Biomedical Research PhD projects for 2010 at the Murdoch Childrens Research Institute

Peanut allergy has been reported to be increasing in industrialised countries. Children with IgE-mediated food allergies such as peanut allergy are at risk of life-threatening episodes of anaphylaxis. Along with obesity, atopy has been touted as the new epidemic of the 21st century. This project aims to examine the epidemiology of food allergy in a large cohort of Melbourne children. The primary goal will be to catalogue the prevalence of peanut allergy in the community and measure if there are modifiable factors that can alter this prevalence. As up to 20% of individuals develop tolerance to food allergy, a secondary focus of this project will be to elucidate what mechanisms promote tolerance to foods. Infants who are 12-month-old and pre-peanut ingestion will be recruited from the community at vaccination sessions in and across metropolitan Melbourne via council-led immunisation clinics. Skin prick test for food allergens will be administered and a questionnaire completed. Children with positive skin prick tests will be invited to attend the Royal Children’s Hospital to be offered an inpatient-based food challenge to confirm whether the infant has true peanut allergy. Other genetic and biochemical analyses will be undertaken as potential markers to predict allergy or development of tolerance.

2. Arthritis Research: Detecting bioactivity in a naturally-occurring aggrecan fragment

A/Professor Amanda Fosang
T 83416466
E

Dr Fraser Rogerson
T 83416467
E

ARTHRITIS disturbs the dynamic balance of anabolic and catabolic processes in healthy cartilage by increasing catabolism leading to irreparable cartilage damage. We will study the ability of a naturally-occurring aggrecan fragment to modulate cartilage catabolism. Our in vitro and in vivo experiments suggest that the aggrecan fragment limits cartilage destruction. This project will explore the mechanism by which the naturally occurring aggrecan fragment antagonises cartilage damage and promotes cartilage repair.

3. Using children's genes in research

Dr Merle Spriggs
T 90905237
E

A/Professor Lynn Gillam
T 90905203
E

Increasingly, genetic testing of children is becoming part of pediatric research. While a considerable amount of attention has been paid to the ethics of predictive testing in children for adult onset conditions there is little written about the ethical conduct of pediatric genetic research, especially that involving complex behavioural traits. Questions that arise include: • Is it ethically acceptable to enroll children and young people in gene-based prevention trials for traits such as obesity, addiction and ADHD? • When is it ethically defensible for a parent to consent to their child taking part in such research? Ethical issues include competence to consent, proxy consent, autonomy and developing autonomy, best interests, discrimination, stigma, privacy, genetic determinism and the right not to know. This project could be literature based, interview based or based on a questionnaire. The precise topic is negotiable and the methods are negotiable. Other ethics projects can be negotiated.

4. The ethics of surgically assigning sex to children

Dr Merle Spriggs
T 90905237
E

A/Professor Lynn Gillam
T 90905203
E

Intersex conditions are variously referred to as ‘developmental anomalies of the external genitalia’, ‘atypical sexual differentiation’, and ‘ambiguous genitalia’. Controversy surrounding the surgical management of intersex conditions in newborns is an important ethical issue because it: • Raises questions about the authority of parents and others to make irrevocable decisions for young children • Tests the idea that surgery is only justified when it is for disease or malfunction • Raises questions about what constitutes disease or malfunction • Poses questions about what we should base treatment decisions on when there is little guidance in terms of evidence of outcomes • Illustrates the shift from physician-centred medicine and paternalism to patient-centred medicine • Highlights the need for evidence in the form of systematic outcome studies This project could be literature based, interview based or based on a questionnaire. The precise topic is negotiable and the methods are negotiable. Other ethics projects can be negotiated

5. SchoolNuts - Food Allergy in School-Aged Children

A/Professor Katie Allen
T 93455060
E

Dr Nick Osborne
T 90905260
E

Childhood food allergy has become a major public health problem and the apparently rising incidence of food allergy is magnified by the devastating but extremely rare sudden death of a healthy child. There is considerable uncertainty surrounding the resolution of food allergy by adolescence. We know that some children with food allergy will grow out of it before adolescence. However the proportion that outgrows an allergy, and the factors that predict this, are not known. A second area of uncertainty concerns the paradox that while anaphylaxis related to food allergy is most prevalent in children under 5 years it poses a far greater risk of death to adolescents, accounting for two of every three anaphylaxis deaths. We aim to determine the prevalence of, and environmental risk factors for food allergy, and to characterise co-existing atopic manifestations (asthma, hayfever & eczema) in childhood and adolescence; and to identify knowledge about and attitudes to food allergy and anaphylaxis in both allergic and non-allergic school children during the transition from primary to secondary school. We also aim to examine amongst those school children aged 10-14 years identified with self-reported food allergy to assess the diagnostic positive predictive values of skin prick test for food allergy. This study has the potential to have a significant impact on public health policy regarding the prevention and management of allergy and anaphylaxis in schools.

6. Analysis of mouse models of human birth defects

Dr Peter Farlie
T 83416409
E

Professor John Bateman
T 83416422
E

Birth defects involving the face affect approximately 1% of all babies but the genes involved in most of these conditions are unknown. ENU mutagenesis is a forward genetics approach that allows phenotypes of interest to be identified without any prior knowledge of specific genes involved in the development of the organ system of interest. Once useful phenotypes are established, rapid gene mapping approaches have been developed to identify the mutated gene. We have a number of mouse strains harbouring birth defects involving both the face and limbs that appear similar to human syndromes. Identification of the mutated genes in these strains will help us understand how the normal developmental program is altered in human birth defects and will facilitate identification of disease genes in humans. This project will provide an opportunity for students to learn developmental biology approaches to understanding human birth defects and gain skills in a wide range of molecular biology techniques. Upon completion of this project, students will be in a strong position to initiate their own research into the genetic and developmental basis of human birth defects.

7. Large-scale screen of genes controlling skeletal development

Dr Peter Farlie
T 83416409
E

Professor John Bateman
T 83416422
E

Congenital defects of the skeleton are common and have a major impact on health and well being of affected children. Microarray RNA expression analysis of skeletal development is a powerful genome scale screening technology that is beginning to reveal essential pathways in skeletogenesis. However, a major limitation in this process is the functional analysis of identified candidate genes. To address this limitation in the analysis of our microarray data, we have developed a high-throughput screen to analyse the function of candidate genes in early skeletal development using avian retroviral delivery of expression and knockdown constructs. This screen will allow the student to rapidly analyse gene function in a whole animal model and will facilitate large-scale functional analysis of the genes controlling skeletal development and causing human skeletal defects and disease. Students will use cutting edge approaches to dissecting the genetic networks controlling complex developmental events during formation and growth of the craniofacial and limb skeletons. Experience gained in this project will allow students to initiate investigations into the mechanisms controlling development of any organ system.

8. Evidence based paediatric bioethics in Australia

A/Professor Lynn Gillam
T 90905203
E

Dr Craig Fry
T 90905216
E

Paediatric bioethics is a new and developing field in Australia, and internationally. Whilst there are some useful theoretical analyses of child and adolescent capacity to consent, and the basis and limits to parents’ rights to make medical decisions for their children, there have been no attempts to test the applied utility of these theories across a range of health conditions and social contexts. Significant ethical dilemmas currently exist in relation to for example: child and adolescent decision-making on their own health and medical treatment; and in the case of adolescent alcohol and drug use and treatment. At the Children's Bioethics Centre we are establishing an integrated program of world-class research in paediatric bioethics, to inform policy, practice and education, and deliver enhanced outcomes in paediatric health. In this project we will: (1) Document current ethical challenges and dilemmas in paediatric health practice (service delivery and research) and policy in Australia; (2) Explore the attitudes, knowledge and practices of health professionals, children and adolescents, and families in relation to these ethical challenges; (3) Develop practical resources and decision-making strategies for addressing these ethical challenges. Students could work on one or a number of aspects of this project.

9. Ethical challenges in new public health research methods.

Dr Craig Fry
T 90905216
E

A/Professor Lynn Gillam
T 90905203
E

Public health encompasses diverse settings, target groups, disciplines and skills in the quest to improve prevention, health promotion and health care. Success depends on innovative research and practice methods which often push the boundaries of knowledge and current ethical standards. Examples of new research methods currently being trialled in public health include: SMS messaging in health promotion research with difficult to access groups; Internet-based survey research and counselling; respondent driven sampling; brain imaging techniques to inform pharmacotherapy policy and treatments; photo/video research to engage specific target groups; and data linkage of health and other personal records. New health research methods like these give rise to important ethical questions, including: How do existing research ethics guidelines apply to these new forms of research participation? Do these new methods result in different outcomes for participants in relation to benefits and harms? Are existing definitions and guidelines around autonomy and consent applicable? Do new research methods like these alter participant confidentiality requirements and researcher responsibilities? What are the ethical limitations of methods innovation in health research with vulnerable populations? How can methods innovation be supported by ethical analysis? This project will: (1) document current ethical challenges encountered in new and emerging public health research methods; (2) explore the views, practices and needs of health researchers in relation to these ethical challenges; and (3) develop practical research ethics resources and guidelines to address identified needs. This will be the first mixed methods empirical study of ethical challenges in public health research in Australia and is also internationally unique.

10. Addiction and moral identity: Theoretical and empirical approaches

Dr Craig Fry
T 90905216
E

A/Professor Lynn Gillam
T 90905203
E

Research in neuroscience and genetics is increasingly revealing the role of the brain in drug addiction, and the impact of drug use upon brain function, human decisions about drug use and behaviour related to drug use. Advances in this area potentially have widespread implications for public policy and the treatment of people who use drugs. Addiction neuroscience reinvigorates long-standing philosophical questions about free will, self-control, responsibility, and identity. Such issues are crucial for the practical translation of this new science and for ethical and effective public policies and practices in the addictions field. This project will examine the moral self-conception, practical identity, and values of people who currently use drugs and drug addicted persons. It will review philosophical accounts of responsible agency and self-control against the empirical data, and perceptions currently informing treatment. This project utilises a mixed methods approach incorporating literature review, focus groups, in-depth interviews, structured survey, and key informant interviews.

11. Development of the human plasma proteome

Dr Vera Ignjatovic
T 99366520
E

Professor Paul Monagle
T 93455161
E

Major diseases such as cardiovascular disease, cancer and diabetes and their related mortality increase with age and are the major causes of death in the Australian population, as well as world-wide. As an example, cardiovascular disease related mortality for children is 3% compared with 40% for adults. This data indicates that children are in some way protected from serious disease outcomes. We want to improve the understanding of the mechanisms of this protection by focusing on the age-related differences in the plasma proteome. This has not been investigated to date and is what makes our study novel and highly clinically significant. With an increase in number of elderly Australians, the total burden of major diseases (cardiovascular, cancer, diabetes) is likely to increase significantly over the coming decades. Successful completion of this project will improve our understanding of the differences between children and adults, in particular the age of onset and proteins likely to be involved and will therefore increase the potential for prevention and decrease in burden of these age-related events in Australia and world-wide. The proposed study is only possible because of our ability to combine state of the art proteomic methodology with access to adequate samples from neonates, children and adults. The overall objective of this proposal is to determine the age-specific differences of the human plasma proteome in the healthy population in order to understand the implications of these differences in disease processes.

12. Understanding age-related differences in the structure of coagulation proteins and their interaction with anticoagulants

Dr Vera Ignjatovic
T 99366520
E

Professor Paul Monagle
T 93455161
E

Haemostatic system of children evolves with age, with marked physiological differences in the concentration of most haemostatic proteins, a concept known as Developmental Haemostasis. We have previously observed that these quantitative differences in haemostatic proteins do not explain all of the age-related differences in the effect of anticoagulants, suggesting the role for qualitative differences. Studies performed in our laboratory confirmed that fibrinogen isolated from neonatal and child plasma is qualitatively different to that isolated from adult plasma. In addition, we have demonstrated clinically significant age-related differences in the anticoagulation effect of the anticoagulant Heparin, hypothesized to be due to the age-specific differences in binding of this drug to coagulation as well as other plasma proteins. Using state of the art proteomic methodology, this proposal will build on our current and previous work and contribute significantly towards developing treatment strategies for children based on sound experimental evidence. This proposal will be the first attempt to: 1: Determine the extent of age-related differences in structure and binding kinetics of key coagulation proteins in humans (Fibrinogen, Antithrombin, and Thrombin); 2: Investigate the age-related differences in the interaction of haemostatic proteins with clinically relevant anticoagulants.

13. Neuropathogenic mechanisms of mitochondrial dysfunction

Dr Ann Frazier
T 83416287
E

A/Professor David Thorburn
T 83416235
E

Mitochondrial dysfunction causes a range of early-onset neurological conditions and contributes to neurodegenerative conditions such as Parkinson Disease. The mechanisms of neuronal damage are unknown, and the study of these at a cellular level may lead to improved treatment and greater understanding of the role of both nuclear- and mitochondrial-DNA mutations in both rare and common conditions. This project will focus on complex I deficiency, the most common mitochondrial respiratory chain defect. Using multiple primary and established cell culture models, it will study the effects of mutations on mitochondrial membrane potential, reactive oxygen species, ATP production, apoptosis and cellular calcium dynamics, primarily using techniques in fluorescent microscopy and cell biology, as well as biochemistry and molecular biology. We already have data on most of these parameters for patient fibroblast cell lines with characterised mutations in complex I subunits and assembly factors. This project will use three other cell culture models that more closely reflect neuronal function to study possible mechanisms of neuronal damage: 1. Primary neural cell cultures established from two mouse models with complex I deficiency resulting from mutations in two different nuclear encoded complex I subunits. 2. Olfactory stem cell cultures derived from nasal epithelial biopsies from patients with mtDNA mutations affecting complex I activity or with Parkinson disease, which can be grown as neurospheres and differentiated into neurons and glia. 3. Mouse embryonic stem cells with mitochondrial DNA mutations, which can be differentiated into neurons and glia.

14. Exploring the process of genetic counselling to facilitate family communication

A/Professor Sylvia Metcalfe T 83416309 E	Dr Jan Hodgson T 83416308 E
A/Professor Lesley Stirling T 8344 5192 E

We are conducting an NHMRC funded project of a randomised controlled trial of a genetic counselling intervention to facilitate communication to at-risk family members after diagnosis and genetic testing of an inherited condition. To augment this study, the process of genetic counselling will be explored in a number of different settings using qualitative methods, including discourse analysis. Perspectives of the genetic health professionals and the patients will be examined to further inform practice.

15. Offering population carrier screening for fragile X syndrome

A/Professor Sylvia Metcalfe
T 83416309
E

A/Professor Jane Halliday
T 83416260
E

Fragile X syndrome (FXS) is the most common cause of inherited intellectual disability, with other medical, behavioural and emotional features of varying expression. The condition is due expansions of a CGG repeat in the promoter region of the gene on the X chromosome, such that the risk of being affected relates to the length of this repeat. Carriers of FXS are at risk of developing a late-onset tremor ataxia and female carriers have an additional risk of primary ovarian insufficiency including early menopause, as well a risk of passing on an expanded allele to their children (unlike male carriers). Carrier frequency in females is about 1 in 150. We are conducting a study in which carrier screening is being offered to non-pregnant and pregnant women with the aim of assessing informed decision-making as one of the outcomes. Data collection will involve the use of questionnaires and interviews.

16. Identifying TRPV4 interacting proteins using proteomics and pharmacology

Dr Shireen Lamande
T 83416465
E

Professor Peter McIntyre
T 8344 5745
E

Mutations in the calcium channel TRPV4 cause defective skeletal development. Consistent with the disease phenotypes, TRPV4 is expressed in cartilage and bone cells, but it is also found in many other tissues including nerves and kidney and we don’t yet understand why mutations predominantly affect the skeleton. The mutant TRPV4 proteins are not glycosylated normally and appear to be relatively unstable, possibly due to misfolding. We would like to understand how TRPV4 is regulated and activated in cartilage cells by identifying proteins that interact with the intracellular N-terminal domain of TRPV4. This project will screen for interacting proteins by expressing Strep-tagged TRPV4 proteins in mammalian cells, using affinity pull-down approaches to recover TRPV4 and interacting proteins followed by mass spectrometry to identify the interacting proteins. The effect of co-expressing TRPV4 and its partner proteins will be studied using established ion-channel assays.

17. TRPV4 and skeletal development

Dr Shireen Lamande
T 83416465
E

Professor John Bateman
T 83416422
E

Mutations in the calcium channel TRPV4 cause defective skeletal development but very little is known about the temporal and spatial expression of TRPV4 during cartilage and bone development. This project will characterise TRPV4 mRNA and protein expression during skeletal development in the mouse using in situ hybridization and immunohistochemistry. We know that the Trpv4 knockout mouse has some abnormal skeletal features but to date only the knee joints have been studied and so another aspect of this project will involve detailed analyses of the skeleton in this mouse during development using histology and a range of imaging techniques. We are developing a knockin mouse carrying a disease causing Trpv4 mutation and this project will also involve characterising the skeletal phenotype in this mouse model.

18. mRNA surveillance in human disease: How cells detect and degrade deleterious mutant mRNA (nonsense-mediated mRNA decay)

Professor John Bateman
T 83416422
E

Dr Shireen Lamande
T 83416465
E

Cells have several critical quality control processes to reduce the impact of mutations on cell function. We are studying nonsense-mediated decay (NMD), a mRNA quality mechanism that degrades mRNA containing premature stop codons. Since mutations that introduce premature stop codons account for one-third of inherited disorders, NMD is of immense importance in many diseases as well as normal development [see Hum Mol Genet. 8:1893 (1999); Am J Hum Genet 82:786 (2008)]. Our studies will explore the molecular basis of NMD by the production of mutations in reporter gene constructs we have developed to measure NMD in vitro by transfection of cells and determination of mRNA levels by PCR and primer extension assays. The project will characterise the mRNA sequences that specify NMD in different cell types and determine role of known and novel RNA binding proteins using electromobility shift assays. These trans-acting proteins will be identified by proteomics (electrophoresis and mass spectrometry) and their role in NMD tested by suppression of expression using RNA interference.

19. The molecular signalling pathways that cause osteoarthritis

Professor John Bateman
T 83416422
E

Dr Richard Wilson
T 93456601
E

Degeneration of articular cartilage is the central pathological feature of osteoarthritis (OA) and it is this progressive erosion of cartilage that leads to joint failure and necessitates joint replacement surgery. We have a major research program determining the molecular events in the initiation and progression of cartilage breakdown. Using microarray analysis to look at gene expression changes and proteomic approaches we have determined new osteoarthritis candidate genes. Several research projects are available in this program exploring the detailed biology of these genes and the signalling pathways that result in the onset and progression of OA. These studies will involve the study of the biological function of these genes in cultured cartilage and bone cells, and how both over-expression and expression knockdown by RNAi affects cellular signalling and cell phenotype in vitro. This will compared with the changes found in osteoarthritic tissues. The projects will use of a wide range of molecular biology, biochemical, cell biology and proteomic techniques.

20. The contribution of protein misfolding (“unfolded protein response”) to inherited cartilage and bone disease

Professor John Bateman
T 83416422
E

Dr Richard Wilson
T 93456601
E

Inherited musculoskeletal disorders are a significant disease burden and although many mutations have been defined, our knowledge on the molecular mechanisms that cause them, and ultimately how these mechanisms could be manipulated, is only just beginning to be explored. Many of the gene mutations result in the production of mutant protein that is compromised in its ability to form the correct 3-D folded functional structures. Recent research has shown that these unfolded proteins can cause cellular stress and activate intracellular signalling pathways that have profound effects on cell gene expression that may contribute to cellular pathology (see Bateman et al.,Nature Reviews Genetics 2009 Mar;10(3):173-83). The proposed studies will explore the molecular signalling pathways using in vitro and transgenic mouse models and a range of immunohistochemical, biochemical, molecular methods and proteomic analysis (2D-electrophoresis and mass spectrometry) skills. In addition, our studies will explore the use of new therapeutic agents to overcome protein misfolding and cell stress, as a proof-of-principle that some of these diseases can be effectively treated.

21. Characterisation of the role of PArkin Co-Regulated Gene (PACRG) in neurodegenerative disease

Dr Paul Lockhart
T 83416322
E

Dr Juliet Taylor
T 83416295
E

Parkinson’s disease (PD) is a common progressive neurodegenerative disorder that is a major cause of morbidity and mortality. Mutations in the parkin gene are the most common cause of early onset-PD, and altered parkin function is a risk factor for several different neurodegenerative diseases. We have recently shown that Parkin Co-Regulated Gene (PACRG) shares a bi-directional promoter with parkin and the two proteins interact. We hypothesise that this interaction facilitates the degradation of misfolded and toxic proteins within the brain. Failure or compromise of the function of either parkin or PACRG results in the accumulation of toxic proteins and results in the development of neurodegenerative disease. This project will determine the function of PACRG, with a particular focus on its role in the brain. This will be achieved through a range of approaches including gene expression studies, protein analysis and the characterisation of cell and animal models.

22. Characterisation of a novel gene and mouse model of ciliary dyskinesia

Dr Paul Lockhart
T 83416322
E

Miss Gabrielle Wilson
T 83416295
E

Cilia are evolutionarily conserved microtubule-based hair-like organelles that project from nearly all mammalian cell types. Although they perform remarkably diverse functions they share a similar basic structure, consisting of a basal body, axoneme and ciliary membrane. Defects in cilial function have classically being associated with human phenotypes such as neural tube and patterning defects, male infertility and sinusitis. However, recent studies have broadened the range of associated syndromes and phenotypes to include obesity, diabetes and hypertension. There is limited understanding of the genes and proteins involved in the formation and function of cilia, but recent studies have taken advantage of mice models to study the pathogenesis of ciliary dysfunction in vivo. We have identified a novel mouse model characterised by male infertility and hydrocephalus (enlarged ventricles within the brain). We have identified the defective gene and have preliminary data suggesting it is a key protein required for the functioning of motile cilia. This project will utilise a range of molecular and cellular techniques, including the development of cell and animal models, to investigate the role of the protein and potential contribution to human cases of hydrocephalus.

23. Determining of the molecular basis of childhood dystonia

Dr Paul Lockhart
T 83416322
E

Dr Kirstee Martin
T 83416286
E

Dystonia is a common movement disorder which is characterised by involuntary sustained muscle contractions and abnormal movement. The condition affects approximately 1 in 5000 people, but remains poorly understood with limited treatment options. Mutation of the TorsinA gene causes dominant early-onset general torsion dystonia, the most common heritable form of the disease. TorsinA is highly expressed in a subset of neuron within the brain, particularly the basal ganglia and associated motor circuits. Although the normal function of TorsinA is currently unknown we have preliminary data suggesting the protein functions as a chaperone and transports substrates within the neuron. We have identified several proteins that interact with TorsinA. The aim of this project is to further characterise these interacting proteins using a range of molecular and cellular techniques and investigate their contribution to the disease phenotype. In addition, we have established mouse models and human patient-derived cell lines specific defects in the TorsinA gene. These will allow us to identify the molecular pathways disrupted during disease and provide the means to develop and test novel therapeutic treatments.

24. Cardiac molecular signaling mechanisms during the progression of heart failure

Dr Salvatore Pepe T 93454114 E	A/Professor Joe Smolich T 93454571 E
Professor Dan Penny T 93455922 E

Congenital and acquired myocardial disorders, despite diverse etiology, commonly involve a reduced capacity to manage oxygen and nitrogen free radical metabolism. Chronic augmented oxidative stress, particularly in fetal and neonatal development, not only leads to post-translational structural modification of proteins, but also impacts gene transcription, ultimately with consequences to structural, metabolic and functional remodeling during adaptive and maladaptive heart failure. These pathological changes remain to be well defined in the developing heart at molecular and cellular level in order for potential therapeutic targets to be identified. Students ideally should have a background in at least one of the following: biochemistry, immunology or pharmacology. Studies will explore novel molecular signaling pathways (intracellular/mitochondrial/nuclear) using unique in vitro and ex vivo models and a range of immunohistochemical, biochemical, molecular, genetic and cell biology methods.

25. Determining cord blood stem cells with cardiac fate for the repair of congenital myocardial dysfunction

Dr Salvatore Pepe T 93454114 E	Ms Faten Zaibak T 99366523 E
Dr Ngaire Elwood T 93456398 E	Dr Christian Brizard T 93455200 E

As the heart has recently been found to be capable of self renewal, the current work is aimed at acquiring a basic understanding of the growth and differentiation of cardiac progenitor cells. Cord blood, obtained from the placenta and umbilical cord, contains cells called unrestricted somatic stem cells (USSC) that are capable of forming many different tissues including the heart. Related genetic transcriptional signaling, immune and endocrine regulatory factors that are involved in determining what drives cardiac cell fate will be studied to develop models of myocardial cell recruitment for potential treatment of congenital heart disorders which currently only have palliative surgical treatment options. Beyond cord cell line manipulation and characterization, our goals are projected to facilitate the iterative development of experimental surgical models, working with surgeons and clinicians. Students ideally should have a background in one or more areas such as immunology, genetics, biochemistry or pharmacology, and will predominantly utilise genetic, molecular and cellular techniques.

26. Cardiac molecular signaling mechanisms in survival adaptation to hypoxia and post-operative stress recovery

Dr Salvatore Pepe T 93454114 E	Dr Michael Cheung T 93455714 E
Professor Igor Konstantinov T 93455200 E

Many congenital heart disorders, involve chronic hypoxic conditions due to one or more cardiovascular structural defects which compromise normal cardiopulmonary blood flow and thus blood reoxygenation. During heart surgery cardioplegic heart arrest and cardiopulmonary bypass impose additional inflammatory and ischemia-reperfusion stress. Ischemic preconditioning (IPC) activates a powerful innate protection via brief intermittent periods of coronary artery ischemia-reperfusion prior to a sustained period of ischemia, thus reducing post-ischemic injury. In animal and human models of ischemia-reperfusion injury, a simple stimulus known as remote ischemic preconditioning (RIPC) has been shown to reduce post-ischemic tissue damage and inflammation. RIPC can be invoked by causing IPC at a site remote from the heart, ie using a pressure cuff to intermittently occlude and reperfuse blood vessels in limbs. In numerous cell types mitochondria have been recognised to be central to IPC where multiple signalling pathways appear to converge to regulate metabolic function. However the molecular and cellular mechanisms that underly the cardioprotection induced by RIPC remain to be defined. Thus, our current goals are to define these intracellular/ mitochondrial/ nuclear signaling pathways using animal models and cell-based studies. New understanding of RIPC will identify specific targets to harness more potent cardioprotective effects in our clinical setting. Students should have a background in one or more of the following: biochemistry, immunology, genetics, physiology, pharmacology.

27. Collagen VI and WARP interactions during neurological development

Dr Shireen Lamande
T 83416465
E

Professor John Bateman
T 83416422
E

WARP is a recently identified extracellular matrix molecule with expression restricted to permanent cartilages and a distinct set of basement membranes in peripheral nerves, muscle, and the central nervous system vasculature. WARP knockout mice are healthy, viable, and fertile with no overt abnormalities; however, they have a significantly delayed response to acute painful stimulus and impaired fine motor coordination, suggesting compromised peripheral nerve function. WARP interacts with the extracellular matrix protein collagen VI and the collagen VI microfibrillar network is severely reduced and mislocalised in peripheral nerves of WARP knockout mice. Collagen VI is broadly distributed and mutations in humans cause muscular dystrophy. Other tissues such as cartilage, bone and tendons are also affected although these phenotypes have been poorly defined. Our data suggests that collagen VI may also be important in peripheral nerves and this project will define the role of collagen VI in the nervous system using collagen VI knockout mice, WARP knockout mice and collagen VI/WARP double knockout mice. This project will also characterise the phenotype in other tissues where collagen VI and WARP are coexpressed such as cartilage and skeletal muscle.

28. Role of ADAMTS5 in muscular dystrophy

Dr Jason White T 83416418 E	Dr Shireen Lamande T 83416465 E
A/Professor Amanda Fosang T 83416466 E

Skeletal muscle is a major and important component of the mammalian body and the consequences of loss of control of the regulatory factors which govern skeletal muscle development can be devastating. Muscular dystrophy is a progressive degenerative disease affecting nearly 1 in every 1000 Australians. The most significant feature of muscular dystrophy is the progressive loss of skeletal muscle tissue and function. This project will focus on characterising the role of AMADTS5 in skeletal muscle formation, regeneration, growth and degeneration in muscular dystrophy. Using a range of biochemical, molecular biology, genetic, cell and whole animal techniques we are investigating the function of ADAMTS5 and why it is perturbed in muscular dystrophy (MD) as well as identifying potential (pro and anti-apoptotic) target genes that may be used to develop therapies to treat MD. Initially muscle cell cultures will be used but we have access to genetically-modified mice, with knock-in and knock-out mutations designed to help elucidate the role of ADAMTS5 in muscular dystrophy.

29. Genes involved in Disorders of Sex Development: identification and regulation

Dr Stefan White T 83416426 E	Dr Thomas Ohnesorg T 83416426 E
Professor Andrew Sinclair T 83416424 E

Disorders of Sex Development (DSD), ranging in severity from genital abnormalities to complete sex reversal, are surprisingly common and as such represent a major paediatric concern. The cause of these problems is most often the failure of the complex network of genes that regulate development of testes or ovaries. Our research seeks to understand the molecular basis of testis and ovary development and how mutations in key genes can lead to abnormalities. Mutations in known genes explain 20% of DSD patients but we have no explanation for the remaining 80%. DNA samples from a large number of DSD patients with gonadal dysgenesis (XX males and XY females) have been collected, and we are currently applying a range of powerful methodologies to look for mutations in these patients. These techniques include screening for deletions and duplications using high-density microarrays and multiplex ligation-dependent probe amplification, and identifying sequence changes using high-throughput deep sequencing and DNA denaturation analysis. We are also currently studying regulatory elements controlling a range of genes involved in gonad differentiation. Methods that are being applied include DNaseI hypersensitivity analysis, Chromatin Immunoprecipitation and reporter assays. Other methods involved include cell culture, quantitative PCR and expression analysis.

30. Analysis of genes responsible for male germ cell development and germ cell tumours.

Dr Patrick Western
T 83416353
E

Professor Andrew Sinclair
T 83416424
E

Germ cells mediate passage of all genetic information to the offspring and lay the foundation for embryonic development. To achieve this the germ line must differentiate into highly specialised cells while maintaining complete developmental potency. Primordial germ cells are derived from the pluripotent epiblast and share features with embryonic stem cells, including the expression of core genes that regulate developmental potency. In mice, at embryonic day 12.5, the male germ line is specified from the primordial germ cells. These early male germ cells ultimately differentiate into the various components of the male germ cell lineage required for sperm production. However, occasionally differentiation of male germ cells fails, and the male germ cells retain undifferentiated fetal germ cell characteristics and establish tumours, which exhibit aberrant control of cell cycle and pluripotency. Over the past five years we have studied the molecular regulation of male germ cell specification and differentiation with particular focus on the control of cell cycle and pluripotency (Western et. al. 2005 Stem Cells 23:1436-1442; Maldonando-Saldivia et. al. 2007 Stem Cells 25:19-28; Western et. al. 2008 Stem Cells 26:339-347; van den Bergen et. al. 2009 Biology of Reproduction 81:362-70; Western 2009 International Journal of Developmental Biology 53:393-409). Our work shows that male germ line differentiation involves the suppression of pluripotency both at the transcriptional and post-transcriptional levels. Central to this differentiation process is the strict regulation of germ cell mitotic arrest, which is associated with activation of key regulatory components such as retinoblastoma, and cell cycle inhibitors p27 and p15. Using molecular techniques, such as micro-array screening of gene and micro-RNA expression, we have identified genes/micro-RNAs that are specifically regulated during the specification and early differentiation of male germ cells. These data are being used to further explore male germ cell differentiation and the regulation of germ cell tumour initiation and development in mice. Genes identified in the mouse system will then be analysed for mutations or aberrant expression in germ cells tumours of patients with testicular cancer. Our work involves the use of a wide range of state of the art molecular and genetic tools such as analysis of gene knock-outs, flow cytometry, organ/tissue culture, immuno-fluorescence, confocal microscopy, quantitative real time PCR.

31. Analysis of candidate sex-determining genes in an avian model

Dr Craig Smith
T 83416353
E

Professor Andrew Sinclair
T 83416424
E

Sex determination is a fundamental and fascinating developmental process common to all animals. In humans and other vertebrates, sex determination results in the differentiation of either testes or ovaries during embryogenesis. Mutations in the sex-determining pathway can lead to gonadal abnormalities, ambiguous genitalia and /or sex reversal at birth. Our research seeks to understand the molecular and cellular basis of human sex determination, and how mutations in key genes can lead to these abnormalities. While most groups studying sex determination and gonadal sex differentiation use the mouse embryo as a model system, we have been utilising the chicken embryo. The chicken embryo has a number of experimental advantages over traditional mammalian models. Fertile eggs are readily available and, because embryogenesis occurs outside the maternal body, gonadal development is very accessible to experimental manipulation. Furthermore, draft sequence of the chicken genome is now available. The chicken embryo therefore represents a powerful model for the analysis of sex determination and gonadal development. Our lab is a world leader using this organism model to study sex determination (recently published in Nature; Smith CA, et al., 2009). This project will analyse candidate sex-determining genes and cellular processes underlying gonadal differentiation in this model system. Both molecular and cell biology-based methods will be used to functionally analyse key candidate genes that we have already identified. Techniques include expression analysis (PCR, in situ hybridisation, immunofluorescence, etc.), cell and organ culture, and manipulation of candidate genes using expression-plasmids and avian retroviruses, and RNA interference technology.

32. Using brain imaging to understand cognitive deficits in neurodevelopmental disorders.

Dr Tim Silk
T 8341 5637
E

A/Professor Alasdair Vance
T 93454666
E

Childhood neurodevelopmental disorders including Attention Deficit Hyperactivity Disorder (ADHD), Dysthymic Disorder (DD) and Obsessive Compulsive Disorder (OCD), are associated with cognitive deficits in addition to the clinical symptoms and behaviours. While clinically distinct disorders, they are highly comorbid with each other as well as other psychiatric problems, and overlap lies in the neuropsychological profile of executive function. This project will use Magnetic Resonance Imaging to examine both the functional and structural similarities or differences in children with ADHD, DD and OCD.

33. Epigenetic determinants of neocentromere and centromere chromatin

Dr Lee Wong
T 83416240
E

Professor KH Andy Choo
T 83416306
E

This project aims to study the role of genetic and epigenetic factors in regulating the structural and functional integrity of chromosomes and chromatin. We will use normal centromeres, neocentromeres (a new class of centromere devoid of alpha-satellite repetitive DNA first discovered by us), and human artificial chromosomes to investigate how different chromatin-modifying proteins (including constitutive centromere proteins, histone variants, boundary element insulator and DNA repair checkpoint proteins) and non-coding RNA components (such as various classes of centromeric alpha-satellite transcripts and retrolements) are organised at the centromere regions. The organisation will be defined at the linear chromatin level using chromatin immunoprecipitation and microarray analysis. The knowledge gained will be fundamental to our understanding of how genetic and epigenetic factors regulate centromere hierarchical assembly and its function in the maintenance of mitotic activity.

34. Epigenetic regulation of telomere chromatin in embryonic stem cells

Dr Lee Wong
T 83416240
E

Professor KH Andy Choo
T 83416306
E

cell pluripotency is controlled, and what (epigenetic) changes occur at the chromatin level during differentiation. However, until the present study, no one has investigated the chromatin status of the telomere in pluripotent and differentiating ES cells. In our study, we have found that the telomere chromatin of the pluripotent ES cells is unique compared to that of the differentiating ES cells. Specifically we show enrichment of histone variant H3.3 and ATRX (alpha thalassemia mental retardation) at the telomeric chromatin in mouse ES cells. The study involving RNAi-depletion of H3.3 and ATRX that results in impairment of the telomere structure also confirms that H3.3 and ATRX are essential for the maintenance of telomeric integrity in these cells. This project involves the investigation of the roles of H3.3 and ATRX, and their interacting partner as a ‘reprogramming cue’ for the maintenance of prolonged telomere-self renewal in pluripotent ES cells.

35. Hearing loss: identifying the genetic causes underlying childhood and adult deafness

A/Professor Henrik Dahl
T 83416253
E

Dr Shehnaaz Manji
T 83416254
E

Hearing loss affects 1:400 young people and many more adults and elderly people. The major objective of our research is to identify and understand the underlying causes of deafness in children and adults. Research in the hearing field has to a large extent advanced through the use of animal models. We have identified mouse strains with recessively inherited deafness, the most common form of inherited deafness in humans. These mice provide a new, unique and valuable resource for studying the contribution of genetic and environmental factors to hearing loss. We are identifying “deafness” genes by genetic and molecular studies in our mouse strains. Candidate genes are identified through database analysis, bioinformatics and DNA sequencing. The study of the function and expression of novel “deafness” genes is critical for our understanding of ear development and function. Expression of a “deafness” gene is analysed by in-situ and immunohistochemical techniques in mice as well as by biochemical methods in tissue culture cells. These studies are followed by screening for mutations in humans using novel techniques such as high resolution melt DNA profiling. These studies are providing much needed insights into the mechanisms leading to hearing loss in humans and will provide a foundation for developing new strategies for delaying, preventing or treating genetic deafness, including age-related hearing loss.

36. Using Next Generation Sequencing to Discover Novel Genes that Cause Mitochondrial Disorders.

A/Professor David Thorburn
T 83416235
E

Dr Alison Compton
T 6287
E

Mitochondria are the powerhouses of the cell, generating cellular energy through the oxidative phosphorylation (OXPHOS) system. Pathogenic mutations in genes required for correct assembly of the OXPHOS protein complexes result in a variety of neurodegenerative disorders collectively known as mitochondrial disorders. Nearly 100 (nuclear and mitochondrial) genes are known causes of mitochondrial disease, however 50% of patients still do not have a molecular diagnosis with many more novel disease genes awaiting discovery. We recently identified four novel (nuclear) disease genes in which mutations cause severe childhood-onset OXPHOS complex I deficiency, the most common mitochondrial enzyme defect in humans. Our collaborators at the Broad Institute, Harvard have used phylogenetic profiling to identify another 19 novel genes proposed to be involved in OXPHOS complex I biogenesis (Pagliarini et al., 2008 Cell 134:112–123). Recently we performed high throughput sequencing of 89 ‘mitochondrial’ genes in 103 of our patients with defined complex I defects and have identified mutations in putative novel ‘disease genes’. This project will follow up on several of the many sequence variants identified to discover novel OXPHOS disease genes and determine their normal function and disease pathogenesis using a combination of cell biology, molecular biology and biochemical approaches.

37. Mouse models for mitochondrial disease: Mendelian genetics and synergistic heterozygosity

Dr Bi-Xia Ke T 83416287 E	Dr Jasper Komen T 83416287 E
A/Professor David Thorburn T 83416235 E

Disorders of mitochondrial energy generation cause a wide range of diseases. Severe mitochondrial defects affect ~1/5000 individuals, often causing childhood neurodegenerative diseases. Increasing evidence suggests that some patients have digenic or multigenic disorders rather than simple single gene defects of one mtDNA or nuclear gene. In the general population at least 1 in 10 people carry nuclear or mtDNA genetic variants that cause milder mitochondrial dysfunction, which may contribute to common conditions such as Parkinson disease and diabetes. We have generated two mouse models of Complex I deficiency, the most common type of mitochondrial disease. Ndufs4-/- mice have a systemic Complex I defect and neurodegenerative disease while Ndufs6 GeneTrap mice have a Complex I defect primarily affecting heart and develop cardiomyopathy. This project will complete characterization of the phenotype of heterozygous and homozygous mice using a range of physiological, molecular, immunochemical and neuropathological approaches. Homozygous mice will be used in studies of therapeutic approaches such as high fat diet or upregulation of mitochondrial biogenesis using bezafibrate or resveratrol. Heterozygous mice will be used to investigate the role of mild mitochondrial dysfunction as a risk factor for common diseases. In addition, doubly heterozygous mice (ie, heterozygous for both Ndufs6 and Ndufs4 mutations) will be studied to investigate possible effects of synergistic heterozygosity.

38. Novel mechanisms of chromosome and genome regulation and disease aetiology

Dr Damien Hudson
T 83416300
E

Professor KH Andy Choo
T 83416306
E

In order for our genetic material to be faithfully segregated into two daughter cells, the chromosomes must compact nearly 10,000 fold. Prior to this event chromosomes are an amorphous mass of DNA, but upon compaction they form visible X-shaped structures known as mitotic chromosomes. A key component in this process is a multi subunit complex termed condensin. The aims of this project are to understand how condensin directs chromosome condensation and to find which components condensin interacts using gene knockout technology, and integrated proteomics and biochemistry. Furthermore we aim to look at the non-mitotic roles of condensin where a growing body of evidence suggests condensin has key roles in gene regulation and DNA repair. Critically malfunction of condensin is associated with human disease including cancer and immune deficiency. We expect to find novel interactors contributing to chromosome structure and to understand the mechanism of action of condensin and how it might contribute to disease.

39. ANALYSIS OF THE ROLE OF AKT SIGNALING IN RIBOSOME BIOGENESIS AND CELL GROWTH

A/Professor Paul Ekert
T 93455823
E

A/Professor Rick Pearson
T 03 96561247
E

The Akt/mTOR/S6K signalling pathway is a critical regulator of many fundamental cellular processes including cell survival, growth and proliferation and differentiation. A major focus of our laboratory is to understand how growth factors, such as Interleukin-3 and GM-CSF, engage this pathway and how this signalling is “hi-jacked” in tumour cells to produce proliferation and survival in the absence of growth factors. The availability of functional ribosomes is a fundamental rate-limiting step for growth and proliferation in mammalian cells Furthermore, increased cell growth is a key feature of transformed cells and absolutely requires sustained increases in the synthesis of functional ribosomes. The primary focus of this project will be to understand the role of AKT in cell growth and ribosomal biogenesis. The project will employ established models of growth factor signalling, inducible AKT expression and AKT-deficient mice to establish the signalling pathways involved in ribosome biogenesis and the function of these pathways in normal cells and in cancer. This PhD project is a joint project based at Peter Mac Research Division and the Murdoch Children’s Research Institute. You will be supported by two well-established and funded laboratories and become part of an exciting team of scientists and other students. You will become proficient in many innovative techniques of cell and cancer biology and molecular biology and will have opportunities to develop bioinformatic skills using microarrays and other techniques. For more information about this project contact: Assoc. Prof. Rick Pearson, Tel: 9656 1247; Email: rick.pearson@petermac.org Assoc. Prof. Paul Ekert, Tel: 9345 5823; Email: paul.ekert@rch.org.au

40. RNAi therapy: Applications in ß-thalassaemia

Dr Jim Vadolas
T 83416233
E

Dr Heidi Peters
T 83416257
E

Severe ß-thalassaemia (ß-thalassaemia major) is an inherited haemoglobinopathy arising from mutated ß-globin genes, resulting in reduced ß-globin chain synthesis. Much of the pathology of this disease is due to excess a-globin chains forming toxic insoluble precipitates in erythroid cells resulting in cell death, ineffective erythropoiesis and severe anaemia. Decreased a-globin chain synthesis leads to milder symptoms, exemplified by individuals who co-inherit a- and ß-thalassaemia. Therefore, a possible therapeutic strategy in the treatment of ß-thalassemia could include targeted reduction of a-globin chains to mimic co-inheritance of a/ß-thalassemia. RNA interference (RNAi) is an innovative new strategy for modulating gene expression and this pathway can potentially be exploited to mediate reductions in a-globin. Our group has identified key regions in the a-globin mRNA sequence which can be targeted with high efficiency using short-interfering RNA (siRNA) to mediate significant reductions in a-globin expression. We have also successfully demonstrated that RNAi-mediated reduction of a-globin results in phenotypic improvements in ß-thalassaemic cells. This project aims to develop strategies for targeted delivery of siRNA into erythroid progenitor cells. Initial studies will be conducted in vitro and will involve culture of both cell lines and primary cells. Further studies will also be conducted in vivo using our unique humanised ß-thalassaemia mouse models and patient-derived cells.

41. Stem cells and gene therapy: Targeted integration of functional genomic loci

Dr Jim Vadolas
T 83416233
E

Dr Heidi Peters
T 83416257
E

One of the major obstacles to successful gene therapy is the random integration of the therapeutic transgene, which is associated with insertional mutagenesis and oncogenesis. Using specific elements derived from adeno-associated virus (AAV) our research group has developed a novel strategy to enhance the delivery, and site-specific integration of large DNA molecules into the human genome. We have recently shown that we can enhance the delivery, and facilitate the site-specific integration of the entire human ß-globin locus. This project will investigate the site-specific integration of functional genomic loci into stem cells. Reporter gene expression and fluorescence in situ hybridisation will be used to monitor targeted integration and tissue-specific expression. In vitro differentiation will be used to assess the capacity of modified stem cells to differentiate along multiple lineages. The transplantation potential of modified stem cells will be investigated using the immunodeficient NOD/SCID mouse model. We propose that this non-viral gene therapy strategy may be used in conjunction with patient-derived stem cells to facilitate persistent and stable transgene expression while avoiding the risks associated with random integration.

42. Investigations into chromosome instability and human disease predisposition

Dr Paul Kalitsis
T 83416300
E

Professor KH Andy Choo
T 83416306
E

Approximately 10 quadrillion cell divisions occur in the lifetime of a human. Each divisional event requires the accurate distribution of the newly-replicated chromosomes to the daughter cells. Any faults occurring during this process can cause an imbalance in chromosome number and lead to clinical conditions such as Down syndrome, pregnancy loss, infertility, and cancer. Our laboratory investigates the cellular and molecular mechanisms that are responsible for such chromosome imbalances. One project involves the use of a fluorescent protein chromosome instability mutant screening assay in mouse embryonic stem cells to identify genes and environmental agents that contribute to chromosome missegregation events. Another project uses affinity purification and mass spec/proteomic techniques to identify novel chromatin protein components using known essential chromosome proteins as affinity baits. We anticipate finding many new genes/proteins whose functions will be further studied using techniques such as RNAi gene knockdown and gene knockout in cells and mice. These studies are expected to contribute important new insight into key mechanisms regulating chromosome stability and their potential role in causing the plethora of known chromosome-related human diseases.

43. Project 1. Stop codon readthrough in a mouse model of MMA

Dr Heidi Peters
T 83416257
E

Dr Nicole Buck
T 83416236
E

44. Project 1. Stop codon readthrough in a mouse model of MMA

Dr Heidi Peters
T 83416257
E

Dr Nicole Buck
T 83416236
E

A large number of diseases including Methylmalonic aciduria (MMA), cystic fibrosis, b-thalassemia and Duchenne muscular dystrophy are caused by premature stop mutations. One way to treat these diseases is to reduce the efficiency of translation termination at stop codons and produce some full length protein. Drugs such as gentamicin can influence the fidelity of the stop codon recognition process and enhance the extent of read-through. We have developed a mouse colony of MMA mice with a stop codon mutation. This project involves characterising the model and treatment of the mice with gentamicin and potentially PTC124 (a new drug currently being trialled). The work will involve the acquisition of a broad range of molecular and cellular biological techniques including tissue culture, flow cytomtery, liver enzymology and measurement of metabolite levels by mass-spectrometry.

45. Project 2. Stem cell transplantation for the treatment of MMA

Dr Heidi Peters
T 83416257
E

Dr Nicole Buck
T 83416236
E

Methylmalonic aciduria is an autosomal recessive inborn error of organic acid metabolism, affecting approximately 1/140,000 children. The condition results from a functional defect in the enzyme methylmalonyl CoA mutase. This project aims to investigate the degree to which a transplanted immature liver cell line can reduce disease and biochemical phenotypes observed in a mouse model with an intermediate phenotype for the human disorder MMA. We have established colonies of transgenic mice which will be transplanted and then characterised biochemically and phenotypically. Tissues will be examined for the presence and level of EGFP expression using fluorescent microscopy, RT-PCR of mRNA, western blot and flow cytometry. The activity of the transplanted cells will also be confirmed by specific liver enzyme assays and measurement of metabolite levels by mass-spectrometry. This project will lead on to extending the work to examine methods of increasing the level of production of MMA enzyme from the cell line. This would involve the use of both viral gene therapy techniques and non viral methods prior to transplantation.

46. Control of nerve cell migration: what goes wrong in Hirschprung’s Disease and how to fix it.

Dr Don Newgreen
T 83416276
E

Heather Young
T 83440007
E

The nervous system of the intestine is crucial for peristalsis. Nerve precursor cells (neural crest stem cells) migrate from the vagal level of the brainstem (hindbrain) into the foregut intestine (duodenum and stomach) at 3 weeks post-conception in humans. They then colonize the rest of the small and large intestine, reaching the rectum by 7 weeks. A common and potentially fatal birth defect, Hirschsprung’s Disease (HSCR) is due to abnormalities in this migration ---the cells do not reach the far end. This is the clearest clinical example of a cell migration defect and this project focuses on understanding migration in normal and HSCR conditions. Mutations in at least 11 genes predispose to HSCR but the inheritance pattern is complex. Our group has made fundamental advances in linking phenotype to genotype in this disease. In this project, molecular and genetic control of intestinal neuron precursor cell migration will be explored in animal (mouse, chick, quail) models, in the whole embryo and in organ culture. We have available techniques to manipulate gene expression and function including transgenic mice and very recently developed and powerful techniques of in vivo gene transfer into chick and quail embryos. Functional outcomes will be followed with time-lapse observations of cells moving in living tissues. This project will develop towards methods of replacing the neural crest cells missing in HSCR via neural crest stem cell therapy. For recent reviews (pdfs), contact above email.

47. Folate supplementation, neurodevelopment and epigenetics

Dr Richard Saffery
T 83416341
E

Dr David Godler
T 83416240
E

DNA methylation has been implicated in chromatin condensation, regulation of global transcriptional activity and nuclear organization. Folate is a principal methyl donor in the majority of biochemical reactions, and is an indirect substrate for S-adenosyl-L-methionine (SAM). Although folate deficiency can cause genome-wide DNA hypomethylation through depletion of SAM; limited folate intake has been also shown to induce silencing of many tumour suppressor genes, attributed to regional hypermethylation. To date the molecular relationship between these two paradoxical phenomena is unknown, however it indicates presence of a finely tuned regulatory mechanism of site-specific epigenetic changes affected by folic acid supplementation – a mechanism that is evident from our preliminary findings. Furthermore, there is ample evidence to suggest that these disturbances result in aberrant gene expression associated with abnormal neurodevelopment. This project aims to study the epigenetic bases behind the neurodevelopmental defects associated with folate over or under supplementation in a mouse model, with a longer-term view to extend the study to humans.

48. The role of altered epigenetics in Paediatric Leukaemia development and outcome?

Dr Richard Saffery T 83416341 E	Dr Nicholas Wong T 83416205 E
Dr Jeff Craig T 83416346 E

Leukaemia is the most common form of cancer in children, accounting for over 30% of newly diagnosed cases. Most cases involved specific genomic rearrangements (translocations). However, these are neither sufficient nor absolutely necessary for disease development. Despite the fact that ~80% of cases are successfully treated by chemotherapy, the underlying causes of childhood leukaemia remain unclear and cannot be explained by genetic or environmental factors alone. Epigenetics is an emerging field examining the modulation of gene expression in the absence of underlying genetic change. We believe disruption of epigenetic profile could play a major role in the aetiology of paediatric leukaemia in conjunction chromosome translocations. This project will catalogue epigenetic changes at gene promoters from archived matched leukaemia and remission bone marrow samples in an attempt to identify changes in associated with development or outcome of specific leukaemia subtypes.

49. What is the role of Epigenetics in Paediatric Leukaemia?

Dr Richard Saffery T 83416341 E	A/Professor Jane Halliday T 83416260 E
Dr Jeff Craig T 83416346 E

50. Investigating the role of altered methylation in schizophrenia

Dr Jeff Craig
T 83416346
E

Dr Richard Saffery
T 83416341
E

Despite the relatively high prevalence (approaching 1%) and devastating social and financial impact, there is presently no “objective” biological test to screen for Schizophrenia risk. The identification of SZ biomarkers is a crucial step towards improving current diagnosis, developing new presymptomatic treatments, identifying high-risk individuals and disease subgroups, and assessing the efficacy of preventative interventions at a rate that is not currently possible. In addition, the identification of brain-specific biomarkers of SZ has the potential to reveal valuable insights into the development of this disorder.
We have data demonstrating that, SZ cases have lower serum folate level than controls with altered epigenetic modification of specific genes in the prefrontal cortex compared to disease free brains.
We now aim to further characterise specific epigenetic biomarkers of SZ in post-mortem brain samples, to identify peripheral epigenetic biomarkers of SZ in blood; and to characterise the downstream functional consequences of this altered methylation profile.

51. Epigenetics and the interaction between folate and vitamin D metabolism at the fetomaternal interface.

Dr Jeff Craig
T 83416346
E

Dr Richard Saffery
T 83416341
E

The fetomaternal interface (placenta: decidua) represents a major site of accumulation of active vitamin D. However the exact role of this remains to be elucidated but may involve immune modulation, regulation of cell division, and/or maximal transfer of VitD to the developing fetus.
Recent data have demonstrated a role of epigenetic modification generally (and DNA methylation specifically) in the regulation of genes involved vitamin D metabolic enzymes that control vitamin D bioavailability and action. As one-carbon donors derived from maternal dietary folate are critical for the establishment of DNA methylation, we believe that sub-optimal circulating levels of vitamin D and folate may act cooperatively to alter vitamin D bioavailability in the developing pregnancy.

52. Epigenetic variation in newborn twins: effect of maternal diet and environment and underlying genetic make up.

Dr Jeff Craig
T 83416346
E

Dr Richard Saffery
T 83416341
E

Many chronic diseases have an environmental component, and can be influenced even by the environment experienced in the womb. We are searching for the factors that, during pregnancy, influence the epigenetic profile of the fetus and with this, the health of the individual at birth and in later life. We have established a cohort of mothers and their newborn twins and have collected maternal blood and various tissues (including cords, cord blood and placenta) from newborns. Maternal nutrition and other environmental factors will be measured in mothers and we will use state-of-the-art methods to analyse epigenetic markers in the twins. We are studying dizygotic twins to investigate the role dietary/lifestyle and genetic factors have on epigenetic variation of newborns. We are also studying monozygotic twins to investigate the extent to which the intra-uterine micro-environment induces the kinds of epigenetic change that have been shown to be associated with increased disease risk. This project will involve analysis of DNA methylation and will techniques such as locus-specific and genome-wide microarray analysis. The student will be working in a supportive environment of fifteen researchers skilled in all the required techniques.

53. Probiotic and Peanut Oral Immunotherapy (P-POIT) for the Treatment of Peanut Allergy

A/Professor Mimi Tang
T 93455911
E

Professor Len Harrison
E

Food allergy is a major public health problem of childhood. 5-8% of children have food allergy, and more than 1 in 70 have peanut allergy. Peanut allergy is of particular concern as a substantial proportion of reactions are life-threatening anaphylaxis, allergy is usually lifelong, and peanut is the most common cause of death due to food anaphylaxis. A promising new treatment approach is the combined administration of a probiotic adjuvant with peanut oral immunotherapy (P-POIT). Our pilot studies show that oral immunotherapy is safe when administered within a careful regimen, is well accepted, and shows preliminary evidence of efficacy with reduced peanut specific IgE and increased peanut specific IgG4. The probiotic Lactobacillus rhamnosus GG has immunomodulatory effects that are expected to enhance the tolerogenic potential of oral immunotherapy.

Students

Please come to our Information Night on: Thursday August 27th, 5.00 - 6.30 PM Ella Latham Theatre Royal Children's Hospital

Biomedical Research PhD Projects in Child & Adolescent Health offered during 2010

Please come to our Information Night on:
Thursday August 27th, 5.00 - 6.30 PM
Ella Latham Theatre
Royal Children's Hospital