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  • 1
    Publication Date: 2015-07-02
    Description: Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org . Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2012-12-12
    Description: Stockwell, J. D., Weber, T. C., Baukus, A. J., and Jech, J. M. 2013. On the use of omnidirectional sonars and downwards-looking echosounders to assess pelagic fish distributions during and after midwater trawling. – ICES Journal of Marine Science, 70:196–203. Small pelagic fish can play an important role in the structure and function of ecosystems, and there is increasing interest in their non-market value. At the scale of fish aggregations, however, the impact of fishing has received relatively little attention, with most effort devoted to impacts of vessel and gear avoidance on stock size estimates. We used concurrent deployment of a downwards-looking echosounder (Simrad ES60 system) and an omnidirectional sonar (Simrad SP90 system) during commercial pairtrawling operations for Atlantic herring ( Clupea harengus ) in the Gulf of Maine to examine their potential for studying the impacts of fishing on herring aggregations. We compared a number of aggregation metrics to illustrate similarities and differences between the two systems, and then qualitatively examined their properties during and after pairtrawling events to illustrate potential applications. Our results suggest that using both downwards-looking and omnidirectional systems provides complementary information on fish aggregation metrics. Future applications of these systems in before–after–control-impact (BACI) designs may help inform management agencies when evaluating potential impacts of fishing at the time and space scales of pelagic fish aggregations.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
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  • 3
    Publication Date: 2013-06-23
    Description: Microbial secondary metabolites are a potent source of antibiotics and other pharmaceuticals. Genome mining of their biosynthetic gene clusters has become a key method to accelerate their identification and characterization. In 2011, we developed antiSMASH, a web-based analysis platform that automates this process. Here, we present the highly improved antiSMASH 2.0 release, available at http://antismash.secondarymetabolites.org/ . For the new version, antiSMASH was entirely re-designed using a plug-and-play concept that allows easy integration of novel predictor or output modules. antiSMASH 2.0 now supports input of multiple related sequences simultaneously (multi-FASTA/GenBank/EMBL), which allows the analysis of draft genomes comprising multiple contigs. Moreover, direct analysis of protein sequences is now possible. antiSMASH 2.0 has also been equipped with the capacity to detect additional classes of secondary metabolites, including oligosaccharide antibiotics, phenazines, thiopeptides, homo-serine lactones, phosphonates and furans. The algorithm for predicting the core structure of the cluster end product is now also covering lantipeptides, in addition to polyketides and non-ribosomal peptides. The antiSMASH ClusterBlast functionality has been extended to identify sub-clusters involved in the biosynthesis of specific chemical building blocks. The new features currently make antiSMASH 2.0 the most comprehensive resource for identifying and analyzing novel secondary metabolite biosynthetic pathways in microorganisms.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 4
    Publication Date: 2016-09-24
    Description: Active- and passive-acoustic methods are widely used tools for observing, monitoring, and understanding marine ecosystems. From 25 to 28 May 2015, 214 scientists from 31 nations gathered for an ICES symposium on Marine Ecosystem Acoustics (SoME Acoustics) to discuss three major themes related to acoustic observations of marine ecosystems: (i) recent developments in acoustic and platform technologies; (ii) acoustic characterisation of aquatic organisms, ecosystem structure, and ecosystem processes; and (iii) contribution of acoustics to integrated ecosystem assessments and management. The development of, and access to new instruments, such as broad bandwidth systems, enables insightful ecological studies and innovative management approaches. Unresolved ecological questions and the increasing move towards ecosystem based management pose further challenges to scientists and instrument developers. Considering the SoME Acoustics presentations in the context of three previous ICES symposia on fisheries acoustics, topics increasingly emphasize ecosystem studies and management. The continued expansion of work and progress in marine ecosystem acoustics is due to the cross-disciplinary work of fisheries acousticians, engineers, ecologists, modellers, and others. An analysis of the symposium co-authorship network reveals a highly connected acoustic science community collaborating around the globe.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
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  • 5
    Publication Date: 2017-01-05
    Description: Secondary metabolites produced by microorganisms are the main source of bioactive compounds that are in use as antimicrobial and anticancer drugs, fungicides, herbicides and pesticides. In the last decade, the increasing availability of microbial genomes has established genome mining as a very important method for the identification of their biosynthetic gene clusters (BGCs). One of the most popular tools for this task is antiSMASH. However, so far, antiSMASH is limited to de novo computing results for user-submitted genomes and only partially connects these with BGCs from other organisms. Therefore, we developed the antiSMASH database, a simple but highly useful new resource to browse antiSMASH-annotated BGCs in the currently 3907 bacterial genomes in the database and perform advanced search queries combining multiple search criteria. antiSMASH-DB is available at http://antismash-db.secondarymetabolites.org/ .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 6
    Publication Date: 1983-03-11
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 7
    Publication Date: 2009-09-01
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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