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Lee M.Y.,University of Nevada, Reno | Lee M.Y.,Wonkwang University | Park C.,University of Nevada, Reno | Berent R.M.,University of Nevada, Reno | And 12 more authors.
PLoS ONE | Year: 2015

Genome-scale expression data on the absolute numbers of gene isoforms offers essential clues in cellular functions and biological processes. Smooth muscle cells (SMCs) perform a unique contractile function through expression of specific genes controlled by serum response factor (SRF), a transcription factor that binds to DNA sites known as the CArG boxes. To identify SRF-regulated genes specifically expressed in SMCs, we isolated SMC populations from mouse small intestine and colon, obtained their transcriptomes, and constructed an interactive SMC genome and CArGome browser. To our knowledge, this is the first online resource that provides a comprehensive library of all genetic transcripts expressed in primary SMCs. The browser also serves as the first genome-wide map of SRF binding sites. The browser analysis revealed novel SMC-specific transcriptional variants and SRF target genes, which provided new and unique insights into the cellular and biological functions of the cells in gastrointestinal (GI) physiology. The SRF target genes in SMCs, which were discovered in silico, were confirmed by proteomic analysis of SMC-specific Srf knockout mice. Our genome browser offers a new perspective into the alternative expression of genes in the context of SRF binding sites in SMCs and provides a valuable reference for future functional studies. Copyright: © 2015 Lee et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Hebert S.S.,Laval University | Wang W.-X.,University of Kentucky | Zhu Q.,LC science | Nelson P.T.,University of Kentucky
Journal of Alzheimer's Disease | Year: 2013

MicroRNAs (miRNAs) are small (20-22 nucleotides) regulatory non-coding RNAs that strongly influence gene expression. Most prior studies addressing the role of miRNAs in neurodegenerative diseases (NDs) have focused on individual diseases such as Alzheimer's disease (AD), making disease-to-disease comparisons impossible. Using RNA deep sequencing, we sought to analyze in detail the small RNAs (including miRNAs) in the temporal neocortex gray matter from non-demented controls (n = 2), AD (n = 5), dementia with Lewy bodies (n = 4), hippocampal sclerosis of aging (n = 4), and frontotemporal lobar dementia (FTLD) (n = 5) cases, together accounting for the most prevalent ND subtypes. All cases had short postmortem intervals, relatively high-quality RNA, and state-of-the-art neuropathological diagnoses. The resulting data (over 113 million reads in total, averaging 5.6 million reads per sample) and secondary expression analyses constitute an unprecedented look into the human cerebral cortical miRNome at a nucleotide resolution. While we find no apparent changes in isomiR or miRNA editing patterns in correlation with ND pathology, our results validate and extend previous miRNA profiling studies with regard to quantitative changes in NDs. In agreement with this idea, we provide independent cohort validation for changes in miR-132 expression levels in AD (n = 8) and FTLD (n = 14) cases when compared to controls (n = 8). The identification of common and ND-specific putative novel brain miRNAs and/or short-hairpin molecules is also presented. The challenge now is to better understand the impact of these and other alterations on neuronal gene expression networks and neuropathologies. © 2013 - IOS Press and the authors. All rights reserved.


Lang Q.,Zhejiang University | Lang Q.,Zhejiang Sci-Tech University | Jin C.,Zhejiang Sci-Tech University | Gao X.,LC science | And 5 more authors.
Journal of Nanoscience and Nanotechnology | Year: 2011

Cucumber mosaic virus (CMV) is widely spread worldwide, causing typical systemic mosaic and other symptoms in tomato (Solanum lycopersicum). Host responses to CMV and molecular mechanisms associated with the development of disease symptoms caused by this virus in tomato are largely unexplored. To investigate plant responses activated during this interaction, we used microarray analysis to monitor changes in host gene expression during disease development. Compared with genes from mock-inoculated control plants, seedlings to adults, 214 of the 3313 tomato genes represented on the array were differentially expressed in CMV-infected plants. Functional classification of CMV-responsive genes revealed that CMV activated typical basal defense responses in the host during the infection process, including induction of defense-related genes, production and scavenging of free oxygen radicals, and hormone synthesis. CMV infection also suppressed a subset of host genes involved in photosynthesis and metabolism. Our results indicate that a wide range of genes play an important role in regulation of the tomato susceptibility response to CMV. Copyright © 2011 American Scientific Publishers.


Liu Z.,Hunan Normal University | Zhu Q.,LC science | Hu W.,Hunan Normal University | Liang S.,Hunan Normal University
Protein and Peptide Letters | Year: 2013

Hainantoxin-III (HNTX-III) purified from the venom of the spider Ornithoctonus hainana is a novel neurotoxin preferentially inhibiting tetrodotoxin-sensitive voltage-gated sodium channels in rat dorsal root ganglion cells. The structure of this toxin in aqueous solution was investigated using 2-D 1H-NMR techniques. The complete sequencespecific assignments of proton resonances in the 1H-NMR spectra were obtained by analyzing a series of 2-D spectra, including DQF-COSY, TOCSY and NOESY spectra, in H 2O or D2O. All the backbone protons and more than 95% of the side-chain protons have been assigned by dαN, d βN, and dNN connectivities in NOESY spectrum. Furthermore, the secondary structure of HNTX-III was identified from NMR data. It consists mainly of a short triple-stranded antiparallel sheet formed by Asp7 to Cys9, Tyr21 to Ser23, and Lys27 to Val30. Because HNTX-III shares high sequence identity (>70%) with HWTX-I and HNTX-I, we proposed that they all share a structural scaffold known as the inhibitor cystine knot architectural motif. This study provides a basis for the further determination of the solution conformation of HNTX-III. © 2013 Bentham Science Publishers.


Krishnamoorthy S.,University of Houston | Liu Z.,University of Houston | Liu Z.,Hunan Normal University | Hong A.,LC science | And 5 more authors.
PLoS ONE | Year: 2013

The architecture of cellular proteins connected to form signaling pathways in response to internal and external cues is much more complex than a group of simple protein-protein interactions. Post translational modifications on proteins (e.g., phosphorylation of serine, threonine and tyrosine residues on proteins) initiate many downstream signaling events leading to protein-protein interactions and subsequent activation of signaling cascades leading to cell proliferation, cell differentiation and cell death. As evidenced by a rapidly expanding mass spectrometry database demonstrating protein phosphorylation at specific motifs, there is currently a large gap in understanding the functional significance of phosphoproteins with respect to their specific protein connections in the signaling cascades. A comprehensive map that interconnects phospho-motifs in pathways will enable identification of nodal protein interactions that are sensitive signatures indicating a disease phenotype from the physiological hemostasis and provide clues into control of disease. Using a novel phosphopeptide microarray technology, we have mapped endogenous tyrosine-phosphoproteome interaction networks in breast cancer cells mediated by signaling adaptor protein GRB2, which transduces cellular responses downstream of several RTKs through the Ras-ERK signaling cascade. We have identified several previously reported motif specific interactions and novel interactions. The peptide microarray data indicate that various phospho-motifs on a single protein are differentially regulated in various cell types and shows global downregulation of phosphoprotein interactions specifically in cells with metastatic potential. The study has revealed novel phosphoprotein mediated signaling networks, which warrants further detailed analysis of the nodes of protein-protein interaction to uncover their biomarker or therapeutic potential. © 2013 Krishnamoorthy et al.

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