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Correction: Satellite DNA Modulates Gene Expression in the Beetle Tribolium castaneum after Heat Stress.
No full textNon-coding repetitive DNAs have been proposed to perform a gene regulatory role, however for tandemly repeated satellite DNA no such role was defined until now. Here we provide the first evidence for a role of satellite DNA in the modulation of gene expression under specific environmental conditions. The major satellite DNA TCAST1 in the beetle Tribolium castaneum is preferentially located within pericentromeric heterochromatin but is also dispersed as single repeats or short arrays in the vicinity of protein-coding genes within euchromatin. Our results show enhanced suppression of activity of TCAST1-associated genes and slower recovery of their activity after long-term heat stress relative to the same genes without associated TCAST1 satellite DNA elements. The level of gene suppression is not influenced by the distance of TCAST1 elements from the associated genes up to 40 kb from the genes’ transcription start sites, but it does depend on the copy number of TCAST1 repeats within an element, being stronger for the higher number of copies. The enhanced gene suppression correlates with the enrichment of the repressive histone marks H3K9me2/3 at dispersed TCAST1 elements and their flanking regions as well as with increased expression of TCAST1 satellite DNA. The results reveal transient, RNAi based heterochromatin formation at dispersed TCAST1 repeats and their proximal regions as a mechanism responsible for enhanced silencing of TCAST1-associated genes. Differences in the pattern of distribution of TCAST1 elements contribute to gene expression diversity among T. castaneum strains after long-term heat stress and might have an impact on adaptation to different environmental conditions
Dispersed satellite DNA elements and their effect on gene expression
No full textDifferent from dispersed transposable elements whose role in evolution of gene regulation was investigated in diverse model organism, influence of satellites DNA on gene regulation was not investigated till now. To perform potential regulatory function, satellite DNA elements are predicted not only to be present within heterochromatin, but to be distributed in euchromatic portion of the genome, in the vicinity of genes. Within insect species Tribolium castaneum satellite DNAs make a substantial portion of the genome and are major constituents of pericentromeric heterochromatin. The expression of a major heterochromatic T. castaneum satellite DNA TCAST1 proceeds in the form of long double-strand transcripts which are rapidly processed into small interfering RNAs (siRNAs). Satellite DNA expression is strongly induced by heat shock, and increased level of satellite-derived siRNAs is accompanied by increase of repressive epigenetic modifications of histones, H3K9me2-3 at satellite DNA regions. Single repeats or short stretches of the same TCAST1 satellite DNA are also dispersed in the close vicinity of protein-coding genes within euchromatin of T. castaneum. To explore the potential gene-regulatory role of TCAST1 satellite elements, we examined variation of TCAST1 elements among 10 T. castaneum wild-type strains originating from diverse geographic locations, and followed expression of genes that either contain or have in the vicinity polymorphic TCAST1 elements. Gene expression was explored at normal as well as under heat stress conditions. Expression analysis of genes that contain polymorphic TCAST1 elements within introns indicates influence of TCAST1 elements on gene expression under heat stress conditions. The gene expression is effected by the presence of TCAST1 element as well as by the number of repeats within dispersed TCAST1 satellite element. In all cases, TCAST1 elements partially repressed activity of genes after heat shock treatment. It is proposed that TCAST1-associated siRNAs, significantly induced after heat stress, affect epigenetic state of euchromatic regions containing dispersed TCAST1 satellite elements by increasing repressive epigenetic modifications of histones. This is the first demonstration of satellite DNA involvement in the modulation of protein-gene expression and indication for the role of satellite DNA in the evolution of gene regulation
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
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
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