University of Alberta

64 articles published in JoVE

• Neuroscience

  
  Enrichment of Adult Mouse Dorsal Root Ganglia Neuron Cultures by Immunopanning Aislinn D. Maguire¹, Jason R. Plemel^1,2,3, Bradley J. Kerr^{1,4,5 1}Neuroscience and Mental Health Institute, University of Alberta, ²Department of Medicine, Division of Neurology, University of Alberta, ³Department of Medical Microbiology and Immunology, University of Alberta, ⁴Department of Pharmacology, University of Alberta, ⁵Department of Anesthesiology and Pain Medicine, University of Alberta This paper describes an immunopanning protocol for adult mouse dorsal root ganglia. By adhering antibodies to culture plates, we can negatively select and remove non-neuronal cells. We show that the cultures are enriched for neurons using this protocol, allowing for an in-depth study of neuronal responses to manipulation.

• Medicine

  
  A Piglet Perinatal Asphyxia Model to Study Cardiac Injury and Hemodynamics after Cardiac Arrest, Resuscitation, and the Return of Spontaneous Circulation Eydis Oddsdottir Stenersen^1,2, Annette Olsen², Maria Melheim³, Rønnaug Solberg^3,4, Ingrid Dannevig⁵, Georg Schmölzer^6,7, Po-Yin Cheung^6,7, Britt Nakstad^8,9, Ola Didrik Saugstad^10,11, Arild Rønnestad^1,2, Anne Lee Solevåg^{2 1}Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, ²Department of Neonatal Intensive Care, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, ³Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, ⁴Department of Pediatrics, Vestfold Hospital Trust, ⁵Department of Anesthesiology, Oslo University Hospital Rikshospitalet, ⁶Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, ⁷Centre for the Studies of Asphyxia and Resuscitation, Neonatal Research Unit, Royal Alexandra Hospital, ⁸Division of Paediatric and Adolescent Medicine, Institute of Clinical Medicine, University of Oslo, ⁹Department of Paediatrics and Adolescent Health, University of Botswana, ¹⁰Department of Pediatric Research, Oslo University Hospital, University of Oslo, ¹¹Department of Pediatrics, Robert H Lurie Medical Research Center, Northwestern University Chicago This piglet model involves surgical instrumentation, asphyxiation until the cardiac arrest, resuscitation, and post-resuscitation observation. The model allows for multiple sampling per animal, and by using continuous invasive arterial blood pressure, ECG, and non-invasive cardiac output monitoring, it provides knowledge about hemodynamics and cardiac pathophysiology in perinatal asphyxia and neonatal cardiopulmonary resuscitation.

• Medicine

  
  Normothermic Negative Pressure Ventilation Ex Situ Lung Perfusion: Evaluation of Lung Function and Metabolism Keir A. Forgie^1,2, Nicholas Fialka³, Max Buchko^1,2, Sayed Himmat⁴, Sanaz Hatami⁴, Xiao Qi⁴, Xiuhua Wang⁴, Katie-Marie Buswell⁵, Ryan Edgar⁵, Darren H. Freed^1,2,6,7, Jayan Nagendran^{1,2,6,7 1}Division of Cardiac Surgery, Department of Surgery, Faculty of Medicine, University of Alberta, ²Mazankowski Alberta Heart Institute, ³Faculty of Medicine and Dentistry, University of Alberta, ⁴Department of Surgery, Faculty of Medicine, University of Alberta, ⁵Ray Rajotte Surgical-Medical Research Institute (SMRI), University of Alberta, ⁶Alberta Transplant Institute, ⁷Canadian Donation and Transplantation Research Program This paper describes a porcine model of negative pressure ventilation ex situ lung perfusion, including procurement, attachment, and management on the custom-made platform. Focus is made on anesthetic and surgical techniques, as well as troubleshooting.

• Immunology and Infection

  
  Screening Peptides that Activate MRGPRX2 using Engineered HEK Cells Shammy Raj¹, Lei Lu², Larry D. Unsworth^{1 1}Department of Chemical and Materials Engineering, Donadeo Innovation Centre for Engineering, University of Alberta, ²School of Life Science and Engineering, Southwest Jiaotong University Techniques for generating a library of short peptides that can activate mast cells via the MRGPRX2 receptor are described. Associated techniques are easy, inexpensive, and can be extended to other cell receptors.

• Medicine

  
  A Protocol for Roux-en-Y Gastric Bypass in Rats using Linear Staplers Jerry T. Dang¹, Valentin Mocanu¹, Breanna Fang², Michael Laffin¹, Shahzeer Karmali¹, Karen Madsen³, Daniel W. Birch^{1 1}Department of Surgery, University of Alberta, ²Faculty of Medicine and Dentistry, University of Alberta, ³Department of Medicine, University of Alberta Roux-en-Y gastric bypass (RYGB) is performed to treat obesity and diabetes. However, the mechanisms underlying RYGB's efficacy are not fully understood, and studies are limited by technical difficulty leading to high mortality in animal models. This article provides instructions on how to perform RYGB in rats with high success rates.

• Bioengineering

  
  Fabrication of a Crystalline Nanocellulose Embedded Agarose Biomaterial Ink for Bone Marrow-Derived Mast Cell Culture Leshern Karamchand¹, Ashley Wagner¹, Syed Benazir Alam¹, Marianna Kulka^{1,2 1}Nanotechnology Research Center, National Research Council Canada, ²Department of Medical Microbiology and Immunology, University of Alberta This protocol highlights a method to rapidly assess the biocompatibility of a crystalline nanocellulose (CNC)/agarose composite hydrogel biomaterial ink with mouse bone marrow-derived mast cells in terms of cell viability and phenotypic expression of the cell surface receptors, Kit (CD117) and high-affinity IgE receptor (FcεRI).

• Medicine

  
  Focal Laser Ablation of Prostate Cancer: An Office Procedure Wayne G. Brisbane¹, Shyam Natarajan¹, Alan Priester¹, Ely R. Felker¹, Adam Kinnaird², Leonard S. Marks^{1 1}University of California Los Angeles, ²University of Alberta This article presents and describes an outpatient treatment for prostate cancer using focal laser ablation. Laser catheter placement is guided by MRI-ultrasound fusion imaging in a fashion similar to prostate needle biopsy. Treatment is monitored in real-time with a thermal probe, placed adjacent to the laser fiber.

• Cancer Research

  
  Discovery of Metastatic Regulators using a Rapid and Quantitative Intravital Chick Chorioallantoic Membrane Model Konstantin Stoletov¹, Lian Willetts², Perrin H. Beatty¹, John D. Lewis^{1 1}Department of Oncology, University of Alberta, Edmonton, Alberta, Canada, ²Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary This is an effective method to screen for suppressors or drivers of cancer metastasis. Cells, transduced with an expression library, are injected into the chicken chorioallantoic membrane vasculature to form metastatic colonies. Colonies having decreased or increased invasiveness are excised, expanded, reinjected to confirm their phenotype, and finally, analyzed using high throughput sequencing.

• Engineering

  
  Cryogenic Liquid Jets for High Repetition Rate Discovery Science Chandra B. Curry*^1,2, Christopher Schoenwaelder*^1,3, Sebastian Goede⁴, Jongjin B. Kim¹, Martin Rehwald^5,6, Franziska Treffert^1,7, Karl Zeil⁵, Siegfried H. Glenzer¹, Maxence Gauthier^{1 1}SLAC National Accelerator Laboratory, ²University of Alberta, ³Friedrich-Alexander-Universität Erlangen-Nürnberg, ⁴European XFEL, ⁵Helmholtz-Zentrum Dresden-Rossendorf, ⁶Technische Universität Dresden, ⁷Technische Universität Darmstadt This protocol presents the operation and principles of micron-scale cylindrical and planar cryogenic liquid jets. Until now, this system has been used as a high repetition rate target in laser-plasma experiments. Anticipated cross-disciplinary applications range from laboratory astrophysics to material science, and eventually next-generation particle accelerators.

• Behavior

  
  Fully Automated Leg Tracking in Freely Moving Insects using Feature Learning Leg Segmentation and Tracking (FLLIT) Animesh Banerjee¹, Shuang Wu², Li Cheng³, Sherry Shiying Aw^{1 1}Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, ²Bioinformatics Institute, Agency for Science, Technology and Research, ³Department of Electrical and Computer Engineering, University of Alberta We describe detailed protocols for using FLLIT, a fully automated machine learning method for leg claw movement tracking in freely moving Drosophila melanogaster and other insects. These protocols can be used to quantitatively measure subtle walking gait movements in wild type flies, mutant flies and fly models of neurodegeneration.

• Chemistry

  
  ¹⁸F-Labeling of Radiotracers Functionalized with a Silicon Fluoride Acceptor (SiFA) for Positron Emission Tomography David Connolly*¹, Justin J. Bailey*¹, Harun Ilhan^2,3, Peter Bartenstein^2,3, Carmen Wängler⁴, Björn Wängler⁵, Melinda Wuest¹, Frank Wuest¹, Ralf Schirrmacher^{1 1}Department of Oncology, University of Alberta, ²Department of Nuclear Medicine, University Hospital of Munich, ³ENETS Centre of Excellence, Interdisciplinary Center of Neuroendocrine Tumors of the GastroEnteroPancreatic System, LMU Munich, ⁴Biomedical Chemistry, Department of Clinical Radiology and Nuclear Medicine, Medical Faculty Mannheim of Heidelberg University, ⁵Molecular Imaging and Radiochemistry, Department of Clinical Radiology and Nuclear Medicine, Medical Faculty Mannheim of Heidelberg University The synthesis of fluorine-18 (¹⁸F) labeled radiopharmaceuticals for positron emission tomography typically requires months of experience. When incorporated into a radiotracer, the silicon-fluoride acceptor (SiFA) motif enables a simple ¹⁸F-labeling protocol that is independent of costly equipment and preparatory training, while reducing precursor quantity needed and utilizing milder reaction conditions.

• Medicine

  
  Generation of Porcine Testicular Organoids with Testis Specific Architecture using Microwell Culture Sadman Sakib¹, Yang Yu^3,4, Anna Voigt², Mark Ungrin^2,3,4, Ina Dobrinski^{1,2 1}Biochemistry and Molecular Biology, University of Calgary, ²Comparative Biology and Experimental Medicine, University of Calgary, ³Biomedical Engineering Graduate Program, University of Calgary, ⁴Alberta Diabetes Institute, University of Alberta Here, we present a protocol for the reproducible generation of porcine testicular organoids with testis specific tissue architecture using the commercially available microwell culture system.

• Neuroscience

  
  Non-Invasive Modulation and Robotic Mapping of Motor Cortex in the Developing Brain Adrianna Giuffre^1,2, Lauran Cole^1,2,3, Hsing-Ching Kuo^4,5, Helen L. Carlson^2,4,5, Jeff Grab⁶, Adam Kirton^2,3,4,5,7, Ephrem Zewdie^{3,4,5 1}Department of Neurosciences, University of Calgary, ²Hotchkiss Brain Institute, University of Calgary, ³Cumming School of Medicine, University of Calgary, ⁴Department of Pediatrics, University of Calgary, ⁵Alberta Children's Hospital Research Institute, University of Calgary, ⁶Faculty of Medicine and Dentistry, University of Alberta, ⁷Department of Clinical Neurosciences, University of Calgary We demonstrate protocols for the modulation (tDCS, HD-tDCS) and mapping (robotic TMS) of the motor cortex in children.

• Editorial

  
  JoVE Methods Collection Highlights: Protein-Protein Interactions Alastair Barr¹, Michael Overduin^{2 1}School of Life Sciences, University of Westminster, ²Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta

• Medicine

  
  Brachial Artery Catheterization in Swine Richard R.E. Uwiera¹, Amirali Toossi^2,3, Dirk G. Everaert^3,4, Trina C. Uwiera⁵, Vivian K. Mushahwar^{2,3,6 1}Department of Agricultural, Food and Nutritional Science, University of Alberta, ²Neuroscience and Mental Health Institute, University of Alberta, ³Sensory Motor Adaptive Rehabilitation Technology (SMART) Network, University of Alberta, ⁴Division of Physical Medicine and Rehabilitation, University of Alberta, ⁵Division of Pediatric Surgery, Department of Surgery, University of Alberta, ⁶Division of Physical Medicine and Rehabilitation, University of Alberta The video describes in detail the catheterization of the distal brachial artery in swine. This procedure accurately measures arterial blood pressure and is a simple and fast method to collect samples for arterial blood gas measurements.

• Developmental Biology

  
  Visualization of the Superior Ocular Sulcus during Danio rerio Embryogenesis Kevin H. Yoon¹, Sonya A. Widen^1,2, Melissa M. Wilson¹, Jennifer C. Hocking^2,3,4,5, Andrew J. Waskiewicz^{1,2,6 1}Department of Biological Sciences, University of Alberta, ²Women & Children's Health Research Institute, University of Alberta, ³Division of Anatomy, Department of Surgery, University of Alberta, ⁴Department of Cell Biology, University of Alberta, ⁵Department of Medical Genetics, University of Alberta, ⁶Neuroscience and Mental Health Research Institute, University of Alberta Here, we present a standardized series of protocols to observe the superior ocular sulcus, a recently-identified, evolutionarily-conserved structure in the vertebrate eye. Using zebrafish larvae, we demonstrate techniques necessary to identify factors that contribute to the formation and closure of the superior ocular sulcus.

• Behavior

  
  A Vibrotactile Feedback Device for Seated Balance Assessment and Training Andrew D. Williams¹, Albert H. Vette^{1,2,3 1}Department of Biomedical Engineering, University of Alberta, ²Department of Mechanical Engineering, University of Alberta, ³Glenrose Rehabilitation Hospital, Alberta Health Services A sitting platform has been developed and assembled that passively destabilizes sitting posture in humans. During the user's stabilizing task, an inertial measurement unit records the device's motion, and vibrating elements deliver performance-based feedback to the seat. The portable, versatile device may be used in rehabilitation, assessment, and training paradigms.

• Medicine

  
  Normothermic Ex Situ Heart Perfusion in Working Mode: Assessment of Cardiac Function and Metabolism Sanaz Hatami¹, Christopher W. White¹, Martin Ondrus¹, Xiao Qi¹, Max Buchko¹, Sayed Himmat¹, Lily Lin², Katie Cameron³, David Nobes⁴, Hyun-Joong Chung⁵, Jayan Nagendran^1,6, Darren H. Freed^{1,3,6,7 1}Department of Surgery, Faculty of Medicine, University of Alberta, ²Department of Pediatrics, Faculty of Medicine, University of Alberta, ³Department of Biomedical Engineering, Faculty of Medicine, University of Alberta, ⁴Department of Mechanical Engineering, Faculty of Engineering, University of Alberta, ⁵Department of Chemical and Materials Engineering, Faculty of Engineering, University of Alberta, ⁶Canadian National Transplant Research Program, ⁷Department of Physiology, Faculty of Medicine, University of Alberta Normothermic ex situ heart perfusion (ESHP), preserves the heart in a beating, semi-physiologic state. When performed in a working mode, ESHP provides the opportunity to perform sophisticated assessments of donor heart function and organ viability. Here, we describe our method for myocardial performance evaluation during ESHP.

• Biochemistry

  
  Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering Tyler Mrozowich¹, Steffane McLennan², Michael Overduin^2,4, Trushar R. Patel^{1,3,4 1}Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, ²Department of Biochemistry, University of Alberta, ³Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, ⁴DiscoveryLab, Faculty of Medicine & Dentistry, University of Alberta Here, we present how Small Angle X-Ray Scattering (SAXS) can be utilized to obtain information on low-resolution envelopes representing the macromolecular structures. When used in conjunction with high-resolution structural techniques such as X-Ray Crystallography and Nuclear Magnetic Resonance, SAXS can provide detailed insights into multidomain proteins and macromolecular complexes in-solution.

• Biochemistry

  
  Measuring Interactions of Globular and Filamentous Proteins by Nuclear Magnetic Resonance Spectroscopy (NMR) and Microscale Thermophoresis (MST) Graeden Winkelaar¹, Catharine Trieber¹, Jitendra Kumar¹, Michael Overduin^{1 1}Department of Biochemistry, University of Alberta Here, we present a protocol for the production and purification of proteins that are labeled with stable isotopes, and subsequent characterization of protein-protein interactions using Nuclear Magnetic Resonance (NMR) spectroscopy and MicroScale Thermophoresis (MST) experiments.

• Immunology and Infection

  
  Antigenic Liposomes for Generation of Disease-specific Antibodies Kyle J. Bednar*¹, Lakeya Hardy*^2,3, Johanna Smeekens*^3,4, Dharmendra Raghuwanshi⁵, Shiteng Duan⁶, Mike D. Kulis^3,4, Matthew S. Macauley^{5,7 1}Janssen R&D, ²Department of Microbiology and Immunology, University of North Carolina, ³UNC Food Allergy Initiative, University of North Carolina, ⁴Department of Pediatrics, University of North Carolina, ⁵Department of Chemistry, University of Alberta, ⁶Department of Molecular Medicine, Scripps Research Institute, ⁷Department of Medical Microbiology and Immunology, University of Alberta Described is the preparation of antigenic liposomal nanoparticles and their use in stimulating B-cell activation in vitro and in vivo. Consistent and robust antibody responses led to the development of a new peanut allergy model. The protocol for generating antigenic liposomes can be extended to different antigens and immunization models.

• Environment

  
  Determination of the Settling Rate of Clay/Cyanobacterial Floccules Tiffany Playter¹, Kurt Konhauser¹, George W. Owttrim², Denise S. Whitford², Tyler Warchola¹, Cheryl Hodgson^1,3, Aleksandra M. Mloszewska⁴, Bruce Sutherland¹, J.-P. Zonneveld¹, S. George Pemberton¹, Murray K. Gingras^{1 1}Department of Earth and Atmospheric Sciences, University of Alberta, ²Department of Biological Sciences, University of Alberta, ³Department of Earth Sciences, Simon Fraser University, ⁴Earth Sciences Department, University of Toronto The interaction and sedimentation of the clay and bacterial cells within the marine realm, observed in natural environments, can be best investigated in a controlled lab environment. Here, we describe a detailed protocol, which outlines a novel method for measuring the sedimentation rate of clay and cyanobacterial floccules.

• Medicine

  
  Novel Approach for Simultaneous Recording of Renal Sympathetic Nerve Activity and Blood Pressure with Intravenous Infusion in Conscious, Unrestrained Mice. Shereen M. Hamza¹, John E. Hall^{2 1}Department of Pediatrics, University of Alberta, ²Department of Physiology & Biophysics, University of Mississippi Medical Center, ³Mississippi Center for Obesity Research Anesthetized mice exhibit non-physiological systemic blood pressure, which precludes meaningful assessment of autonomic tone given the intimate relationship between blood pressure and the autonomic nervous system. Thus, a novel method to simultaneously record renal sympathetic nerve activity and blood pressure with intravenous infusion in conscious mice is outlined.

• Engineering

  
  All-electronic Nanosecond-resolved Scanning Tunneling Microscopy: Facilitating the Investigation of Single Dopant Charge Dynamics Mohammad Rashidi^1,2, Wyatt Vine¹, Jacob A.J. Burgess^3,4,5, Marco Taucer^1,2,6, Roshan Achal¹, Jason L. Pitters², Sebastian Loth^3,4, Robert A. Wolkow^{1,2 1}Department of Physics, University of Alberta, ²National Institute for Nanotechnology, National Research Council of Canada, Edmonton, ³Max Planck Institute for the Structure and Dynamics of Matter, ⁴Max Planck Institute for Solid State Research, ⁵Department of Physics and Astronomy, University of Manitoba, ⁶Joint Attosecond Science Laboratory, University of Ottawa We demonstrate an all-electronic method to observe nanosecond-resolved charge dynamics of dopant atoms in silicon with a scanning tunneling microscope.

• Bioengineering

  
  Improved 3D Hydrogel Cultures of Primary Glial Cells for In Vitro Modelling of Neuroinflammation Kyle M. Koss^1,2, Matthew A. Churchward^1,2, Andrea F. Jeffery^1,3, Vivian K. Mushahwar^1,2,4, Anastasia L. Elias³, Kathryn G. Todd^{1,2,5 1}Department of Psychiatry, University of Alberta, ²Alberta Innovates-Health Solutions Interdisciplinary Team in Smart Neural Prostheses (Project SMART), University of Alberta, ³Department of Chemical and Materials Engineering, University of Alberta, ⁴Division of Physical Medicine and Rehabilitation, University of Alberta, ⁵Centre for Neuroscience, University of Alberta Herein, we present a protocol for the 3D culture of rat brain-derived glia cells, including astrocytes, microglia, and oligodendrocytes. We demonstrate primary cell culture, methacrylated hyaluronic acid (HAMA) hydrogel synthesis, HAMAphoto-polymerization and cell encapsulation, and sample processing for confocal and scanning electron microscopic imaging.

• Bioengineering

  
  A Test Bed to Examine Helmet Fit and Retention and Biomechanical Measures of Head and Neck Injury in Simulated Impact Henry Y. Yu¹, Brooklynn M. Knowles¹, Christopher R. Dennison^{1 1}Department of Mechanical Engineering, University of Alberta Using an anthropometric head and neck, optical fiber-based fit force transducers, an array of head acceleration and neck force/moment transducers, and a dual high speed camera system, we present a test bed to study helmet retention and effects on biomechanical measures of head and neck injury secondary to head impact.

• Behavior

  
  Neurodevelopmental Reflex Testing in Neonatal Rat Pups Antoinette T. Nguyen¹, Edward A. Armstrong¹, Jerome Y. Yager^{1 1}Department of Pediatrics, University of Alberta Behavioral testing is the gold standard for determining outcomes following brain injury, and can identify the presence of developmental disabilities in infants and children. Neurodevelopmental reflexes are an early indicator of these abnormalities. A host of easily accomplished developmental reflex tests in the neonatal rodent were developed and described here.

• Neuroscience

  
  Bioluminescence Imaging of Neuroinflammation in Transgenic Mice After Peripheral Inoculation of Alpha-Synuclein Fibrils Sara Breid¹, Maria E. Bernis¹, Julius B. Tachu¹, Maria C. Garza², Holger Wille², Gültekin Tamgüney^{1 1}German Center for Neurodegenerative Diseases (DZNE), ²Centre for Prions and Protein Folding Diseases & Department of Biochemistry, University of Alberta Peripheral injection of alpha-synuclein fibrils into the peritoneum or tongue of Tg(M83^+/-:Gfap-luc^+/-) mice, which express human alpha-synuclein with the familial A53T mutation and firefly luciferase, can induce neuropathology, including neuroinflammation, in their central nervous system.

• Engineering

  
  In Situ Visualization of the Phase Behavior of Oil Samples Under Refinery Process Conditions Cedric Laborde-Boutet¹, William C. McCaffrey^{1 1}Department of Chemical and Materials Engineering, University of Alberta This article describes a setup and method for the in situ visualization of oil samples under a variety of temperature and pressure conditions that aim to emulate refining and upgrading processes. It is primarily used for studying isotropic and anisotropic media involved in the fouling behavior of petroleum feeds.

• Cancer Research

  
  Live Imaging to Study Microtubule Dynamic Instability in Taxane-resistant Breast Cancers Richard Wang¹, Harris Wang¹, Zhixiang Wang^{1 1}Department of Medical Genetics, Signal Transduction Research Group, Faculty of Medicine and Dentistry, University of Alberta In this paper, we report a protocol describing an in vivo method to measure microtubule dynamic instability in docetaxel-resistant breast cancer cells (MCF-7TXT). In this method, a deconvolution microscopy imaging system is used to detect the expression of GFP-tubulin in target cells.

• Medicine

  
  Assessment of Pulmonary Capillary Blood Volume, Membrane Diffusing Capacity, and Intrapulmonary Arteriovenous Anastomoses During Exercise Vincent Tedjasaputra^1,2, Sean van Diepen³, Sophie É Collins^1,4, Wade M. Michaelchuk^1,2, Michael K. Stickland^{1,5 1}Division of Pulmonary Medicine, University of Alberta, ²Faculty of Physical Education and Recreation, University of Alberta, ³Divisions of Critical Care and Cardiology, University of Alberta, ⁴Faculty of Rehabilitation Medicine, University of Alberta, ⁵G.F. MacDonald Centre for Lung Health To assess the pulmonary diffusion and vasculature responses to exercise, we describe the multiple-inspired oxygen diffusion capacity technique to determine capillary blood volume and membrane diffusing capacity, as well as agitated saline contrast echocardiography to assess the recruitment of intrapulmonary arteriovenous anastomoses.

• Biology

  
  A Web Tool for Generating High Quality Machine-readable Biological Pathways Miguel Ramirez-Gaona¹, Ana Marcu¹, Allison Pon¹, Jason Grant¹, Anthony Wu¹, David S. Wishart^{1,2 1}Department of Computer Science, University of Alberta, ²Department of Biological Sciences, University of Alberta PathWhiz is a comprehensive, online pathway drawing tool for generating biochemical and biological pathways. It uses publicly accessible databases and easily expandable palettes consisting of pre-drawn pathway components. This protocol describes how to easily build new pathways, replicate and edit existing pathways, and propagate previously drawn pathways to different organisms.

• Developmental Biology

  
  Transcriptome Profiling of In-Vivo Produced Bovine Pre-implantation Embryos Using Two-color Microarray Platform Reza Salehi*¹, Stephen C.M. Tsoi*¹, Marcos G. Colazo², Divakar J. Ambrose^1,2, Claude Robert³, Michael K. Dyck^{1 1}Department of Agricultural, Food and Nutritional Science, University of Alberta, ²Livestock Research Branch, Alberta Agriculture and Forestry, ³Laboratory of Functional Genomics of Early Embryonic Development, Université Laval Microarray technology allows quantitative measurement and gene expression profiling of transcripts on a genome-wide basis. Therefore, this protocol provides an optimized technical procedure in a two-color custom made bovine array using Day 7 bovine embryos to demonstrate the feasibility of using low amount of total RNA.

• Environment

  
  Extraction and Analysis of Microbial Phospholipid Fatty Acids in Soils Sylvie A. Quideau¹, Anne C.S. McIntosh², Charlotte E. Norris¹, Emily Lloret³, Mathew J.B. Swallow⁴, Kirsten Hannam^{5 1}Department of Renewable Resources, University of Alberta, ²Department of Science, Augustana Faculty, University of Alberta, ³Laboratoire Génie Civil et géo-Environnement, Université de Lille, ⁴Department of Earth and Environmental Sciences, Mount Royal University, ⁵Forest Ecology & Production, Great Lakes Forestry Centre, Natural Resources Canada Phospholipid fatty acids provide information about the structure of soil microbial communities. We present methods for extraction from soil samples with a single-phase chloroform mixture, fractionation of extracted lipids using solid phase extraction columns, and methanolysis to produce fatty acid methyl esters, which are analyzed by capillary gas chromatography.

• Bioengineering

  
  Microbiologically Induced Calcite Precipitation Mediated by Sporosarcina pasteurii Swayamdipta Bhaduri¹, Nandini Debnath¹, Sushanta Mitra², Yang Liu³, Aloke Kumar^{1 1}Department 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.

• Chemistry

  
  An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions Mohameedyaseen Syedbasha¹, Janina Linnik^1,2,3, Deanna Santer⁴, Daire O'Shea⁵, Khaled Barakat^4,6, Michael Joyce⁴, Nina Khanna⁷, D. Lorne Tyrrell⁴, Michael Houghton⁴, Adrian Egli^{1,8 1}Applied Microbiology Research, Department of Biomedicine, University of Basel, ²Department of Biosystems Science and Engineering, ETH Zurich, and Swiss Institute of Bioinformatics, ³Swiss Institute of Bioinformatics, ⁴Li Ka Shing Institute for Virology, University of Alberta, ⁵Regional Infectious Diseases Unit, University of Edinburgh, ⁶Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, ⁷Infection Biology, Department of Biomedicine, University of Basel, ⁸Clinical Microbiology, University Hospital Basel The presented protocols describe two enzyme-linked immunosorbent assay (ELISA) based techniques for the rapid investigation of ligand-receptor interactions: The first assay allows the determination of dissociation constant between ligand and receptor. The second assay enables a rapid screening of blocking peptides for ligand-receptor interactions.

• Medicine

  
  Long-Term Catheterization of the Intestinal Lymph Trunk and Collection of Lymph in Neonatal Pigs Richard R. Uwiera¹, Rabban Mangat¹, Sandra Kelly¹, Trina C. Uwiera², Spencer D. Proctor^{1 1}Department of Agricultural, Food and Nutritional Science, University of Alberta, ²Department of Surgery, University of Alberta We present a surgical procedure to catheterize the intestinal lymph trunk in neonatal pigs to collect large quantities of lipid metabolism components from efferent lymph.

• Developmental Biology

  
  Accurate and Phenol Free DNA Sexing of Day 30 Porcine Embryos by PCR Milena S. Blanes*¹, Stephen C.M. Tsoi*¹, Michael K. Dyck^{1 1}Department of Agricultural, Food and Nutritional Science, University of Alberta This protocol describes an accurate, inexpensive, rapid and non-toxic method to determine the sex of Day 30 porcine embryo using PCR method after grinding an embryo into powder without phenol chloroform extraction and DNA column purification.

• Biology

  
  Visualization of miniSOG Tagged DNA Repair Proteins in Combination with Electron Spectroscopic Imaging (ESI) Hilmar Strickfaden¹, Zhi Zhong Xu¹, Michael J. Hendzel^{1 1}Department of Oncology, Faculty of Dentistry and Medicine, University of Alberta Electron spectroscopic imaging can image and distinguish nucleic acid from protein at nanometer resolution. It can be combined with the miniSOG system, which is able to specifically label tagged proteins in transmission electron microscopy samples. We illustrate the use of these technologies using double-strand break repair foci as an example.

• Bioengineering

  
  Engineering 3D Cellularized Collagen Gels for Vascular Tissue Regeneration Sébastien Meghezi¹, Dawit G. Seifu^1,2, Nina Bono^1,3, Larry Unsworth^2,4,5, Kibret Mequanint⁶, Diego Mantovani^{1,2 1}Laboratory for Biomaterials and Bioengineering, Department Min-Met-Materials Eng & CHU de Québec Research Center, Canada Research Chair I for the Innovation in Surgery, Laval University, ²NSERC CREATE Program for Regenerative Medicine (NCPRM), Laval University, ³Department Electronics, Information and Bioengineering, Politecnico di Milano, ⁴Department of Chemical and Materials Engineering, University of Alberta, ⁵National Institute for Nanotechnology, National Research Council (Canada), ⁶Department of Chemical and Biochemical Engineering, University of Western Ontario In this work, we present a technique for the rapid fabrication of living vascular tissues by direct culturing of collagen, smooth muscle cells and endothelial cells. In addition, a new protocol for the mechanical characterization of engineered vascular tissues is described.

• Neuroscience

  
  Quantitative Analysis of Climbing Defects in a Drosophila Model of Neurodegenerative Disorders Surya T. Madabattula¹, Joel C. Strautman¹, Andrew M. Bysice¹, Julia A. O’Sullivan¹, Alaura Androschuk¹, Cory Rosenfelt¹, Kacy Doucet¹, Guy Rouleau², Francois Bolduc^{1 1}Department of Pediatrics, University of Alberta, ²Montreal Neurological Institute and Hospital, McGill University We present an optimized inexpensive and reliable negative geotaxis assay in Drosophila melanogaster as a model for neurodegenerative disorders. Being more sensitive to mild locomotor defects, this assay will help screen for potential genetic interactions and drug targets.

• Engineering

  
  Surface Enhanced Raman Spectroscopy Detection of Biomolecules Using EBL Fabricated Nanostructured Substrates Robert F. Peters^1,2, Luis Gutierrez-Rivera^1,2, Steven K. Dew^1,2, Maria Stepanova^{1,2 1}Department of Electrical and Computer Engineering, University of Alberta, ²National Institute for Nanotechnology, National Research Council of Canada We describe the fabrication and characterization of nano-biological systems interfacing nanostructured substrates with immobilized proteins and aptamers. The relevant experimental steps involving lithographic fabrication of nanostructured substrates, bio-functionalization, and surface-enhanced Raman spectroscopy (SERS) characterization, are reported. SERS detection of surface-immobilized proteins, and probing of protein-ligand and aptamer-ligand binding is demonstrated.

• Environment

  
  A Small Volume Bioassay to Assess Bacterial/Phytoplankton Co-culture Using WATER-Pulse-Amplitude-Modulated (WATER-PAM) Fluorometry Anna R. Bramucci¹, Leen Labeeuw¹, Teaghan J. Mayers¹, Julie A. Saby¹, Rebecca J. Case^{1 1}Department of Biological Sciences, University of Alberta The goal of this procedure is to demonstrate the reproducibility and adaptability of using a microtiter plate format for microalgal screening. This rapid screen combines WATER-Pulse-Amplitude-Modulated (WATER-PAM) fluorometry to measure photosynthetic yield as an indicator of Photosystem II (PSII) health with small volume bacterial-algal co-cultures.

• Medicine

  
  Murine Ileocolic Bowel Resection with Primary Anastomosis Troy Perry¹, Anna Borowiec¹, Bryan Dicken¹, Richard Fedorak², Karen Madsen^{2 1}Department of Surgery, University of Alberta, ²Department of Medicine, University of Alberta Ileocolic resection is commonly performed in several human diseases; however, little is known regarding the impact of intestinal resection on surgical illnesses. This article provides instruction on executing the procedure in mice with high success, providing a means to study the effects of ileocolic resection in models of disease.

• Bioengineering

  
  Protocol for Biofilm Streamer Formation in a Microfluidic Device with Micro-pillars Mahtab Hassanpourfard¹, Xiaohui Sun², Amin Valiei¹, Partha Mukherjee³, Thomas Thundat¹, Yang Liu², Aloke Kumar^{4 1}Department of Chemical and Material Engineering, University of Alberta, ²Department of Civil and Environmental Engineering, University of Alberta, ³Department of Mechanical Engineering, Texas A&M University, ⁴Department of Mechanical Engineering, University of Alberta Protocols for the study of biofilm formation in a microfluidic device that mimics porous media are discussed. The microfluidic device consists of an array of micro-pillars and biofilm formation by Pseudomonas fluorescens in this device is investigated.

• Chemistry

  
  A Simple and Rapid Protocol for Measuring Neutral Lipids in Algal Cells Using Fluorescence Zachary J. Storms¹, Elliot Cameron¹, Hector de la Hoz Siegler^1,2, William C. McCaffrey^{1 1}Department of Chemical and Materials Engineering, University of Alberta, ²Department of Chemical and Petroleum Engineering, University of Calgary A simple protocol to determine the neutral lipid content of algal cells using a Nile Red staining procedure is described. This time-saving technique offers an alternative to traditional gravimetric-based lipid quantification protocols. It has been designed for the specific application of monitoring bioprocess performance.

• Medicine

  
  A Three-dimensional Tissue Culture Model to Study Primary Human Bone Marrow and its Malignancies Mukti R. Parikh¹, Andrew R. Belch^2,3, Linda M Pilarski^2,3, Julia Kirshner^{1 1}Department of Biological Sciences, Purdue University, ²Department of Oncology, University of Alberta, ³Cross Cancer Institute In standard culture methods cells are taken out of their physiological environment and grown on the plastic surface of a dish. To study the behavior of primary human bone marrow cells we created a 3-D culture system where cells are grown under conditions recapitulating the native microenvironment of the tissue.

• Biology

  
  Rapid Protocol for Preparation of Electrocompetent Escherichia coli and Vibrio cholerae Miguel F. Gonzales¹, Teresa Brooks², Stefan U. Pukatzki², Daniele Provenzano^{1,3 1}Department of Biological Sciences, University of Texas Brownsville, ²Department of Medical Microbiology and Immunology, University of Alberta, ³Department of Biomedical Sciences, University of Texas Brownsville Electroporation is a commonly employed method for introducing DNA into bacteria in a process known as transformation. Traditional protocols for the preparation of electrocompetent cells are time consuming and labor intensive. This article describes an alternate, rapid, and efficient method for the preparation of electrocompetent cells presently employed by some laboratories.

• Neuroscience

  
  Patch Clamp Recordings from Embryonic Zebrafish Mauthner Cells Birbickram Roy¹, Declan William Ali^{1 1}Department of Biological Sciences, University of Alberta We have developed an intact brain-spinal cord preparation to record and monitor electrical activity via patch clamp recording from the Mauthner neurons and other reticulospinal cells in zebrafish embryos. Thus, we are able to record excitatory and inhibitory synaptic currents, voltage-gated channel activity and action potentials from key neurons in a developing embryo.

• Engineering

  
  Ultrahigh Density Array of Vertically Aligned Small-molecular Organic Nanowires on Arbitrary Substrates Ryan Starko-Bowes¹, Sandipan Pramanik^{1 1}Electrical and Computer Engineering, University of Alberta We report a simple method for fabricating an ultrahigh density array of vertically ordered small-molecular organic nanowires. This method allows for synthesis of complex heterostructured hybrid nanowire geometries, which can be inexpensively grown on arbitrary substrates. These structures have potential applications in organic electronics, optoelectronics, chemical sensing, photovoltaics and spintronics.

• Immunology and Infection

  
  A Simple and Efficient Method to Detect Nuclear Factor Activation in Human Neutrophils by Flow Cytometry Erick García-García¹, Eileen Uribe-Querol², Carlos Rosales^{3 1}Department of Biological Sciences, University of Alberta, ²División de Estudios de Posgrado e Investigación, Facultad de Odontología, Universidad Nacional Autónoma de México, ³Department of Immunology, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México Neutrophils are the most abundant leukocytes in blood. Neutrophils possess transcriptionally regulated functions such as production of proinflammatory cytokines and inhibition of apoptosis. These functions can be studied with the method presented here, which allows detection and quantification of nuclear factors by flow cytometry in isolated nuclei

• Engineering

  
  Synthesis and Operation of Fluorescent-core Microcavities for Refractometric Sensing Shalon McFarlane¹, C.P.K. Manchee¹, Joshua W. Silverstone¹, Jonathan Veinot¹, Al Meldrum^{1 1}Department of Physics, University of Alberta Fluorescent-core microcavity sensors employ a high-index quantum-dot coating in the channel of silica microcapillaries. Changes in the refractive index of fluids pumped into the capillary channel cause shifts in the microcavity fluorescence spectrum that can be used to analyze the channel medium.

• Immunology and Infection

  
  Examination of Thymic Positive and Negative Selection by Flow Cytometry Qian Hu*¹, Stephanie A. Nicol*¹, Alexander Y.W. Suen*¹, Troy A. Baldwin^{1 1}Department of Medical Microbiology and Immunology, University of Alberta We present a flow cytometry-based method to examine T cell development in vivo using genetically manipulated mice on a wildtype or T cell receptor transgenic background.

• Medicine

  
  Human Internal Mammary Artery (IMA) Transplantation and Stenting: A Human Model to Study the Development of In-Stent Restenosis Xiaoqin Hua^1,2, Tobias Deuse^1,2, Evangelos D. Michelakis³, Alois Haromy³, Phil S. Tsao⁴, Lars Maegdefessel⁴, Reinhold G. Erben⁵, Claudia Bergow⁵, Boris B. Behnisch⁶, Hermann Reichenspurner^1,2, Robert C. Robbins⁷, Sonja Schrepfer^{1,2,7 1}University Heart Center Hamburg, TSI-Lab, Germany, ²Cardiovascular Research Center, University of Hamburg, ³Department of Medicine, Cardiology Division, Pulmonary Hypertension Program, University of Alberta, ⁴Department of Medicine, Stanford University School of Medicine, ⁵Department of Biomedical Sciences, Institute of Physiology, Pathophysiology, and Biophysics, University of Veterinary Medicine, Vienna, ⁶Translumina GmbH, Hechingen, ⁷Department of Cardiothoracic Surgery, Stanford University School of Medicine This video shows a model to study the development of intimal hyperplasia after stent deployment using a human vessel (IMA) in an immunodeficient rat model.

• Neuroscience

  
  Brain Imaging Investigation of the Impairing Effect of Emotion on Cognition Gloria Wong^1,2, Sanda Dolcos^1,3, Ekaterina Denkova¹, Rajendra Morey^4,5,6, Lihong Wang^4,5, Gregory McCarthy^6,7, Florin Dolcos^{1,2,3,8,9 1}Department of Psychiatry, University of Alberta, ²Centre for Neuroscience, University of Alberta, ³Department of Psychology, University of Illinois, ⁴Brain Imaging and Analysis Center, Duke University, ⁵Department of Psychiatry and Behavioral Sciences, Duke University, ⁶Mid-Atlantic Mental Illness Research Education and Clinical Center, VA Medical Center, ⁷Department of Psychology, Yale University, ⁸Neuroscience Program, University of Illinois, ⁹Beckman Institute for Advanced Science & Technology, University of Illinois We present a protocol that allows investigation of the neural mechanisms mediating the detrimental impact of emotion on cognition, using functional magnetic resonance imaging. This protocol can be used with both healthy and clinical participants.

• Medicine

  
  A Swine Model of Neonatal Asphyxia Po-Yin Cheung¹, Richdeep S. Gill², David L. Bigam^{2 1}Departments of Pediatrics, Pharmacology and Surgery, University of Alberta, ²Department of Surgery, University of Alberta Large animal models have good translational values in the examination of physiology and pharmacology of neonatal asphyxia. Using newborn piglets, we develop an experimental protocol to simulate neonatal asphyxia which has advantages of studying the systemic and regional hemodynamics, oxygen transport with biochemical and pathologic pathways and correlations.

• Medicine

  
  Guide Wire Assisted Catheterization and Colored Dye Injection for Vascular Mapping of Monochorionic Twin Placentas Eric B. Jelin¹, Samuel C. Schecter¹, Kelly D. Gonzales¹, Shinjiro Hirose¹, Hanmin Lee¹, Geoffrey A. Machin², Larry Rand³, Vickie A. Feldstein^{4 1}Division of Pediatric and Fetal Surgery, Department of Surgery, University of California, San Francisco, ²Department of Pathology, University of Alberta, ³Department of Obstretics and Gynecology, University of California, San Francisco, ⁴Department of Radiology, University of California, San Francisco Vascular mapping of monochorionic (MC) twin placentas after birth provides a means for detailed demonstration of vascular connections between the twins’ circulations. Imbalance of these connections is thought to play a pivotal role in the development of complications of MC twinning including twin-to-twin transfusion syndrome.

• Neuroscience

  
  Brain Imaging Investigation of the Neural Correlates of Emotion Regulation Sanda Dolcos¹, Keen Sung², Ekaterina Denkova³, Roger A. Dixon^4,5, Florin Dolcos^{1,6,7 1}Department of Psychology, University of Illinois, Urbana-Champaign, ²Department of Computing Science, University of Alberta, Edmonton, ³Department of Psychiatry, University of Alberta, Edmonton, ⁴Department of Psychology, University of Alberta, Edmonton, ⁵Centre for Neuroscience, University of Alberta, Edmonton, ⁶Neuroscience Program, University of Illinois, Urbana-Champaign, ⁷Beckman Institute, University of Illinois, Urbana-Champaign We present a protocol that allows investigation of the neural correlates of deliberate and automatic emotion regulation, using functional magnetic resonance imaging. This protocol can be used in healthy participants, both young and older, as well as in clinical patients.

• Neuroscience

  
  Brain Imaging Investigation of the Neural Correlates of Emotional Autobiographical Recollection Ekaterina Denkova¹, Trisha Chakrabarty¹, Sanda Dolcos^1,2, Florin Dolcos^{1,2,3,4 1}Department of Psychiatry, University of Alberta, Edmonton, ²Psychology Department, University of Illinois, Urbana-Champaign, ³Neuroscience Program, University of Illinois, Urbana-Champaign, ⁴Beckman Institute for Advanced Science & Technology, University of Illinois, Urbana-Champaign We present a protocol that allows investigation of the neural correlates of recollecting emotional autobiographical memories, using functional magnetic resonance imaging. This protocol can be used with both healthy and clinical participants.

• Neuroscience

  
  Brain Imaging Investigation of the Neural Correlates of Observing Virtual Social Interactions Keen Sung¹, Sanda Dolcos², Sophie Flor-Henry³, Crystal Zhou³, Claudia Gasior⁴, Jennifer Argo⁵, Florin Dolcos^{2,6,7 1}Department of Computing Science, University of Alberta, ²Department of Psychology, University of Illinois, ³Centre for Neuroscience, University of Alberta, ⁴Department of Psychology, University of Alberta, ⁵Department of Marketing, Business Economics, and Law, University of Alberta, ⁶Neuroscience Program, University of Illinois at Urbana-Champaign, ⁷Beckman Institute, University of Illinois at Urbana-Champaign This article demonstrates an experimental design in which whole-body animated characters are used in conjunction with functional magnetic resonance imaging (fMRI) to investigate the neural correlates of observing virtual social interactions.

• Biology

  
  Swimming Performance Assessment in Fishes Keith B. Tierney^{1 1}Department of Biological Sciences, University of Alberta The lives of the majority of fish are predicated on swimming. This protocol describes techniques for capturing a range of swimming modes available to individual and schooling fish, and includes metrics associated with swimming physiology and behaviour.

• Neuroscience

  
  Brain Imaging Investigation of the Memory-Enhancing Effect of Emotion Andrea Shafer¹, Alexandru Iordan², Roberto Cabeza³, Florin Dolcos^{1,4 1}Centre for Neuroscience, University of Alberta, ²Neuroscience Program, University of Illinois, Urbana-Champaign, ³Center for Cognitive Neuroscience, Duke University, ⁴Psychology Department, Neuroscience Program, & Beckman Institute, University of Illinois, Urbana-Champaign We present a protocol that uses functional magnetic resonance imaging to investigate the neural correlates of the memory-enhancing effect of emotion. This protocol allows identification of brain activity specifically linked to memory-related processing, contrary to more general perceptual processing, and can be used with healthy and clinical populations.

• Biology

  
  Modified Annexin V/Propidium Iodide Apoptosis Assay For Accurate Assessment of Cell Death Aja M. Rieger¹, Kimberly L. Nelson¹, Jeffrey D. Konowalchuk¹, Daniel R. Barreda^{1,2 1}Department of Biological Sciences, University of Alberta, ²Department of Agriculture, Food and Nutrition Sciences, University of Alberta An accurate method for the assessment of cell death is described. The protocol improves upon conventional Annexin V/ propidium iodide (PI) protocols, which display up to 40% false- positive events in cell lines and primary cells from a broad range of animal models.

• Biology

  
  Catheterization of Intestinal Loops in Ruminants Richard R. E. Uwiera¹, John P. Kastelic², G. Douglas Inglis^{2 1}Department of Agricultural, Food and Nutritional Science, University of Alberta, ²Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge We describe a novel surgical method for catheterizing 'intestinal loops' within the ileum of sheep. Once animals have recovered from surgery and have cleared antibiotics and analgesics, multiple treatments can be deposited directly in loops via the catheters.