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.
- 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
About the Author
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.
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