Edinburgh Infectious Diseases
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Supervisors and projects

There are 25 supervisors currently associated with the Programme. Find out about their research and the types of projects that you might work on in their labs.

Find out about the researchers who contribute to the programme.

The supervisors contributing to the Programme are mainly based in The Roslin Institute at Easter Bush, the Centres for Inflammation Research and Cardiovascular Research at Little France and the Usher Institute in the Old Medical School.

This page has information on the research each supervisor is involved in and details about a possible project that you could work on if you chose to undertake your PhD in that lab. 

Please note that when you apply to join the Programme you are not choosing a supervisor - you will select your PhD project toward the end of your first year in Edinburgh. 

Programme directors

The One Health Models of Disease PhD programme is directed by Prof Ross Fitzgerald, Chair of Molecular Bacteriology and Director of Edinburgh Infectious Diseases, at the Roslin Institute and Dr Martyn Pickersgill, Reader in the Social Studies of Biomedicine at the Usher Institute of Population Health Sciences and Informatics.

University profile of Ross Fitzgerald

University profile of Martyn Pickersgill

Supervisors and example projects

Prof Matt Bailey – Centre for Cardiovascular Science

Matt is chair of Renal Physiology at Edinburgh.  He investigates physiological and molecular pathways of cardiovascular and renal dysfunction in hypertension and renal disease. His research group has longstanding expertise in using innovative methodologies to assessment of hypertension and renal dysfunction in mice, including measurement of vascular and tubular function in vivo and ex vivo. He has published 75 papers and has been awarded >£2.5M in research funding and >£7.5M for Doctoral Training.  He currently has grants from Kidney Research UK, British Heart Foundation and Diabetes UK.

Website

Possible project title:  Salt & steroids: the molecular basis of vascular dysfunction in hypertension

Project description:  Advanced physiological assessment of cardiovascular functional will be combined with vascular transcriptomics to define the molecular basis of vascular dysfunction in models of glucocorticoid excess and salt-sensitive hypertension.

Dr Kenny Baillie – The Roslin Institute

The Baillie lab focuses on translation genomics in sepsis.  They are trying to understand the mechanisms that make people desperately sick in sepsis, so that they can find new treatments. This is their approach: (1) there is biological variation in the host response to injury; (2) some of this variation is genetic; (3) we can use this genetic variation to find new treatments.  They believe that a functional genomics approach can lead us to biological processes that might be amenable to treatment.  They develop and apply computational tools, and use in vitro and in vivo models to generate and test hypotheses, using influenza as a model for the host response to injury.  

Baillie lab website

Possible project title:  Genome editing in primary cells, tissues and in vivo in Cas9 transgenic pigs to promote survival in humans with sepsis

Project description:  Use CRISPR/Cas9 genome editing using cells and tissues available from Cas9 transgenic pigs, and in vivo, to investigate mechanisms of severe sepsis.

Prof Andy Baker – Centre for Cardiovascular Science

Andy's lab is interested in the mechanisms that control vascular damage and how to influence repair and regeneration of the vascular system using innovative therapies, including gene-, cell- and RNA-based approaches. Focusing on vascular smooth muscle and endothelial cells, they are defining the non-coding RNA pathways and networks that influence cell function in health and disease and developing interventions to influence beneficially repair and regeneration.

They also have a focus on gene therapy, both in the translational and basic sense. They have developed an innovative gene therapy approach to prevent pathological vascular remodelling associated with coronary artery bypass graft failure and are pursuing this at the clinical interface. They are also generating endothelial cells from human embryonic stem cells for regeneration in ischaemic conditions, and developing an understanding in mechanisms that control endothelial cell commitment and specification.

Lab website

Possible project:  Using human embryonic stem cell-derived endothelial cells to understand endothelial function and dysfunction.

Prof Debby Bogaert – Centre for Inflammation Research

Respiratory infections are a leading cause of morbidity and mortality in children worldwide. The respiratory and bacterial pathogens causing these infections are actually common colonizers of the upper respiratory tract as well, living mostly in full harmony with the host. The reason why in one child colonization with those pathogens is followed by disease, and in others not, is not fully understood. 

Debby's research group has a major focus on investigating the physiology and pathophysiology of respiratory infections and inflammation from an ecological perspective, with the ultimate goal to design new or improved treatment and preventive measures for respiratory infections in susceptible populations. To this purpose, the team uses a fully translational approach, combining epidemiological, molecular microbiological, immunological and systems biology approaches to answer their research questions. Moreover, we execute mechanistic studies in vitro and in vivo. Debby still has a research team in Utrecht, the Netherlands, working on continuation of several birth cohorts and clinical studies.

Lab website

Possible project title:  Drivers of the human microbiome; the influence of pets and livestock.

Project description:  In this project we aim to study how the environment, in particular contact with animals, shape the human microbiome in childhood.  To study this, we can use of a molecular epidemiological and system science approach to cohort data, complemented by mechanistic work using in vitro models.

Dr David Collie – The Roslin Institute

David's group has a longstanding interest in developing a closer understanding of the mechanisms that underlay lung disease in domestic animals and man such that appropriate directed therapies can be developed and validated in a pre-clinical setting prior to their evaluation in a clinical context. Current research is directed towards understanding the mechanisms that underlay individual susceptibility to radiation-induced lung injury, and developing strategies to mitigate this risk. 

In addition our group is currently working towards understanding the way in which microbial communities develop and are arrayed within the healthy lung microbiota and how these communities are influenced by chronic lung infection, particularly in the context of Pseudomonas aeruginosa, and/or treatment with antimicrobials.  These interests complement our longer term involvement in developing lung-directed gene therapy as a viable clinical entity. The driver in this instance is our involvement within the UK Cystic Fibrosis Gene Therapy Consortium, a grouping of the leading gene therapists in the UK. This involvement contributed to a major UK initiative that culminated in the largest ever human gene therapy trial for this condition.

Lab website

Possible project (1):  Exploring the impact of radiation-induced remodelling of the lung vascular bed in dictating susceptibility to lung injury following radiation exposure

Possible project (2):  Assessing the periodicity of respiratory microbiota in small ruminants, and exploring its impact on susceptibility to respiratory disease

Dr Megan Davey – The Roslin Institute

The Davey Group examines the causative alterations of gene expression which lead to variations in phenotype using comparative anatomy, genomics and embryonic manipulation of avian species. She has expertise in gene expression analysis, particularly the molecular anatomy of the developing limb bud and in the function of TALPID3, a ciliopathy locus. Additionally Dr Davey is the Roslin Institute Lead for Public Engagement.

 

Lab website

Possible Project 1: Investigation of Joubert Syndrome and TALPID3 related ciliopathies with gene engineering approaches.

TALPID3 is a ciliopathy disease locus in humans and animals. Using pioneering gene engineering approaches in a chicken embryonic model we will create and study an allelic series of human TALPID3 mutations to investigate the underlying  cell biology, anatomy and immune system of Joubert syndrome patients.

Possible Project 2: The role of TALPID3 in the immune synapse

TALPID3 is a centrosomal protein, essential for ciliogenesis and normal polarised cell behaviour. Using transgenic and genome engineering approaches we will investigate the role of TALPID3 in immune synapse formation in macrophages.

Prof Kev Dhaliwal – Centre for Inflammation Research

Current research is directed towards understanding the mechanisms that underlay individual susceptibility to radiation-induced lung injury, and developing strategies to mitigate this risk.

Prof David Dockrell – Centre for Inflammation Research

Macrophages play a key role in the pathogenesis of infectious diseases. We are interested in understanding how key macrophage innate immune functions protect healthy individuals against infection, despite recurring challenge, and how these core responses are perturbed by human disease inducing susceptibility to infection. We believe that by optimising innate immune responses we can limit our reliance on antimicrobial therapy and provide an alternative strategy to that focused on targeting pathogens by vaccine responses or with antimicrobials to which they can develop resistance. 

We study a variety of bacterial infections but focus in particular on Streptococcus pneumoniae and other respiratory pathogens. We also examine Staphylococcus aureus and are interested in how HIV and other viral infections alter the macrophage responses to bacteria. We use a variety of models to interrogate the macrophages' function both in isolation and as part of an immune cell network. These approaches include working with patients with chronic diseases such as Chronic Obstructive Pulmonary Disease and HIV. We are also interested in developing effective screening approaches to identify and manipulate key innate immune responses.

Lab website

Possible project title:  Enhancing macrophage microbicidal responses to limit bacterial pathogens in livestock

Project description:  Innate immune responses are broadly conserved and this project will build on knowledge of microbicidal responses in humans to determine their utility as therapeutic targets in livestock.

Prof David Gally – The Roslin Institute

The main research focus of David's group is the pathogenesis of Escherichia coli, in particular zoonoses caused by enterohaemorrhagic E. coli (EHEC).  They study the colonization of cattle by EHEC strains and aim to understand the genetic factors that lead to infections in humans. 

Specifically, his recent work is making use of whole genome sequencing to define the subset of animal strains that are a threat to human health.  By analyzing the accessory genome content of both human and cattle strains we are able to predict the strains more likely to cause serious human disease.  This work is combined with his other main research area, the development of vaccines to prevent EHEC excretion from cattle.  The vaccine research has been built on his lab's studies of surface organelle expression in Escherichia coli, in particular of flagella and type III secretion systems.   As it is now possible to predict which farms carry strain with a high zoonotic threat then targeted interventions are possible. Ongoing work is aiming to licence the vaccine, and they are also developing flagellin-based fusions for stimulation of mucosal immunity.

Personal profile

Dr Agomoni Ganguli-Mitra – School of Law

Dr. Ganguli-Mitra’s background is in bioethics, with a special interest in global bioethics, structural and gender justice. She has written on ethical issues related to global surrogacy, sex-selection, biomedical research in low-income countries, social value in research governance and the concepts of exploitation and vulnerability in bioethics. 

Her current research interests include Global bioethics and justice in global health and the ethics of global health emergencies, biomedical research, and public health

Research Profile

Possible project title:  Beyond public health ethics? Novel ethical challenges in the era of One Health

Project description:  Bioethics and public health ethics have developed with the person at their focus of moral attention. Yet, global challenges such as antimicrobial resistance, the spread of infectious diseases, and public health emergencies, increasingly point to the need to approach bioethics and public health ethics in ways that look beyond the person and the human body. This project, to be co-designed between the student and supervisory team, will explore the new ethical tensions arising in the face of emerging threats to health, human wellbeing and animal welfare. The lead supervisor will be Dr. Agomoni Ganguli-Mitra, a bioethicist based at Edinburgh University School of Law, and  member of the Centre for Biomedicine, Self and Society (Associate Lead of Beyond Global theme).

Prof Gillian Gray – Centre for Cardiovascular Science

Survival following acute myocardial infarction (MI), or heart attack, has increased thanks to efficient intervention to restore blood supply to the myocardium, or heart muscle. However, the myocardium still incurs damage, and as the adult heart does cannot efficiently regenerate new tissue, a fibrous scar is formed that does not contribute to contraction. In the longer term the remaining healthy heart undergoes remodelling while trying to maintain cardiac output, leading to an increased chance of developing of debilitating chronic heart failure. 

My research is focused primarily on understanding how to limit the loss of contractile tissue that occurs immediately after MI, but in particular the processes involved in infarct healing (inflammation, fibroblast activation & angiogenesis) and how these might be targeted therapeutically to prevent infarct expansion during repair. We also work on development of new imagingtechniques to identify vulnerable peri-infarct myocardium and on the mechanisms that support neonatal heart regeneration after injury.

Lab website

Dr Finn Grey – The Roslin Institute

The Grey Lab uses cutting-edge tools to examine the interactions between the host and pathogens such as cytomegalovirus, influenza virus and African Trypanosomiasis.  Pathogens interact with hosts in complex and intricate ways. Understanding how pathogens interact with the host can provide valuable information on how the pathogen replicates and teach us how the host responds to infections, ultimately leading to the development of better vaccines, drugs and treatment regimes.

Systematic high throughput screens are powerful approaches that allow us to examine the role of host genes during infection.  Our group uses cutting-edge high throughput approaches including small interfering RNA (siRNA) and CRISPR/Cas9 screens, arrayed interferon stimulated gene (ISG) expression libraries and microRNA target identification to discover and characterise novel host-pathogen interactions. We work on human clinical diseases including human cytomegalovirus, diseases important to livestock, and pathogens that span both human and livestock, such as influenza virus and African Trypanosomiasis.

Lab website

Possible project title:  Identification of novel host-virus interactions through phenotypic screening

Project description:  Our group uses cutting-edge high throughput approaches to discover and characterise novel host-pathogen interactions to improve our basic understanding of pathogens and to identify therapeutic targets.

Prof Jayne Hope – The Roslin Institute

The group focuses on cellular immune responses aiming to define the mechanisms whereby natural immunity is achieved and how protective immunity is induced by vaccination. We focus specifically on antigen presenting cells and their interactions with other cells of the innate immune system including natural killer cells and gamma delta TCR+ T lymphocytes. The overall aim is to define the functional and phenotypic characteristics of innate immune cells and to assess their role in protective immunity to mycobacterial pathogens including Mycobacterium bovis and M. avium paratuberculosis. These pathogens cause economically important diseases in cattle: bovine tuberculosis and Johne’s disease.

Alongside this we are interested in defining host-pathogen interactions in feline tuberculosis. Effective control of mycobacterial diseases requires the development of effective vaccines and/or diagnostic tests: this requires detailed knowledge of protective immune mechanisms. The development of new immunological tools, reagents and assays and validation across species is also an important area of research. This will provide the capacity to determine immunological correlates of protection against a number of strategically important diseases.

Lab website

Possible project title:  Using stem cell-derived macrophages to investigate infection mechanisms of Mycobacterium bovis

Project description:  This project will investigate the mechanisms by which Mycobacterium bovis, which causes TB in cattle and humans, infects host macrophages and causes disease.

Dr Vicky Macrae

Our group undertakes research in bone formation and vascular calcification. We examine the mechanisms of differentiation and calcification in growth plate chondrocytes, osteoblasts, vascular smooth muscle cells and valvular interstitial cells.

Our research employs transgenic models and clinical samples and utilises use a range of molecular, histological and imaging techniques. The elucidation of new mechanisms of bone formation and vascular calcification may identify new potential therapeutic targets in human and animal disease.

Lab website

Possible project title: Using large animal models to discover new molecular pathways of cardiovascular calcification

Project description:  This project will employ sheep and pig in vitro and ex vivo models of blood vessel and aortic valve calcification to investigate new mechanisms underpinning cardiovascular calcification.

Dr Gerry McLachlan – The Roslin Institute

The main long-term focus of my research has been on developing lung-directed gene therapy as a viable clinical entity. My group is part of the UK Cystic Fibrosis Gene Therapy Consortium (CFGTC), a grouping of leading gene therapists in the UK. Over two decades the CFGTC has pooled the resources of three major groups in the UK (University of Edinburgh, University of Oxford and Imperial College London), progressing from laboratory studies, to the first demonstration that gene therapy can produce improvements in the lungs of CF patients in the largest ever human gene therapy trial for this condition. 

We are now in a position to take advantage of unique expertise in Edinburgh in delivery, sampling and lung function measurement in a large mammalian lung model that we have established. An added objective of the CFGTC is the translation of gene therapy for a Portfolio of diseases by exploiting the synergies provided by our respiratory gene delivery platform technology, a critical mass of researchers with complementary extensive expertise, the use of common resources, and respiratory gene transfer expertise.  Other interests include studies in the sheep lung to explore the functional relevance of the respiratory microbiota.

We are investigating potential spatial heterogeneity within different regions of the healthy lung, the longitudinal stability and the potential changes following infection and/or antibiotic treatment.  We also have an interest in evaluating protocols to manipulate the composition of the respiratory microbiota in vivo.

Personal profile

Possible project title:  Ovine and Porcine lung organoids and cultured Precision Cut Lung Slices (PCLS) to predict efficacy of gene therapy vectors for respiratory disease

Project description:  Development of lung organoids and PCLS from large animal species potentially give greater scope for understanding and intervening with human pathogenic processes in the lung.  We have pioneered the use of sheep and pigs to improve translational potential of respiratory gene therapy vectors.

Dr James Mittra – Science, Technology and Innovation Studies, School of Social and Political Science

My interests include: Impact of the life science and new biology on the pharmaceutical and biotechnology industries; New business models and value systems in the bioeconomy; New approaches to value and pricing in healthcare; Translational research and collaborative approaches to R&D; Risk governance and regulation of advanced technoogies; Genetic risk, probability and insurance; and Stakeholder engagement with science and technology.

Personal profile

Prof John Mullins – Centre for Cardiovascular Science

My research focusses on the molecular and cellular mechanisms that regulate blood pressure.

We use molecular, cellular and in vivo tools, including state-of-the-art imaging and genetic techniques to understand how key genes work, to dissect pathways through which they operate, and to understand the function of specialized cells that secrete hormones and control fluid and salt balance.

Lab website

Dr Martyn Pickersgill – Centre for Biomedicine Self and Society, Usher Institute

Martyn Pickersgill is Wellcome Trust Reader in Social Studies of Biomedicine. Based in Edinburgh Medical School, he conducts research in the social sciences and medical humanities. Martyn's primary expertise is in the sociology of biomedicine and mental health. In particular, his work has considered the social, historical, and normative dimensions of epigenetics, neuroscience, and psychiatry.

Personal profile

Possible project title:  Sociological Dimensions of Animal Welfare and Gene Editing

Project description:  This project will be co-designed between student and the supervisory team, and relate to the social dimensions of gene editing, and specifically how welfare concerns are constructed, negotiated, and (potentially) resolved within gene editing research.

Prof Rob Semple – Centre for Cardiovascular Science

My overarching interest is in the causes and consequences of abnormal insulin action in human disease. I aim ultimately to gain insights into the nature and mechanisms of "common" insulin resistance, and into potentially modifiable mechanisms linking it to major diseases such as type 2 diabetes, fatty liver, dyslipidaemia, subfertility and cancer.

To achieve this, my lab focuses on the genetic, cellular and molecular basis of extreme human disorders of insulin action, whether genetic or antibody-mediated, and ranging from severe insulin resistance to spontaneous non insulin-dependent hypoglycaemia. Many of the conditions we study feature primary abnormalities either the insulin receptor (INSR) or downstream phosphatidylinositol-3-kinase (PI3K).  

As well as undertaking mechanistically informative studies of relevance to common disease, I have a major translational interest in improving diagnostic pathways and therapy for patients with these rare disorders. Core approaches include physiological phenotyping of humans with rare genetic syndromes, dissection of insulin action in primary cells from affected patients ex vivo, and identification of causative genetic defects using hypothesis-led and non hypothesis-driven genetic approaches.

Lab website

Prof Devi Sridhar – Global Health Governance Programme, Usher Institute

Devi's work focuses on the three core areas of research within the Global Health Governance Programme: improving the effectiveness of international health organizations; tracking financing to global public health and developing better tools for priority-setting.

Her work is conducted in close collaboration with Ministries of Foreign Affairs, Health and Finance and researchers in low and middle income countries, as well as policy-makers in international institutions. Devi's current projects include: (1) The Economic Gaze. The World Banks Influence on Global Public Health (Funder: WT Wellcome Trust); (2) RESPIRE:  Global Health Research Unit focussing on respiratory health in Asia (Funder: NIHR); (3) Assessing the impact of CHNRI method for setting global health research priorities.

Personal profile

Prof Mark Stevens - The Roslin Institute

Research in the Stevens laboratory aims to improve food safety and enhance the health and welfare of farmed animals by defining the role of host and bacterial factors during Salmonella, Campylobacter and Escherichia coli infections. These agents have been estimated to collectively cause 174 million cases of acute diarrhoeal illness in humans and 80,000 deaths worldwide each year and infections can be complicated by life-threatening sequelae. Such infections are frequently acquired via the food chain and environment from farm animals and control of the agents in reservoir hosts is expected to reduce the incidence of human disease.

Toward this aim, a mix of fundamental, strategic and applied projects exploit knowledge of the role of bacterial and host factors in pathogenesis to develop and evaluate methods of disease control. His research is conducted at all levels from molecules to target animals and provides insights that cannot be obtained in surrogate rodent- or cell-based assays. Current emphasis is placed on identifying bacterial virulence factors and their mode of action, understanding the genetic architecture of host resistance to guide selective breeding, evaluating novel vaccines and studying the dynamics of transfer of antimicrobial resistance.

Personal profile

Possible project title:  Analysis of the role of bacterial factors in the pathogenesis of typhoid using novel surgical & 3Rs approaches

Project description:  My laboratory has developed novel surgical and 3Rs models to study Salmonella pathogenesis in cattle, which closely resembles disease in humans. The project will combine these models with genetic approaches to study the role of specific bacterial factors in persistence, pathology and protection.

Dr Christine Tait-Burkard – The Roslin Institute

Prof Bruce Whitelaw – The Roslin Institute

Bruce Whitelaw's group is focused on animal genetic engineering. Through evaluating application of genetic engineering and advanced reproductive technologies we aim to improve livestock health, develop new livestock breeding strategies to enhance overall agriculatural productivity, and progress innovative biotech solutions in biomedicine. By altering livestock genomes using precise genome editing technology like CRISPR-Cas9 we tackle costly livestock diseases, devise innovative breeding strategies, address the challenge of increasing protein production in livestock agriculture, investigate how gene drives could be applied in animals and explore opportunities to develop new disease-treatments.

Lab website

Possible project title:  Engineering resistance to pestivirus

Project description:  Can we exploit CRISPR/cas9 technology to identify host genetic resistance to pestivirus infections that has application in farmed animals and humans.

Prof Andrea Wilson – The Roslin Institute

Research in the Doeschl-Wilson group focuses on the development of mathematical models and computational tools that enhance our understanding how the genetics of individuals and diverse non-genetic factors together influence the dynamics of infectious diseases and their impact on the health and performance of individuals and of entire livestock populations. We use these tools to (1) DESIGN infection experiments and sampling strategies that let us detect the genetic signal from disease and performance data; (2) IDENTIFY individuals or genomic regions associated with high genetic resistance or tolerance to infections, or high genetic risk for transmitting infections (infectivity); (3) PREDICT the impact of genetic and non-genetic control strategies on future disease prevalence and pathogen evolution.

We use a wide range of modelling techniques that combine methods from mathematical dynamical systems theory, Bayesian statistics, and quantitative genetics. Applications include virus infections in pigs (Porcine Reproductive and Respiratory Syndrome, PRRS) and chicken (Marek’s disease), gastro-intestinal parasite infections in sheep, bacterial infections in cattle (bovine Tuberculosis), to virus and protozoa infections in fish.   We also apply mathematical tools to study genetic effects and group dynamics underlying aggressive behaviour in pigs.

Personal profile

Possible project title:  Genetic dissection of individual health trajectories and their role in disease transmission

Project description:  We will use novel mathematical and computational techniques such hidden Markov models and deep learning to dissect individuals’ health trajectories and how manipulation of these may affect disease transmission dynamics in the future

Dr Tom Wishart – The Roslin Institute

Research in the Wishart laboratory is aimed at understanding the cellular and molecular processes which underpin the development and stability of the nervous system in health and disease, with a more specific focus on the biology of the neuron.It is accepted that the neuron can be compartmentalized (grossly speaking) with respect to both form and function into three units: the cell body (or soma and associated dendrites), the axon and the synapse.

It is also known that stability of the axon and synapse can be affected independently of one another. Synapses are of special interest to us as it is becoming increasingly accepted that they are a primary pathological target in a number of neurodegenerative conditions, including but by no means limited to; Alzheimer’s disease, Parkinson’s disease, Huntington’s disease and motor neuron diseases. That is to say, synapses go first and the rest of the neuron follows. As age increases the susceptibility to many of these neurodegenerative conditions, the ever increasing life expectancy of current society means that the costs associated with neurodegenerative diseases are only going to escalate over the coming years. It is therefore critical that we develop a clearer understanding of the mechanisms which underpin healthy development and stability of synapses and the regulators of altered synaptic/neuronal vulnerability.

Personal profile

Possible project title:  Multi species investigation of PPT1 and Nervous system stability in health and disease.

Project description:  Analysis of the anatomical and molecular consequences of the childhood neurodegeneration inducing PPT1 mutation in mouse, sheep and human tissue samples with assessment of subsequently identified novel regulators in rapid in vivo systems.