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Centre for Cell Biology of Chronic Diseases

Advancing 3D imaging and visualisation of cell surfaces

Supervisor: Professor Jennifer Stow (j.stow@imb.uq.edu.au)

Biochemical and structural studies of membrane trafficking protein complexes involved in neurodegeneration

Supervisor: Professor Brett Collins (b.collins@imb.uq.edu.au)

Blocking nutrient uptake to limit cancer cell survival

Supervisor: Professor Jennifer Stow (j.stow@imb.uq.edu.au)

Cancer metastasis and stem-like reprogramming via mechanical signatures

Supervisors: Dr Samantha Stehbens (s.stehbens@uq.edu.au), Dr Melanie White (melanie.white@imb.uq.edu.au)

Tumour cells spread via the circulation. Here, travelling as clusters facilitates their survival and ability to seed into new tissues. This project will investigate how tumour cells form clusters and the role of physical forces.

Characterising the impact of neurological injury on coronary sinus biomarker profile in an ovine model of circulatory determination of death

Supervisors: Dr Jacky Suen (j.suen1@uq.edu.au); Ms Molly McInerney (m.mcinerney@imb.uq.edu.au)

To characterise the coronary sinus (CS) biomarker profile and catecholamine surge after neurological injury in an ovine model of circulatory determination of death (DCD). The molecular characterisation of the CS profile will improve our understanding of the physiological changes directly inside the heart during DCD for the purpose of heart transplantation.

Characterising the impact of neurological injury on cytokine profile in an ovine model of circulatory determination of death

Supervisors: Dr Jacky Suen (j.suen1@uq.edu.au); Ms Molly McInerney (m.mcinerney@imb.uq.edu.au)

To determine if neurological injury impacts circulating inflammatory cytokines and cardiac injury markers within an ovine model of circulatory determination of death (DCD). The identification of this biomarker profile will improve our understanding of the physiological changes during DCD and their implications for heart transplantation.

Characterising the impact of neurological injury on hearts reconditioned with hypothermic oxygenated machine perfusion (HOPE) in a model of circulatory determination of death (DCD) for heart transplantation

Supervisors: Dr Jacky Suen (j.suen1@uq.edu.au); Ms Molly McInerney (m.mcinerney@imb.uq.edu.au)

To determine the impact of neurological injury on hearts reconditioned with hypothermic oxygenated machine perfusion (HOPE) in an ovine model of circulatory determination of death (DCD) for the purpose of heart transplantation.

Circadian regulation of protein glycosylation

Supervisor: Associate Professor Frederic Gachon (f.gachon@uq.edu.au)

Controlling cell fate through transcription factor-based reprogramming

Supervisor: Dr Christian Nefzger (c.nefzger@imb.uq.edu.au)

Deciphering the DNA-protein interactions that reset the ageing clock during reprogramming

Supervisor: Dr Christian Nefzger (c.nefzger@imb.uq.edu.au)

Designing mini-protein chaperones for dementia treatment.

Supervisors: Dr Michael Healy (michael.healy@uq.edu.au)

At the heart of neurodegeneration is the concept of proteostasis, the tight regulation of protein synthesis, transport, degradation, and recycling. Defective proteostasis results in the toxic accumulation of proteins and peptides such as amyloid β (Aβ) and phosphorylated tau. The major pathway that regulates proteostasis is the sorting and degradation of transmembrane proteins in the endolysosomal system, and associated autophagic and lysosomal destruction of toxic cytosolic molecules. Retromer is a trimeric protein complex that is a central player in regulating the endolysosomal system and is downregulated in the hippocampus of patients with Alzheimer’s disease. Molecules (termed molecular chaperones) that stabilise this complex increase Retromer levels in neurons and decrease levels of neurotoxic Aβ, however, to date no molecule has made it into the clinic. Here I will use our knowledge of fundamental Retromer biology to design a suite of ‘mini-protein’ molecular chaperones using revolutionary machine learning techniques (Alphafold, RFdiffusion) and test their ability to stabilise Retromer in vitro and reverse dysfunction in known cellular models of neurodegeneration. Unlike traditional drug screening approaches, these revolutionary techniques allow for the generation of novel protein backbones that bind to specified regions of a protein or protein complex. If successful, these molecular chaperones could represent novel therapeutics for the treatment of the underlying molecular pathology that is common in neurodegeneration.  

Determining the impact of neurological injury on cardiac contractile function in an ovine model of circulatory determination of death

Supervisors: Dr Jacky Suen (j.suen1@uq.edu.au); Ms Molly McInerney (m.mcinerney@imb.uq.edu.au)

To determine myocardial catecholamine sensitivity and cardiac contractility after neurological injury in an ovine model of circulatory determination of death (DCD).

Do cells experience nuclear damage in the absence of microtubules?

Supervisors: Dr Samantha Stehbens (s.stehbens@uq.edu.au), Dr Robert Ju (r.ju@uq.edu.au)

Cells can generate and transmit mechanical forces. Physical compression of cells (such as a cell invading through a dense tissue) can result in damage to the nucleus. This can drive adaptations in nuclear biology. This project will examine how the nucleus responds to force in the absence of the microtubule cytoskeleton.

Endocytosis of Endothelial Nitric Oxide Synthase in Cardiovascular Disease

Supervisor: Dr Nicholas Ariotti (n.ariotti@uq.edu.au)

Engineering cell identity: Using human pluripotent stem cells to program cells with customised functions not seen in the natural world

Supervisor: Dr Nathan Palpant (n.palpant@uq.edu.au)

This project seeks to explore the frontier of cell engineering by utilizing pluripotent stem cells as a model system. These stem cells, known for their ability to differentiate into any cell type, will be manipulated to remove the epigenetic barriers that conventionally restrict cell identity. By transcending these intrinsic limitations, the study aims to engineer cells with functions and characteristics not observed in the natural world. The potential impact of this work extends not only to fundamental discovery science, where it may open new avenues in understanding cellular differentiation and control, but also to translational applications. Innovations in synthetic biology could emerge from this research, impacting areas such as tissue engineering, regenerative medicine, and the development of novel therapeutic strategies.

Examining a novel regulator of blood vessel integrity

Supervisors: Dr Anne Lagendijk (a.lagendijk@uq.edu.au)

A healthy vasculature is central to a functioning cardiovascular system. One aspect imperative to a homeostatic vascular system is stability of the endothelial cell (EC) monolayer, which forms the inner wall of all vessels. We have recently identified striking vascular defects in zebrafish lacking a selected soluble peptide receptor. CRISPR/Cas9 targeting of the gene encoding this receptor induced severe bleedings in the zebrafish brain by three days post fertilisation (dpf). This data suggests that this receptor is essential to strengthen the vasculature and prevent bleedings. This project aims to further characterise this unique phenotype and uncover the underlying mechanisms.

Fighting infection: Enhancing phagocytosis and pathogen killing

Supervisor: Professor Jennifer Stow (j.stow@imb.uq.edu.au)

How (ab)normal mechanics controls the health (or not) of the eye epithelium

Supervisors: Professor Alpha Yap (a.yap@uq.edu.au), Dr Ivar Noordstra (i.noordstra@imb.uq.edu.au)

How cytokines increase sensitivity to inflammation triggered by apoptosis in epithelia

Supervisors: Professor Alpha Yap (a.yap@uq.edu.au), Dr Kinga Duszyc (k.duszyc@imb.uq.edu.au)

How does the tumour mechano-environment facilitate melanoma brain metastasis?

Supervisors: Dr Samantha Stehbens (s.stehbens@uq.edu.au), Dr Melanie White (melanie.white@imb.uq.edu.au), Dr Meg McFetridge

Melanoma spreads from the skin to the brain. The brain is a unique environment, both biochemically and physically. This project will explore the role of the physical environment in mediating the survival and spread of melanoma to the brain.

How immune cells eat and digest pathogens; phagocytosis

Supervisor: Professor Jennifer Stow (j.stow@imb.uq.edu.au)

Immune navigation: changing signals to control inflammation in disease

Supervisor: Professor Jennifer Stow (j.stow@imb.uq.edu.au)

Investigating a newly identified mechanism of innate immune defence using tissue culture and zebrafish models

Supervisors: Dr Harriet Lo (h.lo@imb.uq.edu.au), Dr Tom Hall (thomas.hall@imb.uq.edu.au)

We recently discovered a novel process whereby eukaryotic cells are able to kill invading pathogens using lipid droplets. This project will use cell-based infection models and live imaging in zebrafish to identify and characterise the proteins involved.

Investigating a novel pathway that controls venous blood vessel integrity

Supervisor: Dr Anne Lagendijk (a.lagendijk@imb.uq.edu.au)

A healthy vasculature is central to a functioning cardiovascular system. One aspect imperative to a homeostatic vascular system is the integrity of junctions between adjacent endothelial cells (ECs). It is appreciated that arteries and veins display different adhesive properties at EC junctions, underpinning their distinct functions. However, the molecular mechanisms controlling this heterogeneous adhesion and junction integrity across divergent vessel types are not well understood.

Preliminary data in our lab has uncovered a novel factor that specifically controls venous EC adhesion. We have shown this specific role in both loss-of-function zebrafish and 3D bioengineered human vessels, displaying disrupted venous endothelial junctions and venous vessel dysmorphia. Notably, arteries are unaffected. Such vessel-restricted phenotypes are rare, and this project aims to characterise the cellular mechanisms that determine this specificity. We are seeking an enthusiastic and driven Honours student to assist in the phenotyping of novel zebrafish CRISPR knockout lines that have been generated as part of this project. You will gain skills in zebrafish handling, molecular cloning, CRISPR/Cas9 gene editing and high-resolution live imaging of functioning blood vessels. Specific project aims include:

1. Phenotypic rescue experiments by re-expressing genes in zebrafish knockout models

2. Determine the functional consequences of compromised ECs (i.e. vessel hyperpermeability or breakdown) using dextran injections

3. Assist in phenotyping of novel CRISPR/Cas9 zebrafish mutant lines to help delineate the key players in this novel venous specific pathway

Investigating the role of the vasculature in COVID-19

Supervisors: Dr Emma Gordon (e.gordon@imb.uq.edu.au), Dr Larisa Labzin (l.labzin@uq.edu.au)

Leveraging single cell multiome data to identity drivers of organ ageing (dry lab/computational project)

Supervisor: Dr Christian Nefzger (c.nefzger@imb.uq.edu.au)

Live imaging of cell lineage differentiation in a novel transgenic quail model

Supervisor: Dr Mel White (melanie.white@imb.uq.edu.au)

Mitochondrial transplantation for cardiac transplantation

Supervisors: Dr Jacky Suen (j.suen1@uq.edu.au)

Donor hearts experienced secondary injury during transplantation which increases the risk of primary graft dysfunction and patient mortality. One approach to improve donor heart condition is through mitochondrial transplantation. Student will work with our collaborator at Harvard Medical School to optimise the extraction, preparation and application of mitochondria onto donor heart in a preclinical model.

Modelling human genetic variants for muscle and adipose phenotypes using the zebrafish

Supervisors: Dr Tom Hall (thomas.hall@imb.uq.edu.au), Dr Harriet Lo (h.lo@imb.uq.edu.au)

The results of genetic testing in humans are often difficult to interpret. This project will use live imaging and CRISPR/Cas9 technology to introduce human variants into zebrafish and examine the effects on muscle and adipose tissue.

Oxygenator-induced haemolysis in advanced life support

Supervisors: Dr Jacky Suen (j.suen1@uq.edu.au)

Student will conduct benchtop experiments to examine the role of oxygenator in device-related haemolysis. Patients with cardio-respiratory failure are often supported by advanced life support, and face complications such as bleeding. The student will build on our previous data showing that oxygenator is a cause of haemolysis that has not been reported before.

Regulation of liver protein secretion and its regulation by circadian and feeding rhythms

Supervisor: Associate Professor Frederic Gachon (f.gachon@uq.edu.au)

Role of macrophage metabolism in driving inflammation

Supervisor: Professor Matt Sweet (m.sweet@imb.uq.edu.au)

Role of macrophage metabolism in host defence against bacterial infections

Supervisor: Professor Matt Sweet (m.sweet@imb.uq.edu.au)

Screening for metastasis inhibitory markers in cancer

Supervisor: Professor Jennifer Stow (j.stow@imb.uq.edu.au)

Specific role of the circadian clocks in the different liver cell types and how they interact

Supervisor: Associate Professor Frederic Gachon (f.gachon@uq.edu.au)

Studies of membrane trafficking protein complexes involved in neurodegenerative disease using X-ray crystallography and cryoelectron microscopy

Supervisors: Professor Brett Collins (b.collins@imb.uq.edu.au), Dr Michael Healy (m.healy@imb.uq.edu.au)

Targeting Nanoparticles to Fight Cancer

Supervisors: Dr Ye-Wheen Lim (y.lim@uq.edu.au), Professor Rob Parton (r.parton@imb.uq.edu.au)

How are nanoparticles transported across different biological barriers from the bloodstream to their target sites? This project will use tumor xenograft models and live imaging in the zebrafish to uncover the trafficking of nanoparticles in a live organism.

Targeting stress and protein quality control pathways in skeletal muscle disease

Supervisors: Amy Hanna (a.hanna@imb.uq.edu.au); A/Prof Nathan Palpant (n.palpant@uq.edu.au)

Skeletal muscle is an active, highly dynamic tissue that is constantly building new proteins to perform integral muscle activities like contraction, temperature regulation and energy expenditure.  In healthy muscle, misfolded proteins are removed before they can affect cellular health but in some muscle diseases these misfolded proteins remain in the cell and aggregate, causing activation of stress pathways. How these misfolded proteins affect the ability of muscle to function is poorly understood. This project will examine the factors that regulate protein folding in skeletal muscle and determine how the accumulation of misfolded proteins affects muscle contraction and muscle size. We will also determine if these stress pathways can be targeted to treat congenital myopathy by testing novel pharmacological agents in models of human muscle disease. 

The role of BAR proteins in directing collective cell migration during blood vessel development

Supervisors: Dr Anne Lagendijk (a.lagendijk@uq.edu.au)

The growth of new blood vessels is governed by polarisation and directional collective migration of the endothelial cells that make up these vessels. BAR proteins are a protein family characterised by the BAR domain, a membrane curvature sensing module that senses and actively induces membrane curvatures. As part of an international collaboration, we have identified BAR proteins that specifically regulate polarisation and collective cell migration in confluent endothelial cell cultures subjected to scratch wounds as well as in growing blood vessels in zebrafish. We have now generated stable zebrafish knockout lines for these BAR proteins. This project will utilise these novel zebrafish lines to identify how these BAR proteins control collective cell migration by high resolution live imaging of developing vasculature. Overall this project provides the unique opportunity to be part of an international team and perform state-of-the art live imaging to reveal novel cellular behaviours that are relevant to blood vessel function. 

The role of caveolae in cancer

Supervisors: Dr. Kerrie-Ann McMahon (k.mcmahon@imb.uq.edu.au), Dr. Yeping Wu (yeping.wu@imb.uq.edu.au)

Caveola mutations or dysfunction have been linked to human diseases including cancer. This project will use genome-edited cell models and confocal microscopy to investigate the roles of caveolar components in cellular pathways involved in cancer development.

Understanding acid sensitivity of the heart: identifying genes and drugs that block the injury response of the heart during ischemic stress

Supervisor: Dr Nathan Palpant (n.palpant@uq.edu.au)

This project aims to explore heart injury mechanisms that occur under low-oxygen conditions. Drawing insights from studies on high altitude adaptation, the project aims to uncover genetic factors that may confer tolerance to hypoxic environments. These discoveries are anticipated to facilitate the identification of novel genetic targets that can be employed in the treatment of patients suffering from heart attacks. Utilizing human pluripotent stem cells, ischemia will be modeled in vitro to test new genes or pharmacological agents that prevent cell death under acute stress conditions. Given that heart attacks represent the leading cause of death globally, the findings of this project will offer innovative strategies to alleviate the substantial burden associated with cardiac diseases. 

Understanding microtubule-dependent cell invasion to enhance innate immune responses

Supervisors: Dr Samantha Stehbens (s.stehbens@uq.edu.au), Dr Larisa Labzin (l.labzin@uq.edu.au), Dr Robert Ju (r.ju@uq.edu.au)

Microtubules are required for tumour cells to invade tissues. Disruption of microtubules results in cell rupture during invasion. This project will determine if melanoma cells secrete factors to elicit an immune response.

Unlocking Vascular Control: Investigation of a Novel Gene Regulating Blood Pressure for Therapeutic Development

Supervisor: Dr Nathan Palpant (n.palpant@uq.edu.au)

This project aims to study a newly discovered gene that plays a crucial role in controlling vascular development and regulating blood pressure. We aim to understand the mechanisms and functions of this gene to open new avenues for the development of novel therapeutics specifically tailored for blood pressure management. Utilizing an integrative approach that combines animal models, stem cell models, and genetics, the study will dissect the pathways and functions of this gene. The project will contribute to the expanding body of knowledge surrounding genetic control of vascular function, thus enhancing our comprehension of blood pressure regulation at a molecular level. The outcomes may lead to the creation of new drugs, providing approaches to treat hypertension and other blood pressure-related diseases. 

Water bears (tardigrades) as a system to study stress resistance

Supervisors: Dr Harriet Lo (h.lo@imb.uq.edu.au), Professor Rob Parton (r.parton@imb.uq.edu.au)

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.

Zinc toxicity as an antimicrobial weapon of macrophages

Supervisor: Professor Matt Sweet (m.sweet@imb.uq.edu.au)

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