Science Honours Projects - 2021
CRICOS Provider No. 00103D Contents
Bachelor of Science Honours……………………. 2
How to apply for Honours…………………….…... 3
Biomedical Science………………………….…….. 4
Environmental Science……………………………. 8
Mathematical Science…………………………….. 14
Food Science…………………………...... 15
Veterinary and Wildlife Science…………………. 16
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 1 Bachelor of Science Honours
Students who excel in their undergraduate degree are eligible to apply for entry into the Bachelor of Science Honours program. Honours is an intensive research-based program requiring an extra year of full- time study (or 18 months part-time study) on top of your undergraduate degree.
What is Honours? The Bachelor of Science Honours program (SZ8) is an additional fourth year of Undergraduate studies, completed over 9 months full-time (FT), or 18 months part-time (PT). The main objective of the program is to train students as professional research scientists. Honours students engage in an individual research project under the close supervision of an academic staff member with relevant expertise in their chosen field. Students also complete theoretical coursework designed to complement their research and develop key skills in communication, critical analysis and project management, equipping them for independent research roles in the workplace or for entry into postgraduate research programs. For more program information, see Honours course outline and Honours courses and assessment.
Why complete an Honours year? For some students completing honours is the first step towards building an academic research career and pursuing post graduate study. However, completing an Honours year also offers many benefits to those looking to boost their marketability in an increasingly competitive job market. Honours gives you the opportunity to: • Get experience in real scientific research • Extend your knowledge in a specialist field of interest • Contribute new knowledge to your field (with possibility of publication) • Develop workplace skills attractive to employers • Use advanced techniques and equipment and broaden your technical skill set
Honours can be challenging, with a level of independence expected of students representing a significant change from previous undergraduate courses. However, most students find that their Honours year is an extremely rewarding experience.
School of Science, Psychology and Sport Honours Research projects are available in the following discipline areas, as listed in this Information Booklet: • Biomedical Science • Environmental Science • Mathematical Science • Food Science • Veterinary and Wildlife Science
For more information on the Bachelor of Science Honours Program, contact the Science Honours course coordinator at your campus:
Mt Helen Campus Gippsland Campus Dr Morgan Wallace Dr Phill Brook -Carter [email protected] [email protected] +61 3 5327 9939 +61 3 5122 6783
Berwick Campus Dr Rob Bischof [email protected] +61 3 4313 7930
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 2 How to apply for Honours
Qualification for the Honours program requires studentso t have a GPA>6.0 (or equivalent) in a relevant undergraduate degree, and the support of an academic supervisor. In addition to completing an Online Application for entry to the Bachelor of Science (Honours) programs, students will need to submit a completed Research Proposal Form, outlining their intended research project which is also signed by their chosen supervisor(s).
Step 1 Find a Project and Supervisor An Honours information session will be held as a webinar in Semester 2, which will provide you with an introduction to the Bachelor of Science Honours program and the scope of research projects available to students in 2021. You can also contact academic staff working in areas that interest you directly and ask them if they would consider supervising you. This Information Booklet contains a listing of Research projects suitable for Honours students in 2021. Note that this is not a complete list of available projects for 2021, so students are encouraged to contact academic staff that they are interested in working with at the School of Science, Psychology and Sport to discuss possible Honours projects. It is a good idea to talk to a number of prospective supervisors to assess whether their research focus aligns with your interests and whether you feel you could work well with their research group. If possible, talk to other students in the group or past students who have worked with them as well. Some questions to help you refine what you want to work on • What aspects of your undergraduate degree have you found most interesting? • Which courses did you enjoy the most? • What topics or issues did you wish you could have studied in more depth? • Which academic staff had a teaching style that you liked in undergraduate courses? • Which academic staff are working in areas that interest you?
Step 2: Apply for Honours FedUni students can complete an Online Application for entry into the honours program (SZ8). You will also need to submit a completed Research Proposal Form signed by your prospective supervisor. Students wanting to enrol in Honours at FedUni, who completed their undergraduate degree elsewhere should contact the relevant Science Honours Program Coordinator to discuss eligibility requirements.
Step 3: Accept your offer If you are offered a place in the honours program you need to formally accept your offer in writing. You should also get in touch with your supervisor to discuss any additional requirements (eg ethics approvals, laboratory safety training) for your project prior to starting your research work. Semester 1 intake typically starts at the beginning of February, Semester 2 intake starts at the beginning of August. Additional discipline-based information sessions may also be run, dates and details to be advised by email to eligible students.
School of Science, Psychology and Sport Honours Scholarships The School of Science, Psychology and Sport is offering 5 Honours Scholarships ($3,000 each) to be awarded to applicants entering Honours in 2021. Applications will be assessed on the applicant’s academic performance within their undergraduate degree. For further information, contact the Science Honours course coordinator at your campus.
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 3 Biomedical Science
Characterising immune changes in specific The Y chromosome microRNA - a new paradigm of disease settings coronary artery disease in men
Location: Mt Helen Campus Location: Mt Helen Campus Project Leaders: Prof Stuart Berzins, Dr Morgan Wallace Project Leaders: Prof Fadi Charchar, Prof Stephen Harrop Email: [email protected], (University of Melbourne) [email protected] Email: [email protected] Phone: (03) 5334 4963 (Prof Berzins) Phone: (03) 5327 6098 (03) 5327 9939 (Dr Wallace) Project description: There is a well-known “male Project description: Comparing blood from patients with that disadvantage” in heart disease – men develop and die of it of healthy people can reveal immune changes associated with more frequently than women. The cause of this disparity is still disease progression. This not clear and is not explained by many traditional risk factors type of characterisation is such as diet. We have shown in a recent that the male sex Y being considered for chromosome is associated with increased risk of heart disease. patients with blood cancers The current proposed project will utilise molecular techniques such as multiple myeloma, to measure the expression of Y genes in patients with CAD. respiratory diseases such This may improve our understanding of why men are more as asthma, and for patients prone to heart disease and could help to develop sex-specific with virus infections. This methods for prevention and treatment of heart disease in the approach provides useful future. insights into normal immune Key words: genetics, human disease function and may identify novel prognostic markers that can be used to improve diagnosis and assist with the selection of appropriate treatment strategies for patients. Key words: immunology, T cells, immune responses, cancer, Using RNA-Seq to determine the long-non coding viruses RNA profile of hypertensive human kidneys
Location: Mt Helen Campus Project Leaders: Prof Fadi Charchar, Characterising the function of innate-like T cells Dr Maciej Tomaszewski (University of Manchester, UK) Location: Mt Helen Campus Email: [email protected] Project Leaders: Prof Stuart Berzins, Dr Morgan Wallace Phone: (03) 5327 6098 Email: [email protected], [email protected] Project description: Hypertension is the number one risk Phone: (03) 5334 4963 (Prof Berzins) factor for many cardiovascular diseases. It is not clear which (03) 5327 9939 (Dr Wallace) genes and transcripts are association with increased risk of hypertension. Our hypothesis is that non-coding RNA or/and Project description: We are interested in studying the the aberrant expression of long-non coding RNA (exciting new response of innate like T cells to different forms of stimulation RNA molecules previously thought of as JUNK RNA) may be to better understand how they function in different disease one of the drivers. We will be using next generation sequencing settings. This project will stimulate T cells isolated from human and a range of cutting-edge technologies to determine which blood and tissues and analyse their gene expression, long non-coding RNA are expressed on the human Kidney. proliferation and cytokine production responses to determine Key words: genetics, human disease how they influence immune responses. Key words: immunology, T cells, immune responses, cancer, viruses Self-assembling peptides as building blocks for 3D printable hydrogels
Understanding how innate like T cells are activated Location: Mt Helen Campus Project Leader: Dr Benjamin Long Location: Mt Helen Campus Email: [email protected] Project Leaders: Prof Stuart Berzins, Dr Morgan Wallace Phone: (03) 5327 9452 Email: [email protected], [email protected] Project description: Short self-assembling peptides have Phone: (03) 5334 4963 (Prof Berzins) been shown to be useful building blocks for self-assembled (03) 5327 9939 (Dr Wallace) hydrogels. This project aims to make enzymatically and spontaneously cross-linkable peptides for 3D printing hydrogel Project description: T cells need to interact with antigen implants that mimic the extracellular matrix. These hydrogels presenting cells to become activated. This project aims to can be tuned for anticancer properties, stroke rehabilitation and identify novel cancer antigens that are capable of activating neuron growth promotion. In this project you will become innate like T cells. Understanding what antigens are being familiar with solid phase peptide synthesis, organic synthesis recognised in the cancer environment and the signalling that and a range of chemical characterisation techniques (IR, UV takes place between APCs and T cells may allow us to develop and NMR Spectroscopy; HPLC-MS; Small Angle X-ray therapies to either promote or suppress immune responses. Scattering) Key words: immunology, T cells, immune responses, cancer, Key words: hydrogels, peptides viruses
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 4 Biomedical Science (continued)
The role of zinc in cell signalling Treatment of atherosclerosis after renal denervation in mice Location: Mt Helen Campus Project Leaders: A/Prof Mark Myers, Dr Scott Nankervis Location: Mt Helen Campus Email: [email protected] Project Leader: Dr Yutang Wang Phone: (03) 5327 9291 Email: [email protected] Phone: (03) 5327 9394 Project description: Insulin resistance in muscle, liver and fat tissues is an underlying cause of diabetes. While calcium ions Project description: Hypertension is a major risk factor for have long been recognized as second messengers in cells, a cardiovascular diseases, and decreasing blood pressure can similar role for zinc has only recently emerged. Dysfunctional save lives. Disconnecting the nerves in the kidney (renal zinc signalling has been associated with important diseases denervation) has shown to low pressure in humans. However, including diabetes, obesity, cardiovascular disease and renal denervation may also increase atherosclerosis, a disease cancer. Our previous studies have shown that insulin causes a associated with inflammation. This project, funded by an transient increase in the concentration of free zinc ions in NHMRC project grant, will investigate whether inhibition of muscle cells. Understanding how this occurs may reveal new inflammation by atorvastatin and aspirin decreases ways of treating diabetes. The project will use genetic atherosclerosis after renal denervation in mice. This project manipulation of the expression of genes involved in zinc control involves surgery in mice, blood pressure measurement, and confocal microscopy imaging of live cells and intracellular histology, immunohistochemistry and biochemical analysis. zinc sensors to work out how zinc signalling is controlled. Techniques will include cell biology, advanced live cell Key words: atherosclerosis, heart hypertrophy, abdominal microscopy, cell transfection to manipulate gene expression, aortic aneurysm, cholesterol efflux and qPCR. Key words: zinc, diabetes, human disease The effect of antihypertensive drugs on cholesterol efflux
Location: Mt Helen Campus Project Leader: Dr Yutang Wang Email: [email protected] Phone: (03) 5327 9394
Project description: Atherosclerosis is the major underlying mechanism for stroke and heart attack. Treatment of atherosclerosis can protect us from these diseases. Atherosclerosis is characterised by the build-up of cholesterol in the arteries. However, most research on atherosclerosis Novel pancreatic micro-peptides encoded by small focuses on inflammation. One under-investigated area for open reading frames (sORFs) in “non-coding” RNA atherosclerosis is the imbalance of cholesterol in the arteries. This project will investigate the effect of several antihypertensive drugs, which can inhibit atherosclerosis, on Location: Mt Helen Campus cholesterol efflux from aortic smooth muscle cells. The Project Leaders: A/Prof Mark Myers, Dr Scott Nankervis techniques involved include cell culture, confocal microscopy, Email: [email protected] biochemical analysis, and quantitative-PCR. Phone: (03) 5327 9291 Key words: atherosclerosis, hypertension, cholesterol efflux Project description: The pancreatic islets of Langerhans produce many important regulatory peptides including insulin and glucagon and numerous other peptides that also modulate metabolic control. Over recent years there has been an Functionalised peptides for the detection of explosion in the study of non-coding RNA e.g. long non-coding pyrophosphate in biological samples RNA or lncRNA and this is uncovering a whole new level of genomic regulation. More recently it has become clear that a Location: Mt Helen/Gippsland Campus small proportion of lncRNA actually does encode small Project Leader: Dr Benjamin Long, Dr David Smith proteins, or micro-peptides, which also have biological Email: [email protected] importance. We have discovered a lncRNA expressed in a Phone: (03) 5327 9452 pancreatic islet cell line that potentially encodes a peptide that modulates insulin activity. The project will use bioinformatics Project description: Solid phase peptide synthesis allows for and molecular biology to characterise lncRNA and proteomics rapid prototyping of molecules for the binding and detection of to identify encoded micropeptides. Techniques will include pyrophosphate. The detection of pyrophosphate could allow for PCR, cDNA sequencing, cell transfection, and liquid rapid diagnosis of diseases such as pseudogout and chromatography and mass spectrometry to identify renal/vascular calcification; as well as being a potential probe micropeptides.. for cell viability. In this project you will become familiar with Key words: diabetes, micropeptides, human disease solid phase peptide synthesis, organic synthesis and a range of chemical characterisation techniques (IR, UV and NMR Spectroscopy; HPLC-MS). Key words: detection, host-guest chemistry, diagnostics, peptides
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 5 Biomedical Science (continued)
Transcriptomics study of Host Parasite Interactions DNA damage repair pathways and mutagenesis
Location: Gippsland Campus Location: Gippsland Campus Project Leader: Dr Phillip Brook-Carter Project Leader: Dr Gregory Davis Email: [email protected] Email: [email protected] Phone: (03) 5122 8054 Project description: The projects on offer will focus on the analysis of the interactions that take place between the Project description: DNA damage repair contributes to parasite Giardia Duodenalis and the host intestinal epithelial genomic stability in all eukaryotes. Due to this, the pathways cells in an attempt to further the understanding of the associated with DNA damage repair are highly conserved from mechanisms of parasitism that lead to giardiasis. Projects will yeast through to humans. While these are well characterised, focus on the generation and / or analysis of transcriptomic data the recruitment and maintenance of these repair mechanisms representing host cell responses to Giardia infection, as well is largely unknown. This project will use the multicellular model as the transcriptome of the parasite itself during parasitism. We organism, Caenorhabditis elegans, to explore key genes have already identified thousands of gene transcription required for repairing DNA damage and their contribution to changes in host cells during parasitism and we will explore this maintaining chromosomal integrity in early embryonic events. area more closely in individual projects. This project will involve several approaches including genetics, There are up to 2 projects available (upon discussion) that immunohistochemistry, cloning and fluorescence microscopy. would suit both molecular biologists and / or those with a desire Key words: DNA damage, genome, mutagenesis to utilise bioinformatics on complex data sets. Key words: Giardia, Transcriptomics, Bioinformatics
The role of an eosinophil-specific galectin (galectin-14) in allergic airway inflammation Germline specific small non-coding RNAs and epigenetic control Location: Berwick/Gippsland/Mt Helen Campus Project Leaders: Dr Rob Bischof, A/Prof David Piedrafita, Location: Gippsland Campus Dr Benjamin Long Project Leader: Dr Gregory Davis Email: [email protected]; Email: [email protected] [email protected]; Phone: (03) 5122 8054 [email protected] Phone: (03) 4313 7930 Project description: Small non-coding RNAs are short stretches of RNA which are associated with regulating gene Project description: Members of the galectin family have expression at the post-transcriptional level (e.g., microRNAs), been shown to mediate a variety of important cellular functions but also guard the genome against viruses, pseudogenes and including inflammation and immune responses through binding cryptic loci. This project will utilise the model organism and crosslinking with glycoproteins. Galectin-14 was identified Caenorhabditis elegans to explore how specific subgroups of in sheep and is elevated in the mucus of asthmatic airways, small RNAs contribute to the development of viable germ cells similar to its human homologue galectin-10. This project will that are free from genomic lesions, mutations, and insertions. focus on the role of galectin-14 in mucus thickening, which is This requires analysis of the mechanisms that control stem cell known to contribute to fatal asthma, and whether targeted quiescence through to the early stages of embryogenesis and galectin inhibition can alter the properties of this mucus. Using will apply a variety of techniques including genetics, a sheep model of allergic asthma, airway mucus samples will epigenetics (histone analysis), molecular biology and be collected and assessed for galectin-14 content and fluorescence microscopy. viscoelastic properties. In vitro experiments will examine the Key words: DNA damage, genome, RNA, reproduction function of galectin-14 in mucus viscosity and eosinophil degranulation. Techniques to be used will include Western blot, immunology and rheology. Outcomes of this work will provide further insights into potential therapeutic targets to treat allergic diseases. Key words: galectin-14, mucus viscosity, allergic airway disease
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 6 Biomedical Science (continued)
Characterisation of ACE2 expression in the lungs A sheep model of chronic obstructive pulmonary disease (COPD) Location: Berwick/Gippsland Campus Project Leaders: Dr Rob Bischof, A/Prof David Piedrafita Location: Berwick/Gippsland Campus Email: [email protected]; Project Leaders: Dr Rob Bischof, A/Prof David Piedrafita, [email protected] Dr Andrew Davies (Monash University) Phone: (03) 4313 7930 Email: [email protected]; [email protected] Project description: Angiotensin-converting enzyme 2 Phone: (03) 4313 7930 (ACE2) is the cellular receptor for the severe acute respiratory syndrome coronavirus SARS-CoV-2 (also known as COVID- Project description: Chronic obstructive pulmonary disease 19). The ACE2 receptor/protein is expressed in the upper and (COPD) is a chronic inflammatory disease of the airways. lower respiratory tract and Sheep have similar lung size and physiology to that of humans plays a critical role in and thus represent a suitable large animal preclinical model for covid-19 infection and respiratory studies. This project will provide the opportunity for transmission. With lungs a more ‘realistic’ large animal model that can be used to better similar to human lungs, understand how COPD develops and how we can effectively sheep are widely treat the disease with new therapies. Techniques will include recognised as a good whole-animal physiology and cell and tissue immune studies. translational model for Key words: COPD, translational model, sheep human respiratory diseases. This study will examine cellular localisation and tissue distribution of the ACE2 protein in the sheep respiratory tract, using molecular, biochemical and immunological techniques. This work may help to clarify potential targets for the development of more effective antiviral therapies against COVID-19. Key words: ACE2 receptor, COVID-19, sheep airways
Determining the age of infant gastrointestinal Functional and phenotypic characterisation of pathogen colonisation in Papua New Guinea airway macrophages Location: Berwick/Gippsland Campus Location: Berwick/Gippsland Campus Project Leaders: Dr Richard Bradbury, Project Leaders: Dr Rob Bischof, A/Prof David Piedrafita A/Prof Andrew Greenhill Email: [email protected]; Email: [email protected]; [email protected] Phone: (03) 5327 6584 Phone: (03) 4313 7930 Project description: Gastrointestinal pathogens can cause Project description: Airway macrophages are prominent considerable illness and potentially death in children, immune cells that are known to play an important role in particularly in the first year of life. The greatest impacts on healthy and diseased lungs. Macrophage M1/M2 polarisation health occur in low-income and middle-income countries, and functional differentiation is affected by a range of stimuli, where basic nutrition is lower and risk of infection higher than but we know very little about the ’altered’ state of macrophages in high income countries. We have conducted a preliminary in the context of airway disease. The aim of these studies is to study to investigate the development of the gut microbiota in examine and better understand the characteristics of airway infants, and how that collates with macrophages in healthy and inflamed lung tissues. This project carriage of pathogens. A cohort of will include immunohistology, microscopy, immunology and `20 infants from the highlands of cell biology techniques. Papua New Guinea have had faecal Key words: airway macrophages, inflammation samples collected monthly over the first 12 months of life. Faecal samples have also been collected from mothers of infants. This study will focus on gastrointestinal parasites. Faecal samples will be tested for the presence of targeted parasites using real-time polymerase chain reaction. Outcomes of the study will be a) age of first infection of specific parasites; b) determine correlation between mother’s infection status and age/likelihood of infant infection; and c) correlation between general health status of infant and parasite infection history. Key words: parasites, infant health, global health, nutrition, lab diagnostics
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 7 Environmental Science
Biodiversity of insect decomposers in Kosciusko Climatological characteristics of tropical cyclone NP rainfall in the Pacific Islands
Location: Mt Helen Campus Location: Mt Helen Campus Project Leader: Dr Philip Barton Project Leader: Dr Savin Chand Email: [email protected] Email: [email protected] Phone: (03) 5327 6868 Phone: (03) 5327 6901
Project description: An exciting research project is currently Project description: Pacific island countries have high underway examining the biodiversity of insect and vertebrate concentrations of settlements in close proximities to coastlines. scavengers found at deer and kangaroo carcasses in These communities are highly vulnerable to extreme tropical Kosciusko National Park. This project will look at the flies and cyclone rainfalls, and at present there is little quantitative beetles collected from carcasses, and to answer questions information on how these risks have changed over the past about seasonal changes in important species. There is scope decades and will change under a warmer climate. The to conduct field work in the mountains, as well as learn new frequency and magnitude of tropical cyclones are likely to skills in insect identification in the laboratory. Work will be done change and so are the risks they pose for coastal communities in collaboration with experts at Federation University and the and infrastructure. This project will emphasise on magnitude- University of Sydney. frequency relationship of tropical cyclone rainfall on selected Key words: ecosystem function, insect, carrion, scavengers, Pacific island countries. Understanding the impact of climate Kosciusko NP change on the magnitude of tropical cyclone rainfalls provides one indication of conditions under a changed climate, but it is also useful to understand the expected changes in the frequency of extreme rainfalls. Effect of artificial light at night on insects as food for fish and birds at Lake Wendouree Downscaling bushfire conditions to the station- Location: Mt Helen Campus Project Leaders: Dr Philip Barton, Dr Penelope scale in regional Victoria Greenslade, Dr Teresa Jones (University of Melbourne) Location: Mt Helen Campus Email: [email protected]; Project Leader: Dr Savin Chand [email protected] Email: [email protected] Phone: (03) 5327 6868; (03) 5327 6205 Phone: (03) 5327 6901
Project description: There is considerable evidence Project description: Climate models are very useful tools to accumulating on the deleterious effects of artificial lights at understand how climate change may affect bushfire conditions night on wildlife. This has recently been emphasised in the in Australia. However, due to their coarse resolution and other press and elsewhere on the damage to bogong moth inherent deficiencies (such as parametrization issues), populations along their migratory route to montane areas resolving the station-scale changes in the climate conditions is where they aestivate and provide food for the mountain pygmy problematic. The main emphasis of this project is to downscale possum. Lake Wendouree is the most important habitat in climate model output to the station-scale in order to better Ballarat for aquatic insects that, as larvae, are food for fish and understand the changes at local-scale. Several case studies birds and as will be used, utilising data from regional and remote locations adults are a in Victoria. resource for bats as well as some birds. There is a plan to place Long-term changes in tropical cyclone landfall artificial lights at over Australia 20 m intervals all around lake Location: Mt Helen Campus Wendouree for Project Leader: Dr Savin Chand the benefit of Email: [email protected] runners at night. It has been observed that the existing trial Phone: (03) 5327 6901 lights attract large numbers of flying insects at certain times of the year with the result that massive deaths occur from the heat Project description: Tropical cyclones are one of the costliest and insect debris that accumulates under them which has even natural disasters affecting coastal communities around tropical been observed smouldering. It is proposed that this Honours Australia. However, due to quality and quantity issues work would involve sampling flying insects both at lights and surrounding tropical cyclone database and the presence of where there are no lights in close proximity to the lake. The large variability from natural sources at multiple timescale, it is method to be used would be yellow sticky cards. If the results difficult to ascertain how TC characteristics have changed over show a significant difference between catches at lights Australia. This project utilises results from climate model compared to away from lights, it is planned that they will be simulations to examine high-impact features of our past and submitted to local councils for consideration in future lighting future tropical cyclone activity over Australia. In particular, we plans in the city. will examine model-derived TCs for past several decades over Key words: insects, artificial lights, fish, birds, bats Australia and determine how the landfall characteristics of tropical cyclones have changes over the coastal regions.
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 8 Environmental Science (continued)
Statistical assessment of tropical cyclone intensity The vegetation history of Enfield - what does from climate models Dereel Swamp tell us?
Location: Mt Helen Campus Location: Mt Helen Campus Project Leader: Dr Savin Chand Project Leader: Prof Peter Gell Email: [email protected] Email: [email protected] Phone: (03) 5327 6901 Project description: Dereel Swamp is a large, seasonal Project description: Over the past few years, our wetland in the Enfield Forest. While there have been numerous understanding of tropical cyclones has improved considerably records of vegetation change revealed from the lakes of through improvements in climate model simulations of ocean western Victoria, none have come from wetlands within the and atmospheric processes. However, there are still forested uplands. This study promises to reveal how vegetation reservations around model simulation of tropical cyclone responded to past climate change, how fire-vegetation intensities, which need very fine model resolution to be dynamics evolved in the millennia before European arrival, and explicitly resolved. Such fine-resolution simulation is difficult how European settlement modified the regional landscape. due high computation cost, as well as issues with model Key words: water quality, pollen, diatoms, climate change, fire parametrization. Regardless, cutting-edge mathematical and statistical techniques can now provide opportunities to examine high-impact features of tropical cyclones – such as tropical cyclone intensity – through drawing “links” with large- Wastewater treatment and the state of the scale environment in which tropical cyclones form. The main emphasis of this work is to examine the relationship between Yarrowee River tropical cyclone intensity and several large-scale features, and develop statistical models to assess changes in cyclone Location: Mt Helen Campus Project Leader: Prof Peter Gell intensity in current and future climate scenarios. Email: [email protected]
Project description: The Yarrowee River is important Spatial variations in the seed ecology, effect of regionally as it has a guaranteed flow. Its condition is compromised by the release of treated wastewater from ponds. elevated CO2 and effect of soil moisture on This project will use water quality monitoring, and diatom- agricultural and environmental weeds based biomonitoring, to examine seasonal variation in the nutrient status of the River, with a view to informing the next Location: Mt Helen Campus stage of the Yarrowee Corridor plan of the City of Ballarat. Project Leader: Prof S. K. Florentine (Florry) Key words: water quality, diatoms, eutrophication Email: [email protected] Phone: (03) 5327 9231
Project description: One of the most challenging issues in natural resource management is the control of elevated or unbalanced populations of weed species. Although substantial financial and other resources have been directed towards the control of some weeds, natural resource management agencies in Australia continue to struggle with who or what management. Invasive species tend to adapt to new areas so overcoming any environmental limitations. Knowledge of the ecology of weeds is essential for the selection and development of control strategies. Such information is also needed to ensure appropriate management of fragile Lake Cartcarrong: relative impact of people and ecosystems which might be prone to invasion, particularly in climate the light of future climatic changes. This project aims to collect empirical data on spatial variations in seed ecology, effect of Location: Mt Helen Campus elevated CO2and water availability on key environmental and Project Leader: Prof Peter Gell agricultural weeds. Australian environments are subject to El Email: [email protected] Niño–Southern Oscillation (ENSO) and, as a result, drought, fire, and flood may occur at unpredictable intervals. Under this Project description: Lake Cartcarrong is among few volcanic scenario, there is a high probability that weeds species will plains wetlands that have not been analysed for climate increase in abundance, significantly impacting on community change over time. Situated in the dairy country of western composition and ecosystem function. It is essential to Victoria, it offers an opportunity to contrast the relative impact understand how all species will respond to elevated CO2 and of a changing climate and landscape development on wetland water availability. To date, very limited studies have been condition over centuries. conducted and thus a comprehensive study on these issues is needed. This research would link ecological understanding of Key words: water quality, pollen, diatoms, climate change, fire current variations in different populations and predict how this aggressive species would respond to future climatic variations in particular elevated CO2 and water availability. This research will address critical issues affecting Australia and equivalent systems in other parts of the world.
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 9 Environmental Science (continued)
Barmah Lake: Understanding the Natural Management of native grassland remnant reserves ecological character of a Ramsar wetland for maintenance of native invertebrate diversity
Location: Mt Helen Campus Location: Mt Helen Campus Project Leader: Prof Peter Gell Project Leaders: Dr Nick Schultz, Dr Penelope Greenslade Email: [email protected] Email: [email protected]; [email protected] Project description: Barmah Lake is a Ramsar listed wetland Phone: (03) 5327 9681; (03) 5327 6205 of international significance. Fossil remains within sediments records will provide evidence of its natural character prior to Project description: There are a fairly large number of native river regulation and how it has changed through time since. grassland reserves within 50 km of Ballarat under the This will inform plans for the local CMA and the Yorta Yorta management of the Ballarat Environmental Network. They are people. of varying sizes and under different types of management. For Key words: water quality, diatoms, pollen, MDB wetlands, fire instance, some have been burnt using local indigenous methods others have been manage to enhance indigenous food plants and/or control weeds. Native grasses are a habitat for a surprisingly large number of endemic species, even endemic genera of invertebrates that are restricted to certain grass genera such as Themeda, Danthonia and the like. Until now the conservation status and protection of this part of the native grass fauna has received no attention. This honours project will involve sampling a number of these reserves for invertebrates to investigate the effect of size of reserve, management and lack of weeds on this fauna. Methods will include suction sampling, sweeping and pitfall trapping. It is anticipated that the results will make an important contribution to the future management of native grassland in Victoria. Key words: conservation, indigenous burning, native grasslands, invertebrates Bioaccumulation and effect of emerging contaminants in the environment
Location: Mt Helen/Gippsland Campus Project Leader: Dr Benjamin Long, Dr Nick Schultz, Dr David Smith Email: [email protected] Phone: (03) 5327 9452
Project description: Emerging contaminants such as Pharmaceuticals, PFAS and microplastics are known to be discharged to the environment. Little is known about the concentrations of these contaminants in the Australian Restoration success of native grasslands environment and their penetration through the food web. In this project you will contribute to the characterisation of the problem Location: Mt Helen Campus and help measure the effects of these contaminants on the Project Leaders: Dr Nick Schultz, Dr Penelope Greenslade environment (through environmental sampling and or Email: [email protected]; microcosm studies). You will become familiar with field [email protected] sampling techniques, solid phase extraction (SPE and Phone: (03) 5327 9681; (03) 5327 6205 QuEChERS) and HPLC-MS/MS. Key words: pharmaceuticals, emerging contaminants, Project description: Environmental offsets are a key tool for detection the management and conservation of biodiversity in Victoria, but we do not adequately understand how well we can improve and restore biodiversity at offset sites. In particular, we have a poor understanding of how invertebrate communities change with restoration efforts. This project will work in collaboration with industry to sample the invertebrates and vegetation of grassland offset sites in various stages of restoration, as well as high-quality reference sites. The project will ask how well restored sites reflect the condition and composition of high- quality grasslands, and will consider the rate at which biodiversity improvements proceed. The main site is a 95 Ha Northern Grassland reserve that is an offset for Boral Cement Company. The project will provide vital data on outcomes of biodiversity offsetting and may contribute directly to Environmental Management Plans for endangered grassland communities. Key words: native grasslands, invertebrates
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 10 Environmental Science (continued)
Gold containing fluorescent metallo-hydrogels Living Bung Yarnda (Lake Tyers) environmental stewardship plan Location: Gippsland Campus/Mt Helen Project Leaders: Dr David Smith, Dr Benjamin Long Location: Gippsland Campus Email: [email protected]; Project Leader: Dr Jess Reeves [email protected] Email: [email protected] Phone: (03) 5122 6023 Phone: (03) 5327 9049
Project description: This project will explore the creation of Project description: This project involves both the gold-containing fluorescent metallo-hydrogels. You will development of an integrated citizen science environmental investigate the optimal conditions required for gelation to occur, program and analysis of the community and project and how the relative proportion of the components influences development itself. The environmental aspect will include a fluorescent properties, and thermal and mechanical stability. review of existing monitoring programs including water quality, You will characterise the gels through various techniques waterbugs, fish, birds, vegetation and mammal scats and including UV-vis and fluorescence spectroscopy, FT-IR scratchings. A database will be developed, specific to Lake spectroscopy, dynamic scanning calorimetry, Rheology and Tyers, but contributing to larger, extant monitoring programs. It small angle X-ray scattering. will also involve recruitment and training of volunteer Key words: metals, hydrogels, fluorescence participants and analysis of the first 6 months of data collected, to be presented at a community forum. The social science aspect of the project will map the process of recruitment, engagement and community outreach of the program, beyond Sensing arrays for organic contamination in the participants. It will also map the environmental values of surface water and groundwater the various interest groups around Lake Tyers, to assist in development of the Environmental Stewardship program. Location: Gippsland Campus/Mt Helen Project Leaders: Dr David Smith, Dr Benjamin Long Email: [email protected]; [email protected] Phone: (03) 5122 6023
Project description: Sensing arrays use several non- selective probes in combination to create a unique finger-print response to an analyte or range of analytes. This project aims to create a sensing array for the detection of organic contaminants (artificial sweeteners, pharmaceuticals, PFAS). This will be developed to quantify concentrations of common organics pollutants in surface water and ground water as an Ecology and Water Chemistry of the Morwell indicator of wastewater contamination. The project would involve time in the laboratory and data analysis. Wetlands Key words: sensing array, detection, water Location: Gippsland Campus Project Leader: Dr Jess Reeves Email: [email protected] Phone: (03) 5327 9049 Palaeoecology of Lake Reeve Project description: This project will look at the seasonal Location: Gippsland Campus water quality variability and ecology of the Morwell Wetlands. Project Leader: Dr Jess Reeves Depending on your interest, the project can either focus on the Email: [email protected] flora (aquatic vegetation, algal communities) or the fauna Phone: (03) 5327 9049 (invertebrate assemblages) of the wetlands. Sampling will be undertaken in March-April and again in August-September and Project description: This project will look at sediment cores related to both climatic events and discharge regimes of the from the Lake Reeve wetlands to look at changes in ecology local industries. There is scope to improve the ecological and water quality over a longer (decadal-centennial) time values of Morwell Wetlands, so this project will provide a scale. Depending on your interest, you may focus on sediment ‘before’ study, to determine the current condition and variability chemistryr o preserved ecology, such as macroinvertebrates of the wetland system, prior to changes in the flow of the or diatoms. There is also the possibility to visit the Australian Morwell, in light of the mine site rehabilitation project. Nuclear Science and Technology Organisation (ANSTO) to undertake iTRAX sediment chemistry sampling and dating of the core material. This project will determine the natural conditions and variability of the wetland complex prior to major impacts in the catchment, such as channel diversion and the significant industrial and urban activity in the region. Key words: wetlands, ecology, climate change, rehabilitation, water chemistry
Key words: wetlands, ecology, climate change, rehabilitation, water chemistry
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 11 Environmental Science (continued)
Efficacy of Traralgon Artificial Wetlands Lichens as indicators of ecosystem functionality in revegetated forests Location: Gippsland Campus Project Leader: Dr Jess Reeves Location: Gippsland/Berwick Campus Email: [email protected] Project Leaders: Dr Simone Louwhoff, Phone: (03) 5327 9049 A/Prof Wendy Wright Email: [email protected], Project description: The Latrobe City Council has established [email protected] a number of vegetated wetlands for treatment of both industrial Phone: (03) 5122 8026 and urban stormwaters. The council are interested to see how effective their design is. This will be tested by undertaking bi- Project description: In Victoria, as elsewhere, clearing of our monthly sampling of the wetlands for water quality, nutrients, native vegetation and associated loss of habitat and invertebrates and vegetation. There are also parallel projects biodiversity has been extensive. In an effort to remediate this, related to the construction of the wetland and flow regimes revegetation programs aim to return fragmented landscapes to (engineering) and social value of the wetland sites (social a more functional state. Lichens are sensitive to microclimatic science). conditions and have long been known as good indicators of Key words: wetlands, ecology, climate change, habitat continuity. They also play an important ecological role Rehabilitation, water chemistry and it is important to recognise their potential contribution to revegetated forests. Lichens have been used to monitor ecosystem function or health (described as including maintenance of productivity, nutrient cycling, and disturbance response) of a forest. Their presence can, therefore, be used as an indication that this has been re-created at a revegetated site. The overall objective is to determine if individual lichen species or lichen assemblages can be used to determine the success of a revegetation project in mimicking the ecosystem functionality usually associated with remnant vegetation. Students will develop: vegetation and lichen identification skills Healthy Agricultural Soils
Location: Gippsland Campus Project Leader: Dr Jess Reeves Email: [email protected] Phone: (03) 5327 9049
Project description: This is a two phase project looking at the chemistry and biology of agricultural soils in Southern Gippsland. We are working with 8 properties who are interested in improving their soil health. They have employed a range of techniques, including compost, mulch, organic fertilisers, grazing and crop rotation. The project will look at the efficacy of each of these methods on soil health across a range of agricultural landscapes and produce types. The project forms part of Growing Southern Gippsland, funded by the (including microscopy and thin layer chromatography), and DELWP Climate Change Adaptation grants and led by Bass skills in analysing the success of different revegetation Coast Landcare Network. techniques. Project aims are to: identify the lichen flora of revegetation projects in different successional stages; compare lichen species in revegetated patches with those in remnant patches in similar ecological vegetation classes (EVCs); to investigate if the revegetation method employed has an impact on lichen richness. Key words: lichen, indicators, ecosystem functionality, revegetation, monitoring, restoration
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 12 Environmental Science (continued)
Habitat specificity and competitive traits of Seed ecology and agronomy of a selected Australian acacias invaded to natural landscapes Murnong (Microseris) yam daisy species in Asia Pacific: a global review Location: Berwick/Mt Helen Campus Location: Berwick/Mt Helen Campus Project Leader: Dr Kushan Tennakoon, Project Leader: Dr Kushan Tennakoon, Prof S. K. Florentine (Florry) Prof S. K. Florentine (Florry) Dr Nick Schultz Email: [email protected] Email: [email protected] Phone: (03) 4313 7954 Phone: (03) 4313 7954
Project description: The genus Acacia (Family: Fabaceae; Project description: Murnong (Microseris sp.) has long been subfamily: Mimosoideae) commonly known as Wattles are recognised as one of the most important staple food sources native to both Australia and Africa. The Acacia lineage native for Aboriginal people of the grassy plains of south-eastern to Australia comprise over 900 species are found in different Australia. However, Murnong on the plains became scarce habitats: from coastal to subalpine regions, from high rainfall to after the introduction of sheep and rabbits. Murnong persist arid areas, in tropical, sub-tropical and temperate regions. now in isolated undisturbed grassland remnants and dry Approximately 300 Acacia spp. of Australian origin have been sclerophyll forests in Victoria. Recently, Walsh (2016) introduced around the world as timber and ornamental plants conducted a taxonomic revision which increased Microseris and approximately 23 of them have become highly invasive in from two to three species. In Victoria Microseris walteri (largely many terrestrial ecosystems and causing significant impact on found in central and western Victoria), M. scapigera (south- biodiversity. Ten Acacia spp. (with six species of Australian west Victoria), and M. lancelota (eastern part of Victoria) exist. origin viz. A. longifolia subsp. sophorae, A. mangium, A. The Murnong SEED Citizen Science Project (SEED - Studies mearnsii, A. melanoxylon, A. retinodes. and A. saligna) are Exploring Edible Daisies) is a joint Higher Ed and TAFE FedUni listed in the Global Invasive Species Database with one project, with the assistance of more than 200 citizen scientists species (A. mearnsii) being in the 100 most invasive species and gardeners. It aims to explore the growth form and list. distribution of the two local species, analyse their nutritional and medicinal value and build up stocks for education and revegetation projects here in Victoria. This project will investigate the seed ecology and agronomy of one of the Murnong species. Knowledge of optimum growth requirements of Murnong species is critically important to develop cultivation protocols for eventual bushland and grassland revegetation projects using this culturally significant species. A suitable candidate can (i) examine the influence selected environmental factors such as temperature, light, pH, Salinity, soil moisture, and burial depth on the germination and emergence of the seeds of one of Microseris species in Victoria, and (ii) examine the effect of different soil types, light It is vital to identify a discrete set of characteristics which and application of synthetic fertilisers on the growth and facilitate successful invasion by exotic plants such as Acacia establishment of the same Microseris species under controlled species n i non-original regions. It has been claimed that conditions (plant house study to be conducted in the Ballarat invasive plants typically possess novel traits or exhibit more Campus). extreme trait values which confer on their competitive advantage over native flora such characteristics: (i) rapid growth, (ii) high N–fixing ability, (iii) heteroblasty and (iv) high flexibility in physiological performance found in Australian Acacia spp. However, no clear separation of particular trait sets has been reported for either highly invasive or less invasive Acacia spp. Furthermore, these facilitations may vary in different environmental conditions. We found that plant invasion studies have been unevenly distributed biogeographically, with the majority conducted in either Temperate or Mediterranean climate regions. The Mediterranean climate is shared by the Mediterranean Basin, California, Chile, the Western Cape of South Africa and Southern Australia. In contrast, related studies in other climate types such as the seasonal tropics are still scarce. Thus, an assessment of the contribution of traits to success of Australian Acacia species’ invasions under these largely unstudied conditions/climates in the Asia Pacific will help us to better understand invasive mechanisms and subsequently develop control approaches. This project will aim to provide insights into Australian Acacia invasiveness for the more efficacious selection of management practices, including control.
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 13 Mathematical Science
Optimisation methods for machine learning Reducing high dimensional convex sets
Location: Mt Helen Campus Location: Mt Helen Campus Project Leaders: Dr Minh Dao Project Leaders: Dr David Yost Email: [email protected] Email: [email protected] Phone: (03) 5327 6793 Project description: A convex set P which is symmetric about Project description: Since conceptualised, mathematical the origin, is called reducible, if there is a nonsymmetric convex optimisation has always been an effective tool in problem- set Q for which P is the set of all differences of the elements of solving and decision-making processes. Many real-life Q. Otherwise, P is irreducible. In two dimensions, every square problems can be treated as optimisation problems, requiring or parallelogram is irreducible, but everything else is reducible. the best solution among a set of possible ones. In the current For example, the difference set of a triangle is a regular era of big data, the explosion in size and complexity of datasets hexagon. has greatly influenced the focus of optimisation research. In higher dimensions, deciding reducibility is not a such an However, existing methods and theories for large-scale easy problem. Perhaps surprisingly, any d-dimensional problems have not yet taken full advantages of specific symmetric polyhedron with less than 4d vertices is irreducible structures and hence, faced major difficulties in handling (unless it is a hexagon). Nevertheless, there is an algorithm for increasingly massive and distributed datasets. This work finding a nonsymmetric polytope Q which reduces P, or proving provides a deep understanding of structures of optimisation that no such Q exists. This algorithm has barely been studied, problems and complexity analysis of numerical algorithms in in dimension three or higher. For example, it remains unknown order to explore the frontier of research in big data optimisation whether a reducing set (when one exists) can be found with and machine learning. fewer vertices than the original symmetric set. This project will examine a large collection of examples in three and four dimensions, and attempt to find relationships.
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 14 Food Science
Compositional evaluation of Murnong Role of lactic acid bacteria in flavour formation of whiskey Location: Mt Helen Campus Project Leaders: Dr Lara Wakeling, Dr Benjamin Long Location: Mt Helen/Gippsland Campus Email: [email protected]; Project Leader: Dr David Bean, A/Prof Andrew Greenhill Phone: (03) 5327 9250 Email: [email protected]; [email protected] Project description: Murnong, commonly referred to as the yam daisy, is known as a key food source for Aboriginal people Project description: Whiskey has a complex flavour profile, of south eastern Australia. There are two local species of which is derived in part from the microbial communities murnong: Microseris walteri and Microseris scapigera. Little is involved in fermentation. Yeast are used in the fermentation known about process and are well recognised for their contribution to flavour the nutritional profiles; however, other microbes are also likely to play a role composition of in flavour profile of whiskey and other spirits. The murnong and microorganisms with a potential role in flavour are possibly how it changes, endogenous distillery microbes, potentially originating from yet anecdotal grain. This endogenous microbiota potentially contributes to evidence the unique flavour profile of different whiskeys. suggests that Despite the prospective role of endogenous microbes in the sweetness, whiskey flavour profiles, there is a dearth of scientific literature in particular, investigating the contribution of the “secondary” microbes (i.e., changes across the year. In this project you will the complete microbes other than those added specifically to convert a comprehensive analysis of nutritional composition of the two fermentable sugars to ethanol) to the flavour of whiskey. This local species of murnong and evaluate how the composition project would recover and characterise organisms for a changes across the seasons. You will become familiar with distillery with the aim of understanding their role in formation of many techniques involved in food analysis. flavour compounds.
Hydration of yeast in brewing: adding value or Fluorescent sensing arrays for hops in beer unnecessary risk? Location: Gippsland/Mt Helen Campus Location: Mt Helen/Gippsland Campus Project Leaders: Dr David Smith, Dr David Bean, Project Leader: Dr David Bean, A/Prof Andrew Greenhill A/Prof Andrew Greenhill Email: [email protected]; Email: [email protected]; [email protected] [email protected] Phone: (03) 5122 6023 Project description: There has been great advancements in dry yeasts for the brewing industry in the past 10 – 15 years. Project description: Sensing arrays use several non- Until recently there were relatively few brewing yeast strains selective probes in combination to create a unique finger-print available as dry yeast; though now there is a greater range and response to an analyte or range of analytes. This project aims an increasing acceptance of dried yeast. However, there are to use fluorescent sensing arrays to detect and quantify the still some reservationsn i some sectors of brewing fraternity, presence of the acid and essential oil components of different perhaps in part because large breweries have their own yeasts hop varieties. The aim would be to create new methods for the strains thuso d not depend on dried yeast. However, amongst determination of these compounds within the brewing process. manyn i the craft brewing industry dried yeasts have gained Key words: fluorescence, sensing array, brewing acceptance. Dried yeast has many advantages over liquid yeast, not the least the storage life of dried yeast. Craft brewing is a key potential market for dried yeast producers. Beyond acceptability of dried yeast, there remains debate over the need to rehydrate dried yeast prior to pitching. Some manufacturers suggest pitching yeast directly, others recommend rehydrating the yeast first. To add to the confusion, texts and brewing websites (many targeting home-brewers) provide opinions, often conflicting. Currently, decisions are being made on whether to rehydrate yeast before pitching based on opinions rather than data. Moreover, many of the opinions are influenced by dried yeast characteristics of >10 years ago, not on the current product. The value of rehydrating dried yeast is an important research question. Dried yeast is a highly convenient product; however, the need to rehydrate does detract from that convenience. Moreover, there may be quality risks associated with rehydration, not the least the risk of contamination. This study seeks to determine the value of re-hydrating various strains of brewer’s yeast.
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 15 Veterinary and Wildlife Science
Biodiversity of insect decomposers in Kosciusko Drone- and community- monitoring of declining NP wildlife populations in the Ballarat region
Location: Mt Helen Campus Location: Mt Helen Campus Project Leaders: Dr Philip Barton Project Leaders: Dr Sarah Preston, Dr Truong Phang, Email: [email protected] Dr Adriene Lavinia (Ballarat Wildlife Park), Dr Grant Palmer Project description: An exciting research project is currently Email: [email protected] underway examining the biodiversity of insect and vertebrate Phone: (03) 5327 6880 scavengers found at deer and kangaroo carcasses in Kosciusko National Park. This project will look at the flies and Project description: A collaboration between the Ballarat beetles collected from carcasses, and to answer questions Wildlife Park (BWP), and Federation Universities’ School about seasonal changes in important species. There is scope of Engineering, Information Technology and Physical Sciences to conduct field work in the mountains, as well as learn new and School of Science, Psychology and Sport will provide the skills in insect identification in the laboratory. Work will be done BWP and community with an open access database of in collaboration with experts at Federation University and the historical and current wildlife populations. To begin, the student University of Sydney. will conduct a literature review to identify historical numbers Key words: ecosystem function, insect, carrion, scavengers, and best practice for identification and recording of wildlife, Kosciusko NP particularly relating to koalas. Next the student will work with Fed Uni scientists to develop an automated koala tracker using drone surveillance technology. Machine learning approaches will be optimised to automatically count koalas from the thermal images taken by the drone. This will be integrated with counts already collected from the community. The integration of technology and community surveillance will result in an open access research and community tracking App. Tourists and locals and members that visit to BWP will be educated on the declining koala habitat and encouraged to download the App and help monitor the declining population. BWP will use this data to make animal conservation decisions, growing their business in local wildlife conservation.
Assessment of night time distribution of Latham’s Snipe Understanding the effect of PPID on parasite Location: Mt Helen Campus burden in horses Project Leaders: Dr Birgita Hansen, Dr Nick Schultz Email: [email protected] Location: Mt Helen Campus Project Leaders: Dr Sarah Preston, A/Prof David Piedrafita Project description: Latham’s Snipe is a migratory shorebird Email: [email protected]; that breeds in Japan and spends the austral summer in south- [email protected] eastern Australia. In its non-breeding range, it typically roosts Phone: (03) 5327 6880 in shallow vegetated wetlands during the day, and departs at dusk to forage in the surrounding landscape at night. Previous Project description: Pituitary pars intermedia dysfunction research in Port Fairy has revealed that snipe have relatively (PPID) is an endocrine condition affecting twenty percent of aged equines. PPID results in elevated cortisol levels causing immunosuppression and hence commonly suffer fatal infections and/or inflammatory conditions. Furthermore, immunosuppression may lead to increased parasite susceptibility. Research on PPID associated parasite burden is sparse. High worm burden may manifest as weight loss, short commuting distanc e between daytime and night time illness and colic. habitats, and that day time and night time habitats differ Colic presents as markedly in their wetland characteristics. As much of the abdominal pain surveyed population of snipe occurs in small urban wetlands, and can require this has implications for foraging habitat availability in built-up surgery or areas. This project will develop and test a night time survey euthanasia. This method for this species, targeting sites in Melbourne and study aims to determine if equines with PPID have increased Western Victoria that are known to support large numbers of susceptibility to parasites. Resulting information may help snipe. The outcomes of this research will inform the devise new parasite treatment and management plans for development of best practice methods for environmental PPID and healthy equines. This study (in collaboration with the impact assessment of this species. This project will require a University of Melbourne) will also investigate the immune cells mid-year start. in horses with PPID compared to age-matched horses and Key words: shorebird monitoring, wetland ecology, remote susceptibility to parasites. sensing Key words: parasites, immune system, worms, equine
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 16 Veterinary and Wildlife Science (continued)
Development of a vaccine for scour worms in Antibiotic resistance in bacteria from the sheep environment
Location: Mt Helen/Gippsland Campus Location: Mt Helen/Gippsland Campus Project Leaders: Dr Sarah Preston, A/Prof David Piedrafita Project Leaders: Dr David Bean, Dr Andrew Greenhill Email: [email protected]; Email: [email protected]; [email protected] [email protected] Phone: (03) 5327 6880 Phone: (03) 5327 9247
Project description: Due to widespread drench resistance, Project description: Antibiotic resistance is one of the new non-chemical control methods are required for sustainable greatest threats facing human medicine. Only one-third of parasite control in the red meat industry. This is particularly antibiotics purchased in Australia are used in human medicine, important for Trichostrongylus worms (scour worms) which the remainder being for mostly for veterinary and food cause weight loss and scouring. Molecular vaccines are a production purposes. This gives the potential for antibiotic sustainable non-chemical control method. A vaccine resistance to develop in the environment and eventually be (Barbervax) has recently been marketed for control of Barbers transmitted to humans. This project aims to investigate the Pole worm, reviving the possibility of a vaccine for producers burden of antibiotic resistance in the environment and better to use to control worms. This project will investigate whether a understand the potential threat to human medicine. Bacteria vaccine developed against will be recovered from diverse environment origins: wildlife, Barbers Pole worm can veterinary, food production animals and the environment itself, protect sheep against other and be tested for the presence of antibiotic resistance. The related worms such as project will provide important data on antimicrobial resistance Trichostrogylus species in non-medical niches and potentially identify hotspots for the and Teladorsagia development of resistance in Australia. circumcincta. This project Key words: antibiotic-resistance, E. coli, Salmonella, wildlife will be performed in collaboration with Latrobe University. Key words: parasites, vaccine, immune system, worms, ovine
Life cycle adaptions of Little penguins in captivity
Location: Mt Helen/Berwick Campus Project Leaders: Dr Sarah Preston, Dr Philip Barton, Dr Meagan Dewar, Dr Adriene Lavinia (Ballarat Wildlife Park) Detection, isolation and characterisation of Email: [email protected] Enterobacteriaceae from wild birds in Australia Phone: (03) 5327 6880 Location: Gippsland/Mt Helen Campus Project description: Ballarat Wildlife Park (BWP) is home to Project Leader: A/Prof Andrew Greenhill, Dr David Bean a colony of 20 Little penguins (Eudyptula minor). In the wild, Email: [email protected]; Little penguins spend approximately 80% of their time at sea, [email protected] returning to land to breed, moult and rest. It is un known how this lifecycle structure and associated feeding habits are Project description: Due to habitat destruction and other adapted in captivity. This project will use advanced statistical anthropogenic effects on the environment, humans have approaches such as mixed model non-linear regression increasingly closer contact with wildlife. This increases the models to analyse three years of daily feed intake data from potential health risks to both wildlife populations and humans. the Little penguin colony and correlate weight gain/losses to An existing research project within the School has led to the their lifecycle. Trends in this dataset will be identified and collection and culture-based detection of selected bacteria compared to similar datasets of wild Little penguin colonies from 1022 wild birds. These samples represent 12 bird species, where possible. The project will also involve site visits to the and have been collected from 22 collection sites across three park where the student states. This study seeks to use these archived samples to will have the detect both recognised pathogens such as Salmonella, and opportunity to weigh potential novel and emerging bacterial pathogens of the family and handle the little Enterobacteriaceae, arguably the most important taxonomic penguins and network group of bacterial pathogens. The study will first screen with the staff at the samples using specific PCR assays to detect target pathogens. BWP. A major outcome Samples that are PCR positive for targeted pathogens will be of the project will then cultured to isolate the pathogen, thus allowing provide new insight to comprehensive phenotypic and genotypic characterisation of the habituation of little isolates. The study will contribute important findings to our penguins in captivity. research program that investigates the role of migratory birds in global pathogen dissemination. Skills acquired will include molecular biology, bacterial culture and antimicrobial sensitivity testing.
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 17 Veterinary and Wildlife Science (continued)
Diet and feeding selectivity of Tasmanian common Sniffing out koala diet wombats Location: Berwick/Gippsland Campus Location: Gippsland Campus Project Leaders: Dr Fiona Hogan, A/Prof Wendy Wright, Project Leader: A/Prof Wendy Wright, Dr Georgia Roberts Dr Faye Wedrowicz Email: [email protected]; Email: [email protected] [email protected] Phone: (03) 5122 6466
Project description: The seasonal diets and feeding Project description: In this project you will join the team at selectivity of common wombats (Vombatus ursinus) has OWAD Environment and their detector dogs to search for koala previously been investigated in the mountainous region of scats in SE Queensland. Specially trained detector dogs will NSW using faecal analysis (Evans et al., 2006). Very little is be employed to sniff out koala scats in the field. Koala scats currently known about the feeding habits or diet of the will be collected, along with leaf samples from close by trees. Tasmanian common wombat (Vombatus ursinus Back in the laboratory you will develop molecular markers tasmaniensis), a distinct genetic subspecies of the mainland which can be used to identify common wombat. This pilot project will aim to collect the the species of the leaf, DNA baseline data necessary to do a similar study of wombats from isolated from the scat Cradle Mountain – Lake St sample will then be matched Claire National Park in to the references, and the north western Tasmania. diet of the koala revealed. The project will involve Knowledge of koala diet will direct field observation of help land managers to direct diet and feeding behaviours conservation efforts, as well of wombat populations as provide information about within a 10 km radius of the what plant species should be Cradle Mountain visitors centre. Students will need to observe used in revegetation efforts feeding animals and identify plant species. The study will aimed at koala conservation. conclude with the collection of samples of dietary vegetation to Skills acquired in this project use in a later study, which will use faecal material collected will include experience from road killed animals to investigate seasonal changes in working as an environmental diet. consultant, working knowledge of detector dog work for conservation, animal scat ID training, field skills, and laboratory skills including DNA isolation, PCR, Next Gen Improved methods for identifying, characterising Sequencing and bioinformatics. This project will involve and phenotyping immune cells in sheep spending around one month in the field with OWAD Environment http://www.owad.com.au/ in SE Queensland. Location: Berwick/Gippsland Campus Timing of this trip is unknown and as such you must be Project Leaders: Dr Rob Bischof, A/Prof David Piedrafita available to travel and stay away from home for the time Email: [email protected] required. You must also have a very good fitness level, as field Phone: (03) 4313 7930 work with detection dogs is intense and involves long days.
Project description: Immune cells feature in many organs and tissues of the body, and play a huge role in health, infection and disease. Our capacity to study the different classifications of immune cells is aided by the availability of markers or antibodies that help identify the phenotype of immune cell subpopulations and allow assessment of the health status of an individual. Antibody binding or staining in histology, Melzi et al. Immunophenotyping of Sheep Lymph Nodes Melzi et al. however, is often affected by conditions around the preparation Immunophenotyping of Sheep Lymph Nodes and fixation of tissues. These studies will investigate and optimise antibody staining in healthy and inflamed tissues collected and fixed in different ways. Techniques will include histology, immunohistology, microscopy and image analysis. Key words: immune cells, tissue staining, sheep
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 18
FIGURE 3 | Differential expression of MHC II in dendritic cells and macrophages. Representative confocal micrographs of sheep lymph node sections. (A) Sections stained for MHC II (green) and CD83 (red). (B) Sections stained for MHC II (green) and fascin (red) to visualize the extension of DCs in the paracortical area. (C) Sections stained for MHC II (green) and CD163 (red). Markers expression in different areas of the lymph node is shown at higher magnification, DAPI (blue). immune complexes, whereas in the dark zone they display positively labeled with an anti-human antibody targeting CD54 fewer cytoplasmic extensions and present a low capacity to trap reported to work in sheep (Figure 5A). CD54 (also known as immune complexes (80). intercellular adhesion molecule 1–ICAM-1) is a transmembrane We found sheep FDCs to react positively with the anti- protein expressed by the endothelial cells and leukocytes whichis human CNA.42 antibody (15)(Figure 5)asalreadydescribedfor implicated in the process of transmigration of leucocytes across cattle (38). The epitope recognized by CNA.42 is a membrane- lymphatic vessels (83). Both mouse and human FDCs have been associated 120 kD antigen resistant to fixation that is expressed already shown to express CD54 (84, 85). CNA.42 and CD54 were on FDCs. CNA.42 is commonly used in human diagnostic expressed in the same cell population in the follicles of the sheep settings for the histological classification of malignancies of FDCs LNs (Figure 5A). origin (such as follicular dendritic reticulum cell sarcoma and We also detected a second population of FDC localized EBV-positive inflammatory pseudotumors) (39, 81, 82). In the in the dark zone of the sheep germinal centers. These cells, sheep LNs under study, this antigen was also expressed by some have been previously described in the literature as “dark mononuclear cells present in the paracortical area of the LN zone FDC” (dzFDC) or “dark zone reticular cells” but their as describedFIGURE for 2 human| Identification LNs (39 of). markers We identified for sheep sheep macrophages FDC function and dendritic has yetcells. to be Representative defined (80, 86 immunohistochemistry, 87). DzFDC lacked micrographs of sheep lymph node sections as cells forming a reticular pattern in the light zone of the expression of the classical FDC marker CNA.42, but stained fixed using zinc salt solution. Sequential tissue sections stained for CD11b, CD163, CD169, CD208, and fascin. Insets show the paracortical area at higher germinal centers. Furthermore, FDC in the light zone were positively for CD83 and S100 (Figure 5). CD83 was also magnification. The expression of these markers in different anatomical areas of the lymph node allowed the identification ofvariouspopulationsofmononuclear phagocytes. Scale bar: 100 µmforcortexand20µmforparacortexandmedulla.
Frontiers in Immunology | www.frontiersin.org 8 December 2018 | Volume 9 | Article 2892 is mostly expressed on tissue-resident macrophages (63)andin macrophages: SCS and medullary (65). These macrophages are sheep is considered to be exclusively expressed by monocytes strategically placed along the sinuses where they are involved and macrophages and not expressed by neutrophils (unlike in antigen acquisition and their delivery to lymphocytes. Here CD68 for example) (28, 64). To identify CD163 expression, we we used the anti-human CD169 antibody clone HSn 72D, that used the anti-human CD163 mAb (clone EDHu-1) previously in zinc salt fixed tissues labeled a population of macrophages validated in ovine tissues (28). CD163 was expressed by a few present along trabecular and medullary sinuses but not in the cells in the paracortical area and by numerous cells present along SCS. This pattern of expression starkly contrast with what has the trabecular and medullary sinuses (Figure 2), in a similar been described in the mouse (Figure 2)(66). localisation as CD11b+ macrophages. The sialoadhesin CD169 We then screened antibodies targeting markers normally (Siglec-1) is a lectin with Ig superfamily domains binding sialic expressed by dendritic cells. Dendritic cells can be found in acid and in the mouse lymph node is expressed by macrophages. the paracortical area of the LN, where they interact with T In mouse LNs, CD169 characterizes two different types of cells for antigen presentation and activation. In humans, CD208
Frontiers in Immunology | www.frontiersin.org 6 December 2018 | Volume 9 | Article 2892 Veterinary and Wildlife Science (continued)
Hidden diversity, discovering burrowing crayfish Wildlife forensics
Location: Berwick/Gippsland Campus Location: Berwick/Gippsland Campus Project Leaders: Dr Fiona Hogan, A/Prof Wendy Wright, Project Leaders: Dr Fiona Hogan, A/Prof Wendy Wright, Dr Faye Wedrowicz Dr Faye Wedrowicz Email: [email protected] Email: [email protected]; Phone: (03) 5122 6466 [email protected] Phone: (03) 5122 6466 Project description: Invertebrate diversity is critical for healthy ecosystems, however, we know very little about these Project description: Do you know what a pangolin is? If not tiny creatures as they are often hidden in the environment. you are not alone. The pangolin is a mammal, but looks more Burrowing crayfish are a cryptic invertebrate species that live like a reptile, and is the most traffic species in the world. The in underground burrows. Five species of burrowing crayfish are illegal traffic of wildlife is a serious issue and is having grave endemic to the western Strzelecki Ranges, including three impacts on biodiversity. Rarely are whole animals traded, more which are considered under threat of extinction; Narracan often, it is animal parts that are sold at market. It is often difficult Burrowing Crayfish, South Gippsland Burrowing Crayfish and to identify which species an animal part has come from, so that Warragul Burrowing Crayfish. As burrowing crayfish live is where genetics can help. This project will involve extracting underground, populations decline, largely caused by adverse DNA from pangolin scats and then using species specific impacts on their habitat, can go unnoticed. The ability of these crays to recover naturally from a decline is severely hampered by their limited ability to disperse and re-occupy abandoned territory. Relatively little is known about the ecology, population dynamics or habitat requirements of burrowing crayfish. One of the reasons for this is that surveying is difficult and often involves invasive sampling where crayfish are removed from burrows. The aim of this project is to use eDNA (environmental DNA) to determine the species diversity of burrowing crayfish in the South Gippsland area. The project will involve you working with a specialised invertebrate ecologist to find potential burrowing crayfish burrows. Burrows will be sampled non-invasively, where either a water or soil sample will be taken. DNA isolated from the sample will be used to identify whether burrowing crayfish occupy the burrow, and if so which microsatellite molecular markers to obtain genetic data. Data species. In this project you will acquire the following skills: will then be used to investigate the genetic diversity of the experience working as an environmental consultant, burrow ID pangolin across Nepal and reveal for the first time how many training, field skills, and laboratory skills including DNA genetically distinct populations exist. Population genetic isolation, PCR, Next Generation Sequencing, bioinformatics signatures can then be used to match seize parts of pangolin, and spatial analysis skills using GIS. This project will involve thus providing an insight to where poachers are targeting spending time in the field with an invertebrate ecologist in pangolin. If live pangolin are seized, then knowledge of Gippsland. Timing of field trips are unknown at this stage, it is population genetics will allow for individuals to be returned to anticipated that you will spend up to a month in the field and their own habitat. Skills acquired in this project include cultural you may need to be away from home during this period. You experience of working and living in a developing country, should have a good fitness level, as working in the field can be experience working in a DNA laboratory in the jungles of Nepal, intense and involve long days. laboratory skills including DNA isolation, PCR, population Key words: conservation, wildlife, genetics genetic analysis. It is not clear whether this project will go ahead in 2020 or not. If you are interested in this project please have a chat with either Fiona (Berwick) or Wendy (Churchill). We expect that there might be considerable interest in this project, and there may be a selection process put in place. If you are selected for the project, flights, accommodation and most meals will be covered during your time in Nepal. Key words: conservation, wildlife, genetics
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 19 Veterinary and Wildlife Science (continued)
Assessing the impact of nutrition, heat stress and Intestinal parasites of non-human primates from grazing behaviour on the immune status of dairy Asia and Africa cows Location: Berwick Campus Location: Berwick Campus Project Leaders: Dr Richard Bradbury, Dr Jennifer Cramer Project Leaders: Dr Rob Bischof, Dr Danielle Auldist (American Public University), Email: [email protected] Dr Vito Colella (University of Melbourne), Phone: (03) 4313 7930 Dr Indu Panicker Email: [email protected]; Project description: The Gippsland dairy industry supplies Phone: (03) 5327 6584 >20% of Australia’s milk and is a major employer. Knowledge of ruminant nutrition and its impact on herd health and Project description: This project will involve the productivity assists farmers to make decisions about feeding parasitological screening of non-human primate faecal levels of supplements (grains, proteins, oils) to optimise rumen samples collected in Kampong Chhnang province of Central fermentation as well as milk production and composition Cambodia and Tonkolili District of Sierra Leone (West Africa). (lactoferrin, lactose and types of fat and protein). This project Non-human primates share many parasitic helminths and will be carried out in protozoa with humans, this study will examine the prevalence, collaboration with Ellinbank distribution and species of gastrointestinal parasites infecting Research Institute, and will monkeys in Africa and Asia, including the implications for both assess the impact of various human and animal health. Approximately 90 samples are factors including grazing available for screening now. The student will learn microscopic behaviour, heat stress and techniques for the detection of parasitic agents, including milk quality on the immune special stains and will gain a broad experience in diagnostics status of dairy cows. and parasitology. Next generation sequencing to determine the Methods will include genotypes of any Strongylida and Rhabditida present will be immunology, biochemistry performed. The skills acquired are transferable to the and cell-based studies. molecular biology, diagnostics and veterinary industry, public health and research roles. Key words: immune status, ruminant nutrition, heat stress, grazing behaviour, milk composition, feed quality Key words: parasites, primatology, public health, veterinary health, laboratory diagnostics, one-health
Toxocara in dogs from Mississippi
Location: Berwick Campus Project Leaders: Dr Richard Bradbury, Dr. Indu Panicker, Assoc. Prof. Charlotte Hobbs (University of Mississippi) Email: [email protected] Phone: (03) 5327 6584
Project description: There are many parasitic diseases which may affect both dogs and humans. Recently, it has been Seabird and Elasmobranch Microbiomes discovered that human toxocariasis, caused by exposure to the dog parasite Toxocara canis, is unusually common in Location: Berwick Campus Mississippi, the most underserved state in the United States. Project Leader: Dr Meagan Dewar, Dr Andrew Greenhill An unusual cluster of ocular infections Email: [email protected] with this parasite has also been Phone: (03) 5122 8919 observed. This study will involve screening faecal samples from stray Project description: A number of projects are available to dogs in Mississippi for Toxocara and examine the microbial composition of sharks (great white, other zoonotic parasites. The student tigers and bull) and Temperate (little) and Antarctic penguins will learn microscopic techniques for (Adelie, Emperor). These projects focus on characterising the the detection of parasitic agents, microbial community that lives inside these host species using including special stains and will gain a genomic sequencing and bioinformatics analysis. The aim of broad experience in parasitic disease these projects is to further our knowledge into the microbes diagnostics and parasitology. This is a colonising these species and our understanding of the role that largescale (260 samples) study and the microbiome plays in host health, nutrition and metabolism. thus statistical methods for Key words: microbiome, genome, microbial ecology, epidemiological investigation will also bacteria, seabirds, sharks be applied to the analysis. If time permits, multiplex real-time PCR for hookworm species identification may be performed. The skills acquired are transferable to the diagnostics and veterinary industry, public health and research roles. Key words: parasites, dogs, public health, epidemiology, veterinary health, laboratory diagnostics, one-health
School of Science, Psychology and Sport – BSc Honours Research Projects 2021 20 Contact our Supervisors
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