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Found 17 matching student topics

Displaying 1–12 of 17 results

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
Faculty of Science
School
School of Computer Science
Research centre(s)
Centre for Data Science

High-performance bioinformatic analysis of gene editing targets using Python Standard Libraries

The CRISPR-Cas9 technology allows the modification of 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. It is vital that the modification is made efficiently and at the desired location. This calls for bioinformatic approaches to design these guide RNAs.Our existing Python-based bioinformatic pipeline is …

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

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)

Centre for Microbiome Research

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

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

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 evolution …

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

Centre for Microbiome Research

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

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

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)

Centre for Microbiome Research

Exploring global viral diversity with conserved sequence tags

Viruses control much of the world indirectly through infection of microbial cells. Modern metagenomics provides the raw data to investigate their dynamics and patterns of co-occurrence with the microbial hosts, but extracting signal from these datasets at the large scale remains challenging. Marker-gene based approaches, such as SingleM, have shown great promise for microbial data, converting metagenomic datasets into community profiles by concentrating on reads which derive from conserved sections of prevalent genes.

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

Centre for Microbiome Research

Prostate cancer transcriptomics (Honours and Master of Philosophy)

At the Australian Prostate Cancer Research Centre QLD, we are interested in the cellular adaptive response processes leading to therapy resistance in advanced prostate cancer.A focus area of our research is studying the transcriptome changes in prostate cancer cell lines, xenograft models and patient samples using RNA sequencing technologies.By integrating our large in-house repository of RNAseq data sets with publicly available studies, this project will further explore the cellular heterogeneity of prostate tumours and the plasticity of cancer cells in …

Study level
Master of Philosophy, Honours
Faculty
Faculty of Health
School
School of Biomedical Sciences

Metabolic diversity of the 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 aims for a potential Honours/MSc project will be to uncover the metabolic diversity of the Methanoperedenaceae and to understand the evolutionary mechanisms responsible for these adaptations.

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

Centre for Microbiome Research

Estimating the evolutionary history of plasmids and viruses

In the case of cellular life - bacteria, archaea and eukaryotes - determining the 'tree of life' is a comparatively well-studied problem.This vertical evolutionary history can be estimated using concatenated gene phylogenies, where single copy marker genes are concatenated into a single multiple sequence alignment which is then used in a phylogenetic tree reconstruction algorithm.Viral genomes and plasmid sequences, meanwhile, are more challenging to fit into a phylogenetic framework.

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

Centre for Microbiome Research

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