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.

Phylogenomics, taxonomy, and evolution of the salt- and drought-tolerant sea heaths (Frankenia; Frankeniaceae)

Supervisor: Dr Steven Dodsworth

Frankenia consists of around 90 species, the sole genus within Frankeniaceae (Caryophyllales). These taxa are (sub)shrubs and herbaceous plants that are well-adapted to saline and dry environments, with a few taxa in cultivation as ornamental plants. Frankenia are widespread across temperate and subtropical regions, particularly coastal and arid regions. Many species are found in arid parts of Australia, where the greatest diversity occurs, but it is unclear how these are related to Eurasian, American, and African species. This project will build the first major phylogenetic assessment of the group, using a novel whole-genome sequencing approach based on high-throughput nanopore sequencing, and utilising a recent reference genome of the native Frankenia laevis, coming from the Darwin Tree of Life project. This phylogenomic framework will then be used to investigate the biogeography of the group, the likely geographic origin of the family, and of major clades within the genus. Climatic factors (e.g., aridity, salinity) can also then be mapped in order to provide insight into the evolution and level of salt- and drought-tolerance within the group. A focus on the Australian clade will provide an opportunity to define species boundaries and broad taxonomic inquiry, studying the key morphological characters that are important for defining and identifying the taxa, and an opportunity to uncover new species.

Evolutionary development of flower traits that impact pollination and diversification

Supervisor: Dr Steven Dodsworth

Flowers are a key evolutionary innovation of the angiosperms (flowering plants), the largest group of green plants, that dominate terrestrial ecosystems and provide humans with many vital ecosystem services (food, shelter, medicines). Floral structures themselves are highly variable and this great diversity of floral features can be related to pollinator specialisation. Many angiosperm species rely on successful zoophily (pollination by animals) for reproduction, including several important fruit and vegetable crop species. Investigating the biology of novel floral traits is therefore very significant for understanding the dynamics of plant-pollinator interactions. Key overarching research questions concern the repeatability of trait evolution, and the parallel (molecular) evolution of important traits across different species. Several projects are possible within this general area in our group utilising diverse systems, including: (i) investigations into the repeated evolution of nectar spurs; (ii) flower colour polymorphisms in natural populations; (iii) dynamics of flower size change. Techniques will likely involve a combination of molecular techniques (expression analysis, functional analyses), microscopy and imaging analyses (e.g. microCT, SEM).

Plant community ecology, pollinator ecology, and eco-evolutionary dynamics

Supervisor: Dr Steven Dodsworth

A wide range of projects focussing on plant community dynamics, as well as pollinator ecology and autecology, are possible. A key interest of our group is the impact of specific plant species on the overall diversity and dynamics (e.g. composition) of particular plant communities. This could be the impact of (hemi)parasitic taxa on local and regional plant communities, which has important longer-term impacts that may also relate to policy that aims to increase biodiversity. Other projects might focus on a specific taxon, particularly in the context of pollinator ecology and linking with ongoing projects on floral development and diversity. For example, this could include the influence of flower colour polymorphism on pollinator attraction, pollinator assemblages, and reproductive success, or the relationship between reproductive investment and reward. Techniques for such projects are likely to involve field ecology, species identification, herbarium specimen preparation and using collections, as well as novel use of camera traps and eDNA technologies to identify pollinator taxa. Projects are also possibly in collaboration with the Portsmouth herbarium (Portsmouth Museums), particularly when looking at historical trends in phenology and other trait data.

Investigating the role of chromosomal rearrangements in speciation

Supervisor: Dr Steven Dodsworth

Chromosomal change is pervasive in plant evolution, and most dramatic in the flowering plants, whereby chromosome number increases (following whole genome duplication, or polyploidy) are followed by decreases (through dysploidy and diploidisation). Whilst these structural changes to the genome are very widespread, much less is known regarding their stochastic or adaptive nature, as well as the repeatability of evolution. The idea that the diploidisation process itself is important to adaptive evolution is thus far relatively untested. This project will focus on recent chromosomal reduction in Nicotiana (Solanaceae), a group of wild tobaccos from the arid zone of Australia. Within this group we have found populations of several species that harbour individuals with different chromosome numbers and therefore can use this as an excellent study of recent chromosomal change. Utilising long-read datasets constructed through nanopore DNA sequencing, you will assemble high quality genome sequences and investigate the nature of structural variation. Comparing rearranged and unrearranged regions of the genomes, we will investigate the potential for adaptive evolution through structural rearrangement of the genome.

Phylogenetics and recent evolution of a species complex

Supervisor: Dr Steven Dodsworth

Nicotiana section Suaveolentes represents the majority of taxa within the genus of tobaccos, most of which are found across Australia, and with most diversity in the central arid regions of Australia. Over the past decade collaborative research has helped to collect and verify populations from across the range of most taxa within the group. This has enabled us to produce a new phylogenetic framework for section Suaveolentes and to gain a better understanding of the recent and rapid radiation of species within this group. What has become apparent is that within major clades, there are ongoing radiations that are extremely recent (<100,000 years old), and which represent taxa with more subtle morphological differences and ecologies. Using a high-throughput DNA dataset (RADseq) you will focus on reconstructing the phylogenetic history of one of these species’ complexes, and help to delimit the species units as well as investigate key morphological and ecological traits that define taxa. The phylogenetic analyses will be used to reciprocally illuminate morphological comparisons. This may also provide evidence for the recognition of new taxa that have been hiding within an understudied group of plants.

Antimicrobial resistance in Cornwall, is mining pollution selecting for AMR?

Supervisors: Dr Carmen Falagan and Dr Samuel Robson

With the raise in the use of antibiotics there is the general concern that antimicrobial resistance (AMR) is going to be the major cause of fatalities worldwide. More and more studies are showing how the antibiotics used in farming and for human use end up in the marine and freshwater environments selecting those microorganisms resistant to antibiotics. There are several factors that affect the spread of AMR in the environment, for example, misuse and overuse of antibiotics, lack of sanitation. However, there are other less well-known factors that also affect the degree of AMR, one of these is exposure to heavy metals.

The heavy metal zinc can increase the resistance of Escherichia coli by five times and exposure to copper and zinc was seen to coselect for antibiotic resistance in soil microorganisms. Cornwall has a long history of mining since the Bronze Age, which has caused the significant release of mining water containing high amounts of heavy metals into the rivers of the area. For example, the Carnon river fails the environmental quality standards for many heavy metals (e.g. cadmium, nickel, arsenic, copper, zinc) making it one of the most polluted of the region.

Thus, it is important that we understand how metal pollution affect AMR to better understand how AMR spread can be prevented. To that end, you will be using samples collected from metal polluted environments in Cornwall and using next generation sequencing to identify how metals affect AMR in the environment. Additionally, mesocosms experiments may be run to better understand which individual metals are positively selecting for AMR in selected samples.

This research will help to understand the hidden connections between heavy metal pollution and AMR ultimately contributing to the global battle against AMR and safeguarding our planet's health.

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.

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.

Characterisation of key polyphosphate-accumulating bacteria from wastewater treatment plants

Supervisor: Dr Kenneth Wasmund

Polyphosphate-accumulating organisms (PAOs) are key functional members of microbial communities in wastewater treatment plants (WWTPs), where they play critical roles in removing excess phosphorus from the wastewater before it’s discharged. Bacteria of the genus Tetrasphaera are one of the most abundant PAOs in WWTPs, but the strains that are abundant in situ in WWTPs are only known via sequencing and genomic methods, and have never been cultivated in the laboratory, or their metabolic properties specifically tested. This project would therefore use newly acquired metagenomic-based information to design strategies to selectively isolate the sought-after strains, as well as test their physiological/metabolic capabilities.

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

Enzymatic production of novel bioplastics

Supervisor: Dr Michael Zahn

Plastic products have revolutionized the world, but unsustainable production from fossil oil and poor degradability due to their recalcitrant nature are causing major pollution problems. The goal for the future is to produce bioplastics from renewable carbon (biobased or directly from carbon dioxide) and, if recycling is not possible, to provide adequate biodegradability to match the intended lifetime. In principle, polyesters have a built-in degradability, since these polymers carry hydrolysable ester groups that link the monomer units. However, conventional polyesters, such as polyethylene terephthalate (PET) and polycarbonates, are difficult to degrade by naturally occurring microorganisms, leading to their accumulation in the environment.

The aim of the project is to develop new enzymatically produced biopolyesters to replace conventional plastic products with new bio-based and biodegradable polymers for a sustainable life cycle. Methods will involve protein expression and purification as well as protein structure determination and biochemical enzyme characterisation.

Structural and biochemical characterisation of Nylon degrading enzymes

Supervisor: Dr Michael Zahn

Plastic products have become an important part of our modern lives, but due to their recalcitrant nature, synthetic polymers have also become one of the biggest global waste problems. Although they have only been around for less than a century, plastic pollution is everywhere on our planet and poses a major threat, especially to marine organisms, but also to humans in the form of microplastics.

The project aim is to express and purify potential Polyurethane degrading enzymes as well as to determine the enzyme structures and to characterise the enzymatic activities with biochemical assays.

Structural and biochemical characterisation of Polyurethane degrading enzymes

Supervisor: Dr Michael Zahn

Plastic products have become an important part of our modern lives, but due to their recalcitrant nature, synthetic polymers have also become one of the biggest global waste problems. Although they have only been around for less than a century, plastic pollution is everywhere on our planet and poses a major threat, especially to marine organisms, but also to humans in the form of microplastics.

The project aim is to express and purify potential Polyurethane degrading enzymes as well as to determine the enzyme structures and to characterise the enzymatic activities with biochemical assays.

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.

Investigating metabolite-RNase communication

Supervisor: Professor Anastasia Callaghan

Understanding how metabolism is controlled within a cell is fundamentally important and is directly applicable to medical, environmental and biotechnological advances. Our studies have recently identified that a molecule of central metabolism interacts with an RNase and affects its ability to destroy mRNA. This project will unravel some of the details of this newly discovered mechanism and investigate whether it represents a conserved metabolite-RNase coammunicative link in prokaryotes and eukaryotes.

Developing novel technologies for the study of RNA-interactions

Supervisor: Professor Anastasia Callaghan

With their versatile functions and the recent explosion of interest in transcriptomics, RNAs, and their interactions with proteins, nucleic acids and small molecules, are currently the subject of intense scientific research. RNA may represent an, as yet, untapped resource in the search for novel pharmaceutical drug targets. Characterization of bio-molecular interactions with RNAs is becoming increasingly necessary as the repertoire of RNA functions continues to expand. Such interactions are regularly investigated using sensor technique instrumentation that involves the immobilisation of one of the molecules being studied. This project will involve working on developing a novel method to tag RNA molecules for sensor surface immobilization in order to support bio-molecular interaction studies of this important family of biological molecules using sensor technique instrumentation.

Studying a novel mechanism linked to pathogenic bacterial virulence

Supervisor: Professor Anastasia Callaghan

With antibiotic resistance on the rise, research into understanding the workings of bacterial organisms is crucially important, as are new approaches to combating the infections they cause. The aim of this project is to increase our understanding of a recently discovered mechanism of genetic regulation which has potential applications in the field of antibacterial research. Specifically, the interplay of small non-coding RNAs, their mRNA targets, and an RNA chaperone protein, result in a finely balanced mechanism of communication leading to either transcript destruction, or stabilization and subsequent translation. The project will address how this communication occurs and whether this mechanism, with a direct impact on pathogenic bacterial virulence, can be exploited in the search for novel antibacterial approaches and/or targets.

Investigating the inhibition of the novel antibacterial target, RNase E

Supervisor: Professor Anastasia Callaghan

In an era of increasing antibiotic resistance, new antibacterial targets are urgently required. Found only in bacteria, the essential endoribonuclease RNase E represents such a potential target. Extensive structural characterisation of RNase E from the model organism, Escherichia coli, has provided molecular level details of the workings of the protein, enabling the first steps to be taken towards structure based inhibitor design. This project focuses on furthering the understanding of the inhibition of E. coli RNase E and its homologues in pathogenic bacteria. Expanding on existing in silico inhibitor design studies, potential small molecule inhibitors will be tested experimentally and their mechanisms of inhibition characterised prior to assessment of in vivo effectiveness.

Understanding novel bacterial molecular switches applicable to synthetic biology

Supervisor: Professor Anastasia Callaghan

Bacteria can use specific molecules to either promote or repress protein translation through a novel post-transcriptional mechanism. This ability to turn genes on or off at the right times and at the right levels demonstrates a potential role for these specific molecules as molecular switches, ripe for exploitation within a synthetic biology context. This project will seek to explore the application of these specific molecules as artificial molecular switches.

Role of histones and histone variants in the first stages of reprogramming fibroblasts into pluripotent stem cells

Supervisors: Dr Fiona Myers

Changing cell fate holds the potential for therapy in regenerative medicine. If a patient’s cells, e.g. skin fibroblasts, could be turned into the cell type in need of regeneration all problems associated with tissue rejection would be eliminated. For this to develop we require a full understanding of how the gene expression profile of the initiator cell is altered to determine cell fate. This project, in collaboration with Prof Colyn Crane-Robinson, will investigate the role of both modified and variant replacement histones in the earliest stages of re-programming fibroblasts into pluripotent stem cells.

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.

Purification and Characterisation of DNA Ligase Domains (3 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. The 3D structure of LigA is known, though one part of it - the BRCT domain - has never been determined by X-ray structural analysis. We are looking to use the technique of NMR to solve the solution structure of the BRCT domain and examine its effect on nick closure and ligation efficiency. The work will initially involve gene-fragment cloning, followed by growing E.coli cultures and harvesting and purifying recombinant proteins. If successful, the work will then move to NMR theory and training before attempting to undertake 1H and/or 15N 2D NMR experiments on the BRCT domain (and other relevant LigA or LigB constructs).

The effect of pollution on the ecology of plankton in Langstone Harbour

Supervisor: Dr Joanne Preston

Langstone Harbour receives a range of anthropogenic inputs, including frequent storm water discharges (a mixture of rain and untreated sewage). The increased nutrient status associated with this pollution can drive phytoplankton blooms and lead to decreased water quality. This project will examine the relationship between nutrient status, phytoplankton community and zooplankton diversity, with a focus on the larvae of ecologically important marine species (the native oyster Ostrea edulisand the invasive mollusc Crepidula fornicata). The project will involve boat and fieldwork, and utilise microscopy, flow cytometry and molecular techniques to analyse the plankton community.

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.

Microplastic uptake in filter feeding marine invertebrates in the Solent

Supervisor: Dr Joanne Preston

Plastic pollution is pervasive in the marine environment and has devastating impacts on marine ecosystems and the organisms therein. Often, the first entry into the animal food web is via invertebrate filter feeders. This project will examine a range of filter feeding marine species (sponges, oysters, mussels, tunicates) for their microplastic uptake and retention. The microplastic content of the water will also be analysed. The project will involve boat and fieldwork, and utilise microscopy, fluorescent microscopy, flow cytometry and aquarium based experiments.

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.

The translational control of retinoid receptor expression

Supervisor: Dr Colin Sharp

The retinoid receptors mediate retinoid signaling, which, in the early embryo, is important for axial patterning and for neuronal differentiation. Examination of the transcripts that encode the retinoid receptor RAR alpha 2 show that it has an extensive 5’ untranslated region (UTR) that precedes the open reading frame encoding the receptor. Preliminary experiments show that the 5’UTR determines when, during Xenopus development, RAR alpha 2 mRNA is converted into protein. Sequence analysis indicates that this mechanism is conserved across the vertebrates. The aim of the project is to determine the regions of the 5’UTR that mediate this regulation and identify the factors in the embryo that determine when the mRNA is translated. This will involve molecular biology to construct minigenes that can be injected into Xenopus embryos and then Western blotting as an assay for protein production. The project requires an interest in molecular biology, gene expression and embryology.

Improving urban air-quality using plants

Supervisor: Dr Mike Fowler

This project will involve characterising the composition and deposition rates of a range of urban air-pollutants to different forms of urban vegetation. Road-side plants and street trees will be examined in both the urban environment and under controlled conditions.

Particulate-matter air-pollution is responsible for approximately 50, 000 premature deaths each year in the UK and ranked the 13th leading cause of human mortality worldwide. Urban vegetation is a very effective way of filtering particulate pollution from the atmosphere so saving lives and money. Key to the effectiveness of this approach is identifying the best vegetation forms for specific environments.

This project will help identify the vegetation forms needed to optimise particulate pollution removal in urban environments. The project would suit a student with interests in sustainability, plants and air-pollution.

Improving the health benefits from greenhouse grown crops

Supervisor: Dr Mridula Chorpa

This project will investigate the effect changes in growth, harvest and storage conditions have on the shelf-life and nutritional content for selected greenhouse grown crops.

Dietary consumption of salads, fruits and vegetables have been linked to human health benefits by providing beneficial nutrients and antioxidant compounds. However, the nutrient content of such crops can change depending on growth and storage conditions. The aims of this project are to quantify the impacts different growing, harvest and storage conditions have on yield, antioxidant content and shelf life of selected greenhouse grown crops.

This project would suit a student with interests in plants, agronomy and nutrition.

Cell polarity during vascular ingression

Supervisor: Dr Frank Schubert

The blood supply of the central nervous system is provided by mesoderm-derived endothelial cells. These initially aggregate around the neural tube to form the perineural vascular plexus (PNVP), but eventually penetrate the basal lamina and ingress radially into the neural tube. Each angiogenic sprout is led by a specialised tip cell, followed by stalk cells. Previous work in the lab has described the process anatomically and has characterised the activity of matrix metalloproteinases. In contrast, little is known about the polarity of the PNVP, tip cells and stalk cells. The aim of this project is to study the location of apical or basal marker proteins during vascular ingression by immunofluorescence.

Axon guidance signals that organise the early axon scaffold in the vertebrate brain

Supervisor: Dr Frank Schubert

The first neurons that differentiate in the embryonic vertebrate brain establish an evolutionary conserved array of longitudinal, transversal and commissural axon tracts, the early axon scaffold. Despite the stereotypical arrangement of these tracts, little is known about the signals that underlie the guidance of the axons. We have characterised the expression of the main axon guidance molecules in the early brain, providing candidate genes for analysis. The aim of the project is to test the function of these genes in the guidance of early axons by in-ovo electroporation and loss-of-function approaches.

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.

Neuroendocrine disruption in crustaceans

Supervisors: Professor Alex Ford

Studies in our labs have recently found that antidepressants (SSRIs) can impact the behaviour of crustaceans at environmentally relevant concentrations. The aim of the study is to define whether exposure to SSRIs alters the serotonergic and dopaminergic activity in shrimp using immunohistochemistry.

Phylogeny of Antarctic coralline algae

Supervisor: Dr Jo Preston

The Corallinales, along with the Sporolithales (Corallinophycidae, Rhodophyta), is a red algal order characterized by the presence of Mg-calcite in their cell walls. This calcification capacity confers them a crucial ecological role by creating new habitats sand therefore increasing biodiversity.

However, coralline identification is complicated by phenotypic plasticity depending on environmental conditions as well as the need for decalcification prior to the observation of anatomical features.

The aim of this project is to create a phylogenetic tree of Antarctic coralline algae by combining morphological (histology, SEM) and genetic analysis.

The effects of antidepressants on embryonic development and adult behaviour in zebrafish

Supervisors: Professor Alex Ford and Dr Matt Parker

Antidepressants can be detected in aquatic ecosystems at concentrations believed to be causing harm to wildlife. This study aims to investigate the effects of fluoxetine on early embryonic development and adult behaviour using zebrafish as a model species.

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.

Protein engineering of lignin-active enzymes

Supervisor: Professor Simon Cragg

Lignin is a heterogeneous, aromatic biopolymer found in abundance in plant cell walls where it is used for defence, structure, and nutrient and water transport. Given its prevalence in plant tissues, lignin is the largest reservoir of renewable, aromatic carbon found in nature.

This project is part of a collaborative UK-US project with the goal of identifying and characterising novel enzymes that are active on lignin monomers. The potential is for the development on new pathways for converting lignin waste into valuable fine chemicals and biofuels. While our US colleagues are providing extensive molecular biology support, the Portsmouth team will focus on the characterisation of potential lignin-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, characterise, and optimise key enzymes that can transform this important resource.

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.

Predator-Prey interactions of the Oyster drill (Ocenebra erinacea) and assessment of implications for restoration of the native oyster Ostrea edulis

Supervisors: Dr Joanne Preston and Dr Luke Helmer (Blue Marine Foundation) 

Ocenebra erinaceus is a predatory gastropod native to European waters that is known to feed on a variety of bivalves, including the European flat oyster Ostrea edulis. As populations of O. edulis have decline predation levels of O. erinacea have become more apparent. This is coupled with the ban of Tributyltin (TBT) antifoulant paints that severely depleted populations of O. erinacea. Key and Davidson (1981) estimated that 30 million individual tingles were present within the Solent during 1976/77 oyster fishing season and Lockwood (1985) estimated that 60% of O. edulis mortalities within the Solent during the 1980s occurred as a result of tingle drilling activity. Predation of the Pacific oyster Crassostrea gigas has also recently been observed in the area. Alongside boat and intertidal work to conduct ecological surveys, a range of aquarium experiments will be performed. This MRes aims establish the preferred prey species to inform oyster restoration site selection based on predation pressure. This research will also determine the size preference for O. edulis prey to inform seabed deployment strategy as part of the wider Solent Oyster Restoration Project. 

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.

Unravelling metal resistance mechanisms in acidophiles used for biotechnology

Supervisor: Dr Carmen Falagan

Acidophiles are microorganisms found in extreme environments with pH < 3. They are used in biotechnological processes, such as bioleaching, for the extraction of metals. These microorganisms are exposed to high concentrations of metals, other cations (e.g. magnesium), and sulfates which are toxic for many other microorganisms found in the environment.

Metal resistance mechanisms in man-made environments, such as in bioleaching heap operations, remain largely unstudied. While metals such as cobalt and copper have attracted attention, other metals, like aluminium, have been overlooked.

Through bioinformatics, this project will focus on determining metal resistance mechanisms, with special focus on aluminium, in acidophiles (bacteria and archaea) used in column bioleaching experiments that mimic the conditions found in a bioleaching heap. This project will be mainly computer based and will use samples from bioleaching experiments collected during previous years. Additionally, some laboratory experiments may be run if proven of interest for the study.

Evolution of flight – investigating the microstructure and mechanics of bones using advanced X-ray imaging techniques

Supervisor: Dr Katherine Williams

Vertebrate evolution is driven and constrained by the ways in which animals can move. Flight, swimming, jumping, running; all are supported by highly specialised skeletal adaptations both in terms of macro and microstructure. The combination of structures at different scales is related to the strength of the bone, and also whether the bone is strongest when it is being compressed or is under tension or twisted. The type of loading varies with anatomical region and type of locomotion (e.g. bird wings twist during flight), but the relationship between bone microstructure and mechanical function in birds is not well studied.

In this project, the student will investigate how bone has adapted to flight in different modern avian bones. This will build understanding of the evolution of flight as well as provide data which will allow interpretation of fossil bones. This project will use 3D X-ray microscopy, and will likely involve a trip to the most advanced scientific facilities in the UK - Diamond Light Source synchrotron radiation facility. This project will be data intensive and will involve image analysis but will also provide the opportunity to carry out experiments.