School of Biodiversity, One Health & Veterinary Medicine

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 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 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 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 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:

• 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

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.