A public key encryption based on third order linear sequences

Based on third order linear sequences, an improvement version of the Diffie-Hellman distribution key scheme and the ElGamal public key cryptosystem scheme are proposed, together with an implementation and computational cost. The security relies on the difficulty of factoring an RSA integer and on the difficulty of computing the discrete logarithm.

Origine des populations de rainette verte (Hyla spp.) de l'ouest de la Suisse

DNA-based techniques are important tools for species assignment, in particular when identification with morphological criteria is difficult. The aim of this study was to genetically determine the species identity of tree frogs (Hyla spp.) populations from western and northern Switzerland (Swiss Plateau), this area being frequently subjected to introductions of species or sub-species from south of the Alps. We sequenced 261 base pairs of the mitochondrial DNA cytochrome b gene from 24 samples of tree frogs from the Swiss Plateau, Ticino (southern Switzerland) and the Dombes region (Ain, France), and compared them with homologous sequences retrieved from DNA databases. The phylogenetic analyses revealed two distinct clades. The first one is represented by samples of Green tree frog (Hyla arborea) from the Swiss Plateau, France, Germany and Greece, confirming the current knowledge about the species' distribution. The second clade includes samples belonging to the Italian tree frog (Hyla intermedia) from south of the Alps (Ticino and Italy), and unexpectedly from the Grangettes site in western Switzerland. These results suggest the introduction of the Italian tree frog H. intermedia north of the Alps, and raise questions about the management of the Grangettes protected area.

Les TIC a l'ensenyament de la modelització matemàtica en Ciències Econòmiques i en Ciències Experimentals

Aquest projecte proposa materials didàctics per a un nou plantejament de les assignatures de Matemàtiques dels primers cursos de Ciències Empresarials i d'Enginyeria Tècnica, més acord amb el procés de convergència europea, basat en la realització de projectes que anomenem “Tallers de Modelització Matemàtica” (TMM) en els quals: (1) Els alumnes parteixen de situacions i problemes reals per als quals han de construir per sí mateixos els models matemàtics més adients i, a partir de la manipulació adequada d’aquests models, poden obtenir la informació necessària per donar-los resposta. (2) El treball de construcció, experimentació i avaluació dels models es realitza amb el suport de la calculadora simbòlica Wiris i del full de càlcul Excel com a instruments “normalitzats” del treball matemàtic d’estudiants i professors. (3) S’adapten els programes de les assignatures de matemàtiques de primer curs per tal de poder-les associar a un petit nombre de Tallers que parteixen de situacions adaptades a cada titulació. L’assignatura de Matemàtiques per a les Ciències Empresarials s’articula entorn de dos tallers independents: “Matrius de transició” pel que fa a l’àlgebra lineal i “Previsió de vendes” per a la modelització funcional en una variable. L’assignatura de Matemàtiques per a l’Enginyeria s’articula entorn d’un únic taller, “Models de poblacions”, que abasta la majoria de continguts del curs: successions i models funcionals en una variable, àlgebra lineal i equacions diferencials. Un conjunt d’exercicis interactius basats en la calculadora simbòlica WIRIS (Wiris-player) serveix de suport per al treball tècnic imprescindible per al desenvolupament de les dues assignatures. L’experimentació d’aquests tallers durant 2 cursos consecutius (2006/07 i 2007/08) en dues universitats catalanes (URL i UAB) ha posat en evidència tant els innegables avantatges del nou dispositiu docent per a l’aprenentatge dels estudiants, així com les restriccions institucionals que actualment dificulten la seva gestió i difusió.

trEST, trGEN and Hits: access to databases of predicted protein sequences.

High throughput genome (HTG) and expressed sequence tag (EST) sequences are currently the most abundant nucleotide sequence classes in the public database. The large volume, high degree of fragmentation and lack of gene structure annotations prevent efficient and effective searches of HTG and EST data for protein sequence homologies by standard search methods. Here, we briefly describe three newly developed resources that should make discovery of interesting genes in these sequence classes easier in the future, especially to biologists not having access to a powerful local bioinformatics environment. trEST and trGEN are regularly regenerated databases of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Hits is a web-based data retrieval and analysis system providing access to precomputed matches between protein sequences (including sequences from trEST and trGEN) and patterns and profiles from Prosite and Pfam. The three resources can be accessed via the Hits home page (http://hits. isb-sib.ch).

Development and testing of novel chloroplast microsatellite markers for Lolium perenne and other grasses (Poaceae) from de novo sequencing and in silico sequences

Twelve primers to amplify microsatellite markers from the chloroplast genome of Lolium perenne were designed and optimized using de novo sequencing and in silico sequences. With one exception, each locus was polymorphic with a range from two to nine alleles in L. perenne. The newly developed primer pairs cross-amplified in different species of Lolium and in 50 other grass species representing nine grass subfamilies.

Desenvolupament d'eines d'alta ressolució per al cribatge (screening) de l'activitat de fàrmacs

Projecte de recerca elaborat a partir d’una estada a la Satandford University, EEUU, entre 2007 i 2009. Els darrers anys, hi ha hagut un avanç espectacular en la tecnologia aplicada a l’anàlisi del genoma i del proteoma (microarrays, PCR quantitativa real time, electroforesis dos dimensions, espectroscòpia de masses, etc.) permetent la resolució de mostres complexes i la detecció quantitativa de diferents gens i proteïnes en un sol experiment. A més a més, la seva importància radica en la capacitat d’identificar potencials dianes terapèutiques i possibles fàrmacs, així com la seva aplicació en el disseny i desenvolupament de noves eines de diagnòstic. L’aplicabilitat de les tècniques actuals, però, està limitada al nivell al que el teixit pot ser disseccionat. Si bé donen valuosa informació sobre expressió de gens i proteïnes implicades en una malaltia o en resposta a un fàrmac per exemple, en cap cas, s’obté una informació in situ ni es pot obtenir informació espacial o una resolució temporal, així com tampoc s’obté informació de sistemes in vivo. L’objectiu d’aquest projecte és desenvolupar i validar un nou microscopi, d’alta resolució, ultrasensible i de fàcil ús, que permeti tant la detecció de metabòlits, gens o proteïnes a la cèl•lula viva en temps real com l’estudi de la seva funció. Obtenint així una descripció detallada de les interaccions entre proteïnes/gens que es donen dins la cèl•lula. Aquest microscopi serà un instrument sensible, selectiu, ràpid, robust, automatitzat i de cost moderat que realitzarà processos de cribatge d’alt rendiment (High throughput screening) genètics, mèdics, químics i farmacèutics (per aplicacions diagnòstiques i de identificació i selecció de compostos actius) de manera més eficient. Per poder realitzar aquest objectius el microscopi farà ús de les més noves tecnologies: 1)la microscopia òptica i d’imatge, per millorar la visualització espaial i la sensibilitat de l’imatge; 2) la utilització de nous mètodes de detecció incloent els més moderns avanços en nanopartícules; 3) la creació de mètodes informàtics per adquirir, emmagatzemar i processar les imatges obtingudes.

Impacte de la variabilitat climàtica ràpida de l'últim període glacial sobre la vegetació del sud-est de Nord Amèrica

Projecte de recerca elaborat a partir d’una estada a UMR-CNRS - Géologie et Océanographie, França, entre 2007 i 2009. Els canvis climàtics ràpids de l’últim període glacial (cicles Dansgaard/Oeschger i Heinrich Stadials-HS), han estat documentats en testimonis marins, de gel i dipòsits continentals, generalment de l’hemisferi nord. Mentre que la majoria dels estudis paleoclimàtics i paleoceanogràfics de l’Atlàntic Nord sobre l’últim període glacial s’han centrat en la part nord i est, les latituds mitjanes de la part occidental han estat menys estudiades. Particularment, els canvis de la vegetació de l’est de Nord Amèrica durant l’últim glacial es coneixen molt poc degut a la manca de seqüències pol.líniques llargues en aquesta regió. Només dues seqüències de pol.len del llac Tulane (Florida) mostren canvis de la vegetació significatius i interessants durant l’últim glacial, que suggereixen HS càlids i humits, que contrasta amb el que s’observa a l’altre costat de l’Atlàntic Nord. El treball realitzat al UMR-CNRS 5805 EPOC, Université Bordeaux 1, EPHE, des del 23 d’abril 2007 al 22 d’abril 2009, gràcies a la beca Beatriu de Pinós, implica una reconstrucció a alta resolució dels canvis de la vegetació a partir de l’anàlisi d’un testimoni marí, localitzat a l’oest de l’Atlàntic Nord subtropical (MD99-2203, 34º58’N, 75º12’W), durant l’Estadi Isotòpic Marí 3 (MIS 3). Les dades pal.linològiques del testimoni mostren una alternança entre Picea i Quercus. En general, les associacions pol.líniques indiquen que les variacions de la vegetació segueixen un patró bosc boreal/temperat durant l’últim glacial. El model d’edat preliminar basat en edats radiomètriques suggereix un augment del bosc temperat acompanyat d’una reducció del boreal entre el H4 i el H3. La comparació amb registres pol.línics marins d’alta resolució de la regió est subtropical, a latituds similars, mostren, per primer cop, que els canvis en les formacions forestals associats als canvis climàtics ràpids de l’últim glacial van ser menys intensos al sud-est de Nord Amèrica que a la Península Ibèrica.

Le rôle de la matérialité dans l'apprentissage de la lecture : aspects du curriculum enseigné, pratique enseignante et développement chez l'élève : une étude de cas à l'école primaire française

Notre étude consiste en une recherche longitudinale pour laquelle une cohorte d'élèves a été suivie depuis la Grande Section de l'école maternelle française (élèves de 5-6 ans) jusqu'au Cours Élémentaire 1re année de l'école élémentaire française (élèves de 7-8 ans) dans des situations ordinaires de classe. À ces niveaux scolaires, l'un des principaux objectifs du curriculum est l'apprentissage de la lecture. Nous considérons que l'élève construit les compétences de lecture à acquérir, i.e. les compétences caractérisant son développement potentiel, en s'appuyant sur les compétences caractérisant son développement actuel (Vygotski, 1934/1997). Lorsqu'il apprend à lire, l'élève a à sa disposition des moyens sémiotiques relatifs à la connaissance des objets et leurs usages, ainsi qu'aux gestes et leur signification (Moro & Rodriguez, 2005), ce que nous appelons globalement la matérialité. En conséquence, dans cette recherche, nous faisons l'hypothèse que ces premières habiletés relatives à la matérialité, constituent une ressource dans les situations d'enseignement- apprentissage de la lecture. Nous réalisons une étude de cas dont le recueil des données, à caractère ethnographique, est constitué de moments de classe enregistrés en vidéo, et ce, quatre fois par année scolaire. Ces douze enregistrements vidéo sont complétés par deux entretiens semi-directifs et un entretien d'auto- confrontation ; ils sont aussi mis en lien avec les Instructions officielles (programmes scolaires). L'analyse est à la fois macrogénétique et microgénétique. Pour chaque observation, concernant l'analyse macrogénétique, nous réalisons le synopsis à partir duquel nous sélectionnons des épisodes significatifs porteurs de matérialité. Les épisodes significatifs sont constitués des événements remarquables dont les analyses microgénétiques nécessitent l'utilisation d'outils, à savoir les tableaux des matérialités et les photogrammes. Notre étude montre que la matérialité permet aux élèves de devenir lecteurs et que les formes de cette matérialité changent en fonction de l'avancée des acquisitions des élèves et des dimensions de la lecture (code et compréhension) à apprendre. - Our research consists of a longitudinal study in which one group of pupils in ordinary classroom situations has been followed from the top level of French pre-elementary school (5- to 6 year-old pupils) to the second level of French primary school (7- to 8 year-old pupils). For these three school grades, one of the main objectives in the curriculum is learning to read. We consider that pupils build their new reading skills, i.e. the skills characterizing their potential development, by relying on skills characterizing their actual development (Vygotski, 1934/1997). When learning to read, pupils yet have at their disposal semiotic abilities related to knowledge both of material objects and their uses, and of basic gestures and their meaning (Moro & Rodriguez, 2005), all of this we sum up under the term of materiality. Consequently, in our research, we make the hypothesis that the children's basic abilities related to materiality constitute a resource in teaching-learning situations. We have chosen to carry out a case study. The data collected consist of videos of class sequences carried out four times a year for three years. These twelve videos are supplemented by two semi- structured interviews with the teacher, one "self-confronting" interview in which the teacher is brought to discuss her actions and by the analysis of the ministry's school curricula. Our analysis is both macrogenetic and microgenetic. For each teaching sequence, on the level of macrogenetic analysis, we have made up the synopsis from which we have selected significant episodes in terms of materiality. The significant episodes are composed of remarkable events the microgenetic analysis of which requires the use of tools such as materiality boards and photograms. Our study shows that materiality enables pupils to develop reading skills and that the forms that materiality takes on change according to the pupils' acquisition progress and the aspects of reading (code and comprehension) still to be learned.

Production of full-length cDNA sequences by sequencing and analysis of expressed sequence tags from Schistosoma mansoni

The number of sequences generated by genome projects has increased exponentially, but gene characterization has not followed at the same rate. Sequencing and analysis of full-length cDNAs is an important step in gene characterization that has been used nowadays by several research groups. In this work, we have selected Schistosoma mansoni clones for full-length sequencing, using an algorithm that investigates the presence of the initial methionine in the parasite sequence based on the positions of alignment start between two sequences. BLAST searches to produce such alignments have been performed using parasite expressed sequence tags produced by Minas Gerais Genome Network against sequences from the database Eukaryotic Cluster of Orthologous Groups (KOG). This procedure has allowed the selection of clones representing 398 proteins which have not been deposited as S. mansoni complete CDS in any public database. Dedicated sequencing of 96 of such clones with reads from both 5' and 3' ends has been performed. These reads have been assembled using PHRAP, resulting in the production of 33 full-length sequences that represent novel S. mansoni proteins. These results shall contribute to construct a more complete view of the biology of this important parasite.

Morphology of the larvae, male genitalia and DNA sequences of Anopheles (Kerteszia) pholidotus (Diptera: Culicidae) from Colombia

Since 1984, Anopheles (Kerteszia) lepidotus has been considered a mosquito species that is involved in the transmission of malaria in Colombia, after having been incriminated as such with epidemiological evidence from a malaria outbreak in Cunday-Villarrica, Tolima. Subsequent morphological analyses of females captured in the same place and at the time of the outbreak showed that the species responsible for the transmission was not An. lepidotus, but rather Anopheles pholidotus. However, the associated morphological stages and DNA sequences of An. pholidotus from the foci of Cunday-Villarrica had not been analysed. Using samples that were caught recently from the outbreak region, the purpose of this study was to provide updated and additional information by analysing the morphology of female mosquitoes, the genitalia of male mosquitoes and fourth instar larvae of An. pholidotus, which was confirmed with DNA sequences of cytochrome oxidase I and rDNA internal transcribed spacer. A total of 1,596 adult females were collected in addition to 37 larval collections in bromeliads. Furthermore, 141 adult females, which were captured from the same area in the years 1981-1982, were analysed morphologically. Ninety-five DNA sequences were analysed for this study. Morphological and molecular analyses showed that the species present in this region corresponds to An. pholidotus. Given the absence of An. lepidotus, even in recent years, we consider that the species of mosquitoes that was previously incriminated as the malaria vector during the outbreak was indeed An. pholidotus, thus ending the controversy.

On spectral approximation, Folner sequences and crossed products

In this article we review first some of the possibilities in which the notions of Fo lner sequences and quasidiagonality have been applied to spectral approximation problems. We construct then a canonical Fo lner sequence for the crossed product of a concrete C* -algebra and a discrete amenable group. We apply our results to the rotation algebra (which contains interesting operators like almost Mathieu operators or periodic magnetic Schrödinger operators on graphs) and the C* -algebra generated by bounded Jacobi operators.

Folner sequences and finite operators

This article analyzes Folner sequences of projections for bounded linear operators and their relationship to the class of finite operators introduced by Williams in the 70ies. We prove that each essentially hyponormal operator has a proper Folner sequence (i.e. a Folner sequence of projections strongly converging to 1). In particular, any quasinormal, any subnormal, any hyponormal and any essentially normal operator has a proper Folner sequence. Moreover, we show that an operator is finite if and only if it has a proper Folner sequence or if it has a non-trivial finite dimensional reducing subspace. We also analyze the structure of operators which have no Folner sequence and give examples of them. For this analysis we introduce the notion of strongly non-Folner operators, which are far from finite block reducible operators, in some uniform sense, and show that this class coincides with the class of non-finite operators.

Contribution pollinique à l'étude du pléistocène de la région lémanique (Suisse) : paléoenvironnement des derniers 800'000 ans

Abstact : Pollinic contribution to a Pleistocene study of the Lake Geneva region (Switzerland) Palaeoenvironment of the last 800,000 years. Although the "Plateau Romand" (tableland of French-speaking Switzerland) has been marked by the repetitive action of different Quaternary glacial thrusts, numerous preserved outcrops here and there, thanks to favourable topographical conditions, provide sufficient pollinic content to reconstitute the significant botanical fluctuations and allow bio- and chrono-stratigraphical correlations with the long European sequences. The present study examines around ten Pleistocene deposits rich in pollens, whose presumed ages cover a range of 800,000 years. - The Early and Early-Middle Pleistocene are examined at Ecoteaux (VD), undeniably the oldest site in this study. The "Lower Formation of Ecoteaux", whose low pollinic content reveals an environment of the cold desert type, shows an inverse palaeomagnetic remanence. An age earlier than 780,000 years BP (Matuyama period or earlier) is proposed. The "Upper Formation of Ecoteaux" contains over eight major fluctuations in the vegetal covering, of which at least four temporal phases and one climatic optimum. The presence of botanical genera, relics of the Tertiary in particular Pterocarya and Carya, associated with the vegetal dynamic made up of short oscillations, contrives to link this formation to the Cromerian Complex. The thermomeres recorded could correspond to one or several interglacial periods from Middle Pleistocene. Possible correlations with marine isotopic stages 15, 17 and 19 are discussed. - The Middle and Late Pleistocene is approached through the sediments of Onnens (VD), Creux d'Enfer (FR), Port-Valais (VS), La Dénériaz (VD) and Cortaillod (NE). Each site provides a temperate interglacial flora, whose pollinic content is evaluated according to the different conceivable bio-stratigraphic correlations. - Finally the Würm is studied thanks to the outcrop of Marly (FR), together with the excavations at Villars-sous-Yens (VD), Versoix (GE) and Ollon (VD). Together, these observations tend to show that the west of the Swiss Plateau is a zone of transition between the meridian vegetation of the lower Rhone valley and that of beyond the Jura. At the outlet of the Rhone glacier, and on the borders of the prealpine and Jurassian glaciers, the region is situated at the crossroads of post-glacial botanical migrations, between the major axis of the Rhone valley and the Eastern refuge zones; this situation confers particular importance on it. Although believed to be deeply scraped by ice, one notices today that the "Plateau Romand" harbours overtwenty interglacial and interstadial sites. The abrasive action of the Rhone glacier has thus been more modest than previously estimated. The effective extension of glacial tongues, together with atmospheric circulation, are doubtless varying from one interglacial to another. Finally, the speeds of glacial movements, and the unbelievable vegetal vitality, are important parameters, capable of leading to deposits, very early enriched in pollens. RÉSUMÉS : Contribution pollinique à l'étude du Pléistocène de la région lémanique (Suisse) - Paléoenvironnement des derniers 800'000 ans Bien que le Plateau romand soit marqué par l'action répétitive des différentes poussées glaciaires quaternaires, de nombreux affleurements préservés ça et là, à la faveur de conditions topographiques favorables, livrent un contenu pollinique suffisant pour reconstituer des fluctuations botaniques significatives et autoriser des corrélations bioet chronostratigraphiques avec les longues séquences européennes. Le présent travail étudie une dizaine de dépôts pléistocènes riches en pollens, dont les âges présumés balaient un éventail de plus de 800'000 ans. - Le Pléistocène Ancien et Moyen inférieur, sont examinés à Ecoteaux (VD); indéniablement le site le plus ancien de cette étude. La "Formation inférieure d'Ecoteaux", dont le maigre contenu pollinique traduit un environnement de type désertique froid, présente une rémanence magnétique inverse. Un âge antérieur à 780'000 ans BP (période de Matuyama ou antérieure) est proposé. La "Formation supérieure d'Ecoteaux" comprend plus de huit fluctuations majeures du couvert végétal, parmi lesquelles on compte au moins quatre épisodes tempérés et un optimum climatique. La présence de genres botaniques reliques du Tertiaire, en particulier Pterocarya et Carya, associée à la dynamique végétale faite de courtes oscillations, concourent à lier cette formation au Complexe Cromérien. Les thermomères enregistrées pourraient correspondre à un- ou plusieurs interglaciaires du Pléistocène moyen. Les corrélations possibles avec les stades isotopiques marins, MIS 15, 17 et 19 sont discutées. - Le Pléistocène Moyen et Récent est abordé à travers les sédiments d'Onnens (VD), du Creux d'Enfer (FR), de Port-Valais (VS), de La Dénériaz (VD) et de Cortaillod (NE). Chaque site livre une flore tempérée interglaciaire, dont le contenu pollinique est évalué en fonction des différentes corrélations bio-stratigraphiques envisageables. - Enfin le Würm est étudié grâce à l'affleurement de Marly (FR), accompagné des forages de Villars-sous-Yens (VD), Versoix (GE) et Ollon (VD). L'ensemble de ces observations tend à montrer que l'ouest du Plateau suisse est une zone charnière entre la végétation méridionale de la basse vallée du Rhône et celle d'au-delà du Jura. Au débouché du glacier du Rhône et aux confins des glaciers préalpins et jurassiens, cette région est située au carrefour des migrations botaniques post-glaciaires, entre l'axe majeur de la vallée du Rhône et les zones refuges de l'Est. Cette situation lui confère une importance toute particulière. Alors qu'on pensait le Plateau romand profondément raboté par les glaces, on constate aujourd'hui qu'il recèle plus d'une vingtaine de sites interglaciaires et interstadiaires. L'action abrasive du glacier rhodanien a donc été plus modeste qu'envisagée jusqu'ici. L'extension effective des langues glaciaires, tout comme la circulation atmosphérique, diffèrent sans doute d'un interglaciaire à l'autre. Enfin la vitesse des mouvements glaciaires et l'incroyable vitalité végétale sont des paramètres importants, susceptibles d'avoir entraîné des dépôts, très précocement enrichis en pollens.

Genometrics as an essential tool for the assembly of whole genome sequences: the example of the chromosome of Bifidobacterium longum NCC2705.

BACKGROUND: Analysis of the first reported complete genome sequence of Bifidobacterium longum NCC2705, an actinobacterium colonizing the gastrointestinal tract, uncovered its proteomic relatedness to Streptomyces coelicolor and Mycobacterium tuberculosis. However, a rapid scrutiny by genometric methods revealed a genome organization totally different from all so far sequenced high-GC Gram-positive chromosomes. RESULTS: Generally, the cumulative GC- and ORF orientation skew curves of prokaryotic genomes consist of two linear segments of opposite slope: the minimum and the maximum of the curves correspond to the origin and the terminus of chromosome replication, respectively. However, analyses of the B. longum NCC2705 chromosome yielded six, instead of two, linear segments, while its dnaA locus, usually associated with the origin of replication, was not located at the minimum of the curves. Furthermore, the coorientation of gene transcription with replication was very low. Comparison with closely related actinobacteria strongly suggested that the chromosome of B. longum was misassembled, and the identification of two pairs of relatively long homologous DNA sequences offers the possibility for an alternative genome assembly proposed here below. By genometric criteria, this configuration displays all of the characters common to bacteria, in particular to related high-GC Gram-positives. In addition, it is compatible with the partially sequenced genome of DJO10A B. longum strain. Recently, a corrected sequence of B. longum NCC2705, with a configuration similar to the one proposed here below, has been deposited in GenBank, confirming our predictions. CONCLUSION: Genometric analyses, in conjunction with standard bioinformatic tools and knowledge of bacterial chromosome architecture, represent fast and straightforward methods for the evaluation of chromosome assembly.