MRes Projects – Biological Sciences

Studying our Master of Research (MRes) Science allows you to focus your research interests on one or two areas of science and work towards translating your learning into research related outputs – such as a submission for a peer-reviewed publication; a peer reviewed research/knowledge transfer grant application, or a presentation.

MRes Science can be studied either full time (1-year) or part time (2-years). You will develop a wide variety of skills, experience and competence on this course, and the MRes will provide a thorough grounding for students moving towards Doctoral (PhD) studies, or pursuing research related activities as a career.

Please note this list of projects is not exhaustive and you'll need to meet and discuss the project you're interested in with a member of research staff before you apply.

Cool microbiology: Exploring the Antarctic seafloor microbiome

Supervisor: Dr Carmen Falagan

Antarctica is one of the most inhospitable environments on Earth, many organisms have adapted to the extreme conditions including bacteria, archaea, and microalgae. While the microbiome of ice-covered lakes and subglacial environments have been studied, the microbiology of the Antarctic seafloor remains largely unexplored. Understanding the microbiology of these extreme environments has implications not only for climate change but also for astrobiology.

Microorganisms play a crucial role in carbon and other macro- and micronutrient cycles, which are key to understanding the ecosystem dynamics. For example, the microbial composition of seabed communities determines the rate at which carbon returns as CO2 to the environment by decomposing organic matter (remineralisation). Examining the microbial composition of Antarctic seafloor environments offers valuable insights into the microbial carbon cycle in the Southern Ocean. This research addresses a significant knowledge gap in understanding how these communities may be impacted by climate change and their role in carbon cycling in the Antarctic seafloor.

Furthermore, studying the microbiome of Antarctica offers insights into the limits of life on our planet with implications for astrobiology as it provides a valuable analogue for studying life in extreme extraterrestrial environments.

This is a laboratory-based project where you will be determining the microbial composition of sediment samples collected from the Antarctic seafloor using next-generation sequencing techniques.

The annual breeding cycle and diet of Xenopus tropicalis within their natural habitat

Supervisor: Prof John Measey, Dr Annie Godwin, Prof Matt Guille

The tropical clawed frog, Xenopus tropicalis, is increasingly being used as the model frog in developmental biology as it is easy to maintain and has a diploid genome – the only known 2n in the genus Xenopus. Laboratory work depends on breeding this species, but we have little to no information about natural breeding of X. tropicalis in its native West African habitat. Most laboratory populations are derived from lineages that originated in Nigeria or Cote d’Ivoire, yet the species ranges from Senegal to Cameroon. In this project, we will investigate the autecology of X. tropicalis, by taking monthly samples from the native range in Nigeria. We will also monitor the native habitat of the population. Individuals collected will be dissected to determine the sexual-cycle of X. tropicalis as well as changes in the diet throughout the year. The project requires a student who is comfortable in the field environment and meticulous with dissections and recording data. Identification of aquatic vertebrates/invertebrates would be an advantage.

Please note this project is not funded and is split between UK and Nigeria. All field work will be conducted in Nigeria. 

Getting to the root of the problem – an underground look at the interactions between plants and their environments

Supervisor: Katherine Williams

The below-ground world of roots and soils is perhaps the least visible but most important environment for sustainable agriculture, rewilding, conservation efforts, and carbon capture. Complex interactions between plant roots, soil structure and chemistry, water, and microbiomes have profound influences on plant productivity and communities. However, there are still fundamental processes within soil that remain poorly understood. Plants can exude 20-40% of their fixed carbon into the soil in the form of root mucilage, but the exact function of root mucilage is still under debate. Key processes are likely to involve microbial interactions, root lubrication, and regulation of water and nutrient uptake.

This project will investigate the role of root exudates in processes such as water uptake by roots, drought tolerance, and mobilisation of nutrients, and could include work on soil microbiomes. It could focus on agricultural, general ecological, or extreme environments. It will involve setting up laboratory assays including both standard soil methods and development of novel techniques. It could also include X-ray CT imaging for understanding the 3D structure of roots within the soil.

Screening Environmental Microbes for PET Degradation Capabilities

Supervisors: Dr Sam Robson and Prof Joy Watts

Accumulation of plastics in the environment is one of the major global challenges facing us today. Natural enzymes, such as those produced by micro-organisms (e.g., bacteria), may hold the key to breaking down plastics, with the potential to be deployed on an industrial scale.

The Centre for Enzyme Innovation (CEI) at the University of Portsmouth aims to identify and exploit such enzymes from the environment. They have developed a biobank of environmental samples collected from a range of sources, with potential for plastic-degrading enzymes to be present (waste sites, recycling plants, fuel tanks, sea sponges, etc.). The successful candidate will explore these samples to identify and characterise potential enzyme targets of interest for further research, and potential use for industrial deployment in the future.

In this project, you'll first select bacterial isolates of interest from the CEI biobank, culture these isolates, and perform DNA extraction in order to carry out PCR screening for known PET-degrading genes. Any isolates indicating a positive result from this PCR screening will then undergo confirmatory tests using microbiological techniques developed within the CEI (including screening using Coomassie blue staining of M9 agar and 5% PEG), as well as a novel technique developed by Charnock, 2021.

During this screening project, you'll undergo whole genome sequencing and RNA sequencing, providing the successful candidate with experience of Nanopore sequencing, bioinformatics analysis, and data exploration (e.g. de novo genome assembly, gene annotation).

Machine learning-based prediction of i-motif structures from Nanopore sequencing signal data

Supervisors: Dr Sam Robson, Dr Daniela Lopes Cardoso, Dr Garry Scarlett and Dr Fiona Myers

The aim of this project is to identify novel methods for the detection of non-standard 4-stranded ‘i-motif’ DNA structures from commonly used biophysical assays. In particular, this project will combine biophysics and genomics with machine learning approaches, to develop cutting-edge approaches for the high-throughput identification of these structures. As we understand more about the role that such structures play in metabolism and cellular function, such advanced approaches will be necessary to accurately distinguish i-motif from B-form DNA.

The i-motif is a non-standard DNA structure, very different to the typical Watson-Crick double-helix shape. The currently accepted sequence-specific definition of an i-motif over-estimates the number and misses potential i-motif forming sequences that do not follow the standard precisely. In particular, work by our collaborator Dr John Brazier has shown that the loops present in the 4-stranded structure are of great importance in the structure formation. It was previously believed that the i-motif structure was not biologically relevant and would not be seen under normal physiological conditions. However, recent evidence has directly visualised i-motif structures in the genomes of living cells under such cellular conditions. This, along with other recent evidence, strongly suggests that i-motifs play a currently under-explored role in molecular function and genomic regulation.

We have recently studied the effect of i-motifs on helicase enzymes, which act to unwind DNA during replication and translation. By using Oxford Nanopore Technologies (ONT) flow cells as real time helicase models, we have shown that helicase activity is affected by the secondary structure of i-motifs, resulting in a change to the translocation speed through the nanopore and effects at the raw signal transduction level. The successful candidate will further explore this effect and help to develop machine learning models for the prediction of i-motif structures from nanopore sequencing data.

This project will provide a powerful toolkit for identification of i-motif structures, and will link with further work within the group. This work will help in understanding the role that i-motifs play in development and disease, leading to a greater understanding of the complex machinery underpinning gene regulation, and the identification of novel targets for small molecule therapeutics.

Nanopore sequencing of cell-free DNA for early identification of prosthetic joint infection (PJI)

Supervisors: Dr Sam Robson and Dr Sharon Glaysher

Prosthetic joint infection (PJI) represents one of the most common reasons for failure among hip and knee arthroplasty, with an incidence of around 1-2%. Infection can occur early (within days of surgery) or late (over a year after surgery), and no specific early markers for infection onset exist. Given the significant costs to the NHS for corrective revision surgery, the added suffering and risks to patients from surgery, and the risk of enhancing antimicrobial resistance through the use of broad-spectrum antibiotics, a more specific predictive test for early onset of infection is required.

Over 80% of human infection is estimated to be a result of biofilm formation. Biofilms are an accumulation of microorganisms on a surface, resulting in a functional community which provides antibiotic resistance and a beneficial environment for the growth of pathogenic species that would otherwise be removed by the body’s defences. Biofilms can rupture, allowing pathogens to spread infection. To date, biofilm development and diversity on periprosthetic implants is poorly understood. It is not known whether biofilms associated with PJI differ from those in infection-free patients, or whether characteristic biofilms are associated with providing a microenvironment suitable for PJI-associated pathogens to thrive.

In this project, you'll explore the possibility of early detection of PJI from cell free DNA from blood samples collected from individuals who have undergone hip joint prosthetic replacement. This data will link to a wider-scale data set exploring the characteristic microbiome of hip joint prosthetic biofilms. This has the possibility of providing a relatively non-invasive diagnostic tool for PJI detection, with potential benefits for many.

Modelling paediatric brain tumours in chicken embryos

Supervisors: Dr Frank Schubert

This project aims at establishing and utilising the chicken embryo as a new model for paediatric brain tumours. Diffuse intrinsic paediatric glioma is a deadly brain tumour for which currently there is no cure. While substantial progress has been made in identifying driver mutations for DIPG, most notably the K27M mutation in variant histone 3 genes, there are still considerable gaps in our understanding of the biology of DIPG and its microenvironment. This is partly due to the lack of an easily accessible in vivo model. By introducing driver mutations into the embryonic chicken brain, we hope to establish a new, more ethical and more usable model to study aspects of DIPG biology.

Exploring the gene regulatory network for neurogenesis

Supervisors: Dr Frank Schubert

By using a combination of pharmacological and molecular genetics approaches, this project aims at elucidating the gene regulatory network regulating the onset of neurogenesis. The embryonic vertebrate brain provides an excellent model, since neurogenesis is initially restricted to a few clusters of cells. Preliminary results suggest that neurogenesis is inhibited by Fgf signalling in one these clusters, but promoted in the other two. Other signalling pathways like Shh and Wnt signalling are likely to also play a role. We'll explore the molecular mechanisms through which cell signalling controls the expression of proneural genes, and thus the onset of neurogenesis.

Challenging LEGO plastics: Designing novel enzymes for biodegradation

Supervisors: Dr Binuraj Menon, Professor Joy Watts and Professor Andrew Pickford

Plastic pollution has become one of the most pressing environmental issues, with around 400 million tonnes ending up in landfills and 8 million tonnes in the aquatic environment every year. A major portion of this waste is made up of LEGO plastics (or ABS plastics) found in LEGOs, computer keyboards, and wall sockets which are produce over 12.49 million metric tons worldwide per annum. These plastics are not readily biodegradable and can take thousands of years, calling for an innovative biocatalytic solution to address this.

This project is built-up on our success to identify and develop several industrially viable enzymatic processes that use plant microbiomes and natural product enzymes. At the Centre for Enzyme Innovation (CEI), we develop enzymes that break down waste plastic into its building blocks. We engineer to make faster and more efficient enzymes that otherwise take millions of years via natural selection. Also, we've collaborated with leading Artificial intelligence (AI) researchers to help us engineer faster-acting enzymes for recycling some of the world’s most polluting plastics.

The work on this project could involve:

• Studying plastic degrading enzymes via Bio-physical, Bio-catalytic and Structural Biology based techniques
• Investigating and studying the microbial interaction with the environment and each other, and their effects on the degradation of anthropogenic chemicals and polymers
• Directed evolution, high-throughput screening and AI-based computational studies to identify and evolve a new generation of plastic eating enzymes
   

Engineering microbial chemical factories to produce renewable and modified biomaterials

Supervisors: Dr Binuraj Menon and Professor Steve Wood

Polymers, such as plastics, are ever-present and integral in everyday human life with many applications that vary from medical, transport, electrical, construction and packaging. As the current polymer production completely depends on petrochemicals, the manufacturing process is not sustainable along with its high environmental and economic risks. With the advancement of synthetic biology and metabolic engineering, the genomic information and mechanisms of which bacterial cells produce several linear polyesters in nature are about to emerge. These materials have a potential advantage over petrochemical derived polymers in the manufacturing of either thermoplastic or elastomeric polymer materials and are completely biodegradable, which could be used to produce bioplastics. The plan is to identify the genes that act up from the early stages of polyester biosynthesis in bacteria and recreate biosynthetic pathways in E. coli and other host organisms. The initial pathway components are derived from a previously reported butanol pathway, which was shown to produce biofuel propane from E. coli cells (Menon et al, 2015: A microbial platform for renewable propane synthesis based on a fermentative butanol pathway. Biotechnology for Biofuels). With the presence of a corresponding transporter genes, it will produce various halogenated polymer units which could be further modified via chemo-catalysis or via incorporating other modifying enzymes. Our aim is to incorporate new modifications (via biosynthetically and chemically) on the derived biopolymers to render them readily available for the preparation of bio-molecular conjugates and hybrid biomaterials that could act as a potential and promising new class of biocompatible biomaterials.

The work on this project could involve:

• Bioinformatics – analysing gene cluster, protein structural prediction and metabolite prediction, protein-protein interactions
• Molecular biology – Manipulation with DNA (PCR, cloning, Gene knockouts, etc), site-directed mutagenesis
• Protein expression and purification, optimisation and analysis of protein quality
• Metabolic engineering, pathway construction in different hosts and pathway optimisation, separation and characterisation of metabolites, analysis of polymers and biomaterials
• Enzymology – enzyme activity assays and assay development, enzyme kinetics (UV-Vis spectroscopy, Fluorescence spectroscopy. HPLC, GC, IR, Mass spec, NMR)
• Chemical synthesis – of metabolites/intermediates, cross coupling chemistry and developing chemo-enzymatic reactions

Development of novel halogenase enzymes for biopharmaceutical applications

Supervisors: Dr Binuraj Menon and Professor Steve Wood

Identification of new halogenated synthetic, natural and non-natural compounds, and further exploitation and synthesis of these compounds are of extreme importance in this modern era. This is due to the profound role of organo halides as pharmaceuticals, agrochemicals and valuable synthons in various organic reactions. As an organic synthetic intermediate, halogenated molecules are of importance in many metal-catalysed cross-coupling reactions. Nature has evolved several biocatalysts to regio-selectively halogenate a diverse range of biosynthetic precursors and secondary metabolites, and this unexplored repertoire is ever growing. Biosynthetic halogenation can occur over simple to extremely complex ring structures of natural compounds and in some cases, it initiates the formation of complex structures and scaffolds. These reactions often range from simple aromatic substitutions to complex stereoselective C-H functionalisation and activation of remote carbon centres. These reliable, simple and cleaner biosynthetic routes have potential value and greater demand over traditional nonenzymatic halogenation chemistry that requires deleterious reagents and lacks regio-control. In the past few years we have identified several pharmaceutically important halogenase systems by genome mining in natural product pathways. In this project, we're planning to explore their enzyme structure and substrate scope, along with their potential applications in organic synthesis. The aim is to incorporate these enzymes into synthetic and biosynthetic pathways and into various natural product pathways for biotechnological and pharmaceutical applications.

The work on this project could involve:

• Bioinformatics – analyzing gene cluster, protein structural prediction and metabolite prediction, protein-protein interactions
• Molecular biology – manipulation with DNA (PCR, cloning, Gene knockouts etc), site-directed mutagenesis
• Protein expression and purification, optimisation and analysis of protein quality
• Metabolic engineering, pathway construction in different hosts and pathway optimisation, separation and characterisation of metabolites, analysis of polymers and biomaterials
• Enzymology – enzyme activity assays and assay development, enzyme kinetics (UV-Vis spectroscopy, Fluorescence spectroscopy. HPLC, GC, IR, Mass spec, NMR)
• Protein X-ray crystallography, crystallisation and protein structure resolution
• Chemical synthesis of metabolites/intermediates, cross coupling chemistry and developing chemo-enzymatic reactions.
   

Enhancing seagrass restoration efficiency: Designing and assessing innovative solutions to seed sorting and deployment

Supervisors: Dr Joanne Preston, Dr Ian Hendy and Dr Tim Ferrero

Seagrass restoration has the potential to benefit the ecology and environment locally and at a wider scale. However, seagrass restoration is often challenging, given the dynamic environment that seagrasses inhabit and the multi-step processes to restoration activities.

This MRes would work alongside our project partner the Hampshire and Isle of Wight Wildlife Trust to increase the efficiency of intertidal seagrass restoration to support the scalability and application of such restoration. This research will aim to increase restoration efficiency and quality in intertidal seagrass, through mechanisation of seed separation and trialling different novel seed deployment techniques.

This may mean developing bespoke equipment such as a Zostera noltii seed separator to assess the quality (size and density) of seagrass seeds to retain high quality seeds for restoration and/or trial innovative seed deployment strategies in muddy seagrass habitats i.e. direct seed injection, or biodegradable hessian seed bags.

This project will involve muddy intertidal fieldwork and seagrass seed culturing on site at the Institute of Marine Science. This MRes represents an exciting opportunity to work alongside a partner stakeholder on active seagrass restoration research.

Assessing carbon storage within intertidal seagrass, above and below ground biomass

Supervisors: Dr Joanne Preston, Dr Ian Hendy and Dr Tim Ferrero

Seagrass habitats are one of the world’s most threatened ecosystems. Seagrasses provide a multitude of benefits, ranging from habitat for many species to providing various ecological services such as, nutrient cycling, sediment stabilisation and carbon sequestration.

Research regarding carbon sequestration has received growing interest due to its potential to incentivise habitat restoration through finance accreditation mechanisms. This research involves having a holistic understanding of the different carbon compartments (sedimentary and plant) within seagrass habitats. This MRes research will focus on characterising the carbon stored within the plant compartment (above and below ground plant biomass, seed biomass) of Solent seagrass habitats.

This Master’s involves intertidal fieldwork across the Solent in muddy and sandy seagrass habitats, the project will also likely involve supporting seagrass culturing on site at the Institute of Marine Science. This MRes represents an exciting opportunity to work alongside wider research currently ongoing at IMS within the growing area of blue carbon research.

Morphometrics of deep-sea hydrothermal vent taxa

Supervisors: Dr C. Nicolai Roterman and Katherine Williams

Studying the life history and behaviour of animals adapted to the extreme environment of deep-sea hydrothermal vents, such as the yeti crab Kiwa tyleri can provide a unique insight into evolution and adaptation. However, many species inhabiting deep-sea hydrothermal vents are poorly understood, with large gaps in our basic knowledge of their life history and behaviour. These environments are challenging to access, so animals cannot easily be observed long term and in fact K. tyleri was only formally described in 2015.

One way to better understand these enigmatic animals is to systematically characterise their morphology at different stages of maturity. For K. tyleri (amongst other taxa), enough specimens have been collected from vents in the Southern and Indian Oceans to allow for a systematic analysis. This will involve a variety of methods, from traditional morphometric techniques to more recent geometric morphometric analyses of images; and also 3D scanning techniques.

The aims of the project will be to characterise key aspects of morphology relating to survival in low oxygen environments, as well as feeding, mating and behaviour. This project will provide new insights into species living in some of the most extreme environments on Earth.

Ecology of an invasive spider

Supervisors: Dr C. Nicolai Roterman and Dr Lena Grinsted

The false widow spider (Steatoda nobilis) – an invasive species in the UK and around the world – has received a lot of publicity in recent years. They are reported to have arrived on the English south coast from the Canary Islands in the 19th century and have since been expanding northwards in the UK, becoming prevalent around buildings. Understanding the spread of S. nobilis around the world and why they are successful invasives will provide valuable information for stakeholders concerned with the impacts of invasives.

In this project, the student will use primarily population genetics tools to reveal patterns of population connectivity and demography in the UK and potentially, globally. Some specimens have already been collected and the COI gene sequenced. Initially, this will therefore be a data analysis project. The student will learn to use a suite of bioinformatic tools to characterise patterns of genetic diversity, with the additional possibility of further specimen collection and DNA-based lab work (DNA extraction, PCR, DNA sequencing). There is also scope for an additional project focusing more on the behaviour of the spider, along with other aspects of its biology which might involve either field or lab-based experiments.

Phylogeography and population genetics of deep-sea urchins (Echinoidea)

Supervisor: Dr C Nicolai Roterman

Some of the most extensive coral habitats on the planet are far below the surface of the ocean; down to depths of 1000m or greater, where there is little or no light and ambient temperatures are well below 10 ̊C. These corals are sustained by organic material sinking from the sea surface, providing a huge amount of habitat complexity; and hosting a range of associated fauna. In recent years there has been increased interest in such habitats owing their importance in sequestering carbon, their role as fish nurseries, their high biodiversity, and the increasing threats of human activity.

While much of the research focus is on the habitat forming coral, much less is known about the associated fauna. One of the more prominent grazers and predators in habitats are cidaroid urchins. The diversity and distribution of these urchins – ‘considered living fossils’ – is little known. The student will employ phylogenetic and population genetic tools to reveal patterns of evolution and population connectivity in deep-sea urchins from DNA sequences already acquired. Additionally there is scope to acquire more specimens and to employ DNA-based lab techniques (DNA extraction, PCR, DNA sequencing).

Demographic stability of deep-sea invertebrate populations in the Pleistocene and Holocene

Supervisor: Dr C. Nicolai Roterman

In recent years there has been an increased public interest in the deep sea relating – amongst other things – to its importance in sequestering carbon and the looming anthropogenic impacts of climate change, pollution and mining. A key question is how large and resilient are deep-sea populations? One way to answer this is to employ population genetic analyses to infer the size and demographic stability of populations in the recent past.

Over the past 30 years there has been an explosion of population genetic studies on invertebrate species inhabiting the deep-sea floor (depths >200 m) and there are now enough studies published to allow for the analyses of these datasets together (meta-analyses). Population genetic research on shallow-water temperate marine species has revealed a general trend of demographic expansion (population growth) occurring since the last glacial maximum (~20,000 years ago), when the climate began to warm.

However, little is known of how a changing climate impacted deep-sea species, which live in more thermally constant conditions (<10  ̊C). In this project, the student will compile relevant studies and re-analyse those data to model past demographic patterns in order to provide better insight into the resilience of deep-sea populations to future anthropogenic impacts.

Identification of nucleic acid (DNA/RNA)-degrading bacteria from the environment

Supervisor: Dr Kenneth Wasmund

Nucleic acids (DNA and RNA) are abundant and prevalent molecules in the environment, and microorganisms that degrade and consume them are important components of biogeochemical cycles. Identifying which microorganisms carry-out these specialised metabolisms is therefore important for understanding the cycling of nutrients and niches of microorganisms in the environment.

Projects can be developed in discussion with the student:

• Identify bacteria that consume DNA and/or RNA from environmental sources, e.g., marine or wastewater
• Identify bacteria that consume nucleotide-based metabolites (e.g., NADH) from environmental sources, e.g., marine or wastewater

The project will involve molecular and cultivation techniques, including nucleic acid extractions and purification, molecular identification of bacteria (e.g., PCR, sequencing), fluorescence microscopy.

Molecular sequencing of marine sediment microbiomes from Portsmouth

Supervisor: Dr Kenneth Wasmund

Marine sediment-benthic ecosystems represent one of the Earth’s largest biomes for microorganisms, and are key sites for the biogeochemical recycling of organic material from the oceans. Tidal flat sediments are good model ecosystems for global marine sediment ecosystems, because they contain similar organisms and processes, and are easily accessible. In order to establish a study site for tidal flat sediments at the University of Portsmouth, we aim to gain initial insights into the microbial communities at a model study site in the Portsmouth area.

Projects can be developed in discussion with the student:

1. Molecular characterisation of microbial communities: extract DNA, PCR, clone, and Sanger & Illumina sequencing. Analyse sequences bioinformatically. Potentially some metagenomic work. Fluorescence microscopy
2. Develop novel isolation strategies to grow bacteria using unusual organic compounds. Isolate and identify bacteria by DNA/16S rRNA gene sequencing
3. Detection and characterization of newly discovered sulfur-cycling Acidobacteriota in tidal flat sediments.

Modified triplex-forming oligonucleotides as therapeutic agents

Supervisor: Dr David Rusling

Oligonucleotides are short synthetic strands of DNA or RNA that can be used to treat or manage a wide range of diseases, for example by silencing specific genes. In recent years, various oligonucleotides have made it through clinical trials and have now reached the clinic to some fanfare. They often elicit their affects via antisense or RNAi mechanisms by acting on messenger RNA molecules and modulating protein expression inside living cells. Although this has been hugely successful, a better strategy, at least in principle, would be to use oligonucleotides to target genomic DNA directly and prevent messenger RNA expression altogether. Oligonucleotides that might prove useful in this manner are known as triplex-forming oligonucleotides, on account of their binding to specific duplex sequences and generating a triplex structure.

Our research group has recently overcome a long-standing problem associated with these molecules using oligonucleotides containing modified DNA bases. We are now at the stage of developing these molecules as gene-targeting agents and this MRes project will help us in attaining that goal. The student will gain experience in a wide variety of biochemical, biophysical and biological techniques used to characterise the formation of triplex DNA, and the project will involve a large amount of assay design and optimisation.

Targeted delivery of large macromolecular cargoes to subcellular environments

Supervisor: Dr Bruce R Lichtenstein

One of the grand challenges in biology is the targeted delivery of macromolecular complexes to specific sites in eukaryotic cells. Recent mRNA vaccines highlight the potential of delivered macromolecules to effect physiological changes in organisms, but we still remain quite distant from our goal of making selective changes to cellular physiology down to the organelle level.

To meet this challenge, extracellular macromolecules must be delivered to sites of interest within selected eukaryotic cells. Our recent work with engineering AB5 toxins highlights the flexibility of these carriers to transport cargoes of unconstrained identity into eukaryotic cells.

This project will define the limits of the delivery system towards applications in targeted therapies and cell engineering, by examining the delivery of supramolecular protein assemblies targeted to different subcellular environments. This research project would suit a biology, biochemistry, or biomedical student with interest in molecular biology, protein engineering, tissue culture, and confocal or super-resolution microscopy.

Directed evolution of a de novo designed peroxidase

Supervisor: Dr Bruce R Lichtenstein

One of the grand challenges in biology is the targeted delivery of macromolecular complexes to specific sites in eukaryotic cells. Recent mRNA vaccines highlight the potential of delivered macromolecules to effect physiological changes in organisms, but we still remain quite distant from our goal of making selective changes to cellular physiology down to the organelle level.

To meet this challenge, extracellular macromolecules must be delivered to sites of interest within selected eukaryotic cells. Our recent work with engineering AB5 toxins highlights the flexibility of these carriers to transport cargoes of unconstrained identity into eukaryotic cells.

This project will define the limits of the delivery system towards applications in targeted therapies and cell engineering, by examining the delivery of supramolecular protein assemblies targeted to different subcellular environments. This research project would suit a biology, biochemistry, or biomedical student with interest in molecular biology, protein engineering, tissue culture, and confocal or super-resolution microscopy.

Rational engineering of plastic degrading enzymes

Supervisor: Dr Bruce R Lichtenstein

Plastics have revolutionised our way of life, touching everything from every day packaging to ensuring the safety of our medicines. However, their value as robust materials makes them challenging to recycle conventionally, allowing them to accumulate harmfully in the environment; thus our ability to continue to use them is directly tied to finding sustainable end-of-life solutions. For this, we need routes that allow their unlimited recycling (or upcycling), and enzymes offer an economical, biological means to effect this process. Because plastics are relatively new, enzymes with plastic degrading function have notably not evolved for this activity, leaving room for enhancing their catalytic proficiency and suitability for industrial applications.

This project will focus on tracking the laboratory evolution of a plastic degrading enzyme through deep sequencing and bioinformatics from an evolving library. Sequence and functional details will be used in the rational engineering of novel depolymerases, which will then be characterised using a range of biophysical techniques in the wet lab. This project would suit a biochemistry, or biology student with interest in bioinformatics, molecular biology, and protein engineering.

The effects of legacy contaminants on reproductive morphometrics and fertility of the harbour porpoise

Supervisors: Professor Alex Ford and Dr Rosie Williams (Zoological Society of London)

Porpoise around the UK have recently been shown to have lower testes size in relation to PCB contamination in their tissues. To determine whether there might be links between industrial pollution and other reproductive abnormalities, this study will determine the relationships between tissue contaminants and reproductive morphometrics of male and female porpoises. We also aim to conduct some histological examinations of archived testicular tissues from male porpoises. The study would be conducted in collaboration between Prof Alex Ford (University of Portsmouth) and Dr Rosie Williams (Zoological Society of London).

Intertidal seagrass restoration in the Solent – mapping changes in carbon and diversity services

Supervisors: Dr Joanne Preston, Dr Ian Hendy, Tim Ferrero (HIWWT)

Seagrass habitats are one of the world’s most threatened ecosystems. Seagrass restoration could provide a multitude of benefits, ranging from habitat for many species to providing various ecological services such as, nutrient cycling, sediment stabilisation and carbon sequestration. Seagrass restoration therefore has the potential to benefit the ecology and environment locally and at a wider scale. However, seagrass restoration is often challenging, given the dynamic environment that seagrasses inhabit.

This MRes would work alongside our project partner the Hampshire and Isle of Wight Wildlife Trust to undertake trials of seagrass bed restoration in the Solent. This research will aim to characterise the seagrass restoration sites to assess post restoration change at the sites and in the ecosystem services they provide, ultimately gauging the success of restoration. Alongside intertidal work at the restoration sites the project will likely involve seagrass seed culturing on site at the Institute of Marine Science. This MRes represents an exciting opportunity to work alongside a partner stakeholder on seagrass restoration research.

Epitope labelling at endogenous loci using gene editing (2 projects)

Supervisor: Professor Matt Guille

Proteins are the major “doing molecules” in cells and visualising them relies on antibodies. For many key proteins however effective antibodies cannot be raised consistently; this has been identified as a major problem for biomedical science. Introducing genes/mRNAs encoding epitope-tagged versions of proteins has been a way of overcoming this, but it has limitations because the expression of these tagged proteins is not at endogenous levels and is unlikely to be in the precise cells expressing the target protein. To overcome this we have used gene editing to introduce an HA-tag to the gata2locus; we need now to test if other loci can be similarly targeted, optimise the pipeline for producing these gene edited, transgenic animals and test whether these proteins can be visualised using an anti-HA antibody. The students will learn gene editing, microinjection, embryo culture, mutant screening, advanced experimental design, western blotting and immunostaining.

Structural biology of plastic-digesting enzymes

Supervisor: Dr Andy Pickford

This project is part of a collaborative UK-US project with the goal of addressing one of our most imminent global challenges, plastic pollution. Plastics are now part of our everyday life, and polymers such as poly(ethylene terephthalate), or PET, are highly versatile, but are accumulating in the environment at a staggering rate as discarded packaging and textiles. The chemical properties that make PET so useful also endow it with an alarming resistance to natural biodegradation, likely lasting several centuries in the environment. We are working on newly discovered enzymes that have the ability to depolymerise plastics including PET. While our US colleagues are providing extensive molecular biology support, the Portsmouth team will focus on the characterisation of potential plastic-degrading enzymes using X-ray crystallography as a platform for protein engineering. Using a combination of biophysics and structural biology approaches, the goal of this MRes will be to join our growing team in order to identify, characterize, and optimize key enzymes that can degrade man-made plastics.

DNA Target-Site Location by Restriction Endonucleases or DNA Ligases (1 of 3)

Supervisor: Dr Darren Gowers

This research group focus on understanding the kinetics and binding of enzymes that interact with specific sequences or specific structures of DNA. These include a large number of DNA restriction enzymes (such as SfiI or BbvCI) that have to locate a specific target site; exonucleases (such as lambda exo) that have to locate a DNA end, and ligases (such as E.coli DNA ligases A and B) that have to locate a specific nick site within a long DNA chain. The work will involve growing E.coli cultures, harvesting and purifying proteins, using PCR, checking enzyme purities on SDS gels, designing experiments, running accurate timecourses, analysing DNA fragments by electrophoresis through agarose or polyacrylamide, gel imaging, quantitation and data fitting.

Bacterial DNA ligases as novel targets for inhibiting nucleic acid repair and replication (2 of 3)

Supervisor: Dr Darren Gowers

This research group focus on understanding the kinetics and binding of enzymes that interact with specific sequences or specific structures of DNA. Two E.coli proteins that we are very interested in are LigA and LigB. These repair enzymes seal breaks in the phosphodiester backbone that arise during DNA replication, and also as the terminal step in all DNA repair pathways. Inhibition of one or both of these ligases would lead to loss of bacterial genome integrity and cell death: that is, an antibacterial action. This project will involve elements of in-silico (computer-based) molecular docking, in-vitro testing of compounds in ligase activity assays and in-vivo experiments to see if the novel compounds can enter bacteria and cause a bacteriocidal effect. The work will involve use of MOE software, harvesting and purifying proteins, using PCR, checking enzyme purities on SDS gels, designing experiments, running accurate timecourses, analysing DNA fragments by electrophoresis through agarose or polyacrylamide, gel imaging, quantitation, data fitting and Kirby-Bauer in-vivo plate testing.

Analysis of Ostrea edulis larval recruitment and settlement in the Solent

Supervisor: Dr Joanne Preston

Historically the Solent supported one of the largest native Oyster (Ostrea edulis) fisheries in Europe. The oyster population suffered a catastrophic crash in 2006 due to overfishing, habitat destruction, pollution and potentially climate change impacts. The recovery of the native oyster has been poor despite closure of the fishery, and a large project is underway to restore the native oyster population and oyster seabed habitat. This project will be part of the larger restoration work, and will analyse the onset and duration of spawning, planktonic larvae behaviour and settlement rates of juvenile oyster spat. The project will involve boat and fieldwork, and utilise microscopy, flow cytometry and molecular techniques to analyse the life history of this ecologically and commercially important species.

The microbial community associated with marine plastics

Supervisors: Dr Joy Watts and Dr Michelle Hale

Using a range of techniques such as direct counts, fecal coliform numbers and DNA extraction and community analysis the effects of marine litter on microbial community stability and function in Langstone harbour will be examined. Microbial source tracking from sewage outfall and sediment resuspension will also be an area of focus.

Turning mats into money

Supervisor: Dr Gordon Watson

Protecting and enhancing transitional and coastal water (TAC) ecosystems are essential to growing a sustainable blue economy (e.g. fisheries, tourism), meeting conservation objectives (e.g. protecting habitats/birds) and improving public health (e.g. shellfish consumption). Despite this, all urbanised TAC waters have elevated nutrient levels leading to poor water quality caused by inputs of fertilizers, livestock and human waste. This results in the excessive growth of plant life (termed eutrophication). Coastal eutrophication results in the rapid growth of green seaweeds on intertidal mudflats forming mats 10 cms deep and covering thousands of hectares. These have significant ecological impacts (a key measure for not achieving GES [Good Ecological Status] via the WFD [Water Framework Directive]), as well as economic and human health issues. This project will develop and test innovative, sustainable and cost-effective methods that will rapidly reduce algal mat coverage of these habitats and contribute to reductions in nutrient levels. Feeding algal mats to polychaete worms and converting these to AC (aquaculture) feed will be tested under controlled conditions to maximise growth and assess the conversion of algal biomass to polychaete biomass.

Intersexuality and metal pollution in amphipods crustaceans

Supervisor: Professor Alex Ford

Some recent studies have linked reproductive abnormalities such as intersexuality in amphipods to pollution and parasites. This study aims to determine the metal concentrations and incidence of intersexuality in amphipods clean and polluted coastal locations.

Assessing the global marine ornamental trade

Supervisors: Dr Gordon Watson and Dr Harriet Wood

The global trade in marine organisms collected for aquariums is worth hundreds of millions of pounds per annum, yet very little is known about the species removed from coral reefs and their suitability for specific roles in an aquarium. Using gastropod species that are sold as ‘cleanup crew’ this project will assess the diversity of species collected; the accuracy of the identification of each and assess their function in a marine aquarium in the context of grazing and other processes.

Genetic variation, local adaptation and climate change: How do wild crop relatives respond to drought?

Supervisors: Dr Gordon Watson and Beatrice Landoni

At global scale, one of the most important signs of climate change is the increasing drought resulting from raising temperatures. Changes in drought are not necessarily similar across a latitudinal gradient. For example, summer drought is the SW Europe is more intense than in the UK. Hence, species with wide geographic distributions are likely to respond differently at local scale. Wild flax is the wild crop relative of linseed. It is distributed in the Mediterranean and in the W Europe. In this project, we will investigate genetic variation and local adaptation to drought with the aim to identify if different populations have evolved different strategies to cope with climate change. With this project, we will also investigate the value of a wild crop relative to increase food security.

Antibiotic Resistance in the Environment

Supervisors: Dr Joy Watts and Dr Michelle Hale 

Extensive antibiotic resistant strains are now being detected in all environments; the spread of these strains could greatly reduce medical treatment options available and increase deaths from previously curable infections. By their nature, aquaculture systems contain high numbers of diverse bacteria, which exist in combination with the current and past use of antibiotics, probiotics, prebiotics, and other treatment regimens—singularly or in combination. These systems have been designated as “genetic hotspots” for gene transfer.

It is essential that we identify the sources and sinks of antimicrobial resistance, and monitor and analyse the transfer of antimicrobial resistance between the microbial community, the environment, in order to better understand the implications to human and environmental health.

In this project different environments will be examined for the presence and transfer of clinically important antimicrobial resistance genes, using a number of molecular and traditional tools. To better understand the resistome laboratory based studies will be employed, to model the transfer frequencies and hot spots. Transfer of antimicrobial resistance provides a global threat to healthcare systems and human longevity, it is therefore critical that we better understand how AMR genes persist in the environment and spread - especially into clinically relevant pathogen species.

Teaching how to identify and avoid fake news: Digital literacy in the era of post-truth

Supervisor: Dr Alessandro Siani

With the public trust in science being undermined by the uncontrolled spreading of anti-scientific and pseudo-scientific fake news, it is imperative that tomorrow’s citizens are taught from a young age how to discriminate between credible sources and unreliable ones.

The aim of the project is to develop a teaching instrument or intervention to foster critical thinking and awareness of what constitutes a reliable source in school-age pupils.

Prior to developing and carrying out an intervention, you will be tasked with researching current literature to understand the causes of the spreading of fake news and investigate strategies to teach students how to look for appropriate sources and identify fake news.

Using Virtual Reality to facilitate learning and engagement in school-age students with special educational needs

Supervisor: Dr Alessandro Siani

The aim of the project is to develop a VR-based teaching strategy to facilitate engagement and on-task behaviour in students with special educational needs.

Prior to developing and carrying out an intervention, you will be tasked with researching current literature to understand the nature and features of selected learning disabilities, how these affect students’ learning and daily life, and what pedagogical strategies are currently used to address them.

Antimicrobial Resistance in Biofilms found in Waste Water Treatment Plant (WWTP)

Supervisors: Athanasios Rizoulis

This project will focus on understanding AMR found within bacterial biofilms in WWTP when compared to planktonic bacteria. In addition, we aim to investigate the possibility of microplastics found in WWTP serving as vectors for AMR. Several techniques will be used for this project such as molecular microbiology techniques, advanced microscopy (e.g. SEM) and traditional cultural methods.