DTP3 Cohort 1 Details

Adam John Hart

Newcastle University

Supervisor: Prof Robert Hirt

Comparative functional genomics of trichomonads infecting animals and humans: new insights into their zoonotic capacity and diverse mucosal life styles

Project Description: Some microbial eukaryotes have the capacity to jump between various animal hosts. This includes zoonotic pathogens that can represent important threat to global human and/or animal health. The zoonotic potential of microbial eukaryotes species belonging to the Trichomonads is becoming increasingly more recognised. Comparative genomics coupled with functional characterisation of inferred colonisation/virulence factors will help move towards understanding the broad capacity of Trichomonad symbionts to colonise various mucosal surfaces among a broad diversity of hosts including human, pet and farm animals and wild avian populations and by doing so contribute to gain new insights into the complex roles of mucosal microbes in both health and disease. This multidisciplinary study will integrate an evolutionary and comparative framework, genomics, transcriptomics, microbiology and biochemistry, to investigate the molecular basis of animal host-bacteriafungi- parasite interactions at mucosal surfaces across important and common trichomonads symbionts. The project will specifically test the hypothesis that the capacity of trichomonads species to target members of the microbiota contributes at these parasites tremendous plasticity to thrive in various mucosal surfaces across diverse hosts.

NLD Research Thematic Areas: Agriculture and Food Security; Systems Biology and Technology Development

Personal Background: I have an Msci in Biomedical Sciences from Newcastle University. My research interests include Molecular biology, Microbiology and Bioinformatics. During my undergraduate and

Master’s degrees I developed a keen interest in Parasitology and infectious disease and as such wanted to hone my learned skills to pursue research in this area. I am looking forward to carrying on the research started in my masters with my supervisor, Professor Robert Hirt, during the course of my PhD.

Alex Faulkner

Newcastle University 

Supervisors: Dr Miguel Velazquez, Dr Adam Benham and Dr Edward Okello

Impact of mycotoxins of agricultural relevance on reproductive cell biology in cattle

Project Description: In dairy cattle herds, mycotoxins (i.e. toxic secondary metabolites produced by fungi) such as deoxynivalenol (DON) and zearalenone (ZEN) are highly prevalent in feedstuffs, but clinical presentation of mycotoxicosis is not observed due to the low level of exposure. Hence, their potential impact on cattle reproductive performance is unknown. In vitro studies in pigs showed that DON and ZEN can impair oocyte development competence (i.e. the capacity of an oocyte to develop into a preimplantation embryo), but their effects on the developmental competence of bovine oocytes is virtually unknown. My project therefore aims to generate novel mechanistic knowledge on the impact of DON and ZEN on bovine oocyte developmental competence using physiologically relevant values, as previous mycotoxin studies used concentrations not representative of real-life exposure. Cellular and molecular endpoints will be analysed in an in vitro bovine model of preimplantation embryo production. This would allow for the mechanisms of action of mycotoxins to be determined, generating opportunities for future therapeutic development to prevent early pregnancy loss, and hence improving animal welfare and profitability for farmers. The relevance of this research is further highlighted by prediction models indicating an increase in mycotoxin crop contamination as a consequence of climate change.                                                                                                                                                             

NLD Research Thematic Areas: Agriculture and Food Security

Personal Background: I originally studied for a BSc in Biological Sciences, specialising in microbiology, followed by an MSc in Cancer Cell and Molecular Biology at the University of Leicester. Throughout these experiences, I have developed a variety of research interests surrounding antibiotic resistant pathogens and the mammalian cell cycle, with a particular fascination for chromosome missegregation events and aneuploidy. I am equally intrigued by the field of reproductive cell biology and the techniques that are utilised to combat infertility, including IVF. I am therefore excited to experience such techniques for my PhD project, where I shall be investigating the potential of fungal mycotoxins to impact the reproductive performance of cattle, at concentrations more representative of real-life exposure. Here I intend to convey my passion for microscopy to identify potential mechanisms in which mycotoxins may compromise oocyte and embryo development, generating opportunities for future therapeutic development and intervention, to prevent early pregnancy loss.

Ben Slater

Newcastle University

Supervisors: Professor Chris Petkov and Dr Alex Easton

Causal Neural Mechanisms for Decision Making: Putting Rules into Context

Project Description: Rule learning is pivotal to living in the world. The rules we learn often only apply to certain situations; X does not always define Y, sometimes the presence of an additional variable is

required. The question, therefore, is how does a natural system, like the brain, learn and remember these rules?

The aim of this project is to understand how the brain learns and makes decisions under different contextual situations. The project itself will involve designing and implementing a computationally informed paradigm in both primates and rodents and assessing their behavioural choices and how they are guided by rules or context. Then with the use of an innovative technique called ultrasound stimulation, brain function in primates will be modulated to identify brain areas that are required for rule/context learning. Parallel work in rodents will identify evolutionary origins and the dependence on the hippocampus and frontal systems, providing vital information from two key laboratory animals.

This knowledge is highly relevant for humans with frontal or hippocampal cognitive impairment and may lead to better artificially intelligent systems that currently inefficiently learn every rule under every context and may also enhance medical understanding concerning disorders that involve maladaptation of memory and cognition.      

NLD Research Thematic Areas: Regenerative Biology, Stem Cells and Neuroscience

Personal Background: The neurobiology of behaviour is a strong interest of mine and has shaped my academic/scientific career. During my Neuroscience degree at the University of Leeds, my dissertation focussed on anxiety in rodents and how the absence of the gene PDZD8 affects behaviour during exploration of the elevated plus maze. I have also spent a year-long placement at Newcastle University studying how humans combine semantics and syntax during learning artificial grammar and developed a touchscreen experiment to see if primates could learn in the same manner.

Moving forward, I am keen to learn more about the neural pathways involved in learning and decision making and would like to explore the similarities/differences in neurobiology between humans and other species.

For recreation I enjoy cycling, climbing (particularly bouldering) and birdwatching. The Northumbrian coastline is fantastic for all three and I am excited for the next four years living in Newcastle.

Bethan Morris

Newcastle University

Supervisors: Dr Maxim Kapralov, Dr Stephen Chivasa and Dr Martin Edwards

Investigating the molecular basis for Rubisco acclimation to increasing temperature

Project Description: Photosynthesis is an intricate process that is fundamental to life on earth. It underpins all-natural ecosystems and food chains. Ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco) is an enzyme complex that con-verts of inorganic CO2 into organic carbon compounds during photosynthesis. However, like all enzyme-driven processes, CO2 fixation is a temperature-sensitive process. Rubisco is a bifunctional enzyme with a photosynthesis driving activity and a counter-productive activity, that fixes oxygen. The later activity decreases photo-synthetic efficiency as temperature increases, leading to reduced plant productivity. This project aims to understand the mechanism by which Rubisco acclimates to high temperatures via a comparative study of the temperature sensitivity and the resilience of photosynthetic systems, from contrasting climates. It will also investigate different isoforms of Rubisco and the changes in its kinetic properties under different temperatures. A modelling exercise will use recent methodologies and recent data to test plant productivity with different Rubisco modifications under future climates.           

NLD Research Thematic Areas: Agriculture and Food Security; Systems Biology and Technology Development

Personal Background: I gained a BSc in Biological Sciences from Queen’s University Belfast. As part of my degree, I completed a year in industry working at the Max Planck Institute for Molecular Plant Physiology. During this time, I developed my interest in plant biology, particularly focusing on the molecular basis to changing environmental stimulus and adaptations to stress responses. I am looking forward to further developing my data processing skills, proteomics and biochemical skills as I start my PhD.

Christopher Miller

Newcastle University

Supervisors: Dr. Colline Poirier, Prof. Melissa Bateson, Dr. Yujiang Wang and Prof Joanna Setchell

Welfare assessment of rhesus macaques: from field observation to computational models of brain network

Project description: Rhesus macaques (Macaca mulatta) are the most commonly used non-human primate in biomedical research. Maximising their welfare is both a moral obligation for researchers, and a requirement for the collection of valid neurobiological data. In captivity, non-human primates are subjected to significant levels of stress from both their environment and research procedures. Current biological indicators measure only the intensity of an individual’s affective state and not its valence (positive or negative), leading to potential misinterpretation of welfare. Wild rhesus macaques live in strongly hierarchical societies, with stress-levels hypothesised to vary between individuals of different social ranks. By assessing differences in behaviour relative to social rank, this study aims to identify potential behavioural indicators of affective state, before confirming the valence of these behaviours in captive macaques, using recently validated neural biomarkers. Finally, the neurological underpinnings of the stress response will be further explored using computational modelling. The results of this study will not only advance our understanding of the primate stress response, but will also inform future welfare-based decisions for captive macaque colonies.                                                                                                                                                               

NLD Research Thematic Areas: Regenerative Biology, Stem Cells and Neuroscience

Personal Background: I have a BSc in Zoology and an MSc in Animal Behaviour. My research interests include behavioural ecology and cognition, and more specifically their applications to welfare science. Through studying behavioural welfare at master’s level and going on to work with captive macaques at Public Health England, I developed an interest and motivation to work towards the improvement of macaque welfare in research facilities. I am excited to start my PhD, which will have important ramifications for our ability to measure affective states in rhesus macaques, allowing researchers to make more informed decisions regarding welfare implications of management strategies.

Cosette Darby

Newcastle University

Supervisors: Dr David Bolam, Professor Dan Rigden and Dr Jon Marles-Wright

Investigating the mechanism of dietary fibre breakdown by the human and animal gut Microbiota

Project Description: My project aims to investigate the enzymatic pathways by which members of the human and animal gut microbiota breakdown complex carbohydrates (fibre) from dietary sources. Whilst much work has been done on Bacteroidetes, mechanisms of fibre breakdown by members of the Firmicutes phylum are less well defined. Utilisation of bioinformatics, combined with biochemical, structural and cell biology techniques will allow characterisation of these mechanisms and improve our understanding of their role in nutrient supply to the host organism. The data generated will benefit in informing nutritional strategies to improve feed utilisation and host health across a range of species, as well as underpinning strategies to improve the nutritional value of plant-based foods.

NLD Research Thematic Areas: Systems Biology and Technology Development; Industrial Biotechnology, Synthetic Biology and Structural Biology

Personal Background: At undergraduate level I studied Animal Science at Aberystwyth University and following this spent time working in the equine nutrition industry. During this period, I became particularly interested in the gut microbiome and its links with diet, health and disease across humans and animals. This inspired me to complete my MRes at Aberystwyth, focussing on the effect of tapeworm infection of horses on the equine gut microbiome.


Daniele Francesco Mega

University of Liverpool

Supervisors: Prof James Stewart, Prof Julian Hiscox and Dr Anja Kipar

The antiviral role and therapeutic potential of novel seaweed-derived compounds

Project Description: Influenza A virus (IAV) causes severe respiratory illness resulting in up to 650,000 deaths and 3 to 5 million cases of severe illness globally each year, with previous pandemics drastically increasing these numbers. The potential of zoonotic transmission is a major worldwide health concern and the rapid evolution of the virus often results in vaccines and antivirals becoming ineffective, highlighting the importance to develop novel therapies. This study works alongside an industrial partner, Byotrol, who has isolated a compound from seaweed with potent anti-viral properties and low toxicity. This project aims to use IAV as a model animal virus to define the precise mechanism of inhibition and therapeutic potential of this seaweed derived compound.

NLD Research Thematic Areas: Ageing, Diet and Health

Personal Background: I have a BSc in Biochemistry and a MSc by research in Molecular and Cellular biology. I initially developed a keen interest in virus-host interactions during my undergraduate research project and furthered this interest during my masters utilising molecular biology techniques to study the role of non-coding regions in Hazara virus multiplication. I am eager to start my PhD, working alongside an industrial partner, to determine the potential antiviral role of a seaweed compound for an important pathogen such as Influenza A virus.

Diana Githwe

Newcastle University

Supervisors: Dr Elisabeth Lowe, Dr James Connolly and Dr Alan Cartmell

How do hybrid two-component systems in gut bacteria regulate global gene expression?

Project description: The human gut microbiome comprises bacteria which, among various functions, are able to break down complex host and dietary sugars. Polysaccharide breakdown has been extensively characterised as a major function of the bacterial genus Bacteroides, which utilise hybrid two-component systems (HTCS) to sense and regulate gene expression for the variety of proteins needed for the catabolic process. The main aims of the project are to gain an understanding of the activities that occur at the cytoplasmic membrane and how they’re modulated, namely: how the HTCS domains sense oligosaccharide fragments and the mechanisms by which ligand binding signals the regulation of global gene expression.

NLD Research Thematic Areas: Industrial Biotechnology, Synthetic Biology and Structural Biology; Ageing, Diet and Health

Personal Background: I have recently completed an MSci in Microbiology at the University of Strathclyde in Glasgow. During my undergraduate and Master’s degree I developed a deep appreciation for the fusion of biochemistry and microbiology, the commercial aspects of scientific research and the experimental nature of scientific discovery. I am interested in all aspects of scientific communication and linking the gap between medicine, science and industry to improve overall health and patient care. My PhD project excites me as it brings forward previous theoretical knowledge of sugar biochemistry and molecular microbiology together with the practical applications of cutting-edge research science to answer long-standing questions regarding sugar degradation by Bacteroides, which are pivotal to gut health.

Eva Cea Torrescassana

Newcastle University 

Supervisors: Dr Thomas Howard, Prof Marc Knight, Dr Maria del Carmen Montero Calasanz and Dr Jem Stach

Enhancing plant productivity using engineered microbes

Project Description: The productivity and resilience of agricultural systems faces multiple challenges and there is an increasing global demand for introducing environmentally and eco-friendly practices in agriculture. The plant/microbe interactions have promising potential to enhance the crop productivity in a sustainable way. In general, favorable endophytes promote plant growth, increase plant nutrient uptake, reduce disease and pathogen growth and increase plant stress tolerance.

The objective of this project is to engineer plant endophytic relationships without genetically manipulating the host plant but developing a bacterial species suitable for use as a synthetic biology model organism. For that purpose, I will study and engineer interactions between a root-colonizing endophyte (Pseudomonas) and A. Thaliana.

NLD Research Thematic Areas: Agriculture and Food Security; Industrial Biotechnology, Synthetic Biology and Structural Biology

Personal Background: My passion for science has been evident since I was little. My devotion was intensified due to a passionate biology teacher I had just before having to choose my degree. From then on, I decided to study Biotechnology. After two years in the University I decided to specialize in Microbial and Plant Biotechnology. During my last year I worked in CBGP where I studied the Expression, Function and Recognition of Type VI Secretion System in Rhizobium-legume Symbiosis and elaborate my final degree project with the results obtained. After that, I decided to do an internship abroad in order to push my boundaries. After much research, I was lucky enough to join Andrew Truman’s group in John Innes Centre which gave me one of my biggest challenges. There I worked in three different projects related to natural products in Streptomyces.

Grisial Hedd Roberts

University of Liverpool

Supervisors: Dr John Graham-Brown, Dr Hannah Vineer and Prof Mark Viney

Determining the epidemiology and immune responses of UK cattle to natural challenge with Dictyocaulus viviparus

Project Description: Dictyocaulus viviparus is a nematode parasite that infects the lungs of grazing cattle, leading to a disease called bovine parasitic bronchitis (BPB). This can lead to pneumonia and death in cattle, which subsequently causes £5.2 million in economic damages in the UK per annum. Prevalence is increasing due to weather changes, which is in turn impacting animal welfare and health. It is therefore the aim of this project to evaluate the immune responses of cattle in the UK to infection using immunoassays such as ELISA, to determine the prevalence, distribution and variation in risk across the UK using immunological assays, to identify the immune responses of cattle to natural infection by collecting serum and faecal samples from infected cattle and analysing them for antibodies, and finally to investigate the mechanisms of the immune responses using in vitro functional assays. The data collected will be essential for the further understanding of BPB, its prevalence and treatments.

NLD Research Thematic Areas: Agriculture and Food Security

Personal Background: I previously studied at Aberystwyth University where I completed a bachelor’s degree in biology, and a Master of Research degree in Parasite Control. Here I focused my studies on flukes, including Fasciola hepatica (liver fluke) which causes Fascioliasis in sheep and cattle, and Schistosoma mansoni (Blood fluke) which causes Schistosomiasis in humans. Over the course of my studies I developed a great interest in helminths (parasitic worms), as well as veterinary medicine, agriculture and disease control, including pathology, immunology and epidemiology.

Harry Collier

University of Liverpool

Supervisors: Prof. Sonia Rocha, Prof. Claire Eyers and Prof. Neil Perkins

SINHCAF, a previously unknown link between HIF and NF-kappaB signalling

Project Description: My project will investigate the physiological significance of a relatively unstudied protein called SINHCAF. Previous work carried out by Prof. Sonia Rocha’s research group uncovered a link between SINHCAF, and both hypoxia and inflammation pathways. This information will be further investigated by examining the functional interaction of SINHCAF with the transcription factor families of HIF and NF-kappaB. In particular, there will be an emphasis on mass spectrometry to examine how the binding partners of SINHCAF affect its function. The project will be under the supervision of Prof. Sonia Rocha, Prof. Claire Eyers and Prof. Neil Perkins (Newcastle).

NLD Research Thematic Areas:  Ageing, Diet and Health

Personal Background: I completed my integrated Masters (MBiolSci) studies at the University of Liverpool in 2020. My undergraduate project involved the study of novel myoglobin transcriptional variants in the mouse brain tissue. It is during this project I was enlightened to the importance of hypoxia across various key and pathological processes, most notably its behaviour in cancer. I was then fortunate enough to work at the Chulalongkorn University in Thailand during which I studied a treatment that could potentially reverse replicative senescence. I then moved on to my Masters year where I investigated how the post-translational modification status of HIF- 2α affects its ability to induce gene expression. This project piqued my interest of HIF and hypoxia whilst allowing me to gain a great deal of understanding of the functions of HIF in the context of its post-translational modifications.

Ieva Andrulyte

University of Liverpool

Supervisors: Dr Simon Keller, Dr Peter Taylor and Dr Laura Bonnett

Brain connectivity and networks as the basis of human hemispheric language dominance

Project Description: The left cerebral hemisphere is dominant for our ability to speak and understand spoken words for the majority of people. The reasons for such lateralised brain function are unknown. One hypothesis is that brain structural asymmetry may provide the basis for functional asymmetry, but there is limited support for this. Interestingly, it has been shown that macroscopic cerebral asymmetry of the insula is related to side of hemispheric language dominance (HLD) in groups of healthy people whereas interhemispheric asymmetry of ‘classical’ language cortical regions – such as Broca’s area – has limited significance. However, using macroscopic brain morphology to determine the functional organisation of the brain provides only limited answers. Significant new insights into the functional organisation of the human brain will only be achieved when we consider the structural organisation of the microstructural brain environment, brain connectivity, and brain networks. The aim of this project is to use Magnetic Resonance Imaging (MRI) and structural and functional connectomes between people with left, bilateral and right HDL.                                                                                                                                                                                       

NLD Research Thematic Areas: Systems Biology and Technology Development; Regenerative Biology, Stem Cells and Neuroscience

Personal Background: I have a BSc in Molecular Biology and Genetics and MSc in Neuroimaging for Clinical and Cognitive Neuroscience. During my bachelor’s degree, I focused on developing bioinformatics skills. I undertook two internships (one after second year and another after third year), learning how to do basic coding and using R. In my dissertation, I also used R, and other genomics techniques. During MSc degree, I expanded my knowledge about computational biology, learning new neuroimaging techniques. I learnt how to analyse EEG, fMRI and sMRI images using SPM and FSL. I'm really excited to start my PhD and try to incorporate the skills I gained during my University years. I strongly believe that neuroscience and genetics are highly related, and studying both aspects would help to answer even more questions.

Isabella Endacott

University of Liverpool

Supervisors: Dr Hannah Vineer, Dr Jakob Bro-Jorgensen and Prof Andy Fenton

How does ecological community influence livestock parasite transmission?

Project Description: Parasites and vectorborne diseases severely impact the health and productivity of livestock worldwide. In many regions of Southern Africa humans, livestock and wildlife live in close proximity. Though this can result in conflict, livestock-wildlife sympatry can also be beneficial by improving forage quality and reducing parasite abundance. My project will investigate the role of community ecology in ungulate parasite transmission in the species-diverse region of Makgadikgadi Pans National Park, Botswana. I will use a combination of empirical data collection and computational methods to develop a network model to characterize the ecological community in and around the study region. With support from the project partner Elephants for Africa, the overarching aim is to use subsequent findings to devise strategies to prevent parasite and VBD transmission, and to advance human-wildlife conflict mitigation.

NLD Research Thematic Areas: Agriculture and Food Security

Personal Background: I graduated with a BSc (Hons) in Zoology from the University of Exeter and subsequently undertook a Masters in One Health (Infectious Diseases) at the London School of Hygiene and Tropical Medicine and the Royal Veterinary College. My MSc thesis investigated transmission dynamics of Peste des petits ruminant’s virus between livestock and wildlife in the Masai Mara ecosystem. Thereafter I have spent the last two years working at the University of Surrey Veterinary School as a Research Assistant on a Bill & Melinda Gates Foundation initiative to improve livestock health and production in Sub-Saharan Africa. Through my academic and professional experiences, I have become particularly interested in research incorporating a One Health approach to tackle livestock diseases, food security, and human-wildlife conflict, and as such I am looking forward to pursuing this multidisciplinary PhD project.

Jesse McCarthy

University of Liverpool

Supervisors: Dr Diarmuid Ó'Maoiléidigh and Dr Vasilios Andriotis

Molecular mechanisms underlying floral organ photosynthesis

Project Description: Flowers evolved from leaves. Although we know some of the master regulators of this process, we do not completely understand how they shaped floral evolution. One aspect of development that these master regulators control is photosynthesis. Leaves are often the focus of photosynthetic research, however, a large body of research indicates that photosynthesis in other organs, such as fruits, is important to provide resources for developing seeds. The molecular mechanisms that control the establishment and activity of photosynthesis in fruits are largely unclear, however, novel links between fruit development and photosynthetic activity have been identified.

To investigate this further, we are using a comparative approach between several members of the mustard family to investigate how the regulation of photosynthesis in leaves is rewired during flower and fruit development. We will focus on the transcriptional regulation of key genes involved in photosynthesis and identify and/or characterize the cis regulatory elements required for their transcription in different tissues. The information generated during this project will be directly applicable to agriculture in the effort to improve yield, nutrition, and reduce environmental impacts of agriculture.                                                                                                                                                                                                      

NLD Research Thematic Areas:  Agriculture and food security; Systems Biology and Technology Development; Ageing, Diet and Health

Personal Background: I completed an integrated Master’s in Biological Sciences at the University of Liverpool (UoL). A lecture series that I attended during my first year at university highlighted the need to dramatically improve crop yields by up to 70% by 2050 to feed an ever-growing population, which sparked my initial interest in plant science. The modules and research projects I completed during the rest of my degree helped expand my knowledge of and fuel my passion for plant science. Projects involved investigating CAM and floral organ photosynthesis at UoL; and investigating plant-insect interactions at The James Hutton Institute (Dundee) and Chulalongkorn University (Bangkok). The information generated during my PhD project will be directly applicable to agriculture in the effort to improve yield, nutrition, and reduce environmental impacts of agriculture and I’m excited to play a part in tackling the global food security challenges, that initially inspired me to study plant science.

John Clark-Corrigall

Newcastle University

Supervisors: Dr Anjam Khan, Dr James Connolly and Dr Heather Allison

Unravelling the dynamic interactions between protective, probiotic Escherichia coli and pathogenic Salmonella

Project Description: Salmonella are responsible for causing food-poisoning and remain a major global health problem. The bacteria reside in the intestines of humans and animals and can subsequently enter the food chain. Our intestinal microbiota harbour trillions of commensal bacteria that play a pivotal role in maintaining good health. Bacterial probiotics provide huge health benefits to their hosts including protection against invading pathogens, thus preventing disease, and helping to reduce antibiotic usage. Furthermore, screening extracellular metabolites produced by probiotic bacteria of anti-bacterial effects may provide a new pipeline for novel antibiotics. This study aims to provide detailed molecular and cellular insights in to the fierce competition which takes place within the intestinal niche for nutrients and space between the probiotic Escherichia coli Nissle and invading Salmonella, as the probiotic bacterium competes with the pathogen to maintain its niche.

NLD Research Thematic Areas: Agriculture and Food Security

Personal Background: I have a BSc in Biomedical Sciences and an MRes in Stem Cells and Regenerative Medicine. My research interests are in molecular microbiology; particularly interbacterial warfare and bacterial genetics. I was captivated by microbiology, particularly the microbiota after an initial foray into cancer research. I am looking forward to the multitude of unique opportunities doctoral study can afford and getting stuck into learning new techniques and developing skills.

Matthew Quinn

Durham University

Supervisors: Dr O Riabinina , Dr V Nityananda ,Dr N Hempel de Ibarra and Dr V Croset

Visual processing in mosquito larvae

Project Description: Malaria is a mosquito-borne disease that affects half of the world population, and increasingly presents risk to Europe, due to climate change. The fight against malaria has currently stalled, and new methods are needed to make further progress.

Larval control methods have proved efficient in the past but were abandoned due to their low specificity. More precise targeting of larvae requires new knowledge about larval behaviour and responses to sensory stimuli, such as visual and olfactory cues. The knowledge about larval visual and olfactory processing is very limited, but when acquired, could lead to the development of new, highly-specialised traps and repellents. In addition, important insights about evolution and function of insect sensory systems will be gained by exploring this new model organism.

This project will study anatomy of the visual system and behavioural responses to visual stimuli in larvae of Anopheles gambiae mosquitoes. The larvae, uniquely, possess both the larval and the developing adult eyes that are likely both functional, and respond to different wavelengths of light. This project will explore how the signals from the two systems are integrated and lead to behavioural responses. The project will also investigate possible modulation of visual responses by concurrently presented olfactory stimuli. Techniques, employed in this project, include behavioural assays, regulation of gene expression by RNAi, in vivo imaging on a light-sheet microscope, immunohistochemistry and confocal imaging, with corresponding image analysis.                                                                                                                                                                       

NLD Research Thematic Areas: Industrial Biotechnology, Synthetic Biology and Structural Biology; Regenerative Biology, Stem Cells and Neuroscience

Personal Background: I have undertaken a research masters in University college Dublin to be the first person to publish work on the parasites and pathogens of the wild ungulate population in Phoenix park, Dublin. The types of parasites discovered as part of my Msc were Dictyocaulus eckerti, a strongyle spp and Toxoplasma gonddii. I completed a 4 years honours degree in applied freshwater and marine biology in Galway-Mayo institute of technology. In my career up to this point I have focused on understanding the role of climate, animal movement and hormones in predicting parasitic infection in wild ungulates. Management of parasites is further challenged by drug resistance, which undermines farming systems that rely on chemical treatment. Working with collaborators in UCD veterinary medicine and Vienna my research aims to suggest more adaptive strategies. I use a combination of experiments on parasite biology, predictive statistical modelling, and observations of field epidemiology. The outcomes of my research seeks to move toward more sustainable methods to manage the challenges parasites pose to both human and animal health.

Megan Parker

University of Liverpool

Supervisors: Dr Sharon Zytynska and Professor Angharad Gatehouse

Reducing insect pests on cereal crops by exploiting beneficial species interactions

Project Description: Insect pests are a growing problem for agriculture due to range expansion and desynchrony with natural pest species due to climate change. Not only can insecticides be harmful to the environment, but pest populations are becoming resistant to their effects. This has led to the use of soil microbiome manipulation as a promising pest control strategy. The project will focus on inoculating barley crop plants with root bacterium to promote plant growth and reduce insect pests. In particular, we aim to understand how inoculation of root bacteria can alter plant volatiles that attract natural enemies of pest insects to the plant for increased pest control. This will be done through a combination of greenhouse and chemical analyses, with the aim to provide practical benefits for agriculture and food security.

NLD Research Thematic Areas: Agriculture and food security

Personal Background: I graduated from University of Liverpool in 2020 with a Masters in Biological Sciences with Honours in Zoology. For my Master’s research I examined the effect of alcohol on mating behaviour in Drosophila melanogaster and also completed an internship at Blue Planet Aquarium, assisting in a study on the impact of climate change on jellyfish. Throughout my degree I have been especially interested in Animal Behaviour and Evolution, and in particular, between species interactions. I am really looking forward to the opportunities for learning my PhD research will provide me with whilst using my interests in a way that could positively impact the agricultural industry.


Milan Collins

University of Liverpool

Supervisors: Dr Tobias Zech, Dr Iakowos Karakesisoglou and Prof Luning Liu

The Cell Matrix Connection to Premature Ageing

Project Description: The nuclei of cells are directly linked to their extracellular environment via a bridge which encompasses focal adhesions, the actin cytoskeleton, and the LINC complex. This bridge can act as a conduit via which extracellular forces are channelled to the nuclear interior and the Lamin A/C nucleo-cytoskeletal network, triggering changes in cellular behaviour and transcription. Hutchinson-Gilford Progeria Syndrome (HGPS) is a degenerative premature ageing disease resulting from de novo point mutations within the LMNA gene that causes the accumulation of the truncated isoform called progerin to be translated. Remaining farnesylated, progerin accumulation induces functional and morphological changes to the nuclear envelope and is known to inhibit nuclear import/export of proteins resulting in alterations to transcription, DNA repair, and chromatin organisation. Defects in nuclear import/export have been shown to be causative of the cellular phenotypes seen in HGPS. Overexpression of wildtype Lamin A/C and Progerin has shown that Progerin expressing cells show less nuclear force coupling (via Nesprin-2 based tension sensor), as well as reduced tension at focal adhesions (via a Talin-tension sensor). This project will investigate how the altered nucleo-cytoskeletal architecture in ageing cells and HGPS patients affects cell matrix adhesions and leads to nuclear import defects that cause HGPS symptoms.

NLD Research Thematic Areas:  Systems Biology and Technology Development; Ageing, Diet and Health

Personal Background: I have a BSc in Biochemistry and an MRes in Biomedical Science and Translational Medicine (Cellular and Molecular Physiology) from the University of Liverpool. A focal point of my interest is centred around biochemical signal transductions and the signalling mechanisms that govern cancer pathogenesis and other age-related pathologies. I am intrigued by the multifactorial nature of tumour progression, the biochemical mechanisms that influence premature aging, and the interplay between the cytoskeleton and other cellular components to perform various cellular processes and physiological mechanisms. During my masters, I also developed a keen interest in the protein, KIAA1217, in which I was able to identify as a novel focal adhesion protein. I am excited to begin my PhD research, which will define the characteristics of cell matrix adhesions alterations cause by changes in the nucleocytoskeleton of HGPS patients and aged cells. We will deepen our understanding of the causes of HGPS symptoms and the underlying mechanisms of HGPS and ageing.

Morgan Lee

Durham University

Supervisors: Dr Heather Knight and Dr James Hartwell

Engineering crops for improved freezing tolerance and better yields

Project Description: Freezing temperatures cause considerable damage to crops. This damage is primarily through desiccation, as water becomes unavailable to the cell when ice forms. The vacuolar proton-pumping pyrophosphatase, AVP1, has been identified as improving plant desiccation tolerance, likely through increased solute accumulation and water uptake. These factors may also influence freezing tolerance, and AVP1 has previously been implicated in this process. However, AVP1 also promotes auxin transport, enhances heterotrophic growth, and increases transport of sucrose from source to sink tissues due to its additional localisation at the plasma membrane of sieve element companion cell. As such, this study aims to identify which of AVP1’s enzymatic activities and localisations contribute to freezing tolerance, and if manipulation of the protein can be used to improve it. AVP1 may represent a unique route to improving freezing tolerance without sacrificing yield, due to its role in plant growth (by facilitating auxin transport).

NLD Research Thematic Areas:  Agriculture and food security

Personal Background: I have a Biosciences MBiol. My primary research interest is molecular biology, specifically plant abiotic stress responses. I also have an interest in cell signalling, plant physiology, and microscopy. My PhD research has the potential to be applied to agriculture, and is particularly exciting due to the possibility to simultaneously boost crop freezing tolerance and yield.

Natasha Chavda

University of Liverpool

Supervisors: Dr K Hamill, Prof CAB Jahoda, Dr H Levis

Determining the role and mechanism of spatially restricted basement membrane remodelling in regulating mesenchymal-epithelial interactions in skin and limbal stem cell niches

Project Description: Stem cells are formed and modified in environments called niches. Focussing on the epithelial stem cell niches of the corneal-limbus and hair follicle bulge regions, this study hopes to answer fundamental biological questions by investigating how the cells that form these niches interact with one another. Seminal work from the Hamill lab has shown that cross-talk occurs between epithelial and stromal cells in these regions, via disruption of the basement membrane barrier between the two stem cell populations. These regions are important for maintaining the cornea and skin during normal and wound repair conditions and defects lead to severe clinical diseases. By predicting the composition and mechanisms of the proteins involved in these contact points, we hope to elucidate the function behind these interactions and their importance for stem cell survival in the niche environment and potentially provide future therapeutic targets.

NLD Research Thematic Areas: Regenerative Biology, Stem Cells and Neuroscience

Personal Background: I have an MSci in Natural Sciences, where I specialised in Biomedical Sciences and Medical Physics. Due to the emphasis on interdisciplinary study during my degree, I gained skills in a wide range of areas including physiology, biophysics, programming and statistics. Whilst working with Drosophila at the Francis Crick Institute and the University of Birmingham, I gained interest in Developmental Biology and Stem Cell research, leading me to my PhD project. I am greatly looking forward to investigating the interactions between epithelial and mesenchymal stem cells, by learning and using cutting-edge techniques, that include super resolution microscopy, advanced electron microscopy and 3D cell culture models.

Nicola Rudling

University of Liverpool

Supervisors: Daniel Canniffe, Luning Liu and Daniel Rigden

Engineered expansion of photosynthesis into the near-infrared

Project Description: Oxygenic phototrophs such as plants contain two photosystems that both use chlorophyll; these photosystems have overlapping absorption spectra and so partially compete with each other for light of the same wavelength. Bacteriochlorophyll absorbs near-infrared light, which cannot be absorbed by chlorophyll, so engineering one photosystem to contain bacteriochlorophyll would prevent the two photosystems competing for light and would increase light-harvesting capacity and potentially improve the efficiency of photosynthesis. The enzyme chlorophyllide oxidoreductase (COR), found in anoxygenic phototrophs, reduces a carbon-carbon double bond in the tetrapyrrole ring of chlorophyllide, the first step in bacteriochlorophyll biosynthesis branching from chlorophyll. This enzyme is oxygen-sensitive so cannot function in oxygenic phototrophs. By expressing, purifying and crystallising both CORa and CORb (which are involved in producing bacteriochlorophyll a and b) this project hopes to determine the structures of these two enzyme forms, elucidating their catalytic mechanism and identifying ways to engineer oxygen-tolerant variants. If successful, these enzymes could be used to synthesise bacteriochlorophyll in oxygenic phototrophs, with the long-term goal of using this technology to increase crop plant growth.

NLD Research Thematic Areas:  Agriculture and food security; Industrial Biotechnology, Synthetic Biology and Structural Biology

Personal Background: I recently completed an integrated Master’s degree in biochemistry at the University of Bristol. My main research interests are in protein structure, protein engineering and photosynthesis. During my Master’s degree I conducted research into creating synthetic photosystems using purified light-harvesting proteins from different photosynthetic organisms to maximise light absorption. I am now excited to be able to complete my PhD carrying out further research into photosynthesis, taking a different approach to increasing light absorption by altering pigment synthesis within living cells.

Ravina Mistry

University of Liverpool

Supervisors: Professor David Fernig, Dr Igor Barsukov and Dr Edwin Yates

Engineering algae polysaccharide sulfotransferases for biotechnology

Project Description: Enzymatic modification of polysaccharides has the potential to replace oil-based polymers and encourage companies to use green technologies into their products. The goal of the project is to engineer polysaccharide modifying enzymes to develop unique polysaccharidebased

materials to replace existing compounds produced by traditional chemical means. Chemical modification by sulfation is of interest due to its use by plants and algae to create materials with unique properties, and as sulfated molecules are key components of many personal care and food products. The project will incorporate a variety of techniques for enzyme characterisation, crystal structure determination and protein engineering. The evolutionary history of sulfotransferases will also be explored to identify the unique structural features conferring their distinct catalytic activity. The in-depth analysis of sulfotransferase structure and activity will guide the design of enzyme variants with altered enzyme activity or substrate preference (e.g. polysaccharides of terrestrial plants) selected via a highthroughput screen. Successful enzyme variants and resulting active sulphated compounds may then undergo further evaluation for their incorporation into manufacturing processes or products.

NLD Research Thematic Areas:  Industrial Biotechnology, Synthetic Biology and Structural Biology

Personal Background: I studied Biological Sciences with an Integrated Masters (Biotechnology) with industrial experience. My masters project took place in Unilever which focused on polyesterases, where I gained experience in protein expression, protein purification, enzyme characterisation and activity studies. Following my placement, I gained further experience in the protein purification of lipases and high-throughput study design at the Materials Innovation Factory, Unilever. I find biotechnology an exciting field of study and look forward to contributing to the development of green technologies.

Prior to my industrial placement, I was introduced to structural biology through a summer research placement awarded through the Biochemical Society. I was part of a project studying the peptide inhibition of alpha-synuclein aggregation. This project measured protein interactions through a variety of techniques, such as NMR spectroscopy, fluorescence assays and isothermal titration calorimetry which were fascinating studies to perform and learn about.

Ryan Nolan

University of Liverpool

Supervisors: Professor Jane Hurst, Professor Candy Rowe, Dr Matthew Leach

Do rewards change an animal’s emotional state?

Project Description: Punishing or threatening events lead to long lasting negative emotional (affective) states in animals, such as fear, anxiety and depression. Improving welfare of farm, laboratory and companion animals predominantly focuses on removal of these negative events; however, it is believed that an animal’s long-term emotional state is shaped by the cumulative experience of both negative experiences and positive rewarding events. Using mice as a model species, the aim of my project is to establish the long- and short-term impacts of rewards schedules on animal emotional states, and compare the effectiveness of different types of rewards (social and nutritional). I will assess whether these rewards can help reduce stress reactivity and increase resilience to future negative events, and increase both physical and emotional wellbeing.

NLD Research Thematic Areas:  Agriculture and Food Security

Personal Background: My research interests are animal behaviour and welfare. I studied BSc Wildlife Biology and completed an MRes in Biological Sciences (Wildlife Behaviour and Conservation), during which I gained experience of behavioural research with primates; from the social behaviour of bush babies in Tanzania, to habitat preferences of forest monkeys in Ghana. Since then, I have been working as a Research Assistant at Newcastle University, looking at the effects of food insecurity on behaviour and body mass regulation of European starlings.

Ryan Waite

Durham University

Supervisors: Dr Carrie Ambler, Dr Gary Sharples and Dr Nawaporn Onkokesung

Investigating PDT as Targeted Herbicidal and Antimicrobial Agents

Project Description: Photodynamic Therapies are beginning to show clinical efficacy, however, application of the technology in non-mammalian species has been limited due to difficulties generating photoactivatable compounds. LightOx has developed novel photochemistry that allows the development of small molecular weight photosensitive chemicals. These compounds can be taken up by bacteria and plant cells and show no toxicity in the absence of irradiation. The mechanism by which PDT kills cells is different from that of conventional antibiotics and herbicides. As the problem of antibiotic and herbicide resistance is on the rise globally, this project aims is to generate evidence on the potential of these compounds to selectively target and destroy antibiotic-resistant microbes and herbicide-resistant weeds. Providing new treatment methods to aid in the fight against these global issues.

NLD Research Thematic Areas: Agriculture and Food Security

Personal Background: I have a BSc in Biochemistry and Microbiology from the University of Sheffield. I spent time working in the pharmaceutical industry but was drawn back into research as my undergraduate project I saw first-hand the ease with which resistance to antimicrobials could spread. Whilst working in research, I developed a keen interest in the manipulation of bacteria to alter protein expression, as well as the protein-protein interactions underpinning essential bacterial cellular processes I am looking forward to starting my PhD to get the chance to work with a novel technology with the potential to treat resistant bacteria as well as protect crops from herbicide-resistant weeds to increase food security.

Shireen Al-Momani

University of Liverpool

Supervisors: Prof Andy Jones, Prof Ari Sadanandom and Prof Claire Eyers

Using machine learning to identify the functional consequences of post-translational modifications in the rice proteome

Project Description: Under normal field conditions, plants can be exposed to various biotic and abiotic environmental stresses. Plant stress tolerance and acclimation depends on significant changes in post-translational modifications (PTMs) of specific proteins to rapidly switch protein function. It is expected that environmental stresses, such as drought and heat will become more prevalent in the coming decades. Future successful solutions will undoubtedly involve applying next-generation technologies to improve the breeding of agro-economically important crops. This study aims to identify and quantify PTMs in the rice proteome to deliver a detailed protein functional characterisation that will improve our understanding of how plants acquire stress tolerance and will allow the prediction of functional consequences of PTMs that are associated with desirable traits, with a long term objective of improving rice breeding efforts.

NLD Research Thematic Areas: Agriculture and food security; Systems Biology and Technology Development

Personal Background: I have a BSc in Plant Sciences and an MSc in Advanced Biological Sciences (Bioinformatics). My research interests include data science, machine learning, and cell signalling. During my Masters, I developed a keen interest in writing my own code in Python to analyse mass spectrometry phosphoproteomics data. I am looking forward to starting my PhD research, which has the potential for involvement with major international research programmes to improve rice, through allele mining and advanced breeding techniques.

Sukhmani Kaur

Newcastle University

Supervisors: Prof Brian Morgan, Prof Janet Quinn and Dr Niall Kenneth

The functions and regulation of ubiquitin and ubiquitin-like modifications

Project Description: Reactive oxygen species (ROS) are produced as the by-product of cellular processes. High levels of ROS are a vital defense mechanism against pathogens (e.g Candida albicans), whereas low levels regulate important cell signalling pathways. However, high levels of ROS can cause oxidative stress, leading to age-related conditions including cancer, diabetes and neurodegenerative disease. Therefore, to improve human heath it is important to understand how cells respond to ROS.

Recent work in model yeast revealed that oxidation of catalytic cysteine residues within conserved antioxidants (e.g. thioredoxin system) plays a key role in ROS responses. Interestingly, other enzymes which utilize catalytic cysteine residues, such as those involved in ubiquitin (Ub) and ubiquitin-like (Ubl) modification (e.g. SUMO, NEDD), are also oxidized. In particular, oxidation of the Ub E2 enzyme Cdc34 led to cell cycle arrest in yeast in response to oxidative stress. Furthermore, specific Ub/Ubl conjugation pathway enzymes are also regulated by conserved antioxidants. Ub/Ubl modifications regulate the cell cycle, development and DNA repair, and alterations are linked to common human diseases. Therefore, the project aim is to build upon this research to understand the function and regulation of Ub/Ubl modifications and their links with ROS responses and human disease.

NLD Research Thematic Areas:  Ageing, Diet and Health

Personal Background: have a BSc in Biomedical Sciences, and during my undergraduate studies I undertook a vacation studentship funded by the Biochemical Society investigating the role of phosphorylation within the NFkB signalling pathway. Furthermore, my final year project investigated the effects of mitochondrial dysfunction in intestinal tumour progression. From these two projects, I developed a keen interest in cell signalling and post-translational modifications which drew me to this PhD project. I am excited to start my PhD research which explores the molecular basis of cellular responses to ROS and the relationship with ubiquitin/ubiquitin-like modifications, to ultimately improve our understanding of these mechanisms and how they influence human health.

Suzannah Tasker

University of Liverpool

Supervisors: Dr Violaine see, Dr Anne Herrmann, Prof Patricia Murray and Dr Dermott O’Callaghan

Single cell live imaging in vivo, to understand cell activity in the context of regenerative medicine and cancer biology

Project Description: 

Stem cell-based therapies have shown promising results across many disciplines in medicine. However, several recent clinical studies have led to disappointing results, due to the fundamental mechanisms underpinning their effects not being understood. This project will monitor and track the interaction over time of multiple cell types transplanted in vivo and how they interact with the host tissues. Non-invasive cell imaging techniques are essential to obtain real-time, quantitative, and long-term monitoring of transplanted cells and information on cell migration, distribution, viability, differentiation etc. The well-established chick embryo model will be used either by direct injection of cells in the vasculature/organs or by exploiting the chorioallantoic membrane (CAM). CAM has the ability to support the growth and maintenance of live tissue/cells placed on its surface, making it an ideal bioreactor and a core resource to evaluate biological processes in regenerative medicine and cancer research. The chick embryo is not under home office regulation until Embryonic day 14, thereby contributing to Replace/Reduce animal use. StreamBio have developed Conjugated Polymer Nanoparticles (CPNs™), which are highly stable, fluorescent labelling probes immensely brighter than conventional technologies, and have an iron oxide component for MRI contrast enhancing, making them multi-modal. Using the advanced imaging technologies at the University of Liverpool Centre for Preclinical Imaging -CPI- and Centre for Cell Imaging -CCI for cellular and in vivo imaging; we will determine how neural undifferentiated/dedifferentiated cells interact with immune cells, the host tissue and vasculature, and how this environment impacts differentiation, survival and migratory capabilities.                                                                                                                                                                                                  

NLD Research Thematic Areas:  Systems Biology and Technology Development; Regenerative Biology, Stem Cells and Neuroscience; Ageing, Diet and Health

Personal Background: I have a BSc in Biological and Medical Science and an MRes in Advanced Biological sciences (Molecular Oncology). My research interest’s include molecular oncology, cell signalling and microscopy. During my MRes I developed a key interest in the development of new in vivo tools within preclinical drug testing, in particular the chick embryo model which implements the 3R’s. I am now looking forward to starting my PhD which will use state of the art live-cell imaging and longitudinal imaging techniques with CPN labelled neural cells in the chick embryo to gain a mechanistic understanding of neural cell differentiation and migratory properties.

Tanya Horne

University of Liverpool

Supervisors: Dr Heather Allison, Dr Tim Blower, Prof Jay Hinton and Dr James Hall

Conflicts in the pangenome: integrating evolutionary and structural microbiology to understand plasmid costs and genome defence

Project Description: Horizontal gene transfer (HGT) enables bacteria to gain advantageous traits including antimicrobial resistance and novel catabolic activities from their neighbours. However, this openness to new genetic material can come at a high cost. Incoming genes, such as those from a bacteriophage, may be harmful or even lethal. Bacteria have therefore evolved a wide range of genome defence systems, which not only mitigate the risk posed to bacteria by HGT but have also been developed into indispensable biological research tools such as CRISPR. This project will investigate a newly identified family of ‘domain-of-unknown-function’ proteins that appear to act as a barrier to HGT and defend against bacteriophage in divergent species of bacteria. Through analysis of their distribution across bacteria and their effects on fitness, as well as the determination of the molecular basis of their action, this project will establish whether these proteins comprise a novel genomic defence mechanism with potential applications. It will also add to our understanding of patterns of gene exchange in bacteria.

NLD Research Thematic Areas:  Industrial Biotechnology, Synthetic Biology and Structural Biology

Personal Background: After more than a decade spent working in politics and health administration, I entered higher education as a mature student, graduating from the University of Liverpool with a BSc (Hons) in Microbiology in 2020. My research interests include evolutionary microbiology and biotechnology, with a passion for widening participation and outreach. I am excited to be joining the lab of Dr J Hall in October 2020 to undertake a four-year PhD exploring the trade-off between openness to horizontal gene transfer and genome defence in Pseudomonas and E. coli.

Emilia Dwyer

Newcastle University

Supervisors: Elizabeth Veal, Patrick Eyers

Targeting redox-active cysteine residues in protein kinases as a new therapeutic approach to ageing and age-associated diseases.

Project Description:

Aaron Brooks

Newcastle University

Supervisors: Josana Rodriguez, Tim Davies.

The importance of staying together; a cellular perspective. 

Project Description:

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