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First year IITM students showcase rotation projects with poster presentations

by Hannah Sharpe

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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 Donat

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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 Johnson

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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 Nussbaum

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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 SharpeIMG_20180208_153759842

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 Wideman

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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 Dr. Jack Dorling

Congratulations to Dr. Jack Dorling who recently passed his DPhil Viva exam!

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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.

In his first year, Jack rotated with Prof. Keith Gull at the Dunn School and Dr. Jeanne Salje at MORU, Bangkok before deciding on the Ligoxygakis lab for his main project.

Good luck Jack with your future career!

Congratulations Dr. Laura Makin

Congratulations to IITM student, Laura Makin, who recently passed her DPhil viva!

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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 Dr. Florian Brod

Congratulations to Florian Brod who completed a viva exam and successfully defended his DPhil thesis today.

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Post-viva celebrations. Left to right: Prof. Sumi Biswas (supervisor), Dr. Gavin Wright (examiner), Dr. Florian Brod and Prof. Kevin Marsh (examiner)

 

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.

 

 

The IITM Symposium 2017 – A small symposium discussing big science

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.

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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.

 

 

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Meike Assman and Robert Donat review the second years’ posters

 

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.

 

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Marianne Clemence presents her project

 

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.

 

 

References

  1. Veiga-Fernandes H, Freitas AA. The S(c)ensory Immune System Theory. Trends Immunol. 2017;38(10):777-88.
  2. 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.
  3. 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.

Congratulations Ben Nilsson

Congratulations to Dr. Ben Nilsson who successfully defended his thesis yesterday (December 4th 2017). 

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Ben and Ervin in celebration

Ben has spent the past 3 years working on the influenza A virus RNA polymerase in Ervin Fodor‘s lab at the Dunn School, University of Oxford.

You can read more about what Ben got up to during his project in a post he wrote earlier this year summarising the paper published on his work.

The Programme wishes Ben all the very best with his future career.

Welcome to new IITM students

Welcome to the latest cohort of IITM students! Find out more about them and their interests here.

Last month (October 2017) we welcomed five new students to the IITM DPhil programme: Robert Friedrich-Donat, Mari Johnson, Lea Nussbaum, Hannah Sharpe and Sarah Wideman.

Robert studied Immunology at the University of Edinburgh and is now working in Simon Draper‘s lab investigating red blood cell invasion by the malaria parasite. Mari is also focusing on malaria during her first rotation, designing epitopes for a potential vaccine in Matt Higgins‘ lab. Before coming to Oxford, Mari studied Cellular and Molecular Medicine at the University of Bristol. Lea studied Molecular Biotechnology at Heidelberg University in Germany. She is currently working in William James‘ lab, examining cellular interactions during HIV infection. Hannah studied Biology and Immunology here at Oxford and is now working in Ellie Barnes‘ lab characterising immune responses to hepatitis C vaccination. Sarah studied Biomedicine at the Karolinska Institute in Sweden. She is now undertaking a rotation in Hal Drakesmith‘s lab looking at the effect of iron deficiency on immune function.

Author: Layal Liverpool

If you would like to write a piece for the IITM blog please get in touch by emailing iitm@path.ox.ac.uk.

Global Perspectives: unexpected takeaways from my lab rotation in Ho Chi Minh City, Vietnam

Rob Ragotte describes his experiences on rotation in Ho Chi Minh City, Vietnam.

When I accepted my place in the IITM programme in February 2016, I prepared myself for what I thought would be an interesting, illuminating, exciting, challenging, stressful, and sometimes demoralising few years. What I did not prepare for was wandering around a grocery store for an hour unable to identify a single food I could confidently cook. I did not imagine myself cruising through the streets of Ho Chi Minh City on the back of a motorcycle. And it never crossed my mind that the words cảm ơn (thanks) and không đường (no sugar) would be essential additions to my vocabulary.

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Eating out at the Street Food Market in Ho Chi Minh City

 

As part of the IITM programme, all first year students undertake three lab rotations. For many, this will allow them to get comfortable in three different labs around Oxford where they will learn new techniques and refine their research interests.

However, students are also able, and encouraged, to explore labs at one of Oxford’s major overseas programmes. This allows students to travel to Bangkok, Thailand; Ho Chi Minh City, Vietnam; or Kilifi, Kenya, to work at the Oxford/Wellcome Trust centres situated in those cities.

For my third rotation, I opted to go to Ho Chi Minh City, to work under the supervision of Prof. Stephen Baker at the Oxford University Clinical Research Unit (OUCRU).  The goal of my project was to understand the genetic factors that enable Klebsiella pneumoniae, a common and normally harmless bacteria, to cause disease in otherwise healthy individuals. K. pneumoniae can sometimes cause life-threatening infections if it enters the bloodstream or brain.

For the project, I analysed the all the genes contained in 83 suspected K. pneumoniae samples isolated from patients with infection of the blood. Although I had limited experience doing complex computational analyses before, I quickly found myself mastering a host of new skills needed to carry out my project.

I found an abundance of genes transferred from other disease-causing bacteria, as well as genes that confer resistance to a range of antibiotics in the blood isolates. This might help to explain why K. pneumoniae sometimes causes disease and sometimes does not.

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Entrance to the Hospital for Tropical Diseases, Ho Chi Minh City

 

While working on this project, it was not immediately clear to me why I needed to be in Vietnam. After all, most of what I did was computer based and much of my day-to-day supervision was via email. My physical presence in Vietnam seemed unnecessary. I could just as easily do my work from Cardiff or Calgary. So I thought.

As my project progressed, I realised not only was it beneficial to be in Vietnam, it was absolutely essential. By living in Vietnam, albeit briefly, I began to understand some of the unique challenges faced by clinicians and scientists alike. The realities of clinical care in a middle-income country profoundly impact not only the type of research that is conducted, but also the how we think about and implement potential solutions. It is not enough to merely identify a problem from afar. Though antimicrobial resistance is particularly problematic in Vietnam, it is not localised to single region, country or continent. It is a global problem and requires global partnerships, coupled with a mutual understanding of the specific goals and challenges, if it is to be solved. My immersive experience emphasised and contextualised the importance of conducting research on a major global health problem.

I do not mean to suggest that I now understand the intricacies of the Vietnamese health care system, or the particular nuances of operating in a middle-income country. I know very little. However, some of the unknown unknowns have now become known unknowns, which is a substantial improvement. Recognising that there are fundamental differences between conducting health research and providing clinical care in a middle-income setting will ensure conversations about global health interventions evolve from paternalistic to empowering. It will allow us to move from a prescriptive approach to one where local idiosyncrasies are considered.

My time in Vietnam was not as orderly as I initially envisioned. Certainly there were challenges and it was, at times, tumultuous. Though, I was fortunate to have an excellent supervisor and resourceful colleagues that ensured I was both productive in my work, and enjoyed my Vietnamese experience. I fly back to the UK grateful for the opportunity and optimistic about the next three years.

Author: Rob Ragotte

Rob is an IITM student entering his second year of the programme.

If you would like to write a piece for the IITM blog please get in touch by emailing iitm@path.ox.ac.uk.

Sensing viruses: shape matters

Layal Liverpool summarises the findings of a recent study she was involved in during her rotation and the first year of her DPhil in Jan Rehwinkel‘s lab. This article was first posted on the WIMM blog.

Viruses are basically packets of nucleic acid, DNA or it’s sister molecule RNA. Our cells have therefore evolved to recognise these molecules as a sign of virus infection. A recent study from Jan Rehwinkel’s lab in the MRC WIMM has revealed a new way in which cells sense and respond to invading viruses.

Infection is one of the biggest threats faced by our cells. To combat this, cells have evolved a highly-tuned detection system that relies on proteins called sensors. Viruses rely on nucleic acids, DNA or RNA, to infect cells and propagate themselves. Nucleic acid sensors in our cells exploit this by recognising DNA or RNA from invading viruses and activating potent anti-viral responses.

These early anti-viral responses are the cell’s first line of defence against an invading virus. One such response is a form of cell suicide called necroptosis. One of the nucleic acid sensors, called ZBP1 or DAI, can activate this form of cell death upon detecting herpes virus infection. By committing suicide, the infected cell sacrifices itself to stop the spread of the virus to other cells in the body.

Necroptosis is a “messy” form of cell death because it essentially involves the explosion of the cell, releasing all its contents into its surroundings. Here they can be picked up by patrolling immune cells, alerting them to the fact that there is a virus around.

Although ZBP1 was already known to activate cell suicide, exactly what from the virus ZBP1 was detecting had been a mystery. In their study, Jonathan Maelfait and colleagues in Jan Rehwinkel’s lab demonstrate that ZBP1 recognises RNA from the invading virus.

Like viruses, our cells also contain their own nucleic acids, for example the DNA that makes up our genes. A big question then is how nucleic acid sensors, like ZBP1, can tell the difference between the cells own nucleic acids and those coming from invading viruses.

Well, it might all come down to shape. In addition to the classical DNA double helix structure on the cover of every GCSE biology textbook, DNA – and RNA – can adopt another, more jagged, zig-zag shape named ‘Z’. In fact, ZBP1 is so-called because of its special ability to recognise Z-shape nucleic acids.

Maelfait and colleagues found that when they made cells with a broken version of ZBP1, which could no longer recognise Z-nucleic acids, the cells lost the ability to activate cell suicide in response to virus infection. Mice that have the same broken version of ZBP1 are more vulnerable to virus infection, probably because the lack of cell suicide allows the virus to persist and spread through the body more easily. This discovery suggests that the Z-shape might be an important molecular sign of virus infection, allowing cells to distinguish their own nucleic acids from those of viruses.

Understanding exactly how our cells make this distinction is important because when it goes wrong, it can lead to auto-immune or auto-inflammatory diseases. Clearly it would not be useful for our cells to start committing suicide when there is no virus! In the future, further investigation of nucleic acid sensing may reveal novel therapeutic targets for the treatment of viral infections and auto-inflammatory diseases.

References:
J. Maelfait, L. Liverpool, A. Bridgeman, K. B. Ragan, J. W. Upton, and J. Rehwinkel, “Sensing of viral and endogenous RNA by ZBP1/DAI induces necroptosis,” EMBO J, Jul. 2017.

Author: Layal Liverpool

If you would like to write a piece for the IITM blog please get in touch by emailing iitm@path.ox.ac.uk

 

Malaria Hotspots and How to Find Them

Richard Morter explains the findings of a recent study he was involved in during his rotation project at the KEMRI-Wellcome Trust Research Programme in Kenya.

Malaria is a mosquito-transmitted parasitic infection and although it is treatable if diagnosed early enough, approximately half a million people die each year from malaria. Around 70% of these deaths are in children under the age of five.

Malaria therefore presents a huge burden to global health. Although incidence is reducing globally, there is still a long way to go to reach elimination. The most effective tools currently used to control the spread of malaria are the insecticide-treated bed nets and indoor residual spraying (the application of insecticides to the walls of people’s homes where mosquitos might rest).

 

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Credit: UNICEF

 

Traditionally, malaria control programmes have involved blanket coverage of endemic areas, where every single house in an area is given bed nets or has their houses sprayed. However there is growing interest in adopting more targeted approaches where only those most at-risk are selected for intervention.

The advantage of this is largely economic. The hope would be that targeted intervention in a defined geographic area would yield the same overall reduction in malaria transmission as blanket coverage, but using fewer resources. This would mean more areas could be covered for the same cost leading to a more universal reduction in malaria transmission.

Malaria transmission intensity is inherently uneven across different areas. It’s unevenly spread across the tropical world with sub-Saharan Africa accounting for over 90% of all cases. It’s unevenly spread within Africa too. This unevenness is called spatial heterogeneity of transmission intensity.

 

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Credit: Malaria Atlas Project – University of Oxford

 

In fact; as we zoom in on smaller geographic areas, we continue to see spatial heterogeneity. We can even see it right down at the single homestead level – infected children are not uniformly spread across a village but instead are tightly clustered together, living in either the same or adjacent homesteads. These locations are described as ‘hotspots’ of malaria transmission and could be targeted for control interventions.

Hotspots have been identified by our group in nearby villages along the Kenyan coast, Junju, Ngerenya and Ganze. Junju has moderately high transmission intensity whereas Ngerenya and Ganze have very low transmission intensity.

For targeted interventions to work, hotspots need to be detected accurately. In this paper, we investigated just how accurate current methods are in detecting hotspots.

The first question to ask is; do hotspots remain stable over time? In other words, if we use a previous year’s hotspot data, and direct control interventions to those locations, will the hotspots be in the same place the next year or are we chasing a moving target? In this study, we discovered that the hotspots are indeed stable over time in the high-transmission village, however there appears to be less stability in the lower-transmission villages. What may be required in the future is a more real-time approach where hotspots are detected as they form and immediately targeted.

The second question we addressed is; what method should be used to detect hotspots? We used three different methods to detect parasite infection and subsequently identify hotspots; microscopy, rapid diagnostic testing (RDT) and qPCR.

The gold standard method for malaria diagnosis is microscopy. It’s cheap and already almost universally available in malaria endemic areas, however it lacks sensitivity meaning infections with low numbers of parasites are often not detected.

 

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Malaria-causing P. falciparum parasites in a thin blood film

 

RDTs work in a similar way to pregnancy tests and a band appears on the test stick if the blood sample contains parasites. They are also relatively cheap and might have slightly better sensitivity to microscopy.

A much newer and more sensitive tool is qPCR where parasite DNA in a blood sample is amplified in an enzymatic reaction. This amplification is detected and indicates a positive sample. qPCR can detect positive samples with much lower parasite counts than microscopy or RDTs, however it’s expensive and requires more specialist equipment.

We compared the abilities of microscopy, RDTs and qPCR to detect hotspots in settings of different transmission intensities and assessed the degree of overlap between hotspots detected by the methods. We found that hotspots were easily detected by all methods in the high transmission setting but microscopy was less reliable in the low transmission setting. The degree of overlap was least for RDTs. Microscopy also became more inconsistent and the hotspots it was detecting overlapped less with qPCR in the low transmission setting.

This is because RDTs and microscopy are less sensitive methods so are less reliable in being able to accurately detect hotspots especially when there are fewer positive samples. Because of this, we suggest that qPCR should preferentially be used particularly as transmission intensity decreases.

Overall, targeted malaria control programmes are an important part of elimination campaigns. Hotspots become more apparent as transmission intensity falls and becomes patchier, therefore hotspot targeting will become even more important in the future as global malaria incidence gradually declines. We found that qPCR becomes more important in this situation. More needs to be done to increase the accessibility of qPCR in malaria-endemic low and middle income countries by reducing cost and simplifying technologies.

Together, these strategies may help contribute to controlling and eventually eliminating malaria worldwide.

The full paper can be accessed at: https://doi.org/10.1093/infdis/jix321

Polycarp Mogeni, Thomas N. Williams, Irene Omedo, Domtila Kimani, Joyce M. Ngoi, Jedida Mwacharo, Richard Morter, Christopher Nyundo, Juliana Wambua, George Nyangweso, Melissa Kapulu, Gregory Fegan, Philip Bejon; Detecting Malaria Hotspots: a comparison between RDT, Microscopy and Polymerase Chain Reaction. J Infect Dis 2017 jix321. doi: 10.1093/infdis/jix321

Author: Richard Morter

Richard is now undertaking a collaborative DPhil project between the Jenner Institute, University of Oxford and the KEMRI-Wellcome Trust Research Programme, supervised by Professors Adrian Hill and Philip Bejon. He is characterising the Regulatory T cell response in a human malaria challenge model and looking at the consequences of malaria-induced Regulatory T cells on effective vaccination against malaria.

If you would like to write a piece for the IITM blog please get in touch by emailing iitm@path.ox.ac.uk