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A Unified Structure for Dutch Dialect Dictionary Data
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41452.pdf (author's version ) (Open Access)The fifth international conference on Language Resources and EvaluationGenoa, Ital
Genomics, proteomics and secondary metabolites biosynthesis research on Streptomyces asterosporus DSM 41452
No full textAbstraktStreptomyceten, als eine Art wichtiger industrieller Stamm für die Herstellung von Antibiotika, wurden über Jahrzehnte hinweg untersucht. Es wurde als spezielles Bakterium mit einem komplexen pilzartigen Lebenszyklus charakterisiert (Ohnishi et al. 2005). Die Sporulation von Streptomyceten wurde eindeutig als signifikant mit der Produktion von Antibiotika in Verbindung gebracht (Chandra und Chater 2014). Nicht-Sporulations-Mutanten erzeugen das Luftmyzel aus unterschiedlichen Gründen nicht. Bis heute sind mindestens 20 beschriebene Gene an der Luftmyzelbildung beteiligt (Takano et al. 2003). Wir berichteten bereits, dass das defekte bldA-Gen die Bildung von Lufthyphen und die Bildung von Sekundärmetaboliten in Streptomyces calvus verhindert, indem es die Expression des TTA-haltigen adpA-Gens hemmt (Gessner et al. 2015; Hackl und Bechthold 2015). Unsere folgenden Untersuchungen haben jedoch ergeben, dass die konstitutive Expression von bldA in einigen "kahlen" Streptomyceten-Stämmen, die von der DSMZ gekauft wurden, die Sporulation nicht effizient wiederherstellt, was unser Interesse geweckt hat. Einer der Stämme ist Streptomyces asterosporus DSM 41452. Das Phänomen zeigt an, dass ein potentieller unbekannter Mechanismus den "schwach sporulierenden" Phänotyp in S. asterosporus DSM 41452 verursacht. In dieser Dissertation wurde das vollständige Genom von S. asterosporus DSM 41452 sequenziert und kommentiert. Durch detaillierte vergleichende Genomsequenzanalyse wurde ein Transposon-Gen stromaufwärts des adpA-Gens von S. asterosporus DSM 41452 gefunden, das die Transkription von adpA behindert. Durch Komplementierung des adpA-Gens mit einem funktionellen Promotor in diesem Stamm wurde die Sporulation wiederhergestellt.Die Proteomik war schon immer eine effiziente Methode, um die zelluläre Physiologie und den Stoffwechsel eines Organismus zu untersuchen. In dieser Arbeit verwenden wir zum ersten Mal den SILAC-basierten komparativen Proteomik-Ansatz, um das AdpA-Regulon im nativen nicht-sporulierenden S. asterosporus DSM 41452 zu profilieren. In unserer Studie wurden mehr als 1200 Proteine identifiziert, einschließlich Proteine, die am Stamm-Stoffwechsel, der zellulären Verarbeitung und Signalisierung, Informationsspeicherung und -verarbeitung usw. beteiligt sind. Am wichtigsten ist, dass wir gezeigt haben, dass der SILAC-Ansatz in der Streptomyceten-Proteomik effizient angewendet werden kann.In Bezug auf seine Sekundärmetabolite von S. asterosporus DSM 41452 wurden Gencluster von WS9326A (Johnston et al. 2015) und Annimycin (Kalan et al. 2013), die zuvor in S. calvus ATCC 13382 gefunden wurden, durch bioinformatische Analyse der Genomsequenz von S. asterosporus DSM 41452 identifiziert. Sechs Verbindungen, WS9326A und seine Derivate WS9326B, WS9326D, WS9326E, WS9326F und WS9326G wurden aus der Scale-Up-Fermentation von S. asterosporus DSM 41452 isoliert. Überraschenderweise wurden zwei neue Analoga SY11 und SY12 isoliert aus einem Annimycin-Defekt-Mutantenstamm S. asterosporus DSM 41452::pUC19Δ3100spec und ihre Strukturen teilweise gemäß den Massenspektrometrie- und NMR-Daten charakterisiert. Die Titer von WS9326A in der entsprechenden S. asterosporus-Mutante waren leicht verbessert. Darüber hinaus wurde die Grenze des WS9326A-Genclusters durch Aufbrechen des Gens orf (-1) und sas1 am Terminus des Genclusters bestimmt. In-frame-Gen-Knockout des Gens, das die N-Methyltransferase (MTase) in Modul 2 der WS9326A-NRPSs kodiert, führt zur Unterbrechung der WS9326A-Produktion, was auf die Bedeutung des Methyl-Tyrosins für die Substraterkennung durch die Kondensationsdomäne hinweist. Die Geninaktivierung von sas13 durch single crossover scheint die Produktion von WS9326A nicht zu beeinflussen, was die Möglichkeit ausschließt, dass sas13 an der Bildung des nichtproteinogenen Dehydrotyrosinrests in WS9326A beteiligt ist. Zusätzlich führte die In-frame-Gen-Deletion von sas16 durch doppelten Crossover zum Verlust von WS9326A, und die Produktion von WS9326A wurde nach der Komplementation des Gens sas16 wiederhergestellt. Daher wird vorgeschlagen, dass dieses Gen an der Bildung des Dehydrotyrosins in WS9326As beteiligt ist.Um die biochemische Rolle von Sas16 während der Biosynthese des N-Methyl-Dehydro-Tyrosin-Proteins zu verstehen, wurde Sas16 heterolog für In-vitro-Enzymtests exprimiert. In der Zwischenzeit haben wir erfolgreich die Architektur von Sas16 aufgeklärt, um die zugrundeliegende molekulare Basis der Substratselektivität dieses Cytochrom P450 Enzyms aufzudeckenAbstract Many important industrial strains for antibiotic production belong to the genus of Streptomyces. They are characterized as special bacteria with a complex fungus-like life cycle (Ohnishi et al. 2005). The sporulation of Streptomyces has been clearly demonstrated to have a significant association with the production of antibiotics (Chandra and Chater 2014). Non-sporulation mutants fail to generate the aerial mycelium due to different reason. To date at least 20 reported genes are involved in the aerial mycelium formation (Takano et al. 2003). We previously reported that the defective bldA gene prevents the generation of aerial hyphae and the formation of secondary metabolites in Streptomyces calvus by inhibiting the expression of the TTA-containing adpA gene (Gessner et al. 2015; Hackl and Bechthold 2015). However, our following research found that the constitutive expression of bldA in some “bald” Streptomyces strains didn’t efficiently restore the sporulation, which attracts our interests. One of the strain is Streptomyces asterosporus DSM 41452. Experimental data indicate that there is a potential unknown mechanism causing the “poorly sporulating” phenotype in S. asterosporus DSM 41452. In this dissertation, the complete genome of S. asterosporus DSM 41452 was sequenced and annotated. By detailed comparative genome sequence analysis, a transposon gene was found upstream of adpA gene of S. asterosporus DSM 41452 which hinder the transcription of adpA. By complementation of adpA gene with a functional promoter in this strain, the sporulation was restored. Proteomics has always been an efficient method to investigate the cellular physiology and metabolism of an organism. In this thesis, we first time employ SILAC-based comparative proteomic approach to profile the AdpA regulon in the native non-sporulating S. asterosporus DSM 41452. In our study, more than 1200 proteins were identified, including proteins involved in strain’s metabolism, cellular processing and signaling, information storage and processing, etc. Most importantly, we managed to demonstrated that SILAC approach can be efficiently applied for Streptomyces proteomics research. In terms of its secondary metabolites of S. asterosporus DSM 41452, from the genome of S. asterosporus DSM 41452, we found the gene clusters for WS9326A (Johnston et al. 2015) and Annimycin (Kalan et al. 2013), which both have been detected in S. calvus ATCC 13382 were identified through bioinformatics analysis of genome sequence of S. asterosporus DSM 41452. Six compounds, WS9326A and its derivatives WS9326B, WS9326D, WS9326E, WS9326F, and WS9326G were isolated from the scale-up fermentation of S. asterosporus DSM 41452. Surprisingly, two new WS9326A derivatives SY11 and SY12 were isolated from one Annimycin-defect mutant strain S. asterosporus DSM 41452::pUC19Δ3100spec, structures of SY11 and SY12 were partially characterized by mass spectrometry and NMR. The boundary of WS9326A gene cluster was determined by disrupting gene orf(-1) and sas1 at the terminus of the gene cluster. In-frame gene knockout of the gene encoding the N-methyltransferase(MTase) in module 2 of WS9326A NRPSs resulted in the disruption of WS9326A production, suggesting that the methylation of the tyrosine residue is essential for the substrate recognition by the downstream condensation domain. Gene inactivation of sas13 by single crossover seem didn’t influence the production of WS9326A, which exclude the possibility of sas13 participating the formation of the nonproteinogenic dehydrotyrosine residue in WS9326A production. In addition, in-frame gene deletion of sas16 by PCR-targeting method led to the loss of WS9326A, and the production of WS9326A was restored after the complementation of gene sas16. Therefore, this gene is proposed to participate in the formation of the dehydrotyrosine moiety. For an in-depth understanding of the biochemical role of Sas16 during the biosynthesis of the N-methyl-dehydrotyrosine protein, the gene was heterologously expressed for in vitro enzymatic assay. We successfully elucidated the protein structure of Sas16 to reveal the underlying molecular basis of substrate selectivity of this Cytochrome P450 enzyme
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
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