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  1. Article ; Online: Extensive Mendelian randomization study identifies potential causal risk factors for severe COVID-19

    Yitang Sun / Jingqi Zhou / Kaixiong Ye

    Communications Medicine, Vol 1, Iss 1, Pp 1-

    2021  Volume 11

    Abstract: Sun et al. perform a two-sample Mendelian randomization study of a large number of traits with the aim of identifying risk factors of severe COVID-19. They show that body mass index-related traits, specific white blood cells, and some circulating ... ...

    Abstract Sun et al. perform a two-sample Mendelian randomization study of a large number of traits with the aim of identifying risk factors of severe COVID-19. They show that body mass index-related traits, specific white blood cells, and some circulating proteins are risk factors for the development of severe COVID-19.
    Keywords Medicine ; R
    Language English
    Publishing date 2021-12-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: White Blood Cells and Severe COVID-19

    Yitang Sun / Jingqi Zhou / Kaixiong Ye

    Journal of Personalized Medicine, Vol 11, Iss 195, p

    A Mendelian Randomization Study

    2021  Volume 195

    Abstract: Increasing evidence shows that white blood cells are associated with the risk of coronavirus disease 2019 (COVID-19), but the direction and causality of this association are not clear. To evaluate the causal associations between various white blood cell ... ...

    Abstract Increasing evidence shows that white blood cells are associated with the risk of coronavirus disease 2019 (COVID-19), but the direction and causality of this association are not clear. To evaluate the causal associations between various white blood cell traits and the COVID-19 susceptibility and severity, we conducted two-sample bidirectional Mendelian Randomization (MR) analyses with summary statistics from the largest and most recent genome-wide association studies. Our MR results indicated causal protective effects of higher basophil count, basophil percentage of white blood cells, and myeloid white blood cell count on severe COVID-19, with odds ratios (OR) per standard deviation increment of 0.75 (95% CI: 0.60–0.95), 0.70 (95% CI: 0.54–0.92), and 0.85 (95% CI: 0.73–0.98), respectively. Neither COVID-19 severity nor susceptibility was associated with white blood cell traits in our reverse MR results. Genetically predicted high basophil count, basophil percentage of white blood cells, and myeloid white blood cell count are associated with a lower risk of developing severe COVID-19. Individuals with a lower genetic capacity for basophils are likely at risk, while enhancing the production of basophils may be an effective therapeutic strategy.
    Keywords COVID-19 ; white blood cells ; basophils ; Mendelian randomization ; Medicine ; R
    Subject code 610
    Language English
    Publishing date 2021-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Plumeriapropionics A–E, Carboxyl-Substituted Phenylpropionic Acid Derivatives with Anti-Inflammatory Activity from Plumeria rubra L.

    Xueming Zhou / Minlin Gan / Meizhu Wu / Ting Zheng / Chuluunbaatar Enkhchimeg / Haixiang Li / Shuo Feng / Jingqi Zhou / Xinming Song

    Molecules, Vol 29, Iss 1, p

    2023  Volume 115

    Abstract: Five rare carboxyl-substituted phenylpropionic acid derivatives, plumeriapropionics A–E ( 1 – 5 ), together with one known analog, cerberic acid B ( 6 ), were isolated from flowers of Plumeria rubra L. Their structures were elucidated using comprehensive ...

    Abstract Five rare carboxyl-substituted phenylpropionic acid derivatives, plumeriapropionics A–E ( 1 – 5 ), together with one known analog, cerberic acid B ( 6 ), were isolated from flowers of Plumeria rubra L. Their structures were elucidated using comprehensive spectroscopic methods. To date, only one compound of this structural type has been reported. The inhibitory activities of compounds 1 – 6 against nitric oxide (NO) production induced by lipopolysaccharide (LPS) were evaluated in vitro using mouse macrophage RAW264.7 cells. Compounds 1 – 6 showed remarkable inhibitory activities on NO production, with IC 50 values in the range of 6.52 ± 0.23 to 35.68 ± 0.17 µM. These results indicate that the discovery of carboxyl-substituted phenylpropionic acid derivatives from the flowers of P. rubra , which show significant anti-inflammatory properties, could be of great importance for the research and development of novel natural anti-inflammatory agents.
    Keywords Plumeria rubra ; plumeriapropionics ; carboxyl-substituted phenylpropionic acid ; anti-inflammatory activity ; Organic chemistry ; QD241-441
    Subject code 540
    Language English
    Publishing date 2023-12-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Paralog-divergent Features May Help Reduce Off-target Effects of Drugs

    Zhining Sa / Jingqi Zhou / Yangyun Zou / Zhixi Su / Xun Gu

    Genomics, Proteomics & Bioinformatics, Vol 15, Iss 4, Pp 246-

    Hints from Glucagon Subfamily Analysis

    2017  Volume 254

    Abstract: Side effects from targeted drugs remain a serious concern. One reason is the nonselective binding of a drug to unintended proteins such as its paralogs, which are highly homologous in sequences and have similar structures and drug-binding pockets. To ... ...

    Abstract Side effects from targeted drugs remain a serious concern. One reason is the nonselective binding of a drug to unintended proteins such as its paralogs, which are highly homologous in sequences and have similar structures and drug-binding pockets. To identify targetable differences between paralogs, we analyzed two types (type-I and type-II) of functional divergence between two paralogs in the known target protein receptor family G-protein coupled receptors (GPCRs) at the amino acid level. Paralogous protein receptors in glucagon-like subfamily, glucagon receptor (GCGR) and glucagon-like peptide-1 receptor (GLP-1R), exhibit divergence in ligands and are clinically validated drug targets for type 2 diabetes. Our data showed that type-II amino acids were significantly enriched in the binding sites of antagonist MK-0893 to GCGR, which had a radical shift in physicochemical properties between GCGR and GLP-1R. We also examined the role of type-I amino acids between GCGR and GLP-1R. The divergent features between GCGR and GLP-1R paralogs may be helpful in their discrimination, thus enabling the identification of binding sites to reduce undesirable side effects and increase the target specificity of drugs.
    Keywords Paralog ; Functional divergence ; Functional site ; Drug specificity ; Evolutionary conservation ; Biology (General) ; QH301-705.5
    Subject code 571
    Language English
    Publishing date 2017-08-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: Paralog-divergent Features May Help Reduce Off-target Effects of Drugs: Hints from Glucagon Subfamily Analysis

    Sa, Zhining / Jingqi Zhou / Xun Gu / Yangyun Zou / Zhixi Su

    Genomics, proteomics & bioinformatics. 2017 Aug., v. 15, no. 4

    2017  

    Abstract: Side effects from targeted drugs remain a serious concern. One reason is the nonselective binding of a drug to unintended proteins such as its paralogs, which are highly homologous in sequences and have similar structures and drug-binding pockets. To ... ...

    Abstract Side effects from targeted drugs remain a serious concern. One reason is the nonselective binding of a drug to unintended proteins such as its paralogs, which are highly homologous in sequences and have similar structures and drug-binding pockets. To identify targetable differences between paralogs, we analyzed two types (type-I and type-II) of functional divergence between two paralogs in the known target protein receptor family G-protein coupled receptors (GPCRs) at the amino acid level. Paralogous protein receptors in glucagon-like subfamily, glucagon receptor (GCGR) and glucagon-like peptide-1 receptor (GLP-1R), exhibit divergence in ligands and are clinically validated drug targets for type 2 diabetes. Our data showed that type-II amino acids were significantly enriched in the binding sites of antagonist MK-0893 to GCGR, which had a radical shift in physicochemical properties between GCGR and GLP-1R. We also examined the role of type-I amino acids between GCGR and GLP-1R. The divergent features between GCGR and GLP-1R paralogs may be helpful in their discrimination, thus enabling the identification of binding sites to reduce undesirable side effects and increase the target specificity of drugs.
    Keywords adverse effects ; amino acids ; antagonists ; binding sites ; drugs ; glucagon ; glucagon receptors ; glucagon-like peptide 1 ; ligands ; noninsulin-dependent diabetes mellitus ; physicochemical properties
    Language English
    Dates of publication 2017-08
    Size p. 246-254.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2240213-5
    ISSN 2210-3244 ; 1672-0229
    ISSN (online) 2210-3244
    ISSN 1672-0229
    DOI 10.1016/j.gpb.2017.03.004
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: XBSeq2

    Yuanhang Liu / Ping Wu / Jingqi Zhou / Teresa L. Johnson-Pais / Zhao Lai / Wasim H. Chowdhury / Ronald Rodriguez / Yidong Chen

    BMC Bioinformatics, Vol 18, Iss S11, Pp 57-

    a fast and accurate quantification of differential expression and differential polyadenylation

    2017  Volume 65

    Abstract: Abstract Background RNA sequencing (RNA-seq) is a high throughput technology that profiles gene expression in a genome-wide manner. RNA-seq has been mainly used for testing differential expression (DE) of transcripts between two conditions and has ... ...

    Abstract Abstract Background RNA sequencing (RNA-seq) is a high throughput technology that profiles gene expression in a genome-wide manner. RNA-seq has been mainly used for testing differential expression (DE) of transcripts between two conditions and has recently been used for testing differential alternative polyadenylation (APA). In the past, many algorithms have been developed for detecting differentially expressed genes (DEGs) from RNA-seq experiments, including the one we developed, XBSeq, which paid special attention to the context-specific background noise that is ignored in conventional gene expression quantification and DE analysis of RNA-seq data. Results We present several major updates in XBSeq2, including alternative statistical testing and parameter estimation method for detecting DEGs, capacity to directly process alignment files and methods for testing differential APA usage. We evaluated the performance of XBSeq2 against several other methods by using simulated datasets in terms of area under the receiver operating characteristic (ROC) curve (AUC), number of false discoveries and statistical power. We also benchmarked different methods concerning execution time and computational memory consumed. Finally, we demonstrated the functionality of XBSeq2 by using a set of in-house generated clear cell renal carcinoma (ccRCC) samples. Conclusions We present several major updates to XBSeq. By using simulated datasets, we demonstrated that, overall, XBSeq2 performs equally well as XBSeq in terms of several statistical metrics and both perform better than DESeq2 and edgeR. In addition, XBSeq2 is faster in speed and consumes much less computational memory compared to XBSeq, allowing users to evaluate differential expression and APA events in parallel. XBSeq2 is available from Bioconductor: http://bioconductor.org/packages/XBSeq/
    Keywords Differential expression analysis ; XBSeq ; XBSeq2 ; Alternative polyadenylation ; RNA-seq ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
    Subject code 612
    Language English
    Publishing date 2017-10-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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