Examinando por Materia "ecology"

Mostrando 1 - 4 de 4
  • No hay miniatura disponible
    Ítem
    IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
    (BioMed Central Ltd., 2016-12-16) Narayanasamy, S.; Jarosz, Y.; Muller, E.E.L.; Heintz-Buschart, A.; Herold, M.; Kaysen, A.; Laczny, C.C.; Pinel, N.; May, P.; Wilmes, P.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
    Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning, as well as genomic signature-based visualizations. The IMP-based data integration strategy enhances data usage, output volume, and output quality as demonstrated using relevant use-cases. Finally, IMP is encapsulated within a user-friendly implementation using Python and Docker. IMP is available at http://r3lab.uni.lu/web/imp/ (MIT license).
  • Miniatura
    Ítem
    Malezas incomprendidas - Portada Revista Universidad EAFIT Descubre y Crea Vol. 58 No. 179
    (Universidad EAFIT, 2024-08-23) Solís Marin, Juan Camilo; Eslava, Maria Luisa; Universidad EAFIT
  • Miniatura
    Ítem
    Rebellion against Pavement: the Network of Gardeners in Medellin
    (Universidad EAFIT, 2018-11-01) Giraldo Cerón, Andrés Felipe; Equipo Universidad de los niños
  • No hay miniatura disponible
    Ítem
    Reviewing microbial behaviors in ecosystems leading to a natural quorum quenching occurrence
    (INST TECNOLOGIA PARANA, 2017-01-01) Sierra Zapata, Laura; Romero Tabarez, Magally; Correa Alvarez, Javier; Villegas Escobar, Valeska; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
    Quorum sensing is considered one of the most important discoveries in cell-to-cell communication. Although revealed in Bacteria, it has been identified as well as a mechanism present in the other two domains, Eukaryota and Archaea. This phenomenon consists mainly of an exchange and sensing of "words" produced by each cell: chemical signals known as autoinducers. The process takes places at high cell densities and confined environments, triggering the expression of specific genes that manifest in a determined phenotype. Quorum sensing has a fundamental importance in the organisms' fitness in natural ecosystems since it activates many of the traits needed by cells to survive under specific conditions, and thus a wide variety of chemical signals, which are detailed throughout the review, have evolved in response to the needs of an organism in the ecosystem it inhabits. As a counterpart, derived from the natural occurrence of quorum sensing, comes it's antagonistic process named quorum quenching. Acting in the exact opposite way, quorum quenching interferes or degrades the autoinducers confusing and stopping communication, hence affecting transcriptional regulation and expression of a specific phenotype. The main reasons for stopping this mechanism go from fading their own signals when perceiving scarce nutrients conditions, to degrading competitors' signals to take advantage in the ecosystem. Some of the most studied purposes and means known up to date to be used by cells for making quorum quenching in their ecosystems is what will be discussed along this review, offering information for future works on quorum quencher molecules bioprospection.