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  • Oxford University Press (OUP)  (11)
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  • Oxford University Press (OUP)  (11)
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  • 1
    Online Resource
    Online Resource
    Microbial adaptation in vertical soil profiles contaminated by an antimony smelting plant
    Oxford University Press (OUP) ; 2020
    In:  FEMS Microbiology Ecology Vol. 96, No. 11 ( 2020-10-29)
    Details
    In: FEMS Microbiology Ecology, Oxford University Press (OUP), Vol. 96, No. 11 ( 2020-10-29)
    Abstract: Antimony mining has resulted in considerable pollution to the soil environment. Although studies on antinomy contamination have been conducted, its effects on vertical soil profiles and depth-resolved microbial communities remain unknown. The current study selected three vertical soil profiles (0–2 m) from the world's largest antimony mining area to characterize the depth-resolved soil microbiota and investigate the effects of mining contamination on microbial adaptation. Results demonstrated that contaminated soil profiles showed distinct depth-resolved effects when compared to uncontaminated soil profiles. As soil depth increased, the concentrations of antimony and arsenic gradually declined in the contaminated soil profiles. Acidobacteria, Chloroflexi, Proteobacteria and Thaumarchaeota were the most variable phyla from surface to deep soil. The co-occurrence networks were loosely connected in surface soil, but obviously recovered and were well-connected in deep soil. The metagenomic results indicated that microbial metabolic potential also changed with soil depth. Genes encoding C metabolism pathways were negatively correlated with antimony and arsenic concentrations. Abundances of arsenic-related genes were enriched by severe contamination, but reduced with soil depth. Overall, soil depth-resolved characteristics are often many meters deep and such effects affected the indigenous microbial communities, as well as their metabolic potential due to different contaminants along vertical depths.
    Type of Medium: Online Resource
    ISSN: 1574-6941
    URL: Article
    DOI: 10.1093/femsec/fiaa188
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1501712-6
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  • 2
    Online Resource
    Online Resource
    Bacteria responsible for antimonite oxidation in antimony-contaminated soil revealed by DNA-SIP coupled to metagenomics
    Oxford University Press (OUP) ; 2021
    In:  FEMS Microbiology Ecology Vol. 97, No. 5 ( 2021-04-13)
    Details
    In: FEMS Microbiology Ecology, Oxford University Press (OUP), Vol. 97, No. 5 ( 2021-04-13)
    Abstract: Antimony (Sb), the analog of arsenic (As), is a toxic metalloid that poses risks to the environment and human health. Antimonite (Sb(III)) oxidation can decrease Sb toxicity, which contributes to the bioremediation of Sb contamination. Bacteria can oxidize Sb(III), but the current knowledge regarding Sb(III)-oxidizing bacteria (SbOB) is limited to pure culture studies, thus underestimating the diversity of SbOB. In this study, Sb(III)-oxidizing microcosms were set up using Sb-contaminated rice paddies as inocula. Sb(III) oxidation driven by microorganisms was observed in the microcosms. The increasing copies and transcription of the arsenate-oxidizing gene, aioA, in the microcosms during biotic Sb(III) oxidation indicated that microorganisms mediated Sb(III) oxidation via the aioA genes. Furthermore, a novel combination of DNA-SIP and shotgun metagenomic was applied to identify the SbOB and predict their metabolic potential. Several putative SbOB were identified, including Paracoccus, Rhizobium, Achromobacter and Hydrogenophaga. Furthermore, the metagenomic analysis indicated that all of these putative SbOB contained aioA genes, confirming their roles in Sb(III) oxidation. These results suggested the concept of proof of combining DNA-SIP and shotgun metagenomics directly. In addition, the identification of the novel putative SbOB expands the current knowledge regarding the diversity of SbOB.
    Type of Medium: Online Resource
    ISSN: 0168-6496 , 1574-6941
    URL: Article
    DOI: 10.1093/femsec/fiab057
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1501712-6
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Effects of fermented wheat bran and yeast culture on growth performance, immunity, and intestinal microflora in growing-finishing pigs
    Oxford University Press (OUP) ; 2021
    In:  Journal of Animal Science Vol. 99, No. 11 ( 2021-11-01)
    Details
    In: Journal of Animal Science, Oxford University Press (OUP), Vol. 99, No. 11 ( 2021-11-01)
    Abstract: This study was conducted to evaluate the effects of feeding fermented wheat bran (FWB) and yeast culture (YC) on growth performance, immune levels, and intestinal microflora in growing-finishing pigs. In total, 96 crossbred pigs were randomly distributed into four treatments with four replicates pens and six pigs per pen. This study was performed using a 2 × 2 factor design: 1) CON (basal diet), 2) FWB (basal diet + 5% FWB), 3) YC (basal diet + 2% YC), and 4) FWB + YC (basal diet + 5% FWB + 2% YC). Dietary FWB supplementation significantly increased the average daily gain and significantly decreased the feed gain ratio of growing-finishing pigs (P & lt; 0.05). Supplementation of FWB and YC improved the immune capacity and reduced the inflammation level of growing-finishing pigs (P & lt; 0.05). In addition, pigs fed FWB, YC, and FWB + YC diets showed better intestinal development and morphology compared with those CON pigs. The relative abundance of Streptococcus in the FWB group was significantly lower than that in the CON group (P & lt; 0.05), and the relative abundance of probiotics (unclassified_f_Lachnospiraceae, Turicibacter) increased significantly (P & lt; 0.05). Furthermore, the relative abundance of probiotics (Lactobacillus, norank_f_Muribaculaceae) in the YC group was significantly increased compared with the CON group (P & lt; 0.05). The results of this study observed positive effects of FWB and YC on growing-finishing pigs, which provides insights into the application of biological feed in swine industry.
    Type of Medium: Online Resource
    ISSN: 0021-8812 , 1525-3163
    URL: Article
    DOI: 10.1093/jas/skab308
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1490550-4
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Multiomics comparison among populations of three plant sources of Amomi Fructus
    Oxford University Press (OUP) ; 2023
    In:  Horticulture Research Vol. 10, No. 8 ( 2023-08-04)
    Details
    In: Horticulture Research, Oxford University Press (OUP), Vol. 10, No. 8 ( 2023-08-04)
    Abstract: Amomi Fructus (Sharen, AF) is a traditional Chinese medicine (TCM) from three source species (or varieties), including Wurfbainia villosa var. villosa (WVV), W. villosa var. xanthioides (WVX), or W. longiligularis (WL). Among them, WVV has been transplanted from its top-geoherb region, Guangdong, to its current main production area, Yunnan, for & gt;50 years in China. However, the genetic and transcriptomic differentiation among multiple AF source species (or varieties) and between the origin and transplanted populations of WVV is unknown. In our study, the observed overall higher expression of terpenoid biosynthesis genes in WVV than in WVX provided possible evidence for the better pharmacological effect of WVV. We also screened six candidate borneol dehydrogenases (BDHs) that potentially catalyzed borneol into camphor in WVV and functionally verified them. Highly expressed genes at the P2 stage of WVV, Wv05G1424 and Wv05G1438, were capable of catalyzing the formation of camphor from (+)-borneol, (−)-borneol and DL-isoborneol. Moreover, the BDH genes may experience independent evolution after acquiring the ancestral copies, and the following tandem duplications might account for the abundant camphor content in WVV. Furthermore, four populations of WVV, WVX, and WL are genetically differentiated, and the gene flow from WVX to WVV in Yunnan contributed to the greater genetic diversity in the introduced population (WVV-JH) than in its top-geoherb region (WVV-YC), which showed the lowest genetic diversity and might undergo genetic degradation. In addition, terpene synthesis (TPS) and BDH genes were selected among populations of multiple AF source species (or varieties) and between the top- and non-top-geoherb regions, which might explain the difference in metabolites between these populations. Our findings provide important guidance for the conservation, genetic improvement, and industrial development of the three source species (or varieties) and for identifying top-geoherbalism with molecular markers, and proper clinical application of AF.
    Type of Medium: Online Resource
    ISSN: 2052-7276
    URL: Article
    DOI: 10.1093/hr/uhad128
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2781828-7
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  • 5
    Online Resource
    Online Resource
    VARIDT 1.0: variability of drug transporter database
    Oxford University Press (OUP) ; 2020
    In:  Nucleic Acids Research Vol. 48, No. D1 ( 2020-01-08), p. D1042-D1050
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 48, No. D1 ( 2020-01-08), p. D1042-D1050
    Abstract: The absorption, distribution and excretion of drugs are largely determined by their transporters (DTs), the variability of which has thus attracted considerable attention. There are three aspects of variability: epigenetic regulation and genetic polymorphism, species/tissue/disease-specific DT abundances, and exogenous factors modulating DT activity. The variability data of each aspect are essential for clinical study, and a collective consideration among multiple aspects becomes crucial in precision medicine. However, no database is constructed to provide the comprehensive data of all aspects of DT variability. Herein, the Variability of Drug Transporter Database (VARIDT) was introduced to provide such data. First, 177 and 146 DTs were confirmed, for the first time, by the transporting drugs approved and in clinical/preclinical, respectively. Second, for the confirmed DTs, VARIDT comprehensively collected all aspects of their variability (23 947 DNA methylations, 7317 noncoding RNA/histone regulations, 1278 genetic polymorphisms, differential abundance profiles of 257 DTs in 21 781 patients/healthy individuals, expression of 245 DTs in 67 tissues of human/model organism, 1225 exogenous factors altering the activity of 148 DTs), which allowed mutual connection between any aspects. Due to huge amount of accumulated data, VARIDT made it possible to generalize characteristics to reveal disease etiology and optimize clinical treatment, and is freely accessible at: https://db.idrblab.org/varidt/ and http://varidt.idrblab.net/.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkz779
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Catalytically active atomically thin cuprate with periodic Cu single sites
    Oxford University Press (OUP) ; 2023
    In:  National Science Review Vol. 10, No. 1 ( 2023-01-14)
    Details
    In: National Science Review, Oxford University Press (OUP), Vol. 10, No. 1 ( 2023-01-14)
    Abstract: Rational design and synthesis of catalytically active two-dimensional (2D) materials with an abundance of atomically precise active sites in their basal planes remains a great challenge. Here, we report a ligand exchange strategy to exfoliate bulk [Cu4(OH)6][O3S(CH2)4SO3] cuprate crystals into atomically thin 2D cuprate layers ([Cu2(OH)3]+). The basal plane of 2D cuprate layers contains periodic arrays of accessible unsaturated Cu(II) single sites (2D-CuSSs), which are found to promote efficient oxidative Chan-Lam coupling. Our mechanistic studies reveal that the reactions proceed via coordinatively unsaturated CuO4(II) single sites with the formation of Cu(I) species in the rate-limiting step, as corroborated by both operando experimental and theoretical studies. The robust stability of 2D-CuSSs in both batch and continuous flow reactions, coupled wi th their recyclability and good performance in complex molecule derivatization, render 2D-CuSSs attractive catalyst candidates for broad utility in fine chemical synthesis.
    Type of Medium: Online Resource
    ISSN: 2095-5138 , 2053-714X
    URL: Article
    DOI: 10.1093/nsr/nwac100
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2745465-4
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  • 7
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    Online Resource
    Study of miRNA interactome in active rheumatoid arthritis patients reveals key pathogenic roles of dysbiosis in the infection–immune network
    Oxford University Press (OUP) ; 2021
    In:  Rheumatology Vol. 60, No. 3 ( 2021-03-02), p. 1512-1522
    Details
    In: Rheumatology, Oxford University Press (OUP), Vol. 60, No. 3 ( 2021-03-02), p. 1512-1522
    Abstract: To characterize serum microRNA (miR) and the miR interactome of active RA patients in RA aetiology and pathogenesis. Methods The differentially expressed miRs (DEmiRs) in serum of naïve active RA patients (NARAPs, n = 9, into three pools) vs healthy controls (HCs, n = 15, into five pools) were identified with Agilent human miR microarray analysis. Candidate driver genes in epigenetic and pathogenic signalling pathway modules for RA were analysed using miRTarBase and a molecular complex detection algorithm. The interactome of these DEmiRs in RA pathogenesis were further characterized with gene ontology and Kyoto Encyclopaedia of Genes and Genomes. Results Three upregulated DEmiRs (hsa-miR-187-5p, -4532, -4516) and eight downregulated DEmiRs (hsa-miR-125a-3p, -575, -191-3p, -6865-3p, -197-3p, -6886-3p, -1237-3p, -4436b-5p) were identified in NARAPs. Interactomic analysis from heterogeneous experimentally validated sources yielded 1719 miR–target interactions containing 5.67% strong and 94.33% less strong experimental evidence. Gene ontology and Kyoto Encyclopaedia of Genes and Genomes analyses allocated the upregulated DEmiRs in the infection modules and the downregulated DEmiRs in the immune signalling pathways. Specifically, these DEmiRs revealed the significant contributions of the intestinal microbiome dysbiosis in the infection–inflammation–immune network for activation of T cells, immune pathways of IL-17, Toll-like receptor, TNF, Janus kinase-signal transducer and activator of transcription, osteoclast cell differentiation pathway and IgA production to the active RA pathogenesis. Conclusions Our experiment-based interactomic study of DEmiRs in serum of NARAPs revealed novel clinically relevant miRs interactomes in the infection–inflammation–immune network of RA. These results provide valuable resources for understanding the integrated function of the miR network in RA pathogenesis and the application of circulating miRs as biomarkers for early aetiologic RA diagnosis.
    Type of Medium: Online Resource
    ISSN: 1462-0324 , 1462-0332
    URL: Article
    DOI: 10.1093/rheumatology/keaa369
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1474143-X
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  • 8
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    Programmable Single and Multiplex Base-Editing in Bombyx mori Using RNA-Guided Cytidine Deaminases
    Oxford University Press (OUP) ; 2018
    In:  G3 Genes|Genomes|Genetics Vol. 8, No. 5 ( 2018-05-01), p. 1701-1709
    Details
    In: G3 Genes|Genomes|Genetics, Oxford University Press (OUP), Vol. 8, No. 5 ( 2018-05-01), p. 1701-1709
    Abstract: Genome editing using standard tools (ZFN, TALEN, and CRISPR/Cas9) rely on double strand breaks to edit the genome. A series of new CRISPR tools that convert cytidine to thymine (C to T) without the requirement for DNA double-strand breaks was developed recently and quickly applied in a variety of organisms. Here, we demonstrate that CRISPR/Cas9-dependent base editor (BE3) converts C to T with a high frequency in the invertebrate Bombyx mori silkworm. Using BE3 as a knock-out tool, we inactivated exogenous and endogenous genes through base-editing-induced nonsense mutations with an efficiency of up to 66.2%. Furthermore, genome-scale analysis showed that 96.5% of B. mori genes have one or more targetable sites that can be edited by BE3 for inactivation, with a median of 11 sites per gene. The editing window of BE3 reached up to 13 bases (from C1 to C13 in the range of gRNA) in B. mori. Notably, up to 14 bases were substituted simultaneously in a single DNA molecule, with a low indel frequency of 0.6%, when 32 gRNAs were co-transfected. Collectively, our data show for the first time that RNA-guided cytidine deaminases are capable of programmable single and multiplex base editing in an invertebrate model.
    Type of Medium: Online Resource
    ISSN: 2160-1836
    URL: Article
    DOI: 10.1534/g3.118.200134
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2018
    detail.hit.zdb_id: 2629978-1
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  • 9
    Online Resource
    Online Resource
    VARIDT 1.0: variability of drug transporter database
    Oxford University Press (OUP) ; 2020
    In:  Nucleic Acids Research Vol. 48, No. D1 ( 2020-01-08), p. D1171-D1171
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 48, No. D1 ( 2020-01-08), p. D1171-D1171
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkz878
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 10
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    Biochemical evidence for a mitochondrial genetic modifier in the phenotypic manifestation of Leber’s hereditary optic neuropathy-associated mitochondrial DNA mutation
    Oxford University Press (OUP) ; 2016
    In:  Human Molecular Genetics Vol. 25, No. 16 ( 2016-08-15), p. 3613-3625
    Details
    In: Human Molecular Genetics, Oxford University Press (OUP), Vol. 25, No. 16 ( 2016-08-15), p. 3613-3625
    Type of Medium: Online Resource
    ISSN: 0964-6906 , 1460-2083
    URL: Article
    DOI: 10.1093/hmg/ddw199
    RVK:
    XA 10000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2016
    detail.hit.zdb_id: 1474816-2
    SSG: 12
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