262 research outputs found

    ZoomQuant: An application for the quantitation of stable isotope labeled peptides

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    The main goal of comparative proteomics is the quantitation of the differences in abundance of many proteins between two different biological samples in a single experiment. By differentially labeling the peptides from the two samples and combining them in a single analysis, relative ratios of protein abundance can be accurately determined. Protease catalyzed 18O exchange is a simple method to differentially label peptides, but the lack of robust software tools to analyze the data from mass spectra of 18O labeled peptides generated by common ion trap mass spectrometers has been a limitation. ZoomQuant is a stand-alone computational tool that analyzes the mass spectra of 18O labeled peptides from ion trap instruments and determines relative abundance ratios between two samples. Starting with a filtered list of candidate peptides that have been successfully identified by Sequest, ZoomQuant analyzes the isotopic forms of the peptides using high-resolution zoom scan spectrum data. The theoretical isotope distribution is determined from the peptide sequence and is used to deconvolute the peak areas associated with the unlabeled, partially labeled, and fully labeled species. The ratio between the labeled and unlabeled peptides is then calculated using several different methods. ZoomQuant’s graphical user interface allows the user to view and adjust the parameters for peak calling and quantitation and select which peptides should contribute to the overall abundance ratio calculation. Finally, ZoomQuant generates a summary report of the relative abundance of the peptides identified in the two samples

    Wrestling with tradition: revitalizing the Orkney chair and other culturally significant crafts

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    Across the world, "culturally significant" designs, products, and practices – such as traditional crafts – have been pushed to the margins by the forces of modernization and globalization. Appreciation of the positive attributes of these traditions drive widespread revitalization initiatives, often involving designers. Awareness of the cultural ramifications of design-led revitalization may deter enthusiasm for radical initiatives and instead promote preservation efforts. Yet a deconstruction of the popular understandings of tradition and origin indicates a need for change and cross-cultural contact. This article proposes that social value – central to a traditional craft's cultural significance – should be used to guide revitalization

    Flood resilience community pathfinder evaluation: rapid evidence assessment

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    The increase in the risk of flooding as a result of extreme weather and climate change makes it essential for local authorities and communities to engage with this issue. Defra is providing grant funding to 13 local authorities throughout England under a new Flood Resilience Community Pathfinder (FRCP) scheme aimed at stimulating community action to increase resilience. The measures being developed include property-level protection, flood resilience groups, volunteer flood wardens and community champions, engagement with more vulnerable groups and efforts to increase financial resilience

    Dietary soy and meat proteins induce distinct physiological and gene expression changes in rats

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    This study reports on a comprehensive comparison of the effects of soy and meat proteins given at the recommended level on physiological markers of metabolic syndrome and the hepatic transcriptome. Male rats were fed semi-synthetic diets for 1 wk that differed only regarding protein source, with casein serving as reference. Body weight gain and adipose tissue mass were significantly reduced by soy but not meat proteins. The insulin resistance index was improved by soy, and to a lesser extent by meat proteins. Liver triacylglycerol contents were reduced by both protein sources, which coincided with increased plasma triacylglycerol concentrations. Both soy and meat proteins changed plasma amino acid patterns. The expression of 1571 and 1369 genes were altered by soy and meat proteins respectively. Functional classification revealed that lipid, energy and amino acid metabolic pathways, as well as insulin signaling pathways were regulated differently by soy and meat proteins. Several transcriptional regulators, including NFE2L2, ATF4, Srebf1 and Rictor were identified as potential key upstream regulators. These results suggest that soy and meat proteins induce distinct physiological and gene expression responses in rats and provide novel evidence and suggestions for the health effects of different protein sources in human diets

    Performance of a Large-Area GEM Detector Prototype for the Upgrade of the CMS Muon Endcap System

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    Gas Electron Multiplier (GEM) technology is being considered for the forward muon upgrade of the CMS experiment in Phase 2 of the CERN LHC. Its first implementation is planned for the GE1/1 system in the 1.5<η<2.21.5 < \mid\eta\mid < 2.2 region of the muon endcap mainly to control muon level-1 trigger rates after the second long LHC shutdown. A GE1/1 triple-GEM detector is read out by 3,072 radial strips with 455 μ\murad pitch arranged in eight η\eta-sectors. We assembled a full-size GE1/1 prototype of 1m length at Florida Tech and tested it in 20-120 GeV hadron beams at Fermilab using Ar/CO2_{2} 70:30 and the RD51 scalable readout system. Four small GEM detectors with 2-D readout and an average measured azimuthal resolution of 36 μ\murad provided precise reference tracks. Construction of this largest GEM detector built to-date is described. Strip cluster parameters, detection efficiency, and spatial resolution are studied with position and high voltage scans. The plateau detection efficiency is [97.1 ±\pm 0.2 (stat)]\%. The azimuthal resolution is found to be [123.5 ±\pm 1.6 (stat)] μ\murad when operating in the center of the efficiency plateau and using full pulse height information. The resolution can be slightly improved by \sim 10 μ\murad when correcting for the bias due to discrete readout strips. The CMS upgrade design calls for readout electronics with binary hit output. When strip clusters are formed correspondingly without charge-weighting and with fixed hit thresholds, a position resolution of [136.8 ±\pm 2.5 stat] μ\murad is measured, consistent with the expected resolution of strip-pitch/12\sqrt{12} = 131.3 μ\murad. Other η\eta-sectors of the detector show similar response and performance.Comment: 8 pages, 32 figures, submitted to Proc. 2014 IEEE Nucl. Sci. Symposium, Seattle, WA, reference adde
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