1,721,121 research outputs found
Time to Network : The Molecular Blueprint of the Circadian Timing System in Plants
No full textPlants are exposed to periodic changes of light and darkness in their habitats through the Earth’s rotation around its axis. Accordingly, plants have evolved an endogenous system to schedule their day in synchrony with their surroundings. Here, we review the blueprint of the core clockwork in plants and how the core clockwork orchestrates time-of-day-specific gene expression programmes.Fil: Danisman, Selahattin. Universitat Bielefeld; AlemaniaFil: Mateos, Julieta Lisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Staiger, Dorothee. Universitat Bielefeld; Alemani
Plant RNA Biology
No full textThis eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contac
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
Expression of UGT76E12 and UGT76E11 : two UDP-glycosyltransferases involved in biotic and abiotic stress responses, is differentially regulated by their antisense lncRNAs
Full text linkIn den letzten Jahren wurde festgestellt, dass eukaryotische nicht-kodierende RNAs eine wichtige Rolle in einer Vielzahl von Prozessen spielen, die von der Regulation der Genexpression bis zur Translation reichen. Bei Pflanzen hat sich gezeigt, dass sie an einer Vielzahl biologischer Prozesse beteiligt sind, darunter Blütezeitregulation, Wurzelentwicklung sowie Hormon- und Stressreaktionen. Natürliche Antisense-lange nicht-kodierende RNAs (lncNATs), ein Subtyp von lncRNAs, die vom komplementären DNA-Strang eines Protein-kodierenden Gens transkribiert werden, haben die Entwicklung verschiedener Pflanzenarten beeinflusst. Anhand des Modellorganismus Arabidopsis thaliana untersuchten wir das regulatorische Potential einer lncNAT, die das Gen UDP-GLYCOSYLTRANSFERASE 76E12 (UGT76E12) überlappt.In recent years, eukaryotic non-coding RNAs were found to play an important role in a variety of processes ranging from gene expression regulation to translation. In plants, they have been shown to be involved in a wide range of biological processes including flowering time regulation, root development, and hormone and stress responses. Natural antisense long non-coding RNAs (lncNATs), a sub-type of lncRNAs that are transcribed from the complementary DNA strand of a protein-coding gene, have been revealed to influence development in various plant species. Using the model organism Arabidopsis thaliana, we investigated the regulatory potential of a lncNAT which overlaps the UDP-GLYCOSYLTRANSFERASE 76E12 gene (UGT76E12)
Functional and evolutionary characterization of flowering-related long non-coding RNAs
Full text linkGenomweite Bemühungen haben eine große Anzahl langer nichtkodierender RNAs (lncRNAs) identifiziert, obwohl ihre möglichen Funktionen weitgehend rätselhaft bleiben. Hier verwendeten wir ein System zur synchronisierten Blüteninduktion in Arabidopsis, um 4106 blütenbezogene lange intergene RNAs (lincRNAs) zu identifizieren. Blütenbezogene lincRNAs sind typischerweise mit funktionellen Enhancern assoziiert, die bidirektional transkribiert werden und mit verschiedenen funktionellen Genmodulen assoziiert sind, die mit der Entwicklung von Blütenorganen zusammenhängen, die durch Koexpressionsnetzwerkanalyse aufgedeckt wurden. Die Master-regulatorischen Transkriptionsfaktoren (TFs) APETALA1 (AP1) und SEPALLATA3 (SEP3) binden an lincRNA-assoziierte Enhancer. Die Bindung dieser TFs korreliert mit der Zunahme der lincRNA-Transkription und fördert möglicherweise die Zugänglichkeit von Chromatin an Enhancern, gefolgt von der Aktivierung einer Untergruppe von Zielgenen. Darüber hinaus ist die Evolutionsdynamik von lincRNAs in Pflanzen, einschließlich nicht blühender Pflanzen, noch nicht bekannt, und das Expressionsmuster in verschiedenen Pflanzenarten war ziemlich unbekannt. Hier identifizierten wir Tausende von lincRNAs in 26 Pflanzenarten, einschließlich nicht blühender Pflanzen. Ein direkter Vergleich von lincRNAs zeigt, dass die meisten lincRNAs speziesspezifisch sind und das Expressionsmuster von lincRNAs einen hohen Transkriptionsumsatz nahe legt. Darüber hinaus zeigen konservierte lincRNAs eine aktive Regulation durch Transkriptionsfaktoren wie AP1 und SEP3. Konservierte lincRNAs zeigen eine konservierte blütenbezogene Funktionalität sowohl in der Brassicaceae- als auch in der Grasfamilie. Die Evolutionslandschaft von lincRNAs in Pflanzen liefert wichtige Einblicke in die Erhaltung und Funktionalität von lincRNAs.Genome-wide efforts have identified a large number of long non-coding RNAs (lncRNAs), although their potential functions remain largely enigmatic. Here, we used a system for synchronized floral induction in Arabidopsis to identify 4106 flower-related long intergenic RNAs (lincRNAs). Flower-related lincRNAs are typically associated with functional enhancers which are bi-directionally transcribed and are associated with diverse functional gene modules related to floral organ development revealed by co-expression network analysis. The master regulatory transcription factors (TFs) APETALA1 (AP1) and SEPALLATA3 (SEP3) bind to lincRNA-associated enhancers. The binding of these TFs is correlated with the increase in lincRNA transcription and potentially promotes chromatin accessibility at enhancers, followed by activation of a subset of target genes. Furthermore, the evolutionary dynamics of lincRNAs in plants including non-flowering plants still remain to be elusive and the expression pattern in different plant species was quite unknown. Here, we identified thousands of lincRNAs in 26 plant species including non-flowering plants, and allow us to infer sequence conserved and synteny based homolog lincRNAs, and explore conserved characteristics of lincRNAs during plants evolution. Direct comparison of lincRNAs reveals most lincRNAs are species-specific and the expression pattern of lincRNAs suggests their high evolutionary gain and loss. Moreover, conserved lincRNAs show active regulation by transcriptional factors such as AP1 and SEP3. Conserved lincRNAs demonstrate conserved flower related functionality in both the Brassicaceae and grass family. The evolutionary landscape of lincRNAs in plants provide important insights into the conservation and functionality of lincRNAs
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
Regulation and evolution of alternative splicing in plants
Full text linkRecent studies showed that alternative splicing (AS) is much more prevalent in plants than previously thought. Both genome-wide analyses and cases studies of AS in response to abiotic stresses indicate the importance of AS for plant adaptation in a changing environment. However, how plants regulate their AS in response to herbivore attack, one of major biotic stresses that threaten plant fitness, remains unknown. The tight association between AS and environmental stresses also points to the rapid evolution of AS. However, the underlying mechanisms for this rapid evolution are unknown in plants. In this thesis, I aimed to address these two main questions by investigating the genome-wide insect herbivore-induced AS alteration in wild tobacco (Nicotiana attenuata) and by systematically studying the mechanisms that contributed to the evolution of AS among six plant species
Characterization of the long non-coding RNA encoded by the At4g14548 gene from Arabidopsis thaliana
Full text linkSeit ihrer Entdeckung durch die ersten genomweiten Studien in den frühen 2000er Jahren wurde die funktionelle Bedeutung langer nicht-kodierender RNAs (lncRNAs) diskutiert. Ursprünglich erfolgte die Einstufung der lncRNAs als "Transkriptionsrauschen" ohne biologische Funktion, aber die Forschung des letzten Jahrzehnts hat gezeigt, dass sie wichtige Modulatoren der Genexpression in Eukaryoten sind. In Pflanzen sind lncRNAs an der Regulierung einer Vielzahl von biologischen Prozessen beteiligt, darunter Blütezeit, Wurzelentwicklung und Reaktion auf abiotischen und biotischen Stress. Eine bestimmte Klasse von lncRNAs sind natürliche Antisense-Transkripte (lncNATs), die vom komplementären DNA-Strang eines proteinkodierenden Gens transkribiert werden. Im Focus dieser Arbeit steht ein lncNAT, das vom Gen At4g14548 der Modellpflanze Arabidopsis thaliana kodiert wird, und dessen regulatorisches Potenzial auf die Expression des proteinkodierenden Gens INDOLE-3-ACETIC ACID INDUCIBLE 14 (IAA14).Since their discovery by the first genome-wide studies in the early 2000s, the functional relevance of long non-coding RNAs (lncRNAs) has been debated. They were initially classified as 'transcriptional noise' without biological function, but research in the last decade has shown that they are important modulators of gene expression in eukaryotes. In plants, lncRNAs are involved in the regulation of a variety of biological processes, including flowering time, root development, and response to abiotic and biotic stress. A particular sub-class of lncRNAs are natural antisense transcripts (lncNATs) that are transcribed from the complementary DNA strand of a protein-coding gene. This thesis focuses on a lncNAT encoded by the At4g14548 gene of the model plant Arabidopsis thaliana and its regulatory potential on the expression of the protein-coding gene INDOLE-3-ACETIC ACID INDUCIBLE 14 (IAA14)
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