A combined computational and functional approach identifies new residues involved in pH-dependent gating of ASIC1a.

Acid-sensing ion channels (ASICs) are key receptors for extracellular protons. These neuronal nonvoltage-gated Na(+) channels are involved in learning, the expression of fear, neurodegeneration after ischemia, and pain sensation. We have applied a systematic approach to identify potential pH sensors in ASIC1a and to elucidate the mechanisms by which pH variations govern ASIC gating. We first calculated the pK(a) value of all extracellular His, Glu, and Asp residues using a Poisson-Boltzmann continuum approach, based on the ASIC three-dimensional structure, to identify candidate pH-sensing residues. The role of these residues was then assessed by site-directed mutagenesis and chemical modification, combined with functional analysis. The localization of putative pH-sensing residues suggests that pH changes control ASIC gating by protonation/deprotonation of many residues per subunit in different channel domains. Analysis of the function of residues in the palm domain close to the central vertical axis of the channel allowed for prediction of conformational changes of this region during gating. Our study provides a basis for the intrinsic ASIC pH dependence and describes an approach that can also be applied to the investigation of the mechanisms of the pH dependence of other proteins.

Efficiency of five biosolids to supply nitrogen and phosphorus to ryegrass

Biosolids have been considered satisfactory to supply crops and plant nutrients. The ideal biosolids application rate should result in high crop yields and nutrient uptake, and leave low concentrations of nutrients in soils to avoid environmental problems. The objective of this study was to estimate the capacity of five biosolids to supply N and P to ryegrass (Lolium perenne) after a single application of either fertilizers or biosolids to a Spodosol and an Oxisol. Results showed that 6% - 36% of N and 3% - 7% of P applied as biosolids were recovered in plants grown on the Spodosol, while the range on the Oxisol was 26%-75% for N and 1.2%-3.7% for phosphorus. Biosolids' efficiency on supplying N and P to plants was similar to fertilizer on the Spodosol, but on the Oxisol it refrained to 65%-67% fertilizer's efficiency. After a single application of biosolids followed by six consecutive harvests, 25%-94% of the N and 93%-99% of the P were not used by plants and remain in the soils.

Computational problems in perfect phylogeny haplotyping: Typing without calling the allele

A haplotype is an m-long binary vector. The XOR-genotype of two haplotypes is the m-vector of their coordinate-wise XOR. We study the following problem: Given a set of XOR-genotypes, reconstruct their haplotypes so that the set of resulting haplotypes can be mapped onto a perfect phylogeny (PP) tree. The question is motivated by studying population evolution in human genetics and is a variant of the PP haplotyping problem that has received intensive attention recently. Unlike the latter problem, in which the input is '' full '' genotypes, here, we assume less informative input and so may be more economical to obtain experimentally. Building on ideas of Gusfield, we show how to solve the problem in polynomial time by a reduction to the graph realization problem. The actual haplotypes are not uniquely determined by the tree they map onto and the tree itself may or may not be unique. We show that tree uniqueness implies uniquely determined haplotypes, up to inherent degrees of freedom, and give a sufficient condition for the uniqueness. To actually determine the haplotypes given the tree, additional information is necessary. We show that two or three full genotypes suffice to reconstruct all the haplotypes and present a linear algorithm for identifying those genotypes.

A high-efficiency HeLa cell nuclear transcription extract.

A HeLa cell nuclear transcription extract that is approximately 20 times more efficient than standard HeLa cell transcription extracts was developed. Transcription of the strong adenovirus II major late promoter by this extract results in the synthesis of 1.5-4 molecules of product RNA per molecule of template, indicating that the extract is capable of multiple rounds of initiation. Standard HeLa cell nuclear extracts transcribe closed circular and linear adenovirus major late promoter templates with equal efficiency. In contrast, the new extract exhibits an increase of approximately twofold on transcription of a closed circular, as opposed to a linear, major late promoter template.

Pollination efficiency of the stingless bee Melipona subnitida on greenhouse sweet pepper

The present study was carried out in Northeastern Region of Brazil, in order to investigate the use of stingless bee Melipona subnitida Ducke in the pollination of greenhouse sweet pepper (Capsicum annuum L.). Treatments of hand cross-pollination, hand self-pollination, pollination by bees and restricted pollination were performed. Results showed that despite sweet pepper flowers are considered autogamous, this crop benefits from pollination by M. subnitida, producing fruits significantly heavier and wider, containing a greater number of seeds and of better quality (lower percentage of malformed fruits) than self-pollinated sweet pepper. Thus, M. subnitida can be considered an efficient pollinator of greenhouse sweet pepper.

Growth components and zinc recovery efficiency of upland rice genotypes

The objective of this work was to evaluate Zn use efficiency by upland rice genotypes. The experiment was carried out in a greenhouse, with ten upland rice genotypes grown on an Oxisol (Typic Hapludox) with no application, and with application of 10 mg kg-1 Zn, applied as zinc sulfate. Shoot dry weight, grain yield, Zn harvest index, Zn concentration in shoot and in grain were significantly influenced by soil Zn levels and genotypes. However, panicle number and grain harvest index were significantly affected only by genotype. Genotypes CNA8557, CNA8540 and IR42 produced higher grain yield than other genotypes. Genotypes showed significant variability in Zn recovery efficiency. On average, 13% of the applied Zn was recovered by upland rice genotypes. Genotypes with high Zn recovery efficiency could be used in breeding of Zn efficient upland rice cultivars. Higher level of soil Zn (10 mg kg-1) increased significantly the concentrations of plant Cu and Mn. However, Fe concentrations in plant (shoot and grain) were not influenced by soil Zn levels.

Phosphorus acquisition and internal utilization efficiency in tropical maize genotypes

The objective of this work was to determine the relative importance of phosphorus acquisition efficiency (PAE - plant P uptake per soil available P), and phosphorus internal utilization efficiency (PUTIL - grain yield per P uptake) in the P use efficiency (PUE - grain yield per soil available P), on 28 tropical maize genotypes evaluated at three low P and two high P environments. PAE was almost two times more important than PUTIL to explain the variability observed in PUE, at low P environments, and three times more important at high P environments. These results indicate that maize breeding programs, to increase PUE in these environments, should use selection index with higher weights for PAE than for PUTIL. The correlation between these two traits showed no significance at low or at high P environments, which indicates that selection in one of these traits would not affect the other. The main component of PUTIL was P quotient of utilization (grain yield per grain P) and not the P harvest index (grain P per P uptake). Selection to reduce grain P concentration should increase the quotient of utilization and consequently increase PUTIL.

Computational and statistical analysis of copy number variants in normal and cancer genomes

AbstractAlthough the genomes from any two human individuals are more than 99.99% identical at the sequence level, some structural variation can be observed. Differences between genomes include single nucleotide polymorphism (SNP), inversion and copy number changes (gain or loss of DNA). The latter can range from submicroscopic events (CNVs, at least 1kb in size) to complete chromosomal aneuploidies. Small copy number variations have often no (lethal) consequences to the cell, but a few were associated to disease susceptibility and phenotypic variations. Larger re-arrangements (i.e. complete chromosome gain) are frequently associated with more severe consequences on health such as genomic disorders and cancer. High-throughput technologies like DNA microarrays enable the detection of CNVs in a genome-wide fashion. Since the initial catalogue of CNVs in the human genome in 2006, there has been tremendous interest in CNVs both in the context of population and medical genetics. Understanding CNV patterns within and between human populations is essential to elucidate their possible contribution to disease. But genome analysis is a challenging task; the technology evolves rapidly creating needs for novel, efficient and robust analytical tools which need to be compared with existing ones. Also, while the link between CNV and disease has been established, the relative CNV contribution is not fully understood and the predisposition to disease from CNVs of the general population has not been yet investigated.During my PhD thesis, I worked on several aspects related to CNVs. As l will report in chapter 3, ! was interested in computational methods to detect CNVs from the general population. I had access to the CoLaus dataset, a population-based study with more than 6,000 participants from the Lausanne area. All these individuals were analysed on SNP arrays and extensive clinical information were available. My work explored existing CNV detection methods and I developed a variety of metrics to compare their performance. Since these methods were not producing entirely satisfactory results, I implemented my own method which outperformed two existing methods. I also devised strategies to combine CNVs from different individuals into CNV regions.I was also interested in the clinical impact of CNVs in common disease (chapter 4). Through an international collaboration led by the Centre Hospitalier Universitaire Vaudois (CHUV) and the Imperial College London I was involved as a main data analyst in the investigation of a rare deletion at chromosome 16p11 detected in obese patients. Specifically, we compared 8,456 obese patients and 11,856 individuals from the general population and we found that the deletion was accounting for 0.7% of the morbid obesity cases and was absent in healthy non- obese controls. This highlights the importance of rare variants with strong impact and provides new insights in the design of clinical studies to identify the missing heritability in common disease.Furthermore, I was interested in the detection of somatic copy number alterations (SCNA) and their consequences in cancer (chapter 5). This project was a collaboration initiated by the Ludwig Institute for Cancer Research and involved other groups from the Swiss Institute of Bioinformatics, the CHUV and Universities of Lausanne and Geneva. The focus of my work was to identify genes with altered expression levels within somatic copy number alterations (SCNA) in seven metastatic melanoma ceil lines, using CGH and SNP arrays, RNA-seq, and karyotyping. Very few SCNA genes were shared by even two melanoma samples making it difficult to draw any conclusions at the individual gene level. To overcome this limitation, I used a network-guided analysis to determine whether any pathways, defined by amplified or deleted genes, were common among the samples. Six of the melanoma samples were potentially altered in four pathways and five samples harboured copy-number and expression changes in components of six pathways. In total, this approach identified 28 pathways. Validation with two external, large melanoma datasets confirmed all but three of the detected pathways and demonstrated the utility of network-guided approaches for both large and small datasets analysis.RésuméBien que le génome de deux individus soit similaire à plus de 99.99%, des différences de structure peuvent être observées. Ces différences incluent les polymorphismes simples de nucléotides, les inversions et les changements en nombre de copies (gain ou perte d'ADN). Ces derniers varient de petits événements dits sous-microscopiques (moins de 1kb en taille), appelés CNVs (copy number variants) jusqu'à des événements plus large pouvant affecter des chromosomes entiers. Les petites variations sont généralement sans conséquence pour la cellule, toutefois certaines ont été impliquées dans la prédisposition à certaines maladies, et à des variations phénotypiques dans la population générale. Les réarrangements plus grands (par exemple, une copie additionnelle d'un chromosome appelée communément trisomie) ont des répercutions plus grave pour la santé, comme par exemple dans certains syndromes génomiques et dans le cancer. Les technologies à haut-débit telle les puces à ADN permettent la détection de CNVs à l'échelle du génome humain. La cartographie en 2006 des CNV du génome humain, a suscité un fort intérêt en génétique des populations et en génétique médicale. La détection de différences au sein et entre plusieurs populations est un élément clef pour élucider la contribution possible des CNVs dans les maladies. Toutefois l'analyse du génome reste une tâche difficile, la technologie évolue très rapidement créant de nouveaux besoins pour le développement d'outils, l'amélioration des précédents, et la comparaison des différentes méthodes. De plus, si le lien entre CNV et maladie a été établit, leur contribution précise n'est pas encore comprise. De même que les études sur la prédisposition aux maladies par des CNVs détectés dans la population générale n'ont pas encore été réalisées.Pendant mon doctorat, je me suis concentré sur trois axes principaux ayant attrait aux CNV. Dans le chapitre 3, je détaille mes travaux sur les méthodes d'analyses des puces à ADN. J'ai eu accès aux données du projet CoLaus, une étude de la population de Lausanne. Dans cette étude, le génome de plus de 6000 individus a été analysé avec des puces SNP et de nombreuses informations cliniques ont été récoltées. Pendant mes travaux, j'ai utilisé et comparé plusieurs méthodes de détection des CNVs. Les résultats n'étant pas complètement satisfaisant, j'ai implémenté ma propre méthode qui donne de meilleures performances que deux des trois autres méthodes utilisées. Je me suis aussi intéressé aux stratégies pour combiner les CNVs de différents individus en régions.Je me suis aussi intéressé à l'impact clinique des CNVs dans le cas des maladies génétiques communes (chapitre 4). Ce projet fut possible grâce à une étroite collaboration avec le Centre Hospitalier Universitaire Vaudois (CHUV) et l'Impérial College à Londres. Dans ce projet, j'ai été l'un des analystes principaux et j'ai travaillé sur l'impact clinique d'une délétion rare du chromosome 16p11 présente chez des patients atteints d'obésité. Dans cette collaboration multidisciplinaire, nous avons comparés 8'456 patients atteint d'obésité et 11 '856 individus de la population générale. Nous avons trouvés que la délétion était impliquée dans 0.7% des cas d'obésité morbide et était absente chez les contrôles sains (non-atteint d'obésité). Notre étude illustre l'importance des CNVs rares qui peuvent avoir un impact clinique très important. De plus, ceci permet d'envisager une alternative aux études d'associations pour améliorer notre compréhension de l'étiologie des maladies génétiques communes.Egalement, j'ai travaillé sur la détection d'altérations somatiques en nombres de copies (SCNA) et de leurs conséquences pour le cancer (chapitre 5). Ce projet fut une collaboration initiée par l'Institut Ludwig de Recherche contre le Cancer et impliquant l'Institut Suisse de Bioinformatique, le CHUV et les Universités de Lausanne et Genève. Je me suis concentré sur l'identification de gènes affectés par des SCNAs et avec une sur- ou sous-expression dans des lignées cellulaires dérivées de mélanomes métastatiques. Les données utilisées ont été générées par des puces ADN (CGH et SNP) et du séquençage à haut débit du transcriptome. Mes recherches ont montrées que peu de gènes sont récurrents entre les mélanomes, ce qui rend difficile l'interprétation des résultats. Pour contourner ces limitations, j'ai utilisé une analyse de réseaux pour définir si des réseaux de signalisations enrichis en gènes amplifiés ou perdus, étaient communs aux différents échantillons. En fait, parmi les 28 réseaux détectés, quatre réseaux sont potentiellement dérégulés chez six mélanomes, et six réseaux supplémentaires sont affectés chez cinq mélanomes. La validation de ces résultats avec deux larges jeux de données publiques, a confirmée tous ces réseaux sauf trois. Ceci démontre l'utilité de cette approche pour l'analyse de petits et de larges jeux de données.Résumé grand publicL'avènement de la biologie moléculaire, en particulier ces dix dernières années, a révolutionné la recherche en génétique médicale. Grâce à la disponibilité du génome humain de référence dès 2001, de nouvelles technologies telles que les puces à ADN sont apparues et ont permis d'étudier le génome dans son ensemble avec une résolution dite sous-microscopique jusque-là impossible par les techniques traditionnelles de cytogénétique. Un des exemples les plus importants est l'étude des variations structurales du génome, en particulier l'étude du nombre de copies des gènes. Il était établi dès 1959 avec l'identification de la trisomie 21 par le professeur Jérôme Lejeune que le gain d'un chromosome supplémentaire était à l'origine de syndrome génétique avec des répercussions graves pour la santé du patient. Ces observations ont également été réalisées en oncologie sur les cellules cancéreuses qui accumulent fréquemment des aberrations en nombre de copies (telles que la perte ou le gain d'un ou plusieurs chromosomes). Dès 2004, plusieurs groupes de recherches ont répertorié des changements en nombre de copies dans des individus provenant de la population générale (c'est-à-dire sans symptômes cliniques visibles). En 2006, le Dr. Richard Redon a établi la première carte de variation en nombre de copies dans la population générale. Ces découvertes ont démontrées que les variations dans le génome était fréquentes et que la plupart d'entre elles étaient bénignes, c'est-à-dire sans conséquence clinique pour la santé de l'individu. Ceci a suscité un très grand intérêt pour comprendre les variations naturelles entre individus mais aussi pour mieux appréhender la prédisposition génétique à certaines maladies.Lors de ma thèse, j'ai développé de nouveaux outils informatiques pour l'analyse de puces à ADN dans le but de cartographier ces variations à l'échelle génomique. J'ai utilisé ces outils pour établir les variations dans la population suisse et je me suis consacré par la suite à l'étude de facteurs pouvant expliquer la prédisposition aux maladies telles que l'obésité. Cette étude en collaboration avec le Centre Hospitalier Universitaire Vaudois a permis l'identification d'une délétion sur le chromosome 16 expliquant 0.7% des cas d'obésité morbide. Cette étude a plusieurs répercussions. Tout d'abord elle permet d'effectuer le diagnostique chez les enfants à naître afin de déterminer leur prédisposition à l'obésité. Ensuite ce locus implique une vingtaine de gènes. Ceci permet de formuler de nouvelles hypothèses de travail et d'orienter la recherche afin d'améliorer notre compréhension de la maladie et l'espoir de découvrir un nouveau traitement Enfin notre étude fournit une alternative aux études d'association génétique qui n'ont eu jusqu'à présent qu'un succès mitigé.Dans la dernière partie de ma thèse, je me suis intéressé à l'analyse des aberrations en nombre de copies dans le cancer. Mon choix s'est porté sur l'étude de mélanomes, impliqués dans le cancer de la peau. Le mélanome est une tumeur très agressive, elle est responsable de 80% des décès des cancers de la peau et est souvent résistante aux traitements utilisés en oncologie (chimiothérapie, radiothérapie). Dans le cadre d'une collaboration entre l'Institut Ludwig de Recherche contre le Cancer, l'Institut Suisse de Bioinformatique, le CHUV et les universités de Lausanne et Genève, nous avons séquencés l'exome (les gènes) et le transcriptome (l'expression des gènes) de sept mélanomes métastatiques, effectués des analyses du nombre de copies par des puces à ADN et des caryotypes. Mes travaux ont permis le développement de nouvelles méthodes d'analyses adaptées au cancer, d'établir la liste des réseaux de signalisation cellulaire affectés de façon récurrente chez le mélanome et d'identifier deux cibles thérapeutiques potentielles jusqu'alors ignorées dans les cancers de la peau.

Ultraweak photon emission in assessing bone growth factor efficiency using fibroblastic differentiation.

Photons participate in many atomic and molecular interactions and changes. Recent biophysical research has shown the induction of ultraweak photons in biological tissue. It is now established that plants, animal and human cells emit a very weak radiation which can be readily detected with an appropriate photomultiplier system. Although the emission is extremely low in mammalian cells, it can be efficiently induced by ultraviolet light. In our studies, we used the differentiation system of human skin fibroblasts from a patient with Xeroderma Pigmentosum of complementation group A in order to test the growth stimulation efficiency of various bone growth factors at concentrations as low as 5 ng/ml of cell culture medium. In additional experiments, the cells were irradiated with a moderate fluence of ultraviolet A. The different batches of growth factors showed various proliferation of skin fibroblasts in culture which could be correlated with the ultraweak photon emission. The growth factors reduced the acceleration of the fibroblast differentiation induced by mitomycin C by a factor of 10-30%. In view that fibroblasts play an essential role in skin aging and wound healing, the fibroblast differentiation system is a very useful tool in order to elucidate the efficacy of growth factors.

Sugarcane crop efficiency in two growing seasons in São Paulo State, Brazil

A conceptual framework for crop production efficiency was derived using thermodynamic efficiency concept, in order to generate a tool for performance evaluation of agricultural systems and to quantify the interference of determining factors on this performance. In Thermodynamics, efficiency is the ratio between the output and input of energy. To establish this relationship in agricultural systems, it was assumed that the input energy is represented by the attainable crop yield, as predicted through simulation models based on environmental variables. The method of FAO's agroecological zones was applied to the assessment of the attainable sugarcane yield, while Instituto Brasileiro de Geografia e Estatística (IBGE) data were used as observed yield. Sugarcane efficiency production in São Paulo state was evaluated in two growing seasons, and its correlation with some physical factors that regulate production was calculated. A strong relationship was identified between crop production efficiency and soil aptitude. This allowed inferring the effect of agribusiness factors on crop production efficiency. The relationships between production efficiency and climatic variables were also quantified and indicated that solar radiation, annual rainfall, water deficiency, and maximum air temperature are the main factors affecting the sugarcane production efficiency.

Genetic control of grain yield and nitrogen use efficiency in tropical maize

The objectives of this work were to study the genetic control of grain yield (GY) and nitrogen (N) use efficiency (NUE, grain yield/N applied) and its primary components, N uptake efficiency (NUpE, N uptake/N applied) and N utilization efficiency (NUtE, grain yield/N uptake), in maize grown in environments with high and low N availability. Experiments with 31 maize genotypes (28 hybrid crosses and three controls) were carried out in soils with high and low N rates, in the southeast of the state of Minas Gerais, Brazil. There was a reduction of 23.2% in average GY for maize grown in soil with low N, in comparison to that obtained with high N. There were 26.5, 199 and 400% increases in NUtE, NUpE, and NUE, respectively, for maize grown with low N. The general combining ability (GCA) and specific combining ability (SCA) were significant for GY, NUE and NUpE for maize grown in high N soil. Only GCA was significant for NUpE for maize grown in low N soil. The GCA and SCA for NUtE were not significant in either environment. Additive and non-additive genetic effects are responsible for the genetic control of NUE and GY for maize grown in soils with high N availability, although additive effects are more important.

Estimating water application efficiency for drip irrigation emitter patterns on banana

The objective of this work was to evaluate root and water distribution in irrigated banana (Musa sp.), in order to determine the water application efficiency for different drip irrigation emitter patterns. Three drip emitter patterns were studied: two 4-L h-1 emitters per plant (T1), four 4-L h-1 emitters per plant (T2), and five 4-L h-1 emitters per plant (T3). The emitters were placed in a lateral line. In the treatment T3, the emitters formed a continuous strip. The cultivated area used was planted with banana cultivar BRS Tropical, with a 3-m spacing between rows and a 2.5-m spacing between plants. Soil moisture and root length data were collected during the first production cycle at five radial distances and depths, in a 0.20x0.20 m vertical grid. The experiment was carried out in a sandy clay loam Xanthic Hapludox. Soil moisture data were collected every 10 min for a period of five days using TDR probes. Water application efficiency was of 83, 88 and 92% for the systems with two, four and five emitters per plant, respectively. It was verified that an increase in the number of emitters in the lateral line promoted better root distribution, higher water extraction, and less deep percolation losses.

EADock : design of a new molecular docking algorithm and some of its applications

3 Summary 3. 1 English The pharmaceutical industry has been facing several challenges during the last years, and the optimization of their drug discovery pipeline is believed to be the only viable solution. High-throughput techniques do participate actively to this optimization, especially when complemented by computational approaches aiming at rationalizing the enormous amount of information that they can produce. In siiico techniques, such as virtual screening or rational drug design, are now routinely used to guide drug discovery. Both heavily rely on the prediction of the molecular interaction (docking) occurring between drug-like molecules and a therapeutically relevant target. Several softwares are available to this end, but despite the very promising picture drawn in most benchmarks, they still hold several hidden weaknesses. As pointed out in several recent reviews, the docking problem is far from being solved, and there is now a need for methods able to identify binding modes with a high accuracy, which is essential to reliably compute the binding free energy of the ligand. This quantity is directly linked to its affinity and can be related to its biological activity. Accurate docking algorithms are thus critical for both the discovery and the rational optimization of new drugs. In this thesis, a new docking software aiming at this goal is presented, EADock. It uses a hybrid evolutionary algorithm with two fitness functions, in combination with a sophisticated management of the diversity. EADock is interfaced with .the CHARMM package for energy calculations and coordinate handling. A validation was carried out on 37 crystallized protein-ligand complexes featuring 11 different proteins. The search space was defined as a sphere of 15 R around the center of mass of the ligand position in the crystal structure, and conversely to other benchmarks, our algorithms was fed with optimized ligand positions up to 10 A root mean square deviation 2MSD) from the crystal structure. This validation illustrates the efficiency of our sampling heuristic, as correct binding modes, defined by a RMSD to the crystal structure lower than 2 A, were identified and ranked first for 68% of the complexes. The success rate increases to 78% when considering the five best-ranked clusters, and 92% when all clusters present in the last generation are taken into account. Most failures in this benchmark could be explained by the presence of crystal contacts in the experimental structure. EADock has been used to understand molecular interactions involved in the regulation of the Na,K ATPase, and in the activation of the nuclear hormone peroxisome proliferatoractivated receptors a (PPARa). It also helped to understand the action of common pollutants (phthalates) on PPARy, and the impact of biotransformations of the anticancer drug Imatinib (Gleevec®) on its binding mode to the Bcr-Abl tyrosine kinase. Finally, a fragment-based rational drug design approach using EADock was developed, and led to the successful design of new peptidic ligands for the a5ß1 integrin, and for the human PPARa. In both cases, the designed peptides presented activities comparable to that of well-established ligands such as the anticancer drug Cilengitide and Wy14,643, respectively. 3.2 French Les récentes difficultés de l'industrie pharmaceutique ne semblent pouvoir se résoudre que par l'optimisation de leur processus de développement de médicaments. Cette dernière implique de plus en plus. de techniques dites "haut-débit", particulièrement efficaces lorsqu'elles sont couplées aux outils informatiques permettant de gérer la masse de données produite. Désormais, les approches in silico telles que le criblage virtuel ou la conception rationnelle de nouvelles molécules sont utilisées couramment. Toutes deux reposent sur la capacité à prédire les détails de l'interaction moléculaire entre une molécule ressemblant à un principe actif (PA) et une protéine cible ayant un intérêt thérapeutique. Les comparatifs de logiciels s'attaquant à cette prédiction sont flatteurs, mais plusieurs problèmes subsistent. La littérature récente tend à remettre en cause leur fiabilité, affirmant l'émergence .d'un besoin pour des approches plus précises du mode d'interaction. Cette précision est essentielle au calcul de l'énergie libre de liaison, qui est directement liée à l'affinité du PA potentiel pour la protéine cible, et indirectement liée à son activité biologique. Une prédiction précise est d'une importance toute particulière pour la découverte et l'optimisation de nouvelles molécules actives. Cette thèse présente un nouveau logiciel, EADock, mettant en avant une telle précision. Cet algorithme évolutionnaire hybride utilise deux pressions de sélections, combinées à une gestion de la diversité sophistiquée. EADock repose sur CHARMM pour les calculs d'énergie et la gestion des coordonnées atomiques. Sa validation a été effectuée sur 37 complexes protéine-ligand cristallisés, incluant 11 protéines différentes. L'espace de recherche a été étendu à une sphère de 151 de rayon autour du centre de masse du ligand cristallisé, et contrairement aux comparatifs habituels, l'algorithme est parti de solutions optimisées présentant un RMSD jusqu'à 10 R par rapport à la structure cristalline. Cette validation a permis de mettre en évidence l'efficacité de notre heuristique de recherche car des modes d'interactions présentant un RMSD inférieur à 2 R par rapport à la structure cristalline ont été classés premier pour 68% des complexes. Lorsque les cinq meilleures solutions sont prises en compte, le taux de succès grimpe à 78%, et 92% lorsque la totalité de la dernière génération est prise en compte. La plupart des erreurs de prédiction sont imputables à la présence de contacts cristallins. Depuis, EADock a été utilisé pour comprendre les mécanismes moléculaires impliqués dans la régulation de la Na,K ATPase et dans l'activation du peroxisome proliferatoractivated receptor a (PPARa). Il a également permis de décrire l'interaction de polluants couramment rencontrés sur PPARy, ainsi que l'influence de la métabolisation de l'Imatinib (PA anticancéreux) sur la fixation à la kinase Bcr-Abl. Une approche basée sur la prédiction des interactions de fragments moléculaires avec protéine cible est également proposée. Elle a permis la découverte de nouveaux ligands peptidiques de PPARa et de l'intégrine a5ß1. Dans les deux cas, l'activité de ces nouveaux peptides est comparable à celles de ligands bien établis, comme le Wy14,643 pour le premier, et le Cilengitide (PA anticancéreux) pour la seconde.

Efficiency in inventories of ants in a forest reservein Central Amazonia

The objective of this work was to evaluate an inventory method efficiency for ants. We used subsamples collected in 24 transects of 100 m, distributed in 6 plots of 600 ha each in primary forest, as part of a long-term project. Ten litter subsamples were extracted per transect using Winkler extractors. Ants were identified to genus level, and Crematogaster, Gnamptogenys and Pachycondyla genera to species/morphospecies level. To evaluate the consequences of reduced sampling on the retention of ecological information, we estimated the lowest number of subsamples needed to detect the effects of environmental variables. Multidimensional scaling (MDS) was used to generate dissimilarity matrices, and Mantel correlations between each reduced-sampling effort and maximum effort were used as an index of how much information was maintained and could still be used in multivariate analyses. Lower p-values was observed on the effect of soil pH in the community of genera, and on the effect of the litter volume for the community of Crematogaster. The trend was still detectable in the analysis based on reduced-sampling. The number of subsamples can be reduced, and the cost-efficiency of the protocol can be improved with little loss of information.

Solar radiation use efficiency by soybean under field conditions in the Amazon region

The objective of this work was to evaluate the efficiency of soybean (Glycine max) in intercepting and using solar radiation under natural field conditions, in the Amazon region, Brazil. The meteorological data and the values of soybean growth and leaf area were obtained from an agrometeorological experiment carried out in Paragominas, Pará state, during 2007 and 2008. The radiation use efficiency (RUE) was obtained from the ratio between the above-ground biomass production and the intercepted photosynthetically active radiation (PAR) accumulated to 99 and 95 days after sowing, in 2007 and 2008, respectively. Climatic conditions during the experiment were very distinct, with reduction in rainfall in 2007, which began during the soybean mid-cycle, due to the El Niño phenomenon. An important reduction in the leaf area index and biomass production was observed during 2007. Under natural field conditions in the Amazon region, the values of RUE were 1.46 and 1.99 g MJ-1 PAR in the 2007 and 2008 experiments, respectively. The probable reason for the differences found between these years might be associated to the water restriction in 2007 coupled with the higher air temperature and vapor pressure deficit, and also to the increase in the fraction of diffuse radiation that reached the land surface in 2008.