Open Access
An integrated computational and experimental studyto investigate Staphylococcus aureus metabolism
Mohammad Mazharul Islam,Vinai Chittezham Thomas,Matthew Van Beek,Jongsam Ahn,Abdulelah A. Alqarzaee,Chunyi Zhou,Paul D. Fey,Kenneth W. Bayles,Rajib K. Saha +8 more
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TLDR
An updated and enhanced genome-scale metabolic model of S. aureus that combines genome annotation data, reaction stoichiometry, and regulation information from biochemical databases and previous strain-specific models to enhance the functional utility of omics data and to augment staphylococcal research worldwide is reconstructed and experimentally validated.About:
The article was published on 2020-01-01 and is currently open access. It has received 8 citations till now. The article focuses on the topics: Staphylococcus aureus.read more
Citations
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Journal ArticleDOI
Virulence and Metabolism.
TL;DR: This chapter essentially connects many recent observations that link the metabolism of S. aureus to its overall pathogenesis and hints that the mere presence of a plethora of virulence factors may not entirely explain the extraordinary pathogenic potential of S-Aureus.
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Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens.
Mustafa Sertbas,Kutlu O. Ulgen +1 more
TL;DR: The current knowledge of genome-scale metabolic modeling in pathogen cells as well as pathogen host interaction systems and the promising applications in the extension of curative strategies against pathogens for global preventative healthcare are reviewed.
Journal ArticleDOI
Interplay of CodY and CcpA in Regulating Central Metabolism and Biofilm Formation in Staphylococcus aureus
Logan L. Bulock,Jong Sam Ahn,Dhananjay D. Shinde,Sanjit Pandey,Cleofes Sarmiento,Vinai Chittezham Thomas,Chittibabu Guda,Kenneth W. Bayles,Marat R. Sadykov +8 more
TL;DR: Combined, the results of this study suggest that the coordinated action of CodY and CcpA modulate central metabolism, virulence gene expression, and biofilm-associated genes to optimize growth on preferred carbon sources until starvation sets in.
Journal ArticleDOI
Investigation of microbial community interactions between Lake Washington methanotrophs using -------genome-scale metabolic modeling.
TL;DR: This work attempted to predict the response of a simplified methane cycling microbial community from Lake Washington to varying environments and also provides an insight into the difference of dynamics in sediment-incubated microcosm community and synthetic co-cultures.
Journal ArticleDOI
Genome-Scale Metabolic Modelling Approach to Understand the Metabolism of the Opportunistic Human Pathogen Staphylococcus epidermidis RP62A
Teresa Díaz Díaz Calvo,Noemi Tejera,Iain McNamara,Gemma C. Langridge,John Wain,Mark G. Poolman,Dipali Singh +6 more
TL;DR: It is shown that this strain has no real substrate auxotrophies, although removal of proline from the media has the highest impact on the model and the experimental growth characteristics, and Amino acids, proline, valine, alanine, glutamate and arginine are preferred sources of energy and biomass production.
References
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Journal ArticleDOI
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Journal ArticleDOI
The Universal Protein Resource (UniProt)
Amos Marc Bairoch,Rolf Apweiler,Cathy H. Wu,Winona C. Barker,Brigitte Boeckmann,Serenella Ferro,Elisabeth Gasteiger,Hongzhan Huang,Rodrigo Lopez,Michele Magrane,Maria Jesus Martin,Darren A. Natale,Claire O'Donovan,Nicole Redaschi,Lai-Su L. Yeh +14 more
TL;DR: During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; the UniProt keyword list got augmented by additional keywords; the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications.
Journal ArticleDOI
Invasive Methicillin-Resistant Staphylococcus aureus Infections in the United States
R. Monina Klevens,Melissa Morrison,Joelle Nadle,Ken Gershman,Lee H. Harrison,Ruth Lynfield,Ghinwa Dumyati,John M. Townes,Allen S. Craig,Elizabeth R. Zell,Gregory E. Fosheim,Linda K. McDougal,Roberta B. Carey,Scott K. Fridkin +13 more
TL;DR: Invasive MRSA infection affects certain populations disproportionately and is a major public health problem primarily related to health care but no longer confined to intensive care units, acute care hospitals, or any health care institution.
Journal ArticleDOI
The Pfam protein families database in 2019.
Sara El-Gebali,Jaina Mistry,Alex Bateman,Sean R. Eddy,Aurelien Luciani,Simon C. Potter,Matloob Qureshi,Lorna Richardson,Gustavo A. Salazar,Alfredo Smart,Erik L. L. Sonnhammer,Layla Hirsh,Layla Hirsh,Lisanna Paladin,Damiano Piovesan,Silvio C. E. Tosatto,Robert D. Finn +16 more
TL;DR: A significant comparison to the structural classification database that led to the creation of 825 new families based on their set of uncharacterized families (EUFs) was carried out and Pfam entries were connected to the Sequence Ontology (SO) through mapping of the Pfam type definitions to SO terms.
Journal ArticleDOI
What is flux balance analysis
TL;DR: This primer covers the theoretical basis of the approach, several practical examples and a software toolbox for performing the calculations.