Undergraduate Programs

IMB offers a range of opportunities for undergraduate students, whether you are enrolled at UQ or elsewhere, advance your studies and contribute to the world-leading discoveries of the institute.

Undergraduates may be eligible for the Director's Award for Research Training (DART).

IMB supports the UQ Winter Research Program, allowing exceptional students the opportunity to gain valuable research experience working alongside some of the university’s leading academics and researchers. Participation will extend your knowledge of an area of interest and develop your analytical, critical thinking and communication skills.

IMB Undergraduate Research Projects are available in select IMB Research Groups for a duration between 4-5 weeks over the winter vacation period, commencing 21 June 2021.

For eligibility criteria, additional information and to submit your application, please see the UQ Student Employability Centre website.

IMB values diversity and encourages applications from individuals who identify as being Aboriginal or Torres Strait Islander.

For a summary of the type of research undertaken by each IMB group, please visit the IMB Research Groups website.

Available Projects for Winter 2021

Project title: 

Regulation of liver physiology by circadian and feeding rhythms

Project duration, hours of engagement & delivery mode

4 – 5 weeks and applicant will be required on-site for the project

30-36hrs per week

Description:

This project aims at characterizing the molecular mechanism involved in the circadian regulation of protein secretion by the liver by circadian and feeding rhythms. The student will participate to omics data analysis to develop hypothesis and use classical biochemistry techniques on samples from mouse tissue or cultured cells to confirm the signalling pathways involved in this regulation.

Expected outcomes and deliverables:

The student will gain knowledge in data analysis and physiology and develop skills and technical expertise in biochemistry and molecular biology.

Suitable for:

Considering the multidisciplinary background of the project (physiology, molecular biology, biochemistry and data analysis), any science student (after 3rd year) could be interested by the project.

 

Primary Supervisor:

 

A/Prof Frederic Gachon

 

Further info:

https://imb.uq.edu.au/physiology-of-circadian-rhythms

f.gachon@uq.edu.au

Tel: 0428 579 696

 

 

Project title: 

Characterising gene regulatory networks that underpin cell identity and age-stage

Project duration & delivery

5 weeks and applicant will be required on-site for the project, but some aspects can also be performed off-site. Dry lab/computational biology project

Description:

The group’s research is centred around the study of cell fate transitions that occur rapidly as a consequence of forced cellular reprogramming (i.e. transdifferentiation), as well as the subtler and slower, albeit functionally meaningful, changes that occur as part of cellular ageing. To uncover transcription factors (TFs) that drive these processes, we have created a molecular atlas (RNAseq, ATACseq) comprised of dozens of mammalian cell types from both young and aged subjects.  

We are currently looking for “dry-lab” students interested in purely computational projects to dissect the TF network and how it is changing in the context of ageing, differentiation and transdifferentation (using techniques like TF motive prediction & network analysis). In collaboration with wet lab scientists, hypotheses derived from the candidate’s analyses will be tested using in vitro cell models (e.g. can we “reprogramme” aged cells to work more efficiently by targeting age-altered transcriptional circuits).

Expected outcomes and deliverables:

The student will gain experience in working with state-of-the-art computational pipelines and advanced methods in the field of computational biology. Students will be asked to communicate their findings to the lab (e.g. short report or oral presentation) at the end of their project, and will be given detailed feedback, to help develop their science communication skills. The work will be embedded within ongoing research studies and, if performed well, incorporated into publications (authorship on these studies can be expected).

Suitable for:

This project is suitable for 3rd – 4th year students. The ideal candidate has some demonstrated background in computational bioinformatics and as such is comfortable writing code in languages such as R, Matlab, Perl, or Python. 

Primary Supervisor:

 

Dr Christian Nefzger

Dr Marina Naval-Sanchez

Dr Amin Esmail

Further info:

For all enquires please email c.nefzger@imb.uq.edu.au

 

Project title: 

How diabetes mellitus disrupts the foundation of the nervous system

Project duration, hours of engagement & delivery mode

4 -5 weeks and the applicant will be required to be onsite (minimum 20hrs/week).

Description:

Diabetes mellitus is associated with a higher incidence of congenital abnormalities such as neural tube defects, but the underlying mechanisms are unknown. The neural tube is formed by remodelling of the actin cytoskeleton and gives rise to the brain and the spinal cord.

This project will use a chick embryo model of diabetes mellitus to understand how hyperglycemia affects the actin cytoskeleton and disrupts neural tube formation.

Expected outcomes and deliverables:

The applicant will learn embryology, immunostaining and microscopy techniques.

Suitable for:

This project is open to applications from students with interests in cell and developmental biology, physiology or molecular biology.

Primary Supervisor:

 

Dr Melanie White

Further info:

For further information, students may contact Dr Melanie White: melanie.white@imb.uq.edu.au

 

Project title: 

Understanding microtubules in cell migration

Project duration, hours of engagement & delivery mode

4-5 weeks and the applicant will be required on-site for the project.

COVID-19 considerations: The project will be mostly wet-lab (80%), accompanied by analysis of microscopy data (20%). The analysis could be completed under a remote working arrangement.

Description:

Cancer cells spread aggressively through tissues by adapting their cell shape to fit the environment in addition to altering their environment so they can squeeze through tight tissue spaces. Cancer cells sense and become more invasive following changes in the biophysical properties of their microenvironment including increases in stromal stiffness and interstitial fluid pressures. These changes make cancer cells more compliant and adaptive to fluctuations in their surrounding environment allowing them to alter their shape to squeeze through tight spaces more effectively.

Cells have integrative sensory mechanisms where key proteins undergo conformational changes or activation in response to force to induce biochemical signalling. This allows forces felt at the cell membrane to be transmitted and interpreted as a biochemical signal- similar to a ligand binding to a surface receptor. Several properties of the microtubule cytoskeleton make it an ideal structure integrate and translate these forces.

This project extends our work investigating the role of the microtubule binding protein, CLASP, in regulating microtubule functions in cell migration. CLASPs bind to microtubules, acting to stabilise them and promote their growth – key functions in migration. This project will investigate how CLASPs regulate cytoskeletal crosstalk in migration and invasion.

Expected outcomes and deliverables:

The scholars will gain skills in cell culture, shRNA, immunoblotting, immunofluorescence, cancer culture models, microscopy, image analysis and figure assembly for publications. Students will be expected to produce a summary document the end of their project.

Suitable for:

This project is suited to applications with a background in cell biology who are interested in undertaking post graduate studies in their future education.  (Honours, Masters, PhD).

Primary Supervisor:

 

Dr Samantha Stehbens

Further info:

Please feel free to contact Dr Stehbens with any questions regarding the project. S.stehbens@uq.edu.au

Project title: 

Ex vivo study of new antimicrobials

Project duration, hours of engagement & delivery mode

For the Winter program, duration of this project is anticipated for 5 weeks and hours of engagement about 36hrs per week.

COVID-19 considerations:

The project is design for the on-site work, but can be completed under a remote working arrangement for the review writing instead.

Description:

There is an urgent demand for antimicrobial agents effective against multi-drug resistant bacteria (MDR). Careless use of antibiotics has led to untreatable infections, and this rise and spread of resistant bacteria is a serious threat for health systems across the globe. With the ongoing increase in drug resistance, the topical skin treatment of bacterial diseases necessitating the development of alternative approaches.

As one possible solution, we propose testing nature derived potential antimicrobials as alternative to antibiotics.

In this study, several nature-derived compounds will be tested and analytical techniques such as isothermal titration calorimetry and mass spectroscopy will be used to examine their structures and interactions. They will be also tested for their antimicrobial activity by micro-broth dilution.

Expected outcomes and deliverables:

This project will suit students who are interested in chemistry and analytical chemistry and will enable the students to get hands on experience with analytical chemistry equipment and techniques, such ITC, LCMS and MS.

With the pre-existing data there is a high possibility that the manuscript for the publication will be written in the end of the project and after edition will be submitted for publication.

Suitable for:

This project is open to applications from students with a background in (bio)-chemistry and analytical chemistry with skills in processing generated data, 3-4-year students.

Primary Supervisor:

 

Dr Zyta Ziora

Further info:

z.ziora@uq.edu.au

m.blaskovich@uq.edu.au

IMB supports the UQ Summer Research Program, allowing exceptional students the opportunity to gain valuable research experience working alongside some of the university’s leading academics and researchers. Participation will extend your knowledge of an area of interest and develop your analytical, critical thinking and communication skills.

IMB Undergraduate Research Projects are available in select IMB Research Groups for a duration between 6-10 weeks over the summer vacation period, commencing from 30 November 2020.

For eligibility criteria, additional information and to submit your application, please see the UQ Student Employability Centre website.

For a summary of the type of research undertaken by each IMB group, please visit the IMB Research Groups website.

Available Projects for Summer 2020/2021

Project title: 

Advanced Microbial Biodiscovery

 

Project duration & delivery

6-8 weeks full time and will be required on-site for the project

 

Description:

Background: Natural selection relentlessly drives adaptations in microbial secondary metabolism, with successive generations acquiring ever more diverse natural products, capable of enhancing survival in complex communities and ecosystems. As a result, the global microbiome has evolved to encompass a vast arsenal of ecologically and biologically potent natural chemicals. For over 70 years readily accessible microbial natural products have fuelled a revolution in science, inspiring new pharmaceuticals and agrochemicals, improving the quality of life for millions, and driving global commerce. This success is perhaps most clearly exemplified in modern antibiotics, which are overwhelmingly inspired by microbial natural products. Notwithstanding past successes, the threat of multi-drug resistance presents an urgent need to innovate, to deepen and broaden the search, to discover new antibiotics.

 

Hypothesis: Microbes isolated from Qld soils produce valuable new chemistry that exhibit promising antibiotic properties.

 

Aim: To cultivate bacteria and fungi from a library of Qld soil samples, and assess their capacity to produce new antibiotics.

 

The project will be part of a new IMB Citizen Science initiative, Soils for Science.  https://imb.uq.edu.au/soils-science-antibiotics-australia

 

Expected outcomes and deliverables:

Successful candidates will gain skills spanning microbiology and chemistry, while working in a dedicated research laboratory. More specifically they will gain experience in;

  • cultivation of microbes from soils
  • isolation and cryopreservation of pure microbial strains
  • microbial taxonomy (morphology and sequencing)
  • chemical and antibiotic profiling of microbial extracts

Candidates will also acquire skills in safe lab practice, and scientific data acquisition, analysis, archive and communication.

Suitable for:

This project is suitable for 3rd – 4th year students majoring in microbiology, and with knowledge of organic chemistry.

 

Primary Supervisor:

 

Prof. Robert J. Capon

Dr Zeinab Khalil

Further info:

For all enquires please email z.khalil@uq.edu.au

 

 

Project title: 

Molecular evolution of caveolae

 

Project duration & delivery

6 weeks - will be required on-site for some of the project but other aspects could be completed off-site

Description:

The research project involves assessing the evolutionary conservation of surface structures called caveolae and the major protein components of caveolae. This will involve genomic searching and molecular biology.

Expected outcomes and deliverables:

Scholars will gain skills in database searching and genome analysis as well as molecular biology, and may have an opportunity to be involved in electron microscopy. Students will be asked to produce a report or oral presentation at the end of their project.

Suitable for:

This project is open to applications from students with a background in biology or biochemistry and an interest in evolutionary analysis.

 

Primary Supervisor:

 

Professor Rob Parton/Dr. Tom Hall

 

Further info:

Please contact Rob Parton (R.Parton@imb.uq.edu.au) or Tom Hall (thomas.hall@imb.uq.edu.au) prior to submitting an application.

 

 

Project title: 

Regulation of liver physiology by circadian and feeding rhythms

 

Project duration:

10 weeks and will be required on-site for the project.

Description:

This project aims at characterizing the molecular mechanism involved in the circadian regulation of protein secretion by the liver by circadian and feeding rhythms. The student will participate to omics data analysis to develop hypothesis and use classical biochemistry techniques on samples from mouse tissue or cultured cells to confirm the signalling pathways involved in this regulation.

Expected outcomes and deliverables:

The student will gain knowledge in data analysis and physiology and develop skills and technical expertise in biochemistry and molecular biology.

Suitable for:

Considering the multidisciplinary background of the project (physiology, molecular biology, biochemistry and data analysis), any science student (after 2nd year) could be interested by the project.

 

Primary Supervisor:

 

A/Prof Frederic Gachon

 

Further info:

https://imb.uq.edu.au/physiology-of-circadian-rhythms

Frederic.gachon@uq.edu.au

Tel: 0428579696

 

 

Project title: 

Synthesis of novel Octapeptin antibiotics

 

Project duration & delivery

8-10 weeks and will be required on-site for the project

Description:

Antibiotics are the “wonder drugs” of the 20th century. We use antibiotics to treat bacterial infections and to kill bacteria without harming the patient. It has been estimated that antibiotics have extended human life expectancy by ten to twenty years. Unfortunately, antibiotics are losing their activity against bacterial infections. Bacteria are rapidly becoming resistant to all current antibiotics, and can quickly share the genes that make them resistant. Currently, the polymyxin class of lipopeptide antibiotics is used as a last-line therapy in critically ill patients with multidrug-resistant (MDR) infections. Unfortunately, resistance to polymyxins is now becoming widespread throughout the world.

We have been working on a new class of antibiotics, called the octapeptins, which have potential to target polymyxin-resistant superbugs. Octapeptins were first discovered over 40 years ago but received little attention until our recent publications. This project is focused on the design and synthesis of new Octapeptin analogues, with the goal of improving microbiological, pharmacological, and toxicological properties. Variations of a key component of the structure will be synthesised and attached to the rest of the molecule.

Expected outcomes and deliverables:

This project will provide training in organic chemistry, peptide chemistry, analytical technics (purification, LCMS analysis, HPLC analysis and 1H, 13C-NMR analysis) and toxicity studies.  Good results could lead to a publication in an international journal.

 

Suitable for:

This project is open to applications from students with a background in synthetic chemistry.

 

Primary Supervisor:

Dr. Mark Blaskovich, Director, IMB Centre for Superbug Solutions

Mr Raghu Bolisetti

 

Further info:

m.blaskovich@uq.edu.au

  07 3346 2994

 

Project title: 

Fluorescence based Gram typing of bacteria

 

Project duration & delivery

10 weeks, wet laboratory based

Description:

In our laboratory, we have developed technologies to capture bacteria from different clinical samples using magnetic nanoparticles functionalised with bacteria-specific capture agents. The bacteria are then phenotypically and genotypically classified by new generation technologies like MALDI-TOF mass spectrometry or long read sequencing. These approaches still require time for analysis: rapid methods that can quickly identify the type of bacteria would improve the ability to treat patients with the correct antibiotic. Gram typing is a conventional technique that distinguishes the two major types of bacteria.

In this project, we will extend our capacity to selectively capture bacteria by combining the technique with bacteria-selective fluorescent probes developed in our laboratory, with the goal of rapidly identifying the Gram type of the bacteria.

 

Expected outcomes and deliverables:

Scholars will gain laboratory skills in bacterial growth and culture, fluorescent assay development & flow cytometry. They will have an opportunity to gain skills in flow cytometry data analysis and interpretation.

 

Suitable for:

This project is open to applications from students with interest in microbiology and biotechnology.

Primary Supervisor:

 

Dr. Mark Blaskovich, Director, IMB Centre for Superbug Solutions

Dr. Sanjaya KC

Further info:

m.blaskovich@uq.edu.au

  07 3346 2994

sanjaya.kc@imb.uq.edu.au

 

Project title: 

In vivo bioluminescent models of bacterial infection

 

Project duration & delivery

10 weeks, wet laboratory based

Description:

New antibiotics are desperately needed to fight the rise of antimicrobial resistance. A key step in evaluating the potential of new antibacterial agents is testing their efficacy in mouse models of infection. Traditional models are time consuming and use many mice: by using bioluminescent bacteria and an optical imaging system infections can be monitored much more easily. In this project, we will work on establishing and validating different models of infection using a new AMI HTX Optical Imaging System. The goal is to combine imaging of the bacteria with imaging of fluorescently labelled antibiotics, to track the co-localisation of antibiotic and bacteria.

Expected outcomes and deliverables:

Scholars will gain laboratory skills in bacterial growth and culture, mouse handling, and fluorescent/bioluminescent in vivo imaging. They will have an opportunity to gain skills in image analysis and interpretation.

Suitable for:

This project is open to applications from students with interest in microbiology, biotechnology and pharmacology.

Primary Supervisor:

Dr. Mark Blaskovich, Director, IMB Centre for Superbug Solutions

Further info:

m.blaskovich@uq.edu.au

  07 3346 2994

 

Project title: 

Disrupting cellular forces underlying morphogenesis

 

Project duration & delivery

10 weeks and the applicant will be required to be onsite.

Description:

The actomyosin cytoskeleton plays critical roles in both sensing and generating contractile forces within cells to cause changes in cellular properties such as size, shape, position and gene expression. These cellular forces are transmitted to neighbouring cells and integrated across tissues to cause global changes in embryo morphology.

Cellular forces are also transmitted across cell membranes to remodel the extracellular matrix (ECM), which in turn feeds back to regulate cell–ECM and cell–cell adhesions. Disruption in the balance of cell-cell and cell-ECM forces causes embryonic defects and is associated with diseases such as cancer, fibrosis, atherosclerosis and asthma.

 

This project will knockdown regulators of the actomyosin cytoskeleton and/or ECM components and investigate the effects on actin dynamics and cell morphology using live fluorescence microscopy. The applicant will generate constructs for RNA interference and test their efficacy in cultured cell lines. They will then use their constructs to disrupt cellular forces in human induced pluripotent stem cells and developing avian embryos and characterise the cytoskeletal and morphological changes.

 

Expected outcomes and deliverables:

The applicant will learn cloning, cell culture, immunofluorescence and microscopy.

Suitable for:

This project is open to applications from students with a background in cell and developmental biology or molecular biology.

Primary Supervisor:

 

Dr Melanie White

 

Further info:

For further information, students may contact Dr Melanie White: melanie.white@imb.uq.edu.au

 

 

Project title: 

Inflammasome signalling in infection and/or disease

 

Project duration & delivery

6-10 weeks and will be required on-site for the project (2 opportunities available)

Description:

During injury or infection, our body’s immune system protects us by launching inflammation. But uncontrolled inflammation drives diseases such as gout, diabetes, neurodegenerative disease and cancer. The Inflammasome Lab is defining the molecular and cellular processes of inflammation. We seek to unravel the secrets of inflammasomes – protein complexes at the heart of inflammation and disease – to allow for new therapies to fight human diseases.

 

We will offer 2 projects investigating aspects of inflammasome signalling in infection and disease. Projects will be tailored to the specific interests of the student, and may involve techniques such as molecular cloning, cell culture, microscopy, infection, ELISA, western blot, cell death assays and/or assessment of mouse disease phenotypes.

 

Expected outcomes and deliverables:

Scholars will gain methodological skills in molecular and cellular biology. Scholars will have the opportunity to contribute to a larger project and generate publications from their research.  Students will be asked to communicate their findings to the lab (e.g. short report or oral presentation) at the end of their project, and will be given detailed feedback, to help develop their science communication skills. In all, the project will allow scholars to get experience in a research lab setting, and the opportunity to contribute to our understanding of inflammation biology.

Suitable for:

This project is open to applications from students with a background in immunology, microbiology  and/or cell biology.

Primary Supervisor:

 

Prof Kate Schroder

 

Further info:

K.Schroder@imb.uq.edu.au

 

 

Project title: 

Using Transposon Directed Insertion Sequencing (TraDIS) to elucidate conditionally essential genes in Gram negative bacteria

 

Project duration & delivery

The project required 10 weeks of on-site attendance (2 opportunities available)

Description:

Transposon directed insertion site sequencing (TraDIS) is a powerful tool for investigating bacterial genes that are required for growth/survival in many conditions. The method of TraDIS involves creating 200,000 transposon mutants that are pooled into one library, and this library can be used to assess the requirement of each gene at once under certain conditions, using a high throughput transposon junction sequencing approach. If a gene is important for growth/survival in the test conditions, the corresponding transposon mutants will not grow, and therefore when the genomes are sequenced, that gene is determined to be” conditionally essential”. We aim to identify genes that are essential for the survival of bacteria under stress conditions such as antibiotics and specialised growth media.

 

Expected outcomes and deliverables:

The participating students get experience in designing experiments, in addition to collecting and analysing data. They will learn techniques related to microbiology and DNA sequencing. The outcomes of the experiments in this project could result in research publications.

 

Suitable for:

This project would require student in their 3rd and 4th years with a background in molecular biology, microbiology, and biochemistry.

 

Primary Supervisor:

 

Professor Ian Henderson

Further info:

For further information interested students can contact Dr. Karthik Pullela by sending an email to k.pullela@uq.edu.au. Students can submit the application without contacting the supervisor beforehand.

 

Project title: 

Engineering plants for the production of therapeutic peptides

 

Project duration & delivery

10 weeks and the project can only be performed on site

Description:

Plants naturally produce a wide range of peptides that function in cell signalling and plant defence. The overall aim of this project is to investigate if plants can be engineered to express designer therapeutic peptides of high value. In this project the scholar will learn techniques to transform a model plant species for the expression of a lead therapeutic peptide candidate Vc1.1, which is a potent inhibitor of neuropathic pain.

 

Expected outcomes and deliverables:

The scholar will learn techniques in plant transformation and analysis of transgenic plants. This will include assembly of expression vectors and Agrobacterium-mediated plant transformation. Resulting transgenic plants  will be characterised for transgene expression levels using real time PCR and peptide production using MALDI-MS methods. The scholar will be asked to generate a short report at the conclusion of the project.

 

Suitable for:

This project will suit a scholar with an interest in plant biotechnology and drug design.

 

Primary Supervisor:

 

Professor David Craik, Dr Mark Jackson and Dr Edward Gilding

 

Further info:

Please email m.jackson1@uq.edu.au

 

 

Project title: 

Analysing how the cells differentiate at single cell resolution

 

Project duration & delivery

This project can be carried out for the maximum time of the summer project and involves computational work that can be completed remotely should there be any restrictions due to COVID-19

Description:

My laboratory has developed data on thousands of stem cells undergoing differentiation into diverse cell types of the body including heart, kidney, gut and more. This project will involve work with the team of bioinformaticians in the laboratory to deconstruct the genetic basis of heart development. The goal is to understand how different cell types are made by studying the genes controlling their differentiation.

 

 

Expected outcomes and deliverables:

These projects are likely to contribute to research quality data that will be incorporated into publications that are being prepared for submission. Provided the data quality are up to standard, authorship on these studies can be expected. The student will gain experience in working with the most current and advanced methods in computational bioinformatics to study large scale genomic data at single cell resolution.

Suitable for:

Students should have for computational bioinformatics course work completion and can bring advanced proficiency in coding, specifically in use of R and Python. Familiarity working with large scale genomic data would be beneficial.

Primary Supervisor:

 

Nathan Palpant

 

Further info:

I have one position available for this project, so please contact me for scheduling an interview (n.palpant@uq.edu.au)

 

 

Project title: 

Uncovering the role of acid sensing ion channels in cardiac ischemia

 

Project duration & delivery

10 weeks and will be required on-site for the duration of the project

 

 

Description:

Ischemic injuries of the heart account for the majority of the cardiovascular disease burden in Australia and worldwide. Despite decades of research, there are no drugs which can prevent ischemic injury. We have identified an important ion channel, the acid sensing ion channel 1a (ASIC1a), to be a key modulator of the cell death pathway during injury. Inhibition of ASIC1a with a novel spider venom peptide, Hi1a, provides potent therapeutic protection in multiple models of cardiac ischemia, but the molecular mechanisms that underlie ASIC1a-induced cell death are unknown. The summer research project will involve assessing how acid sensing ion channels modulate the cellular responses to ischemic injury, by looking for molecular interactors of the channel and identifying signal pathway activation. The project will utilize advanced differentiation techniques to generate human cardiomyocytes from stem cells, followed by in vitro disease modelling and downstream molecular analyses of samples.

 

Expected outcomes and deliverables:

Student will learn how to use human pluripotent stem cells to model human disease and may learn laboratory techniques such as cell culture, quantitative real time PCR, immunohistochemistry, western blots, etc. This project is a part of a larger program within the lab working towards identifying novel targets for the treatment of heart disease The student will be asked to write a report and prepare an oral presentation at the end of the project. Depending on the outcomes of the study, there may be an opportunity to publish key results and findings.

 

Suitable for:

3rd or 4th year students with an academic background in biology are encouraged to apply.

Primary Supervisor:

 

Nathan Palpant

 

Further info:

n.palpant@imb.uq.edu.au  

 

 

Project title: 

Understanding how microtubule +TIPs drive tumour cell migration and invasion

 

Project duration & delivery

For 6-10 weeks the applicant will be required on-site for the project.

COVID-19 considerations: The project will be mostly wet-lab (80%), accompanied by analysis of microscopy data (20%). The analysis could be completed under a remote working arrangement.

 

 

Description:

Despite our significant progress, metastatic melanoma remains a highly aggressive, incurable disease and current therapies, although effective, result in resistance and recurrence. The hurdle in understanding and treating melanoma is due to its highly heterogeneous and adaptive nature, complicated by the biomechanical influence of the microenvironment and the reciprocal adaptive responses mounted by melanoma cells. Melanoma successfully navigates a variety of microenvironments, spreading to distal organs which is fatal for patients. It presents a clinical opportunity for the development of ‘migrastatics’, therapies used in the adjuvant setting which act to inhibit tumour cell invasion machinery to prevent metastatic spread.  Even with our greater understanding of cancer genomes, it is striking how this genetic diversity converges on several basic cell behaviours that, at a fundamental level, require cells to alter they shape. Cell migration is one such process that is exploited by tumour cells during metastasis. Innovative imaging and cell biology approaches have recently uncovered novel biology in cells navigating confined 3Dimensional matrices vs 2D, underlining the significance of understanding melanoma invasion in mechanically relevant cell culture models. This project focuses on understanding the fundamental mechanisms governing the mechanoreciprocity between the microtubule cytoskeleton and the extracellular matrix during metastatic melanoma invasion.

 

“Mechanosensing” is the ability of cells to move through complex microenvironments by adapting their shape to fit the physical attributes of the extracellular matrix (ECM). Adaptive cellular plasticity in response to changes in matrix topography involves two principle mechanisms: (1) spatio-temporal remodelling of the cell-matrix adhesions and the cytoskeleton, and (2) the ability to move through confined spaces, either through proteolytic ECM degradation or squeezing through small pores. Inhibition of matrix remodelling or cell squeezing results in invasion inhibition.

 

We have identified that Cytoplasmic Linker Associated Proteins (CLASPs) are highly overexpressed in multiple metastatic melanoma cell lines. CLASPs belong to a family of microtubule interacting proteins known as +TIPs and act to regulate microtubule dynamics, targeting and tethering. We discovered that CLASPs tether microtubules at cell-matrix connections to establish a transport pathway for localised delivery of matrix metalloproteinases (MMPs), facilitating cell–matrix connection severing (Stehbens et al., Nature Cell Biology, 2014). Exocytic secretion of MMPs needs to be tightly controlled as they facilitate metastatic invasion by remodelling the extracellular matrix to breakdown tissue barriers. Translocation of the nucleus through interstitial spaces is one of the greatest obstacles for invasive cells. It requires nuclear deformation which is often attributed to actin. We know that confined modes of migration are dependent on microtubules, microtubules are mechanically coupled to the nuclear envelope and that microtubules can resist compression. A recent finding identified that microtubule flexibility is modified by acetylation, a post-translational modification that is lost with CLASP depletion; indicating that CLASP-dependent microtubule stability may play significant mechanical roles in nuclear translocation and resistance to mechanical compression during migration through crowded, confined microenvironments.

 

Aim 1. Generate 3D ‘mini tumours’ from control and CLASP-depleted melanoma cells. Embed the tumours into collagen matrix to create a 3D microenvironment. Analyse their invasion into the matrix using time-lapse microscopy.

 

Aim 2. Generate 3D organotypic culture models of control and CLASP-depleted melanoma cells. Analyse their invasion into the underlying fibroblast-organised matrix using static analysis of fixed time points.

 

Expected outcomes and deliverables:

These aims form part of a project being completed for publication. The scholar will work side-by-side with a highly experienced lab member who is proficient in these models. Tools are established, troubleshooting has been completed, and preliminary results already generated- ensuring high feasibility of the project. The scholars will gain skills in cell culture, shRNA, immunoblotting, immunofluorescence, 3D cancer culture models, microscopy, image analysis and figure assembly for publications. Students will be expected to produce a summary document and an oral presentation at the end of their project.

 

Suitable for:

This project is suited to applications with a background in cell biology who are interested in undertaking honours in 2021.

Primary Supervisor:

 

Dr Samantha Stehbens

 

Further info:

Please feel free to contact Dr Stehbens with any questions regarding the project.

 

 

Project title: 

Using gene expression data to identify potentially unknown effects of statin medication

 

Project duration & delivery

10 weeks - applicant can work remotely or on-site

Description:

Observational studies suggest that statin medication, which are used to lower cholesterol levels, may have some beneficial effects on depression ( https://pubmed.ncbi.nlm.nih.gov/31299405/). But there are studies with suggest the opposite (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276028/).

 

The project has two aims:

1.Use the Connectivity Map (CMap) database to explore if statin medication perturbs pathways that may be similar to those perturbed by antidepressants.

2.Mendelian randomisation analysis (https://www.bmj.com/content/362/bmj.k601) to determine the effect of statins on psychiatric disorders.

 

Expected outcomes and deliverables:

They will apply statistical genetic approaches to answer questions driven by translational potential. The project may lead to publication as a first author.

Suitable for:

Students who are familiar with using R programming and have a background in genetics/bioinformatics would be favoured.

 

The project is particularly suitable for students who have completed the Statistical Analysis of Genetic Data (STAT7306) at UQ (https://my.uq.edu.au/programs-courses/course.html?course_code=STAT7306)

 

 

Primary Supervisor:

 

Dr Sonia Shah

 

Further info:

Please email me for an informal chat if you are interested in this project s.shah1@uq.edu.au

 

 

Project title: 

Towards the synthesis of new immunomodulators from a bacterial natural product

 

Project duration & delivery

8-10 weeks, on-site at St Lucia campus for laboratory work.

Description:

Background: MAIT cells (mucosal associated invariant T cells) are a major population of T cells in humans, especially in liver, blood, and lungs, but have only recently gained attention. In 2014, we discovered that the bacterial natural product 5-OP-RU activates MAIT cells with exquisite potency. We have since synthesised 5-OP-RU, which has become an essential research tool for studying MAIT cells worldwide .

 

Gap: However, 5-OP-RU is too chemically unstable for future medicines (half-life 88 mins), including as potential treatments for COVID19.

 

Approach: Recent studies in our laboratory have identified components of 5-OP-RU that could be potentially modified to confer chemical stability without affecting biological function. Based on these, we have designed a new stable molecule that mimics 5-OP-RU. This molecule needs to be synthesised in order to determine its immunological properties and chemically stability.

 

Aim: This project aims to establish synthetic methodology for accessing a new stable analogue of 5-OP-RU.

 

Expected outcomes and deliverables:

The student will:

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

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

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

4.contribute to publications, depending on project outcomes

 

The student will be expected to:

1.contribute to the synthesis of the new 5-OP-RU analogue

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

3. 

Suitable for:

This project is suitable for 2nd or 3rd year students who are enthusiastic about organic chemistry and aim to study (or have already studied) CHEM3001.

Primary Supervisor:

 

Dr Jeffrey Mak

Institute for Molecular Bioscience

University of Queensland

Further info:

Dr Mak (j.mak@uq.edu.au) would be happy to provide further information

 

 

Project title: 

Investigation of cell permeability of coiled coil peptides

 

Project duration & delivery

8-10 weeks and applicant will be required to be on-site

 

Description:

Background: Proteins featuring a coiled coil-structure are involved in important biological functions such as regulation of gene expression. Recent studies reported that some supercoil proteins are able to cross cell membranes and translocate to the nucleus. Understanding the cell uptake mechanism of such large molecules may lead to the discovery of novel cell-penetrating motifs with useful applications in biochemistry and drug delivery.

 

Aim: This project aims to prepare a series of peptides featuring sequences from the supercoil proteins thought to be responsible for their cell permeation abilities. The identity and structure of the peptides will be assessed by mass spectroscopy and circular dichroism and their cell uptake will be compared to other cell-penetrating peptides using flow cytometry.

 

Expected outcomes and deliverables:

The student will experience working in a multidisciplinary research environment, in a research institute of international reputation.

 

The student will gain technical skills in synthetizing bioorganic molecules (peptides), including exposure to analytical and preparative HPLC techniques and compound characterization by mass spectroscopy. Biophysical properties of the synthetic peptides will be analysed by circular dichroism and fluorescence spectroscopy.

 

The outcome of this research project is expected to be presented by the student to our group by the end of the project. Depending on the findings, it may be suitable for publication.

 

Suitable for:

This project is suitable for 3rd-4th applicants with a background in chemistry or biochemistry.

Primary Supervisor:

 

Dr Aline Dantas

Further info:

Contact:

Dr Aline Dantas de Araujo
Institute for Molecular Bioscience
The University of Queensland
Brisbane, Australia
Email: a.dantasdearaujo@imb.uq.edu.au
Phone: (61) 7 33462988

 

Project title: 

Structures of Cyclic Peptides by NMR and Circular Dichroism Spectroscopy

 

Project duration & delivery

6 weeks and applicant will be required on-site

Description:

The research project involves hands-on laboratory work of sample preparations, operating and analysing data from CD and NMR experiments for a library of cyclic peptides. Using these data for elucidating their 3-dimensional solution structures and investigating the relationship between the structure and bio/physio-chemistry properties.

 

Expected outcomes and deliverables:

Scholars will: gain skills in working in a structural chemistry/biology laboratory, using computers to determine three-dimensional structure, data collection, drawing correlations between experimental data. They will have hands-on involvement in generating documents for scientific publication from their research.  Students will be asked to produce a short report and oral presentation at the end of their project.

 

Suitable for:

This project is open to applications from students with a background in chemistry or 3rd – 4th year students with enthusiasm in scientific research.

Primary Supervisor:

 

Dr Huy Hoang

Institute for Molecular Bioscience

University of Queensland

Further info:

h.hoang@imb.uq.edu.au

 

Project title: 

Inflammation in Atherosclerosis

 

Project duration & delivery

10-12 weeks, and applicant will be required on-site for the project.

If required (due to COVID restrictions), it is possible for 2-4 weeks of the project can be completed remotely (i.e. quantification and data analysis).

 

Description:

Atherosclerosis is a maladaptive inflammatory disease characterised by the accumulation of cholesterol and other inflammatory molecules within the vessel wall, that ultimately cause life-threatening cardiovascular events such as heart attacks and stroke. Traditional lipid-lowering therapies (e.g. statins) only reduce cardiovascular disease by only 40-50%. Thus, the pursuit for alternative therapies, specifically that which target inflammation is highly sought after.

 

In our laboratory, we’re currently studying several novel inflammatory molecules in atherosclerosis. We are testing specific inhibitors that target these inflammatory pathways in atherosclerotic mouse models. The summer project will involve the analysis of atherosclerotic lesion size and complexity, and/or in vitro experiments using cells found in atherosclerotic lesions (e.g. macrophages) to test the effect of these inhibitors in the activation of various inflammatory and cell death pathways.

 

Together, these studies will definite specific inflammatory pathways, and potentially identify novel therapeutic strategies to treat cardiovascular diseases.

 

Expected outcomes and deliverables:

Scholars will gain work experience in a laboratory setting and will be part of a larger team of scientists working on this project. Specifically, they will learn biochemistry and immunology techniques such as western blot, qPCR, ELISAs, tissue culture, histology and/or confocal microscopy. They will also learn scientific communication skills (written and oral).

 

Any quality data produced by the scholar will be duly acknowledged as authorship in abstracts and/or publications etc. Further, this project has potential to lead to a very successful honours project within the lab as well.

Suitable for:

This project is suited ideally for a 3rd or 4th year undergraduate student who is interested in pursuing an honours degree at UQ.

*Highly desirable: GPA > 6.0, previous research experience

Primary Supervisor:

 

Primary Supervisor: Dr Denuja Karunakaran

(Secondary Supervisor: Prof Jenny Stow)

Further info:

For further information, please contact Dr Denuja Karunakaran: d.karunakaran@imb.uq.edu.au

 

Project title: 

Targeting inflammation and cell death in obesity

 

Project duration & delivery

10-12 weeks, and applicant will be required on-site for the project.

If required (due to COVID restrictions), it is possible for 2-4 weeks of the project can be completed remotely (i.e. quantification and data analysis).

 

Description:

Obesity is a major public health burden worldwide, greatly increasing the risk of diabetes, cardiovascular diseases and cancer. Obesity is characterized by excessive fat accumulation, adipose tissue inflammation and insulin resistance. There’s a huge misconception that obesity is simply the result of ‘lack of exercise’ or ‘excessive eating’, however, our research, along with others’, suggest that the equation is far more complex, involving genetics, sleep cycle (circadian rhythms) and/or inflammation. 

 

RIPK1 and MLKL are important regulators of inflammation and cell death pathways, and our preliminary studies show that therapeutically targeting these molecules reduce diet-induced obesity in mice. Importantly, in humans, we found several genetic variants with the RIPK1 gene that is associated with adipose tissue inflammation and increased risk of obesity. However, the mechanisms by which these molecules alter inflammatory responses, cell death pathways and cellular rhythms in adipose tissue cells (e.g. macrophages or adipocytes) remains unclear, and the focus on our laboratory.

 

Here, we will use unique tools to study how inflammatory stimuli alter gene expression that drives inflammation and/or alter normal rhythms within these cells, and long-term studies will investigate how adipocytes interact with these immune cells in the adipose tissue.

 

Expected outcomes and deliverables:

Scholars will gain work experience in a laboratory setting and will be part of a larger team of scientists working on this project. Specifically, they will learn biochemistry and immunology techniques such as western blot, qPCR, ELISAs, tissue culture, histology and/or confocal microscopy. They will also learn scientific communication skills (written and oral).

 

Any quality data produced by the scholar will be duly acknowledged as authorship in abstracts and/or publications etc. Further, this project has potential to lead to a very successful honours project within the lab as well.

Suitable for:

This project is suited ideally for a 3rd or 4th year undergraduate student who is interested in pursuing an honours degree at UQ.

*Highly desirable: GPA > 6.0, previous research experience

Primary Supervisor:

 

Primary Supervisor: Dr Denuja Karunakaran

(Secondary Supervisor: Prof Jenny Stow)

Further info:

For further information, please contact Dr Denuja Karunakaran: d.karunakaran@imb.uq.edu.au

 

Project title: 

Characterising gene regulatory networks that underpin cell identity and age-stage

Project duration & delivery

8-10 weeks and applicant will be required on-site for the project, but some aspects can also be performed off-site. Dry lab/computational biology project

Description:

The group’s research is centred around the study of cell fate transitions that occur rapidly as a consequence of forced cellular reprogramming (i.e. transdifferentiation), as well as the subtler and slower, albeit functionally meaningful, changes that occur as part of cellular ageing. To uncover transcription factors (TFs) that drive these processes, we have created a molecular atlas (RNAseq, ATACseq) comprised of dozens of mammalian cell types from both young and aged subjects.  

 

We are currently looking for “dry-lab” students interested in purely computational projects to dissect the TF network and how it is changing in the context of ageing, differentiation and transdifferentation (using techniques like TF motive prediction & network analysis). In collaboration with wet lab scientists, hypotheses derived from the candidate’s analyses will be tested using in vitro cell models (e.g. can we “reprogramme” aged cells to work more efficiently by targeting age-altered transcriptional circuits).

 

Expected outcomes and deliverables:

The student will gain experience in working with state-of-the-art computational pipelines and advanced methods in the field of computational biology. Students will be asked to communicate their findings to the lab (e.g. short report or oral presentation) at the end of their project, and will be given detailed feedback, to help develop their science communication skills. The work will be embedded within ongoing research studies and, if performed well, incorporated into publications (authorship on these studies can be expected).

Suitable for:

This project is suitable for 3rd – 4th year students. The ideal candidate has some demonstrated background in computational bioinformatics and as such is comfortable writing code in languages such as R, Matlab, Perl, or Python. 

Primary Supervisor:

 

Dr Christian Nefzger

Dr Marina Naval-Sanchez

Further info:

For all enquires please email c.nefzger@imb.uq.edu.au