1,720,989 research outputs found
Emergence of two distinct spatial folds in a pair of plant virus proteins encoded by nested genes
No full textVirus genomes may encode overlapping or nested open reading frames that increase their coding capacity. It is not known whether the constraints on spatial structures of the two encoded proteins limit the evolvability of nested genes. We examine the evolution of a pair of proteins, p22 and p19, encoded by nested genes in plant viruses from the genus Tombusvirus. The known structure of p19, a suppressor of RNA silencing, belongs to the RAGNYA fold from the alpha+beta class. The structure of p22, the cell-to-cell movement protein from the 30K family widespread in plant viruses, is predicted with the AlphaFold approach, suggesting a single jelly-roll fold core from the all-beta class, structurally similar to capsid proteins from plant and animal viruses. The nucleotide and codon preferences impose modest constraints on the types of secondary structures encoded in the alternative reading frames, nonetheless allowing for compact, well-ordered folds from different structural classes in two similarly-sized nested proteins. Tombusvirus p22 emerged through radiation of the widespread 30K family, which evolved by duplication of a virus capsid protein early in the evolution of plant viruses, whereas lineage-specific p19 may have emerged by a stepwise increase in the length of the overprinted gene and incremental acquisition of functionally active secondary structure elements by the protein product. This evolution of p19 toward the RAGNYA fold represents one of the first documented examples of protein structure convergence in naturally occurring proteins.This work was supported by grant PID2022-136912NB-I00 funded by MCIN/AEI/
10.13039/501100011033 and European Union NextGenerationEU/PRTR and by Generalitat Valenciana grant CIPROM/2022/59 to S. F. E. E. G. L. was supported by grant FPU21/00410 funded by MCIN/AEI/10.13039/501100011033 and by “ESF Invest in Your Future”. A. R. M. was supported by the U.S. National Science Foundation Independent Research and Development program.Peer reviewe
The Drosophila Beat protein is related to adhesion proteins that contain immunoglobulin domains
No full textEvolution of plant virus movement proteins from the 30K superfamily and of their homologs integrated in plant genomes
No full textHomologs of Tobacco mosaic virus 30K cell-to-cell movement protein are encoded by diverse
plant viruses. Mechanisms of action and evolutionary origins of these proteins remain obscure.
We expand the picture of conservation and evolution of the 30K proteins, producing sequence
alignment of the 30K superfamily with the broadest phylogenetic coverage thus far and
illuminating structural features of the core all-beta fold of these proteins. Integrated copies of
pararetrovirus 30K movement genes are prevalent in euphyllophytes, with at least one copy
intact in nearly every examined species, and mRNAs detected for most of them. Sequence
analysis suggests repeated integrations, pseudogenizations, and positive selection in those
provirus genes. An unannotated 30K-superfamily gene in Arabidopsis thaliana genome is likely
expressed as a fusion with the At1g37113 transcript. This molecular background of
endopararetrovirus gene products in plants may change our view of virus infection and
pathogenesis, and perhaps of cellular homeostasis in the hosts.S.F.E.issupportedbygrantBFU2012-30805
fromSpainMinistryofEconomyandCompetitivenessandbygrant
PROMETEOII/2014/021fromGeneralitatValenciana.A.R.M.isaPro-
gramDirectorattheU.S.NationalScienceFoundation(NSF);hiswork
on thisprojectwassupportedbytheNSFIndependentResearchand
Developmentprogram,butthestatementsandopinionsexpressed
hereinaremadeinthepersonalcapacity anddonotconstitutethe
endorsementbyNSForthegovernmentoftheUnitedStates.Peer reviewe
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
- …
