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Wellcome Trust Research Round-up: 1/9/14

1 Sep, 2014

Our fortnightly round-up of news from the Wellcome Trust research community…

Genes linked to development of glaucoma

N0022146 Testing for GlaucomaA new study funded by the Wellcome Trust and Fight for Sight has identified four new gene locations associated with glaucoma, an eye condition that can lead to blindness and visual impairment. It is hoped the finding could lead to earlier diagnosis and new therapies for treating the condition.

Glaucoma is the leading cause of irreversible blindness in the world. It is caused by damage to the optic nerve, usually due to the eye pressure inside the eye (intraocular pressure) being too high because eye fluid does not drain properly.

In the study published in Nature Genetics, researchers carried out a meta-analysis of more than 35,000 people from seven countries, including subjects of Asian and European descent, with data drawn from the International Glaucoma Genetics Consortium (IGGC).

A site on the ABO gene, which determines blood group, is one of the locations identified, and higher eye pressure appears to be linked to blood group B.

The study also found that a genetic change in the ABCA1 gene is associated with an increased risk of developing both high inner eye pressure and glaucoma. ABCA1 is a major regulator of cellular cholesterol and lipid levels, although further research is required to understand how this mechanism works in the eye.

Early diagnosis of glaucoma is crucial because if it is treated early enough, damage to vision can be prevented. In future it may be possible to provide intensive screening to those identified as being at higher genetic risk.

Professor Chris Hammond from the Department of Twin Research and Genetic Epidemiology at King’s College London, who directed the study, said: “Although eye drops are already available to treat glaucoma, these are not always effective. These findings help us to understand why some people get glaucoma and explain why the condition tends to run in families.”

Male fruit flies’ chemical demand for monogamy

fly sexA new study in The Journal of Cell Biology provides an insight into how male fruit flies

improve their reproductive success by stopping females from mating with other flies.

In addition to sperm, semen carries products that foster sperm survival, promote egg fertilization, and serve other functions that optimise a male’s chances of passing along his genes.

In male fruit flies’, reproductive accessory glands (thought to be equivalent to the prostate gland in humans) secrete signalling chemicals into the seminal fluid that make the recipient females less inclined to mate again with other flies.

But it’s unclear how some of these signalling chemicals are produced and delivered in order to reprogram a female’s behaviour against her own self-interest. Researchers funded by the Wellcome Trust have identified tiny membrane-bound vesicles called exosomes that are secreted into the seminal fluid by the so-called “secondary cells” of male accessory glands.

The authors showed that, after mating, the exosomes fuse with sperm and interact with cells along the female reproductive tract.

When the researchers reduced the number of exosomes produced by secondary cells, the female flies were more inclined to re-mate. This indicates that the exosomes are responsible for the behavioural changes, by interacting with the targeted female cells to overpower normal signalling pathways.

Puberty in girls influenced by one parent more than the other

AS0000131F03 Teenage girlsThe age at which girls reach sexual maturity is influenced by ‘imprinted’ genes, a small sub-set of genes whose activity differs depending on which parent passes on that gene, according to new research published today in the journal Nature.

The findings come from an international study of more than 180,000 women involving scientists from 166 institutions worldwide. The researchers identified 123 genetic variations that were associated with the timing of when girls experienced their first menstrual cycle, by analysing the DNA of 182,416 women of European descent from 57 studies. Six of these variants were found to be clustered within imprinted regions of the genome.

Lead author Dr John Perry, a Henry Wellcome Postdoctoral Fellow at the University of Cambridge said, “Normally, our inherited physical characteristics reflect a roughly average combination of our parents’ genomes, but imprinted genes place unequal weight on the influence of either the mother’s or the father’s genes. Our findings imply that in a family, one parent may more profoundly affect puberty timing in their daughters than the other parent.”

The activity of imprinted genes differs depending on which parent the gene is inherited from – some genes are only active when inherited from the mother, others are only active when inherited from the father. Both types of imprinted genes were identified as determining puberty timing in girls, indicating a possible biological conflict between the parents over their child’s rate of development.

Further evidence for the parental imbalance in inheritance patterns was obtained by analysing the association between these imprinted genes and timing of puberty in a study of over 35,000 women in Iceland, for whom detailed information on their family trees were available.

In other news…

Congratulations to Professor Rob Klose who has been awarded the Royal Society Francis Crick Lecture for his research into how chromatin-based, and epigenetic processes, contribute to gene regulation. Professor Klose has been supported throughout his career by the Wellcome Trust, beginning with his PhD studentship.

Another Wellcome Trust-funded PhD student, Dr Jenny Bangham, has won the Marc-Auguste Pictet Prize for her dissertation “Blood groups and the rise of human genetics in mid-twentieth century Britain”. The prize is given out every other year by the Société de Physique et d’Histoire Naturelle de Genève on a different theme pertaining to the history of science.

Image credits: Testing for Glaucoma – Libby Welch, Wellcome Images, Drosophila melanogaster mating – ImageEditor on Flickr, CC-BY 2.0, Teenage girls – Anthea Sieveking , Wellcome Images

Image of the week: Ebola

29 Aug, 2014

L0076142 Ebola. Sculpture by Luke Jerram, c. 2004

This week’s image is of a sculpture of the Ebola virus, created by artist Luke Jerram.

It is an unusual, and artistic, take on Ebola. With the virus continuing to spread in West Africa and the responses from the global health community regularly in the news, we’ve found that journalists and health writers have been requesting images of the virus, but they are not easy to come by.

Made entirely of glass, Luke’s sculpture is approximately one million times larger than the virus itself, and is part of a series of similar glass-works called Glass Microbiology.

All the pieces in this series are transparent and colourless, in deliberate contrast to artificially coloured scientific images. Being smaller than the wavelength of light, viruses in fact have no colour. To create the series, Luke worked in consultation with virologists from the University of Bristol, and photographs of his work have been used in medical journals, media stories, and one has even appeared on the front cover of Nature.

Not only is this a precise visual representation of Ebola, its jewel-like finish carries great beauty. This complex tension between the beauty of an object and what it represents lies at the heart of Luke’s sculptures, which have been created as a means of contemplating the global impact of disease.

This particular artwork was commissioned by a museum in Holland last year, but will be on display in the redeveloped Reading Room at Wellcome Collection in 2015.

Image Credit: Luke Jerram

A summer of science journalism with the Wellcome Trust-New Statesman scholarship

28 Aug, 2014

 Earlier this year the Wellcome Trust and New Statesman announced a joint programme offering paid internships to aspiring science writers from traditionally underrepresented backgrounds. The recipients of the first two scholarships spent eight weeks working at New Statesman. Ajit Niranjan, tells us about the experience…


This summer I worked as a science writer for the New Statesman, a weekly British magazine that is famous for its progressive take on politics, arts and current affairs. I had a Wellcome Trust scholarship that enabled me to complete an internship programme for aspiring science writers at the magazine.

In an attempt to combat the lack of diversity in science journalism, the placement is only open to students and graduates from ethnic minorities. I know this doesn’t sit well with many people – I certainly wrestled with the idea of accepting any form of positive discrimination – but if you’re an eligible candidate I’d strongly urge you to apply. Schemes like this are essential to levelling the playing field.

I joined the online team at the start of June and was thrown straight into the deep end, writing four articles in my first week and conducting phone interviews with researchers in the UK and abroad. Essentially, I was given the same level of independence as the rest of the staff. My day-to-day role was finding interesting developments from press releases or the news, find a ‘science-y’ angle (there usually is one) and write a blog post that a school child would be able to understand.

It’s a simple formula that works pretty well. Every article was edited before going up online and so I got feedback on my writing on a daily basis.

During the two-month placement I learned a great deal – not just about writing and journalism, but also about areas of science I’d never studied before. The scope is huge. Topics that fell under my remit as a science writer ranged from opinion pieces on drugs policy to reporting on the latest gadgets in the tech world – which even saw me trying Google Glass when it first launched in the UK.

googleglass AjitAlongside the regular short blog posts, I did a couple of longer pieces including a 3000-word essay on China’s growing environmental issues. Having the New Statesman’s name behind me meant I could confidently approach important figures for interviews, including CEOs of tech companies and even my local MP (and scientist) Julian Huppert.

Outside of the regular writing, New Statesman kept me busy. I attended all the editorial meetings, spoke on the weekly podcast about science and technology, and joined the political editor on a trip to Westminster for Prime Minister’s Questions.

Best of all, I was allowed to pitch ideas for publication in the printed magazine’s Observations section. The work was always varied and the perks – including free tickets to New Statesman events including a Laurie Penny/Mary Beard debate and the incredible Latitude festival – just added to the excitement of working in London.

The staff at New Statesman invested time in training the interns up. Helen Lewis, the deputy editor, set us a challenge popular in journalism schools, to give us some reporting practice – to take the Tube out to a nearby station and cover a local story on the ground in a single afternoon. A daunting task, but well worth it for the feedback we received.

Mainstream media, more so than any other profession, really suffers from its artificially homogeneous make-up and ethnicity is just one area that is disproportionately represented in what is overwhelmingly an old boys’ club. The Wellcome Trust Scholarship provides an imperfect solution to a very serious problem of a lack of diversity in journalism. It’s a tricky issue for a number of reasons but I strongly recommend checking out this piece by ex-New Statesman writer Rafael Behr for a bit of background.

There’s a lot you can get out of the placement if you choose to apply, and the application process itself is pretty straightforward – simply write an 800-word blog post on a recent scientific development. My advice is to choose a topic you’re genuinely interested in.

Working at the New Statesman this summer was hugely educational and I’m now very set on pursuing a career in journalism. If you’re thinking of applying in future I’d be happy to answer your questions on Twitter.

You can read Ajit’s articles on the New Statesman website and follow him on Twitter as @NiranjanAjit. The Wellcome Trust is committed to supporting a new generation of science journalists – find our more in this blog post.

Researcher Spotlight: Dr Faith Osier

26 Aug, 2014

Faith OsierDr Faith Hope Among’in Osier is a Clinical Research Fellow and Group leader at the KEMRI-Wellcome Research Institute in Kenya. She holds a Wellcome Trust Intermediate Fellowship in Public Health and Tropical Medicine and was recently awarded the Royal Society Pfizer Prize, one of the most prestigious prizes for African science. Here, Dr Osier shares her passion for research on the mechanisms of developing immunity to malaria, especially in children…

What are you working on?

I try to understand how adults in Africa learn to live in harmony with the parasite responsible for malaria, such that infections do not make them ill. This knowledge could help us design vaccines that would protect children, who can die as a result of a malaria infection.

What does your average day involve?

My average day has evolved over the years as I have graduated from being a junior to a more senior researcher. Earlier on, I’d spend a lot of time in the laboratory generating data and less time in the office – reading scientific literature, analysing data and writing up my work.

More recently, I spend most of my time in the office, still reading, analysing data and writing research grants and papers. Importantly I meet with my students and research assistants to discuss their work. I also spend at least one to two hours each day on administrative issues and/or academic meetings within my department.

Why is your work important?

Malaria still claims the lives of hundreds of thousands of children each year and has a major economic impact on the lives of many in sub-Saharan Africa. Children that survive severe malaria can be left with permanent physical disability that takes many forms. It’s really important that we find ways to control and eventually eliminate malaria for the health and economic empowerment of Africa.

Osier_photo5 blog

Children in Kilifi county, Kenya present to a local dispensary for testing (Photo credit: Juliana Wambua)

What do you hope the impact of your work will be?

My dream is that I can contribute to “making malaria history” through effective vaccination.

Imagine a world where young babies and infants are vaccinated for malaria in rural clinics, alongside other vaccines in the Expanded Programme for Immunisation. I’d love to see this happen, children getting vaccinated and having the opportunity to live, improve their lives and those of their communities.

How did you come to be working on this topic/in this field?

I joined the KEMRI-Wellcome Trust Research Programme in 1998 as a junior doctor and was interested in training in paediatrics. It was here that I was introduced to research on malaria in general, and begun to understand that we know so little about this disease that has been with humans for such a long time.

I met a vibrant team of enthusiastic researchers, and this really drew me in. Before I joined the immunology research team, I would joke that the immunologists asked the same question about malaria over and over again, and did not seem to get any wiser. Now that joke is on me, and I appreciate better why it is that we still do not understand how humans become immune to malaria.

How has Wellcome funding helped you/your research/your career?

The Wellcome Trust has been instrumental to getting me established as a credible African research scientist. I competed and won a training fellowship that supported my PhD studies. My current work is supported by an intermediate fellowship, and this has enabled me to compete successfully for an MRC/DFID African Research Leader award.

Osier_photo1 blog

Research mentorship Kilifi style!

The Wellcome Trust also supported (and continues to support) other brilliant researchers, who have mentored me in different ways and contributed significantly to my development.

Funding from the Trust has also allowed me to mentor and train younger researchers and I have a research team that I am really proud of! I commend the Trust for their international portfolio, for opening up funding opportunities for researchers for tropical and developing countries. Without this, I doubt that I would have taken up a career in research.

What’s the most frequently asked question about your work?

When will we have a malaria vaccine?

faith_gathoni blog

Faith Osier and Gathoni Kamuyu doing malaria antibody testing in the lab. (Photo credit: Brett Lowe)

Which question about your work do you most dread – and why?

Why is it that after so many years we still do not have a malaria vaccine? What are you researchers doing?

This question often comes from laymen – and it is challenging to explain in lay language why basic science research takes time, and why we must remain nevertheless optimistic!

Tell us something about you that might surprise us…

I love international rugby matches and am a strong supporter of our Kenya Sevens Team

What keeps you awake at night?

The fact that people are developing immunity to malaria all around me – I feel that this process is staring me in the face- if you like, and I must be able to see and understand how it is happening.

What’s the best piece of advice you’ve been given?

It’s a funny statement but I think its true… “Life is not a rehearsal, LIVE IT!”

The ‘chain reaction’ question, set by Prof Scott Waddell is this: “If you were able to start again, what would you rather work on? Or do?”

If I could start again, I’d still work on malaria…it is a fascinating disease.

You can find out more about Dr Osier and her research on the KEMRI-Wellcome website.

Top 10 things about doing a summer internship at the Wellcome Trust

22 Aug, 2014

Wellcome Trust Summer Internship

Each year, the Wellcome Trust offers a number of paid summer internships at Trust HQ. These are aimed at giving current undergraduates the chance to experience working an area of the Trust that interests them, and we hope to inspire, support and develop the next generation of people who can make a difference.

As the eight-week placements of the 2014 cohort of interns come to an end, we caught up with some of them to find out what they most enjoyed about being at the Trust, and what advice they have for future applicants…

The top 10 things about working at the Wellcome Trust

  • The diversity of people – their careers, backgrounds, and skills – and the diversity of the work done that is done here
  • The friendliness and atmosphere – “Everyone is super friendly & helpful– from the staff in the kitchen to Jeremy Farrar”
  • The food! Cheap, tasty, healthy food
  • The glass lifts – and the chats you have in them
  • The sense of improving the world and being able to see real outcomes of your work
  • The opportunity to learn outside your field
  • Working alongside the greatest minds (someone’s been reading our vision statement!)
  • The free gym
  • The free tea and coffee (and hot-chocolate)
  • The great views from the upper floors of the building

Even though they’ve only been with us for eight weeks, it seems like this bright bunch of interns have already found many of the things that make working at the Wellcome Trust so enjoyable. But what will they take away from the experience?

The Internship Experience

Eloisa Tovee, Legal Intern
“Eight weeks interning at the Wellcome Trust is a substantial amount of time and has been the origin of an amazing learning curve. Over the summer internship I have developed communication skills, gained experience in legal writing and negotiation and more importantly, learnt to think outside the box.”

Kate Taylor - 2014 SPPU Evaluation Intern

Kate Taylor – 2014 SPPU Evaluation Intern

Kate Taylor
 Strategic Planning and Policy Unit – Evaluation Intern
“I’ve learned that most people change careers and move about quite a lot – it’s okay not to know exactly what you want to do as that will probably change anyway throughout your life! I’ve also learnt how to handle many different projects at the same time, and to always provide updates and feedback to your supervisors.”

Jamie Gore, Marketing Communications Intern
“I’ve learned all about the different tasks that come under the umbrella term ‘Marketing’, I’ve improved a number of my skills Excel for example) and learned that the Trust gets involved with much more than just medical research.”

Bethany Summers, Science Intern
“I’ve learnt more about what the Wellcome Trust does and from that been able to complete a whole project complete with presentation to the division in only 8 weeks! My newfound Excel skills are certainly a bonus and I’m geekily excited about being able to use them in my final year of university. I must credit the Neuroscience and Mental Health team in Science for all their support and including me as one of the ‘family’.”

Sophie Ward, Education and Learning Intern
“I’ve learnt a lot of transferrable skills to take back to university with me next year, including research/report writing skills. I’ve also had the chance to listen to a funding committee, which gave me lots of things to think about when completing application forms in the future.”

Meesha Patel – Broadcast, Games and Film Intern
“One of the main and most important things I have learnt from my experience here is that you shouldn’t plan too far ahead. As long as you have a general idea of where you are going and you have ambition, you are helping yourself along the way by getting involved with projects that interest you. Your plan isn’t set in stone. It has got to be fluid – as most things are in life.”

Advice for future applicants

Ben Stockton

Ben Stockton – 2014 Intern in the Editorial team

We asked what advice they would give people who are considering applying for the Wellcome Trust internship scheme in future. Lots of good advice came back – including these top tips:

Go for it!
“You would need a very good reason not to apply!” says Eloisa Tovee. “The opportunities to network, gain experience in what interests you, develop personal skills and transferrable career skills are boundless. It is the perfect place to spend eight weeks learning!”

It’s not just for science students
“As a non-science student I nearly let this put me off applying” says Sophie Ward. “I thought that I wouldn’t have much of a chance, however it turns out that this isn’t true! Just make sure you can show a real interest in the role you are applying for and can articulate why you want to work here.”

Be Passionate
Meesha Patel shares her advice on producing a good application “Show how passionate you are” she says. “Interest and dedication really shines through in an application or in an interview and being able to convey that will help you a great deal.”

Be yourself
“Don’t try to fit the model of a ‘perfect applicant’” says Ben Stockton, “there’s no set career path needed to work here.” Jamie Gore agrees, “being a little bit different helps you stand out, I did my interview on Skype from a hostel in Morocco in harem pants and I think that made me stand out somewhat” he says.

Learn about the Trust
“I would highly recommend developing an understanding of the uniqueness of the Trust and an appreciation for how influential and important its role is in the scientific community” says Gore.

Ask questions
If you’re successful, then Kate Taylor has this advice for getting the most out of the experience: “Don’t be afraid to ask questions or speak up when you don’t know something. People are really friendly here and willing to help.”

We’d like to thank all of our 21 summer interns for their hard work this summer. They’ve worked on projects and initiatives too numerous to count within every department in the Trust, and contributed greatly to our work. A final word from the Wellcome Trust Director Jeremy Farrar “From all of us: thank you, goodbye and remember to stay in touch!”

If you’re interested in applying for a summer internship next year, be sure to keep an eye on the internship section of the Wellcome Trust website. We also run a graduate development scheme and offer a range of funding options, including Biomedical Vacation Scholarships.

Image of the Week: Xenopus

22 Aug, 2014

C0011036 Xenopus

Move over Paul the Octopus, this friendly looking creature can tell if you’re pregnant or not…

.. well, sort of. This week’s image is of a Xenopus, a type of aquatic frog native to southern Africa, which was used in pregnancy testing.

In the 1930s it was discovered that injecting a woman’s urine into a live female Xenopus could test if the woman was pregnant. If the urine contained the pregnancy hormone human chorionic gonadotropin, it prompted the female frog to ovulate, so if the frog laid eggs, it was confirmation of pregnancy.

Between the 1940s and 1960s, it was common practice in the UK to send urine samples to pregnancy-testing laboratories where this test was performed.

Xenopus, more commonly known as the African clawed frog, has slippery smooth skin, the result of a mucus antibiotic coating, which results in incredible healing properties for the frog. The back legs are webbed making them powerful swimmers, a handy attribute when you spend pretty much all of your time in the water.

No longer used as a living pregnancy test, these frogs can still be found in life science laboratories around the world. Xenopus leavis is used as a model organism and has played an important role in helping scientists better understand developmental biology.

As well as being used in research around the globe, Xenopus has made it into space. Embryos were first taken to the Russian space station Salyut, and further research involved successful fertilisation of eggs in space, and experiments on the International Space Station, where the affect of microgravity on development could be studied.

Image credit: Wellcome Library, London

Wellcome Images is one of the world’s richest and most unusual collections, with themes ranging from medical and social history to contemporary healthcare and biomedical science. Over 100,000 high resolution images from our historical collections are now free to use under the Creative Commons-Attribution only (CC-BY) licence.


Estimating how many people need treatment during an Ebola outbreak

21 Aug, 2014

Ebola virus virionToday the Wellcome Trust has announced a multi-million pound funding package to support research during the current Ebola epidemic in West Africa. There’s no sign of an end to the outbreak and many people believe things will get worse before they get better, so it’s important to understand the scale of the challenge we face. Oliver Brady is an epidemiologist from the University of Oxford, who has been working in this area with colleagues Professor Simon Hay and Dr Peter Horby. Here, he explains why this outbreak requires special attention…

Last week a World Health Organisation (WHO) Expert Committee reached the conclusion that it would be ethical to consider unproven drugs during this exceptional Ebola outbreak in West Africa.

This ground-breaking decision raises some immediate questions: what investigational drugs and vaccines are available, and what volume of each would be required in the current epidemic?

Rapid answers to these questions are necessary in order to plan the development of any of the candidate drugs or vaccines, for this, and future outbreaks.

Prof Simon Hay, Dr Peter Horby and I have spent some time looking at how we might come up with some figures to provide a useful starting point for discussions. It is important to note that it is not our intention to provide exact figures, but rather to enable us to judge the potential need in an epidemic of this scale, compared to previous outbreaks.

To reach these estimates we extracted a range of published data from 22 previous outbreaks of Ebola spanning back to 1976. This data includes contact-tracing studies and staffing needs during the outbreaks, which allowed us to approximate the number of people that may have been exposed to the Ebola virus per infected person or per bed.

We created four different categories to reflect the different groups potentially exposed to Ebola virus. These categories are: Ebola patients and their close contacts, healthcare providers and those who dispose of the bodies and infectious material, other essential service providers including logistics personnel and a contingency stockpile for controlling infections that spread outside West Africa.

By estimating the numbers of people in each of these categories who might be exposed to infectious individuals, we were able to work out how many people could have been eligible for treatment or vaccination over the course of the outbreak so far.

While the people in these different categories may be at very different levels of risk for developing the disease, until we have a better understanding exactly what constitutes a significant contact we have to assume that all of these individuals may require treatment or prophylaxis.

Our results show that, under a conservative scenario, up to 30,000 people may have been eligible for treatment or vaccination between the start of the current epidemic in December 2013 and 19th August 2014.

This scenario is considered conservative as it is based on data from past Ebola epidemics in isolated rural communities. The difference in scale of the current urban outbreak means that many of these historical parameters may be underestimates.

It is clear that the magnitude of need for the current on-going epidemic is already significantly higher than any previous Ebola outbreaks. Furthermore we are seeing no signs of the epidemic easing and action is urgently required given the considerable gap between need and the tools we currently have available.

The next step is for those involved in manufacturing or commissioning potential therapies to refine our initial estimates, taking into account the specific therapeutic or preventive characteristics of each drug or vaccine. The financing and roll-out of investigational drugs will also have an effect on the number of treatments required, but we hope that the groundwork that we have put in will assist in this process.

Mathematical models of the epidemic will also be important in refining the numbers and helping to determine the optimum intervention scenarios when the effectiveness and modes of action of the candidates are known.

The scale of the current Ebola outbreak in West Africa means that we have no time to waste. Now is the time for decisions to be made on financing, scaling up production and evaluating investigational and novel Ebola therapeutics.

Our preliminary estimates of the number of people that might have been eligible for treatment or vaccination since the start of this outbreak, if the products were available, gives us an a better idea of the scale of the challenge we face.

We hope that our tool will facilitate prompt, evidence-based decisions on the scale of financing and manufacturing required for these potential therapeutics and vaccines.

Made now, these decisions may have the capacity to mitigate the mortality and improve the control of the current Ebola outbreak, as well as those that may occur in the future.

You can read Oliver Brady’s article on in their ‘World View’ section and find the spreadsheet they used for calculating the number here. Oliver Brady (BBSRC funded) and Prof Simon Hay (Wellcome Trust funded) are in the Spatial Ecology and Epidemiology Group, University of Oxford, and Dr Peter Horby is from the Epidemic Diseases Research Group, Centre for Tropical Medicine and Global Health, also at the University of Oxford.

The Wellcome Trust has announced new funding to support research that could take place during the current Ebola outbreak and in future epidemics. More information can be found in the news section of the Wellcome Trust website.

Image credits: Ebola virus – CDC/Cynthia Goldsmith/Public Health Image Library, Vaccination – Barbara Bellingham, Wellcome Images

The Discoverability Challenge – How Can We Make Research Data Easier to Find and Use?

20 Aug, 2014


Enhancing the discoverability of public health and epidemiology research data is a key to ensuring that it gets more widely used. This was the topic of a recent workshop hosted by the London School of Hygiene and Tropical Medicine, where researchers and data experts explored the findings of a recent Wellcome Trust report on data discoverability. Dave Carr, Policy Adviser at the Wellcome Trust, highlights some of the key themes that emerged from a lively and productive debate.

The Wellcome Trust is committed to ensuring that the data outputs generated by the research we fund can be accessed and used in a way that maximises the health and societal benefit. We are a member of the Public Health Research Data Forum, which brings together a consortium of like-minded funding global funders with a shared vision of increasing the availability of health research data, in ways that are equitable, ethical and efficient.

While some research disciplines have well-established community-level resources that store and curate datasets and make these available to potential users, this type of infrastructure has been much slower to develop in other fields.

For public health and epidemiology research, the vast and rich datasets collected from human populations in the course of research are often held locally by the groups that have gathered the data. In many cases, there is no easy way for potential users to find out whether a particular dataset exists, let alone to gain access to the data in a useable form. This severely limits the potential value that may be derived.

Screen Shot 2014-08-20 at 14.00.24The need to make data more readily discoverable to users is widely recognised as one of the fundamental barriers to more effective data sharing. On behalf of the Public Health Research Data Forum, the Wellcome Trust commissioned an expert team to explore how the public health and epidemiology field could best take on this challenge. Their report was published in July 2014.

The workshop gave participants the opportunity to discuss the team’s findings with a panel of invited experts – including Arofan Gregory of the Open Data Foundation, Steve Kern of the Bill and Melinda Gates Foundation, David Leon of the London School of Hygiene and Tropical Medicine, Brian Hole of Ubiquity Press, and Matthew Wollard of the UK Data Service. The panel discussion was chaired by Jimmy Whitworth, Head of Population Sciences at the Wellcome Trust.

One of the important messages was that making data discoverable is certainly not an impossible challenge. The required technology already exists and successful approaches have been applied in related fields (such as the social sciences). These could be built upon and adapted to provide workable solutions for public health and epidemiology research data.

Panellists and delegates highlighted several pioneering initiatives that are already widening access to research datasets. But the picture that currently exists is a fragmented one, with a lack of overarching community standards and agreed best practice across the piece. A key challenge for any initiative to enhance data discoverability would therefore be linking up existing initiatives and effectively building on what is already in place.

Two other messages emerged very strongly from the discussion. Firstly, that data usability is at least as big a challenge as discoverability, and as it is inextricably linked, cannot be ignored.

The adoption of robust approaches for collecting adequate metadata is critical for both discoverability and usability. Metadata must be gathered as the research is conducted (and not added in as an afterthought).

7995656412_18df90cfc2_nSecondly, in order to encourage researchers to put in the effort required to make their data discoverable and useable, appropriate incentive structures must exist. This point resonates strongly with the findings of a report of Expert Advisory Group on Data Access on incentives and culture change for data sharing that was published earlier this year.

In building support in the research community, it was emphasised that the principal argument must always be that enhancing the discoverability and usability of data enables better science.

Over the weeks ahead the Trust and our partners in the Forum will crystallise plans for taking forward the report’s recommendations. We are committed to ensuring we progress in a way that best meets the community’s needs, and want the issues to be discussed and debated as widely as possible. This workshop provided an excellent first step in this progress, and we would welcome your further feedback and comments.

The workshop was filmed and is available to view on the London School of Hygiene and Tropical Medicine’s Vimeo Channel. The report, “Enhancing Discoverability of Public Health and Epidemiology Research Data” is available from the Public Health Research Data Forum site.

Image credit: Lederle Laboratory - G. Terry Sharrer, Ph.d. National Museum Of American History/NIH, Carrot on a string – by nist6dh on Flickr CC-BY-SA

Wellcome Trust Research Round-Up: 18/08/14

18 Aug, 2014

Our fortnightly round-up up of news from the Wellcome Trust research community…

Mind and body: link between immune system and mental health

The immune system may have a role to play in mental illness, suggests research from the University of Cambridge, published in JAMA Psychiatry last week.

With funding from the Trust, as well as the NIHR and the MRC, the team from Cambridge carried out the first ever longitudinal study to examine the link between inflammatory markers, such as the protein interleukin-6 (IL-6), in childhood and subsequent mental illness.

ALSPAC - Children of the 90sThey took blood samples from 4,500 individuals (from the Avon Longitudinal Study of Parents and Children, or Children of the 90s), at age 9 and followed up at age 18 to see if they had experienced episodes of depression or psychosis. They found that those participants whose levels of IL-6 were deemed ‘high’ when children were nearly twice as likely to have experienced such episodes later in life, than those whose levels were ‘low’.

Dr Golam Khandaker from the Department of Psychiatry at the University of Cambridge, who led the study, says: “Our immune system acts like a thermostat, turned down low most of the time, but cranked up when we have an infection. In some people, the thermostat is always set slightly higher, behaving as if they have a persistent low-level infection – these people appear to be at a higher risk of developing depression and psychosis.

It’s too early to say whether this association is causal, and we are carrying out additional studies to examine this association further.”

The study indicates that chronic physical illness such as coronary heart disease and type 2 diabetes may share a common mechanism with mental illness. People with depression and schizophrenia are known to have a much higher risk of developing heart disease and diabetes, and elevated levels of IL-6 have previously been shown to increase the risk of heart disease and type 2 diabetes. The research also hints at interesting ways of potentially treating illnesses such as depression with anti-inflammatory drugs.

Momentary subjective well-being: an equation to predict happiness spectrum_by_JoeLercio

Researchers from University College London, including one of the team behind the Great Brain Experiment, have developed an equation to predict how happy people will say they are from moment to moment, based on recent events relating to rewards and expectations.

26 subjects completed a decision-making task where they either lost or gained money, while answering the question: ‘how happy are you right now?’

The participants’ neural activity was measured throughout using fMRI, and this data was used to develop one of the games in the Great Brain Experiment app, called ‘What makes me happy?’ Data from a subsequent 18,420 players found that the same equation could be used to predict their happiness, even though they were only winning points and not money.

Lead author of the study, Dr Robb Rutledge from the UCL Wellcome Trust Centre for Neuroimaging and the new Max Planck UCL Centre for Computational Psychiatry and Ageing, commented: “It is often said that you will be happier if your expectations are lower…The new equation captures these different effects of expectations and allows happiness to be predicted based on the combined effects of many past events”.

PNAS equation

With the data from players of the smartphone app fitting the same equation as the smaller lab-based experiments, the team are optimistic about the app’s potential to produce robust results. “It demonstrates the tremendous value of this approach for studying human well-being on a large scale,” said Dr Rutledge.

The research was published in the Proceedings of the National Academy of Sciences and was reported widely by outlets including the BBC and the Telegraph.

Toxic proteins implicated in brain diseases

B0005749 Human brain from aboveA specific genetic mutation may damage nerve cells in frontotemporal dementia and motor neurone disease, suggesting a potential new target for treating the two brain diseases.

Scientists at UCL and the Max Planck Institute for Biology of Ageing used fruit flies to better understand the effects of the C9orf72 gene, which has been linked to both frontotemporal dementia (FTD) and motor neurone disease. A faulty version of the C9orf72 gene was recently shown to cause both diseases, and is thought to be responsible for roughly 8% of all cases of each in the UK.

The faulty gene contains a short section of genetic code that is repeated thousands of times. This repeated code results in extra molecules called RNA, as well as repeated fragments of protein, and the challenge has been to uncover whether the RNA or the protein – or both – may be harmful to nerve cells. By ‘cloning’ sections of DNA to test separately, the team were able to identify that toxic protein fragments are the main culprit in causing brain cell death in both diseases.

Dr Brian Dickie, Director of Research Development at the Motor Neurone Disease Association, said:

“Since the discovery of C9orf72 in 2011, researchers have been continually trying to understand how this gene causes both motor neurone disease and FTD. This detailed and elegant research has given us an important insight into how C9orf72 causes disease, which will guide the MND and FTD research communities in their efforts to develop new approaches to treatment.”

This work was funded by the Trust, alongside Alzheimer’s Research UK, the Motor Neurone Disease Association and the MRC. The paper is published in the journal Science.

In other news…

  • Researchers at the University of Reading have provided new understanding into how our brain processes information to change how we view the world. Using a simple 3D computer game (not un-like Pong) they found that the brain uses an internal simulation of the laws of physics to change its perception of slant in order to ‘score’ consistently. The Wellcome Trust and EPSRC funded study, Humans Use Predictive Kinematic Models to Calibrate Visual Cues to Three-Dimensional Surface Slant, is published in the Journal of Neuroscience.
  • A study published in Nature Communications has found that new-born babies generate a genetic code to indicate whether or not a bacterial infection is present in the bloodstream; an infection distress signal. Researchers from the University of Edinburgh have identified a signal consisting of 52 molecular characters specific to bacterial infection, likening it to a ‘biological tweet’.
  • Researchers from the KEMRI-Wellcome Trust Research Programme in Kenya and Imperial College have published the results from a pilot randomized controlled trial looking at the effects of Mesalazine in malnourished children. The study is available on BioMed Central and is part of their series on Medicine for Global Health.
  • Congratulations to the Wellcome Trust Centre for Molecular Parasitology, Institute of Infection Immunity and Inflammation for being shortlisted in the Excellence in Communication category of the Glasgow Business Awards.

Image of the Week: Wiring of the human brain

15 Aug, 2014

Wiring of the human brain

Spark the imagination… submit your images for the 2015 Wellcome Image Awards now! If you are a research scientist, photographer or illustrator, your images could reach a global audience. The winning images will go on display at science centres and public galleries across the UK. We are looking for high quality imagery that relates to biomedical science and contemporary healthcare, and are interested in all artistic media and imaging techniques, from hand-drawn illustrations to super-resolution microscopy and functional MRI scans. Any images we receive before 30 September 2014 will be considered for the Wellcome Image Awards 2015. Email Sabrina Taner for more information about this.

To inspire you, this week’s image focuses on one of the 2014 Award winners, a bird’s-eye view of nerve fibres in a normal, healthy adult human brain. The back of the brain is on the left of the image and the left side of the brain is at the top of the image. Brain cells communicate with each other through these nerve fibres, which have been visualised by diffusion-weighted magnetic resonance imaging (DWI MRI). Diffusion-weighted imaging is a specialised type of MRI scan; here it is measuring the movement of water in many directions in order to reconstruct the orientation of the nerve fibres. As this is a 3D image the direction of the nerve fibres has been colour-coded. Fibres travelling up and down (between the top of the head and the neck) are coloured blue, fibres travelling forwards and backwards (between the face and back of the head) are coloured green, and fibres travelling left and right (between the ears) are coloured red.

This image was taken by Zeynep Saygin, a postdoctoral fellow at the McGovern Institute for Brain Research at the Massachusetts Institute of Technology (MIT). Zeynep’s work focuses on understanding how different regions in the brain work together to process information and how this changes in people as they develop or in those with dyslexia. She said “I am continually astounded by the sheer number and complexity of the nerve fibres of the human brain, this image only shows a small portion of its neuronal connections. There is something utterly provocative and powerful about seeing the physical architecture that makes up the human mind.”

This year, for the first time, the Wellcome Image Awards went on display simultaneously in all four countries of the UK: at the Glasgow Science Centre, the Museum of Science and Industry (MOSI) in Manchester, Techniquest in Cardiff and W5 in Belfast. In 2015 the winning images will go on display in simultaneous exhibitions at even more science centres and public galleries across the UK.

Image credit: Zeynep M. Saygin, McGovern Institute, MIT/Wellcome Images

Wellcome Images is one of the world’s richest and most unusual collections, with themes ranging from medical and social history to contemporary healthcare and biomedical science. All our images are available in digital form so please click the link above if you would like to use the picture that features in this post, or to quickly find related ones. Many are free to use non-commercially under the terms of a Creative Commons licence and full details of the specific licence for each image are provided.

Researcher Spotlight: Professor Scott Waddell

12 Aug, 2014
Professor Scott Waddell

Professor Scott Waddell (Credit: Wellcome Images)

Professor Scott Waddell is a Professor of Neurobiology at the University of Oxford and a Wellcome Trust Senior Research Fellow. Scott studied biochemistry as an undergraduate and completed a PhD in cancer biology before taking a leap across the atlantic and in to the field of neuroscience for his post-doctoral research. He studied at the Massachusetts Institute of Technology and spent 10 years leading a research group at the Department of Neurobiology at the University of Massachusetts Medical School. We talked to Scott about his current research and what drew him to neuroscience. 

What are you working on?

We work on many things. How and where are memories formed? Why do some memories last a lifetime and others are transient? How are memories retrieved so that you can use them when they are needed? Recently we have also started to work on neural transposition; that is the unexpected alteration of the genome within neurons caused by the somewhat random activity of small pieces of mobile, or ‘jumping’, DNA. Transposition could in principle lead to individual differences in behaviour, sporadic neurological disease and so forth.

What does your average day involve?

Drop off daughter at school, bike to work, check the overnight email, chat to people in the lab getting an update on progress, lab meeting if we have it, lunch with the group, more discussion with lab sucking in the new data, writing mostly in afternoon, check on those doing the most exciting experiments of the day, ride the bike home, run, dinner, family time, write, sleep, repeat.

Why is your work important?

I study the fabric of life and I try to explain where intelligent behaviour comes from. What could be more interesting and important than that?! A better understanding of the brain will likely improve our chances of treating a number of neurological disorders.

What do you hope the impact of your work will be?

I hope our work will help us to understand how the brain works and that it will interest and inspire others.

How did you come to be working on this topic/in this field?

From university onward I was fascinated by research and followed opportunity. My PhD advisor John Jenkins used to irregularly leave photocopied articles on my desk and it was one of those that initiated my switch from cancer biology to neuroscience.

Yeast studies of cell-cycle control and the circadian clockwork in flies tipped me towards using genetics to study memory in Drosophila. From then on I have been lead by the data in front of me; new approaches, my curiosity, the scientific literature and old science books.

A fly brain

A fly brain

How has Wellcome funding helped you/your research/your career?

The Wellcome Trust has been instrumental. They funded my transition from cancer to neuroscience as a postdoctoral fellow in the USA and 15 years later, they facilitated my return. I would still be in the USA without my Senior Research Fellowship.  Support from the Trust to myself and the Centre for Neural Circuits and Behaviour, allows us to continue to follow the most interesting and difficult avenues of our work in Oxford.

What’s the most frequently asked question about your work?

Why do you work on flies?

Which question about your work do you most dread – and why?

There’s nothing I dread. I think it’s important to think about and explain what we are doing and why.

Tell us something about you that might surprise us…

Hmm, tough choice. There are a few things! How about a brain one? 10 years ago I had a 5cm left frontal lobe bleed.

What keeps you awake at night?

My hectic life-style.

What’s the best piece of advice you’ve been given?

To learn to say ‘no’ to some of the many requests for my time.

The chain reaction question, posed by the previous spotlight participant, Dr Nichola Lax, is this: How do you see your career progressing and what would be your ideal post?

Hopefully forward!  My current position is pretty good.

You can find out more about Scott and the Centre for Neural Circuits and Behaviour on the Centre’s website or by following Scott on Twitter. You might also like to read Scott’s papers: Transposition-Driven Genomic Heterogeneity in the Drosophila Brain and Layered reward signaling through octopamine and dopamine in Drosophila.

Image of the Week: Grey Drone Fly

8 Aug, 2014

L0034687 Robert Hooke, Micrographia, head and eyes of drone-fly

This week’s image depicts the head of a drone fly. It is an engraving featured in Robert Hooke’s 1665 publication Micrographia: Or Some Physiological Descriptions of Minute Bodies Made by Magnifying Glasses With Observations and Inquiries Thereupon (catchy title).

Although Hooke is more often associated with his contributions to science, the image here demonstrates his remarkable talent as a draftsman.

Hooke’s small lettered annotations remind you that this is, in fact, an anatomical diagram, though this hardly detracts from the intricate detailing in the eyes and surrounding hairs.

Micrographia is an extraordinary book and the first of its kind. It gave the public their first look at the weird and wonderful things that exist beyond the naked eye. After finding a copy in a local bookshop and staying up until 2am reading it, Samuel Pepys declared in his diary that it was ‘the most ingenious book I read in my life’.

Hooke’s own personal story is a fascinating as his illustrations. As a Fellow of the Royal Society, Hooke and Isaac Newton were absorbed in a bitter rivalry. Rumours say that Newton waited until Hooke had died before becoming more active in the Society. However, it may only be coincidence that Newton was elected President in 1703, the year of Hooke’s death.

No contemporary portraits of Hooke remain, any painted after his death have relied on written physical descriptions. Some say that once he had passed away, Newton destroyed all paintings of Hooke, but this is a mystery. Today, he remains a relatively enigmatic figure in history.

Image credit: Wellcome Images

Wellcome Images is one of the world’s richest and most unusual collections, with themes ranging from medical and social history to contemporary healthcare and biomedical science. Over 100,000 high resolution images from our historical collections are now free to use under the Creative Commons-Attribution only (CC-BY) licence.

Keeping open access simple

8 Aug, 2014
Piece of cake

Piece of cake?

The Wellcome Trust believes that access to the published outputs of research should be open and unrestricted. But, argue Robert Kiley, Head of Digital Services at Wellcome Library, and Chris Bird, Senior Legal Counsel for the Wellcome Trust, policies and licences designed to support open access publication must also be easy for researchers to understand and use.

In April 2013 we simplified our open access policy: now, where we pay an open access fee our research must be published under the Creative Commons Attribution licence (CC-BY). Why did we do this? Because we passionately believe in the power of sharing knowledge, and because CC-BY is the strongest available tool to deliver access to and re-use of our funded research. We also believe that CC-BY has become the globally recognised open access licence. Now, The International Association of Scientific, Technical and Medical Publishers (STM) has published a new set of open access licence and is encouraging its publisher members to adopt them: unfortunately, we feel this can only confuse the picture.

The great thing about CC-BY is freedom to re-use, and interoperability with other platforms and technologies. Anyone can re-use CC-BY content without getting permission: all they need to do is give credit to the author.

Under CC-BY, anyone can take an article and translate it to a different language, use text and graphics such as figures and tables in their own presentations or blogs, and use the power of computers to create links and generate new knowledge.

Anyone can post CC-BY content to any web site, including commercial ones, allowing much wider reach. For example, if new research was published which described new approaches to reduce cot death, this could be re-published without permission on Mumsnet and BabyCentre (both highly commercial sites) in order to reach more parents who may not generally search journal web sites or repositories like Europe PMC.

Since announcing our move to CC-BY, we have worked with publishers, and the overwhelming majority who offer a paid open access model have moved with us and provide our researchers the option to choose the right licence.

We are very conscious that authors still get asked to choose their licence when they publish open access, and that the choice can be confusing and complex (typically they are offered the Creative Commons attribution (CC-BY), attribution with no commercial re-use (CC-BY-NC), and attribution with no commercial re-use and no right to create derivatives (CC-BY-NC-ND)). We understand that many researchers will have little interest in the nuances of the “NC” licence versus the “BY” licence – it would be easy to think that a charity like the Wellcome Trust would not want its funded research to be used commercially, for example – so we try to work behind the scenes to make the choice that bit easier.

So while we’re happy that the licensing landscape has been getting simpler in recent years, we are concerned that the publication of the STM model open access licences will make the author’s life unnecessarily complex. Put simply, we see no value in these new licences, and believe that if a publisher wishes to restrict how content can be used (excluding Wellcome funded, OA papers which must always be published under the CC-BY licence), the existing Creative Commons licences (e.g. CC-BY-NC and CC-BY-NC-ND) are more than adequate.

Of course, first and foremost we also believe that anything describing itself as “open access” should truly be open, which means CC-BY – tested by users, interoperable, and globally recognised.

Chris Bird, Senior Legal Counsel, Wellcome Trust

Robert Kiley, Head of Digital Services, Wellcome Library

You can find the Trust’s Open access policy on our website.

Image: “Creative Commons 10th Birthday Celebration San Francisco” by tvol on Flickr

Experimental Medicine in a Time of Ebola

6 Aug, 2014
Ebola nurse

This Zairian nurse was prepared to enter the Ebola VHF isolation ward during the a 1995 outbreak in Kikwit, Zaire.

As the deadly outbreak of Ebola in West Africa continues to claim lives, Wellcome Trust director Dr Jeremy Farrar calls for Africans to be given access to experimental Ebola medication. This joint statement with Prof David Heymann, head of the Chatham House Centre on Global Health Security, and Prof Peter Piot, director of the London School of Hygiene and Tropical Medicine, expresses the urgent need for action. It was originally published in the Wall Street Journal.

A virologist carrying out mouse experiments in a lab in Hamburg five years ago accidentally pricked her finger. The syringe contained the Zaire Ebola virus, the same strain wreaking havoc today in Guinea, Liberia and Sierra Leone. There is no approved treatment or vaccine for Ebola, or even one that has passed the first phase of safety trials in human volunteers. Yet unlike those exposed to Ebola in West Africa recently, the Hamburg virologist was quickly offered an experimental vaccine.

This vaccine hadn’t yet been tested on humans, but it had been shown to offer primates some protection against Ebola infections. For the virologist, it wasn’t a good option, but it was the only one available in the face of a virus with an extremely high mortality rate. She chose to take the vaccine.

We expect it is a risk we would take if one of us were exposed to Ebola. The Hamburg researcher didn’t fall ill. It is unclear exactly how the vaccine worked, or indeed whether she was ever infected. What is important is that immediate access to an experimental vaccine allowed her to try something with the potential to protect her.

It is highly likely that if Ebola were now spreading in Western countries, public-health authorities would give at-risk patients access to experimental drugs or vaccines. Indeed, there are reports that two U.S. relief workers infected with Ebola in Liberia have been offered experimental therapies, which they have accepted.

There are antiviral drugs, monoclonal antibodies and vaccines under study that have shown varying degrees of effectiveness in animals that have been infected with or exposed to the Ebola virus. Medical agencies in rich counties affected by Ebola would begin discussions with companies and labs developing these products and then make rapid decisions about which of them might be appropriate for compassionate use.

Ebola virions

This scanning electron micrograph (SEM) depicts a number of Ebola virions.

The African countries where the current outbreaks of Ebola are occurring should have the same opportunity. African governments should be allowed to make informed decisions about whether or not to use these products, for example to protect and treat health-care workers who run especially high risks of infection.

The World Health Organization could assist African countries with developing rigorous protocols for the use and study of experimental approaches to treatment and prevention, while coordinating more traditional containment measures. As the only body with the necessary international authority, it must take on this greater leadership role.

Affected communities would need to be made fully aware regarding treatment options through open and responsible communication. And the international community must work hard to break down the barriers of fear and mistrust. In a region racked by civil war and poverty, international agencies need to be aware of infrastructure limitations, as well as those imposed by cultural and religious sensitivities.

Experimental treatments shouldn’t be rolled out generally without prior safety testing. But in the face of the critical challenge in West Africa, the WHO and Western medical agencies should be helping countries weigh the risks and benefits of a limited deployment of the best candidates to those in the greatest need, while continuously monitoring safety and efficacy.

This epidemic is now so extensive that we can expect it to last for some months yet. That means the West must fast-track safety testing of drugs and vaccines in unaffected countries, so that those which perform well could go into fuller trials in the affected region before the outbreak ends. Even if results come too late to allow trials this time around, this approach would allow studies to begin quickly when Ebola next strikes. Ultimately, the only way of discovering whether these new interventions are effective will be to test them in an Ebola epidemic.

Experimental treatments aren’t a substitute for standard infection-control measures. Past Ebola outbreaks have demonstrated which containment approaches are effective: hospital-infection control, self-protection of health workers, community education about how to avoid infection, and placing those exposed under fever surveillance and isolation for a full 21 days.

These measures, however, have failed to stop the West African outbreak, because of profound distrust in authorities and health services, strong traditional beliefs concerning disease causation and funeral practices, and, until recently, a lack of leadership. Populations have grown, people travel more and there are more people living in major cities—all of which complicate the containment of Ebola and other highly infective diseases and multiply the risks of catastrophic outcomes. These dire circumstances call for a more robust international response.

This comment piece was originally posted in the Wall Street Journal on 5th August 2014. You can hear Prof Peter Piot, who co-discovered Ebola in 1976, talking about the situation in this interview with BBC Radio 4’s Today Programme.

Wellcome Trust Research Round-Up: 4/8/14

4 Aug, 2014

Our fortnightly look at research from around the Wellcome Trust community…

8.2% of our DNA is ‘functional’

B0004905 DNA double helix

Only 8.2% of human DNA is likely to be doing something important – or ‘functional’ – say Oxford University researchers funded by the Wellcome Trust and the MRC.

This figure is very different from one given in 2012, when some scientists involved in the ENCODE (Encyclopaedia of DNA Elements) project stated that 80% of our genome has some biochemical function.

That 80% claim has been controversial, with many in the field arguing that the biochemical definition of ‘function’ was too broad, and that just because an activity on DNA occurs, it does not necessarily have a consequence. They said that for true functionality you need to demonstrate that an activity matters.

To reach the new figure, the Oxford University group took advantage of the ability of evolution to discern which activities matter and which do not. They identified how much of our genome has avoided accumulating changes over 100 million years of mammalian evolution – a clear indication that this DNA matters, with functionality that needs to be retained.

“This is in large part a matter of different definitions of what is “functional” DNA,” says joint senior author Professor Chris Ponting of the MRC Functional Genomics Unit at Oxford University. “We don’t think our figure is actually too different from what you would get looking at ENCODE’s bank of data using the same definition for functional DNA.

“But this isn’t just an academic argument about the nebulous word “function”. These definitions matter. When sequencing the genomes of patients, if our DNA was largely functional, we’d need to pay attention to every mutation. In contrast, with only 8% being functional, we have to work out the 8% of the mutations detected that might be important. From a medical point of view, this is essential to interpreting the role of human genetic variation in disease.”

The researchers Chris Rands, Stephen Meader, Chris Ponting and Gerton Lunter report their findings in the journal PLOS Genetics.

New malaria vaccine targets found in large-scale study of patients in Kenya

Researchers have discovered new vaccine targets that could help in the battle against malaria. Taking a new, large-scale approach to this search, researchers tested a library of proteins from the Plasmodium falciparum parasite with antibodies produced by the immune systems of a group of infected children.

The tests measured which proteins the children’s immune systems responded to, revealing antigens that had not previously been identified, that could be used as possible vaccine targets. They also gained new insights into the ways antigens could be used in combination to increase protection.

“Resistance to malaria drugs is an increasing problem so vaccines are desperately needed to battle the Plasmodium falciparum parasite before it has a chance to make people sick,” says Dr Faith Osier, first author of the study, from the KEMRI-Wellcome Trust Research Programme. “This study presents us with a large number of new vaccine candidates that offer real hope for the future.”

Kenyan childrenA group of children infected with malaria were followed over a six-month period by scientists at KEMRI-Wellcome. While some patients became sick, others were protected by naturally occurring antibodies that stopped the malaria parasite from penetrating their red blood cells during the blood stage of the disease, which produces severe symptoms such as fever and anaemia.

Researchers used samples taken from these children to identify combinations of antibodies that provided up to 100 per cent protection against clinical episodes of malaria.

The study used a library of parasite proteins employing an approach that was developed at the Wellcome Trust Sanger Institute by Dr Gavin Wright and Dr Julian Rayner. These researchers had previously developed a new approach to express large panels of correctly folded, full-length proteins from the Plasmodium falciparum parasite, targeting proteins involved in the invasion of human red blood cells. In this study, published in Science Translational Medicine, Sanger Institute scientists collaborated with colleagues in Kenya to see which of them the children’s immune systems had developed antibodies against.

Brain scans examine response to food in genetically obese and normal weight

People who have the most common genetic mutation linked to obesity respond differently to pictures of appetising foods than overweight or obese people who do not have the genetic mutation, according to a new study by researchers at the Wellcome Trust-MRC Institute of Metabolic Science at Addenbrooke’s Hospital in Cambridge.

Obesity typically results from a combination of eating too much, getting too little physical activity, and genetics. Foods such as chocolate trigger signals in the brain that give a feeling of pleasure and reward, and these cravings can contribute to overeating. Reward signals are processed in specific areas of the brain, where sets of neurons release chemicals such as dopamine. However, very little is known about whether the reward centres of the brain work differently in some people who are overweight or obese.

choc and brocThe most common genetic cause of obesity involves mutations in the melanocortin 4 receptor (MC4R), which occur in about 1% of obese people and contribute to weight gain from an early age.

The researchers compared three groups of people: eight people who were obese due to a problem in the MC4R gene, 10 people who were overweight or obese without the gene mutation, and eight people who were normal weight. They performed functional Magnetic Resonance Imaging (fMRI) scans to look at how the reward centres in the brain were activated by pictures of appetising food such as chocolate cake, compared to bland food such as rice or broccoli, and non-food items such as staplers.

“In our study, we found that people with the MC4R mutation responded in the same way as normal weight people, while the overweight people without the gene problem had a lower response,” said lead researcher Dr Agatha van der Klaauw. “In fact the brain’s reward centres light up when people with the mutation and normal weight people viewed pictures of appetising foods. But overweight people without the mutation did not have the same level of response.”

The study is published in the Journal of Clinical Endocrinology & Metabolism.

In other news…

Scientists at the University of Sussex are beginning a £4 million project to develop an innovative new drug for treating the devastating psychiatric condition, schizophrenia. The project is funded by a Wellcome Trust Seeding Drug Discovery award.

Two new papers in the New England Journal of Medicine by Professor Nicholas White at the Wellcome Trust-funded Mahidol Oxford Tropical Medicine Research Unit have shown that malaria resistance has spread across Southeast Asia, but also that a new antimalarial drug in development at Novartis has shown some promising results.

Image credits: DNA by Peter Artymiuk, Wellcome Images; Kenyan Children by Brad Ruggles on Flickr, CC-BY-NC-SA; Chocolate cake by Ron Paul on Flickr, CC-BY-NC-SA; Broccoli by keithloaf1961 on Flickr, CC-BY-ND.

The genetic building blocks of future healthcare

1 Aug, 2014

Sanger Institute

The Wellcome Trust has long been involved in the area of genomics, most notably funding the creation of the Wellcome Trust Sanger Institute, which spearheaded the UK contribution to the Human Genome Project. Today we announce that we are supporting Genomics England by pledging £27 million to pay for a new sequencing facility in Hinxton. Dr Michael Dunn, head of the Genetic and Molecular Sciences Team at the Wellcome Trust, explains why the Trust believes genomics is so important…

For many, the Wellcome Trust’s name will long be associated with the bold and ambitious plans to sequence the human genome. The Human Genome Project’s history is well documented and now, 10 years on from the completion of the ‘gold standard’ sequence of one human genome, technology is enabling the sequencing of hundreds of thousands of human genomes.

Why is this important? The variation between each person’s genome underlies the basis for many diseases, whether it’s a single faulty gene responsible for a child having neonatal diabetes, or the mutations and variations that cause cancer. Sequencing the genomes of pathogens also promises to revolutionise the tracking and control of infectious diseases.

DNA sequencingThese are exciting times for human genetics research, but the benefits to patients will only be realised if sequencing technology becomes part of our health service and if getting a genetic test or whole genome sequence becomes as routine as a blood test.

We are a long way from routinely using genetics to diagnose and treat a variety of diseases, but the Wellcome Trust’s £27 million investment today takes us one step closer. This will support a new building on the Wellcome Trust Genome Campus at Hinxton, part of which will be used to house Genomics England’s new sequencing facility. This will share a site with the Wellcome Trust Sanger Institute’s sequencing facility, facilitating collaborations and further strengthening this world-leading DNA science and technology hub.

Genomics England has ambitious plans to sequence 100,000 genomes from 75,000 people, some of whom will also have cancer cells sequenced. The sheer scale of the plans is pretty daunting. The genetic information arising from this project will be immense and a huge challenge for computational analysis as well as clinical interpretation. It will also raise a number of issues regarding privacy of patient data. Ensuring that these genetic data can be used maximally for patient benefit whilst protecting the rights of the individual participant must be at the heart of this project.

At the beginning of the Human Genome Project, scientists and funders like the Wellcome Trust knew they were on a journey that would be fraught with difficulties and challenges, but the long-term vision was clear. And so it is with the plans for Genomics England, it will most certainly not be easy, but the future benefits to our nation’s health promise to be immense.

You can read our funding announcement on the Wellcome Trust website.

Image of the Week: Dopamine

1 Aug, 2014

B0004541 Dopamine crystals viewed with polarized light

It appears like a psychedelic landscape – sharp ridges and dark valleys – softened by a sprawl of colour. There’s something remarkably mountainous about the scene, but the flow of pink, blue green and orange may prompt the question; what actually is it?

Despite appearing other-worldly, this is an image of a substance that occurs naturally within all of us. This micrograph, created by Spike Walker, depicts dopamine crystals illuminated by polarised light. The orientation of each crystal within the structure determines how they refract light. As a result, the wavelength of the reflected light varies, creating this spectral wonder captured under a microscope.

Dopamine is a neurotransmitter that mediates a variety of brain processes. Its release, in the parts of the brain known as the limbic system, is associated with pleasurable activities, such as eating or having sex. Some recreational drugs such as MDMA (otherwise known as ecstasy) exploit this, flooding the limbic system with dopamine to create the feeling of euphoria (though studies indicate the drug can also damage neurons).

It’s not all about pleasure when it comes to talking about dopamine. Loss of dopamine-secreting nerve cells causes movement problems in people with Parkinson’s disease. Unfortunately in most cases, we don’t know the cause of this cell death, which is why preventing Parkinson’s has proved so difficult. Knowledge of the role that dopamine plays in Parkinson’s disease has enabled the development of dopamine agonist drugs, which act like dopamine to stimulate your nerve cells, and are used to control the symptoms.

Image Credit: Spike Walker, Wellcome Images

Wellcome Images is one of the world’s richest and most unusual collections, with themes ranging from medical and social history to contemporary healthcare and biomedical science. Over 100,000 high resolution images from our historical collections are now free to use under the Creative Commons-Attribution only (CC-BY) licence.

We must learn lessons from this Ebola outbreak

30 Jul, 2014

Ebola virus virion

The current outbreak of Ebola in West Africa is the worst since the virus was first identified in 1976. Wellcome Trust Director Dr Jeremy Farrar, explains why we mustn’t underestimate the huge challenges presented by this deadly infectious disease…

It is easy to think of Ebola as an outlier, a rare and exotic disease that is particularly hard to learn about due to the sporadic nature of its outbreaks. Yet there is much we could and should learn from this outbreak, and quickly.

From the spread of countries affected, to the number of those who have lost their lives, this situation cannot be ignored. It is compounded by the movement of people, the pressures on infrastructure, and the capacity of the healthcare systems in the regions trying to cope with the crisis they face.

Information is hard to come by and rumours abound, and there are a surprising number of basic elements that we still do not understand. For example, we know little about the characteristics of this virus infection and the clinical response in humans. Despite the large number of deaths reported, the mortality rate during this outbreak has so far been lower than might be expected for the strain of the virus we believe is responsible.

Does this mean there is more to this virus than we know? Or perhaps there are differences in the human physiological response that we don’t yet appreciate or in the clinical care of the patients.

As the disease tightens its grip it surely threatens the resolve of those on the ground, who are doing all they can despite incredibly difficult circumstances.

These issues affect all of us.  Even if Ebola does not reach our shores, other emerging infectious diseases or drug resistant pathogens will, and this must be addressed in an equitable and globally responsible way.

Indeed SARS, avian and swine flu outbreaks have already had an impact much closer to home, and while we are much better at the surveillance of such outbreaks we are still not tackling them – or learning from them – fast enough.

In a world made so much smaller by the ease and speed of travel, what is happening in Lagos or Shanghai today may be relevant in London tomorrow, and vice versa. This means we have to get much better at dealing with outbreaks if we are to be truly prepared for the global damage they may bring.

We need to work with at-risk communities and national governments to discuss potential new treatments and how they might work within ethical, logistical and assessment frameworks, and we need them to be ready to go within days.

We also have to work out how to ethically, and practically, undertake the essential clinical research in an emergency that is critical to save lives and reduce disease transmission.

This needs extensive preparation in the period between epidemics, full engagement with all countries – particularly those most at risk of epidemics – and full consideration of the ethical and health frameworks involved.

It is a huge undertaking, complex and challenging in many ways. But our ability to control this and future outbreaks may depend on it.

Dr Jeremy Farrar is the director for the Wellcome Trust. Before joining the Trust he spent almost two decades in Vietnam, where his research focussed on emerging infectious diseases.


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