Honours Projects for 2015
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SCHOOL OF MATHEMATICAL AND PHYSICAL SCIENCES
Bachelor of Science (Honours) in Applied Chemistry
2016 PROJECTS
3
The value of an Honours degree
An Honours degree provides an opportunity to be involved in a research program in an area that
interests you, and provides training in research techniques and experience with modern research
instrumentation. The Honours programme adds a new dimension to the skills that you have acquired
during your undergraduate years and enhances your immediate employment prospects and, more
significantly, your future career potential. An Honours degree provides a pathway to postgraduate
research degrees (MSc or PhD), with possible financial support from an Australian Postgraduate
Award (APA) or some other postgraduate scholarship.
Eligibility
Applicants must have completed a UTS recognised bachelor's degree in a relevant discipline at an
appropriate level. The honours program is normally open to students who have attained at least a
credit average over the final two-thirds of the undergraduate program.
Assessment
In the Honours year, students undertake original research projects under the supervision of
academic staff. Students write a thesis about the project and present a talk on the outcomes. There
is also a coursework component, with assessment tasks on advanced chemistry topics.
Choosing a project
It is advisable to contact a potential supervisor and discuss a project during the semester prior to
enrolment in the Honours project. A number of research projects are on offer in the school and are
outlined in this booklet. Feel free to discuss any of these with the appropriate supervisor.
If you have an interest in carrying out a project in an area that is not listed, it may be possible to
arrange suitable supervision. For instance, a number of previous students have carried out their
work-based projects in conjunction with the CSIRO, ANSTO or an industrial partner.
How to apply
After discussing deciding on a project with a supervisor, fill out the forms available at:
http://www.uts.edu.au/future-students/science/go-further/honours-program/school-chemistry-and-
forensic-science-honours
Applications should be submitted by November 30, 2015 to be considered for a first round offer, but
final round applications are accepted until January 29, 2016. Students generally begin work on their
project in February. There are Autumn and Spring semester intakes for the programme.
Advice
If you have any questions about the programme, please feel free to discuss them with the Chemistry
Honours Coordinator, A/Prof. Andrew McDonagh ([email protected]).
Honours Projects for 2016
6
UNIVERSITY OF TECHNOLOGY, SYDNEY
Bachelor of Forensic Science (Honours) in Applied Chemistry
Bachelor of Science (Honours) in Applied Chemistry
Honours Projects 2016
#
Title Screening for lung infections: volatile profiling of bacteria in cystic fibrosis patients
Nature of problem
work is intended to
address
In Australia, the most common inherited disease,
Cystic Fibrosis (CF), is characterised by recurrent,
progressive lung infections. Early detection and
treatment of these infections is important to prevent
lung damage and scarring. Many different infections
are common in CF so identification of the specific
bacterial species is important to optimise antibiotic
therapy. While sputum culture is useful in some situations, it may take days or weeks
to diagnose depending on the organism. Hence, a rapid and non-invasive technique
capable of diagnosing, identifying and monitoring early bacterial infection in CF
patients is desired, and will contribute significantly to improving their quality of life.
New techniques involve chemical analysis of the volatile bacterial by-products which
are present in the air exhaled by people with infections. This project will assess the
volatile by-products produced by the bacterial species characteristic of CF lung
infections. The results of the project will assist in determining unique volatile profiles
which can be used to detect lung infections in CF adults. This information will
facilitate the long-term goal of developing a portable instrument which will rapidly
detect lung infections in CF patients.
Outline of
goals/objectives
The goals of this project are as follows:
To optimise an advanced gas chromatography-mass spectrometry method
for the analysis of volatile compounds produced by CF-associated bacteria
To compare the volatile profiles of breath samples collected from a control
group with a clinical group of cystic fibrosis patients
To identify volatile profiles for each bacterial species which can be used to
rapidly screen cystic fibrosis patients for bacterial lung infection
Special requirements
None
Industry/Ext partner Westmead Millennium Institute
UTS supervisor Professor Shari Forbes
Dr Katie Nizio
External supervisor Clinical Associate Professor Peter Middleton (Westmead Millennium Institute for
Medical Research, University of Sydney)
Contact information [email protected]
Honours Projects for 2016
7
UNIVERSITY OF TECHNOLOGY, SYDNEY
Bachelor of Forensic Science (Honours) in Applied Chemistry
Bachelor of Science (Honours) in Applied Chemistry
Honours Projects 2016
#
Title Wildlife forensics: Chemical odour profiling to identify illegal wildlife products
Nature of problem
work is intended to
address
A major issue in the enforcement of
wildlife trafficking is the lack of a rapid
and accurate method to distinguish legal
from illegal wildlife parts. While
detector dogs are trained to alert to
threatened wildlife parts they cannot
provide a species-level identification. However, chemical odour profiling of
confiscated trafficked samples has the potential to provide a rapid discrimination of
species-type and determine whether or not the sample is illegal. Rapid identification
can greatly assist law enforcement to prosecute offenders, thus preventing future
wildlife crimes. Determination of the species' geographic origin based on their odour
'fingerprint' will also assist customs to track current trafficking routes.
This project will chemically profile the odour produced by rhino horn, elephant ivory
and other wildlife parts identified and supplied by the Australian Museum. Samples
will be analysed using an advanced gas chromatography-mass spectrometry
technique. Data will be analysed statistically to identify unique ‘fingerprints’ for each
species type. This information will be used to build a database of odour profiles for
trafficked wildlife parts into and out of Australia.
Outline of
goals/objectives
The goals of this project are as follows:
To optimise an advanced gas chromatography-mass spectrometry method
for the analysis of volatile compounds produced by wildlife parts
To apply statistical analysis to determine unique odour fingerprints for each
species type
To build a database of unique odour profiles for trafficked wildlife in
Australia
Special requirements
None
Industry/Ext partner Australian Museum
UTS supervisor Professor Shari Forbes
Maiken Ueland
External supervisor Dr Rebecca Johnson, Director of the Australian Museum Research Institute
Contact information [email protected]
Honours Projects for 2016
8
Title Synthesis of RAFT Mediated Cationic Glycopolymer for Nucleic Acid delivery
Project Description Diseases cause by genetic disorder has affected the health and lifestyle of many individuals around the world. The current method of treatment involves very high doses of drugs to suppress the symptoms. Small interfering RNA (siRNA) is the most recent nucleic acid molecule employed to silence gene expression, thereby, arresting the disease-causing genes. However, the effective delivery of siRNA is an arduous task.
Glycopolymers are polymers bearing carbohydrate moieties and they have very strong binding abilities with cell receptors due to their multivalent interactions between the sugar repeating unit from the glycopolymers and the cell surface receptors. There have already been delivery systems (e.g. lipid based system) out in the market concerning gene knockdown technology, but none of these are specific toward targeting the affected areas. Receptor mediated delivery of siRNA using targeting glycopolymers paves the way to efficient therapeutic window for delivering siRNA.
Figure 1: Schematic of glucose-based glycopolymer with thiocarbonylthio end-functional group (bracketed) of RAFT agent.
Objectives In this project, students will have hands on experience on performing reversible addition-fragmentation transfer (RAFT) polymerization to generate cationic glycopolymers. Due to the controlled/living nature of RAFT polymerization, complex glycopolymer architectures such as diblock copolymers could be synthesized. Glycomonomer synthesis will initially be carried out and analysed using the nuclear magnetic resonance (NMR). This will be followed by performing polymerization in solution and resulting polymers will also be analysed using NMR and gel permeation chromatography (GPC).
Supervisors Dr Simon Ting (Centre for Health Technologies, UTS)
Contact information [email protected]
Honours Projects for 2016
9
Project title Characterization of bonding and surface structure of self-assembled
quantum effect devices
Name of supervisor(s) Dr. Charlene Lobo, Prof. Milos Toth, Dr. Avi Bendavid (CSIRO)
Email address [email protected]
Project description & aims
(250 words max, summary
written for prospective
students)
Next-generation nanophotonic, plasmonic and optoelectronic circuits
rely on accurate positioning of fluorescent nanoparticles, plasmonic elements and single photon emitters to each other and to desired
locations on the substrate (Fig. 1). This project will employ a variety of
surface-sensitive characterization techniques (such as low energy ion scattering, x-ray photoelectron spectroscopy and Raman scattering),
optical and electrical measurements to analyze the extent of surface functionalization and nature of bonding between the individual
elements in these circuits, in order to improve the fidelity,
reproducibility, and yield of the circuit assembly process.
Figure 1: Positioning of nanodiamond optical emitters at desired
locations in an optical circuit using linking molecules. The student will work with other group members who are developing
electron beam processes for fabricating, aligning and contacting a
device component with nano-scale spatial resolution. The work will be done in a dynamic UTS research group comprised of numerous PhD
students, postdocs and academic staff who work together on electron beam techniques, nanophotonics, nanoplasmonics and
nanoelectronics, publish their work in top nanotechnology, physics and materials science journals, and collaborate with FEI Company
(http://www.fei.com) and CSIRO.
Techniques the student would
be working with Chemical self-assembly, electron beam microscopy, low energy ion
scattering (LEIS), x-ray photoelectron spectroscopy (XPS), and a
variety of other nanofabrication and electrical characterization techniques.
Infrastructure and support
required for project execution This project will employ facilities presently available at UTS. Occasional visits to CSIRO Lindfield (where the LEIS and XPS instrumentation is
located) will also be required. Degree Nanotechnology/Physics Honours, Engineering Capstone
Honours Projects for 2016
10
Project title Design of precursor molecules for electron beam induced chemistry
Name of supervisor(s) Dr Charlene Lobo, A.Prof Andrew McDonagh, Prof. Milos Toth
Email address [email protected]
Project description & aims
(250 words max, summary
written for prospective
students)
Electron beam induced chemistry (EBIC) is a cutting edge technique for the fabrication and editing of advanced functional materials at the
nano-scale. Emerging EBIC applications include the fabrication of next-
generation optoelectronic devices made from diamond, chemical manipulation of single photon emitters (Fig. 1), and electrical
contacting of carbon nanotubes. In order to expand the applications of EBIC, understanding of the
underlying chemical pathways and reaction mechanisms must be
improved. Recent advances made at UTS have made it possible to identify the properties of precursor molecules that lead to improved
purity and specificity in bonding of EBIC-synthesized nanostructures to the substrate and to other nanostructures. The present project will use
this knowledge to design, synthesize and test a new generation of EBIC precursor molecules for nanofabrication of functional materials.
The honours student will work with a PhD student focusing on the
design and chemical synthesis phases of the project, and will have the opportunity to collaborate with a team of PhD students working on
applications of the synthesized precursors.
Figure 1: Chemical switching of the quantum states of single photon
emitters by EBIC. The emitters are embedded in nanoparticles processed by a scanned electron beam.
Techniques the student would
be working with Chemical and photochemical synthesis, mass spectrometry (LC and
GCMS), electron beam induced chemistry, electron microscopy, thermogravimetric analysis, among other techniques.
Infrastructure and support
required for project execution This project will employ facilities presently available at UTS.
Degree Chemistry/Nanotechnology/Physics Honours
Honours Projects for 2016
11
Title Antibacterial agents derive from Boldine
Project description Recent studies have identified that the Methicillin-resistant Staphylococcus aureus (MRSA) strain, a strain resistant to all penicillin derivatives, now accounts for 40-50% of all S. aureus isolates within hospitals in America and 25-30% in Australia. The review ordered by British Prime Minister in 2014 on antimicrobial resistance found that if immediate action were not taken, antimicrobial resistance would be responsible for more deaths than cancer by the year 2050. Therefore, it is an urgent need to pursue antibacterial drug discovery and overcome this impending issue of resistance. The Filamenting temperature-sensitive mutant Z (FtsZ) protein in recent years has become an ever more important focus for antibiotic research due to its potential as a novel target. FtsZ is an essential cell division protein conserved in the majority of bacterial species, including S. aureus and Mycobacterium tuberculosis. Boldine is a natural alkaloid found in the leaves and bark of a medicinal plant (Peumus boldus) use in the treatment of liver diseases. Boldine also has other beneficial biological activities such as antioxidant, antimalarial, anti-inflammation, antiplatelet, anti-cancer, antimicrobial and antiviral activities.
In this project, therefore, we are focusing on Design and Synthesis of potential FtsZ inhibitors from Boldine, as novel antibacterial agents.
Project aims To synthesise compound 1 and its analogues from Boldine (Fig 1).
To determine antibacterial activity (MIC) of the synthesised compounds
against S. aureus.
To explore the FtsZ inhibitory activity of the synthesised compounds.
To investigate SAR (structure-activity relationship) of the synthesised
compound via computer-aided molecular modelling.
Supervisors A/Prof Alison Ung and Prof Elizabeth Harry
Contact information
Honours Projects for 2016
12
Title Natural Products for Drug Discovery
Project description A recent review by Newman and Cragg, clearly documented the pivotal role Natural Products play in drug discovery, especially in the key areas such as anticancer, anti-infective and metabolic diseases. More than 60% and 75% of chemotherapeutic drugs for cancer and infectious disease, respectively are of plant origin.
Plant volatile, beta-caryophyllene 1 and the oxide 2 are found in relatively high concentrations in many spices, medicinal and edible plants. They exhibit a wide variety of pharmacological effects, demonstrating antibacterial, antifungal, immunomodulatory, anti-inflammatory, antirheumatic, antioxidant and anticancer properties.
In this project, we are focusing on Design and Synthesis of novel natural product-derived compounds 3 and 4 from beta-caryophyllene, for drug discovery targeting human diseases, such as cancer and bacterial injections.
Project aims To synthesise optically active tricyclic hydro-amides from beta-caryophyllene 1 and 2, via the Ritter reaction.
To assess the broad-spectrum biological activities of the synthesised compounds.
To determine SAR (structure activity relationship) of synthesised compounds via computer-aided molecular modelling study.
Supervisors A/Prof Alison Ung
Contact information
Honours Projects for 2016
13
Title Synthesis of flavonoid-derived FtsZ inhibitors as antibacterial agents
Project description The increase of antibiotic resistance among an array of bacteria is of growing concern in both hospitals and community settings. Particularly, Methicillin-resistant Staphylococcus aureus (MRSA) has shown resistance towards traditional targets and every class of antibiotics available. In 2011, roughly 80,000 cases of methicillin-resistant S. aureus (MRSA) infections occurred in the United States alone. The FtsZ (Filamentous temp.-sensitive protein Z) is an essential protein for bacterial cell division, viability and cell growth. FtsZ is one such emerging target for antibacterial drug discovery. Inhibition of FtsZ has been shown to cause bacterial cell death and reduced the MRSA in the animal model. Therefore, we hypothesised that FtsZ-inhibitors are potential broad-spectrum antibiotics. The results on computational docking have indicated that flavonol-benzamides such as 1 can bind to the inter-domains cleft of S. aureus-FtsZ with excellent ligand efficiency. Based on this computer-aided drug design, a series of novel flavonol-benzamides targeting FtsZ will be synthesised.
.
Fig 1. (a) Compound 1 binds in the FtsZ inter-domains pocket (simulated docking) (b) Compound 1 pose-view and detailed interactions in the binding pocket.
Project aims To synthesise compound 1 and its analogues (Fig 1).
To determine antibacterial activity (MIC) of the synthesised
compounds against S. aureus
To explore the FtsZ inhibitory activity of the synthesised compounds
To investigate SAR (structure-activity relationship) of the synthesised
compound via computer-aided molecular modelling.
Supervisors A/Prof Alison Ung and Prof Elizabeth Harry
Contact information
Honours Projects for 2016
14
Title Development of a sulfonyl-[18F]fluoride-based radiosynthon for applications in nuclear medicine
Project description Positron emission tomography (PET) is able to give detailed three-dimensional information on functional processes in the body and is used to diagnose and treat conditions such as neurological disorders and cancer. Fluorine-18 ([18F]) is one of the most popular radioisotopes for PET due to its short-life (110 min) and
favourable physical and chemical properties. Proteins and other macromolecules used in the diagnosis and treatment of diseases are generally difficult to radiolabel with [18F]fluoride due to the high temperatures often required, which consequently damage the protein. To overcome this hurdle, this project will involve the development of a radiosynthon for potential conjugation to a therapeutically useful macromolecule. Our previous research has shown that para-substituted benzenesulfonyl [18F]fluorides can be rapidly prepared using continuous flow chemistry (microfluidics) and show great potential to be used within a radiosynthon. In this project the student will use cutting-edge, high-throughput microfluidic flow chemistry techniques to synthesise a sulfonyl fluoride-based synthon and subsequently produce the radiosynthon by radiolabelling with [18F]fluoride. The [18F]radiosynthon will be coupled onto a macromolecule and the bioconjugation scope will be explored to verify the stability of the sulfonyl fluoride group, before conjugation to a more therapeutically useful peptide or protein e.g. for cancer or neuroimaging.
Project aims Use microfluidic flow chemistry to produce a sulfonyl fluoride-based
synthon
Develop skills in analytical chemistry and instrumentation
Learn the fundamentals of [18F]radiochemistry, through one-on-one training and supervision using equipment and facilities unique in Australia
Use microfluidic flow chemistry to produce a [18F]radiosynthon
Conjugate the [18F]radiosynthon to a therapeutically useful macromolecule
Supervisor A/Prof Alison Ung (UTS) and Dr Lidia Matesic (ANSTO)
Additional Information
Financial Support for this project is potentially available through Australian Institute for Nuclear Science and Engineering (AINSE)
Contact information
Honours Projects for 2016
15
Title Investigation of the interaction and complexation of peptides with radiometals
Project Description Radiometals such as lanthanides (Lu-177), Tc-99m and Cu-64 are important diagnostic and therapeutic tools in nuclear medicine. As such, it is important to understand the interactions between radiometals and biologically relevant molecules such as peptides in order to understand and predict their behaviour in vivo. The aim of this research is to develop peptides with a high affinity and selectivity for radiometals, in particular lanthanides, so as to elucidate what structural and functional features are responsible for coordination. The design of these novel peptides will be based on peptide structures that have previously been shown to have a high affinity or selectivity for the targeted elements. Systematic variation of the peptide structure will then allow us to answer questions such as “which amino acids provide the highest affinity/selectivity”, “what is the effect of cyclisation” and “what is the effect of changing the sequence/position of the amino acids in the peptide chain”. This project will involve organic synthesis, characterization and testing of the affinity and selectivity of the peptides for radiometal complexation as well as potentially molecular computer modelling.
Supervisors Associate Professor Alison Ung and Dr Tracey Hanley (Australian Nuclear Science and Technology Organisation)
Additional Information
Financial Support for this project is potentially available through Australian Institute for Nuclear Science and Engineering (AINSE)
Contact information Please contact Alison Ung ([email protected]) for further details.
Honours Projects for 2016
16
Project title High performance cathode material: NaCrO2, for Na-ion batteries
Name of supervisors Dr Dawei Su
Email address [email protected]
Project description & aims
Sodium-ion batteries (Na-ion batteries) are considered as a
promising technology for large-scale energy storage applications
owing to their low cost. However, there are many challenges for
developing Na-ion batteries with high capacity, long cycle life
and high-rate capability. Recently, NaCrO2 was identified as the
great cathode candidate for the Na-ion batteries, which
demonstrates high specific capacity and great cycling
performance. In this project we will attempt to synthesize nano-
sized NaCrO2 single crystals exposed with the unique crystal
planes, which present the necessary channels to accommodate
and intercalate Na ions. Through this project, we can improve the
electrochemical performance of the NaCrO2, particularly, the
high rate performance. We will also investigate the mechanism
of the Na ions intercalation process through the ex-situ SEM,
TEM, XPS and in-situ XRD (the instrument is just installed and
tested, which is cutting-edge technique for the analysis of the
batteries system) measurements.
Furthermore, I recently found that an ether-based electrolyte
exhibits an improved electrochemical performance over the pure
alkyl carbonate electrolytes for Na-ion batteries. Electrochemical
testing and first-principle calculations demonstrate that the ether-
based solvent can facilitate the overall transport of electrons and
reduce the energy barrier for sodium ion diffusion. Therefore, we
will combine the nano-sized NaCrO2 single crystal electrode and
ether based electrolyte to develop the Na-ion batteries with high
reversible sodium storage capacity, high Coulombic efficiencies,
and extended cycle life.
Techniques the student
would be working with
Chemical reaction techniques: hydrothermal method, solid state
method.
Electrochemical measurements techniques: galvanostatic charge-
discharge testing, A.C. impedance testing, cyclic voltammetry
Materials characterization techniques: XRD, SEM, TEM, EDS,
XPS
Infrastructure and support
required for project
execution
Autoclave for the hydrothermal reactions, vacuum tube furnace
for the solid state reaction
Electrochemical workstation, Battery testing system
SEM, XRD, TEM, EDS, XPS (external to UTS)
Major
(Applied Physics or
Nanotechnology)
Nanotechnology. Also suitable for Applied Chemistry
Honours Projects for 2016
17
Project title Synthesis and optical properties of ‘cesium bronze’ and ‘sodium
bronze’
Name of supervisors Prof. Michael B Cortie, co-supervisor A/Prof. Andrew
McDonagh
Email address [email protected]
Project description & aims
(
‘Tungsten bronzes’ are an unusual family of conducting oxides.
They can be manipulated to be metal-like, semi-conducting or
insulating, with an associated effect on their optical properties.
They are of interest for switchable windows and other active
optical devices. In this project we will investigate the chemical
synthesis and the optical properties of cesium and sodium
tungsten bronzes. These have been identified as having potential
for application plasmonic and spectrally selective applications.
Our objective is to be able to develop a material with controllable
band-gap and optimized dielectric function.
Techniques the student
would be working with
Wet chemical synthesis, X-ray diffraction, heat treatment in
controlled atmospheres, measurement of optical properties,
Raman spectroscopy
Infrastructure and support
required for project
execution
All facilities are available from within UTS.
Major
(Applied Physics or
Nanotechnology)
Applied Physics, Nanotechnology, Applied Chemistry
Honours Projects for 2016
18
Title Fluorination of model boronates using flow chemistry techniques
Project description Fluorine substituents are widely used in medicinal chemistry to tune the
ADMET profile of several drugs. The availability of the positron emitter 18
F
(109min half-life) makes late-stage radiofluorination reactions of paramount
importance in building novel PET radiopharmaceuticals for molecular
imaging studies. However, using this radionuclide involves stringent
requirements on the speed and reliability of the reactive process; for this
reason only few simple routes are available for usefully radiofluorinating
desired structures. In particular, there is an evident lack of effective aromatic
nucleophilic radiofluorinations to obtain non-activated fluoro-arenes.
In this project we will study the nucleophilic fluorination of model boronic
acid esters using fluoride and Cu2+
catalysis as a new late-stage fluorination
methodology. We will employ high-throughput microfluidic techniques, in
order to screen a wider range of conditions by employing the minimal
possible quantity of chemicals and experimental time.
The use of microfluidic system will allow a straightforward translation of the
best conditions to the 18
F radiolabelling of important drugs that are not
obtainable using current radiofluorination methodologies.
Project aims Literature review of fluorination conditions and choice of model
compounds
Setting of flow system and variables (materials, pumps, heaters,
pressures, oxygenation)
Setting of analytical systems and methods
Execution of experiments and variation of parameters (temperature,
pressure, residence time)
Collection of data, identification of best conditions and fluidic set-up
UTS supervisor Prof. Alison Ung
External supervisor Dr. Giancarlo Pascali (ANSTO), Dr. Lidia Matesic (ANSTO), Dr. Benjamin
Fraser (ANSTO), Tien Q. Pham (ANSTO)
Contact information [email protected] ; [email protected]
B
OR2
OR1
<F->, <Cu2+>
solvent, heat
residence time
microf luidicsF
Honours Projects for 2016
19
Title In-flow CO2-generated CO and direct utilization in metal-catalyzed
carbonylations
Project description Carbon monoxide represents a very useful synthon that can be used in metal-
catalyzed insertive carbonylation reactions, giving access to a wide series of
medicinally relevant compounds. Instead of using pressurized cylinders, it is
preferable to generate CO in-situ, and several routes are available to this
scope. 11
C (20min half-life) is also an important PET nuclide that gives
access to highly valuable molecular imaging information; its use is however
mandated by the starting chemical form utilizable, 11
C-CO2. Therefore, there
exists a relevant demand of ways to transform 11
C-CO2 into 11
C-CO, which
are efficient and quick enough to cope with the time and handling constraints
imposed by this radionuclide. A recent method has been published on the use
of silyl acid esters as a mild storage and release systems for CO starting
directly from CO2.
Our group is accumulating experience in the use of tube-in-tube systems to
allow the safe and efficient performance of gas-liquid reactions. Therefore, in
this project we will apply this straightforward flow approach to improve the
applicability of this silicon based reaction on a series of model compounds. In
particular, we will use a double tube-in-tube system for a) trapping the
gaseous CO2 in solution as silyl acid ester and, after flow reaction with an
activator (CsF), b) releasing the CO gas into the metal catalyzed insertive
carbonylation environment.
The use of microfluidic system will allow a straightforward translation of the
best conditions to the 11
C radiolabelling of important drugs that are not
obtainable using current methodologies.
Project aims Literature review of reaction conditions and choice of model compounds
Setting of flow system and variables (tubing set-up, pumps, heaters,
pressures)
Setting of analytical systems and methods
Execution of experiments and variation of parameters (temperature,
backpressures, residence time)
Collection of data, identification of best conditions and fluidic set-up
UTS supervisor Prof. Alison Ung
External supervisor Dr. Giancarlo Pascali (ANSTO), Dr. Benjamin Fraser (ANSTO), Dr. Gary
Perkins
Contact information [email protected] ; [email protected]
SiSi
PhPh
PhPh
CO2
Si
PhPh
COH
O
CO
CsF
R''-X + R'-NH2
<Pd>
Ph2MeSiOSiMePh2 +
C
HN
R'R''
OAF2400tubing
Honours Projects for 2016
20
Project title Synthesis of Activated Carbon with High Absorption
Properties from the Australian Almond Shells and Hulls
UTS supervisor Assoc. Prof. Andrew McDonagh
Email address [email protected]
External supervisor Dr Amir Moezzi
Project description & aims
There is an increasing interest in resource recovery from various
waste materials. Among the waste materials available
abundantly are agricultural residues such as shells and hulls
from various sources e.g. from coconut shells, pecan shells,
wood industry and almond shells. In Australia, thousands of
tonnes of almond are produced every year in processing
facilities, leaving behind thousands of tonnes of almond shells
and hulls as the low value residues. Despite the potentials of
resource recovery and creation of added value to the almond
shell residues, such materials are currently used as a low value
animal feed product.
Almond shells are lignocellulosic materials consisting of around
50% carbon content in the form of hemicellulose, lignin and
cellulose. Lignocellulosic materials are naturally porous, which
makes them important materials for the production of activated
carbon for various applications such as filtration, catalysis,
heavy element separation, adsorption of VOCs, gas adsorption
and storage. When these materials are converted to activated
carbon via a series of physical/chemical process, the product
provides a high specific surface area with high adsorption
properties.
The aim of the current project is to perform the resource
recovery from the Australian almond shells/hulls, which are
abundantly available with low value and to produce activated
carbon with high absorption properties with added value.
Techniques the student
would be working with
Separation techniques, NMR, IR, UV-vis, MS
Infrastructure and support
required for project
execution
All facilities are available from within UTS
Major Suited to Applied Chemistry
Honours Projects for 2016
21
Project title Extraction of d-Limonene from Citrus Peel Waste or Pulp
from Juice Factories
UTS supervisor Assoc. Prof. Andrew McDonagh
Email address [email protected]
External supervisor Dr Amir Moezzi
Project description & aims
Thousands of tonnes of citrus
fruit are juiced or used to
produce concentrates. Tonnes of
citrus fruit are also dumped
every year due to improper
resource management.
Apart from the juice and flesh
of the fruit, citrus peel, which is
often discarded is a source of d-limonene with the chemical
structure as shown in Figure 1. Limonene has a citrus scent and
used as a food additive and fragrance, solvent, natural pesticide
and insect repellent. As a solvent, it is a very good degreaser.
Citrus peel is composed of the white flesh as
well as the rind. Most of the limonene is
concentrated in the rind, however, the white
flesh also contains significant amount of
limonene.
Here, we aim to design a feasible and practical
extraction process for separating limonene
from citrus peel, starting with Australian
orange or lemon pulp.
Process design will be based on
separation techniques such as
steam distillation and solvent
extraction. Selection of a suitable and simple process, which can
be upgradable to pilot size unit operation is of importance.
Parameters such as extraction yield, optimum temperature for
the separation and optimum concentrations of extractants will be
studied. Extracted materials will also be analysed in terms of
purity and composition by various analytical methods.
Techniques the student
would be working with
Separation techniques, NMR, IR, UV-vis, MS
Infrastructure and support
required for project
execution
All facilities are available from within UTS
Major Suited to Applied Chemistry
Figure 1. Molecular structure of
limonene.
Honours Projects for 2016
22
Title
Amino acid diastereomers in recent and ancient bone collagen
Nature of problem
work is intended to
address
Amino acid racemization has previously been employed as a relative dating
tool, for example using aspartic acid for bone (eg. Bada et al, Nature 312,
442-444, 1984) and isoleucine for eggshell (eg. Miller et al, Science 309,
287-290, 2005), but the optical isomers of the secondary amino acids proline
and hydroxyproline have not been routinely measured. Hydroxyproline is the
best potential target for radiocarbon dating because it is found at ~10%
abundance in collagen but occurs rarely elsewhere. Current methods for the
isolation of the secondary amino acids are cumbersome (eg. Marom et al,
Radiocarbon 55, 698–708, 2013).
Outline of
goals/objectives
This novel research will determine the 14
C/12
C ratio and racemization ratios
of the amino acids found in collagen and dentine, with particular emphasis on
the optical isomers of proline and hydroxyproline. Recently-deceased bodies
will provide the initial human samples. For comparison, the same analyses
will be performed on marsupial collagen and dentine.
This project will explore different derivatisation reagents and instrumental
techniques (HPLC, TLC, GC) with mass spectrometry and/or
UV/VIS/fluorescence detection, to establish:
(a) suitable chiral separation parameters for high-resolution abundance
measurements of the proline and hydroxyproline optical isomers; and
(b) a simpler method for isolating sufficient (~0.5 mg) of the most abundant
single optical isomer of proline and hydroxyproline for compound-specific
AMS radiocarbon dating and stable C & N isotope measurements.
We expect this baseline analytical data for modern human and marsupial
collagen/dentine will have future applications to both ancient human skeletal
remains and sub-fossil marsupial bones, particularly the extinct Australian
megafauna. Hydroxyproline racemization ratios may benefit chronological
studies particularly for material beyond the 50,000-year limit of radiocarbon
dating.
Special requirements
Industry/Ext partner University of Wollongong, Australian National University
UTS supervisor Prof Shari Forbes
External supervisor Dr Richard Gillespie, Dr Susan Luong
Contact information [email protected]
Honours Projects for 2016
23
UNIVERSITY OF TECHNOLOGY, SYDNEY
Bachelor of Forensic Science (Honours) in Applied Chemistry
Forensic Honours Projects 2016
Title Developing a Lab-on-a-chip devices for the analysis of Amphetamines
Nature of problem
work is intended to
address
Lab-on-a-chip (LOC) is a device that integrates several laboratory functions on a single chip
to achieve automation and high-throughput screening. Printed microchips made of tonner-
polyester are one of the most promising platforms for the production of low-cost LOC
disposable devices. This project will design and produce an entirely printed LOC device for
the analysis of amphetamine related substances.
Example of a Lab-on-a-chip device
Reference:
Do Lago et al; A Dry Process for Production of Microfluidic Devices Based on the
Lamination of Laser-Printed Polyester Films. Anal. Chem., 2003, 75 (15), pp 3853–3858
Outline of
goals/objectives
1) Design microchips and print them using a toner printer and a 3D printer
2) Optimize the channel and sensors
3) Perform the analysis of amphetamines
Industry/Ext partner
UTS supervisor Lucas Blanes, Philip Doble
External supervisor
Contact information [email protected]
Honours Projects for 2016
24
Title Determination of ions present in post-blast explosive samples employing the Agilent
Bioanalyzer lab-on-a-chip
Nature of problem
work is intended to
address
The Bioanalizer is a microchip capillary electrophoresis instrument designed to detect
DNA, RNA and proteins. Recently we have shown that this instrument also can be used to
detect illicit drugs and explosives [1-2]. This project will test the feasibility of employing this
instrument for the determination of cations and anions present in post-blast explosive
samples using laser fluorescence detection. The analysis of explosive residues are important
in the forensic perspective to determine which explosives where employed in the terrorist
activity.
The Bioanalyzer instrument and chip
1- Lloyd, A et al, 2011, 'A Rapid Method For The In-Field Analysis Of Amphetamines
Employing The Agilent Bioanalyzer', Analytical Methods, vol. 3, no. 7, pp. 1535-
1539.
2- Pesenti, A, et al 2014, 'Coupling Paper-Based Microfluidics and Lab on a Chip
Technologies for Confirmatory Analysis of Trinitro Aromatic Explosives', Analytical
Chemistry, vol. 86, pp. 4707-4714.
Outline of
goals/objectives
Develop a simple and ultra-fast portable method to detect major ions present in post blast
samples.
Industry/Ext partner
UTS supervisor Lucas Blanes and Claude Roux
External supervisor
Contact information [email protected]
Honours Projects for 2016
25
Title Development of a self-powered peroxide sensor made of filter paper
Nature of problem
work is intended to
address
Microfluidic paper-based analytical devices (µPADs) present a new generation/class in
microfluidics. Filter paper is used as a fabrication substrate on which hydrophobic
microfluidic patterns are imparted to control fluid movement and compartmentalise chemical
reactions. In comparison to other micro devices, µPADs have particular benefits such as, no
requirement for pumps, adsorption of fluids, availability in a range of thickness, easy
disposal, flexibility, and suitability for colorimetric tests. In this project the student will
develop a µPADs with an internal chemical battery that will power the microchip device
when the device is put in contact with water. This device will be used to detect hydrogen
peroxide compounds that can be used to manufacture home-made explosives like TATP.
Example of a self-powered µPAD device
References:
1- Hong Liu, at al. Aptamer-Based Origami Paper Analytical Device for
Electrochemical Detection of Adenosine. Angew. Chem, 2012, 124, 1 – 5
2- Lucas Blanes at al; Garcia Lab-on-a-Chip Biosensor for Glucose Based on a Packed
Immobilized Enzyme Reactor. Electroanalysis 19, 2007, No. 23, 2451 – 2456
Outline of
goals/objectives 1- Develop a µPADs that produce electricity
2- Test and optimize the use of hydrogen peroxidase on paper devices
3- Optimize the chips to detect hydrogen peroxide using an electrochemical sensor
Industry/Ext partner
UTS supervisor Lucas Blanes and Philip Doble
External supervisor
Contact information [email protected]
Honours Projects for 2016
26
Title Printing chemical reagents onto µPADs to detect explosives
Nature of problem
work is intended to
address
Microfluidic paper-based analytical devices (µPADs) have been explored to a wide range of
applications including the detection of explosives. In this research, the student will develop a
cost effective method to print chemicals reagents onto µPADs as part of an automated
process to detect explosives.
References:
[1]Hong, L., et al; 2013, 'Inkjet printing lanthanide doped nanorods test paper for visual
assays of nitroaromatic explosives', Analytica chimica acta, vol. 802, pp. 89-94.
[2]Peters, K.L.,et al 2015, 'Simultaneous colorimetric detection of improvised explosive
compounds using microfluidic paper-based analytical devices (μPADs)', Analytical Methods,
vol. 7, no. 1, pp. 63-70.
Outline of
goals/objectives
Develop µPADs
Optimize reagent and printing conditions
Develop µPADs that will be used as swabs for direct detection of explosives
Industry/Ext partner
UTS supervisor Lucas Blanes; Andrew McDonagh; Philip Maynard
External supervisor
Contact information [email protected]
Honours Projects for 2016
27
Detection of Toxic Food Contaminants by Surface-Enhanced Raman Spectroscopy
Supervisors: Dr. Annette Dowd, Dr Linda Xiao and Dr Shanlin Fu
In recent years, food safety issues caused by contamination of toxic chemical substances or microbial
species have raised a great deal of concern in the world. Conventional chromatography-based
methods for detection of chemical contaminants and microbial plating methods for detection of food-
borne pathogens are time-consuming and labour intensive. In this project, we aim to explore the use
surface-enhanced Raman spectroscopy (SERS) (e.g. commercial SERS substrates, fractal-like metal
nanosponges, metal nanodendrites) as alternative and speedy analytical tools to detect and
characterise various toxic food contaminants, including patulin, melamine and its analogues, some
restricted antibiotics, prohibited dyes and fertilisers found in food matrices. SERS is a technique that
enhances the Raman signal from Raman-active analye molecules and reduces the fluorescence from
food matrices. The limit of detection of SERS could reach parts per billion level for chemical
samples. These results indicate a great potential of using SERS techniques for rapid detection,
classification, and quantification of chemical and biochemical contaminants in food products.
Nanostructured silver SERS substrates (image: Declan Stockdale 2015)
Honours Projects for 2016
28
Durable High Performance Cements
Supervisors Paul Thomas (CFS), Kirk Vessalas (Civil Engineering)
Concrete and precast concrete systems are important construction materials that shape the built
environment. These versatile construction materials provide strength to support high loads allowing the
building of high rise structures, but are also formable so can be used in complex architectural designs. The
growth and development of our built environment has resulted in consumption of local resources and with
the desire to design and build green building with minimal environmental impact, optimisation of
construction materials is required. From a materials perspective, the production of durable long life
structures is the primary focus of efforts to minimise environmental impact as a long life building reduces the
average annual impact of a building over the life of the building.
In order to attain durable constructions, durable materials need to be employed. Durability is attained by
mitigating the effects of environment on the construction materials. Two areas are of particular current
interest to the construction materials sector; delayed ettringite formation (DEF) and alkali silica reaction
(ASR). Both ASR and DEF result in cracking and failure of cement based construction materials due to the
formation of expansive phases during the aging of concretes.
DEF is associated with the recrystallization of ettringite after the hardening process has occurred. Ettringite is
an expansive phase and the resulting volume increase causes cracking in the cement binder. ASR is the
reaction of alkalis with ‘reactive’ aggregates forming expansive alkali substituted calcium-silicate-hydrate gels
which expand and cause cracking. In order to mitigate the effect of these processes, an understanding of the
chemistry is required. Projects investigating phase development using typical characterisation techniques,
XRD, thermal analysis and spectroscopic methods, will be carried out in conjunction with physical
characterisation methods such as expansion, strength and porosity measurements. These projects will be
carried out as part of a larger program investigating durability of cement based construction materials
involving industry (Humes and Cement Australia), the industry peak body (Cement and Concrete Aggregates
Association(CCAA)) and cross faculty collaboration (Science and FEIT).
Honours Projects for 2016
29
Characterisation of Precious Opal
Supervisor Paul Thomas
Natural precious opal is an amorphous hydrous silica (SiO2.nH2O) containing circa 8% water and 1% trace
elements and is formed through a dissolution-precipitation mechanism through the weathering of minerals.
Although a number of models have been debated for the formation of opal, mounting evidence is suggesting
that opal is formed through the homogeneous precipitation of a surface charge stabilised monodispersed
silica colloid with particle growth to a size (circa 150 to 400 nm) which can diffract visible light resulting in the
observed play of colour. This process is most likely to occur under gentle conditions (ambient temperature
and pressure, low electrolyte concentration, slightly elevated pH (8-10)) and close to equilibrium. This has
been recently demonstrated by neutron diffraction (USANS) and small angle x-ray scattering (SAXS) studies of
a Coober Pedy opal which was found to be face centred cubic (FCC) in structure (the thermodynamically
stable close packed structure – hexagonal close packed (HCP) is the kinetically derived structure).
Understanding how this crystallisation process can occur requires the understanding of the chemical and
physical properties of opal. This project proposes to characterise opal sourced from around the world using
typical characterisation techniques of XRD, SEM-EDS, NIR, Raman and thermal analysis to elucidate the
composition of opal to further understand the formation process.
Natural specimens (left to right) from Winton (QLD), Mintabie (SA), Coober Pedy (SA) and Lightning Ridge
(NSW)
SEM micrographs showing the sphere packing arrays in natural precious play of colour opal (left) and random
packing of common non-precious opal (right).
Honours Projects for 2016
30
Quantification of proteins using isotope dilution ChipLC-ICP-MS
In this project, you will develop and validate a method for the quantification of proteins using isotope
dilution chipLC-ICP-MS.
Trace elements (<0.01% of human body weight) are critical in biological processes. For example,
protein phosphorylation cascades play a central role in cell signaling and development, particularly in
cancer cells. Cyanocobalamin (vitamin B12), which forms two coenzymes responsible for biological
transformations, contains cobalt. Iron in haemoglobin binds oxygen and carbon dioxide, reactants and
products of cellular respiration. Copper and zinc are key components of superoxide dismutase (SOD),
an important enzyme in oxidation–reduction reactions. It is currently thought that around one-third of
all proteins in the human body contain at least one metal ion. These ions can act as structural features
or active sites for catalysis [1]. Trace metals are so important to cell function that cell chemistry must
be characterised by the distribution of the metals and metalloids among different biomolecules –
defined as the ‘metallome’.
Hyphenated technologies such as liquid
chromatography-inductively coupled
plasma-mass spectrometry (LC-ICP-
MS) are the most effective way to detect
trace elements in biological samples. LC
separates the sample fractions prior to
detection by ICP-MS. ICP-MS has
isotope specificity, versatility (virtually
any element can be detected), high
sensitivity, and enormous linear
dynamic range (105–10
6) needed for
efficient element detection. Figure 1 is
one example of the analysis of
metallothionein isoforms by LC-ICP-
MS. These isoforms are metal-binding
proteins associated with numerous disease states [2-4]. Recent improvements in ICP-MS
instrumentation also detect non-metals such as phosphorous and sulfur, expanding LC-ICP-MS
analysis to phosphorylated proteins [5-6]. Recently we achieved a world first hyphenation between
microfluidic chipLC and ICP-MS, designed to mitigate issues associated with standard LC-ICP-MS
analyses. It also standardises the analysis with molecular MS for identification of analytes.
The aim of this project is to quantify proteins using isotope dilution chipLC-ICP-MS; you will also
learn LC-MS to positively identify the proteins. You will apply your validated technique to determine
the concentration of SOD in C elegans.
For further information please contact David at [email protected], or Philip Doble
1. Dudev, T. and C. Lim, Principles governing Mg, Ca, and Zn binding and selectivity in proteins. Chem. Rev., 2003. 103: 773-787.
2. Aschner, M., et al., Metallothioneins in neurodegeneration. Metal Ions and Neurodegenerative Disorders, 2003: p. 307-322.
3. Cherian, M.G., et al., Contemporary Issues in Toxicology : Role of Metallothionein in Carcinogenesis. Toxicology and Applied
Pharmacology, 1994. 126(1): p. 1-5.
4. Chung, R.S. and A.K. West, A role for extracellular metallothioneins in CNS injury and repair. Neuroscience, 2004. 123(3): p.
595.
5. Bandura, D.R., O.I. Ornatsky, and L. Liao, Characterization of phosphorus content of biological samples by ICP-DRC-MS:
potential tool for cancer research. Journal of Analytical Atomic Spectrometry, 2004. 19(1): p. 96-100.
6. Bandura, D.R., V.I. Baranov, and S.D. Tanner, Detection of ultratrace phosphorus and sulfur by quadrupole ICPMS with dynamic
reaction cell. Analytical Chemistry, 2002. 74(7): p. 1497-1502.
Figure 1: Separation metallothionein isoforms by LC-ICP-MS
Honours Projects for 2016
31
Elemental bio-imaging of proteins using immunohistochemical mass spectrometry
Elemental bio-imaging using laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-
MS) was developed to target natural elemental tags in biological tissue. However, only around one-
third of all proteins contain a metal cofactor. Immunohistochemical mass spectrometry is a new field
designed to take advantage of the sensitivity of LA-ICP-MS and the selectivity of
immunohistochemical antibody tagging techniques. Antibodies selectively bind to a target, and are
themselves labelled with a lanthanide for detection (see Figure 1).
Figure 1. Mouse brain neurons tagged with an Nd-labelled antibody.
Aptamers are short synthetic strands of DNA, RNA or amino acids with complex three dimensional
structures that bind unique protein or small molecule targets with exquisite specificity. Aptamer
technology is relatively new and has the capability to distinguish between closely related isoforms.
Like antibodies, they are able to be labelled with lanthanides before binding to their target. They have
not yet been used for elemental bio-imaging.
In this project you will validate and standardise the aptamer tagging procedure. The optimal
procedure will be applied to the in situ analysis of cobalamin in mouse brain. Cobalamin has been
chosen because of its clinical relevance in a number of disease states such as pernicious anaemia and
neurological disorders and as it is currently measured using a time-consuming competitive binding
luminescence assay which requires removal of serum binding proteins before measurement. Other
short comings of this complex assay are interfering factors; in May 2012 there was a voluntary recall
of a cobalamin assay reagent (Siemens Healthcare Diagnostics, NY) due to inference issues.
For further information please contact David at [email protected], or Philip Doble
Honours Projects for 2016
32
Developing new applications for next generation elemental analysis instrumentation
Agilent Technologies is the world’s leading vendor of analytical instrumentation and leads the way in
atomic spectroscopy and elemental analysis innovation. Its optical spectroscopy headquarters is
located in Melbourne and has been the site of multiple new product developments in the past 2 years
that have pushed back some of the long-term barriers in atomic spectroscopy. Agilent’s Microwave
Plasma – Atomic Emission Spectroscopy (MP-AES) is a prime example of the continuing innovation
around instrumentation. The MP-AES is a world’s first product that provides excellent performance
without the need for expensive, difficult to obtain and often hazardous bottled gases, thereby allowing
it to be used remotely, at a mine site for example, or in developing countries where access to bottled
gases is difficult if not impossible.
There are a number of projects available to students with an interest in developing novel applications
for the MP-AES and Agilent’s next generation Inductively Coupled Plasma – Optical Emission
Spectroscopy (ICP-OES), instruments that are used in labs around the world for accurate
measurement of trace levels of a broad range of elements. Think measurement of mercury in drinking
water, trace levels of gold in mine tailings, melamine adulteration of milk and infant formula and lead
in toys.
In these projects you will research and develop novel analytical protocols for use with the MP-AES
and/or ICP-OES in the fields of food and agriculture and environmental analysis. Results will be
compared to those obtained by other analytical measurement techniques and a range of international
standards. The protocols and results developed will be used to establish real world applications for use
by researchers and analytical chemists around the world.
Students working on these projects will have the opportunity to spend time at Agilent’s state of the art
Spectroscopy Technology Innovation Centre in Melbourne.
Examples of projects available (actual project to be determined by mutual agreement, based on the
interests of the student), include developing protocols to determine:
Trace elements in drinking water
Major and trace elements in infant formula
Minor nutrients in fertilizers
Heavy metals in toys
Toxic elements in green ink
For further information please contact Philip Doble at [email protected] or David at
Honours Projects for 2016
33
Figure 1- SELEX workflow (a) The degenerate nucleic acid library is incubated with the target molecule under defined solution conditions; (b) the target-bound nucleic acids are separated from the non-bound; (c) the low affinity nucleic acids are removed (d) the bound targets are eluted; (e) the nucleic acids, now known as aptamers, are amplified.
Tagged Aptamer Evolution for Elemental Bio-imaging
Aptamer selection was originally developed by two independent laboratories with a technique known as “Systematic evolution of ligands by exponential enrichment (SELEX)”. SELEX evolves aptamers from a random library of DNA or RNA in 5 steps as shown in Figure 1. A typical SELEX procedure will undergo up to 20 cycles before aptamer characterisation. Technological advances have reduced aptamer evolution time from months to a few days. The most rapid of recent methods of aptamer evolution is by micro free-flow electrophoresis
(FFE) which is capable of screening 1.8 x 1014 random sequences in 30 minutes. FFE consists of microfluidic channels connected to a planar free-flow chamber. A solutions of the library incubated with the molecules are pumped laterally at constant flow rates across the chamber upon which a potential is applied. The separation of the bound and unbound species under the influence of the electric field is observed via fluorescence microscopy with bound fractions collected at a suitably placed exit channel. These fractions are
then unbound from the target for subsequent PCR and continued evolution. FFE devices are usually fabricated from etched borofloat wafers and require specialised equipment for photolithography procedures.
Objective : To construct novel printed
free-flow electrophoresis chips for
aptamer evolution and amplification
A printed free-flow electrophoresis chip will be designed in Coral Draw similar to that shown in Figure 2. The design will be laser printed onto wax paper followed by transfer to a glass substrate with a heat press, and covered with a thin cover slip [26]. The separation buffer and a pre-incubated aptamer-target solution will be pumped at continuous flow rates into the free-flow planar chamber. A potential difference applied laterally across the separation chamber will separate bound and unbound fractions. The fastest moving species (free DNA) will migrate towards well 8, whilst DNA with increasing affinity will be collected in wells 7 to 2 as target binding will decrease the electrophoretic mobility of the aptamer, decreasing the distance travelled within a given time frame. As the electrolyte and aptamer-target solutions are pumped at constant flow rates, extended operation of the chip will increase the amount of aptamer collected in the wells. High affinity aptamer species will be collected from the high affinity reservoirs and subjected to PCR. The amplified product will be cycled through the chip up to six times resulting in a highly specific aptamer for the target molecules.
For further information please contact
Philip Doble at [email protected] or
David at [email protected]
Figure 2- SELEX printed chip
The chip will separate bound and unbound target molecules with collection of products in well 2 to 7 for subsequent amplification by PCR.
Honours Projects for 2016
34
Professor Graham Pyke and Dr John Kalman Projects below:
Frogs as bio-indicators of environmental quality and change
Frogs are suspected to be important and useful environmental bio-indicators, but evidence to
support this view is generally lacking. This project would pursue this by examining all life
stages of frogs, in situations with varying nature and extent of likely pollution, relating
physical and physiological abnormalities to pollutant composition and concentration.
Floral nectar: It’s biology & chemistry
Floral nectar exhibits patterns within and between individual plants, and across plant species,
depending on pollinator type. However, we do not fully understand the nature of these
patterns, nor the ways in which they have arisen through co-evolution of plants and their
pollinators, nor the chemical processes involved in nectar secretion. This project would
address these issues by considering both floral nectar chemistry and pollinator foraging
behaviour.
Biology and chemistry of frog secretions
We know that frogs produce secretions, as we can sometimes see, smell or taste them.
Presumably these secretions are related to stressful conditions, interactions between male and
female frogs (as in courtship, mating etc), other interactions between frogs (such as
aggression, dominance), interactions between frogs and other organisms (warding off
predators or diseases), and so on. However, little is known about the occurrence (when, where
etc), nature (incl chemical), or function of such secretions. This project would consider the
levels of secretion by frogs and their chemical composition in relation to circumstances.
Honours Projects for 2016
35
Title New phthalocyanine complexes as photodynamic therapy agents
Description
Photodynamic therapy (PDT) is a procedure used as a treatment for cancer. PDT
utilises compounds that can react with molecular oxygen to produce cytotoxic reactive
oxygen species when irradiated with light. The reactive oxygen species cause damage
to tumour cells and can lead to cell death.
Photosensitisers are typically strongly coloured compounds (to absorb plenty of light)
and so phthalocyanine compounds are an ideal choice.
An example of a metal-containing phthalocyanine (RuPc).
This project involves the synthesis of new phthalocyanine complexes that have
potential as PDT agents. To do this, ligands will be attached to the complex that enable
the complex be absorbed, distributed and eliminated from the body.
The synthetic methods will rely on organic techniques but will be coupled with
inorganic coordination chemistry. The project will utilise NMR spectroscopy together
with other techniques to characterize the new compounds.
Name of
supervisor(s)
Dr Andrew McDonagh
Contact [email protected]
Honours Projects for 2016
36
Spectroscopic probing of biological nanomachines: elucidating the structure of CLIC proteins in cell
membrane models
Supervisors: Dr Annette Dowd, A/Prof Barbara Stuart, A/Prof Stella Valenzuela
Raman and FTIR spectroscopy are powerful techniques to monitor modification in the lipid bilayer and also
the protein structure. Characteristic vibrations of chemical bonds can be subtly changed by their nanoscale
local environment, e.g. the frequency associated with the peptide bond depends on whether it is situated in an
alpha-helix or a beta-sheet structure. These spectroscopic tools can interrogate these chemical bonds in a
noninvasive way.
The aim of this project is to add to knowledge about the structure of the CLIC protein machinery and its
insertion into lipid bilayer membranes. This student will study the effect of cholesterol on the lipid structure,
protein structure and its insertion. The student may also develop the spectroscopic technique by investigating
different types of membrane preparation (liposomes, single tethered layers etc) and the use of nanostructured
SERS substrates for signal enhancement.
This multidisciplinary project will be undertaken in PAM, CFS & MMB labs. Opportunities will be available
to access state-of-the-art equipment at the Vibrational Spectroscopy Facility at the University of Sydney.
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