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Biological imaging is now a quantitative technique for probing cellular structure and dynamics and is increasingly used for cell-based screens. However, the bioinformatics tools required for hypothesis-driven analysis of digital images are still immature. We are developing the Open Microscopy Environment (OME) as an informatics solution for the storage and analysis of optical microscope image data. OME aims to automate image analysis, modeling, and mining of large sets of images and specifies a flexible data model, a relational database, and an XML-encoded file standard that is usable by potentially any software tool. With this design, OME provides a first step toward biological image informatics. 相似文献
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A greenhouse experiment was conducted by growing oats (Avenasativa L.) in a continuously 13CO2 labeled atmosphere. The allocation of 13C-labeled photosynthates in plants, microbial biomass in rhizosphere and root-free soil, pools of soil organic C, and CO2 emissions were examined over the plant's life cycle. To isolate rhizosphere from root-free soil, plant seedlings were placed into bags made of nylon monofilament screen tissue (16 μm mesh) filled with soil. Two peaks of 13C in rhizosphere pools of microbial biomass and dissolved organic carbon (DOC), as well as in CO2 emissions at the earing and ripeness stages were revealed. These 13C maxima corresponded to: (i) the end of rapid root growth and (ii) beginning of root decomposition, respectively. The δ13C values of microbial biomass were higher than those of DOC and of soil organic matter (SOM). The microbial biomass C accounted for up to 56 and 39% of 13C recovered in the rhizosphere and root-free soil, respectively. Between 4 and 28% of 13C assimilated was recovered in the root-free soil. Depending on the phenological stage, the contribution of root-derived C to total CO2 emission from soil varied from 61 to 92% of total CO2 evolved, including 4-23% attributed to rhizomicrobial respiration. While 81-91% of C substrates used for microbial growth in the root-free soil and rhizosphere came from SOM, the remaining 9-19% of C substrates utilized by the microbial biomass was attributable to rhizodeposition. The use of continuous isotopic labelling and physical separation of root-free and rhizosphere soil, combined with natural 13C abundance were effective in gaining new insight on soil and rhizosphere C-cycling. 相似文献
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Structured water molecules near redox cofactors were found recently to accelerate electron-transfer (ET) kinetics in several systems. Theoretical study of interprotein electron transfer across an aqueous interface reveals three distinctive electronic coupling mechanisms that we describe here: (i) a protein-mediated regime when the two proteins are in van der Waals contact; (ii) a structured water-mediated regime featuring anomalously weak distance decay at relatively close protein-protein contact distances; and (iii) a bulk water-mediated regime at large distances. Our analysis explains a range of otherwise puzzling biological ET kinetic data and provides a framework for including explicit water-mediated tunneling effects on ET kinetics. 相似文献
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Phytochemical composition and metabolic performance-enhancing activity of dietary berries traditionally used by Native North Americans 总被引：1，自引：0，他引：1
Burns Kraft TF Dey M Rogers RB Ribnicky DM Gipp DM Cefalu WT Raskin I Lila MA 《Journal of agricultural and food chemistry》2008,56(3):654-660
Four wild berry species, Amelanchier alnifolia, Viburnum trilobum, Prunus virginiana, and Shepherdia argentea, all integral to the traditional subsistence diet of Native American tribal communities, were evaluated to elucidate phytochemical composition and bioactive properties related to performance and human health. Biological activity was screened using a range of bioassays that assessed the potential for these little-known dietary berries to affect diabetic microvascular complications, hyperglycemia, pro-inflammatory gene expression, and metabolic syndrome symptoms. Nonpolar constituents from berries, including carotenoids, were potent inhibitors of aldose reductase (an enzyme involved in the etiology of diabetic microvascular complications), whereas the polar constituents, mainly phenolic acids, anthocyanins, and proanthocyanidins, were hypoglycemic agents and strong inhibitors of IL-1beta and COX-2 gene expression. Berry samples also showed the ability to modulate lipid metabolism and energy expenditure in a manner consistent with improving metabolic syndrome. The results demonstrate that these berries traditionally consumed by tribal cultures contain a rich array of phytochemicals that have the capacity to promote health and protect against chronic diseases, such as diabetes. 相似文献
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Ilya V. Senechkin Leonard S. van Overbeek Hong Ling Er Oscar de Vos Ariena H. C. van Bruggen 《European journal of plant pathology / European Foundation for Plant Pathology》2013,136(4):789-802
Collimonas sp. IS343, isolated from an organically-farmed arable soil and characterized as a broad-range oligotrophic bacterium, was shown to degrade chitin and to suppress R. solani mycelium growth under in vitro conditions at high and low carbon availabilities. In contrast to C. fungivorans Ter331, strain IS343 did not respond with an increase in growth rate to higher carbon levels in liquid medium, it reached higher cell numbers in carbon-poor media and it showed better survival in bulk soil. Therefore, it was concluded that strain IS343 cells are better adapted to circumstances of low carbon availability as present in bulk soils than strain Ter331 cells. Further, strain IS343 cells were more suppressive towards R. solani than strain Ter331 cells in vitro. When introduced into soil, strain IS343 cells delayed disease development caused by R. solani AG2-2IIIB in sugar beet plants. These results suggest that strain IS343 cells are able to tentatively suppress R. solani AG2-2IIIB mycelium growth in soil. Potential mechanisms behind the observed suppressive effects can be competition for available nutrients between strain IS343 cells and R. solani mycelium in soil or the production of chitinase as shown for this and other Collimonas species. 相似文献
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An aqueous ethanol extract of Bergenia crassifolia rhizomes strongly inhibited human pancreatic lipase activity and increased scavenging of DPPH free radicals in vitro. Chromatographic separation of this extract led to isolation of the hydrolysable tannins (+)-catechin 3,5-di-O-gallate () and (+)-catechin 3-O-gallate (). This is the first report of the isolation of compound 1 from plant material. This compound strongly inhibited human pancreatic lipase (with an IC50 value of 0.42 μg/ml) and exhibited a remarkable free radical-scavenging ability (with an SC50 value of 1.04 μg/ml). The chemical structures of 1 and 2 were elucidated using MS, NMR and chemical approaches. 相似文献
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Ethanolic extracts of diploid Artemisia dracunculus L. (wild tarragon) from populations in the U.S., and polyploid tarragon from a variety of sources, were screened for the anti-diabetic compounds davidigenin; sakuranetin; 2’,4’-dihydroxy-4-methoxydihydrochalcone; 4,5-di-O-caffeoylquinic acid; 5-O-caffeoylquinic acid and 6-demethoxycapillarisin using LC-MS. Only decaploid plants contained all six target compounds and were the only plants that contained davidigenin and 2,4-dihydroxy-4-methoxydihydrochalcone. These results exhibit the importance of germplasm selection and provenance when studying plants for medicinal activity. Relying only on the “right species” for consistent medicinal activities may not be sufficient, as intraspecific variation may be highly significant. 相似文献
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Molecular noise restricts the ability of an individual cell to resolve input signals of different strengths and gather information about the external environment. Transmitting information through complex signaling networks with redundancies can overcome this limitation. We developed an integrative theoretical and experimental framework, based on the formalism of information theory, to quantitatively predict and measure the amount of information transduced by molecular and cellular networks. Analyzing tumor necrosis factor (TNF) signaling revealed that individual TNF signaling pathways transduce information sufficient for accurate binary decisions, and an upstream bottleneck limits the information gained via multiple integrated pathways. Negative feedback to this bottleneck could both alleviate and enhance its limiting effect, despite decreasing noise. Bottlenecks likewise constrain information attained by networks signaling through multiple genes or cells. 相似文献
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Philip W. Atkinson Graham E. Austin Mark M. Rehfisch Helen Baker Peter Cranswick Mel Kershaw James Robinson Rowena H.W. Langston David A. Stroud Chris Van Turnhout Ilya M.D. Maclean 《Biological conservation》2006,130(4):549-559
To manage and conserve wildlife populations effectively it is necessary to use methods that identify the often non-linear trends in populations, have an inbuilt assessment of trend quality and can analyse count data from a range of spatial scales. We present a method of trend analysis using generalised additive models. These produce smoothed indices of abundance that can be used to assess population change from one or more sites or time periods, with any number of estimates of abundance per index period. We apply this method to count data collected under the Wetland Bird Survey, a national scheme that monitors waterbirds in the United Kingdom. To highlight declining populations, ‘alerts’ were raised if the population decline was equal to or greater than 50%. Significance was determined using bootstrapped confidence intervals for analyses that included many sites, or a novel Monte-Carlo method for single site analyses. The impact of missing data, species count variability and the number of months used to calculate the population change was greater at individual sites than for national datasets, which were relatively insensitive to changes in the above parameters. For single sites it is essential that three or more counts be made per index period if reliable estimates of population change are required. We propose that the method presented could be applied to a wide range of national or other monitoring schemes for a variety of taxa. 相似文献