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Author (up) Cortes, M.P.; Mendoza, S.N.; Travisany, D.; Gaete, A.; Siegel, A.; Cambiazo, V.; Maass, A. pdf  doi
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  Title Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing Type
  Year 2017 Publication Frontiers In Microbiology Abbreviated Journal Front. Microbiol.  
  Volume 8 Issue Pages 15 pp  
  Keywords pathogen; genome-scale; metabolism; constraint-based; Piscirickettsia; salmonis  
  Abstract Piscirickettsia salmonis is an intracellular bacterial fish pathogen that causes piscirickettsiosis, a disease with highly adverse impact in the Chilean salmon farming industry. The development of effective treatment and control methods for piscireckttsiosis is still a challenge. To meet it the number of studies on P. salmonis has grown in the last couple of years but many aspects of the pathogen's biology are still poorly understood. Studies on its metabolism are scarce and only recently a metabolic model for reference strain LF-89 was developed. We present a new genomescale model for P. salmonis LF-89 with more than twice as many genes as in the previous model and incorporating specific elements of the fish pathogen metabolism. Comparative analysis with models of different bacterial pathogens revealed a lower flexibility in P. salmonis metabolic network. Through constraint-based analysis, we determined essential metabolites required for its growth and showed that it can benefit from different carbon sources tested experimentally in new defined media. We also built an additional model for strain A1-15972, and together with an analysis of P. salmonis pangenome, we identified metabolic features that differentiate two main species clades. Both models constitute a knowledge-base for P. salmonis metabolism and can be used to guide the efficient culture of the pathogen and the identification of specific drug targets.  
  Address [Cortes, Maria P.; Mendoza, Sebastian N.; Travisany, Dante; Maass, Alejandro] Univ Chile, Ctr Math Modeling, Math, Santiago, Chile, Email: mpcortes@dim.uchile.cl  
  Corporate Author Thesis  
  Publisher Frontiers Media Sa Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1664-302x ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000417578100001 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 787  
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Author (up) Perez-Lara, G.; Moyano, T.C.; Vega, A.; Larrondo, L.F.; Polanco, R.; Alvarez, J.M.; Aguayo, D.; Canessa, P. doi  openurl
  Title The Botrytis cinerea Gene Expression Browser Type
  Year 2023 Publication Journal of Fungi Abbreviated Journal J. Fungi  
  Volume 9 Issue 1 Pages 84  
  Keywords Botrytis cinerea; RNA-Seq; phytopathogen; transcriptomics; Botrytis Expression Browser; BEB  
  Abstract For comprehensive gene expression analyses of the phytopathogenic fungus Botrytis cinerea, which infects a number of plant taxa and is a cause of substantial agricultural losses worldwide, we developed BEB, a web-based B. cinerea gene Expression Browser. This computationally inexpensive web-based application and its associated database contain manually curated RNA-Seq data for B. cinerea. BEB enables expression analyses of genes of interest under different culture conditions by providing publication-ready heatmaps depicting transcript levels, without requiring advanced computational skills. BEB also provides details of each experiment and user-defined gene expression clustering and visualization options. If needed, tables of gene expression values can be downloaded for further exploration, including, for instance, the determination of differentially expressed genes. The BEB implementation is based on open-source computational technologies that can be deployed for other organisms. In this case, the new implementation will be limited only by the number of transcriptomic experiments that are incorporated into the platform. To demonstrate the usability and value of BEB, we analyzed gene expression patterns across different conditions, with a focus on secondary metabolite gene clusters, chromosome-wide gene expression, previously described virulence factors, and reference genes, providing the first comprehensive expression overview of these groups of genes in this relevant fungal phytopathogen. We expect this tool to be broadly useful in B. cinerea research, providing a basis for comparative transcriptomics and candidate gene identification for functional assays.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 2309-608X ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000917555600001 Approved  
  Call Number UAI @ alexi.delcanto @ Serial 1756  
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