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Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods 2016; 13:741-8. [DOI: 10.1038/nmeth.3959] [Citation(s) in RCA: 365] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/27/2016] [Indexed: 12/28/2022]
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Abstract
Outer hair cells were isolated from the guinea pig cochlea using a micromechanical non-enzymatic procedure. Depolarization of outer hair cells in the presence of 25-125 mM K+ was accompanied by a longitudinal contraction of the isolated cells. A decrease of [K+] to 5.4 mM interrupted contraction and induced a relaxation. Individual hair cells were able to undergo as many as 5 cycles of contraction and relaxation. External Ca2+ was required for relaxation of the contracted hair cells. The contractile event led to the production of a visible cytoplasmic network between the supranuclear area and the cuticular plate.
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Rosenberger G, Bludau I, Schmitt U, Heusel M, Hunter CL, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, Reiter L, Röst HL, Tate S, Ting YS, Collins BC, Aebersold R. Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nat Methods 2017; 14:921-927. [PMID: 28825704 PMCID: PMC5581544 DOI: 10.1038/nmeth.4398] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 07/07/2017] [Indexed: 12/18/2022]
Abstract
Liquid chromatography coupled to tandem mass spectrometry is the main method for high-throughput identification and quantification of peptides and inferred proteins. Within this field, data-independent acquisition (DIA) combined with peptide-centric scoring, exemplified by SWATH-MS, emerged as a scalable method to achieve deep and consistent proteome coverage across large-scale datasets. Here we discuss the adaptation of statistical concepts developed for discovery proteomics based on spectrum-centric scoring to large-scale DIA experiments analyzed with peptide-centric scoring strategies and provide guidance on their application. We show that optimal tradeoffs between sensitivity and specificity require careful considerations of the relationship between proteins in the samples and proteins represented in the spectral library. We propose the application of a global analyte constraint to prevent accumulation of false positives across large-scale datasets. Furthermore, to increase the quality and reproducibility of published proteomic results, well-established confidence criteria should be reported for detected peptide queries, peptides and inferred proteins.
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Journal Article |
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154 |
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Schmitt U, Hiemke C. Strain differences in open-field and elevated plus-maze behavior of rats without and with pretest handling. Pharmacol Biochem Behav 1998; 59:807-11. [PMID: 9586835 DOI: 10.1016/s0091-3057(97)00502-9] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Behavior of two rat strains was analyzed with and without 1-week pretest handling. Male rats (150-200 g body weight) of the strains PVG/OlaHsd (PVG) and Hsd:Sprague-DawleySD (SPRD) were tested once in a standard open field and an enriched open field and twice in an elevated plus-maze. Behavioral analysis revealed significant differences between the two strains and differential effects of the pretest handling procedure. SPRD rats displayed higher levels of activity and exploratory behavior than the PVG rats, whereas PVG rats were obviously less anxious. One-week pretest handling had an "anxiolytic" effect and changed activity and exploration-related behavior of the animals in both strains. Activity-related parameters were mainly affected in SPRD rats and anxiety-related ones in PVG rats. The data give evidence that differences in behavior of rats are not only determined genetically but also by preceding handling procedures. Because the two rat strains responded differentially to the pretest handling, we recommend to use a well-defined handling procedure before starting a behavioral test, especially when drug applications are included.
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Comparative Study |
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Wagner A, Donaldson L, Kim H, Phillips L, Flint H, Steward D, Torr K, Koch G, Schmitt U, Ralph J. Suppression of 4-coumarate-CoA ligase in the coniferous gymnosperm Pinus radiata. PLANT PHYSIOLOGY 2009; 149:370-83. [PMID: 18971431 PMCID: PMC2613735 DOI: 10.1104/pp.108.125765] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Accepted: 10/26/2008] [Indexed: 05/18/2023]
Abstract
Severe suppression of 4-coumarate-coenzyme A ligase (4CL) in the coniferous gymnosperm Pinus radiata substantially affected plant phenotype and resulted in dwarfed plants with a "bonsai tree-like" appearance. Microscopic analyses of stem sections from 2-year-old plants revealed substantial morphological changes in both wood and bark tissues. This included the formation of weakly lignified tracheids that displayed signs of collapse and the development of circumferential bands of axial parenchyma. Acetyl bromide-soluble lignin assays and proton nuclear magnetic resonance studies revealed lignin reductions of 36% to 50% in the most severely affected transgenic plants. Two-dimensional nuclear magnetic resonance and pyrolysis-gas chromatography-mass spectrometry studies indicated that lignin reductions were mainly due to depletion of guaiacyl but not p-hydroxyphenyl lignin. 4CL silencing also caused modifications in the lignin interunit linkage distribution, including elevated beta-aryl ether (beta-O-4 unit) and spirodienone (beta-1) levels, accompanied by lower phenylcoumaran (beta-5), resinol (beta-beta), and dibenzodioxocin (5-5/beta-O-4) levels. A sharp depletion in the level of saturated (dihydroconiferyl alcohol) end groups was also observed. Severe suppression of 4CL also affected carbohydrate metabolism. Most obvious was an up to approximately 2-fold increase in galactose content in wood from transgenic plants due to increased compression wood formation. The molecular, anatomical, and analytical data verified that the isolated 4CL clone is associated with lignin biosynthesis and illustrated that 4CL silencing leads to complex, often surprising, physiological and morphological changes in P. radiata.
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research-article |
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110 |
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Tacke M, Schmolke S, Schlueter V, Sauleda S, Esteban JI, Tanaka E, Kiyosawa K, Alter HJ, Schmitt U, Hess G, Ofenloch-Haehnle B, Engel AM. Humoral immune response to the E2 protein of hepatitis G virus is associated with long-term recovery from infection and reveals a high frequency of hepatitis G virus exposure among healthy blood donors. Hepatology 1997; 26:1626-33. [PMID: 9398008 DOI: 10.1002/hep.510260635] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The second envelope protein (E2) of the hepatitis G virus (HGV) was expressed in Chinese hamster ovary (CHO) cells and showed a molecular weight of approximately 60 to 70 kd, with 15 to 25 kd of the size contributed by N-linked glycosylation. An enzyme-linked immunosorbent assay (ELISA) using HGV-E2 was developed to test for antibodies to this protein (anti-E2) in human sera. High sensitivity was achieved by developing monoclonal antibodies (mAbs) to HGV-E2, which were used as capture antibodies in the ELISA. Our studies revealed that 16% of healthy Spanish blood donors were exposed to HGV, indicating that additional routes of viral transmission besides parenteral exposure might exist. An even higher prevalence of exposure to HGV (52%-73%) was found in several groups at risk of parenteral exposure to infectious agents, i.e., intravenous drug users, transfusion history, hemophiliacs, and hepatitis C virus (HCV)-positive patients. Most anti-E2-positive patients were HGV-RNA-negative and vice versa, indicating an inverse correlation of these two viral markers. A panel of 16 posttransfusion patients followed for up to 16 years revealed that patients who develop an anti-E2 response become HGV-RNA-negative, while patients who do not develop anti-E2 are persistently infected. Immunity to HGV seems to be long-lasting, because circulating antibody to E2 could still be detected 14 years after seroconversion. Sequence comparisons showed that E2 is highly conserved among isolates collected worldwide, indicating that immune escape variants are not common in HGV infections. This reflects on a molecular level why HGV infections usually are cleared spontaneously by the host. However, possible mechanisms of HGV persistence, as found in some patients, remain to be elucidated.
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Röst HL, Schmitt U, Aebersold R, Malmström L. pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library. Proteomics 2014; 14:74-7. [PMID: 24420968 DOI: 10.1002/pmic.201300246] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/11/2013] [Accepted: 10/11/2013] [Indexed: 11/07/2022]
Abstract
pyOpenMS is an open-source, Python-based interface to the C++ OpenMS library, providing facile access to a feature-rich, open-source algorithm library for MS-based proteomics analysis. It contains Python bindings that allow raw access to the data structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping, and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ, and SWATH analysis tools). pyOpenMS thus allows fast prototyping and efficient workflow development in a fully interactive manner (using the interactive Python interpreter) and is also ideally suited for researchers not proficient in C++. In addition, our code to wrap a complex C++ library is completely open-source, allowing other projects to create similar bindings with ease. The pyOpenMS framework is freely available at https://pypi.python.org/pypi/pyopenms while the autowrap tool to create Cython code automatically is available at https://pypi.python.org/pypi/autowrap (both released under the 3-clause BSD licence).
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Research Support, Non-U.S. Gov't |
11 |
92 |
8
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Häber T, Schmitt U, Emmeluth C, Suhm MA. Ragout-jet FTIR spectroscopy of cluster isomerism and cluster dynamics: from carboxylic acid dimers to N2O nanoparticles. Faraday Discuss 2002:331-59; discussion 361-71. [PMID: 11605275 DOI: 10.1039/b009312m] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Direct absorption supersonic jet Fourier transform spectroscopy provides a panoramic view of the dynamics of molecular clusters over the entire IR spectral range. The new and generally applicable ragout-jet technique compensates for the sensitivity limits inherent in the incoherent FTIR approach by the use of synchronized giant gas pulses expanding into a large vacuum buffer. A modification based on fragmented interferograms is proposed and demonstrated, by which the spectral resolution can be extended to the limit of the available FTIR spectrometer. The power of the method is illustrated for two classes of compounds. For acetic acid and its isotopomers, the supersonic jet spectra of dimers and oligomers are investigated for the first time, concentrating on the very complex OH/CH stretching domain and on the more regular C=O/C-O stretching range. Issues of cluster isomerism, hydrogen exchange tunneling, anharmonic resonances, intermolecular Franck-Condon sequences, methyl group substitution and cluster coating with argon are explored. For the more weakly interacting nitrous oxide, stretching fundamentals and combination bands of clusters in the 1-3 nm range are studied as a function of composition. Surface vibrations are investigated in detail and modeled quantum mechanically. The semiempirical AM1 approach is found to provide a remarkably accurate description of the cluster structure, energetics and dynamics.
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Teleman J, Röst HL, Rosenberger G, Schmitt U, Malmström L, Malmström J, Levander F. DIANA--algorithmic improvements for analysis of data-independent acquisition MS data. ACTA ACUST UNITED AC 2014; 31:555-62. [PMID: 25348213 DOI: 10.1093/bioinformatics/btu686] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
MOTIVATION Data independent acquisition mass spectrometry has emerged as a reproducible and sensitive alternative in quantitative proteomics, where parsing the highly complex tandem mass spectra requires dedicated algorithms. Recently, targeted data extraction was proposed as a novel analysis strategy for this type of data, but it is important to further develop these concepts to provide quality-controlled, interference-adjusted and sensitive peptide quantification. RESULTS We here present the algorithm DIANA and the classifier PyProphet, which are based on new probabilistic sub-scores to classify the chromatographic peaks in targeted data-independent acquisition data analysis. The algorithm is capable of providing accurate quantitative values and increased recall at a controlled false discovery rate, in a complex gold standard dataset. Importantly, we further demonstrate increased confidence gained by the use of two complementary data-independent acquisition targeted analysis algorithms, as well as increased numbers of quantified peptide precursors in complex biological samples. AVAILABILITY AND IMPLEMENTATION DIANA is implemented in scala and python and available as open source (Apache 2.0 license) or pre-compiled binaries from http://quantitativeproteomics.org/diana. PyProphet can be installed from PyPi (https://pypi.python.org/pypi/pyprophet). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Research Support, Non-U.S. Gov't |
11 |
72 |
10
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Schmitt U, Hiemke C. Combination of open field and elevated plus-maze: a suitable test battery to assess strain as well as treatment differences in rat behavior. Prog Neuropsychopharmacol Biol Psychiatry 1998; 22:1197-215. [PMID: 9829298 DOI: 10.1016/s0278-5846(98)00051-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
1. A test battery consisting of a standard open field, an enriched open field and an elevated plus maze was used to study behavior in rats. 2. Male rats of the strains PVG/OlaHsd (PVG) and Sprague-Dawley-Hsd (SPRD) (150-200 g body wt) were used to assess interstrain differences as well as handling effects. In a subsequent experiment an other set of male PVG rats (150-200 g body wt) treated either with diazepam or zolpidem was used to evaluate the test battery for pharmacological purposes. 3. SPRD rats displayed higher motor activity levels and also higher levels of exploratory behavior than the PVG rats. In contrast plus-maze activity indicated more anxiety of SPRD than PVG rats. One week pre-test handling increased the activity of both strains but it increased explorative behavior in the enriched open field only in SPRD rats. Diazepam had a substantial anxiolytic effect. Zolpidem enhanced the explorative activity in a differently to diazepam and exerted only minor anxiolytic properties. 4. We concluded that the test battery used here enables to reveal differentially strain, and treatment effects in rats.
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Comparative Study |
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Erb C, Troost J, Kopf S, Schmitt U, Löffelholz K, Soreq H, Klein J. Compensatory mechanisms enhance hippocampal acetylcholine release in transgenic mice expressing human acetylcholinesterase. J Neurochem 2001; 77:638-46. [PMID: 11299326 DOI: 10.1046/j.1471-4159.2001.00287.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Central cholinergic neurotransmission was studied in learning-impaired transgenic mice expressing human acetylcholinesterase (hAChE-Tg). Total catalytic activity of AChE was approximately twofold higher in synaptosomes from hippocampus, striatum and cortex of hAChE-Tg mice as compared with controls (FVB/N mice). Extracellular acetylcholine (ACh) levels in the hippocampus, monitored by microdialysis in the absence or presence of 10(-8)-10(-3) M neostigmine in the perfusion fluid, were indistinguishable in freely moving control and hAChE-Tg mice. Muscarinic receptor functions were unchanged as indicated by similar effects of scopolamine on ACh release and of carbachol on inositol phosphate formation. However, when the mice were anaesthetized with halothane (0.8 vol. %), hippocampal ACh reached significantly lower levels in AChE-Tg mice as compared with controls. Also, the high-affinity choline uptake (HACU) in hippocampal synaptosomes from awake hAChE-Tg mice was accelerated but was reduced by halothane anaesthesia. Moreover, hAChE-Tg mice displayed increased motor activity in novel but not in familiar environment and presented reduced anxiety in the elevated plus-maze test. Systemic application of a low dose of physostigmine (100 microgram/kg i.p.) normalized all of the enhanced parameters in hAChE-Tg mice: spontaneous motor activity, hippocampal ACh efflux and hippocampal HACU, attributing these parameters to the hypocholinergic state due to excessive AChE activity. We conclude that, in hAChE-Tg mice, hippocampal ACh release is up-regulated in response to external stimuli thereby facilitating cholinergic neurotransmission. Such compensatory phenomena most likely play important roles in counteracting functional deficits in mammals with central cholinergic dysfunctions.
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Comparative Study |
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Kiefer P, Schmitt U, Vorholt JA. eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows. ACTA ACUST UNITED AC 2013; 29:963-4. [PMID: 23418185 PMCID: PMC3605603 DOI: 10.1093/bioinformatics/btt080] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SUMMARY The Python-based, open-source eMZed framework was developed for mass spectrometry (MS) users to create tailored workflows for liquid chromatography (LC)/MS data analysis. The goal was to establish a unique framework with comprehensive basic functionalities that are easy to apply and allow for the extension and modification of the framework in a straightforward manner. eMZed supports the iterative development and prototyping of individual evaluation strategies by providing a computing environment and tools for inspecting and modifying underlying LC/MS data. The framework specifically addresses non-expert programmers, as it requires only basic knowledge of Python and relies largely on existing successful open-source software, e.g. OpenMS. AVAILABILITY The framework eMZed and its documentation are freely available at http://emzed.biol.ethz.ch/. eMZed is published under the GPL 3.0 license, and an online discussion group is available at https://groups.google.com/group/emzed-users. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Research Support, Non-U.S. Gov't |
12 |
46 |
13
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Schmitt U, Abou El-Ela A, Guo LJ, Glavinas H, Krajcsi P, Baron JM, Tillmann C, Hiemke C, Langguth P, Härtter S. Cyclosporine A (CsA) affects the pharmacodynamics and pharmacokinetics of the atypical antipsychotic amisulpride probably via inhibition of P-glycoprotein (P-gp). J Neural Transm (Vienna) 2005; 113:787-801. [PMID: 16252067 DOI: 10.1007/s00702-005-0367-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Accepted: 08/28/2005] [Indexed: 01/16/2023]
Abstract
The importance of P-glycoprotein (P-gp) in the pharmacokinetics of amisulpride and the effects of a P-gp inhibitor cyclosporine A (CsA) was investigated both, in vitro and in vivo. In vitro and in vivo results indicated amisulpride as a substrate of P-gp. Amisulpride was not metabolized by rat liver microsomes. Open field behavior showed time dependent abolishment in locomotion by amisulpride (50 mg kg(-1)). Co-administration of CsA (50 mg kg(-1)) resulted in a higher and significantly longer antipsychotic effect (24 h after drug administration). Accordingly, the area under concentration-time curve in serum and brain was higher in CsA co-treated rats (13.5 vs. 29.8 micromol h l(-1) for serum and 2.16 vs 2.98 micromol h l(-1) for brain tissue) while renal clearance was not affected. These results pointed to a pharmacokinetic drug interaction between CsA and amisulpride most likely caused by inhibition of P-gp.
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Journal Article |
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Van Kampen M, Schmitt U, Hiemke C, Fuchs E. Diazepam has no beneficial effects on stress-induced behavioural and endocrine changes in male tree shrews. Pharmacol Biochem Behav 2000; 65:539-46. [PMID: 10683496 DOI: 10.1016/s0091-3057(99)00190-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The present study evaluated the effect of subchronic oral treatment of psychosocially stressed male tree shrews with diazepam on locomotor activity, marking behavior, avoidance behavior, and urinary cortisol and noradrenaline. To mimic a realistic situation of anxiolytic intervention, the treatment started 14 days after the beginning of psychosocial stress; at that time, the stress-induced behavioral and endocrine alterations had been established. The drug (5 mg/kg/day) was administered orally in the morning, while the psychosocial stress continued during the whole treatment period; the therapeutic action of diazepam treatment was followed across 7 days. Twenty-four hours after the last application serum concentrations of diazepam and its major metabolites were determined via HPLC. The results revealed concentrations of 7 ng/ml for diazepam, 106 ng/ml for nordiazepam, 22 ng/ml for temazepam, and 30 ng/ml for oxazepam. Treatment of subordinate animals with diazepam did not reveal a beneficial effect to any of the parameters studied. This contrasts to earlier findings showing that the behavioral and neuroendocrine alterations produced by this stress paradigm are sensitive to chronic treatment with the tricyclic antidepressant clomipramine. The present results support the view that in male tree shrews the state induced by psychosocial stress might be more depression related than anxiety related.
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Wölfel T, Herr W, Coulie P, Schmitt U, Meyer zum Büschenfelde KH, Knuth A. Lysis of human pancreatic adenocarcinoma cells by autologous HLA-class I-restricted cytolytic T-lymphocyte (CTL) clones. Int J Cancer 1993; 54:636-44. [PMID: 8514455 DOI: 10.1002/ijc.2910540419] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
From the primary site of a pancreatic adenocarcinoma (patient BE) a permanent cell line (MZ-PC-2) was established in tissue culture. In the course of mixed lymphocyte-tumor-cell cultures (MLTC) with autologous blood-derived lymphocytes, we isolated CTL clones that lysed autologous tumor cells but not autologous EBV-transformed B cells (EBV-B) and not K562. Pre-treatment of MZ-PC-2 cells with IFN-gamma was required to obtain significant lysis in 4-hr cytotoxicity assays. IFN-gamma was superior to IFN-alpha in that respect. Among MLTC responder lymphocytes, tumor-reactive CTL proliferated more strongly in response to MZ-PC-2 cells treated with IFN-gamma than to untreated tumor cells. Three CTL clones derived from MLTC were chosen for further analysis. They were CD3+, CD8+, TCR-alpha/beta+ and behaved identically in all functional aspects tested. They all expressed the same TCR-beta chain, indicating that they descended from a common precursor lymphocyte and were directed against the same antigen. According to antibody-inhibition experiments, BE-CTL recognized their targets via an HLA-B molecule carrying the Bw6 supertypic determinant. Irrespective of pre-incubation with IFN-gamma, low levels of tumor-cell lysis, or none, were seen when MZ-PC-2 cells were kept in medium supplemented with autologous serum or serum pooled from healthy volunteers instead of FCS. Lysability was restored when TNF-alpha was added to human serum. Serum-free medium was found to enhance the susceptibility of MZ-PC-2 cells to lysis by autologous CTL.
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MESH Headings
- Adenocarcinoma/immunology
- Adenocarcinoma/pathology
- Adult
- Antibodies, Monoclonal/pharmacology
- Base Sequence
- Histocompatibility Antigens Class I/immunology
- Humans
- Interferon-gamma/pharmacology
- Lymphocyte Culture Test, Mixed
- Molecular Sequence Data
- Pancreatic Neoplasms/immunology
- Pancreatic Neoplasms/pathology
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- T-Lymphocytes, Cytotoxic/drug effects
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/pathology
- Tumor Cells, Cultured/immunology
- Tumor Cells, Cultured/pathology
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Seo JW, Eckstein D, Jalkanen R, Rickebusch S, Schmitt U. Estimating the onset of cambial activity in Scots pine in northern Finland by means of the heat-sum approach. TREE PHYSIOLOGY 2008; 28:105-12. [PMID: 17938119 DOI: 10.1093/treephys/28.1.105] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We estimated the date of onset (Date(est)) of cambial activity by the pinning method in Scots pine (Pinus sylvestris L.) trees at Vanttauskoski (Site 1) and Laanila (Site 2) near the latitudinal limit of Scots pine in northern Finland. In each year and at each site, observations were made on a different set of five trees. The estimated dates of onset of cambial activity were compared with the corresponding heat sums, calculated in degree-days according to two models. Within years, Date(est) varied among trees by up to 15 days at Site 1 and up to 13 days at Site 2. Among years, mean Date(est) varied by 15.3 days at Site 1 and 12.0 days at Site 2. The overall mean Date(est) differed between sites by 6 days (June 5 at Site 1 and June 11 at Site 2). Among all trees in all years, the mean number of degree days (d.d.) calculated from mean daily temperature above a threshold of 5 degrees C before Date(est) ranged from 68.7 to 135 d.d. at Site 1 and from 37.4 to 154.7 d.d. at Site 2. Among years, the mean heat sum before Date(est )ranged from 94 to 112.5 d.d. at Site 1 and from 61.4 to 136 d.d. at Site 2. Variation among years in heat sum before Date(est) at Site 2 was highly significant, indicating that one or more factors other than, or in addition to, heat sum determines the onset of cambial activity in Scots pine. Similar results were obtained when heat sum was computed from the area between the sine wave generated by daily maximum and minimum temperature and the threshold temperature.
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Ross RS, Viazov S, Schmitt U, Schmolke S, Tacke M, Ofenloch-Haehnle B, Holtmann M, Müller N, Da Villa G, Yoshida CF, Oliveira JM, Szabo A, Paladi N, Kruppenbacher JP, Philipp T, Roggendorf M. Distinct prevalence of antibodies to the E2 protein of GB virus C/hepatitis G virus in different parts of the world. J Med Virol 1998; 54:103-6. [PMID: 9496367 DOI: 10.1002/(sici)1096-9071(199802)54:2<103::aid-jmv6>3.0.co;2-a] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Since the identification of the new human virus, GB virus C (GBV-C)/hepatitis G-virus (HGV), in 1995/1996, reverse transcription polymerase chain reaction remained the sole available diagnostic tool for GBV-C/HGV infection. Recently, a serologic test based on the detection of antibodies to the putative envelope protein 2 (anti-E2) has been introduced. We used this assay for a seroepidemiological survey including 3,314 healthy individuals from different parts of the world, 123 patients from Germany who were suspected to have an increased risk of acquiring GBV-C/HGV infection, 128 multiple organ donors, and 90 GBV-C/HGV RNA positive persons. In European countries, anti-E2 seropositivity ranged from 10.9% (Germany) to 15.3% (Austria). In South Africa (20.3%) and Brazil (19.5%), even higher anti-E2 prevalence rates were recorded. In Asian countries like Bhutan (3.9%), Malaysia (6.3%), and the Philippines (2.7%), anti-E2 positivity was significantly lower. GBV-C/HGV anti-E2 prevalence in potential "risk groups," i.e., patients on hemodialysis and renal transplant recipients, did not vary significantly from anti-E2 seroprevalence in German blood donors. Anti-E2 and GBV-C/HGV RNA were found to be mutually exclusive, confirming the notion that anti-E2 has to be considered as a marker of past infection.
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Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, Ori A, Iskar M, Gillet L, Bi R, Zhang J, Zhang H, Yu C, Zhong Q, Varma S, Schmitt U, Qiu P, Zhang Q, Zhu Y, Wild PJ, Garnett MJ, Bork P, Beck M, Liu K, Saez-Rodriguez J, Elloumi F, Reinhold WC, Sander C, Pommier Y, Aebersold R. Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines. iScience 2019; 21:664-680. [PMID: 31733513 PMCID: PMC6889472 DOI: 10.1016/j.isci.2019.10.059] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 12/15/2022] Open
Abstract
Here we describe a proteomic data resource for the NCI-60 cell lines generated by pressure cycling technology and SWATH mass spectrometry. We developed the DIA-expert software to curate and visualize the SWATH data, leading to reproducible detection of over 3,100 SwissProt proteotypic proteins and systematic quantification of pathway activities. Stoichiometric relationships of interacting proteins for DNA replication, repair, the chromatin remodeling NuRD complex, β-catenin, RNA metabolism, and prefoldins are more evident than that at the mRNA level. The data are available in CellMiner (discover.nci.nih.gov/cellminercdb and discover.nci.nih.gov/cellminer), allowing casual users to test hypotheses and perform integrative, cross-database analyses of multi-omic drug response correlations for over 20,000 drugs. We demonstrate the value of proteome data in predicting drug response for over 240 clinically relevant chemotherapeutic and targeted therapies. In summary, we present a novel proteome resource for the NCI-60, together with relevant software tools, and demonstrate the benefit of proteome analyses.
High-quality NCI-60 proteotypes created using pressure cycling technology and SWATH-MS Proteotypes improve drug response prediction in multi-omics regression analysis ∼3000 measured proteins allow investigation into protein complex stoichiometry CellMinerCDB (discover.nci.nih.gov/cellminercdb) portal allows dataset exploration
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Schmitt U, Hiemke C. Effects of GABA-transporter (GAT) inhibitors on rat behaviour in open-field and elevated plus-maze. Behav Pharmacol 1999; 10:131-7. [PMID: 10780826 DOI: 10.1097/00008877-199903000-00002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The behavioural consequences of inhibition of gamma-aminobutyric acid (GABA) uptake were studied. Two GABA uptake inhibitors, tiagabine and SKF 89976-A, were administered to rats, and behaviour was analysed 30 min later in a standard open field, an enriched open field, and an elevated plus-maze. Eight groups of animals received either saline (0.9%), tiagabine, or SKF 89976-A. At a dose of 18.5 mg/kg, tiagabine, an established antiseizure drug, impaired motor coordination, enhanced exploratory activity and reduced anxiety related behaviour. SKF 89976-A exhibited minimal effects over the dose range tested. These results indicate that inhibition of GABA uptake might be a pharmacological strategy to treat not only epilepsy, but also anxiety disorders.
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Zenner HP, Gitter A, Zimmermann U, Schmitt U, Frömter E. Die isolierte, lebende Haarzelle - Ein neues Modell zur Untersuchung der Hörfunktion. Laryngorhinootologie 2008. [DOI: 10.1055/s-2007-1008225] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Darvas F, Schmitt U, Louis AK, Fuchs M, Knoll G, Buchner H. Spatio-temporal current density reconstruction (stCDR) from EEG/MEG-data. Brain Topogr 2001; 13:195-207. [PMID: 11302398 DOI: 10.1023/a:1007855119092] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Among the different approaches to the bioelectromagnetic inverse problem, the current-density reconstruction methods (CDR) provide the most general solutions. Since the inverse problem does not have a unique solution, model assumptions have to be taken into account. Multi-channel measurements contain not only spatial, but also temporal information about the sources, so a naturally extension to existing methods leads to spatio-temporal model constraints. Spatio-temporal CDR's (stCDR) have been tested in simplified volume conductor models, assuming different spatial model constraints and a smooth temporal activation model. Comparison to existing spatial model constraints showed a significant improvement of spatial and temporal resolution of the reconstructed sources for the spatio-temporal models especial in noisy data.
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Amrein A, Hollenstein H, Quack M, Schmitt U. High resolution interferometric fourier transform infrared spectroscopy in supersonic free jet expansions: N2O, CBrF3 and CF3I. ACTA ACUST UNITED AC 1989. [DOI: 10.1016/0020-0891(89)90099-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Schmitt U, Sabel BA. MK-801 reduces retinal ganglion cell survival but improves visual performance after controlled optic nerve crush. J Neurotrauma 1996; 13:791-800. [PMID: 9002064 DOI: 10.1089/neu.1996.13.791] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Excitotoxicity is implicated in secondary cell death after ischemic or traumatic brain injury. We therefore evaluated the role of excitotoxicity mediated by the NMDA glutamate receptor subtype on retinal ganglion cell (RGC) survival and visual performance after optic nerve injury in adult rats. To monitor visual deficits after mild optic nerve crush, rats were trained in a two-choice pattern discrimination task. Immediately after the crush and on postoperative day 1, MK-801 (1 nmol), a noncompetitive open channel blocker of the NMDA-receptor, was injected intraocularly. Within the first few days after crush, all rats showed a loss of their discrimination ability that was followed by a significant recovery within a 3-week testing period. Although animals treated with MK-801 had a significantly smaller initial deficit compared with PBS-injected controls, anatomic investigations using retrograde HRP tracing revealed a significant retrograde loss of RGC in lesioned rats that was significantly exacerbated by MK-801. These results confirm our earlier studies suggesting that neuronal damage does not uniformly match behavioral defects in CNS injury paradigms and that near-normal visual performance occurs in rats with only about 10% of RGC being connected to their target. The observation that after traumatic injury MK-801 is neuroprotective functionally while being neurotoxic anatomically is a structural-functional paradox that needs to be explored further.
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Schmitt U, Lüddens H, Hiemke C. Anxiolytic-like effects of acute and chronic GABA transporter inhibition in rats. J Neural Transm (Vienna) 2002; 109:871-80. [PMID: 12111474 DOI: 10.1007/s007020200071] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acute GABA transporter inhibition can induce anxiolytic-like behaviors. The present analysis addressed whether chronic treatment (23 days via drinking water) with a GABA transporter inhibitor affects rat behavior similar to acute treatment and interferes with additional benzodiazepine-receptor agonistic treatment. Seventy-one rats divided into seven groups were acutely treated with either vehicle, diazepam (2 mg/kg), zolpidem (0.05 mg/kg), tiagabine (19 mg/kg) or chronically with tiagabine with or without acute diazepam or zolpidem. Animals were behaviorally characterized in an elevated plus-maze. None of the treatments induced changes in the activity of the animals. Acute and chronic treatment with tiagabine induced anxiolytic-like effects, similar to acute doses of diazepam. Acute diazepam did not enhance chronic tiagabine effects, whereas acute zolpidem attenuated the anxiolytic-like effects of chronic tiagabine. It is concluded that anxiolytic effects of acute GABA-uptake inhibition by tiagabine persist under chronic treatment and are sensitive to concomitant use of benzodiazepine receptor ligands.
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Heid M, Chen T, Schmitt U, Kiefer W. Spectrally resolved fs-CARS as a probe of the vibrational dynamics of a large polyatomic molecule: magnesium octaethylporphyrin. Chem Phys Lett 2001. [DOI: 10.1016/s0009-2614(00)01456-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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