Establecimiento de módulo funcionales de secuencia en familias de metiltransferasas de RNA y su uso en la búsqueda de genes de resistencia a antibióticos en patógenos humanos

En el presente trabajo realizó un estudio a nivel biocomputacional y a nivel molecular que permitiera dilucidar las relaciones funcionales y filogenéticas de las metiltransferasa de RNA con el fin de: (i) Esclarecer su origen e historia evolutiva (ii) caracterizar nuevas metiltransferasas de RNA (iii) Identificar nuevos genes de MTasas asociados a la resistencia a antibióticos en paleógenos humanos y (iv) establecer patrones consenso de aminoácidos y nucleótidos que permitan el diseño de marcadores moleculares para la identificación experimental de genes responsables de resistencias. Para el análisis bioinformático se emplearon aproximadamente 34 familias de metiltransferasas de RNA correspondientes a las enzimas endógenas identificadas en Escherichia coli asociadas a metilaciones en el rRNA y tRNA. Este análisis estuvo compuesto por cuatro etapas. Para el análisis experimental se emplearon 6 aislamientos de pseudomona aeruginosa de origen clínico resistentes a aminoglucósidos y obtenidos a partir de, muestras de orina, hueso, secreciones e isopado rectal de pacientes afectados por infecciones asociadas a la atención de salud (IAAS).Departamento Administrativo de Ciencia, Tecnología e Innovación [CO] Colciencias5817-569-34856Establecimiento de módulo funcionales de secuencia en familias de metiltransferasas de RNA y su uso en la búsqueda de genes de resistencia a antibióticos en patógenos humanosn

Colombia, an unknown genetic diversity in the era of Big Data

Abstract Background Latin America harbors some of the most biodiverse countries in the world, including Colombia. Despite the increasing use of cutting-edge technologies in genomics and bioinformatics in several biological science fields around the world, the region has fallen behind in the inclusion of these approaches in biodiversity studies. In this study, we used data mining methods to search in four main public databases of genetic sequences such as: NCBI Nucleotide and BioProject, Pathosystems Resource Integration Center, and Barcode of Life Data Systems databases. We aimed to determine how much of the Colombian biodiversity is contained in genetic data stored in these public databases and how much of this information has been generated by national institutions. Additionally, we compared this data for Colombia with other countries of high biodiversity in Latin America, such as Brazil, Argentina, Costa Rica, Mexico, and Peru. Results In Nucleotide, we found that 66.84% of total records for Colombia have been published at the national level, and this data represents less than 5% of the total number of species reported for the country. In BioProject, 70.46% of records were generated by national institutions and the great majority of them is represented by microorganisms. In BOLD Systems, 26% of records have been submitted by national institutions, representing 258 species for Colombia. This number of species reported for Colombia span approximately 0.46% of the total biodiversity reported for the country (56,343 species). Finally, in PATRIC database, 13.25% of the reported sequences were contributed by national institutions. Colombia has a better biodiversity representation in public databases in comparison to other Latin American countries, like Costa Rica and Peru. Mexico and Argentina have the highest representation of species at the national level, despite Brazil and Colombia, which actually hold the first and second places in biodiversity worldwide. Conclusions Our findings show gaps in the representation of the Colombian biodiversity at the molecular and genetic levels in widely consulted public databases. National funding for high-throughput molecular research, NGS technologies costs, and access to genetic resources are limiting factors. This fact should be taken as an opportunity to foster the development of collaborative projects between research groups in the Latin American region to study the vast biodiversity of these countries using ‘omics’ technologies

BMC Gebomics

Background. Duck treatments and vaccine designs against the opportunistic human pathogen Pseudomonas aeruginosa have multiple issues, all associated with the diverse genetic traits present in this pathogen, ranging from multi-drug resistant genes to the molecular machinery for the biosynthesis of biofilms. Several candidate vaccines against P. aeruginosa have been developed, which target the outer membrane proteins; However, major issues arise when attempting to establish complete protection against this pathogen due to its presumably genotypic variation at the strain level. To shed light on this concern, we propose this study to assess the P. aeruginosa pangenome and its molecular evolution across multiple strains. Results the P. aeruginosa pangenome was estimated to contain almost 17,000 non-redundant genes, and approximately 15% of these constituted the core genome. Functional analyzes of the accessory genome indicated a wide presence of genetic elements directly associated with pathogenicity. An in-depth molecular evolution analysis revealed the full landscape of selection forces acting on the P aeruginosa pangenome, in which purifying selection drives evolution in the genome of this human pathogen. We also detected distinctive selection wide variety of outer membrane proteins, with the data supporting the concept of substantial genetic variation in proteins probably recognized antigens. Approaching the evolutionary information of genes under extremely positive selection, we designed a new multi-locus sequencing typing assay for and informative, rapid and cost-effective genotyping of P. Aeruginosa on a large scale.Departamento Administrativo de Ciencia, Tecnología e Innovación [CO] Colciencias5817-569-34856Establecimiento de módulo funcionales de secuencia en familias de metiltransferasas de RNA y su uso en la búsqueda de genes de resistencia a antibióticos en patógenos humanosn

Additional file 1: of Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species

Metadata associated with the 181 strains used in this study to reconstruct the P. aeruginosa pangenome. All the information regarding the genome size, ORF predicted, RNA genes, host, geographic location, virulence, and resistance genes were recovered from PATRIC database. NA indicates no information available. (PDF 808 kb