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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 Heavy metals are well known for their toxicity. One method used for the removal of STRUCTURE STREAMS aqueous metals from water isCOURSE adsorption, which AND 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 drugcarrier 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. Tony Hollenkamp (CSIRO), Russell Newnham (Electric Applications Incorporated) & Peter Mahon Why do Lead-Acid Batteries Lose their High-Power Capability when operated under HighRate Partial-State-of-Charge Duty Cycles? Hayden Webb, Song Ha Nguyen & Peter Mahon Electrochemical and spectroscopic analysis of redox mediators secreted by electricityCOURSE STRUCTURE AND STREAMS producing bacteria Peter Mahon & Hayden Webb Direct electrochemical detection using an ionic liquid to selectively pre-concentrate redox mediators during solvent extraction Peter Mahon The application of electrochemistry to mimic metabolism 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-of-flight 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 specificity of the test will be examined. COURSE STRUCTURE AND STREAMS 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 PCRamplifications, 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 PCR-amplifications, 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 gelassisted method to form giant unilamellar vesicles (GUVs) and investigated using timelapsed 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 Plasma polymerization modifies surfaces via the deposition of a thin film containing 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. COURSE STRUCTURE AND STREAMS 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. This project will involve sampling in appropriate field locations in ports/harbours and the subsequent identification of microorganisms in the samples. Some of the overall aims are to determine: - Presence of microorganisms previously implicated in MIC COURSE AND STREAMS - What other microorganisms tendSTRUCTURE 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 SRB - Test metal sample orientation - Test metal type - Test metal surface preparation OURSE STRUCTURE AND STREAMS During the project the student C 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 in Mid-November 2016, prior to the beginning of the honours project (inquiry: [email protected]). Without participation of the experiment will not affect the project. COURSE STRUCTURE AND STREAMS 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 antioxidative compounds will be detected, and potentially other bio-protective agents, such as quorum sensing inhibitors may be present. The project will also aim at demonstrating the bioprotective effectiveness of these compounds for the protection of metallic and non-metallic surfaces. COURSE STRUCTURE AND STREAMS 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