Neil Chi, MD, PhD

Neil ChiNeil C. Chi, MD, PhD
Assistant Professor
Department of Medicine
UC San Diego School of Medicine
Lab Website


Our goal is to investigate the central mechanisms of structural brain defects (SBD). Specifically, we will perform in vivo cellular, molecular, and genetic analysis on zebrafish SBD mutants and morphants in order to analyze the fundamental mechanisms that guide vertebrate brain morphogenesis and function during central nervous system (CNS) development. These studies will employ techniques that our laboratory routinely uses to study the developmental programs for organogenesis and include immunohistochemical confocal microscopy imaging, in vivo cell morphometric analysis, time-lapse in vivo brain imaging using neurai specific transgenic lines, and transgene-assisted forward genetic screens.
The zebrafish is typically used as an outstanding fonward genetic vertebrate system for studying developmental embryologic events. However, because of my medical training, I realized that the system was limited in its ability to analyze and model the pathophysiology of human diseases. Thus, I created a new calcium sensitive GFP (gCaMP) transgenic line to develop a novel in vivo calcium imaging system for analyzing the electrical activity of the zebrafish heart. Using this tool, we have performed fon/vard genetic screens to identify and analyze novel zebrafish cardiac conduction mutants to dissect cellular and molecular pathways that regulate the development of the vertebrate cardiac conduction system (Chi et al., 2008 PLoS biology).

Furthermore, exploiting the optical transparency of zebrafish, our group has generated a collection of zebrafish transgenics to investigate in vivo the morphogenetic events that transpire during cardiac development (Chi et al., 2008 Genes and Development, Chi et al., 2010 PNAS).

Finally, in collaboration with Henwig Baler at UCSF, we have performed a Tol2 enhancer trap Gal4 driver screen to generate a library of new brain specific Gal4 driver lines that permit detailed analysis of CNS/brain development as well as neural activity during behavioral responses (Scott et al., 2006 Nature Methods). Overall, these techniques and tools will be particularly useful towards our proposed fonward genetic screens of SBD mutants as well as the cellular, molecular, and genetic analysis of brain morphogenesis and function.
Thus, our lab's expertise in using the zebrafish to study the underlying mechanisms of vertebrate organogenesis synergizes well with our colleagues using mammalian systems including mouse and human to study brain morphogenesis. Toward this end, the Gleeson lab already collaborates with our lab to study the role of polarity genes and primary cilia in cardiovascular and neural development/function. Furthermore, we currently collaborate with the Frazer lab to perform Next Generation sequencing and genomic analysis of human pluripotent stem cell derived cardiac lineages.

Because of the proximity of our labs, this sharing of reagents, ideas and expertise has been straightfonward and seamless. Thus, we anticipate that these past collaborations with the Co-Pls of this proposal will facilitate the execution of our proposed studies to elucidate the underlying mechanisms involved in brain structure and function.

Overall, we believe the full potential of this proposal will be to ultimately provide novel insights into the mechanisms of how polarity genes may influence brain morphogenesis and function, and my past successful and productive research on using the zebrafish to understand the developmental programs of organogenesis has provided me the background and expertise to co-lead the proposed project.