York University View Institution's Website 13 articles published in JoVE Bioengineering Soybean Hairy Root Transformation for the Analysis of Gene Function Jie Lin1, Dasol Wi1, Melissa Ly1, Md Asraful Jahan2, Sarah Pullano1, Izabella Martirosyan1, Nik Kovinich1 1Department of Biology, York University, 2Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology Here, we present a protocol for the high-efficiency production of transgenic soybean hairy roots. Biochemistry Measurement of Protein Import Capacity of Skeletal Muscle Mitochondria Ashley N. Oliveira1, Brandon J. Richards1, David A. Hood1 1Muscle Health Research Center, School of Kinesiology and Health Science, York University Mitochondria are key metabolic organelles that exhibit a high level of phenotypic plasticity in skeletal muscle. The import of proteins from the cytosol is a critical pathway for organelle biogenesis, essential for the expansion of the reticulum and the maintenance of mitochondrial function. Therefore, protein import serves as a barometer of cellular health. Biology Studying the Activity of Neuropeptides and Other Regulators of the Excretory System in the Adult Mosquito Aryan Lajevardi*1, Farwa Sajadi*1, Andrew Donini1, Jean-Paul V. Paluzzi1 1Department of Biology, York University This protocol outlines methodologies behind the Ramsay assay, ion-selective microelectrodes, Scanning Ion-selective Electrode Technique (SIET) and in vitro contraction assays, applied to study the adult mosquito excretory system, comprised of the Malpighian tubules and hindgut, to collectively measure ion and fluid secretion rates, contractile activity, and transepithelial ion transport. Developmental Biology Application of Chronic Stimulation to Study Contractile Activity-induced Rat Skeletal Muscle Phenotypic Adaptations Yuho Kim1,2,3, Jonathan M. Memme1,2, David A. Hood1,2 1Muscle Health Research Centre, York University, 2School of Kinesiology and Health Science, York University, 3National Heart, Lung, and Blood Institute, National Institutes of Health This protocol describes the use of the chronic contractile activity model of exercise to observe stimulation-induced skeletal muscle adaptations in the rat hindlimb. Biochemistry Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions Robert W. Harkness V1, Philip E. Johnson2, Anthony K. Mittermaier1 1Department of Chemistry, McGill University, 2Department of Chemistry, York University We present a protocol for rapid characterization of biomolecular folding and binding interactions with thermolabile ligands using differential scanning calorimetry. Biochemistry Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics Cristina Lento1, Shaolong Zhu1, Kerene A. Brown1, Ruth Knox1, Peter Liuni1, Derek J. Wilson1,2,3 1Department of Chemistry, York University, 2The Centre for Research in Mass Spectrometry, York University, 3The Centre for Research on Biomolecular Interactions, York University Conformational flexibility plays a critical role in protein function. Herein, we describe the use of time-resolved electrospray ionization mass spectrometry coupled to hydrogen-deuterium exchange for probing the rapid structural changes that drive function in ordered and disordered proteins. Genetics Conjugative Mating Assays for Sequence-specific Analysis of Transfer Proteins Involved in Bacterial Conjugation Fettah Erdogan1, Cristina Lento1, Ayat Yaseen1, Roksana Nowroozi-Dayeni1, Sasha Kheyson1, Gerald F. Audette1,2 1Department of Chemistry, York University, 2The Centre for Research on Biomolecular Interactions, York University Here, we present a protocol to knockout a gene of interest involved in plasmid conjugation and subsequently analyze the impact of its absence using mating assays. The function of the gene is further explored to a specific region of its sequence using deletion or point mutations. Biology Automated Quantification and Analysis of Cell Counting Procedures Using ImageJ Plugins Jacob O'Brien1, Heyam Hayder1, Chun Peng1 1Department of Biology, York University This paper describes the quantification of hemocytometer and migration/invasion micrographs through two new open-source ImageJ plugins Cell Concentration Calculator and migration assay Counter. Furthermore, it describes image acquisition and calibration protocols as well as discusses in detail the input requirements of the plugins. Neuroscience Measuring Connectivity in the Primary Visual Pathway in Human Albinism Using Diffusion Tensor Imaging and Tractography Anahit Grigorian1, Larissa McKetton1, Keith A. Schneider1 1Department of Biology, Centre for Vision Research, York University This manuscript describes deterministic and probabilistic algorithms for white matter (WM) reconstruction, used to examine differences in optic radiation (OR) connectivity between albinism and controls. Although probabilistic tractography follows the true course of nerve fibers more closely, deterministic tractography was run to compare the reliability and reproducibility of both techniques. Bioengineering Microbiologically Induced Calcite Precipitation Mediated by Sporosarcina pasteurii Swayamdipta Bhaduri1, Nandini Debnath1, Sushanta Mitra2, Yang Liu3, Aloke Kumar1 1Department of Mechanical Engineering, University of Alberta, 2Department of Mechanical Engineering, York University, 3Department of Civil and Environmental Engineering, University of Alberta Protocols for microbiologically induced calcite precipitation (MICP) using the bacterium Sporosarcina pasteurii are presented here. The precipitated calcium carbonate was characterized through optical microscopy and scanning electron microscopy (SEM). It is also shown that exposure to MICP increases the compressive strength of sponge. Behavior Testing Tactile Masking between the Forearms Sarah D'Amour1, Laurence R. Harris1 1Department of Psychology, York University Here we explore contralateral tactile masking between the forearms in which tactile detection thresholds are modulated by vibration applied to a remote site. The details of which remote sites have an effect can tell us about how the body is represented in the brain. Neuroscience High-resolution Structural Magnetic Resonance Imaging of the Human Subcortex In Vivo and Postmortem Larissa McKetton1, Joy Williams2, Joseph D. Viviano1, Yeni H. Yücel3, Neeru Gupta3, Keith A. Schneider1 1Department of Biology and Centre for Vision Research, York University, 2York MRI Facility, York University, 3Department of Ophthalmology & Vision Sciences, Laboratory Medicine & Pathobiology, University of Toronto Here we present a protocol to determine the minimum number images that needed to be registered and averaged to resolve subcortical structures and test whether the individual layers of the LGN could be resolved in the absence of physiological noise. Neuroscience Correlating Behavioral Responses to fMRI Signals from Human Prefrontal Cortex: Examining Cognitive Processes Using Task Analysis Joseph F.X. DeSouza1,2, Shima Ovaysikia1, Laura K. Pynn1 1Department of Psychology, Centre for Vision Research, York University, 2Department of Biology, Centre for Vision Research, York University The goal of our research is to correlate behavior to brain activity. Accurate behavioral measures and imaging techniques allow us to elucidate brain-behavior relationships.