Student projects

These are the research projects available at IMB. Depending on the enrolment type of student (Honours, Master's or PhD), projects can be scaled accordingly.

2020/2021 Summer undergraduate-specific courses can be found here.

Cell and Developmental Biology

GACHON group: Physiology of Circadian Rhythms

Contact: A/Prof Frederic Gachon
f.gachon@imb.uq.au 07 3346 2017

Our group studies the regulation of mammalian physiology by the circadian clock, focussing on liver metabolism. Circadian clocks have been conserved throughout the evolution, allowing the adaptation of the physiology to the time of day in an anticipatory way. As a demonstration of their crucial role, perturbation of the circadian clock leads to numerous pathologies including obesity, type 2 diabetes and cancer.

Our goal is to determine how the circadian clock regulates mammalian physiology and understand how the perturbation of the circadian clock leads to pathologies.

We use a wide variety of techniques, including animal biology, molecular biology, biochemistry, genomics, proteomics and bioinformatic analysis of the data to make conclusions at the biological system level.

Traineeships, honours and PhD projects include:

Determine the regulation of liver protein secretion and its regulation by circadian and feeding rhythms.
Study the role of the autonomic nervous system in the rhythmic regulation of liver physiology.
Demonstrate the specific role of the circadian clocks in the different liver cell types and how they interact.
Study the rhythmic organisation of the different liver cell types and its consequence on physiology.

GORDON Group: Vessel growth and stability

Contact: Dr Emma Gordon
e.gordon@imb.uq.edu.au

Vessels form complex branched networks that supply oxygen and nutrients to all body tissues. The focus of our research is to understand the signals that regulate how blood vessels grow and are maintained during development and disease. Specifically, we are interested in how cells within the vessel wall interact with each other and their surrounding environment. If the signals controlling these interactions become deregulated, normal vessel growth and function is lost. This contributes to the progression of a wide range of human diseases, including cancer growth and metastasis, diabetic eye disease and stroke.

We use a range of novel biological models, biochemical assays and imaging techniques to better understand vessel biology, which will enable a better understanding of human development and improved treatment of disease.

Traineeships, honours and PhD projects include:

Identifying cellular signals guiding blood vessel sprouting
Imaging protein movements and activity in living cells
Therapeutic strategies in pathological eye disease
Understanding how the tumour environment affects vascular dysfunction

LAGENDIJK group: Mechanobiology of the vasculature in health and disease

Contact: Dr. Anne Karine Lagendijk
a.lagendijk@imb.uq.edu.au 07 3346 2105

Our group aims to understand how our blood vessel network is established during embryonic development and how its function is maintained during life. The development of an aberrant vessel network contributes to a range of cardio-vascular diseases. For example leaky vessels in the brain can cause stroke. In the lab we employ the zebrafish as a model organism since zebrafish embryos are viable ex utero and can be imaged at extremely high resolution which gives us a unique, live, view of vascular development. We make use of existing and novel biosensors in zebrafish to reveal dynamics of adhesion complexes at the cell-cell and cell-matrix interface whilst also examining distribution of tension at these mechanical hubs. By combining these high-end imaging approaches with detailed, innovative molecular genetics approaches, like CRISPR mutagenesis, we explore the fundamental importance of cell-matrix adhesion in vascular biology. In addition to in vivo analysis, we are currently implementing in Australia a novel technique to grow and manipulate bioengineered human micro-vessels.

Traineeships, honours and PhD projects include:

The role of neuropeptides in establishing and maintaining blood vessels in zebrafish and 3D bioengineered human vessels.
Using CRISPR mutagenesis to uncover changes in cellular mechanics that drive a vascular disease called Cerebral Cavernous Malformation (CCM).
Profiling changes in tension across wild-type and mutant forms of the adhesion protein VE-cadherin using in vivo live imaging.
The impact of cell-matrix interactions on vascular growth in zebrafish mutant models.
Mathematical modelling of cell shapes and adhesion dynamics that underlie vessel morphology and diameter.

PALPANT Group: Cardiovascular medicine: from stem cells to drug discovery

Contact: Dr Nathan Palpant
n.palpant@imb.uq.edu.au 07 334 62054

In recent years, bioengineering and biotechnology approaches have emerged for studying complex developmental processes with high resolution and precision. My lab uses human stem cells to study mechanisms underlying heart development with the goal of applying our knowledge to find new therapeutic strategies for cardiovascular disease. We utilize tools in cellular genomics including genome editing and single cell level RNA-sequencing to study mechanisms of cell differentiation. My lab also aims to identify new genes controlling how heart cells respond to disease and developing new therapeutics for cardiovascular medicine.

Traineeships, honours and PhD projects include:

Use stem cells, genome engineering, and single cell RNA-sequencing to study how cells differentiate into cell types of the heart
Modify stem cells to generate cells with custom engineered functions to create synthetic cell states
Use bioinformatics approaches to analyse large scale genomic data to study what features of the genome control cell decisions
Study novel genes that control how heart cells respond to stress like ischemia and work with chemists to develop novel drugs that could be used to treat patients who have heart attacks
Use computational genomics and cell biology approaches to study how the heart adapts to extreme environments (like high altitude) to learn what genes control stress responses in cells.
Study the biology of how venoms of marine and terrestrial species impact heart function using cells, whole organ models, and animal models.

PARTON group: The cell surface in health and disease

Contact: Prof Rob Parton
r.parton@imb.uq.edu.au 07 3346 2032

The plasma membrane that envelops each mammalian cell plays a crucial role in detecting signals for growth or in taking nutrients into the cell. At the same time, the plasma membrane protects the cell against unwanted invaders. Many human disease conditions, including cancer and muscular dystrophy, are caused by dysfunction of the plasma membrane.

Our current research analyses the organisation, dynamics, and functions of this crucial structure – with a particular focus on surface domains termed caveolae, that are linked to signal transduction, endocytosis, and lipid regulation, to understand their role in healthy cells and their aberrant function in disease.

We use a wide range of techniques, including advanced 3D electron microscopy and real-time light microscopy together with animal models of human disease to gain insights into plasma membrane dynamics and domain organisation.

Traineeships, honours and PhD projects include:

Zebrafish as a model to understand human muscle diseases
Structure and function of a new family of caveolar coat proteins
Novel pathways of endocytosis in cultured cells and in tissues
Bioengineering of novel nanovesicles for drug delivery.

COLLINS group: Membrane trafficking at atomic resolution

Contact: Prof Brett Collins
b.collins@imb.uq.edu.au 07 3346 2043

Our group studies the process of membrane trafficking in the human cell. This is fundamental for normal physiology, and is important in neurodegenerative diseases, including Alzheimer’s and Parkinson’s.

Our goal is to determine the molecular basis of how ‘protein coats’ bind to receptors, such as the amyloid precursor protein involved in Alzheimer’s, and control their packaging into membrane-bound vesicles.

We use a wide variety of techniques, including molecular biology, protein X-ray crystallography, biochemical and biophysical studies of protein-protein and protein-lipid interactions, and cellular studies of protein localisation, to build coherent molecular models of how molecules are trafficked within the cell.

Traineeships, honours and PhD projects include:

Molecular basis for the function of the retromer protein complex, and implications for neurodegenerative diseases.
Determining the role of ‘sorting nexin’ proteins in controlling the homeostasis of receptors in neurons.
Discovery of small molecules that modulate the assembly of protein trafficking coats.
Structural studies of proteins that form membrane structures called caveolae.

Dr NICHOLAS HAMILTON: Modelling, Visualisation and Classification of Bio-Imaging

Contact: Dr Nick Hamilton
n.hamilton@imb.uq.edu.au 07 334 62033

Biological imaging is undergoing rapid growth and development in microscope technology. High throughput screens for drug and genomic discovery are leading to massive image sets in need of new methods of quantification, modelling, analysis, classification, feature extraction, organisation, visualisation, comparison, hypothesis testing and inference. The core of the groups research is to develop the methodologies, algorithms and tools to maximise the benefit of the new data sources becoming available. The group collaborates closely with cell biology, developmental biology, bioinformatics and mathematics groups in creating these methodologies and utilises and develops techniques in areas such as machine learning, data clustering, graph algorithms, image segmentation, statistical testing amathematical modelling.

Traineeships, honours and PhD projects include:

Machine learning approaches to bio-imaging
Information visualisation and clustering methodologies
Segmentation and quantification of microscopy imaging
Mathematical modelling from microscopy imaging

NEFZGER group: Cellular reprogramming and ageing

Contact: Dr Christian Nefzger:
c.nefzger@imb.uq.edu.au

The group’s research is centred around the study of cell fate transitions that occur rapidly as a consequence of forced cellular reprogramming (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.

The diverse background of researchers within the Nefzger group (including computational biologist Dr Marina Naval-Sanchez), will provide the candidate with access to state-of-the-art training in the area of computational biology. 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 and in vivo cell models. For example, by pinpointing and targeting age-related transcriptional circuits, we want to find ways to “reprogramme” aged cells to work more efficiently, like young cells do.

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.

Traineeships, honours and PhD projects include:

Study of age-related transcription factor network changes
Identification of transcription factors that underpin cell type identity
Tool development

SCHRODER group: Inflammasomes in infection and inflammatory disease

Contact: A/Prof Kate Schroder
k.schroder@imb.uq.edu.au 07 3346 2058

The innate immune system is critical to defence against infection, but also drives unhealthy processes in inflammatory disease. An important pathway in innate immunity is the inflammasome.

Inflammasomes are molecular machines that trigger cytokine maturation and immune system activation in response to signals indicating cellular ‘danger’. While the inflammasome pathway is critical for host defence against infection, it is also a key driver of unhealthy inflammation in many human diseases.

We use a wide variety of molecular and cell biology techniques, in conjunction with animal models and human clinical samples, to investigate the biology of inflammasomes in host defence and inflammatory disease at the molecular, cellular and organismal levels.

Traineeships, honours and PhD projects include:

Inflammasome function in host defence against infection
Human-specific inflammasome and caspase pathways
Pathogenic inflammasome function in human diseases
Inflammasome inhibition by small molecule drugs and cellular pathways
Neutrophil inflammasome function during infection and disease.

SWEET Group: Innate immunity, infection and inflammation

Contact: Prof Matt Sweet
m.sweet@imb.uq.edu.au 07 3346 2082

Innate immune cells, such as macrophages, express a broad repertoire of pattern recognition receptors that act as danger sensors. For example, members of the Toll-like receptor (TLR) family detect a number of pathogen-associated molecular patterns such as LPS from Gram-negative bacteria. Macrophage activation through TLRs regulates expression of genes involved in antimicrobial responses and inflammation. Thus, TLR signalling is required for effective control of invading microorganisms, but if dysregulated, contributes to acute and chronic inflammatory diseases.

Our team studies TLR signalling pathways and the functions of TLR-regulated genes in inflammation, as well as in host defence against bacterial pathogens (e.g. Salmonella, uropathogenic E. coli).

Traineeships, honours and PhD projects include:

TLR-inducible zinc toxicity as a macrophage antimicrobial weapon against bacterial pathogens
Role of TLR-inducible mitochondrial fission in macrophage responses against bacterial pathogens
Characterization and targeting of TLR-inducible pro-inflammatory signalling in macrophages
Roles of protein deacetylases in innate immunity
Regulated immunometabolism in macrophages
Control of TLR-inducible inflammatory and antimicrobial responses by circadian rhythm

STOW group: Cell regulation in inflammation and cancer

Contact: Prof Jenny Stow
j.stow@imb.uq.edu.au 07 3346 2034

Macrophages are key immune cells in inflammation, infection and cancer where they detect, phagocytose and kill pathogens or cancerous cells, and secrete cytokine messengers to control inflammatory responses. Inflammation is a powerful response that is normally turned on and off under tight control. Loss of these controls allows inflammation to contribute to many chronic diseases, including diseases of the liver, kidney, brain, lungs, joints and skin. Our research aims to control macrophage-induced inflammation by identifying the relevant genes, proteins, membrane domains and signalling pathways in order to devise new treatments based on new or existing drugs. Our molecular cell biology laboratory uses advanced live cell imaging and microscopy, advanced protein biochemistry and cell-based assays with multidisciplinary collaborations and clinical partners.

Traineeships, honours and PhD projects include:

Toll-like receptor signalling and kinase inhibitors in cancer and inflammation
Rab-mediated phagocytosis and endocytosis
TLR-mediated neuroinflammation in Alzheimer’s disease
Turning off pulmonary inflammation in cystic fibrosis
Targeting macrophage activation in lupus and kidney diseases

Dr Lin Luo, STOW Group: Controlling inflammation in chronic disease

Contact: Dr Lin Luo
l.luo@imb.uq.edu.au 07 3346 2035

Inflammation is a fundamental response to danger in all-higher organisms. It is a rapid and robust response, designed to kill pathogens and limit the spread of infection. Macrophages are elemental cells of the innate immune system, tasked with tissue surveillance and pathogen destruction. As key proponents of inflammatory responses, activated macrophages elicit temporally-controlled programs of cytokines in order to mount robust immune responses and then to promote tissue repair. The differential expression of many cytokines and their varied time of release allow macrophages to tailor their inflammatory responses for different pathogens, tissues and situations. Just how cytokine expression is normally programmed with such precision is not fully understood. Defining the underlying molecular regulators of inflammation and cytokine release is imperative for extending our knowledge of inflammatory systems and for applications aimed at infection and immunity for a wide range of organisms. Our team aims to identify key regulators of inflammatory responses. Our research entails multiple approaches including proteomics, structural biology, protein biochemistry and cell imaging.

Traineeships, honours and PhD projects include:

The function of pTRAPs in Toll-like receptor (TLR) driven inflammation
The regulation of Src family kinases in TLR signalling
Characterisation of Rab-PI3K functions in macrophages
The role of integrin in lupus and kidney diseases

WHITE Group: Dynamics of Morphogenesis

Contact: Mel White
melanie.white@imb.uq.edu.au 07 3346 2494

The Dynamics of Morphogenesis Lab is focused on understanding the dynamic mechanisms controlling tissue formation and cell fate determination in vivo. Morphogenesis requires the precise spatiotemporal coordination of processes occurring across multiple scales: from the expression of individual genes, to the behaviour of single cells, to the forces that drive the simultaneous movement of thousands of cells. Our lab is interested in how molecular events are translated into, and integrated with, cellular properties and mechanical forces to orchestrate tissue formation. We are particularly interested in how these processes interact to direct the formation of the neural tube – the embryonic precursor to the brain and spinal cord. Incorrect formation of the neural tube results in neural tube defects (NTDs) which are amongst the most common and severe birth defects. Understanding the dynamic mechanisms driving neural tube formation may ultimately assist in the development of methods for the prediction and treatment of NTDs.

Traineeships, honours and PhD projects include:

Remodelling of actomyosin networks during neural tube formation in the living embryo
Tissue-scale forces driving neural tube formation in the living embryo
Creation and characterisation of a Rainbow transgenic avian line
Disrupting cellular forces underlying morphogenesis

YAP Group: Epithelial homeostasis in health and disease

Contact: Prof Yap
a.yap@imb.uq.edu.au 07 3346 2013

Epithelial tissues are the principal barriers in our body and the source of common diseases, notably cancer and inflammation. The surprising thing is that despite the fact that they are subject to constant bombardment by toxins, infection and transformation, epithelia stay healthy most of the time – and keep us healthy. This is because epithelia possess mechanisms to maintain homeostasis: to detect potential insults and respond appropriately. We believe that a major early-warning system involves changes in mechanical tension upon injury or transformation, that are detected by the neighbouring epithelium, which responds by eliminating the affected cells. These changes in mechanical force are transmitted through cell-cell junctions and detected at those junctions by mechanotransduction. Conversely, events that compromise junctional mechanotransduction can render epithelia vulnerable to disease. Thus, we aim to understand the cellular mechanisms of junctional mechanosensing; determine how they support tissue homeostasis; and test how they are compromised in disease. To do this, we combine cell biology with biophysics, collaborating with developmental biologists, cancer biologists, mathematicians, engineers and physicists.

Traineeships, honours and PhD projects include:

Understanding how tissue hypertension in epithelia promotes cancer development
Sensing forces at cell-cell junctions: its role in homeostasis and epithelial inflammation
Regulation and dysregulation of junctional mechanics: impact for epithelial organisation and tumour invasion

STEHBENS Group: Cell migration and invasion

Contact: Dr Samantha Stehbens
s.stehbens@uq.edu.au 07 3346 2444

Cells in living organisms must be able to navigate highly crowded 3D environments, where their coordinated migration provides the driving force behind developmental and homeostatic tissue maintenance. During metastasis, cancer cells navigate a wide range of physically challenging microenvironments to spread to distal tissues. Our research aims to understand the fundamental principles underpinning how cells integrate secreted and biomechanical signals from their local microenvironment to facilitate cell movement and survival. We apply these findings to understand how cancer cells exploit this to become metastatic. We hypothesise that targeting the ‘basic’ processes of cell motility, mediated by crosstalk between the cytoskeleton and the mechanical micro-environment, can be developed as an anti-metastatic approach. Our work will help provide a molecular basis to uncover novel therapeutic targets and develop mechano-medicines to prevent the metastatic spread of cancer. Specifically, we focus on understanding at the molecular level, how the microtubule cytoskeleton and microtubule associated proteins called +TIPs, regulate how cells move through physically challenging environments. To do this we utilize cutting-edge methodology including microchannel fabrication, novel light sheet microscopy, quantitative imaging methods in combination with patient-derived cell and 3D hydrogel models to recapitulate the metastatic microenvironment.

Traineeships, honours and PhD projects include:

Microtubule-dependent positioning of organelles
Understanding the role of microtubules in protecting cells from mechanical stress
The role of the mechano-environment in metastatic disease and therapy resistance
Regulation of protease secretion by microtubule-dependent targeting to cell-matrix attachments

KARUNAKARAN group: Cardiometabolic Diseases and Therapeutics

Contact: Dr Denuja Karunakaran
d.karunakaran@imb.uq.edu.au 07 3346 2055

Cardiometabolic diseases such as atherosclerosis, diabetes and obesity remain the leading cause of mortality and/or morbidity worldwide. Importantly, risk factors such as obesity and diabetes markedly accelerate the progression of atherosclerosis, the underlying cause of heart attacks and stroke.

Central to these complex diseases are chronic inflammation, cell death and/or the clearance of dying cells (aka efferocytosis). Our team focuses on how immune cells such as macrophages regulate inflammation, cell death and efferocytosis, and how these immune cells interact with other cells within the tissues in these cardiometabolic diseases (e.g. macrophages and adipocytes during adipose tissue inflammation in obesity). With the long-term goal of identifying novel therapeutic strategies to treat these conditions, we also routinely test novel drugs that target inflammation and/or cell death in our experimental disease models in vivo.

Our laboratory employs a range of unique mouse models, biochemistry, molecular biology, genetics, histology and imaging techniques to better understand the intricate molecular mechanisms by which inflammation, cell death and efferocytosis occurs in health and disease.

Traineeships, honours and PhD projects include

Targeting and validating novel inflammatory pathways in atherosclerosis
Identifying novel genes that regulate effective or defective macrophage efferocytosis
Understanding the specific role of inflammatory genes in adipose tissue cells during obesity
Study the complex interaction between inflammation, circadian clock, behaviour and obesity

Chemistry and Structural Biology Division

CAPON group: Biodiscovery: from biodiversity and biology, to bioactives and beyond

Contact: Prof Rob Capon
r.capon@imb.uq.edu.au 07 3346 2979

We specialise in the detection, isolation, identification and evaluation of biologically active small molecules from Nature (natural products). The aim of this research is to acquire knowledge of the chemical and biological properties of natural products, including how and why they are made, and to use this knowledge to better understand living systems, and inspire innovative solutions for important scientific and societal challenges. Natural products uncovered during our investigations represent valuable new leads in the search for drugs in the fields of human and animal health, as well as crop and environmental protection (eg new antibiotics and antiparasitics, and pest control solutions). They also have potential application as molecular probes to better interrogate, understand and manage living systems.

Traineeships, honours and PhD projects include:

Marine biodiscovery
Microbial biodiscovery
Chemical communication in Nature
Cane toad chemical ecology

Dr Mark Blaskovich (IMB Fellow): Antimicrobial Drug Discovery and Diagnostics

Contact: Dr Mark Blaskovich
m.blaskovich@uq.edu.au

Antimicrobial resistance threatens the viability of modern medicine. Our research is aimed at discovering new ways of diagnosing and treating viral and bacterial infections.

We have a major focus on the discovery, design and development of novel antibiotics and antibiotic adjuvants active against drug-resistant bacteria (also known as ‘superbugs’) through the application of medicinal chemistry and chemical biology. We are searching for new classes of antibiotics through an international collaborative screening initiative (the Community for Open Antimicrobial Drug Discovery, www.co-add.org), improving existing classes of antibiotics, and developing novel strategies that combine different types of antibacterial activity. Complementary research programs are developing antibiotic-derived probes, as tools to better understand how antibiotics work, and as diagnostics for the detection and visualisation of bacterial infections. Another theme is focused on creating functionalised nanoparticles that can selectively capture microorganisms from biological matrices or the environment. Our lab is committed to translating our discoveries into the real world, and have a range of collaborations with industry partners and global antimicrobial organisations.

Traineeships, honours and PhD projects include:

Antibacterial and antifungal medicinal chemistry
Development of antibiotic-derived probes to visualise bacteria and bacterial infections
Antibiotic mode of action studies
Chemoinformatics and microbiology applied to antimicrobial drug discovery
Nanotechnology for diagnostics

Dr Karl Hansford (COOPER Group): Antimicrobial drug discovery

Contact: Dr Karl Hansford k.hansford@uq.edu.au
Prof Matt Cooper m.cooper@imb.uq.edu.au

My research passion is devoted to the strategic application of small molecule organic synthesis, peptide synthesis and peptide mimicry toward the design of antimicrobials, and its interface with cellular and animal based assays to better understand the relationship between function and toxicity, and the underlying mechanisms leading to resistance development. Projects of this nature enable students to apply their detective skills to overcome the many and varied difficulties encountered during the synthesis of small molecules and peptides, and gain a first hand appreciation of how their compounds become critical pieces of the puzzle toward answering a broader set of questions in support of various hypotheses.

Traineeships, honours and PhD projects include:

Organic synthesis/chemistry (synthesis design and execution, structure determination, method development)
Medicinal chemistry/drug discovery (structure activity/structure toxicity relationships, optimisation of drug likeness, in vitro and in vivo testing, assay development)
Microbiology & biophysical studies – application of various techniques to assess microbiological potency, resistance development, and mode of action

CRAIK Group: NMR spectroscopy

Contact: Prof David Craik
d.craik@imb.uq.edu.au 07 3346 2019

Our group focuses on cyclic peptides, which are small stable peptides that can be tailored for treating a range of diseases, including cardiovascular disease, chronic pain, cancer and Alzheimer’s disease. We investigate all aspects of cyclic peptides, including their discovery from plants, determining their structure using NMR spectroscopy, testing their activity, synthesising and re-engineering them to make them more active and also producing them in plant ‘biofactories’.

Traineeships, honours and PhD projects include:

Discovery and structural characterisation of medicinal plant proteins
Structure-activity studies of conotoxins
Design of novel anticancer agents
Protein engineering and drug design
Molecular biology and evolution of cyclotides.

FAIRLIE Group: Chemistry and human therapeutics

Contact: Prof David Fairlie
d.fairlie@imb.uq.edu.au

Our group investigates (1) Chemistry - design and synthesis, NMR structures, molecular mechanisms of chemical reactions; (2) Biochemistry - protein-protein interactions, enzymology, cell signalling; (3) Pharmacology - mechanisms of disease development and drug action in human cells and mice/rats; (4) Immunology - innate and innate-like immune cells in disease. Understanding how molecules interact, how chemical and biological reactions work and how structure influences activity enables us to design, synthesize and evaluate enzyme inhibitors, receptor agonists/antagonists and protein-binding ligands. Chemists in our group discover new reactions, mechanisms, drugs and biological probes. Pharmacologists, biochemists and immunologists in our group study proteins, protein interactions in cells, signalling mechanisms, and experimental drugs in animal models of cancer, infectious diseases, inflammatory disorders, type 2 diabetes, obesity and Alzheimer’s disease.

Traineeships, honours and PhD projects include:

Chemistry (organic synthesis, medicinal chemistry, NMR structures, drug development)
Drug design and discovery (computer-modelling, structure, dynamics)
Biochemistry (protein-protein interactions, peptide and protein mimetics, peptide synthesis, NMR structures, enzymology)
G-protein coupled receptor (GPCR) drug discovery and signalling in cell metabolism, inflammation and cancer
Molecular Pharmacology (drug mechanisms of action, cell biology, signalling pathways, enzymology, GPCRs)
Experimental Pharmacology (rodent models of inflammatory, respiratory, metabolic, neurodegenerative diseases, type 2 diabetes, cancers)
Immunology (innate and adaptive immune cells in health and disease; chemical immunology)

HANKAMER group: The Centre for Solar Biotechnology: Developing solar driven industries

Contact: Prof Ben Hankamer
b.hankamer@imb.uq.edu.au 07 3346 2012

By 2050 the human population is forecast to expand from 7.5 to 9.6 billion people. We will require 70% more food (United Nations), 50% more fuel (International Energy Agency), and 50% more water (Organization for Economic Co-operation and Development). We also need to reduce CO2 emissions by over 80% (Intergovernmental Panel on Climate Change). All of these will have to be achieved to ensure economic, social, political, climate, food, water and fuel security.

The Centre for Solar Biotechnology connects ~30 international research teams and its industry partners to accelerate the innovation and commercialisation of new solar powered technologies and industries, based on photosynthetic green algae. Our technologies tap into the huge energy resource of the sun and absorb CO2 to provide economic solar driven solutions that will help supply the world’s growing energy, food and water needs, and a path for CO2 utilisation. Our technologies also open up a suite of high value opportunities in the nutraceutical and pharmaceutical sectors.

Collectively our work actively supports the development of new job opportunities, sustainable regional development, export industries and a clean, green and renewable future.

Traineeships, honours and PhD projects include:

Molecular and Cell Biology
- Optimising light capture efficiency: transcript and protein analysis of the light harvesting complex proteins
- Optimising protein expression for the production of peptide therapeutics
- Solar driven H2 production from water
Structural Biology
- High resolution single particle analysis: Membrane protein structure determination - purification and structural characterisation of the cyclic-electron flow – Photosystem I super complex using electron microscopy and high resolution single particle analysis
Chemical Engineering/Bioprocess
- Optimising and testing of pilot scale microalgae systems
Techno-Economics & Life Cycle Analysis
- Microalgae process modelling: model-guided design of high-efficiency microalgae systems

HENDERSON Group: Antibiotics and Antimicrobial Resistance

Contact: Prof Ian Henderson
i.henderson@uq.edu.au

Across the history the vast majority of humans have died due to infection; TB and malaria are estimated to have caused the deaths of 50% of all people who have ever lived. The introduction of vaccines and antibiotics has significantly reduced the burden of death and morbidity due to infectious disease. However, the widespread and inappropriate use of antibiotics over the lasqq22hnkjkkkbgre2t century has resulted in the global spread of antibiotic resistant organisms. Epidemiological data indicate that infections will regain their prominence as a leading cause of death by 2050, outstripping deaths due to cancer. Our research is aimed at discovering new ways to treat and prevent bacterial infections.

Our major research focus is understanding the molecular basis for the assembly of the bacterial cell membrane. We use this understanding as the basis for the discovery of novel therapies for infection and the design of new vaccines to prevent infection.

Traineeships, honours and PhD projects include:

Development of new vaccines
Microbial pathogenesis studies to understand the contribution of bacterial cell surface components to disease
Chemical biology screens to understand gene function
High throughput genetic screening to identify novel antimicrobial targets

KING Group: Bugs and drugs

Contact: Prof Glenn King
glenn.king@imb.uq.edu.au 07 3346 2025

Animal venoms are increasingly being used in drug discovery efforts as they constitute a vast and largely untapped source of pharmacologically active molecules. Our group uses animal venoms as a source of ion channel modulators for targeting nervous system disorders (pain, epilepsy and stroke) in which the underlying molecular problem is dysfunction or altered expression of an ion channel. We maintain the world’s largest collection of >600 venoms that can be used in screens against drug targets of interest. We have developed a drug discovery pipeline that allows venom peptides to be efficiently isolated, structurally and functionally characterised, and tested in animal models of disease.

Traineeships, honours and PhD projects include:

Development of first-in-class anti-stroke therapeutics
Discovery and development of analgesic venom peptides
Discovery and development of anti-epileptic venom peptides
Discovery and characterisation of novel compounds that target human parasites
Structural characterisation of the interaction between venom peptides and their ion channel targets using NMR spectroscopy, X-ray crystallography, and cryoelectron microscopy.

LEWIS Group: Venoms to drugs

Contact: Prof Richard Lewis
r.lewis@imb.uq.edu.au 07 3346 2984

Researchers in this area are focused on the discovery and biochemical characterisation of venoms and marine toxins, especially the conotoxins produced by cone snails to rapidly immobilise their prey. These toxins modulate a variety of membrane proteins, including important drug targets like sodium and calcium channels, nicotinic acetylcholine receptors (nAChRs), mc research.

Traineeships, honours and PhD projects include:

Discovery of novel analgesic venom peptides from cone snails
Integrated proteomics and transcriptomics to investigate the evolution and structure-function of cone snail venoms
Ultrastructural studies of the venom apparatus of cone snails
Mechanisms of venom peptide regulation in cone snails
Genomics studies of cone snails.

VETTER Group: Neuropharmacology and pain mechanisms

Contact: A/Prof Irina Vetter
i.vetter@imb.uq.edu.au 07 3346 2660

Sensory neurons are fundamental for our interaction with the external world by detecting stimuli including cold, heat, touch, pressure, vibration and tissue injury. These external stimuli are then transformed to electrical signals through specialised molecules, which detect temperature, mechanical stimulation and various chemicals. Although significant progress has been made towards determining the molecular identity of selected receptors and ion channels involved in sensory perception, our understanding of how these contribute to sensory perception, and in particular pain, is limited. Toxins from plants and animal venoms have provided highly specific tools, which allow dissection of the mechanisms of sensory perception and pain and may provide novel molecules with analgesic potential.

Traineeships, honours and PhD projects include:

Fundamental basis of peripheral sensory perception
Identifying and characterising the effect of venoms and toxins on peripheral sensory neurons
Identifying, characterising and optimising molecules with therapeutic potential from natural sources
Understanding the pathophysiology of pain and optimising analgesic treatment approaches.

SMYTHE Group: Drug Discovery and Development

Contact: A/Prof Mark Smythe
m.smythe@imb.uq.edu.au 07 3346 2977

We work on developing new drug candidates to treat diseases that have significant unmet medical need. This includes both applied research; the discovery and development of drug candidates at specific disease targets, and basic research; the development of new methods and tools to facilitate the drug discovery process. Research outcomes are typically commercialised in spin-out companies, with numerous discoveries successfully translated to the clinic and in late-stage preclinical development. We have strong linkages to clinicians and the pharmaceutical industry. Projects are offered in the disciplines of drug design, mathematics, chemistry and biology, as related to the development of drugs for specific therapeutic targets.

Traineeships, honours and PhD projects include:

Optimisation of drug candidates for treatment of breast cancer
Synthesizing new chemical probes to unravel biological pathways
Expanding constrained peptide evolution strategies to facilitate drug discovery
Antibodies with teeth, a new therapeutic modality.

Dr Christina Kulis, SMYTHE Group: The quest for drug discovery

Contact: Dr Christina Kulis
c.kulis@imb.uq.edu.au 07 3346 2368

My research interests are focused on the discovery, design and development of new drugs. Using a plethora of medicinal chemistry techniques, including virtual screening, organic chemistry, peptide synthesis, enzyme and cell assays, we are able to target different diseases ranging from balding to asthma. These multidisciplinary projects give students the opportunity to be exposed to different research skills and techniques used to develop pharmaceutical drug candidates.

Traineeships, honours and PhD projects include:

Drug discovery and development for the treatment of hair loss
Drug optimisation for hthe treatment of asthma and allergic diseases
Development of nitroxide spin label probes as ‘rulers’ for structural biology

MUTTENTHALER Group: Neuropeptide Research - Molecular probes to study health and disease

Contact: A/Prof Markus Muttenthaler
m.muttenthaler@imb.uq.edu.au

We work at the interface of chemistry and biology, with a strong passion for translational research. Our interests lie in neuropeptides and the exploration of nature's diversity to develop advanced molecular probes, diagnostics and therapeutics. We use chemistry, molecular biology, and pharmacology to study the interactions of these highly potent and selective molecules with human physiology, with therapeutic applications in gastrointestinal disorders, neuropathic pain, autism, breast cancer and neurodegenerative disorders.

Traineeships, honours and PhD projects include:

The therapeutic potential of oxytocin in autism and breast cancer
Molecular probe development to study memory formation
Venom peptide drug discovery
Therapeutic peptide dendrimers
Development of novel and innovative peptide chemistry strategies
Study of bioactive peptides in human breast milk
Therapeutic lead development for the treatment of gastrointestinal disorders

Genetics and Genomics

NGUYEN Group: Disease in single cells and intact tissues

Contact: Dr Quan Nguyen
quan.nguyen@imb.uq.edu.au 07 3346 2611

Nguyen group’s research is focused on understanding cancer complexity at tissue level by applying single-cell sequencing, spatial transcriptomics and tissue imaging, statistical learning and deep learning, and high performance computing. Most molecular biological data are from dissociated cells, which were separated from their original tissues, and thus the spatial information is missing. Furthermore, these data often represent average measurements of millions of cells, which mask subtle differences that are specific for individual cells. From sequencing and imaging data, the group aims to computationally reconstruct biological regulatory networks underlying human diseases in every single cell within an intact tissue. The group develops both experimental and analytical methods to integrate genomics and imaging data for earlier and more accurate diagnosis and prognosis of diseases in tissue biopsies. Particularly, the group focuses on cancer (brain and skin cancer) and neuronal inflammation responses. Through advancing the understanding of biomarkers and cellular regulatory networks that are specific to individuals and cell types, the group contributes to early disease diagnosis, targeted drug discovery and precision medicine.

Traineeships, honours and PhD projects include:

Analyse spatial transcriptomics data of brain and skin cancer tissue to find cell-cell interactions, cell-type specific responses and cancer microenvironment evolution
Develop experimental approaches to study spatial transcriptomics of human cancer cells in brain cancer xenograft models
Develop experimental approaches to study formalin-fixed tissue sections for human skin cancer tissue sections
Develop analysis methods to combine sequencing and imaging data from spatial transcriptomics experiments of skin cancer tissue sections
Develop analysis methods to combine spatial transcriptomics, immuno-fluorescence images and histopathological images
Find single cell gene regulatory networks in healthy and diseased cells from single cell and spatial datasets of human skin cancer samples

Dr Cheong Xin Chan, NGUYEN Group: Genomics and evolution of coral reef symbionts

Contact: Dr CX Chan
c.chan@imb.uq.edu.au 07 3346 2617

Our group uses advanced bioinformatic approaches to study genome evolution of microbes, and to explore and develop highly scalable phylogenomic approaches. A core theme is the genome sequencing of Symbiodinium, a specialised group of dinoflagellate algae that grow symbiotically with diverse coral reef animals including corals and sponges. These algae are critical primary producers in the oceans, and contribute to the survival of coral reefs. We are interested in the genome evolution of these algae and their closely related polar species, specifically related to their evolutionary transition from free-living to symbiotic lifestyles, and its functional implications for the coral host and health of the coral reefs in light of global climate change. Our research routinely involves de novo assembly and analysis of next-generation sequencing data, and high performance-computing.

Traineeships, honours and PhD projects include:

Discovery of gene functions critical to coral-algae symbiosis
Microbial genome evolution and environmental adaptation
De novo genomics of non-model organisms
Bioinformatics and development of scalable phylogenomic approaches

MONTGOMERY Group: Genetics and genomics in health and disease

Contact: Prof Grant Montgomery
g.montgomery@imb.uq.edu.au 07 3346 2612

We use genetic approaches to discover critical genes and pathways increasing risk for complex diseases (including endometriosis, inflammatory bowel disease, and melanoma). Follow-up genomic studies aim to understand how these genetic differences regulate gene expression and epigenetics to alter disease risk. A major focus is women’s health and the pathogenesis of endometriosis. We have identified genomic regions strongly associated with increased endometriosis risk and are analysing gene expression and methylation patterns in the endometrium to understand how these genetic variants contribute to increased disease risk. Endometriosis is associated with other reproductive traits and diseases including ovarian cancer and we also study the mechanisms of shared genetic risk.

Traineeships, honours and PhD projects include:

Analysis of genomic regions associated with endometriosis risk and other diseases.
Integrating omic data to identify target genes for endometriosis.
Visualisation of multi-omic datasets projects

VISSCHER Group: Causes and consequences of human trait variation

Contact: Prof Peter Visscher
peter.visscher@uq.edu.au 07 3346 6348

Virtually all human traits that vary between individuals have unknown genetic and non-genetic factors that contribute to the observed variation – they are called ‘complex traits’. We discover specific factors that explain individual differences between people across a wide range of complex traits; such as risk to common disease, anthropomorphic traits such as height, genomic traits such as gene expression and gene methylation. The team is interested in quantifying and dissecting trait variation in the population into genetic and non-genetic factors, and in identifying specific gene variants that contribute to genetic variation. We use large datasets and sophisticated statistical models to address fundamental questions about genetic variation in the human population and to predict individual complex trait phenotypes using genetic and genomic data.

Traineeships, honours and PhD projects include:

Quantification of pleiotropy for complex traits in the human genome
Estimation of genetic variation from whole genome sequence data
Developing better genetic and phenotypic predictors for common diseases and quantitative traits using advanced statistical methods

Dr Loic Yengo, VISSCHER Group: Statistical Methods for Complex Traits Genetics

Contact: Dr Loic Yengo
l.yengodimbou@uq.edu.au 07 3346 2095

Genome-wide association studies (GWAS) now stand as a well-established experimental design to identify gene variants associated with complex traits and diseases. Findings from GWAS can be used to predict as yet unobserved phenotypes from DNA samples or to refine our understanding of the underlying biology connecting the genome to trait variation. Our team develops and applies scalable statistical models to address these questions. Our research strategy involves statistical modelling, extensive computer simulations and analysis of large genomic datasets in human populations.

Traineeships, honours and PhD projects include:

Quantifying loss of information in heterogeneous genome-wide association studies (Ga)
Quantifying DNA motifs in flanking sequences of GWAS-hits and eQTL
Quantifying transferability of findings from genome-wide association studies across ethnic groups

Dr Kath Kemper, VISSCHER Group: Maximising genomic predictions in biobank-style data

Contact: Dr Kath Kemper
k.kemper@imb.uq.edu.au

Complex traits in humans, such as height and body mass index, are influenced by environmental and genetic factors. Genetic factors affecting a trait can be further subdivided into genetic factors shared between or within families, and population-level genetic information. To date, genomic analyses have primarily focused on population-level genetic information. The aim of this PhD project is to utilise and combine all possible sources of information to increase the accuracy of genomic predictions for complex traits in biobank-style data. The applicant will work on large datasets such as the UK Biobank which, in the near future, will have whole genome sequence information on approximately 500K individuals and extensive phenotypes.

WRAY Group: Quantitative genomics of common disorders of the brain

Contact: Prof Naomi Wray
n.wray@imb.uq.edu.au 07 3346 6374

The last five years have seen unprecedented advances in our understanding of the genetics of complex common disorders of the brain. Given the clinical complexity of these disorders, perhaps it is not surprising that the empirical data are revealing complex genetic heterogeneity and a genetic architecture of hundreds of genetic variants of small effect. We combine in-house genetic and ‘omic data with publicly available data sets to further understanding of the etiology of disorders of the brain. We use quantitative genetic modelling to add objective evaluation of empirical data – for example, we recently quantified the likely contribution of de novo mutations, to the association between paternal age and psychiatric disorder.

Traineeships, honours and PhD projects include:

Genomics of neurological disorders, particularly motor neurone disease and Parkinson’s disease
Genomics of psychiatric disorders, particularly autism spectrum disorders and major depression
Quantitative genetic modelling of disease – using theory to understand empirical data

Dr Zeng, VISSCHER Group: Statistical methods for risk prediction of common diseases

Contact: Dr Jian Zeng
j.zeng@uq.edu.au 07 3346 2685

Polygenic risk predictors based on a large number of genetic variants can identify a subgroup of individuals at high risk of developing a common disease, such as coronary artery disease, type 2 diabetes, or breast cancer. This risk stratification will greatly facilitate precision medicine through opportunities for early disease diagnosis, prevention and intervention. The overall aim of our team is to develop and implement optimised statistical methods and software to best predict an individual’s disease risk through the use of genetic and non-genetic data. Data available for the analysis include large-scale genetic data from genome-wide association studies, whole-genome sequence data, molecular quantitative phenotypes across tissues and cell types, functional annotations on genomic regions, and longitudinal health conditions and lifestyle phenotypes from biobanks.

Traineeships, honours and PhD projects include:

Develop a powerful whole-genome prediction model using summary statistics from large-scale GWAS with imputed or whole-genome sequence variants.
Enhance methodology by incorporating functional genomic annotations.
Develop a multivariate method to integrate multi-dimensional GWAS data for common diseases and molecular phenotypes.
Incorporate both genetic and environmental risk factors into the prediction model.