OrganismTagger: detection, normalization and grounding of organism entities in biomedical documents

Motivation: Semantic tagging of organism mentions in full-text articles is an important part of literature mining and semantic enrichment solutions. Tagged organism mentions also play a pivotal role in disambiguating other entities in a text, such as proteins. A high-precision organism tagging system must be able to detect the numerous forms of organism mentions, including common names as well as the traditional taxonomic groups: genus, species and strains. In addition, such a system must resolve abbreviations and acronyms, assign the scientific name and if possible link the detected mention to the NCBI Taxonomy database for further semantic queries and literature navigation. Results: We present the OrganismTagger, a hybrid rule-based/machine learning system to extract organism mentions from the literature. It includes tools for automatically generating lexical and ontological resources from a copy of the NCBI Taxonomy database, thereby facilitating system updates by end users. Its novel ontology-based resources can also be reused in other semantic mining and linked data tasks. Each detected organism mention is normalized to a canonical name through the resolution of acronyms and abbreviations and subsequently grounded with an NCBI Taxonomy database ID. In particular, our system combines a novel machine-learning approach with rule-based and lexical methods for detecting strain mentions in documents. On our manually annotated OT corpus, the OrganismTagger achieves a precision of 95%, a recall of 94% and a grounding accuracy of 97.5%. On the manually annotated corpus of Linnaeus-100, the results show a precision of 99%, recall of 97% and grounding accuracy of 97.4%. Availability: The OrganismTagger, including supporting tools, resources, training data and manual annotations, as well as end user and developer documentation, is freely available under an open-source license at http://www.semanticsoftware.info/organism-tagger. Contact: [email protected]

Antifungal activity of Comamonas acidovorans isolated from water pond in south Jordan

A bacterial strain identified as Comamonas acidovorans NB-10II was isolated from water pond in South Jordan. It was found to have an antifungal activity against filamentous fungi (Aspergillus niger SQ 40,Fusarium oxysporium SQ 11, Verticillium dahliae SQ 42), yeasts (Saccharomyces cerevisiae SQ 46, Candida albicans SQ 47). All gram-positive bacteria (Bacillus megaterium SQ 5, Bacillus cereus SQ 6, Staphylococcus aureus SQ 9, Streptococcus pyogenes SQ 10) and gram-negative bacteria (Escherichia coli SQ 22, Klepsiella spp SQ 33, Pseudomonas mallei SQ 34) were found to be resistant. The isolateNB-10II was found to accumulate the main portion of the antimicrobial substances in their cells. In batch culture, the active antimicrobial substances accumulated at the late growth cycle, reaching theirmaximum at 42 h of growth. The data clearly show an antifungal activity of C. acidovorans against filamentous fungi and yeasts, and indicated the possibility of using NB-10II as a source of antimicrobialsubstances or as a biocontrol agent of some plant diseases in Jordan

Production of a rhamnolipid-type biosurfactant by Pseudomonas aeruginosa LBM10 grown on glycerol

The work herewith investigated the effect of the culture medium composition on rhamnolipid production by Pseudomonas aeruginosa LBM10, previously isolated from an estuarine environment in Southern Brazil. Experimental design and surface response methodology were used in order to improve biosurfactant production using glycerol, a renewable carbon source. The assays were carried out in a rotary shaker at 30°C and 180 rpm for 120 h and the parameters studied were glycerol concentration, C/N (carbon/nitrogen) and C/P (carbon/phosphorus) ratios. Low glycerol concentration and a phosphorus-limiting condition were favorable for rhamnolipid production. Contour plots constructed by predictive polynomial equations led to a glycerol concentration of 13.2 g/l, a C/N ratio of 12.8 and a C/P ratio of 40 in order to maximize rhamnolipid concentration (4.15 g/l) associated with a high emulsification index (61%).Keywords: Biosurfactant, surface-active compounds, experimental design, phosphorus limitatio

When genome-based approach meets the “Old but Good”: revealing genes involved in the antibacterial activity of Pseudomonas sp. P482 against soft rot pathogens

Dickeya solani and Pectobacterium carotovorum subsp. brasiliense are recently established species of bacterial plant pathogens causing black leg and soft rot of many vegetables and ornamental plants. Pseudomonas sp. strain P482 inhibits the growth of these pathogens, a desired trait considering the limited measures to combat these diseases. In this study, we determined the genetic background of the antibacterial activity of P482, and established the phylogenetic position of this strain. Pseudomonas sp. P482 was classified as Pseudomonas donghuensis. Genome mining revealed that the P482 genome does not contain genes determining the synthesis of known antimicrobials. However, the ClusterFinder algorithm, designed to detect atypical or novel classes of secondary metabolite gene clusters, predicted 18 such clusters in the genome. Screening of a Tn5 mutant library yielded an antimicrobial negative transposon mutant. The transposon insertion was located in a gene encoding an HpcH/HpaI aldolase/citrate lyase family protein. This gene is located in a hypothetical cluster predicted by the ClusterFinder, together with the downstream homologs of four nfs genes, that confer production of a non-fluorescent siderophore by P. donghuensis HYS(T). Site-directed inactivation of the HpcH/HpaI aldolase gene, the adjacent short chain dehydrogenase gene, as well as a homolog of an essential nfs cluster gene, all abolished the antimicrobial activity of the P482, suggesting their involvement in a common biosynthesis pathway. However, none of the mutants showed a decreased siderophore yield, neither was the antimicrobial activity of the wild type P482 compromised by high iron bioavailability. A genomic region comprising the nfs cluster and three upstream genes is involved in the antibacterial activity of P. donghuensis P482 against D. solani and P. carotovorum subsp. brasiliense. The genes studied are unique to the two known P. donghuensis strains. This study illustrates that mining of microbial genomes is a powerful approach for predictingthe presence of novel secondary-metabolite encoding genes especially when coupled with transposon mutagenesis

When genome-based approach meets the “Old but Good”: revealing genes involved in the antibacterial activity of Pseudomonas sp. P482 against soft rot pathogens

Dickeya solani and Pectobacterium carotovorum subsp. brasiliense are recently established species of bacterial plant pathogens causing black leg and soft rot of many vegetables and ornamental plants. Pseudomonas sp. strain P482 inhibits the growth of these pathogens, a desired trait considering the limited measures to combat these diseases. In this study, we determined the genetic background of the antibacterial activity of P482, and established the phylogenetic position of this strain. Pseudomonas sp. P482 was classified as Pseudomonas donghuensis. Genome mining revealed that the P482 genome does not contain genes determining the synthesis of known antimicrobials. However, the ClusterFinder algorithm, designed to detect atypical or novel classes of secondary metabolite gene clusters, predicted 18 such clusters in the genome. Screening of a Tn5 mutant library yielded an antimicrobial negative transposon mutant. The transposon insertion was located in a gene encoding an HpcH/HpaI aldolase/citrate lyase family protein. This gene is located in a hypothetical cluster predicted by the ClusterFinder, together with the downstream homologs of four nfs genes, that confer production of a non-fluorescent siderophore by P. donghuensis HYS(T). Site-directed inactivation of the HpcH/HpaI aldolase gene, the adjacent short chain dehydrogenase gene, as well as a homolog of an essential nfs cluster gene, all abolished the antimicrobial activity of the P482, suggesting their involvement in a common biosynthesis pathway. However, none of the mutants showed a decreased siderophore yield, neither was the antimicrobial activity of the wild type P482 compromised by high iron bioavailability. A genomic region comprising the nfs cluster and three upstream genes is involved in the antibacterial activity of P. donghuensis P482 against D. solani and P. carotovorum subsp. brasiliense. The genes studied are unique to the two known P. donghuensis strains. This study illustrates that mining of microbial genomes is a powerful approach for predictingthe presence of novel secondary-metabolite encoding genes especially when coupled with transposon mutagenesis

Молекулярно-генетическая идентификация возбудителей бактериальной водянки различных древесных пород

Объектом исследования явились образцы с пораженных бактериальной водянкой различных древесных пород : березы, лещины, ивы. В ходе данной работы были изучены ПДРФ-спектры локусов гена 16S pРНК бактериальной ДНК. Проведена видовая идентификация возбудителей бактериальной водянки на основании секвенирования гена 16S pРНК . Полученные результаты будут включены в молекулярно-генетическую базу патогенов Беларуси для разработки системы ранней диагностики и идентификации патогенов

Antagonistic, biofilm-forming rhizospheric Pseudomonas spp. isolated from Hail province

Background: The objectives of this study were to characterize Pseudomonas rhizospheric strains, that have a biocontrol activity, in rhizosphere soil in Hail province and study their ability to form biofilm.Methods: Rhizosphere soil samples were collected from rhizosphere of soil plantation areas, to be used for bacteria isolation. The identified bacteria were qualitatively tested for their ability to produce slime and subsequently develop biofilm.Results: The cultural and biochemical identification techniques, including morphological, biochemical and molecular methods revealed that the antagonistic bacteria- from the distinctive rhizosphere soil samples belong to Pseudomonas genus in particular, P. aeruginosa (PF1a, pf2a, PF-8) and P. putida (PF-7). These identified isolates inhibited Aspergillus niger development with percentage of parasitic growth inhibition greater than (48.095 ± 2.182)% for P. aeruginosa (pf-8). In addition, these identified isolates were significantly shown to be able to produce exopolysaccharide and subsequently develop biofilm on polystyrene and glass surfaces.Conclusion: Superior strains of these bio-control and plant growth promoting rhizobacteria will enable for better biological control of fungal and bacterial plant diseases and may reduce chemical pesticide usage. The indigenous strains isolated could potentially have a great impact on controlling plant diseases, in particular, those caused by microorganisms, and could be used as an alternative bio control agents instead of harmful chemical pesticides. Most of the tried microbes produced exopolysaccharides as well as formed biofilm on polystyrene and glass surfaces.Keywords: Biological control, Rhizosphere; Biofilm; Pseudomonas; Antimicrobial

Atividades de importação e exportação do Laboratório de Quarentena "Costa Lima" no período de 1991 a 2000.

Resumo: O Laboratório "Costa Lima", da Embrapa Meio Ambiente, realizou entre 1991 e 2000 170 introduções referentes a 42 espécies de organismos benéficos (6 fungos, 12 bactérias, 2 nematóides entomopatogênicos, 7 ácaros predadores, 13 insetos parasitóides e 2 insetos predadores) e de outros microrganismos. Este trabalho relata todas essas introduções e exportações oficiais de agentes de controle biológico e de outros organismos úteis.bitstream/item/131402/1/2001DC01.pdfNa publicação, ISSN incorreto 1516-4675

Interagency monitoring action plan (I-MAP) for quagga mussels in Lake Mead, Nevada-Arizona, USA

Following the discovery of quagga mussels in Lake Mead, Nevada-Arizona, USA, a variety of federal, state and regional agencies set up monitoring programs to evaluate and gain information to help minimize the impacts, or potential impacts, of quagga mussels to their facilities and lake ecology. While the agencies have worked closely and shared monitoring data and findings from the beginning of the infestation, there has been no documented comprehensive monitoring program to describe and record the various quagga mussel-related monitoring needs. Ad hoc interagency quagga mussel meeting representatives established an Interagency Monitoring Action Plan (I-MAP), which outlines agency objectives related to quagga mussel monitoring and provides approaches to realize these objectives. I-MAP team members and their respective agencies provide technical, logistical, and financial support in monitoring quagga mussels and their environmental impacts to Lake Mead. The goal of this effort is to develop a long-term, cost-effective, and consistent monitoring plan for quagga mussels in Lake Mead to inform various agencies and to gain efficiencies from shared operations and information. The plan attempts to build upon current monitoring activities and capabilities, identifies the next steps that can occur within existing capabilities and, finally, outlines gaps and areas of future need