Contact Information:


Zachery Smith

The Salk Institute

Plant Molecular and Cellular Biology Lab

10010 N. Torrey Pines Rd.

San Diego, CA 92109

858-453-4100 x1907






I am a graduate student in the Department of Biology at UCSD.I am currently performing research in the laboratories of Jeff Long (Plant Biology Department, The Salk Institute) and Shankar Subramaniam (Bioengineering Department, UCSD).The goal of my research is to understand the transcriptional network architecture underlying polarity establishment and cell fate determination in lateral organ development of the model plant Arabidopsis thaliana.


My previous research employed forward genetic and molecular biology methodology to identify genes involved in embryonic polarity and organ patterning.We have identified and characterized a transcription factor gene family (HD-ZIP III) that specifies apical and central fate in the early embryo.This gene family also directs dorsal polarity to most lateral organs of the vegetative plant body.The knowledge of this pathway is almost exclusively based on genetic evidence.We aim to add large scale as well as discrete biochemical evidence to our understanding of this process.In Jeff Longís laboratory, I plan to take a top down approach and find direct targets of these transcription factors through microarray and chromatin immunoprecipitation methods.I also plan to use genetic, molecular biology, and biochemical techniques to elucidate feed forward and feedback loops that modulate the action of these transcription factors.


In Arabidopsis, robustness of key developmental processes is thought to be provided through genetic redundancy and modularity of signaling networks.The data obtained from our transcriptional profiling and biochemical studies will facilitate computational analysis and modeling to elucidate the underlying transcriptional network structure.In Shankar Subramaniamís laboratory, I plan to analyze our microarray data to identify direct targets and binding motifs of the HD-ZIP III transcription factors.After confirmation of these targets, I plan to use our data as well as published data to reconstruct the transcriptional network in which the HD-ZIP III transcription factors play a central role in lateral organ development.


Understanding the underlying network architecture to this central developmental process will help us understand how redundancy and modularity are utilized in plant development.Furthermore, the pathway that we are studying patterns leaf, vascular, flower, fruit, and stem cell development.The information that we obtain from these studies can be directly applied towards crop improvement for the goal of increasing the nutritional and economic value of food products as well as toward the production of biofuels.






Jeff A. Long, Carolyn Ohno, Zachery R. Smith, Elliot M. Meyerowitz.TOPLESS Regulates Apical Embryonic Fate in Arabidopsis.2006.Science, 312: 1520-1523.


Zachery Smith and Jeff Long.Apical-Basal and Adaxial-Abaxial Polarity in Arabidopsis Embryogenesis.2005.Poster presentation at the 16th International Conference on Arabidopsis research.


Todd C. Mockler, Xuhong Yu, Dror Shalitin, Dhavan Parlkh, Todd P. Michael, Jasmine Liou, Jie Huang, Zachery Smith, Jose M. Alonso, Joseph Ecker, Joanne Chory, and Chentao Lin.Regulation of flowering time in Arabidopsis by K homology domain proteins.2004.PNAS, vol. 101, no. 34, 12759-12764.





The Long Lab:


The Subramanaim Lab: