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Echinoderms Part B - 1st Edition - ISBN: 9780128170724, 9780128170731

Echinoderms Part B, Volume 151

1st Edition

Serial Volume Editors: Amro Hamdoun Kathleen Foltz
Hardcover ISBN: 9780128170724
eBook ISBN: 9780128170731
Imprint: Academic Press
Published Date: 2nd April 2019
Page Count: 550
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Table of Contents

1. Fertilization
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

2. Cytokenesis and Embryology
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

3. 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
Gregory A. Cary, R. Andrew Cameron and Veronica F. Hinman
2. Methods for the experimental and computational analysis of gene regulatory networks in sea urchins
Isabelle S. Peter
3. Using ATAC-seq and RNA-seq to increase resolution in GRN connectivity
Elijah K. Lowe, Claudia Cuomo, Danila Voronov and Maria I. Arnone
4. Identifying gene expression from single cells to single genes
Nathalie Oulhen, Stephany Foster, Greg Wray and Gary Wessel
5. Multiplex cis-regulatory analysis
Jongmin Nam
6. Whole mount in situ hybridization techniques for analysis of the spatial distribution of mRNAs in sea urchin embryos and early larvae
Eric M. Erkenbrack, Jenifer C. Croce, Esther Miranda, Sujan Gautam, Marina Martinez-Bartolome, Shunsuke Yaguchi and Ryan C. Range
7. Techniques for analyzing gene expression using BAC-based reporter constructs
Katherine M. Buckley and Charles A. Ettensohn
8. Genome-wide analysis of chromatin accessibility using ATAC-seq
Tanvi Shashikant and Charles A. Ettensohn

Section 2 - Genome-editing and proteomics
9. Expression of exogenous mRNAs to study gene function in echinoderm embryos
Maria Dolores Molina, Christian Gache and Thierry Lepagef
10. Trapping, tagging and tracking: Tools for the study of proteins during early development of the sea urchin
Michelle M. Roux-Osovitz, Kathy R. Foltz, Nathalie Oulhen and Gary Wessel
11. CRISPR/Cas9-mediated genome editing in sea urchins
Che-Yi Lin, Nathalie Oulhen, Gary Wessel and Yi-Hsien Su
12 .Analysis of microRNA functions
Carolyn Remsburg, Kalin Konrad, Nina Faye Sampilo and Jia L. Song
13. In vivo analysis of protein translation activity in sea urchin eggs and embryos
Héloïse Chassé, Sandrine Boulben, Virginie Glippa, Florian Pontheaux, Patrick Cormier and Julia Morales
14. Generation, expression and utilization of single-domain antibodies for in vivo protein localization and manipulation in sea urchin embryos
Catherine S. Schrankel, Tufan Gökirmak, Chang-Wook Lee, Geoffrey Chang and Amro Hamdoun

Section 3 - Imaging of echinoderm embryos
15. Live-cell fluorescence imaging of echinoderm embryos
Silvia P. Sepúlveda-Ramírez, Leslie Toledo-Jacobo, Chelsea Garno, Debadrita Pal, Clara Ross,
Andrea Ellis and Charles B. Shuster
16. 3D + time imaging of normal and twin sea urchin embryos for the reconstruction of their cell lineage
Antonio Ortiz, Elena Kardash and Nadine Peyriéras
17. High resolution imaging of the cortex isolated from sea urchin eggs and embryos
J.H. Henson, Bakary Samasa and E.C. Burg
18. Spatially mapping gene expression in sea urchin primary mesenchyme cells
Daniel T. Zuch and Cynthia A. Bradham

Section 4 - Methods for measurement of intracellular signals in eggs, sperm and embryos
19. Probing Ca2+ release mechanisms using sea urchin egg homogenates
Yu Yuan, Gihan S. Gunaratne, Jonathan S. Marchant and Sandip Patel
20. Measuring voltage and ion concentrations in live embryos
Nahomie Rodriguez-Sastre, Christopher F. Thomas and Cynthia A. Bradham
21. Analysis of sperm chemotaxis
Héctor Vicente Ramírez-Gómez, Idán Tuval, Adán Guerrero and Alberto Darszon
22. Kinetic and photonic techniques to study chemotactic signaling in sea urchin sperm
Hussein Hamzeh, Luis Alvarez, Timo Strünker, Michelina Kierzek, Christoph Brenker, Parker E. Deal, Evan W. Miller, Reinhard Seifert and U. Benjamin Kaupp
23. 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


No. of pages:
© Academic Press 2019
2nd April 2019
Academic Press
Hardcover ISBN:
eBook ISBN:

Ratings and Reviews

About the Serial Volume Editors

Amro Hamdoun

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

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