School of Biological Sciences & Biotechnology

Our Research Students

Genetic structure and abundance of fishery-impacted dolphins of the Pilbara region, north-western Australia

The bycatch of non-target wildlife in fisheries is a global problem. The significance of this research lies in quantifying the level of impact a commercial fishery has on a protected species population,and then providing recommendations toward reducing impacts and promoting sustainable fisheries.

Some of the objectives of this research are to:

1. Examine dolphin population genetic structure, effective population size and gene flow across the Pilbara Trawl Fishery,

2. Estimate the abundance of dolphins in the fishery by conducting an aerial survey.

PhD Candidate – Simon Allen

Coral growth and survival on Hall Bank Reef; a high latitude marginal reef in Fremantle, WA

Over the last few decades global climatic changes have caused wide scale disturbances to coral reef systems and although high latitude reefs are also suffering, their resilience appears much higher than tropical reefs.

Therefore the corals found on high-latitude reefs have significant research potential in terms of the mechanisms necessary for coral reef survival.

Some of the objectives of this project are to:

1) Document the growth rates, mortality and lesion recovery of juveniles corals for 1 year;

2) Record physical parameters at Hall Bank Reef such as temperature, light, nutrients, currents and wave conditions.

Honours student – Kaija Antipas

Symbiotic specificity and nodulation in the southern African legume clade Lotononis s. l. and description of novel

rhizobial species…

Several species in the southern African legume clade Lotononis s. l have shown potential as perennial pasture legumes in southern Australian agricultural systems.

This project examines the symbiotic relationships between species of Lotononis s. l and their associated rhizobia.

Some of the objectives of this research are to:

1. contribute to sustainable agricultural systems, 2. help decipher how plants and bacteria communicate with

each other, 3. provide a better understanding of the signal transduction

pathways which may eventually allow to develop nitrogen fixation in cereals.

PhD Candidate – Julie Ardley

Effect of silencing Myzus persicae (green peach aphid) genes by RNAi by feeding with dsRNA and or via transgenic plants

Aphids reduce crop yields both directly by feeding damage and indirectly by transmission of virus diseases. With the development of resistance against not only chemicals but also genetically resistant varieties of crops, exploiting the naturally occurring cellular process of RNAi is an exciting field of research in terms of developing transgenic crops.

The objective of this project is to silence the expression of genes vital for aphids to complete their life cycle using RNAi.

This will provide an excellent method of control that is both economical and environmentally safe.

PhD Candidate – Vineeta Bilgi

Green peach aphids

Abundance, residency and genetic connectivity of Australian snubfin (Orcaella heinsohni) and Indo-Pacific humpback (Sousa

chinensis) dolphins in the Kimberley region

Little is known about the snubfin and humpback dolphins in north-west Australia, and insufficient data exist for DEC in Western Australia to effectively assess their conservation status. Increasing pressure from coastal development in WA is threatening coastal habitats and the species that rely on them, such as coastal dolphins.

Some of the objectives of this research are to:

1. Quantify abundance and residency patterns for Australian snubfin, Indo-Pacific humpback and Indo-Pacific bottlenose dolphins in state waters at several locations in the Kimberley region.

2. Use a landscape genetics approach to identify levels of structure and connectivity within and between dolphin populations across the Kimberley region.

PhD Candidate – Alex Brown

The congruence between bat and vegetation succession in restored bauxite minesites in the jarrah forests of south-

western Australia

Joanna’s research project will be the first, nationally or internationally, to specifically examine the impacts of mining on bat activity, including foraging and roosting behaviour,It should inform future land managers on how to maintain bat populations in production landscape.

Some of the objectives of this research are to:

1) identify patterns of bat succession in restored minesites2) investigate congruence between these successional patterns and

vegetation succession3) identify patterns of bat foraging in restored minesites

PhD Candidate – Joanna Burgar

Coral-associated microbial communities in reef-building corals of Ningaloo Reef, Western Australia

Climate change imposes measurable effects and represents a major threat to coral reefs. The balance of the complex multi-partner symbiotic relationship in coral reef ecosystem is disrupted by:

• increases in atmospheric concentrations of carbon dioxide contributing to ocean warming, • as well as ocean acidification

Each of these stressors and their synergistic effects can result in coral stress or disease and ultimately in coral death.

Some of the findings of this project are:1. microbial shifts in adult corals over one year are structured by environmental

parameters; 2. brooding and broadcast spawning corals show distinct differences in microbial

profiles; 3. coral reproduction as well as the environmental effects of coral mass spawning

influence changes in coral-microbial communities;

PhD Candidate – Janja Ceh

Population biology of bottlenose dolphins (Tursiops aduncus) in the metropolitan waters of Perth, Western Australia

Six bottlenose dolphins were found dead within a five month period in the Swan Canning Estuary, Perth, in 2009 and were reported as an Unusual Mortality Event (UME). Recent tests came back positive for morbillivirus, a rare virus caught by cetacean in the open ocean.

Some of the main objectives of this project are:

1. Long-term study of the dolphins inhabiting the estuary and Inner harbour,

2. Provide more scientific data in order to improve conservation basis of the Swan River’s dolphin population.

PhD Candidate – Delphine Chabanne

Ranging patterns of resident and transient populations and their time spent in the Swan-Canning estuary vs coastal waters, Gage Roads (North), Owen Anchorage (Middle) and Cockburn Sound (South).

Colonisation of Jetty Pilings at Busselton Jetty

The development of Busselton jetty started over 200 years ago providing a new habitat for a variety of marine organisms.

The information collected on the colonisation of steel pilings may also be relevant to other studies related to fouling of steel structures such as oil rigs.

Some of the objectives of this research are:

1) To monitor over an extended period the progressive colonisation of the new wood pilings vs the new steel pilings recently established at the Busselton Jetty;

2) A comparison of these new pilings against the well colonised old wood pilings will also be an interesting endeavour.

Honours student – Fionna Cosgrove

A standardized method for the comparison of skin lesions among bottlenose dolphin population in coastal areas

Lisa’s research will focus on skin lesions in bottlenose dolphins. Skin lesions can offer insights into the health of the ecosystem and the strength of the dolphin’s immune system. Currently there is no standardised method for classifying lesions, making it difficult to compare different studies.

The objectives of this research are to:

1. Develop a classification system for skin lesions in bottlenose dolphins, especially lesions caused by Poxvirus, also called Tattoo Skin Disease.

2. Reduce the subjectivity in lesion classification and allow lesions to be classified more accurately.

3. It will also make it easier to compare results across studies.

Honours student – Lisa-Marie Harrison

Comparative and Functional Analysis of Trans-spliceosome Units of Cyst and Root Lesion Nematodes.

The research aims at interfering the expression of genes encoding trans-spliceosome units of Heterodera schachtii (Beet cyst nematode) and Pratylenchus thornei (a root lesion nematode).

The objective of this project is to validate the chosen targets by functional analysis, using two approaches – ‘soaking’ and ‘in planta’ delivery of dsRNA - to identify genes which if knocked out by RNAi will confer plant resistance to major plant parasitic nematodes.

PhD Candidate – Harshini Herath

The Regulation of neuregulin-1β gene expression in lung fibroblasts and its role in perinatal lung development.

George’s research project is investigating the role of neuregulin-1β (NRG-1β) in perinatal lung development and its mode of action.

A better understanding of the molecular regulation and release of surfactant synthesis is needed to improve the treatment of premature infants who suffer from respiratory distress as a result of diminished surfactant production.

Some of the objectives of this research are to:

1) Determine whether purified NRG-1β can stimulate surfactant lipid biosynthesis;

2) Ascertain the effect of glucocorticoids on NRG-1β gene expression;3) Evaluate the effect of NRG-1β on the level of β-adrenergic receptors and its

corresponding mRNA in type II cells.

PhD Candidate – George King

The ecology of the grazing urchin Echinometra mathaei at Ningaloo Marine Park

Sea urchins are important grazers in many marine systems and can cause major changes in the ecosystem when their populations reach high levels …The role of sea urchins in influencing the composition and structure of coral reef habitats has rarely been explored.

Some of the objectives of this research are to:

1. Determine what factors influence the distribution and population of the grazing urchin (Echinometra mathaei) within the Ningaloo Marine Park,

2. Quantify urchin grazing rates and subsequent bioerosion of substrates.

This will be the first time urchin grazing, bioerosion, movement and behaviour will be quantified at Ningaloo Reef.

PhD Candidate – Mark Langdon

The diet and foraging ecology of a population of bottlenose dolphins in south west Australia

In order to better manage human activity to lessen stressful impacts on the dolphins it is imperative to have a better understanding of potential direct and indirect competition of fisheries, likely avenues of contaminant exposure, and general areas use patterns. The role of sea urchins in influencing the composition and structure of coral reef habitats has rarely been explored.

Some of the specific aims of this project are to:

1. Estimate the relative abundance, composition, and energy content of prey species in the nearshore waters of Bunbury in summer and winter months.

2. Investigate trophic level interactions of dolphins and prey using stable isotope analyses.

3. Develop a spatially explicit model of environmental drivers in the coastal region that influence dolphin movement and behavior.

PhD Candidate – Shannon McCluskey

Are the volatile chemicals from wheat and grain insects related with inter-communication between insects and host?

This project proposes to understand the biological and chemical based signals between insects and their hosts which could lead to new approaches to the diagnosis and bio-treatment of insect pest . It is hoped this will help solve some of the key biosecurity problems related to insects control.

Some of the objectives of this research are to:

1. Identify volatile compounds which could be used as signals for insect receivers.

2. Develop rapid method for analysis of the volatile compounds by HS-SPME and GC-MS.

3. Determine the influence of the signals on behaviour of the receivers and develop a model for describing their relationship.

PhD Candidate – Yonghao Niu

The Dynamic Eukaryote Genome: Evolution and the TE-Thrust Hypothesis

There are many questions about the adequacy of the ‘Modern Synthesis’ to account for many known aspects of evolution. Keith’s project is examining the expansion of the Modern Synthesis to include the hypothesised TE-Thrust, and other new data and concepts, which may go a long way towards obtaining a better match between the theory and the realities of evolution.

The main objectives of this project are:

1. to expand the theoretical basis for the understanding of evolution, with particular attention paid to the part played by transposable elements in evolution and,

2. to make this theoretical understanding widely available to all interested evolutionary biologists, other biologists or students.

PhD Candidate – Keith Oliver

The Ecology and Demography of Stingrays (Dasyatidae) at Ningaloo Reef, Western Australia

Most rays have life history traits such as slow growth, late maturation to adulthood and low fecundity, which make them vulnerable to anthropogenic pressures, such as overfishing (both as by-catch and in targeted fisheries), and habitat destruction. Despite this, there has been little research on the demography and role of stingrays in coral reef communities and much of what is known is inferential or based on modeling studies.

Some of the objectives of this research are to:

1. Describe the distribution, abundance, movement patterns, age & growth, trophic ecology, and ecosystem impact of stingrays within the Ningaloo Reef Marine Park.

2. Highlight key ecological functions, predator-prey relationships and bio-geophysical impacts of stingrays at multiple spatial scales.

PhD Candidate – Owen O’Shea

Enhanced Nodulation of Grain Legumes Co-inoculated with Rhizobia and Plant Growth Promoting Rhizobacteria

Rhizobia occupy nodules on the roots of plants and it is within these nodules that they are able to convert atmospheric N2 to NH3.

It has been shown that nodule formation is enhanced by co-inoculating with plant growth promoting rhizobacteria (PGPRs).

Some of the objectives of this research are to:

1. Determine genes associated with enhanced nodulation and growth ,

2. Increase knowledge about the mechanisms which contribute to enhanced nodulation, plant growth and nitrogen fixation.

PhD Candidate – Liza Parkinson

Nodules observed on Glycine max when inoculated with Bradyrhizobium japonicum CB1809 and when co-

inoculated with Bacillus spp. WSM4548

Headspace Solid-Phase Microextraction Gas Chromatography-Mass Spectrum method for detection and

identification of Phytophthora species

Phytophthora species is a serious plant pathogen to agriculture and forest; This project aims at developing reliable, cheap and quick diagnostic techniques like HS-SPME GC/MS method for Phytophthora diagnosis. This may become a useful tool to solve some of the biosecurity problems related to plant health.

Some of the objectives of this research are to:

1. Identify the specific VOCs of Phytophthora species, develop new diagnostic methods for Phytophthora

2. Develop new treatment of Phytophthora according to biological and chemical signals of Phytophthora.

PhD Candidate – Rui Qiu

Identification of humpback whale breeding areas in the Great Barrier Reef Marine Park: validation of a spatial habitat

model

The breeding areas for Australian humpback whales in the Great Barrier Reef Marine Park (GBRMP) are not well defined. More information about the distribution and habitat use of these whales is needed for a more effective management of interactions between breeding whales and human activities in the BGRMP.

The overall objective of this project is to identify areas and habitat important to mating and calving whales and to:

1. Determine distribution and quantify relative abundance of breeding whales within four regions of the GBRMP.

2. Identify human use in areas of important habitat to breeding humpback whales.

Postdoc – Josh Smith

Predictive habitat modelling and population dynamics of Indo-Pacific bottlenose dolphins (Tursiops aduncus) in south western Australia.

Animals prefer to use an area based on its physical environment, food availability, protection from predators, suitability as a breeding or calving ground and lack of anthropogenic pressures. Detecting these critical areas and explaining the factors that influence habitat use and movements (through predictive habitat modelling techniques) are important for conservation and management efforts of a species.

Some of the objectives for this project on the Bunbury dolphin population are to:

1. Investigate the distribution and habitat use using predictive habitat modelling techniques,

2. Calculate current abundance estimates & determine home ranges and population dynamics.

PhD Candidate – Kate Sprogis

Characterising the ‘secretome’ and establishing a protocol to use root lesion nematodes as a model for RNA

interference in plant parasitic nematodes

The aim of this project is to investigate the use of RNAi as an alternative method of nematode control and to identify and silence genes related to plant parasitism in Pratylenchus spp. The application of RNAi and its delivery via transgenic plants can provide a strategy which is not only environmentally friendly, but also able to confer broad resistance to numerous plant parasites.

Root lesion nematodes (Pratylenchus spp.) reduce the yield of wheat and barley crops in WA by 7-15%.

PhD Candidate – Jo-Anne Tan

This project is focusing on nematode diagnostics using existing and novel molecular approaches to identify plant parasitic nematodes.

The main objectives are to: • develop ‘anti-primer’ technology for plant parasitic

nematode identification,• use existing nematode diagnostic techniques and

compare them with new approaches such as protein profiling using mass spectroscopy .

Nematode pathogens cause losses of at least $450 million per annum in Australia and US$120 billion

each year in crop losses worldwide.

Molecular approaches to diagnostics for plant parasitic nematodes of biosecurity concern

PhD Candidate – Matthew Tan

Quantifying the effects of human interactions on spinner dolphins in resting bays in Hawaii, and assessing the

effectiveness of time area closures…

This study aims to collect baseline data on the local abundance, distribution and behaviour of spinner dolphins (Stenella longirostris) using a suite of modern visual and acoustic techniques in four resting bays along the Kona coast of Hawai'i island. This data will then be used to investigate the effects of human interactions on the spinner dolphins and assess the effectiveness of time area closures as a mitigation approach.

Some of the objectives of this research are to:1. Quantify spinner dolphin daytime habitat use and resting behaviour in

proposed time area closures2. Produce quantitative measures of spinner dolphin exposure to human

activities within resting bays and in near shore shallow water environments outside resting bays.

3. Produce predictive habitat models and individual based models of spinner dolphin behaviour in relation to human interactions

PhD Candidate – Julian Tyne

Impact of Plant Pathogens in Irrigation Water on Biosecurity in the Ord River Irrigation Area (ORIA)

The ORIA, currently under expansion, is subject to various environmental controls, including the implementation of irrigation tailwater management systems. This management system involves recycling of tailwater and has the potential to aid in the dispersal of plant pathogens if they are present in the water.

The main objectives of this research are to:

1. Determine the presence of Phytophthora and Pythium species in the irrigation water of the ORIA; and

2. ascertain what impact they could have on biosecurity in the region if tailwater is recycled.

PhD candidate – Rebecca Zappia