1,721,049 research outputs found
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
Gene regulatory network in Escherichia coli
No full textL'adaptation d'une bactérie aux changements de son environnement est contrôlée par un réseau de régulation large et complexe, faisant intervenir de nombreux acteurs et modules différents. Dans ce travail, nous avons étudiés un module de régulation spécifique, contrôlant l'adaptation de la bactérie Escherichia coli à un changement de sources de carbone. Dans un milieu contenant du glucose et de l'acétate, la croissance est divisée en deux phases : les bactéries utilisent préférentiellement le glucose et commencent à métaboliser l'acétate qu'après l'épuisement du glucose. En effet, la présence du glucose réprime la transcription d'un gène nécessaire à la croissance sur acétate, le gène acs (codant pour l'acétyl-CoA synthétase). Le mécanisme régulateur fait intervenir le facteur de transcription Crp-AMPc et le système de transfert de phosphate (PTS), qui permet l'import du glucose. Plusieurs modèles décrivent en détail la cascade de réactions moléculaires à l'origine de cette « répression catabolique ». Cependant, certaines de nos observations expérimentales ne sont pas correctement prédites par les modèles actuels. Ces modèles doivent être révisés ou complétés. L'outil majeur que nous employons pour les expériences est la fusion transcriptionnelle : une région promotrice fusionnée en amont d'un gène rapporteur (GFP, luciferase). Avec ces constructions, nous mesurons la dynamique de l'expression génique dans différentes souches (mutants) et différentes conditions environnementales. Les observations à l'échelle de la population sont corroborées par des mesures similaires à l'échelle de la cellule unique. Nous utilisons cette même technologie pour construire de petits systèmes synthétiques qui sondent davantage le phénomène de répression catabolique. Nous avons ainsi créé un interrupteur génétique dont le fonctionnement est contrôlé par le flux glycolytique et nous avons construit un petit système de communication intercellulaire basé sur la molécule AMPc. Enfin, nous proposons une manière originale de mesurer l'état métabolique des cellules en utilisant la dépendance énergétique de la luciferase.The adaptation of bacteria to changes in their environment is controlled by a large and complex regulatory network involving many different actors and modules. In this work, we have studied a specific module controlling the adaptation of Escherichia coli to a change in carbon sources. In a medium containing glucose and acetate, growth is divided into two phases : the bacteria preferentially use glucose and start to metabolize acetate only after glucose exhaustion. Indeed, the presence of glucose represses the transcription of a gene needed for growth on acetate : the acs gene (coding for acetyl-CoA synthetase). The regulatory mechanism involves the Crp-cAMP regulator and the phosphate transfer system (PTS), which is responsible for glucose import. Several models describe the cascade of molecular reactions responsible for this « catabolite repression ». However, our work shows that many of our experimental observations are incorrectly predicted by current models. These models have to be amended.We use transcriptional fusion, i.e., the fusion of a promoter region upstream of a reporter gene (GFP, luciferase), to measure the dynamics of gene expression in different genetic backgrounds and environmental conditions. Observations at the population level are corroborated by similar measurements at the single cell level. We use this same technology to construct small synthetic systems that probe further aspects of the phenomenon of catabolite repression. We have thus created a genetic toggle switch controlled by the glycolytic flux and we have built an inter-cellular communication system mediated by cAMP. Finally, we propose a novel way to measure the metabolic state of cells by using the energy dependence of the luciferase enzyme
Import of cyclic adenosine monophosphate in Escherichia coli
No full textL'adénosine monophosphate cyclique (AMPc) est une molécule très largement conservée dans le monde du vivant. Chez les bactéries, cette molécule signal est impliquée, entre autres, dans l'adaptation aux changements de milieu, au développement de la virulence, à la sporulation et la compétence. Bien qu'il fut démontré dans les années 1970 que cette molécule nécessitait un transporteur afin de traverser la membrane cellulaire, l'identité de celui-ci restait jusqu'à très récemment inconnue. Ce n'est qu'en 2011 que Hantke et ses collègues démontrèrent l'implication de la protéine TolC dans l'export de l'AMPc. Au cours de ma thèse, j'ai démontré le rôle prépondérant du complexe Opp dans l'import d'AMPc chez Escherichia coli. Ce complexe, formé des protéines OppABCD et F, est connu pour transporter des oligopeptides et se trouve dans la membrane interne de nombreuses bactéries. Pour arriver à la conclusion de son implication dans le transport d'AMPc, une banque de mutants a été créée dans une souche ne produisant pas d'AMPc (cyaA-). Afin d'identifier le transporteur responsable de l'import de l'AMPc, différents cribles qui testent la présence de cette molécule dans la cellule, ont ensuite été réalisée sur ces clones. Après analyse des résultats obtenus, l'opéron opp a été pressenti comme étant nécessaire à l'entrée de l'AMPc dans la cellule. Le double mutant cyaA-oppA- a été créé et de nouvelles expériences sont venues confirmer notre hypothèse. La protéine OppA a ensuite était surexprimée et purifiée pour nous permettre de faire des tests biochimiques d'interaction entre AMPc et OppA, basés sur la fluorescence émise par la protéine elle-même ou un homologue de l'AMPc, l'ε-AMPc. Ces expériences nous ont permis de confirmer l'interaction entre la protéine OppA et l'AMPc. Le système Opp est donc le principal importateur d'AMPc chez Escherichia coli, mais il ne semble pas être l'unique transporteur impliqué. Un autre candidat très intéressant est le complexe Dpp, connu pour transporter les dipeptides. En effet, les expériences préliminaires effectuées démontrent une diminution de la concentration intracellulaire d'AMPc dans une cellule cyaA-dppA- comparée à celle observée dans une souche cyaA-. Les travaux réalisés pendant ces trois dernières années permettent de conclure que le complexe Opp est le principal importateur d'AMPc, très probablement secondé par le complexe Dpp.Cyclic adenosine monophosphate (cAMP) is a signalling molecule conserved in all reigns of life. In bacteria, cAMP plays an important role in processes as diverse as the adaptation to a changing environment, the control of virulence, sporulation and competence. Although it has been proven in the 1970s that this molecule needs an active transporter to traverse the plasma membrane, the first one of these transporters was discovered only a few years ago. In 2011, Hantke et al have shown that the TolC protein is involved in the efflux of cAMP. During my PhD work I have identified the Opp complex as a major player of cAMP import into Escherichia coli. This complex, composed of proteins called OppABCD and F, is known to transport oligopeptides across the inner membrane of numerous bacterial species. To prove the involvement of the Opp complex in cAMP transport, I have used transposon mutagenesis to generate a collection of random mutants in a strain that does not produce cAMP (cyaA-). Different screens were used to detect mutants with impaired transport of extracellular cAMP into the cell. The opp operon emerged as the most promising candidate from this screen. The double mutant cyaA-oppA- was constructed and experiments designed to test the function of OppA confirmed our hypothesis. Subsequently, I overexpressed and purified OppA in order to perform biochemical experiments destined to measure the physical interaction between cAMP and OppA. I show that the Opp system is the major importer of cAMP in Escherichia coli. However, it seems that Opp is not the unique importer of cAMP. The other, very interesting candidate is the complex Dpp, known to transport dipeptides. Preliminary experiments revealed a decreased amount of cAMP in strain cyaA-dppA- compared to strain cyaA-. The experiments carried out during the last three years allow us to conclude that the Opp complex is the major importer of cAMP into E. coli and that the Dpp complex is probably a secondary transporter
Variations on the Author
Get PDF“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
Get PDFWe 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
Get PDFWe 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
Design and in vivo implementation of synthetic RNA switches in E.coli
No full textCe travail de thèse s’inscrit dans le thème général de la biologie de synthèse de l’ARN et vise à construire et tester le fonctionnement de commutateurs ARN contrôlés par des petits ARN antisens. La question fondamentale correspondante concerne les relations entre séquence, repliement et fonction d’une molécule d’ARN. Nous avons conçus des ARN commutateurs qui adoptent deux conformations alternatives : une conformation forme un terminateur de la transcription, empêchant l’expression d’un gène en aval, tandis que la conformation alternative ne conduit pas à la terminaison de la transcription. La sélection de la conformation dépend de la présence ou absence d’un petit ARN antisens fournit ou exprimé en trans. Nous avons validé le fonctionnement de commutateurs répressibles et inductibles in vitro. Afin d’évaluer leur fonctionnement in vivo, nous avons construit et optimisé une plateforme génétique chez la bactérie Escherichia coli. Le fonctionnement du commutateur est mesuré par l’expression d’une protéine fluorescente en aval du commutateur. Nous avons ainsi fourni la preuve de concept du fonctionnement de commutateurs activables et répressibles in vivo. Nos expériences in vitro et in vivo nous ont permis de découvrir de nouveaux principes du designs des ARN synthétiques, d’optimiser les conditions d’expression des commutateurs et les méthodes de mesure de l’expression in vivo. La gamme dynamique de la régulation par les petits ARN antisens in vivo doit être augmentée et nous avons identifié les pistes à explorer. Plus généralement, nos résultats ouvrent la voie à l’exploration plus systématique du lien séquence-repliement-fonction des ARN.This thesis work is a contribution to the general field of synthetic biology of RNA and aims at constructing and testing the functioning of RNA switches controlled by small anti-sense RNAs. The corresponding topic of fundamental research addresses the relationship between sequence, folding and function of an RNA molecule.We have devised RNA switches that adopt two alternative conformations. In one conformation, the RNA forms a transcriptional terminator, stopping the expression of a downstream gene. The alternative conformation undoes the terminator structure and allows read-through to the downstream DNA. The choice of which conformation the RNA molecule adopts depends on the presence or absence of a small regulatory anti-sense RNA. We have validated the functioning of our repressible and inducible switches in vitro. In order to validate the functioning of the switches in vivo, we have constructed and optimized a genetic testing system in the bacterium Escherichia coli. The performance of the switch is measured by the expression of a fluorescent reporter gene cloned downstream of the switch. We have thus been able to provide a proof of concept of the design, construction and in vivo functioning of activatable and repressible RNA switches.Our in vitro and in vivo experiments have allowed us to discover new principles of the design of synthetic RNA switches. We have also been able to optimize the expression conditions of the switches and the measurements methods of the in vivo experiments. The dynamic range of our RNA switches needs to be improved and we have discovered several promising avenues to accomplish this goal. More generally, our results form the basis of a more systematic exploration of the relationships between sequence, folding and functioning of RNA molecules
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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