987 resultados para plant genome


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1. Accumulating evidence indicates that plant resistance against above-ground herbivores can be affected by the presence of arbuscular mycorrhizal fungi (AMF) in association with the host plant. Little is known, however, about how AMF composition can influence herbivore choice to feed on a particular plant. 2. Unravelling the preference-performance hypothesis in a multitrophic context is needed to expand our knowledge of complex multitrophic interactions in natural systems. If given mycorrhizal fungal genotypes increase attractiveness for a herbivore (reduced plant resistance), then the benefits of increased unpalatability provided by the mycorrhizal fungi (increased plant resistance) might be outweighed by the increased herbivore recruitment. 3. This was addressed by designing three experiments to test the effects of different AMF genotypes, inoculated either alone or in combination, to measure intraspecific AMF effects on plant resistance and insect herbivore preference. Using strawberry (Fragaria vesca L.) plants that were colonised by eight different combinations of Rhizophagus irregularis isolates, we measured effects on plant growth, insect growth and survival, as well as feeding preferences of a generalist herbivore caterpillar (Spodoptera littoralis Boisduval). 4. Overall, it was found that: (i) AMF influenced plant resistance in an AMF genotype-specific manner; (ii) some AMF inoculations decreased insect performance; (iii) insects preferentially chose to feed more on leaves originating from non-mycorrhizal plants; but also that (iv) in a whole plant bioassay, insects preferentially chose the biggest plant, regardless of their mycorrhizal status. 5. Therefore, AMF-mediated trade-offs between growth and resistance against herbivores have been shown. Such trade-offs, particularly driven by plant attractiveness to herbivores, buffer the positive effects of the mycorrhizal symbiosis on enhanced plant growth.

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Nitrogen supply and plant population are basic parameters for cereal-legume intercropping. In order to study plant population and nitrogen fertilizer effects on yield and yield efficiency of maize-bean intercropping, a field experiment was established. Three bean plant populations and three nitrogen levels were used. Maize dry matter accumulation decreased with increases in bean plant population. Competitive effect of intercrop beans on maize yields was high at higher plant populations, being decreased by nitrogen fertilizer; application of 50 kg ha-1 N was very efficient in increasing maize cob yield. Intercropping significantly decreased harvest index of beans in all plant population and nitrogen fertilizer situations. The efficiency of intercropping, compared to sole cropping, was evidenced by the values obtained for Land Equivalent Ratio (LER) for biomass, cob and pod yields that increased with increases in bean plant populations and nitrogen fertilizer levels.

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BACKGROUND: HIV-infected individuals have an increased risk of myocardial infarction. Antiretroviral therapy (ART) is regarded as a major determinant of dyslipidemia in HIV-infected individuals. Previous genetic studies have been limited by the validity of the single-nucleotide polymorphisms (SNPs) interrogated and by cross-sectional design. Recent genome-wide association studies have reliably associated common SNPs to dyslipidemia in the general population. METHODS AND RESULTS: We validated the contribution of 42 SNPs (33 identified in genome-wide association studies and 9 previously reported SNPs not included in genome-wide association study chips) and of longitudinally measured key nongenetic variables (ART, underlying conditions, sex, age, ethnicity, and HIV disease parameters) to dyslipidemia in 745 HIV-infected study participants (n=34 565 lipid measurements; median follow-up, 7.6 years). The relative impact of SNPs and ART to lipid variation in the study population and their cumulative influence on sustained dyslipidemia at the level of the individual were calculated. SNPs were associated with lipid changes consistent with genome-wide association study estimates. SNPs explained up to 7.6% (non-high-density lipoprotein cholesterol), 6.2% (high-density lipoprotein cholesterol), and 6.8% (triglycerides) of lipid variation; ART explained 3.9% (non-high-density lipoprotein cholesterol), 1.5% (high-density lipoprotein cholesterol), and 6.2% (triglycerides). An individual with the most dyslipidemic antiretroviral and genetic background had an approximately 3- to 5-fold increased risk of sustained dyslipidemia compared with an individual with the least dyslipidemic therapy and genetic background. CONCLUSIONS: In the HIV-infected population treated with ART, the weight of the contribution of common SNPs and ART to dyslipidemia was similar. When selecting an ART regimen, genetic information should be considered in addition to the dyslipidemic effects of ART agents.

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The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (that is, bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of genome-wide gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated non-sterile sand, compared with regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing dibenzodioxins and dibenzofurans. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well as during growth and stationary phase in sand. Cells during transition show stationary phase characteristics, evidence for stress and for nutrient scavenging, and adjust their primary metabolism if they were not precultured on the same contaminant as found in the soil. Cells growing and surviving in sand degrade dibenzofuran but display a very different transcriptome signature as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous 'soil-specific' expressed genes. Studies focusing on inoculation efficacy should test behaviour under conditions as closely as possible mimicking the intended microbiome conditions.

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The objective of this study was to evaluate the efficiency of spatial statistical analysis in the selection of genotypes in a plant breeding program and, particularly, to demonstrate the benefits of the approach when experimental observations are not spatially independent. The basic material of this study was a yield trial of soybean lines, with five check varieties (of fixed effect) and 110 test lines (of random effects), in an augmented block design. The spatial analysis used a random field linear model (RFML), with a covariance function estimated from the residuals of the analysis considering independent errors. Results showed a residual autocorrelation of significant magnitude and extension (range), which allowed a better discrimination among genotypes (increase of the power of statistical tests, reduction in the standard errors of estimates and predictors, and a greater amplitude of predictor values) when the spatial analysis was applied. Furthermore, the spatial analysis led to a different ranking of the genetic materials, in comparison with the non-spatial analysis, and a selection less influenced by local variation effects was obtained.

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In Illinois and Iowa, the author finds that plants with approximately 750 employees have suffered the highest strike-frequency rate. Why at this size? Among other explanations, it is posited that in significantly smaller plants labor-management relations can be personalized-and tensions reduced-while in appreciably larger plants sophistication in dealing with disputes may, of necessity, have been developed. C. Fred Eisele is a graduate teaching assistant at the University of Iowa's College of Business Administration.

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Résumé La diminution de la biodiversité, à toutes les échelles spatiales et sur l'ensemble de la planète, compte parmi les problèmes les plus préoccupants de notre époque. En terme de conservation, il est aujourd'hui primordial de mieux comprendre les mécanismes qui créent et maintiennent la biodiversité dans les écosystèmes naturels ou anthropiques. La présente étude a pour principal objectif d'améliorer notre compréhension des patrons de biodiversité végétale et des mécanismes sous jacents, dans un écosystème complexe, riche en espèces et à forte valeur patrimoniale, les pâturages boisés jurassiens. Structure et échelle spatiales sont progressivement reconnues comme des dimensions incontournables dans l'étude des patrons de biodiversité. De plus, ces deux éléments jouent un rôle central dans plusieurs théories écologiques. Toutefois, peu d'hypothèses issues de simulations ou d'études théoriques concernant le lien entre structure spatiale du paysage et biodiversité ont été testées de façon empirique. De même, l'influence des différentes composantes de l'échelle spatiale sur les patrons de biodiversité est méconnue. Cette étude vise donc à tester quelques-unes de ces hypothèses et à explorer les patrons spatiaux de biodiversité dans un contexte multi-échelle, pour différentes mesures de biodiversité (richesse et composition en espèces) à l'aide de données de terrain. Ces données ont été collectées selon un plan d'échantillonnage hiérarchique. Dans un premier temps, nous avons testé l'hypothèse élémentaire selon laquelle la richesse spécifique (le nombre d'espèces sur une surface donnée) est liée à l'hétérogénéité environnementale quelque soit l'échelle. Nous avons décomposé l'hétérogénéité environnementale en deux parties, la variabilité des conditions environnementales et sa configuration spatiale. Nous avons montré que, en général, la richesse spécifique augmentait avec l'hétérogénéité de l'environnement : elle augmentait avec le nombre de types d'habitats et diminuait avec l'agrégation spatiale de ces habitats. Ces effets ont été observés à toutes les échelles mais leur nature variait en fonction de l'échelle, suggérant une modification des mécanismes. Dans un deuxième temps, la structure spatiale de la composition en espèces a été décomposée en relation avec 20 variables environnementales et 11 traits d'espèces. Nous avons utilisé la technique de partition de la variation et un descripteur spatial, récemment développé, donnant accès à une large gamme d'échelles spatiales. Nos résultats ont montré que la structure spatiale de la composition en espèces végétales était principalement liée à la topographie, aux échelles les plus grossières, et à la disponibilité en lumière, aux échelles les plus fines. La fraction non-environnementale de la variation spatiale de la composition spécifique avait une relation complexe avec plusieurs traits d'espèces suggérant un lien avec des processus biologiques tels que la dispersion, dépendant de l'échelle spatiale. Dans un dernier temps, nous avons testé, à plusieurs échelles spatiales, les relations entre trois composantes de la biodiversité : la richesse spécifique totale d'un échantillon (diversité gamma), la richesse spécifique moyenne (diversité alpha), mesurée sur des sous-échantillons, et les différences de composition spécifique entre les sous-échantillons (diversité beta). Les relations deux à deux entre les diversités alpha, beta et gamma ne suivaient pas les relations attendues, tout du moins à certaines échelles spatiales. Plusieurs de ces relations étaient fortement dépendantes de l'échelle. Nos résultats ont mis en évidence l'importance du rapport d'échelle (rapport entre la taille de l'échantillon et du sous-échantillon) lors de l'étude des patrons spatiaux de biodiversité. Ainsi, cette étude offre un nouvel aperçu des patrons spatiaux de biodiversité végétale et des mécanismes potentiels permettant la coexistence des espèces. Nos résultats suggèrent que les patrons de biodiversité ne peuvent être expliqués par une seule théorie, mais plutôt par une combinaison de théories. Ils ont également mis en évidence le rôle essentiel joué par la structure spatiale dans la détermination de la biodiversité, quelque soit le composant de la biodiversité considéré. Enfin, cette étude souligne l'importance de prendre en compte plusieurs échelles spatiales et différents constituants de l'échelle spatiale pour toute étude relative à la diversité spécifique. Abstract The world-wide loss of biodiversity at all scales has become a matter of urgent concern, and improving our understanding of local drivers of biodiversity in natural and anthropogenic ecosystems is now crucial for conservation. The main objective of this study was to further our comprehension of the driving forces controlling biodiversity patterns in a complex and diverse ecosystem of high conservation value, wooded pastures. Spatial pattern and scale are central to several ecological theories, and it is increasingly recognized that they must be taken -into consideration when studying biodiversity patterns. However, few hypotheses developed from simulations or theoretical studies have been tested using field data, and the evolution of biodiversity patterns with different scale components remains largely unknown. We test several such hypotheses and explore spatial patterns of biodiversity in a multi-scale context and using different measures of biodiversity (species richness and composition), with field data. Data were collected using a hierarchical sampling design. We first tested the simple hypothesis that species richness, the number of species in a given area, is related to environmental heterogeneity at all scales. We decomposed environmental heterogeneity into two parts: the variability of environmental conditions and its spatial configuration. We showed that species richness generally increased with environmental heterogeneity: species richness increased with increasing number of habitat types and with decreasing spatial aggregation of those habitats. Effects occurred at all scales but the nature of the effect changed with scale, suggesting a change in underlying mechanisms. We then decomposed the spatial structure of species composition in relation to environmental variables and species traits using variation partitioning and a recently developed spatial descriptor, allowing us to capture a wide range of spatial scales. We showed that the spatial structure of plant species composition was related to topography at the coarsest scales and insolation at finer scales. The non-environmental fraction of the spatial variation in species composition had a complex relationship with several species traits, suggesting a scale-dependent link to biological processes, particularly dispersal. Finally, we tested, at different spatial scales, the relationships between different components of biodiversity: total sample species richness (gamma diversity), mean species .richness (alpha diversity), measured in nested subsamples, and differences in species composition between subsamples (beta diversity). The pairwise relationships between alpha, beta and gamma diversity did not follow the expected patterns, at least at certain scales. Our result indicated a strong scale-dependency of several relationships, and highlighted the importance of the scale ratio when studying biodiversity patterns. Thus, our results bring new insights on the spatial patterns of biodiversity and the possible mechanisms allowing species coexistence. They suggest that biodiversity patterns cannot be explained by any single theory proposed in the literature, but a combination of theories is sufficient. Spatial structure plays a crucial role for all components of biodiversity. Results emphasize the importance of considering multiple spatial scales and multiple scale components when studying species diversity.

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Agreed-upon procedures report on the Villisca Municipal Power Plant for the period January 1, 2014 through December 31, 2014

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The objective of this work was to evaluate the response of rangpur lime (Citrus limonia) to arbuscular mycorrhiza (Glomus intraradices), under P levels ranging from low to excessive. Plants were grown in three levels of soluble P (25, 200 and 1,000 mg kg-1), either inoculated with Glomus intraradices or left noninoculated, evaluated at 30, 60, 90, 120 and 150 days after transplanting (DAT). Total dry weight, shoot P concentration and specific P uptake by roots increased in mycorrhizal plants with the doses of 25 and 200 mg kg-1 P at 90 DAT. With 1,000 mg kg-1 P, mycorrhizal plants had a transient growth depression at 90 and 120 DAT, and nonmycorrhizal effects on P uptake at any harvesting period. Root colonization and total external mycelium correlated positively with shoot P concentration and total dry weight at the two lowest P levels. Although the highest P level decreased root colonization, it did not affect total external mycelium to the same extent. As a result, a P availability imbalance affected negatively the mycorrhizal symbiosis and, consequently, the plant growth.

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The objective of this work was to compare the relative efficiency of initial selection and genetic parameter estimation, using augmented blocks design (ABD), augmented blocks twice replicated design (DABD) and group of randomised block design experiments with common treatments (ERBCT), by simulations, considering fixed effect model and mixed model with regular treatment effects as random. For the simulations, eight different conditions (scenarios) were considered. From the 600 simulations in each scenario, the mean percentage selection coincidence, the Pearsons´s correlation estimates between adjusted means for the fixed effects model, and the heritability estimates for the mixed model were evaluated. DABD and ERBCT were very similar in their comparisons and slightly superior to ABD. Considering the initial stages of selection in a plant breeding program, ABD is a good alternative for selecting superior genotypes, although none of the designs had been effective to estimate heritability in all the different scenarios evaluated.

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Given that retroposed copies of genes are presumed to lack the regulatory elements required for their expression, retroposition has long been considered a mechanism without functional relevance. However, through an in silico assay for transcriptional activity, we identify here >1,000 transcribed retrocopies in the human genome, of which at least approximately 120 have evolved into bona fide genes. Among these, approximately 50 retrogenes have evolved functions in testes, more than half of which were recruited as functional autosomal counterparts of X-linked genes during spermatogenesis. Generally, retrogenes emerge "out of the testis," because they are often initially transcribed in testis and later evolve stronger and sometimes more diverse spatial expression patterns. We find a significant excess of transcribed retrocopies close to other genes or within introns, suggesting that retrocopies can exploit the regulatory elements and/or open chromatin of neighboring genes to become transcribed. In direct support of this hypothesis, we identify 36 retrocopy-host gene fusions, including primate-specific chimeric genes. Strikingly, 27 intergenic retrogenes have acquired untranslated exons de novo during evolution to achieve high expression levels. Notably, our screen for highly transcribed retrocopies also uncovered a retrogene linked to a human recessive disorder, gelatinous drop-like corneal dystrophy, a form of blindness. These functional implications for retroposition notwithstanding, we find that the insertion of retrocopies into genes is generally deleterious, because it may interfere with the transcription of host genes. Our results demonstrate that natural selection has been fundamental in shaping the retrocopy repertoire of the human genome.

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We developed a semiquantitative job exposure matrix (JEM) for workers exposed to polychlorinated biphenyls (PCBs) at a capacitor manufacturing plant from 1946 to 1977. In a recently updated mortality study, mortality of prostate and stomach cancer increased with increasing levels of cumulative exposure estimated with this JEM (trend p values = 0.003 and 0.04, respectively). Capacitor manufacturing began with winding bales of foil and paper film, which were placed in a metal capacitor box (pre-assembly), and placed in a vacuum chamber for flood-filling (impregnation) with dielectric fluid (PCBs). Capacitors dripping with PCB residues were then transported to sealing stations where ports were soldered shut before degreasing, leak testing, and painting. Using a systematic approach, all 509 unique jobs identified in the work histories were rated by predetermined process- and plant-specific exposure determinants; then categorized based on the jobs' similarities (combination of exposure determinants) into 35 job exposure categories. The job exposure categories were ranked followed by a qualitative PCB exposure rating (baseline, low, medium, and high) for inhalation and dermal intensity. Category differences in other chemical exposures (solvents, etc.) prevented further combining of categories. The mean of all available PCB concentrations (1975 and 1977) for jobs within each intensity rating was regarded as a representative value for that intensity level. Inhalation (in microgram per cubic milligram) and dermal (unitless) exposures were regarded as equally important. Intensity was frequency adjusted for jobs with continuous or intermittent PCB exposures. Era-modifying factors were applied to the earlier time periods (1946-1974) because exposures were considered to have been greater than in later eras (1975-1977). Such interpolations, extrapolations, and modifying factors may introduce non-differential misclassification; however, we do believe our rigorous method minimized misclassification, as shown by the significant exposure-response trends in the epidemiologic analysis.

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RÉSUMÉ: Le génome de toute cellule est susceptible d'être attaqué par des agents endogènes et exogènes. Afin de préserver l'intégrité génomique, les cellules ont développé des multitudes de mécanismes. La réplication de l'ADN, une étape importante durant le cycle cellulaire, constitue un stress et présente un danger important pour l'intégrité du génome. L'anémie de Fanconi est une maladie héréditaire rare dont les protéines impliquées semblent jouer un rôle crucial dans la réponse au stress réplicatif. La maladie est associée à une instabilité chromosomique ainsi qu'à une forte probabilité de développer des cancers. Les cellules des patients souffrant de l'anémie de Fanconi sont sensibles à des agents interférant avec la réplication de l'ADN, et plus particulièrement àdes agents qui fient les deux brins d'ADN d'une manière covalente. L'anémie de Fanconi est une maladie génétiquement hétérogène. Treize protéines ont pu être identifiées. Elles semblent figurer dans une même voie de signalisation qui est aussi connue sous le nom de « FA/BRCA pathway », car un des gènes est identique au gène BRCA2 (breast cancer susceptibility gene 2). Huit protéines forment un complexe nucléaire dont l'intégrité est nécessaire à la monoubiquitination de deux autres protéines, FANCD2 et FANCI, en réponse à un stress réplicatif. A ce jour, la fonction moléculaire des protéines du « FA/BRCA pathway »reste encore mal décrite. Au début de mon travail de thèse, nous avons donc décidé de purifier les protéines du complexe nucléaire et d'étudier leurs propriétés biochimiques. Nous avons tout d'abord étudié les cinq protéines connues à l'époque qui sont FANCA, FANCC, FANCE, FANCF et FANCG. Par la suite, nous avons étendu notre étude à des protéines découvertes plus récemment, FANCL, FANCM et FAAP24, en concentrant finalement notre travail sur la caractérisation de FANCM. FANCM, contrairement aux autres protéines du complexe, est constituée de deux domaines conservés suggérant un rôle important dans le métabolisme de l'ADN. Il s'agit d'un domaine « DEAH box hélicase »situé dans la partie N-terminale et d'un domaine « ERCC4 nuclease »situé dans la partie C-terminale de la protéine. Dans cette étude, nous avons purifié avec succès la protéine FANCM entière à partir d'un système hétérologue. Nous montrons que FANCM s'attache de manière spécifique à des jonctions de Holliday et des fourches de réplication. De plus, nous démontrons que FANCM peut déplacer le point de jonction de ces structures via son domaine hélicase de manière dépendante de l'ATP. FANCM est aussi capable de dissocier de grands intermédiaires de la recombinaison, via la migration de jonctions de Holliday à travers une région d'homologie de 2.6 kb. Tous ces résultats suggèrent que FANCM peut s'attacher spécifiquement à des fourches de réplication et à des jonctions de Holliday in vitro et que son domaine hélicase est associé à une activité migratoire efficace. Nous pensons que FANCM peut avoir un rôle direct sur les intermédiaires de réplication. Ceci est en accord avec l'idée que les protéines de l'anémie de Fanconi coordonnent la réparation de l'ADN au niveau des fourches de réplication arrêtées. Nos résultats donnent une première indication quant au rôle de FANCM dans la cellule et peuvent contribuer à élucider la fonction de cette voie de signalisation peu comprise jusqu'à présent. SUMMARY: The genome of every cell is subject to a constant offence by endogenous and exogenous agents. Not surprisingly; cells have evolved a multitude of mechanisms which aim at preserving genomic integrity. A key step during the life cycle of a cell, DNA replication itself, constitutes a special danger to the integrity of the genome. The proteins defective in the rare hereditary disease Fanconi anemia (FA) are suspected to play a crucial role in the cellular response to DNA replication stress. The disease is associated with chromosomal instability and pronounced cancer susceptibility. Cells from Fanconi anemia patients are sensitive to a variety of agents which interfere with DNA replication, DNA interstrand cross-linking agents being particularly threatening to their survival. Fanconi anemia is a genetically heterogeneous disease with 13 different proteins identified, which seem to work together in a common pathway. Since one of the FA genes is identical to the breast cancer susceptibility gene BRCA2, it is also referred to as the FA/BRCA pathway. Eight proteins form a nuclear complex, whose integriry is required for the monoubiquitination of two other FA proteins, FANCD2 and FANCI, in response to DNA replication stress. Despite intensive research, the function of the FA/BRCA pathway at a molecular level has remained largely elusive so far. At the beginning of my thesis, we therefore decided to purify the proteins of the FA core complex and to investigate their biochemical properties. We started with the five proteins which were known at that time, FANCA, FANCC, FANCE, FANCF, and FACG. Later on, we extended our studies to the newly discovered proteins FANCL, FANCM, and FAAP24, and eventually focused our work on the characterisation of FANCM. In contrast to the other core complex proteins, FANCM contains two conserved domains, which point to a role in DNA metabolism: an N-terminal DEAH box helicase domain and a C-terminal ERCC4 nuclease domain. In this study, we have successfully purified full-length FANCM from a recombinant source. We show that purified FANCM binds to branched DNA molecules, such as Holliday junctions and replication forks, with high specificity and affinity. In addition, we demonstrate that FANCM can translocate the junction point of branched DNA molecules due to its helicase domain in an ATPase-dependent manner. FANCM can even dissociate large recombination intermediates, via branch migration of Holliday junctions through a 2.6 kb region of homology. Taken together, our data suggest that FANCM can specifically bind to replication forks and Holliday junctions in vitro, and that its DEAH box helicase domain is associated with a potent branch migration activity. We propose that FANCM might have a direct role in the processing of DNA replication intermediates. This is consistent with the current view that FA proteins coordinate DNA repair at stalled replication forks. Our findings provide a first hint as to the context in which FANCM might play a role in the cell. We are optimistic that they might be key to further elucidate the function of a pathway which is far from being understood.

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The aim of this work was to evaluate a protocol for plant regeneration by means of somatic embryos obtained from isolated adult pejibaye leaf primordia, and to describe histological origin of embryos and morphogenetic response. Explants were cultivated in modified MS medium. Mesophyll parenchymatous cells originated meristemoids (preembryonic complex formation) induced with 7.1 µM BAP in the first two subculture periods. After polarized structures with 12.9 µM NAA and 3.55 µM BAP were formed in the third subculture, somatic embryos developed and regenerated normal plants. The mesophyll parenchymatous cells display high capacity of direct response to the auxin and cytokinin.