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Environmental Bloom of Lingulodinium polyedrum in Southern California: Potential Health Risks
Full text linkHarmful algal blooms (HABs) have been documented to harbor algae capable of producing toxins harmful to both humans and marine life. Lingulodinium polyedrum, the major dinoflagellate species in the recent algal blooms in southern California in 2011 and 2013, has been shown to induce allergic responses in humans exposed to the bloom. The chemical natures of the compounds produced by L. polyedrum which induce this response are as of yet unknown. This study had the goal of determining whether L. polyedrum contains any pro-inflammatory compounds and to discern whether these compounds could induce an allergic reaction. Bioassay guided fractionation and chemical separation of cultured L. polyedrum has led to the isolation of a glycolipid produced by L. polyedrum, monogalactosyldiacylglycerol (20:5/18:5). Evaluation of the pro-inflammatory capacity of this glycolipid revealed that this glycolipid does not induce a pro-inflammatory response
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On the evolution of the sghC1q gene family, with bioinformatic and transcriptional case studies in zebrafish
Full text linkIn this thesis the evolution of the sghC1q gene family is explored throughout the metazoan lineage and within the zebrafish (Danio rerio) genome. This involved novel bioinformatic analyses, extensive synthesis of the literature, development of a bioinformatic tool, and the transcriptional assessment of the full complement of sghC1q genes within D. rerio during infection and early development. The secreted globular head C1q (sghC1q) genes can be characterized as a family of genetic loci each encoding a signal peptide followed by a complement component 1q globular (gC1q) motif. Members of this family have been referred to as precerebellin-like (cblnl), C1q-like or ovary specific C1q-like factors. Previous studies have found gene family members in multiple organisms with varying numbers of copies within a species. The genes are known to be transcribed in response to infection and/or during development. The domain of the C1q globular head (gC1q or ghC1q) appears to be ancient; present even in prokaryotes. With increasing complexity of organisms, this domain can sometimes be found accompanying first a signal peptide motif (indicative of secretion), and later with a collagen region. A comprehensive naming scheme is suggested based on these evolutionary adaptations. Computational modeling shows the globular head to be structurally conserved throughout the metazoa. The EST Keeper program was developed to facilitate these studies in identification of sets of non-redundant homologous genes from BLAST results that often contain redundant copies and gene fragments. It was built as a Flash based webservice and can be used to find gene families within genomes and EST datasets. Twenty sghC1q genes were found in the D. rerio genome (Zv9) and transcriptionally assessed. Two of the examined twenty genes showed significant up-regulation within 24 h of infection with the fish pathogen Streptococcus iniae, and eleven were expressed during early development. Due to the clustered nature of these genes on chromosomes two and seven, intrachromosomal duplication events are hypothesized and explored
Combined LC-MS/MS and Molecular Networking Approach Reveals New Cyanotoxins from the 2014 Cyanobacterial Bloom in Green Lake, Seattle
No full textCyanotoxins obtained from a freshwater cyanobacterial collection at Green Lake, Seattle during a cyanobacterial harmful algal bloom in the summer of 2014 were studied using a new approach based on molecular networking analysis of liquid chromatography tandem mass spectrometry (moleculrLC-MS/MS) data. This MS networking approach is particularly well-suited for the detection of new cyanotoxin variants and resulted in the discovery of three new cyclic peptides, namely microcystin-MhtyR (6), which comprised about half of the total microcystin content in the bloom, and ferintoic acids C (12) and D (13). Structure elucidation of 6 was aided by a new microscale methylation procedure. Metagenomic analysis of the bloom using the 16S-ITS rRNA region identified Microcystis aeruginosa as the predominant cyanobacterium in the sample. Fragments of the putative biosynthetic genes for the new cyanotoxins were also identified, and their sequences correlated to the structure of the isolated cyanotoxins
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
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Comparative genomics and genome mining insights into natural product rich marine cyanobacteria
Full text linkNumerous advantages of systematic genomics have been leveraged in other areas, such as transcriptomics, proteomics and human microbiome studies, but it has yet to be effective in stimulating the increased discovery of natural products (secondary metabolites).1 Since the discovery of the first microbial genome (2002), the surprisingly high percentage of cryptic biosynthetic pathways per genome (genes not connected to any known secondary metabolite, aka natural product) has continued as a consistent theme.2 Cyanobacteria from benthic environments are prolific producers of natural products but genomes from these organisms remain scarce in public repositories. Hence, this dissertation focused on sequencing and performing genomic analysis in prolific cyanobacteria collected from several tropical benthic ecosystems around the planet. First, we analyzed the relationship between a cyanobacterium host and its associated heterotrophic microbiome. By evaluation the non-axenic culture of Moorea producens JHB, we characterized a novel uncultured acidobacteria heterotroph living with the cyanobacterial host.3 This heterotroph was only 85% similar to the closest cultured representative, it presented a large number of genes encoding for transcriptional regulators and it was auxotrophic for several proteogenic amino acids. Next, we expanded our genome comparison by deeper analyzing 4 Moorea genomes. Our genome comparison revealed that Moorea, already a prolific producer of secondary metabolites, harbored an even richer metabolic potential, four times above the cyanobacterial average. We observed that Moorea conserved its primary metabolism while evolved an intricate secondary metabolism machinery, accounting for 20% of their genomic content. These findings were very promising for future genome mining efforts in those four strains. Thereby, we further expanded our sequencing efforts by sampling 165 metagenomes of filamentous marine cyanobacteria collected from around the globe. Our new metagenomic pipeline was able to generated 85 high-quality genomes, including 32 Moorea and 29 Okeania strains. Our genome comparison highlighted that these two genera are among the most diverse and prolific producers of natural products in our dataset (comparing pairwise 506 cyanobacterial genomes, 425 from the NCBI database). Gene networking revealed the abundance of unique (only encountered in a single strain) and “extended families” (found in several strains). Using genomes with paired mass spectrometry data, we correlated the distribution of gene families with the distribution of metabolic families and automatically annotated a new dehydromicrosclerodermin B homologue
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
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