1,720,964 research outputs found
Dynamics and impact of mobile genetic elements in the moss physcomitrium patens|
No full textEls elements genètics mòbils son material genètic amb la capacitat de moure's en el genoma o, en alguns casos, entre diferents organismes o cèl·lules. Podem distingir dues classes d'elements genètics mòbils, els virus, que tenen la capacitat de transferir el seu material gènic entre organismes, i els transposons, que es mouen i es repliquen dins el genoma de l'hoste. Els transposons ocupen una fracció important dels genomes eucariotes i mitjançant el seu moviment poden alterar-ne la seva estructura, tenint un paper clau en l'evolució dels genomes. En aquesta tesi s'ha estudiat la dinàmica i l'impacte en Physcomitrium patens de diferents elements mòbils. El primer capítol es centra en l'anàlisi i la comparació de diferents metodologies per tal de detectar la transcripció i mobilització dels transposons utilitzant dades de seqüenciació basades en tecnologies de short-reads, Aquesta anàlisi ens va permetre definir les metodologies que millor s'adapten als objectius d'aquesta tesi. En el segon capítol es van emprar les metodologies seleccionades amb la finalitat d'estudiar la dinàmica dels transposons en el genoma de Physcomitrium patens, detectant varies famílies de retrotransposons i transposons d'ADN que son transcripcionalment actives i que en alguns casos son polimòrfiques a la població. En el tercer capítol es descriu l'anàlisi de l'impacte dels transposons, i en concret d'un retrotransposó amb LTRs anomenat RLG1, tant en l'estructura del genoma com en els gens de Physcomitrium patens, eliminant o, en algun cas, introduint de nou elements RLG1 en llocs concrets del genoma. Finalment, el darrer capítol es centra en la detecció i dinàmica del primer virus descrit a P. patens. Aquest virus, al que hem anomenat Physcomitrium patens Amalagavirus 1 (PPAV1) és un virus endogen present només en algunes accessions de P. patens i que es transmet verticalment, tant per la línia paterna com materna.Los elementos genéticos móviles son material genético con la capacidad de moverse en el genoma o, en algunos casos, entre diferentes organismos o células. Pueden distinguirse dos clases de elementos genéticos móviles, los virus, que tienen la capacidad de transferir su material génico entre organismos, y los transposones, que se mueven y replican dentro del genoma del organismo huésped. Los transposones ocupan una fracción importante de los genomas eucariotas y mediante su movimiento pueden alterar su estructura, teniendo un papel clave en la evolución de los genomas. En esta tesis se ha estudiado la dinámica y el impacto de Physcomitrium patens de diferentes elementos móviles. El primer capitulo se centra en el análisis y la comparación de diferentes metodologías para detectar la transcripción y movilización de los transposones utilizando datos de secuenciación basados en tecnologías de short-reads. Este análisis nos permitió definir las metodologías que mejor se adaptan a los objetivos de esta tesis. En el segundo capítulo se utilizaron estas metodologías seleccionadas con la finalidad de estudiar la dinámica de los transposones en el genoma de Physcomitrium patens, detectando varias familias de retrotransposones y transposones de ADN que son transcripcionalmente activas y que en algunos casos son polimórficas en la población. En el tercer capítulo se describe el análisis del impacto de los transposones, y en concreto de un retrotransposón con LTRs nombrado RLG1, tanto en la estructura del genoma como en los genes de Physcomitrium patens, eliminando o en algunos casos, introduciendo de nuevo elementos RLG1 en lugares concretos del genoma. Finalmente, el último capítulo se centra en la detección y dinámica del primer virus descrito en P. patens. Este virus, que hemos nombrado Physcomitrium patens Amalgavirus 1 (PPAV1) es un virus endógeno presente únicamente en algunas accesiones de P. patens y que se transmite verticalmente, tanto por la línea paterna como materna.Mobile genetic elements are genetic material with the ability to move within the genome or, in some cases, between different organisms or cells. Two classes of mobile genetic elements can be distinguished, viruses, which have the ability to transfer their genetic material between organisms, and transposons, which move and replicate within the genome of the host organism. Transposons occupy an important fraction of eukaryotic genomes and through their movement can alter their structure, playing a key role in the evolution of genomes. In this thesis we have studied the dynamics and impact of Physcomitrium patens of different mobile elements.
The first chapter focuses on the analysis and comparison of different methodologies to detect transcription and mobilization of transposons using sequencing data based on short-reads technologies. This analysis allowed us to define the methodologies that best fit the objectives of this thesis. In the second chapter, these selected methodologies were used to study transposon dynamics in the genome of Physcomitrium patens, detecting several families of retrotransposons and DNA transposons that are transcriptionally active and, in some cases, polymorphic in the population. The third chapter describes the analysis of the impact of transposons, and in particular of a retrotransposon with LTRs named RLG1, on both the genome structure and genes of Physcomitrium patens, eliminating or in some cases, reintroducing RLG1 elements at specific locations in the genome. Finally, the last chapter focuses on the detection and dynamics of the first virus described in P. patens. This virus, which we have named Physcomitrium patens Amalgavirus 1 (PPAV1), is an endogenous virus present only in some P. patens accessions and transmitted vertically, both from the paternal and maternal lines.Universitat Autònoma de Barcelona. Programa de Doctorat en Biologia i Biotecnologia Vegeta
Anàlisis de l'evolució del genoma de Physcomitrella patens
Get PDFEn aquest treball s'ha analitzat l'evolució de Physcomitrella patens. Es realitzen dues aproximacions: per una part s'ha estudiat els elements transposables polimòrfics en diferents ecotips de l'organisme a partir de dades de Next Generation Sequencing. Per altra banda, s'ha estudiat l'evolució del genoma de P. patens en un clon reproduït vegetativament durant els darrers 8 anys. Aquest clon prové de l'utilitzat per realitzar l'anotació publicada l'any 2008, el genoma de referència. Això s'ha realitzat gràcies a la disposició de diferents reseqüenciacions en anys diferents. Totes aquestes anàlisis s'han realitzat utilitzant programes de detecció de polimorfismes de transposons que permetenl 'anàlisis de seqüenciacions en format paired-end.In this paper, we analyzed the Physcomitrella patens evolution. We carried out two approximations to study this evolution. On the one side, we analyzed the polymorphisms in two ecotypes: Villersexel and Reute through data obtained by Next Generation Sequencing. On the other side, we analyzed the evolution of P. patens through multiple resequencing from the original clone used to generate the annotation that had been vegetative propagated during the last 8 years. This has been possible due to some resequencing samples that come from other ones resequenced during that time.En este trabajo se ha analizado la evolución de Physcomitrella patens. Se realizan dos aproximaciones: por una parte se ha estudiado los elementos transposables polimórficos en diferentes ecotips del organismo a partir de datos de Next Generation Sequencing. Por otro lado, se ha estudiado la evolución del genoma de P. patens en un clon reproducido vegetativamente durante los últimos 8 años. Este clon proviene del utilizado para realizar la anotación publicada en 2008, el genoma de referencia. Esto se ha realizado gracias a la disposición de diferentes reseqüenciacions en años diferentes. Todos estos análisis se han realizado utilizando programas de detección de polimorfismos de transposons que permiten ¿análisis de secuenciaciones en formato paired-end
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
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
How LTR retrotransposons target their insertion sites in plants / Identification and characterization of plant endophytic bacteria for novel biosynthetic gene clusters discovery
No full textTrabajo presentado en el Internal Seminar del Centre de Recerca Agrigenómica (CRAG), celebrado el 30 de abril de 2021.Peer reviewe
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
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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