PhD studentships

We regularly offer studentships for research students throughout the year, including those from our EnvEast Doctoral Training Partnership. When they are advertised you will find information on this page or the EnvEast page. You can also contact us with any studentship enquiries.

Previously offered studentships

Recently offered studentships have included:

Determination of extent to which anatomical stomatal characters determine leaf transcription, temperature and CO2 assimilation in wheat

BBSRC Industrial studentship - School of Biological Sciences, University of Essex; NIAB Cambridge and Bayer Crop Science

Stomal density is known to vary significantly between and within species (Weyers & Lawson, 1997). Manipulations to increase stomatal numbers per unit leaf area has not only have the potential for greater CO2 diffusion for photosynthesis (Tanaka et al., 2013) but could also enhance leaf cooling, ensuring the leaf is maintained at temperatures optimal for photosynthesis. On the other hand reductions in numbers could increase water use efficiency (Franks et al., 2015).

Computational Biology of Epigenetic regulation in Chromatin

The proposed project is devoted to modelling epigenetic regulation in chromatin using approaches of theoretical biophysics and computational biology, based on experimental data from different types of next generation sequencing techniques. Our long-term mission is to understand how Nature “computes” molecular assembly in chromatin, which determines changes in gene expression during normal cell differentiation or cancer progression. See examples of our recent publications: Beshnova et al. (2014) PLoS Comput Biol 10, e1003698; Teif et al. (2014) Genome Research, 24, 1285-95; Teif et al. (2012) Nature Struct Mol Biol 19, 1185-92. Our most frequently used techniques for this project are: (1) methods of statistical mechanics to construct theoretical biophysical models of macromolecular binding and parameterize those using experimental data from multiple sources, and (2) methods of bioinformatics and computational biology to analyse and integrate different high-throughput sequencing datasets.

Elucidating Interactions within Bacterial Tripartite Drug-efflux Pumps

A PhD studentship is available to study the mechanisms of recognition between the components of tripartite multidrug-efflux (MDR) pumps. These pumps are key contributors to the rising global problem of multidrug resistance in Gram-negative bacteria and are composed of tree components spanning both the outer and inner membranes of the Gram-negative cell, namely the outer-membrane proteins (OMPs) [1], the energy-coupled inner-membrane proteins (IMPS) [2] and the periplasmic adapter proeins (PAPs) providing a link between the two [3,4].

Mechanistic Models of Gene Regulation

The DNA in all cells of an organism is the same. What makes the great variety of tissues, or the difference between healthy and diseased tissue, is the specific set of genes that are active. Transcription factors are proteins that bind in the vicinity of genes and determine whether a gene is on or off.

Unravelling the Origins and Evolution of the Animal Kingdom using Genomics

The Animal Kingdom comprises some of the major transitions in the evolution of life, embracing a spectacular diversity product of hundreds of million of years. Intriguing questions on its beginnings and major transitions are still a mystery: which genomic events are related to the advent multicellular animals from single cell organisms? What are the causes of the major transitions such as the emergence from animals with radial symmetry (as sponges or jellyfish) of creatures with a bilateral architecture like ourselves?

Deciphering the Function of Histone Modifications and Noncoding Transcription at Distal cis Regulatory Elements

Interplay among histone modifying complexes that recognise these modifications, along with chromatin remodelers are likely to play key role in enhancer function. However, there are no thorough investigations on the importance of histone modifications and protein complexes associated with enhancers and their effect on target genes in vivo.

Free Radical Mechanism of ferritins

A PhD studentship will be available at the Biomedical EPR Facility to study ferritins – ubiquitous enzymes that accumulate iron for cell’s needs and handle iron’s intrinsic toxicity. Ferritins from different organisms exhibit structural differences and, consequently, demonstrate rather different mechanisms of iron acquisition. We recently demonstrated [1], that iron acquisition in E. coli ferritin is associated with free radical formation on the enzyme. The mechanism of this free radical driven iron mineralisation, in ferritins from different organisms, is in the focus of the PhD studentship programme. Successful output of the programme is expected to be accurate kinetic characterisation, by several spectroscopic methods, of the mineralisation process which would allow creation of kinetic models. The candidate is expected to be fluent in basic biochemistry, to be familiar with several spectroscopic methods including fast kinetic techniques. Knowledge of and experience in EPR spectroscopy will be considered advantageous. Successful candidate will benefit from learning several wet lab and computational protocols exercised in the friendly and diverse research environment of the School as well as from collaborative contacts with the University of East Anglia which has very a strong record of ferritins studies.

Computational Chemistry Assisted Simulation of the EPR Spectra of Protein Radicals

A PhD studentship will be available at the Biomedical EPR Facility to develop a new method of simulation of Electron Paramagnetic Resonance (EPR) spectra of protein radicals. Free radicals are often formed on proteins and enzymes during many biologically important reactions. To understand the mechanism of such reactions, it is important to know where exactly on the protein the free radical is located [1]. Computer simulation of experimentally detected free radical EPR spectra provides information about the radical structure and its micro-environment. This information can be related to the protein structure, if known, and the radical location can be found. This approach, however, suffers from ambiguity: there are too many variables in a protein radical EPR spectrum simulation which can yield many local minima in a search for an optimal simulated spectrum.

Modelling Epigenetic Regulation in Chromatin

The proposed project is devoted to modelling epigenetic regulation in chromatin using approaches of theoretical biophysics and computational biology, based on experimental data from different types of next generation sequencing techniques. Our long-term mission is to understand how Nature “computes” molecular assembly in chromatin, which determines changes in gene expression during normal cell differentiation or cancer progression..

New Insights into Temperature Adaptation of Diatom Growth

Do you want to undertake research on one of the challenges facing marine organisms, which is to understand how the base of the ocean food chain is going to cope with global warming? The microscopic plants (phytoplankton) that inhabit the ocean are being driven out of their climatic comfort zone as global warming continues. The phytoplankton account for about 50% of global photosynthesis and form the base of open ocean food webs. This project will allow you to undertake innovative fundamental research on important questions including: What are the physiological mechanisms that allow marine phytoplankton to cope with high and low temperature stress, and what sets the limits on the efficacy of these mechanisms? How is primary production likely to change in response to rising water temperature?

Evolution of the Optimal Leaf

Local and global environmental conditions and atmospheric gas concentrations have played a major role in shaping plant evolution. Evolution has selected for plants that have greater densities of stomata and veins as well as heterogeneous patterns of veins and stomata, facilitating spatial variation in gas exchange, photosynthesis and evaporative cooling. It is assumed that veins and stomata show coordination in patterning however this has only been examined in modern angiosperms. This project will focus on mapping patterns and heterogeneity in stomatal density in parallel with vein density in relation to photosynthetic capacity, hydraulic conductance and stomatal responses in different species from across an evolutionary gradient. The project is a collaborative effort between the University of Essex (EnvEast partner) and Prof Jenny McElwain at University College Dublin (UCD). UCD have unique climate control facilities for growing plants in a range of climatic conditions. The successful candidate will have the opportunity to work with Prof McElwain at UCD to evaluate the impact of climate change on spatial patterns of anatomical and functional traits.

Why Aren't Marine Organisms Permanently Hungover? Understanding Microbial Consumption of Acetaldehyde in the Ocean

Acetaldehyde is a simple, highly soluble and volatile organic compound that contributes to global warming and significantly changes the ‘self-cleaning’ capacity of the atmosphere. Acetaldehyde also has many other societal impacts from wine spoilage to damaging human health. Globally, the amount of acetaldehyde entering the atmosphere is between 80-160 million tonnes per year, with the oceans contributing 17-125 million tonnes per year. Thus, the oceans are potentially the largest global source of acetaldehyde to the atmosphere. In seawater the concentration of acetaldehyde is in the low nano-molar range, and is thought to be largely controlled by marine microbes. What we do not know is ‘who’ is using this compound and ‘how’ they are doing it.

Sea Ice and Clouds - Modelling their Climate Connections over the Southern Ocean

The aim of this project is to explore processes affecting Southern Ocean clouds, to try to improve the performance of the UK Earth System Model (UKESM1). During this project, you will learn to use the UKESM1, and to test a range of influences on Southern Ocean clouds. These include a recently-identified source of sea salt aerosol source from blowing snow over sea ice zone. You will implement this new aerosol source into the UKESM1 to check its effect on sea surface temperature and atmospheric circulation, and evaluate it against observations.

Coral Survivors: Local Adaptation to Extreme Conditions

Never have coral reefs been under greater threat. The third global coral bleaching event is currently underway, putting at risk the survival of corals around the world. This project will provide insight into how corals can survive harsh environmental conditions, such as those that cause bleaching.

Do Fungi Regulate Terrestrial Biodiversity?

In this project, you will examine the strength and specificity of belowground plant-fungal interactions, and examine if these interactions are able to contribute towards regulating plant-species coexistence. You will conduct field sampling of grassland plant species from a number of European sites. This will involve plant surveys and, collecting plant roots for molecular analysis (Next Generation Sequencing) to quantify the fungal assemblages present. Additional experimental work will allow assessment of fungal effect on plant productivity and physiology.

Development of Methods and Instrumentation for Collection, Analysis and Validation of Damage-Free Protein Structures in Defined Redox States

X-ray crystallography underpins much of our knowledge of biology. However, radiation damage caused by X-rays to the protein crystal druing data collection remains a major challenge. Such damage takes two forms: global and site-specific. Global damage is typically observed through decay in diffracting power or loss of high-resolution data while site-specific damage (including X-ray driven photoreduction of metal redox centres) is much more difficult to track and occurs at much lower absorbed doses. This is a critical problem for structural biology as incorrect information regarding biological function may be inadvertently inferred from damage structures.

The Role of Thermal Adaptation in contraining Long-term Biogeochemical Responses to Global Warming

Forecasting and mitigating damaging levels of climate change is set to be the defining scientific challenge of our age. Central to this is an understanding of the mechanisms underpinning biogeochemical feedbacks with the climate system. Biogeochemical cycles (e.g. C and N cycles) are driven by metabolic processes, which transform and exchange elements between the biosphere and the atmosphere. Despite major progress in the past decade, we currently lack a mechanistic understanding of how ecological and evolutionary processes mediate biogeochemical responses to global warming. Thermal adaptation is known to be an important process giving rise to taxa or lineages with distinct thermal niches that can differ in the parameters which characterise their thermal performance curves - e.g. thermal optima, activation energy, specific rate. This studentship will utilse microbial communities across our long-term warming experiments and field sites, to determine the extent to which evolutionary adaptation influences the long-term thermal responses of key fluxes in the carbon and nitrogen cycle.

Using Thermal Niche Theory to Predict Community Dynamics in Freshwater Ecosystems

Climate warming is one of the biggest drivers of change in many ecological systems. However, we remain largely ignorant about its impacts on many groups of organisms and their ecological interactions, particularly in freshwater environments. Within these systems, bacterivorous micro- and meiofauna are key taxa in regulating bacterial communities, and thus have consequences for bacterial-driven ecosystem functions (e.g. nutrient cycling). In the context of warming environments, it is critical to know how warming alters the complex web of interactions between bacteria and the grazer community, if we are to understand the functional implications of climate change. The studentship will use the ecological niche concept as a foundation to understand component and community wide responses to simulated global warming and the concomitant ecosystem functioning outcomes. The overall goal of the studentship will be to investigate how ecological niche breadth influences tipping points and community interactions, including food webs within freshwater lentic microbial eukaryote communities associated with warming.

Performing under pressure: Helping athletes to meet the challenge

The biopsychosocial model proposes that challenge and threat states are important predictors of performance variation under pressure. Athletes who experience a challenge state (i.e. resources evaluated as outweighing demands, increased cardiac output, and decreased total peripheral resistance) display more favourable emotions, gaze behaviour, kinematic responses, and performance compared to those who experience threat state (e.g. Moore et al, 2012). The purpose of this PhD project is to advance understanding into what leads athletes to experience a challenge rather than a threat state.

Structural and biophysics characterisation of S6K2

This PhD project will focus on unravelling the molecular mechanism of S6K2 (RPS6KB2) signalling pathway. In particular the aim is to characterize S6K2 protein-protein interactions and not redundant with its closely related isoform S6K1 (Roy, R., et al. Nucleic Acids Res, 2014). At the moment there is a complete lack of biochemical and structural information about S6K2. Using a range of biophysical and biochemical techniques we aim to characterize S6K2 protein complexes and ultimately solve their crystal structures.