Marine Genomics: Methods and Protocols

ISBN-13: 9781071623121 / Angielski / Twarda / 2022

Verde, Cinzia

Opis

This detailed volume provides an overview of recent advances in the application of genomic technologies in several domains of marine biology, raising awareness of various DNA- and RNA-based technologies. Genomic methods are essential in identifying previously undetected taxonomic (e.g. DNA barcoding), genetic (e.g. sequencing), and functional (e.g. gene expression, analysis of metabolites) diversity, as shown in the chapters of this book, with sections focusing on next generation sequencing (NGS) technologies, bioinformatics in marine genomics research, marine biotechnology, as well as a variety of methods successfully applied in fish. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Marine Genomics: Methods and Protocols highlights the utility of numerous lab protocols and their potential to provide deeper insight into physiological and ecological mechanisms in marine life.

Spis treści

1. Mitochondrial Genome of Non-Model Marine Metazoans by Next-Generation Sequencing (NGS)

            Tullia I. Terraneo, Kiruthiga G. Mariappan, Zac Forsman, and Roberto Arrigoni

 

2. Genome-Wide DNA Methylation Protocol for Epigenetics Studies

            Annalaura Mancia

 

3. Transcriptome Mining to Identify Genes of Interest: From Local Databases to Phylogenetic Inference

            Daniele De Luca and Chiara Lauritano

 

4. Detecting Structural Variants and Associated Gene Presence-Absence Variation Phenomena in the Genomes of Marine Organisms

            Marco Sollitto, Nathan J. Kenny, Samuele Greco, Carmen Federica Tucci, Andrew D. Calcino, and Marco Gerdol

 

5. From Sequences to Enzymes: Comparative Genomics to Study Evolutionary Conserved Protein Functions in Marine Microbes

            Angelina Cordone, Alessandro Coppola, Angelica Severino, Monica Correggia, Matteo Selci, Antonio Cascone, Costantino Vetriani, and Donato Giovannelli

 

6. VenomFlow: An Automated Bioinformatic Pipeline for Identification of Disulfide-Rich Peptides from Venom Arsenals

            Eleonora Achrak, Jennifer Ferd, Jessica Schulman, Trami Dang, Konstantinos Krampis, and Mande Holford

 

7. Population Genomics Analysis with RAD, Reprised: Stacks 2

            Angel G. Rivera-Colón and Julian Catchen

 

8. A Metabarcoding Protocol to Analyze Coastal Planktic Communities Collected by Desalination Plant Filters: From Sampling to Bioinformatic Exploratory Analyses

            Matteo Cecchetto, Andrea Di Cesare, Ester Eckert, Isabella Moro, Diego Fontaneto, and Stefano Schiaparelli

 

9. Barcoding of Antarctic Marine Invertebrates: From Field Sampling to Lab Procedures

            Stefano Schiaparelli, Maria Chiara Alvaro, Matteo Cecchetto, and Alice Guzzi

 

10. DNA Barcoding Procedures for Taxonomical and Phylogenetic Studies in Marine Animals: Porifera as Case Study

            Laura Núñez-Pons, Valerio Mazzella, Francesca Rispo, Jana Efremova, and Barbara Calcinai

 

11. Environmental DNA from Marine Waters and Substrates: Protocols for Sampling and eDNA Extraction

            Dominique A. Cowart, Katherine R. Murphy, and C.-H. Christina Cheng

 

12. Metataxonomic Analysis of Bacterial Diversity Associated with Marine Organisms

            Nadia Ruocco, Roberta Esposito, Valerio Zupo, and Maria Costantini

 

13. From Sequences to Enzymes: Heterologous Expression of Genes from Marine Microbes

            Angelica Severino, Alessandro Coppola, Monica Correggia, Costantino Vetriani, Donato Giovannelli, and Angelina Cordone

 

14. Expression of Recombinant Cold-Adapted (Hemo)Globins from Marine Bacteria

            Daniela Giordano and Cinzia Verde

 

15. Isolation of UV-Resistant Marine Bacteria by UV-C Assays

            Daniela Coppola, Cinzia Verde, and Daniela Giordano

 

16. Fractionation Protocol of Marine Metabolites

            Genoveffa Nuzzo, Emiliano Manzo, Carmela Gallo, Giuliana d'Ippolito, and Angelo Fontana

 

17. Detection and Quantification of Small Non-Coding RNAs in Marine Diatoms

            Alessandra Rogato and Angela Falciatore

 

18. Optimized Proteolistic Protocol for the Delivery of the Cas9 Protein in Phaeodactylum tricornutum

            Monia Teresa Russo, Anna Santin, Alessandra Rogato, and Maria Immacolata Ferrante

 

19. Production of a Chimeric Mouse-Fish Monoclonal Antibody by the CRISPR/Cas9 Technology

            Alessia Ametrano and Maria Rosaria Coscia

 

20. Identification, Characterization, and Expression Analysis of Immunoglobulin Genes from Antarctic Fish by PCR Methods

            Alessia Ametrano and Maria Rosaria Coscia

 

21. Physical Mapping of Repeated Sequences on Fish Chromosomes by Fluorescence In Situ Hybridization (FISH)

            Laura Ghigliotti, Juliette Auvinet, and Eva Pisano

 

22. Functional Genomics of Fish Erythrocytes

            Mikko Nikinmaa and Amélie Crespel

 

23. Stain-Free Approach for Western Blot Analysis of Zebrafish Embryos

            Jianmin Xue and Paola Corti

 

24. Proteomics of Fish White Muscle and Western Blotting to Detect Putative Allergens

            Liliana Anjos, Arsenios-Zafeirios Loukissas, and Deborah Mary Power

 

25. In Vitro Assays for the Bifunctional Acylpeptide Hydrolase (APEH) Enzyme from Antarctic Fish

            Carmela Fusco, Bruna Agrillo, Marta Gogliettino, Gianna Palmieri, and Ennio Cocca