NSF Project: Program Participants
Mendes, Pedro - PI of the project. He is responsible for the complete bioinformatics system, for data analysis, and for integrative modeling.

Dixon, Richard - Co-PI of the project. He is responsible for overseeing all experimental activities. He is directly responsible for supervision of the cell cultures and elicitation, and for profiles of triterpenes.

Sumner, Lloyd - Lead scientist on the metabolite and protein profiling.

May, Greg - Lead scientist on the mRNA profiling and the co-coordinator for the summer course.

Smith, Joel T. - Metabolic profiling of carbohydrates, amino acids and ionic species.

Post-doc
Asirvatham, Victor - performing and enhancing protein identifications of Medicago truncatula proteins using custom databases. This is a critical effort in improving our protein identifications in an organism without a sequenced genome but one with large EST sequence resources

Aziz, Naveed - Optimization of microarray protocols, RNA purification from time course samples, and the generation and analyses of expression profiling data.

Elmer, Aaron - Generation and analyses of expression profiling using 2-DE for the methyl jasomonate time course

Lei, Zhentian - Protein profiles and their data processing.

Mehrotra, Bharat - data curation, the project website, and research in data mining.

Naoumkina, Marina - RNA purification as well as the generation and analyses of expression profiling data from the yeast elicitor time course. 

Graduate Students
Technician, Programmer
Riner, Lisa - Laboratory technician responsible for cell culture establishment and elicitation of cell cultures.

Broeckling, Corey - Sr. Research Associate on metabolite profiling

Undergraduate Students
Self, Sara - student at Southeastern Oklahoma State University, participated in the Noble Foundation's Summer Intern Program while in the Dr May's laboratory last summer.

Williams, Brad - worked with Dr. Smith in the development of CE protocols for the carbohydrate and amino acid profiling. He is a graduating senior who will begin his graduate career at Texas A&M in chemistry starting in the fall of 2003.

Rhodes, Gary - worked with Dr. Smith in the development of CE protocols for the carbohydrate profiling.

Staff not funded by NSF

Other Participants

Research Experience for Undergraduates

Organizational Partners
The Samuel Roberts Noble Foundation
The Noble Foundation is a major partner in this project, with roughly equal proportion of work than the lead institution (VT). The Noble Foundation has contributed with matching funds ($200k) for the purchase of Q-TOF mass spectrometer. The Foundation has also contributed with staff that are not paid from this grant but that have worked a substancial amount of time (notably Mr. Jack Blount). The Noble Foundation has also contributed with facilities for holding the summer course (teaching rooms and lodging in its conference center) at no cost to NSF or participants.

Southeastern Oklahoma State University
Dr. Tim Smith (senior personnel in the grant) works at this institution. Project work here is on profiling of amino acids and ionic metabolites. 

Contributions within Discipline:
The group of Dr. Sumner has developed LC/MS protocols for profiling and identification of flavonoids and saponins.

The group of Dr. Sumner has found that the biological variation of samples from M. truncatula roots exceed considerably the proteomic analytical variation.

The group of Dr. Dixon has identified ESTs coding for the first three enzymes in the triterpene pathway.

The group of Dr. Mendes has developed the concept of 'metabolite neighborhoods', useful for metabolic network analysis and for functional genomic data visualization and integration.

The group of Dr. Mendes has developed (and is currently validating) an XML format for GC/MS and LC/MS raw data.

Dr. May led the development of a 16,000 oligonucleotide set for M. truncatula expression analyses.

The group of Dr. May has optimized microarray experimental protocols.

The group of Dr. May has identified differences in expression profiling experimental results when polysomal RNA is substituted for total RNA as template for probe synthesis.

The group of Dr. May, in collaboration with Dr. Liangjiang Wang, Noble Foundation, is characterizing a class of genes unique to legumes.

Dr. May is a member of the International M. truncatula Steering Committee.

Dr. Smith's group has developed capillary electrophoresis protocols for profiling for inorganic and organic anions and cations, carbohydrates, and amino acids in M. truncatula plant tissue and cell culture tissue.

Other Collaborators or Contacts
In the course of this year's progress project we initiated a series of new collaborations and contacts related with the current project.

Dr. Pedro Mendes collaborated with Phenomenome Discoveries, Inc. of Saskatoon, Canada. The project sponsored financially by this company aimed at developing software for metabolomics data visualization. It consisted of the construction of a software, MetExViewer, for visualization of Phenomenome's MetEx data (which uses FTICR mass spectrometry). The software is now ready and major portions of it will be reused for the present project.

Dr. Pedro Mendes has started collaboration with two new faculty colleagues at the Virginia Bioinformatics Institute. Dr. John Lennon is a proteomics speciallist (who came from Large Scale Biology) and Dr. Vladymir Shulaev is a plant metabolomics speciallist. Dr. Mendes and Dr. Shulaev are now planning research projects similar with the current one on a series of other plant organisms.

Dr. Rick Dixon has established a collaboration with Dr Seiichi Matsuda, Departments of Chemistry and Biochemistry and Cell Biology, Rice University, Houston, Texas, for functional analysis of triterpene pathway genes. The present project has as one of its goals the use of integrated Annual Report: 0109732 functional genomics to elucidate the genes encoding the enzymes of triterpene saponin biosynthesis in M. truncatula. Dr Matsuda is an expert in terpenoid chemistry and production of terpenoids using recombinant DNA technology. As a part of the functional characterization of the M. truncatula triterpene cyclase, Dr Matsuda generated a yeast strain producing active beta-AS enzyme. This will be used in Dr Matsuda's lab for subsequent functional identification of candidate downstream cytochrome P450 enzymes that act on beta-amyrin. These candidates will be identified based on the transcriptome vs metabolome profiles generated in the present project.

Dr. Lloyd Sumner initiated collaborations with Dr. Ben Matthews, USDA-ARS-PSI, Soybean Genomics and Improvement Laboratory, Beltsville, MD on metabolomic studies of soybean-nematode resistence, and with Dr. Jack Dillwith, Department of Entomology and Plant Pathology, Oklahoma State University, on proteomics and metabolomics of aphid interactions with M. truncatula. Integrated metabolomic and proteomic studies are central to this project and these new collaborations will allow application of the findings of this project onto host-pathogen interactions in legumes.

Both Dr. Pedro Mendes and Dr. Lloyd Sumner have become members of the International Committee on Plant Metabolomics (together with Drs. Raoul Bino, Wageningen University, Oliver Fiehn, Max-Plank Institute for Plant Physiology, and John Draper, University of Wales Aberystwyth). This committee was formed at the First International Conference on Plant Metabolomics (Wageningen, April 2002) with the intention of stimulating and coordinating the actions of the Platform Plant Metabolomics. This is a group aiming to facilitate interaction between the various groups in the plant metabolomics community.

Dr. Pedro Mendes initiated collaborations with Dr. Walling Cyre, Electrical and Computer Engineering Department, Virginia Tech. Dr. Cyre is an expert in natural language processing and wants to apply this technology to biological texts. This collaboration will enhance the ability of the bioinformatics team of this project to scan the literature for relevant information on M. truncatula (which is needed as reference information for annotation).

Dr. Pedro Mendes has had several contacts with senior members of the I3C organization (www.i3c.org, of which VBI is a member) with the intention of initiating discussions leading to the drafting of standards for metabolomics data exchange. In parallel with this, Dr. Mendes is now in contact with a British group for the same purpose. Such data standards would suit a role in metabolomics similar to the MIAME and MAGE protocols in trasncriptomics, and follow the reccomendations that came out of the NSF-sponsored meeting on the Future of Plant Genome Databases, held at TIGR September 10-11, 2001.

Dr. Gregory May collaborated with Drs. Kate Vandenbosch, University of Minnesota and Chris Town, TIGR on the development of the Medicago Array-Ready Oligonucleotide Set Version 1.0 that is commercially available through Qiagen Operon.

Dr. Gregory May collaborated with Drs. Charles Brummer, Iowa State University and Ian Ray, New Mexico State University on determining the transferability of M. truncatula genomics data and resources towards the improvement M. sativa varieties.

Training and Development:
Workshop on Gene Expression Methods, Design, and Analysis ? August 19-21, 2002 Noble Foundation. (http://medicago.vbi.vt.edu/workshops/2002/index.html) The workshop examined gene expression technologies, experimental design and the informatics and statistical methods involved in data analysis. Overviews of cDNA and oligonucleotide DNA microarrays, quantitative RT-PCR, serial analysis of gene expression, AFLP, and microbead-based systems were provided. The workshop was coordinated by Drs. Jennifer Weller and Gregory May with lectures provided by Drs. Jennifer Weller and Karen Schlauch.

Dr. Olga Brazhnik, a database administrator for the project (at VBI), attended the Plant and Animal Genome meeting in San Diego. This was in order for her to become more familiar with the plant genomics area and to meet members of the community (she is a physicist by training).

Outreach activities:
Dr. Smith was an invited speaker to two universities this year. These included Oklahoma Christian University, Edmond, OK, on March 5, 2003 and University of Tulsa, Tulsa, OK, on April 10, 2003. These presentations included an overview of this project and as well as a detailed description of Dr. Smith?s research.

Dr. Mendes participated in the NSF-sponsored workshop on 'Linking Teachers to Research Experience' held at the Howard Community College Campus on February 23, 2002. While at this workshop the PI established contact with one teacher who showed interested in participating in the project, however the collaboration did not materialize due to geographical distance. On return from the workshop, Dr. Mendes has excahnged views with Dr. Neysa Call (VBI's head of public relations and outreach) towards organizing a similar workshop in the south Virginia-North Carolina area.

Dr. Mendes has supervised a visiting Masters student from the International University (Germany). Dr. Sinan Gueler (a PhD in plant Physiology) was a computer science Masters student who joined the Mendes lab for three months. Dr. Gueler was trained in XML and implemented a DTD and schema for GC/MS raw data.

Dr. Mendes is scheduled to be interviewed by The Scientist on functional genomics data visualization, in the first week of June 2002.

Dr. Rick Dixon has given a public lecture to heads of six university and institutes' librarians, at the Noble Foundation, and another public lecture on Food and Society, at the Oklahoma Historical Society. Dr. Dixon has also participated in a meeting of the Oklahoma State Office of Careers Development where he discussed training for support technicians in biotechnology and genomics.

Dr. Rick Dixon supervised a summer undergraduate student from the University of Oklahoma (Courtney Allen) and a summer high school student (Shannon Gonzales).

Dr. Lloyd Sumner supervised two summer undergraduate students in his laboratory, providing basic laboratory training as well as exposure to biological and analytical sciences.