Progress 11/01/03 to 09/30/09

Outputs
OUTPUTS: MENTORING ACTIVITIES Graduate Students (Committee Chair /Co-Chair) Luyen He (2007-present): Translational regulation in corn Rebecca Hammond (2006-2007): Transcriptional and translational regulation in corn. Rebecca received an undergraduate fellowship award from the NC RNA biology group to work with me during Spring/Summer 2006, Undergraduate Research Award Spring 2007, Presented a poster at the National conference of the American Society for Gravitational and Space Biology in Washington, DC, November 2006 and won the 2nd price in the undergraduate research competition. Rebecca also presented her research at the NC Undergraduate Research and Creativity Symposium in Raleigh, November 2006. Her research will result in co-authorship for two publications. POSTDOCTORAL ASSOCIATES: Dr. Cassi Myburg-Nichols (2004-2007): Transcriptional and translational regulation of gravitropism in the maize pulvinus. Dr. Raul Salinas Mondragon (2003-2008): Role of Inositol phosphate in gravity and light induced gene expression changes. Regulation of translation efficiency by miRNA in corn. INVITED SEMINARS AND WORKSHOP PRESENTATIONS: "Gravity-Induced Gene Expression in Plants." Heike Winter Sederoff, Steffen Heber, Brian Howard, Henrietta Myburg-Nichols, Rebecca Hammond, Raul Salinas-Mondragon, and Christopher S. Brown, COSPAR 37th Assembly, Palais des Congres de Montreal, Canada, July 2008. "Transcriptional and Translational regulation of gravitropism in maize." Plant Genomes Meeting, Cold Spring Harbor Laboratory, March 2007, NY. "Gravity and Light: The role of membrane components in tropic responses." Annual Meeting of the American Society for Gravitational and Space Biology, Washington, DC, Nov. 2006 " Microarray technology: Applications in Plant Research" at the Microarray Pre-meeting Workshop, American Society for Gravitational and Space Biology, New York , Nov. 2004 "Microarrays for Space" Guest lecture on microarray analysis in BIT 815J (2003/04) "Regulatory Networks in Plant Gravitropic Signal Transduction." Departmental Seminar Biochemistry, NCSU, Raleigh, Nov. 2004. Poster Presentations and published abstracts (underlined - undergraduate, graduate and postdoctoral advisees): Luyan He, Rebecca Boston, Heike Winter Sederoff. "The roles of miRNAs in Translational Regulation I nZea Mays Gene Expression in Plants." Annual Plant Molecular Biology Retreat, Ashville North Carolina, September 2008. Heike Winter Sederoff, Steffen Heber, Brian Howard, Henrietta Myburg-Nichols, Rebecca Hammond, Raul Salinas-Mondragon, and Christopher S. Brown. " Gravity-Induced Gene Expression in Plants." COSPAR 37th Assembly, Palais des Congres de Montreal, Canada, July 2008. R.L. Hammond, H. Myburg, I.Y. Perera, C.S. Brown and H. Winter Sederoff. Is Transcriptional Regulation of Gravitropism Conserved Between Dicots and Monocots Gravitational and Space Biology 20(1), p.5.(Second place Undergraduate poster comptetition) PARTICIPANTS: Dr. Heike Sederoff Dr. Imara Perera Dr. Henrietta Myburg Nichols Dr. Raul Salinas-Mondragon Rebecca Hammond Luyan He All North Carolina State University, Dept. Plant biology. TARGET AUDIENCES: Scientific community investigating gene regulation. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
The outcome of this project enabled us to identify genes in corn that are regulated on the transcriptional and translational level. This now enables us and other groups to research the mechanistic basis for this regulation which has already let to the identification of nobel miRNA. The data sets are published and as such a resource for the entire community.

Publications

• Howard, B.E., Sick, B. Perera, I., Im, Y.J., Winter-Sederoff, H., Heber, S. (2007) "Quality Assessment of Affymetrix GeneChip Data using the EM Algorithm and a Naive Bayes Classifier," Bioinformatics and Bioengineering, 2007. BIBE 2007. Proceedings of the 7th IEEE International Conference, pp.145-150.
• Christopher S. Brown, Heike Winter Sederoff, Eric Davies, Robert J. Ferl, and Bratislav Stanković, (2007) Plan(t)s for Space Exploration. In: Plant Tropisms P. Masson & S. Gilroy (eds.). Blackwell Publishing, Iowa, USA. pp.183-196.
• H. Myburg, R. Salinas-Mondragon, R.L. Hammond, I.Y. Perera, E. Davis, C.S. Brown and H. Winter Sederoff. 2006. Effects of gravity on gene expression in the maize pulvinus: Unraveling the roles of transcription and translation. Gravitational and Space Biology 20(1), p.37.
• A manuscript (2009) on the findings from this research project is prepared and will be submitted to a peer-review scientific journal.

Progress 10/01/06 to 09/30/07

Outputs
OUTPUTS: We modified methods for the separation and quantitative analysis of transcripts associated with ribosomes or non-ribosomal components. Polysomal and non-polysomal fractions were separated and analyzed using Affymetric gene chips. We identified transcriptionally and translationally regulated genes in corn pulvini and other tissues (root, young immature leaf) and are in the process of quanifying specific miRNA that could be involved in the translational regulation and transcript stability. Training undergraduate and advising postdoctoral Research Associate and Researcher: Undergraduate Student: Rebecca Hammon received an undergraduate fellowship award from the NC RNA biology group to work with me during Spring/Summer 2006, Undergraduate Research Award Spring 2007, Presented a poster at the National conference of the American Society for Gravitational and Space Biology in Washington, DC, November 2006 and won the 2nd price in the undergraduate research competition. Rebecca also presented her research at the NC Undergraduate Research and Creativity Symposium in Raleigh, November 2006. Her research will result in co-authorship for two publications. Postdoctoral Research Associate: Dr. Cassi Myburg-Nichols (2004-2007): Transcriptional and translational regulation of gravitropism in the maize pulvinus. Researcher: Raul Salinas-Mondragon (2007): Separation and identification of polysome-associated and non-polysome associated mRNAs and miRNAs in corn. Invited Presentations: "Transcriptional and Translational regulation of gravitropism in maize." Plant Genomes Meeting, Cold Spring Harbor Laboratory, March 2007, NY. "Signal Integration of Tropic Responses in Plant Roots." School of Environmental and Biological Sciences, Rutgers University, February 2007, NJ. PARTICIPANTS: Rebecca Hammond, Undergraduate student Dr. Henrietta Myburg-Nichols, postdoctoral research associate Dr. Raul Salinas-Mondragon, researcher Collaborators: Brian Howard, Graduate Student IFAS Dr. Steffen Heber, Assistant Professor, computer Engineering

Impacts
Research Outcomes/impacts: We have identified 3821 transcripts which are regulated in their association with ribosomes and therefore their translational efficiency. None of these transcripts responded differentially to gravity stimulation. However we identified a large group of transcripts that were transcriptionally but not translationally regulated after reorientation. We compared the changes in transcript abundance between these genes with those from our work on Arabidopsis in an effort to identify evolutionary conserved mechanisms regulating transcription in response to gravity stimulation. In collaboration with the Bioinformatics Group at NCSU (Prof. Heber, Brian Howard) we developed tools for "phylogenomics" analysis - an analysis of microarray experiments across species. This led to submission (and award) of a grant from the NC RNA biology group on "An intelligent User-Guided Microarray Analysis Server", 2006-2007, $10,500. The collaboration resulted in one peer-reviewed paper, and a second one to be submitted this Fall. A poster applying this method was presented at the Plant and Animal Genome conference in San Diego 2007:

Publications

• Mariya Khodakovskaya, Henrietta Myburg, Raul Salinas-Mondragon, Rebecca Hammond, Steffen Heber, Christopher S. Brown and Heike Winter Sederoff (2007) "Cross-species comparison of transcript profiles from root tissue of Arabidopsis and tomato expressing the same transgene" (XV International Plant and Animal Genome Conference (2007, January, San Diego, CA). Poster presentation. Abstract: P. 279.
• Paper in Proceedings: Howard, B., Heber, S., Perera, I., Im, J., Winter Sederoff, H., Sick, B. "Quality Assessment of Affymetrix GeneChip Data using the EM Algorithm and a Naive Bayes Classifier. IEEE-BIBE 2007. in press

Progress 10/01/05 to 09/30/06

Outputs
The initial set of slides for the microarray experiment turned out to be faulty and the data essentially useless. We therefore repeated the experiment with a different technology (Affymetrix GeneChip) which became available in the summer this year. We identified all significant differentially expressed genes and were able to distinguish transcriptionally regulated genes from those that are regulated on the translational level. Specific transcripts were monitored using realtime PCR and their changes confirmed. We are currently writing the first manuscript. In collaboration with collegues from Computer Science, we are comparing those sets of genes differentially translated in corn with data from Arabidopsis. This has sofar identified a cluster of genes which are orthologs conserved in their functional response to gravity stimulation.

Impacts
same as last year We trained three undergraduate students in the lab this year (2 from minority backgrounds). One of these students won second price in a national meeting for her presentation and all students presented their work at the NC Undergraduate Research Symposium in Spring and Fall 2006.

Publications

• in progress. The results have been presented in a talk at a National conference in Washington in November 2006 (American Society for Gravitational and Space Biology) by the postdoctoral associate.

Progress 10/01/04 to 09/30/05

Outputs
The experimental part for this project has been carried out during the summer 05. Maize plants were grown for 7 weeks in the phytotron greenhouse. Gravity stimulation was carried out by reorientation of the plants by 90 degree to the vertical and pulvinus tissue was harvested before and at different timepoints after stimulation. We extracted total and polysomal mRNA from the upper and lower pulvini to compare transcriptional and translational regulation. We have amplified and labelled the cRNA and are currently hybridizing the second biological replicate to the microarrays. Differentially expressed genes from the first biorep in the process of being confirmed by realtime PCR.

Impacts
same as last year.

Publications

• No publications reported this period

Progress 10/01/03 to 09/30/04

Outputs
This project officially started in 03/2004. We were able to hire an excellent postdoc with expertise in microarray design and analysis. THis postdoc started in July this year (2004). Sofar we were able to carry out the experiemental part - grow maize plants, gravity stimulate and harvest specific tissues in a time course after stimulation and in vertical controls - in four biological replicates. RNA extraction of total and polysomal mRNA, amplification and labelling has been carried out and the samples are ready to be hybridized to the microarrays. The microarrays are expected to arrive any day - they have been released from the NSF Maize Microarray Project in October 2004. We were able to receive test arrays and carried out technical replicates to evaluate the gene specific variations and dye effects. Due to our expertise in microarray analysis we were able to secure a position as beta testers for the NSF Microarray Project which provides us with additional free maize arrays. We expect to have first results from this experiment in Spring 2005.

Impacts
These experiments will be the first to identify on a whole genome basis the translational regulation of stress response genes in maize. It will help us to understand how the plant regulates differential cell elongation on the gene expression level.

Publications

• No publications reported this period