PhD studentships

We expect to be offering a range of PhD projects funded by the UK Research Councils (BBSRC, MRC and NERC), the Wellcome Trust and other funding bodies in late autumn.

Details of these projects will be advertised on this page, on the College's Graduate School page and at FindAPhd.com.

Funded Positions Recruiting Now

Doctoral Landscape Award in Exascale Computing for Earth, Environmental, and Sustainability Solutions 

ExaGEO PhD - GPU-accelerated multiscale modelling for glacier sliding

ExaGEO: https://www.exageo.org – closing date Monday 17th February

The projects that involve SBOHVM supervisors are as follows, contact them for further details:

Scalable Inference and Uncertainty Quantification for Ecosystem Modelling

Project supervisor(s): Dr Vinny Davies, Prof Richard Reeve, Prof David Johnson (Lancaster University), Prof Christina Cobbold and Dr Neil Brummitt (Natural History Museum)

Developing GPU-accelerated digital twins of ecological systems for population monitoring and scenario analyses

Project supervisor(s): Prof Colin Torney, Prof Juan Morales, Prof Rachel McCrea (Lancaster University), Dr Tiffany Vlaar and Prof Dirk Husmeier 

Building the Next Generation of Numerical Landscape and Species Evolvers to Quantify Geo-Biological Linkages in Changing Environments

Project supervisor(s): Dr Paul Eizenhöfer, Prof Jason Matthiopoulos, Dr Shan Huang (University of Birmingham) and Prof Kathryn Elmer

AI Meets Glasgow’s Trees: Metrics Prediction, 3D Mapping, and Socio-Ecosystem Impact Simulations

Project supervisor(s): Dr Meiliu Wu , Dr Davide Dominoni, Dr Luigi Cao Pinna, Dr Dominic McCafferty, Dr Alex Bush (Lancaster University), Doug McNeil (EOLAS Insights Ltd) and Gillian Dick (Glasgow City Council)

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Leverhulme Programme for Doctoral Training in Ecological Data Science

Ecological Data Science: https://ecological-data-science.github.io/about.html - closing date Friday 7th March 

The projects that led by SBOHVM supervisors are as follows, contact them for further details:

Leveraging large language models to provide insights into global plant biodiversity 

Primary supervisor: Prof Richard Reeve

What do wild insects do? Leveraging AI to describe wild insect behaviour and to uncover their functions for fitness

Primary supervisor: Dr Jelle Boonekamp

Text mining with large language models to enhance infectious disease ecology

Primary supervisor: Dr Maxwell Farrell

Implications of mosquito community composition changes for vector control

Primary supervisor: Dr Mafalda Viana

 

 

PhD project outlines

You can get an idea of some the types and fields of research that might interest you by visiting a listing of past PhD projects advertisments.

The listing below contains information on example project areas and potential supervisors that we hope wil be particularly useful to people who have their own scholarships and are looking for a project.  You can also see the Research Themes here. 

 

Project: Levaraging pathogen genomics...
Supervisor: Dr Roman Biek

Project Title: Levaraging pathogen genomics and phylodynamics to control endemic anthrax

Project Description:

Recent advances in sequencing technology have revolutionised our ability to track infectious disease dynamics using pathogen genomes, such as during outbreak investigations. However, these tools remain underutilised for addressing endemic disease threats, especially those affecting human and animal health in low-resource settings.  

Anthrax is a classic example of a neglected bacterial zoonosis, affecting marginalised communities in many parts of the global south, including much of Sub-Saharan Africa. It causes significant mortality in people as well as livestock losses, but tends to be undiagnosed and underreported. Although vaccination of livestock plays a key role in preventing infection in both people and animals, it is often not affordable. Moreover, because the spores of the anthrax bacterium Bacillus anthracis can remain infectious within the environment for decades, it is not clear how long livestock vaccination would have to be maintained before a measurable reduction in infection risk is achieved. Obtaining genome data from detected cases, and incorporating genomic and epidemiological data into phylodynamic models provide a novel and powerful means to track residual anthrax transmission and quantify progress towards its elimination.

This project aims to create the necessary framework for guiding anthrax control programmes in endemic settings through the use of pathogen genomics and phylodynamic modelling. Building on robust partnerships and research platforms established in northern Tanzania by the Glasgow supervisors, including existing genomic data, our project will:

1) Extend current analytical tools and molecular clock models to accommodate the alternation between extended environmental persistence and periodic rapid replication typical for B. anthracis

2) Develop a simulation model combining genomic, spatial, temporal and epidemiological information to examine the effect of vaccination on B. anthracis genetic diversity and transmission in silico

Supervisors:

Project: Fish behaviour in shallow and mesophotic coral ecosystems
Supervisor: Dr David Bailey

Supervisors: Dr David Bailey, Dr Deborah McNeill

Project outline: Mesophotic Coral Ecosystems (MCEs) are large, diverse tropical marine systems at depths of 40-100 m and which have remained relatively unstudied. Apart from a small number of teams in the US, Caribbean and Australia the mixture of technical and scientific abilities needed to carry out work in these systems remains extremely rare. As a result, work to understand MCEs is in its infancy. This is unfortunate as existing studies suggest that MCEs are coupled to the more familiar shallow reefs by many shared species.

As a result MCEs probably provide a degree of buffering when shallow reefs are affected by human activities, but it is also likely that shallow impacts spread deeper through similar mechanisms to those documented in bathyal systems. As tourism and fishing move deeper there will be a further need to understand MCEs so that impacts can be understood and managed. An essential prerequisite for management is an understanding how fish use MCEs and how fish behaviour links shallow and deep systems.

Aim: This project will investigate the distribution and behaviour of key fish species and individual animals over periods of weeks to months at sites in the Egyptian Red Sea. We hypothesise that many species move between MCE and shallow reefs either during their ontogeny or over day-night or seasonal cycles. Differences in these behaviours mediate the effects of fishing on each species, including which size classes are most affected within species. MCEs provide a refuge for some large, predatory fish that are the main targets of fishers where their behaviour limits their vertical movement.

Techniques to be used: Diver surveys will require the use of Closed Circuit Rebreathers and trimix. Two Inner Space Systems Megalodon rebreathers are available for use in this project. The candidate must either be trained to do such dives or their scholarship must provide sufficient funds to support the training.

Use of  diver-operated and baited high definition stereo video systems to determine the locations, sizes and individual identifications of key species and individual fish. Analytical methods will involve the use of Interactive Individual Identification (I3S) software and the photogrammetry system EventMeasure. These allow individual fish to be identified, measured and their precise location on the reef to be determined. Analyses of coral type, cover and other measures of habitat complexity and health may be carried out using ImageProPlus software and Coral Point Count (CPCe).

 

Contact: Dr David Bailey (david.bailey@glasgow.ac.uk)

Project: Parasitic nematode gene regulation and function
Supervisor: Dr Collette Britton

Project outline: This is an exciting time in parasitic nematode research with the availability of genome and transcriptome data for a large number of species. We are using this data to better understand how parasites invade and survive within their hosts and how their development is regulated. We have identified small non-coding microRNAs in Haemonchus and Brugia which, from their expression profiles, have potential roles in larval activation on host invasion and in modulating host immune responses which may benefit parasite survival.

The pathways regulated by these microRNAs are being identified both bioinformatically and biochemically and the importance of specific microRNAs is being tested using miRNA mimics and inhibitors. In addition, we have previously shown that RNAi-mediated gene silencing is feasible in parasitic nematodes and a current aim is to develop reliable RNAi delivery systems to identify genes essential to parasite development. A focus will be on genes conserved across related nematode species, as potential targets of novel therapeutic control.

Aim: To identify microRNAs involved in regulating parasitic nematode development and host-parasite interactions. To develop RNAi tools to interrogate the available genome data and identify essential gene functions. The information gained by these approaches will be applied to the design of new drug or vaccine therapies.

Techniques to be used: RT-PCR, RNAi, gene cloning, nematode and cell culture, miRNA technologies, bioinformatics

References:

  • Britton, C., Winter, A. D., Gillan, V. and Devaney, E. (2014) microRNAs of parasitic helminths – identification, characterization and potential as drug targets. International Journal for Parasitology: Drugs and Drug Resistance 4 (2), 85-94.
  • Laing, R. et al. (2013) The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery. Genome Biology 14 (8), R88.
  • Samarasinghe, S.B., Knox, D.P. and Britton, C. (2011) Factors affecting susceptibility to RNA interference in Haemonchus contortus and in vivo silencing of an H11 aminopeptidase gene. International Journal for Parasitology 41 (1), 51-59.
  • Winter, A.D., Weir, W., Hunt, M., Berriman, M., Gilleard, J.S., Devaney, E. and Britton, C. (2012) Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel. BMC Genomics 13 (1), 4.

Contact: Dr Collette Britton

Project: Ecological genomics and ecological transcriptomics
Supervisor: Dr Kathryn R. Elmer

Project outline: Myriad forces shape biodiversity, including its evolutionary history, demography, genomic variation, and ecological opportunity. The relative influence each of these forces is not well understood but may underlie the dramatically uneven distribution of diversity and speciation rates across geography and within and among lineages.

This is particularly fascinating to examine in fishes and in amphibians, both of which are closely tied to the ecological and environmental parameters of their habitats. A combination of genomic and phenotypic analyses in evolutionary context will offer great potential for disentangling these fundamental processes. A wealth of projects is available in this area to motivated PhD students interested in joining our research team.

Aim: To identify the genomic patterns and processes associated with adaptive phenotypes in extant biodiversity.

Techniques to be used: Sampling populations in the wild (fishes, amphibians, reptiles); next-generation sequencing of reduced genomes (e.g. RAD seq) and/ or transcriptomes (RNAseq); analysis of phenotypic variability.

References:

  • Elmer KR, Meyer A (2011) Adaptation in the age of ecological genomics: insights from parallelism and convergence. Trends in Ecology & Evolution, 26, 298–306.

Contact: Dr. Kathryn Elmer

Project: The consequences of flexibility in metabolic rate
Supervisor: Prof Neil B. Metcalfe

Project outline: Metabolic rates can vary as much as 3-fold among individuals of the same size and age in a population. The persistence of this variation has intrigued biologists, since this implies a 3-fold difference in the energetic cost of living. Studies of the consequences of this variation have revealed a range of traits (e.g. activity, dominance, rate of digestion and growth) that are connected to metabolic rate, and it seems that different rates of metabolism are favoured in different environments.

However, it also seems to be the case that some individuals are able to adjust their metabolic rate more than others (e.g. in response to a change in food availability). This project will examine the consequences of variation in this metabolic flexibility – there must be some cost or constraint to having a flexible metabolic rate, otherwise selection would have led to all individuals having an equally high degree of plasticity in this trait, which we know not to be the case.

Aim: To determine the fitness advantages and disadvantages of being able to adjust the basal and maximal level of metabolism.

Techniques to be used: Measurements of metabolic rate under different environmental conditions will be made using species of freshwater fish, and the degree of flexibility related to fitness traits such as growth, reproduction, lifespan etc.

References: 

  • Burton, T., Killen, S.S., Armstrong, J.D. & Metcalfe, N.B. 2011. What causes intra-specific variation in resting metabolic rate and what are its ecological consequences? Proc. R. Soc. B 278: 3465-3473.
  • Hoogenboom, M.O., Armstrong, J.D., Groothuis, T.G.G. & Metcalfe, N.B. 2013. The growth benefits of aggressive behavior vary with individual metabolism and resource predictability. Behav. Ecol. 24: 253-261.
  • Reid, D., Armstrong, J.D. & Metcalfe, N.B. 2011. Estimated standard metabolic rate interacts with territory quality and density to determine growth rates of juvenile Atlantic salmon. Funct. Ecol. 25: 1360-1367.
  • Reid, D., Armstrong, J.D. & Metcalfe, N.B. 2012. The performance advantage of a high resting metabolic rate in juvenile salmon is habitat dependent. J. Anim. Ecol. 81: 868-875.

Contact: Prof Neil B. Metcalfe

Project: The nematode moulting pathway as a potential novel drug target
Supervisor: Prof Tony Page

Project outline: The Trichostrongylid gastrointestinal (GI) nematodes of grazing livestock have a worldwide prevalence and cause morbidity and death with a consequential serious economic impact to farming. Teladorsagia circumcincta is the most important and widespread GI nematode of sheep in temperate areas, whereas on a global scale Haemonchus contortus is the most significant.

In cattle the related species Ostertagi ostertagi has a direct impact on meat production and milk yields. As a consequence of single and multiple drug resistance, there is an urgent need to develop new drugs against these important parasites. This studentship will characterize and target novel cuticle biosynthetic and moulting astacin enzymes that play essential nematode-specific roles. We have identified key enzymes in a model nematode Caenorhabditis elegans and we will now focus on these metalloproteinases in UK endemic trichostrongylid sheep and cattle parasites. This pathway has not previously been targeted in drug development schemes, and if successful, will provide an effective means of treating the existing anthelmintic resistant strains that are currently widespread worldwide. This project will involve the molecular identification and biochemical characterization of these drug targets and the testing and validation of synthesised inhibitors in vivo and in vitro.

Aim: The focus here will be to translate the findings from the C. elegans model into key GI nematodes of sheep and cattle. This will involve the cloning and characterization of the key astacin encoding genes from T. circumcinta and O. ostertagi, expression of recombinant proteins, heterologous expression in C. elegans and complementation of C. elegans mutants and examination of function via RNA interference.

Following on from this initial characterization, the student will focus on in vitro drug assays against larval and adult stages of T. circumcincta and O. ostertagi. This will be based on the classes of novel anthelmintics that we have developed in collaboration with Edinburgh University, that have shown dramatic effects on C. elegans. Based on these initial hits, we will carry out Structure Activity Relationship (SAR) studies and in conjunction with Chemistry colleagues to optimize the candidates for efficacy against T. circumcincta and O. ostertagi based on in vitro assays.

Techniques to be used: This project will involve a wide range of systems biology approaches, diverse techniques and training opportunities for the student. Including molecular genetics, biochemistry, drug testing, molecular modelling and animal studies. This project represents an excellent example of combining diverse but complementary skills.

References:

  • Stepek, G., et al. Int. J. Parasitol. 40: 533-542. (2010)
  • Davis, M. W. et al. Development 131, 6001-6008 (2004)
  • Novelli, J. et al. Genetics 172: 2253-2267 (2006)
  • Stepek, G., et al. Parasitol. 138: 237-248 (2011)

Contact: Prof. Tony Page

Project: Regulation of stage differentiation in the parasite Theileria
Supervisor: Prof Brian Shiels

Project outline: Apicomplexan parasites are one of the most important causes of disease in humans and animals at the global level. They include Plasmodium parasites that cause malaria, and the tick borne parasites Babesia and Theileria that cause disease syndromes that are a huge constraint to livestock productivity in many regions of the world.

These three types of parasite all have complex life cycles and current research indicates that the mechanisms that determine how the parasite changes from one life cycle form to another may be closely related and involve the same or similar types of proteins. The ability to change form is critical for both establishing and transmitting infection in human and animal host. Defining the mechanism and molecules involved in this process will provide targets for novel control strategies that may operate across a range of important parasites.

Aim: To characterise further a family of DNA binding proteins indicated to operate in the mechanism that determines when and how a parasite changes from one form to the next. Investigation of how the mechanism operates at a functional level will be performed.

Techniques to be used: Many standard molecular biology techniques: DNA cloning, sequencing, RNA expression profiling, generation of fusion proteins and competitive binding assays. Cell culture, Immunofluorescence, Bioinformatics and Chromatin immune-precipitation methodology: design and testing of inhibitors.

References:

Contact: Prof. Brian Shiels

Health and Productivity of Livestock in East Africa
Dr Tiziana Lembo & Dr Jo Halliday

Supervisors: & Dr Tiziana Lembo (Main supervisors, Glasgow)

The programme will provide postgraduate training opportunities to a cohort of sixteen PhD students focusing on closely linked projects addressing issues related to animal health and productivity to enhance the economic and food security of smallholder farmers in sub-Saharan Africa. Research projects will centre on improving health, and productivity while safeguarding animal welfare, public health and the environment.

Potential projects: Potential projects supported through this scheme for the positions at the University of Glasgow are given below. There is scope for candidates to develop their research projects based on the options below or formulate their own project ideas in line with the livestock focus of the Agricultural Development strategy of the Bill & Melinda Gates Foundation.

(1) Characterising spatial and temporal patterns of Foot-and-Mouth Disease (FMD) virus circulation in livestock populations -FMD causes significant losses for smallholder farmers in sub-Saharan Africa through livestock mortality and condition/milk loss, lack of access to local markets, and constraints to regional and international market development. Current vaccines are ineffective in East Africa, and work is needed to identify the most appropriate strains for vaccine selection and to design effective livestock vaccination strategies for the East African region. This project will involve investigation of FMD outbreaks in northern Tanzania. In addition to molecular characterisation of virus variants, data from outbreaks will be linked with information on livestock populations, livestock movement patterns and market networks to identify determinants of regional spread for different circulating virus variants, and the spatial scale across which different FMD vaccine strain combinations are likely to be effective. The study will also investigate temporal patterns of infection, involving a longitudinal study that applies newly-developed analytical approaches to identify infection patterns of FMD viruses from serological analysis of cattle herds experiencing successive outbreaks. This will allow the timing of epidemics of specific virus types to be predicted and control measures to be targeted as they are needed. 

(2) Development of surveillance and typing schemes for anthrax epidemiological studies in endemic areas - In Africa, anthrax, caused by Bacillus anthracis, affects humans, livestock and wildlife, although under-reporting and under-/mis-diagnosis of cases result in a limited appreciation of the scale of the disease problem. Existing records do not reflect human disease incidence, particularly in relation to the more severe (gastrointestinal and inhalation) disease, as opposed to the less serious, cutaneous, form. Underreporting of cases is common also for animal anthrax. There is a need for improved case reporting, and surveillance and diagnostic capacity for correctly quantifying the magnitude of the zoonotic disease problem and animal losses due to anthrax. This project will establish capacity for surveillance in anthrax-endemic areas of northern Tanzania through developing mechanisms involving the veterinary, medical and wildlife sectors, including grassroots-level information networks; improved information flow; and ‘field-friendly’ diagnosis. Molecular detection and typing assays for anthrax suitable for non-containment laboratories will also be developed, including assessing the sensitivity of polymerase chain reaction (PCR)-based techniques compared to rapid diagnosis by microscopy using improved staining procedures; assessing the sensitivity of PCR-based techniques on inactivated samples carried out in-country in Tanzania compared to standard diagnostic and PCR-based methods in western laboratories; and exploring genetic markers to develop culture-independent typing methods. This study will ultimately improve our ability to conduct in-depth anthrax molecular epidemiological studies in sub-Saharan Africa in order to study epidemiological links between animal and human anthrax cases.

(3) The etiology and productivity impacts of ruminant abortions in northern Tanzania -Infectious diseases that cause abortion in livestock species (principally cattle, sheep and goats) have significant impacts on ruminant productivity and thus on the livelihoods of smallholder farmers in sub-Saharan Africa. Many abortigenic pathogens are also zoonotic, which poses additional risks to the health of livestock keepers. This project will (1) quantify the frequency of abortion and basic reproductive parameters in cattle, sheep and goats owned by pastoralist smallholders in Tanzania; (2) quantify the economic impacts of livestock abortion and reduced reproductive productivity on smallholders; (3) generate diagnostic test data to identify the pathogens responsible for livestock abortions; and (4) identify control measures (e.g pathogen specific vaccination programmes, generic measures to improve herd nutrition etc.) that can be implemented to control the pathogens identified and reduce the socio-economic and health impacts of abortigenic pathogens. Data collection elements will include repeat household surveys to generate data (animal and human) on pathogen presence and quantify the frequency and economic impacts of livestock abortions and impaired reproductive productivity in ruminants; establishment of syndromic surveillance systems to quantify the incidence of livestock abortions; and follow-up sampling of reported livestock abortions to gather diagnostic material to determine the etiology of ruminant abortions.