RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12

RegulonDB is a database on mechanisms of transcription regulation and operon organization in Escherichia coli K-12. The current version has considerably increased numbers of regulatory elements such as promoters, binding sites and terminators. The complete repertoire of known and predicted DNA-binding transcriptional regulators can be considered to be included in this version. The database now distinguishes different allosteric conformations of regulatory proteins indicating the one active in binding and regulating the different promoters. A new set of operon predictions has been incorporated. The relational design has been modified accordingly. Furthermore, a major improvement is a graphic display enabling browsing of the database with a Java-based graphic user interface with three zoom-levels connected to properties of each chromo­somal element. The purpose of these modifications is to make RegulonDB a useful tool and control set for tran­scriptome experiments. RegulonDB can be accessed on the web at the URL: http://www.cifn.unam.mx/Computational_Biology/regulondb/

Corneal collagen fibril structure in three dimensions: Structural insights into fibril assembly, mechanical properties, and tissue organization

The ability of the cornea to transmit light while being mechanically resilient is directly attributable to the formation of an extracellular matrix containing orthogonal sheets of collagen fibrils. The detailed structure of the fibrils and how this structure underpins the mechanical properties and organization of the cornea is understood poorly. In this study, we used automated electron tomography to study the three-dimensional organization of molecules in corneal collagen fibrils. The reconstructions show that the collagen molecules in the 36-nm diameter collagen fibrils are organized into microfibrils (≈4-nm diameter) that are tilted by ≈15° to the fibril long axis in a right-handed helix. An unexpected finding was that the microfibrils exhibit a constant-tilt angle independent of radial position within the fibril. This feature suggests that microfibrils in concentric layers are not always parallel to each other and cannot retain the same neighbors between layers. Analysis of the lateral structure shows that the microfibrils exhibit regions of order and disorder within the 67-nm axial repeat of collagen fibrils. Furthermore, the microfibrils are ordered at three specific regions of the axial repeat of collagen fibrils that correspond to the N- and C-telopeptides and the d-band of the gap zone. The reconstructions also show macromolecules binding to the fibril surface at sites that correspond precisely to where the microfibrils are most orderly.

The physical and genomic organization of microsatellites in sugar beet.

Microsatellites, tandem arrays of short (2-5 bp) nucleotide motifs, are present in high numbers in most eukaryotic genomes. We have characterized the physical distribution of microsatellites on chromosomes of sugar beet (Beta vulgaris L.). Each microsatellite sequence shows a characteristic genomic distribution and motif-dependent dispersion, with site-specific amplification on one to seven pairs of centromeres or intercalary chromosomal regions and weaker, dispersed hybridization along chromosomes. Exclusion of some microsatellites from 18S-5.8S-25S rRNA gene sites, centromeres, and intercalary sites was observed. In-gel and in situ hybridization patterns are correlated, with highly repeated restriction fragments indicating major centromeric sites of microsatellite arrays. The results have implications for genome evolution and the suitability of particular microsatellite markers for genetic mapping and genome analysis.

Glutamate receptor blockade at cortical synapses disrupts development of thalamocortical and columnar organization in somatosensory cortex.

The segregation of thalamocortical inputs into eye-specific stripes in the developing cat or monkey visual cortex is prevented by manipulations that perturb or abolish neural activity in the visual pathway. Such findings show that proper development of the functional organization of visual cortex is dependent on normal patterns of neural activity. The generalisation of this conclusion to other sensory cortices has been questioned by findings that the segregation of thalamocortical afferents into a somatotopic barrel pattern in developing rodent primary somatosensory cortex (S1) is not prevented by activity blockade. We show that a temporary block of N-methyl-D-aspartate (NMDA) and non-NMDA glutamate receptors in rat S1 during the critical period for barrel development disrupts the topographic refinement of thalamocortical connectivity and columnar organization. These effects are evident well after the blockade is ineffective and thus may be permanent. Our findings show that neural activity and specifically the activation of postsynaptic cortical neurons has a prominent role in establishing the primary sensory map in S1, as well as the topographic organization of higher order synaptic connections.

Visualization of glucocorticoid receptor translocation and intranuclear organization in living cells with a green fluorescent protein chimera.

A highly fluorescent mutant form of the green fluorescent protein (GFP) has been fused to the rat glucocorticoid receptor (GR). When GFP-GR is expressed in living mouse cells, it is competent for normal transactivation of the GR-responsive mouse mammary tumor virus promoter. The unliganded GFP-GR resides in the cytoplasm and translocates to the nucleus in a hormone-dependent manner with ligand specificity similar to that of the native GR receptor. Due to the resistance of the mutant GFP to photobleaching, the translocation process can be studied by time-lapse video microscopy. Confocal laser scanning microscopy showed nuclear accumulation in a discrete series of foci, excluding nucleoli. Complete receptor translocation is induced with RU486 (a ligand with little agonist activity), although concentration into nuclear foci is not observed. This reproducible pattern of transactivation-competent GR reveals a previously undescribed intranuclear architecture of GR target sites.

The genomic and physical organization of Ty1-copia-like sequences as a component of large genomes in Pinus elliottii var. elliottii and other gymnosperms.

A DNA sequence, TPE1, representing the internal domain of a Ty1-copia retroelement, was isolated from genomic DNA of Pinus elliottii Engelm. var. elliottii (slash pine). Genomic Southern analysis showed that this sequence, carrying partial reverse transcriptase and integrase gene sequences, is highly amplified within the genome of slash pine and part of a dispersed element >4.8 kbp. Fluorescent in situ hybridization to metaphase chromosomes shows that the element is relatively uniformly dispersed over all 12 chromosome pairs and is highly abundant in the genome. It is largely excluded from centromeric regions and intercalary chromosomal sites representing the 18S-5.8S-25S rRNA genes. Southern hybridization with specific DNA probes for the reverse transcriptase gene shows that TPE1 represents a large subgroup of heterogeneous Ty1-copia retrotransposons in Pinus species. Because no TPE1 transcription could be detected, it is most likely an inactive element--at least in needle tissue. Further evidence for inactivity was found in recombinant reverse transcriptase and integrase sequences. The distribution of TPE1 within different gymnosperms that contain Ty1-copia group retrotransposons, as shown by a PCR assay, was investigated by Southern hybridization. The TPE1 family is highly amplified and conserved in all Pinus species analyzed, showing a similar genomic organization in the three- and five-needle pine species investigated. It is also present in spruce, bald cypress (swamp cypress), and in gingko but in fewer copies and a different genomic organization.

El audiovisual como herramienta de cambio social de jóvenes en situación de exclusión en Guatemala (2004-2014)

The audiovisual as a tool for social change among youth in social exclusion situations in Guatemala (2004-2014)” is the title of this research paper which aims to study the organizations and projects that have worked with video tools and participatory methodology with young people in marginalized social sectors in order to improve their opportunities and social inclusion. The purpose of this study also includes the analysis of the finish video products as well as the impact of the projects on the youth participants. Guatemala is a country with deep rooted and historical social inequality. This situation is currently reflected by the high violence rates, the extreme poverty and the exclusion of populations, including youth. As social participants, young people have much to say about the construction of a future plan for the country, but they are not heard. That’s why it is so important to facilitate a youth voice and research the tools that can help reach that goal. The participatory methodologies are based on the popular education theories developed by the Latinamerican School with authors such as Paulo Freire, Juan Díaz Bordenave, Jesús Martín Barbero and Mario Kaplún, among others. These methodologies have proved to be a lateral way to face the educational process by promoting dialogue, analysis, consensus search and consciousness-raising. In addition, these methodologies provide a more democratic way to format educational processes that provide students tools to promote an active attitude towards social questions. They can develop their own role of responsibility in the improvement of their own lives and contribute to the progress of their community. This research is based on observation, an extensive bibliographical review, analysis protocols for the study of video materials and projects and closed structured interviews with facilitators and project coordinators. It includes open qualitative interviews with some selected participants and with other specialists in order to complete the necessary information to structure the historical, social and political context of Guatemala...

The cognitive mobilization index: crises and political generations

This article shows how the cognitive mobilization index, designed for use in observing potential political participation, can be used as an indicator of the political climate that a particular society is going through. Following a discussion of the theoretical elaborations (and their working definitions) of the concept of cognitive mobilization, a longitudinal study of various European countries is used to consider the question of how political crises influence cognitive mobilization indexes and what effects they have on the political socialization process among the youngest cohorts.

Social and immigration factors in intimate partner violence among Ecuadorians, Moroccans and Romanians living in Spain

Background: Intimate partner violence (IPV) against women occurs in all countries, all cultures and at every level of society; however, some populations may be at greater risk than others. The aim of this study was to explore IPV prevalence among Ecuadorian, Moroccan and Romanian immigrant women living in Spain and its possible association with their personal, family, social support and immigration status characteristics. Methods: Cross-sectional study of 1607 adult immigrant women residing in Barcelona, Madrid and Valencia (2011). Prevalence rates and adjusted odds ratios (AORs) were calculated, with current IPV being the outcome. Different women’s personal (demographic), family, social support and immigration status characteristics were considered as explicative and control variables. All analyses were separated by women’s country of origin. Results: Current IPV prevalence was 15.57% in Ecuadorians, 10.91% in Moroccans and 8.58% in Romanians. Some common IPV factors were found, such as being separated and/or divorced. In Romanians, IPV was also associated with lack of social support [AOR 5.96 (1.39–25.62)] and low religious involvement [AOR 2.17 (1.06–4.43)]. The likelihood of current IPV was lower among women without children or other dependants in this subgroup [AOR 0.29 (0.093–0.92)]. Conclusion: The IPV prevalence rates obtained for Moroccan, Romanian and Ecuadorian women residing in Spain were similar. Whereas the likelihood of IPV appeared to be relatively evenly distributed among Moroccan and Ecuadorian women, it was higher among Romanian women in socially vulnerable situations related to family responsibilities and the lack of support networks. The importance of intervention in the process of separation and divorce was common to all women.

The Iron Age landscape of Alcoi Valley, eastern Iberia: Agricultural intensification and sociopolitical dynamics

New archaeological survey data are combined with previous evidence to examine the rural landscape during the Iberian Iron Age in the Valencia region of eastern Spain. One goal was to understand the settlement pattern and agricultural intensification through manuring. The second objective was to address the socioeconomic aspects of changes in the landscape. It is possible to trace the emergence of a hierarchical settlement pattern in the Iberian Iron Age in which large fortified settlements carried out the most important functions of control and exploitation of the territory, extending their authority over small rural villages and farmsteads. This pattern is associated with the complex socioeconomic structures and political organization of early Iberian states.

Culture and World Vision: The Cognitive Mythical Mode

Culture is the system of knowledge, from whose meanings the human being screened and selected their understanding of Reality in the broad sense, and interprets and regulates the facts and data of social behavior. In this sense, culture is a program for social action and acting in humans during the process of socialization and social interaction. The meanings of each culture are the cumulative product of collective and individual thinking, in ecological economic, social and political specific situations, so are the expression of each particular cultural historical conjuncture. Moreover, the universal cognitive structure for the apprehension of cultural reality is the World Vision (WV). Due to its importance and significance as substratum of religious and political belief systems, we will gird our study to mythical cognitive mode or mythical WV.

Socialising Around Media (SAM): Dynamic Social and Media Content Syndication for Second Screen

Today's generation of Internet devices has changed how users are interacting with media, from passive and unidirectional users to proactive and interactive. Users can use these devices to comment or rate a TV show and search for related information regarding characters, facts or personalities. This phenomenon is known as second screen. This paper describes SAM, an EU-funded research project that focuses on developing an advanced digital media delivery platform based on second screen interaction and content syndication within a social media context, providing open and standardised ways of characterising, discovering and syndicating digital assets. This work provides an overview of the project and its main objectives, focusing on the NLP challenges to be faced and the technologies developed so far.

Differences between the personal, social and emotional profiles of teaching and computer engineering professionals and students

The evidence suggests that emotional intelligence and personality traits are important qualities that workers need in order to successfully exercise a profession. This article assumes that the main purpose of universities is to promote employment by providing an education that facilitates the acquisition of abilities, skills, competencies and values. In this study, the emotional intelligence and personality profiles of two groups of Spanish students studying degrees in two different academic disciplines – computer engineering and teacher training – were analysed and compared. In addition, the skills forming part of the emotional intelligence and personality traits required by professionals (computer engineers and teachers) in their work were studied, and the profiles obtained for the students were compared with those identified by the professionals in each field. Results revealed significant differences between the profiles of the two groups of students, with the teacher training students scoring higher on interpersonal skills; differences were also found between professionals and students for most competencies, with professionals in both fields demanding more competencies that those evidenced by graduates. The implications of these results for the incorporation of generic social, emotional and personal competencies into the university curriculum are discussed.

Dynamic Social and Media Content Syndication for Second Screen

Social networking apps, sites and technologies offer a wide range of opportunities for businesses and developers to exploit the vast amount of information and user-generated content produced through social networking. In addition, the notion of second screen TV usage appears more influential than ever, with viewers continuously seeking further information and deeper engagement while watching their favourite movies or TV shows. In this work, the authors present SAM, an innovative platform that combines social media, content syndication and targets second screen usage to enhance media content provisioning, renovate the interaction with end-users and enrich their experience. SAM incorporates modern technologies and novel features in the areas of content management, dynamic social media, social mining, semantic annotation and multi-device representation to facilitate an advanced business environment for broadcasters, content and metadata providers, and editors to better exploit their assets and increase their revenues.