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Alkaline Phosphatase: An enzyme that catalyzes the conversion of an orthophosphoric monoester and water to an alcohol and orthophosphate. EC 3.1.3.1.

DNA Ligation Reactions

JoVE 5069

In molecular biology, ligation refers to the joining of two DNA fragments through the formation of a phosphodiester bond. An enzyme known as a ligase catalyzes the ligation reaction. In the cell, ligases repair single and double strand breaks that occur during DNA replication. In the laboratory, DNA ligase is used during molecular cloning to join DNA fragments of inserts with vectors – carrier DNA molecules that will replicate target fragments in host organisms. This video provides an introduction to DNA ligation. The basic principle of ligation is described as well as a step-by-step procedure for setting up a generalized ligation reaction. Critical aspects of ligation reactions are discussed, such as how the length of a sticky end overhang affects the reaction temperature and how the ratio of DNA insert to vector should be tailored to prevent self-ligation. Molecular tools that assist with ligations like the Klenow Fragment and shrimp alkaline phosphatase (SAP) are mentioned, and applications , such as proximity ligations and the addition of linkers to fragments for sequencing are also presented.


 Basic Methods in Cellular and Molecular Biology

Whole-Mount In Situ Hybridization

JoVE 5330

Whole-mount in situ hybridization (WMISH) is a common technique used for visualizing the location of expressed RNAs in embryos. In this process, synthetically produced RNA probes are first complementarily bound, or "hybridized," to the transcripts of target genes. Immunohistochemistry or fluorescence is then used to detect these RNA hybrids, revealing spatial and temporal patterns of gene expression. Unlike traditional in situ hybridization techniques, which require thin tissue sections whose images will need to be computationally reassembled, the whole-mount technique allows gene expression patterns to be assessed over the entire embryo or structure. This video will introduce the basic concepts of whole mount staining and detail key procedural steps, including probe design and production, embryo fixation and staining, and post-hybridization signal detection. Viewers will then learn about how developmental biologists are applying WMISH to current research studies.


 Developmental Biology

The Western Blot

JoVE 5065

Western Blotting is used to identify the presence of specific proteins in electrophoretically separated samples. Following separation by a technique known as sodium dodecyl sulfate polyacrylamide gel electrophoresis, or SDS-PAGE, western transfer is used to move proteins from a polyacrylamide gel onto a piece of membrane which traps the proteins in their respective locations. Next, the membranes are probed with antibodies in a process called immunboblotting. Immunoblotting uses antibody-protein and antibody-antibody binding through specific recognition sites, providing the high specificity required for identifying a single protein. The detection of antibodies takes place using reporter systems which includes the use of enzymes. Enzymes can be attached to the end of an antibody and react with substrates to produce changes in color or light. These signals can then be imaged and quantified using a process called densitometry. This video-article presents an overview of the western blot technique by describing western transfer, the use of antibody detection, and image analysis. The steps involved with western transfer such as the assembly of the transfer sandwich and transfer conditions are discussed in detail as well as the theory behind antibody binding and detection of those antibodies. The broad applications of this technique are described through severa


 Basic Methods in Cellular and Molecular Biology

Site-Directed Immobilization of Bone Morphogenetic Protein 2 to Solid Surfaces by Click Chemistry

1Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik (IGB), Translationszentrum Würzburg 'Regenerative Therapien für Krebs- und Muskuloskelettale Erkrankung', Institutsteil Würzburg, 2Lehrstuhl für Tissue Engineering und Regenerative Medizin, Universitätsklinikum Würzburg, 3Lehrstuhl für Pharmazeutische Technologie und Biopharmazie, Universität Würzburg, 4Lehrstuhl für molekulare Pflanzenphysiologie und Biophysik, Julius-von-Sachs Institut für Biowissenschaften, Universität Würzburg

JoVE 56616


 Bioengineering

Modeling Osteosarcoma Using Li-Fraumeni Syndrome Patient-derived Induced Pluripotent Stem Cells

1Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 2Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth, 3Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, 4Women's Health Institute, Cleveland Clinic Foundation, 5Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, 6Center for Precision Health, School of Biomedical Informatics and School of Public Health, The University of Texas Health Science Center at Houston

JoVE 57664


 Cancer Research

Generation of Induced Pluripotent Stem Cells from Frozen Buffy Coats using Non-integrating Episomal Plasmids

1Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), 2Laboratory of Medical Genetics, Fondazione IRCCS Ca´ Granda, Ospedale Maggiore Policlinico, 3Del E. Webb Center for Neuroscience, Aging & Stem Cell Research, Sanford-Burnham Medical Research Institute

JoVE 52885


 Developmental Biology

Flat Mount Imaging of Mouse Skin and Its Application to the Analysis of Hair Follicle Patterning and Sensory Axon Morphology

1Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 2Department of Neuroscience, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 3Department of Ophthalmology, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine

JoVE 51749


 Neuroscience

Prediction of HIV-1 Coreceptor Usage (Tropism) by Sequence Analysis using a Genotypic Approach

1Institute of Virology, University of Cologne, 2Max Planck Institute for Informatics, 3Institute for Immune genetics, 4Department of Gastroenterology, Hepatology and Infectiology, University of Duesseldorf, 5Department of Dermatology, University of Essen, 6Department of Internal Medicine, University of Cologne, 7Augustinerinnen Hospital

JoVE 3264


 Immunology and Infection

Quantitation of Protein Expression and Co-localization Using Multiplexed Immuno-histochemical Staining and Multispectral Imaging

1Division of Urologic Surgery, Washington University in St. Louis School of Medicine, 2Department of Urology, University of Wisconsin School of Medicine and Public Health, 3Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, 4O’Brien Urology Research Center, University of Wisconsin School of Medicine and Public Health

JoVE 53837


 Biology

High-Throughput, Multi-Image Cryohistology of Mineralized Tissues

1Department of Reconstructive Sciences, University of Connecticut Health Center, 2Department of Computer Science and Engineering, University of Connecticut, 3Department of Orthopaedic Surgery, University of Connecticut Health Center, 4Department of Orthopaedics, University of Rochester

JoVE 54468


 Biology

Human Pluripotent Stem Cell Culture on Polyvinyl Alcohol-Co-Itaconic Acid Hydrogels with Varying Stiffness Under Xeno-Free Conditions

1Department of Chemical and Materials Engineering, National Central University, 2Department of Botany and Microbiology, King Saud University, 3Cathay Medical Research Institute, Cathay General Hospital, 4Graduate Institute of Systems Biology and Bioinformatics, National Central University, 5Department of Medical Microbiology and Parasitology, Universiti Putra Malaysia, 6Department of Internal Medicine, Taiwan Landseed Hospital, 7Department of Zoology, Bharathiar University, 8Thiruvalluvar University

JoVE 57314


 Bioengineering

Understanding Early Organogenesis Using a Simplified In Situ Hybridization Protocol in Xenopus

1Developmental and Stem Cell Biology, Hospital for Sick Children, 2Children's Health Research Institute, University of Western Ontario, 3Department of Physiology and Pharmacology, University of Western Ontario, 4Neurosciences and Mental Health, Hospital for Sick Children, 5Department of Paediatrics, University of Western Ontario

JoVE 51526


 Developmental Biology

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

1Molecular Genetics of Chronic Inflammation and Allergic Disease, Max-Delbrück Center for Molecular Medicine, 2Murdoch Childrens Research Institute, 3Department of Paediatrics, University of Melbourne, 4Centre for Social and Early Emotional Development, Faculty of Health, Deakin University, 5Department of Paediatrics, University of Western Australia

JoVE 57601


 Genetics

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