Gloria M. Coruzzi
Carroll and Milton Petrie Professor; Professor of Biology
Ph.D./M.S. 1979 (Molecular and Cell Biology), New York University; B.S. 1976 (Biology), Fordham.
|New York University|
|Department of Biology|
|Center for Genomics and Systems Biology|
|12 Waverly Place, Room 505|
|New York, NY 10003|
Plant Systems Biology. Our goal is to identify gene regulatory networks in plants using a combination of genetic, genomic, bioinformatic, and systems biological approaches. Our lab has two main areas of inquiry: 1. A systems approach to nitrogen networks & the Virtual Plant; 2. Comparative Genomics of Seed Evolution.
A Systems Approach to Nitrogen Networks & the VirtualPlant.
The long term goal of this project is to understand how internal and external perturbations affect gene regulatory networks that link plant metabolism and development. Succeeding in this endeavor will allow us to (1) explain mechanistically how changes in gene networks evoke systems-wide responses to external treatments such as nitrogen, and (2) to predict network states under untested conditions or in response to modifications. In the long term, this systems biology approach to gene networks should enable researchers to test the effects of biotechnological strategies for gene modifications in silico, prior to implementation in transgenic plants. Our approach starts with the integration of all available information on Arabidopsis genomic data into a "multinetwork" where the "edges" connecting gene "nodes" are supported by multiple evidence including: metabolic pathway connections, protein:protein and protein:DNA interactions, microarray data, microRNA:target datasets, and literature-based interactions. At present, the Arabidopsis multinetwork we have created contains approximately 7,000 gene nodes and 230,000 interactions between them. As proof-of-principle, we have used this Arabidopsis multinetwork to identify the gene networks controlled by light, carbon and nitrogen signals. In selected cases, the networks identified in wild-type plants have been validated using microarray data from Arabidopsis signaling mutants. Our studies include analysis of gene networks in specific organs (leaves, roots or seeds) or in specific cell-types based on analysis of microarray data obtained from cell-sorted samples of roots. The network analysis of gene lists generated from the microarray data in a network view is shown in Figure 1.
FIGURE 1: Nitrogen Networks and the VirtualPlant.
The VirtualPlant Project. In order to go beyond data integration to conceptual integration of genomic data, we recognize that scientists pattern recognition skills often lead to the most enduring qualitative biological insights. To support those skills in a data-rich environment, have implemented a set of data integration, analysis and visualization tools into a system called the "VirtualPlant" (www.virtualplant.org). This system encompasses visualization techniques that render the multivariate genomic information in visual formats that facilitate the extraction of biological concepts and enable a "Systems Biology" view of the genomic data. While our project relates specifically to Arabidopsis, the data structures, algorithms, and visualization tools we have developed have been designed in a species-independent fashion. Thus, with the proper data uploads, the system can be used to visualize and model the molecular basis and underlying genomic responses in any organism for which genomic data is available.
Comparative Genomics of Seed Evolution
This NSF Plant Genome project (NSF DBI-0421604) involves the comparative genomic analysis of non-model, non-crop species, to uncover genes important to the evolution of seeds, an important agronomic trait. This project is being conducted with our partners in the NY Plant Genomic Consortium that include coPIs from NYU Biology (Coruzzi), NYU Courant (Shasha), NYBG (Stevenson), AMNH (DeSalle) and CSHL (McCombie & Martienssen). Our approach is to generate and mine EST data from the the most primitive living-seed plants, the nodal Gymnosperms and the heterosporous lycophyte, Selaginella (as an outgroup), to resolve their phylogenetic relationship and to uncover novel genes and characters associated with the evolution and development of seeds. This project is being conducted collaboratively by scientists at three NY area institutions specializing in evolution, genomics and bioinformatics, who comprise The New York Plant Genomics Consortium (www.nypgenomics.org). Participants in this project include PIs who collaborate in the training of post docs and graduate students from New York University, The New York Botanical Garden, Cold Spring Harbor, and The American Museum of Natural History. We aim to achieve three goals:
- Evolutionary Genomics: We have generated 18,437 ESTs from three "nodal" Gymnosperm species which have enabled us to create genome-scale phylogenies to resolve evolutionary relationships in the Gymnosperms and identify putative genes involved in the evolution of seeds.
- Phylogenomics/Informatics: We developed new informatic tools to automate orthology determination in a parsimony framework and the construction of phylogenomic scale trees. These tools include: and Ortholog ID, ViCoGenta (Viewer for Comparing Genomes to Arabidopsis), and a newer tool under development ASAP (Automatic Systematic Analysis Program).
- Functional Genomics: To test the function of genes supporting the node for seed plant evolution we have begun to test the expression in Gymnosperm tissues (RNA and in situs) and perform analysis of Arabidopsis mutants in orthologous genes.
FIGURE 2. Comparative Genomics of Seed Evolution: Use of ESTs in functional phylogenomic studies to identify genes associated with the evolution of seeds
NIH NIGMS GRANT GM32877: "Regulation of amino acid biosynthesis genes in plants"
P.I.: Gloria Coruzzi
NSF Arabidopsis 2010 Genome Grant (IBN0115586):"N2010: Nitrogen Networks in Plants" P.I. Gloria Coruzzi, Co-PIs; D. Shasha (NYU Courant), N.Crawford (UCSD), Ken Birnbaum (NYU Center for Comparative Functional Genomics).
NSF Plant Genome Grant: DBI-0421604. "Genomics of Comparative Seed Evolution" P.I.: Gloria Coruzzi; Co-PIs: Stevenson (NYBG), McCombie (CSHL), DeSalle (AMNH).
NSF Database Activities: DBI-0445666, "Conceptual Data Integration for the Virtual Plant". Coruzzi , PI, CoPIs: Gutierrez R (U Catolica de Chile), Shasha D (NYU Courant).
DOE GRANT DEFG02-89ER14034: "Asparagine synthetase gene regulation and plant nitrogen metabolism" P.I. Coruzzi
Gloria Coruzzi is currently the Carroll & Milton Petrie Professor of Biology at New York University. Her research in Plant Systems Biology combines genomic, bioinformatic and system biology approaches to identify gene networks involved in biological regulatory mechanisms controlling nitrogen use and the evolution of seeds. A native New Yorker, Dr. Coruzzi received her Ph.D. in Molecular & Cell Biology at New York University School of Medicine in yeast genetics where she decoded the yeast mitochondrial genome. Her studies on plant genes began during her studies as an Assistant and Associate Professor at Rockefeller University. Since joining NYU a professor, Dr. Coruzzi's lab initiated Plant Systems Biology approaches to perform functional genomic studies in Arabidopsis and other species. This work including the development of new informatic tools encompassed in a software platform called VirtualPlant which is being performed in collaboration with colleagues at NYU Courant Institute for Math & Computer Science. Dr. Coruzzi is also engaged in a collaborative genomic project on the Comparative Genomics of Seed Evolution with co-PIs at the New York Botanical Garden, the American Museum of Natural History and Cold Spring Harbor labs. Dr. Coruzzi's research is currently funded by The National Institutes of Health, The NSF 2010 Project, The NSF Plant Genome Project, the NSF Database and Information Project, and The Department of Energy. Dr. Coruzzi was named an AAAS Fellow in 2005 and currently serves on numerous science advisory and editorial boards.
I have been involved in developing a specialized graduate training track that concerns the molecular evolution of plants and animals called BRIDGES: Biotic Resources: Integrating Development, Genetics, Evolution and Systematics which is currently run by Dr. David Fitch. The BRIDGES PhD track was developed jointly by NYU faculty and faculty the New York Botanical Garden (NYBG) and the American Museum of Natural History (AMNH). I teach in the following undergradiate and graduate courses: V23.0012 Principles of Biology II, V230014 Honors Principles of Biology II, V23.0022 Molecular and Cellular Biology; G23.1072 Molecular Controls of Organism Form and Function, G23.1128 Genomics; G23.1002/2004 BioCore II & IV: Genes, Systems and Evolution.
See Coruzzi Laboratory Webpage for more information on people & projects.
Editorial Board; Current Opinions in Plant Biology, 1998-present; Board of Directors, International Society of Plant Molecular Biology, 1996-1999; New York Botanical Garden, Advisory Committee for Systematic Botany, 1995-present; Board Member, North American Arabidopsis Steering Committee, 1994-1997; Associate Editor, Plant Physiology, 1992-1998.
AAAS Fellow, 2005; Carroll and Milton Petrie Chair in Biology, NYU 1996- present; National Institutes of Health Grant, GM32877, 1996-2000; National Science Foundation Grant, MCB93-04913, 1996-1999; United States Department of Energy Grant, DEFG0292ER20071, 1995-1998; Herbert and Margaret Sokol Award in the Sciences, NYU Dec. 1996.