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  • Oxford University Press (OUP)  (8)
  • 1
    In: Journal of Experimental Botany, Oxford University Press (OUP), Vol. 73, No. 7 ( 2022-04-05), p. 2222-2237
    Abstract: Cold stress is a major environmental factor affecting plant growth and development. Although some plants have developed resistance to cold stress, the molecular mechanisms underlying this process are poorly understood. Using genome-wide association mapping with 200 cotton accessions collected from different regions, we identified variations in the short chain alcohol dehydrogenase gene, GhSAD1, that responds to cold stress. Virus-induced gene silencing and overexpression in Arabidopsis revealed that GhSAD1 fulfils important roles in cold stress responses. Ectopic expression of a haploid genotype of GhSAD1 (GhSAD1HapB) in Arabidopsis increased cold tolerance. Silencing of GhSAD1HapB resulted in a decrease in abscisic acid (ABA) content. Conversely, overexpression of GhSAD1HapB increased ABA content. GhSAD1HapB regulates cold stress responses in cotton through modulation of C-repeat binding factor activity, which regulates ABA signalling. GhSAD1HapB induces the expression of COLD-REGULATED (COR) genes and increases the amount of metabolites associated with cold stress tolerance. Overexpression of GhSAD1HapB partially complements the phenotype of the Arabidopsis ABA2 mutant, aba2-1. Collectively, these findings increase our understanding of the mechanisms underlying GhSAD1-mediated cold stress responses in cotton.
    Type of Medium: Online Resource
    ISSN: 0022-0957 , 1460-2431
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1466717-4
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2021
    In:  Genome Biology and Evolution Vol. 13, No. 2 ( 2021-02-03)
    In: Genome Biology and Evolution, Oxford University Press (OUP), Vol. 13, No. 2 ( 2021-02-03)
    Abstract: Silver sillago, Sillago sihama is a member of the family Sillaginidae and found in all Chinese inshore waters. It is an emerging commercial marine aquaculture species in China. In this study, high-quality chromosome-level reference genome of S. sihama was first constructed using PacBio Sequel sequencing and high-throughput chromosome conformation capture (Hi-C) technique. A total of 66.16 Gb clean reads were generated by PacBio sequencing platforms. The genome-scale was 521.63 Mb with 556 contigs, and 13.54 Mb of contig N50 length. Additionally, Hi-C scaffolding of the genome resulted in 24 chromosomes containing 96.93% of the total assembled sequences. A total of 23,959 protein-coding genes were predicted in the genome, and 96.51% of the genes were functionally annotated in public databases. A total of 71.86 Mb repetitive elements were detected, accounting for 13.78% of the genome. The phylogenetic relationships of silver sillago with other teleosts showed that silver sillago was separated from the common ancestor of Sillago sinica ∼7.92 Ma. Comparative genomic analysis of silver sillago with other teleosts showed that 45 unique and 100 expansion gene families were identified in silver sillago. In this study, the genomic resources provide valuable reference genomes for functional genomics research of silver sillago.
    Type of Medium: Online Resource
    ISSN: 1759-6653
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2495328-3
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  • 3
    In: FEMS Microbiology Ecology, Oxford University Press (OUP), Vol. 91, No. 10 ( 2015-10), p. fiv112-
    Type of Medium: Online Resource
    ISSN: 1574-6941
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2015
    detail.hit.zdb_id: 1501712-6
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  • 4
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2016
    In:  Journal of Chromatographic Science
    In: Journal of Chromatographic Science, Oxford University Press (OUP)
    Type of Medium: Online Resource
    ISSN: 0021-9665 , 1945-239X
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2016
    detail.hit.zdb_id: 2044085-6
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  • 5
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 50, No. 18 ( 2022-10-14), p. 10586-10600
    Abstract: Type II toxin–antitoxin (TA) systems are widely distributed in bacterial and archaeal genomes and are involved in diverse critical cellular functions such as defense against phages, biofilm formation, persistence, and virulence. GCN5-related N-acetyltransferase (GNAT) toxin, with an acetyltransferase activity-dependent mechanism of translation inhibition, represents a relatively new and expanding family of type II TA toxins. We here describe a group of GNAT-Xre TA modules widely distributed among Pseudomonas species. We investigated PacTA (one of its members encoded by PA3270/PA3269) from Pseudomonas aeruginosa and demonstrated that the PacT toxin positively regulates iron acquisition in P. aeruginosa. Notably, other than arresting translation through acetylating aminoacyl-tRNAs, PacT can directly bind to Fur, a key ferric uptake regulator, to attenuate its DNA-binding affinity and thus permit the expression of downstream iron-acquisition-related genes. We further showed that the expression of the pacTA locus is upregulated in response to iron starvation and the absence of PacT causes biofilm formation defect, thereby attenuating pathogenesis. Overall, these findings reveal a novel regulatory mechanism of GNAT toxin that controls iron-uptake-related genes and contributes to bacterial virulence.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2023
    In:  Cerebral Cortex Vol. 33, No. 11 ( 2023-05-24), p. 7088-7099
    In: Cerebral Cortex, Oxford University Press (OUP), Vol. 33, No. 11 ( 2023-05-24), p. 7088-7099
    Abstract: Previous studies investigated the age-related positivity effect in terms of emotion perception and management, whereas little is known about whether the positivity effect is shown in emotion utilization (EU). If yes, the EU-related intrinsic functional connectivity and its age-associated alterations remain to be elucidated. In this study, we collected resting-state functional magnetic resonance imaging data from 62 healthy older adults and 72 undergraduates as well as their self-ratings of EU. By using the connectome-based predictive modeling (CPM) method, we constructed a predictive model of the positive relationship between EU self-ratings and resting-state functional connectivity. Lesion simulation analyses revealed that the medial-frontal network, default mode network, frontoparietal network, and subcortical regions played key roles in the EU-related CPM. Older subjects showed significantly higher EU self-ratings than undergraduates, which was associated with strengthened connectivity between the left dorsolateral prefrontal cortex and bilateral frontal poles, and between the left frontal pole and thalamus. A mediation analysis indicated that the age-related EU network mediated the age effect on EU self-ratings. Our findings extend previous research on the age-related “positivity effect” to the EU domain, suggesting that the positivity effect on the self-evaluation of EU is probably associated with emotion knowledge which accumulates with age.
    Type of Medium: Online Resource
    ISSN: 1047-3211 , 1460-2199
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1483485-6
    SSG: 12
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  • 7
    In: Genome Biology and Evolution, Oxford University Press (OUP), Vol. 13, No. 6 ( 2021-06-08)
    Abstract: The spotted scat, Scatophagus argus is a member of the family Scatophagidae found in Indo-Pacific coastal waters. It is an emerging commercial aquaculture species, particularly in East and Southeast Asia. In this study, the first chromosome-level genome of S. argus was constructed using PacBio and Hi-C sequencing technologies. The genome is 572.42 Mb, with a scaffold N50 of 24.67 Mb. Using Hi-C data, 563.28 Mb (98.67% of the genome) sequences were anchored and oriented in 24 chromosomes, ranging from 12.57 Mb to 30.38 Mb. The assembly is of high integrity, containing 94.26% conserved single-copy orthologues, based on BUSCO analysis. A total of 24,256 protein-coding genes were predicted in the genome, and 96.30% of the predicted genes were functionally annotated. Evolutionary analysis showed that S. argus diverged from the common ancestor of Japanese puffer (Takifugu rubripes) approximately 114.8 Ma. The chromosomes of S. argus showed significant correlation to T. rubripes chromosomes. A comparative genomic analysis identified 49 unique and 90 expanded gene families. These genomic resources provide a solid foundation for functional genomics studies to decipher the economic traits of this species.
    Type of Medium: Online Resource
    ISSN: 1759-6653
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2495328-3
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  • 8
    In: Bioinformatics, Oxford University Press (OUP), Vol. 30, No. 4 ( 2014-02-15), p. 581-583
    Abstract: Summary: Experimental MSn mass spectral libraries currently do not adequately cover chemical space. This limits the robust annotation of metabolites in metabolomics studies of complex biological samples. In silico fragmentation libraries would improve the identification of compounds from experimental multistage fragmentation data when experimental reference data are unavailable. Here, we present a freely available software package to automatically control Mass Frontier software to construct in silico mass spectral libraries and to perform spectral matching. Based on two case studies, we have demonstrated that high-throughput automation of Mass Frontier allows researchers to generate in silico mass spectral libraries in an automated and high-throughput fashion with little or no human intervention required. Availability and implementation: Documentation, examples, results and source code are available at http://www.biosciences-labs.bham.ac.uk/viant/hammer/. Contact:  m.viant@bham.ac.uk Supplementary information:  Supplementary data are available at Bioinformatics online.
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2014
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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