Undergraduate summer studentships

Dean's Vacation Research Scholarships

Overview
Dean's Vacation Research Scholarships

The 2022 scheme is now open. Deadline for applications is 28^th January 2022 at noon. Please send your application via email to fbsris@leeds.ac.uk. Applications should consist of a covering letter, along with your curriculum vitae.

These projects are offered by Faculty postdocs and internally funded. Applicants will be shortlisted and invited for interview. The intention of these awards is that successful candidates will be supervised in the lab by the postdoc leading the project. However, whilst every effort will be made to offer lab placements, in light of the COVID-19 pandemic, it may be that an alternative literature project has to be offered. The stipend offered to the undergraduate is £200 per week.

Project Supervisor	Project details
Dr Samantha Hover Job Description	Imaging Influenza virus RNA genome assembly with high spatial and temporal resolutions. We have generated an IAV strain containing an eGFP tag which allows fluorescent localisation of the viral polymerase, including those attached to vRNPs. Using density gradient fractionation of infected cells, we have enriched a fraction containing eGFP fluorescent ICVs and confirmed their presence using a fluorescent plate reader and by negative stain EM. This project will aim to: 1) Confirm the presence of Rab11 (a cellular component known to be associated with ICVs) and vRNPs on ICVs. 2) Determine the presence of a lipid bilayer; confirming these are in fact vesicles. 3) Identify the origin of ICVs using cellular markers for different organelles. This project will involve fixing ICVs to coverslips and fluorescently immunolabelling with a variety of antibodies already available in our lab, similarly to an approach employed for labelling components of virions (PMID: 10482613). We will test multiple cellular markers alongside both the eGFP tag on the viral polymerase and co-staining for the viral nucleoprotein (another vRNP component), to confirm fluorescent puncta are ICVs. These studies will be complemented by cryo-EM of the ICVs, performed in parallel to this project. This work will provide an improved understand of ICVs and potential host cell targets to inhibit influenza infection.
Dr Gemma Lyall Job Description	Molecular mechanisms of vascular impairment in heart failure with preserved ejection fraction Alongside alterations in the myocardium, heart failure with preserved ejection fraction (HFpEF) is associated with vascular dysfunction and myopathy of the peripheral skeletal muscles (SKM). A family of E3 ligases, including muscle ring finger protein 1 (MuRF1) and muscle atrophy F-box protein (MAFBx) promote atrophic stress in SKM and hypertrophy in the myocardium. The objective of this project is to investigate the molecular mechanisms underlying changes to vascular function in HFpEF and to determine whether MAFbx and MuRF-1 contribute to pathological vascular changes in HFpEF. The student will perform western blots and PCR to assess proteins and genes of interest in vascular tissue, specifically aorta and carotid artery samples, from rats with HFpEF. We have found differences in vascular function in HFpEF versus control animals. Therefore, the student will examine proteins and genes which may play a role in vascular dysfunction in HFpEF, namely eNOS, p-eNOS, MAFbx, MuRF-1, ICAM-1, VCAM-1 and MCP-1. A further objective is to explore whether supplementation of a novel MuRF-1 inhibitor alters levels of MuRF-1 and therefore vascular dysfunction in HFpEF. The student will be taught how to carry out the experimental procedures, analyse and interpret the results, and write a short report to present to the lab group at an informal meeting. We will also help the student develop their teamwork skills and, through lab meetings, gain a theoretical understanding of the wider project.
Dr Lauryn New Job Description	Investigating the presence of glial endozepines in the dorsal vagal complex and their proposed role in glucose homeostasis Glial endozepines such as DBI and ODN may be involved in the neuronal regulation of homeostatic feeding behaviours including food intake, energy expenditure, and brain glucose-sensing. The DBI gene is expressed by neurones and glia within the hypothalamus relative to nutritional status and ODN in the DVC acts to inhibit autonomic feeding related behaviour. Our lab has recently shown how NTS astrocytes influence food intake and body weight and is investigating how GABAergic neurones, which are influenced by DBI and ODN, may be insulin sensing. However, it is still unclear which specific neuronal and glial populations within the DVC are involved in DBI or ODN-mediated negative neuronal-glial feedback loops. The successful candidate will therefore carry out immunofluorescent staining of ex-vivo rat brain tissue to characterise these ODN+ and DBI+ populations in the DVC. The student will section tissue and use double labelling IHC for the detection of ODN and DBI alongside several well-known markers of neurones, glia, and specific neurochemistry. They will also quantify and analyse findings using ImageJ software. There is also scope to carry out similar work in high-fat diet fed insulin resistant animals.
Dr Karl Norris Job Description	Investigating the role of IFRD1 in ribosome specialisation and male fertility Ribosomes are the macromolecular machines that catalyse protein synthesis. Studies over the last decade have shown that ribosomes can become specialised by changes in their composition (1). These specialised ribosomes target specific mRNA transcripts for translation and are crucial for organismal development (2). Subsequently, they have been implicated in cancers, Alzheimer’s disease and a class of diseases known as ribosomopathies (2). We recently characterised the protein composition of ribosomes from several tissues of Drosophila melanogaster using quantitative mass spectrometry and cryo-electron microscopy (3). We discovered significant heterogeneity in ribosome composition in the gonads, implying that specialised ribosomes are important for reproduction. We discovered a ribosome associated protein, IFRD1, sitting in the mRNA channel of our testis ribosome structure. Although the role of IFRD1’s association with the ribosome remains unknown, we hypothesise that it could result in a population of specialised ribosomes that are playing a pivotal role in translational regulation. IFRD1 has previously been found associated with mammalian ribosomes and therefore, this may represent a novel and conserved mechanism of translational regulation (4). By understanding the role IFRD1 plays in translational regulation by virtue of ribosome association, we may gain novel and important insight into the mechanisms that underpin male fertility. The successful candidate will investigate the importance of IFRD1 to male fertility using Drosophila melanogaster as a model organism. Using the UAS-GAL4 system, IFRD1 RNAi will be targeted to the testis and knockdown will be confirmed via RT-qPCR. The impact of IFRD1 knockdown on translational regulation and male fertility will be assessed using puromycin incorporation assays, immunostaining and fertility assays. 1. Xue, S. and Barna, M. (2012) Specialized ribosomes: a new frontier in gene regulation and organismal biology. Nat Rev Mol Cell Biol, 13, 355-369. 2. Norris, K., Hopes, T. and Aspden, J.L. (2021) Ribosome heterogeneity and specialization in development. Wiley Interdiscip Rev RNA, e1644. 3. Hopes, T., Norris, K., Agapiou, M., McCarthy, C.G.P., Lewis, P.A., O'Connell, M.J., Fontana, J. and Aspden, J.L. (2021) Ribosome heterogeneity in Drosophila melanogaster gonads through paralog-switching. Nucleic Acids Res. 4. Brown, A., Baird, M.R., Yip, M.C., Murray, J. and Shao, S. (2018) Structures of translationally inactive mammalian ribosomes. Elife, 7.
Dr James Warren Job Description	Self-assembling peptide hydrogels for the treatment of cartilage damage The objectives of the project would be to investigate the effects of altering the composition of the SAP:GAG ratio. This would be achieved by: 1) Systematically adjusting the ratio of GAG:SAP from the one previously studied and investigate the effect of increasing this ratio of GAGs relative to the SAP. 2) Additionally, altering the specific SAP – as many different variants are currently available within the SAP family, would alter the net charge and subsequent chemical and material properties of the SAP. This in turn could alter the effect that increasing GAG content would have. 3) The effects of these systematic changes would be investigated through visual changes in the hydrogel appearance (apparent turbidity, viscosity, state) as well as chemical changes such as pH, rate of assembly. The material properties of the systems could be assessed using an in-house BOSE material testing set up to measure material properties such as the rheology of the systems. 4) Successful candidate systems (ones with improved clinical relevance – such as increased rate of assembly/strength of assembly) would then be assessed through injection into a relevant tissue model currently used within our group that attempts to replicate the GAG depleted state of early stage osteoarthritis.

Project Supervisor

Project details

Dr Samantha Hover

Job Description

Imaging Influenza virus RNA genome assembly with high spatial and temporal resolutions.

We have generated an IAV strain containing an eGFP tag which allows fluorescent localisation of the viral polymerase, including those attached to vRNPs. Using density gradient fractionation of infected cells, we have enriched a fraction containing eGFP fluorescent ICVs and confirmed their presence using a fluorescent plate reader and by negative stain EM. This project will aim to:

1) Confirm the presence of Rab11 (a cellular component known to be associated with ICVs) and vRNPs on ICVs.
2) Determine the presence of a lipid bilayer; confirming these are in fact vesicles.
3) Identify the origin of ICVs using cellular markers for different organelles.

This project will involve fixing ICVs to coverslips and fluorescently immunolabelling with a variety of antibodies already available in our lab, similarly to an approach employed for labelling components of virions (PMID: 10482613). We will test multiple cellular markers alongside both the eGFP tag on the viral polymerase and co-staining for the viral nucleoprotein (another vRNP component), to confirm fluorescent puncta are ICVs. These studies will be complemented by cryo-EM of the ICVs, performed in parallel to this project. This work will provide an improved understand of ICVs and potential host cell targets to inhibit influenza infection.

Dr Gemma Lyall

Job Description

Molecular mechanisms of vascular impairment in heart failure with preserved ejection fraction

Alongside alterations in the myocardium, heart failure with preserved ejection fraction (HFpEF) is associated with vascular dysfunction and myopathy of the peripheral skeletal muscles (SKM). A family of E3 ligases, including muscle ring finger protein 1 (MuRF1) and muscle atrophy F-box protein (MAFBx) promote atrophic stress in SKM and hypertrophy in the myocardium. The objective of this project is to investigate the molecular mechanisms underlying changes to vascular function in HFpEF and to determine whether MAFbx and MuRF-1 contribute to pathological vascular changes in HFpEF.

The student will perform western blots and PCR to assess proteins and genes of interest in vascular tissue, specifically aorta and carotid artery samples, from rats with HFpEF. We have found differences in vascular function in HFpEF versus control animals. Therefore, the student will examine proteins and genes which may play a role in vascular dysfunction in HFpEF, namely eNOS, p-eNOS, MAFbx, MuRF-1, ICAM-1, VCAM-1 and MCP-1. A further objective is to explore whether supplementation of a novel MuRF-1 inhibitor alters levels of MuRF-1 and therefore vascular dysfunction in HFpEF. The student will be taught how to carry out the experimental procedures, analyse and interpret the results, and write a short report to present to the lab group at an informal meeting. We will also help the student develop their teamwork skills and, through lab meetings, gain a theoretical understanding of the wider project.

Dr Lauryn New

Job Description

Investigating the presence of glial endozepines in the dorsal vagal complex and their proposed role in glucose homeostasis

Glial endozepines such as DBI and ODN may be involved in the neuronal regulation of homeostatic feeding behaviours including food intake, energy expenditure, and brain glucose-sensing. The DBI gene is expressed by neurones and glia within the hypothalamus relative to nutritional status and ODN in the DVC acts to inhibit autonomic feeding related behaviour. Our lab has recently shown how NTS astrocytes influence food intake and body weight and is investigating how GABAergic neurones, which are influenced by DBI and ODN, may be insulin sensing. However, it is still unclear which specific neuronal and glial populations within the DVC are involved in DBI or ODN-mediated negative neuronal-glial feedback loops. The successful candidate will therefore carry out immunofluorescent staining of ex-vivo rat brain tissue to characterise these ODN+ and DBI+ populations in the DVC. The student will section tissue and use double labelling IHC for the detection of ODN and DBI alongside several well-known markers of neurones, glia, and specific neurochemistry. They will also quantify and analyse findings using ImageJ software. There is also scope to carry out similar work in high-fat diet fed insulin resistant animals.

Dr Karl Norris

Job Description

Investigating the role of IFRD1 in ribosome specialisation and male fertility

Ribosomes are the macromolecular machines that catalyse protein synthesis. Studies over the last decade have shown that ribosomes can become specialised by changes in their composition (1). These specialised ribosomes target specific mRNA transcripts for translation and are crucial for organismal development (2). Subsequently, they have been implicated in cancers, Alzheimer’s disease and a class of diseases known as ribosomopathies (2).
We recently characterised the protein composition of ribosomes from several tissues of Drosophila melanogaster using quantitative mass spectrometry and cryo-electron microscopy (3). We discovered significant heterogeneity in ribosome composition in the gonads, implying that specialised ribosomes are important for reproduction. We discovered a ribosome associated protein, IFRD1, sitting in the mRNA channel of our testis ribosome structure. Although the role of IFRD1’s association with the ribosome remains unknown, we hypothesise that it could result in a population of specialised ribosomes that are playing a pivotal role in translational regulation. IFRD1 has previously been found associated with mammalian ribosomes and therefore, this may represent a novel and conserved mechanism of translational regulation (4). By understanding the role IFRD1 plays in translational regulation by virtue of ribosome association, we may gain novel and important insight into the mechanisms that underpin male fertility.

The successful candidate will investigate the importance of IFRD1 to male fertility using Drosophila melanogaster as a model organism. Using the UAS-GAL4 system, IFRD1 RNAi will be targeted to the testis and knockdown will be confirmed via RT-qPCR. The impact of IFRD1 knockdown on translational regulation and male fertility will be assessed using puromycin incorporation assays, immunostaining and fertility assays.

1. Xue, S. and Barna, M. (2012) Specialized ribosomes: a new frontier in gene regulation and organismal biology. Nat Rev Mol Cell Biol, 13, 355-369.
2. Norris, K., Hopes, T. and Aspden, J.L. (2021) Ribosome heterogeneity and specialization in development. Wiley Interdiscip Rev RNA, e1644.
3. Hopes, T., Norris, K., Agapiou, M., McCarthy, C.G.P., Lewis, P.A., O'Connell, M.J., Fontana, J. and Aspden, J.L. (2021) Ribosome heterogeneity in Drosophila melanogaster gonads through paralog-switching. Nucleic Acids Res.
4. Brown, A., Baird, M.R., Yip, M.C., Murray, J. and Shao, S. (2018) Structures of translationally inactive mammalian ribosomes. Elife, 7.

Dr James Warren

Job Description

Self-assembling peptide hydrogels for the treatment of cartilage damage

The objectives of the project would be to investigate the effects of altering the composition of the SAP:GAG ratio. This would be achieved by:

1) Systematically adjusting the ratio of GAG:SAP from the one previously studied and investigate the effect of increasing this ratio of GAGs relative to the SAP.

2) Additionally, altering the specific SAP – as many different variants are currently available within the SAP family, would alter the net charge and subsequent chemical and material properties of the SAP. This in turn could alter the effect that increasing GAG content would have.

3) The effects of these systematic changes would be investigated through visual changes in the hydrogel appearance (apparent turbidity, viscosity, state) as well as chemical changes such as pH, rate of assembly. The material properties of the systems could be assessed using an in-house BOSE material testing set up to measure material properties such as the rheology of the systems.

4) Successful candidate systems (ones with improved clinical relevance – such as increased rate of assembly/strength of assembly) would then be assessed through injection into a relevant tissue model currently used within our group that attempts to replicate the GAG depleted state of early stage osteoarthritis.