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Collecting tissue for genetic analysis

The Plant Genomics Consortium with Cold Spring Harbor Laboratory, New York University, and the American Museum of Natural History endeavors to contribute to the creation and dissemination of scientific knowledge in the field of comparative plant genomics. Ongoing genomics projects integrate Garden research expertise in plant systematics and economic botany with cutting-edge genomic techniques, breaking ground for the new fields of molecular biodiversity and genome evolution.

The Consortium
What is Genomics?
Plant Neuroactive Compounds Gymnosperm Genomics Project

The Consortium

The New York Botanical Garden has conducted field and laboratory research in the areas of systematic and economic botany for 113 years. With more than 150 scientists and technical support staff, NYBG has the expertise to identify applicable plant genomics projects and has access to the study plants. The Plant Genomics Consortium has recently been awarded a five year, NSF Plant Genomics Grant to study the evolution of seed. The Plant Genomics Consortium is a natural extension to the current molecular research conducted by The Lewis B. and Dorothy Cullman Program for Molecular Systematics Studies. Participants include: Dr. Dennis Stevenson and Dr. Eric D. Brenner.

New York University Department of Biology has launched its new Genomic Feacility in conjunction with the NYU Courant Institute of Mathematical Sciences. Research includes the development of novel computational biology approaches to identify networks of gene regulation by applying combinatorial theory to bioinformatics analysis. Participants include: Dr. Gloria Coruzzi, Dr. Dennis Shasha

Cold Spring Harbor Laboratory, a private, non-profit basic research and educational institution, is a leader in the field of plant molecular biology and genomics. The plant genomics center at the Lita Annenberg Hazen Genome Center was largely responsible for the completion of the first fully sequenced plant genome, Arabidopsis thaliana. Participants include: Dr. Richard McCombie and Dr. Robert Martienssen

American Museum of Natural History is committed to expanding public awareness of the Earth's diverse life forms and the role of biodiversity on the planet. A new frozen tissue collection, the Ambrose Monell Collection for Molecular and Microbial Research, opened in early 2001. It has the capacity to store many tens of thousands of frozen samples in liquid-nitrogen-cooled vats for the long-term preservation of samples for DNA sequencing. In recent years, the AMNH has hosted conferences on the human genome, conservation genetics, supercomputing, and constructing the tree of life. Participants include: Dr. Rob DeSalle.
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What is Genomics?

The term "genome" originated in 1930; it was used to denote the totality of genes on all chromosomes in the nucleus of a cell. Incredibly, DNA was not identified as the genetic material of all living organisms until 1944. The genetic code was elucidated in 1961 and with these fundamental insights in hand, it was possible to contemplate the concept that biological organisms had a blueprint consisting of finite numbers of genes. The sequence of these genes encoded all of the information required to specify the reproduction, development, and adult function of an individual organism. The massive interest and commitment of resources in both the public and private sectors flows from the generally-held perception that genomics will be the single most fruitful approach to the acquisition of new information in basic and applied biology in the next several decades.

"The new paradigm, now emerging, is that all genes will be known (in the sense of being resident in databases available electronically), and that the starting point of a biological investigation will be theoretical." (Walter Gilbert 1993)

Genomics is operationally defined as investigations into the structure and function of very large numbers of genes undertaken in a simultaneous fashion. Because all modern genomes have arisen from common ancestral genomes, the relationships between genomes can be studies with this fact in mind. This commonality means that information gained in one organism can have application in other even distantly related organisms. Comparative genomics enables the application of information gained from facile model systems to agricultural or non-model taxa. The nature and significance of differences between genomes also provides a powerful tool for determining the relationship between genotype and phenotype through comparative genomics and morphological and physiological studies. Genotype is the term applied to specific changes in DNA sequence found in a mutant, while phenotype refers to all biological consequences from the presence of the mutation in question.

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Cycad and Gymnosperm Genomics Project

We are taking a genomics approach to answer fundamental questions in plant biology. In particular, we are probing the evolutionary origins of the seed and the flower. Our strategy has focused on analysis of the gymnosperms, and especially cycads. Using a comparative genomics approach, we have prepared cDNA libraries and ?Expressed Sequence Tags? (ESTs) from developing vegetative and reproductive tissue for our chosen taxa. Using these methods, we have obtained the DNA sequence for several genes with high similarity to genes known in higher plants to be involved with development of seeds and flowers. Current studies are investigating the role of these genes in gymnosperms to help us form hypotheses about how these genes may have been recruited to create seeds and flowers.

Another classical botanical question we are addressing with cycads is of important medicinal value. Several compounds isolated from cycads have been shown to be neurologically toxic, including a compound called BMAA, which mimics the neurotransmitter, glutamate. BMAA toxicity is believed to act by over stimulating glutamate receptor in human neurons. Using our EST based approach, we have identified genes that may be involved in BMAA biosynthesis. We have also identified a cycad EST similar to human glutamate receptors, which may play a important role in signaling mechanisms responsible for growth and development. By understanding the role of BMAA in cycads and its relationship to the native plant glutamate receptors, we may gain a clearer insight into glutamate receptor function or dysfunction in both plants and humans.

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Eric Brenner

Gloria Coruzzi

Rob DeSalle

Robert Martienssen

Richard McCombie

Dennis Shasha

Dennis Stevenson

Laboratory Technicians

Suzan Runko

Walter Moss

Post Docs

Ernest Lee

Mary Egan

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