• Login
    View Item 
    •   Home
    • Research
    • Datasets
    • View Item
    •   Home
    • Research
    • Datasets
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Browse

    All of KAUSTCommunitiesIssue DateSubmit DateThis CollectionIssue DateSubmit Date

    My Account

    Login

    Quick Links

    Open Access PolicyORCID LibguideTheses and Dissertations LibguideSubmit an Item

    Statistics

    Display statistics

    A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance

    • CSV
    • RefMan
    • EndNote
    • BibTex
    • RefWorks
    Type
    Dataset
    Authors
    Sheen, Patricia
    Requena, David
    Gushiken, Eduardo
    Gilman, Robert H.
    Antiparra, Ricardo
    Lucero, Bryan
    Lizárraga, Pilar
    Cieza, Basilio
    Roncal, Elisa
    Grandjean, Louis
    Pain, Arnab cc
    McNerney, Ruth
    Clark, Taane G.
    Moore, David
    Zimic, Mirko
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Program
    Pathogen Genomics Laboratory
    Date
    2017
    Permanent link to this record
    http://hdl.handle.net/10754/663880
    
    Metadata
    Show full item record
    Abstract
    Abstract Background Tuberculosis (TB) is a major global health problem and drug resistance compromises the efforts to control this disease. Pyrazinamide (PZA) is an important drug used in both first and second line treatment regimes. However, its complete mechanism of action and resistance remains unclear. Results We genotyped and sequenced the complete genomes of 68Â M. tuberculosis strains isolated from unrelated TB patients in Peru. No clustering pattern of the strains was verified based on spoligotyping. We analyzed the association between PZA resistance with non-synonymous mutations and specific genes. We found mutations in pncA and novel genes significantly associated with PZA resistance in strains without pncA mutations. These included genes related to transportation of metal ions, pH regulation and immune system evasion. Conclusions These results suggest potential alternate mechanisms of PZA resistance that have not been found in other populations, supporting that the antibacterial activity of PZA may hit multiple targets.
    Citation
    Sheen, P., Requena, D., Gushiken, E., Gilman, R., Antiparra, R., Lucero, B., LizĂĄrraga, P., Cieza, B., Roncal, E., Grandjean, L., Arnab Pain, McNerney, R., Taane Clark, Moore, D., & Zimic, M. (2017). A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance. Figshare. https://doi.org/10.6084/M9.FIGSHARE.C.3902473.V1
    Publisher
    figshare
    DOI
    10.6084/m9.figshare.c.3902473.v1
    Relations
    Is Supplement To:
    • [Article]
      Sheen P, Requena D, Gushiken E, Gilman RH, Antiparra R, et al. (2017) A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance. BMC Genomics 18. Available: http://dx.doi.org/10.1186/s12864-017-4146-z.. DOI: 10.1186/s12864-017-4146-z HANDLE: 10754/625883
    ae974a485f413a2113503eed53cd6c53
    10.6084/m9.figshare.c.3902473.v1
    Scopus Count
    Collections
    Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Datasets

    entitlement

     

    Related items

    Showing items related by title, author, creator and subject.

    • Thumbnail

      Additional file 4: of Silica diatom shells tailored with Au nanoparticles enable sensitive analysis of molecules for biological, safety and environment applications

      Onesto, V.; Villani, M.; Coluccio, M. L.; Majewska, R.; Alabastri, A.; Battista, E.; Schirato, A.; Calestani, D.; Coppedé, N.; Cesarelli, M.; Amato, F.; Di Fabrizio, Enzo M.; Gentile, F. (figshare, 2018) [Data File]
      Supporting figures to the Numerical Simulation Methods of the main text. (DOCX 608Â kb)
    • Thumbnail

      Impact of data preprocessing on cell-type clustering based on single-cell RNA-seq data

      Wang, Chunxiang; Gao, Xin; Liu, Juntao (figshare, 2020) [Dataset]
      Abstract Background Advances in single-cell RNA-seq technology have led to great opportunities for the quantitative characterization of cell types, and many clustering algorithms have been developed based on single-cell gene expression. However, we found that different data preprocessing methods show quite different effects on clustering algorithms. Moreover, there is no specific preprocessing method that is applicable to all clustering algorithms, and even for the same clustering algorithm, the best preprocessing method depends on the input data. Results We designed a graph-based algorithm, SC3-e, specifically for discriminating the best data preprocessing method for SC3, which is currently the most widely used clustering algorithm for single cell clustering. When tested on eight frequently used single-cell RNA-seq data sets, SC3-e always accurately selects the best data preprocessing method for SC3 and therefore greatly enhances the clustering performance of SC3. Conclusion The SC3-e algorithm is practically powerful for discriminating the best data preprocessing method, and therefore largely enhances the performance of cell-type clustering of SC3. It is expected to play a crucial role in the related studies of single-cell clustering, such as the studies of human complex diseases and discoveries of new cell types.
    • Thumbnail

      Supplementary Material for: Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

      Horiuchi, Youko; Harushima, Yoshiaki; Fujisawa, Hironori; Mochizuki, Takako; Fujita, Masahiro; Ohyanagi, Hajime; Kurata, Nori (figshare, 2015) [Dataset]
      Abstract Background Since the development of transcriptome analysis systems, many expression evolution studies characterized evolutionary forces acting on gene expression, without explicit discrimination between global expression differences and tissue specific expression differences. However, different types of gene expression alteration should have different effects on an organism, the evolutionary forces that act on them might be different, and different types of genes might show different types of differential expression between species. To confirm this, we studied differentially expressed (DE) genes among closely related groups that have extensive gene expression atlases, and clarified characteristics of different types of DE genes including the identification of regulating loci for differential expression using expression quantitative loci (eQTL) analysis data. Results We detected differentially expressed (DE) genes between rice subspecies in five homologous tissues that were verified using japonica and indica transcriptome atlases in public databases. Using the transcriptome atlases, we classified DE genes into two types, global DE genes and changed-tissues DE genes. Global type DE genes were not expressed in any tissues in the atlas of one subspecies, however changed-tissues type DE genes were expressed in both subspecies with different tissue specificity. For the five tissues in the two japonica-indica combinations, 4.6 ± 0.8 and 5.9 ± 1.5 % of highly expressed genes were global and changed-tissues DE genes, respectively. Changed-tissues DE genes varied in number between tissues, increasing linearly with the abundance of tissue specifically expressed genes in the tissue. Molecular evolution of global DE genes was rapid, unlike that of changed-tissues DE genes. Based on gene ontology, global and changed-tissues DE genes were different, having no common GO terms. Expression differences of most global DE genes were regulated by cis-eQTLs. Expression evolution of changed-tissues DE genes was rapid in tissue specifically expressed genes and those rapidly evolved changed-tissues DE genes were regulated not by cis-eQTLs, but by complicated trans-eQTLs. Conclusions Global DE genes and changed-tissues DE genes had contrasting characteristics. The two contrasting types of DE genes provide possible explanations for the previous controversial conclusions about the relationships between molecular evolution and expression evolution of genes in different species, and the relationship between expression breadth and expression conservation in evolution.
    DSpace software copyright © 2002-2023  DuraSpace
    Quick Guide | Contact Us | KAUST University Library
    Open Repository is a service hosted by 
    Atmire NV
     

    Export search results

    The export option will allow you to export the current search results of the entered query to a file. Different formats are available for download. To export the items, click on the button corresponding with the preferred download format.

    By default, clicking on the export buttons will result in a download of the allowed maximum amount of items. For anonymous users the allowed maximum amount is 50 search results.

    To select a subset of the search results, click "Selective Export" button and make a selection of the items you want to export. The amount of items that can be exported at once is similarly restricted as the full export.

    After making a selection, click one of the export format buttons. The amount of items that will be exported is indicated in the bubble next to export format.