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AN INTEGRATED APPROACH TO THE STUDY OF EMBRYONIC DEVELOPMENT IN SEA URCHINS

Summary: 
The major focus of research in our laboratory is the systems biology of the gene regulatory networks (GRNs) that control development, and the evolution of these networks.  Our research is done on sea urchin embryos, which provide key experimental advantages.  Among these are:  an easy gene transfer technology, with high throughput technologies available, which makes the sea urchin embryo an experimental system of choice for studying the genomic regulatory code; reliable methods for high throughput measurement and for specific perturbation of gene expression in the embryo; sensitive and dramatic means of visualizing spatial gene expression; availability of embryonic material at all seasons of the year; an optically clear, easily handled embryo that is remarkably able to withstand micromanipulations, injections and blastomere recombination and disaggregation procedures; a very well understood and relatively simple embryonic process, known from over a century of research; and in-house egg-to-egg culture of the species we work with, Strongylocentrotus purpuratus (in a special culture system we have developed, located at Caltech's Kerckhoff Marine Laboratory).  Recent additions to our special research arsenal include the NanoString nCounter for simultaneous measurement of hundreds of transcript levels and a NanoString codeset targeting >200 interesting regulatory genes and some signaling ligands and receptors expressed during embryogenesis; plus >100 custom recombineered BACs, most including relevant regulatory genes and some also special vectors or regulatory mutants.  We have a rich collection of arrayed cDNA and BAC libraries for many other species of sea urchin, at various degrees of relatedness to S. purpuratus.  The genome of S. purpuratus has been sequenced and annotated at the Human Genome Sequencing Center (Baylor College of Medicine).  We utilize additional experimental echinoderm models for evolutionary GRN comparisons, viz. the starfish Patiria miniata also of local provenance, and the (in certain respects) pleisiomorphic "pencil urchin" Eucidaris tribuloides.  The embryos of both these animals prove to be as excellent subjects for gene regulation molecular biology as is that of the sea urchin.  We pursue an integrated, "vertical" mode of experimental analysis, in that our experiments are directed at all levels of biological organization, extending from the transcription factor-DNA interactions that control spatial and temporal expression of specific genes to the system-level analysis of large regulatory networks, to the sets of downstream effector genes they control.  It has become apparent that only from the GRN system level of analysis can causal explanations of major developmental phenomena directly emerge, and this is our main focus.  The main research initiatives in our laboratories at the present time are as follows:  RESEARCH OVERVIEW