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GenerationResearch Equity in summer research

The studentships below are for University of Leeds and University of Sheffield 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.

Jacobs Studentship

The following studentship is open to all 2nd and 3rd year students (including 3rd year leavers and those going onto an integrated Masters degree) and 4th year students finishing an integrated Masters degree.

Investigating inorganic carbon uptake in the algal C02 concentrating mechanism

Location: York 

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

BBSRC Studentships: the building blocks of life

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

Furthering the capabilities of CryoEM at York

Location: York 

Project Supervisor and description: Dr Jamie Blaza, YSBL, Dept. Chemistry, 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 of protein translation in humans

Location: York 

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

Understanding viral recoding of protein translation in humans

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 an error rate 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 single-molecule fluorescence microscopy 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 in E.coli and purification, fluorescent dye labelling, biophysical techniques including isothermal titration calorimetry and surface plasmon resonance.  Quantitative data analysis, time management, and record keeping will also be as 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, Dept. Chemistry, 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.

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.