Sample records for efficient isotopic labeling

  1. A method for efficient isotopic labeling of recombinant proteins

    Microsoft Academic Search

    Jonathan Marley; Min Lu; Clay Bracken

    2001-01-01

    A rapid and efficient approach for preparing isotopically labeled recombinant proteins is presented. The method is demonstrated for 13C labeling of the C-terminal domain of angiopoietin-2, 15N labeling of ubiquitin and for 2H\\/13C\\/15N labeling of the Escherichia coli outer-membrane lipoprotein Lpp-56. The production method generates cell mass using unlabeled rich media followed by exchange into a small volume of labeled

  2. Efficient and selective isotopic labeling of hemes to facilitate the study of multiheme proteins

    SciTech Connect

    Fonseca, Bruno M.; Tien, Ming; Rivera, Mario; Shi, Liang; Louro, Ricardo O.

    2012-04-02

    Specific isotopic labeling of hemes provides a unique opportunity to characterize the structure and function of heme-proteins. Unfortunately, present day methods do not allow efficient labeling in high yields of multiheme cytochromes c, which are of great biotechnological interest. Here, a method for production of recombinant multiheme cytochromes c in Escherichia coli with isotopically labeled hemes is reported. A small tetraheme cytochrome of 12 kDa from Shewanella oneidensis MR-1 was used to demonstrate the method, achieving a production of 4 mg of pure protein per liter. This method achieves, in a single step, efficient expression and incorporation of hemes isotopically labeled in specific atom positions adequate for spectroscopic characterization of these complex heme proteins. It is, furthermore, of general application to heme proteins opening new possibilities in the characterization of this important class of proteins.

  3. An efficient and cost-effective isotope labeling protocol for proteins expressed in shape Escherichia coli

    Microsoft Academic Search

    Mengli Cai; Ying Huang; Kazuyasu Sakaguchi; G. Marius Clore; Angela M. Gronenborn; Robert Craigie

    1998-01-01

    A cost-effective protocol for uniform 15N and\\/or13 C isotope labeling of bacterially expressed proteins is presented. Unlike most standard protocols, cells are initially grown in a medium containing nutrients at natural abundance and isotopically labeled nutrients are only supplied at the later stages of growth and during protein expression. This permits the accumulation of a large cell mass without the

  4. A novel design for a dual stable isotope continuous labeling chamber: results on labeling efficiency and C and N allocation in Andropogon gerardii

    NASA Astrophysics Data System (ADS)

    Soong, J.; Stewart, C.; Reuss, D.; Pinney, C.; Cotrufo, F. M.

    2010-12-01

    The use of stable isotope enriched plant material can provide an unobstructed method of studying ecosystem nutrient dynamics between plants, soil, and atmosphere. However, the production of uniformly labeled perennial plant material is challenging due to plant physiological constraints and the mechanics of building and operating an isotope labeling system. In this study we present the design of a novel dual 13C and 15N continuous isotope labeling chamber located at Colorado State University. The chamber is equipped with automatic controls for CO2 concentration, temperature, and humidity, and has successfully been used to grow and label the tallgrass perennial Andropogon gerardii in pots from rhizomes. Three different nitrogen fertilization levels were applied to assess how substrate availability may alter growth and overall performance in the system. The efficiency of the 13C and 15N labeling chamber, its design and overall performance, as well as a full C, N, 13C, and 15N budget of the aboveground biomass, belowground biomass, and soil will be presented. Solid samples were analyzed on an EA-IRMS, while air samples from the chamber were analyzed using a precon-GC-IRMS system. The dual stable isotope labeled A. gerardii produced from this chamber will be used in a decomposition experiment to quantify the relative contribution of aboveground litter derived C to soil respiration, dissolved organic carbon, and various soil organic matter pools. Based on the results of our A. gerardii 13C and 15N labeling experiment we believe that this chamber design can be used to successfully produce dual stable isotope labeled plants for a wide variety of terrestrial nutrient flux experiments.

  5. Efficient production of isotopically labeled proteins by cell-free synthesis: A practical protocol

    Microsoft Academic Search

    Takuya Torizawa; Masato Shimizu; Masato Taoka; Hiroshi Miyano; Masatsune Kainosho

    2004-01-01

    We provide detailed descriptions of our refined protocols for the cell-free production of labeled protein samples for NMR spectroscopy. These methods are efficient and overcome two critical problems associated with the use of conventional Escherichia coli extract systems. Endogenous amino acids normally present in E. coli S30 extracts dilute the added labeled amino acids and degrade the quality of NMR

  6. A novel design for a dual stable isotope continuous labeling chamber: results on labeling efficiency and C and N allocation in Andropogon gerardii

    Microsoft Academic Search

    J. Soong; C. Stewart; D. Reuss; C. Pinney; F. M. Cotrufo

    2010-01-01

    The use of stable isotope enriched plant material can provide an unobstructed method of studying ecosystem nutrient dynamics between plants, soil, and atmosphere. However, the production of uniformly labeled perennial plant material is challenging due to plant physiological constraints and the mechanics of building and operating an isotope labeling system. In this study we present the design of a novel

  7. Isotope-labeled immunoassays without radiation waste

    E-print Network

    Hammock, Bruce D.

    Isotope-labeled immunoassays without radiation waste Guomin Shan*, Wei Huang*, Shirley J. Gee with radioactive materials, and (iii) short shelf-life of the labeled re- agents. The advantage of isotopic with ELISA or fluorescent detection systems. We developed a format for isotope label immunoassay

  8. Isotope Labeling in Mammalian Cells

    PubMed Central

    Dutta, Arpana; Saxena, Krishna; Klein-Seetharaman, Judith

    2011-01-01

    Isotope labeling of proteins represents an important and often required tool for the application of nuclear magnetic resonance (NMR) spectroscopy to investigate the structure and dynamics of proteins. Mammalian expression systems have conventionally been considered to be too weak and inefficient for protein expression. However, recent advances have significantly improved the expression levels of these systems. Here, we provide an overview of some of the recent developments in expression strategies for mammalian expression systems in view of NMR investigations. PMID:22167668

  9. Synthesis of isotopically labeled epothilones.

    PubMed

    Ganesh, Thota; Brodie, Peggy J; Banerjee, Abhijit; Bane, Susan; Kingston, David G I

    2014-02-01

    The epothilones, including epothilones B and D, are macrocyclic lactones, which have potent cytotoxicities and promote the polymerization of tubulin to mictotubules by binding to and stabilizing the tubulin polymer. They have a very similar mechanism of action to paclitaxel (Taxol®). The determination of the microtubule-binding conformation of the epothilones is an important piece of information in designing improved analogs for possible clinical use, and internuclear distance information that will assist the determination of this conformation can be obtained by rotational echo double resonance (REDOR) NMR studies of microtubule-bound epothilones with appropriate stable isotope labels. Analogs of epothilone B and epothilone D with [(2) H3 ] and [(19) F] labels were prepared from an advanced precursor for potential use in REDOR NMR studies to determine internuclear distances in tubulin-bound ligand. PMID:24307484

  10. Stereospecific Multiple Isotopic Labeling of Benzyl Alcohol

    PubMed Central

    Roston, Daniel; Kohen, Amnon

    2015-01-01

    Isotopically labeled enzymatic substrates and biological metabolites are useful for many mechanistic analyses, particularly the study of kinetic and equilibrium isotope effects, determining the stereospecificity of enzymes, and resolving metabolic pathways. Here we present the 1-pot synthesis, purification, and kinetic analysis of 7R-[2H]-phenyl-[14C]-benzyl alcohol. The procedure involves a chemoenzymatic synthesis that couples formate dehydrogenase to alcohol dehydrogenase with a catalytic amount of nicotinamide cofactor. The reaction goes to completion overnight, and the measurement of a competitive kinetic isotope effect on the enzymatic oxidation of the purified product identified no 1H contamination. This measurement is very sensitive to such isotopic contamination and verified the high level of isotopic and enantiomeric purity yielded by the new synthetic procedure. PMID:24327376

  11. Stereospecific multiple isotopic labeling of benzyl alcohol.

    PubMed

    Roston, Daniel; Kohen, Amnon

    2014-02-01

    Isotopically labeled enzymatic substrates and biological metabolites are useful for many mechanistic analyses, particularly the study of kinetic and equilibrium isotope effects, determining the stereospecificity of enzymes, and resolving metabolic pathways. Here, we present the one-pot synthesis, purification, and kinetic analysis of 7R-[(2) H]-phenyl-[(14) C]-benzyl alcohol. The procedure involves a chemoenzymatic synthesis that couples formate dehydrogenase to alcohol dehydrogenase with a catalytic amount of nicotinamide cofactor. The reaction goes to completion overnight, and the measurement of a competitive kinetic isotope effect on the enzymatic oxidation of the purified product identified no (1) H contamination. This measurement is very sensitive to such isotopic contamination and verified the high level of isotopic and enantiomeric purity yielded by the new synthetic procedure. PMID:24327376

  12. SILEC: a protocol for generating and using isotopically labeled coenzyme A mass spectrometry standards

    PubMed Central

    Basu, Sankha S; Blair, Ian A

    2013-01-01

    Stable isotope labeling by essential nutrients in cell culture (SILEC) was recently developed to generate isotopically labeled coenzyme A (CoA) and short-chain acyl-CoA thioesters. This was accomplished by modifying the widely used technique of stable isotope labeling by amino acids in cell culture to include [13C315N]-pantothenate (vitamin B5), a CoA precursor, instead of the isotopically labeled amino acids. The lack of a de novo pantothenate synthesis pathway allowed for efficient and near-complete labeling of the measured CoA species. This protocol provides a step-by-step approach for generating stable isotope-labeled short-chain acyl-CoA internal standards in mammalian and insect cells as well as instructions on how to use them in stable isotope dilution mass spectrometric-based analyses. Troubleshooting guidelines, as well as a list of unlabeled and labeled CoA species, are also included. This protocol represents a prototype for generating stable isotope internal standards from labeled essential nutrients such as pantothenate. The generation and use of SILEC standards takes approximately 2–3 weeks. PMID:22157971

  13. Quantifying Peptides in Isotopically Labeled Protease Digests by Ion Mobility/Time-of-Flight

    E-print Network

    Clemmer, David E.

    Quantifying Peptides in Isotopically Labeled Protease Digests by Ion Mobility/Time-of-Flight Mass of isotopically labeled peptides. The isotopic labels were generated by treatment of peptides with N isobaric interferences. Mass spectrometry (MS) techniques and isotopic labeling strategies have been used

  14. Analysis of proteome dynamics in mice by isotopic labeling.

    PubMed

    Price, John C; Ghaemmaghami, Sina

    2014-01-01

    Recent advances in mass spectrometry and in vivo isotopic labeling have enabled proteome-wide analyses of protein turnover in complex organisms. Here, we describe a protocol for analyzing protein turnover rates in mouse tissues by comprehensive (15)N labeling. The procedure involves the complete isotopic labeling of blue green algae (Spirulina platensis) with (15)N and utilizing it as a source of dietary nitrogen for mice. We outline a detailed protocol for in-house production of (15)N-labeled algae, labeling of mice, and analysis of isotope incorporation kinetics by mass spectrometry. The methodology can be adapted to analyze proteome dynamics in most murine tissues and may be particularly useful in the analysis of proteostatic disruptions in mouse models of disease. PMID:24791984

  15. Production of stable isotope-labeled acyl-coenzyme A thioesters by yeast stable isotope labeling by essential nutrients in cell culture.

    PubMed

    Snyder, Nathaniel W; Tombline, Gregory; Worth, Andrew J; Parry, Robert C; Silvers, Jacob A; Gillespie, Kevin P; Basu, Sankha S; Millen, Jonathan; Goldfarb, David S; Blair, Ian A

    2015-04-01

    Acyl-coenzyme A (CoA) thioesters are key metabolites in numerous anabolic and catabolic pathways, including fatty acid biosynthesis and ?-oxidation, the Krebs cycle, and cholesterol and isoprenoid biosynthesis. Stable isotope dilution-based methodology is the "gold standard" for quantitative analyses by mass spectrometry. However, chemical synthesis of families of stable isotope-labeled metabolites such as acyl-CoA thioesters is impractical. Previously, we biosynthetically generated a library of stable isotope internal standard analogs of acyl-CoA thioesters by exploiting the essential requirement in mammals and insects for pantothenic acid (vitamin B5) as a metabolic precursor for the CoA backbone. By replacing pantothenic acid in the cell medium with commercially available [(13)C3(15)N1]-pantothenic acid, mammalian cells exclusively incorporated [(13)C3(15)N1]-pantothenate into the biosynthesis of acyl-CoA and acyl-CoA thioesters. We have now developed a much more efficient method for generating stable isotope-labeled CoA and acyl-CoAs from [(13)C3(15)N1]-pantothenate using stable isotope labeling by essential nutrients in cell culture (SILEC) in Pan6-deficient yeast cells. Efficiency and consistency of labeling were also increased, likely due to the stringently defined and reproducible conditions used for yeast culture. The yeast SILEC method greatly enhances the ease of use and accessibility of labeled CoA thioesters and also provides proof of concept for generating other labeled metabolites in yeast mutants. PMID:25572876

  16. Intrinsic stable isotope labeling of plants for nutritional investigations in humans

    Microsoft Academic Search

    Michael A. Grusak

    1997-01-01

    Although plant foods provide an array of nutrients in the human diet, our knowledge of how efficiently these nutrients are absorbed has been limited by our ability to selectively monitor their absorption from a complex food matrix. Intrinsic labeling of plants with low-abundance stable isotopes can provide a safe, traceable product to investigate absorptive phenomena in the gut. Various techniques,

  17. Author's personal copy Systematic approach to group-specific isotopic labeling

    E-print Network

    Gerwert, Klaus

    Author's personal copy Systematic approach to group-specific isotopic labeling of proteins November 2007 Abstract Group-specific isotopic labeling of proteins using stable isotopes such as 15 N, 13 able to quantify the degree of both the incorporation and the spreading of the isotopic label

  18. ICPLQuant - A software for non-isobaric isotopic labeling proteomics.

    PubMed

    Brunner, Achim; Keidel, Eva-Maria; Dosch, Dominik; Kellermann, Josef; Lottspeich, Friedrich

    2010-01-01

    The main goal of many proteomics experiments is an accurate and rapid quantification and identification of regulated proteins in complex biological samples. The bottleneck in quantitative proteomics remains the availability of efficient software to evaluate and quantify the tremendous amount of mass spectral data acquired during a proteomics project. A new software suite, ICPLQuant, has been developed to accurately quantify isotope-coded protein label (ICPL)-labeled peptides on the MS level during LC-MALDI and peptide mass fingerprint experiments. The tool is able to generate a list of differentially regulated peptide precursors for subsequent MS/MS experiments, minimizing time-consuming acquisition and interpretation of MS/MS data. ICPLQuant is based on two independent units. Unit 1 performs ICPL multiplex detection and quantification and proposes peptides to be identified by MS/MS. Unit 2 combines MASCOT MS/MS protein identification with the quantitative data and produces a protein/peptide list with all the relevant information accessible for further data mining. The accuracy of quantification, selection of peptides for MS/MS-identification and the automated output of a protein list of regulated proteins are demonstrated by the comparative analysis of four different mixtures of three proteins (Ovalbumin, Horseradish Peroxidase and Rabbit Albumin) spiked into the complex protein background of the DGPF Proteome Marker. PMID:19953540

  19. Raman spectroscopic and mass spectrometric investigations of the hydrogen isotopes and isotopically labelled methane

    Microsoft Academic Search

    Fluor Daniel Hanford

    1997-01-01

    Suitable analytical methods must be tested and developed for monitoring the individual process steps within the fuel cycle of a fusion reactor and for tritium accountability. The utility of laser-Raman spectroscopy accompanied by mass spectrometry with an Omegatron was investigated using the analysis of all hydrogen isotopes and isotopically labeled methanes as an example. The Omegatron is useful for analyzing

  20. IDEAL-Q, an Automated Tool for Label-free Quantitation Analysis Using an Efficient

    E-print Network

    Hsu, Wen-Lian

    , various stable isotope labeling techniques, e.g. ICAT (1), en- zymatic labeling using 18 O/16 O (2, 3), stable isotope labeling by amino acids in cell culture (4), and isobaric tagging for relative in isotopic labeling experiments, and the high cost of reagents, limit the applicability of isotopic labeling

  1. Isotope labeling experiments in metabolomics and fluxomics.

    PubMed

    Klein, Sebastian; Heinzle, Elmar

    2012-01-01

    Metabolomics, the study of all the small molecules in and outside a cell and fluxomics, comprising all conversion rates in a cell, are increasingly used in fundamental and applied sciences to unravel structures and activities of cellular networks and their regulation, to investigate mechanisms of diseases and toxicity, and to improve producing strains among other applications. For both fluxomics and metabolomics the application of isotopes became almost indispensable. Their use in these techniques is discussed, focusing primarily on studies applying stable isotopes and using mass spectrometry. This includes the underlying principles, experimental and computational methods used, and examples of application. PMID:22447740

  2. SILEC: a protocol for generating and using isotopically labeled coenzyme A mass spectrometry standards

    Microsoft Academic Search

    Sankha S Basu; Ian A Blair

    2011-01-01

    Stable isotope labeling by essential nutrients in cell culture (SILEC) was recently developed to generate isotopically labeled coenzyme A (CoA) and short-chain acyl-CoA thioesters. This was accomplished by modifying the widely used technique of stable isotope labeling by amino acids in cell culture to include [13C315N]-pantothenate (vitamin B5), a CoA precursor, instead of the isotopically labeled amino acids. The lack

  3. Proteome Analysis using Selective Incorporation of Isotopically Labeled Amino Acids

    SciTech Connect

    Veenstra, Timothy D.; Martinovic, Suzana; Anderson, Gordon A.; Pasa-Tolic, Liljiana; Smith, Richard D.

    2000-01-01

    A method is described for identifying intact proteins from genomic databases using a combination of accurate molecular mass measurements and partial amino acid content. An initial demonstration was conducted for proteins isolated from Escherichia coli (E. coli) using a multiple auxotrophic strain of K12. Proteins were extracted from the organism grown in natural isotopic abundance minimal medium and also minimal medium containing isotopically labeled leucine (Leu-D10), were mixed and analyzed by capillary isoelectric focusing (CIEF) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR). The incorporation of the isotopically labeled Leu residue has no effect on the CIEF separation of the protein, therefore both versions of the protein are observed within the same FTICR spectrum. The difference in the molecular mass of the natural isotopic abundance and Leu-D10 isotopically labeled proteins is used to determine the number of Leu residues present in that particular protein. Knowledge of the molecular mass and number of Leu residues present can be used to unambiguously identify the intact protein. Preliminary results show the efficacy of using this method to unambiguously identify proteins isolated from E. coli.

  4. Synthesis of Isotopically-Labeled Graphite Films by Cold-Wall Chemical Vapor Deposition and Electronic

    E-print Network

    Synthesis of Isotopically-Labeled Graphite Films by Cold-Wall Chemical Vapor Deposition the synthesis of isotopically-labeled graphite films on nickel substrates by using cold-wall chemical vapor from such isotopically-labeled graphite films by mechanical methods have electron mobility values

  5. Evolution of Graphene Growth on Ni and Cu by Carbon Isotope Labeling

    E-print Network

    Evolution of Graphene Growth on Ni and Cu by Carbon Isotope Labeling Xuesong Li, Weiwei Cai, Luigi used carbon isotope labeling in conjunction with Raman spectroscopic mapping to track carbon during-limiting. In this work, we used isotopic labeling of the carbon precursor to study the mechanism and kinetics of CVD

  6. Preparation of Uniformly Isotope-labeled DNA Oligonucleotides for NMR Spectroscopy*

    E-print Network

    Clore, G. Marius

    Preparation of Uniformly Isotope-labeled DNA Oligonucleotides for NMR Spectroscopy* (Received for the large scale preparation of uni- formly isotope-labeled DNA for NMR studies have been developed grown with 15 N- and 13 C-enriched nutrients (7­11). Isotope labeling of DNA has been difficult and most

  7. From isotope labeled CH3CN to N2 inside single-walled carbon nanotubes

    E-print Network

    Maruyama, Shigeo

    From isotope labeled CH3CN to N2 inside single-walled carbon nanotubes Christian Kramberger to this peculiar place? We have used N15 and C13 isotope labeled acetonitrile during the synthesis of single- cation of the reaction pathway by isotope labeling has not yet been achieved. Moreover, it remains

  8. Existing and emerging technologies for measuring stable isotope labelled retinol in biological samples: isotope dilution analysis of body retinol stores.

    PubMed

    Preston, Tom

    2014-01-01

    This paper discusses some of the recent improvements in instrumentation used for stable isotope tracer measurements in the context of measuring retinol stores, in vivo. Tracer costs, together with concerns that larger tracer doses may perturb the parameter under study, demand that ever more sensitive mass spectrometric techniques are developed. GCMS is the most widely used technique. It has high sensitivity in terms of sample amount and uses high resolution GC, yet its ability to detect low isotope ratios is limited by background noise. LCMSMS may become more accessible for tracer studies. Its ability to measure low level stable isotope tracers may prove superior to GCMS, but it is isotope ratio MS (IRMS) that has been designed specifically for low level stable isotope analysis through accurate analysis of tracer:tracee ratios (the tracee being the unlabelled species). Compound-specific isotope analysis, where GC is interfaced to IRMS, is gaining popularity. Here, individual 13C-labelled compounds are separated by GC, combusted to CO2 and transferred on-line for ratiometric analysis by IRMS at the ppm level. However, commercially-available 13C-labelled retinol tracers are 2 - 4 times more expensive than deuterated tracers. For 2H-labelled compounds, GC-pyrolysis-IRMS has now become more generally available as an operating mode on the same IRMS instrument. Here, individual compounds are separated by GC and pyrolysed to H2 at high temperature for analysis by IRMS. It is predicted that GC-pyrolysis-IRMS will facilitate low level tracer procedures to measure body retinol stores, as has been accomplished in the case of fatty acids and amino acids. Sample size requirements for GC-P-IRMS may exceed those of GCMS, but this paper discusses sample preparation procedures and predicts improvements, particularly in the efficiency of sample introduction. PMID:25537104

  9. Segmental Isotopic Labeling of Proteins for Nuclear Magnetic Resonance

    PubMed Central

    Dongsheng, Liu; Xu, Rong; Cowburn, David

    2009-01-01

    Nuclear Magnetic Resonance (NMR) spectroscopy has emerged as one of the principle techniques of structural biology. It is not only a powerful method for elucidating the 3D structures under near physiological conditions, but also a convenient method for studying protein-ligand interactions and protein dynamics. A major drawback of macromolecular NMR is its size limitation caused by slower tumbling rates and greater complexity of the spectra as size increases. Segmental isotopic labeling allows specific segment(s) within a protein to be selectively examined by NMR thus significantly reducing the spectral complexity for large proteins and allowing a variety of solution-based NMR strategies to be applied. Two related approaches are generally used in the segmental isotopic labeling of proteins: expressed protein ligation and protein trans-splicing. Here we describe the methodology and recent application of expressed protein ligation and protein trans-splicing for NMR structural studies of proteins and protein complexes. We also describe the protocol used in our lab for the segmental isotopic labeling of a 50 kDa protein Csk (C-terminal Src Kinase) using expressed protein ligation methods. PMID:19632474

  10. The use of oxygen isotopic labeling to understand oxidation mechanisms

    SciTech Connect

    Aakermark, T. [Royal Inst. of Tech., Stockholm (Sweden). Div. of Corrosion Science] [Royal Inst. of Tech., Stockholm (Sweden). Div. of Corrosion Science

    1998-10-01

    Isotopic labeling is a powerful tool to evaluate transport and reaction mechanisms of oxidation. The evaluation can answer the essential question in high-temperature oxidation: which is the dominating migrating species? Isotopic labeling can be used in two different ways: analysis of the gas phase and analysis of the oxide formed. By using as-reported, depth-profiling data from the literature, the oxygen exchange was evaluated and compared with oxide growth. Gas-phase analysis was used to evaluate the oxygen-exchange reactions, O{sub 2} {leftrightarrow} H{sub 2}O, O{sub 2} {leftrightarrow} O{sub 2}, and O{sub 2}{leftrightarrow} Me{sub x}O{sub y}, in relation to the oxidation of Si and Fe-Cr-Al alloys in {approximately}10 mbar isotopically-labeled H{sub 2}O/O{sub 2}-gas mixtures at 900 to 950 C. The time dependence of the rate of the oxygen exchange was used to explain the deviation from parabolic oxidation kinetics. The results of this study suggest that atomic oxygen is the migrating species during the oxidation of Si and alumina-forming alloys.

  11. Efficient palladium isotope chromatograph for hydrogen (EPIC)

    SciTech Connect

    Embury, M.C.; Ellefson, R.E.; Melke, H.B. (EG and G Mound Applied Technologies, Miamisburg, OH (US))

    1992-03-01

    The Efficient Palladium Isotope Chromatograph (EPIC) is a rapid cycling, computer-operated displacement chromatograph for the separation of hydrogen isotopes. EPIC incorporates several features that optimize product throughput and purity. This paper describes this palladium displacement chromatograph, the operations with protium and deuterium, and the design modifications for operation with tritium.

  12. Isotopic Labeling of Red Cabbage Anthocyanins with Atmospheric 13-CO2

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Isotopic labeling of plants provides a unique opportunity for understanding metabolic processes. A significant challenge of isotopic labeling during plant growth is that isotopes must be administered without disrupting plant development and at sufficient levels for mass spectral analysis. We describ...

  13. Determination of Phytochelatins in Rice by Stable Isotope Labeling Coupled with Liquid Chromatography-Mass Spectrometry.

    PubMed

    Liu, Ping; Cai, Wen-Jing; Yu, Lei; Yuan, Bi-Feng; Feng, Yu-Qi

    2015-07-01

    A highly sensitive method was developed for the detection of phytochelatins (PCs) in rice by stable isotope labeling coupled with liquid chromatography-electrospray ionization-tandem mass spectrometry (IL-LC-ESI-MS/MS) analysis. A pair of isotope-labeling reagents [?-bromoacetonylquinolinium bromide (BQB) and BQB-d(7)] were used to label PCs in plant sample and standard PCs, respectively, and then combined prior to LC/MS analysis. The heavy labeled standards were used as the internal standards for quantitation to minimize the matrix and ion suppression effects in MS analysis. In addition, the ionization efficiency of PCs was greatly enhanced through the introduction of a permanent charged moiety of quaternary ammonium of BQB into PCs. The detection sensitivities of PCs upon BQB labeling improved by 14-750-fold, and therefore, PCs can be quantitated using only 5 mg of plant tissue. Furthermore, under cadmium (Cd) stress, we found that the contents of PCs in rice dramatically increased with the increased concentrations and treatment time of Cd. It was worth noting that PC5 was first identified and quantitated in rice tissues under Cd stress in the current study. Taken together, this IL-LC-ESI-MS/MS method demonstrated to be a promising strategy in detection of PCs in plants with high sensitivity and reliability. PMID:26073168

  14. Quantitating isotopic molecular labels with accelerator mass spectrometry.

    PubMed

    Vogel, John S; Love, Adam H

    2005-01-01

    Accelerator mass spectrometry (AMS) traces isotopically labeled biochemicals and provides significant new directions for understanding molecular kinetics and dynamics in biological systems. AMS traces low-abundance radioisotopes for high specificity but detects them with MS for high sensitivity. AMS reduces radiation exposure doses to levels safe for use in human volunteers of all ages. Total radiation exposures are equivalent to those obtained in very short airplane flights, a commonly accepted radiation risk. Waste products seldom reach the Nuclear Regulatory Commission (NRC) definition of radioactive waste material for (14)C and (3)H. Attomoles of labeled compounds are quantified in milligram-sized samples, such as 20 microl of blood. AMS is available from several facilities that offer services and new spectrometers that are affordable. Detailed examples of designing AMS studies are provided, and the methods of analyzing AMS data are outlined. PMID:16401517

  15. Design and operation of a continuous 13C and 15N labeling chamber for uniform or differential, metabolic and structural, plant isotope labeling.

    PubMed

    Soong, Jennifer L; Reuss, Dan; Pinney, Colin; Boyack, Ty; Haddix, Michelle L; Stewart, Catherine E; Cotrufo, M Francesca

    2014-01-01

    Tracing rare stable isotopes from plant material through the ecosystem provides the most sensitive information about ecosystem processes; from CO2 fluxes and soil organic matter formation to small-scale stable-isotope biomarker probing. Coupling multiple stable isotopes such as (13)C with (15)N, (18)O or (2)H has the potential to reveal even more information about complex stoichiometric relationships during biogeochemical transformations. Isotope labeled plant material has been used in various studies of litter decomposition and soil organic matter formation(1-4). From these and other studies, however, it has become apparent that structural components of plant material behave differently than metabolic components (i.e. leachable low molecular weight compounds) in terms of microbial utilization and long-term carbon storage(5-7). The ability to study structural and metabolic components separately provides a powerful new tool for advancing the forefront of ecosystem biogeochemical studies. Here we describe a method for producing (13)C and (15)N labeled plant material that is either uniformly labeled throughout the plant or differentially labeled in structural and metabolic plant components. Here, we present the construction and operation of a continuous (13)C and (15)N labeling chamber that can be modified to meet various research needs. Uniformly labeled plant material is produced by continuous labeling from seedling to harvest, while differential labeling is achieved by removing the growing plants from the chamber weeks prior to harvest. Representative results from growing Andropogon gerardii Kaw demonstrate the system's ability to efficiently label plant material at the targeted levels. Through this method we have produced plant material with a 4.4 atom%(13)C and 6.7 atom%(15)N uniform plant label, or material that is differentially labeled by up to 1.29 atom%(13)C and 0.56 atom%(15)N in its metabolic and structural components (hot water extractable and hot water residual components, respectively). Challenges lie in maintaining proper temperature, humidity, CO2 concentration, and light levels in an airtight (13)C-CO2 atmosphere for successful plant production. This chamber description represents a useful research tool to effectively produce uniformly or differentially multi-isotope labeled plant material for use in experiments on ecosystem biogeochemical cycling. PMID:24457314

  16. Simplified Synthesis of Isotopically Labeled 5,5-Dimethyl-pyrroline N-Oxide

    PubMed Central

    Leinisch, Fabian; Jiang, JinJie; Deterding, Leesa J.; Mason, Ronald P.

    2011-01-01

    5,5-Dimethylpyrroline N-oxide (15N) and 5,5-di(trideuteromethyl)pyrroline N-oxide were synthesized from the respective isotopically labeled 2-nitropropane analogs obtained from the reaction of sodium nitrate with 2-halopropanes. This facile, straightforward process allows synthesizing isotopically labeled DMPO analogs in a 4-step reaction without special equipment. PMID:21986521

  17. Melting of Rodlike Molecules on Pt(111). Infrared Spectroscopic Studies of Isotopically Labeled n-Alkanes

    E-print Network

    Girolami, Gregory S.

    Melting of Rodlike Molecules on Pt(111). Infrared Spectroscopic Studies of Isotopically Labeled n 61801 ReceiVed: May 12, 1998; In Final Form: August 24, 1998 The melting of monolayers of isotopically labeled n-alkanes on Pt(111) surfaces has been followed by reflection-absorption infrared (RAIR

  18. New developments in isotope labeling strategies for protein solution NMR spectroscopy

    Microsoft Academic Search

    Natalie K Goto; Lewis E Kay

    2000-01-01

    The development of novel isotope labeling strategies for proteins has facilitated the study of the structure and dynamics of these molecules. In addition, the recent emergence of alternative methods of bacterial expression for obtaining isotopically labeled proteins permits the study of new classes of important proteins by solution NMR methods.

  19. Use of stable isotopically labeled tracers for studies of metabolic kinetics: An overview

    Microsoft Academic Search

    Bruce W. Patterson

    1997-01-01

    Stable isotopically labeled tracers offer a reliable and safe alternative to the use of radioactive tracers for studies of metabolic kinetics. This overview examines some of the principles and technical issues regarding mass spectrometry instrumentation, and reviews some of the approaches used in the application of stable isotopically labeled tracers to studies of protein, lipid, and carbohydrate metabolic kinetics.

  20. Table I. Column 4, labelled f, lists isotopic abundance fractions from Anders and Grevesse [11]. Columns 5 through 7 are from Table of Isotopes [12]. Column

    E-print Network

    Kurucz, Robert L.

    Table I. Column 4, labelled f, lists isotopic abundance fractions from Anders and Grevesse [11]. Columns 5 through 7 are from Table of Isotopes [12]. Column 5, labelled I, is the nuclear spin. Column 6, labelled ¯, is the magnetic dipole moment in nuclear magnetons. Column 7, labelled Q, is the electric

  1. Using phylogenetic probes for quantification of stable isotope labeling and microbial community analysis

    DOEpatents

    Brodie, Eoin L; DeSantis, Todd Z; Karaoz, Ulas; Andersen, Gary L

    2014-12-09

    Herein is described methods for a high-sensitivity means to measure the incorporation of stable isotope labeled substrates into RNA following stable isotope probing experiments (SIP). RNA is hybridized to a set of probes such as phylogenetic microarrays and isotope incorporation is quantified such as by secondary ion mass spectrometer imaging (NanoSIMS).

  2. Split-Field Drift Tube/Mass Spectrometry and Isotopic Labeling Techniques for Determination of Single Amino Acid Polymorphisms

    E-print Network

    Clemmer, David E.

    Split-Field Drift Tube/Mass Spectrometry and Isotopic Labeling Techniques for Determination/mass spectrometry and isotopic labeling techniques is evaluated as a means of identifying single amino acid, and the peptides are labeled at primary amine groups [using either a light (H3)- or heavy (D3)-isotopic reagent

  3. Investigation of the Effects of Isotopic Labeling at a PS/PMMA Interface Using SIMS and Mean-Field Theory

    E-print Network

    Investigation of the Effects of Isotopic Labeling at a PS/PMMA Interface Using SIMS and Mean ReceiVed December 4, 2005 ABSTRACT: Isotopic labeling (deuteration) is known to affect the phase qualitatively, using previously reported changes in for PS/PMMA due to isotopic labeling. The previously

  4. 2D-IR Study of a Photoswitchable Isotope-Labeled r-Helix Ellen H. G. Backus,,

    E-print Network

    Caflisch, Amedeo

    2D-IR Study of a Photoswitchable Isotope-Labeled r-Helix Ellen H. G. Backus,, Robbert Bloem, Paul M spectroscopy (2D-IR). Single-isotope labeling with 13 C18 O at various positions in the sequence was employed information, 2D-IR spectroscopy is often used in combination with isotope labeling14,17,18 to spectrally

  5. Isotopic labeling studies of interactions of nitric oxide and nitrous oxide with ultrathin oxynitride layers on silicon

    E-print Network

    Gustafsson, Torgny

    Isotopic labeling studies of interactions of nitric oxide and nitrous oxide with ultrathin depth profiling using medium energy ion scattering and isotopic labeling methods. We observe that, after atoms are incorporated near the SiO2/Si interface.3,7,17,20­22 A recent isotopic labeling study using

  6. Accurate determination of leucine and valine side-chain conformations using H-(methine/methyl)-Leu/Val] isotope labeling, NOE

    E-print Network

    Clore, G. Marius

    H]/[1 H-(methine/methyl)-Leu/Val] isotope labeling, NOE pattern recognition, and methine Cc 2005; Accepted 14 July 2005 Key words: isotope labeling, Leu and Val conformation, NMR, NOE, residual dipolar couplings, solution structure Abstract An isotope labeling scheme is described in which specific

  7. Evaluation of the Variation in Sample Preparation for Comparative Proteomics Using Stable Isotope Labeling by Amino Acids in Cell

    E-print Network

    Chait, Brian T.

    with sample preparation. In this study, we report the strategy of using SILAC (stable isotope labeling on quantitative accuracy. For example, for approaches based on stable isotope labeling, the "light" and "heavy" samples can be mixed after differential isotope labeling so that subsequent sample handling will introduce

  8. FTIR Difference Spectroscopy in Combination with Isotope Labeling for Identification of the Carbonyl Modes of P700

    E-print Network

    Hastings, Gary

    FTIR Difference Spectroscopy in Combination with Isotope Labeling for Identification; Sivakumar et al., 2003), and here we have used FTIR DS in combination with isotope labeling to gain a more Synechocystis sp. PCC 6803 that are unlabeled, uniformly 2 H labeled, and uniformly 15 N labeled. Spectra were

  9. Experimental investigation of rates and mechanisms of isotope exchange (O, H) between volcanic ash and isotopically-label ed water

    Microsoft Academic Search

    Gary S. Nolan; Ilya N. Bindeman

    2013-01-01

    The hydrogen and oxygen isotope ratios in hydrous minerals and volcanic glass are routinely used as paleo-proxies to infer the isotopic values of meteoric waters and thus paleo-climatic conditions. We report a series of long-term exposure experi- ments of distal 7700 BP Mt. Mazama ash (? 149& d 2 H, +7 & d 18 O, 3.8 wt.% H2O) with isotopically-labeled

  10. Determination of Multimodal Isotopic Distributions: The Case of a (15)N Labeled Protein Produced into Hairy Roots.

    PubMed

    Trouillard, Romain; Hubert-Roux, Marie; Tognetti, Vincent; Guilhaudis, Laure; Plasson, Carole; Menu-Bouaouiche, Laurence; Coquet, Laurent; Guerineau, François; Hardouin, Julie; Ele Ekouna, Jean-Pierre; Cosette, Pascal; Lerouge, Patrice; Boitel-Conti, Michèle; Afonso, Carlos; Ségalas-Milazzo, Isabelle

    2015-06-16

    Isotopic labeling is widely used in various fields like proteomics, metabolomics, fluxomics, as well as in NMR structural studies, but it requires an efficient determination of the isotopic enrichment. Mass spectrometry is the method of choice for such analysis. However, when complex expression systems like hairy roots are used for production, multiple populations of labeled proteins may be obtained. If the isotopic incorporation determination is actually well-known for unimodal distributions, the multimodal distributions have scarcely been investigated. Actually, only a few approaches allow the determination of the different labeled population proportions from multimodal distributions. Furthermore, they cannot be used when the number of the populations and their respective isotope ratios are unknown. The present study implements a new strategy to measure the (15)N labeled populations inside a multimodal distribution knowing only the peptide sequence and peak intensities from mass spectrometry analyses. Noteworthy, it could be applied to other elements, like carbon and hydrogen, and extended to a larger range of biomolecules. PMID:25973921

  11. Raman spectroscopic and mass spectrometric investigations of the hydrogen isotopes and isotopically labelled methane

    SciTech Connect

    Jewett, J.R., Fluor Daniel Hanford

    1997-02-24

    Suitable analytical methods must be tested and developed for monitoring the individual process steps within the fuel cycle of a fusion reactor and for tritium accountability. The utility of laser-Raman spectroscopy accompanied by mass spectrometry with an Omegatron was investigated using the analysis of all hydrogen isotopes and isotopically labeled methanes as an example. The Omegatron is useful for analyzing all hydrogen isotopes mixed with the stable helium isotopes. The application of this mass spectrometer were demonstrated by analyzing mixtures of deuterated methanes. In addition, it was employed to study the radiochemical Witzbach exchange reaction between tritium and methanes. A laser-Raman spectrometer was designed for analysis of tritium-containing gases and was built from individual components. A tritium-compatible, metal-sealed Raman cuvette having windows with good optical properties and additional means for measuring the stray light was first used successfully in this work. The Raman spectra of the hydrogen isotopes were acquired in the pure rotation mode and in the rotation-vibration mode and were used for on. The deuterated methanes were measured by Raman spectroscopy, the wavenumbers determined were assigned to the corresponding vibrations, and the wavenumbers for the rotational fine-structure were summarized in tables. The fundamental Vibrations of the deuterated methanes produced Witzbach reactions were detected and assigned. The fundamental vibrations of the molecules were obtained with Raman spectroscopy for the first time in this work. The @-Raman spectrometer assembled is well suited for the analysis of tritium- containing gases and is practical in combination with mass spectrometry using an Omegatron, for studying gases used in fusion.

  12. EFFICIENT LEARNING WITH SOFT LABEL INFORMATION AND MULTIPLE ANNOTATORS

    E-print Network

    Hauskrecht, Milos

    and other fields. These data provide us with a great resource for building automated learn- ing systems examples to be labeled next are selected online using active learning. Second, we study waysEFFICIENT LEARNING WITH SOFT LABEL INFORMATION AND MULTIPLE ANNOTATORS by Quang Nguyen BS, Moscow

  13. Soil water utilization by herbaceous species of the southern Great Plains: evidence from isotopically labeled water 

    E-print Network

    Yoder, Carolyn Kay

    1993-01-01

    Understanding spatial and temporal patterns of soil water utilization by plants has broad implications for physiological, ecological, and hydrological processes. Water labeled with the stable isotopes deuterium ('H) or oxygen-18 ("'O) was injected...

  14. Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities

    PubMed Central

    Verastegui, Y.; Cheng, J.; Engel, K.; Kolczynski, D.; Mortimer, S.; Lavigne, J.; Montalibet, J.; Romantsov, T.; Hall, M.; McConkey, B. J.; Rose, D. R.; Tomashek, J. J.; Scott, B. R.

    2014-01-01

    ABSTRACT Soil microbial diversity represents the largest global reservoir of novel microorganisms and enzymes. In this study, we coupled functional metagenomics and DNA stable-isotope probing (DNA-SIP) using multiple plant-derived carbon substrates and diverse soils to characterize active soil bacterial communities and their glycoside hydrolase genes, which have value for industrial applications. We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon (12C) or stable-isotope-labeled (13C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates. Among characterized taxa, Actinomycetales (Salinibacterium), Rhizobiales (Devosia), Rhodospirillales (Telmatospirillum), and Caulobacterales (Phenylobacterium and Asticcacaulis) were bacterial indicator species for the heavy substrates and soils tested. Both Actinomycetales and Caulobacterales (Phenylobacterium) were associated with metabolism of cellulose, and Alphaproteobacteria were associated with the metabolism of arabinose; members of the order Rhizobiales were strongly associated with the metabolism of xylose. Annotated metagenomic data suggested diverse glycoside hydrolase gene representation within the pooled heavy DNA. By screening 2,876 cloned fragments derived from the 13C-labeled DNA isolated from soils incubated with cellulose, we demonstrate the power of combining DNA-SIP, multiple-displacement amplification (MDA), and functional metagenomics by efficiently isolating multiple clones with activity on carboxymethyl cellulose and fluorogenic proxy substrates for carbohydrate-active enzymes. PMID:25028422

  15. Fluorination of isotopically labeled turbostratic and Bernal stacked bilayer graphene.

    PubMed

    Ek Weis, Johan; Costa, Sara D; Frank, Otakar; Bastl, Zdenek; Kalbac, Martin

    2015-01-12

    Fluorination of graphene opens up a bandgap, which creates opportunities for optoelectronics, and also paves the way for the creation of extremely thin insulating layers, which can be important for applications in devices. However, in spite of many interesting features offered by, for example, unequally doped layers in multilayered systems, most of the work has concerned the fluorination of graphene monolayers. Here, the fluorination process of graphene bilayers is investigated through high-resolution Raman mapping followed by analysis of more than 10,000 spectra of bilayer graphene. Isotopically labeled bilayers are used, allowing each individual layer in bilayer graphene to be addressed unambiguously. The fluorinated graphene is prepared through exposure to XeF2. Monolayer graphene is found to be significantly more sensitive to fluorination than bilayer graphene. Through comparison of the D/G area ratio and the position of the G band for turbostratic and Bernal stacked (AB) bilayers, it is found that the fluorination process is more effective for turbostratic than for AB-stacked bilayer graphene. The fluorination changes the electronic structure similarly for the top and bottom layers in turbostratic bilayers. However, the top layer is more sensitive than the bottom layer in AB-stacked bilayers. PMID:25394738

  16. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC)

    Microsoft Academic Search

    Matthias Mann; Shao-En Ong

    2007-01-01

    Stable isotope labeling by amino acids in cell culture (SILAC) is a simple, robust, yet powerful approach in mass spectrometry (MS)-based quantitative proteomics. SILAC labels cellular proteomes through normal metabolic processes, incorporating non-radioactive, stable isotope-containing amino acids in newly synthesized proteins. Growth medium is prepared where natural (“light”) amino acids are replaced by “heavy” SILAC amino acids. Cells grown in

  17. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC)

    Microsoft Academic Search

    Shao-En Ong; Matthias Mann

    2006-01-01

    Stable isotope labeling by amino acids in cell culture (SILAC) is a simple, robust, yet powerful approach in mass spectrometry (MS)-based quantitative proteomics. SILAC labels cellular proteomes through normal metabolic processes, incorporating non-radioactive, stable isotope-containing amino acids in newly synthesized proteins. Growth medium is prepared where natural (''light'') amino acids are replaced by ''heavy'' SILAC amino acids. Cells grown in

  18. An isotopic labeling study of the growth of thin oxide films on Si(100) H. C. Lu and T. Gustafsson

    E-print Network

    Gustafsson, Torgny

    An isotopic labeling study of the growth of thin oxide films on Si(100) H. C. Lu and T. Gustafsson.1­1 Torr oxygen pressure regime. Isotopic labeling experiments demonstrate that the Deal­Grove model breaks-resolution medium energy ion scattering in combination with oxygen isotope substitution in the T 800­ 900 °C and 0

  19. Examination of the rate of peptide biosynthesis in neuroendocrine cell lines using a stable isotopic label and mass spectrometry

    E-print Network

    Tian, Weidong

    isotopic label and mass spectrometry Fa-Yun Che,*,1 Quan Yuan,* ,1 Elena Kalinina* and Lloyd D. Fricker. These results are consistent with the acidic pH optima for peptide processing enzymes. Stable isotopic labeling of peptides. In the present study, we labeled cell lines with L-leucine containing 10 deuterium residues (d10

  20. Respiratory Carbon Metabolism following Illumination in Intact French Bean Leaves Using 13C\\/12C Isotope Labeling

    Microsoft Academic Search

    Salvador Nogues; Guillaume Tcherkez; Gabriel Cornic; Jaleh Ghashghaie

    2004-01-01

    system coupled online to an elemental analyzer and linked to an isotope ratio mass spectrometer. The isotopic analysis of the CO2 respired in the dark after a light period revealed that the CO2 was labeled, but the labeling level decreased progressively as the dark period increased. The pattern of disappearance depended on the amount of carbon fixed during the labeling

  1. Autotrophic production of stable-isotope-labeled arginine in Ralstonia eutropha strain H16.

    PubMed

    Lütte, Steffen; Pohlmann, Anne; Zaychikov, Evgeny; Schwartz, Edward; Becher, Johannes R; Heumann, Hermann; Friedrich, Bärbel

    2012-11-01

    With the aim of improving industrial-scale production of stable-isotope (SI)-labeled arginine, we have developed a system for the heterologous production of the arginine-containing polymer cyanophycin in recombinant strains of Ralstonia eutropha under lithoautotrophic growth conditions. We constructed an expression plasmid based on the cyanophycin synthetase gene (cphA) of Synechocystis sp. strain PCC6308 under the control of the strong P(cbbL) promoter of the R. eutropha H16 cbb(c) operon (coding for autotrophic CO(2) fixation). In batch cultures growing on H(2) and CO(2) as sole sources of energy and carbon, respectively, the cyanophycin content of cells reached 5.5% of cell dry weight (CDW). However, in the absence of selection (i.e., in antibiotic-free medium), plasmid loss led to a substantial reduction in yield. We therefore designed a novel addiction system suitable for use under lithoautotrophic conditions. Based on the hydrogenase transcription factor HoxA, this system mediated stabilized expression of cphA during lithoautotrophic cultivation without the need for antibiotics. The maximum yield of cyanophycin was 7.1% of CDW. To test the labeling efficiency of our expression system under actual production conditions, cells were grown in 10-liter-scale fermentations fed with (13)CO(2) and (15)NH(4)Cl, and the (13)C/(15)N-labeled cyanophycin was subsequently extracted by treatment with 0.1 M HCl; 2.5 to 5 g of [(13)C/(15)N]arginine was obtained per fed-batch fermentation, corresponding to isotope enrichments of 98.8% to 99.4%. PMID:22941075

  2. Autotrophic Production of Stable-Isotope-Labeled Arginine in Ralstonia eutropha Strain H16

    PubMed Central

    Lütte, Steffen; Pohlmann, Anne; Zaychikov, Evgeny; Becher, Johannes R.; Heumann, Hermann; Friedrich, Bärbel

    2012-01-01

    With the aim of improving industrial-scale production of stable-isotope (SI)-labeled arginine, we have developed a system for the heterologous production of the arginine-containing polymer cyanophycin in recombinant strains of Ralstonia eutropha under lithoautotrophic growth conditions. We constructed an expression plasmid based on the cyanophycin synthetase gene (cphA) of Synechocystis sp. strain PCC6308 under the control of the strong PcbbL promoter of the R. eutropha H16 cbbc operon (coding for autotrophic CO2 fixation). In batch cultures growing on H2 and CO2 as sole sources of energy and carbon, respectively, the cyanophycin content of cells reached 5.5% of cell dry weight (CDW). However, in the absence of selection (i.e., in antibiotic-free medium), plasmid loss led to a substantial reduction in yield. We therefore designed a novel addiction system suitable for use under lithoautotrophic conditions. Based on the hydrogenase transcription factor HoxA, this system mediated stabilized expression of cphA during lithoautotrophic cultivation without the need for antibiotics. The maximum yield of cyanophycin was 7.1% of CDW. To test the labeling efficiency of our expression system under actual production conditions, cells were grown in 10-liter-scale fermentations fed with 13CO2 and 15NH4Cl, and the 13C/15N-labeled cyanophycin was subsequently extracted by treatment with 0.1 M HCl; 2.5 to 5 g of [13C/15N]arginine was obtained per fed-batch fermentation, corresponding to isotope enrichments of 98.8% to 99.4%. PMID:22941075

  3. Incorporation of a stable isotopically labeled amino acid into multiple human apolipoproteins

    Microsoft Academic Search

    Bruce W. Patterson; David L. Hachey; Gary L. Cook; Joseph M. Amann; Peter D. Klein

    Procedures are presented for the separation and de- termination of the isotopic enrichment of multiple human apoli- poproteins labeled in vivo with a stable isotope amino acid. The isotopic enrichments of plasma lysine and plasma apolipopro- teins were monitored for 16 days after a single intravenous dose of (4,4,5,5-2H4)lysine (5 mg\\/kg body weight). The use of a mul- tiply deuterated

  4. Stable isotope-labeling studies in metabolomics: new insights into structure and dynamics of metabolic networks

    PubMed Central

    Chokkathukalam, Achuthanunni; Kim, Dong-Hyun; Barrett, Michael P; Breitling, Rainer; Creek, Darren J

    2014-01-01

    The rapid emergence of metabolomics has enabled system-wide measurements of metabolites in various organisms. However, advances in the mechanistic understanding of metabolic networks remain limited, as most metabolomics studies cannot routinely provide accurate metabolite identification, absolute quantification and flux measurement. Stable isotope labeling offers opportunities to overcome these limitations. Here we describe some current approaches to stable isotope-labeled metabolomics and provide examples of the significant impact that these studies have had on our understanding of cellular metabolism. Furthermore, we discuss recently developed software solutions for the analysis of stable isotope-labeled metabolomics data and propose the bioinformatics solutions that will pave the way for the broader application and optimal interpretation of system-scale labeling studies in metabolomics. PMID:24568354

  5. Relative quantification of biomarkers using mixed-isotope labeling coupled with MS

    PubMed Central

    Chapman, Heidi M; Schutt, Katherine L; Dieter, Emily M; Lamos, Shane M

    2013-01-01

    The identification and quantification of important biomarkers is a critical first step in the elucidation of biological systems. Biomarkers take many forms as cellular responses to stimuli and can be manifested during transcription, translation, and/or metabolic processing. Increasingly, researchers have relied upon mixed-isotope labeling (MIL) coupled with MS to perform relative quantification of biomarkers between two or more biological samples. MIL effectively tags biomarkers of interest for ease of identification and quantification within the mass spectrometer by using isotopic labels that introduce a heavy and light form of the tag. In addition to MIL coupled with MS, a number of other approaches have been used to quantify biomarkers including protein gel staining, enzymatic labeling, metabolic labeling, and several label-free approaches that generate quantitative data from the MS signal response. This review focuses on MIL techniques coupled with MS for the quantification of protein and small-molecule biomarkers. PMID:23157360

  6. Oxygen Atom Transfer and Oxidative Water Incorporation in Cuboidal Mn3MOn Complexes Based on Synthetic, Isotopic Labeling,

    E-print Network

    Goddard III, William A.

    on Synthetic, Isotopic Labeling, and Computational Studies Jacob S. Kanady,§, Jose L. Mendoza-Cortes,, Emily YIII 4O3, was observed experimentally upon treatment with water, base, and oxidizing equivalents. 18 O-labeling

  7. NMR Study of 100 kDa HCV IRES RNA Using Segmental Isotope Labeling Insil Kim, Peter J. Lukavsky, and Joseph D. Puglisi*

    E-print Network

    Puglisi, Joseph

    NMR Study of 100 kDa HCV IRES RNA Using Segmental Isotope Labeling Insil Kim, Peter J. Lukavsky labeling of RNA, in which part of the RNA is labeled with stable isotope, reduces the complexity of spectra assignments have been achieved through selective isotope labeling of RNAs using T4 DNA ligase, T4 RNA ligase

  8. Isotopic labeling of mammalian G protein-coupled receptors heterologously expressed in Caenorhabditis elegans.

    PubMed

    Salom, David; Cao, Pengxiu; Yuan, Yiyuan; Miyagi, Masaru; Feng, Zhaoyang; Palczewski, Krzysztof

    2015-03-01

    High-resolution structural determination and dynamic characterization of membrane proteins by nuclear magnetic resonance (NMR) require their isotopic labeling. Although a number of labeled eukaryotic membrane proteins have been successfully expressed in bacteria, they lack post-translational modifications and usually need to be refolded from inclusion bodies. This shortcoming of bacterial expression systems is particularly detrimental for the functional expression of G protein-coupled receptors (GPCRs), the largest family of drug targets, due to their inherent instability. In this work, we show that proteins expressed by a eukaryotic organism can be isotopically labeled and produced with a quality and quantity suitable for NMR characterization. Using our previously described expression system in Caenorhabditis elegans, we showed the feasibility of labeling proteins produced by these worms with (15)N,(13)C by providing them with isotopically labeled bacteria. (2)H labeling also was achieved by growing C. elegans in the presence of 70% heavy water. Bovine rhodopsin, simultaneously expressed in muscular and neuronal worm tissues, was employed as the "test" GPCR to demonstrate the viability of this approach. Although the worms' cell cycle was slightly affected by the presence of heavy isotopes, the final protein yield and quality was appropriate for NMR structural characterization. PMID:25461480

  9. Plasma appearance of labeled  -carotene, lutein, and retinol in humans after consumption of isotopically labeled kale

    Microsoft Academic Search

    Janet A. Novotny; Anne C. Kurilich; Steven J. Britz; Beverly A. Clevidence

    2005-01-01

    The bioavailability of carotenoids from kale was investigated by labeling nutrients in kale with 13 C, feeding the kale to seven adult volunteers, and analyzing serial plasma samples for labeled lutein, ? -carotene, and retinol. Ingested doses of labeled carotenoids were 34 ? mol for ? -carotene and 33 ? mol for lutein. Peak plasma concentra- tions, areas under the

  10. Immunoproteomics Using Polyclonal Antibodies and Stable Isotope–labeled Affinity-purified Recombinant Proteins*

    PubMed Central

    Edfors, Fredrik; Boström, Tove; Forsström, Björn; Zeiler, Marlis; Johansson, Henrik; Lundberg, Emma; Hober, Sophia; Lehtiö, Janne; Mann, Matthias; Uhlen, Mathias

    2014-01-01

    The combination of immuno-based methods and mass spectrometry detection has great potential in the field of quantitative proteomics. Here, we describe a new method (immuno-SILAC) for the absolute quantification of proteins in complex samples based on polyclonal antibodies and stable isotope–labeled recombinant protein fragments to allow affinity enrichment prior to mass spectrometry analysis and accurate quantification. We took advantage of the antibody resources publicly available from the Human Protein Atlas project covering more than 80% of all human protein-coding genes. Epitope mapping revealed that a majority of the polyclonal antibodies recognized multiple linear epitopes, and based on these results, a semi-automated method was developed for peptide enrichment using polyclonal antibodies immobilized on protein A–coated magnetic beads. A protocol based on the simultaneous multiplex capture of more than 40 protein targets showed that approximately half of the antibodies enriched at least one functional peptide detected in the subsequent mass spectrometry analysis. The approach was further developed to also generate quantitative data via the addition of heavy isotope–labeled recombinant protein fragment standards prior to trypsin digestion. Here, we show that we were able to use small amounts of antibodies (50 ng per target) in this manner for efficient multiplex analysis of quantitative levels of proteins in a human HeLa cell lysate. The results suggest that polyclonal antibodies generated via immunization of recombinant protein fragments could be used for the enrichment of target peptides to allow for rapid mass spectrometry analysis taking advantage of a substantial reduction in sample complexity. The possibility of building up a proteome-wide resource for immuno-SILAC assays based on publicly available antibody resources is discussed. PMID:24722731

  11. Energy-efficient appliance labeling in China: Lessons for successful labeling programs in varied markets

    SciTech Connect

    Lin, Jiang; Townend, Jeanne; Fridley, David; McNeil, Gary; Silva, Tony; Clark, Robin

    2002-08-20

    Appliance ownership and production has increased dramatically in China in the past two decades. From extremely low levels in 1980, China's appliance industry has become one of the largest in the world, with sales topping U.S. $14.4 billion in 2000. In 1981, less than 1 percent of urban Chinese households owned a refrigerator; by 1998, that number had increased to over 75 percent. This dramatic increase in sales and ownership leads to an excellent opportunity to impact energy consumption in China by affecting the energy efficiency of appliances being bought and sold. In general, Chinese consumers value energy efficiency and are knowledgeable about the operating costs of major appliances. However, the Chinese marketplace does not provide information that consumers trust about the energy consumption of specific products. Thus, several interdependent organizations have emerged in China to provide information and market supports for energy efficiency. This paper describes the appliance market in China and the evolution of its standards and labeling programs and the agencies that implement them. It discusses the authors' work with these organizations in developing energy efficiency criteria and supporting an energy efficiency endorsement labeling program in China. It describes how the authors have used their experience with ENERGY STAR{reg_sign} and other programs in the U.S. to work with China to develop a successful program specific to Chinese conditions, with a particular emphasis on refrigerators. It then gives the author's market assessment of the Chinese refrigerator market and recommendations for a successful labeling program and transferable lessons for developing energy efficiency labeling programs in varied markets. This paper is based on the authors' market research, their support in setting energy efficiency criteria in China, interviews with Chinese manufacturers, retailers, and sales staff, and the development and implementation of labeling strategies and promotion in China.

  12. Metal Oxide-Based Selective Enrichment Combined with Stable Isotope Labeling-Mass Spectrometry Analysis for Profiling of Ribose Conjugates.

    PubMed

    Chu, Jie-Mei; Qi, Chu-Bo; Huang, Yun-Qing; Jiang, Han-Peng; Hao, Yan-Hong; Yuan, Bi-Feng; Feng, Yu-Qi

    2015-07-21

    Some modified ribonucleosides in biological fluids have been evaluated as cancer-related metabolites. Detection of endogenous modified ribonucleosides in biological fluids may serve as a noninvasive cancers diagnostic method. However, determination of modified ribonucleosides is still challenging because of their low abundance and serious matrix interferences in biological fluids. Here, we developed a novel strategy for comprehensive profiling of ribose conjugates from biological fluids using metal oxide-based dispersive solid-phase extraction (DSPE) followed with in vitro stable isotope labeling and double neutral loss scan-mass spectrometry analysis (DSPE-SIL-LC-DNLS-MS). Cerium dioxide (CeO2) was used to selectively recognize and capture ribose conjugates from complex biological samples under basic environment. The enriched ribose conjugates were subsequently labeled with a pair of isotope labeling reagents (acetone and acetone-d6). The glucosidic bond of acetone labeled ribose conjugates is readily ruptured, and the generated ribose that carries an isotope tag can be lost as a neutral fragment under collision induced dissociation (CID). Since the light (acetone) and heavy (acetone-d6) labeled compounds have the same chemical structures and can generate different neutral loss fragments (NL 172 and 178 Da), it is therefore highly convenient to profile ribose conjugates by double neutral loss scan mode in mass spectrometry analysis. In this respect, the light and heavy labeled compounds were ionized at the same condition but recorded separately on MS spectra, which can significantly improve the detection specificity and facilitate the identification of ribose conjugates. Using the developed DSPE-SIL-LC-DNLS-MS strategy, we profiled the ribose conjugates in human urine, and 49 ribose conjugates were readily identified, among which 7 ribose conjugates exhibited significant contents change between healthy controls and lymphoma patients. The DSPE-SIL-LC-DNLS-MS strategy combines the selective enrichment, stable isotope labeling, and double neutral loss scan - MS analysis, which therefore can efficiently minimize false positive results, facilitate the relative quantification, and notably increase the numbers of identified ribose conjugates in biological fluids samples. Taken together, this study established a promising strategy for the effective profiling of urinary modified ribonucleosides, and simultaneous evaluation of the contents change of multiple modified ribonucleosides should provide more accurate and conclusive results for the use of urinary modified ribonucleosides as indicators of cancers. PMID:26086917

  13. X13CMS: global tracking of isotopic labels in untargeted metabolomics.

    PubMed

    Huang, Xiaojing; Chen, Ying-Jr; Cho, Kevin; Nikolskiy, Igor; Crawford, Peter A; Patti, Gary J

    2014-02-01

    Studies of isotopically labeled compounds have been fundamental to understanding metabolic pathways and fluxes. They have traditionally, however, been used in conjunction with targeted analyses that identify and quantify a limited number of labeled downstream metabolites. Here we describe an alternative workflow that leverages recent advances in untargeted metabolomic technologies to track the fates of isotopically labeled metabolites in a global, unbiased manner. This untargeted approach can be applied to discover novel biochemical pathways and characterize changes in the fates of labeled metabolites as a function of altered biological conditions such as disease. To facilitate the data analysis, we introduce X(13)CMS, an extension of the widely used mass spectrometry-based metabolomic software package XCMS. X(13)CMS uses the XCMS platform to detect metabolite peaks and perform retention-time alignment in liquid chromatography/mass spectrometry (LC/MS) data. With the use of the XCMS output, the program then identifies isotopologue groups that correspond to isotopically labeled compounds. The retrieval of these groups is done without any a priori knowledge besides the following input parameters: (i) the mass difference between the unlabeled and labeled isotopes, (ii) the mass accuracy of the instrument used in the analysis, and (iii) the estimated retention-time reproducibility of the chromatographic method. Despite its name, X(13)CMS can be used to track any isotopic label. Additionally, it detects differential labeling patterns in biological samples collected from parallel control and experimental conditions. We validated the ability of X(13)CMS to accurately retrieve labeled metabolites from complex biological matrices both with targeted LC/MS/MS analysis of a subset of the hits identified by the program and with labeled standards spiked into cell extracts. We demonstrate the full functionality of X(13)CMS with an analysis of cultured rat astrocytes treated with uniformly labeled (U-)(13)C-glucose during lipopolysaccharide (LPS) challenge. Our results show that out of 223 isotopologue groups enriched from U-(13)C-glucose, 95 have statistically significant differential labeling patterns in astrocytes challenged with LPS compared to unchallenged control cells. Only two of these groups overlap with the 32 differentially regulated peaks identified by XCMS, indicating that X(13)CMS uncovers different and complementary information from untargeted metabolomic studies. Like XCMS, X(13)CMS is implemented in R. It is available from our laboratory website at http://pattilab.wustl.edu/x13cms.php . PMID:24397582

  14. A new method for the labelling of proteins with radioactive arsenic isotopes

    NASA Astrophysics Data System (ADS)

    Jennewein, M.; Hermanne, A.; Mason, R. P.; Thorpe, P. E.; Rösch, F.

    2006-12-01

    Radioarsenic labelled radiopharmaceuticals could be a valuable asset to positron emission tomography. In particular, the long half-lives of 72As ( T=26 h) and 74As ( T=17.8 d) allow to investigate slow physiological or metabolical processes, like the enrichment and distribution of monoclonal antibodies (mab) in tumour tissue. In this work, a new method for the labelling of proteins with various radioactive arsenic isotopes was developed. For this purpose, two proteins, namely a chimeric IgG 3 monoclonal antibody, ch3G4, directed against anionic phospholipids, and Rituxan (Rituximab), were labelled as a proof of principle with no-carrier-added radioarsenic isotopes ( 74As and 77As). The developed labelling chemistry gives high yields (>99.9%), is reliable and could easily be transferred to automated labelling systems in a clinical environment. At least for the mab used in this work, this route of radioarsenic labelling does not affect the immunoreactivity of the product. The arsenic label stays stable for up to 72 h at the molecular mass of the monoclonal antibody, which is in particular relevant to follow the pharmacology and pharmacokinetics of the labelled mab for several days.

  15. Efficient synthesis of deuterium labeled hydroxyzine and aripiprazole.

    PubMed

    Vohra, Mohit; Sandbhor, Mahendra; Wozniak, Andrew

    2015-06-15

    Hydroxyzine and aripiprazole are active pharmaceutical ingredients that have been largely acknowledged for their antipsychotic properties. Deuterium labeled isotopes of hydroxyzine and aripiprazole are internal standards that can aid in the further research of non-isotopic forms via quantification analysis using HPLC-MS/MS. The synthesis of hydroxyzine-d8 was accomplished by coupling piperazine-d8 with 4-chlorobenzhydryl chloride followed by the reaction of the first intermediate with 2-(2-chloroethoxy) ethanol to afford 11.7% of hydroxyzine-d8 with 99.5% purity. The synthesis of aripiprazole-d8 was also achieved in two steps. 1,4-Dibromobutane-d8 reacted with 7-hydroxy-3,4-dihydro-2(1H)-quinolinone. The first intermediate was then coupled with 1-(2, 3-dichlorophenyl)piperazine hydrochloride to produce 33.4% of aripiprazole-d8 with 99.93% purity. PMID:26011470

  16. Production and use of stable isotope-labeled proteins for absolute quantitative proteomics.

    PubMed

    Lebert, Dorothée; Dupuis, Alain; Garin, Jérôme; Bruley, Christophe; Brun, Virginie

    2011-01-01

    In the field of analytical chemistry, stable isotope dilution assays are extensively used in combination with liquid chromatography-mass spectrometry (LC-MS) to provide confident quantification results. Over the last decade, the principle of isotope dilution has been adopted by the proteomic community in order to accurately quantify proteins in biological samples. In these experiments, a protein's concentration is deduced from the ratio between the MS signal of a tryptic peptide and that of a stable isotope-labeled analog, which serves as an internal standard. The first isotope dilution standards introduced in proteomics were chemically synthesized peptides incorporating a stable isotope-tagged amino acid. These isotopically labeled peptide standards, which are currently widely used, are generally added to samples after protein isolation and digestion. Thus, if protein enrichment is necessary, they do not allow correction for protein losses that may occur during sample pre-fractionation, nor do they allow the tryptic digestion yield to be taken into account. To reduce these limitations we have developed the PSAQ (Protein Standard Absolute Quantification) strategy using full-length stable isotope-labeled proteins as quantification standards. These standards and the target proteins share identical biochemical properties. This allows standards to be spiked into samples at an early stage of the analytical process. Thanks to this possibility, the PSAQ method provides highly accurate quantification results, including for samples requiring extensive biochemical pre-fractionation. In this chapter, we describe the production of full-length stable isotope-labeled proteins (PSAQ standards) using cell-free expression devices. The purification and quality control of protein standards, crucial for good-quality and accurate measurements, are also detailed. Finally, application of the PSAQ method to a typical protein quantification assay is presented. PMID:21604118

  17. Synthesis of [(2) H6 ]ceftazidime as a stable isotopically labeled internal standard.

    PubMed

    Bian, Lei; Bushby, Nick

    2015-06-15

    Ceftazidime is a third generation cephalosporin antibiotic that has activity against a wide range of Gram-negative and Gram-positive bacterial pathogens, including Escherichia coli and Pseudomonas aeruginosa. Stable isotope-labeled ceftazidime was required for use as an internal standard in LC-MS/MS assays, and a route was developed to make [(2) H6 ]ceftazidime in eight steps from the commercially available labeled starting material [(2) H7 ]isobutyric acid. PMID:26017617

  18. Mass Spectral Fragmentation Patterns of Deuterated Butyl and Ethyl Acetates: An Easy Microscale Isotopic Labeling Experiment

    Microsoft Academic Search

    Hengameh Zahedkargaran; Leverett R. Smith

    2001-01-01

    We have developed an experimentally uncomplicated microscale second-semester organic lab exercise that illustrates the use of isotopic labeling, in this case deuteration, to help confirm and interpret mass spectral fragmentation patterns in butyl acetate and ethyl acetate. Preparation and gas chromatographic-mass spectrometric (GC-MS) analysis of unlabeled and labeled esters is followed by pooling of student data for interpretation and write-up.

  19. Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy

    Microsoft Academic Search

    Vitali Tugarinov; Voula Kanelis; Lewis E Kay

    2006-01-01

    The development of isotope labeling methodology has had a significant impact on NMR studies of high-molecular-weight proteins and macromolecular complexes. Here we review some of this methodology that has been developed and used in our laboratory. In particular, experimental protocols are described for the production of highly deuterated, uniformly 15N- and 13C-labeled samples of large proteins, with optional incorporation of

  20. Affordable uniform isotope labeling with (2)H, (13)C and (15)N in insect cells.

    PubMed

    Sitarska, Agnieszka; Skora, Lukasz; Klopp, Julia; Roest, Susan; Fernández, César; Shrestha, Binesh; Gossert, Alvar D

    2015-06-01

    For a wide range of proteins of high interest, the major obstacle for NMR studies is the lack of an affordable eukaryotic expression system for isotope labeling. Here, a simple and affordable protocol is presented to produce uniform labeled proteins in the most prevalent eukaryotic expression system for structural biology, namely Spodoptera frugiperda insect cells. Incorporation levels of 80 % can be achieved for (15)N and (13)C with yields comparable to expression in full media. For (2)H,(15)N and (2)H,(13)C,(15)N labeling, incorporation is only slightly lower with 75 and 73 %, respectively, and yields are typically twofold reduced. The media were optimized for isotope incorporation, reproducibility, simplicity and cost. High isotope incorporation levels for all labeling patterns are achieved by using labeled algal amino acid extracts and exploiting well-known biochemical pathways. The final formulation consists of just five commercially available components, at costs 12-fold lower than labeling media from vendors. The approach was applied to several cytosolic and secreted target proteins. PMID:25929326

  1. Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics

    Microsoft Academic Search

    Tamar Geiger; Jacek R Wisniewski; Juergen Cox; Sara Zanivan; Marcus Kruger; Yasushi Ishihama; Matthias Mann

    2010-01-01

    Mass spectrometry (MS)-based proteomics is increasingly applied in a quantitative format, often based on labeling of samples with stable isotopes that are introduced chemically or metabolically. In the stable isotope labeling by amino acids in cell culture (SILAC) method, two cell populations are cultured in the presence of heavy or light amino acids (typically lysine and\\/or arginine), one of them

  2. Phosphorus cycling in the Sargasso Sea: Investigation using the oxygen isotopic composition of phosphate, enzyme-labeled

    E-print Network

    Paytan, Adina

    : Investigation using the oxygen isotopic composition of phosphate, enzyme-labeled fluorescence, and turnoverPhosphorus cycling in the Sargasso Sea: Investigation using the oxygen isotopic composition of phosphate, enzyme-labeled fluorescence, and turnover times Karen McLaughlin,1 Jill A. Sohm,2 Gregory A

  3. Sample-efficient learning with auxiliary class-label information.

    PubMed

    Nguyen, Quang; Valizadegan, Hamed; Seybert, Amy; Hauskrecht, Milos

    2011-01-01

    Building classification models from clinical data collected for past patients often requires additional example labeling and annotation by a human expert. Since example labeling may require to review a complete electronic health record the process can be very time consuming and costly. To make the process more cost-efficient, the number of examples an expert needs to label should be reduced. We develop and test a new approach for the classification learning in which, in addition to class labels provided by an expert, the learner is provided with auxiliary information that reflects how strong the expert feels about the class label. We show that this information can be extremely useful for practical classification tasks based on human assessment and can lead to improved learning with a smaller number of examples. We develop a new classification approach based on the support vector machines and the learning to rank methodologies capable of utilizing the auxiliary information during the model learning process. We demonstrate the benefit of the approach on the problem of learning an alert model for Heparin Induced Thrombocytopenia (HIT) by showing an improved classification performance of the models that are trained on a smaller number of labeled examples. PMID:22195160

  4. Sample-efficient learning with auxiliary class-label information

    PubMed Central

    Nguyen, Quang; Valizadegan, Hamed; Seybert, Amy; Hauskrecht, Milos

    2011-01-01

    Building classification models from clinical data collected for past patients often requires additional example labeling and annotation by a human expert. Since example labeling may require to review a complete electronic health record the process can be very time consuming and costly. To make the process more cost-efficient, the number of examples an expert needs to label should be reduced. We develop and test a new approach for the classification learning in which, in addition to class labels provided by an expert, the learner is provided with auxiliary information that reflects how strong the expert feels about the class label. We show that this information can be extremely useful for practical classification tasks based on human assessment and can lead to improved learning with a smaller number of examples. We develop a new classification approach based on the support vector machines and the learning to rank methodologies capable of utilizing the auxiliary information during the model learning process. We demonstrate the benefit of the approach on the problem of learning an alert model for Heparin Induced Thrombocytopenia (HIT) by showing an improved classification performance of the models that are trained on a smaller number of labeled examples. PMID:22195160

  5. UV Raman Spatially Resolved Melting Dynamics of Isotopically Labeled Polyalanyl Peptide: Slow r-Helix Melting Follows 310-Helices and -Bulges Premelting

    E-print Network

    Asher, Sanford A.

    UV Raman Spatially Resolved Melting Dynamics of Isotopically Labeled Polyalanyl Peptide: Slow r) to examine the spatial dependence of the T-jump secondary structure relaxation of an isotopically labeled 21

  6. Isotopic Labeling Experiments That Elucidate the Mechanism of DNA Strand Cleavage by the Hypoxia-Selective Antitumor Agent 1,2,4-

    E-print Network

    Gates, Kent. S.

    Isotopic Labeling Experiments That Elucidate the Mechanism of DNA Strand Cleavage by the Hypoxia produced nondeuterated mono-N-oxide metabolites. This and the results of other isotopic labeling studies

  7. Profiling and relative quantitation of phosphoinositides by multiple precursor ion scanning based on phosphate methylation and isotopic labeling.

    PubMed

    Cai, Tanxi; Shu, Qingbo; Hou, JunJie; Liu, Peibin; Niu, Lili; Guo, Xiaojing; Liu, Charles C; Yang, Fuquan

    2015-01-01

    Phosphoinositides, the phosphorylated derivatives of phosphatidylinositol (PtdIns), are key regulators of many fundamental biological processes, including cell growth, proliferation, and motility. Here, we present a novel method for rapid, sensitive, and simultaneous profiling of phosphatidylinositol trisphosphate (PtdInsP3), phosphatidylinositol bisphosphate (PtdInsP2), and phosphatidylinositol phosphate (PtdInsP) of different fatty acid compositions. This method is based on a technique called "charged diacylglycerol fragment ion-specific multiple precursor ion scanning" (DAG(+)-specific MPIS), coupled with prior phosphate methylation. Using DAG(+)-specific MPIS, we were able to identify 32 PtdIns, 28 PtdInsP, 30 PtdInsP2, and 3 PtdInsP3 molecular species from bovine brain extracts or prostatic cancer cell lines in an efficient and time-saving manner. Our analysis revealed a large range of fatty acyl compositions in phosphoinositides not obtained previously from mammalian samples. We also developed a method that involves isotopic labeling of endogenous phosphoinositides with deuterated diazomethane (CD2N2) for quantitation of phosphoinositides. CD2N2 was generated in situ through acid-catalyzed H/D exchange and methanolysis of trimethylsilyl diazomethane (TMS-diazomethane). Phosphoinositides, extracted from a PC3 prostatic cancer cell line, were labeled either with CH2N2 or CD2N2 and mixed in known proportions for DAG(+)-specific MPIS-based mass spectrometry (MS) analysis. The results indicate that isotopic labeling is capable of providing accurate quantitation of PtdInsP3, PtdInsP2, and PtdInsP with adequate linearity as well as high reproducibility with an average coefficient variation of 18.9%. More importantly, this new methods excluded the need for multiple phosphoinositide internal standards. DAG(+)-specific MPIS and isotopic labeling based MS analysis of phosphoinositides offers unique advantages over existing approaches and presents a powerful tool for research of phosphoinositide metabolism. PMID:25495789

  8. In situ Raman spectroscopy of supported chromium oxide catalysts: {sup 18}O{sub 2}-{sup 16}O{sub 2} isotopic labeling studies

    SciTech Connect

    Weckhuysen, B.M.; Wachs, I.E. [Lehigh Univ., Bethlehem, PA (United States)] [Lehigh Univ., Bethlehem, PA (United States)

    1997-04-10

    The isothermal isotopic exchange reaction of {sup 18}O{sub 2} with {sup 16}O of chromium(VI) oxide supported on zirconia, alumina, and titania has been investigated with in situ laser Raman spectroscopy. The isotopic exchange reaction is dependent on the support type, the Cr loading, and the reaction temperature. Complete isotopic exchange of chromium(VI) oxide with {sup 18}O{sub 2} is difficult to achieve and requires several successive butane reduction-{sup 18}O{sub 2} oxidation cycles at relatively high temperatures. The efficiency of the isothermal isotopic exchange reaction increases from alumina over titania to zirconia and with increasing Cr loading and reduction temperature. The observed Raman shifts upon isotopic labeling are consistent with a mono-oxo surface chromium oxide(VI) species. 25 refs., 5 figs.

  9. Quantitative approaches for analysing fluxes through plant metabolic networks using NMR and stable isotope labelling

    Microsoft Academic Search

    N. J. Kruger; R. G. Ratcliffe; A. Roscher

    2003-01-01

    The quantitative analysis of metabolic networks is a prerequisite for understanding the integration and regulation of plant metabolism and for devising rational approaches for manipulating resource allocation in plants. The analysis of steady state stable isotope labelling experiments using nuclear magnetic resonance (NMR) spectroscopy has developed into a powerful method for determining these fluxes in micro-organisms and its application to

  10. Ion-Surface Reactions Involving Isotopically Labeled Langmuir-Blodgett Films

    E-print Network

    Wysocki, Vicki H.

    (i.e., secondary ion mass spectrometry, SIMS11 ). Various mechanisms for alkyl and/or hydrogen for investigating ion-surface reactions is a custom tandem mass spectrometer equipped with two Extrel (PittsburghIon-Surface Reactions Involving Isotopically Labeled Langmuir-Blodgett Films Chungang Gu and Vicki

  11. UNiquant, a Program for Quantitative Proteomics Analysis Using Stable Isotope Labeling

    Microsoft Academic Search

    Xin Huang; Aleksey V. Tolmachev; Yulei Shen; Miao Liu; Lin Huang; Zhixin Zhang; Gordon A. Anderson; Richard D. Smith; Wing C. Chan; Steven Hinrichs; Kai Fu; Shi-Jian Ding

    2011-01-01

    We present UNiquant, a new software program for analyzing stable isotope labeling (SIL) based quantitative proteomics data. UNiquant surpassed the performance of two other platforms, MaxQuant and Mascot Distiller, using complex proteome mixtures having either known or unknown heavy\\/light ratios. UNiquant is compatible with a broad spectrum of search engines and SIL methods, providing outstanding peptide pair identification and accurate

  12. Chemical Ligation of Folded Recombinant Proteins: Segmental Isotopic Labeling of Domains for NMR Studies

    Microsoft Academic Search

    Rong Xu; Brenda Ayers; David Cowburn; Tom W. Muir

    1999-01-01

    A convenient in vitro chemical ligation strategy has been developed that allows folded recombinant proteins to be joined together. This strategy permits segmental, selective isotopic labeling of the product. The src homology type 3 and 2 domains (SH3 and SH2) of Abelson protein tyrosine kinase, which constitute the regulatory apparatus of the protein, were individually prepared in reactive forms that

  13. Protein N- and C-Termini Identification Using Mass Spectrometry and Isotopic Labeling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new method for protein N- and C-terminal analysis using mass spectrometry is introduced. A novel stable isotopic labeling scheme has been developed to identify terminal peptides generated from an enzyme digestion for the determination of both N- and C-termini of the protein. This method works dire...

  14. Unambiguous assignment of short- and long-range structural restraints by solid-state NMR spectroscopy with segmental isotope labeling.

    PubMed

    Schubeis, Tobias; Lührs, Thorsten; Ritter, Christiane

    2015-01-01

    We present an efficient method for the reduction of spectral complexity in the solid-state NMR spectra of insoluble protein assemblies, without loss of signal intensity. The approach is based on segmental isotope labeling by using the split intein DnaE from Nostoc punctiforme. We show that the segmentally (13)C, (15)N-labeled prion domain of HET-s exhibits significantly reduced spectral overlap while retaining the wild-type structure and spectral quality. A large number of unambiguous distance restraints were thus collected from a single two-dimensional (13)C, (13)C cross-correlation spectrum. The observed resonances could be unambiguously identified as intramolecular without the need for preparing a dilute, less sensitive sample. PMID:25394265

  15. A 15N stable isotope semen label to detect mating in the malaria mosquito Anopheles arabiensis Patton

    Microsoft Academic Search

    Michelle EH Helinski; Rebecca C Hood; Doris Gludovacz; Leo Mayr; Bart GJ Knols

    2008-01-01

    In previous studies it was determined that the stable isotope 13-carbon can be used as a semen label to detect mating events in the malaria mosquito Anopheles arabiensis. In this paper we describe the use of an additional stable isotope, 15-nitrogen (15N), for that same purpose. Both stable isotopes can be analysed simultaneously in a mass spectrometer, offering the possibility

  16. Analysis of Isotopic Labeling in Peptide Fragments by Tandem Mass Spectrometry

    PubMed Central

    Allen, Doug K.; Evans, Bradley S.; Libourel, Igor G. L.

    2014-01-01

    Phenotype in multicellular organisms is the consequence of dynamic metabolic events that occur in a spatially dependent fashion. This spatial and temporal complexity presents challenges for investigating metabolism; creating a need for improved methods that effectively probe biochemical events such as amino acid biosynthesis. Isotopic labeling can provide a temporal-spatial recording of metabolic events through, for example, the description of enriched amino acids in the protein pool. Proteins are therefore an important readout of metabolism and can be assessed with modern mass spectrometers. We compared the measurement of isotopic labeling in MS2 spectra obtained from tandem mass spectrometry under either higher energy collision dissociation (HCD) or collision induced dissociation (CID) at varied energy levels. Developing soybean embryos cultured with or without 13C-labeled substrates, and Escherichia coli MG1655 enriched by feeding 7% uniformly labeled glucose served as a source of biological material for protein evaluation. CID with low energies resulted in a disproportionate amount of heavier isotopologues remaining in the precursor isotopic distribution. HCD resulted in fewer quantifiable products; however deviation from predicted distributions were small relative to the CID-based comparisons. Fragment ions have the potential to provide information on the labeling of amino acids in peptides, but our results indicate that without further development the use of this readout in quantitative methods such as metabolic flux analysis is limited. PMID:24626471

  17. Combining Stable Isotope Labeling and Molecular Networking for Biosynthetic Pathway Characterization.

    PubMed

    Klitgaard, Andreas; Nielsen, Jakob B; Frandsen, Rasmus J N; Andersen, Mikael R; Nielsen, Kristian F

    2015-07-01

    Filamentous fungi are a rich source of bioactive compounds, ranging from statins over immunosuppressants to antibiotics. The coupling of genes to metabolites is of large commercial interest for production of the bioactives of the future. To this end, we have investigated the use of stable isotope labeled amino acids (SILAAs). SILAAs were added to the cultivation media of the filamentous fungus Aspergillus nidulans for the study of the cyclic tetrapeptide nidulanin A. Analysis by UHPLC-TOFMS confirmed that the SILAAs were incorporated into produced nidulanin A, and the change in observed m/z could be used to determine whether a compound (known or unknown) incorporated any of the added amino acids. Samples were then analyzed using MS/MS and the data used to perform molecular networking. The molecular network revealed several known and unknown compounds that were also labeled. Assisted by the isotope labeling, it was possible to determine the sequence of several of the compounds, one of which was the known metabolite fungisporin, not previously described in A. nidulans. Several novel analogues of nidulanin A and fungisporin were detected and tentatively identified, and it was determined that these metabolites were all produced by the same nonribosomal peptide synthase. The combination of stable isotope labeling and molecular network generation was shown to very effective for the automated detection of structurally related nonribosomal peptides, while the labeling was effective for determination of the peptide sequence, which could be used to provide information on biosynthesis of bioactive compounds. PMID:26020678

  18. Vibrational Energy Relaxation of Isotopically Labeled Amide I Modes in Cytochrome c: Theoretical Investigation of Vibrational Energy Relaxation Rates and Pathways

    E-print Network

    Straub, John E.

    Vibrational Energy Relaxation of Isotopically Labeled Amide I Modes in Cytochrome c: Theoretical theory, vibrational energy relaxation (VER) of isotopically labeled amide I modes in cytochrome c studied were isotopically labeled according to IR experiment.30,31 We decompose the VER rate into two

  19. Solution structure of the two RNA recognition motifs of hnRNP A1 using segmental isotope labeling: how the relative orientation

    E-print Network

    Paris-Sud XI, Université de

    1 Solution structure of the two RNA recognition motifs of hnRNP A1 using segmental isotope labeling with segmental isotope labeling techniques to carefully analyze the inter-RRM contacts present in solution isotope labeling; expressed protein ligation; intein; structural biology; hnRNP A1; UP1; RRM; NMR; inter

  20. Stable Isotope Labeling in Zebrafish Allows in Vivo Monitoring of Cardiac Morphogenesis*

    PubMed Central

    Konzer, Anne; Ruhs, Aaron; Braun, Helene; Jungblut, Benno; Braun, Thomas; Krüger, Marcus

    2013-01-01

    Quantitative proteomics is an important tool to study biological processes, but so far it has been challenging to apply to zebrafish. Here, we describe a large scale quantitative analysis of the zebrafish proteome using a combination of stable isotope labeling and liquid chromatography-mass spectrometry (LC-MS). Proteins derived from the fully labeled fish were used as a standard to quantify changes during embryonic heart development. LC-MS-assisted analysis of the proteome of activated leukocyte cell adhesion molecule zebrafish morphants revealed a down-regulation of components of the network required for cell adhesion and maintenance of cell shape as well as secondary changes due to arrest of cellular differentiation. Quantitative proteomics in zebrafish using the stable isotope-labeling technique provides an unprecedented resource to study developmental processes in zebrafish. PMID:23412571

  1. Isotope labeling pattern study of central carbon metabolites using GC/MS.

    PubMed

    Jung, Joon-Young; Oh, Min-Kyu

    2015-01-01

    Determination of fluxes by (13)C tracer experiments depends on monitoring the (13)C labeling pattern of metabolites during isotope experiments. In metabolome-based (13)C metabolic flux analysis, liquid chromatography combined with mass spectrometry or tandem mass spectrometry (LC/MS or LC/MS/MS, respectively) has been mainly used as an analytical platform for isotope pattern studies of central carbon metabolites. However, gas chromatography with mass spectrometry (GC/MS) has several advantages over LC/MS, such as high sensitivity, low cost, ease of operation, and availability of mass spectra databases for comparison. In this study, analysis of isotope pattern for central carbon metabolites using GC/MS was demonstrated. First, a proper set of mass ions for central carbon metabolites was selected based on carbon backbone information and structural isomers of mass fragment ions. A total of 34 mass fragment ions was selected and used for the quantification of 25 central carbon metabolites. Then, to quantify isotope fractions, a natural mass isotopomer library for selected mass fragment ions was constructed and subtracted from isotopomer mass spectra data. The results revealed a surprisingly high abundance of partially labeled (13)C intermediates, such as 56.4% of fructose 6-phosphate and 47.6% of dihydroxyacetone phosphate at isotopic steady state, which were generated in the pentose phosphate pathway. Finally, dynamic changes of isotope fragments of central metabolites were monitored with a U-(13)C glucose stimulus response experiment in Kluyveromyces marxianus. With a comprehensive study of isotope patterns of central carbon metabolites using GC/MS, 25 central carbon metabolites and their isotopic fractions were successfully quantified. Dynamic and precise acquisition of isotope pattern can then be used in combination with proper kinetic models to calculate metabolic fluxes. PMID:25463204

  2. Proteome analysis using selective incorporation of isotopically labeled amino acids

    Microsoft Academic Search

    Timothy D. Veenstra; Suzana Martinovi?; Gordon A. Anderson; Ljiljana Paša-Toli?; Richard D. Smith

    2000-01-01

    A method is described for identifying intact proteins from genomic databases using a combination of accurate molecular mass\\u000a measurements and partial amino acid content. An initial demonstration was conducted for proteins isolated from Escherichia coli (E. coli) using a multiple auxotrophic strain of K12. Proteins extracted from the organism grown in natural isotopic abundance minimal\\u000a medium and also minimal medium

  3. Global Potential of Energy Efficiency Standards and Labeling Programs

    SciTech Connect

    McNeil, Michael A; McNeil, Michael A.; Letschert, Virginie; de la Rue du Can, Stephane

    2008-06-15

    This report estimates the global potential reductions in greenhouse gas emissions by 2030 for energy efficiency improvements associated with equipment (appliances, lighting, and HVAC) in buildings by means of energy efficiency standards and labels (EES&L). A consensus has emerged among the world's scientists and many corporate and political leaders regarding the need to address the threat of climate change through emissions mitigation and adaptation. A further consensus has emerged that a central component of these strategies must be focused around energy, which is the primary generator of greenhouse gas emissions. Two important questions result from this consensus: 'what kinds of policies encourage the appropriate transformation to energy efficiency' and 'how much impact can these policies have'? This report aims to contribute to the dialogue surrounding these issues by considering the potential impacts of a single policy type, applied on a global scale. The policy addressed in this report is Energy Efficient Standards and Labeling (EES&L) for energy-consuming equipment, which has now been implemented in over 60 countries. Mandatory energy performance standards are important because they contribute positively to a nation's economy and provide relative certainty about the outcome (both timing and magnitudes). Labels also contribute positively to a nation's economy and importantly increase the awareness of the energy-consuming public. Other policies not analyzed here (utility incentives, tax credits) are complimentary to standards and labels and also contribute in significant ways to reducing greenhouse gas emissions. We believe the analysis reported here to be the first systematic attempt to evaluate the potential of savings from EES&L for all countries and for such a large set of products. The goal of the analysis is to provide an assessment that is sufficiently well-quantified and accurate to allow comparison and integration with other strategies under consideration.

  4. An efficient on-column expressed protein ligation strategy: Application to segmental triple labeling of human apolipoprotein E3

    PubMed Central

    Zhao, Wentao; Zhang, Yonghong; Cui, Chunxian; Li, Qianqian; Wang, Jianjun

    2008-01-01

    Expressed protein ligation (EPL) is an intein-based approach that has been used for protein engineering and biophysical studies of protein structures. One major problem of the EPL is the low yield of final ligation product, primarily due to the complex procedure of the EPL, preventing EPL from gaining popularity in the research community. Here we report an efficient on-column EPL strategy, which focuses on enhancing the expression level of the intein-fusion protein that generates thioester for the EPL. We applied this EPL strategy to human apolipoprotein E (apoE) and routinely obtained 25–30 mg segmental, triple-labeled apoE from 1-L cell culture. The approaches reported here are general approaches that are not specific for apoE, thus providing a general strategy for a highly efficient EPL. In addition, we also report an isotopic labeling scheme that double-labels one domain and keeps the other domain of apoE deuterated. Such an isotopic labeling scheme can only be achieved using the EPL strategy. Our data indicated that the segmental triple-labeled apoEs using this labeling scheme produced high-quality, simplified NMR spectra, facilitating NMR spectral assignment. For large proteins, such as apoE, perdeuterated protein samples have to be used to reduce the linewidth of NMR signals, causing a major problem for the NOE-based NMR method, since perdeuterated proteins lack protons for NOE measurement. The new labeling strategy solves this problem and provides 13C/15N double-labeled, protonated protein domains, allowing for determination of high-resolution NMR structure of these large proteins. PMID:18305193

  5. Quantifying proteomes and their post-translational modifications by stable isotope label-based mass spectrometry

    PubMed Central

    Merrill, Anna E.; Coon, Joshua J.

    2013-01-01

    Stable isotope labeling coupled with mass spectrometry has revolutionized the scope and impact of protein expression studies. Label incorporation can occur metabolically or chemically, and each method bears specific strengths and weaknesses. Quantitative proteomics confidently identifies specific interactions between proteins and other biological species, such as nucleic acids and metabolites. Extending label-based methods to phosphorylation-modified forms of proteins enables the construction of signaling networks and their temporal responses to stimuli. The integration of multiple data types offers systems-level insight on coordinated biological processes. Finally, the development of methods applicable to tissue quantification suggests the emerging role of label-based, quantitative mass spectrometry in translational science. PMID:23835517

  6. Isotopic labeling of mouse interferon by incorporation of radioactive amino acids during synthesis

    SciTech Connect

    DeMaeyer-Guignard, J.; Cachard, A.; DeMaeyer, E.

    1982-07-30

    Mouse interferon produced by C-243 cells induced with Newcastle disease virus was isotopically labeled by adding either (/sup 35/S)methionine or a /sup 14/C-labeled amino acid mixture to the culture medium. A method combining butyric acid and theophylline treatment and resulting in high interferon yields was used. Following purification by two-step affinity chromatography on poly(U) and antibody columns, the resulting material was analyzed on SDS-PAGE. The migration pattern of radioactivity and interferon coincided well and autoradiography revealed three major bands at migration distances corresponding, respectively, to 35, 28, and 22 K. Interferon represented 3.8% of all (/sup 35/S)methionine-labeled proteins and 2.6% of all /sup 14/C-amino acid-labeled proteins released into the medium.

  7. Stable isotope labeling of glycoprotein expressed in silkworms using immunoglobulin G as a test molecule.

    PubMed

    Yagi, Hirokazu; Nakamura, Masatoshi; Yokoyama, Jun; Zhang, Ying; Yamaguchi, Takumi; Kondo, Sachiko; Kobayashi, Jun; Kato, Tatsuya; Park, Enoch Y; Nakazawa, Shiori; Hashii, Noritaka; Kawasaki, Nana; Kato, Koichi

    2015-06-01

    Silkworms serve as promising bioreactors for the production of recombinant proteins, including glycoproteins and membrane proteins, for structural and functional protein analyses. However, lack of methodology for stable isotope labeling has been a major deterrent to using this expression system for nuclear magnetic resonance (NMR) structural biology. Here we developed a metabolic isotope labeling technique using commercially available silkworm larvae. The fifth instar larvae were infected with baculoviruses for co-expression of recombinant human immunoglobulin G (IgG) as a test molecule, with calnexin as a chaperone. They were subsequently reared on an artificial diet containing (15)N-labeled yeast crude protein extract. We harvested 0.1 mg of IgG from larva with a (15)N-enrichment ratio of approximately 80 %. This allowed us to compare NMR spectral data of the Fc fragment cleaved from the silkworm-produced IgG with those of an authentic Fc glycoprotein derived from mammalian cells. Therefore, we successfully demonstrated that our method enables production of isotopically labeled glycoproteins for NMR studies. PMID:25902760

  8. Stable isotopic labeling-based quantitative targeted glycomics (i-QTaG).

    PubMed

    Kim, Kyoung-Jin; Kim, Yoon-Woo; Kim, Yun-Gon; Park, Hae-Min; Jin, Jang Mi; Hwan Kim, Young; Yang, Yung-Hun; Kyu Lee, Jun; Chung, Junho; Lee, Sun-Gu; Saghatelian, Alan

    2015-05-01

    Mass spectrometry (MS) analysis combined with stable isotopic labeling is a promising method for the relative quantification of aberrant glycosylation in diseases and disorders. We developed a stable isotopic labeling-based quantitative targeted glycomics (i-QTaG) technique for the comparative and quantitative analysis of total N-glycans using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). We established the analytical procedure with the chemical derivatizations (i.e., sialic acid neutralization and stable isotopic labeling) of N-glycans using a model glycoprotein (bovine fetuin). Moreover, the i-QTaG using MALDI-TOF MS was evaluated with various molar ratios (1:1, 1:2, 1:5) of (13) C6 /(12) C6 -2-aminobenzoic acid-labeled glycans from normal human serum. Finally, this method was applied to direct comparison of the total N-glycan profiles between normal human sera (n?=?8) and prostate cancer patient sera (n?=?17). The intensities of the N-glycan peaks from i-QTaG method showed a good linearity (R(2) ?>?0.99) with the amount of the bovine fetuin glycoproteins. The ratios of relative intensity between the isotopically 2-AA labeled N-glycans were close to the theoretical molar ratios (1:1, 1:2, 1:5). We also demonstrated that the up-regulation of the Lewis antigen (?82%) in sera from prostate cancer patients. In this proof-of-concept study, we demonstrated that the i-QTaG method, which enables to achieve a reliable comparative quantitation of total N-glycans via MALDI-TOF MS analysis, has the potential to diagnose and monitor alterations in glycosylation associated with disease states or biotherapeutics. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:840-848, 2015. PMID:25832445

  9. An Efficient Method to Estimate Labelled Sample Size for Transductive LDA(QDA/MDA)

    E-print Network

    An Efficient Method to Estimate Labelled Sample Size for Transductive LDA(QDA/MDA) Based on Bayes to Estimate Labelled Sample Size 275 kernel, and by maximizing the margin based on the unlabelled data labelled sample size becomes a necessity. Moreover, a detailed analysis of labelled sample size under

  10. Novel approaches in selective tryptophan isotope labeling by using Escherichia coli overexpression media.

    PubMed

    Schörghuber, Julia; Sára, Tomáš; Bisaccia, Marilena; Schmid, Walther; Konrat, Robert; Lichtenecker, Roman J

    2015-03-23

    NMR-based investigations of large protein complexes require optimized isotopic labeling schemes. We report new methods to introduce stable isotopes into tryptophan residues; these are fine-tuned to the requirements of the particular protein NMR experiment. Selective backbone labeling was performed by using a new ?-ketoacid precursor as an additive in cell-based overexpression media. Additionally, we developed synthetic routes to certain isotopologues of indole with (13)C-(1)H spin systems surrounded by (12)C and (2)H. The corresponding proteins, overexpressed in the presence of these precursor compounds, can be effectively analyzed for conformational changes in tryptophan residues in response to external stimuli, such as interaction with other proteins or small molecules. PMID:25703586

  11. UNiquant, a Program for Quantitative Proteomics Analysis Using Stable Isotope Labeling

    SciTech Connect

    Huang, Xin; Tolmachev, Aleksey V.; Shen, Yulei; Liu, Miao; Huang, Lin; Zhang, Zhixin; Anderson, Gordon A.; Smith, Richard D.; Chan, Wing C.; Hinrichs, Steven; Fu, Kai; Ding, Shi-Jian

    2011-03-04

    We present UNiquant, a new software program for analyzing stable isotope labeling (SIL) based quantitative proteomics data. UNiquant surpassed the performance of two other platforms, MaxQuant and Mascot Distiller, using complex proteome mixtures having either known or unknown heavy/light ratios. UNiquant is compatible with a broad spectrum of search engines and SIL methods, providing outstanding peptide pair identification and accurate measurement of the relative peptide/protein abundance.

  12. Use of stable isotopically labeled tracers to measure very low density lipoprotein-triglyceride turnover

    Microsoft Academic Search

    Bruce W. Patterson; Bettina Mittendorfer; Nizar Elias; Raj Satyanarayana; Samuel Klein

    Tracer methods for VLDL-TG kinetics vary in their ability to account for the effect of tracer recycling, which can influence the calculation of VLDL-TG fractional catabolic rates (FCRs). We evaluated a novel approach, in- volving stable isotopically labeled glycerol or palmitate tracers in conjunction with compartmental modeling, for measur- ing VLDL-TG kinetics in normolipidemic human subjects. When administered as a

  13. Apolipoprotein B metabolism in humans: studies with stable isotope-labeled amino acid precursors

    Microsoft Academic Search

    Julian B. Marsh; Francine K. Welty; Alice H. Lichtenstein; Stefania Lamon-Fava; Ernst J. Schaefer

    2002-01-01

    This article reviews the literature from 1986 to early 2001 relating to apoB100 and apoB48 kinetics in humans using amino acid precursors labeled with stable isotopes. The following subjects are reviewed: (1) methodology; (2) normal individuals and the effects of aging; (3) diet; (4) hereditary dyslipidemias: familial hypercholesterolemia, familial combined hyperlipidemia, cholesteryl ester storage disease, cholesteryl ester transfer protein deficiency,

  14. Identification of miRNA targets with stable isotope labeling by amino acids in cell culture

    Microsoft Academic Search

    Jeppe Vinther; Mads M. Hedegaard; Paul P. Gardner; Jens S. Andersen; Peter Arctander

    2006-01-01

    miRNAs are small noncoding RNAs that regulate gene expression. We have used stable isotope labeling by amino acids in cell culture (SILAC) to investigate the effect of miRNA-1 on the HeLa cell proteome. Expression of 12 out of 504 investigated proteins was repressed by miRNA-1 transfection. This repressed set of genes significantly overlaps with miRNA-1 regulated genes that have been

  15. Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase.

    PubMed

    Luk, Louis Y P; Ruiz-Pernía, J Javier; Adesina, Aduragbemi S; Loveridge, E Joel; Tuñón, Iñaki; Moliner, Vincent; Allemann, Rudolf K

    2015-07-27

    Chemical ligation has been used to alter motions in specific regions of dihydrofolate reductase from E.?coli and to investigate the effects of localized motional changes on enzyme catalysis. Two isotopic hybrids were prepared; one with the mobile N-terminal segment containing heavy isotopes ((2) H, (13) C, (15) N) and the remainder of the protein with natural isotopic abundance, and the other one with only the C-terminal segment isotopically labeled. Kinetic investigations indicated that isotopic substitution of the N-terminal segment affected only a physical step of catalysis, whereas the enzyme chemistry was affected by protein motions from the C-terminal segment. QM/MM studies support the idea that dynamic effects on catalysis mostly originate from the C-terminal segment. The use of isotope hybrids provides insights into the microscopic mechanism of dynamic coupling, which is difficult to obtain with other studies, and helps define the dynamic networks of intramolecular interactions central to enzyme catalysis. PMID:26079622

  16. Enhanced sample multiplexing for nitrotyrosine-modified proteins using combined precursor isotopic labeling and isobaric tagging.

    PubMed

    Robinson, Renã A S; Evans, Adam R

    2012-06-01

    Current strategies for identification and quantification of 3-nitrotyrosine (3NT) post-translationally modified proteins (PTM) generally rely on biotin/avidin enrichment. Quantitative approaches have been demonstrated which employ isotopic labeling or isobaric tagging in order to quantify differences in the relative abundances of 3NT-modified proteins in two or potentially eight samples, respectively. Here, we present a novel strategy which uses combined precursor isotopic labeling and isobaric tagging (cPILOT) to increase the multiplexing capability of quantifying 3NT-modified proteins to 12 or 16 samples using commercially available tandem mass tags (TMT) or isobaric tags for relative and absolute quantification (iTRAQ), respectively. This strategy employs "light" and "heavy" labeled acetyl groups to block both N-termini and lysine residues of tryptic peptides. Next, 3NT is reduced to 3-aminotyrosine (3AT) using sodium dithionite followed by derivatization of light and heavy labeled 3AT-peptides with either TMT or iTRAQ multiplex reagents. We demonstrate the proof-of-principle utility of cPILOT with in vitro nitrated bovine serum albumin (BSA) and mouse splenic proteins using TMT(0), TMT(6), and iTRAQ(8) reagents and discuss limitations of the strategy. PMID:22509719

  17. A novel stable isotope labelling assisted workflow for improved untargeted LC-HRMS based metabolomics research.

    PubMed

    Bueschl, Christoph; Kluger, Bernhard; Lemmens, Marc; Adam, Gerhard; Wiesenberger, Gerlinde; Maschietto, Valentina; Marocco, Adriano; Strauss, Joseph; Bödi, Stephan; Thallinger, Gerhard G; Krska, Rudolf; Schuhmacher, Rainer

    2014-01-01

    Many untargeted LC-ESI-HRMS based metabolomics studies are still hampered by the large proportion of non-biological sample derived signals included in the generated raw data. Here, a novel, powerful stable isotope labelling (SIL)-based metabolomics workflow is presented, which facilitates global metabolome extraction, improved metabolite annotation and metabolome wide internal standardisation (IS). The general concept is exemplified with two different cultivation variants, (1) co-cultivation of the plant pathogenic fungi Fusarium graminearum on non-labelled and highly (13)C enriched culture medium and (2) experimental cultivation under native conditions and use of globally U-(13)C labelled biological reference samples as exemplified with maize and wheat. Subsequent to LC-HRMS analysis of mixtures of labelled and non-labelled samples, two-dimensional data filtering of SIL specific isotopic patterns is performed to better extract truly biological derived signals together with the corresponding number of carbon atoms of each metabolite ion. Finally, feature pairs are convoluted to feature groups each representing a single metabolite. Moreover, the correction of unequal matrix effects in different sample types and the improvement of relative metabolite quantification with metabolome wide IS are demonstrated for the F. graminearum experiment. Data processing employing the presented workflow revealed about 300 SIL derived feature pairs corresponding to 87-135 metabolites in F. graminearum samples and around 800 feature pairs corresponding to roughly 350 metabolites in wheat samples. SIL assisted IS, by the use of globally U-(13)C labelled biological samples, reduced the median CV value from 7.1 to 3.6 % for technical replicates and from 15.1 to 10.8 % for biological replicates in the respective F. graminearum samples. PMID:25057268

  18. Profiling of aldehyde-containing compounds by stable isotope labelling-assisted mass spectrometry analysis.

    PubMed

    Yu, Lei; Liu, Ping; Wang, Ya-Lan; Yu, Qiong-Wei; Yuan, Bi-Feng; Feng, Yu-Qi

    2015-07-13

    We developed a strategy for non-targeted profiling of aldehyde-containing compounds by stable isotope labelling in combination with liquid chromatography-double neutral loss scan-mass spectrometry (SIL-LC-DNLS-MS) analysis. A pair of stable isotope labelling reagents (4-(2-(trimethylammonio)ethoxy)benzenaminium halide, 4-APC and d4-4-(2-(trimethylammonio)ethoxy)benzenaminium halide, 4-APC-d4) that can selectively label aldehyde-containing compounds were synthesized. The 4-APC and 4-APC-d4 labelled compounds were capable of generating two characteristic neutral fragments of 87 Da and 91 Da, respectively, under collision induced dissociation (CID). Therefore, double neutral loss scans were carried out simultaneously to record the signals of the potential aldehyde-containing compounds. In this respect, the aldehyde-containing compounds from two samples labelled with 4-APC and 4-APC-d4 were ionized at the same time but recorded separately by mass spectrometry. The peak pairs with characteristic mass differences (n × 4 Da) can be readily extracted from the DNLS spectra and assigned as potential aldehyde-containing candidates, which facilitates the identification of the target aldehydes. 4-APC and 4-APC-d4 labelling also dramatically increased detection sensitivities of the derivatives. Using the SIL-LC-DNLS-MS strategy, we successfully profiled the aldehyde-containing compounds in human urine and white wine. Our results showed that 16 and 19 potential aldehyde-containing compounds were discovered in human urine and white wine, respectively. In addition, 5 and 4 aldehyde-containing compounds in human urine and white wine were further identified by comparison with aldehyde standards. Altogether, SIL-LC-DNLS-MS demonstrated to be a promising approach in the identification and relative quantification of aldehyde-containing compounds from complex samples. PMID:26086784

  19. Expression and isotopic labelling of the potassium channel blocker ShK toxin as a thioredoxin fusion protein in bacteria

    PubMed Central

    Chang, Shih Chieh; Galea, Charles A.; Leung, Eleanor W W.; Tajhya, Rajeev B.; Beeton, Christine; Pennington, Michael W.; Norton, Raymond S.

    2012-01-01

    The polypeptide toxin ShK is a potent blocker of Kv1.3 potassium channels, which play a crucial role in the activation of human effector memory T-cells (TEM). Selective blockers constitute valuable therapeutic leads for the treatment of autoimmune diseases mediated by TEM cells, such as multiple sclerosis, rheumatoid arthritis, and type-1 diabetes. We have established a recombinant peptide expression system in order to generate isotopically-labelled ShK and various ShK analogues for in-depth biophysical and pharmacological studies. ShK was expressed as a thioredoxin fusion protein in Escherichia coli BL21 (DE3) cells and purified initially by Ni2+ iminodiacetic acid affinity chromatography. The fusion protein was cleaved with enterokinase and purified to homogeneity by reverse-phase HPLC. NMR spectra of 15N-labelled ShK were similar to those reported previously for the unlabelled synthetic peptide, confirming that recombinant ShK was correctly folded. Recombinant ShK blocked Kv1.3 channels with a Kd of 25 pM and inhibited the proliferation of human and rat T lymphocytes with a preference for TEM cells, with similar potency to synthetic ShK in all assays. This expression system also enables the efficient production of 15N-labelled ShK for NMR studies of peptide dynamics and of the interaction of ShK with Kv1.3 channels. PMID:22659540

  20. Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics

    Microsoft Academic Search

    Shao-En Ong; Blagoy Blagoev; Irina Kratchmarova; Dan Bach Kristensen; Hanno Steen; Akhilesh Pandey; Matthias Mann

    2002-01-01

    Quantitative proteomics has traditionally been performed by two-dimensional gel electrophoresis, but recently, mass spectrometric methods based on stable isotope quantitation have shown great promise for the simultane- ous and automated identification and quantitation of complex protein mixtures. Here we describe a method, termed SILAC, for stable isotope labeling by amino acids in cell culture, for the in vivo incorporation of

  1. Phosphorus cycling in the Sargasso Sea: Investigation using the oxygen isotopic composition of phosphate, enzyme-labeled

    E-print Network

    Paytan, Adina

    Phosphorus cycling in the Sargasso Sea: Investigation using the oxygen isotopic composition of phosphate, enzyme-labeled fluorescence, and turnover times Karen McLaughlin,1 Jill A. Sohm,2 Gregory A in these regions. We explore the use of oxygen isotopic signature of dissolved phosphate (d18 OPO4) to investigate

  2. Application of stable isotope labelling in cell culture experiments: [2-13 C]pyruvate as novel and superior substrate for in vitro

    E-print Network

    Application of stable isotope labelling in cell culture experiments: [2-13 C]pyruvate as novel, Germany Introduction: Use of stable isotope labeling in cell culture experiments is a widely applied and powerful technique to study metabolic pathways and fluxes. In particular, the incorporation of 13 C-labels

  3. Stable isotope labels as a tool to determine the iron absorption by Peruvian school children from a breakfast meal

    Microsoft Academic Search

    T. Walczyk; Lena Davidsson; Nelly Zavaleta; Richard F. Hurrell

    1997-01-01

    Fractional iron absorption from a breakfast meal was determined in Peruvian children employing stable iron isotopes as labels.\\u000a Iron isotopic analysis was performed by the recently developed negative thermal ionization technique for high-precision iron\\u000a isotope ratio measurements using FeF4\\u000a – ions. By increasing the ascorbic acid content of the standard breakfast meal as served within the Peruvian school-breakfast\\u000a program from

  4. IMPACT OF DURATION OF INFUSION OF CHOICE ISOTOPE LABEL ON ISOTOPE RECYCLING IN GLUCOSE HOMEOSTASIS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The purposes of this study were to quantitate the impact of the duration of infusion and choice of stable isotope of glucose on measures of glucose rate of appearance (glucose Ra) and to determine whether the differences observed were due to tracer recycling via the glycogen pool (direct pathway) or...

  5. Systematic NMR Analysis of Stable Isotope Labeled Metabolite Mixtures in Plant and Animal Systems: Coarse Grained Views of Metabolic Pathways

    PubMed Central

    Chikayama, Eisuke; Suto, Michitaka; Nishihara, Takashi; Shinozaki, Kazuo; Hirayama, Takashi; Kikuchi, Jun

    2008-01-01

    Background Metabolic phenotyping has become an important ‘bird's-eye-view’ technology which can be applied to higher organisms, such as model plant and animal systems in the post-genomics and proteomics era. Although genotyping technology has expanded greatly over the past decade, metabolic phenotyping has languished due to the difficulty of ‘top-down’ chemical analyses. Here, we describe a systematic NMR methodology for stable isotope-labeling and analysis of metabolite mixtures in plant and animal systems. Methodology/Principal Findings The analysis method includes a stable isotope labeling technique for use in living organisms; a systematic method for simultaneously identifying a large number of metabolites by using a newly developed HSQC-based metabolite chemical shift database combined with heteronuclear multidimensional NMR spectroscopy; Principal Components Analysis; and a visualization method using a coarse-grained overview of the metabolic system. The database contains more than 1000 1H and 13C chemical shifts corresponding to 142 metabolites measured under identical physicochemical conditions. Using the stable isotope labeling technique in Arabidopsis T87 cultured cells and Bombyx mori, we systematically detected >450 HSQC peaks in each 13C-HSQC spectrum derived from model plant, Arabidopsis T87 cultured cells and the invertebrate animal model Bombyx mori. Furthermore, for the first time, efficient 13C labeling has allowed reliable signal assignment using analytical separation techniques such as 3D HCCH-COSY spectra in higher organism extracts. Conclusions/Significance Overall physiological changes could be detected and categorized in relation to a critical developmental phase change in B. mori by coarse-grained representations in which the organization of metabolic pathways related to a specific developmental phase was visualized on the basis of constituent changes of 56 identified metabolites. Based on the observed intensities of 13C atoms of given metabolites on development-dependent changes in the 56 identified 13C-HSQC signals, we have determined the changes in metabolic networks that are associated with energy and nitrogen metabolism. PMID:19030231

  6. Synthesis of isotopically labeled P-site substrates for the ribosomal peptidyl transferase reaction

    PubMed Central

    Zhong, Minghong

    2010-01-01

    Isotopomers of the ribosomal P-site substrate, the trinucleotide peptide conjugate CCA-pcb,1 have been designed and synthesized in 26–350020steps. These include individual isotopic substitution at the ?-proton, carbonyl carbon, and carbonyl oxygen of the amino acid, the O2' and O3' of the adenosine, and a remote label in the N3 and N4 of both cytidines. These isotopomers were synthesized by coupling cytidylyl-(3'5')-cytidine phosphoramidite isotopomers, as the common synthetic intermediates, with isotopically substituted A-Phe-cap-biotin (A-pcb). The isotopic enrichment is higher than 99% for 1-13C (Phe), 2-2H (Phe), and 3,4-15N2 (cytidine), 93% for 2'/3'- 18O (adenosine), and 64% for 1-18O (Phe). A new synthesis of highly enriched [1-18O2] phenylalanine has been developed. The synthesis of [3'-18O] adenosine was improved by Lewis acid aided regioselective ring opening of the epoxide and by an economical SN2-SN2 method with high isotopic enrichment (93%). Such substrates are valuable for studies of the ribosomal peptidyl transferase reaction by complete kinetic isotope effect analysis and of other biological processes catalyzed by nucleic acid related enzymes, including polymerases, reverse transcriptases, ligases, nucleases, and ribozymes. PMID:18081346

  7. Selectively Dispersed Isotope Labeling for Protein Structure Determination by Magic Angle Spinning NMR

    PubMed Central

    Eddy, Matthew T.; Belenky, Marina; Sivertsen, Astrid; Griffin, Robert G.; Herzfeld, Judith

    2013-01-01

    The power of nuclear magnetic resonance spectroscopy derives from its site-specific access to chemical, structural and dynamic information. However, the corresponding multiplicity of interactions can be difficult to tease apart. Complimentary approaches involve spectral editing on the one hand and selective isotope substitution on the other. Here we present a new “redox” approach to the latter: acetate is chosen as the sole carbon source for the extreme oxidation numbers of its two carbons. Consistent with conventional anabolic pathways for the amino acids, [1-13C] acetate does not label ? carbons, labels other aliphatic carbons and the aromatic carbons very selectively, and labels the carboxyl carbons heavily. The benefits of this labeling scheme are exemplified by magic angle spinning spectra of microcrystalline immunoglobulin binding protein G (GB1): the elimination of most J-couplings and one- and two-bond dipolar couplings provides narrow signals and long-range, intra- and inter-residue, recoupling essential for distance constraints. Inverse redox labeling, from [2-13C] acetate, is also expected to be useful: although it retains one-bond couplings in the sidechains, the removal of CA-CO coupling in the backbone should improve the resolution of NCACX spectra. PMID:23990199

  8. Stable Isotope Labeling Strategy for Curcumin Metabolite Study in Human Liver Microsomes by Liquid Chromatography-Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Gao, Dan; Chen, Xiaowu; Yang, Xiaomei; Wu, Qin; Jin, Feng; Wen, Hongliang; Jiang, Yuyang; Liu, Hongxia

    2015-04-01

    The identification of drug metabolites is very important in drug development. Nowadays, the most widely used methods are isotopes and mass spectrometry. However, the commercial isotopic labeled reagents are usually very expensive, and the rapid and convenient identification of metabolites is still difficult. In this paper, an 18O isotope labeling strategy was developed and the isotopes were used as a tool to identify drug metabolites using mass spectrometry. Curcumin was selected as a model drug to evaluate the established method, and the 18O labeled curcumin was successfully synthesized. The non-labeled and 18O labeled curcumin were simultaneously metabolized in human liver microsomes (HLMs) and analyzed by liquid chromatography/mass spectrometry (LC-MS). The two groups of chromatograms obtained from metabolic reaction mixture with and without cofactors were compared and analyzed using Metabolynx software (Waters Corp., Milford, MA, USA). The mass spectra of the newly appearing chromatographic peaks in the experimental sample were further analyzed to find the metabolite candidates. Their chemical structures were confirmed by tandem mass spectrometry. Three metabolites, including two reduction products and a glucuronide conjugate, were successfully detected under their specific HLMs metabolic conditions, which were in accordance with the literature reported results. The results demonstrated that the developed isotope labeling method, together with post-acquisition data processing using Metabolynx software, could be used for fast identification of new drug metabolites.

  9. Stable isotope labeling strategy for curcumin metabolite study in human liver microsomes by liquid chromatography-tandem mass spectrometry.

    PubMed

    Gao, Dan; Chen, Xiaowu; Yang, Xiaomei; Wu, Qin; Jin, Feng; Wen, Hongliang; Jiang, Yuyang; Liu, Hongxia

    2015-04-01

    The identification of drug metabolites is very important in drug development. Nowadays, the most widely used methods are isotopes and mass spectrometry. However, the commercial isotopic labeled reagents are usually very expensive, and the rapid and convenient identification of metabolites is still difficult. In this paper, an (18)O isotope labeling strategy was developed and the isotopes were used as a tool to identify drug metabolites using mass spectrometry. Curcumin was selected as a model drug to evaluate the established method, and the (18)O labeled curcumin was successfully synthesized. The non-labeled and (18)O labeled curcumin were simultaneously metabolized in human liver microsomes (HLMs) and analyzed by liquid chromatography/mass spectrometry (LC-MS). The two groups of chromatograms obtained from metabolic reaction mixture with and without cofactors were compared and analyzed using Metabolynx software (Waters Corp., Milford, MA, USA). The mass spectra of the newly appearing chromatographic peaks in the experimental sample were further analyzed to find the metabolite candidates. Their chemical structures were confirmed by tandem mass spectrometry. Three metabolites, including two reduction products and a glucuronide conjugate, were successfully detected under their specific HLMs metabolic conditions, which were in accordance with the literature reported results. The results demonstrated that the developed isotope labeling method, together with post-acquisition data processing using Metabolynx software, could be used for fast identification of new drug metabolites. PMID:25592681

  10. Stable Isotope Labeling of Phosphoproteins for Large-scale Phosphorylation Rate Determination*

    PubMed Central

    Molden, Rosalynn C.; Goya, Jonathan; Khan, Zia; Garcia, Benjamin A.

    2014-01-01

    Signals that control responses to stimuli and cellular function are transmitted through the dynamic phosphorylation of thousands of proteins by protein kinases. Many techniques have been developed to study phosphorylation dynamics, including several mass spectrometry (MS)-based methods. Over the past few decades, substantial developments have been made in MS techniques for the large-scale identification of proteins and their post-translational modifications. Nevertheless, all of the current MS-based techniques for quantifying protein phosphorylation dynamics rely on the measurement of changes in peptide abundance levels, and many methods suffer from low confidence in phosphopeptide identification due to poor fragmentation. Here we have optimized an approach for the stable isotope labeling of amino acids by phosphate using [?-18O4]ATP in nucleo to determine global site-specific phosphorylation rates. The advantages of this metabolic labeling technique are increased confidence in phosphorylated peptide identification, direct labeling of phosphorylation sites, measurement phosphorylation rates, and the identification of actively phosphorylated sites in a cell-like environment. In this study we calculated approximate rate constants for over 1,000 phosphorylation sites based on labeling progress curves. We measured a wide range of phosphorylation rate constants from 0.34 min?1 to 0.001 min?1. Finally, we applied stable isotope labeling of amino acids by phosphate to identify sites that have different phosphorylation kinetics during G1/S and M phase. We found that most sites had very similar phosphorylation rates under both conditions; however, a small subset of sites on proteins involved in the mitotic spindle were more actively phosphorylated during M phase, whereas proteins involved in DNA replication and transcription were more actively phosphorylated during G1/S phase. The data have been deposited to the ProteomeXchange with the identifier PXD000680. PMID:24532841

  11. Stable isotope labeling of phosphoproteins for large-scale phosphorylation rate determination.

    PubMed

    Molden, Rosalynn C; Goya, Jonathan; Khan, Zia; Garcia, Benjamin A

    2014-04-01

    Signals that control responses to stimuli and cellular function are transmitted through the dynamic phosphorylation of thousands of proteins by protein kinases. Many techniques have been developed to study phosphorylation dynamics, including several mass spectrometry (MS)-based methods. Over the past few decades, substantial developments have been made in MS techniques for the large-scale identification of proteins and their post-translational modifications. Nevertheless, all of the current MS-based techniques for quantifying protein phosphorylation dynamics rely on the measurement of changes in peptide abundance levels, and many methods suffer from low confidence in phosphopeptide identification due to poor fragmentation. Here we have optimized an approach for the stable isotope labeling of amino acids by phosphate using [?-¹?O?]ATP in nucleo to determine global site-specific phosphorylation rates. The advantages of this metabolic labeling technique are increased confidence in phosphorylated peptide identification, direct labeling of phosphorylation sites, measurement phosphorylation rates, and the identification of actively phosphorylated sites in a cell-like environment. In this study we calculated approximate rate constants for over 1,000 phosphorylation sites based on labeling progress curves. We measured a wide range of phosphorylation rate constants from 0.34 min?¹ to 0.001 min?¹. Finally, we applied stable isotope labeling of amino acids by phosphate to identify sites that have different phosphorylation kinetics during G1/S and M phase. We found that most sites had very similar phosphorylation rates under both conditions; however, a small subset of sites on proteins involved in the mitotic spindle were more actively phosphorylated during M phase, whereas proteins involved in DNA replication and transcription were more actively phosphorylated during G1/S phase. The data have been deposited to the ProteomeXchange with the identifier PXD000680. PMID:24532841

  12. Chemical imaging of biological materials by NanoSIMS using isotopic and elemental labels

    SciTech Connect

    Weber, P K; Fallon, S J; Pett-Ridge, J; Ghosal, S; Hutcheon, I D

    2006-04-10

    The NanoSIMS 50 combines unprecedented spatial resolution (as good as 50 nm) with ultra-high sensitivity (minimum detection limit of {approx}200 atoms). The NanoSIMS 50 incorporates an array of detectors, enabling simultaneous collection of 5 species originating from the same sputtered volume of a sample. The primary ion beam (Cs{sup +} or O{sup -}) can be scanned across the sample to produce quantitative secondary ion images. This capability for multiple isotope imaging with high spatial resolution provides a novel new approach to the study of biological materials. Studies can be made of sub-regions of tissues, mammalian cells, and bacteria. Major, minor and trace element distributions can be mapped on a submicron scale, growth and metabolism can be tracked using stable isotope labels, and biogenic origin can be determined based on composition. We have applied this technique extensively to mammalian and prokaryotic cells and bacterial spores. The NanoSIMS technology enables the researcher to interrogate the fate of molecules of interest within cells and organs through elemental and isotopic labeling. Biological applications at LLNL will be discussed.

  13. Determining metal assimilation efficiency in aquatic invertebrates using enriched stable metal isotope tracers

    USGS Publications Warehouse

    Croteau, M.-N.; Luoma, S.N.; Pellet, B.

    2007-01-01

    We employ a novel approach that combines pulse-chase feeding and multi-labelled stable isotopes to determine gut passage time (GPT), gut retention time (GRT), food ingestion rate (IR) and assimilation efficiency (AE) of three trace elements for a freshwater gastropod. Lettuce isotopically enriched in 53Cr, 65Cu and 106Cd was fed for 2 h to Lymnaea stagnalis. The release of tracers in feces and water was monitored for 48 h, during which unlabelled lettuce was provided ad libidum. The first defecation of 53Cr occurred after 5 h of depuration (GPT), whereas 90% of the ingested 53Cr was recovered in the feces after 22.5 h of depuration (GRT). 53Chromium was not significantly accumulated in the soft tissues upon exposure. In contrast, 65Cu and 106Cd assimilation was detectable for most experimental snails, i.e., 65/63Cu and 106/114Cd ratios in exposed snails were higher than those for controls. Food IR during the labelled feeding phase was 0.16 ?? 0.07 g g-1 d-1. IR was inferred from the amount of 53Cr egested in the feces during depuration and the concentration of 53Cr in the labelled lettuce. Assimilation efficiencies (??95% CI) determined using mass balance calculations were 84 ?? 4% for Cu and 85 ?? 3% for Cd. The ratio method yields similar AE estimates. Expanding the application of this novel stable isotope tracer technique to other metals in a wide variety of species will provide unique opportunities to evaluate the interplay between digestive processes and dietary influx of metals. Understanding the biological processes that modulate dietborne metal uptake is crucial to assess the toxicity of dietborne metals. ?? 2007 Elsevier B.V. All rights reserved.

  14. Dual amino acid-selective and site-directed stable-isotope labeling of the human c-Ha-Ras protein by cell-free synthesis

    Microsoft Academic Search

    Takashi Yabuki; Takanori Kigawa; Naoshi Dohmae; Koji Takio; Tohru Terada; Yutaka Ito; Ernest D. Laue; Jonathan A. Cooper; Masatsune Kainosho; Shigeyuki Yokoyama

    1998-01-01

    We developed two methods for stable-isotope labeling of proteins by cell-free synthesis. Firstly, we applied cell-free synthesis to the dual amino acid-selective 13C-15N labeling method, originally developed for in vivo systems by Kainosho and co-workers. For this purpose, we took one of the advantages of a cell-free protein synthesis system; the amino acid-selective stable-isotope labeling is free of the isotope

  15. Quantitative cross-linking/mass spectrometry using isotope-labelled cross-linkers?

    PubMed Central

    Fischer, Lutz; Chen, Zhuo Angel; Rappsilber, Juri

    2013-01-01

    Dynamic proteins and multi-protein complexes govern most biological processes. Cross-linking/mass spectrometry (CLMS) is increasingly successful in providing residue-resolution data on static proteinaceous structures. Here we investigate the technical feasibility of recording dynamic processes using isotope-labelling for quantitation. We cross-linked human serum albumin (HSA) with the readily available cross-linker BS3-d0/4 in different heavy/light ratios. We found two limitations. First, isotope labelling reduced the number of identified cross-links. This is in line with similar findings when identifying proteins. Second, standard quantitative proteomics software was not suitable for work with cross-linking. To ameliorate this we wrote a basic open source application, XiQ. Using XiQ we could establish that quantitative CLMS was technically feasible. Biological significance Cross-linking/mass spectrometry (CLMS) has become a powerful tool for providing residue-resolution data on static proteinaceous structures. Adding quantitation to CLMS will extend its ability of recording dynamic processes. Here we introduce a cross-linking specific quantitation strategy by using isotope labelled cross-linkers. Using a model system, we demonstrate the principle and feasibility of quantifying cross-linking data and discuss challenges one may encounter while doing so. We then provide a basic open source application, XiQ, to carry out automated quantitation of CLMS data. Our work lays the foundations of studying the molecular details of biological processes at greater ease than this could be done so far. This article is part of a Special Issue entitled: New Horizons and Applications for Proteomics [EuPA 2012]. PMID:23541715

  16. Efficiency of background suppression for arterial spin labeling

    E-print Network

    Garcia, Dairon, 1980-

    2005-01-01

    Arterial spin labeling (ASL), a technique developed for the measurement of local tissue perfusion with MRI, is heavily dependent on distinguishing irrelevant static tissue signal from the labeled blood. Background suppression ...

  17. Deletion of Genes Encoding Arginase Improves Use of “Heavy” Isotope-Labeled Arginine for Mass Spectrometry in Fission Yeast

    PubMed Central

    Borek, Weronika E.; Zou, Juan; Rappsilber, Juri; Sawin, Kenneth E.

    2015-01-01

    The use of “heavy” isotope-labeled arginine for stable isotope labeling by amino acids in cell culture (SILAC) mass spectrometry in the fission yeast Schizosaccharomyces pombe is hindered by the fact that under normal conditions, arginine is extensively catabolized in vivo, resulting in the appearance of “heavy”-isotope label in several other amino acids, most notably proline, but also glutamate, glutamine and lysine. This “arginine conversion problem” significantly impairs quantification of mass spectra. Previously, we developed a method to prevent arginine conversion in fission yeast SILAC, based on deletion of genes involved in arginine catabolism. Here we show that although this method is indeed successful when 13C6-arginine (Arg-6) is used for labeling, it is less successful when 13C615N4-arginine (Arg-10), a theoretically preferable label, is used. In particular, we find that with this method, “heavy”-isotope label derived from Arg-10 is observed in amino acids other than arginine, indicating metabolic conversion of Arg-10. Arg-10 conversion, which severely complicates both MS and MS/MS analysis, is further confirmed by the presence of 13C515N2-arginine (Arg-7) in arginine-containing peptides from Arg-10-labeled cells. We describe how all of the problems associated with the use of Arg-10 can be overcome by a simple modification of our original method. We show that simultaneous deletion of the fission yeast arginase genes car1+ and aru1+ prevents virtually all of the arginine conversion that would otherwise result from the use of Arg-10. This solution should enable a wider use of heavy isotope-labeled amino acids in fission yeast SILAC. PMID:26075619

  18. Deletion of Genes Encoding Arginase Improves Use of "Heavy" Isotope-Labeled Arginine for Mass Spectrometry in Fission Yeast.

    PubMed

    Borek, Weronika E; Zou, Juan; Rappsilber, Juri; Sawin, Kenneth E

    2015-01-01

    The use of "heavy" isotope-labeled arginine for stable isotope labeling by amino acids in cell culture (SILAC) mass spectrometry in the fission yeast Schizosaccharomyces pombe is hindered by the fact that under normal conditions, arginine is extensively catabolized in vivo, resulting in the appearance of "heavy"-isotope label in several other amino acids, most notably proline, but also glutamate, glutamine and lysine. This "arginine conversion problem" significantly impairs quantification of mass spectra. Previously, we developed a method to prevent arginine conversion in fission yeast SILAC, based on deletion of genes involved in arginine catabolism. Here we show that although this method is indeed successful when 13C6-arginine (Arg-6) is used for labeling, it is less successful when 13C615N4-arginine (Arg-10), a theoretically preferable label, is used. In particular, we find that with this method, "heavy"-isotope label derived from Arg-10 is observed in amino acids other than arginine, indicating metabolic conversion of Arg-10. Arg-10 conversion, which severely complicates both MS and MS/MS analysis, is further confirmed by the presence of 13C515N2-arginine (Arg-7) in arginine-containing peptides from Arg-10-labeled cells. We describe how all of the problems associated with the use of Arg-10 can be overcome by a simple modification of our original method. We show that simultaneous deletion of the fission yeast arginase genes car1+ and aru1+ prevents virtually all of the arginine conversion that would otherwise result from the use of Arg-10. This solution should enable a wider use of heavy isotope-labeled amino acids in fission yeast SILAC. PMID:26075619

  19. Carbon allocation belowground in Pinus pinaster using stable carbon isotope pulse labeling technique

    NASA Astrophysics Data System (ADS)

    Dannoura, M.; Bosc, A.; Chipeaux, C.; Sartore, M.; Lambrot, C.; Trichet, P.; Bakker, M.; Loustau, D.; Epron, D.

    2010-12-01

    Carbon allocation belowground competes with aboveground growth and biomass production. In the other hand, it contributes to resource acquisition such as nutrient, water and carbon sequestration in soil. Thus, a better characterization of carbon flow from plant to soil and its residence time within each compartment is an important issue for understanding and modeling forest ecosystem carbon budget. 13C pulse labeling of whole crown was conducted at 4 seasons to study the fate of assimilated carbon by photosynthesis into the root on 12 year old Pinus pinaster planted in the INRA domain of Pierroton. Maritime pine is the most widely planted species in South-West Europe. Stem, root and soil CO2 effluxes and their isotope composition were measured continuously by tunable diode laser absorption spectroscopy with a trace gas analyzer (TGA 100A; Campbell Scientific) coupled to flow-through chambers. 13CO2 recovery and peak were observed in respiration of each compartment after labeling. It appeared sequentially from top of stem to bottom, and to coarse root. The maximum velocity of carbon transfer was calculated as the difference in time lag of recovery between two positions on the trunk or on the root. It ranged between 0.08-0.2 m h-1 in stem and between 0.04-0.12 m h-1 in coarse root. This velocity was higher in warmer season, and the difference between time lag of recovery and peak increased after first frost. Photosynthates arrived underground 1.5 to 5 days after labeling, at similar time in soil CO2 effluxes and coarse root respiration. 0.08-1.4 g of carbon was respired per tree during first 20 days following labeling. It presented 0.6 -10% of 13C used for labeling and it is strongly related to seasons. The isotope signal was detected in fine root organs and microbial biomass by periodical core sampling. The peak was observed 6 days after labeling in early summer while it was delayed more than 10 days in autumn and winter with less amount of carbon allocated belowground.

  20. 4. Isotopically-Labeled Amino Acids (for R6K6, R6K4 and R10K8 media) Source: Cambridge Isotope Lab (CIL; North America; www.isotope.com). UK distributor of CIL is: CK GAS Products Ltd. (3 Murrell Green Business Park,

    E-print Network

    Lamond, Angus I.

    #12;4. Isotopically-Labeled Amino Acids (for R6K6, R6K4 and R10K8 media) Source: Cambridge Isotope of Arg or Lys in order to to prevent the cells from converting the isotope labels into other Lab (CIL; North America; www.isotope.com). UK distributor of CIL is: CK GAS Products Ltd. (3 Murrell

  1. METHOD TO TEST ISOTOPIC SEPARATION EFFICIENCY OF PALLADIUM PACKED COLUMNS

    SciTech Connect

    Heung, L; Gregory Staack, G; James Klein, J; William Jacobs, W

    2007-06-27

    The isotopic effect of palladium has been applied in different ways to separate hydrogen isotopes for many years. At Savannah River Site palladium deposited on kieselguhr (Pd/k) is used in a thermal cycling absorption process (TCAP) to purify tritium for over ten years. The need to design columns for different throughputs and the desire to advance the performance of TCAP created the need to evaluate different column designs and packing materials for their separation efficiency. In this work, columns with variations in length, diameter and metal foam use, were tested using an isotope displacement method. A simple computer model was also developed to calculate the number of theoretical separation stages using the test results. The effects of column diameter, metal foam and gas flow rate were identified.

  2. In-Gel Stable-Isotope Labeling (ISIL): a strategy for mass spectrometry-based relative quantification.

    PubMed

    Asara, John M; Zhang, Xiang; Zheng, Bin; Christofk, Heather H; Wu, Ning; Cantley, Lewis C

    2006-01-01

    Most proteomics approaches for relative quantification of protein expression use a combination of stable-isotope labeling and mass spectrometry. Traditionally, researchers have used difference gel electrophoresis (DIGE) from stained 1D and 2D gels for relative quantification. While differences in protein staining intensity can often be visualized, abundant proteins can obscure less abundant proteins, and quantification of post-translational modifications is difficult. A method is presented for quantifying changes in the abundance of a specific protein or changes in specific modifications of a protein using In-gel Stable-Isotope Labeling (ISIL). Proteins extracted from any source (tissue, cell line, immunoprecipitate, etc.), treated under two experimental conditions, are resolved in separate lanes by gel electrophoresis. The regions of interest (visualized by staining) are reacted separately with light versus heavy isotope-labeled reagents, and the gel slices are then mixed and digested with proteases. The resulting peptides are then analyzed by LC-MS to determine relative abundance of light/heavy isotope pairs and analyzed by LC-MS/MS for identification of sequence and modifications. The strategy compares well with other relative quantification strategies, and in silico calculations reveal its effectiveness as a global relative quantification strategy. An advantage of ISIL is that visualization of gel differences can be used as a first quantification step followed by accurate and sensitive protein level stable-isotope labeling and mass spectrometry-based relative quantification. PMID:16396506

  3. Quantitative Metabolome Analysis Based on Chromatographic Peak Reconstruction in Chemical Isotope Labeling Liquid Chromatography Mass Spectrometry.

    PubMed

    Huan, Tao; Li, Liang

    2015-07-21

    Generating precise and accurate quantitative information on metabolomic changes in comparative samples is important for metabolomics research where technical variations in the metabolomic data should be minimized in order to reveal biological changes. We report a method and software program, IsoMS-Quant, for extracting quantitative information from a metabolomic data set generated by chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS). Unlike previous work of relying on mass spectral peak ratio of the highest intensity peak pair to measure relative quantity difference of a differentially labeled metabolite, this new program reconstructs the chromatographic peaks of the light- and heavy-labeled metabolite pair and then calculates the ratio of their peak areas to represent the relative concentration difference in two comparative samples. Using chromatographic peaks to perform relative quantification is shown to be more precise and accurate. IsoMS-Quant is integrated with IsoMS for picking peak pairs and Zero-fill for retrieving missing peak pairs in the initial peak pairs table generated by IsoMS to form a complete tool for processing CIL LC-MS data. This program can be freely downloaded from the www.MyCompoundID.org web site for noncommercial use. PMID:26086729

  4. Chemical ligation of folded recombinant proteins: Segmental isotopic labeling of domains for NMR studies

    PubMed Central

    Xu, Rong; Ayers, Brenda; Cowburn, David; Muir, Tom W.

    1999-01-01

    A convenient in vitro chemical ligation strategy has been developed that allows folded recombinant proteins to be joined together. This strategy permits segmental, selective isotopic labeling of the product. The src homology type 3 and 2 domains (SH3 and SH2) of Abelson protein tyrosine kinase, which constitute the regulatory apparatus of the protein, were individually prepared in reactive forms that can be ligated together under normal protein-folding conditions to form a normal peptide bond at the ligation junction. This strategy was used to prepare NMR sample quantities of the Abelson protein tyrosine kinase-SH(32) domain pair, in which only one of the domains was labeled with 15N. Mass spectrometry and NMR analyses were used to confirm the structure of the ligated protein, which was also shown to have appropriate ligand-binding properties. The ability to prepare recombinant proteins with selectively labeled segments having a single-site mutation, by using a combination of expression of fusion proteins and chemical ligation in vitro, will increase the size limits for protein structural determination in solution with NMR methods. In vitro chemical ligation of expressed protein domains will also provide a combinatorial approach to the synthesis of linked protein domains. PMID:9892643

  5. The evaluation of new and isotopically labeled isoindoline nitroxides and an azaphenalene nitroxide for EPR oximetry

    NASA Astrophysics Data System (ADS)

    Khan, Nadeem; Blinco, James P.; Bottle, Steven E.; Hosokawa, Kazuyuki; Swartz, Harold M.; Micallef, Aaron S.

    2011-08-01

    Isoindoline nitroxides are potentially useful probes for viable biological systems, exhibiting low cytotoxicity, moderate rates of biological reduction and favorable Electron Paramagnetic Resonance (EPR) characteristics. We have evaluated the anionic (5-carboxy-1,1,3,3-tetramethylisoindolin-2-yloxyl; CTMIO), cationic (5-( N, N, N-trimethylammonio)-1,1,3,3-tetramethylisoindolin-2-yloxyl iodide, QATMIO) and neutral (1,1,3,3-tetramethylisoindolin-2-yloxyl; TMIO) nitroxides and their isotopically labeled analogs ( 2H 12- and/or 2H 12- 15N-labeled) as potential EPR oximetry probes. An active ester analogue of CTMIO, designed to localize intracellularly, and the azaphenalene nitroxide 1,1,3,3-tetramethyl-2,3-dihydro-2-azaphenalen-2-yloxyl (TMAO) were also studied. While the EPR spectra of the unlabeled nitroxides exhibit high sensitivity to O 2 concentration, deuteration resulted in a loss of superhyperfine features and a subsequent reduction in O 2 sensitivity. Labeling the nitroxides with 15N increased the signal intensity and this may be useful in decreasing the detection limits for in vivo measurements. The active ester nitroxide showed approximately 6% intracellular localization and low cytotoxicity. The EPR spectra of TMAO nitroxide indicated an increased rigidity in the nitroxide ring, due to dibenzo-annulation.

  6. Effect of acetaminophen on the leukocyte-labeling efficiency of indium oxine In 111

    SciTech Connect

    Augustine, S.C.; Schmelter, R.F.; Nelson, K.L.; Petersen, R.J.; Qualfe, M.A.

    1983-11-01

    The effect of acetaminophen on the labeling efficiency of leukocytes with indium oxine In 111 was studied. A blood sample was obtained from eight healthy men before and after they received acetaminophen 650 mg every four hours for 24 hours. After dividing the plasma from each sample into three portions, leukocytes were separated and labeled with indium oxine In 111. In an in vitro study, 200 ml of blood was obtained from one of the men, and the plasma was separated into four portions. Acetaminophen in 95% ethanol was added to three of the plasma fractions to produce acetaminophen concentrations of 4, 20, and 100 micrograms/ml; ethanol was added to the fourth fraction as a control. Each plasma fraction was then subdivided into three aliquots, and leukocytes were labeled as in the in vivo study. Mean leukocyte labeling efficiencies in both studies were calculated from the ratios of leukocyte radioactivity to initial radioactivity in the samples, expressed as percentages. Leukocyte labeling efficiencies before acetaminophen administration ranged from 79 to 85%; after administration, labeling efficiencies ranged from 70 to 87%. No significant differences in mean labeling efficiency before and after acetaminophen administration were noted in any of the subjects. Leukocyte labeling efficiencies in all in vitro plasma fractions were reduced, ranging from 54 to 63%, but no significant differences in labeling efficiency between any of the plasma fractions were found. Using the labeling procedures in this study, exposure of leukocytes from healthy men to acetaminophen in vivo or in vitro does not affect labeling efficiency with indium oxine In 111.

  7. Stable Carbon Isotopes As Indicators of Plant Water Use Efficiency

    Microsoft Academic Search

    E. M. Powers; J. D. Marshall; N. Ubierna Lopez

    2007-01-01

    Stable carbon isotopes have been utilized to better understand how environmental variables influence the efficiency of photosynthesis, specifically what factors limit the uptake and absorption of CO2 during photosynthesis. An understanding of the controls over both gas exchange and stomatal conductance can provide an explanation for the possible environmental influences on plant WUE. The delta13C of extractive-free wood was used

  8. Ultrasonic Energy as a New Tool for Fast Isotopic 18O Labeling of Proteins for Mass Spectrometry-Based Techniques: Preliminary Results

    SciTech Connect

    Carreira, R.J.; Rial-Otero, R.; Lopez-Ferrer, Dani; Lodeiro, C.; Capelo, J.L.

    2008-07-15

    Preliminary results regarding fast isotopic labeling of proteins with 18O in conjunction with matrix assisted laser desorption ionization time of flight mass spectrometry technique are presented. Similar 16O/18O isotopic labeling ratios were found for the overnight procedure (12 h) and the new fast ultrasonic one (30 min) for the BSA, ovalbumin and ?-lactalbumin proteins. The procedure, however, failed to promote double 18O isotopic labeling for the proteins ovalbumin and ?-lactalbumin. Two different sonication frequencies, 35 kHz and 130 kHz, were studied at two different sonication times of 15 min and 30 min, being best results obtained with the procedure at 130 kHz of sonication frequency and 30 min of sonication time. For comparative purposes the overnight isotopic 18O labeling procedure was done. In addition, the new fast isotopic labeling procedure was also studied without ultrasonication, in a water bath at 60 ºC.

  9. Development of versatile isotopic labeling reagents for profiling the amine submetabolome by liquid chromatography-mass spectrometry.

    PubMed

    Zhou, Ruokun; Huan, Tao; Li, Liang

    2015-06-30

    Metabolomic profiling involves relative quantification of metabolites in comparative samples and identification of the significant metabolites that differentiate different groups (e.g., diseased vs. controls). Chemical isotope labeling (CIL) liquid chromatography-mass spectrometry (LC-MS) is an enabling technique that can provide improved metabolome coverage and metabolite quantification. However, chemical identification of labeled metabolites can still be a challenge. In this work, a new set of isotopic labeling reagents offering versatile properties to enhance both detection and identification are described. They were prepared by a glycine molecule (or its isotopic counterpart) and an aromatic acid with varying structures through a simple three-step synthesis route. In addition to relatively low costs of synthesizing the reagents, this reaction route allows adjusting reagent property in accordance with the desired application objective. To date, two isotopic reagents, 4-dimethylaminobenzoylamido acetic acid N-hydroxylsuccinimide ester (DBAA-NHS) and 4-methoxybenzoylamido acetic acid N-hydroxylsuccinimide ester (MBAA-NHS), for labeling the amine-containing metabolites (i.e., amine submetabolome) have been synthesized. The labeling conditions and the related LC-MS method have been optimized. We demonstrate that DBAA labeling can increase the metabolite detectability because of the presence of an electrospray ionization (ESI)-active dimethylaminobenzoyl group. On the other hand, MBAA labeled metabolites can be fragmented in MS/MS and pseudo MS(3) experiments to provide structural information on metabolites of interest. Thus, these reagents can be tailored to quantitative profiling of the amine submetabolome as well as metabolite identification in metabolomics applications. PMID:26041526

  10. Effectiveness of isotopically labelled and non-isotopically labelled internal standards in the gas chromatography/mass spectrometry analysis of sulfur compounds in wines: use of a statistically based matrix comprehensive approach.

    PubMed

    Lavagnini, Irma; Fedrizzi, Bruno; Versini, Giuseppe; Magno, Franco

    2009-04-01

    The effectiveness of isotopically and non-isotopically labelled internal standards in reducing matrix-induced effects is evaluated. The question is addressed in the quantitative analysis by gas chromatography/mass spectrometry (GC/MS) of dimethyl sulphide, chosen as a typical example of volatile sulphur compounds, in wine matrices. When matrix/run effects are not cancelled out the use of a variance component model (VCM) to handle the linear calibrations obtained by regression technique is successful. The method implies the estimation of an overall calibration straight line, which properly takes into account the uncertainty due to different matrices, the calibration run and the measurement error, making the use of an isotopically labelled internal standard not necessary. The obtained results show that the benefits of lowering times and costs for routine analyses compensate for the small increase in uncertainty in the concentration values obtained in the regression analysis and the slight increase in the detection limit. PMID:19291680

  11. A stable isotope dual-labelling approach to detect multiple insemination in un-irradiated and irradiated Anopheles arabiensis mosquitoes

    Microsoft Academic Search

    Michelle EH Helinski; Rebecca C Hood; Bart GJ Knols

    2008-01-01

    BACKGROUND: In the context of a Sterile Insect Technique programme, the occurrence of multiple insemination in the malaria mosquito Anopheles arabiensis Patton was studied using a novel labelling system with the stable isotopes 15N and 13C. The incidence of multiple insemination in the absence of radiation, and when males were irradiated in the pupal stage and competed against un-irradiated males

  12. Probing in Vivo Metabolism by Stable Isotope Labeling of Storage Lipids and Proteins in Developing Brassica napus Embryos

    Microsoft Academic Search

    Jorg Schwender; John B. Ohlrogge

    2002-01-01

    Developing embryos of Brassica napus accumulate both triacylglycerols and proteins as major storage reserves. To evaluate metabolic fluxes during embryo development, we have established conditions for stable isotope labeling of cultured embryos under steady-state conditions. Sucrose supplied via the endosperm is considered to be the main carbon and energy source for seed metabolism. However, in addition to 220 to 270

  13. Bioavailability of imipramine tablets relative to a stable isotope-labeled internal standard: Increasing the power of bioavailability tests

    Microsoft Academic Search

    Henry d'A Heck; Sidney E. Buttrill; Norman W. Flynn; Robert L. Dyer; Michael Anbar; Thomas Cairns; Shrikant Dighe; Bernard E. Cabana

    1979-01-01

    A new methodology for comparative bioavailability testing is described in which each drug formulation is compared with a stable isotope-labeled variant of the drug that is consumed orally in solution at the same time the tested formulation is ingested. The methodology is used to determine the comparative bioavailabilities of two commercially available brands of imipramine hydrochloride. The power of the

  14. Stable Isotope Labeling Strategy for Protein-Ligand Binding Analysis in Multi-Component Protein Mixtures

    NASA Astrophysics Data System (ADS)

    DeArmond, Patrick D.; West, Graham M.; Huang, Hai-Tsang; Fitzgerald, Michael C.

    2011-03-01

    Described here is a stable isotope labeling protocol that can be used with a chemical modification- and mass spectrometry-based protein-ligand binding assay for detecting and quantifying both the direct and indirect binding events that result from protein-ligand binding interactions. The protocol utilizes an H{2/16}O2 and H{2/18}O2 labeling strategy to evaluate the chemical denaturant dependence of methionine oxidation in proteins both in the presence and absence of a target ligand. The differential denaturant dependence to the oxidation reactions performed in the presence and absence of ligand provides a measure of the protein stability changes that occur as a result of direct interactions of proteins with the target ligand and/or as a result of indirect interactions involving other protein-ligand interactions that are either induced or disrupted by the ligand. The described protocol utilizes the 18O/16O ratio in the oxidized protein samples to quantify the ligand-induced protein stability changes. The ratio is determined using the isotopic distributions observed for the methionine-containing peptides used for protein identification in the LC-MS-based proteomics readout. The strategy is applied to a multi-component protein mixture in this proof-of-principle experiment, which was designed to evaluate the technique's ability to detect and quantify the direct binding interaction between cyclosporin A and cyclophilin A and to detect the indirect binding interaction between cyclosporin A and calcineurin (i.e., the protein-protein interaction between cyclophilin A and calcineurin that is induced by cyclosporin A binding to cyclophilin A).

  15. Multi-isotope labelling (13C, 18O, 2H) for studying organic matter cycling within plant-soil systems

    NASA Astrophysics Data System (ADS)

    Studer, M. S.; Abiven, S.; Schmidt, M. W. I.; Siegwolf, R. T. W.

    2012-04-01

    Carbon cycling has become of major interest for the understanding and mitigation of global climatic change. Terrestrial ecosystems have a large carbon sequestration potential, but many processes and fluxes of organic matter (OM) cycling within the plant-soil system are not yet well understood [1]. The dynamics of OM cycling within the plant soil-system are determined by environmental parameters, as well as chemical quality of OM input. A well-known technique to study OM dynamics is to label OM inputs with stable isotopes (e.g 13C). Changes in OM quality in the plant and in the soil can be assessed by compound specific isotopic analysis [2]. These techniques give a precise insight of the OM composition, but are laborious and expensive. Here we suggest a new multi-isotope labelling technique using stable 13C in combination with stable 18O and 2H isotopes, which provides information on OM quality by simple bulk material analysis. The method is based on the creation of an isotopic van Krevelen diagram, which is used to describe different compound groups by plotting the atomic ratios of O/C vs. H/C [3]. We could show that new assimilates can be labelled with 13C, 18O and 2H by adding the stable isotopes (continuously) in the gaseous phase (CO2 and water vapour) to the plants atmosphere. The label has been traced within the bulk material of different compartments of the plant-soil system (e.g. leaves, stems, roots, bulk soil). Our first results showed that after 2, 8 and 14 days of labelling the 18O/13C(new) ratio was notably different in leaf, stem and root tissue (0.0024, 0.0011 and 0.0007, respectively), suggesting a change in OM quality towards more C-rich compounds. d2H analysis will follow and an isotopic van Krevelen diagram will be produced (18O/13C(new) vs. 2H/13C(new)) to describe the changes in OM quality. The new multi-isotope labelling approach represent a powerful tool to address open questions in plant and soil research such as the allocation of organic molecules within the plant-soil system under changing environmental conditions or the influence of plant roots on soil organic matter stabilization and destabilization processes.

  16. Stable Carbon Isotopes As Indicators of Plant Water Use Efficiency

    NASA Astrophysics Data System (ADS)

    Powers, E. M.; Marshall, J. D.; Ubierna Lopez, N.

    2007-12-01

    Stable carbon isotopes have been utilized to better understand how environmental variables influence the efficiency of photosynthesis, specifically what factors limit the uptake and absorption of CO2 during photosynthesis. An understanding of the controls over both gas exchange and stomatal conductance can provide an explanation for the possible environmental influences on plant WUE. The ?13C of extractive-free wood was used as an index of plant water use efficiency at Mica Creek Experimental Watershed, Shoshone County, ID. The ?13C values of tree rings were used to determine the effects of clear cut and partial cut harvesting practices, the effect of elevation, and species differences in intrinsic water use efficiency (WUE) among coniferous species including: Thuja plicata, Larix occidentalis, Picea engelmannii, Pseudotsuga menziesii, Abies lasiocarpa, and Abies grandis. We found significant effects of harvest treatments (p=0.0197), elevation (p= 0.0268), and species (p<0.001) on tree ?13C. The significantly more enriched isotopic signatures observed in Thuja plicata (?13C = -23.37 ±0.17‰), indicate that it is a more water use efficient species compared to Larix occidentalis (?13C = -25.66 ±0.43‰), and Abies grandis (?13C = -25.83 ±0.15‰). There was also an overall trend of ?13C enrichment with elevation. The isotopic composition of tree rings has been estimated to increase by 0.003 ‰ per meter of elevation gain, which may be related to a decrease in soil moisture with elevation. Finally, the mean ?13C values observed on partial cut (?13C = -24.73 ±0.10‰) and clear cut treatments (?13C = -24.45 ±0.29‰) were significantly more enriched than the mean value for the control treatment (?13C = -25.25 ±0.19‰). The more enriched isotopic signatures observed on the harvested treatments indicate that the trees are more water use efficient, which may be a result of increased photosynthetic capacity with an increase in the availability of water, foliar nitrogen, and light to individual trees on the harvested treatments. The reduction of stand density through harvesting may reduce the transpirational water losses on a stand level, thus increasing the water availability for individual trees.

  17. Allocation of Recent Photosynthetic Products Using a Dual Isotope (13C and 14C) Pulse-Chase Labeling Technique

    NASA Astrophysics Data System (ADS)

    Carbone, M. S.; Trumbore, S.; McDuffee, K.; Xu, X.

    2005-12-01

    Pulse-chase labeling studies provide a non-destructive way to follow the allocation of recent photosynthetic products to above and belowground plant pathways. In August 2005, we applied a CO2 label enriched in 13C and low-levels of 14C, to elucidate differences in carbon allocation patterns between two plant communities (perennial grasses and shrubs) in the Owens Valley, CA. Following the label application, we sampled the CO2 flux and isotopic content of respiration from the leaves and stems, the soil surface, the soil profile, and the total ecosystem. The 13C signal was intended to quantify allocation to fast cycling respiration pathways (<6 days), where as the 14C signal was designed to follow the fate of the label into longer-lived plant carbon pools including respiration, growth, and storage (>6 days). The low-level 14C label was measured by accelerator mass spectrometry (AMS), and had radioactivity levels below what is classified as harmful or hazardous waste. This combination of stable and radiocarbon isotope tracers allowed us to safely label in the field, at ambient CO2 concentrations, yet minimize the expense of AMS analyses. Our preliminary 13C results show differences in the depth distribution and persistence of the label in the soil CO2 between the grass and shrub communities. The 14C results show that the label signal is still measurable in respiration four weeks after labeling. We believe this application will provide valuable insight into carbon cycling, particularly belowground, where carbon used for root respiration, growth, and storage are not easily observed nor well quantified.

  18. Cell-free synthesis and amino acid-selective stable isotope labeling of proteins for NMR analysis

    Microsoft Academic Search

    Takanori Kigawa; Yutaka Muto; Shigeyuki Yokoyama

    1995-01-01

    For the application of multidimensional NMR spectroscopy to larger proteins, it would be useful to perform selective labeling of one of the 20 amino acids. For some amino acids, however, amino acid metabolism drastically reduces the efficiency and selectivity of labeling in in vivo expression systems. In the present study, a cell-free protein synthesis system was optimized, so that highly

  19. Global Potential of Energy Efficiency Standards and Labeling Programs

    E-print Network

    McNeil, Michael A

    2008-01-01

    and Efficiency Scenario The exception is residential air conditioningEfficiency Scenarios .. 41 Lighting.. 41 Refrigeration 43 Air Conditioning air conditioning depends on the penetration of equipment and the efficiency

  20. Isotopic labeling for the understanding of the alteration of limestone used in built cultural heritage

    NASA Astrophysics Data System (ADS)

    Saheb, Mandana; Chabas, Anne; Mertz, Jean-Didier; Rozenbaum, Olivier; Verney-Carron, Aurélie

    2015-04-01

    This project belongs to a specific work aiming at developing isotopic tools to better understand the alteration of materials used in the built cultural heritage. It is focused on the study of the alteration of limestone used in the facades of historic buildings subject to atmospheric polluted environment. Actually in the elevated parts of the buildings, water as rainfall (runoff or wet deposition) or in vapor form (condensation or dry deposition) is the main agent of alteration. Thus, the rock/water interactions need to be well understood to propose adapted solution to better preserve the buildings. To identify the water transfer within the porous limestone and locate the reaction preferential sites, two isotopic tracers (D and 18O) are used to monitor the alteration solution (D) and locate the zones containing the secondary phases (18O). The Saint-Maximin limestone used in many monuments in the suburbs of Paris (France) as a building and restoration stone has been specifically studied. Pristine materials, stones from monuments (monuments in the Paris area) and samples altered in laboratory constitute the analytical corpus to compare different stages of alteration. In a first step the stones are characterized at different scales to identify the alteration pattern (SEM-EDS, Raman microspectrometry, XRD, rugosimetry) and study the water transfers (X-ray tomography, mercury porosimetry, imbibition kinetics). The samples are then altered in the laboratory by realistic and controlled wet or dry deposition using isotopically labeled solutions to locate the reaction zones by SIMS. The multiscale characterization of the alteration pattern has allowed proposing alteration mechanisms linked to the properties of the stones and their location inside the building. Moreover, the location of the reactive zones inside the materials determined by the isotopic experiments helps examining the role of the evolution of porosity and formation of alteration products within the material, in order to estimate the alteration rate. This innovative methodology will contribute to improve the knowledge of stone alteration processes in order to develop appropriate conservation strategies for the buildings.

  1. Tracking the metabolic pulse of plant lipid production with isotopic labeling and flux analyses: Past, present and future.

    PubMed

    Allen, Doug K; Bates, Philip D; Tjellström, Henrik

    2015-04-01

    Metabolism is comprised of networks of chemical transformations, organized into integrated biochemical pathways that are the basis of cellular operation, and function to sustain life. Metabolism, and thus life, is not static. The rate of metabolites transitioning through biochemical pathways (i.e., flux) determines cellular phenotypes, and is constantly changing in response to genetic or environmental perturbations. Each change evokes a response in metabolic pathway flow, and the quantification of fluxes under varied conditions helps to elucidate major and minor routes, and regulatory aspects of metabolism. To measure fluxes requires experimental methods that assess the movements and transformations of metabolites without creating artifacts. Isotopic labeling fills this role and is a long-standing experimental approach to identify pathways and quantify their metabolic relevance in different tissues or under different conditions. The application of labeling techniques to plant science is however far from reaching it potential. In light of advances in genetics and molecular biology that provide a means to alter metabolism, and given recent improvements in instrumentation, computational tools and available isotopes, the use of isotopic labeling to probe metabolism is becoming more and more powerful. We review the principal analytical methods for isotopic labeling with a focus on seminal studies of pathways and fluxes in lipid metabolism and carbon partitioning through central metabolism. Central carbon metabolic steps are directly linked to lipid production by serving to generate the precursors for fatty acid biosynthesis and lipid assembly. Additionally some of the ideas for labeling techniques that may be most applicable for lipid metabolism in the future were originally developed to investigate other aspects of central metabolism. We conclude by describing recent advances that will play an important future role in quantifying flux and metabolic operation in plant tissues. PMID:25773881

  2. IsoMS: automated processing of LC-MS data generated by a chemical isotope labeling metabolomics platform.

    PubMed

    Zhou, Ruokun; Tseng, Chiao-Li; Huan, Tao; Li, Liang

    2014-05-20

    A chemical isotope labeling or isotope coded derivatization (ICD) metabolomics platform uses a chemical derivatization method to introduce a mass tag to all of the metabolites having a common functional group (e.g., amine), followed by LC-MS analysis of the labeled metabolites. To apply this platform to metabolomics studies involving quantitative analysis of different groups of samples, automated data processing is required. Herein, we report a data processing method based on the use of a mass spectral feature unique to the chemical labeling approach, i.e., any differential-isotope-labeled metabolites are detected as peak pairs with a fixed mass difference in a mass spectrum. A software tool, IsoMS, has been developed to process the raw data generated from one or multiple LC-MS runs by peak picking, peak pairing, peak-pair filtering, and peak-pair intensity ratio calculation. The same peak pairs detected from multiple samples are then aligned to produce a CSV file that contains the metabolite information and peak ratios relative to a control (e.g., a pooled sample). This file can be readily exported for further data and statistical analysis, which is illustrated in an example of comparing the metabolomes of human urine samples collected before and after drinking coffee. To demonstrate that this method is reliable for data processing, five (13)C2-/(12)C2-dansyl labeled metabolite standards were analyzed by LC-MS. IsoMS was able to detect these metabolites correctly. In addition, in the analysis of a (13)C2-/(12)C2-dansyl labeled human urine, IsoMS detected 2044 peak pairs, and manual inspection of these peak pairs found 90 false peak pairs, representing a false positive rate of 4.4%. IsoMS for Windows running R is freely available for noncommercial use from www.mycompoundid.org/IsoMS. PMID:24766305

  3. Auto-inducing media for uniform isotope labeling of proteins with (15)N, (13)C and (2)H.

    PubMed

    Guthertz, Nicolas; Klopp, Julia; Winterhalter, Aurélie; Fernández, César; Gossert, Alvar D

    2015-06-01

    Auto-inducing media for protein expression offer many advantages like robust reproducibility, high yields of soluble protein and much reduced workload. Here, an auto-inducing medium for uniform isotope labelling of proteins with (15)N, (13)C and/or (2)H in E. coli is presented. So far, auto-inducing media have not found widespread application in the NMR field, because of the prohibitively high cost of labeled lactose, which is an essential ingredient of such media. Here, we propose using lactose that is only selectively labeled on the glucose moiety. It can be synthesized from inexpensive and readily available substrates: labeled glucose and unlabeled activated galactose. With this approach, uniformly isotope labeled proteins were expressed in unattended auto-inducing cultures with incorporation of (13)C, (15)N of 96.6 % and (2)H, (15)N of 98.8 %. With the present protocol, the NMR community could profit from the many advantages that auto-inducing media offer. PMID:25893498

  4. ­Characterization of Reduced Magmatic C-O-H-N Volatiles By Isotopic Labeling

    NASA Astrophysics Data System (ADS)

    Falksen, E.; Armstrong, L. S.; Hirschmann, M. M.

    2014-12-01

    Characterization of COHN species in silicate melts [1-10] is required to understand the role of reduced volatiles in planetary and early Earth processes, including partitioning between planetary cores, mantles, and atmospheres during early differentiation. Vibrational spectroscopy has been used to examine volatile speciation, but for a number of absorptions there is uncertainty as to whether they relate to species containing N, C, or both [1,3]. In particular, an IR band at 3370 cm-1 is commonly attributed to N-H stretching [1,4,5,7], but associated Raman bands near 3280 cm-1 have also been attributed to alkyne (C-H) bonds [8-10]. The 3370 cm-1 IR band appears even in nominally N-free experiments owing to trapped air and is accompanied by a feature at 1615 cm-1 which could be caused by C=O or N-H bonds [1,3,8]. We sought to determine whether N and C were responsible for various IR bands by dissolving different isotopes of N and C in basaltic melts at high pressure and temperature and observing the shift in position of the resulting absorptions. Experiments were conducted at 1.2 GPa and 1400 oC and volatiles were added to a basaltic oxide mix in the form of unlabeled, 13C labeled, and 15N labeled urea [(NH2)2CO]. The resulting glasses were analyzed using FTIR and the theoretical band shifts were predicted based on a classical approximation of a diatomic molecule. Relative to isotopically normal glasses, bands at both 3370 cm-1 and 1615 cm-1 decrease by 4-8 wavenumbers for 15N and not at all for 13C, consistent with origination by N-H bonds in amines or metal-ammine complexes. [1] Stanley et al. (2014) GCA 129, 54-76. [2] Wetzel et al. (2013) PNAS 110, 8010-8013. [3] Armstrong et al. (in prep). [4] Kadik et al. (2011) Geochem. Int. 49, 429-438. [5] Kadik et al. (2013) PEPI 214, 14-24. [6]Mysen (2013) Chem. Geo. 346, 113-124. [7] Mysen et al. (2008) Am. Min. 93, 1760-1770. [8] Mysen et al. (2009) GCA 73, 1696-1710. [9] Dasgupta et al. (2013) GCA 102, 191-212. [10] Chi et al. (2014) 139, 447-471. [11] Socrates (2001).

  5. Elemental analysis of complex organic aerosol using isotopic labeling and unit-resolution mass spectrometry.

    PubMed

    Hicks, Raea K; Day, Douglas A; Jimenez, Jose L; Tolbert, Margaret A

    2015-03-01

    Elemental analysis of unit-mass resolution (UMR) mass spectra is limited by the amount of information available to definitively elucidate the molecular formula of a molecule ionized by electron impact. The problem is compounded when a mixture of organic molecules (such as those found in organic aerosols) is analyzed without the benefit of prior separation. For this reason, quadrupole mass spectrometry is not usually suited to the elemental analysis of organic mixtures. Here, we present a mathematical method for the elemental analysis of UMR mass spectra of a complex organic aerosol through the use of isotopic labeling. Quadrupole aerosol mass spectrometry was used to obtain UMR data of (13)C-labeled and unlabeled aerosol generated by far ultraviolet (FUV) photochemistry of gas mixtures containing 0.1% of either CH4 or (13)CH4 in N2. In this method, the differences in the positions of ion groups in the resulting spectra are used to estimate the mass fraction of carbon in the aerosol, and estimation of the remaining elements follows. Analysis of the UMR data yields an elemental composition of 63 ± 7% C, 8 ± 1% H, and 29 ± 7% N by mass. Unlabeled aerosols formed under the same conditions are found by high-resolution time-of-flight aerosol mass spectrometry to have an elemental composition of 63 ± 3% C, 8 ± 1% H, 20 ± 4% N, and 9 ± 3% O by mass, in good agreement with the UMR method. This favorable comparison verifies the method, which expands the UMR mass spectrometry toolkit. PMID:25645140

  6. Simultaneous measurement of phosphorus and carbon uptake in Lake Kinneret by multiple isotopic labeling and differential filtration

    Microsoft Academic Search

    T. Berman; M. Stiller

    1977-01-01

    Differential filtration and multiple isotopic labeling were combined to study the uptake of [14C]bicarbonate, [14C]glucose, and [32P]orthophosphate by microplakton in Lake Kinneret, Israel. Short-term (4 hr) uptake experiments showed seasonal changes in the size distributions of organisms taking up inorganic carbon, glucose carbon, and orthophosphate in the lake water. In a time-course experiment of 48 hr (Jan 1976) most, but

  7. Systematic NMR Analysis of Stable Isotope Labeled Metabolite Mixtures in Plant and Animal Systems: Coarse Grained Views of Metabolic Pathways

    Microsoft Academic Search

    Eisuke Chikayama; Michitaka Suto; Takashi Nishihara; Kazuo Shinozaki; Takashi Hirayama; Jun Kikuchi; Lucia Banci

    2008-01-01

    BackgroundMetabolic phenotyping has become an important ‘bird's-eye-view’ technology which can be applied to higher organisms, such as model plant and animal systems in the post-genomics and proteomics era. Although genotyping technology has expanded greatly over the past decade, metabolic phenotyping has languished due to the difficulty of ‘top-down’ chemical analyses. Here, we describe a systematic NMR methodology for stable isotope-labeling

  8. LC/MS Method for the Determination of Stable Isotope Labeled Promethazine in Human Plasma

    NASA Technical Reports Server (NTRS)

    Zuwei, Wang; Boyd, Jason; Berens, Kurt L.; Putcha, Lakshmi

    2004-01-01

    Promethazine (PMZ) is taken by astronauts orally (PO), intramuscularly (IM) or rectally (PR) for space motion sickness. LC/MS method was developed with off-line solid phase extraction to measure plasma concentrations of PMZ given as stable isotope-labeled (SIL) formulations by the three different routes of administration simultaneously. Samples (0.5ml) were loaded on to Waters Oasis HLB co-polymer cartridges and eluted with 1.0 mL methanol. HPLC separation of the eluted sample was performed using an Agilent Zorbax SB-CN column (50 x 2.1 mm) at a flow rate of 0.2 mL/min for 6 min. Acetonitrile/ ammonium acetate (30 mM) in water (3:2, v/v), pH 5.6 plus or minus 0.1, was used as the mobile phase for separation. Concentrations of PMZ, PMZ-d4 and PMZ-d7 and chlorpromazine (internal standard) were determined using a Micromass ZMD single quadrupole mass spectrometer with Electrospray Ionization (ESI). ESI mass spectra were acquired in positive ion mode with selected ion monitoring of [M+ H]dot plus. The method is rapid, reproducible and the assay specific parameters are listed in a table. A novel, sensitive and specific method for the measurement of PMZ and SIL PMZ in human plasma is reported.

  9. Absolute Quantitation of Glycosylation Site Occupancy Using Isotopically Labeled Standards and LC-MS

    PubMed Central

    Zhu, Zhikai; Go, Eden P.; Desaire, Heather

    2014-01-01

    N-linked glycans are required to maintain appropriate biological functions on proteins. Underglycosylation leads to many diseases in plants and animals; therefore, characterizing the extent of glycosylation on proteins is an important step in understanding, diagnosing, and treating diseases. To determine the glycosylation site occupancy, protein N-glycosidase F (PNGase F) is typically used to detach the glycan from the protein, during which the formerly glycosylated asparagine undergoes deamidation to become an aspartic acid. By comparing the abundance of the resulting peptide containing aspartic acid against the one containing non-glycosylated asparagine, the glycosylation site occupancy can be evaluated. However, this approach can give inaccurate results when spontaneous chemical deamidation of the non-glycosylated asparagine occurs. To overcome this limitation, we developed a new method to measure the glycosylation site occupancy that does not rely on converting glycosylated peptides to their deglycosylated forms. Specifically, the overall protein concentration and the non-glycosylated portion of the protein are quantified simultaneously by using heavy isotope-labeled internal standards coupled with LC-MS analysis, and the extent of site occupancy is accurately determined. The efficacy of the method was demonstrated by quantifying the occupancy of a glycosylation site on bovine fetuin. The developed method is the first work that measures the glycosylation site occupancy without using PNGase F, and it can be done in parallel with glycopeptide analysis because the glycan remains intact throughout the workflow. PMID:24671695

  10. Investigation of bn-44 Peptide Fragments Using High Resolution Mass Spectrometry and Isotope Labeling

    NASA Astrophysics Data System (ADS)

    Wang, Bing; Yu, Jiayi; Wang, Huixin; Wei, Zhonglin; Guo, Xinhua; Xiao, Zhaohui; Zeng, Zhoufang; Kong, Wei

    2014-12-01

    An N-terminal deuterohemin-containing hexapeptide (DhHP-6) was designed as a short peptide cytochrome c (Cyt c) mimetic to study the effect of N-terminal charge on peptide fragmentation pathways. This peptide gave different dissociation patterns than normal tryptic peptides. Upon collision-induced dissociation (CID) with an ion trap mass spectrometer, the singly charged peptide ion containing no added proton generated abundant and characteristic bn-44 ions instead of bn-28 (an) ions. Studies by high resolution mass spectrometry (HRMS) and isotope labeling indicate that elimination of 44 Da fragments from b ions occurs via two different pathways: (1) loss of CH3CHO (44.0262) from a Thr side chain; (2) loss of CO2 (43.9898) from the oxazolone structure in the C-terminus. A series of analogues were designed and analyzed. The experimental results combined with Density Functional Theory (DFT) calculations on the proton affinity of the deuteroporphyrin demonstrate that the production of these novel bn-44 ions is related to the N-terminal charge via a charge-remote rather than radical-directed fragmentation pathway.

  11. Monitoring protein conformational changes and dynamics using stable-isotope labeling and mass spectrometry (CDSiL-MS)

    PubMed Central

    Kahsai, Alem W.; Rajagopal, Sudarshan; Sun, Jinpeng; Xiao, Kunhong

    2015-01-01

    Understanding the mechanism accompanying functional conformational changes associated with protein activation has important implications for drug design. Here, we describe a powerful method, CDSiL-MS (conformational changes and dynamics using stable-isotope labeling and mass-spectrometry), which involves chemical-labeling by isotope-coded forms of N-ethylmaleimide or succinic anhydride to site-specifically label the side-chains of cysteines or lysines, respectively, in native proteins. Subsequent MS-analysis allows the quantitative monitoring of reactivity of residues as a function of time, providing a measurement of the labeling kinetics, thereby enabling elucidation of conformational changes of proteins. We demonstrate the utility of this method using a model G-protein coupled receptor, the ?2-adrenergic receptor including experiments that characterize the functional conformational-changes associated with activation of distinct signaling pathways induced by different ?-adrenoceptor ligands. The procedure requires five days and can easily be adapted to systems where soluble and detergent-solubilized membrane protein targets, which undergo function-dependent conformational-changes, can be interrogated structurally to allow drug screening. PMID:24810039

  12. Molecularly imprinted solid phase extraction using stable isotope labeled compounds as template and liquid chromatography–mass spectrometry for trace analysis of bisphenol A in water sample

    Microsoft Academic Search

    Migaku Kawaguchi; Yoshio Hayatsu; Hisao Nakata; Yumiko Ishii; Rie Ito; Koichi Saito; Hiroyuki Nakazawa

    2005-01-01

    We have developed a molecularly imprinted polymer (MIP) using a stable isotope labeled compound as the template molecule and called it the “isotope molecularly imprinted polymer” (IMIP). In this study, bisphenol A (BPA) was used as the model compound. None imprinted polymer (NIP), MIP, dummy molecularly imprinted polymer (DMIP) and IMIP were prepared by the suspension polymerization method using without

  13. Measuring supply chain carbon efficiency : a carbon label framework

    E-print Network

    Craig, Anthony (Anthony J.)

    2012-01-01

    In the near term, efficiency improvements represent a key option for reducing the impacts of climate change. The growing awareness of climate change has increased the attention regarding the carbon emissions "embedded" in ...

  14. Study on the Appliances Energy Efficiency Label and MultiDimensional Thinking under Low-Carbon Economic Development

    Microsoft Academic Search

    Tibin Liu; Jiao Lu; Honglian Xie

    2011-01-01

    Most of the household appliance energy efficiency label is considered qualified level of energy efficiency index of how to limit the power consumption of the household appliances, rarely consider reducing the power consumption of competitive advantage for the household appliance. This is the first Low-carbon Economic Development from the perspective given the implementation appliance energy efficiency label of Game Theory

  15. Primary Productivity Rates at Station ALOHA Determined by 18O Labeling and the Triple Isotope Composition of Dissolved Oxygen

    NASA Astrophysics Data System (ADS)

    Juranek, L. W.; Quay, P. D.; Karl, D. M.

    2002-12-01

    Although knowledge of accurate Primary Productivity (PPr) rates is essential to the understanding of ocean carbon cycling, the standard method of determining ocean productivity, 14C labeling, often yields uncertain results. Typically, 14C-derived PPr rates fall ambiguously between gross and net productivity because the method is sensitive to recycling of a relatively small POC pool. Bottle incubations using labeled oxygen produced from 18O-enriched water have shown promise in giving a more consistent measure of gross productivity, since the pool of dissolved oxygen is less sensitive to recycling than POC. Typically this method gives gross PPr rates that are 2-3 times 14C-derived rates. Recently Luz and Barkan (2001) have pioneered a new technique to determine PPr rates using the triple isotope composition of dissolved oxygen as an in situ tracer. This relies on the observation that a signature of mass-independent fractionation originating in the stratosphere and imparted to the surface ocean by air-sea exchange is diminished by biological oxygen production. In February 2002 we measured gross productivity using both the 18O-labeling and triple isotope in situ methods at Hawaii Ocean Time-Series station ALOHA in the N. Pacific subtropical gyre. We found the in situ oxygen isotope method yielded double the 14C-derived PPr rates while 18O bottle incubations yielded similar rates as 14C. In addition, comparison of in situ isotope measurements with the biological oxygen saturation state indicate that community respiration is approximately equal to gross photosynthesis in the upper 60 m while from 80-200 m respiration exceeds photosynthesis by at most 10 %. We will present these results along with new results from upcoming measurements at station ALOHA.

  16. Stable Isotope Labeled n-Alkanes to Assess Digesta Passage Kinetics through the Digestive Tract of Ruminants

    PubMed Central

    Warner, Daniel; Ferreira, Luis M. M.; Breuer, Michel J. H.; Dijkstra, Jan; Pellikaan, Wilbert F.

    2013-01-01

    We describe the use of carbon stable isotope (13C) labeled n-alkanes as a potential internal tracer to assess passage kinetics of ingested nutrients in ruminants. Plant cuticular n-alkanes originating from intrinsically 13C labeled ryegrass plants were pulse dosed intraruminally in four rumen-cannulated lactating dairy cows receiving four contrasting ryegrass silage treatments that differed in nitrogen fertilization level (45 or 90 kg nitrogen ha?1) and maturity (early or late). Passage kinetics through the gastrointestinal tract were derived from the ?13C (i.e. the ratio 13C:12C) in apparently undigested fecal material. Isotopic enrichment was observed in a wide range of long-chain n-alkanes (C27–C36) and passage kinetics were determined for the most abundant C29, C31 and C33 n-alkanes, for which a sufficiently high response signal was detected by combustion isotope ratio mass spectrometry. Basal diet treatment and carbon chain length of n-alkanes did not affect fractional passage rates from the rumen (K1) among individual n-alkanes (3.71–3.95%/h). Peak concentration time and transit time showed a quantitatively small, significant (p?0.002) increase with carbon chain length. K1 estimates were comparable to those of the 13C labeled digestible dry matter fraction (3.38%/h; r?=?0.61 to 0.71; p?0.012). A literature review has shown that n-alkanes are not fermented by microorganisms in the rumen and affirms no preferential depletion of 13C versus 12C. Our results suggest that 13C labeled n-alkanes can be used as nutrient passage tracers and support the reliability of the ?13C signature of digestible feed nutrients as a tool to measure nutrient-specific passage kinetics. PMID:24124493

  17. Seasonal liver protein differences in a hibernator revealed by quantitative proteomics using whole animal isotopic labeling

    PubMed Central

    Rose, J. Cameron; Epperson, L. Elaine; Carey, Hannah V.; Martin, Sandra L.

    2011-01-01

    Hibernation is an energy-saving strategy used by diverse species of mammals to survive winter. It is characterized by cycles between multi-day periods of torpor with low body temperature (Tb), and short periods of rapid, spontaneous rewarming. The ability to retain cellular integrity and function throughout torpor and rewarming is a key attribute of hibernation. Livers from winter hibernators are resistant to cellular damage induced by cold storage followed by warm reperfusion. Identifying proteins that differ between the summer-sensitive and winter-protected phenotypic states is one useful approach that may elucidate the molecular mechanisms that underlie this protection. Here we employ a novel quantitative proteomics screening strategy whereby a newly-weaned 13-lined ground squirrel was metabolically labeled by ingesting heavy-isotope substituted (15N) Spirulina. The liver protein extract from this animal provided a common reference for quantitative evaluation of protein differences by its addition to extracts from pooled samples of summer active (SA) or winter entrance (Ent) phase hibernating ground squirrels. We identified 61 significantly different proteins between the two groups and compared them to proteins identified previously in the same samples using 2D gels. Of the 20 proteins common to the two datasets, the direction and magnitude of their differences were perfectly concordant for 18, providing confidence that both sets of altered proteins reflect bona fide differences between the two physiological states. Furthermore, the 41 novel proteins recovered in this study included many new enzymes in pathways identified previously: specifically, additional enzymes belonging to the urea cycle, amino acid and carbohydrate degradation, and lipid biosynthetic pathways were decreased, whereas enzymes involved in ketone body synthesis, fatty acid utilization, protein synthesis and gluconeogenesis were increased in the samples from entrance hibernators compared to summer active animals, providing additional specific evidence for the importance of these pathways in the hibernating phenotype. PMID:21481655

  18. Development And Evaluation Of Stable Isotope And Fluorescent Labeling And Detection Methodologies For Tracking Injected Bacteria During In Situ Bioremediation

    SciTech Connect

    Mark E. Fuller; Tullis C. Onstott

    2003-12-17

    This report summarizes the results of a research project conducted to develop new methods to label bacterial cells so that they could be tracked and enumerated as they move in the subsurface after they are introduced into the groundwater (i.e., during bioaugmentation). Labeling methods based on stable isotopes of carbon (13C) and vital fluorescent stains were developed. Both approaches proved successful with regards to the ability to effectively label bacterial cells. Several methods for enumeration of fluorescently-labeled cells were developed and validated, including near-real time microplate spectrofluorometry that could be performed in the field. However, the development of a novel enumeration method for the 13C-enriched cells, chemical reaction interface/mass spectrometry (CRIMS), was not successful due to difficulties with the proposed instrumentation. Both labeling methodologies were successfully evaluated and validated during laboratory- and field-scale bacterial transport experiments. The methods developed during this research should be useful for future bacterial transport work as well as other microbial ecology research in a variety of environments. A full bibliography of research articles and meeting presentations related to this project is included (including web links to abstracts and full text reprints).

  19. Nic1 Inactivation Enables Stable Isotope Labeling with 13C615N4-Arginine in Schizosaccharomyces pombe*

    PubMed Central

    Carpy, Alejandro; Patel, Avinash; Tay, Ye Dee; Hagan, Iain M.; Macek, Boris

    2015-01-01

    Stable Isotope Labeling by Amino Acids (SILAC) is a commonly used method in quantitative proteomics. Because of compatibility with trypsin digestion, arginine and lysine are the most widely used amino acids for SILAC labeling. We observed that Schizosaccharomyces pombe (fission yeast) cannot be labeled with a specific form of arginine, 13C615N4-arginine (Arg-10), which limits the exploitation of SILAC technology in this model organism. We hypothesized that in the fission yeast the guanidinium group of 13C615N4-arginine is catabolized by arginase and urease activity to 15N1-labeled ammonia that is used as a precursor for general amino acid biosynthesis. We show that disruption of Ni2+-dependent urease activity, through deletion of the sole Ni2+ transporter Nic1, blocks this recycling in ammonium-supplemented EMMG medium to enable 13C615N4-arginine labeling for SILAC strategies in S. pombe. Finally, we employed Arg-10 in a triple-SILAC experiment to perform quantitative comparison of G1 + S, M, and G2 cell cycle phases in S. pombe. PMID:25368411

  20. MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LCMS

    Microsoft Academic Search

    Chih-chiang Tsou; Yin-hao Tsui; Yi-hwa Yian; Yi-ju Chen; Han-yin Yang; Chuan-yih Yu; Ke-shiuan Lynn; Yu-ju Chen; Ting-yi Sung; Wen-lian Hsu

    2009-01-01

    Isotope labeling combined with liquid chromato- graphy-mass spectrometry (LC-MS) provides a robust platform for analyzing differential protein expression in proteomics research. We present a web service, called MaXIC-Q Web (http:\\/\\/ms.iis .sinica.edu.tw\\/MaXIC-Q_Web\\/), for quantitation analysis of large-scale datasets generated from proteomics experiments using various stable isotope-labeling techniques, e.g. SILAC, ICAT and user-developed labeling methods. It accepts spec- tral files in the

  1. Efficient dominating sets in labeled rooted oriented trees

    Microsoft Academic Search

    Allen J. Schwenk; Bill Quan Yue

    2005-01-01

    An oriented graph G? is said to have an efficient dominating set S if S is a set of vertices of G? and for each vertex v of G?, either v is in S and v is adjacent to no other vertex in S, or v is not in S but is adjacent from precisely one vertex of S. Not

  2. Probing in Vivo Metabolism by Stable Isotope Labeling of Storage Lipids and Proteins in Developing Brassica napus Embryos1

    PubMed Central

    Schwender, Jörg; Ohlrogge, John B.

    2002-01-01

    Developing embryos of Brassica napus accumulate both triacylglycerols and proteins as major storage reserves. To evaluate metabolic fluxes during embryo development, we have established conditions for stable isotope labeling of cultured embryos under steady-state conditions. Sucrose supplied via the endosperm is considered to be the main carbon and energy source for seed metabolism. However, in addition to 220 to 270 mm carbohydrates (sucrose, glucose, and fructose), analysis of endosperm liquid revealed up to 70 mm amino acids as well as 6 to 15 mm malic acid. Therefore, a labeling approach with multiple carbon sources is a precondition to quantitatively reflect fluxes of central carbon metabolism in developing embryos. Mid-cotyledon stage B. napus embryos were dissected from plants and cultured for 15 d on a complex liquid medium containing 13C-labeled carbohydrates. The 13C enrichment of fatty acids and amino acids (after hydrolysis of the seed proteins) was determined by gas chromatography/mass spectrometry. Analysis of 13C isotope isomers of labeled fatty acids and plastid-derived amino acids indicated that direct glycolysis provides at least 90% of precursors of plastid acetyl-coenzyme A (CoA). Unlabeled amino acids, when added to the growth medium, did not reduce incorporation of 13C label into plastid-formed fatty acids, but substantially diluted 13C label in seed protein. Approximately 30% of carbon in seed protein was derived from exogenous amino acids and as a consequence, the use of amino acids as a carbon source may have significant influence on the total carbon and energy balance in seed metabolism. 13C label in the terminal acetate units of C20 and C22 fatty acids that derive from cytosolic acetyl-CoA was also significantly diluted by unlabeled amino acids. We conclude that cytosolic acetyl-CoA has a more complex biogenetic origin than plastidic acetyl-CoA. Malic acid in the growth medium did not dilute 13C label incorporation into fatty acids or proteins and can be ruled out as a source of carbon for the major storage components of B. napus embryos. PMID:12226514

  3. Energy Efficiency Standards and Labels in North America: Opportunities for Harmonization

    SciTech Connect

    Vanwiemcgrory, Laura; Wiel, Stephen; Van Wie McGrory, Laura; Harrington, Lloyd

    2002-05-16

    To support the North American Energy Working Group's Expert Group on Energy Efficiency (NAEWG-EE), USDOE commissioned the Collaborative Labeling and Appliance Standards Program (CLASP) to prepare a resource document comparing current standards, labels, and test procedure regulations in Canada, Mexico, and the United States. The resulting document reached the following conclusions: Out of 24 energy-using products for which at least one of the three countries has energy efficiency regulations, three products -- refrigerators/freezers, split system central air conditioners, and room air conditioners -- have similar or identical minimum energy performance standards (MEPS) in the three countries. These same three products, as well as three-phase motors, have similar or identical test procedures throughout the region. There are 10 products with different MEPS and test procedures, but which have the short-term potential to develop common test procedures, MEPS, and/or labels. Three other noteworthy areas where possible energy efficiency initiatives have potential for harmonization are standby losses, uniform endorsement labels, and a new standard or label on windows. This paper explains these conclusions and presents the underlying comparative data.

  4. Metabolic labeling with stable isotope nitrogen (15N) to follow amino acid and protein turnover of three plastid proteins in Chlamydomonas reinhardtii

    PubMed Central

    2014-01-01

    Background The length of time that a protein remains available to perform its function is significantly influenced by its turnover rate. Knowing the turnover rate of proteins involved in different processes is important to determining how long a function might progress even when the stimulus has been removed and no further synthesis of the particular proteins occurs. In this article, we describe the use of 15N-metabolic labeling coupled to GC-MS to follow the turnover of free amino acids and LC-MS/MS to identify and LC-MS to follow the turnover of specific proteins in Chlamydomonas reinhardtii. Results To achieve the metabolic labeling, the growth medium was formulated with standard Tris acetate phosphate medium (TAP) in which14NH4Cl was replaced with 15NH415NO3 and (14NH4)6Mo7O24.4H2O was replaced with Na2MoO4.2H2O. This medium designated 15N-TAP allowed CC-125 algal cells to grow normally. Mass isotopic distribution revealed successful 15N incorporation into 13 amino acids with approximately 98% labeling efficiency. Tryptic digestion of the 55 kDa SDS-PAGE bands from 14N- and 15N-labeled crude algal protein extracts followed by LC-MS/MS resulted in the identification of 27 proteins. Of these, five displayed peptide sequence confidence levels greater than 95% and protein sequence coverage greater than 25%. These proteins were the RuBisCo large subunit, ATP synthase CF1 alpha and beta subunits, the mitochondrial protein (F1F0 ATP synthase) and the cytosolic protein (S-adenosyl homocysteine hydroxylase). These proteins were present in both labeled and unlabeled samples. Once the newly synthesized 15N-labeled free amino acids and proteins obtained maximum incorporation of the 15N-label, turnover rates were determined after transfer of cells into 14N-TAP medium. The t½ values were determined for the three plastid proteins (RuBisCo, ATP synthase CF1 alpha and beta) by following the reduction of the 15N-fractional abundance over time. Conclusion We describe a more rapid and non-radioactive method to measure free amino acid and protein turnover. Our approach is applicable for determination of protein turnover for various proteins, which will lead to a better understanding of the relationship between protein lifetime and functionality. PMID:24580857

  5. Carbon Allocation of 13CO2-labeled Photoassimilate in Larix gmelinii Saplings - A Physiological Basis for Isotope Dendroclimatology in Eastern Siberia.

    NASA Astrophysics Data System (ADS)

    Kagawa, A.; Sugimoto, A.; Maximov, T. C.

    2006-12-01

    Tree-ring density and widths have been successfully used to reconstruct summer temperatures in high- northern latitudes, although a discrepancy between tree-growth and temperature has been found for recent decades. The so-called "reduced sensitivity" of tree rings to summer temperatures has been observed especially strongly in northern Siberia (Briffa et al., 1998) and drought stress (increased water use efficiency) arose from global warming and/or increasing CO2 are suggested as causes (Barber et al. 2000, Saurer et al. 2004). By using carbon isotope ratio as an indicator of drought stress and ring-width/density as indicators of growth, we can clarify how drought stress caused by recent global warming affects wood formation of Siberian trees. However, isotope dendroclimatology is still in its infancy and our understanding of basic physiological processes of isotope signal transfer from leaves to tree rings is insufficient. In order to understand translocation, storage, and allocation of photoassimilate to different organs of trees, we pulse- labeled ten L. gmelinii growing in a continuous permafrost zone with stable 13CO2. We studied seasonal course of carbon allocation patterns of photoassimilate among needles, branches, stem and roots and also how spring, summer, and autumn photoassimilate is later used for both earlywood and latewood formation. About half of the carbon in new needles was derived from stored material. The starch pool in non- needle parts, which can be used for xylem formation, drew about 43 percent of its carbon from previous year's photoassimilate, suggesting that carbon storage is the key mechanism behind autocorrelation in (isotope) dendroclimatology. Analysis of intra-annual 13C of the tree rings formed after the labeling revealed that earlywood contained photoassimilate from the previous summer and autumn as well as from the current spring. Latewood was mainly composed of photoassimilate from the current year's summer/autumn, although it also relied on stored material in some cases. Carbon isotope chronology of recent 100 years shows that the latewood 13C contains stronger climate signal than the earlywood and is significantly correlated to July temperature and July precipitation, corresponding to the timing of carbon incorporation that constitutes latewood. The results suggest the need for separating earlywood and latewood for isotope dendroclimatological study in Siberia. References: 1) Kagawa A., Sugimoto A., & Maximov, T.C. (2006) 13CO2 pulse-labelling of photoassimilates reveals carbon allocation within and between tree rings. Plant, Cell and Environment 29, 1571-1584. 2) Kagawa A., Sugimoto A., & Maximov, T. C. (2006) Seasonal course of translocation, storage, and remobilization of 13C pulse-labeled photoassimilate in naturally growing Larix gmelinii saplings. New Phytologist 171, 793-804. 3) Kagawa A., Naito D., Sugimoto A. & Maximov T. C. (2003) Effects of spatial and temporal variability in soil moisture on widths and 13C values of eastern Siberian tree rings. Journal of Geophysical Research 108 (D16), 4500, doi:10.1029/2002JD003019.

  6. Energy-efficiency labels and standards: A guidebook for appliances, equipment and lighting

    SciTech Connect

    McMahon, James E.; Wiel, Stephen

    2001-02-16

    Energy-performance improvements in consumer products are an essential element in any government's portfolio of energy-efficiency and climate change mitigation programs. Governments need to develop balanced programs, both voluntary and regulatory, that remove cost-ineffective, energy-wasting products from the marketplace and stimulate the development of cost-effective, energy-efficient technology. Energy-efficiency labels and standards for appliances, equipment, and lighting products deserve to be among the first policy tools considered by a country's energy policy makers. The U.S. Agency for International Development (USAID) and the United Nations Foundation (UNF) recognize the need to support policy makers in their efforts to implement energy-efficiency standards and labeling programs and have developed this guidebook, together with the Collaborative Labeling and Appliance Standards Program (CLASP), as a primary reference. This guidebook was prepared over the course of the past year with significant contribution from the authors and reviewers mentioned previously. Their diligent participation has made this the international guidance tool it was intended to be. The lead authors would also like to thank the following individuals for their support in the development, production, and distribution of the guidebook: Marcy Beck, Elisa Derby, Diana Dhunke, Ted Gartner, and Julie Osborn of Lawrence Berkeley National Laboratory as well as Anthony Ma of Bevilacqua-Knight, Inc. This guidebook is designed as a manual for government officials and others around the world responsible for developing, implementing, enforcing, monitoring, and maintaining labeling and standards-setting programs. It discusses the pros and cons of adopting energy-efficiency labels and standards and describes the data, facilities, and institutional and human resources needed for these programs. It provides guidance on the design, development, implementation, maintenance, and evaluation of the programs and on the design of the labels and standards themselves. In addition, it directs the reader to references and other resources likely to be useful in conducting the activities described and includes a chapter on energy policies and programs that complement appliance efficiency labels and standards. This guidebook attempts to reflect the essential framework of labeling and standards programs. It is the intent of the authors and sponsors to distribute copies of this book worldwide at no charge for the general public benefit. The guidebook is also available on the web at www.CLASPonline.org and can be downloaded to be used intact or piecemeal for whatever beneficial purposes readers may conceive.

  7. Reduce, Reuse & Recycle: Efficiently Solving Multi-Label MRFs Karteek Alahari1

    E-print Network

    Kohli, Pushmeet

    Reduce, Reuse & Recycle: Efficiently Solving Multi-Label MRFs Karteek Alahari1 Pushmeet Kohli2 first method (dynamic - expansion) works by `recycling' results from previous prob- lem instances is becoming increasingly important. The last few years have seen a lot of attention being devoted

  8. Isotopic labeling of DNA in rat adipose tissue: evidence for proliferating cells associated with mature adipocytes

    Microsoft Academic Search

    Barry J. Klyde; Jules Hirsch

    The intraperitoneal administration of (3H)thymi- dine to adult rats resulted in the rapid appearance of label in the adipocyte fraction of collagenase digests of adipose tissue. Low-speed centrifugation followed by freezing and slicing showed the label to be uniformly distributed in the adipocyte fraction. The presence of label in DNA was con- firmed by hydrolysis with deoxyribonuclease and by inhibi-

  9. Sensitive, Efficient Quantitation of 13C-Enriched Nucleic Acids via Ultrahigh-Performance Liquid Chromatography–Tandem Mass Spectrometry for Applications in Stable Isotope Probing

    PubMed Central

    Wilhelm, Roland; Szeitz, András; Klassen, Tara L.

    2014-01-01

    Stable isotope probing (SIP) of nucleic acids is a powerful tool for studying the functional traits of microbial populations within complex communities, but SIP involves a number of technical challenges. Many of the difficulties in DNA-SIP and RNA-SIP experiments can be effectively overcome with an efficient, sensitive method for quantitating the isotopic enrichment of nucleic acids. Here, we present a sensitive method for quantitating 13C enrichment of nucleic acids, requiring a few nanograms of sample, and we demonstrate its utility in typical DNA-SIP and RNA-SIP experiments. All five nucleobases (adenine, guanine, cytosine, thymine, and uracil) were separated and detected by using ultrahigh-performance liquid chromatography–tandem mass spectrometry. We detected all isotopic species in samples with as low as 1.5 atom% 13C above natural abundance, using 1-ng loadings. Quantitation was used to characterize the isotopic enrichment kinetics of cellulose- and lignin-based microcosm experiments and to optimize the recovery of enriched nucleic acids. Application of our method will minimize the quantity of expensive isotopically labeled substrates required and reduce the risk of failed experiments due to insufficient recovery of labeled nucleic acids for sequencing library preparation. PMID:25217022

  10. Sensitive, Efficient Quantitation of 13C-Enriched Nucleic Acids via Ultrahigh-Performance Liquid Chromatography-Tandem Mass Spectrometry for Applications in Stable Isotope Probing.

    PubMed

    Wilhelm, Roland; Szeitz, András; Klassen, Tara L; Mohn, William W

    2014-12-01

    Stable isotope probing (SIP) of nucleic acids is a powerful tool for studying the functional traits of microbial populations within complex communities, but SIP involves a number of technical challenges. Many of the difficulties in DNA-SIP and RNA-SIP experiments can be effectively overcome with an efficient, sensitive method for quantitating the isotopic enrichment of nucleic acids. Here, we present a sensitive method for quantitating (13)C enrichment of nucleic acids, requiring a few nanograms of sample, and we demonstrate its utility in typical DNA-SIP and RNA-SIP experiments. All five nucleobases (adenine, guanine, cytosine, thymine, and uracil) were separated and detected by using ultrahigh-performance liquid chromatography-tandem mass spectrometry. We detected all isotopic species in samples with as low as 1.5 atom% (13)C above natural abundance, using 1-ng loadings. Quantitation was used to characterize the isotopic enrichment kinetics of cellulose- and lignin-based microcosm experiments and to optimize the recovery of enriched nucleic acids. Application of our method will minimize the quantity of expensive isotopically labeled substrates required and reduce the risk of failed experiments due to insufficient recovery of labeled nucleic acids for sequencing library preparation. PMID:25217022

  11. Site-specific relaxation kinetics of a tryptophan zipper hairpin peptide using temperature-jump IR spectroscopy and isotopic labeling.

    PubMed

    Hauser, Karin; Krejtschi, Carsten; Huang, Rong; Wu, Ling; Keiderling, Timothy A

    2008-03-12

    Two antiparallel beta-strands connected by a turn make beta-hairpins an ideal model system to analyze the interactions and dynamics of beta-sheets. Site-specific conformational dynamics were studied by temperature-jump IR spectroscopy and isotopic labeling in a model based on the tryptophan zipper peptide, Trpzip2, developed by Cochran et al. (Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 5578). The modified Trpzip2C peptides have nearly identical equilibrium spectral behavior as Trpzip2 showing that they also form well-characterized beta-hairpin conformations in aqueous solution. Selective introduction of 13C=O groups on opposite strands lead to distinguishable cross-strand coupling of the labeled residues as monitored in the amide I' band. These frequency patterns reflect theoretical predictions, and the coupled 13C=O band loses intensity with increase in temperature and unfolding of the hairpin. Thermal relaxation kinetics were analyzed for unlabeled and cross-strand isotopically labeled variants. T-jumps of approximately 10 degrees C induce relaxation times of a few microseconds that decrease with increase of the peptide temperature. Differences in kinetic behavior for the loss of beta-strand and gain of disordered structure can be used to distinguish localized structure dynamics by comparison of nonlabeled and labeled amide I' components. Analysis of the data supports multistate dynamic and equilibrium behavior, but because of this process it is not possible to clearly define a folding and unfolding rate. Nonetheless, site-specific relaxation kinetics could be seen to be consistent with a hydrophobic collapse hypothesis for hairpin folding. PMID:18278908

  12. USE OF OXYGEN-18 ISOTOPE LABELING FOR MEASUREMENT OF OXIDATIVE STRESS

    EPA Science Inventory

    Oxygen-18 (18-O) labeling provides a sensitive means for quantifying oxygen binding that occurs during in vivo oxidations. Oxidants (ozone, nitrogen oxides, hydrogen peroxide, etc.) are first synthesized using 18-O, then cells or tissues are exposed to the labeled ...

  13. A Software Toolkit and Interface for Performing Stable Isotope Labeling and Top3 Quantification Using Progenesis LC-MS

    PubMed Central

    Brownridge, Philip; Xia, Dong; Mackay, Katherine; Gonzalez-Galarza, Faviel F.; Kenyani, Jenna; Harman, Victoria; Beynon, Robert J.; Jones, Andrew R.

    2012-01-01

    Abstract Numerous software packages exist to provide support for quantifying peptides and proteins from mass spectrometry (MS) data. However, many support only a subset of experimental methods or instrument types, meaning that laboratories often have to use multiple software packages. The Progenesis LC-MS software package from Nonlinear Dynamics is a software solution for label-free quantitation. However, many laboratories using Progenesis also wish to employ stable isotope-based methods that are not natively supported in Progenesis. We have developed a Java programming interface that can use the output files produced by Progenesis, allowing the basic MS features quantified across replicates to be used in a range of different experimental methods. We have developed post-processing software (the Progenesis Post-Processor) to embed Progenesis in the analysis of stable isotope labeling data and top3 pseudo-absolute quantitation. We have also created export ability to the new data standard, mzQuantML, produced by the Proteomics Standards Initiative to facilitate the development and standardization process. The software is provided to users with a simple graphical user interface for accessing the different features. The underlying programming interface may also be used by Java developers to develop other routines for analyzing data produced by Progenesis. PMID:22888986

  14. Stable isotope-labeled tracers for the investigation of fatty acid and triglyceride metabolism in humans in vivo

    PubMed Central

    Magkos, Faidon; Mittendorfer, Bettina

    2008-01-01

    Summary Understanding lipid metabolism and its regulation requires information on the rates at which lipids are produced within the body, absorbed (dietary lipids) into the body, transported within the body, and utilized by various tissues. This article focuses on the use of stable isotope-labeled tracers for the quantitative evaluation of major pathways of fatty acid and triglyceride metabolism in humans in vivo. Adipose tissue lipolysis and free fatty acid appearance in plasma, fatty acid tissue uptake and oxidation, and hepatic very low-density lipoprotein triglyceride secretion are among the metabolic pathways that can be studied by using stable isotope labeled tracers, and will be discussed in detail. The methodology has been in use for many years and is constantly being refined. A variety of tracers and analytical approaches are available and can be used; knowing the advantages, assumptions, and limitations of each is essential for the planning of studies and the interpretation of data, which can provide unique insights into human lipid metabolism. PMID:20161007

  15. Untargeted Profiling of Tracer-Derived Metabolites Using Stable Isotopic Labeling and Fast Polarity-Switching LC–ESI-HRMS

    PubMed Central

    2014-01-01

    An untargeted metabolomics workflow for the detection of metabolites derived from endogenous or exogenous tracer substances is presented. To this end, a recently developed stable isotope-assisted LC–HRMS-based metabolomics workflow for the global annotation of biological samples has been further developed and extended. For untargeted detection of metabolites arising from labeled tracer substances, isotope pattern recognition has been adjusted to account for nonlabeled moieties conjugated to the native and labeled tracer molecules. Furthermore, the workflow has been extended by (i) an optional ion intensity ratio check, (ii) the automated combination of positive and negative ionization mode mass spectra derived from fast polarity switching, and (iii) metabolic feature annotation. These extensions enable the automated, unbiased, and global detection of tracer-derived metabolites in complex biological samples. The workflow is demonstrated with the metabolism of 13C9-phenylalanine in wheat cell suspension cultures in the presence of the mycotoxin deoxynivalenol (DON). In total, 341 metabolic features (150 in positive and 191 in negative ionization mode) corresponding to 139 metabolites were detected. The benefit of fast polarity switching was evident, with 32 and 58 of these metabolites having exclusively been detected in the positive and negative modes, respectively. Moreover, for 19 of the remaining 49 phenylalanine-derived metabolites, the assignment of ion species and, thus, molecular weight was possible only by the use of complementary features of the two ion polarity modes. Statistical evaluation showed that treatment with DON increased or decreased the abundances of many detected metabolites. PMID:25372979

  16. Untargeted profiling of tracer-derived metabolites using stable isotopic labeling and fast polarity-switching LC-ESI-HRMS.

    PubMed

    Kluger, Bernhard; Bueschl, Christoph; Neumann, Nora; Stückler, Romana; Doppler, Maria; Chassy, Alexander W; Waterhouse, Andrew L; Rechthaler, Justyna; Kampleitner, Niklas; Thallinger, Gerhard G; Adam, Gerhard; Krska, Rudolf; Schuhmacher, Rainer

    2014-12-01

    An untargeted metabolomics workflow for the detection of metabolites derived from endogenous or exogenous tracer substances is presented. To this end, a recently developed stable isotope-assisted LC-HRMS-based metabolomics workflow for the global annotation of biological samples has been further developed and extended. For untargeted detection of metabolites arising from labeled tracer substances, isotope pattern recognition has been adjusted to account for nonlabeled moieties conjugated to the native and labeled tracer molecules. Furthermore, the workflow has been extended by (i) an optional ion intensity ratio check, (ii) the automated combination of positive and negative ionization mode mass spectra derived from fast polarity switching, and (iii) metabolic feature annotation. These extensions enable the automated, unbiased, and global detection of tracer-derived metabolites in complex biological samples. The workflow is demonstrated with the metabolism of (13)C9-phenylalanine in wheat cell suspension cultures in the presence of the mycotoxin deoxynivalenol (DON). In total, 341 metabolic features (150 in positive and 191 in negative ionization mode) corresponding to 139 metabolites were detected. The benefit of fast polarity switching was evident, with 32 and 58 of these metabolites having exclusively been detected in the positive and negative modes, respectively. Moreover, for 19 of the remaining 49 phenylalanine-derived metabolites, the assignment of ion species and, thus, molecular weight was possible only by the use of complementary features of the two ion polarity modes. Statistical evaluation showed that treatment with DON increased or decreased the abundances of many detected metabolites. PMID:25372979

  17. Combining position-specific 13C labeling with compound-specific isotope analysis: first steps towards soil fluxomics

    NASA Astrophysics Data System (ADS)

    Dippold, Michaela; Kuzyakov, Yakov

    2015-04-01

    Understanding the soil organic matter (SOM) dynamics is one of the most important challenges in soil science. Transformation of low molecular weight organic substances (LMWOS) is a key step in biogeochemical cycles because 1) all high molecular substances pass this stage during their decomposition and 2) only LMWOS will be taken up by microorganisms. Previous studies on LMWOS were focused on determining net fluxes through the LMWOS pool, but they rarely identified transformations. As LMWOS are the preferred C and energy source for microorganisms, the transformations of LMWOS are dominated by biochemical pathways of the soil microorganisms. Thus, understanding fluxes and transformations in soils requires a detailed knowledge on the biochemical pathways and its controlling factors. Tracing C fate in soil by isotopes became on of the most applied and promising biogeochemistry tools. Up to now, studies on LMWOS were nearly exclusively based on uniformly labeled organic substances i.e. all C atoms in the molecules were labeled with 13C or 14C. However, this classical approach did not allow the differentiation between use of intact initial substances in any process, or whether they were transformed to metabolites. The novel tool of position-specific labeling enables to trace molecule atoms separately and thus to determine the cleavage of molecules - a prerequisite for metabolic tracing. Position-specific labeling of LMWOS and quantification of 13CO2 and 13C in bulk soil enabled following the basic metabolic pathways of soil microorganisms. However, only the combination of position-specific 13C labeling with compound-specific isotope analysis of microbial biomarkers and metabolites allowed 1) tracing specific anabolic pathways in diverse microbial communities in soils and 2) identification of specific pathways of individual functional microbial groups. So, these are the prerequisites for soil fluxomics. Our studies combining position-specific labeled glucose with amino sugar 13C analysis showed that oxidizing catabolic pathways and anabolic pathways, i.e. building-up new cellular compounds, occurred in soils simultaneously. This involved an intensive C recycling within the microorganisms that was observed not only for cytosolic compounds but also for cell wall polymers. Fungal metabolism and fluxes were slower than bacterial intracellular C recycling and turnover. Furthermore, position-specific labeling of glutamate and subsequent 13C analysis of microbial phospholipid fatty acids (PLFA) revealed starvation pathways, which were only active in specific microbial groups in soils. These studies revealed that position-specific labeling enables the reconstruction of metabolic pathways of LMWOS within diverse microbial communities in complex media such as soil. Processes occurring simultaneously in soil i.e. 1) within individual, reversible metabolic pathways and 2) in various microbial groups could be traced by position-specific labeling in soils in situ. Tracing these pathways and understanding their regulating factors are crucial for soil C fluxomics, the extremely complex network of transformations towards mineralization versus the formation of microbial biomass compounds. Quantitative models to assess microbial group specific metabolic networks can be generated and parameterized by this approach. The submolecular knowledge of transformation steps and biochemical pathways in soils and their regulating factors is essential for understanding C cycling and long-term C storage in soils.

  18. Automated LC-HRMS(/MS) approach for the annotation of fragment ions derived from stable isotope labeling-assisted untargeted metabolomics.

    PubMed

    Neumann, Nora K N; Lehner, Sylvia M; Kluger, Bernhard; Bueschl, Christoph; Sedelmaier, Karoline; Lemmens, Marc; Krska, Rudolf; Schuhmacher, Rainer

    2014-08-01

    Structure elucidation of biological compounds is still a major bottleneck of untargeted LC-HRMS approaches in metabolomics research. The aim of the present study was to combine stable isotope labeling and tandem mass spectrometry for the automated interpretation of the elemental composition of fragment ions and thereby facilitate the structural characterization of metabolites. The software tool FragExtract was developed and evaluated with LC-HRMS/MS spectra of both native (12)C- and uniformly (13)C (U-(13)C)-labeled analytical standards of 10 fungal substances in pure solvent and spiked into fungal culture filtrate of Fusarium graminearum respectively. Furthermore, the developed approach is exemplified with nine unknown biochemical compounds contained in F. graminearum samples derived from an untargeted metabolomics experiment. The mass difference between the corresponding fragment ions present in the MS/MS spectra of the native and U-(13)C-labeled compound enabled the assignment of the number of carbon atoms to each fragment signal and allowed the generation of meaningful putative molecular formulas for each fragment ion, which in turn also helped determine the elemental composition of the precursor ion. Compared to laborious manual analysis of the MS/MS spectra, the presented algorithm marks an important step toward efficient fragment signal elucidation and structure annotation of metabolites in future untargeted metabolomics studies. Moreover, as demonstrated for a fungal culture sample, FragExtract also assists the characterization of unknown metabolites, which are not contained in databases, and thus exhibits a significant contribution to untargeted metabolomics research. PMID:24965664

  19. Automated LC-HRMS(/MS) Approach for the Annotation of Fragment Ions Derived from Stable Isotope Labeling-Assisted Untargeted Metabolomics

    PubMed Central

    2014-01-01

    Structure elucidation of biological compounds is still a major bottleneck of untargeted LC-HRMS approaches in metabolomics research. The aim of the present study was to combine stable isotope labeling and tandem mass spectrometry for the automated interpretation of the elemental composition of fragment ions and thereby facilitate the structural characterization of metabolites. The software tool FragExtract was developed and evaluated with LC-HRMS/MS spectra of both native 12C- and uniformly 13C (U-13C)-labeled analytical standards of 10 fungal substances in pure solvent and spiked into fungal culture filtrate of Fusarium graminearum respectively. Furthermore, the developed approach is exemplified with nine unknown biochemical compounds contained in F. graminearum samples derived from an untargeted metabolomics experiment. The mass difference between the corresponding fragment ions present in the MS/MS spectra of the native and U-13C-labeled compound enabled the assignment of the number of carbon atoms to each fragment signal and allowed the generation of meaningful putative molecular formulas for each fragment ion, which in turn also helped determine the elemental composition of the precursor ion. Compared to laborious manual analysis of the MS/MS spectra, the presented algorithm marks an important step toward efficient fragment signal elucidation and structure annotation of metabolites in future untargeted metabolomics studies. Moreover, as demonstrated for a fungal culture sample, FragExtract also assists the characterization of unknown metabolites, which are not contained in databases, and thus exhibits a significant contribution to untargeted metabolomics research. PMID:24965664

  20. Sulfur-34S stable isotope labeling of amino acids for quantification (SULAQ34) of proteomic changes in Pseudomonas fluorescens during naphthalene degradation.

    PubMed

    Herbst, Florian-Alexander; Taubert, Martin; Jehmlich, Nico; Behr, Tobias; Schmidt, Frank; von Bergen, Martin; Seifert, Jana

    2013-08-01

    The relative quantification of proteins is one of the major techniques used to elucidate physiological reactions. Because it allows one to avoid artifacts due to chemical labeling, the metabolic introduction of heavy isotopes into proteins and peptides is the preferred method for relative quantification. For eukaryotic cells, stable isotope labeling by amino acids in cell culture (SILAC) has become the gold standard and can be readily applied in a vast number of scenarios. In the microbial realm, with its highly versatile metabolic capabilities, SILAC is often not feasible, and the use of other (13)C or (15)N labeled substrates might not be practical. Here, the incorporation of heavy sulfur isotopes is shown to be a useful alternative. We introduce (34)S stable isotope labeling of amino acids for quantification and the corresponding tools required for spectra extraction and disintegration of the isotopic overlaps caused by the small mass shift. As proof of principle, we investigated the proteomic changes related to naphthalene degradation in P. fluorescens ATCC 17483 and uncovered a specific oxidative-stress-like response. PMID:23603340

  1. Sulfur-34S Stable Isotope Labeling of Amino Acids for Quantification (SULAQ34) of Proteomic Changes in Pseudomonas fluorescens during Naphthalene Degradation*

    PubMed Central

    Herbst, Florian-Alexander; Taubert, Martin; Jehmlich, Nico; Behr, Tobias; Schmidt, Frank; von Bergen, Martin; Seifert, Jana

    2013-01-01

    The relative quantification of proteins is one of the major techniques used to elucidate physiological reactions. Because it allows one to avoid artifacts due to chemical labeling, the metabolic introduction of heavy isotopes into proteins and peptides is the preferred method for relative quantification. For eukaryotic cells, stable isotope labeling by amino acids in cell culture (SILAC) has become the gold standard and can be readily applied in a vast number of scenarios. In the microbial realm, with its highly versatile metabolic capabilities, SILAC is often not feasible, and the use of other 13C or 15N labeled substrates might not be practical. Here, the incorporation of heavy sulfur isotopes is shown to be a useful alternative. We introduce 34S stable isotope labeling of amino acids for quantification and the corresponding tools required for spectra extraction and disintegration of the isotopic overlaps caused by the small mass shift. As proof of principle, we investigated the proteomic changes related to naphthalene degradation in P. fluorescens ATCC 17483 and uncovered a specific oxidative-stress-like response. PMID:23603340

  2. Multi-Isotope Secondary Ion Mass Spectrometry Combining Heavy Water 2H with 15N Labeling As Complementary Tracers for Metabolic Heterogeneity at the Single-Cell Level

    NASA Astrophysics Data System (ADS)

    Kopf, S.; McGlynn, S.; Cowley, E.; Green, A.; Newman, D. K.; Orphan, V. J.

    2014-12-01

    Metabolic rates of microbial communities constitute a key physiological parameter for understanding the in situ growth constraints for life in any environment. Isotope labeling techniques provide a powerful approach for measuring such biological activity, due to the use of isotopically enriched substrate tracers whose incorporation into biological materials can be detected with high sensitivity by isotope-ratio mass spectrometry. Nano-meter scale secondary ion mass spectrometry (NanoSIMS) combined with stable isotope labeling provides a unique tool for studying the spatiometabolic activity of microbial populations at the single cell level in order to assess both community structure and population diversity. However, assessing the distribution and range of microbial activity in complex environmental systems with slow-growing organisms, diverse carbon and nitrogen sources, or heterotrophic subpopulations poses a tremendous technical challenge because the introduction of isotopically labeled substrates frequently changes the nutrient availability and can inflate or bias measures of activity. Here, we present the use of hydrogen isotope labeling with deuterated water as an important new addition to the isotopic toolkit and apply it for the determination of single cell microbial activities by NanoSIMS imaging. This tool provides a labeling technique that minimally alters any aquatic chemical environment, can be administered with strong labels even in minimal addition (natural background is very low), is an equally universal substrate for all forms of life even in complex, carbon and nitrogen saturated systems, and can be combined with other isotopic tracers. The combination of heavy water labeling with the most commonly used NanoSIMS tracer, 15N, is technically challenging but opens up a powerful new set of multi-tracer experiments for the study of microbial activity in complex communities. We present the first truly simultaneous single cell triple isotope system measurements of 2H/1H, 13C/12C and 15N/14N and apply it to study of microbial metabolic heterogeneity and nitrogen metabolism in a continuous culture case study. Our data provide insight into both the diversity of microbial activity rates, as well as patterns of ammonium utilization at the single cell level.

  3. Kinetic isotope effects significantly influence intracellular metabolite [superscript 13]C labeling patterns and flux determination

    E-print Network

    Stephanopoulos, Gregory

    Rigorous mathematical modeling of carbon-labeling experiments allows estimation of fluxes through the pathways of central carbon metabolism, yielding powerful information for basic scientific studies as well as for a wide ...

  4. Probing the metabolic network in bloodstream-form Trypanosoma brucei using untargeted metabolomics with stable isotope labelled glucose.

    PubMed

    Creek, Darren J; Mazet, Muriel; Achcar, Fiona; Anderson, Jana; Kim, Dong-Hyun; Kamour, Ruwida; Morand, Pauline; Millerioux, Yoann; Biran, Marc; Kerkhoven, Eduard J; Chokkathukalam, Achuthanunni; Weidt, Stefan K; Burgess, Karl E V; Breitling, Rainer; Watson, David G; Bringaud, Frédéric; Barrett, Michael P

    2015-03-01

    Metabolomics coupled with heavy-atom isotope-labelled glucose has been used to probe the metabolic pathways active in cultured bloodstream form trypomastigotes of Trypanosoma brucei, a parasite responsible for human African trypanosomiasis. Glucose enters many branches of metabolism beyond glycolysis, which has been widely held to be the sole route of glucose metabolism. Whilst pyruvate is the major end-product of glucose catabolism, its transamination product, alanine, is also produced in significant quantities. The oxidative branch of the pentose phosphate pathway is operative, although the non-oxidative branch is not. Ribose 5-phosphate generated through this pathway distributes widely into nucleotide synthesis and other branches of metabolism. Acetate, derived from glucose, is found associated with a range of acetylated amino acids and, to a lesser extent, fatty acids; while labelled glycerol is found in many glycerophospholipids. Glucose also enters inositol and several sugar nucleotides that serve as precursors to macromolecule biosynthesis. Although a Krebs cycle is not operative, malate, fumarate and succinate, primarily labelled in three carbons, were present, indicating an origin from phosphoenolpyruvate via oxaloacetate. Interestingly, the enzyme responsible for conversion of phosphoenolpyruvate to oxaloacetate, phosphoenolpyruvate carboxykinase, was shown to be essential to the bloodstream form trypanosomes, as demonstrated by the lethal phenotype induced by RNAi-mediated downregulation of its expression. In addition, glucose derivatives enter pyrimidine biosynthesis via oxaloacetate as a precursor to aspartate and orotate. PMID:25775470

  5. Isotope labelling of Rubisco subunits provides in vivo information on subcellular biosynthesis and exchange of amino acids between compartments

    PubMed Central

    Allen, Doug K; Laclair, Russell W; Ohlrogge, John B; Shachar-Hill, Yair

    2012-01-01

    The architecture of plant metabolism includes substantial duplication of metabolite pools and enzyme catalyzed reactions in different subcellular compartments. This poses challenges for understanding the regulation of metabolism particularly in primary metabolism and amino acid biosynthesis. To explore the extent to which amino acids are made in single compartments and to gain insight into the metabolic precursors from which they derive, we used steady state 13C labelling and analysed labelling in protein amino acids from plastid and cytosol. Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a major component of green tissues and its large and small subunits are synthesized from different pools of amino acids in the plastid and cytosol, respectively. Developing Brassica napus embryos were cultured in the presence of [U-13C]-sucrose, [U-13C]-glucose, [U-13C]-glutamine or [U-13C]-alanine to generate proteins. The large subunits (LSU) and small subunits (SSU) of Rubisco were isolated and the labelling in their constituent amino acids was analysed by gas chromatography-mass spectrometry. Amino acids including alanine, glycine and serine exhibited different 13C enrichment in the LSU and SSU, demonstrating that these pools have different metabolic origins and are not isotopically equilibrated between the plastid and cytosol on the time scale of cellular growth. Potential extensions of this novel approach to other macromolecules, organelles and cell types of eukaryotes are discussed. PMID:22292468

  6. Probing the Metabolic Network in Bloodstream-Form Trypanosoma brucei Using Untargeted Metabolomics with Stable Isotope Labelled Glucose

    PubMed Central

    Creek, Darren J.; Mazet, Muriel; Achcar, Fiona; Anderson, Jana; Kim, Dong-Hyun; Kamour, Ruwida; Morand, Pauline; Millerioux, Yoann; Biran, Marc; Kerkhoven, Eduard J.; Chokkathukalam, Achuthanunni; Weidt, Stefan K.; Burgess, Karl E. V.; Breitling, Rainer; Watson, David G.; Bringaud, Frédéric; Barrett, Michael P.

    2015-01-01

    Metabolomics coupled with heavy-atom isotope-labelled glucose has been used to probe the metabolic pathways active in cultured bloodstream form trypomastigotes of Trypanosoma brucei, a parasite responsible for human African trypanosomiasis. Glucose enters many branches of metabolism beyond glycolysis, which has been widely held to be the sole route of glucose metabolism. Whilst pyruvate is the major end-product of glucose catabolism, its transamination product, alanine, is also produced in significant quantities. The oxidative branch of the pentose phosphate pathway is operative, although the non-oxidative branch is not. Ribose 5-phosphate generated through this pathway distributes widely into nucleotide synthesis and other branches of metabolism. Acetate, derived from glucose, is found associated with a range of acetylated amino acids and, to a lesser extent, fatty acids; while labelled glycerol is found in many glycerophospholipids. Glucose also enters inositol and several sugar nucleotides that serve as precursors to macromolecule biosynthesis. Although a Krebs cycle is not operative, malate, fumarate and succinate, primarily labelled in three carbons, were present, indicating an origin from phosphoenolpyruvate via oxaloacetate. Interestingly, the enzyme responsible for conversion of phosphoenolpyruvate to oxaloacetate, phosphoenolpyruvate carboxykinase, was shown to be essential to the bloodstream form trypanosomes, as demonstrated by the lethal phenotype induced by RNAi-mediated downregulation of its expression. In addition, glucose derivatives enter pyrimidine biosynthesis via oxaloacetate as a precursor to aspartate and orotate. PMID:25775470

  7. Efficient preparation and labeling of human induced pluripotent stem cells by nanotechnology

    PubMed Central

    Ruan, Jing; Shen, Jie; Wang, Zheng; Ji, Jiajia; Song, Hua; Wang, Kan; Liu, Bin; Li, Jinhui; Cui, Daxiang

    2011-01-01

    Efficient preparation and labeling of human induced pluripotent stem (iPS) cells is a great challenge in stem cell research and development. With the aim of investigating the feasibility of using nanotechnology to enhance the preparation efficiency of iPS cells and to label iPS cells for long-term tracing and imaging, in this paper, four transcription factor genes, ie, Oct4, Sox2, LIN28, and Nanog, and packaging plasmids such as PSPAX2 and PMD2.G were cotransfected into 293T cells using Generation 5.0 polyamidoamine dendrimer-modified magnetic nanoparticles (dMNPs) as a delivery system. The resultant supernatant liquids were incubated with human fibroblast cells at 37°C for 21 days, then the embryonic stem (ES) cell-like clones were screened, cultured, and identified. Finally, the prepared iPS cells were labeled with fluorescent magnetic nanoparticles (FMNPs). The results showed that dMNPs can efficiently deliver all vectors into 293T cells. The resultant lentiviruses’ titers were 10-fold more than those based on Lipofectamine™ 2000. Reverse transcription polymerase chain reaction analysis showed that four genes (Oct4, Sox2, LIN28, and Nanog) exhibited different expressions in iPS cells. Immunostaining analysis showed that specific surface markers of ES cells such as SSEA-3, SSEA-4, Tra-1-60, and Tra-1-81 were positive in iPS cells, and the terotomas were formed in NOD-SCID mice that were implanted with iPS cells. Red fluorescent signals could be observed in iPS cells labeled with FMNPs by fluorescent microscopy, and the magnetic signals were detected in labeled iPS cells by magnetic resonance imaging. In conclusion, human iPS cells can be efficiently generated using polyamidoamine dMNPs and lentivirus and labeled with FMNPs for long-term observation and tracking, which has great potential application in the research and development of stem cells in the near future. PMID:21499432

  8. Sulfonium Ion Derivatization, Isobaric Stable Isotope Labeling and Data Dependent CID- and ETD-MS/MS for Enhanced Phosphopeptide Quantitation, Identification and Phosphorylation Site Characterization

    NASA Astrophysics Data System (ADS)

    Lu, Yali; Zhou, Xiao; Stemmer, Paul M.; Reid, Gavin E.

    2012-04-01

    An amine specific peptide derivatization strategy involving the use of novel isobaric stable isotope encoded `fixed charge' sulfonium ion reagents, coupled with an analysis strategy employing capillary HPLC, ESI-MS, and automated data dependent ion trap CID-MS/MS, -MS3, and/or ETD-MS/MS, has been developed for the improved quantitative analysis of protein phosphorylation, and for identification and characterization of their site(s) of modification. Derivatization of 50 synthetic phosphopeptides with S, S'-dimethylthiobutanoylhydroxysuccinimide ester iodide (DMBNHS), followed by analysis using capillary HPLC-ESI-MS, yielded an average 2.5-fold increase in ionization efficiencies and a significant increase in the presence and/or abundance of higher charge state precursor ions compared to the non-derivatized phosphopeptides. Notably, 44% of the phosphopeptides (22 of 50) in their underivatized states yielded precursor ions whose maximum charge states corresponded to +2, while only 8% (4 of 50) remained at this maximum charge state following DMBNHS derivatization. Quantitative analysis was achieved by measuring the abundances of the diagnostic product ions corresponding to the neutral losses of `light' (S(CH3)2) and `heavy' (S(CD3)2) dimethylsulfide exclusively formed upon CID-MS/MS of isobaric stable isotope labeled forms of the DMBNHS derivatized phosphopeptides. Under these conditions, the phosphate group stayed intact. Access for a greater number of peptides to provide enhanced phosphopeptide sequence identification and phosphorylation site characterization was achieved via automated data-dependent CID-MS3 or ETD-MS/MS analysis due to the formation of the higher charge state precursor ions. Importantly, improved sequence coverage was observed using ETD-MS/MS following introduction of the sulfonium ion fixed charge, but with no detrimental effects on ETD fragmentation efficiency.

  9. Highly efficient cellular labeling of mesoporous nanoparticles in human mesenchymal stem cells: implication for stem cell tracking

    Microsoft Academic Search

    Dong-Ming Huang; Yann Hung; Bor-Sheng Ko; Szu-Chun Hsu; Wei-Hsuan Chen; Chung-Liang Chien; Chih-Pin Tsai; Chieh-Ti Kuo; Ju-Chiun Kang; Chung-Shi Yang; Chung-Yuan Mou; Yao-Chang Chen

    2005-01-01

    Tracking the distribution of stem cells is crucial to their therapeutic use. However, the usage of current vectors in cellular labeling is restricted by their low internalizing efficiency. Here, we reported a cellular labeling approach with a novel vector composed of mesoporous silica nanoparticles (MSNs) conjugated with fluorescein isothiocyanate in human bone marrow mesenchymal stem cells and 3T3-L1 cells, and

  10. A ROBUST ABSOLUTE DETECTION EFFICIENCY CALIBRATION METHOD UTILIZING BETA/GAMMA COINCIDENCE SIGNATURES AND ISOTOPICALLY PURIFIED NEUTRON ACTIVATED RADIOXENON ISOTOPES

    SciTech Connect

    McIntyre, Justin I.; Cooper, Matthew W.; Ely, James H.; Haas, Derek A.; Schrom, Brian T.

    2012-09-21

    Efforts to calibrate the absolute efficiency of gas cell radiations detectors have utilized a number of methodologies which allow adequate calibration but are time consuming and prone to a host of difficult-to-determine uncertainties. A method that extrapolates the total source strength from the measured beta and gamma gated beta coincidence signal was developed in the 1960’s and 1970’s. It has become clear that it is possible to achieve more consistent results across a range of isotopes and a range of activities using this method. Even more compelling is the ease with which this process can be used on routine samples to determine the total activity present in the detector. Additionally, recent advances in the generation of isotopically pure radioxenon samples of Xe-131m, Xe-133, and Xe-135 have allowed these measurement techniques to achieve much better results than would have been possible before when using mixed isotopic radioxenon source. This paper will discuss the beta/gamma absolute detection efficiency technique that utilizes several of the beta-gamma decay signatures to more precisely determine the beta and gamma efficiencies. It will than compare these results with other methods using pure sources of Xe-133, Xe-131m, and Xe-135 and a Xe-133/Xe-133m mix.

  11. Efficiency of the Electrolytic Separation of Lithium Isotopes

    Microsoft Academic Search

    Herrick L. Johnston; Clyde A. Hutchison

    1940-01-01

    The electrolytic separation coefficient, ?, has been determined for the lithium isotope separation in the electrolysis of lithium chloride solutions at a mercury cathode. Its value was found to be 1.055± about 0.005 and, within limits of error, was independent of temperature, of the fraction electrolyzed and of the amount of back reaction at the cathode. The factor was the

  12. Sedimented cyanobacterial detritus as a source of nutrient for submerged macrophytes (Vallisneria spiralis and Elodea nuttallii): An isotope labeling experiment using 15N

    Microsoft Academic Search

    Leiyan Zhang; Kuanyi Li; Zhengwen Liu; Jack J. Middelburg

    2010-01-01

    A tracer experiment using the nitrogen isotope 15N investigated the uptake and incorporation of nitrogen from sedimented cyanobacterial detritus by two species of submerged macrophytes, the native Vallisneria spiralis and the exotic Elodea nuttallii, in Lake Taihu (China). The cyanobacterium Microcystis was labeled with 15Nammonium and dried to produce detritus, which was injected into vegetated sediments and traced to establish

  13. Lewis Acid-Base, Molecular Modeling, and Isotopic Labeling in a Sophomore Inorganic Chemistry Laboratory

    ERIC Educational Resources Information Center

    Nataro, Chip; Ferguson, Michelle A.; Bocage, Katherine M.; Hess, Brian J.; Ross, Vincent J.; Swarr, Daniel T.

    2004-01-01

    An experiment to prepare a deuterium labeled adduct of a Lewis acid and Lewis base, to use computational methods allowing students to visualize the LUMO of Lewis acids, the HOMO of Lewis bases and the molecular orbitals of the adduct that is formed is developed. This allows students to see the interplay between calculated and experimental results.

  14. Production of large quantities of isotopically labeled protein in Pichia pastoris by fermentation

    Microsoft Academic Search

    Matthew J. Wood; Elizabeth A. Komives

    1999-01-01

    Heterologous expression in Pichia pastoris has many of the advantages of eukaryotic expression, proper folding and disulfide bond formation, glycosylation, and secretion. Contrary to other eukaryotic systems, protein production from P.pastoris occurs in simple minimal defined media making this system attractive for production of labeled proteins for NMR analysis. P.pastoris is therefore the expression system of choice for NMR of

  15. Combining Raman and FT-IR spectroscopy with quantitative isotopic labeling for differentiation of E. coli cells at community and single cell levels.

    PubMed

    Muhamadali, Howbeer; Chisanga, Malama; Subaihi, Abdu; Goodacre, Royston

    2015-04-21

    There is no doubt that the contribution of microbially mediated bioprocesses toward maintenance of life on earth is vital. However, understanding these microbes in situ is currently a bottleneck, as most methods require culturing these microorganisms to suitable biomass levels so that their phenotype can be measured. The development of new culture-independent strategies such as stable isotope probing (SIP) coupled with molecular biology has been a breakthrough toward linking gene to function, while circumventing in vitro culturing. In this study, for the first time we have combined Raman spectroscopy and Fourier transform infrared (FT-IR) spectroscopy, as metabolic fingerprinting approaches, with SIP to demonstrate the quantitative labeling and differentiation of Escherichia coli cells. E. coli cells were grown in minimal medium with fixed final concentrations of carbon and nitrogen supply, but with different ratios and combinations of (13)C/(12)C glucose and (15)N/(14)N ammonium chloride, as the sole carbon and nitrogen sources, respectively. The cells were collected at stationary phase and examined by Raman and FT-IR spectroscopies. The multivariate analysis investigation of FT-IR and Raman data illustrated unique clustering patterns resulting from specific spectral shifts upon the incorporation of different isotopes, which were directly correlated with the ratio of the isotopically labeled content of the medium. Multivariate analysis results of single-cell Raman spectra followed the same trend, exhibiting a separation between E. coli cells labeled with different isotopes and multiple isotope levels of C and N. PMID:25831066

  16. FTIR Study of the Photoinduced Processes of Plant Phytochrome Phya using Isotope-Labeled Bilins and Density Functional Theory Calculations

    PubMed Central

    Schwinté, Pascale; Foerstendorf, Harald; Hussain, Zakir; Gärtner, Wolfgang; Mroginski, Maria-Andrea; Hildebrandt, Peter; Siebert, Friedrich

    2008-01-01

    Fourier transform infrared spectroscopy was used to analyze the chromophore structure in the parent states Pr and Pfr of plant phytochrome phyA and the respective photoproducts lumi-R and lumi-F. The spectra were obtained from phyA adducts assembled with either uniformly or selectively isotope-labeled phytochromobilin and phycocyanobilin. The interpretation of the experimental spectra is based on the spectra of chromophore models calculated by density functional theory. Global 13C-labeling of the tetrapyrrole allows for the discrimination between chromophore and protein bands in the Fourier transform infrared difference spectra. All infrared difference spectra display a prominent difference band attributable to a stretching mode with large contributions from the methine bridge between the inner pyrrole rings (B-C stretching). Due to mode coupling, frequencies and isotopic shifts of this mode suggest that the Pr chromophore may adopt a distorted ZZZssa or ZZZasa geometry with a twisted A-B methine bridge. The transition to lumi-R is associated with only minor changes of the amide I bands indicating limited protein structural changes during the isomerization site of the C-D methine bridge. Major protein structural changes occur upon the transition to Pfr in which the chromophore adopts a ZZEssa or ZZEasa-like state. In addition, specific interactions with the protein alter the structure of the B-C methine bridge as concluded from the substantial downshift of the respective stretching mode. These interactions are removed during the photoreaction to lumi-F (ZZE?ZZZ), which involves only small protein structural changes. PMID:18390618

  17. Analysis of SRC Oncogenic Signaling in Colorectal Cancer by Stable Isotope Labeling with Heavy Amino Acids in Mouse Xenografts*

    PubMed Central

    Sirvent, Audrey; Vigy, Oana; Orsetti, Beatrice; Urbach, Serge; Roche, Serge

    2012-01-01

    The non-receptor tyrosine kinase SRC is frequently deregulated in human colorectal cancer (CRC), and SRC increased activity has been associated with poor clinical outcomes. In nude mice engrafted with human CRC cells, SRC over-expression favors tumor growth and is accompanied by a robust increase in tyrosine phosphorylation in tumor cells. How SRC contributes to this tumorigenic process is largely unknown. We analyzed SRC oncogenic signaling in these tumors by means of a novel quantitative proteomic analysis. This method is based on stable isotope labeling with amino acids of xenograft tumors by the addition of [13C6]-lysine into mouse food. An incorporation level greater than 88% was obtained in xenograft tumors after 30 days of the heavy lysine diet. Quantitative phosphoproteomic analysis of these tumors allowed the identification of 61 proteins that exhibited a significant increase in tyrosine phosphorylation and/or association with tyrosine phosphorylated proteins upon SRC expression. These mainly included molecules implicated in vesicular trafficking and signaling and RNA binding proteins. Most of these proteins were specific targets of SRC signaling in vivo, as they were not identified by analysis via stable isotope labeling by amino acids in cell culture (SILAC) of the same CRC cells in culture. This suggests that oncogenic signaling induced by SRC in tumors significantly differs from that induced by SRC in cell culture. We next confirmed this notion experimentally with the example of the vesicular trafficking protein and SRC substrate TOM1L1. We found that whereas TOM1L1 depletion only slightly affected SRC-induced proliferation of CRC cells in vitro, it drastically decreased tumor growth in xenografted nude mice. We thus concluded that this vesicular trafficking protein plays an important role in SRC-induced tumor growth. Overall, these data show that SILAC analysis in mouse xenografts is a valuable approach for deciphering tyrosine kinase oncogenic signaling in vivo. PMID:23023324

  18. Highly accurate quantification of hydroxyproline-containing peptides in blood using a protease digest of stable isotope-labeled collagen.

    PubMed

    Taga, Yuki; Kusubata, Masashi; Ogawa-Goto, Kiyoko; Hattori, Shunji

    2014-12-17

    Collagen-derived hydroxyproline (Hyp)-containing dipeptides and tripeptides, which are known to possess physiological functions, appear in blood at high concentrations after oral ingestion of gelatin hydrolysate. However, highly accurate and sensitive quantification of the Hyp-containing peptides in blood has been challenging because of the analytical interference from numerous other blood components. We recently developed a stable isotope-labeled collagen named "SI-collagen" that can be used as an internal standard in various types of collagen analyses employing liquid chromatography-mass spectrometry (LC-MS). Here we prepared stable isotope-labeled Hyp-containing peptides from SI-collagen using trypsin/chymotrypsin and plasma proteases by mimicking the protein degradation pathways in the body. With the protease digest of SI-collagen used as an internal standard mixture, we achieved highly accurate simultaneous quantification of Hyp and 13 Hyp-containing peptides in human blood by LC-MS. The area under the plasma concentration-time curve of Hyp-containing peptides ranged from 0.663 ± 0.022 nmol/mL·h for Pro-Hyp-Gly to 163 ± 1 nmol/mL·h for Pro-Hyp after oral ingestion of 25 g of fish gelatin hydrolysate, and the coefficient of variation of three separate measurements was <7% for each peptide except for Glu-Hyp-Gly, which was near the detection limit. Our method is useful for absorption/metabolism studies of the Hyp-containing peptides and development of functionally characterized gelatin hydrolysate. PMID:25417748

  19. Stable carbon isotope labeling reveals different carry-over effects between functional types of tropical trees in an Ethiopian mountain forest.

    PubMed

    Krepkowski, Julia; Gebrekirstos, Aster; Shibistova, Olga; Bräuning, Achim

    2013-07-01

    We present an intra-annual stable carbon isotope (?(13)C) study based on a labeling experiment to illustrate differences in temporal patterns of recent carbon allocation to wood structures of two functional types of trees, Podocarpus falcatus (a late-successional evergreen conifer) and Croton macrostachyus (a deciduous broadleaved pioneer tree), in a tropical mountain forest in Ethiopia. Dendrometer data, wood anatomical thin sections, and intra-annual ?(13)C analyses were applied. Isotope data revealed a clear annual growth pattern in both studied species. For P. falcatus, it was possible to synchronize annual ?(13) C peaks, wood anatomical structures and monthly precipitation patterns. The labeling signature was evident for three consecutive years. For C. macrostachyus, isotope data illustrate a rapid decline of the labeling signal within half a year. Our ?(13)C labeling study indicates a distinct difference in carryover effects between trees of different functional types. A proportion of the labeled ?(13)C is stored in reserves of wood parenchyma for up to 3 yr in P. falcatus. By contrast, C. macrostachyus shows a high turnover of assimilates and a carbon carryover effect is only detectable in the subsequent year. PMID:23586968

  20. Multi-isotope labelling (13C, 18O, 2H) of fresh assimilates to trace organic matter dynamics in the plant-soil system

    NASA Astrophysics Data System (ADS)

    Studer, M. S.; Siegwolf, R. T. W.; Leuenberger, M.; Abiven, S.

    2014-11-01

    Isotope labelling is a powerful tool to study elemental cycling within terrestrial ecosystems. Here we describe a new multi-isotope technique to label organic matter (OM). We exposed poplars (Populus deltoides x nigra) for 14 days to an atmosphere enriched in 13CO2 and depleted in 2H218O. After one week, the water-soluble leaf OM (?13C = 1346 ± 162‰) and the leaf water were strongly labelled (?18O = -63± 8‰, ?2H = -156 ± 15‰). The leaf water isotopic composition was between the atmospheric and stem water, indicating a considerable diffusion of vapour into the leaves (58-69%). The atomic ratios of the labels recovered (18O/13C, 2H/13C) were 2-4 times higher in leaves than in the stems and roots. This either indicates the synthesis of more condensed compounds (lignin vs. cellulose) in roots and stems, or be the result of O and H exchange and fractionation processes during transport and biosynthesis. We demonstrate that the three major OM elements (C, O, H) can be labelled and traced simultaneously within the plant. This approach could be of interdisciplinary interest for the fields of plant physiology, paleoclimatic reconstruction or soil science.

  1. An efficient method for the production of isotopically enriched cholesterol for NMR[S

    PubMed Central

    Shivapurkar, Rupali; Souza, Cleiton M.; Jeannerat, Damien; Riezman, Howard

    2011-01-01

    13C-Cholesterol was produced with high efficiency by a genetically engineered yeast strain. The method produces ?1 mg of cholesterol per gram of glucose using 100 ml of culture medium. Uniform 94% enrichment where the most abundant product is the fully enriched isotopomer (u-13C27) is obtained using (u-13C6, 99%) glucose medium. High enrichment is very important for relaxation experiments, but for NMR applications where carbon-carbon couplings are measured, this is problematic. A good compromise between sensitivity and cost consists in diluting (u-13C6, 25%) with natural-abundance glucose. With a 2:3 ratio, the maximal amount of singlets can be obtained in 1 dimensional (D) carbon and 2D heteronuclear single-quantum correlation (HSQC) spectra with 6× intensity increase relative to natural-abundance samples. The use of (1-13C1-glucose, 99%) or (2-13C1-glucose, 99%) as isotope sources allows the labeling of the cholesterol in multiple mostly nonvicinal positions and reach 45× intensity increase. As an alternative, the dilution of (u-13C6, 99%) glucose can be used to simultaneously enrich eleven pairs of 13C up to ?1,000× natural-abundance probability, which should be very beneficial to double-quantum NMR experiments including the INADEQUATE and related pulse sequences. The flexibility of the method and the potential to adapt the culture protocol to specific needs should find many applications in chemistry and biology and in different fields of NMR and MS. PMID:21357620

  2. Quantitative proteomic approaches in mouse: stable isotope incorporation by metabolic (SILAC) or chemical labeling (reductive dimethylation) combined with high-resolution mass spectrometry.

    PubMed

    Billing, Anja M; Ben Hamidane, Hisham; Graumann, Johannes

    2015-01-01

    Mass spectrometry-based quantitative proteomics is a powerful method for in-depth exploration of protein expression, allowing researchers to probe its regulation and study signal-transduction networks, protein turnover, secretion, and spatial distribution, as well as post-translational modification and protein-protein interaction, on a large scale. Precise protein quantitation may be achieved by incorporation of stable isotopes, which introduce a mass shift detectable by mass spectrometry, allowing multiplexing of several samples and therefore relative quantification. Stable isotope incorporation into proteins or peptides can be attained either by metabolic labeling (e.g., SILAC) or by chemical labeling (e.g., reductive dimethylation). Both labeling approaches are presented here. They are straightforward and robust and can be applied to murine samples. While both SILAC and reductive dimethylation offer similar multiplexing capabilities and quantitative accuracy, reductive dimethylation is more versatile and can be used with any sample type. PMID:25727197

  3. Absolute quantification of protein and post-translational modification abundance with stable isotope–labeled synthetic peptides

    PubMed Central

    Kettenbach, Arminja N; Rush, John; Gerber, Scott A

    2013-01-01

    In the analysis of biological systems, it is of interest to identify the components of the system and to monitor their changes in abundance under different conditions. The AQUA (for ‘absolute quantification’) method allows sensitive and specific targeted quantification of protein and post-translational modifications in complex protein mixtures using stable isotope–labeled peptides as internal standards. Each AQUA experiment is composed of two stages: method development and application to a biological scenario. In the method development stage, peptides from the protein of interest are chosen and then synthesized with stable isotopes such as 13C, 2H or 15N. The abundance of these internal standards and their endogenous counterparts can be measured by mass spectrometry with selected reaction monitoring or selected ion monitoring methods. Once an AQUA method is established, it can be rapidly applied to a wide range of biological samples, from tissue culture cells to human plasma and tissue. After AQUA peptide synthesis, the development, optimization and application of AQUA analyses to a specific biological problem can be achieved in ~1 week. Here we demonstrate the usefulness of this method by monitoring both Polo-like kinase 1 (Plk1) protein abundance in multiple lung cancer cell lines and the extent of Plk1 activation loop phosphorylation (pThr-210) during release from S phase. PMID:21293459

  4. Investigation of biosynthetic pathways to hydroxycoumarins during post-harvest physiological deterioration in Cassava roots by using stable isotope labelling.

    PubMed

    Bayoumi, Soad A L; Rowan, Michael G; Beeching, John R; Blagbrough, Ian S

    2008-12-15

    Cassava (Manihot esculenta Crantz) is an important starch-rich crop, but the storage roots only have a short shelf-life due to post-harvest physiological deterioration (PPD), which includes the over-production and polymerisation of hydroxycoumarins. Key aspects of coumarin secondary-metabolite biosynthesis remain unresolved. Here we exploit the accumulation of hydroxycoumarins to test alternative pathways for their biosynthesis. Using isotopically labelled intermediates (p-coumarate-2-(13)C, caffeate-2-(13)C, ferulate-2-(13)C, umbelliferone-2-(18)O and esculetin-2-(18)O), we show that the major biosynthetic pathway to scopoletin and its glucoside, scopolin, in cassava roots during PPD is through p-coumaric, caffeic and then ferulic acids. An alternate pathway through 2',4'-dihydroxycinnamate and umbelliferone leads to esculetin and esculin. We have used C(18)O(2)-carboxylate-labelled cinnamic and ferulic acids, and feeding experiments under an atmosphere of (18)O(2), to investigate the o-hydroxylation and cyclisation steps. We demonstrate that the major pathway is through o-hydroxylation and not via a proposed spirolactone-dienone intermediate. PMID:19035613

  5. An automated method for the analysis of stable isotope labeling data in proteomics

    Microsoft Academic Search

    Xiang Zhang; Wade Hines; Jiri Adamec; John M. Asara; Stephen Naylor; Fred E. Regnier

    2005-01-01

    An algorithm is presented for the generation of a reliable peptide component peak table from liquid chromatography-mass spectrometry\\u000a (LC-MS) and subsequent quantitative analysis of stable isotope coded peptide samples. The method uses chemical noise filtering,\\u000a charge state fitting, and deisotoping toward improved analysis of complex peptide samples. Overlapping peptide signals in\\u000a mass spectra were deconvoluted by correlation with modeled peptide

  6. Isomerization of stable isotopically labeled elaidic acid to cis and trans monoenes by ruminal microbes

    Microsoft Academic Search

    Julie M. Proell; Erin E. Mosley; Gary L. Powell; Thomas C. Jenkins

    2002-01-01

    A previous study showed that oleic acid was con- verted by mixed ruminal microbes to stearic acid and also converted to a multitude of trans octadecenoic acid iso- mers. This study traced the metabolism of one of these trans C18:1 isomers upon its incubation with mixed ruminal microbes. Unlabeled and labeled (18-( 13 C) trans -9 C18:1) elaidic acid were

  7. Structure and vibrational dynamics of isotopically labeled lithium borohydride using neutron diffraction and spectroscopy

    Microsoft Academic Search

    Michael R. Hartman; John J. Rush; Terrence J. Udovic; Robert C. Bowman Jr.; Son-Jong Hwang

    2007-01-01

    The crystalline structure of a 7Li and 11B labeled lithium borohydride has been investigated using neutron powder diffraction at 3.5, 360, and 400K. The B–H bond lengths and H–B–H angles for the [BH4]? tetrahedra indicated that the tetrahedra maintained a nearly ideal configuration throughout the temperature range investigated. The atomic displacement parameters at 360K suggest that the [BH4]? tetrahedra become

  8. ZoomQuant: An application for the quantitation of stable isotope labeled peptides

    Microsoft Academic Search

    Brian D. Halligan; Ronit Y. Slyper; Simon N. Twigger; Wayne Hicks; Michael Olivier; Andrew S. Greene

    2005-01-01

    The main goal of comparative proteomics is the quantitation of the differences in abundance of many proteins between two different\\u000a biological samples in a single experiment. By differentially labeling the peptides from the two samples and combining them\\u000a in a single analysis, relative ratios of protein abundance can be accurately determined. Protease catalyzed 18O exchange is a simple method to

  9. Isotope-labeling studies on the formation pathway of acrolein during heat processing of oils.

    PubMed

    Ewert, Alice; Granvogl, Michael; Schieberle, Peter

    2014-08-20

    Acrolein (2-propenal) is classified as a foodborne toxicant and was shown to be present in significant amounts in heated edible oils. Up to now, its formation was mainly suggested to be from the glycerol part of triacylglycerides, although a clear influence of the unsaturation of the fatty acid moiety was also obvious in previous studies. To unequivocally clarify the role of the glycerol and the fatty acid parts in acrolein formation, two series of labeled triacylglycerides were synthesized: [(13)C(3)]-triacylglycerides of stearic, oleic, linoleic, and linolenic acid and [(13)C(54)]-triacylglycerides with labeled stearic, oleic, and linoleic acid, but with unlabeled glycerol. Heating of each of the seven intermediates singly in silicon oil and measurement of the formed amounts of labeled and unlabeled acrolein clearly proved the fatty acid backbone as the key precursor structure. Enzymatically synthesized pure linoleic acid and linolenic acid hydroperoxides were shown to be the key intermediates in acrolein formation, thus allowing the discussion of a radical-induced reaction pathway leading to the formation of the aldehyde. Surprisingly, although several oils contained high amounts of acrolein after heating, deep-fried foods themselves, such as donuts or French fries, were low in the aldehyde. PMID:25105208

  10. International Review of the Development and Implementation of Energy Efficiency Standards and Labeling Programs

    SciTech Connect

    Zhou, Nan; Zheng, Nina; Fridley, David

    2012-02-28

    Appliance energy efficiency standards and labeling (S&L) programs have been important policy tools for regulating the efficiency of energy-using products for over 40 years and continue to expand in terms of geographic and product coverage. The most common S&L programs include mandatory minimum energy performance standards (MEPS) that seek to push the market for efficient products, and energy information and endorsement labels that seek to pull the market. This study seeks to review and compare some of the earliest and most well-developed S&L programs in three countries and one region: the U.S. MEPS and ENERGY STAR, Australia MEPS and Energy Label, European Union MEPS and Ecodesign requirements and Energy Label and Japanese Top Runner programs. For each program, key elements of S&L programs are evaluated and comparative analyses across the programs undertaken to identify best practice examples of individual elements as well as cross-cutting factors for success and lessons learned in international S&L program development and implementation. The international review and comparative analysis identified several overarching themes and highlighted some common factors behind successful program elements. First, standard-setting and programmatic implementation can benefit significantly from a legal framework that stipulates a specific timeline or schedule for standard-setting and revision, product coverage and legal sanctions for non-compliance. Second, the different MEPS programs revealed similarities in targeting efficiency gains that are technically feasible and economically justified as the principle for choosing a standard level, in many cases at a level that no product on the current market could reach. Third, detailed survey data such as the U.S. Residential Energy Consumption Survey (RECS) and rigorous analyses provide a strong foundation for standard-setting while incorporating the participation of different groups of stakeholders further strengthen the process. Fourth, sufficient program resources for program implementation and evaluation are critical to the effectiveness of standards and labeling programs and cost-sharing between national and local governments can help ensure adequate resources and uniform implementation. Lastly, check-testing and punitive measures are important forms of enforcement while the cancellation of registration or product sales-based fines have also proven effective in reducing non-compliance. The international comparative analysis also revealed the differing degree to which the level of government decentralization has influenced S&L programs and while no single country has best practices in all elements of standards and labeling development and implementation, national examples of best practices for specific elements do exist. For example, the U.S. has exemplified the use of rigorous analyses for standard-setting and robust data source with the RECS database while Japan?s Top Runner standard-setting principle has motivated manufacturers to exceed targets. In terms of standards implementation and enforcement, Australia has demonstrated success with enforcement given its long history of check-testing and enforcement initiatives while mandatory information-sharing between EU jurisdictions on compliance results is another important enforcement mechanism. These examples show that it is important to evaluate not only the drivers of different paths of standards and labeling development, but also the country-specific context for best practice examples in order to understand how and why certain elements of specific S&L programs have been effective.

  11. Efficient 18F labeling of cysteine containing peptides and proteins using the tetrazine-trans-cyclooctene ligation

    PubMed Central

    Liu, Shuanglong; Hassink, Matthew; Selvaraj, Ramajeyam; Yap, Li-Peng; Park, Ryan; Wang, Hui; Chen, Xiaoyuan; Conti, Peter S.

    2014-01-01

    18F PET has a number of attributes that make it clinically attractive, including nearly 100% positron efficiency, very high specific radioactivity, and short half-life of ~110 min. However, the short half-life of 18F and the poor nucleophilicity of fluoride introduce challenges for the incorporation of 18F into complex molecules. Recently, the tetrazine-trans-cyclooctene ligation has been introduced as a novel 18F labeling method that proceeds with fast reaction rates without catalysis. Herein, we report an efficient method for 18F-labeling of free cysteines of peptides and proteins based on sequential ligation with a bifunctional tetrazinyl-maleimide and an 18F-labeled trans-cyclooctene. The newly developed method was tested for site specific labeling of both c(RGDyC) peptide and VEGF-SH protein. Starting with 4 mCi of 18F-trans-cyclooctene and only 10 ?g of tetrazine-RGD (80–100 ?M) or 15 ?g of tetrazine-VEGF (6.0 ?M), 18F labeled RGD peptide and VEGF protein could be obtained within five minutes in 95% yield and 75% yield, respectively. The obtained tracers were then evaluated in mice. In conclusion, a highly efficient method has been developed for site-specific 18F labeling of cysteine containing peptides and proteins. The special characteristics of the tetrazine-trans-cyclooctene ligation provide unprecedented opportunities to synthesize 18F-labeled probes with high specific activity for PET applications. PMID:23415400

  12. Design and operation of a continuous 13C and 15N labeling chamber for uniform or differential, metabolic and structural, plant tissue isotope labeling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tracing heavy stable isotopes from plant material through the ecosystem provides the most sensitive information about ecosystem processes; from CO2 fluxes and soil organic matter formation to small-scale stable-isotope biomarker probing. Coupling multiple stable isotopes such as 13C with 15N, 18O o...

  13. Detection of superoxide anion using an isotopically labeled nitrone spin trap: potential biological applications

    Microsoft Academic Search

    Hao Zhang; Joy Joseph; Jeannette Vasquez-Vivar; Hakim Karoui; Cline Nsanzumuhire; Pavel Martásek; Paul Tordo; B Kalyanaraman

    2000-01-01

    We describe the synthesis and biological applications of a novel nitrogen-15-labeled nitrone spin trap, 5-ethoxycarbonyl-5-methyl-1-pyrroline N-oxide ([15N]EMPO) for detecting superoxide anion. Superoxide anion generated in xanthine\\/xanthine oxidase (100 nM min?1) and NADPH\\/calcium-calmodulin\\/nitric oxide synthase systems was readily detected using EMPO, a nitrone analog of 5,5?-dimethyl-1-pyrroline N-oxide (DMPO). Unlike DMPO-superoxide adduct (DMPO–OOH), the superoxide adduct of EMPO (EMPO–OOH) does not spontaneously

  14. The use of stable-isotopically labeled oleic acid to interrogate lipid assembly in vivo: assessing pharmacological effects in preclinical species.

    PubMed

    McLaren, David G; He, Timothy; Wang, Sheng-Ping; Mendoza, Vivienne; Rosa, Raymond; Gagen, Karen; Bhat, Gowri; Herath, Kithsiri; Miller, Paul L; Stribling, Sloan; Taggart, Andrew; Imbriglio, Jason; Liu, Jinqi; Chen, Dunlu; Pinto, Shirly; Balkovec, James M; Devita, Robert J; Marsh, Donald J; Castro-Perez, Jose M; Strack, Alison; Johns, Douglas G; Previs, Stephen F; Hubbard, Brian K; Roddy, Thomas P

    2011-06-01

    The use of stable isotopically labeled substrates and analysis by mass spectrometry have provided substantial insight into rates of synthesis, disposition, and utilization of lipids in vivo. The information to be gained from such studies is of particular benefit to therapeutic research where the underlying causes of disease may be related to the production and utilization of lipids. When studying biology through the use of isotope tracers, care must be exercised in interpreting the data to ensure that any response observed can truly be interpreted as biological and not as an artifact of the experimental design or a dilutional effect on the isotope. We studied the effects of dosing route and tracer concentration on the mass isotopomer distribution profile as well as the action of selective inhibitors of microsomal tri-glyceride transfer protein (MTP) in mice and diacylglycerol acyltransferase 1 (DGAT1) in nonhuman primates, using a stable-isotopically labeled approach. Subjects were treated with inhibitor and subsequently given a dose of uniformly ¹³C-labeled oleic acid. Samples were analyzed using a rapid LC-MS technique, allowing the effects of the intervention on the assembly and disposition of triglycerides, cholesteryl esters, and phospholipids to be determined in a single 3 min run from just 10 ?l of plasma. PMID:21415123

  15. Combining Capillary Electrophoresis Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry and Stable Isotopic Labeling Techniques for Comparative Crustacean Peptidomics

    PubMed Central

    Wang, Junhua; Zhang, Yuzhuo; Xiang, Feng; Zhang, Zichuan; Li, Lingjun

    2010-01-01

    Herein we describe a sensitive and straightforward off-line capillary electrophoresis (CE) matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) interface in conjunction with stable isotopic labeling (SIL) technique for comparative neuropeptidomic analysis in crustacean model organisms. Two SIL schemes, including a binary H/D formaldehyde labeling technique and novel, laboratory-developed multiplexed dimethylated leucine-based isobaric tagging reagents, have been evaluated in these proof-of-concept experiments. We employ these isotopic labeling techniques in conjunction with CE-MALDI MS for quantitative peptidomic analyses of the pericardial organs isolated from two crustacean species, the European green crab Carcinus maenas and the blue crab Callinectes sapidus. Isotopically labeled peptide pairs are found to co-migrate in CE fractions and quantitative changes in relative abundances of peptide pairs are obtained by comparing peak intensities of respective peptide pairs. Several neuropeptide families exhibit changes in response to salinity stress, suggesting potential physiological functions of these signaling peptides. PMID:20334868

  16. Simultaneous determination of seven ?2-agonists in human and bovine urine by isotope dilution liquid chromatography-tandem mass spectrometry using compound-specific minimally (13)C-labelled analogues.

    PubMed

    González-Antuña, Ana; Rodríguez-González, Pablo; Centineo, Giuseppe; García Alonso, J Ignacio

    2014-10-29

    Seven ?2-agonist (clenproperol, clenbuterol, salbutamol, bronbuterol, ractopamine, clenpenterol and clencyclohexerol) were determined simultaneously in human and bovine urine by isotope dilution LC-ESI-MS/MS in a triple quadrupole instrument. The method is based on the application of multiple linear regression in combination with compound-specific minimally (13)C-labelled analogues. Additionally, the increase of the bandpass of the first quadrupole during the selected reaction monitoring (SRM) measurement procedure allowed the simultaneous quantification of the seven compounds at sub ngg(-1) levels in a single chromatogram without resorting to a methodological calibration graph. Recovery values at concentration levels between 5.0 and 0.05ngg(-1) ranged from 95 to 110% in fortified bovine urine and from 91 to 108% in human urine, with relative standard deviations lower than 5% except for salbutamol and ractopamine. The proposed methodology was validated by analyzing the certified reference material BCR-503 (lyophilized bovine urine) certified for clenbuterol and salbutamol. The limits of detection (LOD) for a sample volume of 10mL of both human and bovine urine was found to be lower than 0.012ngg(-1) for all compounds, except to salbutamol in bovine urine which was of 0.029ngg(-1). The use of compound-specific isotopically labelled analogues minimally labelled in (13)C minimized the occurrence of isotope effects and corrected for matrix effects during ESI ionization and can be efficiently applied for the quantification of ultra-trace concentrations of ?2-agonists in human and bovine urine. PMID:25468499

  17. Carbon Isotope Discrimination and Other Surrogates of Water Use Efficiency for Tomato Under Various Soil Moistures

    Microsoft Academic Search

    Surya P. Bhattarai; David J. Midmore

    2007-01-01

    Carbon isotope discrimination (?‰) is negatively correlated with water use efficiency (WUE) in several C3 species and was proposed as a selection criterion for improving WUE. Tomato (Lycopersion esculentumL.), cv. Improved Apollo, was exposed to soil moisture levels, saturated, field capacity (FC) and deficit soil moisture conditions, in a container experiment in a screenhouse. The objective was to test for:

  18. Assessing water-use-efficiency from stable isotopes and eddy covariance data

    NASA Astrophysics Data System (ADS)

    Knohl, A.; Barthel, M.; Kutsch, W. L.; Salmon, Y.; Sturm, P.

    2009-04-01

    The water and carbon cycles in terrestrial ecosystems play an essential role in the earth system by modifying the atmospheric carbon dioxide and water vapor composition and by partitioning energy at the land surface. Carbon uptake during photosynthesis and water release during transpiration are closely linked through stomatal conductance. The efficiency of carbon uptake versus water loss is called water-use-efficiency and is a key factor for agricultural irrigation practices and species competition in water limited ecosystems. Here we review various concepts to assess water-use-efficiency at plant and ecosystem scale and present results from different biomes. We will show that inherent water-use-efficiency (estimated from eddy covariance measurements as the ratio of gross primary productivity over evapotranspiration times vapor pressure deficit) is a fairly conservative ecosystem property and only changes under sever drought conditions. Another approach to assess water-use-efficiency is the stable carbon isotope composition (^13C) of plant material. Typically, in a first approximation a simply linear relationship between leaf ^13C and intrinsic water-use-efficiency (the ratio of assimilation to stomata conductance) is assumed. More recent studies, however, show that various factors influence leaf ^13C independently of the exchange through the stomata leading to incorrect water-use-efficiency estimates. Based on laboratory and field experiments using stable carbon isotopes in various plant components as well as recently developed laser spectroscopy for continuous stable isotope measurements we discuss possibilities and limitations of using stable carbon isotopes to approximate plant water-use-efficiency.

  19. Efficient Analysis of Mass Spectrometry Data Using the Isotope Wavelet

    SciTech Connect

    Hussong, Rene; Hildebrandt, Andreas [Center for Bioinformatics, Computer Science Department, Saarland University, 66041 Saarbruecken (Germany); Tholey, Andreas [Center for Bioinformatics, Institute of Biochemical Engineering, Functional Proteomics Group, Saarland University, 66041 Saarbruecken (Germany)

    2007-09-18

    Mass spectrometry (MS) has become today's de-facto standard for high-throughput analysis in proteomics research. Its applications range from toxicity analysis to MS-based diagnostics. Often, the time spent on the MS experiment itself is significantly less than the time necessary to interpret the measured signals, since the amount of data can easily exceed several gigabytes. In addition, automated analysis is hampered by baseline artifacts, chemical as well as electrical noise, and an irregular spacing of data points. Thus, filtering techniques originating from signal and image analysis are commonly employed to address these problems. Unfortunately, smoothing, base-line reduction, and in particular a resampling of data points can affect important characteristics of the experimental signal. To overcome these problems, we propose a new family of wavelet functions based on the isotope wavelet, which is hand-tailored for the analysis of mass spectrometry data. The resulting technique is theoretically well-founded and compares very well with standard peak picking tools, since it is highly robust against noise spoiling the data, but at the same time sufficiently sensitive to detect even low-abundant peptides.

  20. Quantitative, Time-Resolved Proteomic Analysis by Combining Bioorthogonal Noncanonical Amino Acid Tagging and Pulsed Stable Isotope Labeling by Amino Acids in Cell Culture*

    PubMed Central

    Bagert, John D.; Xie, Yushu J.; Sweredoski, Michael J.; Qi, Yutao; Hess, Sonja; Schuman, Erin M.; Tirrell, David A.

    2014-01-01

    An approach to proteomic analysis that combines bioorthogonal noncanonical amino acid tagging (BONCAT) and pulsed stable isotope labeling with amino acids in cell culture (pSILAC) provides accurate quantitative information about rates of cellular protein synthesis on time scales of minutes. The method is capable of quantifying 1400 proteins produced by HeLa cells during a 30 min interval, a time scale that is inaccessible to isotope labeling techniques alone. Potential artifacts in protein quantification can be reduced to insignificant levels by limiting the extent of noncanonical amino acid tagging. We find no evidence for artifacts in protein identification in experiments that combine the BONCAT and pSILAC methods. PMID:24563536

  1. Residue-Specific Structural Kinetics of Proteins through the Union of Isotope Labeling, Mid-IR Pulse Shaping, and Coherent 2D IR Spectroscopy

    PubMed Central

    Middleton, Chris T.; Woys, Ann Marie; Mukherjee, Sudipta S.; Zanni, Martin T.

    2010-01-01

    We describe a methodology for studying protein kinetics using a rapid-scan technology for collecting 2D IR spectra. In conjunction with isotope labeling, 2D IR spectroscopy is able to probe the secondary structure and environment of individual residues in polypeptides and proteins. It is particularly useful for membrane and aggregate proteins. Our rapid-scan technology relies on a mid-IR pulse shaper that computer generates the pulse shapes, much like in an NMR spectrometer. With this device, data collection is faster, easier, and more accurate. We describe our 2D IR spectrometer, as well as protocols for 13C=18O isotope labeling, and then illustrate the technique with an application to the aggregation of the human islet amyloid polypeptide form type 2 diabetes. PMID:20472067

  2. Relative quantitation of glycans using stable isotopic labels 1-(d0/d5) phenyl-3-methyl-5-pyrazolone by mass spectrometry.

    PubMed

    Zhang, Ping; Zhang, Ying; Xue, Xiangdong; Wang, Chenjian; Wang, Zhongfu; Huang, Linjuan

    2011-11-01

    A deuterium reagent, 1-(d5) phenyl-3-methyl-5-pyrazolone (d5-PMP), has been synthesized and used for relative quantitative analysis of oligosaccharides by mass spectrometry (MS) using d0/d5-PMP stable isotopic labeling. Previously reported permethylation-based isotopic labels generate variable mass differences, and reductive amination-based isotopic labels cause a loss of some acid-labile groups in carbohydrates. In contrast, d0/d5-PMP stable isotopic labeling is performed at the reducing end of glycans under basic conditions without desialylation, and the mass difference (?m=10 Da) between the heavy form (d5-PMP derivative) and light form (d0-PMP derivative) of each glycan is invariable. When the two derivative forms of a glycan are mixed in equimolar amounts, a pair of peaks with a 10-Da mass differences is observed in the MS profile. The difference at relative intensity between the d0- and d5-PMP derivatives reflects the difference in quantity of glycans in two samples, making it possible to carry out both qualitative and relative quantitative analyses of glycans in glycomic studies. Application of this method on DP(2) to DP(6) maltodextrin oligosaccharides and N-linked glycans released from ribonuclease B and bovine fetuin demonstrates a 10-fold relative quantitative dynamic range, a satisfying reproducibility (coefficient of variation [CV] ? 8.34%), and good accuracy (relative error [RE] ? 5.1%) of the method. The suggested technique has been successfully applied for comparative quantitative analysis of free oligosaccharides in human and bovine milk. PMID:21803021

  3. A novel method to measure isotopic labeled gas-phase nitrous acid (HO15NO) in biogeochemical studies

    NASA Astrophysics Data System (ADS)

    Wu, Dianming; Kampf, Christopher; Pöschl, Ulrich; Oswald, Robert; Cui, Junfang; Ermel, Michael; Hu, Chunsheng; Trebs, Ivonne; Sörgel, Matthias

    2014-05-01

    We developed a new method (gas-phase stripping-derivatization coupled to LC-MS) to measure the 15N atom percent excess (APE) of HONO in the gas-phase. Gaseous HONO is quantitatively collected and transferred to an azo dye by the well-known Griess reaction in the Long Path Absorption Photometer (LOPAP). The reaction solutions containing the dye are collected at the outflow of the LOPAP, purified by solid-phase extraction and analyzed using high performance liquid chromatography coupled to mass spectrometry (HPLC-MS). The unlabeled azo dye (C18H19O2N5S) with a monoisotopic molecular mass of 369.41 g mol-1 can be detected as its protonated molecular ion ([M+H+], M) by HPLC-MS at a retention time of 2.8 min. Due to the natural isotope distribution M + 0, M + 1, M + 2, and M + 3 ions were considered for the calculation of the 15N APE. The optimal working range was found to be between 20 and 50% for the 15N/14N ratio. The optimum pH and solvents for extraction by SPE and potential interferences are discussed. The method has been applied for the measurement of HO15NO emissions from soil in a dynamic chamber with and without spiking 15N labeled urea. Our results confirm biogenic HONO emissions from soil as HO15NO was measured after addition of 15N urea.

  4. Live-cell vibrational imaging of choline metabolites by stimulated Raman scattering coupled with isotope-based metabolic labeling.

    PubMed

    Hu, Fanghao; Wei, Lu; Zheng, Chaogu; Shen, Yihui; Min, Wei

    2014-05-21

    Choline is a small molecule that occupies a key position in the biochemistry of all living organisms. Recent studies have strongly implicated choline metabolites in cancer, atherosclerosis and nervous system development. To detect choline and its metabolites, existing physical methods such as magnetic resonance spectroscopy and positron emission tomography are often limited by the poor spatial resolution and substantial radiation dose. Fluorescence imaging, although with submicrometer resolution, requires introduction of bulky fluorophores and thus is difficult in labeling the small choline molecule. By combining the emerging bond-selective stimulated Raman scattering microscopy with metabolic incorporation of deuterated choline, herein we have achieved high resolution imaging of choline-containing metabolites in living mammalian cell lines, primary hippocampal neurons and the multicellular organism C. elegans. Different subcellular distributions of choline metabolites are observed between cancer cells and non-cancer cells, which may reveal a functional difference in the choline metabolism and lipid-mediated signaling events. In neurons, choline incorporation is visualized within both soma and neurites, where choline metabolites are more evenly distributed compared to proteins. Furthermore, choline localization is also observed in the pharynx region of C. elegans larvae, consistent with its organogenesis mechanism. These applications demonstrate the potential of isotope-based stimulated Raman scattering microscopy for future choline-related disease detection and development monitoring in vivo. PMID:24555181

  5. Tracing nitrogenous disinfection byproducts after medium pressure UV water treatment by stable isotope labeling and high resolution mass spectrometry.

    PubMed

    Kolkman, Annemieke; Martijn, Bram J; Vughs, Dennis; Baken, Kirsten A; van Wezel, Annemarie P

    2015-04-01

    Advanced oxidation processes are important barriers for organic micropollutants (e.g., pharmaceuticals, pesticides) in (drinking) water treatment. Studies indicate that medium pressure (MP) UV/H2O2 treatment leads to a positive response in Ames mutagenicity tests, which is then removed after granulated activated carbon (GAC) filtration. The formed potentially mutagenic substances were hitherto not identified and may result from the reaction of photolysis products of nitrate with (photolysis products of) natural organic material (NOM). In this study we present an innovative approach to trace the formation of disinfection byproducts (DBPs) of MP UV water treatment, based on stable isotope labeled nitrate combined with high resolution mass spectrometry. It was shown that after MP UV treatment of artificial water containing NOM and nitrate, multiple nitrogen containing substances were formed. In total 84 N-DBPs were detected at individual concentrations between 1 to 135 ng/L bentazon-d6 equivalents, with a summed concentration of 1.2 ?g/L bentazon-d6 equivalents. The chemical structures of three byproducts were confirmed. Screening for the 84 N-DBPs in water samples from a full-scale drinking water treatment plant based on MP UV/H2O2 treatment showed that 22 of the N-DBPs found in artificial water were also detected in real water samples. PMID:25760315

  6. Live-cell vibrational imaging of choline metabolites by stimulated Raman scattering coupled with isotope-based metabolic labeling

    PubMed Central

    Hu, Fanghao; Wei, Lu; Zheng, Chaogu; Shen, Yihui

    2014-01-01

    Choline is a small molecule that occupies a key position in the biochemistry of all living organisms. Recent studies have strongly implicated choline metabolites in cancer, atherosclerosis and nervous system development. To detect choline and its metabolites, existing physical methods such as magnetic resonance spectroscopy and positron emission tomography, are often limited by the poor spatial resolution and substantial radiation dose. Fluorescence imaging, although with submicrometer resolution, requires introduction of bulky fluorophores and thus is difficult in labeling the small choline molecule. By combining the emerging bond-selective stimulated Raman scattering microscopy with metabolic incorporation of deuterated choline, herein we have achieved high resolution imaging of choline-containing metabolites in living mammalian cell lines, primary hippocampal neurons and multicellular organism C. elegans. Different subcellular distributions of choline metabolites are observed between cancer cells and non-cancer cells, which may reveal functional difference in the choline metabolism and lipid-mediated signaling events. In neurons, choline incorporation is visualized within both soma and neurites, where choline metabolites are more evenly distributed compared to the protein. Furthermore, choline localization is also observed in the pharynx region of C. elegans larvae, consistent with its organogenesis mechanism. These applications demonstrate the potential of isotope-based stimulated Raman scattering microscopy for future choline-related disease detection and development monitoring in vivo. PMID:24555181

  7. Synthesis and Use of Stable-Isotope-Labeled Internal Standards for Quantification of Phosphorylated Metabolites by LC-MS/MS.

    PubMed

    Arrivault, Stéphanie; Guenther, Manuela; Fry, Stephen C; Fuenfgeld, Maximilian M F F; Veyel, Daniel; Mettler-Altmann, Tabea; Stitt, Mark; Lunn, John E

    2015-07-01

    Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is a highly specific and sensitive technique for measuring metabolites. However, coeluting components in tissue extracts can interfere with ionization at the interface of the LC and MS/MS phases, causing under- or overestimation of metabolite concentrations. Spiking of samples with known amounts of stable-isotope-labeled internal standards (SIL-IS) allows measurements of the corresponding metabolites to be corrected for such matrix effects. We describe criteria for selection of suitable SIL-IS and report the enzymatic synthesis and purification of nine SIL-IS for hexose-, pentose-, and triose-phosphates, UDP-glucose, and adenosine monophosphate (AMP). Along with commercially available SIL-IS for seven other metabolites, these were validated by LC-MS/MS analyses of extracts from leaves, nonphotosynthetic plant tissues, mouse liver, and cells of Chlamydomonas reinhardtii, Escherichia coli and baker's yeast (Saccharomyces cerevisiae). With only a few exceptions, spiking with SIL-IS significantly improved the reproducibility of LC-MS/MS-based metabolite measurements across a wide range of extract dilutions, indicating effective correction for matrix effects by this approach. With use of SIL-IS to correct for matrix effects, LC-MS/MS offers unprecedented scope for reliable determination of photosynthetic and respiratory intermediates in a diverse range of organisms. PMID:26010726

  8. Influence of 13C isotopic labeling location of 13C DNP of acetate using TEMPO free radical

    NASA Astrophysics Data System (ADS)

    Parish, Christopher; Niedbalski, Peter; Lumata, Lloyd

    2015-03-01

    Dynamic nuclear polarization (DNP) via the dissolution method enhances the liquid-state magnetic resonance (NMR or MRI) signals of insensitive nuclear spins by at least 10,000-fold. The basis for all these signal enhancements at room temperature is the polarization transfer from the electrons to nuclear spins at cryogenic temperature and high magnetic field. In this work, we have studied the influence of the location of 13C isotopic labeling on the DNP of sodium acetate at 3.35 T and 1.4 K using a wide ESR linewidth free radical 4-oxo-TEMPO. The carbonyl [1-13C]acetate spins produced a polarization level that is almost twice that of the methyl [2-13C]acetate spins. On the other hand, the polarization of the methyl 13C spins doubled to reach the level of [1-13C]acetate when the methyl group was deuterated. Meanwhile, the solid-state nuclear relaxation of these samples are the same and do not correlate with the polarization levels. These behavior implies that the nuclear relaxation for these samples is dominated by the contribution from the free radicals and the polarization levels can be explained by a thermodynamic picture of DNP.

  9. Automated resonance assignment of the 21 kDa stereo-array isotope labeled thioldisulfide oxidoreductase DsbA

    NASA Astrophysics Data System (ADS)

    Schmidt, Elena; Ikeya, Teppei; Takeda, Mitsuhiro; Löhr, Frank; Buchner, Lena; Ito, Yutaka; Kainosho, Masatsune; Güntert, Peter

    2014-12-01

    The automated chemical shift assignment algorithm FLYA has been extended for use with stereo-array isotope labeled (SAIL) proteins to determine the sequence-specific resonance assignments of large proteins. Here we present the assignment of the backbone and sidechain chemical shifts of the 21 kDa thioldisulfide oxidoreductase DsbA from Escherichia coli that were determined with the SAIL-FLYA algorithm in conjunction with automated peak picking. No manual corrections of peak lists or assignments were applied. The assignments agreed with manually determined reference assignments in 95.4% of the cases if 16 input spectra were used, 94.1% if only 3D 13C/15N-resolved NOESY, CBCA(CO)NH, and 2D [13C/15N,1H]-HSQC were used, and 86.8% if exclusively 3D 13C/15N-resolved NOESY spectra were used. Considering only the assignments that are classified as reliable by the SAIL-FLYA algorithm, the degrees of agreement increased to 97.5%, 96.5%, and 94.2%, respectively. With our approach it is thus possible to automatically obtain almost complete and correct assignments of proteins larger than 20 kDa.

  10. Understanding cellular metabolism using stable isotopic labeling, metabolic flux analysis and kinetic modeling

    Microsoft Academic Search

    Neelanjan Sengupta

    2011-01-01

    There is focus on increasing scent production in flowers by metabolic engineering due to its broad impact in the perfume and horticulture industry. Metabolic engineering of flowers to enhance the scent production can be done in an efficient and targeted manner, if there is mechanistic information about the kinetics and regulation of the pathways involved in scent production. Thus a

  11. Stable Isotope Labeled Tracers for Metabolic Pathway Elucidation by GC-MS and FT-MS

    PubMed Central

    Higashi, Richard M.; Fan, Teresa W-M.; Lorkiewicz, Pawel K.; Moseley, Hunter N.B.; Lane, Andrew N.

    2015-01-01

    Advances in analytical methodologies, principally nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS), over the last decade have made large-scale analysis of the human metabolome a reality. This is leading to the reawakening of the importance of metabolism in human diseases, particularly widespread metabolic diseases such as cancer, diabetes, and obesity. Emerging NMR and MS atom-tracking technologies and informatics is poised to revolutionize metabolomics-based research because they deliver the high information throughput (HIT) that is needed for deciphering systems biochemistry. In particular, Stable Isotope Resolved Metabolomics (SIRM) enables unambiguous tracking of individual atoms through compartmentalized metabolic networks, in a wide range of experimental systems, including human subjects. MS offers a wide range of initial capital outlay and operating costs, ranging from gas-chromatography (GC) MS affordable by many individual laboratories, to the HIT-supporting Fourier-transform (FT) class of MS that rivals NMR in cost and infrastructure support. This chapter will focus on sample preparation, instrument, and data processing procedures for these two extremes of MS instrumentation used in SIRM. PMID:25270929

  12. Universal primers for fluorescent labelling of PCR fragments--an efficient and cost-effective approach to genotyping by fluorescence.

    PubMed

    Blacket, M J; Robin, C; Good, R T; Lee, S F; Miller, A D

    2012-05-01

    Directly labelling locus-specific primers for microsatellite analysis is expensive and a common limitation to small-budget molecular ecology projects. More cost-effective end-labelling of PCR products can be achieved through a three primer PCR approach, involving a fluorescently labelled universal primer in combination with modified locus-specific primers with 5' universal primer sequence tails. This technique has been widely used but has been limited largely due to a lack of available universal primers suitable for co-amplifying large numbers of size overlapping loci and without requiring locus-specific PCR conditions to be modified. In this study, we report a suite of four high-performance universal primers that can be employed in a three primer PCR approach for efficient and cost-effective fluorescent end-labelling of PCR fragments. Amplification efficiency is maximized owing to high universal primer Tm values (approximately 60+?°C) that enhance primer versatility and enable higher annealing temperatures to be employed compared with commonly used universal primers such as M13. We demonstrate that these universal primers can be combined with multiple fluorophores to co-amplify multiple loci efficiently via multiplex PCR. This method provides a level of multiplexing and PCR efficiency similar to microsatellite fluorescent detection assays using directly labelled primers while dramatically reducing project costs. Primer performance is tested using several alternative PCR strategies that involve both single and multiple fluorophores in single and multiplex PCR across a wide range of taxa. PMID:22268566

  13. Structure and vibrational dynamics of isotopically labeled lithium borohydride using neutron diffraction and spectroscopy

    SciTech Connect

    Hartman, Michael R. [NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899-8562 (United States)], E-mail: mike.hartman@oregonstate.edu; Rush, John J. [NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899-8562 (United States); Udovic, Terrence J. [NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899-8562 (United States); Bowman, Robert C. [Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109 (United States); Hwang, Son-Jong [Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 (United States)

    2007-04-15

    The crystalline structure of a {sup 7}Li and {sup 11}B labeled lithium borohydride has been investigated using neutron powder diffraction at 3.5, 360, and 400 K. The B-H bond lengths and H-B-H angles for the [BH{sub 4}]{sup -} tetrahedra indicated that the tetrahedra maintained a nearly ideal configuration throughout the temperature range investigated. The atomic displacement parameters at 360 K suggest that the [BH{sub 4}]{sup -} tetrahedra become increasingly disordered as a result of large amplitude librational and reorientational motions as the orthorhombic to hexagonal phase transition (T=384 K) is approached. In the high-temperature hexagonal phase, the [BH{sub 4}]{sup -} tetrahedra displayed extreme disorder about the trigonal axis along which they are aligned. Neutron vibrational spectroscopy data were collected at 5 K over an energy range of 10-170 meV, and were found to be in good agreement with prior Raman and low-resolution neutron spectroscopy studies. - Graphical abstract: The structure of {sup 7}Li{sup 11}BH{sub 4} in the low-temperature Pnma phase, including atomic displacement ellipsoids, at 3.5 K.

  14. Estimation efficiency and statistical power in arterial spin labeling fMRI

    PubMed Central

    Mumford, Jeanette A.; Hernandez-Garcia, Luis; Lee, Gregory R.; Nichols, Thomas E.

    2009-01-01

    Arterial spin labeling (ASL) data are typically differenced, sometimes after interpolation, as part of preprocessing before statistical analysis in fMRI. While this process can reduce the number of time points by half, it simplifies the subsequent signal and noise models (i.e., smoothed box-car predictors and white noise). In this paper, we argue that ASL data are best viewed in the same data analytic framework as BOLD fMRI data, in that all scans are modeled and colored noise is accommodated. The data are not differenced, but the control/label effect is implicitly built into the model. While the models using differenced data may seem easier to implement, we show that differencing models fit with ordinary least squares either produce biased estimates of the standard errors or suffer from a loss in efficiency. The main disadvantage to our approach is that non-white noise must be modeled in order to yield accurate standard errors, however, this is a standard problem that has been solved for BOLD data, and the very same software can be used to account for such autocorrelated noise. PMID:16860577

  15. 15N- and 13C-labeled media from Anabaena sp. for universal isotopic labeling of bacteriocins: NMR resonance assignments of leucocin A from Leuconostoc gelidum and nisin A from Lactococcus lactis.

    PubMed

    Sailer, M; Helms, G L; Henkel, T; Niemczura, W P; Stiles, M E; Vederas, J C

    1993-01-12

    A procedure for universal 13C and/or 15N labeling of microbial peptides which are produced by fermentation in complex media and its application to two food-preserving bacteriocins from lactic acid bacteria are described. Isotopic enrichment of nisin A (from Lactococcus lactis) and of leucocin A (from Leuconostoc gelidum) is readily achieved using a soluble peptone derived from enzymatic hydrolysis (pepsin and chymopapain) of Anabaena sp. ATCC 27899 cells grown on sodium [13C]bicarbonate and/or sodium [15N]nitrate as sole carbon and nitrogen sources. Combustion of this peptone followed by mass spectrometric analysis indicates that 45% of the labeled carbon and 65% of the labeled nitrogen added to the Anabaena culture are utilized in the amino acids of the peptone and that the isotopic purity for both 13C and 15N remains essentially unchanged provided that the cells are grown under argon atmosphere to avoid nitrogen fixation. NMR analyses of [13C,15N]nisin A using H[13C]MQC, H[13C]MBC, 2D INADEQUATE, and H[15N]MQC techniques confirmed 1H spectral assignments previously reported for unlabeled material and readily provided carbon and nitrogen assignments. The results show that universal but not uniform 13C labeling occurs unless the nutrient source is completely isotopically enriched at high level (> or = 98%) because of differential levels of de novo amino acid synthesis. Application of NMR techniques such as TOCSY, DQF-COSY, NOESY, and H[13C]MQC to unlabeled and [13C]leucocin A afforded the complete 1H and 13C assignment. Leucocin A does not possess clearly defined conformational structure in DMSO or aqueous solutions. PMID:8418850

  16. Stable isotope labeling confirms mixotrophic nature of streamer biofilm communities at alkaline hot springs.

    PubMed

    Schubotz, Florence; Hays, Lindsay E; Meyer-Dombard, D'Arcy R; Gillespie, Aimee; Shock, Everett L; Summons, Roger E

    2015-01-01

    Streamer biofilm communities (SBC) are often observed within chemosynthetic zones of Yellowstone hot spring outflow channels, where temperatures exceed those conducive to photosynthesis. Nearest the hydrothermal source (75-88°C) SBC comprise thermophilic Archaea and Bacteria, often mixed communities including Desulfurococcales and uncultured Crenarchaeota, as well as Aquificae and Thermus, each carrying diagnostic membrane lipid biomarkers. We tested the hypothesis that SBC can alternate their metabolism between autotrophy and heterotrophy depending on substrate availability. Feeding experiments were performed at two alkaline hot springs in Yellowstone National Park: Octopus Spring and "Bison Pool," using various (13)C-labeled substrates (bicarbonate, formate, acetate, and glucose) to determine the relative uptake of these different carbon sources. Highest (13)C uptake, at both sites, was from acetate into almost all bacterial fatty acids, particularly into methyl-branched C15, C17 and C19 fatty acids that are diagnostic for Thermus/Meiothermus, and some Firmicutes as well as into universally common C16:0 and C18:0 fatty acids. (13)C-glucose showed a similar, but a 10-30 times lower uptake across most fatty acids. (13)C-bicarbonate uptake, signifying the presence of autotrophic communities was only significant at "Bison Pool" and was observed predominantly in non-specific saturated C16, C18, C20, and C22 fatty acids. Incorporation of (13)C-formate occurred only at very low rates at "Bison Pool" and was almost undetectable at Octopus Spring, suggesting that formate is not an important carbon source for SBC. (13)C-uptake into archaeal lipids occurred predominantly with (13)C-acetate, suggesting also that archaeal communities at both springs have primarily heterotrophic carbon assimilation pathways. We hypothesize that these communities are energy-limited and predominantly nurtured by input of exogenous organic material, with only a small fraction being sustained by autotrophic growth. PMID:25699032

  17. Stable isotope labeling confirms mixotrophic nature of streamer biofilm communities at alkaline hot springs

    PubMed Central

    Schubotz, Florence; Hays, Lindsay E.; Meyer-Dombard, D'Arcy R.; Gillespie, Aimee; Shock, Everett L.; Summons, Roger E.

    2015-01-01

    Streamer biofilm communities (SBC) are often observed within chemosynthetic zones of Yellowstone hot spring outflow channels, where temperatures exceed those conducive to photosynthesis. Nearest the hydrothermal source (75–88°C) SBC comprise thermophilic Archaea and Bacteria, often mixed communities including Desulfurococcales and uncultured Crenarchaeota, as well as Aquificae and Thermus, each carrying diagnostic membrane lipid biomarkers. We tested the hypothesis that SBC can alternate their metabolism between autotrophy and heterotrophy depending on substrate availability. Feeding experiments were performed at two alkaline hot springs in Yellowstone National Park: Octopus Spring and “Bison Pool,” using various 13C-labeled substrates (bicarbonate, formate, acetate, and glucose) to determine the relative uptake of these different carbon sources. Highest 13C uptake, at both sites, was from acetate into almost all bacterial fatty acids, particularly into methyl-branched C15, C17 and C19 fatty acids that are diagnostic for Thermus/Meiothermus, and some Firmicutes as well as into universally common C16:0 and C18:0 fatty acids. 13C-glucose showed a similar, but a 10–30 times lower uptake across most fatty acids. 13C-bicarbonate uptake, signifying the presence of autotrophic communities was only significant at “Bison Pool” and was observed predominantly in non-specific saturated C16, C18, C20, and C22 fatty acids. Incorporation of 13C-formate occurred only at very low rates at “Bison Pool” and was almost undetectable at Octopus Spring, suggesting that formate is not an important carbon source for SBC. 13C-uptake into archaeal lipids occurred predominantly with 13C-acetate, suggesting also that archaeal communities at both springs have primarily heterotrophic carbon assimilation pathways. We hypothesize that these communities are energy-limited and predominantly nurtured by input of exogenous organic material, with only a small fraction being sustained by autotrophic growth. PMID:25699032

  18. An optimal defense strategy for phenolic glycoside production in Populus trichocarpa--isotope labeling demonstrates secondary metabolite production in growing leaves.

    PubMed

    Massad, Tara Joy; Trumbore, Susan E; Ganbat, Gantsetseg; Reichelt, Michael; Unsicker, Sybille; Boeckler, Andreas; Gleixner, Gerd; Gershenzon, Jonathan; Ruehlow, Steffen

    2014-07-01

    Large amounts of carbon are required for plant growth, but young, growing tissues often also have high concentrations of defensive secondary metabolites. Plants' capacity to allocate resources to growth and defense is addressed by the growth-differentiation balance hypothesis and the optimal defense hypothesis, which make contrasting predictions. Isotope labeling can demonstrate whether defense compounds are synthesized from stored or newly fixed carbon, allowing a detailed examination of these hypotheses. Populus trichocarpa saplings were pulse-labeled with 13CO2 at the beginning and end of a growing season, and the 13C signatures of phenolic glycosides (salicinoids), sugars, bulk tissue, and respired CO2 were traced over time. Half of the saplings were also subjected to mechanical damage. Populus trichocarpa followed an optimal defense strategy, investing 13C in salicinoids in expanding leaves directly after labeling. Salicinoids turned over quickly, and their production continued throughout the season. Salicin was induced by early-season damage, further demonstrating optimal defense. Salicinoids appear to be of great value to P. trichocarpa, as they command new C both early and late in the growing season, but their fitness benefits require further study. Export of salicinoids between tissues and biochemical pathways enabling induction also needs research. Nonetheless, the investigation of defense production afforded by isotope labeling lends new insights into plants' ability to grow and defend simultaneously. PMID:24739022

  19. Non-homogeneity of isotopic labelling in 15N gas flux studies: theory, some observations and possible lessons

    NASA Astrophysics Data System (ADS)

    Well, Reinhard; Buchen, Caroline; Deppe, Marianna; Eschenbach, Wolfram; Gattinger, Andreas; Giesemann, Anette; Krause, Hans-Martin; Lewicka-Szczebak, Dominika

    2015-04-01

    Quantifying dinitrogen (N2) and nitrous oxide (N2O) fluxes from different soil N pools and processes can be accomplished using the 15N tracer technique but this is subject to four different sources of bias (i. - iv.). This approach includes 15N labelling of selected N pools in soil and subsequent isotope analysis of all relevant N pools as well as of gas samples from enclosures, i.e. mixtures of soil-derived and atmospheric N2 and N2O. Depending on the processes of interest, there may be 15N labelling of one or several N pools, were several labelling treatment are needed in the latter case (e.g. Müller et al., 2004). Measuring pool-derived N2 or N2O has been shown to include two calculation problems, (i.) arising from multiple pools (e.g. Arah, 1992) and (ii.) dealing with the non-random distribution of N2 and N2O mole masses (Hauck et al., 1958). Non-randomness can be solved if m/z 28, 29 and 30 are correctly analysed and the 15N enrichment of one (to distinguish two pools, i.e. soil and atmosphere) or two pools (in case of three pools) is known (Spott & Stange, 2008). Moreover (iii.), NO3- pools generating N2 and N2O via denitrification can be identical or different, e.g. if N2O evolved from higher enriched NO3- in deeper soil was more reduced to N2 compared to N2O evolved from N2O from shallow soil with lower enrichment, or vice versa. Apportioning N2O fluxes to NH4+ (nitrification and/or nitrifier denitrification) and NO3- (denitrification) is often conducted by NO3-labeling, measuring ?15N of emitted N2O and applying mixing equations were the measured 15N enrichment of NH4+and NO3-pool is used. However, this assumes that the average 15N enrichment of NH4+and NO3-in the soil is identical to the enrichment in the active soil domain producing N2 and/or N2O. Violation of this precondition must lead to bias in source apportionment (iv.), but to our knowledge this has not been investigated until now. Here we present conceptual models and model calculations addressing cases iii. and iv.. Furthermore we present some experimental data illustrating this. These include two data sets from denitrification experiments exhibiting substantial deviations in 15N enrichment between the N pools producing N2 and N2O. Moreover, results from a lab incubation study to quantify NH4+-derived N2O with increasing NH4+ amendment under conditions favouring nitrification are shown, were non-labelled NH4+ was added together with 15N labelled NO3-. Here we found large deviations between the 15N enrichment of NO3- in extracted soil water and the 15N enrichment of the labelled N pool as calculated from N2O isotopologues (Bergsma et al., 2001). We think that this reflects type iv. bias, probably because enrichment of NO3- in anoxic micro-sites was less diluted by non-labelled NO3- from nitrification compared to NO3- in oxic zones. Our data analysis provides a means to overcome bias iv. and thus to obtain correct source apportionment. References: Arah, J.R.M. (1992): Soil Sci. Soc. Am. J. 56, 795 - 800, 1992. Bergsma, T. et al. (2001): Env. Sci. & Technol. 35(21): 4307-4312. Hauck, R.D., et al.(1958): Soil Science 86, 287 - 291, 1958. Lewicka-Szczebak, D. et al.(2013): Rapid Comm. Mass Spectrom., 27 1548-1558. Müller, C. et al. (2004): Soil Biol. Biochem. 36(4): 619-632. Mulvaney, R.L.(1984):. Soil Sci. Soc. Am. J. 48:690 - 692. Spott, O, et al.. (2006): Rapid Comm. Mass Spectrom., 20: 3267-3274. Spott, O. and C. F. Stange (2007): Rapid Comm. Mass Spectrom., 21: 2398-2406.

  20. Nonuniform isotope patterns produced by collision-induced dissociation of homogeneously labeled ubiquitin: implications for spatially resolved hydrogen/deuterium exchange ESI-MS studies.

    PubMed

    Ferguson, Peter L; Konermann, Lars

    2008-06-01

    There is an ongoing debate whether collision-induced dissociation (CID) of electrosprayed proteins after solution-phase hydrogen/deuterium exchange (HDX) is a viable approach for determining spatially resolved deuteration patterns. This work explores the use of two methods, source-CID and hexapole tandem mass spectrometry (MS/MS) on a quadrupole time-of-flight (Q-TOF) mass spectrometer, for measuring the fragment deuteration levels of regioselectively labeled ubiquitin. Both methods reveal that b-ions exhibit HDX levels significantly below that of the intact protein, whereas several y'' fragments are labeled to a much greater extent. These results are consistent with earlier source-CID data (Akashi, S.; Naito, Y.; Takio, K. Anal. Chem. 1999, 71, 4974-4980). However, the measured b-ion deuteration levels are in disagreement with the known solution-phase behavior of ubiquitin. Partial agreement is observed for y''-ions. Control experiments on homogeneously labeled ubiquitin (having the same average deuteration level at every exchangeable site) result in highly nonuniform fragment HDX levels. In particular, b-ions exhibit deuteration levels significantly below that of intact ubiquitin, thereby mimicking the behavior seen for the regioselectively labeled protein. This effect is likely caused by isotope fractionation during collisional activation, facilitated by the high mobility of charge carriers (scrambling) in the gas phase. The observation that the b-ion labeling behavior is largely independent of the spatial isotope distribution within solution-phase ubiquitin invalidates these ions as reporters of the protein deuteration pattern. This work questions the common practice of interpreting any nonuniformities in fragment deuteration as being indicative of regioselective solution-phase labeling. Artifactual deuterium enrichment or depletion during collisional activation may have contributed to the current lack of consensus as to whether HDX/CID represents a potentially viable tool for measuring solution-phase deuteration patterns. PMID:18459737

  1. Human studies using isotope labeled fatty acids: answered and unanswered questions.

    PubMed

    Emken, Edward

    2013-01-01

    Human studies using deuterium-labeled fatty acids have answered many questions related to the metabolism and health effects of dietary fats. These studies also raised a number of unanswered questions and unresolved issues. For example, studies with cis and trans positional isomers dispelled concerns and allegations that the isomers in partially hydrogenated fats were poorly absorbed, accumulate in undesirable phospholipid acyl positions, mimic stearic acid and competed with oleic acid. Trans 18:1 isomers were metabolically intermediate between 16:0 and 18:0, so the unanswered question is why are the metabolic properties of trans fatty acids not consistent with their physiological effects? Results from ²H-18:0 studies address questions regarding stearic acid absorption and desaturation. Contrary to accepted dogma, stearic acid was well absorbed and less than 10% was desaturation to oleic acid. The still unanswered question is what is the metabolic basis for why 18:0 is less hypercholesterolemic than other saturated fatty acids? The question of whether humans convert 18:3n-3 to EPA and DHA was investigated by feeding male subjects a mixture of ²H-18:3n-3 and ²H-18:2n-6. The unequivocal answer was that 18:3n-3 is converted to EPA and DHA and the conversions for 18:3n-3 to 20:5n-3 and 18:2n-6 to 20:4n-6 were about equal. A major issue that remains unresolved is the wide variability between studies for the estimated conversion of 18:3n-3 to 20:5n-3 and 22:6n-3. The commercial availability of liquid oils hardened by interesterified with 18:0 has raised the question of whether fatty acids in the sn-2 and sn-1,3 TAG positions are metabolically equivalent. To answer this question, subjects were fed triglycerides containing ²H-16:0 and ²H-18:2n-6 at specific sn-1(3) and sn-2 acyl positions. The result was that dietary fatty acids at the sn-1(3) and sn-2 triacylglycerol positions are essentially metabolically equivalent. PMID:23648399

  2. Energy-Efficiency Labels and Standards: A Guidebook forAppliances, Equipment, and Lighting - 2nd Edition

    SciTech Connect

    Wiel, Stephen; McMahon, James E.

    2005-04-28

    Energy-performance improvements in consumer products are an essential element in any government's portfolio of energy-efficiency and climate change mitigation programs. Governments need to develop balanced programs, both voluntary and regulatory, that remove cost-ineffective, energy-wasting products from the marketplace and stimulate the development of cost-effective, energy-efficient technology. Energy-efficiency labels and standards for appliances, equipment, and lighting products deserve to be among the first policy tools considered by a country's energy policy makers. The U.S. Agency for International Development (USAID) and several other organizations identified on the cover of this guidebook recognize the need to support policy makers in their efforts to implement energy-efficiency standards and labeling programs and have developed this guidebook, together with the Collaborative Labeling and Appliance Standards Program (CLASP), as a primary reference. This second edition of the guidebook was prepared over the course of the past year, four years after the preparation of the first edition, with a significant contribution from the authors and reviewers mentioned previously. Their diligent participation helps maintain this book as the international guidance tool it has become. The lead authors would like to thank the members of the Communications Office of the Environmental Energy Technologies Division, Lawrence Berkeley National Laboratory for their support in the development, production, and distribution of the guidebook. This guidebook is designed as a manual for government officials and others around the world responsible for developing, implementing, enforcing, monitoring, and maintaining labeling and standards setting programs. It discusses the pros and cons of adopting energy-efficiency labels and standards and describes the data, facilities, and institutional and human resources needed for these programs. It provides guidance on the design, development, implementation, maintenance, and evaluation of the programs and on the design of the labels and standards themselves. In addition, it directs the reader to references and other resources likely to be useful in conducting the activities described and includes a chapter on energy policies and programs that complement appliance efficiency labels and standards. This guidebook attempts to reflect the essential framework of labeling and standards programs. It is the intent of the authors and sponsor to distribute copies of this book worldwide, at no charge, for the general public benefit. The guidebook is also available on the web at www.clasponline.org and may be downloaded to be used intact or piecemeal for whatever beneficial purposes readers may conceive.

  3. Methyl-coenzyme M reductase from methanogenic archaea: isotope effects on label exchange and ethane formation with the homologous substrate ethyl-coenzyme M.

    PubMed

    Scheller, Silvan; Goenrich, Meike; Thauer, Rudolf K; Jaun, Bernhard

    2013-10-01

    Ethyl-coenzyme M (CH3CH2-S-CH2CH2-SO3(-), Et-S-CoM) serves as a homologous substrate for the enzyme methyl-coenzyme M reductase (MCR) resulting in the product ethane instead of methane. The catalytic reaction proceeds via an intermediate that already contains all six C-H bonds of the product. Because product release occurs after a second, rate-limiting step, many cycles of intermediate formation and reconversion to substrate occur before a substantial amount of ethane is released. In deuterated buffer, the intermediate becomes labeled, and C-H activation in the back reaction rapidly leads to labeled Et-S-CoM, which enables intermediate formation to be detected. Here, we present a comprehensive analysis of this pre-equilibrium. (2)H- and (13)C-labeled isotopologues of Et-S-CoM were used as the substrates, and the time course of each isotopologue was followed by NMR spectroscopy. A kinetic simulation including kinetic isotope effects allowed determination of the primary and ?- and ?-secondary isotope effects for intermediate formation and for the C-H/C-D bond activation in the ethane-containing intermediate. The values obtained are in accordance with those found for the native substrate Me-S-CoM (see preceding publication, Scheller, S.; Goenrich, M.; Thauer, R. K.; Jaun, B. J. Am. Chem. Soc. 2013, 135, DOI: 10.1021/ja406485z) and thus imply the same catalytic mechanism for both substrates. The experiment by Floss and co-workers, demonstrating a net inversion of configuration to chiral ethane with CH3CDT-S-CoM as the substrate, is compatible with the observed rapid isotope exchange if the isotope effects measured here are taken into account. PMID:24003767

  4. Transport of indole-3-butyric acid and indole-3-acetic acid in Arabidopsis hypocotyls using stable isotope labeling.

    PubMed

    Liu, Xing; Barkawi, Lana; Gardner, Gary; Cohen, Jerry D

    2012-04-01

    The polar transport of the natural auxins indole-3-butyric acid (IBA) and indole-3-acetic acid (IAA) has been described in Arabidopsis (Arabidopsis thaliana) hypocotyls using radioactive tracers. Because radioactive assays alone cannot distinguish IBA from its metabolites, the detected transport from applied [3H]IBA may have resulted from the transport of IBA metabolites, including IAA. To test this hypothesis, we used a mass spectrometry-based method to quantify the transport of IBA in Arabidopsis hypocotyls by following the movement of [13C1]IBA and the [13C1]IAA derived from [13C1]IBA. We also assayed [13C6]IAA transport in a parallel control experiment. We found that the amount of transported [13C1]IBA was dramatically lower than [13C6]IAA, and the IBA transport was not reduced by the auxin transport inhibitor N-1-naphthylphthalamic acid. Significant amounts of the applied [13C1]IBA were converted to [13C1]IAA during transport, but [13C1]IBA transport was independent of IBA-to-IAA conversion. We also found that most of the [13C1]IBA was converted to ester-linked [13C1]IBA at the apical end of hypocotyls, and ester-linked [13C1]IBA was also found in the basal end at a level higher than free [13C1]IBA. In contrast, most of the [13C6]IAA was converted to amide-linked [13C6]IAA at the apical end of hypocotyls, but very little conjugated [13C6]IAA was found in the basal end. Our results demonstrate that the polar transport of IBA is much lower than IAA in Arabidopsis hypocotyls, and the transport mechanism is distinct from IAA transport. These experiments also establish a method for quantifying the movement of small molecules in plants using stable isotope labeling. PMID:22323783

  5. ABRF Research Group Development and Characterization of a Proteomics Normalization Standard Consisting of 1,000 Stable Isotope Labeled Peptides

    PubMed Central

    Dufresne, Craig; Hawke, David; Ivanov, Alexander R.; Koller, Antonius; MacLean, Brendan; Phinney, Brett; Rose, Kristie; Rudnick, Paul; Searle, Brian; Shaffer, Scott; Colangelo, Christopher M.

    2014-01-01

    The ABRF Proteomics Standards Research Group (sPRG) is reporting the progress of a two-year study (2012–2014) which focuses on the generation of interassay, interspecies, and interlaboratory peptide standard that can be used for normalization of protein abundance measurements in mass spectrometry based quantitative proteomics analyses. The standard has been formulated as two mixtures: 1,000 stable isotope 13C/15N-labeled (SIL) synthetic peptides alone, and peptides mixed with a tryptic digest of a HEK 293 cell lysate. The sequences of the synthetic peptides were derived from 552 proteins conserved across proteomes of commonly analyzed species: Homo sapiens, Mus musculus and Rattus norvegicus. The selected peptides represent a full range of hydrophobicities and isoelectric points, typical of tryptic peptides derived from complex proteomic samples. The standard was designed to represent proteins of various concentrations, spanning three orders of magnitude. First year efforts were focused on selection of appropriate protein and peptide candidates, peptide synthesis, quality assessment and LC-MS/MS evaluation conducted in laboratories of sPRG members. Using a variety of instrumental configurations and bioinformatics approaches, a thorough characterization of all 1,000 peptides was established. In the second year, the group launched the study to the entire proteomics community. A lyophilized mixture of HEK 293 tryptic digest cell lysate spiked with the 1,000 SIL peptide standards was provided to each participant. Also provided were a Skyline tutorial, tutorial datasets, three MS/MS spectral libraries generated from linear ion-trap (CID), Q-TOF/QQQ (CID), or Orbitrap (HCD) instrumentation, and a Panorama data repository. Participants were asked to analyze the sample in triplicate and calculate ratios of the spiked SIL to endogenous peptides and coefficients of variance for each peptide. Over 40 datasets were returned, and results following thorough characterization of the standard using various instrumental configurations will be reported.

  6. Phosphorus cycling in the Sargasso Sea: Investigation using the oxygen isotopic composition of phosphate, enzyme-labeled fluorescence, and turnover times

    NASA Astrophysics Data System (ADS)

    McLaughlin, Karen; Sohm, Jill A.; Cutter, Gregory A.; Lomas, Michael W.; Paytan, Adina

    2013-04-01

    Dissolved inorganic phosphorus (DIP) concentrations in surface water of vast areas of the ocean are extremely low (<10 nM) and phosphorus (P) availability could limit primary productivity in these regions. We explore the use of oxygen isotopic signature of dissolved phosphate (?18OPO4) to investigate biogeochemical cycling of P in the Sargasso Sea, Atlantic Ocean. Additional techniques for studying P dynamics including 33P-based DIP turnover time estimates and percent of cells expressing alkaline phosphatase (AP) activity as measured by enzyme-labeling fluorescence are also used. In surface waters, ?18OPO4 values were lower than equilibrium by 3-6‰, indicative of dissolved organic phosphorous (DOP) remineralization by extracellular enzymes. An isotope mass balance model using a variety of possible combinations of enzymatic pathways and substrates indicates that DOP remineralization in the euphotic zone can account for a large proportion on P utilized by phytoplankton (as much as 82%). Relatively short DIP turnover times (4-8 h) and high expression of AP (38-77% of the cells labeled) are consistent with extensive DOP utilization and low DIP availability in the euphotoc zone. In deep water where DOP utilization rates are lower, ?18OPO4 values approach isotopic equilibrium and DIP turnover times are longer. Our data suggests that in the euphotic zone of the Sargasso Sea, DOP may be appreciably remineralized and utilized by phytoplankton and bacteria to supplement cellular requirements. A substantial fraction of photosynthesis in this region is supported by DOP uptake.

  7. 1H-detected 1H- 1H correlation spectroscopy of a stereo-array isotope labeled amino acid under fast magic-angle spinning

    NASA Astrophysics Data System (ADS)

    Takahashi, Hiroki; Kainosho, Masatsune; Akutsu, Hideo; Fujiwara, Toshimichi

    2010-04-01

    The combined use of selective deuteration, stereo-array isotope labeling (SAIL), and fast magic-angle spinning effectively suppresses the 1H- 1H dipolar couplings in organic solids. This method provided the high-field 1H NMR linewidths comparable to those achieved by combined rotation and multiple-pulse spectroscopy. This technique was applied to two-dimensional 1H-detected 1H- 1H polarization transfer CHH experiments of valine. The signal sensitivity for the 1H-detected CHH experiments was greater than that for the 13C-detected 1H- 1H polarization transfer experiments by a factor of 2-4. We obtained the 1H- 1H distances in SAIL valine by CHH experiments with an accuracy of about 0.2 Å by using a theory developed for 1H- 1H polarization transfer in 13C-labeled organic compounds.

  8. Recent developments in solid-state magic-angle spinning, nuclear magnetic resonance of fully and significantly isotopically labelled peptides and proteins.

    PubMed Central

    Straus, Suzana K

    2004-01-01

    In recent years, a large number of solid-state nuclear magnetic resonance (NMR) techniques have been developed and applied to the study of fully or significantly isotopically labelled ((13)C, (15)N or (13)C/(15)N) biomolecules. In the past few years, the first structures of (13)C/(15)N-labelled peptides, Gly-Ile and Met-Leu-Phe, and a protein, Src-homology 3 domain, were solved using magic-angle spinning NMR, without recourse to any structural information obtained from other methods. This progress has been made possible by the development of NMR experiments to assign solid-state spectra and experiments to extract distance and orientational information. Another key aspect to the success of solid-state NMR is the advances made in sample preparation. These improvements will be reviewed in this contribution. Future prospects for the application of solid-state NMR to interesting biological questions will also briefly be discussed. PMID:15306412

  9. Allocation of Recent Photosynthetic Products Using a Dual Isotope (13C and 14C) Pulse-Chase Labeling Technique

    Microsoft Academic Search

    M. S. Carbone; S. Trumbore; K. McDuffee; X. Xu

    2005-01-01

    Pulse-chase labeling studies provide a non-destructive way to follow the allocation of recent photosynthetic products to above and belowground plant pathways. In August 2005, we applied a CO2 label enriched in 13C and low-levels of 14C, to elucidate differences in carbon allocation patterns between two plant communities (perennial grasses and shrubs) in the Owens Valley, CA. Following the label application,

  10. Quantitation of cortisol and related 3-oxo-4-ene steroids in urine using gas chromatography\\/mass spectrometry with stable isotope-labeled internal standards

    Microsoft Academic Search

    Mario Palermo; Celso Gomez-Sanchez; Esther Roitman; Cedric H. L. Shackleton

    1996-01-01

    A method for the profiling of several important 3-oxo-4-ene urinary steroids is reported. The methodology is combined gas chromatography\\/mass spectrometry (GC\\/MS) utilizing stable isotope-labeled internal standards. The following standards were obtained or easily synthesized: [9,11,12,12-2H4]cortisol, [1,2-2H2] and [9,12,12-2H2]cortisone, [1,2-2H2]6?-hydroxycortisol, and [1,2-2H2]18-hydroxycortisol. We found the following excretions of free steroids for normal adult males and females: cortisol (males mean ± SD,

  11. An aggregated perylene-based broad-spectrum, efficient and label-free quencher for multiplexed fluorescent bioassays.

    PubMed

    Liu, Tao; Hu, Rong; Lv, Yi-Fan; Wu, Yuan; Liang, Hao; Huan, Shuang-Yan; Zhang, Xiao-Bing; Tan, Weihong; Yu, Ru-Qin

    2014-08-15

    Fluorescent sensing systems based on the quenching of fluorophores have found wide applications in bioassays. An efficient quencher will endow the sensing system a high sensitivity. The frequently used quenchers are based on organic molecules or nanomaterials, which usually need tedious synthesizing and modifying steps, and exhibit different quenching efficiencies to different fluorophores. In this work, we for the first time report that aggregated perylene derivative can serve as a broad-spectrum and label-free quencher that is able to efficiently quench a variety of fluorophores, such as green, red and far red dyes labeled on DNA. By choosing nucleases as model biomolecules, such a broad-spectrum quencher was then employed to construct a multiplexed bioassay platform through a label-free manner. Due to the high quenching efficiency of the aggregated perylene, the proposed platform could detect nuclease with high sensitivity, with a detection limit of 0.03U/mL for EcoRV, and 0.05U/mL for EcoRI. The perylene quencher does not affect the activity of nuclease, which makes it possible to design post-addition type bioassay platform. Moreover, the proposed platform allows simultaneous and multicolor analysis of nucleases in homogeneous solution, demonstrating its value of potential application in rapid screening of multiple bio-targets. PMID:24662061

  12. Dynamic interval-based labeling scheme for efficient XML query and update processing

    E-print Network

    Chung, Chin-Wan

    relationships, several node labeling and index schemes have been suggested (Li and Moon, 2001; Zhang et al., 2001; Wu et al., 2004; Tatarinov et al., 2002; Kaplan et al., 2002; Catania et al., 2005; Chen et al the case of the interval-based labeling scheme (Li and Moon, 2001; Zhang et al., 2001) that assigns start

  13. Large-scale synthesis of isotopically labeled 13C2-tenuazonic acid and development of a rapid HPLC-MS/MS method for the analysis of tenuazonic acid in tomato and pepper products.

    PubMed

    Lohrey, Lilia; Marschik, Stefanie; Cramer, Benedikt; Humpf, Hans-Ulrich

    2013-01-01

    Tenuazonic acid is a fungal secondary metabolite that is produced by a number of Alternaria species and is therefore a natural contaminant of food and feed samples. This paper describes a new strategy for the efficient and economical large-scale synthesis of the isotopically labeled internal standard (13)C(2)-tenuazonic acid via a three-step procedure. Furthermore, a new reliable and quick method based on QuEChERS (Quick, Easy, Cheap, Effective, Rugged, and Safe) cleanup is presented for the determination of tenuazonic acid in food and feed samples utilizing high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) by application of the stable isotope dilution analysis. This new method has a limit of detection (LOD) of 0.86 ?g/kg and a limit of quantitation (LOQ) of 2.89 ?g/kg. In total 26 tomato samples and 4 bell pepper samples from the German market were analyzed. Tenuazonic acid was found in each sample with levels from 3 to 2330 ?g/kg. PMID:23230907

  14. Measurement of cell proliferation by labeling of DNA with stable isotope-labeled glucose: Studies in vitro, in animals, and in humans

    Microsoft Academic Search

    DEREK C. MACALLAN; CATHERINE A. FULLERTON; RICHARD A. NEESE; KATHERINE HADDOCK; SUNNY S. PARK; MARC K. HELLERSTEIN

    1998-01-01

    A method for measuring DNA synthesis and, thus, cell proliferation, in vivo is presented. The technique consists of administering (6,6-2H2)Glc or (U-13C)Glc, isolat- ing genomic DNA, hydrolyzing enzymatically to free deoxyri- bonucleosides, and derivatizing for GC-MS analysis of dA or dG isotopic enrichments, or both. Comparison of dA or dG to extracellular Glc enrichment (with a correction for intracel- lular

  15. Transient isotopic labeling studies under steady-state Conditions in partial oxidation of methane to formaldehyde over MoO[sub 3] catalysts

    SciTech Connect

    Smith, M.R.; Ozkan, U.S. (Ohio State Univ., Columbus (United States))

    1993-07-01

    The oxygen insertion pathway over MoO[sub 3] catalysts has been investigated for the partial oxidation of methane to formaldehyde using transient isotopic labeling under steady-state reaction conditions. Catalyst samples preferentially exposing basal (010) and side (100) planes have been characterized using various techniques including scanning electron microscopy with three-dimensional imaging, BET surface area, X-ray diffraction, X-ray photoelectron spectroscopy, and laser Raman spectroscopy. In addition to isotopic labeling studies, these catalysts have also been examined under steady-state reaction conditions to assess the effect of the concentration of gas-phase oxygen. Results of the characterization and reaction studies suggest that the production of HCHO proceeds via utilization of lattice oxygen through the Mo[double bond]O sites. These sites are then preferentially replenished through bulk diffusion of oxygen. The bridging Mo-O-Mo sites, on the other hand, appear to be involved in complete oxidation and are more easily regenerated by gas-phase oxygen. 19 refs., 8 figs., 3 tabs.

  16. Anaerobic central metabolic pathways in Shewanella oneidensis MR-1interpreted in the light of isotopic metabolite labeling, enzymeactivities and genome annotation

    SciTech Connect

    Tang, Yinjie J.; Meadows, Adam L.; Kirby, James; Keasling, Jay D.

    2006-06-27

    It has been proposed that during growth under anaerobic oroxygen-limited conditions Shewanella oneidensis MR-1 uses theserine-isocitrate lyase pathway common to many methylotrophic anaerobes,in which formaldehyde produced from pyruvate is condensed with glycine toform serine. The serine is then transformed through hydroxypyruvate andglycerate to enter central metabolism at phosphoglycerate. To examine itsuse of the serine-isocitrate lyase pathway under anaerobic conditions, wegrew S. oneidensis MR-1 on [1-13C]lactate as the sole carbon source witheither trimethylamine N-oxide (TMAO) or fumarate as an electron acceptor.Analysis of cellular metabolites indicates that a large percentage(>75 percent) of lactate was partially oxidized to either acetate orpyruvate. The 13C isotope distributions in amino acids and other keymetabolites indicate that, under anaerobic conditions, a complete serinepathway is not present, and lactate is oxidized via a highly reversibleserine degradation pathway. The labeling data also suggest significantactivity in the anaplerotic (malic enzyme and phosphoenolpyruvatecarboxylase) and glyoxylate shunt (isocitrate lyase and malate synthase)reactions. Although the tricarboxylic acid (TCA) cycle is often observedto be incomplete in many other anaerobes (absence of 2-oxoglutaratedehydrogenase activity), isotopic labeling supports the existence of acomplete TCA cycle in S. oneidensis MR-1 under TMAO reductioncondition.

  17. Importance of bacterivory and preferential selection toward diatoms in larvae of Crepidula fornicata (L.) assessed by a dual stable isotope (13C, 15N) labeling approach

    NASA Astrophysics Data System (ADS)

    Leroy, Fanny; Riera, Pascal; Jeanthon, Christian; Edmond, Frédérique; Leroux, Cédric; Comtet, Thierry

    2012-05-01

    In Europe, the gastropod Crepidula fornicata is an invasive species characterized by a long reproductive period (from February to November). Thus, its larvae are exposed to variations in available food sources (in terms of quantity and quality). We aimed to investigate if bacteria could contribute to larval food both in presence or absence of phytoplankton, and to compare these results to seasonal variations of bacteria and phytoplankton abundances at a coastal site in the English Channel. First, ingestion of fluorescent beads of 0.5 to 2 ?m diameter, showed that larvae were able to ingest particles of typical bacterial size. Then we used a dual stable isotope labeling approach which consisted in labeling a bacterial pelagic community with 15N and a diatom (Chaetoceros gracilis) culture with 13C, and supplying larvae with 15N-labeled bacteria, 13C-labeled diatoms, and both labeled sources. This technique has, to our knowledge, never been applied to invertebrate larvae. After 24 h of experiment, larvae were significantly enriched in all treatments: + 21.5‰ (??13C) when supplied with diatoms, + 1364‰ (??15N) when supplied with bacteria, and + 24‰ (??13C) and + 135‰ (??15N) when supplied with the two mixed sources. These results indicated that bacteria can contribute to the larval nutrition in C. fornicata, even in the presence of phytoplankton. Our results however suggested that larvae of C. fornicata preferentially used diatoms and showed that the supply of free bacteria did not alter the uptake of diatoms. Considering the seasonal variations of bacteria and phytoplankton abundances at the study site, these results suggested that bacteria may constitute a complementary resource for the larvae of C. fornicata when phytoplankton is abundant and may become a substitute resource when phytoplankton is less available. This approach offers promising perspectives to trace food sources and assess nitrogen and carbon fluxes between planktotrophic larvae and their preys.

  18. Stimulating carbon efficient supply chains : carbon labels and voluntary public private partnerships

    E-print Network

    Tan, Kwan Chong

    2009-01-01

    This thesis looks at the potential of labeling products with life cycle greenhouse gas emission information as a bottom-up, complementary alternative to carbon cap and trade systems. By improving the transparency of product ...

  19. A stable isotope-labeled internal standard is essential for correcting for the interindividual variability in the recovery of lapatinib from cancer patient plasma in quantitative LC-MS/MS analysis

    PubMed Central

    Wu, Jianmei; Wiegand, Richard; LoRusso, Patricia; Li, Jing

    2013-01-01

    The development and validation of a LC-MS/MS method is often performed using pooled human plasma, which may fail to account for variations in interindividual matrices. Since calibrator standards and quality control samples are routinely prepared in pooled human plasma, variations in the extraction recovery and/or matrix effect between pooled plasma and individual patient plasma can cause erroneous measurements. Using both pooled human plasma as well as individual healthy donor and cancer patient plasma samples, we evaluated the analytical performance of two classes of internal standards (i.e., non-isotope-labeled and isotope-labeled) in the quantitative LC-MS/MS analysis of lapatinib. After exhaustive extraction with organic solvent, the recovery of lapatinib, a highly plasma protein-bound drug, varied up to 2.4-fold (range, 29 – 70%) in 6 different donors of plasma and varied up to 3.5-fold (range, 16 – 56%) in the pretreatment plasma samples from 6 cancer patients. No apparent matrix effects were observed for lapatinib in both pooled and individual donor or patient plasma samples. The calibration curve range was 5 – 5000 ng/ml of lapatinib in plasma. Both the non-isotope-labeled (zileuton) and isotope-labeled (lapatinib-d3) internal standard methods showed acceptable specificity, accuracy (within 100 ± 10%), and precision (< 11%) in the determination of lapatinib in pooled human plasma. Nevertheless, only the isotope-labeled internal standard could correct for the interindividual variability in the recovery of lapatinib from patient plasma samples. As inter- and intra-patient matrix variability is commonly presented in the clinical setting, this study provides an example underscoring the importance of using a stable isotope-labeled internal standard in quantitative LC-MS/MS analysis for therapeutic drug monitoring or pharmacokinetic evaluation. PMID:24189203

  20. [Microbial synthesis of deuterium labelled L-phenylalanine with different levels of isotopic enrichment by facultative methylotrophic bacterium Brevibacterium methylicum with RMP assimilation of carbon].

    PubMed

    Mosin, O V; Shvets, V I; Skladnev, D A; Ignatov, I

    2014-01-01

    The preparative microbial synthesis of amino acids labelled with stable isotopes, including deuterium ( 2 H), suitable for biomedical applications by methylotrophic bacteria was studied using L-phenylalanine as example. This amino acid is secreted by Gram-negative aerobic facultative methylotrophic bacteria Brevibacterium methylicum, assimilating methanol via ribulose-5-monophosphate (RMP) cycle of assimilation of carbon, The data on adaptation of L-phenylalanine secreted by methylotrophic bacterium ?. methylicum to the maximal concentration of deuterium in the growth medium with 98% 2 ? 2 O and 2% [ 2 ?]methanol, and biosynthesis of deuterium labelled L-phenylalanine With different levels of enrichment are presented. The strain was adapted by means of plating initial cells on firm (2% agarose) minimal growth media with an increasing gradient of 2 ? 2 O concentration from 0; 24.5; 49.0; 73.5 up to 98% 2 ? 2 O followed by subsequent selection of separate colonies stable to the action of 2 ? 2 O. These colonies were capable to produce L-phenylalanine. L-phenylalanine was extracted from growth medium by extraction with isopropanol with the subsequent crystallization in ethanol (output 0.65 g/l). The developed method of microbial synthesis allows to obtain deuterium labelled L-phenylalanine with different levels of isotopic enrichment, depending on concentration of 2 ? 2 O in growth media, from 17% (on growth medium with 24,5% 2 ? 2 O) up to 75% (on growth medium with 98% 2 ? 2 O) of deuterium in the molecule that is confirmed with the data of the electron impact (EI) mass- spectrometry analysis of methyl ethers of N-dimethylamino(naphthalene)-5-sulfochloride (dansyl) phenylalanine in these experimental conditions. PMID:25249528

  1. Nano-Mole Scale Side-Chain Signal Assignment by 1H-Detected Protein Solid-State NMR by Ultra-Fast Magic-Angle Spinning and Stereo-Array Isotope Labeling

    PubMed Central

    Nishiyama, Yusuke; Endo, Yuki; Nemoto, Takahiro; Yamauchi, Kazuo; Asakura, Tetsuo; Takeda, Mitsuhiro; Terauchi, Tsutomu; Kainosho, Masatsune; Ishii, Yoshitaka

    2015-01-01

    We present a general approach in 1H-detected 13C solid-state NMR (SSNMR) for side-chain signal assignments of 10-50 nmol quantities of proteins using a combination of a high magnetic field, ultra-fast magic-angle spinning (MAS) at ~80 kHz, and stereo-array-isotope-labeled (SAIL) proteins [Kainosho M. et al., Nature 440, 52–57, 2006]. First, we demonstrate that 1H indirect detection improves the sensitivity and resolution of 13C SSNMR of SAIL proteins for side-chain assignments in the ultra-fast MAS condition. 1H-detected SSNMR was performed for micro-crystalline ubiquitin (~55 nmol or ~0.5mg) that was SAIL-labeled at seven isoleucine (Ile) residues. Sensitivity was dramatically improved by 1H-detected 2D 1H/13C SSNMR by factors of 5.4-9.7 and 2.1-5.0, respectively, over 13C-detected 2D 1H/13C SSNMR and 1D 13C CPMAS, demonstrating that 2D 1H-detected SSNMR offers not only additional resolution but also sensitivity advantage over 1D 13C detection for the first time. High 1H resolution for the SAIL-labeled side-chain residues offered reasonable resolution even in the 2D data. A 1H-detected 3D 13C/13C/1H experiment on SAIL-ubiquitin provided nearly complete 1H and 13C assignments for seven Ile residues only within ~2.5 h. The results demonstrate the feasibility of side-chain signal assignment in this approach for as little as 10 nmol of a protein sample within ~3 days. The approach is likely applicable to a variety of proteins of biological interest without any requirements of highly efficient protein expression systems. PMID:25856081

  2. Nano-mole scale side-chain signal assignment by 1H-detected protein solid-state NMR by ultra-fast magic-angle spinning and stereo-array isotope labeling.

    PubMed

    Wang, Songlin; Parthasarathy, Sudhakar; Nishiyama, Yusuke; Endo, Yuki; Nemoto, Takahiro; Yamauchi, Kazuo; Asakura, Tetsuo; Takeda, Mitsuhiro; Terauchi, Tsutomu; Kainosho, Masatsune; Ishii, Yoshitaka

    2015-01-01

    We present a general approach in 1H-detected 13C solid-state NMR (SSNMR) for side-chain signal assignments of 10-50 nmol quantities of proteins using a combination of a high magnetic field, ultra-fast magic-angle spinning (MAS) at ~80 kHz, and stereo-array-isotope-labeled (SAIL) proteins [Kainosho M. et al., Nature 440, 52-57, 2006]. First, we demonstrate that 1H indirect detection improves the sensitivity and resolution of 13C SSNMR of SAIL proteins for side-chain assignments in the ultra-fast MAS condition. 1H-detected SSNMR was performed for micro-crystalline ubiquitin (~55 nmol or ~0.5mg) that was SAIL-labeled at seven isoleucine (Ile) residues. Sensitivity was dramatically improved by 1H-detected 2D 1H/13C SSNMR by factors of 5.4-9.7 and 2.1-5.0, respectively, over 13C-detected 2D 1H/13C SSNMR and 1D 13C CPMAS, demonstrating that 2D 1H-detected SSNMR offers not only additional resolution but also sensitivity advantage over 1D 13C detection for the first time. High 1H resolution for the SAIL-labeled side-chain residues offered reasonable resolution even in the 2D data. A 1H-detected 3D 13C/13C/1H experiment on SAIL-ubiquitin provided nearly complete 1H and 13C assignments for seven Ile residues only within ~2.5 h. The results demonstrate the feasibility of side-chain signal assignment in this approach for as little as 10 nmol of a protein sample within ~3 days. The approach is likely applicable to a variety of proteins of biological interest without any requirements of highly efficient protein expression systems. PMID:25856081

  3. Highly efficient fluorescent interstrand photo-crosslinking of DNA duplexes labeled with 5-fluoro-4-thio-2'-o-methyluridine.

    PubMed

    Nowak-Karnowska, Joanna; Chebib, Ziad; Milecki, Jan; Franzen, Stefan; Skalski, Bohdan

    2014-09-22

    The formation of a fluorescent photoadduct between 5-fluoro-4-thiouridine ((FS) U), in the sequence context 5'-A(FS) UA-3' and incorporated into a synthetic oligonucleotide either at its 3'- or 5'-end, and one of the thymines of the TAT motif in a complementary target DNA strand led to photo-crosslinking of the two strands for several oligonucleotide constructs. Enzymatic digestion, MS, UV, and fluorescence spectral analyses of the interstrand crosslinked oligonucleotides revealed the identity of the thymidine that participates in the photo-crosslinking reaction as well as the diastereomeric structures of the crosslinks. The proposed pathways of interstrand photo-crosslinking are supported by experiments with isotopically labeled oligonucleotide constructs and visualized by means of molecular dynamics simulations. PMID:25111776

  4. Efficient method for iodine radioisotope labeling of cyclooctyne-containing molecules using strain-promoted copper-free click reaction.

    PubMed

    Jeon, Jongho; Kang, Jung Ae; Shim, Ha Eun; Nam, You Ree; Yoon, Seonhye; Kim, Hye Rim; Lee, Dong Eun; Park, Sang Hyun

    2015-07-01

    Herein we report an efficient method for iodine radioisotope labeling of cyclooctyne-containing molecules using copper-free click reaction. For this study, radioiodination using the tin precursor 2 was carried out at room temperature to give (125)I-labeled azide ([(125)I]1) with high radiochemical yield (85%) and excellent radiochemical purity. Dibenzocyclooctyne (DBCO) containing cRGD peptide and gold nanoparticle were labeled with [(125)I]1 at 37°C for 30min to give triazoles with good radiochemical yields (67-95%). We next carried out tissue biodistribution study of [(125)I]1 in normal ICR mice to investigate the level of organ accumulation which needs to be considered for pre-targeted in vivo imaging. Large amount of [(125)I]1 distributed rapidly in liver and kidney from bloodstream and underwent rapid renal and hepatobiliary clearance. Moreover [(125)I]1 was found to be highly stable (>92%) in mouse serum for 24h. Therefore [(125)I]1 could be used as a potentially useful radiotracer for pre-targeted imaging. Those results clearly indicated that the present radiolabeling method using copper free click reaction would be quite useful for both in vitro and in vivo labeling of DBCO group containing molecules with iodine radioisotopes. PMID:25960325

  5. Preparation of stable isotope-labeled 2-nitrobenzaldehyde derivatives of four metabolites of nitrofuran antibiotics and their comprehensive characterization by UV, MS, and NMR techniques.

    PubMed

    Delatour, Thierry; Gremaud, Eric; Mottier, Pascal; Richoz, Janique; Arce Vera, Francia; Stadler, Richard H

    2003-10-22

    A convenient method is presented for the preparation of the carbon-13-labeled 2-nitrobenzaldehyde derivatives of the nitrofuran metabolites 3-amino-2-oxazolidinone (AOZ), semicarbazide (SC), 1-aminohydantoin (AH), and 3-amino-5-morpholinomethyl-2-oxazolidinone (AMOZ), with the purpose of using them as internal standards for the quantification of trace levels of nitrofuran residues by liquid chromatography-tandem mass spectrometry in foods of animal origin. The synthesis encompasses the nitration of [1,2,3,4,5,6-(13)C(6)]toluene prior to chromyl compound-mediated oxidation of the methyl group into the corresponding aldehyde. The four metabolites of nitrofuran antibiotics were derivatized independently with the resulting ring-labeled 2-nitrobenzaldehyde (NBA) to obtain the target compounds. Both the isotopically enriched and native substances were used to perform a comprehensive fragmentation study by electrospray ionization (ESI) collision-induced dissociation (CID) mass spectrometry (MS). Full characterization of the nitrofuran derivatives was accomplished with ultraviolet (UV) and exhaustive nuclear magnetic resonance (NMR) analysis. A major advantage of the described procedure is that it can be extended to the preparation of other carbon-13-labeled derivatives of metabolites of nitrofuran antibiotics. PMID:14558749

  6. Production of 18F-Labeled Radiopharmaceuticals

    E-print Network

    Shen, Jun

    candidates for isotopic labeling, and for radioligand or radiotracer development · Compounds may be labeled by adding groups containing 18F (non-isotopic labeling) · A mono-fluoro derivative of an endogenous compoundProduction of 18F-Labeled Radiopharmaceuticals Part 1 (PET radiochemistry lecture #4) Contents

  7. Qualitative Metabolome Analysis of Human Cerebrospinal Fluid by 13C-/12C-Isotope Dansylation Labeling Combined with Liquid Chromatography Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Guo, Kevin; Bamforth, Fiona; Li, Liang

    2011-02-01

    Metabolome analysis of human cerebrospinal fluid (CSF) is challenging because of low abundance of metabolites present in a small volume of sample. We describe and apply a sensitive isotope labeling LC-MS technique for qualitative analysis of the CSF metabolome. After a CSF sample is divided into two aliquots, they are labeled by 13C-dansyl and 12C-dansyl chloride, respectively. The differentially labeled aliquots are then mixed and subjected to LC-MS using Fourier-transform ion cyclotron resonance mass spectrometry (FTICR MS). Dansylation offers significant improvement in the performance of chromatography separation and detection sensitivity. Moreover, peaks detected in the mass spectra can be readily analyzed for ion pair recognition and database search based on accurate mass and/or retention time information. It is shown that about 14,000 features can be detected in a 25-min LC-FTICR MS run of a dansyl-labeled CSF sample, from which about 500 metabolites can be profiled. Results from four CSF samples are compared to gauge the detectability of metabolites by this method. About 261 metabolites are commonly detected in replicate runs of four samples. In total, 1132 unique metabolite ion pairs are detected and 347 pairs (31%) matched with at least one metabolite in the Human Metabolome Database. We also report a dansylation library of 220 standard compounds and, using this library, about 85 metabolites can be positively identified. Among them, 21 metabolites have never been reported to be associated with CSF. These results illustrate that the dansylation LC-FTICR MS method can be used to analyze the CSF metabolome in a more comprehensive manner.

  8. Optical Label Switching Technology and Energy-Efficient Future Networks S. J. Ben Yoo

    E-print Network

    Kolner, Brian H.

    of Electrical and Computer Engineering, University of California, Davis, California 95616, U.S.A. Abstract Switching Network Wireline O-CDMA LAN Satellite Network Reconfigurable Wireless Network DATA Center Figure 1. Future Internet with optical-label switching, wireless, and wireline networking in support of cloud

  9. Parallel ?-sheet vibrational couplings revealed by 2D IR spectroscopy of an isotopically labeled macrocycle: Quantitative benchmark for the interpretation of amyloid and protein infrared spectra

    PubMed Central

    Woys, Ann Marie; Almeida, Aaron M.; Wang, Lu; Chiu, Chi Cheng; McGovern, Michael; de Pablo, Juan J.; Skinner, James L.; Gellman, Samuel H.; Zanni, Martin T.

    2012-01-01

    Infrared spectroscopy is playing an important role in the elucidation of amyloid fiber formation, but the coupling models that link spectra to structure are not well tested for parallel ?-sheets. Using a synthetic macrocycle that enforces a two stranded parallel ?-sheet conformation, we measured the lifetimes and frequency for six combinations of doubly 13C=18O labeled amide I modes using 2D IR spectroscopy. The average vibrational lifetime of the isotope labeled residues was 550 fs. The frequen cies of the labels ranged from 1585 to 1595 cm?1, with the largest frequency shift occurring for in-register amino acids. The 2D IR spectra of the coupled isotope labels were calculated from molecular dynamics simulations of a series of macrocycle structures generated from replica exchange dynamics to fully sample the conformational distribution. The models used to simulate the spectra include through-space coupling, through-bond coupling, and local frequency shifts caused by environment electrostatics and hydrogen bonding. The calculated spectra predict the linewidths and frequencies nearly quantitatively. Historically, the characteristic features of ?-sheet infrared spectra have been attributed to through-space couplings such as transition dipole coupling. We find that frequency shifts of the local carbonyl groups due to nearest neighbor couplings and environmental factors are more important, while the through space couplings dictate the spectral intensities. As a result, the characteristic absorption spectra empirically used for decades to assign parallel ?-sheet secondary structure arises because of a redistribution of oscillator strength, but the through-space couplings do not themselves dramatically alter the frequency distribution of eigenstates much more than already exists in random coil structures. Moreover, solvent exposed residues have amide I bands with >20 cm?1 linewidth. Narrower linewidths indicate that the amide I backbone is solvent protected inside the macrocycle. This work provides calculated and experimentally verified couplings for parallel ?-sheets that can be used in structure-based models to simulate and interpret the infrared spectra of ?-sheet containing proteins and protein assemblies, such as amyloid fibers. PMID:23113791

  10. Evaluation of the mass spectrometric fragmentation of codeine and morphine after 13C-isotope biosynthetic labeling.

    PubMed

    Poeaknapo, Chotima; Fisinger, Ursula; Zenk, Meinhart H; Schmidt, Jürgen

    2004-05-01

    All major fragment ions of codeine and morphine were elucidated using LC-electrospray MS/MS and high resolution FT-ICR-MS combined with an IRMPD system. Nanogram quantities of labeled codeine were isolated and purified from Papaver somniferum seedlings, which were grown for up to 9 days in the presence of [ring-13C6]-l-tyrosine, [ring-13C6]-tyramine and [1,2-13C2], [6-O-methyl 13C]-(R,S)-coclaurine. The labeling degree of codeine up to 57% into morphinans was observed. PMID:15231415

  11. Luminescent dye-doped or rare-earth-doped monodisperse silica nanospheres as efficient labels in DNA microarrays

    NASA Astrophysics Data System (ADS)

    Enrichi, F.; Riccò, R.; Meneghello, A.; Pierobon, R.; Marinello, F.; Schiavuta, P.

    2009-08-01

    Luminescent nanoparticles are gaining more and more interest in bio-labeling and bio-imaging applications, like for example DNA microarray. This is a high-throughput technology used for detection and quantification of nucleic acid molecules and other ones of biological interest. The analysis is resulting by specific hybridization between probe sequences deposited in array and a target ss-DNA usually expressed by PCR and functionalized by a fluorescent dye. These organic labels have well known disadvantages like photobleaching and limited sensitivity. Quantum dots may be used as alternatives, but they present troubles like blinking, toxicity and excitation wavelengths out of the usual range of commercial instruments, lowering their efficiency. Therefore in this work we investigate a different strategy, based on the use of inorganic silica nanospheres incorporating standard luminescent dyes or rare earth doped nanocrystals. In the first case it is possible to obtain a high luminescence emission signal, due to the high number of dye molecules that can be accommodated into each nanoparticle, reduced photobleaching and environmental protection of the dye molecules thanks to the encapsulation in the silica matrix. In the second case, rare earths exhibit narrow emission bands (easy identification), large Stokes shifts (efficient discrimination of excitation and emission) and long luminescence lifetimes (possibility to perform time-delayed analysis) which can be efficiently used for the improvement of signal to noise ratio. The synthesis and characterization of good luminescent silica spheres either by organic dye-doping or by rare-earth-doping are investigated and reported. Moreover, their application in the DNA microarray technology in comparison to the use of standard molecular fluorophores or commercial quantum dots is discussed. The cheap and easy synthesis of these luminescent particles, the stability in water, the surface functionalization and bio-compatibility makes them very promising for present and future applications in bio-labeling and bio-imaging.

  12. Plasma nitrogen isotopic fractionation and feed efficiency in growing beef heifers.

    PubMed

    Wheadon, N M; McGee, M; Edwards, G R; Dewhurst, R J

    2014-05-01

    Fractionation of N isotopes occurs in many metabolic reactions which causes tissue proteins to become enriched in ¹?N while urea (urine) is depleted in ¹?N relative to the diet. We investigated ¹?N enrichment of whole plasma and its relationship with feed conversion efficiency (FCE) in growing beef heifers (n 84) offered 2 kg/d of concentrates with grass silage ad libitum. Heifers were on average 299 (SD 48·3) d old and weighed 311 (SD 48·8) kg. Plasma was obtained on day 79 (n 84) of the experiment and from a subset of animals (n 20) on four occasions between days 16 and 79. Silage DM intake (DMI) averaged 4·1 (SD 0·74) kg/d and concentrate DMI was 1·72 kg/d. Mean mid-test live weight was 333 (SD 47·6) kg, daily gain was 0·53 (SD 0·183) kg, FCE (g live-weight gain/g DMI) was 0·09 (SD 0·028) and residual feed intake (RFI) was 0 (SD 0·428). N isotopic fractionation (?¹?N; plasma ?¹?N - diet ?¹?N) averaged 3·58 ‰ on day 79 (n 84) and 3·90 ‰ for the subset of heifers. There was no relationship between ?¹?N and RFI. Plasma ?¹?N and ?¹?N were related to both FCE (negative) and animal weight (positive) for the whole population, and repeatable for the subset of animals over four time points. These relationships of ?¹?N with FCE and animal weight are consistent with the anticipated negative relationship with N-use efficiency. There is potential to use ?¹?N to provide rapid, low-cost estimates of FCE in cattle. PMID:24387820

  13. To appear, 8th Int'l Conf. on Intelligent Systems for Molecular Biology, August, 2000, San Diego, CA. Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling

    E-print Network

    Richardson, David

    , CA. Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling #3; Chris Bailey-Kellogg y John-Activity Re- lation by Mass Spectrometry (SAR by MS), for elu- cidating the function of protein-DNA and protein- protein complexes. SAR by MS enzymatically cleaves a crosslinked complex and analyzes

  14. Absolute quantification of protein NP24 in tomato fruit by liquid chromatography/tandem mass spectrometry using stable isotope-labelled tryptic peptide standard.

    PubMed

    Ippoushi, Katsunari; Sasanuma, Motoe; Oike, Hideaki; Kobori, Masuko; Maeda-Yamamoto, Mari

    2015-04-15

    Protein NP24 is a thaumatin-like protein contained in tomato (Lycopersicon esculentum Mill.). This protein is reported to be a putative tomato allergen and is listed as a food allergen in Structural Database of Allergenic Proteins (SDAP). In this research, we developed the quantitative analysis of NP24 by employing the protein absolute quantification (AQUA) technology composed of stable isotope-labelled internal standard (SIIS) peptide (GQTWVINAPR[(13)C6,(15)N4]) and liquid chromatography/tandem mass spectrometry (LC/MS/MS). A linear relationship (r(2)>0.99) was found throughout the concentration range (2.0-500 fmol/?L). The coefficients of variation (CVs) measured on each of the five days when NP24 contained in the tomato skin was analysed did not exceed 13%. Our developed assay of NP24 will contribute to the allergological examination of tomato and its derived products. PMID:25466018

  15. Comparative analysis of monoclonal antibody N-glycosylation using stable isotope labelling and UPLC-fluorescence-MS.

    PubMed

    Millán Martín, Silvia; Delporte, Cédric; Farrell, Amy; Navas Iglesias, Natalia; McLoughlin, Niaobh; Bones, Jonathan

    2015-03-01

    A twoplex method using (12)C6 and (13)C6 stable isotope analogues (?mass = 6 Da) of 2-aminobenzoic acid (2-AA) is described for quantitative analysis of N-glycans present on monoclonal antibodies and other glycoproteins using ultra performance liquid chromatography with sequential fluorescence and accurate mass tandem quadrupole time of flight (QToF) mass spectrometric detection. PMID:25623139

  16. Quantitation of changes in protein phosphorylation: A simple method based on stable isotope labeling and mass spectrometry

    Microsoft Academic Search

    Débora Bonenfant; Tobias Schmelzle; Estela Jacinto; José L. Crespo; Thierry Mini; Michael N. Hall; Paul Jenoe

    2003-01-01

    Reversible protein phosphorylation plays an important role in many cellular processes. However, a simple and reliable method to measure changes in the extent of phosphorylation is lacking. Here, we present a method to quantitate the changes in phosphorylation occurring in a protein in response to a stimulus. The method consists of three steps: (i) enzymatic digestion in H216O or isotopically

  17. ISOTOPIC LABELING AND LC-APCI-MS QUANTIFICATION FOR INVESTIGATING ABSORPTION OF CAROTENOIDS AND VITAMIN K1 FROM KALE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ability to study bioavailability of nutrients from plant-based foods is an important step in determining the potential health impact of those nutrients. This work describes a new method for studying bioavailability of nutrients from green, leafy vegetables by labeling the nutrients in kale with ...

  18. Multi-isotope labelling of organic matter by diffusion of 2H/18O-H2O vapour and 13C-CO2 into the leaves and its distribution within the plant

    NASA Astrophysics Data System (ADS)

    Studer, M. S.; Siegwolf, R. T. W.; Leuenberger, M.; Abiven, S.

    2015-03-01

    Isotope labelling is a powerful tool to study elemental cycling within terrestrial ecosystems. Here we describe a new multi-isotope technique to label organic matter (OM). We exposed poplars (Populus deltoides × nigra) for 14 days to an atmosphere enriched in 13CO2 and depleted in 2H218O. After 1 week, the water-soluble leaf OM (?13C = 1346 ± 162‰) and the leaf water were strongly labelled (?18O = -63 ± 8, ?2H = -156 ± 15‰). The leaf water isotopic composition was between the atmospheric and stem water, indicating a considerable back-diffusion of vapour into the leaves (58-69%) in the opposite direction to the net transpiration flow. The atomic ratios of the labels recovered (18O/13C, 2H/13C) were 2-4 times higher in leaves than in the stems and roots. This could be an indication of the synthesis of more condensed compounds in roots and stems (e.g. lignin vs. cellulose) or might be the result of O and H exchange and fractionation processes during phloem transport and biosynthesis. We demonstrate that the three major OM elements (C, O, H) can be labelled and traced simultaneously within the plant. This approach could be of interdisciplinary interest in the fields of plant physiology, palaeoclimatic reconstruction or soil science.

  19. Isotope-Coded and Affinity-Tagged Cross-Linking (ICATXL): An Efficient Strategy to Probe Protein Interaction Surfaces

    E-print Network

    Craik, Charles S.

    Isotope-Coded and Affinity-Tagged Cross-Linking (ICATXL): An Efficient Strategy to Probe Protein of Pharmaceutical Chemistry, UniVersity of California, San Francisco, California 94143-0446 Received March 11, 2006; E-mail: alb@cgl.ucsf.edu Protein bait affinity studies on the yeast proteome have begun to reveal

  20. The oxidation technique for efficient ionization of lanthanides by a helium-jet loaded on-line isotope separator

    Microsoft Academic Search

    Yoichi Kawase; Kotoyuki Okano

    1989-01-01

    The oxidation technique has successfully been developed for efficient ionization of lanthanides by a He-jet type on-line isotope separator for fission products. By introducing a small amount of oxygen to the helium-jet, monoxides of lanthanides (LaO, CeO, PrO, NdO and PmO) can be ionized with a very high efficiency (40-86%) by a surface ionization ion source. The ionization characteristics have

  1. Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein-Protein Interactions by Chemical Cross-Linking

    SciTech Connect

    Merkley, Eric D.; Baker, Erin Shammel; Crowell, Kevin L.; Orton, Daniel J.; Taverner, Thomas; Ansong, Charles; Ibrahim, Yehia M.; Burnet, Meagan C.; Cort, John R.; Anderson, Gordon A.; Smith, Richard D.; Adkins, Joshua N.

    2013-02-20

    Chemical cross-linking of proteins followed by proteolysis and mass spectrometric analysis of the resulting cross-linked peptides can provide insights into protein structure and protein-protein interactions. However, cross-linked peptides are by necessity of low stoichometry and have different physicochemical properties than linear peptides, routine unambiguous identification of the cross-linked peptides has remained difficult. To address this challenge, we demonstrated the use of liquid chromatography and ion mobility separations coupled with mass spectrometry in combination with a heavy-isotope labeling method. The combination of mixed-isotope cross-linking and ion mobility provided unique and easily interpretable spectral multiplet features for the intermolecular cross-linked peptides. Application of the method to two different homodimeric proteins ? SrfN, a virulence factor from Salmonella Typhimurium and SO_2176, a protein of unknown function from Shewanella oneidensis? revealed several cross-linked peptides from both proteins that were identified with a low false discovery rate (estimated using a decoy approach). A greater number of cross-linked peptides were identified using ion mobility drift time information in the analysis than when the data were summed across the drift time dimension before analysis. The identified cross-linked peptides migrated more quickly in the ion mobility drift tube than the unmodified peptides.

  2. Quantitation of methadone enantiomers in humans using stable isotope-labeled (2H3)-, (2H5)-, and (2H8)Methadone

    SciTech Connect

    Nakamura, K.; Hachey, D.L.; Kreek, M.J.; Irving, C.S.; Klein, P.D.

    1982-01-01

    A new technique for simultaneous stereoselective kinetic studies of methadone enantiomers was developed using three deuterium-labeled forms of methadone and GLC-chemical-ionization mass spectrometry. A racemic mixture (1:1) of (R)-(-)-(2H5)methadone (l-form) and (S)-(R)-(2H3)methadone (d-form) was administered orally in place of a single daily dose of unlabeled (+/-)-(2H0)methadone in long-term maintenance patients. Racemic (+/-)-(2H8)methadone was used as an internal standard for the simultaneous quantitation of (2H0)-, (2H3)-, and (2H5)methadone in plasma and urine. A newly developed extraction procedure, using a short, disposable C18 reversed-phase cartridge and improved chemical-ionization procedures employing ammonia gas, resulted in significant reduction of the background impurities contributing to the ions used for isotopic abundance measurements. These improvements enabled the measurement of labeled plasma methadone levels for 120 hr following a single dose. This methodology was applied to the study of methadone kinetics in two patients; in both patients, the analgesically active l-enantiomer of the drug had a longer plasma elimination half-life and a smaller area under the plasma disappearance curve than did the inactive d-form.

  3. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry

    Microsoft Academic Search

    Hui Zhang; Xiao-jun Li; Daniel B Martin; Ruedi Aebersold

    2003-01-01

    Quantitative proteome profiling using stable isotope protein tagging and automated tandem mass spectrometry (MS\\/MS) is an emerging technology with great potential for the functional analysis of biological systems and for the detection of clinical diagnostic or prognostic marker proteins. Owing to the enormous complexity of proteomes, their comprehensive analysis is an as-yet-unresolved technical challenge. However, biologically or clinically important information

  4. Efficient labeling in vitro with non-ionic gadolinium magnetic resonance imaging contrast agent and fluorescent transfection agent in bone marrow stromal cells of neonatal rats

    PubMed Central

    LI, YING-QIN; TANG, YING; FU, RAO; MENG, QIU-HUA; ZHOU, XUE; LING, ZE-MIN; CHENG, XIAO; TIAN, SU-WEI; WANG, GUO-JIE; LIU, XUE-GUO; ZHOU, LI-HUA

    2015-01-01

    Although studies have been undertaken on gadolinium labeling-based molecular imaging in magnetic resonance imaging (MRI), the use of non-ionic gadolinium in the tracking of stem cells remains uncommon. To investigate the efficiency in tracking of stem cells with non-ionic gadolinium as an MRI contrast agent, a rhodamine-conjugated fluorescent reagent was used to label bone marrow stromal cells (BMSCs) of neonatal rats in vitro, and MRI scanning was undertaken. The fluorescent-conjugated cell uptake reagents were able to deliver gadodiamide into BMSCs, and cell uptake was verified using flow cytometry. In addition, the labeled stem cells with paramagnetic contrast medium remained detectable by an MRI monitor for a minimum of 28 days. The present study suggested that this method can be applied efficiently and safely for the labeling and tracking of bone marrow stromal cells in neonatal rats. PMID:25816076

  5. Efficient 18F-Labeling of Large 37-Amino Acid pHLIP Peptide Analogues and their Biological Evaluation

    PubMed Central

    Daumar, Pierre; Wanger-Baumann, Cindy A.; Pillarsetty, NagaVaraKishore; Fabrizio, Laura; Carlin, Sean D.; Andreev, Oleg A.; Reshetnyak, Yana K.; Lewis, Jason S.

    2012-01-01

    Solid tumors often develop an acidic microenvironment, which plays a critical role in tumor progression and is associated with increased level of invasion and metastasis. The 37-residue pH (low) insertion peptide (pHLIP®) is under study as an imaging platform because of its unique ability to insert into cell membranes at a low extracellular pH (pHe<7). Labeling of peptides with [18F]-fluorine is usually performed via prosthetic groups using chemoselective coupling reactions. One of the most successful procedures involves the alkyne-azide copper(I) catalyzed cycloaddition (CuAAC). However, none of the known “click” methods have been applied to peptides as large as pHLIP. We designed a novel prosthetic group and extended the use of the CuAAC “click chemistry” for the simple and efficient 18F-labeling of large peptides. For the evaluation of this labeling approach, a D-amino acid analogue of WT-pHLIP and a L-amino acid control peptide K-pHLIP, both functionalized at the N-terminus with 6-azidohexanoic acid, were used. The novel 6-[18F]fluoro-2-ethynylpyridine prosthetic group, was obtained via nucleophilic substitution on the corresponding bromo-precursor after 10 min at 130 °C with a radiochemical yield of 27.5 ± 6.6% (decay corrected) with high radiochemical purity ? 98%. The subsequent CuI catalyzed “click” reaction with the azido functionalized pHLIP peptides was quantitative within 5 min at 70 °C in a mixture of water and ethanol using Cu-acetate and sodium L-ascorbate. [18F]-D-WT-pHLIP and [18F]-L-K-pHLIP were obtained with total radiochemical yields of 5–20% after HPLC purification. The total reaction time was only 85 min including formulation. In vitro stability tests revealed high stability of the [18F]-D-WT-pHLIP in human and mouse plasma after 120 min, with the parent tracer remaining intact at 65 and 85%, respectively. PET imaging and biodistribution studies in LNCaP and PC-3 xenografted mice with the [18F]-D-WT-pHLIP and the negative control [18F]-L-K-pHLIP revealed pH-dependent tumor retention. This reliable and efficient protocol promises to be useful for the 18F-labeling of large peptides such as pHLIP and will accelerate the evaluation of numerous [18F]-pHLIP analogues as potential PET tracers. PMID:22784215

  6. Efficient In Vitro Labeling Rabbit Bone Marrow-Derived Mesenchymal Stem Cells with SPIO and Differentiating into Neural-Like Cells

    PubMed Central

    Zhang, Ruiping; Li, Jing; Li, Jianding; Xie, Jun

    2014-01-01

    Mesenchymal stem cells (MSCs) can differentiate into neural cells to treat nervous system diseases. Magnetic resonance is an ideal means for cell tracking through labeling cells with superparamagnetic iron oxide (SPIO). However, no studies have described the neural differentiation ability of SPIO-labeled MSCs, which is the foundation for cell therapy and cell tracking in vivo. Our results showed that bone marrow-derived mesenchymal stem cells (BM-MSCs) labeled in vitro with SPIO can be induced into neural-like cells without affecting the viability and labeling efficiency. The cellular uptake of SPIO was maintained after labeled BM-MSCs differentiated into neural-like cells, which were the basis for transplanted cells that can be dynamically and non-invasively tracked in vivo by MRI. Moreover, the SPIO-labeled induced neural-like cells showed neural cell morphology and expressed related markers such as NSE, MAP-2. Furthermore, whole-cell patch clamp recording demonstrated that these neural-like cells exhibited electrophysiological properties of neurons. More importantly, there was no significant difference in the cellular viability and [Ca2+]i between the induced labeled and unlabeled neural-like cells. In this study, we show for the first time that SPIO-labeled MSCs retained their differentiation capacity and could differentiate into neural-like cells with high cell viability and a good cellular state in vitro. PMID:25234466

  7. Impact of isotopic effect on density limit and LHCD efficiency in the FT-2 experiments

    NASA Astrophysics Data System (ADS)

    Lashkul, S. I.; Altukhov, A. B.; Gurchenko, A. D.; Gusakov, E. Z.; Dyachenko, V. V.; Esipov, L. A.; Irzak, M. A.; Kantor, M. Yu.; Kouprienko, D. V.; Perevalov, A. A.; Saveliev, A. N.; Shatalin, S. V.; Stepanov, A. Yu.

    2015-07-01

    Current drive by lower hybrid waves (LHCD) is the most effective method to sustain the plasma current, but it is feasible only at the plasma density not exceeding some density limit nDL. In the present work the main attention is paid to the investigation of this effect on the FT-2 (R = 0.55 m, a = 0.08 m, BT ? 3 T, Ipl = 19–40 kA, f0 = 920 MHz) tokamak. The dependence of LHCD efficiency on isotopic plasma content (hydrogen/deuterium) is studied. Characteristic features of such an experiment are a strong influence of the isotope plasma composition on the LH resonance density nLH. For hydrogen plasma nLH ? 3.5 × 1019 m?3, while for deuterium plasma nLH ? 2 × 1020 m?3. The suppression of the LHCD and beginning of the interaction of LH waves with ions are determined by the hydrogen/deuterium plasma density rise. In the hot hydrogen plasma (Te(r = 0 cm) ? 700 eV) the density limit nDL of LHCD is approximately equal to the resonance value nLH ? nLC, where nLC is the point of linear conversion. In the hot deuterium plasma one could expect an increase of nDL because of a much higher value of nLH ? nLC ? 1020 m?3. However it appeared that the observed density limit for LHCD generation nDL ? (3.5–4) × 1019 m?3 is not determined by nLH. The role of parametric instabilities in CD switch-off is considered in both cases. The cooling of the plasma column and density rise could lead to a reduction of the threshold for the parametric decay of f0 and result in early suppression of LHCD. In both cases the LHCD was inversely proportional to the density, which corresponds to the theoretical predictions. In order to analyse the experimentally observed LHCD efficiency the GRILL3D and FRTC codes have been used.

  8. Quantitative Proteomics Isotope Coding Proteomics

    E-print Network

    Richardson, David

    Quantitative Proteomics Isotope Coding Proteomics ­ In-vitro labeling » ICAT » Acid cleavable ICAT quantitation Increased isotope spacing ­ 9 Daltons rather than 8 Daltons ­ Less interference from oxidation;Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach

  9. Characterization of TATP gas phase product ion chemistry via isotope labeling experiments using ion mobility spectrometry interfaced with a triple quadrupole mass spectrometer.

    PubMed

    Tomlinson-Phillips, Jill; Wooten, Alfred; Kozole, Joseph; Deline, James; Beresford, Pamela; Stairs, Jason

    2014-09-01

    Identification of the fragment ion species associated with the ion reaction mechanism of triacetone triperoxide (TATP), a homemade peroxide-based explosive, is presented. Ion mobility spectrometry (IMS) has proven to be a key analytical technique in the detection of trace explosive material. Unfortunately, IMS alone does not provide chemical identification of the ions detected; therefore, it is unknown what ion species are actually formed and separated by the IMS. In IMS, ions are primarily characterized by their drift time, which is dependent on the ion?s mass and molecular cross-section; thus, IMS as a standalone technique does not provide structural signatures, which is in sharp contrast to the chemical and molecular information that is generally obtained from other customary analytical techniques, such as NMR, Raman and IR spectroscopy and mass spectrometry. To help study the ion chemistry that gives rise to the peaks observed in IMS, the hardware of two different commercial IMS instruments has been directly coupled to triple quadrupole (QQQ) mass spectrometers, in order to ascertain each ion?s corresponding mass/charge (m/z) ratios with different dopants at two temperatures. Isotope labeling was then used to help identify and confirm the molecular identity of the explosive fragment and adduct ions of TATP. The m/z values and isotope labeling experiments were used to help propose probable molecular formulas for the ion fragments. In this report, the fragment and adduct ions m/z 58 and 240 of TATP have been confirmed to be [C3H6NH·H](+) and [TATP·NH4](+), respectively; while the fragment ions m/z 73 and 89 of TATP are identified as having the molecular formulas [C4H9NH2](+) and [C4H9O2](+), respectively. It is anticipated that the work in this area will not only help to facilitate improvements in mobility-based detection (IMS and MS), but also aid in the development and optimization of MS-based detection algorithms for TATP. PMID:24913870

  10. Characterization of electron ionization mass spectral (EIMS) fragmentation patterns of chloropropanol esters of palmitic acid using isotope labeling technique.

    PubMed

    Rahn, Anja K K; Yaylayan, Varoujan A

    2014-01-01

    Chloropropanol (CP) esters are a class of thermally-induced toxicants that are mainly formed in refined edible oils. The structural diversity of these esters presents significant analytical challenges which have often been overcome through analysis of their corresponding free alcohols after a hydrolysis step. Mass spectrometry-based methodologies incorporating characteristic fragmentation patterns of particular isomers of CP esters greatly facilitates their identification. The electron ionization mass spectra (EIMS) of various isomers of synthetic and commercially available (13)C- and (2)H-labeled CP ester standards of palmitic (C16) and other short chain fatty acids (C3 to C10) were generated and analyzed using GC/MS. Short chain CP esters were synthesized by reacting their respective acid anhydrides with the corresponding 3-chloro- and 2-chloro- propanediols in addition to 1,3-dichloro- and 1,2-dichloropropanols. Five fragmentation pathways were identified. Four of the five pathways, such as ?-cleavage, McLafferty rearrangement, ?-H rearrangement and cyclic acyloxonium ion formation, were characteristic of CP mono- and diesters. The remaining pathway generating chloronium ion was found only in dichlorinated isomers. The proposed fragmentation pathways for the palmitic acid esters were confirmed through the use of (13)C- and (2)H-labeled CP ester standards of palmitic acid, and the generality of identified fragmentation patterns was confirmed through the identification of equivalent ions in the mass spectra of short chain fatty acids (C3 to C16). Characteristic ions that were identified in this study retaining the chlorine atom in their structures can be considered as potential markers for the presence of CP esters. PMID:25213450

  11. Acetylation and glycation of fibrinogen in vitro occur at specific lysine residues in a concentration dependent manner: A mass spectrometric and isotope labeling study

    SciTech Connect

    Svensson, Jan, E-mail: jan.svensson@ki.se [Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital (Solna), SE-171 76 Stockholm (Sweden) [Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital (Solna), SE-171 76 Stockholm (Sweden); Karolinska Institutet, Department of Clinical Sciences, Danderyd Hospital, SE-182 88 Stockholm (Sweden); Bergman, Ann-Charlotte [Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital (Solna), SE-171 76 Stockholm (Sweden)] [Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital (Solna), SE-171 76 Stockholm (Sweden); Adamson, Ulf [Karolinska Institutet, Department of Clinical Sciences, Danderyd Hospital, SE-182 88 Stockholm (Sweden)] [Karolinska Institutet, Department of Clinical Sciences, Danderyd Hospital, SE-182 88 Stockholm (Sweden); Blombaeck, Margareta [Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital (Solna), SE-171 76 Stockholm (Sweden)] [Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital (Solna), SE-171 76 Stockholm (Sweden); Wallen, Hakan; Joerneskog, Gun [Karolinska Institutet, Department of Clinical Sciences, Danderyd Hospital, SE-182 88 Stockholm (Sweden)] [Karolinska Institutet, Department of Clinical Sciences, Danderyd Hospital, SE-182 88 Stockholm (Sweden)

    2012-05-04

    Highlights: Black-Right-Pointing-Pointer Fibrinogen was incubated in vitro with glucose or aspirin. Black-Right-Pointing-Pointer Acetylations and glycations were found at twelve lysine sites by mass spectrometry. Black-Right-Pointing-Pointer The labeling by aspirin and glucose occurred dose-dependently. Black-Right-Pointing-Pointer No competition between glucose and aspirin for binding to fibrinogen was found. -- Abstract: Aspirin may exert part of its antithrombotic effects through platelet-independent mechanisms. Diabetes is a condition in which the beneficial effects of aspirin are less prominent or absent - a phenomenon called 'aspirin resistance'. We investigated whether acetylation and glycation occur at specific sites in fibrinogen and if competition between glucose and aspirin in binding to fibrinogen occurs. Our hypothesis was that such competition might be one explanation to 'aspirin resistance' in diabetes. After incubation of fibrinogen in vitro with aspirin (0.8 mM, 24 h) or glucose (100 mM, 5-10 days), we found 12 modified sites with mass spectrometric techniques. Acetylations in the {alpha}-chain: {alpha}K191, {alpha}K208, {alpha}K224, {alpha}K429, {alpha}K457, {alpha}K539, {alpha}K562, in the {beta}-chain: {beta}K233, and in the {gamma}-chain: {gamma}K170 and {gamma}K273. Glycations were found at {beta}K133 and {gamma}K75, alternatively {gamma}K85. Notably, the lysine 539 is a site involved in FXIII-mediated cross-linking of fibrin. With isotope labeling in vitro, using [{sup 14}C-acetyl]salicylic acid and [{sup 14}C]glucose, a labeling of 0.013-0.084 and 0.12-0.5 mol of acetylated and glycated adduct/mol fibrinogen, respectively, was found for clinically (12.9-100 {mu}M aspirin) and physiologically (2-8 mM glucose) relevant plasma concentrations. No competition between acetylation and glycation could be demonstrated. Thus, fibrinogen is acetylated at several lysine residues, some of which are involved in the cross-linking of fibrinogen. This may mechanistically explain why aspirin facilitates fibrin degradation. We find no support for the idea that glycation of fibrin(ogen) interferes with acetylation of fibrinogen.

  12. Precise quantitation of 136 urinary proteins by LC/MRM-MS using stable isotope labeled peptides as internal standards for biomarker discovery and/or verification studies.

    PubMed

    Percy, Andrew J; Yang, Juncong; Hardie, Darryl B; Chambers, Andrew G; Tamura-Wells, Jessica; Borchers, Christoph H

    2015-06-15

    Spurred on by the growing demand for panels of validated disease biomarkers, increasing efforts have focused on advancing qualitative and quantitative tools for more highly multiplexed and sensitive analyses of a multitude of analytes in various human biofluids. In quantitative proteomics, evolving strategies involve the use of the targeted multiple reaction monitoring (MRM) mode of mass spectrometry (MS) with stable isotope-labeled standards (SIS) used for internal normalization. Using that preferred approach with non-invasive urine samples, we have systematically advanced and rigorously assessed the methodology toward the precise quantitation of the largest, multiplexed panel of candidate protein biomarkers in human urine to date. The concentrations of the 136 proteins span >5 orders of magnitude (from 8.6?g/mL to 25pg/mL), with average CVs of 8.6% over process triplicate. Detailed here is our quantitative method, the analysis strategy, a feasibility application to prostate cancer samples, and a discussion of the utility of this method in translational studies. PMID:25858257

  13. Bio-generation of stable isotope-labeled internal standards for absolute and relative quantitation of phase II drug metabolites in plasma samples using LC-MS/MS.

    PubMed

    Li, Pei; Li, Zi; Beck, Wayne D; Callahan, Patrick M; Terry, Alvin V; Bar-Peled, Maor; Bartlett, Michael G

    2015-05-01

    Quantification of drug metabolites in biological samples has been of great interest in current pharmaceutical research, since metabolite concentrations and pharmacokinetics can contribute to a better understanding of the toxicity of drug candidates. Two major categories of Phase II metabolites, glucuronide conjugates and glutathione conjugates, may cause significant drug toxicity and therefore require close monitoring at early stages of drug development. In order to achieve high precision, accuracy, and robustness, stable isotope-labeled (SIL) internal standards (IS) are widely used in quantitative bioanalytical methods using liquid chromatography and tandem mass spectrometry (LC-MS/MS), due to their capability of compensating for matrix effects, extraction variations and instrument response fluctuations. However, chemical synthesis of SIL analogues of Phase II metabolites can often be very difficult and require extensive exploratory research, leading to higher cost and significant delays in drug research and development. To overcome these challenges, we have developed a generic method which can synthesize SIL analogues of Phase II metabolites from more available SIL parent drugs or SIL conjugation co-factors, using in vitro biotransformation. This methodology was successfully applied to the bio-generation of SIL glucuronide conjugates and glutathione conjugates. The method demonstrated satisfactory performance in both absolute quantitation and assessment of relative exposure coverage across species in safety tests of drug metabolites (MIST). This generic technique can be utilized as an alternative to chemical synthesis and potentially save time and cost for drug research and development. PMID:25804729

  14. Promotion of expression of interferon-stimulated genes in U937 monocytic cells by HIV RNAs, measured using stable isotope labeling with amino acids in cell culture (SILAC).

    PubMed

    Li, Yulan; Wen, Bin; Chen, Ran; Jiang, Feng; Zhao, Xiaofang; Deng, Xin

    2015-05-01

    Type I interferon (IFN) exerts strong antiviral activity, particularly against human immunodeficiency virus (HIV), and although several viral proteins have been shown to deregulate IFN induction, little is known about the induction of type I IFNs by HIV RNAs. In the present study, we used the stable isotope labeling with amino acids in cell culture (SILAC) method to determine the proteomic profile in U937 monocytic cells after transfection with viral RNA of HIV. We then used a western blot assay to validate the proteomic results. It was revealed by the SILAC method that there were 1624 non-redundant peptides with quantitative information and 281 proteins with quantitative information in the HIV-RNA-transfected U937 cells when compared to cells transfected with control RNA. In particular, 6, 8 or 12 hours post-transfection, HIV RNA transfection promoted the expression of such interferon stimulated genes (ISGs) as interferon-induced proteins with tetratricopeptide repeats (IFITs), interferon-induced transmembrane proteins (IFITMs), interferon-induced gene 15 protein (ISG15), myxovirus (influenza virus) resistance protein 1 (MX1), and interferon-induced guanylate-binding protein 1 (GBP1), and this was confirmed by western blot assay. In conclusion, HIV RNA is a strong stimulator of IFNs, promoting the expression of such ISGs as IFITs, IFITMs, ISG15, MX1 and GBP1. PMID:25772570

  15. Inter-residue coupling and equilibrium unfolding of PPII helical peptides. Vibrational spectra enhanced with (13)C isotopic labeling.

    PubMed

    Chi, Heng; Lakhani, Ahmed; Roy, Anjan; Nakaema, Marcelo; Keiderling, Timothy A

    2010-10-01

    Unordered proteins, unfolded peptides, and several "random coil" models have been shown to have local conformations similar to that of polyproline II (PPII). Inter-residue coupling of selected residues in a series of related peptides having predominantly PPII conformations were measured using IR, VCD, and Raman spectra of selected variants that were doubly C(1)-labeled with (13)C on the amide C?O. The characteristics of the (13)C?O component of the IR, VCD, and Raman amide I' bands and their sensitivity to the local structure of the peptide are compared to predictions based on DFT level calculations for related structures and used to estimate coupling interactions between pairs of C?O groups along the backbone of this helical structure. In the PPII case, the coupling is relatively weak, due to the extended structure, yet by combining IR, Raman, and VCD observations with results of DFT level model calculations, we have determined bounds for experimental interaction constants for this structure. Correlation of properties for PPII structures with those of "random coils" can be done by comparing Pro(n) and Pro-rich sequences with Lys-rich sequences. The experimental band shifts and implied couplings reflect the computed results in both cases. Thermal unfolding of these peptides appears to be multistate, with monotonic spectral changes but little evidence of a cooperative (sigmoidal) transition. For the Lys-rich series, a transition from PPII to ?-helix structure was induced by TFE addition, and the spectra were fit to an equilibrium model. These spectral changes show a large variation in (13)C?O coupling that occurs with a local conformational change from PPII- to ?-helical, which is both well-fit by our theoretical results and offers a new site-specific method of assigning local PPII/disordered vs ?-helical (or other) structure. PMID:20831224

  16. Comparative cytochrome P450 proteomics in the livers of immune-deficient mice using 18O stable isotope labeling

    PubMed Central

    Lane, Catherine S.; Wang, Yuqin; Betts, Richard; Griffiths, William J.; Patterson, Laurence H

    2008-01-01

    Quantitative changes in cytochrome P450 (CYP) proteins involved in drug metabolism as a consequence of drug treatment are important parameters in predicting the fates and pharmacological consequences of xenobiotics and drugs. In this study we undertake comparative P450 proteomics using liver from control and 1,4 bis 2-(3,5-dichloropyridyloxybenzene) (TCPOBOP)-dosed mice. The method involved separation of microsomal proteins by SDS-PAGE, trypsin digestion and post-digest 18O/16O-labeling, followed by nano-liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) for peptide identification, and LC-MS for relative quantification. Seventeen P450 proteins were identified from mouse liver, of which sixteen yielded data sufficient for relative quantification. All the P450s detected were unambiguously identified except the highly homologous CYP2A4/2A5. With the exception of CYP2A12, 2D10 and 2F2, the levels of all the P450s quantified were affected by treatment with TCPOBOP (3 mg/kg). CYP1A2, 2A4/5, 2B10, 2B20, 2C29, 2C37, 2C38, 3A11 and 39A1 were up-regulated, and CYP2C40, 2E1, 3A41 and 27A1 down-regulated. The response of CYP2B20 to stimulation has not previously been distinguished from that of CYP2B10 because of the poor discrimination between these two proteins (they share 87% sequence identity). Differential response to chemical stimulation by closely related members of the CYP2C subfamily was also observed. PMID:17296599

  17. A new strategy for sequential assignment of intrinsically unstructured proteins based on 15N single isotope labelling

    NASA Astrophysics Data System (ADS)

    Lopez, Juan; Ahuja, Puneet; Gerard, Melanie; Wieruszeski, Jean-Michel; Lippens, Guy

    2013-11-01

    We describe a new efficient strategy for the sequential assignment of amide resonances of a conventional 15N-1H HSQC spectrum of intrinsically unfolded proteins, based on composite NOESY-TOCSY and TOCSY-NOESY mixing times. These composite mixing times lead to a H?-proton mediated unidirectional transfer of amide to amide proton. We have implemented the composite mixing times in an HSQC-NOESY-HSQC manner to obtain directional connectivity between amides of neighbouring residues. We experimentally determine the optimal mixing times for both transfer schemes, and demonstrate its use in the assignment for both a fragment of the neuronal tau protein and for ?-synuclein.

  18. Plasma-treated polystyrene film that enhances binding efficiency for sensitive and label-free protein biosensing

    NASA Astrophysics Data System (ADS)

    Guo, Bihong; Li, Shaopeng; Song, Lusheng; Yang, Mo; Zhou, Wenfei; Tyagi, Deependra; Zhu, Jinsong

    2015-08-01

    A plasma-treated ultrathin polystyrene (PS) film surface was explored as a simple, robust, and low-cost surface chemistry solution for protein biosensing applications. This surface could dramatically improve the binding efficiency of the protein-protein interactions, which is defined as the binding signal per immobilized ligand. The PS-modified protein biosensor was readily fabricated by spin coating and plasma treatment. Various parameters for fabrication, including the concentration of the PS solution, rate of spin coating, and duration of plasma treatment, were systematically optimized based on the improvement of fluorescence signal yielded by the microfluidic network-aided fluorescence immunoassay. The performance of the label-free protein detection on the optimized surfaces was further evaluated by surface plasmon resonance imaging (SPRi). PS surfaces with optimal fabrication parameters exhibited up to an 620% enhancement of the protein binding response and approximately 210% of the protein binding per immobilized protein ligand compared with a self-assembled monolayer (SAM) surface of 11-mercapto undecanoic acid (MUA). The relationship between the fabrication parameters used and changes to the surface chemistry and the morphological properties were characterized with atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared spectroscopy (FTIR). It was revealed that the morphological changes observed in the plasma-treated PS film were the dominant factor for the improvement of the protein bioassay performance, rather than the chemical changes.

  19. A new and efficient synthetic method for 15N3-labeled cytosine nucleosides: Dimroth rearrangement of cytidine N3-oxides.

    PubMed

    Sako, Magoichi; Kawada, Hiroyoshi

    2004-11-12

    The treatment of (15)N(4)-labeled cytidine N(3)-oxide and (15)N(4)-labeled 2'-deoxycytidine N(3)-oxide, prepared from the appropriate unprotected uridines in three reaction steps, with benzyl bromide in the presence of excess lithium methoxide allowed the smooth occurrence of their Dimroth rearrangement even under mild conditions leading to the corresponding (15)N(3)-labeled uridine 4-O-benzyloximes which can easily undergo the reductive N-O bond cleavage to give the desirable (15)N(3)-labeled cytosine nucleosides in high total yields. PMID:15527310

  20. Prediction of equilibrium Li isotope fractionation between minerals and aqueous solutions at high P and T: an efficient ab initio approach

    E-print Network

    Kowalski, Piotr M

    2011-01-01

    The mass-dependent equilibrium stable isotope fractionation between different materials is an important geochemical process. Here we present an efficient method to compute the isotope fractionation between complex minerals and fluids at high pressure, P, and temperature, T, representative for the Earth's crust and mantle. The method is tested by computation of the equilibrium fractionation of lithium isotopes between aqueous fluids and various Li bearing minerals such as staurolite, spodumene and mica. We are able to correctly predict the direction of the isotope fractionation as observed in the experiments. On the quantitative level the computed fractionation factors agree within 1.0 permil with the experimental values indicating predictive power of ab initio methods. We show that with ab initio methods we are able to investigate the underlying mechanisms driving the equilibrium isotope fractionation process, such as coordination of the fractionating elements, their bond strengths to the neighboring atoms, c...

  1. DETERMINATION OF THE EFFICIENCY OF AN ION EXCHANGE SYSTEM IN SEPARATING THE LITHIUM ISOTOPES (PRELIMINARY STUDY)

    Microsoft Academic Search

    R. E. Blanco; A. H. Kibbey; J. T. Roberts

    1954-01-01

    The lithium isotopic separation factors for the ion exchange systems ; studied appear to be quite low, of the magnitude of 1.003. Any possible effects ; on the separation factor attributable to concentration or the presence of ; complexing agents were within the limits of experimental error. The HTU for ; lithium ion exchange is low, i.e., a fraction of

  2. Absolute quantification of UGT1A1 in various tissues and cell lines using isotope label-free UPLC-MS/MS method determines its turnover number and correlates with its glucuronidation activities.

    PubMed

    Xu, Beibei; Gao, Song; Wu, Baojian; Yin, Taijun; Hu, Ming

    2014-01-01

    Uridine 5'-diphosphate-glucuronosyltransferase (UGT)1A1 is a major phase II metabolism enzyme responsible for glucuronidation of drugs and endogenous compounds. The purpose of this study was to determine the expression level of UGT1A1 in human liver microsomes and human cell lines by using an isotope label-free LC-MS/MS method. A Waters Ultra performance liquid chromatography (UPLC) system coupled with an API 5500Qtrap mass spectrometer was used for the analysis. Two signature peptides (Pep-1, and Pep-2) were employed to quantify UGT1A1 by multiple reaction monitoring (MRM) approach. Standard addition method was used to validate the assay to account for the matrix effect. 17?-Estradiol was used as the marker substrate to determine UGT1A1 activities. The validated method has a linear range of 200-0.0195nM for both signature peptides. The precision, accuracy, and matrix effect were in acceptable ranges. UGT1A1 expression levels were then determined using 8 individual human liver microsomes, a pooled human liver microsomes, three UGT1A1 genotyped human liver microsomes, and four cell lines (Caco-2, MCF-7, Hela, and HepG2). The correlations study showed that the UGT1A1 protein levels were strongly correlated with its glucuronidation activities in human liver microsomes (R(2)=0.85) and in microsomes prepared from cell lines (R(2)=0.95). Isotope-labeled peptides were not necessary for LC-MS/MS quantitation of proteins. The isotope label-free absolute quantification method used here had good accuracy, sensitivity, linear range, and reproducibility, and were used successfully for the accurate determination of UGT1A1 from tissues and cell lines. PMID:24055854

  3. Atmospheric CO2 level affects plants' carbon use efficiency: insights from a 13C labeling experiment on sunflower stands

    NASA Astrophysics Data System (ADS)

    Gong, Xiaoying; Schäufele, Rudi; Schnyder, Hans

    2015-04-01

    The increase of atmospheric CO2 concentration has been shown to stimulate plant photosynthesis and (to a lesser extent) growth, thereby acting as a possible sink for the additional atmospheric CO2. However, this effect is dependent on the efficiency with which plants convert atmospheric carbon into biomass carbon, since a considerable proportion of assimilated carbon is returned to the atmosphere via plant respiration. As a core parameter for carbon cycling, carbon use efficiency of plants (CUE, the ratio of net primary production to gross primary production) quantifies the proportion of assimilated carbon that is incorporated into plant biomass. CUE has rarely been assessed based on measurements of complete carbon balance, due to methodological difficulties in measuring respiration rate of plants in light. Moreover, foliar respiration is known to be inhibited in light, thus foliar respiration rate is generally lower in light than in dark. However, this phenomenon, termed as inhibition of respiration in light (IRL), has rarely been assessed at the stand-scale and been incorporated into the calculation of CUE. Therefore, how CUE responses to atmospheric CO2 levels is still not clear. We studied CUE of sunflower stands grown at sub-ambient CO2 level (200 ?mol mol-1) and elevated CO2 level (1000 ?mol mol-1) using mesocosm-scale gas exchange facilities which enabled continuous measurements of 13CO2/12CO2 exchange. Appling steady-state 13C labeling, fluxes of respiration and photosynthesis in light were separated, and tracer kinetic in respiration was analyzed. This study provides the first data on CUE at a mesocosm-level including respiration in light in different CO2 environments. We found that CUE of sunflower was lower at an elevated CO2 level than at a sub-ambient CO2 level; and the ignorance of IRL lead to erroneous estimations of CUE. Variation in CUE at atmospheric CO2 levels was attributed to several mechanisms. In this study, CO2 enrichment i) affected the size of respiratory substrate pools and the relative contribution of temporary storage pools and current assimilation pools; ii) affected the extent of inhibition of stands' respiration in light, which was related to leaf-level re-fixation of respired CO2; and iii) influenced the ratio of leaf mass to total plant mass. Our study highlights the necessity of integrating measurement of respiration in light in assessing carbon cycling. If the decrease of CUE by CO2 enrichment is a general response of terrestrial ecosystems, the buffering effect of plants C acquisition to the rise of atmospheric CO2 is lower than estimated so far.

  4. Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC)-based Quantitative Proteomics Study of a Thyroid Hormone-regulated Secretome in Human Hepatoma Cells*

    PubMed Central

    Chen, Cheng-Yi; Chi, Lang-Ming; Chi, Hsiang-Cheng; Tsai, Ming-Ming; Tsai, Chung-Ying; Tseng, Yi-Hsin; Lin, Yang-Hsiang; Chen, Wei-Jan; Huang, Ya-Hui; Lin, Kwang-Huei

    2012-01-01

    The thyroid hormone, 3, 3?,5-triiodo-l-thyronine (T3), regulates cell growth, development, differentiation, and metabolism via interactions with thyroid hormone receptors (TRs). However, the secreted proteins that are regulated by T3 are yet to be characterized. In this study, we used the quantitative proteomic approach of stable isotope labeling with amino acids in cell culture coupled with nano-liquid chromatography-tandem MS performed on a LTQ-Orbitrap instrument to identify and characterize the T3-regulated proteins secreted in human hepatocellular carcinoma cell lines overexpressing TR?1 (HepG2-TR?1). In total, 1742 and 1714 proteins were identified and quantified, respectively, in three independent experiments. Among these, 61 up-regulated twofold and 11 down-regulated twofold proteins were identified. Eight proteins displaying increased expression and one with decreased expression in conditioned media were validated using Western blotting. Real-time quantitative RT-PCR further disclosed induction of plasminogen activator inhibitor-1 (PAI-1), a T3 target, in a time-course and dose-dependent manner. Serial deletions of the PAI-1 promoter region and subsequent chromatin immunoprecipitation assays revealed that the thyroid hormone response element on the promoter is localized at positions –327/–312. PAI-1 overexpression enhanced tumor growth and migration in a manner similar to what was seen when T3 induced PAI-1 expression in J7-TR?1 cells, both in vitro and in vivo. An in vitro neutralizing assay further supported a crucial role of secreted PAI-1 in T3/TR-regulated cell migration. To our knowledge, these results demonstrate for the first time that proteins involved in the urokinase plasminogen activator system, including PAI-1, uPAR, and BSSP4, are augmented in the extra- and intracellular space of T3-treated HepG2-TR?1 cells. The T3-regulated secretome generated in the current study may provide an opportunity to establish the mechanisms underlying T3-associated tumor progression and prognosis. PMID:22171322

  5. Depletion optimization and photon efficiency in laser isotope separation of deuterium.

    PubMed

    Vanderleeden, J C

    1978-03-01

    The depletion optimization of one of the isotopic components in a gas stream is considered, using a one-photon laser separation process, when the absorption path is in the kilometer range. A multiple-pass cylindrical geometry is proposed with the gas flowing through a tube enclosed by aspherical mirrors. Radiation is injected such that adjustment of the mirror parameters establishes a flux distribution which optimizes the depletion while it minimizes losses from incomplete absorption. The mirror parameters are derived and application to deuterium separation is discussed. This approach it also useful in optical amplifiers and resonators to maximize energy extraction. PMID:20197874

  6. Evaluation of a Method for Nitrotyrosine Site Identification and Relative Quantitation Using a Stable Isotope-Labeled Nitrated Spike-In Standard and High Resolution Fourier Transform MS and MS/MS Analysis

    PubMed Central

    Seeley, Kent W.; Fertig, Alison R.; Dufresne, Craig P.; Pinho, Joao P. C.; Stevens, Stanley M.

    2014-01-01

    The overproduction of reactive oxygen and nitrogen species (ROS and RNS) can have deleterious effects in the cell, including structural and possible activity-altering modifications to proteins. Peroxynitrite is one such RNS that can result in a specific protein modification, nitration of tyrosine residues to form nitrotyrosine, and to date, the identification of nitrotyrosine sites in proteins continues to be a major analytical challenge. We have developed a method by which 15N-labeled nitrotyrosine groups are generated on peptide or protein standards using stable isotope-labeled peroxynitrite (O15NOO?), and the resulting standard is mixed with representative samples in which nitrotyrosine formation is to be measured by mass spectrometry (MS). Nitropeptide MS/MS spectra are filtered using high mass accuracy Fourier transform MS (FTMS) detection of the nitrotyrosine immonium ion. Given that the nitropeptide pair is co-isolated for MS/MS fragmentation, the nitrotyrosine immonium ions (at m/z = 181 or 182) can be used for relative quantitation with negligible isotopic interference at a mass resolution of greater than 50,000 (FWHM, full width at half-maximum). Furthermore, the standard potentially allows for the increased signal of nitrotyrosine-containing peptides, thus facilitating selection for MS/MS in a data-dependent mode of acquisition. We have evaluated the methodology in terms of nitrotyrosine site identification and relative quantitation using nitrated peptide and protein standards. PMID:24736779

  7. Does a stable isotopically labeled internal standard always correct analyte response? A matrix effect study on a LC/MS/MS method for the determination of carvedilol enantiomers in human plasma.

    PubMed

    Wang, Sherry; Cyronak, Matthew; Yang, Eric

    2007-01-17

    A stable isotopically labeled (SIL) analogue is believed to be the most appropriate internal standard in a quantitative bioanalytical liquid chromatography/tandem mass spectrometry (LC/MS/MS) assay. It is assumed that a SIL internal standard always compensates for variability in chemical derivatization, sample extraction and LC/MS/MS analysis due to its nearly identical chemical and physical properties to the unlabeled analyte. Hence, the analyte to internal standard peak area ratio should be constant despite any variations in sample processing or analysis. However, in our laboratories, a deuterium labeled internal standard of carvedilol demonstrated an unexpected behavior-the analyte to internal standard peak area ratio changed with two specific lots of commercially supplied human plasma. Several experiments, including dilution of the extract with LC mobile phase and post-column infusion of the carvedilol solution followed by the injection of extracted blank plasma, have indicated that a high level of matrix suppression affected the ionization of the carvedilol-S enantiomer and its deuterated internal standard differently in these two lots of plasma. For the first time, it was clearly demonstrated that a slight difference in retention time between the analyte and the SIL internal standard, caused by deuterium isotope effect, has resulted in a different degree of ion suppression between these two analogues. This difference was significant enough to change the analyte to internal standard peak area ratio and affect the accuracy of the method. PMID:16959461

  8. Carbon transfer from photosynthesis to below ground fine root/hyphae respiration in Quercus serrata using stable carbon isotope pulse labeling

    NASA Astrophysics Data System (ADS)

    Dannoura, M.; Kominami, Y.; Takanashi, S.; Takahashi, K.

    2013-12-01

    Studying carbon allocation in trees is a key to better understand belowground carbon cycle and its response to climate change. Tracing 13C in tree and soil compartments after pulse labeling is one of powerful tool to study the fate of carbon in forest ecosystems. This experiment was conducted in Yamashiro experimental forest, Kyoto, Japan. Annual mean temperature and precipitation from 1994 to 2009 are 15.5 ° C and 1,388 mm respectively. The branch pulse labeling were done 7 times in 2011 using same branch of Quercus serrata (H:11.7 m, DBH; 33.7 cm) to see seasonal variations of carbon velocity. Whole crown labeling of Quercus serrata (H:9 m, DBH; 13.7 cm) was done in 2012 to study carbon allocation and to especially focus on belowground carbon flux until to the hyphae respiration. Pure 13CO2 (99.9%) was injected to the labeling chamber which was set to branch or crown. Then, after one hour of branch labeling and 3.5 hour for crown labeling, the chamber was opened. Trunk respiration chambers, fine root chambers and hyphae chambers were set to the target tree to trace labeled carbon in the CO2 efflux. 41 ?m mesh was used to exclude ingrowth of roots into hyphae chambers. The results show that the velocity of carbon through the tree varied seasonally, with higher velocity in summer than autumn, averaging 0.47 m h-1. Half-lives of labeled carbon in autotrophic respiration were similar above and below ground during the growing season, but they were twice longer in trunk than in root in autumn. From the whole crown labeling done end of growing season, the 13CO2 signal was observed 25 hours after labeling in trunk chamber and 34-37.7 hours after labeling in fine root and hyphae respiration almost simultaneously. Half-lives of 13 was longer in trunk than below ground. Trunk respiration was still using labelled carbon during winter suggesting that winter trunk respiration is partly fueled by carbon stored in the trunk at the end of the growing season.

  9. Growth of Adlayer Graphene on Cu Studied by Carbon Isotope Qiongyu Li,

    E-print Network

    Growth of Adlayer Graphene on Cu Studied by Carbon Isotope Labeling Qiongyu Li, Harry Chou, Jin and multilayer graphene on copper foils was studied by isotopic labeling of the methane precursor. Isotope: Graphene, adlayer, isotope-labeling, micro-Raman mapping, TOF SIMS Chemical vapor deposition (CVD

  10. Quantitative analysis of N-glycans from human alfa-acid-glycoprotein using stable isotope labeling and zwitterionic hydrophilic interaction capillary liquid chromatography electrospray mass spectrometry as tool for pancreatic disease diagnosis.

    PubMed

    Giménez, Estela; Balmaña, Meritxell; Figueras, Joan; Fort, Esther; de Bolós, Carme; Sanz-Nebot, Victòria; Peracaula, Rosa; Rizzi, Andreas

    2015-03-25

    In this work we demonstrate the potential of glycan reductive isotope labeling (GRIL) using [(12)C]- and [(13)C]-coded aniline and zwitterionic hydrophilic interaction capillary liquid chromatography electrospray mass spectrometry (?ZIC-HILIC-ESI-MS) for relative quantitation of glycosylation variants in selected glycoproteins present in samples from cancer patients. Human ?1-acid-glycoprotein (hAGP) is an acute phase serum glycoprotein whose glycosylation has been described to be altered in cancer and chronic inflammation. However, it is not clear yet whether some particular glycans in hAGP can be used as biomarker for differentiating between these two pathologies. In this work, hAGP was isolated by immunoaffinity chromatography (IAC) from serum samples of healthy individuals and from those suffering chronic pancreatitis and different stages of pancreatic cancer, respectively. After de-N-glycosylation, relative quantitation of the hAGP glycans was carried out using stable isotope labeling and ?ZIC-HILIC-ESI-MS analysis. First, protein denaturing conditions prior to PNGase F digestion were optimized to achieve quantitative digestion yields, and the reproducibility of the established methodology was evaluated with standard hAGP. Then, the proposed method was applied to the analysis of the clinical samples (control vs. pathological). Pancreatic cancer samples clearly showed an increase in the abundance of fucosylated glycans as the stage of the disease increases and this was unlike to samples from chronic pancreatitis. The results gained here indicate the mentioned glycan in hAGP as a candidate structure worth to be corroborated by an extended study including more clinical cases; especially those with chronic pancreatitis and initial stages of pancreatic cancer. Importantly, the results demonstrate that the presented methodology combining an enrichment of a target protein by IAC with isotope coded relative quantitation of N-glycans can be successfully used for targeted glycomics studies. The methodology is assumed being suitable as well for other such studies aimed at finding novel cancer associated glycoprotein biomarkers. PMID:25732693

  11. NTFD--a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data

    E-print Network

    Kelleher, Joanne Keene

    Summary: Most current stable isotope-based methodologies are targeted and focus only on the well-described aspects of metabolic networks. Here, we present NTFD (non-targeted tracer fate detection), a software for the ...

  12. Allocation of atmospheric CO2 into labile sub-surface carbon pools: a stable isotope labelling approach in a tundra wetland

    NASA Astrophysics Data System (ADS)

    Rüggen, Norman; Knoblauch, Christian; Pfeiffer, Eva-Maria

    2015-04-01

    Greenhouse gas emissions from permafrost-affected wetlands are intensively studied due to their important role in the global carbon cycle. There are concerns of increasing methane and carbon dioxide fluxes from tundra wetlands due to permafrost degradation and hydrology changes in a warming Arctic. Understanding the sub-surface carbon pool interactions will improve the prediction on how trace gas fluxes from these ecosystems will respond to changing environmental conditions. Partitioning the sources of greenhouse gas fluxes will help to evaluate the quantitative role of recently produced plant photosynthates. Furthermore, partitioning allows separating respiration of long-term stored organic matter and freshly produced plant products. This knowledge is crucial for understanding the response of greenhouse gas fluxes in such wetlands to environmental changes. An in situ 13CO2 pulse-labelling experiment has been conducted in the northeast Siberian tundra (Samoylov island, Lena river delta) in August 2013 to quantify interactions among sub-surface carbon pools (DIC, DOC, CH4) in three depths (6, 16 and 36 cm) of the active layer. The experimental site was a low-centred polygon centre in a polygonal tundra landscape, with a sedge-moss (Carex-Scorpidium) plant association. The water table was at the soils' surface and the permafrost table in a depth of 50 cm. After the system has been 13CO2 pulse labelled, all three studied subsurface carbon pools (CH4, DIC and DOC) were clearly 13C-enriched, which accounts for atmospheric C incorporated into these pools. One day after the labelling, in 6 cm depth 1.5 percent of DIC and 0.1 percent of CH4were replaced by label C, which then steadily declined over a ten days period. The label C content of DOC increased gradually over the same period. In 16 cm depth, the label C increased gradually after labelling in both DIC and CH4. Label C was found in DIC and CH4 even in a depth of 36 cm, although in less pronounced concentrations. Carex material, exposed to the label, also substantially incorporated the label. Deduced from the results, we will present carbon exchange fluxes among sub-surface DIC, DOC and CH4 in a sedge-moss covered polygon-centre.

  13. Stable carbon isotope ratios and intrinsic water-use efficiency of Miocene fossil leaves compared to modern congeners

    SciTech Connect

    Marshall, J.D.; Zhang, J.; Rember, W.C.; Jennings, D.; Larson, P. (Univ. of Idaho, Moscow, ID (United States))

    1994-06-01

    Miocene fossil leaves of forest trees were extracted from the Clarkia, Idaho fossil beds and their stable carbon isotope ratios were analyzed. Fossils had higher lignin concentrations and lower cellulose concentrations that modern leaves due to diagenesis and the HF used to extract the fossils. Therefore, [delta][sup 13]C of extracted fossil lignin was compared to that of modern lignin. Fossil lignin [delta][sup 13]C was significantly different from that of congeneric modern leaves (paired t-test, P<0.0001), but was 1.9% less negative. Gymnosperms (Metasequoia, Taxodium) were less negative than angiosperms (e.g., Magnolia, Quercus, Acer, Persea), but no difference between evergreen and deciduous species was detected. Using published estimates of the concentration and [delta][sup 13]C of atmospheric CO[sub 2] during the Miocene was estimated the CO[sub 2] partial pressure gradient across the stomata (intrinsic water-use efficiency). Intrinsic water-use efficiency was at least 70% higher during this past [open quotes]greenhouse[close quotes] period than at present.

  14. Isotope-based analysis of modified tRNA nucleosides correlates modification density with translational efficiency.

    PubMed

    Brandmayr, Caterina; Wagner, Mirko; Brückl, Tobias; Globisch, Daniel; Pearson, David; Kneuttinger, Andrea Christa; Reiter, Veronika; Hienzsch, Antje; Koch, Susanne; Thoma, Ines; Thumbs, Peter; Michalakis, Stylianos; Müller, Markus; Biel, Martin; Carell, Thomas

    2012-10-29

    Useful diversity: Quantification of modified tRNA nucleobases in different murine and porcine tissues reveals a tissue-specific overall modification content. The modification content correlates with rates of protein synthesis in?vitro, suggesting a direct link between tRNA modification levels and tissue-specific translational efficiency. PMID:23037940

  15. Silicon isotopes indicate enhanced carbon export efficiency in the North Atlantic during deglaciation.

    PubMed

    Hendry, Katharine R; Robinson, Laura F; McManus, Jerry F; Hays, James D

    2014-01-01

    Today's Sargasso Sea is nutrient starved, except for episodic upwelling events caused by wind-driven winter mixing and eddies. Enhanced diatom opal burial in Sargasso Sea sediments indicates that silicic acid, a limiting nutrient today, may have been more available in subsurface waters during Heinrich Stadials, millennial-scale climate perturbations of the last glacial and deglaciation. Here we use the geochemistry of opal-forming organisms from different water depths to demonstrate changes in silicic acid supply and utilization during the most recent Heinrich Stadial. We suggest that during the early phase (17.5-18 ka), wind-driven upwelling replenished silicic acid to the subsurface, resulting in low Si utilization. By 17 ka, stratification reduced the surface silicic acid supply leading to increased Si utilization efficiency. This abrupt shift in Si cycling would have contributed to high regional carbon export efficiency during the recent Heinrich Stadial, despite being a period of increasing atmospheric CO2. PMID:24452197

  16. Comparison of (64)Cu-complexing bifunctional chelators for radioimmunoconjugation: labeling efficiency, specific activity, and in vitro/in vivo stability.

    PubMed

    Cooper, Maggie S; Ma, Michelle T; Sunassee, Kavitha; Shaw, Karen P; Williams, Jennifer D; Paul, Rowena L; Donnelly, Paul S; Blower, Philip J

    2012-05-16

    High radiolabeling efficiency, preferably to high specific activity, and good stability of the radioimmunoconjugate are essential features for a successful immunoconjugate for imaging or therapy. In this study, the radiolabeling efficiency, in vitro stability, and biodistribution of immunoconjugates with eight different bifunctional chelators labeled with (64)Cu were compared. The anti-CD20 antibody, rituximab, was conjugated to four macrocyclic bifunctional chelators (p-SCN-Bn-DOTA, p-SCN-Bn-Oxo-DO3A, p-SCN-NOTA, and p-SCN-PCTA), three DTPA derivatives (p-SCN-Bn-DTPA, p-SCN-CHX-A?-DTPA, and ITC-2B3M-DTPA), and a macrobicyclic hexamine (sarcophagine) chelator (sar-CO2H) = (1-NH2-8-NHCO(CH2)3CO2H)sar where sar = sarcophagine = 3,6,10,13,16,19-hexaazabicyclo[6.6.6]icosane). Radiolabeling efficiency under various conditions, in vitro stability in serum at 37 °C, and in vivo biodistribution and imaging in normal mice over 48 h were studied. All chelators except sar-CO2H were conjugated to rituximab by thiourea bond formation with an average of 4.9 ± 0.9 chelators per antibody molecule. Sar-CO2H was conjugated to rituximab by amide bond formation with 0.5 chelators per antibody molecule. Efficiencies of (64)Cu radiolabeling were dependent on the concentration of immunoconjugate. Notably, the (64)Cu-NOTA-rituximab conjugate demonstrated the highest radiochemical yield (95%) under very dilute conditions (31 nM NOTA-rituximab conjugate). Similarly, sar-CO-rituximab, containing 1/10th the number of chelators per antibody compared to that of other conjugates, retained high labeling efficiency (98%) at an antibody concentration of 250 nM. In contrast to the radioimmunoconjugates containing DTPA derivatives, which demonstrated poor serum stability, all macrocyclic radioimmunoconjugates were very stable in serum with <6% dissociation of (64)Cu over 48 h. In vivo biodistribution profiles in normal female Balb/C mice were similar for all the macrocyclic radioimmunoconjugates with most of the activity remaining in the blood pool up to 48 h. While all the macrocyclic bifunctional chelators are suitable for molecular imaging using (64)Cu-labeled antibody conjugates, NOTA and sar-CO2H show significant advantages over the others in that they can be radiolabeled rapidly at room temperature, under dilute conditions, resulting in high specific activity. PMID:22471317

  17. SHORT COMMUNICATION Carbon-13 Labeling for Improved Tracer

    E-print Network

    the effects of isotopic labeling using both deuterium substitution (dPS) and 13 C labeling (13 C-PS). ClearSHORT COMMUNICATION Carbon-13 Labeling for Improved Tracer Depth Profiling of Organic Materials Carolina State University, Raleigh, North Carolina, USA 13 C labeling is introduced as an alternative

  18. Cell-specific labeling enzymes for analysis of cell-cell communication in continuous co-culture.

    PubMed

    Tape, Christopher J; Norrie, Ida C; Worboys, Jonathan D; Lim, Lindsay; Lauffenburger, Douglas A; Jørgensen, Claus

    2014-07-01

    We report the orthologous screening, engineering, and optimization of amino acid conversion enzymes for cell-specific proteomic labeling. Intracellular endoplasmic-reticulum-anchored Mycobacterium tuberculosis diaminopimelate decarboxylase (DDC(M.tub-KDEL)) confers cell-specific meso-2,6-diaminopimelate-dependent proliferation to multiple eukaryotic cell types. Optimized lysine racemase (Lyr(M37-KDEL)) supports D-lysine specific proliferation and efficient cell-specific isotopic labeling. When ectopically expressed in discrete cell types, these enzymes confer 90% cell-specific isotopic labeling efficiency after 10 days of co-culture. Moreover, DDC(M.tub-KDEL) and Lyr(M37-KDEL) facilitate equally high cell-specific labeling fidelity without daily media exchange. Consequently, the reported novel enzyme pairing can be used to study cell-specific signaling in uninterrupted, continuous co-cultures. Demonstrating the importance of increased labeling stability for addressing novel biological questions, we compare the cell-specific phosphoproteome of fibroblasts in direct co-culture with epithelial tumor cells in both interrupted (daily media exchange) and continuous (no media exchange) co-cultures. This analysis identified multiple cell-specific phosphorylation sites specifically regulated in the continuous co-culture. Given their applicability to multiple cell types, continuous co-culture labeling fidelity, and suitability for long-term cell-cell phospho-signaling experiments, we propose DDC(M.tub-KDEL) and Lyr(M37-KDEL) as excellent enzymes for cell-specific labeling with amino acid precursors. PMID:24820872

  19. Isotope ratio analysis of actinides, fission products, and geolocators by high-efficiency multi-collector thermal ionization mass spectrometry

    SciTech Connect

    Bürger, Stefan [New Brunswick Laboratory, Argonne, IL; Riciputi, Lee R [Los Alamos National Laboratory (LANL); Bostick, Debra A [ORNL; Turgeon, Steven [University of Alberta, Edmondton, Canada; McBay, Eddie H [ORNL; Lavelle, Mark [ORNL

    2009-01-01

    A ThermoFisher 'Triton' multi-collector thermal ionization mass spectrometer (MC-TIMS) was evaluated for trace and ultra-trace level isotoperatioanalysis of actinides (uranium, plutonium, and americium), fission products and geolocators (strontium, cesium, and neodymium). Total efficiencies (atoms loaded to ions detected) of up to 0.5-2% for U, Pu, and Am, and 1-30% for Sr, Cs, and Nd can be reported employing resin bead load techniques onto flat ribbon Re filaments or resin beads loaded into a millimeter-sized cavity drilled into a Re rod. This results in detection limits of <0.1 fg (10{sup 4} atoms to 10{sup 5} atoms) for {sup 239-242+244}Pu, {sup 233+236}U, {sup 241-243}Am, {sup 89,90}Sr, and {sup 134,135,137}Cs, and {le} 1 pg for natural Nd isotopes (limited by the chemical processing blank) using a secondary electron multiplier (SEM) or multiple-ion counters (MICs). Relative standard deviations (RSD) as small as 0.1% and abundance sensitivities of 1 x 10{sup 6} or better using a SEM are reported here. Precisions of RSD {approx} 0.01-0.001% using a multi-collector Faraday cup array can be achieved at sub-nanogram concentrations for strontium and neodymium and are suitable to gain crucial geolocation information. The analytical protocols reported herein are of particular value for nuclear forensic and nuclear safeguard applications.

  20. Long term changes in Intrinsic Water Use Efficiency, the palaoe record derived from stable carbon isotope measurements from tree rings.

    NASA Astrophysics Data System (ADS)

    Gagen, Mary; McCarroll, Danny; Loader, Neil; Young, Giles; Robertson, Iain

    2015-04-01

    Stable carbon isotope (?13C) measurements from the annual rings of trees are increasingly used to explore long term changes in plant-carbon-water relations, via changes in intrinsic water use efficiency (iWUE); the ratio of photosynthetic rate to stomatal conductance. Many studies report a significant increase in iWEU since industrialisation, which tracks rising global atmospheric CO2. Such changes are logical are trees are known to change their stomatal geometry, number and action in response to rising CO2. However, which increasing iWUE suggests physiological changes which should lead to increased growth increasing iWUE is rarely matched by enhanced tree growth when tree rings are measured, despite increases of up to 30% in iWUE over the recent past (van der Sleen et al 2015). Explanations for the mismatch between iWUE and tree growth records encompass questions over the veracity of ?13C records for recording physiological change (Silva and Howarth 2013), suggestions that moisture stress in warming climates becomes a limit to growth and prevents opportunistic use of rising CO2 by trees (Andreu-Hayles et al 2011) and questions regarding the use of tree ring width, which does not record tree height gain, to record growth. Here we present an extensive range of long term iWUE records, derived broadly from the temperate, high latitude and one tropical forest site to explore the palaeoclimatic perspective on the iWUE-fertilization conundrum in a spatio temporally extensive manner.

  1. Efficient Blind Spectral Unmixing of Fluorescently Labeled Samples Using Multi-Layer Non-Negative Matrix Factorization

    PubMed Central

    Zudaire, Isabel; Ortiz-de-Solorzano, Carlos

    2013-01-01

    The ample variety of labeling dyes and staining methods available in fluorescence microscopy has enabled biologists to advance in the understanding of living organisms at cellular and molecular level. When two or more fluorescent dyes are used in the same preparation, or one dye is used in the presence of autofluorescence, the separation of the fluorescent emissions can become problematic. Various approaches have been recently proposed to solve this problem. Among them, blind non-negative matrix factorization is gaining interest since it requires little assumptions about the spectra and concentration of the fluorochromes. In this paper, we propose a novel algorithm for blind spectral separation that addresses some of the shortcomings of existing solutions: namely, their dependency on the initialization and their slow convergence. We apply this new algorithm to two relevant problems in fluorescence microscopy: autofluorescence elimination and spectral unmixing of multi-labeled samples. Our results show that our new algorithm performs well when compared with the state-of-the-art approaches for a much faster implementation. PMID:24260120

  2. [15N-labeling of fishes using 15N isotopes in aquarium water and the effect of a different protein nutrient on the 15N elimination after the labeling period].

    PubMed

    Bergner, H; Götz, K P; Simon, M; Rennert, B

    1993-01-01

    In a preexperiment of 12 days fishes (Cyprinus carpio L.) were labelled with 15N by means of 15NH4Cl and 15N-urea resp. in the aquarium water and by feeding a protein free diet. 15NH4Cl yielded a higher atom-% 15N excess (15N') in the tissues of fishes. In the main experiment 75 fishes (Cyprinus carpio L.) were 15N-labelled with 100 mg 15N'/l water from 15NH4Cl (95 atom-% 15N') in a protein free preperiod of 12 days. In the following main period the fishes received different protein sources in their diets in maintenance. A group of 20 fishes received an animal protein (fish meal) and two groups of 20 fishes each received plant proteins (soybean meal and wheat gluten resp.). The atom-% 15N' reached after the 15N-labelling period following values: digestive tract with content--7.15, liver--5.65, gills--5.89, muscle--0.81 and chorda dorsalis--1.09 respectively. During the main period (with protein feeding) the atom-% 15N' decreased in the tissues with high protein turnover (liver and gills) on the 2nd and 4th day to 4.31 +/- 0.11 (animal protein) and 4.64 +/- 0.14 (plant proteins) in average. The corresponding values in the tissues with low protein turnover (muscle and chorda dorsalis) were 0.73 +/- 0.04 and 0.80 +/- 0.04 atom-% 15N' in average. From the measurements on the 6th, 8th and 10th day of protein feeding resulted an atom-% 15N' in average of liver and gills of 4.08 +/- 0.13 (animal protein) and 4.11 +/- 0.15 (plant proteins). In muscle and chorda dorsalis the atom-% 15N' ascended in this time upon 0.80 +/- 0.04 (animal protein) and 0.90 +/- 0.03 (plant proteins). It seems that the protein metabolism of fishes is favoured from the amino acid of plant protein in comparison to animal protein to reduce the 15N-loss of the 15N-labelled body in maintenance, like the results from experiments with rats (Hernandez et al., 1981). PMID:7487475

  3. Stable Carbon Isotope Composition (deltaC), Water Use Efficiency, and Biomass Productivity of Lycopersicon esculentum, Lycopersicon pennellii, and the F(1) Hybrid.

    PubMed

    Martin, B; Thorstenson, Y R

    1988-09-01

    Three tomatoes, Lycopersicon esculentum Mill. cv UC82B, a droughttolerant wild related species, Lycopersicon pennellii (Cor.) D'Arcy, and their F(1) hybrid, were grown in containers maintained at three levels of soil moisture. Season-long water use was obtained by summing over the season daily weight losses of each container corrected for soil evaporation. Plant biomass was determined by harvesting and weighing entire dried plants. Season-long water use efficiency (gram dry weight/kilogram H(2)O) was calculated by dividing the dry biomass by the season-long water use. The season-long water use efficiency was greatest in the wild parent, poorest in the domestic parent, and intermediate (but closer to the wild parent) in the F(1) hybrid. Instantaneous water-use efficiency (micromole CO(2)/millimole H(2)O) determined by gas exchange measurements on individual leaves was poorly correlated with season-long water use efficiency. However, the relative abundance of stable carbon isotopes of leaf tissue samples was strongly correlated with the season-long water use efficiency. Also, the isotopic composition and the season-long water use efficiency of each genotype alone were strongly negatively correlated with plant dry weight when the dry weight varied as a function of soil moisture. PMID:16666269

  4. On the reaction mechanism for hydrocarbon formation from methanol over SAPO-34: 1. Isotopic labeling studies of the Co-reaction of ethene and methanol

    Microsoft Academic Search

    I. M. Dahl; S. Kolboe

    1994-01-01

    ¹³C-Methanol and ¹²C-ethene (fed as ethanol) have been co-reacted over SAPO-34 in a flow system at 400°C using argon as a carrier (diluent) gas. The feed contained an equal number of ¹³C and ¹²C atoms. The products were analyzed by GC-MS, allowing the determination of the isotopic composition of the reactor effluent. The ethanol was immediately converted to ethene, so

  5. Energy Efficiency in the Future Internet: The Role of Optical Packet Switching and Optical-Label Switching

    Microsoft Academic Search

    S. J. Ben Yoo

    2011-01-01

    This paper reviews the energy efficiency of optical- packet-switching (OPS) systems in comparison with electronic packet switching and hybrid packet switching in the context of future networks. The paper will first discuss the energy efficiency metrics that should include considerations for life-cycle analy- sis, applications, and network-wide goodput. The state-of-the-art electronic packet switching router is currently energy-limited in scalability as

  6. Cross-Strand Coupling and Site-Specific Unfolding Thermodynamics of a Trpzip ?-Hairpin Peptide Using 13 C Isotopic Labeling and IR Spectroscopy

    Microsoft Academic Search

    Rong Huang; Ling Wu; Dan McElheny; Petr Bour?; Anjan Roy; Timothy A. Keiderling

    2009-01-01

    Conformational properties of a 12-residue tryptophan zipper (trpzip) ? -hairpin peptide (AWAWENGKWAWK- NH2, a modification of the original trpzip2 sequence) are analyzed under equilibrium conditions using ECD and IR spectra of a series of variants, singly and doubly C1-labeled with 13C on the amide CdO. The characteristic features of the 13CdO component of the amide IIR band and their sensitivity

  7. Cross-strand coupling and site-specific unfolding thermodynamics of a trpzip beta-hairpin peptide using 13C isotopic labeling and IR spectroscopy.

    PubMed

    Huang, Rong; Wu, Ling; McElheny, Dan; Bour, Petr; Roy, Anjan; Keiderling, Timothy A

    2009-04-23

    Conformational properties of a 12-residue tryptophan zipper (trpzip) beta-hairpin peptide (AWAWENGKWAWK-NH(2), a modification of the original trpzip2 sequence) are analyzed under equilibrium conditions using ECD and IR spectra of a series of variants, singly and doubly C(1)-labeled with (13)C on the amide CO. The characteristic features of the (13)CO component of the amide I' IR band and their sensitivity to the local structure of the peptide are used to differentiate stabilities for parts of the hairpin structure. Doubly labeled peptide spectra indicate that the ends of the beta-strands are frayed and that the center part is more stable as would be expected from formation of a stable hydrophobic core consisting of four tryptophan residues, and supported by MD simulations. NMR analyses were used to determine a best fit solution structure that is in close agreement with that of trpzip2, except for a small variation in the turn geometry. The distinct vibrational coupling patterns of the labeled sites based on this structure are also well matched by ab initio DFT-level calculations of their IR spectral patterns. Thermal unfolding of the peptides as studied with CD spectra could be fit with an apparent two-state transition model. ECD senses only the tryptophan interactions (tertiary-like) and their overall environment, as shown by TD-DFT modeling of the Trp-Trp pi-pi ECD. However, variation of the amide I IR spectra of (13)C-isotopomers showed that the thermal unfolding process is not cooperative in terms of the peptide backbone (secondary structure), since the transition temperatures sensed for labeled modes differ from those for the whole peptide. The thermal data also evidence dependence on concentration and pH but these cause little spectral variation. This study illustrates the consequences of multistate conformational change at the residue- or sequence-specific level in a system whose structure is dominated by hydrophobic collapse. PMID:19326892

  8. Interactive labeling of facial action units

    Microsoft Academic Search

    Lei Zhang; Yan Tong; Qiang Ji

    2008-01-01

    For many computer vision problems, it is very important to produce the ground truth data. Manual data labeling is labor-intensive and prone to the human errors, whereas fully automatic data labeling is not feasible and reliable. In this paper, we propose an interactive labeling technique for efficient and accurate data labeling. Constructed on a Bayesian network (BN), the automatic image

  9. Evaluation of the efficiency of Pd/H2 -catalyzed benzylic H/D exchange of dehydroabietinal with D(2) O and synthesis of a tritium-labeled analogue.

    PubMed

    Petros, Robby A; Shah, Jyoti

    2014-01-01

    Dehydroabietinal (DA) has been identified as an important signaling molecule in systemic acquired resistance in plants. Deuterium and tritium-labeled DA were synthesized to confirm its role in signaling and to further elucidate the mechanism by which DA induces systemic acquired resistance. Pd/H2 -catalyzed exchange of benzylic hydrogen atoms of DA with (2) H-H2 O or (3) H-H2 O was conducted with >97% label incorporation for (2) H-DA and a specific activity of 12.6?mCi/mmol for (3) H-DA synthesized from 90?mCi/mmol (3) H-H2 O. The extent of deuterium labeling at each benzylic position was determined via an inverse-gated (13) C NMR experiment. C7 and C15 were 87% and 81% labeled, respectively. Isotope-induced chemical shift changes at C6 were used to approximate the amount of singly (66%) and doubly (17%) labeled (2) H-DA at C7. Results also indicated that two of the three benzylic protons in DA underwent facile exchange. Exchange at the remaining position was likely hampered by steric interactions of nearby methyl groups at the surface of the Pd catalyst. PMID:24448746

  10. Spin labeling EPR

    Microsoft Academic Search

    Johann P. Klare; Heinz-Jürgen Steinhoff

    2009-01-01

    Site-directed spin labeling in combination with electron paramagnetic resonance spectroscopy has emerged as an efficient tool\\u000a to elucidate the structure and conformational dynamics of biomolecules under native-like conditions. This article summarizes\\u000a the basics as well as recent progress of site-directed spin labeling. Continuous wave EPR spectra analyses and pulse EPR techniques\\u000a are reviewed with special emphasis on applications to the

  11. ISOTOPE METHODS IN HOMOGENEOUS CATALYSIS.

    SciTech Connect

    BULLOCK,R.M.; BENDER,B.R.

    2000-12-01

    The use of isotope labels has had a fundamentally important role in the determination of mechanisms of homogeneously catalyzed reactions. Mechanistic data is valuable since it can assist in the design and rational improvement of homogeneous catalysts. There are several ways to use isotopes in mechanistic chemistry. Isotopes can be introduced into controlled experiments and followed where they go or don't go; in this way, Libby, Calvin, Taube and others used isotopes to elucidate mechanistic pathways for very different, yet important chemistries. Another important isotope method is the study of kinetic isotope effects (KIEs) and equilibrium isotope effect (EIEs). Here the mere observation of where a label winds up is no longer enough - what matters is how much slower (or faster) a labeled molecule reacts than the unlabeled material. The most careti studies essentially involve the measurement of isotope fractionation between a reference ground state and the transition state. Thus kinetic isotope effects provide unique data unavailable from other methods, since information about the transition state of a reaction is obtained. Because getting an experimental glimpse of transition states is really tantamount to understanding catalysis, kinetic isotope effects are very powerful.

  12. Estimation of the efficiency of hydrocarbon mineralization in soil by measuring CO2-emission and variations in the isotope composition of carbon dioxide

    NASA Astrophysics Data System (ADS)

    Dubrovskaya, Ekaterina; Turkovskaya, Olga

    2010-05-01

    Estimation of the efficiency of hydrocarbon mineralization in soil by measuring CO2-emission and variations in the isotope composition of carbon dioxide E. Dubrovskaya1, O. Turkovskaya1, A. Tiunov2, N. Pozdnyakova1, A. Muratova1 1 - Institute of Biochemistry and Physiology of Plants and Microorganisms, RAS, Saratov, 2 - A.N. Severtsov Institute of Ecology and Evolution, RAS, Moscow, Russian Federation Hydrocarbon mineralization in soil undergoing phytoremediation was investigated in a laboratory experiment by estimating the variation in the 13?/12? ratio in the respired ??2. Hexadecane (HD) was used as a model hydrocarbon pollutant. The polluted soil was planted with winter rye (Secale cereale) inoculated with Azospirillum brasilense strain SR80, which combines the abilities to promote plant growth and to degrade oil hydrocarbon. Each vegetated treatment was accompanied with a corresponding nonvegetated one, and uncontaminated treatments were used as controls. Emission of carbon dioxide, its isotopic composition, and the residual concentration of HD in the soil were examined after two and four weeks. At the beginning of the experiment, the CO2-emission level was higher in the uncontaminated than in the contaminated soil. After two weeks, the quantity of emitted carbon dioxide decreased by about three times and did not change significantly in all uncontaminated treatments. The presence of HD in the soil initially increased CO2 emission, but later the respiration was reduced. During the first two weeks, nonvegetated soil had the highest CO2-emission level. Subsequently, the maximum increase in respiration was recorded in the vegetated contaminated treatments. The isotope composition of plant material determines the isotope composition of soil. The soil used in our experiment had an isotopic signature typical of soils formed by C3 plants (?13C,-22.4‰). Generally, there was no significant fractionation of the carbon isotopes of the substrates metabolized by the soil microbiota. The plants and microorganisms used had the isotopic signatures similar to that of the soil, whereas the ?13C of HD was -47.9‰. The HD mineralization level was assessed by determining the difference between the isotopic compositions of soil CO2 immediately after pollution and during remediation. In the unvegetated soil, about 13% of initially added HD was mineralized, the phytoremediation increased the total decomposition of the contaminant to 19%, and an additional plant inoculation with strain SR80 raised it to 33%. The GC analysis of soil demonstrated that contaminant loss in the plant treatments and in the inoculated plant treatment was 71 and 72%, respectively, whereas in the nonvegetated treatments, it was 64 and 66%, respectively. Thus, the elimination of the contaminant resulted from its total mineralization (CO2 emission) and partial chemical transformation.

  13. Sulfonium Ion Derivatization, Isobaric Stable Isotope Labeling and Data Dependent CID and ETD-MS\\/MS for Enhanced Phosphopeptide Quantitation, Identification and Phosphorylation Site Characterization

    Microsoft Academic Search

    Yali Lu; Xiao Zhou; Paul M. Stemmer; Gavin E. Reid

    An amine specific peptide derivatization strategy involving the use of novel isobaric stable isotope encoded ‘fixed charge’\\u000a sulfonium ion reagents, coupled with an analysis strategy employing capillary HPLC, ESI-MS, and automated data dependent ion\\u000a trap CID-MS\\/MS, -MS3, and\\/or ETD-MS\\/MS, has been developed for the improved quantitative analysis of protein phosphorylation, and for identification\\u000a and characterization of their site(s) of modification.

  14. Efficient Utilization of the Expanded Criteria Donor (ECD) Deceased Donor Kidney Pool: An Analysis of the Effect of Labeling

    PubMed Central

    Hirth, Richard A.; Pan, Qing; Schaubel, Douglas E.; Merion, Robert M.

    2015-01-01

    We investigated the effect of the expanded criteria donor (ECD) label on (i) recovery of kidneys and (ii) acceptance for transplantation given recovery. An ECD is age ? 60, or age 50–59 with ? 2 of 3 specified comorbidities. Using data from the Scientific Registry of Transplant Recipients from 1999 to 2005, we modeled recovery rates through linear regression and transplantation probabilities via logistic regression, focusing on organs from donors just-younger versus just-older than the ECD age thresholds. We split the sample at July 1, 2002 to determine how decisions changed at the approximate time of implementation of the ECD definition. Before July 2002, the number of recovered kidneys with 0-1 comorbidities dropped at age 60, but transplantation probabilities given recovery did not. After July 2002, the number of recovered kidneys with 0-1 comorbidities rose at age 60, but transplantation probabilities contingent on recovery declined. No similar trends were observed at donor age 50 among donors with ? 2 comorbidities. Overall, implementation of the ECD definition coincided with a reversal of an apparent reluctance to recover kidneys from donors over age 59, but increased selectiveness on the part of surgeons/centers with respect to these kidneys. PMID:20055795

  15. Direct Detection and Characterization of Chloride in the Active Site of the Low-pH Form of Sulfite Oxidase Using ESEEM Spectroscopy, Isotopic Labeling, and DFT Calculations

    PubMed Central

    Klein, Eric L.; Astashkin, Andrei V.; Ganyushin, Dmitry; Riplinger, Christoph; Johnson-Winters, Kayunta; Neese, Frank; Enemark, John H.

    2009-01-01

    Electron spin echo envelope modulation (ESEEM) investigations were carried out on samples of the low-pH (lpH) form of vertebrate sulfite oxidase (SO) prepared with 35Cl- and 37Cl-enriched buffers as well as with buffer containing the natural abundance of Cl isotopes. The isotope-related changes observed in the ESEEM spectra provide direct and unequivocal evidence that Cl? is located in close proximity to the Mo(V) center of lpH SO. The measured isotropic hyperfine interaction constant of about 4 MHz (35Cl) suggests that the Cl? ion is either weakly coordinated to Mo(V) at its otherwise vacant axial position, trans to the oxo ligand, or is hydrogen-bonded to the equatorial exchangeable OH ligand. Scalar relativistic all-electron density functional theory (DFT) calculations of the hyperfine and nuclear quadrupole interaction parameters, along with steric and energetic arguments, strongly support the possibility that Cl? is hydrogen-bonded to the equatorial OH ligand rather than being directly coordinated to the Mo(V). PMID:19402624

  16. Seasonal variations in photosynthesis, intrinsic water-use efficiency and stable isotope composition of poplar leaves in a short-rotation plantation

    PubMed Central

    Broeckx, L.S.; Fichot, R.; Verlinden, M.S.; Ceulemans, R.

    2014-01-01

    Photosynthetic carbon assimilation and transpirational water loss play an important role in the yield and the carbon sequestration potential of bioenergy-devoted cultures of fast-growing trees. For six poplar (Populus) genotypes in a short-rotation plantation, we observed significant seasonal and genotypic variation in photosynthetic parameters, intrinsic water-use efficiency (WUEi) and leaf stable isotope composition (?13C and ?18O). The poplars maintained high photosynthetic rates (between 17.8 and 26.9??mol?m?2?s?1 depending on genotypes) until late in the season, in line with their fast-growth habit. Seasonal fluctuations were mainly explained by variations in soil water availability and by stomatal limitation upon photosynthesis. Stomatal rather than biochemical limitation was confirmed by the constant intrinsic photosynthetic capacity (Vcmax) during the growing season, closely related to leaf nitrogen (N) content. Intrinsic water-use efficiency scaled negatively with carbon isotope discrimination (?13Cbl) and positively with the ratio between mesophyll diffusion conductance (gm) and stomatal conductance. The WUEi?–??13Cbl relationship was partly influenced by gm. There was a trade-off between WUEi and photosynthetic N-use efficiency, but only when soil water availability was limiting. Our results suggest that seasonal fluctuations in relation to soil water availability should be accounted for in future modelling studies assessing the carbon sequestration potential and the water-use efficiency of woody energy crops. PMID:25074859

  17. An Efficient and Compact Difference-Frequency-Generation Spectrometer and Its Application to 12CH3D/12CH4 Isotope Ratio Measurements

    PubMed Central

    Tsuji, Kiyoshi; Teshima, Hiroaki; Sasada, Hiroyuki; Yoshida, Naohiro

    2010-01-01

    We have developed an efficient and compact 3.4 ?m difference-frequency-generation spectrometer using a 1.55 ?m distributed feedback (DFB) laser diode, a 1.06 ?m DFB laser diode, and a ridge-waveguide periodically poled lithium niobate. It is continuously tunable in the 30 cm?1 span and is applied to 12CH3D/12CH4 isotope ratio measurements. The suitable pair of 12CH3D ?4 pP(7,6) and 12CH4 ? 2+?4 R(6) F1(1) lines enabled us to determine their isotope ratio with a precision repeatability of 0.8‰ using a sample and a working standard of pure methane with an effective signal averaging time of 100 ms. PMID:22163569

  18. Efficient Estimators for Quantum Instanton Evaluation of theKinetic Isotope Effects: Application to the Intramolecular HydrogenTransfer in Pentadiene

    SciTech Connect

    Vanicek, Jiri; Miller, William H.

    2007-06-13

    The quantum instanton approximation is used to compute kinetic isotope effects for intramolecular hydrogen transfer in cis-1,3-pentadiene. Due to the importance of skeleton motions, this system with 13 atoms is a simple prototype for hydrogen transfer in enzymatic reactions. The calculation is carried out using thermodynamic integration with respect to the mass of the isotopes and a path integral Monte Carlo evaluation of relevant thermodynamic quantities. Efficient 'virial' estimators are derived for the logarithmic derivatives of the partition function and the delta-delta correlation functions. These estimators require significantly fewer Monte Carlo samples since their statistical error does not increase with the number of discrete time slices in the path integral. The calculation treats all 39 degrees of freedom quantum-mechanically and uses an empirical valence bond potential based on a modified general AMBER force field.

  19. Characterization of metabolic profile of honokiol in rat feces using liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry and (13)C stable isotope labeling.

    PubMed

    Dong, Yinfeng; Tang, Minghai; Song, Hang; Li, Rong; Wang, Chunyu; Ye, Haoyu; Qiu, Neng; Zhang, Yongkui; Chen, Lijuan; Wei, Yuquan

    2014-03-15

    As fecal excretion is one of important routes of elimination of drugs and their metabolites, it is indispensable to investigate the metabolites in feces for more comprehensive information on biotransformation in vivo. In this study, a sensitive and reliable approach based on ultra-performance liquid chromatography/quadrupole-time-of-flight-mass spectrometry (UHPLC-Q-TOF-MS) was applied to characterize the metabolic profile of honokiol in rat feces after the administration of an equimolar mixture of honokiol and [(13)C6]-labeled honokiol. Totally 42 metabolites were discovered and tentatively identified in rat feces samples, 26 metabolites were first reported, including two novel classes of metabolites, methylated and dimeric metabolites of honokiol. Moreover, this study provided basic comparative data on the metabolites in rat plasma, feces and urine, which gave better understanding of the metabolic fate of honokiol in vivo. PMID:24566334

  20. Labeling Theory

    Microsoft Academic Search

    Jón Gunnar Bernburg

    Labeling theory provides a distinctively sociological approach that focuses on the role of social labeling in the development\\u000a of crime and deviance. The theory assumes that although deviant behavior can initially stem from various causes and conditions,\\u000a once individuals have been labeled or defined as deviants, they often face new problems that stem from the reactions of self\\u000a and others

  1. An Enhanced In Vivo Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) Model for Quantification of Drug Metabolism Enzymes*

    PubMed Central

    MacLeod, A. Kenneth; Fallon, Padraic G.; Sharp, Sheila; Henderson, Colin J.; Wolf, C. Roland; Huang, Jeffrey T.-J.

    2015-01-01

    Many of the enzymes involved in xenobiotic metabolism are maintained at a low basal level and are only synthesized in response to activation of upstream sensor/effector proteins. This induction can have implications in a variety of contexts, particularly during the study of the pharmacokinetics, pharmacodynamics, and drug–drug interaction profile of a candidate therapeutic compound. Previously, we combined in vivo SILAC material with a targeted high resolution single ion monitoring (tHR/SIM) LC-MS/MS approach for quantification of 197 peptide pairs, representing 51 drug metabolism enzymes (DME), in mouse liver. However, as important enzymes (for example, cytochromes P450 (Cyp) of the 1a and 2b subfamilies) are maintained at low or undetectable levels in the liver of unstimulated metabolically labeled mice, quantification of these proteins was unreliable. In the present study, we induced DME expression in labeled mice through synchronous ligand-mediated activation of multiple upstream nuclear receptors, thereby enhancing signals for proteins including Cyps 1a, 2a, 2b, 2c, and 3a. With this enhancement, 115 unique, lysine-containing, Cyp-derived peptides were detected in the liver of a single animal, as opposed to 56 in a pooled sample from three uninduced animals. A total of 386 peptide pairs were quantified by tHR/SIM, representing 68 Phase I, 30 Phase II, and eight control proteins. This method was employed to quantify changes in DME expression in the hepatic cytochrome P450 reductase null (HRN) mouse. We observed compensatory induction of several enzymes, including Cyps 2b10, 2c29, 2c37, 2c54, 2c55, 2e1, 3a11, and 3a13, carboxylesterase (Ces) 2a, and glutathione S-transferases (Gst) m2 and m3, along with down-regulation of hydroxysteroid dehydrogenases (Hsd) 11b1 and 17b6. Using DME-enhanced in vivo SILAC material with tHR/SIM, therefore, permits the robust analysis of multiple DME of importance to xenobiotic metabolism, with improved utility for the study of drug pharmacokinetics, pharmacodynamics, and of chemically treated and genetically modified mouse models. PMID:25561501

  2. An enhanced in vivo stable isotope labeling by amino acids in cell culture (SILAC) model for quantification of drug metabolism enzymes.

    PubMed

    MacLeod, A Kenneth; Fallon, Padraic G; Sharp, Sheila; Henderson, Colin J; Wolf, C Roland; Huang, Jeffrey T-J

    2015-03-01

    Many of the enzymes involved in xenobiotic metabolism are maintained at a low basal level and are only synthesized in response to activation of upstream sensor/effector proteins. This induction can have implications in a variety of contexts, particularly during the study of the pharmacokinetics, pharmacodynamics, and drug-drug interaction profile of a candidate therapeutic compound. Previously, we combined in vivo SILAC material with a targeted high resolution single ion monitoring (tHR/SIM) LC-MS/MS approach for quantification of 197 peptide pairs, representing 51 drug metabolism enzymes (DME), in mouse liver. However, as important enzymes (for example, cytochromes P450 (Cyp) of the 1a and 2b subfamilies) are maintained at low or undetectable levels in the liver of unstimulated metabolically labeled mice, quantification of these proteins was unreliable. In the present study, we induced DME expression in labeled mice through synchronous ligand-mediated activation of multiple upstream nuclear receptors, thereby enhancing signals for proteins including Cyps 1a, 2a, 2b, 2c, and 3a. With this enhancement, 115 unique, lysine-containing, Cyp-derived peptides were detected in the liver of a single animal, as opposed to 56 in a pooled sample from three uninduced animals. A total of 386 peptide pairs were quantified by tHR/SIM, representing 68 Phase I, 30 Phase II, and eight control proteins. This method was employed to quantify changes in DME expression in the hepatic cytochrome P450 reductase null (HRN) mouse. We observed compensatory induction of several enzymes, including Cyps 2b10, 2c29, 2c37, 2c54, 2c55, 2e1, 3a11, and 3a13, carboxylesterase (Ces) 2a, and glutathione S-transferases (Gst) m2 and m3, along with down-regulation of hydroxysteroid dehydrogenases (Hsd) 11b1 and 17b6. Using DME-enhanced in vivo SILAC material with tHR/SIM, therefore, permits the robust analysis of multiple DME of importance to xenobiotic metabolism, with improved utility for the study of drug pharmacokinetics, pharmacodynamics, and of chemically treated and genetically modified mouse models. PMID:25561501

  3. Isotopic labeling experiments that elucidate the mechanism of DNA strand cleavage by the hypoxia-selective antitumor agent 1,2,4-benzotriazine 1,4-di-N-oxide

    PubMed Central

    Shen, Xiulong; Rajapakse, Anuruddha; Gallazzi, Fabio; Junnotula, Venkatraman; Fuchs-Knotts, Tarra; Glaser, Rainer; Gates, Kent S.

    2014-01-01

    The 1,2,4-benzotriazine 1,4-dioxides are an important class of potential anticancer drugs that selectively kill the low-oxygen (hypoxic) cells found in solid tumors. These compounds undergo intracellular one-electron enzymatic reduction to yield an oxygen-sensitive drug radical intermediate that partitions forward, under hypoxic conditions, to generate a highly reactive secondary radical that causes cell killing DNA damage. Here we characterized bioreductively-activated, hypoxia-selective DNA-strand cleavage by 1,2,4-benzotriazine 1,4-dioxide. We found that one-electron enzymatic activation of 1,2,4-benzotriazine 1,4-dioxide under hypoxic conditions in the presence of the deuterium atom donor methanol-d4 produced non-deuterated mono-N-oxide metabolites. This and the results of other isotopic labeling studies provided evidence against the generation of atom-abstracting drug radical intermediates and are consistent with a DNA-damage mechanism involving release of hydroxyl radical from enzymatically-activated 1,2,4-benzotriazine 1,4-dioxides. PMID:24328261

  4. 18O stable isotope labeling, quantitative model experiments, and molecular dynamics simulation studies on the trans-specific degradation of the bitter tasting iso-alpha-acids of beer.

    PubMed

    Intelmann, Daniel; Demmer, Oliver; Desmer, Nina; Hofmann, Thomas

    2009-11-25

    The typical bitterness of fresh beer is well-known to decrease in intensity and to change in quality with increasing age. This phenomenon was recently shown to be caused by the conversion of bitter tasting trans-iso-alpha-acids into lingering and harsh bitter tasting tri- and tetracyclic degradation products such as tricyclocohumol, tricyclocohumene, isotricyclocohumene, tetracyclocohumol, and epitetracyclocohumol. Interestingly, the formation of these compounds was shown to be trans-specific and the corresponding cis-iso-alpha-acids were found to be comparatively stable. Application of 18O stable isotope labeling as well as quantitative model studies combined with LC-MS/MS experiments, followed by computer-based molecular dynamics simulations revealed for the first time a conclusive mechanism explaining the stereospecific transformation of trans-iso-alpha-acids into the tri- and tetracyclic degradation products. This transformation was proposed to be induced by a proton-catalyzed carbon/carbon bond formation between the carbonyl atom C(1') of the isohexenoyl moiety and the alkene carbon C(2'') of the isoprenyl moiety of the trans-iso-alpha-acids. PMID:19860448

  5. Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein-Protein Interactions by Chemical Cross-Linking

    PubMed Central

    Merkley, Eric D.; Baker, Erin S.; Crowell, Kevin L.; Orton, Daniel J.; Taverner, Thomas; Ansong, Charles; Ibrahim, Yehia M.; Burnet, Meagan C.; Cort, John R.; Anderson, Gordon A.; Smith, Richard D.; Adkins, Joshua N.

    2013-01-01

    Chemical cross-linking of proteins followed by proteolysis and mass spectrometric analysis of the resulting cross-linked peptides provides powerful insight into the quaternary structure of protein complexes. Mixed-isotope cross-linking (a method for distinguishing intermolecular cross-links) was coupled with liquid chromatography and ion mobility separations and mass spectrometry (LC-IMS-MS) to provide an additional separation dimension to the traditional cross-linking approach. This method produced multiplet m/z peaks that are aligned in the IMS drift time dimension and serve as signatures of intermolecular cross-linked peptides. We developed an informatics tool to use the amino acid sequence information inherent in the multiplet spacing for accurate identification of the cross-linked peptides. Because of the separation of peptides and cross-linked peptides in drift time, our LC-IMS-MS approach was able to confidently detect more intermolecular cross-linked peptides than LC-MS alone. PMID:23423792

  6. 18O-Labeled Proteome Reference as Global Internal Standards for Targeted Quantification by Selected Reaction Monitoring-Mass Spectrometry

    SciTech Connect

    Kim, Jong Seo; Fillmore, Thomas L.; Liu, Tao; Robinson, Errol W.; Hossain, Mahmud; Champion, Boyd L.; Moore, Ronald J.; Camp, David G.; Smith, Richard D.; Qian, Weijun

    2011-10-11

    Selected reaction monitoring-mass spectrometry (SRM-MS) is an emerging technology for high throughput targeted protein quantification and verification in biological and biomarker discovery studies; however, the cost associated with the use of stable isotope labeled synthetic peptides as internal standards is prohibitive for quantitatively screening large numbers of candidate proteins as often required in the pre-verification phase of biomarker discovery. Herein we present the proof-of-concept experiments of using an 18O-labeled 'universal' reference as comprehensive internal standards for quantitative SRM-MS analysis. With an 18O-labeled whole proteome sample as reference, every peptide of interest will have its own corresponding heavy isotope labeled internal standard, thus providing an ideal approach for quantitative screening of a large number of candidates using SRM-MS. Our results showed that the 18O incorporation efficiency using a recently improved protocol was >99.5% for most peptides investigated, a level comparable to 13C/15N labeled synthetic peptides in terms of heavy isotope incorporation. The accuracy, reproducibility, and linear dynamic range of quantification were further assessed based on known ratios of standard proteins spiked into mouse plasma with an 18O-labeled mouse plasma reference. A dynamic range of four orders of magnitude in relative concentration was obtained with high reproducibility (i.e., coefficient of variance <10%) based on the 16O/18O peak area ratios. Absolute and relative quantification of C-reactive protein and prostate-specific antigen were demonstrated by coupling an 18O-labeled reference with standard additions of protein standards. Collectively, our results demonstrated that the use of 18O-labeled reference provides a convenient and effective strategy for quantitative SRM screening of large number of candidate proteins.

  7. ABRF-sPRG 2013 Study: Development and Characterization of a Proteomics Normalization Standard Consisting of 1000 Stable Isotope Labeled Peptides and a Qualitative Stability Study of Peptides from the ABRF-sPRG 2012 Study

    PubMed Central

    Dufresne, Craig P.; Ivanov, Alexander R.; Koller, Antonius; Phinney, Brett S.; Rose, Kristie L.; Rudnick, Paul A.; Searle, Brian C.; Colangelo, Christopher

    2013-01-01

    The Proteomics Standards Research Group (sPRG) is reporting the first year progress in a two-year sPRG 2012-2013 study which focuses on the generation of a standard that can be used for interassay, interspecies, and interlaboratory normalization in both label-free and stable isotope label-based quantitative proteomics analysis. The standard has been formulated as two mixtures: 1000 stable isotope 13C/15N-labeled synthetic tryptic peptides alone, and peptides mixed with a tryptic digest from a HEK 293 cell lysate. The sequences of the synthetic peptides were derived from approximately 400 proteins and were conserved across proteomes of the most commonly analyzed species: Homo sapiens, Mus musculus and Rattus norvegicus. The selected peptides represent the full range of hydrophobicities and isoelectric points typical to tryptic peptides from complex proteomic samples. The standard was designed to represent proteins of various concentrations, spanning three orders of magnitude. This year we focused our efforts on selection of appropriate protein and peptide candidates, peptide synthesis, quality assessment and LC-MS evaluation by several sPRG member laboratories. The sPRG study design and initial results of a thorough characterization of the standard using a variety of instrumental configurations and bioinformatics approaches will be presented in this talk. The sPRG is hopeful that the designed formulation will become a valuable resource in various mass spectrometry-based proteomic applications, including quantitative and differential profiling, as well as general benchmarking (e.g. chromatographic retention time). The sPRG plans to start recruiting study participants in April 2013, complete the study by the end of the year 2013, and present the results at the ABRF 2014 meeting. The sPRG encourages proteomics laboratories to participate in the study and sign in at www.abrf.org/sprg. The second half of the session will discuss the qualitative stability study performed using purified synthetic peptides containing a variety of modifications selected from the 2012 sPRG ABRF sample. The stability of the selected synthetic peptides was evaluated by the sPRG using different storage conditions over a three-month period. After storage at either at room temperature, +4°C or ?80°C for one week, one month, or three months. Quantitative LC-MS/MS analysis was used to monitor the stability and degradation of the peptides, and to determine the effect of modifications and storage conditions on peptide degradation rates. The data presented have been built on the quantitative study that was presented at both the 2012 ABRF and ASMS conferences. All forms of degraded peptides were separated and identified using nano-LC tandem mass spectrometry on a Thermo Scientific Q-Exactive hybrid mass spectrometer. Integrated extracted ion chromatograms were used to measure relative amounts of degradation to identify which pathways are most prevalent during storage.

  8. Assessment of effects of the rising atmospheric nitrogen deposition on nitrogen uptake and long-term water-use efficiency of plants using nitrogen and carbon stable isotopes.

    PubMed

    Yao, F Y; Wang, G A; Liu, X J; Song, L

    2011-07-15

    This study assesses the effects of the atmospheric nitrogen (N) deposition on the N uptake and the long-term water-use efficiency of two C(3) plants (Agropyron cristatum and Leymus chinensis) and two C(4) plants (Amaranthus retroflexus and Setaria viridis) using N and C stable isotopes. In addition, this study explores the potential correlation between leaf N isotope (?(15)N) values and leaf C isotope (?(13)C) values. This experiment shows that the atmospheric N deposition has significant effects on the N uptake, ?(15)N and leaf N content (N(m)) of C(3) plants. As the atmospheric N deposition rises, the proportion and the amount of N absorbed from the simulated atmospheric deposition become higher, and the ?(15)N and N(m) of the two C(3) plants both also increase, suggesting that the rising atmospheric N deposition is beneficial for C(3) plants. However, C(4) plants display different patterns in their N uptake and in their variations of ?(15)N and N(m) from those of C(3) plants. C(4) plants absorb less N from the atmospheric deposition, and the leaf N(m) does not change with the elevated atmospheric N deposition. Photosynthetic pathways may account for the differences between C(3) and C(4) plants. This study also shows that atmospheric N deposition does not play a role in determining the ?(13)C and in the long-term water-use efficiency of C(3) and C(4) plants, suggesting that the long-term water-use pattern of the plants does not change with the atmospheric N input. In addition, this study does not observe any relationship between leaf ?(15)N and leaf ?(13)C in both C(3) and C(4) plants. PMID:21638358

  9. Soil organic carbon can be up-taken by plant roots and stored in plant biosilica: NanoSIMS and isotopic labeling evidences

    NASA Astrophysics Data System (ADS)

    Alexandre, Anne; Santos, Guaciara M.; balesdent, Jerôme; Basile-Doelsch, Isabelle; Borschneck, Daniel; Cazevieille, Patrick; Chevassus-Rosset, Claire; Doelsch, Emmanuel; Harutyunyan, Araks; Lemee, Laurent; Mazur, Jean-Charles; Reyerson, Paul; Signoret, Patrick

    2015-04-01

    Plant biosilica particles called phytoliths contain occluded organic compounds (phytC). Over the last few years, phytC content, nature, origin, paleoenvironmental meaning and impact in the global C cycle has been the subject of increasing debate[1, 2]. Inconsistencies in phytC quantification were fed by the scarcity of in-situ characterization of phytC in phytoliths and by inadequate extraction methods[3]. Very recently, 14C-AMS analyses of soil organic matter (SOM), amendments, plant tissues, atmospheric CO2 and phytolith samples, evidenced that a small but significant pool of phytC is not photosynthetic but derived from old SOM[4,5]. From there, several investigations were started to go further into the characterization of phytC and the mechanisms in play behind old SOM absorption by plant roots and old SOM occlusion in plant biosilica. Here, we first reconstruct at high spatial resolution the 3-dimentional location of phytC and its C/N signature using 3D X-ray microscopy and Nano-scale Secondary Ion Mass Spectrometry (NanoSIMS). A pool of phytC appears homogeneously distributed in the silica structure and its C:N estimate is in the range of amino acid signatures[6]. Then, we use 13C and 15N-labelled amino acids monitored from an hydroponic solution to grass roots, stems, leaves and phytoliths to evidence that amino acids are absorbed as such by the roots and are concentrated in phytC rather than in the plant tissues. These findings strengthen and complement the 14C evidences. Both of them dissuade attempts to use phytC as a proxy of plant C. Further, they open new avenues of investigation regarding the processes which drive SOM mobilization by plant uptake, for a better understanding of soil/plant interactions involved in the terrestrial C cycle. [1] Santos et al. 2010. Radiocarbon 52:113 [2] Santos et al. 2012. Biogeosci. 9:1873 [3] Corbineau et al. 2013 R. Paleobot. Palyn. 197: 179 [4] Reyerson et al. 2013 AGU Fall meeting 2013 (1803125) [5] Santos et al. 2014 AGU Fall meeting 2014 (B51A-0011) [6] Alexandre, et al., 2014. Biogeosci. Discuss. 11, 14699 :14727.

  10. Plasma Biomarker Discovery Using 3D Protein Profiling Coupled with Label-Free Quantitation

    PubMed Central

    Beer, Lynn A.; Tang, Hsin-Yao; Barnhart, Kurt T.; Speicher, David W.

    2011-01-01

    In-depth quantitative profiling of human plasma samples for biomarker discovery remains quite challenging. One promising alternative to chemical derivatization with stable isotope labels for quantitative comparisons is direct, label-free, quantitative comparison of raw LC–MS data. But, in order to achieve high-sensitivity detection of low-abundance proteins, plasma proteins must be extensively pre-fractionated, and results from LC–MS runs of all fractions must be integrated efficiently in order to avoid misidentification of variations in fractionation from sample to sample as “apparent” biomarkers. This protocol describes a powerful 3D protein profiling method for comprehensive analysis of human serum or plasma proteomes, which combines abundant protein depletion and high-sensitivity GeLC–MS/MS with label-free quantitation of candidate biomarkers. PMID:21468938

  11. High-Resolution Twin-Ion Metabolite Extraction (HiTIME) Mass Spectrometry: Nontargeted Detection of Unknown Drug Metabolites by Isotope Labeling, Liquid Chromatography Mass Spectrometry, and Automated High-Performance Computing.

    PubMed

    Leeming, Michael G; Isaac, Andrew P; Pope, Bernard J; Cranswick, Noel; Wright, Christine E; Ziogas, James; O'Hair, Richard A J; Donald, William A

    2015-04-21

    The metabolic fate of a compound can often determine the success of a new drug lead. Thus, significant effort is directed toward identifying the metabolites formed from a given molecule. Here, an automated and nontargeted procedure is introduced for detecting drug metabolites without authentic metabolite standards via the use of stable isotope labeling, liquid chromatography mass spectrometry (LC/MS), and high-performance computing. LC/MS of blood plasma extracts from rats that were administered a 1:1 mixture of acetaminophen (APAP) and (13)C6-APAP resulted in mass spectra that contained "twin" ions for drug metabolites that were not detected in control spectra (i.e., no APAP administered). Because of the development of a program (high-resolution twin-ion metabolite extraction; HiTIME) that can identify twin-ions in high-resolution mass spectra without centroiding (i.e., reduction of mass spectral peaks to single data points), 9 doublets corresponding to APAP metabolites were identified. This is nearly twice that obtained by use of existing programs that make use of centroiding to reduce computational cost under these conditions with a quadrupole time-of-flight mass spectrometer. By a manual search for all reported APAP metabolite ions, no additional twin-ion signals were assigned. These data indicate that all the major metabolites of APAP and multiple low-abundance metabolites (e.g., acetaminophen hydroxy- and methoxysulfate) that are rarely reported were detected. This methodology can be used to detect drug metabolites without prior knowledge of their identity. HiTIME is freely available from https://github.com/bjpop/HiTIME . PMID:25818563

  12. Integrated Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) Quantitative Proteomic Analysis Identifies Galectin-1 as a Potential Biomarker for Predicting Sorafenib Resistance in Liver Cancer.

    PubMed

    Yeh, Chao-Chi; Hsu, Chih-Hung; Shao, Yu-Yun; Ho, Wen-Ching; Tsai, Mong-Hsun; Feng, Wen-Chi; Chow, Lu-Ping

    2015-06-01

    Sorafenib has become the standard therapy for patients with advanced hepatocellular carcinoma (HCC). Unfortunately, most patients eventually develop acquired resistance. Therefore, it is important to identify potential biomarkers that could predict the efficacy of sorafenib. To identify target proteins associated with the development of sorafenib resistance, we applied stable isotope labelling with amino acids in cell culture (SILAC)-based quantitative proteomic approach to analyze differences in protein expression levels between parental HuH-7 and sorafenib-acquired resistance HuH-7 (HuH-7(R)) cells in vitro, combined with an isobaric tags for relative and absolute quantitation (iTRAQ) quantitative analysis of HuH-7 and HuH-7(R) tumors in vivo. In total, 2,450 quantified proteins were identified in common in SILAC and iTRAQ experiments, with 81 showing increased expression (>2.0-fold) with sorafenib resistance and 75 showing decreased expression (<0.5-fold). In silico analyses of these differentially expressed proteins predicted that 10 proteins were related to cancer with involvements in cell adhesion, migration, and invasion. Knockdown of one of these candidate proteins, galectin-1, decreased cell proliferation and metastasis in HuH-7(R) cells and restored sensitivity to sorafenib. We verified galectin-1 as a predictive marker of sorafenib resistance and a downstream target of the AKT/mTOR/HIF-1? signaling pathway. In addition, increased galectin-1 expression in HCC patients' serum was associated with poor tumor control and low response rate. We also found that a high serum galectin-1 level was an independent factor associated with poor progression-free survival and overall survival. In conclusion, these results suggest that galectin-1 is a possible biomarker for predicting the response of HCC patients to treatment with sorafenib. As such, it may assist in the stratification of HCC and help direct personalized therapy. PMID:25850433

  13. High-efficiency astatination of antibodies using N-iodosuccinimide as the oxidising agent in labelling of N-succinimidyl 3-(trimethylstannyl)benzoate

    Microsoft Academic Search

    S. Lindegren; H. Andersson; T. Bäck; L. Jacobsson; B. Karlsson; G. Skarnemark

    2001-01-01

    Monoclonal antibodies C215, reactive with colorectal carcinomas, and MOv18, reactive with most of the ovarian carcinomas, were radiohalogenated with [211At]astatine. The radiohalogen was conjugate coupled to antibodies via the intermediate labelling reagent N-succinimidyl-3-(trimethylstannyl)benzoate (m-MeATE) in a two-step, single-pot reaction. Optimisation of the labelling of the reagent was achieved using N-iodosuccinimide, NIS, as the oxidising agent. The yields ranged from 69–95%

  14. An analysis of ash and isotopic carbon discrimination (delta13C) methods to evaluate water use efficiency in apple

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Apple cultivars are selected for fruit quality, disease and insect resistance, not water use efficiency (WUE), however, the need for more water use efficient crops is accelerating due to climate change and increased competition for water resources. On a whole plant basis, calculation of water use e...

  15. Protein-based stable isotope probing

    Microsoft Academic Search

    Nico Jehmlich; Frank Schmidt; Jana Seifert; Felipe Bastida; Martin von Bergen; Hans-Hermann Richnow; Carsten Vogt; Martin Taubert

    2010-01-01

    We describe a stable isotope probing (SIP) technique that was developed to link microbe-specific metabolic function to phylogenetic information. Carbon (13C)- or nitrogen (15N)-labeled substrates (typically with >98% heavy label) were used in cultivation experiments and the heavy isotope incorporation into proteins (protein-SIP) on growth was determined. The amount of incorporation provides a measure for assimilation of a substrate, and

  16. Extrinsic Labeling Method May Not Accurately Measure Fe Absorption from Cooked Pinto Beans (Phaseolus vulgaris):Comparison of Extrinsic and Intrinsic labeling of Beans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Isotopic labeling of food has been widely used for the measurement of Fe absorption in determining requirements and evaluating the factors involved in Fe bioavailability. An extrinsic labeling technique will not accurately predict the total Fe absorption from foods unless complete isotopic exchange ...

  17. Iodine-Labeled Plasma Proteins. Vol. 1

    SciTech Connect

    Regoeczi, E.

    1984-01-01

    This volume presents the technical background necessary for manipulating plasma proteins and critically evaluates physicochemical changes brought about by introducing iodine atoms into various proteins. The chemistry of iodine and its inorganic derivatives, emissions of various iodine isotopes, analysis of radioiodine by chromatography, and methods for substitution of iodine isotopes in plasma proteins are discussed. Techniques used for separating labeled proteins from iodination mixtures, the reactivities of various amino acids with iodine, properties and analysis of iodoamino acids and the occurrence of labeled residues in a variety of plasma proteins are also examined. Many illustrations and over 800 references support the text.

  18. Femtosecond laser ablation molecular isotopic spectrometry for zirconium isotope analysis.

    PubMed

    Hou, Huaming; Chan, George C-Y; Mao, Xianglei; Zorba, Vassilia; Zheng, Ronger; Russo, Richard E

    2015-05-01

    Laser ablation molecular isotopic spectrometry (LAMIS) for rapid isotopic analysis of zirconium at atmospheric pressure was studied with a femtosecond-laser system operated under high repetition rate (1 kHz) and low pulse energy (160 ?J). The temporal evolution of zirconium neutral-atomic and ionic lines, as well as zirconium oxide molecular bands, were studied. Six molecular bands, belonging to the d(3)?-a(3)? (i.e., the ? system) and E(1)?(+)-X(1)?(+) transitions, were observed with appreciable isotopic shifts. The assignments of the isotopic bandheads were first based on theoretical predictions of the band origins and the associated isotopic shifts of various dipole-allowed ZrO electronic transitions, followed by an experimental confirmation with a (94)Zr-enriched ZrO2 sample. In this work, the ?(0,1) band from the d(3)?3-a(3)?3 subsystem was utilized for Zr isotope analysis based on a compromise between the magnitude of isotopic shifts in emission wavelengths, emission strengths, signal-to-background ratios, and spectral interferences. The analysis was performed in a standardless calibration approach; the isotopic information was extracted from the experimentally measured molecular spectra through theoretical spectral fitting. The results demonstrate the feasibility to obtain isotopic information for a spectrally complicated element like zirconium, without the need to use isotopically labeled calibration standards. The availability of comprehensive molecular constants will further improve the analytical accuracy of this standardless calibration approach. PMID:25821993

  19. Capillary Electrophoresis-Electrospray Ionization-Mass Spectrometry for Quantitative Analysis of Glycans Labeled with Multiplex Carbonyl-Reactive Tandem Mass Tags.

    PubMed

    Zhong, Xuefei; Chen, Zhengwei; Snovida, Sergei; Liu, Yan; Rogers, John C; Li, Lingjun

    2015-07-01

    Recently developed carbonyl-reactive aminoxy tandem mass tag (aminoxyTMT) reagents enable multiplexed characterization and quantitative comparison of structurally complex glycans between different biological samples. Compared to some previously reported isotopic labeling strategies for glycans, the use of the aminoxyTMT method features a simple labeling procedure, excellent labeling efficiency, and reduced spectral complexity at the MS(1) level. Presence of the tertiary amine functionality in the reporter region of the aminoxyTMT labels leads to increased ionization efficiency of the labeled glycans thus improving electrospray ionization (ESI)-mass spectrometry (MS) detection sensitivity. The use of the labeling reagent also makes electrophoretic separation of the labeled neutral and acidic glycans feasible. In this work, we characterized the ESI and collision induced dissociation (CID) behavior of the aminoxyTMT-labeled neutral and sialylated glycans. For the high-mannose N-glycans and small sialylated oligosaccharides, CID fragmentation of [M + Na + H](2+) provides the most informative MS(2) spectra for both quantitative and qualitative analysis. For complex N-glycans, MS(3) of the protonated Y1(H) ion can be used for relative quantification without interference from the HexNAc fragments. Online capillary electrophoresis (CE)-ESI-MS/MS analyses of multiplexed aminoxyTMT-labeled human milk oligosaccharides (HMOs) and different types of N-glycans released from glycoprotein standards were demonstrated. Improved resolution and quantification accuracy of the labeled HMO isomers was achieved by coupling CE with traveling wave ion mobility (TWIM)-CID-MS/MS. N-Glycans released from human serum protein digests were labeled with six-plex aminoxyTMT and subjected to CE-ESI-MS/pseudo-MS(3) analysis, which demonstrated the potential utility of this glycan relative quantification platform for more complex biological samples. PMID:25981625

  20. Proteomic response to 5,6-dimethylxanthenone 4-acetic acid (DMXAA, vadimezan) in human non-small cell lung cancer A549 cells determined by the stable-isotope labeling by amino acids in cell culture (SILAC) approach

    PubMed Central

    Pan, Shu-Ting; Zhou, Zhi-Wei; He, Zhi-Xu; Zhang, Xueji; Yang, Tianxin; Yang, Yin-Xue; Wang, Dong; Qiu, Jia-Xuan; Zhou, Shu-Feng

    2015-01-01

    5,6-Dimethylxanthenone 4-acetic acid (DMXAA), also known as ASA404 and vadimezan, is a potent tumor blood vessel-disrupting agent and cytokine inducer used alone or in combination with other cytotoxic agents for the treatment of non-small cell lung cancer (NSCLC) and other cancers. However, the latest Phase III clinical trial has shown frustrating outcomes in the treatment of NSCLC, since the therapeutic targets and underlying mechanism for the anticancer effect of DMXAA are not yet fully understood. This study aimed to examine the proteomic response to DMXAA and unveil the global molecular targets and possible mechanisms for the anticancer effect of DMXAA in NSCLC A549 cells using a stable-isotope labeling by amino acids in cell culture (SILAC) approach. The proteomic data showed that treatment with DMXAA modulated the expression of 588 protein molecules in A549 cells, with 281 protein molecules being up regulated and 306 protein molecules being downregulated. Ingenuity pathway analysis (IPA) identified 256 signaling pathways and 184 cellular functional proteins that were regulated by DMXAA in A549 cells. These targeted molecules and signaling pathways were mostly involved in cell proliferation and survival, redox homeostasis, sugar, amino acid and nucleic acid metabolism, cell migration, and invasion and programed cell death. Subsequently, the effects of DMXAA on cell cycle distribution, apoptosis, autophagy, and reactive oxygen species (ROS) generation were experimentally verified. Flow cytometric analysis showed that DMXAA significantly induced G1 phase arrest in A549 cells. Western blotting assays demonstrated that DMXAA induced apoptosis via a mitochondria-dependent pathway and promoted autophagy, as indicated by the increased level of cytosolic cytochrome c, activation of caspase 3, and enhanced expression of beclin 1 and microtubule-associated protein 1A/1B-light chain 3 (LC3-II) in A549 cells. Moreover, DMXAA significantly promoted intracellular ROS generation in A549 cells. Collectively, this SILAC study quantitatively evaluates the proteomic response to treatment with DMXAA that helps to globally identify the potential molecular targets and elucidate the underlying mechanism of DMXAA in the treatment of NSCLC. PMID:25733813

  1. Protected Amine Labels: A Versatile Molecular Scaffold for Multiplexed Nominal Mass and Sub-Da Isotopologue Quantitative Proteomic Reagents

    PubMed Central

    Ficarro, Scott B.; Biagi, Jessica M.; Wang, Jinhua; Scotcher, Jenna; Koleva, Rositsa I.; Card, Joseph D.; Adelmant, Guillaume; He, Huan; Askenazi, Manor; Marshall, Alan G.; Young, Nicolas L.; Gray, Nathanael S.; Marto, Jarrod A.

    2014-01-01

    We assemble a versatile molecular scaffold from simple building blocks to create binary and multiplexed stable isotope reagents for quantitative mass spectrometry. Termed Protected Amine Labels (PAL), these reagents offer multiple analytical figures of merit including, (i) robust targeting of peptide N-termini and lysyl side chains, (ii) optimal mass spectrometry ionization efficiency through regeneration of primary amines on labeled peptides, (iii) an amino acid-based mass tag that incorporates heavy isotopes of carbon, nitrogen, and oxygen to ensure matched physicochemical and MS/MS fragmentation behavior among labeled peptides, and (iv) a molecularly efficient architecture, in which the majority of hetero-atom centers can be used to synthesize a variety of nominal mass and sub-Da isotopologue stable isotope reagents. We demonstrate the performance of these reagents in well-established strategies whereby up to four channels of peptide isotopomers, each separated by 4 Da are quantified in MS-level scans with accuracies comparable to current commercial reagents. In addition we utilize the PAL scaffold to create isotopologue reagents in which labeled peptide analogs differ in mass based on the binding energy in carbon and nitrogen nuclei, thereby allowing quantification based on MS or MS/MS spectra. We demonstrate accurate quantification for reagents that support 6-plex labeling and propose extension of this scheme to 9-channels based on a similar PAL scaffold. Finally we provide exemplar data that extends the application of isotopologe-based quantification reagents to medium resolution, quadrupole time-of-flight mass spectrometers. PMID:24496597

  2. Rare-isotope and kinetic studies of Pt/SnO2 catalysts

    NASA Technical Reports Server (NTRS)

    Upchurch, Billy T.; Wood, George M.; Schryer, David R.; Hess, Robert V.; Miller, Irvin M.; Kielin, Erik J.

    1990-01-01

    Closed-cycle pulsed CO2 laser operation requires the use of an efficient CO-O2 recombination catalyst for these dissociation products which otherwise would degrade the laser operation. The catalyst must not only operate at low temperatures but also must operate efficiently for long periods. In the case of the Laser Atmospheric Wind Sounder (LAWS) laser, an operational lifetime of 3 years is required. Additionally, in order to minimize atmospheric absorption and enhance aerosol scatter of laser radiation, the LAWS system will operate at 9.1 micrometers with an oxygen-18 isotope CO2 lasing medium. Consequently, the catalyst must not only operate at low temperatures but must also preserve the isotopic integrity of the rare-isotope composition in the recombination mode. Several years ago an investigation of commercially available and newly synthesized recombination catalysts for use in closed-cycle pulsed common and rare-isotope CO2 lasers was implemented at the NASA Langley Research Center. Since that time, mechanistic efforts utilizing both common and rare oxygen isotopes have been implemented and continue. Rare-isotope studies utilizing commercially available platinum-tin oxide catalyst have demonstrated that the catalyst contributes oxygen-16 to the product carbon dioxide thus rendering it unusable for rare-isotope applications. A technique has been developed for modification of the surface of the common-isotope catalyst to render it usable. Results of kinetic and isotope label studies using plug flow, recycle plug flow, and closed internal recycle plug flow reactor configuration modes are discussed.

  3. INCORPORATING CONCENTRATION DEPENDENCE IN STABLE ISOTOPE MIXING MODELS

    EPA Science Inventory

    Stable isotopes are often used as natural labels to quantify the contributions of multiple sources to a mixture. For example, C and N isotopic signatures can be used to determine the fraction of three food sources in a consumer's diet. The standard dual isotope, three source li...

  4. Isotopic Biogeochemistry

    NASA Technical Reports Server (NTRS)

    Hayes, J. M.

    1985-01-01

    An overview is provided of the biogeochemical research. The funding, productivity, personnel and facilities are reviewed. Some of the technical areas covered are: carbon isotopic records; isotopic studies of banded iron formations; isotope effects in microbial systems; studies of organic compounds in ancient sediments; and development in isotopic geochemistry and analysis.

  5. Efficient Human Computation

    E-print Network

    Gilad-Bachrach, Ran; Ein-Dor, Liat

    2009-01-01

    Collecting large labeled data sets is a laborious and expensive task, whose scaling up requires division of the labeling workload between many teachers. When the number of classes is large, miscorrespondences between the labels given by the different teachers are likely to occur, which, in the extreme case, may reach total inconsistency. In this paper we describe how globally consistent labels can be obtained, despite the absence of teacher coordination, and discuss the possible efficiency of this process in terms of human labor. We define a notion of label efficiency, measuring the ratio between the number of globally consistent labels obtained and the number of labels provided by distributed teachers. We show that the efficiency depends critically on the ratio alpha between the number of data instances seen by a single teacher, and the number of classes. We suggest several algorithms for the distributed labeling problem, and analyze their efficiency as a function of alpha. In addition, we provide an upper b...

  6. Correlated optical and isotopic nanoscopy

    PubMed Central

    Saka, Sinem K.; Vogts, Angela; Kröhnert, Katharina; Hillion, François; Rizzoli, Silvio O; Wessels, Johannes T.

    2014-01-01

    The isotopic composition of different materials can be imaged by secondary ion mass spectrometry. In biology, this method is mainly used to study cellular metabolism and turnover, by pulsing the cells with marker molecules such as amino acids labelled with stable isotopes (15N, 13C). The incorporation of the markers is then imaged with a lateral resolution that can surpass 100?nm. However, secondary ion mass spectrometry cannot identify specific subcellular structures like organelles, and needs to be correlated with a second technique, such as fluorescence imaging. Here, we present a method based on stimulated emission depletion microscopy that provides correlated optical and isotopic nanoscopy (COIN) images. We use this approach to study the protein turnover in different organelles from cultured hippocampal neurons. Correlated optical and isotopic nanoscopy can be applied to a variety of biological samples, and should therefore enable the investigation of the isotopic composition of many organelles and subcellular structures. PMID:24718107

  7. COMMUNICATION An efficient protocol for incorporation of an unnatural amino acid

    E-print Network

    Clore, G. Marius

    . Keywords Site-specific labeling Á Isotopic labeling Á Unnatural amino acids Á Spin-labeling In vivo-specific methyl- labeled proteins used in the study of large molecular weight systems). The method consists of pre to exchanging the culture into a D2O-based medium. Our protocol results in high level of isotopic incorporation

  8. Variation in the carbon and oxygen isotope composition of plant biomass and its relationship to water-use efficiency at the leaf- and ecosystem-scales in a northern Great Plains grassland.

    PubMed

    Flanagan, Lawrence B; Farquhar, Graham D

    2014-02-01

    Measurements of the carbon (?(13) Cm ) and oxygen (?(18) Om ) isotope composition of C3 plant tissue provide important insights into controls on water-use efficiency. We investigated the causes of seasonal and inter-annual variability in water-use efficiency in a grassland near Lethbridge, Canada using stable isotope (leaf-scale) and eddy covariance measurements (ecosystem-scale). The positive relationship between ?(13) Cm and ?(18) Om values for samples collected during 1998-2001 indicated that variation in stomatal conductance and water stress-induced changes in the degree of stomatal limitation of net photosynthesis were the major controls on variation in ?(13) Cm and biomass production during this time. By comparison, the lack of a significant relationship between ?(13) Cm and ?(18) Om values during 2002, 2003 and 2006 demonstrated that water stress was not a significant limitation on photosynthesis and biomass production in these years. Water-use efficiency was higher in 2000 than 1999, consistent with expectations because of greater stomatal limitation of photosynthesis and lower leaf ci /ca during the drier conditions of 2000. Calculated values of leaf-scale water-use efficiency were 2-3 times higher than ecosystem-scale water-use efficiency, a difference that was likely due to carbon lost in root respiration and water lost during soil evaporation that was not accounted for by the stable isotope measurements. PMID:23862667

  9. Trypsin-catalyzed oxygen-18 labeling for quantitative proteomics

    SciTech Connect

    Qian, Weijun; Petritis, Brianne O.; Nicora, Carrie D.; Smith, Richard D.

    2011-07-01

    Stable isotope labeling based on relative peptide/protein abundance measurements is commonly applied for quantitative proteomics. Recently, trypsin-catalyzed oxygen-18 labeling has grown in popularity due to its simplicity, cost-effectiveness, and its ability to universally label peptides with high sample recovery. In (18)O labeling, both C-terminal carboxyl group atoms of tryptic peptides can be enzymatically exchanged with (18)O, thus providing the labeled peptide with a 4 Da mass shift from the (16)O-labeled sample. Peptide (18)O labeling is ideally suited for generating a labeled "universal" reference sample used for obtaining accurate and reproducible quantitative measurements across large number of samples in quantitative discovery proteomics.

  10. Isotopic Diversity and Plume Strength

    NASA Astrophysics Data System (ADS)

    Chauvel, C.; Maury, R. C.; Gutscher, M.

    2012-12-01

    The scale and geometry of isotopic heterogeneities in the source of plumes are poorly known but have important scientific implications for the origin of plumes, for the processes occurring during magma ascent through the mantle and for the timing of differentiation and mixing within the mantle. Isotopic heterogeneities occur at all scales in mantle rocks. Melt inclusions in mantle minerals have remarkably diverse isotopic compositions compared to their host lavas. At a much larger scale, the isotopic compositions of plume magmas are significantly different from ridge volcanics. Here we address the relationship between isotopic heterogeneity and magma productivity in mantle plumes. We compare several plumes, some very strong and long-lived like Hawaii and others very weak with sporadic magmatic activity. For the latter, we concentrate on the Polynesian Archipelago in the South Pacific which comprises several arrays of oceanic islands build over the past 20 Ma. We calculate, for several radiogenic isotopic systems, the isotopic amplitude within each island or island group and normalize these values to the total known variability in ocean island basalts worldwide. Our calculations show that isotopic diversity exists in all island groups, but where extreme isotopic compositions occur, they are always accompanied by FOZO-like compositions (the mean composition of all oceanic island). For example, the largest amplitudes for Pb isotopic compositions are found in the Austral chain where HIMU-type basalts erupt together with lavas with much lower Pb isotopes; and the largest amplitude for Nd isotopic compositions occurs in Pitcairn chain where EM I-type magmas coexist with lavas with much more radiogenic Nd isotopes. Additionally, our compilation shows that the isotopic diversity increases drastically as magma flux diminishes. We conclude that weak plumes selectively sample the source isotopic diversity through preferential low degree melting of small-scale heterogeneities. In contrast, strong plumes which produce large amounts of magma have much more homogeneous isotopic compositions as a consequence of efficient mixing of source heterogeneities during high-degree melting.

  11. Project EARTH-13-DP1: Understanding biological processes controlling metal isotopes in the oceans

    E-print Network

    Henderson, Gideon

    Project EARTH-13-DP1: Understanding biological processes controlling metal isotopes in the oceans) on different plankton, diatoms, and other biological materials. Techniques using isotopic labelling of metals onto surfaces may also lead to isotopic fractionation, leading to isotopic shifts in the remaining

  12. Isotopic Effect on Ion Mobility and Separation of Isotopomers by High-Field Ion Mobility

    E-print Network

    Clemmer, David E.

    application,4 and isotopic labeling is intrinsic to MS quantification methods. The issue of isotopesIsotopic Effect on Ion Mobility and Separation of Isotopomers by High-Field Ion Mobility of Chemistry, Indiana University, Bloomington, Indiana 47405 Distinguishing and separating isotopic molecular

  13. Comparison of water-use efficiency estimates based on tree-ring carbon isotopes with simulations of a dynamic vegetation model

    NASA Astrophysics Data System (ADS)

    Saurer, Matthias; Renato, Spahni; Fortunat, Joos; David, Frank; Kerstin, Treydte; Rolf, Siegwolf

    2015-04-01

    Tree-ring d13C-based estimates of intrinsic water-use efficiency (iWUE, reflecting the ratio of assimilation A to stomatal conductance gs) generally show a strong increase during the industrial period, likely associated with the increase in atmospheric CO2. However, it is not clear, first, if tree-ring d13C-derived iWUE-values indeed reflect actual plant and ecosystem-scale variability in fluxes and, second, what physiological changes were the drivers of the observed iWUE increase, changes in A or gs or both. To address these questions, we used a complex dynamic vegetation model (LPX) that combines process-based vegetation dynamics with land-atmosphere carbon and water exchange. The analysis was conducted for three functional types, representing conifers, oaks, larch, and various sites in Europe, where tree-ring isotope data are available. The increase in iWUE over the 20th century was comparable in LPX-simulations as in tree-ring-estimates, strengthening confidence in these results. Furthermore, the results from the LPX model suggest that the cause of the iWUE increase was reduced stomatal conductance during recent decades rather than increased assimilation. High-frequency variation reflects the influence of climate, like for example the 1976 summer drought, resulting in strongly reduced A and g in the model, particularly for oak.

  14. Multiple linear regression for isotopic measurements

    NASA Astrophysics Data System (ADS)

    Garcia Alonso, J. I.

    2012-04-01

    There are two typical applications of isotopic measurements: the detection of natural variations in isotopic systems and the detection man-made variations using enriched isotopes as indicators. For both type of measurements accurate and precise isotope ratio measurements are required. For the so-called non-traditional stable isotopes, multicollector ICP-MS instruments are usually applied. In many cases, chemical separation procedures are required before accurate isotope measurements can be performed. The off-line separation of Rb and Sr or Nd and Sm is the classical procedure employed to eliminate isobaric interferences before multicollector ICP-MS measurement of Sr and Nd isotope ratios. Also, this procedure allows matrix separation for precise and accurate Sr and Nd isotope ratios to be obtained. In our laboratory we have evaluated the separation of Rb-Sr and Nd-Sm isobars by liquid chromatography and on-line multicollector ICP-MS detection. The combination of this chromatographic procedure with multiple linear regression of the raw chromatographic data resulted in Sr and Nd isotope ratios with precisions and accuracies typical of off-line sample preparation procedures. On the other hand, methods for the labelling of individual organisms (such as a given plant, fish or animal) are required for population studies. We have developed a dual isotope labelling procedure which can be unique for a given individual, can be inherited in living organisms and it is stable. The detection of the isotopic signature is based also on multiple linear regression. The labelling of fish and its detection in otoliths by Laser Ablation ICP-MS will be discussed using trout and salmon as examples. As a conclusion, isotope measurement procedures based on multiple linear regression can be a viable alternative in multicollector ICP-MS measurements.

  15. Carbon-13 Labeling for Quantitative Analysis of Molecular Movement in Heterogeneous Organic

    E-print Network

    ,22,23 and therefore, techniques such as isotopic labeling have been utilized in an attempt to overcome these drawbacksCarbon-13 Labeling for Quantitative Analysis of Molecular Movement in Heterogeneous Organic of macromolecules in heterogeneous or- ganic systems. Using 13C tracer labeling and two model systems, polystyrene

  16. Changes in Thermodynamic Interactions at Highly Immiscible Polymer/Polymer Interfaces due to Deuterium Labeling

    E-print Network

    ) with its isotopic analogue (2H). Although this method of labeling seems simple and unobtrusive, it has been to Deuterium Labeling Shane E. Harton, Frederick A. Stevie, Zhengmao Zhu, and Harald Ade*,§ Department, 2006 Deuterium labeling has been shown previously to affect thermodynamic interactions at polymer

  17. State-Selective Metabolic Labeling of Cellular Proteins John T. Ngo1

    E-print Network

    Schuman, Erin M.

    in isotopic labeling, non-canonical amino acids (ncAAs) bearing azide or alkyne side chains are introduced 1 State-Selective Metabolic Labeling of Cellular Proteins John T. Ngo1 , Brett M. Babin1-determined physiological states can be identified. The approach is demonstrated by proteome-wide labeling of bacterial

  18. Comparison of various rhenium-188-labeled diphosphonates for the treatment of bone metastases

    Microsoft Academic Search

    Bor-Tsung Hsieh; Jih-Fang Hsieh; Shih-Chuan Tsai; Wan-Yu Lin; Shyh-Jen Wang; Gann Ting

    1999-01-01

    In the past, many diphosphonates were introduced as bone scan radiopharmaceuticals. In addition, diphosphonates have been labeled with beta-emitted isotopes and developed into useful therapeutic drugs for bone metastases. However, it is not clear which diphosphonate is the best choice when labeling with Re-188. In this study, we labeled methylene diphosphonate (MDP), hydroxyethylidene diphosphonate (HEDP), and hydroxymethane diphosphonate (HDP) with

  19. 5, 24252444, 2008 Stable isotopes and

    E-print Network

    Paris-Sud XI, Université de

    BGD 5, 2425­2444, 2008 Stable isotopes and multiple sources M. N. Bugalho et al. Title Page of Biogeosciences Stable isotopes as ecological tracers: an efficient method for assessing the contribution Union. 2425 #12;BGD 5, 2425­2444, 2008 Stable isotopes and multiple sources M. N. Bugalho et al. Title

  20. Comparison of Ecosystem Water-use Efficiency Among Douglas fir Forest, Aspen Forest and Grassland Using Eddy Covariance and Carbon Isotope Techniques

    NASA Astrophysics Data System (ADS)

    Flanagan, L. B.; Ponton, S.; Alstad, K. P.; Johnson, B. G.; Morgenstern, K.; Kljun, N.; Black, T. A.; Barr, A. G.

    2005-12-01

    Comparisons were made among Douglas fir forest, aspen (broad leaf deciduous) forest and wheatgrass (C3) grassland for ecosystem-level water-use efficiency. Water-use efficiency (WUE) was defined as the ratio of photosynthetic CO2 assimilation rate and evapo-transpiration (ET) rate. The ET data measured by eddy covariance were screened so that they overwhelmingly represented transpiration. The three sites used in this comparison spanned a range of vegetation (plant functional) types and environmental conditions within western Canada. When compared in the relative order Douglas fir (located on Vancouver Island, B.C), aspen (northern Saskatchewan), grassland (southern Alberta), the sites demonstrated a progressive decline in precipitation and a general increase in maximum air temperature and atmospheric saturation deficit (D) during the mid-summer. The average WUE at the grassland site was 2.6 mmol mol-1, which was much lower than the average values observed for the two other sites (aspen: 5.4, Douglas fir: 8.1). The differences in WUE among sites were primarily due to variation in ET. The highest maximum ET rates were approximately 5, 3.2 and 2.7 mm day-1 for the grassland, aspen and Douglas fir sites, respectively. There was a strong negative correlation between WUE and D for all sites. We also made seasonal measurements of the carbon isotope ratio of ecosystem respired CO2 (?R) in order to test for the expected correlation between shifts in environmental conditions and changes to the ecosystem-integrated ratio of leaf intercellular to ambient CO2 concentration (ci/ca). There was a consistent increase in ?R values in the grassland, aspen forest and Douglas fir forest associated with a seasonal reduction in soil moisture. Comparisons were made between WUE measured using eddy covariance with that calculated based on atmospheric saturation deficit and ?R measurements. There was excellent agreement between WUE values calculated using the two techniques. Our ?R measurements indicated that ci/ca values were quite similar among the Douglas fir, aspen and grassland sites, despite large variation in environmental conditions among sites. This implied that the shorter-lived grass species had relatively high ci/ca values for the D of their habitat. By contrast, the longer-lived Douglas fir trees were more conservative in water-use with lower ci/ca values relative to their habitat D. This illustrates the interaction between biological and environmental characteristics influencing ecosystem-level water-use efficiency.

  1. Bcl-2-functionalized ultrasmall superparamagnetic iron oxide nanoparticles coated with amphiphilic polymer enhance the labeling efficiency of islets for detection by magnetic resonance imaging

    PubMed Central

    Yang, Bin; Cai, Haolei; Qin, Wenjie; Zhang, Bo; Zhai, Chuanxin; Jiang, Biao; Wu, Yulian

    2013-01-01

    Based on their versatile, biocompatible properties, superparamagnetic iron oxide (SPIO) or ultrasmall superparamagnetic iron oxide (USPIO) nanoparticles are utilized for detecting and tracing cells or tumors in vivo. Here, we developed an innoxious and concise synthesis approach for a novel B-cell lymphoma (Bcl)-2 monoclonal antibody-functionalized USPIO nanoparticle coated with an amphiphilic polymer (carboxylated polyethylene glycol monooleyl ether [OE-PEG-COOH]). These nanoparticles can be effectively internalized by beta cells and label primary islet cells, at relatively low iron concentration. The biocompatibility and cytotoxicity of these products were investigated by comparison with the commercial USPIO product, FeraSpin™ S. We also assessed the safe dosage range of the product. Although some cases showed a hypointensity change at the site of transplant, a strong magnetic resonance imaging (MRI) was detectable by a clinical MRI scanner, at field strength of 3.0 Tesla, in vivo, and the iron deposition/attached in islets was confirmed by Prussian blue and immunohistochemistry staining. It is noteworthy that based on our synthesis approach, in future, we could exchange the Bcl-2 with other probes that would be more specific for the targeted cells and that would have better labeling specificity in vivo. The combined results point to the promising potential of the novel Bcl-2-functionalized PEG-USPIO as a molecular imaging agent for in vivo monitoring of islet cells or other cells. PMID:24204136

  2. Understanding Food Labels

    MedlinePLUS

    ... Healthy eating for girls Understanding food labels Understanding food labels There is lots of info on food ... need to avoid because of food allergies. Other food label terms top In addition to the Nutrition ...

  3. Read the Label First

    MedlinePLUS

    ... Fact Sheets Health & Safety Read the Label First Read the Label First Need help with product labels? ... effectively. It contains pertinent information that you should read and understand before you use a pesticide product. ...

  4. Calendar Year 2009 Program Benefits for ENERGY STAR Labeled Products

    Microsoft Academic Search

    Gregory K Homan; Marla C. Sanchez; Richard E. Brown

    2010-01-01

    ENERGY STAR is a voluntary energy efficiency labeling program operated jointly by the Environmental Protection Agency (US EPA) and the U.S. Department of Energy (US DOE), designed to identify and promote energy-efficient products, buildings and practices. Since the program inception in 1992, ENERGY STAR has become a leading international brand for energy efficient products, and currently labels more than thirty

  5. Multi-focus cluster labeling.

    PubMed

    Eikvil, Line; Jenssen, Tor-Kristian; Holden, Marit

    2015-06-01

    Document collections resulting from searches in the biomedical literature, for instance, in PubMed, are often so large that some organization of the returned information is necessary. Clustering is an efficient tool for organizing search results. To help the user to decide how to continue the search for relevant documents, the content of each cluster can be characterized by a set of representative keywords or cluster labels. As different users may have different interests, it can be desirable with solutions that make it possible to produce labels from a selection of different topical categories. We therefore introduce the concept of multi-focus cluster labeling to give users the possibility to get an overview of the contents through labels from multiple viewpoints. The concept for multi-focus cluster labeling has been established and has been demonstrated on three different document collections. We illustrate that multi-focus visualizations can give an overview of clusters along axes that general labels are not able to convey. The approach is generic and should be applicable to any biomedical (or other) domain with any selection of foci where appropriate focus vocabularies can be established. A user evaluation also indicates that such a multi-focus concept is useful. PMID:25869415

  6. Trends in carbon isotope fractionation in atmospheric carbon dioxide constrain water use efficiency of northern ecosystems from the 1980s to 2010

    NASA Astrophysics Data System (ADS)

    Welp, L. R.; Piper, S. C.; Graven, H. D.; Bollenbacher, A.; Meijer, H. A.; Keeling, R. F.

    2013-12-01

    Atmospheric CO2 concentrations have increased by approximately 120 ppm since preindustrial times and have reached levels higher than any other time during the last three to five million years ago with uncertain consequences for the modern terrestrial biosphere. When plants take up CO2 for photosynthesis from the atmosphere through stomata openings in their leaves, water escapes due to the gradient in water vapor pressure from the leaf interior to the atmospheric boundary layer. The amount of carbon assimilated by photosynthesis per water lost determines the water use efficiency (WUE) of the plant. The extra CO2 in the atmosphere has been shown to increase WUE in growth chamber studies, allowing plants to take up the same or more CO2 with reduced stomatal conductance, thereby reducing water loss. Carbon isotope fractionation by plants is related to the CO2 concentration gradient from inside the leaf (Ci) to that in the atmosphere (Ca) (e.g. Farquhar model). Therefore intrinsic water use efficiency (iWUE) of the biosphere, defined as the amount of net photosynthesis divided by the stomatal conductance, leaves an imprint on the record of ?13C in atmospheric CO2. We will present estimates of the biological carbon isotope fractionation of atmospheric CO2 from the Scripps Institution of Oceanography flask network from the 1980s to 2010 and discuss the constraints it provides on trends in iWUE over this period. Using the seasonal co-variation of 13C and CO2, we calculate effective fractionation. This data can be used to test hypothetical trends in iWUE and Ci. The conventional wisdom in the field has been that the ratio of Ci/Ca would remain approximately constant as CO2 rises, which would result in no change in fractionation but a modest increase in iWUE. Keenan et al. (2013) recently published an analysis of FluxNet eddy covariance measurements suggesting that Ci has stayed nearly constant since the mid-1990s, translating to a large ~3% yr-1 increase in iWUE. Atmospheric records from Barrow, Alaska, and Alert, Canada stations, suggest an increase in fractionation of northern ecosystems over the last few decades. These atmospheric results seem generally consistent with a constant Ca-Ci scenario, which increases fractionation, but corresponds to a constant iWUE. At the same time that fractionation has been increasing, the amplitude of the seasonal cycle of CO2 has increased dramatically (Graven et al., 2013). One possible explanation for both trends is that the deciduous fraction in the boreal forests has increased as these forest species have shorter, more intense periods of CO2 uptake and have been shown to have greater 13C fractionation and lower iWUE than evergreen species.

  7. Genetic Control of Water Use Efficiency and Leaf Carbon Isotope Discrimination in Sunflower (Helianthus annuus L.) Subjected to Two Drought Scenarios

    PubMed Central

    Adiredjo, Afifuddin Latif; Navaud, Olivier; Muños, Stephane; Langlade, Nicolas B.; Lamaze, Thierry; Grieu, Philippe

    2014-01-01

    High water use efficiency (WUE) can be achieved by coordination of biomass accumulation and water consumption. WUE is physiologically and genetically linked to carbon isotope discrimination (CID) in leaves of plants. A population of 148 recombinant inbred lines (RILs) of sunflower derived from a cross between XRQ and PSC8 lines was studied to identify quantitative trait loci (QTL) controlling WUE and CID, and to compare QTL associated with these traits in different drought scenarios. We conducted greenhouse experiments in 2011 and 2012 by using 100 balances which provided a daily measurement of water transpired, and we determined WUE, CID, biomass and cumulative water transpired by plants. Wide phenotypic variability, significant genotypic effects, and significant negative correlations between WUE and CID were observed in both experiments. A total of nine QTL controlling WUE and eight controlling CID were identified across the two experiments. A QTL for phenotypic response controlling WUE and CID was also significantly identified. The QTL for WUE were specific to the drought scenarios, whereas the QTL for CID were independent of the drought scenarios and could be found in all the experiments. Our results showed that the stable genomic regions controlling CID were located on the linkage groups 06 and 13 (LG06 and LG13). Three QTL for CID were co-localized with the QTL for WUE, biomass and cumulative water transpired. We found that CID and WUE are highly correlated and have common genetic control. Interestingly, the genetic control of these traits showed an interaction with the environment (between the two drought scenarios and control conditions). Our results open a way for breeding higher WUE by using CID and marker-assisted approaches and therefore help to maintain the stability of sunflower crop production. PMID:24992022

  8. Assessing the Cr(VI) reduction efficiency of a permeable reactive barrier using Cr isotope measurements and 2D reactive transport modeling.

    PubMed

    Wanner, Christoph; Zink, Sonja; Eggenberger, Urs; Mäder, Urs

    2012-04-01

    In Thun, Switzerland, a permeable reactive barrier (PRB) for Cr(VI) reduction by gray cast iron was installed in May 2008. The PRB is composed of a double array of vertical piles containing iron shavings and gravel. The aquifer in Thun is almost saturated with dissolved oxygen and the groundwater flow velocities are ca. 10-15m/day. Two years after PRB installation Cr(VI) concentrations still permanently exceed the Swiss threshold value for contaminated sites downstream of the barrier at selected localities. Groundwater ?(53/52)Cr(SRM979) measurements were used to track Cr(VI) reduction induced by the PRB. ?(53/52)Cr(SRM979) values of two samples downstream of the PRB showed a clear fractionation towards more positive values compared to four samples from the hotspot, which is clear evidence of Cr(VI) reduction induced by the PRB. Another downstream sample did not show a shift to more positive ?(53/52)Cr(SRM979) values. Because this latter location correlates with the highest downstream Cr(VI) concentration it is proposed that a part of the Cr(VI) plume is bypassing the barrier. Using a Rayleigh fractionation model a minimum present-day overall Cr(VI) reduction efficiency of ca. 15% was estimated. A series of 2D model simulations, including the fractionation of Cr isotopes, confirm that only a PRB bypass of parts of the Cr(VI) plume can lead to the observed values. Additionally, the simulations revealed that the proposed bypass occurs due to an insufficient permeability of the individual PRB piles. It is concluded that with this type of PRB a complete and long-lasting Cr(VI) reduction is extremely difficult to achieve for Cr(VI) contaminations located in nearly oxygen and calcium carbonate saturated aquifer in a regime of high groundwater velocities. Additional remediation action would limit the environmental impact and allow to reach target concentrations. PMID:22343010

  9. Evaluation of stable labeled compounds as internal standards for quantitative GC\\/MS determinations. Final report Jul 79Jul 81

    Microsoft Academic Search

    Colby

    1983-01-01

    The report gives results of an investigation of the use of stable isotopically labeled compounds as internal standards for quantitative isotope dilution GC\\/MS determinations. The availability of labeled compounds and the costs associated with using them for routine analyses were evaluated using the volatile, acid, and base\\/neutral fraction priority pollutants as a target component base. About 75 percent of these

  10. A fully enzymatic method for site-directed spin labeling of long RNA

    PubMed Central

    Lebars, Isabelle; Vileno, Bertrand; Bourbigot, Sarah; Turek, Philippe; Wolff, Philippe; Kieffer, Bruno

    2014-01-01

    Site-directed spin labeling is emerging as an essential tool to investigate the structural and dynamical features of RNA. We propose here an enzymatic method, which allows the insertion of a paramagnetic center at a specific position in an RNA molecule. The technique is based on a segmental approach using a ligation protocol with T4 RNA ligase 2. One transcribed acceptor RNA is ligated to a donor RNA in which a thio-modified nucleotide is introduced at its 5?-end by in vitro transcription with T7 RNA polymerase. The paramagnetic thiol-specific reagent is subsequently attached to the RNA ligation product. This novel strategy is demonstrated by introducing a paramagnetic probe into the 55 nucleotides long RNA corresponding to K-turn and Specifier Loop domains from the Bacillus subtilis tyrS T-Box leader RNA. The efficiency of the coupling reaction and the quality of the resulting spin-labeled RNA were assessed by Mass Spectrometry, Electron Paramagnetic Resonance (EPR) and Nuclear Magnetic Resonance (NMR). This method enables various combinations of isotopic segmental labeling and spin labeling schemes, a strategy that will be of particular interest to investigate the structural and dynamical properties of large RNA complexes by NMR and EPR spectroscopies. PMID:24981512

  11. Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research.

    PubMed

    Wiese, Sebastian; Reidegeld, Kai A; Meyer, Helmut E; Warscheid, Bettina

    2007-02-01

    A novel, MS-based approach for the relative quantification of proteins, relying on the derivatization of primary amino groups in intact proteins using isobaric tag for relative and absolute quantitation (iTRAQ) is presented. Due to the isobaric mass design of the iTRAQ reagents, differentially labeled proteins do not differ in mass; accordingly, their corresponding proteolytic peptides appear as single peaks in MS scans. Because quantitative information is provided by isotope-encoded reporter ions that can only be observed in MS/MS spectra, we analyzed the fragmentation behavior of ESI and MALDI ions of peptides generated from iTRAQ-labeled proteins using a TOF/TOF and/or a QTOF instrument. We observed efficient liberation of reporter ions for singly protonated peptides at low-energy collision conditions. In contrast, increased collision energies were required to liberate the iTRAQ label from lysine side chains of doubly charged peptides and, thus, to observe reporter ions suitable for relative quantification of proteins with high accuracy. We then developed a quantitative strategy that comprises labeling of intact proteins by iTRAQ followed by gel electrophoresis and peptide MS/MS analyses. As proof of principle, mixtures of five different proteins in various concentration ratios were quantified, demonstrating the general applicability of the approach presented here to quantitative MS-based proteomics. PMID:17177251

  12. Synthesis Of Labeled Metabolites

    DOEpatents

    Martinez, Rodolfo A. (Santa Fe, NM); Silks, III, Louis A. (Los Alamos, NM); Unkefer, Clifford J. (Los Alamos, NM); Atcher, Robert (White Rock, NM)

    2004-03-23

    The present invention is directed to labeled compounds, for example, isotopically enriched mustard gas metabolites including: [1,1',2,2'-.sup.13 C.sub.4 ]ethane, 1,1'-sulfonylbis[2-(methylthio); [1,1',2,2'-.sup.13 C.sub.4 ]ethane, 1-[[2-(methylsulfinyl)ethyl]sulfonyl]-2-(methylthio); [1,1',2,2'-.sup.13 C.sub.4 ]ethane, 1,1'-sulfonylbis[2-(methylsulfinyl)]; and, 2,2'-sulfinylbis([1,2-.sup.13 C.sub.2 ]ethanol of the general formula ##STR1## where Q.sup.1 is selected from the group consisting of sulfide (--S--), sulfone (--S(O)--), sulfoxide (--S(O.sub.2)--) and oxide (--O--), at least one C* is .sup.13 C, X is selected from the group consisting of hydrogen and deuterium, and Z is selected from the group consisting of hydroxide (--OH), and --Q.sup.2 --R where Q.sup.2 is selected from the group consisting of sulfide (--S--), sulfone(--S(O)--), sulfoxide (--S(O.sub.2)--) and oxide (--O--), and R is selected from the group consisting of hydrogen, a C.sub.1 to C.sub.4 lower alkyl, and amino acid moieties, with the proviso that when Z is a hydroxide and Q.sup.1 is a sulfide, then at least one X is deuterium.

  13. Changes in 131I-Labelled Immune Bovine gamma -globulin during Transmission to the Circulation after Oral Adminstration to the Young Rat

    Microsoft Academic Search

    F. W. R. Brambell; R. Halliday; W. A. Hemmings

    1961-01-01

    Bovine gamma -globulin, trace-labelled with 131I, reaches the circulation in substantial amounts although bacterial agglutinins from bovine antisera appear to be completely excluded. Thus when the bovine globulin is both isotopically labelled and immune, the labelled protein which reaches the circulation is still precipitable by antisera to bovine globulin but is without antibody activity. When the labelled bovine gamma -globulin

  14. Development of an efficient signal amplification strategy for label-free enzyme immunoassay using two site-specific biotinylated recombinant proteins.

    PubMed

    Tang, Jin-Bao; Tang, Ying; Yang, Hong-Ming

    2015-02-15

    Constructing a recombinant protein between a reporter enzyme and a detector protein to produce a homogeneous immunological reagent is advantageous over random chemical conjugation. However, the approach hardly recombines multiple enzymes in a difunctional fusion protein, which results in insufficient amplification of the enzymatic signal, thereby limiting its application in further enhancement of analytical signal. In this study, two site-specific biotinylated recombinant proteins, namely, divalent biotinylated alkaline phosphatase (AP) and monovalent biotinylated ZZ domain, were produced by employing the Avitag-BirA system. Through the high streptavidin (SA)-biotin interaction, the divalent biotinylated APs were clustered in the SA-biotin complex and then incorporated with the biotinylated ZZ. This incorporation results in the formation of a functional macromolecule that involves numerous APs, thereby enhancing the enzymatic signal, and in the production of several ZZ molecules for the interaction with immunoglobulin G (IgG) antibody. The advantage of this signal amplification strategy is demonstrated through ELISA, in which the analytical signal was substantially enhanced, with a 32-fold increase in the detection sensitivity compared with the ZZ-AP fusion protein approach. The proposed immunoassay without chemical modification can be an alternative strategy to enhance the analytical signals in various applications involving immunosensors and diagnostic chips, given that the label-free IgG antibody is suitable for the ZZ protein. PMID:25622607

  15. Imaging of inflammation with indium-111 tropolonate labeled leukocytes

    Microsoft Academic Search

    A. Michael Peters; Sethna H. Saverymuttu; Helen J. Reavy; Heather J. Danpure; Safiye Osman; J. Peter Lavender

    1983-01-01

    Indium-111 tropolonate has recently been introduced as a new cell-labeling agent. It has the interesting property of labeling cells in plasma with high efficiency, and may therefore promote an improvement in viability of labeled cells. This paper describes researchers initial experience with ¹¹¹In tropolonate as a leukocyte label for abscess imaging. Pure populations of separated granulocytes, as well as crude

  16. SPECIAL ARTICLE: The use of radioactive isotopes in metallurgy

    Microsoft Academic Search

    R. Shuttleworth

    1953-01-01

    The ?-radiation from radioactive isotopes is used for radiography, and the ?-radiation for gauging the thickness of foils or, by back-scattering, the thickness of a coating on a base metal. The high sensitivity and ease with which isotopes can be detected and measured provides an easy method of estimating minute amounts of metal that have been labelled by pile irradiation.

  17. Long-term tree growth rate, water use efficiency, and tree ring nitrogen isotope composition of Pinus massoniana L. in response to global climate change and local nitrogen deposition in Southern China

    Microsoft Academic Search

    Fangfang Sun; Yuanwen Kuang; Dazhi Wen; Zhihong Xu; Jianli Li; Weidong Zuo; Enqing Hou

    2010-01-01

    Purpose  We aimed to investigate long-term tree growth rates, water use efficiencies (WUE), and tree ring nitrogen (N) isotope compositions\\u000a (?15N) of Masson pine (Pinus massoniana L.) in response to global climate change and local N deposition in Southern China.\\u000a \\u000a \\u000a \\u000a \\u000a Materials and methods  Tree annual growth rings of Masson pine were collected from four forest sites, viz. South China Botanical Garden (SBG),

  18. Calendar Year 2008 Program Benefits for ENERGY STAR Labeled Products

    Microsoft Academic Search

    GregoryK Homan; Marla Sanchez; RichardE Brown; Judy Lai

    2010-01-01

    This paper presents current and projected savings for ENERGY STAR labeled products, and details the status of the model as implemented in the September 2009 spreadsheets. ENERGY STAR is a voluntary energy efficiency labeling program operated jointly by the Environmental Protection Agency (US EPA) and the U.S. Department of Energy (US DOE), designed to identify and promote energy-efficient products, buildings

  19. RNA Stable Isotope Probing, a Novel Means of Linking Microbial Community Function to Phylogeny

    Microsoft Academic Search

    Mike Manefield; Andrew S. Whiteley; Robert I. Griffiths; Mark J. Bailey

    2002-01-01

    accountable for it. In this study stable-isotope-labeled (13C)phenol was fed into a phenol-degrading community from an aerobic industrial bioreactor, and the 13C-labeled RNA produced was used to identify the bacteria responsible for the process. Stable-isotope-labeled RNA was analyzed by equilibrium density centrifugation in concert with reverse transcription-PCR and denaturing gradient gel electrophoresis. In contradiction with findings from conventional methodologies, this

  20. Use of stable isotopes to determine compliance.

    PubMed

    Schwarcz, H P

    1984-12-01

    The natural variation in the abundance of stable isotopes of light elements (C, H, O, N) in humans is less than 0.5%. Much larger variations can be induced through administration of drugs labeled with enriched isotopes of these elements. Such labels thus can be used as tracers of compliance. Variations of several percent can be generated without adverse physiological effect. An example is presented of the use of deuterium oxide as a tracer, and a scheme of sampling moisture in expired air is proposed, in which the subject can easily collect a sample and present it for rapid analysis. Tracer levels can be used to estimate the degree of compliance. The labeled compound can be selected to match the drug being tested with respect to residence time in the body. Except for deuterium, the cost of such stable isotope tracers is at present prohibitive. The main problem with the use of stable isotopes in compliance studies is the cost of the tracer, a biologically acceptable substance labeled with a rare-stable isotope. Our original experiments were carried out using 13C-glucose, which costs at present about $600/g. To carry out a tracer experiment on an individual, approximately 10 mg of uniformly labeled tracer would be administered, which would result in a 5% shift of the 13C/12C ratio, which is easily detectable. To minimize the cost of such a study, we proposed utilizing the cheapest enriched light isotope that is available, namely, deuterium. Using a ratio-detecting mass spectrometer in which a sample is compared with a standard, it is possible to detect enrichment or depletion of deuterium with respect to 1H at the level of 0.1%.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:6518787

  1. Assessment of vitamin A status in rats by isotope dilution: A simplified model

    SciTech Connect

    Furr, H.C.; Cooper, D.A.; Olson, J.A. (Iowa State Univ., Ames (United States))

    1990-02-26

    Isotope-dilution analysis of vitamin A status requires giving a known quantity of labeled vitamin A to the subject and measuring the ratio of labeled to unlabeled retinol in the blood after a period for equilibration. To calculate total body stores from the isotopic ratio of plasma retinol, several assumptions must be made. In considering new ways of better calculating liver vitamin A stores from isotope-dilution data, the authors used the data of Green et al. to estimate loss of vitamin A tracer as a function of time and of vitamin A status. This correction markedly improves the correlation between calculated and analyzed liver vitamin A stores and also quantitively explains the hyperbolic relationship between fraction of tracer dose recovered in liver and mass of liver vitamin A stores. Agreement of this model with experimental data suggests that efficiency of absorption and storage of vitamin A is not affected by vitamin A status. This model can be used to estimate both the amount of tracer needed for a given lower limit of detection and an optimum sampling time.

  2. Active site structure of Rieske-type proteins: electron nuclear double resonance studies of isotopically labeled phthalate dioxygenase from Pseudomonas cepacia and Rieske protein from Rhodobacter capsulatus and molecular modeling studies of a Rieske center.

    PubMed

    Gurbiel, R J; Doan, P E; Gassner, G T; Macke, T J; Case, D A; Ohnishi, T; Fee, J A; Ballou, D P; Hoffman, B M

    1996-06-18

    Continuous wave electron nuclear double resonance (CW ENDOR) spectra of [delta-15N,epsilon(-14)N]histidine-labeled phthalate dioxygenase (PDO) from Pseudomonas cepacia were recorded and found to be virtually identical to those previously recorded from [delta,epsilon-15N2]histidine-labeled protein [Gurbiel, R. J., Batie, C. J., Sivaraja, M., True, A. E., Fee, J. A., Hoffman, B. M., & Ballou, D. P. (1989) Biochemistry 28, 4861-4871]. Thus, the two histidine residues, previously shown to ligate one of the irons in the cluster [cf. Gurbiel et al. 1989)], both coordinate the metal at the N(delta) position of their imidazole rings. Pulsed ENDOR studies showed that the "remote", noncoordinating nitrogen of the histidine imidazole ring could be observed from the Rieske protein in a sample of Rhodobacter capsulatus cytochrome bc1 complex uniformly labeled with 15N but not in a sample of PDO labeled with [delta-15N,epsilon-14N]histidine, but this atom was easily observed with a sample of Rh. capsulatus cytochrome bc1 complex that had been uniformly labeled with 15N; this confirmed the conclusion from the CW ENDOR studies that ligation is exclusively via N(delta) for both ligands in the PDO center. Modifications in the algorithms previously used to simulate 14N ENDOR spectra permitted us to compute spectra without any constraints on the relative orientation of hyperfine and quadrupole tensors. This new algorithm was used to analyze current and previously published spectra, and slightly different values for the N-Fe-N angle and imidazole ring rotation angles are presented [cf. Gurbiel et al. (1989) Gurbiel, R. J., Ohnishi, T., Robertson, D. E., Daldal, F., and Hoffman, B. M. (1991) Biochemistry 30, 11579-11584]. This analysis has permitted us to refine the proposed structure of the [2Fe-2S] Rieske-type cluster and rationalize some of the properties of these novel centers. Although the spectra of cytochrome bc1 complex from Rh. capsulatus are of somewhat lower resolution than those obtained with samples of PDO, our analysis nevertheless permits the conclusion that the geometry of the cluster is essentially the same for all Rieske and Rieske-type proteins. Structural constraints inferred from the spectroscopic results permitted us to apply the principles of distance geometry to arrive at possible three-dimensional models of the active site structure of Rieske protein from Rh. capsulatus. Results from this test case indicate that similar procedures should be generally useful in metalloprotein systems. We also recorded the pulsed and CW ENDOR spectra of 57Fe-labeled PDO, and the resulting data were used to derive the full hyperfine tensors for both Fe(III) and Fe(II) ions, including their orientations relative to the g tensor. The A tensor of the ferric ion is nominally isotropic, while the A tensor of the ferrous ion is axial, having A(parallel) > A(perpendicular); both tensors are coincident with the observed g tensor, with A(parallel) of the ferrous ion lying along the maximum g-value, g1. These results were examined using refinements of existing theories of spin-coupling in [2Fe-2S]+ clusters, and it is concluded that current theories are not adequate to fully describe the experimental results. PMID:8672484

  3. Deciphering Food Labels

    MedlinePLUS

    ... choices to help meet your family's nutritional needs. Food Labels Information The Food and Drug Administration (FDA) ... values; and important nutrients, vitamins, and minerals. Continue Food Label Claims Manufacturers often make claims about the ...

  4. Mapping photoautotrophic metabolism with isotopically nonstationary 13C flux analysis

    PubMed Central

    Young, Jamey D.; Shastri, Avantika A.; Stephanopoulos, Gregory; Morgan, John A.

    2011-01-01

    Understanding in vivo regulation of photoautotrophic metabolism is important for identifying strategies to improve photosynthetic efficiency or re-route carbon fluxes to desirable end products. We have developed an approach to reconstruct comprehensive flux maps of photoautotrophic metabolism by computational analysis of dynamic isotope labeling measurements and have applied it to determine metabolic pathway fluxes in the cyanobacterium Synechocystis sp. PCC6803. Comparison to a theoretically predicted flux map revealed inefficiencies in photosynthesis due to oxidative pentose phosphate pathway and malic enzyme activity, despite negligible photorespiration. This approach has potential to fill important gaps in our understanding of how carbon and energy flows are systemically regulated in cyanobacteria, plants, and algae. PMID:21907300

  5. Transuranium isotopes

    SciTech Connect

    Hoffman, D.C.

    1985-12-01

    The needs of the research community for the production of transuranium isotopes, the quantities required, the continuity of production desired, and what a new steady state neutron source would have to provide to satisfy these needs are discussed. Examples of past frontier research which need these isotopes as well as an outline of the proposed Large Einsteinium Activation Program, LEAP, which requires roughly ten times the current production of /sup 254/Es are given. 15 refs., 5 figs., 4 tabs.

  6. Eco-labelling, Competition and Environment: Endogenization of Labelling Criteria

    E-print Network

    Paris-Sud XI, Université de

    Eco-labelling, Competition and Environment: Endogenization of Labelling Criteria Adel Ben Youssef not to set up a label. Keywords: Eco-label, Labelling Criteria, Environmental Quality, Price Competition, Firms' Position. JEL Classification: C72, L13, Q20. 1 Introduction An eco-label is defined

  7. Improvement of multi jet low pressure impactor for high collection efficiency of UF5 in the molecular laser isotope separation of uranium

    Microsoft Academic Search

    Yoshikazu Kuga; Benjamin Jurcik; Sakae Satooka; Kazuo Takeuchi

    1995-01-01

    A numerical and experimental study for the collection of photo-produced UF5 particles was performed for the low pressure impactors which have different design factors at typical flow conditions (upstream pressure of the impactor = 10–15 Torr, pressure ratio of downstream to upstream of the impactor, PdownPup = 0.2–0.5) in the molecular laser isotope separation of uranium at RIKEN (RIMLIS). Smaller

  8. Relationships of stable carbon isotopes, plant water potential and growth: an approach to asses water use efficiency and growth strategies of dry land agroforestry species

    Microsoft Academic Search

    Aster Gebrekirstos; Meine van Noordwijk; Henry Neufeldt; Ralph Mitlöhner

    2011-01-01

    The relationships between annual wood stable carbon isotope composition (?13C), dry season midday plant water potential, and annual growth rate were investigated to asses the ability of agroforestry\\u000a species to adapt to climate changes. 6–8 stem disks from four co-occurring species (Acacia senegal, A. seyal, A. tortilis and Balanites aegyptiaca) were collected for radial growth measurements using tree-ring analysis spanning

  9. Mass Spectrometry-Based Label-Free Quantitative Proteomics

    PubMed Central

    Zhu, Wenhong; Smith, Jeffrey W.; Huang, Chun-Ming

    2010-01-01

    In order to study the differential protein expression in complex biological samples, strategies for rapid, highly reproducible and accurate quantification are necessary. Isotope labeling and fluorescent labeling techniques have been widely used in quantitative proteomics research. However, researchers are increasingly turning to label-free shotgun proteomics techniques for faster, cleaner, and simpler results. Mass spectrometry-based label-free quantitative proteomics falls into two general categories. In the first are the measurements of changes in chromatographic ion intensity such as peptide peak areas or peak heights. The second is based on the spectral counting of identified proteins. In this paper, we will discuss the technologies of these label-free quantitative methods, statistics, available computational software, and their applications in complex proteomics studies. PMID:19911078

  10. BIOAVAILABILITY OF LUTEIN IN HUMANS FROM INTRINSICALLY LABELED VEGETABLES DETERMINED BY LC-APCI-MS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The aim of the investigation was to assess a stable isotope method for determining the relative bioavailability of food-derived lutein in humans. Subjects were administered a single dose of deuterium-labeled carotenoids from intrinsically labeled spinach or collard green; 10 mL blood samples were d...

  11. Metabolic flux analysis using 13C peptide label measurements

    Technology Transfer Automated Retrieval System (TEKTRAN)

    13C metabolic flux analysis (MFA) has become the experimental method of choice to investigate cellular metabolism. MFA has established flux maps of central metabolism for dozens of microbes, cell cultures, and plant seeds. Steady-state MFA utilizes isotopic labeling measurements of amino acids obtai...

  12. Isotope chemistry; a useful tool in the drug discovery arsenal.

    PubMed

    Elmore, Charles S; Bragg, Ryan A

    2015-01-15

    As Medicinal Chemists are responsible for the synthesis and optimization of compounds, they often provide intermediates for use by isotope chemistry. Nevertheless, there is generally an incomplete understanding of the critical factors involved in the labeling of compounds. The remit of an Isotope Chemistry group varies from company to company, but often includes the synthesis of compounds labeled with radioisotopes, especially H-3 and C-14 and occasionally I-125, and stable isotopes, especially H-2, C-13, and N-15. Often the remit will also include the synthesis of drug metabolites. The methods used to prepare radiolabeled compounds by Isotope Chemists have been reviewed relatively recently. However, the organization and utilization of Isotope Chemistry has not been discussed recently and will be reviewed herein. PMID:25499878

  13. Biosynthetic production of universally (13)C-labelled polyunsaturated fatty acids as reference materials for natural health product research.

    PubMed

    Le, Phuong Mai; Fraser, Catherine; Gardner, Graeme; Liang, Wei-Wan; Kralovec, Jaroslav A; Cunnane, Stephen C; Windust, Anthony J

    2007-09-01

    Long-chain polyunsaturated fatty acids (LCPUFA) including eicosapentaenoic acid (EPA, 20:5n-3) and docosahexaenoic acid (DHA, 22:6n-3) have become important natural health products with numerous proven benefits related to brain function and cardiovascular health. Not only are omega-3 fatty acids available in a plethora of dietary supplements, but they are also increasingly being incorporated as triglycerides into conventional foods, including bread, milk, yoghurt and confectionaries. Recently, transgenic oil seed crops and livestock have been developed that enhance omega-3 fatty acid content. This diverse array of matrices presents a difficult analytical challenge and is compounded further by samples generated through clinical research. Stable isotope (13)C-labelled LCPUFA standards offer many advantages as research tools because they may be distinguished from their naturally abundant counterparts by mass spectrometry and directly incorporated as internal standards into analytical procedures. Further, (13)C-labelled LCPUFAs are safe to use as metabolic tracers to study uptake and metabolism in humans. Currently, (13)C-labelled LCPUFAs are expensive, available in limited supply and not in triglyceride form. To resolve these issues, marine heterotrophic microorganisms are being isolated and screened for LCPUFA production with a view to the efficient biosynthetic production of U-(13)C-labelled fatty acids using U-(13)C glucose as a carbon source. Of 37 isolates obtained, most were thraustochytrids, and either DHA or omega-6 docosapentaenoic acid (22:5n-6) were produced as the major LCPUFA. The marine protist Hyalochlorella marina was identified as a novel source of EPA and omega-3 docosapentaenoic acid (22:5n-3). As proof of principle, gram-level production of (13)C-labelled DHA has been achieved with high chemical purity ( >99%) and high (13)C incorporation levels (>90%), as confirmed by NMR and MS analyses. Finally, U-(13)C-DHA was enzymatically re-esterified to glycerol to yield a (13)C-labelled tridocosahexaenoin. PMID:17486321

  14. Lead isotopes in environmental sciences: A review

    Microsoft Academic Search

    Michael Komárek; Vojt?ch Ettler; Vladislav Chrastný; Martin Mihaljevi?

    2008-01-01

    Lead (Pb) isotopic analyses proved to be a very efficient tool for tracing the sources of local and global Pb pollution. This review presents an overview of literature published on the use of Pb isotopic analyses of different environmental matrices (atmospheric aerosols, lichens, tree rings, peat deposits, lake, stream, marine sediments, soils, etc.). In order to gain more insight, the

  15. Autologous platelet-labeling in thrombocytopenia

    SciTech Connect

    Sinzinger, H.; Virgolini, I.; Vinazzer, H. (Univ. of Vienna (Austria))

    1990-11-01

    Field studies performed with peripheral platelets obtained from 6 male volunteers aged 23 to 29 years revealed an extraordinary dependence of labeling efficiency on incubation time and platelet concentration after {sup 111}In-oxine platelet labeling. Since the monitoring of in vivo-platelet function in patients with thrombocytopenia may cause problems due to insufficient labeling results and homologous platelets may show a different in vivo behaviour to autologous ones, we have searched for the minimal amount of platelets necessary to allow appropriate labeling and imaging in patients with thrombocytopenia. In 15 patients with untreated thrombocytopenia aged 14 to 79 years demonstrating a mean peripheral platelet count of 2.509 +/- 1.45 x 10(4) cells/microliters autologous {sup 111}In-oxine platelet labeling was performed. The results indicate that approximately 1 x 10(8) (concentrated) platelets/ml are necessary to obtain an adequate labeling efficiency and recovery. This platelet concentration can be easily achieved by drawing one more Monovette of whole blood per each 5 x 10(4) platelets/microliter peripheral platelet count less than 2 x 10(5)/microliter. It is concluded, that calculation of the required number of platelets in advance, variation of the blood volume drawn and the volume of incubation buffer allow informative, qualitative and quantitative results using autologous platelets. The method presented effectively circumvents the requirement of homologous platelets for radiolabeling in thrombocytopenia.

  16. Isotope Science and Production

    E-print Network

    Isotope Science and Production 35 years of experience in isotope production, processing. Contact: Kevin John LANL Isotope Program Manager kjohn@lanl.gov 505-667-3602 Sponsored by the Department of Energy National Isotope Program http://www.nuclear.energy.gov/isotopes/nelsotopes2a.html Isotopes

  17. Facile labeling of lipoglycans with quantum dots

    SciTech Connect

    Morales Betanzos, Carlos; Gonzalez-Moa, Maria [Center for Innovations in Medicine, Biodesign Institute, Arizona State University, 1001 S. McAllister Av, Tempe, AZ 85287 (United States); Johnston, Stephen Albert [Center for Innovations in Medicine, Biodesign Institute, Arizona State University, 1001 S. McAllister Av, Tempe, AZ 85287 (United States); School of Life Sciences, Arizona State University 1711 S. Rural Road, Tempe, AZ 85287 (United States); Svarovsky, Sergei A. [Center for Innovations in Medicine, Biodesign Institute, Arizona State University, 1001 S. McAllister Av, Tempe, AZ 85287 (United States)], E-mail: Sergei.Svarovsky@asu.edu

    2009-02-27

    Bacterial endotoxins or lipopolysaccharides (LPS) are among the most potent activators of the innate immune system, yet mechanisms of their action and in particular the role of glycans remain elusive. Efficient non-invasive labeling strategies are necessary for studying interactions of LPS glycans with biological systems. Here we report a new method for labeling LPS and other lipoglycans with luminescent quantum dots. The labeling is achieved by partitioning of hydrophobic quantum dots into the core of various LPS aggregates without disturbing the native LPS structure. The biofunctionality of the LPS-Qdot conjugates is demonstrated by the labeling of mouse monocytes. This simple method should find broad applicability in studies concerned with visualization of LPS biodistribution and identification of LPS binding agents.

  18. Bar Code Labels

    NASA Technical Reports Server (NTRS)

    1988-01-01

    American Bar Codes, Inc. developed special bar code labels for inventory control of space shuttle parts and other space system components. ABC labels are made in a company-developed anodizing aluminum process and consecutively marketed with bar code symbology and human readable numbers. They offer extreme abrasion resistance and indefinite resistance to ultraviolet radiation, capable of withstanding 700 degree temperatures without deterioration and up to 1400 degrees with special designs. They offer high resistance to salt spray, cleaning fluids and mild acids. ABC is now producing these bar code labels commercially or industrial customers who also need labels to resist harsh environments.

  19. Tips for Adding Labels How Do I Add Labels

    E-print Network

    Brownstone, Rob

    Tips for Adding Labels How Do I Add Labels Right Click on the data layer in the Table of Contents Label Field dropdown o Change desired Font Tips With Labels you are not able to move/colour/size/delete them individually. To do that you must convert the labels to Annotation o Right click on the name

  20. Quantification of peptide m/z distributions from 13C-labeled cultures with high-resolution mass spectrometry.

    PubMed

    Allen, Doug K; Goldford, Joshua; Gierse, James K; Mandy, Dominic; Diepenbrock, Christine; Libourel, Igor G L

    2014-02-01

    Isotopic labeling studies of primary metabolism frequently utilize GC/MS to quantify (13)C in protein-hydrolyzed amino acids. During processing some amino acids are degraded, which reduces the size of the measurement set. The advent of high-resolution mass spectrometers provides a tool to assess molecular masses of peptides with great precision and accuracy and computationally infer information about labeling in amino acids. Amino acids that are isotopically labeled during metabolism result in labeled peptides that contain spatial and temporal information that is associated with the biosynthetic origin of the protein. The quantification of isotopic labeling in peptides can therefore provide an assessment of amino acid metabolism that is specific to subcellular, cellular, or temporal conditions. A high-resolution orbital trap was used to quantify isotope labeling in peptides that were obtained from unlabeled and isotopically labeled soybean embryos and Escherichia coli cultures. Standard deviations were determined by estimating the multinomial variance associated with each element of the m/z distribution. Using the estimated variance, quantification of the m/z distribution across multiple scans was achieved by a nonlinear fitting approach. Observed m/z distributions of uniformly labeled E. coli peptides indicated no significant differences between observed and simulated m/z distributions. Alternatively, amino acid m/z distributions obtained from GC/MS were convolved to simulate peptide m/z distributions but resulted in distinct profiles due to the production of protein prior to isotopic labeling. The results indicate that peptide mass isotopologue measurements faithfully represent mass distributions, are suitable for quantification of isotope-labeling-based studies, and provide additional information over existing methods. PMID:24387081

  1. High-efficiency labeling of sialylated glycoproteins

    E-print Network

    Cai, Long

    by either oxime and hydra- zone ligations, we used the oxime ligation, which gives a more stable product incorporation of sialic acids, we used a hyposialylated human B-cell line, BJA-B subclone K20 (hence- forth referred to as K20), that cannot synthesize its own sialic acids15. As a control, we used the BJA-B

  2. Isotope dependent, temperature regulated, energy repartitioning in a low-barrier, short-strong hydrogen bonded cluster

    E-print Network

    Iyengar, Srinivasan S.

    Isotope dependent, temperature regulated, energy repartitioning in a low-barrier, short/deuterium isotope effects, in a fundamental organic hydrogen bonded system using multiple experimental infrared the isotopically labeled systems arises from an analysis of the simulated cluster spectroscopy and leads

  3. Tritium labeling of detonation nanodiamonds.

    PubMed

    Girard, Hugues A; El-Kharbachi, Abdelouahab; Garcia-Argote, Sébastien; Petit, Tristan; Bergonzo, Philippe; Rousseau, Bernard; Arnault, Jean-Charles

    2014-03-18

    For the first time, the radioactive labeling of detonation nanodiamonds was efficiently achieved using a tritium microwave plasma. According to our measurements, the total radioactivity reaches 9120 ± 120 ?Ci mg(-1), with 93% of (3)H atoms tightly bonded to the surface and up to 7% embedded into the diamond core. Such (3)H doping will ensure highly stable radiolabeled nanodiamonds, on which surface functionalization is still allowed. This breakthrough opens the way to biodistribution and pharmacokinetics studies of nanodiamonds, while this approach can be scalable to easily treat bulk quantities of nanodiamonds at low cost. PMID:24492594

  4. Protein-based stable isotope probing.

    PubMed

    Jehmlich, Nico; Schmidt, Frank; Taubert, Martin; Seifert, Jana; Bastida, Felipe; von Bergen, Martin; Richnow, Hans-Hermann; Vogt, Carsten

    2010-12-01

    We describe a stable isotope probing (SIP) technique that was developed to link microbe-specific metabolic function to phylogenetic information. Carbon ((13)C)- or nitrogen ((15)N)-labeled substrates (typically with >98% heavy label) were used in cultivation experiments and the heavy isotope incorporation into proteins (protein-SIP) on growth was determined. The amount of incorporation provides a measure for assimilation of a substrate, and the sequence information from peptide analysis obtained by mass spectrometry delivers phylogenetic information about the microorganisms responsible for the metabolism of the particular substrate. In this article, we provide guidelines for incubating microbial cultures with labeled substrates and a protocol for protein-SIP. The protocol guides readers through the proteomics pipeline, including protein extraction, gel-free and gel-based protein separation, the subsequent mass spectrometric analysis of peptides and the calculation of the incorporation of stable isotopes into peptides. Extraction of proteins and the mass fingerprint measurements of unlabeled and labeled fractions can be performed in 2-3 d. PMID:21127489

  5. Monitoring electron donor metabolism under variable electron acceptor conditions using 13C-labeled lactate

    NASA Astrophysics Data System (ADS)

    Bill, M.; Conrad, M. E.; Yang, L.; Beller, H. R.; Brodie, E. L.

    2010-12-01

    Three sets of flow-through columns constructed with aquifer sediment from Hanford (WA) were used to study reduction of Cr(VI) to poorly soluble Cr(III) under denitrifying, sulfate-reducing/fermentative, and iron-reducing conditions with lactate as the electron donor. In order to understand the relationship between electron donors and biomarkers, and to determine the differences in carbon isotope fractionation resulting from different microbial metabolic processes, we monitored the variation in carbon isotopes in dissolved inorganic carbon (DIC), in total organic carbon (TOC), and in lactate, acetate and propionate. The greatest enrichment in 13C in columns was observed under denitrifying conditions. The ?13C of DIC increased by ~1750 to ~2000‰ fifteen days after supplementation of natural abundance lactate with a 13C-labeled lactate tracer (for an influent ?13C of ~2250‰ for the lactate) indicating almost complete oxidation of the electron donor. The denitrifying columns were among the most active columns and had the highest cell counts and the denitrification rate was highly correlated with Cr(VI) reduction rate. ?13C values of DIC ranged from ~540 to ~1170‰ for iron-reducing conditions. The lower enrichment in iron columns was related to the lower biological activity observed with lower yields of RNA and cell numbers in the column effluents. The carbon isotope shift in the sulfate-reducing ~198 to ~1960‰ for sulfate-reducing conditions reflecting the lower levels of the lactate in these columns. Additionally, in two of the sulfate columns, almost complete fermentation of the lactate occurred, producing acetate and propionate with the labeled carbon signature, but relatively smaller amounts of inorganic carbon. For all electron-accepting conditions, TOC yielded similar ?13C values as lactate stock solutions. Differences in C use efficiency, metabolic rate or metabolic pathway contributed to the differing TOC ?13C to DIC ?13C ratios between treatments. Carbon isotope signatures of DIC can be useful for monitoring the efficiency of 13C-enriched electron donor consumption associated with bioactivity under reducing conditions.

  6. Introduction Balanced Group Labeled Graphs

    E-print Network

    Diwan, Ajit A

    Introduction Results Summary Balanced Group Labeled Graphs M. Joglekar N. Shah A.A. Diwan.A.Diwan Balanced Group Labeled Graphs #12;Introduction Results Summary Outline 1 Introduction Group Labeled Graphs Balanced Labellings Characterization 2 Results Counting Number of Balanced labellings Proof Markable Graphs

  7. Fluorescent Labeling Reagents Optimized for Capillary Electrophoretic Separations

    E-print Network

    Estrada, Roy Tonacao, III

    2012-02-14

    . The fluorophore is di-anionic and is based on pyrene. The SPR was designed to allow the simultaneous capture and labeling of an analyte and the efficient release of the label-analyte conjugate under mild acidic conditions. The use of the SPR allowed...

  8. Using Food Labels

    NSDL National Science Digital Library

    Nancy P. Moreno

    2011-01-01

    In this nutrition activity, learners explore food labels and consider the nutritional value of foods. Learners also explore units of measurement commonly used on food labels. Learners will be surprised to find out how much sugar soft drinks contain. This lesson guide includes background information and bilingual (English/Spanish) handouts.

  9. Production of carbon isotopes by laser separation

    NASA Astrophysics Data System (ADS)

    Baranov, Vladimir Y.; Dyad'kin, A. P.; Maluta, D. D.; Kuzmenko, V. A.; Pigulskiy, S. V.; Mezhevov, Vladimir S.; Letokhov, Vladilen S.; Laptev, Vladimir B.; Ryabov, Evgeny A.; Yarovoi, I. V.; Zarin, V. B.; Podoryashy, A. S.

    2000-07-01

    Since the advent of lasers, these unique sources of highly intense and monochromatic radiation have been proposed as excellent tools to induce or catalyze chemical reactions. Due to the great interest to the problem of isotope production, investigation and application, the laser method of isotope separation has received the most attention worldwide and may be the first major commercial application of lasers to chemistry. Laser methods of isotope separation are based on high selectivity and power of laser sources of radiation. One of the most prominent method is based on the effect is isotope-selective multiphoton dissociation of molecules by IR-radiation (MLIS-method). This phenomena was discovered in Russia in 1974 and developed from scientific investigations to industrial scale production of 13C isotopes in collaboration between the Kurchatov Institute of Atomic Energy, TRINITI and Institute of Spectroscopy of RAS. Demonstration facilities for sulfur and carbon isotope separation with average productivity up to 2 g/h have been created as a result of collaboration and these systems are aimed at optimization of MLIS process and evaluation of its cost efficiency. Experiments show that laser produced isotopes are far cheaper as compared to any conventional technique. Results of basic scientific research, existing technological cooperation allow to start building a laser isotope separation plant. Light element isotopes produced there can answer a wide variety of demands in many technologies. These isotopes can be readily used in medicine, agriculture, environmental monitoring, etc.

  10. How to Read Drug Labels

    MedlinePLUS

    ... and alternative medicine Healthy Aging How to read drug labels Printer-friendly version How to Read Drug ... read drug labels How to read a prescription drug label View a text version of this picture. ...

  11. Comprehensive analysis of metabolic pathways through the combined use of multiple isotopic tracers

    E-print Network

    Antoniewicz, Maciek Robert

    2006-01-01

    Metabolic Flux Analysis (MFA) has emerged as a tool of great significance for metabolic engineering and the analysis of human metabolic diseases. An important limitation of MFA, as carried out via stable isotope labeling ...

  12. Noise labeling in Brazil

    NASA Astrophysics Data System (ADS)

    de Araujo, Marco A. N.; Massarani, Paulo M.; de Azevedo, Jose A. J.; Gerges, Samir N. Y.

    2002-11-01

    The Brazilian Silence Program, created in 1990 by the Brazilian Ministry of Environment, advocates the production and use of equipment with lower noise level. The subcommittee of Noise Labeling of the Brazilian Committee of Certification is composed of INMETRO acoustic specialists to organize and implement the Brazilian Labeling Program. This subcommittee elaborated the label form and test procedure. The noise-labeling program will first concentrate on the following household devices, both manufactured in Brazil or imported from abroad; mixers, blenders, hairdryers, refrigerators, and vacuum cleaners. The label should contain the sound-power level in dBA. INMETRO or other credited laboratories are responsible for the measurements. The ISO 4871, 3740 (1 to 5), ISO 8960, and IEC 704 (1 to 4) and also the equivalent Brazilian standards are used for the measurements, such as ABNT NBR 13910-1. The main objective of the label is to inform the consumer about the emitted noise level. The label offers the noise parameter to be used by the consumer when comparing devices, considering price, performance, and now also noise. No restriction for noise level was established.

  13. 15N-DNA STABLE ISOTOPE PROBING (SIP) FOR THE ANALYSIS OF CONTAMINANT-DEGRADING MICROORGANISMS: ASSESSMENT OF FEASIBILITY AND LIMITATIONS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Stable isotope probing (SIP) is a novel method allowing for the separation and subsequent identification of organisms actively assimilating isotopically labeled compounds. Thus far the method has focused on the incorporation of 13C-labeled substrates into nucleic acids or other biomarkers, advantage...

  14. Capacitive label reader

    DOEpatents

    Arlowe, H.D.

    1985-11-12

    A capacitive label reader includes an outer ring transmitting portion, an inner ring transmitting portion, and a plurality of insulated receiving portions. A label is the mirror-image of the reader except that identifying portions corresponding to the receiving portions are insulated from only one of two coupling elements. Positive and negative pulses applied, respectively, to the two transmitting rings biased a CMOS shift register positively to either a 1 or 0 condition. The output of the CMOS may be read as an indication of the label. 5 figs.

  15. Capacitive label reader

    DOEpatents

    Arlowe, H.D.

    1983-07-15

    A capacitive label reader includes an outer ring transmitting portion, an inner ring transmitting portion, and a plurality of insulated receiving portions. A label is the mirror-image of the reader except that identifying portions corresponding to the receiving portions are insulated from only one of two coupling elements. Positive and negative pulses applied, respectively, to the two transmitting rings biased a CMOS shift register positively to either a 1 or 0 condition. The output of the CMOS may be read as an indication of the label.

  16. Utraviolet-B effects on stomatal density, water use efficiency, and stable carbon isotope discrimination in four glasshouse-grown soybean cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Interactions between UV-B radiation and drought stress have been observed but the underlying mechanisms have not been thoroughly investigated. We hypothesized that UV-B radiation would improve water use efficiency by its effects on epidermal development, specifically stomatal density and leaf gas e...

  17. 1. Isotope Definitions and terms a) Isotopes and isotope ratios.

    E-print Network

    Saleska, Scott

    -- The Compensation Point for C3 and C4 differ http://www.steve.gb.com/science/photosynthesis_and_respiration.html Net fractionation c) Simple illustration with the water cycle 2. CO2 isotopes in photosynthesis a) Photosynthetic discrimination in C3 plants b) C3 vs C4 photosynthesis and the distinction in isotopes c) Measuring isotopic

  18. Probes labelled with energy transfer coupled dyes

    DOEpatents

    Mathies, R.A.; Glazer, A.; Ju, J.

    1997-11-18

    Compositions are provided comprising sets of fluorescent labels carrying pairs of donor and acceptor dye molecules, designed for efficient excitation of the donors at a single wavelength and emission from the acceptor in each of the pairs at different wavelengths. The different molecules having different donor-acceptor pairs can be modified to have substantially the same mobility under separation conditions, by varying the distance between the donor and acceptor in a given pair. Particularly, the fluorescent compositions find use as labels in sequencing nucleic acids. 7 figs.

  19. Probes labelled with energy transfer coupled dyes

    DOEpatents

    Mathies, Richard A. (El Cerrito, CA); Glazer, Alexander (Orinda, CA); Ju, Jingyue (Berkeley, CA)

    1997-01-01

    Compositions are provided comprising sets of fluorescent labels carrying pairs of donor and acceptor dye molecules, designed for efficient excitation of the donors at a single wavelength and emission from the acceptor in each of the pairs at different wavelengths. The different molecules having different donor-acceptor pairs can be modified to have substantially the same mobility under separation conditions, by varying the distance between the donor and acceptor in a given pair. Particularly, the fluorescent compositions find use as labels in sequencing nucleic acids.

  20. Fluorescent labels and their use in separations

    DOEpatents

    Mathies, Richard A. (El Cerrito, CA); Glazer, Alexander (Orinda, CA); Ju, Jingyue (Berkeley, CA)

    1997-01-01

    Compositions are provided comprising sets of fluorescent labels carrying pairs of donor and acceptor dye molecules, designed for efficient excitation of the donors at a single wavelength and emission from the acceptor in each of the pairs at different wavelengths. The different molecules having different donor-acceptor pairs can be modified to have substantially the same mobility under separation conditions, by varying the distance between the donor and acceptor in a given pair. Particularly, the fluorescent compositions find use as labels in sequencing nucleic acids.

  1. Spectral Label Fusion

    E-print Network

    Wachinger, Christian

    We present a new segmentation approach that combines the strengths of label fusion and spectral clustering. The result is an atlas-based segmentation method guided by contour and texture cues in the test image. This offers ...

  2. Behind the Label "Alcoholic."

    ERIC Educational Resources Information Center

    Wright, Deborah M.

    1989-01-01

    Relates individual's personal story of her childhood influenced by her parent's alcoholism, her own alcoholism as a young adult, and her experiences with counseling. Asks others not to reject her because of the label "alcoholic." (ABL)

  3. Novel mass spectrometry imaging software assisting labeled normalization and quantitation of drugs and neuropeptides directly in tissue sections.

    PubMed

    Källback, Patrik; Shariatgorji, Mohammadreza; Nilsson, Anna; Andrén, Per E

    2012-08-30

    MALDI MS imaging has been extensively used to produce qualitative distribution maps of proteins, peptides, lipids, small molecule pharmaceuticals and their metabolites directly in biological tissue sections. There is growing demand to quantify the amount of target compounds in the tissue sections of different organs. We present a novel MS imaging software including protocol for the quantitation of drugs, and for the first time, an endogenous neuropeptide directly in tissue sections. After selecting regions of interest on the tissue section, data is read and processed by the software using several available methods for baseline corrections, subtractions, denoising, smoothing, recalibration and normalization. The concentrations of in vivo administered drugs or endogenous compounds are then determined semi-automatically using either external standard curves, or by using labeled compounds, i.e., isotope labeled analogs as standards. As model systems, we have quantified the distribution of imipramine and tiotropium in the brain and lung of dosed rats. Substance P was quantified in different mouse brain structures, which correlated well with previously reported peptide levels. Our approach facilitates quantitative data processing and labeled standards provide better reproducibility and may be considered as an efficient tool to quantify drugs and endogenous compounds in tissue regions of interest. PMID:22841942

  4. Routing and Label Space Reduction in Label Switching Networks

    NASA Astrophysics Data System (ADS)

    Solano, Fernando; Caro, Luis Fernando; Stidsen, Thomas; Papadimitriou, Dimitri

    This chapter is devoted to the analysis and modeling of some problems related to the optimal usage of the label space in label switching networks. Label space problems concerning three different technologies and architectures - namely Multi-protocol Label Switching (MPLS), Ethernet VLAN-Label Switching (ELS) and All-Optical Label Switching (AOLS) - are discussed in this chapter. Each of these cases yields to different constraints of the general label space reduction problem. We propose a generic optimization model and, then, we describe some adaptations aiming at modeling each particular case. Simulation results are briefly discussed at the end of this chapter.

  5. Comparison of ecosystem water-use efficiency among Douglas-fir forest, aspen forest and grassland using eddy covariance and carbon isotope techniques

    Microsoft Academic Search

    STEPHANE P ONTON; BRUCE G. J OHNSON; K AI; T. A NDREW

    Comparisons were made among Douglas-fir forest, aspen (broad leaf deciduous) forest and wheatgrass (C3) grassland for ecosystem-level water-use efficiency (WUE). WUE was defined as the ratio of photosynthetic CO2 assimilation rate and evapotranspiration (ET) rate. The ET data measured by eddy covariance were screened so that they overwhel- mingly represented transpiration. The three sites used in this comparison spanned a

  6. saliva and urine samples were collected before and 4, 5, 6,7 and 8 h after labeling 41

    E-print Network

    Boyer, Edmond

    saliva and urine samples were collected before and 4, 5, 6,7 and 8 h after labeling 41 healthy a determination of TBW using 10% 180 water (enrichment of TBW increased by 307 ppm). Isotopic enrichments were measured by gas-chromatography isotope ratio mass spectrometry. TBW (in % of body weight) did not differ

  7. China Refrigerator Information Label: Specification Development and Potential Impact

    SciTech Connect

    Fridley, David; Fridley, David; Zheng, Nina; Zhou, Nan; Aden, Nathaniel; Lin, Jiang; Jianhong, Cheng; Sakamoto, Tomoyuki

    2008-02-01

    In the last five years, China's refrigerator market has grown rapidly, and now urban markets are showing signs of saturation, with ownership rates in urban households reaching 92%. Rural markets continue to grow from a much lower base. As a result of this growth, the Chinese government in 2006 decided to revise the refrigerator standards and its associated efficiency grades for the mandatory energy information label. In the Chinese standards process, the efficiency grades for the information label are tied to the minimum standards. Work on the minimum standards revision began in 2006 and continued through the first half of 2007, when the draft standard was completed under the direction of the China National Institute of Standardization (CNIS). Development of the information label grades required consideration of stakeholder input, continuity with the previous grade classification, ease of implementation, and potential impacts on the market. In this process, CLASP, with the support of METI/IEEJ, collaborated with CNIS to develop the efficiency grades, providing technical input to the process, comment and advice on particular technical issues, and evaluation of the results. After three months of effort and three drafts of the final grade specifications, this work was completed. In addition, in order to effectively evaluate the impact of the label on China's market, CLASP further provided assistance to CNIS to collect data on both the efficiency distribution and product volume distribution of refrigerators on the market. The new information label thresholds to be implemented in 2008 maintain the approach first adopted in 2005 of establishing efficiency levels relative to the minimum standard, but increased the related required efficiency levels by 20% over those established in 2003 and implemented in 2005. The focus of improvement was on the standard refrigerator/freezer (class 5), which constitutes the bulk of the Chinese market. Indeed, the new requirements to achieve grade 1 on the label are now virtually as stringent as those for US Energy Star-qualified or EU A-grade refrigerators. When the energy information label went into effect in March 2005, refrigerator manufacturers were required to display their declared level of efficiency on the label and report it to the China Energy Label Center (CELC), a newly established unit of CNIS responsible for label program management. Because of the visible nature of the label, it was found, through a METI/IEEJ-supported study, that MEPS non-compliance dropped from 4% to zero after the label became mandatory, and that the percentage of higher-grade refrigerators increased. This suggests that the label itself does have potential for shifting the market to higher-efficiency models (Lin 2007). One challenge, however, of assessing this potential impact is the lack of a comprehensive baseline of market efficiency and a program to evaluate the market impact on a yearly basis. As a result, the impact evaluation in this study draws upon the market transformation experience of the related EU energy information label, for which quantitative assessments of its market impact exist. By assuming a parallel process unfolding in China, it is possible to look at the potential impact of the label to 2020. The results of the analysis demonstrates that a robust market transformation program in China focused on the energy information label could save substantial amounts of electricity by 2020, totaling 16.4 TWh annually by that year, compared to a case in which the efficiency distribution of refrigerators was frozen at the 2007 level. Remarkably, the impact of a successful market transformation program with the label would essentially flatten the consumption of electricity for refrigerator use throughout most of the next decade, despite the expectations of continued growth in total stock by nearly 190 million units. At the end of this period, total consumption begins to rise again, as the least efficient of the units have been mostly removed from the market. Such a level of savings would reduce CO{sub

  8. Cytotoxic activity, tumor accumulation, and tissue distribution of ruthenium-103-labeled bleomycin

    SciTech Connect

    Stern, P.H.; Helpern, S.E.; Hagan, P.L.; Howell, S.B.; Dabbs, J.E.; Gordon, R.M.

    1981-05-01

    Bleomycin (BLM) was labeled with gamma-emitting 103Ru. Yields of 103Ru-labeled BLM as high as 50.6% were attained. 103Ru-labeled BLM was stable in vitro and the 103ru label was not displaced by large excesses of Cu (II) and Co (II) or Fe (III). Chromatography of the urine following 103Ru-labeled BLM injection indicated no in vivo decomposition. Pharmacokinetic studies in healthy inbred SD and tumor-bearing inbred BUF rats demonstrated tumor accumulations, tissue distributions, and clearance nearly identical with those reported for 3H-labeled BLM. Cytotoxicity studies on a WI-L2 human B-cell line showed that BLM labeled with nonradioactive Ru retained 100% of the activity demonstrated by native BLM. Thus BLM may be labeled with isotopes of Ru to form stable complexes by a simple, rapid reaction without loss of its chemotherapeutic properties or variations in its in vivo distribution. BLM labeled with the proper Ru isotope should prove useful as a gamma-emitting tracer for BLM or a beta-emitting compound capable of providing combination chemotherapy and radiotherapy of tumors.

  9. Manifold Adaptive Label Propagation for Face Clustering.

    PubMed

    Pei, Xiaobing; Lyu, Zehua; Chen, Changqing; Chen, Chuanbo

    2015-08-01

    In this paper, a novel label propagation (LP) method is presented, called the manifold adaptive label propagation (MALP) method, which is to extend original LP by integrating sparse representation constraint into regularization framework of LP method. Similar to most LP, first of all, MALP also finds graph edges from given data and gives weights to the graph edges. Our goal is to find graph weights matrix adaptively. The key advantage of our approach is that MALP simultaneously finds graph weights matrix and predicts the label of unlabeled data. This paper also derives efficient algorithm to solve the proposed problem. Extensions of our MALP in kernel space and robust version are presented. The proposed method has been applied to the problem of semi-supervised face clustering using the well-known ORL, Yale, extended YaleB, and PIE datasets. Our experimental evaluations show the effectiveness of our method. PMID:25291812

  10. Elementary metabolite units (EMU): A novel framework for modeling isotopic distributions

    Microsoft Academic Search

    Maciek R. Antoniewicz; Joanne K. Kelleher; Gregory Stephanopoulos

    2007-01-01

    Metabolic flux analysis (MFA) has emerged as a tool of great significance for metabolic engineering and mammalian physiology. An important limitation of MFA, as carried out via stable isotope labeling and GC\\/MS and nuclear magnetic resonance (NMR) measurements, is the large number of isotopomer or cumomer equations that need to be solved, especially when multiple isotopic tracers are used for

  11. Bioavailability of xenobiotics in unsaturated soils – implications for nucleic acid based stable isotope probing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The use of stable isotopes to label phylogenetically informative biomolecules (phospholipid fatty acids, DNA, or RNA), typically referred to as stable isotope probing (SIP) has the potential of providing definitive evidence that a detected population is active in a specific process, if that process ...

  12. Liquid chromatography, chemical oxidation, and online carbon isotope dilution mass spectrometry as a universal quantification system for nonvolatile organic compounds.

    PubMed

    Díaz, Sergio Cueto; Encinar, Jorge Ruiz; Sanz-Medel, Alfredo; Alonso, J Ignacio García

    2013-02-01

    A procedure for the universal detection and quantification of polar organic compounds separated by liquid chromatography (LC) based on postcolumn carbon isotope dilution mass spectrometry (IDMS) was developed. The eluent from the LC column is mixed online with a continuous flow of (13)C-enriched sodium bicarbonate, and the sodium persulfate oxidation reaction in acidic media is employed to achieve isotope equilibration. All carbon-containing compounds eluting from the column are oxidized to (12)CO(2) and (13)CO(2), respectively, and the carbon dioxide is separated from the aqueous phase using a gas-permeable membrane. The gaseous carbon dioxide is then carried to the mass spectrometer for isotope ratio measurements. Different water-soluble organic compounds were evaluated using a flow injection configuration to assess the efficiency of the oxidation process. Most water-soluble organic compounds tested showed quantitative oxidation. However, chemical structures involving conjugated C?N double bounds and guanidinium-like structures were found to be resistant to the oxidation and were further studied. For this purpose, (13)C(1)-labeled creatine (with the isotopic label in the guanidinium group) was employed as model compound. Specific conditions for the quantitative oxidation of these compounds required lower flow rates and the addition of metallic catalysts. This novel approach was tested as a universal detection and quantification system for LC. A simple standard mixture of four amino acids was separated under 100% aqueous conditions and quantified without the need for specific standards with good accuracy and precision using potassium hydrogen phthalate as internal standard. The main field of application of the developed method is for the purity assessment of organic standards with direct traceability to the International System of Units (SI). PMID:23252800

  13. 15N-labeled glycine synthesis.

    PubMed

    Tavares, Claudinéia R O; Bendassolli, José A; Coelho, Fernando; Sant'ana Filho, Carlos R; Prestes, Clelber V

    2006-09-01

    This work describes a method for 15N-isotope-labeled glycine synthesis, as well as details about a recovery line for nitrogen residues. To that effect, amination of alpha-haloacids was performed, using carboxylic chloroacetic acid and labeled aqueous ammonia (15NH3). Special care was taken to avoid possible 15NH3 losses, since its production cost is high. In that respect, although the purchase cost of the 13N-labeled compound (radioactive) is lower, the stable tracer produced constitutes an important tool for N cycling studies in living organisms, also minimizing labor and environmental hazards, as well as time limitation problems in field studies. The tests were carried out with three replications, and variable 15NH3aq volumes in the reaction were used (50, 100, and 150 mL), in order to calibrate the best operational condition; glycine masses obtained were 1.7, 2, and 3.2 g, respectively. With the development of a system for 15NH3 recovery, it was possible to recover 71, 83, and 87% of the ammonia initially used in the synthesis. With the required adaptations, the same system was used to recover methanol, and 75% of the methanol initially used in the amino acid purification process were recovered. PMID:16936934

  14. [Solid state isotope hydrogen exchange for deuterium and tritium in human gene-engineered insulin].

    PubMed

    2014-01-01

    The reaction of high temperature solid state catalytic isotope exchange in peptides and proteins under the action of catalyst-activated spillover hydrogen was studied. The reaction of human gene-engineered insulin with deuterium and tritium was conducted at 120-140° C to produce insulin samples containing 2-6 hydrogen isotope atoms. To determine the distribution of the isotope label over tritium-labeled insulin's amino acid residues, oxidation of the S-S bonds of insulin by performic acid was performed and polypeptide chains isolated; then their acid hydrolysis, amino acid analysis and liquid scintillation counts of tritium in the amino acids were conducted. The isotope label was shown to be incorporated in all amino acids of the protein, with the peptide fragment FVNQHLCGSHLVE of the insulin ?-chain showing the largest incorporation. About 45% of the total protein isotope label was incorporated in His5 and His10 of this fragment. For the analysis of isotope label distribution in labeled insulin's peptide fragments, the recovery of the S-S bonds by mercaptoethanol, the enzymatic hydrolysis by glutamyl endopeptidase from Bacillus intermedius and HPLC division of the resulting peptides were carried out. Attribution of the peptide fragments formed due to hydrolysis at the Glu-X bond in the ?-chain was accomplished by mass spectrometry. Mass spectrometry analysis data of the deuterium-labeled insulin samples' isotopomeric composition showed that the studied solid state isotope exchange reaction equally involved all the protein molecules. Biological studying of tritium-labeled insulin showed its physiological activity to be completely retained. PMID:25898721

  15. Quantification of Pantothenic Acid and Folates by Stable Isotope Dilution Assays

    Microsoft Academic Search

    Michael Rychlik; Achim Freisleben

    2002-01-01

    Stable isotope dilution assays for the quantification of pantothenic acid and folates in foods by using four-fold labeled isotopomers of the vitamins as internal standards (IS) were developed. The use of labeled IS enabled to exactly correct losses during cleanup and derivatization.Pantothenic acid and its labeled isotopomer were detected as trimethylsilyl derivatives by gas chromatography–mass spectrometry. In starch a detection

  16. Stable isotope studies

    SciTech Connect

    Ishida, T.

    1992-01-01

    The research has been in four general areas: (1) correlation of isotope effects with molecular forces and molecular structures, (2) correlation of zero-point energy and its isotope effects with molecular structure and molecular forces, (3) vapor pressure isotope effects, and (4) fractionation of stable isotopes. 73 refs, 38 figs, 29 tabs.

  17. Labelling and metabolism of methionine-methyl- 11 C

    Microsoft Academic Search

    Dominique Comar; Jean-Claude Cartron; Mariannick Maziere; Christian Marazano

    1976-01-01

    Carbon 11 which is a 20.4 minutes half life isotope emitting positrons was used for methionine labelling on the methyl group by action of 11C-methyl-iodide on DL or L homocysteine. With the method described, 20 to 30 mCi of 11C-methyl-methionine (Specific activity 50 mCi\\/M) may be obtained within 25 minutes. The 20 Mev proton beam used for 11C production was

  18. Comparison of Tc-99m labeled liver and liver pate as markers for solid-phase gastric emptying

    SciTech Connect

    Christian, P.E.; Moore, J.G.; Datz, F.L.

    1984-03-01

    A radionuclide marker for studies of solid-phase gastric emptying should have a high labeling efficiency and remain relatively stable during gastric emptying. The availability of materials and the ease of preparation are also considerations in selecting radionuclide markers. The stability of intracellularly labeled chicken liver, surface-labeled chicken liver, and labeled pureed meat (liver pate) incubated with hydrochloric acid solution or gastric juice have been compared. Intracellularly labeled chicken liver and labeled liver pate were also compared in gastric emptying studies in humans. In vitro results demonstrated labeling efficiencies greater than 92% for both intracellularly labeled liver and labeled liver pate. The pate labeled with Tc-99m sulfur colloid was more stable than Tc-99m surface-labeled liver in vitro and its prepartion was easier than with the intracellular labeling technique. Gastric emptying studies on normal subjects demonstrated equal performance of the intracellularly labeled liver and the labeled liver pate. Labeled liver pate is thus an alternative to intracellularly labeled chicken liver in measuring solid-phase gastric emptying.

  19. A Streptavidin-Metallothionein Chimera that Allows Specific Labeling of Biological Materials with Many Different Heavy Metal Ions

    NASA Astrophysics Data System (ADS)

    Sano, Takeshi; Glazer, Alexander N.; Cantor, Charles R.

    1992-03-01

    We have designed a streptavidin-metallothionein chimeric protein in which the streptavidin moiety provides a means of binding the metallothionein moiety tightly to specific biological targets. A gene fusion of streptavidin with mouse metallothionein I was efficiently expressed in Escherichia coli, and the expressed chimeric protein was purified to homogeneity by a simple procedure. The purified chimera, consisting of four identical subunits, bound one biotin and approximately seven Cd2+ ions per subunit (19.5 kDa). This indicates that both the streptavidin and the metallothionein moieties are fully functional. The high binding affinity of the chimera both for biotin and for heavy metal ions allows the specific labeling or conjugation of any biological material containing unhindered biotin with a variety of different heavy metal ions and their isotopes, thereby opening the way for simultaneous assay systems for a large number of biological targets.

  20. An inexact labeling problem 

    E-print Network

    Murray, Margaret Shuey

    1984-01-01

    with colinear centers. The best prototype is selected as the label for the candidate object. A degree of accuracy for the match is determined. The author would like to thank Dr. Norman Griswold for his assistance in this research and in the preparation... of prototype and candidate objects - . 1'7 3 ~ Tree showing possible unit-label assignments for the example of Figut'e 2 (p. 17) 4. Candidate and prototype objects 5. A 3x3 pixel window . . . ~ 6. S, r parameterization of a line 20 30 36 38 7. A...

  1. STABLE ISOTOPE PROBING TO INVESTIGATE MICROBIAL FUNCTION IN SOIL

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Most approaches for in situ phylogenetic characterization of soil microorganisms lack the ability to establish a causal relationship to function within the community. Recently, the use of stable isotopes to label phylogenetically informative biomolecules (phospholipid fatty acids, DNA, or RNA), typ...

  2. Labeling and functionalizing amphipols for biological applications.

    PubMed

    Le Bon, Christel; Popot, Jean-Luc; Giusti, Fabrice

    2014-10-01

    Amphipols (APols) are short amphipathic polymers developed as an alternative to detergents for handling membrane proteins (MPs) in aqueous solution. MPs are, as a rule, much more stable following trapping with APols than they are in detergent solutions. The best-characterized APol to date, called A8-35, is a mixture of short-chain sodium polyacrylates randomly derivatized with octylamine and isopropylamine. Its solution properties have been studied in detail, and it has been used extensively for biochemical and biophysical studies of MPs. One of the attractive characteristics of APols is that it is relatively easy to label them, isotopically or otherwise, without affecting their physical-chemical properties. Furthermore, several variously modified APols can be mixed, achieving multiple functionalization of MP/APol complexes in the easiest possible manner. Labeled or tagged APols are being used to study the solution properties of APols, their miscibility, their biodistribution upon injection into living organisms, their association with MPs and the composition, structure and dynamics of MP/APol complexes, examining the exchange of surfactants at the surface of MPs, labeling MPs to follow their distribution in fractionation experiments or to immobilize them, increasing the contrast between APols and solvent or MPs in biophysical experiments, improving NMR spectra, etc. Labeling or functionalization of APols can take various courses, each of which has its specific constraints and advantages regarding both synthesis and purification. The present review offers an overview of the various derivatives of A8-35 and its congeners that have been developed in our laboratory and discusses the pros and cons of various synthetic routes. PMID:24696186

  3. Synthetic procedures for the preparation of deuterium-labeled analogs of naturally occurring steroids

    SciTech Connect

    Wudy, S.A. (Universitaetskinderklinik Ulm, Donau (Germany, F.R.))

    1990-10-01

    The object of this article is to review the procedures that have been published concerning the preparation of deuterium-labeled analogs of naturally occurring steroid hormones. In combination with mass spectrometric methods, these stable isotope-labeled compounds should be applicable for human metabolism studies or as internal standards. Deuteration techniques for the elucidation of stereochemical problems, procedures for the preparation of monodeuterated steroids, and synthesis of deuterated analogs of nonbiologic steroids have therefore not been included in this review. 41 refs.

  4. Calendar Year 2007 Program Benefits for ENERGY STAR Labeled Products

    Microsoft Academic Search

    Marla Christine Sanchez; Gregory Homan; Richard Brown

    2008-01-01

    ENERGY STAR is a voluntary energy efficiency-labeling program operated jointly by the United States Department of Energy and the United States Environmental Protection Agency (US EPA). Since the program inception in 1992, ENERGY STAR has become a leading international brand for energy efficient products. ENERGY STAR's central role in the development of regional, national, and international energy programs necessitates an

  5. Biosynthetic Approaches to Isotope Enrichment for Applications in Neutron Scattering and High Field NMR Spectroscopy: Methylotrophic

    SciTech Connect

    Mary E. lidstrom

    2004-09-15

    Limitations in current isotopic labeling methods present a substantial bottleneck for the application of advanced structural techniques to many important biochemical problems. New tools are required to efficiently produce the necessary labeling patterns in biochemical precursors and incorporate them into protein molecules for structural studies. This project proposed involved one aspect of this problem, the development of expression vectors for a methylotrophic bacterium, Methylobacterium extorquens AM1. If high-level, efficient expression could be obtained in such a bacterium, it would be possible to use low-cost {sup 2}H- and/or {sup 13}C-labeled substrates such as methanol to label proteins. The Lidstrom laboratory at the University of Washington worked closely with the collaborators at Los Alamos National Laboratories in the development and use of these vectors. (1) Overexpression of a target gene, bacterial dehalogenase--This enzyme was expressed in Methylobacterium extorquens AM1 using a high level methanol-inducible promoter, the mxaF promoter. High expression was achieved, but most was in an insoluble form. They expressed this protein in a mutant lacking polybetahydroxybutyrate granules, and high expression was achieved, up to 10% of the total soluble protein. The recombinant protein was purified and shown to be active, with characteristics similar to the enzyme produced in E. coli. (2) Development of regulated expression systems--A number of regulated promoters were tested in M. extorquens AM1, the most promising of which appeared to be the E. coli lac promoter coupled to the Laciq regulator. The repressor was shown to be active and a chromosomal insertion construct was generated that repressed the low-level lac promoter activity in M. extorquens AM1. However, IPTG induced this system only poorly. A number of studies were carried out leading to the conclusion that IPTG entered the cell but was exported by one or more export pumps. Target genes for such pumps were mutated but none of these showed increased induction. A number of methods were used to permeabilize the cell, and a 2-fold increase in induction was obtained with one of these. The activity of the lac promoter was increased by inserting a recently-identified M. extorquens AM1 enhancer element upstream. The promoter increased in activity 5-6 fold with this addition. In summary, they have developed a suite of expression tools and host mutant strains for expressing a variety of heterologous proteins in this methylotroph. These are now available for testing by the LANL collaborators in labeling reactors to obtain labeled proteins of interest.

  6. Label switched ethernet technology

    Microsoft Academic Search

    Jaihyung Cho

    2005-01-01

    In this paper, we propose a technique that employs advantage of MPLS in Ethernet. Major goals are improving QoS capability of Ethernet and facilitating secure access of commercial service, such as IP-TV or videophone, in local area network. Key solution to achieve the goal is MAC address swapping which uses 48 bits of Ethernet address in MAC header as labels.

  7. Understanding Pesticide Labels

    E-print Network

    Liskiewicz, Maciej

    environment problems as well ­ beneficial insects, earthworms, birds, and even pets may be harmed or killed of certain pesticides may induce resistance in the pests they are designed to control. Some pesticides do Services. It is illegal to use a pesticide on a crop or site unless it is listed on the label. It is also

  8. List Group Label

    NSDL National Science Digital Library

    2012-01-01

    This web page describes a vocabulary strategy, List-Group-Label, that provides students with a way to recognize the relationships between words and concepts using their prior knowledge about a topic. The page describes the benefits of using the strategy and provides an instructional sequence for teachers to follow when implementing the strategy. A blank graphic organizer and references are included.

  9. IP SwitchingIP Switching and Label Switchingand Label Switching

    E-print Network

    Jain, Raj

    Raj Jain 1 IP SwitchingIP Switching and Label Switchingand Label Switching Raj Jain Professor Switching vs routing q IP Switching (Ipsilon) q Tag Switching (CISCO) q Multi-protocol label switching (Cont)Routing vs Switching (Cont) On ATM networks: q IP routers use IP addresses Reassemble IP

  10. A diagram retrieval method with multi-label learning

    NASA Astrophysics Data System (ADS)

    Fu, Songping; Lu, Xiaoqing; Liu, Lu; Qu, Jingwei; Tang, Zhi

    2015-01-01

    In recent years, the retrieval of plane geometry figures (PGFs) has attracted increasing attention in the fields of mathematics education and computer science. However, the high cost of matching complex PGF features leads to the low efficiency of most retrieval systems. This paper proposes an indirect classification method based on multi-label learning, which improves retrieval efficiency by reducing the scope of compare operation from the whole database to small candidate groups. Label correlations among PGFs are taken into account for the multi-label classification task. The primitive feature selection for multi-label learning and the feature description of visual geometric elements are conducted individually to match similar PGFs. The experiment results show the competitive performance of the proposed method compared with existing PGF retrieval methods in terms of both time consumption and retrieval quality.

  11. Use of indium-111 as a red cell label

    SciTech Connect

    AuBuchon, J.P.; Brightman, A.

    1989-02-01

    To select the most promising 111In chelate for use as a second red cell (RBC) label for comparison of the survival of autologous and allogeneic cells, 49 normal RBC samples were studied in vitro after being labeled with 111In-8-hydroxyquinolinol (111In-oxine) prepared by three different methods, 111In-tropolone, and 111In-acetylacetone. Labeling efficiencies reached 99 percent and did not decline when the amount of 111In used was increased from 1.75 to 50 muCi per ml of RBCs. Storage of labeled RBCs in normal AB plasma at 4, 22, and 37 degrees C for up to 48 hours resulted in a similar rate of loss of the label from the RBCs with all labeling methods. These rates were time- and temperature-dependent and were accurate predictions of the rates found in later in vivo experimentation. Fresh RBCs from 11 subjects were labeled with 111In chelated with oxine in the presence of the RBCs or chelated with tropolone just prior to the labeling. RBC mass determinations using these autologous RBCs labeled with 111In accurately reflected the subjects' RBC masses as predicted through standard morphometric formulae. The rate of disappearance of the radionuclide after reinfusion of the autologous RBCs decreased with time. At 24 hours after reinfusion, 89.5 +/- 1.29 percent (mean +/- SEM) of the 111In-tropolone and 87.3 +/- 1.25 percent of the 111In-oxine continued in circulation. 111In is a simple and efficient agent for the labeling of RBCs for blood volume determinations and short-term survivals.

  12. 99m tc labeled liposomes

    SciTech Connect

    Phillips, W.T.; Klipper, R.W.; Timmons, J.H.; Rudolph, A.S.

    1992-10-27

    This patent describes a method of preparing stable gamma-emitting radionuclide-labeled alkyleneamine oxime, the incubating being for a period of time sufficient to form labeled liposome-encapsulated protein.

  13. HAZARDOUS WASTE LABEL DEPAUL UNIVERSITY

    E-print Network

    Schaefer, Marcus

    - Hazardous Ignitable Reactive Toxic Oxidizer Other ( explain ) Generator Building Dept. HAZARDOUS WASTE LABELHAZARDOUS WASTE LABEL DEPAUL UNIVERSITY ENVIRONMENTAL HEALTH & SAFETY 5-4170 Corrosive Non DEPAUL UNIVERSITY ENVIRONMENTAL HEALTH & SAFETY 5-4170 HAZARDOUS WASTE LABEL DEPAUL UNIVERSITY

  14. Application of Screening Experimental Designs to Assess Chromatographic Isotope Effect upon Isotope-Coded Derivatization for Quantitative Liquid Chromatography–Mass Spectrometry

    PubMed Central

    2015-01-01

    Isotope effect may cause partial chromatographic separation of labeled (heavy) and unlabeled (light) isotopologue pairs. Together with a simultaneous matrix effect, this could lead to unacceptable accuracy in quantitative liquid chromatography–mass spectrometry assays, especially when electrospray ionization is used. Four biologically relevant reactive aldehydes (acrolein, malondialdehyde, 4-hydroxy-2-nonenal, and 4-oxo-2-nonenal) were derivatized with light or heavy (d3-, 13C6-, 15N2-, or 15N4-labeled) 2,4-dinitrophenylhydrazine and used as model compounds to evaluate chromatographic isotope effects. For comprehensive assessment of retention time differences between light/heavy pairs under various gradient reversed-phase liquid chromatography conditions, major chromatographic parameters (stationary phase, mobile phase pH, temperature, organic solvent, and gradient slope) and different isotope labelings were addressed by multiple-factor screening using experimental designs that included both asymmetrical (Addelman) and Plackett–Burman schemes followed by statistical evaluations. Results confirmed that the most effective approach to avoid chromatographic isotope effect is the use of 15N or 13C labeling instead of deuterium labeling, while chromatographic parameters had no general influence. Comparison of the alternate isotope-coded derivatization assay (AIDA) using deuterium versus 15N labeling gave unacceptable differences (>15%) upon quantifying some of the model aldehydes from biological matrixes. On the basis of our results, we recommend the modification of the AIDA protocol by replacing d3-2,4-dinitrophenylhydrazine with 15N- or 13C-labeled derivatizing reagent to avoid possible unfavorable consequences of chromatographic isotope effects. PMID:24922593

  15. Nuclear spins and magnetic moments of some cesium isotopes

    Microsoft Academic Search

    C. Ekström; S. Ingelman; G. Wannberg; M. Skarestad

    1977-01-01

    Using an atomic-beam magnetic resonance apparatus connected on-line with the ISOLDE isotope separator, CERN, hyperfine structure measurements have been performed in the 2S1\\/2 electronic ground state of some cesium isotopes. An on-line oven system which efficiently converts a mass separated ion beam of alkali isotopes to an atomic beam is described in some detail. Experimentally determined nuclear spins of 120,

  16. Optimizing two-pass connected-component labeling algorithms

    Microsoft Academic Search

    Kesheng Wu; Ekow J. Otoo; Kenji Suzuki

    2009-01-01

    Wepresent two optimization strategiestoimprove connected component labeling algorithms. Taking together, they form an efficient two-pass labeling algorithm that is fast and theoretically optimal. The first optimization strategy re- duces the number of neighboring pixels accessed through the use of a decision tree, and the second one streamlines the union-find algorithms usedto trackequivalentlabels.Weshow that thefirst strategyreducestheaveragenumber of neighbors accessed by a

  17. Food Labels Tell the Story!

    MedlinePLUS

    From the Label to the Table! Food Labels Tell the Story! What is in food? Food provides your body with all of the materials it needs to grow, and ... your food choices. Nutrition Facts—the Labels on Food Products Beginning in 1994, the US government began ...

  18. Eco-labelling: Policy Considerations

    Microsoft Academic Search

    Aaditya Mattoo; HARSHA V. SINGH

    1994-01-01

    This paper argues that eco-labeling could lead to an adverse effect on the environment. In every society there are some consumers who are concerned about environmental problems and others who are not. Labeling may stimulate concern for the environment and increase the demand for environment-friendly products. However, it is precisely this consequence of labeling that can lead to perverse results.

  19. Nutrition Marketing on Food Labels

    ERIC Educational Resources Information Center

    Colby, Sarah E.; Johnson, LuAnn; Scheett, Angela; Hoverson, Bonita

    2010-01-01

    Objective: This research sought to determine how often nutrition marketing is used on labels of foods that are high in saturated fat, sodium, and/or sugar. Design and Setting: All items packaged with food labels (N = 56,900) in all 6 grocery stores in Grand Forks, ND were surveyed. Main Outcome Measure(s): Marketing strategy, nutrient label

  20. 79 FR 11879 - Food Labeling: Revision of the Nutrition and Supplement Facts Labels

    Federal Register 2010, 2011, 2012, 2013, 2014

    2014-03-03

    ...Labeling: Revision of the Nutrition and Supplement Facts Labels...Labeling: Revision of the Nutrition and Supplement Facts Labels...their declarations on the Nutrition Facts label are necessary...development in infants; and adverse pregnancy outcome. Vitamin D is...