If you are interested in applying for any of these PhD positions we strongly encourage you to contact the identified project supervisor before or simultaneously with submitting a formal application, so that we can look out for, and if necessary help you with the submission of your application.
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.
Funded positions recruiting now
- Please check for opportunities on FindAPhD.co
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 currently available 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.
Project: Levaraging pathogen genomics...
Supervisor: Dr Roman Biek
Project Title: Levaraging pathogen genomics and phylodynamics to control endemic anthrax
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
Validate this model by generating genomic data obtained during a livestock vaccination program expected to start in the study area in 2019.
Interested? Please contact the Supervisors below -
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.
The student will use 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).
The student will be trained in survey methods, image analysis, statistics and the biology and ecology of fish and coral reefs.
Contact: Dr David Bailey (firstname.lastname@example.org)
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
- 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.
- 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.
- 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.
- 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.
- Shiels B.R. Should I stay or should I go now: a stochastic model of stage differentiation in Theileria annulata. Para. Today 15(6): 241-245, 1999, ISSN: 0169-4758.
- Sinha A, Hughes KR, Modrzynska KK, Otto TD, Pfander C, Dickens NJ, Religa AA, Bushell E, Graham AL, Cameron R, Kafsack BF, Williams AE, Llinás M, Berriman M, Billker O, Waters AP. A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium. Nature. 2014 Mar 13;507(7491):253-7.
- Campbell TL, De Silva EK, Olszewski KL, Elemento O, Llinás M. Identification and genome-wide prediction of DNA binding specificities for the ApiAP2 family of regulators from the malaria parasite. PLoS Pathog. 2010 Oct 28;6(10):e1001165.
Contact: Prof. Brian Shiels