Nicholas_Provart

50 years of Arabidopsis research: highlights and future directions

Posted on by biota

Provart NJ, Alonso J, Assmann SM, Bergmann D, Brady SM, Brkljacic J, Browse J, Chapple C, Colot V, Cutler S, Dangl J, Ehrhardt D, Friesner JD, Frommer WB, Grotewold E, Meyerowitz E, Nemhauser J, Nordborg M, Pikaard C, Shanklin J, Somerville C, Stitt M, Torii KU, Waese J, Wagner D, McCourt P

New Phytol. 2015 Oct;

PMID: 26465351

Abstract

I. II. III. IV. V. VI. VII. VIII. IX. X. XI. XII. XIII. Natural variation and genome-wide association studies XIV. XV. XVI. XVII. References SUMMARY: The year 2014 marked the 25(th) International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in Göttingen, Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published. We present herein a citational network analysis of these papers, and touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species. We also look to the future, highlighting some outstanding questions that can be readily addressed in Arabidopsis. Topics that are discussed include Arabidopsis reverse genetic resources, stock centers, databases and online tools, cell biology, development, hormones, plant immunity, signaling in response to abiotic stress, transporters, biosynthesis of cells walls and macromolecules such as starch and lipids, epigenetics and epigenomics, genome-wide association studies and natural variation, gene regulatory networks, modeling and systems biology, and synthetic biology.

Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice

Posted on by biota

Wang L, Czedik-Eysenberg A, Mertz RA, Si Y, Tohge T, Nunes-Nesi A, Arrivault S, Dedow LK, Bryant DW, Zhou W, Xu J, Weissmann S, Studer A, Li P, Zhang C, LaRue T, Shao Y, Ding Z, Sun Q, Patel RV, Turgeon R, Zhu X, Provart NJ, Mockler TC, Fernie AR, Stitt M, Liu P, Brutnell TP

Nat. Biotechnol. 2014 Oct;

PMID: 25306245

Abstract

C4 and C3 photosynthesis differ in the efficiency with which they consume water and nitrogen. Engineering traits of the more efficient C4 photosynthesis into C3 crops could substantially increase crop yields in hot, arid conditions. To identify differences between C4 and C3 photosynthetic mechanisms, we profiled metabolites and gene expression in the developing leaves of Zea mays (maize), a C4 plant, and Oryza sativa (rice), a C3 plant, using a statistical method named the unified developmental model (UDM). Candidate cis-regulatory elements and transcription factors that might regulate photosynthesis were identified, together with differences between C4 and C3 nitrogen and carbon metabolism. The UDM algorithms could be applied to analyze and compare development in other species. These data sets together with community viewers to access and mine them provide a resource for photosynthetic research that will inform efforts to engineer improvements in carbon fixation in economically valuable grass crops.

Taking the next step: building an Arabidopsis information portal

Posted on by biota

Plant Cell 2012 Jun;24(6):2248-56

PMID: 22751211

Abstract

The Arabidopsis information portal (AIP), a resource expected to provide access to all community data and combine outputs into a single user-friendly interface, has emerged from community discussions over the last 23 months. These discussions began during two closely linked workshops in early 2010 that established the International Arabidopsis Informatics Consortium (IAIC). The design of the AIP will provide core functionality while remaining flexible to encourage multiple contributors and constant innovation. An IAIC-hosted Design Workshop in December 2011 proposed a structure for the AIP to provide a framework for the minimal components of a functional community portal while retaining flexibility to rapidly extend the resource to other species. We now invite broader participation in the AIP development process so that the resource can be implemented in a timely manner.