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

Information Sheet.

RNAi Pathways in Fasciola hepatica: Understanding Gene Silencing in Parasitic Worms

Parasitic worms, also known as helminths, cause major health and agricultural problems worldwide. In livestock, these parasites reduce animal health and productivity, while increasing reliance on chemical treatments that can lead to drug resistance.

RNA interference, or RNAi, is a natural gene-silencing process controlled by small RNAs. While RNAi is well understood in model organisms such as Caenorhabditis elegans, very little is known about how this pathway works in parasitic worms.

This project will investigate RNAi pathways in the liver fluke Fasciola hepatica, an important parasitic worm affecting livestock.

This project aims to:

Identify and compare RNAi genes across parasitic and free-living worms.
Characterise small RNA profiles during different stages of Fasciola hepatica development.
Investigate whether Fasciola hepatica has an active RNAi/RISC gene-silencing system.
Identify RNAi-associated proteins that may be unique to parasitic worms.

The findings from this study will improve our understanding of gene regulation in parasitic worms and may help support future RNA-based approaches for parasite control.

Using Saliva to Detect and Stratify HPV16-Positive Oropharyngeal Cancer

Human Papillomavirus type 16 (HPV16) is a major driver of oropharyngeal squamous cell carcinoma (OPSCC). While many HPV-positive patients respond well to treatment, a subset of HPV16-positive tumours contain high-risk viral SNPs associated with more aggressive disease and poorer survival.

Current HPV16 testing usually relies on tumour tissue from biopsy or FFPE samples. This project will develop a saliva-based liquid biopsy assay as a less-invasive approach for detecting HPV16 and identifying high-risk patients.

Using multiplex qPCR, the project will detect HPV16 E6, E7 and the upstream regulatory region (URR) to assess viral presence and activity. It will also investigate qPCR-based detection of high-risk HPV16 SNPs in saliva.

This project aims to:

Develop a saliva-based assay to detect transcriptionally active HPV16.
Optimise multiplex qPCR for HPV16 E6, E7 and URR.
Detect high-risk HPV16 SNPs associated with poorer clinical outcomes.
Evaluate the assay using Australian and independent patient cohorts.

The findings may support non-invasive HPV16 detection, improved patient monitoring and more personalised treatment decisions for patients with OPSCC.

Decoding MicroRNA Circuits in Parasitic Worm Development

This project investigates how parasitic worms use microRNAs and their sequence variants, known as isomiRs, to regulate development and adapt to life inside a mammalian host.

The focus is on Fasciola hepatica, an important liver fluke, and how small RNA networks control the transition from newly excysted juveniles to more mature parasite stages.

This project aims to:

Characterise microRNAs and isomiRs involved in early parasite development.
Compare small RNA networks across different parasitic worms.
Identify key microRNAs and isomiRs required for parasite growth and maturation.
Investigate how parasite RNAs may interact with mammalian host RNA pathways.

The findings from this project will improve our understanding of how parasitic worms regulate development and communicate with their hosts. This work may also help identify new RNA-based strategies to disrupt parasite infection without relying solely on traditional chemical treatments.

Investigating isomiR Biogenesis and RNAi-Mediated microRNA Regulation

MicroRNAs are small non-coding RNAs that regulate gene expression. However, each microRNA can also exist as multiple sequence variants, known as isomiRs.

These variants can differ at their 5′ or 3′ ends, or contain internal sequence changes, potentially altering their stability, target selection and biological function.

This project will investigate how isomiRs are produced and regulated in cells. A key focus will be to examine isomiR production when major RNAi components, including Dicer and PAGO/AGO proteins, are absent or disrupted. This will help determine which parts of the RNAi pathway are required for isomiR biogenesis.

This project aims to:

Characterise isomiR profiles in cells with altered Dicer and PAGO/AGO activity.
Investigate how loss of key RNAi components changes microRNA processing.
Identify RNAi-dependent and RNAi-independent mechanisms of isomiR production.
Explore how changes in isomiR profiles may alter microRNA target selection and gene regulation.

The findings from this project will improve our understanding of how microRNA variants are generated and regulated, and may provide new insights into the broader role of isomiRs in cancer and disease.