1,721,014 research outputs found
Examining the contribution of cell wall polysaccharides to the mechanical properties of apple parenchyma tissue using exogenous enzymes
No full textThe viscoelastic mechanical properties of water-rich plant tissues are fundamental for many aspects of organ physiology and plant functioning. These properties are determined partly by the water in cellular vacuole and partly by the mechanical properties of the cell wall, the latter varying according to the composition and organization of its polysaccharides. In this study, relationships between the viscoelastic properties of apple cortex parenchyma tissue and cell wall pectin, hemicelluloses, and cellulose structures were studied by infusing the tissue with selected sets of purified enzymes in a controlled osmoticum. The results showed that tissue elasticity and viscosity were related, and controlled to variable extents by all the targeted polysaccharides. Among them, pectic homogalacturonan domains, crystalline cellulose, and fucosylated xyloglucan were revealed as being of prime importance in determining the viscoelastic mechanical properties of apple cortex tissue
Impact of climate on quantitative disease resistance of A. thaliana against S. sclerotiorum
No full textLe dérèglement climatique se traduit par l'augmentation globale des températures de surface, l'augmentation d'épisodes de fortes précipitations et la modification des vents. Ces modifications de l'environnement abiotique ne sont pas sans conséquence pour les interactions plantes-pathogènes. Si des études ont déjà montré que l'élévation de la température pouvait rendre les plantes plus sensibles aux infections, nous ne savons encore que très peu de choses sur les mécanismes génétiques impliqués. L'identification de gènes clés impliqués dans la modulation de l'immunité par le climat est pourtant une étape nécessaire à une meilleure compréhension de la résistance de la plante dans un environnement physique fluctuant. Au cours de ma thèse, je me suis intéressée à l'identification de gènes impliqués dans la modulation de la résistance quantitative par le climat. Pour cela, j'ai étudié les dépendances génétiques de ce type de résistance le long d'une trajectoire de réchauffement climatique probable. La résistance quantitative des plantes qui est mise en place pour faire face à certains champignons nécrotrophes est fortement multigénique. Les gènes impliqués sont majoritairement non spécifiques à la défense et sont modulés en réponse à des fluctuations de l'environnement abiotique. Cette caractéristique fait de cette forme de résistance un système idéal pour identifier des acteurs génétiques clés dans la modulation de la résistance par le climat. L'étude du pathosystème composé de la plante modèle Arabidopsis thaliana et du champignon nécrotrophe à large spectre d'hôte Sclerotinia sclerotiorum nous a permis d'identifier plusieurs acteurs génétiques clés. En combinant analyse transcriptomique, biologie moléculaire et bioinformatique, j'ai mis en évidence un réseau de gènes impliqué dans la résistance dont l'expression est sensiblement modulée par le climat ainsi qu'une protéine de la famille des facteurs de transcription NAC pour laquelle nous avons identifié des cibles potentielles. L'analyse de données transcriptomiques a également permis d'impliquer dans la modulation de la résistance par le climat un nombre conséquent de gènes appartenant à une famille de fonction inconnue baptisée, suite à cette étude, famille PADRE (plastid movement, cadmium tolérance, calmodulin and response regulator interaction). Comme les fluctuations thermiques ont pour conséquence la modification de la vitesse du vent, je me suis également intéressée à l'effet du vent sur la résistance des plantes. J'ai montré que le vent était un facteur environnemental modulant fortement la résistance des plantes et que l'augmentation de la sensibilité constatée dépendait du génotype et de la fréquence à laquelle les épisodes venteux se répètent.Climate change leads to global warming, more recurring events of heavy precipitations, and modification of winds. These modifications of the abiotic environment influence the interaction between plants and pathogens. Studies showed that temperature elevation leads to a higher susceptibility in plants, however little is known about the molecular mechanisms involved. Identification of key genes involved in the modulation of immunity by climate is however necessary to a better understanding of plant resistance within a fluctuating environment. During my thesis, I focused on the identification of genes involved in the modulation of Quantitative Disease Resistance (QDR) by the climate. To do so, I studied the genetic dependence of QDR along a trajectory simulating climate change. The QDR that takes place to counter some necrotrophic fungi is highly polygenic. QDR genes are widely unspecific to immunity and are sensitive to changes in the abiotic environment. This characteristic makes QDR an ideal system to identify key molecular actors of the modulation of immunity by climate. The study of the pathosystem composed of the model plant A. thaliana and the broad-spectrum necrotrophic fungus S. sclerotiorum allowed us to identify several of these key molecular actors. By combining transcriptomic analyses, molecular biology and bioinformatics, we highlighted a network of genes involved in resistance whose expression depends on climate as well as a NAC transcription factor family gene for which we identified the putative targets. The transcriptomic analyses also showed that a number of genes from a family of unknown function (subsequently coined PADRE for plastid movement, cadmium tolerance, calmodulin and response regulator interaction) were involved in the modulation of resistance by climate. As temperature variations lead to wind speed modifications, we also studied the effect of wind on plant resistance to pathogens. We showed that wind strongly modulated plant resistance and that higher susceptibility depended on the genotype and the frequency of the wind events
Classification and inference of gene networks from very short time series : Application to the modeling of plant transcriptional memory associated with repeated sound stimulations
No full textLes avancées des nouvelles technologies de séquençage ont ouvert l'accès aux données d'expression dynamique des gènes à l'échelle du génome. Les approches ensemblistes classiques, habituellement utilisées en biologie, ne permettent pas la compréhension des mécanismes moléculaires complexes sous-jacents. Par conséquent, le développement de méthodes analytiques permettant d'appréhender de manière plus satisfaisante ce type de données représente un défi majeur pour la biologie contemporaine. Cependant, les coûts techniques et expérimentaux associés aux données de transcriptomiques limitent la dimension des jeux de données réels et, par conséquent, leurs méthodes d'analyse. Au cours de ma thèse, à l'interface entre les mathématiques appliquées et la biologie végétale, j'ai travaillé sur la mise en place d'une méthode d'inférence de réseaux de régulations dynamiques adaptée à un jeu de données réelles et originales décrivant l'effet de stimulations sonores répétées sur l'expression des gènes d'Arabidopsis thaliana. J'ai ainsi proposé une méthode de classification adaptée aux séries temporelles très courtes qui regroupe les gènes par variations temporelles, permettant d'ajuster la dimension des données à l'inférence de réseau. La comparaison de cette méthode aux méthodes classiques a permis de montrer qu'elle était la plus adaptée aux séries temporelles très courtes avec un pas de temps irrégulier. Pour l'inférence de réseau dynamique, j'ai proposé un modèle qui prend en compte la variabilité intra-classe et qui intègre un terme constant décrivant explicitement la stimulation externe du système. L'évaluation de ces méthodes de classification et d'inférence a été effectuée sur des données de séries temporelles simulées et réelles, ce qui a permis d'établir la bonne qualité des performance en terme de précision, de rappel et d'erreur de prédiction. L'implémentation de ces méthodes a permis d'étudier le priming de la réponse immunitaire d'Arabidopsis thaliana par des ondes sonores répétées. Nous avons montré l'existence de la formation d'une mémoire transcriptionnelle associée aux stimulations qui fait passer la plante d'un état naïf à un état primé et plus résistant en 3 jours. Cet état résistant, entretenu d'une part par les stimulations et d'autre part par des cascades de facteurs de transcription, augmente la résistance immunitaire de la plante en déclenchant l'expression de gènes de résistance chez la plante saine, en diversifiant le nombre de gènes participant à la réponse immunitaire et en intensifiant l'expression de nombreux gènes de résistance. L'inférence du réseau décrivant la mémoire transcriptionnelle associée aux stimulations sonores répétées nous a permis d'identifier les propriétés qu'elle confère à la plante. Ces prédictions, validées expérimentalement, ont montré par exemple que l'augmentation de la cadence entre stimulations ne permettait pas d'obtenir un gain de résistance plus conséquent et que la mémoire transcriptionnelle ne dure que 1.5 jours après la dernière stimulation.Advancements in new sequencing technologies have paved the way for accessing dynamic gene expression data on a genome-wide scale. Classical ensemble approaches traditionally used in biology fall short of comprehending the underlying the complex molecular mechanisms. Consequently, developing analytical methods to understand further such data poses a significant challenge for current biology. However, the technical and experimental costs associated with transcriptomic data severely limit the dimension of real datasets and their analytical methods. Throughout my thesis, at the intersection of applied mathematics and plant biology, I focused on implementing an inference method for dynamic regulatory networks tailored to a real and original dataset describing the effect of repeated acoustic stimulations on genes expressions of Arabidopsis thaliana. I proposed a clustering method adapted to very-short time series that groups genes based on temporal variations, adjusting the data dimension for network inference. The comparison of this method with classical methods showed that it was the most suitable for very-short time series with irregular time points. For the network inference, I proposed a model that takes into account intra-class variability and integrates a constant term explicitly describing the external stimulation of the system. The evaluation of these classification and inference methods was conducted on simulated and real-time series data, which established their high performance in terms of accuracy, recall, and prediction error. The implementation of these methods to study the priming of the immune response of Arabidopsis thaliana through repeated sound waves. We demonstrated the formation of a transcriptional memory associated with stimulations, transitioning the plant from a naïve state to a primed and more resistant state within 3 days. This resistant state, maintained by stimulations and transcription factor cascades, enhances the plant's immune resistance by triggering the expression of resistance genes in healthy plants, diversifying the number of genes involved in the immune response, and intensifying the expression of numerous resistance genes. The inference of the network describing the transcriptional memory associated with repeated sound stimulations allowed us to identify the properties conferred to plants. Experimentally validated predictions showed that increasing the frequency between stimulations does not result in a more significant resistance gain, and the transcriptional memory lasts only 1.5 days after the last stimulation
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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