1,721,121 research outputs found
Coupling metabolite flux to transcriptomics: insights into the molecular mechanisms underlying primary productivity by the hydrothermal vent tubeworm Ridgeia piscesae
No full textDeep-sea hydrothermal vents host highly productive ecosystems. Many of these communities are dominated by vestimentiferan tubeworms that house endosymbiotic chemoautotrophic bacteria that provide the hosts with their primary nutritional needs. Rates of carbon fixation by these symbioses are also among the highest recorded. Despite the breadth of physiological and biochemical research on these associations, the underlying molecular mechanisms that regulate host and symbiont metabolite flux and carbon fixation are largely unknown. Here we present metabolite flux and transcriptomics data from shipboard high-pressure respirometry experiments in which we maintained Ridgeia piscesae tubeworms at conditions comparable to those in situ. Host trophosome was used for cDNA library construction and sequencing. Of the 19,132 clones sequenced, 10,684 represented unique expressed sequence tags (ESTs). The highest proportions of genes are involved with translation, ribosomal structure and biogenesis, cellular processing, and signal transduction. There was moderate representation of genes involved in metabolite exchange and acid-base regulation. These data represent the first concomitant surveys of metabolite flux rates and gene expression for a chemoautotrophic symbiosis during net autotrophy, and they suggest that-in the case of Ridgeia piscesae-host-symbiont interactions such as cell cycle regulation may play a significant role in maintaining physiological poise during high productivity
Linking Hydrothermal Geochemistry to Organismal Physiology: Physiological Versatility in Riftia pachyptila from Sedimented and Basalt-hosted Vents
Full text linkMuch of what is known regarding Riftia pachyptila physiology is based on the wealth of studies of tubeworms living at diffuse flows along the fast-spreading, basalt-hosted East Pacific Rise (EPR). These studies have collectively suggested that Riftia pachyptila and its chemoautotrophic symbionts are physiologically specialized, highly productive associations relying on hydrogen sulfide and oxygen to generate energy for carbon fixation, and the symbiont's nitrate reduction to ammonia for energy and biosynthesis. However, Riftia also flourish in sediment-hosted vents, which are markedly different in geochemistry than basalt-hosted systems. Here we present data from shipboard physiological studies and global quantitative proteomic analyses of Riftia pachyptila trophosome tissue recovered from tubeworms residing in the EPR and the Guaymas basin, a sedimented, hydrothermal vent field. We observed marked differences in symbiont nitrogen metabolism in both the respirometric and proteomic data. The proteomic data further suggest that Riftia associations in Guaymas may utilize different sulfur compounds for energy generation, may have an increased capacity for energy storage, and may play a role in degrading exogenous organic carbon. Together these data reveal that Riftia symbionts are far more physiologically plastic than previously considered, and that -contrary to previous assertions- Riftia do assimilate reduced nitrogen in some habitats. These observations raise new hypotheses regarding adaptations to the geochemical diversity of habitats occupied by Riftia, and the degree to which the environment influences symbiont physiology and evolution.Organismic and Evolutionary BiologyVersion of Recor
Characterizing microbial community and geochemical dynamics at hydrothermal vents using osmotically-driven continuous fluid samplers
No full textMicrobes play a key role in mediating aquatic biogeochemical cycles. However, our understanding of the relationships between microbial phylogenetic/physiological diversity and habitat physicochemical characteristics is restrained by our limited capacity to concurrently collect microbial and geochemical samples at appropriate spatial and temporal scales. Accordingly, we have developed a low-cost, continuous fluid sampling system (the Biological OsmoSampling System, or BOSS) to address this limitation. The BOSS does not use electricity, can be deployed in harsh/remote environments, and collects/preserves samples with daily resolution for >1 year. Here, we present data on the efficacy of DNA and protein preservation during a 1.5 year laboratory study as well as the results of two field deployments at deep-sea hydrothermal vents, wherein we examined changes in microbial diversity, protein expression, and geochemistry over time. Our data reveal marked changes in microbial composition co-occurring with changes in hydrothermal fluid composition as well as the temporal dynamics of an enigmatic sulfide-oxidizing symbiont in its free-living state. We also present the first data on in situ protein preservation and expression dynamics highlighting the BOSS’s potential utility in meta-proteomic studies. These data illustrate the value of using BOSS to study relationships among microbial and geochemical phenomena and environmental conditions
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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