The complete genome sequence of the gram-positive bacterium Bacillus subtilis.

Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.

Teaching, sustainability and environment in UPC buildings

Universities must motivate future professionals so that they are able to apply their experience over and beyond the scientific and technological context. These professionals should also be trained so that they are aware of the current position as regards the economy and limited energy resources, and they must be creative, knowledgeable and committed if they are to rethink the current model.The Departments of Architectural Technology II and Applied Physics, in collaboration with the Interdisciplinary Centre of Technology, Innovation and Education for Sustainability (CITIES), believed that students could be given the opportunity to specialise in the area of sustainable development by means of their final theses [2]. With this objective in mind, a line of theses called Energy Assessments was created as part of the Plan for Resource Consumption Efficiency (PECR). The line was based on a learning strategy that focused on the student.The teaching staff was able to observe that, in terms of cognitive aspects, the students improved their knowledge of environmental issues and the associated skills, and that they were more able to solve problems in the area of sustainability and had greater concerns about this subject matter after having completed their theses.

Complete DNA sequence of Kuraishia capsulata illustrates novel genomic features among budding yeasts (Saccharomycotina)

The numerous yeast genome sequences presently available provide a rich source of information for functional as well as evolutionary genomics but unequally cover the large phylogenetic diversity of extant yeasts. We present here the complete sequence of the nuclear genome of the haploid-type strain of Kuraishia capsulata (CBS1993(T)), a nitrate-assimilating Saccharomycetales of uncertain taxonomy, isolated from tunnels of insect larvae underneath coniferous barks and characterized by its copious production of extracellular polysaccharides. The sequence is composed of seven scaffolds, one per chromosome, totaling 11.4 Mb and containing 6,029 protein-coding genes, ~13.5% of which being interrupted by introns. This GC-rich yeast genome (45.7%) appears phylogenetically related with the few other nitrate-assimilating yeasts sequenced so far, Ogataea polymorpha, O. parapolymorpha, and Dekkera bruxellensis, with which it shares a very reduced number of tRNA genes, a novel tRNA sparing strategy, and a common nitrate assimilation cluster, three specific features to this group of yeasts. Centromeres were recognized in GC-poor troughs of each scaffold. The strain bears MAT alpha genes at a single MAT locus and presents a significant degree of conservation with Saccharomyces cerevisiae genes, suggesting that it can perform sexual cycles in nature, although genes involved in meiosis were not all recognized. The complete absence of conservation of synteny between K. capsulata and any other yeast genome described so far, including the three other nitrate-assimilating species, validates the interest of this species for long-range evolutionary genomic studies among Saccharomycotina yeasts.

Targeted sequence capture and Ultra High Throughput sequencing for gene discovery in inherited diseases

L'introduction des technologies de séquençage de nouvelle génération est en vue de révolutionner la médecine moderne. L'impact de ces nouveaux outils a déjà contribué à la découverte de nouveaux gènes et de voies cellulaires impliqués dans la pathologie de maladies génétiques rares ou communes. En revanche, l'énorme quantité de données générées par ces systèmes ainsi que la complexité des analyses bioinformatiques nécessaires, engendre un goulet d'étranglement pour résoudre les cas les plus difficiles. L'objectif de cette thèse a été d'identifier les causes génétiques de deux maladies héréditaires utilisant ces nouvelles techniques de séquençage, couplées à des technologies d'enrichissement de gènes. Dans ce cadre, nous avons développé notre propre méthode de travail (pipeline) pour l'alignement des fragments de séquence (reads). Suite à l'identification de gènes, nous avons réalisé une analyse fonctionnelle pour élucider leur rôle dans la maladie. Dans un premier temps, nous avons étudié et identifié des mutations impliquées dans une forme récessive de la rétinite pigmentaire qui est à ce jour la dégénérescence rétinienne héréditaire la plus fréquente. En particulier, nous avons constaté que des mutations faux-sens dans le gène FAM161A étaient la cause de la rétinite pigmentaire préalablement associé avec le locus RP28. De plus, nous avons démontré que ce gène avait des fonctions au niveau du cil du photorécepteur, complétant le large spectre des cilliopathies rétiniennes héréditaires. Dans un second temps, nous avons exploré la possibilité qu'un syndrome, relativement fréquent en pédiatrie de fièvre récurrente, appelé PFAPA (acronyme de fièvre périodique avec adénite stomatite, pharyngite et cervical aphteuse) puisse avoir une origine génétique. L'étiologie de cette maladie n'étant pas claire, nous avons tenté d'identifier le spectre génétique de patients PFAPA. Comme nous n'avons pas pu mettre à jour un nouveau gène unique muté et responsable de la maladie chez tous les individus dépistés, il semblerait qu'un modèle génétique plus complexe suggérant l'implication de plusieurs gènes dans la pathologie ait été identifié chez les patients touchés. Ces gènes seraient notamment impliqués dans des processus liés à l'inflammation ce qui élargirait l'impact de ces études à d'autres maladies auto-inflammatoires.

Cenomanian-Turonian transition in a shallow water sequence of the Sinai, Egypt

Environmental and depositional changes across the Late Cenomanian oceanic anoxic event (OAE2) in the Sinai, Egypt, are examined based on biostratigraphy, mineralogy, delta(13)C values and phosphorus analyses. Comparison with the Pueblo, Colorado, stratotype section reveals the Whadi El Ghaib section as stratigraphically complete across the late Cenomanian-early Turonian. Foraminifera are dominated by high-stress planktic and benthic assemblages characterized by low diversity, low-oxygen and low-salinity tolerant species, which mark shallow-water oceanic dysoxic conditions during OAE2. Oyster biostromes suggest deposition occurred in less than 50 m depths in low-oxygen, brackish, and nutrient-rich waters. Their demise prior to the peak delta(13)C excursion is likely due to a rising sea-level. Characteristic OAE2 anoxic conditions reached this coastal region only at the end of the delta(13)C plateau in deeper waters near the end of the Cenomanian. Increased phosphorus accumulations before and after the delta(13)C excursion suggest higher oxic conditions and increased detrital input. Bulk-rock and clay mineralogy indicate humid climate conditions, increased continental runoff and a rising sea up to the first delta(13)C peak. Above this interval, a dryer and seasonally well-contrasted climate with intermittently dry conditions prevailed. These results reveal the globally synchronous delta(13)C shift, but delayed effects of OAE2 dependent on water depth.

Complementary DNA cloning of complement C8 beta and its sequence homology to C9.

The complete amino acid sequence of mature C8 beta has been derived from the DNA sequence of a cDNA clone identified by expression screening of a human liver cDNA library. Comparison with the amino acid sequence of C9 shows an overall homology with few deletions and insertions. In particular, the cysteine-rich domains and membrane-inserting regions of C9 are well conserved. These findings are discussed in relation to a possible mechanism of membrane attack complex formation.

Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility.

The flexibility of different regions of HIV-1 protease was examined by using a database consisting of 73 X-ray structures that differ in terms of sequence, ligands or both. The root-mean-square differences of the backbone for the set of structures were shown to have the same variation with residue number as those obtained from molecular dynamics simulations, normal mode analyses and X-ray B-factors. This supports the idea that observed structural changes provide a measure of the inherent flexibility of the protein, although specific interactions between the protease and the ligand play a secondary role. The results suggest that the potential energy surface of the HIV-1 protease is characterized by many local minima with small energetic differences, some of which are sampled by the different X-ray structures of the HIV-1 protease complexes. Interdomain correlated motions were calculated from the structural fluctuations and the results were also in agreement with molecular dynamics simulations and normal mode analyses. Implications of the results for the drug-resistance engendered by mutations are discussed briefly.

La enseñanza de estrategias de resolución de problemas matemáticos en la ESO: un ejemplo concreto

Within this article is included a description and justification of a didactical sequence to improve the learning of problem solving strategies of Secondary Education students. The design of the didactical sequence is guided by four principles: a) to context the activities and problems to solve in students’ every day practices; b) to use teaching methods that show the problem solving processes; c) to design didactical materials in order to guide strategies such as selection, organisation and control; d) to facilitate the co-operative learning of problem solving strategies.

Teaching fundamentals of computing theory: a constructivist approach

A Fundamentals of Computing Theory course involves different topics that are core to the Computer Science curricula and whose level of abstraction makes them difficult both to teach and to learn. Such difficulty stems from the complexity of the abstract notions involved and the required mathematical background. Surveys conducted among our students showed that many of them were applying some theoretical concepts mechanically rather than developing significant learning. This paper shows a number of didactic strategies that we introduced in the Fundamentals of Computing Theory curricula to cope with the above problem. The proposed strategies were based on a stronger use of technology and a constructivist approach. The final goal was to promote more significant learning of the course topics.

Emergency department visits for non-life-threatening conditions : evolution over 13 years in a Swiss urban teaching hospital

INTRODUCTION: A large proportion of visits to our Emergency Department (ED) are for non-life-threatening conditions. We investigated whether patients' characteristics and reasons for consultation had changed over 13 years. METHODS: Consecutive adult patients with non-life-threatening conditions at triage were included in the spring of 2000 and in the summer of 2013. In both years patients completed a similar questionnaire, which addressed their reasons for consultation and any previous consultation with a general practitioner (GP). RESULTS: We included 581 patients in 2013 vs 516 in 2000, with a mean age of 44.5 years vs 46.4 years (p=0.128). Of these patients, 54.0% vs 57.0% were male (p=0.329), 55.5% vs 58.7% were Swiss (p=0.282), 76.4% were registered with a GP in both periods, but self-referral increased from 52.0% to 68.8% (p<0.001); 57.7% vs., 58.3% consulted during out-of- hours (p=0.821). Trauma-related visits decreased from 34.2% to 23.7% (p<0.001). Consultations within 12 hours of onset of symptoms dropped from 54.5% to 30.9%, and delays of ≥1 week increased from 14.3% to 26.9% (p<0.001). The primary motive for self-referral remained unawareness of an alternative, followed in 2013 by dissatisfaction with the GP's treatment or appointment. Patients who believed that their health problem would not require hospitalisation increased from 52.8% to 74.2% and those who were actually hospitalised decreased from 24.9% to 13.9% (all p<0.001). CONCLUSION: The number of visits for non-life-threatening consultations continue to increase. Our ED is used by a large proportion of patients as a convenient alternative source of primary care.

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10 000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.

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.

Translation as a Process and Translation as a Product in Teaching Translation

L'ensenyament de la traducció s'ha utilitzat tradicionalment en algunes titulacions de filologia com a eina d'aprenentatge d'habilitats de la llengua. Aquesta circumstància, però, no ha d'estar renyida amb la producció d'una traducció acceptable. En aquest article es pretén analitzar si pot aconseguir-se aquest objectiu mitjançant la incorporació d'informació extratextual en l'enunciat de l'exercici de traducció. Els resultats obtinguts amb un grup d'estudiants de filologia mostren que en les seves decisions lingüístiques va tenir un pes important el tipus d'informació extratextual adjunta als textes originals anglesos. Si bé caldria fer un esforç investigador més sistemàtic per poder afirmar-ho categòricament, aquest estudi intenta esbossar la qüestió tan discutida de fins on l'aprenentatge d'una llengua s'ha de realitzar junt amb l'aprenentatge de la traducció. Aquest estudi, també, planteja la necessitat d'incorporar informació extratextual en l'aprenentatge de la traducció, independentment de la titulació que en aquests estudis s'insereixen.