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  • Oxford University Press (OUP)  (48)
  • 1
    Online Resource
    Online Resource
    CTR-DB, an omnibus for patient-derived gene expression signatures correlated with cancer drug response
    Oxford University Press (OUP) ; 2022
    In:  Nucleic Acids Research Vol. 50, No. D1 ( 2022-01-07), p. D1184-D1199
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 50, No. D1 ( 2022-01-07), p. D1184-D1199
    Abstract: To date, only some cancer patients can benefit from chemotherapy and targeted therapy. Drug resistance continues to be a major and challenging problem facing current cancer research. Rapidly accumulated patient-derived clinical transcriptomic data with cancer drug response bring opportunities for exploring molecular determinants of drug response, but meanwhile pose challenges for data management, integration, and reuse. Here we present the Cancer Treatment Response gene signature DataBase (CTR-DB, http://ctrdb.ncpsb.org.cn/), a unique database for basic and clinical researchers to access, integrate, and reuse clinical transcriptomes with cancer drug response. CTR-DB has collected and uniformly reprocessed 83 patient-derived pre-treatment transcriptomic source datasets with manually curated cancer drug response information, involving 28 histological cancer types, 123 drugs, and 5139 patient samples. These data are browsable, searchable, and downloadable. Moreover, CTR-DB supports single-dataset exploration (including differential gene expression, receiver operating characteristic curve, functional enrichment, sensitizing drug search, and tumor microenvironment analyses), and multiple-dataset combination and comparison, as well as biomarker validation function, which provide insights into the drug resistance mechanism, predictive biomarker discovery and validation, drug combination, and resistance mechanism heterogeneity.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkab860
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 2
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    Production of reactive oxygen species by PuRBOHF is critical for stone cell development in pear fruit
    Oxford University Press (OUP) ; 2021
    In:  Horticulture Research Vol. 8, No. 1 ( 2021-12)
    Details
    In: Horticulture Research, Oxford University Press (OUP), Vol. 8, No. 1 ( 2021-12)
    Abstract: The production of reactive oxygen species (ROS) by NADPH oxidase, which is also referred to as respiratory burst oxidase homolog (RBOH), affects several processes in plants. However, the role of RBOHs in cell wall lignification is not well understood. In this study, we show that PuRBOHF , an RBOH isoform, plays an important role in secondary wall formation in pear stone cells. ROS were closely associated with lignin deposition and stone cell formation according to microscopy data. In addition, according to the results of an in situ hybridization analysis, the stage-specific expression of PuRBOHF was higher in stone cells than in cells of other flesh tissues. Inhibitors of RBOH activity suppressed ROS accumulation and stone cell lignification in pear fruit. Moreover, transient overexpression of PuRBOHF caused significant changes in the amount of ROS and lignin that accumulated in pear fruit and flesh calli. We further showed that PuMYB169 regulates PuRBOHF expression, while PuRBOHF -derived ROS induces the transcription of PuPOD2 and PuLAC2 . The findings of this study indicate that PuRBOHF -mediated ROS production, which is regulated by a lignin-related transcriptional network, is essential for monolignol polymerization and stone cell formation in pear fruit.
    Type of Medium: Online Resource
    ISSN: 2662-6810 , 2052-7276
    URL: Article
    DOI: 10.1038/s41438-021-00674-0
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2781828-7
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  • 3
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    SPIDR is required for homologous recombination during mammalian meiosis
    Oxford University Press (OUP) ; 2023
    In:  Nucleic Acids Research Vol. 51, No. 8 ( 2023-05-08), p. 3855-3868
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 51, No. 8 ( 2023-05-08), p. 3855-3868
    Abstract: Meiotic recombinases RAD51 and DMC1 mediate strand exchange in the repair of DNA double-strand breaks (DSBs) by homologous recombination. This is a landmark event of meiosis that ensures genetic diversity in sexually reproducing organisms. However, the regulatory mechanism of DMC1/RAD51-ssDNA nucleoprotein filaments during homologous recombination in mammals has remained largely elusive. Here, we show that SPIDR (scaffold protein involved in DNA repair) regulates the assembly or stability of RAD51/DMC1 on ssDNA. Knockout of Spidr in male mice causes complete meiotic arrest, accompanied by defects in synapsis and crossover formation, which leads to male infertility. In females, loss of Spidr leads to subfertility; some Spidr−/− oocytes are able to complete meiosis. Notably, fertility is rescued partially by ablation of the DNA damage checkpoint kinase CHK2 in Spidr−/− females but not in males. Thus, our study identifies SPIDR as an essential meiotic recombination factor in homologous recombination in mammals.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkad154
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1472175-2
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  • 4
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    The LSF1–MDH complex functions as a scaffold to recruit β-amylase to promote starch degradation
    Oxford University Press (OUP) ; 2023
    In:  The Plant Cell ( 2023-10-06)
    Details
    In: The Plant Cell, Oxford University Press (OUP), ( 2023-10-06)
    Abstract: In plant leaves, starch is composed of glucan polymers that accumulate in chloroplasts as the products of photosynthesis during the day; starch is mobilized at night to continuously provide sugars to sustain plant growth and development. Efficient starch degradation requires the involvement of several enzymes, including β-amylase and glucan phosphatase. However, how these enzymes cooperate remains largely unclear. Here, we show that the glucan phosphatase LIKE SEX FOUR 1 (LSF1) interacts with plastid NAD-dependent malate dehydrogenase (MDH) to recruit β-amylase (BAM1), thus reconstituting the BAM1–LSF1–MDH complex. The starch hydrolysis activity of BAM1 drastically increased in the presence of LSF1–MDH in vitro. We determined the structure of the BAM1–LSF1–MDH complex by a combination of cryo-electron microscopy, crosslinking mass spectrometry, and molecular docking. The starch-binding domain of the dual-specificity phosphatase (DSP) and carbohydrate-binding module (CBM) of LSF1 were docked in proximity to BAM1, thus facilitating BAM1 access to and hydrolysis of the polyglucans of starch, thus revealing the molecular mechanism by which the LSF1–MDH complex improves the starch degradation activity of BAM1. Moreover, LSF1 is phosphatase-inactive, and the enzymatic activity of MDH was dispensable for starch degradation, suggesting non-enzymatic scaffold functions for LSF1–MDH in starch degradation. These findings provide important insights into the precise regulation of starch degradation.
    Type of Medium: Online Resource
    ISSN: 1040-4651 , 1532-298X
    URL: Article
    DOI: 10.1093/plcell/koad259
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 623171-8
    detail.hit.zdb_id: 2004373-9
    SSG: 12
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  • 5
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    L-shaped association between dietary zinc intake and cognitive decline in Chinese older people
    Oxford University Press (OUP) ; 2024
    In:  Age and Ageing Vol. 53, No. 1 ( 2024-01-02)
    Details
    In: Age and Ageing, Oxford University Press (OUP), Vol. 53, No. 1 ( 2024-01-02)
    Abstract: The prospective association between dietary zinc (Zn) intake and cognitive decline remains uncertain. We aimed to assess the relationship of dietary Zn intake with the risk of cognitive decline in the Chinese older people, and examine the possible effect modifiers on this association. Methods A total of 3,106 older Chinese adults aged 55 years or older from China Health and Nutrition Survey were included. Dietary nutrients intake information was collected by combined 24-h dietary recalls with weighing food inventory. The cognitive decline was defined as the 5-year decline rate in global and composite cognitive scores, based on a subset of items from the Telephone Interview for Cognitive Status–modified. Results The median follow-up duration was 5.9 years. There was an L-shaped association between dietary Zn intake and the 5-year decline rates in global and composite cognitive scores, with an inflection point at 8.8 mg/day of dietary Zn. For the composite cognitive scores, compared with the first quantile ( & lt;7.9 mg/day) of dietary Zn intake, quantiles 2–6 (≥7.9 mg/day) had a significantly slower cognitive decline rate (β: −0.24; 95% confidence interval: −0.40 to −0.07). Similar results were found for the global cognitive scores. Moreover, the inverse association between dietary Zn intake and cognitive decline in composite cognitive scores was significantly stronger in those with lower levels of physical activity (P-interactions = 0.041). Conclusion Dietary Zn intake was negatively associated with cognitive decline in the older people. Maintaining appropriate dietary Zn levels may prevent cognitive decline.
    Type of Medium: Online Resource
    ISSN: 0002-0729 , 1468-2834
    URL: Article
    DOI: 10.1093/ageing/afae008
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 2065766-3
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  • 6
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    The landscape of innate and adaptive immune cell subsets in patients with adult-onset Still’s disease
    Oxford University Press (OUP) ; 2023
    In:  Rheumatology ( 2023-09-26)
    Details
    In: Rheumatology, Oxford University Press (OUP), ( 2023-09-26)
    Abstract: Adult-onset Still’s disease (AOSD) is a systemic autoinflammatory disorder. The understanding of the changes in adaptive immune cells and the crosstalk between innate and adaptive immune systems in AOSD is limited. This study aimed to examine the peripheral immune cell composition and inflammatory protein levels in AOSD patients. Methods Twenty-nine active AOSD patients were enrolled. Flow cytometry was used to analyze the cell populations in peripheral blood. Antibody chips were utilized to detect the protein expression profile in serum. Results In active AOSD patients, there was an increase in the percentage of classical and non-classical monocytes among peripheral blood mononuclear cells. The proportion of natural killer (NK) cells decreased, with an increase in CD56dim NK1 cells and a decrease in CD56bright NK2 cells compared with healthy controls (HC). The percentage of naïve central memory T cells was decreased, while the percentage of effector and effector memory T cells was increased among adaptive lymphocytes. The proportion of naïve B and memory B cells was decreased, while plasma cells were increased in AOSD patients, indicating activation of the adaptive immune system. Additionally, the serum levels of 40 proteins were elevated in AOSD patients, primarily involved in cytokine-cytokine receptor interaction, inflammatory response, and regulation of MAPK cascade. Conclusion Our findings showed the activation of the innate and adaptive immune system in AOSD. The protein-protein interaction analysis suggested potential communication between innate and adaptive cell subsets. These findings provide new insights into the pathogenesis of the disease and the development of targeted therapies.
    Type of Medium: Online Resource
    ISSN: 1462-0324 , 1462-0332
    URL: Article
    DOI: 10.1093/rheumatology/kead507
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1474143-X
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  • 7
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    Exploration of Target Spaces in the Human Genome for Protein and Peptide Drugs
    Oxford University Press (OUP) ; 2022
    In:  Genomics, Proteomics & Bioinformatics Vol. 20, No. 4 ( 2022-08-01), p. 780-794
    Details
    In: Genomics, Proteomics & Bioinformatics, Oxford University Press (OUP), Vol. 20, No. 4 ( 2022-08-01), p. 780-794
    Abstract: After decades of development, protein and peptide drugs have now grown into a major drug class in the marketplace. Target identification and validation are crucial for the discovery of protein and peptide drugs, and bioinformatics prediction of targets based on the characteristics of known target proteins will help improve the efficiency and success rate of target selection. However, owing to the developmental history in the pharmaceutical industry, previous systematic exploration of the target spaces has mainly focused on traditional small-molecule drugs, while studies related to protein and peptide drugs are lacking. Here, we systematically explore the target spaces in the human genome specifically for protein and peptide drugs. Compared with other proteins, both successful protein and peptide drug targets have many special characteristics, and are also significantly different from those of small-molecule drugs in many aspects. Based on these features, we develop separate effective genome-wide target prediction models for protein and peptide drugs. Finally, a user-friendly web server, Predictor Of Protein and PeptIde drugs’ therapeutic Targets (POPPIT) (http://poppit.ncpsb.org.cn/), is established, which provides not only target prediction specifically for protein and peptide drugs but also abundant annotations for predicted targets.
    Type of Medium: Online Resource
    ISSN: 1672-0229 , 2210-3244
    URL: Article
    DOI: 10.1016/j.gpb.2021.10.007
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2233708-8
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  • 8
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    Triple deletion of clpC , porB , and mepA enhances production of small ubiquitin-like modifier-N-terminal pro-brain natriuretic peptide in Corynebacterium glutamicum
    Oxford University Press (OUP) ; 2019
    In:  Journal of Industrial Microbiology and Biotechnology Vol. 46, No. 1 ( 2019-01-01), p. 67-79
    Details
    In: Journal of Industrial Microbiology and Biotechnology, Oxford University Press (OUP), Vol. 46, No. 1 ( 2019-01-01), p. 67-79
    Abstract: In our previous work, a two-plasmid CRISPR/Cas9 system was constructed for genome editing in Corynebacterium glutamicum. To increase the transformation efficiency and simplify the plasmid curing steps, an all-in-one CRISPR/Cas9 system was constructed for efficient genome editing. In addition, to research proteolysis during the production of recombinant proteins and generate a host for enhanced expression of recombinant proteins, the system was used to delete three genes, clpC, porB, and mepA in C. glutamicum CGMCC1.15647, which encoded the Clp protease subunit ClpC, anion selective channel protein B, and metallopeptidase A, respectively. After the evaluation of different plasmids and hosts, small ubiquitin-like modifier-N-terminal pro-brain natriuretic peptide (SUMO-NT-proBNP), an important protein used for the diagnosis of mild heart failure was successfully expressed in the triple mutant ΔclpCΔporBΔmepA, which exhibit threefold higher levels of protein expression compared with the wild-type. In conclusion, we created a simplified CRISPR tool for genome editing in C. glutamicum, provided a method to generate a host for enhanced expression of recombinant proteins and successfully expressed SUMO-NT-proBNP in C. glutamicum. This tool and method will greatly facilitate genetic engineering and metabolic optimization of this important platform organism.
    Type of Medium: Online Resource
    ISSN: 1476-5535 , 1367-5435
    URL: Article
    DOI: 10.1007/s10295-018-2091-8
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 1482484-X
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  • 9
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    Deacetylase-independent function of SIRT6 couples GATA4 transcription factor and epigenetic activation against cardiomyocyte apoptosis
    Oxford University Press (OUP) ; 2020
    In:  Nucleic Acids Research Vol. 48, No. 9 ( 2020-05-21), p. 4992-5005
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 48, No. 9 ( 2020-05-21), p. 4992-5005
    Abstract: SIRT6 deacetylase activity improves stress resistance via gene silencing and genome maintenance. Here, we reveal a deacetylase-independent function of SIRT6, which promotes anti-apoptotic gene expression via the transcription factor GATA4. SIRT6 recruits TIP60 acetyltransferase to acetylate GATA4 at K328/330, thus enhancing its chromatin binding capacity. In turn, GATA4 inhibits the deacetylase activity of SIRT6, thus ensuring the local chromatin accessibility via TIP60-promoted H3K9 acetylation. Significantly, the treatment of doxorubicin (DOX), an anti-cancer chemotherapeutic, impairs the SIRT6–TIP60–GATA4 trimeric complex, blocking GATA4 acetylation and causing cardiomyocyte apoptosis. While GATA4 hyperacetylation-mimic retains the protective effect against DOX, the hypoacetylation-mimic loses such ability. Thus, the data reveal a novel SIRT6–TIP60–GATA4 axis, which promotes the anti-apoptotic pathway to prevent DOX toxicity. Targeting the trimeric complex constitutes a new strategy to improve the safety of DOX chemotherapy in clinical application.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkaa214
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1472175-2
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  • 10
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    Inactivated SARS-CoV-2 vaccine does not increase the risk of relapse in patients with clinically inactive adult-onset Still’s disease
    Oxford University Press (OUP) ; 2023
    In:  Rheumatology Vol. 62, No. 6 ( 2023-06-01), p. 2262-2266
    Details
    In: Rheumatology, Oxford University Press (OUP), Vol. 62, No. 6 ( 2023-06-01), p. 2262-2266
    Abstract: A succession of cases have reported flares of adult-onset Still’s disease (AOSD) after vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), raising concerns. We aimed to investigate the impact of inactivated SARS-CoV-2 vaccines on disease activity in patients with AOSD. Methods We prospectively enrolled clinically inactive AOSD patients visiting the outpatient clinics of our department. The patients received SARS-CoV-2 vaccines (BBIBP-CorV, Sinopharm, Beijing, China) voluntarily. The occurrence of relapse in the participants was recorded during the follow-up period, and a propensity score matching (PSM) method was used to compare the relapse rates between vaccinated and unvaccinated patients. Localized and systemic symptoms were assessed in the vaccinated patients. Results A total of 122 patients with inactive AOSD were included, of which 49.2% (n = 60) voluntarily received the inactivated SARS-CoV-2 vaccine. The relapse rate did not increase significantly in vaccinated patients in comparison with unvaccinated patients (after PSM: 6.8% vs 6.8%), and no relapse occurred within 1 month after vaccination. No obvious adverse reactions were reported in 75.0% of the participants, and none of the patients reported severe reactions. Conclusion Increased disease activity or relapse following vaccination with inactivated SARS–CoV-2 was rare in patients with inactive AOSD. Local and systemic adverse reactions were found to be mild and self-limiting. These safety profiles of inactivated SARS–CoV-2 vaccines in patients with AOSD may assist in eliminating vaccine hesitancy and increase the vaccination rate against SARS-CoV-2.
    Type of Medium: Online Resource
    ISSN: 1462-0324 , 1462-0332
    URL: Article
    DOI: 10.1093/rheumatology/keac620
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1474143-X
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