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Christopher J Mungall Georgios V Gkoutos Cynthia L Smith Melissa A Haendel Suzanna E Lewis Michael Ashburner 《Genome biology》2010,11(1):R2
Phenotype ontologies are typically constructed to serve the needs of a particular community, such as annotation of genotype-phenotype
associations in mouse or human. Here we demonstrate how these ontologies can be improved through assignment of logical definitions
using a core ontology of phenotypic qualities and multiple additional ontologies from the Open Biological Ontologies library.
We also show how these logical definitions can be used for data integration when combined with a unified multi-species anatomy
ontology. 相似文献
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Androniki Psifidi Chrysostomos I. Dovas Georgios Bramis Thomai Lazou Claire L. Russel Georgios Arsenos Georgios Banos 《PloS one》2015,10(1)
Over the recent years, next generation sequencing and microarray technologies have revolutionized scientific research with their applications to high-throughput analysis of biological systems. Isolation of high quantities of pure, intact, double stranded, highly concentrated, not contaminated genomic DNA is prerequisite for successful and reliable large scale genotyping analysis. High quantities of pure DNA are also required for the creation of DNA-banks. In the present study, eleven different DNA extraction procedures, including phenol-chloroform, silica and magnetic beads based extractions, were examined to ascertain their relative effectiveness for extracting DNA from ovine blood samples. The quality and quantity of the differentially extracted DNA was subsequently assessed by spectrophotometric measurements, Qubit measurements, real-time PCR amplifications and gel electrophoresis. Processing time, intensity of labor and cost for each method were also evaluated. Results revealed significant differences among the eleven procedures and only four of the methods yielded satisfactory outputs. These four methods, comprising three modified silica based commercial kits (Modified Blood, Modified Tissue, Modified Dx kits) and an in-house developed magnetic beads based protocol, were most appropriate for extracting high quality and quantity DNA suitable for large-scale microarray genotyping and also for long-term DNA storage as demonstrated by their successful application to 600 individuals. 相似文献
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The aim of this study was to investigate the impact of early colonizing species on the structure and the composition of the bacterial community developing in a subgingival 10-species biofilm model system. The model included Streptococcus oralis, Streptococcus anginosus, Actinomycesoris, Fusobacterium nucleatum subsp. nucleatum, Veillonella dispar, Campylobacter rectus, Prevotella intermedia, Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola. Based on literature, we considered Streptococcus oralis, Streptococcus anginosus, and Actinomyces oris as early colonizers and examined their role in the biofilms by either a delayed addition to the consortium, or by not inoculating at all the biofilms with these species. We quantitatively evaluated the resulting biofilms by real-time quantitative PCR and further compared the structures using confocal laser scanning microscopy following fluorescence in situ hybridisation. The absence of the early colonizers did not hinder biofilm formation. The biofilms reached the same total counts and developed to normal thickness. However, quantitative shifts in the abundances of individual species were observed. In the absence of streptococci, the overall biofilm structure appeared looser and more dispersed. Moreover, besides a significant increase of P. intermedia and a decrease of P. gingivalis , P. intermedia appeared to form filamented long chains that resembled streptococci. A. oris, although growing to significantly higher abundance in absence of streptococci, did not have a visible impact on the biofilms. Hence, in the absence of the early colonizers, there is a pronounced effect on P. intermedia and P. gingivalis that may cause distinct shifts in the structure of the biofilm. Streptococci possibly facilitate the establishment of P. gingivalis into subgingival biofilms, while in their absence P. intermedia became more dominant and forms elongated chains. 相似文献
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McCool F. D.; Tzelepis G. E.; Leith D. E.; Hoppin F. G. Jr 《Journal of applied physiology》1989,66(5):2045-2055
When a subject breathes against an inspiratory resistance, the inspiratory pressure, the inspiratory flow, and the lung volume at which the breathing task takes place all interact to determine the length of time the task can be sustained (Tlim). We hypothesized that the mechanism actually limiting tasks in which these parameters were varied involved the rate of energy utilization by the inspiratory muscles. To test this hypothesis, we studied four experienced normal subjects during fatiguing breathing tasks performed over a range of pressures and flows and at two different lung volumes. We assessed energy utilization by measuring the increment in the rate of whole body O2 consumption due to the breathing task (VO2 resp). Power and mean esophageal pressure correlated with Tlim but depended also on lung volume and inspiratory flow rate. In contrast, VO2 resp closely correlated with Tlim, and this relationship was not systematically altered by inspiratory flow or lung volume. The shape of the VO2 resp vs. Tlim curve was approximately hyperbolic, with high rates of VO2 resp associated with short endurance times and lower rates of VO2 resp approaching an asymptotic value at high Tlim. These findings are consistent with a mechanism whereby a critical rate of energy utilization determines the endurance of the inspiratory pump, and that rate varies with pressure, flow, and lung volume. 相似文献
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Christos Arvanitidis Georgios Chatzigeorgiou Drosos Koutsoubas Theodoros Kevrekidis Costas Dounas Anastasios Eleftheriou Panayota Koulouri Athanasios Mogias 《Helgoland Marine Research》2005,59(3):177-186
An attempt is made to compare the results of different rapid biodiversity assessment techniques at the pan-Mediterranean, sectorial and local levels. A uniform multivariate pattern exists at the pan-Mediterranean and national (sectorial) levels: lagoons can be different when they host only a few species, but as species numbers increase, lagoons become homogenous in composition. Multivariate techniques cannot distinguish anthropogenically-impacted lagoons from those, which are naturally disturbed. In the pan-Mediterranean context it is the higher taxonomic levels, but in the national and local context it is the most abundant macrobenthic groups (polychaetes, molluscs and crustaceans) and meiobenthos which provide patterns closest to that derived from the species level. Taxonomic distinctness indices applied to polychaete and mollusc inventories provide meaningful results at most levels and scales of observation. These indices seem to be robust enough to discriminate anthropogenically impacted from naturally disturbed lagoons. 相似文献