Maryam Waseem-Sayeed and Asha Omar are Year 12 students at Burntwood School and are members of our Student Advisory Panel. Over the summer, they spent a day in the lab watching one of our studies, and have produced this video showing many of the techniques we use. Thanks Asha and Maryam for your hard work and we look forward to more cinematic genius to come!
Rosalind Franklin has always been a personal heroine of mine, both as a scientist and as a feminist. She was integral to the discovery of the double helix structure of DNA, and her work in X-Ray Crystallography was pioneering. So when I got an email from Vicky saying that on my work experience, I would be spending a morning working in Professor Brian Sutton‘s X-ray Crystallography labs in the same department that Franklin worked in, it was fair to say I was pretty excited!
However, although I have always admired Franklin’s work, I had only the shakiest understanding of what on earth X-ray crystallography even was. During my morning in the Randall department of Bio-physics, Katy and Sneha, two women working in the department, explained to me what they do in the labs, and how it all works. I’ve tried my best to explain it here. Spoiler alert – it’s even more confusing than the name suggests.
The Biology The best way to explain a protein is to say it is a lock and key. Each protein binds with a partner in a specific disease, so it needs a specific drug to fit into the lock and block the disease. In order to produce enough different proteins to study, and to develop new drugs, you have to grow them in bacteria. You replace a section of the bacterial genes with those of the protein, and the bacteria grow. Bacteria reproduce by splitting into identical copies of themselves so each new bacterium will contain the protein you want. In this way, we can express large quantities of proteins with relatively little effort.
The Chemistry However, they then need to be purified. This is done using chromatography. Huge channels are made, lined with nickel. The protein is bound with a histidine tag and fed down the channel. The histidine tag binds with nickel, binding the proteins to the sides and leaving all the impurities to be washed away. You then remove the nickel and the tag, and are left with pure protein.
You then need to crystallise the proteins. The protein is put into a round well next to a reservoir and mixed with a higher concentration of the substance that you want to bind with the protein than the concentration of the protein. Due to the process of equilibrium (of which I understand enough to pass Chemistry GCSE but not enough to explain) the protein becomes more concentrated, and eventually crystallised. However, this process is also down to a lot of luck. The protein crystals are then frozen in liquid nitrogen.
The Physics Electrons scatter waves, and in a microscope, lenses focus the scattered light rays, meaning you can see the image of the object you are focusing. X-rays are types of waves. However, they have a much higher frequency than light rays. They are also much stronger, meaning that there is currently no lens that can focus them, so we cannot use a microscope to see things diffracted using X-rays.
Crystals amplify the signal given out by the X-rays. The definition of a crystal is that it is an ordered arrangement of atoms, in this case proteins. This produces an ordered diffraction pattern. When waves pass through a crystal, they produce a diffraction pattern made up of different spots. Each spot corresponds to a point in the lattice, and represents the amplitude and the phase. Due to the phase problem (http://www-structmed.cimr.cam.ac.uk/Course/Basic_phasing/Phasing.html) it’s difficult to determine the structure of the protein, so lots of complicated maths goes on at this point, usually on a computer. The protein’s structure is then mapped.
Why Is It Important? X-ray crystallography maps proteins. Each pathogen has a specific antigen on the surface of its cells, and the immune system creates antibodies (which are proteins) to latch onto these antigens and destroy the pathogen. If we can map proteins, we can work out which ones lock onto the antigens, coming back to the idea of a lock and a key. This way, we can create drugs that successfully destroy pathogens in the same way that the immune system does, leading to more and more diseases being eradicated over time.
There. That wasn’t too complicated now, was it?
Many people may imagine a career in research to be non-stop, action-packed fun from 9 till 5, 7 days a week. When we, budding young scientists, flick through articles in New Scientist, we assume someone got up one morning and thought “I want to do this project”, and then soon enough their findings are published as articles in national journals. But, as we learnt this week, life as a researcher is far from this idyllic fantasy.
One of the first things we learnt during our week of work experience at the lab is that life as a researcher is very unpredictable. Each morning when you arrive, you have no idea what kinds of tasks you’ll have completed by the end of the day. This may seem rather daunting, however it means you are never bored, and are always kept on your toes!
On our first day at the lab, Vicky had planned for us to have a go at taking some lung function measurements. Collecting the data was reasonably straight-forward – the difficult part was setting up the equipment! As a researcher, you are responsible for locating equipment and making sure you have what you need to conduct your research. It is evident that being organised and patient are two vital skills to have as a researcher.
One would often think of a researcher as a solitary scientist alone at a work bench. In reality, there is a great deal of teamwork and collaboration involved, making it a very social job. Every Wednesday morning, all members of the muscle lab come together to discuss their recent findings, often seeking guidance from one another about something unexpected they’ve come across. This aspect of the job means that you are never alone as a researcher; there will always be someone in another field who is able to assist you.
Something which we found really exciting to see during the week was the ability that researchers have to develop their specific areas of personal interest in the scientific field. For example, Dr Clark (who we were lucky enough to spend a whole day with) has a particular interest in cardiovascular physiology, so is currently working with some masters students on a project looking into the physiological processes which occur during heart failure. To be able to learn new things every day and develop a deeper understanding in an area you’re fascinated by is incredible. We also spent some time with Professor Sutton, who works in X-ray crystallography, a technique which was used by Franklin and Wilkins – leading to the discovery of the structure of DNA. The development of new technology allows processes which would previously have taken 4 years, to take a matter of hours. Unfortunately, researchers need to manage to get the funding first which we have learnt is not an easy task!
As well as that, we also really enjoyed learning about a longitudinal study which Vicky is currently carrying out, looking at premature babies and their risk of developing a respiratory disorder. We observed her doing some lung function tests with a participant, who had carried out similar tests when he was a baby. Over 100 premature babies were involved in the original data collection, and Vicky is now in the process of contacting the same participants to collect further data 6 years on. Research projects often take many years to complete, but often the discoveries made are very valuable, so in the end the years of hard work and dedication pay off!
We had an amazing week at the muscle lab and learnt so much in such a short space of time. Thank you to Vicky for organising it all, as well as to the many other academics we were lucky enough to spend time with during the week!
Laura Schuz and Beth Tobiansky, Student Panel members, JFS School Sixth Form
As we mentioned in a previous post, Ged and Vicky recently attended The Physiological Society‘s conference in Cardiff. One of the great things about going to scientific conferences is that it gives you an opportunity to see what research other people are doing, often in areas quite different to your own. One of the other researchers at Physiology 2015 was Andrew O’Leary, who is working towards his PhD in the Physiology Department at University College Cork in Ireland, under the supervision of Professor Ken O’Halloran. He has been working on some research examining the effect of low oxygen levels on breathing muscles, but using mice instead of people. We thought you might be interested to hear about his work and why we thought Irish mice could be useful in our own.
We know that when people get certain types of breathing problems, particularly those severe enough to require Intensive Care Unit (ICU) admission, they often suffer from very low oxygen levels (called ‘hypoxia’). We don’t really know at present what hypoxia over a long period of time does to the respiratory muscles. In this study, Andrew took two groups of mice and made one group breath air containing only 10% oxygen for up to 8 hours. The other group breathed normal air (21% oxygen). The amount of air the mice breathed in and out throughout the experiment was recorded constantly by placing the mice in a special measurement chamber. At the end of the experiment, the mice were humanely killed and their respiratory muscles were carefully measured in a number of ways.
The first interesting thing is that the mice in the hypoxic gas breathed a bit faster and deeper to start with (this is what humans would do – increasing the amount of air going in and out of the lungs in order to try and compensate for the lower availability of oxygen) but then went back to their normal breathing after about 20 minutes. Mice are a bit different to humans in that they can reduce their metabolic rate so that their body doesn’t require as much oxygen, like hibernating animals, so this is probably why their breathing rate and depth went back to normal despite the lower oxygen levels.
The respiratory muscles (the diaphragm and a muscle in the neck called the sternohyoid) were weaker in the hypoxic mice at the end of the experiment, with the diaphragms in the hypoxic mice only able to generate 70% of the force of the diaphragms from the control mice. Other tests that Andrew did showed that genes in the respiratory muscles were behaving differently in the hypoxic mice’s muscles. The changes in these genes suggested that the mitochondria (the ‘battery packs’ in cells) were not as efficient at generating energy for muscle contractions, and that the cells may have been releasing less calcium (which is used by the ‘contractile machinery’ of the muscle cells) to help the muscle produce force.
While obviously what happens in mice might be very different to what happens in people, we were still very interested in Andrew’s findings. We have known for a long time that people who are on ICU get weakness in their breathing muscles, and that this is often due to the fact that these patients spend long periods of time on a ventilator. This means that their breathing muscles don’t have to do much or any work, and so can waste away – a bit like someone’s leg if they break it and it’s put in a plaster cast. What Andrew’s work might suggest, though, is that the initial illness that causes people’s oxygen levels to drop might also play a part in the weakness developing. What’s really useful about doing animal research is that you can get a much more detailed picture about how all of the different aspects of muscle function are affected by the hypoxia – it wouldn’t be possible to make all of these measurements in people, and in a patient group there would be a large number of other factors that might be influencing any changes seen. We think this is a great example of how different types of research can complement one another to move the scientific field forward. Thanks to Andrew O’Leary and his supervisor Prof O’Halloran for allowing us to write about their research – and for the really fascinating discussion that we had at his poster during the conference. Watch this space for more Irish mouse news in future perhaps!
After our first Student Advisory Panel meeting, we mentioned that we were going to develop a logo for the blog and our Facebook and Twitter. A brilliant guy called Lee Taniwha has designed these for us. Lee spent a bit of time a few years ago on the receiving end of Vicky’s physio talents (he might have called it bullying at the time – physios make people work pretty hard). He’s now a graphic designer (https://www.behance.net/taniwhazdname) and has kindly donated his time and fantastic skills to help us out by designing this selection of logos.
We now need you to vote for your favourite! Either leave a comment on here saying which number (1-5) you like best, or go onto Facebook and like the one you think is the best. We will collect all of the votes from here, Facebook, Twitter and from asking around the less technically-literate people in the lab, and we will announce the winner at our next Student Advisory Panel meeting on 25th June. The winning logo will be used at the top of the blog and as our banner photo on Facebook and Twitter.
The student advisory panel is 16 students from various London schools who attended a conference at King’s College London today. Panel members discussed the ongoing partnership to develop the laboratory public engagement strategy. The students had fantastic suggestions about our social media presence, blog content, as well as their career aspirations and what they’d like to know about research. They also gained an insight into research careers. The long-term aim of the Panel is to improve the blog’s user interface, content and style. The first step on the road to change is a new “King’s Muscle Lab” logo, which will be designed by students from the schools involved – we are waiting for students to pitch their ideas! Other students are also going to assist with filming laboratory experiments and writing posts.
The Panel will meet again in late June, and hopefully every three months after that.
We recently posted on here that we were doing a survey where we wanted to hear from parents of young children with asthma. We worked with the charity Asthma UK on this project and they were kind enough to post the survey on their Twitter and Facebook pages. We were thrilled to see well over 200 people complete the survey in just one week! The information from the survey is really useful in helping us consider what areas to concentrate our research on in the future, which was the main aim of the survey at the start. It’s very important to us that we do research that deals with real problems that affect real people, rather than things we as scientists have just decided are interesting to look at. This process of asking patients and their families about what is important to them and how they think we should do our research is called Patient and Public Involvement, or PPI.
The results of the survey have also shown us very clearly how frightening it can be for parents to have a young child who has asthma or a wheezing illness. We think it’s really important for the doctors, nurses and other healthcare staff to understand how parents feel when they have a child with this type of illness The huge number of responses we’ve got means that we can look at the results in great detail and can write an article for a scientific journal, so that the people who look after sick children can understand how parents might be feeling and possibly support them better. We are really grateful to all of the parents who completed the survey for being so honest and for taking the time to give us such useful information. We’d also like to thank Asthma UK for their help in promoting the survey.
The Science Museum have a regular feature where they look at a new invention and then ask people who might use it for their opinion. They contacted Vicky to ask her what she thought of a new machine to test the oxygen levels in people’s blood, which has been invented by a Brazilian scientist who is also linked to King’s. You can see Vicky’s quote, along with other people’s thoughts, here.
Over the last few years, Alan and Vicky have worked with Burntwood School, which is a girls’ senior school in Wandsworth, South London. A very kind science teacher, Ms Budd, has brought small groups of students in to the lab to help with our research, and in turn we have showed the girls around the lab and talked to them about what it’s like to work in science and in hospitals. We have also had some girls come to us to do work experience. Hosting the group visits and the work experience students is really fun as the girls are enthusiastic and enjoy seeing the workings of a real hospital and research department, and it’s always really interesting to hear their opinions of what we do.
Last week, I asked Ms Budd if she would look at our blog and tell us whether it might be useful for her science classes, and to help her students decide whether they might be interested to do a science job in the future. She very kindly asked her students to look at the blog too and to write down what they thought of it. We were thrilled to see that they found it useful and interesting. The girls also told us what else they’d like to see on the blog, which included things like videos of us doing our research, information on how we use what we find in our research, and more detail of how we publish our results in journals. This information is really useful and we will be trying to add things like this to the blog in the next few weeks. Thank you, Ms Budd and the Burntwood girls, for your enthusiasm and helpful comments.
We are really keen to hear from anyone who wants to understand more about our work. If there’s anything you’d like to see on here, please leave a comment and we will do our best!
Recently, Ged and Vicky have been talking to Evangelia Kolyra, who is a dancer and choreographer currently working on a project all about breath and breathing. Evangelia asked King’s College London for some help and advice with the project, and so we have done our best to be helpful! Evangelia visited our lab a while ago to help with our research, which she said helped her to understand what we do. Last week, Ged and Vicky went to visit Evangelia and the other dancers who are working on the project (Justyna Janiszewska, Elsa Petit, Elli Sikorski and Antonio de la Fe) to watch them rehearse.
Watching the rehearsal was really interesting – it was so different to what we normally do! The fascinating thing was that many of the things that the dancers had noticed while they were practicing were things that fitted with our research and knowledge of breathing. We had some great discussions, talking about the science of why certain movements or ways of breathing might be easier or more difficult, as well as about how some of what they had experienced might be similar to how people with breathing problems can feel. Having problems with your breathing can be quite scary but this is often hard to explain to people who have never had those feelings. Perhaps dance could show this in a way that’s easier for people to understand.
We hope that we will be able to continue to work with Evangelia on this project. Although it’s not – at the moment – something that we can directly use in our research, we think that Evangelia and her colleagues might be able to use their very impressive skills to help show what lung disease can feel like. Our visit has pushed us to consider doing something completely new – this could be an exciting adventure! Thank you, Evangelia, for inviting us along and we look forward to continuing to work with you.