Dr. Juan Zalapa

Genetics Undergraduate research projects

Centers for Excellence in Genomic Science (CEGS) supports undergraduate summer research through the California Institute of Technology 's (Caltech) Summer Undergraduate Research Fellowship (SURF) and Minority Undergraduate Research Fellowship (MURF) programs. Applications are encouraged from students who wish to work in a modern academic research laboratory under the guidance of experienced scientists and engineers. The program will expose students to the excitement and opportunities of a research career in genomics and systems biology. This experience will provide excellent preparation for students interested in subsequently pursuing a Ph.D. Qualified minority undergraduates will work on diverse projects at the interface between genomics, imaging, developmental biology, and bioinformatics. In exceptional cases, high school students will also be considered for summer fellowships. Applicants must be U.S. citizens or permanent residents.

Post-Graduate Internship Program

Fellowships are available to fund minority M.D.s and Ph.D.s (or those pursuing M.D.s and/or Ph.D.s) to pursue genomic research. Stipends will be awarded to work in the laboratory of one of the four P.I.s on the CEGS grant and will have a duration of 2 to 3 years. Applicants must be U.S. citizens or permanent residents.

Project 1: Comprehensive spatiotemporal analysis of gene expression and function of the developing vertebrate embryo

We are developing techniques for performing in toto imaging that allow us to repeatedly image multiple vertebrate embryos throughout their embryonic development using in vivo time-lapse, confocal microscopy. We will generate a large collection of zebrafish lines using a transposon-based gene-trapping technology called "flip trapping". The FlipTrap cassette forms a functional fusion protein with a green fluorescent tag (GFP variant) when inserted into an intron. When exposed to cre-recombinase, the cassette assumes a second conformation, and generates a red fluorescent tag (RFP variant) gene trap and a mutant allele for the trapped gene. Thus, each flip trap line can be used to reveal the protein expression pattern (using the GFP fusion trap) and the mutant phenotype (using the RFP gene trap). Using in toto imaging, this information can be read out from the embryo in vivo and non-invasively. Once validated in the zebrafish, our goal is to apply this strategy to quail, an amniote that much more closely resembles the developing human embryo.

Project 2: Design of quantitative, multiplexed, "hybridization chain reaction" (HCR) amplifiers for in vivo imaging with active background suppression

We have designed and are testing a new in situ amplification approach based on the mechanism of hybridization chain reaction, in which fluorescently labeled DNA monomers self-assemble non-covalently into tethered "polymers" only when triggered by probes bound specifically to target mRNAs or proteins. The design principles underlying this approach promise to achieve specific and high resolution detection of multiple labels simultaneously.

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