Honours Projects at Other Institutes

Adult Cancer Program

Dr Anthony Don
Project 1: Anti-cancer properties of synthetic sphingosine analogues. In this project we are testing the relationship between compound structure and anti-cancer (pro-apoptotic) properties of synthetic sphingosine derivatives, aiming to create a very potent and selective anti-cancer agent. The project involves biochemistry, molecular, and cell biology techniques and is carried out in collaboration with the laboratory of A/Prof Jonathan Morris in the School of Chemistry.
Project 2: Alterations to the abundant myelin lipid galactosylceramide in the pathogenesis of Alzheimer's Disease. In this project we are using sophisticated mass spectrometry and biochemical methods to describe alterations to myelin sphingolipids in Alzheimer's Disease, and aim to determine whether these alterations occur in the early stages of the disease, thereby destabilising myelin and accelerating neurodegeneration.

Dr Caroline Ford
The role of the Ror2 receptor tyrosine kinase in cancer.
The Wnt signalling pathway plays an important role in many human cancers, and research into regulation of the pathway has become an area of interest in recent years as a strategy to identify targets for novel drug development. Ror2 is a novel Wnt receptor that appears to play a key role in regulation of downstream Wnt signalling, and is frequently lost in cancer. This project will determine the expression and epigenetic regulation of this receptor in ovarian and colorectal cancer. The downstream effects of Ror2 on epithelial to mesenchymal transition (EMT), and metastatic potential will also be investigated. This project will involve protein work, cell culture, epigenetics and cell signalling analyses.

Dr Caroline Ford / Dr Viola Heinzelmann-Schwarz
Modulation of Wnt antagonists in ovarian cancer.
Wnt signalling is essential for crucial components of carcinogenesis and metastasis including differentiation, polarity, migration, adhesion and survival, and hence the role of Wnt signalling in human cancer is increasingly being investigated along with strategies to target pathway components. The Wnt pathway is regulated at multiple levels, with the Wnt antagonists or “gatekeeper proteins” receiving attention in recent years, due to their frequent loss in cancer. Secreted frizzled receptor proteins (SFRPs) are extracellular inhibitors of Wnt signalling that act by binding directly to Wnt ligands or Frizzled receptors, and have been shown to function as tumour suppressors in other cancer types. We have previously shown that the expression of these gatekeepers is lost in ovarian cancer. This project will focus on the regulation of these proteins, and will involve cell culture, qPCR, protein work and epigenetics.

Prof Philip Hogg
Studying the concept of biological regulation through protein disulfide interchange. We have shown that disulfide interchange events are critical for new blood vessel formation in tumours and HIV infection of blood cells.

Dr John Pimanda
Role of Mesenchymal Stem Cells in Cancer Biology.
Mesenchymal stem cells are precursors of bone, cartilage, fat and other cell types. Their role in tumour vascularisation is not well characterised. The objective of this project is to use cells derived from a genetically marked mouse to establish their relationship with endothelial cells in culture. These data will form the platform for future experiments designed to perturb cellular interactions in vivo to study their effect on tumour progression.

Dr Jason Wong
Identification of splice variants in cancer proteomes. Splice variants have been implicated in many cancers. Identification of these variants will enhance our understanding of the how they affect protein function.
Skills learnt: Bioinformatics, Proteomics, Mass spectrometry.

A/Prof Jia-Lin Yang / Dr Luke Hesson
Project 1: DNA MMR deficiency and cancer sensitivity to calcium channel blockers. We have been the only group in the world to have confirmed that DNA mismatch repair (MMR) gene deficient cancer cell lines are more sensitive to calcium channel blockers. It is unknown whether cancer cell lines having normal MMR genes but with epigenetic changes would have the same drug sensitivity. This study will investigate selective drug sensitivity on MMR epimutation cell lines comparing with wild type or epimutation reverted controls. Further study can compare wild-type with siRNA MMR gene inhibited cell lines and investigate the mechanism behind.
Project 2: Investigation of Mir34 and its promoter in a panel of cancer cell lines and tissue samples. From our published literature review (see reference), we knew that MiR34 is an important p53 downstream tumour suppressor. It was reported to be dysregulated in cancers and restoration of MiR34 will have a therapeutic significance to particularly p53 mutant cancers. This study will measure MiR34 promoter epigenetic change, as well as MiR34 mutation or deletion in a panel of cancer cell lines. Further study will focus on MiR34 restoration in its dysregulated cell lines and their sensitivity to targeted therapy, chemotherapy and/or radiotherapy.

Childrens' Cancer Institute Australia

Dr Jamie Fletcher
Characterization and inhibition of the tumour-stroma interaction in neuroblastoma.
Children with the solid tumour neuroblastoma often have metastatic disease in the bone and bone marrow that is resistant to conventional chemotherapy. The bone marrow microenvironment is likely to play an important role in drug insensitivity and subsequent relapse. The tumour-stroma interaction is therefore an attractive target for therapeutic intervention. Paracrine loops established between stromal and tumour cells have long been recognised to contribute to proliferation and drug resistance in other tumours, and similar loops have recently been demonstrated for neuroblastoma. Molecular analysis of tumour and stromal cells as both mono- and co-cultures can facilitate the characterization of these interactions. Furthermore, high throughput screening can be used to identify small molecule inhibitors to disrupt these interactions or to target weaknesses arising from them.
Aims:
1. To characterise the interaction between bone marrow stromal cells and neuroblastoma cells using gene expression analysis and other molecular profiling techniques.
2. To identify small molecule inhibitors of the tumour-stroma interaction using recently developed bioluminescence based high-throughput screening techniques.
Techniques: Cell culture, bioluminescence assays, whole-genome expression analysis, high-throughput small molecule inhibitor screening, real-time PCR analysis and other in vitro techniques.

Dr Jamie Fletcher/ Prof Michelle Haber
Genes underlying bone marrow metastasis in neuroblastoma.
The overwhelming majority of tumour-related deaths are attributable to metastases. Different tumour types infiltrate and colonise different organs, however little is currently known about the genes that underlie these abilities. The paediatric tumour neuroblastoma arises in the sympathetic nervous system and frequently metastasizes to the bone and bone marrow. In mouse models, xenografted human neuroblastoma cells also grow in these sites. Re-isolation of tumour cells from mouse bone marrow can enrich for cells with enhanced ability to grow at this site. These cells often grow more aggressively in bone marrow upon xenografting into secondary recipients. Comparative gene expression analysis of these populations can identify candidate genes governing enhanced ability to grow in bone marrow. These genes are potential therapeutic targets for patients with metastatic disease.
Specific aims:
1. Produce tumour cell populations with enhanced ability to colonize bone marrow using vivo selection.
2. Identify candidate genes contributing to efficient bone marrow colonization.
3. Validate these genes using databases, mouse models and cell culture systems.
Techniques: Human neuroblastoma cell xenografts in immunodeficient mice, cell culture, whole-genome expression analysis, real-time PCR analysis and other in vitro techniques.

Dr Tao Liu
Project 1: Histone demethylases in modulating gene transcription, tumour initiation and progression. One of the most important advances in cancer research in the last 5 years is the identification of histone demethylases as the critical players in gene transcription, tumour initiation and progression. In collaboration with researchers at University of North Carolina (USA) and Nagoya City University (Japan), we are currently investigating histone demethylases in modulating gene transcription, tumour initiation and progression, and investigating histone demethylase inhibitors as novel anti-cancer agents in human cancer cell lines and in animal models of human cancers.
Techniques: Cell culture, cell proliferation and apoptosis assays, RT-PCR, immunoblot, protein immunoprecipitation and chromatin immunoprecipitation assays.
Project 2: The critical role of long noncoding RNAs in cancer. Long intergenic noncoding RNAs (lincRNAs), which range in size from two hundred to tens of thousands of bases, comprise a distinct class of newly discovered noncoding RNAs. Although >3,000 human lincRNAs have been manually annotated and predicted by bioinformatics analysis, <1% of these have been experimentally characterized. Recent studies demonstrate that the expression of lincRNAs is regulated by key transcription factors and by biological processes such as tumour initiation, progression and metastasis. We have made the novel finding that gene amplification of a lincRNA is essential for the transcription of a critical oncogene, and is essential for neuroblastoma cell proliferation. We are currently investigating how the lincRNA modulates gene transcription of oncogenes and how to target the lincRNA for cancer therapy.
Techniques: Cell culture, cell proliferation and apoptosis assays, RT-PCR, immunoblot, protein immunoprecipitation and chromatin immunoprecipitation assays.

Dr Karen MacKenzie
Project 1: Anti-apoptotic mechanisms involved in cancer cell immortalisation. One characteristic that is common to most (if not all) cancer cells, and distinct from normal cells is that cancer cells proliferate indefinitely (they are immortal), whereas the replicative lifespan of normal human cells is maintained within programmed limits. Our investigations have revealed that immortalised human fibroblasts are resistant to apoptosis and express elevated levels of the Inhibitor of Apoptosis Protein (IAP) survivin. This project will make use of a panel of cell lines that have been immortalised in our laboratory to delineate the molecular mechanisms by which survivin confers resistance to apoptosis during the immortalisation process. Results from this study will provide opportunity for the development of targeted therapeutics that act by reverse the immortal phenotype of premalignant and malignant cells.
Project 2: Reversing the immortal phenotype of neuroblastoma cells. The enzyme telomerase is expressed in 80-90% of cancers, including neuroblastoma, which is the most common extracranial solid tumour that affects children. Telomerase functions to maintain the integrity of chromosomal-end structures (telomeres) and is central to the immortalisation process, which is an essential step in carcinogenesis. The molecular mechanisms that are responsible for the activation of telomerase are ideal for targeted anti-cancer therapeutics. Hence the objective of this Student project will be to delineate mechanisms that are involved in the activation of telomerase in neuroblastoma cells. The results will provide insight to effective ways of targeting telomerase and reversing the immortal phenotype of neuroblastoma cells.
Project 3: Regulation and function of telomerase in acute myeloid leukaemia cells. Telomerase is activated in 80-90% of all cancers and leukaemias, where it promotes the continual replication of malignant cells. In this project, the function and regulation of individual components of the telomerase holoenzyme will be further investigated in acute myeloid leukaemia cell lines. siRNA knockdown and overexpression systems will be employed to investigate the function of telomerase components and the consequences of their ablation. The transcriptional mechanisms that regulate specific telomerase components in leukaemia cells will also be explored. Results from these investigations will provide insight to the most effective strategies for targeting telomerase in acute leukaemia.

Centre for Vascular Research

Prof Miles Davenport
Mathematical and statistical analysis and bioinformatics of infectious diseases. Current projects involve study of viral-immune dynamics in HIV, and red cell destruction in malaria. Students with some background in (or just not afraid of) mathematics, bioinformatics, or computer science are encouraged to come and discuss the possibilities.

A/Prof Katharina Gaus
The role of membrane structure and the organization of membrane domains (lipid rafts) in signal transduction processes.

Prof Wendy Jessup
Cell biology of atherosclerosis. Interests are in how cells in the artery wall store and export excess cholesterol. Current projects: role of membrane transporter proteins in cholesterol export; plasma membrane structure and function in arterial cells; how diabetes stimulates atherosclerosis. Techniques include gene silencing (siRNA), transient and stable overexpression systems, real-time PCR, HPLC, Western blotting, functional assays of cholesterol transport, cell culture and microscopy.

Prof Levon Khachigian
Uncovering the roles of key transcription factors in neointima formation (arterial thickening), angiogenesis, tumour growth, myocardial ischemia, and inflammation. Novel uses of DNAzymes, siRNA and modified antisense oligonucleotides as gene-silencing "molecular assassins" in cellular and animal models of human disease. Isolation and characterisation of novel genes that are involved in narrowing of blood vessels.

Dr Shane Thomas
Project 1: Role of oxidative stress in cardiovascular disease
This project aims to define the biochemical and molecular mechanisms by which oxidative stress causes endothelial dysfunction in cardiovascular disease patients.
Project 2: Roles and regulation of an immune regulatory protein in antigen presenting and cancer cells
This project aims to better understand the biochemical and molecular mechanisms through which tumour cells avoid removal by the cancer patient’s immune system.
Skills learnt: Tissue culture of vascular, immune or cancer cells, molecular biology (PCR), cell signalling and western blotting, analytical chemistry (spectrometry, high performance liquid chromatography, mass spectrometry), recombinant protein expression and site-directed mutagenesis, measurement of blood vessel function, animal models of vascular disease, histology, immunohistochemistry and confocal microscopy.

Prince of Wales Hospital

Dr Tim Brighton
Project 1: Investigation of a case of acquired von Willebrand’s Disease. This project revolves around a patient with apparent acquired VWD. The project involves purification of patient immunoglobulin, proving patient’s antibody reproduces the phenotype, and establishing new assay to detect auto-antibodies to VWF. Genotyping the patient to exclude heritable Type II VWD will be required. The work would be completed by literature review and preparing a manuscript for publication.
Project 2: Investigation of Type III VWD.The Dept of Haematology has 5 known kindreds of Type III von Willebrand’s Disease. This project would involve detailed family investigations of phenotype and laboratory assays. DNA would be collected, extracted, amplified and direct sequenced to identify mutations in the cases and parents. The size of the VWF gene makes it more efficient to screen for mutations in and deletions of exons by PCR amplification and denaturating gradient gel electrophoresis prior to sequence analysis of exons in which mutations are suspected.
Project 3: Characterisation of Familial Thrombocytopenia. Candidate genes carrying mutations account for approximately 50% of cases of familial thrombocytopenia described in the existing literature. The project will focus on characterising the gene(s) involved in several kindreds of familial thrombocytopenia within the Department. Linkage analysis using single nucleotide polymorphisms will be used to identify/exclude candidates in these families, followed by sequence analysis of relevant genes. Genome-wide snp analysis may be required where no clear candidates emerge from the initial analysis.
Project 4: Characterisation of Platelet Dysfunction in Patients with ITP. Occasional patients with immune thrombocytopenia have unusually severe bleeding given their platelet count and platelet dysfunction. In these cases the autoantibody inhibits platelet function. This project will focus on 2 cases and involve total Ig and IgG preparations from patient’s serum,  platelet aggregation experiments to reproduce the platelet aggregation defect, and determination of the specificity of the autoantibodies.
Project 5: Characterisation of Scott Syndrome Platelets. Scott Syndrome is a rare poorly characterised but fascinating inherited platelet membrane disorder. This project will continue ongoing research into kindreds with bleeding who may have Scott Syndrome or other functional platelet defects. The work will involve a variety of functional platelet assays (aggregation, thrombin generation), flow cytometric analysis, and novel laboratory assays to be established. If individuals with Scott Syndrome are found, characterisation of the gene(s) involved would potentially make a significant contribution to platelet physiology.

Virology Research, POWH and UNSW Research Laboratories

Dr Cristina Baleriola
Project (1 place available): Clinical molecular diagnosis of blood-borne viruses’ transmission. Research projects include the development and evaluation of real-time molecular techniques for the rapid characterization of blood-borne viruses (HIV, HCV, HBV and CMV) and use of these tests in investigating cases of transmission, particularly in health-care settings, and tissue and organ transplantation.

A/Prof Maria Craig
Project 1 (1 place available): Enterovirus infections and type 1 diabetes. Type 1 (insulin dependent) diabetes (T1D) is increasing in childhood and we do not know why. The rise has occurred rapidly, suggesting a major role for environmental factors in T1D aetiology. Enteroviruses (EV) are the most common viruses affecting children and are strongly associated with T1D. We have found EV infections are more common in children who develop islet autoantibodies (an early marker of diabetes) and at onset of T1D, compared with controls. This study will investigate the molecular characteristics of EV isolates in children at risk of developing diabetes and at diabetes onset.
Project 2 (1 place available): Molecular mechanisms for enterovirus induced beta cell lysis. Enterovirus (EV) infection is a major environmental factor in the aetiology of type 1 diabetes. Little is known about the mechanism by which these viruses induce apoptosis and/or functionally impair pancreatic β-cells. We have recently shown that EV infection induces cytokine and chemokine production by β-cells. This project will apply a wide range of molecular techniques to investigate the abilities of enteroviruses to induce cellular and functional damage to β-cells, using insulin producing cell lines and human islets.

Dr Jenna Iwasenko
Project (1 place available): Pathogens associated with stillbirth. Stillbirth is an enormous personal, family, community, and medical loss. Despite investigation by routine autopsy, ~30% of stillbirths are unexplained. We have detected cytomegalovirus and other infectious agents in stillborn babies. This project will investigate the proportion of stillbirths where viruses, cell-wall deficient bacteria and anaerobic organisms are present, demonstrate the location of the infecting agent/s from the placenta and tissues from stillborn babies and investigate the host protein changes associated with CMV infection and transplancental transmission of CMV.

Dr Gillian Scott
Project (1 place available): CMV pathogenesis. Human cytomegalovirus (CMV) is now the leading viral cause of malformation and disease in newborns. CMV also causes significant morbidity and mortality in immunocompromised individuals such as transplant recipients receiving immunosuppressive therapy, and can be further complicated by the development of resistance to the antiviral agents used to treat these infections. We study the pathways of CMV transplacental transmission in humans and in the murine animal model, the factors influencing disease outcomes in infected individuals and the mutations that confer antiviral resistance.

Dr Sacha Stelzer-Braid/ Prof Bill Rawlinson
Project (1 place available): Respiratory Viruses. Respiratory infections are a common cause of illness and an important cause of death in the community. The recent H1N1’09 pandemic (‘swine flu’) showed there is much to be understood about the transmission and containment of respiratory viruses. Using novel methods developed in collaboration with researchers at The Woolcock Institute and The University of Sydney, we collect viruses from mucus and aerosols produced by patients with chronic respiratory diseases suffering respiratory infections, and detect these viruses using molecular PCR and real-time assays.
We are interested in examining:

• Bio-aerosol production over the time course of a natural respiratory virus infection
• The role of respiratory viruses in exacerbation of chronic airway diseases (e.g. asthma, cystic fibrosis)
• Mechanisms of respiratory virus transmission in the environment

Victor Chang Cardiac Research Institute

A/Prof Sally Dunwoodie/ Dr Duncan Sparrow (Developmental Biology Division)
Project 1: Congenital scoliosis is a birth defect in which vertebral malformation causes a lateral curvature of the spine. Up until now there has been no genetic explanation for its occurrence. We have identified human gene mutations that cause congenital scoliosis and we are currently investigating why there is not an exact correlation between genotype and phenotype. This project will investigate the interplay of genetic and environmental factors on vertebral formation in the mouse embryo. The student will gain a comprehensive introduction to the process of embryonic vertebral development, and experience in mammalian embryology, molecular biology and histology.
Project 2: Congenital heart disease occurs in many forms. Although it is the most common type of birth defect, representing a third of the total, only about 10% of cases can be identified as having a genetic cause. This project will generate information about the effects of environmental conditions on heart formation in the mouse embryo. The student will gain an introduction to the process of embryonic heart development, and experience in mammalian embryology, molecular biology and histology.
Project 3: Of the genetically defined cases of congenital heart disease (CHD), there is variable penetrance and expressivity of the heart defects, that is a single human gene mutation may cause different types of CHD or indeed no CHD. This project investigates what non-genetic factors influence the genesis and nature of genetically-defined CHD in the mouse. This project will provide the student with a comprehensive introduction to the process of embryonic heart development, and experience in mammalian embryology, molecular biology, and histology.

A/Prof Sally Dunwoodie/ Dr Gavin Chapman (Developmental Biology Division)
The Notch signalling pathway is a well conserved and widely utilised pathway in embryogenesis and in the adult in situations where cell-cell interactions are important for cell fate changes and differentiation events.
Project 1: The role of Notch4 in patterning the developing vasculature. Notch signalling is essential for the proper formation of the vasculature. This project seeks to understand signalling through the Notch4 receptor and how it relates to the formation and remodelling of the vasculature. Techniques include embryo and retina dissection, immunofluorescence, confocal microscopy, immunoprecipitation and western blotting.
Project 2: Characterising the function of Notch ligands in vertebral column formation. Mutations of in Notch pathway genes cause abnormal vertebral segmentation. This project takes advantage of live confocal microscopy, whole-mount immunofluorescence and immunoprecipitation techniques in order to decypher the role of ligands during formation of the vertebral column.

A/Prof Diane Fatkin (Molecular Cardiology Program)
Project 1: Identification of novel disease genes for familial AF. This study is examining DNA from AF patients for mutations in candidate genes.
Project 2: Characterisation of the atrial ³environment². This study will use cell models to evaluate the effects of mechanical stress on atrial wall properties and AF development.
Skills learnt: DNA and RNA extraction, PCR, sequencing, mutation analysis, genome analysis, cell culture, molecular and cell biology techniques, stretch studies.

Prof Michael Feneley / Dr J Yu (Cardiovascular Mechanics Program)
The overall research strategy is to employ a series of different transgenic/knockout mouse models to dissect the different candidate pathways to the induction of left ventricular hypertrophy (LVH) in low-renin and high-renin LV pressure overload by cardiac-targeted inhibition of critical steps in each pathway.
Project 1: /TgGqI mouse/. This mouse has inhibition of Gq receptor function. This project will examine relative role of activation of Gq receptors in the induction of pressure overload LVH in the presence and absence of elective renin levels.
Project 2: /GSK3//b// mouse/. This mouse has effective blockade of the calcineurin-mediated pathway to LVH induction. This project will explore the relative role of the calcineurin pathway in induction of pressure overload LVH in the presence and absence of elective renin levels.

Bioanalytical Mass Spectrometry Facility

Dr Valerie Wasinger
Project: Proteomic biomarkers in the assessment of Inflammatory Bowel Disease; severity and prediction of treatment response.
Skills learnt: Application of proteomic technologies for elucidation of novel markers using in-house developed technologies, fractionation, liquid chromatography and 'state of the art' mass spectrometry techniques, quantitative and qualitative data evaluation and multivariate stat analysis. Project will involve liasing with clinicians at Bankstown and Concord Hopsitals in association with A/Prof Rupert Leong.

Stem Cell Lab, School of Psychiatry

A/Prof Kuldip Sidhu
Project 1: Role of GLP-1 receptors in hESCs and iPS cells in maintaining pluripotency. Our preliminary data on micro RNA indicate that GLP-1 receptors in human embryonic stem cells (hESCs) and induced pluripotent stem (iPS) cells may have a role in maintaining pluripotency in these cells. This project is to understand the mechanism how GLP-1 receptors are involved in this process.
Project 2: Disease modelling by using iPS cells derived from patients with early stage Parkinson’s and Alzheimer’s diseases. We have produced and characterised iPS cells by using fetal and adult human skin-derived fibroblasts. The next phase is to derive disease-specific iPS cells using our optimised procedure and to use these iPS cells for disease modelling.
Project 3: Reprogramming somatic cells to a pluripotent state by non-genetic means. We have partially reprogrammed human fetal fibroblasts (HFFs) using a combinatorial approach of changing the epigenetic status and by using human embryonic stem cell (hESC) extracts. These partial reprogrammed cells were able to be differentiated into neuronal cells. However, apoptotic genes were found to be up-regulated in the reprogrammed cells, which may have a negative effect on cell growth and survival. Initial data also suggest that the culture medium may have a role in the process of reprogramming. This project will further investigate the improvement of the reprogramming efficiency, which would lead to a better understanding of the mechanisms involved in maintaining these partially reprogrammed cells in culture.