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GenerationResearch Equity in summer research

University of York only studentships

The studentships below are for University of York students only. Please note the location of each project supervisor as this will be where the project will be hosted.

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In your application, you can choose two projects from any of the drop down projects on this webpage.

University and Industry funded studentships

The following studentships are open to all 2nd and 3rd year York students (including 3rd year leavers and those going onto an integrated Masters degree) and 4th year students finishing an integrated Masters degree. Studentships are also open to HYMS students in Phase 1 of their studies.

Novel fluorescent polymer nanoparticles as a biomarker for cells

Location: York

Project Supervisor and description: Dr. Karen Hogg, Technology Facility, York

Novel fluorescent polymer nanoparticles as a biomarker for cells

10 weeks (full time 37 hours per week, £9.77 per hour, £1,000 consumables)

The use of fluorescently tagged antibodies, recognising specific proteins has been invaluable to scientists in identifying immune cells and to visualise cell structures using flow cytometry and microscopy. Stream Bio have developed fluorescent polymer nanoparticles (CPNs) as probes for a variety of life science applications including imaging ELISA, Western blot and lateral flow tests. The probes are extremely bright compared to other fluorescent makers and are very photostable. Students will work closely with the industrial partner to assess the ability of antibody conjugated CPNs to bind cells and use as fluorescence biomarkers for light microscopy, flow cytometry, and other novel applications. Samples of conjugated CPNs will be supplied by Stream Bio and tested alongside proven commercially available reagents on relevant research samples. Weekly updates with the product development development team will be required to ensure modifications or improvements to the CPNs performance can be implemented rapidly. Flow cytometry and light microscopy training will be provided and the student will present findings at a research day in York.

Studying antigen expression factories in African trypanosome parasites

Location: York

Project Supervisor and description: Dr. Joana Faria, Biology Dept., York

Studying antigen expression factories in African trypanosome parasites

10 weeks (full time 37 hours per week, £9.77 per hour, £700 consumables)

Antigenic variation is a highly sophisticated virulence mechanism. Several pathogens, such as African trypanosomes and malaria parasites, are able to systematically alter the identity of proteins displayed to the host immune system. At any given time, trypanosomes express only one variant-surface-glycoprotein (VSG) from thousands of possible genes. Notably, the single active-VSG coding-locus is transcribed at very high levels within a dedicated nuclear body, like an ‘antigen expression factory’.  To study its architecture, ultra-structure expansion microscopy (U-ExM), will be used. Perturbations of known protein components will also be studied by RNAi, global or site-specific transcription inhibition using chemicals, and genetic reporters. The successful candidate will learn how to culture and genetically manipulate trypanosomes, as well as to prepare, image and analyse U-ExM samples in order to visualise specific proteins and DNA sequences, using a technique which is quickly becoming an important molecular biology tool.  Students will present their work at a research day in York.

Seeing the light: Quantifying LED light emissions in controlled environments

Location: York

Project Supervisor and description: Mr. Jason Daff, Horticultural Facility, York

Seeing the light: Quantifying LED light emissions in controlled environments 

10 weeks (full time 37 hours per week, £9.77 per hour)

The horticultural technical team at University of York involves a network of highly experienced technicians that support the work of the Centre for Novel Agricultural Products, which is tasked with improving food security, plant technology, and climate-resilience. The student will be based within this team to help manage the controlled environment plant-growing facilities, including watering and propagation. Alongside this, the student will undertake a research project sponsored by the UK Controlled Environment Users’ Group (CEUG) investigating the intricacies of quantifying the outputs of artificial light sources using Photosynthetically Active Radiation (PAR) quantum sensors and spectrophotometers. The student will be given all necessary training, present their findings at a research day, and be supported (fees and travel expenses) to attend the UK CEUG Annual Conference at the University of Birmingham in September 2022.

Identification and characterisation of novel inflammasome mediators

Location: York

Project Supervisor and description: Dr Dave Boucher, Biology Dept., York

Identification and characterisation of novel inflammasome mediators

9 weeks (full time 37 hours per week, £9.77 per hour)

The innate immune system is the body's first line of defence against infections, orchestrating inflammation to protect the host. Our lab is studying the inflammasome, large molecular signalling platforms that activate signalling proteases called inflammatory caspases. These responses involve the maturation and secretion of inflammatory cytokines and the execution of a process called pyroptosis. Although caspases are critical drivers of immune disease (Crohn’s disease, sepsis) our knowledge of caspase substrates is currently limited. We recently identified novel substrates in human epithelial cells. Through this exciting project (funded via York Unlimited), the selected candidate will be trained in biochemical approaches (protein expression and purification, enzymology) to validate and characterise these substrates (DNA transfection and western blotting). The selected candidate will be directly involved in the lab activities, as well as presenting their findings at a research day.

The Laboratory of Molecular Biology

Location: Cambridge 

Project Supervisor and description: Laboratory of Molecular Biology, Cambridge

The Laboratory of Molecular Biology, Cambridge, funded by the Max Perutz Fund

10 weeks (full time 37.5 hours per week, paid at LMB rate, Band 7)

The Laboratory of Molecular Biology, the flagship institute of the Medical Research Council, is considered one of the birthplaces of molecular biology, with its scientists winning numerous Nobel Prizes over the last 70 years for discoveries such as monoclonal antibody technology, DNA sequencing, and CryoEM. For this studentship the LMB will host a York student to gain hands-on experience in a research project at this world famous laboratory. You will join one of the research groups at LMB and carry out original research, working alongside LMB scientists or work within one of the world-class facilities at the LMB. You will meet other undergraduates and will take part in activities with our postgraduate research students. The internship is fully funded by the Max Perutz Fund and students will present their work at a research day in York.

Investigating the role of TRIM24 in macrophage signalling

Location: York

Project Supervisor and description: Dr. Elmarie Myburgh, Biology Dept., York

Investigating the role of TRIM24 in macrophage signalling

10 weeks (full time 37 hours per week, £9.77 per hour, £700 consumables)

HYMS Logo

Macrophages are immune cells vital to combating infection and ensuring homeostasis. They are extremely heterogeneous, possessing a plethora of functions ranging from the capture and removal of invading pathogens to aiding in wound healing and tissue repair. We are interested in investigating the molecular mechanisms present within macrophages that fine tune their activation during inflammation and infection. We have previously identified the cell regulatory protein TRIM24 as a predicted negative regulator of pro-inflammatory macrophage activation. For this project, the student will investigate wild-type and TRIM24-deficient macrophages, exposed to pro-inflammatory stimuli, using a cutting-edge flow cytometry-based technique called phosphoflow. The aim is to provide a broader view of how these pathways change over time after stimulation, and how they are affected by the absence or overexpression of TRIM24. The student will learn valuable techniques such as the in vitro culture of primary immune cells and flow cytometry and students will present their work at a research day in York.

Investigating inorganic carbon uptake in the algal C02 concentrating mechanism

Location: York 

Project Supervisor and description: Dr. Charlotte Walker, Biology Dept., York

Investigating inorganic carbon uptake in the algal CO2 concentrating mechanism

10 weeks (full time 37 hours per week, £9.77 per hour, £700 consumables)

Approximately 30% of global photosynthesis is conducted by eukaryotic algae. To enhance their photosynthetic output, algae operate a CO2 concentrating mechanism (CCM). My research focuses on characterising bicarbonate channels in the algal CCM. The impact of the research is to understand algal carbon fixation but also feeds directly into an effort to engineer a CCM into C3 crop plants. If successfully introduced, a CCM could increase yield by up to 60% and directly alleviate global food security issues. We have recently generated several bicarbonate channel knock-out mutants using CRISPR Cas9. These mutants need extensive characterisation to fully understand the impact the knock-out has on the algal CCM. Techniques applicable include algal culturing and growth experiments; general molecular biology (PCR, cloning etc); protein biochemistry and confocal microscopy. I am open to tailoring a project based on the student’s interests and career development goals. The project would be laboratory based, with some data analysis as the project develops. The students will take part in regular lab meetings and journal clubs, so they get a well-rounded research experience. Students will present their work at a research day in York.

Extending the data analysis pipeline to understand Long COVID

Location: York

Project Supervisor and description: Dr. Adar Pelah, Engineering Dept., York

Extending the data analysis pipeline to understand Long COVID

10 weeks (full time 37 hours per week, £9.77 per hour, £1000 consumables)

YBRI logo

Estimates suggest over 1.3 million people in the UK are suffering From Long COVID, the name given to multi-system effects that may persist for weeks, months and possibly even years after recovery from COVID19 infection. Using technology developed by the Laboratory for Intelligent Virtual Environments (LIVE) a functional movement and cognition dataset is being collected with clinical partners on a large cohort of post-acute COVID patients. Analysis of this dataset may extend our understanding of long COVID, leading to the development of new diagnostics and treatments. The student would be part of a core team of researchers and other students tasked with identifying hypotheses, devising methods, applying analyses, testing for statistical correlation, and building models of the disease. Medical advisory is available from clinical partners, including an NHS rheumatology consultant, senior NHS research physiotherapists, PhD students, HYMS medical students and others engaged with the study. Project outcomes would include a pragmatic research toolset and clinical resource that exploits the opportunities presented by the dataset, with specific activities tailored to the skills and interests of the student. Students will present their work at a research day in York.

Inducing barriers to DNA replication in yeast to study genomic instability

Project Supervisor and description: Dr. Aisha Syeda, Biology Dept., York

Inducing barriers to DNA replication in yeast to study genomic instability

8 weeks (full time 37 hours per week, £9.77 per hour, £1,000 consumables)

DNA replication (R) is a highly orchestrated process that occurs exclusively in the S-phase of the eukaryotic cell cycle to avoid conflicts with other DNA-associated processes. Transcription (T) is another fundamental process that also utilises DNA as the template. To avoid collisions between these important pathways, cells have evolved many mechanisms to protect DNA integrity and prevent genome instability, such as that seen in cancer. Genetic manipulation of the rDNA locus in budding yeast, S. cerevisiae provides a perfect model to study the effects of these R-T collisions. In the Leake lab the student will use molecular cloning to introduce an artificial barrier to replication in yeast and establish conditions in which we see compromised yeast viability, in order to provide an assay where nucleoprotein libraries can be assessed for their role in genome stability. Students will also be exposed to experimental planning and data analysis. Students will present their work at a research day in York.

Studying ESR1 dysregulation in oestrogen receptor-positive breast cancer

Location: York 

Project Supervisor and description: Dr. Weiye Zhao, Biology Dept., York

Studying ESR1 dysregulation in oestrogen receptor-positive breast cancer

8 weeks (full time 37 hours per week, £9.77 per hour, £960 consumables)

Breast cancer is one of the most common forms of solid tumour, malignant disease. We now understand that this disease exists in many forms, depending on the particular genetic mutations contained within the tumour.  Understanding these differences and the molecules involved has and will continue to unlock new therapeutic options. In the Holding lab we wish to understand the role of ESR1 in oestrogen receptor-positive breast cancer.  ESR1 is dysregulated in this form of breast cancer, but the transcriptional regulators that control expression are unknown. The student will study ESR1 by developing an unbiased proteomics platform, new to York, in order to investigate ESR1 interacting partners. Students will receive training in in vitro tissue culture, plasmid design, CRISPR/Cas9, immunoprecipitation, and data analysis. Students will present their work at a research day in York.

Measuring plant growth in response to seasonal change using machine learning

Location: York 

Project Supervisor and description: Dr Sarah Lock, Biology Dept., York

Measuring plant growth in response to seasonal change using machine learning

8 weeks (full time 37 hours per week, £9.77 per hour, £640 consumables)

Developing crops with similar growth rates to ensure that during harvest more plants are at an appropriate stage would increase yield and reduce waste. In this project the student will work in the Ezer lab to first measure the effect of shifts in photoperiods on hypocotyl lengths in different Arabidopsis populations before developing a novel machine learning approach to automate this process.  Thus, this will provide an excellent opportunity to work on an interdisciplinary project to gain experience in lab-based experimental techniques, bioinformatics analysis, experimental design, and time management. Students will present their work at a research day in York.

The effect of extracellular matrix proteins on blood stem cell purity, in vitro

Location: York 

Project Supervisor and description: Dr. Juan Rubio-Lara, Biology Dept., York

The effect of extracellular matrix proteins on blood stem cell purity, in vitro

8 weeks (full time 37 hours per week, £9.77 per hour, £1,000 consumables)

Haematopoietic stem cells (HSCs) are essential in the generation of the billions of red and white blood cells we need everyday. In the Kent lab we are interested in investigating the molecular pathways that control these cells. It is not only necessary for understanding this process of haematopoiesis, but also holds great promise for generating red blood cells and immune cells outside of the body for therapeutic applications. The project combines the fields of material science and biology to investigate the effects of extracellular matrix proteins on HSC quiescence and fitness. To do this the student would be trained in flow cytometry, in vitro cell culture, and the engineering of artificial cell niches and would also have the opportunity to collaborate with the Krauss and Johnson labs in the engineering Department. Students will present their work at a research day in York.

BBSRC Studentships: the building blocks of life

The following studentships are open to second year (BSc) and third year (integrated Masters) York students.

Furthering the capabilities of CryoEM at York

Location: York 

Project Supervisor and description: Dr Jamie Blaza, YSBL, Chemistry Dept., York

Furthering the capabilities of CryoEM at York 

10 weeks (full time 37 hours per week, £9.77 per hour, £700 consumables)

Electron cryo-microscopy (cryoEM) is a rapidly expanding field that allows biological molecules to be imaged to resolve their 3-dimensional structure. Recently, the University of York has established a powerful Glacios electron microscope housed within a custom-designed building. We are beginning a program of further exploring the capabilities of the Glacios, optimising our experimental workflows and installing new capabilities. The successful candidate will work closely with academics, facility staff, and representatives from Thermo Scientific, the manufacturer of the microscope to help us do this. We will explore how best to run our sensitive detector by making measurements of its sensitivity (‘detective quantum efficiency’) at different electron exposure rates (‘fluences’). Then, we will collect real datasets on test samples and reconstruct 3D maps using advanced computational techniques. This project will provide in-depth training in sample preparation, operating an electron microscope, and processing data. Given the rapidly expanding use of cryoEM and its application to fields such as drug design, the project is an excellent way to prepare an undergraduate to work at the cutting-edge of molecular bioscience. Students will present their work at a research day in York.

Understanding viral ‘recoding’ during protein synthesis

Location: York 

Project Supervisor and description: Dr. Chris Hill, Biology Dept., York

Understanding viral ‘recoding’ during protein synthesis

10 weeks (full time 37 hours per week, £9.77 per hour, £700 consumables)

Accurate translation of mRNA by the ribosome is essential for all life, with spontaneous error rates of only ~ 1 in 100,000 codons. When RNA viruses infect cells, they frequently make proteins that differ from the genetically encoded sequences, using mechanisms such as frameshifting, StopGo peptide release and stop codon readthrough. These highly regulated ‘recoding’ events are vitally important to viral gene expression. We are developing a new in vitro reporter assay to study the kinetics of viral recoding events. This system uses fluorescently labelled nanobodies to directly observe single ribosomes in real time. The student will purify nanobodies and their target peptides, and investigate these interactions using a variety of biophysical techniques. Training and close experimental supervision will be provided to allow you to develop skills in protein expression (E.coli) and purification, fluorescent dye labelling and biophysical techniques including isothermal titration calorimetry and surface plasmon resonance. Quantitative data analysis, time management and record keeping will also be expected and the student will present their findings at a research day in York.

Characterisation of the host recognition apparatus of a gene transfer agent

Location: York 

Project Supervisor and description: Dr. Pavol Bardy, YSBL, Chemistry Dept., York

Characterisation of the host recognition apparatus of a gene transfer agent

10 weeks (full time 37 hours per week, £9.77 per hour, £700 consumables)

Bacteria are a key component of our microbiome and the causative agents of many infectious diseases. Although there is an arsenal of common therapies to fight major pathogens, many bacterial species become resistant to antimicrobials. Gene transfer agents (GTAs) are virus-like particles capable of transferring antimicrobial resistance genes among bacteria at high frequencies. It remains elusive what is the clinical impact of this transfer as the host range determinants of the GTAs are poorly studied. This project aims to describe how the host recognition apparatus of a model GTA particle works. The student will be responsible for producing chimeric GTA virions that contain putative host receptor-binding domains originating from GTAs that recognise different species. The putative binding domains will be cloned into expression vectors as translational fusions to produce functional hybrid proteins. Then, the recombinant constructs will be transformed into the GTA producer strain. Recombinant GTA production will be induced, and their adsorption and gene delivery abilities tested using gene transfer bioassays and selective screening. The project is suitable for Biology or Chemistry students with a deep interest in microbiology, molecular biology, or gene engineering. Students will present their work at a research day in York.

A mechanical model of cell rounding to understand eukaryotic cell division

Location: Sheffield 

Project Supervisor and description: Dr Buddho Chakrabarti, Physics Dept., Sheffield

A mechanical model of cell rounding to understand eukaryotic cell division 

10 weeks (full time 37.5 hours per week, £9.77 per hour, £700 consumables)

Cell division in eukaryotes has been widely studied and while the key molecular components have been identified, their collective properties continue to elude us. This project will develop a mechanical model of cell rounding and force generation based on statistical physics of soft active matter. We will build a hypothesis to address the collective behaviour of pliant components of a dividing cell. Our model will connect the elastic constants that dictate the mechanics of the cell at a macroscale to the interaction energies among constituent biomolecules and their associated chemical reaction rates. This will identify key criteria for cell rounding in mitosis, The student will be exposed to theoretical and computational techniques at the forefront of soft-matter and biophysics research. These include coarse-grained simulation packages and parallel computing on the Sheffield High Performance Computing Cluster. In addition, we will explore analytical methods involving active hydrodynamics applied to cell division. Although this project is primarily computational, the student will also have the opportunity to work with Dr. Matthews’ Lab to assist with cell culture experiments in this collaborative project and will also present their work at a research day with other summer students in York.

Using CryoEM to understand nucleosome and transcription factor binding

Location: Sheffield 

Project Supervisor and description: Dr. Archna Shah, Biosciences Dept., Sheffield

Using CryoEM to understand nucleosome and transcription factor binding 

10 weeks (full time 37.5 hours per week, £9.77 per hour, £700 consumables)

Understanding the rules which transcription factors (TFs) follow in the cell nucleus in order to regulate gene expression changes forms a fundamental field in cell biology. This question, combined with the cutting edge technology, Electron cryo-microscopy (cryoEM) allows a unique opportunity for us to visualise these transcriptional interactions to resolve their 3-dimensional structure. The successful student will work on a model enhancer system in order to understand how TFs  access the DNA in this area. Nucleosomes will be reconstituted from purified histones and DNA in vitro and their quality checked by EM. Alongside data processing, TFs will be expressed and purified, leading towards CryoEM of nucleosome/enhancer, DNA/TF complexes. The student will become a fully integrated member of the lab, learn protein expression and purification, participate in EM data acquisition, and become independent in their experiments and time management. The student will present their work at a research day in York along with other summer students from the scheme.

Network approaches to metabolic pathways in cancer

Location: Sheffield 

Project Supervisor and description: Dr. Giuliano Punzo, Engineering Dept., Sheffield

Network approaches to metabolic pathways in cancer

10 weeks (full time 37.5 hours per week, £9.77 per hour, £700 consumables)

Regulation of tissue growth can be achieved by altering cell metabolism. Fine control of cell metabolism can be achieved through either altering substrates availability in the environment, or enabling/inhibiting reactions in various metabolic pathways. Set at the intersection of network science, bioinformatics and cell metabolism, this project aims at identifying systemic approaches to identifying, hence modifying, metabolic pathways by solving the minimum cut problem on metabolic networks, obtained through experimental data by Dr Elena Rainero, which are known to be involved in the growth of tumour masses. The Rainero lab performed metabolomics experiments resulting in the identification of extracellular matrix (ECM)-derived metabolites that are used by cancer cells grown under nutrient starvation. The successful student will use the  Recon-2 model to define which metabolic pathways are used by the identified metabolites and present their work at a research day in York along with other summer students from the scheme.

Generating a transcriptomic expression atlas to understand gene transfer in plants

Location: Sheffield 

Project Supervisor and description: Dr. Lara Pereira Garcia Bioscience Dept, Sheffield

Generating a transcriptomic expression atlas to understand gene transfer in plants

10 weeks (full time 37.5 hours per week, £9.77 per hour, £700 consumables)

Lateral gene transfer (LGT) among grasses allows species to develop new phenotypes that were out of reach of the native genome. While comparative genomics have established the frequency of LGT in different groups, the regulatory consequences of foreign genes landing in a new genome remain unknown. In this project, we will use comparative transcriptomics to test the hypothesis that interspecific gene movements were followed by drastic changes of gene expression. The student will collect plant samples from Alloteropsis semialata, perform RNA extraction, and DNA preparation, then generate and analyse the RNA Sequencing data. This will result in the generation of an expression atlas. Similar transcriptomes atlases will be generated for three distantly related species known to have donated in total >50 LGT to Alloteropsis. The expression profiles of the LGT will then be compared between the recipient and donor species, providing a direct test of the regulatory effect of LGT in grasses. The student will present their work at a research day in York along with other summer students from the scheme.

Improving the bioactivity profile of medically important antifungal agents

Location: Leeds 

Project Supervisor and description: Dr. Asif Fazal, Biology Dept, Leeds

Improving the bioactivity profile of medically important antifungal agents

10 weeks (full time 37.5 hours per week, £9.77 per hour, £700 consumables)

Most clinically used antibiotics are derived from microbial natural products, a large proportion of which are biosynthesised by assembly line-like non-ribosomal peptide synthetases or polyketide synthases. The antimycins are produced by such a system and are potent antifungals, as well as possessing other notable bioactivities. Thus, understanding the functionality of the antimycin biosynthetic system in detail would enable refactoring of the assembly line for the production of novel compounds, with improved bioactivity profiles and characteristics. The student will aim to reconstitute antimycin biosynthesis in vitro so that mechanistic questions about biosynthesis can be addressed. This will involve training in techniques such as gene cloning, protein purification, mutational analysis, and enzymatic assays; and following the lab project, the student will have the chance to present their work at a research day in York along with other students from the scheme.

Towards food security: Understanding trigger temperatures in wheat development

Location: Leeds 

Project Supervisor and description: Dr. Laura Dixon, Biology Dept, Leeds

Towards food security: Understanding trigger temperatures in wheat development

10 weeks (full time 37.5 hours per week, £9.77 per hour, £700 consumables)

Our cereal crops are experiencing increasingly variable temperature conditions during the annual growth cycle in the UK. This project is aiming to understand how one of the major known genetic loci in temperature regulation in cereals VERNALIZATION 2 (VRN2) functions to respond and regulate the wheat plants growth at different temperatures. To do this the student will use newly developed genetic resources to identify how different alleles of VRN2 respond to realistic field temperatures during early plant development. This developmental analysis will be complemented by qPCR expression analysis under a selection of the temperature conditions for known expression targets of VRN2. In combination this will provide vital information on the trigger temperature for VRN2 responses in cereals. These techniques would be relevant to any biology degree and also to a lot of plant science related industry jobs, e.g. plant breeding companies. In addition to the skills acquired in the lab the student will also be welcomed to the lab group, giving short presentations, reviewing scientific papers, discussing scientific results, and presenting their work at a research day in York along with other summer students from the scheme.

Understanding mechanisms of human norovirus infection

Location: Leeds

Project Supervisor and description: Dr. Jake Mills, Biology Dept, Leeds

Understanding mechanisms of human norovirus infection

10 weeks (full time 37.5 hours per week, £9.77 per hour, £700 consumables)

There is currently no efficacious vaccine or therapy for human norovirus infection, which causes >200,000 deaths yearly. The norovirus capsid comprises two structural proteins, which assemble around the viral genome to generate virions. Assembling virions is essential to spread infection, however the mechanism by which assembly occurs is undefined. Our research aims to understand the mechanism of norovirus capsid assembly, using the tractable murine norovirus (MNV) model system. The student will undergo training in techniques such as virological TCID50 assays and qPCR to understand wild type versus mutated viral infection mechanisms.  The student will also be required to critically evaluate data they generate, and will be encouraged to present their findings at a laboratory group meeting, and also offered the opportunity to work on the public engagement project, Keepin’ It Real Education, organised by the lab. The student will present their work at a research day in York along with other summer students from the scheme.