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Role of microRNAs (miRNA) in progression and development of liver disease

Liver disease is a significant burden on society, accounting for more than 2 million deaths worldwide. miRNAs can exert causal roles, being pro- or anti-inflammatory, as well as pro- or antifibrotic mediators or being oncogenes as well as tumour suppressor genes. In this project we will identify novel miRNAs which play a role in the progression and development of liver disease and delineate the mechanisms utilised by these miRNAs using cell and mouse models of disease.Aim 1: To identify differentially …

Study level
PhD, Master of Philosophy, Honours
Faculty
Faculty of Health
School
School of Biomedical Sciences
Research centre(s)

Computational drug repurposing for neuropsychiatric disease

While hundreds of robust genetic associations have been found for neuropsychiatric disease (such as schizophrenia, major depression, and anxiety) understanding the exact molecular mechanisms leading to disease onset and progression remains challenging. Inherited (i.e. genetic) risk factors for many neuropsychiatric diseases converge on genes that are co-ordinately expressed (co-expressed) in a disease-relevant tissue (e.g. brain). The study of how genetic risk factors affect co-expressed genes (i.e. gene co-expression analysis) has the potential to uncover new biological processes underlying disease onset. …

Study level
Honours
Faculty
Faculty of Health
School
School of Biomedical Sciences
Research centre(s)

Adaptive evolution of anaerobic methanotrophic (ANME) archaea mediating methane oxidation in freshwater environments

The as-yet-uncultured archaeal lineage Methanoperedenaceae are anaerobic methanotrophs with a key role in mitigating the atmospheric release of methane in freshwater environments. The metabolic diversity of these microorganisms directly links methane with several key biochemical cycles and suggests a remarkable ability of these microorganisms to adapt to diverse environmental conditions. The overall aim of this PhD project will be to uncover the metabolic diversity of the Methanoperedenaceae and to understand the evolutionary mechanisms responsible for these adaptations.Approaches/skills and techniquesThe project …

Study level
Master of Philosophy, Honours
Faculty
Faculty of Health
School
School of Biomedical Sciences
Research centre(s)

Giant viruses in the human gut microbiome

The human body is home to a vast ecosystem of microorganisms including bacteria, archaea, fungi, viruses, and bacteriophages that make up the human microbiota. These microbes and their collective genetic material, known as the microbiome, influence a wide range of physiological functions including nutrient production and absorption, the development and regulation of our immune system, protection against potential pathogens, and even our mood and mental health. While distinct microbial communities exist throughout the body, the gut microbiome has gained particular …

Study level
Master of Philosophy, Honours
Faculty
Faculty of Health
School
School of Biomedical Sciences
Research centre(s)

DNA markers of burn injury and trauma

Burns cause physical and psychological trauma. Patients often experience prolonged treatment to enable their wounds to heal, and may experience scarring and repeated operations. Patients often experience distress related to the initial injury and ongoing management, and are at risk of developing PTSD. The patients who are more likely to develop heightened trauma reactions, long-term psychological sequelae and wound healing with scarring and surgery, need to be identified early in the treatment pathway, for improved management. It is also important …

Study level
Master of Philosophy, Honours
Faculty
Faculty of Health
School
School of Biomedical Sciences
Research centre(s)

Identifying protein and metabolite markers of burn injury and trauma

It can be difficult for clinical teams to determine the severity of burn injuries when the patient first presents to the hospital. This is because burn wounds continue to deepen/progress over time, in a process known as burn wound conversion. Some wounds may deepen over days or weeks and require aggressive surgical treatment e.g. grafting, and some wounds don’t progress, stay superficial in depth, and they can be managed conservatively with the application of different bandages or dressings. We have …

Study level
PhD, Master of Philosophy, Honours
Faculty
Faculty of Health
School
School of Biomedical Sciences
Research centre(s)

Identifying biomarkers in children for predicting burn wound healing, to optimise wound care (BIOM02)

Project code:BIOM02Project aim:To identify protein biomarkers which are associated with poor wound healing outcomes in patients (e.g. needing a skin graft, scarring, delayed healing).Project methodology and resources:Blister fluid samples collected from patients are processed and analysed using mass spectrometry-based proteomic approaches. Proteins within the sample are identified and their abundance level characterised. The presence and amount of proteins within the sample are related to patient clinical parameters, using bioinformatic techniques. Students will gain an understanding of all these processes and …

Study level
Vacation research experience scheme
Faculty
Faculty of Health
School
School of Biomedical Sciences
Research centre(s)

Illuminating the microbial world using genome-based fluorescence microscopy

Our understanding of microbial diversity on Earth has been fundamentally changed by metagenomic characterisation of natural ecosystems. Traditional approaches for visualising microbial communities are time-consuming and provide limited information about the identity of specific microorganisms.The proposed research aims to combine single cell genomics and super resolution microscopy for novel, high-throughput, genome-based techniques to visualise microorganisms, plasmids and viruses, with strain level specificity. The application of these highly scalable approaches will provide comprehensive and unprecedented insight into the fine-scale dynamics and …

Study level
PhD
Faculty
Faculty of Health
School
School of Biomedical Sciences
Research centre(s)

Adaptive evolution of anaerobic methanotrophic (ANME) archaea mediating methane oxidation in freshwater environments

The as-yet-uncultured archaeal lineage Methanoperedenaceae are anaerobic methanotrophs with a key role in mitigating the atmospheric release of methane in freshwater environments. The metabolic diversity of these microorganisms directly links methane with several key biochemical cycles and suggests a remarkable ability of these microorganisms to adapt to diverse environmental conditions.The overall aim of this PhD project will be to uncover the metabolic diversity of the Methanoperedenaceae and to understand the evolutionary mechanisms responsible for these adaptations.Methods and ResourcesThe project will …

Study level
PhD
Faculty
Faculty of Health
School
School of Biomedical Sciences
Research centre(s)

High-performance scoring of CRISPR targets

The CRISPR-Cas9 technology allows the modification of virtually any gene in any organism of interest. It's generated a lot of interest, both in the research community and the general population.One of the crucial components of CRISPR experiments is the design of the "guide RNAs" that will control where modifications occur. It's vital that the modification is made at the desired location and not elsewhere.We developed a method utilising high-performance computing to efficiently assess the "off-target risk" of each guide RNA …

Study level
Honours, Vacation research experience scheme
Faculty
Science and Engineering Faculty
School
School of Computer Science
Research centre(s)
Centre for Data Science

Visualisation of CRISPR targets

CRISPR-Cas9 technology allows us to modify virtually any gene in any organism of interest. It has generated a lot of interest, both in the research community and the general population.One of the crucial components of CRISPR experiments is the design of the “guide RNAs” that will control where modifications occur.We have developed a software pipeline, named Crackling, to identify safe and effective guide RNAs across entire genomes. We're now seeking to develop a visualisation to communicate the results produced by …

Study level
Honours, Vacation research experience scheme
Faculty
Science and Engineering Faculty
School
School of Computer Science
Research centre(s)
Centre for Data Science

Investigation of genetic factors that contribute to concussion and its outcomes

The health outcomes from traumatic brain injuries (TBIs) and concussion depend on the nature of the injury, but response also varies greatly between individuals, suggesting that genetic factors may play a role. In particular, due to effects of head trauma on balances of ions, neurotransmitters and energy use in the brain, there is suggestion that variation in the genes that encode proteins involved in these pathways, e.g. ion channels, may affect the risk of, as well as response to a …

Study level
PhD, Master of Philosophy, Honours
Faculty
Faculty of Health
School
School of Biomedical Sciences
Research centre(s)

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