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: 1st April 2019
Page Count: 362
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Table of Contents

1. Echinoderm Genome Databases
Greg Cary, Veronica Hinman and Robert Andrew Cameron
2. Analysis of gene regulatory networks
Isabelle S. Peter
3. Using ATAC-seq and RNA-seq to increase resolution in GRN connectivity
Ina Arnone
4. Analysis of metabolomic and proteomic data
Greg Wray
5. Multiplex cis-regulatory Analysis
Jongmin Nam
6. Nanostring analysis of gene expression
Paola Oliveri
7. Experimental approaches GRN/signal pathways
Ryan Range
8. BACs
Kate Michele Buckley
9. Genome-Wide Analysis of Chromatin Accessibility Using ATAC-seq Tanvi Shashikant and Charles Ettensohn
Charles Ettensohn and Kate Michele Buckley
10. Injection of exogenous mRNAs to study gene function in echinoderm embryos
Thierry Lepage
11. Analysis of sea urchin proteins /Click IT
Michelle Marie Roux-Osovitz
12. CRISPR/Cas9-mediated genome editing in sea urchins
Yi-Hsien Su
13. scRNA and ChIP Analysis
Gary M. Wessel
14. Analysis of micro RNAs
Jia Song
15. Polysome isolation and methods for analysis of protein translation
Julia Morales
16. Generation, expression and utilization of single domain antibodies
Amro Hamdoun, Geoffrey Chang and Catherine Sarah Schrankel
17. Fluorescence and transmitted light microscopy
Charles Bradley Schuster
18. In toto imaging
Nadine Peyrarias
19. Isolation of the egg cortex for high resolution imaging
John Henson
20. Spatially mapping gene expression in sea urchin primary mesenchyme cells
Cynthia Bradham
21. Calcium Imaging
Sandip Patel
22. Measuring ion and voltage gradients across the embryo
Cynthia Bradham
23. Analysis of sperm
Alberto Darszon
24. Kinetic and photonic techniques to study chemotatic signaling in urchin sperm
u. benjamin kaupp
25. Calcium sensors and imaging
Robert Burke


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
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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