Echinoderms Part B

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. 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.

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