Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638

In recent years, there has been a large increase in the amount of experimental evidence for diverse archaeal organisms, and these findings allow for a comprehensive analysis of archaeal genetic organization. However, studies about regulatory mechanisms in this cellular domain are still limited. In this context, we identified a repertoire of 86 DNA-binding transcription factors (TFs) in the archaeon Pyrococcus furiosus DSM 3638, that are clustered into 32 evolutionary families. In structural terms, 45% of these proteins are composed of one structural domain, 41% have two domains, and 14% have three structural domains. The most abundant DNA-binding domain corresponds to the winged helix-turn-helix domain; with few alternative DNA-binding domains. We also identified seven regulons, which represent 13.5% (279 genes) of the total genes in this archaeon. These analyses increase our knowledge about gene regulation in P. furiosus DSM 3638 and provide additional clues for comprehensive modeling of transcriptional regulatory networks in the Archaea cellular domain

Deciphering the functional diversity of DNA-binding transcription factors in Bacteria and Archaea organisms.

DNA-binding Transcription Factors (TFs) play a central role in regulation of gene expression in prokaryotic organisms, and similarities at the sequence level have been reported. These proteins are predicted with different abundances as a consequence of genome size, where small organisms contain a low proportion of TFs and large genomes contain a high proportion of TFs. In this work, we analyzed a collection of 668 experimentally validated TFs across 30 different species from diverse taxonomical classes, including Escherichia coli K-12, Bacillus subtilis 168, Corynebacterium glutamicum, and Streptomyces coelicolor, among others. This collection of TFs, together with 111 hidden Markov model profiles associated with DNA-binding TFs collected from diverse databases such as PFAM and DBD, was used to identify the repertoire of proteins putatively devoted to gene regulation in 1321 representative genomes of Archaea and Bacteria. The predicted regulatory proteins were posteriorly analyzed in terms of their genomic context, allowing the prediction of functions for TFs and their neighbor genes, such as genes involved in virulence, enzymatic functions, phosphorylation mechanisms, and antibiotic resistance. The functional analysis associated with PFAM groups showed diverse functional categories were significantly enriched in the collection of TFs and the proteins encoded by the neighbor genes, in particular, small-molecule binding and amino acid transmembrane transporter activities associated with the LysR family and proteins devoted to cellular aromatic compound metabolic processes or responses to drugs, stress, or abiotic stimuli in the MarR family. We consider that with the increasing data derived from new technologies, novel TFs can be identified and help improve the predictions for this class of proteins in complete genomes. The complete collection of experimentally characterized and predicted TFs is available at http://web.pcyt.unam.mx/EntrafDB/

Kéfir, fuente de enzimas hidrolasas y bacterias con potencial para degradar plásticos tipo pet

Kefir is a fermented milk product that contains a symbiotic microbiota that generates health benefits by synthesizing different metabolites and enzymes with diverse metabolic capacities. For their part, synthetic plastics used in the home and industrial sectors have caused an environmental problem around the world due to excessive use, their high durability and lack of recycling. For this reason, Kefir consortia are studied as a source of hydrolytic enzymes and microorganisms capable of degrading plastics. For this, two kefir metagenomes (NCBI under the BioProject PRJNA704713) were analyzed, using bioinformatic tools, aimed at the search for sequences homologous to hydrolases, as well as the isolation of microorganisms that degrade PET-type plastics. The results obtained allowed the identification of two kefir sequences homologous to the dienelactone hydrolase enzyme (DLH-1 and DHL-2), which can participate in the degradation of plastic compounds. Both sequences presented a shared domain with the alpha/beta hydrolase superfamily; this type of motif has been observed in PET hydrolases obtained from different species of actinomycetes. Likewise, microorganisms with the capacity to degrade PLC plastics were isolated, suggesting that they possess enzymes with hydrolytic activity of industrial compounds for the manufacture of PET. In conclusion, our data demonstrate that kefirs are sources of hydrolytic enzymes of PET hydrolases and that it is possible to isolate PET-degrading microorganisms from themEl kéfir es un producto de leche fermentada que contiene una microbiota simbiótica que genera beneficios para la salud al sintetizar diferentes metabolitos y enzimas con diversas capacidades metabólicas. Por otra parte, los plásticos sintéticos utilizados en sectores del hogar e industrial, han originado un problema ambiental alrededor del mundo debido a su uso desmedido, su alta durabilidad y la falta de reciclado. Por tal motivo, el estudio de los consorcios de kéfir representa una fuente para la obtención de microorganismos productores de enzimas hidrolíticas capaces de degradar plásticos. En este estudio, se analizaron dos metagenomas de kéfir (NCBI proyecto PRJNA704713), mediante herramientas bioinformáticas, dirigidos a la búsqueda de secuencias homólogas a hidrolasas, así como el aislamiento de microorganismos relacionados con la degradación de plásticos tipo PET. Los resultados obtenidos permitieron la identificación de dos secuencias de kéfir homólogas a las enzimas dienolactona hidrolasa (DLH-1 y DLH-2) que han sido relacionadas con la degradación de compuestos plásticos. Ambas secuencias presentan un dominio compartido con la superfamilia alfa/beta hidrolasas; este tipo de motivo se ha observado en las PET hidrolasas obtenidas en diferentes especies de actinomicetos. Así mismo, se aislaron seis bacterias que mostraron diferentes características y capacidades para degradar plásticos PLC. En conclusión, los metagenomas del kéfir presentan secuencias de enzimas asociadas a la degradación de plásticos tipo PET y los microorganismos aislados del kéfir fueron capaces de degradar PLC, lo que sugiere que representan un potencial para la degradación de plásticos PET

Intermediate-Salinity Systems at High Altitudes in the Peruvian Andes Unveil a High Diversity and Abundance of Bacteria and Viruses

Intermediate-salinity environments are distributed around the world. Here, we present a snapshot characterization of two Peruvian thalassohaline environments at high altitude, Maras and Acos, which provide an excellent opportunity to increase our understanding of these ecosystems. The main goal of this study was to assess the structure and functional diversity of the communities of microorganisms in an intermediate-salinity environment, and we used a metagenomic shotgun approach for this analysis. These Andean hypersaline systems exhibited high bacterial diversity and abundance of the phyla Proteobacteria, Bacteroidetes, Balneolaeota, and Actinobacteria; in contrast, Archaea from the phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota were identified in low abundance. Acos harbored a more diverse prokaryotic community and a higher number of unique species compared with Maras. In addition, we obtained the draft genomes of two bacteria, Halomonas elongata and Idiomarina loihiensis, as well as the viral genomes of Enterobacteria lambda-like phage and Halomonas elongata-like phage and 27 partial novel viral halophilic genomes. The functional metagenome annotation showed a high abundance of sequences associated with detoxification, DNA repair, cell wall and capsule formation, and nucleotide metabolism; sequences for these functions were overexpressed mainly in bacteria and also in some archaea and viruses. Thus, their metabolic profiles afford a decrease in oxidative stress as well as the assimilation of nitrogen, a critical energy source for survival. Our work represents the first microbial characterization of a community structure in samples collected from Peruvian hypersaline systems

LINC00460 Is a Dual Biomarker That Acts as a Predictor for Increased Prognosis in Basal-Like Breast Cancer and Potentially Regulates Immunogenic and Differentiation-Related Genes

International audienceBreast cancer (BRCA) is a serious public health problem, as it is the most frequent malignant tumor in women worldwide. BRCA is a molecularly heterogeneous disease, particularly at gene expression (mRNAs) level. Recent evidence shows that coding RNAs represent only 34% of the total transcriptome in a human cell. The rest of the 66% of RNAs are non−coding, so we might be missing relevant biological, clinical or regulatory information. In this report, we identified two novel tumor types from TCGA with LINC00460 deregulation. We used survival analysis to demonstrate that LINC00460 expression is a marker for poor overall (OS), relapse-free (RFS) and distant metastasis-free survival (DMFS) in basal-like BRCA patients. LINC00460 expression is a potential marker for aggressive phenotypes in distinct tumors, including HPV-negative HNSC, stage IV KIRC, locally advanced lung cancer and basal-like BRCA. We show that the LINC00460 prognostic expression effect is tissue-specific, since its upregulation can predict poor OS in some tumors, but also predicts an improved clinical course in BRCA patients. We found that the LINC00460 expression is significantly enriched in the Basal-like 2 (BL2) TNBC subtype and potentially regulates the WNT differentiation pathway. LINC00460 can also modulate a plethora of immunogenic related genes in BRCA, such as SFRP5, FOSL1, IFNK, CSF2, DUSP7 and IL1A and interacts with miR-103-a-1, in-silico, which, in turn, can no longer target WNT7A. Finally, LINC00460:WNT7A ratio constitutes a composit

. 11-12 Año 6 (2017) enero-agosto. CR. Conservación y restauración

- Editorial por Manuel Alejandro González Gutiérrez y Magdalena Rojas Vences. -Proyecto de atención del acervo documental de Ixcamilpa de Guerrero por Patricia de la Garza Cabrera, Marie Vander Meeren, Laura Olivia Ibarra Carmona, Nora A. Pérez Castellanos, Carlos Orejel Delgadillo, Silvia Yocelin Pérez Ramírez, Débora Y. Ontiveros Ramírez, Denisse Ochoa Gutiérrez, Hugo Arriaga González y Gerardo Gutiérrez. - Haciendo frente a los embates medioambientales: conservación integral del sitio rupestre Cuevas Pintas,Baja California Sur por Sandra Cruz Flores, Alejandra Bourillón Moreno, Anacaren Morales Ortiz, Rodrigo Ruiz Herrera y María Fernanda López-Armenta. - Estrategia para la accesibilidad e inclusión de las personas con discapacidad a zonas arqueológicas “El pasado es de todos” por Daniela Tovar Ortiz y Luis Antonio Huitrón Santoyo. - Atención a grupos sociales. Sistematización de actividades por Manuel González Gutiérrez y Denisse Ochoa Gutiérrez. - Tañendo campanas: trabajando en equipo. Intervención de las campanas robadas en la capilla de Nuestra Señora de la Concepción, Escobedo, Nuevo León por Gabriela Peñuelas Guerrero, Carlos I. Cañete Ibáñez, Claudia Sánchez Gándara, Jannen Contreras Vargas e Ingrid K. Jiménez Cosme. - La apropiación del patrimonio cultural de El Ocote. Una aportación etnográfica para la sostenibilidad por Hugo Arriaga González. - Churubusco. 50 años en la memoria. Una muestra conmemorativa de la conservación en el INAH por Mónica Badillo Leal, Gabriela Gómez Llorente y Mariana Pascual Cáceres. - Los órganos y su conservación en la CNCPC por Norma Cristina Peña Peláez, Sandra María Álvarez Jacinto, José Luis Acevedo Guzmán y Fanny Magaña Nieto. - Conservación de cestería en espiral proveniente de la Cueva de la Candelaria, Torreón, Coahuila: criterios, tratamientos y líneas de investigación por Gloria Martha Sánchez Valenzuela, Miriam Elizabeth Castro Rodríguez y Adriana Reyes García. - Evaluación de recubrimientos de protección para metales. Caso de estudio: Imagen de México, relieve escultórico del Museo Nacional de Antropología. Primera etapa por Aline Moreno Núñez, Arturo A. Egea Salas, Gilda E. Salgado Manzanares, Mauricio B. Jiménez Ramírez, Armando Arciniega Corona y Nora A. Pérez Castellanos. - Patrimonio arqueológico digital. Uso de las tecnologías de la información y la comunicación para la divulgación del patrimonio arqueológico por Eduardo Andrés Escalante Carrillo y Luis Antonio Huitrón Santoyo. - El laboratorio de documentación y análisis tridimensional de la CNCPC. Resultados a un año de operación María Fernanda López-Armenta, Gilberto García Quintana y Celedonio Rodríguez Vidal. - La conservación-restauración de los bienes culturales en el Museo Regional de Querétaro: retos y perspectivas por María del Rosario Bravo Aguilar Conocer y reconocer a los actores sociales en la conservación de los bienes patrimoniales por Mitzi Vania García Toribio y Fanny Magaña Nieto. - Foro Anual de Trabajo. Una historia sin historia en el archivo de la CNCPC por Débora Y. Ontiveros Ramírez. - Expediente de incidentes en el tiempo. El Ehécatl-Quetzalcóatl de Coyoacán y cómo su caso puede ser usado para difundir la conservación en museos por Roberto Velasco Alonso. - Conservación en la vida cotidiana por María Bertha Peña Tenorio. - La Mediateca del INAH por Thalía E. Velasco Castelán. - Finaliza CNCPC la recuperación de sillares simulados originales en la bóveda del templo franciscano de Huaquechula, Puebla por Oscar Adrián Gutiérrez Vargas. - San Francisco de Asís en Huejotzingo, Puebla María Eugenia Rivera Pérez. - Investiga INAH factores de deterioro en la pirámide de la Serpiente Emplumada por Oscar Adrián Gutiérrez Vargas. - Lo que querías saber y no te atrevías a preguntar sobre el INAH en El Ocote por Oscar Adrián Gutiérrez Vargas. - Para saber más de El Caballito por Oscar Adrián Gutiérrez Vargas

International Nosocomial Infection Control Consortiu (INICC) report, data summary of 43 countries for 2007-2012. Device-associated module

We report the results of an International Nosocomial Infection Control Consortium (INICC) surveillance study from January 2007-December 2012 in 503 intensive care units (ICUs) in Latin America, Asia, Africa, and Europe. During the 6-year study using the Centers for Disease Control and Prevention's (CDC) U.S. National Healthcare Safety Network (NHSN) definitions for device-associated health care–associated infection (DA-HAI), we collected prospective data from 605,310 patients hospitalized in the INICC's ICUs for an aggregate of 3,338,396 days. Although device utilization in the INICC's ICUs was similar to that reported from ICUs in the U.S. in the CDC's NHSN, rates of device-associated nosocomial infection were higher in the ICUs of the INICC hospitals: the pooled rate of central line–associated bloodstream infection in the INICC's ICUs, 4.9 per 1,000 central line days, is nearly 5-fold higher than the 0.9 per 1,000 central line days reported from comparable U.S. ICUs. The overall rate of ventilator-associated pneumonia was also higher (16.8 vs 1.1 per 1,000 ventilator days) as was the rate of catheter-associated urinary tract infection (5.5 vs 1.3 per 1,000 catheter days). Frequencies of resistance of Pseudomonas isolates to amikacin (42.8% vs 10%) and imipenem (42.4% vs 26.1%) and Klebsiella pneumoniae isolates to ceftazidime (71.2% vs 28.8%) and imipenem (19.6% vs 12.8%) were also higher in the INICC's ICUs compared with the ICUs of the CDC's NHSN