Transposable element derived DNaseI-hypersensitive sites in the human genome

BACKGROUND: Transposable elements (TEs) are abundant genomic sequences that have been found to contribute to genome evolution in unexpected ways. Here, we characterize the evolutionary and functional characteristics of TE-derived human genome regulatory sequences uncovered by the high throughput mapping of DNaseI-hypersensitive (HS) sites. RESULTS: Human genome TEs were found to contribute substantially to HS regulatory sequences characterized in CD4+ T cells: 23% of HS sites contain TE-derived sequences. While HS sites are far more evolutionarily conserved than non HS sites in the human genome, consistent with their functional importance, TE-derived HS sites are highly divergent. Nevertheless, TE-derived HS sites were shown to be functionally relevant in terms of driving gene expression in CD4+ T cells. Genes involved in immune response are statistically over-represented among genes with TE-derived HS sites. A number of genes with both TE-derived HS sites and immune tissue related expression patterns were found to encode proteins involved in immune response such as T cell specific receptor antigens and secreted cytokines as well as proteins with clinical relevance to HIV and cancer. Genes with TE-derived HS sites have higher average levels of sequence and expression divergence between human and mouse orthologs compared to genes with non TE-derived HS sites. CONCLUSION: The results reported here support the notion that TEs provide a specific genome-wide mechanism for generating functionally relevant gene regulatory divergence between evolutionary lineages. REVIEWERS: This article was reviewed by Wolfgang J. Miller (nominated by Jerzy Jurka), Itai Yanai and Mikhail S.Gelfand

Many sequence-specific chromatin modifying protein-binding motifs show strong positional preferences for potential regulatory regions in the Saccharomyces cerevisiae genome

Initiation and regulation of gene expression is critically dependent on the binding of transcriptional regulators, which is often temporal and position specific. Many transcriptional regulators recognize and bind specific DNA motifs. The length and degeneracy of these motifs results in their frequent occurrence within the genome, with only a small subset serving as actual binding sites. By occupying potential binding sites, nucleosome placement can specify which sequence motif is available for DNA-binding regulatory factors. Therefore, the specification of nucleosome placement to allow access to transcriptional regulators whenever and wherever required is critical. We show that many DNA-binding motifs in Saccharomyces cerevisiae show a strong positional preference to occur only in potential regulatory regions. Furthermore, using gene ontology enrichment tools, we demonstrate that proteins with binding motifs that show the strongest positional preference also have a tendency to have chromatin-modifying properties and functions. This suggests that some DNA-binding proteins may depend on the distribution of their binding motifs across the genome to assist in the determination of specificity. Since many of these DNA-binding proteins have chromatin remodeling properties, they can alter the local nucleosome structure to a more permissive and/or restrictive state, thereby assisting in determining DNA-binding protein specificity

Clonación del gen de la cápside protéica de una cepa colombiana del Virus del Mosaico del Pepino (CMV) para su expresión en plantas por transformación mediante Agrobaderium

Research Note.Cucumber Mosaic Virus (CMV) is a member of the cucumuvirus group in the Bromoviridaefa mily which membersh ave divided genomes consisting of three positive-strand RNAs and a subgenomic RNA 4 that is generated from the transcriptionof RNA ¡ and servesa s a messengerR NA for the viral coat protein (Davies, 1988). CMV can infect over 8oo specieso f plants and has a world-wide distribution.Nota de Investigación.  El Virus del Mosaico del Pepíno (Cucumber Mosaic Virus, CMV) forma parte del grupo Cucumuvirus de la familia romoyiridae:este virus tiene su genoma dividido en tres cadenas positivas de ARN y un ARN-4 subgenómico el cual se genera de la transcripción delARN-3 y sirve como ARN mensajerop aral a síntesisd e proteínad e la cápside (Davies, 1988). EI.CMV puede infectarm ásd e 8oo especieds e plantasy se encuentra distribuido en todo el mundo. 

Clonación del gen de la cápside protéica de una cepa colombiana del virus del mosaico del pepino (CMV) para su expresión en plantas por transformación mediante Agribacterium

El Virus del Mosaico del Pepino (Cucumber Mosaic Virus, CMV) forma parte del grupo Cucumuvirus de la familia Bromoviridae, este virus tiene su genoma dividido en tres cadenas positivas de ARN y un ARN-4 subgenómico el cual se genera de la transcripción del ARN-3 y sirve como ARN mensajero para la síntesis de proteína de la cápside (Davies, 1988). El CMV puede infectar más de 800 especies de plantas y se encuentra distribuido en todo el mundo. El gen de la cápside proteica (CP) del CMV se ha usado para producir plantas transgénicas que han mostrado protección contra infecciones causadas por el CMV (Nakajima, 1993, Quemada, 1991), recientemente un gen CP, procedente de una cepa de CMV que infecta el plátano, ha sido caracterizado (Reichel, 1996) y su secuencia fue depositada en el Banco de Genes (GenBank) (Benson, 1996). A continuación se describe la construcción de dos vectores binarios para la expresión del gen CP en plantas.Pepino-Cucumis sativ

Complete mitochondrial genome of the nesting Colombian Caribbean Hawksbill Turtle

The hawksbill turtle, Eretmochelis imbricata (Linnaeus, 1766), is an endangered sea turtle in Colombian Caribbean beach. In this study, we report the complete mitochondrial DNA sequences of hawksbill turtle. The entire genome comprised 16,386 base pairs, and a nucleotide frequency of T: 25.6%, C: 26.9%, A: G 35.4% and 12.1%. The mitogenome sequence of hawksbill turtle would contribute to better understand population genetics, and evolution of sea turtles. Molecule was deposited at the GenBank database under the accession number KP221806

Comunicación participativa en perspectiva de construcción a la comunidad desde la emisora comunitaria los Andes Stereo.

Se entiende por radiodifusión sonora comunitaria cuando la programación de una emisora está orientada a generar espacios de expresión, información, educación, comunicación, promoción cultural, formación, debate y concertación que conduzcan al encuentro entre las diferentes identidades sociales y expresiones culturales de la comunidad, dentro de un ámbito de integración y solidaridad ciudadana y, en especial, a la promoción de la democracia, la participación y los derechos fundamentales de los colombianos que aseguren una convivencia pacífica. El decreto 2805 de 2008 define el servicio comunitario de radiodifusión sonora como un servicio público participativo y pluralista, orientado a satisfacer necesidades de comunicación en el municipio o área objeto de cubrimiento; a facilitar el ejercicio del derecho a la información y la participación de sus habitantes, a través de programas radiales realizados por distintos sectores sociales, de manera que promueva el desarrollo social, la convivencia pacífica, los valores democráticos, la construcción de ciudadanía y el fortalecimiento de las identidades culturales y sociales En este caso se aborda La Emisora Comunitaria Los Andes stereo, Málaga– Santander, una asociación comunitaria sin ánimo de lucro, la cual se compone por habitantes de la misma población con el propósito de solucionar problemáticas presentadas en el entorno mencionado y a través de la comunicación participativa. En esta Asociación se realiza un diagnóstico pertinente dentro de los procesos internos de la misma para observar aquellas falencias comunicacionales con base a los conocimientos adquiridos desde el Diplomado en Construcción de Redes Sociales de Comunicación de la UNAD, fortaleciendo las herramientas para contribuir a la participación colectiva y analizar el enfoque de comunicación participativa desde sus técnicas utilizadas, esto con el fin de intervenir a través estrategias que contribuyan al mejoramiento de su gestión desde la Investigación Acción.Community sound broadcasting is understood when the programming of a radio station is oriented to generate spaces of expression, information, education, communication, cultural promotion, training, debate and consensus that lead to the meeting between the different social identities and cultural expressions of the community, within a scope of integration and citizen solidarity and, in particular, to the promotion of democracy, participation and fundamental rights of Colombians that ensure a peaceful coexistence. Decree 2805 of 2008 defines the community service of sound broadcasting as a participatory and pluralistic public service, aimed at satisfying communication needs in the municipality or area covered by it; to facilitate the exercise of the right to information and the participation of its inhabitants, through radio programs carried out by different social sectors, in a way that promotes social development, peaceful coexistence, democratic values, the construction of citizenship and strengthening of cultural and social identities In this case, the community broadcaster Los Andes stereo, Málaga-Santander, a non-profit community association, is composed of inhabitants of the same population with the purpose of solving problems presented in the environment mentioned and through participatory communication. In this Association a pertinent diagnosis is made within the internal processes of the same to observe those communicational shortcomings based on the knowledge acquired from the Diploma in Construction of Social Communication Networks of UNAD, strengthening the tools to contribute to collective participation and analyze the participatory communication approach from its used techniques, this in order to Intervene through strategies that contribute to the improvement of its management from the Action Research

Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites

<p>Abstract</p> <p>Background</p> <p>Biologically active sequence motifs often have positional preferences with respect to a genomic landmark. For example, many known transcription factor binding sites (TFBSs) occur within an interval [-300, 0] bases upstream of a transcription start site (TSS). Although some programs for identifying sequence motifs exploit positional information, most of them model it only implicitly and with <it>ad hoc </it>methods, making them unsuitable for general motif searches.</p> <p>Results</p> <p>A-GLAM, a user-friendly computer program for identifying sequence motifs, now incorporates a Bayesian model systematically combining sequence and positional information. A-GLAM's predictions with and without positional information were compared on two human TFBS datasets, each containing sequences corresponding to the interval [-2000, 0] bases upstream of a known TSS. A rigorous statistical analysis showed that positional information significantly improved the prediction of sequence motifs, and an extensive cross-validation study showed that A-GLAM's model was robust against mild misspecification of its parameters. As expected, when sequences in the datasets were successively truncated to the intervals [-1000, 0], [-500, 0] and [-250, 0], positional information aided motif prediction less and less, but never hurt it significantly.</p> <p>Conclusion</p> <p>Although sequence truncation is a viable strategy when searching for biologically active motifs with a positional preference, a probabilistic model (used reasonably) generally provides a superior and more robust strategy, particularly when the sequence motifs' positional preferences are not well characterized.</p

Lineamientos teóricos para promover la cultura de paz en los hogares

El objetivo de la presente sistematización fue formular los lineamientos para realizar una cartilla que promueva pautas de crianza y estrategias de resolución de conflictos dirigidas al óptimo desarrollo de los niños, niñas, adolescentes y jóvenes, al fomentar la cultura de paz en los hogares del barrio Rincón del Diamante, en la localidad de Ciudad Bolívar en Bogotá D.C. Para ello, se realizó el análisis de la información recolectada durante el año 2016 desde una perspectiva sistémica, a partir de talleres dirigidos a padres de familia de la comunidad y acompañamientos psicosociales a familias vinculadas a la Fundación Proyecto de Vida. La metodología implementada estuvo enmarcada desde el enfoque cualitativo, al considerar las narrativas de los participantes. El análisis de la información se realizó por medio de matrices de contenido en las cuales se especificaron las categorías de análisis: significados de familia, pautas de crianza y resolución de conflictos. Los resultados de los análisis contrastaron la información obtenida en los talleres con la información de las sesiones del acompañamiento a familias. Se logró realizar una primera caracterización de la población lo cual permitió la formulación de los lineamientos teóricos para la creación de una cartilla que transmita a las familias, la cultura de paz.The purpose of the present systematization was formulate the guidelines to carry out a primer that promote parenting guidelines and strategies for the conflicts resolution, guided to the optimum development of boys, girls, teenagers and young people, by promoting a culture of peace in the community of Rincón del Diamante neighborhood, in the sector of Ciudad Bolivar, Bogotá, D.C. For that reason, an analysis based on the information recollected during the year 2016 from a systemic perspective has been made, this through workshops directed to the parents in the community as well as psychosocial accompaniments to the families linked to the foundation called Proyecto de Vida. The methodology implemented was based on a qualitative approach, taking into account the participant’s narratives. The analysis of the information has been done through content tables, in which the analysis categories were specified: family meanings, parenting guidelines and conflict resolution. The analysis’s results were contrasting the information obtained in the workshops and the information picked up on the sessions during the families’ accompaniment. A first characterization of the population was achieved, allowing the formulation of theoretical guidelines for the creation of a primer that will be able to transmit a peace culture to the families.Psicólogo (a)Pregrad

Effect of the Transposable Element Environment of Human Genes on Gene Length and Expression

Independent lines of investigation have documented effects of both transposable elements (TEs) and gene length (GL) on gene expression. However, TE gene fractions are highly correlated with GL, suggesting that they cannot be considered independently. We evaluated the TE environment of human genes and GL jointly in an attempt to tease apart their relative effects. TE gene fractions and GL were compared with the overall level of gene expression and the breadth of expression across tissues. GL is strongly correlated with overall expression level but weakly correlated with the breadth of expression, confirming the selection hypothesis that attributes the compactness of highly expressed genes to selection for economy of transcription. However, TE gene fractions overall, and for the L1 family in particular, show stronger anticorrelations with expression level than GL, indicating that GL may not be the most important target of selection for transcriptional economy. These results suggest a specific mechanism, removal of TEs, by which highly expressed genes are selectively tuned for efficiency. MIR elements are the only family of TEs with gene fractions that show a positive correlation with tissue-specific expression, suggesting that they may provide regulatory sequences that help to control human gene expression. Consistent with this notion, MIR fractions are relatively enriched close to transcription start sites and associated with coexpression in specific sets of related tissues. Our results confirm the overall relevance of the TE environment to gene expression and point to distinct mechanisms by which different TE families may contribute to gene regulation