Master’s by Research opportunities

In the School of Biosciences, we offer five Master’s by Research courses in Biochemistry, Cell Biology, Computational Biology, Genetics, and Microbiology. Each offers a range of projects – scroll down to discover more.

How to apply

Once you have identified a project you are interested in, contact the named supervisor by email to discuss the possibility of undertaking an MSc under their supervision. Please outline your interest in the research project and supply a CV, including all relevant experience and details of how you will fund your study. After securing a project and a supervisor, you can proceed to make an online application.

For further information on how to apply online for Postgraduate research degrees, see our website. Alternatively, please contact information@kent.ac.uk with any questions on how to proceed.

Please note that additional research fees of £1,500 apply to each of the listed projects.

Our projects

Click on the headings for details of the projects offered:

Cancer and Ageing (led by Professor Michelle Garratt)

Investigation of drug-adapted cancer cell lines: Professor Mark Wass (jointly supervised with Professor Martin Michaelis

We host the Resistant Cancer Cell Line (RCCL) collection, the worldwide largest collection of drug-adapted cancer cell lines and models of acquired drug resistance in cancer at Kent. In this project, drug-adapted cancer cell lines will be characterised and investigated to gain novel insights into the processes underlying resistance formation and to identify novel therapy candidates (including biomarkers).

Probing the mechanism of INDY (I’m not dead yet) transporters: a target for the treatment of cancer, diabetes and obesity: Dr Christopher Mulligan

In eukaryotic cells, disrupting the activity of INDY transporters can extend lifespan, reduce cancer cell proliferation, and protect against metabolic disease such as diabetes and obesity. To develop inhibitors for INDY proteins, we first need to understand their transport mechanism.

In this project, we will investigate the mechanism of the bacterial representative of this family, VcINDY. We will probe substrate and inhibitor interactions, and proteins dynamics using biochemical and biophysical approaches. The student will receive training in molecular biology techniques, such as site-directed mutagenesis, integral membrane protein expression and purification, transporter characterisation, protein biochemistry and biophysical techniques.

The microbiome-muscle connection – how gut microbes improve muscle function: Dr Marina Ezcurra (jointly supervised with Professor Dan Mulvihill)

The gut microbiome affects many important functions including gut health, immunity and cognition. Recent exciting studies in athletes and mice suggest gut microbes also alter muscle function and performance, raising the exciting possibility that the microbiome can be targeted to improve muscle function and health. In this project we will investigate microbiome effects on molecular determinants of muscle contraction, muscle morphology and physical output using the model organism C elegans. The project will provide with training in a range of biochemical, molecular, genetic and imaging approaches.

The molecules underlying microbiome health benefits: Dr Marina Ezcurra

The gut microbiome profoundly impacts human health, but how it does this is largely unknown.  Studies suggest that the microbiome acts through the transcription factor Nrf, a regulator of stress-responses, lifespan and appetite. A major challenge in studying host-microbiome interactions is the difficulty and cost of mammalian models and the complexity of the human microbiome. This project will use a simple and versatile organism C. elegans to explore the molecular basis of the gut-brain-axis by which the microbiome and Nrf impact health. Training: Microbiology, molecular-biology, immunology, biochemistry, microscopy, genetics, bioinformatics.

Using cancer genomics to identify biomarkers of cancer resistance: Professor Mark Wass (jointly supervised with Professor Martin Michaelis

At Kent we host the Resistant Cancer Cell Line (RCCL) collection, the largest collection of cancer cell lines worldwide that have been adapted to anti-cancer drugs. These cells represent a model of drug resistance in tumours. This project will analyse exome sequencing data of a set of cell lines to identify mechanisms of resistance and biomarkers.

A new approach to bladder cancer treatment: Prof Michelle Garrett, Prof Dan Mulvihill and Prof Jennifer Hiscock

Bladder cancer kills over 5,000 people per year in the UK with 10-year survival being less than 50%. Treatment includes chemotherapy to the bladder with effectiveness limited by inadequate cellular uptake. Supramolecular Self-associating Amphiphiles (SSAs, inventor Prof Jen Hiscock) are a new class of molecule which in a collaboration between Garrett and Hiscock have been shown to act as anticancer agents and enhancers of anticancer agent efficacy (1). The aim of this current MSc project is to investigate the use of 10 new SSAs to increase the efficacy of chemotherapy drugs including mitomycin C and gemcitabine in bladder cancer cells in the laboratory and provide a route to a proof-of concept clinical trial for SSAs in bladder cancer patients. This project will be part of a wider collaboration which is ongoing between Garrett and Hiscock on the use of SSAs in bladder cancer. Techniques that the student will learn include human cell culture, cell proliferation assays, western blot analysis for protein detection, cell cycle analysis by flow cytometry and fluorescence microscopy (microscopy in collaboration with Prof Dan Mulvihill).

1. Dora, N.O. et al. (2021) RSC Adv.11:14213-1421. doi: 10.1039/d1ra02281d

Investigating the role of chaperones in the stability and assembly of multi-protein complexes: Dr Mohinder Pal

Heat Shock Protein 90 (HSP90) is a molecular chaperone and is an essential protein for cell survival. It is involved in the folding and assembly of several proteins called clients of HSP90. Some of these client proteins cause several diseases in humans, such as cancer, making HSP90 a potent anti-cancer target. The interaction of HSP90 with its client proteins does not occur directly. Instead, it relies on helper proteins called “co-chaperones of HSP90”, which bind and recruit client proteins for their folding and assembly. Upon recognising the client proteins bound to its co-chaperone, HSP90 utilises its ATPase activity to facilitate the folding and activation of its clients. Despite the structural and biochemical work, it is still unknown how HSP90 interacts with a variety of its client proteins via its diverse co-chaperones. In these two projects, we will investigate how HSP90 interacts with and recognises its client protein presented by its co-chaperone.

Research questions: In these two projects, we will investigate how HSP90 interacts with its co-chaperones when bound to different client proteins and how these clients are activated by HSP90 molecular chaperone?

To answer these questions, we will employ biochemistry and structural biology techniques such as single particle cryo-electron microscopy (Cryo-EM) and X-ray crystallography to determine the three-dimension structure of HSP90 bound co-chaperone-client protein complexes at the highest possible resolution.

The learning outcome for potential students: Students will learn protein over-expression using bacterial and eukaryotic expression systems. They will have hands-on biochemistry techniques such as affinity and size exclusion chromatography and protein-protein interaction studies using pull-down and Iso-thermal Titration Calorimetry (ITC). For structural work, students will learn X-ray crystallography and single-particle cryo-electron microscopy (Cryo-EM) techniques to determine high-resolution structures of multi-protein complexes.

Industrial Biotechnology

Developing an oxygen sensitive protein expression system based on proteins from anaerobic protozoa: Dr Anastasios D Tsaousis (jointly supervised with Dr Tobias von der Haar

Fe-S clusters are ubiquitous and essential co-factors in all living cells. They are present in important proteins involved in transcription, translation, DNA replication, DNA repair, amino acid synthesis, nucleotide metabolism, iron uptake and regulation, etc. Fe-S cluster biosynthesis is also considered the reason for the universal existence of mitochondria in all eukaryotes, since Fe-S cluster maturation involves essential cellular functions. Heterologous expression of eukaryotic Fe-S proteins is one of the most difficult tasks in synthetic biology, due to the sensitivity of these proteins to different environmental factors (e.g. oxygen). Anaerobic microbial eukaryotes (protozoa) have developed unique tools to overcome these difficulties. Among these are Fe-S cluster assembly machineries that have diversified their functions to survive the specialised lifestyles of these organisms.

The purpose of the proposed project is to modify the Fe-S maturation machinery of yeast, a widespread fungal synthetic biology chassis, with proteins from anaerobic protozoa. The efficacy of the heterologous systems will be tested using specific Fe-S cluster proteins with potential biotechnological application.

This project will provide knowledge and tools that can be used to: (i) improve the roles and associations of the eukaryotic Fe-S cluster assembly and translational machineries in synthetic biology, (ii) develop yeast strains with novel functions and adaptations in different environmental conditions that can be used for bioproduction and/or bioremediation, and (iii) establish novel expression systems for the production of anaerobic proteins and systems to be used in the synthesis of oxygen-sensitive biocompounds. The project will bring together the expertise and supervisory roles of an anaerobic biochemist (Dr. Tsaousis) with that of a systems biologist (Dr von der Haar) to ensure that all goals will be met.

Enhancing a microbial solution to drastic plastic pollution:  Dr Christopher Mulligan

Phthalic acids (PA) are major constituents of plastics, acting as either part of the polymeric structure (e.g. in polyethylene terephthalate, PET) or as essential non-covalently associated plasticisers. PA plasticisers, which have carcinogenic properties, readily leach out of waste plastics leading to contamination of the environment, and are classified as major man-made priority pollutants due to their ability to cause ill health in both humans and animals.

The development of microbes to take up and degrade PA plasticisers would provide a cost effective and environmentally friendly solution to this growing problem. A critically important step in this bioremediation process is the efficient transport of the PA plasticisers from the environment into the bacteria where they can be broken down. Microbial degradation of PA plasticisers removes these pollutants from the environment, but also provides the opportunity to use them as a feedstock for high value chemicals.

In this project, we will interrogate the structure and mechanism of predicted bacterial PA transport proteins that are currently very poorly understood. To do this, we will use an integrated approach combining molecular biology, biochemical and biophysical analyses, and microbiological approaches. The goal of this project is to further our understanding of the PA uptake mechanisms that bacteria employ to remove this major pollutant from the environment. Please get in touch if you would ike more details about this project.

Enzymatic routes to obtain added-value chemicals from biomass: Dr Max Cardenas-Fernandez

Hemicellulose and pectin are the main by-product from the food industry and considered a low price biomass feedstock. From the chemical point of view, they are heteropolymers formed of a combination of several C5 and C6 monosaccharides, that can be biotransformed into added-value chemicals such as commodities and polymers.

This project aims to establish an efficient routes to valorise sugar rich biomass feedstock through biotechnological means (e.g sugar alcohols and pre-polymers). The candidate will work on enzyme discovery from thermophilic microorganisms, cloning and expression, high-throughput activity screening and enzyme characterisation.

Understanding the biosynthesis of polyamide biopolymers: Dr Max Cardenas-Fernandez

Synthetic polymers derived from petrochemicals represent an important source of environmental contamination. In contrast, some microorganisms are able to naturally synthesise extracellular biopolymers such as biopolyamides (nylon-like biopolymers) which are environmental friendly and suitable for industrial applications. Our in-silico results have revealed the protein structure of the synthetase involved in the biosynthesis of the biopolyamide g-polyglutamate (PGA).

The MSc-R candidate will clone the PGA-synthetase from Bacillus subtilis, and carry out site-directed mutagenesis experiments in the potential active site (based on model) to confirm activity. Ultimately, recombinant PGA will be produced in specific media and characterised.

Building a Vitamin B12 future: Dr Andrew Simkin

Vitamin B12 (B12) is made exclusively by a small group of prokaryotes (bacteria and archaea). Some of these bacteria are found in the flora of ruminant mammals where they proliferate in the stomach. This source of B12 therefor accumulates in animal product including meat, eggs, milk and is the key dietary source of B12 in the population. B12 is absent from fruits and vegetables.
B12 is an essential nutrient for animals and B12 deficiency can result in a range of symptoms including depression, loss of memory (reduced cognitive performance), fatigue, lethargy and headaches and in some people mania and psychosis. Research has shown that as much as 40% of the world’s population are deficient in B12.

Biofortification of plants via feeding mechanisms has demonstrated that Lepidium sativum (garden cress) can take up B12 if grown in B12 enriched media, where it accumulates in the vacuole of the cotyledons.

In this project, you will use Golden Gate construct assembly to generate constructs for the expression of Vitamin B12 biosynthetic enzymes, and Vitamin B12 binding proteins in transgenic plants. You will carry out PCR, bacterial transformation, sequencing, and tissue culture (transformation of Arabidopsis and tomato material) in the first instance.

Evolution, reproduction and genome organisation

Exploring a role for APOBEC3 genes in mammalian evolution: Dr Marta Farre Belmonte (jointly supervised by Dr Tim Fenton)

The apolipoprotein-B mRNA editing enzyme catalytic polypeptide like (APOBEC) genes encode polynucleotide (deoxy)cytidine deaminases that fulfil important roles in metabolism and immune responses via their ability edit DNA and RNA sequences. The APOBEC3 sub-family genes restrict replication of exogenous retroviruses and retrotransposons but at a cost; off-target APOBEC3 editing activity generates somatic mutations in human cancer.

The APOBEC3 locus has diversified considerably during mammalian evolution: humans have 7 APOBEC3 genes, while mice have only one. APOBEC3 activity in the germline has recently been implicated as a source of heritable mutations in humans but the contribution of APOBEC3 activity to evolution remains unclear. This project will utilise computational and wet-lab approaches, leveraging genome sequencing data from a range of mammalian species with different APOBEC3 gene repertoires to examine the APOBEC3 contribution to heritable mutations and to further define its role as an evolutionary driver.

References:
https://genome.cshlp.org/content/27/2/175.full
https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-12-71#Sec2
https://jme.bioscientifica.com/view/journals/jme/62/4/JME-19-0011.xml

Investigating the adaptation of South Asian cattle breeds to extreme climates – can we identify genomic regions responsible for these traits? Dr Marta Farre Belmonte (jointly supervised by Dr Anastasios Tsaousis)

Thousands of years of artificial selection coupled with human-driven migration and adaptation to diverse continents resulted in ~1,000 cattle breeds. Most of them, highly adapted to local environmental conditions and possessing unique genetic profiles. In this project, using a combination of wet-lab and bioinformatics, the student will genotype ~300 samples from several cattle breeds from South Asia adapted to extreme conditions with the aim to understand where these breeds originated and identify their unique genetics.

Study the genetic diversity of the Defassa waterbuck (Kobus ellipsiprymnus): Dr Marta Farre Belmonte (This project is in collaboration with the Aspinall Foundation)

Waterbuck, a species of African antelope, is usually considered to comprise two subspecies: Ellipsen and Defassa, based on differences in phenotype and geographical distribution. The Defassa waterbuck is Near Threatened, while the Ellipsen waterbuck is classified as Least Concern by the IUCN Red List. Waterbuck formerly occurred throughout most of sub-Saharan Africa; however, it has been widely eliminated within its former range but survives in many protected areas.

Studies on the genetic differences between subspecies studies showed some degree of genetic differentiation in the Defassa populations; however, these studies did not include individuals from all the distribution range, particularly from central Africa (including Democratic Republic of the Congo and Angola) and more distal populations in west Africa (Mali and Guinea-Bissau). To address this issue, we have collected samples from these areas. The student, using a combination of wet-lab and bioinformatics, will quantify genetic variation across these samples and establish a phylogeography of the species. This will have a direct impact on the conservation strategies for the Defassa waterbuck.

The host perspective: studying the genetics of animals infected with the parasite Cryptosporidium: Dr Marta Farre Belmonte (jointly supervised by Dr Anastasios Tsaousis)

Cryptosporidium is the pathogenic agent of cryptosporidiosis, a disease mainly characterized by diarrhoea in humans and livestock. Transmission of Cryptosporidium can result from ingestion of contaminated food/water, or by direct transmission from host to host. In humans, prevalence and severity of infection is increased in infants, in the elderly and in immunodeficient people including AIDS patients. In Africa and Asia, Cryptosporidium was described as the second infectious agent responsible for infant mortality, related to severe diarrhoea in children under 5 years of age. In a context of human health concern, cattle have been considered to be Cryptosporidium oocysts primary reservoirs. A sick animal could produce and disseminate in the environment millions or even billions of infectious parasites per day. Cryptosporidiosis in calves leads to stunted growth, loss of yield and the death of the most vulnerable animals. Reducing the presence and spread of this parasite in farms will have an impact not only on the economic balance of farms, but also on the threat raised by this parasite to human health.

In this project, the student will use genomic data from 3,500 cattle with different levels of parasite infection load to identify the regions of the DNA that might be responsible to confer resistance to infection. This is a combined wet-lab and bioinformatics project where the student will learn the most up-to-date techniques to genotype and perform GWAS analysis.

Developing gregarine apicomplexans as aquatic symbiosis model system: Dr Anastasios Tsaousis (jointly supervised by Dr Sonja Rueckert)

Apicomplexans are widely distributed, single-celled organisms that are always described as obligate parasitic. Despite their importance for human health (malaria, toxoplasmosis) and their virulence in animals, there is substantial evidence for mutualistic attributes of some apicomplexans. Gregarine apicomplexans infect almost all invertebrates and are highly abundant across ecosystems. The early diverging gregarines span the whole range of symbiosis from mutualism to parasitism and thus are critical links in the evolution of symbiosis in the apicomplexans. Despite their importance, information on the biology and evolution of these organisms is lacking with e.g. only a handful of transcriptome and genome data available.

In-vitro culturing has not been achieved for any gregarine. Thus, the aim of this project is to develop an in-vitro tissue culture for aquatic Gregarine apicomplexans. The student will establish an invertebrate in-vitro 2D tissue culture for gregarine apicomplexans. They will develop invertebrate cell cultures using tissues from various gut areas of invertebrate hosts. This approach will be assessed by infecting the host cells with the target species and monitor the success of gregarine development and propagation using an in-house automated microscopy system, under controlled atmospheric conditions.

Understanding the engine of evolution: Dr Peter Ellis (jointly supervised by Dr Marta Farre Belmonte)

All genetic variation ultimately stems from the introduction of new mutations during gametogenesis. While the mutational processes operating in tumorigenesis are beginning to be unravelled, leading to the known COSMIC mutational signatures, those operating in the germline are much less well characterised. In this bioinformatics project, we will take advantage of the recent availability of several high quality genomes from different mouse species to identify mutations specific to lab mouse using comparative genomics methods.

Comparison with existing data sets will then allow identification of the types of mutations associated with meiotic strand breaks, overall recombinational hotspots, spermatid-specific strand breaks occurring during sperm maturation, and oxidative damage incurred by mature sperm. This will allow us to develop a comprehensive all-round overview of the mutational pressures during male gametogenesis and how this relates to the rates of evolutionary change in different parts of the genome.

Infectious Diseases

Blastocystis metabolites: what does a “questionable parasite” produces and why? Dr Anastasios Tsaousis (jointly supervised with Dr Gary Thompson)

Blastocystis sp. is an obligate anaerobic parasite, frequently found in patients with irritable bowel syndrome. The actual pathogenicity of Blastocystis is still questionable, since currently there is no direct link between the parasite and the disease caused. Preliminarily data by the Tsaousis Laboratory have shown that Blastocystis produces metabolites that are currently produced only by plant or algal organisms. Since Blastocystis does not have any evolutionary relation with these organisms, these results suggest that Blastocystis has acquired a peculiar pathway from plants in order to overcome potential obstacles in its life cycle.

This is a project that combines both bioinformatics and wet-lab techniques. The student will investigate the presence/absence of proteins related to the metabolites and he/she will attempt to reconstruct any relevant metabolic pathway(s). Any hypothesis arose from the analysis will be tested using molecular and cellular biological techniques along with sophisticated biochemical methodologies. The successful student will have the chance to use the state of the art biomolecular and NMR facilities that are present in the School of Biosciences.

Caught in a TRAP: probing the mechanism of tripartite ATP-independent periplasmic (TRAP) transporters as new antimicrobial targets: Dr Christopher Mulligan

The uptake of nutrients from the environment is an essential requirement of all cellular life. In certain bacterial pathogens, host-derived nutrients can be used for growth during infection but can also be used to enhance colonisation and virulence. Pathogens such as Haemophilus influenzae and Vibrio cholerae take up sialic acid from the host and can present it on the cell surface, which allows the bacteria to evade the innate immune response. Therefore, these sialic acid uptake routes are prime targets for the development of inhibitors to treat and prevent bacterial infection.

In this project, we will interrogate the structure and mechanism of the sialic acid-specific TRAP transporter from H. influenzae. TRAP transporters have an extremely fascinating, but poorly understood mechanism, which employs a unique combination of an essential soluble substrate binding protein and a Na+-driven, elevator-like movement of the transmembrane domain to facilitate transport across the membrane. This project will probe the interaction of the substrate binding protein with the membrane component and assess the contribution of selected amino acids to the transport mechanism. To do this, we will use a combination of molecular biology, biochemical and microbiological approaches.

Drug repurposing to target respiratory complexes of antibiotic-resistant bacterial pathogens: Dr Mark Shepherd

Loss of bd-type respiratory oxidases is well-known to diminish survival of a variety of bacterial pathogens during infection. The current project will involve screening of drug libraries using in silico and biochemical approaches to design new strategies to inhibit bd-type respiratory complexes. This project will focus on multidrug-resistant E. coli, Pseudomonas aeruginosa, and Mycobacterium tuberculosis.

Elucidating the role of the host environment in controlling the fungal-host pathogen interaction: Dr Becky Hall

Candida albicans is an opportunistic fungal pathogen that forms part of the natural flora of the oral, genital and gastrointestinal tracts of healthy individuals. However, changes in the host’s environment, activate adaptation responses in the fungus that enable the fungus to switch from commensal growth to a more pathogenic state. One of these adaptation events is the structural remodelling of the fungal cell wall. As the cell wall is the first point of contact between the invading pathogen and innate immune system, modification of its structure affects the host-pathogen interaction, enabling the fungus to either evade the immune system, or to hyperactivate pro-inflammatory immune responses and induce host damage. However, the host environmental signals and fungal signalling cascades that control cell wall adaptation are largely unknown. The aim of this project is to determine which host environmental signals drive fungal pathogenicity through modulation of the fungal cell wall and to elucidate the novel fungal signalling pathways that mediate this adaptation.

Establishing and developing an advance culturing platform for Cryptosporidium: Dr Anastasios D Tsaousis

Cryptosporidium is an obligate intracellular intestinal parasite of various animals that causes cryptosporidiosis, a diarrheal disease that is most common in young children and is severe in immunosuppressed humans. The goal of this project is to develop a more advance culturing platform for Cryptosporidium parasite. The student will make use of the newly develop culturing system from our lab, not only to test it, but also to explore 3D culturing methods and organoids to increase the in vitro production of the parasite.

Exploring Cryptosporidium transportome and how it affects the intracellular interactions with its host: Dr Anastasios D Tsaousis (jointly supervised by Dr Christopher Mulligan)

Cryptosporidium is an obligate intracellular intestinal parasite of various animals that causes cryptosporidiosis, a diarrheal disease that is most common in young children and is severe in immunosuppressed humans. Its genome is highly reduced, encoding for 4800 proteins, 151 of which are carrier proteins. We hypothesise that these transporters play significant role in the adaptations of the parasite in an intracellular lifestyle and its interactions/communication with the host . The purpose of this project is to explore the localisation and function(s) of these transporters, identify potential links associated with the adaptation to parasitic lifestyle, while exploring probable candidates for tackling cryptosporidiosis.

Exploring the eukaryotic gut microbiome among animals: Dr Anastasios D Tsaousis

While there have been numerous studies exploring the gut microbiome of different animals, these were mainly focused on identifying the bacterial residents of the gut microflora. In addition, not much is known about the eukaryotic residents of the gut and their contribution to the health and disease. This project will be in collaboration with local conservation parks in the Kent region, where the student will use multidisciplinary approaches to investigate the eukaryotic residents of the gut microflora from different animals, either living in the wild or in captivity (including farms). To tackle these aims, the student will use an integrative approach combining culturomics, microscopy, molecular and phylogenetic methods.

Exploring the potential use of bacteria to kill fungal pathogens: Dr Becky Hall

In their natural environment fungi and bacteria compete with each other for space and nutrients. This natural competition has led the evolution of chemical weapons to give one species the advantage over another. For example, penicillin is produced by the fungus Penicillium chrysogenum to kill bacteria giving the fungus the upper hand. However, there are very limited examples of bacterial products that have significant antifungal activity, with clinical potential. Therefore, there is large potential for the discovery of natural, bacterial secreted antifungal compounds. We have identified that the bacterium Pseudomonas aeruginosa is able to kill fungi through an unknown mechanism. The aim of this project is to identify how the bacterium kills fungi. To achieve these objectives, you will employ molecular biology, together with advanced microscopy techniques (super resolution, scanning electron and transmission electron microscopy). This project has the potential to not only improve the efficacy of our current antifungal drugs, but to also identify a novel antifungal agent which will be of considerable clinical importance.

Exploring the presence and distribution of cryptosporidiosis in cow farms: Dr Anastasios D Tsaousis

Cryptosporidium is a major cause of waterborne outbreaks worldwide. This protozoan parasite is the etiologic agent of a disease called cryptosporidiosis that affects both humans and animals. In cattle farms, this common infectious disease induces stunting growth, and high mortality rate of animals that further threaten the economic viability of a sector, which already faces frequent crises. The MSc by Research student will use multidisciplinary approaches to investigate the prevalence and distribution of Cryptosporidium species in cow farms around Europe. To tackle these aims, the student will use an integrative approach combining fieldwork with culturomics, microscopy, molecular and phylogenetic methods along with gut microbiome studies. Stool samples have already been collected from the Netherlands, France, Belgium (as part of an EU-funded project), but also from Czech Republic and Cyprus. As part of this project, we will also collect stool samples from farms in the South region of UK.

This project will provide us with a better understanding of Cryptosporidium infection and its long-term effect in the cow’s health. The prospective MSc by Research student will be trained and have access to state-of-the-art facilities within the School of Biosciences at University of Kent, including Imaging facility, proteomics and NMR and will also take advantage of the large-scale network under the Heath-4-Dairy-Cows project.

Investigating determinants of virus pathogenicity: Professor Mark Wass (jointly supervised with Professor Martin Michaelis)

Our research has recently compared different species of Ebolaviruses to identify parts of their proteins that determine if they are pathogenic. This project will apply these computational approaches to different types of viruses (e.g. Zika virus, west Nile, human papillomavirus) to identify determinants of virus pathogenicity and gain insight into what make some viruses highly virulent while others are harmless.

Investigating the determinants of SARS Coronavirus-2 pathogenicity: Professor Mark Wass (jointly supervised with Professor Martin Michaelis)

Severe Acute Respiratory Coronavirus-2 (SARS-CoV-2) is currently causing a pandemic with much of the world in a lockdown state to limit the spread of the virus and number of cases and deaths that it causes. Due to the latest genome sequencing technologies there are now many thousands of SARS-CoV-2 genome sequences obtained from those infected. These can be analysed to advance our understanding of the genetic and molecular features that determine the properties of the virus.

This project will focus on using computational approaches to compare the thousands of SARS-CoV-2 genome sequences with those of SARS-CoV, the related virus that caused the 2002-2003 SARS Coronavirus outbreak. While these two viruses are closely related there are important differences in the disease that they cause. For example SARS-CoV-2 has a much lower death rate and appears to be more easily transmitted. We have already begun research in this area (see our preprint here: https://www.biorxiv.org/content/10.1101/2020.04.03.024257v1) and this project will expand on this work.

Investigating the effect of both symptomatic and asymptomatic COVID-19 infections in the diversity of the human gut microbiome: Dr Anastasios D Tsaousis (jointly supervised by Dr Jeremy Rossman)

The Coronavirus (COVID-19) pandemic has had a significant impact in our lifestyle during the last year. Despite the fact that this virus is mainly affecting the respiratory tract, several reports have demonstrated its presence in the gastrointestinal (GI) tract of humans as well. Therefore, the presence of the virus could have long-term consequences in the health of an individual. In this project, using a combination of wet-lab techniques and bioinformatics, the MSc by Research student will investigate the effects of COVID-19 infection in the diversity and function of the gut microbiome. Results from this project will: (1) provide us with new diagnostic tools, (2) allow us to explore the effect of the virus in the gut microbiome composition and abundance, and lastly (3) elucidate whether detected shifts are conducive to causing potential future GI-related diseases (e.g. explore whether changes in the gut microbiome of COVID-19 positive individuals will make them susceptible to infections by other gut pathogens). Thus, this project will significantly contribute in elucidating the long-term pathogenesis of the virus in the gut.

Investigating the role of polymicrobial interactions in antimicrobial resistance: Dr Becky Hall

Polymicrobial interactions play an essential role in life and are important for agriculture, food production, and disease. Polymicrobial communities normally form biofilms, which are complex communities of microorganisms encased in a self-produced extracellular matrix. Biofilms provide a unique habitat for microbial growth and as a result, gene expression profiles of cells isolated from biofilms are significantly different compared to planktonic growing cells. Biofilms readily form on indwelling medical devices, and are one of the leading causes of nosocomial infections due to their increased resistance to antimicrobial therapy. Currently our understanding of the interactions that occur in polymicrobial biofilms, and the impact these interactions have on antimicrobial drug resistance is poorly understood. The aim of this project is to investigate the impact of polymicrobial interactions on antimicrobial resistance.

The CydDC transporter of E. coli: biochemical characterisation of an antimicrobial target: Dr Mark Shepherd

CydDC is an ABC transporter that is important for bacterial virulence, resistance to β-lactam antibiotics, and tolerance to the host immune response. This project aims to gain a better understanding of how CydDC interacts haem and how this transporter contributes to the assembly of respiratory complexes. Techniques: purification of membrane proteins, ATPase assays, mutagenesis, spectroscopic analyses.

The path to least resistance: probing the mechanism of integral membrane transport proteins essential for antimicrobial resistance in bacteria: Dr Christopher Mulligan

Antimicrobial resistance is a major global health concern. One of the most effective mechanisms bacteria have developed to resist the effects of antimicrobial agents is to use drug efflux transporters to pump them out of the cell before they can do any damage. Understanding the structure and function of these proteins will lay the foundation for the development of future inhibitors, which could be used to enhance the efficacy of current antimicrobials and breathe new life into antimicrobials rendered ineffective due to the development of resistance.

In this project, we will elucidate the functional mechanism of a family of integral membrane transport proteins that strongly influence the antibiotic resistance of several bacterial pathogens. This project will take an integrated approach to probing the structure and function of these membrane proteins, which will include protein biochemistry, biophysical approaches and microbial phenotypic assays.

Cellular Architecture and Dynamics

Boosting Plant Disease Resistance Through RNAi: Dr Helen Cockerton

Plant pathogens can cause extensive damage to crops, and if left untreated, epidemics can lead to complete crop destruction. Host Induced Gene Silencing (HIGS) can be used to provide an environmentally friendly strategy for disease control. Through this project we will study the efficacy of HIGS through the construction of vectors containing hairpins that target plant pathogen genes. These vectors will then be transformed into the model plant Arabidopsis and pathogenicity assays will be conducted with two fungal pathogens (Botrytis and Verticillium) in order to assess the disease resistance status of Arabidopsis mutants.

Cold-shock, translational reprogramming and development of treatments to prevent neurodegeneration and cancer: Dr Mark Smales

With colleagues we have shown that mammalian cells respond to cold-shock by reprogramming protein synthesis, particularly by utilising transcripts with different codon usage. Some of these proteins whose synthesis is regulated can be neuroprotective. This project will look to further explore the mammalian responses to cold-shock and how these could be harnessed for the development of treatments in the clinic.

Computational structural biology of amyloid assemblies: Dr Wei-Feng Xue

The aim of this project is to identify and understand the structural organisation of amyloid aggregates using nano-scale imaging methods. In this computational project, training in image data analysis will be offered and AFM image data will be analysed using state of the art 3D reconstruction methods developed in the Xue lab to characterise and compare the molecular structures involved in the formation, growth and the division of amyloid aggregates grown from disease associated amyloidogenic proteins. There will also be opportunities to learn computer coding and data analysis software algorithm development. This computational project can be carried out through remote working.

Development of diagnostics and potential vaccines for Mycoplasma bovis: Dr Mark Smales

Mycoplasma bovis is a pathogen that is found globally in the bovine (cattle) population and results in respiratory disease and calf pneumonia. Antibiotic resistant strains are also emerging and this, along with the movement of cattle and people, a lack of a vaccine or low cost rapid diagnostic tests that can be used to monitor and detect the disease in the filed have combined to present a significant problem. This project will look to recombinantly produce Mycoplasma bovis antigens (proteins) so that they can be used in the development of rapid diagnostics for the presence of the pathogen in infected animals in the field and as potential vaccine candidates. The project will involve training in bioinformatics, molecular biology/cloning, recombinant protein expression, purification and characterisation and assay development.

Docking of large protein complexes using sparse NMR Restraints: Dr Gary Thompson

An MSc in structural biology using NMR is available shared between the NMR Facility and the Laboratory of Jose Ortega Roldan. The calculation of the structures of protein complexes by NMR remains an important area of research. This project will aim to improve protein-protein docking methodologies by using chemical shifts to restrain the proteins during docking so as to achieve a more natural soft docked structure. The project will examine two test systems a large protein-protein complex involved in antibiotic resistance (FusB-EFG) and a large multimeric protein multimer using solid state NMR data. The project will offer both an opportunity to learn how to carry out protein NMR experiments and a thorough grounding in python programming and structural biology. No previous programming experience is required.

Evolution of the muscle sarcomere. A bioinformatics approach to the interaction between myosin and myosin binding protein-C: Professor Mark Wass (jointly supervised by Professor M Geeves)

Following on from a study of how muscle-type myosins have adapted, over evolutionary timescales, for different types of muscle contraction, we will explore the co-evolution of myosin and the myosin binding proteins C. MyBP-C is well known to carry mutations linked to inherited heart disease.

Fast protein structure assignment and validation: Dr Gary Thompson

An MSc in structural biology using NMR is available shared between the NMR Facility and the Laboratory of Jose Ortega Roldan. New structure prediction algorithms such as alpha fold from deep mind offer the possibility of very fast validation and refinement of predicted protein structures using NMR based experimental restraints. The project will build a protocol to quickly validate protein structures using automatically assigned protein backbone and sidechain shifts [including 4D experiments], residual dipolar couplings and un-labelling approaches. The project will offer both an opportunity to learn how to carry out protein NMR experiments and a thorough grounding in python programming and structural biology. No previous programming experience is required.

Generation of Coronavirus protein antigens, diagnostics and vaccines: Dr Mark Smales

This project will build upon the on-going work to recombinantly produce key protein antigens from the coronavirus and then utilise these in diagnostics and the development of new vaccine candidates. Candidates will be involved in the cloning, expression and characterisation of the major protein components of the virus and various truncations and modifications thereof, and subsequent attachment of these to bacterial microcompartments such that these can be used to generate proof-of-concept data on the utility of this approach to elicit an appropriate immune response indicative of good vaccine candidates. Such technologies will also be explored for application into other areas of vaccine need in collaboration with colleagues in the UK and abroad.

In-cell structural biology: CLIC1 structure, function and drug binding inside tumour cells: Dr Jose Ortega Roldan

CLIC1 is a chloride channel that gets upregulated in different tumour cells and whose inhibition has been shown to halt tumour progression. The aim of this project is to study the activation and inhibition mechanisms with atomic detail using a range of structural biology techniques, including NMR, X-Ray crystallography and fluorescence microscopy.

Investigating metabolic dysfunction as a driver of Motor Neuron Disease: Professor Campbell Gourlay

Amyotrophic lateral sclerosis (ALS), also known as motor neurone disease (MND) is a devastating and incurable disease. Significant research efforts have increased our understanding of the cellular dysfunction that underpins ALS pathology, but we have much to learn. Recent findings suggest that metabolic defects play an important role in the onset and progression of ALS, offering the tantalising prospect of new avenues to therapy. We have developed a rapid high throughput yeast model of ALS that enables us to probe the metabolic nature of cellular toxicity associated with defects in the protein Superoxide dismutase 1 (Sod1). Mutations in Sod1 lead to familial ALS and are also linked to sporadic forms of the disease. The project will establish the metabolic defects associated with Sod1 mutations found in ALS patients. The outcomes of this research will lead to a significant increase in our understanding of the metabolic dysfunction associated with ALS.

Making Super Mammalian Cell Factories for the Production of Biological Drugs – Biotherapeutic Proteins and Gene Therapy Applications: Dr Mark Smales

Mammalian cells are a major expression system for the production of biotherapeutic recombinant protein drugs used to treat a range of diseases and for the generation of gene therapies. The Chinese hamster ovary (CHO) cell is the current industrial system of choice for the expression of complex, post-translationally modified recombinant biopharmaceutical proteins for use in humans in the clinic to treat a variety of diseases. Current CHO host cells have been manipulated and ‘optimised’ for the commercial manufacture of monoclonal antibodies (mAbs) in particular, however many new protein biologics in development are difficult to express (DTE) in these systems. As such the product yields and quality are not sufficient to be used in the clinic and potentially life changing and saving drugs thus never reach the market. The programme of work here will take a novel approach to solving this challenge and provide a fundamental understanding of the impact of metabolic engineering on the CHO and HEK cell factories and their ability to produce biotherapeutic proteins and gene therapies at high yield and quality, particularly those that are DTE in CHO cells or any other system. The project will particularly involve training in molecular biology (particularly new approaches to cloning), protein analysis and characterisation, analytics, cell culture, genome/cell editing/engineering, microscopy.samples

Nano-imaging and structural biology of amyloid assemblies: Dr Wei-Feng Xue

A number of human disorders, for example Alzheimer’s disease (AD), Parkinson’s disease (PD), type 2 diabetes, and transmissible spongiform emcephalopathies (TSEs), are associated with the abnormal folding and assembly of proteins. The aim of this project is to identify and understand the structural organisation and structural polymorphism of amyloid aggregates using nano-scale imaging methods. This project will include training on atomic force microscopy (AFM) and electron microscopy (EM), and cutting-edge image analysis methods developed in the Xue laboratory.

Predicting protein function: Professor Mark Wass

Advances in sequencing technologies have identified millions of protein sequences but the function of many of these proteins remains unknown. This project will focus on developing a computational method to predict protein function.

Further reading:
Cell-Free Synthetic Biology: https://www.frontiersin.org/research-topics/12103/cell-free-synthetic-biology
Streptomyces CFPS: https://www.biorxiv.org/content/10.1101/2020.11.16.384693v2.full
An automated platform for ESKAPE pathogen antimicrobial discovery
The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp) are multidrug-resistant bacteria found in nosocomial clinical infections and a growing concern for hospitals; novel antibiotics with distinct modes of action are required. We are interested in the development of an automated workflow for novel antimicrobial discovery. We will specifically study methicillin-resistant Staphylococcus aureus (MRSA) for drug screening using a unique approach to detect bioactivity, potentially at a high-throughput scale.

Synthetic biology approach to self-assembled fibrous bio-materials: Dr Wei-Feng Xue

The aims for this project is to design and produce functional amyloid fibrils displaying a specific structural organisation or a selection of enzymes or small molecule/metal binding motifs, and to evaluate the structure and of these fibrils using cutting-edge AFM imaging analysis, as well as the designed function of these fibrils in vitro or in vivo in cells.

The roles of RAS in controlling cell fate – a yeast model of oncogenic potential: Professor Campbell Gourlay

RAS proteins are small GTPases that couple cell signals to fate. Mutations in Ras that cause a loss of its regulation are found in around 30% of all human cancers. The role of RAS as an oncogene can be attributed to it being a master regulator of proliferation and viability, however the processes by which RAS controls cell fate are not fully understood. In this MSc project you will investigate the consequences of altering RAS activity in a yeast model system to help understand its oncogenic potential. The project will involve the use of a number of techniques such as advanced live cell imaging techniques, gene editing technology, flow cytometry and cell culture.

Understanding antimicrobial activity in live cells: Dr Jose Ortega Roldan

The mechanism of action of peptides and compounds with antimicrobial activity is not fully understood. We will combine in-cell NMR and in-vivo fluorescence imaging to understand how different peptides and organic molecules with antimicrobial activity kill bacteria. This information will enable the optimisation of these compounds for the next generation of antimicrobial agents.

Age-related changes in the gut: more than just a gut feeling?: Dr Lorraine Fisher

The intestine plays a crucial role in the digestion and processing of our food as well as acting as a sort of “second brain” that relays signals about your nutrition to distant organs such as the liver and the brain. The intestine needs to be maintained by a set of adult intestinal stem cells (ISCs) in both mammals as well as fruit flies (Drosophila melanogaster) to support the high cell turnover in this tissue. Our research focuses on how stem cells function in the intestine of Drosophila and how this tissue is affected by ageing. We have several projects to work on in our recently established group. These include 1) The role of targets of the transcription factor Klumpfuss (Klu, Korzelius et al., Nature Communications 2019) in the establishment of enterocyte cell fate 2) Cell cycle phasing of ISCs under different conditions (see Zielke, Korzelius et al., Cell Reports 2014) and 3) Transcriptional rewiring of the intestine during aeging. Techniques used will include Drosophila genetics and husbandry, immunofluorescence, transcriptomics and molecular cloning. Additional research costs: £1500.

Cleaning up the rubbish in the cell: the role of the proteasome in healthy ageing: Dr Jerome Korzelius

Damaged proteins in the cell end up in the proteasome: the cell’s rubbish bin. The proteasome makes sure damaged proteins are properly broken up and recycled. If this does not happen, damaged proteins can aggregate and clog up the cell. In the brain for instance, this build-up of aggregated proteins is a leading cause of diseases like Alzheimer’s and dementia. Increased age is the major risk factor for these diseases due to the fact that the proteasome does not function properly anymore at advanced age. You will study the proteasome in different tissues and at different ages in the fruit fly (Drosophila melanogaster). We will use in vivo proximity labeling, that will label the proteasome and its interactors and identify regulators of this protein complex. In collaboration with Dr. Alessandro Ori (FLI-Leibniz institute on Aging, Germany), you will identify novel proteasome regulators that change with ageing and test these for their effect on proteasome function. Techniques include fly genetics, immunohistochemistry, protein purification and Western blotting.

Dormant viruses on demand: Dr Sara Lopez-Gomollon

Plants genomes have dormant viruses, called EPRV. Abiotic stress or hybridisation can cause the activation of these “sleeping agents” that may lead to viral disease. Some plants fight this infection by activating an immune response, RNA silencing, to cleave the viral RNA into small RNAs. We have identified DCL2 (Dicer-like2) as the protein involved in the cleavage of small RNAs, but we don’t know yet how DCL2 recognise specifically the viral RNA molecules, or if there are other proteins involved in this interaction. As virus activation occurs during stress, it is difficult to differentiate the effects of one from the other.

During this master project, you will develop an inducible system to activate on demand EPRV, independently of any environmental signal, using synthetic biology. This ON-OFF mechanism will be a valuable tool to understand and characterise the pathway, such as identifying other proteins apart from DCL2 involved, using tomato as a model organism. The system will include a fluorescent molecule to monitor in time and space the cleavage of EPRV into sRNAs. You will get skills into molecular biology, synthetic biology, proteomics, bioinformatics and microscopy.

A better knowledge of how some plants can cope with the infection will be key to develop strategies that can be use to “vaccinate” plants against this disease, and therefore have an impact in food security.

More info in references: PMID: 35597968; PMID: 35710830.

Viruses that change the colour of flowers: Dr Sara Lopez-Gomollon

How cells with identical genomes can differentiate into cell types? The answer to this central question of developmental biology relies partly on differential gene expression. And among other regulatory mechanisms, transposable elements are known for being able to jump and interrupt genes, changing their expression. Some of these elements are specifically activated during development, and research from my group shows that some transposons can be processed into small RNAs, changing the expression of genes, likely to control developmental processes.

In petunia, a group of transposon are activated during development, producing a visible change in the bicolour pattern of flowers. This transposons are processed into small RNAs by the RNA silencing machinery In the cell. During your master, you will explore how transposons, and the small RNAs that are produced from them, can regulate gene expression. For that you will use Next Generation Sequencing techniques, such as sRNAseq, among other molecular biology approaches, and bioinformatics. Your research will contribute to understanding plant development, but also will shed light on the genetic role of transposons, considered for a long time as junk DNA.

More info in references: PMID: 35597968; PMID: 35710830, PMCID: 7496347.

Plant virus activation in response to extreme weather conditions: Dr Sara Lopez-Gomollon

By the end of the century, it is expected that there will be an increase in the world temperature of 3.5°C. Each degree increase correlates with about a 10% reduction in crop yields, which, added to the threat of new pathogens, may further reduce crop yields. Food security is a real challenge, and one actionable solution is to understand possible threats that can affect crop production. Currently, there are global virus diseases pandemics and epidemics affecting our staple crops with a terrible effect on crop yield and quality. The addition of new viral pandemics will exacerbate the challenge of food security.

Plants genomes have dormant viruses, called EPRV. Abiotic stress can cause the activation of these “sleeping agents” that may lead to viral disease. The conditions that lead to activation is only know for a few plants, although these viruses are present in almost all plant genomes. Plants fight this infection by activating an immune response, RNA silencing, to cleave the viral RNA into small RNAs. Our group has recently discovered that the size of these sRNAs is very specific, 22 nucleotides. During your master, you will search for the presence of EPRV-derived 22nucleotide sRNAs in published datasets, using this trademark as a proxy to identify which conditions lead to viral activation and in which plants. This analysis will be experimental analysis of your results using molecular biology techniques, including Next Generation Sequencing. This information will be essential to understand which conditions can lead to viral activation and in which plants, so preventive technologies can be applied to control the infection.

More info in references: PMID: 35597968; PMID: 35710830.

Growing Kent and Medway

Investigating the impact of high temperature during berry growth and prior harvest on shelf life of strawberries: Dr Lorraine Fisher

This is an exciting opportunity to conduct research situated directly within the fresh produce sector, helping reduce food waste, whilst gaining industry experience.
Following a literature review, an experimental design for heat stress application will be developed. Fruit will be packaged, mishandled and then analysed for quality e.g., firmness, colour.
The student must have their own transport, as pre-harvest work will be carried out at Berry Gardens, postharvest mishandling treatments, storage and analysis will be carried out at the University of Kent.

Determining the mechanism of genotype specific AMF colonisation in strawberry: Jointly supervised by Dr Helen Cockerton and Dr Gary Robinson

Arbuscular mycorrhizae fungi (AMF) colonies the roots of plants and provide nutrients in exchange for carbon. AMF are able to protect strawberry plants from drought stress and boost yields in low nutrient environments.
Two cultivars of strawberry have been shown to have contrasting root system architecture. You will investigate the relative propensity of these cultivars to form mycorrhizal associations, in tissue culture and soil less substrate. You will then study the plasticity of root system architecture of the strawberry cultivars when grown in low and high nutrient environments and determine the impact of nutrient level on mycorrhizal association and root system architecture. Although largely aseptic we will also examine any associated microbiome and the metabolome of the rhizosphere in each cultivar.

This project will require quantification of AMF levels both through microscopy and qPCR, supplemented with 16S amplicon sequencing and rhizosphere quantification by extraction and analysis.