Download honours projects for february 2017

Faculty of Science, Engineering & Technology
Department of Chemistry and Biotechnology
HONOURS PROJECTS
FOR
FEBRUARY 2017
Biochemistry, Biotechnology,
Chemistry & Environmental Science
PREFACE
If we knew what it was we were doing, it would not be called research, would it?
Albert Einstein
Honours is an intellectually rewarding and personally fulfilling experience.
Intellectually, you will undertake study at a higher level than in your undergraduate
degree both in your honours units and when you carry out research for your thesis,
report or dissertation. The report allows you to focus on an area of particular interest
and provides the opportunity to make contribution to knowledge and wider debates in
your discipline.
On a personal basis, the skills acquired during this period will enhance your future
career prospects in a broad range of occupations, in both the public and private
sectors, giving you an edge compared with a straight undergraduate pass degree.
While your bachelor’s degree provides you with fundamental knowledge
underpinning the scientific principles related to real-life applications, during your
honours year you will have an opportunity to develop soft and transferable skills.
Research is about discovery, the proposal of new ideas and the assessment of new
hypotheses. It is about the establishment of facts through enquiry and exploration,
and its outcome is new knowledge, leading to deeper understanding of mechanisms
and the development of new and improved procedures. To ensure that the use of
research results is maximised, it must be disseminated in a suitable format, and you
will learn a lot about scientific writing (abstract, poster, journal article, thesis, etc.)
The purpose of this guide, intended for students completing their bachelor’s degree
in Science, is to provide a list of research projects available to those planning to
pursue an Honours year in Biochemistry, Biotechnology, Chemistry or
Environmental Science.
Interested students are strongly recommended to meet with the respective academic
to discuss details of projects. Should you need any information about application
process, please contact me directly.
Dr Huseyin Sumer
Honours Coordinator (Science)
School of Science
http://www.swinburne.edu.au/study/course/bachelor-of-science-honours/
FOR PERSONAL USE ONLY
PLEASE DO NOT PRINT, COPY, DISTRIBUTE OR SHARE
2
TABLE OF CONTENTS
Preface……………………………………………………………………………………….....ii
Table of Contents……………………………………………………………………………....iii
Contact Details of Staff…………………………………………………………………….......iv
Summary of Application Process……………………………………………………………...v
Course Structure and Streams………………………………………………………………....vi
Draft Timetable for 2017 ........................................................................................................ .vii
Projects .................................................................................................................................... .viii
CONTACT DETAILS OF STAFF
Title
Name
Email
Phone
Location
Professor
Bhave, Mrinal
mbhave@swin
5759
AS228
Professor
Blackall, Linda
lblackall@swin
8209
AS208
Professor
Harding, Ian
iharding@swin
8715
AS212
Professor
Ivanova, Elena
eivanova@swin
5137
AS222
Professor
Kingshott, Peter
pkingshott@swin
5033
AS-224
Professor
Mainwairing, David
demainwaring@swin
5421
AS204
Professor
Palombo, Enzo
epalombo@swin
8571
AS226
Professor
Associate
Wang, Feng
fwang@swin
5065
AS206
Professor
Yu, Aimin
aiminyu@swin
8161
AS 214
Dr
Barton, Tony
pbarton@swin
8893
AS217
Dr
Eldridge, Daniel
deldridge@swin
5681
AS227
Dr
Krishnamurthy,
Ajay
akrishnamurthy@swin
5129
ATC 811
Dr
Mahon, Peter
pmahon@swin
4880
AS219
Dr
Malherbe, Francois
fmalherbe@swin
5361
AS210
Dr
Sumer, Huseyin
hsumer@swin
8687
AS 218
Dr
Webb, Hayden
hkwebb@swin
5183
AS229
Dr
Zaferanloo, Bita
bzaferanloo@swin
5183
AS229
Note:
All staff emails end with @swin.edu.au
All staff phone numbers start with (03) 9214
SUMMARY OF APPLICATION PROCESS
Basic Eligibility
Bachelor of Science in relevant field with
an overall Credit Average or above
Introspection
What is my preferred field of research?
What do I like/am passionate about?
What are my research strengths/skills?
Am I interested in a PhD?
Approach Academic Staff
Browse through the list of projects
Following your choice of topic(s), contact
and arrange a meeting with the respective
academic(s) to discuss their offerings and
your credentials
Secure a Project
Once you are offered a project, make sure
you and your supervisor agree on the
modalities of attendance, course
components, etc…
Submit an application
You can do that online
https://swinburne.onlineappform.com.au/
COURSE STRUCTURE AND STREAMS
To qualify for a Bachelor of Science (Honours), a student must complete 100 credit points
comprising coursework and thesis units within ONE area of specialisation: Biotechnology/
Biochemistry; Chemistry; Environmental Science; Physics. A unit of study can only be
counted once.
An overall Honours Grading is based on a weighted average of all units, with each unit’s
contribution weighted by its credit point value.




BSc
BSc
BSc
BSc
(Hons)
(Hons)
(Hons)
(Hons)
Unit
Code
with
with
with
with
First Class Honours (H1): 80%-100%
Upper Second Class Honours (H2A): 70% – 79%
Lower Second Class Honours (H2B): 60% – 69%
Third Class Honours (H3): 50%-59%
Unit Name
Level
Credit
Points
Outcome
Unit
4
4
4
4
4
12.5
12.5
12.5
12.5
50
Y
Y
Y
Y
Y
4
4
4
4
4
12.5
12.5
12.5
12.5
50
Y
Y
Y
Y
Y
4
4
4
4
4
12.5
12.5
12.5
12.5
50
Y
Y
Y
Y
Y
Biotechnology/Biochemistry
Students must complete the following five units (100 credit points):
BCH40002 Honours Lectures Part A
BCH40003 Honours Lectures Part B
NPS40010 Research and Professional Skills
NPS40007 Honours Project A
NPS40009 Honours Project C
Chemistry
Students must complete the following five units (100 credit points):
CHE40003 Chemistry Honours Lectures Part A
CHE40004 Chemistry Honours Lectures Part B
NPS40010 Research and Professional Skills
NPS40007 Honours Project A
NPS40009 Honours Project C
Environmental Science
Students must complete the following five units (100 credit points):
BCH40002 Honours Lectures Part A
CHE40003 Chemistry Honours Lectures Part A
NPS40010 Research and Professional Skills
NPS40007 Honours Project A
NPS40009 Honours Project C
DRAFT TIMETABLE FOR 2017
COURSE STRUCTURE AND STREAMS
AM
Sem 1
Monday
Tuesday
Wednesday
Thursday
Friday
BCH40002/
CHE40003
Project A
Project A
Project A
Project A
Project A
Project A
Project A
Project A
Project B
Project B
Project B
Project B
Project B
Project B
Project B
Science
Colloquia
Project B
Project B
BCH40003
CHE40004
PM
NPS40010
AM
Sem 2
PM






Core Lectures
Advanced Lectures
R&P Skills
Research Project A
Research Project B
Science Colloquia
:
:
:
:
:
:
12.5 CP - BCH40002, CHE40003 (generic, common)
12.5 CP - BCH40003, CHE40004 (discipline specific)
12.5 CP - NPS40010 (common)
12.5 CP (topic specific)
50 CP (topic specific)
Built-in Project B and is common to all streams (TBC)
Notes:
 Total research hours for each component is topic specific
 Lab attendance is normally Mon-Fri 9am-5pm, unless otherwise agreed with the
supervisor
 The above timetable is for illustration only
COURSE STRUCTURE AND STREAMS
Project Descriptions of 2017 Chemistry & Environmental Honours Research
Projects
Generation of New Material Surfaces by Self-Assembly of Anisotropically Shaped
Particles (Chemistry)
Supervisors: Professor Peter Kingshott and Dr George Wang
The project aims to develop new exciting material surfaces by designing new methods for
the specific control of colloidal crystal morphologies using particles of different shape
prepared by optical lithography.
Polymeric brushes as ‘non-stick’ surfaces in biointerface science (Chemistry)
Supervisors: Professor Peter Kingshott and Dr George Wang
Surfaces will be modified polymer brushes on surfaces to prevent proteins, cells and
bacteria from sticking to surfaces. Such surfaces are highly relevant in the medtech area
to prevent adverse responses to biomedical materials.
Clean Energy (Chemistry)
Supervisors: A/Prof Chenghua Sun; A/Prof Aimin Yu
Catalysts Design for Better Solar Energy Harvest. The project aims to develop novel 2D
graphene based catalysts for solar hydrogen production and ammonia synthesis at room
temperature. It contains two sections: computational searching (60%) and experimental
validation (40%).
Material Synthesis and Application (Chemistry)
Main Supervisor: A/Prof Aimin Yu
(1) Synthesis of gold nanoparticle modified graphene sheets for photothermal ablation
therapy
(2) Preparation of electroactive graphene-polymer hydrogels for controlled drug release
Material Synthesis and Application (Chemistry)
Main Supervisor: A/Prof Aimin Yu; Rory Mccallum
Encapsulation of phase change materials as latent heat thermal storage for building
applications
Colloid and Surface Chemistry, Water Science
Associate Professor Aimin Yu & Dr Daniel Eldridge
Surface functionalization for the creation of more efficient and effective adsorbents
Adsorption has proven to be a cost efficient and effective means of removing pollutants
from wastewater without the use of any harsh chemical treatment. The push continues to
produce adsorbents that can be more versatile, selective and efficient. Surface-modified
mesoporous silica (MS) has proven to be an adsorbent of particular interest due to its
high surface area, porosity and the reactivity of its surface sites. This project will involve
the synthesis, characterization and employment of MS adsorbents with a view towards
advancing current adsorption capabilities.
COURSE STRUCTURE AND STREAMS
Colloid and Surface Chemistry, Microbiology
Daniel Eldridge, Enzo Palombo, Ajay Krishnamurthy & Ian Harding*
Investigation of the ability of Solid Lipid Nanoparticles (SLNs) to inhibit biofilm formation
In environmental settings and on biomedical surfaces, the formation of biofilms can be
detrimental. Recently, an exciting development has come about where solid lipid
nanoparticles have been shown to inhibit biofilm formation. This project will combine a
new novel microwave SLN formulation technique with the study of what properties are
desirable in order to mitigate biofilm formation. There is a potential for this project to
involve clinical strains of bacteria and to have direct medical impact.
Colloid and Surface Chemistry
Professor Ian Harding & Dr Daniel Eldridge
Determination of surface area in an aqueous environment
The surface area and surface properties of materials are of great importance in a variety
of industries including surface coatings, catalysis, cosmetics and pharmaceuticals.
Despite the obvious need for particle surface area data, at this stage, available areas are
typically estimated by gas adsorption and assumed to be the same – at least on a relative
scale – in water.
This commonly accepted approximation is in clear need of
improvement. This project will involve the investigation of the variation in measured
surface area using a variety of techniques. Such a study will provide an assessment of
the validity of gas adsorption surface areas and may lead to more useful and accurate
determinations of particle surface area in an aqueous environment.
Colloid and Surface Chemistry
Professor Ian Harding & Dr Daniel Eldridge
The effect of electrolyte on colloidal stability
Differing electrolyte types and concentrations have been theoretically and experimentally
shown to affect the stability of colloid suspensions. However, there have been reported
cases were abnormal stability has been observed for particular systems. If this effect can
be understood and reproduced it could be of great benefit. This project will involve the
synthesis of a selection of colloidal materials followed by characterisation of their colloidal
stability in a variety of electrolyte conditions in order to better understand the way that
electrolyte affects their properties.
Colloid and Surface Chemistry, Water Science
Professor Ian Harding & Dr Daniel Eldridge
Formulation of nano-sized polystyrene latex particles
Interest in the synthesis of polystyrene latex particles has been rapidly growing in recent
years. A particularly interesting characteristic of polystyrene lattices is the potential for
them to be synthesised as nano-sized but still monodisperse particles with controllable
surface charge. A systematic optimisation has not been previously attempted. This
project will involve the synthesis of polystyrene latex samples with a view to achieving a
small particle size, high sample yield and highly monodisperse formulation.
Colloid and Surface Chemistry
Professor Ian Harding & Dr Daniel Eldridge
Adsorption of variable metal valencies onto adsorbing surfaces
STRUCTURE
Heavy metals are well knownCOURSE
for their
toxicity. AND
OneSTREAMS
method used for the removal of
aqueous metals from water is adsorption, which involves binding the metals to a solid
surface and then removing the bulk material from solution. This phenomenon has been
thoroughly studied, revealing some expected behavioural patterns for a variety of
adsorbents. One particular trend of note is the common correlation between the pH at
which a metal is removed and the metal’s hydrolysis constants. Exploring this trend for
metals of varying valency on several substrates may yield further information regarding
the mechanisms involved during metal adsorption.
Colloid and Surface Chemistry, Microbiology
Professor Ian Harding, Professor Enzo Palombo & Dr Daniel Eldridge
Use of the HLB system to predict the stability of drug carrier systems
Emulsion formulations have proven to be effective carriers for the delivery of a variety of
pharmaceutical compounds. A great deal of research goes into the synthesis of safe,
stable emulsions suitable for this application. This research project will focus on the study
of drug-carrier emulsion stability and optimization as the formulation components are
varied.
Colloid and Surface Chemistry
Professor Ian Harding & Dr Daniel Eldridge
Adsorption/coprecipitation of a dye showing unusual behaviour
Dyes are used throughout many industries and present themselves as a significant
pollutant in industrial wastewater. An effective method for the removal of dyes is
adsorption, which has been well studied and displays many benefits over other methods
of removal. A particular dye has shown some unusual adsorption behaviour where at
high concentrations the dye does not adsorb as typically expected. This project will
continue on from previous studies in an attempt to determine why this system is behaving
in an unexpected manner.
Colloid and Surface Chemistry
Professor Ian Harding & Dr Daniel Eldridge
Adsorption of aqueous heavy metals onto TiO2
Heavy metals are well known for their toxicity. One method used for the removal of
aqueous metals from water is adsorption, which involves binding the metals to a solid
surface and then removing the bulk material from solution. This phenomenon has been
thoroughly studied, revealing some expected behavioural patterns for a variety of
adsorbents. However, when using TiO2 as the adsorbent, some unusual trends appear.
This project will involve the synthesis and characterisation of a TiO2 sample, followed by
the variation of some of the parameters that may be responsible for this abnormal
adsorption behaviour in order to determine what makes TiO2 an unusual adsorbent.
Direct electrochemical detection using an ionic liquid to selectively pre-concentrate
redox mediators during solvent extraction
Peter Mahon & Hayden Webb
Ionic liquids are also known as room temperature molten salts but can also be immiscible
when mixed with water and therefore used for liquid-liquid extraction. In this project, this
method will be developed in order to detect low concentrations of redox mediators that
are produced in aqueous solutions by bacteria. The partitioning of the redox mediator in
each phase will be directly measured using microelectrode voltammetry.
COURSE STRUCTURE AND STREAMS
The application of electrochemistry to mimic metabolism
Peter Mahon
Many metabolic processes involve a simple electron transfer process that can be
mimicked in an electrochemical reactor. The generated metabolite(s) can be detected by
mass spectrometry and the reaction pathway(s) can be determined for the metabolite(s).
This approach is complimentary to traditional in-vivo and in-vitro methods but has the
advantage that it is more rapid. In this project you will setup an electrochemical flow cell
with a liquid chromatograph-mass spectrometer (LC-MS) and test various substrates.
COURSE STRUCTURE AND STREAMS
Project Descriptions of 2017 Biotechnology & Environmental Sciences Honours
Research Projects
Peptide Modified Surfaces to Control Bacterial Colonisation (Chemistry or
Biotechnology)
Supervisors: Professor Peter Kingshott and Professor Mrinal Behave
Surfaces will be modified with a range of antibacterial peptides that have shown activity
against planktonic bacterial. By immobilisation of the peptides on the surfaces it is
hypothesised that biofilm formation can be minimised.
Controlled Release of Antimicrobial Peptides from Electrospun Polymer Nanofibres
(Chemistry or Biotechnology)
Supervisors: Professor Mrinal Bhave and Professor Peter Kingshott
Polymer nanofibers made by electrospinning will be used to release antimicrobial
peptides in a controlled way in order to prevent bacterial attachment and subsequent
biofilm formation that leads to infections.
Stem Cell Growth on Complex Biomaterials Surfaces (Biotechnology)
Supervisors: Dr Huseyin Sumer, Dr George Wang and Professor Peter Kingshott
Control stem cell behaviour on surfaces that contain micro- and nanopatterns to different
chemistry and topography aimed at controlling attachment, proliferation and
differentiation. These surfaces will be based on colloidal assembly of particles from a few
nms to 5ums.
Use of proteomics approaches to understanding complex protein adsorption to
biomaterial surfaces (Chemistry or Biotechnology).
Supervisors: Professor Peter Kingshott and Professor Enzo Palombo
Precise control of protein adsorption remains elusive due to a lack of understanding of the
molecular processes involved in protein-surface and protein-protein interactions,
particularly in complex protein solutions such as human plasma. The project will use the
highly specific technique of surface-matrix assisted laser desorption/ionisation time-offlight mass spectrometry (surface-MALDI-ToF-MS) as a direct method for investigating
adsorption of proteins with different surface affinities.
Clinical and Diagnostic Microbiology (Biotechnology)
Supervisors – Prof Enzo Palombo and Dr James Knox (Melbourne Pathology)
Project Title – Improved detection of carbapenemase-producing Enterobacteriaceae
using MALDI-TOF mass spectrometry
Abstract – The global spread of carbapenemase-producing Enterobacteriaceae (CPE) is
a major threat to public health. Currently, these are most important group of multiresistant “super-bugs” threatening to take hold in Australia. The efficient laboratory
detection of these agents requires a rapid, robust and inexpensive diagnostic test. In this
study, a recently developed method for detecting CPE using an imipenem hydrolysis
assay and matrix-assisted laser desorption ionization–time of flight mass spectrometry
(MALDI-TOF MS) will be further optimised using a large collection of CPE isolates. In
addition, modifications to the current protocol aimed at increasing the sensitivity and
COURSE STRUCTURE AND STREAMS
specificity of the test will be examined.
Public Health Microbiology (Biotechnology)
Supervisors – Prof Enzo Palombo
Project Title – Investigating the antibacterial properties of aloe-based hand sanitisers
Abstract – Hand hygiene is one of the most effective ways to prevent infectious disease
transmission. Many commercial hand sanitisers incorporate antibacterial compounds,
however the safety and efficacy of these has recently been questioned by the US FDA.
This project will investigate the effectiveness of a hand sanitiser incorporating aloe as the
active ingredient against common bacterial pathogens.
Aquatic Microbiology (Biotechnology)
Supervisors – Prof Enzo Palombo
Project Title – Natural products with antibacterial activity against the fish pathogen,
Streptococcus iniae
Abstract – Infectious diseases of fish affect productivity of aquaculture industries and are
linked to major economic losses. Treatment of infected fish has traditionally focussed on
the use of antibiotic therapy. However, the problems associated with antibiotic residues in
food products and the alarming levels of antimicrobial resistance among common
bacterial pathogens of fish (and the potential spread of these bacteria to humans via the
food chain) have focussed attention on new approaches to disease management. This
project will explore the use of natural products to inhibit Streptococcus iniae, which is a
leading fish pathogen in aquaculture operations worldwide.
Food Microbiology (Biotechnology)
Supervisors – Prof Enzo Palombo
Project Title – Autochthonous (indigenous) bacterial cultures isolated from raw milk:
development of novel adjunct cultures that impart regional Australian flavours in cheesemaking
Abstract – Cheeses made from unpasteurised milk generally have more distinctive and
complex flavour/aroma profiles than equivalent cheeses made from pasteurised milk. This
difference is largely due to the natural live microbiota of the milk. Is it possible for cheesemakers to reintroduce microbial complexity into cheeses made with pasteurised milk?
This project will involve the characterisation of an existing collection of bacteria isolated
from raw milks to determine their potential to be developed into adjunct cultures that will
impart desirable flavours and aromas to cheeses made with pasteurised milk. This will
involve a detailed examination of the stability, safety, behaviour and biochemical
properties of the cultures during the cheese-making process.
Controlling bacterial biofilms using a novel nanotechnology approach
Supervisor: Dr Ajay Krishnamurthy
Microbial biofilms and nanotechnology (Chemistry and Biotechnology)
COURSE STRUCTURE AND STREAMS
Molecular analysis of the puroindoline genes, related to grain hardness in wheat
Supervisor: Mrinal Bhave
Grain hardness of wheat is an extremely important characteristic that dictates its end- use
(i.e. what type of food product it can be used for), and its commercial/export dollar
value. Two genes, called puroindoline A and puroindoline B, are considered the main
genetic factor determining grain hardness. A number of mutations have been reported in
the Pin genes that lead to hard endosperm, which is desirable for breads and certain
other food products. Novel mutations in these genes are thus of commercial interests.
There is a lot of evidence also that the PIN proteins are antimicrobial in nature. The
project will involve characterisation of the Pin genes from seeds of various lines of wheat
by PCR-amplifications, RFLP studies, and cloning and DNA sequencing if required and if
time
permits.
Molecular analysis of the hordoindoline genes, related to grain hardness in barley
Supervisor: Mrinal Bhave
Grain hardness of wheat is an extremely important characteristic that dictates its end- use
(i.e. what type of food product it can be used for), and its commercial/export dollar
value. Two genes, called puroindoline A and puroindoline B, are considered the main
genetic factor determining grain hardness. The equivalents of these genes in barley are
called hordoindolines, and these have also been found to be involved in determining the
grain texture of barley, which is related to its malting quality. Hence novel mutations in
these genes in barley are of commerce interests. There is a lot of evidence also that the
PIN proteins are antimicrobial, and the HIN proteins may be too. The project will involve
characterisation of Hin genes from seeds of various lines of barley, by PCRamplifications, RFLP studies, and cloning and DNA sequencing if required and if time
permits.
Testing the activity and mechanism of action of antimicrobial peptides.
Supervisors: Mrinal Bhave; Enzo Palombo
The synthetic peptides are based on the Trp-rich domain of puroindoline proteins (see
above projects). Their activity is to be tested against bacteria, yeast, fungi, spores,
biofilms (choices: specifics to be worked out in discussions).
Testing the anticancer-activity of antimicrobial peptides
Supervisor: Mrinal Bhave; co-supervisors Nadin Shagaghi, Rohan Shah
A number of antimicrobial pepetides are also known to have anti-cancerous activities, but
vary in their activity against different cell lines. In this project, synthetic peptides based on
the Trp-rich domain of puroindoline proteins, as well as other peptides based on certain
biochemical parameters, are to be tested against several cell lines for testing their anticancer activity potential. (specifics to be worked out in discussions).
COURSE STRUCTURE AND STREAMS
Development of antifungal surfaces
Supervisors: Dr. Vy Khanh Truong and Prof. Elena Ivanova (Scholarship available)
Swinburne University of Technology is a member of the Australian Research Council (ARC)
Research Hub for Australian Steel Manufacturing, hosted by the University of Wollongong (UOW).
The Steel Research Hub aims to develop breakthrough process and product innovations to
enable the Australian steel industry to improve its global competitiveness using integrated
approachs in the steel sector, including projects on innovation in coating and surface engineering
technology. This project will focus on how fungi interact with the surfaces at the nano-, micro-, and
macro-scales. Newly proposed to be developed emerging range of fungicidal surfaces that are
capable of killing fungi and other cell types that attach to them based primarily on their surface
structure will initiate an innovative direction in the antimicrobial surfaces design as an alternative
to traditional, chemical-based approaches. In order to understand the nature of autogenous
fungicidal mechanism several reference nanostructured surfaces with apparent biocidal effect will
be investigated using laboratory protocols developed in Nano-biotechnology laboratory at SUT.
An Honours Scholarship stipend of $5,000 maybe offered to a prospective candidate.
Investigation of the interactions between giant unilamellar vesicles and nanostructured
surfaces
Supervisors: Prof. Elena Ivanova and Dr. Vy Khanh Truong (Scholarship available)
It was recently reported that an array of regularly spaced nanopillar structures found on the wings
of the cicada Psaltoda claripennis displayed potent bactericidal activity against Pseudomonas
aeruginosa bacteria, an opportunistic human pathogen. It was shown that the bactericidal nature
of the cicada wing arose from physical phenomena alone, which was based on the nanostructure
of the surface rather than on the chemical properties of the surface, with the cells being killed as a
result of their cell membrane stretching to the point of rupture between the superhydrophobic
nanopillars present on the surface. In this project, the aim will be to construct lipid membranes
which are mimicking the cell membrane and to monitor imposed interaction forces induced by
nanostructures of insect wing surfaces or their synthetic analogues. The artificial cell membranes
will be constructed using the gel-assisted method to form giant unilamellar vesicles (GUVs) and
investigated using time-lapsed confocal laser scanning microscopy. This project being conducted
in collaboration with Prof. Carlos Marques’ group (Institut Charles Sadron, Strasbourg, France).
An Honours Scholarship stipend of $5,000 maybe offered to a prospective candidate.
Investigating the long term antibacterial activity of plasma polymerized cineole films
Supervisors - Prof. Sally McArthur and Dr. Karyn Jarvis
COURSE
STRUCTURE
AND
STREAMS of a thin film containing
Plasma polymerization modifies
surfaces
via the
deposition
specific functional groups. The organic monomer is introduced into the chamber as a
vapour, fragmented via radio frequency and deposited onto all surfaces in contact with
the plasma. Antibacterial surfaces have been produced using plasma polymerised
cineole. Cinole, also known as eucalyptol, is a major component of eucalyptus oil. While
plasma polymerized cineole films are initially antibacterial, the surface does not remain
antibacterial. This project will investigate the reasons behind this loss in the antibacterial
nature and if the antibacterial nature can be extended by modifying the surface
properties. This project will involve thin film deposition via plasma polymerization. A
number of surface characterisation techniques such as X-ray photoelectron spectroscopy
(XPS) and spectroscopic ellipsometry will be utilized. Bacterial culture work will also be
conducted.
Colloid and Surface Chemistry, Microbiology
Professor Ian Harding, Professor Enzo Palombo & Dr Daniel Eldridge
How do the physicochemical properties of bacteria influence their behavior?
Bacteria, being small, have colloidal dimensions and can be treated in a physico-chemical
fashion as well as a microbial fashion. Their behaviour may be a mixture of their well
understood microbiological function combined with their less well known physical
properties such as surface charge. The surface charge of colloidal particles results in an
electrical potential which can make those particle repel and stop them sticking. The
potential can be measured, under appropriate conditions, and is referred to as the
zetapotential. Does the zetapotential of bacteria (and other micro-organisms) therefore
influence bacterial ability to attach and/or modify the behaviour of those bacteria? What
is the zeta potential of bacteria? How does it relate to their microbiological function, for
example do gram positive bacteria have a different zetapotential to gram negative
bacteria? This project will involve the study of the physicochemical properties of bacteria
in order to better understand why they behave the way they do.
Identifying Bacterial Consortia Involved in Microbiologically Influenced Corrosion
Supervisors: Prof. Linda Blackall & Assoc. Prof. Scott Wade
Microbiologically influenced corrosion (MIC) can lead to localised material degradation
rates that are orders of magnitude higher than would normally be expected from standard,
abiotic corrosion. This can lead to the premature failure of a wide range of important
structures that can not only be costly to repair, but in some cases can have fatal
consequences.
In addition to field tests there has been a significant effort to understand MIC through
controlled laboratory tests. One of the difficulties in carrying out such tests is to truly
simulate the environment in which MIC is being observed. Indeed for many of the tests
performed in the laboratory the corrosion rates observed have been significantly lower
than that experienced in the field. While it is widely recognised that MIC is caused by the
combined effects of a consortia of microorganisms many laboratory tests continue to be
performed using single strains of bacteria, typically sulphate reducing bacteria. This is
one of the potential reasons for the differences in laboratory and field measurements.
COURSE
STRUCTUREfield
AND S
TREAMS in ports/harbours and the
This project will involve sampling
in appropriate
locations
subsequent identification of microorganisms in the samples. Some of the overall aims are
to determine:
- Presence of microorganisms previously implicated in MIC
- What other microorganisms tend to form consortia with the MIC-related bacteria
Some of the variables that may be studied in conjunction with the sampling include:
- Seasonal effects
- Location effects
- Local pollution
During the project the student will develop skills in field sampling, identification of
microorganism through the use a range of molecular biological methods that allow the
study of mixed microbial communites. Methods will include DNA extraction, PCR
amplification of specific genes (e.g. 16S rRNA, dissimilatory sulfite reductase,
hydrogenase), cloning, sequencing of representative clones, bioinformatics and
phylogenetic analysis. Quantitative PCR will be a likely method used for quantitation of
specific microbes. Additional methods will include fluorescence in situ hybridisation and
confocal laser scanning microscopy for microbial community analysis on corroded
materials.
Role of Sulphate Reducing Bacteria in Microbiologically Influenced Corrosion
Assoc. Prof. Scott Wade and Prof. Linda Blackall
Microbiologically influenced corrosion (MIC) can lead to localised material degradation
rates that are orders of magnitude higher than would normally be expected from standard,
abiotic corrosion. This can lead to the premature failure of a wide range of important
structures that can not only be costly to repair, but in some cases can have fatal
consequences. Understanding the processes that cause MIC is an exciting and active
area of research.
In addition to field tests there has been a significant effort to understand MIC through
controlled laboratory tests. One of the difficulties in carrying out such tests is to truly
simulate the environment in which MIC is being observed. Indeed for many of the tests
performed in the laboratory the corrosion rates observed have been significantly lower
than that experienced in the field. While it is widely recognised that MIC is caused by the
combined effects of a consortia of microorganisms many laboratory tests continue to be
performed using single strains of bacteria, typically sulphate reducing bacteria. This is
one of the potential reasons for the differences in laboratory and field measurements.
This project will involve studies of the role of sulphate reducing bacteria (SRB) in MIC.
SRB are the most commonly reported microorganisms in MIC and many tests are
routinely performed with these bacteria to look at corrosion. A key issue however is that
many of the testing procedures used in these studies are poorly understood, which in turn
can have a significant effect on the subsequent results. Some of the areas that could be a
part of the project involve looking at how the following affect the testing:
- Oxygen
- Nutrients
- Different strains of SRBCOURSE STRUCTURE AND STREAMS
- Test metal sample orientation
- Test metal type
- Test metal surface preparation
During the project the student will develop a range of relevant skills in microbiology,
chemistry and corrosion.
Baculovirus gene delivery for production of induced pluripotent stem (iPS) cells.
Novel approaches to differentiate stem cells through the use of aerosol printers.
Analysis of pluripotent stem cells grown and differentiated on novel surfaces.
Co-supervisors for various projects Dr Tony Barton, Prof Peter Kingshott, Prof Paul
Stoddart, Prof Simon Moulton.
Embryonic/pluripotent stem cells have the unique ability to differentiate into all cell types
and tissues of the body making them ideal for the use in cellular therapies. However, the
transplanted cells need to be matched to the patient as they may be rejected by the hosts
immune system. One of the most exciting advances in cell biology has been the ability to
wind back the developmental clock of an adult cell back to an embryonic state restoring
pluripotency. The process of reprogramming a differentiated adult cell to a pluripotent
state involves the forced expression of a number of pluripotency genes. A number of
projects are available to generate, analyse and explore the use of pluripotent stem cells
for applications in biotechnology including the ones listed above.
Linking early life environment with child health: a longitudinal twin study
Supervisors: A/Prof Craig and Prof Saffery (MCRI), Dr Scurrah (UoM), Dr Sumer
(Swinburne)
What happens in the womb can last a lifetime. Factors such as maternal diet and lifestyle
during pregnancy are linked with a lifetime risk for chronic diseases, ranging from
cardiometabolic to neurodevelopmental. Twin studies are ideal for studying such diseases
because of their ability to resolve genetic, shared (maternal and early life) and individual
environments. This project takes advantage of the unique data collected in the
Peri/postnatal epigenetic Twin Study (PETS) of Drs. Craig and Saffery. This rich dataset
enables a number of potential projects based on the student’s interests and is ideal for a
wide range of disciplines from genetics to medicine. Our main outcomes of interest are
cardiometabolic (weight, height, skin fold thickness, blood pressure) and infectious and
other illnesses.
COURSE STRUCTURE AND STREAMS
An epigenetic analysis of twins discordant for epilepsy
Supervisors: Prof Jeff Craig and Dr Jane Loke (MCRI), Dr Lata Vadlamudi (RBWH), Dr
Huseyin Sumer (Swinburne)
Epilepsy is the most common serious neurological disorder and affects over 70 million
people worldwide. Epilepsy can have debilitating consequences with significant
economic, social and quality of life implications. The importance of genetics in the
causation of epilepsy has long been recognized and there has been significant progress
with the identification of genes for certain monogenic epilepsy syndromes. This Honours
project will involve “validation” of the top genomic regions whose methylation state is most
likely to associate with or predict epilepsy in twins as identified using methylation
microarrays. This validation will use the method of Sequenom MassArray EpiTyping,
which measures DNA methylation at specific or groups of CpG sites within a region of
200-400 base pairs. This technique involves techniques such as bisulphite conversion,
PCR and mass spectrometry and had been used in A/Prof Craig’s lab for over ten years.
The project will provide a valuable contribution to a future research publication
Analysis of human mesenchymal stem cells (MSCs) obtained from adipose tissue
cultured in different media
Supervisors: Dr Kiran Shah, Dr Tony Barton, Dr Huseyin Sumer
Human mesenchymal stem cells (MSCs) can be obtained from adipose tissue via a small
liposuction procedure. These MSCs can be used for a range of stem cell treatments –
treatments based on using stem cells obtained from each individual patient (autologous
treatments) and stem cell treatments based on the use of stem cells from a donor
(allogeneic stem cell treatments). In this project the gene expression profile of MSCs
grown in a number of conditions will be analysed using a number of techniques such as
qRTPCR array analysis.
Computer aided metal complex catalysis study
Supervisors: Prof. Feng Wang and Dr. Stephen Best (The Univ. of Melbourne)
Computational chemistry methods will be applied to study structures of tricarbonyl(η4diene)Iron and/or salicylaldiminato Nikle (II) in the application of catalyst design. In
collaboration with on-going projects with the Univ. of Melb. Some experiments such as Xray and FTIR spectroscopy will be conducted at the Australian Synchrotron in Clayton.
Participation of the experimental measurements will depend on the synchrotron beamline
time allocation (not guaranteed during the honours year). There is a scheduled FTIR time
COURSE
STRUCTURE
AND S
in Mid-November 2016, prior
to the
beginning
ofTREAMS
the honours project (inquiry:
[email protected]). Without participation of the experiment will not affect the project.
Does the colour of anticancer drugs (pharmacophores) help us to understand how
they work?
Supervisors: Prof. Feng Wang and A/Prof. Andrew Clayton (CMP)
Cancer is one of the biggest killers worldwide. Quinazoline based pharmacophores are a
class of organic compounds used in the clinic to help stop the growth of tumours. These
compounds have been widely used to synthesize molecules with medical benefits,
including antimalarial, antimicrobial and anticancer activities. Unfortunately, these drugs
are effective in only a sub-set of patients and we need to know why. Quinazolines also
display environmentally-sensitive spectroscopic properties which may provide clues to
how these drugs work or don’t work in vivo. This project aims to combine experiment and
theory to measure and understand the basis of drug color and drug interactions. The
incumbent will gain valuable experience in using UV-vis spectrometry and/or fluorescence
spectroscopy and detailed theoretical analysis.
Spectroscopic studies of Electronic structure and fragmentation patterns of fatty
acids
Supervisors: Prof. Feng Wang and Prof. Kevin Prince (Elettra, Italy)
Supercomputers and synchrotron sourced spectroscopic methods are employed to study
fatty acids. Fatty acids provide an avenue of ion dynamics and photoionization mass
spectroscopy of biomolecules. At low photon energies, we wish to know if soft ionization
can reduce fragmentation.
Metabolic mining of endophytic fungi for bio-protective agents.
Supervisors: Hayden Webb and Bita Zaferanloo
Microorganisms are ubiquitous in most environments, and are responsible for the
degradation, corrosion and fouling of numerous materials surfaces. Given the high
incidence rate of microbes in general, individual species need to develop a competitive
edge in order to thrive. In many cases, microbes produce metabolites that are toxic to
potential interlopers, however they may also manufacture other components that inhibit
invasion by other means, e.g. by preventing microbial attachment.
Endophytic fungi colonise the internal tissues of plants, and in many cases protect the
plant from infection by other, potentially pathogenic microbes. Endophytes have been
established as a rich source of a variety of interesting compounds with bio-protective
potential, including antibacterials and antioxidants. This project will investigate a variety of
unclassified and potentially novel strains of endophytic fungi to determine their potential
for producing bio-protective compounds. It is anticipated that antibacterial and
OURSE
STRUCTURE
AND STREAMS
antioxidative compounds will Cbe
detected,
and potentially
other bio-protective agents,
such as quorum sensing inhibitors may be present. The project will also aim at
demonstrating the bio-protective effectiveness of these compounds for the protection of
metallic and non-metallic surfaces.
Defining the role played by mitochondrial DNA in fertilisation outcome
Project description
Mitochondrial DNA plays a critical role in fertilisation and early development. Eggs with
low mitochondrial copy number often fail to fertilise. However, these eggs can be rescued
by supplementing them with autologous populations of mitochondria carrying
mitochondrial DNA. Little is known about how mitochondrial DNA copy number can alter
fertilisation and developmental outcomes. This project aims to define the processes using
a pig embryology model and state-of-the-art next generation sequencing approaches to
identify the key gene pathways and gene regulators involved. Along with learning egg
culture and fertilisation techniques, you will use real time PCR, next generation
sequencing and bioinformatics.
Project Leaders: Prof Jus St. John and Dr Huseyin Sumer
Email: [email protected]
Phone: 03 8572 2678
Centre for Genetic Diseases, Hudson Institute of Medical Research