BNMC Seminar:  In Toto Imaging of Vertebrate Development

Sean G. Megason
Postdoctoral Fellow
Biological Imaging Center, Beckman Institute, Caltech

We have recently been awarded a grant from the National Human Genome Research Institute for the establishment of a Center of Excellence in Genomic Science for the "In Toto Genomic Analysis of Vertebrate Development." The principle goal of this center is to create a "Digital Fish" using an integrated approach combining imaging, genetics, genomics, and information technology.

Understanding how the genomic code is executed through development requires moving from the one-dimensional string of letters that has now been determined for the genome sequence towards understanding how the genome functions in the 4-dimensions of space and time of a developing embryo. The goal of this center is to perform a comprehensive, systems-based analysis of gene function across the space and time of the developing vertebrate embryo.

The center has four aims: 1) The first aim is to develop a technology called "in toto imaging" that can digitize in vivo data in a systematic, high-throughput, and quantitative fashion. In toto imaging uses confocal/2-photon laser scanning microscopy to image whole developing embryos at single-cell resolution and special software to digitize and quantify this 4-dimensional data at the level of the cell. Acquiring data that is comprehensive (across the genome, space, and time), quantitative, cell-based, and centralized is essential for taking a system approach to biology. 2) The second aim is to develop a gene-trap-like technology called "flip trapping." In the initial conformation flip trap alleles produce a functional YFP fusion protein. After Cre mediated recombination, flip trap alleles produce a non-functional RFP gene trap. Each flip trap allele thus reveals: protein expression pattern, transcriptional expression pattern, protein subcellular localization; and a conditional mutant phenotype.

Importantly, this information can be read out from the embryo in vivo and non-invasively. 3) The third aim is to develop a flexible, muliplex, fluorescent-based in situ hybridization technique using the Hybridization Chain Reaction (HCR) 4) In the fourth aim, we will integrate these technologies into a production phase. We will use in toto imaging to upload data fluorescently marked by flip traps and HCR on a genome-wide scale to create a "Digital Fish" that provides the foundation to model the execution of the genomic program that turns an egg into and embryo. Our data, software, and fish lines will be released rapidly to the community in the spirit of the Bermuda Principles.

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About the BNMC: The Beckman Institute Biological Network Modeling Center (BNMC: http://bnmc.caltech.edu) is an interdisciplinary effort whose goal it is to bring together Caltech biologists, bioengineers, mathematicians, and computer scientists to develop and apply state-of-the-art computational tools for modeling and analyzing complex biological systems.  Its key members come from multiple Caltech divisions and groups, including Biology, Control and Dynamical Systems, and CACR (the Center for Advanced Computing Research).  As part of its mission, the BNMC holds a regular seminar series on topics relevant to computational modeling in biology.