scholarly journals The Eucalyptus Tonoplast Intrinsic Protein (TIP) Gene Subfamily: Genomic Organization, Structural Features, and Expression Profiles

2016 ◽  
Vol 7 ◽  
Author(s):  
Marcela I. Rodrigues ◽  
Agnes A. S. Takeda ◽  
Juliana P. Bravo ◽  
Ivan G. Maia
Keyword(s):  
Genomic Organization ◽  
Expression Profiles ◽  
Structural Features ◽  
Tonoplast Intrinsic Protein ◽  
Intrinsic Protein ◽  
Gene Subfamily

scholarly journals Tonoplast Intrinsic Protein Isoforms as Markers for Vacuolar Functions

1999 ◽  
Vol 11 (10) ◽  
pp. 1867-1882 ◽  
Author(s):  
Guang-Yuh Jauh ◽  
Thomas E. Phillips ◽  
John C. Rogers
Keyword(s):  
Protein Isoforms ◽  
Tonoplast Intrinsic Protein ◽  
Intrinsic Protein

scholarly journals Identification, characterization, and quantitative expression analysis of rainbow trout myostatin-1a and myostatin-1b genes

2006 ◽  
Vol 190 (3) ◽  
pp. 879-888 ◽  
Author(s):  
Dilip K Garikipati ◽  
Scott A Gahr ◽  
Buel D Rodgers
Keyword(s):  
Rainbow Trout ◽  
Genomic Organization ◽  
Expression Profiles ◽  
Muscle Growth ◽  
Fish Tissue ◽  
Tissue Expression ◽  
Negative Regulator ◽  
Cdna Clones ◽  
Mrna Levels ◽  
Quantitative Expression

Myostatin is a potent negative regulator of skeletal muscle growth. Although several cDNA clones have been characterized in different vertebrates, the genomic organization and bioactivity of non-mammalian homologs have not. The intron/exon organization and promoter subsequence analysis of two rainbow trout myostatin genes, rtMSTN-1a and rtMSTN-1b (formerly 1 and 2 respectively), as well as a quantitative assessment of their embryonic, larval, and adult tissue expression profiles are reported herein. Each gene was similarly organized into three exons of 490, 368, and 1600 bp for MSTN-1a and 486, 386, and 1419 bp for MSTN-1b. Comparative mapping of coding regions from several vertebrate myostatin genes revealed a common organization between species, including conserved pre-mRNA splice sites; the first among the fishes and the second across all vertebrate species. In silico subsequence analysis of the promoter regions identified E-boxes and other putative myogenic response elements. However, the number and diversity of elements were considerably less than those found in mammalian promoters or in the recently characterized zebrafish MSTN-2 gene. A quantitative analysis of the embryonic expression profile for both genes indicates that rtMSTN-1a expression is consistently greater than that of rtMSTN-1b and neither gene is significantly expressed throughout gastrulation. Expression of both steadily increases fourfold during somitogenesis and subsides as this period ends. After eyeing, however, rtMSTN-1a mRNA levels ultimately rise 20-fold by day 49 and peak before hatching and yolk sac absorption (YSA). Levels of rtMSTN-1b rise similarly, but do not peak before YSA. An analysis of adult (2-year-old fish) tissue expression indicates that both transcripts are present in most tissues although levels are highest in brain, testes, eyes, muscle, and surprisingly spleen. These studies suggest that strong selective pressures have preserved the genomic organization of myostatin genes throughout evolution. However, the different expression profiles and putative promoter elements in fishes versus mammals suggests that limitations in myostatin function may have evolved recently.

scholarly journals  -Tonoplast intrinsic protein defines unique plant vacuole functions

1998 ◽  
Vol 95 (22) ◽  
pp. 12995-12999 ◽  
Author(s):  
G.-Y. Jauh ◽  
A. M. Fischer ◽  
H. D. Grimes ◽  
C. A. Ryan ◽  
J. C. Rogers
Keyword(s):  
Tonoplast Intrinsic Protein ◽  
Intrinsic Protein ◽  
Plant Vacuole

scholarly journals Why Polyphenols have Promiscuous Actions? An Investigation by Chemical Bioinformatics

2016 ◽  
Vol 11 (5) ◽  
pp. 1934578X1601100
Author(s):  
Guang-Yan Tang
Keyword(s):  
Redox Potential ◽  
Bioinformatics Analysis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Critical Factor ◽  
Structural Features ◽  
Molecular Structures ◽  
Pharmacological Effects ◽  
Protein Targets ◽  
Structure Activity

Despite their diverse pharmacological effects, polyphenols are poor for use as drugs, which have been traditionally ascribed to their low bioavailability. However, Baell and co-workers recently proposed that the redox potential of polyphenols also plays an important role in this, because redox reactions bring promiscuous actions on various protein targets and thus produce non-specific pharmacological effects. To investigate whether the redox reactivity behaves as a critical factor in polyphenol promiscuity, we performed a chemical bioinformatics analysis on the structure-activity relationships of twenty polyphenols. It was found that the gene expression profiles of human cell lines induced by polyphenols were not correlated with the presence or not of redox moieties in the polyphenols, but significantly correlated with their molecular structures. Therefore, it is concluded that the promiscuous actions of polyphenols are likely to result from their inherent structural features rather than their redox potential.

ASSOCIATION OF FEATURE GENE EXPRESSION WITH STRUCTURAL FINGERPRINTS OF CHEMICAL COMPOUNDS

2011 ◽  
Vol 09 (04) ◽  
pp. 503-519 ◽  
Author(s):  
YUN LI ◽  
KANG TU ◽  
SIYUAN ZHENG ◽  
JINGFANG WANG ◽  
YIXUE LI ◽  
...  
Keyword(s):  
Gene Expression ◽  
Structural Information ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Structural Difference ◽  
Structural Features ◽  
Molecular Structures ◽  
Transcriptomics Data ◽  
Function Relationship ◽  
Relationship Of

Exploring the relationship between a chemical structure and its biological function is of great importance for drug discovery. For understanding the mechanisms of drug action, researchers traditionally focused on the molecular structures in the context of interactions with targets. The newly emerged high-throughput "omics" technology opened a new dimension to study the structure–function relationship of chemicals. Previous studies made attempts to introduce transcriptomics data into chemical function investigation. But little effort has been made to link structural fingerprints of compounds with defined intracellular functions, i.e. expression of particular genes and altered pathways. By integrating the chemical structural information with the gene expression profiles of chemical-treated cells, we developed a novel method to associate the structural difference between compounds with the expression of a definite set of genes, which were called feature genes. A subtraction protocol was designed to extract a minimum gene set related to chemical structural features, which can be utilized in practice as markers for drug screening. Case studies demonstrated that our approach is capable of finding feature genes associated with chemical structural fingerprints.

Genomic organization, phylogenetic comparison and expression profiles of annexin gene family in tomato (Solanum lycopersicum)

Gene ◽  
2012 ◽  
Vol 499 (1) ◽  
pp. 14-24 ◽  
Author(s):  
Yongen Lu ◽  
Bo Ouyang ◽  
Junhong Zhang ◽  
Taotao Wang ◽  
Chen Lu ◽  
...  
Keyword(s):  
Gene Family ◽  
Solanum Lycopersicum ◽  
Genomic Organization ◽  
Expression Profiles ◽  
Phylogenetic Comparison ◽  
Annexin Gene

scholarly journals Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11052
Author(s):  
Sushma Naithani ◽  
Daemon Dikeman ◽  
Priyanka Garg ◽  
Noor Al-Bader ◽  
Pankaj Jaiswal
Keyword(s):  
Gene Ontology ◽  
Abiotic Stress ◽  
Differential Expression ◽  
Functional Annotation ◽  
Expression Profiles ◽  
Abiotic Stress Tolerance ◽  
Family Members ◽  
Gene Families ◽  
Structural Features ◽  
Response Expression

The S-domain subfamily of receptor-like kinases (SDRLKs) in plants is poorly characterized. Most members of this subfamily are currently assigned gene function based on the S-locus Receptor Kinase from Brassica that acts as the female determinant of self-incompatibility (SI). However, Brassica like SI mechanisms does not exist in most plants. Thus, automated Gene Ontology (GO) pipelines are not sufficient for functional annotation of SDRLK subfamily members and lead to erroneous association with the GO biological process of SI. Here, we show that manual bio-curation can help to correct and improve the gene annotations and association with relevant biological processes. Using publicly available genomic and transcriptome datasets, we conducted a detailed analysis of the expansion of the rice (Oryza sativa) SDRLK subfamily, the structure of individual genes and proteins, and their expression.The 144-member SDRLK family in rice consists of 82 receptor-like kinases (RLKs) (67 full-length, 15 truncated),12 receptor-like proteins, 14 SD kinases, 26 kinase-like and 10 GnK2 domain-containing kinases and RLKs. Except for nine genes, all other SDRLK family members are transcribed in rice, but they vary in their tissue-specific and stress-response expression profiles. Furthermore, 98 genes show differential expression under biotic stress and 98 genes show differential expression under abiotic stress conditions, but share 81 genes in common.Our analysis led to the identification of candidate genes likely to play important roles in plant development, pathogen resistance, and abiotic stress tolerance. We propose a nomenclature for 144 SDRLK gene family members based on gene/protein conserved structural features, gene expression profiles, and literature review. Our biocuration approach, rooted in the principles of findability, accessibility, interoperability and reusability, sets forth an example of how manual annotation of large-gene families can fill in the knowledge gap that exists due to the implementation of automated GO projections, thereby helping to improve the quality and contents of public databases.

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