JoVE Neuroscience
Assessing Burrowing, Nest Construction, and Hoarding in Mice
Department of Experimental Psychology, University of Oxford
Burrowing, nesting, and hoarding are species-typical activities that mice readily perform in the laboratory. This article describes how they can be easily and cheaply assessed. These protocols are extremely sensitive to mouse strain, brain lesions and diseases. Moreover they constitute “environmental enrichment” for the mice, and embody the “Refinement” aspect of the “3 Rs”18.
JoVE Neuroscience
Peering into the Dynamics of Social Interactions: Measuring Play Fighting in Rats
Department of Neuroscience, University of Lethbridge
Play fighting in the rat involves attack and defense of the nape of the neck, which if contacted, is gently nuzzled with the snout. Because the movements of one animal are countered by the actions of its partner, play fighting is a complex, dynamic interaction. This dynamic complexity raises methodological problems about what to score for experimental studies. We present a scoring schema that is sensitive to the correlated nature of the actions performed. Two experiments illustrate how these measurements can be used to detect the effect of brain damage on play fighting even when there is no effect on overall playfulness. That is, the schema presented here is designed to detect and evaluate changes in the content of play following an experimental treatment.
JoVE Neuroscience
Hyponeophagia: A Measure of Anxiety in the Mouse
Department of Experimental Psychology, University of Oxford
Mice and rats, due to their innate cautiousness, are initially slow in consuming a novel food, particularly in a novel place. This hyponeophagia can readily be measured in the laboratory, even though laboratory animals are much less anxious than their wild counterparts
JoVE General
A Simple Protocol for Extracting Hemocytes from Wild Caterpillars
Department of Biological Sciences, The George Washington University
Insect hemocytes carry out many important functions, both immune and non-immune, throughout all stages of insect development. Our present knowledge of hemocyte types and function comes from studies on insect genetic models. Here, we present a method for extracting, quantifying and visualizing hemocytes from wild caterpillars.
JoVE General
Chromatographic Purification of Highly Active Yeast Ribosomes
1Department of Cell Biology and Molecular Genetics, University of Maryland, 2Department of Biotechnology and Microbiology, Vilnius University
Contamination of preparations of eukaryotic ribosomes purified by traditional methods by co-purifying nucleases and proteases negatively impacts on downstream biochemical and structural analyses. A rapid and simple chromatographic purification method is used to solve this problem using yeast ribosomes as a model system.
JoVE Applied Physics
Probing and Mapping Electrode Surfaces in Solid Oxide Fuel Cells
1Center for Innovative Fuel Cells and Battery Technologies, School of Materials Science and Engineering, Georgia Institute of Technology, 2School of Chemistry and Biochemistry, Georgia Institute of Technology
We present a unique platform for characterizing electrode surfaces in solid oxide fuel cells (SOFCs) that allows simultaneous performance of multiple characterization techniques (e.g. in situ Raman spectroscopy and scanning probe microscopy alongside electrochemical measurements). Complementary information from these analyses may help to advance toward a more profound understanding of electrode reaction and degradation mechanisms, providing insights into rational design of better materials for SOFCs.
JoVE Immunology and Infection
Cutaneous Leishmaniasis in the Dorsal Skin of Hamsters: a Useful Model for the Screening of Antileishmanial Drugs
1Program for the Study and Control of Tropical Diseases -PECET-School of Medicine, University of Antioquia, 2School of Agrarian Sciences, University of Antioquia
Optimization of the experimental hamster model for cutaneous leishmaniasis by intradermal injection of Leishmania promastigotes at the dorsal skin. This approach is useful during inoculation, follow-up, characterization of lesions, application of treatments and obtaining of clinical samples. Locomotion, search for food and water, play and social activities are preserved.
JoVE Immunology and Infection
Rearing and Injection of Manduca sexta Larvae to Assess Bacterial Virulence
Department of Bacteriology, University of Wisconsin-Madison
The method described here utilizes direct injection of entomopathogenic bacteria into the hemocoel of Manduca sexta insect larvae. M. sexta is a commercially available and well-studied insect. Thus, this method represents a simple approach to analyzing host-bacterial interactions from the perspective of one or both partners.
JoVE Immunology and Infection
Colon Ascendens Stent Peritonitis (CASP) - a Standardized Model for Polymicrobial Abdominal Sepsis
Department of Surgery, University of Greifswald
The Colon Ascendens Stent Peritonitis (CASP) is a highly standardized model for polymicrobial abdominal sepsis in rodents. This article describes the surgical procedure of CASP. The CASP model and its variants allow the systematic investigation of various problems concerning the subject of sepsis.
JoVE General
Measurement of Leaf Hydraulic Conductance and Stomatal Conductance and Their Responses to Irradiance and Dehydration Using the Evaporative Flux Method (EFM)
University of California, Los Angeles
We describe a relatively rapid (30 min) and realistic method for simultaneously measurement of leaf hydraulic conductance (Kleaf) and stomatal conductance (gs) for transpiring excised leaves. The method can be modified to measure the light and dehydration responses of Kleaf and gs.
JoVE General
Depletion of Ribosomal RNA for Mosquito Gut Metagenomic RNA-seq
Department of Biology, New Mexico State University
A ribosomal RNA (rRNA) depletion protocol was developed to enrich messenger RNA (mRNA) for RNA-seq of the mosquito gut metatranscriptome. Sample specific rRNA probes, which were used to remove rRNA via subtraction, were created from the mosquito and its gut microbes. Performance of the protocol can result in the removal of approximately 90-99% of rRNA.
JoVE Clinical and Translational Medicine
The Use of Reverse Phase Protein Arrays (RPPA) to Explore Protein Expression Variation within Individual Renal Cell Cancers
1Edinburgh Urological Cancer Group, University of Edinburgh, 2School of Medicine, University of St Andrews, 3Division of Pathology, University of Edinburgh, 4MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, 5Department of Pathology, Western General Hospital, 6Breakthrough Breast Cancer Research Unit, University of Edinburgh, 7St Bartholomew's Cancer Institute, Experimental Cancer Medicine Centre, Queen Mary University of London
RPPA enables the protein expression of hundreds of samples, printed on nitrocellulose slides to be interrogated simultaneously, using fluorescently labelled antibodies. This technique has been applied to study the effect of drug treatment heterogeneity within clear cell renal carcinoma.
JoVE General
Electron Spin Resonance Micro-imaging of Live Species for Oxygen Mapping
Schulich Faculty of Chemistry, The Technion, Israel Institute of Technology
This protocol describes a method for micron-scale three-dimensional imaging of oxygen concentration in the immediate environment of live cells by electron spin resonance microscopy.
JoVE General
Chronic Salmonella Infected Mouse Model
Department of Medicine, University of Rochester
Establish a chronic bacterial infected mouse model with persistent Salmonella typhimurium colonization in intestine for 27 weeks.
JoVE Immunology and Infection
RNA Interference in Ticks
1Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, 2(CSIC-UCLM-JCCM), Instituto de Investigación en Recursos Cinegéticos IREC
A method for RNA interference (RNAi) by injection of dsRNA into unfed ticks is described. RNAi is the most widely used gene-silencing technique in ticks where the use of other methods of genetic manipulation has been limited.
JoVE General
Identification and Analysis of Mouse Erythroid Progenitors using the CD71/TER119 Flow-cytometric Assay
A flow-cytometric method for identification and molecular analysis of differentiation-stage-specific murine erythroid progenitors and precursors, directly in freshly –harvested mouse bone marrow, spleen or fetal liver. The assay relies on cell-surface markers CD71, Ter119, and cell size.
JoVE Clinical and Translational Medicine
Analytical Techniques for Assaying Nitric Oxide Bioactivity
1Texas Therapeutics Institute, University of Texas Health Science Center at Houston, 2Deptartment of Pediatrics, Baylor College of Medicine
The endogenous production of nitric oxide (NO) regulates a wide variety of biological functions. It is becoming increasingly clear that disruption or dysregulation of NO based signaling is involved in many human diseases. Methods to quantify relevant NO metabolites may provide novel diagnostic or prognostic biomarkers for human disease.
JoVE Chemistry
Production of Disulfide-stabilized Transmembrane Peptide Complexes for Structural Studies
1Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 2The University of Melbourne
Biophysical and biochemical studies of interactions among membrane-embedded protein domains face many technical challenges, the first of which is obtaining appropriate study material. This article describes a protocol for producing and purifying disulfide-stabilized transmembrane peptide complexes that are suitable for structural analysis by solution nuclear magnetic resonance (NMR) and other analytical applications.
JoVE General
Establishing Primary Adult Fibroblast Cultures From Rodents
Department of Biology, University of Rochester
This article describes a protocol for isolation and maintenance of primary fibroblast cultures from skin and lung tissue of wild rodents.
JoVE Bioengineering
Characterizing Bacterial Volatiles using Secondary Electrospray Ionization Mass Spectrometry (SESI-MS)
School of Engineering, University of Vermont
Secondary electrospray ionization mass spectrometry (SESI-MS) enables the detection of volatile organic compounds (VOCs) without the need for any sample pretreatment. This protocol provides instructions for the rapid (within minutes) characterization of bacterial VOCs using SESI-MS.
JoVE Bioengineering
Continuously-stirred Anaerobic Digester to Convert Organic Wastes into Biogas: System Setup and Basic Operation
Department of Biological and Environmental Engineering, Cornell University
Laboratory-scale anaerobic digesters allow scientists to research new ways of optimizing existing applications of anaerobic biotechnology and to evaluate the methane producing potential of various organic wastes. This article introduces a generalized model for the construction, inoculation, operation, and monitoring of a laboratory-scale continuously stirred anaerobic digester.
JoVE General
Brain Banking: Making the Most of your Research Specimens
1Department of Physiology, University of Montreal, 2School of Optometry, University of Montreal
Brain banking and systematic sampling of biological material provides the basis for unbiased stereology and maximizes the potential data obtained from each specimen.
JoVE General
Label-free in situ Imaging of Lignification in Plant Cell Walls
1Energy Biosciences Institute, University of California, Berkeley, 2Molecular Foundry, Lawrence Berkeley National Laboratory, 3Physical Biosciences Division, Lawrence Berkeley National Laboratory
A method based on confocal Raman microscopy is presented that affords label-free visualization of lignin in plant cell walls and comparison of lignification in different tissues, samples or species.
JoVE General
Using High Resolution Computed Tomography to Visualize the Three Dimensional Structure and Function of Plant Vasculature
1U.S. Department of Agriculture, 2Department of Viticulture and Enology, University of California - Davis, 3Hawkesbury Institute for the Environment, University of Western Sydney, 4Advanced Light Source, Lawrence Berkeley National Lab, 5Citrus Research & Education Center, University of Florida
High resolution x-ray computed tomography (HRCT) is a non-destructive diagnostic imaging technique that can be used to study the structure and function of plant vasculature in 3D. We demonstrate how HRCT facilitates exploration of xylem networks across a wide range of plant tissues and species.
JoVE Bioengineering
Fluorescence detection methods for microfluidic droplet platforms
1Department of Chemistry, Imperial College London, 2Department of Biochemistry, Protein Chip Research Center, Chungbuk National University, 3Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich
Droplet-based microfluidic platforms are promising candidates for high throughput experimentation since they are able to generate picoliter, self-compartmentalized vessels inexpensively at kHz rates. Through integration with fast, sensitive and high resolution fluorescence spectroscopic methods, the large amounts of information generated within these systems can be efficiently extracted, harnessed and utilized.
JoVE General
Conversion of a Capture ELISA to a Luminex xMAP Assay using a Multiplex Antibody Screening Method
1Chemistry Research and Development, Luminex Corporation, 2Global Marketing, Luminex Corporation
An ELISA can be easily converted to a Luminex xMAP assay and, through the benefits of multiplexing, several antibodies can be screened simultaneously to identify an optimum antibody pair, resulting in increased sensitivity and dynamic range, while reducing assay cost.
JoVE Immunology and Infection
Mass Spectrometric Analysis of Glycosphingolipid Antigens
1Undergraduate Program, Rice University, 2Proteomics Facility, Department of Pathology, University of Texas MD Anderson Cancer Center, 3Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, 4University of Texas Graduate School of Biological Sciences at Houston
A specific and sensitive method to gain insight into the expression profile of glycosphingolipid antigens in immune organs and cells is described. The method takes advantage of the ion trap mass spectrometry allowing step-wise fragmentation of glycosphingolipid molecules for structural analysis in comparison to chemically synthesized standards.
JoVE General
Pharmacological and Functional Genetic Assays to Manipulate Regeneration of the Planarian Dugesia japonica
Department of Pharmacology and The Stem Cell Institute, University of Minnesota Medical School
An attractive model for studying stem cell differentiation within a live animal is the planarian flatworm. Regeneration is studied by simple amputation experiments that are easily performed in a basic laboratory and are amenable to pharmacological and genetic (in vivo RNAi) manipulation as detailed by protocols in this article.
JoVE General
Quantitative Comparison of cis-Regulatory Element (CRE) Activities in Transgenic Drosophila melanogaster
1Department of Biology, University of Dayton, 2Department of Biology, Center for Tissue Regeneration and Engineering at Dayton, University of Dayton
Phenotypic variation for traits can result from mutations in cis-regulatory element (CRE) sequences that control gene expression patterns. Methods derived for use in Drosophila melanogaster can quantitatively compare the levels of spatial and temporal patterns of gene expression mediated by modified or naturally occurring CRE variants.
JoVE General
Optimized PCR-based Detection of Mycoplasma
Product Management, Sigma-Aldrich
The LookOut Mycoplasma PCR Detection Kit utilizes the polymerase chain reaction (PCR), which is established as the method of choice for highest sensitivity in the detection of Mycoplasma, Acholeplasma, and Ureaplasma contamination in cell cultures and other cell culture derived biologicals.
JoVE Applied Physics
Fabrication of Nano-engineered Transparent Conducting Oxides by Pulsed Laser Deposition
1Department of Energy and NEMAS - Center for NanoEngineered Materials and Surfaces, Politecnico di Milano, 2Center for Nano Science and Technology, Instituto Italiano di Tecnologia
We describe the experimental method to deposit nanostructured oxide thin films by nanosecond Pulsed Laser Deposition (PLD) in the presence of a background gas. By using this method Al-doped ZnO (AZO) films, from compact to hierarchically structured as nano-tree forests, can be deposited.
JoVE Bioengineering
Adhesion Frequency Assay for In Situ Kinetics Analysis of Cross-Junctional Molecular Interactions at the Cell-Cell Interface
Biomedical Engineering Department, Georgia Institute of Technology
An adhesion frequency assay for measuring receptor-ligand interaction kinetics when both molecules are anchored on the surfaces of the interacting cells is described. This mechanically-based assay is exemplified using a micropipette-pressurized human red blood cell as adhesion sensor and integrin αLβ2 and intercellular adhesion molecule-1 as interacting receptors and ligands.
JoVE Neuroscience
The Vermicelli and Capellini Handling Tests: Simple quantitative measures of dexterous forepaw function in rats and mice
1Institute for Neuroscience, University of Texas at Austin, 2Department of Psychology, University of Texas at Austin, 3Department of Neurology, University of Florida, 4Department of Psychiatry, University of Texas Southwestern Medical Center, 5Department of Neuroscience, McKnight Brain Institute, University of Florida
The Vermicelli and Capellini Handling Tests of forepaw dexterity take advantage of the natural inclination of rodents to manipulate food items using skillful forepaw and digit movements. Animals are videotaped while handling short strands of uncooked dry pasta. Slow motion video playback allows for the quantification of forepaw adjustments.
JoVE General
Electroantennographic Bioassay as a Screening Tool for Host Plant Volatiles
Plant Mycotoxin Research, U.S. Department of Agriculture, Agricultural Research Service
A method to rapidly screen host plant volatiles by measurement of the electrophysiological response of adult navel orangeworm (Amyelois transitella) antennae to single components and blends via electroantennographic analysis is demonstrated.
JoVE Neuroscience
A Lightweight, Headphones-based System for Manipulating Auditory Feedback in Songbirds
1Department of Biology, Emory University, 2Neuroscience Graduate Program, Emory University, 3Program in Neuroscience and Behavioral Biology, Emory University
We describe the design and assembly of miniaturized headphones suitable for replacing a songbird’s natural auditory feedback with a manipulated acoustic signal. Online sound processing hardware is used to manipulate song output, introduce real-time errors in auditory feedback via the headphones, and drive vocal motor learning.
JoVE General
Agar-Block Microcosms for Controlled Plant Tissue Decomposition by Aerobic Fungi
Department of Bioproducts and Biosystems Engineering, University of Minnesota
This video demonstrates a controlled environment approach to study degradation of lignocellulosic plant tissues by aerobic fungi. The ability to control nutrient sources and moisture is a key advantage of agar-block microcosms, but the approach often yields mixed success. We address critical pitfalls to yield reproducible, low-variability results.
JoVE General
Non-radioactive in situ Hybridization Protocol Applicable for Norway Spruce and a Range of Plant Species
1Department of Evolutionary Functional Genomics, Evolutionary Biology Center, Uppsala University, 2Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences
We describe a modified DIG in situ hybridization protocol, which is fast and applicable on a wide range of plant species including Norway spruce. With just a few adjustments, including altered RNase treatment and proteinase K concentration, the protocol may be used in studies of different tissues and species.
JoVE General
Knowing What Counts: Unbiased Stereology in the Non-human Primate Brain
1Department of Physiology, University of Montreal, 2Ecole d’optometrie, University of Montreal, 3Stereology Resource Center
The anatomical organization of the primate brain can provide important insights into normal and pathological conditions in humans. Unbiased stereology is a method for accurately and efficiently estimating the total neuron number (or other cell type) in a given reference space1.
JoVE General
Comprehensive Compositional Analysis of Plant Cell Walls (Lignocellulosic biomass) Part II: Carbohydrates
1Great Lakes Bioenergy Research Center, Michigan State University (MSU), 2Great Lakes Bioenergy Research Center and DOE-Plant Research Lab, Michigan State University (MSU)
Plant biomass is a major carbon-neutral renewable resource that could be used for the production of biofuels. Plant biomass consists mainly of cell walls, a structurally complex composite material termed lignocellulosics. Here we describe a protocol for a comprehensive analysis of the content and composition of wall derived carbohydrates.
JoVE Neuroscience
Investigating Outer Hair Cell Motility with a Combination of External Alternating Electrical Field Stimulation and High-speed Image Analysis
Division of Cell Biology and Genetics, House Ear Institute
A reliable method to investigate outer hair cell (OHC) motile responses, including electromotility, slow motility and bending, is described. OHC motility is elicited by stimulation with an external alternating electrical field, and the method takes advantage of high-speed image recording, LED-based illumination, and last generation image analysis software.
JoVE General
Identification and Characterization of Protein Glycosylation using Specific Endo- and Exoglycosidases
Using specific glycosidases to remove sugars from glycoproteins followed by SDS-PAGE is a valuable method to detect glycan modifications on protein samples and is a good choice for initial glycobiology studies. Changes following deglycosylation can be detected as shifts in gel mobility or by staining with glycan sensitive reagents.
JoVE Clinical and Translational Medicine
The Use of Cystometry in Small Rodents: A Study of Bladder Chemosensation
1Laboratory of Experimental Urology, Department of Development and Regeneration, KU Leuven, Belgium, 2Laboratory for Ion Channel Research, Department of Cellular and Molecular Medicine, KU Leuven, Belgium, 3TRP Research Platform Leuven (TRPLe), KU Leuven, Belgium
Cystometry is an efficient technique to measure bladder function of small animals in vivo. The bladder is continuously infused at rates controlled through an intravesical catheter, whereas the urethra is left free for micturition. This allows for repetitive filling and emptying of the bladder, while intravesical pressure and voided volume are recorded.
JoVE General
Detection of Viral RNA by Fluorescence in situ Hybridization (FISH)
1Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, 2Department of Microbiology and Immunology, McGill University, 3Department of Medicine, Division of Experimental Medicine, McGill University
A fluorescence in situ hybridization (FISH) method was developed to visually detect viral genomic RNA using fluorescence microscopy. A probe is made with specificity to the viral RNA that can then be identified using a combination of hybridization and immunofluorescence techniques. This technique offers the advantage of identifying the localization of the viral RNA or DNA at steady-state, providing information on the control of intracellular virus trafficking events.
JoVE Clinical and Translational Medicine
Staining Protocols for Human Pancreatic Islets
Department of Pathology, Immunology, and Laboratory Medicine, University of Florida
This video demonstrates procedures for characterization of human pancreatic islets using hematoxylin and eosin (H&E) and immunohistochemistry (IHC). Pancreatic sections from head, body, and tail regions are stained by both H&E and IHC to determine islet endocrine composition (insulin, glucagon, and pancreatic polypeptide), cell replication (Ki67), and inflammatory infiltrates (H&E, CD3). The uncinate region is localized using IHC for pancreatic polypeptide.
JoVE Neuroscience
A Low Cost Setup for Behavioral Audiometry in Rodents
Experimental Otolaryngology, University of Erlangen-Nuremberg
A fast and inexpensive method for the behavioral determination of hearing parameters like hearing thresholds, hearing impairments or phantom perceptions (subjective tinnitus) is described. It uses pre-pulse inhibition of the acoustic startle response and can be easily implemented in a personal computer using a programmable AD/DA-converter and a piezo sensor.
JoVE General
Transmembrane Domain Oligomerization Propensity determined by ToxR Assay
Department of Chemistry and Biochemistry, University of Colorado at Boulder
An efficient procedure to assess the oligomerization propensity of single-pass transmembrane domains (TMDs) is described. Chimeric proteins consisting of the TMD fused to ToxR are expressed in an E. coli reporter strain. TMD-induced oligomerization causes dimerization of ToxR, activation of transcription and production of the reporter protein, -galactosidase.
JoVE Immunology and Infection
High and Low Throughput Screens with Root-knot Nematodes Meloidogyne spp.
Department of Nematology, University of California, Riverside
Two distinct methods to screen plants with root-knot nematodes are described. The described approaches include high-throughput screens with nematodes in a nondestructive manner facilitating the use of these plants in breeding programs.
JoVE General
Optimized Transfection Strategy for Expression and Electrophysiological Recording of Recombinant Voltage-Gated Ion Channels in HEK-293T Cells
Department of Biology, University of Waterloo
Reliable method for highly efficient in vitro expression and subsequent electrophysiological recording of recombinant voltage-gated ion channels in cultured human embryonic kidney cells (HEK-293T).
JoVE General
Two Types of Assays for Detecting Frog Sperm Chemoattraction
1Department of Animal Sciences, University of Illinois, Urbana-Champaign, 2School of Life Sciences, Arizona State University
Eggs and the extracellular coatings around eggs frequently release peptides, proteins and small molecules that communicate with sperm to guide them to the egg thereby promoting fertilization. Using frog sperm we describe and compare two classes of assays used to detect sperm chemoattraction – sperm accumulation assays and sperm tracking assays.
JoVE General
Purification of the M. magneticum Strain AMB-1 Magnetosome Associated Protein MamAΔ41
MamA is a unique Magnetosome associated protein which was shown to be involved in magnetosome activation. Here we present the purification protocol of MamA deletion mutant (MamAΔ41) from M. magneticum AMB-1.
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