JoVE General
An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
Wellcome Trust Centre for Human Genetics, University of Oxford
Genetic associations often remain unexplained at a functional level. This method aims to assess the effect of phenotype-associated genetic markers on gene expression by analyzing cells heterozygous for transcribed SNPs. The technology allows accurate measurement by MALDI-TOF mass spectrometry to quantify allele-specific primer extension products.
JoVE General
Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources
Max-Planck Institute for Evolutionary Anthropology, Leipzig
We present a method of targeted ancient DNA sequence retrieval, which we used to reconstruct the complete mitochondrial genomes of five Neandertal individuals. Comparison of these sequences with present day humans suggests that Neandertals had a long term low effective population size.
JoVE General
Measuring Plant Cell Wall Extension (Creep) Induced by Acidic pH and by Alpha-Expansin
Department of Biology, Penn State University
We demonstrate the use of a constant-force extensometer to measure long-term extension (creep) of plant cell wall specimens induced by acidic buffers and expansin protein.
JoVE Bioengineering
Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers
1LSA Biophysics, University of Michigan, 2LSA Biophysics, Department of Physics, University of Michigan
We illustrate the use of a constant force axial optical tweezers to explore the mechanical properties of short DNA molecules. By stretching DNA axially, we minimize steric hindrances and artifacts arising in conventional lateral manipulation, allowing us to study DNA molecules as short as ~100 nm.
JoVE Immunology and Infection
Examination of the Telomere G-overhang Structure in Trypanosoma brucei
Biological, Geo. & Env. Sciences, Cleveland State University
Telomeres are essential for chromosome stability and the telomere G-overhang structure is essential for telomerase-mediated telomere maintenance. We have recently adopted two methods for detecting the telomere G-overhang structure in Trypanosoma brucei, which are native in-gel hybridization and ligation-mediated primer extension, which will be described.
JoVE Clinical and Translational Medicine
Development of Obliterative Bronchiolitis in a Murine Model of Orthotopic Lung Transplantation
1Departments of Medicine, Microbiology and Immunology, Indiana University School of Medicine, 2Center for Immunobiology, Indiana University School of Medicine
Obliterative bronchiolitis is the key impediment to the long-term survival of lung transplant recipients and the lack of a robust preclinical model precludes examining obliterative bronchiolitis immunopathogenesis. Unlike other solid organ transplants, vascularized mouse lung transplantation has only recently been developed. Here we show our independently developed obliterative bronchiolitis model after murine orthotopic single-lung transplantation.
JoVE General
An Analytical Tool that Quantifies Cellular Morphology Changes from Three-dimensional Fluorescence Images
1Medications Development, Ernest Gallo Clinic and Research Center, University of California, San Francisco, 2Clinical Pharmacology and Experimental Therapeutics, University of California, San Francisco, 3Translational Research Institute and the Institute for Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
We developed a software platform that utilizes Imaris Neuroscience, ImarisXT and MATLAB to measure the changes in morphology of an undefined shape taken from three-dimensional confocal fluorescence of single cells. This novel approach can be used to quantify changes in cell shape following receptor activation and therefore represents a possible additional tool for drug discovery.
JoVE Bioengineering
Tri-layered Electrospinning to Mimic Native Arterial Architecture using Polycaprolactone, Elastin, and Collagen: A Preliminary Study
1Department of Biomedical Engineering, Virginia Commonwealth University, 2Department of Anatomy and Neurobiology, Virginia Commonwealth University, 3Department of Cardiovascular Surgery, University Hospital of Geneva
The aim of this study was to mimic the native three layered architecture of the arterial wall. To accomplish this, electrospinning was employed with the use of a 3-1 (input-output) nozzle and blends of polycaprolactone, elastin, and collagen.
JoVE Neuroscience
High Sensitivity 5-hydroxymethylcytosine Detection in Balb/C Brain Tissue
Applications and Product Development, New England Biolabs
The EpiMark 5-hmC and 5-mC Analysis Kit can be used to analyze and quantitate 5-methylcytosine and 5-hydroxymethylcytosine within a spe cific locus. The kit distinguishes 5-mC from 5-hmC by the addition of glucose to the hydroxyl group of 5-hmC via an enzymatic reaction utilizing β-glucosyltransferase (T4-BGT). When 5-hmC occurs In the context of CCGG, this modification converts a cleavable MspI site to a non-cleavable site.
JoVE General
Polymerase Chain Reaction: Basic Protocol Plus Troubleshooting and Optimization Strategies
Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles
PCR has emerged as a common technique in many molecular biology laboratories. Provided here is a quick guide to several conventional PCR protocols. Because each reaction is a unique experiment, optimal conditions required to generate a product vary. Understanding the variables in a reaction will greatly enhance troubleshooting efficiency, thereby increasing the chance to obtain the desired result.
JoVE Clinical and Translational Medicine
A Murine Model of Muscle Training by Neuromuscular Electrical Stimulation
1Department of Physical Medicine and Rehabilitation, University of Pittsburgh, 2Department of Physical Therapy, University of Pittsburgh, 3McGowan Institute for Regenerative Medicine, University of Pittsburgh
A murine model of neuromuscular electrical stimulation (NMES), a safe and inexpensive clinical modality, to the anterior compartment muscles is described. This model has the advantage of modifying a readily available clinical device for the purpose of eliciting targeted and specific muscle contractions in mice.
JoVE Clinical and Translational Medicine
Rat Model of Blood-brain Barrier Disruption to Allow Targeted Neurovascular Therapeutics
Department of Neurological Surgery, Vanderbilt University School of Medicine
Blood-brain barrier disruption aids the delivery of certain drugs to the brain. Mannitol delivered intra-arterially shrinks cells surrounding blood vessels in order to physically disrupt the barrier.
JoVE Clinical and Translational Medicine
In Vivo Canine Muscle Function Assay
1Department of Neurology and Wake Forest Institute for Regenerative Medicine, Wake Forest University, 2Department of Human Nutrition, Foods and Exercise, Virginia Polytechnic Institute and State University, 3Departments of Pathology and Laboratory Medicine and Neurology and the Gene Therapy Center , University of North Carolina-Chapel Hill
We describe a minimally-invasive and painless method to measure canine hindlimb muscle strength and muscle response to repeated eccentric contractions.
JoVE Clinical and Translational Medicine
Manual Muscle Testing: A Method of Measuring Extremity Muscle Strength Applied to Critically Ill Patients
1Outcomes After Critical Illness and Surgery (OACIS) Group, Division of Pulmonary and Critical Care Medicine, Johns Hopkins University, 2Critical Care Physical Medicine and Rehabilitation Program, Johns Hopkins Hospital, 3Department of Physical Medicine and Rehabilitation, Johns Hopkins University, 4Department of Rehabilitation Services, University of Maryland Medical System
Survivors of acute respiratory distress syndrome (ARDS) and critical illness frequently develop long-lasting muscle weakness. Manual muscle testing (MMT) is a standardized clinical examination commonly used to measure strength of peripheral skeletal muscle groups. This video demonstrates MMT using the 6-point Medical Research Council scale.
JoVE Clinical and Translational Medicine
Methods to Quantify Pharmacologically Induced Alterations in Motor Function in Human Incomplete SCI
1Sensory Motor Performance Program, Rehabilitation Institute of Chicago, 2Department of Kinesiology and Nutrition, University of Illinois at Chicago, 3Department of Physical Therapy, University of Illinois at Chicago
This video demonstrates modulation of reflex activity, volitional strength and ambulation through clinical and quantitative assessments in individuals with motor incomplete SCI as a result of acute oral administration of a serotonin reuptake inhibitor (SSRI).
JoVE Clinical and Translational Medicine
Breathing-controlled Electrical Stimulation (BreEStim) for Management of Neuropathic Pain and Spasticity
1Department of Physical Medicine and Rehabilitation, University of Texas Health Science Center at Houston, 2UTHealth Motor Recovery Laboratory, TIRR Memorial Hermann Hospital, 3The Institute of Rehabilitation and Research (TIRR), TIRR Memorial Hermann Hospital
The purpose is to present a new method, breathing-control electrical stimulation (BreEStim) for management of neuropathic pain and spasticity.
JoVE General
Measuring Replicative Life Span in the Budding Yeast
1Department of Biochemistry, University of Washington, 2Department of Pathology, University of Washington
In this article we present a general protocol for measuring the replicative life span of yeast mother cells.
JoVE General
Genotyping of Plant and Animal Samples without Prior DNA Purification
Thermo Scientific Molecular Biology Products, Thermo Fisher Scientific
The Direct PCR approach presented here facilitates PCR amplification directly from small amounts of unpurified plant and animal tissue.
JoVE Neuroscience
Automated Sholl Analysis of Digitized Neuronal Morphology at Multiple Scales
1Department of Cell Biology and Neuroscience, Rutgers University, 2Graduate Program in Biomedical Engineering, Rutgers University
We have developed a computer program to analyze neuronal morphology. In combination with two existing open source analysis tools, our program performs Sholl analysis and determines the number of neurites, branch points, and neurite tips. The analyses are performed so that local changes in neurite morphology can be observed.
JoVE Neuroscience
Investigating the Neural Mechanisms of Aware and Unaware Fear Memory with fMRI
Department of Psychology, University of Alabama at Birmingham
A methodology to investigate the neural mechanisms that support aware and unaware memory processes during fear conditioning is described. This method monitors blood oxygen level dependent (BOLD) functional magnetic resonance imaging, skin conductance response, and unconditioned stimulus expectancy during Pavlovian fear conditioning to assess the neural correlates of distinct memory processes.
JoVE Neuroscience
Neural Tube Closure in Mouse Whole Embryo Culture
Department of Neurology/Neuroscience, Weill Cornell Medical College
A method allowing for direct pharmacological manipulation of mouse embryos during neurulation that bypasses maternal metabolism is described. The technique can be adapted to study different aspects of neurulation by varying the time point and pharmacological agent.
JoVE Clinical and Translational Medicine
Vascular Occlusion Training for Inclusion Body Myositis: A Novel Therapeutic Approach
1School of Physical Education and Sport, University of São Paulo, 2Division of Rheumatology, School of Medicine, University of São Paulo
The present article presents the details pertaining to the application of resistance training associated to vascular occlusion in IBM patients.
JoVE Editorial
JoVE 3rd Issue
This third issue of JoVE draws attention to issues on the intersection of the basic and applied biomedical research. In this context, the interview with Ole Isacson (McLean Hospital/Harvard Medical School) provides an in-depth look at contemporary challenges of Parkinson’s disease research. The candid interview grants insights that reach beyond the pure scientific problems, as it addresses...
JoVE Clinical and Translational Medicine
Surgical Procedures for a Rat Model of Partial Orthotopic Liver Transplantation with Hepatic Arterial Reconstruction
1Institute for Laboratory Animal Science and Experimental Surgery, RWTH-Aachen University, 2Department of Hepato-Biliary-Pancreatic Surgery and Transplantation, Graduate School of Medicine, Kyoto University
Orthotopic liver transplantation in rats is an indispensable experimental model for biomedical research. Here we present our surgical procedures for orthotopic rat liver transplantation with hepatic arterial reconstruction using a 50% partial graft.
JoVE Bioengineering
Axon Stretch Growth: The Mechanotransduction of Neuronal Growth
1Departments of Biomedical Engineering, New Jersey Institute of Technology, 2Graduate School of Biomedical Sciences, University of Medicine and Dentistry of New Jersey
A unique tissue engineering method was developed to elongate numerous nerve fibers in culture by recapitulating axon stretch growth; a form of nervous system growth whereby nerves elongate in conjunction with growth of the enlarging body.
JoVE Clinical and Translational Medicine
Remote Magnetic Navigation for Accurate, Real-time Catheter Positioning and Ablation in Cardiac Electrophysiology Procedures
1Cardiology, Robotic Cardiac Electrophysiology and Arrhythmia Unit, La Paz University Hospital, 2Magnetecs Corp., 3Cardiology, Geffen School of Medicine at UCLA Los Angeles
This report provides a detailed description of a new remote navigation system based on magnetic driven forces, which has been recently introduced as a new robotic tool for human cardiac electrophysiology procedures.
JoVE General
Fluorescence in situ hybridization (FISH) Protocol in Human Sperm
Unitat de Biologia Cel·lular (Facultat de Biociències), Universitat Autónoma de Barcelona
This video-article describes, step by step, how to process a semen sample to achieve good-quality fluorescence in situ hybridization on human spermatozoa. Preparations obtained can be used for aneuploidy screening in the context of clinical diagnosis.
JoVE Neuroscience
Tactile Conditioning And Movement Analysis Of Antennal Sampling Strategies In Honey Bees (Apis mellifera L.)
In this protocol we show how to condition harnessed honey bees to tactile stimuli and introduce a 2D motion capture technique for analyzing the kinematics of fine-scale antennal sampling pattern.
JoVE Clinical and Translational Medicine
Guidelines for Elective Pediatric Fiberoptic Intubation
1Department of Anesthesia, St. Jude Children's Research Hospital, 2Department of Anesthesia, Children's Hospital of Michigan, 3Department of Anesthesiology, Children's Hospital of Michigan
We describe guidelines to perform a safe and efficient elective fiberoptic intubation in pediatric patients while maintaining spontaneous ventilation.
JoVE General
In vivo Ca2+- Imaging of Mushroom Body Neurons During Olfactory Learning in the Honey Bee
1Institut für Biologie - Neurobiologie, Freie Universität Berlin, 2Institut für Biologie - Neurobiologie, Free University Berlin - Freie Universitaet Berlin
Bees can be conditioned in an appetitive olfactory learning paradigm (PER-conditioning). Using odors as stimuli, we established a method in which behavior is recorded while simultaneously Calcium Imaging is used to measure odor evoked activity in mushroom body neurons in vivo.
JoVE General
Trajectory Data Analyses for Pedestrian Space-time Activity Study
1School of Environmental and Life Sciences, Kean University, 2Department of Geography, University of Wisconsin-Madison
A suite of spatiotemporal processing methods are presented to analyze human trajectory data, such as that collected using a GPS device, for the purpose of modeling pedestrian space-time activities.
JoVE General
Assessing Signaling Properties of Ectodermal Epithelia During Craniofacial Development
Department of Orthopaedic Surgery, University of California San Francisco
This article describes a tissue transplantation technique that was designed to test the signaling and patterning properties of surface cephalic ectoderm during craniofacial development.
JoVE General
Measuring Caenorhabditis elegans Life Span in 96 Well Microtiter Plates
1Department of Chemical Physiology, The Scripps Research Institute, 2Department of Molecular and Experimental Medicine, The Scripps Research Institute
In this protocol we present a method to measure Caenorhabditis elegans lifespan in 96 well microtiter plates.
JoVE Bioengineering
A Chitosan Based, Laser Activated Thin Film Surgical Adhesive, 'SurgiLux': Preparation and Demonstration
The fabrication of a novel, flexible thin film surgical adhesive from FDA approved ingredients, chitosan and indocyanine green is described. Bonding of this adhesive to collagenous tissue through a simple activation process with a low-powered infra-red laser is demonstrated.
JoVE Neuroscience
Behavioural Pharmacology in Classical Conditioning of the Proboscis Extension Response in Honeybees (Apis mellifera)
Fachbereich Bio/Chem/Pharm, Institut für Biologie – Neurobiologie, Freie Universität Berlin
We demonstrate how to implement a behavioral pharmacology method in an appetitive olfactory conditioning paradigm in honeybees (Apis mellifera) by systemic application of drugs. This method allows investigation of the mechanisms underlying learning and memory formation in a simple and reliable way.
JoVE General
Quantitative Real-Time PCR using the Thermo Scientific Solaris qPCR Assay
Thermo Scientific Solaris qPCR Products
The Solaris qPCR Gene Expression Assays are novel pre-designed qPCR primer/probe combinations designed to simplify the qPCR process without sacrificing the specificity and robustness of the assay.
JoVE General
Bromodeoxyuridine (BrdU) Labeling and Subsequent Fluorescence Activated Cell Sorting for Culture-independent Identification of Dissolved Organic Carbon-degrading Bacterioplankton
1Biological Sciences, Kent State University, 2Marine Sciences, University of Georgia (UGA)
Environmental bacterioplankton are incubated with a model dissolved organic carbon (DOC) compound and a DNA labeling reagent, bromodeoxyuridine (BrdU). Afterward, DOC-degrading cells are separated from the bulk community based on their elevated BrdU incorporation using fluorescence activated cell sorting (FACS). These cells are then identified by subsequent molecular analyses.
JoVE Neuroscience
Simultaneous Recording of Calcium Signals from Identified Neurons and Feeding Behavior of Drosophila melanogaster
Department of Neurobiology, University of Massachusetts Medical School
The fruit fly, Drosophila melanogaster, extends its proboscis for feeding, responding to a sugar stimulus from its proboscis or tarsus. I have combined observations of the proboscis extension response (PER) with a calcium imaging technique, allowing us to monitor the activity of neurons in the brain, simultaneously with behavioral observation.
JoVE Clinical and Translational Medicine
Measuring Cardiac Autonomic Nervous System (ANS) Activity in Children
1Department of Public Health, Academic Medical Center - University of Amsterdam, 2Department of Epidemiology, Documentation and Health Promotion, Public Health Service of Amsterdam (GGD), 3Department of Biological Psychology, VU University, 4EMGO+ Institute, VU University Medical Center, 5Institute of Health Sciences, VU University, 6Department of Pediatrics, VU University Medical Center
Measurement of autonomic nervous system activity usually confines the researcher and participant to the laboratory, which may provide an intimidating environment to children. The VU University Ambulatory Monitoring System (VU-AMS) device can record cardiac autonomic control in any setting. The VU-AMS proved very amenable to testing in children.
JoVE General
Proboscis Extension Response (PER) Assay in Drosophila
Department of Molecular, Cellular, and Developmental Biology, Yale University
Proboscis extension response or PER is a taste behavior assay that has been used in flies as well as in honeybees. When the proboscis makes contact with an attractive substance, the fly extends its proboscis to consume the substance. Solutions of various sugars are very attractive to the fly.
JoVE General
Rapid PCR Thermocycling using Microscale Thermal Convection
1Department of Mechanical Engineering, Texas A&M University, 2Department of Mechanical Engineering and Department of Nuclear Engineering, Texas A&M University, 3Department of Chemical Engineering, Texas A&M University
We describe a novel method to perform DNA replication via the polymerase chain reaction (PCR). Thermal convection is harnessed to continuously shuttle reagents between denaturing, annealing, and extension conditions by maintaining opposing surfaces of the reactor at constant temperature. This inherently simple design promises to make rapid PCR more accessible.
JoVE Bioengineering
Creating Adhesive and Soluble Gradients for Imaging Cell Migration with Fluorescence Microscopy
1Centre for Vascular Research and Australian Centre for Nanomedicine, The University of New South Wales, 2School of Chemistry and Australian Centre for Nanomedicine, The University of New South Wales
A method for the assembly of adhesive and soluble gradients in a microscopy chamber for live cell migration studies is described. The engineered environment combines antifouling surfaces and adhesive tracks with solution gradients and therefore allows one to determine the relative importance of guidance cues.
JoVE General
In-vivo Centrifugation of Drosophila Embryos
Department of Biology, University of Rochester
We describe a method to separate organelles by density in living Drosophila embryos. Embryos are embedded in agar and centrifuged. This technique yields reproducible separation of major organelles along the anterior-posterior embryo axis. This method facilitates colocalization experiments and yields organelle fractions for biochemical analysis and transplantation experiments.
JoVE General
A Practical and Novel Method to Extract Genomic DNA from Blood Collection Kits for Plasma Protein Preservation
1Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine and Children's Health Care of Atlanta, 2Division of Rheumatology, Department of Pediatrics, Emory University School of Medicine and Children's Health Care of Atlanta
We are describing a new method of isolating genomic DNA from whole blood collected for plasma/serology. After plasma collection, the compacted blood is usually discarded. Our novel method represents a significant improvement over existing methods and makes DNA and plasma available from a single collection, without requesting additional blood.
JoVE Neuroscience
Strategies for Study of Neuroprotection from Cold-preconditioning
Department of Neurology, The University of Chicago Medical Center
We seek to define the neural immune signaling responsible for cold-preconditioning as means to identify novel targets for therapeutics development to protect brain before injury onset. We present strategies for such work that require biological systems, experimental manipulations plus technical capacities that are highly reproducible and sensitive.
JoVE Neuroscience
Analysis of Dendritic Spine Morphology in Cultured CNS Neurons
1Department of Physiology, Northwestern University Feinberg School of Medicine, 2Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine
Numerous recent studies have identified mutations in synaptic proteins associated with brain pathologies. Primary cultured cortical neurons offer great flexibility in examining the effects of these disease-associated proteins on dendritic spine morphology and motility.
JoVE General
Robotics and Dynamic Image Analysis for Studies of Gene Expression in Plant Tissues
1Department of Horticulture and Crop Science, The Ohio State University, 2Department of Plant Pathology, North Carolina State University
We report a method for introduction, tracking and quantitative analysis of GFP expression in plant cells. This method utilizes a custom-designed robotics system for semi-continuous image collection from large numbers of samples, over time. We also demonstrate the use of ImageJ and ImageReady for analysis of image series.
JoVE General
Small Volume (1-3L) Filtration of Coastal Seawater Samples
Department of Microbiology and Immunology, University of British Columbia - UBC
This video documents small volume (~1 L) filtration of microbial biomass from the water column.
JoVE Neuroscience
Mechanical Manipulation of Neurons to Control Axonal Development
Department of Zoology, Michigan State University, East Lansing
Application and direct measurements of forces on neurons in the 2-1000 microdyne range are achieved with high precision using calibrated glass needles. This methodology can be used to control and measure several aspects of axonal development, including axonal initiation, axonal tension, velocity of axonal elongation, and force vectors.
JoVE General
Generation of RNA/DNA Hybrids in Genomic DNA by Transformation using RNA-containing Oligonucleotides
School of Biology, Georgia Institute of Technology
This work shows how to form an RNA/DNA hybrid at the chromosomal level and reveal transfer of genetic information from RNA to genomic DNA in yeast cells.
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