Assemblage of benthic foraminifera in sediment core GIK23414-8

Marine isotope stage (MIS) 9 is one of the least investigated Pleistocene interglaciations. The present study describes reconstructions of deepwater conditions during this time interval based on benthic foraminiferal assemblages from sediment core M23414 (Rockall Plateau, North Atlantic). The results of faunal analysis were supported by planktic d18O, sea surface temperature reconstructions based on planktic foraminiferal assemblages and content of ice rafted debris. Statistical data processing using principal component analysis revealed five climaterelated benthic foraminiferal associations that changed in response to alterations of deepwater circulation.

Assemblage d’ADN avec graphes de de Bruijn sur FPGA

Ce mémoire est consacré à la parallélisation d’un algorithme d’assemblage d’ADN de type de novo sur différentes plateformes matérielles, soit les processeurs multicoeurs et les accélérateurs de type FPGA. Plus précisément, le langage OpenCL est utilisé pour accélérer l’algorithme dont il est question, et de permettre un comparatif direct entre les les plateformes. Cet algorithme est d’abord introduit, puis son implémentation originale, développée pour une exécution sur une grappe de noeuds, est discutée. Les modifications apportées à l’algorithme dans le but de faciliter la parallélisation sont ensuite divulgées. Ensuite, le coeur du travail est présenté, soit la programmation utilisant OpenCL. Finalement, les résultats sont présentés et discutés.

L'impact du pays de conception et du pays d'assemblage des produits industriels sur les évaluations des acheteurs professionnels: une approche multi-attributs multi-produits

Dans la réalité complexe d'aujourd'hui, caractérisée par une globalisation des marchés et une internationalisation accrue des échanges, les produits industriels ont souvent plus d'une origine nationale. Ce facteur constitue un attribut important dans l'évaluation de la qualité de fabrication des produits industriels et la formation de jugements évaluatifs à leur égard. L'objet principal de cette étude porte sur la distinction entre le pays de conception et le pays d'assemblage et leurs influences relatives sur les évaluations de la qualité et la valeur de l'achat des produits de nature industrielle. L'appréciation des acheteurs professionnels pour des profils d'analyse conjointe est examinée pour trois catégories de produits différents de par l'importance de leur achat et le risque qui leur est associé: systèmes informatiques, télécopieurs et stylos à bille. Chacun de ces trois produits est caractérisé par trois niveaux hiérarchiques sur cinq attributs: le pays de conception, le pays d'assemblage, la marque, le prix et la garantie accordée. 306 questionnaires ont été administrés auprès d'un échantillon probabiliste d'acheteurs industriels québécois, membres de l'Association Canadienne de Gestion des Achats (ACGA). Les résultats indiquent l'existence d'une distinction importante entre le pays de conception et celui d'assemblage et que celle-ci est plus marquée pour des pays en voie de développement. Le pays de conception et le pays d'assemblage sont les attributs les plus importants pour l'évaluation de la qualité perçue des produits et de la valeur perçue de leur achat et ce, quel que soit le niveau de complexité du produit considéré. Le prix constitue cependant le facteur le plus déterminant lorsque l'importance et le risque associé au produit sont faibles. Plus un produit suscite une implication personnelle forte, plus le nombre et l'importance des attributs déterminants augmentent. Et plus l'implication et l'importance de l'achat diminuent, plus l'acheteur industriel a recours à des compromis entre les attributs étudiés. Les implications managériales et étatiques sont discutées dans le cadre de la globalisation des marchés et du traité de libre-échange nord-américain.

Utilisation d'une méthode de correction de retards pour la vérification d'un assemblage de fonctions RTL par rapport à un assemblage de fonctions au niveau fonctionnel

National audience

Étude du comportement de la chromatine, de la régulation de la transcription et réparation des gènes de l’ARNr avant la réplication de l’ADN et assemblage de la réparation par excision de nucléotides chez Saccharomyces cerevisiae

Résumé : Le nucléole est considéré comme étant une « usine » à produire des ribosomes. Cette production est la fonction la plus énergivore de la cellule. Elle met en jeu les trois ARN polymérases et représente 80% de l’activité de transcription au sein d’une cellule. Les trois quarts de cette activité de transcription correspondent à la synthèse des ARNr par l’ARN polymérase I (ARNPI). Ainsi mieux comprendre les mécanismes cellulaires se déroulant à l’intérieur de ce compartiment permettra le développement de nouveaux traitements contre le cancer. La synthèse d’ARNr par l’ARNPI est régulée à trois niveaux : l’initiation de la transcription, l’élongation et le nombre de gènes de l’ARNr en transcription. La plupart des travaux qui se sont intéressés à ces niveaux de régulation ont été réalisés avec des cellules en phase exponentielle de croissance. Au cours de mes travaux, je me suis attardé sur la régulation de la transcription par l’ARNPI au cours de la phase G1 du cycle cellulaire et au début de la phase S. Ainsi mes résultats ont montré que si la chromatine des gènes de l’ARNr est essentiellement dépourvue de nucléosomes, la régulation de l’ARNPI diffère dans des cellules en G1 et au début de la phase S. J’ai pu de ce fait observer qu’en G1, la transcription de l’ARNPI se concentre sur un nombre réduit de gènes en transcription. Dans des cellules arrêtées au début de la phase S avec de l’hydroxyurée, la transcription de l’ARNPI est perturbée par un défaut de maturation de l’ARNR. Fort de ces résultats sur la nature des gènes ribosomaux en phase G1, je me suis attardé à la réparation de ces gènes lors de cette phase. Alors que dans des cellules en phase exponentielle de croissance irradiées avec des UVC, la chromatine des gènes de l’ARNr se ferme ; je n’ai pas observé la formation de nucléosomes suite à l’irradiation de cellules synchronisée en G1. Mes résultats montrent également que la réparation est plus efficace. Parallèlement, j’ai exploré l’assemblage du complexe de réparation par excision de nucléotides. Toutefois, les résultats obtenus sont peu concluants.

Determining phosphine resistance in rust red flour beetle, Tribolium castaneum (Herbst.) (Coleoptera : Tenebrionidae) populations from Turkey

Fumigation with phosphine gas is the primary method of controlling stored grain pests. In Turkey, phosphine has been used extensively since the 1950's. Even though high levels of phosphine resistance have been detected in several key stored products pests across the world, it has never been studied in Turkey despite this long history of phosphine use. High-level phosphine resistance has been detected and genetically characterised previously in the rust red flour beetle, Tribolium castaneum in other countries. Since this pest is also a common problem in stored grain environment in Turkey, the current study was undertaken for the first time, to investigate the distribution and strength of phosphine resistance in T. castaneum. Four strains of T. castaneum were tested through bioassays for determining the weak and strong phosphine resistance phenotypes on the basis of the response of adults to discriminating phosphine concentrations of 0.03 mg/L and 0.25 mg/L, for 20 hour exposures respectively. Phenotype testing showed all strains exhibited some level of phosphine resistance with a maximum level of 196 fold. Sequencing and genetic testing of seven field-collected strains showed that all of them carried a strong resistance allele in at the rph2 locus similar to the one previously reported. Our results show that strong resistance to phosphine is common in Turkish strains of T. castaneum.

Brachyuran soft-bottom assemblage from marine shallow waters in the southeastern Brazilian littoral.

The present investigation examined the assemblages of brachyuran crabs in three bays of southeastern So Paulo State, analyzing the numbers of species and individuals, biomass, and diversity. The crabs were collected monthly in Ubatumirim, Ubatuba, and Mar Virado bays in the Ubatuba region over 2 years (1998 and 1999). In each bay, six tows were made from a fishing boat. A total of 39,820 specimens, representing 11 super families, 39 genera, and 65 species of brachyurans, were obtained. The mean number of specimens and biomass varied seasonally, which can be mainly related with the population tendencies of two dominant species in the area (Callinectes ornatus and Hepatus pudibundus). The highest numbers of individuals and species were found in Ubatuba Bay, followed by Ubatumirim and Mar Virado. The highest diversity index was estimated for Ubatumirim (H' = 2.44), followed by Ubatuba (H' = 2.37) and Mar Virado (H' = 1.86). In general, the coastal region supported high abundance and species richness concerning brachyurans, with high diversity indices, probably because of its more-heterogeneous substrate, which may afford more refuges for certain species. These results suggested that environmental conditions in this area, although they showed certain differences, are favorable for the establishment and development of a diverse brachyuran guild.

Dinocyst assemblage constraints on oceanographic and atmospheric processes in the eastern equatorial Atlantic over the last 44 kyr

A new 44 kyr long record of dinoflagellate (phytoplanktonic organisms) cysts (dinocysts) is presented from a marine sediment core collected on the Congolese margin with the aim of reconstructing past hydrological changes in the equatorial eastern Atlantic Ocean since Marine Isotopic Stage (MIS) 3. Our high-resolution dinocyst record indicates that significant temperature and moisture variations occurred across the glacial period, the last deglaciation and the Holocene. The use of specific dinocyst taxa, indicative of fluvial, upwelling and Benguela Current past environments for instance, provides insights into the main forcing mechanisms controlling palaeohydrological changes on orbital timescales. In particular, we are able, for the last 44 kyr, to correlate fluvial-sensitive taxa to monsoonal mechanisms related to precession minima–obliquity maxima combinations. While upwelling mechanisms appear as the main drivers for dinoflagellate productivity during MIS 2, dissolved nutrient-enriched Congo River inputs to the ocean also played a significant role in promoting dinoflagellate productivity between approximately 15.5 and 5 ka BP. Finally, this high-resolution dinocyst study permits us to precisely investigate the suborbital timing of the last glacial–interglacial termination, including an atypical warm and wet oceanic LGM signature, northern high-latitude abrupt climate change impacts in the equatorial eastern Atlantic, as well as a two-step decrease in moisture conditions during the Holocene at around 7–6 and 4–3.5 ka BP.

A field study to describe diel, tidal and semilunar rhythms of larval release in an assemblage of tropical rocky shore crabs

Available information on the larval release rhythms of brachyurans is biased to temperate estuarine species and outcomes resulting from some sort of artificial manipulation of ovigerous females. In this study we applied field methods to describe the larval release rhythms of an assemblage of tropical rocky shore crabs. Sampling the broods of ovigerous females of Pachygrapsus transversus at two different shores indicated a spatially consistent semilunar pattern, with larval release maxima around the full and new moon. Yet, synchronism between populations varied considerably, with the pattern obtained at the site exposed to a lower wave action far more apparent. Breeding cohorts at one of the sampled shores apparently belonged to actual age groups composing the ovigerous population. The data suggest that these breeding groups release their larvae in alternate syzygy periods, responding to a lunar cycle instead of the semilunar pattern observed for the whole population. For the description of shorter-term rhythms, temporal series at hour intervals were obtained by sampling the plankton and confinement boxes where ovigerous females were held. Unexpectedly, diurnal release activity prevailed over nocturnal hatching. Yet, only grapsids living higher on the shore exhibited strong preferences over the diel cycle, with P. transversus releasing their larvae during the day and Geograpsus lividus during the night. The pea crab Dissodactylus crinitichelis, the spider crab Epialtus brasiliensis and a suite of xanthoids undertook considerable releasing activity in both periods. Apart from the commensal pea crab D. crinitichelis, all other taxa revealed tide-related rhythms of larval release, with average estimates of the time of maximum hatching always around the time of high tides; usually during the flooding and slack, rather than the ebbing tide. Data obtained for P. transversus females held in confinement boxes indicated that early larval release is mostly due to nocturnal hatching, while zoeal release in diurnal groups took place at the time of high tide. Since nocturnal high tides at the study area occurred late, sometimes close to dusk, early release would allow more time for offshore transport of larvae when the action of potential predators is reduced.

Composition and temporal dynamics of a temperate rocky cryptobenthic fish assemblage

Temporal variation in a temperate cryptobenthic fish assemblage at the Arrabida Marine Park (Portugal) was assessed by visual Surveys during 2002 and 2003. A total of 9596 fish from 11 families and 30 species was recorded. There were no changes in structure or density at the assemblage level between years, whereas diversity changed significantly due to a higher number of abundant species in the second year. A similar seasonal trend was found between years, with a significant overall density increase in autumn. This is partially explained by the arrival of new recruits of some of the most abundant species in the assemblage. Assemblage diversity and structure also changed across seasons. A group of species encompassing Gobius xanthocephalus, Tripterygion delaisi, Parablennius pilicornis, Gobius paganellus, Lepadogaster candollii and Lepadogaster spp. were analysed in detail. The temporal patterns of two of the most abundant species, G. xanthocephalus and T delaisi, mimicked the overall temporal patterns of the assemblage. We suggest that the inter-annual stability in density of this subtidal fish assemblage may be similar to what has been reported for the intertidal and that strong post-settlement processes are probably shaping this assemblage.

Enzymatic activity on sediments and nematode assemblage responses during seagrass beds habitat recovery following the disturbance of the traditional digging activity of bivalves harvesting.

Sediment digging is an anthropogenic activity connected to the exploitation of living resources in estuarine and marine environments. The knowledge on the functional responses of the benthic assemblages to the physical disturbance is an important baseline to understand the ecological processes of the habitat recovery and restoration and to develop tools for the management of the harvesting activities. To investigate the effects of the digging activity of the bivalves on Zostera noltii seagrass beds a manipulative field experiment was conducted that included the enzymatic activity of sediments and the associated nematode assemblages. Four plots (two undisturbed serving as control and two dug to collect bivalves - treatment) with 18 subplots were randomly located at seagrass beds in the Mira estuary at the SW coast of Portugal. Samples were randomly and unrepeatably collected from three subplots of each plot in five different occasions, before sediment digging (T0) up to six months after disturbance (T5). Microbial activity in sediments was assess by determining the extracelular enzymatic activity of six hydrolytic enzymes (sulfatase, phosphatase, b -N-acetilglucosaminidase, b-glucosidase, urease, protease) and two oxidoreductases (phenol oxidase and peroxidase). The microbial community status was also assessed through the measurement of dehydrogenase, which reflects microbial respiration. The nematode assemblages composition, biodiversity and trophic composition at different sampling occasions were also analyzed. The fluorometric and biochemical parameters analysed of the Z. noltii plants during the experimental period showed a recovery of the seagrass beds, and it was detected an increase of the enzymatic activity of the sediments after disturbance. The nematodes assemblages were similar in all sampling occasions. The seagrass beds and the nematodes assemblages associated showed a high resilience to the stress caused by the traditional bivalves digging activity. The obtained results allow the development of a management programme for the commercial fishing activity to maintain the good environmental status and minimized the secondary environmental effects on marine and estuarine habitats through the establishment of a baseline for the regulation of the harvesting frequency.

Benthic nematode assemblage composition and diversity during a natural recovery process of Zostera noltii seagrass beds,

In 2008, the stable seagrass beds of the Mira estuary (SW Portugal) disappeared completely; however, during 2009, they have begun to present early symptoms of natural recovery, characterised by a strongly heterogeneous distribution. This study was designed to investigate the spatial and temporal variability patterns of species composition, densities and trophic composition of the benthic nematode assemblages in this early recovery process, at two sampling sites with three stations each and at five sampling occasions. Because of the erratic and highly patchy seagrass recovery and the high environmental similarity of the two sampling sites, we expected within-site variability in nematode assemblages to exceed between-site variability. However, contrary to that expectation, whilst nematode genus composition was broadly similar between sites, nematode densities differed significantly between sites, and this between-site variability exceeded within-site variability. This may be linked to differences in the Zostera recovery patterns between both sites. In addition, no clear temporal patterns of nematode density, trophic composition and diversity were evident.

Changes in fish assemblage structure after implementation of Marine Protected Areas in the south western coast of Portugal.

Marine Protected Areas (MPAs) are increasingly being recommended as management tools for biodiversity conservation and fisheries. With the purpose of protecting the region's biodiversity and prevent the over exploitation of marine resources, in February 2011 the no-take MPAs of Ilha do Pessegueiro and Cabo Sard~ao were implemented within the “Parque Natural do Sudoeste Alentejano e Costa Vicentina “(PNSACV) Marine Park, south western coast of Portugal. As such, commercial and recreational fishing became prohibited in these areas. In order to evaluate the effects of these no-take MPAs, the structure of their fish assemblages and of adjacent control areas without fishing restrictions were studied between 2011 (immediately after implementation) and 2013 (two years after implementation). A total of 4 sampling campaigns were conducted (summer 2011, winter 2012, summer 2013 and winter 2013) using trammel nets and bottom trawl. Ichthyofaunal assemblages from the no-take MPAs (treatment) were compared with adjacent areas (controls) and changes evaluated as a function of time since protection. Results revealed significant increase in fish abundance after the implementation of the no-take MPAs. Furthermore, significant differences in the structure of fish assemblages (abundance and fish size) between protected and neighbouring areas were rapidly observed upon the implementation of the no-take MPAs. In addition, specimens of larger size occurred more frequently within Ilha do Pessegueiro no-take MPA in the last year of the study. Overall, despite the young age of these no-take MPAs, changes on the structure of their fish assemblages were already evident after only two years of protection, indicating that management measures such as MPA designation may play an important role to promote fisheries sustainable exploitation as well as to protect species with conservation interest.