Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study.

Bacterial small RNAs (sRNAs) play a vital role in pathogenesis by enabling rapid, efficient networks of gene attenuation during infection. In recent decades, there has been a surge in the number of proposed and biochemically-confirmed sRNAs in both Gram-positive and Gram-negative pathogens. However, limited homology, network complexity, and condition specificity of sRNA has stunted complete characterization of the activity and regulation of these RNA regulators. To streamline the discovery of the expression of sRNAs, and their post-transcriptional activities, we propose an integrative in vivo data-mining approach that couples DNA protein occupancy, RNA-seq, and RNA accessibility data with motif identification and target prediction algorithms. We benchmark the approach against a subset of well-characterized E. coli sRNAs for which a degree of in vivo transcriptional regulation and post-transcriptional activity has been previously reported, finding support for known regulation in a large proportion of this sRNA set. We showcase the abilities of our method to expand understanding of sRNA RseX, a known envelope stress-linked sRNA for which a cellular role has been elusive due to a lack of native expression detection. Using the presented approach, we identify a small set of putative RseX regulators and targets for experimental investigation. These findings have allowed us to confirm native RseX expression under conditions that eliminate H-NS repression as well as uncover a post-transcriptional role of RseX in fimbrial regulation. Beyond RseX, we uncover 163 putative regulatory DNA-binding protein sites, corresponding to regulation of 62 sRNAs, that could lead to new understanding of sRNA transcription regulation. For 32 sRNAs, we also propose a subset of top targets filtered by engagement of regions that exhibit binding site accessibility behavior in vivo. We broadly anticipate that the proposed approach will be useful for sRNA-reliant network characterization in bacteria. Such investigations under pathogenesis-relevant environmental conditions will enable us to deduce complex rapid-regulation schemes that support infection.

Diversidad y caracterización de maíces nativos de la Reserva de la Biósfera "El Cielo", Tamaulipas, México / Diversity and characterization of native maize from the "El Cielo" Biosphere Reserve, Tamaulipas, Mexico

Resumen La diversidad del maíz en México se fundamenta por la presencia de 59 a 64 razas; Tamaulipas como estado productor contribuye a mantener la variabilidad entre razas, especialmente en las regiones aisladas. La reserva de la Biósfera "El Cielo" localizada en una región montañosa, que comprende los municipios de Jaumave, Ocampo, Gómez Farías y Llera de Canales, ha sido escasamente estudiada, a pesar de que existen riesgos de degradación o extinción de poblaciones nativas de maíz, por factores como cambios de uso de suelo y fenómenos naturales. El objetivo de este trabajo fue analizar la diversidad morfológica de poblaciones nativas de maíz de la Reserva de la Biósfera "El Cielo". Durante los meses de febrero, marzo y abril del 2016, se realizaron recolectas de maíces nativos en los municipios que comprenden la reserva. El tamaño de la muestra varió, entre 20 y 30 mazorcas de cada población, y de estas, se eligieron 10 mazorcas para registrar variables cuantitativas y cualitativas. Se utilizaron los métodos multivariados de análisis de componentes principales y conglomerados. El 62.45 % correspondió a la variación total, la cual fue explicada por los dos primeros componentes principales, y las variables con mayor contribución a la variación fueron longitud de mazorca, número de granos por hilera, peso de mazorca, peso y volumen de 100 granos, diámetro de mazorca y de olote, número de hileras por mazorca y la relación diámetro/longitud de mazorca. En las poblaciones nativas de maíz que aún se cultivan en la Reserva de la Biósfera "El Cielo", se encontró amplia diversidad morfológica de mazorca, así como variación en la combinación de colores de grano y olote, lo que sugiere que las poblaciones nativas representan un amplio potencial como acervo genético y reservorio de genes.

Abstract The diversity of maize in Mexico is based on the presence of breeds that range from 59 to 64 varieties. Tamaulipas is a corn-producing state that contributes to sustain this enormous variation of breeds, especially in isolated regions. The biosphere ecological reserve "El Cielo" is located in a mountainous region, which comprises Jaumave, Ocampo, Gómez Farías and Llera de Canales municipalities. This region has been scarcely studied in spite of the degrada tion or extinction risks of native populations of maize due to factors such as changes in land use and natural phenomena. The objective of this work was to analyze the morphologic diversity of native maize varieties of "El Cielo" biosphere ecological reserve. Native maize harvests were collected in the municipalities that comprise the reserve during the months of February, March and April of 2016. The sample size ranged between 20 and 30 cobs of each variety, out of this sample 10 cobs were selected in order to register quantitative and qualitative variables. A multivariate analysis method of main components and conglomerates was used. Results show that 62.45 % of the samples were correspondent with total variation, which was explained by the first two main compo nents. The variables with greater contribution to the variation were cob length, number of grains per row, cob weight, weight and volume of 100 grains, cob diameter, number of rows per hob and the relation of diameter/length in each cob. The native maize populations that are still cultivated at the biosphere ecological reserve "El Cielo" there was a wide morphological diversity of cob, as well as variation in the com bination of grain and corncob color. This sug gests that native populations possess a substantial potential as a gene pool and gene reservoir.