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McMaster University

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27 articles published in JoVE

Biochemistry

Advancing High-Resolution Imaging of Virus Assemblies in Liquid and Ice Liza-Anastasia DiCecco*^1,2, Samantha Berry*¹, G. M. Jonaid*^1,3, Maria J. Solares^1,4, Liam Kaylor^1,4, Jennifer L. Gray⁵, Carol Bator⁶, William J. Dearnaley¹, Michael Spilman⁷, Madeline J. Dressel-Dukes⁸, Kathryn Grandfield², Sarah M. McDonald Esstman⁹, Deborah F. Kelly^1,5,6 ¹Department of Biomedical Engineering, Pennsylvania State University, ²Department of Materials Science and Engineering, McMaster University, ³Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, ⁴Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, ⁵Materials Research Institute, Pennsylvania State University, ⁶Huck Institutes of the Life Sciences, Pennsylvania State University, ⁷Applications team, Direct Electron, ⁸Application Scientist, Protochips, Inc., ⁹Department of Biology, Wake Forest University Here protocols are described to prepare virus assemblies suitable for liquid-EM and cryo-EM analysis at the nanoscale using transmission electron microscopy.
Biology

Isolation of Culturable Yeasts and Molds from Soils to Investigate Fungal Population Structure Himeshi Samarasinghe¹, Gregory Korfanty¹, Jianping Xu¹ ¹Department of Biology, McMaster University This protocol is an effective, speedy method of culturing yeasts and the mold Aspergillus fumigatus from large sets of soil samples in as little as 7 days. The methods can be easily modified to accommodate a range of incubation media and temperatures as needed for experiments.
Immunology and Infection

Antibiotic Dereplication Using the Antibiotic Resistance Platform Haley L. Zubyk¹, Georgina Cox², Gerard D. Wright¹ ¹Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, McMaster University, ²Department of Molecular and Cellular Biology, University of Guelph We describe a platform that utilizes a library of isogenic antibiotic resistant Escherichia coli for the dereplication of antibiotics. The identity of an antibiotic produced by bacteria or fungi can be deduced by the growth of E. coli expressing its respective resistance gene. This platform is economically effective and time-efficient.
Chemistry

High-throughput and Comprehensive Drug Surveillance Using Multisegment Injection-Capillary Electrophoresis-Mass Spectrometry Meera Shanmuganathan¹, Sabrina Macklai¹, Clara Barrenas Cárdenas¹, Zachary Kroezen¹, Marcus Kim², William Zizek³, Howard Lee³, Philip Britz-McKibbin¹ ¹Department of Chemistry and Chemical Biology, McMaster University, ²Agilent Technologies Inc., ³Seroclinix Corporation Here we describe a high-throughput method for comprehensive drug surveillance that allows for the improved resolution and detection of large panels of drugs of abuse and their metabolites, with quality control based on multisegment injection-capillary electrophoresis-mass spectrometry.
Biology

Growing Magnetotactic Bacteria of the Genus Magnetospirillum: Strains MSR-1, AMB-1 and MS-1 Lucas Le Nagard¹, Viviana Morillo-López², Cecile Fradin¹, Dennis A. Bazylinski² ¹Department of Physics & Astronomy, McMaster University, ²School of Life Sciences, University of Nevada Las Vegas We present a procedure for growing several strains of Magnetospirillum in two different types of growth media. Magnetospirillum gryphiswaldense strain MSR-1 is grown in both liquid and O2 concentration gradient semi-solid media while M. magneticum strain AMB-1 and M. magnetotacticum strain MS-1 are grown in liquid medium.
Engineering

A 3D-printed Chamber for Organic Optoelectronic Device Degradation Testing Emma Mogus¹, Benjamin Torres-Kulik¹, Christopher Gustin², Ayse Turak¹ ¹Department of Engineering Physics, McMaster University, ² Here, we present a protocol for the design, manufacture, and use of a simple, versatile 3D-printed and controlled atmospheric chamber for the optical and electrical characterization of air-sensitive organic optoelectronic devices.
Bioengineering

Fabricating Degradable Thermoresponsive Hydrogels on Multiple Length Scales via Reactive Extrusion, Microfluidics, Self-assembly, and Electrospinning Daryl Sivakumaran¹, Emilia Bakaic¹, Scott B. Campbell¹, Fei Xu¹, Eva Mueller¹, Todd Hoare¹ ¹Department of Chemical Engineering, McMaster University Protocols are described for the fabrication of degradable thermoresponsive hydrogels based on hydrazone cross-linking of polymeric oligomers on the bulk scale, microscale, and nanoscale, the latter for preparation of both gel nanoparticles and nanofibers.
Genetics

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease Allison A. Dilliott^1,2, Sali M.K. Farhan³, Mahdi Ghani⁴, Christine Sato⁴, Eric Liang⁵, Ming Zhang⁴, Adam D. McIntyre¹, Henian Cao¹, Lemuel Racacho^6,7, John F. Robinson¹, Michael J. Strong^1,8, Mario Masellis^9,10, Dennis E. Bulman^6,7, Ekaterina Rogaeva⁴, Anthony Lang^10,11, Carmela Tartaglia^4,10, Elizabeth Finger^12,13, Lorne Zinman⁹, John Turnbull¹⁴, Morris Freedman^10,15, Rick Swartz⁹, Sandra E. Black^9,16, Robert A. Hegele^1,2 ¹Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, ²Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, ³Analytic and Translational Genetics Unit, Center for Genomic Medicine, Harvard Medical School, Massachusetts General Hospital, Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, ⁴Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, ⁵ Targeted next-generation sequencing is a time- and cost-efficient approach that is becoming increasingly popular in both disease research and clinical diagnostics. The protocol described here presents the complex workflow required for sequencing and the bioinformatics process used to identify genetic variants that contribute to disease.
Chemistry

Preparation and Evaluation of ^99mTc-labeled Tridentate Chelates for Pre-targeting Using Bioorthogonal Chemistry Holly A. Bilton*¹, Zainab Ahmad*¹, Nancy Janzen¹, Shannon Czorny¹, John F. Valliant¹ ¹Department of Chemistry and Chemical Biology, McMaster University Here, we describe a protocol for radiolabeling and in vivo testing of tridentate ^99mTc(I) chelate-tetrazine derivatives for pre-targeting and bioorthogonal chemistry.
Biology

Colorimetric Detection of Bacteria Using Litmus Test Kha Tram¹, Sepehr Manochehry¹, Qian Feng², Dingran Chang¹, Bruno J. Salena³, Yingfu Li¹ ¹Department of Biochemistry and Biomedical Sciences, McMaster University, ²Department of Chemistry and Chemical Biology, McMaster University, ³Department of Medicine, McMaster University We describe a protocol for colorimetric detection of E. coli using a modified litmus test that takes advantage of an RNA-cleaving DNAzyme, urease, and magnetic beads.
Behavior

Combining Multiple Data Acquisition Systems to Study Corticospinal Output and Multi-segment Biomechanics Michael J. Asmussen¹, Aaron Z. Bailey¹, Peter J. Keir¹, Jim Potvin¹, Tim Bergel², Aimee J. Nelson¹ ¹Department of Kinesiology, McMaster University, ²2Els Espots The use of transcranial magnetic stimulation (TMS) to study human motor control requires the integration of data acquisition systems to control TMS delivery and simultaneously record human behavior. The present manuscript provides a detailed methodology for integrating data acquisition systems for the purpose of investigating human movement via TMS.
Behavior

Design and Implementation of an fMRI Study Examining Thought Suppression in Young Women with, and At-risk, for Depression Caitlin L. Carew¹, Erica L. Tatham², Andrea M. Milne¹, Glenda M. MacQueen³, Geoffrey B.C. Hall⁴ ¹Department of Psychiatry and Behavioural Neurosciences, McMaster University, ²McMaster Integrative Neuroscience Discovery and Study, McMaster University, ³Department of Psychiatry, University of Calgary, ⁴Department of Psychology, Neuroscience & Behaviour, McMaster University We aim to identify the neural correlates underlying sustained and transient thought suppression, and thought re-emergence in controls, at-risk and depressed individuals. Activation was greatest for controls compared to the at-risk and the depressed group in the dorsolateral prefrontal cortex during thought suppression and anterior cingulate cortex during thought re-emergence.
Behavior

Behavioral Phenotyping of Murine Disease Models with the Integrated Behavioral Station (INBEST) Boris Sakic¹, Marcella P. A. Cooper², Sarah E. Taylor², Milica Stojanovic², Bosa Zagorac², Minesh Kapadia³ ¹Department of Psychiatry and Behavioral Neurosciences, McMaster University, ²Department of Psychology, Neuroscience & Behaviour, McMaster University, ³Neuroscience Program, McMaster University Prolonged and comprehensive monitoring of mice in a home-cage environment provides a deeper understanding of aberrant behavior in murine models of brain diseases. This paper describes the Integrated Behavioral Station (INBEST) as the key component of contemporary behavioral analysis.
Medicine

Handling of the Cotton Rat in Studies for the Pre-clinical Evaluation of Oncolytic Viruses Breanne Cuddington¹, Meghan Verschoor¹, Karen Mossman¹ ¹Department of Pathology and Molecular Medicine, McMaster Immunology Research Centre, Institute for Infectious Disease Research, McMaster University Cotton rats are extremely excitable and have a strong flight-or-fight response. A handling method optimized to reduce the stress of the animals is described which will make cotton rats more accessible as a preclinical model.
Immunology and Infection

Characterization of Inflammatory Responses During Intranasal Colonization with Streptococcus pneumoniae Alicja Puchta¹, Chris P. Verschoor¹, Tanja Thurn¹, Dawn M. E. Bowdish¹ ¹Department of Pathology and Molecule Medicine, McMaster University Colonization of the murine nasopharynx with Streptococcus pneumoniae and the subsequent extraction of adherent or recruited cells is described. This technique involves flushing the nasopharynx and collection of the fluid through the nares and is adaptable for various readouts, including differential cell quantification and analysis of mRNA expression in situ.
Medicine

Quantitative Analysis and Characterization of Atherosclerotic Lesions in the Murine Aortic Sinus Daniel E. Venegas-Pino¹, Nicole Banko¹, Mohammed I. Khan², Yuanyuan Shi², Geoff H. Werstuck^1,2 ¹Department of Biochemistry and Biomedical Sciences, McMaster University, ²Thrombosis and Atherosclerosis Research Institute, McMaster University We describe procedures to quantify and characterize atherosclerotic lesions in mouse models using precision sectioning of the aortic sinus and ascending aorta combined with histochemical and immunohistochemical analysis.
Medicine

Tibial Nerve Transection - A Standardized Model for Denervation-induced Skeletal Muscle Atrophy in Mice Jane A. E. Batt¹, James Ralph Bain² ¹Keenan Research Centre of the LiKaShing Knowledge Institute, St Michaels Hospital, ²Department of Surgery, McMaster University The tibial nerve transection model is a well-tolerated, validated, and reproducible model of skeletal muscle atrophy. The model surgical protocol is described and demonstrated in C57Black6 mice.
Chemistry

A Guided Materials Screening Approach for Developing Quantitative Sol-gel Derived Protein Microarrays Blake-Joseph Helka¹, John D. Brennan¹ ¹Department of Chemistry and Chemical Biology, McMaster University A guided material screening approach to develop sol-gel derived protein doped microarrays using an emerging pin-printing method of fabrication is described. This methodology is demonstrated through the development of acetylcholinesterase and multikinase microarrays, which are used for cost-effective small-molecule screening.
Bioengineering

Microfluidic-based Electrotaxis for On-demand Quantitative Analysis of Caenorhabditis elegans' Locomotion Justin Tong¹, Pouya Rezai², Sangeena Salam¹, P. Ravi Selvaganapathy², Bhagwati P. Gupta¹ ¹Department of Biology, McMaster University, ²Department of Mechanical Engineering, McMaster University A semi-automated micro-electro-fluidic method to induce on-demand locomotion in Caenorhabditis elegans is described. This method is based on the neurophysiologic phenomenon of worms responding to mild electric fields (“electrotaxis”) inside microfluidic channels. Microfluidic electrotaxis serves as a rapid, sensitive, low-cost, and scalable technique to screen for factors affecting neuronal health.
Biology

Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes Yu Seon Chung¹, Alba Guarné¹ ¹Department of Biochemistry and Biomedical Sciences, McMaster University Crystal structure of protein–DNA complexes can provide insight into protein function, mechanism, as well as, the nature of the specific interaction. Here, we report how to optimize the length, sequence and ends of duplex DNA for co-crystallization with Escherichia coli SeqA, a negative regulator of replication initiation.
Medicine

Processing of Primary Brain Tumor Tissue for Stem Cell Assays and Flow Sorting Chitra Venugopal¹, Nicole M. McFarlane¹, Sara Nolte¹, Branavan Manoranjan¹, Sheila K. Singh¹ ¹Stem Cell and Cancer Research Institute, McMaster University The identification of brain tumor initiating cells (BTICs), the rare cells within a heterogeneous tumor possessing stem cell properties, provides new insights into human brain tumor pathogenesis. We have refined specific culture conditions to enrich for BTICs, and we routinely use flow cytometry to further enrich these populations. Self-renewal assays and transcript analysis by single cell RT-PCR can subsequently be performed on these isolated cells.
Immunology and Infection

Analysis of Pulmonary Dendritic Cell Maturation and Migration during Allergic Airway Inflammation Rahul Kushwah¹, Jim Hu² ¹Stem Cell and Cancer Research Institute, McMaster University, Hamilton, ²Physiology and Experimental Medicine Research Program, Hospital for Sick Children, University of Toronto We describe a strategy to monitor maturation and migration of pulmonary dendritic cells in response to ovalbumin in the setting of ovalbumin induced allergic airway inflammation. This strategy can be modified to assess migration of pulmonary dendritic cells in settings of infection.
Immunology and Infection

Detection of Bacteria Using Fluorogenic DNAzymes Sergio D. Aguirre¹, M. Monsur Ali¹, Pushpinder Kanda¹, Yingfu Li^1,2 ¹Department of Biochemistry and Biomedical Sciences, McMaster University, ²Department of Chemistry and Chemical Biology, McMaster University We have recently reported a novel approach for generating fluorogenic DNAzyme probes that can be applied to set up a simple, "mix-and-read" fluorescent assay for bacterial detection. These special DNA probes catalyze the cleavage of a chromophore-modified DNA-RNA chimeric substrate in the presence of crude extracellular mixture (CEM) produced by a specific bacterium, thereby translating bacterial detection into fluorescence signal generation. In this report we will describe key experimental procedures where a specific DNAzyme probe denoted "RFD-EC1" is employed for the detection of the model bacterium, Escherichia coli (E. coli).
Biology

Investigating Intestinal Inflammation in DSS-induced Model of IBD Janice J. Kim¹, Md. Sharif Shajib¹, Marcus M. Manocha¹, Waliul I. Khan¹ ¹Farncombe Family Digestive Health Research Institute, Department of Pathology and Molecular Medicine, McMaster University Experimental models of inflammatory bowel disease have allowed us to examine the complex innate and adaptive immune responses associated with pathogenesis. Using histological scoring, quantification of pro-inflammatory cytokines and myeloperoxidase activity, one can begin to assess these responses seen in inflammatory bowel disease.
Biology

Primary Human Bronchial Epithelial Cells Grown from Explants Asma Yaghi¹, Aisha Zaman¹, Myrna Dolovich¹ ¹Medicine, Faculty of Health Sciences, McMaster University Here we describe a detailed method for growing primary human bronchial epithelial cells from explants of human bronchial airway tissue including differentiated growth on an air-liquid interface. This method provides an abundant source of primary cells for investigating the role of the airway epithelium in human lung health and disease.
Biology

A Tactile Automated Passive-Finger Stimulator (TAPS) Daniel Goldreich^1,2, Michael Wong², Ryan M. Peters², Ingrid M. Kanics¹ ¹Department of Occupational Therapy, Duquesne University, ²Department of Psychology, Neuroscience and Behaviour, McMaster University We describe a computer-controlled device for investigating the sense of touch: the Tactile Automated Passive-finger Stimulator (TAPS). We describe the components of TAPS, and show how TAPS is used to administer a two-interval forced-choice tactile grating orientation test.
Biology

Culture of myeloid dendritic cells from bone marrow precursors Jeanette Boudreau^1,2, Sandeep Koshy^2,3, Derek Cummings², Yonghong Wan² ¹Medical Sciences Program, McMaster University, ²Centre for Gene Therapeutics, McMaster University, ³Department of Chemical Engineering, University of Waterloo This video demonstrates the procedure for differentiating myeloid dendritic cells from mouse bone marrow. Isolation of mouse tibia and femur, and processing of bone marrow are demonstrated. Pictures demonstrating cell morphology before and after differentiation, and figures depicting cell phenotype and IL-12 production following maturation using CpG are shown.

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