Honours Project Booklet - Deakin University...All three Honours courses run on a semester structure,...

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Honours Project Booklet School of Life and Environmental Sciences

2021

School of Life and Environmental Sciences Honours 2021 Information Booklet

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What is Honours? During Honours, students undertake independent research, under supervision, that forms the majority (75%) of their activity for the year. The research may involve field work, laboratory work and data analysis, depending on the nature of the project. The major assessment component is the written thesis produced at the end of the year. Honours students also must present their research via oral presentations. There are also two coursework units (comprising the remaining 25% of activity) which vary according to the Honours program you are enrolled in.

Why do Honours? An Honours degree provides an important year for further acquisition of scientific skills. In addition to the specialised research training you obtain during your research project, all Honours students gain further competence in critical thinking and data analysis, information technology, computer software, and scientific communication via oral and written presentations. These skills are recognised by external employers as essential in the workplace. Thus, completion of an Honours year will make you more employable. An Honours degree also exposes you to research of national and international significance, and is the springboard to further study as a postgraduate student undertaking Masters or PhD level research.

How do I get into Honours? Admission to the Honours program normally require students to have a Bachelor’s degree with an average of at least 65% or greater in their level-3 units. There is an alternative entry pathway with consideration of relevant work experience through an interview process. Furthermore, admission to the Honours program is dependent on a suitable research project and the availability of a supervisor.

Honours structure There are three Honours courses:

• S400 Bachelor of Science (Honours) • S401 Bachelor of Forensic Science (Honours) • S494 Bachelor of Environmental Science (Honours)

All three Honours courses run on a semester structure, with Honours requiring 2 semesters of study. In each semester you will do 4 credit points. Two of these credit points in semester 1 or semester 2 will be for the two stand-alone coursework units. The remaining 6 credit points will be for your research project running across both semesters. Activities for Semester 1 Honours will commence on Monday 22nd February 2021 with thesis submission in mid-late November. Semester 2 Honours commence on Monday 28th June 2021 with thesis submission the following April 2022. You must be available to commence Honours on the specified start dates.

Applications The first step in securing a place in the program for 2021 is to contact supervisors and discuss projects. Once you have met with a supervisor and agreed on a project, please complete the application form on the website. Application forms must be completed and signed by the nominated Supervisor and attached to your online application via the Deakin applicant portal.

Applications close on Monday 1st February 2021 for the Semester 1, 2021 intake and Friday 4th June 2021 for the Semester 2, 2021 intake.

Further information Contact your local Honours coordinator (Burwood: Assoc Prof Peter Beech; Waurn Ponds: Dr Annalisa Durdle; Warrnambool: Assoc Prof Julie Mondon) and via the School Honours website at deakin.edu.au/les-honours

https://www.deakin.edu.au/les-honours

https://www.deakin.edu.au/application-portal

https://www.deakin.edu.au/les-honours


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Burwood Projects ...............................................................................................................................5

Prof John Arnould .......................................................................................................................5

A/Prof Lambert Brau ...................................................................................................................5

Dr Damien Callahan ....................................................................................................................5

Dr Adam Cardilini ........................................................................................................................6

A/Prof Raylene Cooke and A/Prof John White .............................................................................6

A/Prof Raylene Cooke, A/Prof John White and A/Prof Mike Weston ...........................................7

Dr Bernhard Dichtl ......................................................................................................................7

Prof Don Driscoll .........................................................................................................................7

Dr Georgia Dwyer .......................................................................................................................8

Dr Galen Holt ..............................................................................................................................8

Dr Scarlett Howard .....................................................................................................................9

A/Prof Rebecca Lester.................................................................................................................9

Dr Ashley Macqueen ................................................................................................................. 10

Dr Alex McQueen...................................................................................................................... 10

A/Prof Kelly Miller .................................................................................................................... 11

Dr Nick Porch ............................................................................................................................ 11

Prof Jenny Pringle ..................................................................................................................... 11

A/Prof Euan Ritchie ................................................................................................................... 12

Dr Anthony Somers ................................................................................................................... 12

A/Prof Matthew Symonds ......................................................................................................... 13

Dr Stacey Trevathan-Tackett ..................................................................................................... 13

Dr Susanna Venn ...................................................................................................................... 13

Dr Mark Warne ......................................................................................................................... 14

Dr Liz Weldon ........................................................................................................................... 14

A/Prof Mike Weston ................................................................................................................. 15

Dr Tricia Wevill ......................................................................................................................... 17

Dr Desley Whisson .................................................................................................................... 17

A/Prof Barbara Wilson and A/Prof John White .......................................................................... 17

Dr Kaori Yokochi ....................................................................................................................... 18

Waurn Ponds Projects ........................................................................... 19

A/Prof Luis Afonso .................................................................................................................... 19

Dr Ben Allardyce and Dr Stuart Linton ....................................................................................... 19

A/Prof Peter Biro ...................................................................................................................... 20

Prof Kate Buchanan .................................................................................................................. 20

Dr Adam Cardilini ...................................................................................................................... 21

Dr Georgia Dwyer ..................................................................................................................... 21


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Prof Paul Francis ....................................................................................................................... 22

A/Prof Michelle Harvey ............................................................................................................. 22

Prof Luke C. Henderson............................................................................................................. 23

Dr Galen Holt ............................................................................................................................ 25

Dr Tim Jessop............................................................................................................................ 26

Prof Marcel Klaassen ................................................................................................................ 26

A/Prof Rebecca Lester............................................................................................................... 27

Dr Stuart Linton ........................................................................................................................ 27

Dr Ashley Macqueen ................................................................................................................. 28

Dr Matthew McKenzie .............................................................................................................. 28

Dr Adam Miller and Dr Craig Sherman....................................................................................... 29

Dr Ryan Nai ............................................................................................................................... 29

A/Prof Fred Pfeffer ................................................................................................................... 29

Dr Justin Rizzari ......................................................................................................................... 31

Dr Aaron Schultz ....................................................................................................................... 31

Dr Aaron Schultz and A/Prof Luis Afonso ................................................................................... 33

Dr Aaron Schultz and A/Prof Fred Pfeffer .................................................................................. 33

Dr Madeleine Schultz ................................................................................................................ 34

A/Prof Craig Sherman ............................................................................................................... 34

A/Prof Cenk Suphioglu .............................................................................................................. 36

Dr Erica Todd ............................................................................................................................ 37

Dr Eric A Treml .......................................................................................................................... 37

Dr Mark Ziemann ...................................................................................................................... 38

Warrnambool Projects .......................................................................... 39

Dr Adam Miller and Dr Susanna Venn ....................................................................................... 39

Dr Adam Miller, Dr John Morrongiello and Dr Eric Treml ........................................................... 39

Dr Adam Miller and Dr Craig Sherman....................................................................................... 40

Queenscliff Projects .............................................................................. 41

A/Prof David Francis ................................................................................................................. 41

Dr Ty Matthews ........................................................................................................................ 41

Dr Erica Todd ............................................................................................................................ 42

Victorian Fisheries Authority ..................................................................................................... 42


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Burwood Projects

Prof John Arnould Campus: Burwood

Contact details: [email protected]

Project or research area description: My research interests focus on the physiological and behavioural adaptations of higher vertebrates to environmental variability, with a focus on marine mammals and seabirds. I have ongoing research programmes on numerous seabird and marine mammal species covering aspects of their foraging ecology, habitat use, breeding biology and demography. There are always opportunities to run Honours thesis projects that align with these programme aims. Most of my Honours projects are mid-year starts, to match with the breeding seasons of the various study species. Students interested in any of these research areas are encouraged to contact me by email to discuss potential project opportunities.

A/Prof Lambert Brau Campus: Burwood


Project or research area description: The group’s research focus is on plant growth promoting bacteria PGPBs, nitrogen fixation, soil microbiology and plant microbe interactions to improve crop production and reduce fertilizer inputs in farming systems. Plant growth promoting bacteria facilitate plant growth via numerous via various mechanisms and this interaction occurs in the rhizosphere, a specialised micro-niche for bacteria immediately adjacent to the plant roots that is characterized by an active exchange of signals between host plant and bacteria. PGPBs use a variety of mechanisms to facilitate plant growth and one of the major mechanisms used by these bacteria involves the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase which cleaves the compound ACC, the immediate precursor of the phytohormone ethylene in all higher plants. PGPB strains that contain ACC deaminase provide a wide range of different plant species with a significant level of protection from the damage caused by various environmental stresses including pathogens, flooding, heavy metals, drought, and high salt.

Dr Damien Callahan Campus: Burwood


Project or research area description: The research conducted by Dr Callahan’s laboratory is spans environmental chemistry, chemical ecology and advanced analytical chemistry. This includes the application of metabolomics, lipidomics, elemental profiling and trace chemical analysis. The analytical methods used are applied to projects that are focused on improving our understanding chemicals in the environment and to study the biochemical mechanisms that support extreme traits in organisms which have potential practical applications, such as, metal hyperaccumulating plants. This is multidisciplinary research and involves analytical chemistry, biochemistry and bioinformatics and has many potential applications. For this reason the methodology applied in this research area enables a diverse collaborative research portfolio.

mailto:[email protected]




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Specific projects on offer: 1) Per and polyfluoroalkyl substances (PFAS) are an emerging pollutant of concern and are used solar

panels. This project will determine if roof top solar panels are a source for human PFAS exposure. 2) The Forensic Identification of Illegal Firewood: An elemental ‘fingerprint’ can be developed from wood

taken from a particular location. Matching a fingerprint could provide a novel tool for identifying the point of origin of a wood sample.

3) MALDI-TOF to identify insects - This project aims to evaluate the potential for MALDI-TOF MS (a mass spectrometry technique) to identify insects that cannot be efficiently and rapidly identified to species-level using existing methods. This project will be carried out Dept Ag, Water and the Environment and will include a $5,000 scholarship.

Dr Adam Cardilini Campus: Burwood and Waurn Ponds


Project or research area description: I am an environmental scientist working on questions related to ecology, conservation and society. I am interested in how our relationship with non-human Animals shapes science, the environment and society. My current research focusses on how concern for Animals informs environmental values and practice, and critically assessing how the sciences consider Animals. A simple provocation drives my research: how would research, the environment and society change if we meaningfully considered the moral claims of other Animals?

Specific projects on offer:

1) Transparency of animal use in ecology, conservation and environmental science publications: developing a methodology and metric

2) Investigating the role for compassionate conservation in urban biodiversity and conservation initiatives

3) Do individual animals matter: the role of intrinsic value in peoples acceptance of conservation initiatives

Each project is desktop based and Covid-19 ready. You will need strong desktop research skills and attention to detail. Some projects involve social research skills, so an understanding of, or interest and willingness to learn, social science methodologies will be valuable. Finally, each project requires a critical understanding of human-animal relationships and respect for the lives of Animals.

The list of projects above is not exhaustive, if you have an idea that aligns with the themes above please get in touch and we can chat about it.

A/Prof Raylene Cooke and A/Prof John White Campus: Burwood

Contact details: [email protected] and [email protected] Project or research area description:

1) Determining the spatial ecology of powerful owls within urban environments using GPS technologies. 2) Determining the diet of powerful owls within urban environments through the analysis of regurgitated

pellets collected from beneath their roosting sites.





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3) Identifying the remaining populations of long-nosed potoroo and southern brown bandicoot in the Grampians (Gariwerd) landscape. Requires a manual license, experience with GIS would be useful.

4) Investigating the long-term (14 years of data) impact of fire and climate on small mammal communities in the Grampians (Gariwerd) landscape. Requires a manual license.

A/Prof Raylene Cooke, A/Prof John White and A/Prof Mike Weston Campus: Burwood

Contact details: [email protected], [email protected] and [email protected] Specific projects on offer:

1) Assessing the effectiveness of quail-callers in attracting stubble quail. This project will be based in the western district of Victoria, requiring a student who can drive and spend periods away from campus.

Dr Bernhard Dichtl Campus: Burwood

Contact details: [email protected], http://dichtllab.com

Project or research area description: The Dichtl lab is investigating the function and assembly of molecular machines. We study protein complexes involved in gene expression and use yeast and human cell culture systems. Major areas of investigation include:

1) Function of Set1C histone methyltransferase. Post-translational modification of histone proteins is a central regulatory mechanism of chromatin-associated processes and we linked meiotic recombination to histone methylation (Acquaviva, Science, 2013). The Set1C methyltransferase methylates lysine 4 on histone H3 and chromosomal translocations of the human MLL gene, encoding a homologue of Set1, give rise to acute myeloid and lymphoid leukemia. Studying Set1C and H3K4 methylation in yeast thus provides important insight into the underlying causes of cancer.

2) Alternative polyadenylation in health and disease. 3) 3’ end formation is an essential RNA maturation step that impacts all aspects of mRNA function. The

process adds 250 adenosines to the 3’ end of primary transcripts and determines the length of the 3’ untranslated region (3’UTR), which is targeted by regulatory factors. Control of 3’UTR length via Alternative Polyadenylation (APA) is an important mechanism to control gene expression. We identified factors that mediate APA (Turner, RNA, 2020) and now study how APA it is integrated with cellular signaling pathways.

Prof Don Driscoll Campus: Burwood


Project or research area description: Frogs have suffered enormous declines around the world due to habitat loss, often associated with agriculture, and the global pandemic disease caused by the chytrid fungus. Major declines and even extinctions have occurred before scientists or land managers have had time to react because data have often been lacking. In these projects, the successful applicants will undertake extensive field surveys then use statistical models to





http://dichtllab.com/



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discover which environmental covariates explain patterns of occurrence of threatened or declining frogs. Covariates may include different impacts of humans, such as land clearing and cropping, but also biological covariates that might represent disease risk, such as the presence of the reservoir host Crinia signifera. We will also consider landscape variables, like number of nearby wetlands and amount of native vegetation. To complete one of these projects you must be willing to work at night in the field, in challenging environmental conditions. You must have a license to drive a manual car. You may be able to use your own car for the project, with costs reimbursed.

Specific projects on offer: 1) Land-sharing despite intensifying agriculture. In collaboration with the community group Beyond

Bolac, this project aims to discover the management regimes and landscape variables that determine where the endangered frog Litoria raniformis is able to survive. Suits mid-year start.

2) Frogs versus forest management. Pseudophryne semimarmorata is listed as vulnerable in Victoria due to reported declines. In collaboration with the Ecology Centre, this project aims to discover how fire management influences this autumn-breeding frog. Suits February start.

Dr Georgia Dwyer Campus: Burwood and Waurn Ponds


Project or research area description:

My prior research is in the field of nutritional ecology. A key concept in nutritional ecology is that organisms are able to select foods based on nutritional content to increase fitness. This has been demonstrated in a wide range of organisms under laboratory conditions, but demonstrating this in the wild and relating this to the ecology of organisms is more difficult. A new interest of mine, is linking host selection by pathogens to host nutrient composition. In particular, I am interested in the ability of the pathogen Saprolegnia to locate caddisfly hosts via chemical cues. Freshwater ecosystems are ideal systems to investigate this, as the aquatic environment allows movement of pathogens to reach potential hosts. Further, both Saprolegnia and caddisflies have complex life cycles, which allows us to investigate nutritional dynamics in a wide range of research avenues.

Dr Galen Holt Campus: Burwood and Waurn Ponds



I study how biodiversity depends on the large-scale outcomes of interactions between environmental conditions and life history. Specifically, I am interested in how species’ responses to variable environmental conditions affect local interactions, and how those interactions scale up to affect the dynamics of ecological communities. I study these issues using a combination of empirical studies, community dynamics models and coexistence theory. My recent projects include theoretical investigations of the maintenance of diversity at regional scales in stream networks, modelling studies of community dynamics in caddisflies, large-scale models informing management of aquatic environments, and empirical work (field and laboratory) with caddisfly communities. A current focus of my research is characterising an emerging disease affecting caddisfly eggs, and how the disease process might depend on the environment and caddisfly egg-laying behaviours. This is an emerging area of research, with a wide range of potential directions and methods, including field, lab, and modelling approaches. Additional projects related to my broader interests are also possible.




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1) Investigation of post-hatching drift behaviour in response to predators, density, or environmental conditions (flow speed, temperature, etc) in a flume

2) Investigation of stressors increasing susceptibility of caddisfly egg masses to Saprolegnia infection, such as temperature, damage, or dessication, and their duration

3) Isolation of Saprolegnia life stages to investigate their differing ability to initiate infection of caddisfly egg masses

4) Studying density-dependent infection processes at one of several scales. Possibilities include Saprolegnia chemotaxis responding to egg density, or how the number and distance of nearby egg masses affect transmission.

Dr Scarlett Howard Campus: Burwood



Dr Scarlett Howard is currently conducting research on the effect of anthropogenic environmental change on native and introduced pollinators with a focus on bees. She is examining the impact of urbanization on native bee morphology, distribution, behaviour, pollination ability, floral preferences, and evolution. By implementing both novel and traditional techniques, she will map the distribution of pollinators across urban, rural, suburban and native habitat using surveys, trap nests, pan-traps, sweep netting, observation, community/citizen science, and social media. Her past and current research explores conceptual learning, neurobiology, and visual perception in honeybees as well as insect diversity, pollinator preferences, and plant-pollinator interactions.

Specific projects on offer: 1) How do bees adapt to anthropogenic change? 2) Utilizing community science and social media to track pollinators

A/Prof Rebecca Lester Campus: Burwood and Waurn Ponds


Project or research area description: I am an ecologist with experience in freshwater, estuarine and marine systems. I have wide-ranging research interests, but am primarily focused on the management of aquatic ecosystems. My current research is focused on understanding how an emerging infectious disease is altering population and community dynamics in aquatic insects (specifically caddisflies). Specifically, I am interested in identifying where and in which caddisfly species the disease occurring, which mechanisms of transmission allow the disease to proliferate, and what are the effects of this on caddisfly populations. This work is in its early stages and will require further field surveys and laboratory experiments to continue to answer these questions. Other research related to my broader interest are also feasible. These projects would require an enthusiastic student who is open to learning a range of skills from a variety of disciplines (ecology, microbiology, and genetics).





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1) Understanding how an emerging infectious disease (Saprolegnia) is altering population and community dynamics in aquatic insects (caddisflies) using field surveys and laboratory experiments.

2) Investigating chemotaxis of Saprolegnia to aquatic insect eggs under static and turbulent conditions using laboratory experiments.

3) Using a laboratory experiment to investigate the effect of temperature on Saprolegnia infection in caddisflies to gain an understanding of how climate change might influence the arms race between these organisms.

Dr Ashley Macqueen Campus: Burwood and Waurn Ponds


Project or research area description: I have a strong interest in understanding the drivers of spatial and temporal variability in populations of freshwater organisms and how these can be distilled and combined with remotely sensed and other large-scale datasets to provide insights into the likely distribution of organism under various future scenarios. Furthermore, I ask how empirical data can be soundly scaled up to catchment level, and potentially extrapolated to data-poor locations, to inform management decision making. I am currently supervising PhD students working on ecosystem and food-web models in the Three Gorges Dam. Potential projects could involve leveraging large datasets collected for EPA and Murray-Darling Basin Authority to interrogate management-relevant problems through an ecological lens.

Dr Alex McQueen Campus: Burwood


Project or research area description: Birds can increase blood flow to their highly vascularised bills to dissipate excess body heat, allowing them to keep cool in hot conditions. Having a large bill is advantageous in hot weather, but bill size also varies widely among species in warm climates, suggesting small-billed species can use other means to avoid heat stress. In particular, it is predicted that small-billed species rely on behavioural strategies to minimise heat stress, such as seeking shade or cooler microhabitats and becoming less active in hot weather. Such adaptations may be useful in the short term, but come at the cost of time spent on other activities, such as foraging, and may be impractical during prolonged exposure to hot conditions. Determining whether species differ in their strategies for avoiding heat stress is important for predicting their survival in a warming world.

Our research (as part of Matthew Symonds’ lab) uses a combination of fieldwork involving observations of wild birds and comparative, literature-based studies. We aim to assess the evolution of bird bills, and how birds use their bills to mitigate heat stress. We further consider how different thermoregulatory strategies impact species survival.


Potential field-based projects include: 1) Assessment of whether birds use human-made roosting platforms as thermal refuges 2) Whether bill size impacts shorebird foraging behaviour in hot conditions.




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Comparative research projects on bill size and/or shorebird ecology are also possible, to be discussed with the applicant.

A/Prof Kelly Miller Campus: Burwood


Project or research area description: Projects focusing on sustainable behaviours and the human dimensions of wildlife/environmental management (e.g. human values, attitudes, perceptions) are available and will be developed around the student’s specific interests e.g. wildlife, conservation, sustainability, environmental protection. Previous Honours projects have focused on wildlife/wildlife management e.g. bird feeding, threatened species, wildlife tourism; habitat management/conservation e.g. gardening practices, park/reserve visitation; and environmental education in a range of contexts. Specific projects on offer:

Human Usage of the Wyndham Coast Wyndham City Council manages a diverse coastline from little River to Skeleton Creek on the western side of Port Phillip Bay. The coast is backed by nature reserve, residential and agricultural development, and recreational infrastructure. The municipality is one of the fastest growing human populations in Australia. This project will quantify human usage of the coastline, explicitly documenting variation in that usage in time and space. The successful student will need to travel to the area frequently (even better if they live nearby), and would ideally have some basic GIS capacity. The results of this project will contribute to sustainable coastal planning in the municipality and offers strong connections with a local government.

Dr Nick Porch Campus: Burwood


Project or research area description: Human impact on island ecosystems: projects in this area are laboratory-based investigations into the nature of the recent fossil record of plants and animals on Indo-Pacific oceanic islands. Materials for projects in this area are in hand and projects would be laboratory based.

Diversity and ecology of Australian insect faunas: wide range of potential projects including studies examining patterns of invertebrate richness and endemism, taxonomic revision of beetle genera, and projects assessing the ecology/conservation of invertebrate species or communities. Some projects would require fieldwork, some laboratory work and others could be entirely desktop.

Prof Jenny Pringle Campus: Burwood







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Our research group makes new electrolytes for next generation “beyond lithium ion” batteries. The development of advanced, high performance rechargeable energy storage devices, such as lithium metal or sodium batteries, is important for reducing our reliance on fossil fuels as these devices can support renewable technologies such as solar, wind etc.

Good electrolytes are critical for efficient batteries, and our research involves making new kinds of cations and anions for these electrolytes and investigating their physical, thermal and electrochemical properties when mixed with different lithium or sodium salts (i.e. for lithium or sodium batteries). These new salt mixtures may be used neat, or dissolved in solvent, or the new ions may be most beneficial as additives to improve existing battery electrolytes.

The honours projects on offer would investigate the effect of the new ions, made by other members of the group or by our Industry partners, on electrolyte properties such as viscosity, conductivity and melting point for different salt mixtures and compositions. Understanding how different ion structures influence these electrolyte properties is very important for developing more efficient, longer lasting batteries. The insights from this project will benefit the novel battery prototyping work led by our team in the StorEnergy centre and Deakin’s new BatTri-Hub facility.

A/Prof Euan Ritchie Campus: Burwood


Project or research area description: Our research group, the Applied Ecology and Conservation Research group https://euanritchie.org/, is focused on addressing a range of issues that apply to wildlife management, environmental policy and biodiversity conservation, and these include: fire ecology; invasive species; landscape ecology; mammal ecology; predator-prey interactions; species reintroductions and urban ecology.


We have a range of exciting and well-supported honours projects on offer in 2021 and in collaboration with our industry partners (DELWP, Parks Victoria, Phillip Island Nature Parks, The Mornington Peninsula Shire and Zoos Victoria). We are also very happy to discuss project ideas that students may have.

Dr Anthony Somers Campus: Burwood


Project or research area description: Our research group makes new multifunctional inhibitors to mitigate both abiotic and microbiologically influenced corrosion. With the drive to more eco-friendly methods of inhibition and the ever-increasing cost of corrosion there is a need to discover new compounds to meet these challenges.

The research within our group has concentrated on the synthesis, evaluation and characterisation of new inhibitors in order to discover the structural requirements for improved performance. The problem and its investigation require a multidisciplinary approach through the use of a range of chemical, electrochemical, biological and surface analysis techniques.

The honours projects offered would investigate the performance of a new family of corrosion inhibitors. Such an investigation would involve electrochemical, chemical and surface analysis techniques in order to evaluate the performance and determine mechanisms of protection. In conjunction with comparisons to previous work,


https://euanritchie.org/



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the findings of this study will elucidate structural aspects of inhibitors that result in the protection of metal surfaces from corrosion.

A/Prof Matthew Symonds Campus: Burwood


Project or research area description: I’m interested in trying to explain, from an evolutionary perspective, what has generated differences in behaviour, morphology and physiology between closely related species. Much of my research involves using phylogenies (evolutionary trees) to answer questions about how and why traits have evolved, either by looking at the mode of evolution and extent of phylogenetic signal in the trait of interest (e.g. insect pheromone chemical composition), or by carrying out phylogenetic comparative analyses to identify ecological traits that are correlated with that trait (e.g. identifying that bird species that live in warm climates tend to have larger beaks). For 2021, especially in the light of potential Covid-based restrictions on research, I am offering Honours projects that involve analyses of large cross-species datasets (and hence can easily be done from home) – be they on insects (e.g. evolution of host breadth in parasitoid wasps), mammals (e.g. influence of hibernation on mammalian life-history evolution) or other vertebrates, or even plants. I’m open to suggestions! Feel free to contact me to ask me more about these. If you want to get the best idea of the breadth of my research interests and projects, look no further than the publications page on my website www.symondslab.wordpress.com/publications/

Dr Stacey Trevathan-Tackett Campus: Burwood


Project or research area description: Wetland habitats provide important ecosystem services, including building biodiversity, filtering toxins and removing greenhouse gases from the atmosphere. However, continued wetland degradation and loss pose a serious threat to the ecological, human and climate-protecting services they provide the world. Our research examines the factors that have the potential to maximise wetland carbon preservation and biosequestration in the fight against climate change.

The Honours project will focus on carbon cycling in coastal and freshwater wetlands using ‘tea litter’ decomposition. As part of the global TeaComposition H2O initiative, the student will assess how the process of decomposition differs across ecosystems and plant types, and how that could affect carbon and nitrogen preservation in the soil. The student should have a basic understanding of statistics, as well as knowledge in chemistry, biogeochemistry and/or a willingness to learn. We are looking for an independent and motivated student, with skills in organising and managing data, and an enthusiasm for working in the lab and in a team environment.

Dr Susanna Venn Campus: Burwood


mailto:[email protected]%20u

http://www.symondslab.wordpress.com/publications/


https://www.bluecarbonlab.org/teacomposition-h2o/



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Project or research area description: I’m a botanist and plant ecologist with a keen interest in the processes that shape vegetation patterns in alpine areas, and I lead the eXtreme Plant Ecology Research Team at Deakin Burwood. I’m interested in testing ecological theory in the mountains and investigating the ways in which alpine plant communities are coping with environmental change. This could involve focusing on community (re) assembly patterns, how snow drives community composition, ecological function or ecological processes in the mountains, treeline dynamics, vegetation responses to heat, frost, drought or fire, and regeneration strategies of alpine plants. These topics can be undertaken using experimental manipulations in the field and/or lab. I’m happy to discuss ideas for honours projects that overlap with any of these topics – or possibly other plant ecology projects in extreme environments. In general, a field based project will require a mid-year (July) start to accommodate the alpine field season over summer. More info: https://susannavenn.wordpress.com


1) Investigating the interactions between freezing resistance and high light levels in Australian alpine plants. Test the freezing resistance of various alpine species in a series of lab-based and field-based experiments, and determine how high-light levels interact with freezing temperatures to cause plant-tissue death, using a range of real and simulated scenarios.

2) Alpine shrubs as facilitative nurse plants. Using data from a global field experiment, determine how alpine shrubs act to facilitate the growth of adjacent plants as they create a windbreak and allow for extra snow to build up on their leeside.

3) Investigating the germination niche of alpine species. Using a Temperature Gradient Plate in the lab, test the germination strategies of several alpine grasses, forbs and shrubs which are known to be distributed over a wide geographical range, compared with those that are more narrowly distributed.

Dr Mark Warne Campus: Burwood



1) Early Pleistocene marine palaeoecology of the Werrikoo Limestone, western Victoria. Early Pleistocene sedimentary rocks known as the Werrikoo Limestone occur in cliffs along the Glenelg River valley of southwest Victoria. These rocks are 2.6 to 1.8 million years old, and contain a very rich fossil fauna including abundant fossil shells of marine Ostracoda (microscopic crustaceans). This project will involve (1) the description of ostracod fossils from the Werrikoo Limestone, and (2) fossil-based interpretations of sea level history and past coastal maritime climates for western Victoria. This project offers an opportunity to develop skills in the systematic description of invertebrate taxa, and (ii) in the use of fossils for assessing coastal landscape and seascape evolution. Note: This project will require sample processing and microscope work in a Deakin University Laboratory. Field work is optional.

Dr Liz Weldon Campus: Burwood



https://susannavenn.wordpress.com/




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Research supervision capabilities in palaeontology, earth science, and geoconservation.

Major themes: 1) Geodiversity and geoconservation.

Projects centred on raising awareness of the significance of our geoheritage and geodiversity. Theresearch involves developing regionally and culturally appropriate quantitative methodology to assessgeosites and geoheritage for geoconservation, in different international contexts. This research issuitable for both Honours and Master of Sustainability students.

2) Palaeontology.Ttaxonomic studies or quantitative analysis of marine macro-invertebrates applied topalaeobiogeography or palaeoecology. The projects can be developed with Museum Victoria.

3) Quaternary Lancefield megafauna site.Research investigating the processes and causes of the accumulation of an estimated 10,000individuals from a range of extinct species in a Victorian swamp deposit. The research can be appliedto understanding changing climate patterns and its impact on ecosystems over time. This research willbe co-supervised with Dr Sanja Van Huet.

4) Morphology of extinct and extant kangaroos and emus.This research involves quantitative analysis of teeth and bones. The aims are to devise methods thatdetermine age and gender in the fossil record, and record biotic responses to environmental change,such as dwarfism or disease. This research will be co-supervised with Dr Sanja Van Huet.

A/Prof Mike Weston Campus: Burwood


Project or research area description: The ecology of fear. Fear (propensity to escape) is a major force in the way animals live their lives and is also a management and conservation issue. A range of projects are available on measuring flight-initiation distances among wildlife. Some of these projects have occurred overseas, and most (but not all) require good bird identification skills, a driver’s license, and access to a vehicle. Please discuss specifics with Mike.


1) Examining responses in relation to different stimuli or stimulus behavior. In particular, wildlifephotography and the use of drones are growing and controversial aspects of human behavior whichmay disturb wildlife.

2) As part of ongoing efforts at mapping fear among birds globally, many countries require datacollection. These projects require excellent birdwatching skills, preferably local experience or support,and the ability to contribute to some costs.

3) As part of documenting the fear responses of Australia’s avifauna, many interstate and remote partsof Australia require data collection. Again, excellent bird identification skills are required.

Project or research area description: The ecology of Red-capped Plovers and Masked Lapwings Marked populations of Red-capped Plovers and Masked Lapwings have been studied for over 9 years and a series of key questions remain regarding their behavioral, breeding, general and conservation ecology. Some of these projects require banding experience, all require some training, a driver’s license and access to a vehicle. Some Red-capped fieldwork is available in SA. Lots of field work, and great species and questions to work on! Contact Mike for more details.



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Project or research area description: The conservation of Hooded Plovers and sandy shore ecology (including beach invertebrates)

Hooded Plovers are a threatened sandy shore obligate which is nationally Vulnerable. A range of projects are available exploring the conservation ecology and testing management effectiveness of a variety of conservation tools.

Specific projects on offer: 1) The role of parental footprints in egg crypsis. Human disturbance is known to increase the amount of

adult footprints around a nest. This project will examine if this is associated with heighten rates of egg depredation.

2) The features of non-breeding flocking sites. Current evidence suggests some locations are used as non-breeding flocking sites, while others are not. This study will compare the biophysical and ecological attributes of flocking and non-flocking sites to establish the habitat requirements of this species during winter.

3) The distribution of beach invertebrates in time and space.

Project or research area description: The ecology of Venus Bay and it’s dunes

There are few studies of the ecology of life in coastal sand dunes, especially those adjacent to high-energy ocean beaches. Venus Bay, in southern central Victoria, represents an ideal study system. Several human settlements and long unbroken sections of dunes enable the assessment of how human habitation may modify dune fauna. Key questions include:

• Is there zonation in dunes, in terms of habitat and occupancy by birds/mammals/reptiles?

• Do human settlements alter the occupancy of dunes by birds/mammals?

• Do the above patterns occur in terrestrial vertebrates, mammals and birds?

Project or research area description: The ecology of gardening

Several projects have been developed in conjunction with Whitehorse City Council and a private landscape gardening provider regarding eco-friendly gardening. These projects aim to provide input into guidelines for eco-friendly gardening. All projects require the capacity to conduct fieldwork and a driver’s license.


1) Invertebrate/skink abundance in different garden mulches (no mulch, pinebark, natural mulch - pitfalls)

2) Nestbox use in gardens (and how this is affected by nestbox dimensions)

3) Use of "bee hotels" in parks vs gardens

4) Bird baths and disease

5) Habitat characteristics of gardens with skinks

6) Effects of dogs/cats on reptile/bird/frog fauna in gardens

7) Pond characteristics and frog use in gardens

8) Invertebrate/skink abundance and understory cover in gardens

9) Invertebrate/skink abundance and pesticide use in gardens

10) Bird bath characteristics and position and use in gardens

11) Aggression at bird baths and feeders

12) Health of birds that regularly use feeders (cholestrol, fat, etc).


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Dr Tricia Wevill Campus: Burwood


Project or research area description: Plant ecology. Students who are interested in working in the area of fire and vegetation management should contact Tricia Wevill to discuss the potential to develop other projects.


1) Mapping and assessing Phytophthora dieback in the eastern Otways 2) Assessment of long-term condition and changes in the habitat of the threatened New Holland mouse

in the eastern Otways: impacts of fire management and rainfall variability 3) Developing spatial models to estimate regional bryophyte richness trajectories in Victoria: This project

will develop models to predict regional bryophyte richness as a function of ecologically relevant predictors, under various future climate and landscape composition scenarios.

4) Ecophysiological limitations of asexual reproduction in a rare moss: This project will measure the ecophysiological thresholds of asexual recruitment in a rare moss—Trachyloma planifolium—under various microclimate conditions. Results will assist to better understand the conservation needs of bryophytes.

Dr Desley Whisson Campus: Burwood


Project or research area description: I am broadly interested in the ecology and management of terrestrial wildlife with a focus on their spatial ecology (home range, movements, distribution). I am particularly interested in arboreal species (koalas and gliders) and impacts of landscape change and anthropogenic factors on their distribution. I also am interested in using bioacoustics for wildlife survey. This method allows for the survey of more sites than can be achieved through traditional methods. I can offer honours projects that are GIS-based and/or utilise bioacoustics as a survey approach. A few options are provided below.


1) Using bioacoustics to assess biodiversity values in modified landscapes

2) The influence of bushfire on habitat suitability for koalas (mid-year start)

A/Prof Barbara Wilson and A/Prof John White Campus: Burwood

Contact details: [email protected] and [email protected]







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Assessment of the characteristics of habitat refuges for threatened mammals in the Otways: impacts of fire management and rainfall variability

Dr Kaori Yokochi Campus: Burwood


Project or research area description: Finding ways to minimise the impacts of urbanisation on wildlife, especially those posed by our infrastructure. Ongoing and previous research includes investigating impacts of ALAN (artificial light at night) on microbat communities, and investigating and mitigating impacts of roads on arboreal mammals.

Specific projects on offer: 1) Impacts of intense temporary lighting on microbats of Melbourne (2021 S2 start), co-supervised by

Anthony Rendall (Deakin) and Dr Lindy Lumsden (Arthur Rylah Institute/ DELWP)



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Waurn Ponds Projects

A/Prof Luis Afonso Campus: Waurn Ponds


Project or research area description: Individual variation in stress response in fishes: molecular and endocrine responses.

I am interested in understanding the stress response in fish to aquaculture-related and environmental stressors. An integrated and multi-level approach, including physiological, endocrine, and cellular responses, is used to: 1) examining the ability of fish to cope with stress, and 2) developing novel and reliable biomarkers of stress in fish for a variety of applications. Projects will allow learning opportunities in field sampling collection, and techniques such as standard and quantitative polymerase chain reaction (PCR), enzyme-linked immunosorbent assays (ELISAS) for determining hormone levels, other biochemical assays for determining enzyme and intermediate metabolites levels, SDS-PAGE and Western blot. Stressors to be studied include thermal stress, crowding, transport, hypoxia, and environmental pollutants.


1) Changes in gill Na+,K+ ATPase levels in Atlantic salmon (Salmo salar) prior to and after transfer to saltwater; 2) Endocrine and molecular responses in Atlantic salmon (Salmo salar) exposed to short and long-term

stressors, and 3) Sex differentiation and sex reversal in Atlantic salmon.

Dr Ben Allardyce and Dr Stuart Linton Campus: Waurn Ponds

Contact details: [email protected] or [email protected]

Project or research area description: My work focusses on the development of silk based biomaterials, most notably the “silk eardrum” a graft material to support tissue regeneration after chronic eardrum perforation. I am interested in understanding silk’s unique biochemistry and biophysical properties and how this understanding can lead to new and innovative biomedical materials.


1) Development of new extraction methods to purify fibroin, the main structural protein in silk, from silkworm cocoons. The use of regenerated silk materials can be challenging due to limitations in our ability to remove sericin and extract purified fibroin without causing extensive degradation.

2) Development of a “gold standard” method to measure the molecular weight of silk. Accurate characterisation of silk’s molecular weight is critical for designing biomaterials with controllable degradation within the body. Current methods involve SDS-PAGE, however, electrophoresis is not ideal for silk since it produces a heterogenous molecular mass range. Chromatography offers higher resolution but is better suited to globular proteins. This project would understand how silk behaves during chromatographic separation and design a set of protocols to inform the silk research community.

Both projects would offer a chance to learn key protein purification and characterisation principals including FPLC and low pressure chromatography and SDS-PAGE.





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A/Prof Peter Biro Campus: Waurn Ponds


Specific projects on offer: 1) Growing up athletic: developmental effects of exercise on metabolism and personality traits in

zebrafish. Recent research suggests that personality traits in animals are linked to metabolic physiology, and emphasize the genetic basis for these links. Less well known is how developmentally plastic this association is. That is, can we use a developmental programming approach to possibly ‘engineer’ individuals with greater physiological capacity for work and behavioural tendencies for higher levels of activity? Results will have ramifications for human lifestyles given the well-known and various health benefits of activity. The project will involve measuring activity of fish using state of the art tracking systems, and possibly also metabolic rates; there is also an option to induce cancer in these fish to study if innate propensity to exercise affects cancer risk and progression as literature suggests it may. Student will also learn about general fish husbandry.

2) Evolution of song in female birds. While birdsong is a model system for animal communication studies, our knowledge is derived primarily from the study of only one sex and is therefore incomplete. Bird song has long been considered a male trait, sexually selected to enhance attractiveness to females. However, in some species, females may also produce songs even with comparable complexity to that of males. This study will examine song and singing behaviour in both male and female grey fantails, with the aim of contrasting song complexity and singing behaviour between the sexes. This project may make use of existing recordings from which to gather data, or include field work such as song recording, behavioural observations, and trapping and banding birds. Field work will be conducted in Brisbane Ranges National Park (30 min drive from the Geelong Campus).

3) Avian Nest Construction. Nest structures are essential for successful reproduction in most bird species. Many bird species go to great lengths to camouflage their nests in order to avoid detection by predators, such as building nests that are shaped to blend into their surroundings. Using an experimental approach, this study will examine the effects of nest shape on nest predation rates. This project can be a lab or field based project.

Prof Kate Buchanan Campus: Waurn Ponds


Project or research area description: I am interested in the impact of early developmental conditions on long term health, welfare and fitness in birds. I use zebra finches as a model species to ask questions about developmental conditions, early life constraints and the evolution of signals of quality.





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1) A project examining the role of mitochondrial respiration in contributing to developmental constraints in birds, in collaboration with Dr Matthew McKenzie. This project will involve breeding birds on campus and sampling to determine mitochondrial function. This project works best with a July start.

2) A joint project with School of Medicine (with Drs Crowley and Craven) on the evolution of avian lactation. This project involves sampling from breeding birds in a range of locations, however Covid 2021 restrictions will factor in determining these. This project is best for a July start.

There may be additional projects on offer which are less temporally constrained using existing samples, looking at prenatal impacts on development, immune function in relation to early life conditions or the responses of birds to heat.

For any project the student needs to be Geelong based throughout to manage data gathering effectively. Ideally these projects are best with a July 2021 start for practical constraints.

Dr Adam Cardilini Campus: Burwood and Waurn Ponds


Project or research area description: I am an environmental scientist working on questions related to ecology, conservation and society. I am interested in how our relationship with non-human Animals shapes science, the environment and society. My current research focusses on how concern for Animals informs environmental values and practice, and critically assessing how the sciences consider Animals. A simple provocation drives my research: how would research, the environment and society change if we meaningfully considered the moral claims of other Animals?


1) Transparency of animal use in ecology, conservation and environmental science publications: developing a methodology and metric

2) Investigating the role for compassionate conservation in urban biodiversity and conservation initiatives

3) Do individual animals matter: the role of intrinsic value in peoples acceptance of conservation initiatives

Each project is desktop based and Covid-19 ready. You will need strong desktop research skills and attention to detail. Some projects involve social research skills, so an understanding of, or interest and willingness to learn, social science methodologies will be valuable. Finally, each project requires a critical understanding of human-animal relationships and respect for the lives of Animals.

The list of projects above is not exhaustive, if you have an idea that aligns with the themes above please get in touch and we can chat about it.

Dr Georgia Dwyer Campus: Burwood and Waurn Ponds






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My prior research is in the field of nutritional ecology. A key concept in nutritional ecology is that organisms are able to select foods based on nutritional content to increase fitness. This has been demonstrated in a wide range of organisms under laboratory conditions, but demonstrating this in the wild and relating this to the ecology of organisms is more difficult. A new interest of mine, is linking host selection by pathogens to host nutrient composition. In particular, I am interested in the ability of the pathogen Saprolegnia to locate caddisfly hosts via chemical cues. Freshwater ecosystems are ideal systems to investigate this, as the aquatic environment allows movement of pathogens to reach potential hosts. Further, both Saprolegnia and caddisflies have complex life cycles, which allows us to investigate nutritional dynamics in a wide range of research avenues.

Prof Paul Francis Campus: Waurn Ponds


Project or research area description: The capacity to effectively diagnose disease in the human body and identify dangerous pollutants in our environment is fundamentally limited by the speed, selectivity, accuracy and sensitivity that we can measure molecules. We create new analytical approaches based on chemical reactions that produce light, for clinical diagnostic, environmental and forensic science applications. We are particularly interested in the use of simple consumer devices, such as mobile phones as portable analytical devices for at-scene or in-field detection.

Our team is also exploring the use of visible light as a source of energy for the synthesis of new molecules. The growing awareness of the environmental impact of traditional chemical processes by scientists, authorities and the public has spurred extensive research into ‘green’ chemistry. The use of ‘photo-active’ metal-complexes has enabled various important chemical transformations to be powered by the energy of visible light. We examine the action of these photocatalysts using a variety of analytical and spectroscopic techniques, to develop novel routes to synthesise new molecules.


1) A New Sensing Platform for Molecular Biomarkers of Disease (Supervisors: Paul Francis (LES), Emily Kerr (IFM)).

2) Illicit Drug Screening by Multi-Coloured Electrochemiluminescence (ECL) (Supervisors: Paul Francis (LES), Egan Doeven (CeRRF), Emily Kerr (IFM)).

3) Synthesis of New Metal Complexes for Multi-Coloured Electrochemiluminescence (ECL) (Supervisors: Paul Francis (LES), David Hayne (IFM), Luke Henderson (IFM).

4) Photoredox Catalysis for Controlled Chemical Synthesis (Supervisors: Paul Francis (LES), David Hayne (IFM), Tim Connell (RMIT)).

5) Light-Emitting Devices for Low-Cost Functional Displays (Supervisors: Paul Francis (LES), Emily Kerr (IFM), David Hayne (IFM)).

A/Prof Michelle Harvey Campus: Waurn Ponds






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Research in the areas of entomology and forensic biology. This includes: general insect taxonomy projects, blowfly biology, attraction of insects, growth studies, maggot therapy in chronic human wounds, flystrike by maggots on sheep, bacterial relationships with insects. Forensic projects concern factors affecting field-based decomposition of remains, scavenging of remains, insect succession, effect of substances in/on remains on the development of insects and rate of decay, burial studies, vegetation and aquatic studies.

Prof Luke C. Henderson Campus: Waurn Ponds

Contact details: [email protected] Specific projects on offer:

1) Using Light Activation of Surface Bound Molecules for Polymerisation on Carbon Fibre. The ability to control and achieve chemoselective modification of surfaces is critically important in materials science, since many of the properties of a given material are largely governed by surface interactions induced with its environment. An excellent example is Teflon coating, which confers water repelling, anti-icing, and non-stick properties to materials that otherwise exhibit none of these properties.

In the field of composites, the performance of a carbon fiber reinforced plastic (CFRP) is ultimately dictated by the interfacial adhesion between the fibers and supporting polymer. Due to the huge scale on which carbon fibers are used (estimated to be ~117,000 tons by 2020), even slight improvements in performance can have significant impact on modern materials design, manufacture and reduction of downstream emissions from mass transport. The engineering of carbon interfaces has application in fields such as energy storage, electrode modification for detection, among others. In this project light will be used as a stimulus for the generation of reactive surface bound species to initiate polymerization, leading to increased material performance. This project will allow the development of skills from chemistry, materials science, composites, and engineering.

2) Preventing the formation of bacterial biofilms in joint replacements.



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Degeneration of articular joint surfaces in humans with resultant osteoarthritis (OA) is part of aging and can pose major limitations to quality of life. Contemporary surgical techniques and implants have made joint (hip, knee, shoulder, elbow, etc.) replacements one of the most common and quality of life improving advances in medicine, restoring mobility to millions of people in recent decades. Nevertheless, the potential for post-operative infection remains a serious and unresolved concern as it can pose substantial health risk and disability to patients.

This project will examine the use of surface coatings on metal used in medical implants and obtain data related to their adhesion to ‘bone-cement’, physical and chemical characteristics such as water contact angle, surface topology by Atomic Force Microscopy (AFM), Scanning Electron Microscopy (SEM), and mechanical tests. This project is being carried out in collaboration with St. John of God hospital and Barwon Health.

3) Multifunctional carbon fibers for advanced materials. The use of carbon fiber reinforced plastics in light-weighting and in the effort to reduce fuel consumption is increasing at an exponential rate. While they are light and strong, they possess an inherent weakness, the interface of the fibers and the plastic they are reinforcing. The degree of chemical communication between these two phases, to a large extent, determines the overall performance of the material. In this project an array of chemistries will be applied to the surface of the fibers to increase the compatibility of the fiber surface with the intended plastic it is reinforcing. In our previous work we have increased the interfacial shear strength, mitigating a typical failure mechanism, by up to 270%.


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This project has aspects of synthetic organic chemistry, electrochemistry, materials science, engineering, and polymer science. This work has interest from the USA department of defense (Army, Navy, and Air Force), Solvay Chemicals, and Boeing, among others.

4) Examining Solvate Ionic Liquids (SILs) for their potential as a replacement for organic solvents.

The use of organic solvents to allow chemical reactions is critical to many areas of science. Traditional solvents such (e.g. chloroform, toluene, diethyl ether, etc.) are flammable, toxic, and require specialized disposal methods. Ionic liquids, a class of solvent which is liquid at room temperature but composed entirely of ions, represent a potential alternative to traditional solvents which have many benefits such as: non-flammability, negligible vapor pressure, and controllable solvating power. We recently reported the use of Solvate Ionic Liquids (SILs) as a potential media for organic reactions, demonstrating both reaction rate, and yield benefits over traditional molecular solvents. In this project a range of chemical reactions, which are not traditionally viable in ionic liquids, will be attempted to explore the potential of SILs as reaction media.

5) Development of fire resistant plastics using amino-acid mimetics. The use of plastics in everyday lift is unavoidable, their high process-ability, high volume manufacture, and ability to be molded into complex shapes makes them perfect for almost any application. Unusually, when exposed to a fire, it is not uncommon for the polymer from which these plastics are derived to degrade and liberate flammable monomeric materials, effectively feeding the material’s own combustion. A means to stop this process is to dope a system with a phosphorus containing compound, these are typically just dissolved in the plastic during fabrication. In this project a range of phosphorus analogues of naturally occurring amino acids will be covalently incorporated into polymeric materials, using the reactive amino group. This will incorporate the flame retardant into the polymer backbone itself, and confer unique properties into the material for application in high temperature environments such as firefighting, aerospace, and naval applications.

Dr Galen Holt Campus: Burwood and Waurn Ponds





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I study how biodiversity depends on the large-scale outcomes of interactions between environmental conditions and life history. Specifically, I am interested in how species’ responses to variable environmental conditions affect local interactions, and how those interactions scale up to affect the dynamics of ecological communities. I study these issues using a combination of empirical studies, community dynamics models and coexistence theory. My recent projects include theoretical investigations of the maintenance of diversity at regional scales in stream networks, modelling studies of community dynamics in caddisflies, large-scale models informing management of aquatic environments, and empirical work (field and laboratory) with caddisfly communities. A current focus of my research is characterising an emerging disease affecting caddisfly eggs, and how the disease process might depend on the environment and caddisfly egg-laying behaviours. This is an emerging area of research, with a wide range of potential directions and methods, including field, lab, and modelling approaches. Additional projects related to my broader interests are also possible.


1) Investigation of post-hatching drift behaviour in response to predators, density, or environmental conditions (flow speed, temperature, etc) in a flume

2) Investigation of stressors increasing susceptibility of caddisfly egg masses to Saprolegnia infection, such as temperature, damage, or dessication, and their duration

3) Isolation of Saprolegnia life stages to investigate their differing ability to initiate infection of caddisfly egg masses

4) Studying density-dependent infection processes at one of several scales. Possibilities include Saprolegnia chemotaxis responding to egg density, or how the number and distance of nearby egg masses affect transmission.

Dr Tim Jessop Campus: Waurn Ponds

Contact details: [email protected] Project or research area description: I am offering multiple projects that will assess how native animals respond to the impacts of environmental, ecological and anthropogenic disturbances. Projects will vary in scope and address these issues using different techniques that will range from desk top modelling exercises to field-based studies.


1) Komodo dragon ecology, evolution, and conservation. Undertake desktop studies to aid conservation and understanding of one of the world’s most iconic animals.

2) Macroecology and Macrophysiology: Globalscale analyses addressing how animal respond to ecological and environmental phenomena.

3) Predictive Ecology: addressing how animals respond to natural and global change-related environmental variation using predictive biophysical models.

4) Functional Ecology: Developing functional monitoring frameworks to assess the impacts of disturbance on biodiversity.

5) Evaluating the consequences of environmental management actions for Australian biodiversity.

Prof Marcel Klaassen Campus: Waurn Ponds





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Project or research area description: My research is mainly centred around migratory shorebirds and waterfowl and focussed on (1) modelling migration, population dynamics and conservation strategies, and (2) disease ecology and the connecting powers of migrants (see https://scholar.google.com/citations?user=OrKqLoAAAAAJ&hl=en for publications). Global change has a particularly noticeable effect on long-distance migratory birds in our, East-Asian Australasian flyway. Habitat loss and massively changing conditions on their migratory staging sites along the East-Asian coast are taking their toll. Also climate chance in the breeding grounds appears to play a role. So far, there has been little attention for how the dynamics of these shorebird populations are impacted by (changing) conditions on their Australian wintering grounds. Still, these birds spent almost half their life in Australia. The Victorian Wader Study Group and the Australasian Wader Studies Group established more than 30-year long mark-recapture banding databases on a range of shorebird species. Aside from the possibility for honours students (COVID19 situation permitting) to participate in further extending these databases and assist in catching and banding shorebirds, these data bases also provide a unique source of information for detailed studies on the consequences of various global change processes on the survival, breeding success and movements of these shorebirds.

A/Prof Rebecca Lester Campus: Burwood and Waurn Ponds


Project or research area description: I am an ecologist with experience in freshwater, estuarine and marine systems. I have wide-ranging research interests, but am primarily focused on the management of aquatic ecosystems. My current research is focused on understanding how an emerging infectious disease is altering population and community dynamics in aquatic insects (specifically caddisflies). Specifically, I am interested in identifying where and in which caddisfly species the disease occurring, which mechanisms of transmission allow the disease to proliferate, and what are the effects of this on caddisfly populations. This work is in its early stages and will require further field surveys and laboratory experiments to continue to answer these questions. Other research related to my broader interest are also feasible. These projects would require an enthusiastic student who is open to learning a range of skills from a variety of disciplines (ecology, microbiology, and genetics).


1) Understanding how an emerging infectious disease (Saprolegnia) is altering population and community dynamics in aquatic insects (caddisflies) using field surveys and laboratory experiments.

2) Investigating chemotaxis of Saprolegnia to aquatic insect eggs under static and turbulent conditions using laboratory experiments.

3) Using a laboratory experiment to investigate the effect of temperature on Saprolegnia infection in caddisflies to gain an understanding of how climate change might influence the arms race between these organisms.

Dr Stuart Linton Campus: Waurn Ponds



https://scholar.google.com/citations?user=OrKqLoAAAAAJ&hl=en




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My work focuses on the purification and characterisation of hemicellulase and cellulase enzymes from herbivorous invertebrates. In particular, I am interested in how terrestrial crustaceans such as the Christmas Island red crab, Gecarcoidea natalis are able to digest leaf litter using endogenously produced cellulase and hemicellulase enzymes. Molecular biology, enzymology and protein purification is used to characterise the biochemistry of cellulose digestion. One possible project would be “Purification and characterisation of an endo-β-1,4-mannase, an important digestive hemicellulase”. Students within my laboratory would have a chance to learn, enzymology, protein purification through liquid chromatography, PAGE electrophoresis and a range of molecular biology techniques (PCR and DNA sequencing).

Dr Ashley Macqueen Campus: Burwood and Waurn Ponds


Project or research area description: I have a strong interest in understanding the drivers of spatial and temporal variability in populations of freshwater organisms and how these can be distilled and combined with remotely sensed and other large-scale datasets to provide insights into the likely distribution of organism under various future scenarios. Furthermore, I ask how empirical data can be soundly scaled up to catchment level, and potentially extrapolated to data-poor locations, to inform management decision making. I am currently supervising PhD students working on ecosystem and food-web models in the Three Gorges Dam. Potential projects could involve leveraging large datasets collected for EPA and Murray-Darling Basin Authority to interrogate management-relevant problems through an ecological lens.

Dr Matthew McKenzie Campus: Waurn Ponds


Project or research area description: Defects in mitochondrial function can cause human mitochondrial disease, affecting approximately 1 in every 4,500 people. My research is investigating how defects in both mitochondrial sugar and fat metabolism cause disease, as well as new ways to treat affected patients. We use both patient cells and knockout cell lines to determine how specific inherited genetic defects disrupt mitochondrial ATP production. To do this, we use a range of cutting-edge molecular, biochemical and electrophoresis techniques. We are also testing new compounds that can stimulate mitochondrial biogenesis as a potential treatment strategy for these diseases.

In addition, alterations of mitochondrial metabolism are involved in cancer progression, and my research is also investigating how mitochondrial function can be modulated to specifically kill cancer cells. Using different cancer cell lines that we have in the lab, we are investigating how we can increase oxidative stress to inhibit proliferation and trigger cell death.


1) Identifying Mitochondrial Oxidative Phosphorylation (OXPHOS) and Fatty Acid Oxidation (FAO) Protein Complex Defects in Human Disease

2) Development of Compounds that Stimulate Mitochondrial Biogenesis as Potential Treatments for Mitochondrial Disease

3) Modulating Mitochondrial Metabolism and Oxidative Stress to Kill Cancer Cells




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Dr Adam Miller and Dr Craig Sherman Campus: Waurn Ponds and Warrnambool

Contact details: [email protected] Project or research area description: Assessing the resilience of marine foundation species to climate change

The speed and magnitude of environmental shifts associated with climate change poses a significant challenge for marine biodiversity conservation. Rising ocean temperatures, increasing acidification, and changing ocean currents are major environmental threats. Species living close to their physiological limits are of particular concern and will become increasingly dependent on their ability to overcome environmental change via dispersal, physical tolerance and evolutionary adaptation. Understanding the environmental resilience of ‘keystone’ and ‘foundation’ species is of critical importance, given their response to environmental change will have the greatest impact on community dynamics and structure, and ultimately ecosystem function. The availability of such information will provide the necessary basis for marine conservation planning at local and regional scales. We have several potential and ongoing projects investigating the adaptive capacity of marine foundation species including kelps, seagrasses and mangroves. These projects involve the integration of genomic data and quantitative data generated from controlled laboratory and field experiments to assess the potential roles of gene flow, plasticity, and genetic adaptation in assisting adaptation to changes in the physical ocean climate. These projects will involve a combination of exciting field and laboratory-based activities.

Dr Ryan Nai Campus: Waurn Ponds


Project or research area description: I am a researcher with a strong focus on applied research, and more pertinently, on the translation of fundamental research to deliver outcomes to society. I am part of Professor Rosanne Guijt’s Smart Sensor research team within Centre for Regional and Rural Futures (CeRRF), and my research expertise is trans-disciplinary research and connects microbiology, molecular biology, analytical chemistry, engineering, and agricultural technology. I was previously involved in developing a ‘Lab on a Chip’ device, carrying responsibility for bio-functionalisation and molecular biological processes. The aim was to develop a commercialisable and manufacturable diagnostic device for sample in-answer out detection of zoonotic disease in an agricultural setting. My primary research interests are in the areas of DNA/RNA amplification especially isothermal amplification, rapid plant pathogens DNA detection using dipstick technology (similar to pregnancy rapid test), electroporation of CRISPR plasmid with Isotachophoresis, and recombinant protein expression for applied molecular biology application.

A/Prof Fred Pfeffer Campus: Waurn Ponds


Project or research area description: My research interests cover both supramolecular and medicinal chemistry with a key theme being the understanding of molecular level interactions and behaviour i.e. how molecules interact. This enhanced understanding is relevant to a number of fields including molecular recognition and sensing, biomolecular





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science and medicinal chemistry. I am happy to discuss a modified project if you are interested in this field or have an idea you would like to explore.

One aspect of my research is the development of high yielding methodology to access a broad range of naphthalimide based fluorophores [Chem. Commun. 2017, 12298, Chem. Commun., 2020, 6866]. Fluorescent tags are valuable commodities in a number of biological settings as they allow the tracking of proteins and other biomolecules of interest.

Another theme in my research is the use of large conformationally preorganised molecular frameworks to assemble larger architectures (coordination cage assembly) that can selectively interact with other species and in collaboration with Professor Guido Clever (Dortmund) the customised interior of the cage was used for six-point binding of an octahedral guest [Chem. Eur J., 2016, 10791].

Students gain valuable “hands on” organic chemistry skills, in particular the use of NMR spectroscopy to characterise molecules. For projects in which naphthalimides are developed the photophysical properties of the fluorophores are also determined. The projects listed below involve collaboration with a number of research groups in Australia and potentially overseas.


1) Functionalised naphthalimides for the fluorescent labelling of biomolecules. (With UniSA and Monash In this project the further functionalisation of naphthalimide fluorophores will be pursued. A number of functional groups, commonly used in the literature for the tagging of biomolecules, will be incorporated and the reactivity of the resultant naphthalimide tag will be evaluated.

2) New, highly fluorescent, HDAC inhibitors (With UTas and Monash

The naphthalimide core is present in the anticancer agent Scriptaid. We have now made analogues that offer superior selectivity—an important consideration for side effects (Eur J Med Chem, 2019, p 321-333). These fluorescence probes have been tracked both in cells and in zebrafish and in this project you would synthesise new analogues for this medicinal chemistry project.

3) Catching cations and anions (with UNSW)


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The project would initially involve the synthesis of the norbornene crown ether highlighted below and in turn this compound would be incorporated into larger hosts. Both the smaller and the larger hosts will be evaluated in terms of their host:guest interactions.

4) Molecular assembly using hydrogen bonding (with Melbourne and Adelaide universities We have previously use metal ligand interactions to construct cages such as that shown below (Chem. Eur J., 2016, 10791). In this project we will examine the use of hydrogen bonding as the principal interaction to drive the assembly of larger cages and networks.

Dr Justin Rizzari Campus: Waurn Ponds

Contact details: [email protected] Project or research area description: Dr Justin Rizzari is a Lecturer in Fisheries Science. His research interests span a diverse portfolio encompassing fisheries biology, quantitative fisheries science, assessments of commercial and recreational fisheries, marine conservation, spatial ecology, social science, and the impacts of global change on fisheries. He also has a strong research interest in elasmobranch communities.


1) Angler perspectives on the impact of the COVID-19 pandemic on recreational fisheries in Victoria The overarching purpose of this project is to gain a better understand of how COVID-19 has impacted recreational fishers in Victoria through the use of online social surveys.

Dr Aaron Schultz Campus: Waurn Ponds





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Project or research area description: Cardiovascular toxicity of metal nanomaterials in aquatic animals. Rapid advances in nanosciences have led to a much greater use of engineered nanomaterials (NMs) in a variety of applications, ranging from medicine (e.g. drug delivery and medical imaging) and materials science (e.g. paints), to environmental remediation and consumer products (e.g. clothing, sunscreens, and cosmetics). Several of the main materials used in these applications are engineered metal-containing and metal oxide NMs, including silver (Ag), titanium dioxide (TiO2) and copper (Cu). The growing interest and use of these NMs for future applications globally and in Australia will undoubtedly result in their infiltration into aquatic environments where the NMs themselves and/or the ionic metals they release have the potential to impact aquatic ecosystems. Despite the extensive research conducted in aquatic nanotoxicology to date, very little research has been conducted on the effects that NMs may pose on the blood vasculature and cardiovascular system of aquatic organisms. This is extremely important to determine, as it is the first biological system to come into contact with NMs after their entry into an animal. Please see the new Environmental Science: Nano Hot Article published by our group in this research area: https://doi.org/10.1039/D0EN00229A Specific projects on offer:

1) This research project aims to investigate the cardiovascular toxicity of NPs using zebrafish embryo’s as a model test organism. Standard OECD toxicity procedures, cardiovascular toxicity assays, and microscopy methods will be used in this important project and you will develop key skills in toxicology, nanomaterial characterization, cardiovascular physiology, molecular biology, and/or microscopy.

2) This research project aims to investigate the toxic effects and uptake of engineered NMs in isolated cane toad blood vessels, using physiological, toxicological, and microscopy techniques. The project provides an opportunity to develop key skills in toxicology, nanomaterial characterization, cardiovascular physiology, myography, and microscopy.

Project or research area description: Potential therapeutic application of copper-containing nanomaterial’s as “trojan horses” to deliver ionic copper into cancer cells or neuronal cells.

Nanomaterial’s (NMs) exhibit special properties at the nanometer scale (<100 nm) that dramatically increases their surface area, binding properties and charge distribution. Manufacturers have exploited these properties to develop and improve NMs for use in medicine as fluorescent agents for cell imaging and as vehicles for drug delivery. However, the potential for optimizing and using copper (Cu) NMs to treat cancer or neurological disorders, such as Menkes disease (MD) has not been investigated. Some cancer cells have increased basal Cu levels so increasing their internal Cu with NMs may induce selective toxicity. For MD, a devastating Cu deficiency disorder, Cu NMs may restore essential Cu to brain cells. This research project will investigate the cellular uptake and biocompatibility of Cu NMs in brain cell or cancer cell models, to assess their therapeutic value. The project provides an opportunity to develop key skills in nanomaterial characterization, toxicology, cell biology, and/or microscopy.

https://doi.org/10.1039/D0EN00229A


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Dr Aaron Schultz and A/Prof Luis Afonso Campus: Waurn Ponds

Contact details: [email protected] and [email protected]

Project or research area description: The potential threat of emerging contaminants (nanomaterials and nano-plastics) to aquatic ecosystems.

What do socks, wound dressings, cosmetics, sunscreens, and medical devices all have common? Each of these products can contain engineered nanomaterial’s (NMs), which are man-made materials ranging in size from 1 – 100 nm. Due to their small size and unique surface properties, NMs have many desirable and useful properties, and in recent years they have shown great promise for improving the treatment of a number of diseases, including cancer. However, NMs can also interact with living cells and animals in potentially undesirable and toxic manners and it is, therefore, very important for us to understand any potential adverse effects of NMs on organisms in both freshwater and marine aquatic environments

Specific projects on offer: 1) This research project aims to investigate the potential threat engineered NMs pose to freshwater

aquatic ecosystems using zebrafish embryo’s as a model test organism. Standard OECD toxicity procedures, toxicity assays and microscopy methods will be used in this important project and you will develop key skills in toxicology, nanomaterial characterization, molecular biology, and/or microscopy.

2) This research project aims to investigate the potential threat engineered NMs pose to marine aquatic ecosystems using mussels as a model test organism. Standard OECD toxicity procedures, toxicity assays and microscopy methods will be used in this important project and you will develop key skills in toxicology, nanomaterial characterization, molecular biology, and/or microscopy. A major component of this project will be conducted at the Queenscliff Marine Science Centre

For more information on nanotoxicology please see review article: Schultz, A.G, et al. Environmental Chemistry, 2014, 11, 207-226.

Dr Aaron Schultz and A/Prof Fred Pfeffer Campus: Waurn Ponds

Contact details: [email protected] and [email protected] Project or research area description: The role of HDAC6 selective HDAC inhibitors on Zebrafish development.

Compounds known as Histone Deacetylase Inhibitors (HDACi) have now been established as clinically relevant cancer therapeutics. The family of HDAC enzymes is divided into a number of classes and isoforms and it is now believed that specifically targeting one isoform (as opposed to all isoforms) is a viable means to mitigate the side effects of the current clinically used non-selective HDACi. HDAC6 is a particular focus as (i) it has a proven role in cancer and (ii) mice with HDAC6 deletion are still viable.

Our group has designed and synthesised a number of potent highly fluorescent HDAC6 selective inhibitors.[1] In our preliminary studies using compound 6 in zebrafish the fluorescence enabled the tracking of






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these compounds into the vasculature of zebrafish (confirms uptake) and it also appeared that the phenotypical outcome for compound 6 was less severe than that of the broad spectrum inhibitors tested (such as TSA).

In this project a more comprehensive set of compounds will be evaluated for their uptake, tissue distribution, and potential developmental impacts on zebrafish embryos. The student will gain valuable skills in animal handling, zebrafish embryo toxicity procedures, developmental toxicology, and fluorescent and bright field microscopy methods.

[1] C. L. Fleming, A. Natoli, J. Schreuders, M. Devlin, P. Yoganantharajah, Y. Gibert, K. G. Leslie, E. J. New, T. D. Ashton, F. M. Pfeffer, Eur. J. Med. Chem. 2019, 162, 321–333.

Dr Madeleine Schultz Campus: Waurn Ponds


Project or research area description: My research is in the area of chemistry education. This spans multiple topics including:

• student engagement and the impact of different forms of engagement on performance;

• concept acquisition and remediation of chemical misconceptions;

• professional development of both secondary and tertiary chemistry teachers, including demonstrators;

• chemistry teacher attitudes towards pedagogical content knowledge;

• incorporation of sustainability throughout chemistry education.

Specific project details will be based on student interests and can span multiple topics. Co-supervisors are Dr Seamus Delaney or Dr Damien Callahan (both at Burwood campus). The results of this research are important to help structure effective chemistry education that will allow diverse students to tackle complex problems.

Educational research includes training in correct ethical conduct in research involving human subjects, as well as discipline-specific literature reviews and writing. Depending on whether the project is qualitative, quantitative or mixed methods, the project will involve training in statistical techniques and software.

This research can be conducted fully online and does not involve any laboratory or field work.

A/Prof Craig Sherman Campus: Waurn Ponds






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1) Developing the tools for seagrass restoration. As key ecosystem engineers, seagrasses provide a range of important ecosystem services including nutrient cycling, carbon sequestration, coastal protection, and providing a structurally complex habitat to a variety of vertebrate and invertebrate species. Given these important roles, there has been increasing concern about the rapid decline seagrass populations are now experiencing globally. This project will develop restoration and recovery methodology for intertidal seagrass meadows in Western Port, Australia. The project will use a combination of field-based trials and nursery experiments to develop the appropriate methodologies needed for seagrass restoration in Western Port. This project offers opportunities to develop skills in field ecology, GIS, drone mapping and genetics.

2) Assessing patters of connectivity and genetic structure in the purple sea urchin. Understanding the population genetic structure and patterns of connectivity are crucial for understanding the ability of populations to be maintained by locally derived recruits versus migrants from neighbouring populations. In Victoria reef systems are inherently patchy in their spatial distribution. These reefs offer important habitat to a wide diversity of invertebrates, macroalgae and fish species, including ecosystem engineers such as the purple sea urchin Heliocidaris erythrogramma. Urchins play an important grazing role on temperate reefs, however, if their populations are not controlled, they can cause urchin barrens which strip the local reef habitats of macroalgae. This can lead to a dramatic decline in species biodiversity. Understanding patterns of connectivity and dispersal are crucial for determining if populations form isolated self-recruiting populations, or if populations are maintained through the exchange of recruits from neighbouring populations (i.e. stepping stone populations). This project will undertake genetic analysis, using the latest genomic approaches, to characterise the population structure of H. erythrogramma in Victoria.

3) Assessing the use of environmental DNA (eDNA) for detecting invasive marine species. Environmental DNA (eDNA) refers to DNA that is collected and extracted from environmental samples such as water or soil, rather than directly sampling the DNA from the organisms. The eDNA results from cellular material continuously being lost from organisms into the environment and typically lasts for several hours to several weeks. This approach can be used to identify potentially invasive species and their geographical ranges, and is emerging as a crucial tool for biodiversity and pest species management. The project will involve the collection of eDNA samples and use quantitative real-time PCR (qPCR) to detect invasive pest species. The student will have the opportunity to spend time in the field and laboratory and will develop important skills in field sampling, DNA extraction and qPCR. The student will also have the opportunity to make valuable industry contacts within the Department of Economic Development, Jobs, Transport and Resources and Parks Victoria.

4) Understanding the role and changes in microbiome composition of declining seagrass meadows.

As key ecosystem engineers, seagrasses play a crucial role in nutrient cycling, sediment stabilisation, reducing turbidity, reducing coastal erosion and providing a structurally complex habitat to a variety of vertebrate and invertebrate species. Given these important roles in providing habitat and a range of ecosystem services, there has been increasing concern about the rapid decline seagrass populations are now experiencing globally. Seagrass support a wide diversity of microbes that are found on, within and closely associated with their roots and leaves. Associations with these microbial communities can directly influence the fitness of seagrass. Given the significance and diversity of microbial influence on seagrass health and maintenance of ecosystem services, an understanding of the composition and functional diversity of seagrass microbiomes is essential for understanding seagrass health and resilience. This project will undertake the characterisation of the microbiome of seagrass meadows using targeted PCR and next generation sequencing approaches. The student will undertake field sampling of microbiomes, conduct DNA extractions, sequencing and bioinformatic analyses to characterise microbiomes from impacted and healthy seagrass sites.

5) The effect of global climate change on seed survival and germination success of seagrass meadows. Sea surface temperatures have been increasing due to the effects of global climate change and are already having significant impacts on marine life. Rising temperatures can directly affect the


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metabolism, life cycle, and behaviour of marine organisms and their ability to cope and adapt with rising water temperatures will determine the long-term viability of these species. Seagrasses are important ecosystem engineers, providing habitat to a range of species, nutrient cycling, sediment stabilisation, and reducing coastal erosion. Their reproductive cycles are highly seasonal and temperature dependent, yet we know little about how increasing temperature may affect their reproductive output and recruitment. Seagrasses produce seeds that often accumulate in a soil-stored seedbank. This project will look at the effect of climate change and adaption of Zostera muelleri seeds along a latitudinal gradient on the east coast of Australia to determine germination success of seeds under different temperatures. This information will provide crucial data on the ability of seagrass seeds to germinate under future climate change scenarios and the long-term viability of Australian seagrass populations. The student will be involved in field collections and mesocosm experiments based at the Queenscliff marine research station.

6) Determining the chemical basis of detection of an invasive predator by scallops.

The introduction of non-native species provides an excellent opportunity to study rapid evolutionary change. This is because invasive species have to adapt to a range of novel conditions, while native species often have to evolve novel responses to invasive predators. The Northern Pacific sea star is ranked as one of the top ten most potentially damaging invasive species. It is a ferocious marine predator of marine bivalves and other invertebrates and can have a devastating effect on the biodiversity of native marine communities. Recent work has demonstrated that native scallops in populations exposed to the Northern Pacific sea star show predator avoidance behaviours, while populations with no exposure to this invasive predator show no anti-predator behaviours. This project will explore the chemical basis of this anti-predator behavior and identify the key chemical species involved in predator detection. Students will undertake fieldwork to collect samples and laboratory analysis including a multidimensional approach to detection chemistry with the aid of Mass spectrometry, 2D-HPLC and chemiluminescence detection.

A/Prof Cenk Suphioglu Campus: Waurn Ponds


Project or research area description: Allergy is a chronic disease affecting up to 50% of the population worldwide and costing more than $7 billion per annum in Australia alone. Exposure to environmental allergens through contact with the skin, airways or gastrointestinal track can trigger an immediate hypersensitive (Type I) response in genetically predisposed individuals, which may prove fatal. Such allergic responses involves IL-4 signalling and the production of allergen-specific IgE antibodies by B cells, which are then bound on basophils and mast cells via the high affinity IgE receptors. On subsequent allergen exposure, the cell-bound IgE antibodies are crosslinked, causing cell degranulation and thereby releasing the pharmacological mediators of the allergic reaction. Airborne grass pollen are ubiquitous and are important triggers of allergic diseases such as allergic rhinitis and allergic asthma. We have shown that grass pollen can rupture during a thunderstorm and thus release hundreds of highly allergenic particles that have the capacity to penetrate the lower airways to trigger allergic asthma and cause epidemic events known as Epidemic Thunderstorm Asthma (ETSA), which can be life-threatening. Indeed, on 21 November of 2016, thousands of Melbournians, who were grass pollen allergic, required emergency medical attention and 10 people died as a result of ETSA.


1) Inhibition of IL-4 signalling pathway for allergy treatment In this project, the student will use our in-house synthetic peptide inhibitors of human IL-4 signalling in a cell line model to evaluate their potential for allergy treatment.



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2) Production and characterisation of allergen specific human IgE antibodies via Polymerase Incomplete Primer Extension (PIPE). In this project, the student will use PIPE to clone and characterise recombinant human IgE antibodies to ryegrass pollen allergens for allergen detection and diagnostics for grass pollen allergies.

3) Importance of grass pollen rupture in epidemic thunderstorm asthma (ETSA). In this project, the student will use Deakin AIRwatch air sampling to investigate the importance of weather factors for airborne grass pollen rupture and its links to acute asthma presentations.

Dr Erica Todd Campus: Waurn Ponds and Queenscliff

Contact details: [email protected] Project or research area description: Sexual development, ecology and aquaculture.

My research combines the latest tools in genomics and bioinformatics with traditional molecular biology techniques to address questions about the ecology, evolution, and reproductive biology of marine and freshwater species. In particular, sexual development patterns in fishes are remarkably diverse and often reversible – some fishes change sex naturally (e.g. barramundi), whereas the sexual fate of many fishes is reversible by environmental stressors (e.g. temperature). This has important consequences for fisheries biology and conservation, and there is considerable interest in controlling sexual development in aquaculture species. Potential Honours projects in these areas will allow learning opportunities in bioinformatics, gene expression analyses (PCR, transcriptomics) and/or epigenetics. Please contact me to discuss potential projects.

Dr Eric A Treml Campus: Waurn Ponds

Contact details: [email protected], https://mseaclab.com/

Project or research area description: In our Marine Spatial Ecology and Conservation (MSEaC) group, our research interests are in marine ecology, fisheries science, and conservation planning in coral and rocky reef systems. Our specific focus is on understanding the causes and consequences of population connectivity (e.g., larval dispersal) and the implications for biodiversity and climate adaptation.

Population connectivity (i.e., larval dispersal or migration) is critical for metapopulation persistence, range expansion, a species’ ability to cope with climate change. Connectivity is also fundamental to our understanding of population dynamics, biodiversity patterns, and the conservation and management of species. Unfortunately, quantifying this complex bio-physical process and identifying the important biological drivers and the resultant geographic patterns remains a great challenge. We use a variety of quantitative tools, along with field and lab research to tackle these challenging questions. Our quantitative approaches include geographic information systems (GIS), spatially-explicit dynamic modelling and statistics, network analysis, oceanographic modelling/data, and remote sensing data.

An Honours project in our lab will help you further develop critical and employable skills in spatial analysis (ArcGIS), statistics (R), programming (MATLAB and/or R), and quantitative ecology. In addition, you will be embedded within a broad professional network including international academics and industry partners.




https://mseaclab.com/


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1) Applying network approaches to marine conservation problems. This project aims to use network analysis to quantify marine metapopulation ‘health’ and identify conservation priorities across the Indo-Pacific and/or Port Phillip Bay reef systems.

2) Quantifying source-sink relationships of plastic pollution in Port Philip Bay. In this project, the student will choose a vulnerable habitat (e.g., mangroves, seagrass, reef) and conduct a thorough empirical and model-based source-sink assessment of plastic pollution. Associate Supervisor: Dr Kay Critchell

3) Invasive Species modelling in New Zealand. This project will assist with the development of a maritime network model for New Zealand, and the use of this model for simulating invasion scenarios to understand risk mitigation strategies. Associate Supervisor: Dr Kay Critchell

Dr Mark Ziemann Campus: Waurn Ponds

Contact details: [email protected] Project or research area description: Our group is focused on building data resources and software tools to accelerate biomedical discovery. We also collaborate closely with biologists and clinicians to get the most out of their 'omics experiments. Our lab is committed to reproducibility, open science, and diversity. In 2021 there will be an opportunity for an Honours student to join our group to investigate the role of epigenetics in experimental evolution in guppies. This role will involve significant bioinformatics analysis and can be undertaken remotely or on-campus.



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Warrnambool Projects

Dr Adam Miller and Dr Susanna Venn Campus: Warrnambool


Project or research area description: The ECOGENETICS LAB’s research program focusses on a range of fundamental and applied questions relating to the ecology and evolution of native and invasive species. The team is particularly interested in research that provides insights into the evolutionary processes that shape patterns of biodiversity, environmental resilience, and the ability of species and ecosystems to adapt to environmental change. We have a range of projects happening in the field of conservation genetics and wildlife monitoring, environmental stress and adaptation research, pest control and biosecurity, fisheries genetics, and ecological restoration. Three potential 2021 Honours projects are provided below, but students are encouraged to contact us to discuss other options (please visit: https://www.ecogeneticslab.com/)

Population genomics of Australian alpine plants: Identifying vulnerable plant species and climate-ready seed sources

The Australian Alps are recognized as one of the world’s major biodiversity hotspots and critically vulnerable to climate change. Here, plant communities are already showing signs of climate stress, threatening environmental and associated cultural and socio-economic values in the region. The persistence of alpine plant species under climate change will largely depend on plastic responses or rapid evolutionary change. Some species will likely tolerate substantial environmental fluctuations via existing plasticity, while others are expected to be pushed to physiological limits and become increasingly dependent on evolving to maintain current distributions. The Honours project will be linked within a larger research program using a combination of common garden and genomic approaches to decipher the likely contributions of plasticity, local adaptation and gene flow to future adaptive responses in a range of functionally important alpine plant species. This study will help to improve biodiversity outcomes under climate change by identifying key plant species with reduced adaptive potential and in need of intervention, as well ‘climate-ready’ seed sources for restoration purposes. This project will involve a combination of exciting fieldwork in the Australian alps, as well as laboratory and glasshouse experiments.

Dr Adam Miller, Dr John Morrongiello and Dr Eric Treml Campus: Warrnambool


Project or research area description: Estimating population genetic structure in the common pipi (Donax deltoides) for future fisheries management

A fisheries long-term viability and profitability is intrinsically linked to its sustainability. Sustainable fisheries management requires an understanding of how harvested populations are structured (population connectivity), and the spatio-temporal dynamics in their abundance and demography (assessed by monitoring). Previous genetic work indicates that Australian pipi stocks consist of two large and reproductively isolated populations occurring on Australia’s east and south coasts, however, we lack information on more relevant finer-scale stock structure. This Honours projects will involve sampling pipis from across the Victorian coastline and using genetic markers to test for spatial autocorrelation and fine scale genetic structure. This data will be combined with estimates of connectivity from biophysical models (provided by Eric Treml’s team) to determine the true extent of stock connectivity across Victorian fisheries (strength and directionality of juvenile migration) and the recruitment potential of individual fisheries. This project will help guide future management of Victorian pipi fisheries ensuring the industries long-term viability and profitability.


https://www.ecogeneticslab.com/



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Dr Adam Miller and Dr Craig Sherman Campus: Warrnambool and Waurn Ponds


Project or research area description: Assessing the resilience of marine foundation species to climate change The speed and magnitude of environmental shifts associated with climate change poses a significant challenge for marine biodiversity conservation. Rising ocean temperatures, increasing acidification, and changing ocean currents are major environmental threats. Species living close to their physiological limits are of particular concern and will become increasingly dependent on their ability to overcome environmental change via dispersal, physical tolerance and evolutionary adaptation. Understanding the environmental resilience of ‘keystone’ and ‘foundation’ species is of critical importance, given their response to environmental change will have the greatest impact on community dynamics and structure, and ultimately ecosystem function. The availability of such information will provide the necessary basis for marine conservation planning at local and regional scales. We have several potential and ongoing projects investigating the adaptive capacity of marine foundation species including kelps, seagrasses and mangroves. These projects involve the integration of genomic data and quantitative data generated from controlled laboratory and field experiments to assess the potential roles of gene flow, plasticity, and genetic adaptation in assisting adaptation to changes in the physical ocean climate. These projects will involve a combination of exciting field and laboratory-based activities.



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Queenscliff Projects

A/Prof David Francis Campus: Queenscliff


Project or research area description: Fish in hot water: future-proofing aquaculture via nutritional innovation The Nutrition and Seafood Laboratory (NuSea.Lab) is a multidisciplinary team with a focused research effort in the nutrition-based sciences. We work towards the development of innovative approaches and solutions to support the aquaculture and seafood industries. Our specific areas of interest include sustainable aquafeed development, nutritional biomarkers of organism health, fatty acid metabolism, and marine genetics. Current NuSea.Lab associated projects explore salmon farming in the face of climate change, the nutritional requirements of farmed abalone, flavour enhancement in farmed fish, investigations into sustainable aquafeed development, and the assessment of novel bioactive efficacy in aquafeeds.

NuSea.Lab currently has multiple opportunities available for highly motivated Honours students commencing in 2021 to further explore these areas of industry priority. The successful realisation of each project will see students develop a series of practical and analytical skills related to aquaculture nutrition, including fish husbandry and laboratory analyses.

Dr Ty Matthews Campus: Queenscliff


Project or research area description: Ty is an aquatic ecologist based at the Queenscliff Marine Station that works in marine, estuarine and freshwater ecosystems. He is particularly interested in how varying flow regimes influence aquatic plants and animals and in assessing ecological restoration efforts. The projects described below are a small sample of the possible projects on offer and he is happy to discuss other project ideas with interested students. Ty is often willing to tailor projects around student interest. Other potential projects include the ecology of estuarine fish and invertebrates and also sandy beach ecology.

Ty also collaborates with researchers from the Centre of Rural and Regional Futures (CeRRF - Associate Professor Rebecca Lester and her team) and environmental consultants (Dr Dion Iervasi, Austral Research and Consulting & Dr Travis Howson, Australian Private Fisheries Resources) on a range of joint freshwater and estuarine projects. This provides additional opportunities and networking for Honours students that are interested in working with Ty.

NOTE: Students working with Ty would be predominantly based at the Queenscliff Marine Station, but will also spend some time at the Waurn Ponds campus.

1) Diversity of Fish and Invertebrates in Urban and Agricultural Wetlands Co-supervisors: Rebecca Lester, David Dodemaide (CeRRF) and Dr Dion Iervasi (AR&C).

2) Spawning Ecology of River Blackfish Associate Supervisor: Dr Travis Howson, APFR)

3) Invasive species ecology (specifically common carp), conservation and management Associate Supervisor: Dr Dion Iervasi (AR&C)




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4) Influence of stream confluences on diversity of stream invertebrates Associate Supervisors: Associate Professor Belinda Robson (Murdoch University, WA).

Marine 1) Influence of oyster reef and man-made infrastructure on adjacent benthic faunal assemblages

Co-supervisor: Associate Professor Craig Sherman (Waurn Ponds Campus) 2) Examining the symbiotic relationship between sea anemones (Anthopleura sp.) and infaunal clams

(Katelysia spp.) in Port Phillip Bay (or broad distribution and abundance of subtidal clams) 3) Recreational Fishing Efforts and Catch Per Unit Effort data for pipis (Donax deltoidalis) in south-west

Victoria

Dr Erica Todd Campus: Waurn Ponds and Queenscliff

Contact details: [email protected] Project or research area description: Sexual development, ecology and aquaculture. My research combines the latest tools in genomics and bioinformatics with traditional molecular biology techniques to address questions about the ecology, evolution, and reproductive biology of marine and freshwater species. In particular, sexual development patterns in fishes are remarkably diverse and often reversible – some fishes change sex naturally (e.g. barramundi), whereas the sexual fate of many fishes is reversible by environmental stressors (e.g. temperature). This has important consequences for fisheries biology and conservation, and there is considerable interest in controlling sexual development in aquaculture species. Potential Honours projects in these areas will allow learning opportunities in bioinformatics, gene expression analyses (PCR, transcriptomics) and/or epigenetics. Please contact me to discuss potential projects.

Victorian Fisheries Authority Campus: Queenscliff


Supervisor: Dependent of project

Project or research area description: Several research projects on fisheries population dynamics, biology, ecology and management are potentially available through a partnership between the Victorian Fisheries Authority (VFA) and Deakin University. These projects offer hands on experience in developing a range of potential skills from fisheries modeling, data analysis of large multi-year data sets, collection of life history data and a range of field and technical skills. Students work closely with VFA staff and other stakeholders, providing them with important industry experience and networking opportunities that will provide real opportunity in expanding our knowledge in effectively managing species in marine, estuarine and freshwater systems. Students successful in their application for a VFA-Deakin honours project will be assigned a Deakin and VFA supervisor. Interested students should contact the school representative and outline in their email why they are interested in doing a VFA-Deakin honours project and the type of fisheries research area they are interested in.

Project examples could include:

1) Optimizing trout and native fish production through improved feeding strategies 2) Understanding the population dynamics of greenlip abalone in Victoria




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3) Gaining greater understanding of spider crab population dynamics

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