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  • Oxford University Press (OUP)  (9)
  • 1
    Online Resource
    Online Resource
    Nutritional quality of different potassium efficiency types of vegetable soybean as affected by potassium nutrition
    Oxford University Press (OUP) ; 2022
    In:  Food Quality and Safety Vol. 6 ( 2022-01-01)
    Details
    In: Food Quality and Safety, Oxford University Press (OUP), Vol. 6 ( 2022-01-01)
    Abstract: Pot experiments were conducted in 2017, 2019, and 2020 to examine the effects of potassium nutrition on the nutritional components of vegetable soybeans with different K efficiency at immature and mature stages. Two vegetable soybean varieties with higher K efficiency and two varieties with lower K efficiency were studied in the low available K soil under the conditions of no K and normal K fertilization. The results indicated that almost all nutritional components in vegetable soybean were affected by K, genotypes, interannual differences, and their interactions. In general, no K fertilization increased protein and amino acid concentrations but decreased oil, soluble sugar, sucrose, K, Mg, and Fe concentrations in immature and mature vegetable soybean. The sensitivity of nutritional components to K nutrition differed among varieties. For instance, K high-efficiency varieties generally exhibited higher protein and amino acid concentrations without K application. K high-efficiency vegetable soybeans are low-K tolerance varieties to isoflavones. The results of this study provide insights for high yield and quality vegetable soybean breeding against soil K deficiency.
    Type of Medium: Online Resource
    ISSN: 2399-1399 , 2399-1402
    URL: Article
    DOI: 10.1093/fqsafe/fyab039
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2899899-6
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  • 2
    Online Resource
    Online Resource
    NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses
    Oxford University Press (OUP) ; 2020
    In:  Nucleic Acids Research Vol. 48, No. 14 ( 2020-08-20), p. e83-e83
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 48, No. 14 ( 2020-08-20), p. e83-e83
    Abstract: Mass spectrometry (MS)-based quantitative proteomics experiments frequently generate data with missing values, which may profoundly affect downstream analyses. A wide variety of imputation methods have been established to deal with the missing-value issue. To date, however, there is a scarcity of efficient, systematic, and easy-to-handle tools that are tailored for proteomics community. Herein, we developed a user-friendly and powerful stand-alone software, NAguideR, to enable implementation and evaluation of different missing value methods offered by 23 widely used missing-value imputation algorithms. NAguideR further evaluates data imputation results through classic computational criteria and, unprecedentedly, proteomic empirical criteria, such as quantitative consistency between different charge-states of the same peptide, different peptides belonging to the same proteins, and individual proteins participating protein complexes and functional interactions. We applied NAguideR into three label-free proteomic datasets featuring peptide-level, protein-level, and phosphoproteomic variables respectively, all generated by data independent acquisition mass spectrometry (DIA-MS) with substantial biological replicates. The results indicate that NAguideR is able to discriminate the optimal imputation methods that are facilitating DIA-MS experiments over those sub-optimal and low-performance algorithms. NAguideR further provides downloadable tables and figures supporting flexible data analysis and interpretation. NAguideR is freely available at http://www.omicsolution.org/wukong/NAguideR/ and the source code: https://github.com/wangshisheng/NAguideR/.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkaa498
    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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  • 3
    Online Resource
    Online Resource
    Tumor Size, Not Small Vessel Invasion, Predicts Survival in Patients With Hepatocellular Carcinoma
    Oxford University Press (OUP) ; 2022
    In:  American Journal of Clinical Pathology Vol. 158, No. 1 ( 2022-07-01), p. 70-80
    Details
    In: American Journal of Clinical Pathology, Oxford University Press (OUP), Vol. 158, No. 1 ( 2022-07-01), p. 70-80
    Abstract: The 8th edition American Joint Committee on Cancer (AJCC) staging system for hepatocellular carcinoma (HCC) has been criticized for failing to stratify patients. We aimed to reassess and modify the tumor staging criteria for HCC. Methods Three independent study cohorts were collected and analyzed. Results The initial cohort consists of 103 patients with HCC. By Kaplan-Meier survival analysis, the 8th edition failed to distinguish between T1b and T2. Only tumor size and large vessel invasion, but not small vessel invasion or other histopathologic parameters, predicted HCC survival. We modified the T staging criteria by eliminating small vessel invasion while emphasizing tumor size in the middle categories (T2 and T3), which achieved more even distribution of cases and significantly improved risk stratifications (P  & lt; .001). This modification was then validated in a cohort of 250 consecutive patients from Mount Sinai Hospital and an online Surveillance, Epidemiology, and End Results data set comprising 9,685 patients, which showed similar results. Small vessel invasion was not an independent prognostic factor in either validation cohort. Conclusions Our study showed that tumor size, but not small vessel invasion, predicts survival in patients with HCC. We suggest incorporating our modified T staging criteria in future AJCC revisions.
    Type of Medium: Online Resource
    ISSN: 0002-9173 , 1943-7722
    URL: Article
    DOI: 10.1093/ajcp/aqac001
    RVK:
    YV 2000
    RVK:
    XA 18700
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2039921-2
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  • 4
    Online Resource
    Online Resource
    Evolution of higher mesenchymal CD44 expression in the human lineage
    Oxford University Press (OUP) ; 2022
    In:  Evolution, Medicine, and Public Health Vol. 10, No. 1 ( 2022-01-05), p. 447-462
    Details
    In: Evolution, Medicine, and Public Health, Oxford University Press (OUP), Vol. 10, No. 1 ( 2022-01-05), p. 447-462
    Abstract: CD44 is an extracellular matrix receptor implicated in cancer progression. CD44 increases the invasibility of skin (SF) and endometrial stromal fibroblasts (ESF) by cancer and trophoblast cells. We reasoned that the evolution of CD44 expression can affect both, the fetal–maternal interaction through CD44 in ESF as well as vulnerability to malignant cancer through expression in SF. We studied the evolution of CD44 expression in mammalian SF and ESF and demonstrate that in the human lineage evolved higher CD44 expression. Isoform expression in cattle and human is very similar suggesting that differences in invasibility are not due to the nature of expressed isoforms. We then asked whether the concerted gene expression increase in both cell types is due to shared regulatory mechanisms or due to cell type-specific factors. Reporter gene experiments with cells and cis-regulatory elements from human and cattle show that the difference of CD44 expression is due to cis effects as well as cell type-specific trans effects. These results suggest that the concerted expression increase is likely due to selection acting on both cell types because the evolutionary change in cell type-specific factors requires selection on cell type-specific functions. This scenario implies that the malignancy enhancing effects of elevated CD44 expression in humans likely evolved as a side-effect of positive selection on a yet unidentified other function of CD44. A possible candidate is the anti-fibrotic effect of CD44 but there are no reliable data showing that humans and primates are less fibrotic than other mammals.
    Type of Medium: Online Resource
    ISSN: 2050-6201
    URL: Article
    DOI: 10.1093/emph/eoac036
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2684837-5
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  • 5
    Online Resource
    Online Resource
    Characterization and engineering of the Lrp/AsnC family regulator SACE_5717 for erythromycin overproduction in Saccharopolyspora erythraea
    Oxford University Press (OUP) ; 2019
    In:  Journal of Industrial Microbiology and Biotechnology Vol. 46, No. 7 ( 2019-07-01), p. 1013-1024
    Details
    In: Journal of Industrial Microbiology and Biotechnology, Oxford University Press (OUP), Vol. 46, No. 7 ( 2019-07-01), p. 1013-1024
    Abstract: In this work, we found that the Lrp/AsnC family protein SACE_5717 negatively regulated erythromycin biosynthesis in S. erythraea. Disruption of SACE_5717 led to a 27% improvement in the yield of erythromycin in S. erythraea A226. SACE_5717 directly repressed its own gene expression, as well as that of the adjacent gene SACE_5716 by binding to the target sequence 5′-GAACGTTCGCCGTCACGCC-3′. The predicted LysE superfamily protein SACE_5716 directly influenced the export of lysine, histidine, threonine and glycine in S. erythraea. Arginine, tyrosine and tryptophan were characterized as the effectors of SACE_5717 by weakening the binding affinity of SACE_5717. In the industrial S. erythraea WB strain, deletion of SACE_5717 (WBΔSACE_5717) increased erythromycin yield by 20%, and by 36% when SACE_5716 was overexpressed in WBΔSACE_5717 (WBΔSACE_5717/5716). In large-scale 5-L fermentation experiment, erythromycin yield in the engineered strain WBΔSACE_5717/5716 reached 4686 mg/L, a 41% enhancement over 3323 mg/L of the parent WB strain.
    Type of Medium: Online Resource
    ISSN: 1476-5535 , 1367-5435
    URL: Article
    DOI: 10.1007/s10295-019-02178-2
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 1482484-X
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    A new animal model for Polygonum multiflorum Thunb-induced liver injury in rats and its potential mechanisms
    Oxford University Press (OUP) ; 2015
    In:  Toxicology Research Vol. 4, No. 4 ( 2015), p. 1085-1097
    Details
    In: Toxicology Research, Oxford University Press (OUP), Vol. 4, No. 4 ( 2015), p. 1085-1097
    Type of Medium: Online Resource
    ISSN: 2045-452X , 2045-4538
    URL: Article
    DOI: 10.1039/C5TX00054H
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2015
    detail.hit.zdb_id: 2684701-2
    SSG: 15,3
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  • 7
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    Online Resource
    The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics
    Oxford University Press (OUP) ; 2023
    In:  Nucleic Acids Research ( 2023-11-24)
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), ( 2023-11-24)
    Abstract: The SysteMHC Atlas v1.0 was the first public repository dedicated to mass spectrometry-based immunopeptidomics. Here we introduce a newly released version of the SysteMHC Atlas v2.0 (https://systemhc.sjtu.edu.cn), a comprehensive collection of 7190 MS files from 303 allotypes. We extended and optimized a computational pipeline that allows the identification of MHC-bound peptides carrying on unexpected post-translational modifications (PTMs), thereby resulting in 471K modified peptides identified over 60 distinct PTM types. In total, we identified approximately 1.0 million and 1.1 million unique peptides for MHC class I and class II immunopeptidomes, respectively, indicating a 6.8-fold increase and a 28-fold increase to those in v1.0. The SysteMHC Atlas v2.0 introduces several new features, including the inclusion of non-UniProt peptides, and the incorporation of several novel computational tools for FDR estimation, binding affinity prediction and motif deconvolution. Additionally, we enhanced the user interface, upgraded website framework, and provided external links to other resources related. Finally, we built and provided various spectral libraries as community resources for data mining and future immunopeptidomic and proteomic analysis. We believe that the SysteMHC Atlas v2.0 is a unique resource to provide key insights to the immunology and proteomics community and will accelerate the development of vaccines and immunotherapies.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkad1068
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Corrections to: Enhanced lincomycin production by co‑overexpression of metK1 and metK2 in Streptomyces lincolnensis
    Oxford University Press (OUP) ; 2018
    In:  Journal of Industrial Microbiology and Biotechnology Vol. 45, No. 6 ( 2018-06-01), p. 447-448
    Details
    In: Journal of Industrial Microbiology and Biotechnology, Oxford University Press (OUP), Vol. 45, No. 6 ( 2018-06-01), p. 447-448
    Abstract: In the online published article, row value “pIB139-metK1-metK2” in table 1 has been processed incorrectly. The correct table is given below
    Type of Medium: Online Resource
    ISSN: 1476-5535 , 1367-5435
    URL: Article
    DOI: 10.1007/s10295-018-2036-2
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2018
    detail.hit.zdb_id: 1482484-X
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    Enhanced lincomycin production by co-overexpression of metK1 and metK2 in Streptomyces lincolnensis
    Oxford University Press (OUP) ; 2018
    In:  Journal of Industrial Microbiology and Biotechnology Vol. 45, No. 5 ( 2018-05-01), p. 345-355
    Details
    In: Journal of Industrial Microbiology and Biotechnology, Oxford University Press (OUP), Vol. 45, No. 5 ( 2018-05-01), p. 345-355
    Abstract: Streptomyces lincolnensis is generally utilized for the production of lincomycin A (Lin-A), a clinically useful antibiotic to treat Gram-positive bacterial infections. Three methylation steps, catalyzed by three different S-adenosylmethionine (SAM)-dependent methyltransferases, are required in the biosynthesis of Lin-A, and thus highlight the significance of methyl group supply in lincomycin production. In this study, we demonstrate that externally supplemented SAM cannot be taken in by cells and therefore does not enhance Lin-A production. Furthermore, bioinformatics and in vitro enzymatic assays revealed there exist two SAM synthetase homologs, MetK1 (SLCG_1651) and MetK2 (SLCG_3830) in S. lincolnensis that could convert l-methionine into SAM in the presence of ATP. Even though we attempted to inactivate metK1 and metK2, only metK2 was deleted in S. lincolnensis LCGL, named as ΔmetK2. Following a reduction of the intracellular SAM concentration, ΔmetK2 mutant exhibited a significant decrease of Lin-A in comparison to its parental strain. Individual overexpression of metK1 or metK2 in S. lincolnensis LCGL either elevated the amount of intracellular SAM, concomitant with 15% and 22% increase in Lin-A production, respectively. qRT-PCR assays showed that overexpression of either metK1 or metK2 increased the transcription of lincomycin biosynthetic genes lmbA and lmbR, and regulatory gene lmbU, indicating SAM may also function as a transcriptional activator. When metK1 and metK2 were co-expressed, Lin-A production was increased by 27% in LCGL, while by 17% in a high-yield strain LA219X.
    Type of Medium: Online Resource
    ISSN: 1476-5535 , 1367-5435
    URL: Article
    DOI: 10.1007/s10295-018-2029-1
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2018
    detail.hit.zdb_id: 1482484-X
    SSG: 12
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