Gene Promoter Evolution Targets the Center of the Human Protein Interaction Network

Assessing the contribution of promoters and coding sequences to gene evolution is an important step toward discovering the major genetic determinants of human evolution. Many specific examples have revealed the evolutionary importance of cis-regulatory regions. However, the relative contribution of regulatory and coding regions to the evolutionary process and whether systemic factors differentially influence their evolution remains unclear. To address these questions, we carried out an analysis at the genome scale to identify signatures of positive selection in human proximal promoters. Next, we examined whether genes with positively selected promoters (Prom+ genes) show systemic differences with respect to a set of genes with positively selected protein-coding regions (Cod+ genes). We found that the number of genes in each set was not significantly different (8.1% and 8.5%, respectively). Furthermore, a functional analysis showed that, in both cases, positive selection affects almost all biological processes and only a few genes of each group are located in enriched categories, indicating that promoters and coding regions are not evolutionarily specialized with respect to gene function. On the other hand, we show that the topology of the human protein network has a different influence on the molecular evolution of proximal promoters and coding regions. Notably, Prom+ genes have an unexpectedly high centrality when compared with a reference distribution (P = 0.008, for Eigenvalue centrality). Moreover, the frequency of Prom+ genes increases from the periphery to the center of the protein network (P = 0.02, for the logistic regression coefficient). This means that gene centrality does not constrain the evolution of proximal promoters, unlike the case with coding regions, and further indicates that the evolution of proximal promoters is more efficient in the center of the protein network than in the periphery. These results show that proximal promoters have had a systemic contribution to human evolution by increasing the participation of central genes in the evolutionary process.

Constraints on effective field theory parameters for the Lambda N -> NN transition

The relation between the low-energy constants appearing in the effective field theory description of the Lambda N -> NN transition potential and the parameters of the one-meson-exchange model previously developed is obtained. We extract the relative importance of the different exchange mechanisms included in the meson picture by means of a comparison to the corresponding operational structures appearing in the effective approach. The ability of this procedure to obtain the weak baryon-baryon-meson couplings for a possible scalar exchange is also discussed.

Constraints on effective field theory parameters for the Lambda N -> NN transition

The relation between the low-energy constants appearing in the effective field theory description of the Lambda N -> NN transition potential and the parameters of the one-meson-exchange model previously developed is obtained. We extract the relative importance of the different exchange mechanisms included in the meson picture by means of a comparison to the corresponding operational structures appearing in the effective approach. The ability of this procedure to obtain the weak baryon-baryon-meson couplings for a possible scalar exchange is also discussed.

Interaction of Spiral Waves in the Complex Ginzburg-Landau Equation

Solutions of the general cubic complex Ginzburg-Landau equation comprising multiple spiral waves are considered, and laws of motion for the centers are derived. The direction of the motion changes from along the line of centers to perpendicular to the line of centers as the separation increases, with the strength of the interaction algebraic at small separations and exponentially small at large separations. The corresponding asymptotic wave number and frequency are also determined, which evolve slowly as the spirals move

Technology educational affordance: Bridging the gap between patterns of interaction and technology usage

Peer-reviewed

Designing online interaction to address disciplinary competencies: A cross-country comparison of faculty perspectives

This study was conducted at colleges in three countries (United States, Venezuela, and Spain) and across three academic disciplines (engineering, education, and business), to examine how experienced faculty define competencies for their discipline, and design instructional interaction for online courses. A qualitative research design employing in-depth interviews was selected. Results show that disciplinary knowledge takes precedence when faculty members select competencies to be developed in online courses for their respective professions. In all three disciplines, the design of interaction to correspond with disciplinary competencies was often influenced by contextual factors that modify faculty intention. Therefore, instructional design will vary across countries in the same discipline to address the local context, such as the needs and expectations of the learners, faculty perspectives, beliefs and values, and the needs of the institution, the community, and country. The three disciplines from the three countries agreed on the importance of the following competencies: knowledge of the field, higher order cognitive processes such as critical thinking, analysis, problem solving, transfer of knowledge, oral and written communication skills, team work, decision making, leadership and management skills, indicating far more similarities in competencies than differences between the three different applied disciplines. We found a lack of correspondence between faculty¿s intent to develop collaborative learning skills and the actual development of them. Contextual factors such as faculty prior experience in design, student reluctance to engage in collaborative learning, and institutional assessment systems that focus on individual performance were some of these reasons.

Building a usable and accessible semantic web interaction platform

Semantic Web applications take off is being slower than expected, at least with respect to “real-world” applications and users. One of the main reasons for this lack of adoption is that most Semantic Web user interfaces are still immature from the usability and accessibility points of view. This is due to the novelty of these technologies, but this also motivates the exploration of alternative interaction paradigms, different from the “traditional” Web or Desktop applications ones. Our proposal is realized in the Rhizomer platform, which explores the possibilities of the object–action interaction paradigm at the Web scale. This paradigm is well suited for heterogeneous resource spaces such as those common in the Semantic Web. Resources, described by metadata, correspond to the objects in the paradigm. Semantic web services, which are dynamically associated to these objects, correspond to the actions. The platform is being put into practice in the context of a research project in order to build an open application for media distribution based on Semantic Web technologies. Moreover, its usability and accessibility have been evaluated in this real setting and compared to similar systems.

The Impact of ICTs on Lecturer and Student Interaction in University Education Processes

Interaction is a basic element in any educational process, and it is something that needs to be reconsidered in the light of technology. In order to examine the methodological changes that ICTs bring to teaching from an interaction perspective, a study was carried out at the University of Lleida to observe interaction processes in various face-to-face, blended learning and e-learning subjects. The methodological design was based on three data collection techniques: documentary analysis of subject curricula, lecturer and student questionnaires, and lecturer interviews. The data showed that, as the online component of subjects increased, the lecturers and students used more technological tools to communicate (e-mail, forums, chats, social networks, etc.). Furthermore, we found that the lecturers and students basically communicated for academic purposes. While they hardly ever communicated for personal reasons (guidance, support, etc.), they claimed that closer contact with a non-academic focus would be preferable. We also observed that the students’ work was more individual in e-learning subjects. Although there is still a considerable way to go in ICT-mediated lecturer-student interaction, both the lecturers and students recognise the potential of such technologies, even though they still do not use them as they feel they should.

Teaching how to learn with a wiki in Primary Education: what classroom interaction can tell us

Understanding how wikis are used to support collaborative learning is an important concern for researchers and teachers. Adopting a discourse analytic approach, this paper attempts to understand the teaching processes when a wiki is embedded in a science project in primary education to foster collaborative learning. Through studying interaction between the teacher and students, our findings identify ways in which the teacher prompts collaborative learning but also shed light on the difficulties for the teacher in supporting student collective collaboration. It is argued that technological wiki features supporting collaborative learning can only be realized if teacher talk and pedagogy are aligned with the characteristics of wiki collaborative work: the freedom of students to organize and participate by themselves, creating dialogic space and promoting student participation. We argue that a dialogic approach for examining interaction can be used to help to design a more effective pedagogic approach in the use of wikis in education, to shift into Web 2.0 learning paradigm and to equip learners with the competences they need to participate in knowledge co-construction.

Cell-Cell interaction in erythropoiesis: role of human monocytes

Erythroid burst forming units (BFU-E) are proliferative cells present in peripheral blood and bone marrow which may be precursors of the erythroid colony forming cell found in the bone marrow. To examine the possible role of monocyte-macrophages in the modulation of erythropoiesis, the effect of monocytes on peripheral blood BFU-E proliferation in response to erythropoietin was investigated in the plasma clot culture system. Peripheral blood mononuclear cells from normal human donors were separated into four fractions. Fraction-I cells were obtained from the interface of Ficoll-Hypaque gradients (20-30% monocytes; 60-80% lymphocytes); fraction-II cells were fraction-I cells that were nonadherent to plastic (2-10% monocytes; 90-98% lymphocytes); fraction-III cells were obtained by incubation of fraction-II cells with carbonyl iron followed by Ficoll-Hypaque centrifugation (>99% lymphocytes); and fraction-IV cells represented the adherent population of fraction-II cells released from the plastic by lidocaine (>95% monocytes). When cells from these fractions were cultured in the presence of erythropoietin, the number of BFU-E-derived colonies was inversely proportional to the number of monocytes present (r = ¿0.96, P < 0.001). The suppressive effect of monocytes on BFU-E proliferation was confirmed by admixing autologous purified monocytes (fraction-IV cells) with fraction-III cells. Monocyte concentrations of ¿20% completely suppressed BFU-E activity. Reduction in the number of plated BFU-E by monocyte dilution could not account for these findings: a 15% reduction in the number of fraction-III cells plated resulted in only a 15% reduction in colony formation. These results indicate that monocyte-macrophages may play a significant role in the regulation of erythropoiesis and be involved in the pathogenesis of the hypoproliferative anemias associated with infection and certain neoplasia in which increased monocyte activity and monopoiesis also occur.

Protein interaction studies point to new functions for Escherichia coli glyceraldehyde-3-phosphate dehydrogenase

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is considered a multifunctional protein with defined functions in numerous mammalian cellular processes. GAPDH functional diversity depends on various factors such as covalent modifications, subcellular localization, oligomeric state and intracellular concentration of substrates or ligands, as well as protein-protein interactions. In bacteria, alternative GAPDH functions have been associated with its extracellular location in pathogens or probiotics. In this study, new intracellular functions of E. coli GAPDH were investigated following a proteomic approach aimed at identifying interacting partners using in vivo formaldehyde cross-linking followed by mass spectrometry. The identified proteins were involved in metabolic processes, protein synthesis and folding or DNA repair. Some interacting proteins were also identified in immunopurification experiments in the absence of cross-linking. Pull-down experiments and overlay immunoblotting were performed to further characterize the interaction with phosphoglycolate phosphatase (Gph). This enzyme is involved in the metabolism of 2-phosphoglycolate formed in the DNA repair of 3"-phosphoglycolate ends generated by bleomycin damage. We show that interaction between Gph and GAPDH increases in cells challenged with bleomycin, suggesting involvement of GAPDH in cellular processes linked to DNA repair mechanisms.

Social network extraction and analysis based on multimodal dyadic interaction

Social interactions are a very important component in people"s lives. Social network analysis has become a common technique used to model and quantify the properties of social interactions. In this paper, we propose an integrated framework to explore the characteristics of a social network extracted from multimodal dyadic interactions. For our study, we used a set of videos belonging to New York Times" Blogging Heads opinion blog. The Social Network is represented as an oriented graph, whose directed links are determined by the Influence Model. The links" weights are a measure of the"influence" a person has over the other. The states of the Influence Model encode automatically extracted audio/visual features from our videos using state-of-the art algorithms. Our results are reported in terms of accuracy of audio/visual data fusion for speaker segmentation and centrality measures used to characterize the extracted social network.

Approaches to the study of individual–landscape interaction as an evocation of intrapersonal communication Aproximaciones al estudio de la interacción individuo-paisaje a modo de evocación comunicativa intrapersonal

Analysis of the interaction between landscape and the individual opens up many research avenues linked to the generation and interpretation of symbolisms and imaginaries. The capacity of landscape for significant and/or communicative evocation finds in intrapersonal communication a relevant argument for the construction of a theoretical framework to study the process of appropriation and experience of the landscape in terms of communicative expression. The principal aim of this paper is to set up the theoretical framework that enables us to interpret the language of landscape and to decode its intangible discourse.

Dynamically generated resonances from the vector octet-baryon octet interaction

We study the interaction of vector mesons with the octet of stable baryons in the framework of the local hidden gauge formalism using a coupled channels unitary approach. We examine the scattering amplitudes and their poles, which can be associated to known J P = 1/2- , 3/2- baryon resonances, in some cases, or give predictions in other ones. The formalism employed produces doublets of degenerate J P = 1/2- , 3/2- states, a pattern which is observed experimentally in several cases. The findings of this work should also be useful to guide present experimental programs searching for new resonances, in particular in the strange sector where the current information is very poor.