Skip to content

The Reckoning: An Analysis of Wellcome Trust Open Access Spend 2013-14

3 Mar, 2015

Cost of Open Access

To help make the costs around open access more transparent, the Wellcome Trust has published details on how much it spent on article processing charges in the year 2013-14. The data also shows to what extent the services the Trust has paid for – i.e. that the final, publisher-formatted versions of articles are freely available in Europe PubMed Central with a CC-BY licence – have been delivered. Robert Kiley, Head of Digital Services at the Wellcome Library, provides an analysis of what the latest data reveals...

Once a year we ask all those institutions in receipt of an open access (OA) grant from the Trust to provide details on how the grant has been spent. In addition to simply calculating the total spend, and the average article processing charge (APC), we have, for the first time, done an analysis of the licence types that have been applied to these articles. The licence analysis was undertaken to determine to what extent articles had been published under the Creative Commons Attribution licence (CC-BY), in line with our OA policy.

Cost data

In headline terms, some 2556 articles were published under an APC model, and the total spend for the year 2013-14 was just under £4.7 million. The average APC was around £1837, whilst the median cost was £1800. Table one, shows how these figures compare with the previous year (2012-13).
Open access spend Wellcome Trust

The takeaway form this is that more Trust-funded articles are being published via the OA APC route – an increase of 20% – whilst APC fees are relatively static (an increase in the average APC of just 0.8%).

Focusing just on 2013-14 data, Table two provides a breakdown of the type of journal where the articles were published, and the average APC for each type. A fully OA journal is one in which every article is made OA (e.g. PLOS One, Cell Reports etc.), whereas a hybrid journal is one which is still published under a subscription model, but where individual articles can be made OA. The “unknowns” in table two are those that we were unable (programmatically) to determine if the article was published in a fully OA or a hybrid journal.

Open access spend Wellcome Trust

Although Wellcome Trust authors are publishing large numbers of papers in fully OA journals (around 24% of all papers in this cohort), there is still a very strong desire to publish in traditional, subscription-based journals, albeit via the OA, hybrid route (in line with the Wellcome Trust policy).

The second key finding is that the average APC levied by hybrid journals is 64% higher than the average APC charged by a fully OA title. This higher average fee is despite the fact that hybrid journals also enjoy a revenue stream from subscriptions.

Faced with similar data showing the high price of APCs charged by hybrid journals, a number of organisations – including the German Research Foundation, DFG, and the Norwegian Research Council – do not allow OA grants to be used to fund APCs in hybrid journals.

Given the scale of hybrid OA publishing amongst Trust-funded researchers, such an approach would seriously limit the ability of many of our researchers to publish in their journal of choice, and therefore we have (to date) decided not to go down this path.

However, we do feel that the hybrid APC market is not working effectively and we are actively exploring other ways to tackle this marketplace’s current dysfunctions. By way of example, the FWF (Austrian Science Fund) have recently imposed a cap of €1500 for hybrid articles. We will watch with interest whether this cap leads to any change in author behaviour (i.e. authors start to consider price when they are submitting an article for publication), or changes to publishers’ APCs.

Our final table on costs provides an analysis of the top five publishers (by volume of Trust-attributed articles published).

Open access spend Wellcome Trust

What is significant here is the degree to which the two traditional, subscription-based publishers (Elsevier and Wiley) still dominate the field where Trust authors seek to publish. Together, these two publishers represent some 40% of our total APC spend, and are responsible for 35% of all Trust-funded papers published under the APC model.

It is also interesting to note that the average APCs for the fully OA journals published by Elsevier and Wiley are significantly higher than those charged by competitors at PLOS, BMC and OUP.

Compliance data

The other reason for collecting this data is to check whether the publisher has provided the service we demand in return for paying an APC.

When Trust funding is used to cover an APC, the publisher has to provide a number of specific services. These include depositing the final version of the article in PubMed Central (PMC) at the time of publication (this content is then mirrored to Europe PMC) and attaching a CC-BY licence to the article, thus making is clear that anyone can re-use that work for any purpose, subject to the norm of attribution.

To help us check compliance in a more automated way, we commissioned Cottage Labs to develop a “compliance monitoring” tool to programmatically determine whether the paper is in the Europe PMC repository and what licence (if any) is attached.

A summary of the key compliance findings is presented in table four:
Open access spend Wellcome Trust

The headline data is disappointing – particularly in terms of the relatively high numbers of papers which are not in the Europe PMC repository.

To investigate this further, we undertook a manual exercise to determine if these articles were freely available on the publisher site and/or were published “ahead of print”. The latter distinction is important as the PMC repository only accepts the final version of the article, and thus it not possible for a publisher to deposit a paper that is released online “ahead of print”.

The results of this exercise are shown in table five:

Open access spend Wellcome Trust

Table five shows that typically publishers are making APC-funded papers OA on their sites. This suggests therefore that, for some publishers the problem is confined to being able to consistently deposit papers at PMC. By way of example, of the 325 papers that were not in Europe PMC, 110 of these (34%) were published by Wiley.

It is also interesting to note that 23% of the papers are classified as “early view” papers, and that in the fullness of time we can expect most (all) of these papers will be deposited in PMC (and mirrored to Europe PMC). Looking across this cohort of papers we can see a wide range of early view publication dates, with the oldest article (not yet formally published) originally published online in October 2013.

However, even if we assume that all the early view papers will be deposited, this still means that 237 papers, available in final published form, for which APCs totalling over £480,000 have been paid, are not available in Europe PMC.

This is unacceptable.

Licence compliance was always going to be more problematic – authors do not always fully understand the Trust’s requirements, a situation compounded by some publishers who persist in offering a choice of licences to Trust funded authors – but we do now have a baseline compliance rate (61%) to build on.

Action Areas

As a matter of urgency the Wellcome Trust has started to follow up with all the publishers concerned, to better understand the problems they are experiencing, and how they plan to rectify them. It is encouraging how responsive publishers have been so far.

Their responses have also highlighted the number and variety of obstacles facing articles destined for open access; obstacles which publishers, funders and institutions must identify and navigate when tracking compliance. Problems identified include:

  • Content not available in PMC, even though the publisher believes they have successfully deposited it;
  • Institutions reporting an APC payment – but publisher has no record of that article ever being flagged as an OA paper (and no invoice was ever raised);
  • Articles submitted for publication before the CC-BY requirement was introduced (1st April 2013);
  • Ambiguous (or no) licence information in the article;
  • Contradictory licence information (the human readable text says one licence, the licence encoded in the XML cites a different one);
  • Author has selected an alternative to the CC-BY licence (either erroneously, or otherwise), presumably unaware of the sanctions the Trust has defined for non-compliance).

Pinning down which of the above issues relates to which specific articles is a moving target, but the numbers involved indicate clear trends and challenges.

It is clear that early view articles pose another challenge; it is only possible to identify whether the article is early view manually, and if it is, the months which elapse before its final publication (and deposit in PMC/Europe PMC) are still troubling. The Trust is discussing this issue with staff at PMC to see if a policy change can be made, such that publishers can (for papers funded by named funders) deposit an early view paper and follow-up with the final, published version, in due course.

We will also be following up with institutions with regards to our CC-BY requirement and we will make it clear that, going forward, any APC costs associated with papers that are not licenced CC-BY cannot be met from Trust funds.

We will also be ensuring publishers are aware of their obligations to ensure papers associated with our funding are deposited and licensed in line with our requirements where an APC is being charged. We will also make clear our expectation that the licences are encoded in a consistent, machine-readable way.

Moving forward, in cases where particular journals or publishers consistently fail to deliver the services that have been paid for, we will declare them to be non-compliant with our OA policy, and alert researchers and institutions to this, including through the Sherpa FACT service. More generally, we will encourage all researchers and institutions to actively consider whether the APC they are being charged by a particular journal is justified in light of the quality of service they receive.

Conclusion

Last year, when we released our first set of APC data, I published a blog post that concluded by saying that we expect every publisher who levies on open access fee to provide a first class service to our researchers and their institutions.

One year on, there are still significant problems – especially in terms of depositing content in PMC and licensing this in accordance with our requirements – and the first class service called for still seems to be some way off. These problems are particularly prevalent amongst publishers offering a hybrid OA option, which, as discussed above, is also the more expensive way to comply with our OA policy.

The Trust remains committed to its OA policy, but ultimately if we are to be successful and get to the point where all Trust funded research is OA, then the friction in the system – which is all too evident in this analysis – has to be resolved.

You can read the Wellcome Trust’s OA policy on our website and if you’re interested in exploring our 2013-14 APC data set you can find it on Figshare. The underlying code for the Cottage Lab compliance tool we used has been This piece of software has been made available on github under an Apache open source licence, to enable others to take this code and adapt it to suit their specific needs.

Image Credit: Kate Arkless Gray/Wellcome Trust – CC-BY

Researcher Spotlight: Dr Arun Shukla

2 Mar, 2015

Arun Shukla Dr Arun Shukla is an assistant professor in the Department of Biological Sciences and Bioengineering, at the Indian Institute of Technology. His research focuses on the largest group of cell surface receptors and he hopes that understanding the atomic level structures of these receptors may in future help us design more effective drugs. Here Dr Shukla talks about how he came to be at the forefront of a new line of research in India…

What are you working on?

We are trying to understand how G Protein-Coupled Receptors (GPCRs) work. These receptors are the largest class of cell surface receptors in our body and they are targeted by about half of the currently prescribed medicines.

GPCRs control many physiological processes in our body such as blood pressure, heart beat, pain sensation and appetite – to name a few. Our primary focus is on obtaining atomic resolution information on selected GPCRs to decipher their activation and regulatory mechanisms.

We design and generate synthetic protein binders to stabilise these receptors in specific conformations so that we can trap these conformations by X-ray crystallography.

What does your average day involve?

The first thing I do after coming to the lab is to talk to my students and fellows, get updates on experiments, discuss and design the next steps and so on. Then, I talk to my lab manager and get updates on the status of various orders, visitors etc. Of course, on days when I have to teach a class in the afternoon, I work on slides and read about the topics that I am going to cover in the class.

I like to work on grants and papers in the afternoon and try to spend solid two-three hours if possible. As you can imagine, there are other commitments on some days such as different committee meetings, seminars etc. And yes, a couple of trips to coffee joint and checking emails every five minutes.

Why is your work important?

Protein ShuklaWe believe that our work will not only reveal fundamental mechanistic insights in to very complicated cellular signalling events but it will also provide a framework for translational discoveries. Our research is directly relevant to a number of human diseases and the hope that perhaps our research findings in long run might help somebody, someday, somewhere, is what keeps us motivated and to keep going.

From the Indian science point of view, our work is likely to establish a new line of research in India i.e. Structural Biology of Membrane Proteins, GPCRs in particular. This is an incredibly challenging endeavour and has not received much attention in the Indian research community. Thanks to Wellcome Trust DBT India Alliance fellowship programs, this research domain is picking up some pace in the country.

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

We hope that by understanding their atomic level structures, we will be better positioned to design drugs that will be more effective against various diseases and will have lesser side effects. Although our work primarily focuses on basic research, the potential outcomes have tremendous translational potential. 

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

My lucky break in research came when Professor Rakesh Bhatnagar from Jawaharlal Nehru University (JNU) in New Delhi (India) arranged for me to do a summer research project during my MSc in Professor Shyamal Goswami’s laboratory. That is where I realised that research was my calling.

During my Masters in biotechnology, I started to learn about how critical membrane proteins – especially GPCRs – are for receiving diverse signals outside of the cells and communicating them across the membrane to inside of the cell. This got me fascinated with these incredible molecular machines and I developed a desire to understand their atomic details.

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

The kind of research we do is incredibly expensive and consumables-intensive. And, that perhaps applies to most research areas in life sciences, if not all. I feel very fortunate to have received the Intermediate Fellowship within a couple of months of landing in India. This meant that I don’t have to run after many different funding agencies to accumulate the quantum of funds that I would have liked to begin with.

Moreover, the flexibility to spend the funds as per the needs of the project and the timely release of funds are indeed a blessing. As the India Alliance fellowships are highly competitive, the prestige of being a fellow also has added advantage with respect to visibility in the science community.

Arun Shukla

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

I always talk about how many physiological and cellular functions are mediated by GPCRs. People often ask me how can they regulate so many things with extreme temporal and spatial precision in a very complex cellular context.

I wish that I knew the answer but that is what we are trying to figure out. The other question that I often get, especially from students, is how did I get a chance to work with three different Nobel Laureates during my Ph.D. and post-doctoral research? – I say, “I just got lucky”.

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

Nothing as such but sometimes, people ask me how closely X-ray snapshots represent the native structure of proteins in their natural environment. I do not think that anybody has a very good answer to that.

Tell us something about you that might surprise us…

When I was in college, I developed an interest in journalism and politics. I even considered a career in one of those professions. I wrote many small articles for national newspapers and magazines, and I also contested elections of the students union in college.

I guess writing research papers now satisfies my appetite for getting published and perhaps in future, I would be able to contribute in science policy decisions to my address my cravings for administration.

What keeps you awake at night?

Anticipating data that my students email me late at night, often past midnight. When I go home in the evening, I know what experiments were being run in the lab and which of them will be finished later in the night and yield some data. I have my smartphone under my pillow and when it beeps (indicating an incoming email), I just cannot resist checking it.

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

I guess, the advice given by my post-doctoral mentor, Professor Robert Lefkowitz (Nobel Prize, 2012). He used to say: “there are three keys to success in research, the first is focus, the second is focus and the third is focus”. Even now, I tune to one of his YouTube videos once in a while and hear him say this again.

The chain reaction question – posed by previous spotlit researcher, Dr Daniel Streicker, is this: If you had a time machine, what year would you travel to and why?

I would love to travel 20 years into the future and see how the projects that we worked on progressed over the years. Of course, I would be lot wiser when I return because I would know what did not work, and we could tweak the experiments accordingly.

If you’d like to read more about Dr Arun Shukla’s research, the following papers may be of interest: Methodological advances: the unsung heroes of the GPCR structural revolution and Visualization of arrestin recruitment by a G-protein-coupled receptor. You can also follow Dr Shukla on Twitter as @ArShukla.

Image of the Week: The Nutshell Studies of Unexplained Death

27 Feb, 2015
Dark Bathroom (Tub), Corinne May Botz, 2004. Image courtesy of the artist

Dark Bathroom (Tub), Corinne May Botz, 2004. Image courtesy of Corinne Botz and Benrubi Gallery.

This unsettling image of a doll meeting her untimely end, carries a deadly serious purpose. It is a close up portrait of one the twenty miniature crime scenes created by American heiress and criminologist Frances Glessner Lee in the 1940s and 50s. Termed ‘The Nutshell Studies of Unexplained Death’, each of these macabre dollhouse scenes was based on a composite of actual crimes. Their purpose was to train police investigators in a more methodical approach when observing and collecting evidence, while encouraging better interaction between law enforcement and the medical community. The Nutshells are still used for police training in Baltimore today.

Our featured image this week was created by artist and author Corinne May Botz, who spent several years photographing the Nutshells and researching the work and life of Glessner Lee. She was particularly fascinated by the ways in which these meticulously crafted crime scenes, created by a self-taught, wealthy socialite, subvert the notion of the home as a safe haven, especially for their (mostly female) victims. Her photographs magnify Glessner Lee’s miniature worlds of domestic violence to an unnervingly human scale.

A selection of Corinne May Botz’s compelling photographs are on display, alongside one of Glessner Lee’s original Nutshell studies, as part of Wellcome Collection’s new (and free!) exhibition ‘Forensics: The anatomy of crime’, which opened this week.

Clinical trials not immune from poor quality drugs

26 Feb, 2015

B0006919 Capsules

There is an increasing body of evidence to suggest that significant quantities of medicines and medical products, especially in low and middle-income countries, are of poor quality. Malaria researcher and drug quality expert Professor Paul Newton, of the Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit in Laos, explains the latest research findings and explores some of the recommendations to improve medicine provision for clinical trials…

Substandard medicines (due to errors in factory production) and falsified medicines (due to criminal fraud) are profoundly neglected global health problems. Poor quality drugs have the potential to deny patients and their families the full and expected benefits of modern medicine.

Global and national health policy decisions are often made using evidence generated from clinical trial reports. Until recently it was believed that trials were immune from the issue of medicine quality. However, recent research investigations suggest worrying evidence of poor quality medicines administered during patient trials.

Clinical trials are the trusted method of providing the results needed to make important policy decisions about whether medicines are safe, efficacious and provide value for money. Patients who volunteer to participate in trials do so with the knowledge that the results will be reported transparently, and without bias, so that ultimately many other patients can benefit from the scientific findings.

N0018981 Pills and vitaminsPolicy guidelines have improved the practice of medical research, especially clinical trials, and helped to ensure that trials are more carefully planned, implemented and reviewed. However, some guidelines need to be strengthened further to include clear guidance on how to monitor and safeguard the quality of medicines used in patient trials.

Working with a team of international medical experts, we recently compiled a number of findings published today in the British Medical Journal. The results highlight the apparent inadequacies of existing clinical trial guidelines, and the absence of sufficient checks in place to safeguard the quality of medicines used during patient trials.

One report of antimalarial drugs that were planned to be used in pregnant women in Africa, describes that one of the brands contained less than 90% of what the label stated. Our study also describes problems with a trial of the efficacy of vitamin A in Tanzania, Africa. Thirteen months into the trial it was found that the amount of Vitamin A supplement had deteriorated to only 32% of the stated amount of vitamin A, despite appropriate storage conditions.

Perhaps surprisingly for some, our research team found that the issue is not just confined to the developing world. A cardiac drug shipment worth £1 million was sent from the UK to a pharmaceutical company in the USA in 2007, for use as a comparator in a clinical trial. Suspicions raised by the tablets’ weight led to the discovery that the entire consignment was falsified, containing only 50-80% of the drug stated in the consignment.

B0007401 pillsAs a global health community we should call for urgent changes in the guidance for checking the quality of clinical trial medicines. Guidelines such as the Consolidated Standards of Reporting Trials (CONSORT) and the International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH) guidelines, be adapted to require that researchers clearly state the quality of medicines and any other medical products used in their clinical trials.

In addition, global health bodies should review more closely the current pharmaceuticals market, where globalisation of production, coupled with insufficient regulatory overview, has created a situation where medicines may be of wildly varying qualities.

If the standards aren’t tightened, it is likely that poor quality medicines used in medical research may lead to wrongful conclusions that useful medicines are not useful and that harmful medicines are safe to use.

If these critical amendments are made, the chain of evidence for health policy decision-making should be significantly reinforced, less money on trials will be wasted and patient confidence restored in the quality of medicines being used in clinical trials.

Read the full research findings in the British Medical Journal, and discover more of Paul Newton and colleagues’ work on Antimalarial Drug Quality at the Worldwide Antimalarial Resistance Network (WWARN).

Image credits: Anna Tanczos, Wellcome Images, Kate Whitley, Wellcome Images and Spooky Pooka, Wellcome Images.

House of Lords votes to approve mitochondrial donation techniques in UK

24 Feb, 2015

After four hours of intense debate in the House of Lords, peers have voted to approve regulations that will allow mitochondrial donation to be licensed for use. The techniques, pioneered by scientists at the Wellcome Trust Centre for Mitochondrial Research at the University of Newcastle, give hope to families suffering from mitochondrial disease. Wellcome Trust Director, Dr Jeremy Farrar shares his thoughts on this momentous decision…

Vicky and Jessica2Families who know what it is like to care for a child with a devastating disease are the people best placed to decide whether mitochondrial donation is the right option for them.

Parliament is to be commended for a considered and compassionate decision to give these families that choice, with proper safeguards under the UK’s internationally-admired regulatory system.

Parliament’s decision is a credit to the patients, scientists, doctors and ethicists who have worked so hard over the past decade to explain this complex research to politicians, the public and the media, and to the exemplary process for reviewing scientific, ethical and public opinion led by the Human Fertilisation and Embryology Authority.

We have again seen how science advances most effectively through engagement with wider society.

If you want to find out more about the techniques, scientific and ethical reviews and the public consultation that were mentioned today’s debate before the vote to allow the technique to be used, check out the Wellcome Trust policy pages. The first applications to the HFEA for mitochondrial donation could come later this year, you can read our previous posts on the subject on our blog.

Pathways of resistance: from mercury to methicillin

24 Feb, 2015

Mercury

In a climate of rising fear over the diminishing efficacy of antibiotics, Wellcome-supported microbiologists have looked back at the bacteria-killing substances of the pre-antibiotic era – toxic metals. Jemima Hodkinson looks at how resistance to these metals may be linked to drug resistance in bacteria…

Dr Jon Hobman, University of Nottingham, and Dr Lisa Crossman, from the University of East Anglia, recently published a review of bacterial antimicrobial metal ion resistance in the Journal of Medical Microbiology. Their article concludes that the ancient pathways of resistance that bacteria have evolved against metals such as mercury, copper, arsenic and silver may be intimately linked to the antibiotic resistance genes that are circulating in bacterial populations today.

Metals and metallic compounds have been used for medical and biological purposes for millennia: as antiseptics, diuretics, and dental fillings; cosmetics, tonics and chemical weapons. Most are indiscriminately toxic, and you have to wonder whether some of these historical cures were actually worse than the ailments they were intended to treat. Mercury-laced teething powder, anyone?

L0057809 Blue ridged glass bottle for arsenic, Europe, 1701-1935Metals and their ions can damage cells in multiple ways: binding to enzymes, DNA and membranes, disrupting their function; taking part in reactions that generate harmful free radicals; or binding to the cell’s pool of antioxidants that usually protects against free radicals. It is the lethal damage that these mechanisms can inflict on bacterial cells that underlies the utility of metal compounds in controlling infections in plants, animals and humans.

However, bacteria have evolved their own defences against the toxic effects of antimicrobial metals, as they have also done with modern antibiotics. Some methods are generic, such as stress response mechanisms and efflux pumps, which try to bail toxic molecules out of the cell faster than they can come in.

Others are specific weapons against particular metals or ions: these are controlled by a response regulator, a neat signalling system that turns on the genes for the cell’s defensive response when it senses the ion present in the environment. For example, the method that bacteria use to protect themselves against mercury ions involves a protein which ferries the ion into the cell, then hands it over to an enzyme that converts it into non-toxic mercury molecules, which can then diffuse out of the cell. Scientists have identified related mechanisms for several other metals; many are ancient, evolved over millennia in response to metal ions present naturally in the environment.

Today, use of all but a few metals in medicine has now been phased out, superseded by safer, more effective modern antibiotics. Should we care that E. coli is resistant to arsenic, or that mercuric chloride might no longer cure your syphilis?

Thanks to a dramatic increase in available microbial genome sequences, there is increasing evidence that metal ion resistance and antibiotic resistance are linked by being carried on the same mobile genetic elements that are capable of being moved between bacterial species and strains. Antimicrobial metal resistances could be contributing to the more pressing problem of resistance to modern antibiotics.

M0012706 Title-page to: 'A treatise on mercury.'When mercury resistance was beginning to be reported in clinically important bacteria in the 1960s, it was found to be genetically linked to penicillinase plasmids in S. aureus. Comparing these clinical isolates with samples from the ‘pre-antibiotic era’ – some from 10,000 year old Siberian permafrost, others from the first half of the 20th century – leads the authors of this review to conclude that the Tn21 family of mercury resistance transposons – a type of mobile genetic element – could have evolved stepwise into multi-drug resistance transposons, eventually carrying genes conferring resistance to streptomycin, chloramphenicol and tetracycline as well as mercury.

This evidence for the co-carriage – and potential for co-selection – of metal ion resistance and antibiotic resistance genes could be important when thinking about approaches to combat antibiotic resistance, particularly given the increasing use of metals with antimicrobial properties in consumer products, from plasters to water filters.

It could also provide a worrying glimpse into the future of resistance to modern antibiotics. Current advice emphasises the need to limit use of antibiotics, on the assumption that reducing the pressure for bacteria to carry resistance genes will lead to their loss by natural selection. However, mercury resistance has persisted despite the fact that antimicrobial use of mercury compounds has all but stopped – a phenomenon that the authors admit is surprising.

Could antibiotic resistance genes persist in bacterial populations in a similar way, even if use declines?

Hobman and Crossman’s article also reminds us that microbiology can often take a human-centric view. While antibiotic resistance to modern antibiotics is usually seen as a problem of treatment failure, the way that resistance genes spread is an ecological problem. Understanding this could provide important lessons for future attempts to manage antibiotic resistance.

You can read the full article, Bacterial antimicrobial metal ion resistance, in the Journal of Medical Microbiology. Jemima Hodkinson is on the Wellcome Trust Graduate Development Programme and you can find more details of the scheme on the Wellcome Trust website. This post was originally published on Microbe Post – the blog from the Society of General Microbiology.

Image Credits: Top: Mercury byLa Belle Lumière on Flickr, CC-BY-NC-ND, Arsenic and Treatise on Mercury from Wellcome Images

Wellcome Trust Research Round-Up: 23/02/15

23 Feb, 2015

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

The secret life of pollinators in the city

beeCities should not be overlooked as important havens for bees according to research by a team of scientists from universities across the UK.

Pollinators such as bees play an important role in ecosystems but very little is known about how they interact in urban landscapes. With more and more people living in cities, researchers decided to compare and contrast pollinator populations in urban, agricultural and protected landscapes around the UK.

The study, published recently in Proc. R. Soc. B, surveyed 12 large urban centres in the UK. For each city, a nearby nature reserve and farmland site was also surveyed. They recorded a total of 7,412 insects which were visiting flowers. In the study, 11 rare or scarce species were recorded, four of which were found in urban habitats. The ‘species richness’ of bees – the number of species in a given area – was found to be higher in urban zones than farmland site, although there were fewer hover-flies in urban areas.

The team, led by Dr Katherine Baldock of the University of Bristol, said urban landscapes deserve more attention in the drive to protect bees from decline. “Urban areas could be managed in a way to be good to pollinators. What we need to know next is which habitats within urban areas are good for pollinators”, she said.

The research was funded by the Insect Pollinators Initiative, a joint venture between the BBSRC, Defra, NERC, the Scottish Government, the Wellcome Trust, and LWEC.

Genes identified as drug targets for allergies and asthma

asthma34 new genes that make people more likely to suffer from allergies and asthma have been identified, some of which could be targets for new drugs.

This research, published in Nature and led by scientists at Imperial College London, could lead to new treatments for allergic diseases, and help to predict who will respond best to currently available treatments.

The work, involving researchers in the UK, US, Canada and Sweden, studied the genes that regulate the immune response in allergic reactions and asthma. The team looked at ‘epigenetic changes’, which do not affect the genetic code itself but which influence the activity of genes.

Using this approach, the team were able to locate genes that regulate the antibody involved in triggering allergic responses. This antibody, called immunoglobin E (IgE), was known to researchers already but until now scientists had been unable to identify which genes control its activities.

They found strong associations between IgE and increased activity in 34 genes. In people with asthma, these genes are overactive, making them produce more IgE, which contributes to symptoms of asthma.

Professor Miriam Moffatt, Wellcome Trust Senior Investigator and one of the study’s authors said: “The genes we identified represent new potential drug targets for allergic diseases as well as biomarkers that may predict which patients will respond to existing expensive therapies”.

Their research was supported by the Wellcome Trust.

Study predicts Ebola cases in Sierra Leone

ebola wrrA model produced by an international team of researchers suggests that cases of Ebola have peaked in Sierra Leone.

Between August and November 2014, the incidence of Ebola rose dramatically in several districts of Sierra Leone, meaning treatment centres were stretched past capacity and were lacking beds. During December, additional beds were introduced, and incidence declined in many areas. This study, published in PLoS Current Outbreaks, aimed to measure patterns of future demand to help doctors better prepare.

To do this, researchers based in the UK, Switzerland and Sierra Leone and led by the London School of Hygiene and Tropical Medicine used a mathematical model of Ebola infection to estimate how the extent of transmission in the nine worst affected districts of Sierra Leone changed between 10th August 2014 and 18th January 2015. Using the model, they forecasted the number of cases that could occur until the end of March 2015, and compared bed requirements with expected future capacity.

They found that, although Ebola incidence has varied over time and space in Sierra Leone, results suggest that the epidemic may have now peaked. Current numbers of beds appear to be sufficient to keep the epidemic under control in most districts.

The research was funded by R2HC, which is a partnership between the Department for International Development (DFID) and the Wellcome Trust, aimed at improving health outcomes by establishing a strong base of evidence about public health interventions during humanitarian crises.

In other news…

Last week saw the performance of songs developed through partnerships between young people, sexologists and songwriters from across the UK, looking at how sex and sexuality is represented in music and lyrics. You can listen and read about their work here and our most recent image of the week is also about the project.

Brain signatures of intrusions of thought while falling asleep are reported in a paper by Trust-supported researchers in Frontiers in Psychology Research.

A Wellcome Trust funded film about Antoine Yates, who kept a tiger called Ming and a large alligator in his high-rise New York apartment for several years, was screened last Wednesday at the Tate. You can see the trailer here.

Image credits: Wellcome Images

Image of the Week: Songs of Sexology

20 Feb, 2015
credit - Roundhouse Rising, Daily Motion

Manchester group, Level Up. Image courtesy of Roundhouse Rising, Daily Motion

“[It] was the best day of my life… I’d do anything to live that day again!” – A young artist talks about Sounds of Sexology

This picture shows a group of artists performing their music at Sounds of Sexology showcase earlier this week at the Roundhouse. The event was the culmination of months of hard work, talent and passion, as five groups of young performers – from Manchester, Glasgow, Brighton, Havant and London – have worked in partnership with songwriters, sex researchers and incredible youth music organisations on a nationwide Sexology Songwriting project that saw explorations of sex and relationships transformed into touching (and at times provocative) musical works.

Topics like lust, love and consent; the history of sex research; relationships and sexuality inspired an evening of music that touched everyone there (and everyone watching on the live-stream at home). One of the groups looked at young people’s sexual values and experiences, and came up with tracks that championed the right to feel confused and conflicted about relationships. Another focussed on LGBTQ issues and poked fun at the notion that the legalising of homosexual marriage might provoke freak weather incidents…

Event host Greg Foot, one of our Public Engagement Fellows, introduced the aims of the project and welcomed each group in turn, getting them to say a little about the experience of being involved in this project – even the shy ones. As the young artists took to the stage, it became obvious that the songs had personal importance to each and every one of them, and their performances took on extra levels of meaning – there were definitely some leaky eyes in the audience. The evening was neatly rounded off with a special guest performance from Dan Gillespie Sells, songwriter and frontman of UK band The Feeling, who gave an insight into his personal experiences with sexuality as well.

The audience were blown away by the talent of the young artists, who despite having totally different musical styles and experiences – from rap and spoken word poems, to acoustic guitar numbers and indie tracks with multi-part harmonies – threw themselves into their performances and made everyone involved feel truly proud.

All the songs from the project will be made available on the Wellcome Collection website soon, but in the meantime, you can catch a selection of the performances on the Roundhouse website, or visit The Institute of Sexology to hear some of the songs at listening posts in the exhibition that inspired the project.

Image credit: Level Up, the group from Manchester, courtesy of Roundhouse Rising, Daily Motion

Researcher Spotlight: Dr Daniel Streicker

16 Feb, 2015

Daniel StreickerDr Daniel Streicker is a Wellcome Trust/Royal Society Sir Henry Dale Fellow at the University of Glasgow. His research looks at the way that pathogens are transmitted between species, with a hope that a better understanding of the ecological and evolutionary factors will allow us to prevent disease spread in future. Daniel has spent time in Peru investigating the frequency that vampire bats spread rabies to humans and livestock – and not managed to escape their bites! Here he shares his passion for his work, and some great advice from his former lab…

What are you working on?

Some of the most important emerging infectious diseases occur when pathogens are transmitted between species. Dramatic examples include the ongoing Ebola outbreak, the SARS outbreak of 2003 (both likely seeded by bats) and HIV (originally from non-human primates). But, the same epidemiological phenomenon underlies major public health and agricultural burdens from pathogens that don’t necessarily spread in humans or domestic animals, but recurrently emerge from other species.

Which pathogen will emerge next, from which host species, and where it will happen? These are some of the biggest questions at the interface of ecology, evolution, public health and veterinary medicine. We are applying tools ranging from field ecology, to molecular phylogenetics, metagenomics and bioinformatics, to mathematical modelling to try to answer fundamental questions about disease emergence between species and improve prospects for control of known zoonoses.

We focus our work around bats, a key group for both newly emerging and well-established zoonotic diseases. Some of the most exciting questions we are addressing right now are: Is culling an effective tool for the control of vampire bat transmitted rabies in Latin America? What ecological and evolutionary factors govern the diversity of viruses in bats and which of these pose the greatest threats to domestic animals? And are there generalisable genomic signals of RNA virus host range and human adaptation.

What does your average day involve?

Since starting my fellowship, my average day has changed quite a lot. The day-to-day management of a big field project in Peru and the usual routine of preparing talks, analysing data and writing papers still keeps me busy, but having a growing team of researchers in my group is an exciting change, particularly considering the diversity of projects going on. So, one minute I could be talking about sampling strategies to collect bat faeces, the next I could be talking about legal agreements with foreign ministries, or the odd things that go on in RNA virus genomes. This requires a good deal of coffee.

Why is your work important?

In a paper in 2009 in Science, Jamie-Lloyd Smith and colleagues wrote: “Models incorporating spill-over transmission—the defining process of zoonotic dynamics—are dismayingly rare.” That situation is beginning to change, but we still have very few success stories in preventing disease emergence between species and many more instances where we seek to intervene without a solid understanding of the ecological dynamics underlying emergence.

The consequences are severe. Every year it is estimated that over one billion people become ill due to the pathogens of other species, with up to one million deaths. I think ecological and evolutionary approaches can help alleviate this burden by devising control strategies that are grounded in understanding the dynamics of host-pathogen systems.

peru picThe work in Peru has particular significance because of the extraordinary frequency of contact between vampire bats and the humans and livestock that they feed on. A recent presentation from the Ministry of Health reported that over 20,000 people were bitten by vampire bats between 2009 and 2013 and many many thousands of domestic animals are bitten nightly.

This is a tremendous force of infection that causes rabies outbreaks and creates the perfect ecological scenario for other bat viruses to emerge. We want to know how to manage this risk in landscapes undergoing rapid environmental change due to livestock intensification, deforestation and mining.

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

I believe our work sheds light on the ecological and evolutionary factors that allow viruses to jump between species. This moves us one step closer to understanding the origins and outcomes of disease emergence, and eventually prevention.

In parallel, I want to improve the situation for long-neglected disease problems like vampire bat rabies in Latin America by providing and effectively communicating an evidence base for rational control programs that can be adopted by local authorities.

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

peruWhen I was an undergraduate at the University of Virginia, I quickly lost enthusiasm for my major in psychobiology, which involved doing a lot of unfriendly things to lab rats. In my second year, I had the good fortune to volunteer as a field assistant for a study of gut parasites in wild rodents. Over that summer, I was struck to learn both that working on wildlife diseases in beautiful places was a career that could directly or indirectly impact human health and that there were so many unanswered (but completely fundamental) questions about how pathogens are transmitted between species. I quickly changed the course of my studies.

The background I got in infectious disease ecology and evolution over the next two years under the mentorship of Amy Pedersen and Janis Antonovics provided a foundation for my later work on bats, to find a nice middle ground between fundamental question-driven science and the more applied world of bat virology.

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

Receiving the Sir Henry Dale Fellowship had a massive impact. I was in the difficult position of having established during my PhD a field system and international collaborations that I did not want to abandon, but at an early career stage, very few career paths provide the level of independent financial support and the flexibility that I needed. The fellowship enabled a perfect alternative to a postdoc in someone else’s lab or a lectureship/assistant professorship that would have given me additional administrative and teaching responsibilities. Instead, I find myself working in two highly interactive and exciting institutes at Glasgow with a growing team of students and postdocs who bring even more exciting questions.

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

bat biteWorking on vampire bats, I get a lot of questions about bites and blood feeding: do they really drink human blood? Do people sleep through being bitten? Have I been bitten myself? The answer to all three is “yes.”

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

How are your permits applications going? I bring this a question on myself by griping about it all the time, but it is a constant challenge with so many levels of bureaucracy that I feel like I need a white board to answer appropriately.

I attended a workshop recently and was repeatedly reminded of another question I dread: “What is so special about bats as viral reservoirs?” I may be one of the few people who still aren’t totally convinced that bats are actually so special. I’d love to see more science and less hype around that question.

Tell us something about you that might surprise us…

As a wedding gift for a fellow rabies researcher, I once burned a phylogeny of rabies virus with its various host species into an antique table. My grandfather was a physician who took x-rays of plants in his spare time and my dad built a wall out of used wine bottles and test tubes, so I see this as something of a family tradition.phylo table

What keeps you awake at night?

When I’m in Peru, it’s mostly the alarm that goes off every half an hour to check nets for captured bats. In the UK, I must make up for that deprivation because I sleep quite well (aside from jet lag, of course).

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

“Tenacity in the face of adversity…to a point.”

This was the Antonovics lab motto if I recall correctly. It might not sound totally serious, but it does reflect that in science we all have to work hard, but should not do that at the expense of everything else in our lives. It also reminds me of the importance of flexibility – sometimes a change in course pays off a lot more than an endless uphill battle.

The chain reaction question – posed by previous spotlit researcher, Dr Rachel Freathy – is this: If you had the opportunity to meet one scientist (living or dead), who would it be and what would you talk about?

I’ll have to go with Louis Pasteur. I’d want to hear about his early experiments on rabies vaccines and the dramatic ways that he countered disbelief with evidence.

You can find out more about Daniel’s work on the Streicker Group website and by following him on Twitter. You may also be interested in the following articles: Vampire bats remain a holdout on the global stage of rabies control and Host Phylogeny Constrains Cross-Species Emergence and Establishment of Rabies Virus in Bats.

Image of the Week: Under Your Skin – Creutzfeldt-Jakob

13 Feb, 2015
Laurène Pijulet-Balmer, Under Your Skin Creutzfeldt-Jakob, 2013

Laurène Pijulet-Balmer, Under Your Skin Creutzfeldt-Jakob, 2013

This week sees the opening of ‘History is Now: 7 artists take on Britain’ at the Hayward Gallery, featuring the first ever art exhibition to explore the BSE crisis and how it affected the UK in the 1990s – and ever since.

One of the images featured in the exhibition is by Laurène Pijulet-Balmer, an illustrator whose series ‘Under Your Skin’ couples microscopic detail of diseases and viruses with classic fashion and cinematic illustration styles. The series was an attempt by Laurène, a self-confessed hypochondriac, to overcome her own fear of disease by finding the beauty in the shapes and colours revealed under a microscope, and then inserting them into a face, where they cannot be hidden away or ignored.

This image above is based on the human equivalent of BSE, variant Creutzfeldt-Jakob Disease (vCJD), and others in the series include herpes, rotavirus and toxoplasmosis. Each illustration is the product of painstaking research into microscopic disease imaging, looking at different scales, colours, layers and shapes.

The idea for the series sprang from a design project that involved drawing virus-inspired shapes, based on Ernst Haeckel’s 1862 book “Art Forms from the Ocean” – one of the earliest examples of illustrative art and science. At the same time Laurène was working on a portrait for a friend when she began drawing cells instead of the face. She’s not sure why, but we’re glad she did!

She took this further, and later combined her work on viruses with illustrations of faces, as a way of presenting microorganisms in a more familiar light, and bringing them out of the unknown.

Image credit:  Laurène Pijulet-Balmer / 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.

Getting down to busy-ness with Hubbub at The Hub

10 Feb, 2015

The Hubbub Group

 

The £1 million Hub Award is a groundbreaking initiative that provides space and resources to researchers (and other creative minds!) to collaborate on interdisciplinary projects linked to the Trust’s vision of improving human and animal health. Hub Awards last for two years and we are currently open for applications for the 2016-2018 term. The inaugural recipients of the award, currently resident in The Hub space at Wellcome Collection, are the team behind Hubbub. Dr Felicity Callard, Hubbub group leader, tells us how their multifaceted collaboration came about, and why they are so interested in the notion of “busy-ness” and rest…

Our research collective (five core group members and over 30 collaborators) is investigating rest and its opposites by drawing on a wide range of different methods and modes of enquiry from the humanities, social sciences, arts and sciences.

Hubbub’s large group of collaborators includes historians of science and medicine, clinicians, public engagement professionals, social scientists, activists, artists, neuroscientists and broadcasters. We wanted to ensure that our scientific and artistic experiments about rest could benefit from an intense ‘hubbub’ of voices, perspectives and modes of working.

hubbub3Hubbub’s core group came to the problem of rest and its opposites from a range of directions. I had been collaborating with leading resting state neuroscientist Daniel Margulies since 2008 to understand the emergence and exponential growth of ‘resting state’ functional neuroimaging research. I also brought along with me a long-standing, social scientific interest in concepts of the body in states of rest and non-rest (whether through explorations of Marx’s ‘The working day’ or via the study of clinical investigations of anxious or panic-stricken bodies).

James Wilkes, as a poet and humanities researcher, has long explored the aesthetics of voice, silence, and noise. Charles Fernyhough has been preoccupied with improving the methods used to investigate and capture ‘inner experience’ within psychological and neuroscientific paradigms. And Claudia Hammond had previously investigated the experiences of temporality in Time Warped: Unlocking the Mysteries of Time Perception.

We start from the contention that rest is a phenomenon that is curiously hard to define – but one that is of deep cultural, medical, phenomenological, political and scientific interest.

Our work ranges from developing new interdisciplinary neuroscientific paradigms to better investigate states of ‘rest’ in the mind and brain, to tracing the long histories of practices of relaxation. We’re also developing new artistic work that pushes beyond usual aesthetics of noise, silence, signal, and stillness and challenging current practices of ‘workfare’.

It’s not our aim to finally resolve what rest is – and there have undoubtedly been many lively cross-disciplinary arguments since we arrived in the Hub! But I certainly hope our scientific and creative experiments – conducted in collaboration with members of the Wellcome Trust as well as members of the public (in and beyond London) – allow us all to be more attuned to the textures, heterogeneity and contradictions of mental, bodily, and socio-political ‘rest’.

Four months in, we are at the point in which the work plan that the core group designed on paper (in the application phase) is being productively deformed both by our operations, and by the emergence of unpredictable and devolved projects emerging ‘bottom up’ from collaborators. It will be exciting to see where this new phase of experimentation will go.

hubbub postit

I suppose our modes of inhabiting The Hub are actings-out of some of the dilemmas and preoccupations of our research. How, for example, do rest and play exist in the interstices of work? How does living ‘inside’ our funder, the Wellcome Trust, open new opportunities – for us and for the Trust – relating to practices of interdisciplinarity?

How does our rich, dispersed, network of collaborators – who are often in different time zones from one another – help to foment and, at times, retard the emergence of interdisciplinary insights?

As someone whose initial disciplinary training was geography, I am fascinated with how our Hubbub residency inhabits and realises the ‘space’ of the Hub. Our collaboration network extends widely beyond Wellcome Collection into other parts of London – as well as to Durham (the grant-holding organisation), York, and Leipzig (the site of Daniel Margulies’ Neuroanatomy and Connectivity Max Planck Independent Research Group). The question of what and where the Hub is – is it a node within a network, a utopia, a curated space, a field-site, an experimental laboratory? – is always in my mind.

At its starkest, rest – or lack of rest – is, today, one of the most potent of political sites, given the changing nature of work, the unevenness with which any entitlement ‘to rest’ is distributed, as well as the increased surveillance experienced by those not undertaking paid work.

Scientifically, the underspecification of ‘rest’ in cognitive psychology and cognitive neuroscience is a stumbling block for those interested in modelling and conceptualising ‘thought’. That is why we’re developing new methods and paradigms – that draw from the humanities and the arts – to enrich those currently used in the sciences.

There is a lot currently at stake as regards the promise of interdisciplinarity. Many of us within Hubbub have been thinking hard about how to move beyond stale invocations of this term. My hope is that Hubbub, as an experiment in interdisciplinarity, is able to open up different ways of working across the disciplines from those that (explicitly or implicitly) overly constrain the contributions that the arts, humanities and social sciences can make to interdisciplinary research that involves the life sciences.

To keep abreast of Hubbub’s work, and to find out how you might participate in their experiments, follow Hubbub at hubbubgroup.org and on Twitter. Applications for The Hub Award 2016-2018 are now open and we are hosting open days 10th February and 4th March – register your interest here.

Follow

Get every new post delivered to your Inbox.

Join 71,536 other followers

%d bloggers like this: