Whole-Body Regeneration: Methods and Protocols

ISBN-13: 9781071621714 / Angielski / Twarda / 2022

Blanchoud, Simon

Opis

This Open Access volume provides a comprehensive overview of the latest tools available to scientists to study the many facets of whole-body regeneration (WBR). The chapters in this book are organized into six parts. Part One provides a historical overview on the study of the WBR phenomena focusing on the primary challenges of this research. Parts Two and Three explore a series of non-vertebrate zoological contexts that provide experimental models for WBR, showing how they can be approached with cellular tools. Parts Four, Five, and Six discuss the future advancements of WBR, reporting about the cutting-edge techniques in genetics and omics used to dissect the underlying mechanisms of WBR, and systems biology approaches to reach a synthetic view of WBR. Written in the highly successful Methods in Molecular Biology series format, 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 thorough, Whole-Body Regeneration: Methods and Protocols is a valuable resource for scientists and researchers who want to learn more about this important and developing field.

Spis treści

Preface…

Table of Contents…

Contributing Authors…

Part I Historical Overviews

1. The Hazards of Regeneration: From Morgan’s Legacy to Evo-Devo

Chiara Sinigaglia, Alexandre Alié, and Stefano Tiozzo

2. Studying Regeneration in Ascidians: An Historical Overview

Virginia Vanni, Loriano Ballarin, Fabio Gasparini, Anna Peronato, and Lucia Manni

Part II Zoological Approaches

3. Studying Protista WBR and Repair using Physarum polycephalum

Megan M. Sperry, Nirosha J. Murugan, and Michael Levin

4. Studying Porifera WBR using the Calcerous Sponges Leucosolenia

Andrey I. Lavrov and Alexander V. Ereskovsky

5. Studying Ctenophora WBR using Mnemiopsis leidyi 

Julia Ramon-Mateu, Allison Edgar, Dorothy Mitchell, and Mark Q. Martindale

6. Studying Placozoa WBR in the Simplest Metazoan Animal, Trichoplax adhaerens

Hans-Jürgen Osigus, Michael Eitel, Karolin Horn, Kai Kamm, Jennifer Kosubek-Langer, Moritz Jonathan Schmidt, Heike Hadrys, and Bernd Schierwater

7. Collecting and Culturing Kamptozoans for Regenerative Studies

Achim Meyer, Julia Merkel, and Bernhard Lieb

8. Collecting and Culturing Bryozoans for Regenerative Studies

Abigail M. Smith, Peter B. Batson, Katerina Achilleos, and Yuta Tamberg

9. Studying Annelida Regeneration in a Novel Model Organism: The Freshwater Aeolosoma viride 

Chiao-Ping Chen, Sheridan Ke-Wing Fok, Cheng-Yi Chen, Fei-Man Hsu, Yu-Wen Hsieh, and Jiun-Hong Chen

10. Studying Annelida Body Regeneration under Environmental Stress in Diopatra neapolitana

Adília Pires

11. Studying Annelida Regeneration using Platynereis dumerilii

Michel Vervoort and Eve Gazave

12. Collecting and Culturing Lineus sanguineus to Study Nemertea WBR

Eduardo E. Zattara and Fernando A. Fernández-Alvarez

13. Studying Xenacoelomorpha WBR using Isodiametra pulchra 

Bernhard Egger

14. Studying Echinodermata Arm Explant Regeneration using Echinaster sepositus

Cinzia Ferrario, Yousra Ben Khadra, Michela Sugni, M. Daniela Candia Carnevali, Pedro Martinez, and Francesco Bonasoro

15. Studying Hemichordata WBR using Ptychodera flava

Asuka Arimoto and Kuni Tagawa

16. Studying Tunicata WBR using Botrylloides anceps

Arzu Karahan, Esra Öztürk, Berivan Temiz, and Simon Blanchoud

Part III Cellular Approaches

17. In Situ Hybridization to Identify Stem Cells in the Freshwater Sponge Ephydatia fluviatilis

Chiaki Kojima and Noriko Funayama

18. Isolation and Maintenance of In Vitro Cell Cultures from the Ctenophore Mnemiopsis leidyi

Abigail C. Dieter, Lauren E. Vandepas, and William E. Browne

19. Analysis of Spatial Gene Expression at the Cellular Level in Stony Corals 

Nikki Traylor-Knowles and Madison Emery

20. Studying Stem Cell Biology in Intact and Whole-Body Regenerating Hydra by Flow Cytometry

Wanda Buzgariu, Jean-Pierre Aubry-Lachainaye, and Brigitte Galliot

21. Non-Invasive Intra-Vascular Micro-Transfusion in Colonial Tunicates

Luìs Albert Matas Serrato, Alessandro Bilella, and Simon Blanchoud

Part IV Genetic Approaches

22. Gene Manipulation in Hydractinia

Eleni Chrysostomou, Febrimarsa, Timothy DuBuc, and Uri Frank

23. Manipulation of Gene Activity in the Regenerative Model Sea Anemone, Nematostella vectensis

Eric M. Hill, Cheng-Yi Chen, Florencia del Viso, Lacey R. Ellington, Shuonan He, Ahmet Karabulut, Ariel Paulson, and Matthew C. Gibson

24. Monitoring Telomere Maintenance during Regeneration of Annelids

Nithila A. Joseph, Chi-Fan Chen, Jiun-Hong Chen, and Liuh-Yow Chen

25. Analysis of DNA Double Stranded Breaks using the COMET Assay in Planarians 

Paul G. Barghouth, Salvador Rojas, Lacey R. O’Dell, Andrew M. Betancourt, and Néstor J. Oviedo

26. Random Integration Transgenesis in a Free-Living Regenerative Flatworm Macrostomum lignano

Jakub Wudarski, Kirill Ustyantsev, Filipa Reinoite, and Eugene Berezikov

27. RNAi Screening to Assess Tissue Regeneration in Planarians

Rachel H. Roberts-Galbraith

28. Monitoring Chromatin Regulation in Planarians using Chromatin Immunoprecipitation followed by Sequencing (ChIP-seq)

Divya Sridhar and Aziz Aboobaker

29. Assessing Chromatin Accessibility during WBR in Acoels

Andrew R. Gehrke and Mansi Srivastava

Part V OMICS Approaches

30. Single Cell Transcriptomic Analysis in the Regenerating Cnidarian Nematostella vectensis

Flora Plessier, Sandrine Schmutz, Sophie Novault, and Heather Marlow

31. Characterization of Soluble Cell-Free Coelomic Fluid Proteome from the Starfish Marthasterias glacialis

Laidson Paes Gomes, Catarina Gouveia e Silva, Jean-Charles Gaillard, Jean Armengaud, and Ana Varela Coelho

32. Using RNA-Sequencing for Transcriptome Profiling of Botrylloides sp. Regeneration

Michael Meier and Megan J. Wilson

Part VI Integrative Approaches

33. Studying Mechanical Oscillations during Whole-Body Regeneration in Hydra

Jaroslav Ferenc and Charisios D. Tsiairis

34. Combining RNAi-Mediated β-catenin Inhibition and Reaggregation to Study Hydra Whole-Body Regeneration

Matthias Christian Vogg and Brigitte Galliot

35. Creating a User-Friendly and Open-Access Gene Expression Database for Comparing Embryonic Development and Regeneration in Nematostelle vectensis

Olivier Croce and Eric Röttinger

36. Formalizing Phenotypes of Regeneration

Daniel Lobo

Subject Index List…