Winter Research Program - IMB

Primary Supervisor: Dr Fleur Garton | f.garton@uq.edu.au (please contact Dr Garton before submitting an application)

Duration: 4 weeks (20-36 hours per week); onsite

Background: Amyotrophic Lateral Sclerosis is a fatal neurodegenerative condition with a complex genetic architecture. Whole genome and exome sequencing supports the identification of both common and rare variants contributing to disease. Rare variants in known ALS genes have often not been seen before and are labelled as variants of uncertain significance. As more samples are analysed this number becomes larger and prioritising the variants to follow-up is necessary. In-silico prediction tools exist for this purpose. They use empirical data to predict their likelihood to be deleterious but their sensitivity for ALS has not yet been explored. 

Aim: This project will test the sensitivity known pathogenic ALS and benign ALS variants across a range of in-silico tools. We hypothesise that certain tools have better sensitivity at detecting pathogenicity and these are the tools that the community should be used to prioritise variants of unknown significance.  

Approach: This is a computational project requiring variant annotation and analysis. You will be involved in comparing each of these tools using a range of software tools and packages with analyses performed in R. You will use a variety of statistical methods to make conclusions. This may reveal future opportunities for variant interpretation design and/or sensitivity testing for other conditions.  

Expected outcomes: As part of the Centre for Population Genetics and Disease Genomics at IMB, students will be exposed to a variety of research projects and discussions. This project is geared to gaining skills in genetic variant analysis and interpretation. This has not been done before and so there is opportunity to contribute to a publication from this work. Students may also be asked to produce a report and present at the end of their project. 

Suitability: This project is only open to applications from students trained in statistical genetics, bioinformatics and/or related fields.  

Primary Supervisor: Dr Jeffrey Mak | j.mak@uq.edu.au

Duration: 4 weeks (36 hours per week); onsite

Background: Histone deacetylases (HDACs) are enzymes that hydrolyse acetyl groups from the lysine sidechains from histones. They are the targets of a number of known anti-cancer drugs, while some sub-classes of HDACs are emerging as promising drug targets for treating inflammatory diseases. 

Gap: Most HDAC drugs have many deleterious side effects as they are not very selective for their protein targets. There is a need to discover new compound that can confer greater selectivity. 

Approach: The research student will convert known HDAC drug SAHA into new inhibitors that exploit the enzyme’s catalytic mechanism. To our knowledge, this has not been studied before. 

Aim: Synthesise a series of SAHA derivatives to demonstrate a conceptually new way to inhibit HDACs 

Expected outcomes: 

The student will: 

1. experience conducting research in a dynamic and multidisciplinary research laboratory 

2. gain valuable skills in conducting organic synthesis, including advanced reaction techniques and compound characterisation 

3. gain exposure in the design of biologically-active molecules and appropriate synthetic routes 

4. contribute to publications, depending on project outcomes 

The students will be expected to: 

1. contribute to the synthesis of new analogues 

2. give a short oral presentation, depending on project results

Suitability: This project is for enthusiastic organic chemistry students who have completed 2nd year, and aim to study (or have already studied) CHEM3001. 

Primary Supervisor: Dr Hana Starobova | h.starobova@uq.edu.au

Duration: 4 weeks (36 hours per week); onsite

Macrophages are immune cells that are involved in innate immune response and are implicated in many disease pathologies, including neuropathies and pain. Macrophages can be activated via the NLRP3 inflammasome (a danger sensing protein) to release nerve sensitising and pro-inflammatory cytokines such as Interleukin-one beta. The activation of the NLRP3 requires the polymerisation of the ASC protein.  

Aim: To develop high-throughput ASC-Citrine Macrophages Assay 

In this project we will develop a high-throughput NLRP3 activation assay using confocal microscopy. Specifically, we will isolate bone marrow derived macrophages from mice, activate these cells and observe under microscope the polymerisation of the ASC protein. The polymerisation of ASC will be then quantified using a specific software. Supernatants of those cells will be collected and the concentration of released Interleukin-one beta will be analysed using ELISA. 

This assay will be used for future experiments to investigate the kinetics and dose dependency of different NLRP3 activators or inhibitors.   

Expected outcomes: Student will gain skills in primary tissue culture, microscopy, image analysis and cytokine analysis using ELISA.  Additionally, student will learn how to analyse data in GraphPad Prism software. Student will keep laboratory book. At the completion of the project student will produce a short report and give an oral presentation at the weekly Vetter Group meeting.

Suitability: This project is open to applications from students with a background in biology and molecular biology, 4th year students only. Tissue (bone) collection from mice is part of the project. 

Primary Supervisor: A/Prof Nathan Palpant | n.palpant@uq.edu.au

Duration: 4 weeks (up to 36 hours per week); onsite or remote options

The ability to study complex data is important in current project design due to routine high dimensional data generated by sequencing and imaging methods. This project will make use of new computational methods we have developed (see Mizikovsky et al, Nucleic Acids Research, 2022). The goal is to understand and compare data outputs of this and related methods as computational frameworks for determining relationships of objects based on large-scale phenotypic data.

Expected outcomes: The applicants will gain experience working with emerging computational pipelines involving dimensionality reduction and visualisation of complex data. The project will aim to evaluate a set of diverse and pre-selected data types using our established computational methods. We will then use these data to interpret performance accuracy against a reference ground truth. 

Suitability: The work requires applicants with strong computational bioinformatics skills suitable for 3rd-4th year students.

Primary Supervisor: Dr Lilian Schimmel and Dr Emma Gordon  | l.schimmel@imb.uq.edu.au

Duration: 4 weeks; onsite

The research within the Gordon lab is focused on the formation and maintenance of the blood vascular system. Vessels form complex branched networks that supply oxygen and nutrients to all body tissues. The signals controlling blood vessel growth, identity and migration are all downstream of a single, common complex at the cell surface, yet exactly how these signals mediate a diverse range of functions, depending on the physiological need, remains unknown. 
 
The specific focus of this project is to determine the role of endothelial cell caveolae in blood vessel growth. The specific membrane structures that caveolae form are abundantly present in vascular endothelial cells, but their function during vessel growth remains unknown. The project involves the molecular cloning of fluorescently tagged Caveolin-1 mutants to test their effect on blood vessel growth in cultured cells.

Expected outcomes: The student will have the opportunity to gain experience in a wet-lab research group and be involved in imaging of vascular cells using fluorescent microscopy. They will also gain experience in cloning, data collection and analysis to understand how genetic mutations of Caveolin affect cell behaviour. The project will provide experience with molecular cloning in a wet-lab setting, including fluorescently tagging proteins, generating mutants and growing cells to study blood vessel growth.

Suitability: This project is open to applications from students with a strong interest in cell biology, molecular cloning, and (vascular) developmental biology, year 3 undergraduate and postgraduate students. 

Primary Supervisor: Dr James Curson (laboratory of Prof Matt Sweet) | b.curson@uq.edu.au

Duration: 4 weeks (25 hours per week); onsite

Our body innate immune system is constantly surveying for indications of infection or harm. Once the cells of our immune system encounter a threat, such as an invading microorganism, it must convert the recognition of this threat into an inflammatory signal and work to destroy the engulfed pathogen. Both processes rely on the accumulation and mobilisation of an organelle called the lipid droplet. This project seeks to understand what molecular signals are necessary for the production and usage of lipid droplets in innate immune cells such as macrophages.

Expected outcomes: The student will learn in detail about the molecular mechanisms that drive immune cell activation. Practically they will learn wet laboratory skills including hands on experience in tissue culture and biochemical techniques relevant to the field of immunology.  

Suitability: This project is suitable for a student with a background in biology preferably in their 2nd or 3rd year of study with a particular interest in innate immunity. 

Primary Supervisor: Dr Daniel Hwang | d.hwang@uq.edu.au (please contact Dr Hwang before submitting an application)

Duration: 4 weeks (36 hours per week); onsite

Since the deployment of COVID-19 vaccines in autumn 2020, 13.31 billion COVID-19 vaccine doses having been administered worldwide as of 28 February 2023. Various case reports indicate that patients with loss of smell and taste perceived a change in their ability to smell and taste after vaccination. 

This project aims to investigate post-vaccination changes in the perception of smell and taste and other symptoms of long-COVID. The results will help assess the potential impact of COVID-19 vaccines and provide new clues to help us understand recovery from long-COVID. 
 
Participants of this project are asked about their experience following the vaccination through an online survey (https://iu.co1.qualtrics.com/jfe/form/SV_1G1RDda8fcCJHCe). The survey is available in 10 different languages and has received over 2,500 responses from participants all over the world.  

The scholar will assess this whole new dataset and conduct a preliminary analysis using data collected from Australia. 

This is a purely dry-lab computer-based project.

Expected outcomes: The scholar may gain skills in data preparation, data analysis and interpretating data, or have an opportunity to be an author of this international collaborative project when this work is published. The scholar may be asked to produce a report or oral presentation at the end of their project.

Suitability: The project is suitable for students with skills in excel and preferably R language. This project is suitable for students with a background in Biology, nutrition, statistics, psychology, or genetics. 

Primary Supervisor: Dr Zeinab Khalil | z.khalil@uq.edu.au

Duration: 4 weeks (20-36 hours per week); onsite

Background: Microbes have been a new promising source of modern medicines, including antibiotics (e.g. penicillin) and immunosuppressants (e.g. sirolimus) as well as agents to treat cancer (e.g. adriamycin) and cardiovascular (e.g. statins) disease, as well as many more. Recent advances in genomics offer exciting new approaches to discovering the next generation of medicines hidden within the Australian microbiome. 

To this end, in 2020, we launched Soils for Science (S4S) as an Australia broad citizen science initiative designed to engage the public to collect 10's of thousands of soil samples from backyards across the nation, from which we will isolate 100's thousands of unique Australian microbes.  

Hypothesis: Knowledge of microbial metabolites would lead to molecular tools that could be used to access new metabolites with therapeutic potential. 

Aims: This project will include the following; 

(1) analysing the soil microbiome by growing microbes in different media. (2) culturing/photographing communities of microbes.  

(3) isolating/cryopreserving pure microbes.  

(4) uploading images to the S4S Image gallery.  

(5) extracting the pure microbial isolates for chemical analysis to prioritise those genetically and chemically unique. 

Expected outcomes: The successful candidate will join a multi-disciplinary team where, supported by microbiological and genomic sciences, they will gain skills and experience in microbiology, analytical and medicinal chemistry – to inform and inspire the discovery of future medicines. The successful candidate will be asked to produce a report and/or oral presentation at the end of the project to highlight the outcomes.

Suitability: This project is open to applications from students with a background in organic chemistry and/or microbiology or 3rd – 4th year students only, and with an interest in learning multidisciplinary biosciences.

Primary Supervisor: Dr Evans Cheruiyot; Prof Allan McRae | a.mcrae@imb.uq.edu.au

Duration: 4 weeks (36 hours per week); hybrid (onsite or remotely via Zoom/Teams)

The commonly used threshold for genome-wide association studies (GWAS) in humans is 5 x 10-8. This was developed based on samples sizes and marker densities available in the early days of GWAS. We now work with much larger samples sizes and use denser SNP marker panels covering a wider minor allele frequency range. This project will use 
simulation to assess appropriate statistical thresholds for analysis in the UK Biobank, a large-scale biomedical resource containing genetic and health information from half a million people.

Expected outcomes: The student will gain significant hand-on knowledge in: 
     1. Genome-wide association studies 
     2. Handling large complex datasets 
     3. Using high-throughput computing and Linux

Suitability: The project is particularly suitable for honours/master students who are interested in pursuing career research in the biological sciences (e.g., bioinformatics and genetics) 

Primary Supervisor: Dr Harriet Lo; Mr James Rae (Parton Lab) | h.lo@uq.edu.au

Duration: 4 weeks (20 hours per week); onsite

Tardigrades are one of the toughest creatures on earth. In this project we will study the cellular adaptations that allow tardigrades to survive in extreme conditions.  

Expected outcomes: The student will learn how to study tardigrades using state-of-the-art microscopy techniques. Practically they will learn wet laboratory skills including hands on experience in tardigrade culture and techniques for imaging. 

Suitability: This project is suited to applications with a background in cell and molecular biology (3rd or 4th year) who are interested in undertaking postgraduate studies in their future education (Honours, Masters, PhD).

Primary Supervisor: Dr Samantha Stehbens | s.stehbens@uq.edu.au

Duration: 4 weeks (20-36 hours per week); onsite

Melanoma is a cancer that arises in the pigment producing cells of the skin called melanocytes. Whilst curable if treated early -it is often fatal, due to rapid spread throughout the body, especially to the brain. Melanoma brain metastases occur in up to 75% of patients with advanced disease and are associated with very poor prognosis with near 100% mortality. We currently lack a deep molecular understanding of melanoma brain metastases. This project aims to characterise an oncogenic pathway that is altered in melanoma in the brain to understand how cells survive and seed in the brain environment. 

Expected outcomes: The scholar will work with a post-doctoral scientist to gain skills in cell culture, immunoblotting, immunofluorescence, cancer culture models, microscopy, image analysis and figure assembly for publications. Students will be expected to produce a short summary document the end of their project.

Suitability: This project is suited to applications with a background in 2nd or 3rd year cell biology who are interested in undertaking post graduate studies in their future education.  (Honours, Masters, PhD). 

Primary Supervisor: Prof David Evans | d.evans1@uq.edu.au

Duration: 4 weeks (36 hours per week); onsite

The gold standard for demonstrating causal relationships in the epidemiological sciences is the randomized controlled trial. However, these sorts of studies are not always possible due to practical and/or ethical considerations. Nevertheless, in some cases data from genetically related individuals can be used to inform causality in non-experimental (observational) data. The aim of this project is to implement a statistical model we have devised that is capable of distinguishing causal relationships from correlational ones using data from genetically related individuals in non-experimental situations. The successful applicant will use a technique called “structural equation modelling” to construct the model and then test its performance using a mixture of simulated and real genome-wide data from twins/sibling pairs. 

Expected outcomes: Scholars will learn structural equation modelling, data simulation and statistical power analysis. The deliverable will be an R script that implements the model and tests its utility in simulated data. 

Suitability: This project is open to 2nd and 3rd year students who have a statistics major, experience with the R statistics package and/or previous experience in structural equation modelling. The candidate will need to demonstrate outstanding grades in statistics related courses. 

Primary Supervisor: Dr Tom Hall; Dr Harriet Lo (Parton Lab) | thomas.hall@imb.uq.edu.au

Duration: 4 weeks (25 hours per week); onsite

Lipid droplets (LDs) are storage organelles involved in lipid and energy homeostasis. We are interested in using the fast-developing zebrafish embryo as a model to investigate in vivo imaging of adipose tissue in normal biology and in the context of human disease. 

Expected outcomes: Students will have the opportunity to be involved in the live imaging of fluorescent zebrafish, use of state-of-the-art genetic technology, generation/characterisation of transgenic zebrafish lines, as well as gain skills in data collection and analysis. 

Suitability: This project is suited to applications with a background in cell and molecular biology (3rd or 4th year) who are interested in undertaking postgraduate studies in their future education (Honours, Masters, PhD).