Honours Project Booklet Waurn Ponds - School of Life and Environmental Sciences 2019 - Deakin University
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Honours
Project Booklet
Waurn Ponds
School of Life and
Environmental Sciences
2019
Deakin University CRICOS Code: 00113B
School of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
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 fieldwork, 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 have to 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. External employers recognise these skills 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 students 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.
Semester 1 Honours commences on Tuesday 29th January 2019 and finishing in November. Semester 2
Honours commences on Monday 1st July 2019 and finishes the following April. You must be available to
commence Honours on the specified start dates.
Applications
The first step in securing a place in the program for 2019 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:
https://www.deakin.edu.au/students/faculties/sebe/les-students/honours. 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 7 January for the Semester 1, 2019 intake and Monday 24 June for the
Semester 2, 2019 intake. Late applications may be considered pending project availability.
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School of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Further information can be obtained from your local Honours coordinator Dr Annalisa Durdle
a.durdle@deakin.edu.au and via the School website at: http://www.deakin.edu.au/sebe/les/
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School of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Contents
Dr Jacqui Adcock .................................................................................................................................. 4-5
Professor Neil Barnett............................................................................................................................. 6
Associate Professor Peter Biro ............................................................................................................. 7-9
Associate Professor Kate Buchanan and Dr Mylene Mariette .............................................................. 10
Asociate Professor Kate Buchanan…………………………………………………………………………………………………..11
Dr Egan Doeven……………………………………………………………………………………………………………………………….12
Dr Annalisa Durdle ................................................................................................................................ 13
Professor John Endler ...................................................................................................................... 14-19
Dr David Francis …………………………………………………………………………………………………………………………20-21
Professor Paul Francis ...................................................................................................................... 22-24
Dr Prue Francis ...................................................................................................................................... 25
Associate Professor Michelle Harvey ............................................................................................... 26-29
Associate Professor Luke Henderson............................................................................................... 30-33
Professor Marcel Klaassen .................................................................................................................... 34
Dr Stuart Linton..................................................................................................................................... 35
Dr Matthew McKenzie ..................................................................................................................... 36-37
Dr Ryan Nai………………………………………………………………………………………………………………………………………38
Associate Professor Fred Pfeffer...................................................................................................... 39-44
Dr Aaron Schultz .……………………………………………………………………………………………………………………… 45-47
Dr Madeleine Schultz………………………………………………………………………………………………………………… 48-49
Dr Craig Sherman and Dr Adam Miller …………………………………………………………………………………………….50
Dr Craig Sherman ............................................................................................................................ 51-52
Associate Professor Cenk Suphioglu ..................................................................................................... 53
Dr Eric Treml……………………………………………………………………………………………………………………………………54
Dr Beata Ujvari ................................................................................................................................. 55-56
Dr Mark Ziemann ………………………………………………………………………………………………………………………….576
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School of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Dr Jacqui Adcock
Project 1
Project Title: Omega-3 fatty acids – Reactions with lipoxygenase enzymes and characterization of side-
products
Principal Supervisor: Dr Jacqui Adcock
Principal Supervisor contact details: jadcock@deakin.edu.au; 5227 2096; ka4.333
Associate or External Supervisors and their contact details: Prof. Colin Barrow colin.barrow@deakin.edu.au
Start date: Semester 1 2019 or Semester 2 2019
Project description:
Omega-3 fatty acids, like those found in fish oils, are important for good health. Lipoxygenase enzymes
catalyse the transformation of polyunsaturated fatty acids to fatty acid hydro peroxides. These molecules form
important pro- and anti-inflammatory compounds in animal systems, and form defensive compounds in plants.
Under certain conditions, lipoxygenase reactions also generate a range of unusual side-products, including
volatile flavour and fragrance compounds and other complex oxidised lipids, which may also have bioactivity.
The aim of this project is to develop new methods for the analysis and characterisation of side-products from
lipoxygenase reactions with omega-3 fatty acids. This project will include: (i) manipulation of enzymatic
reaction conditions to synthesise a range of products; (ii) analysis of reaction products by HPLC; and (iii)
chemical characterisation of products by GC-MS, LC-MS and NMR.
Project 2
Project Title: Investigating the degradation of pet foods and pet food ingredients
Principal Supervisor: Dr Jacqui Adcock
Principal Supervisor contact details: jadcock@deakin.edu.au; 5227 2096; ka4.333
Associate or External Supervisors and their contact details: Dr Shona Crawford, Kemin Nutrisurance
shona.crawford@kemin.com
Start date: Semester 1 2019 or Semester 2 2019
Project description:
Australians spend over $3 billion per year on pet food, and there is increasing demand for premium products with
added health benefits. Many of the ingredients in pet foods are prone to degradation and as with all food
products, it is essential that food safety standards are met. Animals can be very sensitive to food degradation and
may be able to detect the formation of off flavours even before we can. Food degradation can be a health issue –
eg. Some biogenic amines formed from the breakdown of proteins can cause poisoning; or a taste issue – eg. Lipid
oxidation can lead to rancid flavours even at very low levels. So it is important to be able to detect and
characterise these degradation processes.
The aim of this project is to use a variety of techniques to detect and characterise degradation in pet foods and pet
food ingredients, and to develop strategies to prevent degradation. Techniques used may include HPLC, GC-FID,
GC-MS, FT-NIR, and UV-vis spectroscopy. This project will be run in collaboration with Kemin Nutrisurance, giving
the student access and experience in both University and commercial laboratories.
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School of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Project 3
Project Title: Developing automated methods for fatty acid profiling for industry applications
Principal Supervisor: Dr Jacqui Adcock
Principal Supervisor contact details: jadcock@deakin.edu.au; 5227 2096; ka4.333
Associate or External Supervisors and their contact details: Dr Shona Crawford, Kemin Nutrisurance
(shona.crawford@kemin.com)
Start date: Semester 1 2019 or Semester 2 2019
Project description:
Fatty acids are found in all living things. They have a number of important functions including roles in cell
signalling, cell membranes and energy storage. The essential omega-3 and omega-6 fatty acids are required for
good health. Quantification of fatty acids is crucial in a wide range of applications, such as food manufacturing,
human health and disease, biofuels and plant growth. There are numerous methods available for the
quantification of fatty acids in a variety of sample types, but most are time consuming and involve significant
manual preparation of samples.
This project will investigate the possible automation of the various derivatisation and extraction steps
associated with fatty acid profiling. The developed method will be validated and applied to a range of pet food
ingredients.
The project will provide:
• Experience in sample preparation and chemical derivatisation techniques
• Skills in gas chromatography and data analysis
• Experience in academic and industrial laboratories
• Industry experience in an accredited laboratory
This project will be run in collaboration with Kemin Nutrisurance, giving the student access and experience in
both University and commercial laboratories.
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School of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Professor Neil Barnett
Project Title: Investigations into the origin of heroin metabolites in the urine of chronic pain patients treated with
morphine
Principal Supervisor: Prof Neil Barnett
Principal Supervisor contact details: neil.barnett@deakin.edu.au
Associate Supervisors and their contact details: Dr Zoe Smith, z.smith@deakin.edu.au
Start date: Semester 1 2019
Project description:
Due to the increasing use of powerful opiates for the treatment of chronic pain, it has become common for
patients to be drug tested in order to monitor medication compliance. Physicians test patients’ urine to ensure
that: a) the patient is taking their prescribed medication (not diverting it for profit) and b) they are not using
illicit drugs, which would breach the physicians/patient agreement. Testing positive for illicit drugs results in the
patient being discharged from the clinic, leaving them with no means to legally access pain relief.
In recent years, an unusually large number of patients prescribed with high doses of morphine have tested
positive for the metabolite 6-monoaceytlmorphine (6-MAM) – universally recognised as a definitive sign of
heroin use. Currently, there is no other explanation for the presence of the metabolite in these patients –
however, given the increase in positive detections, it is hypothesised that the 6-MAM may originate from
another source.
This project seeks to determine if heroin metabolites could be formed as an artefact of sample processing
protocols used to prepare urine samples for analysis. Liquid chromatography (with chemiluminescence
detection) will be used to investigate multiple sample preparation methods to identify potential sources of false
positives.
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School of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Associate Professor Peter Biro
Project 1
Project Title: Evolution of song in female birds
Principal Supervisor: Assoc Prof Peter Biro
Principal Supervisor contact details: pete.biro@deakin.edu.au
Associate or External Supervisors and their contact details: Dr. Christa Beckmann, E:
c.beckmann@deakin.edu.au
Start date: Semester 2, 2019
Project description:
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 will require fieldwork, including song recording, behavioural observations, and
trapping and banding birds. Fieldwork will be conducted in Brisbane Ranges National Park (30 min drive from
the Geelong Campus).
Project 2
Project Title: Kleptoparasitism of nesting material in birds
Principal Supervisor: Assoc Prof Peter Biro
Principal Supervisor contact details: pete.biro@deakin.edu.au
Associate or External Supervisors and their contact details: Dr. Christa Beckmann, E:
c.beckmann@deakin.edu.au
Start date: Semester 2, 2019
Project description:
Nest material kleptoparasitism (stealing) commonly occurs among colonially-nesting birds subject to intense
competition for nesting material. Reports of nest material kleptoparasitism in solitary breeding birds is less
frequent, and has been reported for a variety of birds in scattered accounts, yet the ecological context of the
behaviour remains largely untested and speculative. This project will experimentally test several hypothesis
for the existence of nest material kleptoparasitism in the grey fantail, a solitary nesting bird. Five species have
been recorded to steal nest material from the fantails. This is a field- based project, with work will take place
in Brisbane Ranges National Park (a 30 min drive from Geelong).
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School of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Project 3
Project Title: Avian Nest Construction
Principal Supervisor: Assoc Prof Peter Biro
Principal Supervisor contact details: pete.biro@deakin.edu.au
Associate or External Supervisors and their contact details: Dr. Christa Beckmann, E:
c.beckmann@deakin.edu.au
Start date: Semester 2, 2019
Project description:
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 will require field work in Brisbane Ranges National Park.
Project 4
Project Title: Growing up athletic: developmental effects of exercise on metabolism and personality traits in
zebrafish.
Principal Supervisor: A/Prof Peter Biro
Principal Supervisor contact details: pete.biro@deakin.edu.au
Associate Supervisor: Dr Beata Ujvari, Dr. Christa Beckmann
Start date: Semester 1 2019 or Semester 2 2019
Project description:
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 behavioral 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.
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School of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Project 5
Project Title: Is conservation of predators critical for prey population persistence in a changing environment?
Principal Supervisor: A/Prof Peter Biro
Principal Supervisor contact details: pete.biro@deakin.edu.au
Associate Supervisor: Dr Beata Ujvari, Dr Christa Beckmann
Start date: Semester 1 2019 or Semester 2 2019
Project description:
Predation is suggested to encourage among-individual variation in behavior and correlations among different
behaviors. Other traits, like body shape and coloration, are likely related to behavior, but how these traits
might co-evolve under predation is not clear. Why do predators seem to encourage greater variation among
individuals in general, and what genes might be involved?
If predators help maintain ‘adaptive’ variation in prey physiology and behavior, then predators may serve a
critical role in maintaining the ability of prey to adapt to a host of different selection pressures in our rapidly
changing environment. Why? Because variation is needed for animals to adapt and evolve.
Using lab populations of guppies living and breeding for 4 years in ponds either with or without predators, we
can study if predation really does affect the variation in physiological, morphological and behavioural traits in
their prey. The project will involve measuring behavior (such as activity levels), body shape and color of
individuals from each treatment, and testing if the presence of predators does indeed favor evolution of
greater variation of these traits.
The student will learn techniques to measure animal behaviour, colour and morphology, as well as general fish
husbandry.
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Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Associate Professor Kate Buchanan and Dr Mylene Mariette
Project Title: Growing up in a noisy world: Effects of prenatal anthropogenic noise exposure on avian
development
Principle Supervisors: Prof. Kate Buchanan and Dr Mylene Mariette
Principal Supervisor contact details: kate.buchanan@deakin.edu.au
Associate Supervisor: Dr. Alizee Meillere; alizee.meillere@deakin.edu.au
Start date: Semester 2 2019 preferred
Project description:
Today, organisms face dramatic human-induced environmental change, that is likely to be a major factor in
shaping their future. Noise pollution, in particular, has recently received considerable attention, because of
increasing evidence that high noise levels can have major impacts on humans and wildlife; and birds especially.
However, while the effects of noise exposure on adult individuals have been widely studied, little is known
about the effects on developing birds (either as embryos or nestlings). Interestingly, our research group
recently showed that zebra finch embryos are sensitive to "natural" acoustic signals (parental incubation calls)
prior to hatching and that this can affect nestling post-hatch development (Mariette and Buchanan, 2016,
Science). We now seek to assess whether avian embryos are acoustically sensitive to noise pollution. We are
offering an Honours placement for a highly motivated student to investigate the effects of prenatal
anthropogenic noise exposure on offspring development in our colony of captive zebra finches. This project
will be mostly based in the animal house on the Waurn Ponds campus and involve bird handling, bioacoustics
playbacks, morphological and physiological measurements, behavioral observations, and data analyses. Whilst
a July start date is preferable to fit into the natural timing of the breeding season, a February start date may be
possible. The student must be based in Geelong.
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Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Associate Professor Kate Buchanan
Project Title: Mitochondrial function and birds: the effects of the early developmental environment on cellular
metabolism and behaviour
Principle Supervisor: Prof. Kate Buchanan
Principal Supervisor contact details: kate.buchanan@deakin.edu.au
Associate Supervisor: Dr. Ondi Crino; ondi.crino@deakin.edu.au
Start date: Semester 2 2019 preferred.
Project Description:
The environment animals are exposed to during development can have profound effects on their physiology
and behaviour. These effects can be maintained across an animal’s lifetime and, in this way, the
developmental environment can have long-lasting and potent consequences for animals. Although
developmental effects have been widely study, almost no studies to date have examined the cellular
mechanisms that promote such effects. We are currently investigating the effects of the developmental
environment on mitochondrial function in birds. Mitochondria are known as the ‘powerhouses’ of cells
because they produce the majority of energy animals need to function. We have shown that the
developmental environment can have sustained effects on mitochondrial efficiency across an animal’s lifetime.
We are seeking a student to examine the effects of developmental stress (elevated temperature) on
mitochondrial function and behaviour in captive zebra finches. The student will assist with breeding birds,
measuring mitochondrial function in the laboratory, and conducting behavioural assays. Whilst a July start
date is preferable to fit into the natural timing of the breeding season, a February start date may be possible.
The student must be based in Geelong.
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Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Dr Egan Doeven
Project Title: Customised resins for 3D Printing
Principal Supervisor: Dr Egan Doeven
Principal Supervisor contact details: egan.doeven@deakin.edu.au; Geelong Waurn Ponds campus; Room
number kc2.015
Associate Supervisors: Prof. Rosanne Guijt
Start date: Semester 1 2019 or Semester 2 2019
Project description:
3D printing is a disruptive technology, which has changed manufacturing by allowing for a high level of
customisation at little or no extra cost. It is popular in rapid prototyping, but also gaining popularity as stand-
alone manufacturing technique. From the different 3D printing approaches that are available, digital light
projection (DLP) allows for the highest resolution (finest detail) for acceptable build space. The bottleneck for
more widespread use of 3D printing for the fabrication/prototyping of microchemical systems in general, and
for DLP in particular, is the limited availability of materials with different physical/chemical properties. The aim
of this project is to use porogens for making porous structures, which can be used as integrated filters or
membranes. The research will be involve the evaluation of a range of porogens with commercially available
and home-made resins, and the use of the membrane in a simple analytical assay.
12 | P a g eSchool of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Dr Annalisa Durdle
Project 1
Project Title: Fly artefacts in a forensic context
Principal Supervisor: Annalisa Durdle
Principal Supervisor contact details: a.durdle@deakin.edu.au
Associate or External Supervisors and their contact details: TBA
Start date: Semester 1 2019 or Semester 2 2019
Project description:
Fly artefacts (their vomit and faeces) have been shown to be morphologically very similar to bloodstains
generated by blunt force trauma. It is also possible to extract human DNA from these artefacts if the fly has
been feeding on human biological materials. This project will explore variables around fly artefacts in a
forensic context, including distinguishing fly artefacts from human biological material, flies’ feeding behaviour
in relation to various biological materials, and retrieving human DNA from all life stages of the fly.
Project 2
Project Title: Impact of presumptive testing on collection of trace DNA from evidentiary items
Principal Supervisor: Annalisa Durdle
Principal Supervisor contact details: a.durdle@deakin.edu.au
Associate or External Supervisors and their contact details: Roland van Oorschot, Victoria Police
Start date: Semester 1 2019 or Semester 2 2019
Project description:
Presumptive tests are often used on items of evidence to screen for substances that may be biological in
origin. In performing these tests, valuable trace DNA evidence may be lost. This project will quantify the
amount of trace DNA lost and devise procedures to minimise any loss.
Project 3
Project Title: Transfer of microbiomes in a forensic context
Principal Supervisor: Annalisa Durdle
Principal Supervisor contact details: a.durdle@deakin.edu.au
Associate or External Supervisors and their contact details: Roland van Oorschot, Victoria Police
Start date: Semester 1 2019 or Semester 2 2019
Project description:
An emerging discipline in forensic science is that of microbial forensics, and how the human microbiome might
be used to solve crime. The microbiome is the collective DNA of the community of microbes which are present
both internally and externally on a person. Research has shown this community to be unique to an individual,
being able to link them to items and locations. This project will investigate the transfer of microbiomes in a
forensic context.
13 | P a g eSchool of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Professor John Endler
Project 1
Project Title: How does motion and colour interact when guppies track different moving coloured objects and
how does this relate to mating coloration?
Principal Supervisor: John A. Endler
Principal Supervisor contact details: John.Endler@deakin.edu.au , 0488 255 712
Start date: Semester 1 2019 or Semester 2 2019
Project description:
Guppies (Poecilia reticulata) are small freshwater fishes native to clear streams in South America and are feral
in northern Queensland. Males have complex colour patterns with a high diversity of colours which they use to
encourage females to mate. Guppies have far better colour vision than humans, fully as good as birds; they not
only can see UV but their photoreceptors are evenly spaced, so even ignoring UV they can see more colours than
we can. This project involves using a computer programme written by Prof. Endler to generate and move
coloured stimuli. It also involves using a spectrometer to measure the intensity and colour spectrum of the
stimuli. You will investigate the effect of the movement velocity (speed) of the stimuli on the tendency of
guppies to chase the coloured spot. You will be testing the proposed trade-off between motion and colour
detection/perception. There is some evidence that the LWS (long-wavelength-sensitive) cones are responsible
for motion detection. A previous trial of this apparatus showed most sensitivity in the long-wavelength (yellow,
orange and red) colours indicating predominant effects of the LWS cones, so the previous speeds were probably
too high. Consequently you will try much slower spot speeds. This has major implications for the mechanics
and efficiency of the moving coloured displays of male guppies towards females.
Learning outcomes of this project:
1. Discipline-specific knowledge and capabilities. This includes reading the literature, training in experimental
design, quantitative data collection and analysis, and making valid and reasonable conclusions from
results.
2. General: Training in animal research ethics, research integrity, and both quantitative and statistical
methods.
3. Communication. Training in both written and oral skills of communicating science effectively clearly, and
honestly.
4. Digital literacy: Learning how to search the literature online and use computers to collect, collate, and
analyse data.
5. Critical thinking: Learning how to interpret the literature and one’s own results; learning how to be
logical and careful in thinking.
6. Problem solving: Learning how to solve problems as they occur; problems occur in any endeavour.
7. Self-management: Learning how to manage time, work quality and work quantity for maximum efficiency
and best possible results, without being late or superficial.
14 | P a g eSchool of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Project 2
Project Title: Do male guppies choose the best light in which to court females?
Principal Supervisor: John A. Endler
Principal Supervisor contact details: John.Endler@deakin.edu.au , 0488 255 712
Start date: Semester 1 2019 or Semester 2 2019
Project description:
Guppies (Poecilia reticulata) are small freshwater fishes native to clear streams in South America and are feral
in northern Queensland. Males have complex colour patterns with a high diversity of colours which they use to
encourage females to mate. Guppies have far better colour vision than humans, fully as good as birds; they not
only can see UV but their photoreceptors are evenly spaced, so even ignoring UV they can see more colours than
we can. There is a significant interaction between the differently coloured patches in male guppies and the light
environment and we have shown by a long term evolution experiment that different colours appear differently
in different light environments and that different colours increase or decrease in size according to the light
environment over many generations in our laboratory. The question is, do male guppies with different kinds of
colour patterns, choose locations with different light environments so that they maximize their conspicuousness
and/or attractiveness to females? You will be testing this with guppies in wading pools with suspended different
colour filters in 4 sectors.
Learning outcomes of this project:
1. Discipline-specific knowledge and capabilities. This includes reading the literature, training in experimental
design, quantitative data collection and analysis, and making valid and reasonable conclusions from results.
2. General: Training in animal research ethics, research integrity, and both quantitative and statistical methods.
3. Communication. Training in both written and oral skills of communicating science effectively clearly, and
honestly.
4. Digital literacy: Learning how to search the literature online and use computers to collect, collate, and
analyse data.
5. Critical thinking: Learning how to interpret the literature and one’s own results; learning how to be logical
and careful in thinking.
6. Problem solving: Learning how to solve problems as they occur; problems occur in any endeavour.
7. Self-management: Learning how to manage time, work quality and work quantity for maximum efficiency
and best possible results, without being late or superficial.
15 | P a g eSchool of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Project 3
Project Title: Does male guppy courtship movement relate to the elongation of their coloured spots?
Principal Supervisor: John A. Endler
Principal Supervisor contact details: John.Endler@deakin.edu.au , 0488 255 712
Start date: Semester 1 2019 or Semester 2 2019
Project description:
Guppies (Poecilia reticulata) are small freshwater fishes native to clear streams in South America and are feral
in northern Queensland. Males have complex colour patterns with a high diversity of colours which they use to
encourage females to mate. Guppies have far better colour vision than humans, fully as good as birds; they not
only can see UV but their photoreceptors are evenly spaced, so even ignoring UV they can see more colours than
we can. Their sexual display consists of movements in the vertical axis and foraging occurs more along their
body axis, and many spots are elongated horizontally. You will be quantifying motion-blur to investigate the
hypothesis that guppies with less elongated spots may show different kinds of courtship motion than those with
elongated spots.
Learning outcomes of this project:
1. Discipline-specific knowledge and capabilities. This includes reading the literature, training in
experimental design, quantitative data collection and analysis, and making valid and reasonable conclusions
from results.
2. General: Training in animal research ethics, research integrity, and both quantitative and statistical
methods.
3. Communication. Training in both written and oral skills of communicating science effectively clearly,
and honestly.
4. Digital literacy: Learning how to search the literature online and use computers to collect, collate, and
analyse data.
5. Critical thinking: Learning how to interpret the literature and one’s own results; learning how to be
logical and careful in thinking.
6. Problem solving: Learning how to solve problems as they occur; problems occur in any endeavour.
7. Self-management: Learning how to manage time, work quality and work quantity for maximum
efficiency and best possible results, without being late or superficial.
16 | P a g eSchool of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Project 4
Project Title: What are the costs of courtship and does this affect display strategy?
Principal Supervisor: Prof. John A. Endler
Principal Supervisor contact details: John.Endler@deakin.edu.au
Start date: Semester 1 2019 or Semester 2 2019
Project description:
It is commonly thought that courting signals are unlikely to be used unless there is a significant cost to producing
the signals, but this has not been tested except on a very superficial level. Male guppies perform what appears
to be an energetically costly sigmoid display when courting females. By means of a high-speed camera (2000
frames per second) we will record the video displays, quantify the 3D movement during sigmoid displays and
alternative ('sneaky') forms of courtship, estimate the energy required to move rapidly during the displays, and
use this to predict the outcome of displays varying in intensity and estimated energy expenditure. This will give
an estimate of effort and mating return per unit effort as a function of alternative male mating strategies. There
are many other potential ways to analyse this data and other questions which could be asked with motion data.
Experience and confidence in computing and geometry highly recommended.
Learning outcomes of this project:
1. Discipline-specific knowledge and capabilities. This includes reading the literature, training in
experimental design, quantitative data collection and analysis, and making valid and reasonable
conclusions from results.
2. General: Training in animal research ethics, research integrity, and both quantitative and statistical
methods.
3. Communication. Training in both written and oral skills of communicating science effectively clearly, and
honestly.
4. Digital literacy: Learning how to search the literature online and use computers to collect, collate, and
analyse data.
5. Critical thinking: Learning how to interpret the literature and one’s own results; learning how to be
logical and careful in thinking.
6. Problem solving: Learning how to solve problems as they occur; problems occur in any endeavour.
7. Self-management: Learning how to manage time, work quality and work quantity for maximum efficiency
and best possible results, without being late or superficial.
17 | P a g eSchool of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Project 5
Project Title: Can we identify plant geometry or colour cues to bower site selection in Great Bowerbirds?
Principal Supervisor: John A. Endler
Principal Supervisor contact details: John.Endler@deakin.edu.au , 0488 255 712
Start date: Semester 1 2019 or Semester 2 2019
Project description:
Male bowerbirds construct a structure and platform collectively known as a bower, and this is used by males
only for attracting females to mate; females nest separately on their own. Great Bowerbirds place their bower
under a shrub, but we do not understand why they choose particular shrubs. I now have very detailed (1cm
resolution!) aerial photographs of a large study area which are GPS marked, as well as the GPS locations of more
than 50 bowers. This project entails relating each bower to its aerial photograph and looking to see if there are
common shapes or shrub arrangements in photographs with bowers compared to those with no bowers. A
student who is advanced in statistics could also try running discriminant function analysis on the RGB values in
the photos to use this or other multivariate techniques to address this problem. This is for a student who is
reasonably confident with quantitative methods
Learning outcomes of this project:
1. Discipline-specific knowledge and capabilities. This includes reading the literature, training in
experimental design, quantitative data collection and analysis, and making valid and reasonable
conclusions from results.
2. General: Training in animal research ethics, research integrity, and both quantitative and statistical
methods.
3. Communication. Training in both written and oral skills of communicating science effectively clearly, and
honestly.
4. Digital literacy: Learning how to search the literature online and use computers to collect, collate, and
analyse data.
5. Critical thinking: Learning how to interpret the literature and one’s own results; learning how to be
logical and careful in thinking.
6. Problem solving: Learning how to solve problems as they occur; problems occur in any endeavour.
7. Self-management: Learning how to manage time, work quality and work quantity for maximum efficiency
and best possible results, without being late or superficial.
18 | P a g eSchool of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Project 6
Project Title: Project jointly designed with Prof. Endler and yourself
Principal Supervisor: John A. Endler
Principal Supervisor contact details: John.Endler@deakin.edu.au , 0488 255 712
Start date: Semester 1 2019 or Semester 2 2019
Project description:
You are encouraged to come into Prof. Endler's office and discuss projects which you would like to do but which
are not in the booklet, or are possible offshoots of the projects. We would discuss the purpose and mechanics
of the project and it will be designed to be practical and satisfactory in the time permitted. You will test explicit
hypotheses and/or questions what we determine in advance once the project questions are determined. This
is in fact how it is regularly done in other universities and gives you more flexibility. However, it does mean that
you have to discuss the project in detail and get it approved by him long before the start date to ensure that it
can be done on time.
Learning outcomes of this project:
1. Discipline-specific knowledge and capabilities. This includes reading the literature, training in experimental
design, quantitative data collection and analysis, and making valid and reasonable conclusions from results.
2. General: Training in animal research ethics, research integrity, and both quantitative and statistical methods.
3. Communication: Training in both written and oral skills of communicating science effectively clearly, and
honestly.
4. Digital literacy: Learning how to search the literature online and use computers to collect, collate, and analyse
data.
5. Critical thinking: Learning how to interpret the literature and one’s own results; learning how to be logical
and careful in thinking.
6. Problem solving: Learning how to solve problems as they occur; problems occur in any endeavour.
7. Self-management: Learning how to manage time, work quality and work quantity for maximum efficiency and
best possible results, without being late or superficial.
19 | P a g eSchool of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Dr David Francis
Project 1
Project Title: Seasonal trends in the nutritional composition of farmed Atlantic salmon
Principal Supervisor: Dr David Francis
Principal Supervisor contact details: e: d.francis@deakin.edu.au ; t: 5563 3083
Associate Supervisor and their contact details: Prof Giovanni Turchini, t: 5563 3312,
e: giovanni.turchini@deakin.edu.au
Start date: Semester 1 2019 or Semester 2 2019
Project location: Queenscliff Marine Station
Project description:
The farming of Atlantic salmon in Tasmania has significant economic benefits for the nation. This industry
currently generates ~$550 million per year and employs thousands of Australian’s either directly and indirectly.
However, large seasonal fluctuations in water temperature, coupled with a host of adverse water quality
parameters are dramatically affecting the prosperity of industry operations. Little is currently known in relation
to the effects that these fluctuations have on the nutritional quality of farmed salmon, potentially jeopardising
fish health, product quality and subsequent consumer perception.
This honours project will characterise the seasonal nutritional trends of farm salmon. In particular, the project
will place an emphasis on lipid class composition in relation to fluctuating environmental conditions to evaluate
the mobilisation of lipids in response to periods of stress.
Project 2
Project Title: Larval crustacean nutrition – Explorations for new aquaculture candidates
Principal Supervisor: Dr David Francis
Principal Supervisor contact details: e: d.francis@deakin.edu.au ; t: 5563 3083
Associate Supervisor and their contact details: Prof Giovanni Turchini, t: 5563 3312,
e: giovanni.turchini@deakin.edu.au
Start date: Semester 1 2019 or Semester 2 2019
Project location: Queenscliff Marine Station
Project description:
The complex larval life cycle of many bivalve species has severely limited their suitability for commercial
aquaculture. This has not resulted in any reductions in their wild harvest, and as such, many species are being
fished beyond sustainable limits. However, recent technological developments have resulted in unprecedented
advancements in the culture of several significant species with full life cycle closure and reduced co-dependence
on wild fisheries now a reality. Many of these advancements have been made possible via breakthroughs in
nutritional science, with a series of novel dietary formulations that permit the provision of a broad range of
nutrients now available.
This honours project will investigate the suitability of a bivalve species yet to be domesticated for aquaculture.
In particular, we will perform a series assessments relating to its larval life cycle in response to feed sources and
assess characteristics relating to larval progression. The successful realisation of this project will require sound
husbandry skills and a thorough comprehension of related laboratory techniques such as chemical proximate
analysis, fatty acid analysis and digestibility measurement.
20 | P a g eSchool of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Project 3
Project Title: Investigating pigment deposition in farmed fish species and associated feed ingredients
Principal Supervisor: Dr David Francis
Principal Supervisor contact details: e: d.francis@deakin.edu.au ; t: 5563 3083
Associate Supervisor and their contact details: Prof Giovanni Turchini, t: 5563 3312,
e: giovanni.turchini@deakin.edu.au
Start date: Semester 1 2019 or Semester 2 2019
Project location: Queenscliff Marine Station
Project description:
Next to product freshness, pigmentation level represents the most important visual quality criteria for market
acceptance of farmed fish products. In aquaculture, this is dictated entirely via the dietary provision of a pigment
called astaxanthin. As dietary supplements, pigments play many important physiological roles, and in particular,
are well recognised for their antioxidant activities that have been demonstrated to assist in the protection of
cells during adverse environmental periods.
This honours project will assess factors affecting pigment deposition in farmed fish species. It will be largely
analytical in its execution and will aim to establish a series of laboratory protocols for the measurement of fish
tissue pigmentation using High Performance Liquid Chromatography. The successful realisation of this project
will require strong analytical skills and would be best suited to a student with a strong background in chemistry.
21 | P a g eSchool of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Professor Paul Francis
Project 1
Project Title: Multi-coloured Electrogenerated Chemiluminescence (ECL)
Principal Supervisor: Prof. Paul Francis
Principal Supervisor contact details: psf@deakin.edu.au ; Geelong Waurn Ponds campus; Room number
ka5.127
Associate Supervisors: Dr Egan Doeven (CeRRF); Prof. Rosanne Guijt (CeRRF)
Start date: Semester 1 2019 or Semester 2 2019
Project description:
This proposal explores a new approach to chemical detection, in which molecules that emit different coloured
light can be selectively switched-on or switched-off by applying different electrochemical potentials. This
enables unprecedented numbers of simultaneous (multiplexed) detection events for time-critical analytical
applications such as clinical diagnostics. To date, proof-of-concept demonstrations of this multi-coloured
electrogenerated chemiluminescence (ECL) have been limited to only mixtures of 2 or 3 metal complexes in
non-aqueous solvents and not coupled to bioassays. This project marks the next conceptual leap in
multiplexed ECL systems, creating a suite of highly efficient, water-soluble complexes that exploit the full
scope of ECL detection.
Within this large area of research, an honours project can be tailored to provide skills and expertise in areas
such as analytical chemistry, synthetic chemistry, electrochemistry, luminescence spectroscopy and/or clinical
bioassays. (Figure: Doeven, et al., “Red-green-blue electrogenerated chemiluminescence utilizing a digital
camera as detector”, Analytical Chemistry, 86 (2014) 2727).
22 | P a g eSchool of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Project 2
Project Title: New Approaches to Assess Cellular Oxidative Stress and its Links with Disease
Principal Supervisor: Prof. Paul Francis
Principal Supervisor contact details: psf@deakin.edu.au ; Geelong Waurn Ponds campus; Room number
ka5.127
Associate Supervisors: Dr Zoe Smith (LES) and Dr Olivia Dean (School of Medicine)
Start date: Semester 1 2019 or Semester 2 2019
Project description:
This project involves the development of new analytical approaches to assess oxidative stress in biological
samples, based on high performance liquid chromatography (HPLC) with a variety of conventional and novel
modes of detection, including UV absorbance, electrochemistry, mass spectrometry and chemiluminescence.
There is rapidly growing interest in the measurement of thiols and disulfides in human cells, as researchers gain
new insight into their role in a variety of diseases. Particular attention has been paid to glutathione (GSH) and
glutathione disulfide (GSSG). Oxidation of GSH to GSSG is among the earliest responses to increases in reactive
oxygen species in human cells, and therefore assessment of the GSH/GSSG ratio offers great potential for
diagnosing and monitoring pathological and physiological conditions related to oxidative stress. The analytical
methods developed and optimized in this project will be used to determine GSH and GSSG levels in clinical
samples, including those obtained from current clinical trials that are exploring the effects of new medications
for the treatment of disease.
Through this, the student will obtain an excellent understanding and practical expertise in analytical chemistry,
with particular focus on clinical sample preparation, liquid chromatography, and data analysis and
interpretation. (Figure from: McDermott, et al., Analytical Chemistry, 83 (2011) 6034).
23 | P a g eSchool of Life and Environmental Sciences
Honours 2019 Information Booklet – Geelong Waurn Ponds Campus
Project 3
Project Title: Chemiluminescence Reagents for the Detection of Biomolecules and Controlled Drugs
Principal Supervisor: Prof. Paul Francis
Principal Supervisor contact details: psf@deakin.edu.au ; Geelong Waurn Ponds campus; Room number
ka5.127
Associate Supervisors: Dr Zoe Smith and Dr Jacqui Adcock
Start date: Semester 1 2019 or Semester 2 2019
Project description:
A small group of chemiluminescence reagents have been used to detect many compounds of clinical and forensic
science importance at exceedingly low concentrations. Even subtle modifications of these reagents, such as
changing the ligands on the widely used ruthenium complex, Ru(bipy) 3 2+, can have a dramatic effect on reagent
properties. Research at Deakin University has extended this approach to iridium and osmium complexes, which
enable a much wider range of emission colours and greater sensitivity towards certain target analytes (e.g.
heroin and related opiate alkaloids, piperazine designer drugs, fluoroquinolone antibiotics, and synthetic
cannabinoids). This project can have both synthetic and analytical chemistry components (or can focus on one
aspect). The student will prepare new chemiluminescence reagents and evaluate their properties using a wide
range of analytical techniques, including the exploration of their light producing reactions with various
biomolecules, pharmaceuticals and controlled drugs. In addition, the electrochemiluminescence (ECL)
properties of the complexes will be studied to evaluate their potential for clinical diagnostic applications.
Project 4
Project Title: Photoredox Catalysis for Highly Controlled Chemical Synthesis
Principal Supervisor: Prof. Paul Francis
Principal Supervisor contact details: psf@deakin.edu.au ; Geelong Waurn Ponds campus; Room number
ka5.127
Associate Supervisors: A/Prof. Luke Henderson (IFM); Dr David Hayne (LES/IFM)
Start date: Semester 1 2019 or Semester 2 2019
Project description:
The growing awareness of the environmental impact of many traditional chemical processes by scientists,
authorities and the general public has spurred extensive research into more responsible ‘green’ chemistry. In
synthetic chemistry, the use of ‘photo-active’ metal-complexes such as tris(2,2′-bipyridine)ruthenium(II) and
tris(2-phenylpyridine)iridium(III) has enabled various important chemical transformations to be powered by the
energy of visible light, instead of noxious and/or expensive chemical reagents. This project explores new
approaches to photoredox catalysis that will provide extraordinary control of chemical transformations. We will
examine the activity of the photocatalysts and mechanism of the chemical transformations using high-
performance liquid chromatography (HPLC), nuclear magnetic resonance (NMR), and luminescence
spectroscopy. The new understanding of these processes will then be exploited to develop various novel
synthetic procedures. Please talk to one of the supervisor team for the specific details of the reactions involved
in this project.
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