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The Australian National University

11 ARTICLES PUBLISHED IN JoVE

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Engineering

Gradient Echo Quantum Memory in Warm Atomic Vapor
Olivier Pinel 1, Mahdi Hosseini 1, Ben M. Sparkes 1, Jesse L. Everett 1, Daniel Higginbottom 1, Geoff T. Campbell 1, Ping Koy Lam 1, Ben C. Buchler 1
1ARC Centre for Quantum Computation and Communication Technology, Department of Quantum Science, The Australian National University

The gradient echo memory is a protocol for storing optical quantum states of light in atomic ensembles. Quantum memory is a key element of a quantum repeater, which can extend the range of quantum key distribution. We outline the operation of the scheme when implemented in a 3-level atomic ensemble.

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Biology

Identification of Post-translational Modifications of Plant Protein Complexes
Sophie J. M. Piquerez 1, Alexi L. Balmuth 2, Jan Sklenář 2, Alexandra M.E. Jones 1,2, John P. Rathjen 3, Vardis Ntoukakis 1
1School of Life Sciences, University of Warwick, 2The Sainsbury Laboratory, Norwich Research Park, 3Research School of Biology, The Australian National University

We describe here a protocol for the purification and characterization of plant protein complexes. We demonstrate that by immunoprecipitating a single protein within a complex, so we can identify its post-translational modifications and its interacting partners.

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Engineering

Construction and Characterization of External Cavity Diode Lasers for Atomic Physics
Kyle S. Hardman 1, Shayne Bennetts 1, John E. Debs 1, Carlos C. N. Kuhn 1, Gordon D. McDonald 1, Nick Robins 1
1Department of Quantum Science, The Australian National University

This is an instructional paper to guide the construction and diagnostics of external cavity diode lasers (ECDLs), including component selection and optical alignment, as well as the basics of frequency reference spectroscopy and laser linewidth measurements for applications in the field of atomic physics.

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Bioengineering

Micropatterning and Assembly of 3D Microvessels
Meredith A. Roberts *1, Surya S. Kotha *1, Kiet T. Phong 2, Ying Zheng 1,2
1Department of Bioengineering, University of Washington, 2Center for Cardiovascular Biology, Institute for Stem Cell and Regenerative Medicine, University of Washington

This manuscript presents an injection molding method to engineer microvessels that recapitulate physiological properties of endothelium. The microfluidic-based process creates patent 3D vascular networks with tailorable conditions, such as flow, cellular composition, geometry, and biochemical gradients. The fabrication process and examples of potential applications are described.

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Neuroscience

Concurrent Recording of Co-localized Electroencephalography and Local Field Potential in Rodent
Sungmin Kang 1, Michael Bruyns-Haylett 2, Yurie Hayashi 1, Ying Zheng 1
1School of Biological Sciences, Whiteknights, University of Reading, 2Department of Bioengineering, Imperial College

This protocol describes a simple method for concurrent recording of co-localized electroencephalography (EEG) and multi-laminar local field potential in an anesthetized rat. A burr hole drilled in the skull for the insertion of a microelectrode is shown to produce negligible distortion of the EEG signal.

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Biology

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
Pietro Ariani *1, Elodie Vandelle *1, Darren Wong 2, Alejandro Giorgetti 1, Andrea Porceddu 3, Salvatore Camiolo 3, Annalisa Polverari 1
1Dipartimento di Biotecnologie, Università degli Studi di Verona, 2Ecology and Evolution, Research School of Biology, The Australian National University, 3Dipartimento di Agraria, SACEG, Università degli Studi di Sassari

This article describes the procedure for the identification and characterization of a gene family in grapevine applied to the family of Arabidopsis Tóxicos in Levadura (ATL) E3 ubiquitin ligases.

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Biology

Visualization and Quantification of Mesenchymal Cell Adipogenic Differentiation Potential with a Lineage Specific Marker
Jennifer Eom 1, Vaughan Feisst 1, Louis Ranjard 2, Kerry Loomes 1, Tanvi Damani 1, Victoria Jackson-Patel 1,3, Michelle Locke 4,5, Hilary Sheppard 1, Pritika Narayan 1,6, P. Rod Dunbar 1,7
1School of Biological Sciences, The University of Auckland, 2Research School of Biology, The Australian National University, 3Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, 4Department of Plastic Surgery, Counties Manukau District Health Board, 5Department of Surgery, Faculty of Medical and Health Sciences, The University of Auckland, 6Biomedical Imaging Research Unit, Faculty of Medical and Health Sciences, The University of Auckland, 7Maurice Wilkins Centre, The University of Auckland

Traditional methods of assessing adipogenic differentiation are cheap and easy to use, but are not specific to changes in gene expression. We have developed an assay to quantify mesenchymal cell differentiation into mature adipocytes using a lineage specific marker. This assay has diverse applications across basic research and clinical medicine.

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Bioengineering

Fabricating a Kidney Cortex Extracellular Matrix-Derived Hydrogel
Harrison L. Hiraki 1, Ryan J. Nagao 2, Jonathan Himmelfarb 3, Ying Zheng 2
1Department of Bioengineering, University of Washington, 2Department of Bioengineering, Center for Cardiovascular Biology, Institute for Stem Cell and Regenerative Medicine, University of Washington, 3Department of Medicine, Kidney Research Institute, University of Washington

Here we present a protocol to fabricate a kidney cortex extracellular matrix-derived hydrogel to retain the native kidney extracellular matrix (ECM) structural and biochemical composition. The fabrication process and its applications are described. Finally, a perspective on using this hydrogel to support kidney-specific cellular and tissue regeneration and bioengineering is discussed.

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Neuroscience

Evaluation of Hemisphere Lateralization with Bilateral Local Field Potential Recording in Secondary Motor Cortex of Mice
Yunan Chen 1,2, Ming Li 3, Ying Zheng 3, Li Yang 1
1School of Life Sciences, Guangzhou University, 2Institute for Brain Research and Rehabilitation, South China Normal University, 3School of Life Sciences, South China Normal University

We present in vivo electrophysiological recording of the local field potential (LFP) in bilateral secondary motor cortex (M2) of mice, which can be applied to evaluate hemisphere lateralization. The study revealed altered levels of synchronization between the left and right M2 in APP/PS1 mice compared to WT controls.

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Biology

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Gunjan Dixit 1, Ying Zheng 1, Brian Parker 2, Jiayu Wen 1
1Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, 2Department of Biology, New York University

Alternative splicing (AS) and alternative polyadenylation (APA) expand the diversity of transcript isoforms and their products. Here, we describe bioinformatic protocols to analyze bulk RNA-seq and 3' end sequencing assays to detect and visualize AS and APA varying across experimental conditions.

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JoVE Journal

Rapid In Vivo Fixation and Isolation of Translational Complexes from Eukaryotic Cells
Yoshika Janapala *1, Katrina Woodward *1, Jiwon Lee 2, Melanie Rug 2, Thomas Preiss 1,3, Nikolay E. Shirokikh 1
1Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, 2Centre for Advanced Microscopy, The Australian National University, 3Victor Chang Cardiac Research Institute

We present a technique to rapidly stabilize translational (protein biosynthesis) complexes with formaldehyde crosslinking in live yeast and mammalian cells. The approach enables dissecting transient intermediates and dynamic RNA:protein interactions. The crosslinked complexes can be used in multiple downstream applications such as in deep sequencing-based profiling methods, microscopy, and mass-spectrometry.

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