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Projects

The lab has an active research program for  Honors, Masters and PhD projects. Typically the Honors program is full-time research for 12 months and a PhD varies from 3-4 years. Listed are some of the projects on offer. 

The study of long ncRNAs  in prostate cancer exosomes

Each year in Australia, close to 3,300 men die of prostate cancer, and each day about 32 men learn news that they have prostate cancer. An estimate 20,000 new cases will be diagnosed each year and this rate is increasing. One of the major challenges for the treatment of prostate cancer is early detection and currently there are no robust clinical biomarkers.

Our laboratory has identified a set of novel gene(s), which have the potential to become future biomarkers. These genes are unlike the traditional genes but are non-coding RNAs longer then 1 KB. These long ncRNAs are enriched in secreted vesicles, but their current function and application, as biomarkers are unknown.

 

This project will have two major Aims A) to confirm the expression of these ncRNA in micro-particles and exosomes and B) to determine their function in the progression of cancer.

​To understand the role of worm RNA in a mammalian immune response

Supervisors : Dr. Nham Tran (nham.tran@uts.edu.au) and Dr Sheila Donnelly (sheila.Donnelly@uts.edu.au)
 

Helminth parasites have strongly influenced the behaviour of the human immune system. They have developed the capacity to modulate the human immune system to minimise tissue damage and to prevent their expulsion during their life cycle.

 

The continuous presence of this modulatory effect over millennia of co-evolution has resulted in compensatory adjustments to immune-related genes within the human population. We have identified several novel RNA molecules which may drive this immunological phenomenal. However their exact function in altering immune patterns remains unknown.  

 

To explore and characterise the functions of these RNA molecules is subverting the phenotypes of specific immune cells. 
 

The expression of non-coding RNAs in HPV16 positive oral cancers

Human papillomavirus (HPV), notably type 16, is a risk factor for up to 50% of oral squamous cell carcinomas (SCC)s. For many decades, oral cancers were considered to be a disease associated with the older generation.

Today this paradigm has shifted. HPV16 is now a major cause of oral cancers and this is growing around the world. The fastest growing segment for oral cancers, are young women in the 20-24-age range, who are never smokers but are predominantly HPV16 positive. Similar trends for HPV16 incidence are seen in the UK and it is also on the rise.

There is now significant public heath concern for the spread of HPV16 in oral cancers. These HPV16 positive tumours are localised to the posterior of the mouth; in the oropharynx, tonsils, and at the base of the tongue.

 

Non-coding RNAs are known to play a vital role in the transformation process and recent evidence suggests that HPV16 may impact the small and long ncRNA pathways in oral cancers.

 

The project will explore the associations between HPV16 and the expression of non coding RNAs in oral cancer.

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The development of novel living data maps for the analysis of genomic data  

Scientific data representation has been traditionally focused on the use of 2D graphs such as histograms and scatter plots. In the ever increasing research areas of genomics and big data analysis these archetypal data formats are no longer applicable. Our laboratory is seeking to develop novel forms of data representation which is both informative but also embraces visual creativity.
 
To develop a pipeline or GUI for the scientific community to import their data and transform these data points onto an interactive data organism. Specifically, we will focus on delivering a pipeline for creating D3 Data Driven Documents (https://d3js.org/ ) and Circos layouts (http://circos.ca/).


To create a living data map for the analysis of large genomic data sets with the aim of identifying biomarkers for clinical applications.
To combine art and science to create exciting visual tools.

This project will be suited for engineering or science students with a deep knowledge of Perl, Python, Ruby, Java and R languages. Scholarships will be made available to the selected candidate. This is a research only project and is offered as a capstone or PhD program.

Methodology and Skills

These projects cover a range of skills from cell biology to molecular techniques. The candidates will be fully trained in all aspects of the work. The projects are offered as honours or PhD by research. 


 

  • Tissue culture: Growing mammalian cells line using sterile techniques.

  • Isolation of non coding RNAs from in vitro cells and mice samples.

  • RNA sequencing, if needed.

  • Molecular biology skills such as Real Time PCR, cloning and bacterial work.

  • Regulation of genes using siRNAs and LNA antisense.

  • Detection of proteins using western blotting. 

  • Presentation of results at weekly lab meetings. 

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