MSc by Research Project Opportunities for September 2021

We offer MSc by research degrees, whereby the student carries out a research project for a full year in a member of staff’s research group. There are a number of exciting opportunities to join us this September.

Our MSc projects are across five topics – Cancer and ageing; Industrial Biotechnology; Evolution, Reproduction and Genome Organisation; Infectious diseases; and Cellular Architecture and Dynamics. Please apply via the relevant MSc link. The following are available for September 2021 (all listed projects will incur additional research costs of £1500):

Cancer and Ageing

Mark Wass

Investigation of drug-adapted cancer cell lines

Jointly supervised with 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)

Using cancer genomics to identify biomarkers of cancer resistance

Jointly supervised with 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.

Dr Marina Ezcurra

Using microbiome-based compounds to develop new therapeutics (MSc by Research in Microbiology)

Jointly supervised with Dr Simon Moore

Host-microbiome interactions have been associated with a wide range of diseases, including inflammatory bowel disease, cancer, depression and neurodegenerative diseases. An important biological challenge is to determine the molecular mechanisms underlying these effects and use them to improve host health. In this project we will use a laboratory host-microbiome model system – the nematode C. elegans combined with a defined experimental microbiome – to identify microbial compounds that improve host health. The project involves synthesising and purifying candidate compounds in the Moore lab and validating their effects in the C. elegans model in the Ezcurra lab. Our goal is to develop innovative approaches to microbiome-based therapeutics. Therapies based on compounds from the microbiome have massive potential as manipulating the microbiome through probiotics or faecal transplants presents problems in achieving predictable outcomes on microbial communities and host health.

Ben Goult

Deciphering the talin code – a cellular code that enables cells to feel their environment

All cells in the human body are held in the correct place via adhesion to neighbouring cells, and to a dense meshwork of proteins that surround cells called the extracellular matrix. It is becoming evident that cells interpret classical signalling pathways in the context of the mechanical forces experienced by the cells attachment to this matrix, and this “mechanosensing” of the environment is a major determinant of cellular function.  In cancer cells this “mechanosensing” is misregulated, leading to aberrant cell behaviour and metastasis.

The protein talin forms the core of most adhesive structures that mediate cell adhesion to the matrix, holding the cell in place. Furthermore, when the cell adheres to the matrix, talin then functions as a Mechanosensitive Signalling Hub (MSH), engaging different signalling molecules as a function of mechanical force to elicit different cellular behaviours (Goult et al., 2018). This plasticity of talin enables different signalling complexes to assemble on talin scaffolds in different conditions ultimately leading to alterations in gene expression.

The aim of this project is to determine precisely using a combination of biochemistry, structural biology and mechanobiology approaches how talin is able to adopt different conformations to switch “On” and “Off” different cellular pathways. The project will focus on defining the talin interactions that are misregulated in metastatic cell migration.

Mechanical signaling mis-regulation in metastasis
Cell migration requires the coordinated assembly and disassembly of adhesions between the cell and the surrounding extracellular matrix, coupled to force exerted by the cell which enables the cell to pull itself forwards. While cell migration is essential for the development of multicellular life, it must be tightly controlled. Cancer metastasis is a product of uncontrolled cell migration.

The aim of this project is to use structural and biochemical techniques to characterise the protein-protein complexes that drive these processes.

Christopher Mulligan

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

 

Industrial Biotechnology

Dr. Anastasios D. Tsaousis

Developing an oxygen sensitive protein expression system based on proteins from anaerobic protozoa (MSc by Research Genetics)

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.

Mark Smales

Generation of Coronavirus protein antigens for development of diagnostics and novel vaccine approaches (MSc by Research Biochemistry)

Joint supervision between Mark Smales and Prof Martin Warren

This project will build upon the on-going work in the Smales and Warren lab’s at Kent, and the Warren lab at the Quadram Institute in Norwich, to recombinantly produce key protein antigens from the coronavirus and then utilise these in diagnostics and the development of new vaccine candidates based on incorporation into bacteria microcompartments. The project will be undertaken in collaboration with Mologic, commissioned by the Government to develop diagnostics for those who have, or have had, COVID-19, based upon antigen-antibody based tests.

The Warren lab is the world-leading lab on the generation, manipulation and biochemical characterisation of pdu based microcompartments whilst the Smales lab is a world-leading laboratory in the development of systems for the generation of complex glycoproteins in mammalian cells and their application to diagnostics development.

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.

Christopher Mulligan

Enhancing a microbial solution to drastic plastic pollution.

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, 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. Ultimately, we will use this knowledge to improve efficiency of the PA breakdown, which has great industrial potential.

Evolution, Reproduction and Genome Organisation

Peter Ellis

Understanding the engine of evolution (MSc Research by Genetics)

Jointly supervised by 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.

Marta Farre Belmonte

Investigating the adaptation of South Asian cattle breeds to extreme climates – can we identify genomic regions responsible for these traits?
Co-supervisor 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).
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
Co-supervisor 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.

Exploring a role for APOBEC3 genes in mammalian evolution
Co-supervisors: 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

Infectious Diseases

Dr. Anastasios D. Tsaousis

Investigating the effect of both symptomatic and asymptomatic COVID-19 infections in the diversity of the human gut microbiome (MSc by Research Microbiology)
Jointly supervised with 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.

Exploring Cryptosporidium transportome and how it affects the intracellular interactions with its host (MSc by Research Microbiology)
Jointly supervised with 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.

Establishing and developing an advance culturing platform for Cryptosporidium (MSc by Research Microbiology)
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.

Blastocystis metabolites: what does a “questionable parasite” produces and why? (MSc by Research Microbiology)
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.

Exploring the presence and distribution of cryptosporidiosis in cow farms (MSc by Research Microbiology)
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

Exploring the eukaryotic gut microbiome among animals (MSc by Research Microbiology)
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.

Mark Shepherd

Drug repurposing to target respiratory complexes of antibiotic-resistant bacterial pathogens 
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. coliPseudomonas aeruginosa, and Mycobacterium tuberculosis.

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

Mark Wass

Investigating the determinants of SARS Coronavirus-2 pathogenicity

Jointly supervised with 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 determinants of virus pathogenicity

Jointly supervised with 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.

Becky Hall

Elucidating the role of the host environment in controlling the fungal-host pathogen interaction

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.

Investigating the role of polymicrobial interactions in antimicrobial resistance

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.

Exploring the potential use of bacteria to kill fungal pathogens

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.

Marina Ezcurra

Novel model systems to monitor biofilm formation in Pseudomonas aeruginosa chronic infections (MSc by Research Microbiology)

Jointly supervised with Dr Becky Hall 

Pseudomonas aeruginosa is a re-emerging, multidrug-resistant, opportunistic pathogen that causes life-threatening chronic infections. The major characteristic of chronic P. aeruginosa infections is the formation of biofilms, in which the cells are surrounded by exopolysaccharides and form structured aggregates. P. aeruginosa biofilms exhibit increased resistance to antibiotics and host immunity, making these infections almost impossible to eradicate. Novel therapeutic strategies aimed at biofilms are therefore urgently needed.

Currently, standardised microbiological assays of Pseudomonas aeruginosa do not take into account the role that biofilms play in pathogenicity and antibiotic resistance. They are often performed in vitro, in the absence of host immune responses. The aim of this project is to develop a new model system to enable monitoring of Pseudomonas aeruginosa biofilms in real time in a whole animal using the model organism C. elegans as a host. This will enable screening for antimicrobial interventions that specifically target P. aeruginosa biofilms in vivo as means to treat chronic infections.

Christopher Mulligan

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

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

Campbell Gourlay

Investigating metabolic dysfunction as a driver of Motor Neuron Disease (MSc Research Cell biology)

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.

The roles of RAS in controlling cell fate – a yeast model of oncogenic potential (MSc Research Cell biology)
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.

 

Simon Moore

Mining for antimicrobial drugs with synthetic biology 
Synthetic biology is accelerating the discovery of promising new antibiotics and anti-tumour drugs, from microbial genomes. This will project will use Gibson DNA assembly to assembly so-called “cryptic” biosynthetic gene clusters encoded from microbial genomes. We will screen for antimicrobial activity, characterise for cluster function (RT-PCR, SDS-PAGE) and perform natural product purification (e.g. chromatography, HPLC, NMR).
Streptomyces Cell-free Protein Synthesis
Jointly supersvised with Tobias von der Haar
Cell-free protein synthesis is a rapidly developing area in synthetic biology for the implementation of the design-built-test-learn cycle. In this project, we are interested in the potential of a Streptomyces cell-free system for studying gene expression tools and the synthesis of novel antimicrobials. This project will involve Golden Gate DNA assembly and routine techniques in gene expression analysis.
Further reading
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.

Mark Wass

Predicting protein function

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.

Evolution of the muscle sarcomere. A bioinformatics approach to the interaction between myosin and myosin binding protein-C

Joint supervision with Prof 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 dsease.

Jose Ortega Roldan

In-cell structural biology: CLIC1 structure, function and drug binding inside tumour cells (MSc by Research Biochemistry)
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.

Understanding antimicrobial activity in live cells (MSc by Research Biochemistry)

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.

Andrew Lawrence

Investigating the biosynthesis of the unusual base, DMB (MSc by Research Biochemistry)

This project looks at the “chicken or egg” question of whether vitamin B12 is required for the biogenesis of itself. The project will investigate the role of vitamin B12 in the biosynthesis of 5,6-dimethylbenzimidazole (DMB), an essential component part of the vitamin B12 structure. The project will involve microbiology, molecular biology and protein biochemistry.

Vitamin analogues as probes and imaging agents (MSc by Research Biochemistry)

In this project we will use synthetic and chemical biology techniques to produce novel vitamin derivatives which can be used as imaging agents and probes of biological function.  This will be achieved through manipulation of the biosynthetic pathway and the use of cofactor analogues to introduce new functionality into an existing molecular framework.

Ben Goult

How to read a memory – proving the MeshCODE theory

We have recently discovered how protein molecules have molecular memory and can store information in the shape of molecules with memory, that are able to story information, Our research has identified an expansive network of mechanical binary switches that are built into each and every synapse that we hypothesise have the potential to store information, and to alter the synaptic impedance to allow control of synaptic activity.

This theory is based on our discovery of protein molecules, known as talin, containing “switch-like” domains that change shape in response to mechanical force. These switches have two stable states, 0 and 1, and this pattern of binary information stored in each molecule is dependent on previous input, similar to the Save History function in a computer. The information stored in this binary format can be updated by small changes in force generated by the cell’s cytoskeleton.

This project aims to test this MeshCODE theory for how memories might be stored in the brain by actually writing and reading information onto single molecules. Using a combination of biochemistry, biophysics and mechanobiology you will work to measure and observe these changes in shape that represent the signature of memory writing. This project will ultimately develop the tools and reagents to be able to read these patterns of information in synapses and ultimately in animals.

Wiring the brain – deciphering how neurons make the right connections.

The human brain is comprised of trillions of neurons, all linked together to form complex networks.  Quite how our brains are wired up with such precision is a major question in biology. This project will work on the mechanisms that regulate axon guidance, the process by which neurons send out axons that extend and migrate to their correct targets.

The project will focus on defining the talin interactions that are central to its function in axon guidance and neuronal pathfinding.

 

Gary Thompson

MSc Fast protein structure assignment and validation

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.

 

MSc Docking of large protein complexes using sparse NMR Restraints

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.

 

Our Masters by Research fall under one of five postgraduate degrees. For more information, please see the following links:
MSc by Research in Genetics
MSc by Research in Cell Biology
MSc by Research in Biochemistry
MSc by Research in Microbiology
MSc by Research in Computational Biology