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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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Basic Methods in Cellular and Molecular Biology

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Model Organisms I

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Essentials of
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 JoVE Application Notes

Immunohistochemistry Protocol for Paraffin-embedded Tissue Sections - ADVERTISEMENT

1Cell Signaling Technology


JoVE 5064

Immunohistochemistry (IHC) is a technique used to analyze protein expression in the context of tissue morphology. This article describes an IHC protocol optimized by scientists at Cell Signaling Technology, for use with our antibodies, that you can replicate to obtain the best results in your experiments.

 JoVE Biology

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue

1Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry


JoVE 50589

Archival formalin fixed and paraffin embedded (FFPE) clinical samples are valuable material for investigation of diseases. Here we demonstrate a sample preparation workflow allowing in-depth proteomic analysis of microdissected FFPE tissue.

 JoVE Biology

Using Unfixed, Frozen Tissues to Study Natural Mucin Distribution

1Department of Cellular and Molecular Medicine, University of California, San Diego, 2Biosecurity and Public Health, Los Alamos National Laboratory


JoVE 3928

Unfixed frozen tissue samples embedded in Optimal Cutting Temperature medium (OCT) can be used to study natural distribution and glycosylation of secreted mucus. In this approach tissue processing is minimal and the natural presentation of glycolipids, mucins and glycan-epitopes is preserved. Tissue sections can be analyzed by immunohistochemistry using fluorescence or chromogenic detection.

 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 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 Clinical and Translational Medicine

Isolation, Culture, and Imaging of Human Fetal Pancreatic Cell Clusters

1Pediatric Diabetes Research Center, Department of Pediatrics, University of California, San Diego


JoVE 50796

A protocol to isolate, culture, and image islet cell clusters (ICCs) derived from human fetal pancreatic cells is described.  The method details the steps necessary to generate ICCs from tissue, culture as monolayers or in suspension as aggregates, and image for markers of proliferation and pancreatic cell fate decisions.

 JoVE Clinical and Translational Medicine

Quantitative Multispectral Analysis Following Fluorescent Tissue Transplant for Visualization of Cell Origins, Types, and Interactions

1Department of Leukemia, MD Anderson Cancer Center, 2Wake Forest Baptist Medical Center, Institute for Regenerative Medicine


JoVE 50385

Complex tissue masses, from organs to tumors, are composed of various cellular elements. We elucidated the contribution of cellular phenotypes within a tissue utilizing multi-labeled fluorescent transgenic mice in combination with multiparameter immunofluorescent staining followed by spectral unmixing to decipher cell origin as well as cell characteristics based on protein expression.

 JoVE Immunology and Infection

A Novel Microdissection Approach to Recovering Mycobacterium tuberculosis Specific Transcripts from Formalin Fixed Paraffin Embedded Lung Granulomas

1Bacteriology and Parasitology, Tulane National Primate Research Center, 2Microbiology and Immunology, Tulane National Primate Research Center


JoVE 51693

Microdissection has been extensively employed for the examination of DNA, RNA, and protein within tissue. Laser capture microscopy (LCM) is the most commonly used method, but a new milling technique, mesodissection, is recently available. We demonstrate RNA extraction from mesodissected formalin fixed paraffin embedded tissue slides of Mycobacterium tuberculosis granulomas.

 JoVE Clinical and Translational Medicine

RNAscope for In situ Detection of Transcriptionally Active Human Papillomavirus in Head and Neck Squamous Cell Carcinoma

1Advanced Cell Diagnostics, Inc.


JoVE 51426

The presence of high-risk HPV in head and neck tumor tissue is associated with favorable outcomes. The recently developed RNA in situ hybridization technique called RNAscope allows direct visualization of HPV E6/E7 mRNA in FFPE tissue sections.

 JoVE Clinical and Translational Medicine

Method for Novel Anti-Cancer Drug Development using Tumor Explants of Surgical Specimens

1Department of Neurological Surgery, The Ohio State University Medical Center, 2Department of Pathology, The Ohio State University Medical Center


JoVE 2846

Here, we established a method for drug efficacy testing with surgical specimens of brain tumors, termed “tumor explant method”. With this method, we can evaluate drug efficacy without breaking the microenvironment of solid tumors. To validate reliability of this method, we describe representative data with our glioma specimen treated with the current first-line chemotherapeutic agent, temozolomide.

 JoVE Clinical and Translational Medicine

Molecular Profiling of the Invasive Tumor Microenvironment in a 3-Dimensional Model of Colorectal Cancer Cells and Ex vivo Fibroblasts

1Cancer Sciences Unit, University of Southampton School of Medicine, 2University Surgical Unit, University of Southampton School of Medicine, 3Bioinformatics Unit, London Research Institute, Cancer Research UK


JoVE 51475

Molecular profiling of laser microdissected cells and stroma from synthetic, tissue-engineered colorectal cancer models represents a novel and manipulatable approach to characterize and dissect the distinctive biology at the interface between tumor cells at the invasive front and cancer associated stromal cells.  

 JoVE Clinical and Translational Medicine

Mouse Kidney Transplantation: Models of Allograft Rejection

1MRC Centre for Inflammation Research, The Queen's Medical Research Institute, The University of Edinburgh


JoVE 52163

Here, we present a protocol to study the immunology of rejection. The surgical model presented reports a short operating time and a concise technique. Depending on the donor-recipient strain combination, the transplanted kidney may develop acute cellular rejection or chronic allograft damage, defined by interstitial fibrosis and tubular atrophy.

 JoVE Clinical and Translational Medicine

Primary Orthotopic Glioma Xenografts Recapitulate Infiltrative Growth and Isocitrate Dehydrogenase I Mutation

1Department of Neurology, Vanderbilt University Medical Center, 2Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, 3Neurology Service, Veteran Affairs TVHS


JoVE 50865

Malignant gliomas constitute a heterogeneous group of highly infiltrative glial neoplasms with distinct clinical and molecular features. Primary orthotopic xenografts recapitulate the histopathological and molecular features of malignant glioma subtypes in preclinical animal models.

 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 Clinical and Translational Medicine

Assessing Phagocytic Clearance of Cell Death in Experimental Stroke by Ligatable Fluorescent Probes

1Baylor College of Medicine, 2Michael E. DeBakey Veterans Affairs Medical Center


JoVE 51261

We present a new fluorescence technique for selective in situ labeling of active phagocytic cells, which clear off cell corpses in stroke. The approach is important for assessing brain reaction to ischemia because only a small proportion of phagocytes present in ischemic brain participate in clearance of cell death.

 JoVE Clinical and Translational Medicine

The In ovo CAM-assay as a Xenograft Model for Sarcoma

1Department of Orthopaedic Surgery and Traumatology, Ghent University Hospital, 2Department of Radiation Oncology and Experimental Cancer Research, Ghent University, 3Department of Virology, Parasitology, and Immunology, Ghent University, 4Pathlicon


JoVE 50522

The in ovo chorioallantoic membrane (CAM) is grafted with fresh sarcoma-derived tumor tissues, their single cell suspensions, and permanent and transient fluorescently labeled established sarcoma cell lines. The model is used to study graft- (viability, Ki67 proliferation index, necrosis, infiltration) and host (fibroblast infiltration, vascular ingrowth) behavior.

 JoVE Immunology and Infection

Granulocyte-dependent Autoantibody-induced Skin Blistering

1Department of Dermatology, University of Freiburg, 2Kepler High School Freiburg, 3Centre for Biological Signalling Studies (BIOSS), University of Freiburg


JoVE 4250

In the animal model described in our present work, purified IgG antibodies against a stretch of 200 amino acids (aa 757-967) of collagen VII are injected repeatedly into mice reproducing the blistering phenotype as well as the histo- and immunopathological features characteristic to human epidermolysis bullosa acquisita (EBA)1.

 JoVE Bioengineering

In vitro Assembly of Semi-artificial Molecular Machine and its Use for Detection of DNA Damage

1Neurosurgery, Baylor College of Medicine, 2Michael E. DeBakey Veterans Affairs Medical Center, 3Molecular & Cellular Biology, Baylor College of Medicine


JoVE 3628

We demonstrate the assembly and application of a molecular-scale device powered by a topoisomerase protein. The construct is a bio-molecular sensor which labels two major types of DNA breaks in tissue sections by attaching two different fluorophores to their ends.

 JoVE Immunology and Infection

Combination of Adhesive-tape-based Sampling and Fluorescence in situ Hybridization for Rapid Detection of Salmonella on Fresh Produce

1Center for Meat Safety and Quality, Department of Animal Sciences, Colorado State University, 2Rapid Microbial Detection and Control Laboratory, Department of Food Science and Human Nutrition, Iowa State University


JoVE 2308

This protocol describes a simple adhesive-tape-based approach for sampling of tomato and other fresh produce surfaces, followed by rapid whole cell detection of Salmonella using fluorescence in situ hybridization (FISH).

 JoVE Clinical and Translational Medicine

Skin Punch Biopsy Explant Culture for Derivation of Primary Human Fibroblasts

1Basic Research Department, The Parkinson's Institute


JoVE 3779

The fibroblast explant culture protocol from human skin punch biopsies is a technically robust and simple way to derive skin cells within 4-8 weeks for banking of about 15-20 million cells at a low passage number.

 JoVE Biology

An Effective Manual Deboning Method To Prepare Intact Mouse Nasal Tissue With Preserved Anatomical Organization

1Biological Sciences, University of Maryland Baltimore County

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