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  JoVE Biology

  
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  JoVE Immunology and Infection

  
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  JoVE Clinical and Translational Medicine

  
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  JoVE Bioengineering

  
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  JoVE Applied Physics

  
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  JoVE Chemistry

  
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  JoVE Behavior

  
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  JoVE Environment

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JoVE Science Education

General Laboratory Techniques

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Basic Methods in Cellular and Molecular Biology

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Model Organisms I

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Model Organisms II

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Essentials of
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 JoVE Biology

A Hybrid DNA Extraction Method for the Qualitative and Quantitative Assessment of Bacterial Communities from Poultry Production Samples

1Egg Safety and Quality Research Unit, USDA-Agricultural Research Service, 2Poultry Microbiological Safety and Processing Research Unit, USDA-Agricultural Research Service, 3Department of Biochemistry and Biophysics, Oregon State University, 4College of Public Health, University of Georgia, 5Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University


JoVE 52161

A novel semi-automated hybrid DNA extraction method for use with environmental poultry production samples was developed and demonstrated improvements over a common mechanical and enzymatic extraction method in terms of the quantitative and qualitative estimates of the total bacterial communities.

 JoVE Biology

DNA Extraction from Paraffin Embedded Material for Genetic and Epigenetic Analyses

1Department of Integrative Oncology, BC Cancer Research Centre, 2Interdisciplinary Oncology Program, University of British Columbia - UBC, 3Photography/Video Production, Multi-Media Services, BC Cancer Agency, 4Department of Pathology and Laboratory Medicine, University of British Columbia - UBC


JoVE 2763

This video demonstrates the protocol for DNA extraction from formalin-fixed paraffin-embedded material. This is a multi-day procedure in which tissue sections are deparaffinized with xylene, rehydrated with ethanol and treated with proteinase K to purify and isolate DNA for subsequent gene-specific or genome-wide analysis.

 JoVE Immunology and Infection

A Simple Chelex Protocol for DNA Extraction from Anopheles spp.

1Malaria Institute at Macha, 2Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health


JoVE 3281

A rapid and affordable way to extract quality malaria parasite and vector DNA from mosquito specimens is described. Capitalizing on chelating properties of Chelex resin, the simple method enables genotyping of malaria parasites in mosquito mid-gut and salivary gland phases, as well as molecular identification of the Anopheles sibling species by PCR.

 JoVE Biology

DNA Extraction from 0.22 μM Sterivex Filters and Cesium Chloride Density Gradient Centrifugation

1Department of Microbiology and Immunology, University of British Columbia - UBC


JoVE 1352

We describe a method for extraction of high molecular weight genomic DNA from planktonic biomass concentrated on 0.22 μm Sterivex filters, followed by cesium chloride density gradient centrifugation for purification.

 JoVE Bioengineering

High-throughput, Automated Extraction of DNA and RNA from Clinical Samples using TruTip Technology on Common Liquid Handling Robots

1Application Development, Akonni Biosystems, Inc., 2Manufacturing, Akonni Biosystems, Inc., 3Engineering, Akonni Biosystems, Inc., 4Research & Development, Akonni Biosystems, Inc.


JoVE 50356

TruTip is a simple nucleic acid extraction technology whereby a porous, monolithic binding matrix is inserted into a pipette tip. Consequently, the sample preparation format is compatible with most liquid handling instruments, and can be used for many medium to high-throughput clinical applications and sample types.

 JoVE Biology

Polymerase Chain Reaction: Basic Protocol Plus Troubleshooting and Optimization Strategies

1Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles


JoVE 3998

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

Collection and Extraction of Saliva DNA for Next Generation Sequencing

1Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, 2The Interdisciplinary Graduate Program in Biophysics, The Ohio State University, 3Department of Pediatrics, The Ohio State University


JoVE 51697

DNA extraction from saliva can provide a readily available source of high molecular weight DNA, with little to no degradation/fragmentation. This protocol provides optimized parameters for saliva collection/storage and DNA extraction to be of sufficient quality and quantity for downstream DNA assays with high quality requirements.

 JoVE Biology

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


JoVE 4241

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 Biology

Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation

1Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 2A*STAR-Duke-NUS Neuroscience Research Partnership, Singapore, 3Department of Biochemistry, National University of Singapore, Singapore


JoVE 3770

Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) is a method for de novo detection of chromatin interactions, for better understanding of transcriptional control.

 JoVE Biology

qPCR Is a Sensitive and Rapid Method for Detection of Cytomegaloviral DNA in Formalin-fixed, Paraffin-embedded Biopsy Tissue

1Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, 2Department of Pathology and Laboratory Medicine, Indiana University Health


JoVE 51570

This protocol describes qPCR detection of cytomegalovirus in formalin-fixed, paraffin-embedded biopsy tissue, which is rapid, sensitive, specific, and useful for interpreting equivocal hematoxylin and eosin or immunohistochemical staining patterns.

 JoVE Immunology and Infection

Simultaneous Quantification of T-Cell Receptor Excision Circles (TRECs) and K-Deleting Recombination Excision Circles (KRECs) by Real-time PCR

1CREA, Diagnostics Department, Spedali Civili di Brescia


JoVE 52184

Here, we describe a method for simultaneous quantification of T-cell receptor excision circles (TRECs) and K-deleting recombination excision circles (KRECs). The TREC/KREC assay can be used as marker of thymic and bone marrow output.

 JoVE Biology

Genotyping of Plant and Animal Samples without Prior DNA Purification

1Thermo Scientific Molecular Biology Products, Thermo Fisher Scientific


JoVE 3844

The Direct PCR approach presented here facilitates PCR amplification directly from small amounts of unpurified plant and animal tissue.

 JoVE Environment

Unraveling the Unseen Players in the Ocean - A Field Guide to Water Chemistry and Marine Microbiology

1Department of Biology, San Diego State University, 2Scripps Institution of Oceanography, University of California San Diego


JoVE 52131

Here, we present a comprehensive protocol to assess the organic and inorganic nutrient availability and the abundance and structure of microbial and viral communities in remote marine environments.

 JoVE Biology

DNA Stable-Isotope Probing (DNA-SIP)

1Department of Biology, University of Waterloo


JoVE 2027

DNA stable-isotope probing is a cultivation-independent method to identify and characterize active communities of microorganisms that are capable of utilizing specific substrates. Assimilation of substrate enriched in heavy isotope leads to incorporation of labelled atoms into microbial biomass. Density gradient ultracentrifugation retrieves labelled DNA for downstream molecular analyses.

 JoVE Biology

A PCR-based Genotyping Method to Distinguish Between Wild-type and Ornamental Varieties of Imperata cylindrica

1Department of Biological Sciences, The University of Alabama, Huntsville, 2USDA-APHIS-PPQ, Center for Plant Health Science and Technology


JoVE 3265

We provide a cost-effective and rapid molecular genotyping protocol that employs variety-specific PCR primers that target DNA sequence differences within the chloroplast trnL-F spacer region to differentiate between varieties of Imperata cylindrica (cogongrass) that cannot be distinguished by morphology alone. These varieties include the federally listed noxious weed, cogongrass and closely-related, wide-spread ornamental variety, I. cylindrica var. koenigii (Japanese blood grass).

 JoVE Immunology and Infection

DNA Fingerprinting of Mycobacterium leprae Strains Using Variable Number Tandem Repeat (VNTR) - Fragment Length Analysis (FLA)

1Department of Microbiology, Immunology and Pathology, Colorado State University


JoVE 3104

Leprosy, caused by Mycobacterium leprae, is still endemic in many places. In order to learn about the spread and mode of transmission of leprosy, it is important to determine which strain of M. leprae has infected a patient. Variable numbers of tandem repeats (VNTR) typing is one such method.

 JoVE Biology

Efficient and Rapid Isolation of Early-stage Embryos from Arabidopsis thaliana Seeds

1Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich


JoVE 50371

We report an efficient and simple method to isolate embryos at early stages of development from Arabidopsis thaliana seeds. Up to 40 embryos can be isolated in 1 hr to 4 hr, depending on the downstream application. The procedure is suitable for transcriptome, DNA methylation, reporter gene expression, immunostaining and fluorescence in situ hybridization analyses.

 JoVE Biology

Identification of Metabolically Active Bacteria in the Gut of the Generalist Spodoptera littoralis via DNA Stable Isotope Probing Using 13C-Glucose

1Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology


JoVE 50734

The active bacterial community associated with the gut of Spodoptera littoralis, was determined by stable-isotope-probing (SIP) coupled to pyrosequencing. Using this methodology, identification of the metabolically active bacteria species within the community was done with high resolution and precision.

 JoVE Immunology and Infection

Multiplex PCR Assay for Typing of Staphylococcal Cassette Chromosome Mec Types I to V in Methicillin-resistant Staphylococcus aureus

1Centre for Antimicrobial Resistance, Alberta Health Services / Calgary Laboratory Services / University of Calgary, 2Department of Pathology & Laboratory Medicine, University of Calgary, 3Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 4Department of Medicine, University of Calgary, 5The Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, University of Calgary


JoVE 50779

We demonstrate a simple multiplex PCR assay for quick-screening and typing of Staphylococcal Cassette Chromosome mec (SCCmec) types I-V for methicillin-resistant Staphylococcus aureus, and provide some of the vital steps and procedural nuances that make it successful for adapting this assay to individual laboratories.

 JoVE Biology

Ice-Cap: A Method for Growing Arabidopsis and Tomato Plants in 96-well Plates for High-Throughput Genotyping

1Horticulture Department, University of Wisconsin-Madison, 2Department of Zoology, Oregon State University


JoVE 3280

The Ice-Cap method allows one to grow plants in 96-well plates and non-destructively harvest root tissue from each seedling. DNA extracted from this root tissue can be used for genotyping reactions. We have found that Ice-Cap works well for Arabidopsis thaliana, tomato, and rice seedlings.

 JoVE Biology

Large Insert Environmental Genomic Library Production

1Department of Microbiology and Immunology, University of British Columbia - UBC


JoVE 1387

Construction of a fosmid library with environmental genomic DNA isolated from the vertical depth continuum of a seasonally hypoxic fjord is described. The resulting clone library is picked into 384-well plates and archived for downstream sequencing and functional screening by the application of an automated colony picking system.

 JoVE Immunology and Infection

Investigating the Effects of Probiotics on Pneumococcal Colonization Using an In Vitro Adherence Assay

1Pneumococcal Research, Murdoch Childrens Research Institute, 2Allergy & Immune Disorders, Murdoch Childrens Research Institute, 3Department of Otolaryngology, The University of Melbourne, 4Department of Microbiology & Immunology at the Peter Doherty Institute for Infection & Immunity, The University of Melbourne


JoVE 51069

In vitro adherence assays can be used to study the attachment of Streptococcus pneumoniae to epithelial cell monolayers and to investigate potential interventions such as the use of probiotics for inhibiting pneumococcal colonization.

 JoVE Biology

Extraction of High Molecular Weight DNA from Microbial Mats

1Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina


JoVE 2887

We provide an improved protocol for extracting high molecular weight DNA from hypersaline microbial mats. Microbial cells are separated from the mat matrix prior to DNA extraction and purification. This enhances the concentrations, quality, and size of the DNA. The protocol may be used for other refractory samples.

 JoVE Biology

Isolation of Viable Multicellular Glands from Tissue of the Carnivorous Plant, Nepenthes

1Laboratoire Agronomie et Environnement, Université de Lorraine, 2Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 3aura optik


JoVE 50993

Plants glands are specialized structures responsible for the biosynthesis and secretion of many compounds involved in interactions with the biotic environment. To enable studies on their molecular and biochemical features, a mechanical micropreparation technique was established in order to isolate single metabolically active glands, here from the carnivorous plant Nepenthes.

 JoVE Immunology and Infection

Genetic Manipulation in Δku80 Strains for Functional Genomic Analysis of Toxoplasma gondii

1Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth


JoVE 50598

Here we report a method for using type I and type II Δku80 strains of Toxoplasma gondii to efficiently generate targeted gene deletions and gene replacements for functional genomic analysis.

 JoVE Biology

Who is Who? Non-invasive Methods to Individually Sex and Mark Altricial Chicks

1Department of Animal Behavior, Freie Universität Berlin


JoVE 51429

This protocol provides a convenient set of methods, which enables extremely fast, easy, non-invasive, reliable and low-cost, molecular sex determination of birds and their non-invasive, quick, safe and easily recognizable marking shortly after hatching. Only limited handling of chicks is required. This convenient toolbox of methods complies entirely with the RRR-guidelines.

 JoVE Biology

Detection of Live Escherichia coli O157:H7 Cells by PMA-qPCR

1Center for Food Safety and Applied Nutrition, Division of Molecular Biology, Food and Drug Administration


JoVE 50967

A qPCR assay was developed for detection of Escherichia coli O157:H7 targeting a unique genetic marker, Z3276. The qPCR was combined with propidium monoazide (PMA) treatment for live cell detection. This protocol has been modified and adapted to a 96-well plate format for easy and consistent handling of numerous samples

 JoVE Biology

DNA-based Fish Species Identification Protocol

1Agilent Technologies


JoVE 1871

This publication describes how to use the Agilent Fish Species Identification System to identify the species of a fish by extracting DNA and performing PCR and RFLP analysis.

 JoVE Biology

Methylated DNA Immunoprecipitation

1Department of Cancer Genetics and Developmental Biology, BC Cancer Research Centre, 2Interdisciplinary Oncology Program, University of British Columbia - UBC, 3These authors contributed equally., 4Department of Pathology and Laboratory Medicine, University of British Columbia - UBC, 5Photography/Video Production, Multi-Media Services, BC Cancer Agency, 6Department of Medical Genetics, Life Sciences Institute,, University of British Columbia - UBC


JoVE 935

This video demonstrates the protocol for methylated DNA immunoprecipitation (MeDIP). MeDIP is a two day procedure that selectively extracts methylated DNA fragments from a genomic DNA sample using antibodies with specificity for 5 -methylcytosine (anti-5 mC).

 JoVE Clinical and Translational Medicine

Neo-Islet Formation in Liver of Diabetic Mice by Helper-dependent Adenoviral Vector-Mediated Gene Transfer

1Department of Medicine, Baylor College of Medicine, 2Division of Diabetes, Endocrinology & Metabolism, Diabetes & Endocrinology Research Center, Baylor College of Medicine, 3Department of Molecular & Cellular Biology, Baylor College of Medicine


JoVE 4321

We describe hepatic neo-islet formation in STZ (streptozotocin)-induced diabetic mice by gene transfer of Neurogenin3 (Ngn3) and Betacellulin (Btc) using helper-dependent adenoviral vector (HDAd) and the reversal of hyperglycemia. Our method takes advantages of helper-dependent adenoviral vectors with their highly efficient in vivo transduction and the long lasting gene expression.

 JoVE Biology

Competitive Genomic Screens of Barcoded Yeast Libraries

1Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, 2Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 3Donnelly Sequencing Centre, University of Toronto, 4Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, 5Stanford Genome Technology Center, Stanford School of Medicine, Stanford University, 6Department of Pharmaceutical Sciences, University of Toronto


JoVE 2864

We have developed comprehensive, unbiased genome-wide screens to understand gene-drug and gene-environment interactions. Methods for screening these mutant collections are presented.

 JoVE Clinical and Translational Medicine

Sequencing of Bacterial Microflora in Peripheral Blood: our Experience with HIV-infected Patients

1Department of Medicine, Surgery and Dentistry, Clinic of Infectious Diseases, San Paolo Hospital University of Milan, Italy


JoVE 2830

Our experiment will show how to perform a sequencing analysis of bacterial species translocating in peripheral blood of HIV positive patients.

 JoVE Biology

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

1Department of Pathology, Memorial Sloan-Kettering Cancer Center, 2Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center


JoVE 50710

We describe the preparation of barcoded DNA libraries and subsequent hybridization-based exon capture for detection of key cancer-associated mutations in clinical tumor specimens by massively parallel "next generation" sequencing. Targeted exon sequencing offers the benefits of high throughput, low cost, and deep sequence coverage, thus yielding high sensitivity for detecting low frequency mutations.

 JoVE Clinical and Translational Medicine

Using Quantitative Real-time PCR to Determine Donor Cell Engraftment in a Competitive Murine Bone Marrow Transplantation Model

1Division of Hematology-oncology, Department of Medicine, Medical University of South Carolina


JoVE 50193

Determining donor cell engraftment presents a challenge in mouse bone marrow transplant models that lack well-defined phenotypical markers. We described a methodology to quantify male donor cell engraftment in female transplant recipient mice. This method can be used in all mouse strains for the study of HSC functions.

 JoVE Biology

Derivation and Characterization of a Transgene-free Human Induced Pluripotent Stem Cell Line and Conversion into Defined Clinical-grade Conditions

1Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), 2Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles (UCLA)


JoVE 52158

We describe a protocol for deriving lentiviral-based reprogrammed and characterized factor-free human induced pluripotent stem cells and conversion into putative clinical-grade conditions.

 JoVE Immunology and Infection

Parasite Induced Genetically Driven Autoimmune Chagas Heart Disease in the Chicken Model

1Chagas Disease Multidisciplinary Research Laboratory, University of Brasilia


JoVE 3716

The inoculation of Trypanosoma cruzi in fertile eggs prior to incubation renders the parasite kDNA minicircle integration in embryo cells genome. Crossbreeding reveals the vertical transfer of the mutations to progeny. The kDNA integrates into coding regions at several chromosomes and the chickens die with an inflammatory autoimmune heart disease.

 JoVE Biology

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

1Wellcome Trust Centre for Human Genetics, University of Oxford


JoVE 2279

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 Immunology and Infection

Forward Genetic Approaches in Chlamydia trachomatis

1Department of Molecular Genetics and Microbiology, Center for Microbial Pathogenesis, Duke University Medical Center


JoVE 50636

We describe a methodology to perform genetic analysis in Chlamydia based on chemical mutagenesis and whole genome sequencing. In addition, a system for DNA exchange within infected cells is described that can be used for genetic mapping. This method may be broadly applicable to microbial systems lacking transformation systems and molecular genetic tools.

 JoVE Immunology and Infection

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

1Viral Populations and Pathogenesis lab and CNRS 3015, Institut Pasteur


JoVE 2953

The present article describes the steps required to isolate and characterize RNA polymerase fidelity variants of RNA viruses and how to use mutation frequency data to confirm fidelity changes in tissue culture.

 JoVE Biology

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

1Energy, Mining and Environment, National Research Council Canada


JoVE 51709

Characterizing microbial community has been a longstanding goal in environmental microbiology. Next-generation sequencing methods now allow for the characterization of microbial communities at an unprecedented depth with minimal cost and labor. We detail here our approach to sequence bacterial 16S ribosomal RNA genes using a benchtop sequencer.

 JoVE Biology

Multiplex PCR and Reverse Line Blot Hybridization Assay (mPCR/RLB)

1Centre for Infectious Diseases and Microbiology, University of Sydney


JoVE 2781

An inexpensive, high throughput method for simultaneous detection of up to 43 molecular targets is described. Applications of mPCR/RLB include microbial typing and detection of multiple pathogens from clinical samples.

 JoVE Immunology and Infection

Identification of Novel Genes Associated with Alginate Production in Pseudomonas aeruginosa Using Mini-himar1 Mariner Transposon-mediated Mutagenesis

1Department of Biochemistry and Microbiology, Joan C. Edwards School of Medicine, Marshall University


JoVE 51346

Here we describe a protocol using the mini-himar1 mariner transposon-mediated mutagenesis for generating a high-density insertion mutant library to screen, isolate and identify novel alginate regulators in the prototypic Pseudomonas aeruginosa strain PAO1.

 JoVE Biology

Extracting DNA from the Gut Microbes of the Termite (Zootermopsis Angusticollis) and Visualizing Gut Microbes

1Department of Environmental Science and Engineering, California Institute of Technology - Caltech


JoVE 195

This video illustrates the technique for extracting DNA from the species of microbes resident in the termite hindgut. The preparation of a wet mount slide, which is useful for visualizing the gut microbial community is also illustrated, and a tour through the species-rich gut environment is given.

 JoVE Environment

Helminth Collection and Identification from Wildlife

1Department of Forestry and Natural Resources, Purdue University, 2Helm West Laboratory


JoVE 51000

Wild animals are commonly parasitized by a wide range of helminths.  The four major types of helminths are “roundworms” (nematodes), “thorny-headed worms” (acanthocephalans), “flukes” (trematodes), and “tapeworms” (cestodes).  Here we describe how helminths are collected from a vertebrate animal and how they are preserved and taxonomically identified. 

 JoVE Biology

Rapid and Efficient Zebrafish Genotyping Using PCR with High-resolution Melt Analysis

1Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, 2Department of Neurobiology and Anatomy, University of Utah School of Medicine, 3Interdepartmental Program in Neurosciences, University of Utah School of Medicine, 4Mutation Generation and Detection Core, HSC Core Research Facility, University of Utah School of Medicine, 5Department of Neurology, University of Utah School of Medicine


JoVE 51138

PCR combined with high-resolution melt analysis (HRMA) is demonstrated as a rapid and efficient method to genotype zebrafish.

 JoVE Biology

A Noninvasive Hair Sampling Technique to Obtain High Quality DNA from Elusive Small Mammals

1Department of Biology and Centre for Species at Risk and Habitat Studies,, University of British Columbia, Okanagan Campus


JoVE 2791

We present a noninvasive sampling approach to efficiently collect hair samples from elusive small mammals, as shown for the American pika. We demonstrate the utility of this method by extracting DNA from sampled hair and amplifying several types of molecular markers commonly used in studies of wildlife ecology and conservation.

 JoVE Immunology and Infection

Multiplex Detection of Bacteria in Complex Clinical and Environmental Samples using Oligonucleotide-coupled Fluorescent Microspheres

1Saskatoon Research Centre, Agriculture and Agri-Food Canada, 2Department of Veterinary Microbiology, University of Saskatchewan, 3Plant Biotechnology Institute, National Research Council of Canada


JoVE 3344

We describe a multiplex method for the detection of microorganisms within a sample using oligonucleotide-coupled fluorescent beads. Amplicon from all organisms within a sample is hybridized to a panel of probe-coupled beads. A Luminex or Bio-Plex instrument is used to query each bead for bead type and hybridization signal.

 JoVE Clinical and Translational Medicine

A Next-generation Tissue Microarray (ngTMA) Protocol for Biomarker Studies

1Institute of Pathology, University of Bern


JoVE 51893

The protocol aims at optimizing the construction and quality of tissue microarrays for biomarker research. It includes aspects of planning and design, digital pathology, virtual slide annotation, and automated tissue arraying.

 JoVE Biology

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

1Max-Planck Institute for Evolutionary Anthropology, Leipzig


JoVE 1573

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.

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