Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes.

A stringent branch-site codon model was used to detect positive selection in vertebrate evolution. We show that the test is robust to the large evolutionary distances involved. Positive selection was detected in 77% of 884 genes studied. Most positive selection concerns a few sites on a single branch of the phylogenetic tree: Between 0.9% and 4.7% of sites are affected by positive selection depending on the branches. No functional category was overrepresented among genes under positive selection. Surprisingly, whole genome duplication had no effect on the prevalence of positive selection, whether the fish-specific genome duplication or the two rounds at the origin of vertebrates. Thus positive selection has not been limited to a few gene classes, or to specific evolutionary events such as duplication, but has been pervasive during vertebrate evolution.

Torre del Greco distrutta nel 1794 : [vue du site et du Vésuve en éruption] : [peinture]

Collectionneur : Lesouëf, Auguste (1829-1906)

Climbers' perceptions toward sustainable bouldering at the Niagara Glen Nature Reserve

Currently, there are a variety of concerns about the future of bouldering, a form of rock climbing, a t the Niagara Glen Nature Reserve near Niagara Falls, Ontario due to environmental impacts at the site. The purpose of this study was to describe the perceptions ofbouldering participants toward sustainable bouldering practices at the Niagara Glen. The methodological framework for this study was based on action research, which attempts to solve specific problems through having people in a community study, discuss, and act on those problems. Five separate focus group interviews elicited data from nineteen men and seven women, while there were twenty one men and ten women observed through participant observations at the Niagara Glen. Analysis was conducted through coding processes where data were compared repeatedly and then organized into themes. From the open coding process, two main themes were identified and interpreted as 1) Barriers to Sustainable Bouldering at the Niagara Glen Nature Reserve, and 2) Environmental and Social Role and Responsibility ofBoulde r ing Participants at the Niagara Glen. The implications of the findings include a variety of recommendations for the bouldering community and the Niagara Parks Commission to consider for future collaborative planning. Some of these recommendations include more open communication between all stakeholders at the Glen, additional leadership from local climbing access coalitions and the Niagara Parks Commission, and greater implementation of minimum impact practices from the bouldering community. Additionally, these implications are discussed through a three-part framework based on a conceptual intersection of sense of place, community empowerment, and sustainable recreational use as a way to potentially unify the bouldering community's voice and vision toward sustainable practice.

Directed evolution of human dihydrofolate reductase: towards a better understanding of binding at the active site

La dihydrofolate réductase humaine (DHFRh) est une enzyme essentielle à la prolifération cellulaire, ce qui en fait une cible de choix pour le traitement de différents cancers. À cet effet, plusieurs inhibiteurs spécifiques de la DHFRh, les antifolates, ont été mis au point : le méthotrexate (MTX) et le pemetrexed (PMTX) en sont de bons exemples. Malgré l’efficacité clinique certaine de ces antifolates, le développement de nouveaux traitements s’avère nécessaire afin de réduire les effets secondaires liés à leur utilisation. Enfin, dans l’optique d’orienter la synthèse de nouveaux composés inhibiteurs des DHFRh, une meilleure connaissance des interactions entre les antifolates et leur enzyme cible est primordiale. À l’aide de l’évolution dirigée, il a été possible d’identifier des mutants de la DHFRh pour lesquels l’affinité envers des antifolates cliniquement actifs se voyait modifiée. La mutagenèse dite ¬¬de saturation a été utilisée afin de générer des banques de mutants présentant une diversité génétique au niveau des résidus du site actif de l’enzyme d’intérêt. De plus, une nouvelle méthode de criblage a été mise au point, laquelle s’est avérée efficace pour départager les mutations ayant entrainé une résistance aux antifolates et/ou un maintient de l’activité enzymatique envers son substrat natif, soient les phénotypes d’activité. La méthode de criblage consiste dans un premier temps en une sélection bactérienne à haut débit, puis dans un second temps en un criblage sur plaques permettant d’identifier les meilleurs candidats. Plusieurs mutants actifs de la DHFRh, résistants aux antifolates, ont ainsi pu être identifiés et caractérisés lors d’études de cinétique enzymatique (kcat et IC50). Sur la base de ces résultats cinétiques, de la modélisation moléculaire et des données structurales de la littérature, une étude structure-activité a été effectuée. En regardant quelles mutations ont les effets les plus significatif sur la liaison, nous avons commencé à construire un carte moléculaire des contacts impliqués dans la liaison des ligands. Enfin, des connaissances supplémentaires sur les propriétés spécifiques de liaison ont put être acquises en variant l’inhibiteur testé, permettant ainsi une meilleure compréhension du phénomène de discrimination du ligand.

L’outillage sur plaquette en quartzite du site ElFs-010. Étude d’une technologie distinctive en Jamésie, Québec (1900-400 A.A.)

Réalisé en collaboration avec Arkéos Inc.

Information sources selection methodology for recommender systems based on intrinsic characteristics and trust measure

El treball desenvolupat en aquesta tesi presenta un profund estudi i proveïx solucions innovadores en el camp dels sistemes recomanadors. Els mètodes que usen aquests sistemes per a realitzar les recomanacions, mètodes com el Filtrat Basat en Continguts (FBC), el Filtrat Col·laboratiu (FC) i el Filtrat Basat en Coneixement (FBC), requereixen informació dels usuaris per a predir les preferències per certs productes. Aquesta informació pot ser demogràfica (Gènere, edat, adreça, etc), o avaluacions donades sobre algun producte que van comprar en el passat o informació sobre els seus interessos. Existeixen dues formes d'obtenir aquesta informació: els usuaris ofereixen explícitament aquesta informació o el sistema pot adquirir la informació implícita disponible en les transaccions o historial de recerca dels usuaris. Per exemple, el sistema recomanador de pel·lícules MovieLens (http://movielens.umn.edu/login) demana als usuaris que avaluïn almenys 15 pel·lícules dintre d'una escala de * a * * * * * (horrible, ...., ha de ser vista). El sistema genera recomanacions sobre la base d'aquestes avaluacions. Quan els usuaris no estan registrat en el sistema i aquest no té informació d'ells, alguns sistemes realitzen les recomanacions tenint en compte l'historial de navegació. Amazon.com (http://www.amazon.com) realitza les recomanacions tenint en compte les recerques que un usuari a fet o recomana el producte més venut. No obstant això, aquests sistemes pateixen de certa falta d'informació. Aquest problema és generalment resolt amb l'adquisició d'informació addicional, se li pregunta als usuaris sobre els seus interessos o es cerca aquesta informació en fonts addicionals. La solució proposada en aquesta tesi és buscar aquesta informació en diverses fonts, específicament aquelles que contenen informació implícita sobre les preferències dels usuaris. Aquestes fonts poden ser estructurades com les bases de dades amb informació de compres o poden ser no estructurades com les pàgines web on els usuaris deixen la seva opinió sobre algun producte que van comprar o posseïxen. Nosaltres trobem tres problemes fonamentals per a aconseguir aquest objectiu: 1 . La identificació de fonts amb informació idònia per als sistemes recomanadors. 2 . La definició de criteris que permetin la comparança i selecció de les fonts més idònies. 3 . La recuperació d'informació de fonts no estructurades. En aquest sentit, en la tesi proposada s'ha desenvolupat: 1 . Una metodologia que permet la identificació i selecció de les fonts més idònies. Criteris basats en les característiques de les fonts i una mesura de confiança han estat utilitzats per a resoldre el problema de la identificació i selecció de les fonts. 2 . Un mecanisme per a recuperar la informació no estructurada dels usuaris disponible en la web. Tècniques de Text Mining i ontologies s'han utilitzat per a extreure informació i estructurar-la apropiadament perquè la utilitzin els recomanadors. Les contribucions del treball desenvolupat en aquesta tesi doctoral són: 1. Definició d'un conjunt de característiques per a classificar fonts rellevants per als sistemes recomanadors 2. Desenvolupament d'una mesura de rellevància de les fonts calculada sobre la base de les característiques definides 3. Aplicació d'una mesura de confiança per a obtenir les fonts més fiables. La confiança es definida des de la perspectiva de millora de la recomanació, una font fiable és aquella que permet millorar les recomanacions. 4. Desenvolupament d'un algorisme per a seleccionar, des d'un conjunt de fonts possibles, les més rellevants i fiable utilitzant les mitjanes esmentades en els punts previs. 5. Definició d'una ontologia per a estructurar la informació sobre les preferències dels usuaris que estan disponibles en Internet. 6. Creació d'un procés de mapatge que extreu automàticament informació de les preferències dels usuaris disponibles en la web i posa aquesta informació dintre de l'ontologia. Aquestes contribucions permeten aconseguir dos objectius importants: 1 . Millorament de les recomanacions usant fonts d'informació alternatives que sigui rellevants i fiables. 2 . Obtenir informació implícita dels usuaris disponible en Internet.

Improving participatory varietal selection processes: participatory varietal selection and the role of informal seed diffusion mechanisms for upland rice in Ghana

This paper considers the process of Participatory Varietal Selection (PVS) and presents approaches and ideas based on PVS activities conducted on upland rice throughout Ghana between 1997 and 2003. In particular the role of informal seed systems in PVS is investigated and implications for PVS design are identified. PVS programmes were conducted in two main agroecological zones, Forest and Savannah, with 1,578 and 1,143 mm of annual rainfall, respectively, and between 40 and 100 varieties tested at each site. In the Savannah zone IR12979-24-1 was officially released and in the Forest zone IDSA 85 was widely accepted by farmers. Two surveys were conducted in an area of the Forest zone to study mechanisms of spread. Here small amounts (1-2 kg) of seed of selected varieties had been given to 94 farmers. In 2002, 37% of 2,289 farmers in communities surveyed had already grown a PVS variety and had obtained seed via informal mechanisms from other farmers, i.e. through gift, exchange or purchase. A modified approach for PVS is presented which enables important issues identified in the paper to be accommodated. These issues include: utilising existing seed spread mechanisms; facilitating formal release of acceptable varieties; assessing post-harvest traits, and; the need for PVS to be an ongoing and sustainable process.

Social bees and food plant associations in the Nilgiri Biosphere Reserve, India

The diversity of social bees was assessed at 15 sites across five locations of the Nilgiri Biosphere Reserve, Western Ghats, India, from January to December 2007. We also conducted floristic analyses of local vegetation in each site using one-hectare sample plots. All woody species with a dbh (diameter at breast height) : 30 cm were recorded within the plots. A total area of 9.72 ha was assessed for floristic composition. Similarity of floristic composition between sites was determined using the Jaccard's distance measure and a dendrogram constructed based on the hierarchical clustering of floristic dissimilarities between sites. A Bee Importance Index (BII) was developed to give a measure of the bee diversity at each site. This index was a sum of the species richness of bee species in a site and their visitation frequencies to flowers, calculated as mean flower visits hour 1 within 2 focal patches within one hectare plots. The visits of bee species to flowers were also recorded. The Jaccard distance measure indicated that the montane sites were quite dissimilar to the low elevation sites in floristic diversity. The BII was 7-9 for the wet forest sites and ranged from 4-6 for drier forest sites. Seventy three plant species were identified as social bee plants and of them 45% were visited by one species of bee, 37% by two bee species and 18% by more than two bee species, indicating a certain degree of floral specialization among bees.

Dysregulation of granulosal bone morphogenetic protein receptor 1B density is associated with reduced ovarian reserve and the age-related decline in human fertility

Reproductive ageing is linked to the depletion of ovarian primordial follicles, which causes an irreversible change to ovarian cellular function and the capacity to reproduce. The current study aimed to profile the expression of bone morphogenetic protein receptor, (BMPR1B) in 53 IVF patients exhibiting different degrees of primordial follicle depletion. The granulosa cell receptor density was measured in 403 follicles via flow cytometry. A decline in BMPR1B density occurred at the time of dominant follicle selection and during the terminal stage of folliculogenesis in the 23-30 y good ovarian reserve patients. The 40+ y poor ovarian reserve patients experienced a reversal of this pattern. The results demonstrate an association between age-induced depletion of the ovarian reserve and BMPR1B receptor density at the two critical time points of dominant follicle selection and pre-ovulatory follicle maturation. Dysregulation of BMP receptor signalling may inhibit the normal steroidogenic differentiation required for maturation in older patients.

Microhabitat Selection of three Forest Understory Birds in the Brazilian Atlantic Rainforest

When assessing fragmentation effects on species, not only habitat preferences on the landscape scale, but also microhabitat selection is an important factor to consider, as microhabitat is also affected by habitat disturbance, but nevertheless essential for species for foraging, nesting and sheltering. In the Atlantic Rainforest of Brazil we examined microhabitat selection of six Pyriglena leucoptera (white-shouldered fire-eye), 10 Sclerurus scansor (rufous-breasted leaftosser), and 30 Chiroxiphia caudata (blue manakin). We radio-tracked the individuals between May 2004 and February 2005 to gain home ranges based on individual fixed kernels. Vegetation structures in core plots and fringe plots were compared. In C. caudata, we additionally assessed the influence of behavioural traits on microhabitat selection. Further, we compared microhabitat structures in the fragmented forest with those in the contiguous, and contrasted the results with the birds` preferences. Pyriglena leucoptera preferred liana tangles that were more common in the fragmented forest, whereas S. scansor preferred woody debris, open forest floor (up to 0.5 m), and a thin closed leaf litter cover which all occurred significantly more often in the contiguous forest. Significant differences were detected in C. caudata for vegetation densities in the different strata; the distance of core plots to the nearest lek site was significantly influenced by sex and age. However, core sites of C. caudata in fragmented and contiguous forests showed no significant differences in structure. Exploring microhabitat selection and behavior may greatly support the understanding of habitat selection of species and their susceptibility to fragmentation on the landscape scale.

Divergent evolution and purifying selection of the H (FUT1) gene in New World monkeys (Primates, Platyrrhini)

In the present study, the coding region of the H gene was sequenced and analyzed in fourteen genera of New World primates (Alouatta, Aotus, Ateles, Brachyteles, Cacajao, Callicebus, Callithrix, Cebus, Chiropotes, Lagothrix, Leontopithecus, Pithecia, Saguinus, and Saimiri), in order to investigate the evolution of the gene. The analyses revealed that this coding region contains 1,101 nucleotides, with the exception of Brachyteles, the callitrichines (Callithrix, Leontopithecus, and Saguinus) and one species of Callicebus (moloch), in which one codon was deleted. In the primates studied, the high GC content (63%), the nonrandom distribution of codons and the low evolution rate of the gene (0.513 substitutions/site/MA in the order Primates) suggest the action of a purifying type of selective pressure, confirmed by the Z-test. Our analyses did not identify mutations equivalent to those responsible for the H-deficient phenotypes found in humans, nor any other alteration that might explain the lack of expression of the gene in the erythrocytes of Neotropical monkeys. The phylogenetic trees obtained for the H gene and the distance matrix data suggest the occurrence of divergent evolution in the primates.

Carbon isotope fractionation for cotton genotype selection

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genetic gain in the selection by multi-effects index in open-pollinated progenies of Eucalyptus grandis Hill ex Maiden

In Brazil, Eucalyptus grandis Hill ex Maiden is widely used for commercial reforestation, especially for production of pulp, paper and energy. Its genetic variability is being explored in tree improvement programs for over 30 years. The objective of this work was to estimate genetic parameters and compare genetic gains by multi-effects index in a breeding population of E. grandis. Progeny tests were established using open-pollinated seeds from ten provenances ranging from 153 to 160 progenies established in a completely randomized block design in four sites of Sao Paulo State (Anhembi, Avere Itarare e Pratania). At 24 months of age the traits diameter at breast height (DBH), height (ALT) and volume (VOL) were measured. The individual site analyses indicated significant genetic differences among progenies, height genetic variability and the mean progeny heritability (> 0.70). For joint analyses of sites, significant differences in genotype x environmental interaction effects were detected, showing differences of performance of the progenies in different sites. The Itarare site gave high genetic gains, effective size and genetic diversity. The genetic diversity and low effective size are unviable factors; considering that the progeny tests studied should retain adequate levels of genetic variability in order to be transformed in future seedling seed orchards.

Selection of Switching Sites in All-Optical Nework Topology Design

In this paper, we consider the problem of topology design for optical networks. We investigate the problem of selecting switching sites to minimize total cost of the optical network. The cost of an optical network can be expressed as a sum of three main factors: the site cost, the link cost, and the switch cost. To the best of our knowledge, this problem has not been studied in its general form as investigated in this paper. We present a mixed integer quadratic programming (MIQP) formulation of the problem to find the optimal value of the total network cost. We also present an efficient heuristic to approximate the solution in polynomial time. The experimental results show good performance of the heuristic. The value of the total network cost computed by the heuristic varies within 2% to 21% of its optimal value in the experiments with 10 nodes. The total network cost computed by the heuristic for 51% of the experiments with 10 node network topologies varies within 8% of its optimal value. We also discuss the insight gained from our experiments.