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101.
YPED:An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research
Christopher M.Colangelo Mark Shifman Kei-Hoi Cheung Kathryn L.Stone Nicholas J.Carriero Erol E.Gulcicek TuKiet T.Lam Terence Wu Robert D.Bjornson Can Bruce Angus C.Nairn Jesse Rinehart Perry L.Miller Kenneth R.Williams 《基因组蛋白质组与生物信息学报(英文版)》2015,13(1):25-35
We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database(YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry(LC–MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring(MRM)/selective reaction monitoring(SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results. 相似文献
102.
Elisa Damiani Erica Adrario Michele Maria Luchetti Claudia Scorcella Andrea Carsetti Nicoletta Mininno Silvia Pierantozzi Tiziana Principi Daniele Strovegli Rosella Bencivenga Armando Gabrielli Rocco Romano Paolo Pelaia Can Ince Abele Donati 《PloS one》2015,10(5)
BackgroundFree hemoglobin (fHb) may induce vasoconstriction by scavenging nitric oxide. It may increase in older blood units due to storage lesions. This study evaluated whether old red blood cell transfusion increases plasma fHb in sepsis and how the microvascular response may be affected.MethodsThis is a secondary analysis of a randomized study. Twenty adult septic patients received either fresh or old (<10 or >15 days storage, respectively) RBC transfusions. fHb was measured in RBC units and in the plasma before and 1 hour after transfusion. Simultaneously, the sublingual microcirculation was assessed with sidestream-dark field imaging. The perfused boundary region was calculated as an index of glycocalyx damage. Tissue oxygen saturation (StO2) and Hb index (THI) were measured with near-infrared spectroscopy and a vascular occlusion test was performed.ResultsSimilar fHb levels were found in the supernatant of fresh and old RBC units. Despite this, plasma fHb increased in the old RBC group after transfusion (from 0.125 [0.098–0.219] mg/mL to 0.238 [0.163–0.369] mg/mL, p = 0.006). The sublingual microcirculation was unaltered in both groups, while THI increased. The change in plasma fHb was inversely correlated with the changes in total vessel density (r = -0.57 [95% confidence interval -0.82, -0.16], p = 0.008), De Backer score (r = -0.63 [95% confidence interval -0.84, -0.25], p = 0.003) and THI (r = -0.72 [95% confidence interval -0.88, -0.39], p = 0.0003).ConclusionsOld RBC transfusion was associated with an increase in plasma fHb in septic patients. Increasing plasma fHb levels were associated with decreased microvascular density.
Trial Registration
ClinicalTrials.gov NCT01584999相似文献103.
Oxygenation measurement by multi‐wavelength oxygen‐dependent phosphorescence and delayed fluorescence: catchment depth and application in intact heart 下载免费PDF全文
Gianmarco M. Balestra Maurice C.G. Aalders Patricia A.C. Specht Can Ince Egbert G. Mik 《Journal of biophotonics》2015,8(8):615-628
Oxygen delivery and metabolism represent key factors for organ function in health and disease. We describe the optical key characteristics of a technique to comprehensively measure oxygen tension (PO2) in myocardium, using oxygen‐dependent quenching of phosphorescence and delayed fluorescence of porphyrins, by means of Monte Carlo simulations and ex vivo experiments. Oxyphor G2 (microvascular PO2) was excited at 442 nm and 632 nm and protoporphyrin IX (mitochondrial PO2) at 510 nm. This resulted in catchment depths of 161 (86) µm, 350 (307) µm and 262 (255) µm respectively, as estimated by Monte Carlo simulations and ex vivo experiments (brackets). The feasibility to detect changes in oxygenation within separate anatomical compartments is demonstrated in rat heart in vivo.
104.
Post‐translational modifications of transthyretin affect the triiodonine‐binding potential 下载免费PDF全文
Andrea Henze Thomas Homann Mustafa Serteser Ozge Can Ozlem Sezgin Abdurrahman Coskun Ibrahim Unsal Florian J. Schweigert Aysel Ozpinar 《Journal of cellular and molecular medicine》2015,19(2):359-370
Transthyretin (TTR) is a visceral protein, which facilitates the transport of thyroid hormones in blood and cerebrospinal fluid. The homotetrameric structure of TTR enables the simultaneous binding of two thyroid hormones per molecule. Each TTR subunit provides a single cysteine residue (Cys10), which is frequently affected by oxidative post‐translational modifications. As Cys10 is part of the thyroid hormone‐binding channel within the TTR molecule, PTM of Cys10 may influence the binding of thyroid hormones. Therefore, we analysed the effects of Cys10 modification with sulphonic acid, cysteine, cysteinylglycine and glutathione on binding of triiodothyronine (T3) by molecular modelling. Furthermore, we determined the PTM pattern of TTR in serum of patients with thyroid disease by immunoprecipitation and mass spectrometry to evaluate this association in vivo. The in silico assays demonstrated that oxidative PTM of TTR resulted in substantial reorganization of the intramolecular interactions and also affected the binding of T3 in a chemotype‐ and site‐specific manner with S‐glutathionylation as the most potent modulator of T3 binding. These findings were supported by the in vivo results, which indicated thyroid function‐specific patterns of TTR with a substantial decrease in S‐sulphonated, S‐cysteinylglycinated and S‐glutathionylated TTR in hypothyroid patients. In conclusion, this study provides evidence that oxidative modifications of Cys10 seem to affect binding of T3 to TTR probably because of the introduction of a sterical hindrance and induction of conformational changes. As oxidative modifications can be dynamically regulated, this may represent a sensitive mechanism to adjust thyroid hormone availability. 相似文献
105.
Jie Cheng Miook Cho Jin-ming Cen Meng-yun Cai Shun Xu Ze-wei Ma Xinguang Liu Xi-li Yang Can Chen Yousin Suh Xing-dong Xiong 《PloS one》2015,10(2)
SIRT1 exerts protective effects against endothelial cells dysfunction, inflammation and atherosclerosis, indicating an important role on myocardial infarction (MI) pathogenesis. Nonetheless, the effects of SIRT1 variants on MI risk remain poorly understood. Here we aimed to investigate the influence of SIRT1 polymorphisms on individual susceptibility to MI. Genotyping of three tagSNPs (rs7069102, rs3818292 and rs4746720) in SIRT1 gene was performed in a Chinese Han population, consisting of 287 MI cases and 654 control subjects. In a logistic regression analysis, we found that G allele of rs7069102 had increased MI risk with odds ratio (OR) of 1.57 [95% confidence interval (CI) = 1.15–2.16, Bonferroni corrected P (Pc) = 0.015] after adjustment for conventional risk factors compared to C allele. Similarly, the combined CG/GG genotypes was associated with the increased MI risk (OR = 1.64, 95% CI = 1.14–2.35, Pc = 0.021) compared to the CC genotype. Further stratified analysis revealed a more significant association with MI risk among younger subjects (≤ 55 years old). Consistent with these results, the haplotype rs7069102G-rs3818292A-rs4746720T containing the rs7069102 G allele was also associated with the increased MI risk (OR = 1.41, 95% CI = 1.09–1.84, Pc = 0.040). However, we did not detect any association of rs3818292 and rs4746720 with MI risk. Our study provides the first evidence that the tagSNP rs7069102 and haplotype rs7069102G-rs3818292A-rs4746720T in SIRT1 gene confer susceptibility to MI in the Chinese Han population. 相似文献
106.
Construction of a Bacillus thuringiensis engineered strain with high toxicity and broad pesticidal spectrum against coleopteran insects 总被引:1,自引:0,他引:1
Jingjing Liu Guixin Yan Changlong Shu Can Zhao Chunqin Liu Fuping Song Lin Zhou Junlan Ma Jie Zhang Dafang Huang 《Applied microbiology and biotechnology》2010,87(1):243-249
A newly engineered strain, denominated BIOT185, was constructed through integrating the cry8Ca2 gene into the endogenous plasmid of BT185 (contains cry8Ea1) by homologous recombination. The thermosensitive plasmid vector was eliminated by the rising temperature of recombinant
cultures. No antibiotic gene or other unnecessary genes were introduced to the new strain. Sodium dodecyl sulfate–polyacrylamide
gel electrophoresis and Western blot analysis demonstrated that the cry8Ca2 gene was expressed normally and produced a 130-kDa protein in the BIOT185 strain. Bioassay results showed that the new strain
had high toxicity to the pests Anomala corpulenta and Holotrichia parallela, which often damage the same fields. 相似文献
107.
Duman F Aksoy A Ozturk F Ceylan A 《Zeitschrift für Naturforschung. C, Journal of biosciences》2010,65(11-12):675-680
Previous studies have shown that salicylates can change the ion permeability of root cells. Therefore the possible effects of exogenous salicylate application on lead (Pb) and copper (Cu) accumulation and its protective role against DNA damage due to metal exposure in Lemna gibba were studied. L. gibba was exposed to 5, 10, and 25 microM Pb and Cu for six days in the presence and absence of sodium salicylate (SA) (0.1, 0.5, and 1 mM). At all concentrations tested, SA application decreased Pb accumulation. On the other hand, application of 0.5 mM SA increased Cu accumulation. SA did not reduce DNA damage resulting from Pb and Cu toxicity. In summary, SA may be useful for reducing Pb accumulation, and application of SA at 0.5 mM may be useful for the phytoextraction of Cu. 相似文献
108.
Britt-Marie Swahn David Wensbo Johan Sandell Daniel Sohn Can Slivo David Pyring Jonas Malmström Erwan Arzel Michaela Vallin Margareta Bergh Fredrik Jeppsson Allan E. Johnson Anders Juréus Jan Neelissen Samuel Svensson 《Bioorganic & medicinal chemistry letters》2010,20(6):1976-1980
The syntheses and SAR of new series of β-amyloid binding agents are reported. The effort to optimize signal-to-background ratios for these ligands are described. Compounds 8, 21 and 30 displayed desirable lipophilicity and pharmacokinetic properties. Compounds 8 and 21 were evaluated with in vitro autoradiographic studies and in vivo in APP/PS1 transgenic mice. It is shown that it was possible to increase the signal-to-background ratios compared to PIB 1, as demonstrated by compounds 8 and 21. 相似文献
109.
Betul Can Gulnihal Kulaksiz Erkmen Ozlem Dalmizrak I. Hamdi Ogus Nazmi Ozer 《The protein journal》2010,29(4):250-256
Glutathione reductase [GR, E.C.1.8.1.7] catalyses NADPH dependent reduction of glutathione disulfide (GSSG) to reduced glutathione
(GSH). Thus, it is the crucial enzyme to maintain high [GSH]/[GSSG] ratio and physiological redox status in cells. Kidney
and liver tissues were considered as a rich source of GR. In this study, rat kidney GR was purified and some of its properties
were investigated. The enzyme was purified 2,356 fold with a yield of 16% by using heat-denaturation and Sephadex G25 gel
filtration, 2′,5′-ADP Agarose 4B, PBE94 column chromatographies. The purified enzyme had a specific activity (Vm) of 250 U/mg protein and the ratio of absorbances at wavelengths of A
273/A
463,
A
280/A
460, A
365/A
460, and A
379/A
463, were 7.1, 6.8, 1.2 and 1.0, respectively. Each mol of GR subunit bound 0.97 mol of FAD. NADH was used as a coenzyme by rat
kidney GR but with a lower efficiency (32.7%) than NADPH. Its subunit molecular weight was estimated as 53 kDa. An optimum
pH of 6.5 and optimum temperature of 65 °C were found for rat kidney GR. Its activation energy (Ea) and temperature coefficient
(Q10) were calculated as 7.02 kcal/mol and 1.42, respectively. The Km(NADPH) and kcat/Km (NADPH) values were found to be 15.3 ± 1.4 μM and 1.68 × 107 M−1 s−1 for the concentration range of 10-200 μM NADPH and when GSSG is the variable substrate, the Km(GSSG) and the kcat/Km(GSSG) values of 53.1 ± 3.4 μM and 4.85 × 106 M−1 s−1 were calculated for the concentration range of 20–1,200 μM GSSG. 相似文献
110.