Echinoderms Part B

Echinoderms Part B

1st Edition - April 2, 2019
  • Editors: Amro Hamdoun, Kathleen Foltz
  • Hardcover ISBN: 9780128170724
  • eBook ISBN: 9780128170731

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Description

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

Readership

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

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

Product details

  • No. of pages: 550
  • Language: English
  • Copyright: © Academic Press 2019
  • Published: April 2, 2019
  • Imprint: Academic Press
  • Hardcover ISBN: 9780128170724
  • eBook ISBN: 9780128170731

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 (https://www.addgene.org/Amro_Hamdoun/). 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