UQ Winter Research Program

Description: Human-pathogenic fungi are spreading intercontinentally at an unprecedented rate and with high resistance to available drugs, for some there is no available treatment. People with weakened or underdeveloped immune system such as newborns or elderly, chemotherapy patients, organ transplant, HIV/AIDS patients are particularly at risk. We have discovered novel antifungal compounds which have significant potential to treat the worlds most deadly fungal infections. In this project you would be using synthetic organic chemistry skills to synthesise active compounds in our molecular series.

Expected outcomes and deliverables: The student will learn and develop synthetic organic chemistry, purification and analytical skills contributing to our series for future patent and/or publication.

Suitable for: This project is open to applications from UQ enrolled students only with a background and interest in synthetic organic chemistry.

Primary supervisor: Professor Avril Robertson

Before you apply: Contact the primary supervisor. 

Description: The aim of this project is to use structural biology to understand the molecular basis of processes involved in infection and immunity. The work has implications for treating a range of infectious and inflammatory diseases and cancer, or for minimizing plant disease. We are focusing in particular on the proteins involved in cytoplasmic signalling by Toll-like receptors, and effector-triggered immunity by plants. The main techniques will involve protein expression, purification, crystallization and structure determination, molecular interaction analyses and characterization of functional effects of site-directed mutants.

Expected outcomes and deliverables: Scholars will gain skills in various lab techniques mentioned above and have an opportunity to contribute to publications from their research.  Students may also be asked to produce a report or oral presentation at the end of their project.

Suitable for: Students with background in biochemistry, biophysics and other relevant areas are most suitable. We are looking for motivated students with interest in research in the areas the lab works in.

Primary supervisor: Professor Bostjan Kobe

Before you apply: Contact the primary supervisor.

Description: When molecules flow, they can change their conformation and their relative orientation. This can result in different reactivity, assembly and other behaviour.  In this project computer simulations will be carried out. 

Expected outcomes and deliverables: The applicant will learn about modelling systems at the molecular level, and how flow can affect physical and chemical properties.  They will collect, analyse and visualise their data.  They will have the opportunity to propose ways of improving physical or chemical reactions. At the end of the project the student will summarise their findings in a report and present the results to our group.

Suitable for:  This project is open to motivated students with a strong background in chemistry or physics and an interest in computational science.

Primary supervisors: Professor Debra Bernhardt

Before you apply: Contact the primary supervisor.

Description: Conversion of carbon dioxide to useful products could lead to environmental and economic benefits. We are interested in developing simulation methods that can contribute to developing catalysts for this purpose.  The student will be part of a project that aims to reduce the computational effort required to model reactions.

Expected outcomes and deliverables: The applicant will learn about modelling systems at the molecular level, and how heterogeneous catalysis can be modelled.  They will collect, analyse and visualise their data.  They will have the opportunity to propose ways of improving the catalyst. At the end of the project the student will summarise their findings in a report and present the results to our group.

Suitable for: This project is open to motivated students with a strong background in chemistry or physics and an interest in computational science.

Primary supervisor: Professor Debra Bernhardt

Before you apply: Contact the primary supervisor.

Description: High-throughput sequencing and proteomics approaches now mean that tens of thousands of positional variations within genes or proteins can be identified in a single experiment. The vast majority of such variations are patient specific and require advanced methods to identify those that are important for disease or biological mechanism. Our aim is to be able to, for each mutation/modification and for each gene/protein, scalably and effectively assess the overall consequences of the molecular effects and their potential phenotypic outcomes.

This project will aim to combine genetic, biochemical, structural, cellular and clinical data to give insights into disease diagnosis, prognosis and design of treatments.

Expected outcomes and deliverables:  The students will gain skills in bioinformatics, applications of artificial intelligence development and validation. The work in this project will lead to development of new tools for research and clinical use.

Suitable for: Some familiarity with computer coding would be beneficial (Python).

Primary supervisor: Professor David Ascher

Before you apply: Contact the primary supervisor.

Description: Our laboratory uses computer simulations to study how molecules react. By performing quantum chemical modelling we are able to explore the factors that control chemical behaviour, visualising molecules in atomic-level detail. A range of project topics are available, e.g. studying the behaviour of catalysts that degrade plastics, or studying how drug candidates bind to biological molecules leading to desirable or undesirable effects. 

Expected outcomes and deliverables: Scholars will gain advanced skills in molecular modelling and in understanding reaction mechanisms. Scholars may also learn about the activities of the broader research group (e.g. by participating in group meetings and activities) and may be asked to produce a short written report and/or oral presentation at the end of their project.

Suitable for: This project is open to applications from UQ enrolled students majoring in Chemistry who have taken CHEM3011 and/or have a commensurate level of previous practical experience in computational quantum chemistry.

Primary supervisor: Professor Elizabeth Krenske

Before you apply: Contact the primary supervisor.

Description: Kunjin virus is an Australian strain of West Nile virus (WNV) which is transmitted by mosquitoes. Previous work in the RNA Virology laboratory using deep mutational scanning (DMS) has identified mutations in the 5’ UTR, showing different tolerances to mutations in the 5’ end for mammalian or insect cells. 

This project aims to analyse the role of identified amino acids in the Kunjin virus capsid gene in modulating the insect-only and mammalian-only phenotype. 

Expected outcomes and deliverables: Scholars will gain skills in molecular biology such as primer design, PCR, cloning and mutagenesis. Techniques such as cell culturing and analysis of Sanger sequencing will also be gained. The virus isolates generated will be described in publications along with other aspects of the work to which students have the opportunity to share authorship. 

Suitable for: The project is open to Science or Biotechnology students with an interest in virology. A general background in 2^nd-3^rd year genetics, microbiology, virology, immunology or molecular biology is recommended.

Primary supervisor: Dr Rhys Parry

Before you apply: Contact the primary supervisor.

Description: Kunjin virus is an Australian flavivirus with a positive-strand RNA genome that replicates exclusively in the cell cytoplasm. Replicons are generated by deleting viral structural genes and replacing them with heterologous genes (HG) allowing for self-amplifying RNA (saRNA) delivery and expression of HG.  In this project you will generate Kunjin replicons expressing potent anti SARS-CoV-2 Spike nanobodies and monoclonal antibodies. 

After generation and sequence confirmation of these constructs, you will verify their expression in mammalian cells transfected with the resulting saRNAs and verify antigen binding properties of produced antibodies using ELISA with purified SARS-CoV-2 spike antigens from different variants.

If the generation of these saRNAs are of sufficient quantity and quality they will be tested in vivo in future animal studies.

Expected outcomes and deliverables: Scholars will gain skills in molecular biology such as primer design, PCR, cloning and RNA production. Techniques such as cell culturing, RNA transfections, detection of protein expression, and ELISA will also be gained. The results will be described in publications along with other aspects of the work to which students have the opportunity to share authorship 

Suitable for: A general background in 2^nd-3^rd year genetics, microbiology, virology, immunology or molecular biology is recommended.

Primary supervisor: Dr Rhys Parry

Before you apply: Contact the primary supervisor.

Description: Flaviviruses subvert host mRNA decay pathway during an infection to generate a functional non-coding RNA known as Flaviviral Subgenomic RNA (sfRNA). It is produced by incomplete exonuclease (XRN1) digestion of the Flaviviral genomic 3’UTR. The Zika Virus (ZIKV) sfRNA binds and stabilizes the viral non-structural protein 5 (NS5), allowing for intracellular accumulation of NS5 and potent antagonism of the innate antiviral response.

This project aims to investigate whether the sfRNA-NS5 interaction is an evolutionarily conserved mechanism similarly employed by other Flaviviruses, such as the Yellow Fever (YFV) and West Nile (WNV) viruses. It will involve plasmid transfections to express NS5 and sfRNA, utilise western blot to quantitate NS5 expression, and perform interferon treatment followed by western blot for phosphorylated STAT1 to analyse modulation of interferon signalling.

Expected outcomes and deliverables: The student will learn key laboratory techniques, such as mammalian cell culturing, transfections, PCR, and western blotting.

Suitable for: This project is open to applications from 3rd year students with a background in microbiology, biochemistry and/or virology

Primary supervisor: Dr Lachlan De Hayr

Before you apply: Contact the primary supervisor.

Description:

Background: The increase in antibiotic resistance creates an urgent need for new or improved antibiotics. Antimicrobial peptides show potent antibacterial or antifungal activities yet are often not suitable as drug candidates due to their haemolytic activity.

Aim:  To compare the antibacterial and haemolytic activities of a series of peptides to better understand what properties govern the interaction of these peptides with bacterial or mammalian membranes

Approach: In our lab, we use a range of biophysical methods including isothermal calorimetry, tethered lipid bilayer membrane or vesicle leakage assays.

Expected outcomes and deliverables: In this project you will:

• learn biophysical techniques that are usually not taught in undergraduate sciences degrees.
• Learn how to keep lab notes and design, carry-out and analyse your own experiments to a standard required for scientific publications.
• Work in a research group and carry out experiments that form part of a larger project.
• Gain knowledge in membrane biophysics, structural biology, and peptide-based drug design.

Suitable for: Suitable for undergraduates in their 3rd or 4th year, Advanced Sciences students in their 2nd, 3rd or 4^th year, or Masters students.

Students should have an interest in peptides, biophysical chemistry, membrane biology, structural biology.

Students need to be curious, highly motivated and interested in learning something new.

Projects are suitable for students with a background in biochemistry, chemistry or biomedical sciences. Note, this project does NOT use cell-based assays and required students to have a solid background in biochemistry or chemistry.

Primary supervisor: Dr Evelyne Deplazes

Before you apply: Contact the primary supervisor.

Description:

Background: Invasive fungal infections are difficult to treat, and many current drugs are toxic to human cells. This project studies the membrane-altering properties of peptides that increase the potency of existing anti-fungal drugs.

Aim:  To use biophysical chemistry techniques to determine the membrane binding and membrane disrupting properties of various peptides, and their synergy with anti-fungal drugs

Approach: In our lab, we use a range of biophysical methods including isothermal calorimetry, tethered lipid bilayer membrane or vesicle leakage assays.

Expected outcomes and deliverables: In this project you will:

• learn biophysical techniques that are usually not taught in undergraduate sciences degrees.
• Learn how to keep lab notes and design, carry-out and analyse your own experiments to a standard required for scientific publications.
• Work in a research group and carry out experiments that form part of a larger project.
• Gain knowledge in membrane biophysics, structural biology, and peptide-based drug design.

Suitable for:

Suitable for undergraduates in their 3rd or 4th year, Advanced Sciences students in their 2nd, 3rd or 4^th year, or Masters students.

Students should have an interest in peptides, biophysical chemistry, membrane biology, structural biology.

Students need to be curious, highly motivated and interested in learning something new.

Projects are suitable for students with a background in biochemistry, chemistry or biomedical sciences. Note, this project does NOT use cell-based assays and required students to have a solid background in biochemistry or chemistry.

Primary supervisor: Dr Evelyne Deplazes

Before you apply: Contact the primary supervisor.

Description: Transfusion related acute lung injury (TRALI) is a severe lung syndrome that can occur during or after transfusion of blood or blood products. TRALI is one of the leading causes of death due to transfusions. Antibodies against human neutrophil antigen (HNA) 3a and biological response modifiers (BRMs) such as extracellular vesicles (EVs) have been associated with TRALI onset. This project aims to develop monoclonal antibodies against the two alleles of HNA-3 that can then be used in cell-based assays to detect anti-HNA-3a and anti-HNA-3b antibodies in blood donors, in order to prevent transfusions that lead to TRALI. The project also aims to use a combination of purified EVs and bioactive lipids from blood components as well as commercially available lipids in both in vivo mouse and in vitro transfusion models to investigate how BRM-mediated TRALI develops.

If you join the lab, you will be able to contribute to specific aspects of the antibody discovery projects.

Expected outcomes and deliverables: Our goal is to provide you with the best experience, both inside and outside the lab, which will contribute to train you for a career in research. An integral part of the experience in our lab will involve active participation in lab meetings and journal club discussions. We will encourage you to present your findings to the group. We will also endeavour to coach you in effective presentation techniques, scientific writing, ethics in research, good laboratory practices, and team-work. You will be required to prepare a report and do a final oral presentation of your work at the end of the placement.

Suitable for: We are actively looking for enthusiastic, team-oriented, fast-learning, and hard-working students with a background in Biochemistry, Molecular Biology, Microbiology or related fields, and an interest in learning molecular and cellular biology, glycobiology, models of disease, proteomics, or antibody discovery. Previous experience in a molecular biology laboratory is of benefit, but not a requirement (we may request a reference letter).

This project is open to applications from students in 3^rd – 4th year; and only in special cases will 2^nd year students be considered.

Primary supervisor: Dr Lucia Zacchi

Before you apply: Contact the primary supervisor.

Description: Post-translational modifications of proteins with complex sugar groups, known as glycosylation, is critical for regulating protein stability and functions. This is particularly important in viral glycoproteins, where evolution of the precise sites of glycosylation can help in immune evasion by covering antigenic sites. This project will study how glycosylation of glycoproteins from influenza virus can change through sequence evolution, and how this impacts protein function and viral fitness.

Expected outcomes and deliverables: You will learn techniques in bioinformatics, molecular biology, PCR, protein purification, mass spectrometry, and glycoproteomics.

Suitable for: Suitable for students with some experience in microbiology, virology, biochemistry, or analytical chemistry. No specific background is required

Primary supervisor: Professor Ben Schulz

Before you apply: Contact the primary supervisor.

Description: Environmental microbial fungi are a source of extreme biological and chemical diversity, and represent an exciting source of novel biochemistry. This project will investigate the diversity of wild Australian microbial fungi and the range of natural products they can produce during fermentation, with potential applications in novel fermented foods and beverages. The project will identify Australian wild yeast from our established collection and perform LC-MS/MS metabolomic and proteomics to understand their metabolic diversity.

Expected outcomes and deliverables: You will gain experience in yeast culture, PCR, sequencing, LC-MS/MS proteomics and metabolomics.

Suitable for: Suitable for students with some background in microbiology, biochemistry, or analytical chemistry. No specific background or experience is needed.

Primary supervisor: Professor Ben Schulz

Before you apply: Contact the primary supervisor.