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. FertilizationWhen sperm meets egg—Fifty years of surprisesDavid EpelEarly and later studies on action potential and fertilization potential of echinoderm oocytes and Ca2+ response of mammalian oocytesShunichi MiyazakiMy research career on (mainly) sea urchinsVictor D. Vacquier2. Cytokenesis and EmbryologyEchinoderm eggs as a model for discoveries in cell biologyDavid R. BurgessUnlocking mechanisms of development through advances in toolsDavid McClayFrom hemoglobin to urchin spiculesFred Wilt3. Genomics and MorphogenesisThe causes of thingsRobert D. BurkeA personal history of the echinoderm genome sequencingR. Andrew CameronSection 1 - Methods for genome and transcriptome analysis1. Genomic resources for the study of echinoderm development and evolutionGregory A. Cary, R. Andrew Cameron and Veronica F. Hinman2. Methods for the experimental and computational analysis of gene regulatory networks in sea urchinsIsabelle S. Peter3. Using ATAC-seq and RNA-seq to increase resolution in GRN connectivityElijah K. Lowe, Claudia Cuomo, Danila Voronov and Maria I. Arnone4. Identifying gene expression from single cells to single genesNathalie Oulhen, Stephany Foster, Greg Wray and Gary Wessel5. Multiplex cis-regulatory analysisJongmin Nam6. Whole mount in situ hybridization techniques for analysis of the spatial distribution of mRNAs in sea urchin embryos and early larvaeEric M. Erkenbrack, Jenifer C. Croce, Esther Miranda, Sujan Gautam, Marina Martinez-Bartolome, Shunsuke Yaguchi and Ryan C. Range7. Techniques for analyzing gene expression using BAC-based reporter constructsKatherine M. Buckley and Charles A. Ettensohn8. Genome-wide analysis of chromatin accessibility using ATAC-seqTanvi Shashikant and Charles A. EttensohnSection 2 - Genome-editing and proteomics9. Expression of exogenous mRNAs to study gene function in echinoderm embryosMaria Dolores Molina, Christian Gache and Thierry Lepagef10. Trapping, tagging and tracking: Tools for the study of proteins during early development of the sea urchinMichelle M. Roux-Osovitz, Kathy R. Foltz, Nathalie Oulhen and Gary Wessel11. CRISPR/Cas9-mediated genome editing in sea urchinsChe-Yi Lin, Nathalie Oulhen, Gary Wessel and Yi-Hsien Su12 .Analysis of microRNA functionsCarolyn Remsburg, Kalin Konrad, Nina Faye Sampilo and Jia L. Song13. In vivo analysis of protein translation activity in sea urchin eggs and embryosHéloïse Chassé, Sandrine Boulben, Virginie Glippa, Florian Pontheaux, Patrick Cormier and Julia Morales14. Generation, expression and utilization of single-domain antibodies for in vivo protein localization and manipulation in sea urchin embryosCatherine S. Schrankel, Tufan Gökirmak, Chang-Wook Lee, Geoffrey Chang and Amro HamdounSection 3 - Imaging of echinoderm embryos15. Live-cell fluorescence imaging of echinoderm embryosSilvia P. Sepúlveda-Ramírez, Leslie Toledo-Jacobo, Chelsea Garno, Debadrita Pal, Clara Ross, Andrea Ellis and Charles B. Shuster16. 3D　+　time imaging of normal and twin sea urchin embryos for the reconstruction of their cell lineageAntonio Ortiz, Elena Kardash and Nadine Peyriéras17. High resolution imaging of the cortex isolated from sea urchin eggs and embryosJ.H. Henson, Bakary Samasa and E.C. Burg18. Spatially mapping gene expression in sea urchin primary mesenchyme cellsDaniel T. Zuch and Cynthia A. BradhamSection 4 - Methods for measurement of intracellular signals in eggs, sperm and embryos19. Probing Ca2+ release mechanisms using sea urchin egg homogenatesYu Yuan, Gihan S. Gunaratne, Jonathan S. Marchant and Sandip Patel20. Measuring voltage and ion concentrations in live embryosNahomie Rodriguez-Sastre, Christopher F. Thomas and Cynthia A. Bradham21. Analysis of sperm chemotaxisHéctor Vicente Ramírez-Gómez, Idán Tuval, Adán Guerrero and Alberto Darszon22. Kinetic and photonic techniques to study chemotactic signaling in sea urchin spermHussein Hamzeh, Luis Alvarez, Timo Strünker, Michelina Kierzek, Christoph Brenker, Parker E. Deal, Evan W. Miller, Reinhard Seifert and U. Benjamin Kaupp23. Analysis of neural activity with fluorescent protein biosensorsRobert D. Burke and Shunsuke Yaguchi