1,721,127 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
Transient gene expression in Catharanthus roseus flower petals using agroinfiltration
No full textTransient transformation methods are frequently used to determine gene function. However, until recently only a few methods have been available in the model medicinal plant Catharanthus roseus. Here, we describe a rapid and highly reproducible protocol for the overexpression of genes of interest by agroinfiltration of C. roseus flower petals. This high throughput method is particularly suitable for screening purposes, for instance, target gene screening of transcription factor candidates, and complements other available methods
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
Elucidation of the Catharanthus roseus alkaloid pathway and metabolic engineering in yeast
No full textCatharanthus roseus est une plante médicinale produisant divers types d’alcaloïdes indoliques monoterpéniques (AIM) d’intérêt en santé humaine. Ainsi, les AIM dimères comme la vinblastine et la vincristine sont utilisés en chimiothérapie anticancéreuse et les alcaloïdes monomères de type hétéroyohimbine présentent diverses activités pharmacologiques. La fabrication de ces molécules dans la plante est fort complexe. Elle requiert un haut niveau de compartimentation tissulaire et subcellulaire et met en jeu plus d’une trentaine d’étapes enzymatiques, dont certaines sont encore très mal connues. Dans ce contexte, l’objectif de la thèse a consisté à élucider plusieurs étapes enzymatiques de la voie de biosynthèse des AIM. Nos travaux ont permis de caractériser de nouvelles isoformes enzymatiques de la famille des cytochromes P450 ainsi que les réductases qui leur sont associées. Ils ont abouti à l’identification de nouvelles déshydrogénases et mis en évidence, in planta, leurs interactions avec la strictosidine synthase suggérant une biosynthèse orientée vers les divers alcaloïdes de type hétéroyohimbine. Enfin, en ayant recours à l’ingénierie métabolique, un segment de la voie de biosynthèse a été transféré dans la levure Saccharomyces cerevisiae, lui conférant la capacité de bio-transformer la tabersonine en vindoline, l’un des deux précurseurs finaux des alcaloïdes dimères.Catharanthus roseus is a medicinal plant producing various types of monoterpene indole alkaloids (MIA) with a great interest in human health. Dimeric alkaloids such as vinblastine and vincristine are used in cancer chemotherapy and monomeric heteroyohimbine alkaloids exhibit various pharmacological activities. The production of these molecules in the plant is very complex. It requires a high level of tissular and subcellular compartmentalization and involves more than thirty enzymatic steps, some of which are largely unknown. In this context, the aim of this thesis was to elucidate several enzymatic steps of the MIA biosynthetic pathway. Our work allowed us to characterize new enzyme isoforms of cytochrome P450 and their associated reductases. They also resulted in the identification of new dehydrogenases and highlighted their interactions with the strictosidine synthase suggesting a directed biosynthesis towards various heteroyohimbine type of alkaloids. Finally, engineered yeast containing a segment of the MIA biosynthetic pathway was able to convert tabersonine into vindoline, one of the two final precursors of the dimeric alkaloids
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
Elucidation and engineering of the biosynthesis of alkaloids of pharmaceutical interest originated from Apocynaceae
No full textLa pervenche de Madagascar (Catharanthus roseus) est une plante de la famille des Apocynacées produisant des alcaloïdes indoliques monoterpéniques (AIM) dont certains présentent un intérêt thérapeutique majeur. C. roseus est considérée aujourd'hui comme une plante médicinale modèle en devenant la référence en matière d'étude d'un métabolisme spécialisé, celui des AIM. L'avancée des connaissances sur ce métabolisme a été impulsée par les développements de ressources transcriptomiques alliés à des méthodes de caractérisation fonctionnelle des gènes. L'expertise acquise sur C. roseus a également permis la transposition de ces connaissances à d'autres plantes de la famille des Apocynaceae. L'objectif de la thèse a consisté à étudier des enzymes de la famille des O-méthyltransférases du métabolisme alcaloïdique dans le but de les valoriser dans des approches d'ingénierie métabolique. Ainsi, suite à l'exploitation de données omiques, un gène codant une nouvelle isoforme enzymatique de la tabersonine-16-O-méthyltransférase (Cr16OMT2) a été isolé chez C. roseus ainsi qu'un gène orthologue Vm16OMT chez l'espèce Vinca minor. La validation fonctionnelle du gène Cr16OMT2 a été réalisée par des études de pertes de fonction grâce à la technique VIGS (Virus-Induced Gene Silencing) et par des études d'expression transitoire utilisant la méthode d'agroinfiltration. Par ailleurs, les deux enzymes ont été caractérisées sur le plan biochimique et leur localisation subcellulaire déterminée. Des recherches en ingénierie métabolique de la levure Saccharomyces cerevisiae utilisant les gènes Cr16OMT2 et Vm16OMT ont été menées en vue d'optimiser les premières étapes de bioconversion de la tabersonine en vindoline (l'un des deux précurseurs des alcaloïdes à activité anticancéreuse). Au final, en exploitant les résultats obtenus avec le gène Cr16OMT2 et d'autres résultats antérieurs obtenus par l'équipe, ces travaux ont conduit à produire en bioréacteur 264 mg/L de vindoline ouvrant la voie à une future production industrielle de ce métabolite.The Madagascar periwinkle (Catharanthus roseus) is a model medicinal plant of the Apocynaceae family producing indole monoterpene alkaloids (MIA) which became the reference in the study of specialized metabolism. The increased knowledge on this metabolism has been driven by the development of transcriptomic resources combined with new methods of functional characterization of genes, which also allowed the transposition of this knowledge to other plants of the Apocynaceae family. The objective of the thesis was to study the O-methyltransferase family enzymes involved in the alkaloid metabolism, in order to develop them in metabolic engineering approaches. Thus, following the study of the omics data, a gene encoding a new enzyme isoform of tabersonine-16-O-methyltransferase (Cr16OMT2) was isolated in C. roseus, as well as an ortholog gene Vm16OMT in the Vinca minor species. Functional validation of the Cr16OMT2 gene was carried out by loss-of-function studies using the VIGS (Virus-Induced Gene Silencing) technique and by transient expression studies using the agroinfiltration method. In addition, the two enzymes were characterized biochemically and their subcellular localization described. The metabolic engineering of the yeast Saccharomyces cerevisiae was carried out using the Cr16OMT2 and Vm16OMT genes in order to optimize the first steps of tabersonine to vindoline bioconversion (one of the two precursors of alkaloids with anticancer activity). Finally, by exploiting the results obtained with the Cr16OMT2 gene and other previous results obtained by the team, this work led to the production of 264 mg/L of vindoline in a bioreactor, paving the way for future industrial production of this metabolite
Yeast metabolic engineering approaches to secure the production of the anticancer drug Etoposide in Centre-Val de Loire region
No full textL'ETOPOSIDE est un lignane, dérivé de la podophyllotoxine, très couramment employé en chimiothérapie. Actuellement, sa production ne dépend que du sourcing en podophyllotoxine extraite des rhizomes de Podophyllum hexandrum. La pression exercée sur les ressources naturelles qui en découle occasionne des pénuries d'approvisionnement de cette molécule. Dans ce contexte, ces travaux de thèse CIFRE, menés avec le groupe industriel Axyntis, visent à développer une alternative de synthèse par des approches d'ingénierie métabolique via la création de cellules usines de levures productrices d'un précurseur d'ETOPOSIDE. Ils reposent plus spécifiquement sur la création d'une souche de levure capable de bioconvertir la yatéine (YAT, un lignane précurseur de podophyllotoxine) hautement biodisponible chez de nombreuses espèces végétales en (-)-4'-déméthyl-épipodophyllotoxine (4'dEPT) directement utilisable pour la production d'ETOPOSIDE. Pour ce faire, les trois gènes assurant la conversion de YAT en 4'dEPT chez P. hexandrum et codant une dioxygénase et deux cytochromes P450 (CYP71BE54 et CYP82D61) ont été intégrés, via le système CRISPR/Cas9, dans le génome de la souche Saccharomyces cerevisiae CEN-PK713D compatible avec une utilisation industrielle. L'optimisation de l'activité de bioconversion de la souche a été axée sur l'ajustement de la balance des copies de gènes transférés et sur l'amélioration de l'activité catalytique de CYP82D61 décrite pour catalyser l'étape d'hydroxylation terminale de la 4'dEPT à faible rendement. Parmi les stratégies testées, l'utilisation de gènes de synthèse à codons optimisés pour favoriser la traduction en levure et la co-expression d'une cytochrome P450 réductase spécifique de P. hexandrum ont permis une optimisation majeure du flux métabolique permettant la bioconversion de la YAT fournie aux levures en culture en 4'dEPT. En parallèle, un protocole d'extraction et de purification de YAT à partir des parties vertes de plants de Juniperus a été mis en place et est en cours de transfert à échelle industrielle au sein d'Axyntis. A terme, la souche de levure lui sera également transférée pour assurer des cultures en bioréacteurs de grande capacité afin de sécuriser l'approvisionnement en ETOPOSIDE via la relocalisation de production en région Centre Val de Loire. Enfin, une souche productrice de tri-hydroxycinnamoyl spermidines, phénolamides accumulés dans le manteau pollinique, a également été générée et permettra d'étudier plus profondément les fonctions et les applications potentielles de ce type de composés.ETOPOSIDE is a lignan derived from podophyllotoxin, which is widely used in chemotherapy. Currently, its production only relies on the podophyllotoxin extracted from Podophyllum hexandrum rhizomes. The pressure on natural resources resulting from this supply causes recurrent shortages of this molecule. In this context, this CIFRE PhD thesis, carried out with the industrial group Axyntis, aims at developing an alternative approach of synthesis through metabolic engineering and the creation of yeast factory cells producing an ETOPOSIDE precursor. More specifically, this work is based on the creation of a yeast strain capable of bioconverting yatein (YAT, a lignan precursor of podophyllotoxin) highly bioavailable in many plant species into (-)-4'-desmethyl-epipodophyllotoxin (4'dEPT) directly usable for the ETOPOSIDE production. To his end, the three genes ensuring the conversion of YAT into 4'dEPT in P. hexandrum, encoding a dioxygenase and two cytochromes P450 (CYP71BE54 and CYP82D61) were integrated via the CRISPR/Cas9 system into the genome of the Saccharomyces cerevisiae strain CEN-PK713D compatible with an industrial use. To optimize bioconversion efficiency of this strain, we have mainly focused on adjusting the balance of transferred genes copies and on the improvement of CYP82D61 catalytic activity described to catalyze the terminal hydroxylation step of 4'dEPT with a low yield. Among the tested strategies, the use of codon-optimized synthetic genes to promote translation in yeast and the co-expression of a cytochrome P450 reductase specific to P. hexandrum allowed a major improvement of the metabolic flow thus allowing a very efficient bioconversion of the YAT supplied to the yeast in culture into 4'dEPT. On the other hand, a protocol for the extraction and the purification of YAT from the green parts of Juniperus plants has been implemented and is being transferred to an industrial scale at Axyntis. At midterms, the strain will also be transferred to Axyntis to perform the yeast culture in high capacity bioreactors in order to secure the ETOPOSIDE supply by relocating the production to the Centre-Val de Loire region. Finally, a last yeast strain synthesizing tri-hydroxycinnamoyl spermidines, which correspond to phenolamides compounds accumulated in the pollen coat, was also generated in order to initiate the detailed study of their in planta functions but also their potential industrial applications
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
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