Information Technology Research Topics

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					     FACULTY OF SCIENCE &
 INFORMATION TECHNOLOGY




HONOURS RESEARCH TOPICS

                 2009
CONTENTS



School of Design, Communication & IT

    Communication………………………………………………………………..                       2

    Design & Natural History Illustration………………………………….........   2

    Information Technology………………………………………………………                   3


School of Environmental & Life Sciences

    Applied Science (Ourimbah Campus)…………………………………………             7

    Biological Sciences……………………………………………………………….                  9

    Chemistry………………………………………………………………………….                        23

    Earth Sciences……………………………………………………………………                      27

    Geography & Environmental Studies…………………………………………...          33


School of Mathematical & Physical Sciences

    Mathematics……………………………………………………………………..                       34

    Physics……………………………………………………………………………                          36

    Statistics………………………………………………………………………….                       41


School of Psychology

    Psychology……………………………………………………………………….                        43




Faculty of Science and IT - Honours Research Topics (2009)             1
School of Design, Communication & Information Technology

COMMUNICATION:


Documentary Production and Creative Practitioner Research
The research uses a Practitioner-Based Enquiry (PBE) approach in examining how form, format and an
aesthetic style develops through the process of writing/directing independent documentary film. The project
takes a specific focus on various approaches that Australian documentaries take in regard to effective
approaches to the storytelling process. The Tin City project involves the production of a half-hour
documentary program, based on the lives of a small, unique community who reside in tin shacks at the
Stockton Bight, north of Newcastle.

Contact: Ms Susan Kerrigan
Phone: 4985 4517
Email:   Susan.Kerrigan@newcastle.edu.au
Research Group: Design, Information & Human Communication


Creativity and Innovation in Cultural Production
Creativity is not, according to the latest research, a process of self-discovery in a freely expressive romantic
process. Nor is it simply confined to the arts. In fact the latest research is showing that creativity and
innovation involves an agent who necessarily engages with the social and cultural structures that both limit
and enable their creative activity. It is a basic human activity that works across both the arts and sciences. It
is multifactorial in origin. One of the confluence models developed from the current body of research, the
systems model of creativity, is being tested at this University in a number of areas. These include journalism,
children’s literature, songwriting, video and documentary making, website construction, sound and radio
production and so on. Projects are invited that explore similar areas of creative concern via an application of
the systems model. Methodologies include quantitative and qualitative forms (experiments, surveys,
ethnographies and case studies) as well as practitioner-based enquiry (PBE).

Contact: Dr Phillip McIntyre
Phone: 4985 4522
Email:   Phillip.McIntyre@newcastle.edu.au
Research Group: Design, Information & Human Communication




DESIGN & NATURAL HISTORY ILLUSTRATION:

Natural History Illustration
Honours students in Natural History Illustration are encouraged to develop their own projects which will be
reviewed before students are accepted into the program. In the past students have come from a variety of
discipline areas and projects have covered a wide range of topics. Prospective students are encouraged to
submit their proposed project outline for consideration to the Natural History Illustration program convenor Dr
Trevor Weekes. Applicants for admission must have successfully completed a relevant undergraduate
degree or four year diploma in Illustration, Fine Art, Design or equivalent, including science, with a minimum
GPA of 5.0 (Credit Grade Average overall) across the entire program.

Contact: Dr Trevor Weekes
Phone: 492 16371
Email:   Trevor.Weekes@newcastle.edu.au
Research Group: Design, Information & Human Communication




Faculty of Science and IT - Honours Research Topics (2009)                                                   2
INFORMATION TECHNOLOGY:

Applied Techniques in Visual Information Processing
The project aims to investigate various image processing techniques such as filtering, feature extraction,
segmentation, compression and visualization. It will then be applied in solving real problems such medical
imaging, machine vision, robot, scientific visualization. The project requires knowledge of C++ programming,
image formatting and image processing.

Contact: Professor Jesse Jin
Phone: 4985 4505
Email:   Jesse.Jin@newcastle.edu.au
Research Group: Visual Information Processing

Business to Customer Information System
We have developed a B2C (Business to Customer) system and would like to extend it to include some B2B
modules. Various data mining techniques will be used in information management. The project aims to
develop a Web-based E-Business system. Various business portals will be investigated. The project requires
knowledge of apatche, tomcat, J2EE or php programming skills and mysql.

Contact: Professor Jesse Jin
Phone: 4985 4505
Email:   Jesse.Jin@newcastle.edu.au
Research Group: Visual Information Processing


Computer Aided Detection of Intracranial Aneurysms in CT Angiography
The project aims to develop a new generation of computer aided detection (CAD) system that caters for the
emerging needs of scientists, radiologists and industries in assisting the detection and characterisation of
intracranial aneurysms through computer tomography angiography (CAT). Increased accuracy and reduced
time in the detection of intracranial aneurysms on CTA can facilitate earlier detection with the potential to
save lives and function. The CAD system will employ sophisticated image processing algorithms for assisting
radiologists in the detection of suspicious regions that may represent aneurysms. The regions then are
characterised by stochastic and machine learning methods.

Contact: Dr Mira Park
Phone: 4985 4518
Email:   Mira.Park@newcastle.edu.au
Research Group: Visual Information Processing


Computer Aided Detection of Polyp in CT Colonograpy
Colorectal cancer is the most commonly diagnosed, non-cutaneous cancer in Australia. In 2001 there were
12,844 cases of colorectal cancer (6,961 in men and 5,883 in women) and 4,754 deaths (2,601 in men and
2,153 in women). In Australia, the lifetime risk of developing colorectal cancer before 75 years of age is
approximately one in 17 for men, and one in 26 for women. Computerized tomography (CT) colonography,
commonly called virtual colonoscopy, has shown great promise as a non-invasive visualization technique to
search for potentially cancerous polyps since there is no risk of bleeding or colon perforation and intravenous
sedation is unnecessary (RSNA News 2005). Physicians hope it will encourage more people to be screened
for colon cancer. However, the accuracy and efficiency of viewing hundreds of CT images per exam are
limited by human factors such as attention span and eye fatigue. The review of hundreds of images for each
patient is tiring and time-consuming. That is where computer-aided detection (CAD) comes into the picture.
The project aims to develop a computer aided polyp detection (CAPD) system that caters for the emerging
needs of scientists, radiologists and industries in assisting the detection and characterisation of polyps
through CTC.

Contact: Dr Mira Park
Phone: 4985 4518
Email:   Mira.Park@newcastle.edu.au
Research Group: Visual Information Processing




Faculty of Science and IT - Honours Research Topics (2009)                                                 3
Computer modelling in economics, business and the environment
This project offers a number of potential topics for study that include:

a.    Visualisation of massive quantities of model output data
b.    Web interfaces and implementations of models

Contact: Dr Ric Herbert
Phone: 4349 4492
Email:   Ric.Herbert@newcastle.edu.au
Research Group: Visual Information Processing


Finding Temporal Patterns in a 3D Visualisation
In this project the student will develop a generic 3D visualisation of a large data set, such as stock market
data or statistics from a football match. The key aspect of this display is that it will involve opposing and
complementary forces, such as buyers and sellers in the stock market or two opposing football teams. The
aim for the display is to find short temporal patterns in the data that help predict future outcomes, such as the
price of the stock market or the winner of the football match.

Contact: Dr Keith Nesbitt
Phone: 4985 4519
Email:   Keith.Nesbitt@newcastle.edu.au
Research Group: Visual Information Processing


Implementation of Database Privilege Monitor
Eliciting security privilege requirements from users pose a considerable challenge to IT administrators in
today’s complex IT environments. Further, IT users themselves are typically unaware of the different
permissions that are needed to perform their daily activities, thus making it more difficult in determining these
privilege requirements. This project aims to develop a tool, called Database Privilege Monitor, for SQL
Server database server. The tool will allow IT administrators to determine permission requirements of users
by observing the different actions the user performs on a SQL Server database. The student will develop a
program to read SQL Server’s Profiler trace (i.e. XML file) and determine the permissions needed by a
particular user. These permissions will be displayed using a “Privilege Manager Console” to the IT
administrator.

Contact: Dr Rukshan Athauda
Phone: 4952 6964
Email:   Rukshan.Athauda@newcastle.edu.au
Research Group: Visual Information Processing


Information, Perception and Cognition in Multi-sensory Computer Games
Providing players with “Information” is often a critical consideration in the design of computer games. We
may wish to increase or decrease the amount of information depending on the game situation and the
player’s performance. This research investigates how we can manipulate the amount of information being
displayed using multiple senses (visual, sound, touch). This is a broad topic area but it is only expected that
the student will investigate a single relevant issue surrounding perception or cognition in the context of a
current computer game.

Contact: Dr Keith Nesbitt
Phone: 4985 4519
Email:   Keith.Nesbitt@newcastle.edu.au
Research Group: Visual Information Processing




Faculty of Science and IT - Honours Research Topics (2009)                                                   4
Intelligent Reasoning for a ‘Virtual’ Pharmacy Patient
In this project, the student investigates ways to develop the “reasoning” necessary for a computer to act as a
‘virtual’ pharmacy patient. This ‘virtual’ patient is to be used to assess the performance of a pharmacy
student in interviewing, diagnosing, and treating a patient. The reasoning system will simulate typical
responses to questions that the pharmacy student will ask. It will need to recognise the question asked by
the student, and then to match it to a pre-defined list of target questions held in a database. The ‘virtual’
patient will answer the pharmacy student’s questions with an appropriate response, which depends on the
patient’s medical condition and the history of the question/responses that have already occurred during the
interview. The reasoning module is to be implemented in Java. It will interface to other modules that simulate
a face and speech for the virtual patient, and an assessment system that provides the overall assessment
coordination for the pharmacy student.

Contact: Dr Rukshan Athauda
Email:   Rukshan.Athauda@newcastle.edu.au

Contact: Dr Peter Summons
Email:   Peter.Summons@newcastle.edu.au

Contact: Dr Mira Park
Email:   Mira.Park@newcastle.edu.au
Research Group: Visual Information Processing


Issues in Multimedia
The project aims to investigate various multimedia issues such as image retrieval, video cataloguing, 3D
modeling, morphing, animation, special video effects, etc. The student will be required to work in one of the
selected area and develop a workable system for one of the application. For example, the project on video
cataloguing will produce a video database management system which will be capable of archiving and
retrieving video streams. The project requires knowledge of C++ or Java programming and INFT3201
(Multimedia Transmission, Storage and Management)

Contact: Professor Jesse Jin
Phone: 4985 4505
Email:   Jesse.Jin@newcastle.edu.au
Research Group: Visual Information Processing


Modeling Information Flows and Knowledge Retention in Health Practice
Whether it's a busy doctor’s office or a bustling hospital ward, good medical practice can often rely on
efficient transfer and flow of information between doctors, nurses and patients. This area has many potential
projects that focus on how to capture this information, model the flow of knowledge and also develop
effective IT systems for information dissemination and long term knowledge retention. The projects have an
applied focus and will involve working with health professionals in a hospital situation. The primary goal of
these projects is improving patient care.

Contact: Dr Peter Summons
Phone: 4985 4506
Email:   Peter.Summons@newcastle.edu.au
Research Group: Visual Information Processing


Navigating Knowledge using a Metro Map Layout
Metro maps were first introduced on the London Underground and now have become a common place tool
for navigating transport routes around the world. Can more abstract knowledge be represented in this way?
Would such a layout help novice users navigate through the unfamiliar content. For example, a university
subject often contains a number of “tracks” or subject areas that overlap in places. Each track has topics
which can be though of as “stations”. In this project a Metro Map will be developed for a single university
subject and then evaluated in a simple experiment.

Contact: Dr Keith Nesbitt
Phone: 4985 4519
Email:   Keith.Nesbitt@newcastle.edu.au
Research Group: Visual Information Processing

Faculty of Science and IT - Honours Research Topics (2009)                                                5
Real time sensor data on websites
This project offers a number of potential topics for study that include:

a.    How much electricity do solar panels generate: Databases and website display of household solar
      panel data;
b.    Comparing different sensor data.

Contact: Dr Ric Herbert
Phone: (02) 4349 4492
Email:   Ric.Herbert@newcastle.edu.au
Research Group: Visual Information Processing


Reducing e-waste by extending the life of junked computing equipment
This project offers a number of potential topics for study that include:

a.    Constructing grids of e-waste computers ;
b.    Software applications for grids of recycled computers (e.g. data cleaning and mining; database
      servers);
c.    Business models for making grids of recycled computers financially sustainable;
d.    Web and other applications using junked computing equipment.

Contact: Dr Ric Herbert
Phone: (02) 4349 4492
Email:   Ric.Herbert@newcastle.edu.au
Research Group: Visual Information Processing


Simulating Agent-based Emotions
In this project the student will develop an agent-based simulation to be used in a computer game. A key
aspect of these agents is that they will have a simple model of conflicting “emotions” that will influence the
game play. The model of emotion may draw on existing ideas from psychology, neuroscience and artificial
intelligence. The “emotional” model itself will be relatively simple although complex dynamics may emerge
from the interaction of the agents in the game world.

Contact: Dr Keith Nesbitt
Phone: 4985 4519
Email:   Keith.Nesbitt@newcastle.edu.au
Research Group: Visual Information Processing


Using Software Design Principles to ‘improve’ Teaching Materials
This research project investigates the use of software design approaches (object-modelling, processes,
patterns, architectures) to improve the quality of instructional materials? The project will focus on existing
courses in Bit degree and examine how a software engineering design approach could impact on the
reusability, generativity, adaptability, scalability and quality of learning resources?

Contact: Dr Keith Nesbitt
Phone: 4985 4519
Email:   Keith.Nesbitt@newcastle.edu.au
Research Group: Visual Information Processing




Faculty of Science and IT - Honours Research Topics (2009)                                                6
School of Environmental & Life Sciences

APPLIED SCIENCE (OURIMBAH CAMPUS):


Adaptation of resistance training methods to female steroid hormone fluctuations
The female steroid hormone oestrogen is known for its anabolic effects. It would therefore be expected that
conditions for muscle growth are better when oestrogen is elevated. Thus the variability in oestrogen levels
due to the menstrual cycle may affect the ability of skeletal muscle to respond to training. The aim of this
research is to establish if adaptations of resistance training programs to fluctuations in oestrogen will result
in greater strength gains than traditional training programs.

Significant improvements with the oestrogen adapted training would revolutionize training regimes for female
athletes and assist in improving musculoskeletal rehabilitation programs for females.

Contact: Dr Xanne Janse de Jonge
Phone: (02) 4349 4566
Email:   x.jansedejonge@newcastle.edu.au
Research Unit: Exercise & Sport Science


Effects of coagulant type and concentration on the quality attributes of tofu
The quality of tofu is significantly influenced by the type of coagulant and the process followed. Coagulation
of soymilk is the most important step in tofu making and the most difficult to control because it depends on
the interrelationships of many variables. The objective of this study is to determine the effect the type and
concentration of coagulant has on the yield and the quality characteristics of the final product during small
scale tofu manufacture.

Contact: Dr Costas Stathopoulos
Phone: (02) 4348 4124
Email:   costas.stathopoulos@newcastle.edu.au
Research Group: Nutrition, Food & Health


Role of the C1520T-SHMT folate polymorphism in colonic adenoma formation
Serinehydroxymethyltransferase (SHMT) regulates entry of carbon units into folate dependent one-carbon
metabolism. Such carbon units are ultimately used to convert homocysteine into denovo methionine.
Methionine contributes methyl groups for epigenetic modifications that modulate gene expression. If the
common C1520T-SHMT polymorphism alters methionine level it may act as a risk factor for early dysplastic
changes in the colonic epithelium via altered CpG methylation of DNA. The prevalence of this SNP will be
examined in patients with and without colonic polyps.

Contact: Dr Mark Lucock
Phone: (02) 4348 4109
Email:   mark.lucock@newcastle.edu.au

Contact: Dr Zoe Yates
Phone: (02) 4349 4560
Email:   zoe.yates@newcastle.edu.au

Contact: Dr Paul Roach
Phone: (02) 4348 4129
Email:   paul.roach@newcastle.edu.au

Contact: Dr Martin Veysey
Phone: (02) 4320 3022
Email:   mveysey@nsccahs.health.nsw.gov.au
Research Group: Nutrition, Food & Health




Faculty of Science and IT - Honours Research Topics (2009)                                                  7
Role of the C1520T-SHMT folate polymorphism in hypertension
Serinehydroxymethyltransferase (SHMT) regulates entry of carbon units into folate dependent one-carbon
metabolism. Such carbon units are ultimately used to convert homocysteine into methionine. Homocysteine
is a vasculotoxic thiol that acts as an independent risk factor for CVD with the same magnitude of effect as
cholesterol. This study will see if the common C1520T-SHMT polymorphism alters homocysteine level and
acts as a risk factor for hypertension in an elderly Australian population.

Contact: Dr Mark Lucock
Phone: (02) 4348 4109
Email:   mark.lucock@newcastle.edu.au

Contact: Dr Zoe Yates
Phone: (02) 4349 4560
Email:   zoe.yates@newcastle.edu.au

Contact: Dr Paul Roach
Phone: (02) 4348 4129
Email:   paul.roach@newcastle.edu.au

Contact: Dr Martin Veysey
Phone: (02) 4320 3022
Email:   mveysey@nsccahs.health.nsw.gov.au
Research Group: Nutrition, Food & Health


Synthesis of New Chiral Bispidinone Ligand Systems
Coordination compounds exhibiting C2 symmetry are widely used in industry to induce the formation of chiral
products from achiral starting materials. We are interested in developing new tetradentate ligands systems
that incorporate the bispidinone skeleton and a amino acid pendant arms for evaluation as chiral ctatlysts.

Contact: Dr Mike Bowyer
Phone: (02) 4348 4119
Email:     Michael.Bowyer@newcastle.edu.au
Priority Research Centre for Organic Electronics

Contact: Professor Geoffrey Lawrance
Phone: (02) 4921 5474
Email:   Geoffery.Lawrance@newcastle.edu.au
Research Group: Advanced Synthetic Materials




Faculty of Science and IT - Honours Research Topics (2009)                                              8
BIOLOGICAL SCIENCES:


Research in Plant and Cell Development, Functional Genomics and Plant Biotechnology

i)      The Transcriptional Regulation of the Partitioning Between Oil and Protein in the Developing
        Legume Embryo and Seed for Improved Nutrition or Use as Biofuels
        This project will build on the improved understanding we have of the transcriptional regulation and
        cell biology of embryo development in the model legume Medicago truncatula. The use of legume
        grain crops reduces the need for expensive and energy requiring nitrogen fertilisers. A third of
        flowering plants are legumes and different species can make a major contribution to human nutrition
        as well as for biodiesel.

ii)     Investigation of the Transcription Factor MtSERF1 Required for Somatic Embryogenesis
        We have discovered a new transcription factor we call MtSERF1 that is essential for somatic
        embryogenesis and there is evidence that it does this by connecting the development response (due
        to the hormones auxin and cytokinin) to the stress response due to the production of the stress
        hormone ethylene. This Project examines the signalling interactions connecting MtSERF1 to embryo
        induction. This work will provide the potential to enable genetic transformation to be carried out in a
        wider range of plant species and cultivars, can be applied to new plant breeding strategies for hybrid
        vigour and can enable an improved understanding of the regulation of plant development.

iii)    Turning a single somatic cell into a whole plant – the first cell division
        Our recent work has suggested that reactive oxygen species (ROS) are essential signals in the
        induction of cell division and that peroxisome biogenesis and dynamics are part of controlling ROS at
        suitable levels. With an increasing CILR emphasis on unravelling the complexity of RNA biology in
        gene regulation, this work will be extended into visualising P-bodies and their dynamics (size,
        number and location). P-bodies are associated with mRNA degradation and storage and there is
        little information about these structures in plant cells. We hypothesise that P-bodies are connected to
        the genetic reprogramming associated with the induction of cell division.

        Contact: Prof Ray Rose
        Phone: 4921 5711
        Email:   Ray.Rose@newcastle.edu.au
        ARC Centre of Excellence for Integrative Legume Research (CILR)


Biomarkers of Heavy Metal Stress in Mangrove Ecosystems
Examining the effects of metal stress on the up-regulation of genes encoding enzymes specific to metal
detoxification in mangroves for environmental protection.

Contact: Dr Geoff MacFarlane
Phone: 4921 7858
Email:   geoff.macfarlane@newcastle.edu.au
Research Group: Environmental Biology and Biotechnology


Koala Chlamydia Vaccine Development
The Chlamydias, particularly the strains C. pecorum and C. pneumoniae, are a major cause of disease in
koalas. Chlamydial disease in the urogenital tract causes wet bottom, inflammation, lesions and sterility.
Infection of the respiratory tract and eyes causes pneumonia, conjunctivitis and blindness. Yet there is
currently no preventative treatment for this disease in koalas. This project aims to underpin the development
of an effective koala chlamydia vaccine by conducting a comprehensive survey of chlamydial genotypes,
prevalence, and disease transmission in local koala populations. Vaccine formulation and delivery strategies
capable of eliciting appropriate protective immune responses in the marsupial reproductive tract are also
being investigated.

Contact: Dr Merrilee Harris or Prof John Rodger
Phone: 4921 7784
Email:   Merrilee.Harris@newcastle.edu.au
Research Group: Environmental Biology and Biotechnology (Marsupial Research Laboratory)


Faculty of Science and IT - Honours Research Topics (2009)                                                 9
Oral Delivery of Contraceptive Vaccines to Macropods
Fertility regulation is a desirable management tool for over abundant or pest marsupials provided that it can
be delivered in a field effective manner which is humane and poses no significant environmental hazards.
Surgical sterilization and hormone implants have been used for control of captive kangaroos and local koala
populations. However, these techniques are invasive and not cost effective long-term for the control of free-
ranging populations. Our research has indicated that contraceptive or sterilizing vaccines for marsupials
have the potential for specificity to reproductive function, and possibly species, while not perturbing normal
behaviour. The next challenge is field appropriate delivery of the vaccine. The goal of this project is to
develop field deliverable vaccines (via orally delivered baits) for overabundant macropods. The research is
focused on optimizing the formulation and efficacy of orally delivered vaccines. Factors that affect bait
uptake (eg animal behaviour, feeder design) are also being investigated.

Contact: Dr Merrilee Harris or Prof John Rodger
Phone: 4921 7784
Email:   Merrilee.Harris@newcastle.edu.au
Research Group: Environmental Biology and Biotechnology (Marsupial Research Laboratory)


Oyster biomonitor for assessing estrogenic effects of contaminants
The development and validation of the Sydney rock oyster, as a biological sentinel system for assessing the
impact of endocrine disrupting contaminants Biochemical markers, gene expression, proteomics and
reproductive endpoints in oysters are employed as sensitive indicators of exposure and effect allowing
anticipatory monitoring and protection.

Contact: Dr Geoff MacFarlane
Phone: 4921 7858
Email:   Geoff.Macfarlane@newcastle.edu.au
Research Group: Environmental Biology and Biotechnology


Zona Pellucida Based Contraceptives for Koalas and Kangaroos
Marsupials are of fundamental importance to the Australian environment, however some species (e.g. koala
and grey kangaroo) have become over abundant within isolated habitat because of environmental changes
since European settlement. Such overpopulation has negative impacts on the entire ecosystem, including
the abundant species itself. Vaccines based on the zona pellucida, an extracellular matrix surrounding the
egg, have been shown to reduce the fertility of a variety of marsupial species however this effect is not
species specific. This project is refining zona pellucida based immunocontraceptive vaccines for koalas and
kangaroos by testing the contraceptive efficacy of vaccines based on macropod specific immunogenic
peptides and koala zona pellucida 2 sequences. It will also identify critical immunological processes
correlated with infertility so that they can be more effectively targeted by incorporation of immune modulating
molecules or adjuvants.

Contact: Dr Merrilee Harris or Prof John Rodger
Phone: 4921 7784
Email:   Merrilee.Harris@newcastle.edu.au
Research Group: Environmental Biology and Biotechnology (Marsupial Research Laboratory)


Characterisation of bacterial transcription complexes
We still know very little about all the factors that regulate RNA polymerase. This project is designed to rapidly
isolate bacterial transcription complexes using a novel tandem affinity purification (TAP) system. Individual
RNA polymerase genes will be tagged with a TAP epitope and complexes isolated for characterisation by
mass spectroscopy. The involvement of individual proteins in transcription will then be confirmed by
reciprocal tagging, deletion, and GFP tagging.

Contact: A/Prof Peter Lewis
Phone: 4921 5701
Email:   Peter.Lewis@newcastle.edu.au
Research Group: Genomes, Organelles and Development (GOD) - Molecular Microbiology




Faculty of Science and IT - Honours Research Topics (2009)                                                   10
Determination of the RNA polymerase-binding residues of the essential transcription factor NusA
NusA is a transcription factor that is essential and unique to bacteria. Therefore, preventing NusA interacting
with RNA polymerase would lead to cell death, and targeting this interaction represents a promising target
for antibiotic development. We have recently determined the structure of NusA in complex with RNA
polymerase, and determined at low resolution the regions of RNA polymerase and NusA that interact. This
project is designed to carry out mutagenesis on the RNA polymerase binding domain of NusA, followed by
mutant purification and binding assays to establish which specific residues of NusA are involved in its
interaction. Results from this study can then be used in the rational targeting of this area to design inhibitors
of the interaction.

Contact: A/Prof Peter Lewis
Phone: 4921 5701
Email:   Peter.Lewis@newcastle.edu.au
Research Group: Genomes, Organelles and Development (GOD) - Molecular Microbiology


Genetic manipulation of Staphylococcus aureus
Staphylococcus aureus (Golden staph) is a major human pathogen that has acquired resistance to most
commonly used antibiotics. This project is designed to develop genetic tools for the rapid manipulation of
golden staph in order that genes involved in transcription, DNA replication and cell division can be easily
tagged. This will enable the rapid isolation and characterisation of proteins/protein complexes that represent
targets for the development of new antibiotics.

Contact: A/Prof Peter Lewis
Phone: 4921 5701
Email:   Peter.Lewis@newcastle.edu.au
Research Group: Genomes, Organelles and Development (GOD) - Molecular Microbiology


Structural analysis of novel bacterial transcription factors
In order to design new antibiotics it is important to know the structure of the drug targets. Protein
crystallography is a well established technique designed to elucidate the structure of proteins. Several novel
proteins that interact with bacterial RNA polymerase have recently been identified and could potentially
represent new targets for antibiotic development. This project is designed to initiate protein crystallography
studies on these proteins in order to determine how they interact with RNA polymerase and, in turn, how
they could modulate its activity.

Contact: A/Prof Peter Lewis
Phone: 4921 5701
Email:   Peter.Lewis@newcastle.edu.au
Research Group: Genomes, Organelles and Development (GOD) - Molecular Microbiology


Manipulating cell wall biosynthesis for bio-energy and fibre yield
This project will use cotton fibre as a model system to identify gene targets for modification of plant cell wall
composition to increase efficiency of biofuel production and cotton fibre yield.

Contact: A/Prof Yong-Ling Ruan
Phone: 4921 7958
Email:   Yong-Ling.Ruan@newcastle.edu.au
Research Group: Plant Science


Manipulating water channel genes for improvement of drought tolerance of crops
This project will study water channel genes in the control of water movement in plant cells and design
innovative approaches to increase drought tolerance of crops.

Contact: A/Prof Yong-Ling Ruan
Phone: 4921 7958
Email:   Yong-Ling.Ruan@newcastle.edu.au
Research Group: Plant Science



Faculty of Science and IT - Honours Research Topics (2009)                                                   11
Nutrient Allocation
Both fundamental and applied research is directed at:

i)      Nutriomics. Nutrient (especially sugars) transport and metabolism within organs of agronomic
        significance (e.g. fruit and seed).

        Novel membrane transporters
        As membrane transport of sucrose is a key determinant of crop yield, a detailed understanding of
        genes encoding sucrose transporters provides fundamental knowledge towards increasing crop
        yield. This project aims to determine the inter- and intracellular localizations of these important
        proteins.

        Contact: Prof Christopher Grof
        Phone: 4921 5858
        Email:   Chris.Grof@newcastle.edu.au
        Research Group: Plant Science


        Enhancing sugar accumulation in tomato fruit
        Fruit sugar levels are a significant agronomic trait. Sugar transporters have been shown to regulate
        this trait. The project will screen site-directed mutants of transporters in a functional expression
        system to select those with enhanced kinetic properties.

        Contact: A/Prof David McCurdy
        Phone: 4921 5879
        Email:   David.Mccurdy@newcastle.edu.au
        Research Group: Plant Science


i)      Transfer cell development. Specialised cells that play a vital role in nutrient allocation.

        Building transfer cell wall ingrowths
        Transfer cells have intricately-invaginated wall ingrowth labyrinths that greatly amplify their plasma
        membranes which in turn contain high densities of nutrient transporters. The wall ingrowths are
        initially deposited as papillate structures at loci in response to inductive signalling by ethylene,
        reactive oxygen species (ROS) and Ca2+. This project involves isolation of lipid rafts (membrane
        aggregation centres for wall building molecules) and visualization of their distribution when transfer
        cell induction is perturbed using signal cascade inhibitors. The concept of lipid raft involvement in
        wall deposition is new; outcomes of the project will contribute significantly to our understanding of
        wall ingrowth formation.

        Contact: Prof Tina Offler (Conjoint)
        Phone: 4921 5704
        Email:   Tina.Offler@newcastle.edu.au
        Research Group: Plant Science

        Manipulating Transfer Cell Development
        This project will use the model species Arabidopsis to investigate genetic control of transfer cell
        development. Identifying transcriptional cascades involved in this process will provide new avenues
        for manipulating crop yield. The project involves gene expression analysis, fluorescence microscopy,
        and mutant analysis.

        Contact: A/Prof David McCurdy
        Phone: 4921 5879
        Email:   David.Mccurdy@newcastle.edu.au
        Research Group: Plant Science




Faculty of Science and IT - Honours Research Topics (2009)                                                12
iii)    Cotton fibre development. A single-cell system, ideal for studying cell growth and cellulose
        synthesis.

        Cotton is the most important textile crop world-wide due to its cellulose-enriched fibres developed
        from the seed epidermis. Each cotton fibre is a single-cell that elongates up to 3~6 cm long and
        synthesizes a massive amount of cellulose. This project aims to understand the molecular and
        cellular basis of rapid fibre cell expansion and cellulose synthesis with the final goal to improve fibre
        yield, quality and tolerance to drought by manipulating identified key genes and processes.

        Contact: A/Prof Yong-Ling Ruan
        Phone: 4921 7958
        Email:   Yong-Ling.Ruan@newcastle.edu.au
        Research Group: Plant Science

iv)     Biofuels. Maximising carbon capture by key crops as a biofuel feedstock.

        Sorghum, a biofuel feedstock for arid environments.
        Increasing fuel costs, finite resources and the need to develop more carbon neutral and cleaner fuels
        have created a need for renewable resources. Sorghum bicolor (Sorghum) is a crop plant adapted to
        the hot water limited environments of northern Australia, both as a grain and forage crop. As a result
        of its rapid growth rate, sorghum is an ideal crop for biofuel production from grain, sugar and
        biomass accumulation.

        Identification and characterisation of sucrose transporters in sorghum.
        As membrane transport of sucrose is a key determinant of crop yield, a detailed understanding of
        genes encoding sucrose transporters provides fundamental knowledge towards increasing crop
        yield. The project will involve:

               Detailed bio-informatic investigation of the complete sorghum genome to seek out all
               sucrose/hexose transporter sequences.
               Quantitative expression analysis using RT-qPCR from RNA isolated from sorghum tissues and
               organs.
               Immunolocalisation of selected transporters.
               Functional characterisation in yeast mutants.

        Contact: Prof Christopher Grof
        Phone: 4921 5858
        Email:   Chris.Grof@newcastle.edu.au
        Research Group: Plant Science


Reconstructing Sustainable Ecosystems

i)      Rebuilding soils. Use of plant-microbe associations to re-establish nutrient cycling.

        Rebuilding soil function
        In badly disturbed ecosystems such as where logging, grazing and mining have occurred, soil
        function has largely been lost or restricted by erosion, compaction, and physical disturbance. Our
        principal aims are to capture remaining components of soil biota, determine their role in functional
        soil, culture them, and return them to reconstructed forest and woodland using experimental
        methods.

        Contact: Mike Cole (Conjoint), CSER Director
        Phone: 4921 5575
        Email:    Mike.Cole@newcastle.edu.au
        Plant Science Group, Centre for Sustainable Ecosystem Restoration (CSER)




Faculty of Science and IT - Honours Research Topics (2009)                                                   13
ii)     Restoration Potential. Addressing ecological bottlenecks by modifying, monitoring and modelling
        native vegetation communities.

        Restoration Potential, Dispersal, Sustainability and Resilience
        Ecosystems that have suffered loss of structure and function due to logging and grazing can have
        bottlenecks preventing pollination, dispersal and the development of regeneration potential. We are
        using remnant forest and developing dispersal sources to enable understanding of future limitations
        to regeneration potential and modelling of forest composition. As part of this research we are
        building and calibrating models of sustainability and resilience. The ecological conductance model
        seeks to explain the ease or difficulty that organisms confront in completing their life cycles and
        building restoration potential. Current research is focussed on quantifying the resistances to life cycle
        completion, including pollination success; seed production and viability; the ability to be recruited into
        a sustainable population; to form associations with soil microbes; and the development of both
        spatial and temporal dispersal vectors.

        Contact: Mike Cole (Conjoint), CSER Director
        Phone: 4921 5575
        Email:    Mike.Cole@newcastle.edu.au
        Plant Science Group, Centre for Sustainable Ecosystem Restoration (CSER)


Advanced proteomic research – application of molecular imprinting

i)      Recognition of Different Conformations of Protein Secondary Structure by Molecular
        Imprinting
        Turner et al have performed proof of concept studies of using molecular imprinting to recognise
        different isoforms of the same protein. This study suggests that direct discrimination of isoforms via
        an artificial receptor is possible, however this initial work needs validating with further examples.

        This honours project will aim to provide this, by studying alternate model systems (Lysozyme and α-
        lactalbumin) to verify the validity of this technique. As well as using the techniques developed in the
        pilot study, this project will look at modifying the imprint matrix to improve sensitivity and affinity.

        This project would suit a biochemist, with interests in structural biology, molecular recognition, and/or
        chemistry at the biological interface.

        Contact: Dr Nicholas Turner, Dr Mark Baker, Professor John Aitken
        Phone: 4921 6143
        Email:     John.Aitken@newcastle.edu.au
        Priority Research Centre for Reproductive Science

ii)     Removal of Interfering Proteins from Blood Serum
        Human Serum Albumin (HSA) makes up approximately 50-60% of blood serum protein, and as such
        can be a problem when screening serum for biomarkers, which tend to be short peptides. A matrix
        that could specifically filter out this abundant protein, leaving other components behind would be
        highly beneficial.

        Molecular imprinting is a technique which creates artificial recognition sites (binding pockets) in
        polymeric materials, and has demonstrated the potential to specifically bind proteins. This project will
        focus on creating a gel filter matrix that by size exclusion and molecular imprinting will be able to
        specifically remove albumin from serum, without removing any markers of interest. Success will
        create a material which will improve screening processes for molecular biological applications.

        This project would suit a biochemist, with interests in protein chemistry, molecular recognition, and/or
        chemistry at the biological interface.

        Contact: Dr Nicholas Turner, Dr Mark Baker, Professor John Aitken
        Phone: 4921 6143
        Email:     John.Aitken@newcastle.edu.au
        Priority Research Centre for Reproductive Science




Faculty of Science and IT - Honours Research Topics (2009)                                                    14
Analysis of the mechanisms generating DNA damage in human spermatozoa
This project involves examining the nature of the environmental factors that might induce DNA damage in
human spermatozoa. Current emphasis is on the identification of an endonuclease which we believe to be
activated by a variety of stressors (temperature/oxidative stress/electromagnetic radiation/age) and be
responsible for the induction of much of the DNA damage we see in infertile patients. The results of this
research will have a bearing on assisted conception therapy and public awareness of the impact of
environmental factors on reproductive heath.

Contact: Laureate Professor John Aitken, Dr Mark Baker, Dr Ari Pujianto, Dr Geoff De Iuliis
Phone: 4921 6143
Email:     John.Aitken@newcastle.edu.au
Priority Research Centre for Reproductive Science


Assessment of oocyte and embryo quality
A major task in the assisted conception industry is to develop no-invasive methods for the evaluation of
oocyte and embryo quality. We have patented an approach to this problem and now wish to refine the assay
technique, using conditioned embryo culture media from Hunter IVF and samples of follicular fluid. The
same fundamental chemistry will be used to develop a diagnostic test for male infertility.

Contact: Laureate Professor John Aitken, Dr Mark Baker, Dr Ari Pujianto, Dr Geoff De Iuliis
Phone: 4921 6143
Email:     John.Aitken@newcastle.edu.au
Priority Research Centre for Reproductive Science


Translational control of folliculogenesis and oocyte development: role of the RNA binding protein
Musashi-1
Coordinated post-transcriptional regulation of the oocyte mRNA pool is critical for the control of the finite pool
of primordial follicles, normal progression of chromatin condensation and ultimately healthy oocyte
production. Using our mouse and Drosophila model systems, we have recently identified the Musashi family
of RNA binding proteins as key regulators of folliculogenesis and oocyte development. Historically, Musashi
proteins have been identified in both neural and epithelial stem cells where they function as translational
repressors. We have recently identified a novel member of the Musashi family in Drosophila ovary, which
also functions as a translational repressor of key regulators of oocyte nuclear maturation and meiotic
progression and have characterised the expression of the mammalian homologue Musashi-1 in the mouse
ovary. In this project we aim to characterise the signalling pathways of Musashi-1 oocyte specific
overexpression and knockout in transgenic and null mice using gene and protein expression profiling.

Contact: A/Prof Eileen McLaughlin
Phone: 4921 5708
Email:     Eileen.Mclaughlin@newcastle.edu.au
Priority Research Centre for Reproductive Science


Spermatogenesis and Stem Cells

i)      Chemokines and spermatogenesis: roles of SDF-1 and CXCR-4
        In the mammalian testes, numerous spermatozoa are continuously produced throughout adult
        reproductive life. This process, known as spermatogenesis, is dependent on the establishment early
        in neonatal development, of a population of self renewing germ line stem cells known as GSC’s,
        from which the highly differentiated haploid spermatozoa are produced. Little is known about the
        molecular and cellular mechanisms underlying the creation of GSC’s from their immediate
        progenitors, the gonocytes, and how the stem cell niche in which they reside in the testes is defined.
        Recent evidence from our laboratory suggests that a chemokine SDF-1 and its receptor CXCR-4 are
        intimately involved in the processes of gonocyte survival and differentiation in the fetal testes and the
        eventual migration of the GSC population to the stem cell “niche” located in the basement membrane
        in the post natal testes. The aims of this proposal are: to elucidate the mechanism of maintenance
        and migration of male germ cells in the developing testis and the role of SDF-1/CXCR-4 interaction
        in the establishment of stem cell populations in the germ cell niche, to characterize the signalling
        pathways activated by CXCR-4 and their role in germ cell differentiation and to investigate the use of
        knockdown and overexpression technologies in vivo and in vitro to manipulate germ cell survival and
        differentiation.

Faculty of Science and IT - Honours Research Topics (2009)                                                    15
ii)     Retention of Spermatogonial Stem cell phenotype
        Crucial to spermatogenesis are a number of RNA binding proteins, which are expressed in germ
        cells. These proteins are responsible for the control of post-transcriptional regulation of the multitude
        of mRNAs coding for proteins essential for latter stages of germ cell and spermatozoal development.
        Musashi (Msi) is an RNA binding protein family and we recently investigated the role of Musashi
        family in the Drosophila and mouse testes and showed that Drosophila Msi is both expressed and
        required in spermatogonial stem cells for maintenance of stem cell fate. We also found that cell-
        autonomous loss of Msi in the Drosophila testis results in the premature differentiation of
        spermatogonial stem cells, indicating an intrinsic requirement for Msi for regulation of stem cell
        maintenance – we have produced a transgenic msi1 mouse for overexpression studies and this
        project aims to characterise this mouse.

        Contact: A/Prof Eileen McLaughlin
        Phone: 4921 5708
        Email:   Eileen.Mclaughlin@newcastle.edu.au

        Contact: Dr Shaun Roman
        Phone: 4921 6818
        Email:   Shaun.Roman@newcastle.edu.au

        Contact: Dr Brett Nixon
        Phone: 4921 6977
        Email:     Brett.Nixon@newcastle.edu.au
        Priority Research Centre for Reproductive Science


iii)    Molecular Pathways of Germ Cell Differentiation
        We are seeking to understand the transition from spermatogonia to spermatocyte at the molecular
        level. We have identified 2 signalling pathways that interact during spermatogonial differentiation: the
        BMP4 and retinoid pathways. Previously, we have found that the metabolites of vitamin A, known as
        retinoids, regulate BMP4 gene expression. The major metabolite of vitamin A is not the active
        molecule in this case. This challenges a dogma. Testis and germ cells will be examined for vitamin A
        metabolites. Retinoids, both extracted and commercially available, will be tested by assessing their
        affects on BMP4 gene expression in isolated cells.

        Using array technology we have previously identified a number of other genes also regulated by
        retinoids in the testis. We now intend to determine which of these regulated genes are expressed in
        spermatogonia. A separate array approach has suggested some candidates. One project involves
        confirming the expression and regulation of candidates in spermatogonia treated with a number of
        retinoids with a focus on the regulation of BMP4 gene expression. Another project involves further
        analysis of the two sets of array data in combination with published data sets relating to stem cells
        from other populations. We are also developing a number of models of BMP4 signalling in the
        germline. These will allow us to determine the role of BMP4 in spermatogonial differentiation. A
        project exists in characterising the molecular response of the germ line to BMP4.


iv)     Transgenerational toxicity
        We are interested in the response of the male germ line to exposure with foreign compounds
        (xenobiotics). Such exposure can lead to defects in the offspring indicating damage at the level of
        DNA. We are trying to elucidate the mechanism of damage generation. Using microarray technology
        we established the cyp gene profile in the male germ line. Cyp genes encode for the phase I
        detoxifying enzymes; the cytochrome P450s. Further studies on gene expression and toxicology in
        germ cells are required. In particular we are interested in assessing changes in cyp expression in
        response to toxicant treatment. We are also looking to measure the formation toxicant-DNA adducts.
        Currently we are establishing a DNA damage assay based on real time PCR. This work has been
        carried out on human DNA. We are interested in establishing this assay in mouse germ cells with a
        view to high throughput testing of the germ cell response to xenobiotic compounds.

        Contact: Dr Shaun Roman
        Phone: 4921 6818
        Email:     Shaun.Roman@newcastle.edu.au
        Priority Research Centre for Reproductive Science


Faculty of Science and IT - Honours Research Topics (2009)                                                   16
v)      DNA damage in the Germline
        DNA damage in the male germline is associated with poor fertilization rates following IVF, defective
        preimplantation embryonic development, and high rates of miscarriage and morbidity in the offspring,
        including childhood cancer. This damage is poorly characterized, but is known to involve
        hypomethylation of key genes, oxidative base damage, endonuclease mediated cleavage and the
        formation of adducts with xenobiotics and the products of lipid peroxidation. There are many possible
        causes of such DNA damage, including abortive apoptosis, the oxidative stress associated with male
        genital tract infection, exposure to redox cycling chemicals, and defects of spermiogenesis
        associated with the retention of excess residual cytoplasm. Physical factors such as exposure to
        radiofrequency electromagnetic radiation or mild scrotal heating can also induce DNA damage in
        mammalian spermatozoa, although the underlying mechanisms are unclear. Ultimately, resolving the
        precise nature of the DNA lesions present in the spermatozoa of infertile men will be an important
        step towards uncovering the aetiology of this damage and developing strategies for its clinical
        management.

        Contact: Laureate Professor John Aitken
        Phone: 4921 6143
        Email:     John.Aitken@newcastle.edu.au
        Priority Research Centre for Reproductive Science


Cell Biology of Spermatozoa

i)      Epididymal Transit and Maturation
        Upon leaving the testis, spermatozoa are incapable of progressive movement or the cascade of
        cellular events that result in fertilization of the oocyte. These functional characteristics are only
        acquired as spermatozoa undergo maturation during epididymal transit. Given the absolute
        importance of epididymal maturation for the generation of fertile spermatozoa, it is clearly important
        that the molecular mechanisms supporting this functional transformation be elucidated. Success in
        this area will have implications both for development of reversible male contraceptive agents and the
        aetiology of male infertility. This project aims to characterise changes in tyrosine phosphorylation
        and mitochondrial activation which appear to be particularly important parts of epididymal
        maturation.

        Contact: Dr Brett Nixon
        Phone: 4921 6977
        Email:   Brett.Nixon@newcastle.edu.au

        Contact: Laureate Professor John Aitken
        Phone: 4921 6143
        Email:     John.Aitken@newcastle.edu.au
        Priority Research Centre for Reproductive Science

ii)     Capacitation and Development of Fertilizing Ability
        Transcriptionally inactive spermatozoa rely totally on Post-translational modifications in order to
        acquire functional competence. These processes occur in two distinct phases; firstly, spermatozoa
        pass through the epididymal luman, and secondly, inside the female reproductive tract as sperm
        capacitate. Both events are essential for fertility, however, the biochemical mechanisms behind the
        maturation of these cells is unclear. This project aims to characterise the entire gamete of proteins
        present in spermatozoa. It will also decipher which proteins (peptides) are up/down regulated, or
        completely new/lost during both maturation procedures. changes in tyrosine phosphorylation and
        mitochondrial activation which appear to be particularly important parts of epididymal maturation.

iii)    Mitochondrial Function and Reactive Oxygen Species
        Reactive oxygen species (ROS) are conventionally considered as detrimental by-products of cellular
        metabolism, which generate a state of oxidative stress in susceptible cells. Despite the
        pathophysiological significance of ROS generation in the male germ line, neither the sub-cellular
        origin nor the biochemical basis for this activity has been established. The major source of ROS
        generation in somatic cells is postulated to involve electron leakage from the mitochondrial electron
        transport chain during cellular respiration. In view of our poor understanding of mitochondrial
        function in spermatozoa, and the potential importance of these organelles as a potential source of
        oxidative stress in the male germ line in particular, this project is an analysis of the potential
        competence of human sperm mitochondria to generate ROS and to characterise the significance of
        this activity in the aetiology of defective sperm function.
Faculty of Science and IT - Honours Research Topics (2009)                                                17
        Contact: Laureate Professor John Aitken
        Phone: 4921 6143
        Email:     John.Aitken@newcastle.edu.au
        Priority Research Centre for Reproductive Science

iv)     Monotreme sperm biology
        As iconic symbols of Australia’s unique fauna the platypus and echidna generate considerable
        interest from tourists and the Australian public, thus ensuring that their display in zoos is of
        significant commercial value. Nevertheless, the record of breeding the 3 extant monotremes in
        captivity is poor, and the New Guinea echidna faces extinction in the wild. Consequently, knowledge
        of monotreme reproductive biology is important for conservation practices. This project focuses on
        elucidation of the molecular processes leading to fertilization in monotremes, including: the proteins
        which form sperm into bundles to greatly enhance their motility (a unique sperm competition
        strategy) and the mechanisms involved in sperm bundle formation. The work will provide an
        understanding of the biological significance of adaptations unique to mammals, the need for
        maturation of sperm in the epididymis and a subsequent period of capacitation before they are
        capable of fertilizing an ovum.

        Contact: Dr Brett Nixon
        Phone: 4921 6977
        Email:     Brett.Nixon@newcastle.edu.au
        Priority Research Centre for Reproductive Science


Oocytes and Folliculogenesis

i)      Musashi 1 and 2
        There is major interest in the molecular mechanisms regulating the maintenance and development of
        oocytes in the mammalian ovary. Exhaustion of the supply of oocytes results in menopause. The
        deterioration of oocyte quality with age has significant impacts on female fertility, meiotic defects in
        the embryo, particularly trisomy 21, and long term susceptibility to conditions such as cardiac
        disease, diabetes and obesity. Crucial to ovarian function are RNA binding proteins, which control
        post-transcriptional regulation of mRNAs coding for proteins essential for germ cell and follicle
        development. We have localised Musashi 1 and Musashi 2, RNA binding proteins with known roles
        in stem cell specification and meiotic segregation, to the mouse oocyte. This project aims to
        characterise the expression of Musashi 1 and 2 throughout oogenesis and folliculogenesis and to
        identify the mRNA target(s) of Musashi 1 and 2 for translational repression in the oocyte, delivering
        possible therapeutic options for improving human oocyte health.

        Contact: A/Prof Eileen McLaughlin
        Phone: 4921 5708
        Email:     Eileen.Mclaughlin@newcastle.edu.au
        Priority Research Centre for Reproductive Science

ii)     Xenobiotics and folliculogenesis
        All mammalian ovaries contain a finite pool of primordial follicles from which mature oocytes and
        ultimately embryos are derived. Recently it has become apparent that synthetic chemical
        compounds (Xenobiotics), are capable of interfering with normal female reproductive function. Some
        xenobiotics such as 4-vinylcyclohexane that are prevalent in the environment have been shown to
        target primordial follicles and trigger atretic oocyte depletion of the ovary leading to premature
        menopause. Studies of cells other than ovaries have demonstrated that mammalian cells generally
        have two defence mechanisms (termed Phase I and Phase II enzymes) for the elimination of
        xenobiotics. Preliminary findings suggest that activation of the Phase I enzymes in the ovary by
        xenobiotic exposure may have undesirable consequences such as the generation of free oxygen
        radicals and subsequent DNA damage. With many Australian women opting to delay childbirth, then
        life long exposure of ovarian oocytes to xenobiotics has repercussions both for the fertility of these
        women and the welfare of their offspring.

        Contact: A/Prof Eileen McLaughlin
        Phone: 4921 5708
        Email:     Eileen.Mclaughlin@newcastle.edu.au
        Priority Research Centre for Reproductive Science

Faculty of Science and IT - Honours Research Topics (2009)                                                  18
iii)    Cytokines and ovarian folliculogenesis
        Female germ cells or oocytes are sequestered in primordial follicles before birth and remain
        quiescent in the ovary until recruited into the growing pool throughout the reproductive years.
        Programmed follicular cell death continues throughout a woman’s reproductive lifetime and
        ultimately 99.9% of all oocytes are lost prior to ovulation with no opportunity to be fertilised. Very little
        is known about what triggers follicle activation, nor the intracellular mechanism by which the
        coordinated differentiation of somatic cells is harmonized with oocyte growth yet this holds the key to
        female germ cell maintenance as well as optimising oocyte cell health and development. Studies of
        pleiotrophic cytokines have suggested that the mechanisms behind follicle activation involve a
        complex network of bidirectional signalling between cellular components of the ovarian follicle.
        However little is known about the intracellular signaling pathways activated by these pleiotrophic
        cytokines. In our pilot microarray gene expression surveys and confirmed by our protein localisation
        studies, we have identified that two key intracellular signaling molecules Signal Transducers and
        Activators of Transcription 3 (STAT3) and Suppressor of Cytokine Signalling 4 (SOCS-4) are
        induced on activation of the murine primordial follicle. The overall goal of our proposed project is to
        characterise the intracellular cytokine signalling pathways regulating activation and maintenance of
        mammalian ovarian primordial follicles.

        Contact: A/Prof Eileen McLaughlin
        Phone: 4921 5708
        Email:   Eileen.Mclaughlin@newcastle.edu.au

        Contact: Dr Shaun Roman
        Phone: 4921 6818
        Email:   Shaun.Roman@newcastle.edu.au

        Contact: Dr Brett Nixon
        Phone: 4921 6977
        Email:     Brett.Nixon@newcastle.edu.au
        Priority Research Centre for Reproductive Science


Fertilisation and Contraception

i)      Formation of Sperm Zona Receptor Complex
        Mammalian sperm-egg interaction is arguably one of the most remarkable processes in biological
        science. This exquisitely specific cell recognition event depends upon a complex cascade of
        interactions between free-swimming sperm and ovulated eggs. Elucidating the nature of these
        interactions has been the subject of intense investigation by many laboratories. Although this has
        led to extensive characterization of the respective gametes, such studies have failed to elucidate the
        molecular basis of this event. In our considered judgement this lack of success stems from the
        incorrect assumption that the sperm receptor is a single molecular entity that is constitutively
        expressed on the cell surface.

        In contrast, recent research from our laboratory has provided support for a novel hypothesis that
        sperm-egg interaction is mediated by a multimeric sperm receptor complex. Furthermore, we have
        compelling evidence that this complex is assembled on the sperm surface through the concerted
        action of a family of molecular chaperone proteins that reside within specialised membrane domains,
        known as lipid rafts. In this project we aim to confirm the validity of this model, establish the
        molecular composition of the sperm surface receptor complexes and characterise the downstream
        signalling cascades that culminate in fertilisation.

        Contact: Dr Brett Nixon
        Phone: 4921 6977
        Email:   Brett.Nixon@newcastle.edu.au

        Contact: Laureate Professor John Aitken
        Phone: 4921 6143
        Email:   John.Aitken@newcastle.edu.au

        Contact: A/Prof Eileen McLaughlin
        Phone: 4921 5708
        Email:     Eileen.Mclaughlin@newcastle.edu.au
        Priority Research Centre for Reproductive Science
Faculty of Science and IT - Honours Research Topics (2009)                                                       19
ii)     Oolemma sperm receptors
        Post-coitus, sperm encounter the ovulated oocyte within the fallopian tube, which serves as the site
        of fertilisation. By the time sperm reach the site of fertilisation they have undergone the prerequisite
        series of capacitation-associated changes necessary for ultimately achieving fertilisation. Upon
        penetrating the Zona pellucida, sperm must then recognise and bind to the oocyte plasma
        membrane. Together, the molecular machinery present in both cell membranes must then interact in
        a precise manner necessary to facilitate the energetically costly event that is the merger of sperm
        and egg membranes.

        This research aims to identify and characterise egg surface proteins implicated in sperm-egg
        interaction, by identifying the important GPI-anchored protein(s) as well characterising the role of the
        tetraspanins and their interacting web partners. In vitro binding and fusion experiments will be used
        as functional bioassays and mass spectrometry (MS)-based proteomics and bioinformatics-based
        analyses will be employed to compile oocyte protein databases and to identify candidate proteins
        responsible for mediating sperm-egg interaction, such as newly identified candidate GPI-anchored
        proteins.

        Contact: A/Prof Eileen McLaughlin
        Phone: 4921 5708
        Email:   Eileen.Mclaughlin@newcastle.edu.au

        Contact: Dr Shaun Roman
        Phone: 4921 6818
        Email:   Shaun.Roman@newcastle.edu.au

        Contact: Dr Brett Nixon
        Phone: 4921 6977
        Email:     Brett.Nixon@newcastle.edu.au
        Priority Research Centre for Reproductive Science

iii)    Spermicides and microbicides
        There is an urgent clinical need to research novel methods of fertility control that are also protective
        against sexually transmitted diseases (STDs) such as the human immunodeficiency virus (HIV) or
        Chlamydia. The most obvious way to generate such a dual-purpose contraceptive method would be
        to develop safe, effective spermicides that were also active against a wide range of pathogenic
        organisms. The currently available formulations such as nonoxynol-9, gramicidin and benzalkonium
        chloride are effective spermicides but are toxic to the vaginal epithelium and do not provide
        protection against STDs. Over 60 agents are in clinical trials as potentially safer topical spermicides
        and/or microbicides. Compounds that have reached this stage of development include acid buffers,
        detergents, dendrimers, non-nucleoside reverse transcriptase inhibitors and anionic polymers. In
        addition, a number of potential spermicides/microbicides are the subject of preclinical investigation,
        including beta-cyclodextrin, cyanovirin, porphyrins, cyclotriazadisulfonamides, dermaseptins, short-
        interfering RNA (siRNA) and HIV antibodies. This project aims using to characterise the biological
        activities and mode of action of newly developed target specific compounds as novel dual
        spermicides/microbicides.

        Contact: Laureate Professor John Aitken
        Phone: 4921 6143
        Email:     John.Aitken@newcastle.edu.au
        Priority Research Centre for Reproductive Science

iv)     Environmental Impacts on Female Fertility
        All female mammalian ovaries contain a limited supply of primordial follicles which are present from
        birth. Recently it has become apparent that xenobiotics, such as organochlorine pesticides,
        polychlorinated biphenyls, dioxins, alkyl phenolic chemicals, phthalates and synthetic oestrogens are
        capable of interfering with normal female reproductive function in both humans and animals. Some
        xenobiotics that are prevalent in the environment including 4-vinylcyclohexane and benzo[a]pyrene,
        have been shown to target primordial follicles and trigger atretic oocyte depletion of the ovary
        leading to premature menopause. Our recent studies of the effects of xenobiotic exposure in the
        ovary have demonstrated that environmental agents can cause significant primordial follicle loss and
        oocyte damage through oxidative stress. Our proposed model is based on preliminary findings which
        indicate that xenobiotic exposure has direct consequences on ovarian function.

Faculty of Science and IT - Honours Research Topics (2009)                                                  20
        The aims of this project are: To elucidate the action of xenobiotics in the developing ovary and in
        particular the role of the Phase I enzymes (Cytochrome p450’s) in the generation of reactive oxygen
        species. To quantify the role of xenobiotic derived oxidative stress on mitochondrial function, plasma
        membrane fluidity and oocyte dysfunction. To characterize the ovarian follicle signalling pathways
        activated by xenobiotics and their role in oocyte growth, follicle differentiation and survival. Insight
        into these processes will illuminate the origins of primordial follicle loss and oocyte dysfunction
        leading to subsequent ovarian failure and infertility in human females.

        Contact: A/Prof Eileen McLaughlin
        Phone: 4921 5708
        Email:   Eileen.Mclaughlin@newcastle.edu.au

        Contact: Dr Shaun Roman
        Phone: 4921 6818
        Email:   Shaun.Roman@newcastle.edu.au

        Contact: Dr Brett Nixon
        Phone: 4921 6977
        Email:     Brett.Nixon@newcastle.edu.au
        Priority Research Centre for Reproductive Science


v)      What Makes a Good Egg?
        There is major interest in the molecular mechanisms regulating the maintenance and development of
        oocytes in the mammalian ovary. Exhaustion of the supply of oocytes results in menopause. The
        deterioration of oocyte quality with age has significant impacts on female fertility, meiotic defects in
        the embryo, particularly trisomy 21, and long term susceptibility to conditions such as cardiac
        disease, diabetes and obesity. Crucial to ovarian function are RNA binding proteins, which control
        post-transcriptional regulation of mRNAs coding for proteins essential for germ cell and follicle
        development. We have localised Musashi 1 and Musashi 2, RNA binding proteins with known roles
        in stem cell specification and meiotic segregation, to the mouse oocyte.

        This project aims to characterise the expression of Musashi 1 and 2 throughout oogenesis and
        folliculogenesis and to identify the mRNA target(s) of Musashi 1 and 2 for translational repression in
        the oocyte, delivering possible therapeutic options for improving human oocyte health.

        Contact: A/Prof Eileen McLaughlin
        Phone: 4921 5708
        Email:   Eileen.Mclaughlin@newcastle.edu.au

        Contact: Dr Shaun Roman
        Phone: 4921 6818
        Email:   Shaun.Roman@newcastle.edu.au

        Contact: Dr Brett Nixon
        Phone: 4921 6977
        Email:     Brett.Nixon@newcastle.edu.au
        Priority Research Centre for Reproductive Science

vi)     Identification and validation of targets for fertility regulation
        There have been no significant advances in planned fertility regulation since the introduction of the
        oral contraceptive pill in the 1960s. The purpose of this project is to use our advanced proteomics
        platform to identify targets for male and female fertility regulation on the basis of their specificity,
        functional significance and drugability. The current focus is on the identification of phosphoproteins
        that are critical to the process of fertilization and then through a knowledge of the kinases and
        phosphatases that regulate their phosphorylation statu,s to select contraceptive targets that can then
        be validated by functional genomics in vivo and in vitro.

        Contact: Laureate Professor John Aitken
        Phone: 4921 6143
        Email:     John.Aitken@newcastle.edu.au
        Priority Research Centre for Reproductive Science


Faculty of Science and IT - Honours Research Topics (2009)                                                  21
Assisted Conception and Early Development
The overall purpose of the studies grouped under this heading is to improve the management of human
infertility by evaluating the causes of diminished gamete quality and resolving the impact of this damage on
the developmental potential of the embryo.

i)      Proteomic and Metabolomic Analyses of Gamete and Embryo quality
        This clinically–orientated project research project involves the development of a close interface with
        collaborators in assisted conception clinics to refine our understanding of gamete and embryo
        quality. This project will use state-of-the-art techniques in metabolomics and proteomics to define
        the molecular basis of impaired gamete function and to identify markers for the assessment of
        embryo quality. Current emphasis is on resolving the molecular basis of impaired gamete interaction
        at fertilization and the role of oxidative stress in the disruption of fertilization and impaired embryonic
        development. This project would provide training in advanced mass spectrometry as well as insights
        into the assisted conception industry.

        Contact: Laureate Professor John Aitken
        Phone: 4921 6143
        Email:   John.Aitken@newcastle.edu.au

        Contact: Dr Brett Nixon
        Phone: 4921 6977
        Email: Brett.Nixon@newcastle.edu.au
        Priority Research Centre for Reproductive Science


ii)     Epigenetic Defects
        Preliminary clinical data is available to suggest that infertile males generate gametes that possess
        methylation defects that might have an impact on the developmental potential of the embryo and the
        health and well being of the subsequent offspring.               These defects are characterized by
        hypomethylation of key sites, which we have hypothesised is due to oxidative damage to the
        corresponding CpG islands. High-throughput DNA methylation profiling will be used to screen for
        genome wide methylation defects in the gametes of infertile men. These profiles will subsequently be
        correlated with presence of oxidative base damage to the sperm DNA. In addition we shall correlate
        any defects seen in the methylation profiles with the developmental potential of the embryo and the
        normality of DNA methylation in the offspring.

        Contact: Laureate Professor John Aitken
        Phone: 4921 6143
        Email:     John.Aitken@newcastle.edu.au
        Priority Research Centre for Reproductive Science




Faculty of Science and IT - Honours Research Topics (2009)                                                     22
CHEMISTRY:

Chemometrics/Development of advanced methods for analysis of chemical data. Theory and
industrial applications. Strong international collaboration.
Academic research is performed under very strict control of external parameters such as temperature, pH,
ionic strength, etc. Such control is not feasible for industrially relevant processes. Adaptation of the modelling
algorithms with the goal of taking into account non-constant conditions is the main thrust of on-going
research at the Discipline of Chemistry. Research involves programming in Matlab. The main application
includes analysis of processes relevant for CO2 capture.

Contact: Prof Marcel Maeder
Phone: 4921 5478
Email:   Marcel.Maeder@newcastle.edu.au
Advanced Synthetic Materials Group, Priority Research Centre for Energy


Coordination chemistry involving metal complexes of polydentate and macrocyclic ligands
Compounds involving metal ions bound by synthetic cyclic and acyclic organic molecules have fascinating
physical properties that offer potential applications across broad areas, and as models of metalloenzymes.
Development of ligands with new topologies, their complexation by metal ions, and determination of their
physical properties and structures lies at the core of this work, with a diversity of projects available.

Contact: Prof Geoff Lawrance
Phone: 4921 5474
Email:   Geoffrey.Lawrance@newcastle.edu.au
Research Group: Advanced Synthetic Materials


Effect of Copolymer Composition on Linear Copolymer-based Molecularly Imprinted Films
Molecularly imprinted polymeric films (MIPfs) can be prepared utilising linear copolymers (and not the
conventional crosslinked polymers) by the techniques of phase inversion (polymer solution immersed in a
non-solvent) and/or spin-casting. A linear copolymer-based MIPf is prepared using a ‘functional’ monomer
that shows favourable interaction (usually by H-bonding) with the analyte-template and a matrix monomer,
typically acrylonitrile, that imparts rigidity and controls the quality of the film. The performance of the MIPfs
developed by our group has been shown to be affected by the composition of the copolymers. For example,
the binding efficiency of the analyte-template, L-ephedrine, is exceptionally high when methyl methacrylate is
used as a matrix monomer with minimal non-selective surface binding. This project will examine the effect of
various matrix (e.g. acrylate, styrenic) monomers (other than acrylonitrile) on the performance of MIPfs. In
particular, the morphology of the MIPfs, believed to greatly influence the formation of binding packets in this
type of MIP, will be studied by differential scanning calorimetry (DSC) thermal analysis method.

Contact: Dr Clovia Holdsworth
Phone: 4921 5481
Email:   Clovia.Holdsworth@newcastle.edu.au
Research Group: Advanced Synthetic Materials


In situ studies of polymeric biolubricants
The human body produces effective water-based polymeric lubricants that are the envy of the engineering
profession. The aim of this project is to study why certain polymers are better lubricants than others and to
gain the knowledge necessary to design novel lubricants for bioimplants and other important applications.
The key to the success of the project lies in the combination of in situ spectroscopy and atomic force
microscopy, allowing us to ‘see’ and ‘feel’ the polymer film whilst it is under pressure. To be conducted in
collaboration with Dr David Beattie (University of South Australia).

Contact: A/Prof Erica Wanless
Phone: 4921 8846
Email:   Erica.Wanless@newcastle.edu.au
Research Group: Advanced Synthetic Materials


Faculty of Science and IT - Honours Research Topics (2009)                                                    23
Reduction of greenhouse gas emissions by absorption of CO2 with subsequent sequestration
The bulk of scientific evidence points to the necessity of reducing greenhouse gas emissions. A prominent
approach is Post Combustion Capture (PCC) of CO2 with subsequent sequestration. As a major coal user
and exporter this is most relevant for Australia. The most promising PCC technology is based on the simple
fact that CO2 in aqueous solution acts as an acid (carbonic acid) and interacts reversibly with organic
amines. Surprisingly little is known about these reactions. The project includes investigations of the reactions
between amines and CO2 in aqueous solution using NMR and FT-IR spectroscopies.

Contact: Prof Marcel Maeder
Phone: 4921 5478
Email:   Marcel.Maeder@newcastle.edu.au

Contact: Dr Robert Burns
Phone: 49215479
Email:   Robert.Burns@newcastle.edu.au
Advanced Synthetic Materials Group, Priority Research Centre for Energy


The selective oxidation of small alkanes by new generation heterogeneous catalysts
This project deals with the study of new solid-state catalysts for the oxidation of isobutane to methacrolein
and methacrylic acid, which lead to the commercially important Perspex. The catalysts are
heteropolyoxometalates and related oxide-based materials. Studies will involve the design, synthesis,
characterisation and application of the catalysts, and there are many aspects of this work applicable to both
Honours and PhD projects.

Contact: Dr Robert Burns
Phone: 49215479
Email:   Robert.Burns@newcastle.edu.au
Research Group: Advanced Synthetic Materials


Mineral processing using minimal water
There is a need to develop methods to process minerals that will reduce the need to use the large quantity of
water that is currently used. An important characteristic of any new method is that it must be selective to
differences in the physical or chemical properties of the valuable mineral, which is often a sulfide, as distinct
from the host rock in the ore, which is usually a silicate. The aim of this project is to investigate the selective
adsorption of molecules from the vapour phase on the surfaces of typical minerals. We will then attempt to
separate these modified materials using triboelectric (surface charging) separation, thus obviating the need
for water intensive processes such as flotation.

Contact: A/Prof Erica Wanless
Phone: 4921 8846
Email:     Erica.Wanless@newcastle.edu.au
Priority Research Centre for Advanced Particle Processing


Structure-function relationships in short fibre liquid composites
Novel short fibre composites offer exciting prospects for the safer manufacture of strong lightweight materials
in a greater variety of formats than is possible with traditional fibreglass. However, these materials are
currently poorly understood in terms of the relationship between their mechanical properties and their
molecular scale structure. In this project we will examine these relationships. In particular, the surface
chemistry of the fibre-resin interface and the polymerisation reactions with the resin will be investigated. To
be co-supervised by Dr Clovia Holdsworth.

Contact: A/Prof Erica Wanless
Phone: 4921 8846
Email:     Erica.Wanless@newcastle.edu.au
Priority Research Centre for Advanced Particle Processing




Faculty of Science and IT - Honours Research Topics (2009)                                                     24
Switchable polymeric coatings
The growth of polymers from solid surfaces offers exciting prospects for new surface-engineered materials.
In this project surface initiated polymerisation will be used to grow well-defined polymer brushes. These
brushes may be synthesised to respond to various triggers such as pH or temperature. Rapid and profound
changes in brush thickness and surface wettability can then be achieved by adjusting the trigger. Switchable
copolymer coatings will be designed for various surface and colloid science applications. This project can
have a polymer synthesis, characterisation (atomic force microscopy, optical reflectometry etc), or materials
engineering focus.

Contact: A/Prof Erica Wanless
Phone: 4921 8846
Email:     Erica.Wanless@newcastle.edu.au
Priority Research Centre for Advanced Particle Processing


Advanced Battery Systems
Modern society is very dependent on electrical energy, and for portable devices batteries are the power
source of choice. There are a number of options available to postgraduate students in this research area,
particularly related to the system being studied. Currently there are projects available focussed on battery
materials such as MnO2, LiMPO4 (where M=Fe, Mn, Ni, Co or combinations thereof), LiMn2O4 and CuO.
Irrespective of the system, the focus is on material synthesis to produce superior performance, as well as on
fundamentally understanding the processes occurring.

Contact: A/Prof Scott Donne
Phone: 4921 5477
Email:     Scott.Donne@newcastle.edu.au
Priority Research Centre for Energy


Advanced Fuel Cell Catalysts
The development of fuel cells has been ongoing for many years, and as a result numerous configurations
have been developed. However, a common feature they all possess is that oxygen from the air is the
oxidant. Furthermore, it is the aspect of the fuel cell technology that is most limiting to performance. Our
research efforts here focus on the development of advanced non-noble catalysts that have comparable of
superior performance compared to Pt. Another objective is to understand the effects of adsorption on
electrode behaviour.

Contact: A/Prof Scott Donne
Phone: 4921 5477
Email:     Scott.Donne@newcastle.edu.au
Priority Research Centre for Energy


Pseudo-Capacitance in Materials
While batteries have been the power source of choice for portable electronic devices, recent advances in
micro-electronics have meant that they are suffering performance limitations in modern devices. A strategy to
alleviate this problem is the use of materials that exhibit pseudo-capacitance; i.e., fast charge transfer
reactions combined with conventional double-layer charge storage. The research focus here is on the
synthesis of materials (typically manganese oxides) with appropriate morphologies that exhibit pseudo-
capacitance.

Contact: A/Prof Scott Donne
Phone: 4921 5477
Email:     Scott.Donne@newcastle.edu.au
Priority Research Centre for Energy




Faculty of Science and IT - Honours Research Topics (2009)                                               25
Medicinal Chemistry
1% of the world’s population suffers epilepsy, and of this 1% 1 person in 3 does not respond to treatment.
Over the past decade we have pioneered the inhibition of a protein called dynamin as a potential treatment
for epilepsy. Recently, via the National Institute for Neurological Diseases and Stroke, we have acquired
compelling animal data that confirms our original hypothesis. Our AEDs operate by a novel mechanism of
action and hold considerable promise against this resistant population. Student working in this area will
design, synthesise and have tested potential new drugs for the treatment of epilepsy (AEDs).

Contact: A/Prof Adam McCluskey
Phone: 4921 6486
Email:     Adam.McCluskey@newcastle.edu.au
Priority Research Centre for Organic Electronics


Molecular Weight Control of Poly (3-alkylthiophenes)
Poly(3-alkylthiophenes) are an important class of organic conductive polymers. They are soluble, therefore
processable, and exhibit high electrical conductivities. Nanoparticulate films of poly(3-hexylthiophene),
P3HT, in particular, blended with [6,6]-phenyl-C61 butyric acid methyl ester (PCBM) have been utilised as
the electroactive layer in organic photovoltaic devices (OPVs). A key determinant of the efficiency of OPV
devices is the morphology of the electroactive layer of the device which can be controlled by regulating the
size distribution of the nanoparticles and the molecular weight and MW distribution of the electroactive
polymers. This project will investigate the influence of polymer MW and MW distribution on the morphology
and electronic properties of P3HT. P3HT is chosen as the model system to be aligned with an on-going
PRCOE study on P3HT:PCBM based OPVs. The project consists of two parts: (1) fractionation of
commercially available P3AT by precipitation and size exclusion chromatography, and (2) synthesis of P3AT
of controlled molecular weight and MW distribution using chain transfer agents (e.g. thiols). This project will
be co-supervised by Dr Warwick Belcher.

Contact: Dr Clovia Holdsworth
Phone: 4921 5481
Email:     Clovia.Holdsworth@newcastle.edu.au
Priority Research Centre for Organic Electronics


Surface chemistry for improved organic solar cells
One problem with current plastic photovoltaic cells is phase separation of the polymer blends used during
device construction. We believe that this unfavourable behaviour can be prevented by controlling the
interfaces between the various components in the device. With a combined focus on the polymer chemistry,
the surface chemistry and the device fabrication, advances in solar cell efficiency can be made. This project
concerns the manufacture, surface organisation and ultimately incorporation of conducting polymer
nanoparticles into polymeric photovoltaic devices. The project may be cosupervised by either Dr Clovia
Holdsworth or Dr Warwick Belcher depending on the desired level of polymer synthesis or device
construction respectively.

Contact: A/Prof Erica Wanless
Phone: 4921 8846
Email:     Erica.Wanless@newcastle.edu.au
Priority Research Centre for Organic Electronics

Synthesis of New Chiral Bispidinone Ligand Systems
Coordination compounds exhibiting C2 symmetry are widely used in industry to induce the formation of chiral
products from achiral starting materials. We are interested in developing new tetradentate ligands systems
that incorporate the bispidinone skeleton and an amino acid pendant arms for evaluation as chiral ctatlysts.

Contact: Dr Mike Bowyer
Phone: 4348 4119
Email:     Michael.Bowyer@newcastle.edu.au
Priority Research Centre for Organic Electronics

Contact: Professor Geoffrey Lawrance
Phone: 4921 5474
Email:   Geoffery.Lawrance@newcastle.edu.au
Advanced Synthetic Materials Group

Faculty of Science and IT - Honours Research Topics (2009)                                                 26
EARTH SCIENCES:


Acid Mine Drainage
A student is required for a project related to the treatment and management of acid mine drainage at a site
near Cessnock. The project is at a derelict mine site and trials are proposed for the remediation of
contaminated water at the site. There is likely to be some funding available from the Department of Primary
Industry.

Contact: A/Prof Phil Geary
Phone: 4921 6726
Email:   Phil.Geary@newcastle.edu.au
Research Group: Environmental & Climate Change


An east Australian palaeoclimate record for isotope stage 5
The last warm climatic stage in Australia (from about 130 to 120 ka) is poorly understood, as is the period
when Earth’s climate slid towards glacial conditions. Did Australia follow the patterns observed in Antarctic
ice cores or were the tropics more influential? These two projects focus on two cave systems in eastern
NSW from where we have sampled speleothems known to have grown through this time interval. A
combination of stable isotope and trace element geochemistry, as well as radiometric dating, will be used to
unravel the palaeoclimate. The results will provide the first detail reconstruction through this time interval in
Australia and lead to high quality publications.

Contact: Dr Russell Drysdale
Phone: 4921 5749
Email:   Russell.Drysdale@newcastle.eduy.au
Research Group: Environmental & Climate Change


An investigation of dissolved organic carbon in stream waters
Soil organic matter movement on the hillslope and catchment scale is poorly understood. What is even less
well known is how soil carbon enters stream and river waters and is ultimately transported out to sea for
deep storage. In this project the student will investigate the concentration of dissolved organic carbon in a
branch of the Hunter River in which Hancock and his research team have installed water quality
instrumentation. The student will be integrated into an existing project and research team investigating soil C
on the catchment scale. The project is ideally suited to someone with a GIS and Remote Sensing interest as
well as a background in chemistry/biology. End goal will be potentially publishable findings relating soil C to
hydrology and catchment behaviour. This project is funded by an ARC Discovery Project grant.

Contact: Dr Greg Hancock
Phone: 4921 5090
Email:   Greg.Hancock@newcastle.edu.au
Research Group: Environmental & Climate Change


Biomediated calcite precipitation: the mysterious Moonmilk
Moonmilk is a plastic deposit formed in caves which consists of pliable calcite fibres, water and microbial
filaments. There is a strong debate on the role of microbial activity in its formation. Recently, we found
evidence of an indirect role of cave bacteria in moonmilk calcite fibre formation. This has important
implications in the whole field of carbonate mineral genesis, but also, indirectly, in CO2 sequestration.
Moonmilk is also one of the most promising archives of seasonal temperature variability as related to global
changes. Study on moonmilk calcite and water isotope show that moonmilk grows through seasonal cycles
when mean annual temperature is above 3°C. Because moonmilk can be dated by radiocarbon on the
organic fraction, it has great potential as palaeoclimate archive.

I propose the study of calcite moonmilk from some alpine caves. In collaboration with Russell Drysdale we
could also explore Australian moonmilk and recognize differences and similarities. The study implies at first
the documentation of the relationships between filaments and fibres as observed by Scanning and the
Transmission Electron Microscopy at UoN. Subsequently, spectroscopic analyses by FT-IR (Fourier
Transform Infra Red) spectroscopy shall be carried out to detect the organic compounds present within the
moonmilk.

Faculty of Science and IT - Honours Research Topics (2009)                                                   27
Stable isotopic analyses in Russell’s lab of well dated moonmilk shall then be carried out. Some dated
moonmilk samples are already available. Isotope time series will be interpreted them in terms of climate
changes, and this will allow us to recognize conditions conducive to massive moonmilk formation. The
massive deposits are those expected to efficiently sequester CO2 in the cave environments. Results from the
study shall prompt further investigation about the potential of moonmilk bacteria in promoting CO2
sequestration. I expect mutual exchange of information with the Honours candidate in a shared research
experience.

Contact: Dr Silvia Frisia
Phone: 4921 5402
Email:   Silvia.Frisia@newcastle.edu.au
Research Group: Environmental & Climate Change


Can we detect ENSO-like signals in Wombeyan Holocene stalagmites?
We’re currently working on a major project with the Sydney Catchment Authority which seeks to reconstruct
the Sydney Basin drought history over the last 1000 years. Potential exists to conduct a parallel study to
explore earlier periods during the Holocene. This would involve carrying out stable isotope and trace element
analyses, as well as radiometric dating. In a similar vain to Project 3, this would allow us to determine the
presence of dry-wet cycles and ascertain whether their frequency matches known ENSO periodicities.

Contact: Dr Russell Drysdale
Phone: 4921 5749
Email:   Russell.Drysdale@newcastle.eduy.au
Research Group: Environmental & Climate Change


Do Flores stalagmites preserve an ENSO-related flood record?
Flores (Indonesia) is host to the famous ‘Hobbit’ hominid remains. Our group has been working at the site for
several years to explore past climates associated with human occupation history. We have some stalagmites
which clearly preserve regular mud layers, and may record flood frequencies that are linked to ENSO events.
In this project, the student will conduct geochemical, microscopic and radiometric dating analysis to
determine whether these mud layers are flood deposits, and whether they frequency matches known ENSO
periodicities.

Contact: Dr Russell Drysdale
Phone: 4921 5749
Email:   Russell.Drysdale@newcastle.eduy.au
Research Group: Environmental & Climate Change


Exploratory radiocarbon dating of Corchia Cave (Italy) speleothems
To use radiocarbon dating effectively over its time range, we need to know the background variations in
atmospheric radiocarbon (known to have fluctuated markedly with time). One way of doing this is to conduct
radiocarbon measurements on materials that have already been dated using an independent technique,
such as uranium-thorium dating. Speleothems can be used to perform this, but they suffer from having a
mixture of ‘dead carbon’ (sourced from ancient limestone) and ‘modern carbon’ (from the soil and
atmosphere) at the time of calcite deposition. Soil carbon input is a problem because it changes with climate.
However, in areas where soil coverage is very low, the variable contribution from soil C may be minimal,
leaving only atmospheric and bedrock contributions. In this project, the aim is to conduct a series of parallel
radiocarbon and uranium-thorium age measurements on Corchia speleothems through a period where the
atmospheric radiocarbon signal is well constrained. This will allow us to determine whether Corchia
speleothems are suited to exploring periods where atmospheric variations are poorly known. This project
may involve a trip to the dating laboratory in Glasgow, UK.

Contact: Dr Russell Drysdale
Phone: 4921 5749
Email:   Russell.Drysdale@newcastle.eduy.au
Research Group: Environmental & Climate Change




Faculty of Science and IT - Honours Research Topics (2009)                                                 28
Global vs local Holocene climate changes from stalagmites
Stalagmites from Cogola di Giazzera, a cave located at 1025 m above sea level in the Dolomites of N-E Italy
preserve a record of Holocene climate variability at annual scale. So far, only one stalagmite has been
studied. But it revealed a very promising topic of general interest for the climate community.
Recent published work on speleothems from the alpine Spannagel cave prompted a large debate as it
suggested that the European Middle Age Warm Period (ca. XII and XIII century C.E.) was characterized by
higher temperatures than today. By contrast, Cogola di Giazzera reveals a trend in past temperature
changes similar to the famous “hockey-stick” curve that is at the basis of the predictions for future warming
trends. Hence, the study of more Giazzera stalagmites will enable to recognize if the Spannagel record has
a very local significance. I’d like to stress that a key issue in the debate of global changes is the recognition
of the unique nature of the current warming.

I propose to study more Giazzera stalagmites, starting with the observation of fabrics (the arrangement in
space of calcite crystals), which are indicative of changes in rainfall rate. Then, C and O isotope ratio shall
be analysed in Russell’s isotope lab. Focus is on the past 2500 years, and in particular on the Warm Roman
Period (ca. 2000 years ago), the Medieval Warm Period and Little Ice Age.
FT-IR spectroscopy shall be carried out to extract information on the organic molecules which should provide
insight on climate-related soil processes. I hope to obtain also insight on land-use.
I propose to carry out the study in collaboration with the Spannagel people, because we want to understand
why the two cave records are so different. The Spannagel team, which is based in Innsbruck and
Heidelberg, offered to perform dating of new stalagmites and carry out trace element analyses.
Much is already known about the present-day environment of formation of calcite in Giazzera. This is a great
baseline for the interpretation of past data.

I expect the Honours candidate to be confident to work within an international group and be ready to submit,
as first author, the results to a peer reviewed journal.

Contact: Dr Silvia Frisia
Phone: 4921 5402
Email:   Silvia.Frisia@newcastle.edu.au
Research Group: Environmental & Climate Change


Groundwater Quality and Waste Disposal
A student is required to work on a project examining the impacts of waste disposal on soil and groundwater.
The field work would be undertaken locally and would look at various land uses and waste disposal
practices.

Contact: A/Prof Phil Geary
Phone: 4921 6726
Email:   Phil.Geary@newcastle.edu.au
Research Group: Environmental & Climate Change


High resolution stable isotope record for the period 390 ka to 280 ka
In 2004, we published a low resolution stable isotope record from an Italian speleothem (CC1) which showed
good agreement with sea-surface temperatures (SSTs) in the North Atlantic. Recently, the level of detail of
the N Atlantic SST record has been improved, but, as with all marine cores, dating is not possible over much
of their records. In this project, the aim is to re-sample the speleothem at high-resolution for stable isotope
analysis and carry out uranium-thorium dating to improve the CC1 record. This will enable us to re-tune the
SST record, and thus provide the first independent radiometric chronology for this part of the marine
sequence.

Contact: Dr Russell Drysdale
Phone: 4921 5749
Email:   Russell.Drysdale@newcastle.eduy.au
Research Group: Environmental & Climate Change




Faculty of Science and IT - Honours Research Topics (2009)                                                   29
Prediction of soil moisture across catchments from limited spatial data
Soil moisture is a driving factor in plant growth, runoff processes and agricultural systems. This project will
examine soil moisture data from a number of sites in the Upper Hunter and examine how different sites
within a number of catchments respond to rainfall. The project will assess how many and where soil moisture
should be measured so that catchment scale predictions can be reliably made. The project is part of an ARC
Discovery project looking at the spatial and temporal variability of soil carbon. This research is ideally suited
to someone with an interest in soils and soil moisture and has good GIS and data management skills.

Contact: Dr Greg Hancock
Phone: 4921 5090
Email:   Greg.Hancock@newcastle.edu.au
Research Group: Environmental & Climate Change

Relationship between soil carbon and soil erosion
Soil is the 2nd largest store of organic carbon globally. There appears to be a dearth of studies examining
soil carbon at the hillslope and catchment scale. It is important that hillslope soil processes be understood if
we are to model carbon dynamics at the catchment scale and better understand the role of soil carbon in
climate change. In this project the student will investigate the relationship between soil carbon and its
position in the landscape using an existing data set held by Hancock and research team. The student will be
integrated into an existing project and research team investigating this issue. End goal will be potentially
publishable findings relating soil C to soil erosion and deposition on the hillslope and catchment scale. This
project is funded by an ARC Discovery Project grant.

Contact: Dr Greg Hancock
Phone: 4921 5090
Email:   Greg.Hancock@newcastle.edu.au
Research Group: Environmental & Climate Change

Spatial patterns of vegetation and soil in relation to geomorphology and hydrology in an undisturbed
catchment in Kakadu National Park, NT
In April 2006 Cyclone Monica, a Category 5 Cyclone hit the Northern Territory coast. Monica had a higher
intensity than Cyclone Tracey with winds greater than 300km/hr. In mid 2006 an assessment of the impact of
the cyclone on vegetation and erosion was done to ascertain the impact of such severe storms. It is
important that such assessment be carried out as the climate change models predict a greater frequency
and greater intensity of such storms in the future. This knowledge is also important for mine site rehabilitation
especially in regard to the safe encapsulation of uranium mining waste. At present there is a large data base
ready to be assessed regarding the number of trees and trees species damaged/fallen in the storm in
relation to soil type, geomorphic position and storm intensity. The project will require several months in
Darwin and Jabiru in the Northern Territory and be supported by the Environmental Research Institute of the
Supervising Scientist, Department of Environment and Heritage.

Contact: Dr Greg Hancock
Phone: 4921 5090
Email:   Greg.Hancock@newcastle.edu.au
Research Group: Environmental & Climate Change


Stormwater Quality & Management
A student is required for a project related to stormwater water quality management around Lake Macquarie.
The project is concerned with assessing the effectiveness of control structures being built around the lake.
Some funding from Council is available to help with project costs.

Contact: A/Prof Phil Geary
Phone: 4921 6726
Email:   Phil.Geary@newcastle.edu.au
Research Group: Environmental & Climate Change




Faculty of Science and IT - Honours Research Topics (2009)                                                   30
The evaluation of erosion models for the assessment of mine site rehabilitation stability and off-site
water quality
Mining is a central component of the Australian economy. It is vital that best practice environmental
assessments and technology be employed to assess post-mining rehabilitation designs. This project will
assess the use of the SIBERIA and CAESAR models for their ability to predict erosion and landscape
evolution on the ERA Ranger mine in the Northern Territory. These models are state of the art assessment
tools and require calibration, validation and then analysis of their suitability as rehabilitation tools. The project
is ideally suited for someone with an interest in GIS and Remote Sensing and environmental modelling. The
project will require several months in Darwin and Jabiru in the Northern Territory and be supported by the
Environmental Research Institute of the Supervising Scientist, Department of Environment and Heritage.

Contact: Dr Greg Hancock
Phone: 4921 5090
Email:   Greg.Hancock@newcastle.edu.au
Research Group: Environmental & Climate Change


The fluvial geomorphology of Mars
In recent years a number of high quality maps and digital elevation models of Mars have been available.
These are all free to those undertaking research. This data clearly show evidence of fluid flows on Mars.
Hancock has developed a range of novel tools in recent years to analyse catchments and this will be applied
to Martian landforms. In 2004-2005 Hancock undertook a pilot study and showed that Martian landforms are
indeed similar to earth and that techniques developed for analysis on earth are applicable on Mars. This is
blue-sky research which could have endless possibilities. End goal will be a better understanding of Martian
landforms and the base for a research publication. The project would be ideally suited to someone who has
a strong interest in geomorphology/geology as well as GIS and Remote Sensing skills/interest

Contact: Dr Greg Hancock
Phone: 4921 5090
Email:   Greg.Hancock@newcastle.edu.au
Research Group: Environmental & Climate Change


The geomorphology and hydrology of mesas
Mesas are a relatively common landform in arid areas of both Australia and overseas. Relatively little
research has been conducted on their geomorphology, hydrology and vegetation patterns. Mesas are
thought to be relatively stable landforms consequently the research interest in mesas comes from proposals
for their flat caps to used as radioactive waster storage areas and in Australia mining companies such as
Newcrest are very interested in constructing mesas as large waste rock dumps. This project has a number of
aspects that could be undertaken:

      The geomorphological modelling of mesas using the SIBERIA landform evolution model;
      Rates of soil erosion down mesa hillslopes;
      Rock and vegetation surface cover in relation to soil depth.

It is likely that some travel will be required to both Perth and the Telfer mine in the East Pilbara. This project
is funded by an ARC Linkage Grant and is in conjunction with The University of Western Australia.

Contact: Dr Greg Hancock
Phone: 4921 5090
Email:   Greg.Hancock@newcastle.edu.au
Research Group: Environmental & Climate Change


The use of remote sensing for the determination of soil carbon, soil erosion and soil
biogeochemistry
Remote sensing offers the ability to quantify spatial and temporal changes in vegetation, soil quality and
potentially soil biogeochemistry especially in relation to soil carbon and soil nitrogen. This project will
examine a range of remote sensed data (MODIS, Landsat, ALOS and Quickbird) for their ability to predict
above ground biomass, soil C and N as well as soil type and properties. The project is ideally suited for
someone with an interest in GIS and Remote Sensing. The project will largely focus on the Upper Hunter
Valley but may also examine data from Arnhem Land in the Northern Territory. This project is funded by an
ARC Discovery Project grant and be supported by the Environmental Research Institute of the Supervising
Scientist, Department of Environment and Heritage.
Faculty of Science and IT - Honours Research Topics (2009)                                                       31
Contact: Dr Greg Hancock
Phone: 4921 5090
Email:   Greg.Hancock@newcastle.edu.au
Research Group: Environmental & Climate Change


Tracing Sources of Contamination
A student is required to examine several tracers used to track sources of contamination in the environment.
In particular, the student would examine the fluorometric properties of various fluorescing whitening agents in
a laboratory investigation and assist with determining a method for their analysis in environmental samples.
Field work would also be required to test the usefulness of a number of the studied tracers in particular
environmental applications.

Contact: A/Prof Phil Geary
Phone: 4921 6726
Email:   Phil.Geary@newcastle.edu.au
Research Group: Environmental & Climate Change


On the tectonic and sedimentary structures of forearc systems
World-class examples of tectonic and sedimentary structures that form in a tectonically active forearc trench
are exposed in the Pacific Palms region of northeastern NSW. Our current understanding of the structural
architecture of forearc systems is primarily known from seismic studies and ocean drilling programs; whereas
few attempts to characterise these systems on the basis of field observations have been carried out. This is
primarily due to most modern forearc systems being submerged by water, and most ancient systems being
reworked by collision events. This project will involve detailed field mapping through a section of exposed
forearc rocks that have not been reworked by later collision events. Field mapping will require the
compilation of balanced cross-sections that illustrate the main structural and sedimentary architecture of the
forearc system. This project has the scope to provide important insights into tectonic processes associated
with the evolution of continental margins along convergent tectonic plate boundaries.

Contact: Dr Glenn Phillips
Phone: 4921 5410
Email:   Glenn.Phillips@newcastle.edu.au
Research Group: Tectonics and Earth Resources


The exhumation of eclogites and blueschists – a tectonic ambiguity?
The exhumation of deep crustal depths is an enigmatic process not comprehensively explained by tectonic
theory. In the New England Orogen, eclogite and blueschist facies rocks (from depths of 20-60 km) are
exposed and are generally enveloped by highly deformed serpentenite. This project will use a detailed
analysis of fabric relationships in serpentenite to provide inferences on structural processes responsible for
the exhumation of these deep crustal rocks. The results of this project will provide important information on a
long-standing tectonic ambiguity that has puzzled tectonicists for years. This project will involve 6-8 weeks of
fieldwork.

Contact: Dr Glenn Phillips
Phone: 4921 5410
Email:   Glenn.Phillips@newcastle.edu.au
Research Group: Tectonics and Earth Resources




Faculty of Science and IT - Honours Research Topics (2009)                                                  32
The formation of eclogites and blueschists – what can they tell us about plate tectonics?
Eclogite and blueschist facies rocks form under high-pressure tectonic conditions and are generally
associated with processes occurring along plate margins. This project will use detailed petrography and
thermodynamic modelling to provide constraints on the evolution of eclogite to blueschist facies rocks
exposed in the New England Orogen, NSW. Thermodynamic modelling will be carried out using the
computer software THERMOCALC and will involve the calculation of phase diagrams with the aim of
constructing pressure-temperature paths. The primary aim of this project is to provide robust tectonic
constraints on lower crustal process associated with continental evolution along plate margins. This project
will involve 2-3 weeks of fieldwork.

Contact: Dr Glenn Phillips
Phone: 4921 5410
Email:   Glenn.Phillips@newcastle.edu.au
Research Group: Tectonics and Earth Resources


Unravelling the structural characteristics of accretionary wedges
This project will involve combining field mapping with geophysics to interpret the internal structure of the
Carboniferous to Triassic accretionary wedge of the New England Orogen, NSW. The primary aim of this
project is to characterise the internal structure of an accretionary wedge to provide insight in to the structural
processes of wedge evolution, continental obduction and subsequent accretion and continental growth. This
work will add to our understanding of how accretionary wedges evolve, and provide important insights into
the main mechanisms associated with continental growth by accretion. This project will involve 6-8 weeks of
fieldwork.

Contact: Dr Glenn Phillips
Phone: 4921 5410
Email:   Glenn.Phillips@newcastle.edu.au
Research Group: Tectonics and Earth Resources



GEOGRAPHY & ENVIRONMENTAL STUDIES:


Please refer to the Honours opportunities outlined in the brochures, available at the Geography &
Environmental Studies display at the EXPO, for the following research areas:

        Geography and Environmental Studies;
        Development Studies.




Faculty of Science and IT - Honours Research Topics (2009)                                                    33
School of Mathematical and Physical Sciences

MATHEMATICS:

Aircraft Tail Assignment and Maintenance Scheduling
Most airline operational planning activities, particularly for crews, are supported by the use of mathematical
algorithms embedded in decision support software. These algorithms are based on integer linear
programming models, which arise in the field of mathematics known as optimization, and use a technique
known as “column generation”. However relatively little work has been done on the assignment of lines of
work to aircraft, and the detailed scheduling of maintenance. This project will develop an understanding of
the key models and techniques in mathematical optimization, investigate the effectiveness of column
generation for this problem, and explore alternative approaches, testing each for computational effectiveness
and solution quality.

Contact: Prof Natashia Boland
Phone: 4921 6717
Email:   Natashia.Boland@newcastle.edu.au
Research Group: Computer Assisted Research in Mathematics and its Applications (CARMA)


Computer assisted discovery and proof / Experimental Mathematics
To work on the implementation and analysis of algorithms to assist with the discovery and or proof of analytic
inequalities in one and more variables.

Contact: Laureate Professor Jon Borwein
Phone: 4921 5535
Email:   Jonathan.Borwein@newcastle.edu.au
Research Group: Computer Assisted Research in Mathematics and its Applications (CARMA)


Conformal Symmetries and Electromagnetisms
Symmetries are intimately related to conservation laws. The isometries of Minkowski space underlie the
existence of conserved energy and momenta for any relativistic theory. Maxwell's equations are additionally
invariant under conformal motions. Some of the consequences of this will be explored, in particular in
relation to electromagnetic radiation.

Contact: Dr Ian Benn
Phone: 4921 5531
Email:   Ian.Benn@newcastle.edu.au
Research Group: Computer Assisted Research in Mathematics and its Applications (CARMA)


High Precision Integration / Computational Mathematics
To work on the implementation and analysis of algorithms to compute physically meaningful integrals to at
least double precision in more than two dimensions.

Contact: Laureate Professor Jon Borwein
Phone: 4921 5535
Email:   Jonathan.Borwein@newcastle.edu.au
Research Group: Computer Assisted Research in Mathematics and its Applications (CARMA)


Integral Directed Graphs / Graph Theory
The adjacency matrix encodes a complete description of a graph and its eigenvalues can give some useful
information about the graph. Some information is already known about which simple graphs have integer
eigenvalues. In this project we will try to learn what we can do about which directed graphs have integer
eigenvalues.

Contact: Dr Jim MacDougall
Phone: 4921 6792
Email:   jim.macdougall@newcastle.edu.au
Research Group: Computer Assisted Research in Mathematics and its Applications (CARMA)
Faculty of Science and IT - Honours Research Topics (2009)                                                34
Optimization of Cancer Treatment using Wedge Radiotherapy
The treatment of cancer using radiation therapy is delivered using sophisticated technologies for shaping
and modulating the field of radiation delivered. Treatment planning seeks to design the treatment for a
patient so as to maximize its effectiveness, whilst ensuring healthy organs suffer as little side-effect as
possible. This planning is based on mathematical optimization algorithms, which are embedded in treatment
planning software. This project will investigate optimization of treatment delivered using wedge radiotherapy,
in which a wedge is used to shape the radiation field. New mathematical models and algorithms will be
developed, with the goal of improving treatment processes. This project will be collaborative with Medical
Physicists based in the Radiation Oncology Department of the Mater Hospital.

Contact: Prof Natashia Boland
Phone: 4921 6717
Email:   Natashia.Boland@newcastle.edu.au
Research Group: Computer Assisted Research in Mathematics and its Applications (CARMA)


The Two-Across Cutting Stock Problem: Theoretical Analysis and/or Effective Algorithms
The two-across cutting stock problem arises as a special and mathematically interesting case of the general
cutting stock problem, which is important in manufacturing for minimizing waste, for example, in the
production of paper, or steel beams. The problem has a fascinating mathematical structure, which can be
investigated through combinatorial structure, or via polyhedral analysis. Both exact and heuristic techniques
for finding good quality solutions in reasonable computation time are of interest. Depending on the interest
of the student, the project could be entirely theoretical, focussing, for example, on polyhedral analysis, or
could be more computational, investigating algorithms.

Contact: Prof Natashia Boland
Phone: 4921 6717
Email:   Natashia.Boland@newcastle.edu.au
Research Group: Computer Assisted Research in Mathematics and its Applications (CARMA)




Faculty of Science and IT - Honours Research Topics (2009)                                                35
PHYSICS:


Applications of Generalised Coordinate Eigenvalue Problems to Space Physics
Processes in near-Earth space are usually described in an orthogonal dipole coordinate system. However, in
some situations non-orthogonal coordinates are more appropriate. This project focuses on numerical
solution of an EM wave equation, eigenvalue problem in non-orthogonal coordinates. The particular
application involves the realistic damping and mode structure of a geomagnetic field line resonance and how
these respond to different ionosphere conductances.

Contact: Dr Murray Sciffer
Phone: 4921 5800
Email:    Murray.Sciffer@newcastle.edu.au
Centre for Space Physics


Determination of Magnetic Topology Using Ultra Low Frequency Waves Recorded in Antarctica
Quasi-sinusoidal, mHz frequency variations of the geomagnetic field at high latitudes are associated with
local field line resonances. The resonant frequency depends on magnetospheric dimensions and hence
solar wind conditions. In this project magnetohydrodynamic theory will be used in combination with
geomagnetic field and plasma density models to determine the expected resonance frequencies and
compare these to observations from four closely spaced magnetometers near Davis station, Antarctica.


Contact: Dr Sean Ables
Phone: 4921 2005
Email:    Sean.Ables@newcastle.edu.au
Centre for Space Physics


Electromagnetic fields near Power lines
Electric power generation authorities are interested in the electric and magnetic fields surrounding power
transmission lines. An Energy Australia consultant has requested a solution to the simplified problem of a
long, single wire suspended above a uniform conducting ground. Of interest are fields for a wire carrying
currents that vary up to ~kHz. The project will look at some of the existing analytic solutions and will involve
the computer simulation of more interesting variations of the parameters.

Contact: A/Prof Colin Waters
Phone: 4921 5421
Email:    Colin.Waters@newcastle.edu.au
Centre for Space Physics


Estimation of Pipeline-soil voltages due to Geomagnetically Induced Ground Currents
Gas and oil pipelines are susceptible to corrosion due to space weather. Cathode protection systems are
used to control the voltage between the pipeline and ground, but natural variations of the geomagnetic field
drive currents that cause changes in the pipe-to-soil potentials. In this project real magnetic field data and a
ground conductance model from Geoscience Australia will be used estimate the geo-electric field and hence
the pipe-soil voltages. This work may help reduce space weather effects on long pipelines.

Contact: A/Prof Colin Waters
Phone: 4921 5421
Email:    Colin.Waters@newcastle.edu.au
Centre for Space Physics


Field-Aligned Currents Measured Using FedSat
FedSat, Australia's only scientific satellite, operated December 2002 to August 2007. One of the primary
science payloads was the Newcastle Magnetometer (NewMag). This project will use NewMag and other data
sources to study the relationship between the interplanetary magnetic field (IMF) and the field-aligned
currents found in Earth's auroral zones. This is vital to understanding how the solar wind couples to our
geospace environment.


Faculty of Science and IT - Honours Research Topics (2009)                                                  36
Contact:    Dr Steve Morley
Phone:      4921 5425
Email:      Steve.Morley@newcastle.edu.au
Centre for Space Physics


Mapping the Radio Sky at Southern Polar Latitudes
We have operated an imaging riometer at the Australian Antarctic station Davis for some years. This space
weather instrument measures variations in radio noise reaching the ground from the sky. This project will (a)
determine whether individual radio stars or galaxies are detected; (b) use such discrete sources to check the
calibration of the antenna beam pattern and sensitivity; and (c) investigate scintillation effects.


Contact:    Professor Fred Menk
Phone:      4921 2005
Email:      Fred.Menk@newcastle.edu.au
Centre for Space Physics


Microscale Fluctuations in GPS Signals
Many navigation and aircraft landing systems rely upon precise radio signals transmitted from GPS
spacecraft at 20,200 km altitude. These signals suffer amplitude and phase perturbations due to plasma
density irregularities along the transmission path. This project will use high time resolution GPS data and
ground magnetometer observations from the Australian sector to investigate whether such perturbations are
caused by ULF (few mHz) plasma waves propagating through space. Such waves occur for hours every day
at all locations, and their presence in GPS data may have important implications for precise navigation
systems.

Contact:    Professor Fred Menk
Phone:      4921 2005
Email:      Fred.Menk@newcastle.edu.au
Centre for Space Physics


Polar Cap Boundary Dynamics
Magnetospheric substorms are large scale reconfigurations of the terrestrial magnetic field throughout
geospace that are analogous to earthquakes. On average they occur every 5 hours and deposit vast
amounts of energy in the upper atmosphere. The reconfiguration, through magnetic reconnection, drives
convection in geospace and causes motion of the poleward extent of aurorae. These high-latitude magnetic
disturbances can induce currents in the ground, causing damage to technological systems. This project will
investigate the motion of the boundary between the polar cap and the auroral zones usingdata from a variety
of space- and ground-based platforms, and through development of suitable software.


Contact:    Dr Steve Morley
Phone:      4921 5425
Email:      Steve.Morley@newcastle.edu.au
Centre for Space Physics


Remote Sensing of ULF Waves in Geospace Plasma Using SuperDARN Radars
This project uses HF radars in Tasmania and New Zealand to study the signatures of of ULF plasma waves
in the high latitude ionosphere. The project focuses on advanced analysis techniques used in geophysics,
including spectral and correlation algorithms, to elucidate the spatio-temporal and spectral structure of ULF
waves and obtain new information on their generation and propagation mechanisms.

Contact:    Dr Pavlo Ponomarenko
Phone:      4921 2005
Email:      phpp@alinga.newcastle.edu.au
Centre for Space Physics



Faculty of Science and IT - Honours Research Topics (2009)                                               37
Solar Physics – Magnetic Equilibrium of Solar Structure
This project will study the influence of multiple sources of magnetic flux on the equilibrium of magnetic field
structures in the solar atmosphere, and the quasi-static evolution of such fields. This will involve numerically
solving the force balance equation on a magnetised plasma representative of the solar surface, using a
nonlinear Grad-Shafranov approach. A parameter study will show how the solar magnetic structure evolves
over time.

Contact:    Dr Murray Sciffer
Phone:      4921 5800
Email:      Murray.Sciffer@newcastle.edu.au
Centre for Space Physics


Statistical Characteristics of ULF Waves in the Polar Cap
Plasma waves with 0-50 mHz frequency propagate throughout geospace and form an important diagnostic
tool for Space Weather applications. They are usually studied using ground-based magnetometers, but their
properties in the polar cap are largely unknown. This project will investigate (1) statistical characteristics of
the wave amplitude and phase (propagation) distribution inside the polar cap and (2) their physical
interpretation.

Contact:    Professor Brian Fraser
Phone:      4921 5445
Email:      Brian.Fraser@newcastle.edu.au
Centre for Space Physics


The Global Ionosphere Current System
The Iridium constellation of >70 polar orbiting 800 km altitude communications satellites provides global data
and voice services. This project will use proprietary data from the satellite attitude control systems to
investigate the ~million amp currents associated with auroras, and their relation to current systems closer to
the equator. These upset spacecraft attitude control systems and also cause corrosion in gas pipelines.

Contact:    A/Prof Colin Waters
Phone:      4921 5421
Email:      Colin.Waters@newcastle.edu.au
Centre for Space Physics


The Ionospheric Alfven Resonator
The Earth’s ionosphere acts as a resonant cavity for electromagnetic plasma waves. This project will involve
numerically solving the time dependent Maxwell wave equations to explore the properties of this cavity, and
comparison with experimental data. The model is unique in combining realistic descriptions of the
conductivity and geomagnetic field.

Contact:    Dr Murray Sciffer
Phone:      4921 5800
Email:      Murray.Sciffer@newcastle.edu.au
Centre for Space Physics


Effect of patient immobilization devices on dose calculations for radiotherapy
Immobilisation devices such as masks with associated metal and plastic mountings perturb high energy
photon beams used for radiation therapy treatment. This perturbation must be accurately predicted by the
treatment planning algorithm that calculates dose within the patient. This project will measure the two
dimensional perturbation of various immobilization devices used for patient setup in radiotherapy and
compared them to predictions from radiation therapy planning algorithms. This project will assist with
improving the accuracy of patient dose calculations and treatments in radiation therapy.

Contact:  Dr Peter Greer
Phone:    4921 1510
Email:    Peter.Greer@newcastle.edu.au
Research Group: Medical Physics
Faculty of Science and IT - Honours Research Topics (2009)                                                   38
Near Infrared Optical Fibre Power Monitor
Low-band gap conductive polymers can detect optical radiation in the near infrared. The project is to detect
the evanescent or bending loss field from an optical fibre carrying a NIR signal with a conductive polymer
detector. The end goal is to fabricate a polymer detector bonded to the fibre.

Contact: Dr John Holdsworth
Phone: 4921 5436
Email:     John.Holdsworth@newcastle.edu.au
Priority Research Centre for Organic Electronics


Organic semiconductor electronics
This project will explore the full capacity of organic conductive polymers in electronics applications. The
world class facilities at Priority Centre for Organic Electronics (PROCE) hosted by the University of
Newcastle have been established to allow us to fabricate flexible electronics, including organic light-emitting
display (OLED), organic field-effect transistor (OFET) and organic photovoltaic cell (OPVC) and their
combination organic integration circuit (OCI).

Contact: Dr Xiaojing.Zhou
Phone: 4921 6732
Email:     Xiaojing.Zhou@newcastle.edu.au
Priority Research Centre for Organic Electronics


Organic silicon hybrid devices
By using a scanning tunnelling microscopy (STM), this project involves a fundamental understanding on the
interactions between organic molecules and silicon surfaces at an atomic level. The formed structures will be
used to make organic silicon hybrid devices for biosensor applications.
Contact: Dr Xiaojing.Zhou
Phone: 4921 6732
Email:     Xiaojing.Zhou@newcastle.edu.au
Priority Research Centre for Organic Electronics


Polymer lasers
Conductive polymers will emit light and may be made into optically pumped lasers. The project entails filling
selected holes in a microstructured optical fibre with conductive polymer and optically pumping the structure
within a resonator to obtain laser emission.

Contact: Dr John Holdsworth
Phone: 4921 5436
Email:     John.Holdsworth@newcastle.edu.au
Priority Research Centre for Organic Electronics


Predicting optical properties of materials
Predicting and understanding the optical properties of materials from first principles can be considered as
one of the “last frontiers” in solid state physics. The challenge lies in the fact that the optical properties are
related to the excited electron states within the material. This project will compare a variety of calculations
based first principles calculations based in quantum mechanics.

Contact: Dr Vicki Keast
Phone: 4921 6653
Email:   Vicki.Keast@newcastle.edu.au
Research Group: Surface and Nancoscience




Faculty of Science and IT - Honours Research Topics (2009)                                                    39
Reaction energetics of 2-chlorophenol with Cu2O surfaces
Polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/F’s) are among the most
harmful pollutants to health and the environment. Despite the enormous amount of research on PCDD/F’s in
the last two decades, driven largely by their high toxicity, their formation mechanisms are not yet understood
in sufficient detail. This project will explore the role copper and copper oxides in the catalytic formation of
PCDD/F’s The adsorption (and its energetics) of a 2-chlorophenol molecule on the clean Cu2O surfaces
using first principles density functional theory calculations will be performed.

Contact: Dr Marian Radny
Phone: 4921 5447
Email:   Marian.Radny@newcastle.edu.au
Research Group: Surface and Nancoscience


Secondary Ion Mass Spectrometry of Implant Diffusion in Silicon
In the NASA Genesis mission, a spacecraft circled the sun for 27 months collecting atoms ejected by the sun
– the solar wind – onto wafers of Si, SiC and diamond. These experiments are significant for understanding
how stars from dust clouds. In collaboration with scientists at Argonne National Laboratory in Chicago, King
has measured the depth distribution of Mg and Ca atoms in Genesis wafers and found that the impurities
have moved in the wafer from where we expect them to be. Inital modelling of this movement has been
made but we need to know the parameters (eg segregation and diffusion energies) for the impurity motion.
To do this we will use Secondary Ion Mass Spectrometry (SIMS) to measure, as a function of temperature,
the distribution of Mg and Ca atoms with depth in implanted Si samples. We will then model these
distributions by using MAPLE to solve coupled differential equations describing the motion of impurities and
defects. This project has both experimental and computer simulation aspects which can both be extended or
reduced depending on progress.

Contact: Professor Bruce King
Phone: 4921 5548
Email:   Bruce.King@newcastle.edu.au
Research Group: Surface and Nancoscience




Faculty of Science and IT - Honours Research Topics (2009)                                                 40
STATISTICS:


Adaptive estimation in Threshold AR models
The Threshold Autoregressive (TAR) model is one class of nonlinear times series models that has been
applied in many areas, from Finance to Ecology. The aim of the project is to explore the adaptive estimation
of TAR models by weakening the assumption on the distribution of the errors. For example, if the error
follows a t-distribution, then under some conditions, we should be able to obtain the efficient estimates as
when it was normally distributed. This project will include understanding the established theory in the
literature, a bit of programming and their applications.

Contact: Dr Darfiana Nur
Phone: 4921 5547
Email:   Darfiana.Nur@newcastle.edu.au
Research Group: Statistics


Assessing Ecological Models
Goodness-of-fit assessment for models generated in theoretical ecology.

Contact Dr Robert King
Phone: 4921 5548
Email:   Robert.King@newcastle.edu.au
Research Group: Statistics


Bayesian Hierarchical Modelling
In the past decade, Bayesian techniques have increasingly been used in the analysis and reporting of
performance measures in health care, education and industry. This project will explore the effects of various
Bayesian models on parameter estimation, with a focus on the model’s use in organisational quality
improvement. The methods may be applied to health care, education or industry depending upon the
student’s preferences.

Contact: Dr Peter Howley
Phone: 4921 5518
Email:   Peter.Howley@newcastle.edu.au
Research Group: Statistics


Change-point detection
Developing algorithms for automatic detection of change points in time series data.

Contact: Dr Robert King
Phone: 4921 5548
Email:   Robert.King@newcastle.edu.au
Research Group: Statistics


Estimation methods for flexibly shaped statistical distribution
The problem of estmating the parameters of statistical distributions that can take on a wide variety of shapes
contributes to our understanding of distributional shape. Such distributions are of particular interest to
psychologists. This project could either focus on algebraicapproaches, or be based on simulation studies of
different methods.

Contact: Dr Robert King
Phone: 4921 5548
Email:   Robert.King@newcastle.edu.au
Research Group: Statistics




Faculty of Science and IT - Honours Research Topics (2009)                                                41
Modelling uncertainty in meta-analysis
Data from different studies are often combined for the purpose of conducting meta-analyses. This project will
assess various forms of modelling uncertainty in the meta-analyses framework. In particular an assessment
of the association between the presence of a particular gene and Ewing's Sarcome (a form of childhood
cancer) will be assessed. A Bayesian approach to meta-analysis will be investigated.

Contact: Dr Elizabeth Stojanovski
Phone: 4921 5346
Email:   Elizabeth.Stojanovski@newcastle.edu.au
Research Group: Statistics


Psychosocial effects of Cancer
The death rate from colorectal cancer has declined in recent years due to improved screening methods and
advances in treatment. Hence a growing population of people are living with a history of colon cancer. This
project will assess the psychosocial outcomes of longer term survivors using structural equation modelling, a
multivariate technique. Bayesian approaches will be implemented to account for some of the data
characteristics (non-normality for example) within this modelling framework.

Contact: Dr Elizabeth Stojanovski
Phone: 4921 5346
Email:   Elizabeth.Stojanovski@newcastle.edu.au
Research Group: Statistics


Socio-spatial statistics
The spatial pattern of disadvantage shows different features at different geographic levels. This project will
consider the role of geographic level and investigate social statistics of areas in the Hunter region.

Contact Dr Robert King
Phone: 4921 5548
Email:   Robert.King@newcastle.edu.au
Research Group: Statistics


Testing Homogeneity of Variances/ Inference
In two univariate samples the standard parametric test of equality of variances in normal populations is
based on the quotient of the unbiased sample variances. Wald tests based on the difference will have good
optimality properties and should be more robust to failure of the normality assumption. Similar considerations
apply to the corresponding multiple sample problem. This topic will involve verifying the derivation of the new
tests and an empirical study of their properties.

Contact: Professor John Rayner
Phone: 4921 554
Email:   John.Rayner@newcastle.edu.au
Research Group: Statistics




Faculty of Science and IT - Honours Research Topics (2009)                                                 42
School of Psychology

PSYCHOLOGY:

Exploring the psychosocial well-being of athletes post-retirement

Contact: A/Prof Jenny Bowman
Phone: 4921 5958
Email:   Jenny.Bowman@newcastle.edu.au
Research Group: Clinical and Health Psychology


Harm perception of cannabis versus other drug use among people with psychotic disorders

Contact: Dr Martin Johnson
Phone: 4921 8864
Email:   Martin.Johnson@newcastle.edu.au
Research Group: Clinical and Health Psychology


Obesity: psychological aspects

Contact: A/Prof Jenny Bowman
Phone: 4921 5958
Email:   Jenny.Bowman@newcastle.edu.au
Research Group: Clinical and Health Psychology


Psychosocial wellbeing of young adults diagnosed with cancer

Contact: A/Prof Jenny Bowman
Phone: 4921 5958
Email:   Jenny.Bowman@newcastle.edu.au
Research Group: Clinical and Health Psychology


Self-efficacy for change and homework compliance: Predictors of therapeutic outcome
The University Psychology Clinic provides a group program “Cool Kids” for children with anxiety. Research
has shown that client expectations and homework compliance may be important factors in treatment
efficacy. This study aims to provide a framework for ongoing assessment of these variables to improve
treatment outcomes.

Contact: Dr Rosemary Webster
Phone: 4921 5975
Email:   Rosemary.Webster@newcastle.edu.au
Research Group: Clinical and Health Psychology

Don’t stand so close to me: The relationship between self-construal and interpersonal closeness
The term self-construal means how people construe, or perceive, themselves in relation to other people.
Markus and Kitayama (1991) proposed that there are two types of self-construal: independent self-construal
and interdependent self-construal. Independent self-construal refers to a conception of the self as an
autonomous, independent person, separate from others. Interdependent self-construal refers to conception
of the self as existing in relationships with others. Following Holland, Roeder, van Baaren, Brandt, and
Hannover (2004), we will investigate the hypothesis that people with an independent self-construal should be
motivated to distance themselves from other people in order to maintain their sense of autonomy and
independence, and that people with an interdependent self-construal should be motivated to increase their
closeness to other people in order to enhance their sense of relatedness and connectedness with others.

Contact: Dr Mark Rubin
Phone: 4921 6706
Email:   Mark.Rubin@newcastle.edu.au
Research Group: Human Experimental and Applied Dynamics (HEAD)

Faculty of Science and IT - Honours Research Topics (2009)                                              43
Feedback and Absolute Identification

Contact: A/Prof Andrew Heathcote
Phone: 4921 6778
Email:   Andrew.Heathcote@newcastle.edu.au
Research Group: Human Experimental and Applied Dynamics (HEAD)


Gender Bias in Spatial Cognition Performance
Investigates whether gender bias exists in test performance on spatial ability tasks. Research provides
evidence that differences do exist. This study examines whether differences are still prevalent today. It
investigates if changes in study, work and leisure activities which are currently more uniform across genders
will show test performance to be similar. This study compares the performance of two groups (male and
female) using a range of psychometric spatial ability paper tests and a recently developed computer-based
test of 3D understanding. Both skilled and unskilled subgroups may be investigated.

Contact: Mr Ken Sutton
Phone: 4921 6361
Email:   Ken.Sutton@newcastle.edu.au
Research Group: Human Experimental and Applied Dynamics (HEAD)


Improving 3D Understanding
Investigates performance on a computer-based psychometric test of 3D understanding after exposure to a
set of interactive learning tasks designed to improve 3D understanding. Examines active exploration
(learning by doing) as opposed to the conventional approach of passive learning. Compares test
performance of a control group with an experimental group consisting of participants with no prior learning
experience. Learning tasks will be selected from a set currently under development. Both male and female
subgroups may be investigated.

Contact: Mr Ken Sutton
Phone: 4921 6361
Email:   Ken.Sutton@newcastle.edu.au
Research Group: Human Experimental and Applied Dynamics (HEAD)


Mapping the Spatial Ability Profile of Designers
Spatial ability refers to performance on tasks that require the mental rotation of objects, the ability to
understand how objects appear in different positions and the ability to conceptualise how objects relate to
each other in space. Specific spatial ability tasks will be used to profile novice designers from a range of
design disciplines. The tasks consist of sets of test items called subtests that represent different elements of
spatial ability considered appropriate to designers. This project will investigate differences in performance
and whether distinct factors of spatial ability can be identified.

Contact: Mr Ken Sutton
Phone: 4921 6361
Email:   Ken.Sutton@newcastle.edu.au
Research Group: Human Experimental and Applied Dynamics (HEAD)


Personality and Cognitive Conflict
Using Festinger’s (1957) model of cognitive dissonance this project will examine the personality differences
of people who experience greater dissonance compared to those who report less dissonance.

Contact: Dr Miles Bore
Phone: 4921 6585
Email:   Miles.Bore@newcastel.edu.au
Research Group: Human Experimental and Applied Dynamics (HEAD)




Faculty of Science and IT - Honours Research Topics (2009)                                                  44
Personality and Psychological Health
This project explores the relationships between trait models of personality and the frequency and intensity of
symptoms of poor psychological health. The study will focus on possible curvilinear relationships.

Contact: Dr Miles Bore
Phone: 4921 6585
Email:   Miles.Bore@newcastel.edu.au
Research Group: Human Experimental and Applied Dynamics (HEAD)


Personality and Social Behaviour
The predictive validity of a model consisting of three global traits will tested in this study. An experimental
task will be designed to elicit measurable individual differences that will be used as outcome variables.

Contact: Dr Miles Bore
Phone: 4921 6585
Email:   Miles.Bore@newcastel.edu.au
Research Group: Human Experimental and Applied Dynamics (HEAD)


Presentation Frequency and Absolute Identification

Contact: A/Prof Andrew Heathcote
Phone: 4921 6778
Email:   Andrew.Heathcote@newcastle.edu.au
Research Group: Human Experimental and Applied Dynamics (HEAD)


Spacing Effects in Absolute Identification

Contact: A/Prof Andrew Heathcote
Phone: 4921 6778
Email:   Andrew.Heathcote@newcastle.edu.au
Research Group: Human Experimental and Applied Dynamics (HEAD)


Stimulus Noise and Choice

Contact: A/Prof Andrew Heathcote
Phone: 4921 6778
Email:   Andrew.Heathcote@newcastle.edu.au
Research Group: Human Experimental and Applied Dynamics (HEAD)


The Gambler’s Fallacy
The Gambler's Fallacy is well known - when people are asked to predict the outcome of a coin toss, they
increasingly bet on heads after a long run of tails. This behaviour is statistically sub-optimal, but it happens
very reliably, and in a wide range of tasks and under a wide range of conditions. We investigate the causes
of the Gambler's Fallacy, by searching for conditions where it is not observed.

Contact: Dr Scott Brown
Phone: 4921 5760
Email:   Scott.Brown@newcastle.edu.au
Research Group: Human Experimental and Applied Dynamics (HEAD)


Analytical/synthetic perception and hedonics of odour/taste mixtures

Contact: A/Prof John Prescott
Phone: 4348 4145
Email:   John.Prescott@newcastle.edu.au
Research Group: Neuroscience


Faculty of Science and IT - Honours Research Topics (2009)                                                  45
Binaural and monaural mechanisms in auditory temporal processing

Contact: Dr Bill Budd
Phone: 4348 4135
Email:   Bill.Budd@newcastle.edu.au
Research Group: Neuroscience


Defining contextual relevance in sound processing
The brain automatically models patterns in sound activity in the environment. These models serve the
function of representing a current context against which the relevance of subsequent sounds can be
automatically evaluated outside of our awareness. This function contributes to the efficiency of attention and
neural processing and is dysfunctional in certain clinical groups. Studies will be conducted using
electrophysiological, psychophysical and/or neurocognitive measures to determine the parameters that
define the boundaries of this context.

Contact: Dr Juanita Todd
Phone: 4921 5977
Email:   Juanita.Todd@newcastle.edu.au
Research Group: Neuroscience


Developmental trajectories of cognitive control
Executive control functions are amongst the last to mature – often not reaching peak function until early
adulthood. Our research aims at defining maturational pathways of different aspects of cognitive control
across childhood to early adulthood. We examine individual variability in developmental trajectories with a
view to mapping specific patterns of executive function development to problem behaviours in childhood and
adolescence.

Contact: Dr Frini Karayanidis
Phone: 4921 5457
Email:   Frini.Karayanidis@newcastle.edu.au
Research Group: Neuroscience


Global spatial perceptual processes as cues in coherent motion perception

Contact: Dr Stuart Marlin
Phone: 4921 6323
Email:   Stuart.Marlin@newcastle.edu.au
Research Group: Neuroscience


Judging facial emotions – accuracy and discriminability of emotion expression

Contact: A/Prof Mick Hunter
Phone: 4921 5953
Email:   Mick.Hunter@newcastle.edu.au
Research Group: Neuroscience




Faculty of Science and IT - Honours Research Topics (2009)                                                46
Impact of early life infection on the development of the pain system*

Impact of neonatal endotoxin exposure on adulthood anxiety-like behaviour and the underlying
neural mechanisms*

Long-term alterations in neuroimmune responses after neonatal exposure to lipopolysaccharide*

Maternal Probiotic Treatment Protects Against Colonic and Immune Dysfunctions Induced by
Neonatal Stress*

Role of early life factors in susceptibility to cancer in rodents*

* Laboratory of Neuroimmunology

Animal research has previously demonstrated that exposure of infant pups to stress during the prenatal
and/or early neonatal period temporarily disrupts the physiological and behavioural functioning of the
offspring. Recent research has demonstrated that exposure to stress during this period can also produce
permanent physiological changes in the offspring. Specifically, perinatal stressors alter physiological systems
involved in regulating responses to stress in adulthood. Research in our laboratory has provided new
evidence to suggest that exposure to these stressors during the early neonatal period can also have an
impact on immune and behavioural functioning and ultimately alter long term health outcomes. Our current
research is investigating the mechanisms underlying these effects. An animal model is used in this research
(rats).

Contact: Dr Deborah Hodgson
Phone: 4921 6701
Email:   Deborah.Hodgson@newcastle.edu.au
Research Group: Neuroscience


Local temporal processes as cues in coherent motion perception

Contact: Dr Stuart Marlin
Phone: 4921 6323
Email:   Stuart.Marlin@newcastle.edu.au
Research Group: Neuroscience


Maturation in the Chicken – changes in EEG power during the first 6 weeks of life

Contact: A/Prof Mick Hunter
Phone: 4921 5953
Email:   Mick.Hunter@newcastle.edu.au
Research Group: Neuroscience


Mechanisms of Auditory Attention:

i)      Attention isolates multiple sound characteristics
        Auditory change detection occurs by comparison of an averaged representation of preceding sounds
        to each new sound. Attention can isolate the representation of a single sound source to prevent it
        being averaged with other sound’s representations, thus maximising acuity of change detection for
        the attended sound. This has been demonstrated only for one sound attribute (duration), but should
        be true for all attributes (e.g. intensity, location etc). This project aims to establish that multiple
        characteristics of the attended sound source are isolated.

        Contact: Mr David McKenzie
        Phone: 4921 6319
        Email:   David.McKenzie@Newcastle.edu.au
        Research Group: Neuroscience




Faculty of Science and IT - Honours Research Topics (2009)                                                 47
ii)     Dynamics of the MMN representation
        This project aims to examine the fit of various models describing the absolute duration
        representation when a train of different-duration sounds is presented. Clearly this representation will
        increase or decrease as the duration of the sounds presented increases or decreases, and will be a
        function of the time between the sounds. The auditory change detection mechanism (mismatch
        negativity), can be used to probe the absolute value of the duration representation. In this project
        the represented duration will be compared to predictions of dynamic models of the representation’s
        absolute value.

        Contact: Mr David McKenzie
        Phone: 4921 6319
        Email:   David.McKenzie@Newcastle.edu.au
        Research Group: Neuroscience


Mind control - EEG mu rhythm neurofeedback and control of dynamic visual displays

Contact: A/Prof Mick Hunter
Phone: 4921 5953
Email:   Mick.Hunter@newcastle.edu.au
Research Group: Neuroscience


Processing time cues in sound – changes in central auditory processing associated with aging
As we age, many individuals with intact audiograms (normal hearing sensitivity) will experience difficulty
hearing speech in noisy environments. One hypothesis for why this occurs is that there is a decline in the
ability to track important temporal/timing cue in the speech signal. Studies will be conducted using
electrophysiological, psychophysical and/or neurocognitive measures to determine the pattern of temporal
processing of age-related decline in central auditory processing.

Contact: Dr Juanita Todd
Phone: 4921 5977
Email:   Juanita.Todd@newcastle.edu.au
Research Group: Neuroscience


Sequence effects in Go/NoGo and two-choice tasks
Reaction time in two-choice tasks is dependent on the sequence of trials preceding the current trial. For
example, responses are slow and errors are common if a participant has to change from a train of response
X to a different response Y. This change from an expected response will elicit greater response inhibition
and competition than after a run of the same type of trials. The project will examine the effect of sequence on
event-related potentials in a Go/NoGo task and a two-choice RT task.

Contact: Dr Janette Smith
Phone: 4921 7096
Email:   Janette.Smith@newcastle.edu.au
Research Group: Neuroscience


Structural and functional organisation of cognitive control processes
Our research program aims at understanding the cognitive and neural architecture of executive control
processes. We use a range of paradigms that allow us to examine the role of voluntary mechanisms vs
contextual factors that affect the way we control our intentions and actions. Our program integrates across
mathematical models of behaviour and neuroimaging methods such as event-related potentials (ERP) and
functional magnetic resonance imaging (fMRI) in order to develop integrative models of cognitive control.

Contact: Dr Frini Karayanidis
Phone: 4921 5457
Email:   Frini.Karayanidis@newcastle.edu.au
Research Group: Neuroscience




Faculty of Science and IT - Honours Research Topics (2009)                                                 48
The role of control processes in cognitive decline in normal ageing and psychopathology
Executive dysfunction is associated with many clinical conditions and normal ageing. Our work aims to
examine specific patterns of cognitive control decline in psychopathologies associated with frontal lobe
dysfunction and develop cognitive remediation programs targeted to different clinical groups.

Contact: Dr Frini Karayanidis
Phone: 4921 5457
Email:   Frini.Karayanidis@newcastle.edu.au
Research Group: Neuroscience


Vision Science: Myopia
1. Reversing myopia with plus lenses

Contact: Dr Sally McFadden
Phone: 4921 5634
Email:   Sally.McFadden@newcastle.edu.au
Research Group: Neuroscience


What is learnt with neurofeedback?
Neurofeedback is a method for supplying information about bodily systems to an individual, so they may
better control that system. For example, information about muscle tension may help an individual to avoid
tension headaches. It is not clearly understood what is learnt during the neurofeedback process, nor how
long the effect lasts. This study will investigate these questions in healthy adults training brain waves.

Contact: Dr Janette Smith
Phone: 4921 7096
Email:   Janette.Smith@newcastle.edu.au
Research Group: Neuroscience


Investigating why intergroup interactions can be detrimental to the relations between rival social
groups
Area: Social stereotyping, prejudice, and discrimination
Fifty years ago, Gordon Allport, an influential social psychologist, proposed that face-to-face interactions, or
‘contact’, between individuals of potentially rival groups may reduce prejudice, discrimination, and conflict
and lead to more harmonious intergroup relations. Since then, this idea has inspired desegregation policies
in Australia and around the world. Recent reviews of the intergroup contact literature have confirmed that
positive contact with individuals of the ‘other’ group or ‘outgroup’ improves intergroup relations. This
optimistic view of the future, however, is at odds with a sharp increase in intergroup conflict that our
multicultural society is experiencing. In the proposed research, we aim to clarify why intergroup conflict
continues to be a key social issue in Australia and abroad despite increased contact between social groups.
In particular, we use a variety of social psychological research methods to address the following critical
questions:

    Does negative (i.e., unpleasant) contact with outgroup members make people more aware of their
    respective group memberships than positive (i.e., pleasant) contact and does it have a greater impact on
    group attitudes?

    Why might negative intergroup contact have a disproportionate impact on intergroup relations?

    Are there conditions under which negative contact does not make people more aware of their group
    memberships and does not have a greater impact on group attitudes?

Contact: Dr Stefania Paolini
Phone: 4921 5938
Email:     Stefania.Paolini@newcastle.edu.au
Priority Research Centre for Brain and Mental Health Research




Faculty of Science and IT - Honours Research Topics (2009)                                                  49

				
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