Honours project list - RMIT University

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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 Sci
ences

RMIT University

PO Box 71
,
Bundoora
,
Vic 3083

Tel. (03) 9925 7157
,
Fax (03) 9925 7110

Email
aclawrie@rmit.edu.au

http://www.rmit.edu.au/applied
-
scien
ces

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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 researc
h for Honours, M.App.Sc. or Ph.D. degrees in the areas indicated below to contact the staff
directly (
firstname.lastname@rmit.edu.au
)or the Honours and Postgraduate Coordinator for further information
(A/Prof. Ann Lawrie, tel. 03 9925 7157, fax 03 9925 7110, e
-
mail
aclawrie@rmit.edu.au
).


MICROBIAL
BIOTECHNOLOGY
/H
UMAN & ANIMAL DISEASE

Prof. Peter Coloe

(Head of School)

Molecular biology and microbiology; vir
ulence factors and vaccines for enteric
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. M
argaret
Deighton

Molecular pathogenesis and epidemiology of staphylococcal and streptococcal
infections of humans and dairy cattle; detection of pathogens in biosolids

Dr Duncan Rouch

Pathogen die
-
off in biosolids (treated sewage)

Dr Danilla Grando

Diagn
ostic 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 Pau
l 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) again
st 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/F
OOD 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 b
lue genes in cotton

A/Prof. Trevor
Stevenson

Molecular biology and biotechnology of plants, in
the high level expression and
stability of foreign proteins expressed in genetically engineered plant chloroplasts

Dr Greg Nugent

Plant tissue culture and tran
sformation 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 diseas
e 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

O
rchidology: Tissue culture, propagation, mycorrhizal associations, molecular
biology, immunoblotting, microscopy


ENVIRONMENTAL
BIOLOGY/ECO
TOXICOLOGY

A/Prof. Dayanthi
Nugegoda

Ecotoxicology of heavy metals, pesticides and organics esp. in fish and inverte
brates.
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 ac
idification.

Dr Jeff Shimeta

Microbial ecology in impacted coastal sediments, emphasizing protozoa

A/P Bruce Anderson*

*adjunct appointment

Biodegradation of toxic chemicals

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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 BR
AMWELL

................................
................................
................................
................................
....

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 NUGEG
ODA

................................
................................
................................
...

10

DR BEN KEFFORD

................................
................................
................................
................................
.........

11

DR JEFF SHIMETA

................................
................................
................................
................................
.........

12


ADVANTAGES OF COMPL
ETING 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 BIOTECHNOL
OG
Y/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 projec
t 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 fr
om
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 aro
A
-

S.

typhimu
r
ium
and eval
uation of the antibody and cell
-
mediated responses that are evoked to the
various vaccine strains.



DR TAGHRID ISTIVAN


Epidemiology and pathogenesis of Campylobacter concis
us

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 t
he 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 investig
ated through the
capability of these clinical strains to invade differ
ent tissue culture cell lines.


Molecular an
alysis of the
pld
A 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 in
vasion 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
fla
A
and
fla
B

genes
encode for

endoflagella,
a spe
cific character in spirochaetes
. Our
preliminary
investigations
indicated that the
fla
B1 gene nucleotide sequence is conserved
(
to some extent
)

in
Brachyspira

spp.
This project
will investigate the differences in
fla
B1

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 C
hildren’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 regulatio
n 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 subt
ractive 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
.


Det
ection 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 biosol
ids 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 fertilis
ing
agricultural crops. While standard methods have been developed to estimate the pathogen load at various stages
of the treatme
nt 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. Recen
tly
,

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 t
o 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 an
d 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 m
olecular 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 chic
ken 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 ly
ophilisation 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
o
C. 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 a
nd 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 con
centration 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 whil
e a 96
-
well
plate most probable number method ha
s 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 Ab
s 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 effec
tively 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 im
mune 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 d
iagnostic, 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 molecula
r 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
depend
ing 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 cha
racterisation 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 tar
gets 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 anti
-
peptide 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
purificati
on, 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 signi
ficant public health concern througho
ut 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 media
ted 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 variou
s 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 consumer
s

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 offer
ed 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 w
ork would normally be based off
-
campus at one of
the establ
ishments 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 an
d 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 m
ediated
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 wil
d 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 pr
okaryotic 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 ex
amined.



ASSOC. PROF. EDDIE PANG


Identification of differentially expressed genes during flavour development in varieties of strawberry
(Fragaria spp.) by DNA microarrays (2
nd

Stage)

In recent times, strawberry breeders have produced varieties with consi
stent 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 de
velopment (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 fac
tors 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 waterl
ogging, 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 var
ieties, 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.


Con
struction 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 effect
ive 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 gra
sspea 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
susceptibl
e, 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 salt
-
tolerance 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
-
tol
erance 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 caus
e 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 lupi
n 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 Botan
ic Gardens, and Ms Ruth Raleigh,
DSE
)

Spider orchids (
Caladenia

spp.) need
the mycorrhizal fungus
Sebacina vermifera

for germination and grow
th.
These fungi

have been
traced

on eucalypt and epacrid roots
using specific

primers that detect only
S. vermife
ra
.
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 pro
ject 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 specie
s

(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
questio
ns 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 o
rchids
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 prev
ent 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 w
hat 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 betwee
n 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 ha
bitats 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 a
im 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

orchi
ds 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 m
ethods 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 col
laboration 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
p
lant 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.

DAYANTH
I 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 sa
linity 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 o
ffered 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 t
race 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
Cher
ax 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 lev
el 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. Th
is 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 molecula
r 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 r
ange 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 herbicide
s 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 researc
h 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
pestic
ides and herbicides on its survival, growth and reproduction assessed



DR BEN KEFFORD


What is the effect of increasing atmospheric CO
2

on calcifying animals?

(
with

Dr Peter Obendorf)

The potential of increasing atmospheric
CO
2

c
oncentrations to cause glo
bal warming has attracted considerable
attention.

By

contrast
,

much less attention has been given to the resultant increase in the concentration of
dissolved
CO
2

i
n the oceans
that

is acidifying (lowering pH) the oceans and reducing the concentration of
c
arbonate (CO
3
2
-
).

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
p
roject would involve exposing
suitable temperate animal

species to various dissolved
CO
2

concentrations and
determining the biological effects.


Chloride cells as

novel biomarker
s

of salinity stress

Increasing salinity in rivers and wetlands is a major environmental problem and is likely to have negative effec
ts
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 happene
d 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
macro
invertebrates 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 sa
linity 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, wher
e
metal pollution, from disused tips, appears to be impacting on marine communities.

Our o
n
-
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 tempe
rate species.

Antarctic
marine waters are cold,
-
1.8
o
C to +1
o
C, 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 lo
w 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.

Th
e
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, ecotoxic
ologists have conventionally accurately and precisely m
easure
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
-
ran
dom 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 meas
ures
of the tolerance of each is made.

Somewhat paradoxically
,

more accurate estimates of the effect of all species
can be made
from this larger s
ample of approximate tolerances

than from a smaller sample of more accurate
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tolerances.


This project would a
pply 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 macroinvertebrate
s

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 know
n

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 macroinvertebrate
s

will be inve
stigated
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 le
vel of stress that it
expe
riences 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 conc
entrations at
diff
erent 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 stu
died 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 activ
ities 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 gra
zing 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 b
acteria 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, Indus
try 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 rese
arch 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 d
egree. 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 acade
mically
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 co
-
ordinator 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 three
-
year degree B.App.Sc. (Applied Biology/Biotechnology) or equivalent.


ADVANTAGES OF COMPLETING THE HONOURS YEAR


General:

1. development of

-

ability to think critica
lly 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 thre
e
-

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. ch
ance 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 assess
ed 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 minute
s 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
compr
ises 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 mid
-
year and the other at the e
nd 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 f
or 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/Biotechno
logy) 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 approv
ed 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 th
e 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 pref
erred 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 supervisor
s

and research project
s

(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 Roun
d 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 applican
ts 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
aclawrie@rmit.edu.au
)


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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.







---------------------------------------------------------------------------------------------------------

3.








PLEASE ATTACH THIS FORM TO YOUR DI
RECT 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
.