Aureolib — A Proteome Signature Library: Towards an Understanding of Staphylococcus aureus Pathophysiology
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{"title"=>"Aureolib - A Proteome Signature Library: Towards an Understanding of Staphylococcus aureus Pathophysiology", "type"=>"journal", "authors"=>[{"first_name"=>"Stephan", "last_name"=>"Fuchs", "scopus_author_id"=>"7202421519"}, {"first_name"=>"Daniela", "last_name"=>"Zühlke", "scopus_author_id"=>"8929053300"}, {"first_name"=>"Jan", "last_name"=>"Pané-Farré", "scopus_author_id"=>"9336960200"}, {"first_name"=>"Harald", "last_name"=>"Kusch", "scopus_author_id"=>"6601998997"}, {"first_name"=>"Carmen", "last_name"=>"Wolf", "scopus_author_id"=>"24469462100"}, {"first_name"=>"Swantje", "last_name"=>"Reiß", "scopus_author_id"=>"54909759900"}, {"first_name"=>"Le Thi Nguyen", "last_name"=>"Binh", "scopus_author_id"=>"55821439700"}, {"first_name"=>"Dirk", "last_name"=>"Albrecht", "scopus_author_id"=>"9245778700"}, {"first_name"=>"Katharina", "last_name"=>"Riedel", "scopus_author_id"=>"7101773056"}, {"first_name"=>"Michael", "last_name"=>"Hecker", "scopus_author_id"=>"26643644600"}, {"first_name"=>"Susanne", "last_name"=>"Engelmann", "scopus_author_id"=>"7004606226"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84881517255", "doi"=>"10.1371/journal.pone.0070669", "pui"=>"369566664", "pmid"=>"23967085", "scopus"=>"2-s2.0-84881517255", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic) 1932-6203 (Linking)"}, "id"=>"d749a745-fc80-3f01-88cb-7b7e89aea074", "abstract"=>"Gel-based proteomics is a powerful approach to study the physiology of Staphylococcus aureus under various growth restricting conditions. We analyzed 679 protein spots from a reference 2-dimensional gel of cytosolic proteins of S. aureus COL by mass spectrometry resulting in 521 different proteins. 4,692 time dependent protein synthesis profiles were generated by exposing S. aureus to nine infection-related stress and starvation stimuli (H2O2, diamide, paraquat, NO, fermentation, nitrate respiration, heat shock, puromycin, mupirocin). These expression profiles are stored in an online resource called Aureolib (http://www.aureolib.de). Moreover, information on target genes of 75 regulators and regulatory elements were included in the database. Cross-comparisons of this extensive data collection of protein synthesis profiles using the tools implemented in Aureolib lead to the identification of stress and starvation specific marker proteins. Altogether, 226 protein synthesis profiles showed induction ratios of 2.5-fold or higher under at least one of the tested conditions with 157 protein synthesis profiles specifically induced in response to a single stimulus. The respective proteins might serve as marker proteins for the corresponding stimulus. By contrast, proteins whose synthesis was increased or repressed in response to more than four stimuli are rather exceptional. The only protein that was induced by six stimuli is the universal stress protein SACOL1759. Most strikingly, cluster analyses of synthesis profiles of proteins differentially synthesized under at least one condition revealed only in rare cases a grouping that correlated with known regulon structures. The most prominent examples are the GapR, Rex, and CtsR regulon. In contrast, protein synthesis profiles of proteins belonging to the CodY and sigma(B) regulon are widely distributed. In summary, Aureolib is by far the most comprehensive protein expression database for S. aureus and provides an essential tool to decipher more complex adaptation processes in S. aureus during host pathogen interaction.", "link"=>"http://www.mendeley.com/research/aureolib-proteome-signature-library-towards-understanding-staphylococcus-aureus-pathophysiology", "reader_count"=>27, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Student > Doctoral Student"=>3, "Researcher"=>5, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>1, "Student > Master"=>4, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Student > Doctoral Student"=>3, "Researcher"=>5, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>1, "Student > Master"=>4, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>11, "Medicine and Dentistry"=>1, "Veterinary Science and Veterinary Medicine"=>2, "Chemistry"=>2, "Computer Science"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>11}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>2}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"Denmark"=>1, "India"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1167804"], "description"=>"<p><i>Aureolib</i> uses a MySQL database to store expression data and relevant information on protein annotation, statistical analyses, and experimental setups.</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "gene expression", "Biological data management", "microbiology", "Bacterial pathogens", "staphylococci", "Host-pathogen interaction", "Microbial physiology", "Molecular cell biology", "Cellular stress responses", "proteomics", "Proteomic databases", "Spectrometric identification of proteins", "Information technology", "databases", "Infectious diseases", "Bacterial diseases", "Staphylococcus aureus", "relational"], "article_id"=>770958, "categories"=>["Information And Computing Sciences", "Medicine", "Biological Sciences"], "users"=>["Stephan Fuchs", "Daniela Zühlke", "Jan Pane-Farre", "Harald Kusch", "Carmen Wolf", "Swantje Reiß", "Le Thi Nguyen Binh", "Dirk Albrecht", "Katharina Riedel", "Michael Hecker", "Susanne Engelmann"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0070669.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_relational_database_model_/770958", "title"=>"The relational database model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-13 01:33:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1167805"], "description"=>"<p>(A) <i>Aureolib</i> consists of three different levels for data management, data processing and visualization of data. (<b>B</b>) Combined with an intuitive user interface accessible by generic web browsers <i>Aureolib</i> provides helpful tools for expression data analyses and data visualization.</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "gene expression", "Biological data management", "microbiology", "Bacterial pathogens", "staphylococci", "Host-pathogen interaction", "Microbial physiology", "Molecular cell biology", "Cellular stress responses", "proteomics", "Proteomic databases", "Spectrometric identification of proteins", "Information technology", "databases", "Infectious diseases", "Bacterial diseases", "Staphylococcus aureus", "graphical", "interface"], "article_id"=>770959, "categories"=>["Information And Computing Sciences", "Medicine", "Biological Sciences"], "users"=>["Stephan Fuchs", "Daniela Zühlke", "Jan Pane-Farre", "Harald Kusch", "Carmen Wolf", "Swantje Reiß", "Le Thi Nguyen Binh", "Dirk Albrecht", "Katharina Riedel", "Michael Hecker", "Susanne Engelmann"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0070669.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Functions_and_graphical_user_interface_of_Aureolib_/770959", "title"=>"Functions and graphical user interface of <i>Aureolib</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-13 01:33:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1167808"], "description"=>"<p>Quantification data for all detected protein spots were normalized (total) and standardized (z-score). Significant changes of spot intensities were determined for each experiment (ANOVA, α = 0.1, distribution based on 1000 permutations) and the corresponding expression values were used for hierarchical sample clustering (HCL, Euclidean distance, complete linkage). Accordingly, the stimuli can be divided into two classes: (<b>A</b>) Stimuli causing continuous changes of the protein synthesis pattern and (<b>B</b>) stimuli transiently affecting the protein synthesis pattern.</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "gene expression", "Biological data management", "microbiology", "Bacterial pathogens", "staphylococci", "Host-pathogen interaction", "Microbial physiology", "Molecular cell biology", "Cellular stress responses", "proteomics", "Proteomic databases", "Spectrometric identification of proteins", "Information technology", "databases", "Infectious diseases", "Bacterial diseases", "Staphylococcus aureus", "synthesis", "patterns"], "article_id"=>770961, "categories"=>["Information And Computing Sciences", "Medicine", "Biological Sciences"], "users"=>["Stephan Fuchs", "Daniela Zühlke", "Jan Pane-Farre", "Harald Kusch", "Carmen Wolf", "Swantje Reiß", "Le Thi Nguyen Binh", "Dirk Albrecht", "Katharina Riedel", "Michael Hecker", "Susanne Engelmann"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0070669.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Intra_experimental_comparison_of_protein_synthesis_patterns_in_response_to_different_stimuli_/770961", "title"=>"Intra-experimental comparison of protein synthesis patterns in response to different stimuli.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-13 01:33:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1167810"], "description"=>"<p>Inter-experimental analyses of stress induced protein synthesis patterns revealed general and specific effects on global protein synthesis. (<b>A</b>) The majority of the synthesis profiles showed a significant (ANOVA, α = 0.1, p-values based on 1000 permutations, absolute threshold of 2.5) induction or repression rate in response to one or two stimuli. (<b>B</b>) To identify more general effects a pairwise comparison of all experiments was performed using protein synthesis profiles significantly changed at least one time point following exposure to the different stimuli (t-test, α = 0.1; p-values based on all possible permutations, adjusted Bonferroni correction). The number of induced (orange) and repressed (blue) protein synthesis profiles shared by the respective stimuli is shown. The total number of synthesis profiles significantly induced or repressed by the respective stimulus are given on the right side. (<b>C</b>) Overlap of marker proteins induced in response to diamide, puromycin, and heat as well as to nitric oxide, fermentation, and nitrate respiration are shown.</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "gene expression", "Biological data management", "microbiology", "Bacterial pathogens", "staphylococci", "Host-pathogen interaction", "Microbial physiology", "Molecular cell biology", "Cellular stress responses", "proteomics", "Proteomic databases", "Spectrometric identification of proteins", "Information technology", "databases", "Infectious diseases", "Bacterial diseases", "Staphylococcus aureus", "aspects"], "article_id"=>770962, "categories"=>["Information And Computing Sciences", "Medicine", "Biological Sciences"], "users"=>["Stephan Fuchs", "Daniela Zühlke", "Jan Pane-Farre", "Harald Kusch", "Carmen Wolf", "Swantje Reiß", "Le Thi Nguyen Binh", "Dirk Albrecht", "Katharina Riedel", "Michael Hecker", "Susanne Engelmann"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0070669.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_General_aspects_of_S_aureus_stress_response_/770962", "title"=>"General aspects of <i>S. aureus</i> stress response.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-13 01:33:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1167811"], "description"=>"<p>Synthesis ratios (stress <i>vs.</i> control) are shown as log<sub>2</sub> values. Fold changes above 2.5 and below 0.4 are colored in orange and blue, respectively. Significant changes are marked by an asterisk (*). Synthesis profiles of proteins belonging to the Rex (<b>A</b>) and Ctsr/HrcA (<b>B</b>) regulon as well as proteins involved in leucine biosynthesis (<b>C</b>) are shown in more detail.</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "gene expression", "Biological data management", "microbiology", "Bacterial pathogens", "staphylococci", "Host-pathogen interaction", "Microbial physiology", "Molecular cell biology", "Cellular stress responses", "proteomics", "Proteomic databases", "Spectrometric identification of proteins", "Information technology", "databases", "Infectious diseases", "Bacterial diseases", "Staphylococcus aureus", "profiles"], "article_id"=>770963, "categories"=>["Information And Computing Sciences", "Medicine", "Biological Sciences"], "users"=>["Stephan Fuchs", "Daniela Zühlke", "Jan Pane-Farre", "Harald Kusch", "Carmen Wolf", "Swantje Reiß", "Le Thi Nguyen Binh", "Dirk Albrecht", "Katharina Riedel", "Michael Hecker", "Susanne Engelmann"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0070669.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Inter_experimental_expression_profiles_of_selected_proteins_/770963", "title"=>"Inter-experimental expression profiles of selected proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-13 01:33:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1167813"], "description"=>"<p>Sectors of 2D gels covering the regions where CysK, GuaB, Upp, SACOL0618 and SACOL1895 are located. Proteins represented by multiple spots indicate post translational modifications. In the present approach the synthesis of protein isoforms differing in p<i>I</i> and/or molecular weight was separately analyzed.</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "gene expression", "Biological data management", "microbiology", "Bacterial pathogens", "staphylococci", "Host-pathogen interaction", "Microbial physiology", "Molecular cell biology", "Cellular stress responses", "proteomics", "Proteomic databases", "Spectrometric identification of proteins", "Information technology", "databases", "Infectious diseases", "Bacterial diseases", "Staphylococcus aureus", "isoforms", "diamide", "nitrosative"], "article_id"=>770965, "categories"=>["Information And Computing Sciences", "Medicine", "Biological Sciences"], "users"=>["Stephan Fuchs", "Daniela Zühlke", "Jan Pane-Farre", "Harald Kusch", "Carmen Wolf", "Swantje Reiß", "Le Thi Nguyen Binh", "Dirk Albrecht", "Katharina Riedel", "Michael Hecker", "Susanne Engelmann"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0070669.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differential_expression_of_protein_isoforms_in_response_to_diamide_A_and_nitrosative_stress_B_/770965", "title"=>"Differential expression of protein isoforms in response to diamide (A) and nitrosative stress (B).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-13 01:33:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1167819"], "description"=>"<p>(<b>A</b>) Hierarchical clustering (Euclidian distance/complete linkage) of synthesis profiles of proteins for which transcription of the respective genes has been shown to be influenced by σ<sup>B </sup><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070669#pone.0070669-Bischoff1\" target=\"_blank\">[48]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070669#pone.0070669-PanFarr1\" target=\"_blank\">[49]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070669#pone.0070669-Gertz1\" target=\"_blank\">[50]</a>. (<b>B</b>) Expression profiles of solely σ<sup>B</sup>-dependent proteins. Abbreviations for stress conditions are: O (H<sub>2</sub>O<sub>2</sub>), D (diamide), P (paraquat), N (nitrogen monoxide), F (fermentation), A (nitrate respiration), H (heat stress), U (puromycin), and M (mupirocin). <sup>1)</sup> Support for a σ<sup>B</sup>-dependent transcriptional start point: experimental (black square), predicted (gray square), not identified yet (white square) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070669#pone.0070669-Fuchs2\" target=\"_blank\">[37]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070669#pone.0070669-Potrykus1\" target=\"_blank\">[43]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070669#pone.0070669-Vinella1\" target=\"_blank\">[70]</a>. <sup>2)</sup> Impact of σ<sup>B</sup>: solely σ<sup>B</sup>-dependent/major effect on expression (black square), co-regulated by additional factors (gray squares), or not determined (white square) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070669#pone.0070669-Gertz1\" target=\"_blank\">[50]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070669#pone.0070669-Vinella1\" target=\"_blank\">[70]</a>. Csb (<u>c</u>ontrolled by <u>s</u>igma <u>B</u>) nomenclature based on Gertz <i>et al. </i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070669#pone.0070669-Gertz1\" target=\"_blank\">[50]</a>.</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "gene expression", "Biological data management", "microbiology", "Bacterial pathogens", "staphylococci", "Host-pathogen interaction", "Microbial physiology", "Molecular cell biology", "Cellular stress responses", "proteomics", "Proteomic databases", "Spectrometric identification of proteins", "Information technology", "databases", "Infectious diseases", "Bacterial diseases", "Staphylococcus aureus", "clusters"], "article_id"=>770971, "categories"=>["Information And Computing Sciences", "Medicine", "Biological Sciences"], "users"=>["Stephan Fuchs", "Daniela Zühlke", "Jan Pane-Farre", "Harald Kusch", "Carmen Wolf", "Swantje Reiß", "Le Thi Nguyen Binh", "Dirk Albrecht", "Katharina Riedel", "Michael Hecker", "Susanne Engelmann"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0070669.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_clusters_of_B_dependent_proteins_/770971", "title"=>"Expression clusters of σ<sup>B</sup>-dependent proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-13 01:33:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1167820"], "description"=>"<p>(<b>A</b>) <i>S. aureus</i> COL was cultivated in synthetic medium at 37°C and treated with 10 mM H<sub>2</sub>O<sub>2</sub> at OD<sub>500</sub> 0.5 (0 min). (<b>B</b>) Protein synthesis profiles were normalized using total normalization and standardized (z-score). Significantly changed synthesis profiles were determined by ANOVA (α = 0.1, distribution based on all permutations, absolute threshold of 2.5). Based on their expression kinetics in response to H<sub>2</sub>O<sub>2</sub>, proteins can be allocated to three groups: proteins which are induced during the acute phase immediately after imposition of stress (red lines), proteins induced during resumption of growth (blue lines) and proteins highly expressed in the tolerance phase (green lines).</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "gene expression", "Biological data management", "microbiology", "Bacterial pathogens", "staphylococci", "Host-pathogen interaction", "Microbial physiology", "Molecular cell biology", "Cellular stress responses", "proteomics", "Proteomic databases", "Spectrometric identification of proteins", "Information technology", "databases", "Infectious diseases", "Bacterial diseases", "Staphylococcus aureus"], "article_id"=>770972, "categories"=>["Information And Computing Sciences", "Medicine", "Biological Sciences"], "users"=>["Stephan Fuchs", "Daniela Zühlke", "Jan Pane-Farre", "Harald Kusch", "Carmen Wolf", "Swantje Reiß", "Le Thi Nguyen Binh", "Dirk Albrecht", "Katharina Riedel", "Michael Hecker", "Susanne Engelmann"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0070669.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Response_of_S_aureus_to_H_2_O_2_/770972", "title"=>"Response of <i>S. aureus</i> to H<sub>2</sub>O<sub>2</sub>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-13 01:33:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1167821"], "description"=>"<p>Regulators or regulatory elements and the number of assigned proteins which are significantly and at least 2.5-fold induced (up) or repressed (down) on synthesis level.</p>1<p>number of corresponding proteins identified on the master gel belonging to the respective regulon.</p>a<p>source: <a href=\"http://regprecise.lbl.gov\" target=\"_blank\">http://regprecise.lbl.gov</a><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070669#pone.0070669-Novichkov2\" target=\"_blank\">[32]</a>.</p>b<p>source: Pagels <i>et al.</i> (2010) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070669#pone.0070669-Pagels1\" target=\"_blank\">[36]</a>.</p>c<p>source: Bischoff et al. 2004 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070669#pone.0070669-Bischoff1\" target=\"_blank\">[48]</a>, Pané-Farré et al. 2006 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070669#pone.0070669-PanFarr1\" target=\"_blank\">[49]</a>, Ziebandt et al. 2001 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070669#pone.0070669-Ziebandt2\" target=\"_blank\">[71]</a>, Ziebandt et al. 2004 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070669#pone.0070669-Ziebandt3\" target=\"_blank\">[72]</a>.</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "gene expression", "Biological data management", "microbiology", "Bacterial pathogens", "staphylococci", "Host-pathogen interaction", "Microbial physiology", "Molecular cell biology", "Cellular stress responses", "proteomics", "Proteomic databases", "Spectrometric identification of proteins", "Information technology", "databases", "Infectious diseases", "Bacterial diseases", "Staphylococcus aureus"], "article_id"=>770973, "categories"=>["Information And Computing Sciences", "Medicine", "Biological Sciences"], "users"=>["Stephan Fuchs", "Daniela Zühlke", "Jan Pane-Farre", "Harald Kusch", "Carmen Wolf", "Swantje Reiß", "Le Thi Nguyen Binh", "Dirk Albrecht", "Katharina Riedel", "Michael Hecker", "Susanne Engelmann"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0070669.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Regulons_in_S_aureus_/770973", "title"=>"Regulons in <i>S. aureus</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-13 01:33:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1167822"], "description"=>"1<p>CDM = chemically defined medium.</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "gene expression", "Biological data management", "microbiology", "Bacterial pathogens", "staphylococci", "Host-pathogen interaction", "Microbial physiology", "Molecular cell biology", "Cellular stress responses", "proteomics", "Proteomic databases", "Spectrometric identification of proteins", "Information technology", "databases", "Infectious diseases", "Bacterial diseases", "Staphylococcus aureus", "experiments", "included", "proteome"], "article_id"=>770974, "categories"=>["Information And Computing Sciences", "Medicine", "Biological Sciences"], "users"=>["Stephan Fuchs", "Daniela Zühlke", "Jan Pane-Farre", "Harald Kusch", "Carmen Wolf", "Swantje Reiß", "Le Thi Nguyen Binh", "Dirk Albrecht", "Katharina Riedel", "Michael Hecker", "Susanne Engelmann"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0070669.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Stress_experiments_included_in_the_proteome_signature_library_/770974", "title"=>"Stress experiments included in the proteome signature library.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-13 01:33:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1167825", "https://ndownloader.figshare.com/files/1167826", "https://ndownloader.figshare.com/files/1167835", "https://ndownloader.figshare.com/files/1167838", "https://ndownloader.figshare.com/files/1167843", "https://ndownloader.figshare.com/files/1167844", "https://ndownloader.figshare.com/files/1167845", "https://ndownloader.figshare.com/files/1167846", "https://ndownloader.figshare.com/files/1167847", "https://ndownloader.figshare.com/files/1167851", "https://ndownloader.figshare.com/files/1167852"], "description"=>"<div><p>Gel-based proteomics is a powerful approach to study the physiology of <i>Staphylococcus aureus</i> under various growth restricting conditions. We analyzed 679 protein spots from a reference 2-dimensional gel of cytosolic proteins of <i>S. aureus</i> COL by mass spectrometry resulting in 521 different proteins. 4,692 time dependent protein synthesis profiles were generated by exposing <i>S. aureus</i> to nine infection-related stress and starvation stimuli (H<sub>2</sub>O<sub>2</sub>, diamide, paraquat, NO, fermentation, nitrate respiration, heat shock, puromycin, mupirocin). These expression profiles are stored in an online resource called <i>Aureolib</i> (<a href=\"http://www.aureolib.de\" target=\"_blank\">http://www.aureolib.de</a>). Moreover, information on target genes of 75 regulators and regulatory elements were included in the database. Cross-comparisons of this extensive data collection of protein synthesis profiles using the tools implemented in <i>Aureolib</i> lead to the identification of stress and starvation specific marker proteins. Altogether, 226 protein synthesis profiles showed induction ratios of 2.5-fold or higher under at least one of the tested conditions with 157 protein synthesis profiles specifically induced in response to a single stimulus. The respective proteins might serve as marker proteins for the corresponding stimulus. By contrast, proteins whose synthesis was increased or repressed in response to more than four stimuli are rather exceptional. The only protein that was induced by six stimuli is the universal stress protein SACOL1759. Most strikingly, cluster analyses of synthesis profiles of proteins differentially synthesized under at least one condition revealed only in rare cases a grouping that correlated with known regulon structures. The most prominent examples are the GapR, Rex, and CtsR regulon. In contrast, protein synthesis profiles of proteins belonging to the CodY and σ<sup>B</sup> regulon are widely distributed. In summary, <i>Aureolib</i> is by far the most comprehensive protein expression database for <i>S. aureus</i> and provides an essential tool to decipher more complex adaptation processes in <i>S. aureus</i> during host pathogen interaction.</p></div>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "gene expression", "Biological data management", "microbiology", "Bacterial pathogens", "staphylococci", "Host-pathogen interaction", "Microbial physiology", "Molecular cell biology", "Cellular stress responses", "proteomics", "Proteomic databases", "Spectrometric identification of proteins", "Information technology", "databases", "Infectious diseases", "Bacterial diseases", "Staphylococcus aureus", "proteome", "pathophysiology"], "article_id"=>770975, "categories"=>["Information And Computing Sciences", "Medicine", "Biological Sciences"], "users"=>["Stephan Fuchs", "Daniela Zühlke", "Jan Pane-Farre", "Harald Kusch", "Carmen Wolf", "Swantje Reiß", "Le Thi Nguyen Binh", "Dirk Albrecht", "Katharina Riedel", "Michael Hecker", "Susanne Engelmann"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0070669.s001", "https://dx.doi.org/10.1371/journal.pone.0070669.s002", "https://dx.doi.org/10.1371/journal.pone.0070669.s003", "https://dx.doi.org/10.1371/journal.pone.0070669.s004", "https://dx.doi.org/10.1371/journal.pone.0070669.s005", "https://dx.doi.org/10.1371/journal.pone.0070669.s006", "https://dx.doi.org/10.1371/journal.pone.0070669.s007", "https://dx.doi.org/10.1371/journal.pone.0070669.s008", "https://dx.doi.org/10.1371/journal.pone.0070669.s009", "https://dx.doi.org/10.1371/journal.pone.0070669.s010", "https://dx.doi.org/10.1371/journal.pone.0070669.s011"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Aureolib_A_Proteome_Signature_Library_Towards_an_Understanding_of_Staphylococcus_aureus_Pathophysiology/770975", "title"=>"<i>Aureolib</i> — A Proteome Signature Library: Towards an Understanding of <i>Staphylococcus aureus</i> Pathophysiology", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-08-13 01:33:12"}

PMC Usage Stats | Further Information

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Relative Metric

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