1st Edition

Molecular Analyses

Edited By Scott Orland Rogers Copyright 2022
    375 Pages 20 Color & 68 B/W Illustrations
    by CRC Press

    375 Pages 20 Color & 68 B/W Illustrations
    by CRC Press

    DNA and RNA extraction methods from a variety of tissues and samples are now routine, including extraction from single cells. Many methods are now automated. Sequencing efficiency has reached the point where it is now possible to obtain gigabases of data, both quickly and inexpensively. Such methods permit the identification of gene versions, including those associated with disease (e.g. small nucleotide polymorphism analyses, or SNPs). The general public as well as clinicians can now access a wide variety of literature on the molecular bases of diseases, allowing them to better assess disease risks and treatments. This volume concentrates on medically-focused methods, and therefore the major audience will be medical professionals, students, and those involved in medically-related research endeavors. There are also papers in this volume dealing specifically with methods developed to analyze large sequence data sets. Many methods reviewed herein are more broadly applicable to other fields in biology, chemistry, bioinformatics, and bioengineering, and are intended for a broad readership.

    Key Features

    • Summarizes nucleic acid extractions from a wide variety of tissues and cells
    • Describes processes of nucleic acid preservation
    • Reviews forensic sampling, detection of nucleic acids, and delivery of nucleic acids to multicellular organisms
    • Provides essential guidance for sequencing, sequence analysis, database searches, and phylogenetic analyses
    • Includes additional methods useful for analysis of nucleic acids and proteins

    Related Titles

    DeSalle, et al. Phylogenomics: A Primer (ISBN 978-0-3670-2849-7).

    Jennings, W. B. Phylogenomic Data Acquisition: Principles and Practice (ISBN 978-0-3678-6980-9).

    Wang, X. Next-Generation Sequencing Data Analysis (ISBN 978-1-4822-1788-9)

    Sung, W.-K. Algorithms for Next-Generation Sequencing (ISBN 978-0-3676-5797-0)


    List of Contributors

    1. Nucleic Acid Extraction from Diverse Samples

    Scott O. Rogers

    2. DNA Extraction from Mummified Tissues

    Yayoi Sato

    3. Commercial DNA Extraction Kits

    Stuart C. Clarke

    4. Automated Nucleic Acid Extraction

    Juergen Loeffler, Kathrin D. Schmidt, Holger Hebart, Hermann Einsele

    5. Forensic DNA Samples: Collection and Handling

    Mark Benecke

    6. DNA Preservation

    C. William Kilpatrick

    7. RNA Storage

    Martin Hofmann

    8. Disposable Electrochemical DNA Biosensors

    Kagan Kerman and Mehmet Ozsoz

    9. Handheld Nucleic Acid Analyzer

    James A. Higgins

    10. DNA-Binding Fluorophores

    Mikael Kubista, Jonas Karlsson, Martin Bengtsson, Neven Zoric, Gunar Westman

    11. Fluorescence Resonance Energy Transfer (FRET)

    Dino A. De Angelis

    12. LightUp® Probes

    Mikael Leijon

    13. Invader® Assay

    Stephen Day, Andrea Mast

    14. Laser-Capture Microdissection

    Falko Fend

    15. Helper-Dependent Adenoviral Vectors

    Philip Ng

    16. Retroviral Vectors

    Erin L. Weber, Paula M. Cannon

    17. Liposomal Nonviral Delivery Vehicles

    Nancy Smyth Templeton

    18. Polymer-Based Nonviral Nucleic Acid Delivery and Genome Editing

    Janin Germer, Ernst Wagner

    19. Automated DNA Sequencing

    Alexandre Izmailov

    20. DNA Sequencing Methods

    Scott O. Rogers

    21. Differential Sequencing by Mass Spectrometry

    Christian Jurinke, Christiane Honisch, Dirk van den Boom

    22. Brief Guide to Conducting Biological Database Searches

    John Gray

    23. Accessing Genomic Databases

    Robert J. Trumbly

    24. Phylogenetics, Comparative Genomics, and Phylogenomics

    Scott O. Rogers

    25. DNannotator: Annotation Software Tool Kit for Regional Genomic Sequences

    Chunyu Liu

    26. ESTAnnotator: A Tool for High-Throughput EST Annotation

    Agnes Hotz-Wagenblatt and Thomas Hankeln

    27. The Basics of Omics

    Scott O. Rogers

    28. Ribotyping

    Tim J. Inglis

    29. Forensic DNA Typing: Y Chromosome

    Lluís Quintana-Murci

    30. Forensic Identification: An Overview on Molecular Diagnostic Technology

    Adrian Linacre, Yvonne E. Cruickshank

    31. Denaturing Gradient Gel Electrophoresis (DGGE)

    Luciana Cresta de Barros Dolinsky

    32. Heteroduplex Analysis (HA)

    Philip L. Beales

    33. NEBcutter: A Program to Cleave DNA with Restriction Enzymes

    Janos Posfai, R. J. Roberts, Tamas Vincze

    34. Differential Display (DD) Analysis

    Farid E. Ahmed

    35. Protein Truncation Test (PTT)

    Sadanand Gite, Mark Lim, Kenneth Rothschild



    Scott Orland Rogers is a professor of molecular biology and evolution at Bowling Green State University, Bowling Green, Ohio. He received his PhD in plant molecular biology from the University of Washington, Seattle. He was an assistant professor and associate professor at the State University of New York College of Environmental Science and Forestry before moving to BGSU. He has taught courses in biology, botany, cell physiology, molecular biology, molecular genetics, bioinformatics, and molecular evolution. Research in his lab includes studies of microbes and nucleic acids preserved in ice, life in extreme environments, group I introns, molecular microbial phylogenetics, microbial metagenomics/metatranscriptomics, ancient DNA, and plant development.