Studentship projects 2020

Mapping the epigenetic modifications of DNA and RNA

CRISPR gene-editing tools to enable structural studies of multi-protein complexes

Crystallography-based fragment screening to discover pharmacological chaperones for misfolding diseases

Causes of genomic instability in endometrial cancer

Understanding carbon fixation by Rubisco in cyanobacteria

NDM Studentship: Cytomegalovirus infection and vaccine efficacy in Influenza vaccination

Potential for prophylaxis to prevent forest malaria in the Greater Mekong Subregion

Retrospective analysis of a malaria outbreak in the Greater Mekong Subregion

Mapping to support dengue control in Myanmar

Mapping potential malaria transmission sites in the Greater Mekong Subregion

The role of the Pre-Exposure Prophylaxis (PreP) in stabilizing the HIV epidemics among Men Who Have Sex with Men (MSM) in Kyrgyzstan

Characterisation of non-specific antibody responses induced by BCG vaccination

Summer student position:  Systematic review to understand how changes in behaviour might contribute to reducing AMR

AfOx/NDM summer studentship project

Mapping the epigenetic modifications of DNA and RNA

Supervisor: Chunxiao Song, Oxford Ludwig Institute, NDM Research Building

Our genome is not a static state; it contains dynamic epigenetic modifications that play crucial roles from development to pathogenesis. Recently, many new nucleotide variants have been discovered in DNA and RNA, which triggered an explosion of new information in the epigenetics field. Chemical and biological transformations of nucleotide variants have always been the core of crucial methodologies in epigenetic research. Our group is working on the technology development, functional studies and clinical applications in epigenetics and epitranscriptomics. We combine various chemical biology and genome technologies to develop novel tools to analyse the epigenome. In this project, you will help to further develop our recent technologies into single-cell and long-read epigenetic sequencing, as well as to develop new chemistry in epigenetics and epitranscriptomics.

Reference:

Liu Y, Siejka-Zielińska P, Velikova G, Bi Y, Yuan F, Tomkova M, Bai C, Chen L, Schuster-Böckler B, Song CX. (2019). Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution. Nat. Biotechnol. 37, 424-429.
Yuan F, Bi Y, Siejka-Zielinska P, Zhou YL, Zhang XX, Song CX. (2019). Bisulfite-free and base-resolution analysis of 5-methylcytidine and 5-hydroxymethylcytidine in RNA with peroxotungstate. Chem. Commun. (Camb.) 55, 2328-2331.

CRISPR gene-editing tools to enable structural studies of multi-protein complexes

Supervisor: Assoc Prof Wyatt Yue, SGC

Living cells have evolved complex metabolic machines, where functionally related enzymes do not work in isolation but instead cluster into supramolecular complexes, to provide spatial and temporal control of key molecules in the cell. Our team is interested in studying the molecular architecture of these multiprotein machines, which often remain elusive due to difficulty in generating recombinant material for study.

Using CRISPR gene-editing, we have recently inserted fusion tags into the genomic locus of one subunit of an 8-protein megadalton complex. This allows tag-mediated isolation of the entire complex from endogenous human cells, resulting in its structure determination by cryo-electron microscopy to 2.5 Å resolution. This project builds on this pioneering result, and aims to explore the wider applicability of this CRISPR-tagging approach for various multi-protein complexes across different biological pathways. Techniques involved in this project include cell culture, affinity purification, and sample preparation for electron microscopy.

Crystallography-based fragment screening to discover pharmacological chaperones for misfolding diseases

Supervisor: Assoc Prof Wyatt Yue, SGC

Small molecules that bind specifically to a target protein resulting in its stabilization in the cell (pharmacological chaperones, PC) would have therapeutic benefits for protein misfolding diseases. This PC approach has advanced from concept to market approval for Migalastat, developed for the treatment of the lysosomal storage disorder Fabry disease. Migalastat and other PCs under development are typically substrate mimetics that rescue the folding of the effected mutant enzyme but can also have inhibitory effects. Therefore, developing PC molecules that exert the stabilisation effect away from the active site would be more beneficial.

Fragment screening using crystallography (XChem) offers promise in identifying novel binding pockets away from the active site. Here crystals of the target protein are soaked with a library of fragments and their binding are identified by x-ray crystallography. These fragments can then act as starting points for further development into drug-like molecules. This project aims to carry out XChem screening for several metabolic enzymes associated with protein misfolding, capitalizing on our previous success in crystallizing these proteins and determining their structures in high throughput.

Causes of genomic instability in endometrial cancer

Church group NDM summer studentship (David Church), Wellcome Centre for Human Genetics

Endometrial cancer is the most common gynaecological malignancy in Western populations and is increasing in incidence. A large and expanding body of evidence indicates that many if of not most cases display some form of genomic instability. This includes somatic copy number alterations and structural variants of chromosomal instability often associated with somatic TP53 mutation, the hypermutation and microsatellite instability associated with DNA mismatch repair deficiency, and the ultramutation caused by somatic mutation of the replicative DNA polymerase POLE. This project will use both human cancers and model systems to understand the causes and consequences of genomic instability in cancer, with particular focus on identifying novel therapeutic avenues for further investigation. Training will be provided in all techniques required, including experimental and bioinformatic methods.

Understanding carbon fixation by Rubisco in cyanobacteria

Peijun Zhang Lab (Peijun Zhang), Structural Biology, Wellcome Centre for Human Genetics

Rubisco is an enzyme involved in the first major step of carbon fixation, a process by which the atmospheric carbon dioxide is converted by plants and other photosynthetic organisms to energy-rich molecules such as glucose. It is probably the most abundant enzyme on Earth. RuBisCO is important biologically because it catalyzes the primary chemical reaction by which inorganic carbon enters the biosphere. Given its important role in the biosphere, the genetic engineering of RuBisCO is of continuing interest. In our recent study, we found that Rubisco-GFP activity is more than 20% higher than WT Rubisco. To understand the structural mechanism of activity enhancement, this project is aimed at high resolution cryoEM structures of both WT Rubisco and Rubisco-GFP.

NDM Studentship: Cytomegalovirus infection and vaccine efficacy in Influenza vaccination

Supervisor: Dr Teresa Lambe

Jenner Institute

Cytomegalovirus (CMV) is a global herpesvirus that infects approximately 50% of individuals in the UK (1). CMV infection has a senescent and exhaustive effect on the immune system, exacerbating the process of immune aging and inducing permanent phenotypic changes of terminal differentiation on immune cells (2). CMV seropositivity and older age are both factors for reduced vaccine efficacy (3,4), although the immunological process behind this phenomenon is not yet clear. It is important to understand the effect of CMV and of older age on the immune system and vaccine response, and how this compares to younger and CMV seronegative individuals, in order to develop efficacious vaccines for older adults.

Previously, we have shown that individuals who are CMV seropositive in the UK and Senegal have a lower antibody response, less T-cell IFNg production, and a more senescent T cell phenotype in response to ChAd-MVA EBOV(GP) vaccination (Bowyer et al, manuscript under review).

This project

This project will look at a cohort of vaccine trial samples collected from older individuals vaccinated against Influenza. Project work will include serotyping the cohort for CMV serostatus via CMV diagnostic ELISA. Following this, we will assess the immune response to the vaccinations in association with CMV seropositivity across a range of adaptive and innate immune cells. Techniques will include ELISA and multicolour flow cytometry, with relevant statistical analysis.

Significance of work

A reduction in vaccine efficacy with age poses a significant problem for an aging global population. Influenza infection mortality is predominantly distributed towards older individuals, and currently seasonal flu vaccines are also not as efficacious in older adults compared to younger adults (4,5). This work will delineate the impact of CMV infection and age on vaccine response. This will contribute towards the development of an influenza vaccine that will offer higher protection towards the most at-risk populations.

  1. Adland et al, Ongoing burden of disease and mortality from HIV/CMV coinfection in Africa in the antiretroviral therapy era. 2015. Front Microbiol. PMID26441939
  2. Ouyang, Q. Age-associated accumulation of CMV-specific CD8+ T cells expressing the inhibitory killer like receptor G1 (KLRG1). 2003. Exp Gerontol. PMID 12915213
  3. Olsson, J et al. Age-related change in peripheral blood T-lymphocyte subpopulations and cytomegalovirus infection in the very old: the Swedish longitudinal OCTO immune study. 2000. Mech Ageing Dev. PMID 11164473
  4. Merani et al, Impact of aging and cytomegalovirus on immunological response to influenza vaccination and infection. 2017. Front Immunol. PMID 28769922
  5. Merani, S, et al. Influenza vaccine-mediated protection in older adults: impact of influenza infection, cytomegalovirus serostatus and vaccine dosage. 2018. Exp Gerontol. PMID 28958701

Potential for prophylaxis to prevent forest malaria in the Greater Mekong Subregion

Professor Richard J Maude (Epidemiology Dept, Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand)

Location: Bangkok, Thailand

Most malaria in the Greater Mekong Subregion (GMS) is transmitted in and around forests. However risk behaviours leading to infection have not been well characterized which makes it challenging to design appropriate interventions to prevent and treat infections. One proposed intervention that could reduce forest malaria is antimalarial prophylaxis for forest goers and we are running the first large clinical trial of this to assess its efficacy in Cambodia. If prophylaxis proves to be effective in the trial, it is not clear how it would be administered and monitored and by whom in different healthcare settings. It is also not known which interventions populations in the GMS prefer and how acceptable prophylaxis would be to them. Together with the trial, we are conducting interviews among forest goers, healthcare workers, community leaders and policy makers in Cambodia, Lao PDR and Thailand to assess opinions and preferences about different malaria prevention measures among high risk groups and the feasibility of prophylaxis as a strategy.

This project will help to analyse these interviews under the guidance of an experienced social scientist and team of epidemiologists and clinicians. It will provide training in relevant qualitative methods and will result in a peer-reviewed research publication. The results will help National Malaria Control Programmes to decide how to roll out this intervention in their country.

Retrospective analysis of a malaria outbreak in the Greater Mekong Subregion

Professor Richard J Maude (Epidemiology Dept, Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand)

Location: Bangkok, Thailand, Vientiane, Lao PDR or Oxford, UK

There have also been a number of focal outbreaks of malaria in the Greater Mekong Subregion (GMS) in the past few years. In many cases the causes of these outbreaks were not well understood and responses suboptimal due to limitations in data and capacity for analysis. This limits countries’ ability to act efficiently to contain these outbreaks and to prevent future outbreaks and has the potential to threaten the achievement of planned elimination timelines.

This project will help to analyse retrospective surveillance data together with intervention data to describe a recent malaria outbreak in the GMS and investigate possible causes. Questions that the project may address include: what was the contribution of climate factors to this outbreak/epidemic? What was the contribution of changes in treatment/vector control measures to this outbreak/epidemic? What are the geographical and temporal extent of the epidemic? Which demographic and risk groups were affected? Where data are available what was the contribution of changes in population movement patterns and antimalarial resistance to this epidemic?

Methods will include statistical analysis, GIS and spatial analysis and it will result in a peer-reviewed research publication. The results will help the National Malaria Control Programme understand which factors contributed to the outbreak should report as possible causes of the epidemic/outbreak and inform planning of interventions for future outbreaks. The results will be used in a peer-reviewed research publication.

Mapping potential malaria transmission sites in the Greater Mekong Subregion

Professor Richard J Maude (Epidemiology Dept, Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand)

Location: Bangkok, Thailand or Oxford, UK

Countries in the Greater Mekong Subregion (GMS) aim to eliminate malaria by 2020. Most of the transmission occurs among people visiting the forest however little is known about where this occurs. We are working with the European Space Agency and government partners in Cambodia, Lao PDR and Thailand with research staff on the ground in areas with high malaria risk to map forest cover and identify locations in the forest where malaria transmission might be occurring. This project will analyse satellite images, GPS data and photographs to identify and characterize these potential transmission sites. There will be opportunity to visit field sites to validate the results on the ground. The results will be shared with the national malaria control programme in each country to help them design interventions to prevent transmission and protect high risk populations and will form part of a peer-reviewed research publication.

Mapping to support dengue control in Myanmar

Professor Richard J Maude (Epidemiology Dept, Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand)

Location: Yangon, Myanmar

Dengue is a major public health problem in urban areas in Southeast Asia. Occurring in epidemics every few years, it is challenging to control requiring participation of the general public in control measures. Monitoring and responding to dengue epidemics is hampered by weak surveillance systems and lack of essential geographic information. We are running a large cluster-randomised trial of community-based dengue prevention measures in partnership with 40 schools in Yangon, Myanmar. To measure the impact of the interventions we are strengthening the surveillance system with diagnostic testing and standardized reporting together with detailed mapping of the study townships.

This project will support the trial at an early stage to help collect baseline data on the locations and catchment areas of schools and health facilities. Methods for collection of GPS data, annotation of satellite images and analysis with GIS software will be taught.

The role of the Pre-Exposure Prophylaxis (PreP) in stabilizing the HIV epidemics among Men Who Have Sex with Men (MSM) in Kyrgyzstan

Supervisor: Prof Lisa White

Big Data Institute, Nuffield Department of Medicine, University of Oxford, UK

Introduction

Kyrgyzstan is in the top list of countries with the highest HIV incidence level in the world. The UNAIDS reports that the Incidence: prevalence ratio (IPR) remains higher (0.08) than the global threshold of 0.03, thus indicating the potential for a further growth of the population in the country with HIV positive status (UNAIDS, 2018).

Men who have sex with men (MSM) are among other key populations in Kyrgyzstan mostly affected with HIV epidemic. The HIV prevalence in this group is 33 times higher than of the general population (6.6% vs. 0.2%), with highest rate of 10.1% observed in the capital city (MOH, 2016).

Since the emergence of the epidemics, the country has undertaken various measures and interventions among MSM, including expanded HIV cascade of services and educational interventions and advocacy.

Thus, following the global recommendations to improve the cascade of HIV services, Kyrgyzstan has introduced new tools, such as assisted and self- testing, active case findings, index tracing, immediate launch of treatment after diagnosing, and peer HIV positive case management.
In light of the increasing epidemics, the country has recently introduced Pre-Exposure Prophylaxis (PrEP) as an additional method to prevent HIV transmission among MSM. Currently, the PrEP is available through the pilot project in the capital city, Bishkek. The country is now discussing about the potential for expanding the use of this tool nationwide and accordingly collecting evidence for its effectiveness and implications.

The proposed project will look at the potential effect of PrEP on the force of infection and accordingly the course of HIV epidemics among MSM. The findings of the study will serve as an additional evidence for the policy decision-making process.

Particularly, the proposed research will attempt to answer the following questions:

Methods

Dynamic compartmental model will be applied in analysing and modelling the HIV epidemics among MSM. At the initial stage, the model will consider some key parameters, like HIV transmission and progression rates, testing rates, enrolment and adherence rates for ARV treatment and other parameters in the analysis of the current course of HIV epidemics among MSM. At the following stage, the model will include PrEP as a prevention method, which will be a part of the force of infection, and will project the change in the course of infection with and without this additional parameter.

Proposed ways of visualising the research outputs

Description of the HIV epidemics among MSM in Kyrgyzstan:

Moving forward: Analysis of the potential role of PrEP in reducing HIV epidemics among MSM in Kyrgyzstan

From analysis to policy decision making

Who are we looking for?

The ideal candidate would have a strong background in mathematics, with knowledge of dynamical systems and ordinary differential equations. They would be adept at the R programming language (essential) and experience of R Shiny would be desirable. Some fluency in Russian would be desirable but not essential.

S/he will be working with Prof Lisa White and Ainura Moldokmatova at BDI in Oxford on a collaboration with state and non-governmental HIV health providers in Kyrgyzstan.

References

MOH. (2016). РЕЗУЛЬТАТЫ ДОЗОРНОГО ЭПИДЕМИОЛОГИЧЕСКОГО НАДЗОРА ЗА ВИЧ-ИНФЕКЦИЕЙ В КЫРГЫЗСКОЙ РЕСПУБЛИКЕ 2016.

UNAIDS. (2018). UNAIDS DATA 2018.

WHO. (2007). WHO CASE DEFINITIONS OF HIV FOR SURVEILLANCE AND REVISED CLINICAL STAGING AND IMMUNOLOGICAL CLASSIFICATION OF HIV-RELATED DISEASE IN ADULTS AND CHILDREN HIV/AIDS Programme.

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Characterisation of non-specific antibody responses induced by BCG vaccination

Supervisors: Helen McShane and Rachel Tanner

Jenner Institute

BCG is the only currently licenced vaccine against tuberculosis (TB). In addition to the specific protection it confers against TB meningitis and miliary disease in infants and variable protection against adult pulmonary TB, it has been hypothesised that BCG has non-specific effects on the immune system. Randomised and observational studies conducted in low-income countries indicate lower all-cause mortality rates within the first 6-12 months of life for BCG-vaccinated neonates; the most consistent effect is a reduction in the cases of sepsis, respiratory infection and fever. Some studies also suggest that BCG vaccination at birth contributes to responses to subsequent vaccinations such as those for Haemophilus Influenzae type b, pertussis, hepatitis B and pneuomococcal infections. Such non-specific effects have also been reported for other live-attenuated vaccines including the measles and oral polio vaccines. While evidence in favour of this phenomenon is arguably strongest for BCG, studies have yielded conflicting findings and the concept remains contentious. An improved understanding of this phenomenon is essential as new TB vaccine candidates under development must also be non-inferior to BCG in this regard. We are currently characterising the specific antibody response to BCG vaccination, and have a valuable resource of samples from multiple BCG vaccination studies from different human populations and across species including mice, non-human primates and cattle. This internship will aim to characterise the antibody response to antigens from a range of different pathogens using samples from baseline and at multiple time-points post-BCG vaccination. Training will be provided in immunological laboratory techniques such as ELISA assays as well as statistical analysis and presentation of results.

Summer student position: Systematic review to understand how changes in behaviour might contribute to reducing AMR

Supervisors: Dr Catrin Moore and Philip Hogan

Big Data Institute, Nuffield Department of Medicine, University of Oxford, UK

Project duration: 8 weeks
Project Summary:
Drug resistant infections are a major global health threat. Many estimates have been published recently, one study estimates that 700,000 people die of resistant infections every year, with low and middle income countries (LMICs) being disproportionally affected.
A wide range of behavioural changes will be needed if the rise in drug resistant infections is to be challenged.

The Global Burden of Disease group in Oxford is working with the Institute for Health Metrics and Evaluation (IHME) at the University of Washington, USA to determine the global burden of disease and excess mortality due to AMR. The project aims to synthesize drug resistance data worldwide, create geospatial maps as far as possible with the available data, of the distribution of resistance of selected bug-drug combinations and lead the incorporation of the impact of AMR into the disease estimates of the Global Burden of Disease Study. At BDI we are also working with FIND, WHO/TDR, the Oxford Africa and Asia programmes and other research organisations in LMICS, to both reduce prescribing of antibiotics through the use of pathogen diagnostics, and to identify behaviour change determinants to adherence to prescriptions and in the uptake of diagnostics.

This summer internship will focus on behavioural change related to inappropriate antibiotic prescribing, use of diagnostics and adherence to prescriptions as drivers of AMR. It is unlikely that the burden of disease will change without a change in behaviour such as reducing the unnecessary use of non-prescription antibiotics. The project involves performing a systematic review of the available literature to inform a new study to determine the approaches that may be successful in implementing behaviour change to reduce the mortality due to AMR, particularly in LMICs. The candidate will perform a systematic review to examine the evidence of behaviour change and more broadly social science in altering behaviours associated with antimicrobial resistance.

AfOx/NDM summer studentship project

Sarah Rowland-Jones’ lab

NDM Research Building

Our group has collaborated for over a decade with investigators in Harare, Zimbabwe, who are studying the clinical complications experienced by older children and adolescents with perinatally-acquired HIV infection (PHIV). These young people may suffer from multiple comorbidities, including chronic lung and heart disease, as well as stunting and other complications. The SR-J group is investigating the role of host genetics, chronic inflammation and persistent infection with cytomegalovirus (CMV) in the pathogenesis of these comorbidities in Zimbabwean cohorts of older children with PHIV. We would welcome the involvement of a summer student to work with D. Phil. students and post-docs who are engaged in these studies. This is likely to involve molecular studies of host and viral genes in samples collected from the cohorts, as well as cellular studies looking at the immunological consequences of polymorphisms in the HLA class I associated antigen processing pathway detected in Zimbabwean populations.