EastBio Student Cohort 2020

Project title

Stochastic modelling of translation dynamics 

Louis Headley

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Project title

Co-benefits and trade-offs of bioenergy with carbon capture and storage – The role of feedstock sustainability

Personal note

I have recently completed my undergraduate studies with the University of Aberdeen where I achieved a First-class BSc in Environmental Science with honours. This course allowed me to develop a keen interest in conservation and climate change. I also took the opportunity to volunteer for roles as class representative during my course which involves liaising between students and staff, providing course feedback, and attending the Staff-Student Liaison Committee meetings. I also volunteered as a mentor to new students through the universities Students 4 Students mentoring programme.

I am a co-author of a paper titled “Implementation of Carbon Capture and Storage: Is this Cost-Effective in the UK?” which has been submitted to the International Journal of Greenhouse Gas Control for review and publication. I find that drawing on my experience as a retail manager helps me to organize my time, work efficiently to meet deadlines and complete self-study in support of my courses and research.

I try and balance my work, study, and family life as best as I can, spending time with my wife and two children, who love to climb trees and spend time in the countryside. I like to consider myself an amateur wildlife photographer and enjoy wildlife spotting when I get the chance.

Conservation and environmental issues, carbon capture and storage and climate change are all areas that I have an interest in. I am looking to find a career in one of these areas in the future once I have completed my PhD, although a career in research or academia is also a possibility.

I look forward to meeting and engaging with everyone in the (hopefully) near future.

David Knight

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Project title

Assembly of the matrix that supports bacteria living in biofilms

Personal note

After completing a BSc (Hons) & MRes at the University of Strathclyde I worked for several years at PHE Porton as a microbiologist with a focus on water microbiology & biofilms. I am now based at the University of Dundee under the supervision of Prof. Nicola Stanley-Wall & Prof. Cait E. MacPhee (Edinburgh). My PhD project will involve using an interdisciplinary approach to explore the mechanisms of biofilm matrix assembly in the soil bacterium Bacillus subtilisis. Focusing on three key components of this matrix (exopolysaccharide, BslA, TasA) and their role in the structure and function of the biofilm.

David Stevenson

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Project title

Exploring the Untapped Chemical Potential of the Microbial Word – a cellular and synthetic biology approach to organic synthesis

Personal note

Hi, I’m Connor and I have moved to Edinburgh from just south of the border where I completed my MBiol in Biology at Newcastle University. During this time, I participated in the iGEM competition twice which set me on the path of research within Synthetic Biology and Biochemistry. In my downtime I like going on long walks and taking photos of as many dogs I can find.

My PhD within the Stephen Wallace lab at the University of Edinburgh seeks to systematically explore the native metabolism of a diverse range of unsequenced microbes to identify species which can complete interesting chemistries. The project will specifically aim to identify unmodified strains capable of novel and pharmaceutically relevant chemical transformations. Once such microbes are identified, the potential to use unmodified cells in whole cell biocatalysis will be evaluated and optimised to provide potential alternatives to environmentally harmful chemical synthesis methods.

Connor Trotter

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Project title

Expanding enzymatic fluorination: development of artificial fluorinases

Personal note

My PhD studies within Dr Amanda Jarvis group at the University of Edinburgh focus on the design of artificial metalloenzymes. In particular, I am interested in the development of fluorinases, which, in fact, are very uncommon in nature. As a result, there is only a handful of fluorinated molecules from the natural product biosynthetic pathways. However, the demand for sustainable and selective fluorination methods in the pharmaceutical and agrochemical industries is very high. Thus, in this interdisciplinary project we aim to expand the biocatalytic fluorination toolbox and provide a much greener and efficient strategy for selective C-F bond formation.

Prior to this PhD programme, I completed an MSc degree in Medicinal and Biological Chemistry at the University of Edinburgh where I developed my interest in biocatalysis. Consequently, my MSc research project focused on the structural analysis of the thermophilic biocatalysts from a combined chemo- and bio-cascade synthesis of pyrroles. I also hold a BSc Chemistry degree from the University of Aberdeen where I completed my final year project on the chemoenzymatic peptide synthesis. I very much look forward to continuing my academic journey in Scotland!

Evelina Venckute

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Project title

Exploiting enzymes from halophilic archaea for fructan biosynthesis

Personal note

Hello everyone! I am Anna and I have just started my PhD at the University of St Andrews. My research will explore the biotechnological potential of GH68 family fructosyltransferases from evolutionary diverse haloarchaea, and it is a result of the collaboration between Dr Stuart MacNeill and Dr Tracey Gloster. My focus will be to characterise the enzymes and mechanisms of fructan biosynthesis by haloarchaea with the aim to establish a haloarchaeal platform for the production of fructans industrially. This could have the potential to reduce reliance on chemical processes in the current fructan production, improve performance, lower operational costs and reduce carbon emissions.

I completed my undergraduate degree on Biology with a Year in Industry at the University of York. The internship I undertook was at the University of Edinburgh where I researched the salt tolerance of microbes from the International Space Station under the supervision of Professor Charles Cockell.

I am originally from Greece, I absolutely adore dogs, and in my free time I like playing music, reading fantasy and science fiction books, watching anime, exercising and exploring. Travelling and enjoying a drink with friends would be up in the list but for obvious reasons there has been a halt to that.

Anna Zolotariof

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Project title

Developing effective rat control for rural Madagascar landscapes – using individual based modelling approaches to inform strategies to increase agricultural productivity and reduce zoonotic disease risk

Personal note

My research typically applies a multidisciplinary approach of spatial analysis, individual modelling and bioinformatics etc. to best inform environmental and conservation strategies. I have worked on and developed projects (in partnership with Bristol Zoological Society, Bristol Museum and Art Gallery, and Liverpool John Moores University) ranging from social network analysis of lowland western gorillas to best improve captive breeding programs; modelling the environmental factors in chimpanzee nest site selection in Cameroon to support forest protection schemes; reviewing community-based well-being projects in Madagascar; and non-invasive survey techniques (using bioacoustics, camera traps and faecal DNA analysis) to study the Negros bleeding-heart Dove in the Philippines to molecular identification of ticks and tick-borne diseases as a threat to population growth and survival of infants (Cercocebus sanjei), providing significant outputs; and directly informing the IUCN’s primate specialist group species action plan on mangabeys.  I have previously completed a BSc (Hons) Wildlife Ecology and Conservation Science at University of the West of England (UWE) and an MSc Primate Behaviour and Conservation at Liverpool John Moores University (LJMU). Both these courses have stressed that successful research tends to produce outcomes which are: (1) fully accessible to the stakeholders involved; (2) provide cost-effective benefits; and (3) provides a framework/resources for future development and longevity. Hence my current focus at the University of Aberdeen and as an EastBio student is to develop strategies to increase agricultural productivity and reduce zoonotic disease risk owing from rodent infestation in Madagascar.  The project focuses on the effectiveness of targeting rat control in different habitats and different seasons, using a model parameterised with existing trapping data and land-cover maps; and Incorporate individual disease status into RangeShifter (a modelling platform that allows for incorporated life history traits and dispersal strategies to illustrate eco-evolutionary dynamics and species’ responses to environmental changes) and investigate the impact of control on the landscape epidemiology of different pathogens, including plague and leptospirosis.

Daniel Dornan

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Project title

What are the causes and impacts of woody encroachment in the herbivore dominated savannas? A comparison of South Africa and Madagascar

Personal noteMy name is Susan and I am starting my PhD at the University of Edinburgh under the advisement of Dr. Caroline Lehmann and Dr. Graham Stone. My project will be focusing on woody encroachment onto grazing lawns in herbivore dominated savannas, with research to be conducted in South Africa and Madagascar. My research aims to address important questions around the mechanisms of encroachment in areas utilized by wildlife, livestock, and mixtures of both, along with impacts on ecosystem services such as nutrient cycling and pollination services

Previously, I received my Bachelor of Science in Biology- Evolution, Ecology, and Behavior from the University of Texas at Austin in 2015 and my Masters of Science in Biodiversity and Conservation from Trinity College Dublin in 2017. I conducted my master's dissertation project in the Limpopo region of South Africa, focusing on the effects of abandoned kraals on surrounding habitat vegetation and local herbivore populations. Following grad school, I worked for over a year in South Africa and Malawi as an ecologist. In my free time, I enjoy running, hiking, traveling, and hanging out with my friends and family (in person or over video chat).

Susan Eshelman

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Project title

Crosstalk between the circadian clock and innate immune system in plants.

Personal note

I am joining Dr. Gerben van Ooijen’s lab at the University of Edinburgh. My project focuses on the interaction between Arabidopsis and the bacterial pathogen Pseudomonas to test the specific points of cross talk between immune pathways and the circadian clock. Before starting my PhD, I completed my BSc in Plant Sciences at the University of Edinburgh. Outside of the lab, I enjoy running, playing sports and hiking.

Olivia Fraser

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Project title

Is mob grazing beneficial for soil health and the environment?

Personal note

I am a Sheep and Grassland Specialist with SAC Consulting, a division of SRUC. My PhD will be part time and supervised by Dr Joanna Cloy (SRUC), Professor Liz Baggs (University of Edinburgh), Dr Gillian MacKinnon (SUERC/University of Glasgow), Dr Sarah Buckingham (SRUC) and Professor Christine Watson (SRUC). I am keen to further my understanding of grazing management practises that improve carbon storage. Mob grazing is a method of livestock grazing management that mimics wild herbivore grazing - short intensive grazing followed by a long rest period. The theory is that this encourages root growth and organic matter returns for greater carbon sequestration and improved soil health. However, evidence is required to back these claims – hence the PhD!

Poppy Frater

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Project title

Barley Single Cell Transcriptomics

Personal note

Hi, I'm Laura. I am former Police Officer and I graduated with a BSc (Hons) in Biological Sciences (Bioinformatics) from the University of Dundee this year. For my honours year project, I did a computational and statistical analysis of Spring Barley microbiome samples and performed species identification using the 16S rRNA gene. My PhD project will be in Sarah McKim's lab at the University of Dundee's division of Plant Sciences where I will developing techniques for single-cell transcriptomics in Barley. 

I am a Captain in the Army Reserves specialising in logistics and have been working this summer in support of the NHS supply chain in response to the Coronavirus pandemic. I sing alto in the Dundee University Chamber Choir and enjoy playing piano and cello.

Laura Pugh

Project title

Molecular characterisation of plant disease resistance genes through novel Next-Generation Sequencing applications

Lynn Simpson

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Project title

Resistance in crop roots: Functional analysis of the H2-mediated response to nematodes

Personal note

Following my graduation from the University of Glasgow with a BSc in Molecular & Cellular Biology, I joined the James Hutton Institute to pursue a PhD with a focus on food security. My project will focus on characterising the H2 resistance gene which provides resistance against the potato cyst nematode (PCN) Globodera pallida, a parasitic nematode that attacks the roots of the potato crop causing extensive yield loss. PCN is responsible for £26 million of crop losses each year in the UK, and whilst several resistance genes have been characterised and deployed against the related species G. rostochiensis, to date no effective resistance genes for G. pallida have been identified. Developing a clear understanding of the H2 resistance gene is crucial for its potential deployment in commercial potato crops to provide protection against this ‘invisible enemy’. In my spare time I enjoy mid-distance running, or open water swimming during the summer!

Moray Smith

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Project title

Reconciling food security and biodiversity conservation: An integrative modelling approach

Personal note

Hello, I’m Tamsin and I am a PhD student at the University of Aberdeen. My PhD project focuses on how we can sustainably increase global food production while conserving biodiversity and is co-supervised by Professor Justin Travis, Professor David Burslem and Dr Peter Alexander (University of Edinburgh). The aim of my project is to integrate computational land-use and ecological models to predict the combined effect of land-use and climate change on pollinators and crop pests, and potential feedbacks on crop productivity. Prior to starting my PhD, I completed an MSci in Natural Sciences at the University of Cambridge where I studied Ecology and Systems Biology. I have also worked as a software developer and a research assistant in bioinformatics, and I am looking forward to applying my previous experience in coding to my PhD.

Tamsin Woodman

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Project title

Engineering novel RNA Polymerases for RNA vaccine production

Personal note

Having greatly enjoyed a BA and MSci in Biochemistry at the University of Cambridge, I decided to pursue academic research further with a PhD project and I’m very excited to be joining the Rosser Lab in Edinburgh this year. I’m particularly interested in synthetic biology and bioengineering and I’ll be exploring that area through engineering of novel RNA polymerases first isolated in ocean cyanophages. Whilst my initial work will be focussed on evaluating and improving the activity of these polymerases there is a hope to later put this activity to work in RNA vaccine production. Outside the lab I’m a keen runner and tennis player and will be trying to make the most of the amazing Scottish surroundings through walking and mountaineering trips.  

Benjamin Baker

Project title

Impact of steroid hormone environment on immune cell phenotype and function

Erin Brown

Project title

Understanding the pathogenesis of life-threatening Burkholderia cenocepacia infections using blocking antibodies and novel chemistry scaffolds to untangle complex aspects of AMR

Emily Candlish

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Project title

The impact of soft-fruit phytochemicals on the gut microbiome and bile acid metabolism

Personal note

I am doing my PhD project at the Rowett Institute of Nutrition and Health where molecular science is translated into real-life health and dietary interventions. During my project I will be looking at the phytochemicals contained in the Arctic berries such as blueberries, trying to unravel their effect on microbiome and understand molecular pathways that change bile acid and lipid metabolism and ultimately lead to weight-loss and anti-obesogenic effects that have been shown in mice and humans. This is an exciting project that will keep me busy working with animal model systems, in vitro models of microbial digestion, and human intervention trials, and I will need all the experience I gained during my MSci in Genetics with Immunology and industry placements at AstraZeneca, The Scottish Biologics Facility and Marine Laboratories, where I worked with transgenic animal cell lines, monoclonal antibodies and phage display technologies. I look forward to working with Dr. Andreas Kolb, Dr. Karen Scott and Dr. Claus-Dieter Mayer from the Rowett Institute, as well as with Dr. Gordon McDougall from the James Hutton Institute, who will be jointly supervising this inter-disciplinary project. And if there is any spare time left, I am sure to be hill walking somewhere in the Northern Hemisphere foraging for wild berries!

Tatiana Dovgan

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Project title

Using the eye to unlock changes in the health of the aging brain: A state of the art data analysis approach

Personal note

I’m Sam. I’ll be looking at images of the retina (eye) and MR images (brain scans) in a large group of elderly participants – the Lothian Birth Cohort. Almost everyone born in Scotland in 1921 and 1936 was given an intelligence test when they were aged 11. Many decades later, around 1999, these same people living in the Lothians (the county to which Edinburgh belongs), were asked to participate in further studies. Over the next twenty years these groups have contributed a vast amount of scientific data, including cognitive, psychosocial, lifestyle, medical, biomarker, genetic, and brain imaging, which has enabled us to learn a great deal about healthy ageing in humans. With over 400 publications to date, and growing, many scientists have built their careers working with these wonderful people, and the data they provide. Building on the work of others, my particular research will use the latest machine learning and statistical techniques to uncover patterns in retinal images that relate to aspects of cognition. We can think of the retina as a “window to the brain”, as it shares blood supply, and has common embryological origins. Unlike MRI, which is incredibly specialised and expensive, retinal photography is relatively cheap and easy, so one thing that motivates me a lot in this project is the the potential scalability of any findings to the wider population, and to less developed parts of the world. For example, the discovery of robust retinal biomarkers could enable widespread screening programmes, at a fraction of the cost of brain scans.

I’ll be working with Dr Thomas MacGillivray, an imaging specialist at the Centre for Clinical Brain Sciences, Edinburgh, and Prof. Emanuele Trucco, a computer vision specialist at Dundee. Our work will depend upon, and feed into the VAMPIRE project. VAMPIRE is world-leading software that generates a large number of parameters from retinal images.

Samuel Gibbon

Project title

Artificial intelligence mediated discovery and biovalidation of novel regulators of nervous system stability

Somya Iqbal

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Project title

Unravelling the circuit changes mediating the development of episodic memory

Personal note

I completed my undergraduate degree in Neuroscience at the University of Edinburgh, and I have stayed here to continue the investigation of how memory works. The project I am involved in is particularly interesting as it involves episodic memory (remembering events and experiences), which emerges fairly late in development, and is often disrupted in neurodevelopmental and neurodegenerative diseases, as well as during ageing. My aim is to identify the circuit changes that mediate the emergence of episodic memory in rats. Outside of my work, I enjoy pole dancing, foraging, brewing, and pony trekking.

Lucja Kostrzewa

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Project title

Untangling the role of microglia in colonising brain tumours through targeted drug delivery

Personal note

Hi, my name is Ellen! I just finished my integrated master’s degree in biomedical sciences at the University of York. During my undergraduate degree, I found myself drawn towards a variety of research areas, including immunology, neuroscience, and oncology. Luckily, I was able to find a PhD incorporating these areas. Under the supervision of Professor Alison Hulme, Dr Dirk Sieger and Professor Val Brunton, I will be generating a nanoparticle delivery system able to deliver therapeutics to microglia in zebrafish. It is our hope that we will be able to switch microglial behaviour from supporting tumour growth to tumour suppression. Outside of the lab I enjoy walking, mountain biking and baking (especially eating it afterwards!).

Ellen Poot

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Project title

How is the activity of IL-33 controlled by the speed of its release, and how could this affect obesity?

Personal note

Hi, I'm Josh, 25 and from Dunfermline, Scotland. I spent 5 years at the University of Edinburgh - carrying out a BSc (Hons) in Biological Sciences (Immunology) followed by a MScR in Biomedical Sciences. I left the University of Edinburgh after my MScR degree to join Professor Rick Maizels' lab at the University of Glasgow - where I have been working for 18 months prior to starting in Dundee. My studies have mostly been on the mammalian immune system - with an interest on the interface between host and pathogen.  My PhD project is asking the question - "How is the activity of IL-33 controlled by the speed of its release, and how could this affect obesity?" In this project, I will be working with Dr Henry McSorley and Professor Simon Arthur at the University of Dundee - also with Dr Cecile Benezech at the University of Edinburgh.

Josh Richards

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Project Title

How CHIP ensures health and wellbeing across the life-course

Personal Note

Hello, I’m Ailish and I will be joining Professor Kathryn Ball and Dr Maria Doitsidou’s labs at the University of Edinburgh. My project will investigate how the E3-ubiquitin ligase CHIP supports healthy ageing and wellbeing in both mammals and nematodes by identifying CHIP regulated pathways and studying how these pathways are suppressed or activated throughout the life-course. The dual functions of CHIP, as a part of the protein quality control network and as a chaperone-independent E3 ligase, make it an attractive target for therapeutic intervention in certain neurodegenerative disorders. Targeting this protein offers the prospect of abrogating the early events in toxic protein formation that are associated with ageing and cognitive decline, whilst at the same time promoting healthy ageing. Prior to undertaking this project, I completed my BSc(Hons) in Neuroscience at the University of Glasgow and then my MScR in Integrative Neuroscience at the University of Edinburgh. In my free time I enjoy singing in the uni choir, baking and listening to a good podcast!

Ailish Tynan

Project title

Modelling bovine tuberculosis infection in stem cell-derived macrophages

Personal note

Hello, I’m Emily and I’m excited to be joining Professor Hope’s lab at the Roslin Institute. I previously completed my undergraduate degree in Virology and Immunology at the University of Bristol.

Mycobacterium bovis is an important pathogen; it causes TB in cattle leading to significant economic costs and is also responsible for some cases of human TB. When M. bovis enters the lung, the bacteria are engulfed by innate immune cells called macrophages. Macrophages usually kill invading pathogens, however, M. bovis utilises various mechanisms to evade destruction and establish an infection. During my project I aim to develop methods of differentiating bovine stem cells into macrophages. I will then infect these macrophages with M. bovis and use specialised imaging techniques to investigate how M. bovis survives within macrophages.

Emily Charlton

Project title

Dynamics of mitochondrial genome complexity in trypanosomes

Zihao Chen

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Project title

Directed evolution for optimization of industrially-relevant protists (CASE)

Personal note

Hi, I’m Martina and I’m a part of Dr Andrew Free Lab at the Institute of Quantitative Biology, Biochemistry and Biotechnology, based at The University of Edinburgh. My project will be looking at enhancing the performance of Omega-3 rich protist species and developing desired phenotypes through the process of directed evolution. Depending on the selection pressure, directed evolution strategies can mediate many different evolutionary trajectories. As well, chosen strains will be characterized biochemically to shed light on various metabolic pathways and how they interconnect to produce a desired compound. The project is in collaboration with MiAlgae Ltd., a green start-up company that cultivates Omega-3 rich microalgae, by recycling industrial co-products.

Before starting my PhD I did an MSc in Biotechnology at The University of Edinburgh, with my final project investigating the structure and composition of microbial communities associated with microalga in photobioreactors under different cultivation conditions. After that I worked on a project investigating the role of CreChar® in Direct Interspecies Electron Transfer (DIET) during Anaerobic digestion, after which I spent almost two years working in the industry, in the field of algal biotechnology, as a part of a start-up microalgae production company.

Martina Dajak

Project title

Developing ovine immune 'Omics for sheep genomic improvement  

Katie Dubarry

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Project Title

Functional role of transcript diversity in salmon immunity: development of full-length RNA sequencing

Personal note

Hi, I’m Oliver and I’m part of the Macqueen lab at the Roslin Institute. My PhD project focuses on understanding transcript diversity in the immune function of Atlantic salmon, Salmo salar. The project is centred on developing methods for full-length RNA sequencing using Oxford Nanopore technology with the aim of identifying a diverse range of RNA transcripts expressed during immune challenge. The research is closely linked to the H2020 AQUA-FAANG project, which will be providing immune tissue samples for analysis, for which additional functional genomics data will be generated. Prior to my PhD, I graduated with a 1st class BSc. Marine Biology from the University of Aberdeen in June 2019 and was awarded the Gordon Rae Memorial Prize for Outstanding Performance. For my final year research project, I investigated B-cell formation and IgNAR expression in the memory response of the Nurse shark. Aside from academia, I’m an avid musician and enjoy SCUBA diving, travelling and eating!

Oliver Eve

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Project title

The role and optimisation of the microbiome in molluscum larval development

Personal note

Hi, I’m Hannah. My PhD project is focused around characterising and determining the role of the microbiome in the development of the larval stages of oysters, specifically Crassostrea gigas. Understanding more about the role of the microbiome in this way will allow us to determine better control methods for large scale mortality events in oyster hatcheries. These morality events come at a huge economic loss for the industry and make for less sustainable food production.

Before starting my PhD at the Roslin institute I completed by BSc in Biology and Biotechnology and Bangor University in North Wales where I discovered my interest in environmental microbiology. I then went on to complete my MSc in Tropical Disease Biology at the Liverpool School of Tropical Medicine where I was able to investigate the microbiome of mosquitos. I enjoyed these past studies and am excited to be continuing research in the world of microbiomes at Roslin! 

Outside of my studies I enjoy running, baking,  watercolour painting and hope to explore as much of Scotland as possible during my time here.

Hannah Farley

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Project title

Genome editing for resistance to white spot syndrome virus in whiteleg shrimp

Personal note

Hi, I’m Alex. Before starting my journey as a postgraduate student, I worked for two years under the Scottish Aquaculture group in Aberdeen focusing on salmonid immunology, viral kinetics and transcriptomics.  Now, I am a PhD student at the Roslin Institute in Edinburgh working under Prof Ross Houston and Dr. Diego Robledo. The main goal of my project is to generate whiteleg shrimp that are resistant to whitespot syndrome virus (WSSV), one of the most widespread and lethal viruses for shrimp populations. The experimental work will require understanding the mechanisms of host response to the virus to generate potential targets, and optimization of genome editing techniques in shrimp.

Alexandra Florea

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Project title

A holistic approach to internal parasite control on hill and upland sheep farms

Personal note

Hello, I am Eilidh and I have recently started my PhD studentship at Moredun Research Institute, in collaboration with the SRUC and University of Edinburgh. This project aims to optimise internal parasite control on hill and upland sheep farms at a farm level. Hill and upland sheep farming represents around 60% of the whole agricultural area in Scotland, yet is becoming increasingly challenging particularly due to parasite infections. Therefore, effective parasite management is essential, especially when faced with increasing resistance to anthelmintic products.

I previously completed BSc in Veterinary Biosciences from the University of Glasgow, with my final year project investigating the occurrence and pathogenicity of adult rumen fluke. I have also since completed a 12-month Master of Veterinary Medicine by research programme, also at the University of Glasgow, to improve the use of existing and new data sources for the scanning surveillance of sheep scab.

Away from research I enjoy baking, playing in a big band, and I also run a small business drawing pet portraits.

Eilidh Geddes

Project title

A global assessment of aquaculture products from a food systems and value chain perspective towards the development of a personal environmental/health impact tool

Project title

Pesticide problems for honey bees: a closer look in our towns

Linnet McGregor

Project title

Genomic epidemiology of bovine mastitis pathogens

Logan Newstead

Project title

Improving the efficiency of beef production through the use of precision farming technologies and machine learning techniques

Holly Nisbet

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Project title

Novel approaches to improving calf health: new technology and data analytics

Personal note

I graduated as a veterinary surgeon from Liverpool University in 2016. After this I spent 3 years in rural mixed practice in Northern Ireland and west Wales before returning to academia and have recently completed my MSc in Livestock Science at Aberystwyth University. I am passionate about herd health and early detection and intervention in disease. My PhD project is supervised by Marie Haskell, Carol Anne-Duthie and Colin Mason at SRUC as well as Alex Corbishley from the Edinburgh vet school. Calves are the future of any herd and it is crucial to get the first months of life right. I’m really excited to be working on research that could provide tools to farmers in for early diagnosis and treatment of disease. I will also be working to further our understanding of nutrition and immunology in early life. In my spare time I enjoy walking, circus skills and relaxing with my cats.

Bethan Riley

Project title

Design of breeding programs to improve honeybee health and production

Laura Strachan

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Project title

Genome, epigenome and environmental interactions in RAS reared Atlantic salmon

Personal note

Hi I’m Mette. I previously studied marine biology at university of Aberdeen, and evolutionary genetics at Edinburgh University am now going be working on a PhD mainly based at the University of Stirling, within the Institute of Aquaculture, focusing on the genetics of important traits of farmed Atlantic salmon and the way in which domestication and aquaculture environments interact and affect these. This is with the aim to aid future selective breeding programs and contribute to farmed salmon as a sustainable food source. 

Mette Tollervey

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Project title

The epidemiology of bovine viral diarrhoea (BVD) in the Tanzanian small holder dairy sector

Personal Note

I recently started my Phd  at the University of Edinburgh and I will be based at the RDVS and Roslin institute researching on the epidemiology of BVD. BVD is a disease with significant negative impact on any economy and, among other infections, it one of the neglected infectious diseases in Africa. Focusing on LMIC, we are collecting serum samples form dairy farms in East Africa to test for antibodies and viral sequencing. The aim of the project is to understand the susceptibility or resistance of cross breeds of cattle to BVD using data on age, location, calving history and other parameters; also, to develop statistical and dynamic models to identify risk factors In order to estimate transmission of the disease and the economic impact, thereby  formulate effective control and prevention measures.

This project will be supervised by Dr Rob Kelly and Prof Mark Bronsvoort in Edinburgh and Dr Annie Cook at the ILRI.  

I have an MSC in Public Health Research obtained from the University of Edinburgh and a Doctor of Veterinary Medicine (DVM) degree from Nigeria. 

Bibiana Zirra-Shallangwa

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Project title

Regulation of plant cell-to-cell communication

Personal note

Plasmodesmata are the channels between adjacent plant cells that allow for direct cell-to-cell communication essential for development, however, viruses also use plasmodesmata to spread throughout the plant . My project is to study the interactions of plasmodesmata associated proteins and investigate plasmodesmata phenotypes.

At King’s College London, I completed my undergraduate in biochemistry, became fascinated with protein function and (with a more medically inclined department) frequently found myself wondering why we weren’t always talking about plants. I am excited to begin working at the James Hutton Institute supervised by Dr Jens Tilsner, Dr Piers Hemsley and Dr Alison Roberts.

Away from biochemistry, I’m happiest swimming (if not in the lab, find me in the nearest pool, lake or sea) or wandering an art gallery.

Bibiana Zirra-Shallangwa

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Project title

Novel regulatory mechanisms in peripheral nerve development and disease

Personal note

Hi, I’m Stephen. I’m a PhD student in the Centre for Discovery Brain Sciences. My supervisors are Prof Dies Meijer and Dr Alasdair MacKenzie. My project focuses on the peripheral nervous system, specifically the molecular interactions between Schwann cells and axons. I will investigate the roles that the protein LGI4 and transmembrane receptor ADAM22 play in myelination and disease.   

Before starting my PhD, I completed a BSc in Biomedical Sciences at the University of Sheffield and an MSc in Translational Neuroscience at the Sheffield Institute of Translational Neuroscience (SITraN). Most recently, I have worked as a research technician at SITraN on the Fox Foundation project; Does Mitochondrial Dysfunction in the skin predict that in the Brain?  (Prof Oliver Bandmann, Dr Heather Mortiboys & Dr Thomas Payne). Outside of science, I spend my time doing CrossFit, photography and Munro bagging.

Stephen Bradley

Project title

Cerebellar and basal ganglia contributions to motor learning

Personal note

My project is supervised by Professor Ian Duguid and aims to understand how signals from the cerebellum and basal ganglia develop during the learning of a novel motor task. Prior to my PhD, I studied Medicine at Oxford before moving to UCL to study Neuroscience. I then came to Edinburgh for my Masters and am excited to be continuing to study the motor system as part of the EASTBIO DTP.

Thomas Clarke

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Project title

Temporal Adaptation to Antifungal Treatment in Pathogenic Fungi

Personal note

Hi, I am Eszter, my project is co-supervised by Dr Delma Childers (University of Aberdeen) and Dr Edward Wallace (University of Edinburgh). The aim of my project is to improve our understanding how fungal cells initially sense and respond to antifungal agents using the model yeast, Saccharomyces cerevisiae, and the clinically relevant yeast, Candida glabrata. First, I will focus on how antifungal exposure over time alters gene expression and protein translation. Later the validity of these observations will be tested on genetically modified yeast created by CRISPR-Cas9 gene editing.

I’ve completed my undergraduate degree at the University of Aberdeen as well. In my free time I enjoy fencing, cooking, and reading fiction.

Honours and prizes: Molecular Biology Project Prize, University of Aberdeen 2020

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Project title

Control of the ParaHox genes in chordate evolution and development

Personal note

Hi, my name is Anastasia. I am a PhD student in the Evolutionary Developmental Genomics (EDGe) research group at St Andrews University. My PhD is going to investigate how ParaHox genes are regulated in the chordates using two model species, the chicken and the sea squirt (web search "Ciona intestinalis").  

ParaHox genes are important in body plan patterning during development. When they are mis-regulated they are linked with disorders such as type II diabetes and colon cancer. To investigate how ParaHox genes are regulated I will be using specialist techniques such as electroporation, generation of gene reporter constructs, comparative genomics and gene expression analysis.  

I am a graduate from St Andrews University, where I did my BSc in Biochemistry. During my degree I was awarded The Laidlaw Leadership and Research Scholarship, where I had the opportunity to develop my leadership skills and I undertook a research project with the EDGe group.

This research was both enjoyable and influential in my pursuit of this topic through a PhD.

In my very little spare time I enjoy painting, badminton and improvisation on my saxophone. 

Anastasia Ellis

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Project title

Understanding the activation and control of bacterial cyclic-oligonucleotide based anti-phage systems, in mediating bacterial protection

Personal note

Hi, I’m Laura. I have recently started my PhD studentship at the University of St Andrews, under the supervision of Professor Malcolm White. My research will be focusing on developing understanding of the activation and control of complex anti-phage CBASS systems within bacteria.  CBASS utilise cyclic oligonucleotide signalling to provide immunity via the activation of a range of abortive mechanisms, such as endonuclease activity, within the infected cell. These systems are incredibly widespread and diverse with links to type III CRISPR systems and human cGAS-STING. However, fundamentals regarding their activation and regulation are unknown.

I completed my undergraduate at the University of Exeter in Biosciences, specialising in Molecular and Cellular Biology, having undertaken a placement year in Shell Biodomain, Houston. Here, I worked on optimising the microbial production of high value chemicals and confirmed my ambition to build a career within research.

Alongside my research, I enjoy rock-climbing and travelling, both of which I can’t wait to do more of as soon as COVID allows!

Laura Gaskell-Mew

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Project title

New plant species from old genes?

Personal note

I completed my undergraduate degree in Evolutionary Biology at the University of Edinburgh and an MSc in Bioinformatics at the University of Glasgow. I am now returning to Edinburgh for my PhD, investigating adaptive evolution in Antirrhinums, supervised by Andrew Hudson. This project aims to examine whether hybridisation can account for rapid evolution in the plant genus Antirrhinum. There are two forms of Antirrhinums, either small alpines or larger lowland plants. The two forms are typified by two sympatric species in South-East Spain, which hybridize and share much of their genomes but remain morphologically distinct. I aim to test whether the alpine and lowland forms of Antirrhinum are maintained by ecological adaptations and whether the two species evolved from hybridisation between older lowland and alpine species.

Emily Haley

Project title

The RNA-bound proteome

Michaela Kompauerova

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Project title

Fluorescent lifetime imaging of proteins in the brain

Personal note

I have completed a Master’s degree in Medicinal and Biological Chemistry at Edinburgh which included a 12-month industrial placement at AstraZeneca. I am hoping to use my experience and skillset as a chemist to tackle multidisciplinary research during my PhD at Edinburgh, in Dr Mathew Horrocks’ lab. My project will focus on developing fluorescent peptide probes as visualisation tools for fluorescent lifetime brain imaging. Through combining highly specific and sensitive probes with a novel microscopy technique, we hope to gain a better understanding of protein aggregation and its role in aging and disease-related processes.

Outside of the lab, I am a theatre-lover (with some voice acting experience and a performance during Edinburgh Fringe under my belt), and an experimental baker (specialising in bakes with weird/non-cake-like ingredients).

Zuzanna Konieczna

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Project title

Evolutionary consequences of mutation rate variation in bacteria

Personal note

Hi I'm Lucy! I studied physics and mathematics at the University of Cologne in Germany. During my masters I specialised on statistical and biological physics which convinced me to do research in the field of evolutionary biology. Previously I have worked on Contingency and Entrenchment in Fitness Landscapes at the Institute for Biological Physics in Cologne and on Evolutionary Rescue from Mutational Meltdown at the Instituto Gulbenkian de Ciência in Oeiras, Portugal. Starting October 2020 I will be part of Helen Alexander's lab at The University of Edinburgh to work on Evolutionary Consequences of Mutation Rate Variation in Bacteria. I am excited to apply my mathematical skills to this fundamental question and keen to learn more about microbial biology. In my free time I enjoy climbing and hiking and am looking forward to explore Scotland's nature.

Lucy Lansch-Justen

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Project title

Functional genomics for understanding behaviour and learning in a single-celled brainless blob, the slime mould Physarum polycephalum  

Personal note

My name is Anastasia Leligdowicz, I will be starting a PhD at the University of Aberdeen using epigenetics (changes in gene expression) and functional genomics (assigning function to genes) to understand the learning and memory of a single-celled brainless blob, the slime mould Physarum polycephalum.

Physarum polycephalum is an intriguing creature! It’s a protist who can solve ‘intelligent’ problems, such as finding its way through a maze and create an efficient intercellular network for the transportations of food and nutrients. My project endeavours to try to understand the learning and memory of this peculiar creature and to see what this reveals about the concept of memory.

Physarum polycephalum

I am a graduate from Queen Mary University of London, with a BSc Honours in Biology. At my time at Queen Mary, I worked as a member of the Hanson Lab researching microbial ecology of Desulfotomaculum (a thermophilic sulphate reducing bacteria found in the arctic sediment). Where I looked into the spatial distribution of the bacteria in arctic sediments, to see that it would reveal about it’s source.

Personal website

Anastasia Leligdowicz

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Project title

Trimming the Fat – Identification of De-S-Acylating Enzymes from Plants

Personal note

Hi, I’m Kara and I graduated with a BSc in Biological Sciences (Plant Sciences) from the University of Dundee. During my undergraduate honours project, I investigated the mechanisms which regulate Phospholipase C membrane association in growing tobacco pollen tubules. I will be completing my PhD with the University of Dundee, carrying out my research at the James Hutton Institute with Dr Piers Hemsley. The aim of my project is to identify and characterise members of the enzyme family which carry out protein de-S-acylation in plants. S-acylation is a reversible post-translational modification involved in the regulation of many important plant processes ranging from growth and development, to defence against pathogens. In my spare time I enjoy baking, reading, and gardening. I also love live music, theatre, and watching football.

Kara McHugh

Project title

Molecular basis of environmental sensing in fungi and protozoan parasites

Rachael Murray

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Project title

Scalable cell-free manufacturing of diverse therapeutic proteins

Personal note

I am working on the scaling up of industrial Cell-Free Protein Expression in partnership with Fujifilm-Diosynth. Prior to joining the cohort, I completed an MRes in Synthetic Biology at Imperial College under the watchful eyes of Drs Polizzi and Ceroni, where I worked on optimising Quorum-Sensing devices using directed-evolution and investigating of metabolic burden via RNA-seq analysis.

In the private sector, I spent a stint working under Dr Martin on neonatal stem-cell storage and differentiation at Cells4Life and collaborated with OpenCell to develop a cheap, opensource, automated, high-throughput Covid-19 RT-qPCR testing system.

As a fresh-faced undergraduate, I obtained Biomed BSc from UCL, where I focused on molecular mechanisms of HepC-induced cellular changes and the lasting effects of Ebola Virus during convalescence.

Generally, I am interested in how modern computing and statistical methods can be applied to Bio-Big Data to find better solutions in bioengineering applications.

Alex Perkins

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Project title

Surveying epigenetic regulation of differentiation and pluripotency in developmental cell models

Personal note

I am undertaking my PhD project in Professor Richard Meehan’s lab at the Institute for Genetics and Molecular Medicine at the University of Edinburgh, co supervised by Prof. Sari Pennings (Edinburgh) and Prof. Frank Gunn-Moore (St. Andrews).

My project is aimed at understanding fundamental epigenetic processes in embryonic development. These mechanisms are involved in regulating gene expression during the differentiation of stem cells into the range of cell types present in an adult organism, however their exact roles at different stages are unclear. Part of my project will involve generating 3D cell models of the early embryo as well as imaging by light sheet microscopy.

Previously I completed my undergraduate degree at the University of York during which I spent a year doing a research placement at the Centre for Genomic Regulation in Barcelona. Experiences at both institutes got me interested in epigenetics, gene regulation and microscopy. Since graduating I have also worked as an intern in the technology transfer department of Cancer Research UK. Outside the lab I enjoy baking and exploring the beautiful Scottish outdoors.

Katherine Pickup

Project title

Forward engineering of pattern formation: Models and experiments towards predictive multicellular self-organisation

Miguel Robles Garcia

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Project title

Prediction of specificity determining sites in proteins from human population genetic variation by deep learning

Personal note

Hi, I am Javier. I graduated with a BSc in Genetics from Universitat Autònoma de Barcelona in 2018. After that, I graduated with an MSc in Bioinformatics for Health Sciences from Universitat Pompeu Fabra. I carried out my master thesis at the Barton Group, in the University of Dundee. My work consisted in exploring the distribution of human variants in the ankyrin repeat protein family and explaining the observed variant distribution patterns with structural features such as protein-protein interactions and intra-domain contacts.

The results of this research

My PhD project is supervised by Prof Geoff Barton and Prof Ulrich Zachariae. It revolves around the prediction of specificity determining sites in proteins by means of population genetic variation, amino acid conservation across homologues and structural features. Amongst other things, I enjoy running, good coffee, meeting friends and a good movie.

Javier Sanchez Utges

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Project title

Dissecting centromere identity and epigenetic inheritance  

Personal note

Hi, thank you for reading this, I’m Hwei Ling, from Singapore (SG). I feel great honour and privilege to be embarking on my PhD project under the tutelage of my supervisors Dr Patrick Heun and Dr A. Jeyaprakash Arulanandam, and lab mates at the Michael Swann building, University of Edinburgh, with thanks to the EASTBIO program for this opportunity. My project will be focusing on the detailed investigation of the protein-protein interactions between the Drosophila spp. Centromere protein A (an essential histone H3 variant that epigenetically defines the centromere) and its deposition factors to understand how these factors contribute to the mechanism of CENP-A nucleosomal deposition and propagation at the centromere. The experimental work will borrow knowledge and technical expertise from areas like proteomics and mass spectrometry, protein purification technology, structural biology, protein crystallography and microscopy. 

I have completed both my BSc in Cell and Molecular Biology and MSc (by research) at the National University of Singapore. I have worked as a Research Assistant prior and during my Masters, and have been fortunate to participate in a wide range of projects, from the study and classification of renal cell carcinoma to the study of epigenetics and centromere inheritance, with main interests in the systematic investigation of the function of the fission yeast CENP-A amino-terminal domain. 

Out of lab, I enjoy reading. On days of fine weather, I like taking nature walks, hikes, gardening and general exploration on my kick scooter.  

Hwei Ling Tan

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Project title

The neural basis of descending motor control (CASE)

Personal note

Hi, I’m Annamaria! My project is supervised by Dr Maarten Zwart and Dr Stefan Pulver at the School of Psychology and Neuroscience at the University of St. Andrews. Before undertaking this PhD, I completed a BSc (Hons) Biochemistry just across town- at the University of St. Andrews’ School of Biology.

My project aims to investigate the extent to which the brain controls how movements and the finer details thereof are performed, using the fruit fly as a model organism. By doing so, I will be further investigating previous findings which evidenced that the brain’s involvement in neural pathways goes beyond sending commands to the spinal cord for it to start, stop, or change movements, as previously thought. Using connectomics, optogenetics, as well as lightsheet microscopy and voltage imaging to detect neural activity, I hope to contribute to the collaborative effort of producing a full wiring diagram of the fruit fly’s nervous system. I will also be working with Cairn Research as part of my Industrial CASE Studentship to develop or test open-access software for synchronising multiple data streams. In addition to my studies, I enjoy listening to music, painting, photography, reading, and going on walks.

Annamaria Wakileh