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12 ARTICLES PUBLISHED IN JoVE

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Bioengineering

Microbiologically Induced Calcite Precipitation Mediated by Sporosarcina pasteurii
Swayamdipta Bhaduri 1, Nandini Debnath 1, Sushanta Mitra 2, Yang Liu 3, Aloke Kumar 1
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.

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Neuroscience

High-resolution Structural Magnetic Resonance Imaging of the Human Subcortex In Vivo and Postmortem
Larissa McKetton 1, Joy Williams 2, Joseph D. Viviano 1, Yeni H. Yücel 3, Neeru Gupta 3, Keith A. Schneider 1
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.

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Behavior

Testing Tactile Masking between the Forearms
Sarah D'Amour 1, Laurence R. Harris 1
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.

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Neuroscience

Measuring Connectivity in the Primary Visual Pathway in Human Albinism Using Diffusion Tensor Imaging and Tractography
Anahit Grigorian 1, Larissa McKetton 1, Keith A. Schneider 1
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.

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Biology

Automated Quantification and Analysis of Cell Counting Procedures Using ImageJ Plugins
Jacob O'Brien 1, Heyam Hayder 1, Chun Peng 1
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.

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Genetics

Conjugative Mating Assays for Sequence-specific Analysis of Transfer Proteins Involved in Bacterial Conjugation
Fettah Erdogan 1, Cristina Lento 1, Ayat Yaseen 1, Roksana Nowroozi-Dayeni 1, Sasha Kheyson 1, Gerald F. Audette 1,2
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.

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Biochemistry

Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics
Cristina Lento 1, Shaolong Zhu 1, Kerene A. Brown 1, Ruth Knox 1, Peter Liuni 1, Derek J. Wilson 1,2,3
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.

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Biochemistry

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions
Robert W. Harkness V 1, Philip E. Johnson 2, Anthony K. Mittermaier 1
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.

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Developmental Biology

Application of Chronic Stimulation to Study Contractile Activity-induced Rat Skeletal Muscle Phenotypic Adaptations
Yuho Kim 1,2,3, Jonathan M. Memme 1,2, David A. Hood 1,2
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.

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Biology

Studying the Activity of Neuropeptides and Other Regulators of the Excretory System in the Adult Mosquito
Aryan Lajevardi *1, Farwa Sajadi *1, Andrew Donini 1, Jean-Paul V. Paluzzi 1
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.

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JoVE Journal

Measurement of Protein Import Capacity of Skeletal Muscle Mitochondria
Ashley N. Oliveira 1, Brandon J. Richards 1, David A. Hood 1
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.

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Bioengineering

Soybean Hairy Root Transformation for the Analysis of Gene Function
Jie Lin 1, Dasol Wi 1, Melissa Ly 1, Md Asraful Jahan 2, Sarah Pullano 1, Izabella Martirosyan 1, Nik Kovinich 1
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.

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