Timothy Mark Nelson

Professor of Molecular, Cellular, and Developmental Biology; Director, Marsh Botanical Garden

Research Interests

Arabidopsis; Zea mays; vascular patterning


Research Summary

Our work is aimed at pattern formation in the development of leaves. The leaf is ideal for evaluating cell lineage, local cell interactions, and positional information in these processes, since the patterns of cells are simple and reiterative. One recent research focus has been on the formation of the regular venation pattern that appears to guide leaf cell differentiation on a fine scale. In Arabidopsis, we are using genetic screens to isolate vascular pattern mutants, characterizing genes with provascular specific expression patterns, and using laser-capture microdissection (LCM) to compare expression profiles of provascular and vascular cells. Another focus has been on the interactions of cell types and transcriptional networks in developing leaves. We have recently used LCM and transcriptional profiling to isolate cell-specific RNAs for a complete cell type transcriptome atlas of rice (>100 cell types) and to identify C4-photosynthesis-specific transcriptional networks in developing maize leaf mesophyll and bundle sheath cells.

Extensive Research Description

One effort in the lab is aimed at understanding the formation of the regular venation pattern that appears to guide leaf cell differentiation on a fine scale. We have used three strategies to identify the genes and pathways that form the simple venation pattern of Arabidopsis leaves: 1) cloning of vascular pattern mutants, 2) screening of genes with provascular (PV)-specific expression patterns, and 3) analysis of expression profiles of PV cells by laser-capture microdissection (LCM) and microarray analysis. Recently, we characterized the roles of specific phosphoinositols (PIs) that regulate intracellular vesicle traffic essential for vein polarity and vascular cell continuity in developing leaves, and characterized several mutants with defective vein patterns that correspond to the proteins that produce or perceive these PIs. In collaboration with the Deng and Zhao labs, we mined our growing cell-specific transcriptome atlas for rice (http://plantgenomics.biology.yale.edu/riceatlas/) to identify a host of features specific to individual cell types, including cell-specific genes and promoter motifs, cell-specific pathways and hormone-response centers. In a third (collaborative) area of effort, we are undertaking a systems biology comparison of developing leaves of three grass species: rice (a C3-type plant), maize (moderate C4 plant), and sorghum (extreme C4 plant), to attempt to learn the molecular developmental basis of high-efficiency C4-type photosynthesis. We have thus far obtained the inventories of transcriptomes, proteomes and metabolites from maize developmental stages and physiological states and are now obtaining comparable data from corresponding stages and states of rice.


Selected Publications

  • Nelson, T., et al. (2007). A rice cell type transcriptional atlas: cellular profiles for a comparative approach to regulation of pathways and venation patterns. In: IRRI Workshop on C4 Rice (In press).
  • Nelson, T., Tausta, S.L., Gandotra, N., and Liu, T. (2006). Laser microdissection of plant tissue: what you see is what you get. Ann. Rev. Plant Biol. 57:181-201.
  • Jiao Y, Tausta SL, Gandotra N, Sun N, Liu T, Clay NK, Ceserani T, Chen M, Ma L, Holford M, Zhang HY, Zhao H, Deng XW, Nelson T. (2009) A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat Genet. 41:258-63.
  • Ceserani T, Trofka A, Gandotra N, Nelson T. (2009) VH1/BRL2 receptor-like kinase interacts with vascular-specific adaptor proteins VIT and VIK to influence leaf venation. Plant J. 57:1000-14.
  • Petricka JJ, Clay NK, Nelson TM (2008) Vein patterning screens and the defectively organized tributaries mutants in Arabidopsis thaliana. Plant J. 56:251-63.
  • Carland F, NelsonT. (2009) CVP2- and CVL1-mediated phosphoinositide signaling as a regulator of the ARF GAP SFC/VAN3 in establishment of foliar vein patterns. Plant J., in press.

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