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Unrestricted modification search reveals lysine methylation as major modification induced by tissue formalin fixation and paraffin embedding 下载免费PDF全文
Bo Xu Yutaka Yoshida Oliver Horlacher Frederic Nikitin Samuel Garessus Sameh Magdeldin Naohiko Kinoshita Hidehiko Fujinaka Eishin Yaoita Miki Hasegawa Frederique Lisacek Tadashi Yamamoto 《Proteomics》2015,15(15):2568-2579
Formalin‐fixed paraffin‐embedded (FFPE) tissue is considered as an appropriate alternative to frozen/fresh tissue for proteomic analysis. Here we study formalin‐induced alternations on a proteome‐wide level. We compared LC‐MS/MS data of FFPE and frozen human kidney tissues by two methods. First, clustering analysis revealed that the biological variation is higher than the variation introduced by the two sample processing techniques and clusters formed in accordance with the biological tissue origin and not with the sample preservation method. Second, we combined open modification search and spectral counting to find modifications that are more abundant in FFPE samples compared to frozen samples. This analysis revealed lysine methylation (+14 Da) as the most frequent modification induced by FFPE preservation. We also detected a slight increase in methylene (+12 Da) and methylol (+30 Da) adducts as well as a putative modification of +58 Da, but they contribute less to the overall modification count. Subsequent SEQUEST analysis and X!Tandem searches of different datasets confirmed these trends. However, the modifications due to FFPE sample processing are a minor disturbance affecting 2–6% of all peptide‐spectrum matches and the peptides lists identified in FFPE and frozen tissues are still highly similar. 相似文献
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Distinct Roles of Urinary Liver-Type Fatty Acid-Binding Protein in Non-Diabetic Patients with Anemia
Naohiko Imai Takashi Yasuda Atsuko Kamijo-Ikemori Yugo Shibagaki Kenjiro Kimura 《PloS one》2015,10(5)
BackgroundVarious stresses including ischemia are known to up-regulate renal L-FABP gene expression and increase the urinary excretion of L-FABP. In diabetic patients with anemia, the urinary excretion of L-FABP is significantly increased. We studied the clinical significance of urinary L-FABP and its relationship with anemia in non-diabetic patients.ResultsUrinary L-FABP levels were significantly higher in patients with anemia compared to those in patients without anemia. Similarly, the urinary L-FABP levels were significantly higher in patients with albuminuria compared to those in patients without albuminuria. Urinary L-FABP levels correlated with urinary albumin-to-creatinine ratios, estimated glomerular filtration rates, body mass index, and hemoglobin levels. Multivariate linear regression analysis determined that hemoglobin levels (β = -0.249, P = 0.001) and urinary albumin-to-creatinine ratios (β = 0.349, P < 0.001) were significant predictors of urinary L-FABP levels.ConclusionsUrinary L-FABP is strongly associated with anemia in non-diabetic patients. 相似文献
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Ryotaro Yabe Akane Miura Tatsuya Usui Ingrid Mudrak Egon Ogris Takashi Ohama Koichi Sato 《PloS one》2015,10(12)
Protein phosphatase 2A (PP2A) is a conserved essential enzyme that is implicated as a tumor suppressor based on its central role in phosphorylation-dependent signaling pathways. Protein phosphatase methyl esterase (PME-1) catalyzes specifically the demethylation of the C-terminal Leu309 residue of PP2A catalytic subunit (PP2Ac). It has been shown that PME-1 affects the activity of PP2A by demethylating PP2Ac, but also by directly binding to the phosphatase active site, suggesting loss of PME-1 in cells would enhance PP2A activity. However, here we show that PME-1 knockout mouse embryonic fibroblasts (MEFs) exhibit lower PP2A activity than wild type MEFs. Loss of PME-1 enhanced poly-ubiquitination of PP2Ac and shortened the half-life of PP2Ac protein resulting in reduced PP2Ac levels. Chemical inhibition of PME-1 and rescue experiments with wild type and mutated PME-1 revealed methyl-esterase activity was necessary to maintain PP2Ac protein levels. Our data demonstrate that PME-1 methyl-esterase activity protects PP2Ac from ubiquitin/proteasome degradation. 相似文献
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Summary We have characterized the two dominant genes, IND 1 and IND 2, responsible for inducible sexual agglutinability. The strains carrying these genes differ from the inducible strains carrying the recessive gene, saa 1 in the following points. The former strains produce agglutination substance at 22°, 28°, and 37° C only in response to sex pheromone of the opposite mating type, but the latter strains produce the substance constitutively without the pheromone at 22° C, only in response to the pheromone at 28° C, and do not produce the substance, even in the presence of the pheromone, at 37° C.We suggest that strains carrying one of the dominant, inducible genes are wild type and have a pheromone-controlled regulatory system of sexual agglutinability. 相似文献
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Yasuo Noda Yoshiki Ida Shinichi Tanaka Taku Toyama Murilo Felix Roggia Yasuhiro Tamaki Naohiko Sugita Mamoru Mitsuishi Takashi Ueta 《PloS one》2013,8(1)
Purpose
To elucidate the merits of robotic application for vitreoretinal maneuver in comparison to conventional manual performance using an in-vitro eye model constructed for the present study.Methods
Capability to accurately approach the target on the fundus, to stabilize the manipulator tip just above the fundus, and to perceive the contact of the manipulator tip with the fundus were tested. The accuracies were compared between the robotic and manual control, as well as between ophthalmologists and engineering students.Results
In case of manual control, ophthalmologists were superior to engineering students in all the 3 test procedures. Robotic assistance significantly improved accuracy of all the test procedures performed by engineering students. For the ophthalmologists including a specialist of vitreoretinal surgery, robotic assistance enhanced the accuracy in the stabilization of manipulator tip (from 90.9 µm to 14.9 µm, P = 0.0006) and the perception of contact with the fundus (from 20.0 mN to 7.84 mN, P = 0.046), while robotic assistance did not improve pointing accuracy.Conclusions
It was confirmed that telerobotic assistance has a potential to significantly improve precision in vitreoretinal procedures in both experienced and inexperienced hands. 相似文献8.
Michael J. Miller Yoshito Chikaraishi Nanako O. Ogawa Yoshiaki Yamada Katsumi Tsukamoto Naohiko Ohkouchi 《Biology letters》2013,9(1)
What eel larvae feed on in the surface layer of the ocean has remained mysterious. Gut contents and bulk nitrogen stable isotope studies suggested that these unusual larvae, called leptocephali, feed at a low level in the oceanic food web, whereas other types of evidence have suggested that small zooplankton are eaten. In this study, we determined the nitrogen isotopic composition of amino acids of both natural larvae and laboratory-reared larvae of the Japanese eel to estimate the trophic position (TP) of leptocephali. We observed a mean TP of 2.4 for natural leptocephali, which is consistent with feeding on particulate organic matter (POM) such as marine snow and discarded appendicularian houses containing bacteria, protozoans and other biological materials. The nitrogen isotope enrichment values of the reared larvae confirm that the primary food source of natural larvae is consistent only with POM. This shows that leptocephali feed on readily available particulate material originating from various sources closely linked to ocean primary production and that leptocephali are a previously unrecognized part of oceanic POM cycling. 相似文献
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Akira Sakurai Saburo Tamura Naohiko Yanagishima Chikashi Shimoda Michio Hagiya Narao Takao 《Bioscience, biotechnology, and biochemistry》2013,77(1):231-232
5-Fluorotryptophan (5FT), indolmycin (IM), 4-fluorotryptophan and 7-azatryptophan were found on screening to be tryptophan antagonists among various chemically synthesized and naturally occurring tryptophan analogues for the isolation of l-tryptophan (l-Trp) producing mutants of Bacillus subtilis K.From among 5FT resistant mutants, potent l-Trp producers were obtained using an improved isolation medium. Growth of the isolated 5FT-resistant l-Trp producer, AJ 11709, was inhibited by IM. From among 5FT and IM resistant mutants, the best strain, AJ 11979, which produced 9.0 g/liter of l-Trp from 13% glucose on 120hr cultivation, was selected. 相似文献
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Kosuke Kurosawa Seiji Sugita Ko Ishibashi Sunao Hasegawa Yasuhito Sekine Nanako O. Ogawa Toshihiko Kadono Sohsuke Ohno Naohiko Ohkouchi Yoichi Nagaoka Takafumi Matsui 《Origins of life and evolution of the biosphere》2013,43(3):221-245
Cyanide compounds are amongst the most important molecules of the origin of life. Here, we demonstrate the importance of mid-size (0.1–1 km in diameter) hence frequent meteoritic impacts to the cyanide inventory on the early Earth. Subsequent aerodynamic ablation and chemical reactions with the ambient atmosphere after oblique impacts were investigated by both impact and laser experiments. A polycarbonate projectile and graphite were used as laboratory analogs of meteoritic organic matter. Spectroscopic observations of impact-generated ablation vapors show that laser irradiation to graphite within an N2-rich gas can produce a thermodynamic environment similar to that produced by oblique impacts. Thus, laser ablation was used to investigate the final chemical products after this aerodynamic process. We found that a significant fraction (>0.1 mol%) of the vaporized carbon is converted to HCN and cyanide condensates, even when the ambient gas contains as much as a few hundred mbar of CO2. As such, the column density of cyanides after carbon-rich meteoritic impacts with diameters of 600 m would reach ~10 mol/m2 over ~102 km2 under early Earth conditions. Such a temporally and spatially concentrated supply of cyanides may have played an important role in the origin of life. 相似文献