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  • Oxford University Press  (34)
  • Blackwell Publishing Ltd  (7)
  • 2010-2014  (30)
  • 1985-1989  (11)
  • 1
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    Structural analysis of the yeast Dhh1-Pat1 complex reveals how Dhh1 engages Pat1, Edc3 and RNA in mutually exclusive interactions (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-26
    Description: Translational repression and deadenylation of eukaryotic mRNAs result either in the sequestration of the transcripts in a nontranslatable pool or in their degradation. Removal of the 5' cap structure is a crucial step that commits deadenylated mRNAs to 5'-to-3' degradation. Pat1, Edc3 and the DEAD-box protein Dhh1 are evolutionary conserved factors known to participate in both translational repression and decapping, but their interplay is currently unclear. We report the 2.8 Å resolution structure of yeast Dhh1 bound to the N-terminal domain of Pat1. The structure shows how Pat1 wraps around the C-terminal RecA domain of Dhh1, docking onto the Phe-Asp-Phe (FDF) binding site. The FDF-binding site of Dhh1 also recognizes Edc3, revealing why the binding of Pat1 and Edc3 on Dhh1 are mutually exclusive events. Using co-immunoprecipitation assays and structure-based mutants, we demonstrate that the mode of Dhh1-Pat1 recognition is conserved in humans. Pat1 and Edc3 also interfere and compete with the RNA-binding properties of Dhh1. Mapping the RNA-binding sites on Dhh1 with a crosslinking–mass spectrometry approach shows a large RNA-binding surface around the C-terminal RecA domain, including the FDF-binding pocket. The results suggest a model for how Dhh1-containing messenger ribonucleoprotein particles might be remodeled upon Pat1 and Edc3 binding.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions (2012)
    Oxford University Press
    Details
    Publication Date: 2012-03-14
    Description: The Gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria ( Xcv ) is an important model to elucidate the mechanisms involved in the interaction with the host. To gain insight into the transcriptome of the Xcv strain 85–10, we took a differential RNA sequencing (dRNA-seq) approach. Using a novel method to automatically generate comprehensive transcription start site (TSS) maps we report 1421 putative TSSs in the Xcv genome. Genes in Xcv exhibit a poorly conserved –10 promoter element and no consensus Shine-Dalgarno sequence. Moreover, 14% of all mRNAs are leaderless and 13% of them have unusually long 5'-UTRs. Northern blot analyses confirmed 16 intergenic small RNAs and seven cis -encoded antisense RNAs in Xcv . Expression of eight intergenic transcripts was controlled by HrpG and HrpX, key regulators of the Xcv type III secretion system. More detailed characterization identified sX12 as a small RNA that controls virulence of Xcv by affecting the interaction of the pathogen and its host plants. The transcriptional landscape of Xcv is unexpectedly complex, featuring abundant antisense transcripts, alternative TSSs and clade-specific small RNAs.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Evaluating Topological Conflict in Centipede Phylogeny Using Transcriptomic Data Sets (2014)
    Oxford University Press
    Details
    Publication Date: 2014-05-24
    Description: Relationships between the five extant orders of centipedes have been considered solved based on morphology. Phylogenies based on samples of up to a few dozen genes have largely been congruent with the morphological tree apart from an alternative placement of one order, the relictual Craterostigmomorpha, consisting of two species in Tasmania and New Zealand. To address this incongruence, novel transcriptomic data were generated to sample all five orders of centipedes and also used as a test case for studying gene-tree incongruence. Maximum likelihood and Bayesian mixture model analyses of a data set composed of 1,934 orthologs with 45% missing data, as well as the 389 orthologs in the least saturated, stationary quartile, retrieve strong support for a sister-group relationship between Craterostigmomorpha and all other pleurostigmophoran centipedes, of which the latter group is newly named Amalpighiata. The Amalpighiata hypothesis, which shows little gene-tree incongruence and is robust to the influence of among-taxon compositional heterogeneity, implies convergent evolution in several morphological and behavioral characters traditionally used in centipede phylogenetics, such as maternal brood care, but accords with patterns of first appearances in the fossil record.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Correlation of hyaluronan deposition with infiltration of eosinophils and lymphocytes in a cockroach-induced murine model of asthma (2012)
    Oxford University Press
    Details
    Publication Date: 2012-11-24
    Description: Asthma is a chronic inflammatory disease that exhibits airway remodeling with changes in the extracellular matrix (ECM). The role of the ECM in mediating these changes is poorly understood. Hyaluronan (HA), a major component of the ECM, has been implicated in many biological processes in diseases. This study investigates the processes involved in HA synthesis, deposition and localization during the propagation of cockroach-induced asthma. Mice were sensitized and challenged with cockroach antigen, and sacrificed at various time points during an 8-week challenge protocol. Analysis of bronchoalveolar lavage (BAL) fluid revealed an increase in total nucleated cells as early as 6 h, which peaked at 6 days. Histopathologic analysis of the lung tissue revealed an influx of inflammatory cells at the peribronchial and perivascular regions starting at 12 h, which peaked at 6 days and persisted to 8 weeks. Eosinophils predominated in the early time points while lymphocytes predominated during the late time points. Quantitative polymerase chain reaction (PCR) data showed that hyaluronan synthase 1 (HAS1) mRNA peaked within 6 h and then declined. HAS2 mRNA also peaked within 6 h but remained elevated throughout the 8-week exposure course. HA levels in lung tissue and BAL increased at 12 h and peaked by 6 and 8 days, respectively. Inflammatory cells and new collagen formation localized in areas of HA deposition. Taken together, these data support a role for HA in the pathogenesis in asthma.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    SMMRNA: a database of small molecule modulators of RNA (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-29
    Description: We have developed SMMRNA, an interactive database, available at http://www.smmrna.org , with special focus on small molecule ligands targeting RNA. Currently, SMMRNA consists of ~770 unique ligands along with structural images of RNA molecules. Each ligand in the SMMRNA contains information such as Kd, Ki, IC50, Tm, molecular weight (MW), hydrogen donor and acceptor count, XlogP, number of rotatable bonds, number of aromatic rings and 2D and 3D structures. These parameters can be explored using text search, advanced search, substructure and similarity-based analysis tools that are embedded in SMMRNA. A structure editor is provided for 3D visualization of ligands. Advance analysis can be performed using substructure and OpenBabel-based chemical similarity fingerprints. Upload facility for both RNA and ligands is also provided. The physicochemical properties of the ligands were further examined using OpenBabel descriptors, hierarchical clustering, binning partition and multidimensional scaling. We have also generated a 3D conformation database of ligands to support the structure and ligand-based screening. SMMRNA provides comprehensive resource for further design, development and refinement of small molecule modulators for selective targeting of RNA molecules.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
    Electronic Resource
    Electronic Resource
    Multivariate Analysis in Relation to Genetic Improvement in Lavender, Lavandula officinalis Chaix (1989)
    Oxford, UK : Blackwell Publishing Ltd
    Plant breeding 102 (1989), S. 0 
    Details
    ISSN: 1439-0523
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Forty-three genotypes of lavender, Lavandula officinalis Chaix, comprising 20 parental stocks including variety ‘Karlovo’, and 23 promising clones were subjected to genetic divergence analysis by Mahalanobis D2 statistics. All the clones were grouped in 12 clusters. Intracluster D2 was highest for cluster × followed by cluster IX and I. Highest intercluster D2 value was observed between cluster VII and IX. Major emphasis was given to including Sher-i-Kashmir, B 10, E 2, A3 and one from each cluster I, II, V, VII, VIII and × for polycross for maximum chance of transgressive segregants of practical utility.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1439-0523.1989.tb01259.x
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  • 7
    Electronic Resource
    Electronic Resource
    Inheritance of Isoproturon Tolerance in Durum Wheat Transferred from Triticum monococcum (1989)
    Oxford, UK : Blackwell Publishing Ltd
    Plant breeding 102 (1989), S. 0 
    Details
    ISSN: 1439-0523
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: The inheritance of isoproturon tolerance exhibited by the selected progenies of durum wheat was investigated. This tolerance to the herbicide isoproturon had been transferred from Triticum monococcum to durum wheat cultivars. It was shown to be conditioned by a single dominant gene
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1439-0523.1989.tb00331.x
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  • 8
    Electronic Resource
    Electronic Resource
    The Rhizobium meliloti host range nodQ gene encodes a protein which shares homology with translation elongation and initiation factors. (1989)
    Oxford, UK : Blackwell Publishing Ltd
    Molecular microbiology 3 (1989), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: The Rhizobium meliloti nod region lib is involved in host-range determination: (i)the presence of region lib is necessary for transfer of alfalfa root hair curling ability to Rhizobium legumlnosarum biovar trifolii; (ii) a mutation in region llb extends the R. meliloti infection host range to Vicia sativa nigra; (iii) dominance of R. meliloti nod genes over R. leguminosarum biovar viciae nod genes is abolished by mutations in region llb. The nucleotide sequence of this region has been determined. Genes corresponding to the two open reading frames identified are designated nodP and nodQ. The predicted amino acid sequence of the NodQ protein shows homology with translation initiation and elongation factors. The consensus sequence involved in the GTP-binding domain is conserved.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-2958.1989.tb00223.x
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  • 9
    Electronic Resource
    Electronic Resource
    COMPLETE CODING REGION SEQUENCE OF Eβk cDNA CLONES: LACK OF POLYMORPHISM IN THE NH2-TERMINUS BETWEEN Eβk AND Eβb MOLECULES (1988)
    Oxford, UK : Blackwell Publishing Ltd
    International journal of immunogenetics 15 (1988), S. 0 
    Details
    ISSN: 1744-313X
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Sequence analysis of two independently isolated Eβk cDNA clones revealed that the Eβk molecule is identical to the Eβb molecule at the NH2-terminus. These data resolve a discrepancy between previously published amino acid and nucleotide sequences and indicate that the Eβ NH2-terminus is not as polymorphic as was once believed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1744-313X.1988.tb00423.x
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  • 10
    Electronic Resource
    Electronic Resource
    Effect of iron on early changes in Escherichia coli-induced ascending pyelonephritis in rats (1987)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 41 (1987), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Uptake of d-glucose, l-lysine and l-proline and the kinetic parameters of alkaline phosphatase and γ-glutamyl-transpeptidase were evaluated in renal brush border membrane (BBM) vesicles prepared from control, pyelonephritic and iron-administered pyelonephritic rats. The uptake of d-glucose and amino acids and Vmax of both the enzymes studied were found to be altered in pyelonephritic and iron-administered pyelonephritic rats, but changes appeared earlier and more severely in iron-administered infected animals than in other infected animals. These early physiological alterations were accompanied by higher bacterial colonisation in iron-administered rats.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1987.tb02214.x
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