An increased tendency of the Genome
to acquire Mutations
when various processes involved in maintaining and replicating the genome are dysfunctional.
JoVE Immunology and Infection
1Greehey Children's Cancer Research Institute, UT Health Science Center at San Antonio, 2Department of Cellular and Structural Biology, UT Health Science Center at San Antonio, 3Department of Pathology, UT Health Science Center at San Antonio, 4Department of Microbiology, UT Health Science Center at San Antonio, 5Cancer Therapy and Research Center, UT Health Science Center at San Antonio
Here we describe an in vivo mutagenesis assay for small numbers of purified hematopoietic cells using the LacI transgenic mouse model. The LacI gene can be isolated to determine the frequency, location, and type of DNA mutants spontaneously arisen or after exposure to genotoxins.
Published February 24, 2014. Keywords: Infection, In vivo mutagenesis, hematopoietic stem/progenitor cells, LacI mouse model, DNA mutations, E. coli
1Irell & Manella Graduate School of Biological Sciences, 2Department of Molecular and Cellular Biology, City of Hope Comprehensive Cancer Center and Beckman Research Institute, 3Department of Biochemistry and Molecular Biology, University of Southern California, Norris Comprehensive Cancer Center
The HO-stimulated translocation assay monitors single-strand annealing following the creation of DNA double-strand breaks at multiple loci in diploid Saccharomyces cerevisiae. This mechanism may model genome rearrangements in somatic cells of higher eukaryotes following exposure to high doses of ionizing radiation.
Published September 23, 2011. Keywords: Genetics, translocation formation, HO-endonuclease, Genomic Southern blot, Chromosome blot, Pulsed-field gel electrophoresis, Homologous recombination, DNA double-strand breaks, Single-strand annealing
JoVE Immunology and Infection
1Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey
DNA repair pathways are essential for maintenance of genomic integrity and preventing mutation and cancer. The goal of this protocol is to quantify genomic instability by direct observation of chromosome aberrations in metaphase spreads from mouse B cells using fluorescent in situ hybridization (FISH) for telomeric DNA repeats.
Published August 19, 2014. Keywords: Immunology, genomic instability, DNA repair, mouse, metaphase spread, FISH, primary culture
1Department of Biochemistry, University of Oxford
Exonucleases play critical roles in ensuring genome stability. Loss of WRN exonuclease function results in premature aging. Studying substrates and other requirements of the nuclease in vitro can help elucidate its role in vivo. Here we demonstrate a rapid and reproducible fluorescence-based assay to measure its nuclease activity.
Published December 23, 2013. Keywords: Biochemistry, Aging, Premature, Exonucleases, Enzyme Assays, biochemistry, WRN, exonuclease, nuclease, RecQ, progeroid disease, aging, DmWRNexo
JoVE Immunology and Infection
1Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, 2Department of Pathology and Laboratory Medicine, Emory University
HIV-1 pathogenesis is defined by both viral characteristics and host genetic factors. Here we describe a robust method that allows for reproducible measurements to assess the impact of the gag gene sequence variation on the in vitro replication capacity of the virus.
Published August 31, 2014. Keywords: Infectious Diseases, HIV-1, Gag, viral replication, replication capacity, viral fitness, MJ4, CEM, GXR25
1Department of Genetics, Louisiana State University Health Science Center
Chromosomes can be isolated from live cells such as lymphocytes or skin fibroblasts, and from organisms including humans or mice. These chromosome preparations can be further utilized for routine G-banding and molecular cytogenetic procedures such as fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH), and spectral karyotyping (SKY).
Published January 28, 2014. Keywords: Basic Protocol, chromosome, cytogenetic, harvesting, karyotype, fluorescence in situ hybridization, FISH
1Environmental Health Science and Research Bureau, Health Canada, Environmental Health Centre
De novo mutations in the male germline may contribute to adverse health outcomes in subsequent generations. Here we describe a protocol for the use of a transgenic rodent model for quantifying mutations in male germ cells induced by environmental agents.
Published August 6, 2014. Keywords: Genetics, sperm, spermatogonia, male germ cells, spermatogenesis, de novo mutation, OECD TG 488, transgenic rodent mutation assay, N-ethyl-N-nitrosourea, genetic toxicology
JoVE Clinical and Translational Medicine
1Joint Unit Hospices de Lyon-bioMérieux, 2Medical Diagnostic Discovery Department, BioMérieux, 3Department of Pathology and Cytology, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, 4Medical Faculty, Lyon 1 University, 5Data and Knowledge Laboratory, BioMérieux, 6Department of Biochemistry and Molecular Biology, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, 7Department of Urology, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon
Human endogenous retroviruses (HERV), which occupy 8% of the human genome, retain scarce coding capacities but a hundred thousand long terminal repeats (LTRs). A custom Affymetrix microarray was designed to identify individual HERV locus expression and was used on prostate cancer tissues as a proof of concept for future clinical studies.
Published November 2, 2013. Keywords: Medicine, Cancer Biology, Genetics, Molecular Biology, Prostate, Retroviridae, Biomarkers, Pharmacological, Tumor Markers, Biological, Prostatectomy, Microarray Analysis, Gene Expression, Diagnosis, Human Endogenous Retroviruses, HERV, microarray, Transcriptome, prostate cancer, Affymetrix
1Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles
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.
Published May 22, 2012. Keywords: Basic Protocols, PCR, optimization, primer design, melting temperature, Tm, troubleshooting, additives, enhancers, template DNA quantification, thermal cycler, molecular biology, genetics
1Department of Pathology, New York University School of Medicine, 2New York University Center for Health Informatics and Bioinformatics, 3NYU Cancer Institute, 4Department of Pathology and Yale Cancer Center, Yale University School of Medicine
Here we describe a protocol for simultaneous detection of histone modifications by immunofluorescence and DNA sequences by DNA FISH followed by 3D microscopy and analyses (3D immuno-DNA FISH).
Published February 3, 2013. Keywords: Genetics, Molecular Biology, Bioinformatics, Cancer Biology, Pathology, Biomedical Engineering, Immunology, Intranuclear Space, Nuclear Matrix, Fluorescence in situ Hybridization, FISH, 3D DNA FISH, DNA, immunofluorescence, immuno-FISH, 3D microscopy, Nuclear organization, interphase nuclei, chromatin modifications