Episode 2 Transcript

Introduction: From Diamond Light Source, this is the Diamond podcast.

Meera Senthilingam: Welcome to the Diamond Light Source podcast. This second edition of the podcast will be a special insight into the life sciences. We’ll be finding out what Diamond got up to at the American Association for the Advancement of Science conference, or AAAS, as well as finding out how Diamond is revolutionising biomedical research.

Martin Walsh: This really is an exciting opportunity for cell biologists as it will allow them to illuminate a single cell with the micron sized infrared beam that the beamline will produce.

Meera: Martin Walsh will be telling us about the beamlines coming soon to Diamond that will allow scientists to understand more about human cells. We’ll also be investigating how to design drugs to target and combat specific diseases.

Stephen Curry: If you want to design or develop a drug which will stick very precisely, very specifically to your target then it’s very helpful to have a detailed picture of what it looks like.

Meera: Stephen Curry will be explaining how he’s used X-rays to visualise the virus behind foot and mouth disease. And moving from farm animals to humans, Joanna Collingwood will be discussing how monitoring iron levels in certain cells in our brain could help us understand more about Parkinson’s disease.

Joanna Collingwood: We know that typically 80% of these particular cells will be lost in Parkinson’s disease and we also know that the concentration of iron in these cells is significantly higher in Parkinson’s patients than in comparable healthy brains.

Meera: But how can monitoring iron levels help treat this condition? I’m Meera Senthilingam and this is the Diamond Light Source podcast.  

Voiceover: This is the Diamond podcast. For more information look us up online at www.diamond.ac.uk/podcast.

Meera: Before we take a look at how Diamond is helping the life sciences let’s join Sarah Bucknall from Diamond’s Communications team to find out what Diamond’s been up to over the past couple of months.

Sarah Bucknall: Well it’s been a really busy time at Diamond – in February we were at the AAAS in Chicago, that’s the American Association for the Advancement of Science, they had their annual meeting. Lots of people go along to hear about the latest scientific research.

Meera: And so what did Diamond get up to there? 

Sarah: Diamond took part in two scientific sessions, they did one all about the latest health research at Diamond, which was called Bright Light for Better Health, and they also took part in a collaborative session with other light sources which was called Casting New Light on Ancient Secrets.

Meera: And what was involved with Bright Light for Better Health?

Sarah: We had our Life Science Director, Professor Dave Stuart, and two of our users, Professor Keith Meek from the University of Cardiff and Dr Joanna Collingwood from Keele University, they each gave a talk about their latest research which they’d carried out at Diamond. Professor Stuart was talking about the latest development in the study of viruses, Professor Meek was talking about his research into the cornea and how to improve laser eye surgery. 

Meera: And so going back to what they found out about viruses, what were the developments there?

Sarah: Well Dave Stuart actually unveiled the structure of a protein from the Vaccinia virus which was a large complex virus that was used as the vaccine to eradicate smallpox.

Meera: What did they actually discover about it?

Sarah: They discovered that although it’s a complicated member of the pox virus family it’s actually related to a large number of simpler viruses, which shows Darwinism at work, in providing clues as to how viruses have been evolving.

Meera: So you mentioned that Professor Keith Meek from Cardiff was also there, talking about his work on the cornea? 

Sarah: That’s right, he was looking at the structure of the collagen in the cornea, and this can relate to an eye disease called keratoconus, where the collagen is laid out differently to that in a normal eye. So this is really important research because their findings may be able to improve corneal surgery, and also advance the technology of laser eye surgery.

Meera: What was the second session that you did at the AAAS?

Sarah: So this one was called Casting New Light on Ancient secrets, this was actually a group session with other light sources, some in America, some in Europe, and one of our scientists was speaking there, Dr Jen Hiller. And she was talking about a new beamline that we’ve got coming up this year or next year, and how that can be used for cultural heritage science.

Sarah: This is the Joint Engineering and Environmental Processing beamline, JEEP for short, it uses X-rays mainly for engineering research but the beauty of it is that it will have a really large experimental hutch, which means for example large engineering components can be brought in, as opposed to really small samples. This is of benefit to the cultural heritage scientific field because they can actually bring in fully formed artefacts and scan them with our X-rays to create the picture that they need to see.

Meera: Ok, well it sounds like Diamond have been very busy at the AAAS, but as well as unveiling all this exciting science you’ve also been a bit creative, and you’ve got an art project going on at the moment?

Sarah: Yes, that’s our World’s Largest Diffraction Pattern. It’s actually a textile project and we’re asking lots of people to contribute, just simply by adding a cross-stitch. It’s basically creating a pattern like some of the ones we collect on our beamlines. This particular one was collected by a company called Evotech who use Diamond. The nice thing about this is that so many people who are interested in Diamond wanted to take part and add a stitch. The next time it is available to the public is at our Inside Diamond Day, on 23 May.  

Sarah: It’s a day when we basically open up to the public, and to give them the opportunity to have a look around, to meet some of our staff and just to get to know a bit more about Diamond really.

Meera: And then people can come along and add a few stitches to the pattern?

Sarah: Definitely! People have to register to visit but it is free, and if they just go to our website they can find out more details about coming along to Inside Diamond.

Meera: Thanks Sarah. Diamond’s Sarah Bucknall will be back with some more of the latest news from Diamond in the next podcast.

Now this month we are finding out how Diamond is supporting the biological sciences. So now we hear from Life Science Coordinator Martin Walsh about how the beamlines created by the synchrotron can help us find out more about living organisms.

Martin: At Diamond one of my roles as Life Science Coordinator is to engage with the UK community to promote the unique capabilities of the Diamond synchrotron. In particular our aims are to encourage the development of new experiments at Diamond which can aid life science research in the UK and provide the infrastructure for biologists to answer important biological questions that can further our understanding of life at the molecular level.

Meera: And so how would a biologist use a synchrotron to answer their questions?

Martin: Well the synchrotron itself produces electromagnetic radiation over a wide range of energies and this spans through infrared to ultraviolet light and finally to X-rays. We can use these different forms of light to answer fundamental biological questions. A good example would be in understanding the role of proteins. Proteins are essential molecules in all different organisms, so by using Diamond biologists are able to visualise the structure of these proteins, which aims at understanding their function and how they work in the cell. Other techniques provide essential tools for cancer research for example. We’re able to allow biologists to image single cells, and this can provide the basis for the development of new methods for identifying normal cells as opposed to cancerous cells, and this can aid researchers in understanding cancer.

Meera: But there are lots of different beamlines at Diamond, so which do you use to look at things like proteins and cells?

Martin: Initially in the first set of beamlines that we have here at Diamond there are three beamlines which have been dedicated towards using crystallography. This is a technique where we use X-rays to interact with biological samples, such as proteins. Amazingly biologists are able to grow crystals of proteins, which can actually be considered as beautiful, and as expensive, as diamond crystals, although protein crystals are usually only tens of microns in size. Now when these crystals are placed in the path of the X-rays at the Diamond beamline they interact with the X-rays and produce a characteristic pattern that we can use to understand the structure of the protein under investigation. Once we have the structure of the protein scientists can use this information to, for example, design drugs to interact with the protein and interfere with it’s function, which could then lead to new therapeutics for preventing a specific disease which that protein is involved in.

Meera: Now you mentioned that you are using X-rays to study these biological functions, but why do people have to use the X-rays at a synchrotron, why can’t they just use something like a hospital X-ray machine?

Martin: Yes Meera, that’s a very good question. The synchrotron is a very specialised machine that produces X-rays that are a billion times more intense than an X-ray source. At a hospital the X-rays are typically quite weak so they don’t actually harm our bodies, and also they cover a very large area, whereas at Diamond we have built a series of beamlines which direct or focus the very intense X-rays that we generate at the synchrotron to a very small area, typically of the order of microns in size. Now by doing this we’re able to have a very intense micron sized beam which then enables the scientist to image the cell and its component parts.

Meera: Is it just X-rays or can you use other forms of synchrotron light as well?

Martin: We also have an infrared and a UV light that we generate and these can also aid biologists in understanding cellular processes. A new beamline that’s coming online at the moment is the circular dichroism beamline and this uses ultraviolet light. One of the things that this beamline will allow us to do is measuring the interactions between proteins and drugs. By measuring these interactions we should be able to aid in the development of new drugs for fighting human disease.

Martin: Yes, we also have an infrared beamline that’s currently in construction at Diamond and this really is an exciting opportunity for cell biologists as it would allow them to illuminate a single cell with the micron sized infrared beam that the beamline will produce. The interaction of the infrared light with the cell will produce a characteristic spectrum from the cell and we can use this spectrum or pattern in a somewhat analogous way to fingerprinting. What I mean by that is that we can build up a library of patterns from healthy cells and we can use this library to identify markers for abnormal or unhealthy cells or, for example, cancerous cells. The final goal would then be to use this technique to apply it to a treatment therapy, for example chemotherapy.

Meera: But chemotherapy is a therapy that’s already used to fight cancers, so how can this make the therapy better?

Martin: The idea is that by using this technique we can follow the chemotherapy treatment and looking at the markers to see if the cells are still cancerous or not, and the really exciting thing here is that hopefully in the future we should be able to refine a treatment regime on a person by person basis.

Meera: So essentially this infrared will allow clinicians to see if a particular patient’s cancerous cells have stopped being cancerous as a result of the chemotherapy and therefore the chemotherapy can stop?

Meera: Now it sounds like there is a lot going on at Diamond already, is there more to come in the future as well?

Martin: Yes Meera, well at present we have seven beamline operational at Diamond, there is another 10 beamlines coming online and in the next 5 years we intend to build another 10 beamlines which will offer a huge range of techniques to both the physical and to the life sciences and will aid in imaging the human body. 

Meera: That was Diamond’s Life Sciences Coordinator Martin Walsh explaining how X-rays, UV and infrared light can help scientists find out more about living organisms, reigning from virus interactions to monitoring chemotherapy treatment on cancerous cells.

Voice over: Did you know that Diamond is so powerful it produces more light than 100 million suns?

Meera: We’ve had an overview of the role that synchrotron light can play in biological research, so now we delve a bit deeper, to the miniscule world where proteins can be visualised – in particular, virus proteins. Foot and mouth disease is a highly contagious virus affecting cloven-hooved animals, which has had a dramatic affect on livestock throughout the world. Vaccinations are available to control the disease, but this involved injecting the animals with inactive virus particles to trigger an immune response, and then it becomes difficult to identify which animals have the disease. So in order to be able to trade animals worldwide farmers can’t use the vaccine continuously. In countries like the UK these vaccines are mainly used during an epidemic, to control its spread rather than to cure the disease. But the vaccines also take a few weeks to kick in. So now, Stephen Curry from Imperial College is trying to create a drug that can be taken by infected livestock that will target the virus and stop it from replicating, so the disease can be stopped more immediately whilst waiting for the vaccine to build up an immune response. He told me more about how the virus works.

Stephen Curry: It’s a mammalian RNA virus, it’s a small sphere made of protein which contains a single molecule of RNA. And that piece of RNA is basically a little messenger piece of RNA which is used to make proteins, so once it gets into the cell the virus immediately starts to make proteins. It starts to re-programme the cell to make new virus particles.

Meera: And so what are the current treatments for foot and mouth disease, or prevention?

Stephen: There’s no particular method for treatment I’m afraid. The main method of prevention is vaccination.

Meera: Now with your research you’re trying to design a drug to control foot and mouth in addition to someone using a vaccine, so you’re focussing on a particular protein that is used by the virus, what are you focussing on?

Stephen: Well we are focussing on the so-called 3C protease from the virus, and this is a very important component of the virus replication machinery, the machinery that it needs to make copies of itself inside an infected animal and inside an infected cell. So when the virus delivers its RNA to the inside of the cell that little piece of messenger RNA starts to programme the cell and it basically tricks the cell into starting to make virus proteins. Now the virus genes are actually rather simple because the virus only carries a single gene in its messenger RNA and that single gene is translated as one great big long poly-protein but before that poly-protein can be put to use it has to be cut up into individual pieces and those individual pieces then become the functional proteins that work together to make new virus particles. And the 3C protease is another protein that’s embedded in that poly-protein and it actually does the job of cutting up the poly-protein into individual bits. The idea is that if you can prevent the protease from cutting up the poly-protein then you stop the replication process at a very early stage and you basically prevent the virus from going any further and that would prevent the replication and the idea then is that it would prevent the spread of the disease.

Meera:  So in order to help you design a drug to target this you’ve been trying to visualise the actual structure of this protein

Stephen: So that’s right, we use a technique known as X-ray crystallography to work out a very detailed picture of what the protease looks like. And the great advantage of this method is that it gives us a detailed 3D depiction of the protease in more or less atomic detail. And if you want to design or develop a drug, a very specific chemical, which will stick very precisely and very specifically to your target, in our case the 3C protease, then it’s very helpful to have a detailed picture of what it looks like.

Meera: So how does X-ray crystallography work, to enable you to see the protein?

Stephen: The first thing that we need to do is make very large quantities of the protein that we are interested in studying, by which I mean we need a few milligrams, and we then have to crystallise that protein and so by crystallising you get the molecules to line up into very orderly rows, and then the rows stack together to form sheets and the sheets stack together to form a sort of array of molecules. And when you shine X-rays at your crystals you find that the crystals actually split the X-ray into many hundreds of different rays which you can then record the position of on a detector. So the image that we see on our detector is basically a whole series of spots and mathematically we know that that pattern is very precisely to the structure of the molecule that’s inside the crystal. Basically we have a three dimensional picture of what the molecule looks like.

Meera: What do you know about the areas you can now target the drug to?

Stephen: We already now have an initial structure of the protease and more recently we have solved the structure of the protease as it’s grabbing on to a piece of protein just before it’s about to cut it, and now we can see not only the structure of the protease but also what it’s doing just before the moment that it cuts the piece of protein that it’s designed to target and so we learn a lot about the chemistry of the interaction. And that information we can then use to think about rational drug design because a drug is very often a molecule that mimics the natural substrate of the enzyme reaction.

Meera: So essentially you want to create a drug that mimics the area that the protease attaches to before it starts cutting, so that the protease would bind to the drug instead so the protease wouldn’t be able to start its cutting?

Stephen: Yes that’s exactly right, and one of the challenges of good drug design is to try and find an inhibitor molecule that binds very tightly to the target, in our case the 3C protease, because if the interaction is not very strong it means that you then have to give very high concentrations of the drug in order to have it work properly.

Meera: Now if you do actually manage to find an effective drug, what will the strategy be?

Stephen: If you do manage to develop an effective drug against foot and mouth, one would probably target it to countries which are normally disease-free, but when an epidemic breaks out of course all hell breaks loose and you want very quickly to damp down the source of infection to prevent the spread of disease, and we would envisage using a drug in that initial window when an outbreak happens in order to control the disease.

Meera: So visualising a virus protein can help us target more specific drugs to stop the virus in its tracks. That was Stephen Curry from Imperial College London. Now moving from the farm to the human brain to disorders affecting our brain. Parkinson’s disease is a neuro-degenerative disease affecting over 120,000 people in the UK, and many millions worldwide. It’s caused by a loss of cells in a particular part of the brain that produces dopamine which is important for coordinating our movements. Scientists have long thought that the death of these cells could be linked to high levels of metal particles, particularly iron in this region. So Joanna Collingwood is analysing samples of autopsy tissue in patients who had the disorder to see whether iron levels really are higher, and how research can be then be used to catch the condition at an earlier stage.  

Joanna Collingwood: Well we’re looking at two forms of brain disease, namely Alzheimer’s disease and Parkinson’s disease. In each of these diseases the regions that are affected that are specific to each disease show changes in metal ions. So we’re using X-rays at the Diamond synchrotron to look at the distribution and form of metal ions in these critical regions.

Joanna: The ones that we can access well at Diamond include iron and copper and zinc amongst others – these are metals you’d normally expect to find in quite high concentrations in these regions in the brain, but they are also implicated to a degree in the diseases.

Meera: And so how are you going about using the synchrotron to look into this?

Joanna: Well we’re working with autopsy tissues so these tissues are from when people die from the diseases concerned we can obtain tissue from the brain banks and prepare them in a way that allows us to bring them to the synchrotron to look directly at very thin slices of these tissues. So we can use a technique called microfocus X-ray fluorescence and what we do is we’re able to focus the beam of X-rays down to a very very small spot, smaller than a lot of the brain cells that we are interested in, and by having a very thin slice of the sample in the beam of the X-rays and moving this sample around on a high precision stage we can make a map by obtaining the fluorescence signal from the metal ions of interest at each point of the map and what we end up with is a contrast map made up entirely of the metal ion signals and so if you change concentration of iron or copper from one spot to the next you will see that in the contrast map afterwards.

The other thing that we do at the beamline is if we have a particular region of interest and we want to know what form that metal ion is in we sit at a particular portion of the map where we know we have a concentration of that metal ion and then we change the energy of the X-rays and by doing that it allows us to collect quite specific information about the form in which the metal ion is stored.

Meera: Which regions of the brain are you focussing on to look at these ions?

Joanna: Well in Parkinson’s disease there is a very critical region called the substantia nigra and this relatively small region of the mid-brain, this has a collection of essential brain cells which are responsible for creating dopamine. Dopamine is a neuro-transmitter and we need that for things like controlled movement.  So one of the symptoms of Parkinson’s disease is the very significant impact on the ability of individuals to manage movement, and we know that typically 80% of these particular cells will be lost in Parkinson’s disease and we also know from our previous studies that the level, the concentration of iron in these individual vulnerable cells is significantly higher in Parkinson’s patients, in the autopsy tissue from Parkinson’s patients than in comparable healthy brains. So we’re looking with particular interest at the iron in this region of the brain, not just at the cell that are lost in this disease but also at the surrounding tissue and the support cells to try and find out where the primary changes are in the iron in this region of the tissue. What the synchrotron allows us to do, that builds upon previous work is look at the form of iron as in what it’s bound to, and its chemical state, in addition to its distribution.

Meera: And so what have you actually found in your research so far?

Joanna: Well in our original study we saw that the concentration of iron in the individual cells almost doubled. Now what we’ve been able to do at Diamond is go on and collect quite a lot of information about the chemical form of the iron in these cells, but we’ve also been able to get the distribution of iron in the surrounding cells and surrounding tissue to build on that initial study. That’s a work in progress.

Meera: And so what are the aims of your current work? Are you hoping that this can be used clinically for treatment or diagnosis of the disease?

Joanna: If we can understand the changes in the tissue and understand the contributions that the metal ions are making to changes in this tissue, this should support some of the current work that’s going on to use magnetic resonance imaging to pick up early changes. It’s assumed in quite a lot of clinical studies at the moment that changes that are being observed clinically in magnetic resonance imaging are due directly to the iron changes, so in effect what we’re doing is looking to validate that assumption from first principles, looking to see whether those changes in the clinical MRI are directly due to iron and therefore whether it could be used in a long term way for picking up chemical changes in the tissue before you start getting damage to the cells if the iron is contributing to that process.

Meera: That was Joanna Collingwood from Keele University. That’s it for this edition of the Diamond podcast, but do join us again in June when we’ll be back with more of the latest news and discoveries from Diamond including a special insight into the tiny world of nanoscience. In the meantime, if you have any questions about Diamond or the research taking place there, the email address is [email protected]. Thank you to Sarah Bucknall, Martin Walsh, Stephen Curry and Joanna Collingwood. I’m Meera Senthilingam, thanks for listening and see you next time.