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| http://dx.doi.org/10.1021/acs.chemrev.5b00034 | DOI Listing |
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The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository.
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Background: Recent advances in high-throughput sequencing technologies have enabled the collection and sharing of a massive amount of omics data, along with its associated metadata-descriptive information that contextualizes the data, including phenotypic traits and experimental design. Enhancing metadata availability is critical to ensure data reusability and reproducibility and to facilitate novel biomedical discoveries through effective data reuse. Yet, incomplete metadata accompanying public omics data may hinder reproducibility and reusability and limit secondary analyses.
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Department of Gastroenterology, Sir Run Run Shaw Hospital, College of Medicine Zhejiang University, Hangzhou, China.
Anti-tumor necrosis factor (TNF) therapy for inflammatory bowel disease (IBD) is hampered by issues of nonresponse and resistance, highlighting the urgent need for alternative or complementary treatments. Our study revealed significant upregulation of taurine in the intestinal tissues of IBD patients, which was inversely related to the severity of the disease. A key discovery was that TNF directly induced taurine synthesis in intestinal epithelial cells and increased the production of angiogenin, a nuclease that degrades mitochondrial RNA, which is known to amplify inflammatory responses.
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View Article and Find Full Text PDFAssessing adult zebrafish despair-like behaviors in the small vertical cylinder immobility test (VCIT).
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View Article and Find Full Text PDFSensitive and specific affinity purification-mass spectrometry assisted by PafA-mediated proximity labeling.
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Lingang Laboratory, Shanghai 201306, China. Electronic address:
While affinity purification-mass spectrometry (AP-MS) has significantly advanced protein-protein interaction (PPI) studies, its limitations in detecting weak, transient, and membrane-associated interactions remain. To address these challenges, we introduced a proteomic method termed affinity purification coupled proximity labeling-mass spectrometry (APPLE-MS), which combines the high specificity of Twin-Strep tag enrichment with PafA-mediated proximity labeling. This method achieves improved sensitivity while maintaining high specificity (4.
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