1,720,963 research outputs found
Insights into the evolution of pre-mRNA splicing from reduced algal genomes
No full textEukaryotic genes are interrupted by non-coding regions known as introns, which are removed through pre-mRNA splicing. This process catalyzed by the spliceosome, a large complex of five small nuclear ribonucleoproteins (snRNPs), and various other proteinaceous accessory complexes. Although this process is highly conserved across eukaryotes, significant divergence is seen in organisms with reduced genomes. My dissertation research explores the evolution of nuclear pre-mRNA splicing and the spliceosome in diverse reduced algal genomes. I examined transcriptomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans for splicing in their nucleomorphs, the remnant nuclei found in their plastids. There, I observed high levels of unspliced transcripts in the intron-sparse G. theta nucleomorphs, and typical eukaryotic levels of splicing in the many tiny nucleomorph introns of B. natans. To determine if this reflects contrasting intron richness and/or differing ancestries of these plastids, I investigated splicing in three species of red algae: the mesophilic Porphyridium purpureum, and the extremophilic Cyanidiales red algae Cyanidioschyzon merolae and Galdieria sulphuraria. A comparison of transcriptome data revealed extremely low levels of splicing in the intron-poor C. merolae, typical splicing in the intron-rich G. sulphuraria, and an intermediate level of splicing in P. purpureum, whose intron richness lies between C. merolae and G. sulphuraria. My analyses present a trend where transcripts more often remain unspliced in genomes with low intron numbers, and spliceosomes exhibit increasing divergence and loss of components. I also showed that an intron’s splicing level is tied to 5′ splice site and branch donor sequence variability, suggesting an increased reliance on base-pairing for intron recognition in an increasingly reduced spliceosome. I explored potential functions of persisting nucleomorph introns of the cryptophytes Guillardia theta and Chroomonas mesostigmatica. I performed differential analysis of light and dark transcriptomes for both, and assembled a nuclear transcriptome for C. mesostigmatica, showing extensive intron retention in cryptophyte nucleomorph transcripts. However, differential splicing and gene expression is limited in nucleomorphs, suggesting that secondary plastids are primarily regulated by nuclear genes. My research highlights patterns of divergence in splicing in genomes evolving under the pressures of reduction.Science, Faculty ofBotany, Department ofGraduat
Spliceosomal evolution in the reduced genomes of microsporidia
No full textEukaryotic genes are mosaics of coding regions and non-coding regions called spliceosomal introns. Introns are removed from pre-mRNA by a ribonucleoprotein complex called the spliceosome. The spliceosome in humans is composed of five small nuclear RNAs and nearly 200 associated proteins. As nuclear genomes reduce, introns are more readily lost and, as a result, there is weakened selection to maintain a complex spliceosome. My dissertation focuses on the evolution of introns and spliceosomes in species with reduced genomes. Microsporidia are intracellular parasites that have extremely reduced nuclear genomes and have lost of many, if not all, introns. I examined all available microsporidian genomes and identified a family of introns that are conserved in all intron-containing microsporidia. These introns differ from typical microsporidian introns: they are longer, are spliced at higher levels, have hyperextended motifs, and contain internal conserved regions that may indicate a non-coding function. Despite the genome of Pseudoloma neurophilia having no annotated introns, I identified the presence of two long introns. I established that the P. neurophilia spliceosome is the most reduced known, and that the retained proteins and small nuclear RNAs are notably divergent from canonical orthologs. Due to extensive sequence evolution in microsporidia, direct comparisons to model organisms can be difficult. I produced the first transcriptomes from the Rozellomycota, the sister group to microsporidia, and found significant plasticity of expression throughout the lifecycle. I also found that Rozella introns are extremely constrained in size but lack conserved spliceosomal motifs. These data, combined with available genomic data from two other related parasites, provide insights into the evolution of microsporidian introns. Spliceosomal reduction extends beyond the loss of proteins. In the red alga Cyanidioschyzon merolae, a regulatory toggle in the core spliceosomal protein Prp8 has been lost. I examined a diverse set of eukaryotes and found that convergent losses occurred in other reduced taxa, including microsporidia. Overall, my dissertation highlights the usefulness of microsporidia as a model for spliceosomal reduction and aids in our understanding of the evolution of splicing in reduced systems.Science, Faculty ofBotany, Department ofGraduat
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
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
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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