University of Aberdeen
Project title: Characterising the skeletal muscle gene expression signature when exercise is performed concomitant with metformin treatment
Project supervisor: Dr Brendan Gabriel (The Rowett Institute, University of Aberdeen & Department of Physiology and Pharmacology, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden)
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Strategic area: Bioscience for an integrated understanding of health
Project Start Date (duration 8 weeks): 1st June 2022
Project summary:
Type 2 Diabetes Mellitus (T2D) is a growing, global health burden. Metformin is widely prescribed as a first-line treatment of T2D, while individuals with T2D are also routinely advised to engage in frequent physical activity. Recent studies suggest that although metformin is an effective treatment strategy of T2D, patients undergoing this treatment may have a reduced beneficial response to exercise, including an ablation of skeletal muscle mitochondrial protein synthesis. We have previously performed bioinformatic, cellular, and human experiments to characterise the skeletal muscle gene expression signature when exercise is performed concomitant with metformin treatment. These data have led us to identify a target-of-interest (TOI) that we hypothesise is central in mediating the skeletal muscle response to metformin and exercise.
Objective: The student will culture skeletal muscle cells and treat with siRNA targeting the TOI. TOI knockdown will be confirmed by RT-qPCR, in addition to mitochondrial gene expression.
Feasibility: These techniques are routinely performed in our lab and are well-established for other targets.
Skills development and confidence: These techniques are core tenets of a cellular/molecular biology lab and form the bedrock for more complex techniques. Mastering these techniques will give the student an excellent starting point for a career in research.
University of Dundee
Project Title: Making biological tools to facilitate cell-based assays in investigating Bet-protein degradation using PROTACs
Project Supervisor: Professor Alessio Ciulli; email a.ciulli@dundee.ac.uk;
Day-to-day supervisor: Dr Selma Gulyurtlu Email scabritagulyurtlu001@dundee.ac.uk
Strategic area: Bioscience for an integrated understanding of health
Project start date: 06/06/22
Project Summary:
Targeted protein degradation has opened new avenues in drug discovery by providing a different modality to targeting proteins. Proteolysis targeting chimeras (PROTACs) are heterobifunctional compounds that link a protein of interest (POI) to an E3 ligase, bypassing the cell’s intrinsic catalytic activity and allowing the POI to be subsequently degraded in a proteosome-dependent manner. The Ciulli lab has made significant breakthroughs in deciphering Bromo- and Extra-terminal (BET) protein degradation, particularly by designing and innovating one of the very first archetypical PROTAC molecule MZ1, a BRD4-selective degrader that recruits the VHL E3 ligase.
The focus of this project is to develop biological tools to help assess BET protein degradation and further explore the nature of a PROTAC’s mechanism of action. It will involve the creation of reporter and knockdown cell lines through gene editing and insertion, using CRISPR-Cas9 and lentiviral systems. These cell lines will then be validated with well-established PROTACs, such as MZ1, to confirm functionality. This will include cell-based assays that are vital in evaluating protein degradation, such as Western blotting and HiBiT luminescence tracking. Overall, the project will give the successful REP student an insightful introduction to molecular cloning, gene editing, cell culture (including category level 2 lentiviral work), stable cell line generation and cell-based assays – all important techniques used everyday in the research laboratory
University of Edinburgh
Project title: Investigating the impact of abiotic stresses on the efficacy of single-stranded DNA-mediated precision gene editing
Project supervisor: MOLNAR Attila (University of Edinburgh, School of Biological Science)
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Strategic area: Clean Growth/Rules of Life
Project Start Date: 1st June 2022
Project Summary:
Single-strand DNA templated repair (SSTR) is one of the most efficient type of CRISPR/Cas-mediated precision gene editing in eukaryotes. However, very little is known about how abiotic stresses, such as nutrient deprivation affect SSTR. The proposed project will investigate the impact of a variety of abiotic stresses on the efficacy of CRISPR/Cas12-mediated SSTR, with the aim to improve precision gene editing. It will also provide a platform for developing transferable skills including experimental design, molecular biology, data analysis and communication.
Further reading: Ferenczi et al., 2021, Nature Communications; doi: 10.1038/s41467-021-27004-1
Project title: Optimising live cell imaging in the cytoplasm: towards deciphering the role of the protein TDP43 in ALS
Project supervisor: Professor Lynne Regan (School of Biological Sciences)
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Strategic area: Bioscience for Heath or Understanding the Rules of Life)
Project start/end dates: June to July 2022
Project summary:
The Regan and Horrocks labs have invented a new way to perform super-resolution fluorescence imaging in live cells. It uses transient interactions of a fluorescent protein with the protein of interest, rather than direct fusion.
Certain proteins can be present in both the nucleus and cytoplasm. An example is TDP43, which in healthy individuals is predominantly nuclear, but in individuals with ALS (Amyotrophic Lateral Sclerosis) is predominantly cytoplasmic. We are interested in extending our method to label a protein only when it is in the cytoplasm, and not in the nucleus. Small proteins (such as a single fluorescent protein) are able to freely diffuse between nucleus and cytoplasm.
The project we propose is for the student to construct different sized fluorescent proteins (by a variety of strategies) and to identify those that prevent diffusion into the nucleus. This is an eminently achievable project for a summer student, and has the definite goal of making a construct that behaves in the desired fashion. Different constructs can be assessed by straightforward microscopy, so the student can test what they make themselves. The student will be fully embedded in the research group, and by having a small sub-project, in consultation with the PI and more senior lab members, will be able to develop planning and analytical skills.
Scotland's Rural College (SRUC)/University of Edinburgh
Project title: The role of hepatic insulin clearance in equine metabolic syndrome
Project supervisor: Ruth Morgan
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Strategic area: Bioscience for an integrated understanding of health
Project duration: 23rd May-8th July 2022
Project summary:
As in humans, obesity is a significant problem in horses with almost 40% of horses in the UK classified as overweight/obese. We study obesity across species to try and understand the mechanisms which lead to conditions such as diabetes and cardiovascular disease in humans and domestic species. Obesity in horses and humans is often accompanied by marked and sustained elevation of insulin levels (hyperinsulinaemia) and we know that this is a major risk factor for cardiovascular disease. Some data in humans suggests that reduced hepatic clearance of insulin is a significant component driving hyperinsulinaemia. In this project we hypothesise that impaired hepatic insulin clearance contributes to hyperinsulinaemia in horses. The project will utilise equine liver samples (fixed and frozen) from horses with and without hyperinsulinaemia. Students will learn molecular biology (quantitative PCR and protein quantification) and immunohistochemistry skills allowing them to address this hypothesis for example through quantification of proteins involved in insulin clearance. Students will be responsible for designing and conducting the experiments and analysing and presenting the data. This unique project is an opportunity to contribute to equine health research in a lab which specialises in comparative biology and its translational impact.
Project title: Developing a novel litter treatment to reduce microbial loads in chicken bedding
Strategic area: Bioscience for sustainable agriculture and food
Project supervisor: Dr Naomi Fox (SRUC, Disease Systems)
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Project start date: June 2022
Project summary:
The high humidity, ample nutrients, and high stocking densities in poultry houses are associated with the spread of pathogens such as Salmonella and Campylobacter. As these pathogens are responsible for most food poisoning cases there is constant pressure on farmers to reduce pathogen levels in their flocks. This project aims to determine the effects of a novel chicken-bedding treatment on environmental loads of pathogenic bacteria.
Objective 1: Test antimicrobial effects of treated versus untreated shavings in vitro.
The student will select the bacteria species to focus on, then develop and execute protocols for liquid and solid bacteria growth experiments.
Objective 2: Characterise bacterial communities in spent treated and untreated chicken-litter.
Following training in DNA extractions and PCR, the student will develop primers for characterisation of bacterial communities in spent treated and untreated chicken litter (collected from experimental trials at the Allermuir Avian Innovation and Skills Centre).
Working within an active research team, the student will learn about current projects, discuss the diverse career paths that Team members have taken, and receive guidance, feedback, and feedforward on their research plans. Through visiting Allermuir’s facilities the student will learn fundamental elements of applied research and gain awareness of industry-research links.
Moredun Research Institute
Project Title: The use of the blood-feeding mite Dermanyssus gallinae in poultry disease detection.
Project supervisor: Dr Francesca Nunn
Strategic Area: Agriculture and Aquaculture
Project start/end date: June to July 2022
Project Summary:
Dermanyssus gallinae or the poultry red mite (PRM) is a blood feeding ectoparasite and a major problem for the egg laying industry in the UK (Flochay et al, 2017). Because it consumes a blood meal, PRM has the potential to transmit a range of pathogens to its’ avian host, however, the role of the parasite as a disease vector has not yet been fully characterised (Schiavone et al, 2022). Recently we described a new method for feeding adult female PRM (Nunn et al, 2020) and have since used this in vitro feeding device to support all of the hematophagous life stages of PRM. This device has the potential to help study the mites’ role as a disease vector in vitro and this project aims to determine the device’s usefulness in the study of PRM and its role in the spread of pathogens.
The aim of the project is to demonstrate that digested DNA can be detected by PCR in all hematophagous life cycle stages following in vitro feeding of a spiked blood meal.
The mites’ blood meal will be spiked with a harmless plasmid and PCR used to detect the plasmid at different time points post-feeding. The project will provide the student with foundation laboratory skills in microscopy, parasitology, in vitro feeding methods, DNA extraction techniques, PCR optimisation, sample handling and data analysis and experimental design while being involved in a novel project in the red mite lab at the Moredun Research Institute, Edinburgh.
University of St Andrews
Project title: Combining data sets to understand methylation-regulated gene expression in renal cancer.
Project Supervisor: Andy Lynch (School of Mathematics and Statistics)
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Strategic area: Bioscience for Health, Rules of Life
Expected Project Start Date: June 2022
Project summary:
DNA methylation is an important regulator of gene expression that is typically rewritten in cancer. We can investigate this by treating cell lines (or other models of tissue/disease) with an inhibitor of DNA methylation such as 5-Azacytidine. By comparing the resultant gene expression profiles with those from control (untreated) cells, we can see which genes are regulated by methylation in the tissue or disease that the cell line represents.
Several studies of renal cancer have included such experiments. However, cell lines are not perfect representations of disease, and certainly don’t capture all of the heterogeneity seen within and between cancers, so these experiments tend only to tell part of the story.
This project will look to meta-analyse several such data sets to understand better the role of methylation in renal cancer. Different disease models, different treatments, and different expression platforms will be combined to gain both better understanding of the heterogeneity and of whether a common core set of regulated genes exists.
The project will provide practical experience of handling high-throughput molecular data. Being at the interface of disciplines it will develop skills and knowledge on either the statistical or biological aspects, depending on the student’s background.
