The Experts below are selected from a list of 273 Experts worldwide ranked by ideXlab platform

Wenfeng Li - One of the best experts on this subject based on the ideXlab platform.

  • re analysis of rna seq transcriptome data reveals new aspects of Gene Activity in arabidopsis root hairs
    Frontiers in Plant Science, 2015
    Co-Authors: Wenfeng Li
    Abstract:

    Root hairs, tubular-shaped outgrowths from root epidermal cells, play important roles in the acquisition of nutrients and water, interaction with microbe, and in plant anchorage. As a specialized cell type, root hairs, especially in Arabidopsis, provide a pragmatic research system for various aspects of studies. Here, we re-analyzed the RNA-seq transcriptome profile of Arabidopsis root hair cells by Tophat software and used Cufflinks program to mine the differentially expressed Genes. Results showed that, ERD14, RIN4, AT5G64401 were among the most abundant Genes in the root hair cells; while ATGSTU2, AT5G54940, AT4G30530 were highly expressed in non-root hair tissues. In total, 5409 Genes, with a fold change greater than 2-fold (FDR adjusted P<0.05), showed differential expression between root hair cells and non-root hair tissues. Of which, 61 were expressed only in root hair cells. 136 out of 5409 Genes have been reported to be “core” root epidermal Genes, which could be grouped into nine clusters according to expression patterns. Gene ontology (GO) analysis of the 5409 Genes showed that processes of “response to salt stress”, “ribosome bioGenesis”, “protein phosphorylation”, and “response to water deprivation” were enriched. Whereas only process of “intracellular signal transduction” was enriched in the subset of 61 Genes expressed only in the root hair cells. 121 unannotated transcripts were identified and 14 of which were shown to be differentially expressed between root hair cells and non-root hair tissues, with transcripts XLOC_000763, XLOC_031361, and XLOC_005665 being highly expressed in the root hair cells. The comprehensive transcriptomic analysis provides new information on root hair Gene Activity and sets the stage for follow-up experiments to certify the biological functions of the newly identified Genes and novel transcripts in root hair cell morphoGenesis.

  • mapping Gene Activity of arabidopsis root hairs
    Genome Biology, 2013
    Co-Authors: Wenfeng Li, Simonetta Santi, Wolfgang Schmidt
    Abstract:

    Background: Quantitative information on Gene Activity at single cell-type resolution is essential for the understanding of how cells work and interact. Root hairs, or trichoblasts, tubular-shaped outgrowths of specialized cells in the epidermis, represent an ideal model for cell fate acquisition and differentiation in plants. Results: Here, we provide an atlas of Gene and protein expression in Arabidopsis root hair cells, Generated by paired-end RNA sequencing and LC/MS-MS analysis of protoplasts from plants containing a pEXP7-GFP reporter construct. In total, transcripts of 23,034 Genes were detected in root hairs. High-resolution proteome analysis led to the reliable identification of 2,447 proteins, 129 of which were differentially expressed between root hairs and nonroot hair tissue. Dissection of pre-mRNA splicing patterns showed that all types of alternative splicing were cell type-dependent, and less complex in EXP7-expressing cells when compared to non-root hair cells. Intron retention was repressed in several transcripts functionally related to root hair morphoGenesis, indicative of a cell type-specific control of Gene expression by alternative splicing of pre-mRNA. Concordance between mRNA and protein expression was Generally high, but in many cases mRNA expression was not predictive for protein abundance. Conclusions: The integrated analysis shows that Gene Activity in root hairs is dictated by orchestrated, multilayered regulatory mechanisms that allow for a cell type-specific composition of functional components.

Wolfgang Schmidt - One of the best experts on this subject based on the ideXlab platform.

  • mapping Gene Activity of arabidopsis root hairs
    Genome Biology, 2013
    Co-Authors: Wenfeng Li, Simonetta Santi, Wolfgang Schmidt
    Abstract:

    Background: Quantitative information on Gene Activity at single cell-type resolution is essential for the understanding of how cells work and interact. Root hairs, or trichoblasts, tubular-shaped outgrowths of specialized cells in the epidermis, represent an ideal model for cell fate acquisition and differentiation in plants. Results: Here, we provide an atlas of Gene and protein expression in Arabidopsis root hair cells, Generated by paired-end RNA sequencing and LC/MS-MS analysis of protoplasts from plants containing a pEXP7-GFP reporter construct. In total, transcripts of 23,034 Genes were detected in root hairs. High-resolution proteome analysis led to the reliable identification of 2,447 proteins, 129 of which were differentially expressed between root hairs and nonroot hair tissue. Dissection of pre-mRNA splicing patterns showed that all types of alternative splicing were cell type-dependent, and less complex in EXP7-expressing cells when compared to non-root hair cells. Intron retention was repressed in several transcripts functionally related to root hair morphoGenesis, indicative of a cell type-specific control of Gene expression by alternative splicing of pre-mRNA. Concordance between mRNA and protein expression was Generally high, but in many cases mRNA expression was not predictive for protein abundance. Conclusions: The integrated analysis shows that Gene Activity in root hairs is dictated by orchestrated, multilayered regulatory mechanisms that allow for a cell type-specific composition of functional components.

Asit B. Mukherjee - One of the best experts on this subject based on the ideXlab platform.

  • A longitudinal study of human age-related ribosomal RNA Gene Activity as detected by silver-stained NORs
    Mechanisms of Ageing and Development, 1996
    Co-Authors: Samuel Thomas, Asit B. Mukherjee
    Abstract:

    The relative frequencies of silver-stained nucleolar organizing regions (Ag-NORs) as a function of age have been analyzed in skin fibroblasts derived from eight adult individuals participating in the Gerontology Research Center (GRO) Longitudinal Study, NIA, Baltimore, MD. Since silver staining of NORs is correlated with rRNA Gene Activity, we used this cytological method to examine the pattern of rRNA Gene Activity in specific individuals, each at two different ages. Our results show that the average number of Ag-NORs/cell decreases significantly with advancing age of each individual, presumably indicating a General pattern of age-related decline/alteration in rRNA Gene Activity and this pattern is individual-specific. The findings of our longitudinal study is consistent with the results of previous cross-sectional (population) studies on rRNA Gene Activity as detected by Ag-NORs. However, it appears that the relative rate in the age-related decline of rRNA Gene Activity, as evidenced by lower Ag-NOR frequencies with age, is variable from person to person.

John J. Fortin - One of the best experts on this subject based on the ideXlab platform.

A Preiss - One of the best experts on this subject based on the ideXlab platform.

  • Neural hyperplasia induced by RNA interference with m4/mα Gene Activity
    Mechanisms of Development, 2000
    Co-Authors: Anja C. Nagel, Y Apidianakis, I Wech, D Maier, C Delidakis, A Preiss
    Abstract:

    Abstract The E(spl) complex ( E(spl)-C ) contains three different classes of Genes that are downstream of Notch signaling. The bHLH Genes mediate the Notch signal by repressing proneural Gene Activity, for example during the singularization of mechanosensory organ precursor cells (SOPs). Genes of the second class, the E(spl) m4/mα family, antagonize this process if overexpressed. Here we show that this is based on dominant-negative effects since RNA interference gives neurogenic phenotypes indistinguishable from E(spl)-C mutations. Furthermore, a third member of the m4/mα Gene family, named bbu/tom , behaves differently with respect to RNA expression patterns, its regulation by Notch signaling and loss of function phenotypes.

  • Neural hyperplasia induced by RNA interference with m4/malpha Gene Activity.
    Mechanisms of development, 2000
    Co-Authors: A C Nagel, Y Apidianakis, I Wech, D Maier, C Delidakis, A Preiss
    Abstract:

    The E(spl) complex (E(spl)-C) contains three different classes of Genes that are downstream of Notch signaling. The bHLH Genes mediate the Notch signal by repressing proneural Gene Activity, for example during the singularization of mechanosensory organ precursor cells (SOPs). Genes of the second class, the E(spl) m4/malpha family, antagonize this process if overexpressed. Here we show that this is based on dominant-negative effects since RNA interference gives neurogenic phenotypes indistinguishable from E(spl)-C mutations. Furthermore, a third member of the m4/malpha Gene family, named bbu/tom, behaves differently with respect to RNA expression patterns, its regulation by Notch signaling and loss of function phenotypes.