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Baskin II, Lozano S, Durot M, Marcou G, Horvath D, Varnek A. Autoignition temperature: comprehensive data analysis and predictive models. SAR QSAR Environ Res 2020; 31:597-613. [PMID: 32646236 DOI: 10.1080/1062936x.2020.1785933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
Here we report a new predictive model for autoignition temperature (AIT), an important physical parameter widely used to assess potential safety hazards of combustible materials. Available structure-AIT data extracted from different sources were critically analysed. Support vector regression (SVR) models on different data subsets were built in order to identify a reliable compound set on which a realistic model could be built. This led to a selection of the dataset containing 875 compounds annotated with AIT values. The thereupon-based SVR model performs reasonably well in cross-validation with the determination coefficient r 2 = 0.77 and mean absolute error MAE = 37.8°C. External validation on 20 industrial compounds missing in the training set confirmed its good predictive power (MAE = 28.7°C).
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Affiliation(s)
- I I Baskin
- Laboratory of Chemoinformatics, University of Strasbourg, UMR 7140 CNRS/UniStra , Strasbourg, France
| | - S Lozano
- BioLab, Centre de Recherche de Solaize, Total , Solaize, France
| | - M Durot
- BioLab, Centre de Recherche de Solaize, Total , Solaize, France
| | - G Marcou
- Laboratory of Chemoinformatics, University of Strasbourg, UMR 7140 CNRS/UniStra , Strasbourg, France
| | - D Horvath
- Laboratory of Chemoinformatics, University of Strasbourg, UMR 7140 CNRS/UniStra , Strasbourg, France
| | - A Varnek
- Laboratory of Chemoinformatics, University of Strasbourg, UMR 7140 CNRS/UniStra , Strasbourg, France
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Dequivre M, Diel B, Villard C, Sismeiro O, Durot M, Coppée JY, Nesme X, Vial L, Hommais F. Small RNA Deep-Sequencing Analyses Reveal a New Regulator of Virulence in Agrobacterium fabrum C58. Mol Plant Microbe Interact 2015; 28:580-589. [PMID: 26024442 DOI: 10.1094/mpmi-12-14-0380-fi] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Novel ways of regulating Ti plasmid functions were investigated by studying small RNAs (sRNAs) that are known to act as posttranscriptional regulators in plant pathogenic bacteria. sRNA-seq analyses of Agrobacterium fabrum C58 allowed us to identify 1,108 small transcripts expressed in several growth conditions that could be sRNAs. A quarter of them were confirmed by bioinformatics or by biological experiments. Antisense RNAs represent 24% of the candidates and they are over-represented on the pTi (with 62% of pTi sRNAs), suggesting differences in the regulatory mechanisms between the essential and accessory replicons. Moreover, a large number of these pTi antisense RNAs are transcribed opposite to those genes involved in virulence. Others are 5'- and 3'-untranslated region RNAs and trans-encoded RNAs. We have validated, by rapid amplification of cDNA ends polymerase chain reaction, the transcription of 14 trans-encoded RNAs, among which RNA1111 is expressed from the pTiC58. Its deletion decreased the aggressiveness of A. fabrum C58 on tomatoes, tobaccos, and kalanchoe, suggesting that this sRNA activates virulence. The identification of its putative target mRNAs (6b gene, virC2, virD3, and traA) suggests that this sRNA may coordinate two of the major pTi functions, the infection of plants and its dissemination among bacteria.
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Affiliation(s)
- M Dequivre
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 3CNRS, UMR 5240 Microbiologie Adaptation et Pathogénie, F-69622 Villeurbanne, France
| | - B Diel
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 3CNRS, UMR 5240 Microbiologie Adaptation et Pathogénie, F-69622 Villeurbanne, France
- 4CNRS, UMR 5557 Ecologie Microbienne, F-69622 Villeurbanne, France
- 5INRA, USC 1364 Ecologie Microbienne, F-69622 Villeurbanne, France
| | - C Villard
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 3CNRS, UMR 5240 Microbiologie Adaptation et Pathogénie, F-69622 Villeurbanne, France
| | - O Sismeiro
- 6Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Institut Pasteur, 25 rue du Dr. Roux, F75015 Paris, France
| | - M Durot
- 7CEA/DSV/FAR/IG/Genoscope and CNRS UMR8030 Laboratoire d'Analyses Bioinformatiques en Métabolisme et Génomique, 2 rue Gaston Crémieux 91057 Evry cedex, France
- 8Total New Energies USA, 5858 Horton Street, Emeryville, CA 94608, U.S.A
| | - J Y Coppée
- 6Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Institut Pasteur, 25 rue du Dr. Roux, F75015 Paris, France
| | - X Nesme
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 4CNRS, UMR 5557 Ecologie Microbienne, F-69622 Villeurbanne, France
- 5INRA, USC 1364 Ecologie Microbienne, F-69622 Villeurbanne, France
| | - L Vial
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 4CNRS, UMR 5557 Ecologie Microbienne, F-69622 Villeurbanne, France
- 5INRA, USC 1364 Ecologie Microbienne, F-69622 Villeurbanne, France
| | - F Hommais
- 1Université de Lyon, F-69622, Lyon, France
- 2Université Lyon 1, F-69622 Villeurbanne, France
- 3CNRS, UMR 5240 Microbiologie Adaptation et Pathogénie, F-69622 Villeurbanne, France
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Le Fèvre F, Smidtas S, Combe C, Durot M, d'Alché-Buc F, Schachter V. CycSim--an online tool for exploring and experimenting with genome-scale metabolic models. Bioinformatics 2009; 25:1987-8. [PMID: 19420054 PMCID: PMC2712333 DOI: 10.1093/bioinformatics/btp268] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Summary:CycSim is a web application dedicated to in silico experiments with genome-scale metabolic models coupled to the exploration of knowledge from BioCyc and KEGG. Specifically, CycSim supports the design of knockout experiments: simulation of growth phenotypes of single or multiple gene deletions mutants on specified media, comparison of these predictions with experimental phenotypes and direct visualization of both on metabolic maps. The web interface is designed for simplicity, putting constraint-based modelling techniques within easier reach of biologists. CycSim also functions as an online repository of genome-scale metabolic models. Availability:http://www.genoscope.cns.fr/cycsim Contact:cycsim@genoscope.cns.fr
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Affiliation(s)
- F Le Fèvre
- CEA, DSV, IG, Genoscope, UMR 8030, Evry F-91057, France
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