic, but if it experiences oxygen it really needs to change its lifestyle very quickly. So it has an oxygen sensor on it which we think is really key to this change.
Meera: So it’s all very clever really, taking place in these miniscule bacteria, but knowing how they survive in these environments is one thing, but how can this knowledge also be used in, say, for particular applications?
Jon: So if we know how these bacteria can respond to different signals we might be able to change the signals in the molecules themselves and elicit very specific signals or change the downstream response to these stresses, say to produce a specific drug or a specific module as an activating signal.
Meera: So if you can understand how particular signals are set off you can use these to thrn tune in drug production or other applications, so basically you can kind of tune how much of a drug say is produced, or something like that?
Jon: Yes, or we could, say, design a bacteria that responds to an environmental stress and maybe change its colour, so the level of colour change in the bacteria is indicative of exactly how much of this particular molecule is in this environment.
Meera: What’s the kind of current stage or what’s the next step in this research?
Jon: So at the moment we actually looking at the changes in the proteins themselves on the introduction of the stress signal, so we’re looking at what the molecular differences are between the resting state and the activated state of the protein, to really look at how it’s working.
Meera: Jon Marles-Wright from the University of Newcastle explaining that it’s not just us humans that lead stressful lives as some bacteria are constantly fighting for their life. So we’ve heard some of the biological science Diamond had on display, but what about the chemical and physical sciences? One scientist batting for that team was Jenny Rogers from the Centre for Science at Extreme Conditions at the University of Edinburgh who, as her institution name suggests, does some extreme science.
Jenny Rogers: Ok, so my main focus is using high pressures and temperatures to synthesise new materials. So I run a large volume press, that’s a massive machine that’s about 2 m high and weighs about 9 tons and can produce a forces of about 1,000 tons, so we can generate pressures of about 100,000 atmospheres, which is equivalent to about six elephants all balanced on top of each other and the bottom elephant wearing a high-heeled shoe, and the pressure at the high heeled shoe point, that’s the kind of pressure we can generate with the machine I run.
Meera: So that’s an extremely high pressure, but what are the benefits of looking at materials at these pressures and conditions and what kind of materials do you look at there?
Jenny: So the exciting thing about using high pressure is that we can access materials that we can’t access using normal pressures. We’re just trying to make new stuff basically! So we squeeze and heat metals and oxides together and then with the large volume press we make enough, say 10 – 20 mg so we can recover them and then do property measurements on them, say do electronic measurements or magnetic measurements, and so one of the groups of materials we’ve been working on recently are a group known as superconductors. One of the properties these have is that when you pass a current through them they have zero resistance so basically you don’t lose any energy as heat. So obviously if you can have a superconductor at room temperature it would be fantastic because you could send electrical currents through wires and not have any energy getting lost. But the superconductors we’ve been looking at work at much lower temperatures but they’re still really interesting materials, not that much is understood about them so it’s always important to work on these materials.
Meera: So what kind of materials are these superconductors made of?
Jenny: So the ones that we’ve been working on are actually made up of a mixture of iron and arsenic and some other elements in there as well, so they’re maybe not so user friendly, but they are very exciting! The first one was discovered a couple of years ago by a group in Japan and since then there has been worldwide excitement would you believe around chemists and physicists trying to make this new iron / arsenic superconductors.
Meera: So I can see it’s so obviously so beneficial to be able to conduct electricity with minimal energy loss, but as you’ve mentioned it is at particular pressures that aren’t ambient, how can it possibly be adapted then to be used?
Jenny: So actually the materials I’m making with the large volume press can be recovered to normal pressures, so these properties remain at normal pressures, we just use the high pressure to synthesise the materials.
Meera: So how is this studied at Diamond, what can you actually see about the particular superconductor?
Jenny: Sure, we use Diamond Light Source to give us information about the structure of the materials that we’ve made, so we can use these ultra high energy X-rays and they will bounce off the atoms and tell us information about where the atoms are. So we can find out more information about the structure that’s related back to the property measurements that we’ve made back at the lab. We also have people working at the Centre for Science at Extreme Conditions that take along what is known as a Diamond anvil cell, so that’s two diamonds and they have points that are pointed towards each other. And basically we squeeze those diamonds together and generate very high pressures so they can do experiments at the Diamond Light Source where they are looking at what’s happening to materials under pressure so they start to squeeze it and see the changes that start to happen as you squeeze something. So for example oxygen has about six different forms, so as you squeeze oxygen at high pressures it actually turns into a red crystal, an amazingly beautiful red crystal, so there’s some really cool things that happen at high pressures!
Meera: So how high a pressure are we talking here?
Jenny: I think oxygen goes to a red crystal at about 170,000 atmospheres, so it’s pretty high.
Meera: So that’s quite a wide range of things, you’ve got superconductors, you’ve got oxygen in it’s different forms, what other areas of science could be looked at at these extreme conditions?
Jenny: So there are lots of other areas, for example there are some groups in the UK that are looking at ultra-hard material at high pressure. A well known example of this is diamond itself, so if you squeeze graphite so if you apply a high enough pressure, so 50,000 time atmospheric pressure and then heat it to about 2000 degrees Celsius you can transform graphite into diamond and diamond is of course an incredibly hard material and diamond is the hardest naturally occurring material and what we’re doing there is mimicking conditions deep within the Earth and replicating them here on Earth.
Meera: Now part of being here at the Royal Society Summer Exhibition is about engaging the public, so we’ve got a few hands-on demos here to explain a bit about your work. So I’m seeing here a wine bottle filled with marshmallows – what’s this about?
Jenny: Exactly, so marshmallows are made up basically of sugar and air, and what we’re going to do is use a vacuum pump, so this is just used to keep wine good actually! And what we’re going to do is remove the air from the wine bottle and see what happens to the marshmallows. So I’m going to pump the air out … [pumps] … and hopefully you’ll see as we take the air out the marshmallows are expanding. That’s because we’re removing the air particles and there’s more empty space – we’re creating a vacuum and there’s more space for the remaining air particles and they are increasing in size and what we’re going to do is allow some of the air back in so we’re going to increase the pressure again …
Meera: And you heard the air just there go back in!
Jenny: And the marshmallows have shrunk quite considerably back down in size.
Meera: And it was very instant, so quite a quick demo as well.
Jenny: Yes, it’s quite as fun demo, a nice one, and you can try it at home. But the key to getting the marshmallow in the wine bottle, top tip, is to use cornflour, otherwise the marshmallows will stick to the side of your bottle! But it’s a good one to try at home.
Meera: So what would you summarise are the benefits of looking at materials at high, extreme conditions?
Jenny: Lots of different benefits depending on the area. One area of research is looking at pharmaceuticals under pressure, so as you squeeze something the atoms rearrange and often have quite different properties. So for example, Professor Colin Pulham has been looking at paracetamol under pressure and found that the molecules rearrange and the stacking rearranges and the idea would be that that might have different properties, so different absorption properties so maybe the drug might be absorbed better so the pharmaceutical industry are interested in very high pressure measurements too.
Meera: That was Jenny Rogers from the University of Edinburgh. Now that’s almost it for this addition of the podcast, but before we go, I also had a chat to members of the public that were visiting Diamond’s stand to see what they thought.
Child: I think it’s really good and it will get children excited about science with all these, like, things that you can get here, and the activities are really like, when you do this…
Meera: So you’re making a magnet levitate there aren’t you? Were you expecting it to do that when you put it on top?
Child: Well, yeah, because they are the same poles so this will make them levitate.
Meera: And so what interests you about science, what bits have you found really exciting? Is it the universe?
Child: Well yes, cosmology and physics and chemistry.
Visitor 1: I just learned many things, like this one.
Meera: So we’re here at the Diamond stand now and you’ve pointed out the X-ray bit over here that’s caught your eye, so what’s particularly interesting about that, or what have you enjoyed?
Visitor 1: Some good diagrams.
Meera: What have you learnt about what they do at Diamond?
Visitor 1: I just learnt about how the joints work and secondly I just learnt like what can use for our surgery for joints.
Visitor 2: I’m really really very surprised that you can look at the investigation of the universities and you understand everything. Here for example they show us that materials change with pressure and temperature and how they investigated making new materials for example.
Visitor 3: I knew it existed, in fact I had seen it from an aeroplane once and I didn’t know what it was, I thought it was a stadium or something and I looked it up and discovered it was an accelerator.
Meera: And so what have you learnt today about how it works or what’s done there.
Visitor 3: Well they explained to me the basic thing it does, which is that it’s an accelerator, looks like an electron accelerator, and the accelerator produces X-rays which here are called light, which is a bit confusing.
Meera: What’s your kind of interest in science usually, do you tend to come to these kinds of exhibitions a lot?
Visitor 3: I trained as a scientist and now I work in IT, so it’s good just to come back and see what’s going on and what is interesting out there, and it is amazing actually.
Meera: So the exhibition has clearly sparked some interest in children as well as adults. Now that is it for this edition of the Diamond podcast brought to you from the Royal Society Summer Exhibition, but do join us again in September when we’ll be investigating the environmental sciences. In the meantime if you have any questions about Diamond about the research taking place there the email address is firstname.lastname@example.org. You can also listen to previous editions of this programme online at www.diamond.ac.uk/podcast or www.nakedscientists.com/diamond. You can also subscribe to the podcast on itunes. Now thank you this month to Peter Cotgreave, Laura Holland, Elizabeth Lowe, Jon Marles-Wright and Jenny Rogers. I’m Meera Senthilingam, thank you for listening and speak to you in September!