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PhD projects list
| Biomedical Imaging | Structural Biology and Chemistry | Imaging Technology Development and Engineering | Polymer Chemistry |
Please note that the availability of these projects are subject to funding. If you would like to discuss another project, please contact the Postgraduate Administrator.
Biomedical Imaging
Responsible Scientist Dr Gary Cowin gary.cowin@cai.uq.edu.au
1. Determination of liver fat and fibrosis by MR methods
2. Development of localizations methods of prostate cancer by MR
3. Assessment of ADC estimates by clinical MRI systems
4. Development and optimization of contrast enhanced imaging for magnetic resonance microscopy.
Responsible Scientist Dr Nyoman Kurniawan nyoman.kurniawan@cai.uq.edu.au
1. Studies of human neurological diseases in mouse animal models
2. Method developments in high-magnetic field diffusion imaging and image processing

Mouse cerebellum fibertracks video
Responsible Scientist Dr Katie McMahon Katie.MacMahon@cai.uq.edu.au
1. Diffusion imaging in spine: In collaboration with the physiotherapy department, looking at the diffusion in normal and damaged lumbar and/or neck muscles. This project would suit people with physiotherapy or MR backgrounds.
2. Functional brain imaging of language: Investigating the various information processing models of language production and comprehension, using functional magnetic resonance imaging. There are several projects being undertaken in this field, in collaboration with psychology and/or Language Neuroscience Laboratory. This type of project would suit people with backgrounds in speech therapy, psychology, language, or imaging.
3. Functional brain imaging of episodic and semantic memory: Looking at various aspects of recall and memory encoding effects with functional magnetic resonance imaging. Projects within this field would suit people from a psychology or imaging background.
4. Neuroimaging of genetics: Using various structural and functional MR images of identical and fraternal twins, plus their siblings, we are investigating the heritability of brain structures and task-related activity. This is in collaboration with QIMR and UCLA, and would suit people with any of the following backgrounds: psychology, anatomy, medical imaging, or genetics.
5. Neurorehabilitation and plasticity in aphasia patients: In conjunction with the language neuroscience laboratory, we investigate the brain mechanisms underlying language disorders and their recovery and treatment using a combination of structural, diffusion and functional imaging.
Responsible Scientist A/Prof Stephen Rose stephen.rose@cai.uq.edu.au
1. Generation of new cortical atlases based on functional connectivity information acquired using MR diffusion tractography.
2. Investigating the relationship between white matter lesion (WML) load, cortical atrophy and aging.
3. Development of novel methods to quantitatively measure white matter injury and endogenous reorganisation / recovery mechanisms associated with stroke and hypoxic injury in neonates.
4. Development of novel MRI markers of early treatment response in patients with brain tumours.
5. Investigating novel fMRI and MR diffusion tractography technology to improve neurosurgical planning for patients with brain tumours.
6. Development of novel segmentation and cortical mantle extraction techniques for the neonate brain.
Responsible Scientist Dr Andrew Janke andrew.janke@cai.uq.edu.au
Structural Biology and Chemistry
Responsible Scientist Prof Ian Brereton ian.brereton@cai.uq.edu.au
Biological Inorganic Chemistry
Responsible Scientist: Prof. Graeme Hanson Graeme.Hanson@cai.uq.edu.au
Metalloenzymes are ubiquitous in nature containing complex metal ion cofactors intimately involved in the enzymes biological function. We are employing multifrequency continuous wave and orientation selective pulsed EPR in conjunction with computer simulation (XSophe, Molecular Sophe and iResonanz) and density functional theory to elucidate the geometric and electronic structure of these metal ion cofactors in the resting enzyme, enzyme-substrate and product complexes, which in turn provides a detailed understanding of the enzymes catalytic mechanism.
In collaboration with scientists in the School of Chemistry (Assoc. Prof. Lawrence Gahan) and Molecular Biosciences (UQ) and the University of Heidelberg, Germany (Prof. Peter Comba) we are employing multifrequency continuous wave and orientation selective pulsed EPR in conjunction with computer simulation (XSophe, Molecular Sophe and iResonanz) and density functional theory to characterise the geometric and electronic structures of dinuclear copper(II) cyclic peptide complexes. We have recently shown that a synthetic analogue (H4L4) of ascidiacyclamide with four methylimidazole donor groups and four isopropyl substituents in an (S)-configuration hydrolyses CO2 to form CO32- which may be biologically relevant in the native marine cyclic peptides (patellamides A-D, ascidiacyclamide) found in ascidians on the Great Barrier Reef and offers insights into the sequestration of CO2.
We are extending these studies to other cyclic peptides in order to gain an understanding of the important structural moieties required for hydrolysis. The projects will involve (i) spectroscopic (UV-vis, CD, infrared, EPR) and mass spectrometry to characterise the mono and dinuclear copper(II) complexes, (ii) computational chemistry calculations using the spectroscopic constraints to determine the geometric and electronic structures of these dinuclear centres, (iii) development of methodology for quantitating the formation of carbonate and subsequently determining the kinetics of CO2 hydrolysis by these dinuclear copper(II) cyclic peptide complexes and (iv) the use of multiple imaging modalities to probe whether CO2 fixation is biologically relevant to the ascidians.
There is an option for a talented student to undertake a dual PhD degree between the University of Queensland the University of Heidelberg. This will involve the student spending ~50% of their time in Heidelberg, for which funding will be available.
Required Skills: Expertise in biological inorganic chemistry, marine chemistry, EPR spectroscopy and DFT calculations would be beneficial.
Metallohydrolases
Dinuclear metallohydrolases that include Ser/Thr protein phosphatases, organophosphate-degrading triesterases, ureases, arginases, aminopeptidases and antibiotics-degrading metallo-β-lactamases. Due to their widespread metabolic functions several of these enzymes have become targets for the development of chemotherapeutic agents, or are used as bioremediators.
Project 2: Purple Acid Phosphatase Metalloenzymes
Purple acid phosphatases (PAPs) belong to the family of Specifically, PAP activity in animals has been shown to be directly linked to bone resorption; overexpression of this enzyme by bone-resorbing osteoclasts leads to osteoporosis. Consequently, PAP has become a major target in the development of anti-osteoporotic drugs.
The currently accepted paradigm is that the purple acid phosphatases (PAPs) require a heterovalent, dinuclear metal ion centre for catalysis. It is believed that this is an essential feature for these enzymes in order for them to operate under acidic conditions. A PAP from sweet potato is unusual in that it appears to have a specific requirement for manganese, forming a unique FeIII-µ-(O)-MnII centre under catalytically optimal conditions (Schenk et al., Proc. Natl. Acad. Sci. USA, 2005, 102, 273). Detailed EPR spectroscopic and kinetic studies of this enzyme have shown that the chromophoric FeIII can be replaced by MnII, forming a catalytically active, unprecedented antiferromagnetically coupled homodivalent MnII-μ-(H)OH-µ-carboxylato-MnII centre in a PAP. However, while the enzyme is still active, it no longer functions as an acid phosphatase, having optimal activity at neutral pH (Hanson, et al. J. Amer. Chem. Soc., 2009, 131, 8173-8179.) provides the basis for the full interpretation of the EPR spectra from other dinuclear Mn metalloenzymes.
Projects in collaboration with Assoc. Profs. Lawrence Gahan and Gary Schenk (School of Chemistry and Molecular Biosciences) and Prof. Peter Comba (University of Heidelberg) involve:
- applying high resolution pulsed EPR spectroscopy and isotope substitution to gain further catalytic insights into the mechanism of PAP's,
- applying multifrequency EPR, ENDOR and computer simulation to characterise the dinuclear Mn centres in a range of other hydrolases of interest to the group.
- applying multifrequency EPR, ENDOR and computer simulation to characterise transition metal ion complexes which mimic PAP's and provide insights into enzymes catalytic mechanism.
There is an option for a talented student to undertake a dual PhD degree between the University of Queensland the University of Heidelberg. This will involve the student spending ~50% of their time in Heidelberg, for which funding will be available.
Required Skills: Expertise in bioinorganic chemistry, EPR spectroscopy and DFT calculations would be beneficial.
Project 3: Alpha lactalbumin
Responsible Scientist: Prof. Graeme Hanson Graeme.Hanson@cai.uq.edu.au
Alpha lactalbumin and a modified form (HAMLET) has been shown to kill cancer cells, though the mechanism is as yet unknown. In conjunction with Prof. Lawrence Berliner (University of Denver) we will undertake the characterisation of the metal binding sites in this metalloenzyme utilizing multifrequency continuous wave and pulsed EPR.
Required Skills: Expertise in bioinorganic chemistry, EPR spectroscopy and DFT calculations would be beneficial.
Project 4: Melanin
Responsible Scientists: Prof. Graeme Hanson Graeme.Hanson@cai.uq.edu.au and Prof. Paul Meredith (School of Mathematics and Physics) meredith@physics.uq.edu.au
The melanins are responsible for multiple critical functions in humans such as photo-protection and free-radical-scavenging. They are also found in the substantia nigra of the human brain stem where their exact biological role is unkown, but is has been speculated that beuromelanin maybe involved in neural transmission, and melanin photo-toxicity is implicated in deadly melanoma skin cancer. Despite decades of intense studies across biology, chemistry and physics, the full details of the structure and functions of the melanins are still not clearly understood. Two physical properties of melanin have particularly intrigued physicists and chemists for decades: i) melanins are electrical and photo-conductors in the solid state; and ii) melanins are black with broad featureless optical absorption and near unity non-radiative conversion of absorbed photon energy. In the solid state melanin contains radicals (termed extrinsic) arising from incomplete polymerisation, while in solution semiquinone radicals (termed extrinsic) are present.
We are currently employing EPR spectroscopy to examine the origin of the electrical and photo-conductivity of melanin at neutral pH in the solid state as a function of hydration and have shown that they arise from the presence of extrinsic spins. The project, a continuation of current hydration dependent studies, extends the current research to examine the properties and spectroscopic signatures as a function of pH and utilize pulsed EPR, ENDOR and ELDOR methods to characterise the intrinsic and extrinsic spins in melanin. In addition these results will be correlated with conductivity, photoconductivity and muon spectroscopy.
Electron Spin Quantum Computing and Magnetic Materials
Responsible Scientists: Prof. Graeme Hanson Graeme.Hanson@cai.uq.edu.au and Dr. Aaron Micallef aaron.micallef@cai.uq.edu.au
The organisation of open-shell molecular building blocks to give structurally well-defined solid state materials is crucial in the physical implementation of both Electron-Spin Quantum Computing (ES-QC) and Molecular Magnetic Materials (MMMs). In both ES-QC and MMMs the relative physical arrangement of the spin carrying units in the solid state material is crucial. The connectivity, distance between, and relative geometry of different spin centres, both within molecules and between molecules, controls the ensuing spin-spin exchange interactions. Materials for ES-QC and MMM lie at opposite extremes of the continuum of exchange interactions.
In ES-QC, weak (but non-zero) exchange interactions within isolated multi-spin molecules are essential. In contrast, for MMM strong co-operative exchange interactions between large numbers of spin carriers are required. We are exploiting Halogen Bond directed self-assembly, co-crystallisation, and crystal engineering strategies to organise stable Nitroxide Radicals in structurally well-defined solid state (single crystal) materials for both ES-QC and molecular magnetism. Projects in collaboration with Prof. Takui (Osaka University) involve:
- chemical synthesis,
- geometric and electronic structural characterisation using X-ray crystallography, continuous wave and pulsed EPR spectroscopy,
- magnetic susceptibility measurements and
- quantum computing applications.
Required Skills: Expertise in organic and inorganic chemistry, EPR spectroscopy, quantum computing and DFT calculations would be beneficial.
Chemiluminesence
Responsible Scientists: Prof. Graeme Hanson Graeme.Hanson@cai.uq.edu.au and Prof Neil Barnett (Deakin University) neil.barnett@deakin.edu.au
Chemically and electrochemically generated luminescence of the tris(2,2'-bipyridyl)ruthenium(II) complex ([Ru(bipy)3]2+) has been exploited for a diverse range of medically and industrially significant applications including immunodiagnostics, DNA probe assays, detection of biological agents for homeland defense, illicit drug screening, and monitoring opiate alkaloids during the pharmaceutical production-scale extraction process. Despite this, current understanding of the chemical functionalities required by a substrate to elicit quantitative light emission from [Ru(bipy)3]2+ has largely evolved from empirical observations made throughout the historic and continued use of the title reagent in detection science. Another phenomenon that has garnered considerable attention and is inextricably linked to the selectivity of [Ru(bipy)3]2+ luminescence is the quenching of emission observed when the reaction is conducted in the presence of certain compounds, most notably, those bearing (poly)phenolic functionality.
We are employing EPR spectroscopy to structurally characterise the reactive radical intermediates formed during the chemiluminescent reactions which also provides insights into why some substrates can quench the luminescence.
Required Skills: Expertise in analytical chemistry, EPR spectroscopy and DFT calculations would be beneficial.
Imaging Informatics
Responsible Scientist: Prof. Graeme Hanson Graeme.Hanson@cai.uq.edu.au
EPR Spectroscopy
Project: Spectroscopic, Structural (Geometric and Electronic) and Image Analysis - iResonanz
Spectral simulation has evolved over the years from simple spin systems (XSophe) to simulations including the full molecular structure (Molecular Sophe). These software tools employ perturbation theory and matrix diagonalization together with EPR computational techniques to generate the spectra for which interpretation of the spin Hamiltonian parameters can give the scientist structural clues to the paramagnetic species being studied. These spin Hamiltonian parameters can also be reproduced using quantum chemistry techniques including crystal field theory, ligand field theory and density functional theory but to name a few and correlated with those from EPR computational spectroscopy to enhance the interpretation.
iResonanz, a distributed quantum system simulation environment incorporates a new paradigm for the analysis of spin Hamiltonian parameters from EPR (continuous wave and orientation selective pulsed EPR and ENDOR) spectra of metal ion cofactors in metalloenzymes and the determination of their geometric and electronic structure using computational chemistry. The combination of these multiple computational processes in a single environment can only be achieved through the careful integration of their data, computation and communication requirements. The efficient exploitation of these integrated systems required a new work flow approach (shown opposite) by computational steering of these integrated components (Explorer, Navigator and Viewer all accessing a central database) towards elucidation of the electronic and geometric structure of paramagnetic centres. The navigation phase of this steering loop employs an advanced distributed network of tiered clients and servers to conduct the computations, yet the Navigator application is still the gateway in this steering process for the simulation phase. The Explorer provides a graphical user interface (generated dynamically from the database at run time) for the implementation of the quantum model data sets and the analysis is performed by the Viewer graphical user interface to permit the analysis of real time data interactively. These three major applications are the core of the iResonanz system together with the database.
Projects offered to computer science, applied mathematics students or physics students involve:
- the continued development of iResonanz,
- the extension of iResonanz to enable MRI and PET image analysis, both visually and computationally
- the extension of iResonanz to enable the inclusion of molecular dynamics and the simulation of motionally averaged nitroxide spectra (in collaboration with Dr. Vasiliy Oganesyan (UK) and
- development of an EPR structural database. This will involve collaborations with Assoc. Prof. Brian Bennett (Medical College of Wisconsin, USA), Prof. Peter Comba (University of Heidelberg, Germany) and Dr. Vasiliy Oganesyan (UK)
There is an option for a talented student to undertake a dual PhD degree between the University of Queensland the University of Heidelberg. This will involve the student spending ~50% of their time in Heidelberg, for which funding will be available.
Required Skills: A working knowledge of C++, MySQL databases, grid computing and Linux. An understanding of EPR spectroscopy and image analysis would be an advantage, but is not necessary.
Imaging Technology Development and Engineering
Responsible Scientist Dr Viktor Vegh viktor.vegh@cai.uq.edu.au
1. Low field magnetic resonance imaging – the research and development of low cost / low field imaging methodologies
2. Radio Frequency coils for high resolution imaging – the research and development of MRI radio frequency coils for object specific imaging
3. Optimisation based image enhancement – to research and develop methods such as topology optimisation for improved delineation of imaged objects
Polymer Chemistry
POLYMER HYDROGELS
Project 1: Novel Tri-Block Co-Polymers for Controlled Release of Proteins for Osteogenesis
Responsible Scientist Dr Firas Rasoul : f.rasoul@uq.edu.au
The aim of this project is to produce a biodegradable controlled drug / protein release material for tissue engineering applications. Gene sequences, angiogenic and osteogenic factors are finding regular application in the clinical setting, however their efficacy is highly dependent on the correct dose that is delivered. Most delivery systems, particularly those based on hydrogels, rely on Fickian diffusion, which doesn’t mimic the profile required by the body to initiate wound healing. Non-hydrogel delivery systems, such as PLGA microspheres, require the growth factors to be loaded from an organic solvent which inherently denature the protein. The basis of this project is to synthesise a triblock copolymer that is predominantly a hydrogel-like material, with interlinking hydrophobic groups that can encapsulate and release the growth factor. The hydrophilic region enables aqueous growth factor loading is also important for controlling degradation rate, swelling, growth factor loading and biological response. The hydrophobic segments encapsulate the protein and enable release profiles that follow the degradation rate instead of the diffusion rate. This project will involve polymer synthesis and characterisation using IR, NMR, SEM and mechanical testing.
POLYMERS FOR TISSUE ENGINEERING
Project 2: Bio-polymer Beads for Drug Delivery
Responsible Scientist Dr Firas Rasoul : f.rasoul@uq.edu.au
This project aims at synthesis and characterisation of biopolymers (a flexible polymeric template) specifically targeting the delivery of drugs with poor bioavailability. This polymeric template will be made from a water soluble hyper-branched nano beads having several reactive sites that can be functionalised with different polymeric chains. The objective of this project is to use combination of polymerisation techniques (for example ATRP and the newly developed Click-Chemistry) to initiate polymerisation with controlled architecture and hydrophilicity. These newly developed nono-beads with unique features can be used for delivering multi-drug systems. Project in this area would involve
polymer synthesis and characterisation using techniques such as FT-IR, NMR and GPC. The developed polymer will be tested for drug delivery.
Project 3: Surface Grafting of Bio-Compatible Polymers
Responsible Scientists Dr Idriss Blakey i.blakey@uq.edu.au, Dr Firas Rasoul f.rasoul@uq.edu.au and Prof Andrew Whittaker a.whittaker@uq.edu.au
Although many bulk commodity plastics are relatively cheap and have good mechanical properties, often they perform poorly when placed in contact with biological media. For example, proteins will denature on the surface of many commodity plastics, which is often undesirable. Recently, we have developed a number of methods for the modification of commodity plastics such as polyolefins and fluoropolymers. The objective of this project is to modify the surface of commodity plastics using these techniques to generate bio-compatible surfaces, which will find applications such as, membranes for protein separation or non-adsorbing surfaces for protein and other biomolecules packaging. The project would involve preparation of grafted surfaces using a variety of conditions such as radiation grafting and surface re-initiation. Several analytical and spectroscopic techniques will be used to characterise and evaluate the grafted surfaces including XPS, FTIR, SEM and protein adhesion assays.
Project 4: Water-born Biodegradable Polyurethane foam for biomedical applications
Responsible Scientist Dr Firas Rasoul : f.rasoul@uq.edu.au
Biodegradable polyurethane elastomers are expected to be suited for any application requiring the use of a flexible elastic material such as soft-porous tissue engineering scaffolds for skin grafting and vasculature. Biodegradable polyurethane (PU) is generally achieved by incorporating labile moieties susceptible to hydrolysis in the polymer chain (soft segment). The most common method of introducing these hydrolysable linkages into polyurethanes has been to utilize hydrolysable soft segments such as PCL or PLA into the backbone. The other component of the polyurethane is the hard segment which can be either aromatic or aliphatic diisocyanates. Aromatic diisocyanates are known to produce toxic degradable by-product. In this project we will utilize aliphatic diisocyanates based on L-lysine which will provide a route to synthesising biodegradable polyurethanes that are expected to yield only non-toxic degradation by-products. The main aim of this project is to develop novel water-crosslinkable biodegradable polyurethane for applications as porous tissue scaffold. The project will involve the use of polycondensation polymerization to synthesise a small library of biodegradable PU with range of mechanical properties and degradation rates. Advanced characterization techniques will be used in this project which includes NMR, FTIR, Differential scanning calorimetry (DSC), SEM and mechanical analysis (tensile strength and modulus of elasticity).
Project 5: Hybrid Biomaterials for Osseointegration
Responsible Scientists Dr Firas Rasoul f.rasoul@uq.edu.au, Dr Imelda Keen i.keen@cai.uq.edu.au and Prof Andrew Whittaker a.whittaker@uq.edu.au
This project aims to develop a range of novel biomaterials which can be delivered and cured in situ, are highly biocompatible and have the potential to promote osseointegration. The materials will be designed to give low shrinkage on polymerisation, to ensure effective bonding to the matrix. The approach adopted in this project will lead to a biodegradable hybrid organic/inorganic biomaterials. The
presence of an inorganic silicate core will impart superior mechanical properties and likely to promote strong interactions with inorganic material deposited by the body. The materials will have many applications as load- and non-load-bearing materials, for example in repair of bone defects, as tissue scaffolds and as drug delivery biomaterial. The project will involve the synthesis and characterization of biodegradable polymers using different polymerization techniques such as ring-opening polymerization and control free radical polymerization. Modern characterization techniques will be used in this project which includes NMR, FTIR, Differential scanning calorimetry (DSC), and mechanical analysis (tensile strength and modulus of elasticity).
POLYMER DEVICES
Project 6: Polymer Stabilised Nanoparticle Devices for Bio-sensing Applications
Responsible Scientist Dr Idriss Blakey i.blakey@uq.edu.au
Noble metal nanoparticles such as gold nanoparticles have a range of interesting optical properties, which make them useful in the field of in vitro diagnostics. However, on their own they lack physiochemical stability and functionality. In this project a range polymer-stabilised nanoparticles will be prepared. The polymer will serve to stabilise the gold nanoparticles and also contain functionality for bio-sensing and bio-recognition. The project will involve polymer synthesis, polymer-nanoparticle self assembly and advanced characterisation.
Project 7: Thermo-responsive Polymers for Biomedical Applications
Responsible Scientists Dr Idriss Blakey i.blakey@uq.edu.au and Dr Kris Thurecht k.thurecht@uq.edu.au
Thermo-responsive polymers have a change in solubility as a result of a temperature change. These types of polymers have applications in drug delivery devices. In this project a range of polymers will be synthesised where the composition is varied to tune the point at which the change is solubility occurs. These polymers will be assembled into polymer micelles and the thermoresponsive properties will be studied with a range of advanced characterisation techniques.
Project 8: Hyperbranched polymers for drug delivery and medical imaging.
Responsible Scientists Dr Idriss Blakey i.blakey@uq.edu.au and Dr Kris Thurecht k.thurecht@uq.edu.au
Hyperbranched polymers are a class of dendritic macromolecules that have received increased attention due to their favourable structural properties. In general, hyperbranched polymers are simple to synthesise by a range of polymerisation techniques and thus have the ability to present a wide range of chemical functionalities. As a result, hyperbranched polymers have found application in areas ranging from biomedicine to catalytic supports to process modifiers in polymer engineering. In this project, hyperbranched polymers formed via controlled free-radical polymerization will be investigated. By incorporating various functionalities into the polymer, it can be assessed in terms of hydrolytic degradation, duel hydrophilicity and its applicability as a contrast agent for magnetic resonance imaging (MRI). A range of interesting chemistries will be utilized in the polymer synthesis (including RAFT, ATRP and click chemistry) in addition to characterization by various advanced techniques (NMR, MRI, GPC, electron microscopy, thermal analysis and vibrational spectroscopy).
Project 9: 19F MRI imaging agents for cancer detection
Responsible Scientists Dr Hui Peng h.peng@uq.edu.au; Dr Kris Thurecht k.thurecht@uq.edu.au and Prof Andrew Whittaker a.whittaker@uq.edu.au
Early detection of cancer cells leads to a dramatic improvement in treatment outcomes. World-wide there is enormous interest in developing new, more sensitive and selective methods for early detection, and for delineation of tumour volumes. We have recently developed several platforms for in vivo imaging based on partially-fluorinated copolymers and hyperbranched copolymers. These perform extremely well in animal models, and have been shown that they can be directed to cancer cells if labelled with appropriate ligands. In this project a series of optimised partially-fluorinated agents will be prepared and conjugated to targetting agents for prostate, skin, breast and brain cancer. Animal models are available for all of these cancers. The project will entail training in advanced synthesis and characterisation, in MRI and in small animal MRI. This project will also potentially involve development of multi-mode agents for sequential or simultaneous MRI-PET-optical imaging.
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