News and Blog
As a PhD student at MRC HIU, I usually spend my days in a white lab coat peering down a microscope, but this July I temporarily gave all that up to undertake a placement on the science desk at The Guardian newspaper.
Commuting through busy central London to The Guardian offices was a sharp change from my usual fifteen-minute cycle uphill to the lab in Oxford. My mentors were Ian Sample, science editor, and Hannah Devlin, science correspondent – two people I admire greatly for their unique flair for translating complex science into engaging news items.
When Ian led me into the newsroom on my first day, I was overwhelmed with excitement. The newsroom is a large, modern office with huge glass windows and rows upon rows of desks. It was somewhat messier and noisier than I had anticipated, with old books and newspapers piled up on the desks and journalists having loud phone conversations in the background. Every morning began with a meeting called ‘conference’ – the journalists’ equivalent of scientists’ laboratory meetings. Representatives from the various news desks ran through what their main stories of the day were going to be, before they became ‘news’.
At the science desk, I dived straight in. My first published article was a page 3 story on sperm and fertility, complete with a catchy headline. Unfortunately, I can’t take credit for any of the headlines on my articles as these are usually added by the sub-editors. The science writers, including me last month, pitch ideas for stories to the commissioning editor, who in turn pitches the main ideas from the science desk during a daily meeting with other editors. Once an idea is given the greenlight, the article is written and undergoes one or more rounds of editing – including the addition of a headline – before it is filed for publication.
To look for ideas, I often used EurekAlert! – an online platform run by AAAS, which collates the newest and most exciting upcoming scientific papers under embargo at various different journals. This gives journalists a heads up, so they can start putting together a news story to be released simultaneously with the paper.
During my PhD, I’m training to become an expert in a very specific subject area. Writing for The Guardian, I suddenly had to broaden my perspective and apply what I had learnt about analysing and interpreting scientific data to subject matters outside my area of expertise. Luckily, I was not alone in this endeavour. None of my articles would have been possible without valuable discussions with the experts in the relevant fields. Much like the scientific process of peer review, getting opinions about new research from one or more independent experts is an essential part of deciding whether something is worth writing about.
Something that pleasantly surprised me was how willing and happy scientists were to speak to me about their research and about the work of others, even at short notice. The reputation of The Guardian was certainly helpful in getting responses from busy professors and it was a fantastic privilege to be able to speak directly with world-leading scientific experts on an almost daily basis.
Alongside scientific robustness, I learnt that another vital ingredient in good science writing is the hook. A typical response I would get when pitching ideas to the editors was “what’s the top-line?” Summarising a complicated scientific paper in one sentence is a valuable skill, which I will definitely apply as I continue my PhD.
As a researcher who has been involved in the process of generating data for the revision of a scientific paper, I thought I was pretty familiar with working to tight deadlines. I could not have been more wrong. During my placement, I quickly learnt how to read scientific papers and write articles within a few hours. To meet deadlines, usually dictated by embargo times set by scientific journals, I also needed to promptly contact and interview the scientists who did the work, as well as independent experts. I discovered that my role as a science writer was to represent my readers rather than scientists. The readers were not there to ask their questions themselves and so it was my job to do this on their behalf. This was a massive responsibility and so asking the right questions was critical.
Sometimes, I needed to get comments from people other than scientists too. Scientific research can have far-reaching implications for society. Society, in turn, has a say on how and whether potential applications of scientific research are implemented. I will never forget the first press conference I attended. The Nuffield Council on Bioethics were about to release their comprehensive report on the social and ethical issues surrounding genome editing and reproduction. Sitting beside journalists from various media outlets it occurred to me that more people would read the news stories about the council’s report than would ever leaf through the actual 183-page document.
The reporters in the room were tasked with the responsibility of communicating the report’s key messages to a wider audience and igniting an important and necessary public debate. I believe this is a responsibility that scientists should also share. Engaging the public with the (often publicly funded) research that we do is also an important part of our jobs as scientists.
I was certainly sad to leave The Guardian science desk at the end of the month, but also extremely grateful for the phenomenal experience I had covering the latest science stories from antibiotics to aliens. My placement was part of a British Science Association Media Fellowship awarded to me earlier in the year, funded by the Society for Applied Microbiology. I would like to thank my PhD supervisor, Jan Rehwinkel, for supporting my application. My PhD is funded by the Wellcome Trust and I am based at the MRC Human Immunology Unit.
This article was originally published on the MRC WIMM blog. Available here.
In her first week on placement at The Guardian, Layal Liverpool has already published two articles in the newspaper reporting on recent scientific breakthroughs.
The first article described research, which revealed that adding a small amount of mixed nuts to a man’s diet could boost fertility by increasing the quality and quantity of sperm produced. The results are based on a clinical study recently conducted in Spain.
Layal’s second article reported on a novel ‘immunobiotic’ which could be used to fight infections. Growing antibiotic resistance is a major concern for medical researchers who are now looking for new ways of eliminating infectious microorganisms. These new findings reveal a very different mode of action compared to conventional antibiotics. They are designed to alert components of the immune system to the presence of the bacteria, which will then come along and kill them.
The placement at The Guardian is part of a British Science Association media fellowship funded by the Society for Applied Microbiology, which Layal was recently awarded. Layal is being mentored at The Guardian by Ian Sample, Science Editor and Hannah Devlin, Science Correspondent. She will spend a further 3 weeks at the newspaper, continuing to develop her journalistic skills before returning to Oxford to continue her DPhil project.
We look forward to many more exciting articles from Layal over the coming weeks! Keep track of them as they are published, here.
The Royal Society’s annual summer science exhibition took place last week (2nd-8th July) in London and a team of researchers from the University where there to present exciting advances in the race to develop a vaccine against malaria. Second year IITM student Rob Ragotte was part of the presenting team, led by Professors Matt Higgins (Dept. of Biochemistry), Simon Draper and Sumi Biswas (Jenner Institute – Nuffield Dept. of Medicine).
The team were there to talk about their most recent data on an experimental malaria vaccine. Most malaria infections in humans are caused by the parasite Plasmodium falciparum. The Draper and Biswas groups have identified as a leading malaria vaccine candidate a protein on the surface of the parasite, called RH5. The group has designed a vaccine that targets RH5, which is now being tested in humans. The Higgins group have simultaneously been working to solve the protein structure of RH5 as well as the human protein it binds to, basigin
3D printed models of RH5 and basigin were developed to explain how the vaccine works as well as two interactive games for visitors to try to identify other proteins on the parasite surface which might be suitable vaccine targets and to explore how a vaccination campaign might impact spread of disease amongst populations. An estimated 10,000 people visited the exhibition, from members of the public to MPs and eminent scientists.
They also developed a short video which summarises the key points of their research:
Further work to test the vaccine in the UK and in malaria-endemic countries is currently underway. The interactions between antibodies isolated from immunized volunteers and the RH5 protein are also being mapped to hopefully improve vaccine design and to develop novel therapeutics.
Rob undertook rotations in both the Higgins and Draper labs before settling at the Jenner Institute for his DPhil project. Rob is working to develop adeno-associated viruses as a platform to deliver monoclonal antibodies, such as those against RH5, as a gene therapy against malaria.
Final-year IITM student Corinna Kulicke features in a video aimed at teaching school children how antibodies can be used as tools in biomedical research. As part of the public engagement activities at the MRC Human Immunology Unit at the MRC Weatherall Institute of Molecular Medicine, researchers there have designed a set of tools to help teach 10-11 year-olds about science. Partnering with Abingdon Science Partnership, the team identified learning objectives in the national science curriculum they could fulfil whilst aiming to increase engagement and participation in science. The tools will hopefully be used by teachers in schools in the local area.
The tool Corinna helped to deliver is an educational video showcasing some of the ways we use antibodies in a biomedical research laboratory to help answer questions about health and disease. Antibodies are important components of the immune system, but scientists have also engineered ways to make use of them in the lab too. Corinna explores two ways; microscopy and flow cytometry, in which antibodies have helped advance science. Corinna is the main presenter in the video and interviews two experts from the MRC Human Immunology Unit at the MRC WIMM, University of Oxford.
Watch Corinna’s video here:
You can also find out more about the series of public engagement activities that have been produced, here.
Watch out Prof Brian Cox, because Corinna is after your job!
Third year IITM student, Layal Liverpool, has been awarded a prestigious BSA media fellowship, funded by the Society for Applied Microbiology. The fellowship will allow Layal to spend 2-6 weeks this summer working at a large media outlet to develop skills in science communication and journalism.
BSA Media Fellows are mentored by professional journalists and learn how the media operates and reports on science, how to communicate with the media and to engage the wider public with science through the media. Layal is yet to find out which media outlet will host her placement, however previous Fellows have worked in major organisations such as the BBC, The Guardian and Nature News.
Following their media placement, Fellows attend the British Science Festival in September, where they have the opportunity to gain valuable experience working in the BSA Press Centre alongside a range of media organisations from all over the UK.
In response to being awarded the fellowship, Layal said “I am absolutely delighted and extremely grateful for this fantastic opportunity!”.
The application process for the fellowship is extremely competitive and the IITM Programme is very proud of Layal for being selected. We hope she finds the experience fulfilling in shaping the direction of her scientific career.
by Hannah Sharpe
The first year of the IITM DPhil consists of three rotations in different labs, covering a broad range of disciplines and research. To summarise the outcomes of the first rotation, the students gave poster presentations to their peers and supervisors. Here is an outline of the achievements of each project.
Robert’s first rotation was in Simon Draper’s lab at the Jenner Institute, and contributed towards the development of a blood-stage vaccine for Plasmodium falciparum malaria infection. PfCyRPA forms part of a triple complex of proteins involved in Plasmodium merozoite erythrocyte invasion. Robert designed and made mutants of PfCyRPA through altering amino acids on the surface of PfCyRPA, and through addition of glycosylation sites. These mutants were tested in a growth inhibition assay using monoclonal and polyclonal anti-PfCyRPA antibodies.
Mari’s project was also related to malaria, and was conducted Dr Matt Higgins’ lab in the Biochemistry department. During her project, she investigated the widely-conserved HAP2 fusion protein involved in gametocyte fusion of Plasmodium, and how it could be used as a potential vaccine against malaria. During this project, Mari used Phyre and Pross modelling programmes to design structurally homologous proteins to HAP2, consisting of fused HAP2 alpha helical bundles and fusion loops, as well as whole HAP2 protein vaccines. These proteins were cloned into E. coli, and some of these protein constructs were successfully purified.
Lea worked in the lab of William James at the Dunn School. Here, she studied multinucleated fusion cells that arise during HIV-1 infection through the interaction of membrane-bound HIV-1 envelope proteins with CD4 and co-receptor molecules, and which can act as HIV-1 reservoirs in the brain. Lea showed that multinucleated macrophage-T cell fusion cells have similar gene expression pattern to macrophages but increased SAMHD1 phosphorylation. This was ascertained through development of a CEM T cell line expressing the HIV-1 Bal envelope protein, exposing them to macrophages, and using RNA expression analysis to measure gene expression.
Hannah’s first rotation project was with Professor Ellie Barnes, and aimed to characterise the T cell responses to rodent hepacivirus in infected and vaccinated rodents. Hannah used ELISpot assays to map the T cell epitopes in rats infected with RHV, and rats and mice vaccinated against RHV using a chimpanzee adenovirus-vectored vaccine. She then conducted intracellular cytokine staining to ascertain whether the epitopes elicited a CD4+ or CD8+ T cell response. The ultimate aim is to use RHV to develop an animal model of closely-related hepatitis C virus infection, in order to improve vaccine development and further research into HCV.
Sarah’s first rotation project took her to Hal Drakesmith’s lab at the Weatherall Institute of Molecular Medicine. The Drakesmith lab researches iron deficiency, and how it can affect vaccine efficacy. Here, Sarah investigated how iron deficiency in murine T cells and dendritic cells have impaired proliferation, DNA synthesis, and cytokine production. She demonstrated that iron deficiency alters differentiation of antigen specific CD8+ T cells, and impairs antigen-specific T cell metabolism by using a Seahorse XF analyser to measure glycolysis, and that it also reduces dendritic cell cytokine production through flow cytometry and ELISA assays.
Overall, the first rotations were a success, and the first years are currently enjoying the first few weeks of their second rotation!
Congratulations to Dr. Jack Dorling who recently passed his DPhil Viva exam!
Jack undertook his project in Prof. Petros Ligoxygakis‘ lab in the Department of Biochemistry. His interests in host-microbe interactions took him to study peptidoglycan metabolism and interactions with the host innate immune system at the cell surface of Staphylococcus aureus for his project.
Good luck Jack with your future career!
Congratulations to IITM student, Laura Makin, who recently passed her DPhil viva!
Laura joined the IITM programme in 2013 and undertook rotation projects with Omer Dushek and Anton van der Merwe at the Dunn School and Jeanne Salje and Nick Day at MORU, Bangkok, Thailand before settling in Eva Gluenz‘s lab at the Dunn School for her main project.
Laura’s project looked at host-parasite interactions in Leishmania which causes the neglected tropical disease leishmaniasis. In particular, Laura focussed on the subcellular origin of extracellular vesicles in Leishmania and their effects on host macrophages.
Congratulations again to Laura and good luck for your future career.
Congratulations to Florian Brod who completed a viva exam and successfully defended his DPhil thesis today.
Florian has spent the past three years at the Jenner Institute working with Professor Sumi Biswas and Professor Adrian Hill. His DPhil project focussed on developing multi-stage vaccines against malaria. Florian designed a virus like particle to induce immunity against infection in humans and to block transmission via the mosquito vector. In addition to this he studied protein-protein interactions between the parasite and mosquito to identify further targets that could be exploited for a transmission blocking vaccine.
In his first year, Florian undertook rotations at the Mahidol-Oxford Research Unit, Bangkok, Thailand with Professors Susie Dunachie and Nick Day and at the Dunn School with Professor Quentin Sattentau as well as at the Jenner Institute.
We wish Florian all the best with his future career.
By Felix Richter and Sarah Wideman
Research needs to be communicated and discussed, whether in big conferences or in a smaller format, such as a research symposium. The IITM programme holds an annual research symposium which provides a great platform for students to improve their presentation skills and to receive feedback on their project from course mates, supervisors and professors. In addition, the day provides opportunities to network, get career advice and socialise in an informal setting.
After a quick cup of coffee and biscuits, the fourth-year students were first up to present. With just one year to go until their thesis submission, all projects had interesting and novel findings, but left time to address some final unanswered questions. Topics presented ranged from iminosugars for antiviral defence (Beatrice Tyrrell) to virus RNA structure (Bernadeta Dadonaite) and CRISPR-based immunological screening methods (Corinna Kulicke). We are already looking forward to seeing the final data from these projects and hope to share more information about the projects as soon as they are published.
After a small break, it was the third-years’ turn. One year into their research projects, the amount and quality of the presented research data was impressive. The topics were diverse and included infection projects such as bacterial toxin-antitoxin systems (Hannah Berens), immune cell chemotaxis during HIV infection (Cherrelle Dacon), microbial bioinformatics of Neisseria species (Marianne Clemence) and viral zRNA sensing (Layal Liverpool), as well as more immunological projects about T-cell transcriptomics (Lucy Garner) and the immunological response to malaria (Richard Morter). The presentations engaged both students and researchers in rewarding discussions and the input was seemingly gratefully welcomed by the presenters.
After a combined lunch break and poster session, a familiar face returned to her old alma mater. Dr. Meike Assmann graduated in 2016 from the IITM programme and has left academia to pursue her passion for consultancy, working with Alcimed. She described her path from the lab to her current job as a project developer for clients in the health care industry. She also talked about how we can apply the skills we develop during a PhD to succeed in a career outside the lab. This inspiring talk highlighted the many ways that a DPhil degree from the IITM programme can take you.
The student presentations were concluded by the second-year students. This cohort recently begun their DPhil projects, so the data was still preliminary, but the ideas big and convincing. Once more the variety of topics was one of the highlights of this session. The topics ranged from characterisation of HIV-related genes (Alun Vaughan-Jackson), autophagy in the bone marrow environment (Felix Richter) and T cell signalling (Johannes Pettmann) to antiviral iminosugar therapy (Juliane Brun) and malaria vaccine development (Robert Ragotte). We look forward to seeing more of their results at the IITM symposium 2018 and we all wish them the best of luck for their new projects.
The symposium concluded with this year’s keynote speaker, the first to be invited from outside the UK; Professor Henrique Veiga-Fernandes from the University of Lisbon. He leads research on the S(c)ensory Immune System Theory, describing the potential role of other cell types to govern the behaviour of immune cells in multicellular organisms (1). His presentation captivated the entire room with insights into how communication between the nervous system and the immune system is important in maintaining immune homeostasis, focussing on two recently published papers which discuss the role of neuroregulatory factors in affecting the function of innate lymphoid cells (2, 3).
For the symposium’s grand finale, there was a drinks reception and formal dinner in the Old Dining Hall at St Edmund Hall. Both the students and faculty greatly enjoyed this opportunity to socialise and to continue the day’s scientific discussions. Here, the programme also officially thanked and said farewell to Professor Fiona Powrie. Fiona was one of the founders of the programme and has recently stepped down from her position as programme director. We again express our gratitude to Professor Powrie for her contribution to the programme over the years. Without her hard work, none of the programme’s achievements to date would have been possible.
We are all already looking forward to a new year of science and to see how our work has progressed at the IITM symposium 2018.
- Veiga-Fernandes H, Freitas AA. The S(c)ensory Immune System Theory. Trends Immunol. 2017;38(10):777-88.
- Cardoso V, Chesne J, Ribeiro H, Garcia-Cassani B, Carvalho T, Bouchery T, et al. Neuronal regulation of type 2 innate lymphoid cells via neuromedin U. Nature. 2017;549(7671):277-81.
- Ibiza S, Garcia-Cassani B, Ribeiro H, Carvalho T, Almeida L, Marques R, et al. Glial-cell-derived neuroregulators control type 3 innate lymphoid cells and gut defence. Nature. 2016;535(7612):440-3.