Client applications and Server Side docker for management of RNASeq and/or VariantSeq workflows and pipelines of the GPRO Suite

The GPRO suite is an in-progress bioinformatic project for -omic data analyses. As part of the continued growth of this project, we introduce a client side & server side solution for comparative transcriptomics and analysis of variants. The client side consists of two Java applications called "RNASeq" and "VariantSeq" to manage workflows for RNA-seq and Variant-seq analysis, respectively, based on the most common command line interface tools for each topic. Both applications are coupled with a Linux server infrastructure (named GPRO Server Side) that hosts all dependencies of each application (scripts, databases, and command line interface tools). Implementation of the server side requires a Linux operating system, PHP, SQL, Python, bash scripting, and third-party software. The GPRO Server Side can be deployed via a Docker container that can be installed in the user's PC using any operating system or on remote servers as a cloud solution. The two applications are available as desktop and cloud applications and provide two execution modes: a Step-by-Step mode enables each step of a workflow to be executed independently and a Pipeline mode allows all steps to be run sequentially. The two applications also feature an experimental support system called GENIE that consists of a virtual chatbot/assistant and a pipeline jobs panel coupled with an expert system. The chatbot can troubleshoot issues with the usage of each tool, the pipeline job panel provides information about the status of each task executed in the GPRO Server Side, and the expert provides the user with a potential recommendation to identify or fix failed analyses. The two applications and the GPRO Server Side combine the user-friendliness and security of client software with the efficiency of front-end & back-end solutions to manage command line interface software for RNA-seq and variant-seq analysis via interface environments

Modulation by Lactobacillus rhamnosus GG of microbiota and innate immune functions in chronological old and adult premature ageing mice

Resumen del trabajo presentado al 10th Workshop on Probiotics and Prebiotics, celebrado en Las Palmas de Gran Canaria del 6 al 8 de febrero de 2019.[Background and Aims] Ageing is characterized by an impairment of the homeostatic (nervous and immune) systems and by changes in the intestinal microbiota. The objective of the study was to analyse differences in the gut microbiota and in several innate immune functions in old and prematurely ageing mice (PAM) when compared with adults, and the modulatory effects of supplementing with Lactobacillus rhamnosus GG.[Methods] Prematurely aging mice (PAM), old and adult mice (females ICR-CD1) were divided into two groups (N = 8-10), which received LGG (109 CFU/mice/day; lyophilized in skim milk and added to drink water) or skim milk without the probiotic LGG (controls). After 4 weeks of LGG supplementation, mice were analysed for several innate immune parameters (chemotaxis, phagocytosis and natural killer activity). Faecal samples were collected for microbiota analysis at 0, 2 and 4 weeks of LGG supplementation.[Results] Ageing in ICR-CD1 female mice was related with increase of Lactobacillus and Blautia coccoides/Eubacterium rectale and decrease of Akkermansia. LGG supplementation was related with changes in Bifidobacterium, Faecalibacterium and Ruminococcus counts. PAM and old mice showed lower values of the immune functions analysed than adult mice. After 4 weeks of LGG ingestion all these functions improved, achieving values similar to those in adults.[Conclusion] L. rhamnosus GG can be considered a probiotic supplement useful for upgrading the immune system in ageing and, consequently, for reaching a healthy longevity.FIS (PI15/01787) of Health Institute Carlos III – Regional Developing Aid European Funds (ISCIII-FEDER), AGL2016-75951-R, CDTI (ADAPTEA IDI-20150753) and CYTED (P916PTE0233).Peer reviewe

Lactobacillus rhamnosus GG mejora la respuesta conductual e inmunitaria de ratones prematuramente envejecidos y aumenta su longevidad

Resumen del póster presentado al XII Workshop Sociedad Española de Microbiota, Probióticos y Prebióticos (SEMiPyP) y I Congreso Sociedad Iberoamericana de Microbiota, Probióticos y Prebióticos (SIAMPYP), celebrado de forma virtual del 15 al 18 de septiembre de 2021.[Introducción/Objetivos]: El envejecimiento se asocia con el deterioro del sistema nervioso e inmunitario y la consecuente pérdida de homeostasis que conduce a una mayor morbilidad y mortalidad. Ratones prematuramente envejecidos (PAM), muestran, siendo adultos, un sistema nervioso e inmunitario típicos de animales cronológicamente viejos, teniendo menor longevidad que los no prematuramente envejecidos (E-NPAM) de igual edad. La suplementación con algunos probióticos ha demostrado mejorar los sistemas homeostáticos y conseguir unadecuado mantenimiento de la salud. Lactobacillus rhamnosus GG (LGG) presenta algunos de estos efectos, pero su incidencia en la longevidad saludable no ha sido comprobada en mamíferos. El objetivo del trabajo fue estudiar el efecto de tomar LGG durante 2 y 4 semanas en diversos parámetros conductuales y de funcionalidad inmunitaria de leucocitos peritoneales en PAM, así como sobre la longevidad.[Métodos]: Ratones hembra (ICR-CD1), adultas, fueron clasificadas en PAM y E-NPAM, y se dividieron en los siguientes grupos: 1) PAM suplementados con LGG (PAMLGG) (ingirieron durante 4 semanas 109 ufc/ratón/día disuelto en el agua); 2) PAM control (PAMC), y 3) E-NPAM control (E-NPAMC). PAMC y E-NPAMC recibieron cantidad similar de bebida sin LGG. Tras 2 semanas de tratamiento, se realizaron pruebas conductuales, y a las 2 y 4 semanas se extrajeron leucocitos peritoneales para estudiar su funcionalidad.[Resultados]: PAMLGG presentan mayor coordinación, equilibrio, vigor neuromuscular, y exploración, y menor ansiedad que los PAMC. También, mostraron funciones inmunitarias (quimiotaxis, fagocitosis y linfoproliferación) mejores que las de PAMC, tras 4 semanas y tras 2 semanas de ingestión. En los parámetros estudiados los valores de PAMLGG fueron similares a los de E-NPAMC, e igual sucedió con la longevidad.[Conclusiones]: La administración de LGG, durante un período de tiempo corto, podría ser una buena estrategia nutricional para ralentizar el deterioro asociado al envejecimiento en individuos prematuramente envejecidos, consiguiendo así una mayor longevidad saludable.Peer reviewe