1,720,984 research outputs found
Development of an integrated omics in silico workflow and its application for studying bacteria-phage interactions in a model microbial community
Get PDFMicrobial communities are ubiquitous and dynamic systems that inhabit a multitude of environments. They underpin natural as well as biotechnological processes, and are also implicated in human health. The elucidation and understanding of these structurally and functionally complex microbial systems using a broad spectrum of toolkits ranging from in situ sampling, high-throughput data generation ("omics"), bioinformatic analyses, computational modelling and laboratory experiments is the aim of the emerging discipline of Eco-Systems Biology. Integrated workflows which allow the systematic investigation of microbial consortia are being developed. However, in silico methods for analysing multi-omic data sets are so far typically lab-specific, applied ad hoc, limited in terms of their reproducibility by different research groups and suboptimal in the amount of data actually being exploited. To address these limitations, the present work initially focused on the development of the Integrated Meta-omic Pipeline (IMP), a large-scale reference-independent bioinformatic analyses pipeline for the integrated analysis of coupled metagenomic and metatranscriptomic data. IMP is an elaborate pipeline that incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning as well as genomic signature-based visualizations. The IMP-based data integration strategy greatly enhances overall data usage, output volume and quality as demonstrated using relevant use-cases. Finally, IMP is encapsulated within a user-friendly implementation using Python while relying on Docker for reproducibility. The IMP pipeline was then applied to a longitudinal multi-omic dataset derived from a model microbial community from an activated sludge biological wastewater treatment plant with the explicit aim of following bacteria-phage interaction dynamics using information from the CRISPR-Cas system. This work provides a multi-omic perspective of community-level CRISPR dynamics, namely changes in CRISPR repeat and spacer complements over time, demonstrating that these are heterogeneous, dynamic and transcribed genomic regions. Population-level analysis of two lipid accumulating bacterial species associated with 158 putative bacteriophage sequences enabled the observation of phage-host population dynamics. Several putatively identified bacteriophages were found to occur at much higher abundances compared to other phages and these specific peaks usually do not overlap with other putative phages. In addition, there were several RNA-based CRISPR targets that were found to occur in high abundances. In summary, the present work describes the development of a new bioinformatic pipeline for the analysis of coupled metagenomic and metatranscriptomic datasets derived from microbial communities and its application to a study focused on the dynamics of bacteria-virus interactions. Finally, this work demonstrates the power of integrated multi-omic investigation of microbial consortia towards the conversion of high-throughput next-generation sequencing data into new insights
De-novo assembly and finishing of the genome of neuro-toxin (anatoxin-a) producing cyanobacterium, Anabaena sp. strain 37
No full textCyanobacteria are ancient photosynthetic microorganisms found in both fresh and saline water bodies all over the world. Anabaena is a genus of filamentous heterocystous diazotrophic cyanobacteria that are common in freshwater lakes and often implicated in the formation of blooms. They are known to play a vital role in the nitrogen cycle and to produce harmful toxins. The reason for this toxic producing nature is still unknown. The Anabaena sp. strain 37, isolated from lake Sääksjärvi, western Finland was found to produce the neurotoxin, anatoxin-a which affects the nervous systems of humans and animals, capable of causing paralysis. During the past decade, genome sequencing has aided in the understanding of genetic information in many organisms including cyanobacteria. A whole genome sequencing project was carried out to understand the mechanism of anatoxin-a production in the Anabaena sp. strain 37. The 454 pyrosequencing produced 258,430 reads with a coverage of approximately 22X. The data was subjected to a de novo assembly which produced a draft genome, made up of 828 contigs above 500 bp, an N50 contig of 10,548 bp and a longest contig of 47,660 bp. The draft assembly underwent a finishing procedure which included scaffolding, gap closure and error correction. Two types of mate pair libraries; 3 Kb and 8 Kb were constructed and sequenced for scaffolding. The scaffolding using 196,221 of 3 Kb mate pair reads yielded 31 major scaffolds with an N50 scaffold of 344,872 bp. A second scaffolding using 34,498, 8 Kb mate pair reads resulted in 16 scaffolds, and an N50 scaffold of 1,085,340 bp. Three automated gap closure rounds were carried out using consed autofinish. The primers amplified the genomic DNA with PCR and the products were sequenced using Sanger sequencing. A total of 1,406 Sanger reads were used to closed more than 800 gaps in the draft assembly. In addition, the 454-based draft assembly contained many sequencing errors among single nucleotide homopolymeric regions of three-mers and above. Moreover, these errors were found in coding regions, namely the anatoxin-a synthetase gene cluster and was further confirmed with additional PCR and Sanger sequencing. There were 370,648 single nucleotide homopolymer sites of three mers and above that accounted for 38.18% of the genome length and a density of 668.1 per 10 Kb. A correction procedure was carried out by incorporating 100X coverage Illumina/Solexa data into the assembly. The high depth data corrected an estimated 1,888 single nucleotide homopolymer error sites of three-mers and above which translates to a 454 single nucleotide homopolymer error rate of 0.51% or 3.37 per 10 Kb. The correction also increased the overall quality of the Q20. The current assembly is made up of 14 scaffolds out of which six are major scaffolds. The assembly has an N50 scaffold of 1,085,340 bp where 99.7% of the consensus bases are of phred Q20 bases and an overall error rate of 8.21 per 10 Kb. Finally, the genome has a GC-content of 38.3% with four ribosomal RNA operons and the anatoxin-a synthetase gene cluster confirmed
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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