Research Projects

PhD and Honors/Capstone Projects
The lab has an active research intensive 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 below are some of the projects on offer. 
The study of long ncRNAs  in prostate cancer exosomes and their application as diagnostic markers

Background and aims: 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.

Methodology: 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 master by research or a full PhD program.
  • Tissue culture: Growing cancer cells.
  • Collecting patient samples & tissue banking.
  • Isolation of long RNA from in vitro cells and patient samples.
  • Molecular biology skills such as Real Time PCR, cloning & bacterial work.
  • RNA and miRNA seq methods.
  • Isolation of micro-particles and exosomes from bodily fluids.
  • Detection of proteins using western blotting.
  • Presentation of results at regular lab meetings.
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UTS Science Building
The expression of non-coding RNAs in HPV16 positive oral cancers

Background: 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. Older men were the major demographic group with smoking and alcohol consumption being the main risk factors for oral SCC. Today this paradigm has shifted. HPV16 is now a major cause of oral cancers in the US and this rate 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.

Objectives: To explore the associations between HPV16 and the expression of non coding RNAs in oral cancers.


Methodology: 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 by research or a full PhD program. 
  • Tissue culture: Growing cancer cells.
  • Isolation of small RNAs from in vitro cells and patient samples.
  • RNA sequencing.
  • 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. 

​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)
Groups: noncoding RNA Cancer Laboratory. Centre for Health Technologies & The Molecular Parasitology Laboratory, i3. 

Background: 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. They do this by secreting molecules that stimulate innate immune cells to establish and maintain an anti-inflammatory/regulatory (Th2/Treg) environment while simultaneously preventing excessive pro-inflammatory (Th1/Th17) immunity. 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.  

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

Methodology: 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 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. 

The development of novel living data maps for the analysis of genomic data  
 
Background: 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.
 
Objectives:
  1. 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/).
  2. To create a living data map for the analysis of large genomic data sets with the aim of identifying biomarkers for clinical applications.
  3. To combine art and science to create exciting visual tools.
Selection and Criteria
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.

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Images created with Circos, illustrating links, ribbons, tiles and a variety of 2D data tracks
 The laboratory is seeking an enthusiastic and highly motivated individual to undertake this research. This person must have a passion to learn and be very open to innovative methods of research. These projects are opened to ALL internal and external students with a basic understanding of science. We also accept mid year honours intakes. 
Please contact Dr. Nham Tran for further information. ​​