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  JoVE Biology

  
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  JoVE Neuroscience

  
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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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Institution Web Site

Stanford University

47 articles published in JoVE

 JoVE Bioengineering

Programming Stem Cells for Therapeutic Angiogenesis Using Biodegradable Polymeric Nanoparticles

1Department of Orthopaedic Surgery, Stanford University, 2Department of Bioengineering, Stanford University


JoVE 50736

We describe the method of programming stem cells to overexpress therapeutic factors for angiogenesis using biodegradable polymeric nanoparticles. Processes described include polymer synthesis, transfecting adipose-derived stem cells in vitro, and validating the efficacy of programmed stem cells to promote angiogenesis in a murine hindlimb ischemia model.

 JoVE Applied Physics

In-situ Tapering of Chalcogenide Fiber for Mid-infrared Supercontinuum Generation

1Edward L. Ginzton Laboratory, Stanford University


JoVE 50518

We describe a method for in-situ tapering of As2S3 fibers to achieve efficient mid-infrared supercontinuum generation. By tapering while monitoring the supercontinuum’s spectrum, the spectral width can be maximized for a fiber taper. In-situ fiber tapering can be applied to optimize the performance of other fiber-based devices.

 JoVE Biology

Rapid Genetic Analysis of Epithelial-Mesenchymal Signaling During Hair Regeneration

1Program in Epithelial Biology, Stanford University School of Medicine


JoVE 4344

Tissue-specific analysis of a hair follicle regeneration model using lentivirus to mediate gain- or loss-of-function.

 JoVE Neuroscience

Optogenetic Stimulation of Escape Behavior in Drosophila melanogaster

1Department of Neurobiology, Stanford University


JoVE 50192

Genetically encoded optogenetic tools enable noninvasive manipulation of specific neurons in the Drosophila brain. Such tools can identify neurons whose activation is sufficient to elicit or suppress particular behaviors. Here we present a method for activating Channelrhodopsin2 that is expressed in targeted neurons in freely walking flies.

 JoVE Clinical and Translational Medicine

Probe-based Confocal Laser Endomicroscopy of the Urinary Tract: The Technique

1Department of Urology, Stanford University School of Medicine, 2Veterans Affairs Palo Alto Health Care System


JoVE 4409

Probe-based confocal laser endomicroscopy enables real-time microscopy of the human urinary tract during cystoscopy, providing dynamic, intravital imaging of pathological states such as bladder cancer with cellular resolution. Endomicroscopy may augment the diagnostic accuracy of standard white light endoscopy and provide intraoperative image guidance to improve surgical resection.

 JoVE Clinical and Translational Medicine

Cerenkov Luminescence Imaging (CLI) for Cancer Therapy Monitoring

1Department of Radiology and Bio-X Program Canary Cancer at Stanford for Cancer Early Detection, Stanford University


JoVE 4341

Use of Cerenkov Luminescence Imaging (CLI) for monitoring preclinical cancer treatment is described here. This method takes advantage of Cerenkov Radiation (CR) and optical imaging (OI) to visualize radiolabeled probes and thus provides an alternative to PET in preclinical therapeutic monitoring and drug screening.

 JoVE Bioengineering

Mass Cytometry: Protocol for Daily Tuning and Running Cell Samples on a CyTOF Mass Cytometer

1Human Immune Monitoring Center, Institute for Immunity, Transplantation, and Infection, Stanford University


JoVE 4398

The steps necessary for daily tuning and optimization of the performance of a CyTOF mass cytometer are described. Comments on optimal sample preparation and flow rate are discussed

 JoVE Clinical and Translational Medicine

Repair of a Critical-sized Calvarial Defect Model Using Adipose-derived Stromal Cells Harvested from Lipoaspirate

1Department of Surgery, Stanford University, 2Department of Surgery, Duke University, 3Department of Surgery, Saint Joseph Mercy Hospital, 4School of Medicine, University of California, San Francisco, 5School of Dentistry, University of California, Los Angeles


JoVE 4221

This protocol describes the isolation of adipose-derived stromal cells from lipoaspirate and the creation of a 4 mm critical-sized calvarial defect to evaluate skeletal regeneration.

 JoVE Clinical and Translational Medicine

Collecting And Measuring Wound Exudate Biochemical Mediators In Surgical Wounds

1Department of Anesthesia, Stanford University School of Medicine


JoVE 50133

This article provides a detailed and visual description of a methodology for collecting and measuring biochemical inflammatory and nociceptive mediators at the surgical wound site following cesarean delivery. This human bioassay has been used to determine correlations between wound and serum cytokine concentrations and drug-mediated changes in wound cytokines, chemokines and neuropetides.

 JoVE Biology

Synthesis of an In vivo MRI-detectable Apoptosis Probe

1Division of Cardiovascular Medicine, Department of Medicine, Stanford University Medical Center, 2Division of Cardiology, Department of Medicine, University of California, San Francisco, 3San Francisco VAMC


JoVE 3775

Early detection of apoptosis may identify at-risk cell populations in a variety of diseases. Here we demonstrate a method to link an early apoptosis-detection protein (Annexin V) to a MRI-detectable iron oxide nanoparticle (SPIO). This method may be extended to other proteins of interest to generate MRI-detectable molecular imaging probes.

 JoVE Bioengineering

Multiplexed Single-molecule Force Proteolysis Measurements Using Magnetic Tweezers

1Department of Chemical Engineering, Stanford University


JoVE 3520

In this article we describe the use of magnetic tweezers to study the effect of force on enzymatic proteolysis at the single molecule level in a highly parallelizable manner.

 JoVE Neuroscience

Functional Neuroimaging Using Ultrasonic Blood-brain Barrier Disruption and Manganese-enhanced MRI

1Department of Radiology, Stanford University, 2Center for In Vivo Microscopy, Duke University Medical Center, 3Department of Biomedical Engineering, Duke University


JoVE 4055

A technique is described for broadly opening the blood-brain barrier in the mouse using microbubbles and ultrasound. Using this technique, manganese can be administered to the mouse brain. Because manganese is an MRI contrast agent that accumulates in depolarized neurons, this approach enables imaging of neuronal activity.

 JoVE Bioengineering

Time-lapse Fluorescence Imaging of Arabidopsis Root Growth with Rapid Manipulation of The Root Environment Using The RootChip

1Department of Plant Biology, Carnegie Institution for Science, 2Howard Hughes Medical Institute, 3Departments of Applied Physics and Bioengineering, Stanford University, 4Department of Microsystems Engineering (IMTEK) and Center for Biological Signaling Studies (BIOSS), University of Freiburg


JoVE 4290

This article provides a protocol for cultivation of Arabidopsis seedlings in the RootChip, a microfluidic imaging platform that combines automated control of growth conditions with microscopic root monitoring and FRET-based measurement of intracellular metabolite levels.

 JoVE Clinical and Translational Medicine

Human Internal Mammary Artery (IMA) Transplantation and Stenting: A Human Model to Study the Development of In-Stent Restenosis

1University 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


JoVE 3663

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.

 JoVE Biology

Chromatin Isolation by RNA Purification (ChIRP)

1Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine


JoVE 3912

ChIRP is a novel and rapid technique to map genomic binding sites of long noncoding RNAs (lncRNAs). The method takes advantage of the specificity of anti-sense tiling oligonucleotides to allow the enumeration of lncRNA-bound genomic sites.

 JoVE Bioengineering

On-chip Isotachophoresis for Separation of Ions and Purification of Nucleic Acids

1Mechanical Engineering, Stanford University


JoVE 3890

Isotachophoresis (ITP) is a robust electrokinetic separation and preconcentration technique with applications ranging from toxin detection to sample preparation. We review the physical principles of ITP and the methodology of applying this technique to two specific example applications: separation and detection of small molecules and purification of nucleic acids from cell culture lysate.

 JoVE Neuroscience

Isolating LacZ-expressing Cells from Mouse Inner Ear Tissues using Flow Cytometry

1Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine


JoVE 3432

Flow cytometry is a powerful tool allowing for the isolation and study of specific cell populations. This protocol describes steps for isolating LacZ-expressing cells from cochlear tissues from neonatal transgenic mice. Dissociated cochlear cells were labeled using fluorescent-conjugated substrates of β-galactosidase prior to separation via flow cytometry.

 JoVE Clinical and Translational Medicine

Labeling Stem Cells with Ferumoxytol, an FDA-Approved Iron Oxide Nanoparticle

1Department of Radiology, Molecular Imaging Program at Stanford (MIPS), 2Stanford School of Medicine, Stanford University


JoVE 3482

We describe a technique for labeling and tracking stem cells with FDA-approved, superparamagnetic iron oxide (SPIO), ferumoxytol (Feraheme). This cellular imaging technique that utilizes magnetic resonance (MR) imaging for visualization, is readily accessible for long-term monitoring and diagnosis of successful or unsuccessful stem cell engraftments in patients.

 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

Mouse Bladder Wall Injection

1Department of Urology, Stanford University School of Medicine


JoVE 2523

Mouse bladder wall injection is a useful approach to orthotopically study bladder stem cell and cancer biology. This delicate microsurgical method can be mastered with careful technique and practice.

 JoVE Bioengineering

Bioluminescence Imaging for Assessment of Immune Responses Following Implantation of Engineered Heart Tissue (EHT)

1Transplant and Stem Cell Immunobiology Lab (TSI) and CVRC, University Hospital Hamburg, University Heart Center Hamburg, 2Department of Experimental and Clinical Pharmacology and Toxicology, University Heart Center Hamburg, 3CT Surgery, Stanford University School of Medicine


JoVE 2605

This video demonstrates the use of in vivo bioluminescence imaging to study immune responses after implantation of Engineered Heart Tissue (EHT) in rats.

 JoVE Biology

Lineage Labeling of Zebrafish Cells with Laser Uncagable Fluorescein Dextran

1Department of Biological Sciences, Vanderbilt University, 2Department of Chemical and Systems Biology, Stanford University


JoVE 2672

This protocol delineates a way to label and trace the fate of small groups of cells zebrafish embryos using UV-uncaging of caged fluorescein, followed by whole mount immunolabeling to amplify the signal from the uncaged fluorescein.

 JoVE Biology

Detection of Post-translational Modifications on Native Intact Nucleosomes by ELISA

1Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, 2Department of Molecular and Cell Biology, University of Connecticut, 3Department of Pharmaceutical Sciences, University of Connecticut


JoVE 2593

Nucleosome ELISA (NU-ELISA) is a sensitive and quantitative method to detect global patterns of post-translational modifications in preparations of native, intact nucleosomes. These modifications include methylations, acetylations, and phosphorylations at specific histone amino acid residues, and hence NU-ELISA provides a global proteomic assay of the overall chromatin modification states of specific cell types.

 JoVE Biology

Associated Chromosome Trap for Identifying Long-range DNA Interactions

1Medical Service, VA Palo Alto Health Care System , Stanford University School of Medicine


JoVE 2621

The associated chromosome trap (ACT) assay is a novel unbiased method for identifying long-range DNA interactions. The characterization of long range DNA interactions will allow us to determine the relationship of nuclear architecture to gene expression in both normal physiology and in diseased states.

 JoVE Biology

Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses

1Department of Biological Sciences, University of Alabama Huntsville, 2Department of Biology, Stanford University


JoVE 2498

A major impediment to biochemical analyses of ribosomes containing nascent peptidyl-tRNAs has been the presence of other ribosomes in the same samples, ribosomes not involved in the translation of the specific mRNA sequence being analyzed. We developed a simple methodology to purify, exclusively, the ribosomes containing the nascent peptidyl-tRNA of interest.

 JoVE Clinical and Translational Medicine

Orthotopic Aortic Transplantation: A Rat Model to Study the Development of Chronic Vasculopathy

1University Heart Center Hamburg, Transplant and Stem Cell Immunobiology Lab (TSI), University Hospital Hamburg, 2Stanford University School of Medicine


JoVE 1989

This video demonstrates the orthotopic aortic transplant model as a simple model to study the development of transplant vasculopathy (TVP) in rats.

 JoVE Neuroscience

The Organotypic Hippocampal Slice Culture Model for Examining Neuronal Injury

1Department of Neurology and Neurological Sciences, Stanford University School of Medicine


JoVE 2106

The organoptypic hippocampal slice culture model is an in vitro model used to examine neuronal injury in a variety of paradigms. In this article, we describe the methods for generating slice cultures and quantifying neuronal injury.

 JoVE Immunology and Infection

Transurethral Induction of Mouse Urinary Tract Infection

1Earth Systems Program, School of Earth Sciences, Stanford University, 2Department of Urology, Stanford University School of Medicine


JoVE 2070

This video will demonstrate methods to transurethrally induce mouse urinary tract infections and quantify the extent of resulting infections.

 JoVE Biology

Heterotopic and Orthotopic Tracheal Transplantation in Mice used as Models to Study the Development of Obliterative Airway Disease

1Transplant and Stem Cell Immunobiology Lab (TSI), University Heart Center Hamburg, 2CVRC, University Hospital Hamburg, 3Department of CT Surgery, Stanford University School of Medicine


JoVE 1437

This video shows and compares two experimental models to study the development of obliterative airway disease (OAD) in mice, the heterotopic and orthotopic tracheal transplantation model.

 JoVE Biology

LAD-Ligation: A Murine Model of Myocardial Infarction

1Transplant and Stem Cell Immunobiology Lab (TSI), University Heart Center Hamburg, 2CVRC, University Hospital Hamburg, 3Department of CT Surgery, Stanford University School of Medicine


JoVE 1438

This video demonstrates how to use a fast and reliable model to study pathobiological and pathophysiological processes of myocardial ischemia.

 JoVE Biology

Imaging In-Stent Restenosis: An Inexpensive, Reliable, and Rapid Preclinical Model

1Department of Cardiothoracic Surgery, Stanford University School of Medicine, 2Stanford University School of Medicine


JoVE 1346

This video demonstrates how to use a preclinical inexpensive and reliable model to study pathobiological and pathophysiological processes of in-stent restenosis development. Longitudinal in vivo monitoring using OCT (Optical Coherence Tomography) and analysis of OCT images are also demonstrated.

 JoVE Biology

Creation of Murine Experimental Abdominal Aortic Aneurysms with Elastase

1Department of Cardiovascular Medicine, Stanford University School of Medicine, 2Department of Vascular Surgery, Stanford University School of Medicine


JoVE 1280

This video shows how to induce abdominal aortic aneurysms (AAA) in mice via transient intraluminal infusion of porcine pancreatic elastase into the infrarenal segment of the abdominal aorta. The model has the ability to add broad insight into the pathobiology of AAA due to the emergence of numerous transgenic and gene knockout mice.

 JoVE Biology

Embryonic Stem Cell-Derived Endothelial Cells for Treatment of Hindlimb Ischemia

1Division of Cardiovascular Medicine, Stanford University, 2Department of Radiology, Stanford University


JoVE 1034

The surgical procedure for delivery of embryonic stem cell-derived endothelial cells to the ischemic hindlimb is demonstrated, with non-invasive tracking by bioluminescence imaging.

 JoVE Biology

Murine Model of Hindlimb Ischemia

1Division of Cardiovascular Medicine, Stanford University, 2Department of Anesthesiology, University of California, San Francisco


JoVE 1035

The surgical procedure for induction of unilateral hindlimb ischemia is demonstrated, with confirmation of ischemia by laser Doppler perfusion imaging.

 JoVE Biology

Calcium Imaging of Cortical Neurons using Fura-2 AM

1Department of Neurobiology, Stanford University, 2Department of Neurobiology, Stanford University School of Medicine


JoVE 1067

Calcium signals play a key role in many cellular processes including gene expression, survival and differentiation. Here we demonstrate how to perform calcium imaging using Fura-2 AM. Calcium imaging is a valuable tool to study the regulation of intracellular calcium in real time and its regulation of signaling cascades.

 JoVE Biology

Determining heat and mechanical pain threshold in inflamed skin of human subjects

1Department of Anesthesia, Stanford University School of Medicine


JoVE 1092

Algorithms assessing heat and mechanical pain thresholds in experimentally inflamed skin of human study subjects are shown. The two pain testing paradigms independently examine nociceptive processing by the two major peripheral nerve fiber populations transmitting pain, i.e., non-myelinated C fibers and small myelinated A-delta fibers.

 JoVE Biology

Human In-Vivo Bioassay for the Tissue-Specific Measurement of Nociceptive and Inflammatory Mediators

1Department of Anesthesia, Stanford University School of Medicine, 2Department of Anaesthesiology, University of Mannheim, 3Department of Anaesthesiology, University of Heidelberg


JoVE 1074

A technique is presented for the in-vivo collection of interstitial fluid samples from pertinent tissue sites (here, experimentally inflamed skin) for the measurement of biochemicals mediating pain and inflammation.

 JoVE Biology

The Hypoxic Ischemic Encephalopathy Model of Perinatal Ischemia

1Department of Neurology and Neurological Sciences, Stanford University School of Medicine


JoVE 955

The postnatal rat model for hypoxic-ischemic brain injury is a well-established model of human neonatal hypoxic ischemic encephalopathy (HIE). In this article, we describe the model of HIE in post-natal rat pups.

 JoVE Biology

Collecting and Measuring Nociceptive and Inflammatory Mediators in Surgical Wounds

1Department of Anesthesiology, Stanford University School of Medicine


JoVE 962

A technique to collect and measure surgical wound biochemical mediators at specific time points.

 JoVE Biology

Pressure-polishing Pipettes for Improved Patch-clamp Recording

1Department of Molecular and Cellular Physiology, Stanford University School of Medicine


JoVE 964

This is a guide to modifying the shape of glass micropipettes. Specifically, by using heat and air pressure the taper is widened without increasing the tip opening, leading to lower pipette resistance. This is critical to obtain low noise recordings of small cells but is useful in many applications.

 JoVE Biology

Patch Clamp Recording of Ion Channels Expressed in Xenopus Oocytes

1Department of Molecular and Cellular Physiology, Stanford University, 2Department of Molecular and Cellular Physiology, Stanford University School of Medicine


JoVE 936

This is intended as an introduction to patch clamp recording from Xenopus laevis oocytes. It covers vitelline membrane removal, formation of a gigaohm seal (gigaseal), and the optional conversion of the patch to the outside-out topology.

 JoVE Biology

Making Patch-pipettes and Sharp Electrodes with a Programmable Puller

1Department of Molecular and Cellular Physiology, Stanford University, 2Department of Molecular and Cellular Physiology, Stanford University School of Medicine


JoVE 939

This video shows how to use a programmable puller to make patch pipettes and sharp electrodes for electrophysiology. The same procedure can be used to make a variety of glass tools, including injection needles.

 JoVE Biology

In vitro Labeling of Human Embryonic Stem Cells for Magnetic Resonance Imaging

1Division of Cardiovascular Medicine, Stanford University


JoVE 827

In this video, we are showing how to label human embryonic stem cells (hESC) with manganese chloride (MnCl2) which can enter cells via voltage-gated calcium channels when the cells are biologically active. Additionally, we show the use of MnCl2 as cellular MRI contrast agent to determine the in vitro viability of hESC.

 JoVE Biology

In vitro and in vivo Bioluminescence Reporter Gene Imaging of Human Embryonic Stem Cells

1Departments of Radiology and Medicine (Cardiology), Stanford University School of Medicine


JoVE 740

With the growing interest in stem cell therapies, molecular imaging techniques are ideal for monitoring stem cell behavior after transplantation. Luciferase reporter genes have enabled non-invasive, repetitive assessment of cell survival, location, and proliferation in vivo. This video will demonstrate how to track hESC proliferation in a living mouse.

 JoVE Biology

Orthotopic Mouse Model of Colorectal Cancer

1Department of Surgery, University of California, San Francisco - UCSF, 2Department of Pathology, Stanford University School of Medicine


JoVE 484

Two techniques can be used to establish this model: injection of a cancer cell suspension into the cecal wall or transplantation of a piece of subcutaneous tumor onto the cecum. This model is useful for studying the natural progression of colorectal cancer and testing new therapeutic agents against colorectal cancer.

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