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INFORMATION FOR PROSPECTIVE
RESEARCH STUDENTS
RMIT
BIOTECHNOLOGY &
ENVIRONMENTAL BIOLOGY
RESEARCH DEGREES, RESEARCH
INTERESTS AND RESEARCH
PROJECTS
Contact person:
Assoc. Prof. Ann Lawrie
Biotechnology & Environmental Biology
School of Applied Sciences
RMIT University
PO Box 71, Bundoora, Vic 3083
Tel. (03) 9925 7157, Fax (03) 9925 7110
Email [email protected]
http://www.rmit.edu.au/applied-sciences
874021199
RMIT
BIOTECHNOLOGY & ENVIRONMENTAL BIOLOGY
SCHOOL OF APPLIED SCIENCES
RESEARCH DEGREES, RESEARCH INTERESTS AND RESEARCH PROJECTS
Biotechnology & Environmental Biology at RMIT University invites prospective students interested in
conducting research for Honours, M.App.Sc. or Ph.D. degrees in the areas indicated below to contact the staff
directly ([email protected])or the Honours and Postgraduate Coordinator for further information
(A/Prof. Ann Lawrie, tel. 03 9925 7157, fax 03 9925 7110, e-mail [email protected]).
MICROBIAL BIOTECHNOLOGY/HUMAN & ANIMAL DISEASE
Prof. Peter Coloe
Molecular biology and microbiology; virulence factors and vaccines for enteric
(Head of School)
disease in animals, particularly pigs and poultry
Dr Taghrid Istivan
Molecular microbiology and bacterial pathogenesis including virulence genes in
Campylobacter spp. and molecular detection of pathogens.
A/Prof. Margaret
Molecular pathogenesis and epidemiology of staphylococcal and streptococcal
Deighton
infections of humans and dairy cattle; detection of pathogens in biosolids
Dr Duncan Rouch
Pathogen die-off in biosolids (treated sewage)
Dr Danilla Grando
Diagnostic bacteriology and infection control, especially staphylococci
Dr Brian Meehan
Virology, especially porcine viruses; rapid diagnosis methods and vaccines
A/Prof. Gina Nicoletti
Antimicrobial agents and mechanisms; bacterial toxin inhibitors
Dr Paul Gibbs
Scale-up of veterinary vaccine and other bacterial fermentations. The development of
commercially feasible fermentation and downstream processing strategies
BIOINFORMATICS/NANOTECHNOLOGY
Dr Peter Smooker
Vaccines (protein, DNA, attenuated) against infectious agents. Targeting the immune
system. Structure and function of proteins. Bioinformatics.
Dr John Fecondo
Structure and function studies of proteins, peptide synthesis, proteomics and protein
technology
FOOD SCIENCES/FOOD BIOTECHNOLOGY/FOOD MICROBIOLOGY
Dr Andreas Lopata
Adverse reactions to food with special focus on fish, crustacean and molluscs and the
molecular characterisation of allergenic proteins for diagnosis and therapy
Ms Prue Bramwell
Food microbiology, especially the use of molecular and cultural methods to diagnose
pathogens in foods.
PLANT BIOTECHNOLOGY AND PATHOLOGY
Prof. David Stalker
Molecular biology and biotechnology of plants, in expression and stability of foreign
proteins involved in cellulose biodegradation and blue genes in cotton
A/Prof. Trevor
Molecular biology and biotechnology of plants, in the high level expression and
Stevenson
stability of foreign proteins expressed in genetically engineered plant chloroplasts
Dr Greg Nugent
Plant tissue culture and transformation of model species and brassicas, esp.
expression of genes that alter chloroplast number or confer abiotic stress tolerance.
Dr Eddie Pang
Use of molecular biology in plant breeding, in particular molecular markers for crop
improvement and disease resistance; regeneration systems from tissue culture
A/Prof. Ann Lawrie
Plant-microorganism interactions: nitrogen fixation, mycorrhizae, plant pathology,
use of molecular biology for diagnosis/control of pathogens and weeds, mycology
Dr Tien Huynh
Orchidology: Tissue culture, propagation, mycorrhizal associations, molecular
biology, immunoblotting, microscopy
ENVIRONMENTAL BIOLOGY/ECOTOXICOLOGY
A/Prof. Dayanthi
Ecotoxicology of heavy metals, pesticides and organics esp. in fish and invertebrates.
Nugegoda
Aquaculture, nutrient pollution. Hormones in fish development and as biomarkers
Dr Ben Kefford
Rapid ecotoxicology testing, comparing laboratory results to effects of toxicants in
nature, effect of salinity on freshwater invertebrates and ocean acidification.
Dr Jeff Shimeta
Microbial ecology in impacted coastal sediments, emphasizing protozoa
A/P Bruce Anderson*
Biodegradation of toxic chemicals
*adjunct appointment
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RESEARCH PROJECTS SUITABLE FOR STUDENTS
Please note that this list is not exhaustive; if you are interested in the general topic area, discuss suitable projects
with the staff member concerned.
MICROBIAL BIOTECHNOLOGY/HUMAN & ANIMAL DISEASE ................................................................. 4
PROF. PETER COLOE ...................................................................................................................................... 4
DR TAGHRID ISTIVAN ................................................................................................................................... 4
ASSOC. PROF. MARGARET DEIGHTON ...................................................................................................... 5
DR DANILLA GRANDO ................................................................................................................................... 5
DR BRIAN MEEHAN ........................................................................................................................................ 5
DR PAUL GIBBS ............................................................................................................................................... 5
BIOINFORMATICS & NANOTECHNOLOGY ................................................................................................... 6
DR PETER SMOOKER ..................................................................................................................................... 6
DR JOHN FECONDO ........................................................................................................................................ 6
FOOD SCIENCES/FOOD BIOTECHNOLOGY/FOOD MICROBIOLOGY ........................................................ 7
DR ANDREAS LOPATA ................................................................................................................................... 7
MS PRUE BRAMWELL .................................................................................................................................... 7
PLANT BIOTECHNOLOGY & PATHOLOGY ................................................................................................... 7
ASSOC. PROF. TREVOR STEVENSON and PROF. DAVID STALKER ....................................................... 7
DR GREG NUGENT .......................................................................................................................................... 8
ASSOC. PROF. EDDIE PANG .......................................................................................................................... 8
ASSOC. PROF. ANN LAWRIE ......................................................................................................................... 8
DR TIEN HUYNH............................................................................................................................................ 10
ENVIRONMENTAL BIOLOGY & ECOTOXICOLOGY .................................................................................. 10
ASSOC. PROF. DAYANTHI NUGEGODA................................................................................................... 10
DR BEN KEFFORD ......................................................................................................................................... 11
DR JEFF SHIMETA ......................................................................................................................................... 12
ADVANTAGES OF COMPLETING THE HONOURS YEAR .......................................................................... 13
COURSE STRUCTURE AND ASSESSMENT ................................................................................................... 13
GRADES IN HONOURS DEGREE ..................................................................................................................... 14
QUOTA................................................................................................................................................................. 14
ENTRY REQUIREMENTS.................................................................................................................................. 14
HOW TO APPLY ................................................................................................................................................. 14
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MICROBIAL BIOTECHNOLOGY/HUMAN & ANIMAL DISEASE
PROF. PETER COLOE
The distribution of the genes encoding antibiotic resistance, with an emphasis on vancomycin resistance in
bacteria colonising food animals.
Vancomycin resistance in bacteria is an emerging problem. This project will investigate the distribution of the
genes associated with vancomycin in a series of animal and human isolates of selected bacteria. Techniques to
be used will include PCR and DNA probes. The project will involve isolation of enteric organisms from
chickens, pigs and cattle, identification of isolates, characterisation of antibiotic resistance parameters and
identification of resistance genes.
The role of TH-1 and TH-2 responses in salmonella infections in mice.
Salmonellosis can be controlled in food animals by the use of live vaccines where as killed vaccines are not as
effective. This project will investigate the types of immune responses that mice mount to live smooth, live
rough and killed Salmonella typhimurium vaccines. The project will involve the introduction of a galE mutation
into an aroA- S. typhimurium and evaluation of the antibody and cell-mediated responses that are evoked to the
various vaccine strains.
DR TAGHRID ISTIVAN
Epidemiology and pathogenesis of Campylobacter concisus
Campylobacter infections caused by C. jejuni and C. coli are of the most common causes of gastroenteritis
worldwide. However, new emerging Campylobacter spp., such as C. concisus, are associated with
gastroenteritis cases in children, the elderly and the immunocompromised. This research project aims to
investigate the efficiency of current isolation and detection methods used at diagnostic labs in comparison to
molecular detection techniques. The pathogenesis of this emerging pathogen will be investigated through the
capability of these clinical strains to invade different tissue culture cell lines.
Molecular analysis of the pldA gene and its relation to virulence in Campylobacter concisus
Campylobacter concisus is a human oral cavity bacterium and a potential aetiological agent of enteritis. The aim
of this project is to investigate the role of phospholipase A (PLA) in the pathogenesis of C. concisus. This will
involve creating a pldA gene mutant in C. concisus clinical strain and investigate its invasion capabilities as
compared with the parental strain. This will also involve extracting and purifying PLA from both the parental
strain and the pldA mutant and undertaking cytotoxicity studies on the effect of the normal and the truncated
proteins on tissue culture cell lines.
The role of flaA and flaB genes in the pathogenesis of Brachyspira spp.
Brachyspira hyodysenteriae is a gram-negative spirochete and the causative agent of swine dysentery. The flaA
and flaB genes encode for endoflagella, a specific character in spirochaetes. Our preliminary investigations
indicated that the flaB1 gene nucleotide sequence is conserved (to some extent) in Brachyspira spp. This project
will investigate the differences in flaB1 nucleotide sequences from different species and the role of this gene in
the pathogenesis of Brachyspira hyodysenteriae. This will be achieved through nucleotide sequencing and
creating flaB mutants in different Brachyspira. strains and also investigating the capability of these mutants to
adhere to certain tissue culture cell lines.
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ASSOC. PROF. MARGARET DEIGHTON
Coagulase-negative staphylococci in neonatal intensive care
This project is part of a prospective study conducted in collaboration with the Department of Microbiology,
Royal Children’s Hospital. Coagulase-negative staphylococci (CoNS) are major pathogens of very low birth
weight (VLBW) infants in neonatal intensive care units (NICUs). Their virulence is due mainly to their ability to
form biofilm on the surfaces of catheters and other medical devices used in the treatment of these babies. This
project looks at regulation of biofilm in one species of CoNS (Staphylococcus capitis).
Virulence factors of Streptococcus uberis
Streptococcus uberis is an important cause of mastitis in dairy cattle. Infected cows produce low yields of poor
quality milk. Several virulence factors of S. uberis have been proposed, but only the hyaluronic acid capsule and
a plasminogen activator have been studied in detail. Using the technique of subtractive hybridisation, we have
identified several clones that are present in mastitis-associated strains but not in commensals. The aim of this
project is to characterise these isolates in an attempt to detect virulence-associated genes of S. uberis.
Detection of pathogens in biosolids (with Dr Duncan Rouch)
Melbourne produces approximately 330,000 million litres of sewage a year, and so it is important to recycle this
material. Treatment processes of sewage produce biosolids as well as reclaimed water. For biosolids, the
ultimate aim is to generate material that is free from microbial pathogens and is safe to use for fertilising
agricultural crops. While standard methods have been developed to estimate the pathogen load at various stages
of the treatment process, they are slow and rely on conventional microbiological techniques. The aim of this
project is to develop molecular methods for the detection in biosolids of potential pathogenic bacteria and
viruses, and related indicator bacteria and viruses.
DR DANILLA GRANDO
Typing of methicillin resistant Staphylococcus aureus (MRSA)
MRSA has been a cause of nosocomial infection in Victorian hospitals since the late 1960’s. Over that time few
strains have become endemic to the hospital environment. Recently, however, reports have increased as to the
number of MRSA arising in non-hospitalised patients. Some of these strains carry a new virulence determinant.
This study will survey Victorian hospital strains and community strains of MRSA for genomic clues to help track
the incidence and possible further spread of MRSA.
DR BRIAN MEEHAN
A study of the pathogenesis of Marek's disease viruses (MDV) using representatives of an MDV gene library
as molecular probes.
Marek's disease is an oncogenic herpesvirus and is currently the greatest cause of economic loss in the Australian
chicken industry and a significant problem in other countries. Newer approaches to the detection and
characterisation of the virus have been developed in recent years which make use of molecular probes for
detecting the virus genome in infected tissues. We have access to a gene library of the MDV genome and it is
proposed to develop a number of probe and immunohistological techniques on sections of tissues from infected
chickens and chicken embryos. These techniques should assist in characterising Australian isolates of MDV that
have been prepared in recent years.
Development of quantitative PCR for studies of the pathogenesis of viruses.
Recent developments allow rapid estimates to be made of viral genome copy number that can be used to more
precisely define events in the pathogenesis of viral diseases. These techniques are available for studies of both
human respiratory viruses and for avian viruses.
DR PAUL GIBBS
Development of lyophilisation protocols for Mycoplasma vaccine cultures
Several live veterinary Mycoplasma vaccines have been developed and are currently in, or near to, commercial
production. Typically the vaccines are wet frozen and hence are stored and transported at –80 oC. This extreme
cold chain adds significantly to the vaccine cost and prevents access to some markets.
An alternative
stabilisation method such as lyophilisation is desirable and the work will involve manipulating the freeze drier
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cycle parameters and investigating the addition of cryoprotectants. The project will be conducted in conjunction
with Bioproperties Pty Ltd.
Development of enumeration methods for Mycoplasma vaccine production
(with Dr Youssef Abs El-Osta, BIOPROPERTIES Pty Ltd)
Cell concentration is a critical part of the quality testing for vaccines to ensure the safety and efficacy of the
product. Traditional spread plating on solid media is not possible with Mycoplasma cultures and while a 96-well
plate most probable number method has been developed, it takes 14-21 days to return a result. This project will
examine techniques such as real-time PCR and/or flow cytometry in an effort to deliver a rapid enumeration
method. The project will be conducted in conjunction with Dr Youssef Abs El-Osta of Bioproperties Pty Ltd
and may involve some work at the production facility at Glenorie, NSW.
BIOINFORMATICS & NANOTECHNOLOGY
DR PETER SMOOKER
Investigation of the responses of chickens to Campylobacter colonisation
Campylobacter can effectively colonise chickens but does not cause disease. The chicken immune system does
not induce an inflammatory response to the bacterium, and therefore cannot clear the colonisation. We are
investigating the interaction of Campylobacter with the chicken immune system.
Targeting the immune system: strategies to increase the effectiveness of vaccines
The effectiveness of a vaccine depends largely upon its ability to stimulate dendritic cells and induce an
inflammatory response. Ways to improve the delivery of antigen to dendritic cells are being investigated. This
includes the use of attenuated bacterial vaccines to “vector” heterologous antigen to the appropriate cells.
Structure and function of parasite proteins
We are studying a number of proteins with diagnostic, vaccine or therapeutic potential. Secreted parasite proteins
play a key role in infection by the parasite. They can also be useful diagnostic markers. We are studying a
particular class of proteases that are secreted by parasites, using molecular and bioinformatics techniques. We
are also studying another class of proteins that may interact with the host immune system during malaria
infection.
Protein engineering
Several strategies are used to formulate recombinant proteins that are suitable for use as vaccine antigens. This
includes in vitro mutagenesis to create non-active proteins, or the creation of fusion proteins for multivalent
vaccination. Bioinformatics is used in the design. Recombinant proteins are expressed in different systems
depending on the nature of the protein.
DR JOHN FECONDO
Generation and functional studies of anti-peptide antibodies against Fat
(in collaboration with Prof. Andrew Boyd, Queensland Institute of Medical Research)
Abnormal forms of an adhesion protein called Fat have been shown to be expressed in some forms of human T
cell leukaemia and are thought to be responsible for altered cell morphology and movement. In this project,
specific rabbit anti-peptide antibodies will be generated against alternative spliced forms of Fat and used for
probing the function of these altered proteins in vitro. Techniques used included sequence analysis, manual and
automated solid phase synthesis of peptides, analysis by HPLC, CE and MS techniques, generation, purification
and characterisation of antibodies using ELISA techniques.
Analysis of the proteome of Campylobacter species
Recent advances in 2D gel electrophoresis techniques, mass spectrometry and data mining of genomic databases
allow for the analysis of complete proteomes of organisms. In this project, these techniques will be used to
compare the proteomes of different species of Campylobacter with a view to identifying unique proteins that
may be associated with the infectivity process and thus be considered as novel targets for either new vaccines or
anti-infectives.
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Generation and functional studies of anti-peptide antibodies
Antibodies can be powerful tools for probing both the structure and function of proteins. However, many protein
antigens cannot be expressed as native functional proteins due to many reasons including insolubility and
cytotoxic effects of the translated product. One approach to overcome these problems is by generating antipeptide antibodies against predicted epitopes derived from the amino acid sequence of the protein. In this
project, it is intended to generate anti-peptide antibodies against a protein using a combination of protein
sequence analysis, manual and automated solid phase synthesis of peptides, their characterisation and
purification, generation of rabbit polyclonal antibodies and assay using ELISA techniques.
FOOD SCIENCES/FOOD BIOTECHNOLOGY/FOOD MICROBIOLOGY
DR ANDREAS LOPATA
Evaluation of the affects of seafood processing on their allergenicity
Allergies to foods are a significant public health concern throughout the world, effecting up to 4% of adults and
8% of children. More than 90% of allergic reactions can be attributed to exposure to eight food groups, including
fish and shellfish. The allergic response is usually mediated by the interaction of specific IgE antibodies to
allergenic molecules. Food undergoes processing conditions to improve sensory qualities, but proteins undergo
biochemical changes that might influence allergenic proteins. This project will employ various techniques such
as heat and non-thermal processing to evaluate the affect of altered allergenicity of shrimp allergens.
Parasite infections in Australian fish with the nematode Anisakis - a potential health risk for consumers of
infected fish
The World Health Organization has estimated the number of people at risk of parasite infections from seafood,
including those in developed countries, as more than half a billion. Through the growing international market for
seafood and demographic changes of heating habits, increasing reactions to the food-borne parasite Anisakis
have been linked to the ingestion of this nematode, which causes human Anisakiasis and life-threatening allergic
reactions. The project will determine the prevalence of Anisakis infection in five consumed Australian fish
species using microscopy analysis supported by molecular methods (DNA and protein analysis) to identify
subspecies of Anisakis.
MS PRUE BRAMWELL
Various Food Microbiology projects can be offered by RMIT in conjunction with Food Science Australia at
Werribee, Primary Industries Research Victoria (PIRVic) at Attwood or Knoxfield, or at the Australian Starter
Culture Research Centre at Werribee. The honours project work would normally be based off-campus at one of
the establishments above. Please see Prue Bramwell for further details or to discuss other Food Microbiology
project options.
PLANT BIOTECHNOLOGY & PATHOLOGY
ASSOC. PROF. TREVOR STEVENSON and PROF. DAVID STALKER
The examination of the high level expression and stability of foreign proteins expressed in genetically
engineered plant chloroplasts
In particular, these projects will examine the interaction between the nuclear-expressed transgenes and foreign
genes expressed in genetically engineered chloroplasts. The projects will involve molecular biology techniques
(gene cloning, PCR, DNA sequencing) as well as plant tissue culture, nuclear and chloroplast transformation
technologies (Agrobacterium mediated nuclear transformation and microprojectile bombardment mediated
chloroplast transformation).
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DR GREG NUGENT
Macrochloroplast plants – behaviour in vitro
Several lines of transgenic tobacco have been generated which contain only one or a few large chloroplasts
(‘macrochloroplasts”) per cell. This project will examine how these cells behave during cell divisions induced
during tissue culture. The fate of these large organelles will be followed during division and regeneration from
whole tissues and isolated protoplasts. The regeneration will be compared to wild type tobacco to determine
whether cells containing either a greatly reduced or increased number of chloroplasts per cell behave differently
in vitro. The transient expression of reporter genes such as gfp in macrochloroplasts will also be investigated.
Abiotic stress resistance via plastid transformation
Transgenic plastids are an attractive means of attaining high level of foreign gene expression. This project will
combine gene cloning, vector construction and plastid transformation of tobacco with a prokaryotic catalase gene
to determine whether increased tolerance to stress is achievable. These organelles currently have no known
catalase activity, so the addition of an additional enzyme activity, to mitigate the effects of hydrogen peroxide,
will be examined.
ASSOC. PROF. EDDIE PANG
Identification of differentially expressed genes during flavour development in varieties of strawberry
(Fragaria spp.) by DNA microarrays (2nd Stage)
In recent times, strawberry breeders have produced varieties with consistent yield, long fruiting/harvesting
periods and good shelf-life. Unfortunately, current commercial varieties such as “Selva” lack the desirable
flavour of older varieties. Strawberry aroma and flavour are from a mixture of over 300 organic compounds, and
are therefore difficult traits to select for in breeding programs. The aim of this project are (1) to construct a larger
and improved microarray with 300-500 oligonucleotides/ESTs representing genes which may have possible roles
in ripening and flavour development (from a previous Honours project) and to study differential gene expression
in different varieties of strawberry during the various stages of fruit ripening.
Production and characterisation of an enriched cDNA library for hostile soil stress factors for chickpea
“Hostile Soils” are common in many farming regions of Australia, and they are unsuitable for plant growth
because of factors such as excessive acidity, salinity and boron. The aims are (1) to develop hydroponic testing
systems for waterlogging, salinity and acidity tolerance, (2) to identify chickpea varieties which are highly
tolerant to each stress, (3) to challenge each tolerant variety with the corresponding stress factor, and to
subsequently produce a pooled cDNA library from all varieties, and all plant parts, and (4) to construct a
microarray with 200-300 randomly selected cDNAs to reveal those which are up- or down-regulated during
stress, and (4) partially characterise this library by single-pass sequencing of selected cDNAs.
Construction of a microarray for the identification of Chinese medicinal herbs
There are over 400 herbs used in Chinese herbal formulations. An important issue in herbal medicine is the
contamination or substitution of certain herbs with toxic or less effective species. The aim of this project is to
use microarray technology to identify herbal species accurately, both in fresh, and dried/powdered preparations.
If successful, this technique may replace older, and more laborious methods of DNA fingerprinting. A library of
random DNA sequences from a number of herbal species will be used in the construction of a microarray. The
array will be validated with samples of herbal preparations to gauge its sensitivity and accuracy.
Identification of defence-related genes for Ascochyta Blight resistance in Pea (Pisum sativum)
Ascochyta blight is a devastating disease in pea, annually destroying 10-40% of Australia’s pea crop. A cDNA
library enriched for defence-related transcripts was constructed from challenged grasspea plants (a close relative
of pea) by a previous Ph.D. project. The aim of this project is to construct a cDNA microarray with 300-500
selected cDNAs and to use this array to examine the expression of defence-related genes in a selection of
susceptible, tolerant and resistant pea varieties.
ASSOC. PROF. ANN LAWRIE
Salt-tolerance in rhizobia
Salt-tolerant clover rhizobia have been isolated in a recent student project and shown to increase clover
productivity by 20% under moderately saline conditions. The aim of this project is to find the basis for this salttolerance and investigate if it is a common mechanism covering more than one species.
The project will
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involve screening rhizobia from other plant species for salt-tolerance, finding salt-tolerance markers, isolating,
cloning and sequencing the genes and comparing the performance of salt-tolerant and salt-intolerant species in
nodulation using genetically marked strains.
Rhizobial persistence and competitiveness in soil
Rhizobia bacteria cause nitrogen-fixing nodules on legumes (pea family) that allow the plants to access
atmospheric nitrogen and enrich the soil as they die and decay. But where are the rhizobia in soil between
legumes, and why do clover rhizobia survive much better than lupin rhizobia? The project will involve
inoculating genetically marked strains of rhizobia into soils under sterile and non-sterile conditions and
fractionating the soil to find out where they are and how that affects competition for legume nodulation. It will
also involve investigating the high degree of antibiotic production and resistance in rhizobia and how that affects
persistence and competition for soil microsites and nodulation.
Detection of orchid mycorrhizal fungi
(with Mr Rob Cross, Royal Botanic Gardens, and Ms Ruth Raleigh, DSE)
Spider orchids (Caladenia spp.) need the mycorrhizal fungus Sebacina vermifera for germination and growth.
These fungi have been traced on eucalypt and epacrid roots using specific primers that detect only S. vermifera.
The aim of this project is to use these specific primers to find how widely these orchid fungi are distributed, in
what other plants in endemic sites, and if these woody plants indeed act as ‘nurse’ plants for successful orchid
establishment. The project will involve collecting roots and soil from the sites, orchids in season, PCR using the
specific and universal primers and growing orchids in axenic conditions with a variety of suspected ‘nurse’
plants.
Survival and reproduction in endangered species
(with Andrew Pritchard, DSE)
There are many endangered species covered by the Flora and Fauna Guarantee Act for which there is not yet an
effective Recovery Plan because so little is known about the species’ biology. In most cases some critical
questions are vital to writing such a plan, e.g. are discrete populations genetically distinct, why do some
populations seed and others do not? Examples of such species are Westringia crassifolia, Grevillea montiscola,
Daviesia sp., Pimelea spinescens and the orchids Corybas aff. diemenicus and Pterostylis ‘rufa’ (orchids would
need a mid-year start). The aim of the project would be to survey the surviving population(s), sort out genetic
diversity, investigate blockages to seed production and factors that prevent the seeds germinating.
Ericoid mycorrhizal survival in soil
Ericoid mycorrhizal fungi infect species in the endemic Australian family Epacridaceae (heaths) wherever they
grow, but the reservoir for the fungi in soil between plants is not known. The fungi are also important in
detoxification and utilisation of organic matter that is difficult to break down in soil. This may explain the
dominance of epacrid plants after frequent fires in many heathlands and dry sclerophyll forests throughout
southern Australia. The aim of this project is to find what and where the surviving propagules are and what
happens to them during and after a fire that leads to epacrid domination after frequent fires. The project will
also investigate the relationship between the two mycorrhizal fungi that form ericoid mycorrhizae.
Biological control of the weed Arctotheca calendula (Cape Daisy)
(with Dr David McLaren, Keith Turnbull Research Institute, Frankston)
Cape Daisy is becoming an increasing weedy problem in many habitats and has spread considerably in recent
years. It is not well controlled in horticulture, remnant vegetation and native habitats. The aim of this project is
to survey its suitability for biological control by studying the genetic diversity of the host plant using molecular
methods and to find and endemic Australian pathogens that might be developed for inundative control
techniques. The project will also investigate the physiological mechanisms by which it manages to invade and
dominate pastures and turfs.
Basis for variation in the dermatophyte Trichophyton rubrum
Previous studies have shown that T. rubrum, the most common cause of tinea in humans, is spreading and
becoming more variable morphologically, yet it seems uniform genetically. The aim of this project is to study
the reasons for this polymorphism, the effects of infection site and previous antifungal treatment, and to devise a
means of finding a genetic marker. It is likely that the polymorphism in morphology is due to differential
expression of genes for pigmentation and growth rate. This may also be linked to pleiomorphism – the ability of
the fungus to lose its colour and/or sporulation and so complicate diagnosis.
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DR TIEN HUYNH
Viral control in Cymbidium spp.
Cymbidium orchids are susceptible to viral infection, predominantly by Cymbidium mosaic viruse (CymMV) and
Odontoglossom ringspot virus (ORSV). Infection symptoms are ambiguous and difficult to diagnose by visual
inspection. This project will investigate and simplify methods to detect mono, dual and multiple viral infections
using molecular biology, electron microscopy and immunological assays. Experimental treatments on plants will
be conducted to manage viral proliferation and quantified using gene expression qPCR.
Flower pigment gene expression due to environmental factors in Cymbidium spp.
Chalcone synthase is the upstream enzyme responsible for catalysing the reaction for flower colour. The effect
of environmental factors on the regulation of this phenylpropanoid metabolic pathway for the synthesis of
flavonoid metabolites and downstream products will be investigated using qPCR and immunoblotting to detect
gene expression and protein transcription, respectively.
Gene expression of Brassica spp. using qPCR
(in collaboration with Dr Eddie Pang)
The expression of specific genes is often used to aid in the selection for desirable cultivars for agriculture.
Several genomic databases exist for a variety of important food crops on the regulatory mechanisms involved in
plant pathways critical for survival and commercial productivity. Gene expression of important cellular
pathways for disease resistance will be investigated using qPCR from existing databases.
ENVIRONMENTAL BIOLOGY & ECOTOXICOLOGY
ASSOC. PROF. DAYANTHI NUGEGODA
The spatial distribution of salinity tolerance and factors affecting salinity tolerance in invertebrates.
Increase in salinity is a major environmental problem impacting Australian freshwaters. This project will
examine the spatial distribution of the salinity tolerance of two to four species of aquatic invertebrate in the
Barwon River, and the Murray – Darling catchment. Invertebrates would be collected from several sites within
the catchments, which have a different salinity history. Acute salinity tolerance experiments will be conducted on
the invertebrates collected from each of the sites. The effect of acclimation, water temperature and ionic
composition on salinity tolerance of the invertebrates will also be investigated.
N.B. This project is on an LWA (Land and Water, Australia), research grant in collaboration with the NRE,
CSIRO and QNR&M and a scholarship may be offered to an excellent candidate. Those interested in this project
are encouraged to apply for the RMIT summer scholarship offered by DN.
Biomonitoring heavy metals in urban streams and wetlands. – in collaboration with Melbourne Water.
Freshwater fish and crustaceans will be sampled from urban streams and wetlands in the Melbourne metropolitan
area. Samples will be dissected into component tissues, digested and analysed for trace metals on the new
Atomic Absorption Spectrophotometer in our labs. Melbourne water will supply data on water and sediment
quality of the sample sites. Bioaccumulation of heavy metals in biota and food chains will be calculated. In
addition laboratory experiments will be conducted using the same species in simple food chain microcosms to
evaluate the importance of the food and water/sediment exposure. This project will contribute to the evaluation
of trace metal contamination in Melbourne. N.B. This project is on a research collaboration with Melbourne
Water and a scholarship may be offered to an excellent candidate.
Effects of heavy metals and/or pesticides on the early life stages of the yabby Cherax destructor.
The common freshwater crayfish (yabby) Cherax destructor will be used as a laboratory model to assess the
toxicity of selected pesticides to early life stages of an Australian freshwater species. Yabbies will be bred in the
hatchery on level 2 and two week and four week old juveniles used for toxicity testing of the pesticides
according to the ASTM 1998. An Honours project conducted in 2000 successfully assessed the toxicity of
glyphosate and endosulfan to early life stages of the yabby. This work will be extended to examine the effect of
environmental factors on the toxicity of pesticides.
Isolation and characterisation of metallothionein from the yabby Cherax destructor
(with Dr Eddie Pang)
Metallothionein is a cysteine-rich low molecular weight, metal binding protein, induced by heavy metals This
protein thus acts as a detoxification mechanism in animal tissues by sequestering the metal and has been
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investigated as a biomarker of metal pollution. Metallothionein has been isolated in a range of animal species,
however there are few reports on the isolation of this protein from Australian native species. The project seeks
to induce metallothionein in the native yabby by exposure to selected heavy metals; isolate and characterise it
using gene array technology. Molecular probes will be developed to investigate the presence of the gene for
metallothionein.
The toxicity of agricultural chemicals to Daphnia carinata and /or Hydra vulgaris.
Agricultural chemicals like pesticides and herbicides are not routinely tested on Australian species before being
licensed for use in Australia. It is therefore vital that research be conducted on the toxicity of such chemical to
Australian daphnids. This project will an added component to previous research conducted on the toxicity of
herbicides to Daphnia carinata. in collaboration with the Arthur Rylah Research Institute of the NRE. D.
carinata, and/or Hydra vulgaris will be cultured in the laboratory and the effect of commonly used agricultural
pesticides and herbicides on its survival, growth and reproduction assessed
DR BEN KEFFORD
What is the effect of increasing atmospheric CO2 on calcifying animals?
(with Dr Peter Obendorf)
The potential of increasing atmospheric CO2 concentrations to cause global warming has attracted considerable
attention. By contrast, much less attention has been given to the resultant increase in the concentration of
dissolved CO2 in the oceans that is acidifying (lowering pH) the oceans and reducing the concentration of
carbonate (CO32-). It is hypothesised that reduced oceanic carbonate concentrations will disadvantage organisms
with external calcium carbonate skeletons such as gastropods, bivalves and corals. It is predicted that by 2050
large portions of the Antarctic (or Southern) Ocean will pass a threshold where calcifying animals will find it
very difficult to build and maintain their shells, but the effects above the threshold conditions are not clear. This
project would involve exposing suitable temperate animal species to various dissolved CO2 concentrations and
determining the biological effects.
Chloride cells as novel biomarkers of salinity stress
Increasing salinity in rivers and wetlands is a major environmental problem and is likely to have negative effects
on freshwater biodiversity. Current biomonitoring programs measure presence/absence of species and
sometimes their abundance. These programs can detect environmental impacts, i.e. loss of species or decline in
their abundances, after they have happened but they cannot detect that a population is under stress so that
preventive action can be taken to prevent an environmental impact. Chloride cells are involved in the transport
of salt ions into and out of the bodies of aquatic invertebrates and fish. Their numbers vary depending on the
salinity and the osmoregulatory stress an organism is under and it may therefore be possible to use them as a
biomarker that an organism is suffering salinity stress. This project would involve exposing freshwater
macroinvertebrates to various salinity levels and measuring the change in chloride cells as well as effects of
salinity on mortality and growth. Results from the project would be incorporated into an evaluation of the use of
chloride cells as a biomarker of salinity stress. There is an Honours scholarship available for this project.
Effect of water temperature in uptake of metals in marine invertebrates
Marine organisms throughout the world are at risk from metal pollution and Antarctica is no exception, where
metal pollution, from disused tips, appears to be impacting on marine communities. Our on-going research has
measured the sensitivity of Antarctic marine invertebrates to metals (Cu, Zn and Cd). We plan to compare the
sensitivity of Antarctic and temperate species. Antarctic marine waters are cold, -1.8oC to +1oC, and thus the
metabolic rates of exothermic organisms are greatly reduced, relatively to temperate species. It may thus be that
uptake rates of metals by Antarctic marine invertebrates are low relative to temperate species. This project
would expose a temperate marine invertebrate species to various metal concentrations at different water
temperatures and measure the metabolic rate of the organisms, the uptake rate of metal and mortality. The
results of this project would feed into the process of designing water quality guidelines for Antarctic waters.
The rapid toxicity test – the sensitively of freshwater invertebrates to metals or pesticides
In designing water quality guidelines, ecotoxicologists have conventionally accurately and precisely measure the
tolerance of one or a few species to some toxicant. The species selected for testing are not chosen randomly;
indeed they are chosen with specific traits in mind. Then from a small non-random sample of species, the effect
of the toxicant is extrapolated to all species. Rapid testing is a new approach were many species are tested and
they are selected to be reprehensive of the community of interest but for each species only approximate measures
of the tolerance of each is made. Somewhat paradoxically, more accurate estimates of the effect of all species
can be made from this larger sample of approximate tolerances than from a smaller sample of more accurate
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tolerances. This project would apply the rapid toxicity test to measure the tolerance of freshwater
macroinvertebrates to a metal or pesticide.
The effect of salinity in combination with sedimentation on freshwater macroinvertebrates
Increasing salinity in rivers and wetlands is a major environmental problem and is likely to have negative effects
on freshwater biodiversity. Salinity rarely, if ever, occurs in isolation to other changes in the environment, yet
there is little is known of its effect in conjunction with other stresses and there is considerable concern as to the
combined effect of the combined effects of elevated salinity and sedimentation on freshwater macroinvertebrates.
In this project the mechanisms by which sediment impacts on freshwater macroinvertebrates will be investigated
experimentally and the potential for these effects to be alerted by salinity examined.
Biochemical level effect of salinity on a salt-tolerant freshwater damselfly
(with Dr Andreas Lopata)
Despite regularly occurring in freshwaters, the damselfly Ischnura heterosticta grows faster and completes the
aquatic phase of its life-cycle quicker in moderately saline water than in freshwater. The biochemical
adaptations in I. eterosticta that allow this increase in growth rate are not known, nor is the level of stress that it
experiences under different salinities. This project would grow I. heterosticta at different salinities and measure
stress proteins and growth hormones, as well as haemolymph (internal fluid) salinity and ionic concentrations at
different salinities, to determine how I. heterosticta responds to salinity at a biochemical level.
DR JEFF SHIMETA
Protozoa in marine biofilms and their interactions with settling invertebrate larvae
Various sessile marine invertebrates (barnacles, mussels, tunicates, polychaetes, etc.) colonise hard substrata
such as rocks, piers, and boats. The free-swimming larvae of many of these species select a site based on
environmental cues such as the nature of biofilms on the surface. Protozoa such as ciliates and flagellates are a
common but poorly understood component of marine biofilms. Initial studies will document the colonisation and
succession of protozoa in biofilms. The roles of protozoa in facilitating or inhibiting larval settlement will then
be studied using settling plates in the lab and the field.
Microbial ecology in nutrient-enriched or wastewater-impacted coastal sediments
Activities of microbes such as bacteria, microalgae, and protozoa are important for nutrient cycling in coastal
sediments. We hope to establish a long-term seasonal study of microbial dynamics at locations in Port Phillip
Bay that are impacted by excess nutrients, possibly near wastewater discharge. Initial studies will characterise
the microbial communities and their activities at impacted vs nonimpacted sites. Analyses will involve intensive
microscopical identification and counting of organisms.
Direct and indirect interactions between protozoa and contaminant-degrading bacteria in marine sediments
Some hydrocarbons and other toxicants can be metabolised or degraded by certain bacterial species in the
environment. This biodegradation is a key aspect in bioremediation of contaminated sites. The protozoan
community might influence degradation rates, either directly by grazing on contaminant-degrading bacteria, or
indirectly by grazing on competing bacteria. You will investigate these interactions by measuring grazing and
growth rates of protozoa and bacteria in laboratory cultures.
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MASTER OF APPLIED SCIENCE (M.App.Sc.)
DOCTOR OF PHILOSOPHY (Ph.D.)
Research scholarships for postgraduate (and some Honours) students. These include Australian Postgraduate
Awards with stipend, RMIT Postgraduate Awards, School Scholarships, John Storey Junior Memorial
Fellowships, Industry R & D scholarships, etc. Since these typically close about September-October for the
following year, prospective applicants should see staff as soon as possible for February enrolment in Honours,
M.App.Sc. or Ph.D.
Both degrees are available by research within the Department. They require extensive work on original research
and the presentation of a thesis for external assessment. The M.App.Sc. degree normally takes two years and
the Ph.D. degree three years after completing a four-year Honours degree.
Both qualify graduates for
employment as professional scientists at levels above those of first-degree holders. Areas of research available
are similar to those for Honours degrees. Scholarships to cover living expenses are available for academically
competitive students. Topics are within the areas of interest of the staff of the Department. A summary of
these is available in the list of potential projects below, many of which are suitable for either Honours or more
detailed (M.App.Sc. or Ph.D.) study. Details on how to apply are available from the postgraduate students coordinator in the Department (A/Prof. A.C. Lawrie).
N.B. Honours, M.App.Sc. and Ph.D. degrees may be undertaken full-time or part-time.
HONOURS
An optional fourth (Honours) year is available in Applied Biology/Biotechnology for graduates from the threeyear degree B.App.Sc. (Applied Biology/Biotechnology) or equivalent.
ADVANTAGES OF COMPLETING THE HONOURS YEAR
General:
1. development of
- ability to think critically and logically, independent decision-making skills
- specialist skills, greater knowledge and understanding of current research
Employment:
2. qualification for higher levels of employment immediately on graduation
3. competitive advantage over three- year graduates
4. extra qualification after only one more year's study
Further study
5. eligibility for scholarships on completing the Honours degree (four-year degree or equivalent needed)
6. removal of need to complete Master's preliminary year
7. chance to find out if you are suited to conducting your own research.
COURSE STRUCTURE AND ASSESSMENT
Students enrol for five courses: Research Methods, Experimental Design and Analysis, Advanced Biology,
Research Project Planning and Research Project. Within the program, each student completes the following:
a. a supervised project of original scientific investigation
This is worth 65% of the final mark and is assessed by:
1) a project report of not more than 50 A4 double-spaced typed pages, together with relevant illustrations
(worth approximately 60% of the final mark), to be submitted at the end of October and assessed by a
panel of academic staff, which may include an external examiner)
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2) a seminar of about 20 minutes, followed by about 10 minutes of discussion, held about the end of
September and assessed by a panel of academic staff
b. a program of formal work
This is worth 35% of the final mark and has three elements:
1) research methods, run in first semester, comprising lectures, tutorials, assignments and examinations on
topics such as experimental design and analysis, thesis writing and laboratory safety (worth 13% of the
final mark)
2) advanced biology, run in first semester, comprising studies in areas of your project topic; this
comprises associated reading and the writing of a literature review and delivery of a seminar (worth
about 10% of the final mark)
3) experimental design and analysis, run throughout the year and assessed by two examinations, one midyear and the other at the end of the year, after submission of the project report (worth 12% of the final
mark).
GRADES IN HONOURS DEGREE
Five results are possible: Honours 1 (HD), Honours 2A (DI), Honours 2B (CR), Honours 3 (PA) and Fail (NN),
and are decided on aggregate marks for each of the courses.
QUOTA
There is a quota of about 10-15 students, who are selected on the basis of academic achievement.
ENTRY REQUIREMENTS
Candidates must have:
1. completed all formal academic studies for the B.App.Sc. (Applied Biology/Biotechnology) degree at RMIT
(or an approved equivalent degree with major studies in final year in biology)
2. above-average results in the three-year degree (expected average grade of credit or above, or equivalent)
3. obtained minimum grades of credit (or approved equivalent) in studies in the area in which they intend to
pursue their major Honours studies
4. a topic and a supervisor for the research project component
5. the approval of the Head of School.
HOW TO APPLY
1. Before the end of the semester, approach the member(s) of staff with whom you are interested in conducting
the research project, to discuss each in more detail. Feel free to approach several potential supervisors in
order to clarify what you would be doing and to be certain that this is your preferred project.
2.
Obtain a direct application form from the Office for Prospective Students (Level 2, Union Building) or the
RMIT web site. Fill this in and attach an up-to-date transcript of results. Please attach the form from
this information leaflet, giving details of your first three proposed supervisors and research projects
(please note that your application is incomplete without this and will not be considered). Please note
that supervisors are only allowed a maximum of two Honours students (to ensure each has sufficient time to
supervise the students) and so do not nominate all three projects with one supervisor.
3.
Return the form to the Office for Prospective Students by the due date (10 November). Late applications
will be considered for Round 2, but only if places are still available.
Selection will be shortly after final results are available, in early December. Applicants will be ranked on
academic achievements and the first approximately 10-15 applicants offered places. Other applicants will be
placed on a reserve list, in order of ranking, and will be contacted if a place becomes available. Applicants
wishing to know their ranking should contact the Honours Coordinator.
ENROLMENT DATE: Early February 2008
STARTING DATE: the first day of Semester 1 in 2008
HONOURS CO-ORDINATOR: Assoc. Prof. A.C. Lawrie (Room 223.1.68)
(Tel. 03 9925 7157, Fax 03 9925 7110, e-mail [email protected])
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RMIT
BIOTECHNOLOGY & ENVIRONMENTAL BIOLOGY
SCHOOL OF APPLIED SCIENCES
APPLICATION FOR HONOURS
NAME:
STUDENT NO.:
ADDRESS FOR CONTACT IN EARLY DECEMBER:
TELEPHONE NO. FOR CONTACT IN EARLY DECEMBER:
If you supply this number, you will be contacted by telephone if you are to be offered a place. If you do not,
your first notification will be by mail; this may take some time.
PROPOSED SUPERVISOR AND TITLE OF TOPIC (IN ORDER OF PREFERENCE):
Please note that at least the third preference should be for a different supervisor
1.
--------------------------------------------------------------------------------------------------------2.
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PLEASE ATTACH THIS FORM TO YOUR DIRECT APPLICATION FORM. YOUR APPLICATION
IS INCOMPLETE WITHOUT THIS AND WILL NOT BE CONSIDERED.
PLEASE APPLY EVEN IF YOU ARE UNCERTAIN OF YOUR FINAL DECISION AT THIS STAGE,
SINCE LATE APPLICATIONS WILL NOT BE CONSIDERED FOR FIRST ROUND OFFERS.
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