DTP3 Cohort 3 Details
Supervisor: Dr Adam Wollman
Project title: New chemical and microscopy tools targeting the complement system in neuroinflammation
Project Description: Alzheimer’s is perhaps the most well-known cause of dementia and one of the leading causes of late-life disability and death, and in recent years increasing our understanding of the neuroinflammation caused by the disease has been discussed as a potential avenue to finding a cure. Neuroinflammation is caused by a chemical cascade within the body’s innate immune system and by developing our understanding of the molecules driving this cascade it may be possible to block inflammation at some point along the chain reaction. The protein C5 is a promising candidate as a target due to its role in the latter half of the cascade which would reduce the risk of unwanted consequences in the patient immune system such as increases in susceptibility to other diseases.
This project aims to new microscopy and chemical tools to target C5 and observe its impact on inflammation in human cells. A range of techniques will be explored to address the inherent multifaceted nature of this project ranging from the development of microscopy techniques and the computational image analysis it requires; to the use of chemical synthesis alongside neuro-cell biology to produce the chemical targeting systems.
Personal Background: I gained my BSc in Physics from Northumbria University, after which I pursued my MSc in Physics at the University of Leeds with a particular focus on Biophysics and nanoscale physics. During my MSc project, I investigated how the distribution of T-Cell receptors on the surface of Jurkat T-cells is influenced by the 3D topography of the cell membrane. Existing point cloud analysis techniques were explored, however, the production of a novel topography correlated point cloud analysis technique rooted in eigenvalue decomposition was required to fully explain receptor distribution in complex cell membrane topographies. This project allowed me to expand my skillset in a varied scientific environment and introduced me to the engaging field of interdisciplinary science.
Supervisor: Dr Simon Whitehall
Project title: Investigating light-activated therapeutic compounds as antifungal agents
Project Description: Fungal diseases are responsible for more than 1.5 million deaths and affect over a billion people worldwide. Systemic fungal infections are intrinsically difficult to treat as there are limited classes of antifungal drugs and resistance to these agents is increasing rapidly. As a result, there is an urgent need to develop new antifungal drugs. LightOx Ltd has developed a portfolio of small molecule light-activated cytotoxic compounds that are being evaluated in a range of therapeutic contexts. My CASE project will investigate the potential of these compounds as novel antifungal agents and will provide an opportunity to build a successful partnership between academic research labs in the Newcastle Fungal Group and a thriving biotechnology company. The activity of LightOx compounds against a range of fungal species, including the key human pathogens Candida albicans and Cryptococcus neoformans, will be determined. Functional analyses will then be used to identify and characterise modes of drug-uptake, molecular targets, and mechanisms of resistance.
Personal Background: I recently graduate from Newcastle University with a BSc in Biomedical Sciences, having completed my final-year research project within the Newcastle Fungal Group. My project focussed on the Mechanisms underlying stress resistance in the human fungal pathogen Candida albicans. Through my undergraduate degree, I have developed a key interest in fungi, an area which requires more extensive research due to a lack of antifungals available. I am excited to start my PhD project, which is a CASE collaboration with the biotechnology company LightOx, and should therefore provide the opportunity to gain valuable experience of an industrial environment and to be at the forefront of research.
Supervisor: Dr Satomi Miwa
Project title: Developing multi-level pipelines for senolytic discoveries
Project Description: Cellular senescence is identified as the irreversible cell-cycle arrest combined with secretion of pro-inflammatory cytokines and mitochondrial dysfunction. Accumulation of senescent cells has been shown to drive many age-associated conditions, such as osteoarthritis, cancer, Alzheimer disease, and chronic obstructive pulmonary disease (COPD). Due to this association, senolytics (drugs that specifically kill senescent cells) have been investigated. There are promising results that ablation of senescent cells improves health-outcomes. However, there are issues with side-effects, limited specificity and lack of drug administration plans. The aim of my project is to further advance a pipeline for discovery of novel senolytics and other anti-ageing drugs by developing multi-level testing platforms.
Personal Background: I recently gained my BSc and MRes in Medical and Molecular Biosciences from Newcastle University. During my undergraduate study I completed a professional placement year in which I investigated the effect of potential senolytic compounds on diseased cells and tissues. This is where my interest in senescence began and I discovered just how paramount senescent cells are in the development of many age-related diseases. Following this, I studied clinical and molecular ageing within my MRes to further my understanding. I am excited to start my PhD with Dr Satomi to combat senescent cells and improve health outcomes!
Supervisors: Dr Miguel De Lucas Torres, Dr Diarmuid O'Maoileidigh and Dr Ulrike Bechtold
Project title: Characterization of the molecular crosstalk regulating xylem differentiation by environmental signals and its function in photosynthesis optimisation
Project Description: The plant vascular system is composed by two conductive tissues, the xylem and the phloem. Xylem conducts water and minerals from the roots and provides mechanical support to the plant and phloem transports the carbohydrates produced via photosynthesis in the leaves. The formation of new layers of xylem and phloem cells is known as secondary growth, which is balanced by precise regulation of the cell division and differentiation occurring in the vascular cambium at its edges.
Light, photoperiod and temperature are the main environmental factors regulating vascular development in plants, how do they achieve this activity remains unclear. Previously our lab confirmed that vascular development is regulated by an environmentally controlled transcription factor network that modulates the activity of intrinsic signalling processes with function in cambium activity. This finding helped us to understand how vascular development is regulated under different environments, however further research is needed to fully understand the mechanism. To investigate this my PhD project aims to elucidate the molecular mechanisms integrating the environmental signals of light, temperature, photoperiod and sugar with xylem differentiation.
Personal Background: I completed my bachelors in Plant Biotechnology under the supervision of Dr. Sneh Sharma at College of Horticulture and Forestry, Neri, Hamirpur where I learned how plant tissue culture techniques can be effectively utilized for invitro propagation of papaya and pomegranate and how this technique is amazing in creating a complete plant from an explant. Later I went for pursuing masters at UAS, Dharwad, India where I studied how genetic variations in natural accessions govern different traits of plants and how these variations can be identified (as genes and QTLs on chromosomes) and utilized in crop improvement programmes using marker-assisted breeding approach. From October 2022, I am going to start my doctoral studies at Durham University, UK under the supervision of Dr. Miguel de Lucas where I will be exploring the role of Phytochrome-Interacting Factors (a bHLH family of transcription factors) in plant growth and development under different environmental cues.
Research group link: https://mdelucas.com/
Supervisor: Dr. Sarah Rice
Project title: Applying a novel PROTAC technology in stem cells to elucidate the regulatory role of transcription factors in cartilage ageing
Project Description: Transcription factors are small proteins, essential for the initiation of gene transcription during development and throughout the life course. Cartilage development and homeostasis is dependent upon the stringent regulation of multiple transcription factors in a highly ordered pattern. Increased expression of catabolic transcription factors can result in cartilage breakdown in older age, and the development of degenerative diseases, most commonly osteoarthritis. Therefore, the identification and targeted elimination of these catabolic transcription factors could be used to promote healthy ageing of the musculoskeletal system. As transcription factors lack catalytic active sites, small molecule inhibitors fail to target this special class of DNA binding proteins. In this research project, for the very first time, we will utilize Transcription Factor Targeting Chimeras (TRAFTACs) for the targeted proteasomal degradation of catabolic transcription factors in aged chondrocytes, and use a multi-omics approach to assess the impact on cell phenotype, along with histological analysis.
Personal Background: I have pursued Bachelor's Degree in Dental Surgery, from India. After completing my undergraduate degree, I was recruited as a dental surgeon on a contractual period of eighteen months, in government hospital. During this tenure, I had dealt with several cases of bone degenerative diseases, affecting the mandible. These exposures gradually developed my interest towards bone regeneration, and motivated me to pursue higher studies in the field of regenerative medicine. I completed my MSc in Stem Cell Engineering for Regenerative Medicine, from University of Glasgow. To gain further lab experience, I worked as a Lab Scientist in Lighthouse Lab, in Glasgow, for a tenure of six months. However, my ultimate aim to become a researcher in regenerative medicine and actively participate in upgradation of medical science, encouraged me to farther my career in higher studies via pursuing PhD. My PhD research deals with a very promising subject "TRAFTACs". I believe that, mastering the regulation of transcription factors via specially designed TRAFTACs, will enable us to find remedy for several untreatable degenerative diseases, including osteoarthritis (our prime target).
Supervisor: Dr Elizabeth Veal
Project title: Establishing new redox-signalling mechanisms as a therapeutic target to prevent age-associated diseases
Project Description: Reactive oxygen species (ROS) cause cell damage that is a major contributor to many age-associated diseases. However, low levels of ROS have been shown to have important signalling functions - initiating protective responses that maintain cell viability and organism health. Despite the increasing evidence that localised ROS increases can be beneficial, the mechanisms by which these ROS signals are transduced to protect against age-associated disease remain poorly understood.
Several signalling proteins with important roles in health and disease have been identified as candidate ROS targets. The aim of this project is to investigate how ROS-induced oxidation of cysteine residues in these signalling proteins contribute to the positive effects of ROS in both cell and Caenorhabditis elegans models, using a range of molecular techniques including genome editing, RNAi, confocal microscopy and proteomics. By elucidating new signalling mechanisms that mediate effects of ROS and metabolism, this project will provide an essential step towards the goal of therapeutically enhancing ROS-induced protective responses to counter the effects of ageing.
Personal Background: I gained my BSc (Hons) Biomedical Sciences degree from Newcastle University. During my degree I completed a summer internship investigating the epigenetic control of chromatin remodelling and its effects on protein degradation and cell viability in yeast. It was this internship that made me want to continue in research, so I completed an MSc in microbiology at Teesside University where I investigated protein mechanisms in the parasitic organism Microsporidia. I then decided to spend a year at Fujifilm Diosynth Biotechnologies, helping with the production of life-changing medicines including the COVID-19 vaccine. Now, I am excited to be returning to academia for my PhD to work with proteins and cell signalling again and to build on my knowledge and skills.
Supervisor: Dr Elisabeth Lowe
Project title: Assigning activity to proteins of unknown function – enzyme discovery in the gut microbiota
Project Description: An important aspect of living in complex microbial community, such as that of the gut microbiota, is the competition amongst strains for resources. For carbohydrates, this can include dietary sources, host-derived molecules or materials derived from other microbes. Previous work in my supervisor’s lab identified genes and proteins associated with the degradation of microbial cell wall glycans by the human gut microbiota. However, many of these proteins have no information about their potential function and they have yet to be characterised, yet the genetic context in which these enzymes are found suggests differences in specificity and target sugars. Therefore, the aim of my project is to undertake biochemical and structural characterisation of these unstudied proteins, predominantly focusing on a new structural family of glycoside hydrolases, active on glycans from bacterial cell walls, with homologs in both commensal bacteria and pathogens such as Enterococcus faecium. Through implementation of protein biochemistry, glycobiology, and X-ray crystallography, these new enzymes will be characterised, and bacterial genetic manipulation will explore the enzymes role in bacterial physiology. Furthermore, bioinformatics will assess structure/function relationships and develop predictions of substrate specificity for homologs of the enzyme family in the microbiota. Lastly, chemical glycobiology techniques will help to characterise enzyme substrates. Ultimately, an understanding of the genetic and biochemical basis of these enzymes could allow manipulation of gut microbiota to benefit host health.
Personal Background: In 2018, I received my BSc Hons in Microbiology from the University of Dundee. During my BSc I was introduced into a research lab, where I worked for 2 summers, the first funded by the James Black Award and then the second funded by the SfAM student into work grant. After gaining my BSc, I decided to take time out of science to progress skills in communication as well as reacquiring hobbies I had forgotten about during my degree. After 18 months, I continued to crave research, so I looked into moving out of Scotland and re-enter science by undertaking an MSci in Microbiology and Infection at the University of Birmingham in 2021. The experiences, opportunities and skills I have gained throughout my BSc and MSci provided by the many researchers, supervisors, post-docs and PhD students, has fuelled my excitement into learning more about bacterial proteins, how these nanomachines function and how we can manipulate these structures for our own benefit.
University of Liverpool
Supervisors: Dr. Marcus Blagrove, Dr. Olena Riabinina, Prof Matthew Baylis
Project title: A conflict of interests: How do viruses manipulate their mosquito-vector to increase their own transmission?
Project Description: Mosquitoes can be hosts for several different pathogens such as Zika virus, West Nile virus, and dengue virus. Hosts and their pathogens are often in conflict for their optimal survival strategy. Because of this some pathogens have evolved ways to manipulate their hosts behaviour. In this project we will investigate how, and to what extent, viruses can manipulate the temperature preference of their mosquito-vector to increase their own transmission. The results of this investigation will be used to create mosquito-behaviour-aware risk models that can determine if areas that are generally considered too cold for transmission could still be at risk if mosquitoes were to find environmental hotspots. We will infect mosquitoes in the lab and perform behavioural experiments to assess the effects of viral infection on temperature preference. Additionally, we will use RNAi and physical manipulation to isolate the molecular pathways involved in temperature sensing and temperature preference.
Personal Background: I graduated from Wageningen University and Research (the Netherlands) with a BSc and MSc in Biology focussed on human and animal health. During my studies I worked on two large research projects. The first was on the prevalence of a mosquito-associated narnavirus in the Asian bush mosquito, Aedes japonicus. In the second project I studied the distribution and overwintering site choice of mosquitoes of the Anopheles maculipennis complex in the Netherlands. This project was a part of the Dutch citizen science project ‘Muggenradar’.
After graduating I continued my work related to mosquitoes and citizen science as a research assistant in the One Health Entomology group at Wageningen University. I look forward to continuing my work with mosquitoes in this PhD project and hope that we can contribute novel insights into the control of mosquito-borne diseases.
University of Liverpool
Supervisors: Dr Manolis Papamichos Chronakis, Prof D Elliott, Dr A Kanhere
Project title: Investigating the role of chromatin in regulation of co-transcriptional RNA quality control
Project Description: Transcription, the first step in gene expression, underpins life. Elimination of aberrant transcripts is vital for proper gene expression and of paramount importance to cellular homeostasis. In eukaryotes, nuclear RNA surveillance and quality control mechanisms monitor mRNA biogenesis co-transcriptionally and terminate transcription by RNA Polymerase II prematurely for degradation of the nascent RNA transcript. While the RNA degradation pathway has been characterized in molecular detail, the mechanisms regulating abortion of transcription are poorly understood. It is also unclear whether this process is conserved across eukaryotes. These knowledge gaps will be investigated in this project. Epigenetic and chromatin regulation is essential for health and development, while dysregulated epigenome contributes to human disease. However, our mechanistic understanding of the role of chromatin in gene expression remains critically limited. By investigating the unexpected role of chromatin in RNA quality control, this project explores novel concepts in gene regulation, with the potential of creating innovative approaches in clinical intervention.
Personal Background: I completed my BSc in Medical Biology and an MRes in Molecular Medicine at Bangor University, funded through North West Cancer Research. Following this, I worked as a Senior Scientist at an NHS diagnostic laboratory as part of the Test and Trace network. This gave me invaluable experience as both a scientist and as a team leader, however I had the desire to return to research and further explore the mechanisms responsible for genetic instability. I will use the professional and scientific skills I developed during my employment within my project to complete impactful research in a field that is important to myself, and many patients.
I am excited to complete this multi-disciplinary project as part of a talented and enthusiastic laboratory group to explore the roles of Chromatin in the regulation of transcription and RNA-quality control.
Supervisor: Professor Tracy Palmer
Project title: Characterisation of a novel protein toxin family in the animal and human pathogen Staphylococcus aureus
Project Description: The type VII secretion system (T7SS), found in Firmicutes such as Staphylococcus spp. and Actinobacteria such as Mycobacteria spp., is used to secrete effector proteins including toxins. Recently, in the human and livestock pathogen Staphylococcus aureus, new T7SS substrates have been identified with likely antibacterial function. These toxin genes often appear alongside those which encode for specific immunity proteins, which form complexes to protect against self-intoxication. Additionally, the discovery of widespread T7SS immunity genes within strains lacking the toxins themselves points to this likely antibacterial function, and a dynamic interbacterial evolutionary arms-race involving novel toxins and immunity defences. My project is to investigate two novel putative toxins within S. aureus, with aims to elucidate their structure through X-ray crystallography and their function through toxicity assays. Bioinformatics analysis supplementing this should reveal more about the distribution and variety of these novel putative toxins and their evolution. Overall, the aim of this project is to further expand on the understanding of the T7SS in Staphylococcus and the role of type VII secreted toxins in interbacterial competition.
Personal Background: I graduated from the University of York with an Integrated Master's in Biochemistry. My fourth-year project involved exploring the diversity of a previously poorly-characterised bacterial enzyme family and cemented my interest in bacterial genetics. I have also always enjoyed structural biology, and look forward to combining bioinformatics with structural and conventional microbiology methods in this project investigating novel toxins.
University of Liverpool
Supervisors: Prof. Warwick Dunn, Dr Howbeer Muhamad Ali, Dr Christopher Stewart
Project title: Modelling metabolism in the human gut to understand inter-tissue metabolism during ageing
Project Description: The gut microbiome is one of the most important biological drivers of how we process foods including the release of nutrients and other small biochemicals required by the human body. This gut microbiome is the collection of many different microbial species present in our intestines which have many roles including regulating immune responses, providing a protective film over gut epithelial cells, and metabolizing food components into usable metabolites for our bodies. Importantly, metabolites synthesized by the gut microbiota can be unique (are not synthesized elsewhere in the human body), are transported to many tissues (brain, liver, muscle as examples), and can have beneficial or detrimental effects on human function and health and dysfunction can lead to the development of diseases. My project will integrate different research tools to understand which metabolites are synthesized and how these metabolites are influenced by aging in humans and other mammals. This will include measuring and reporting concentrations for metabolites and then applying this assay to study metabolic changes in the microbiome related to age as well as health and disease.
Personal Background: The vast, limitless, and alive science called life sciences leads me to know about live beings ranging from micro-organisms in the deep ocean to humans on the land and understanding molecular reactions in them; moreover, life sciences helps me to know the beautiful, amazing nature and the surroundings in which we live. Therefore, without any extra explanation, it is explicit why I am interested in this science. Since the micro-organisms’ world is the most interesting area of life sciences to me, I decided to fulfil my B.Sc. degree in cell and molecular biology-microbiology at the University of Tehran (UT), Iran. During my bachelor's studies, I liked to know how viral vectors can be beneficial for treating different diseases; hence, I carried out a review study on viral vectors' application in gene therapy for Cystic Fibrosis treatment for my thesis. I pursued my master's studies in microbiology at Shahid Beheshti University (SBU), Tehran, Iran. My passion for microbiology, human gut microbiota-as we are more microbes than human, and molecular microbiology stimulated me to research H. pylori genetics for my thesis. H. pylori is an amazing bacterium, living in the gastric of more than 50 percent of people in the world either as a pathogen or symbiotic. My master’s project aimed at investigating the existence of various H. pylori colonies with different genetic content in a single host, which could relate to the pathogenicity response of the bacteria to their host. I am very interested in human-microbiota interactions, metabolomics, human gut microbiota, and their metabolites; therefore, my upcoming project on modelling metabolism in the human gut to understand inter-tissue metabolism during ageing will fulfil my desire.
Congriev Kumar Kabiraj
University of Liverpool
Supervisor: Dr Kannan Ganapathy
Project title: Development and evaluation of lateral-flow test for rapid detection of Mycoplasma gallisepticum and Mycoplasma synoviae in poultry clinical samples
Project Description: The UK chicken poultry industry loses millions of eggs and hundreds of tons of meat due to Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS). These pathogens cause respiratory, reproductive and musculoskeletal infections, resulting in illnesses, increased medication costs and drops in egg production. To date, for MG and MS, there are no pen-side rapid diagnostic lateral flow (LF) tests available, for either antibody or antigen detection.
Therefore, the PhD research focuses on developing and evaluating a lateral flow test for MG and MS antibody or antigen detections in poultry clinical samples. Single and dual detection LF devices will be developed and validated using laboratory and clinical samples.
The objectives to be achieved include (1) synthesis, purification and characterization of recombinant proteins of MG and MS, (2) production and purification of monoclonal antibodies against mgc2 and vlhA surface proteins of MG and MS respectively, (3) development of procedures for practical running of LF device, including nitrocellulose strip preparation, colloidal-gold conjugation with specific antibodies, and optimization (4) samples of blood/sera and swabs from a) experimentally infected birds, b) field (farm) infections, (5) standardization of the assay for field use. At each stage, ‘sonicated’ whole antigen proteins will be used for comparison.
Personal Background: I have completed my DVM (Doctor of Veterinary Medicine) and MS in Pathology from Bangladesh Agricultural University (BAU). Currently, I am working as a faculty here at BAU. I conducted my MS thesis work in the field of poultry viral disease. I was actively involved in research projects addressing the experimental pathogenesis and molecular epidemiology of important viral diseases of poultry. These projects have opened my eyes to a broad range of research in poultry pathogens and motivated me to undertake further study through a PhD program. In the future, I look forward to incorporating my current understanding and expertise into a relevant field and developing multi-disciplinary research skills and knowledge. After having opportunities to conduct several pieces of research in this field, I aim to advance my research expertise by pursuing a PhD degree.
University of Liverpool
Supervisor: Dr Jennifer Duncan
Project title: Preventing contagious ovine digital dermatitis: Characterisation of bacterial pathogens and development of disease control measures to prevent transmission in sheep
Project Description: Contagious ovine digital dermatitis (CODD) is a severe cause of sheep lameness. It affects approximately half of UK sheep flocks, and is emerging globally. Due to its’ severity, CODD has a substantial and highly visible impact on sheep welfare. The economic consequences and high levels of antibiotic use associated with disease control negatively affect sustainability. CODD is considered to be a highly important endemic disease for the livestock industry, with improved understanding of disease transmission and prevention methods being top priority for research.
Our project aims to inform and devise biosecurity protocols for prevention of between and within farm transmission of CODD. Our first objective will be the field validation of the evidence from previous experimental studies, which demonstrated that CODD occurs as a result of superinfection of pre-existing footrot lesions, with a plethora of laboratory methods employed to compare samples from field cases of CODD and footrot. We will also aim to investigate the possible link between CODD and bovine digital dermatitis (BDD) treponemes and whether inter-species transmission was the cause of the emergence of CODD in farms. We will do so by conducting whole genome typing of the treponeme isolates from farms affected by both BDD and CODD and we will also investigate their bacterial diversity and virulence factors. Our third objective will be the improvement of biosecurity protocols that currently seem inadequate. We will conduct farm RCT trials to investigate the efficacy of disinfection protocols for the elimination of the CODD pathogens from sheep’s feet. These protocols will be based on evidence gathered from the current study and pilot in vivo and in vitro efficacy data. Clinical examination, bacterial culture and qPCR will also be used to assess efficacy.
Personal Background: I graduated as a Doctor of Veterinary Medicine from the Aristotle University of Thessaloniki in Greece. While I was an undergraduate student, I had joined the University of Liverpool’s Livestock and One Health Department as a Research Assistant, through an Erasmus+ Placement. In this capacity, I worked on research regarding cattle hoof health and genomics and, more specifically, I was involved in a project exploring the use of non-steroidal anti-inflammatory drugs for the treatment of Bovine Digital Dermatitis. My experience working at the UoL solidified my passion for research and directed my focus towards the importance of hoof health and the negative impact of lameness on animals in production. After furthering my experience both as a research assistant and as a clinical veterinarian for the last couple of years, I decided to pursue a PhD and focus on veterinary research. I am excited to be part of this PhD project as I believe it will greatly improve our understanding of the aetiopathogenesis of CODD and through that allow us to propose effective disease prevention and control protocols that have the potential of great impact in the sheep farming industry.
Supervisor: Prof Heather Knight
Project title: Understanding the role of the novel gene, SENSITIVE-TO-FREEZING10 (SFR10), in integrating freezing and light acclimation in plants
Project Description: Climate change projections indicate an increase in freezing events in late spring and early autumn. These are periods when plants are unprepared for tolerating such temperatures and may result in the injury of sensitive crops with a knock-on damage to food production. The mitigation of these losses is crucial in the fight to achieve global food security as food production demands continue to rise alongside an increasing population. Another key point to tackle is the inefficient photosynthetic productivity of many (C3) crop plants as this is essential to increasing food production. High light acclimation results in an increased capacity for a plant to photosynthesise under the overabundance of light. This process has been closely linked to cold acclimation, thus freezing tolerance.
SENSITIVE-TO-FREEZING10 (SFR10) is a novel gene encoding a protein involved in the freezing tolerance of plants and the regulation of the expenditure of their photosynthetic energy. Under this project the roles of SFR10 will be identified and their underlying mechanisms unveiled, using the model plant Arabidopsis thaliana and the crop oilseed rape. Findings will ultimately build towards the engineering of improved freezing tolerance and photosynthetic productivity in crops, aiding to mitigate the impact of late spring and early autumn freezing events as well as working towards global food security.
Personal Background: I am a Botany PhD candidate at the University of Durham having freshly graduated with a Master’s degree in Plant Sciences from the University of Dundee. My interests focus on crop improvement and using the power of plants to aid in tackling global issues such as food insecurities and climate change. In particular, I am passionate about working towards producing climate resilient crops which my current project will aim to build understanding towards. My interest in tackling global issues is further reflected under my previous project with the McKim lab at the James Hutton Institute which centred on understanding the underlying genetic and molecular mechanisms of barley architecture (or “shape”) for potential agricultural harnessing. I also have great enthusiasm for science communication which I consider to be one of the most important aspects of modern-day science, having worked at the Edinburgh Science Festival, as well as having written my Honour’s thesis on a self-created science communication activity centring around factors impacting plant diseases and their controls. Aside from my interest in scientific research, I am also an aspiring teacher who hopes to be able to pass on their knowledge to aid future generations.
University of Liverpool
Supervisor: Prof William Paxton
Project title: Development of sensitive molecular viral assays to screen anti-SARS-CoV-2 formulations
Project Description: The aim of the project is to develop novel assays to monitor the anti-SARS-CoV-2 activity of newly developed products. The recent COVID-19 pandemic has highlighted the necessity to specifically develop products with the capacity to neutralise or destroy SARS-CoV-2, the causative virus of the disease. New products would typically be tested using live replication competent virus and assays able to monitor reduction in virus infection and/or replication. We will utilise pseudo-typed viral particles to monitor viral infection and interactions with cells. These non-replicative particles will enable development of assays that eliminate the requirement to test new products using replicative virus, thereby minimising laboratory CL3 capacity and cost. For translation to industrial high through-put screening of formulations this is essential. This can be used as means of quantifying antiviral activity through use of fluorescently labelled viral particles or assays which are tagged with easily identifiable DNA/RNA molecular probes for monitoring their structural integrity or infectivity.
Supervisor: Prof Giles Budge
Project title: Understanding the biological mechanisms underpinning the virulence of Varroa destructor to the European honey bee (Apis mellifera)
Project Description: Insect pollinators are necessary for the reproductive success of 88% of flowering plants globally. Managed Western honey bees (Apis mellifera) offer mobile pollination services to complement wild pollinators and contribute to this ecosystem service. Regional declines of honey bee populations have been reported in the face of multiple interacting pressures that include land-use intensification, agrochemical exposure and the impact of parasites/pathogens.
The ectoparasitic mite Varroa destructor moved from its native host, the Asian honey bee (Apis cerana), onto A. mellifera causing the severe disease Varroosis. The mite is benign to its native host, and yet had led to the loss of millions of A. mellifera colonies worldwide. This project will work with beekeepers as an iCASE partner to better understand the mechanisms behind the extreme virulence of V. destructor on A. mellifera. These include manipulating sex ratios in honey bee colonies to influence mite cell invasion strategies, and investigating the relationship between the ability of mites to carry and transmit the RNA virus called deformed wing virus (DWV) and their gut symbionts.
Supervisor: Prof. Ari Sadanandom
Project title: Novel insect-derived biofertilizers for the sustainable protection of crops against insect attack
Project Description: This project is designed to discover the molecular pathways that lead to defence priming when Arabidopsis plants are treated with insect frass-derived biofertilizers. RNA-Seq analysis will generate a list of target genes that show differential gene expression that we can identify as being key to defence against attack by insect pests and fungal pathogens in Arabidopsis. The project will employ a multidisciplinary approach involving molecular genetics, gene silencing, next-generation sequencing, computational biology and biochemistry to dissect the molecular mechanisms that mediate plant immune responses against pests and pathogens to ascertain if this molecular pathway is triggered by priming agents in insect frass.
Personal Background: I have a BSc in Horticulture from Huazhong Agricultural University in China, where I had my bachelor thesis focused on creating the genetically modified anthocyanin-rich tomato plant. During my bachelor’s study, I had a chance to work as a research assistant at Plant and Food Research in New Zealand, participating in the plant-virus-insect interaction program and gaining experience in host plant resistance towards grapevine leafroll-associated virus 3 (GLRaV-3) which is transmitted by Citrophilus mealybugs. For my master’s degree at Wageningen University in the Netherlands, I studied Plant Science with a specialization in Plant pathology and entomology, and my thesis research focused on fall armyworm and beet armyworm host susceptibility towards specific baculovirus isolate for selecting potential viral biocontrol agents. My past research experience ignited my passion for insect/plant-related research. I am excited about the potential improvement the insect products, which are used as biofertilizers, can bring to the world, especially to countries that have suffered substantial food losses and economic damage because of the infestations of pests.
Supervisor: Dr Olena Riabinina
Project title: Neuronal basis of pheromone perception in mosquitoes
Project Description: Malaria is a mosquito-borne disease that affects half of the world population. With the increase of insecticides resistance and malaria incidences, the fight against malaria has stalled. Therefore, new strategies are required to make further progress. Previous investigations identified 17 sex-specific volatile chemical compounds that are detected by Anopheles gambiae. Understanding the basis of this sexual communication will aid to disrupt mosquitoes mating and spread. The project also aims to identify the olfactory receptor and cells that sense pheromone candidates. And investigate-mediated behaviours in A.gambiae using the identified pheromones.
Personal Background: I undertook my MBiol in Biosciences at Durham University working on bumblebee brains and investigating the dimorphism of the olfactory organ that processes odours and conspecific pheromones between the different species of Bombus around Durham,UK, which I was able to poster present the results at the FENS 2022 conferences in Paris, France. Through my previous summer studentship and MBiol project, I have come to enjoy the lab environment and mentor other research student and as a BNA scholar I was able to enjoy the opportunities given such as funding my first international conference.
LinkedIn - www.linkedin.com/in/iman-muktar-a47032197
University of Liverpool
Supervisor: Dr Malcolm Horsburgh
Project title: Abiotic and biotic effectors of colonisation in the skin microbiome
Project Description: The human skin microbiome represents a complex interconnected network of microorganisms such as bacteria, fungi, and viruses. The main function of the skin microbiome is to ensure skin homeostasis through competitive exclusion of pathogenic microorganisms and prevent infection. Each Individual’s skin microbiome varies dependent on environmental and host factors such as bodily location, diet, gender, and use of cosmetics. One particular genus of bacteria associated with the skin microbiome is Staphylococcus, with over 12 species found within different skin microbiome communities each displaying distinct distributions and frequencies. These Staphylococci species are particularly associated with communities following application of personal care products such as moisturizers and deodorants. However, the relationship between Staphylococci and the wider skin microbiome are not fully characterised in particular their competition with other resident microorganisms for nutrients.
My PhD will focus on the use of genomic and metabolomic techniques to identify abiotic and biotic effector compounds that stabilise or destabilise human skin microbial communities. Particularly, this project will focus on Staphylococcus species and their competitive relationship with other microbial species and compounds associated with survival and success.
Personal Background: I received my BSc in Microbiology from the University of Liverpool where I developed a fundamental understanding and appreciation for biological science. My initial scientific interests were focused on viral and bacterial pathogenesis leading to me gain employment as an associate practitioner within the NHS where I carried out SARS-CoV-2 community testing. To further develop my research skills, I recently completed an MRes in Clinical Sciences following a Clinical Infection and Global Health pathway at the University of Liverpool. Here, I carried out several projects such an investigation into the entry mechanics of SARS-CoV-2 in human myoblast cells using a pseudotyped viral particle system. My research interests have now shifted towards the establishment of the native microbiome and its role relation to infection defence and host interactions. I am very excited to join an interdisciplinary team of established scientists to carry out meaningful research and develop my practical skills and theoretical knowledge.
Supervisor: Dr John Bothwell
Project title: Taking Aim: Substrate Specificity in the Sulfotransferases
Project Description: Carbohydrates are the most abundant biomolecule on the planet, representing approximately two-thirds of Earths biomass. They serve a wide range of biological functions including structural roles, energy metabolism and cell signalling. This versatility owes to their structural diversity, which is further expanded by modifications such as methylation and sulfonation. However, these modifications remain only poorly understood, with a particular challenge being how the enzymes that catalyse this modification recognise their specific carbohydrate substrates.
The focus of my project will be on carbohydrate sulfotransferases, which in addition to being important enzymes in themselves also provide excellent models for understanding carbohydrate modifications in general. By using a combination of structural, biochemical and molecular techniques I aim to characterise the specificity of a number of sulfotransferases and elucidate their structure-function relationship, which in turn will provide insights into how an enzyme family evolves to take on a range of different substrates.
Personal Background: I always loved learning about biology in school, but felt I would never be smart enough to become a scientist and ended up choosing A-levels that I did not enjoy at all. I eventually dropped out, and it wasn't until a few years later that I finally built the confidence to go back to college. I finished an Access to Science HE Diploma in 2018 which is easily the best decision I have made in my life. I went on to complete an undergraduate degree in biochemistry at the University of Essex, during which time I did a protein bioinformatics project based on the structure of a lytic polysaccharide monooxygenase, where I developed an interest the structure-function relationship between enzymes and substrates. I then went on to do an MRes in structural biology at Imperial College which included a 4-month project on protein kinase inhibitors at the Francis Crick Institute. This PhD will help further expand my skills and knowledge which will allow me to tackle a wide range of research questions in the future.
University of Liverpool
Supervisor: Dr Peter Walley
Project title: Characterising the genetic control of quality attributes in Pak Choi Brassica rapa subsp. Chinensis (L.).
Project Description: This new project sets out to develop a molecular breeding pipeline for Pak Choi improvement, focusing on morphological traits key to varietal development and organoleptic quality
1. A molecular definition of assembled resources
CN Seeds have a large collection of Pak Choi germplasm used in their breeding programme. For this new project, we will supplement these resources with assembled B. rapa/ Pak Choi core collections and publicly available bi-parental populations held at JIC and Wageningen University. The first phase of this ICASE award will employ high-throughput Genotype-By-Sequencing to generate high-density genotype data aligned with the latest B. rapa genome assembly. These data will be used to explore population sub-structure and relationships between individuals, to establish a new phylogeny-based description of the genetic resources. Haplotypes will be defined across new and existing germplasm, providing a means to track introgressed segments, speed up creation of advanced backcross lines, and provide a means to define intellectual property within the company’s portfolio.
2. Developing a pipeline for enhanced breeding
The assembled germplasm will be characterised for morphological traits key to varietal development and organoleptic quality, e.g., agronomic characters: plant shape, bolting habit (flowering time), stem cracking (base), suppleness; leaf quality: colour, wilting; post-harvest leaf yellowing. Mean phenotype data for these traits will be combined with new GBS SNP data to dissect the genetic regulation of these traits, define available allelic variation. These data will enable the efficient selection of germplasm and establish a new molecular breeding platform at CN Seeds.
Personal Background: During my undergraduate degree at the University of Liverpool I gained an interest in crop genetic improvement sparked by a lecture given by my now supervisor Dr Peter Walley. I then completed my undergraduate project in CAM photosynthesis and a summer internship looking at floral organ photosynthesis. This then enabled me to move to an MRes project studying the genetic control of senescence within Kale lines. I'm excited to start my PhD and continue working in an area I am passionate about!
Supervisor: Dr Tim Blower
Project title: Harnessing promiscuous DNA-modification dependent enzymes used in phage defence
Project Description: My project will investigate the continuing attack and counter-attack between bacteriophage and bacteria. Phages outnumber bacteria by ten to one, and this selection pressure has led to the evolution of phage-resistance systems that protect bacteria from phage predation. The highly promiscuous and recently characterised restriction enzyme BrxU is able to recognise multiple different DNA modifications and use any nucleotide, together with a wide selection of metals, to cleave modified DNA. The aim of this project is to understand the mechanisms of BrxU by exploring how these ligands are used, how modification recognition leads to cleavage and how phage protein inhibitors of the BrxU family interact with BrxU.
The research will also explore the biotechnological potential of BrxU enzymes due to their ability to recognise cytosine DNA modifications that are present in up to 4% of the human genome. These epigenetic markers have roles in developmental processes, pluripotency of stem cells, neurodegenerative diseases and tumourigenesis. BrxU could therefore be used to map DNA modification sites and provide a platform to better understand the role of epigenetic markers in developmental and disease processes.
Personal Background: I graduated from Durham University in 2021 with an MBiol in Bioscience. My final year project investigated novel mechanisms to target the huanglongbing disease-spreading psyllid in collaboration with the Pre-HLB project. In the last year, I have been working as a laboratory technician at Durham University where I designed and produced recombinant spider-venom-based fusion proteins with the aim of developing environmentally friendly biopesticides.
University of Liverpool
Supervisor: Dr Nick Evans
Project title: Dissecting the bacteriophage:treponeme interactions to develop novel therapeutics for bovine digital dermatitis
Project Description: Bovine digital dermatitis (BDD) is a severe, infectious, foot skin disease affecting cattle worldwide. This disease causes severe pain resulting in ruminant lameness and impacting animal welfare. BDD results in reduced milk yield and poor reproductive performance which equates to costing the UK dairy industry alone a substantial £74 million/year. Anaerobic, spiral microorganisms of the genus Treponema are considered causal of BDD. There remains no comprehensive, efficacious treatment for BDD and stewardship issues abound over antibiotic use, whilst use of heavy metal or formalin footbathing are environmentally damaging and carcinogenic respectively. This project sets out to identify and characterise both lysogenic and obligately lytic bacteriophage of treponemes and their interaction with these bacteria as they represent potential therapeutic/control agents.
Personal Background: I qualified in 2009 and worked in mixed, small and farm animal practice before undertaking a residency at the University of Liverpool and have recently become a European diplomate in Bovine Health Management
University of Liverpool
Supervisor: Dr James Hartwell
Project title: Molecular mechanisms underlying the optimised circadian clock control of Crassulacean acid metabolism and the associated optimisation of plant water-use efficiency.
Project Description: The world is getting hotter and drier due to climate change and the human population is growing rapidly to the extent that it has been predicted that we will need to increase crop yields by 50 - 70 % by 2050 in order to feed the predicted 9 - 10 billion people. Our research aims to leverage a naturally occurring super-charged adaptation of photosynthesis called Crassulacean acid metabolism (CAM). This adaptation can enhance plant water use efficiency well beyond that of any of today's major food crop species such as rice, wheat or maize. Through decoding the genomes and transcriptomes of model CAM species in the genus Kalanchoë and undertaking functional genomics research to investigate the function of candidate CAM genes, our work is establishing the minimal parts list for engineering CAM into C3 crops to enhance water use efficiency and photosynthesis. This project will leverage our recent discoveries by exploring the genes involved in CAM using transgenic approaches to switch genes off or on, and/ or explore gene regulation using reporter gene constructs. In particular, we seek to understand how the endogenous circadian clock (the internal timekeeper that organisms use to optimise their biochemistry relative to the daily light/ dark cycle) signals to the CAM system in order to optimize the steps that occur separately both in the dark and the light.
Personal Background: I completed a BSc in genetics at the University of Liverpool, during which I became particularly interested in plant genetics, before working as an analyst at a pharmaceutical consultancy. Subsequently, I returned to Liverpool in order to complete an MRes in advanced biological sciences, where I had the opportunity to study the regulation of CAM and the circadian clock by putative gene promoters. I’m greatly looking forward to starting my PhD and enjoy climbing, swimming and playing chess in my free time.
University of Liverpool
Supervisor: Dr Hannah Rose Vineer
Project title: Climate-sick reindeer: developing model-based decision support tools to inform veterinary interventions for brainworm in managed reindeer
Project Description: Reindeer herding is central to indigenous Sami culture, identity, and food security. Sustainable herding practices with high levels of animal welfare require up to date knowledge about disease and changing disease risk throughout the year. The nomadic transhumance movement of herds between seasonal grazing areas exposes them to a potentially wide range of pathogens. Some, including the parasite Elaphostrongylus rangiferi (brainworm, causing elaphostrongylosis), are closely linked to climatic factors including temperature and precipitation. Under the right climatic conditions explosive development of infectious larvae in the snail intermediate hosts can result in large disease outbreaks in reindeer.
Outbreaks associated with warmer weather have had a devastating impact on some reindeer herds in recent years and the herders need advice on treatment and on alternative strategies to prevent future outbreaks. Treatment options are limited and time-sensitive – once clinical signs are seen, it is too late. Models that predict exposure of reindeer to infection could allow herders to identify the optimum timing of treatment, movement to new pasture to avoid infection, or altered slaughtering strategies, thus reducing the risk and impact of outbreaks significantly. Such a model would give the Sami herders a much-needed tool to help mitigate a negative impact of climate change on traditional reindeer herding practices and food security.
Personal Background: I have a BSc in Mathematics from the University of Birmingham. During my undergraduate studies I developed a particular interest in mathematical modelling, especially applied to topics in ecology and biology. This interest led me to study for an MSc in Mathematical Modelling (Biology and Medicine) at the University of Exeter, where I had the opportunity to learn more about using mathematics to represent a range of biological systems. I am very interested in population ecology, disease modelling and the impacts of climate change, so I am really pleased to be able to explore all of these interests and learn new skills through this PhD project. It is great to be a part of interdisciplinary research in to managing the impacts of Elaphostrongylus rangiferi.
University of Liverpool
Supervisors: Dr Jude Curran, Prof Eann Patterson
Project title: Interaction of bacteria with cellular and hard surfaces
Project Description: Hygiene from personal care and home care products is a vital consumer benefit and is key to control transmission of communicable diseases in a home setting. There are few technologies that work by preventing the adhesion of bacteria by physical means and thereby blocking initial biofilms and slow bacteria colonisation. Methods to measure microbial control are essential tools. Caustics has successfully been used to track and characterise the movement of synthetic and metallic nanoparticles in an array of biologically relevant solutions. The aim of this project is to use caustic methodology to translate label-free tracking technology to support the development of pre-clinical in vitro testing systems that can characterise and quantify the adherence of bacteria and assess the effectiveness of anti-microbials.
Personal Background: I recently graduated from the University of Liverpool with a BEng degree in Mechanical Engineering where I became interested in Biomedical and Bio-engineering. I chose to do my final year research project on the properties of bone in an osteogenesis imperfecta model where I analysed the viscoelastic properties of bone from nanoindentation creep measurements.
University of Liverpool
Supervisor: Dr Simon Tew
Project title: Mapping chondrocyte inflammatory responses using gene editing approaches
Project Description: Diseased joints are typically associated with inflammation. Therefore, healthy cartilage is essential for the maintenance of a active lifestyle into old age. The cells that maintain cartilage are called chondrocytes. In response to cytokine exposure, chondrocytes exhibit gene expression changes, making them valuable model systems for determining disease mechanisms. Elevated IL-1 cytokine signalling is thought to be related to Osteoarthritis (a painful disease causing the loss of joint cartilage). However, clinical trials targeting IL-1 to treat Osteoarthritis have failed, and more recent evidence suggests that transient physiological levels of inflammatory signalling are important for joint health.
My project aims to investigate the mechanisms by which transient inflammatory stimulation affects chondrocyte function. I will use CRISPR/Cas9 gene editing to knock out inflammatory receptors in chondrocytes. Investigation of these cell lines will then distinguish chondrocyte inflammatory responses from primary inflammatory stimuli. I will also quantify downstream inflammatory factors and use co-culture models to investigate cross-talk between different tissues in the joint. The project should bring us closer towards uncovering the fundamental factors and therapies required to maintain healthy joints.
Personal Background: In 2022 I graduated from the University of York with an integrated masters degree in Biology. During my degree, I explored a range of module choices and gained a broad academic background. More recently, I gravitated towards immunology research and molecular biology techniques. During the summer of 2021, I worked as a protein production assistant for a start-up biotech company, which allowed me to hone my laboratory skills in a fast-paced environment. In the final two years of my degree, I carried out research projects relating to biosensor development and parasitology. I felt a great sense of accomplishment and fulfilment from generating, analysing and presenting data from these, which inspired me to start a PhD and pursue a career in scientific research.
Supervisor: Dr Agnieszka Bronowska
Project title: Selective modulation of NLRP3 inflammasome by bespoke cell-permeable peptides
Project Description: The NLRP3 inflammasome is a multiprotein complex, formed in response to microbial infection and cellular damage. It is involved in the innate immune response and growing evidence links the NLRP3 inflammasome to neurodegenerative diseases such as Alzheimer’s Disease due to the occurrence of neuroinflammation and inflammageing.
The structure of the NLRP3 inflammasome has recently been elucidated experimentally. The regulation and mechanism of assembly however is not fully understood, therefore using peptides as chemical scaffolds is an excellent tool for a better understanding of the NLRP3 inflammasome. This method allows for modification with organic fluorophores to achieve favourable physicochemical properties and generate conformation-selective probes for assays.
Pilot data has identified multiple plausible binding sites of several NLRP3 inhibiting and activating peptides. The aim of this project is to investigate the biology and modulation of the NLRP3 inflammasome by developing selective, cell-active peptide-based tools. Computational structure-guided approaches will be used to design peptides with optimised physicochemical properties, which have potential to modulate the NLRP3 inflammasome during different stages of its assembly. The designed peptides will be synthesised and evaluated for their effect on capase-1, cell permeability, stability, and inhibition of IL-1β release in macrophages in response to known NLRP3 triggers. The binding of the designed peptides to a shortened version of the NLRP3 inflammasome complex will be validated in biophysical assays and the crystal structure of the NLRP3-peptide complexes will be determined.
Personal Background: I graduated from Newcastle University in 2021 with an MChem degree in Chemistry with Medicinal Chemistry. During my final year of University, I completed my master’s research project on the effects of targeting the Complement cascade to reduce excessive neuroinflammation linked to neurodegenerative diseases. My time in the research laboratory allowed me to discover my passion for research within neuroinflammation and my desire to contribute to the neuroscience drug discovery research field. The project also sparked my interest in the use of computational software for protein imaging and drug design, which is a skill I am keen to apply during my PhD. I am also excited about the interdisciplinary nature of this programme, allowing me to expand my scientific knowledge beyond medicinal and computational chemistry!
University of Liverpool
Supervisor: Dr Aditi Kanhere
Project title: Novel role of non-coding RNAs in regulating genomic DNA methylation
Project Description: Studying the effects of ncRNA on DNA methylation changes in the human genome and how these effects the regulation of gene expression in relation to ageing and development of disease.
Personal Background: In 2018-2021 I studied Human Physiology BSc (Hons) at University of Liverpool, throughout this degree I developed an interest in molecular biology and the molecular and genetic mechanisms behind pathophysiology. This led to an interest in genomics and epigenetics, in particular areas such as, aberrant genomic DNA methylation, and how it corresponds with health and disease. Additionally, I am interested in how these pathways can be targeted by novel therapeutics. I have recently completed an Advanced Biological Sciences MRes within the Institute of Systems, Molecular and Integrative Biology, investigating the functional crosstalk mechanisms between methionine adenosyltransferases and cellular responses to hypoxia.
Fatemah Tavakoli Foroushani
Supervisor: Prof Christopher Dennison
Project title: Synthesis, characterisation and biomedical applications of protein-templated gold nanoclusters
Project Description: Recently, there has been an unprecedented demand for novel nanomaterials with healthcare applications. A group of compounds with great potential in this area are gold nanoclusters (Au-NCs). These are particularly attractive for diagnostic cell imaging and phototherapy due to their photoluminescence, photostability and biocompatibility. In this project, an interdisciplinary team will investigate a number of approaches for making biocompatible Au-NCs. This will include using a family of copper storage proteins as templates for synthesising Au-NCs. The complexes made will be characterised and their usefulness in a range of biomedical applications including identification of cancer cells, will be tested. The ultimate aim of the project is the rational design of Au-NCs with desired properties for clinical diagnosis.
Personal Background: Coming from an engineering background, I have completed both my BSc and MSc in top technical universities in Iran (Isfahan University of Technology and Amirkabir University of Technology). My master’s thesis was focused on synthesis and fabrication of tungsten oxide nanofibers and their application in hydrogen gas sensing. In March 2021, I joined an interdisciplinary team at the University of Cape Town for a project about improving biocompatibility of silicone breast implants with biomimetic materials. As an engineer who comes from chemistry background, being in the medicine department and bridging my knowledge with biology has been an amazing adventure. I am very excited to start my PhD research with the wonderful team and I am sure there are a lot to learn and experience.
University of Liverpool
Supervisor: Professor Claire Eyers
Project title: Diversifying the histone code: defining the role of non-canonical phosphorylation in chromatin structure
Project Description: Post-translational modifications (PTMs) of histones are known to direct chromatin structure and thus gene transcription. This so called “histone code” hypothesises that the combination of PTMs on different histones are a driving force that regulate DNA packing and thus the ability of different genes to be accessible for transcription or ‘silenced’. Specific histone codes have also been defined as markers of cancer and other diseases.
Using novel technology for the cell-wide identification of sites of non-canonical phosphorylation (NCP) on e.g. histidine, lysine, arginine using mass spectrometry, recent research has identified NCP sites on numerous histone proteins and enzymes that regulate histone PTM status. These findings raise the possibility that the histone code, as we understand it, may very well be incomplete. This project aims to re-define the histone code and its regulation, using methods that are compatible with retaining sites of non-canonical phosphorylation. Furthermore, I will explore the relationship between this re-defined histone code and chromatin structure, and thus the implications for transcriptional regulation.
Personal Background: I completed my MSci in Chemistry with Biomedicine at King’s College London in 2022, with my Master’s project focusing on the synthesis of N-heterocyclic peptide supramolecular cages for drug/biomolecule transport. My interest in protein research began with a 6-week remote placement at King’s College London in 2020, where I produced a literature report on the interaction partners of the cancer-killing protein Apoptin. However, it was my Master’s thesis combined with a summer laboratory placement at the Hans Knöll Institute in Jena in 2021, where I worked on NRPS engineering and antibiotic design, which led me to discover the exciting area of analytical techniques in biochemistry.
Hammed Abolade Tukur
Supervisor: Dr Suzanne Madgwick
Project title: Unravelling molecular signatures of oocyte developmental competence in cattle
Project Description: My project will investigate the causes of infertility that is due to cell division errors in oocytes. Correct cell cycle regulation through oocyte meiosis is critical to produce an egg able to support the development of a healthy embryo. In bovine oocytes our knowledge of cell cycle regulation is limited. This project aims to resolve this by characterising key regulatory processes in bovine oocytes. This will be largely achieved by live and fixed cell fluorescence imaging of key proteins through meiosis and early embryonic development, followed by scoring for developmental competence. We aim to characterise competent and non-competent protein signatures. This is important to inform future breeding programmes since fertility in cattle is falling, yet globally we rely heavily on their milk and meat production.
Personal Background: I am from Nigeria. There, I began my journey with a first-class honours degree in Animal Breeding and Genetics from the Federal University of Agriculture, Abeokuta. However, my interest in Reproductive Biology and Fertility was born out of curiosity. I wanted to understand the causes of infertility that appear to be an unfortunate side effect of selection for high milk yield in dairy cattle. I, therefore, undertook an MSc where my research focused on in-vitro oocyte maturation in Arabian camel. That was at King Saud University, Riyadh, Saudi Arabia. After my MSc, I had a stint working as a Research Assistant at the Laboratory of Early Mammalian Developmental Biology, Czechia. That's a bit of my science journey. My leisure activities include arts, crafts, and design. More recently I've started playing tennis. I'm super excited to be part of the NLD BBSRC DTP and I really look forward to becoming one of the finest DTP alumni the BBSRC would be proud to have produced.
Research group weblink: https://www.ncl.ac.uk/medical-sciences/research/research-themes/chromosome-biology/
University of Liverpool
Supervisor: Dr Dan Canniffe
Project title: Expanding the metabolism of the most primitive phototroph
Project Description: Specific objectives:
- To express formate dehydrogenase from acetogenic Desulfitobacterium hafniense in Heliobacterium undosum, identifying the conditions under which cells producing this recombinant enzyme perform hydrogenation of CO2 to produce formate
- Add further D. hafniense WLP enzymes to the system in a modular fashion
- Perform metabolic analyses of engineered strains under various conditions, and with different mixtures of syngas, to identify pathway bottlenecks
- Generate a photosynthetic, rather than phototrophic, Heliobacterium able to use CO2 as a sole carbon source.
Supervisor: Dr Viktor Korolchuk
Project title: Investigating the role of autophagy-mitochondria-NAD+ axis in ageing
Project Description: Autophagy is a cellular trafficking pathway mediated by the formation of double-membraned vesicles called autophagosomes, which ultimately fuse with lysosomes where their cargo is degraded. By clearing dysfunctional cellular components, such as protein aggregates and damaged organelles, autophagy maintains cellular homeostasis whilst also providing metabolites and energy during periods of starvation. Studies using a range of laboratory models from yeast to mammals have established that autophagy is essential for cellular and organismal survival, whilst autophagy dysfunction leads to cell death or senescence. My project will test the hypothesis that the controlled metabolism of cellular nicotinamide adenine dinucleotide (NAD+) is essential for optimal autophagic clearance of dysfunctional mitochondria, which are central drivers of age-related disease. Based on our preliminary data, I will also explore the theory that a key evolutionarily conserved role of autophagy from yeast to humans lies in the preservation of NAD+ levels. I will investigate how uncontrolled depletion of the NAD+ pool by PARP and Sirtuin NADases affects mitochondrial function, ageing in the yeast model, and cell viability in human-derived neurons. I will also test the effect of NAD+ precursor supplementation on autophagy, viability and ageing in the models mentioned above. We hope that characterising this bidirectional relationship between NAD+ levels/metabolism and autophagy will improve understanding of the mechanisms underlying age-related diseases, which are increasing in prevalence due to rising life expectancy.
Personal Background: I graduated in Summer 2022 with an MSci degree in Biomedical Sciences at Newcastle University. For my final year project, I worked in a liver fibrosis lab, where I characterised the functional consequences of PD1 knockout in murine liver cancer. I was lucky enough to present this research at the HCC-UK conference in London in 2022, where I won the best poster prize. Both this project, and my previous experience as a lab assistant in a mitochondrial research lab sparked my interest in cell signalling and autophagy. I am excited to continue learning and applying a range of new skills during my PhD, and contribute to the growing body of research surrounding autophagy and ageing.
Research Group Profile: https://www.ncl.ac.uk/medical-sciences/people/profile/viktorkorolchuk.html