Echinoderms Part B - 1st Edition - ISBN: 9780128170724

Echinoderms Part B, Volume 151

1st Edition

Serial Volume Editors: Amro Hamdoun Kathleen Foltz
Hardcover ISBN: 9780128170724
Imprint: Academic Press
Published Date: 12th April 2019
Page Count: 548
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Table of Contents

  1. Fertilization
  2. When sperm meets egg—Fifty years of surprises

    David Epel

    Early and later studies on action potential and fertilization potential of echinoderm oocytes and Ca2+ response of mammalian oocytes

    Shunichi Miyazaki

    My research career on (mainly) sea urchins

    Victor D. Vacquier

  3. Cytokenesis and Embryology
  4. Echinoderm eggs as a model for discoveries in cell biology

    David R. Burgess

    Unlocking mechanisms of development through advances in tools

    David McClay

    From hemoglobin to urchin spicules

    Fred Wilt

  5. Genomics and Morphogenesis

The causes of things

Robert D. Burke

A personal history of the echinoderm genome sequencing

R. Andrew Cameron

Section 1 - Methods for genome and transcriptome analysis

  1. Genomic resources for the study of echinoderm development and evolution
  2. Gregory A. Cary, R. Andrew Cameron and Veronica F. Hinman

  3. Methods for the experimental and computational analysis of gene regulatory networks in sea urchins
  4. Isabelle S. Peter

  5. Using ATAC-seq and RNA-seq to increase resolution in GRN connectivity
  6. Elijah K. Lowe, Claudia Cuomo, Danila Voronov and Maria I. Arnone

  7. Identifying gene expression from single cells to single genes
  8. Nathalie Oulhen, Stephany Foster, Greg Wray and Gary Wessel

  9. Multiplex cis-regulatory analysis
  10. Jongmin Nam

  11. Whole mount in situ hybridization techniques for analysis of the spatial distribution of mRNAs in sea urchin embryos and early larvae
  12. Eric M. Erkenbrack, Jenifer C. Croce, Esther Miranda, Sujan Gautam, Marina Martinez-Bartolome, Shunsuke Yaguchi and Ryan C. Range

  13. Techniques for analyzing gene expression using BAC-based reporter constructs
  14. Katherine M. Buckley and Charles A. Ettensohn

  15. Genome-wide analysis of chromatin accessibility using ATAC-seq
  16. Tanvi Shashikant and Charles A. Ettensohn

    Section 2 - Genome-editing and proteomics

  17. Expression of exogenous mRNAs to study gene function in echinoderm embryos
  18. Maria Dolores Molina, Christian Gache and Thierry Lepagef

  19. Trapping, tagging and tracking: Tools for the study of proteins during early development of the sea urchin
  20. Michelle M. Roux-Osovitz, Kathy R. Foltz, Nathalie Oulhen and Gary Wessel

  21. CRISPR/Cas9-mediated genome editing in sea urchins
  22. Che-Yi Lin, Nathalie Oulhen, Gary Wessel and Yi-Hsien Su

  23. Analysis of microRNA functions
  24. Carolyn Remsburg, Kalin Konrad, Nina Faye Sampilo and Jia L. Song

  25. In vivo analysis of protein translation activity in sea urchin eggs and embryos
  26. Héloïse Chassé, Sandrine Boulben, Virginie Glippa, Florian Pontheaux, Patrick Cormier and Julia Morales

  27. Generation, expression and utilization of single-domain antibodies for in vivo protein localization and manipulation in sea urchin embryos
  28. Catherine S. Schrankel, Tufan Gökirmak, Chang-Wook Lee, Geoffrey Chang and Amro Hamdoun

    Section 3 - Imaging of echinoderm embryos

  29. Live-cell fluorescence imaging of echinoderm embryos
  30. Silvia P. Sepúlveda-Ramírez, Leslie Toledo-Jacobo, Chelsea Garno, Debadrita Pal, Clara Ross,
    Andrea Ellis and Charles B. Shuster

  31. 3D + time imaging of normal and twin sea urchin embryos for the reconstruction of their cell lineage
  32. Antonio Ortiz, Elena Kardash and Nadine Peyriéras

  33. High resolution imaging of the cortex isolated from sea urchin eggs and embryos
  34. J.H. Henson, Bakary Samasa and E.C. Burg

  35. Spatially mapping gene expression in sea urchin primary mesenchyme cells
  36. Daniel T. Zuch and Cynthia A. Bradham

    Section 4 - Methods for measurement of intracellular signals in eggs, sperm and embryos

  37. Probing Ca2+ release mechanisms using sea urchin egg homogenates
  38. Yu Yuan, Gihan S. Gunaratne, Jonathan S. Marchant and Sandip Patel


  39. Measuring voltage and ion concentrations in live embryos
  40. Nahomie Rodriguez-Sastre, Christopher F. Thomas and Cynthia A. Bradham

  41. Analysis of sperm chemotaxis
  42. Héctor Vicente Ramírez-Gómez, Idán Tuval, Adán Guerrero and Alberto Darszon

  43. Kinetic and photonic techniques to study chemotactic signaling in sea urchin sperm
  44. Hussein Hamzeh, Luis Alvarez, Timo Strünker, Michelina Kierzek, Christoph Brenker, Parker E. Deal, Evan W. Miller, Reinhard Seifert and U. Benjamin Kaupp

  45. Analysis of neural activity with fluorescent protein biosensors

Robert D. Burke and Shunsuke Yaguchi


Echinoderms, Volume 151, the latest release in the Methods in Cell Biology series, highlights advances in the field, with this update presenting chapters on Echinoderm Genome Databases, analysis of gene regulatory networks, using ATAC-seq and RNA-seq to increase resolution in GRN connectivity, multiplex cis-regulatory analysis, experimental approaches GRN/signal pathways, BACs, analysis of chromatin accessibility using ATAC-seq, analysis of sea urchin proteins /Click IT, CRISPR/Cas9-mediated genome editing in sea urchins, super-resolution and in toto imaging of echinoderm embryos, and methods for analysis of intracellular ion signals in sperm, eggs and embryos.

Key Features

  • Presents clear, concise protocols provided by experts who have established the echinoderms as a model systems
  • Highlights new advances in the field, with this update presenting interesting chapters on echinoderms


New research scholars who wish to learn the echinoderms as a model system will find this book invaluable and for those already in the field, it will serve as a handy resource for the teaching and research laboratory


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© Academic Press 2019
Academic Press
Hardcover ISBN:

Ratings and Reviews

About the Serial Volume Editors

Amro Hamdoun Serial Volume Editor

Amro Hamdoun is an Associate Professor in the Scripps Institution of Oceanography of the University of California, San Diego. His research bridges developmental biology and environmental toxicology, with a focus on the roles of xenobiotic transporters in the embryo. His research merges biochemical, cellular and structural approaches with high-resolution live imaging of echinoderm development. This work has been featured on the covers of Development, Developmental Dynamics, Molecular Biology of the Cell and Molecular Reproduction and Development. The Hamdoun laboratory is also a leading contributor of reagents for the sea urchin through Addgene ( He was a recipient of the NIH Ruth L. Kirschstein NRSA and Pathway to Independence fellowships, and the Scripps Institution of Oceanography Outstanding Undergraduate Teaching Award.

Affiliations and Expertise

Amro Hamdoun is an Associate Professor at the University of California, San Diego, La Jolla, CA, USA

Kathleen Foltz Serial Volume Editor

Kathy Foltz is a Professor in the Department of Molecular, Cellular and Developmental Biology at the University of California, Santa Barbara. She came to UCSB after her Postdoctoral work at SUNY- Stony Brook with William Lennarz following her PhD work at Purdue University with David Asai. A Searle Scholar, NSF Presidential Faculty Fellow and AAAS Fellow, she has used sea urchins, sea stars and other invertebrate deuterostomes to investigate questions of gamete recognition, egg activation and control of cell division throughout her career. She enjoys sharing her curiosity and knowledge with many undergraduates, graduate students and postdoctoral research colleagues. With the UCSB Marine Lab located on the main campus, over 1,000 undergraduate students have also worked with these fascinating organisms under her guidance in the Developmental Biology Laboratory classroom.

Affiliations and Expertise

Professor, Molecular, Cellular, and Developmental Biology, and the Marine Science Institute, University of California, Santa Barbara, CA. USA