Swinburne University of Technology View Institution's Website 10 articles published in JoVE Biochemistry Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling Vito M. Butardo Jr.1, Christiane Seiler2, Nese Sreenivasulu3, Markus Kuhlmann2 1Department of Chemistry and Biotechnology, Swinburne University of Technology, 2Department of Molecular Genetics, Heterosis Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 3Grain Quality and Nutrition Center, Applied Functional Genomics Cluster, International Rice Research Institute A method for transcriptome profiling of cereals is presented. The microarray-based gene expression profiling starts with the isolation of high-quality total RNA from cereal grains and continues with the generation of cDNA. After cRNA labelling and microarray hybridization, recommendations are given for signal detection and quality control. Environment Combining Eye-tracking Data with an Analysis of Video Content from Free-viewing a Video of a Walk in an Urban Park Environment Marco Amati1,2, Chris McCarthy3, Ebadat Ghanbari Parmehr4, Jodi Sita5 1Visiting Professor, Dipartimento di Scienze Agro-Ambientali e Territoriali, Università degli Studi di Bari, 2Centre for Urban Research, Royal Melbourne Institute of Technology (RMIT University), 3School of Software and Electrical Engineering, Swinburne University of Technology, 4Faculty of Civil Engineering, Babol Noshirvani University of Technology, 5School of Science, Australian Catholic University The objective of the protocol is to detail how to collect video data for use in the laboratory; how to record eye-tracking data of participants looking at the data and how to efficiently analyze the content of the videos that they were looking at using a machine learning technique. Biology Confocal Microscopy Reveals Cell Surface Receptor Aggregation Through Image Correlation Spectroscopy Adam C. Parslow1,2, Andrew H.A. Clayton3, Peter Lock4, Andrew M. Scott1,2,5,6,7 1Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, 2School of Cancer Medicine, La Trobe University, 3Centre for Micro-Photonics, Faculty of Science, Engineering and Technology, Swinburne University of Technology, 4LIMS Bioimaging Facility, La Trobe Institute for Molecular Science, La Trobe University, 5Department of Medical Oncology, Olivia Newton-John Cancer and Wellnes Centre, Austin Health, 6Department of Medicine, University of Melbourne, 7Department of Molecular Imaging and Therapy, Austin Health Antibodies that bind to target receptors on the cell surface can confer conformation and clustering alterations. These dynamic changes have implications for characterizing drug development in target cells. This protocol utilizes confocal microscopy and image correlation spectroscopy through ImageJ/FIJI to quantify the extent of receptor clustering on the cell surface. Engineering Generation and Coherent Control of Pulsed Quantum Frequency Combs Benjamin MacLellan*1, Piotr Roztocki*1, Michael Kues1,2, Christian Reimer1, Luis Romero Cortés1, Yanbing Zhang1, Stefania Sciara1,3, Benjamin Wetzel1,4, Alfonso Cino3, Sai T. Chu5, Brent E. Little6, David J. Moss7, Lucia Caspani8, José Azaña1, Roberto Morandotti1,9,10 1Institut National de la Recherche Scientifique - Centre Énergie, Matériaux et Télécommunications (INRS-EMT), 2School of Engineering, University of Glasgow, 3Department of Energy, Information Engineering and Mathematical Models, University of Palermo, 4School of Mathematical and Physical Sciences, University of Sussex, 5Department of Physics and Material Science, City University of Hong Kong, 6State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Science, 7Centre for Micro Photonics, Swinburne University of Technology, 8Institute of Photonics, Department of Physics, University of Strathclyde, 9Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, 10National Research University of Information Technologies, Mechanics and Optics A protocol is presented for the practical generation and coherent manipulation of high-dimensional frequency-bin entangled photon states using integrated micro-cavities and standard telecommunications components, respectively. Neuroscience Recording Brain Electromagnetic Activity During the Administration of the Gaseous Anesthetic Agents Xenon and Nitrous Oxide in Healthy Volunteers Andria Pelentritou1, Levin Kuhlmann1, John Cormack2, Will Woods3, Jamie Sleigh4, David Liley1 1Centre for Human Psychopharmacology, Swinburne University of Technology, 2 Simultaneous magnetoencephalography and electroencephalography provides a useful tool to search for common and distinct macro-scale mechanisms of reductions in consciousness induced by different anesthetics. This paper illustrates the empirical methods underlying the recording of such data from healthy humans during N-Methyl-D-Aspartate-(NMDA)-receptor-antagonist-based anesthesia during inhalation of nitrous oxide and xenon. Chemistry Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene Rebecca A. Ryan1, Sophie Williams1, Andrew V. Martin1, Ruben A. Dilanian1, Connie Darmanin2, Corey T. Putkunz1, David Wood3, Victor A. Streltsov4, Michael W.M. Jones5, Naylyn Gaffney6, Felix Hofmann7, Garth J. Williams8, Sebastien Boutet9, Marc Messerschmidt10, M. Marvin Seibert11, Evan K. Curwood11, Eugeniu Balaur2, Andrew G. Peele5, Keith A. Nugent2, Harry M. Quiney1, Brian Abbey2 1ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, 2Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, 3Department of Physics, Imperial College London, 4Florey Institute of Neuroscience and Mental Health, 5Science and Engineering Faculty, Queensland University of Technology, 6Swinburne University of Technology, 7Department of Engineering Science, University of Oxford, 8Brookhaven National Laboratory, 9Linac Coherent Light Source, SLAC National Accelerator Laboratory, 10BioXFEL Science and Technology Center, 11Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, 12Australian Synchrotron We describe an experiment designed to probe the electronic damage induced in nanocrystals of Buckminsterfullerene (C60) by intense, femtosecond pulses of X-rays. The experiment found that, surprisingly, rather than being stochastic, the X-ray induced electron dynamics in C60 are highly correlated, extending over hundreds of unit cells within the crystals1. Engineering The Evolution of Silica Nanoparticle-polyester Coatings on Surfaces Exposed to Sunlight Vi Khanh Truong1, Miljan Stefanovic1, Shane Maclaughlin2, Mark Tobin3, Jitraporn Vongsvivut3, Mohammad Al Kobaisi1, Russell J. Crawford4, Elena P. Ivanova1 1School of Science, Faculty of Science, Engineering and Technology, Swinburne University of Technology, 2BlueScope Steel Research, 3Infrared Microspectroscopy Beamline, Australian Synchrotron, 4School of Science, College of Science, Engineering and Health, RMIT University Two types of surfaces, polyester-coated steel and polyester coated with a layer of silica nanoparticles, were studied. Both surfaces were exposed to sunlight, which was found to cause substantial changes in the chemistry and nanoscale topography of the surface. Neuroscience Gold Nanorod-assisted Optical Stimulation of Neuronal Cells Chiara Paviolo1, Sally L. McArthur1, Paul R. Stoddart1 1Biotactical Engineering, Faculty of Science, Engineering and Technology, Swinburne University of Technology This protocol outlines how to use the transient heating associated with the optical absorption of gold nanorods to stimulate differentiation and intracellular calcium activity in neuronal cells. These results potentially open up new applications in neural prostheses and fundamental studies in neuroscience. Neuroscience Whole Cell Patch Clamp for Investigating the Mechanisms of Infrared Neural Stimulation William G. A. Brown1, Karina Needham2, Bryony A. Nayagam2, Paul R. Stoddart1 1Biotactical Engineering, Faculty of Engineering and Industrial Science, Swinburne University of Technology, 2Department of Otolaryngology, The University of Melbourne Infrared nerve stimulation has been proposed as an alternative to electrical stimulation in a range of nerve types, including those associated with the auditory system. This protocol describes a patch clamp method for studying the mechanism of infrared nerve stimulation in a culture of primary auditory neurons. Bioengineering Increasing cDNA Yields from Single-cell Quantities of mRNA in Standard Laboratory Reverse Transcriptase Reactions using Acoustic Microstreaming Wah Chin Boon1, Karolina Petkovic-Duran2, Yonggang Zhu2, Richard Manasseh3, Malcolm K. Horne1, Tim D. Aumann1 1Florey Neuroscience Institutes and Centre for Neuroscience, University of Melbourne, 2Fluid Dynamics Group, CSIRO Materials Science and Engineering, 3Swinburne University of Technology, Faculty of Engineering and Industrial Sciences We describe a novel method for increasing cDNA yield from single-cell quantities of mRNA in otherwise standard laboratory reverse transcription reactions. The novelty resides in the use of a micromixer, which utilizes the phenomenon of acoustic microstreaming, to mix fluids at microliter scales more effectively than shaking, vortexing or trituration.