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Labeling Experiments (labeling + experiment)
Selected AbstractsCalyculin-A, an inhibitor for protein phosphatases, induces cortical contraction in unfertilized sea urchin eggsCYTOSKELETON, Issue 4 2001Yukako Asano Abstract When an unfertilized sea urchin egg was exposed to calyculin-A (CL-A), an inhibitor of protein phosphatases, for a short period and then lysed, the cortex contracted to exclude cytoplasm and became a cup-shaped mass. We call the contracted cortex "actin cup" since actin filaments were major structural components. Electron microscopic observation revealed that the cup consisted of inner electron-dense layer, middle microfilamentous layer, and outermost granular region. Microfilaments were heavily accumulated in the inner electron-dense layer. The middle layer also contained numerous microfilaments, which were determined to be actin filaments by myosin S1 decoration, and they were aligned so that their barbed ends directed toward the outermost region. Myosin II, Arp2, Arp3, and spectrin were concentrated in the actin cup. Immuno-electron microscopy revealed that myosin II was localized to the electron-dense layer. We further found that the cortical tension of the egg increased just after application of CL-A and reached maximum within 10 min. Cytochalasin B or butanedione monoxime blocked the contraction, which suggested that both actin filaments and myosin ATPase activity were required for the contraction. Myosin regulatory light chain (MRLC) in the actin cup was shown to be phosphorylated at the activation sites Ser-19 and Thr-18, by immunoblotting with anti-phosphoepitope antibodies. The phosphorylation of MRLC was also confirmed by a 32P in vivo labeling experiment. The CL-A-induced cortical contraction may be a good model system for studying the mechanism of cytokinesis. Cell Motil. Cytoskeleton 48:245,261, 2001. © 2001 Wiley-Liss, Inc. [source] Ring-Expansion of MCPs in the Presence of DIAD or DEAD and Lewis AcidsEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 2 2004Li-Xiong Shao Abstract Treatment of methylenecyclopropanes (MCPs) with DIAD or DEAD in MeCN under mild conditions in the presence of Lewis acid Zr(OTf)4 gave the cyclobutanone ring-expansion products in good to high yields based on the employed DIAD or DEAD. From a deuterium labeling experiment, the oxygen atom is derived from ambient water. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Plant and microbial N acquisition under elevated atmospheric CO2 in two mesocosm experiments with annual grassesGLOBAL CHANGE BIOLOGY, Issue 2 2005Shuijin Hu Abstract The impact of elevated CO2 on terrestrial ecosystem C balance, both in sign or magnitude, is not clear because the resulting alterations in C input, plant nutrient demand and water use efficiency often have contrasting impacts on microbial decomposition processes. One major source of uncertainty stems from the impact of elevated CO2 on N availability to plants and microbes. We examined the effects of atmospheric CO2 enrichment (ambient+370 ,mol mol,1) on plant and microbial N acquisition in two different mesocosm experiments, using model plant species of annual grasses of Avena barbata and A. fatua, respectively. The A. barbata experiment was conducted in a N-poor sandy loam and the A. fatua experiment was on a N-rich clayey loam. Plant,microbial N partitioning was examined through determining the distribution of a 15N tracer. In the A. barbata experiment, 15N tracer was introduced to a field labeling experiment in the previous year so that 15N predominantly existed in nonextractable soil pools. In the A. fatua experiment, 15N was introduced in a mineral solution [(15NH4)2SO4 solution] during the growing season of A. fatua. Results of both N budget and 15N tracer analyses indicated that elevated CO2 increased plant N acquisition from the soil. In the A. barbata experiment, elevated CO2 increased plant biomass N by ca. 10% but there was no corresponding decrease in soil extractable N, suggesting that plants might have obtained N from the nonextractable organic N pool because of enhanced microbial activity. In the A. fatua experiment, however, the CO2 -led increase in plant biomass N was statistically equal to the reduction in soil extractable N. Although atmospheric CO2 enrichment enhanced microbial biomass C under A. barbata or microbial activity (respiration) under A. fatua, it had no significant effect on microbial biomass N in either experiment. Elevated CO2 increased the colonization of A. fatua roots by arbuscular mycorrhizal fungi, which coincided with the enhancement of plant competitiveness for soluble soil N. Together, these results suggest that elevated CO2 may tighten N cycling through facilitating plant N acquisition. However, it is unknown to what degree results from these short-term microcosm experiments can be extrapolated to field conditions. Long-term studies in less-disturbed soils are needed to determine whether CO2 -enhancement of plant N acquisition can significantly relieve N limitation over plant growth in an elevated CO2 environment. [source] Enantioselective Synthesis of Chiral Tetrahydroisoquinolines by Iridium-Catalyzed Asymmetric Hydrogenation of EnaminesADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 18 2009Pu-Cha Yan Abstract Chiral iridium complexes based on spiro phosphoramidite ligands are demonstrated to be highly efficient catalysts for the asymmetric hydrogenation of unfunctionalized enamines with an exocyclic double bond. In combination with excess iodine or potassium iodide and under hydrogen pressure, the complex Ir/(Sa,R,R)- 3a provides chiral N -alkyltetrahydroisoquinolines in high yields with up to 98% ee. The L/Ir ratio of 2:1 is crucial for obtaining a high reaction rate and enantioselectivity. A deuterium labeling experiment showed that an inverse isotope effect exists in this reaction. A possible catalytic cycle including an iridium(III) species bearing two monophosphoramidite ligands is also proposed. [source] Nicotinic synapses formed between chick ciliary ganglion neurons in culture resemble those present on the neurons in vivoDEVELOPMENTAL NEUROBIOLOGY, Issue 4 2001Min Chen Abstract We studied nicotinic synapses between chick ciliary ganglion neurons in culture to learn more about factors influencing their formation and receptor subtype dependence. After 4,8 days in culture, nearly all neurons displayed spontaneous excitatory postsynaptic currents (sEPSCs), which occurred at about 1 Hz. Neurons treated with tetrodotoxin displayed miniature EPSCs (mEPSCs), but these occurred at low frequency (0.1 Hz), indicating that most sEPSCs are actually impulse driven. The sEPSCs could be classified by decay kinetics as fast, slow, or biexponential and, reminiscent of the situation in vivo, were mediated by two major nicotinic acetylcholine receptor (AChR) subtypes. Fast sEPSCs were blocked by ,-bungarotoxin (,Bgt), indicating dependence on ,Bgt-AChRs, most of which are ,7 subunit homopentamers. Slow sEPSCs were unaffected by ,Bgt, and were blocked instead by the ,3/,2-selective ,-conotoxin-MII (,CTx-MII), indicating dependence on ,3*-AChRs, which lack ,7 and contain ,3 subunits. Biexponential sEPSCs were mediated by both ,Bgt- and ,3*-AChRs because they had fast and slow components qualitatively similar to those comprising simple events, and these were reduced by ,Bgt and blocked by ,CTx-MII, respectively. Fluorescence labeling experiments revealed both ,Bgt- and ,3*-AChR clusters on neuron somata and neurites. Colabeling with antisynaptic vesicle protein antibody suggested that some ,3*-AChR clusters, and a few ,Bgt-AChR clusters are associated with synaptic sites, as is the case in vivo. These findings demonstrate the utility of ciliary ganglion neuron cultures for studying the regulation of nicotinic synapses, and suggest that mixed AChR subtype synapses characteristic of the neurons in vivo can form in the absence of normal inputs or targets. © 2001 John Wiley & Sons, Inc. J Neurobiol 47: 265,279, 2001 [source] A systematic investigation into the recovery of radioactively labeled proteins from sodium dodecyl sulfate-polyacrylamide gelsELECTROPHORESIS, Issue 1 2004Shaobo Zhou Abstract We report the results of a systematic investigation designed to optimize a method for quantifying radioactivity in proteins in sodium dodecyl sulfate-polyacrylamide gels. The method involves dissolving appropriately sized pieces of gel in hydrogen peroxide and heating to 70°C overnight followed by liquid scintillation counting. H2O2 had no effect on the count rates of [14C]bovine serum albumin (BSA) when counted in a conventional liquid scintillation system, and the count rates remained stable for several days. Temperatures below 70°C resulted in incomplete extraction of radioactivity from gels containing [14C]BSA, but there was also a significant reduction in count rates in samples incubated at 80°C. At 70°C recovery was not affected by the amount of sample loaded onto the gel or by the staining procedure (Coomassie Brilliant Blue or SYPRO Ruby). Recoveries were in the range of 89,94%, and the coefficient of variation for five replicate samples was 5,10%. This method offers a reliable way of measuring the amount of radioactivity in proteins that have been separated by electrophoresis. It may be useful, for example, in quantitative metabolic labeling experiments when it is necessary to know precisely how much tracer has been incorporated into a particular protein. [source] Fragmentation of Alkoxo(catecholato)vanadium(V) Complexes[(C6H4O2)V(OR1)(OR2)]+ in the Gas PhaseEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 14 2005Malgorzata Kaczorowska Abstract Electrospray ionization (ESI) mass spectrometry is used to investigate the gas-phase dissociation behavior of vanadium(V) complexes [(C6H4O2)V(OR1)(OR2)]+ containing two identical or different alkoxy groups (R1, R2 = CH3, C2H5, n -C3H7, i -C3H7 and t -C4H9) and a catecholato ligand (C6H4O2). The fragmentation reactions of the complexes are studied by collision-induced dissociation (CID) and labeling experiments. For [(C6H4O2)V(OR1)(OR2)]+ cations with alkoxo groups larger than methyl, a trend for preferential evaporation of hydrocarbon fragments is observed, followed by expulsion of neutral alcohols. Further, the CID spectra of all complexes show a signal which can be assigned to the complex [(C6H4O2)VO]+. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Demonstration of long-range GABAergic connections distributed throughout the mouse neocortexEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 6 2005Ryohei Tomioka Abstract ,-Aminobutyric acid (GABA)ergic neurons in the neocortex have been mainly regarded as interneurons and thought to provide local interactions. Recently, however, glutamate decarboxylase (GAD) immunocytochemistry combined with retrograde labeling experiments revealed the existence of GABAergic projection neurons in the neocortex. We further studied the network of GABAergic projection neurons in the neocortex by using GAD67-green fluorescent protein (GFP) knock-in mice for retrograde labeling and a novel neocortical GABAergic neuron labeling method for axon tracing. Many GFP-positive neurons were retrogradely labeled after Fast Blue injection into the primary somatosensory, motor and visual cortices. These neurons were labeled not only around the injection site, but also at a long distance from the injection site. Of the retrogradely labeled GABAergic neurons remote from the injection sites, the vast majority (91%) exhibited somatostatin immunoreactivity, and were preferentially distributed in layer II, layer VI and in the white matter. In addition, most of GABAergic projection neurons were positive for neuropeptide Y (82%) and neuronal nitric oxide synthase (71%). We confirmed the long-range projections by tracing GFP-labeled GABAergic neurons with axon branches traveled rostro-caudally and medio-laterally. Axon branches could be traced up to 2 mm. Some (n = 2 of 4) were shown to cross the areal boundaries. The GABAergic projection neurons preferentially received neocortical inputs. From these results, we conclude that GABAergic projection neurons are distributed throughout the neocortex and are part of a corticocortical network. [source] Low doses of bromo- and iododeoxyuridine produce near-saturation labeling of adult proliferative populations in the dentate gyrusEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 3 2005Kevin A. Burns Abstract Cell proliferation can be detected by the incorporation of tritiated thymidine (3H-dT) or halopyrimidines during DNA synthesis in progenitor cells. Administration of two thymidine analogues at different times can further determine the cell-cycle kinetics of proliferating cells. Traditionally, this was done by combining bromodeoxyuridine (BrdU) immunocytochemistry and 3H-dT autoradiography, or by BrdU and iododeoxyuridine (IdU) double-labeling using two mouse antibodies. However, these methods either require lengthy exposure time or involve complicated histological procedures for differentiating between two antibodies of the same species. Here we report a simple and reliable method of distinguishing BrdU- and IdU-labeled cells by immunofluorescence. This method uses a mouse monoclonal antibody that recognizes both BrdU and IdU and a rat anti-BrdU antibody that has no cross-reactivity with IdU. When combined with species-specific secondary antibodies that are conjugated to different fluorophores, this method identifies BrdU- and IdU-incorporation as doubly and singly labeled cells, respectively. This method has broad applications. First, we demonstrate that this method can distinguish mouse cortical neurons generated on different embryonic days. Second, by administering IdU and BrdU at varying intervals, we used this method to calculate that the length of S-phase of neural progenitor cells in the adult mouse dentate gyrus is approximately 6 h. Finally, we show that a six-fold higher concentration of IdU detects only 10% more cells than the standard dose of BrdU (50 mg/kg) using the double-labeling method. These results suggest that the standard dose of BrdU is sufficient to label the majority of proliferative populations in the S-phase in pulse labeling experiments. [source] Construction and Characterization of Porous SiO2/Hydrogel Hybrids as Optical Biosensors for Rapid Detection of BacteriaADVANCED FUNCTIONAL MATERIALS, Issue 14 2010Naama Massad-Ivanir Abstract The use of a new class of hybrid nanomaterials as label-free optical biosensors for bacteria detection (E. coli K12 as a model system) is demonstrated. The hybrids combine a porous SiO2 (PSiO2) optical nanostructure (a Fabry,Pérot thin film) used as the optical transducer element and a hydrogel. The hydrogel, polyacrylamide, is synthesized in situ within the nanostructure inorganic host and conjugated with specific monoclonal antibodies (IgGs) to provide the active component of the biosensor. The immobilization of the IgGs onto the hydrogel via a biotin-streptavidin system is confirmed by fluorescent labeling experiments and reflective interferometric Fourier transform spectroscopy (RIFTS). Additionally, the immobilized IgGs maintain their immunoactivity and specificity when attached to the sensor surface. Exposure of these modified-hybrids to the target bacteria results in "direct cell capture" onto the biosensor surface. These specific binding events induce predictable changes in the thin-film optical interference spectrum of the hybrid. Preliminary studies demonstrate the applicability of these biosensors for the detection of low bacterial concentrations in the range of 103,105 cell mL,1 within minutes. [source] Theoretical study of carbon atom scrambling in benzenium ions with ethyl or isopropyl groupsJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 2 2006Bjørnar Arstad Abstract Carbon atom scrambling is observed in benzenium ions in the mass spectrometer and in isotopic labeling experiments in the methanol-to-hydrocarbons reaction over acidic zeolites. We have shown plausible scrambling mechanisms in ethyl- and isopropylbenzenium ions and various intramolecular interconversion reactions that may take place in alkylbenzenium ions. Quantum chemical Density Functional Theory (DFT) modeling at the B3LYP/cc-pVTZ//B3LYP/6-311G(d,p) level of theory has been carried out to investigate carbon atom scrambling reactions in ethyl- and isopropyl(methyl)benzenium ions. A total of 85 stationary points have been calculated (48 minima and 37 transition states). The carbon atom scrambling reactions start with an initial ring expansion of the benzenium ions to a seven-membered ring. The seven-membered ring may rearrange and at a later stage re-contract to the original benzenium species, albeit with some atoms interchanged, i.e. there has been atom scrambling. Copyright © 2005 John Wiley & Sons, Ltd. [source] Real-time adaptive sequential design for optimal acquisition of arterial spin labeling MRI dataMAGNETIC RESONANCE IN MEDICINE, Issue 1 2010Jingyi Xie Abstract An optimal sampling schedule strategy based on the Fisher information matrix and the D-optimality criterion has previously been proposed as a formal framework for optimizing inversion time scheduling for multi-inversion-time arterial spin labeling experiments. Optimal sampling schedule possesses the primary advantage of improving parameter estimation precision but requires a priori estimation of plausible parameter distributions that may not be available in all situations. An adaptive sequential design approach addresses this issue by incorporating the optimal sampling schedule strategy into an adaptive process that iteratively updates the parameter estimates and adjusts the optimal sampling schedule accordingly as data are acquired. In this study, the adaptive sequential design method was experimentally implemented with a real-time feedback scheme on a clinical MRI scanner and was tested in six normal volunteers. Adapted schedules were found to accommodate the intrinsically prolonged arterial transit times in the occipital lobe of the brain. Simulation of applying the adaptive sequential design approach on subjects with pathologically reduced perfusion was also implemented. Simulation results show that the adaptive sequential design approach is capable of incorporating pathologic parameter information into an optimal arterial spin labeling scheduling design within a clinically useful experimental time. Magn Reson Med, 2010. © 2010 Wiley-Liss, Inc. [source] A MS data search method for improved 15N-labeled protein identificationPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 17 2009Yaoyang Zhang Abstract Quantitative proteomics using stable isotope labeling strategies combined with MS is an important tool for biomarker discovery. Methods involving stable isotope metabolic labeling result in optimal quantitative accuracy, since they allow the immediate combination of two or more samples. Unfortunately, stable isotope incorporation rates in metabolic labeling experiments using mammalian organisms usually do not reach 100%. As a consequence, protein identifications in 15N database searches have poor success rates. We report on a strategy that significantly improves the number of 15N-labeled protein identifications and results in a more comprehensive and accurate relative peptide quantification workflow. [source] Analysis of oligomeric peroxides in synthetic triacetone triperoxide samples by tandem mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 3 2009Michael E. Sigman Oligomeric peroxides formed in the synthesis of triacetone triperoxide (TATP) have been analyzed by mass spectrometry utilizing both electrospray ionization (ESI) and chemical ionization (CI) to form sodiated adducts (by ESI) and ammonium adducts (by CI and ESI). Tandem mass spectrometry and deuterium isotopic labeling experiments have been used to elucidate the collision-induced dissociation (CID) mechanisms for the adducts. The CID mechanisms differ for the sodium and ammonium adducts and vary with the size of the oligoperoxide. The sodium adducts of the oligoperoxides, H[OOC(CH3)2]nOOH, do not cyclize under CID, whereas the ammonium adducts of the smaller oligoperoides (n,<,6) do form the cyclic peroxides under CID. Larger oligoperoxide adducts with both sodium and ammonium undergo dissociation through cleavage of the backbone under CID to form acyl- and hydroperoxy-terminated oligomers of the general form CH3C(O)[OOC(CH3)2]xOOH, where x is an integer less than the original oligoperoxide degree of oligomerization. The oligoperoxide distribution is shown to vary batch-to-batch in the synthesis of TATP and the post-blast distribution differs slightly from the distribution in the uninitiated material. The oligoperoxides are shown to be decomposed under gentle heating. Copyright © 2009 John Wiley & Sons, Ltd. [source] Distinct roles of neuropilin 1 signaling for radial and tangential extension of callosal axonsTHE JOURNAL OF COMPARATIVE NEUROLOGY, Issue 4 2009Yumiko Hatanaka Abstract Cortical excitatory neurons migrate from their origin in the ventricular zone (VZ) toward the pial surface. During migration, these neurons exhibit a stellate shape in the intermediate zone (IZ), transform into bipolar cells, and then initiate radial migration, extending a trailing process, which may lead to an axon. Here we examined the role of neuropilin 1 (NRP1) in these developmental events. Both NRP1 mRNA and protein were highly expressed in the IZ, where stellate-shaped cells were located. DiI labeling experiments showed that neuronal migration occurred normally in Nrp1 mutant mice up to embryonic day (E) 14.5, the latest day to which the mutant survives, with only subtle axonal defasciculation. However, interference with Nrp1 signaling at a later stage caused pathfinding errors: when a dominant negative form of Nrp1 was electroporated into the cortical VZ cells at E12.5 or E15.5 and examined perinatally, guidance errors were found in tangential axonal extension toward the midline. In contrast, no significant effect was noted on the migration of cortical excitatory neurons. These findings indicate that NRP1 plays an important role in the guidance of callosal axons originating from cortical excitatory neurons but does not support a role in their migration. Moreover, insofar as radial axonal extension within the cortical plate was unaffected, the present findings imply that molecular mechanisms for the axonal extension of excitatory neurons within the cortical plate are distinct from those in the white matter. J. Comp. Neurol. 514:215,225, 2009. © 2009 Wiley-Liss, Inc. [source] Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockoutBIOTECHNOLOGY & BIOENGINEERING, Issue 2 2003Chen Yang Abstract The gluconeogenic phosphoenolpyruvate (PEP) carboxykinase is active in Escherichia coli during its growth on glucose. The present study investigated the influence of growth rates and PEP carboxykinase knockout on the anaplerotic fluxes in E. coli. The intracellular fluxes were determined using the complementary methods of flux ratio analysis and metabolic flux analysis based on [U- 13C6]glucose labeling experiments and 2D nuclear magnetic resonance (NMR) spectroscopy of cellular amino acids and glycerol. Significant activity of PEP carboxykinase was identified in wild-type E. coli, and the ATP dissipation for the futile cycling via this reaction accounted for up to 8.2% of the total energy flux. Flux analysis of pck deletion mutant revealed that abolishment of PEP carboxykinase activity resulted in a remarkably reduced flux through the anaplerotic PEP carboxylase and the activation of the glyoxylate shunt, with 23% of isocitrate found being channeled in the glyoxylate shunt. The changes in intracellular metabolite concentrations and specific enzyme activities associated with different growth rates and pck deletion, were also determined. Combining the measurement data of in vivo fluxes, metabolite concentrations and enzyme activities, the in vivo regulations of PEP carboxykinase flux, PEP carboxylation, and glyoxylate shunt in E. coli are discussed. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 129,144, 2003. [source] Biochemistry of PUFA Double Bond Isomerases Producing Conjugated Linoleic AcidCHEMBIOCHEM, Issue 12 2008Alena Liavonchanka Dr. Abstract The biotransformation of linoleic acid (LA) into conjugated linoleic acid (CLA) by microorganisms is a potentially useful industrial process. In most cases, however, the identities of proteins involved and the details of enzymatic activity regulation are far from clear. Here we summarize available data on the reaction mechanisms of CLA-producing enzymes characterized until now, from Butyrivibrio fibrisolvens, Lactobacillus acidophilus, Ptilota filicina, and Propionibacterium acnes. A general feature of enzymatic LA isomerization is the protein-assisted abstraction of an aliphatic hydrogen atom from position C-11, while the role of flavin as cofactor for the double bond activation in CLA-producing enzymes is also discussed with regard to the recently published three-dimensional structure of an isomerase from P. acnes. Combined data from structural studies, isotopic labeling experiments, and sequence comparison suggest that at least two different prototypical active site geometries occur among polyunsaturated fatty acid (PUFA) double bond isomerases. [source] Lewis Acid Controlled Regioselectivity in Styrene HydrocyanationCHEMISTRY - A EUROPEAN JOURNAL, Issue 35 2009Laura Bini Abstract According to present knowledge, the Ni-catalyzed hydrocyanation of styrene leads predominantly to the branched product 2-phenylpropionitrile (98,%). We observed a dramatic inversion of the regioselectivity upon addition of a Lewis acid. Up to 83,% of the linear product 3-phenylpropionitrile was obtained by applying phosphite ligands in the presence of AlCl3. The mechanism of the Ni-catalyzed reaction and the influence of additional Lewis acids have been investigated by means of deuterium labeling experiments, NMR studies, and DFT calculations. Furthermore, the behavior of different Lewis acids, such as CuCN, could be rationalized and predicted by DFT calculations. [source] | |||||||||||||