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Find video protocols related to scientific articles indexed in Pubmed.
Elemental analysis in biotechnology.
Curr. Opin. Biotechnol.
PUBLISHED: 08-12-2014
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This article focuses on analytical strategies integrating atomic spectroscopy in biotechnology. The rationale behind developing such methods is inherently linked to unique features of the key technique in elemental analysis, which is inductively coupled plasma mass spectrometry: (1) the high sensitivity and selectivity of state of the art instrumentation, (2) the possibility of accurate absolute quantification even in complex matrices, (3) the capability of combining elemental detectors with chromatographic separation methods and the versatility of the latter approach, (4) the complementarity of inorganic and organic mass spectrometry, (5) the multi-element capability and finally (6) the capability of isotopic analysis. The article highlights the most recent bio-analytical developments exploiting these methodological advantages and shows the potential in biotechnological applications.
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Root exudation of phytosiderophores from soil-grown wheat.
New Phytol.
PUBLISHED: 04-23-2014
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For the first time, phytosiderophore (PS) release of wheat (Triticum aestivum cv Tamaro) grown on a calcareous soil was repeatedly and nondestructively sampled using rhizoboxes combined with a recently developed root exudate collecting tool. As in nutrient solution culture, we observed a distinct diurnal release rhythm; however, the measured PS efflux was c. 50 times lower than PS exudation from the same cultivar grown in zero iron (Fe)-hydroponic culture. Phytosiderophore rhizosphere soil solution concentrations and PS release of the Tamaro cultivar were soil-dependent, suggesting complex interactions of soil characteristics (salinity, trace metal availability) and the physiological status of the plant and the related regulation (amount and timing) of PS release. Our results demonstrate that carbon and energy investment into Fe acquisition under natural growth conditions is significantly smaller than previously derived from zero Fe-hydroponic studies. Based on experimental data, we calculated that during the investigated period (21-47 d after germination), PS release initially exceeded Fe plant uptake 10-fold, but significantly declined after c. 5 wk after germination. Phytosiderophore exudation observed under natural growth conditions is a prerequisite for a more accurate and realistic assessment of Fe mobilization processes in the rhizosphere using both experimental and modeling approaches.
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Reduced quenching and extraction time for mammalian cells using filtration and syringe extraction.
J. Biotechnol.
PUBLISHED: 04-08-2014
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In order to preserve the in vivo metabolite levels of cells, a quenching protocol must be quickly executed to avoid degradation of labile metabolites either chemically or biologically. In the case of mammalian cell cultures cultivated in complex media, a wash step previous to quenching is necessary to avoid contamination of the cell pellet with extracellular metabolites, which could distort the real intracellular concentration of metabolites. This is typically achieved either by one or multiple centrifugation/wash steps which delay the time until quenching (even harsh centrifugation requires several minutes for processing until the cells are quenched) or filtration. In this article, we describe and evaluate a two-step optimized protocol based on fast filtration by use of a vacuum pump for quenching and subsequent extraction of intracellular metabolites from CHO (Chinese hamster ovary) suspension cells, which uses commercially available components. The method allows transfer of washed cells into liquid nitrogen within 10-15s of sampling and recovers the entire extraction solution volume. It also has the advantage to remove residual filter filaments in the final sample, thus preventing damage to separation columns during subsequent MS analysis. Relative to other methods currently used in the literature, the resulting energy charge of intracellular adenosine nucleotides was increased to 0.94 compared to 0.90 with cold PBS quenching or 0.82 with cold methanol/AMBIC quenching.
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Quantitative metabolite profiling utilizing parallel column analysis for simultaneous reversed-phase and hydrophilic interaction liquid chromatography separations combined with tandem mass spectrometry.
Anal. Chem.
PUBLISHED: 04-08-2014
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In this work, a fully automated parallel LC column method was established in order to perform orthogonal hydrophilic interaction chromatography (HILIC) and reversed-phase (RPLC) chromatography within one analytical run for targeted quantitative mass spectrometric determination of metabolites from central carbon metabolism. In this way, the analytical throughput could be significantly improved compared to previously established dual separation work flows involving two separate analytical runs. Two sample aliquots were simultaneously injected onto a dual column setup columns using a ten-port valve, and parallel separations were carried out. Sub 2 ?m particle size stationary phases were employed for both separation methods. HILIC and RPLC eluents were combined post column followed by ESI-MS/MS detection. The orthogonal separations were optimized, aiming at an overall separation with 2 retention time segments, while reversed-phase separation was accomplished within 5.5 min; metabolites on the HILIC phase were retained for a minimum time of 6 min. The overall run time was 15 min. The setup was applied to the quantification of 30 primary intercellular metabolites, including amino acids, organic acids, and nucleotides employing internal standardization by a fully (13)C-labeled yeast extract. The comparison with HILIC-MS/MS and RPLC-MS/MS in separate analytical runs revealed that an excellent analytical performance was achieved by the parallel LC column method. The experimental repeatability (N = 5) was on average <5% (only for 2 compounds >5%). Moreover, limits of detection for the new approach ranging from 0.002-15 ?M were in a good agreement with ones obtained in separate HILIC-MS/MS and RPLC-MS/MS runs (ranging from 0.01-44 ?M).
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Effect of the L499M mutation of the ascomycetous Botrytis aclada laccase on redox potential and catalytic properties.
Acta Crystallogr. D Biol. Crystallogr.
PUBLISHED: 03-24-2014
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Laccases are members of a large family of multicopper oxidases that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of dioxygen to water. These enzymes contain four Cu atoms per molecule organized into three sites: T1, T2 and T3. In all laccases, the T1 copper ion is coordinated by two histidines and one cysteine in the equatorial plane and is covered by the side chains of hydrophobic residues in the axial positions. The redox potential of the T1 copper ion influences the enzymatic reaction and is determined by the nature of the axial ligands and the structure of the second coordination sphere. In this work, the laccase from the ascomycete Botrytis aclada was studied, which contains conserved Ile491 and nonconserved Leu499 residues in the axial positions. The three-dimensional structures of the wild-type enzyme and the L499M mutant were determined by X-ray crystallography at 1.7?Å resolution. Crystals suitable for X-ray analysis could only be grown after deglycosylation. Both structures did not contain the T2 copper ion. The catalytic properties of the enzyme were characterized and the redox potentials of both enzyme forms were determined: E0 = 720 and 580?mV for the wild-type enzyme and the mutant, respectively. Since the structures of the wild-type and mutant forms are very similar, the change in the redox potential can be related to the L499M mutation in the T1 site of the enzyme.
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Sample preparation workflow for the liquid chromatography tandem mass spectrometry based analysis of nicotinamide adenine dinucleotide phosphate cofactors in yeast.
J Sep Sci
PUBLISHED: 03-14-2014
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The accurate quantification of the highly unstable intracellular cofactor nicotinamide adenine dinucleotide phosphate in its oxidized and reduced forms demands a thorough evaluation of the analytical workflow and dedicated methods reflecting their solution chemistry as well as the biological importance of their ratio. In this work, we present a workflow for the analysis of intracellular levels of oxidized and reduced nicotinamide adenine dinucleotide phosphate in the yeast Pichia pastoris, including hot aqueous extraction, chromatographic separation in reversed-phase conditions employing a 100% wettable stationary phase, and subsequent tandem mass spectrometric analysis. A thorough evaluation and optimization of the sample preparation procedure resulted in excellent biological repeatabilities (on average <10%, N = 3) without employing an internal standardization approach. As a consequence, the methodology proved to be appropriate for the relative assessment of intracellular levels of oxidized and reduced nicotinamide adenine dinucleotide phosphate in different P. pastoris strains. The ratio of reduced versus oxidized nicotinamide adenine dinucleotide phosphate was significantly higher in an engineered strain overexpressing glucose-6-phosphate dehydrogenase than in the corresponding wildtype strain. Interestingly, a difference was also observed in the nicotinamide adenine dinucleotide phosphate pool size, which was significantly higher in the wildtype than in the modified strain.
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Flow injection combined with ICP-MS for accurate high throughput analysis of elemental impurities in pharmaceutical products according to USP <232>/<233>.
J Pharm Biomed Anal
PUBLISHED: 02-21-2014
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New guidelines of the United States Pharmacopeia (USP), European Pharmacopeia (EP) and international organization (ICH, International Conference on Harmonization) regulating elemental impurity limits in pharmaceuticals seal the end of unspecific analysis of metal(oid)s as outlined in USP <231> and EP 2.4.8. Chapter USP <232> and EP 5.20 as well as drafts from ICH Q3D specify both daily doses and concentration limits of metallic impurities in pharmaceutical final products and in active pharmaceutical ingredients (API) and excipients. In chapters USP <233> and EP 2.4.20 method implementation, validation and quality control during the analytical process are described. By contrast with the--by now--applied methods, substance specific quantitative analysis features new basic requirements, further, significantly lower detection limits ask for the necessity of a general changeover of the methodology toward sensitive multi element analysis by ICP-AES and ICP-MS, respectively. A novel methodological approach based on flow injection analysis and ICP-SFMS/ICP-QMS for the quick and accurate analysis of Cd, Pb, As, Hg, Ir, Os, Pd, Pt, Rh, Ru, Cr, Mo, Ni, V, Cu, Mn, Fe and Zn in drug products by prior dilution, dissolution or microwave assisted closed vessel digestion according to the regulations is presented. In comparison to the acquisition of continuous signals, this method is advantageous with respect to the unprecedented high sample throughput due to a total analysis time of approximately 30s and the low sample consumption of below 50 ?L, while meeting the strict USP demands on detection/quantification limits, precision and accuracy.
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Fully automated on-line two-dimensional liquid chromatography in combination with ESI MS/MS detection for quantification of sugar phosphates in yeast cell extracts.
Analyst
PUBLISHED: 01-29-2014
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A mass spectrometric quantitative assay was developed for the analysis of 10 sugar phosphates in the yeast Pichia pastoris. As a novelty, two-dimensional chromatography based on a fully automated heart-cutting LC-LC technique was introduced. Using a ten-port valve, ten fractions of the first chromatographic dimension, i.e. anion exchange chromatography (AEC), were transferred and separated by the orthogonal second dimension, i.e. separation on porous graphitized carbon. The chromatographic separation on the second dimension was optimized for each transferred fraction minimizing the separation time and ensuring complete removal of the salt constituents of the AEC eluents. The latter being crucial for electrospray mass spectrometric detection was confirmed by combining the LC-LC separation with on-line ICP-MS detection. These measurements showed that sodium elution was completed after 0.8 min. Consequently, an analysis time of 1 min per transferred peak was established. In this way, the excellent peak capacity given by ion exchange could be conserved in the second dimension at the same time enabling mass spectrometric detection. Sub-?M limits of detection could be obtained by the new LC-LC-MS/MS methods ranging between 0.03 and 0.19 ?M for the investigated compounds (only 3GAP showed a LOD of 1 ?M). The method was applied to the quantification of ten sugar phosphates in yeast extracts utilizing internal standardization with a fully labeled (13)C yeast extract. Typically, the standard uncertainties for N = 3 replicates assessed by the LC-LC-MS/MS set-up were <5%.
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Speciation analysis of orthophosphate and myo-inositol hexakisphosphate in soil- and plant-related samples by high-performance ion chromatography combined with inductively coupled plasma mass spectrometry.
J Sep Sci
PUBLISHED: 01-22-2014
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A novel method based on high-performance ion chromatography inductively coupled plasma mass spectrometry employing strong anion exchange chromatography with HNO3 gradient elution for simultaneous analysis of orthophosphate and myo-inositol hexakisphosphate (IP6 ) in soil solution and plant extracts is presented. As inductively coupled plasma mass spectrometry analysis of phosphorus at m/z 31 is hampered by N-based interferences, (31)P was measured as (31)P(16)O(+) at m/z 47 employing dynamic reaction cell technique with O2 as reaction gas. Orthophosphate and IP6 were separated within a total chromatographic run-time of 12 min revealing a limit of detection of 0.3 ?mol/L. The coefficients of determination obtained in a working range of 1-100 and 1-30 ?mol/L were 0.9991 for orthophosphate and 0.9968 for IP6, respectively. The method was successfully applied to extracts from three different soils as well as root and shoot extracts of Brassica napus L. The precision of three independently prepared soil extracts was in the range of 4-10% relative standard deviation for PO4 (3-) and 3-8% relative standard deviation for IP6. Soil adsorption/desorption kinetics for IP6/orthophosphate were performed for investigating the sorption behavior of the two P species in the experimental soils.
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Model based engineering of Pichia pastoris central metabolism enhances recombinant protein production.
Metab. Eng.
PUBLISHED: 01-20-2014
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The production of recombinant proteins is frequently enhanced at the levels of transcription, codon usage, protein folding and secretion. Overproduction of heterologous proteins, however, also directly affects the primary metabolism of the producing cells. By incorporation of the production of a heterologous protein into a genome scale metabolic model of the yeast Pichia pastoris, the effects of overproduction were simulated and gene targets for deletion or overexpression for enhanced productivity were predicted. Overexpression targets were localized in the pentose phosphate pathway and the TCA cycle, while knockout targets were found in several branch points of glycolysis. Five out of 9 tested targets led to an enhanced production of cytosolic human superoxide dismutase (hSOD). Expression of bacterial ?-glucuronidase could be enhanced as well by most of the same genetic modifications. Beneficial mutations were mainly related to reduction of the NADP/H pool and the deletion of fermentative pathways. Overexpression of the hSOD gene itself had a strong impact on intracellular fluxes, most of which changed in the same direction as predicted by the model. In vivo fluxes changed in the same direction as predicted to improve hSOD production. Genome scale metabolic modeling is shown to predict overexpression and deletion mutants which enhance recombinant protein production with high accuracy.
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Accurate LC-ESI-MS/MS quantification of 2'-deoxymugineic acid in soil and root related samples employing porous graphitic carbon as stationary phase and a ¹³C?-labeled internal standard.
Electrophoresis
PUBLISHED: 01-08-2014
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For the first time the phytosiderophore 2'-deoxymugineic acid (DMA) could be accurately quantified by LC-MS/MS in plant and soil related samples. For this purpose a novel chromatographic method employing porous graphitic carbon as stationary phase combined with ESI-MS/MS detection in selected reaction monitoring was developed. Isotope dilution was implemented by using in-house synthesized DMA as external calibrant and ¹³C?-labeled DMA as internal standard (concentration levels of standards 0.1-80 ?M, determination coefficient of linear regression R² > 0.9995). Sample preparation involved acidification of the samples in order to obtain complete dissociation of metal-DMA complexes. Excellent matrix related LOD and LOQ depending on different experimental setups were obtained in the range of 3-34 nM and 11-113 nM, respectively. Standard addition experiments and the implementation of the internal ¹³C?-DMA standard proved the accuracy of the quantification strategy even in complex matrices such as soil solution. The repeatability of the method, including sample preparation, expressed as short- and long term precision was below 4 and 5% RSD, respectively. Finally, application in the context of plant and soil research to samples from rhizosphere sampling via micro suction cups, from soil solutions and soil adsorption/extraction studies revealed a DMA concentration range from 0.1 to 235 ?M.
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Bacterially induced weathering of ultramafic rock and its implications for phytoextraction.
Appl. Environ. Microbiol.
PUBLISHED: 06-21-2013
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The bioavailability of metals in soil is often cited as a limiting factor of phytoextraction (or phytomining). Bacterial metabolites, such as organic acids, siderophores, or biosurfactants, have been shown to mobilize metals, and their use to improve metal extraction has been proposed. In this study, the weathering capacities of, and Ni mobilization by, bacterial strains were evaluated. Minimal medium containing ground ultramafic rock was inoculated with either of two Arthrobacter strains: LA44 (indole acetic acid [IAA] producer) or SBA82 (siderophore producer, PO4 solubilizer, and IAA producer). Trace elements and organic compounds were determined in aliquots taken at different time intervals after inoculation. Trace metal fractionation was carried out on the remaining rock at the end of the experiment. The results suggest that the strains act upon different mineral phases. LA44 is a more efficient Ni mobilizer, apparently solubilizing Ni associated with Mn oxides, and this appeared to be related to oxalate production. SBA82 also leads to release of Ni and Mn, albeit to a much lower extent. In this case, the concurrent mobilization of Fe and Si indicates preferential weathering of Fe oxides and serpentine minerals, possibly related to the siderophore production capacity of the strain. The same bacterial strains were tested in a soil-plant system: the Ni hyperaccumulator Alyssum serpyllifolium subsp. malacitanum was grown in ultramafic soil in a rhizobox system and inoculated with each bacterial strain. At harvest, biomass production and shoot Ni concentrations were higher in plants from inoculated pots than from noninoculated pots. Ni yield was significantly enhanced in plants inoculated with LA44. These results suggest that Ni-mobilizing inoculants could be useful for improving Ni uptake by hyperaccumulator plants.
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In vitro studies on cisplatin focusing on kinetic aspects of intracellular chemistry by LC-ICP-MS.
Metallomics
PUBLISHED: 03-13-2013
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To date, preclinical studies have addressed drug accumulation and intracellular distribution of cisplatin by determination of the total Pt content. In this work, the use of liquid chromatography in combination with inductively coupled plasma mass spectrometry (LC-ICP-MS) enabled accurate intact cisplatin quantification in cell model experiments. Hence, for the first time, intracellular drug degradation, drug accumulation and drug efflux were studied by actually quantifying the intact drug, along with the total Pt content of the cell nucleus, the cytosol and the low molecular weight fraction of the cytosol. The latter fraction was obtained by centrifugal filtration (cut-off filter of 10 kDa). Flow injection (FI)-ICP-MS was implemented for platinum quantification. In a first step, kinetics of intracellular cisplatin degradation was addressed by incubating cell extracts with sub-?M drug concentration levels. A half-life of 2 hours was observed in cell extracts of two different cancer cell lines (colon carcinoma and human mesothelioma), which was significantly shorter than that observed in sodium chloride. Hence, it was suggested that intact and nonaquated cisplatin was reacting with cellular components. Due to the large excess of potential binding partners pseudo first order kinetics were observed. The drug accumulation experiments revealed rapid uptake of the drug into the cytosol and the nucleus. Moreover, a significant fraction of Pt was bound to intracellular high molecular weight biomolecules after one hour of exposure. With ongoing time, the intracellular Pt concentration was increasing. However, the cisplatin concentration remained constant during 5 hours of continuous exposure. Assuming a cell volume of 10(-12) L, an intracellular concentration corresponding to the cisplatin concentration in the cell culture medium (5 ?M) was estimated. At any time of investigation, intact cisplatin was the predominant species in the low molecular weight fraction of the cytosol. These findings support the hypothesis of passive diffusion as an uptake mechanism. Finally, a model experiment was designed resembling the situation of limited drug exposure time. Human mesothelioma cells were incubated with 5 ?M cisplatin for 3 hours. Then the culture medium was replaced and the drug efflux was studied. The observed efflux was biphasic, with the intact cisplatin being removed within the first hour of investigation, while the Pt-protein adduct fraction was removed only partially (30% were still found in the cytosol after 24 hours). No net transfer of Pt from the cytosol to the nucleus fraction was observed after medium replacement.
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Interlaboratory comparison for quantitative primary metabolite profiling in Pichia pastoris.
Anal Bioanal Chem
PUBLISHED: 02-08-2013
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For the first time, an interlaboratory comparison was performed in the field of quantitative metabolite profiling in Pichia pastoris. The study was designed for the evaluation of different measurement platforms integrating different quantification strategies using internal standardization. Nineteen primary metabolites including amino acids and organic acids were selected for the study. Homogenous samples were obtained from chemostat fermentations after rapid sampling, quenching and filtration, and hot ethanol extraction. Laboratory 1 (BOKU) employed an in vivo-synthesized fully labeled U(13)C cell extracts of P. pastoris for immediate internal standardization upon cell extraction. Quantification was carried out using orthogonal reversed-phase (RP-LC) and hydrophilic interaction chromatography (HILIC) in combination with tandem mass spectrometry. Laboratory 2 (Biocrates) applied a metabolomics kit allowing fully automated, rapid derivatization, solid phase extraction and internal standardization in 96-well plates with immobilized isotopically enriched internal standards in combination with HILIC-MS-MS and RP-LC-MS-MS for organic acids and derivatized amino acids, respectively. In this study, the obtained intracellular concentrations ranged from 0.2 to 108 ?mol g(-1) cell dry weight. The total combined uncertainty was estimated including uncertainty contributions from the corresponding MS-based measurement and sample preparation for each metabolite. Evidently, the uncertainty contribution of sample preparation was lower for the values obtained by laboratory 1, implementing isotope dilution upon extraction. Total combined uncertainties (K = 2) ranging from 21 to 48% and from 30 to 57% were assessed for the quantitative results obtained in laboratories 1 and 2, respectively. The major contribution arose from sample preparation, hence from repeatability precision of the extraction procedure. Finally, the laboratory intercomparison was successful as most of the investigated metabolites showed concentration levels agreeing within their total combined uncertainty, implying that accurate quantification was given. The application of isotope dilution upon extraction was an absolute prerequisite for the quantification of the redox-sensitive amino acid methionine, where no agreement between the two laboratories could be achieved.
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LC- and CZE-ICP-MS approaches for the in vivo analysis of the anticancer drug candidate sodium trans-[tetrachloridobis(1H-indazole)ruthenate(III)] (KP1339) in mouse plasma.
Metallomics
PUBLISHED: 09-21-2011
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Ruthenium-indazole complexes are promising anticancer agents undergoing clinical trials. KP1339 is administered intravenously (i.v.), where serum proteins are the first available biological binding partners. In order to gain a better insight into the mode of action, mice were treated with different doses of KP1339 i.v. and sacrificed at different time points. The blood plasma was isolated from blood samples and analyzed by capillary zone electrophoresis (CZE) and size exclusion/anion exchange chromatography (SEC-IC) both combined on-line to inductively coupled plasma-mass spectrometry (ICP-MS). The performance of the analytical methodology was compared and the interaction of KP1339 with mouse plasma proteins characterized in vivo. Interestingly, the samples of the mice treated with 50 mg kg(-1) and terminated after 24 h showed a ca. 4-fold lowered albumin content and increased ruthenation of albumin aggregates as compared to the untreated control group and the 40 mg kg(-1) group. The majority of Ru was bound to albumin and the stoichiometry of the KP1339 protein binding was determined through the molar Ru/S ratio. In general, good agreement of the data obtained with both techniques was achieved and the SEC-IC method was found to be more sensitive as compared to the CZE-ICP-MS approach, whereas the latter benefits from the shorter analysis time and lower sample consumption.
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Stability assessment of different chelating moieties used for elemental labeling of bio-molecules.
Metallomics
PUBLISHED: 09-16-2011
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Integrating elemental labeling in quantitative LC-ICP-MS based bio-analysis requires fundamental experiments concerning the stability of complexes during analysis. In a competitive approach complex stability of the chelating moieties 1,4,7,10-tetraazacyclododecane-N,N,N,N-tetraaceticacid (DOTA), 1,4,7-triazacyclononane-N,N,N-triacetic acid (NOTA) and diethylenetriaminepentaacetic dianhydride (DTPA) in combination with 11 different lanthanides was investigated under typical chromatographic conditions. Measurements were carried out via LC-ICP-QMS using a novel mixed mode separation method. The influence of chromatographic separation, pH and temperature on complex stability constants was assessed regarding further applications of multiplexing in bio-analytical assays. The limit of detection (LOD) for LC-ICP-QMS was 0.03 nM for all investigated Tm complexes (0.15 fmol absolute). Quantification of the complexes was performed via external, flow injection based calibration. For all investigated complexes the stability was significantly decreased by the chromatographic conditions. Moreover, complexation by DOTA revealed two different signals suggesting the presence of a stable intermediate product. Ln(3+)-DOTA and Ln(3+)-NOTA complexes provided high stability at 5 °C and 37 °C over a time of 12 hours, whereas Ln(3+)-DTPA complexes showed significant degradation at 37 °C.
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High-throughput flow injection analysis of labeled peptides in cellular samples - ICP-MS analysis versus fluorescence based detection.
Int J Mass Spectrom
PUBLISHED: 07-15-2011
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A high throughput method based on flow injection analysis was developed and validated for the quantification of the peptide B?(15-42) in cellular samples comparing different labeling strategies and detection methods. The used labels were 1,4,7,10-tetraazacyclododecane-N, N, N, N-tetraaceticacid (In-DOTA) and 2-(4-isothiocyanatobenzyl) - 1,4,7,10-tetraazacyclododecane-N, N, N, N-tetraacetic acid (In-DOTA-Bn) for elemental labeling. 6-Hydroxy-9-(2-carboxyphenyl)- (3H)-xanthen-3-on (fluorescein) was employed as fluorescence label. The explored peptide (mass = 3 kD) is a novel candidate drug, which shows an anti-inflammatory effect after an event of myocardial infarction. The analysed samples were fractioned cell compartments of human umbilical cord vein endothelial cells (HUVEC) maintained via lysis with Triton X buffer. In order to enhance sensitivity and selectivity of peptide quantification via flow injection the peptide was labeled prior to incubation using elemental and fluorescence labels. Quantification of the elemental and fluorescence labeled peptide was performed via flow injection analysis combined with inductive coupled plasma sector field mass spectrometry (FIA-ICP-SFMS) or fluorescence detection (FIA-FLD), respectively. The employed quantification strategies were external calibration in the case of fluorescence detection and external calibration with and without internal standardization and on-line IDMS in the case of ICP-MS detectionThe limit of detection (LOD) for FIA-ICP-MS was 9 pM In-DOTA-B?(15-42) (0.05 fmol absolute) whereas FIA-FLD showed a LOD of 100 pM (3 fmol absolute) for the fluorescein labeled peptide. Short term precision of FIA-ICP-MS was superior for all ICP-MS based quantification strategies compared to FIA-FLD (FIA-ICP-SFMS: 0.3-3.3%; FIA-FLD: 6.5%). Concerning long term precision FIA-ICP-SFMS with on-line IDMS and internal standardization showed the best results (3.1 and 4.6%, respectively) whereas the external calibration of both applied methodological approaches was only in the range of 10 %.The concentrations in the Triton X soluble fraction relative to the applied amount of Indium in the cell culture were in the range of 0.75-1.8% for In-DOTA or 0.30-0.79% for the 2-(4-isothiocyanatobenzyl) - 1,4,7,10-tetraazacyclododecane-N, N, N, N-tetraacetic acid (In-DOTA-Bn) labeled peptide B?(15-42). In the Triton X insoluble fraction the relative concentrations of Indium were 0.03-0.18% for the In-DOTA labeled peptide and 0.03-0.13% for B?(15-42)-In-DOTA-Bn.
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Time and substrate dependent exudation of carboxylates by Lupinus albus L. and Brassica napus L.
Plant Physiol. Biochem.
PUBLISHED: 05-31-2011
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Root exudates influence significantly physical, chemical and biological characteristics of rhizosphere soil. Their qualitative and quantitative composition is affected by environmental factors such as pH, soil type, oxygen status, light intensity, soil temperature, plant growth, nutrient availability and microorganisms. The aim of the present study was to assess the influence of growth substrate and plant age on the release of carboxylates from Lupinus albus L. and Brassica napus L. Both plant species were studied in continuously percolated microcosms filled with either sand, soil or sand + soil (1:1) mixture. Soil solution was collected every week at 7, 14, 21, 28 and 35 days after planting (DAP). Carboxylate concentrations were determined by reversed-phase liquid chromatography - electrospray ionization - time of flight mass spectrometry (LC-ESI-TOFMS). Oxalate, citrate, succinate, malate and maleate were detected in soil solutions of both plant species. Their concentrations were correlated with the physiological status of the plant and the growth substrate. Oxalate was the predominant carboxylate detected within the soil solution of B. napus plants while oxalate and citrate were the predominant ones found in the soil solutions of L. albus plants. The sampling determination of carboxylates released by plant roots with continuous percolation systems seems to be promising as it is a non-destructive method and allows sampling and determination of soluble low molecular weight organic compounds derived from root exudation as well as the concentration of soluble nutrients, which both might reflect the nutritional status of plants.
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Modeling and measuring intracellular fluxes of secreted recombinant protein in Pichia pastoris with a novel 34S labeling procedure.
Microb. Cell Fact.
PUBLISHED: 05-16-2011
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The budding yeast Pichia pastoris is widely used for protein production. To determine the best suitable strategy for strain improvement, especially for high secretion, quantitative data of intracellular fluxes of recombinant protein are very important. Especially the balance between intracellular protein formation, degradation and secretion defines the major bottleneck of the production system. Because these parameters are different for unlimited growth (shake flask) and carbon-limited growth (bioreactor) conditions, they should be determined under "production like" conditions. Thus labeling procedures must be compatible with minimal production media and the usage of bioreactors. The inorganic and non-radioactive 34S labeled sodium sulfate meets both demands.
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Distantly related plant and nematode core ?1,3-fucosyltransferases display similar trends in structure-function relationships.
Glycobiology
PUBLISHED: 04-21-2011
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Here, we present a comparative structure-function study of a nematode and a plant core ?1,3-fucosyltransferase based on deletion and point mutations of the coding regions of Caenorhabditis elegans FUT-1 and Arabidopsis thaliana FucTA (FUT11). In particular, our results reveal a novel "first cluster motif" shared by both core and Lewis-type ?1,3-fucosyltransferases of the GT10 family. To evaluate the role of the conserved serine within this motif, this residue was replaced with alanine in FucTA (S218) and FUT-1 (S243). The S218A replacement completely abolished the enzyme activity of FucTA, while the S243A mutant of FUT-1 retained 20% of the "wild-type" activity. Based on the results of homology modeling of FucTA, other residues potentially involved in the donor substrate binding were examined, and mutations of N219 and R226 dramatically affected enzymatic activity. Finally, as both FucTA and FUT-1 were shown to be N-glycosylated, we examined the putative N-glycosylation sites. While alanine replacements at single potential N-glycosylation sites of FucTA resulted in a loss of up to 80% of the activity, a triple glycosylation site mutant still retained 5%, as compared to the control. In summary, our data indicate similar trends in structure-function relationships of distantly related enzymes which perform similar biochemical reactions and form the basis for future work aimed at understanding the structure of ?1,3-fucosyltransferases in general.
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Ionic liquids for extraction of metals and metal containing compounds from communal and industrial waste water.
Water Res.
PUBLISHED: 01-17-2011
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In a fundamental study the potential of ionic liquids based on quaternary ammonium- and phosphonium cations and thiol-, thioether-, hydroxyl-, carboxylate- and thiocyanate-functionalized anions has been assessed for future application in advanced sewage treatment. The elimination of the metal(oid)s Ag, As, Cd, Cr, Cu, Hg, Ni, Pb, Pt, Sn, Zn and the cancerostatic platinum compounds cisplatin and carboplatin was screened using a liquid phase micro-extraction set-up. The analytical tool-set consisted of ICP-SFMS and LC-ICP-MS for quantification of metal(oid)s and cancerostatic platinum compounds, respectively. The purity of the ILs was assessed for the investigated metal(oid)s on the base of present EU environmental quality standards and was found to be sufficient for the intended use. In model solutions at environmental relevant concentrations extraction efficiencies?95% could be obtained for Ag, Cu, Hg and Pt with both phosphonium- and ammonium-based ILs bearing sulphur functionality in the form of thiosalicylate and 2-(methylthiobenzoate) anions, as well as with tricaprylmethylammonium thiocyanate within an extraction time of 120 min. All other metals were extracted to a lower extent (7-79%). In the case of cancerostatic platinum compounds a phosphonium-based IL bearing thiosalicylate functionality showed high extraction efficiency for monoaquacisplatin. For the first time, liquid phase micro extraction with ionic liquids was applied to industrial and communal waste water samples. The concentration of all investigated metal(oid)s could be significantly reduced. The degree of elimination varied with the initial concentration of metals, pH and the amount of suspended particulate matter.
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LC-MS analysis of low molecular weight organic acids derived from root exudation.
Anal Bioanal Chem
PUBLISHED: 05-12-2010
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A sensitive method for quantification of citric, fumaric, malic, malonic, oxalic, trans aconitic, and succinic acid in soil- and root-related samples is presented. The method is based on a novel, fast, and simple esterification procedure and subsequent analysis via liquid chromatography-mass spectrometry. Derivatization comprises in situ generation of HCl, which catalyzes the Fischer esterification with benzyl alcohol. As a key advance, the esterification with the aromate allows reversed-phase separation and improves electrospray ionization efficiency. The method provided procedural detection limits of 1 nM for citric, 47 nM for fumaric, 10 nM for malic, 10 nM for malonic, 16 nM for oxalic, 15 nM for succinic, and 2 nM for aconitic acid utilizing 500 ?L of liquid sample. The working range was 3 nM to 10 ?M for citric acid, 158 nM to 10 ?M for fumaric acid, 34 nM to 10 ?M for malic acid, 33 nM to 10 ?M for malonic acid, 53 nM to 10 ?M for oxalic acid, 48 nM to 10 ?M for succinic acid, and 6 nM to 10 ?M for aconitic acid. Quantification of the analytes in soil-related samples was performed via external calibration of the entire procedure utilizing (13)C-labeled oxalic and citric acid as internal standards. The robustness of the method was tested with soil extracts and samples from hydroponic experiments. The latter concerned the regulation of phosphorus solubilization via plant root exudation of citric, malic, and oxalic acid.
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Hydrophilic interaction LC combined with electrospray MS for highly sensitive analysis of underivatized amino acids in rhizosphere research.
J Sep Sci
PUBLISHED: 03-16-2010
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Analysis of underivatized amino acids is challenging regarding the separation as well as the detection of these small polar analytes. Hydrophilic interaction LC using a 2.1x150 mm ZIC (ZIC, zwitterionic)-hydrophilic interaction LC from SeQuant as stationary phase with 1% v/v formic acid in water and ACN as eluents was combined with MS/MS in multiple reaction monitoring mode for the separation and the detection of 16 underivatized amino acids. Regression coefficients of eight or seven point calibrations varied from 0.9454 to 0.9993. Absolute LODs and LOQ (on column) were in the fmol range (0.1-12 and 0.4-41 fmol, respectively). A fast screening method of 19 min total runtime has been developed offering applicability to samples from rhizosphere studies--characterized by low analyte concentrations and complex matrices. A successful application to the analysis of tyrosine in samples from soil adsorption experiments is presented as well as an evaluated enrichment procedure for amino acids derived from plant culture in nutrient solution.
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Complexation of metals by phytosiderophores revealed by CE-ESI-MS and CE-ICP-MS.
Electrophoresis
PUBLISHED: 03-09-2010
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CE-ESI-MS and CE-ICP-MS were implemented for studying three phytosiderophores (mugineic acid, epi-mugineic acid and deoxymugineic acid) and their metal complexes. Free ligands and ferric complexes were analyzed using the first methodology, while six free metals (Co(II), Cu(II), Fe(III), Mn(II), Ni(II) and Zn(II)) together with the corresponding complexes were investigated by the latter technique. CE separation was realized at a voltage of +25 kV employing a BGE containing 20 mM ammonium bicarbonate at pH 7.2. Both techniques revealed limits of detection in the high nM to low microM range. Standard additions to hydroponic samples of H. distichon, cv. Bodega (spring barley) showed regression coefficients for the metal-ligand complexes ranging from 0.984 to 0.999. Additionally, results of a competitivity study allowed the determination of relative metal-phytosiderophore complex stability constants of deoxymugineic/mugineic acid.
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Environmental application of elemental speciation analysis based on liquid or gas chromatography hyphenated to inductively coupled plasma mass spectrometry--a review.
Anal. Chim. Acta
PUBLISHED: 01-19-2010
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In recent years the number of environmental applications of elemental speciation analysis using inductively coupled plasma mass spectrometry (ICP-MS) as detector has increased significantly. The analytical characteristics, such as extremely low detection limits (LOD) for almost all elements, the wide linear range, the possibility for multi-elemental analysis and the possibility to apply isotope dilution mass spectrometry (IDMS) make ICP-MS an attractive tool for elemental speciation analysis. Two methodological approaches, i.e. the combination of ICP-MS with high performance liquid chromatography (HPLC) and gas chromatography (GC), dominate the field. Besides the investigation of metals and metalloids and their species (e.g. Sn, Hg, As), representing "classic" elements in environmental science, more recently other elements (e.g. P, S, Br, I) amenable to ICP-MS determination were addressed. In addition, the introduction of isotope dilution analysis and the development of isotopically labeled species-specific standards have contributed to the success of ICP-MS in the field. The aim of this review is to summarize these developments and to highlight recent trends in the environmental application of ICP-MS coupled to GC and HPLC.
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Ultra-fast HPLC-ICP-MS analysis of oxaliplatin in patient urine.
Anal Bioanal Chem
PUBLISHED: 01-13-2010
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A novel method for rapid HPLC-ICP-MS analysis of oxaliplatin in human urine was developed implementing a stationary HPLC phase with a particle size of 1.8 microm. The method allowed a cycle time of <1 min at a HPLC flow rate of 0.9 mL min(-1). Procedural limits of detection of 0.05 microg L(-1) oxaliplatin (150 fg on column) were obtained. Analysis of oxaliplatin in patient urine showed that accurate quantification of the intact drug demanded for storage at -80 degrees C and rapid measurement after thawing.
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Accurate quantification of the redox-sensitive GSH/GSSG ratios in the yeast Pichia pastoris by HILIC-MS/MS.
Anal Bioanal Chem
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A novel method for the simultaneous quantification of both glutathione (GSH) and its oxidized form glutathione disulfide (GSSG) by hydrophilic interaction chromatography-MS/MS has been developed and is critically discussed. Internal standardization based on isotopically labeled standards for both analytes is an absolute prerequisite for accurate quantification of this redox pair. Hence, a highly efficient and selective miniaturized procedure for the synthesis of isotopically labeled GSSG from commercially available glutathione-(glycine-(13)C(2),(15)N) was established using H(2)O(2) as oxidant and NaI as catalyst. Moreover, a tool is presented to monitor and hence uncover artifactual GSSG formation due to oxidation of GSH during sample preparation, which is the main source of systematic error in GSSG analysis. For this purpose, we propose to monitor the oxidation product formed by reaction of naturally occurring GSH with the isotopically labeled GSH used as internal standard. For the determination of GSH/GSSG ratios in yeast, different extraction methods based on (1) hot extraction with aqueous, acidic, or organic solvents, (2) mechanical cell lysis, and (3) extraction at subambient temperature were investigated in terms of recovery, extraction efficiency, and artifactual formation of GSSG. Total combined uncertainties of as low as 25-30 % (coverage factor=2) for the determination of GSH/GSSG ratios without derivatization were made possible by the addition of the internal standards early in the analytical procedure (before extraction) and immediate analysis of the analytes.
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U13C cell extract of Pichia pastoris--a powerful tool for evaluation of sample preparation in metabolomics.
J Sep Sci
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Quantitative metabolic profiling is preceded by dedicated sample preparation protocols. These multistep procedures require detailed optimization and thorough validation. In this work, a uniformly (13)C-labeled (U(13)C) cell extract was used as a tool to evaluate the recoveries and repeatability precisions of the cell extraction and the extract treatment. A homogenous set of biological replicates (n = 15 samples of Pichia pastoris) was prepared for these fundamental experiments. A range of less than 30 intracellular metabolites, comprising amino acids, nucleotides, and organic acids were measured both in monoisotopic (12)C and U(13)C form by LC-MS/MS employing triple quadrupole MS, reversed phase chromatography, and HILIC. Recoveries of the sample preparation procedure ranging from 60 to 100% and repeatability precisions below 10% were obtained for most of the investigated metabolites using internal standardization approaches. Uncertainty budget calculations revealed that for this complex quantification task, in the optimum case, total combined uncertainty of 12% could be achieved. The optimum case would be represented by metabolites, easy to extract from yeast with high and precise recovery. In other cases the total combined uncertainty was significantly higher.
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Systems biology approach for in vivo photodynamic therapy optimization of ruthenium-porphyrin compounds.
J. Photochem. Photobiol. B, Biol.
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Two arene ruthenium porphyrin compounds showing interesting photodynamic activity in vitro, [Ru(?(6)-p-Pr(i)C(6)H(4)Me)(PMP)Cl(2)] (PMP=5-(3-pyridyl)-10,15,20-triphenylporphyrin) and [Ru(4)(?(6)-p-Pr(i)C(6)H(4)Me)(4)(PTP)Cl8] (PTP=5,10,15,20-tetra(3-pyridyl)porphyrin) coined Rut1 and Rut4 respectively, have been evaluated in vivo. Porphyrins alone and the arene ruthenium porphyrin derivatives (Rut1 and Rut4) showed comparable spectroscopic and photophysical properties. The in vivo study consisted in selecting the optimal arene ruthenium porphyrin photosensitizer by using an original experimental design approach on mice bearing an ectopic human oral carcinoma xenograft. The model of experimental design demonstrated to be well suited to the empirical model-building of photodynamic therapy (PDT) response. Arene ruthenium porphyrins concentration and fluence level demonstrated no statistically significant influence on the tumor growth. On the contrary, the presence of ruthenium groups improved the in vivo photodynamic efficiency. By optical fiber fluorimetry, we demonstrated that both compounds exhibited enhanced accumulation in KB tumors from 24h to 96 h post-intravenous injection. These experiments were completed by inductively coupled plasma mass spectrometry quantification of ruthenium in different organs including tumor tissue. Despite a statistically significant in vivo photodynamic efficiency for Rut4, cellular localization in human oral carcinoma KB cells using fluorescence microscopy demonstrated that both conjugates Rut1 and Rut4 accumulated only in cytoplasm of KB cells but not in the nucleus.
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Monitoring the production process of selenized yeast by elemental speciation analysis.
Metallomics
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Elemental speciation analysis was implemented as an essential tool set addressing optimum fermentation conditions for the production of selenized yeast feed supplements. Accordingly, the study addressed intracellular levels of (1) total selenium and sulfur, (2) seleno methionine (SeMet), (3) cysteine (Cys) and methionine (Met) and (4) selenite and selenate. Dedicated sample preparation- and LC-ICP-MS methods were implemented and validated using the reference material Selm-1. Excellent repeatability precisions <10% (n = 4 biological replicates) could be obtained for all parameters. The study comprised fermentation monitoring over 72 hours (6 different time points) for a Saccharomyces cerevisiae strain under different selenite feed conditions. It was observed that for this strain an increase in the selenium concentration in the fermentation feed by 50% did not result in enhanced selenium accumulation. Fermentation monitoring of three different Saccharomyces cerevisiae strains under the same conditions showed strain specific selenium uptake after 72 hours. The strain with the lowest cell viability of 60% showed the lowest SeMet content. After 47 h of fermentation, all strains reached a critical point, at which seleno methionine accounted for approximately 100% of the total selenium and cell viability started to decrease. This could be explained by sulfur limitation and/or excess of the seleno methionine storage capacity. Strains showing cell viability of approx. 90% after 72 hours of fermentation revealed SeMet concentrations up to 3000 ?g g(-1). In the final product, an apparent threshold level for Met/SeMet of approx. 1 was observed for all strains.
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Elemental labelling combined with liquid chromatography inductively coupled plasma mass spectrometry for quantification of biomolecules: a review.
Anal. Chim. Acta
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This article reviews novel quantification concepts where elemental labelling is combined with flow injection inductively coupled plasma mass spectrometry (FI-ICP-MS) or liquid chromatography inductively coupled plasma mass spectrometry (LC-ICP-MS), and employed for quantification of biomolecules such as proteins, peptides and related molecules in challenging sample matrices. In the first sections an overview on general aspects of biomolecule quantification, as well as of labelling will be presented emphasizing the potential, which lies in such methodological approaches. In this context, ICP-MS as detector provides high sensitivity, selectivity and robustness in biological samples and offers the capability for multiplexing and isotope dilution mass spectrometry (IDMS). Fundamental methodology of elemental labelling will be highlighted and analytical, as well as biomedical applications will be presented. A special focus will lie on established applications underlining benefits and bottlenecks of such approaches for the implementation in real life analysis. Key research made in this field will be summarized and a perspective for future developments including sophisticated and innovative applications will given.
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Removal of Cr, Mn, and Co from textile wastewater by horizontal rotating tubular bioreactor.
Environ. Sci. Technol.
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Environmental pollution by industrial wastewaters polluted with toxic heavy metals is of great concern. Various guidelines regulate the quality of water released from industrial plants and of surface waters. In wastewater treatment, bioreactors with microbial biofilms are widely used. A horizontal rotating tubular bioreactor (HRTB) is a combination of a thin layer and a biodisc reactor with an interior divided by O-ring shaped partition walls as carriers for microbial biomass. Using a biofilm of heavy metal resistant bacteria in combination with this special design provides various advantages for wastewater treatment proven in a pilot study. In the presented study, the applicability of HRTB for removing metals commonly present in textile wastewaters (chromium, manganese, cobalt) was investigated. Artificial wastewaters with a load of 125 mg/L of each metal underwent the bioreactor treatment. Different process parameters (inflow rate, rotation speed) were applied for optimizing the removal efficiency. Samples were drawn along the bioreactor length for monitoring the metal contents on site by UV-vis spectrometry. The metal uptake of the biomass was determined by ICP-MS after acidic microwave assisted digestion. The maximum removal rates obtained for chromium, manganese, and cobalt were: 100%, 94%, and 69%, respectively.
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Mass spectrometry based analysis of nucleotides, nucleosides, and nucleobases--application to feed supplements.
Anal Bioanal Chem
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In this work, accurate MS-based methods for quantitative profiling of nucleotides, nucleosides, and nucleobases in yeast extracts used as additives in animal feedstuff are presented. Reversed-phase chromatography utilizing a stationary phase compatible with 100% aqueous mobile phases resulted in superior analytical figures of merit than HILIC or ion-pair reversed-phase separation. The novel separation method was combined with both molecular and elemental mass spectrometry. By use of RP-LC-MS-MS, excellent limits of detection <1 ?mol L(-1) could be obtained for all the compounds investigated. The elemental speciation analysis approach enabled determination of nucleotides by phosphorus detection. Sensitivity of LC-ICP-MS was 1-2 orders of magnitude lower than that of LC-MS-MS. Quantitative analysis of yeast products using complementary MS detection furnished values in good agreement.
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Analysis of iron-phytosiderophore complexes in soil related samples: LC-ESI-MS/MS versus CE-MS.
Electrophoresis
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Phytosiderophores (PS) form stable complexes with various transition metals. These ligands are exuded by the roots of graminacous plants as a mechanism for mobilizing and acquiring soil iron. To investigate iron mobilization and transport, a novel LC method in combination with ESI-MS/MS for the determination of three Fe(III)-complexes with mugineic acid (MA), 2-epi-MA and 2-deoxymugineic acid (DMA) has been developed. Liquid chromatographic separation was realized using a silica-based mixed-mode reversed phase/weak-anion exchange type stationary phase and a 50 mM ammonium acetate buffer, pH 6.5. Baseline separation of the two complex diastereomers Fe(III)-MA and Fe(III)-epi-MA could be achieved. ESI-MS/MS detection allowed for simultaneous quantification of the complexes and the free ligands. Limits of detection were determined to be 0.001 and 0.05 ?M for DMA and Fe(III)-DMA, respectively. The analytical figures of merit of the novel method were evaluated and compared with a CE-ESI-MS method that we had published earlier. The LC-ESI-MS/MS method has been successfully applied to real samples derived from preliminary extraction experiments.
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Oxidative protein folding and unfolded protein response elicit differing redox regulation in endoplasmic reticulum and cytosol of yeast.
Free Radic. Biol. Med.
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Oxidative protein folding can exceed the cellular secretion machinery, inducing the unfolded protein response (UPR). Sustained endoplasmic reticulum (ER) stress leads to cell stress and disease, as described for Alzheimer, Parkinson, and diabetes mellitus, among others. It is currently assumed that the redox state of the ER is optimally balanced for formation of disulfide bonds using glutathione as the main redox buffer and that UPR causes a reduction of this organelle. The direct effect of oxidative protein folding in the ER, however, has not yet been dissected from UPR regulation. To measure in vivo redox conditions in the ER and cytosol of the yeast model organism Pichia pastoris we targeted redox-sensitive roGFP variants to the respective organelles. Thereby, we clearly demonstrate that induction of the UPR causes reduction of the cytosol in addition to ER reduction. Similarly, a more reduced redox state of the cytosol, but not of the ER, is observed during oxidative protein folding in the ER without UPR induction, as demonstrated by overexpressing genes of disulfide bond-rich secretory proteins such as porcine trypsinogen or protein disulfide isomerase (PDI1) and ER oxidase (ERO1). Cytosolic reduction seems not to be caused by the action of glutathione reductase (GLR1) and could not be compensated for by overexpression of cytosolic glutathione peroxidase (GPX1). Overexpression of GPX1 and PDI1 oxidizes the ER and increases the secretion of correctly folded proteins, demonstrating that oxidative protein folding per se is enhanced by a more oxidized ER and is counterbalanced by a more reduced cytosol. As the total glutathione concentration of these strains does not change significantly, but the ratio of GSH to GSSG is altered, either transport or redox signaling between the glutathione pools of ER and cytosol is assumed. These data clearly demonstrate that protein folding and ER stress have a severe impact on the cytosolic redox balance, which may be a major factor during development of folding-related diseases.
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