School of Chemistry & Molecular Biosciences Faculty of Science BIOTECHNOLOGY
Research Projects 2018 Honours Masters Res Ex Professional Doctorate Graduate Diploma Masters SCMB Biotechnology Research Projects 2018 | Industry Project
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“Every effort has been made to ensure the accuracy of information in this document at the time of publication. The authoritative source of program and course information is the UQ Courses and Programs website at www.uq.edu.au/study/. Where any conflict of information exists, the rules and associated course lists approved by the UQ Senate shall apply.”
Last updated: 18 April 2018
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CONTENTS
INDUSTRY PROJECTS Industry Contributors Organisation/Business Unit Page No. Professor Ross Barnard Director, Biotechnology Program 9 School of Chemistry & Molecular Biosciences Professor Peter Gray Australian Institute for Bioengineering and 10 Nanotechnology (AIBN) Professor Peer Schenk School of Biological Sciences 11 Professor Istvan Toth School of Chemistry & Molecular Biosciences / 12 TETRAQ Professor Matt Trau Australian Institute for Bioengineering and 13 Nanotechnology (AIBN) / School of Chemistry & Molecular Biosciences Advanced Water Management Centre 14 Dr Phil Bond Dr Liu Ye Professor Zhiguo Yuan Dr Bernadino Virdis Dr Damien Batstone Dr Jelena Radjenovic Dr Maria Jose Farre Dr Jens Kroemer Cook Australia Pty Ltd 15 Evolve Group 16 Fitgenes 17 QAAFI Honours Project/s Queensland Alliance for Agricultural and Food 18 Dr Michael Netzel Innovation (QAAFI) A/Prof Yasmina Sultanbawa Professor Neena Mitter Queensland Alliance for Agricultural and Food 19 Innovation (QAAFI)
Dr Linda Lua Australian Institute for Bioengineering and 20 Nanotechnology (AIBN) Associate Professor Craig Williams School of Chemistry & Molecular Biosciences 21
GROUP PROFILES Group Name and Contributors Organisation/Business Unit Page No. Centre for Nutrition and Food Sciences Centre for Nutrition and Food Sciences 22 Dr Eugeni Roura (CNAFS) Dr Nadia de Jager Diamantina Institute for Cancer, Immunology Diamantina Institute for Cancer, Immunology & 23 & Metabolic Medicine Metabolic Medicine Professor Ranjeny Thomas Dr Raymond Steptoe Polymer Chemistry Group Australian Institute for Bioengineering and 24 Professor Andrew Whittaker Nanotechnology (AIBN)
Professor Matt Trau Australian Institute for Bioengineering and 25 Dr Ashley Connolly Nanotechnology (AIBN) / School of Chemistry & Molecular Biosciences Professor Matt Trau Australian Institute for Bioengineering and 26 Dr Muhammad Shiddiky Nanotechnology (AIBN) / School of Chemistry & Molecular Biosciences
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INDIVIDUAL CONTRIBUTORS Individual Contributors Organisation/Business Unit Page No. Associate Professor Sassan Asgari School of Biological Sciences 27 Associate Professor Andrew C. Barnes Centre for Marine Studies 28 Professor Christine Beveridge Centre for Integrative Legume Research 29 Associate Professor Joanne Blanchfield School of Chemistry & Molecular Biosciences 30 Professor Jimmy Botella School of Biological Sciences 31 Professor Paul Burn Centre for Organic Photonics & Electronics 32 (School of Chemistry & Molecular Biosciences) Professor Rob Capon Institute for Molecular Bioscience 33 Professor Bernie Carroll School of Chemistry & Molecular Biosciences 34 Dr Marina Chavchich Australian Army Malaria Institute 35 Professor David Craik Institute for Molecular Bioscience 36 Professor James De Voss School of Chemistry & Molecular Biosciences 37 Dr Annette Dexter Australian Institute for Bioengineering & 38 Nanotechnology (AIBN) Associate Professor Paul Ebert School of Biological Sciences 39 School of Chemistry & Molecular Biosciences Associate Professor Darryl Eyles Queensland Brain Institute 40 Professor David Fairlie Institute for Molecular Bioscience 41 Associate Professor Camile Farah School of Dentistry / UQ Centre for Cancer 42 Research Associate Professor Vito Ferro Deputy Director, Biotechnology Program 43 School of Chemistry & Molecular Biosciences Dr Brett Ferguson Director, Centre for Integrative Legume Research 44 Dr Marina Fortes School of Chemistry & Molecular Biosciences 45 Dr Donald Gardiner CSIRO Plant Industry/Queensland BioScience 46 Precinct, UQ-St. Lucia Campus Professor Ian Gentle School of Chemistry & Molecular Biosciences 47 ARC Centre for Functional Nanomaterials Professor Robert G Gilbert Centre for Nutrition & Food Sciences 48 School of Chemistry & Molecular Biosciences Professor Elizabeth Gillam School of Chemistry & Molecular Biosciences 49 Professor Jeff Gorman Queensland Institute of Medical Research (QIMR) 50 Professor Peter Gresshoff Centre for Integrative Legume Research 51 Dr Ulrike Kappler School of Chemistry & Molecular Biosciences 52 Professor Mark Kendall Australian Institute for Bioengineering & 53 Dr Simon Corrie Nanotechnology (AIBN) Professor Alexander Khromykh School of Chemistry & Molecular Biosciences 54 Professor Glenn King Institute for Molecular Bioscience 55 Professor Bostjan Kobe School of Chemistry & Molecular Biosciences 56 Dr Shih-Chun Lo (Lawrence) Centre for Organic Photonics & Electronics 57 School of Chemistry & Molecular Biosciences Dr Patricia Lopez-Sanchez Centre for Nutrition and Food Science 58 ARC Centre for Excellence in Plant Cell Walls Professor Alan E. Mark School of Chemistry & Molecular Biosciences 59 Professor Daniel Markovich School of Biomedical Sciences 60 Associate Professor Fred Meunier Queensland Brain Institute / School of Biomedical 61 Sciences Associate Professor Chamindie Punyadeera School of Biomedical Sciences 62 - 63 Institute of Health and Biomedical Innovations Queensland University of Technology Dr Kristen Radford Mater Medical Research Institute (MMRI) 64 Dr Steven Reid Deputy Director, Biotechnology Program 65 School of Chemistry & Molecular Biosciences Group Leader AIBN
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Associate Professor Joe Rothnagel School of Chemistry & Molecular Biosciences 66 Associate Professor Mark Schembri School of Chemistry & Molecular Biosciences 67 Dr Horst Joachim Schirra School of Chemistry & Molecular Biosciences 68 Dr Benjamin Schulz School of Chemistry & Molecular Biosciences 69 Associate Professor Conrad Sernia School of Biomedical Sciences 70 Dr Yasmina Sultanbawa Queensland Alliance for Agriculture and Food 71 Innovation (QAAFI) Dr Kate Stacey School of Chemistry & Molecular Biosciences 72 Dr Matt Sweet Institute for Molecular Bioscience 73 Professor Stephen Taylor School of Biomedical Sciences 74 Dr Hang Ta Australian Institute for Bioengineering & 75 Nanotechnology (AIBN) Dr Simon Worrall School of Chemistry & Molecular Biosciences 76 Professor Paul Young School of Chemistry & Molecular Biosciences 77 Dr Adrian WIegmans Queensland Institute of Medical Research (QIMR) 78
Dr Stefano Freguia Centre for Microbial Electrosynthesis 79 Advanced Water Management Centre Professor Richard Lewis Chemistry and Structural Biology Division 80 Centre for Pain Research Dr Zyta Ziora Institute for Molecular Bioscience 81
QUEENSLAND ALLIANCE FOR AGRICULTURE AND FOOD INNOVATION (QAAFI)
Dr Inigo Auzmendi QAAFI 83 Dr Jim Hanan (Ecosciences Precinct, Boggo Road, Dutton Park) Dr Femi Akinsanmi QAAFI 84 Associate Professor Andre Drenth (Ecosciences Precinct, Boggo Road, Dutton Park) Dr Femi Akinsanmi QAAFI 85 (Ecosciences Precinct, Boggo Road, Dutton Park) Dr Femi Akinsanmi/Dr Bruce Topp QAAFI 86 (Ecosciences Precinct, Boggo Road, Dutton Park) Associate Professor Elizabeth Aitken School of Agriculture and Food Sciences St Lucia 87 Dr Lee Hickey campus, The University of Queensland Dr Karine Chenu QAAFI (Toowoomba-Gatton) 88 Dr Sushil Dhital Queensland Alliance for Agriculture and Food 89 Innovation (QAAFI)/UQ, St Lucia. Associate Professor Ralf Dietzgen QAAFI 90 Ritchie Laboratories, St. Lucia Campus Associate Professor Ralf Dietzgen CILR, John Hines Building and QAAFI, Ritchie Bldg, 91 Dr Paul Scott UQ St Lucia Campus Professor Peter Gresshoff Dr Andrew Geering QAAFI 92 Associate Professor John Thomas (Ecosciences Precinct, Boggo Road, Dutton Park)
A/Prof Mary Fletcher Health and Food Sciences Precinct, 93 Coopers Plains Dr Jim Hanan Centre for Horticultural Science 94 QAAFI Dr Jim Hanan Centre for Horticultural Science 95 Dr Chung-Chi (Alex) Wu QAAFI Dr Ala Lew-Tabor Centre for Animal Science 96 QAAFI
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EDUCATION/BUSINESS AND MARKETING PROJECTS Professor Ala Tabor Centre for Animal Science 98 Dr Marina Fortes QAAFI
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INDUSTRY PROJECTS
Would you like to undertake part of your research project in a company outside UQ?
Experience a commercial workplace Make contacts to help you with your career Receive support and guidance from UQ as well as your industry supervisor
Opportunities exist in these industries and more:
Biotechnology Chemical Pharmaceutical Food processing Pathology
As a Biotechnology, Chemistry or Molecular Biosciences student, you may be able to undertake a research project or internship with companies with whom SCMB already has a working relationship. In addition, if there is a particular company you would like to work with, you are welcome to propose it to us.
In the past two years, SCMB students have been hosted for a variety of industry projects at the following organizations:
Patheon Biologics Fitgenes Anteo Diagnostics Perkii Merck Sharpe and Dohme Ground Zero Pharmaceuticals Bayer Crop Science Uniquest Luina Bio Research Directions Queensland Health Perfection Fresh QCIF Integria Healthcare Army Malaria Institute Sugar Research Australia TetraQ
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Summer project benefits student and Biotechnology company
Van Mai was inspired by a lecture in the biotechnology program , to do an industry placement internship that led to her work being incorporated into presentations to customers by a successful Brisbane biotech company.
“Two scientists from Anteo Diagnostics gave a guest lecture in the second year Issues in Biotechnology course I was taking,” she said. “I found it very interesting and thought provoking.” Course coordinator, Associate Professor Vito Ferro, mentioned to students that an eight-week internship at Anteo was available for a student taking the course Biotechnology Industry Placement over the summer semester. Van applied and was chosen.
After two weeks of on-site training about company policy, equipment use, experiment design and record-keeping, Van felt well-equipped to undertake six weeks in the company laboratory.
“I worked with one of Anteo’s signature products, Mix&Go, a high performance substance for surface coating,” said Van. “The product enables fragile biomolecules to correctly orientate and attach to a wide range of surfaces. “Specifically, I worked on optimising protocols for plate-based enzyme linked immunosorbent assays.”
Shaun Cooper of Anteo Diagnostics supervised Van’s project and said that Van was asked to use the underlying theory of Anteo’s novel ligand-metal coordination chemistry to determine its utility in improving sensitivity of an immunoassay in a format were low surface area traditionally limits performance.
“Van identified the performance differences of the product in high and low surface area plate formats,” he said. “Her data demonstrated that sensitivity differences can be observed with the application of Mix&Go and that improvements are greater in the lower surface area format.
“Some of her data was incorporated into technology overview presentations given by the company’s chief scientific officer to prospective customers and partners.”
Van said that the work environment at Anteo was warm and welcoming and that the experience had taught her about the business side of scientific research, including policy, protocols and the importance of discussion and collaboration. “It has also built my confidence,” she said. Van is an international student who won a scholarship from the Vietnamese government to study in Australia. She was awarded Dean’s Commendations for high achievement in her undergraduate studies, worked as a peer tutor and charity volunteer, and is now completing her Honours year in materials chemistry. She praised the quality of UQ’s teaching and learning, the range of courses, lab facilities and the beautiful St Lucia campus.
Anteo Diagnostics has hosted a number of UQ biotechnology students and is keen to host more. “Students who undertake internships like Van’s gain not only general workplace skills, but also some insight into how Australian research contributes to commercial product realisation,” said Mr Cooper. “Support for translational research is currently a topic of government policy debate, and projects like Van’s are a good example of the interface between research and commercialisation.
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PROFESSOR ROSS BARNARD Director, Biotechnology Program School of Chemistry & Molecular Biosciences
Phone: 07 3365 4612 Email: [email protected]
Teaching and other interests: • Biotechnology Program Director • PhD and Honours supervisor • Real-time PCR, Infectious disease diagnosis, Antibody engineering
General Research Outline • Development of novel diagnostic technologies. • Antibody engineering/phage display/for cancer therapy or infectious disease diagnostics.
Current research projects 1. Infectious disease diagnostic development with a focus on Campylobacter, Flaviviruses and banana viruses 2. Novel real-time PCR detection technology. 3. Antibody engineering for infectious disease diagnosis and cancer treatment. 4. Project 4 – Anti-inflammatory effects of transdermal metal ion absorption.
My current research projects involve collaboration with: • Project 1 – Department of Fisheries and Forestry/QAAFI. • Project 3 – UQ Mater Institute and Pharmacy Australia Centre of Excellence • Project 4 – Therapeutics Research Unit, UQ Department of Medicine, Princess Alexandra Hospital
Selected Recent Publications: Lai, R., Liang, F., Pearson,D., Barnett, G., Whiley, D., Sloots, T., Barnard, R.T., Corrie, S.R. (2012) PrimRglo: a multiplexable quantitative real time PCR system for nucleic acid detection. Analytical Biochemistry doi:10.1016/j.ab.2011.12.038
Luke R. Le Grand, Michaela White, Evan B. Siegel, and Ross T. Barnard (2012) Recombinant Vaccines: Development, Production, and Application. In: Kayser, O., Warzecha, H. eds. Pharmaceutical Biotechnology 2nd ed. Wiley-Blackwell.
Barnard, R.T., Hall, R.A. & Gould E.A. (2011) Expecting the unexpected: nucleic acid-based diagnosis and discovery of emerging viruses. Expert Rev. Mol. Diagn. 11(4) 409-423
Barnard, R.T. (2010) Recombinant Vaccines Expert Rev.Vaccines 9(5), 461–463 Macdonald, J., Poidinger, M., Mackenzie, J.S., Russell, R.C., Doggett, S., Broom, A.K., Phillips, D., Potamski, J.,Gard, G., Whelan, P., Weir, R., Young, P.R., Gendle, D., Maher, S., Barnard, R.T. & Hall, R.A. (2010) Molecular phylogeny of Edge Hill Virus supports its position in the Yellow Fever Virus group and identifies a new genetic variant. Evolutionary Bioinformatics 6, 91-96
Liang, F., Lai, R., Arora, N., Zhang, K.L., Yeh , C-C., Graeme R. Barnett, G.R., Voigt, P., Corrie, S.R., Barnard, R.T. (2013) Multiplex–microsphere–quantitative polymerase chain reaction: Nucleic acid amplification and detection on microspheres. Analytical Biochemistry 432, 23–30.
Chandrasekaran, N.C., Weir, C., Alfraji, S., Grice, J., Roberts, M.S. & Barnard, R.T. (2014) Effects of magnesium deficiency-more than skin deep. Exp. Biol. Med. Doi:10.1177/1535370214537745
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PROFESSOR PETER GRAY Australian Institute for Bioengineering and Nanotechnology (AIBN)
Phone: 07 3346 3899 Email: [email protected]
Biopharmaceuticals and mammalian cell culture based biotechnology The acceptance of biopharmaceuticals as human therapeutics has been rapid, with global sales of such products now exceeding $US100 billion per annum. These sales are now growing at over 20% per annum, and there are many new biopharmaceuticals making up the potential product ‘pipelines’ of biotech and pharma companies. Of particular note is the rapid acceptance of human and humanised monoclonal antibodies as therapeutic agents.
Antibodies, and the majority of other biopharmaceuticals, are large complex proteins that have to be produced by mammalian cell culture in order to have the correct post-translational modification they require for full biological activity.
The Gray Lab is focused on engineering mammalian cells in order to improve their efficiency and utility in the production of complex proteins. The approaches used to gain greater understanding of such systems are also being applied to even more complex cells, viz the development of bioprocesses based on embryonic stem cells.
Many of our research projects are collaborative, and often involve interactions with international biotech and pharma companies.
Examples of available projects are: 1. Developing transient protein expression systems which will allow researchers to rapidly produce larger amounts of protein needed for initial characterisation and testing.
2. Developing high throughput approaches which allow the rapid selection of clones which stably express high levels of the desired biopharmaceutical.
3. Using modern ‘omics’ approaches to gain better understanding of cellular metabolism which will allow maximal protein expression by mammalian cell cultures.
4. Development of novel therapeutic antibodies. A drug discovery program in this area aims to develop novel therapeutic monoclonal antibodies for infectious diseases. The drugs will be used for treatment of severe infections caused by antibiotic resistant bacteria. The discovery program aims to create antibody molecules that can be engineered for targeted delivery of polymer-based nanoparticles as well as other novel drugs.
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PROFESSOR PEER SCHENK School of Biological Sciences
Phone: 07 3365 8817 Email: [email protected]
Plant and Microbial Biotechnology, Plant-Microbe Interactions, Functional Genomics & MetaTranscriptomics, Sustainable Biofuel Production. Microalgae Biotechnology The Plant-Microbe Interaction Group specialises in the discovery of interesting new genes from plants and microorganisms (www.plantsandmicrobes.com; www.algaebiotech.org)
Disease resistant plants: We use a Functional Genomics and Biodiscovery approach to study beneficial and parasitic interactions of plants with microbes. Arabidopsis is used as a model plant to study signalling pathways that enable plants to withstand pathogen attack or severe drought. The up- or down-regulation of specific key regulatory genes has led to disease resistance and drought tolerance, and this strategy is used to improve crop species.
Microbial communities associated with plants: We are using molecular profiling tools, such as functional gene microarrays and 454 sequencing, to characterise highly diverse microbial communities that are associated with plants to identify novel compounds for pharmaceutical and agricultural applications. This environmental transcriptomics (metatranscriptomics) approach captures microbial activity profiles with direct implications for crop cultivation (e.g. soil-borne diseases, greenhouse gas emmissions, yield increase or decline).
Biofuel production from algae: We use microalgae strains that are highly efficient producers of hydrogen or biodiesel and further optimise these by using cutting-edge molecular biology and engineering tools. Microalgae are likely the only renewable source of fuel that could match our current and future demand without competing for arable land and food production. Recently, we have developed large-scale microalgae cultivation systems to produce biofuels (biodiesel), protein-rich animal feed and Omega-3 fatty acids. This project is receiving a lot of interest from industry
Projects: 1. Increased disease resistance in plants 2. Plant cell signalling in response to beneficial microbes and plant pathogens 3. Metatranscriptomics of highly diverse microbial communities 4. Biodiesel, omega-3 fatty acids and animal feed from microalgae Selected Recent Publications: 1. Çevik et al. (2012) MED25 acts as an integrative hub for the regulation of jasmonate-responsive gene expression in Arabidopsis. Plant Physiology doi: http://dx.doi.org/10.1104/pp.112.202697 2. Adarme-Vega et al. (2012) Microalgal biofactories: A promising approach towards sustainable omega-3 fatty acid production. Microbial Cell Factories 11:96. 3. Lim et al. (2012) Isolation and evaluation of oil-producing microalgae from subtropical coastal and brackish waters. PLoS ONE 7:e40751 4. Schenk et al. (2011) Unravelling plant-microbe interactions: can multi-species transcriptomics help? Trends in Biotechnology 30:177-184
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PROFESSOR ISTVAN TOTH School of Chemistry & Molecular Biosciences
Phone: 07 3346 9892 Email: [email protected]
Drug and Vaccine Delivery: Many peptides have been identified as potential new drugs or vaccines, but few have progressed into the clinic. This is predominantly due to their rapid enzymatic breakdown, problematic delivery, and/or poor inherent immunogenicity. There is a strong need for new delivery systems that overcome these issues.
Project One: Lipid-Core Peptide (LCP) delivery systems: We have previously developed a lipid-core peptide delivery system that is applicable to the delivery of a wide range of peptides. The LCP system can be optimized to improve the absorption and stability of the peptide. An advantage of the LCP system for vaccine delivery is that the antigen, carrier, and adjuvant can be included in a single chimeric molecule. Models under investigation for the use of the LCP system include vaccines against malaria, hookworm, group A streptococcus, and cancer. Further structure-activity studies are required to optimize the delivery system and to identify the mechanism of action of the delivered peptides on the host immune response. Aim: to perform structure-activity studies to further optimize the LCP delivery system.
Project Two: Chemo-enzymatic synthesis of drug/vaccine delivery systems: This project aims to address shortcomings in peptide delivery by coupling naturally occurring sugars and lipids to the peptides of interest using a combination of organic synthesis and enzymatic transformations. This multidisciplinary approach (chemistry, biotechnology, biology) has the potential to not only improve peptide absorption and metabolic stability, but to enhance the access of peptides to target sites using carbohydrate and/or amino acid transport systems. The combination of chemical and enzymatic synthesis provides access to complex carbohydrate structures that can be used to target drug molecules. One example is the use of glycosyltransferases from Neisseria meningitidis to target Leu-enkephalin peptide derivatives (potential pain drug candidates) to opioid receptors in the central nervous system. Aim: to design and develop a generally applicable, novel drug delivery system (synthesized chemically and chemo-enzymatically) that targets specific cell types.
Project Three: Nanovaccine delivery systems: Recent developments in nanomedicine/vaccinology have identified that the size and morphological characteristics of nanoparticle vaccines affect their efficacy. Preliminary investigations have demonstrated that 20 nm nanoparticles displaying peptide epitopes on their surface were able to induce very strong immune responses against those epitopes. We have also shown that this response was size dependent. This project aims to further explore the effect of size and morphology on the efficacy of nanoparticle vaccines. Aims: 1) Produce and self-assemble multi-epitope vaccine constructs. 2) Fully characterize nanoparticles, including arrangement of the epitopes on the surface.
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PROFESSOR MATT TRAU Australian Institute for Bioengineering and Nanotechnology (AIBN)
Phone: 07 3346 4173 Email: [email protected]
Our Centre for Biomarker Research and Development is located in the Australian Institute for Bioengineering and Nanotechnology (AIBN) and has access to state-of-the-art chemistry synthesis, and characterisation facilities. Students working in the Centre will have the opportunity to create nanoscaled biosensors for applications in cancer, infectious disease, therapeutics and point-of-care devices. Students will also be given the opportunity to work with leading geneticists, epigeneticists and clinical researchers to test these devices in clinical settings. The Centre has a focus on developing diagnostic devices for early detection of diseases such as cancer, when it is most responsive to treatment which also provides the greatest social and economic benefits to society. Nanotechnology offers the promise of miniaturized, inexpensive, flexible and robust “plug-and-play” molecular reading systems which can be effectively deployed to detect diseases in a clinical setting. Current projects available include:
1) Microfluidic Devices for Capturing Rare Circulating Tumour Cells The progression of cancer in patients is characterized by cells that invade locally and travel through the blood stream to metastasize in the other parts of the body. These cells, account for 1 or fewer cells in 106 blood cells and are known as circulating tumour cells (CTCs). Development of advanced technologies for capturing CTCs in blood in the early stage of the metastasis process would transform the treatment of cancer. This project strives to build and test a microfluidic device to enable selective capture and detection of CTCs using threedimensional microstructured electrodes within the the device.
2) Nanodevices/Nanobiosensors for Cancer Biomarker Proteins Detecting low concentrations biomarkers in serum is potentially useful for the diagnosis and prognosis of a disease. The development of a detection method that is rapid and cheap could revolutionize the treatment of diseases such as cancer. In this project, we aim to fabricate nanobiosensors with nanostructured 3D-electrodes to detect single protein molecules in blood. Students will achieve hands on experience in the design, fabrication and application of the microfluidic devices and electrochemical micro(nano)biosensors.
3) DNA Nanomachinery for Early Breast Cancer Detection Subsets of non-coding (nc) RNAs serve as potential biomarkers of diseases. This project involves designing, developing and evaluating novel DNA nanomachinery to perform tasks that are currently beyond the reach of existing molecular readout technologies. We aim to use these nanomachines as a new technology platform to rapidly detect ncRNA biomarkers in breast cancer patients. This interdisciplinary project will provide an opportunity for students to acquire diverse skills in chemistry, molecular biology and bioengineering.
4) Point-of-Care Diagnostics Point-of-care (POC) diagnostics have the potential to revolutionise global health care by enabling diseases to be rapidly diagnosed ‘on the spot’ using minimal specialised infrastructure. POC devices need to be highly sensitive, specific, practical, cost effective and portable if they are to be used in resource limited settings. We are focused on novel and simple (nanotechnology-based) molecular assays to generate new POC diagnostic technologies. Students will be involved in designing, developing and evaluating methods to rapidly detect pathogenic DNA using devices such as mobile telephones. This interdisciplinary project will provide an opportunity to acquire diverse skills in chemistry, molecular biology, bioengineering, and biotechnology.
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THE ADVANCED 2. Turning emissions into fuels using electricity- boosted fermentation. / Dr Jens Kroemer WATER MANAGEMENT Microbial electrosynthesis is a cutting edge technology to produce valuable products from CENTRE (AWMC) oxidised carbon sources. This study will apply bioelectrochemical systems to boost the bio-
production of fermentation products by Clostridia. Honours Projects at The Advanced Water
Management Centre (AWMC) 3. 1,3 propanediol production from glycerol using Students with interests in environmental microbial electrosynthesis with Citrobacter ssp. / microbiology/biotechnology, wastewater Dr Jens Kroemer treatment processes, environmental chemistry, Microbial electrosynthesis is a cutting edge microbial ecology and function, and/or application technology to produce valuable products from of molecular approaches, are encouraged to apply oxidised carbon sources. This study will explore for Honours projects listed here. The AWMC is an the production of 1,3 propanediol from glycerol in international centre of excellence for innovative a engineering Citrobacter species. The project is a wastewater technology and management, with collaboration between the Centre fro Microbial over 15 Research Academics and more than 50 Electrosynthesis at UQ and the University of Ghent graduate students (see in Belgium. http://www.awmc.uq.edu.au/). If you are motivated by our exciting science and interested 4. Determining the microbes that are eating our in honours projects or higher degrees then please sewer pipes. / Dr Guangming Jiang, Dr Phil Bond get in contact with either Dr Phil Bond, and Prof Jurg Keller [email protected]; or directly contact Certain microorganisms cause massive problems the academics listed with the project descriptions in sewers by forming biofilms on the concrete and below. For Honours students that qualify at the producing sulfuric acid that corrodes the concrete AWMC a tax free stipend of $3000 can be available pipes. This project will investigate the molecular (subject to the project). ecology and microbial activities to understand the
effects of treatments aimed to mitigate this Research Interests and Graduate Research problem. Projects
Our research focuses on wastewater treatments 5. Influence of soluble organics on struvite systems, polluted environments, production of crystallization. / Dr Chirag Mehta and Dr. Damien energy from waste, ocean biogeochemistry, water Batstone recycling and solid waste treatment. Below are Struvite crystallization technology is being widely examples of research topics available as Honours applied in full-scale to remove phosphorus from projects at the AWMC; further projects are wastewater. This project will investigate influence available within the centre, please enquire. of soluble organics on struvite crystal formation
through solubility, growth rate, product size 1. Determining the mechanism of free nitrous distribution, and product quality measurements. acid inhibition on biofilm activity of wastewater microorganisms. / Dr Chris Lu Fan, Dr Phil Bond 6. Binders for struvite granulation. / Dr Chirag and Prof Zhiguo Yuan Mehta and Dr. Damien Batstone There is great interest in disruption or destruction There is great interest to formulate and test waste of problem microbial biofilms. This project will derived fertilizer product (struvite). This study will investigate the disruptive effect of a toxin, nitrous investigate role of different binders on mechanical acid, on microorganisms relevant to wastewater and agronomic properties of the granulated treatment biofilms, with the aim to determine product molecular and physiological understanding of the toxic effect.
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COOK AUSTRALIA PTY LTD Address: 12 Electronics Street, Eight Mile Plains QLD 4113
Phone: 07 3365 4612 Email: [email protected]
A range of possible projects is available. Applicants for this project should contact Prof Ross Barnard in the first instance.
Cooks contribution: Cook will provide project supervision and ongoing advice.
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DR NAVIN CHANDRASEKERAN Scientific Research Co-ordinator | Evolve Group
Phone +61 7 3283 1196 | Mobile +61 412031588 Email: [email protected] | Web: www.evolvegrp.com
Improved method for sanitising large bodies of water.
Free chlorine (hypochlorite ions or hypochlorous acid) has been used to disinfect water since the 1800s. However, it was only after an Australian invention in early 1960s, the use of saltwater chlorine generators (SWCGs) for disinfecting large bodies of water such as swimming pool became popular. Over the years, these devices have undergone several iterations to improve the process of electrolysing saline water to produce free chlorine. Recently, the use of reversing polarity has gained significance due to its ability to self-clean any salt deposits off the electrodes.
Even though technology and material science has advanced rapidly in the last few decades, it has not effectively translated to improve the working design of a SWCG. We intend to develop a high efficiency electrolysis unit that can generate free chlorine, with minimum chloride levels such as those present in potable water. This could be approached by using an alternative material or design for electrode, which can improve conductivity, surface area and/or current density. Also, alternative ways of electrolysing salt solution could be explored, such as membrane-based methods.
Free chlorine due its oxidising nature acts as an effective sanitiser, however, results in the formation of harmful disinfection by-products such as trihalomethanes, when it combines with organic substances. To avoid this, in another approach we intend to develop a unit that creates a sanitisation effect in a body of water that is equivalent to levels achieved by maintaining 2 ppm free chlorine, without using any salt or granular chlorine.
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Projects with company Fitgenes: Business Plan Prepare a business plan for Fitgenes and its product - CarbChoice. Carbchoice is offered direct to consumer and as a clinical resource of healthcare practitioners who have completed our accreditation training.
Marketing and Sales Plan As above for Fitgenes and CarbChoice.
Content Writing - Technical, Consumer Preparation of content for websites - FG and CC, based on new research, more in depth analysis for nutrigenomic interventions.
CarbChoice Direct to Consumer Report - editing and writing based on science behind potential interventions for consumers. Content writing for Online learning platforms - CarbChoice online learning platform for training practitioners in understanding CarbChoice science, how to apply this in clinic and use as a clinical application. Goal being to offer the AMY1 gene analysis to their patients as a foundation for intervention planning including dietarty and supplements regime.
Research Literature reviews on AMY1 gene CNV and other Fitgenes references and resources. CONTACT: Tracey Porst | Marketing and Communications Manager
p 1300 348 436 37 m +61 409 302 694 e [email protected] w www.fitgenes.com | www.carbchoice.com.au
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QAAFI Honours Projects 2017 Project/s Australian grown produce as a novel dietary source of folate
The vitamins of the folate group play a crucial role as coenzymes in the metabolism of one-carbon groups, and are decisively involved in DNA synthesis, amino acid metabolism and methylations. However, intake of folate from natural sources is considered to be below the human dietary recommendations. Low dietary intake of folate is associated with the risk of neural tube defects and is suspected to be associated with the development of certain forms of cancer, Alzheimer’s disease and cardiovascular disease. Over 50 countries have introduced mandatory folate fortification. However, apart from fortification, the identification and consumption of fruits/food rich in natural folate are an alternative strategy to increase folate intake. Unique strawberry breeding lines and native Australian fruits such as Kakadu plum, Green plum and desert lime will be assessed for their natural folate content, profiles (different vitamers) and nutritional value by using: (a) state-of-the-art analytical techniques such as Accelerated Solvent Extraction (ASE), Stable Isotope Dilution Assays (SIDA) and UHPLC-MS (b) in vitro models mimicking the human digestion process to determine the matrix release/ bioaccessibility of the different folate vitamers which is crucial for their bioavailability and subsequently physiological activity.
This project presents an excellent opportunity for an Honors student to learn state-of-the-art analytical techniques and to generate novel and significant data for this critical vitamin.
Unique Strawberry breeding lines Native Australian Kakadu Plum Contact Dr Michael Netzel | Email: [email protected] | Phone: +61 7 344 32476 Advisor/s A/Prof. Yasmina Sultanbawa | Email: [email protected] | Phone: +61 7 344 32471
Health & Food Sciences Precinct Coopers Plains, 39 Kessels Road, Coopers Plains, QLD 4108 Webpage [https://qaafi.uq.edu.au/profile/579/michael-netzel] [https://qaafi.uq.edu.au/profile/450/yasmina-sultanbawa]
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PROFESSOR NEENA MITTER
Director of Centre for Horticultural Science QUEENSLAND ALLIANCE FOR AGRICULTURE AND FOOD INNOVATION (QAAFI) Queensland Bioscience Precinct (80), St Lucia Campus. Phone: 07 3346 6513 Email: [email protected] Website: https://qaafi.uq.edu.au/centre-for-horticultural-science
Neena Mitter is the Director of the brand new Centre for Horticultural Science, within QAAFI, UQ. Working with partners, the Queensland Department of Agriculture and Fisheries, Horticulture Innovation Australia, and many growers and industry collaborators in Australia and internationally, this Centre aims to grow the future of horticulture in Australia. Within CHS, Neena’s own Mitter Lab Group works to deliver advanced biotechnological and nanotechnological innovations to some of our most important horticultural industries, including avocado, mango and macadamia. We offer the following Themes that students can apply to work within as Honours, Masters or PhD options.
Project 1: BioClay – Spray-On Crop Protection. RNA silencing has proven to be an emerging strategy to control plant viruses and nematodes in agricultural crops. Transgene- mediated virus resistance is a classical example of RNA silencing and its role in antiviral defence in plants. This technology of transgene induced RNA silencing can be exploited to control crop diseases of economic importance, plus their insect vectors. The project Theme will involve design, delivery and investigation of RNA silencing based host delivered resistance.
Project 2: Avocado Tissue Culture and Molecular Biology. The Mitter lab has developed the world’s first platform for mass-production of avocado plants in tissue culture. This has received world-wide commercial interest and could transform the way we produce avocado plants globally. We have a focus on taking this project forward to real-world commercial outcomes. This Theme will involve projects aimed at translating our tissue culture pipeline to new industry-relevant rootstock cultivars plus all-important field trials of our plants. We also have a dedicated interest in understanding the molecular control of avocado growth and development and disease tolerance.
Interested students can contact us any time to discuss specific project options.
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SCMB Biotechnology Research Projects 2017 | Industry Project
DR LINDA LUA Protein Expression Facility Australian Institute for Bioengineering and Nanotechnology
Phone: 07 3346 3979 Email: [email protected] Website: www.uq.edu.au/pef
Project 1: Mass manufacturing viral vaccines for pandemic influenza The ideal way to protect against pandemic flu is to vaccinate the entire Australian population as soon as possible after a dangerous strain starts to spread. Current manufacturing technology, which begins by making an infectious virus in chicken eggs, is unable to quickly deliver a mass vaccine to the entire Australian population. Recent scientific progress has demonstrated that it is possible to make a non-infectious “empty” virus shell (virus- like particle) inside cells. This new product is able to provide full protection against a lethal influenza challenge, when administered nasally. Our approach relies on the expression and purification of key influenza virus proteins, which are then processed in reactors into non-infectious virus-like particles. Skills: Cloning, site-directed mutagenesis, bacterial protein expression, protein purification, biophysical analysis of protein.
Project 2: High throughput parallelised protein production Obtaining large quantities of pure proteins for structural and functional analysis remains a main bottleneck in biological research and pharmaceutical development. As no universally applicable expression system exists, it is often necessary to test several expression systems to achieve a desired outcome. A HTP platform for parallelised cloning and expression in E.coli is established in our lab. Further development in HTP expression using other eukaryotic systems (yeast, insect cell and mammalian cell) is on-going in our lab. Skills: Cloning, protein expression in different hosts (E.coli, yeast, insect cells and mammalian cells), protein purification, protein analysis.
Project 3: Novel protein purification technologies Recovery of the protein of interest from a culture is just as important as obtaining the expression the protein. The end application of the purified protein determines the level of purity and yield required. Minimising protein lost and maximising protein purity in a simple purification process is desirable. We are developing new purification technologies (chromatographic and non-chromatographic) to improve the purification of different types of proteins and from different expression host systems. Skills: Protein expression in different hosts (E.coli, yeast, insect cells and mammalian cells), protein purification, protein analysis.
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SCMB Biotechnology Research Projects 2017 | Industry Project
PROFESSOR CRAIG WILLIAMS Natural product total synthesis, isolation and associated medicinal chemistry. Drug Design and Development / Green chemistry
Phone: 07 3365 3530 Email: [email protected]
Anti-cancer, neurodegenerative disease and insect active limonoids: [in collaboration with Dr Paul Savage (CSIRO), Prof. Peter Dodd (SCMB. UQ) and A/Prof. Gimme Walter (SBS, UQ)]. Recently we achieved the total syntheses of a number of the limonoid family members, such as, Khayasin 1 and Cipadonoid B 2. The synthesised limonoids 1 and 2 are closely related to Gedunin 3, another limonoid family member, which displays anti-cancer and neurodegenerative disease activity in Heat Shock protein 90 (Hsp90) models. We would now like to investigate the total synthesis of gedunin 3, which has yet to be reported, and explore the gedunin 3 structure against Hsp90 using state of the art medicinal chemistry techniques.
Cubane Chemistry: A Benzene Ring Drug Isostere? [in collaboration with Dr Paul Savage (CSIRO) and Prof. James De Voss (SCMB, UQ)]. Cubane 4, when viewed from the corners (i.e. 5) can be considered roughly the same size as a benzene ring (i.e. 6). This is equally true when you take into consideration the clouds of benzene, that is, cubane 4 is about the same “thickness”. Therefore the 1,2- 1,3- and 1,4- substituted cubanes are similar to ortho-, meta-, and para- substituted benzenes respectively. Furthermore, the cubane structure is actually very stable – cubane ring- opening is thermally disallowed by orbital symmetry. With this in mind the project would involve replacing the phenyl ring in a current drug molecule and comparing bioloical assay data. It would also be expected that cubane 4 has completely different P450 metabolism profiles, which will be explored in collaboration with Prof. James De Voss.
Discovery and Development of Novel Analgesics [in collaboration with Prof. Maree Smith from the Centre for Integrated Preclinical Drug Development (CIPDD)/TetraQ)]: The prevalence of painful diabetic neuropathy (PDN) is 7% within a year of diagnosis of diabetes and 50% by 25 yrs of diabetes. The medicines currently used to treat PDN are not effective in less than 50% of patients. Hence, we propose to develop new, effective medicines for the alleviation of PDN by investigating the biology (Smith lab) of unusual heterocycles (Williams lab) that deliver the neurotransmitter molecule NO (nitric oxide).
Green Chemistry [in collaboration with Prof. Ian Gentle (SCMB, UQ)]. Organic reactions are key to new molecules that are in ever-increasing demand for applications in the pharmaceutical, materials and agrichemical sectors. This demand, however, places growing pressure on synthetic chemists to limit or even eradicate environmentally unfriendly chemical waste production. Steps towards such measures are now commonly termed “Green Chemistry”. Projects looking at developing new solvents and new surfactants are available. Applying physical techniques [e.g. small angle scattering (SAXS), neutron scattering (SANS) and dynamic light scattering (DLS)] to understand macromolecular mechanisms is an important part of the work. A/Prof. Williams (ARC Future Fellow) he has held past and present multimillion dollar industry research contracts in addition to ARC and NHMRC grants. Further projects are available on request.
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SCMB Biotechnology Research Projects 2017 | Group Profiles
CENTRE FOR NUTRITION & FOOD SCIENCES (CNAFS) QUEENSLAND ALLIANCE FOR AGRICULTURE AND FOOD INNOVATION (QAAFI) DR EUGENI ROURA (Left) Phone: 07 3365 2526 Email: [email protected]
DR NADIA DE JAGER (Right) Phone: 07 3365 1865 Email: [email protected]
MOLECULAR NUTRITION, METABOLISM AND TASTE The world of taste perception and our understanding thereof is in the process of undergoing significant expansion. Taste receptors have been uncovered as a network of nutrient sensors present not only in the oral cavity, but also in many other parts of the body, including heart, gastrointestinal tract and brain. The roles that these receptors play outside the mouth is not completely understood, however current findings suggest that they are involved in the fundamental process of controlling the hunger-satiety cycle and food intake. Our research group aims to gain a better understanding of how the taste system responds to different nutritional paradigms. Model systems for studying common eating disorders such as obesity and anorexia are assisting us in addressing our research questions.
Project 1: How are nutrients sensed in the gastrointestinal tract? The role of taste receptors. In order to bridge gaps in the current understanding of how nutrients are sensed in the gastrointestinal tract, a number of molecular and cell biology techniques will be employed. For example immunohistochemistry, gene expression and in situ hybridisation techniques will allow for the identification and quantification of key candidate gene expression and protein levels. A background in biomedical sciences or animal physiology is recommended for this project.
Project 2: Knowing more about your sense of taste – applications to obesity research Humans have 25 different types of bitter taste receptors that can detect and taste many more bitter compounds. Our ability to sense these compounds are believed to be associated with an evolutionary advantage for sensing and therefore avoiding potential toxic or harmful substances. Individual variation exists at the molecular level where the genes encoding the bitter taste receptors can have mutations. Different vegetables contain different kinds and different amounts of bitter compounds. Bitter compounds have been shown to have a remarkable ability to elicit a “fuller for longer” feeling and is therefore relevant to obesity research. This project will investigate mutations in bitter taste receptor genes and links with bitter compounds commonly found in vegetables.
Project 3: Biotechnology and Food Science Fibre is known to have wide reaching health benefits and is being consumed in increasing amounts as part of a human diet. However, there appears to be more to the story, at least in rodents, where it was shown that excessive consumption of dietary fibre was associated with increased susceptibility to bacterial infections. Pigs are ideal model animals for humans and this project will investigate changes occurring in pig tissues (already collected) as a consequence of fibre. To address this objective, modern biotechnology techniques will be used by measuring the relative gene expression levels by real time PCR of candidate genes associated with hunger and satiety as well as genes that serve as markers for inflammation.
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SCMB Biotechnology Research Projects 2017 | Group Profiles
DIAMANTINA INSTITUTE FOR CANCER, IMMUNOLOGY & METABOLIC MEDICINE
PROFESSOR RANJENY THOMAS Arthritis Qld Chair of Rheumatology Immunology Programme
Address: Princess Alexandra Hospital, Buranda Phone: 07 3240 5365 Email: [email protected]
Project 1: Pathogenesis of inflammatory arthritis in skg mice Self-reactive T cells with a low signalling capacity through the T cell receptor have been observed in the SKG mouse model of rheumatoid arthritism, and have been linked to a spontaneous mutation in the ZAP-70 signal transduction molecule. This project examines the role that antigen presenting dendritic cells play in the development of arthritis in this model, and whether dendritic cell immunotherapy can be used to treat arthritic mice. Suitable for: PhD, Masters or Honours.
Project 2: Human type 1 diabetes We have developed a new diagnostic assay which identifies individuals with Type 1 diabetes (T1DM) and some of their relatives at risk of diabetes. Exposure of blood monocytes to the bacterial product lipopolysaccharide led to an abnormally low level of activation of the protein, RelB. We are now extending these studies to determine the value of the assay for predicting whether otherwise healthy siblings of children with T1DM will develop diabetes in the future. This would allow us to identify those at risk so that they could be treated earlier or encouraged to make preventative changes to their lifestyle. This project involves analysis of factors contributing to the abnormal RelB test, and researching ways in which RelB function can be restored in these dendritic cells, for new treatments. Suitable for: PhD, Masters or Honours.
DR RAYMOND J. STEPTOE
Phone: 07 3240 5393 Email: [email protected]
Project: Gene Therapy for Autoimmune Disease Autoimmune diseases develop when the body’s immune system mistakenly attacks normal, healthy body tissues. We are interested in developing approaches to prevent or treat autoimmune disease. Dendritic cells are important educators of the immune system and control both immunity and tolerance to self-tissues. We have demonstrated that steady-state antigen-expressing dendritic cells can turn off responses in not only naïve T cells, but surprisingly, also in memory T cells. We are now seeking ways to apply this knowledge to develop a vaccine-like approach to therapy of autoimmune diseases. Projects are available that examine the basic immune biology of immune tolerance or novel methods of in vivo gene transfer that can achieve immune tolerance.
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SCMB Biotechnology Research Projects 2017 | Group Profiles
PROFESSOR ANDREW WHITTAKER GROUP LEADER, Australian Institute for Bioengineering & Nanotechnology (AIBN)
Phone: 07 3346 3885 Email: [email protected] Website: www.uq.edu.au/polymer-chemistry/
Our research group develops polymeric materials to improve human health. Our large group of researchers have programs of research across the spectrum from bench top-to-bedside. Specifically we work in the fields of sensing of disease, delivery of drugs and regeneration of tissue. The projects listed below are all done in collaboration with experts in clinical application of biomaterials, and will provide a solid foundation in practical and theoretical aspects of the use of polymeric materials as biomaterials. Honours projects are available in the following areas (for project details, please see our website or contact Andrew by email). The web site lists other projects.
1. Functionalisation of the surfaces of titanium alloys for improved osseointegration 2. Development of novel polymer scaffolds to aid the repair of the spinal cord 3. Development of low-fouling, anti-microbial surface coatings 4. Novel polymer molecular imaging agents (MRI) for early disease detection 5. Peptide hydrogels for cell delivery
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SCMB Biotechnology Research Projects 2017 | Group Profiles
PROFESSOR MATT TRAU DR ASHLEY CONNOLLY Centre for Biomaker Research and Development, Australian Institute for Bioengineering & Nanotechnology (AIBN) School of Chemistry & Molecular Bioscience (SCMB)
Phone: 07 3346 4173(Matt) / 07 3346 4172(Ashley) Email: [email protected] / [email protected]
1) DNA Nanomachinery for Early Breast Cancer Detection Every 3 minutes a woman is diagnosed with breast cancer. Despite the increasing incidence of breast cancer in the Western world, death rates have been decreasing since 1990. This is the result of treatment advances, increased awareness and early detection. It is widely accepted that early detection results in much higher survival rates, but it is proving difficult to detect the cancer in its early stages. Subsets of RNA that are not translated into proteins have recently been identified in cancerous growths. These non-coding (nc) RNAs serve as potential biomarkers of disease. Our group is designing, developing and evaluating novel DNA nanomachinery to perform tasks that are currently beyond the reach of existing molecular readout technologies. We aim to use these nanomachines as a new technology platform to rapidly detect ncRNA biomarkers in breast cancer patients.
This interdisciplinary project combines the latest developments in molecular genetics with cutting edge nanobiotechnology and will provide an opportunity for students to acquire diverse skills in chemistry, molecular biology and bioengineering.
2) Point-of-Care Diagnostics Point-of-care (POC) diagnostics have the potential to revolutionise global health care by enabling diseases to be rapidly diagnosed ‘on the spot’ using assays that require minimal specialised infrastructure. The simplicity of POC assays enables them to be performed by health care workers or even the patient, which enables rapid diagnosis of a disease. This improves the time taken to treat a disease, leading to better patient care and a reduced rate of mortality and morbidity. POC devices need to be practical, cost effective and portable with high sensitivity and specificity if they are to be used in resource limited settings.
Within our Centre we have an ongoing research program focused on designing and building simple (nanotechnology-based) molecular assays to generate new POC diagnostic technologies. This Honours project will be involved in designing, developing and evaluating novel methods to rapidly amplify and ultimately detect pathogenic DNA and RNA using everyday devices such as mobile telephones.
This interdisciplinary project combines the latest developments in biological chemistry with cutting edge nanobiotechnology and will provide an opportunity to acquire diverse skills in chemistry, molecular biology, bioengineering, and biotechnology.
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SCMB Biotechnology Research Projects 2017 | Group Profiles
PROFESSOR MATT TRAU DR MUHAMMAD SHIDDIKY Centre for Biomarker Research and Development, Australian Institute for Bioengineering & Nanotechnology (AIBN) School of Chemistry & Molecular Bioscience (SCMB)
Phone: 07 3346 4173 (Matt) or 07 3346 4169 (Muhammad) Email: [email protected] / [email protected]
1) Microfluidic Devices for Capturing Rare Circulating Tumour Cells As cancer mortality rates continue to rise, the national impact of the cancers is beginning to overwhelm healthcare services. The progression of cancer in patients is characterized by cells that invade locally and metastasize to nearby tissues or travel through the blood stream to set up colonies in the other parts of the body. These cells, accounting for 1 or fewer cells in 105 – 106 peripheral blood mononuclear cells, are known as circulating tumour cells (CTCs). Development of advanced technology for capturing CTCs in blood in the early stage of the metastasis process would be transformative in the treatment of cancer. This project strives to build and test a microfluidic device with the capacity to enable selective capture and sensitive detection of CTCs by incorporating three-dimensional microstructured electrodes within the detection/capture domain of the device.
2) Nanodevices/Nanobiosensors for Cancer Biomarker Proteins The clinical use of immunoassays in treatment of cancer at early stages of the disease requires detection of proteins of typically 10-16 to 10-12 M concentration in whole blood, blood plasma or serum samples. Detecting this low concentration of proteins is potentially useful for identifying individuals at risk and for clinicians to prescribe preventive measures for these individuals. Current immunoassay technologies typically measure the proteins at concentration above 10-12 M. The development of a detection method that is rapid, cheap, and more sensitive than those currently available could revolutionize many medical treatments in areas such as cancer. In this project, we aim to fabricate nanobiosensors with nanostructured 3D-electrodes to detect single protein molecules in blood.
Via these projects, students will achieve hands on experience in the design, fabrication and application of the microfluidic devices and electrochemical micro(nano)biosensors.
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SCMB Biotechnology Research Projects 2017 | Individual Contributors
ASSOCIATE PROFESSOR SASSAN ASGARI School of Biological Sciences
Phone: 07 3365 2043 Email: [email protected]
Insect host-pathogen molecular interactions In my laboratory, we are investigating the evolutionary adaptations that are employed by parasites and pathogens of insects to avoid host immune defence reactions. This will further our understanding of the interactions but also lead us to the discovery of biogenic molecules with agrochemical and pharmaceutical properties with potential applications in biotechnology.
Examples of available projects are:
Project 1: Role of microRNAs in host-pathogen interactions MicroRNAs are small non-coding RNAs that play important roles in gene regulation in metazoans, plants and viruses. Their roles in development, cancer, apoptosis, immunity, longevity, and viral infections have been established. We are investigating the role of these small molecules expressed from insect viruses or insect host cells in host-pathogen interactions and virus biology. We are using a variety of host-pathogen systems, including Dengue virus-, West Nile virus-, Wolbachia-mosquito interactions. This project is in the most rapidly developing area of microRNA research and provides a basis for designing smart strategies to control insects of medical or agricultural significance.
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SCMB Biotechnology Research Projects 2017 | Individual Contributors
ASSOCIATE PROFESSOR ANDREW C. BARNES School of Biological Sciences & Centre for Marine Science
Phone: 07 3346 9416 Email: [email protected]
Host-microbial interactions in aquatic animals Marine and aquatic animals exist directly immersed in an environment that supports abundant and diverse microbiota. This provides both unique opportunities and challenges for aquatic animals that are not experienced by their terrestrial counterparts. My research explores the interactions of marine fish and invertebrates with predominantly bacterial associates, both beneficial and pathogenic, focusing on aquatic animal health. Much of my research is applied, having strong collaborations with the aquaculture and veterinary industry both in Australia and overseas.
Comparative immunology At the molecular and cellular level, the first point of contact between aquatic animals and environmental microbes is their immune system. We have explored the immune systems of invertebrates such as corals, prawns and oysters, as well as commercially and ecologically important marine fish at both the molecular and functional level. We have identified roles in pathogen exclusion and symbiont selection. At the applied level we have exploited this to develop commercial vaccines for barramundi, improve vaccine adjuvants for fish and to develop tools for marker-assisted selection of disease resistant oysters. At the fundamental level we have identified the first functional immune proteins in reef-building corals and determined their roles in microbial community control and selection of the symbiotic dinoflagellate.
Bacterial pathogenesis Ultimately, most bacterial invaders are eliminated by macrophages. Therefore, understanding how pathogens circumvent these phagocytic cells is critical in development of vaccine targets. We investigate interactions of pathogenic bacteria with primary leucocyte cultures derived from commercially and ecologically important marine fish species with a view to developing improved vaccines, or explaining why particular epizootics have arisen. Current work focuses on evolution of the capsular operon of S. iniae in response to on-farm vaccination, and on tracing origin and explaining pathogenesis of group B Streptococcus in wild Queensland grouper using genomics and functional assays.
Microbial communities Aquatic animals have complex microbial communities that strongly influence health and growth. The complexity of the communities is confounded further by extremely high variability amongst individuals. We investigate microbial communities with sufficient replication to provide data that can be used predictively or to solve particular issues. In highly replicated studies we have shown strong host –specific selection of bacterial associates in reef-building corals. We have also shown what happens to the metabolically active gut microbiota of Atlantic salmon during the stress of warm summer water temperatures in Tasmania, enabling formulation of novel more sustainable feeds to improve stability of the gut microbiome and improve fish performance during the summer months.
Project 1: Serotype switching in marine streptococcus from barramundi and grouper Project 2: Markers for immune cells in barramundi
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SCMB Biotechnology Research Projects 2017 | Individual Contributors
PROFESSOR CHRISTINE BEVERIDGE Centre for Integrative Legume Research School of Biological Sciences
Phone: 07 3365 7525 Email: [email protected]
Supervisors: Christine Beveridge and Francois Barbier
Involvement of sugars in the control of shoot branching We recently demonstrated that sugars are triggering plant branching. In this process, sugars play a signal role like a hormone to trigger the growth of axillary buds into branches. However, several of these sugar signals occur in plants and we still don’t know exactly which ones are involved in the control of plant branching. This project aims to identify which sugar signals are involved in shoot branching. To achieve this, the project will use a combination of different approaches such as physiology (phenotyping mutants and transgenic lines), molecular biology (gene expression and bioinformatics) and pharmacology (impact of sugar analogues on in vitro-grown axillary buds). The results obtained will help place sugars in the molecular regulatory network controlling shoot branching.
Molecular regulation of strigolactone perception during plant branching A few years ago, our team discovered strigolactones as a new class of plant hormone inhibiting plant branching. This class of hormone is perceived by a molecular complex including the F-box MAX2. Mutation of MAX2 totally disrupts the perception of strigolactones and results in very bushy phenotype. We recently noticed that this gene was highly regulated at the transcriptional level (gene expression). In this project you will (i) analyse in depth the sequence of MAX2 promoter using the public databases; (ii) monitor the expression of transcription factors identified in axillary buds to determine the best candidates in the regulation of MAX2 and (iii) express these transcription factors in arabidopsis protoplasts to test their impact on MAX2 expression with different mutations on its promoter.
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SCMB Biotechnology Research Projects 2017 | Individual Contributors
ASSOCIATE PROFESSOR JOANNE BLANCHFIELD School of Chemistry & Molecular Biosciences
Phone: 07 3365 3622 Email: [email protected]
Synthesis of revolutionary synthetic vaccine constructs (project with Prof. Paul Burn) We have a collaboration with Prof. Paul Burn that concerns the construction of fully synthetic vaccine structures against HIV and Staphlycoccus aureus. For details of the project please contact Joanne Blanchfield or Paul Burn. This project would involve:
• organic synthesis • carbohydrate synthesis • solid phase peptide synthesis • cell culture and plasma stability assays and aseptic techniques • assay development and molecule characterisation including use of HPLC, LC/MS, NMR, GC/MS equipment.
Bioavailability of natural products from herbal extracts. (Project with Prof. James De Voss) Herbal remedies are a major source of medical treatment for much of the world’s population. Unfortunately, little is known about the fate of the natural products in the extracts or which, if any are biologically active. We are offering a project that uses a cellular model of the small intestine (Caco-2 cell monolayers) to investigate which natural products are likely to enter the blood stream after oral intake of some popular herbal remedies. We also look closely at what changes the compounds undergo during digestion and absorption.
• use of preparative and analytical HPLC equipment to isolate and identify potentially active compounds from herbal extracts. • performance of in vitro biological assays to determine permeability (Caco-2 cell assay), stability (CC2 homogenate assay, plasma stability) assays. • Analytical analysis using LC/MS and HPLC of the solutions resulting from the in vitro assays.
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SCMB Biotechnology Research Projects 2017 | Individual Contributors
PROFESSOR JIMMY BOTELLA Plant Genetic Engineering Laboratory, School of Biological Sciences
Phone: 07 3365 1128 Email: [email protected]
Characterisation of heterotrimeric G-proteins in plants Heterotrimeric G-proteins are extremely important in humans but very little is known about them in plants. Our lab has established that G-proteins are involved in disease resistance in plants and are also important contributors to yield. We recently discovered new members of the gene family in Arabidopsis and are now investigating their cellular function. The projects involve molecular biology techniques, gene cloning, produce genetic constructs and production and characterization of genetically modified plants. Specific topics include:
• Characterization of the role of G-proteins in plant defence. • G-protein control of yield. • Role of G-proteins in cell death.
Plant defence against pathogenic fungi Pathogenic fungi cause billions of dollars in loses each year and affect all of the important crops used for human food production. We have recently discovered a number of genes involved in the defence against this type of pathogens and are now devising strategies to produce resistant plants using genetic transformation technologies. The projects involve cloning, molecular characterization of genes and study of a number of transgenic lines with increased disease resistance.
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SCMB Biotechnology Research Projects 2017 | Individual Contributors
PROFESSOR PAUL BURN Director, Centre for Organic Photonics & Electronics (COPE) School of Chemistry & Molecular Biosciences
Phone: 07 3346 7614 Email: [email protected]
The Centre for Organic Photonics and Electronics (COPE) is located on floor 9 of the Chemistry Building. The Centre contains state-of-the-art synthesis laboratories, a Class 1000 clean room and a suite of instrument rooms for the characterization of materials and opto-electronic devices. The mission of the Centre is develop ‘organic materials’ that can be used in high performance cutting edge technologies including sensors, solar cells, flat panel displays, plastic electronics, and fuel cells. Honours students working in these areas will learn the key skills of synthetic chemistry and characterization of small and macromolecules, the latter including dendrimers (branched macromolecules) and polymers. In addition, the Honours student will have the opportunity to work with physics colleagues in interpreting the properties of the materials and device performance, which can lead to the design of the next generation of materials. Of particular relevance to Biotechnology students we are offering projects in the area of new sensing technologies. However, we would also be willing to consider students who have an interest in the other areas of research in COPE.
Project: Sensors
Sensors play a vital role in many different technologies including the detection of pollution, drugs, and explosives. Recent global events have raised concerns over national security and counter-terrorism measures in civilian areas. In particular, the deployment of hidden explosives over large populated areas requires creative and feasible preventative measures. Currently the most sensitive detectors for explosives are canines. We are therefore interested in developing sensors that are more sensitive and selective than canines, and are using the sensing of explosives as a model system for detecting analytes. The aim is to develop a general sensing technology that can be applied across a broad range of analytes. Most current methods for detecting explosives are slow and the equipment cumbersome. To this end we are developing an explosives sensor based on semiconducting organic materials that will be portable, selective and fast. These materials rely on electron-deficient analytes (explosives) to quench their luminescence, giving a reduction of the normal signal upon binding. For example, dendrimer 3 can detect 1,4-dinitrobenzene and we will be synthesizing and testing new materials against a variety of analytes.
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SCMB Biotechnology Research Projects 2017 | Individual Contributors
PROFESSOR ROB CAPON Institute for Molecular Bioscience
Phone: 07 3346 2979 Email: [email protected]
Biodiscovery: From Biodiversity and Bioactives to Biology and Beyond The research interests of my group centre on the detection, isolation, characterisation, identification and evaluation of novel bioactive metabolites from Australian marine and terrestrial biodiversity. These metabolites span all known biosynthetic structure classes including many molecules new to science, and their study requires the use of sophisticated chromatographic, spectroscopic and chemical technologies. Natural products uncovered during our investigations represent valuable new leads in the search for drugs with application in the fields of human and animal health and crop protection, have potential as molecular probes to better interrogate and understand living systems, and could find application as biological control agents.
The research group manages an extensive network of collaborators across many scientific disciplines, in industry, academia and government, both in Australia and overseas, which allow it to target such therapeutic indications as infectious and neurodegenerative diseases, cancer, pain, diabetes and obesity, as well as invasive animal and pest control through chemical ecology, and gene activated microbial biodiscovery.
Individual research projects can (on enquiry) be negotiated and structured around the following:
Natural Products Chemistry: the isolation, and spectroscopic and chemical analysis of, secondary metabolites from marine and terrestrial plants, animals and microbes, with a view to better exploring and understanding “natural” chemical space.
Synthetic Organic Chemistry: synthesizing new bioactive natural products, to test and refine novel pharmacophores, to build knowledge of and prioritize new drug lead candidates, with a view to better exploring and understanding “synthetic” chemical space.
Microbial Metabolism: learning to better regulate and express silent secondary metabolite gene clusters, to better explore and make use of the full spectrum of “natural” chemical space defined by the microbial genome.
Chemical Ecology: to acquire and use knowledge of how invasive pests (ie cane toad) make use of chemistry in the form of defensive secretions and pheromones, and to use this knowledge to develop safe, effective and species selective control solutions.
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SCMB Biotechnology Research Projects 2017 | Individual Contributors
PROFESSOR BERNIE CARROLL School of Chemistry and Molecular Biosciences
Phone: 07 3365 2131 Email: [email protected]
RNA interference (RNAi) and gene silencing in Arabidopsis Gene silencing is a highly conserved process in plants and animals, and is of fundamental importance to developmental regulation of gene expression, defence against viruses, transposon silencing, adaptation to environments and genome evolution. Gene silencing is also of immense relevance to biotechnology. We are using Arabidopsis as a eukaryotic model for studying the mechanisms of gene silencing.
Intercellular spreading of gene silencing. Remarkably, when gene silencing is triggered in cells of plants and animals, it can spread throughout the organism. The intercellular movement of RNA signals plays a fundamental role in plant development and defence against viruses. We are using a forward genetic approach and map-based gene cloning to elucidate the mechanisms of systemic movement of gene silencing in Arabidopsis.
Intron splicing regulates gene expression in Arabidopsis. The role of introns has puzzled molecular biologists since their discovery in 1978. We recently showed that intron splicing protects genes from being silenced in Arabidopsis3. Defective intron splicing has been associated with genetic diseases in both plants and humans. This project aims to identify novel genes and proteins involved in these processes.
Genetic engineering of pest resistance in plants based on RNA. RNAi has immense potential for engineering crop resistance to insect pests, and decreasing the use of toxic insecticides that threaten ecosystems and human health. We are expressing RNAi molecules in plants to silence essential insect genes and confer insect resistance.
MicroRNAs involved in high temperature-tolerance in plants. We are using modern molecular techniques and computing to identify miRNAs for high-temperature tolerance in plants. We are using transgenic approaches to modify the expression of these miRNAs to improve high temperature-tolerance in plants.
Selected recent publications: 1. Brosnan et al. (2007) Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis. PNAS 104, 14741-14746. 2. Gursanscky et al. (2011) Mobile microRNAs hit the target. Traffic 12, 1475-82. 3. Christie et al. (2011) Intron splicing suppresses RNA silencing in Arabidopsis. Plant Journal 68, 159-167.
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SCMB Biotechnology Research Projects 2017 | Individual Contributors
DR MARINA CHAVCHICH Australian Army Malaria Institute
Phone: 07 3332 4826 Email: [email protected]
Malaria Biology, Malaria Drug Discovery and Resistance In my research laboratory we are studying the malaria parasite, Plasmodium falciparum. Malaria infects approximately 200-300 million people annually which results in 2-3 million deaths. Understanding the biology of the parasite will lead to novel therapeutic options to treat and prevent the disease. In particular, we are focussing our studies on the malarial cell cycle machinery and the respective signal transduction pathways to identify and validate novel malaria drug targets. Additionally, we are interested in understanding the molecular mechanisms of antimalarial drugs and the development of drug resistance.
Identification of novel anti-malarial compounds P. falciparum will be cultivated and assayed in an ex vivo/in vitro growth inhibition assay to test compounds for anti-malarial activity. Compounds will be tested against both drug sensitive and resistant parasites to determine a drug resistance index. Selected compounds demonstrating significant activity will be further tested in drug combination studies to find suitable partners that yield a synergistic effect with increased potency. Structure Activity Relationships (SAR) will be evaluated and used to select additional compounds for testing. Compounds will be selected from commercially available libraries and obtained from collaborations with medicinal and natural product chemists. This project will involve dose-response inhibition assays, malaria cultivation, and SAR analysis.
Cell cycle control and developmental regulation of the malaria parasite The malaria parasite undergoes multiple rounds of DNA replication in the absence of mitosis in a process known as schizogony. In most eukaryotic cells, DNA replication is followed immediately by mitosis. Cyclin Dependent protein Kinases (CDKs) regulate the progression of the cell cycle and ensure that DNA replication and mitosis occurs in a highly regulated fashion. CDKs are present in the malaria parasite however their role in cell cycle control must be unique in order to regulate schizogony. To further understand the role of malaria CDKs, studies are underway to determine substrate specificity and the regulatory mechanisms of autophosphorylation and the binding of effector proteins. This project will involve protein expression and purification, kinase assays, enzyme kinetics, DNA replication assays, Western blots, immunofluorescence microscopy, two-hybrid protein-protein interaction assays.
Pursue the cyclin dependent protein kinases (CDK) as novel malaria drug targets CDKs are drug targets for numerous diseases to include cancer, neurological disorders, cardiovascular disease and recently, parasitic infections. Several malarial CDKs have been developed into 96 well microtiter plate inhibition assays. Compounds will be screened against the malarial CDKs with particular emphasis on Pfmrk. Compounds demonstrating significant inhibitory activity, will be tested against the homologous kinases to deselect compounds that cross react with the human homologs. Compounds will also be tested against the malaria parasite to establish a correlation between inhibition of the CDK and parasite death. Iterative screening, along with a detailed SAR analysis, should identify potent and selective malarial CDK inhibitors. Genetically modified parasites that overexpress Pfmrk, will be used to validate Pfmrk as a drug target. This project will involve protein expression and purification, enzyme kinetics, kinase assays and dose-response inhibition assays.
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SCMB Biotechnology Research Projects 2017 | Individual Contributors
PROFESSOR DAVID CRAIK Institute for Molecular Bioscience
Phone: 07 3346 2019 Email: [email protected]
The Craik lab discovers novel peptides for applications in drug design. Their work has the potential to lead to new drugs for the treatment of a wide range of diseases, including cancer, cardiovascular disease, infectious disease and pain.
Project 1: Novel circular proteins: templates in drug design Until a few years ago circular proteins were virtually unknown, but over recent years we have discovered and structurally characterised a family of circular proteins in plants called the cyclotides. These molecules were originally discovered because of their uses in native medicine as uterotonic agents to aid childbirth and in screening programs of plant extracts against HIV. We have found that the molecules contain an unusual structural motif called a cystine knot in which two disulfide bonds and their connecting backbone form a ring in the structure that is threaded by a third disulfide bond. Combined with a circular backbone this knot makes the cyclotides exceptionally stable, making them potentially valuable frameworks in peptide- based drug design. Cyclotides are resistant to enzymatic degradation and are stable in biological fluids, unlike most peptide-based drugs. This project involves the discovery and structural characterisation of new cyclotides in plants. We wish to determine the natural structural diversity of the framework so that we can best design novel analogues in which new biological activities are grafted onto the framework. The project will teach skills in natural products isolation and structure determination by NMR spectroscopy.
Project 2: Structure-activity relationships in conotoxins: leads in drug design Conotxins are small disulfide rich toxins from the venoms of cone snails. They inhibit a range of ion-channels and are regard as valuable leads in drug design, with four conotoxins currently in clinical trials for various neurological conditions and as analgesic molecules. As part of an ARC funded project we are identifying new conotoxins, as well as synthetically varying known conotoxins with the broad goal of producing novel leads in drug design or neuropharmacological probes. The aim of this project is to determine the structures of these novel conotoxins. The project will teach skills in peptide purification and structure determination by NMR spectroscopy.
Project 3: Harnessing plants to produce peptide drugs: drugs in plants We have recently discovered the common machinery that diverse plants use to manufacture stable cyclic peptide frameworks as well as the conserved sequences that allow processing from their precursors. We have performed proof-of-concept work that demonstrates we can genetically modify a reference plant so that it synthesises a protease inhibitor that is a potent lead as a treatment for prostate cancer. Our hypothesis is that we can further enhance this system to produce low-cost synthesis of tailor-made drugs in seeds through genetic engineering. The technology developed from this project will allow stable peptide drugs to be manufactured at low cost and, as a more “organic” drug source, has the potential to improve patient compliance as well as be adaptable to production systems in third-world nations. This project will teach skills in plant genetic transformation, peptide analysis, and genetic analysis.
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SCMB Biotechnology Research Projects 2017 | Individual Contributors
PROFESSOR JAMES DE VOSS School of Chemistry & Molecular Biosciences
Phone: 07 3365 3825 Email: [email protected]
My group is concerned with biological and synthetic chemistry and in particular with the application of chemical principles to the understanding of biological processes. Most projects are a blend of disciplines in bio-organic chemistry: synthesis, structure determination, molecular biology, protein purification. A range of techniques is employed, ranging from the biochemical (e.g. PCR, gel electrophoresis) to the chemical (e.g. NMR, HPLC, GC/MS). The following areas illustrate the research in my laboratory but the exact project will be determined by the student’s interests.
Project 1: Cytochromes P450: P450s catalyse an amazing variety of oxidative transformations, ranging from simple alkene epoxidation all the way through to oxidative C-C bond cleavage. They are of interest as they (i) are often unique enzymes in a biosynthetic pathway and as such represent new targets for chemotherapeutic agents or (ii) are extremely efficient catalysts that offer the potential of developing tailored oxidative catalysts for synthetic transformations. We are interested in understanding the mechanism of action of a number of P450s. One example is CYP61, a unique P450 involved in steroid biosynthesis in fungi and other pathogenic organisms. As such it represents a potential target for novel chemotherapeutics. CYP61 catalyses an unusual reaction for a P450, namely the dehydrogenation of an alkane to an alkene. However, essentially nothing is known about the exact structure of the substrate, the stereochemistry of the reaction or its mechanism. Projects in this area will involve the synthesis of mechanistic probes, the analysis of the products of enzyme-catalysed reactions, characterisation of enzyme mutants and design and synthesis of inhibitors.
Project 2: Constituents of Medicinally Used Herbs: Whilst herbal medicines are widely used and have a long history of such use, their chemical constituents are often poorly characterised. In collaboration with a local company we have embarked upon a program of phytochemical characterisation of a number of therapeutically prescribed herbs. The results have been surprising with a number of previously unknown compounds isolated from supposedly well-characterised species. This project would involve the isolation, chromatographic purification and structure determination (especially employing 1D and 2D nmr) of the chemical constituents of selected herbs. The structures of some recently isolated compounds are given below.
Relevant Recent Publications 1. Slessor, Kate E., Farlow, Anthony J., Cavaignac, Sonia M., Stok, Jeanette E., De Voss, James J. Oxygen activation by P450(cin): Protein and substrate mutagenesis Arch. Biochem. Biophys. 2011, 507 154-162. 2. N. J. Matovic, J. M. U. Stuthe, V. L. Challinor, P. V. Bernhardt, R. P. Lehmann, W. Kitching and J. J. De Voss The Truth about False Unicorn (Chamaelirium luteum): Total Synthesis of 23R,24S-Chiograsterol B Defines the Structure of the Major Saponins from this Medicinal Herb Chem. Eur. J. 2011 17, 7578-91.
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SCMB Biotechnology Research Projects 2017 | Individual Contributors
DR ANNETTE DEXTER Australian Institute for Bioengineering & Nanotechnology (AIBN)
Phone: 07 3346 3199 Email: [email protected]
Research area: Designer peptides for biomedical and industrial applications Designer peptides are attractive building blocks for preparation of novel functional nanomaterials. Peptides offer stimuli-responsiveness, biocompatibility, predictable folding and capacity for sustainable production. By employing and modifying a key structural motif of native proteins, the amphipathic alpha-helix, we have developed short designer peptides that show promise as responsive hydrogels for wound healing, tissue engineering and drug delivery or, in a separate class, as environmentally-friendly switchable surfactants. Dr Dexter is a co-founder of UQ start-up company Pepfactants Pty Ltd, and is involved in commercialization of peptides as “green” surfactants as well as biocompatible gelling agents.
Project 1: Peptide hydrogels for burn healing Burns represent a major category of accidentally acquired injury, with over 130,000 injuries in this class in Australia each year. Currently, all children who sustain deep dermal burns will heal with unsightly scars. Scarred areas fail to grow with the child and often cause contractures that require repeated surgery. The scarred tissue is weaker than normal tissue and is prone to drying and ulceration. Pressure garments and silicone sheets are the only proven methods to reduce scar formation, however they must be worn for at least a year and the results are often disappointing. Prevention of scarring following deep burns is thus an important medical goal with long-term consequences for quality of life of burn victims. We are developing peptide hydrogels as advanced wound dressings with the potential to accelerate re-epithelialisation of burn wounds to prevent scarring. An Honours project is available in formulating and testing hydrogels for the treatment of burn wounds.
Project 2: Peptides as surfactants for eco-friendly industrial fluids Industrial fluids are lubricating and cooling fluids extensively used in industrial machining operations. As currently formulated they represent both an occupational health and safety hazard for machine operators, and a waste disposal problem at the end of their lifecycle. Oil-in-water industrial fluid emulsions are usually formulated with petrochemical surfactants that can break down to give hazardous sulfhydryl gases, cause painful skin lesions on prolonged contact, and form emulsions that are difficult to separate for the disposal of oil and water phases. We are currently investigating the use of peptides as alternate surfactants for industrial fluids, in conjunction with a major industry partner. The peptides offer both lower toxicity as sulfur-free and biocompatible surfactants, and a capacity for emulsion switching to allow clean separation of oil and water at the end of the emulsion lifecycle. An Honours project is available in formulating and testing cutting fluids for lubrication in metal-working and recyclability of the functional components.
Project 3: Bioproduction of peptides as hetero- or homoconcatemers The adoption of peptides for materials applications, either in the biomedical or industrial space, will depend on methods for low-cost, large-scale production. Currently, most peptides tested for drug or other applications are produced by solid-phase synthesis (a costly method with high environmental impact) and are subsequently purified by expensive chromatographic methods. While short peptides can be produced in bacterial hosts by fusion to a carrier protein, this approach has poor efficiency, as most of the product obtained (>80%) is carrier protein rather than the target peptide. We recently developed a novel method for expressing ionic surfactant peptides, by using heteroconcatemers of oppositely-charged peptides to form a coiled-coil miniprotein. The resulting protein is stable to heat and proteases and can be purified by simple precipitation steps. We are now seeking to extend this approach to gel-forming peptides, to facilitate the use of such peptides in biomedical applications. An Honours project is available in the design, expression and downstream processing of a gelling peptide for biomedical use.
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SCMB Biotechnology Research Projects 2017 | Individual Contributors
ASSOCIATE PROFESSOR PAUL EBERT School of Biological Sciences
Phone: 07 3365 2973 Email: [email protected]
Project 1: Functional genomics of ageing Despite a significant increase in human life expectancy, old age is still characterised by physiological changes that manifest themselves as age- related diseases. The ultimate goal of this research is to increase the disease- free lifespan of individuals. We approach this problem in two ways: The first is to investigate the ageing process itself, whereas the second is to model disease of old age and to test the effect of drug therapies. We are using the genetic model organism, Caenorhabditis elegans, as it is the leading model organism for lifespan research. We have identified a novel longevity gene and are now determining its mode of action and potential interaction with diseases of old age. The project involves microarray analysis, targeted epigenetic gene suppression, genome sequencing, bioinformatics and genetics.
Project 2: Cloning of phosphine resistance genes from pest insects: Stored grain is protected from insect pests by fumigation with phosphine, but some insects are now resistant to 600 times the normal lethal dose of phosphine. Several new fumigants have been proposed, but their modes of action and interaction with other fumigants and with phosphine resistant insects is unknown. This project will be carried out in collaboration with the Queensland Department of Agriculture, Fisheries & Forestry and will characterize these new fumigants to help lead the grains industry into a new future. This project will involve toxicology testing, genome sequencing, bioinformatics and perhaps some work with C. elegans.
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SCMB Biotechnology Research Projects 2017 | Individual Contributors
ASSOCIATE PROFESSOR DARRYL EYLES Queensland Brain Institute
Phone: 07 3346 6370 Email: [email protected]
Studies in our lab relate the major epidemiological findings in schizophrenia with how the brain may be altered during development. Projects relate directly to the epidemiology implicating certain risk factors during gestation that correlate with increased schizophrenia in offspring. One prominent risk factor we have established is developmental vitamin D deficiency.
Project: The effect of maternal vitamin D deficiency on dopamine neuron ontogeny The student would examine the brains of embryonic animals from vitamin D deficient Dams. The student would study the timing of the expression of crucial dopaminergic transcription regulators in the developing mesencephalon. The student would also conduct in vitro experiments examining the activation status of the receptor for vitamin D in these same cells. These studies will help to inform the larger structural and behavioural picture emerging in this model strongly implicating dopaminergic dysfunction.
Data from both these studies could have considerable public health implications regarding preventative measures in utero for developmental diseases such as MS and schizophrenia!
Students interested in honours projects or higher degrees should contact me. I can be found in the Queensland Brain Institute, The University of Queensland, Brisbane, Qld 4072, Australia.
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SCMB Biotechnology Research Projects 2017 | Individual Contributors
PROFESSOR DAVID FAIRLIE Division Head Institute for Molecular Bioscience
T: +61 7 3346 2989 E: [email protected] W: http://fairlie.imb.uq.edu.au/
Our research programs (http://fairlie.imb.uq.edu.au/) link chemistry to biologically important proteins in diseases. Our chemistry students develop expertise in organic, medicinal or biological chemistry; learning molecular design, organic synthesis (solid/solution phase, combinatorial chemistry, microwave-assisted), structure determination (2D NMR spectroscopy). Our biology students investigate our new experimental drugs on human proteins, human cells or animal models of human diseases and develop expertise in biochemistry, cell biology, immunology, pharmacology or physiology. Outcomes are new chemical structures and reaction mechanisms, new biological understanding of physiological and disease mechanisms, new experimental drugs.
Our projects are designed to train students in advanced chemistry or biology research methods, to develop research capabilities, and to produce publishable outcomes (e.g. Organic Synthesis of Anticancer Enzyme Inhibitors http://fairlie.imb.uq.edu.au/researchers.php?id=54, Medicinal Chemistry of Antiinflammatory Enzyme Inhibitors http://fairlie.imb.uq.edu.au/researchers.php?id=24; id=22, Inflammatory Signalling in the Innate Immune System in an Allergic Asthma Model http://fairlie.imb.uq.edu.au/researchers.php?id=72). Some representative project areas are:
Project 1: Human G protein coupled receptors. Most drugs target these proteins on surfaces of cells where they play major roles in disease. We synthesize small organic compounds that bind to proteins on cell surfaces and activate/inhibit processes leading to immunity, cancer, inflammatory, cardiovascular and Alzheimer’s disease. The student can focus either on chemical synthesis/structure (J Am Chem Soc 2014,136,11914) or cell biology mechanisms (Nature Commun 2017,8,351; Br J Pharmacol 2014,171,4112), or pharmacology and mouse models of disease intervention (FASEB J 2012,26,2877).
Project 2: Controlling signalling pathways in human cells. We aim to understand how to control signalling pathways in immune cells (mast cells, neutrophils, macrophages, dendritic and T cells), cancer cells, pancreatic/liver/kidney cells that lead to chronic diseases. The student will investigate cellular responses to our experimental drugs using cell biology techniques or mouse studies in which primary tissues/cells are examined (e.g. Nature Commun 2017,8,14599; Glia 2017,65,2070; Nature 2014,509,361; J Immunol 2017,198,2989).
Project 3: Protein mimetics. Protein-protein interactions mediate most bilogical processes. We are downsizing bioactive regions of proteins to a smaller molecules that can structurally and functionally mimic key protein surfaces. The chemical and structural challenges are to recreate protein surfaces in small molecules. The biological challenges are in intervening in processes important in physiology or aberrant in disease (e.g. Angew Chem Int Ed 2014,53,13020, Cancer Research 2014,74,3454, PNAS 2010,107,11686).
For more information: contact David ([email protected]) or visit http://fairlie.imb.uq.edu.au/
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
ASSOCIATE PROFESSOR CAMILE FARAH Group Leader, Oral Oncology Research Program University of Queensland Centre for Clinical Research (UQCCR)
Phone: 07 3346 6030 Email: [email protected]
PROGRAM MEMBERS:Academic & Research Staff • Associate Professor Camile Farah (Group Leader) • Dr Pauline Ford (Senior Lecturer) • Dr Andrew Dalley (Postdoctoral Research Officer) • Mr Anthony Chan (Histology Technician). Adjunct
Academic Staff • Dr Martin Batstone (Maxillofacial Surgeon, RBWH) • Dr Borjana Simanovic (Visiting Dentist) • Dr Maurie Stevens (ENT Surgeon, RBWH) • Dr Colin Ades (QML Pathology)
Research Higher Degree Students • Dr Ahmad Abdul Majeed (PhD), • Dr Glenn Francis (PhD) • Dr Phan Nguyen (PhD) • Dr Maryam Jessri (PhD) • Anthony Crombie (MPhil) • Ms Kelsey Moore (MPhil) • Ms Fatima Dost (MPhil).
Concurrent BDSc/MPhil Students • Ms Kristine Allen • Mr Nirav Bhatia • Mr Sean Currie • Ms Yasitra Lallaq • Ms An Vu • Ms Jennifer Wu • Ms Keziah John • Ms Brie Kwon • Mr Bing Lee • Dr Ian Housego • Dr John Webster
Honours Students • Mr Aidan Major, Mr Luke Pitty
PROGRAM SUMMARY: The Oral Oncology Research Program leverages work regarding various bio-markers of oral cancer and oral epithelial dysplasia which are either unique to the oral mucosal situation or shared across malignancies in other sites. The program leverages a range of novel technologies, including optical fluorescence imaging and narrow band imaging, to be able to diagnose oral cancer at its earliest stages, thus allowing early forms of treatment to be applied with maximal effect. The program also investigates the role that cancer stem cells play in the propagation and recurrence of cancerous and pre-cancerous lesions. The underlying premise of this program looks at creating a molecular signature for pre-cancerous conditions that can be used as a diagnostic test to either replace or supplement standard histopathological interpretation of oral epithelial dysplasia and oral squamous cell carcinoma. To complement the program’s work on the biological mechanisms of oral cancer, we are undertaking projects to examine oral pre-cancerous conditions at the population level. Clinical and epidemiological studies of defined at-risk populations are underway which will determine the burden of oral mucosal disease as well as the relative importance of a range of risk factors for these groups. This information is fundamental to planning for oral health services and public health interventions which are appropriate and cost effective. The work of the group is undertaken at the UQ Centre for Clinical Research based at the Royal Brisbane & Women’s Hospital at Herston. This program is funded by grants from the National Health & Medical Research Council, Cancer Australia, Cancer Council Queensland, Queensland Government Smart Futures Fund, RBWH Foundation, and the Australian Dental Research Foundation. The group has collaborations with Agilent Technologies, Life Technologies, Olympus Australia, Colgate-Palmolive Australia, and the Institute for Urban Indigenous Health.
AVAILABLE PROJECTS: Project 1: Molecular profiling of cancer stem cell / Project 2: miRNA expression in oral epithelial dysplasia
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
ASSOCIATE PROFESSOR VITO FERRO School of Chemistry & Molecular Biosciences
Phone: 07 3346 9598 Email: [email protected] Web: http://staff.scmb.uq.edu.au/staff/vito-ferro
Carbohydrate and Medicinal Chemistry My research interests encompass carbohydrate and medicinal chemistry/chemical biology, with a focus on the synthesis of compounds to probe and/or inhibit carbohydrate-protein interactions involved in disease processes. Of particular interest is heparan sulfate (HS) and the development of HS-mimetics as potential drugs for various other diseases. Available projects include, but are not limited to, the following:
A radical new approach to rare L-sugars Sugars with the L-configuration are relatively rare in nature but play important roles in many biological processes and thus are of great interest for the development of vaccines and other applications. However, they are generally not commercially available and are often difficult to synthesize. This projects aims to explore new, more direct synthetic routes to important L-sugars such L-iduronic acid and 2-acetamido-2-deoxy-L-altruronic acid (L-AltNAcA) via an approach that exploits free radical chemistry.
Synthesis of novel glycopolymers Glycans are ubiquitous on cell surfaces and are important mediators of biological recognition events. Glycopolymers, i.e., synthetic polymers with pendant sugars, exbibit molecular recognition properties and have high affinities for proteins owing to their multivalency. This collaborative project with Assoc Prof Kris Thurect (CAI/AIBN) involves the synthesis of novel HS monomers and their conversion into various glycopolymers with tailored biological properties via RAFT polymerization.
Synthesis of pharmacological chaperones for lysosomal storage diseases Lysosomal storage diseases (LSD) are caused by mutations in enzymes that degrade polysaccharides such as HS, resulting in the accumulation of undegraded substrate in the lysosomes of cells. Some patients may be treated with enzyme replacement therapy. Unfortunately, the replacement enzyme cannot cross the blood-brain barrier and thus cannot treat the neurological symptoms associated with severe cases. The aims of this project are to synthesize small molecules for the treatment of LSD, which unlike enzymes, are capable of crossing the blood-brain barrier and thus may offer relief of neurological symptoms. The compounds are designed to act as “chaperones” to protect the defective enzyme from degradation and restore enzyme activity to sufficient levels to alleviate symptoms.
Techniques you learn in our group may include: organic synthesis, NMR spectroscopy, mass spectrometry, flash chromatography, TLC, IR
Useful Majors: Chemical Sciences / Chemistry / Chemical Biotechnology / Drug Design and Development / Nanotechnology
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR BRETT FERGUSON
Director, Centre for Integrative Legume Research School of Agriculture and Food Sciences [email protected]
SAFS profile: http://www.uq.edu.au/agriculture/brettferguson CILR profile: http://www.cilr.uq.edu.au/brett-ferguson
Topic: Functional Characterisation of Novel Components Required for the Development and Control of Legume Nodules.
Project Description: Nitrogen fertiliser use in agriculture is inefficient, costly and can be environmentally damaging. Legume crops represent an economically and environmentally sound alternative, as their symbiotic relationship with nitrogen- fixing soil bacteria enables them to thrive in the absence of nitrogen fertiliser. The bacteria (commonly referred to as rhizobia) are housed in specialised root organs, called nodules. Identifying critical components of legume nodulation is now needed to optimise the process and improve agriculture sustainability. This project aims to discover and functionally characterise novel factors that act in the development and control of legume root nodule numbers. Findings will considerably enhance the current nodulation model and could help to underpin strategies to reduce the reliance on nitrogen fertiliser use in agriculture.
Expected Outcomes: Findings are anticipated to advance our understanding of how various genes and signals function in the development and regulation of legume nodules. Successful outcomes could also help to generate future publications.
Techniques & Skills: Techniques will include growing and maintaining soybean plants and compatible Bradyrhizobium bacteria, and will incorporate additional methods that may include generating transgenic soybean ‘hairy roots’ using Agrobacterium rhizogenes, fixing and treating roots to detect GUS activity, bioinformatic analyses, primer design and quantitative RT-PCR to confirm the regulation of candidate genes, etc.
Figure 1. Root systems of wild-type (WT) and supernodulating mutant (nod++) soybean plants exhibiting mature nodule structures as a result of a symbiotic
relationship with Bradyrhizobium japonicum.
Relevant Reading: Ferguson BJ, Indrasumunar A, Hayashi S, Lin M-H, Lin Y-H, Reid DE, Gresshoff PM (2010) Genetic analysis of legume nodule development and autoregulation. Journal of Integrative Plant Biology 52: 61-76. Ferguson BJ (2013) The development and regulation of soybean nodules. In: A Comprehensive Survey of International Soybean Research - Genetics, Physiology, Agronomy, and Nitrogen Relationships. Ed: Board JE. InTech – Open Access, http://dx.doi.org/10. 5772/52573, pp 31-47. Gresshoff PM, Hayashi S, Biswas B, Mirzaei S, Indrasumunar A, Reid D, Samuel S, van Hameren B, Hastwell A, Scott P, Ferguson BJ (2015) The value of biodiversity in legume symbiotic nitrogen fixation and nodulation for biofuel and food production. Journal of Plant Physiology 172: 128-136. Reid DE, Ferguson BJ, Hayashi S, Lin Y-H, Gresshoff PM (2011) Molecular mechanisms controlling legume autoregulation of nodulation. Annals of Botany 108: 789-795.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR MARINA FORTES School of Chemistry & Molecular Biosciences
Phone: 07 3365 4258 Email: [email protected] Web: http://staff.scmb.uq.edu.au/staff/marina-fortes
Genetics and genomics of mammalian reproduction Understanding the physiology of mammalian reproduction has broad implications, from human fertility clinics to livestock productivity. In our group we use genetics and genomics as avenues to discover genes, gene networks and pathways associated with various aspects of mammalian reproduction, using livestock as a model. Our goals are to: Identify mutations, genes and pathways associated with fertility Understand the genetic basis and inheritance of reproductive characteristics (aspects of sperm quality, for example) Create diagnostic assays (genotyping for fertility traits) Genomics and gene expression underpinning fertility traits in Australian Brahman cattle Brahman cattle are of particular importance for the beef industry in Queensland and northern Australia because of the breed’s tropical adaptation. However, tropical adaptation comes with associated negative traits such as lower fertility and late puberty. This project has two aims: understanding the biological basis of late puberty in Brahman cattle and delivering a diagnostic tool, a DNA chip, specifically designed to assist selection for improvement in their fertility. Gene expression of key tissues will be measured in pre and post pubertal animals using next generation sequencing. This project is conducted in collaboration with the groups of Prof Stephen Moore (QAAFI), Dr Sigrid Lehnert (CSIRO) and Dr Toni Reverter (CSIRO). RNA and ncRNA in testicular tissues Normal sperm cell differentiation, termed spermatogenesis, requires re-organization of sperm DNA structure. The sperm head is much smaller than the nucleus of other cells and DNA must therefore adopt a highly condensed form in order to fit. This mechanism is hypothesized to be regulated by non-coding RNA (ncRNA). An essential role for ncRNA in regulation of spermatogenesis in mice has been demonstrated spermatogenesis (Yadav & Kotaja 2014). But, the impact of ncRNA on male fertility is poorly understood. This research will further investigate the role of ncRNA in spermatogenesis, profiling sperm ncRNA, RNA and protein content in testicular samples that represent three key stages of spermatogenesis. Genetics of new sperm quality traits Flow cytometric assays are replacing older methods used to define male fertility. Two emerging flow cytometric assays are the focus of this research: the sperm chromatin structure assay (SCSA) and the sperm protamine deficiency assay (SPDA, developed by our group). Sperm DNA damage measured by the SCSA is a known factor of male sub-fertility in mammals, including humans. We aim to investigate the relationship between protamine deficiency and sperm DNA damage, estimating for the first time the heritability of these sperm quality traits. This project is financed by Meat and Livestock Australia and is conduct in collaboration with Dr Gry Boe-Hansen and Dr Nana Satake (SVS). Techniques you learn in our group may include: Quantitative Genetics, molecular genetics, bioinformatics, next generation sequencing, SNP genotyping, flow cytometry, analysis of sperm quality. Useful Majors: Biochemistry & Molecular Biology / Bioinformatics / Biomedical Science / Computational Science / Genetics / Veterinary Science
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR DONALD GARDINER CSIRO Agriculture and Food Queensland BioScience Precinct, UQ-St. Lucia Campus
Phone: 07 3214 2370 Email: [email protected]
FUSARIUM PATHOGENESIS IN WHEAT
My group focusses on mechanisms of pathogenicity of Fusarium species of fungi that infect cereal crops. The Fusarium species we are particularly interested in are Fusarium graminearum and Fusarium pseudograminearum which infect wheat, barley and maize and can have some devastating consequences worldwide. These pathogens are particularly nasty as they produce toxins during infection that contaminate food and feed products. We uses genomic technologies to dissect how these pathogens cause disease. Functional studies are undertaken with a particular focus on regulation and biosynthesis of toxins, biosynthesis of plant hormone mimics and mechanisms of degradation of host produced antimicrobial compounds. These fungi are easily cultured in the lab, have small genomes and can be transformed to create mutants or fluorescently tagged isolates. These organisms’ genomes are also Deoxynivalenol very compact with related genes, such as those for toxin biosynthesis, present in gene toxin clusters. We have recently established genome engineering using CRISPR/Cas9 in these pathogens. Projects currently available in the laboratory include: 1. Using CRISPR/Cas to understand sex in F. graminearum. An important part of the F. graminearum lifecycle is sex. This project will investigate how this pathogen undergoes sex by modifying candidate genes in the pathogen using genome engineering [1] and by undertaking experimental evolutionary biology experiments. An expected outcome is an understanding of how the pathogens sexual cycle might be used against it in the field, by for example designing strains carrying Trojan horse cargo for biological control. 2. Cloning a Fusarium virulence loci. Using a combination of next generation (Illumina and PacBio) sequencing and tradition genetic mapping we recently published a very high quality genome of F. pseudograminearum [2, 3]. The project will involve map based cloning, Toxin+ Toxin- fine mapping and functional studies of candidate genes in the virulence locus. 3. Understanding resistance of native grasses to Fusarium. Fusarium infects native grasses but does not have the devastating consequences that it does on wheat. This project will explore the mechanisms of resistance or tolerance that Australian native grasses have to this pathogen. 1. Selection is required for efficient Cas9-mediated genome editing in Fusarium graminearum https://doi.org/10.1016/j.funbio.2017.11.006. 2. A high resolution genetic map of the cereal crown rot pathogen Fusarium pseudograminearum provides a near complete genome assembly https://doi.org/10.1111/mpp.12519. 3. Comparative pathogenomics reveals horizontally acquired novel virulence genes in fungi infecting cereal hosts https://doi.org/10.1371/journal.ppat.1002952.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
PROFESSOR IAN GENTLE School of Chemistry & Molecular Biosciences ARC Centre of Excellence for Functional Nanomaterials
Phone: 07 3365 4800 Email: [email protected]
Research in the Surface Chemistry Group is concerned with the self-assembly of materials at interfaces, a field of research which encompasses thin film methods and other surface processes. Thin film techniques have important technological applications in the construction of devices with useful electronic, optical or optoelectronic properties, and interfaces are also important to many biological systems. Methods of characterisation used include grazing incidence X-ray and neutron scattering and spectroscopy (facilities at the OPAL Neutron Source in Sydney, the Australian Synchrotron in Melbourne or overseas facilities are normally used for this purpose), X-ray reflectometry, X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM), depending on the project. At UQ, the facilities for characterisation of thin films and materials (in the Centre for Microscopy and Microanalysis) are state of the art. These include a $1.1M imaging XPS, a Digital Instruments NanoScope scanning probe microscope, an Anton Paar Small Angle X-Ray Scattering instrument and two Bruker X-ray diffractometers.
New Directions towards High Energy Supercapacitors: Graphene-based Multifunctional Electrodes Supercapacitors with high power density and long life span are the most promising solutions beyond lithium ion batteries to power electric vehicles, transportation and electronic devices. However, the low energy density of supercapacitors is a major impediment to their development. This project aims to address the materials and device challenges in high energy supercapacitors, and to propose guidelines for electrode design principles, materials synthesis methodology and device configuration strategy. The core concept of this research is to optimize the performance of graphene-based electrodes by tailoring nanoporous structure, lattice dopants, surface functionalities and mechanical properties, and most crucially, to understand the basic electrochemical processes.
Specific objectives are to: •Synthesise heterogeneous graphene-based nanosheets with desirable nanoporosity, lattice dopants and surface functionality; •Assemble multifunctional graphene-based electrodes combining electrochemical reactivity and mechanical flexibility; •Understand the mechanisms of electrochemical interfacial reactions and inner-pore ion transport to optimize overall performance of the graphene-based multifunctional electrodes.
This project will be carried out in collaboration with Dr Da-Wei Wang. It will involve extensive use of chemical and surface synthetic techniques, structural characterisation by advanced methods described above, combined with electrochemical measurements. Depending on the rate of progress, there may be the opportunity for prototype supercapacitor device construction using the new materials developed in the project.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
PROFESSOR ROBERT G GILBERT Centre for Nutrition & Food Sciences School of Chemistry & Molecular Biosciences
Phone: 07 3365 4809 Email: [email protected]
Biosynthesis-structure-property relations for starch and glycogen Starch provides more than half the world population’s calorific intake; glycogen is our body’s glucose buffer. These are at first sight simple homopolymers of glucose, but their structure spans many levels of complexity, with features ranging from nm to mm. These structural features strongly influence nutritional value for humans, and how well glycogen is effective in controlling blood sugar (and hence propensity to diabetes). In synthetic polymer science and technology, the paradigm for understanding material properties, and producing materials with improved properties, is well established as synthesis controls structure controls properties. The equivalent has been impossible for starch and glycogen: one changes the genetics (biosynthesis) to try to obtain cereals with desirable properties—better digestibility for managing and reducing obesity, diabetes and colo-rectal cancers—and drug targets for diabetes through glycogen synthesis enzymes. This project will greatly expand current knowledge, through our unique experimental and theoretical tools, to examine the structure of these polymers and then to relate the structural features to both biosynthesis and to properties.
Examples of available projects :
Project 1: Kinetics of enzymatic degradation of starch and glycogen This project will examine the rates at which starch is degraded by enzymes in human digestion, and how glycogen in different organs is degraded to provide blood sugar when needed physiologically. This project will examine the kinetics of these processes in vitro, to shed light on the corresponding in vivo processes which are of major importance in controlling obesity and diabetes.
Project 2: Genetics/structure relations: experiment There is no detailed knowledge on which genes control the extent of starch/glycogen branching at the micro- or nano-structural level. There is also little information on the effects of environmental conditions on the differential expression of the genes, nor the extent of genetic variation in these gene families. This project will examine polymer structures in varieties obtained and characterized by modern techniques in molecular biology and biotechnology to link the genome (gene) to phenome (structure) with reference to growth conditions. Interpreting these data will yield information on the detailed mechanisms by which enzymes of specific structure control particular aspects of starch structure.
Molecular structural differences between type-2-diabetic and healthy glycogen. MA Sullivan, J Li, C Li, F Vilaplana, D Stapleton, AA Gray-Weale, S Bowen, L Zheng, RG Gilbert. Bio¬macro¬¬¬molecules 12 1983 (2011); Molecular weight distributions of starch branches reveal genetic constraints on biosynthesis. AC Wu, RG Gilbert. Biomacromolecules, 11 3539 (2010); Amylose content in starches: towards optimal definition and validating experimental methods. F Vilaplana, J Hasjim, RG Gilbert. Carbohydrate Polymers 88 103 (2012)
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
PROFESSOR ELIZABETH GILLAM School of Chemistry & Molecular Biosciences
Phone: 07 3365 1410 Email: [email protected]
Catalytic promiscuity and artificial evolution of P450 enzymes The cytochromes P450 are one of the most functionally versatile groups of enzymes known. They carry out diverse roles in Nature because they can catalyse an extraordinary range of chemical transformations, ranging from aromatic/aliphatic hydroxylation and heteroatom oxidation, to group transfers, ring expansion/contraction, coupling reactions, and C-C bond cleavage. This makes them ideal starting materials for engineering designer biocatalysts for difficult chemical reactions. Our group is interested in finding out how P450s work and how they can be made to work better.
Project 1: Artificial evolution: better, faster, more specialised P450s can accelerate drug development and clean up environmental pollutants We are using artificial (or directed) evolution to generate libraries of mutants from naturally-occurring P450 forms with the aim of engineering catalysts with properties enhanced by orders of magnitude over those found in naturally occurring enzymes.
Project 2: What determines the catalytic promiscuity of P450s? Collectively a handful of P450s metabolise ~ 95% of all drugs to which humans are exposed as well as innumerable environmental chemicals. This is a truly exceptional variety of substrates. Our aim is to determine how these enzymes can show such extreme catalytic promiscuity using a range of biophysical and molecular techniques.
Project 3: P450 Nanodiscs for biosensors (with Prof. Paul Bernhardt) Since P450s respond to such a variety of different substrates they are well suited for use as biosensors to detect trace environmental contaminants, drugs and other chemicals. We will formulate P450s into nanodiscs – very small protein-bounded lipid bilayer discs – to characterise their electrical properties by protein electrochemistry.
Project 4: Structural signatures of P450s (with Dr. Mikael Boden) We are using bioinformatics tools to explore the essential sequence and structural features underpinning all ~12000 known P450s so as to determine how P450s work.
Students doing Honours in the Gillam lab gain experience in cutting-edge techniques such as artificial evolution of proteins, high throughput screening, protein design and preparation of nanodiscs as well as fundamental methods of molecular cloning, protein chemistry, enzymology and metabolite analysis.
Our research suits students in biochemistry/molecular biology, chemistry, biotechnology, or bioinformatics who are interested in discovering how enzymes work and how to engineer them to provide clean green alternatives to chemical processes. 49
SCMB Biotechnology Research Projects 2018 | Individual Contributors
PROFESSOR JEFF GORMAN Queensland Institute of Medical Research (QIMR)
Phone: 07 3845 3669 Email: [email protected]
Protein Discovery / Proteomics The QIMR Protein Discovery Centre is arguably the most advanced infrastructure centre in Australia for the analysis of chemical features of proteins and documentation of proteomes of cells, organisms and tissues. We are particularly interested in the interactions between host cells and infectious organisms as reflected by dynamic changes in the protein repertoires (proteomes) of cells infected by viruses. We are also interested in interactions between proteins required to initiate, sustain and perpetuate viral and parasitic invasion of cells. The ultimate aim of our work is to develop a better understanding of interactions between infectious organisms and host cells to develop therapeutic interventions for serious human diseases such as viral respiratory infections and malaria. Our projects involve extensive collaborations with leading Australian and international scientists.
Evasion of host cell innate immunity by respiratory syncytial virus: Respiratory syncytial virus (RSV) is a serious pediatric respiratory pathogen and is increasing recognised as an important pathogen of geriatrics. RSV is a master of evasion of the host cell antiviral response. One specific viral gene product, non-structural protein 1 (NS1) of RSV contributes substantially to blocking the host cell antiviral response. In this project we are using a combination of reverse viral genetics and proteomics to determine the mechanism(s) by which NS1 exerts its influence over the infected cell. This project involves collaboration with Dr Peter Collins and his group from the US National Institutes of Health and Dr Kirsten Spann from UQ who contribute molecular virology expertise.
Click chemistry probes of complex macromolecular assemblies: This project involves the development of a diverse range of click chemistry probes to label the exterior of macromolecular assemblies. These probes are designed to probe the distributions of protein domains within membrane assemblies and to obtain low resolution structural information on externally disposed domains. These probes will be applied to help understand the interactions of viruses and parasites with host cells and the structures of proteins on the surfaces of these infectious agents. This project involves collaboration with Dr Ross McGeary of UQ and scientists from QIMR, including Dr Kathy Andrews (malaria parasites), Dr Greg Anderson (iron transport) and Dr Nathan Subramaniam (iron transport).
Viral proteomics: Using proteomic techniques, we and others have shown that viruses often package cellular proteins into mature virions. These cellular proteins are often from molecular machines that viruses use during trafficking in and budding from the host cell. This project aims to investigate the variation in cellular proteins packaged by different viruses in order to ascertain the likely mechanisms by which different viruses interact with host cell molecular machinery.
Post-translational modifications of malarial proteins: Malaria transitions through a number of different forms during its lifecycle. This project aims to examine the post-translational modifications to malarial proteins, particularly phosphorylation, during these transformations as a way of defining these processes at a molecular level. This is a collaboration with Dr Don Gardiner and his group at QIMR.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
PROFESSOR PETER GRESSHOFF ARC Centre for Integrative Legume Research
Phone: 07 3365 3550 Email: [email protected]
Plants possess stem cells that have the ability to differentiate into multiple cell types. The signals controlling this process are critical in the developmental biology of plant growth (see Beveridge et al, 2007; Curr. Topics in Plant Biology). We are looking at one specific stem cell cluster called the nodule meristem. These develop into new organs. We ask: what are the genes responsible for that? How do they interact? What are the signals and the receptors? How does physiology interact with gene expression? We offer three cutting edge projects for top students willing to learn functional genomics and plant biotechnology. The research is carried out within the ARC Centre of Excellence for Integrative Legume Research (CILR), and interested students should visit the website www.cilr.uq.edu.au.
Project 1: Molecular signalling during stem cell differentiation and lateral organ differentiation in legumes such as soybean, Lotus japonicus and Medicago truncatula): The project utilises our increasing understanding of long distance regulation of plant organ induction and differentiation. Critical genes controlling nodulation (GmNFR1, GmCLE80, GmNARK) have now been cloned and characterised. We are starting to understand what molecular signal activates the receptor kinase, what are the down-stream signals and responses (Kinkema and Gresshoff, 2008, Mol. Plant Microbe Interactions), what are its ligands, what proteins are phosphorylated? (See Miyahara et al, 2008, J. Biol. Chemistry). We recently discovered new peptide signal molecules that may act like hormones (Gresshoff et al, 2009, Plant Signalling & Behaviour). We are testing the similarities of these regulatory circuits with those controlling stem cell proliferation (i.e., GmCLV1, GmWUS, GmCLV2, and GmCLV3). Supervisors: Professor Peter Gresshoff, Dr Arief Indrasunumar, Dr Jacqui Batley and Dr Brett Ferguson.
Project 2: Biotechnology of sustainable biofuel (biodiesel) production from the legume tree Pongamia pinnata: Biofuels are essential for our future. We have initiated a biofuel program using biotechnology and genetics coupled with physiology and biology to develop a scientific basis for that growing industry. We are focusing on a legume to eliminate the energy and environmental costs of nitrogen fertiliser. Our plant of choice is a legume tree Pongamia pinnata (see Scott et al, 2008, BioEnergy Research) from which oil-rich seeds are harvested each year. Already industry such as ORIGIN Energy, Pacific Renewable Energy, and BioEnergy Research, are interested in this biotech project. Several projects exist dealing with the optimisation of nitrogen fixation, seed storage protein gene promoters, gene expression analysis, etc. Supervisors: Dr Paul Scott, Professor Peter Gresshoff, Dr Bandana Biswas, and Dr Qunyi Jiang and.
Project 3: Molecular physiology and biotechnology of ethylene regulation of nodulation and lateral root development in the model legume Lotus japonicus: This legume has a small genome, is easily transformed, and has yielded many valuable mutants. Forward and reverse genetics are available. We have produced the world’s first transgenic legumes expressing an Arabidopsis ethylene receptor gene (see Lohar et al, 2009, Annals of Botany; Gresshoff et al, 2009, Plant Signaling & Behaviour). Furthermore we have isolated both ethylene and ABA insensitive mutants in this model legume. The ethylene insensitive plants have altered physiological properties including increased nodulation, decreased lateral root formation and slowed maturation. The ABA insensitive mutant BEYMA shows extreme wilting because of an inability to regulate stomatal openings (see Biswas et al, 2009, Molecular Plant). Cloning of the BEYMA gene is an immediate goal. We are attempting to eliminate some of the negative effects by using tissue-specific promoters in transformation. Grafting is needed to evaluate the role of shoot vs. root in the physiological stress responses. Supervisors: Professor Peter Gresshoff, Dr Bandana Biswas and Dr Qunyi Jiang 51
SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR ULRIKE KAPPLER School of Chemistry & Molecular Biosciences
Phone: 07 3365 2978 Email: [email protected]
Regulation of gene expression Regulation of bacterial sulfite oxidation – a novel role for extracytoplasmic function (ECF) sigma factors.
Enzymes & their role in bacterial physiology Do metalloenzymes support virulence of human pathogens? Case study: Haemophilus influenzae Molybdenum enzymes. Friend or Foe? – Metabolic interactions between Streptococcus pneumoniae and Haemophilus influenzae.
Environmental microbiology & applications Some like it alkaline – Can we use alikaliphilic sulfur oxidizers to treat sulfur pollution? Co-supervision with Prof. Gordon Southam: “The growth of gold nuggets” – bacterial degradation of thiosulfate gold complexes.
If you find these topics interesting, but would like to work on other aspects of the projects, please contact me – this list is not comprehensive and additional projects are available.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
PROFESSOR MARK KENDALL Australian Institute for Bioengineering & Nanotechnology (AIBN)
Phone: 07 3346 4203 Email: [email protected]
DR SIMON CORRIE Australian Institute for Bioengineering & Nanotechnology (AIBN)
Phone: 07 3346 4209 Email: [email protected] Web: http://www.aibn.uq.edu.au/simon-corrie
Delivering vaccines and sampling diagnostic molecules through the skin The outermost layers of our skin contain a rich and untapped source of immune-sensitive cells and blood- borne biomarkers. We are developing new technologies to deliver vaccines to, or extrac diagnostic biomarkers from, these outer skin layers. Our group is a multidisciplinary mix of scientists (chemists, immunologists, virologists, vaccinologists) and engineers (mechanical, civil, chemical) who together bring a diverse array of expertise and skill sets to solve important technology problems and to learn more about the biology, immunology and mechanical properties of the skin. Our laboratory facilities include a mechanical design suite, a multi-photon microscopy system, a range of immunological and molecular assays and material fabrication and surface modification facilities. We also use the facilities of the Australian National Fabrication Facility QLD node (ANFF-Q – level 2 AIBN), UQ’s Centre for Microscopy and Microanalysis (CMM – especially SEM, XPS) and the University of Queensland Biological Resources (UQBR) animal housing facility (level 6, AIBN to support our manufacturing, analytical and pre-clinical testing needs.
We currently have Honours project opportunities in both vaccine delivery and diagnostics projects. These projects include:
• Engineering, expressing and testing novel vaccine formulations on patches in comparison to standard intramuscular injections • Engineering, expressing and testing new diagnostic capture probes for improved diagnostic performance, based on sensitivity or assay simplicity • New surface chemistry approaches to improve capture and release of biomolecules from patch devices • Microfluidic approaches to detect key biomarkers extracted from skin
Projects are available for a wide array of skill sets. Students with a background in biotechnology, molecular biology or physical/inorganic chemistry should apply. Skills gained will include molecular biological techniques (ELISA/PCR), surface chemistry, microfabrication and pre-clinical animal testing of devices (optional). Opportunities exist for students to continue their work, or start new projects, in MPhil or PhD programs.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
PROFESSOR ALEXANDER KHROMYKH RNA Virology Laboratory School of Chemistry & Molecular Biosciences
Phone: 07 3346 7219 Email: [email protected]
RNA virology laboratory study molecular mechanisms of virus RNA replication and virus-host interactions with the main focus on the West Nile virus (WNV) and more recently on Chikungunya virus. WNV belongs to Flaviviruses, a group of highly pathogenic positive strand RNA viruses causing major outbreaks of potentially fatal diseases and affecting more than 50 million people each year. Chikungunya virus is a member of Alphaviruses and has recently caused large outbreaks of devastating arthritis disease in Reunion Island and Asian countries. We are aiming at a better understanding of how these viruses replicate in the host and cause disease, which will help in the development of antiviral drugs. In addition, we develop and evaluate vaccine candidates to prevent infection and outbreaks. The following projects are available:
Role of Small Subgenomic RNA in Flavivrus Pathogenicity. We recently identified a small subgenomic RNA produced from the 3’ untranslated region of the viral RNA in cells infected with a variety of flaviviruses. This subgenomic flavivirus RNA (sfRNA) is the product of incomplete degradation of genomic RNA by cellular ribonucleases and is required for viral response. We will elucidate the function of sfRNA in the viral life cycle and identifyi cellular and viral interaction partners of sfRNA.
Virulence Determinants and Host Innate Immune Response to West Nile Viruses. We have shown previously that WNV is able to evade innate immune response with more virulent strain able to do it more efficiently. There are a number of projects available in collaboration with leading overseas groups (M Diamond, USA; M Gale, USA; and S Akira, Japan) as well as local virologists (Roy Hall, SCMB) which will focus on the mechanisms by which pathogenic (New York 99) and non-pathogenic (Kunjin) strains of WNV interact with the host innate immune response and how these interactions determine outcome of infection.
KUN Virus DNA-Based Vaccine against Pathogenic Flaviviruses. We recently published the development of a highly effective DNA vaccine against WNV which involves the production of single round infectious particles and has been shown to induce high antibody levels in mice and horses. The project will continue in collaboration with Dr. Roy Hall at SCMB and Dr. Andreas Suhrbier at the QIMR to extend the technology to development of vaccines against other medically important flaviviruses, dengue and Japanese Encephalitis.
The role of miRNAs in Flavivirus-Mosquito Host Interactions. In collaboration with S Asgari (SBMS) we have identified a first miRNA produced by WNV and have shown that it targets a transcription factor in mosquito cells that is essential for virus replication. This project is aimed at further investigations of the role of WNV- induced/produced cellular and viral microRNAs (miRNA) in determining the outcome of virus infection in mosquito vector.
Innate immune response to Chikungunya virus. This project is a collaboration with Andreas Suhrbier (QIMR) and is focused on understanding how the innate immune response to this infection relates to virus-induced disease. Using mouse model of the disease developed at QIMR the studies will employ a wide range of mouse strains deficient in expression of various factors involved in innate immune response and cell lines derived from them to identify host factors involved in response to Chikungunya virus infection and in the development of virus-induced arthritis
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
PROFESSOR GLENN KING Institute of Molecular Biosciences
Phone: 07 3346 2025 Email: [email protected]
Venoms to drugs: translating toxins into therapeutics We are interested in the evolution, structure, pharmacology, and potential therapeutic applications of disulfide-stabilised peptides from the venoms of arthropod predators such as ants, assassin bugs, centipedes, scorpions, and spiders. Our primary focus is the discovery, structure-function characterisation, and therapeutic development of peptides that modulate the activity of neuronal ion channels involved in pain, epilepsy and stroke.
We are currently focussed on developing potent and selective inhibitors of three classes of human ion channel drug targets—acid sensing ion channels, voltage-gated sodium channels, and voltage- gated potassium channels. We have the world’s largest collection of >600 arthropod venoms that can be used to screen for modulators of these ion channels. Using this approach, we have developed the most potent known inhibitors of ASIC1a (involved in stroke), NaV1.1 and KV10.1 (involved in epilepsy), and NaV1.7 (involved in chronic pain).
We are also using a variety of structural biological techniques (NMR spectroscopy, cryoelectron microscopy, and X-ray crystallography) to determine the structure of our peptide-drug leads in complex with their ion channel drug targets.
Current projects include: 1. Development of novel venom-derived analgesic drugs 2. Development of novel venom-derived anti-epileptic drugs 3. Development of novel venom-derived and engineered anti-stroke therapeutics 4. Development of novel venom-derived anti-malarial drugs 5. Characterisation of novel venoms from ants, assassin bugs, and caterpillars 6. Exploration of pain signalling pathways using pain-inducing venoms
Background reading 1. Chassagnon IR et al. (2017) Potent neuroprotection after stroke afforded by a double-knot spider toxin that inhibits acid-sensing ion channel 1a. Proc. Natl.. Acad. Sci. USA 114, 3750–3755
2. Osteen JD et al. (2016) Selective spider toxins reveal a role for the NaV1.1 channel in mechanical pain. Nature 534, 494–499 3. Simons C et al. (2015) Mutations in the voltage-gated potassium channel KCNH1 cause Temple–Baraitser syndrome and epilepsy. Nature Genetics 47, 73–77 4. King GF (2011) Venoms as a platform for human drugs: translating toxins into therapeutics. Expert Opinion in Biological Therapy 11, 1469–1484.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
PROFESSOR BOSTJAN KOBE School of Chemistry & Molecular Biosciences
Phone: 07 3365 2132 Email: [email protected] URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe
Structural Biology of Infection, Immunity and Molecular Recognition The recognition of proteins by other proteins and ligands occurs in essentially every cellular process. We are trying to understand this process at the structural level, focusing particularly on the processes of infection and immunity. Our group is using an integrated approach combining determination of three- dimensional structures (with major emphasis on X-ray crystallography and cryo-electron microscopy) with computational techniques, methods for quantitative evaluation of interactions such as the biosensor, protein chemistry and molecular biology. Project 1: Structural studies of proteins involved in innate immunity in mammals and plants The aim of this project is to use structural biology to understand the molecular basis of processes involved in the innate immune response in mammals and plants, with implications for infectious and inflammatory disease, cancer and agriculture. The projects involve protein expression, purification, characterization of biophysical properties and enzymatic activity, crystallization and structure determination.
Project 2: Structural studies of proteins involved in bacterial pathogenesis The aim of this project is to use structural biology to understand the processes of bacterial pathogenesis by different bacterial pathogens. The projects involve protein expression, purification, crystallization and structure determination.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR SHIH-CHUN LO (LAWRENCE) Centre for Organic Photonics & Electronics School of Chemistry & Molecular Biosciences
Phone: 07 3346 7657 Email: [email protected]
Organic materials and Nanotechnology We are focusing on developing new classes of nanomaterials mainly for energy related applications, such as photon-induced water splitting (for H2 generation), solar cells, and organic light emitting diode (OLEDs) as well as bio-applications. Honours students will learn how to design, synthesise and characterise these frontier functional materials.
Project 1: Clean hydrogen fuel generation The use of hydrogen gas as a renewable and clean fuel has been one of the most exciting research fields, in particular, direct hydrogen creation from water driven by sunlight. Developing efficient and long-lasting water-splitting photosensitisers and catalysts has been the key challenge for the technology. The project is to synthesise and characterise new water-splitting photosensitizers for effective light absorption and catalysts for efficient water decomposition.
Project 2: Advanced materials for opto-electronics (e.g., OLEDs, solar cells, and photodiodes) The project is to develop new electro-active materials for OLEDs, solar cells, and photodiodes for our next generation flat-panel displays (e.g., mobile phones, tablets, monitor displays and TVs for the superior display-quality and superb energy saving), renewable energy generation and high-sensitive detectors. The project will involve organic/organometallic and physical chemistry, and students will learn how to fabricate and characterise these devices by closely working with device physicists.
Project 3: Biomaterials for imaging and treatment Photodynamic therapy (PDT) has been developed to provide non-invasive (compared with conventional surgery) and less side effects (compared to chemotherapy) for cancer treatment. PDT can be accurately targeted, and repeatedly administered without the total-dose limitations related with radiotherapy and result in little or no scarring after healing. To facilitate the advantages of PDT, we are developing novel bio-compatible photodynamic therapy agents for deeper tissue treatment with less photodamage with effective two-photon absorption activities.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR PATRICIA LOPEZ-SANCHEZ Centre for Nutrition and Food Sciences ARC Centre of Excellence in Plant Cell Walls
Phone: 07 3346 7373 Email: [email protected]
Our research focuses on the relationship between the chemical composition-architecture and material properties of cell walls in plants. The physical properties of the cell wall have direct implications for the use of plant material in many technological fields such biomaterials for medical applications, agri-food industry, paper production and environmentally friendly energy sources. Furthermore material properties are relevant for many plant bioprocesses, for example the wall has to be rigid to withstand external and internal forces and at the same time flexible enough to allow for growth and development of the plant. These features make the plant cell wall an outstanding material.
Project 1: Structure-function of engineered cell walls: a way to broaden the biotechnological applications of plant materials This project will make use of model plant systems such as bacterium Gluconacetobacter xylinus which produces pure cellulose in liquid fermentation. By using microbiological techniques and including chosen cell wall polymers in the fermentation medium, a range of cellulose-based composites can be engineered which have many properties remarkably similar to plant cell walls. Their materials properties will be characterized using stress controlled rheometers, before and after being subjected to mechanical forces (MPa) characteristic of the turgor pressure found in growing plants. With this approach, we aim to obtain a first understanding of the molecular basis for plant cell wall properties under active turgor pressure. The implications of such studies will contribute to the use of plant-based materials for food, pharmaceutical and medical applications.
Project 2: Mimicking nature by using polysaccharides as building blocks for cereal endosperms walls Cereals are one of the main components of the human diet worldwide. In their natural form, they are a rich source of vitamins, minerals, carbohydrates (fibre), fats and protein. However, when refined the remaining endosperm (‘white flour’) is mostly carbohydrates, such as starch enclosed by cell walls containing β-glucan and arabinoxylan. Extraction of cell wall components disrupts the architecture of the wall, which is key in determining its material properties. Therefore the development of models to mimic cell wall architecture is highly relevant to study the underlying relationships between their composition, microstructure and material properties. In order to build these cell wall analogues we will make use of enzymatic treatments and cryogelation of polysaccharides, a method which uses freeze-thawing cycles to form physically cross-linked networks .The outcomes of the project will contribute to advancing scientific understanding of plant cell wall biology to enable sustainable biomass production for food security and human health.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
PROFESSOR ALAN E. MARK Molecular Dynamics School of Chemistry & Molecular Biosciences
Phone: 07 3365 4180 Email: [email protected] Websites: http://profiles.bacs.uq.edu.au/Alan.Mark.html http://compbio.chemistry.uq.edu.au/md/
The group uses computer simulation techniques to model the dynamic behaviour of biomolecular systems such as proteins, nucleic acids and lipid aggregates. The simulation software and atomic force fields we develop are used to understand processes such as how peptides fold and self-assemble into functional complexes or how anti-microbial peptides enter cells. We look for students interested in working at the interface between structural biology, chemistry, and computational science.
Possible projects include:
Project 1: The nucleation and growth of amyloid fibrils Amyloid fibrils are self-assembled peptide aggregates associated with a range of neurodegenerative diseases. Molecular dynamics (MD) simulation techniques will be used to shed light on the structure and formation of amyloid fibrils. In particular, simulations will be used to identify the minimal stable structure required for fibril growth.
Project 2: The activation of the growth hormone receptor The activation of cell surface receptors is a critical step in cell regulation. MD simulations will be used to characterize the conformational changes that accompany the binding of growth hormone to its receptor thereby shedding light on the mechanism of action of cytokine receptors in general.
Project 3: Predicting protein-ligand interactions Free energy calculations are a highly accurate but computationally expensive method for predicting binding affinities. You will help refine and test a computationally efficient single-point free energy methodology developed within the group for use in virtual drug screening.
Project 4: Membrane protein assembly (anti- microbial peptides and viral fusion proteins) Despite their importance, little is known about to how membrane peptides and proteins assemble into functional complexes. To investigate this we are studying a range of small anti-microbial peptides that spontaneously self-assemble within membranes inducing pore formation, membrane fusion, or even cell death. On a larger scale we are studying how proteins of The peptide Magianin interacting with a DPPC enveloped viruses such as Dengue and Ebola drive the fusion of the bilayer showing the formation of a viral and cell membranes. This is a key step in the entry of the virus transmembrane pore. into cells and a prime target for therapeutic intervention.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
PROFESSOR DANIEL MARKOVICH Ion Transport and Cell Signalling Molecular Biology and Biotechnology School of Biomedical Sciences
Phone: 07 3365 1400 Email: [email protected] Website: http://www.uq.edu.au/sbms/staff/professor-daniel-markovich
Membrane Transporters: Biochemistry, Molecular Biology and Physiology Prof Daniel Markovich’s interests lie in the study of the biochemistry, (patho)physiology and genomics of mammalian ion transporters, involved in transcellular movement of ions (sulfate, chloride, oxalate) across epithelial cells. In the last few years, several membrane transporters have been cloned, characterised and knock-out mice generated in his laboratory.
The following Honours/MPhil/PhD projects are currently available in his laboratory:
• Project 1: Biochemical roles of polymorphisms in human sulfate transporters • Project 2: Trafficking of human sulfate transporters in mammalian cells • Project 3: Second messenger pathways regulation of human sulfate transporters
Using modern molecular and cellular biological techniques, these projects study the molecular function and regulation of ion transport systems by characterising their protein and mRNA expression in both in vitro (in established cell lines) and in vivo (animal models, Xenopus laevis oocytes) systems. These studies will elucidate the function and molecular regulation of these transporters in the body, which will help in clarifying their roles in ion homeostasis, which will provide important insights into diseases associated with membrane transport processes.
Selected Publications Markovich D (2012) Slc13a1 and Slc26a1 KO models reveal physiological roles of anion transporters. Physiology 27: 7-14
Markovich D (2011) Physiological roles of renal anion transporters Nas1 and Sat1. Am. J. Physiol.-Renal. Physiol. 300: F1267-70
Dawson PA, Russell CS, Lee S, McLeay SC, van Dongen JM, Cowley DM, Clarke LA, Markovich D (2010) Hepatotoxicity and urolithiasis in Sat1 transporter (Slc26a1) null mice. J. Clin. Invest. 120: 706-12
Markovich D and Aronson PS (2007) Specificity and regulation of renal sulfate transporters. Ann. Rev. Physiol. 69:7.1-7.15
Dawson PA and Markovich D (2005) Pathogenetics of the human SLC26 transporters. Curr. Med. Chem. 12: 385-396
Dawson PA, Beck L and Markovich D (2003). Hyposulfatemia, growth retardation, reduced fertility and seizures in mice lacking a functional NaSi-1 gene. Proc.Natl.Acad.Sci.USA 100 (23):13704-9
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
ASSOCIATE PROFESSOR FRED MEUNIER Molecular Dynamics of Synaptic Function Lab Queensland Brain Institute / School of Biomedical Sciences
Phone: 07 3346 6373 Email: [email protected]
The focus of our laboratory is to decipher the dynamics of molecular events taking place during nerve cells communication and plasticity. Our ultimate aim is to understand the sequence of interactions underlying neurotransmitter release and neuronal sprouting and to utilise this knowledge to design therapeutic strategies for treating human diseases affecting the nervous system such as neurodegenerative diseases.
Examples of available projects are:
Project 1: Biotechnology to help treat motoneuronal diseases Motoneuronal diseases are notoriously difficult to treat and one of the main hindrances to treatment is the relative inaccessibility of motoneurons. We are designing probes to deliver fluorescently-labelled molecules specifically in motoneurons.
Project 2: Biotechnology to image dynamic events in living neurons Design novel methods to investigate the neurons’ internal trafficking of vesicles involved in nerve cell communication. This project will aim designing new optical tools and methods for investigating vesicle trafficking in living neurons.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
ASSOCIATE PROFESSOR CHAMINDIE PUNYADEERA School of Biomedical Sciences /Institute of Health and Biomedical Innovations Queensland University of Technology
Phone: 07 3138 0830 Email: [email protected]
Project 1: Early Cancer Detection using a Saliva Sample Background: Cancer is the leading cause of death worldwide and accounted for 7.6 million deaths (around 13% of all deaths) in 2008 (WHO, 2011 February Report). Tobacco use is a major risk factor for head and neck cancer and lung cancers, and smoking kills over 1,000,000 people a year, causing 30% of all cancer-related deaths in the western societies. The direct impact of smoking can clearly be seen in the oral cavity due to its proximity, thus, human saliva is an ideal diagnostic medium for investigating smoking-related cancers. DNA methylation in cells is one of the earliest events that occur during cancer initiation and has demonstrated considerable utility by enabling early disease detection, better disease stratification, and predicting disease relapse and response to therapy in cancer and other diseases (Esteller, M. Epigenetics in Cancer, New England Journal of Medicine, 358: 2008). We are developing cutting-edge tools to diagnose cancer at an early stage, Changing Traditional Health Care Paradigm. Project aims: Identify and validate biomarkers in saliva for early detection and staging of head and neck cancers.
Benefits for you? You will have access to the state of the art facilities and will gain experience in working in a multidisciplinary team, focused on cutting-edge science You will develop laboratory skills in molecular biology, cell cultures and biochemistry You will have an opportunity also work in hospitals
Project 2: Saving Hearts with a Simple Saliva Test Background: Cardiovascular diseases (CVD) including heart, stroke and blood vessel disease, affect about 3.67 million Australians. Every 10 minutes ONE Australian dies from CVD. An increase in CVD in Australia is accelerated by growing as well as an aging population. Human saliva as a diagnostic medium has gained attention in the last decade due to its non-invasiveness, easy sampling and lower threat of transmitting infection. Human saliva is the window to our body and saliva mirrors biomarkers found in blood. Up until now, there have been ~ 2000 proteins found in human saliva and about ~26% are also present in blood, highlighting the importance of saliva for clinical research.
Project aims: To develop non-invasive low cost tools to detect heart disease at an early stage. The Saliva Translational Research Team: Our team is young, dynamic and vibrant, and is multidisciplinary. We are geared at investigating the diagnostic potential of human saliva aimed at translating our research findings into a clinical setting.
Collaborators: Professor Ian Frazer Professor John Atherton Professor Henry Krum (Monash University). Professor James Herman (John Hopkins University, Baltimore, USA) Professor Karam Kostner Professor William B Coman
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
Project-3: Circulating tumour cells as biomarkers in cancer Metastases remains the major cause of death in head and neck cancer (HNC) patients; circulating tumour cells (CTCs) derived from primary and secondary sites provide a comprehensive representation of the tumour burden in cancer patients’ at any one time. We have demonstrated that CTCs can be isolated from HNC patients before clinically evident metastasis, using a novel, microfluidic technology and now we have exciting preliminary data correlating CTC presence to clinical outcomes during the course of treatment. This microfluidic technology has the ability to transform scientific findings into translational outcomes and tangible health benefits by identifying HNC patients at risk of developing metastasis earlier than conventional techniques can. Identifying HNC patients before clinical metastasis (via a blood draw to assess CTCs) will allow us to develop treatment strategies either by intensifying or de-escalating treatments, and could revolutionize the management of HNC patients with concomitant increase in survival rates and significant reduction of healthcare costs.
Project Aim: To develop a robust method to enumerate CTCs from early stage cancer patients bloods.
Collaborators: Clearbridge Biomedics, PTY. LTD – Singapore
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
ASSOCIATE PROFESSOR KRISTEN RADFORD
Cancer Immunotherapies Group Mater Research- UQ, Translational Research Institute
Phone: 07 3443 7638 Email: [email protected]
Development of novel cancer immunotherapeutics that harness human dendritic cells
Dendritic cells (DCs) are the key antigen presenting cells responsible for initiating and directing immune responses. There are distinct dendritic cell subsets that are specialised in the types of immune responses they generate. However, dendritic cells are poorly understood in humans and translation is complicated by differences in human and mouse immune systems. We have identified a rare human DC subtype, termed CD141+ DC, that we hypothesize plays an important role in the induction of immune responses against viruses and cancers by their specialised ability to stimulate cytotoxic T cells. These DC are attractive targets for the design of new vaccines against cancers and infectious diseases. Projects are available that 1) seek to understand the role that CD141+ DC play in human cancers with the objective of identifying and validating novel ways of harnessing them as immunotherapies to improve tumour immune responses.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR STEVEN REID Deputy Director, Biotechnology Program School of Chemistry & Molecular Biosciences
Phone: 07 3365 3991 Email: [email protected]
Research Area: Production of Baculovirus Biopesticides – A Systems Biology Approach Increased resistance to chemical pesticides and concern over their use has renewed interest in the application of biological means to control pests of commercial importance. Many wild type Baculoviruses can specifically infect and kill key agricultural caterpillar pests and some virus strains can also target mosquitoes.
The Reid laboratory has a process patent on a procedure for producing Baculoviruses via fermentation. The lead product is a Baculovirus targeting the Helicoverpa pest species, which is responsible for a current $US3.2 billion per annum market in traditional chemicals.
A baculovirus product manufactured by the Reid Group and formulated by Bioflexus has been registered for use on Australian crops to combat heliothis caterpillars (more widely known as the cotton bollworm), under the trade name of ‘Heliocide’. The Reid Group is undertaking further research to increase current yields, to enable manufacture and evaluation in the niche Australian market.
Currently the Group is collaborating with Professor Lars Nielsen to use a Systems Biology approach utilising transciptomic and metabolomic techniques in an effort to understand how the virus interacts with host cells in culture. The team anticipates further increases in yield, making it cost effective in broader markets, both national and international.
Specific Research projects:
Project 1: Development of a Heliothis BACMID system for manipulation of the H.arm virus genome (gene knockouts). This system will be used to generate altered viruses for further transciptomic and metabolomic studies.
Project 2: The use of Real Time PCR to quantify virus binding kinetics to enable optimisation of early process steps for the manufacture of virus in vitro
Project 3: Development of sample extraction procedures and appropriate HPLC/GC-MS techniques for quantifying intracellular metabolite levels for infected and non infected cells in culture. These procedures are essential to enable our metabolomic studies.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
ASSOCIATE PROFESSOR JOE ROTHNAGEL School of Chemistry & Molecular Biosciences
Phone: 07 3365 4629 Email: [email protected] Website: http://www.scmb.uq.edu.au/staff/index.html?page=142199
Development of the next generation of gene expression systems A major focus of this laboratory is directed towards the development of new eukaryotic expression vectors. We are investigating the role of post-transcriptional mechanisms in gene expression. This work has led to the development of short cis-acting sequences based on small upstream open reading frames (uORFs) that can be used to modulate gene expression; known as GeneDimmerTM and GeneBooster respectively. Both GeneDimmerTM and GeneBooster expression vectors will ultimately be used in cell biology, gene therapy and agriculture. Experiment procedures and approaches include bioinformatics, gene cloning and analysis, cell culture, transgenic plants, and expression analysis.
The development of nucleus - targeting tags for the delivery of gene medicines We have identified a peptide sequence that localises to the nucleolus. We are developing a series of constructs that contain this peptide tag and are evaluating its use in delivering gene medicines to the nucleus. This methodology has the potential to increase the concentration of these genetic constructs in the nucleus thereby increasing their efficacy. We are also developing non-peptide aptamers of this sequence.
Characterisation of peptides encoded by short open reading frames Short peptides (sPEPs) that are encoded by short Open Reading Frames (sORFs) are surprisingly common in eukaryote genomes. Recent bioinformatic and ribosomal footprinting studies have identified several thousand sORFs with coding potential and several sPEPs have been identified by mass spectrometry. However, their role in cellular functions remains to be determined. This project will involve identifying and characterizing sPEPs using bioinformatic tools, proteomics (mass spec) and cell biology.
Biotech Honours Projects will be offered in the following areas: • Development of second generation GeneDimmerTM vectors and their characterisation in eukaryotic cells. • Characterisation of novel small peptides encoded by sORFs (with Amanda Nouwens) • Characterisation of PTPRJ isoforms in skin cells (with Stuart Kellie)
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
PROFESSOR MARK SCHEMBRI School of Chemistry & Molecular Biosciences
Phone: 07 3365 3306 Email: [email protected]
Molecular genetics of multidrug resistant uropathogenic E. coli Urinary tract infections (UTIs) are one of the most common infectious diseases of humans and a major cause of morbidity. Uropathogenic E. coli (UPEC) cause the majority (>80%) of UTIs and are a major contributor to global antibiotic resistance. Research in my lab aims to understand the virulence of multidrug resistant (MDR) UPEC, and to develop new approaches to treat and prevent UTI. The outcomes will address the enormous challenge of combating antibiotic resistance.
Our goals are to: Understand the virulence of MDR UPEC. Develop new methods to treat and prevent UTI. Characterize molecular mechanisms of adhesion, aggregation and biofilm formation utilized by MDR UPEC. UPEC virulence factors Molecular characterisation of UPEC clones MDR UPEC strains from predominant clonal groups, including the globally disseminated MDR E. coli ST131 clone, exhibit important differences in virulence gene content and expression compared to other well- characterised non-resistant UPEC strains. We aim to understand the molecular mechanisms of MDR UPEC virulence using genomic, epigenetic and high throughput gene function analyses. We study E. coli ST131 and other common MDR E. coli sequence types, including carbapenem-resistant strains and MDR strains of animal origin.
Development of new methods to treat and prevent UTI New approaches are urgently needed to treat and prevent UTI caused by MDR UPEC. We aim to (i) identify and characterise novel UPEC vaccine targets, (ii) test novel anti-adhesive molecules for their ability to prevent UPEC adhesion and bladder colonisation, and (iii) develop the asymptomatic bacteriuria E. coli strain 83972 as a novel therapeutic agent for the prevention of UTI.
Molecular characterisation UPEC adhesins and biofilms Aggregation and biofilm formation are critical mechanisms for bacterial resistance to host immune factors and antibiotics. Fimbriae and autotransporter proteins represent adhesins that contribute significantly to these phenotypes. Most UPEC strains produce multiple adhesins. We aim to study the regulation, function and structure of UPEC adhesins, and to determine their role in aggregation, biofilm formation, interaction with epithelial and immune cells, and colonization of the urinary tract. UPEC intracellular biofilm
Techniques you learn in our group may include: PCR, cloning, SDS-PAGE, Western blotting, advanced genetic and proteomic techniques, cell culture, biofilm model systems, animal models.
Useful Majors: Microbiology / Biochemistry & Molecular Biology / Bioinformatics / Genetics 67
SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR HORST JOACHIM SCHIRRA Centre for Advanced Imaging
Phone: 07 3346 0360 Email: [email protected]
NMR-based metabonomics in clinical applications and environmental science (3 projects) We try to solve the puzzle of metabolic pathways with NMR metabonomics. NMR metabonomics is the newest frontier technology in systems biology. It analyses biological or clinical samples, such as cell extracts, urine, and blood, by looking at the global composition of body fluids. We want to identify systematic patterns or metabolic fingerprints that are associated with diseases, specific physiological states, environmental or genetic conditions. Diseases and related conditions, as well as environmental or genetic changes lead to global metabolic changes that are reflected in the composition of biofluids and can thus be identified. These changes can then be used as diagnostic markers for identifying individuals at risk, for identifying successful intervention strategies, and for following and monitoring treatment in patients. The technique is powerful, as it can identify trends and metabolic changes that could be missed by a narrow approach of screening only select metabolites or metabolite classes. We study metabolic changes by investigating the chemical composition of biofluids with NMR spectroscopy. Changes in the metabolic profile of e.g. urine are studied by multivariate statistical analysis and let us pinpoint, which parts of the organism’s metabolism are disturbed. Thus, by understanding how disease affects the metabolism of an individual and by understanding the metabolic consequences of a disease we might learn something about the mechanism of a particular disease itself. I have several projects available in this area, focussing on a variety of model diseases.
Current projects involve the study of the effects of growth hormone receptor mutations in mice, the mechanism of phosphine resistance in C. elegans, as well as several projects aimed at developing NMR metabonomics as a tool for clinical diagnosis. Some of our animal model systems are very well understood, and in these cases we are trying to take the next step by investigating the connection between genotype and phenotype on a systematic level. The practical use of NMR metabonomics involves the analysis of a multitude of NMR spectra and correlation of these data with other data from physiology, biochemistry, or clinical assessments. This multimodal analysis is at the cutting edge of systems biology and requires the development of novel analytical tools and techniques. Thus, students with an interest or background in mutivariate statistics, programming and/or bioinformatics are highly welcome in this environment, apart from students with experience in chemistry and/or biochemistry.
Individual Projects: Three main projects in NMR-based metabonomics are available in 2010: One project centres on the early detection of Prostate Cancer and will be conducted in collaboration with Prof Frank Gardiner (UQ Centre for Clinical Research/Royal Brisbane and Women’s Hospital). The second project focuses on oral diseases and their contribution to the total inflammatory burden of a patient, and will be conducted in collaboration with Dr Pauline Ford (School of Oral Biology/Prince Charles Hospital). The third project aims to close the gap between genotype and phenotype by characterising a cohort of mice with mutations in the growth hormone receptor that leads to late-onset obesity. This project is in collaboration with Prof Mike Waters (IMB) and Prof Lars Nielsen (AIBN). All projects will be conducted in SCMB using the extensive NMR infrastructure of the Centre for Magnetic Resonance and the Institute for Molecular Bioscience. The potential for follow-on PhD projects exists, depending on successful APD scholarships.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR BENJAMIN SCHULZ School of Chemistry & Molecular Biosciences
Phone: 07 336 54875 Email: [email protected]
Molecular Systems Glycobiology My research focuses on the mechanisms, biological roles and applications in biotechnology of glycosylation, the most abundant and complex post-translational modification of proteins. Glycosylation is important in biological processes such as human development, cancer and microbial infection. This is because glycosylation is essential in biological activities as diverse as protein folding, fine-tuning protein enzymatic activity and determining protein-protein interactions. Half of all proteins are glycosylated, and a single protein can be modified by hundreds of different sugar moieties. The diversity of glycoproteins therefore requires that we take a systems biology approach in our research. All of our projects use a core set of methods in molecular biology, genetic manipulation, protein biochemistry, glycoprotein analysis and mass spectrometry. We aim to understand the mechanisms controlling glycosylation in these various systems to develop diagnostics, therapies, vaccines and applications in biotechnology.
Project 1: Engineering glycoprotein biopharmaceuticals Many proteins currently used as pharmaceuticals or in biotechnology are glycoproteins, such as erythropoietin (EPO) and monoclonal antibodies. The glycosylation and other post-translational modifications of these proteins are critical for their function, but recombinant proteins produced from mammalian cell culture are often different to the native proteins. This project will develop mass spectrometry analytics to characterise protein biopharmaceuticals, and engineer cell lines to allow targeted post- translational modifications. This project forms part of the ARC Training Centre for Biopharmaceutical Innovation (http://www.arccbi.org/).
Project 2: Glycosylation in health and disease Altered glycosylation is associated with cancer and infection. We aim to understand the mechanisms controlling this process using in vitro protein biochemistry, a yeast model system and human cell culture, to determine how it affects glycoprotein function. We also develop new mass spectrometry approaches to systematically and globally identify and quantify proteins and their sugar modifications in fundamental biology and disease.
Project 3: Beer Beer brewing is perhaps the most ancient biotechnology. We use modern analytical techniques including proteomics and metabolomics to investigate and improve this complex and important process, including analysis of seed germination during malting, protein biochemistry during mashing, and isolation and characterisation of wild yeast for use in fermentation. Aspects of this project are in collaboration with Newstead Brewing.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
ASSOCIATE PROFESSOR CONRAD SERNIA School of Biomedical Sciences
Phone: 07 3365 3180 Email: [email protected]
Endocrinology of Angiotensin Angiotensin is a small peptide hormone that is commonly associated with blood pressure and salt balance. Two widely prescribed classes of antihypertensive drugs are based on interference with Angiotensin action: the angiotensin receptor antagonists (eg. Losartan) and angiotensin-converting enzyme inhibitors (eg. Captopril). This lab is interested in uncovering links between angiotensin and degenerative diseases that may be consequential to, or independent of, cardiovascular effects.
The current focus is on Alzheimer’s Disease, Oxidative Stress and Osteoporosis.
Project 1: Alzheimer’s Disease: angiotensin regulation of amyloid precursor protein (APP) in neurones Project 2: Osteoporosis: angiotensin action on osteoblasts with particular emphasis on RANKL/OPG regulation. Project 3: Involvement of angiotensin-mediated oxidative stress in (1) and (2) above.
Collaboration: The laboratory collaborates with Prof Lindsay Brown (USQ); Prof Wally Thomas (UQ) and Prof Po Leung (Chinese University of Hong Kong).
Research Techniques: General endocrine methods, cell culture, molecular techniques.
Selected Publications: SERNIA C. A critical appraisal of the intrinsic pancreatic angiotensin-generating system. J Pancreas 2:50- 55. 2001 Leung PS SERNIA C. The renin-angiotensin system and male reproduction: new functions for old hormones. Molec Cell Endocrin 30: 263-70, 2003 Sernia, C., Tang, Z., Kerr, D., & Wyse, B. (1997) Novel perspectives on pituitary and brain angiotensinogen. Front. Neuroendocrin. 18(2): 174-208. Wyse, B. & Sernia, C. (1997) Growth hormone regulates AT1a angiotensin receptors in astrocytes. Endocrinol. 138: 4176-4180. Greenland K SERNIA C. Oestrogenic regulation of brain angiotensinogen. J Neuroendocrin 16: 508-515, 2004. SERNIA C Huang H et al. (2007). Bone Homeostasis: an emerging role for the renin-angiotensin system. In “Proteases of the rennin-angiotensin system in Human Disease” ed. P.Leung, Springer Verlag, pp263-287.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR YASMINA SULTANBAWA Queensland Alliance for Agriculture and Food Innovation (QAAFI)
Phone: 07 3276 6037 Email: [email protected] [email protected]
Project 1: Antimicrobial efficacy of Leptospermum polygalyfolium honey with different levels of methylglyoxal contents against MRSA and Pseudomonas Recent studies on Leptospermum polygalifolium a myrtle native to Australia has shown antibacterial activity against Methicillin-Resistant Staphylococcus aureus (MRSA), Staphylococcus aureus and Escherichia coli (Sultanbawa and Smyth 2010). The most extensively studied leptospermum species is Leptospermum scoparium ((Cooper, Molan et al. 1999; Henriques, Jenkins et al. 2010)) and this is the source of the well known bioactive honey manuka from New Zealand. The honey from Leptospermum polygalifolium which is harvested by the bees from a monofloral source and is only found in Australia could be branded and marketed in a similar manner to the manuka honey. However, scientific evidence for the use of the Australian honey for wound infections is limited and more studies are needed to prove efficacy. Methylglyoxal (MGO) one of the phytochemicals present in this honey has been identified as one of the chemical components responsible for antimicrobial activity ((Adams, Boult et al. 2008; Mavric, Wittmann et al. 2008; Adams, Manley-Harris et al. 2009)). MGO levels of 1.1 – 1.8 mM in Leptospermum scoparium has indicated antibacterial activity ((Mavric, Wittmann et al. 2008)). Our studies indicate higher levels of MGO in honeys from Leptospermum polygalifolium. The aim of this project is to understand the mechanisms that govern the antimicrobial activity of this honey at different levels of MGO ranging from 300 – 1750 mg/kg against MRSA and Pseudomonas aeruginosa.
Project 2: Determining the inhibitory effects of Leptospermum polygalyfolium honey on biofilms of MRSA and Pseudomonas. Honey is well known for its wound healing properties and one of the contributing factors is the antibacterial activity in honey. With the increase use of antibiotics in medicine there has been a rise in prevalence of antibiotic resistance bacteria such as MRSA. As a result there has been an urgent need to find alternative antimicrobial strategies which include bioprospecting for natural sources and also changing the methods used to elucidate antimicrobial activity. Honey as a natural antimicrobial is important as it has a potent in vitro activity against antibiotic resistant bacteria and it has been successfully used in the treatment of chronic wound infections not responding to antibiotic treatment.
Information on the antimicrobial activity of the Australian honey Leptospermum polygalifolium and mechanisms that are responsible for inhibiting quorum sensing signals which in turn affect the growth of biofilms will contribute to scientific evidence for the use of honey as a conventional and natural treatment. The aim of this study is to understand the inhibiting effects of Leptospermum polygalifolium in the formation of biofilms from MRSA and Pseudomonas.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR KATE STACEY School of Chemistry & Molecular Biosciences
Phone: 07 3365 4640 Email: [email protected]
Recognition of Cytosolic DNA as a Danger Signal The DNA of eukaryotic cells is contained within a membrane-bound nucleus, and the appearance of DNA within the cytosol indicates a danger to the cell. Cytosolic DNA can result from viral and bacterial infections or the activity of endogenous retroviruses within the human genome. Responses to cytosolic DNA include production of the anti-viral protein interferon-beta, and cell death. We identified AIM2 as a receptor for cytoplasmic DNA eliciting cell death. AIM2 initiates formation of an “inflammasome” which is a protein complex leading to activation of the protease caspase-1 and lytic cell death. We have recently shown that AIM2 recognition of DNA also recruits and activates caspase-8, which leads to the death of cells by apoptosis. Although the AIM2 pathway is only found in mammals, we find that chicken and insect cells can also die after introduction of DNA into the cytosol. Consequently we propose that defences against invading DNA are essential for defending against infections and guarding the genome of all multicellular organisms. Future studies will focus on:-
1) Characterisation of the role of DNA detection in combatting viral infections 2) Definition of pathways of recognition of foreign DNA in non-mammals 3) Characterisation of the inflammasome complex induced by AIM2, and novel death-domain interactions involved in recruitment of procaspase-8 4) Investigation of the role of AIM2 (absent in melanoma 2) as a tumour suppressor
Inflammasome Deficiency in Autoimmune Disease The human autoimmune disease lupus involves formation of antibodies against self molecules and their deposition as immune complexes in tissues. Inflammasomes lead not only to cell death but also to release of the inflammatory cytokine IL-1b. Although most researchers have assumed that inflammasome pathways will be elevated in autoimmunity, we find the opposite; in a mouse model of lupus there is profound deficiency of three different types of inflammasome structures. We propose this leads to an altered response to commensal organisms and poor clearance of pathogens, and promotes autoimmunity. Projects will include: 1) Establishing the molecular basis for inflammasome deficiency in the mouse 2) Investigating whether human lupus patients have inflammasome deficiency
Relevant Publication: Roberts, T.L., Idris, A., Dunn, J.A., Kelly, G.M., Burnton, C.M., Hodgson, S., Hardy, L.L., Garceau, V., Sweet, M.J., Ross, I.L., Hume, D.A., Stacey, K.J. (2009) HIN-200 proteins regulate caspase activation in response to foreign cytoplasmic DNA. Science 323:1057-1060.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR MATT SWEET Institute for Molecular Bioscience
Phone: 07 3346 2082 Email: [email protected]
Project 1: Targeting Histone Deacetylases in Inflammation Acetylation of lysine side chains on proteins regulates diverse cellular processes including signalling, transcription and protein targeting. Histone deacetylases (HDACs) are a family of enzymes that deacetylate lysine side-chains, and inhibitors of these enzymes have efficacy as anti-cancer agents. HDAC inhibitors also display anti-inflammatory properties. This project will investigate the role of specific HDACs in regulating inflammatory responses of macrophages.
Project 2: Characterizing Human-specific Inflammatory pathways Mice are routinely used in immunological models to study disease processes. Specific immune responses are not necessarily conserved between mice and humans however, because the innate immune system is under strong evolutionary pressure. Using expression profiling, we have identified innate immune genes that have conserved regulation between mice and humans, as well as those that are divergent. This project will explore the function of innate immune genes that display human-specific regulation.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
PROFESSOR STEPHEN TAYLOR School of Biomedical Sciences
Phone: 07 3365 3124 Email: [email protected]
Drug Discovery and Development A major problem in clinical medicine is the effective treatment of many cruel diseases. Many of the worst human ailments concern disorders of the immune and inflammatory systems, where the body seemingly attacks its own tissues. The treatments for these kinds of disorders are limited, or toxic, or just plain ineffective. Some of these diseases can kill in just a few days, some may slowly kill or disable over years or even decades. The human suffering is incalculable and progress seems negligible.
In Dr Taylor’s laboratory, new classes of anti-inflammatory drugs are being developed, in collaboration with chemists at the IMB (Professor David Fairlie’s group). We have successfully discovered and developed orally active complement C5a antagonists and phospholipase A2 inhibitors. The C5a antagonist project has led to the formation of the spin-off company, Promics Pty Ltd, and the filing of several key patents.
Projects are available for students to work on the preclinical pharmacology of lead compounds or with new analogues. The work entails cellular, biochemical and whole animal studies, and is aimed at determining the pharmacological activity of these new agents.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR HANG TA Australian Institute for Bioengineering and Nanotechnology (AIBN) School of Pharmacy The University of Queensland, Brisbane, Australia
Phone: +61 7 3346 3851 Email: [email protected]
Did you know that cardiovascular disease is the greatest health problem globally. It kills more people than any other disease and creates enormous costs for the health care system. It places a heavy burden on individuals and the community due to resulting disabilities. Our group is working on different approaches to improve diagnosis and treatment of these diseases. We are located within Australian Institute for Bioengineering and Nanotechnology (AIBN) and has access to state-of-the-art facilities in bioengineering/biotechnology and nanotechnology. AIBN offers a dynamic research environment and is home to world-class researchers working at the interface of the biological, chemical and physical sciences. Current projects available include:
1. Cardiovascular diseases on the chip Every newly developed drug need to be tested through numerous rounds of animal testing before they can be tested on human. However, a rodent or chimp’s response to a medication does not alsway translate smoothly in a person. This project aims to develop chips that mimics the biological processes of cardiovascular diseases, which allows testing new therapies freely on “subjects” without harming any living creatures and lessen the need for animal testing.
2. Thrombolytic nanomaterials to dissolve blood clots Thrombotic and embolic events such as myocardial infarction and stroke remain a major health issue and are leading causes of mortality and morbidity in Australia and worldwide. This project aims to develop novel thrombolytic nanomaterials to dissolve blood clots and restore the blood flow in life-threatening events caused by thrombosis.
3. Smart nano-sensors for detecting and grading cardiovascular diseases The early detection and accurate characterization of life-threatening diseases such as cardiovascular disease and cancer are critical to the design of treatment. This project will develop smart magnetic resonance imaging and optical nano-sensors that can not only detect, but also sense and report the stage or progression of cardiovascular diseases such as thrombosis, the leading cause of death in Australia and worldwide. Innovative reversible blood clotting agents for emergency treatment of internal bleeding Currently, there is a lack of effective therapeutics for internal bleeding following a traumatic event. In this project, novel reversible blood clotting nanomaterials will be designed to be able to hunt for internal injuries and bleeding and then stop the bleeding quickly.
4. Novel nanomaterials for theranostics of diseases such as cardiovascular disease and inflammatory disease Inflammation is part of the complex biological response of body tissues to harmful stimuli, such as pathogens, damaged cells, or irritants. Chronic inflammation might lead to a host of diseases, such as hay fever, periodontitis, atherosclerosis, rheumatoid arthritis, and even cancer. This project will investigate novel approaches to develop nanomaterials which combine both therapeutic and diagnostic capabilities for these diseases in one dose.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR SIMON WORRALL School of Chemistry & Molecular Biosciences
Phone: 07 3365 4626 Email: [email protected]
Mechanisms of Drug-Induced Tissue Injury Liver, muscle, heart and brain injury have long been associated with the abuse and clinical use of drugs.
My research interests focus on ethanol, perhaps the most commonly abused drug. Ethanol is widely tolerated but induces tissue injury in a small number of individuals. The potential research projects listed below will investigate immunological and genetic phenomena associated with alcohol-induced tissue injury.
The potential projects available are: 1. Studies on the aetiology of ethanol- induced tissue injury to liver, skeletal and cardiac muscle, and brain?
2. Is protein modification by ethanol metabolites involved in the aetiology of: a. Alcoholic liver disease? b. Alcoholic skeletal and cardiac myopathy? c. Alcoholic brain injury (with Peter Dodd)?
3. Novel protein modifications induced by ethanol metabolism (with Prof Craig Williams, chemistry)
4. Discovery of molecular markers for the severity of Alzheimer’s disease.
(Top):A reaction scheme showing the formation of malondialdehyde-acetaldehyde adducts.
(Left):Expression of GFP-tagged human keratin 18 in a primary rat hepatocyte.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
PROFESSOR PAUL YOUNG Head of School
Virology Unit School of Chemistry & Molecular Biosciences
Phone: 07 3365 4646 Email: [email protected]
Dr Young’s group is focused on the molecular biology and immunopathology of viral infections. The primary goals of this research are to gain a clearer understanding of the pathogenesis of severe disease as well as the development of novel vaccine and anti-viral strategies for the control of infections and improved molecular diagnosis. Our laboratory has expertise in the areas of molecular biology, cell biology, structural biology, protein biochemistry and immunology. Additional projects are likely to be available on discussion.
Project 1-Development of a dengue virus DNA vaccine based on a novel chimeric form of an immunogenic viral protein. We have been investigating sub-unit and DNA based vaccine strategies for the dengue viruses for some years. Many of these have been based on expression of the immunogenic NS1 protein and we have successfully demonstrated sold protection against viral challenge using a prime-boost approach using a combination of DNA and recombinant sub-unit protein. We wish to expand our array of immunogenic species through the inclusion of a novel chimeric construct that would provide protection against all four serotypes of dengue virus. The project will involve the PCR amplification, cloning and expression as a single fusion protein of domains from all four dengue virus serotypes. Both E.coli and recombinant baculovirus expression will be examined. If time permits, the expressed product will be trialled in a vaccine/challenge study.
Project 2-Development of a novel epitope tagging system for purification of recombinant fusion proteins. This project would suit a student interested in biotechnology applications of molecular biology. We have identified the linear amino acid sequences recognized by a series of high affinity monoclonal antibodies. We want to test whether the fusion of these short peptide epitopes to foreign proteins can aid in their purification via immuno-affinity chromatography – a well established tool in biotechnology research and development. These epitopes are derived from the dengue virus NS1 protein and the student will be involved initially in generating reporter gene constructs fused to these epitopes in order to examine their suitability as epitope tags. Further studies with defined foreign genes will be examined time permitting.
Project 3-Site-directed mutagenesis and recombinant expression of the dengue virus NS1 protein. The NS1 protein of dengue virus is essential for the replication of the virus at the RNA level. It is also secreted from infected cells and is the target of a protective immune response. Paradoxically, it also appears to be directly involved in the pathogenesis of infection. We have 132 been studying the structure and biophysical features of NS1 for some time in order to help elucidate its exact function and these studies are ongoing. This project will fit in with these studies and involve the cloning and expression of sub-domains of NS1 as well as site-directed mutagenesis to identify key residues involved in the cell membrane-association that is thought
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR ADRIAN WIEGMANS Queensland Institute of Medical Research (QIMR)
Phone: 07 3362 0339 Email: [email protected]
Deciphering the molecular mechanisms of metastasis to design new-targeted therapies for breast cancer. The transformation of normal breast tissue to tumor requires the accumulation of mutations, which is readily achieved by deregulation of DNA repair pathways. We found that metastatic breast cancers have high levels of the DNA repair protein RAD51. Metastatic breast cancer represents a subtype that has poor clinical outcome and RAD51 contributes to this. We have determined that reducing RAD51 levels in aggressive breast cancers results in reduced metastatic growth and sensitivity to chemotherapy. RAD51 supports metastasis via a role in stabilizing cancer genomes however RAD51 also augments metastatic potential through other mechanisms. These include changes in actin dynamics and changes in gene metastatic expression profiles via mechanisms that have yet to be fully elucidated. We believe that other DNA repair proteins could also harbour these roles. Outcomes from these analyses will provide new potential clinical targets in treating metastatic breast cancer.
Individual research projects for developing new therapeutic targets will have a focus around one of the following models;
Actin dynamics and metastasis: We find that DNA repair proteins affect actin dynamics, cell morphology and thus the migration and invasion properties of cancer cells. This determines the metastatic potential of the cancer and could be targeted to inhibit metastatic spread of cancer.
Transcriptional regulation of metastasis: DNA repair proteins also change the profile of pro-metastatic gene expression via unknown mechanisms. The ability of DNA repair proteins to bind DNA and simultaneously bind transcription factors, mean they have the capability to direct gene expression. This is a new function for this class of proteins.
Animal models of metastasis: We are developing new models of metastasis to test new anti-metastatic drugs developed in the lab. We are looking to mimic human diseases, with spontaneous metastasis of breast cancer to specific organs.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR STEFANO FREGUIA Centre for Microbial Electrosynthesis Advanced Water Management Centre
Phone: 07 3346 3221 Email: [email protected]
My research is at the interface between microbial biotechnology and electrochemistry, an area known as microbial electrochemistry, which has seen a research boom in the last decade. Electrochemically active bacteria are ubiquitous in nature and are capable of direct and mediated electron transfer to extracellular insoluble electron acceptors, including mineral oxides and positively polarised electrodes. Some of these bacteria are also capable of electron transfer in the opposite direction, i.e. from insoluble electron donors (e.g. metals, elemental sulfur and negatively polarised electrodes) to soluble electron acceptors. These bacteria can be exploited for a number of biotechnological processes, including wastewater treatment with simultaneous electricity production (microbial fuel cells), reductive removal of water pollutants using electricity instead of chemicals, and the concentration of valuable products from wastewater through the use of ion-selective membranes. In particular, these systems can be used to recover precious nutrients from wastewaters. Currently, these nutrients are either discharged in dilute form into the environment or destroyed in energy-intensive wastewater treatment processes. Their recovery and reuse is an important step towards sustainable resource management. We have currently two projects in this area that are suitable for honour or master thesis students.
Project 1: Nutrient recovery from source-separated urine using a microbial fuel cell. Urine is an ideal substrate for a microbial fuel cell, as a consequence of its high organic content, high salinity and high buffering capacity. Preliminary results have already shown that the organic compounds present in urine can be effectively oxidised to carbon dioxide at a microbial anode, with concomitant electricity generation. In this project, the aim is to prove the concept of a three-compartment microbial fuel cell to simultaneously achieve (i) complete treatment of urine and (ii) recovery of valuable nutrients (primarily nitrogen, phosphorus and potassium) in the form of a salt.
Project 2: Development of a high-rate microbial biocathode for oxygen reduction. For any microbial fuel cell to succeed, a strong cathodic process needs be in place to consume the electrons liberated at the anode. Oxygen is the most suitable electron acceptor in light of its wide availability and high redox potential. The aim of this project is to establish and fully characterise a microbially catalysed oxygen reduction process at a cathode. A number of electrode materials will be tested with mixed microbial cultures supplied only with air and minimal nutrients.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
PROFESSOR RICHARD LEWIS Group Leader, Chemistry and Structural Biology Division Director, Centre for Pain Research
Phone: 07 3346 2984 Email: [email protected]
My groups current research focus on the evolution and pharmacology of venom peptides, especially those useful for the treatment of chronic pain. This research is at the cutting edge of venom research internationally. I can offer projects in two broad areas of venom research:
1. In depth computational analysis on cone snail venoms using integrated proteomics and transcriptomics (venomics) to understand the diversity of cone snail venom peptides and how they contribute to the evolution of distinct predatory and defensive venoms.
2. Discovery and pharmacological characterisation of venom peptides acting at ion channels, GPCRs or transporters, especially those with potential to selectively inhibit or activate pain pathways.
Selected references (PLEASE see my Google Scholar profile for more details): 1. Klint JK, Smith JJ, Vetter I, Rupasinghe DB, Er SY, Senff S, Herzig V, Mobli M, Lewis RJ, Bosmans F, King GF (2015) Seven novel modulators of the analgesic target NaV1.7 uncovered using a high-throughput venom- based discovery approach. Br J Pharmacol. 172:2445-2458. 2. Dutertre S, Jin A-H, Vetter I, Hamilton B, Sunagar K, Lavergne V, Dutertre V, Fry BG, Antunes A, Venter DJ, Alewood PF, Lewis RJ (2014) Evolution of separate predation- and defence-evoked venoms in carnivorous cone snails. Nature Communications 5:3521. 3. Dutertre S, Jin AH, Kaas Q, Jones A, Alewood PF, Lewis RJ (2013) Deep venomics reveals the mechanism for expanded peptide diversity in cone snail venom. Mol Cell Proteomics 12:312-329. 4. Lewis RJ, Dutertre, S, Vetter I, Christie MC (2012) Conus venom peptide pharmacology. Pharmacol. Reviews 60:259-298.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR ZYTA ZIORA Senior Research Officer Institute for Molecular Bioscience
Phone: 07 3346 2067 Email: [email protected]
Workshops and interests: • Writing reviews • ITC (isothermal titration microcalorimetry) • Drug design, action mode, peptide and peptidomimetics chemistry • Thermodynamics of metal ions/antibiotics complexes
General Research Outline • Improving antibiotic potency by complexing with metal ions. • Skin treatment for bacterial infection, burns, injury, inflammation, cancer prevention.
Current research projects 1. Enhancement of bio-compounds activity through complexation with metal ions. 2. Metalodrugs and Natureceuticals: alternative treatments for topical skin problems. 3. Wine tannins, physico-chemical characterization and bio-activity. 4. Bacterial sortase: application to improve antibacterial potency.
Collaboration with: • Project 1 – University of Heidelberg, Germany/UQCCR, UQ. • Project 2 – UQ Oral Health Centre, OHC, School of Dentistry/ Griffiths University. • Project 3 – Edenvale, Australian company/OHC, UQ. • Project 4 – Pharmacy Australia Centre of Excellence, PACE, School of Pharmacy.
Selected Recent Publications: - Mital M., Ziora Z, Biological applications of Ru(II) polypyridyl complexes, Coordination Chemistry Reviews, 2018, accepted. - Naseri-Nosar M., Ziora Z. M., Wound Dressings from Naturally-occurring Polymers: A Review on Homopolysaccharide-based Composites Carbohydrate Polymers, Carbohydrate Polymers, 2018, accepted. - Blaskovich M.A.T., Gong Y., Hansford K., Butler M.S., Muldoon C., Huang J. X., Ziora Z., Premraj R., Ramu S., Silva A., Cheng M., Kavanagh A., Bradford T, Karoli T., Lindahl F., Lee J., Pelingon R., Edwards D., Huda Daud N., Deecke J.E., Sidjabat H.E., Ramaologa S., Zuegg J., Betley J.R., Beevers A.P.G., Smith R.A.G., Roberts J.A., Paterson D.L., Cooper M.A. Protein inspired antibiotics active against vancomycin and daptomycin resistant bacteria, Nature Communication, 2017, DOI: 10.1038/s41467-017-02123-w. - Zhou Hang, Matthew A. Cooper, Zyta M. Ziora, Platinum-based anticancer drugs encapsulated liposome and polymeric micelle formulation in clinical trials, Biochemical Compounds, 2016, 4, 1-10. - McRae, J. M.; Ziora Z. M.; Kassara, S.; Cooper, M.A.; Smith, P. A. Ethanol concentration influences the mechanisms of wine tannin interactions with poly(L-proline) in model wine, J. Agriculture Food Chem., 2015, 63, 4345−4352. - Ziora, Z.; Skwarczynski, M.; Kiso, Y. Medicinal chemistry of a-hydroxy-b-amino acids. In Andrew B. Hughes (Ed.), Amino Acids, Peptides and Proteins in Organic Chemistry: Volume 4 - Protection Reactions, Medicinal Chemistry, Combinatorial Synthesis Weinheim, Germany: Wiley. 2011, pp. 189-234. 81
SCMB Biotechnology Research Projects 2018 | Individual Contributors
Queensland Alliance for Agriculture and Food Innovation
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR INIGO AUZMENDI Research Fellow Centre for Horticultural Science Queensland Alliance for Agriculture and Food Innovation
Phone: +61 7 3365 8234 Email: [email protected]
DR JIM HANAN Centre for Horticultural Science Queensland Alliance for Agriculture and Food Innovation
Phone: 07 3365 1858 Email: [email protected]
Dr. Inigo Auzmendi, Dr. Jim Hanan Using virtual plants to simulate photosynthesis in horticultural plants Plants assimilate the carbon required for maintenance and growth through photosynthesis. Estimating photosynthesis is not straightforward in horticultural plants with a complex canopy structure like avocado, macadamia and mango, because individual leaves within the canopy present different photosynthetic characteristics. Therefore, different approaches to simulate photosynthesis could result into different estimates of carbon assimilation. This project will involve the use of virtual plants to simulate photosynthesis of individual leaves and whole canopy with specific management practices like mechanical hedging or topping, planting density and tree shape. The results of these simulations will be used to evaluate several biochemical and physiological photosynthesis models under various management conditions. The final goal is to determine on each case the most adequate photosynthesis model, and propose new approaches if necessary.
Dr. Jim Hanan, Dr. Inigo Auzmendi Towards better fruit and nut yields: Understanding tree architecture and its effects on light distribution This project will take a computational modelling approach to understanding the dynamics of tree architecture in a selected tropical or sub-tropical fruit or nut tree species. After reviewing what is known about the flushing and branching of the selected species, data on tree architecture will be employed or collected if necessary, and a virtual plant model will be developed. This virtual plant model will be used to evaluate light distribution patterns at different planting density and tree training systems.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR FEMI AKINSANMI Queensland Alliance for Agriculture and Food Innovation Ecosciences Precinct, Boggo Road, Dutton Park
Phone: 07 3255 4338 Email: [email protected]
ASSOCIATE PROFESSOR ANDRE DRENTH Queensland Alliance for Agriculture and Food Innovation Ecosciences Precinct, Boggo Road, Dutton Park
Phone: 07 3255 4338 Email: [email protected]
Phylogenetic analysis of Pseudocercospora macadamiae Our previous study with PCR-RFLP has identified six genotypes in P. macadamiae populations from three geographical areas in Australia. This study will evaluate the phylogenetic relationship between isolates of P. macadamiae obtained from different cultivars in all the macadamia producing regions of Australia. Selected genes will be used to study sequence divergence among the P. macadamiae isolates and Pseudocercospora species. Sequence analysis will help to detect more fine scale genotypic diversity among P. macadamiae and enable a direct comparison of the species causing husk spot in macadamia and leaf spots in other hosts in Australia.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR FEMI AKINSANMI Queensland Alliance for Agriculture and Food Innovation Ecosciences Precinct, Boggo Road, Dutton Park
Phone: 07 3255 4338 Email: [email protected]
Microbial composition of macadamia husk Macadamia husks are lignocellulosic materials therefore, microorganisms including fungi as well as actinomycetes and other bacteria are able to colonise the tissue. Some of these microbes are important in bio-decomposition of the materials or other essential biological functions. This study will elucidate the microbial community dynamics on macadamia husks in relation to seasonality, fruit age and positional canopy height of the tree.
AVAILABLE FROM 2016 SEM 2 AND 2017 SEM 1
Characterisation and diagnostics of blossom blight in macadamia Raceme blight also known as blossom or flower blight and grey mould are used to describe various diseases and disorders of macadamia flowers. Different fungi and oomycetes have been reported as causal agents of blossom blight in macadamia. In spite of distinct and remarkable differences in the pathogens, there is still lack of adequate knowledge of the symptom development and disease epidemiology for each pathogen-host interaction. This study will examine the etiology of the disease and establish the epidemiological conditions necessary for infection. The scholar will use plant pathology research techniques and gain advanced plant science and molecular skills. It is expected that the scholar will contribute to publications from the research. Useful references: Phytopathology (1972) 62: 316-319; (1976) 66: 546-548
Development of LAMP assay to detect husk spot Husk spot is a unique disease of macadamia in Australia. The disease leads to premature abscission of macadamia nut. Existing conventional or traditional diagnostic method for husk spot is laborious and takes 4-6 weeks. Lack of diagnostic tool for early detection of infection before symptom expression hinders studies on infection process. Therefore, the aim of this study is to improve the detection and quantification of husk spot infection. The study will develop a simple and rapid diagnostic tool using the loop mediated isothermal amplification (LAMP) assay for early detection and characterisation of macadamia cultivars. The scholar will use existing DNA sequence data for husk spot fungus isolates to develop the LAMP assay. Scholars will gain advanced plant science and molecular skills and contribute to publications from the research. Useful references: Australasian Plant Pathology (2009) 38: 36-43; International Journal of Food Microbiology (2010) 140 183-191.
How many Botryosphaeriaceae fungi are there in macadamia? Botryosphaeriacae fungi are of significant economic importance. They are major pathogens in several plant hosts in temperate, tropical and subtropical crops including macadamia, an Australian native plant. Many names based on morphological and host association are used to distinguish the species complex. However, these are mostly inaccurate. This project proposes to identify and classify the isolates, and based on molecular phylogenetic evidence, reveal distinct and new taxa in this species complex. This project will identify species within the family Botryosphariaecae that are associated with macadamia. The overall aim of the study is to determine if species of the Botryosphariaecae are able to inhabit macadamia tissues as ‘non- pathogenic’ fungi. The scholar will use general plant pathology research techniques including molecular tools to test the research hypotheses. Scholars will gain advanced plant science and molecular skills and contribute to publications from the research. Useful references: Australasian Plant Pathology (2009) 38: 36-43; International Journal of Food Microbiology (2010) 140 183-191. 85
SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR FEMI AKINSANMI Queensland Alliance for Agriculture and Food Innovation Ecosciences Precinct, Boggo Road, Dutton Park
Phone: 07 3255 4338 Email: [email protected]
DR BRUCE TOPP Queensland Alliance for Agriculture and Food Innovation Ecosciences Precinct, Boggo Road, Dutton Park
Phone: 07 5453-5973 Email: [email protected]
Response of species and cultivars of Macadamia to Phytophthora cinnamomi Our previous study suggests that macadamia is tolerant to Phytophthora cinnamomi, however, in certain conditions the soilborne pathogen is able to cause significant damage to macadamia. This study will evaluate the resistance/susceptibility of Macadamia species and commercial cultivars to root rot and stem canker caused by P. cinnamomi.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
ASSOCIATE PROFESSOR ELIZABETH AITKEN School of Agriculture and Food Sciences St Lucia campus, The University of Queensland
Phone: (07) 3365 4775 Email: [email protected]
DR LEE HICKEY Queensland Alliance for Agriculture and Food Innovation
Phone: (07) 3365 4805 Email: [email protected]
Simultaneous selection for resistance to crown rot and foliar diseases in barley Crown rot, caused by the pathogen Fusarium pseudograminearum, is an important disease of winter cereals such as wheat and barley. This project aims to develop a high-throughput phenotypic screening assay that enables simultaneous selection for resistance to crown rot and foliar diseases (e.g. leaf rust caused by Puccinia hordei Otth., and spot form of net blotch caused by Pyrenophora teres f. maculate) in segregating populations of barley grown under controlled environmental conditions. The screening assay will incorporate rapid generation advance techniques for the purpose of accelerating breeding cycles. Outputs of the Honours research project will be: 1) new screening methodology, 2) improved knowledge of the genetic control of resistance to crown rot in barley, and 3) germplasm enriched for the target traits, which will be a useful resource for further breeding efforts in Australia. The student will gain hands-on experience in pathology, plant breeding and genetics.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR KARINE CHENU Queensland Alliance for Agriculture and Food Innovation (Toowoomba – Gatton)
Phone: 07 4688 1357 Email: [email protected]
Understanding the basis of transpiration efficiency in wheat Wheat productivity is limited by the amount of biomass that plants can produce for the limited water supply they can access. Existing conditions in Australia and future predictions for increased temperature, evaporative demand and water scarcity enhance the need for higher transpiration-efficiency crops (“more crop per drop”). To breed for new wheat varieties with increased transpiration efficiency, the physiological responses of transpiration rate to environment need to be better understood. This work will use the new state-of-the-art UQ-Gatton lysimeter facility to investigate whole-plant and leaf-level transpiration rate and efficiency of contrasting wheat genotypes, and to characterise their response to evaporative demand and soil water status.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR SUSHIL DHITAL Centre for Nutrition and Food Sciences (CNAFS) Queensland Alliance for Agriculture and Food Innovation (QAAFI) ARC Centre of Excellence in Plant Cell Walls Room S426, Hartley Teakle Building, The University of Queensland
Phone: 07 334 67373 Email: [email protected]
Bakery products such as biscuits, cakes and breads are widely consumed processed foods in western society. The major ingredients in bakery products are wheat flour, the other ingredients being fat, sugar etc. On consumption of bakery products, the starch in wheat flour is rapidly digested increasing the postprandial blood glucose level, which might have a negative health effect and is often associated with type II diabetes. This project aims to formulate low fat and low sugar bakery products incorporated with enzyme resistant starch (ERS) and investigate the textural attributes of the baked products as well as change in morphological and micro structure of starches in bakery products.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
ASSOCIATE PROFESSOR RALF DIETZGEN QUEENSLAND ALLIANCE FOR AGRICULTURE AND FOOD INNOVATION (QAAFI) Phone: 07 334 66503 Email: [email protected] Web: http://www.qaafi.uq.edu.au//?page=157981
Molecular plant-virus-vector interactions My research interests are in the discovery and biodiversity of genes, proteins and regulatory RNAs in plants, viruses and vector insects, and their molecular interactions in agricultural systems. Increased knowledge of these interactions will enable improved crop performance and better pest and disease control. Special interests include the characterization of plant rhabdoviruses and tospoviruses, virus diagnosis, taxonomy and molecular evolution, RNA silencing pathways for pest and disease resistance, and genome-wide molecular genetic responses to virus infection.
Research Project areas Negative-sense RNA viruses belong to complex families of established and emerging viruses that infect plants and animals. (1) The genome organization of novel plant rhabdoviruses will be determined to improve classification, diagnosis and phylogeny. (2) Genetic diversity of virus isolates will be studied aimed at establishing evolutionary trajectories and understanding symptom development. (3) RNA interference-mediated defenses to plant virus infection will be characterized by live plant cell imaging using advanced protein-protein interaction techniques and laser scanning confocal microscopy. (4) Plant – virus - insect molecular interactions will be revealed by plant and insect transcriptome analysis, quantitative RT-PCR and circular RNA analysis. (5) Expression of tick serpins in plants to determine potential effects on pests and pathogens.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
ASSOCIATE PROFESSOR RALF DIETZGEN CILR, John Hines Building and QAAFI, Ritchie Bldg, UQ St Lucia Campus
Phone: 07 3346 6503 Email: [email protected]
DR PAUL SCOTT CILR, John Hines Building and QAAFI, Ritchie Bldg, UQ St Lucia Campus
Phone: 07 3346 6206 Email: [email protected]
PROFESSOR PETER GRESSHOFF CILR, John Hines Building and QAAFI, Ritchie Bldg, UQ St Lucia Campus
Phone: 07 3365 3550 Email: [email protected]
Identification & characterization of viruses that infect the biofuel tree Pongamia pinnata Plant functional genomics research can benefit greatly from high throughput silencing of genes to determine their function(s) during development and defense against abiotic and biotic stress. Replicating viruses are efficient inducers of RNA silencing in plants and have been used extensively to silence plant genes in Arabidopsis, legumes, cereals and some horticultural crops. This project aims to identify and characterize viruses that infect P. pinnata trees to subsequently construct suitable viruses into virus-induced gene silencing (VIGS) vectors to allow functional genomic studies. Symptomatic and asymptomatic leaves will be collected from diverse locations and samples analysed by dsRNA extraction and gel electrophoresis analysis and by next generation high-throughput sequencing of total RNA.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR ANDREW GEERING Queensland Alliance for Agriculture and Food Innovation Ecosciences Precinct, Boggo Road, Dutton Park
Phone: 07 32554389 Email: [email protected]
ASSOCIATE PROFESSOR JOHN THOMAS
Phone: 07 3255 4393 Email: [email protected]
Towards a better understanding of how plant pararetroviruses process proteins Banana streak virus (BSV) is a representative of the only group of pararetroviruses in plants. BSV is distantly related to Human immunodeficiency virus (HIV) although it is only infects plants. BSV has a simple replication strategy, producing the majority of the proteins it needs on one large polyprotein, which is then cleaved into functional units through the action of a virus-encoded aspartic protease. Retroviral aspartic proteases (APs) are unusual in that it is impossible to predict their substrate preferences through sequence analysis alone and cleavage sites must be predicted empirically. Recently, in our laboratory, we have determined the boundaries of the BSV capsid protein and using this information, made some predictions as to where the AP is cleaving. The next step in this line of research, which is the topic of this project, is to express the BSV AP in vitro and demonstrate cleavage using synthetic peptides as substrates.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
ASSOCIATE PROFESSOR MARY FLETCHER Health and Food Sciences Precinct, Coopers Plains
Phone: 07 344 32479 Email: [email protected]
The risk of pyrrolizidine alkaloids in honey. Pyrrolizidine alkaloids are natural toxins/carcinogens present in approximately 3 percent of flowering plants. Internationally it has been reported that such toxins can be found in honey due to transfer from the plants, by bees, via pollen and nectar. This project will utilise liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology to investigate the presence/identity of such alkaloids in Queensland honey samples. Students will gain experience in sample preparation and extraction for LCMS analysis of market survey honey samples and will gain experience in data analysis of LC-MS/MS results. A background in chemistry with some knowledge of mass spectrometry is essential for this project, as well as an interest in applying such skills to a common condiment/sweetener.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR JIM HANAN Centre for Horticultural Science Queensland Alliance for Agriculture and Food Innovation
Phone: 07 3365 1858 Email: [email protected]
Small Trees, High Productivity: Understanding tree molecular physiology This project will take a computational modeling approach to understanding the dynamics of molecular physiology behind tree development. The ultimate aim is to intensify tropical orchards for species such as macadamia, mango or avocado. After reviewing what is known about molecular level aspects of flushing and flowering of the selected species, a structural model incorporating molecular and hormonal signalling will be used to explore the interactions and consequences of hypotheses of interest.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
DR JIM HANAN Centre for Horticultural Science Queensland Alliance for Agriculture and Food Innovation
Phone: 07 3365 1858 Email: [email protected]
DR CHUNG-CHI(ALEX) WU Postdoctoral Researcher, ARC Centre of Excellence for Translational Photosynthesis Queensland Alliance for Agriculture and Food Innovation Phone: 07 3346 2780 Email: [email protected]
Using models of crop canopy light absorption to estimate the effects of agronomical practices on crop growth Radiation from the sun absorbed by crop canopies drives leaf photosynthesis, which in turn drives crop growth, development and yield. As the first part of this project, the student will conduct a comparative study between similar, but differing in level of detail, approaches for modelling canopy light absorption. Simpler modelling approaches are efficient and robust for field crops, such as wheat or sorghum monocultures, while more detailed approaches are deemed necessary for orchard crops, such as mango, avocado or macadamia. Agronomical practices, such as planting density and pruning, can modify canopy light absorption by opening up crop canopies to allow more light penetration through the canopy. Effects of these canopy manipulations may be estimated with detailed modelling approach, but may not be the most efficient for long-term simulations. In the second part of this project, the student will have the opportunity to develop balanced and efficient models by combining the simpler and more detailed approaches and demonstrate that the new model can be applied to both field and orchard crops. Lastly, investigate ways of how knowledge gained from this project can be used to better inform agronomical decisions for improving crop productivity.
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
PROFESSOR ALA TABOR Centre for Animal Science, QUEENSLAND ALLIANCE FOR AGRICULTURE AND FOOD INNOVATION
Phone: 07 3346 2176 Email: [email protected]; URL: https://qaafi.uq.edu.au/profile/492/ala-tabor
Prof Ala Tabor joined QAAFI's Centre for Animal Science in October 2010, after 18 years of conducting research with the Queensland Government. She is a research focussed academic with a strong background in industry engagement associated with animal health and translational research outcomes. Her research interests are associated with the application of genomic sequence data to improve animal disease management through: 1) the development of molecular diagnostic and genotyping methods to better identify pathogens; and 2) the study of gene function in relation to virulence and host pathogenicity of infectious diseases, to develop new effective vaccines. Areas studied to date include bovine reproductive diseases (in particular bovine genital campylobacteriosis), Australian paralysis tick (Ixodes holocyclus), cattle tick (Rhipicephalus microplus species complex), and tick-borne diseases (babesiosis and anaplasmosis). Some key outputs of her work include the application of reverse vaccinology for the development of a novel tick vaccines (patents pending) and commercialized diagnostic tools for bovine reproductive diseases. Future research interests available for student research projects include (students are encouraged to discuss options associated with specific interests):
1) Omic approaches to examine skin immunity to cattle ticks – proteomics and transcriptomics – biomarker development 2) Investigating the ‘pathobiome’ of northern cattle for improved fertility through improved diagnostics (point-of-care test development) and host biomarkers 3) ‘Proof of concept’ animal trials for new tick vaccines with commercial partners (ELISA, sequencing, cattle trials, tick monitoring) 4) Omics of ticks
SELECTED RECENT PUBLICATIONS:
1) Tabor, A.E., Ali, A., Rehman, G., Rocha Garcia, G., Zangirolamo, A.F., Malardo, T., Jonsson, N.N. (2017) Cattle Tick Rhipicephalus microplus-Host Interface: A Review of Resistant and Susceptible Host Responses. Front. Cell. Infect. Microbiol., 11 December 2017. https://www.frontiersin.org/articles/10.3389/fcimb.2017.00506/full 2) Rodriguez-Valle, M., Moolhuijzen, P., Barrero, R.A., Ong, C.T., Busch, G., Karbanowicz, T., Booth, M., Clark, R., Koehbach, J., Ijaz, H., Broady, K., Agnew, K., Knowles, A.G., Bellgard, M.I., Tabor, A.E. (2017) Transcriptome and toxin family analysis of the paralysis tick, Ixodes holocyclus. Int. J. Parasitol. 6 October 2017. https://www.sciencedirect.com/science/article/pii/S0020751917302849 3) Lew-Tabor, A.E., Rodriguez Valle, M. (2016). A review of reverse vaccinology approaches for the development of vaccines against ticks and tick borne diseases. Ticks Tick-borne Dis. 7: 573-585. http://www.sciencedirect.com/science/article/pii/S1877959X15300534 4) De la Fuente, J., Kopáček, P., Lew-Tabor, A., Maritz-Olivier, C. (2016) Strategies for new and improved vaccines against ticks and tick-borne diseases. Parasite Immunol. 38: 754-769.
http://onlinelibrary.wiley.com/doi/10.1111/pim.12339/full
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
EDUCATION/ BUSINESS/ MARKETING PROJECTS
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SCMB Biotechnology Research Projects 2018 | Individual Contributors
PROFESSOR ALA TABOR Centre for Animal Science, QUEENSLAND ALLIANCE FOR AGRICULTURE AND FOOD INNOVATION
Phone: 07 3346 2176 Email: [email protected]; URL: https://qaafi.uq.edu.au/profile/492/ala-tabor
DR MARINA FORTES
Phone: 07 3365 4258 Email: [email protected] W: http://staff.scmb.uq.edu.au/staff/marina-fortes
Project 1: Market Research for proposed “Biotechnology in Agriculture” Course. “Students undertaking this project will carry out market research, in order to assess likely demand for the proposed new biotechnology course “Introduction to Biotechnology in Agriculture”. The market research will inform which parts of the world such course demand is likely to come. The project will entail development of a questionnaire to be used in a market research survey. It will also entail literature based research on likely areas of demand, and investigation of other similar courses that are offered at other institutions around the world. The project will also develop skills in questionnaire design, implementation of a survey, statistical analysis of data, and data presentation in oral and written modes.”
The project will be supervised by Prof. Ala Tabor & Dr. Marina Fortes.
Project 2: Market Research for proposed “Biotechnology in Livestock Production” Course. “Students undertaking this project will carry out market research, in order to assess likely demand for the proposed new biotechnology course “Biotechnology in Livestock Production”. The market research will inform which parts of the world such course demand is likely to come. The project will entail development of a questionnaire to be used in a market research survey. It will also entail literature based research on likely areas of demand, and investigation of other similar courses that are offered at other institutions around the world. The project will also develop skills in questionnaire design, implementation of a survey, statistical analysis of data, and data presentation in oral and written modes.”
The project will be supervised by Dr. Marina Fortes & Prof. Ala Tabor.
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