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Horizontal gene transfer through natural competence and recombination in the generalist plant pathogen Xylella fastidiosa
Full text linkHorizontal gene transfer has been implicated as a contributing factor towards the diversity and adaptation of pathogens, and the emergence of new diseases. For naturally competent bacteria, DNA acquired through transformation and recombined into the genome could provide a means for this genetic transfer to occur. The work presented here illustrates that Xylella fastidiosa, a bacterial pathogen responsible for several important plant diseases, is naturally competent and able to homologously recombine acquired DNA into its genome. Xylella fastidiosa is vector-transmitted and often exists in natural environments as an endophyte, but causes disease when it multiplies to high levels inside the xylem vessels of its host plants, causing symptoms such as leaf scorching and stunted growth. Several factors were identified that affect the competence of X. fastidiosa, including nutrient availability, growth stage, and methylation state and size of transforming DNA. Recombination efficiencies for X. fastidiosa were at least 1000-fold higher when cells were grown in a defined nutrient medium compared to cells grown in a rich medium. In addition, surface-attached cells transformed and recombined DNA at efficiencies approximately two orders of magnitude higher than their planktonic counterparts. Maximum recombination efficiencies, defined as the number of recombinant cells recovered divided by the total number of cells, were approximately 10-3 when high concentrations of exogenous plasmid DNA were added to cells, and 10-5 when strains harboring different antibiotic markers were co-cultured on solid medium. For planktonic cells, maximum recombination efficiencies were only approximately 10-5 when DNA was added and 10-7 when different strains were co-cultured. Cells appeared most competent while undergoing exponential growth. For planktonic cells, competence peaked after two days of growth and then rapidly declined, with no recombination observed after 8 days. In biofilms, however, cells remained highly competent for at least five days, with recombination events observed even after 21 days of growth. The transformation mechanism in X. fastidiosa is likely similar to that of other naturally competent bacteria, with mutations in type IV pili, competence-related genes (com genes), and cell-cell signaling genes impacting competence. It was also experimentally determined that flanking homologous sequences as short as 96bp in transforming DNA is sufficient to initiate recombination, with efficiencies increasing exponentially with length of the homologous region up to 1kb. In addition, recombination efficiencies decreased exponentially with the size of non-homologous insert. Integration of up to 4kb of non-homologous DNA was observed experimentally. An in silico analysis of genomic sequences confirmed that the experimental data was consistent with events detected in natural populations, with an estimated mean size of recombination events of 1,906 bp. Each recombination event also modified, on average, 1.79% of the nucleotides in the recombined region. Based on sequence similarity of shared coding regions, it appears that recombination between different subspecies of X. fastidiosa could frequently occur. Originally, it was thought that X. fastidiosa was primarily clonal, but recent studies have suggested that recombination plays a significant role in generating genetic diversity in this bacterium. The work presented here illustrates that X. fastidiosa is naturally competent and that DNA acquired through natural transformation could be a substantial source of donor DNA for recombination. Understanding how this process is regulated and what factors affect its efficiency could provide insight into the genetic diversity of this organism and how new diseases emerge
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Dissecting Novel Grapevine-Mealybug-Virus Interactions
Full text linkThe biological mechanisms underlying vector transmission of grapevine leafroll-associated virus 3 (GLRaV-3) remain poorly understood due to limitations of a technically challenging host- pathogen system in Vitis vinifera. GLRaV-3 was able to infect the model organism Nicotiana benthamiana by insect-vector mediated transmission using the vine mealybug, Planococcus ficus. Working with GLRaV-3 infected N. benthamiana revealed distinct advantages in comparison with its natural host Vitis vinifera, yielding both higher viral protein and virion concentrations in western blot and transmission electron microscopy (TEM) observations, respectively. Immunogold labelling of thin sections through N. benthamiana petioles revealed filamentous particles in the phloem cells of GLRaV-3 positive plants. Comparison of assembled whole genomes from GLRaV-3 infected V. vinifera vs. N. benthamiana revealed identical sequences. High throughput sequencing was used to compare host response to GLRaV-3 infection between V. vinifera and N. benthamiana. General families of differentially expressed genes (DEGs) common in both hosts followed similar expression changes with six upregulated, seven downregulated, and two stably expressed genes in common. Overall, both hosts have many DEGs unique to each host as well as responses in common to GLRaV-3 infection. The vine mealybug, Planococcus ficus, fed through a membrane feeding system on GLRaV-3 viral purifications from both V. vinifera and N. benthamiana, and transmitted the virus to test plants.An immunofluorescence approach was used to localize virions to two retention sites in P. ficus mouthparts. Assays testing molecules capable of blocking virus transmission demonstrated that GLRaV-3 transmission by P. ficus can be disrupted. Our results indicate that our membrane feeding system and transmission blocking assays are a valid approach and can be used to screen other candidate blocking molecules. GLRaV-3 continues to impact grape-growing regions worldwide and the lack of knowledge surrounding virus-vector interactions remains limiting to the field. Elucidating the transmission biology of this important virus contributes to the eventual goal of blocking of transmission in insect vectors and the development of improved control strategies in vineyards
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
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
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe 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
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