Potential MBBS Research Projects:
Honours, MPhil, PhD
Students with a ‘genuine interest’ in any of the following projects or areas of
research are encouraged to enquire by email to the contact person listed and
discuss possible project opportunities
NEW Projects Update #34: September 2014
Please also see individual websites:

Queensland Institute For Medical Research (QIMR) Projects here

Diamantina Institute List of Student Projects below and HERE

Burns, Trauma and Critical Care Research Centre Research projects & opportunities

Centre for Advanced Imaging (CAI) List of projects and research areas HERE

Discipline Of General Practice

QCPRRC: Cerebral Palsy & Rehabilitation Research Centre
o
List of projects for Honours, MPhil or PhD

Faculty Of Health Sciences Research

Queensland Brain Institute (QBI)

UQ Centre for Clinical Research (CCR)

Paediatrics & Child Health Research Opportunities

Centre For Longitudinal and Life-course Research SPH Student Projects

Sunshine Coast Clinical School (SCCS) Projects here

Queensland Children's Medical Research Institute
o Projects: Children's Burns & Trauma Research

Queensland Centre for Intellectual and Developmental Disability

Environment and Population Health Projects HERE

Rural Clinical School Research Centre RCSRC Projects

Centre for Youth Substance Abuse: Centre for Youth Substance Abuse
1
RESEARCH AREA
or TOPIC
CONTACT PERSON -
Oral peptide drug delivery in inflammatory bowel
disease
Jakob Begun
NAME
CONTACT
jakob.begun@mater.uq.edu.au
EMAIL / PHONE
Background: Inflammatory bowel disease(IBD) is a chronic inflammatory condition affecting the
gastrointestinal tract of children and adults due to an inappropriate immune response to resident gut
bacteria. Medical treatment has progressed significantly through a better understanding of the
mechanism of disease, resulting in a better quality of life for many patients, but there remains a need
for more effective and targeted therapy. IL-22 has emerged as an important cytokine produced by
macrophages and type-3 innate lymphoid cells during colonic inflammation. In mice, overexpression
of IL-22 in the colon reduces the level of inflammation. Oral delivery of peptides is challenging due to
the numerous proteases and harsh environment of the gut but nanoparticles have emerged as a
novel mode of delivery that may allow delivery of anti-inflammatory cytokines to sites of gut
inflammation. This project focuses on developing orally available IL-22 and testing its efficacy in a
murine model of colitis.
Project description: Using a stable cell line expressing an IL-22 reporter recombinant IL-22 bound to
a variety of nanoparticles provided by collaborators will be tested for receptor activity. Particles with
optimal stimulation properties will be further tested in epithelial cell lines and activation of
endogenous IL-22 examined using quantitative RT-PCR. Optimal IL-22 coated nanoparticles will then
be used in a chemically induced murine colitis model as well as a spontaneous colitis model to
examine the effect on gut inflammation. In addition to assessing histologic inflammation, RT-PCR will
be utilized to interrogate pro- and anti-inflammatory pathways as well as oxidative stress pathways.
Suitable for: Students pursuing a PhD project with knowledge of molecular biology and basic
immunology.
Type of Research: Wet lab.
2
RESEARCH AREA /
TOPIC
Specialist Pain Physician
Persistent Pain Service, Division of Rehabilitation
CONTACT PERSON -
Dr Aston Wan
NAME
CONTACT EMAIL /
aston.wan@health.qld.gov.au
PHONE
Possible B.Med Sci Projects at MSH Persistent Pain Management Service
1. The effects of culture and socioeconomic difference on the presentation of Chronic
Pain.
2. An audit of the effectiveness of interventional pain procedure.
3. Culture difficulties and socioeconomic factors contributing to the effectiveness of pain
intervention
4. Predictors of outcomes of chronic pain management.
5. Prevalence of Somatoform disorders in chronic pain patients
6. Functional outcome of mindfulness meditation and Acceptance Commitment therapy
7. Role of physiotherapist in Somatoform disorders.
8. Patient satisfaction in MSH Persistent Pain Management Service.
9. Pain Rehabilitation program – what are patient’s expectation / what do patients find
acceptable.
10. Do multiple cancellations affect patient outcomes?
Dr Aston Wan MBBCh MA GDMM MClEpid MPainMed MHeadacheMed PCertMedEd
FFPMANZCA
Director and Specialist Pain Physician
Persistent Pain Service, Division of Rehabilitation
Princess Alexandra Hospital
199 Ipswich Rd, Woolloongabba, Queensland, Australia, 4102
Ph:+61 7 3176 1901 l Fax:+61 7 3176 3969 l
Metro South Health Persistent Pain Management Clinic
Level 3, Network House, 57 Sanders Street, Upper Mount Gravatt,
Queensland, Australia 4122
Ph:+61 3339 5500
Email: aston.wan@health.qld.gov.au
3
RESEARCH AREA /
Cardiac Imaging (Cardiology/Radiology)
TOPIC
CONTACT PERSON -
A/Prof Christian Hamilton-Craig
NAME
CONTACT EMAIL /
PHONE
c.hamiltoncraig@uq.edu.au / chamiltoncraig@gmail.com
3139 5226 or 0411 111 980
New Projects as of September 2014
- Comparison Of Sensitivity And Specificity Of "Reference Centre" Versus "Community" Based
Coronary Ct Angiography Compared To Invasive Xray Angiography (Medical Student / Honours)
- Six Year Follow Up And Outcome Of Cardiac Magnetic Resonance Imaging Detected Left
Ventricular Trabeculation Without Non-Compaction In Dilated Cardiomyopathy (Medical Student /
Honours)
Impact Of Cardiac MRI Results On Management Of Patients Referred To An Advanced
Heart Failure Unit: Improvements In Diagnosis And Management
- Takotsubo Cardiomyopathy By Cardiac MRI - Use Of SSFP Feature Tracking Post-Processing
(Honours/Masters Student)
- Comparison Of Tissue Tagging Versus SSFP Feature Tracking By Cardiac Magnetic
Resonance (MRT / Masters / PhD Student)
Intra-Operative TransOesophageal Echocardiography during Cardiac Valves Surgery with 2D
and 3Dimensionl imaging; comparison between Expert and Novice Readers (Medical Student)
A/Prof. Christian Hamilton-Craig
MBBS, PhD, BMedSci(Hons), FRACP, FCSANZ, FSCCT
Staff Cardiologist, Prince Charles Hospital
Associate Professor, School of Medicine & Centre for Advanced Imaging, UQ
Affiliate Associate Professor of Radiology, University of Washington, Seattle USA
Chair, Society of Cardiovascular CT (ANZ), Vice-President ANZCMR
4
A state wide matched case-control study of bilateral sensorineural
hearing loss in Queensland’s premature infant population between 2007
and 2011: Aetiological factors and screening
(Diagnosis and description of preterm infants with hearing loss detected under
newborn hearing screening)
Introduction: All babies born in Queensland are screened for hearing loss soon after birth
through the Queensland Healthy Hearing, Newborn Hearing Screening Program
(Queensland Health). Hear and Say, a program helping children with hearing loss to learn to
listen and speak, will work in partnership with Professor David Tudehope to conduct a case
control study examining specific aetiological factors for pre-term infants diagnosed with a
permanent hearing loss. This study includes a focussed literature review which has helped
define the aims and objectives of this project, and ensures the study is novel and does not
duplicate already published work. The study has, in 2013-2014 been designed and initiated
by a current MBBS 3-4 Honours student from University of Queensland.
Applications are called for a volunteer MBBS Year 2 student in 2014, with a view to the
successful student continuing on to an Honours program in 2015 and collaborating with the
more senior student to complete data gathering, analysis and write-up. The Year 2 student
will assist with an ongoing literature review to cover any relevant new literature on this topic,
determine current research and identify knowledge gaps. This will be followed by the use of
a data extraction tool to complete a retrospective chart review of cases and matched
controls to determine contributing factors to the hearing loss and its outcomes and any coexisting features of this population. There are a number of different opportunities for
publications emanating from this study.
Aims & Objectives: To gain information on the diagnostic process and aetiology and to
describe the co-existing features of the population of infants diagnosed with hearing loss
through universal newborn hearing screening in Queensland. The outcomes of this study will
be used to inform government and decision makers. This study will also develop the Hear
and Say Foundation for future outcomes research which will enhance the diagnosis,
treatment and counselling for these infants and their parents.
Study Outcomes and Significance:
This study will make a significant contribution to the knowledge of outcomes for preterm
infants with hearing loss. It will be a world-first study in this area.
The selection process will favour students with good writing skills, previous
publications, prior experience with data extraction or chart reviews. Please apply in
writing including your curriculum vitae to:
Adjunct Associate Professor Dimity Dornan dimity@hearandsaycentre.com.au
5
RESEARCH AREA or
Professional Identity, Intergroup Dynamics and Communication in
TOPIC
Health
CONTACT PERSON -
A/Pro David Hewett, Dr Bernadette Watson and Lori Leach
NAME
CONTACT
d.hewett@uq.edu.au
EMAIL / PHONE
bernadette@uq.edu.au
l.leach@uq.edu.au
Research Team:
David G Hewett (in collaboration with Bernadette M Watson and Lori E Leach)
Brief synopsis of our research area:
Our research team specialises in research that combines the viewpoints and
expertise of medical and social science researchers. Our research includes the
examination of intergroup dynamics, the nature of communication in health care, and
their effects on quality of health care delivery and patient safety. Uniquely, our team
investigates communication and its effects through a social psychological lens. We
invoke social identity theory and communication accommodation theory as the
frameworks from which to explore professional identity and communication in health
care. We are currently finalising the design of a number of small studies we will
conduct over the next 36 months.
Title of current project:
Towards better healthcare: The impact of intergroup communication on patient safety.
Duration of the project: Three years
Positions open for volunteer experience (from one month to six weeks), Honours,
Mphil and PhD
For those interested in a taster of research experience with out team, as a volunteer
you would assist in the preparation of aspects of studies conducted under our
broader research domain. You would gain observer experience in one or more of the
research team’s activities. These activities would include participation in research
design and study implementation, preparation of ethics applications and literature
reviews. Active participation in these activities would be apportioned to the volunteer
in line with the successful applicant’s current experience and skill level. For those
interested in a higher level of engagement, research higher degree students
(including Honour’s students) would take on more responsibility and potentially
design a study of their own within the broader research project at a level appropriate
to each academic level.
Prerequisite skills: Nil.
6
RESEARCH AREA / TOPIC
Doctors’ Health
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
Discipline of General Practice, School of Medicine
CONTACT PERSON
Dr Margaret Kay
EMAIL / PHONE
m.kay1@uq.edu.au
Title: What do patients and carers expect from GPs at the end of life?
Description of the project:
This project seeks to investigate the experience of compassion satisfaction / fatigue in
general practice including general practitioners, practice nurses and/or administration staff.
Type of involvement:
The project is suitable for an honours project or can be expanded for an RHD student. It is
also possible to participate in this project as an extra-curricular experience e.g. summer
scholar.
Supervisors:
Dr Margaret Kay, Discipline of General Practice, School of Medicine, The University of
Queensland.
Student profile:
Summer Scholar, Hons Student, RHD Student
More information:
If you are interested in research projects at the Discipline of General Practice, please refer to
our website: www.som.uq.edu.au/about/academic-disciplines/general-practice.aspx
7
RESEARCH AREA / TOPIC
Multi-Morbidity
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
Discipline of General Practice, School of Medicine
CONTACT PERSON
Dr Margo Lane
EMAIL / PHONE
m.lane5@uq.edu.au
Title: The Evaluation of a Pilot Multi-Disciplinary Student–run Health Promotion Program at
the Workplace of Adults with Intellectual Disability (Health and Wellbeing Project).
Brief Description:
This project will be piloted later this year and will need a formal evaluation. Students from
four health disciplines (Medicine, Psychology, Dietetics, Exercise Physiology) will prepare
and present information to adults with intellectual disability at their workplace.
We will collect pre- and post-activity data from students and participants.
We hope to explore student issues including teamwork, knowledge, skills and attitudes
towards adults with ID, as well as health literacy and self-efficacy for adults with ID.
We are also investigating the feasibility and benefits of brief health promotion interventions in
the supported workplace.
Type of involvement:
The project is suitable for an Honours Student Project
Supervisors:
Dr Margo Lane, Discipline of General Practice, School of Medicine, The University of
Queensland
Student profile:
Honours Medical Student
More information:
If you are interested in research projects at the Discipline of General Practice, please refer to
our website: www.som.uq.edu.au/about/academic-disciplines/general-practice.aspx
8
RESEARCH AREA / TOPIC
Immunology-Human Kidney Research
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
Queensland Institute of Medical Research
CONTACT PERSON
Dr Andrew Kassianos
EMAIL / PHONE
Andrew.kassianos@qimr.edu.au / 38453036
Chronic kidney disease (CKD) is the most prevalent chronic disease in Australia. It has been
estimated that more than 1.4 million Australians have CKD and these metrics are
deteriorating rather than improving, emphasising that our current understanding of the
pathogenesis of CKD has not produced effective therapeutic strategies.
Tubulointerstitial fibrosis, the hallmark of CKD, is always preceded by inflammation.
However, current therapeutics for CKD do not target this inflammatory process. This is due
to our poor understanding of the role of inflammatory immune cells in the development of
progressive CKD.
Our research group has been studying the role of specific epithelial cells in the kidney and
how these cells contribute to the disease process and maintain tissue homeostasis at the
early stages of disease. We have published novel findings that these cells are able to
modulate autologous immune responses at the level of T lymphocytes/B lymphocytes and
dendritic cells (Wilkinson et al, NDT, 2011; Kassianos et al, NDT, 2013). We are now
expanding these unique clinical findings to investigate the role of dendritic cells and
lymphocytes in the disease process. We have developed novel methods to dissociate human
disease biopsy tissue and characterise immune-cell subtypes within early and late stage
CKD. Using this methodology we have recently described, for the first time in humans, a role
for dendritic cells in driving tubulointerstitial fibrosis and thus CKD (Kassianos et al, AJP –
Renal Phys, 2013).
Opportunities exist for Honours and PhD projects to extend these studies, including:
 An investigation into the recruitment and retention of inflammatory and pathogenic
immune cells within the kidney interstitium.
 The identification, enumeration and characterisation of lymphocyte subsets (T cells, B
cells, NK, NK-T) within human disease kidney tissue.
 The role of immune cells in clinical transplantation rejection.
These projects are innovative as our group was the first to describe that human kidney
epithelial cells modulate autologous immune responses and we are currently the world
leaders in this field. Furthermore, these projects are conducted in human disease systems in
a strategy to accelerate translation of our results into clinical testing.
These projects will provide students with exposure to many relevant and broad laboratory
techniques, including flow cytometry, immunohistochemistry, molecular biology, western
blotting and cell culture.
9
RESEARCH AREA / TOPIC
Epidemiology/Gastroenterology
CENTRE/INSTITUTE/SCHOOL
School of Population Health
CONTACT PERSON
A/Prof Jolieke van der Pols
EMAIL
j.vanderpols@uq.edu.au
Life-style related risk factors for sessile serrated adenoma
Sessile serrated adenomas are a newly discovered type of bowel polyps that may progress to
colorectal cancer. These polyps were previously grouped with hyperplastic polyps and
thought to be harmless. However, in recent years is has been recognised that sessile serrated
adenomas can progress to cancer through the ‘serrated pathway’.
Much progress has been made in the understanding of how these polyps are clinically and
molecularly different from the more common adenomatous polyps. However, knowledge of
the epidemiology and risk factors for sessile serrated adenomas is still very limited. This is
due to the fact that these lesions have only recently become recognised and recorded
clinically, thus few people have had an opportunity to study these cancer-precursors.
To establish the risk factors for sessile serrated adenoma we are currently carrying out a
case-control study together with a team of gastroenterologists and clinical researchers who
are world-leaders in research of sessile serrated adenoma biology and polyp detection at the
Royal Brisbane and Women’s Hospital, The Prince Charles Hospital and UQ School of
Medicine. This study focusses particularly on lifestyle-related risk factors including smoking,
alcohol intake, physical activity, dietary and other factors. We are recruiting patients who have
been diagnosed with sessile serrated adenoma during colonoscopy and compare these with
patients with conventional adenoma and persons without bowel polyps.
Research opportunities for MBBS students:
There are several possible topics for a systematic literature review linked to this research
project (depending on your interests and experience), which would be very suitable for an
Honours project. Students located outside Brisbane are also invited to apply. Data analysis
may also become available. Applications for MPhil projects will also be considered and topics
can be tailored to your specific interests. Please contact us if you are interested to discuss
further details.
10
RESEARCH AREA
Orthopaedics and Sports Medicine
or TOPIC
CONTACT PERSON -
Dr. Manit Arora
NAME
CONTACT
Manit_arora@hotmail.com
EMAIL / PHONE
Multiple review projects to be lead by undergraduate medical students with a keen interest in
orthopaedics and sports medicine. Optional lab component in affiliation with the university.
Projects available for review:
1. review the literature on which nutritional supplements are best for which hip fractures and
develop a protocol to guide surgeons and geriatricians
2. review the role of various BMPs in the fracture healing process. Can include a lab
component through co-operation with major teaching hospital
3. Review literature on SLAP tears and develop a treatment algorithm based on current
classification system
4. Review literature on chance fractures in TL spine and develop a treatment algorithm
based on the current classification system
11
UQ Diamantina Institute – Student Research Projects
http://www.di.uq.edu.au/research-projects
Cancer
Name
Professor Ian
Frazer
Project Details



Associate
Professor Brian
Gabrielli



Dr Graham
Leggatt



Contact
Regulation of effector T cells by the innate
immune response
Immunotherapy for virus associated skin
cancer
Cervical cancer control in Vanuatu
Phone
+61 7 3443 7715
Email
emma.lee@tri.edu.au
Identifying the molecular basis for defective
checkpoints in melanoma.
Targeting defective cell cycle responses to
ultraviolet radiation and TopoII inhibitors in
melanoma.
Defining the molecular changes in moles
underpinning morphological changes
detectable by non-invasive imaging
techniques to improve their diagnostic and
prognostic ability for early stage melanoma.
Trafficking of T cells to cancerous skin
Immunotherapy of skin tumours after
lymphodepletion
T cell function in normal and cancerous skin
tissue
Phone
+61 7 3443 7092
Email
briang@uq.edu.au
Phone
+61 7 3443 6961
Email
g.leggatt@uq.edu.au
Dr Angus
Harding

Combining computer models and clinical
data to understand, treat and prevent brain
cancer
Phone
+61 7 3443 6926
Email
a.harding1@uq.edu.au
Dr Michelle Hill

Cancer microvesicles as a source of
biomarkers and novel target of anti-cancer
therapy
Systems biology approach to understand
lipid raft and caveolin function in health and
disease
Discovery and validation of novel salivary
and blood biomarkers for head and neck
cancers using lectin magnetic bead arraymass spectrometry, LeMBA-MS (with Dr
Chamindie Punyadeera)
NPM functions associated with acute
myeloid leukemia (with Dr Kerry Inder)
Understanding the molecular basis for the
control of squamous differentiation
Understanding how these processes are
dysregulated during the development of oral
and skin cancers
Exploiting this knowledge in the
development of novel treatments for skin
cancers and oral cancer
Interrogating chemotherapeutic sensitivity
Phone
+61 7 3443 7049
Email
m.hill2@uq.edu.au



Associate
Professor
Nicholas
Saunders




Phone
+ 61 7 344 37091
Email
nsaunders@uq.edu.au
12

Identifying novel strategies to treat
metastatic osteosarcoma
Dr Fiona
Simpson



Improving patient responses to Cetuximab.
Improving patient responses to Herceptin.
The role of Girdin in breast cancer metstasis
Phone
+61 7 3443 6930
Email
f.simpson@uq.edu.au
Dr James Wells

Immunotherapy for the treatment of
established skin cancer
Requirements for the initiation and treatment
of Non-Melanoma skin cancer
Immunophenotyping squamous skin cancer
Investigating the cytokine microenvironment
of squamous cell carcinoma and its
precursor lesions
Uncovering CD8 T-cell control mechanisms
in the skin
Exploring the interaction between
osteosarcoma tumour cells and lung cells to
identify the mechanisms that preferentially
drive tumour cells from the bone to the lung.
Investigation of the interaction between
highly- and poorly-metastatic clonal variants
of osteosarcoma with osteoclasts.
Tumour-secreted exosomes are emerging
mediators of tumourigenesis and
metastasis. This project will initially isolate
and characterise exosomes from metastatic
and non-metastatic OS tumour cells
Antibody-drug conjugates in therapy against
blood cancers.
The effect of chronic stress on immune
surveillance and immunotherapy of cancer.
Immunosuppressive myeloid cell
populations induced by B cell lymphomas.
NKT cell and Toll-like receptor-driven
therapeutic vaccination against blood
cancers.
The cancer biology of chromosome
instability in a transgenic mouse model
Identification of signal transduction
pathways that cause chromosome instability
Transcriptional regulation of cell cycle genes
Development of strategies to specifically
target cancer cells with abnormal
chromosome numbers
Phone
+61 7 3443 6983
Email
j.wells3@uq.edu.au
Targeting the actin cytoskeleton as a
strategy for melanoma therapy.
Disarming Tumor Escape Mechanisms in
Human Melanoma With Epigenetic Modifiers
Real-time cell cycle imaging of melanoma
cells in vitro and in vivo.
Defining the role of Microphthalmiaassociated Transcription Factor (MITF) in
melanoma growth by real-time cell cycle
imaging.
Phone




Dr Liliana Munoz



Dr Stephen
Mattarollo




Dr Pascal Duijf




Associate.
Professor
Nikolas Haass




Phone
+61 (0)7 3443 6929
Email
l.munoz@uq.edu.au
Phone:
+61 7 3443 6985
Email
s.mattarollo@uq.edu.au
Phone
+61 (0)7 3443 6937
Email
p.duijf@uq.edu.au
+61 (0)7 3443 7087
Email
n.haass1@uq.edu.au
13

Associate
Professor
Kiarash
Khosrotehrani




Dr Rehan Villani

Dr Linda Scott



Understanding the role of the underlying
dermis in the genesis and progression of
basal cell carcinoma
Study of epidermal clonal progression
towards cancer.
Tumour heterogeneity towards metastasis.
To understand differences between basal
cell carcinoma subtypes at the genomic,
transcriptomic and proteomic level
Investigating the parallels between hair
follicle and tumour niche in skin cancer
development
Phone
+61 7 3443 7088 (UQDI)
+61 7 3346 6077 (UQCCR)
Email
k.khosrotehrani@uq.edu.au
Molecular pathogenesis and clonal
evolution of the myeloproliferative
neoplasms
Role of dysregulated JAK/STAT signalling in
hematologic malignancies
Epigenetic regulation in normal
hematopoietic stem cells and their malignant
equivalents
Molecular basis of leukemogenesis
Phone
+61 7 3443 7093
Email
l.scott3@uq.edu.au
Email
r.villani@uq.edu.au
Autoimmunity
Name
Dr Antje
Blumenthal
Project Details



Dr Emma
HamiltonWilliams




Dr Tony
Kenna



Dr Ray
Steptoe





Dr Gethin
Thomas


Innate immune recognition of Mycobacterium
tuberculosis and other pathogens
Molecular mechanisms of macrophage
functions
Regulators of immune responses during
infection and inflammation
Discovery of novel anti-microbials
A novel role for the interleukin-2 pathway in
humans and mouse models of type 1
diabetes
Genetic control of intestinal microflora in type
1 diabetes susceptibility
Impaired Regulatory T cell function in type 1
diabetes
Transcriptional regulation of inflammation in
autoinflammatory diseases
Intestinal inflammation in ankylosing
spondylitis
Innate inflammatory pathways in ankylosing
spondylitis.
Cellular and molecular pathways of T-cell
tolerance
Prevention and reversal of autoimmune
diabetes
Novel methods of gene delivery for tolerance
Immunotherapy of allergies and anaphylaxis
Exploring T-cell tolerance in B cell
malignancies
Gene expression profiling in ankylosing
spondylitis
Identification of novel genes in skeletal
disease through large-scale ENU mouse
Contact
Phone
+61 3443 6984
Email
a.blumenthal@uq.edu.au
Phone
+61 7 3443 6989
Email
e.hamiltonwilliams@uq.edu.au
Phone
+61 7 3443 7073
Email
t.kenna@uq.edu.au
Phone
+61 7 3443 6959
Email
r.steptoe@uq.edu.au
Phone
+61 7 3443 7048
Email
14
mutagenesis
Novel treatment approaches to prevent joint
fusion in ankylosing spondylitis
Mechanisms underlying genetic associations
in ankylosing spondylitis
Understanding the molecular control of
dendritic cell function in tolerance
Initiation of inflammatory arthritis
Rheumatoid arthritis antigen-specific therapy
Type 1 (Juvenile) Diabetes Innate Immunity:
mouse models and human longitudinal study
Use of statins to reduce atherosclerosis in
early rheumatoid arthritis
Development of ERAP M1 Aminopeptidase
inhibitors as a novel class of therapeutics for
treatment of Immune-mediated diseases
such as Ankylosing Spondylitis (AS),
Psoriasis, Inflammatory Bowel disease (IBD).
Protein expression and functional studies of
ERAP M1 aminopeptidases in Ankylosing
Spondylitis (AS), Psoriasis and Inflammatory
Bowel disease (IBD).
Wanted Alive not Dead: Isolation and
analyses of “new” human gut bacteria
Bacterial mousetraps: the role of serpins in
gut bacteria


Professor
Ranjeny
Thomas





Dr Nitish
Agrawal


Professor
Mark
Morrison


gethin.thomas@uq.edu.au
Phone
+61 7 3443 6960
Email
ranjeny.thomas@uq.edu.au
Phone
+61 (0)7 3443 7074
Email
n.agrawal1@uq.edu.au
Phone
+61 (0)7 3443 6957
Email
m.morrison1@uq.edu.au
Genomic Medicine
Professor
David Evans





Professor Matt
Brown







Next generation sequencing and genome-wide
association studies
Genetics of common complex traits and diseases
Genetics of osteoporosis, eczema and ankylosing
spondylitis
Using genetics to test whether environmental risk
factors cause disease
Development of statistical methods for disease gene
mapping
Genetics of common bone and joint diseases
Osteoporosis
Interethnic mapping of common human diseases;
ankylosing spondylitis, rheumatoid arthritis,
schizophrenia
ENU mutagenesis and models of musculoskeletal
diseases
Gene deserts involved in ankylosing spondylitis
Genetics of multiple sclerosis
Novel gene-mapping approaches using nextgeneration sequencing
Phone
+61 7 3443 7051
Email
d.evans1@uq.edu.au
Phone
+61 7 3443 7018
Email
di.director@uq.edu.au
15
RESEARCH AREA / TOPIC
Cancer Epigenetics
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
QIMR Berghofer Medical Research Institute
CONTACT PERSON
Jason S Lee, Eva Baxter and Frank Gannon
EMAIL / PHONE
Jason.Lee@qimrberghofer.edu.au
Project title: Defining the components of the complexes involved in the cyclical
processes that result in gene expression
Type of student: Honours/Ph.D
Prerequisite skills: Mammalian culture and some molecular biology techniques (Western
blotting, PCR etc) would be very useful.
Type of research: Wet lab
Drs Jason S Lee, Eva Baxter and Professor Frank Gannon
Introduction
Activation of the estrogen-responsive gene pS2 has demonstrated a requirement for cyclical
changes in the DNA methylation of promoter CpGs. The proteins mediating DNA methylation
have been discovered, however the identification of DNA demethylases in humans has
remained problematic. The recent discovery that DNA methyl groups can be oxidised to
hydroxymethyl groups by the TET family of proteins raises a possible mechanism whereby
the transcriptionally repressive methyl mark can effectively be removed from promoters. We
have demonstrated that DNA methylation and demethylation (Kangaspeska et al., Nature
452, 2008) occurs in a transient cyclical manner. However, detailed relationship between
epigenetic state, recruitment of the estrogen receptor and the RNA polymerase and initiation
of transcription has yet to be investigated.
Hypothesis
Epigenetic modifications are important in the expression of estrogen receptor target genes.
Aims
To determine the crosstalk between epigenetic modifications and gene expression by
estrogen receptor.
To identify the factors responsible for mediating the epigenetic modifications.
Approaches
1. Protein complex purification of the estrogen receptor at target genes
2. DNA methylation analysis by bisulphite sequencing
3. Target validation by Chromatin Immunoprecipitation assays.
4. Gene expression analysis
References
Kangaspeska, S., Stride, B., Métivier, R., Polycarpou-Schwarz, M., Ibberson, D.,
Carmouche, R.P., Benes, V., Gannon, F. & Reid, G. (2008) Transient cyclical methylation of
promoter DNA. Nature 452(7183): 112-115.
Métivier R, Gallais R, Tiffoche C, Le Péron C, Jurkowska RZ, Carmouche RP, Ibberson D,
Barath P, Demay F, Reid G, Benes V, Jeltsch A, Gannon F & Salbert G. (2008) Cyclical DNA
methylation of a transcriptionally active promoter. Nature 452, 45-50
http://www.qimr.edu.au/page/Students/University_students/Projects/Control_of_Gene_Expression_student_projects/
16
RESEARCH AREA / TOPIC
Cancer Epigenetics
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
QIMR Berghofer Medical Research Institute
CONTACT PERSON
Jason S Lee and Frank Gannon
EMAIL / PHONE
Jason.Lee@qimrberghofer.edu.au
Project title: Identification of new epigenetic modification targets in breast cancer
Type of student: Honours/Ph.D
Prerequisite skills: Mammalian culture and some molecular biology techniques (Western
blotting, PCR etc) would be very useful.
Type of research: Wet lab
Drs Jason S Lee, Eva Baxter and Professor Frank Gannon
Introduction
Chromatin remodeling is by the so called “histone-code” involving various covalent
modification of the histones such as acetylation, phosphorylation and methylation has been
subject to many studies and their importance is now very well accepted. However, the
transcriptional state can also be regulated by several chromatin-associated protein
complexes that are either involved in enhancing or fine-tuning of the promoter activity and, of
course some of these respond to the altered contexts that arise from the histone, and DNA
modifications. In this project we will focus on novel aspects of the histone methylation status
and related “off-target” activities of the enzymes involved and their consequences in cellular
physiology.
Hypothesis
Epigenetic modifying enzymes play an important role in regulating breast cancer metastasis
through non-histone targets.
Aim
To discover novel targets of the epigenetic modifiers in by integrating proteomic and high
throughput sequencing techniques.
Approaches
1. Cellular models and treatments
2. Characterisation of the KMT and the KDM change
3. Promoter methylation analysis
4. Protein complex purification and proteomics
5. Immunoprecipitation assays
6. Characterisation of putative methylation target proteins
References
Lee et. al., EZH2-Generates a Methyl Degron that is Recognized by the DCAF1/DDB1/
CUL4 E3 Ubiquitin Ligase Complex. Molecular Cell, 48, 572–586, 2012.
Lee et. al., Negative Regulation of Hypoxia Response by Induced Reptin Methylation.
Molecular Cell. 39, 71-85, 2010.
http://www.qimr.edu.au/page/Students/University_students/Projects/Control_of_Gene_Expression_student_projects/
17
RESEARCH AREA / TOPIC
Cancer Epigenetics
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
QIMR Berghofer Medical Research Institute
CONTACT PERSON
Jason S Lee and Frank Gannon
EMAIL / PHONE
Jason.Lee@qimrberghofer.edu.au
Project title: Elucidation of new epigenetic modifier targets in stem cell differentiation
Type of student: Honours/Ph.D
Prerequisite skills: Mammalian culture and some molecular biology techniques (Western
blotting, PCR etc) would be very useful.
Type of research: Wet lab
Drs Jason S Lee, Eva Baxter and Professor Frank Gannon
Introduction
Embryonic stem cells (ESCs) are pluripotent, self-renewing cells that are derived from the
inner cell mass (ICM) of the developing blastocyst. Transcription factors (TFs), such as Oct4,
Sox2, KLF4 and Nanog (ESC TFs) are critical for establishing and maintaining pluripotent
cell identity by collaborating with each other to activate a substantial fraction of the actively
transcribed protein-coding and miRNA genes in ESCs. We are particularly interested in
expanding our novel description of physiologically relevant consequences of “histone”
modifying enzymes on non-histone targets. We will also utilise our Histone-like protein
database as previously used to determine potential modification sites on key non histone
proteins. Discovery of molecular mechanisms that control ESC pluripotency and self-renewal
are important as they are key to understanding development. Because defects in
development cause many different diseases, improved understanding of control mechanisms
in pluripotent cells may lead to new therapies for these diseases.
Hypothesis
Based on the functional importance of these ESC transcription factors in regulating gene
expression, we hypothesise that the transcriptional activity of ESC TFs are altered by
posttranslational modifications resulting in changes in ESC gene expression program, and
ultimately affect pluripotency and their ability to self-renew.
Aim
Determine whether ESC TFs are modified by several classes of epigenetic modifiers.
Approaches
1. Protein complex purification and proteomics.
2. Generation of genetically modified cell lines.
3. Functional consequences of ESC pluripotency and self-renewal.
4. Transcriptome and ChIP sequencing analysis.
References
Loh et. al., The Oct4 and Nanog transcription network regulates pluripotency in mouse
embryonic stem cells. Nat Genetics 38, 431-440, 2006.
Chen et. al., Integration of external signaling pathways with the core transcriptional network
in embryonic stem cells. Cell 133, 1106-1117, 2008.
http://www.qimr.edu.au/page/Students/University_students/Projects/Control_of_Gene_Expression_student_projects/
18
RESEARCH AREA / TOPIC
Cancer Epigenetics
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
QIMR Berghofer Medical Research Institute
CONTACT PERSON
Jason S Lee and Frank Gannon
EMAIL / PHONE
Jason.Lee@qimrberghofer.edu.au
Project title: Defining the role of epigenetic modifiers in metastatic prostate cancer
Type of student: Honours/Ph.D
Prerequisite skills: Mammalian culture and some molecular biology techniques (Western
blotting, PCR etc) would be very useful.
Type of research: Wet lab
Drs Jason S Lee, Eva Baxter and Professor Frank Gannon
Introduction
Chromatin remodeling is by the so called “histone-code” involving various covalent
modification of the histones such as acetylation, phosphorylation and methylation has been
subject to many studies and their importance is now very well accepted. However, the
transcriptional state can also be regulated by several chromatin-associated protein
complexes that are either involved in enhancing or fine-tuning of the promoter activity and, of
course some of these respond to the altered contexts that arise from the histone, and DNA
modifications. In this project we will focus on protein complexes involved prostate metastasis
and their consequences in cellular physiology.
Hypothesis
Epigenetic modifying enzymes play an important role in regulating metastatic potential of
prostate cancers through complexing with other proteins.
Aim
To discover novel targets of the epigenetic modifiers in by integrating proteomic and high
throughput sequencing techniques.
Approaches
1. Cellular models and treatments
2. Characterisation of the KMT and the KDM change
3. Promoter methylation analysis
4. Protein complex purification and proteomics
5. Immunoprecipitation assays
6. Characterisation of putative methylation target proteins
References
Lee et. al., EZH2-Generates a Methyl Degron that is Recognized by the DCAF1/DDB1/
CUL4 E3 Ubiquitin Ligase Complex. Molecular Cell, 48, 572–586, 2012.
Lee et. al., Negative Regulation of Hypoxia Response by Induced Reptin Methylation.
Molecular Cell. 39, 71-85, 2010.
http://www.qimr.edu.au/page/Students/University_students/Projects/Control_of_Gene_Expression_student_projects/
19
RESEARCH AREA / TOPIC
Infectious Diseases
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
QIMR Berghofer
CONTACT PERSON
Denise Doolan
EMAIL / PHONE
Denise.Doolan@qimrberghofer.edu.au / 3362 0382
Rational vaccine development from genomic sequence information – mining genomic,
proteomic and transcriptomic datasets for next generation malaria vaccine development
Vaccines are one of the most effective health care interventions for infectious diseases but are still
not available for many important public health threats despite decades of research. Malaria is a
priority target but conventional approaches to anti-malaria vaccine development, focused on a very
limited number of antigens, have thus far failed. During the past decade, the genome, proteome and
transcriptome of the Plasmodium parasite, the causative agent of malaria, have been defined. These
datasets provide a unique foundation for a new approach to vaccine development but it has not been
obvious how to identify the important protective antigens from genomic-based information. Beginning
with the full set of open reading frames encoded in the Plasmodium parasite genome, we are
pursuing a rational approach to vaccine design for infectious diseases caused by complex
pathogens, using malaria as a model. We are taking advantage of recent advances in genomic
sequencing, proteomics, transcriptional profiling, bioinformatics, and molecular immunology to
choose from the complete set of Plasmodium proteins those most likely to be effective as vaccine
targets. A key aspect of our strategy is functional significance as assessed by the capacity of the
antigen to be recognized by immune responses in protective human models. We have generated
unique datasets of proteome-wide T cell responses and antibody responses to Plasmodium.
The focus of this project will be to further characterize these antigens for potential as vaccine
candidates by assessing immunogenicity, protective capacity and biological function. In addition to
identifying and prioritizing novel antigens for next generation vaccine development, we are integrating
these genomic-based datasets to develop metrics associated with protection which can be extended
to other complex pathogens for which vaccines are urgently needed. These datasets also provide a
unique opportunity to further our understanding of host-parasite relationships and associated
phenomenon such as immunodominance. This project is expected to result in significance advances
in vaccinology as well as immunology, with important public health outcomes.
Applicants must possess a BSc Hons, MSc., MBBS or equivalent with laboratory-based
experience in immunology, genomics/proteomics or infectious diseases. Excellent computer,
communication, and organisational skills are required. Forward thinking, innovation and
creativity are encouraged.
http://www.qimr.edu.au/page/Lab/Mol_Vaccinology/
20
RESEARCH AREA / TOPIC
Infectious Diseases
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
QIMR Berghofer
CONTACT PERSON
Denise Doolan
EMAIL / PHONE
Denise.Doolan@qimrberghofer.edu.au / 3362 0382
Dissecting the molecular basis of protective immunity to malaria using interdisciplinary
approaches
Malaria remains a leading public health threat with approximately 40% of the world’s population at
risk. The Plasmodium spp. parasite which causes malaria has a complex life cycle and has coevolved with the human host over thousands of years. Protective immunity against malaria can be
induced in experimental systems by immunization with the intact parasite, suggesting that a malaria
vaccine is feasible. However the development of an effective vaccine has been hindered by the
complexities of the parasite and the host, and by our poor understanding of the mechanisms of
protective immunity. Animals or humans exposed to Plasmodium typically develop a multi-faceted
immune response including antibodies and CD8+ and CD4+ T cell components directed against
multiple antigens, but little is known about the fine specificities of protective immunity and how to
induce the correct specificities by vaccination.
To address this, we are investigating the molecular basis of immunity to malaria, taking advantage of
well established rodent models of lethal and non-lethal malaria, a unique controlled humanexperimental blood-stage infection system, and cross-sectional and longitudinal field studies in
malaria-endemic areas. In the rodent models, we employ gene deficient and transgenic mice,
including cytokine- and cell-deficient lines, reporter lines, and transgenic lines that allow depletion of
specific cellular subsets of interest. We have access to state-of-the-art flow cytometry, microscopy
and immunohistochemistry facilities as well as cutting-edge molecular based technologies including
protein microarrays, gene expression platforms, high throughput sequencing, and bioinformatics. A
specific interest is in the field of systems immunology, which differs from reductionist approaches that
analyse isolated components of the immune system, by studying the integration of the various
components using high throughput molecular techniques combined with mathematical and
computational tools.
The focus of this project will be to employ cutting-edge molecular technologies to define the critical
cells and signalling pathways required for long-term protective immunity against malaria, with an
emphasis on the interface between innate and adaptive immunity.
Applicants must possess a BSc Hons, MSc., MBBS or equivalent with laboratory-based
experience in immunology, genomics/proteomics or infectious diseases. Excellent computer,
communication, and organisational skills are required. Forward thinking, innovation and
creativity are encouraged.
http://www.qimr.edu.au/page/Lab/Mol_Vaccinology/
21
RESEARCH AREA / TOPIC
e.g. Cancer/Immunity/Primary Care
Infectious Diseases
CENTRE/INSTITUTE/SCHOOL
QIMR Berghofer
CONTACT PERSON
Christian Engwerda
EMAIL / PHONE
chrisE@qimr.edu.au
Immunology and Infection laboratory, QIMR Berghofer





We study host immune responses during malaria and leishmaniasis, two deadly parasitic
infections.
We seek Honours and PhD students.
An interest in infectious diseases and immunology is required.
Successful candidates will learn flow cytometry, microscopy and various immune assays.
Please see http://www.qimr.edu.au/page/Lab/Immunology_Infection/ for more information.
1. Investigating the influence of the gut microbiome on the outcome of malaria and leishmania.
Commensal organisms (including bacteria, fungi, viruses, protozoa and archaea) occur in distinct
niches within tissue microenvironments throughout the body. They develop an intimate relationship
with their host and play an important role in metabolism, tissue development and maintenance, as
well as host defence. Although the liver is not colonised by commensals, the functions of hepatic
immune cells is likely to be impacted by exposure to microbial ligands and metabolites from the gut
microbiome. Both malaria and leishmaniasis stimulate potent immune responses in the liver that can
determine the outcome of infection. We aim to examine the influence of the gut microbiome on
hepatic immune responses during malaria and leishmania.
2. Characterising the roles of innate lymphoid cells during malaria and leishmania.
Innate lymphoid cells are emerging as critical players in early immune responses to infection. They
play an important role in maintaining gut epithelial cell barrier integrity, regulating the intestinal
microbiota and defence against gut pathogens. However, little is known about their roles in diseases
caused by systemic infections, such as malaria and leishmania. Several distinct families of innate
lymphoid cells have been identified, based on the expression of certain cell surface molecules and
their pattern of cytokine production. We aim to characterise the behaviour of innate lymphoid cells
during malaria and leishmania, and establish their roles in anti-parasitic immunity and disease
pathogenesis.
3. Identifying epigenetic changes that regulate cytokine production by parasite-specific CD4+ T cells
during malaria and leishmania.
CD4+ T cells are critical for the control of many intracellular pathogens, including those that cause
malaria and leishmania. The pattern of cytokines produced by parasite-specific CD4+ T cells during
infection determines whether immunity is established or disease develops. This pattern is influenced
by the early interactions between CD4+ T cells and dendritic cells during parasite antigen
presentation, and in particular, the local cytokine milieu. A major mechanism for switching on and off
cytokine production in cells is via epigenetic modification of gene promoters. We will characterise
changes in the promoters of key cytokine genes in antigen-specific CD4+ T cells during malaria and
leishmania under various conditions and at different times during disease.
22
RESEARCH AREA / TOPIC
Adolescent substance use and misuse
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
Centre for Youth Substance Abuse Research
CONTACT PERSON
A/Prof. Adrian Kelly
EMAIL / PHONE
a.kelly@uq.edu.au
A/Prof Kelly has several research projects available in the area of family and school problems, health
risk behaviours (including substance use and misuse, but also adolescent depression, anxiety,
dietary problems, and antisocial behaviour). His work has primarily focused on factors leading to the
escalation of problems related to alcohol use, tobacco use, and other drug use.
Research projects are available to Masters and PhD students.
Some knowledge of widely used statistical packages, such as SPSS or Stata, is desirable. A/Prof.
Kelly will assist students in building a working knowledge of these packages should it be needed.
Secondary datasets are potentially available through our own Centre and through long standing
collaborations with other centres across Australia. The availability of high quality datasets reduces
the risks associated with timely collection of data, and A/Prof Kelly has an excellent track record in
supporting his students right through to publication of research findings in high level journals.
Examples of A/Prof Kelly’s work are available on Research gate:
https://www.researchgate.net/profile/Adrian_Kelly2/
23
RESEARCH AREA / TOPIC
Surgery
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
Princess Alexandra Hospital
CONTACT PERSON
Pallav Shah
EMAIL / PHONE
pallavshah@ozemail.com.au, 0439726871
Title: Understanding the Genes Responsible for the Development of Bicuspid Aortic Valves (BAV)
and Dilated Ascending Aortas.(AAD)
Student type: Honors Student
Prerequsitive Skills: Dedication and Hard work. Interest in surgery
Project Involves:
Background: Aortic valve is a left sided valve, which pumps blood from the heart through the aorta to
the rest of the body. Usually it has three cusps in 99% of the population. Thus it is called a tricuspid
valve. In 1-2% of the individuals, it is bicuspid ( BAV, two leaflets) These patients with bicuspid valve
have increased stress during cardiac cycle and thus develop stenosis and regurgitation earlier then
tricuspid valves. Further more , it has been shown that bicuspid valves are associated with dilated
aorta (AAD, bicuspid aortopathy) BAV together with AAD is a clinical syndrome with poorly
understood aetiology. They present at a young age suggesting strong underlying genetic influence .
These pathologies lead to heart failure and life threathining emergency like aortic dissections..
Aim: Our aims of the project include 1]To identify the presence of rare exonic mutations in patients
with biscuspid aortic valves and aortic aneurysms 2] To evaluate detailed genotype - phenotype
relationships using our extensive clinical and imaging records.
The research plan involves: 1] recruiting subjects with BAV-AAD, ( 12 patients), 2] obtaining clinical
and imaging data (chart review, database review) , 3] performing genetic sequencing , 4] Data
collection and statistical analysis, 5] Literature review, 6 ]involvement in writing a publication
Importance of the project: -Potential for early screending and disease detection, - Potential for early
therapy and prevention of AAD, - Minimize the need for surgery and medical emergencies,- Provide
insights into other congenital heart diseases
Project area:
Clinical: Department of Cardiology and cardiothoracic surgery, Princess Alexandra Hospital
Genetic Sequencing: The University of Queensland (School of Medicine, Centre for Clinical
Genomics, and Diamantina Institute)
24
RESEARCH AREA / TOPIC
ENT / Rhinology
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
RBWH, School of Medicine
CONTACT PERSON
James Earnshaw / Anders Cervin
EMAIL / PHONE
james@EarnshawENT.com.au or a.cervin@uq.edu.au
Predicting outcome in nasal septal surgery (Honours project)
James Earnshaw, Anders Cervin
Nasal blockage is common condition affecting more than 10 % of the population. It disrupts
sleep and as such causes daytime tiredness and can affect quality of life extensively. There
are numerous conditions that can contribute to nasal blockage such as; nasal polyps,
turbinate hypertrophy, allergic and hyper reactive disease, but a major factor is the deviated
nasal septum. Objective measures aimed at measuring airflow through the nose, or the
space within the nasal cavity, are of limited value. As septal surgery is a common procedure
any measures to reduce the number of unnecessary procedures would be of great benefit.
A literature study involving reviewing
Methods to measure nasal airway resistance or space
Clinical techniques to assess the nasal airway
Systemic workup in nasal blockage
The role of BMI in nasal blockage
The aim of the literature review is to create a management algorithm in patients with a
blocked nose not due to chronic sinusitis nor allergy/hyperreactivity
25
RESEARCH AREA / TOPIC
Otolaryngology
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
RBWH
CONTACT PERSON
Prof Anders Cervin
EMAIL / PHONE
a.cervin@uq.edu.au

Title; Quality of life in chronic sinusitis patients referred to a tertiary ENT center.

Type of student? Honours

What type of research? Data analysis, literature review
Quality of life in chronic rhinosinusitis patients is affected by fatigue, blocked nose, sleep
disturbances etc. We have for the last 8 months used a quality of life questionnaire called
SNOT-22 to investigate the influence on daily activities. The honors project aim to analyse
the available data by creating a data base and using descriptive statistics. Furhermore to
compare in the littterature different sinusitis related quality of life instruments. The results will
influence the development of a electronic QoL database for chronic sinusitis patients.
26
Projects in the Conjoint Kidney Research Lab, QIMR-RBWH
Kidney resident cells modulate migratory T/B lymphocytes and dendritic
cells
Supervisors:
Associate Prof. Ray Wilkinson (ray.wilkinson@qimr.edu.au Ph 33620488)
Dr Andrew Kassianos (andrew.kassianos@qimr.edu.au Ph 38453036)
Dr Helen Healy (Helen.healy@health.qld.gov.au Ph 38367568)
Chronic kidney disease (CKD) is the most prevalent chronic disease in Australia. It has been
estimated that more than 1.4 million Australians have CKD and these metrics are deteriorating rather
than improving, emphasising that our current understanding of the pathogenesis of CKD has not
produced effective therapeutic strategies.
Tubulointerstitial fibrosis, the hallmark of CKD, is always preceded by inflammation. However, current
therapeutics for CKD do not target this inflammatory process. This is due to our poor understanding
of the role of inflammatory immune cells in the development of progressive CKD.
Our research group has been studying the role of specific epithelial cells in the kidney and how these
cells contribute to the disease process and maintain tissue homeostasis at the early stages of
disease. We have published novel findings that these cells are able to modulate autologous immune
responses at the level of T lymphocytes/B lymphocytes and dendritic cells (Wilkinson et al, NDT,
2011; Kassianos et al, NDT, 2013). We are now expanding these unique clinical findings to
investigate the role of dendritic cells and lymphocytes in the disease process. We have developed
novel methods to dissociate human disease biopsy tissue and characterise immune-cell subtypes
within early and late stage CKD. Using this methodology we have recently described, for the first time
in humans, a role for dendritic cells in driving tubulointerstitial fibrosis and thus CKD (Kassianos et al,
AJP – Renal Phys, 2013).
Opportunities exist for Honours and PhD projects to extend these studies, including:

An investigation into the recruitment and retention of inflammatory and pathogenic immune
cells within the kidney interstitium.
 The identification, enumeration and characterisation of lymphocyte subsets (T cells, B cells,
NK, NK-T) within human disease kidney tissue.
 The role of immune cells in clinical transplantation rejection.
These projects are innovative as our group was the first to describe that human kidney epithelial cells
modulate autologous immune responses and we are currently the world leaders in this field.
Furthermore, these projects are conducted in human disease systems in a strategy to accelerate
translation of our results into clinical testing.
These projects will provide students with exposure to many relevant and broad laboratory
techniques, including flow cytometry, immunohistochemistry, molecular biology, western blotting and
cell culture.
27
RESEARCH AREA / TOPIC
Respiratory physiology
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
Queensland Children’s Medical Research Institute
CONTACT PERSON
Dr Dean Mills
EMAIL / PHONE
d.mills2@uq.edu.au / 07 3636 5578
Title: Lung function in children with airway malacia measured with the forced oscillation and multiple
breath nitrogen washout techniques.
Background: Patients with airway malacia have softer airways that are an abnormal shape. This
results in greater changes in airway diameter during tidal breathing and causes a dynamic collapse of
the airways during expiration. The current diagnostic techniques for airway malacia are expensive,
invasive and there are issues with anaesthesia, reliability and/or radiation. Alternatives are lacking;
but the forced oscillation (FOT) and/or multiple breath nitrogen washout (MBNW) lung function
techniques are cost-effective, non-invasive methods that are performed during normal breathing. The
FOT provides information on respiratory system impedance; respiratory resistance, an accurate
measure of airway resistance; and respiratory reactance, the elastic and inertial properties of the
respiratory system. MBNW measures ventilation inhomogeneity and the functional residual capacity.
Aim: To compare lung function in children with airway malacia measured using FOT and MBNW to a
population of healthy children.
Methods: Children aged 3-14 years with airway malacia will have height, body mass, FOT and
MBNW measurements undertaken at the respiratory clinic at the Royal Children’s Hospital, Brisbane
on a single visit.
Significance: The incidence of airway malacia in children is 1 in 2100 and it results in significant
expense, morbidity and mortality. Airway malacia clinically presents as wheeze and cough and, as
the symptoms are similar to asthma and other respiratory conditions, unrecognised or misdiagnosed
airway malacia may also increase morbidity and inappropriate diagnoses. This study will, for the first
time, determine whether these non-invasive lung function tests can define the presence of airway
malacia in children and, if successful, they will help with future diagnoses and reduce the likelihood of
inappropriate investigations and treatments.
Type of student: MPhil and Honours.
Prerequisite skills: None.
Type of research: Clinical research involving the recruitment of participants, lung function
measurements and data analyses.
28
RESEARCH AREA / TOPIC
Respiratory physiology
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
Queensland Children’s Medical Research Institute
CONTACT PERSON
Dr Dean Mills
EMAIL / PHONE
d.mills2@uq.edu.au / 07 3636 5578
Title: Breathing and respiratory muscle recruitment patterns in children measured with structured
light plethysmography.
Background: Assessments of breathing and respiratory muscle recruitment patterns are vital for the
investigation of chronic respiratory disease in children. In clinical practice this is undertaken through
visual observation and palpation. For research purposes breathing and respiratory muscle
recruitment patterns need to be quantified. However, the current techniques to do this can impede
normal breathing patterns or are invasive and/or time consuming. Structured light plethysmography is
a novel technique that measures breathing and respiratory muscle recruitment patterns noninvasively and efficiently by projecting a grid of light onto the patient’s chest. This technique,
however, is yet to be used in children.
Aim: To measure breathing and respiratory muscle recruitment patterns in children with structured
light plethysmography.
Methods: Healthy children and those with asthma and cystic fibrosis aged 3-17 years will have
height, body mass and structured light plethysmography measurements undertaken at the respiratory
clinic at the Royal Children’s Hospital, Brisbane on a single visit.
Significance: Assessments of breathing and respiratory muscle recruitment patterns are vital for the
diagnosis of chronic respiratory disease in children. This study will, for the first time, determine
whether structured light plethysmography can determine differences in breathing and respiratory
muscle recruitment patterns between healthy children and those with chronic respiratory disease and,
if successful, the technique will help with future diagnoses.
Type of student: MPhil and Honours.
Prerequisite skills: None.
Type of research: Clinical research involving the recruitment of participants, lung function
measurements and data analyses.
29
RESEARCH AREA / TOPIC
Respiratory physiology
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
Queensland Children’s Medical Research Institute
CONTACT PERSON
Dr Dean Mills
EMAIL / PHONE
d.mills2@uq.edu.au / 07 3636 5578
Title: The effects of Heliox on exercise tolerance in patients with cystic fibrosis.
Background: Cystic fibrosis (CF) is the most common lethal genetic disease in the Caucasian
population. Many patients with CF do not engage in regular physical activity due to breathlessness
and leg discomfort, secondary to respiratory, muscular and cardiovascular limitations. Patients with
chronic obstructive pulmonary disease (COPD) have similar exercise limitations to those with CF.
Previous research has demonstrated that when patients with COPD breathe a mixture of 21%
oxygen and 79% helium (Heliox) the duration that they can exercise for increases by approximately
50%. Heliox improves exercise tolerance in patients with COPD by reducing breathlessness and leg
discomfort, secondary to reductions in respiratory, muscular and cardiovascular limitations. Whether
Heliox improves exercise tolerance in patients with CF is unknown.
Aim: To determine whether Heliox improves exercise tolerance in patients with CF.
Methods: Child and adult patients with CF will undertake 3 exercise tests. The first will be a maximal
incremental test to determine peak exercise capacity. During the second and third tests, patients will
exercise for as long as possible at 80% of their maximum exercise capacity whilst breathing either
room air or Heliox.
Significance: Maintaining high levels of physical activity is important in the management of CF.
However, due to the heightened breathlessness and leg discomfort during exercise, many patients
remain inactive. This causes further body deconditioning and leads to further inactivity. If exercise
tolerance is improved, then Heliox may be used as a therapeutic aid to improve adherence to
exercise training programmes. Regular physical activity in patients with CF slows the progressive
decline in lung function, increases quality of life and, ultimately, increases life expectancy.
Type of student: MPhil and Honours.
Prerequisite skills: None.
Type of research: Clinical research involving the recruitment of participants, exercise testing, lung
function measurements and data analyses.
30
RESEARCH AREA / TOPIC
Respiratory physiology
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
Queensland Children’s Medical Research Institute
CONTACT PERSON
Dr Dean Mills
EMAIL / PHONE
d.mills2@uq.edu.au / 07 3636 5578
Title: The influence of experimental factors on respiratory impedance measured with the forced
oscillation technique.
Background: The forced oscillation technique (FOT) is a non-invasive lung function technique that is
used in the investigation of chronic respiratory disease. The FOT provides information on respiratory
system impedance; respiratory resistance, an accurate measure of airway resistance; and respiratory
reactance, the elastic and inertial properties of the respiratory system. We have recently developed a
variation of this technique called the wave-tube FOT that can be used to dynamically “track” changes
in respiratory impedance with air flow and lung volumes. How the results of the wave-tube FOT are
influenced by experimental factors such as breathing frequency, lung volumes, breath duration, heart
rate, neck position and the ingestion of food is unknown.
Aim: To examine the influence of experimental factors on respiratory impedance measured with the
FOT.
Methods: Healthy adults will have height, body mass and FOT measurements undertaken at the
respiratory clinic at the Royal Children’s Hospital, Brisbane over 3 visits.
Significance: The FOT is a non-invasive lung function technique that is used in the investigation of
chronic respiratory disease. The wave-tube FOT can dynamically “track” changes in respiratory
impedance with air flow and lung volume either those associated with tidal breathing or with deep
inspiration. Within-breath tracking of respiratory impedance is a promising tool for the investigation of
chronic respiratory disease, but the influence of experimental factors that may occur in clinical
practice or research is unknown.
Type of student: MPhil and Honours.
Prerequisite skills: None.
Type of research: Clinical research involving the recruitment of participants, lung function
measurements and data analyses.
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RESEARCH AREA / TOPIC
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
CONTACT PERSON
EMAIL / PHONE
Cancer and Primary health care
PA-Southside Clinical School
A/Prof Jennifer Martin (PA-Southside Clinical
School)
A/Prof Patricia Valery (Menzies School of Health
Research -Brisbane)
j.martin4@uq.edu.au tel 3176 5663
Patricia.Valery@menzies.edu.au tel 07 3309 3418
Improving systems and quality of cancer care in Aboriginal and
Torres Strait Islander primary health care settings
Chief investigators: P Valery, G Garvey, R Bailie, E Walpole, J Adams, D Williamson, J
Martin
Improving the coordination and continuity of care from cancer diagnosis through to
management of cancer is seen as an important step for improvement in the health of the
increasing numbers of Indigenous Australians with cancer. Gaps in knowledge exist about
Indigenous people with a cancer and their use of health services for their cancer in the
Primary Health Care (PHC) setting.
The project aims to investigate:
1. which systems are in place to identify Indigenous cancer patients in the PHC setting
2. if required report on how these systems or processes can be improved;
3. to examine the patterns of care of Indigenous cancer patients at the PHC level
(mixed methods will be used with medical chart reviews and qualitative interviews
about the follow up and coordination of care of Indigenous cancer patients between
the sectors); and
4. to develop an audit tool for cancer care with a particular focus on culturally
appropriate support, management of comorbidities, follow up and communication
between the tertiary health system (major cancer treating hospitals) and the PHC
system.
Within this project there are sub-studies that are available for volunteers, Honours, MPhil or
PhD students. A small involvement in this project (e.g. medical chart reviews, systematic
literature review on a topic related to this project) will be suitable for ‘honours’ or ‘volunteer’
students, while a large involvement (e.g. develop an audit tool for cancer care) could be
suitable for a MPhil or PhD project (exact topic and scope to be discussed further depending
on experience or interest of the application).
The student will be jointly supervised by A/Prof Patricia Valery and A/Prof Jennifer Martin.
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RESEARCH AREA / TOPIC
Breast Cancer Metastases
e.g. Cancer/Immunity/Primary Care
CENTRE/INSTITUTE/SCHOOL
Queensland Institute of Medical Research
CONTACT PERSON
Dr Adrian Wiegmans
EMAIL / PHONE
adrian.wiegmans@qimrberghofer.edu.au
We are looking for H1/H2A honours students to begin a PhD in 2014 on any of our
“translational” projects focussed on metastatic breast cancer.
Deciphering the molecular mechanisms of metastasis to design new-targeted
therapies for breast cancer.
The transformation of normal breast tissue to tumor requires the accumulation of mutations,
which is readily achieved by deregulation of DNA repair pathways. We found that metastatic
breast cancers have high levels of the DNA repair protein RAD51. Metastatic breast cancer
represents a subtype that has poor clinical outcome and RAD51 contributes to this. We have
determined that reducing RAD51 levels in aggressive breast cancers results in reduced
metastatic growth and sensitivity to chemotherapy. RAD51 supports metastasis via a role in
stabilizing cancer genomes however RAD51 also augments metastatic potential through
other mechanisms. These include changes in actin dynamics and changes in gene
metastatic expression profiles via mechanisms that have yet to be fully elucidated. Outcomes
from these analyses will provide new potential clinical targets in treating metastatic breast
cancer.
Individual research projects for developing new therapeutic targets will have a focus around
one of the following models;
The chemistry of small molecule inhibitors: We are currently in early stage development
of small molecule inhibitor library and will need to screen the compounds using various cell
biology techniques to establish efficacy of activity against breast cancers.
Actin dynamics and metastasis: We find that DNA repair proteins affect actin dynamics,
cell morphology and thus the migration and invasion properties of cancer cells. This
determines the metastatic potential of the cancer and could be targeted to inhibit metastatic
spread of cancer.
Transcriptional regulation of metastasis: DNA repair proteins also change the profile of
pro-metastatic gene expression via unknown mechanisms. The ability of DNA repair proteins
to bind DNA and simultaneously bind transcription factors, mean they have the capability to
direct gene expression. This is a new function for this class of proteins.
Animal models of metastasis: We are developing new models of metastasis to test new
anti-metastatic drugs developed in the lab. We are looking to mimic human diseases, with
spontaneous metastasis of breast cancer to specific organs.
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School of Population Health
A systematic review and meta-analysis of clozapine for
treatment refractory schizophrenia
Clozapine is the most effective treatment for schizophrenia for people who have failed at least two
trials of other antipsychotic agents and has been shown to reduce psychotic symptoms, reduce
rehospitalisation, reduce overall premature mortality and improve treatment adherence, sociooccupational functioning and quality of life. Clozapine has the potential to cause significant adverse
drug effects (ADRs), including neutropenia, agranulocytosis, myocarditis, cardiomyopathy, seizures,
metabolic syndrome, hypersalivation, enuresis, obsessive compulsive symptoms, constipation and
ileus.
A choice to start a person on clozapine must be an informed balance between the efficacy of the
treatment and the potential for ADRs.
There has been no recent systematic review and meta-analysis comparing clozapine to other
antipsychotics for people with treatment refractory schizophrenia to help guide clinician choice.
We propose to conduct a systematic review and meta-analysis of clozapine for treatment refractory
schizophrenia.
Professor Steve Kisely and Dr Dan Siskind, clinical academic psychiatrists based at the Princess
Alexandra Hospital, are coordinating this project. Professor Kisely has extensive experience with
meta-analyses including work with the Cochrane Collaboration.
Tasks for a medical student, under the supervision of Professor Kisely and Dr Siskind, would include:
- Systematically reviewing the literature on the efficacy of clozapine for treatment refractory
schizophrenia
- Selecting relevant articles from the literature
- Extracting relevant data from included articles
- Working with Prof Kisely and Dr Siskind to run a meta-analysis
- Assisting with writing a draft manuscript for submission to a peer-reviewed journal.
This project would be ideal for a medical student with an interest in learning how to systematically
review the literature. Publication of this project in a peer reviewed journal is expected. Prior
experience of literature reviews and/or mental health is not essential.
For more information, contact Dr Dan Siskind
dan_siskind@qcmhr.uq.edu.au or Prof Steve Kisely s.kisely@uq.edu.au
34
Research Assistant
The Inflammatory Bowel Disease Research Unit at the Royal Brisbane and
Women’s Hospital (RBWH) and Queensland Institute of Medical Research,
conducts clinical, genetic and epidemiological research into Crohn’s
disease and ulcerative colitis.
Applications are invited for a Research Assistant to review and collect data for a natural history and
genetics study which aims to elucidate the causes of IBD. The successful applicant will have a
strong work ethic and keen attention to detail, and ideally will have experience in data entry
(Microsoft access). This position would provide an ideal opportunity for a motivated student with an
interest in clinical research methods to gain practical experience in research study design, data
collection, data analysis and manuscript preparation.
This position will be based at the Royal Brisbane and Women’s Hospital in Herston. On an ongoing
basis the position will require a commitment of 8 hours per week, (flexible working hours if needed) .
Over the university summer holiday the position will require a commitment of 40 hours per week.
Data collection work will be renumerated, rate appropriate to experience. (Probably around $20 per
hour).
PRIMARY RESPONSIBILITIES




Managing systematic collection of medical information through review of hospital charts and
electronic records
Entering research data accurately, and maintaining an accurate database through careful
auditing and updating of data
Liaise with key people in the Queensland health system including pathologists,
gastroenterologists, surgeons, general practitioners and hospital administrators to obtain
clinical data on on consented patients with Inflammatory Bowel Disease.
Assist with data analysis and preparation of papers for publication in international scientific
and medical journals
KEY SELECTION CRITERIA (Qualifications, Experience, Skills and Abilities)
Essential




An interest in inflammatory bowel disease and some familiarity with medical concepts relevant
to gastrointestinal illnesses
Excellent organisational and time management skills, and keen attention to detail
Demonstrated ability to use Microsoft Access database applications
Commitment to maintain participant privacy and confidentiality
Desirable


Ability to work independently but also to fit into a project team
Knowledge of statistical methods and experience using statistical programs such as SPSS
and R
Forward your Expression of Interest briefly addressing the above criteria,
along with a copy of your CV, to James_Irwin@health.qld.gov.au by 11th
October 2013.
35
QIMR Berghofer
Supervised by Dr Kate Markey and Prof Geoff Hill, QIMR Berghofer
The Anatomy of Graft-versus-host disease
Bone marrow transplantation, used as curative immunotherapy for haematological malignancy, is
fraught with immunological complications, namely graft-versus-host disease (GVHD) and chronic
immune insufficiency which results in opportunistic infection in transplant patient. Central to GVHD
pathogenesis is (1) gut damage by pre-transplant chemotherapy and radiotherapy, (2) activation of
donor T cells after they are transplanted into the recipient, and (3) subsequent T cell proliferation,
cytokine production, and host tissue apoptosis. This results in a clinical syndrome which primarily
damages skin, liver and further destroys already fragile gut tissue. Importantly, the lung can be a
target organ for both acute and chronic GVHD, and patients who experience lung GVHD
We are developing tools in the lab that have allowed us to gain insight into the anatomy of GVHD,
and these include:


green-fluorescent proteins in various cell types so we can ‘find’ cells in various organs after
transplant
Firefly luciferase expressing cells (eg donor T cells) that we can track via a live animal
imaging system (Xenogen) and therefore follow T cell expansion over time
However, there are unsolved questions regarding the timing and location of many important immune
interactions after transplant (eg, antigen presenting cells and T cells, recipient gut tissue and donor T
cells, donor T cells and residual recipient cells) and there are new tools available at QIMR (eg the
Photonimager instrument which allows CT scanning and concurrent fluorescent imaging of live
animals) which will be critical in answering these questions. The proposed student project will have
the following aims:




Establish the parameters for CT scanning recipient animals after transplant to monitor
development of GVHD, particularly in the gastrointestinal tract and lung
Optimize imaging systems for live animal imaging using injected or ingested near-infrared
fluorescent dyes
Establish near-infrared based assays for measuring local host-tissue damage (eg, local
inflammatory marker release, local apoptosis)
After successful assay development, use these new assays in transplant systems to gain new
insights into GVHD biology.
The student/s successful in applying to work in the lab will be well supported within a group of
motivated scientists, under the supervision of Prof Geoff Hill. Aspects of this project could be
completed by a talented honours student, or expanded to form the basis of an MPhil or PhD project
for the appropriate candidate.
For more information contact:
Kate Markey | NH&MRC Clinical Training Fellow | Bone Marrow Transplantation
Laboratory |The Queensland Institute of Medical Research | Phone: +61 7 3845 3773 |
Fax: +61 7 3845 3509 |Email: kate.markey@qimr.edu.au
36
School of Pharmacy and Institute for Molecular
Biosciences
Project: Using toxins to understand the mechanisms of pain
Toxins have evolved in plants, animals and microbes as part of defensive and/or prey capture
strategies, and have proven to be invaluable research tools as well as providing leads for potential
new therapies. Many venoms and toxins are painful, and this has been instrumental for our
understanding of the mechanisms involved in pain. For example, the active component of “hot” chilli
peppers, capsaicin, has led to the identification of TRPV1 as a putative analgesic target in peripheral
pain sensing neurons. In addition, a surprising number of toxins have been found to be highly
selective for a diverse range of mammalian channels and receptors associated with pain signalling
pathways. Such toxins may find applications as novel analgesics, as exemplified by the frog alkaloid
epibatidine and the conotoxin ziconotide, both of which are several hundred times more potent than
morphine.
We have a variety of projects for students interested in toxins and pain mechanisms, relating to the
identification and characterization of toxins from plants, ants, fish and cone snails with activity at
peripheral pain-sensing neurons.
CONTACT: Dr Irina Vetter
School of Pharmacy and Institute for Molecular Biosciences
The University of Queensland
i.vetter@uq.edu.au
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