1,720,987 research outputs found
A needle in a haystack: tracing bivalve-associated viruses in high-throughput transcriptomic data
Get PDFBivalve mollusks thrive in environments rich in microorganisms, such as estuarine and coastal waters, and they tend to accumulate various particles, including viruses. However, the current knowledge on mollusk viruses is mainly centered on few pathogenic viruses, whereas a general view of bivalve-associated viromes is lacking. This study was designed to explore viral abundance and diversity in bivalve mollusks using transcriptomic datasets. Analyzing RNA-seq data of 58 bivalve species, we have reconstructed 26 nearly complete and over 413 partial RNA virus genomes. Although 96.4 % of the predicted viral proteins refer to new viruses, some sequences belong to viruses associated to bivalve species or other marine invertebrates. We considered short non-coding RNAs (sncRNA) and post-transcriptional modifications occurring specifically on viral RNAs as tools for virus host-assignment. We could not identify virus-derived small RNAs in sncRNA reads obtained from the oyster sample richest in viral reads. SNP analysis revealed 938 A-to-G substitutions occurring on the 26 identified RNA viruses, preferentially impacting the AA di-nucleotide motif. Under-representation analysis revealed that the AA motif is under-represented in these bivalve-associated viruses. These findings improve our understanding of bivalve viromes and set the stage for targeted investigations on the specificity and dynamics of identified viruses
Seawater carbonate chemistry and larval viability, size, development, and shell mineralization of the eastern oyster (Crassostrea virginica)
No full textCalcifying marine organisms, including the eastern oyster (Crassostrea virginica), are vulnerable to ocean acidification (OA) because it is more difficult to precipitate calcium carbonate (CaCO3). Previous investigations of the molecular mechanisms associated with resilience to OA in C. virginica demonstrated significant differences in single nucleotide polymorphism and gene expression profiles among oysters reared under ambient and OA conditions. Converged evidence generated by both of these approaches highlighted the role of genes related to biomineralization, including perlucins. Here, gene silencing via RNA interference (RNAi) was used to evaluate the protective role of a perlucin gene under OA stress. Larvae were exposed to short dicer-substrate small interfering RNA (DsiRNA-perlucin) to silence the target gene or to one of two control treatments (control DsiRNA or seawater) before cultivation under OA (pH ~7.3) or ambient (pH ~8.2) conditions. Two transfection experiments were performed in parallel, one during fertilization and one during early larval development (6 h post-fertilization), before larval viability, size, development, and shell mineralization were monitored. Silenced oysters under acidification stress were the smallest, had shell abnormalities, and had significantly reduced shell mineralization, thereby suggesting that perlucin significantly helps larvae mitigate the effects of OA
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
Probing the Protein Folding Mechanism by Simulation of Dynamics and Nonlinear Infrared Spectroscopy
No full textThis dissertation presents simulation based approaches towards the study of the dynamics and nonlinear spectroscopy of protein folding. The folding mechanisms of two model protein systems, the N-terminal domain of ribosomal protein L9 (NTL9) and the synthetic Beta3s mini-protein were investigated. All-atom molecular dynamics (MD) simulations and two-dimensional infrared spectroscopy (2DIR) computations were employed in the investigation of the folding mechanisms of these model systems. In this work, the folding mechanism and transition state ensemble (TSE) of the 56-residue N-terminal domain of L9 (NTL9) was probed. The TSE was identified from high temperature unfolding all-atom MD simulations in conjunction with experimentally determined phi-values. The TSE ensemble of NTL9 was found to be largely native in composition, with a well defined secondary structure. In the progression to folding after crossing the TSE our data suggests that much of the drive towards the native state ofNTL9 is spent optimizing electrostatic interactions between stable secondary structure elements. This work also proposes the use two-dimensional infrared spectroscopy (2DIR) to characterize the folding mechanism of the mini-protein Beta3s. In this study Beta3s was folded by MD simulation and intermediate conformational ensembles were identified. The two-dimensional infrared spectrum was calculated for the intermediate and native states of the mini-protein. A direct structure-spectra relationship was determined by analysis of conformational properties and specific residue contributions. The structural origins of diagonal and off-diagonal peaks in the 2DIR spectrum were identified for the native and intermediate conformational ensembles in the folding mechanism. This work supports the implementation of computational techniques in conjunction with experimental 2DIR to study the folding mechanism of proteins. In addition to exploring the folding mechanism the work presented here may also be applied in combination with experiment to refine and validate current molecular dynamics force fields.Advisor(s): Jin Wang. John Reinitz. Committee Member(s): David F. Green; Daniel P. Raleigh; Robert C. Rizzo; Dale G. Drueckhammer.Stony Brook University Libraries. SBU Graduate School in Department of Biochemistry and Structural Biology. Lawrence Martin (Dean of Graduate School)
Seawater carbonate chemistry and phenotypic Plasticity in Crassostrea virginica Larvae
No full textOcean acidification (OA) is a major threat to marine calcifiers, and little is known regarding acclimation to OA in bivalves. This study combined physiological assays with next-generation sequencing to assess the potential for recovery from and acclimation to OA in the eastern oyster (Crassostrea virginica) and identify molecular mechanisms associated with resilience. In a reciprocal transplant experiment, larvae transplanted from elevated pCO2 (~1400 ppm) to ambient pCO2 (~350 ppm) demonstrated significantly lower mortality and larger size post-transplant than oysters remaining under elevated pCO2 and had similar mortality compared to those remaining in ambient conditions. The recovery after transplantation to ambient conditions demonstrates the ability for larvae to rebound and suggests phenotypic plasticity and acclimation. Transcriptomic analysis supported this hypothesis as genes were differentially regulated under OA stress. Transcriptomic profiles of transplanted and non-transplanted larvae terminating in the same final pCO2 converged, further supporting the idea that acclimation underlies resilience. The functions of differentially expressed genes included cell differentiation, development, biomineralization, ion exchange, and immunity. Results suggest acclimation as a mode of resilience to OA. In addition, the identification of genes associated with resilience can serve as a valuable resource for the aquaculture industry, as these could enable marker-assisted selection of OA-resilient stocks
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