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Honours Projects 2009            

 

Dr Peter White 

p.white@unsw.edu.au

Molecular microbiology

Viruses and bacteria cause the majority of human, animal and plant illness in the world. Projects are available on a range of human viral and bacterial pathogens. The laboratory is strong in basic molecular biology, recombinant protein expression, viral replication, aptamer development using SELEX, identification of antibiotic resistance genes, diagnostics, bioinformatics, cloning, and applied and fundamental virology. The honours projects are available on hepatitis viruses, norovirus and antibiotic resistance genes, and other projects may become available. All of these projects involve training in molecular methods, bioinformatics, cloning and DNA sequence analysis. The studies are funded by ACH2, ARC, UNSW, NHMRC, NIH, Perpetual Trustees and the Sydney Catchment Authority (SCA).

 

Program 1: Hepatitis C virus replication and evolution
Availability for 2 students. 

In Australia 250,000 people are infected with hepatitis C virus (HCV) and 15,000 new cases are reported each year. The majority (~70%) of all infections become persistent and lead to various clinical outcomes ranging from an asymptomatic carrier state to liver failure. HCV has a positive sense RNA genome that replicates in the cytoplasm of the infected cell via minus-strand RNA intermediates. The lack of proof reading activity of the polymerase means that HCV exists in an individual as a population of closely related variants termed quasispecies. Varied or complex quasispecies are thought to be important in evasion of the host immune response and may correlate with a poor response to interferon and a faster progression to cirrhosis. Using our established methodology we have produced highly purified, soluble and active recombinant RdRps from a range of HCV genotypes and from other viral, plant and bacteriophage sources. Current projects are available to study HCV polymerases to examine the influence of NS5B amino acid sequence heterogeneity on transcriptional activity, fidelity and biochemical properties. A second project is also available to develop an alternative simple, rapid system to analyse HCV quasispecies and viral sequence evolution in patients during treated and untreated HCV infections. 

 

Selected References (Available on request)

Jones, L. A., L. E. Clancy, W. D. Rawlinson and P. A. White. 2006. High affinity aptamers to subtype 3a HCV polymerase display genotypic specificity. Antimicrobial Agents and Chemotherapy 50:3019-2027. 

White, P.A., Y. Pan, A. J. Freeman, G. Marinos, R. A. Ffrench, A. R. Lloyd and W. D. Rawlinson. 2002. Hepatitis C virus quantification in human livers and serum using LightCycler RT-PCR. Journal of Clinical Microbiology. 40:4346-8.

White, P. A., Z. Li., X. Zhai, G. Marinos and W. D. Rawlinson. 2000. Mixed viral infection identified using heteroduplex mobility analysis (HMA). Virology 271:382-389.

White, P. A., X. Zhai, I. Carter, Y. Zhao and W. D. Rawlinson. 2000. Simplified hepatitis C virus genotyping using heteroduplex mobility analysis. Journal of Clinical Microbiology. 38:477-482.

 

Program 2: Norovirus
This project will involve collaboration with Prof Bill Rawlinson and Dr Christopher McIver, Virology Division, Prince of Wales Hospital.
Availability for 1 student

Acute gastroenteritis is common in Australia, with an estimated incidence rate of one episode per person per year.  Two of the major viral causes of gastroenteritis include noroviruses and sapoviruses. We have developed a number of viral detection tools for these viruses over the last few years. These tools have been used for molecular epidemiological studies for the investigation of outbreaks of viral gastroenteritis and determine prevalent norovirus strains in the community.

There is excellent evidence that particular strains, all within genotype II.4, can induce large or even world-wide epidemics of acute gastroenteritis.  In Australia 2004 and 2006 saw dramatic increases in NoV associated gastroenteritis.  The reason for this increase in NoV associated gastroenteritis and whether it correlates to the introduction of a new NoV strain is currently unknown. This honours project proposal aims to conduct a detailed molecular epidemiological analysis of Australian NoV strains and determine if outbreaks are associated with the introduction of novel NoV variant.  Other honours projects are aimed at improving upon current detection methodology for norovirus and sapovirus by the use of enzyme immunoassays (EIAs) and nested RT-PCR.

 

Selected References (Available on request)

Bull, R. A., M. M. Tanaka and P. A. White. 2007.  Norovirus recombination. Journal of General Virology.  In Press.

Tu, E. T-V., T. Nguyen, P. Lee, R. A. Bull, J. Musto, G. S. Hansman, P. A. White, W. D. Rawlinson, C. J. McIver. 2007.  Norovirus GII.4 strains and outbreaks, Australia.  Emerging Infectious Disease. 13:1128-30.

Bull, R. A., E. T. V. Tu, C. J. McIver, W. D. Rawlinson and P. A. White. 2006. Emergence of a new norovirus GII.4 variant associated with global outbreaks of gastroenteritis. Journal of Clinical Microbiology. 44:327-333

 

 

Program 3: Antibiotic resistance in Gram-negative bacteria
Availability for 1 student

The rapid and irrepressible increase in antimicrobial resistance in pathogenic bacteria that has been observed over the last two decades is widely accepted to be one of the major problems of human medicine today.  The most worrying resistance mechanisms that emerge and spread in bacterial populations are those of wide activity spectra which compromise multiple drugs.  Multi-resistant nosocomial infections are a significant cause of hospital acquired disease and a major pest in nearly every hospital world-wide.  These bacteria pose a serious clinical problem due to their widespread nature.

Integrons are naturally occurring expression systems that capture, collect and express antibiotic resistance gene cassettes.  Integrons have a tendency to be located on large transferable plasmids, however, the mechanisms involved which leads them to reside there are poorly understood.  We have recently identified a number of plasmids that contain an integron and other resistance elements.  This renders the bacteria harbouring the plasmid resistant to an alarming array of antibiotics.  Current honours projects involve the analysis and evolutionary study of large resistance plasmids that contain multiple resistance genes. Where do the resistance genes reside on these plasmids and how did they get there?

 

Selected References (Available on request)

Jones, L., A., C. J. McIver, W. D. Rawlinson and P. A. White. 2005. The aadB gene cassette is associated with blaSHV genes in Klebsiella species producing extended spectrum β-lactameses.  Antimicrobial Agents and Chemotherapy. 49:794-797.

 

Jones, L. A., C. J. McIver, W. D. Rawlinson and P. A. White. 2003. Polymerase chain reaction screening for integrons can be used to complement resistance surveillance programs. Commun. Dis. Intell. 27 Suppl:S103-S110.

White, P. A., C. McIver, and W. D. Rawlinson. 2001. Integrons and gene cassettes in the Enterobacteriaceae. Antimicrobial Agents and Chemotherapy. 45:2658-2661.