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排序方式: 共有235条查询结果,搜索用时 31 毫秒
81.
Yu Qian Olga Tchuvatkina Josef Spidlen Peter Wilkinson Maura Gasparetto Andrew R Jones Frank J Manion Richard H Scheuermann Rafick-Pierre Sekaly Ryan R Brinkman 《BMC bioinformatics》2009,10(1):184-7
Background
Flow cytometry technology is widely used in both health care and research. The rapid expansion of flow cytometry applications has outpaced the development of data storage and analysis tools. Collaborative efforts being taken to eliminate this gap include building common vocabularies and ontologies, designing generic data models, and defining data exchange formats. The Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) standard was recently adopted by the International Society for Advancement of Cytometry. This standard guides researchers on the information that should be included in peer reviewed publications, but it is insufficient for data exchange and integration between computational systems. The Functional Genomics Experiment (FuGE) formalizes common aspects of comprehensive and high throughput experiments across different biological technologies. We have extended FuGE object model to accommodate flow cytometry data and metadata. 相似文献82.
Consequences of variation in species diversity in a community of root-feeding herbivores for nematode dynamics and host plant biomass 总被引:5,自引:0,他引:5
To date, no study has explicitly addressed effects of variation in species diversity of root‐feeding herbivores on host plant biomass. Root‐feeding nematodes typically occur in multi‐species communities. In a three‐year field experiment, we investigated how variation in species diversity of root‐feeding nematodes affected nematode dynamics and response of the dune grass Ammophila arenaria to root‐feeder activity. This plant species needs regular burial by fresh beach sand to remain vigorous, suggesting that A. arenaria benefits from a temporary escape from root‐feeding soil organisms and that root‐feeders are involved in plant degeneration in stabilized dunes. We created series of ceased and continued sand burial and added the endoparasitic nematodes Meloidogyne maritima, Heterodera arenaria and Pratylenchus penetrans alone or in combination to A. arenaria. We included treatments with and without the whole soil community, measured plant biomass and quantified numbers of nematodes. Addition of H. arenaria and P. penetrans decreased numbers of M. maritima juveniles and delayed the first appearance in time of both juveniles and females, while numbers of males only decreased when plants had been buried. Burial with sand and addition of the other two endoparasites affected numbers of H. arenaria juveniles, while numbers of P. penetrans were low and not affected. Shoot biomass of A. arenaria was lower when M. maritima had been added alone than when the three species had been added together. Addition of root zone soil decreased biomass of all plant parts. Burial with sand decreased aboveground shoot biomass, whereas it increased belowground shoot and root biomass. Our results point at idiosyncratic effects of nematode diversity on A. arenaria biomass. Heterodera arenaria and P. penetrans protected their host by reducing numbers and delaying activity of M. maritima to a later stage in the growth season, when root‐feeding activity was less harmful for plant biomass development. 相似文献
83.
84.
Minggang Wang Arjen Biere Wim H. van der Putten T. Martijn Bezemer E. Pernilla Brinkman 《Plant and Soil》2017,412(1-2):215-233
Aims
A soil-plant-atmosphere continuum (SPAC) model for simulating tree transpiration (Ep) with variable water stress and water distribution in the soil is presented. The model couples a sun/shade approach for the canopy with a discrete representation of the soil in different layers and compartments.Methods
To test its performance, the outputs from the simulations are compared to those from an experiment using trees of olive ‘Picual’ and almond ‘Marinada’ with the root system split into two. Trees are subjected to different irrigation phases in which one side of the root system is dried out while the other is kept wet.Results
The model is able to accurately predict Ep (R2 and the efficiency factor (EF) around 0.9) in the two species studied. The use of a function that modulates the uptake capacity of a root according to the soil water content was necessary to track the fluxes observed from each split part. It was also appropriate to account for root clumping to match the measured and modelled leaf water potential.Conclusions
Coupling the sun/shade approach with the soil multi-compartment solution provides a useful tool to explore tree Ep for different degrees of water availability and distribution.85.
Minggang Wang T. Martijn Bezemer Wim H. van der Putten E. Pernilla Brinkman Arjen Biere 《Journal of Plant Ecology》2018,11(5):696
Aims
Plants use different types of responses such as tolerance and induced defense to mitigate the effects of herbivores. The direction and magnitude of both these plant responses can vary with plant age. However, most studies have focused on aboveground herbivory, whereas important feeding occurs belowground. Here, we tested the hypothesis that plant tolerance and defense following shoot damage or root herbivory depends on plant age. 相似文献
86.
87.
Federica Villanova Paola Di Meglio Margaret Inokuma Nima Aghaeepour Esperanza Perucha Jennifer Mollon Laurel Nomura Maria Hernandez-Fuentes Andrew Cope A. Toby Prevost Susanne Heck Vernon Maino Graham Lord Ryan R. Brinkman Frank O. Nestle 《PloS one》2013,8(7)
Discovery of novel immune biomarkers for monitoring of disease prognosis and response to therapy in immune-mediated inflammatory diseases is an important unmet clinical need. Here, we establish a novel framework for immunological biomarker discovery, comparing a conventional (liquid) flow cytometry platform (CFP) and a unique lyoplate-based flow cytometry platform (LFP) in combination with advanced computational data analysis. We demonstrate that LFP had higher sensitivity compared to CFP, with increased detection of cytokines (IFN-γ and IL-10) and activation markers (Foxp3 and CD25). Fluorescent intensity of cells stained with lyophilized antibodies was increased compared to cells stained with liquid antibodies. LFP, using a plate loader, allowed medium-throughput processing of samples with comparable intra- and inter-assay variability between platforms. Automated computational analysis identified novel immunophenotypes that were not detected with manual analysis. Our results establish a new flow cytometry platform for standardized and rapid immunological biomarker discovery with wide application to immune-mediated diseases. 相似文献
88.
Nolwenn Le Meur Anthony Rossini Maura Gasparetto Clay Smith Ryan R Brinkman Robert Gentleman 《Cytometry. Part A》2007,71(6):393-403
BACKGROUND: The recent development of semiautomated techniques for staining and analyzing flow cytometry samples has presented new challenges. Quality control and quality assessment are critical when developing new high throughput technologies and their associated information services. Our experience suggests that significant bottlenecks remain in the development of high throughput flow cytometry methods for data analysis and display. Especially, data quality control and quality assessment are crucial steps in processing and analyzing high throughput flow cytometry data. METHODS: We propose a variety of graphical exploratory data analytic tools for exploring ungated flow cytometry data. We have implemented a number of specialized functions and methods in the Bioconductor package rflowcyt. We demonstrate the use of these approaches by investigating two independent sets of high throughput flow cytometry data. RESULTS: We found that graphical representations can reveal substantial nonbiological differences in samples. Empirical Cumulative Distribution Function and summary scatterplots were especially useful in the rapid identification of problems not identified by manual review. CONCLUSIONS: Graphical exploratory data analytic tools are quick and useful means of assessing data quality. We propose that the described visualizations should be used as quality assessment tools and where possible, be used for quality control. 相似文献
89.
Whitehouse DB; Tomkins J; Lovegrove JU; Hopkinson DA; McMillan WO 《Molecular biology and evolution》1998,15(4):456-462
The expanding molecular database provides unparalleled opportunities for
characterizing genes and for studying groups of related genes. We use
sequences drawn from the database to construct an evolutionary framework
for examining the important glycolytic enzyme phosphoglucomutase (PGM).
Phosphoglucomutase plays a pivotal role in the synthesis and utilization of
glycogen and is present in all organisms. In humans, there are three
well-described isozymes, PGMI, PGM2, and PGM3. PGM1 was cloned 5 years ago;
however, repeated attempts using both immunological approaches and
molecular probes designed from PGM1 have failed to isolate either PGM2 or
PGM3. Using a phylogenetic strategy, we first identified 47 highly
divergent prokaryotic and eukaryotic PGM-like sequences from the database.
Although overall amino acid identity often fell below 20%, the relative
order, position, and sequence of three structural motifs, the active site
and the magnesium-- and sugar-binding sites, were conserved in all 47
sequences. The phylogenetic history of these sequences was complex and
marked by duplications and translocations; two instances of transkingdom
horizontal gene transfer were identified. Nonetheless, the sequences fell
within six well-defined evolutionary lineages, three of which contained
only prokaryotes. Of the two prokaryotic/eukaryotic lineages, one contained
bacterial, yeast, slimemold, invertebrate, and vertebrate homologs to human
PGM1 and the second contained likely homologs to human PGM2. Indeed, an
amino acid sequence, derived from a partial human cDNA, that fell within
the second cross-kingdom lineage bears several characteristics expected for
PGM2. A third lineage may contain homologs to human PGM3. On a general
level, our phylogenetic-based approach shows promise for the further
utilization of the extensive molecular database.
相似文献
90.
Incorporation of axonally transported glycoproteins into axolemma during nerve regeneration 总被引:14,自引:4,他引:10
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The insertion of axonally transported fucosyl glycoproteins into the axolemma of regenerating nerve sprouts was examined in rat sciatic motor axons at intervals after nerve crush. [(3)H]Fucose was injected into the lumbar ventral horns and the nerves were removed at intervals between 1 and 14 d after labeling. To follow the fate of the “pulse- labeled” glycoproteins, we examined the nerves by correlative radiometric and EM radioautographic approaches. The results showed, first, that rapidly transported [(3)H]fucosyl glycoproteins were inserted into the axolemma of regenerating sprouts as well as parent axons. At 1 d after delivery, in addition to the substantial mobile fraction of radioactivity still undergoing bidirectional transport within the axon, a fraction of label was already associated with the axolemma. Insertion of labeled glycoproteins into the sprout axolemma appeared to occur all along the length of the regenerating sprouts, not just in sprout terminals. Once inserted, labeled glycoproteins did not undergo extensive redistribution, nor did they appear in sprout regions that formed (as a result of continued outgrowth) after their insertion. The amount of radioactivity in the regenerating nerves decreased with time, in part as a result of removal of transported label by retrograde transport. By 7-14 d after labeling, radioautography showed that almost all the remaining radioactivity was associated with axolemma. The regenerating sprouts retained increased amounts of labeled glycoproteins; 7 or 14 d after labeling, the regenerating sprouts had over twice as much of radioactivity as comparable lengths of control nerves or parent axons. One role of fast axonal transport in nerve regeneration is the contribution to the regenerating sprout of glycoproteins inserted into the axolemma; these membrane elements are added both during longitudinal outgrowth and during lateral growth and maturation of the sprout. 相似文献