Boolean Models of Biosurfactants Production in Pseudomonas fluorescens
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{"title"=>"Boolean models of biosurfactants production in Pseudomonas fluorescens", "type"=>"journal", "authors"=>[{"first_name"=>"Adrien", "last_name"=>"Richard", "scopus_author_id"=>"7102160483"}, {"first_name"=>"Gaelle", "last_name"=>"Rossignol", "scopus_author_id"=>"23669125200"}, {"first_name"=>"Jean Paul", "last_name"=>"Comet", "scopus_author_id"=>"55903518200"}, {"first_name"=>"Gilles", "last_name"=>"Bernot", "scopus_author_id"=>"6602085796"}, {"first_name"=>"Jannine", "last_name"=>"Guespin-Michel", "scopus_author_id"=>"57192359320"}, {"first_name"=>"Annabelle", "last_name"=>"Merieau", "scopus_author_id"=>"6603248882"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84856450357", "pui"=>"364181070", "doi"=>"10.1371/journal.pone.0024651", "pmid"=>"22303435", "scopus"=>"2-s2.0-84856450357", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic) 1932-6203 (Linking)"}, "id"=>"9543f5ef-0d15-33f7-9186-7bd46a0e629a", "abstract"=>"Cyclolipopeptides (CLPs) are biosurfactants produced by numerous Pseudomonas fluorescens strains. CLP production is known to be regulated at least by the GacA/GacS two-component pathway, but the full regulatory network is yet largely unknown. In the clinical strain MFN1032, CLP production is abolished by a mutation in the phospholipase C gene (plcC) and not restored by plcC complementation. Their production is also subject to phenotypic variation. We used a modelling approach with Boolean networks, which takes into account all these observations concerning CLP production without any assumption on the topology of the considered network. Intensive computation yielded numerous models that satisfy these properties. All models minimizing the number of components point to a bistability in CLP production, which requires the presence of a yet unknown key self-inducible regulator. Furthermore, all suggest that a set of yet unexplained phenotypic variants might also be due to this epigenetic switch. The simplest of these Boolean networks was used to propose a biological regulatory network for CLP production. This modelling approach has allowed a possible regulation to be unravelled and an unusual behaviour of CLP production in P. fluorescens to be explained.", "link"=>"http://www.mendeley.com/research/boolean-models-biosurfactants-production-pseudomonas-fluorescens", "reader_count"=>23, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>8, "Student > Ph. D. Student"=>5, "Student > Master"=>3, "Student > Bachelor"=>2, "Professor"=>2, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>8, "Student > Ph. D. Student"=>5, "Student > Master"=>3, "Student > Bachelor"=>2, "Professor"=>2, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Environmental Science"=>3, "Mathematics"=>3, "Agricultural and Biological Sciences"=>13, "Physics and Astronomy"=>1, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>1, "Unspecified"=>1}, "reader_count_by_subdiscipline"=>{"Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Mathematics"=>{"Mathematics"=>3}, "Environmental Science"=>{"Environmental Science"=>3}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Poland"=>2, "France"=>1, "Chile"=>1, "Germany"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/686406"], "description"=>"<p>The asynchronous state graph is represented in a 4D-grid, with in the curved axis (first component), in the vertical axis (second component), in the horizontal axis (third component), and in the last axis (fourth component).</p>", "links"=>[], "tags"=>["boolean"], "article_id"=>356896, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Adrien Richard", "Gaelle Rossignol", "Jean-Paul Comet", "Gilles Bernot", "Jannine Guespin-Michel", "Annabelle Merieau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024651.g003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_minimal_consistent_Boolean_network_with_4_components_/356896", "title"=>"A minimal consistent Boolean network with 4 components.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-31 01:54:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/686630"], "description"=>"<p>Circles represent the proteins in the network and edges represent regulatory interaction (bold lines: known interactions, dotted lines: hypothetical interactions). Arrow headed edges represent positive regulatory interaction, and T-headed edges represent negative interaction. PlcC: phospholipase C; CLPs: cyclolipopeptides production; R: unknown regulator (with positive feedback).</p>", "links"=>[], "tags"=>["clp", "deduced", "boolean"], "article_id"=>357114, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Adrien Richard", "Gaelle Rossignol", "Jean-Paul Comet", "Gilles Bernot", "Jannine Guespin-Michel", "Annabelle Merieau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024651.g006", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hypothetic_biological_regulatory_network_of_CLP_production_with_negative_interactions_deduced_from_the_Boolean_model_/357114", "title"=>"Hypothetic biological regulatory network of CLP production (with negative interactions) deduced from the Boolean model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-31 01:58:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/686244"], "description"=>"<p>The graphical conventions used to described the interaction graph of each network are as follows: normal arrows correspond to positive interactions, and T-end arrows correspond to negative interactions. Asynchronous state graphs are represented in a 3D-grid, with in the vertical axis (first component), in the horizontal axis (second component), and in the third axis (third component).</p>", "links"=>[], "tags"=>["boolean", "networks"], "article_id"=>356730, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Adrien Richard", "Gaelle Rossignol", "Jean-Paul Comet", "Gilles Bernot", "Jannine Guespin-Michel", "Annabelle Merieau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024651.g001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_two_minimal_consistent_Boolean_networks_with_3_components_/356730", "title"=>"The two minimal consistent Boolean networks with 3 components.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-31 01:52:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/686557"], "description"=>"<p><b> on the consistent network of </b><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024651#pone-0024651-g003\" target=\"_blank\"><b>Figure 3</b></a><b>.</b> Asynchronous state graphs are represented in a 4D-grid, as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024651#pone-0024651-g003\" target=\"_blank\">Figure 3</a>. The left graph described the dynamics of network of <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024651#pone-0024651-g003\" target=\"_blank\">Figure 3</a>. The right graph described the dynamics of this network under mutation. Stable states and correspond to strains MFN1032 and group 1 variants complemented by or gene, stable state corresponds to group 1 variants, and stable states corresponds to strains MFN1038 and group 2 variants. Dotted arrows represent the effect of mutation or complementation in . Bold lines represent trajectories followed by the systems.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "computer science"], "article_id"=>357041, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Adrien Richard", "Gaelle Rossignol", "Jean-Paul Comet", "Gilles Bernot", "Jannine Guespin-Michel", "Annabelle Merieau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024651.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illustration_of_property_/357041", "title"=>"Illustration of property", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-31 01:57:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/686467"], "description"=>"<p><b> on the consistent network of </b><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024651#pone-0024651-g003\" target=\"_blank\"><b>Figure 3</b></a><b>.</b> Asynchronous state graphs are represented in a 4D-grid, as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024651#pone-0024651-g003\" target=\"_blank\">Figure 3</a>. The left graph described the dynamics of network of <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024651#pone-0024651-g003\" target=\"_blank\">Figure 3</a>. The right graph described the dynamics of this network under mutation. Stable states , and corresponds to strains MFN1032, MFN1037 and MFN1038, respectively. Dotted arrows represent the effect of mutation or complementation in . Bold lines represent trajectories followed by the systems.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "computer science"], "article_id"=>356957, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Adrien Richard", "Gaelle Rossignol", "Jean-Paul Comet", "Gilles Bernot", "Jannine Guespin-Michel", "Annabelle Merieau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024651.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illustration_of_property_/356957", "title"=>"Illustration of property", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-31 01:55:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/350127"], "description"=>"<div><p>Cyclolipopeptides (CLPs) are biosurfactants produced by numerous <em>Pseudomonas fluorescens strains</em>. CLP production is known to be regulated at least by the GacA/GacS two-component pathway, but the full regulatory network is yet largely unknown. In the clinical strain MFN1032, CLP production is abolished by a mutation in the phospholipase C gene () and not restored by complementation. Their production is also subject to phenotypic variation. We used a modelling approach with Boolean networks, which takes into account all these observations concerning CLP production without any assumption on the topology of the considered network. Intensive computation yielded numerous models that satisfy these properties. All models minimizing the number of components point to a bistability in CLP production, which requires the presence of a yet unknown key self-inducible regulator. Furthermore, all suggest that a set of yet unexplained phenotypic variants might also be due to this epigenetic switch. The simplest of these Boolean networks was used to propose a biological regulatory network for CLP production. This modelling approach has allowed a possible regulation to be unravelled and an unusual behaviour of CLP production in <em>P. fluorescens</em> to be explained.</p> </div>", "links"=>[], "tags"=>["boolean", "models", "biosurfactants"], "article_id"=>129212, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Adrien Richard", "Gaelle Rossignol", "Jean-Paul Comet", "Gilles Bernot", "Jannine Guespin-Michel", "Annabelle Merieau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024651", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Boolean_Models_of_Biosurfactants_Production_in_Pseudomonas_fluorescens_/129212", "title"=>"Boolean Models of Biosurfactants Production in <em>Pseudomonas fluorescens</em>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-31 02:33:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/686676"], "description"=>"<p>: Presence; : Absence (early stationary growth phase in LB medium at C).</p>", "links"=>[], "tags"=>["hemolytic", "phospholipase", "cyclolipopeptides"], "article_id"=>357162, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Adrien Richard", "Gaelle Rossignol", "Jean-Paul Comet", "Gilles Bernot", "Jannine Guespin-Michel", "Annabelle Merieau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024651.t001", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_experimental_results_concerning_the_production_of_hemolytic_activity_phospholipase_C_and_cyclolipopeptides_in_different_genetic_backgrounds_/357162", "title"=>"Summary of experimental results concerning the production of hemolytic activity, phospholipase C and cyclolipopeptides in different genetic backgrounds.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-31 01:59:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/686334"], "description"=>"<p><b> on network 1.</b> Asynchronous state graphs are represented in a grid, as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024651#pone-0024651-g001\" target=\"_blank\">Figure 1</a>. The left graph described the dynamics of network 1. The right graph described the dynamics of network 1 under mutation. Stable states , and correspond to strains MFN1032, MFN1037 and MFN 1038, respectively. Dotted arrows represent the effect of mutation or complementation in . Bold lines represent trajectories followed by the systems.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "computer science"], "article_id"=>356823, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Adrien Richard", "Gaelle Rossignol", "Jean-Paul Comet", "Gilles Bernot", "Jannine Guespin-Michel", "Annabelle Merieau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024651.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illustration_of_property_/356823", "title"=>"Illustration of property", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-31 01:53:43"}

PMC Usage Stats | Further Information

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Relative Metric

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