Stable isotope dimethyl labelling for quantitative proteomics and beyond

Science.gov (United States)

Hsu, Jue-Liang; Chen, Shu-Hui

2016-01-01

Stable-isotope reductive dimethylation, a cost-effective, simple, robust, reliable and easy-to- multiplex labelling method, is widely applied to quantitative proteomics using liquid chromatography-mass spectrometry. This review focuses on biological applications of stable-isotope dimethyl labelling for a large-scale comparative analysis of protein expression and post-translational modifications based on its unique properties of the labelling chemistry. Some other applications of the labelling method for sample preparation and mass spectrometry-based protein identification and characterization are also summarized. This article is part of the themed issue ‘Quantitative mass spectrometry’. PMID:27644970

Noninvasive imaging of protein metabolic labeling in single human cells using stable isotopes and Raman microscopy

NARCIS (Netherlands)

van Manen, H.J.; Lenferink, Aufrid T.M.; Otto, Cornelis

2008-01-01

We have combined nonresonant Raman microspectroscopy and spectral imaging with stable isotope labeling by amino acids in cell culture (SILAC) to selectively detect the incorporation of deuterium-labeled phenylalanine, tyrosine, and methionine into proteins in intact, single HeLa cells. The C−D

Identification of Thioredoxin Target Disulfides Using Isotope-Coded Affinity Tags

DEFF Research Database (Denmark)

Hägglund, Per; Bunkenborg, Jakob; Maeda, Kenji

2014-01-01

Thioredoxins (Trx) are small redox proteins that reduce disulfide bonds in various target proteins and maintain cellular thiol redox control. Here, a thiol-specific labeling and affinity enrichment approach for identification and relative quantification of Trx target disulfides in complex protein...... reduction is determined by LC-MS/MS-based quantification of tryptic peptides labeled with "light" (12C) and "heavy" (13C) ICAT reagents. The methodology can be adapted to monitor the effect of different reductants or oxidants on the redox status of thiol/disulfide proteomes in biological systems....... extracts is described. The procedure utilizes the isotope-coded affinity tag (ICAT) reagents containing a thiol reactive iodoacetamide group and a biotin affinity tag to target peptides containing reduced cysteine residues. The identification of substrates for Trx and the extent of target disulfide...

Determining synthesis rates of individual proteins in zebrafish (Danio rerio) with low levels of a stable isotope labelled amino acid.

Science.gov (United States)

Geary, Bethany; Magee, Kieran; Cash, Phillip; Young, Iain S; Whitfield, Phillip D; Doherty, Mary K

2016-05-01

The zebrafish is a powerful model organism for the analysis of human cardiovascular development and disease. Understanding these processes at the protein level not only requires changes in protein concentration to be determined but also the rate at which these changes occur on a protein-by-protein basis. The ability to measure protein synthesis and degradation rates on a proteome-wide scale, using stable isotope labelling in conjunction with mass spectrometry is now a well-established experimental approach. With the advent of more selective and sensitive mass spectrometers, it is possible to accurately measure lower levels of stable isotope incorporation, even when sample is limited. In order to challenge the sensitivity of this approach, we successfully determined the synthesis rates of over 600 proteins from the cardiac muscle of the zebrafish using a diet where either 30% or 50% of the L-leucine was replaced with a stable isotope labelled analogue ([(2) H7 ]L-leucine]. It was possible to extract sufficient protein from individual zebrafish hearts to determine the incorporation rate of the label into hundreds of proteins simultaneously, with the two labelling regimens showing a good correlation of synthesis rates. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A novel strategy using MASCOT Distiller for analysis of cleavable isotope-coded affinity tag data to quantify protein changes in plasma.

Science.gov (United States)

Leung, Kit-Yi; Lescuyer, Pierre; Campbell, James; Byers, Helen L; Allard, Laure; Sanchez, Jean-Charles; Ward, Malcolm A

2005-08-01

A novel strategy consisting of cleavable Isotope-Coded Affinity Tag (cICAT) combined with MASCOT Distiller was evaluated as a tool for the quantification of proteins in "abnormal" patient plasma, prepared by pooling samples from patients with acute stroke. Quantification of all light and heavy cICAT-labelled peptide ion pairs was obtained using MASCOT Distiller combined with a proprietary software. Peptides displaying differences were selected for identification by MS. These preliminary results show the promise of our approach to identify potential biomarkers.

Auto-inducing media for uniform isotope labeling of proteins with {sup 15}N, {sup 13}C and {sup 2}H

Energy Technology Data Exchange (ETDEWEB)

Guthertz, Nicolas [Institute of Cancer Research, Division of Structural Biology (United Kingdom); Klopp, Julia; Winterhalter, Aurélie; Fernández, César; Gossert, Alvar D., E-mail: alvar.gossert@novartis.com [Novartis Institutes for BioMedical Research (Switzerland)

2015-06-15

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 {sup 15}N, {sup 13}C and/or {sup 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 {sup 13}C, {sup 15}N of 96.6 % and {sup 2}H, {sup 15}N of 98.8 %. With the present protocol, the NMR community could profit from the many advantages that auto-inducing media offer.

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

Science.gov (United States)

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.

Stereoselective synthesis of stable-isotope-labeled amino acids

Energy Technology Data Exchange (ETDEWEB)

Unkefer, C.J.; Martinez, R.A.; Silks, L.A. III [Los Alamos National Laboratory, NM (United States); Lodwig, S.N. [Centralia College, WA (United States)

1994-12-01

For magnetic resonance and vibrational spectroscopies to reach their full potential, they must be used in combination with sophisticated site-specific stable isotope labeling of biological macromolecules. Labeled amino acids are required for the study of the structure and function of enzymes and proteins. Because there are 20 common amino acids, each with its own distinguishing chemistry, they remain a synthetic challenge. The Oppolzer chiral auxiliary provides a general tool with which to approach the synthesis of labeled amino acids. By using the Oppolzer auxiliary, amino acids can be constructed from several small molecules, which is ideal for stable isotope labeling. In addition to directing the stereochemistry at the {alpha}-carbon, the camphorsultam can be used for stereo-specific isotope labeling at prochiral centers in amino acids. By using the camphorsultam auxiliary we have the potential to synthesize virtually any isotopomer of all of the common amino acids.

Stereoselective synthesis of stable-isotope-labeled amino acids

International Nuclear Information System (INIS)

Unkefer, C.J.; Martinez, R.A.; Silks, L.A. III; Lodwig, S.N.

1994-01-01

For magnetic resonance and vibrational spectroscopies to reach their full potential, they must be used in combination with sophisticated site-specific stable isotope labeling of biological macromolecules. Labeled amino acids are required for the study of the structure and function of enzymes and proteins. Because there are 20 common amino acids, each with its own distinguishing chemistry, they remain a synthetic challenge. The Oppolzer chiral auxiliary provides a general tool with which to approach the synthesis of labeled amino acids. By using the Oppolzer auxiliary, amino acids can be constructed from several small molecules, which is ideal for stable isotope labeling. In addition to directing the stereochemistry at the α-carbon, the camphorsultam can be used for stereo-specific isotope labeling at prochiral centers in amino acids. By using the camphorsultam auxiliary we have the potential to synthesize virtually any isotopomer of all of the common amino acids

Cell-free expression and stable isotope labelling strategies for membrane proteins

International Nuclear Information System (INIS)

Sobhanifar, Solmaz; Reckel, Sina; Junge, Friederike; Schwarz, Daniel; Kai, Lei; Karbyshev, Mikhail; Loehr, Frank; Bernhard, Frank; Doetsch, Volker

2010-01-01

Membrane proteins are highly underrepresented in the structural data-base and remain one of the most challenging targets for functional and structural elucidation. Their roles in transport and cellular communication, furthermore, often make over-expression toxic to their host, and their hydrophobicity and structural complexity make isolation and reconstitution a complicated task, especially in cases where proteins are targeted to inclusion bodies. The development of cell-free expression systems provides a very interesting alternative to cell-based systems, since it circumvents many problems such as toxicity or necessity for the transportation of the synthesized protein to the membrane, and constitutes the only system that allows for direct production of membrane proteins in membrane-mimetic environments which may be suitable for liquid state NMR measurements. The unique advantages of the cell-free expression system, including strong expression yields as well as the direct incorporation of almost any combination of amino acids with very little metabolic scrambling, has allowed for the development of a wide-array of isotope labelling techniques which facilitate structural investigations of proteins whose spectral congestion and broad line-widths may have earlier rendered them beyond the scope of NMR. Here we explore various labelling strategies in conjunction with cell-free developments, with a particular focus on α-helical transmembrane proteins which benefit most from such methods.

Isotope labeling strategies for NMR studies of RNA

International Nuclear Information System (INIS)

Lu, Kun; Miyazaki, Yasuyuki; Summers, Michael F.

2010-01-01

The known biological functions of RNA have expanded in recent years and now include gene regulation, maintenance of sub-cellular structure, and catalysis, in addition to propagation of genetic information. As for proteins, RNA function is tightly correlated with structure. Unlike proteins, structural information for larger, biologically functional RNAs is relatively limited. NMR signal degeneracy, relaxation problems, and a paucity of long-range 1 H- 1 H dipolar contacts have limited the utility of traditional NMR approaches. Selective isotope labeling, including nucleotide-specific and segmental labeling strategies, may provide the best opportunities for obtaining structural information by NMR. Here we review methods that have been developed for preparing and purifying isotopically labeled RNAs, as well as NMR strategies that have been employed for signal assignment and structure determination.

Identification of Thioredoxin Disulfide Targets Using a Quantitative Proteomics Approach Based on Isotope-Coded Affinity Tags

DEFF Research Database (Denmark)

Hägglund, Per; Bunkenborg, Jakob; Maeda, Kenji

2008-01-01

Thioredoxin (Trx) is a ubiquitous protein disulfide reductase involved in a wide range of cellular redox processes. A large number of putative target proteins have been identified using proteomics approaches, but insight into target specificity at the molecular level is lacking since the reactivity...... of Trx toward individual disulfides has not been quantified. Here, a novel proteomics procedure is described for quantification of Trx-mediated target disulfide reduction based on thiol-specific differential labeling with the iodoacetamide-based isotope-coded affinity tag (ICAT) reagents. Briefly......, protein extract of embryos from germinated barley seeds was treated +/- Trx, and thiols released from target protein disulfides were irreversibly blocked with iodoacetamide. The remaining cysteine residues in the Trx-treated and the control (-Trx) samples were then chemically reduced and labeled...

Stable isotopes labelled compounds

International Nuclear Information System (INIS)

1982-09-01

The catalogue on stable isotopes labelled compounds offers deuterium, nitrogen-15, and multiply labelled compounds. It includes: (1) conditions of sale and delivery, (2) the application of stable isotopes, (3) technical information, (4) product specifications, and (5) the complete delivery programme

Plasma Protein Turnover Rates in Rats Using Stable Isotope Labeling, Global Proteomics, and Activity-Based Protein Profiling

Energy Technology Data Exchange (ETDEWEB)

Smith, Jordan N.; Tyrrell, Kimberly J.; Hansen, Joshua R.; Thomas, Dennis G.; Murphree, Taylor A.; Shukla, Anil K.; Luders, Teresa; Madden, James M.; Li, Yunying; Wright, Aaron T.; Piehowski, Paul D.

2017-12-06

Protein turnover is important for general health on cellular and organism scales providing a strategy to replace old, damaged, or dysfunctional proteins. Protein turnover also informs of biomarker kinetics, as a better understanding of synthesis and degradation of proteins increases the clinical utility of biomarkers. Here, turnover rates of plasma proteins in rats were measured in vivo using a pulse-chase stable isotope labeling experiment. During the pulse, rats (n=5) were fed 13C6-labeled lysine (“heavy”) feed for 23 days to label proteins. During the chase, feed was changed to an unlabeled equivalent feed (“light”), and blood was repeatedly sampled from rats over 10 time points for 28 days. Plasma samples were digested with trypsin, and analyzed with liquid chromatography-tandem mass spectrometry (LC-MS/MS). MaxQuant was used to identify peptides and proteins, and quantify heavy:light lysine ratios. A system of ordinary differential equations was used to calculate protein turnover rates. Using this approach, 273 proteins were identified, and turnover rates were quantified for 157 plasma proteins with half-lives ranging 0.3-103 days. For the ~70 most abundant proteins, variability in turnover rates among rats was low (median coefficient of variation: 0.09). Activity-based protein profiling was applied to pooled plasma samples to enrich serine hydrolases using a fluorophosphonate (FP2) activity-based probe. This enrichment resulted in turnover rates for an additional 17 proteins. This study is the first to measure global plasma protein turnover rates in rats in vivo, measure variability of protein turnover rates in any animal model, and utilize activity-based protein profiling for enhancing measurements of targeted, low-abundant proteins, such as those commonly used as biomarkers. Measured protein turnover rates will be important for understanding of the role of protein turnover in cellular and organism health as well as increasing the utility of protein

Advances in stable isotope assisted labeling strategies with information science.

Science.gov (United States)

Kigawa, Takanori

2017-08-15

Stable-isotope (SI) labeling of proteins is an essential technique to investigate their structures, interactions or dynamics by nuclear magnetic resonance (NMR) spectroscopy. The assignment of the main-chain signals, which is the fundamental first step in these analyses, is usually achieved by a sequential assignment method based on triple resonance experiments. Independently of the triple resonance experiment-based sequential assignment, amino acid-selective SI labeling is beneficial for discriminating the amino acid type of each signal; therefore, it is especially useful for the signal assignment of difficult targets. Various combinatorial selective labeling schemes have been developed as more sophisticated labeling strategies. In these strategies, amino acids are represented by combinations of SI labeled samples, rather than simply assigning one amino acid to one SI labeled sample as in the case of conventional amino acid-selective labeling. These strategies have proven to be useful for NMR analyses of difficult proteins, such as those in large complex systems, in living cells, attached or integrated into membranes, or with poor solubility. In this review, recent advances in stable isotope assisted labeling strategies will be discussed. Copyright © 2017 Elsevier Inc. All rights reserved.

Bacterial expression and one-step purification of an isotope-labeled heterotrimeric G-protein α-subunit

International Nuclear Information System (INIS)

Abdulaev, Najmoutin G.; Zhang Cheng; Dinh, Andy; Ngo, Tony; Bryan, Philip N.; Brabazon, Danielle M.; Marino, John P.; Ridge, Kevin D.

2005-01-01

Heterologous expression systems are often employed to generate sufficient quantities of isotope-labeled proteins for high-resolution NMR studies. Recently, the interaction between the prodomain region of subtilisin and an active, mutant form of the mature enzyme has been exploited to develop a cleavable affinity tag fusion system for one-step generation and purification of full-length soluble proteins obtained by inducible prokaryotic expression. As a first step towards applying high-resolution NMR methods to study heterotrimeric G-protein α-subunit (G α ) conformation and dynamics, the utility of this subtilisin prodomain fusion system for expressing and purifying an isotope-labeled G α chimera (∼40 kDa polypeptide) has been tested. The results show that a prodomain fused G α chimera can be expressed to levels approaching 6-8 mg/l in minimal media and that the processed, mature protein exhibits properties similar to those of G α isolated from natural sources. To assay for the functional integrity of the purified G α chimera at NMR concentrations and probe for changes in the structure and dynamics of G α that result from activation, 15 N-HSQC spectra of the GDP/Mg 2+ bound form of G α obtained in the absence and presence of aluminum fluoride, a well known activator of the GDP bound state, have been acquired. Comparisons of the 15 N-HSQC spectra reveals a number of changes in chemical shifts of the 1 HN, 15 N crosspeaks that are discussed with respect to expected changes in the protein conformation associated with G α activation

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

International Nuclear Information System (INIS)

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

2015-01-01

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

A Cost-effective Amino-acid-type Selective Isotope Labeling of Proteins Expressed in Leishmania tarentolae

Czech Academy of Sciences Publication Activity Database

Foldynová-Trantírková, Silvie; Matulová, J.; Dötsch, V.; Löhr, F.; Cirstea, I.; Alexandov, K.; Breitling, R.; Lukeš, Julius; Trantírek, Lukáš

2009-01-01

Roč. 26, č. 6 (2009), s. 755-761 ISSN 0739-1102 R&D Projects: GA ČR GP204/08/P585; GA AV ČR 1QS600220554; GA AV ČR KAN200100801; GA MŠk 2B06129 Institutional research plan: CEZ:AV0Z60220518 Keywords : NMR * isotope labeling * protein expression * Leishmania * low-level enrichment Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.124, year: 2009

Bacterial expression and one-step purification of an isotope-labeled heterotrimeric G-protein {alpha}-subunit

Energy Technology Data Exchange (ETDEWEB)

Abdulaev, Najmoutin G. [University of Maryland Biotechnology Institute, Center for Advanced Research in Biotechnology (United States); Zhang Cheng; Dinh, Andy [University of Texas Health Science Center, Center for Membrane Biology, Department of Biochemistry and Molecular Biology (United States); Ngo, Tony; Bryan, Philip N. [University of Maryland Biotechnology Institute, Center for Advanced Research in Biotechnology (United States); Brabazon, Danielle M. [Loyola College in Maryland, Department of Chemistry (United States); Marino, John P. [University of Maryland Biotechnology Institute, Center for Advanced Research in Biotechnology (United States)], E-mail: marino@carb.nist.gov; Ridge, Kevin D. [University of Texas Health Science Center, Center for Membrane Biology, Department of Biochemistry and Molecular Biology (United States)

2005-05-15

Heterologous expression systems are often employed to generate sufficient quantities of isotope-labeled proteins for high-resolution NMR studies. Recently, the interaction between the prodomain region of subtilisin and an active, mutant form of the mature enzyme has been exploited to develop a cleavable affinity tag fusion system for one-step generation and purification of full-length soluble proteins obtained by inducible prokaryotic expression. As a first step towards applying high-resolution NMR methods to study heterotrimeric G-protein {alpha}-subunit (G{sub {alpha}}) conformation and dynamics, the utility of this subtilisin prodomain fusion system for expressing and purifying an isotope-labeled G{sub {alpha}} chimera ({approx}40 kDa polypeptide) has been tested. The results show that a prodomain fused G{sub {alpha}} chimera can be expressed to levels approaching 6-8 mg/l in minimal media and that the processed, mature protein exhibits properties similar to those of G{sub {alpha}} isolated from natural sources. To assay for the functional integrity of the purified G{sub {alpha}} chimera at NMR concentrations and probe for changes in the structure and dynamics of G{sub {alpha}} that result from activation, {sup 15}N-HSQC spectra of the GDP/Mg{sup 2+} bound form of G{sub {alpha}} obtained in the absence and presence of aluminum fluoride, a well known activator of the GDP bound state, have been acquired. Comparisons of the {sup 15}N-HSQC spectra reveals a number of changes in chemical shifts of the {sup 1}HN, {sup 15}N crosspeaks that are discussed with respect to expected changes in the protein conformation associated with G{sub {alpha}} activation.

Uniform isotope labeling of a eukaryotic seven-transmembrane helical protein in yeast enables high-resolution solid-state NMR studies in the lipid environment

International Nuclear Information System (INIS)

Fan Ying; Shi Lichi; Ladizhansky, Vladimir; Brown, Leonid S.

2011-01-01

Overexpression of isotope-labeled multi-spanning eukaryotic membrane proteins for structural NMR studies is often challenging. On the one hand, difficulties with achieving proper folding, membrane insertion, and native-like post-translational modifications frequently disqualify bacterial expression systems. On the other hand, eukaryotic cell cultures can be prohibitively expensive. One of the viable alternatives, successfully used for producing proteins for solution NMR studies, is yeast expression systems, particularly Pichia pastoris. We report on successful implementation and optimization of isotope labeling protocols, previously used for soluble secreted proteins, to produce homogeneous samples of a eukaryotic seven-transmembrane helical protein, rhodopsin from Leptosphaeria maculans. Even in shake-flask cultures, yields exceeded 5 mg of purified uniformly 13 C, 15 N-labeled protein per liter of culture. The protein was stable (at least several weeks at 5°C) and functionally active upon reconstitution into lipid membranes at high protein-to-lipid ratio required for solid-state NMR. The samples gave high-resolution 13 C and 15 N solid-state magic angle spinning NMR spectra, amenable to a detailed structural analysis. We believe that similar protocols can be adopted for challenging mammalian targets, which often resist characterization by other structural methods.

Selectively dispersed isotope labeling for protein structure determination by magic angle spinning NMR

Energy Technology Data Exchange (ETDEWEB)

Eddy, Matthew T. [Massachusetts Institute of Technology, Department of Chemistry (United States); Belenky, Marina [Brandeis University, Department of Chemistry (United States); Sivertsen, Astrid C. [Massachusetts Institute of Technology, Francis Bitter Magnet Laboratory (United States); Griffin, Robert G. [Massachusetts Institute of Technology, Department of Chemistry (United States); Herzfeld, Judith, E-mail: herzfeld@brandeis.edu [Brandeis University, Department of Chemistry (United States)

2013-10-15

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-{sup 13}C] acetate does not label {alpha} 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-{sup 13}C] 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.

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

Energy Technology Data Exchange (ETDEWEB)

Yagi, Hirokazu [Nagoya City University, Faculty and Graduate School of Pharmaceutical Sciences (Japan); Nakamura, Masatoshi [National Institute of Agrobiological Sciences, Genetic Resources Conservation Research Unit, Genetic Resources Center (Japan); Yokoyama, Jun [Taiyo Nippon Sanso Corporation, Tsukuba Laboratories (Japan); Zhang, Ying; Yamaguchi, Takumi [National Institutes of Natural Sciences, Institute for Molecular Science and Okazaki Institute for Integrative Bioscience (Japan); Kondo, Sachiko [Nagoya City University, Faculty and Graduate School of Pharmaceutical Sciences (Japan); Kobayashi, Jun [Yamaguchi University, Department of Biological and Environmental Sciences, Faculty of Agriculture (Japan); Kato, Tatsuya; Park, Enoch Y. [Shizuoka University, Laboratory of Biotechnology, Research Institute of Green Science and Technology (Japan); Nakazawa, Shiori [Nagoya University, Sugashima Marine Biological Laboratory, Graduate School of Science (Japan); Hashii, Noritaka; Kawasaki, Nana [National Institute of Health Sciences, Division of Biological Chemistry and Biologicals (Japan); Kato, Koichi, E-mail: kkato@phar.nagoya-cu.ac.jp [Nagoya City University, Faculty and Graduate School of Pharmaceutical Sciences (Japan)

2015-06-15

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 {sup 15}N-labeled yeast crude protein extract. We harvested 0.1 mg of IgG from larva with a {sup 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.

Melatonin labeled with hydrogen isotopes

International Nuclear Information System (INIS)

Dmitrevskaya, L.I.; Smushkevich, Yu.I.; Kurkovskaya, L.N.; Ponomarenko, N.K.; Suvorov, N.N.

1989-01-01

A study has been made of isotope exchange between melatonin and deuterium (D 2 O) or tritium (HTO) oxide under different conditions. The ease of isotope exchange for the indole ring hydrogens of melatonin in an acidic medium decreases over the series H 4 > H 2 H 6 >> H 7 , enabling the authors to process a route for production of melatonin labeled with hydrogen isotopes at positions 4,6, and 2 of the indole ring. A method has been suggested for producing melatonin labeled with hydrogen isotopes at position 2 by desulfurization of 2-(2,4-dinitro-phenylsulfenyl)melatonin at Ni(Re) (D)

Melatonin labelled by hydrogen isotopes

International Nuclear Information System (INIS)

Dmitrevskaya, L.I.; Smushkevich, Yu.I.; Kurkovskaya, L.N.; Ponomarenko, N.K.; Suvorov, N.N.

1988-01-01

Isotope exchange of melatonin with deuterium (D 2 O) and tritium (HTO) oxides under different conditions is studied. Simplicity of isotope exchange of hydrogens of the indole ring of melatonin in the acidic medium decreases in series H 4 >H 2 >H 6 >>H 7 , that permits to suggest the way of melatonin preparation labelled by hydrogen isotopes in positions 4,6 and 2 of the indole ring. The way of melatonin preparation labelled by hydrogen isotopes in position 2 according to the reaction of desulfation 2-(2,4-dinitrophenylsulphenyl) melatonin at catalyst Ni(Re)(D) is suggested

Performance of isobaric and isotopic labeling in quantitative plant proteomics

DEFF Research Database (Denmark)

Nogueira, Fábio C S; Palmisano, Giuseppe; Schwämmle, Veit

2012-01-01

, and quantitation. In the present work, we have used LC-MS to compare an isotopic (ICPL) and isobaric (iTRAQ) chemical labeling technique to quantify proteins in the endosperm of Ricinus communis seeds at three developmental stages (IV, VI, and X). Endosperm proteins of each stage were trypsin-digested in...

Differential isotope dansylation labeling combined with liquid chromatography mass spectrometry for quantification of intact and N-terminal truncated proteins

International Nuclear Information System (INIS)

Tang, Yanan; Li, Liang

2013-01-01

Graphical abstract: -- Highlights: •LC–MS was developed for quantifying protein mixtures containing both intact and N-terminal truncated proteins. • 12 C 2 -Dansylation of the N-terminal amino acid of proteins was done first, followed by microwave-assisted acid hydrolysis. •The released 12 C 2 -dansyl labeled N-terminal amino acid was quantified using 13 C 2 -dansyl labeled amino acid standards. •The method provided accurate and precise results for quantifying intact and N-terminal truncated proteins within 8 h. -- Abstract: The N-terminal amino acids of proteins are important structure units for maintaining the biological function, localization, and interaction networks of proteins. Under different biological conditions, one or several N-terminal amino acids could be cleaved from an intact protein due to processes, such as proteolysis, resulting in the change of protein properties. Thus, the ability to quantify the N-terminal truncated forms of proteins is of great importance, particularly in the area of development and production of protein-based drugs where the relative quantity of the intact protein and its truncated form needs to be monitored. In this work, we describe a rapid method for absolute quantification of protein mixtures containing intact and N-terminal truncated proteins. This method is based on dansylation labeling of the N-terminal amino acids of proteins, followed by microwave-assisted acid hydrolysis of the proteins into amino acids. It is shown that dansyl labeled amino acids are stable in acidic conditions and can be quantified by liquid chromatography mass spectrometry (LC–MS) with the use of isotope analog standards

Isotopically labelled pyrimidines and purines

International Nuclear Information System (INIS)

Balaban, A.T.; Bally, I.

1987-01-01

Among the three diazines, pyrimidine is by far the most important one because its derivatives uracil, thymine and cytosine are constituents of the ubiquitous deoxynucleic acids (DNA) and ribonucleic acids (RNA). Other derivatives of pyrimidine without condensed rings include barbiturates, alloxan, orotic acid and thiamine or vitamin B 1 . From the polycyclic derivatives of pyrimidine such as pteridine, alloxazine, and purine, the latter, through its derivatives adenine and guanine complete the list of bases which occur in DNA and RNA: in addition, other purine derivatives such as hypoxanthine, xanthine, theobromine, theophylline, caffeine and uric acid are important natural products with biological activity. The paper presents methods for preparing isotopically labeled pyrimidines as well as purine derivatives. For convenience, the authors describe separately carbon-labeled with radioisotopes 11 C (T 1/2 = 20.3 min) and 14 C (T 1/2 = 5736 years) or the stable isotope 13 C (natural abundance 1.1%) and then hydrogen-labeled systems with the radioisotope 3 H ≡ T (T 1/2 = 12.346 years) or with the stable isotope 2 H ≡ D (natural abundance 0.015%). We do not separate stable from radioactive isotopes because the synthetic methods are identical for the same element; however, the introduction of hydrogen isotopes into organic molecules is often performed by reactions such as isotope exchange which cannot take place in the case of carbon isotopes

Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates.

Science.gov (United States)

Kleifeld, Oded; Doucet, Alain; Prudova, Anna; auf dem Keller, Ulrich; Gioia, Magda; Kizhakkedathu, Jayachandran N; Overall, Christopher M

2011-09-22

Analysis of the sequence and nature of protein N termini has many applications. Defining the termini of proteins for proteome annotation in the Human Proteome Project is of increasing importance. Terminomics analysis of protease cleavage sites in degradomics for substrate discovery is a key new application. Here we describe the step-by-step procedures for performing terminal amine isotopic labeling of substrates (TAILS), a 2- to 3-d (depending on method of labeling) high-throughput method to identify and distinguish protease-generated neo-N termini from mature protein N termini with all natural modifications with high confidence. TAILS uses negative selection to enrich for all N-terminal peptides and uses primary amine labeling-based quantification as the discriminating factor. Labeling is versatile and suited to many applications, including biochemical and cell culture analyses in vitro; in vivo analyses using tissue samples from animal and human sources can also be readily performed. At the protein level, N-terminal and lysine amines are blocked by dimethylation (formaldehyde/sodium cyanoborohydride) and isotopically labeled by incorporating heavy and light dimethylation reagents or stable isotope labeling with amino acids in cell culture labels. Alternatively, easy multiplex sample analysis can be achieved using amine blocking and labeling with isobaric tags for relative and absolute quantification, also known as iTRAQ. After tryptic digestion, N-terminal peptide separation is achieved using a high-molecular-weight dendritic polyglycerol aldehyde polymer that binds internal tryptic and C-terminal peptides that now have N-terminal alpha amines. The unbound naturally blocked (acetylation, cyclization, methylation and so on) or labeled mature N-terminal and neo-N-terminal peptides are recovered by ultrafiltration and analyzed by tandem mass spectrometry (MS/MS). Hierarchical substrate winnowing discriminates substrates from the background proteolysis products and

Hydroponic isotope labeling of entire plants and high-performance mass spectrometry for quantitative plant proteomics.

Science.gov (United States)

Bindschedler, Laurence V; Mills, Davinia J S; Cramer, Rainer

2012-01-01

Hydroponic isotope labeling of entire plants (HILEP) combines hydroponic plant cultivation and metabolic labeling with stable isotopes using (15)N-containing inorganic salts to label whole and mature plants. Employing (15)N salts as the sole nitrogen source for HILEP leads to the production of healthy-looking plants which contain (15)N proteins labeled to nearly 100%. Therefore, HILEP is suitable for quantitative plant proteomic analysis, where plants are grown in either (14)N- or (15)N-hydroponic media and pooled when the biological samples are collected for relative proteome quantitation. The pooled (14)N-/(15)N-protein extracts can be fractionated in any suitable way and digested with a protease for shotgun proteomics, using typically reverse phase liquid chromatography nanoelectrospray ionization tandem mass spectrometry (RPLC-nESI-MS/MS). Best results were obtained with a hybrid ion trap/FT-MS mass spectrometer, combining high mass accuracy and sensitivity for the MS data acquisition with speed and high-throughput MS/MS data acquisition, increasing the number of proteins identified and quantified and improving protein quantitation. Peak processing and picking from raw MS data files, protein identification, and quantitation were performed in a highly automated way using integrated MS data analysis software with minimum manual intervention, thus easing the analytical workflow. In this methodology paper, we describe how to grow Arabidopsis plants hydroponically for isotope labeling using (15)N salts and how to quantitate the resulting proteomes using a convenient workflow that does not require extensive bioinformatics skills.

Differential isotope dansylation labeling combined with liquid chromatography mass spectrometry for quantification of intact and N-terminal truncated proteins

Energy Technology Data Exchange (ETDEWEB)

Tang, Yanan; Li, Liang, E-mail: Liang.Li@ualberta.ca

2013-08-20

Graphical abstract: -- Highlights: •LC–MS was developed for quantifying protein mixtures containing both intact and N-terminal truncated proteins. •{sup 12}C{sub 2}-Dansylation of the N-terminal amino acid of proteins was done first, followed by microwave-assisted acid hydrolysis. •The released {sup 12}C{sub 2}-dansyl labeled N-terminal amino acid was quantified using {sup 13}C{sub 2}-dansyl labeled amino acid standards. •The method provided accurate and precise results for quantifying intact and N-terminal truncated proteins within 8 h. -- Abstract: The N-terminal amino acids of proteins are important structure units for maintaining the biological function, localization, and interaction networks of proteins. Under different biological conditions, one or several N-terminal amino acids could be cleaved from an intact protein due to processes, such as proteolysis, resulting in the change of protein properties. Thus, the ability to quantify the N-terminal truncated forms of proteins is of great importance, particularly in the area of development and production of protein-based drugs where the relative quantity of the intact protein and its truncated form needs to be monitored. In this work, we describe a rapid method for absolute quantification of protein mixtures containing intact and N-terminal truncated proteins. This method is based on dansylation labeling of the N-terminal amino acids of proteins, followed by microwave-assisted acid hydrolysis of the proteins into amino acids. It is shown that dansyl labeled amino acids are stable in acidic conditions and can be quantified by liquid chromatography mass spectrometry (LC–MS) with the use of isotope analog standards.

Affordable uniform isotope labeling with {sup 2}H, {sup 13}C and {sup 15}N in insect cells

Energy Technology Data Exchange (ETDEWEB)

Sitarska, Agnieszka; Skora, Lukasz; Klopp, Julia; Roest, Susan; Fernández, César; Shrestha, Binesh; Gossert, Alvar D., E-mail: alvar.gossert@novartis.com [Novartis Institutes for BioMedical Research (Switzerland)

2015-06-15

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 {sup 15}N and {sup 13}C with yields comparable to expression in full media. For {sup 2}H,{sup 15}N and {sup 2}H,{sup 13}C,{sup 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.

Quantitative profiling of O-glycans by electrospray ionization- and matrix-assisted laser desorption ionization-time-of-flight-mass spectrometry after in-gel derivatization with isotope-coded 1-phenyl-3-methyl-5-pyrazolone

International Nuclear Information System (INIS)

Sić, Siniša; Maier, Norbert M.; Rizzi, Andreas M.

2016-01-01

The potential and benefits of isotope-coded labeling in the context of MS-based glycan profiling are evaluated focusing on the analysis of O-glycans. For this purpose, a derivatization strategy using d_0/d_5-1-phenyl-3-methyl-5-pyrazolone (PMP) is employed, allowing O-glycan release and derivatization to be achieved in one single step. The paper demonstrates that this release and derivatization reaction can be carried out also in-gel with only marginal loss in sensitivity compared to in-solution derivatization. Such an effective in-gel reaction allows one to extend this release/labeling method also to glycoprotein/glycoform samples pre-separated by gel-electrophoresis without the need of extracting the proteins/digested peptides from the gel. With highly O-glycosylated proteins (e.g. mucins) LODs in the range of 0.4 μg glycoprotein (100 fmol) loaded onto the electrophoresis gel can be attained, with minor glycosylated proteins (like IgAs, FVII, FIX) the LODs were in the range of 80–100 μg (250 pmol–1.5 nmol) glycoprotein loaded onto the gel. As second aspect, the potential of isotope coded labeling as internal standardization strategy for the reliable determination of quantitative glycan profiles via MALDI-MS is investigated. Towards this goal, a number of established and emerging MALDI matrices were tested for PMP-glycan quantitation, and their performance is compared with that of ESI-based measurements. The crystalline matrix 2,6-dihydroxyacetophenone (DHAP) and the ionic liquid matrix N,N-diisopropyl-ethyl-ammonium 2,4,6-trihydroxyacetophenone (DIEA-THAP) showed potential for MALDI-based quantitation of PMP-labeled O-glycans. We also provide a comprehensive overview on the performance of MS-based glycan quantitation approaches by comparing sensitivity, LOD, accuracy and repeatability data obtained with RP-HPLC-ESI-MS, stand-alone nano-ESI-MS with a spray-nozzle chip, and MALDI-MS. Finally, the suitability of the isotope-coded PMP labeling strategy for

Quantitative profiling of O-glycans by electrospray ionization- and matrix-assisted laser desorption ionization-time-of-flight-mass spectrometry after in-gel derivatization with isotope-coded 1-phenyl-3-methyl-5-pyrazolone

Energy Technology Data Exchange (ETDEWEB)

Sić, Siniša; Maier, Norbert M.; Rizzi, Andreas M., E-mail: Andreas.Rizzi@univie.ac.at

2016-09-07

The potential and benefits of isotope-coded labeling in the context of MS-based glycan profiling are evaluated focusing on the analysis of O-glycans. For this purpose, a derivatization strategy using d{sub 0}/d{sub 5}-1-phenyl-3-methyl-5-pyrazolone (PMP) is employed, allowing O-glycan release and derivatization to be achieved in one single step. The paper demonstrates that this release and derivatization reaction can be carried out also in-gel with only marginal loss in sensitivity compared to in-solution derivatization. Such an effective in-gel reaction allows one to extend this release/labeling method also to glycoprotein/glycoform samples pre-separated by gel-electrophoresis without the need of extracting the proteins/digested peptides from the gel. With highly O-glycosylated proteins (e.g. mucins) LODs in the range of 0.4 μg glycoprotein (100 fmol) loaded onto the electrophoresis gel can be attained, with minor glycosylated proteins (like IgAs, FVII, FIX) the LODs were in the range of 80–100 μg (250 pmol–1.5 nmol) glycoprotein loaded onto the gel. As second aspect, the potential of isotope coded labeling as internal standardization strategy for the reliable determination of quantitative glycan profiles via MALDI-MS is investigated. Towards this goal, a number of established and emerging MALDI matrices were tested for PMP-glycan quantitation, and their performance is compared with that of ESI-based measurements. The crystalline matrix 2,6-dihydroxyacetophenone (DHAP) and the ionic liquid matrix N,N-diisopropyl-ethyl-ammonium 2,4,6-trihydroxyacetophenone (DIEA-THAP) showed potential for MALDI-based quantitation of PMP-labeled O-glycans. We also provide a comprehensive overview on the performance of MS-based glycan quantitation approaches by comparing sensitivity, LOD, accuracy and repeatability data obtained with RP-HPLC-ESI-MS, stand-alone nano-ESI-MS with a spray-nozzle chip, and MALDI-MS. Finally, the suitability of the isotope-coded PMP labeling

Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology.

Science.gov (United States)

von Bergen, Martin; Jehmlich, Nico; Taubert, Martin; Vogt, Carsten; Bastida, Felipe; Herbst, Florian-Alexander; Schmidt, Frank; Richnow, Hans-Hermann; Seifert, Jana

2013-10-01

The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes ((13)C, (15)N, (36)S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed.

Application of SAIL phenylalanine and tyrosine with alternative isotope-labeling patterns for protein structure determination

Energy Technology Data Exchange (ETDEWEB)

Takeda, Mitsuhiro [Nagoya University, Structural Biology Research Center, Graduate School of Science (Japan); Ono, Akira M.; Terauchi, Tsutomu [SAIL Technologies Co., Inc. (Japan); Kainosho, Masatsune, E-mail: kainosho@nmr.chem.metro-u.ac.j [Nagoya University, Structural Biology Research Center, Graduate School of Science (Japan)

2010-01-15

The extensive collection of NOE constraint data involving the aromatic ring signals is essential for accurate protein structure determination, although it is often hampered in practice by the pervasive signal overlapping and tight spin couplings for aromatic rings. We have prepared various types of stereo-array isotope labeled phenylalanines ({epsilon}- and {zeta}-SAIL Phe) and tyrosine ({epsilon}-SAIL Tyr) to overcome these problems (Torizawa et al. 2005), and proven that these SAIL amino acids provide dramatic spectral simplification and sensitivity enhancement for the aromatic ring NMR signals. In addition to these SAIL aromatic amino acids, we recently synthesized {delta}-SAIL Phe and {delta}-SAIL Tyr, which allow us to observe and assign {delta}-{sup 13}C/{sup 1}H signals very efficiently. Each of the various types of SAIL Phe and SAIL Tyr yields well-resolved resonances for the {delta}-, {epsilon}- or {zeta}-{sup 13}C/{sup 1}H signals, respectively, which can readily be assigned by simple and robust pulse sequences. Since the {delta}-, {epsilon}-, and {zeta}-proton signals of Phe/Tyr residues give rise to complementary NOE constraints, the concomitant use of various types of SAIL-Phe and SAIL-Tyr would generate more accurate protein structures, as compared to those obtained by using conventional uniformly {sup 13}C, {sup 15}N-double labeled proteins. We illustrated this with the case of an 18.2 kDa protein, Escherichia coli peptidyl-prolyl cis-trans isomerase b (EPPIb), and concluded that the combined use of {zeta}-SAIL Phe and {epsilon}-SAIL Tyr would be practically the best choice for protein structural determinations.

Application of SAIL phenylalanine and tyrosine with alternative isotope-labeling patterns for protein structure determination.

Science.gov (United States)

Takeda, Mitsuhiro; Ono, Akira M; Terauchi, Tsutomu; Kainosho, Masatsune

2010-01-01

The extensive collection of NOE constraint data involving the aromatic ring signals is essential for accurate protein structure determination, although it is often hampered in practice by the pervasive signal overlapping and tight spin couplings for aromatic rings. We have prepared various types of stereo-array isotope labeled phenylalanines (epsilon- and zeta-SAIL Phe) and tyrosine (epsilon-SAIL Tyr) to overcome these problems (Torizawa et al. 2005), and proven that these SAIL amino acids provide dramatic spectral simplification and sensitivity enhancement for the aromatic ring NMR signals. In addition to these SAIL aromatic amino acids, we recently synthesized delta-SAIL Phe and delta-SAIL Tyr, which allow us to observe and assign delta-(13)C/(1)H signals very efficiently. Each of the various types of SAIL Phe and SAIL Tyr yields well-resolved resonances for the delta-, epsilon- or zeta-(13)C/(1)H signals, respectively, which can readily be assigned by simple and robust pulse sequences. Since the delta-, epsilon-, and zeta-proton signals of Phe/Tyr residues give rise to complementary NOE constraints, the concomitant use of various types of SAIL-Phe and SAIL-Tyr would generate more accurate protein structures, as compared to those obtained by using conventional uniformly (13)C, (15)N-double labeled proteins. We illustrated this with the case of an 18.2 kDa protein, Escherichia coli peptidyl-prolyl cis-trans isomerase b (EPPIb), and concluded that the combined use of zeta-SAIL Phe and epsilon-SAIL Tyr would be practically the best choice for protein structural determinations.

Application of SAIL phenylalanine and tyrosine with alternative isotope-labeling patterns for protein structure determination

International Nuclear Information System (INIS)

Takeda, Mitsuhiro; Ono, Akira M.; Terauchi, Tsutomu; Kainosho, Masatsune

2010-01-01

The extensive collection of NOE constraint data involving the aromatic ring signals is essential for accurate protein structure determination, although it is often hampered in practice by the pervasive signal overlapping and tight spin couplings for aromatic rings. We have prepared various types of stereo-array isotope labeled phenylalanines (ε- and ζ-SAIL Phe) and tyrosine (ε-SAIL Tyr) to overcome these problems (Torizawa et al. 2005), and proven that these SAIL amino acids provide dramatic spectral simplification and sensitivity enhancement for the aromatic ring NMR signals. In addition to these SAIL aromatic amino acids, we recently synthesized δ-SAIL Phe and δ-SAIL Tyr, which allow us to observe and assign δ- 13 C/ 1 H signals very efficiently. Each of the various types of SAIL Phe and SAIL Tyr yields well-resolved resonances for the δ-, ε- or ζ- 13 C/ 1 H signals, respectively, which can readily be assigned by simple and robust pulse sequences. Since the δ-, ε-, and ζ-proton signals of Phe/Tyr residues give rise to complementary NOE constraints, the concomitant use of various types of SAIL-Phe and SAIL-Tyr would generate more accurate protein structures, as compared to those obtained by using conventional uniformly 13 C, 15 N-double labeled proteins. We illustrated this with the case of an 18.2 kDa protein, Escherichia coli peptidyl-prolyl cis-trans isomerase b (EPPIb), and concluded that the combined use of ζ-SAIL Phe and ε-SAIL Tyr would be practically the best choice for protein structural determinations.

Stable-isotope-labeled carbohydrates and nucleosides: Synthesis and applications in chemistry and biology

Energy Technology Data Exchange (ETDEWEB)

Serianni, A.S. [Univ. of Notre Dame, IN (United States)

1994-12-01

Carbohydrates play important roles in many key biochemical processes in living cells. For example, they are metabolized to produce energy, mediate cell-cell recognition, and play an indirect role (as constituents of DNA and RNA) in DNA replication, RNA transcription, and protein synthesis. These roles, and others of comparable biochemical significance, have been studied to varying extends with the use of stable isotopically labeled molecules, usually in conjunction with NMR spectroscopy and/or mass spectrometry. For example, carbohydrate metabolism has been monitored in vitro and in vivo with the use of isotopically labeled compounds. Molecular aspects of cell-cell recognition, mediated by cell-surface glycoproteins and glycolipids, have been probed through NMR studies of isotopically labeled oligosaccharides. More recently, the solution behavior of DNA and RNA has been examined through the use of labeled oligonucleotides. In all of these pursuits, the effort and expense to prepare labeled molecules, both of which can be substantial, are more than offset by the wealth of information derived from these studies. This information often cannot be accessed, or can be accessed only with great difficulty, using natural (unlabeled) compounds.

Stable-isotope-labeled carbohydrates and nucleosides: Synthesis and applications in chemistry and biology

International Nuclear Information System (INIS)

Serianni, A.S.

1994-01-01

Carbohydrates play important roles in many key biochemical processes in living cells. For example, they are metabolized to produce energy, mediate cell-cell recognition, and play an indirect role (as constituents of DNA and RNA) in DNA replication, RNA transcription, and protein synthesis. These roles, and others of comparable biochemical significance, have been studied to varying extends with the use of stable isotopically labeled molecules, usually in conjunction with NMR spectroscopy and/or mass spectrometry. For example, carbohydrate metabolism has been monitored in vitro and in vivo with the use of isotopically labeled compounds. Molecular aspects of cell-cell recognition, mediated by cell-surface glycoproteins and glycolipids, have been probed through NMR studies of isotopically labeled oligosaccharides. More recently, the solution behavior of DNA and RNA has been examined through the use of labeled oligonucleotides. In all of these pursuits, the effort and expense to prepare labeled molecules, both of which can be substantial, are more than offset by the wealth of information derived from these studies. This information often cannot be accessed, or can be accessed only with great difficulty, using natural (unlabeled) compounds

Isotopically labelled vitamin D derivatives and processes for preparing same

International Nuclear Information System (INIS)

Deluca, H.R.; Schnoes, H.K.; Napoli, J.L.; Fivizzani, M.A.

1981-01-01

This invention relates to 26,27-isotopically labelled vitamin D 3 compounds, including radiolabelled vitamin D 3 compounds of high specific activity, methods for their preparation, and intermediates obtained in their synthesis. The method involves reacting an ester of a 26,27-dinor-vitamin D-25-carboxylic acid with an isotopically labelled methyl Grignard reagent or methyl lithium reagent to obtain a 26,27-isotopically labelled compound in which at least some of the H atoms and/or C atoms are heavy isotopes. (author)

Custom synthesis of isotope-labelled Apis mellifera Pheromone

International Nuclear Information System (INIS)

Conanan, Aida P.; Cortes, Nicole Marie A.; Daguno, Cristel Lyn R.; Templonuevo, Jose Angelo A.; Sucgang, Raymond J.

2012-01-01

The object of this study is to determine the optimum conditions for the synthesis of the isotope-labelled isopentyl acetate. Isopentyl acetate is widely used as a raw material in industries, in syntheses, and is utilized as a sex attractant (pheromone) by the bee species, Apis mellifera. The isotope labelling of isopentyl acetate will allow tracking of the fate and movement of the isopentyl acetate in the environment, in chemical transformations, and in biological systems. Esterification by alcoholysis of acetic acid was optimized for the preparation of Carbon-14( 14 C)-labelled isopentyl acetate from 14 C-labelled acetic acid and isoamyl alcohol. The different conditions studied were: (1) The effects of acid catalysis and/or reflux on the incorporation and retention of the isotope label on the product. The efficiency of label incorporation and retention was determined through the beta radioactivity of Carbon 14 in each of the synthetic constructs. Determination of the beta radioactivity concentration of 14 C in the isopentyl acetate product was done using low level liquid scintillation spectrometry. Each of the synthetic products was mixed with Ultima Gold scintillation cocktail in a low potassium glass scintillation vial, and analysed in a low-level Wallac 1414 scintillation counter. The application of catalysis without reflux resulted in the highest yield (35%). The same condition also resulted in the highest abundance of carbon isotope label with 2.40 Bequerels per cubic centimetre, Bq/cc (measurement unit for radioactivity). (author)

Impact of transamination reactions and protein turnover on labeling dynamics in C-13-labeling experiments

DEFF Research Database (Denmark)

Grotkjær, Thomas; Åkesson, M.; Christensen, Bjarke

2004-01-01

A dynamic model describing carbon atom transitions in the central metabolism of Saccharomyces cerevisiae is used to investigate the influence of transamination reactions and protein turnover on the transient behavior of C-13-labeling chemostat experiments. The simulations performed suggest...... that carbon exchange due to transamination and protein turnover can significantly increase the required time needed for metabolites in the TCA cycle to reach isotopic steady state, which is in agreement with published experimental observations. On the other hand, transamination and protein turnover will speed...... behavior until after three residence times. These observations suggest that greater caution should be used while also pointing to new opportunities in the design and interpretation of C-13-labeling experiments....

Highly efficient residue-selective labeling with isotope-labeled Ile, Leu, and Val using a new auxotrophic E. coli strain

International Nuclear Information System (INIS)

Miyanoiri, Yohei; Ishida, Yojiro; Takeda, Mitsuhiro; Terauchi, Tsutomu; Inouye, Masayori; Kainosho, Masatsune

2016-01-01

We recently developed a practical protocol for preparing proteins bearing stereo-selectively 13 C-methyl labeled leucines and valines, instead of the commonly used 13 C-methyl labeled precursors for these amino acids, by E. coli cellular expression. Using this protocol, proteins with any combinations of isotope-labeled or unlabeled Leu and Val residues were prepared, including some that could not be prepared by the precursor methods. However, there is still room for improvement in the labeling efficiencies for Val residues, using the methods with labeled precursors or Val itself. This is due to the fact that the biosynthesis of Val could not be sufficiently suppressed, even by the addition of large amounts of Val or its precursors. In this study, we completely solved this problem by using a mutant strain derived from E. coli BL21(DE3), in which the metabolic pathways depending on two enzymes, dihydroxy acid dehydratase and β-isopropylmalate dehydrogenase, are completely aborted by deleting the ilvD and leuB genes, which respectively encode these enzymes. The ΔilvD E. coli mutant terminates the conversion from α,β-dihydroxyisovalerate to α-ketoisovalerate, and the conversion from α,β-dihydroxy-α-methylvalerate to α-keto-β-methylvalerate, which produce the preceding precursors for Val and Ile, respectively. By the further deletion of the leuB gene, the conversion from Val to Leu was also fully terminated. Taking advantage of the double-deletion mutant, ΔilvDΔleuB E. coli BL21(DE3), an efficient and residue-selective labeling method with various isotope-labeled Ile, Leu, and Val residues was established.

Highly efficient residue-selective labeling with isotope-labeled Ile, Leu, and Val using a new auxotrophic E. coli strain

Energy Technology Data Exchange (ETDEWEB)

Miyanoiri, Yohei [Nagoya University, Structural Biology Research Center, Graduate School of Science (Japan); Ishida, Yojiro [Rutgers University-Robert Wood Johnson Medical School, Center for Advanced Biotechnology and Medicine (United States); Takeda, Mitsuhiro [Nagoya University, Structural Biology Research Center, Graduate School of Science (Japan); Terauchi, Tsutomu [Tokyo Metropolitan University, Graduate School of Science and Engineering (Japan); Inouye, Masayori [Rutgers University-Robert Wood Johnson Medical School, Center for Advanced Biotechnology and Medicine (United States); Kainosho, Masatsune, E-mail: kainosho@tmu.ac.jp [Nagoya University, Structural Biology Research Center, Graduate School of Science (Japan)

2016-06-15

We recently developed a practical protocol for preparing proteins bearing stereo-selectively {sup 13}C-methyl labeled leucines and valines, instead of the commonly used {sup 13}C-methyl labeled precursors for these amino acids, by E. coli cellular expression. Using this protocol, proteins with any combinations of isotope-labeled or unlabeled Leu and Val residues were prepared, including some that could not be prepared by the precursor methods. However, there is still room for improvement in the labeling efficiencies for Val residues, using the methods with labeled precursors or Val itself. This is due to the fact that the biosynthesis of Val could not be sufficiently suppressed, even by the addition of large amounts of Val or its precursors. In this study, we completely solved this problem by using a mutant strain derived from E. coli BL21(DE3), in which the metabolic pathways depending on two enzymes, dihydroxy acid dehydratase and β-isopropylmalate dehydrogenase, are completely aborted by deleting the ilvD and leuB genes, which respectively encode these enzymes. The ΔilvD E. coli mutant terminates the conversion from α,β-dihydroxyisovalerate to α-ketoisovalerate, and the conversion from α,β-dihydroxy-α-methylvalerate to α-keto-β-methylvalerate, which produce the preceding precursors for Val and Ile, respectively. By the further deletion of the leuB gene, the conversion from Val to Leu was also fully terminated. Taking advantage of the double-deletion mutant, ΔilvDΔleuB E. coli BL21(DE3), an efficient and residue-selective labeling method with various isotope-labeled Ile, Leu, and Val residues was established.

Custom isotope-labelling of apis mellifera pheromone

International Nuclear Information System (INIS)

Conanan, Aida P.; Cortes, Nicole Marie A.; Daguno, Cristel Lyn R.; Templonuevo, Jose Angelo A.; Sucgang, Raymond J.

2012-01-01

The object of this study is to determine the optimum conditions for the synthesis of isotope-labelled isoamyl acetate. Esterification by alcoholysis of acetic acid was optimized for the preparation of Carbon - 14 ( 14 C)-labelled isopentyl acetate from 14 C-labelled acetic acid and isopentyl alcohol. The optimization procedure defined the effects of catalysis, reflux time, and temperature. The application of catalysis without reflux resulted to the highest yield (40%); the same condition also resulted to the highest abundance of carbon isotope label with 2.40 disintegrations per minute per cubic centimetre, DPM/cc (measurement unit for radioactivity). Determination of the beta radioactivity concentration of 14 C in the isopentyl acetate product was done using low level liquid scintillation spectrometry. Each of the synthetic constructs was mixed with Ultima Gold scintillation cocktail in a glass scintillation vial, and analysed in a low-level Wallac 1414 scintillation counter. Samples were counted for 2 hours in a chamber temperature maintained at 14 degree centegrade. The catalysed reaction without reflux was established to be the most efficient scheme for the radiolabelling. The radiolabelled isoamyl acetate can give way to the synthesis of more complex substances which can be then tracked when they are introduced to a system through the carbon isotope label. (author)

[Progress in stable isotope labeled quantitative proteomics methods].

Science.gov (United States)

Zhou, Yuan; Shan, Yichu; Zhang, Lihua; Zhang, Yukui

2013-06-01

Quantitative proteomics is an important research field in post-genomics era. There are two strategies for proteome quantification: label-free methods and stable isotope labeling methods which have become the most important strategy for quantitative proteomics at present. In the past few years, a number of quantitative methods have been developed, which support the fast development in biology research. In this work, we discuss the progress in the stable isotope labeling methods for quantitative proteomics including relative and absolute quantitative proteomics, and then give our opinions on the outlook of proteome quantification methods.

Pharmaceuticals labelled with stable isotopes

International Nuclear Information System (INIS)

Krumbiegel, P.

1986-11-01

The relatively new field of pharmaceuticals labelled with stable isotopes is reviewed. Scientific, juridical, and ethical questions are discussed concerning the application of these pharmaceuticals in human medicine. 13 C, 15 N, and 2 H are the stable isotopes mainly utilized in metabolic function tests. Methodical contributions are given to the application of 2 H, 13 C, and 15 N pharmaceuticals showing new aspects and different states of development in the field under discussion. (author)

In vivo stability and inertness of various direct labelled and chelate-tagged protein

International Nuclear Information System (INIS)

Janoki, A.; Korosi, L.; Klivenyi, G.; Spett, B.

1987-01-01

There were looking for methods giving precise information about composition and activity distribution of protein components, both in the initial samples and serum samples after intravenous administration. It was tested the applicability of electroimmunoassay, polyacrilamide gel electrophoresis and high performance liquid chromatography for the assessment of in vivo stability and labelled proteins. The model compound was human serum albumin (HSA) labelled with 99m Tc and 125 I, respectively. Bifunctional chelate labelling was done with desferrioxamine, in this case protein was labelled with 67 Ga. Biodistribution of the labelled compounds and their elimination from the blood were studied in rabbits. Experience with various labelling proteins, especially with Tc-Sn-HSA system indicate that in vivo stability of this compounds are generally low. Following intravenous injection of proteins labelled with metal isotopes, due to dilution and to the presence of considerable amount of compatitive protein in the serum, part of the label is being detached from the carrier protein. Distribution of the detached metal is different from the original distribution of the protein. This problem arises also with radiopharmaceuticals based on monoclonal antibodies. (M.E.L.) [es

An economic approach to efficient isotope labeling in insect cells using homemade 15N-, 13C- and 2H-labeled yeast extracts

International Nuclear Information System (INIS)

Opitz, Christian; Isogai, Shin; Grzesiek, Stephan

2015-01-01

Heterologous expression of proteins in insect cells is frequently used for crystallographic structural studies due to the high yields even for challenging proteins requiring the eukaryotic protein processing capabilities of the host. However for NMR studies, the need for isotope labeling poses extreme challenges in eukaryotic hosts. Here, we describe a robust method to achieve uniform protein 15 N and 13 C labeling of up to 90 % in baculovirus-infected insect cells. The approach is based on the production of labeled yeast extract, which is subsequently supplemented to insect cell growth media. The method also allows deuteration at levels of >60 % without decrease in expression yield. The economic implementation of the labeling procedures into a standard structural biology laboratory environment is described in a step-by-step protocol. Applications are demonstrated for a variety of NMR experiments using the Abelson kinase domain, GFP, and the beta-1 adrenergic receptor as examples. Deuterated expression of the latter provides spectra of very high quality of a eukaryotic G-protein coupled receptor

13C metabolic flux analysis: optimal design of isotopic labeling experiments.

Science.gov (United States)

Antoniewicz, Maciek R

2013-12-01

Measuring fluxes by 13C metabolic flux analysis (13C-MFA) has become a key activity in chemical and pharmaceutical biotechnology. Optimal design of isotopic labeling experiments is of central importance to 13C-MFA as it determines the precision with which fluxes can be estimated. Traditional methods for selecting isotopic tracers and labeling measurements did not fully utilize the power of 13C-MFA. Recently, new approaches were developed for optimal design of isotopic labeling experiments based on parallel labeling experiments and algorithms for rational selection of tracers. In addition, advanced isotopic labeling measurements were developed based on tandem mass spectrometry. Combined, these approaches can dramatically improve the quality of 13C-MFA results with important applications in metabolic engineering and biotechnology. Copyright © 2013 Elsevier Ltd. All rights reserved.

Quantitation of some amino-terminal residues in proteins using 3H-labelled dansyl chloride and 14C labelled amino acids

International Nuclear Information System (INIS)

Flengsrud, R.

1979-01-01

A method for quantitation of amino-terminal residues in proteins is presented. The method is a modification of a double isotope-labelling technique, using 3 H-labelled dansyl chloride and 14 C-labelled amino acids as internal standards. The method is demonstrated on human fibrinogen, horse myoglobin and on mouse myoloma IgA. A linear relationship between the ratio 3 H/ 14 C in the separated amino-terminal amino acid of the protein and the amount of protein added in the labelling mixture was obtained with standard deviations of +- 7.4%, +-3.4% and +-10.3%, respectively. An application of the method is demonstrated by measuring the increase in amino-terminal glycine in fibrinogen following the proteolytic action of thrombin. The method seems to be useful when 0.1 nmol or more of protein is used. (author)

Site-specific labeling of proteins with NMR-active unnatural amino acids

International Nuclear Information System (INIS)

Jones, David H.; Cellitti, Susan E.; Hao Xueshi; Zhang Qiong; Jahnz, Michael; Summerer, Daniel; Schultz, Peter G.; Uno, Tetsuo; Geierstanger, Bernhard H.

2010-01-01

A large number of amino acids other than the canonical amino acids can now be easily incorporated in vivo into proteins at genetically encoded positions. The technology requires an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is added to the media while a TAG amber or frame shift codon specifies the incorporation site in the protein to be studied. These unnatural amino acids can be isotopically labeled and provide unique opportunities for site-specific labeling of proteins for NMR studies. In this perspective, we discuss these opportunities including new photocaged unnatural amino acids, outline usage of metal chelating and spin-labeled unnatural amino acids and expand the approach to in-cell NMR experiments.

Quantitative proteomics by amino acid labeling in C. elegans

DEFF Research Database (Denmark)

Fredens, Julius; Engholm-Keller, Kasper; Giessing, Anders

2011-01-01

We demonstrate labeling of Caenorhabditis elegans with heavy isotope-labeled lysine by feeding them with heavy isotope-labeled Escherichia coli. Using heavy isotope-labeled worms and quantitative proteomics methods, we identified several proteins that are regulated in response to loss or RNAi-med......-mediated knockdown of the nuclear hormone receptor 49 in C. elegans. The combined use of quantitative proteomics and selective gene knockdown is a powerful tool for C. elegans biology.......We demonstrate labeling of Caenorhabditis elegans with heavy isotope-labeled lysine by feeding them with heavy isotope-labeled Escherichia coli. Using heavy isotope-labeled worms and quantitative proteomics methods, we identified several proteins that are regulated in response to loss or RNAi...

21 CFR 610.67 - Bar code label requirements.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Bar code label requirements. 610.67 Section 610.67...) BIOLOGICS GENERAL BIOLOGICAL PRODUCTS STANDARDS Labeling Standards § 610.67 Bar code label requirements. Biological products must comply with the bar code requirements at § 201.25 of this chapter. However, the bar...

Uranium Isotopic Analysis with the FRAM Isotopic Analysis Code

International Nuclear Information System (INIS)

Vo, D.T.; Sampson, T.E.

1999-01-01

FRAM is the acronym for Fixed-Energy Response-Function Analysis with Multiple efficiency. This software was developed at Los Alamos National Laboratory originally for plutonium isotopic analysis. Later, it was adapted for uranium isotopic analysis in addition to plutonium. It is a code based on a self-calibration using several gamma-ray peaks for determining the isotopic ratios. The versatile-parameter database structure governs all facets of the data analysis. User editing of the parameter sets allows great flexibility in handling data with different isotopic distributions, interfering isotopes, and different acquisition parameters such as energy calibration and detector type

Usage of burnt fuel isotopic compositions from engineering codes in Monte-Carlo code calculations

International Nuclear Information System (INIS)

Aleshin, Sergey S.; Gorodkov, Sergey S.; Shcherenko, Anna I.

2015-01-01

A burn-up calculation of VVER's cores by Monte-Carlo code is complex process and requires large computational costs. This fact makes Monte-Carlo codes usage complicated for project and operating calculations. Previously prepared isotopic compositions are proposed to use for the Monte-Carlo code (MCU) calculations of different states of VVER's core with burnt fuel. Isotopic compositions are proposed to calculate by an approximation method. The approximation method is based on usage of a spectral functionality and reference isotopic compositions, that are calculated by engineering codes (TVS-M, PERMAK-A). The multiplication factors and power distributions of FA and VVER with infinite height are calculated in this work by the Monte-Carlo code MCU using earlier prepared isotopic compositions. The MCU calculation data were compared with the data which were obtained by engineering codes.

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

Energy Technology Data Exchange (ETDEWEB)

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.

Quantitative protein expression analysis of CLL B cells from mutated and unmutated IgV(H) subgroups using acid-cleavable isotope-coded affinity tag reagents.

Science.gov (United States)

Barnidge, David R; Jelinek, Diane F; Muddiman, David C; Kay, Neil E

2005-01-01

Relative protein expression levels were compared in leukemic B cells from two patients with chronic lymphocytic leukemia (CLL) having either mutated (M-CLL) or unmutated (UM-CLL) immunoglobulin variable heavy chain genes (IgV(H)). Cells were separated into cytosol and membrane protein fractions then labeled with acid-cleavable ICAT reagents (cICAT). Labeled proteins were digested with trypsin then subjected to SCX and affinity chromatography followed by LC-ESI-MS/MS analysis on a linear ion trap mass spectrometer. A total of 9 proteins from the cytosol fraction and 4 from the membrane fraction showed a 3-fold or greater difference between M-CLL and UM-CLL and a subset of these were examined by Western blot where results concurred with cICAT abundance ratios. The abundance of one of the proteins in particular, the mitochondrial membrane protein cytochrome c oxidase subunit COX G was examined in 6 M-CLL and 6 UM-CLL patients using western blot and results showed significantly greater levels (P < 0.001) in M-CLL patients vs UM-CLL patients. These results demonstrate that stable isotope labeling and mass spectrometry can complement 2D gel electrophoresis and gene microarray technologies for identifying putative and perhaps unique prognostic markers in CLL.

Isotope labeling for NMR studies of macromolecular structure and interactions

International Nuclear Information System (INIS)

Wright, P.E.

1994-01-01

Implementation of biosynthetic methods for uniform or specific isotope labeling of proteins, coupled with the recent development of powerful heteronuclear multidimensional NMR methods, has led to a dramatic increase in the size and complexity of macromolecular systems that are now amenable to NMR structural analysis. In recent years, a new technology has emerged that combines uniform 13 C, 15 N labeling with heteronuclear multidimensional NMR methods to allow NMR structural studies of systems approaching 25 to 30 kDa in molecular weight. In addition, with the introduction of specific 13 C and 15 N labels into ligands, meaningful NMR studies of complexes of even higher molecular weight have become feasible. These advances usher in a new era in which the earlier, rather stringent molecular weight limitations have been greatly surpassed and NMR can begin to address many central biological problems that involve macromolecular structure, dynamics, and interactions

Isotope labeling for NMR studies of macromolecular structure and interactions

Energy Technology Data Exchange (ETDEWEB)

Wright, P.E. [Scripps Research Institute, La Jolla, CA (United States)

1994-12-01

Implementation of biosynthetic methods for uniform or specific isotope labeling of proteins, coupled with the recent development of powerful heteronuclear multidimensional NMR methods, has led to a dramatic increase in the size and complexity of macromolecular systems that are now amenable to NMR structural analysis. In recent years, a new technology has emerged that combines uniform {sup 13}C, {sup 15}N labeling with heteronuclear multidimensional NMR methods to allow NMR structural studies of systems approaching 25 to 30 kDa in molecular weight. In addition, with the introduction of specific {sup 13}C and {sup 15}N labels into ligands, meaningful NMR studies of complexes of even higher molecular weight have become feasible. These advances usher in a new era in which the earlier, rather stringent molecular weight limitations have been greatly surpassed and NMR can begin to address many central biological problems that involve macromolecular structure, dynamics, and interactions.

Gluconeogenesis from labeled carbon: estimating isotope dilution

International Nuclear Information System (INIS)

Kelleher, J.K.

1986-01-01

To estimate the rate of gluconeogenesis from steady-state incorporation of labeled 3-carbon precursors into glucose, isotope dilution must be considered so that the rate of labeling of glucose can be quantitatively converted to the rate of gluconeogenesis. An expression for the value of this isotope dilution can be derived using mathematical techniques and a model of the tricarboxylic acid (TCA) cycle. The present investigation employs a more complex model than that used in previous studies. This model includes the following pathways that may affect the correction for isotope dilution: 1) flux of 3-carbon precursor to the oxaloacetate pool via acetyl-CoA and the TCA cycle; 2) flux of 4- or 5-carbon compounds into the TCA cycle; 3) reversible flux between oxaloacetate (OAA) and pyruvate and between OAA and fumarate; 4) incomplete equilibrium between OAA pools; and 5) isotope dilution of 3-carbon tracers between the experimentally measured pool and the precursor for the TCA-cycle OAA pool. Experimental tests are outlined which investigators can use to determine whether these pathways are significant in a specific steady-state system. The study indicated that flux through these five pathways can significantly affect the correction for isotope dilution. To correct for the effects of these pathways an alternative method for calculating isotope dilution is proposed using citrate to relate the specific activities of acetyl-CoA and OAA

Effects of dietary energy density and digestible protein:energy ratio on de novo lipid synthesis from dietary protein in gilthead sea bream (Sparus aurata) quantified with stable isotopes

DEFF Research Database (Denmark)

Ekmann, Kim Schøn; Dalsgaard, Anne Johanne Tang; Holm, Jørgen

2013-01-01

to trace the metabolic fate of dietary protein, 1·8% fishmeal was replaced with isotope-labelled whole protein (.98% 13C). The experiment was divided into a growth period lasting 89 d, growing fish from approximately 140 to 350 g, followed by a 3 d period feeding isotope-enriched diets. Isotope ratio MS...

An economic approach to efficient isotope labeling in insect cells using homemade {sup 15}N-, {sup 13}C- and {sup 2}H-labeled yeast extracts

Energy Technology Data Exchange (ETDEWEB)

Opitz, Christian; Isogai, Shin; Grzesiek, Stephan, E-mail: Stephan.Grzesiek@unibas.ch [University of Basel, Focal Area Structural Biology and Biophysics, Biozentrum (Switzerland)

2015-07-15

Heterologous expression of proteins in insect cells is frequently used for crystallographic structural studies due to the high yields even for challenging proteins requiring the eukaryotic protein processing capabilities of the host. However for NMR studies, the need for isotope labeling poses extreme challenges in eukaryotic hosts. Here, we describe a robust method to achieve uniform protein {sup 15}N and {sup 13}C labeling of up to 90 % in baculovirus-infected insect cells. The approach is based on the production of labeled yeast extract, which is subsequently supplemented to insect cell growth media. The method also allows deuteration at levels of >60 % without decrease in expression yield. The economic implementation of the labeling procedures into a standard structural biology laboratory environment is described in a step-by-step protocol. Applications are demonstrated for a variety of NMR experiments using the Abelson kinase domain, GFP, and the beta-1 adrenergic receptor as examples. Deuterated expression of the latter provides spectra of very high quality of a eukaryotic G-protein coupled receptor.

Exploiting E. coli auxotrophs for leucine, valine, and threonine specific methyl labeling of large proteins for NMR applications

Energy Technology Data Exchange (ETDEWEB)

Monneau, Yoan R. [Rutgers University, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology (United States); Ishida, Yojiro [Rutgers University, Center for Advanced Biotechnology and Medicine (United States); Rossi, Paolo; Saio, Tomohide; Tzeng, Shiou-Ru [Rutgers University, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology (United States); Inouye, Masayori, E-mail: inouye@cabm.rutgers.edu [Rutgers University, Center for Advanced Biotechnology and Medicine (United States); Kalodimos, Charalampos G., E-mail: ckalodim@umn.edu [Rutgers University, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology (United States)

2016-06-15

A simple and cost effective method to independently and stereo-specifically incorporate [{sup 1}H,{sup 13}C]-methyls in Leu and Val in proteins is presented. Recombinant proteins for NMR studies are produced using a tailored set of auxotrophic E. coli strains. NMR active isotopes are routed to either Leu or Val methyl groups from the commercially available and scrambling-free precursors α-ketoisovalerate and acetolactate. The engineered strains produce deuterated proteins with stereospecific [{sup 1}H,{sup 13}C]-methyl labeling separately at Leu or Val amino acids. This is the first method that achieves Leu-specific stereospecific [{sup 1}H,{sup 13}C]-methyl labeling of proteins and scramble-free Val-specific labeling. Use of auxotrophs drastically decreases the amount of labeled precursor required for expression without impacting the yield. The concept is extended to Thr methyl labeling by means of a Thr-specific auxotroph that provides enhanced efficiency for use with the costly L-[4-{sup 13}C,2,3-{sup 2}H{sub 2},{sup 15}N]-Thr reagent. The Thr-specific strain allows for the production of Thr-[{sup 13}CH{sub 3}]{sup γ2} labeled protein with an optimal isotope incorporation using up to 50 % less labeled Thr than the traditional E. coli strain without the need for {sup 2}H-glycine to prevent scrambling.

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

Science.gov (United States)

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

2012-10-01

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 (T(EM)). Selective blockers constitute valuable therapeutic leads for the treatment of autoimmune diseases mediated by T(EM) 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 K(d) of 25 pM and inhibited the proliferation of human and rat T lymphocytes with a preference for T(EM) 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. Copyright © 2012 Elsevier Ltd. All rights reserved.

Isotopically labelled benzodiazepines

International Nuclear Information System (INIS)

Liebman, A.A.

1987-01-01

This paper reports on the benzodiazepines which are a class of therapeutic agents. Improvements in the analytical methodology in the areas of biochemistry and pharmacology were significant, particularly in the application of chromatographic and spectroscopic techniques. In addition, the discovery and subsequent development of tritium and carbon-14 as an analytical tool in the biological sciences were essentially post-world war II phenomena. Thus, as these new chemical entities were found to be biologically active, they could be prepared in labeled form for metabolic study, biological half-life determination (pharmacokinetics), tissue distribution study, etc. This use of tracer methodology has been liberally applied to the benzodiazepines and also more recently to the study of receptor-ligand interactions, in which tritium, carbon-11 or fluorine-18 isotopes have been used. The history of benzodiazepines as medicinal agents is indeed an interesting one; an integral part of that history is their use in just about every conceivable labeled form

Simple, rapid method for the preparation of isotopically labeled formaldehyde

Science.gov (United States)

Hooker, Jacob Matthew [Port Jefferson, NY; Schonberger, Matthias [Mains, DE; Schieferstein, Hanno [Aabergen, DE; Fowler, Joanna S [Bellport, NY

2011-10-04

Isotopically labeled formaldehyde (*C.sup..sctn.H.sub.2O) is prepared from labeled methyl iodide (*C.sup..sctn.H.sub.3I) by reaction with an oxygen nucleophile having a pendant leaving group. The mild and efficient reaction conditions result in good yields of *C.sup..sctn.H.sub.2O with little or no *C isotopic dilution. The simple, efficient production of .sup.11CH.sub.2O is described. The use of the .sup.11CH.sub.2O for the formation of positron emission tomography tracer compounds is described. The reaction can be incorporated into automated equipment available to radiochemistry laboratories. The isotopically labeled formaldehyde can be used in a variety of reactions to provide radiotracer compounds for imaging studies as well as for scintillation counting and autoradiography.

Characterization and relative quantification of phospholipids based on methylation and stable isotopic labeling[S

Science.gov (United States)

Cai, Tanxi; Shu, Qingbo; Liu, Peibin; Niu, Lili; Guo, Xiaojing; Ding, Xiang; Xue, Peng; Xie, Zhensheng; Wang, Jifeng; Zhu, Nali; Wu, Peng; Niu, Lili; Yang, Fuquan

2016-01-01

Phospholipids (PLs), one of the lipid categories, are not only the primary building blocks of cellular membranes, but also can be split to produce products that function as second messengers in signal transduction and play a pivotal role in numerous cellular processes, including cell growth, survival, and motility. Here, we present an integrated novel method that combines a fast and robust TMS-diazomethane-based phosphate derivatization and isotopic labeling strategy, which enables simultaneous profiling and relative quantification of PLs from biological samples. Our results showed that phosphate methylation allows fast and sensitive identification of the six major PL classes, including their lysophospholipid counterparts, under positive ionization mode. The isotopic labeling of endogenous PLs was achieved by deuterated diazomethane, which was generated through acid-catalyzed hydrogen/deuterium (H/D) exchange and methanolysis of TMS-diazomethane during the process of phosphate derivatization. The measured H/D ratios of unlabeled and labeled PLs, which were mixed in known proportions, indicated that the isotopic labeling strategy is capable of providing relative quantitation with adequate accuracy, reproducibility, and a coefficient of variation of 9.1%, on average. This novel method offers unique advantages over existing approaches and presents a powerful tool for research of PL metabolism and signaling. PMID:26733148

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

DEFF Research Database (Denmark)

Vinther, Jeppe; Hedegaard, Mads Marquardt; Gardner, Paul Phillip

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...

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

Science.gov (United States)

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. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Isotope effect study of κ-(BEDT-TTF)2Cu(NCS)2: Labeling in the anion

International Nuclear Information System (INIS)

Kini, A.M.; Wang, H.H.; Schlueter, J.A.

1995-01-01

Since the initial discovery of organic superconductivity in 1979, a large number of organic superconductors have now been synthesized. However, the mechanism of electron-pairing in these novel superconductors has remained largely unresolved. Isotope effect studies constitute an important experimental tool for the investigation of whether or not the electron-pairing mechanism in organic superconductors is phonon-mediated, as in conventional superconductors. Recent isotope effect studies in the authors' laboratory, involving seven different isotopically labeled BEDT-TTF (or ET) derivatives, have demonstrated the following: (1) intramolecular phonon modes involving C double-bond C and Csingle bondS stretching vibrations in the ET donor molecule are not the dominant mediators of electron-pairing, and (2) in κ-(ET) 2 Cu(NCS) 2 , there exist two competing isotope effects--a normal mass effect, i.e., lowering of T c upon isotopic labeling, when the ET molecular mass is increased by concurrent 13 C and 34 S labeling, in addition to an inverse isotope effect upon deuterium labeling in ET. It is of great interest to investigate if there is an isotope effect when the charge-compensating anions, which are also located within the non-conducting layer in the superconducting cation-radical salts, are isotopically labeled. The existence of an isotope effect when the anions are labeled would be indicative of electron-pairing with the mediation of vibrational frequencies associated with the anions. In this paper, the authors present the results of the first isotope effect study in which isotopic labeling in the anion portion of κ-(ET) 2 Cu(NCS) 2 is carried out. The authors find no isotope effect when the carbon and nitrogen atoms of the thiocyanate groups in the anion are replaced with 13 C and 15 N isotopes

Isotopic labelling with carbon-14 and tritium

International Nuclear Information System (INIS)

Evans, E.A.

1980-01-01

In this paper general methods of isotopic labelling with 14 C and with 3 H are briefly reviewed with special attention to examples of compounds likely to be of wide interest in biological research. (author)

The synthesis of a tritium, carbon-14, and stable isotope-labeled cathepsin C inhibitors.

Science.gov (United States)

Allen, Paul; Bragg, Ryan A; Caffrey, Moya; Ericsson, Cecilia; Hickey, Michael J; Kingston, Lee P; Elmore, Charles S

2017-02-01

As part of a medicinal chemistry program aimed at developing a highly potent and selective cathepsin C inhibitor, tritium, carbon-14, and stable isotope-labeled materials were required. The synthesis of tritium-labeled methanesulfonate 5 was achieved via catalytic tritiolysis of a chloro precursor, albeit at a low radiochemical purity of 67%. Tritium-labeled AZD5248 was prepared via a 3-stage synthesis, utilizing amide-directed hydrogen isotope exchange. Carbon-14 and stable isotope-labeled AZD5248 were successfully prepared through modifications of the medicinal chemistry synthetic route, enabling the use of available labeled intermediates. Copyright © 2016 John Wiley & Sons, Ltd.

NMR studies of isotopically labeled RNA

Energy Technology Data Exchange (ETDEWEB)

Pardi, A. [Univ. of Colorado, Boulder, CO (United States)

1994-12-01

In summary, the ability to generate NMR quantities of {sup 15}N and {sup 13}C-labeled RNAs has led to the development of heteronuclear multi-dimensional NMR techniques for simplifying the resonance assignment and structure determination of RNAs. These methods for synthesizing isotopically labeled RNAs are only several years old, and thus there are still relatively few applications of heteronuclear multi-dimensional NMR techniques to RNA. However, given the critical role that RNAs play in cellular function, one can expect to see an increasing number of NMR structural studies of biologically active RNAs.

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

Science.gov (United States)

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.

Site-selective 13C labeling of proteins using erythrose

International Nuclear Information System (INIS)

Weininger, Ulrich

2017-01-01

NMR-spectroscopy enables unique experimental studies on protein dynamics at atomic resolution. In order to obtain a full atom view on protein dynamics, and to study specific local processes like ring-flips, proton-transfer, or tautomerization, one has to perform studies on amino-acid side chains. A key requirement for these studies is site-selective labeling with 13 C and/or 1 H, which is achieved in the most general way by using site-selectively 13 C-enriched glucose (1- and 2- 13 C) as the carbon source in bacterial expression systems. Using this strategy, multiple sites in side chains, including aromatics, become site-selectively labeled and suitable for relaxation studies. Here we systematically investigate the use of site-selectively 13 C-enriched erythrose (1-, 2-, 3- and 4- 13 C) as a suitable precursor for 13 C labeled aromatic side chains. We quantify 13 C incorporation in nearly all sites in all 20 amino acids and compare the results to glucose based labeling. In general the erythrose approach results in more selective labeling. While there is only a minor gain for phenylalanine and tyrosine side-chains, the 13 C incorporation level for tryptophan is at least doubled. Additionally, the Phe ζ and Trp η2 positions become labeled. In the aliphatic side chains, labeling using erythrose yields isolated 13 C labels for certain positions, like Ile β and His β, making these sites suitable for dynamics studies. Using erythrose instead of glucose as a source for site-selective 13 C labeling enables unique or superior labeling for certain positions and is thereby expanding the toolbox for customized isotope labeling of amino-acid side-chains.

Testing isotopic labeling with [¹³C₆]glucose as a method of advanced glycation sites identification.

Science.gov (United States)

Kielmas, Martyna; Kijewska, Monika; Stefanowicz, Piotr; Szewczuk, Zbigniew

2012-12-01

The Maillard reaction occurring between reducing sugars and reactive amino groups of biomolecules leads to the formation of a heterogeneous mixture of compounds: early, intermediate, and advanced glycation end products (AGEs). These compounds could be markers of certain diseases and of the premature aging process. Detection of Amadori products can be performed by various methods, including MS/MS techniques and affinity chromatography on immobilized boronic acid. However, the diversity of the structures of AGEs makes detection of these compounds more difficult. The aim of this study was to test a new method of AGE identification based on isotope (13)C labeling. The model protein (hen egg lysozyme) was modified with an equimolar mixture of [(12)C(6)]glucose and [(13)C(6)]glucose and then subjected to reduction of the disulfide bridges followed by tryptic hydrolysis. The digest obtained was analyzed by LC-MS. The glycation products were identified on the basis of characteristic isotopic patterns resulting from the use of isotopically labeled glucose. This method allowed identification of 38 early Maillard reaction products and five different structures of the end glycation products. This isotopic labeling technique combined with LC-MS is a sensitive method for identification of advanced glycation end products even if their chemical structure is unknown. Copyright © 2012 Elsevier Inc. All rights reserved.

Differential Isotope Labeling of Glycopeptides for Accurate Determination of Differences in Site-Specific Glycosylation.

Science.gov (United States)

Pabst, Martin; Benešová, Iva; Fagerer, Stephan R; Jacobsen, Mathias; Eyer, Klaus; Schmidt, Gregor; Steinhoff, Robert; Krismer, Jasmin; Wahl, Fabian; Preisler, Jan; Zenobi, Renato

2016-01-04

We introduce a stable isotope labeling approach for glycopeptides that allows a specific glycosylation site in a protein to be quantitatively evaluated using mass spectrometry. Succinic anhydride is used to specifically label primary amino groups of the peptide portion of the glycopeptides. The heavy form (D4(13)C4) provides an 8 Da mass increment over the light natural form (H4(12)C4), allowing simultaneous analysis and direct comparison of two glycopeptide profiles in a single MS scan. We have optimized a protocol for an in-solution trypsin digestion, a one-pot labeling procedure, and a post-labeling solid-phase extraction to obtain purified and labeled glycopeptides. We provide the first demonstration of this approach by comparing IgG1 Fc glycopeptides from polyclonal IgG samples with respect to their galactosylation and sialylation patterns using MALDI MS and LC-ESI-MS.

Stereospecific assignments of glycine in proteins by stereospecific deuteration and {sup 15}N labeling

Energy Technology Data Exchange (ETDEWEB)

Hansen, A.P.; Curley, R.W. Jr.; Panigot, M.J.; Fesik, S.W. [Ohio State Univ., Columbus, OH (United States)

1994-12-01

Stereospecific assignments are important for accurately determining the three-dimensional structures of proteins through the use of multidimensional NMR techniques. It is especially important to stereospecifically assign the glycine {alpha}-protons in proteins because of the potential for different backbone conformations of this residue. These stereospecific assignments are critical for interpreting the {sup 3}J{sub NH,{alpha}H} coupling constants and NOEs involving the glycine {alpha}-protons that determine the conformation of this part of the protein. However, it is often difficult to unambiguously obtain the stereospecific assignments for glycine residues by using only NOE data. In this poster, we present a method for unambiguous, stereospecific assignment of the {alpha}-protons of glycine residues. This method involves synthesis of stereo-specifically deuterated and {sup 15}N-labeled Gly using a slightly modified procedure originally described by Woodard and coworkers for the stereoselective deuteration of glycine. The stereospecifically deuterated and {sup 15}N-labeled Gy has been incorporated into recombinant proteins expressed in both bacterial systems (FKBP) and mammalian cells (u-PA). Two- and three-dimensional isotope-filtered and isotope-edited NMR experiments were used to obtain the stereospecific assignments of the glycine {alpha}-protons for these proteins.

Synthesis of 14C-labeled and stable isotope-labeled CGS 16617

International Nuclear Information System (INIS)

Chaudhuri, N.K.; Markus, B.; Sung Mingsang

1988-01-01

The synthesis of a 14 C-labeled and two stable isotope-labeled analogs of CGS 16617 is described. The synthetic method involved the preparation of tetrahydro-3-bromo-1-benzazepin-2-one, labeled with a 14 C or four deuterium atoms, followed by introduction of two side chains at 1- and 3-positions. The labeled bromobenzazepinones were prepared by Beckmann rearrangement of bromo-oximes of α-tetralones, obtained by cyclization of labeled benzenebutanoic acids. The 14 C-labeled acid was prepared by hydrolysis of the nitrile, prepared by reaction of 3-bromopropylbenzene and K 14 CN. The tetradeutero acid was prepared from ethyl phenylpropynoate by catalytic reduction of the triple bond with deuterium gas, followed by reduction of the deuterated ester with lithium aluminium hydride and conversion of the resulting alcohol into the carboxylic acid. The acetic acid side chain was introduced by N-alkylation with ethyl bromoacetate or ethyl bromoacetate-1, 2- 13 C 2 followed by hydrolysis, and the L-lysine side chain, by reaction with L-(-)-3-amino-ε-caprolactam followed by hydrolysis of the caprolactam ring. (author)

Site-Specific Bioorthogonal Labeling for Fluorescence Imaging of Intracellular Proteins in Living Cells.

Science.gov (United States)

Peng, Tao; Hang, Howard C

2016-11-02

Over the past years, fluorescent proteins (e.g., green fluorescent proteins) have been widely utilized to visualize recombinant protein expression and localization in live cells. Although powerful, fluorescent protein tags are limited by their relatively large sizes and potential perturbation to protein function. Alternatively, site-specific labeling of proteins with small-molecule organic fluorophores using bioorthogonal chemistry may provide a more precise and less perturbing method. This approach involves site-specific incorporation of unnatural amino acids (UAAs) into proteins via genetic code expansion, followed by bioorthogonal chemical labeling with small organic fluorophores in living cells. While this approach has been used to label extracellular proteins for live cell imaging studies, site-specific bioorthogonal labeling and fluorescence imaging of intracellular proteins in live cells is still challenging. Herein, we systematically evaluate site-specific incorporation of diastereomerically pure bioorthogonal UAAs bearing stained alkynes or alkenes into intracellular proteins for inverse-electron-demand Diels-Alder cycloaddition reactions with tetrazine-functionalized fluorophores for live cell labeling and imaging in mammalian cells. Our studies show that site-specific incorporation of axial diastereomer of trans-cyclooct-2-ene-lysine robustly affords highly efficient and specific bioorthogonal labeling with monosubstituted tetrazine fluorophores in live mammalian cells, which enabled us to image the intracellular localization and real-time dynamic trafficking of IFITM3, a small membrane-associated protein with only 137 amino acids, for the first time. Our optimized UAA incorporation and bioorthogonal labeling conditions also enabled efficient site-specific fluorescence labeling of other intracellular proteins for live cell imaging studies in mammalian cells.

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

Science.gov (United States)

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

2015-01-01

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.

Doubly labeled water method: in vivo oxygen and hydrogen isotope fractionation

International Nuclear Information System (INIS)

Schoeller, D.A.; Leitch, C.A.; Brown, C.

1986-01-01

The accuracy and precision of the doubly labeled water method for measuring energy expenditure are influenced by isotope fractionation during evaporative water loss and CO 2 excretion. To characterize in vivo isotope fractionation, we collected and isotopically analyzed physiological fluids and gases. Breath and transcutaneous water vapor were isotopically fractionated. The degree of fractionation indicated that the former was fractionated under equilibrium control at 37 0 C, and the latter was kinetically fractionated. Sweat and urine were unfractionated. By use of isotopic balance models, the fraction of water lost via fractionating routes was estimated from the isotopic abundances of body water, local drinking water, and dietary solids. Fractionated water loss averaged 23% (SD = 10%) of water turnover, which agreed with our previous estimates based on metabolic rate, but there was a systematic difference between the results based on O 2 and hydrogen. Corrections for isotopic fractionation of water lost in breath and (nonsweat) transcutaneous loss should be made when using labeled water to measure water turnover or CO 2 production

Preparation of radioactive labelled compounds. Pt. 2. 82Br labelled organic bromine compounds by isotopic exchange

International Nuclear Information System (INIS)

Otto, R.

1988-05-01

Studies on isotopic exchange between organic bromine compounds and 82 Br labelled dioxane dibromide in the presence of AlCl 3 are described. The results obtained enable to develop a simple and quick preparation method for the labelling with 82 Br [fr

Availability of phosphorus in cow slurry using isotopic labelling technique

International Nuclear Information System (INIS)

Pongsakul, P.; Bertelsen, F.; Gissel-Nielsen, G.

1988-01-01

A pot experiment was conducted to evaluate the influence of cow slurry on P uptake by corn and to estimate the readily available P in the slurry by using an isotopic labelling techique. Water-soluble P in soil was increased and isotopic equilibrium of available P was attained after labelled slurry was mixed thoroughly throughout the soil. Labelled slurry applied at planting increased the P uptake by corn, whereas the same amount applied one week before harvest did not affect the P uptake. It was estimated that 46-54% of the total P uptake in plants is derived from the slurry. The readily available P (the L-value) in the slurry was at least 26 mg/kg which equals 3.7% of the total P. (author)

Classification-based quantitative analysis of stable isotope labeling by amino acids in cell culture (SILAC) data.

Science.gov (United States)

Kim, Seongho; Carruthers, Nicholas; Lee, Joohyoung; Chinni, Sreenivasa; Stemmer, Paul

2016-12-01

Stable isotope labeling by amino acids in cell culture (SILAC) is a practical and powerful approach for quantitative proteomic analysis. A key advantage of SILAC is the ability to simultaneously detect the isotopically labeled peptides in a single instrument run and so guarantee relative quantitation for a large number of peptides without introducing any variation caused by separate experiment. However, there are a few approaches available to assessing protein ratios and none of the existing algorithms pays considerable attention to the proteins having only one peptide hit. We introduce new quantitative approaches to dealing with SILAC protein-level summary using classification-based methodologies, such as Gaussian mixture models with EM algorithms and its Bayesian approach as well as K-means clustering. In addition, a new approach is developed using Gaussian mixture model and a stochastic, metaheuristic global optimization algorithm, particle swarm optimization (PSO), to avoid either a premature convergence or being stuck in a local optimum. Our simulation studies show that the newly developed PSO-based method performs the best among others in terms of F1 score and the proposed methods further demonstrate the ability of detecting potential markers through real SILAC experimental data. No matter how many peptide hits the protein has, the developed approach can be applicable, rescuing many proteins doomed to removal. Furthermore, no additional correction for multiple comparisons is necessary for the developed methods, enabling direct interpretation of the analysis outcomes. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms.

Science.gov (United States)

Jameson, Eleanor; Taubert, Martin; Coyotzi, Sara; Chen, Yin; Eyice, Özge; Schäfer, Hendrik; Murrell, J Colin; Neufeld, Josh D; Dumont, Marc G

2017-01-01

Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of 13 C, 18 O, or 15 N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labeled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labeled populations by targeted gene analysis. Such approaches usually involved fingerprint-based analyses or sequencing of clone libraries containing 16S rRNA genes or functional marker gene amplicons. Although molecular fingerprinting remains a valuable approach for rapid confirmation of isotope labeling, recent advances in sequencing technology mean that it is possible to obtain affordable and comprehensive amplicon profiles, metagenomes, or metatranscriptomes from SIP experiments. Not only can the abundance of microbial groups be inferred from metagenomes, but researchers can bin, assemble, and explore individual genomes to build hypotheses about the metabolic capabilities of labeled microorganisms. Analysis of labeled mRNA is a more recent advance that can provide independent metatranscriptome-based analysis of active microorganisms. The power of metatranscriptomics is that mRNA abundance often correlates closely with the corresponding activity of encoded enzymes, thus providing insight into microbial metabolism at the time of sampling. Together, these advances have improved the sensitivity of SIP methods and allow the use of labeled substrates at ecologically relevant concentrations. Particularly as methods improve and costs continue to drop, we expect that the integration of SIP with multiple omics-based methods will become prevalent components of microbial ecology studies

Mechanistic Insights into Catalytic Ethanol Steam Reforming Using Isotope-Labeled Reactants.

Science.gov (United States)

Crowley, Stephen; Castaldi, Marco J

2016-08-26

The low-temperature ethanol steam reforming (ESR) reaction mechanism over a supported Rh/Pt catalyst has been investigated using isotope-labeled EtOH and H2 O. Through strategic isotope labeling, all nonhydrogen atoms were distinct from one another, and allowed an unprecedented level of understanding of the dominant reaction pathways. All combinations of isotope- and non-isotope-labeled atoms were detected in the products, thus there are multiple pathways involved in H2 , CO, CO2 , CH4 , C2 H4 , and C2 H6 product formation. Both the recombination of C species on the surface of the catalyst and preservation of the C-C bond within ethanol are responsible for C2 product formation. Ethylene is not detected until conversion drops below 100 % at t=1.25 h. Also, quantitatively, 57 % of the observed ethylene is formed directly through ethanol dehydration. Finally there is clear evidence to show that oxygen in the SiO2 -ZrO2 support constitutes 10 % of the CO formed during the reaction. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stable isotope labelling with amino acids in cell culture for human embryonic stem cell proteomic analysis

DEFF Research Database (Denmark)

Harkness, Linda; Prokhorova, Tatyana A; Kassem, Moustapha

2012-01-01

The identification and quantitative measurements of proteins in human embryonic stem cells (hESC) is a fast growing interdisciplinary area with an enormous impact on understanding the biology of hESC and the mechanism controlling self-renewal and differentiation. Using a quantitative mass...... spectroscopic method of stable isotope labelling with amino acids during cell culture (SILAC), we are able to analyse differential expression of proteins from different cellular compartments and to identify intracellular signalling pathways involved in self-renewal and differentiation. In this chapter, we...

Synthesis of 15N isotope labeled alanine

International Nuclear Information System (INIS)

Oliveira, Claudineia R. de; Bendassolli, Jose Albertino; Sant'Ana, Carlos Roberto; Tagliassachi, Romulo Barbieri; Maximo, Everaldo; Prestes, Clelber Vieira

2005-01-01

The application of light chemical elements and their stable isotopes in biological studies have been increased over the last years. The use of 15 N labeled amino acids is an important tool for elucidation of peptides structures. This paper describe a method for the synthesis of 15 N isotope labeled alanine at lower costs than international ones, as well as the details of the recovery system of the nitrogen residues. In the present work an amination of α-haloacids, with the bromopropionic carboxylic acid and labeled aqua ammonia ( 15 NH 3 aq) was carried out. In order to avoid eventually losses of 15 NH 3 , special cares were adopted, since the production cost is high. Although the acquisition cost of the 13 N (radioactive) labeled compounds is lower, the obtained stable tracer will allow the accomplishment of important studies of the nitrogen cycling in living things, less occupational and environment hazards, and the time limitation problems in field studies. The tests took place in triplicates with NH 3 (aq) being employed. With the establishment of the system for 15 NH 3 recovery, an average of 94 % of the ammonia employed in the synthesis process was recovered. The purity of the amino acid was state determined by TLC (Thin Layer Chromatography) and HPLC (High-Performance Liquid Chromatography) with a fluorescence detector. The Rf and the retention time of the synthesized sample were similar the sigma standard. Finally, regarding the established conditions, it was possible to obtain the alanine with a production cost about 40 % lower than the international price. (author)

A Breast Cell Atlas: Organelle analysis of the MDA-MB-231 cell line by density-gradient fractionation using isotopic marking and label-free analysis

Directory of Open Access Journals (Sweden)

Marianne Sandin

2015-09-01

Full Text Available Protein translocation between organelles in the cell is an important process that regulates many cellular functions. However, organelles can rarely be isolated to purity so several methods have been developed to analyse the fractions obtained by density gradient centrifugation. We present an analysis of the distribution of proteins amongst organelles in the human breast cell line, MDA-MB-231 using two approaches: an isotopic labelling and a label-free approach.

Quantitative amino acid profiling and stable isotopically labeled amino acid tracer enrichment used for in vivo human systemic and tissue kinetics measurements

DEFF Research Database (Denmark)

Bornø, Andreas; van Hall, Gerrit

2014-01-01

An important area within clinical functional metabolomics is in vivo amino acid metabolism and protein turnover measurements for which accurate amino acid concentrations and stable isotopically labeled amino acid enrichments are mandatory not the least when tissue metabolomics is determined....... The present study describes a new sensitive liquid chromatography tandem mass-spectrometry method quantifying 20 amino acids and their tracer(s) ([ring-(13)C6]/D5Phenylalanine) in human plasma and skeletal muscle specimens. Before analysis amino acids were extracted and purified via deprotonization....../ion exchange, derivatized using a phenylisothiocyanate reagent and each amino acid was quantitated with its own stable isotopically labeled internal standard (uniformly labeled-(13)C/(15)N). The method was validated according to general recommendations for chromatographic analytical methods. The calibration...

Bacterial production of site specific {sup 13}C labeled phenylalanine and methodology for high level incorporation into bacterially expressed recombinant proteins

Energy Technology Data Exchange (ETDEWEB)

Ramaraju, Bhargavi; McFeeters, Hana; Vogler, Bernhard; McFeeters, Robert L., E-mail: robert.mcfeeters@uah.edu [University of Alabama in Huntsville, Department of Chemistry (United States)

2017-01-15

Nuclear magnetic resonance spectroscopy studies of ever larger systems have benefited from many different forms of isotope labeling, in particular, site specific isotopic labeling. Site specific {sup 13}C labeling of methyl groups has become an established means of probing systems not amenable to traditional methodology. However useful, methyl reporter sites can be limited in number and/or location. Therefore, new complementary site specific isotope labeling strategies are valuable. Aromatic amino acids make excellent probes since they are often found at important interaction interfaces and play significant structural roles. Aromatic side chains have many of the same advantages as methyl containing amino acids including distinct {sup 13}C chemical shifts and multiple magnetically equivalent {sup 1}H positions. Herein we report economical bacterial production and one-step purification of phenylalanine with {sup 13}C incorporation at the Cα, Cγ and Cε positions, resulting in two isolated {sup 1}H-{sup 13}C spin systems. We also present methodology to maximize incorporation of phenylalanine into recombinantly overexpressed proteins in bacteria and demonstrate compatibility with ILV-methyl labeling. Inexpensive, site specific isotope labeled phenylalanine adds another dimension to biomolecular NMR, opening new avenues of study.

Site-selective {sup 13}C labeling of proteins using erythrose

Energy Technology Data Exchange (ETDEWEB)

Weininger, Ulrich, E-mail: ulrich.weininger@physik.uni-halle.de [Lund University, Department of Biophysical Chemistry, Center for Molecular Protein Science (Sweden)

2017-03-15

NMR-spectroscopy enables unique experimental studies on protein dynamics at atomic resolution. In order to obtain a full atom view on protein dynamics, and to study specific local processes like ring-flips, proton-transfer, or tautomerization, one has to perform studies on amino-acid side chains. A key requirement for these studies is site-selective labeling with {sup 13}C and/or {sup 1}H, which is achieved in the most general way by using site-selectively {sup 13}C-enriched glucose (1- and 2-{sup 13}C) as the carbon source in bacterial expression systems. Using this strategy, multiple sites in side chains, including aromatics, become site-selectively labeled and suitable for relaxation studies. Here we systematically investigate the use of site-selectively {sup 13}C-enriched erythrose (1-, 2-, 3- and 4-{sup 13}C) as a suitable precursor for {sup 13}C labeled aromatic side chains. We quantify {sup 13}C incorporation in nearly all sites in all 20 amino acids and compare the results to glucose based labeling. In general the erythrose approach results in more selective labeling. While there is only a minor gain for phenylalanine and tyrosine side-chains, the {sup 13}C incorporation level for tryptophan is at least doubled. Additionally, the Phe ζ and Trp η2 positions become labeled. In the aliphatic side chains, labeling using erythrose yields isolated {sup 13}C labels for certain positions, like Ile β and His β, making these sites suitable for dynamics studies. Using erythrose instead of glucose as a source for site-selective {sup 13}C labeling enables unique or superior labeling for certain positions and is thereby expanding the toolbox for customized isotope labeling of amino-acid side-chains.

Quantitative Proteomics Analysis of VEGF-Responsive Endothelial Protein S-Nitrosylation Using Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and LC-MS/MS.

Science.gov (United States)

Zhang, Hong-Hai; Lechuga, Thomas J; Chen, Yuezhou; Yang, Yingying; Huang, Lan; Chen, Dong-Bao

2016-05-01

Adduction of a nitric oxide moiety (NO•) to cysteine(s), termed S-nitrosylation (SNO), is a novel mechanism for NO to regulate protein function directly. However, the endothelial SNO-protein network that is affected by endogenous and exogenous NO is obscure. This study was designed to develop a quantitative proteomics approach using stable isotope labeling by amino acids in cell culture for comparing vascular endothelial growth factor (VEGFA)- and NO donor-responsive endothelial nitroso-proteomes. Primary placental endothelial cells were labeled with "light" (L-(12)C6 (14)N4-Arg and L-(12)C6 (14)N2-Lys) or "heavy" (L-(13)C6 (15)N4-Arg and L-(13)C6 (15)N2-Lys) amino acids. The light cells were treated with an NO donor nitrosoglutathione (GSNO, 1 mM) or VEGFA (10 ng/ml) for 30 min, while the heavy cells received vehicle as control. Equal amounts of cellular proteins from the light (GSNO or VEGFA treated) and heavy cells were mixed for labeling SNO-proteins by the biotin switch technique and then trypsin digested. Biotinylated SNO-peptides were purified for identifying SNO-proteins by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Ratios of light to heavy SNO-peptides were calculated for determining the changes of the VEGFA- and GSNO-responsive endothelial nitroso-proteomes. A total of 387 light/heavy pairs of SNO-peptides were identified, corresponding to 213 SNO-proteins that include 125 common and 27 VEGFA- and 61 GSNO-responsive SNO-proteins. The specific SNO-cysteine(s) in each SNO-protein were simultaneously identified. Pathway analysis revealed that SNO-proteins are involved in various endothelial functions, including proliferation, motility, metabolism, and protein synthesis. We collectively conclude that endogenous NO on VEGFA stimulation and exogenous NO from GSNO affect common and different SNO-protein networks, implicating SNO as a critical mechanism for VEGFA stimulation of angiogenesis. © 2016 by the Society for the Study of Reproduction

Subcellular SIMS imaging of isotopically labeled amino acids in cryogenically prepared cells

International Nuclear Information System (INIS)

Chandra, Subhash

2004-01-01

Ion microscopy is a potentially powerful technique for localization of isotopically labeled molecules. In this study, L-arginine and phenylalanine amino acids labeled with stable isotopes 13 C and 15 N were localized in cultured cells with the ion microscope at 500 nm spatial resolution. Cells were exposed to the labeled amino acids and cryogenically prepared. SIMS analyses were made in fractured freeze-dried cells. A dynamic distribution was observed from labeled arginine-treated LLC-PK 1 kidney cells at mass 28 ( 13 C 15 N) in negative secondaries, revealing cell-to-cell heterogeneity and preferential accumulation of the amino acid (or its metabolite) in the nucleus and nucleolus of some cells. The smaller nucleolus inside the nucleus was clearly resolved in SIMS images and confirmed by correlative light microscopy. The distribution of labeled phenylalanine contrasted with arginine as it was rather homogeneously distributed in T98G human glioblastoma cells. Images of 39 K, 23 Na and 40 Ca were also recorded to confirm the reliability of sample preparation and authenticity of the observed amino acid distributions. These observations indicate that SIMS techniques can provide a valuable technology for subcellular localization of nitrogen-containing molecules in proteomics since nitrogen does not have a radionuclide tracer isotope. Amino acids labeled with stable isotopes can be used as tracers for studying their transport and metabolism in distinct subcellular compartments with SIMS. Further studies of phenylalanine uptake in human glioblastoma cells may have special significance in boron neutron capture therapy (BNCT) as a boron analogue of phenylalanine, boronophenylalanine is a clinically approved compound for the treatment of brain tumors

Subcellular SIMS imaging of isotopically labeled amino acids in cryogenically prepared cells

Energy Technology Data Exchange (ETDEWEB)

Chandra, Subhash

2004-06-15

Ion microscopy is a potentially powerful technique for localization of isotopically labeled molecules. In this study, L-arginine and phenylalanine amino acids labeled with stable isotopes {sup 13}C and {sup 15}N were localized in cultured cells with the ion microscope at 500 nm spatial resolution. Cells were exposed to the labeled amino acids and cryogenically prepared. SIMS analyses were made in fractured freeze-dried cells. A dynamic distribution was observed from labeled arginine-treated LLC-PK{sub 1} kidney cells at mass 28 ({sup 13}C{sup 15}N) in negative secondaries, revealing cell-to-cell heterogeneity and preferential accumulation of the amino acid (or its metabolite) in the nucleus and nucleolus of some cells. The smaller nucleolus inside the nucleus was clearly resolved in SIMS images and confirmed by correlative light microscopy. The distribution of labeled phenylalanine contrasted with arginine as it was rather homogeneously distributed in T98G human glioblastoma cells. Images of {sup 39}K, {sup 23}Na and {sup 40}Ca were also recorded to confirm the reliability of sample preparation and authenticity of the observed amino acid distributions. These observations indicate that SIMS techniques can provide a valuable technology for subcellular localization of nitrogen-containing molecules in proteomics since nitrogen does not have a radionuclide tracer isotope. Amino acids labeled with stable isotopes can be used as tracers for studying their transport and metabolism in distinct subcellular compartments with SIMS. Further studies of phenylalanine uptake in human glioblastoma cells may have special significance in boron neutron capture therapy (BNCT) as a boron analogue of phenylalanine, boronophenylalanine is a clinically approved compound for the treatment of brain tumors.

Modification degrees at specific sites on heparan sulphate: an approach to measure chemical modifications on biological molecules with stable isotope labelling

Science.gov (United States)

Wu, Zhengliang L.; Lech, Miroslaw

2005-01-01

Chemical modification of biological molecules is a general mechanism for cellular regulation. A quantitative approach has been developed to measure the extent of modification on HS (heparan sulphates). Sulphation on HS by sulphotransferases leads to variable sulphation levels, which allows cells to tune their affinities to various extracellular proteins, including growth factors. With stable isotope labelling and HPLC-coupled MS, modification degrees at various O-sulphation sites could be determined. A bovine kidney HS sample was first saturated in vitro with 34S by an OST (O-sulphotransferase), then digested with nitrous acid and analysed with HPLC-coupled MS. The 34S-labelled oligosaccharides were identified based on their unique isotope clusters. The modification degrees at the sulphotransferase recognition sites were obtained by calculating the intensities of isotopic peaks in the isotope clusters. The modification degrees at 3-OST-1 and 6-OST-1 sites were examined in detail. This approach can also be used to study other types of chemical modifications on biological molecules. PMID:15743272

Formation of Hydroxymethyl DNA Adducts in Rats Orally Exposed to Stable Isotope Labeled Methanol

Science.gov (United States)

Lu, Kun; Gul, Husamettin; Upton, Patricia B.; Moeller, Benjamin C.; Swenberg, James A.

2012-01-01

Methanol is a large volume industrial chemical and widely used solvent and fuel additive. Methanol’s well known toxicity and use in a wide spectrum of applications has raised long-standing environmental issues over its safety, including its carcinogenicity. Methanol has not been listed as a carcinogen by any regulatory agency; however, there are debates about its carcinogenic potential. Formaldehyde, a metabolite of methanol, has been proposed to be responsible for the carcinogenesis of methanol. Formaldehyde is a known carcinogen and actively targets DNA and protein, causing diverse DNA and protein damage. However, formaldehyde-induced DNA adducts arising from the metabolism of methanol have not been reported previously, largely due to the absence of suitable DNA biomarkers and the inability to differentiate what was due to methanol compared with the substantial background of endogenous formaldehyde. Recently, we developed a unique approach combining highly sensitive liquid chromatography-mass spectrometry methods and exposure to stable isotope labeled chemicals to simultaneously quantify formaldehyde-specific endogenous and exogenous DNA adducts. In this study, rats were exposed daily to 500 or 2000 mg/kg [13CD4]-methanol by gavage for 5 days. Our data demonstrate that labeled formaldehyde arising from [13CD4]-methanol induced hydroxymethyl DNA adducts in multiple tissues in a dose-dependent manner. The results also demonstrated that the number of exogenous DNA adducts was lower than the number of endogenous hydroxymethyl DNA adducts in all tissues of rats administered 500 mg/kg per day for 5 days, a lethal dose to humans, even after incorporating an average factor of 4 for reduced metabolism due to isotope effects of deuterium-labeled methanol into account. PMID:22157354

Rapid label-free profiling of oral cancer biomarker proteins using nano-UPLC-Q-TOF ion mobility mass spectrometry.

Science.gov (United States)

Nassar, Ala F; Williams, Brad J; Yaworksy, Dustin C; Patel, Vyomesh; Rusling, James F

2016-03-01

It has become quite clear that single cancer biomarkers cannot in general provide high sensitivity and specificity for reliable clinical cancer diagnostics. This paper explores the feasibility of rapid detection of multiple biomarker proteins in model oral cancer samples using label-free protein relative quantitation. MS-based label-free quantitative proteomics offer a rapid alternative that bypasses the need for stable isotope containing compounds to chemically bind and label proteins. Total protein content in oral cancer cell culture conditioned media was precipitated, subjected to proteolytic digestion, and then analyzed using a nano-UPLC (where UPLC is ultra-performance liquid chromatography) coupled to a hybrid Q-Tof ion-mobility mass spectrometry (MS). Rapid, simultaneous identification and quantification of multiple possible cancer biomarker proteins was achieved. In a comparative study between cancer and noncancer samples, approximately 952 proteins were identified using a high-throughput 1D ion mobility assisted data independent acquisition (IM-DIA) approach. As we previously demonstrated that interleukin-8 (IL-8) and vascular endothelial growth factor A (VEGF-A) were readily detected in oral cancer cell conditioned media(1), we targeted these biomarker proteins to validate our approach. Target biomarker protein IL-8 was found between 3.5 and 8.8 fmol, while VEGF-A was found at 1.45 fmol in the cancer cell media. Overall, our data suggest that the nano-UPLC-IM-DIA bioassay is a feasible approach to identify and quantify proteins in complex samples without the need for stable isotope labeling. These results have significant implications for rapid tumor diagnostics and prognostics by monitoring proteins such as IL-8 and VEGF-A implicated in cancer development and progression. The analysis in tissue or plasma is not possible at this time, but the subsequent work would be needed for validation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A free-air system for long-term stable carbon isotope labeling of adult forest trees

Science.gov (United States)

Stable carbon (C) isotopes, in particular employed in labeling experiments, are an ideal tool to broaden our understanding of C dynamics in trees and forest ecosystems. Here, we present a free-air exposure system, named isoFACE, designed for long-term stable C isotope labeling in...

Quantitative Proteomics Analysis of VEGF-Responsive Endothelial Protein S-Nitrosylation Using Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and LC-MS/MS1

Science.gov (United States)

Zhang, Hong-Hai; Lechuga, Thomas J.; Chen, Yuezhou; Yang, Yingying; Huang, Lan; Chen, Dong-Bao

2016-01-01

Adduction of a nitric oxide moiety (NO•) to cysteine(s), termed S-nitrosylation (SNO), is a novel mechanism for NO to regulate protein function directly. However, the endothelial SNO-protein network that is affected by endogenous and exogenous NO is obscure. This study was designed to develop a quantitative proteomics approach using stable isotope labeling by amino acids in cell culture for comparing vascular endothelial growth factor (VEGFA)- and NO donor-responsive endothelial nitroso-proteomes. Primary placental endothelial cells were labeled with “light” (L-12C614N4-Arg and L-12C614N2-Lys) or “heavy” (L-13C615N4-Arg and L-13C615N2-Lys) amino acids. The light cells were treated with an NO donor nitrosoglutathione (GSNO, 1 mM) or VEGFA (10 ng/ml) for 30 min, while the heavy cells received vehicle as control. Equal amounts of cellular proteins from the light (GSNO or VEGFA treated) and heavy cells were mixed for labeling SNO-proteins by the biotin switch technique and then trypsin digested. Biotinylated SNO-peptides were purified for identifying SNO-proteins by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Ratios of light to heavy SNO-peptides were calculated for determining the changes of the VEGFA- and GSNO-responsive endothelial nitroso-proteomes. A total of 387 light/heavy pairs of SNO-peptides were identified, corresponding to 213 SNO-proteins that include 125 common and 27 VEGFA- and 61 GSNO-responsive SNO-proteins. The specific SNO-cysteine(s) in each SNO-protein were simultaneously identified. Pathway analysis revealed that SNO-proteins are involved in various endothelial functions, including proliferation, motility, metabolism, and protein synthesis. We collectively conclude that endogenous NO on VEGFA stimulation and exogenous NO from GSNO affect common and different SNO-protein networks, implicating SNO as a critical mechanism for VEGFA stimulation of angiogenesis. PMID:27075618

Differential profiling of breast cancer plasma proteome by isotope-coded affinity tagging method reveals biotinidase as a breast cancer biomarker

International Nuclear Information System (INIS)

Kang, Un-Beom; Ahn, Younghee; Lee, Jong Won; Kim, Yong-Hak; Kim, Joon; Yu, Myeong-Hee; Noh, Dong-Young; Lee, Cheolju

2010-01-01

Breast cancer is one of the leading causes of women's death worldwide. It is important to discover a reliable biomarker for the detection of breast cancer. Plasma is the most ideal source for cancer biomarker discovery since many cells cross-communicate through the secretion of soluble proteins into blood. Plasma proteomes obtained from 6 breast cancer patients and 6 normal healthy women were analyzed by using the isotope-coded affinity tag (ICAT) labeling approach and tandem mass spectrometry. All the plasma samples used were depleted of highly abundant 6 plasma proteins by immune-affinity column chromatography before ICAT labeling. Several proteins showing differential abundance level were selected based on literature searches and their specificity to the commercially available antibodies, and then verified by immunoblot assays. A total of 155 proteins were identified and quantified by ICAT method. Among them, 33 proteins showed abundance changes by more than 1.5-fold between the plasmas of breast cancer patients and healthy women. We chose 5 proteins for the follow-up confirmation in the individual plasma samples using immunoblot assay. Four proteins, α1-acid glycoprotein 2, monocyte differentiation antigen CD14, biotinidase (BTD), and glutathione peroxidase 3, showed similar abundance ratio to ICAT result. Using a blind set of plasmas obtained from 21 breast cancer patients and 21 normal healthy controls, we confirmed that BTD was significantly down-regulated in breast cancer plasma (Wilcoxon rank-sum test, p = 0.002). BTD levels were lowered in all cancer grades (I-IV) except cancer grade zero. The area under the receiver operating characteristic curve of BTD was 0.78. Estrogen receptor status (p = 0.940) and progesterone receptor status (p = 0.440) were not associated with the plasma BTD levels. Our study suggests that BTD is a potential serological biomarker for the detection of breast cancer

The choice of label and measurement technique in tracer studies of body protein metabolism in man

International Nuclear Information System (INIS)

James, W.P.T.; Sender, P.M.; Garlick, P.J.; Waterlow, J.C.

1975-01-01

The turnover of non-serum proteins in man has had limited study despite the physiological importance of maintaining the balance between synthesis and breakdown of body proteins. Body protein is usually considered as a single pool and breakdown rates are often measured by monitoring excreted label at intervals after pulse labelling with radioactive or 15 N amino acids. No label has yet been used for measuring tissue protein breakdown in man which is free from the major problem of label re-utilization. All measurements of breakdown rates, eg. with 75 Se-selenomethionine, 15 N- or 14 C-glycine, give rate constants which are too low. The heterogeneity of body proteins also means that an estimate of the weighted average breakdown rate can only be obtained after following the excretion of isotope for a long period, perhaps of the order of 3-4 half-lives which, for man, would be 100 days after labelling. We therefore use infusions with either 14 C- or 15 N-labelled amino acids to measure breakdown and synthesis rates: these values are less affected by problems of protein heterogeneity. Single injection techniques are subject to more error than constant infusions of label because of the difficulty of defining the precursor activity. 15 N labelling need not be confined to essential amino acids if total protein rather than amino acid turnover is studied: the latter involves measurements of the labelled amino acid itself which is difficult with 15 N because of the small amounts of free amino acid nitrogen available. Carbon labelling of non-essential amino acids is unsuitable for studies of protein turnover and the choice of the position of the label on the molecule is important when labelled essential amino acids are employed. Short-term changes in protein metabolism are evaluated better with amino acids with a small pool size; the equilibration time in the excretory bicarbonate pool is also shorter than in the urea pool so that 15 N is less useful than carbon labelling. We

Measuring protein synthesis using metabolic ²H labeling, high-resolution mass spectrometry, and an algorithm.

Science.gov (United States)

Kasumov, Takhar; Ilchenko, Serguey; Li, Ling; Rachdaoui, Nadia; Sadygov, Rovshan G; Willard, Belinda; McCullough, Arthur J; Previs, Stephen

2011-05-01

We recently developed a method for estimating protein dynamics in vivo with heavy water ((2)H(2)O) using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) [16], and we confirmed that (2)H labeling of many hepatic free amino acids rapidly equilibrated with body water. Although this is a reliable method, it required modest sample purification and necessitated the determination of tissue-specific amino acid labeling. Another approach for quantifying protein kinetics is to measure the (2)H enrichments of body water (precursor) and protein-bound amino acid or proteolytic peptide (product) and to estimate how many copies of deuterium are incorporated into a product. In the current study, we used nanospray linear trap Fourier transform ion cyclotron resonance mass spectrometry (LTQ FT-ICR MS) to simultaneously measure the isotopic enrichment of peptides and protein-bound amino acids. A mathematical algorithm was developed to aid the data processing. The most notable improvement centers on the fact that the precursor/product labeling ratio can be obtained by measuring the labeling of water and a protein (or peptide) of interest, thereby minimizing the need to measure the amino acid labeling. As a proof of principle, we demonstrate that this approach can detect the effect of nutritional status on albumin synthesis in rats given (2)H(2)O. Copyright © 2011 Elsevier Inc. All rights reserved.

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

KAUST Repository

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.

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

KAUST Repository

Wang, Songlin

2015-04-09

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.

Evaluation of stable isotope labelling strategies for the quantitation of CP4 EPSPS in genetically modified soya

Energy Technology Data Exchange (ETDEWEB)

Ocana, Mireia Fernandez [Centre for Chemical and Bioanalytical Sciences, Royal Holloway, University of London, Egham TW20 0EX (United Kingdom)], E-mail: Mireia.FernandezOcana@pfizer.com; Fraser, Paul D. [Centre for Chemical and Bioanalytical Sciences, Royal Holloway, University of London, Egham TW20 0EX (United Kingdom); Patel, Raj K.P.; Halket, John M. [Specialist Bioanalytical Services Ltd., Royal Holloway, University of London, Egham TW20 0EX (United Kingdom); Bramley, Peter M. [Centre for Chemical and Bioanalytical Sciences, Royal Holloway, University of London, Egham TW20 0EX (United Kingdom)

2009-02-16

The introduction of genetically modified (GM) crops into the market has raised a general alertness relating to the control and safety of foods. The applicability of protein separation hyphenated to mass spectrometry to identify the bacterial enolpyruvylshikimate-3-phosphate synthase (CP4 EPSPS) protein expressed in GM crops has been previously reported [M.F. Ocana, P.D. Fraser, R.K.P. Patel, J.M. Halket, P.M. Bramley, Rapid Commun. Mass Spectrom. 21 (2007) 319.]. Herein, we investigate the suitability of two strategies that employ heavy stable isotopes, i.e. AQUA and iTRAQ, to quantify different levels of CP4 EPSPS in up to four GM preparations. Both quantification strategies showed potential to determine whether the presence of GM material is above the limits established by the European Union. The AQUA quantification procedure involved protein solubilisation/fractionation and subsequent separation using SDS-PAGE. A segment of the gel in which the protein of interest was located was excised, the stable isotope labeled peptide added at a known concentration and proteolytic digestion initiated. Following recovery of the peptides, on-line separation and detection using LC-MS was carried out. A similar approach was used for the iTRAQ workflow with the exception that proteins were digested in solution and generated tryptic peptides were chemically tagged. Both procedures demonstrated the potential for quantitative detection at 0.5% (w/w) GM soya which is a level below the current European Union's threshold for food-labelling. In this context, a comparison between the two procedures is provided within the present study.

Evaluation of stable isotope labelling strategies for the quantitation of CP4 EPSPS in genetically modified soya

International Nuclear Information System (INIS)

Ocana, Mireia Fernandez; Fraser, Paul D.; Patel, Raj K.P.; Halket, John M.; Bramley, Peter M.

2009-01-01

The introduction of genetically modified (GM) crops into the market has raised a general alertness relating to the control and safety of foods. The applicability of protein separation hyphenated to mass spectrometry to identify the bacterial enolpyruvylshikimate-3-phosphate synthase (CP4 EPSPS) protein expressed in GM crops has been previously reported [M.F. Ocana, P.D. Fraser, R.K.P. Patel, J.M. Halket, P.M. Bramley, Rapid Commun. Mass Spectrom. 21 (2007) 319.]. Herein, we investigate the suitability of two strategies that employ heavy stable isotopes, i.e. AQUA and iTRAQ, to quantify different levels of CP4 EPSPS in up to four GM preparations. Both quantification strategies showed potential to determine whether the presence of GM material is above the limits established by the European Union. The AQUA quantification procedure involved protein solubilisation/fractionation and subsequent separation using SDS-PAGE. A segment of the gel in which the protein of interest was located was excised, the stable isotope labeled peptide added at a known concentration and proteolytic digestion initiated. Following recovery of the peptides, on-line separation and detection using LC-MS was carried out. A similar approach was used for the iTRAQ workflow with the exception that proteins were digested in solution and generated tryptic peptides were chemically tagged. Both procedures demonstrated the potential for quantitative detection at 0.5% (w/w) GM soya which is a level below the current European Union's threshold for food-labelling. In this context, a comparison between the two procedures is provided within the present study

DeuteRater: a tool for quantifying peptide isotope precision and kinetic proteomics.

Science.gov (United States)

Naylor, Bradley C; Porter, Michael T; Wilson, Elise; Herring, Adam; Lofthouse, Spencer; Hannemann, Austin; Piccolo, Stephen R; Rockwood, Alan L; Price, John C

2017-05-15

Using mass spectrometry to measure the concentration and turnover of the individual proteins in a proteome, enables the calculation of individual synthesis and degradation rates for each protein. Software to analyze concentration is readily available, but software to analyze turnover is lacking. Data analysis workflows typically don't access the full breadth of information about instrument precision and accuracy that is present in each peptide isotopic envelope measurement. This method utilizes both isotope distribution and changes in neutromer spacing, which benefits the analysis of both concentration and turnover. We have developed a data analysis tool, DeuteRater, to measure protein turnover from metabolic D 2 O labeling. DeuteRater uses theoretical predictions for label-dependent change in isotope abundance and inter-peak (neutromer) spacing within the isotope envelope to calculate protein turnover rate. We have also used these metrics to evaluate the accuracy and precision of peptide measurements and thereby determined the optimal data acquisition parameters of different instruments, as well as the effect of data processing steps. We show that these combined measurements can be used to remove noise and increase confidence in the protein turnover measurement for each protein. Source code and ReadMe for Python 2 and 3 versions of DeuteRater are available at https://github.com/JC-Price/DeuteRater . Data is at https://chorusproject.org/pages/index.html project number 1147. Critical Intermediate calculation files provided as Tables S3 and S4. Software has only been tested on Windows machines. jcprice@chem.byu.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

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

Science.gov (United States)

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

2012-11-21

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 β-sheets. Using a synthetic macrocycle that enforces a two stranded parallel β-sheet conformation, we measured the lifetimes and frequency for six combinations of doubly (13)C═(18)O labeled amide I modes using 2D IR spectroscopy. The average vibrational lifetime of the isotope labeled residues was 550 fs. The frequencies 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 line widths and frequencies nearly quantitatively. Historically, the characteristic features of β-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 β-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) line width. Narrower line widths indicate that the amide I backbone is solvent

Labeling proteins on live mammalian cells using click chemistry.

Science.gov (United States)

Nikić, Ivana; Kang, Jun Hee; Girona, Gemma Estrada; Aramburu, Iker Valle; Lemke, Edward A

2015-05-01

We describe a protocol for the rapid labeling of cell-surface proteins in living mammalian cells using click chemistry. The labeling method is based on strain-promoted alkyne-azide cycloaddition (SPAAC) and strain-promoted inverse-electron-demand Diels-Alder cycloaddition (SPIEDAC) reactions, in which noncanonical amino acids (ncAAs) bearing ring-strained alkynes or alkenes react, respectively, with dyes containing azide or tetrazine groups. To introduce ncAAs site specifically into a protein of interest (POI), we use genetic code expansion technology. The protocol can be described as comprising two steps. In the first step, an Amber stop codon is introduced--by site-directed mutagenesis--at the desired site on the gene encoding the POI. This plasmid is then transfected into mammalian cells, along with another plasmid that encodes an aminoacyl-tRNA synthetase/tRNA (RS/tRNA) pair that is orthogonal to the host's translational machinery. In the presence of the ncAA, the orthogonal RS/tRNA pair specifically suppresses the Amber codon by incorporating the ncAA into the polypeptide chain of the POI. In the second step, the expressed POI is labeled with a suitably reactive dye derivative that is directly supplied to the growth medium. We provide a detailed protocol for using commercially available ncAAs and dyes for labeling the insulin receptor, and we discuss the optimal surface-labeling conditions and the limitations of labeling living mammalian cells. The protocol involves an initial cloning step that can take 4-7 d, followed by the described transfections and labeling reaction steps, which can take 3-4 d.

[Solid state isotope hydrogen exchange for deuterium and tritium in human gene-engineered insulin].

Science.gov (United States)

Zolotarev, Yu A; Dadayan, A K; Kozik, V S; Gasanov, E V; Nazimov, I V; Ziganshin, R Kh; Vaskovsky, B V; Murashov, A N; Ksenofontov, A L; Haribin, O N; Nikolaev, E N; Myasoedov, N F

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 β-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 β-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.

Can infrared spectroscopy provide information on protein-protein interactions?

Science.gov (United States)

Haris, Parvez I

2010-08-01

For most biophysical techniques, characterization of protein-protein interactions is challenging; this is especially true with methods that rely on a physical phenomenon that is common to both of the interacting proteins. Thus, for example, in IR spectroscopy, the carbonyl vibration (1600-1700 cm(-1)) associated with the amide bonds from both of the interacting proteins will overlap extensively, making the interpretation of spectral changes very complicated. Isotope-edited infrared spectroscopy, where one of the interacting proteins is uniformly labelled with (13)C or (13)C,(15)N has been introduced as a solution to this problem, enabling the study of protein-protein interactions using IR spectroscopy. The large shift of the amide I band (approx. 45 cm(-1) towards lower frequency) upon (13)C labelling of one of the proteins reveals the amide I band of the unlabelled protein, enabling it to be used as a probe for monitoring conformational changes. With site-specific isotopic labelling, structural resolution at the level of individual amino acid residues can be achieved. Furthermore, the ability to record IR spectra of proteins in diverse environments means that isotope-edited IR spectroscopy can be used to structurally characterize difficult systems such as protein-protein complexes bound to membranes or large insoluble peptide/protein aggregates. In the present article, examples of application of isotope-edited IR spectroscopy for studying protein-protein interactions are provided.

Monte-Carlo code calculation of 3D reactor core model with usage of burnt fuel isotopic compositions, obtained by engineering codes

Energy Technology Data Exchange (ETDEWEB)

Aleshin, Sergey S.; Gorodkov, Sergey S.; Shcherenko, Anna I. [National Research Centre ' Kurchatov Institute' , Moscow (Russian Federation)

2016-09-15

A burn-up calculation of large systems by Monte-Carlo code (MCU) is complex process and it requires large computational costs. Previously prepared isotopic compositions are proposed to be used for the Monte-Carlo code calculations of different system states with burnt fuel. Isotopic compositions are calculated by an approximation method. The approximation method is based on usage of a spectral functionality and reference isotopic compositions, that are calculated by the engineering codes (TVS-M, BIPR-7A and PERMAK-A). The multiplication factors and power distributions of FAs from a 3-D reactor core are calculated in this work by the Monte-Carlo code MCU using earlier prepared isotopic compositions. The separate conditions of the burnt core are observed. The results of MCU calculations were compared with those that were obtained by engineering codes.

Label and Label-Free Detection Techniques for Protein Microarrays

Directory of Open Access Journals (Sweden)

Amir Syahir

2015-04-01

Full Text Available Protein microarray technology has gone through numerous innovative developments in recent decades. In this review, we focus on the development of protein detection methods embedded in the technology. Early microarrays utilized useful chromophores and versatile biochemical techniques dominated by high-throughput illumination. Recently, the realization of label-free techniques has been greatly advanced by the combination of knowledge in material sciences, computational design and nanofabrication. These rapidly advancing techniques aim to provide data without the intervention of label molecules. Here, we present a brief overview of this remarkable innovation from the perspectives of label and label-free techniques in transducing nano‑biological events.

Isotopic Changes During Digestion: Protein

Science.gov (United States)

Tuross, N.

2013-12-01

Nutrient and hydrological inputs traverse a complicated route of pH, enzymatic and cellular processes in digestion in higher animals. The end products of digestion are the starting products for biosynthesis that are often used to interpret past life-ways. Using an artificial gut system, the isotopic changes (dD, d18O, d13C and d15N) of protein are documented. Three separate protein sources are subjected to the conditions, chemical and enzymatic, found in the stomach and upper small intestine with only a small shift in the oxygen isotopic composition of the proteins observed. Middle to lower small intestine parameters produced both greater isotopic effects and significantly lower molecular weight products. The role of the gastric enterocyte and the likely involvement of the internal milieu of this cell in the isotopic composition of amino acids that are transported to the liver are reported.

Temporal Profiling and Pulsed SILAC Labeling Identify Novel Secreted Proteins During Ex Vivo Osteoblast Differentiation of Human Stromal Stem Cells*

Science.gov (United States)

Kristensen, Lars P.; Chen, Li; Nielsen, Maria Overbeck; Qanie, Diyako W.; Kratchmarova, Irina; Kassem, Moustapha; Andersen, Jens S.

2012-01-01

It is well established that bone forming cells (osteoblasts) secrete proteins with autocrine, paracrine, and endocrine function. However, the identity and functional role for the majority of these secreted and differentially expressed proteins during the osteoblast (OB) differentiation process, is not fully established. To address these questions, we quantified the temporal dynamics of the human stromal (mesenchymal, skeletal) stem cell (hMSC) secretome during ex vivo OB differentiation using stable isotope labeling by amino acids in cell culture (SILAC). In addition, we employed pulsed SILAC labeling to distinguish genuine secreted proteins from intracellular contaminants. We identified 466 potentially secreted proteins that were quantified at 5 time-points during 14-days ex vivo OB differentiation including 41 proteins known to be involved in OB functions. Among these, 315 proteins exhibited more than 2-fold up or down-regulation. The pulsed SILAC method revealed a strong correlation between the fraction of isotope labeling and the subset of proteins known to be secreted and involved in OB differentiation. We verified SILAC data using qRT-PCR analysis of 9 identified potential novel regulators of OB differentiation. Furthermore, we studied the biological effects of one of these proteins, the hormone stanniocalcin 2 (STC2) and demonstrated its autocrine effects in enhancing osteoblastic differentiation of hMSC. In conclusion, combining complete and pulsed SILAC labeling facilitated the identification of novel factors produced by hMSC with potential role in OB differentiation. Our study demonstrates that the secretome of osteoblastic cells is more complex than previously reported and supports the emerging evidence that osteoblastic cells secrete proteins with endocrine functions and regulate cellular processes beyond bone formation. PMID:22801418

Direct methods and residue type specific isotope labeling in NMR structure determination and model-driven sequential assignment

International Nuclear Information System (INIS)

Schedlbauer, Andreas; Auer, Renate; Ledolter, Karin; Tollinger, Martin; Kloiber, Karin; Lichtenecker, Roman; Ruedisser, Simon; Hommel, Ulrich; Schmid, Walther; Konrat, Robert; Kontaxis, Georg

2008-01-01

Direct methods in NMR based structure determination start from an unassigned ensemble of unconnected gaseous hydrogen atoms. Under favorable conditions they can produce low resolution structures of proteins. Usually a prohibitively large number of NOEs is required, to solve a protein structure ab-initio, but even with a much smaller set of distance restraints low resolution models can be obtained which resemble a protein fold. One problem is that at such low resolution and in the absence of a force field it is impossible to distinguish the correct protein fold from its mirror image. In a hybrid approach these ambiguous models have the potential to aid in the process of sequential backbone chemical shift assignment when 13 C β and 13 C' shifts are not available for sensitivity reasons. Regardless of the overall fold they enhance the information content of the NOE spectra. These, combined with residue specific labeling and minimal triple-resonance data using 13 C α connectivity can provide almost complete sequential assignment. Strategies for residue type specific labeling with customized isotope labeling patterns are of great advantage in this context. Furthermore, this approach is to some extent error-tolerant with respect to data incompleteness, limited precision of the peak picking, and structural errors caused by misassignment of NOEs

Quantitative imaging of subcellular metabolism with stable isotopes and multi-isotope imaging mass spectrometry

Science.gov (United States)

Steinhauser, Matthew L.; Lechene, Claude P.

2014-01-01

Multi-isotope imaging mass spectrometry (MIMS) is the quantitative imaging of stable isotope labels in cells with a new type of secondary ion mass spectrometer (NanoSIMS). The power of the methodology is attributable to (i) the immense advantage of using non-toxic stable isotope labels, (ii) high resolution imaging that approaches the resolution of usual transmission electron microscopy and (iii) the precise quantification of label down to 1 part-per-million and spanning several orders of magnitude. Here we review the basic elements of MIMS and describe new applications of MIMS to the quantitative study of metabolic processes including protein and nucleic acid synthesis in model organisms ranging from microbes to humans. PMID:23660233

A cost-effective approach to produce 15N-labelled amino acids employing Chlamydomonas reinhardtii CC503.

Science.gov (United States)

Nicolás Carcelén, Jesús; Marchante-Gayón, Juan Manuel; González, Pablo Rodríguez; Valledor, Luis; Cañal, María Jesús; Alonso, José Ignacio García

2017-08-18

The use of enriched stable isotopes is of outstanding importance in chemical metrology as it allows the application of isotope dilution mass spectrometry (IDMS). Primary methods based on IDMS ensure the quality of the analytical measurements and traceability of the results to the international system of units. However, the synthesis of isotopically labelled molecules from enriched stable isotopes is an expensive and a difficult task. Either chemical and biochemical methods to produce labelled molecules have been proposed, but so far, few cost-effective methods have been described. The aim of this study was to use the microalgae Chlamydomonas reinhardtii to produce, at laboratory scale, 15 N-labelled amino acids with a high isotopic enrichment. To do that, a culture media containing 15 NH 4 Cl was used. No kinetic isotope effect (KIE) was observed. The labelled proteins biosynthesized by the microorganism were extracted from the biomass and the 15 N-labelled amino acids were obtained after a protein hydrolysis with HCl. The use of the wall deficient strain CC503 cw92 mt+ is fit for purpose, as it only assimilates ammonia as nitrogen source, avoiding isotope contamination with nitrogen from the atmosphere or the reagents used in the culture medium, and enhancing the protein extraction efficiency compared to cell-walled wild type Chlamydomonas. The isotopic enrichment of the labelled amino acids was calculated from their isotopic composition measured by gas chromatography mass spectrometry (GC-MS). The average isotopic enrichment for the 16 amino acids characterized was 99.56 ± 0.05% and the concentration of the amino acids in the hydrolysate ranged from 18 to 90 µg/mL. Previously reported biochemical methods to produce isotopically labelled proteins have been applied in the fields of proteomics and fluxomics. For these approaches, low amounts of products are required and the isotopic enrichment of the molecules has never been properly determined. So far, only 13

Limited proteolysis combined with isotope labeling and quantitative LC-MALDI MS for monitoring protein conformational changes: a study on calcium-binding sites of cardiac Troponin C

International Nuclear Information System (INIS)

McDonald, Chris; Li Liang

2005-01-01

Studies of protein-protein and protein-ligand interactions are important for understanding biological functions of proteins. A new technique based on the partial proteolysis of proteins combined with quantitative mass spectrometry is developed as a means of tracking structural changes after the formation of a protein-ligand complex. In this technique, a protein of interest with and without the binding of a ligand is digested with an enzyme to generate a set of peptides, followed by separation of the peptides by liquid chromatography. Matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) is used to identify chromatographically separated peptides, and locate their sequence alignments in the parent protein. Using an isotopically labeled protein as a sample against an unlabeled protein standard, quantitative information can be gathered. This overcomes the inherent lack of quantitative capability of MALDI MS. The utility of the technique to investigate protein-ligand interactions is demonstrated in a model system involving calcium binding to cardiac Troponin C (cTnC). Using this technique, the general location of the three calcium-binding sites of cTnC can be determined by using several different enzymes to generate overlapping peptide maps of cTnC

Kinetic isotope effects in reaction of ferment oxidation of tritium-labelled D-galactosamine

International Nuclear Information System (INIS)

Akulov, G.P.; Korsakova, N.A.

1992-01-01

Primary, secondary and intramolecular kinetic isotopic effects in reaction of ferment oxidation of D-galactosamine labelled by tritium in position 6, were measured. When comparing values of the effects with previously obtained results for similar reaction D-[6- 3 H]galactose, it was ascertained that the presence of aminogroup in galactopyranosyl mainly affects kinetics of substrate-ferment complex formation stage. The possibility to use kinetic isotope effects for increase in molar activity of D-galactosamine, labelled by tritium in position 6, is shown

Copper absorption from foods labelled intrinsically and extrinsically with Cu-65 stable isotope.

Science.gov (United States)

Harvey, L J; Dainty, J R; Beattie, J H; Majsak-Newman, G; Wharf, S G; Reid, M D; Fairweather-Tait, S J

2005-03-01

To determine copper absorption from copper containing foods labelled either intrinsically or extrinsically with a highly enriched Cu-65 stable isotope label. A longitudinal cross-over study. The study was conducted at the Institute of Food Research, Human Nutrition Unit, Norwich, UK. Subjects were recruited locally via advertisements placed around the Norwich Research Park. A total of 10 volunteers (nine female, one male) took part in the study, but not all volunteers completed each of the test meals. A highly enriched Cu-65 stable isotope label was administered to volunteers in the form of a reference dose or in breakfast test meals consisting of red wine, soya beans, mushrooms or sunflower seeds. Faecal monitoring and mass spectrometry techniques were used to estimate the relative quantities of copper absorbed from the different test meals. True copper absorption from the reference dose (54%) was similar to extrinsically labelled red wine (49%) and intrinsically labelled sunflower seeds (52%), but significantly higher than extrinsically labelled mushrooms (35%), intrinsically (29%) and extrinsically (15%) labelled soya beans and extrinsically labelled sunflower seed (32%) test meals. The use of Cu-65 extrinsic labels in copper absorption studies requires validation according to the food being examined; intrinsic and extrinsic labelling produced significantly different results for sunflower seeds.

Waveguide-type optical circuits for recognition of optical 8QAM-coded label

Science.gov (United States)

Surenkhorol, Tumendemberel; Kishikawa, Hiroki; Goto, Nobuo; Gonchigsumlaa, Khishigjargal

2017-10-01

Optical signal processing is expected to be applied in network nodes. In photonic routers, label recognition is one of the important functions. We have studied different kinds of label recognition methods so far for on-off keying, binary phase-shift keying, quadrature phase-shift keying, and 16 quadrature amplitude modulation-coded labels. We propose a method based on waveguide circuits to recognize an optical eight quadrature amplitude modulation (8QAM)-coded label by simple passive optical signal processing. The recognition of the proposed method is theoretically analyzed and numerically simulated by the finite difference beam propagation method. The noise tolerance is discussed, and bit-error rate against optical signal-to-noise ratio is evaluated. The scalability of the proposed method is also discussed theoretically for two-symbol length 8QAM-coded labels.

Isotope labeling-based quantitative proteomics of developing seeds of castor oil seed (Ricinus communis L.)

DEFF Research Database (Denmark)

Nogueira, Fábio C S; Palmisano, Giuseppe; Schwämmle, Veit

2013-01-01

In this study, we used a mass spectrometry-based quantification approach employing isotopic (ICPL) and isobaric (iTRAQ) labeling to investigate the pattern of protein deposition during castor oil seed (Ricinus communis L.) development, including that of proteins involved in fatty acid metabolism...... give important insights into certain aspects of the biology of castor oil seed development such as carbon flow, anabolism, and catabolism of fatty acid and the pattern of deposition of SSPs, toxins, and allergens such as ricin and 2S albumins. We also found, for the first time, some genes of SSP......, seed-storage proteins (SSPs), toxins, and allergens. Additionally, we have used off-line hydrophilic interaction chromatography (HILIC) as a step of peptide fractionation preceding the reverse-phase nanoLC coupled to a LTQ Orbitrap. We were able to identify a total of 1875 proteins, and from these 1748...

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

International Nuclear Information System (INIS)

Zhou, Ruokun; Huan, Tao; Li, Liang

2015-01-01

Highlights: • Two new reagents were developed for chemical isotope labeling mass spectrometry (MS). • They could be used to label amine-containing metabolites in a metabolomic sample. • The labeled metabolites could be detected with much improved sensitivity in MS. • One of the reagents could also help generate useful MS/MS spectra for structural analysis. • These reagents should be useful for quantitative metabolomics. - Abstract: 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

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

Energy Technology Data Exchange (ETDEWEB)

Zhou, Ruokun; Huan, Tao; Li, Liang, E-mail: Liang.Li@ualberta.ca

2015-06-30

Highlights: • Two new reagents were developed for chemical isotope labeling mass spectrometry (MS). • They could be used to label amine-containing metabolites in a metabolomic sample. • The labeled metabolites could be detected with much improved sensitivity in MS. • One of the reagents could also help generate useful MS/MS spectra for structural analysis. • These reagents should be useful for quantitative metabolomics. - Abstract: 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

Development of uniformly stable isotope labeling system in higher plants for hetero-nuclear NMR experiments in vitro and in vivo

International Nuclear Information System (INIS)

Kikuchi, J.

2005-01-01

Full text: Novel methods for measurement of living systems are making new breakthroughs in life science. In the era of the metabolome (analysis of all measurable metabolites), a MS-based approach is considered to be the major technology, whereas a NMR-based method is recognized as minor technology due to its low sensitivity. Therefore, my laboratory is currently focusing to develop novel methodologies for an NMR-based metabolomics. This will be achieved by uniform stable isotope labeling of higher plants allowing application of multi-dimensional NMR experiments used in protein structure determination. Using these novel methods, I will analyze the dynamic molecular networks inside tissues. Especially, use of stable isotope labeling methods has enormous advantage for discrimination of incorporated or de novo synthesized compounds. Furthermore, potentiality of in vivo-NMR metabolomics will be discussed in the conference. (author)

Expeditious syntheses of stable and radioactive isotope-labeled anticonvulsant agent, JNJ-26990990, and its metabolites.

Science.gov (United States)

Lin, Ronghui; Weaner, Larry E; Hoerr, David C; Salter, Rhys; Gong, Yong

2013-01-01

Syntheses of stable and radioactive isotope-labeled anticonvulsant agent, JNJ-26990990, that is, N-(benzo[b]thien-3-ylmethyl)-sulfamide and its metabolites are described. [(13)C(15)N]Benzo[b]thiophene-3-carbonitrile was first prepared by coupling of 3-bromo-benzo[b]thiophene with [(13)C(15)N]-copper cyanide. The resultant [(13)C(15)N]benzo[b]thiophene-3-carbonitrile was reduced with lithium aluminum deuteride to give [(13)CD2(15)N]benzo[b]thiophen-3-yl-methylamine; which was then coupled with sulfamide to afford [(13)CD2(15)N]-N-(benzo[b]thien-3-ylmethyl)-sulfamide, the stable isotope-labeled compound with four stable isotope atoms. Direct oxidation of [(13)CD2(15)N]-N-(benzo[b]thien-3-ylmethyl)-sulfamide with hydrogen peroxide and peracetic acid gave the stable isotope-labeled sulfoxide and sulfone metabolites. On the other hand, radioactive (14)C-labeled N-(benzo[b]thien-3-ylmethyl)-sulfamide was prepared conveniently by sequential coupling of 3-bromo-benzo[b]thiophene with [(14)C]-copper cyanide, reduction of the carbonitrile to carboxaldehyde, and reductive amination with sulfamide. Copyright © 2013 John Wiley & Sons, Ltd.

Development of a code for the isotopic analysis of Uranium

Energy Technology Data Exchange (ETDEWEB)

Kim, J. H.; Kang, M. Y.; Kim, Jinhyeong; Choi, H. D. [Seoul National Univ., Seoul (Korea, Republic of)

2013-05-15

To strengthen the national nuclear nonproliferation regime by an establishment of nuclear forensic system, the techniques for nuclear material analysis and the categorization of important domestic nuclear materials are being developed. MGAU and FRAM are commercial software for the isotopic analysis of Uranium by using γ-spectroscopy, but the diversity of detection geometry and some effects - self attenuation, coincidence summing, etc. - suggest an analysis tool under continual improvement and modification. Hence, developing another code for HPGe γ- and x-ray spectrum analysis is started in this study. The analysis of the 87-101 keV region of Uranium spectrum is attempted based on the isotopic responses similar to those developed in MGAU. The code for isotopic analysis of Uranium is started from a fitting.

Non-Protein Coding RNAs

CERN Document Server

Walter, Nils G; Batey, Robert T

2009-01-01

This book assembles chapters from experts in the Biophysics of RNA to provide a broadly accessible snapshot of the current status of this rapidly expanding field. The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, highlighting just one example of a large number of non-protein coding RNAs. Because non-protein coding RNAs outnumber protein coding genes in mammals and other higher eukaryotes, it is now thought that the complexity of organisms is correlated with the fraction of their genome that encodes non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic transposons, higher-level organization of eukaryotic chromosomes, and gene expression itself are found to largely be directed by non-protein coding RNAs. The biophysical study of these RNAs employs X-ray crystallography, NMR, ensemble and single molecule fluorescence spectroscopy, optical tweezers, cryo-electron microscopy, and ot...

Heating Isotopically Labeled Bernal Stacked Graphene: A Raman Spectroscopy Study

Czech Academy of Sciences Publication Activity Database

Ek Weis, Johan; da Costa, Sara; Frank, Otakar; Kalbáč, Martin

2014-01-01

Roč. 5, č. 3 (2014), s. 549-554 ISSN 1948-7185 R&D Projects: GA MŠk LL1301 Institutional support: RVO:61388955 Keywords : Bernal * graphene * isotopic labeling Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 7.458, year: 2014

Stable isotope applications in biomolecular structure and mechanisms. A meeting to bring together producers and users of stable-isotope-labeled compounds to assess current and future needs

International Nuclear Information System (INIS)

Trewhella, J.; Cross, T.A.; Unkefer, C.J.

1994-12-01

Knowledge of biomolecular structure is a prerequisite for understanding biomolecular function, and stable isotopes play an increasingly important role in structure determination of biological molecules. The first Conference on Stable Isotope Applications in Biomolecular Structure and Mechanisms was held in Santa Fe, New Mexico, March 27--31, 1994. More than 120 participants from 8 countries and 44 institutions reviewed significant developments, discussed the most promising applications for stable isotopes, and addressed future needs and challenges. Participants focused on applications of stable isotopes for studies of the structure and function of proteins, peptides, RNA, and DNA. Recent advances in NMR techniques neutron scattering, EPR, and vibrational spectroscopy were highlighted in addition to the production and synthesis of labeled compounds. This volume includes invited speaker and poster presentations as well as a set of reports from discussion panels that focused on the needs of the scientific community and the potential roles of private industry, the National Stable Isotope Resource, and the National High Magnetic Field Laboratory in serving those needs. This is the leading abstract. Individual papers are processed separately for the database

Stable isotope applications in biomolecular structure and mechanisms. A meeting to bring together producers and users of stable-isotope-labeled compounds to assess current and future needs

Energy Technology Data Exchange (ETDEWEB)

Trewhella, J.; Cross, T.A.; Unkefer, C.J. [eds.

1994-12-01

Knowledge of biomolecular structure is a prerequisite for understanding biomolecular function, and stable isotopes play an increasingly important role in structure determination of biological molecules. The first Conference on Stable Isotope Applications in Biomolecular Structure and Mechanisms was held in Santa Fe, New Mexico, March 27--31, 1994. More than 120 participants from 8 countries and 44 institutions reviewed significant developments, discussed the most promising applications for stable isotopes, and addressed future needs and challenges. Participants focused on applications of stable isotopes for studies of the structure and function of proteins, peptides, RNA, and DNA. Recent advances in NMR techniques neutron scattering, EPR, and vibrational spectroscopy were highlighted in addition to the production and synthesis of labeled compounds. This volume includes invited speaker and poster presentations as well as a set of reports from discussion panels that focused on the needs of the scientific community and the potential roles of private industry, the National Stable Isotope Resource, and the National High Magnetic Field Laboratory in serving those needs. This is the leading abstract. Individual papers are processed separately for the database.

Isotopic labelling studies for a gold-catalysed skeletal rearrangement of alkynyl aziridines

Directory of Open Access Journals (Sweden)

Neil Spencer

2011-06-01

Full Text Available Isotopic labelling studies were performed to probe a proposed 1,2-aryl shift in the gold-catalysed cycloisomerisation of alkynyl aziridines into 2,4-disubstituted pyrroles. Two isotopomers of the expected skeletal rearrangement product were identified using 13C-labelling and led to a revised mechanism featuring two distinct skeletal rearrangements. The mechanistic proposal has been rationalised against the reaction of a range of 13C- and deuterium-labelled substrates.

Site-Specific Protein Labeling Utilizing Lipoic Acid Ligase (LplA) and Bioorthogonal Inverse Electron Demand Diels-Alder Reaction.

Science.gov (United States)

Baalmann, Mathis; Best, Marcel; Wombacher, Richard

2018-01-01

Here, we describe a two-step protocol for selective protein labeling based on enzyme-mediated peptide labeling utilizing lipoic acid ligase (LplA) and bioorthogonal chemistry. The method can be applied to purified proteins, protein in cell lysates, as well as living cells. In a first step a W37V mutant of the lipoic acid ligase (LplA W37V ) from Escherichia coli is utilized to ligate a synthetic chemical handle site-specifically to a lysine residue in a 13 amino acid peptide motif-a short sequence that can be genetically expressed as a fusion with any protein of interest. In a second step, a molecular probe can be attached to the chemical handle in a bioorthogonal Diels-Alder reaction with inverse electron demand (DA inv ). This method is a complementary approach to protein labeling using genetic code expansion and circumvents larger protein tags while maintaining label specificity, providing experimental flexibility and straightforwardness.

Fluorine-18 labeling of proteins

International Nuclear Information System (INIS)

Kilbourn, M.R.; Dence, C.S.; Welch, M.J.; Mathias, C.J.

1987-01-01

Two fluorine-18-labeled reagents, methyl 3-[ 18 F]fluoro-5-nitrobenzimidate and 4-[ 18 F]fluorophenacyl bromide, have been prepared for covalent attachment of fluorine-18 to proteins. Both reagents can be prepared in moderate yields (30-50%, EOB) in synthesis times of 50-70 min. Reaction of these reagents with proteins (human serum albumin, human fibrinogen, and human immunoglobulin A) is pH independent, protein concentration dependent, and takes 5-60 min at mild pH (8.0) and temperature (25-37 degrees C), in yields up to 95% (corrected). The 18 F-labeled proteins are purified by size exclusion chromatography

Synthesis of 13C and 2H labelled retinals: spectroscopic investigations on isotopically labelled rhodopsin and bacteriorhodopsin

International Nuclear Information System (INIS)

Pardoen, J.A.

1986-01-01

In order to develop probes of the structure of chromophores, the author introduces isotopic modifications at specific chromophoric positions as structural probes. To obtain bacteriorhodopsin, rhodopsin and their photoproducts labelled in the chromophore at selected positions, bacterioopsin and opsin were reacted with the appropriate labelled a11-trans and 11-cis retinals. The author describes the synthesis of a11-trans retinal selectively 13 C labelled at different positions. The characterization of these labelled a11-trans retinals by mass spectrometry, 300 MHz 1 H NMR and 75 MHz 13 C NMR spectroscopy is given. The photochemical preparation and isolation of the pure 9-, 11- and 13-cis forms is described in the experimental part. (Auth.)

Sensing site-specific structural characteristics and chirality using vibrational circular dichroism of isotope labeled peptides.

Science.gov (United States)

Keiderling, Timothy A

2017-12-01

Isotope labeling has a long history in chemistry as a tool for probing structure, offering enhanced sensitivity, or enabling site selection with a wide range of spectroscopic tools. Chirality sensitive methods such as electronic circular dichroism are global structural tools and have intrinsically low resolution. Consequently, they are generally insensitive to modifications to enhance site selectivity. The use of isotope labeling to modify vibrational spectra with unique resolvable frequency shifts can provide useful site-specific sensitivity, and these methods have been recently more widely expanded in biopolymer studies. While the spectral shifts resulting from changes in isotopic mass can provide resolution of modes from specific parts of the molecule and can allow detection of local change in structure with perturbation, these shifts alone do not directly indicate structure or chirality. With vibrational circular dichroism (VCD), the shifted bands and their resultant sign patterns can be used to indicate local conformations in labeled biopolymers, particularly if multiple labels are used and if their coupling is theoretically modeled. This mini-review discusses selected examples of the use of labeling specific amides in peptides to develop local structural insight with VCD spectra. © 2017 Wiley Periodicals, Inc.

The Need to Support and Maintain Legacy Software: Ensuring Ongoing Support for the Isotopics Codes

International Nuclear Information System (INIS)

Weber, A.-L.; Funk, P.; McGinnis, B.; Vo, D.; Wang, T.-F.; Peerani, P.; Zsigrai, J.; )

2015-01-01

Since about four decades, gamma evaluation codes for plutonium and uranium isotope abundance measurements are a key component of international, regional and domestic safeguards inspections. However, the development of these codes still relies upon a very limited number of experts. This led the safeguards authorities to express concerns, and to request continuity of knowledge and maintenance capability for the codes. The presentation describes initiatives undertaken in the past ten years to ensure ongoing support for the isotopic codes. As a follow-up to the 2005 international workshop, the IAEA issued a roadmap for future developments of gamma codes, followed by a request for support in this field to several MSSP's (namely JNT A 01684). The international working group on gamma spectrometry techniques for U and Pu isotopics (IWG-GST) was launched by the European, French and US MSSPs in 2007, to respond to the needs expressed by the IAEA and other national or international inspectorates. Its activities started with the organization in 2008 of a workshop on gamma spectrometry analysis codes for U and Pu isotopics. The working group is currently developing an international database of reference spectra that will be made available to the community of users and developers. In parallel, IRSN contributes to the JNT A 01684 by advising the IAEA on establishing a procedure for validating a new version of isotopics codes compared to the previous version. The most recent initiative, proposed by the IAEA, consists in organizing an inter-comparison exercise to assess the performances of U and Pu isotopics and mass assay techniques based on medium resolution gamma spectrometry (MRGS). All these initiatives contributed to the continuity of knowledge and maintenance of the gamma isotopic codes, but further efforts are needed to ensure the long-term sustainability of the codes. (author)

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

Science.gov (United States)

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.

Myelin-associated proteins labelled by slow axonal transport

International Nuclear Information System (INIS)

Giorgi, P.P.; DuBois, H.

1981-01-01

This paper deals with the problem of protein metabolism and provides evidence that the neuronal contribution to myelin metabolism may be restricted to lipids only. On the other hand this line of research led to the partial characterization of a group of neuronal proteins probably involved in axo-glial interactions subserving the onset of myelination and the structural maintenance of the mature myelin sheath. Intraocular injection of radioactive amino acids allows the study of the anterograde transport of labelled proteins along retinofugal fibres which are well myelinated. Myelin extracted from the optic nerve and tract under these conditions also contains labelled proteins. Three hypotheses are available to explain this phenomenon. To offer an explanation for this phenomenon the work was planned as follows. a) Characterization of the spatio-temporal pattern of labelling of myelin, in order to define the experimental conditions (survival time and region of the optic pathway to be studied) necessary to obtain maximal labelling. b) Characterization (by gel electrophoresis) of the myelin-associated proteins which become labelled by axonal transport, in order to work on a consistent pattern of labelling. c) Investigation of the possible mechanism responsible for the labelling of myelin-associated proteins. (Auth.)

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

International Nuclear Information System (INIS)

Giménez, Estela; Balmaña, Meritxell; Figueras, Joan; Fort, Esther; Bolós, Carme de; Sanz-Nebot, Victòria; Peracaula, Rosa; Rizzi, Andreas

2015-01-01

Highlights: • The method enables relative quantitation of hAGP glycans from pathological samples • Pancreatic cancer samples clearly showed an increase of hAGP fucosylated glycans. • Fucosylated glycans could be potential biomarkers for diagnosing pancreatic cancer. • The established method could be extremely useful to find novel glycoprotein biomarkers - Abstract: 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 (μZIC-HILIC-ESI-MS) for relative quantitation of glycosylation variants in selected glycoproteins present in samples from cancer patients. Human α 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 μZIC-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

Isotopically modified compounds

International Nuclear Information System (INIS)

Kuruc, J.

2009-01-01

In this chapter the nomenclature of isotopically modified compounds in Slovak language is described. This chapter consists of following parts: (1) Isotopically substituted compounds; (2) Specifically isotopically labelled compounds; (3) Selectively isotopically labelled compounds; (4) Non-selectively isotopically labelled compounds; (5) Isotopically deficient compounds.

Novel isotopic N, N-Dimethyl Leucine (iDiLeu) Reagents Enable Absolute Quantification of Peptides and Proteins Using a Standard Curve Approach

Science.gov (United States)

Greer, Tyler; Lietz, Christopher B.; Xiang, Feng; Li, Lingjun

2015-01-01

Absolute quantification of protein targets using liquid chromatography-mass spectrometry (LC-MS) is a key component of candidate biomarker validation. One popular method combines multiple reaction monitoring (MRM) using a triple quadrupole instrument with stable isotope-labeled standards (SIS) for absolute quantification (AQUA). LC-MRM AQUA assays are sensitive and specific, but they are also expensive because of the cost of synthesizing stable isotope peptide standards. While the chemical modification approach using mass differential tags for relative and absolute quantification (mTRAQ) represents a more economical approach when quantifying large numbers of peptides, these reagents are costly and still suffer from lower throughput because only two concentration values per peptide can be obtained in a single LC-MS run. Here, we have developed and applied a set of five novel mass difference reagents, isotopic N, N-dimethyl leucine (iDiLeu). These labels contain an amine reactive group, triazine ester, are cost effective because of their synthetic simplicity, and have increased throughput compared with previous LC-MS quantification methods by allowing construction of a four-point standard curve in one run. iDiLeu-labeled peptides show remarkably similar retention time shifts, slightly lower energy thresholds for higher-energy collisional dissociation (HCD) fragmentation, and high quantification accuracy for trypsin-digested protein samples (median errors <15%). By spiking in an iDiLeu-labeled neuropeptide, allatostatin, into mouse urine matrix, two quantification methods are validated. The first uses one labeled peptide as an internal standard to normalize labeled peptide peak areas across runs (<19% error), whereas the second enables standard curve creation and analyte quantification in one run (<8% error).

An In vitro evaluation of the reliability of QR code denture labeling technique.

Science.gov (United States)

Poovannan, Sindhu; Jain, Ashish R; Krishnan, Cakku Jalliah Venkata; Chandran, Chitraa R

2016-01-01

Positive identification of the dead after accidents and disasters through labeled dentures plays a key role in forensic scenario. A number of denture labeling methods are available, and studies evaluating their reliability under drastic conditions are vital. This study was conducted to evaluate the reliability of QR (Quick Response) Code labeled at various depths in heat-cured acrylic blocks after acid treatment, heat treatment (burns), and fracture in forensics. It was an in vitro study. This study included 160 specimens of heat-cured acrylic blocks (1.8 cm × 1.8 cm) and these were divided into 4 groups (40 samples per group). QR Codes were incorporated in the samples using clear acrylic sheet and they were assessed for reliability under various depths, acid, heat, and fracture. Data were analyzed using Chi-square test, test of proportion. The QR Code inclusion technique was reliable under various depths of acrylic sheet, acid (sulfuric acid 99%, hydrochloric acid 40%) and heat (up to 370°C). Results were variable with fracture of QR Code labeled acrylic blocks. Within the limitations of the study, by analyzing the results, it was clearly indicated that the QR Code technique was reliable under various depths of acrylic sheet, acid, and heat (370°C). Effectiveness varied in fracture and depended on the level of distortion. This study thus suggests that QR Code is an effective and simpler denture labeling method.

Reactor Fuel Isotopics and Code Validation for Nuclear Applications

Energy Technology Data Exchange (ETDEWEB)

Francis, Matthew W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Weber, Charles F. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Pigni, Marco T. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Gauld, Ian C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2015-02-01

Experimentally measured isotopic concentrations of well characterized spent nuclear fuel (SNF) samples have been collected and analyzed by previous researchers. These sets of experimental data have been used extensively to validate the accuracy of depletion code predictions for given sets of burnups, initial enrichments, and varying power histories for different reactor types. The purpose of this report is to present the diversity of data in a concise manner and summarize the current accuracy of depletion modeling. All calculations performed for this report were done using the Oak Ridge Isotope GENeration (ORIGEN) code, an internationally used irradiation and decay code solver within the SCALE comprehensive modeling and simulation code. The diversity of data given in this report includes key actinides, stable fission products, and radioactive fission products. In general, when using the current ENDF/B-VII.0 nuclear data libraries in SCALE, the major actinides are predicted to within 5% of the measured values. Large improvements were seen for several of the curium isotopes when using improved cross section data found in evaluated nuclear data file ENDF/B-VII.0 as compared to ENDF/B-V-based results. The impact of the flux spectrum on the plutonium isotope concentrations as a function of burnup was also shown. The general accuracy noted for the actinide samples for reactor types with burnups greater than 5,000 MWd/MTU was not observed for the low-burnup Hanford B samples. More work is needed in understanding these large discrepancies. The stable neodymium and samarium isotopes were predicted to within a few percent of the measured values. Large improvements were seen in prediction for a few of the samarium isotopes when using the ENDF/B-VII.0 libraries compared to results obtained with ENDF/B-V libraries. Very accurate predictions were obtained for ¹³³Cs and ¹⁵³Eu. However, the predicted values for the stable ruthenium and rhodium isotopes varied

Synthetic routes to some isotopically labelled intermediates for diterpenoid biosynthesis

International Nuclear Information System (INIS)

Dawson, R.M.; Godfrey, I.M.; Hogg, R.W.; Knox, J.R.

1989-01-01

The exo-15-hydrogen of ent-kaurene can be exchanged through a reversible ene reaction in a convenient and efficient procedure which has the potential for giving high specific activity 3 H-labelling. Copalol, the (Z)-double bond stereoisomer, and the allylic alcohol isomers ent-manool and ent-epimanool have been obtained through divergent synthetic pathways involving a 15,16-bisnor ketone intermediate. These pathways have also allowed the four compounds to be obtained with 14 C-labelling. A method, involving a Wittig reaction to form a vinyl bromide intermediate, has been developed for obtaining copalol, as the trityl ether derivative, with stereospecific isotopic labelling of one or the other of the hydrogens of the exocyclic methylene group. 27 refs., figs

A SIMPLE FLUORESCENT LABELING METHOD FOR STUDIES OF PROTEIN OXIDATION, PROTEIN MODIFICATION, AND PROTEOLYSIS

Science.gov (United States)

Pickering, Andrew. M.; Davies, Kelvin. J. A.

2014-01-01

Proteins are sensitive to oxidation, and oxidized proteins are excellent substrates for degradation by proteolytic enzymes such as the Proteasome and the mitochondrial Lon protease. Protein labeling is required for studies of protein turnover. Unfortunately, most labeling techniques involve 3H or 14C methylation which is expensive, exposes researchers to radioactivity, generates large amounts of radioactive waste, and allows only single-point assays because samples require acid-precipitation. Alternative labeling methods, have largely proven unsuitable, either because the probe itself is modified by the oxidant(s) being studied, or because the alternative labeling techniques are too complex or too costly for routine use. What is needed is a simple, quick, and cheap labeling technique that uses a non-radioactive marker, that binds strongly to proteins, is resistant to oxidative modification, and emits a strong signal. We have devised a new reductive method for labeling free carboxyl groups of proteins with the small fluorophore 7-amino-4-methycoumarin (AMC). When bound to target proteins, AMC fluoresces very weakly but when AMC is released by proteinases, proteases, or peptidases, it fluoresces strongly. Thus, without acid-precipitation, the proteolysis of any target protein can be studied continuously, in multiwell plates. In direct comparisons, 3H-labeled proteins and AMC-labeled proteins exhibited essentially identical degradation patterns during incubation with trypsin, cell extracts, and purified proteasome. AMC-labeled proteins are well-suited to study increased proteolytic susceptibility following protein modification, since the AMC-protein bond is resistant to oxidizing agents such as hydrogen peroxide and peroxynitrite, and is stable over time and to extremes of pH, temperature (even boiling), freeze-thawing, mercaptoethanol, and methanol. PMID:21988844

Computer codes for problems of isotope and radiation research

International Nuclear Information System (INIS)

Remer, M.

1986-12-01

A survey is given of computer codes for problems in isotope and radiation research. Altogether 44 codes are described as titles with abstracts. 17 of them are in the INIS scope and are processed individually. The subjects are indicated in the chapter headings: 1) analysis of tracer experiments, 2) spectrum calculations, 3) calculations of ion and electron trajectories, 4) evaluation of gamma irradiation plants, and 5) general software

Syntheses with isotopically labelled carbon. Methyl iodide, formaldehyde and cyanide

International Nuclear Information System (INIS)

Finn, R.D.; Boothe, T.E.; Vora, M.M.; Hildner, J.C.; Emran, A.M.; Kothari, P.J.

1984-01-01

Many of the uniquely labelled synthetic precursors currently employed in the design of sophisticated radiolabelled compounds have their origins in the field of hot atom chemistry. Particularly, the development during the past few years of automated, on-line synthetic procedures which combine the nuclear reaction, hot atom and classical chemistry, and rapid purification methods has allowed the incorporation of useful radionuclides into suitable compounds of chemical and biochemical interest. The application of isotopically labelled methyl iodide, formaldehyde, and cyanide anion as synthetic intermediates in research involving human physiology and nuclear medicine, as well as their contributions to other scientific methodology, is reviewed. (author)

Mass spectrometric studies of stable isotope-labelled carboxylic acid derivatives

International Nuclear Information System (INIS)

Andersson, B.Aa.; Dinger, F.; Dinh-Nguyen, N.

1975-01-01

Low resolution mass spectra of deuterium and carbon-13 labelled fatty acid pyrrolidides are discussed. The simple fragmentation pattern of pyrrolidides makes them superior to other derivatives, regarding location of isotopes. Deuteriation of ethylenic fatty acid pyrrolidides therefore seems to be an improved method to locate carbon-carbon double bonds by mass spectrometry. (author)

Raman spectroscopy of isotopically labeled two-layer graphene

Czech Academy of Sciences Publication Activity Database

Kalbáč, Martin; Kong, J.; Kavan, Ladislav; Dresselhaus, M. S.

2012-01-01

Roč. 249, č. 12 (2012), s. 2500-2502 ISSN 0370-1972 R&D Projects: GA AV ČR IAA400400911; GA AV ČR IAA400400804; GA AV ČR KAN200100801; GA MŠk ME09060; GA ČR GAP204/10/1677; GA ČR GBP208/12/G016; GA ČR(CZ) GAP208/12/1062 Institutional support: RVO:61388955 Keywords : electrochemical doping * isotope labeling * graphene Subject RIV: CG - Electrochemistry Impact factor: 1.489, year: 2012

77 FR 49818 - Agency Information Collection Activities; Proposed Collection; Comment Request; Bar Code Label...

Science.gov (United States)

2012-08-17

...] Agency Information Collection Activities; Proposed Collection; Comment Request; Bar Code Label... allow 60 days for public comment in response to the notice. This notice solicits comments on the bar... technology. Bar Code Label Requirement for Human Drug and Biological Products--(OMB Control Number 0910-0537...

Why do total-body decay curves of iodine-labeled proteins begin with a delay

International Nuclear Information System (INIS)

Regoeczi, E.

1987-01-01

The initial delay that occurs in total-body radiation curves reaching their single-exponential slopes was analyzed from 106 experiments involving several mammalian species (guinea pig, mouse, rabbit, and rat) and plasma proteins (alpha 1-acid glycoprotein, antithrombin III, fibrinogen, immunoglobulin G, and transferrin) in 14 different combinations. The time interval (Td) between injection and the intercept of the slope with the full-dose value was adopted as a measure of curve nonideality. The overall mean Td was 6.6 h, but individual values showed a significant correlation to protein half-lives, whereby proteins of unequal metabolic properties exhibited different mean Td values. Targeting protein to the liver abolished delay. Choice of the isotope ( 125 I or 131 I) and size of the labeled protein had no influence on the magnitude of delay. Whole-body radiation curves of animals that received [ 125 I]iodotyrosines, Na 131 I, or 131 I-polyvinylpyrrolidone exhibited no initial delays. These results do not support the earlier notion that delay is caused by a redistribution of the labeled protein in the body to radiometrically more favorable sites. However, they are compatible with the assumption that delayed passage of a protein dose through the extracellular matrix and/or retarded transfer of proteolytic products from extravascular catabolic sites to plasma may be responsible for the phenomenon

Automatic isotope gas analysis of tritium labelled organic materials Pt. 1

International Nuclear Information System (INIS)

Gacs, I.; Mlinko, S.

1978-01-01

A new automatic procedure developed to convert tritium in HTO hydrogen for subsequent on-line gas counting is described. The water containing tritium is introduced into a column prepared from molecular sieve-5A and heated to 550 deg C. The tritium is transferred by isotopic exchange into hydrogen flowing through the column. The radioactive gas is led into an internal detector for radioactivity measurement. The procedure is free of memory effects, provides quantitative recovery with analytical reproducibility better than 0.5% rel. at a preset number of counts. The experimental and analytical results indicate that isotopic exchange between HTO and hydrogen over a column prepared from alumina or molecular sieve-5A can be successfully applied for the quantitative transfer of tritium from HTO into hydrogen for on-line gas countinq. This provides an analytical procedure for the automatic determination of tritium in water with an analytical reproducibility better than 0.5% rel. The exchange process will also be suitable for rapid tritium transfer from water formed during the decomposition of tritium-labelled organic compounds or biological materials. The application of the procedure in automatic isotope gas analysis of organic materials labelled with tritium will be described in subsequent papers (Parts II and III). (T.G.)

Measurement of Endogenous versus Exogenous Formaldehyde-Induced DNA-Protein Crosslinks in Animal Tissues by Stable Isotope Labeling and Ultrasensitive Mass Spectrometry.

Science.gov (United States)

Lai, Yongquan; Yu, Rui; Hartwell, Hadley J; Moeller, Benjamin C; Bodnar, Wanda M; Swenberg, James A

2016-05-01

DNA-protein crosslinks (DPC) arise from a wide range of endogenous and exogenous chemicals, such as chemotherapeutic drugs and formaldehyde. Importantly, recent identification of aldehydes as endogenous genotoxins in Fanconi anemia has provided new insight into disease causation. Because of their bulky nature, DPCs pose severe threats to genome stability, but previous methods to measure formaldehyde-induced DPCs were incapable of discriminating between endogenous and exogenous sources of chemical. In this study, we developed methods that provide accurate and distinct measurements of both exogenous and endogenous DPCs in a structurally specific manner. We exposed experimental animals to stable isotope-labeled formaldehyde ([(13)CD2]-formaldehyde) by inhalation and performed ultrasensitive mass spectrometry to measure endogenous (unlabeled) and exogenous ((13)CD2-labeled) DPCs. We found that exogenous DPCs readily accumulated in nasal respiratory tissues but were absent in tissues distant to the site of contact. This observation, together with the finding that endogenous formaldehyde-induced DPCs were present in all tissues examined, suggests that endogenous DPCs may be responsible for increased risks of bone marrow toxicity and leukemia. Furthermore, the slow rate of DPC repair provided evidence for the persistence of DPCs. In conclusion, our method for measuring endogenous and exogenous DPCs presents a new perspective for the potential health risks inflicted by endogenous formaldehyde and may inform improved disease prevention and treatment strategies. Cancer Res; 76(9); 2652-61. ©2016 AACR. ©2016 American Association for Cancer Research.

Indirect labeling of proteins with radioiodine

International Nuclear Information System (INIS)

Araujo, Elaine Bortoleti de; Lavinas, Tatiana; Muramoto, Emiko; Pereira, Nilda P.S. de; Silva, Constancia P.G.; Tavares, Leoberto C.

2000-01-01

A procedure is described for the radioiodination of proteins using an iodinated derivative of N succinimidyl 3-(tri-n-butylstannyl)benzoate (ATE), previously described by Zalutsky. ATE was obtained in a high pure form and the iodination has been performed with 131-Iodine in 70-80% yield. Protein labeling studies performed with human IgG indicate that the ATE intermediate is an important alternative to conventional labeling methods. (author)

Comparison of three gamma ray isotopic determination codes: FRAM, MGA, and TRIFID

International Nuclear Information System (INIS)

Cremers, T.L.; Malcom, J.E.; Bonner, C.A.

1994-01-01

The determination of the isotopic distribution of plutonium and the americium concentration is required for the assay of nuclear material by calorimetry or neutron coincidence counting. The isotopic information is used in calorimetric assay to compute the effective specific power from the measured isotopic fractions and the known specific power of each isotope. The effective specific power is combined with the heat measurement to obtain the mass of plutonium in the assayed nuclear material. The response of neutron coincidence counters is determined by the 240 Pu isotopic fraction with contributions from the other even plutonium isotopes. The effect of the 240 Pu isotopic fraction and the other neutron contributing isotopes are combined as 240 Pu effective. This is used to calculate the mass of nuclear material from the neutron counting data in a manner analogous to the effective specific power in calorimeter. Comparisons of the precision and accuracy of calorimetric assay and neutron coincidence counting often focus only on the precision and accuracy of the heat measurement (calorimetry) compared to the precision and accuracy of the neutron coincidence counting statistics. The major source of uncertainty for both calorimetric assay and neutron coincidence counting often lies in the determination of the plutonium isotopic distribution ad determined by gamma ray spectroscopy. Thus, the selection of the appropriate isotopic distribution code is of paramount importance to good calorimetric assay and neutron coincidence counting. Three gamma ray isotopic distribution codes, FRAM, MGA, and TRIFID have been compared at the Los Alamos Plutonium Facility under carefully controlled conditions of similar count rates, count times, and 240 Pu isotopic fraction

Tests of intestinal absorption using carbon-14-labeled isotopes

International Nuclear Information System (INIS)

Fromm, H.; Sarva, R.P.

1983-01-01

Beta radiation-emitting isotopes are being used increasingly in diagnostic gastroenterology for the study of absorption. The major reason for the popularity of radioisotopes is that their use is convenient for patient and physician alike. They often obviate naso- or orointestinal intubation and the collection, storage, and analysis of stool. The radioactivity used for the studies of digestive and absorptive processes is small and is not hazardous. In spite of the safety of the radiolabeled compounds, their use is restricted in children and pregnant women. Therefore, for most tests, promising alternative methods that make use of the stable isotope of carbon, /sup 13/C, instead of the radioactive /sup 14/C have been developed. The analysis of stable isotopes requires more sophisticated technology than that of radioactive compounds, however. Only a few centers presently are equipped and staffed to analyze stable isotopes on a routine basis. In contrast, the analysis of radioactive isotopes has become a routine procedure in almost ever major laboratory. The last decade has brought the development of several radioactive absorption tests. The clinically most useful tests relate to the study of bile acid, fat, lactose, and xylose absorption. All of these tests utilize the excretion rate of /sup 14/CO/sub 2/ in breath after ingestion of a /sup 14/C-labeled compound as a measure of the rate of its absorption or malabsorption

Multi-Label Learning via Random Label Selection for Protein Subcellular Multi-Locations Prediction.

Science.gov (United States)

Wang, Xiao; Li, Guo-Zheng

2013-03-12

Prediction of protein subcellular localization is an important but challenging problem, particularly when proteins may simultaneously exist at, or move between, two or more different subcellular location sites. Most of the existing protein subcellular localization methods are only used to deal with the single-location proteins. In the past few years, only a few methods have been proposed to tackle proteins with multiple locations. However, they only adopt a simple strategy, that is, transforming the multi-location proteins to multiple proteins with single location, which doesn't take correlations among different subcellular locations into account. In this paper, a novel method named RALS (multi-label learning via RAndom Label Selection), is proposed to learn from multi-location proteins in an effective and efficient way. Through five-fold cross validation test on a benchmark dataset, we demonstrate our proposed method with consideration of label correlations obviously outperforms the baseline BR method without consideration of label correlations, indicating correlations among different subcellular locations really exist and contribute to improvement of prediction performance. Experimental results on two benchmark datasets also show that our proposed methods achieve significantly higher performance than some other state-of-the-art methods in predicting subcellular multi-locations of proteins. The prediction web server is available at http://levis.tongji.edu.cn:8080/bioinfo/MLPred-Euk/ for the public usage.

Sulfur Isotope Exchange between S-35 Labeled Inorganic Sulfur-Compounds in Anoxic Marine-Sediments

DEFF Research Database (Denmark)

FOSSING, H.; THODEANDERSEN, S.; JØRGENSEN, BB

1992-01-01

Isotope exchange reactions between S-35-labeled sulfur compounds were studied in anoxic estuarine sediment slurries at 21-degrees-C and pH 7.4-7.7. Two experiments labeled with radioactive elemental sulfur (S-35-degrees) and one labeled with radioactive sulfate ((SO42-)-S-35) were performed as time......% of the total S-35 was recovered in the SIGMA-HS- pool in less than 1.5 h. With no detectable SIGMA-HS- (less than 1-mu-M) in the slurry, 58% of the total S-35 was observed in the pyrite pool within 1.5 h. The FeS pool received up to 31% of all S-35 added. The rapid S-35 incorporation from S-35-degrees...... into SIGMA-HS- and FeS pools was explained by isotope exchange reactions. In contrast, there was evidence that the radioactivity observed in the 'pyrite pool' was caused by adhesion of the added S-35-degrees to the FeS2 grains. In all S-35-degrees-labeled experiments we also observed oxidation...

ISOGEN: Interactive isotope generation and depletion code

International Nuclear Information System (INIS)

Venkata Subbaiah, Kamatam

2016-01-01

ISOGEN is an interactive code for solving first order coupled linear differential equations with constant coefficients for a large number of isotopes, which are produced or depleted by the processes of radioactive decay or through neutron transmutation or fission. These coupled equations can be written in a matrix notation involving radioactive decay constants and transmutation coefficients, and the eigenvalues of thus formed matrix vary widely (several tens of orders), and hence no single method of solution is suitable for obtaining precise estimate of concentrations of isotopes. Therefore, different methods of solutions are followed, namely, matrix exponential method, Bateman series method, and Gauss-Seidel iteration method, as was followed in the ORIGEN-2 code. ISOGEN code is written in a modern computer language, VB.NET version 2013 for Windows operating system version 7, which enables one to provide many interactive features between the user and the program. The output results depend on the input neutron database employed and the time step involved in the calculations. The present program can display the information about the database files, and the user has to select one which suits the current need. The program prints the 'WARNING' information if the time step is too large, which is decided based on the built-in convergence criterion. Other salient interactive features provided are (i) inspection of input data that goes into calculation, (ii) viewing of radioactive decay sequence of isotopes (daughters, precursors, photons emitted) in a graphical format, (iii) solution of parent and daughter products by direct Bateman series solution method, (iv) quick input method and context sensitive prompts for guiding the novice user, (v) view of output tables for any parameter of interest, and (vi) output file can be read to generate new information and can be viewed or printed since the program stores basic nuclide concentration unlike other batch jobs. The sample

Measurement of apolipoprotein E and amyloid β clearance rates in the mouse brain using bolus stable isotope labeling

Science.gov (United States)

2012-01-01

Background Abnormal proteostasis due to alterations in protein turnover has been postulated to play a central role in several neurodegenerative diseases. Therefore, the development of techniques to quantify protein turnover in the brain is critical for understanding the pathogenic mechanisms of these diseases. We have developed a bolus stable isotope-labeling kinetics (SILK) technique coupled with multiple reaction monitoring mass spectrometry to measure the clearance of proteins in the mouse brain. Results Cohorts of mice were pulse labeled with 13 C6-leucine and the brains were isolated after pre-determined time points. The extent of label incorporation was measured over time using mass spectrometry to measure the ratio of labeled to unlabeled apolipoprotein E (apoE) and amyloid β (Aβ). The fractional clearance rate (FCR) was then calculated by analyzing the time course of disappearance for the labeled protein species. To validate the technique, apoE clearance was measured in mice that overexpress the low-density lipoprotein receptor (LDLR). The FCR in these mice was 2.7-fold faster than wild-type mice. To demonstrate the potential of this technique for understanding the pathogenesis of neurodegenerative disease, we applied our SILK technique to determine the effect of ATP binding cassette A1 (ABCA1) on both apoE and Aβ clearance. ABCA1 had previously been shown to regulate both the amount of apoE in the brain, along with the extent of Aβ deposition, and represents a potential molecular target for lowering brain amyloid levels in Alzheimer's disease patients. The FCR of apoE was increased by 1.9- and 1.5-fold in mice that either lacked or overexpressed ABCA1, respectively. However, ABCA1 had no effect on the FCR of Aβ, suggesting that ABCA1 does not regulate Aβ metabolism in the brain. Conclusions Our SILK strategy represents a straightforward, cost-effective, and efficient method to measure the clearance of proteins in the mouse brain. We expect that

Use of fluorescent proteins and color-coded imaging to visualize cancer cells with different genetic properties.

Science.gov (United States)

Hoffman, Robert M

2016-03-01

Fluorescent proteins are very bright and available in spectrally-distinct colors, enable the imaging of color-coded cancer cells growing in vivo and therefore the distinction of cancer cells with different genetic properties. Non-invasive and intravital imaging of cancer cells with fluorescent proteins allows the visualization of distinct genetic variants of cancer cells down to the cellular level in vivo. Cancer cells with increased or decreased ability to metastasize can be distinguished in vivo. Gene exchange in vivo which enables low metastatic cancer cells to convert to high metastatic can be color-coded imaged in vivo. Cancer stem-like and non-stem cells can be distinguished in vivo by color-coded imaging. These properties also demonstrate the vast superiority of imaging cancer cells in vivo with fluorescent proteins over photon counting of luciferase-labeled cancer cells.

A comparative study on the radioactive labelling of proteins

International Nuclear Information System (INIS)

Koch, G.K.; Heertje, I.; Stijn, F. van

1977-01-01

The main methods in protein labelling are exchange labelling, iodination, acylation and alkylation. The universal application of the techniques is evaluated by a number of criteria, derived from the demand that labelled proteins should be as identical to the native ones as possible. From our experiences on labelling methods it is concluded that reductive methylation meets most requirements. (orig.) [de

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

Energy Technology Data Exchange (ETDEWEB)

Giménez, Estela, E-mail: estelagimenez@ub.edu [Department of Analytical Chemistry, University of Barcelona, Diagonal 647, E-08028 Barcelona (Spain); Balmaña, Meritxell [Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, Campus Montilivi s/n, 17071 Girona (Spain); Figueras, Joan [Department of Surgery, Dr. Josep Trueta University Hospital, IdlBGi, 17007 Girona (Spain); Fort, Esther [Digestive Unit, Dr. Josep Trueta University Hospital, 17007 Girona (Spain); Bolós, Carme de [Gastroesophagic Cancer Research Group, Research Programme in Cancer, Hospital del Mar Medical Research Institute (IMIM), Dr. Aiguader, 88, 08003 Barcelona (Spain); Sanz-Nebot, Victòria [Department of Analytical Chemistry, University of Barcelona, Diagonal 647, E-08028 Barcelona (Spain); Peracaula, Rosa [Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, Campus Montilivi s/n, 17071 Girona (Spain); Rizzi, Andreas [Institute of Analytical Chemistry, University of Vienna, Währinger Straße 38, A-1090 Vienna (Austria)

2015-03-25

Highlights: • The method enables relative quantitation of hAGP glycans from pathological samples • Pancreatic cancer samples clearly showed an increase of hAGP fucosylated glycans. • Fucosylated glycans could be potential biomarkers for diagnosing pancreatic cancer. • The established method could be extremely useful to find novel glycoprotein biomarkers - Abstract: In this work we demonstrate the potential of glycan reductive isotope labeling (GRIL) using [{sup 12}C]- and [{sup 13}C]-coded aniline and zwitterionic hydrophilic interaction capillary liquid chromatography electrospray mass spectrometry (μZIC-HILIC-ESI-MS) for relative quantitation of glycosylation variants in selected glycoproteins present in samples from cancer patients. Human α{sub 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 μZIC-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 h

Isotope-labelled folic acid derivatives

International Nuclear Information System (INIS)

Lewin, N.; Wong, E.T.

1976-01-01

The suggestion deals with the production of folic acid derivatives suitable as indicators or tracers for analyses of serum folates. These folic acid derivatives contain folic acid which is bound by one or both carboxyl groups to the amino nitrogen of compounds such as, e.g., tyramine, glycyl tyrosine, tyrosine, or the methyl ester of tyrosine. The derivative obtained can be substituted by a gamma emitter, e.g. the iodine isotope I 125. The radioactive derivative is used in the method for the competitive protein bonding to determine endogenic folates in the serum. (UWI) [de

RFP tags for labeling secretory pathway proteins

Energy Technology Data Exchange (ETDEWEB)

Han, Liyang; Zhao, Yanhua [State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (China); Zhang, Xi; Peng, Jianxin [College of Life Sciences, Central China Normal University, Wuhan 430079, Hubei (China); Xu, Pingyong, E-mail: pyxu@ibp.ac.cn [Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Huan, Shuangyan, E-mail: shuangyanhuan@163.com [State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (China); Zhang, Mingshu, E-mail: mingshu1984@gmail.com [Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)

2014-05-09

Highlights: • Membrane protein Orai1 can be used to report the fusion properties of RFPs. • Artificial puncta are affected by dissociation constant as well as pKa of RFPs. • Among tested RFPs mOrange2 is the best choice for secretory protein labeling. - Abstract: Red fluorescent proteins (RFPs) are useful tools for live cell and multi-color imaging in biological studies. However, when labeling proteins in secretory pathway, many RFPs are prone to form artificial puncta, which may severely impede their further uses. Here we report a fast and easy method to evaluate RFPs fusion properties by attaching RFPs to an environment sensitive membrane protein Orai1. In addition, we revealed that intracellular artificial puncta are actually colocalized with lysosome, thus besides monomeric properties, pKa value of RFPs is also a key factor for forming intracellular artificial puncta. In summary, our current study provides a useful guide for choosing appropriate RFP for labeling secretory membrane proteins. Among RFPs tested, mOrange2 is highly recommended based on excellent monomeric property, appropriate pKa and high brightness.

LACAN Code for global simulation of SILVA laser isotope separation process

International Nuclear Information System (INIS)

Quaegebeur, J.P.; Goldstein, S.

1991-01-01

Functions used for the definition of a SILVA separator require quite a lot of dimensional and operating parameters. Sizing a laser isotope separation plant needs the determination of these parameters for optimization. In the LACAN simulation code, each elementary physical process is described by simplified models. An example is given for a uranium isotope separation plant whose separation power is optimized with 6 parameters [fr

Achievements in testing of the MGA and FRAM isotopic software codes under the DOE/NNSA-IRSN cooperation of gamma-ray isotopic measurement systems

International Nuclear Information System (INIS)

Vo, Duc; Wang, Tzu-Fang; Funk, Pierre; Weber, Anne-Laure; Pepin, Nicolas; Karcher, Anna

2009-01-01

DOE/NNSA and IRSN collaborated on a study of gamma-ray instruments and analysis methods used to perform isotopic measurements of special nuclear materials. The two agencies agreed to collaborate on the project in response to inconsistencies that were found in the various versions of software and hardware used to determine the isotopic abundances of uranium and plutonium. IRSN used software developed internally to test the MGA and FRAM isotopic analysis codes for criteria used to stop data acquisition. The stop-criterion test revealed several unusual behaviors in both the MGA and FRAM software codes.

Stable isotope labeled n-alkanes to assess digesta passage kinetics through the digestive tract of ruminants

NARCIS (Netherlands)

Warner, D.; Ferreira, L.M.M.; Breuer, M.J.H.; Dijkstra, J.; Pellikaan, W.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

ISODEP, A Fuel Depletion Analysis Code for Predicting Isotopic ...

African Journals Online (AJOL)

The trend of results was found to be consistent with those obtained by analytical and other numerical methods. Discovery and Innovation Vol. 13 no. 3/4 December (2001) pp. 184-195. KEY WORDS: depletion analysis, code, research reactor, simultaneous equations, decay of nuclides, radionuclitides, isotope. Résumé

TPASS: a gamma-ray spectrum analysis and isotope identification computer code

International Nuclear Information System (INIS)

Dickens, J.K.

1981-03-01

The gamma-ray spectral data-reduction and analysis computer code TPASS is described. This computer code is used to analyze complex Ge(Li) gamma-ray spectra to obtain peak areas corrected for detector efficiencies, from which are determined gamma-ray yields. These yields are compared with an isotope gamma-ray data file to determine the contributions to the observed spectrum from decay of specific radionuclides. A complete FORTRAN listing of the code and a complex test case are given

Mass spectrometric analysis of protein interactions

DEFF Research Database (Denmark)

Borch, Jonas; Jørgensen, Thomas J. D.; Roepstorff, Peter

2005-01-01

Mass spectrometry is a powerful tool for identification of interaction partners and structural characterization of protein interactions because of its high sensitivity, mass accuracy and tolerance towards sample heterogeneity. Several tools that allow studies of protein interaction are now...... available and recent developments that increase the confidence of studies of protein interaction by mass spectrometry include quantification of affinity-purified proteins by stable isotope labeling and reagents for surface topology studies that can be identified by mass-contributing reporters (e.g. isotope...... labels, cleavable cross-linkers or fragment ions. The use of mass spectrometers to study protein interactions using deuterium exchange and for analysis of intact protein complexes recently has progressed considerably....

Astatine-211 labelled proteins and their stability in vivo

International Nuclear Information System (INIS)

Yi Changhou; Jin Jannan; Zhang Shuyuan; Wang Ketai; Zhang Dayuan; Zhou Maolun

1989-01-01

211 At or 131 I labelled proteins, e.g. 211 At-IgG or 211 At-BSA (bovine serum albumin) were prepared by 211 At reaction with the diazo-compound of para-aminobenzoic acid, which is then conjugated with IgG or BSA via an acylation reaction. The 211 At-carbon bond was found metabolically stable under in vivo conditions. For the labelling of proteins with 211 At or 131 I, other methods of direct oxidation are also described. The results show that for the labelling of proteins with 211 At, high rate of incorporation can be obtained with hydrogen peroxide as oxidant, but the labelling of proteins with 131 I is more favourable with the strong oxidant Chloramine-T. (author) 12 refs.; 6 figs

Enhanced production and isotope enrichment of recombinant glycoproteins produced in cultured mammalian cells

Energy Technology Data Exchange (ETDEWEB)

Skelton, David; Goodyear, Abbey [Florida State University, Department of Chemistry and Biochemistry (United States); Ni, DaQun; Walton, Wendy J.; Rolle, Myron; Hare, Joan T. [Florida State University, Institute of Molecular Biophysics (United States); Logan, Timothy M., E-mail: tlogan@fsu.ed [Florida State University, Department of Chemistry and Biochemistry (United States)

2010-10-15

NMR studies of post-translationally modified proteins are complicated by the lack of an efficient method to produce isotope enriched recombinant proteins in cultured mammalian cells. We show that reducing the glucose concentration and substituting glutamate for glutamine in serum-free medium increased cell viability while simultaneously increasing recombinant protein yield and the enrichment of non-essential amino acids compared to culture in unmodified, serum-free medium. Adding dichloroacetate, a pyruvate dehydrogenase kinase inhibitor, further improves cell viability, recombinant protein yield, and isotope enrichment. We demonstrate the method by producing partially enriched recombinant Thy1 glycoprotein from Lec1 Chinese hamster ovary (CHO) cells using U-{sup 13}C-glucose and {sup 15}N-glutamate as labeled precursors. This study suggests that uniformly {sup 15}N,{sup 13}C-labeled recombinant proteins may be produced in cultured mammalian cells starting from a mixture of labeled essential amino acids, glucose, and glutamate.

Enhanced production and isotope enrichment of recombinant glycoproteins produced in cultured mammalian cells

International Nuclear Information System (INIS)

Skelton, David; Goodyear, Abbey; Ni, DaQun; Walton, Wendy J.; Rolle, Myron; Hare, Joan T.; Logan, Timothy M.

2010-01-01

NMR studies of post-translationally modified proteins are complicated by the lack of an efficient method to produce isotope enriched recombinant proteins in cultured mammalian cells. We show that reducing the glucose concentration and substituting glutamate for glutamine in serum-free medium increased cell viability while simultaneously increasing recombinant protein yield and the enrichment of non-essential amino acids compared to culture in unmodified, serum-free medium. Adding dichloroacetate, a pyruvate dehydrogenase kinase inhibitor, further improves cell viability, recombinant protein yield, and isotope enrichment. We demonstrate the method by producing partially enriched recombinant Thy1 glycoprotein from Lec1 Chinese hamster ovary (CHO) cells using U- 13 C-glucose and 15 N-glutamate as labeled precursors. This study suggests that uniformly 15 N, 13 C-labeled recombinant proteins may be produced in cultured mammalian cells starting from a mixture of labeled essential amino acids, glucose, and glutamate.

Amide or Amine: Determining the Origin of the 3300 cm−1 NH Mode in Protein SFG Spectra Using 15N Isotope Labels

Science.gov (United States)

Weidner, Tobias; Breen, Nicholas F.; Drobny, Gary P.; Castner, David G.

2009-01-01

Sum frequency generation (SFG) vibrational spectroscopy has been employed in biomaterials research and protein adsorption studies with growing success in recent years. A number of studies focusing on understanding SFG spectra of proteins and peptides at different interfaces have laid the foundation for future, more complex studies. In many cases a strong NH mode near 3300 cm−1 is observed in the SFG spectra, but the relationship of this mode to the peptide structure is uncertain since it has been assigned to either a backbone amide mode or a side chain related amine resonance. A thorough understanding of the SFG spectra of these first model systems is an important first step for future experiments. To clarify the origin of the NH SFG mode we studied 15N isotopically labeled 14-amino acid amphiphilic model peptides composed of lysine (K) and leucine (L) in an α-helical secondary structure (LKα14) that were adsorbed onto charged surfaces in situ at the solid-liquid interface. 15N substitution at the terminal amine group of the lysine side chains resulted in a red-shift of the NH mode of 9 cm−1 on SiO2 and 13 cm−1 on CaF2. This clearly shows the 3300 cm−1 NH feature is associated with side chain NH stretches and not with backbone amide modes. PMID:19873996

Amide or amine: determining the origin of the 3300 cm(-1) NH mode in protein SFG spectra using 15N isotope labels.

Science.gov (United States)

Weidner, Tobias; Breen, Nicholas F; Drobny, Gary P; Castner, David G

2009-11-26

Sum frequency generation (SFG) vibrational spectroscopy has been employed in biomaterials research and protein adsorption studies with growing success in recent years. A number of studies focusing on understanding SFG spectra of proteins and peptides at different interfaces have laid the foundation for future, more complex studies. In many cases, a strong NH mode near 3300 cm(-1) is observed in the SFG spectra, but the relationship of this mode to the peptide structure is uncertain, since it has been assigned to either a backbone amide mode or a side chain related amine resonance. A thorough understanding of the SFG spectra of these first model systems is an important first step for future experiments. To clarify the origin of the NH SFG mode, we studied (15)N isotopically labeled 14-amino acid amphiphilic model peptides composed of lysine (K) and leucine (L) in an alpha-helical secondary structure (LKalpha14) that were adsorbed onto charged surfaces in situ at the solid-liquid interface. (15)N substitution at the terminal amine group of the lysine side chains resulted in a red-shift of the NH mode of 9 cm(-1) on SiO(2) and 13 cm(-1) on CaF(2). This clearly shows the 3300 cm(-1) NH feature is associated with side chain NH stretches and not with backbone amide modes.

Addressing Raman features of individual layers in isotopically labeled Bernal stacked bilayer graphene

Czech Academy of Sciences Publication Activity Database

da Costa, Sara; Ek Weis, Johan; Frank, Otakar; Fridrichová, Michaela; Kalbáč, Martin

2016-01-01

Roč. 3, č. 2 (2016), 025022 ISSN 2053-1583 R&D Projects: GA MŠk LL1301 Institutional support: RVO:61388955 Keywords : graphene bilayer * Raman spectroscopy * isotope labeling Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.937, year: 2016

Traceless affinity labeling of endogenous proteins for functional analysis in living cells.

Science.gov (United States)

Hayashi, Takahiro; Hamachi, Itaru

2012-09-18

Protein labeling and imaging techniques have provided tremendous opportunities to study the structure, function, dynamics, and localization of individual proteins in the complex environment of living cells. Molecular biology-based approaches, such as GFP-fusion tags and monoclonal antibodies, have served as important tools for the visualization of individual proteins in cells. Although these techniques continue to be valuable for live cell imaging, they have a number of limitations that have only been addressed by recent progress in chemistry-based approaches. These chemical approaches benefit greatly from the smaller probe sizes that should result in fewer perturbations to proteins and to biological systems as a whole. Despite the research in this area, so far none of these labeling techniques permit labeling and imaging of selected endogenous proteins in living cells. Researchers have widely used affinity labeling, in which the protein of interest is labeled by a reactive group attached to a ligand, to identify and characterize proteins. Since the first report of affinity labeling in the early 1960s, efforts to fine-tune the chemical structures of both the reactive group and ligand have led to protein labeling with excellent target selectivity in the whole proteome of living cells. Although the chemical probes used for affinity labeling generally inactivate target proteins, this strategy holds promise as a valuable tool for the labeling and imaging of endogenous proteins in living cells and by extension in living animals. In this Account, we summarize traceless affinity labeling, a technique explored mainly in our laboratory. In our overview of the different labeling techniques, we emphasize the challenge of designing chemical probes that allow for dissociation of the affinity module (often a ligand) after the labeling reaction so that the labeled protein retains its native function. This feature distinguishes the traceless labeling approach from the traditional

Computer codes for tasks in the fields of isotope and radiation research

International Nuclear Information System (INIS)

Friedrich, K.; Gebhardt, O.

1978-11-01

Concise descriptions of computer codes developed for solving problems in the fields of isotope and radiation research at the Zentralinstitut fuer Isotopen- und Strahlenforschung (ZfI) are compiled. In part two the structure of the ZfI program library MABIF is outlined and a complete list of all codes available is given

Proteins are secreted from heterogeneous prestored sources in the exocrine pancreas

International Nuclear Information System (INIS)

Miller, P.E.; Adelson, J.W.

1987-01-01

Recent studies demonstrating nonparallel regulated secretion of prestored digestive enzymes in tightly linked groups consistent with the exocytosis mechanisms led the authors to predict that digestive enzymes would be found to be secreted from heterogeneous sources within the exocrine pancreas. They explored whether the gland was heterogeneous with respect to its sources of prestored secretory proteins with a double isotopic label method not dependent on activity of secreted digestive enzymes. Rabbit pancreatic proteins were double labeled in vivo by injection of each animal with chemically identical but isotopically distinct mixtures of 3 H- and 14 C-labeled amino acids, which were administered separately or together on consecutive days after partial depletion of prestored proteins by administration of cholecystokinin (CCK), methacholine chloride, or saline in a protocol in which order of both isotope and secretagogue administration was varied. Three days after labeling, proteins were recovered by collection from cannulated pancreatic ducts of anesthetized animals after stimulation with alternating increasing doses of CCK and methacholine chloride. Correlation and regression analysis of isotopic outputs and variance analysis of specific radioactivities of secreted proteins showed sequestration into and secretion from heterogeneous pools of secretory proteins, directly confirming the hypothesis. These results provide a cell biological mechanism explaining regulated nonparallel secretion of digestive enzymes

Stable isotope labeling – Liquid chromatography/mass spectrometry for quantitative analysis of androgenic and progestagenic steroids

International Nuclear Information System (INIS)

Guo, Ning; Liu, Ping; Ding, Jun; Zheng, Shu-Jian; Yuan, Bi-Feng; Feng, Yu-Qi

2016-01-01

Steroid hormones play important roles in mammal at very low concentrations and are associated with numerous endocrinology and oncology diseases. Therefore, quantitative analysis of steroid hormones can provide crucial information for uncovering underlying mechanisms of steroid hormones related diseases. In the current study, we developed a sensitive method for the detection of steroid hormones (progesterone, dehydroepiandrosterone, testosterone, pregnenolone, 17-hydroxyprogesterone, androstenedione and 17α-hydroxypregnenolone) in body fluids by stable isotope labeling coupled with liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) analysis. In this respect, a pair of isotopes labeling reagents, Girard reagent P (GP) and d_5-Girard reagent P (d_5-GP), were synthesized and utilized to label steroid hormones in follicular fluid samples and steroid hormone standards, respectively. The heavy labeled standards were used as internal standards for quantification to minimize quantitation deviation in MS analysis due to the matrix and ion suppression effects. The ionization efficiencies of steroid hormones were greatly improved by 4–504 folds through the introduction of a permanent charged moiety of quaternary ammonium from GP. Using the developed method, we successfully quantified steroid hormones in human follicular fluid. We found that the contents of testosterone and androstenedione exhibited significant increase while the content of pregnenolone had significant decrease in follicular fluid of polycystic ovarian syndrome (PCOS) patients compared with healthy controls, indicating that these steroid hormones with significant change may contribute to the pathogenesis of PCOS. Taken together, the developed stable isotope labeling coupled LC-ESI-MS/MS analysis demonstrated to be a promising method for the sensitive and accurate determination of steroid hormones, which may facilitate the in-depth investigation of steroid hormones related

Stable isotope labeling – Liquid chromatography/mass spectrometry for quantitative analysis of androgenic and progestagenic steroids

Energy Technology Data Exchange (ETDEWEB)

Guo, Ning; Liu, Ping; Ding, Jun; Zheng, Shu-Jian; Yuan, Bi-Feng; Feng, Yu-Qi, E-mail: yqfeng@whu.edu.cn

2016-01-28

Steroid hormones play important roles in mammal at very low concentrations and are associated with numerous endocrinology and oncology diseases. Therefore, quantitative analysis of steroid hormones can provide crucial information for uncovering underlying mechanisms of steroid hormones related diseases. In the current study, we developed a sensitive method for the detection of steroid hormones (progesterone, dehydroepiandrosterone, testosterone, pregnenolone, 17-hydroxyprogesterone, androstenedione and 17α-hydroxypregnenolone) in body fluids by stable isotope labeling coupled with liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) analysis. In this respect, a pair of isotopes labeling reagents, Girard reagent P (GP) and d{sub 5}-Girard reagent P (d{sub 5}-GP), were synthesized and utilized to label steroid hormones in follicular fluid samples and steroid hormone standards, respectively. The heavy labeled standards were used as internal standards for quantification to minimize quantitation deviation in MS analysis due to the matrix and ion suppression effects. The ionization efficiencies of steroid hormones were greatly improved by 4–504 folds through the introduction of a permanent charged moiety of quaternary ammonium from GP. Using the developed method, we successfully quantified steroid hormones in human follicular fluid. We found that the contents of testosterone and androstenedione exhibited significant increase while the content of pregnenolone had significant decrease in follicular fluid of polycystic ovarian syndrome (PCOS) patients compared with healthy controls, indicating that these steroid hormones with significant change may contribute to the pathogenesis of PCOS. Taken together, the developed stable isotope labeling coupled LC-ESI-MS/MS analysis demonstrated to be a promising method for the sensitive and accurate determination of steroid hormones, which may facilitate the in-depth investigation of steroid hormones

Obtention of a prosthetic group for labelling of radioiodinated proteins

International Nuclear Information System (INIS)

Santos, Josefina da S.; Colturato, Maria Tereza; Araujo, Elaine B. de

2000-01-01

Antibodies and peptides labeled with radionuclides has been extensively used in radioimmunotherapy and radioimmunodetection. The principal problem with the use of radioiodinated proteins is the in vivo dehalogenation. The use of prosthetic groups for indirect labeling of proteins with radioiodine has showed to be useful on labeling proteins with greater in vivo stability. A procedure is described for the preparation of an radioiodinated prosthetic group (N-succinimidyl 4-radioiodine-benzoate-SIB), using procedure described by Stocklin et al, with the iodination of p-bromo-benzoic acid and subsequent reaction with TSTU. Preliminary labeling results showed that the prosthetic group can be obtained in a good yield. The coupling of the SIB to the protein will be studied using human IgG as protein model. (author)

Investigation into reaction of heterogenous isotopic exchange with gaseoUs tritium in solution for preparation labelled lipid compounds

International Nuclear Information System (INIS)

Shevchenko, V.P.; Myasoedov, N.F.

1983-01-01

The applicability of the method of heterogeneous catalytic isotopic exchange with gaseous tritium in the solution for the production of labelled lipide preparations is studied. Labelled saturated and unsaturated aliphatic acids, prostaglandins, phospholipides and sphingolipides are prepared

Incorporation of radioactive amino acids into protein in isolated rat hepatocytes

International Nuclear Information System (INIS)

Seglin, P.O.

1976-01-01

The incorporation of radioactivity from a 14 C-labelled amino acid mixture (algal protein hydrolysate) into protein in isolated rat hepatocytes has been studied. The incorporation rate declined with increasing cell concentration, an effect which could be explained by isotope consumption, partly (and largely) by isotope dilution due to the formation of non-labelled amino acids by the cells. At a high extracellular amino acid concentration, the rate of incorporation into protein became independent of cell concentration because the isotope dilution effect was now quantitatively insignificant. The time course of protein labelling at various cell concentrations correlated better with the intracellular than with the extracellular amino acid specific activity, suggesting that amino acids for protein synthesis were taken from an intracellular pool. With increasing extracellular amino acid concentrations, both the intracellular amino acid concentration, the intracellular radioactivity and the rate of incorporation into protein increased. Protein labelling exhibited a distinct time lag at high amino acid concentrations, presumable reflecting the time-dependent expansion of the intracellular amino acid pool. The gradual increase in the rate of protein labelling could be due either to an increased intracellular specific activity, or to a real stimulation of protein synthesis by amino acids, depending on whether the total intracellular amino acid pool or just the expandable compartment is the precursor pool for protein synthesis

Protein Stable Isotope Fingerprinting (P-SIF): Multidimensional Protein Chromatography Coupled to Stable Isotope-Ratio Mass Spectrometry

Science.gov (United States)

Pearson, A.; Bovee, R. J.; Mohr, W.; Tang, T.

2012-12-01

As metagenomics increases our insight into microbial community diversity and metabolic potential, new approaches are required to determine the biogeochemical expression of this potential within ecosystems. Because stable isotopic analysis of the major bioactive elements (C, N) has been used historically to map flows of substrates and energy among macroscopic food webs, similar principles may apply to microbes. To address this challenge, we have developed a new analytical approach called Protein Stable Isotope Fingerprinting (P-SIF). P-SIF generates natural stable isotopic fingerprints of microbial individual or community proteomes. The main advantage of P-SIF is the potential to bridge the gap between diversity and function, thereby providing a window into the "black box" of environmental microbiology and helping to decipher the roles of uncultivated species. Our method implements a three-way, orthogonal scheme to separate mixtures of whole proteins into subfractions dominated by single or closely-related proteins. Protein extracts first are isoelectrically focused in a gel-free technique that yields 12 fractions separated over a gradient of pH 3-10. Each fraction then is separated by size-exclusion chromatography into 20 pools, ranging from >100kD to ~10kD. Finally, each of these pools is subjected to HPLC and collected in 40 time-slices based on protein hydrophobicity. Theoretical calculation reveals that the true chromatographic resolution of the total scheme is 5000, somewhat less than the 9600 resulting fractions. High-yielding fractions are subjected to δ13C analysis by spooling-wire microcombustion irMS (SWiM-irMS) optimized for samples containing 1-5 nmol carbon. Here we will present the method, results for a variety of pure cultures, and preliminary data for a sample of mixed environmental proteins. The data show the promise of this method for unraveling the metabolic complexity hidden within microbial communities.

Measurement of Hepatic Protein Fractional Synthetic Rate with Stable Isotope Labeling Technique in Thapsigargin Stressed HepG2 Cells

Science.gov (United States)

Song, Juquan; Zhang, Xiao-jun; Boehning, Darren; Brooks, Natasha C.; Herndon, David N.; Jeschke, Marc G.

2012-01-01

Severe burn-induced liver damage and dysfunction is associated with endoplasmic reticulum (ER) stress. ER stress has been shown to regulate global protein synthesis. In the current study, we induced ER stress in vitro and estimated the effect of ER stress on hepatic protein synthesis. The aim was two-fold: (1) to establish an in vitro model to isotopically measure hepatic protein synthesis and (2) to evaluate protein fractional synthetic rate (FSR) in response to ER stress. Human hepatocellular carcinoma cells (HepG2) were cultured in medium supplemented with stable isotopes 1,2-13C2-glycine and L-[ring-13C6]phenylalanine. ER stress was induced by exposing the cells to 100 nM of thapsigargin (TG). Cell content was collected from day 0 to 14. Alterations in cytosolic calcium were measured by calcium imaging and ER stress markers were confirmed by Western blotting. The precursor and product enrichments were detected by GC-MS analysis for FSR calculation. We found that the hepatic protein FSR were 0.97±0.02 and 0.99±0.05%/hr calculated from 1,2-13C2-glycine and L-[ring-13C6]phenylalanine, respectively. TG depleted ER calcium stores and induced ER stress by upregulating p-IRE-1 and Bip. FSR dramatically decreased to 0.68±0.03 and 0.60±0.06%/hr in the TG treatment group (pisotope tracer incorporation technique is a useful method for studying the effects of ER stress on hepatic protein synthesis. PMID:22298954

Adaptation of a Commonly Used, Chemically Defined Medium for Human Embryonic Stem Cells to Stable Isotope Labeling with Amino Acids in Cell Culture

DEFF Research Database (Denmark)

Liberski, A. R.; Al-Noubi, M. N.; Rahman, Z. H.

2013-01-01

Metabolic labeling with stable isotopes is a prominent technique for comparative quantitative proteomics, and stable isotope labeling with amino acids in cell culture (SILAC) is the most commonly used approach. SILAC is, however, traditionally limited to simple tissue culture regimens and only ra...

Semantic role labeling for protein transport predicates

Directory of Open Access Journals (Sweden)

Martin James H

2008-06-01

Full Text Available Abstract Background Automatic semantic role labeling (SRL is a natural language processing (NLP technique that maps sentences to semantic representations. This technique has been widely studied in the recent years, but mostly with data in newswire domains. Here, we report on a SRL model for identifying the semantic roles of biomedical predicates describing protein transport in GeneRIFs – manually curated sentences focusing on gene functions. To avoid the computational cost of syntactic parsing, and because the boundaries of our protein transport roles often did not match up with syntactic phrase boundaries, we approached this problem with a word-chunking paradigm and trained support vector machine classifiers to classify words as being at the beginning, inside or outside of a protein transport role. Results We collected a set of 837 GeneRIFs describing movements of proteins between cellular components, whose predicates were annotated for the semantic roles AGENT, PATIENT, ORIGIN and DESTINATION. We trained these models with the features of previous word-chunking models, features adapted from phrase-chunking models, and features derived from an analysis of our data. Our models were able to label protein transport semantic roles with 87.6% precision and 79.0% recall when using manually annotated protein boundaries, and 87.0% precision and 74.5% recall when using automatically identified ones. Conclusion We successfully adapted the word-chunking classification paradigm to semantic role labeling, applying it to a new domain with predicates completely absent from any previous studies. By combining the traditional word and phrasal role labeling features with biomedical features like protein boundaries and MEDPOST part of speech tags, we were able to address the challenges posed by the new domain data and subsequently build robust models that achieved F-measures as high as 83.1. This system for extracting protein transport information from Gene

A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study

Directory of Open Access Journals (Sweden)

Haußmann Ute

2011-06-01

Full Text Available Abstract Background Mass spectrometry-based proteomics has reached a stage where it is possible to comprehensively analyze the whole proteome of a cell in one experiment. Here, the employment of stable isotopes has become a standard technique to yield relative abundance values of proteins. In recent times, more and more experiments are conducted that depict not only a static image of the up- or down-regulated proteins at a distinct time point but instead compare developmental stages of an organism or varying experimental conditions. Results Although the scientific questions behind these experiments are of course manifold, there are, nevertheless, two questions that commonly arise: 1 which proteins are differentially regulated regarding the selected experimental conditions, and 2 are there groups of proteins that show similar abundance ratios, indicating that they have a similar turnover? We give advice on how these two questions can be answered and comprehensively compare a variety of commonly applied computational methods and their outcomes. Conclusions This work provides guidance through the jungle of computational methods to analyze mass spectrometry-based isotope-labeled datasets and recommends an effective and easy-to-use evaluation strategy. We demonstrate our approach with three recently published datasets on Bacillus subtilis 12 and Corynebacterium glutamicum 3. Special focus is placed on the application and validation of cluster analysis methods. All applied methods were implemented within the rich internet application QuPE 4. Results can be found at http://qupe.cebitec.uni-bielefeld.de.

Analytical performance of reciprocal isotope labeling of proteome digests for quantitative proteomics and its application for comparative studies of aerobic and anaerobic Escherichia coli proteomes

International Nuclear Information System (INIS)

Lo, Andy; Weiner, Joel H.; Li, Liang

2013-01-01

Graphical abstract: -- Highlights: •Investigating a strategy of reciprocal isotope labeling of comparative samples. •Filtering out incorrect peptide identification or quantification values. •Analyzing the proteome changes of E. coli cells grown aerobically or anaerobically. •Presenting guidelines for reciprocal labeling experimental design. -- Abstract: Due to limited sample amounts, instrument time considerations, and reagent costs, only a small number of replicate experiments are typically performed for quantitative proteome analyses. Generation of reproducible data that can be readily assessed for consistency within a small number of datasets is critical for accurate quantification. We report our investigation of a strategy using reciprocal isotope labeling of two comparative samples as a tool for determining proteome changes. Reciprocal labeling was evaluated to determine the internal consistency of quantified proteome changes from Escherichia coli grown under aerobic and anaerobic conditions. Qualitatively, the peptide overlap between replicate analyses of the same sample and reverse labeled samples were found to be within 8%. Quantitatively, reciprocal analyses showed only a slight increase in average overall inconsistency when compared with replicate analyses (1.29 vs. 1.24-fold difference). Most importantly, reverse labeling was successfully used to identify spurious values resulting from incorrect peptide identifications and poor peak fitting. After removal of 5% of the peptide data with low reproducibility, a total of 275 differentially expressed proteins (>1.50-fold difference) were consistently identified and were then subjected to bioinformatics analysis. General considerations and guidelines for reciprocal labeling experimental design and biological significance of obtained results are discussed

Temporal Profiling and Pulsed SILAC Labeling Identify Novel Secreted Proteins during ex vivo Osteoblast Differentiation of Human Stromal Stem Cells

DEFF Research Database (Denmark)

Kristensen, Lars P; Chen, Li; Nielsen, Maria Overbeck

2012-01-01

, is not fully established. To address these questions, we quantified the temporal dynamics of the human stromal (mesenchymal, skeletal) stem cell (hMSC) secretome during ex vivo OB differentiation using stable isotope labeling by amino acids in cell culture (SILAC). In addition, we employed pulsed SILAC...... the identification of novel factors produced by hMSC with potential role in OB differentiation. Our study demonstrates that the secretome of osteoblastic cells is more complex than previously reported and supports the emerging evidence that osteoblastic cells secrete proteins with endocrine functions and regulate...... regulators of OB differentiation. Furthermore, we studied the biological effects of one of these proteins, the hormone stanniocalcin 2 (STC2) and demonstrated its autocrine effects in enhancing osteoblastic differentiation of hMSC. In conclusion, combining complete and pulsed SILAC labeling facilitated...

Site-specific Orientation of an α-helical Peptide Ovispirin-1 from Isotope Labeled SFG Spectroscopy

Science.gov (United States)

Ding, Bei; Laaser, Jennifer E.; Liu, Yuwei; Wang, Pengrui; Zanni, Martin T.; Chen, Zhan

2013-01-01

Sum-frequency generation (SFG) vibrational spectroscopy is often used to probe the backbone structures and orientations of polypeptides at surfaces. Using the ovispirin-1 polypeptide at the solid/liquid interface of polystyrene, we demonstrate for the first time that SFG can probe the polarization response of a single isotope labeled residue. To interpret the spectral intensities, we simulated the spectra using an excitonic Hamiltonian approach. We show that the polarization dependence of either the label or the unlabeled amide I band alone does not provide sufficient structural constraints to obtain both the tilt and the twist of the ovispirin helix at a solid/liquid interface, but that both can be determined from the polarization dependence of the complete spectrum. For ovispirin, the detailed analysis of the polarized SFG experimental data shows that the helix axis is tilted at roughly 138 degrees from the surface normal, and the transition dipole of the isotope labeled C=O group is tilted at 23 degrees from the surface normal, with the hydrophobic region facing the polystyrene surface. We further demonstrated that the Hamiltonian approach is able to address the coupling effect and the structural disorder. For comparison, we also collected the FTIR spectrum of ovispirin under similar conditions, which reveals the enhanced sensitivity of SFG for structural studies of single monolayer peptide surfaces. Our study provides insight into how structural and environmental effects appear in SFG spectra of the amide I band and establishes that SFG of isotope labeled peptides will be a powerful technique for elucidating secondary structures with residue-by-residue resolution. PMID:24228619

Site-specific orientation of an α-helical peptide ovispirin-1 from isotope-labeled SFG spectroscopy.

Science.gov (United States)

Ding, Bei; Laaser, Jennifer E; Liu, Yuwei; Wang, Pengrui; Zanni, Martin T; Chen, Zhan

2013-11-27

Sum-frequency generation (SFG) vibrational spectroscopy is often used to probe the backbone structures and orientations of polypeptides at surfaces. Using the ovispirin-1 polypeptide at the solid/liquid interface of polystyrene, we demonstrate for the first time that SFG can probe the polarization response of a single-isotope-labeled residue. To interpret the spectral intensities, we simulated the spectra using an excitonic Hamiltonian approach. We show that the polarization dependence of either the label or the unlabeled amide I band alone does not provide sufficient structural constraints to obtain both the tilt and the twist of the ovispirin helix at a solid/liquid interface, but that both can be determined from the polarization dependence of the complete spectrum. For ovispirin, the detailed analysis of the polarized SFG experimental data shows that the helix axis is tilted at roughly 138° from the surface normal, and the transition dipole of the isotope-labeled C═O group is tilted at 23° from the surface normal, with the hydrophobic region facing the polystyrene surface. We further demonstrate that the Hamiltonian approach is able to address the coupling effect and the structural disorder. For comparison, we also collected the FTIR spectrum of ovispirin under similar conditions, which reveals the enhanced sensitivity of SFG for structural studies of single monolayer peptide surfaces. Our study provides insight into how structural and environmental effects appear in SFG spectra of the amide I band and establishes that SFG of isotope-labeled peptides will be a powerful technique for elucidating secondary structures with residue-by-residue resolution.

Labelling strategies for enhanced application of ICPMS in protein analysis

International Nuclear Information System (INIS)

Bettmer, J.; Kutscher, D.J.

2009-01-01

Full text: Quantitative protein analysis is one of today's challenges in analytical chemistry. Herein, mass spectrometric techniques play an important role with the use of both label-free and labelling approaches. In the field of ICPMS, the latter approach is attractive as it can provide highly sensitive detection of proteins after labelling with metal-containing compounds. Following a brief introduction to the different strategies described in the literature, this presentation will be focussed on protein labelling using a mercury compound (p-hydroxymercuribenzoic acid, pHMB). Besides fundamental studies on the derivatization process itself, a strategy will be presented in which absolute protein quantification can be achieved. Finally, the potential, but also limitations of the technique will be highlighted. (author)

12G: code for conversion of isotope-ordered cross-section libraries into group-ordered cross-section libraries

International Nuclear Information System (INIS)

Resnik, W.M. II; Bosler, G.E.

1977-09-01

Many current reactor physics codes accept cross-section libraries in an isotope-ordered form, convert them with internal preprocessing routines to a group-ordered form, and then perform calculations using these group-ordered data. Occasionally, because of storage and time limitations, the preprocessing routines in these codes cannot convert very large multigroup isotope-ordered libraries. For this reason, the I2G code, i.e., ISOTXS to GRUPXS, was written to convert externally isotope-ordered cross section libraries in the standard file format called ISOTXS to group-ordered libraries in the standard format called GRUPXS. This code uses standardized multilevel data management routines which establish a strategy for the efficient conversion of large libraries. The I2G code is exportable contingent on access to, and an intimate familiarization with, the multilevel routines. These routines are machine dependent, and therefore must be provided by the importing facility. 6 figures, 3 tables

Quantification of isotope-labelled and unlabelled folates in plasma, ileostomy and food samples.

Science.gov (United States)

Büttner, Barbara E; Öhrvik, Veronica E; Witthöft, Cornelia M; Rychlik, Michael

2011-01-01

New stable isotope dilution assays were developed for the simultaneous quantitation of [(13)C(5)]-labelled and unlabelled 5-methyltetrahydrofolic acid, 5-formyltetrahydrofolic acid, folic acid along with unlabelled tetrahydrofolic acid and 10-formylfolic acid in clinical samples deriving from human bioavailability studies, i.e. plasma, ileostomy samples, and food. The methods were based on clean-up by strong anion exchange followed by LC-MS/MS detection. Deuterated analogues of the folates were applied as the internal standards in the stable isotope dilution assays. Assay sensitivity was sufficient to detect all relevant folates in the respective samples as their limits of detection were below 0.62 nmol/L in plasma and below 0.73 μg/100 g in food or ileostomy samples. Quantification of the [(13)C(5)]-label in clinical samples offers the possibility to differentiate between folate from endogenous body pools and the administered dose when executing bioavailability trials.

[Non-invasive analysis of proteins in living cells using NMR spectroscopy].

Science.gov (United States)

Tochio, Hidehito; Murayama, Shuhei; Inomata, Kohsuke; Morimoto, Daichi; Ohno, Ayako; Shirakawa, Masahiro

2015-01-01

NMR spectroscopy enables structural analyses of proteins and has been widely used in the structural biology field in recent decades. NMR spectroscopy can be applied to proteins inside living cells, allowing characterization of their structures and dynamics in intracellular environments. The simplest "in-cell NMR" approach employs bacterial cells; in this approach, live Escherichia coli cells overexpressing a specific protein are subjected to NMR. The cells are grown in an NMR active isotope-enriched medium to ensure that the overexpressed proteins are labeled with the stable isotopes. Thus the obtained NMR spectra, which are derived from labeled proteins, contain atomic-level information about the structure and dynamics of the proteins. Recent progress enables us to work with higher eukaryotic cells such as HeLa and HEK293 cells, for which a number of techniques have been developed to achieve isotope labeling of the specific target protein. In this review, we describe successful use of electroporation for in-cell NMR. In addition, (19)F-NMR to characterize protein-ligand interactions in cells is presented. Because (19)F nuclei rarely exist in natural cells, when (19)F-labeled proteins are delivered into cells and (19)F-NMR signals are observed, one can safely ascertain that these signals originate from the delivered proteins and not other molecules.

ICT: isotope correction toolbox.

Science.gov (United States)

Jungreuthmayer, Christian; Neubauer, Stefan; Mairinger, Teresa; Zanghellini, Jürgen; Hann, Stephan

2016-01-01

Isotope tracer experiments are an invaluable technique to analyze and study the metabolism of biological systems. However, isotope labeling experiments are often affected by naturally abundant isotopes especially in cases where mass spectrometric methods make use of derivatization. The correction of these additive interferences--in particular for complex isotopic systems--is numerically challenging and still an emerging field of research. When positional information is generated via collision-induced dissociation, even more complex calculations for isotopic interference correction are necessary. So far, no freely available tools can handle tandem mass spectrometry data. We present isotope correction toolbox, a program that corrects tandem mass isotopomer data from tandem mass spectrometry experiments. Isotope correction toolbox is written in the multi-platform programming language Perl and, therefore, can be used on all commonly available computer platforms. Source code and documentation can be freely obtained under the Artistic License or the GNU General Public License from: https://github.com/jungreuc/isotope_correction_toolbox/ {christian.jungreuthmayer@boku.ac.at,juergen.zanghellini@boku.ac.at} Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Temperature-induced strain and doping in monolayer and bilayer isotopically labeled graphene

Czech Academy of Sciences Publication Activity Database

Verhagen, Timotheus; Drogowska, Karolina; Kalbáč, Martin; Vejpravová, Jana

2015-01-01

Roč. 92, č. 12 (2015), "125437-1"-"125437-9" ISSN 1098-0121 R&D Projects: GA ČR GA15-02196S; GA MŠk LL1301 Institutional support: RVO:68378271 ; RVO:61388955 Keywords : isotopically labeled graphene * temperature dependence * Raman spectroscopy * phonons Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.736, year: 2014

Retrieval-based Face Annotation by Weak Label Regularized Local Coordinate Coding.

Science.gov (United States)

Wang, Dayong; Hoi, Steven C H; He, Ying; Zhu, Jianke; Mei, Tao; Luo, Jiebo

2013-08-02

Retrieval-based face annotation is a promising paradigm of mining massive web facial images for automated face annotation. This paper addresses a critical problem of such paradigm, i.e., how to effectively perform annotation by exploiting the similar facial images and their weak labels which are often noisy and incomplete. In particular, we propose an effective Weak Label Regularized Local Coordinate Coding (WLRLCC) technique, which exploits the principle of local coordinate coding in learning sparse features, and employs the idea of graph-based weak label regularization to enhance the weak labels of the similar facial images. We present an efficient optimization algorithm to solve the WLRLCC task. We conduct extensive empirical studies on two large-scale web facial image databases: (i) a Western celebrity database with a total of $6,025$ persons and $714,454$ web facial images, and (ii)an Asian celebrity database with $1,200$ persons and $126,070$ web facial images. The encouraging results validate the efficacy of the proposed WLRLCC algorithm. To further improve the efficiency and scalability, we also propose a PCA-based approximation scheme and an offline approximation scheme (AWLRLCC), which generally maintains comparable results but significantly saves much time cost. Finally, we show that WLRLCC can also tackle two existing face annotation tasks with promising performance.

Compliance status of product labels to the international code on marketing of breast milk substitutes.

Science.gov (United States)

Ergin, Ahmet; Hatipoğlu, Celile; Bozkurt, Ali Ihsan; Erdoğan, Aslı; Güler, Serdar; Ince, Gülberat; Kavurgacı, Nuran; Oz, Ahmet; Yeniay, Mustafa K

2013-01-01

The aim of this study was to determine the compliance status of product labels regarding Article 9 of the International Code on Marketing of Breast-milk Substitutes (the Code) in Denizli province, Turkey. A cross-sectional study design was employed to determine the compliance status. The product labels were obtained from a convenience sample of five supermarkets, one store and 5 pharmacies in the City centre and district of Honaz. Using a data collection form prepared by previously published studies, data were collected between July 26, 2010 and August 06, 2010. Data collection form included 13 criteria. In addition, we checked the boxes for the availability of a Turkish written label. Forty product labels of 7 companies were reached and evaluated. These products consisted of 83.0% of the products marketed by these companies in Turkey. Thirty seven (92.5%) of the labels violated Article 9 of the Code in terms of one or more criteria. Thirty four (85.0%) of the labels had photos or pictures idealizing the use of infant formula. Nine (22.5%) had a photo, a picture or any representation of an infant, and five (12.5%) had text which idealize the use of infant formula or discouraging breastfeeding. Eight (20%) did not state that breastfeeding is the best. Four (10%) had a term such as 'similar to breast milk or human milk'. In conclusion, the majority of the product labels of breast milk substitutes marketed in our country violate the Code. It is appropriate that the Turkish Ministry of Health, medical organizations, companies, and NGOs work more actively to increase awareness of this issue.

Multiple optical code-label processing using multi-wavelength frequency comb generator and multi-port optical spectrum synthesizer.

Science.gov (United States)

Moritsuka, Fumi; Wada, Naoya; Sakamoto, Takahide; Kawanishi, Tetsuya; Komai, Yuki; Anzai, Shimako; Izutsu, Masayuki; Kodate, Kashiko

2007-06-11

In optical packet switching (OPS) and optical code division multiple access (OCDMA) systems, label generation and processing are key technologies. Recently, several label processors have been proposed and demonstrated. However, in order to recognize N different labels, N separate devices are required. Here, we propose and experimentally demonstrate a large-scale, multiple optical code (OC)-label generation and processing technology based on multi-port, a fully tunable optical spectrum synthesizer (OSS) and a multi-wavelength electro-optic frequency comb generator. The OSS can generate 80 different OC-labels simultaneously and can perform 80-parallel matched filtering. We also demonstrated its application to OCDMA.

Synthesis of stereoarray isotope labeled (SAIL) lysine via the "head-to-tail" conversion of SAIL glutamic acid.

Science.gov (United States)

Terauchi, Tsutomu; Kamikawai, Tomoe; Vinogradov, Maxim G; Starodubtseva, Eugenia V; Takeda, Mitsuhiro; Kainosho, Masatsune

2011-01-07

A stereoarray isotope labeled (SAIL) lysine, (2S,3R,4R,5S,6R)-[3,4,5,6-(2)H(4);1,2,3,4,5,6-(13)C(6);2,6-(15)N(2)]lysine, was synthesized by the "head-to-tail" conversion of SAIL-Glu, (2S,3S,4R)-[3,4-(2)H(2);1,2,3,4,5-(13)C(5);2-(15)N]glutamic acid, with high stereospecificities for all five chiral centers. With the SAIL-Lys in hand, the unambiguous simultaneous stereospecific assignments were able to be established for each of the prochiral protons within the four methylene groups of the Lys side chains in proteins.

A general procedure for isotopic (deuterium) labelling of non-steroidal antiinflammatory 2-arylpropionic acids

International Nuclear Information System (INIS)

Castell, J.V.; Martinez, L.A.; Universidad Politecnica de Valencia; Miranda, M.A.; Tarrega, Pilar

1994-01-01

Alkaline treatment of nonsteroidal antiinflammatory 2-arylpropionic acids in deuterium oxide led in all cases to isotopic exchange of the proton located at the α-position of the side chain. Monodeuteration was observed in the case of carprofen, ibuprofen, ketoprofen, fenoprofen, flurbiprofen and naproxen. Additional exchange of one or two protons of the heterocyclic ring occurred in indoprofen, suprofen and tiaprofenic acid. The isotopic labelling survived under the conditions required to perform in vitro photoallergic studies (photolysis in non-deuterated aqueous media). (Author)

A general procedure for isotopic (deuterium) labelling of non-steroidal antiinflammatory 2-arylpropionic acids

Energy Technology Data Exchange (ETDEWEB)

Castell, J.V. (Valencia Univ. Hospital (Spain). Centro de Investigacion); Martinez, L.A. (Valencia Univ. Hospital (Spain). Centro de Investigacion Universidad Politecnica de Valencia (Spain). Dept. de Quimica); Miranda, M.A.; Tarrega, Pilar (Universidad Politecnica de Valencia (Spain). Dept. de Quimica)

1994-01-01

Alkaline treatment of nonsteroidal antiinflammatory 2-arylpropionic acids in deuterium oxide led in all cases to isotopic exchange of the proton located at the [alpha]-position of the side chain. Monodeuteration was observed in the case of carprofen, ibuprofen, ketoprofen, fenoprofen, flurbiprofen and naproxen. Additional exchange of one or two protons of the heterocyclic ring occurred in indoprofen, suprofen and tiaprofenic acid. The isotopic labelling survived under the conditions required to perform in vitro photoallergic studies (photolysis in non-deuterated aqueous media). (Author).

Re-partitioning of Cu and Zn isotopes by modified protein expression

Directory of Open Access Journals (Sweden)

Ragnarsdottir K Vala

2008-10-01

Full Text Available Abstract Cu and Zn have naturally occurring non radioactive isotopes, and their isotopic systematics in a biological context are poorly understood. In this study we used double focussing mass spectroscopy to determine the ratios for these isotopes for the first time in mouse brain. The Cu and Zn isotope ratios for four strains of wild-type mice showed no significant difference (δ65Cu -0.12 to -0.78 permil; δ66Zn -0.23 to -0.48 permil. We also looked at how altering the expression of a single copper binding protein, the prion protein (PrP, alters the isotope ratios. Both knockout and overexpression of PrP had no significant effect on the ratio of Cu isotopes. Mice brains expressing mutant PrP lacking the known metal binding domain have δ65Cu isotope values of on average 0.57 permil higher than wild-type mouse brains. This implies that loss of the copper binding domain of PrP increases the level of 65Cu in the brain. δ66Zn isotope values of the transgenic mouse brains are enriched for 66Zn to the wild-type mouse brains. Here we show for the first time that the expression of a single protein can alter the partitioning of metal isotopes in mouse brains. The results imply that the expression of the prion protein can alter cellular Cu isotope content.

Sequencing of Isotope-Labeled Small RNA Using Femtosecond Laser Ablation Time-of-Flight Mass Spectrometry

Science.gov (United States)

Kurata-Nishimura, Mizuki; Ando, Yoshinari; Kobayashi, Tohru; Matsuo, Yukari; Suzuki, Harukazu; Hayashizaki, Yoshihide; Kawai, Jun

2010-04-01

A novel method for the analysis of sequences of small RNAs using nucleotide triphosphates labeled with stable isotopes has been developed using time-of-flight mass spectroscopy combined with femtosecond laser ablation (fsLA-TOF-MS). Small RNAs synthesized with nucleotides enriched in 13C and 15N were efficiently atomized and ionized by single-shot fsLA and the isotope ratios 13C/12C and 15N/14N were evaluated using the TOF-MS method. By comparing the isotope ratios among four different configurations, the number of nucleotide contents of the control RNA sample were successfully reproduced.

Efficient sortase-mediated N-terminal labeling of TEV protease cleaved recombinant proteins.

Science.gov (United States)

Sarpong, Kwabena; Bose, Ron

2017-03-15

A major challenge in attaching fluorophores or other handles to proteins is the availability of a site-specific labeling strategy that provides stoichiometric modification without compromising protein integrity. We developed a simple approach that combines TEV protease cleavage, sortase modification and affinity purification to N-terminally label proteins. To achieve stoichiometrically-labeled protein, we included a short affinity tag in the fluorophore-containing peptide for post-labeling purification of the modified protein. This strategy can be easily applied to any recombinant protein with a TEV site and we demonstrate this on Epidermal Growth Factor Receptor (EGFR) and Membrane Scaffold Protein (MSP) constructs. Copyright © 2017 Elsevier Inc. All rights reserved.

Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system

Energy Technology Data Exchange (ETDEWEB)

Ikeya, Teppei [Goethe University Frankfurt am Main, Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (Germany); Takeda, Mitsuhiro; Yoshida, Hitoshi; Terauchi, Tsutomu; Jee, Jun-Goo; Kainosho, Masatsune [Tokyo Metropolitan University, Graduate School of Science (Japan)], E-mail: kainosho@nmr.chem.metro-u.ac.jp; Guentert, Peter [Goethe University Frankfurt am Main, Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (Germany)], E-mail: guentert@em.uni-frankfurt.de

2009-08-15

Stereo-array isotope labeling (SAIL) has been combined with the fully automated NMR structure determination algorithm FLYA to determine the three-dimensional structure of the protein ubiquitin from different sets of input NMR spectra. SAIL provides a complete stereo- and regio-specific pattern of stable isotopes that results in sharper resonance lines and reduced signal overlap, without information loss. Here we show that as a result of the superior quality of the SAIL NMR spectra, reliable, fully automated analyses of the NMR spectra and structure calculations are possible using fewer input spectra than with conventional uniformly {sup 13}C/{sup 15}N-labeled proteins. FLYA calculations with SAIL ubiquitin, using a single three-dimensional 'through-bond' spectrum (and 2D HSQC spectra) in addition to the {sup 13}C-edited and {sup 15}N-edited NOESY spectra for conformational restraints, yielded structures with an accuracy of 0.83-1.15 A for the backbone RMSD to the conventionally determined solution structure of SAIL ubiquitin. NMR structures can thus be determined almost exclusively from the NOESY spectra that yield the conformational restraints, without the need to record many spectra only for determining intermediate, auxiliary data of the chemical shift assignments. The FLYA calculations for this report resulted in 252 ubiquitin structure bundles, obtained with different input data but identical structure calculation and refinement methods. These structures cover the entire range from highly accurate structures to seriously, but not trivially, wrong structures, and thus constitute a valuable database for the substantiation of structure validation methods.

Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system

International Nuclear Information System (INIS)

Ikeya, Teppei; Takeda, Mitsuhiro; Yoshida, Hitoshi; Terauchi, Tsutomu; Jee, Jun-Goo; Kainosho, Masatsune; Guentert, Peter

2009-01-01

Stereo-array isotope labeling (SAIL) has been combined with the fully automated NMR structure determination algorithm FLYA to determine the three-dimensional structure of the protein ubiquitin from different sets of input NMR spectra. SAIL provides a complete stereo- and regio-specific pattern of stable isotopes that results in sharper resonance lines and reduced signal overlap, without information loss. Here we show that as a result of the superior quality of the SAIL NMR spectra, reliable, fully automated analyses of the NMR spectra and structure calculations are possible using fewer input spectra than with conventional uniformly 13 C/ 15 N-labeled proteins. FLYA calculations with SAIL ubiquitin, using a single three-dimensional 'through-bond' spectrum (and 2D HSQC spectra) in addition to the 13 C-edited and 15 N-edited NOESY spectra for conformational restraints, yielded structures with an accuracy of 0.83-1.15 A for the backbone RMSD to the conventionally determined solution structure of SAIL ubiquitin. NMR structures can thus be determined almost exclusively from the NOESY spectra that yield the conformational restraints, without the need to record many spectra only for determining intermediate, auxiliary data of the chemical shift assignments. The FLYA calculations for this report resulted in 252 ubiquitin structure bundles, obtained with different input data but identical structure calculation and refinement methods. These structures cover the entire range from highly accurate structures to seriously, but not trivially, wrong structures, and thus constitute a valuable database for the substantiation of structure validation methods

Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system.

Science.gov (United States)

Ikeya, Teppei; Takeda, Mitsuhiro; Yoshida, Hitoshi; Terauchi, Tsutomu; Jee, Jun-Goo; Kainosho, Masatsune; Güntert, Peter

2009-08-01

Stereo-array isotope labeling (SAIL) has been combined with the fully automated NMR structure determination algorithm FLYA to determine the three-dimensional structure of the protein ubiquitin from different sets of input NMR spectra. SAIL provides a complete stereo- and regio-specific pattern of stable isotopes that results in sharper resonance lines and reduced signal overlap, without information loss. Here we show that as a result of the superior quality of the SAIL NMR spectra, reliable, fully automated analyses of the NMR spectra and structure calculations are possible using fewer input spectra than with conventional uniformly 13C/15N-labeled proteins. FLYA calculations with SAIL ubiquitin, using a single three-dimensional "through-bond" spectrum (and 2D HSQC spectra) in addition to the 13C-edited and 15N-edited NOESY spectra for conformational restraints, yielded structures with an accuracy of 0.83-1.15 A for the backbone RMSD to the conventionally determined solution structure of SAIL ubiquitin. NMR structures can thus be determined almost exclusively from the NOESY spectra that yield the conformational restraints, without the need to record many spectra only for determining intermediate, auxiliary data of the chemical shift assignments. The FLYA calculations for this report resulted in 252 ubiquitin structure bundles, obtained with different input data but identical structure calculation and refinement methods. These structures cover the entire range from highly accurate structures to seriously, but not trivially, wrong structures, and thus constitute a valuable database for the substantiation of structure validation methods.

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

Directory of Open Access Journals (Sweden)

Kent W. Seeley

2014-04-01

Full Text Available 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.

Foot-printing of Protein Interactions by Tritium Labeling

International Nuclear Information System (INIS)

Mousseau, Guillaume; Thomas, Olivier P.; Agez, Morgane; Thai, Robert; Cintrat, Jean-Christophe; Rousseau, Bernard; Raffy, Quentin; Renault, Jean Philippe; Pin, Serge; Ochsenbein, Francoise

2010-01-01

A new foot-printing method for mapping protein interactions has been developed, using tritium as a radioactive label. As residues involved in an interaction are less labeled when the complex is formed, they can be identified via comparison of the tritium incorporation of each residue of the bound protein with that of the unbound one. Application of this foot-printing method to the complex formed by the histone H3 fragment H3 122-135 and the protein hAsflA 1-156 afforded data in good agreement with NMR results. (authors)

Use of AERIN code for determining internal doses of transuranic isotopes

International Nuclear Information System (INIS)

King, W.C.

1980-01-01

The AERIN computer code is a mathematical expression of the ICRP Lung Model. The code was developed at the Lawrence Livermore National Laboratory to compute the body organ burdens and absorbed radiation doses resulting from the inhalation of transuranic isotopes and to predict the amount of activity excreted in the urine and feces as a function of time. Over forty cases of internal exposure have been studied using the AERIN code. The code, as modified, has proven to be extremely versatile. The case studies presented demonstrate the excellent correlation that can be obtained between code predictions and observed bioassay data. In one case study a discrepancy was observed between an in vivo count of the whole body and the application of the code using urine and fecal data as input. The discrepancy was resolved by in vivo skull counts that showed the code had predicted the correct skeletal burden

The method for production of high purity carrier free ortophosphoric acid labeled with isotopes Phosphorus-32 and Phosphorus-33

International Nuclear Information System (INIS)

Abdukayumov, M.N.; Abdusalyamov, A.N.; Chistyakov, P.G.; Yuldashev, B.S.

2001-01-01

Extensive application for various radioactive isotopes was found in an extremity of the 20-Th century in a science and production. Labeled compounds are used with growing effectiveness in a molecular biology, gene engineering, medicine and other areas. Phosphorus-32 and Phosphorus-33 isotopes as a different labeled compounds that are used mainly in molecular biology are produced at the Radiopreparat enterprise of the Institute of Nuclear Physics of Academy of Sciences of Uzbekistan Republic. The quality of labeled preparations is very high. The specifications for above mentioned preparations corresponds to demands most of customers in different countries. P-32 or P-33 labeled orthophosphoric acid has high radiochemical purity (more than 99 %) and specific radioactivity close to theoretical. Orthophosphoric acid prepared by the described above method has radiochemical purity about 95 % and output of the target product 99%

Labeling of multiple HIV-1 proteins with the biarsenical-tetracysteine system.

Directory of Open Access Journals (Sweden)

Cândida F Pereira

Full Text Available Due to its small size and versatility, the biarsenical-tetracysteine system is an attractive way to label viral proteins for live cell imaging. This study describes the genetic labeling of the human immunodeficiency virus type 1 (HIV-1 structural proteins (matrix, capsid and nucleocapsid, enzymes (protease, reverse transcriptase, RNAse H and integrase and envelope glycoprotein 120 with a tetracysteine tag in the context of a full-length virus. We measure the impact of these modifications on the natural virus infection and, most importantly, present the first infectious HIV-1 construct containing a fluorescently-labeled nucleocapsid protein. Furthermore, due to the high background levels normally associated with the labeling of tetracysteine-tagged proteins we have also optimized a metabolic labeling system that produces infectious virus containing the natural envelope glycoproteins and specifically labeled tetracysteine-tagged proteins that can easily be detected after virus infection of T-lymphocytes. This approach can be adapted to other viral systems for the visualization of the interplay between virus and host cell during infection.

An Overview of Advanced SILAC-Labeling Strategies for Quantitative Proteomics.

Science.gov (United States)

Terzi, F; Cambridge, S

2017-01-01

Comparative, quantitative mass spectrometry of proteins provides great insight to protein abundance and function, but some molecular characteristics related to protein dynamics are not so easily obtained. Because the metabolic incorporation of stable amino acid isotopes allows the extraction of distinct temporal and spatial aspects of protein dynamics, the SILAC methodology is uniquely suited to be adapted for advanced labeling strategies. New SILAC strategies have emerged that allow deeper foraging into the complexity of cellular proteomes. Here, we review a few advanced SILAC-labeling strategies that have been published during last the years. Among them, different subsaturating-labeling as well as dual-labeling schemes are most prominent for a range of analyses including those of neuronal proteomes, secretion, or cell-cell-induced stimulations. These recent developments suggest that much more information can be gained from proteomic analyses if the labeling strategies are specifically tailored toward the experimental design. © 2017 Elsevier Inc. All rights reserved.

An IBM-1620 code for calculation of isotopic composition of irradiated thorium (ISOCOM-2)

International Nuclear Information System (INIS)

Soliman, R.H.; Karchava, G.; Hamouda, I.

1978-01-01

The present work gives a description of an IBM-1620 code to calculate the isotopic composition during the irradiation of a nuclear fuel, which initially contains 232 Th. The numerical results on test calculations are presented. The code has been in operation since 1968

Multi-label learning with fuzzy hypergraph regularization for protein subcellular location prediction.

Science.gov (United States)

Chen, Jing; Tang, Yuan Yan; Chen, C L Philip; Fang, Bin; Lin, Yuewei; Shang, Zhaowei

2014-12-01

Protein subcellular location prediction aims to predict the location where a protein resides within a cell using computational methods. Considering the main limitations of the existing methods, we propose a hierarchical multi-label learning model FHML for both single-location proteins and multi-location proteins. The latent concepts are extracted through feature space decomposition and label space decomposition under the nonnegative data factorization framework. The extracted latent concepts are used as the codebook to indirectly connect the protein features to their annotations. We construct dual fuzzy hypergraphs to capture the intrinsic high-order relations embedded in not only feature space, but also label space. Finally, the subcellular location annotation information is propagated from the labeled proteins to the unlabeled proteins by performing dual fuzzy hypergraph Laplacian regularization. The experimental results on the six protein benchmark datasets demonstrate the superiority of our proposed method by comparing it with the state-of-the-art methods, and illustrate the benefit of exploiting both feature correlations and label correlations.

Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs.

Directory of Open Access Journals (Sweden)

Chen Xie

2012-09-01

Full Text Available Tinkering with pre-existing genes has long been known as a major way to create new genes. Recently, however, motherless protein-coding genes have been found to have emerged de novo from ancestral non-coding DNAs. How these genes originated is not well addressed to date. Here we identified 24 hominoid-specific de novo protein-coding genes with precise origination timing in vertebrate phylogeny. Strand-specific RNA-Seq analyses were performed in five rhesus macaque tissues (liver, prefrontal cortex, skeletal muscle, adipose, and testis, which were then integrated with public transcriptome data from human, chimpanzee, and rhesus macaque. On the basis of comparing the RNA expression profiles in the three species, we found that most of the hominoid-specific de novo protein-coding genes encoded polyadenylated non-coding RNAs in rhesus macaque or chimpanzee with a similar transcript structure and correlated tissue expression profile. According to the rule of parsimony, the majority of these hominoid-specific de novo protein-coding genes appear to have acquired a regulated transcript structure and expression profile before acquiring coding potential. Interestingly, although the expression profile was largely correlated, the coding genes in human often showed higher transcriptional abundance than their non-coding counterparts in rhesus macaque. The major findings we report in this manuscript are robust and insensitive to the parameters used in the identification and analysis of de novo genes. Our results suggest that at least a portion of long non-coding RNAs, especially those with active and regulated transcription, may serve as a birth pool for protein-coding genes, which are then further optimized at the transcriptional level.

Reconstitution of Nucleosomes with Differentially Isotope-labeled Sister Histones.

Science.gov (United States)

Liokatis, Stamatios

2017-03-26

Asymmetrically modified nucleosomes contain the two copies of a histone (sister histones) decorated with distinct sets of Post-translational Modifications (PTMs). They are newly identified species with unknown means of establishment and functional implications. Current analytical methods are inadequate to detect the copy-specific occurrence of PTMs on the nucleosomal sister histones. This protocol presents a biochemical method for the in vitro reconstitution of nucleosomes containing differentially isotope-labeled sister histones. The generated complex can be also asymmetrically modified, after including a premodified histone pool during refolding of histone subcomplexes. These asymmetric nucleosome preparations can be readily reacted with histone-modifying enzymes to study modification cross-talk mechanisms imposed by the asymmetrically pre-incorporated PTM using nuclear magnetic resonance (NMR) spectroscopy. Particularly, the modification reactions in real-time can be mapped independently on the two sister histones by performing different types of NMR correlation experiments, tailored for the respective isotope type. This methodology provides the means to study crosstalk mechanisms that contribute to the formation and propagation of asymmetric PTM patterns on nucleosomal complexes.

Accurate and sensitive determination of molar fractions of "1"3C-Labeled intracellular metabolites in cell cultures grown in the presence of isotopically-labeled glucose

International Nuclear Information System (INIS)

Fernández-Fernández, Mario; Rodríguez-González, Pablo; Hevia Sánchez, David; González-Menéndez, Pedro; Sainz Menéndez, Rosa M.; García Alonso, J. Ignacio

2017-01-01

This work describes a methodology based on multiple linear regression and GC-MS for the determination of molar fractions of isotopically-labeled intracellular metabolites in cell cultures. Novel aspects of this work are: i) the calculation of theoretical isotopic distributions of the different isotopologues from an experimentally measured value of % 13C enrichment of the labeled precursor ii) the calculation of the contribution of lack of mass resolution of the mass spectrometer and different fragmentation mechanism such as the loss or gain of hydrogen atoms in the EI source to measure the purity of the selected cluster for each metabolite and iii) the validation of the methodology not only by the analysis of gravimetrically prepared mixtures of isotopologues but also by the comparison of the obtained molar fractions with experimental values obtained by GC-Combustion-IRMS based on "1"3C/"1"2C isotope ratio measurements. The method is able to measure molar fractions for twenty-eight intracellular metabolites derived from glucose metabolism in cell cultures grown in the presence of "1"3C-labeled Glucose. The validation strategies demonstrate a satisfactory accuracy and precision of the proposed procedure. Also, our results show that the minimum value of "1"3C incorporation that can be accurately quantified is significantly influenced by the calculation of the spectral purity of the measured cluster and the number of "1"3C atoms of the labeled precursor. The proposed procedure was able to accurately quantify gravimetrically prepared mixtures of natural and labeled glucose molar fractions of 0.07% and mixtures of natural and labeled glycine at molar fractions down to 0.7%. The method was applied to initial studies of glucose metabolism of different prostate cancer cell lines. - Highlights: • Determination of molar fractions of "1"3C-labeled metabolites in cell cultures. • The method is based on multiple linear regression and GC-MS. • Validation of the method by

Accurate and sensitive determination of molar fractions of {sup 13}C-Labeled intracellular metabolites in cell cultures grown in the presence of isotopically-labeled glucose

Energy Technology Data Exchange (ETDEWEB)

Fernández-Fernández, Mario [Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo (Spain); Rodríguez-González, Pablo, E-mail: rodriguezpablo@uniovi.es [Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo (Spain); Hevia Sánchez, David; González-Menéndez, Pedro; Sainz Menéndez, Rosa M. [University Institute of Oncology (IUOPA), University of Oviedo, Julián Clavería 6, 33006 Oviedo (Spain); García Alonso, J. Ignacio [Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo (Spain)

2017-05-29

This work describes a methodology based on multiple linear regression and GC-MS for the determination of molar fractions of isotopically-labeled intracellular metabolites in cell cultures. Novel aspects of this work are: i) the calculation of theoretical isotopic distributions of the different isotopologues from an experimentally measured value of % 13C enrichment of the labeled precursor ii) the calculation of the contribution of lack of mass resolution of the mass spectrometer and different fragmentation mechanism such as the loss or gain of hydrogen atoms in the EI source to measure the purity of the selected cluster for each metabolite and iii) the validation of the methodology not only by the analysis of gravimetrically prepared mixtures of isotopologues but also by the comparison of the obtained molar fractions with experimental values obtained by GC-Combustion-IRMS based on {sup 13}C/{sup 12}C isotope ratio measurements. The method is able to measure molar fractions for twenty-eight intracellular metabolites derived from glucose metabolism in cell cultures grown in the presence of {sup 13}C-labeled Glucose. The validation strategies demonstrate a satisfactory accuracy and precision of the proposed procedure. Also, our results show that the minimum value of {sup 13}C incorporation that can be accurately quantified is significantly influenced by the calculation of the spectral purity of the measured cluster and the number of {sup 13}C atoms of the labeled precursor. The proposed procedure was able to accurately quantify gravimetrically prepared mixtures of natural and labeled glucose molar fractions of 0.07% and mixtures of natural and labeled glycine at molar fractions down to 0.7%. The method was applied to initial studies of glucose metabolism of different prostate cancer cell lines. - Highlights: • Determination of molar fractions of {sup 13}C-labeled metabolites in cell cultures. • The method is based on multiple linear regression and GC-MS. �

Isotopic modelling using the ENIGMA-B fuel performance code

International Nuclear Information System (INIS)

Rossiter, G.D.; Cook, P.M.A.; Weston, R.

2001-01-01

A number of experimental programmes by BNFL and other MOX fabricators have now shown that the in-pile performance of MOX fuel is generally similar to that of conventional UO 2 fuel. Models based on UO 2 fuel experience form a good basis for a description of MOX fuel behaviour. However, an area where the performance of MOX fuel is sufficiently different from that of UO 2 to warrant model changes is in the radial power and burnup profile. The differences in radial power and burnup profile arise from the presence of significant concentrations of plutonium in MOX fuel, at beginning of life, and their subsequent evolution with burnup. Amongst other effects, plutonium has a greater neutron absorption cross-section than uranium. This paper focuses on the development of a new model for the radial power and burnup profile within a UO 2 or MOX fuel rod, in which the underlying fissile isotope concentration distributions are tracked during irradiation. The new model has been incorporated into the ENIGMA-B fuel performance code and has been extended to track the isotopic concentrations of the fission gases, xenon and krypton. The calculated distributions have been validated against results from rod puncture measurements and electron probe micro-analysis (EPMA) linescans, performed during the M501 post irradiation examination (PIE) programme. The predicted gas inventory of the fuel/clad gap is compared with the isotopic composition measured during rod puncture and the measured radial distributions of burnup (from neodymium measurements) and plutonium in the fuel are compared with the calculated distributions. It is shown that there is good agreement between the code predictions and the measurements. (author)

Site-directed fluorescence labeling of a membrane protein with BADAN: probing protein topology and local environment

NARCIS (Netherlands)

Koehorst, R.B.M.; Spruijt, R.B.; Hemminga, M.A.

2008-01-01

We present a new and simple method based on site-directed fluorescence labeling using the BADAN label that allows to examine protein-lipid interactions in great detail. We apply this approach to a membrane-embedded mainly -helical reference protein, the M13 major coat protein, of which in a

Protein quantitation using Ru-NHS ester tagging and isotope dilution high-pressure liquid chromatography-inductively coupled plasma mass spectrometry determination.

Science.gov (United States)

Liu, Rui; Lv, Yi; Hou, Xiandeng; Yang, Lu; Mester, Zoltan

2012-03-20

An accurate, simple, and sensitive method for the direct determination of proteins by nonspecies specific isotope dilution and external calibration high-performance liquid chromatography-inductively coupled plasma mass spectrometry (HPLC-ICPMS) is described. The labeling of myoglobin (17 kDa), transferrin (77 kDa), and thyroglobulin (670 kDa) proteins was accomplished in a single-step reaction with a commercially available bis(2,2'-bipyridine)-4'-methyl-4-carboxybipyridine-ruthenium N-succinimidyl ester-bis(hexafluorophosphate) (Ru-NHS ester). Using excess amounts of Ru-NHS ester compared to the protein concentration at optimized labeling conditions, constant ratios for Ru to proteins were obtained. Bioconjugate solutions containing both labeled and unlabeled proteins as well as excess Ru-NHS ester reagent were injected onto a size exclusion HPLC column for separation and ICPMS detection without any further treatment. A (99)Ru enriched spike was used for nonspecies specific ID calibration. The accuracy of the method was confirmed at various concentration levels. An average recovery of 100% ± 3% (1 standard deviation (SD), n = 9) was obtained with a typical precision of better than 5% RSD at 100 μg mL(-1) for nonspecies specific ID. Detection limits (3SD) of 1.6, 3.2, and 7.0 fmol estimated from three procedure blanks were obtained for myoglobin, transferrin, and thyroglobulin, respectively. These detection limits are suitable for the direct determination of intact proteins at trace levels. For simplicity, external calibration was also tested. Good linear correlation coefficients, 0.9901, 0.9921, and 0.9980 for myoglobin, transferrin, and thyroglobulin, respectively, were obtained. The measured concentrations of proteins in a solution were in good agreement with their volumetrically prepared values. To the best of our knowledge, this is the first application of nonspecies specific ID for the accurate and direct determination of proteins using a Ru-NHS ester

Drug-laden 3D biodegradable label using QR code for anti-counterfeiting of drugs.

Science.gov (United States)

Fei, Jie; Liu, Ran

2016-06-01

Wiping out counterfeit drugs is a great task for public health care around the world. The boost of these drugs makes treatment to become potentially harmful or even lethal. In this paper, biodegradable drug-laden QR code label for anti-counterfeiting of drugs is proposed that can provide the non-fluorescence recognition and high capacity. It is fabricated by the laser cutting to achieve the roughness over different surface which causes the difference in the gray levels on the translucent material the QR code pattern, and the micro mold process to obtain the drug-laden biodegradable label. We screened biomaterials presenting the relevant conditions and further requirements of the package. The drug-laden microlabel is on the surface of the troches or the bottom of the capsule and can be read by a simple smartphone QR code reader application. Labeling the pill directly and decoding the information successfully means more convenient and simple operation with non-fluorescence and high capacity in contrast to the traditional methods. Copyright © 2016 Elsevier B.V. All rights reserved.

Metabolic flux analysis of the phenylpropanoid pathway in wound-healing potato tuber tissue using stable isotope-labeled tracer and LC-MS spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Matsuda, Fumio; Morino, Keiko; Miyashita, Masahiro; Miyagawa, Hisashi [Kyoto Univ. (Japan). Department of Agriculture

2003-05-01

The metabolic flux of two phenylpropanoid metabolites, N-p-coumaroyloctopamine (p-CO) and chlorogenic acid (CGA), in the wound-healing potato tuber tissue was quantitatively analyzed by a newly developed method based upon the tracer experiment using stable isotope-labeled compounds and LC-MS. Tuber disks were treated with aqueous solution of L-phenyl-d{sub 5}-alanine, and the change in the ratio of stable isotope-labeled compound to non-labeled (isotope abundance) was monitored for p-CO and CGA in the tissue extract by LC-MS. The time-dependent change in the isotope abundance of each metabolite was fitted to an equation that was derived from the formation and conversion kinetics of each compound. Good correlations were obtained between the observed and calculated isotope abundances for both p-CO and CGA. The rates of p-CO formation and conversion (i.e. fluxes) were 1.15 and 0.96 nmol (g FW){sup -1}h{sup -1}, respectively, and for CGA, the rates 4.63 and 0.42 nmol (g FW){sup -1}h{sup -1}, respectively. This analysis enabled a direct comparison of the biosynthetic activity between these two compounds. (author)

Synthesis of stable isotopically labeled peptides with filter-assisted enzymatic labeling for the diagnosis of hepatitis B virus infection utilizing mass spectrometry-based proteomics strategy

International Nuclear Information System (INIS)

Tsai, Hsing-Fen; Hsiao, He-Hsuan

2017-01-01

A facile method for the preparation of stable isotopically labeled peptides was developed by means of filter-assisted tryptic "1"6O/"1"8O water labeling, which could be directly applied to the determination of hepatitis B virus infection from human serum with tandem mass spectrometry. Tryptic peptides of hepatitis B surface antigen or hepatitis B e antigen from different subtypes of hepatitis B virus were synthesized with traditional solid-phase peptide synthesis as potential biomarkers. Trypsin catalyzed oxygen-18 exchange at their amidated c-terminus of arginine or lysine residue. The protease catalyzed oxygen-18 to oxygen-16 back exchange reaction was eliminated due to the complete removal of trypsin by the centrifugal filter containing a thin membrane associated with molecular weight cut-off of 10 KDa. The synthetic isotopic peptides were spiked into trichloroacetic acid/acetone precipitated human serum as internal standards and were selectively detected with multiplexed parallel reaction monitoring on a hybrid quadrupole-orbitrap mass spectrometer. The limit of detection for all synthetic peptides were in the range of 0.09 fmol–1.13 fmol. The results indicated that the peptide YLWEWASVR derived from hepatitis B surface antigen was quantified approximately 200 fmol per μl serum and may serve as a diagnostic biomarker for the detection of hepatitis B virus infected disease. - Highlights: • Facile synthesis of an inexpensive and highly reproducible stable isotopically labeled peptides. • Complete incorporation of two "1"8O atoms into synthesized peptides with filter-assisted enzymatic labeling. • Targeted analysis with parallel reaction monitoring assay for the disease diagnosis.

Synthesis of stable isotopically labeled peptides with filter-assisted enzymatic labeling for the diagnosis of hepatitis B virus infection utilizing mass spectrometry-based proteomics strategy

Energy Technology Data Exchange (ETDEWEB)

Tsai, Hsing-Fen; Hsiao, He-Hsuan, E-mail: hhhsiao@dragon.nchu.edu.tw

2017-03-01

A facile method for the preparation of stable isotopically labeled peptides was developed by means of filter-assisted tryptic {sup 16}O/{sup 18}O water labeling, which could be directly applied to the determination of hepatitis B virus infection from human serum with tandem mass spectrometry. Tryptic peptides of hepatitis B surface antigen or hepatitis B e antigen from different subtypes of hepatitis B virus were synthesized with traditional solid-phase peptide synthesis as potential biomarkers. Trypsin catalyzed oxygen-18 exchange at their amidated c-terminus of arginine or lysine residue. The protease catalyzed oxygen-18 to oxygen-16 back exchange reaction was eliminated due to the complete removal of trypsin by the centrifugal filter containing a thin membrane associated with molecular weight cut-off of 10 KDa. The synthetic isotopic peptides were spiked into trichloroacetic acid/acetone precipitated human serum as internal standards and were selectively detected with multiplexed parallel reaction monitoring on a hybrid quadrupole-orbitrap mass spectrometer. The limit of detection for all synthetic peptides were in the range of 0.09 fmol–1.13 fmol. The results indicated that the peptide YLWEWASVR derived from hepatitis B surface antigen was quantified approximately 200 fmol per μl serum and may serve as a diagnostic biomarker for the detection of hepatitis B virus infected disease. - Highlights: • Facile synthesis of an inexpensive and highly reproducible stable isotopically labeled peptides. • Complete incorporation of two {sup 18}O atoms into synthesized peptides with filter-assisted enzymatic labeling. • Targeted analysis with parallel reaction monitoring assay for the disease diagnosis.

Design of integrated optics all-optical label swappers for spectral amplitude code label swapping optical packet networks on active/passive InP technology

NARCIS (Netherlands)

Habib, C.; Munoz, P.; Leijtens, X.J.M.; Chen, Lawrence; Smit, M.K.; Capmany, J.

2009-01-01

In this paper the designs of optical label swapper devices, for spectral amplitude coded labels, monolithically integrated on InP active/passive technology are pre sented. The devices are based on cross-gain modulation in a semiconductor optical amplifier. Multi-wavelength operation is enabled by

Evaluation of the impact of matrix effect on quantification of pesticides in foods by gas chromatography-mass spectrometry using isotope-labeled internal standards.

Science.gov (United States)

Yarita, Takashi; Aoyagi, Yoshie; Otake, Takamitsu

2015-05-29

The impact of the matrix effect in GC-MS quantification of pesticides in food using the corresponding isotope-labeled internal standards was evaluated. A spike-and-recovery study of nine target pesticides was first conducted using paste samples of corn, green soybean, carrot, and pumpkin. The observed analytical values using isotope-labeled internal standards were more accurate for most target pesticides than that obtained using the external calibration method, but were still biased from the spiked concentrations when a matrix-free calibration solution was used for calibration. The respective calibration curves for each target pesticide were also prepared using matrix-free calibration solutions and matrix-matched calibration solutions with blank soybean extract. The intensity ratio of the peaks of most target pesticides to that of the corresponding isotope-labeled internal standards was influenced by the presence of the matrix in the calibration solution; therefore, the observed slope varied. The ratio was also influenced by the type of injection method (splitless or on-column). These results indicated that matrix-matching of the calibration solution is required for very accurate quantification, even if isotope-labeled internal standards were used for calibration. Copyright © 2015 Elsevier B.V. All rights reserved.

REDOR NMR of stable-isotope-labeled protein binding sites

Energy Technology Data Exchange (ETDEWEB)

Schaefer, J. [Washington Univ., St. Louis, MO (United States)

1994-12-01

Rotational-echo, double resonance (REDOR) NMR, a new analytical spectroscopic technique for solids spinning at the magic angle, has been developed over the last 5 years. REDOR provides a direct measure of heteronuclear dipolar coupling between isolated pairs of labeled nuclei. In a solid with a {sup 13}C-{sup 15}N labeled pair, for example, the {sup 13}C rotational echoes that form each rotor period following a{sup 1}H-{sup 13}C cross-polarization transfer can be prevented from reaching full intensity by insertion of a {sup 15}N {pi} pulse each half rotor period. The REDOR difference (the difference between a {sup 13}C NMR spectrum obtained under these conditions and one obtained with no {sup 15}N {pi} pulses) has a strong dependence on the {sup 13}C-{sup 15}N dipolar coupling, and hence, the {sup 13}C-{sup 15}N internuclear distance. REDOR is described as double-resonance even though three radio frequencies (typically {sup 1}H, {sup 13}C, and {sup 15}N) are used because the protons are removed from the important evolution part of the experiment by resonant decoupling. The dephasing of magnetization in REDOR arises from a local dipolar {sup 13}C-{sup 15}N field gradient and involves no polarization transfer. REDOR has no dependence on {sup 13}C or {sup 15}N chemical-shift tensors and does not require resolution of a {sup 13}C-{sup 15}N coupling in the chemical-shift dimension.

Cooperation of CMEA member states in the field of the manufacture and use of stable isotopes and compounds thus labelled

International Nuclear Information System (INIS)

Ertel, G.; Ewald, G.

1977-01-01

The contribution presents a survey of scientific-technical cooperation of CMEA member states in the field of stable isotopes, it deals with the specialization of stable isotope production and compounds thus labelled, and gives the prospects for further development of this cooperation. (HK) [de

Isotope label-aided mass spectrometry reveals the influence of environmental factors on metabolism in single eggs of fruit fly.

Directory of Open Access Journals (Sweden)

Te-Wei Tseng

Full Text Available In order to investigate the influence of light/dark cycle on the biosynthesis of metabolites during oogenesis, here we demonstrate a simple experimental protocol which combines in-vivo isotopic labeling of primary metabolites with mass spectrometric analysis of single eggs of fruit fly (Drosophila melanogaster. First, fruit flies were adapted to light/dark cycle using artificial white light. Second, female flies were incubated with an isotopically labeled sugar ((13C(6-glucose for 12 h--either during the circadian day or the circadian night, at light or at dark. Third, eggs were obtained from the incubated female flies, and analyzed individually by matrix-assisted laser desorption/ionization (MALDI mass spectrometry (MS: this yielded information about the extent of labeling with carbon-13. Since the incorporation of carbon-13 to uridine diphosphate glucose (UDP-glucose in fruit fly eggs is very fast, the labeling of this metabolite was used as an indicator of the biosynthesis of metabolites flies/eggs during 12-h periods, which correspond to circadian day or circadian night. The results reveal that once the flies adapted to the 12-h-light/12-h-dark cycle, the incorporation of carbon-13 to UDP-glucose present in fruit fly eggs was not markedly altered by an acute perturbation to this cycle. This effect may be due to a relationship between biosynthesis of primary metabolites in developing eggs and an alteration to the intake of the labeled substrate - possibly related to the change of the feeding habit. Overall, the study shows the possibility of using MALDI-MS in conjunction with isotopic labeling of small metazoans to unravel the influence of environmental cues on primary metabolism.

Photoaffinity labeling of the oxysterol binding protein

International Nuclear Information System (INIS)

Taylor, F.R.; Kandutsch, A.A.; Anzalone, L.; Spencer, T.A.

1986-01-01

A cytosolic receptor protein for oxygenated sterols, that is thought to be involved in the regulation of HMG-CoA reductase and cholesterol biosynthesis, can be labeled covalently by the photoactivated affinity compound [5,6- 3 H]-7,7'-azocholestane-3β,25-diol (I). Several other compounds were tested including 25-hydroxycholesta-4,6-dien-3-one, 25-azido-27-norcholest-5-en-3β-ol,3β,25-dihydroxycholest-5-en-7-one and 3β-hydroxycholesta-8(14),9(11)-dien-15-one. However, these sterols either did not bind to the receptor with adequate affinity or did not react covalently with the receptor during photolysis. Compound I binds to the receptor with very high affinity (K/sub d/ = 30 nM). After activation with long wavelength UV, two tritium labeled proteins, M/sub r/ approximately 95K and 65K daltons, are found upon SDS gel electrophoresis. No labeling occurs when the binding reaction is carried out in the presence of a large excess of 25-hydroxycholesterol. It is possible that the smaller polypeptide is a degradation product. Under the reaction conditions investigated so far labeling is relatively inefficient (< 1% of bound sterol). These results are generally consistent with previous information suggesting that the M/sub r/ of the receptor subunit is 97,000. Covalent labeling of the receptor should greatly facilitate its further purification and characterization

{sup 125}I Labelling of Protein Using Immobilized Enzyme

Energy Technology Data Exchange (ETDEWEB)

Kim, Jae Rok; Park, Kyung Bae; Awh, Ok Doo [Korea Advanced Energy Research Institute, Daejeon (Korea, Republic of)

1984-03-15

For an effective solid-phase labelling of protein with {sup 125}I, studies on the immobilization of lactoperoxidase (LPO) on the inner wall of polystyrene tubes were carried out. Labelling of bovine serum albumin (BSA) and insulin was also practiced using the LPO immobilized tubes. The immobilized enzyme of about 2.5 mu g/tube was sufficient for small scale labelling since the results of radio-paper chromatography of the labelling mixture of insulin indicated that the yields were sufficiently high (80%) even in the reactions conducted at room temperature for 60 sec. The results of the Sephadex column chromatography indicated that the labelled products were not contaminated with LPO-{sup 125}I, and the radiochemical purity of the products was more than 90%. In considering the general trend that the {sup 125}I labelled protein obtained by using LPO maintains its intactness better than those obtained by using chloramine-T, together with the tendency of yield enhancing with increase of reactants-concentration, the LPO immobilized tube method is estimated to be one of the simple methods of labelling. The product might be applicable without further purification.

Tuning a Protein-Labeling Reaction to Achieve Highly Site Selective Lysine Conjugation.

Science.gov (United States)

Pham, Grace H; Ou, Weijia; Bursulaya, Badry; DiDonato, Michael; Herath, Ananda; Jin, Yunho; Hao, Xueshi; Loren, Jon; Spraggon, Glen; Brock, Ansgar; Uno, Tetsuo; Geierstanger, Bernhard H; Cellitti, Susan E

2018-04-16

Activated esters are widely used to label proteins at lysine side chains and N termini. These reagents are useful for labeling virtually any protein, but robust reactivity toward primary amines generally precludes site-selective modification. In a unique case, fluorophenyl esters are shown to preferentially label human kappa antibodies at a single lysine (Lys188) within the light-chain constant domain. Neighboring residues His189 and Asp151 contribute to the accelerated rate of labeling at Lys188 relative to the ≈40 other lysine sites. Enriched Lys188 labeling can be enhanced from 50-70 % to >95 % by any of these approaches: lowering reaction temperature, applying flow chemistry, or mutagenesis of specific residues in the surrounding protein environment. Our results demonstrated that activated esters with fluoro-substituted aromatic leaving groups, including a fluoronaphthyl ester, can be generally useful reagents for site-selective lysine labeling of antibodies and other immunoglobulin-type proteins. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

An IBM-1620 code for calculaton of isotopic composition of irradiated uranium (ISOCOM-1)

International Nuclear Information System (INIS)

Soliman, R.H.; Karchava, G.; Hamouda, I.

1974-01-01

The present work gives a description of an IBM-1620 code to calculate the isotopic composition during the irradiation of a nuclear fuel, which initially consists of 235 U and 238 U. The numerical results of test calculations as well as the ET-RR-1 reactor calculations are presented. The code is in operation since 1968

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

Science.gov (United States)

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

Content Coding of Psychotherapy Transcripts Using Labeled Topic Models.

Science.gov (United States)

Gaut, Garren; Steyvers, Mark; Imel, Zac E; Atkins, David C; Smyth, Padhraic

2017-03-01

Psychotherapy represents a broad class of medical interventions received by millions of patients each year. Unlike most medical treatments, its primary mechanisms are linguistic; i.e., the treatment relies directly on a conversation between a patient and provider. However, the evaluation of patient-provider conversation suffers from critical shortcomings, including intensive labor requirements, coder error, nonstandardized coding systems, and inability to scale up to larger data sets. To overcome these shortcomings, psychotherapy analysis needs a reliable and scalable method for summarizing the content of treatment encounters. We used a publicly available psychotherapy corpus from Alexander Street press comprising a large collection of transcripts of patient-provider conversations to compare coding performance for two machine learning methods. We used the labeled latent Dirichlet allocation (L-LDA) model to learn associations between text and codes, to predict codes in psychotherapy sessions, and to localize specific passages of within-session text representative of a session code. We compared the L-LDA model to a baseline lasso regression model using predictive accuracy and model generalizability (measured by calculating the area under the curve (AUC) from the receiver operating characteristic curve). The L-LDA model outperforms the lasso logistic regression model at predicting session-level codes with average AUC scores of 0.79, and 0.70, respectively. For fine-grained level coding, L-LDA and logistic regression are able to identify specific talk-turns representative of symptom codes. However, model performance for talk-turn identification is not yet as reliable as human coders. We conclude that the L-LDA model has the potential to be an objective, scalable method for accurate automated coding of psychotherapy sessions that perform better than comparable discriminative methods at session-level coding and can also predict fine-grained codes.

Absolute quantitative autoradiography of low concentrations of [125I]-labeled proteins in arterial tissue

International Nuclear Information System (INIS)

Schnitzer, J.J.; Morrel, E.M.; Colton, C.K.; Smith, K.A.; Stemerman, M.B.

1987-01-01

We developed a method for absolute quantitative autoradiographic measurement of very low concentrations of [ 125 I]-labeled proteins in arterial tissue using Kodak NTB-2 nuclear emulsion. A precise linear relationship between measured silver grain density and isotope concentration was obtained with uniformly labeled standard sources composed of epoxy-embedded gelatin containing glutaraldehyde-fixed [ 125 I]-albumin. For up to 308-day exposures of 1 micron-thick tissue sections, background grain densities ranged from about two to eight grains/1000 micron 2, and the technique was sensitive to as little as about one grain/1000 micron 2 above background, which correspond to a radioactivity concentration of about 2 x 10(4) cpm/ml. A detailed statistical analysis of variability was performed and the sum of all sources of variation quantified. The half distance for spatial resolution was 1.7 micron. Both visual and automated techniques were employed for quantitative grain density analysis. The method was illustrated by measurement of in vivo transmural [ 125 I]-low-density lipoprotein [( 125 I]-LDL) concentration profiles in de-endothelialized rabbit thoracic aortic wall

Automation of dimethylation after guanidination labeling chemistry and its compatibility with common buffers and surfactants for mass spectrometry-based shotgun quantitative proteome analysis

Energy Technology Data Exchange (ETDEWEB)

Lo, Andy; Tang, Yanan; Chen, Lu; Li, Liang, E-mail: Liang.Li@ualberta.ca

2013-07-25

Graphical abstract: -- Highlights: •Dimethylation after guanidination (2MEGA) uses inexpensive reagents for isotopic labeling of peptides. •2MEGA can be optimized and automated for labeling peptides with high efficiency. •2MEGA is compatible with several commonly used cell lysis and protein solubilization reagents. •The automated 2MEGA labeling method can be used to handle a variety of protein samples for relative proteome quantification. -- Abstract: Isotope labeling liquid chromatography–mass spectrometry (LC–MS) is a major analytical platform for quantitative proteome analysis. Incorporation of isotopes used to distinguish samples plays a critical role in the success of this strategy. In this work, we optimized and automated a chemical derivatization protocol (dimethylation after guanidination, 2MEGA) to increase the labeling reproducibility and reduce human intervention. We also evaluated the reagent compatibility of this protocol to handle biological samples in different types of buffers and surfactants. A commercially available liquid handler was used for reagent dispensation to minimize analyst intervention and at least twenty protein digest samples could be prepared in a single run. Different front-end sample preparation methods for protein solubilization (SDS, urea, Rapigest™, and ProteaseMAX™) and two commercially available cell lysis buffers were evaluated for compatibility with the automated protocol. It was found that better than 94% desired labeling could be obtained in all conditions studied except urea, where the rate was reduced to about 92% due to carbamylation on the peptide amines. This work illustrates the automated 2MEGA labeling process can be used to handle a wide range of protein samples containing various reagents that are often encountered in protein sample preparation for quantitative proteome analysis.

Coherent spectral amplitude coded label detection for DQPSK payload signals in packet-switched metropolitan area networks

DEFF Research Database (Denmark)

Osadchiy, Alexey Vladimirovich; Guerrero Gonzalez, Neil; Jensen, Jesper Bevensee

2011-01-01

We report on an experimental demonstration of a frequency swept local oscillator-based spectral amplitude coding (SAC) label detection for DQPSK signals after 40km of fiber transmission. Label detection was performed for a 10.7Gbaud DQPSK signal labeled with a SAC label composed of four......-frequency tones with 500MHz spectral separation. Successful label detection and recognition is achieved with the aid of digital signal processing that allows for substantial reduction of the complexity of the detection optical front-end....

Mass spectrometry–based relative quantification of proteins in precatalytic and catalytically active spliceosomes by metabolic labeling (SILAC), chemical labeling (iTRAQ), and label-free spectral count

Science.gov (United States)

Schmidt, Carla; Grønborg, Mads; Deckert, Jochen; Bessonov, Sergey; Conrad, Thomas; Lührmann, Reinhard; Urlaub, Henning

2014-01-01

The spliceosome undergoes major changes in protein and RNA composition during pre-mRNA splicing. Knowing the proteins—and their respective quantities—at each spliceosomal assembly stage is critical for understanding the molecular mechanisms and regulation of splicing. Here, we applied three independent mass spectrometry (MS)–based approaches for quantification of these proteins: (1) metabolic labeling by SILAC, (2) chemical labeling by iTRAQ, and (3) label-free spectral count for quantification of the protein composition of the human spliceosomal precatalytic B and catalytic C complexes. In total we were able to quantify 157 proteins by at least two of the three approaches. Our quantification shows that only a very small subset of spliceosomal proteins (the U5 and U2 Sm proteins, a subset of U5 snRNP-specific proteins, and the U2 snRNP-specific proteins U2A′ and U2B′′) remains unaltered upon transition from the B to the C complex. The MS-based quantification approaches classify the majority of proteins as dynamically associated specifically with the B or the C complex. In terms of experimental procedure and the methodical aspect of this work, we show that metabolically labeled spliceosomes are functionally active in terms of their assembly and splicing kinetics and can be utilized for quantitative studies. Moreover, we obtain consistent quantification results from all three methods, including the relatively straightforward and inexpensive label-free spectral count technique. PMID:24448447

Nitrogen 15 abundance in protein fractions of beans fertilized with (15NH4)2SO4

International Nuclear Information System (INIS)

Chaud, Saula Goulart; Oliveira, Admar Costa de; Trivelin, Paulo Cesar Ocheuze

2002-01-01

Studies evaluating the protein nutritive value of beans labelled with 15 N, using nitrogen balance and the quantitation of faecal and urinary endogenous nitrogen, determined by isotopic dilution, have been extensively used. The objective of this research was to verify if the isotopic labelling of raw, freeze dried beans (Phaseolus vulgaris L., cultivar Pirata 1) with 1.394 atoms % 15 N, resulted in the same abundance of the whole flour and of the protein fractions extracted from the beans with 0.5 mol L -1 NaCl. The isotopic abundance found in the whole bean flour, in the protein extract, in the globulin and albumin fractions were respectively: 1.394 +- 0.011; 1.403 +- 0.012; 1.399 +- 0.007 and 1.399 +- 0.028 atoms % of 15 N, presenting no difference (P > 0.05). However, a difference was found (P < 0.05) between the above mentioned abundances and the isotopic abundance found in the nitrogen of the proteins in the extraction residue, which was 0.969 +- 0.084. Since the abundances did not differ, the protein nutritive indexes, such as digestibility and biological value, determined from the nitrogen balance and corrected for isotopic dilution, would not be affected by extracting the proteins from the beans with 0.5 mol L 1 NaCl. If working with the nitrogen balance of the residual proteins after extraction and even with the whole flours, these indexes could present incorrect values, since the isotopic labelling of the residual proteins was less than that of the protein fractions. (author)

Selective {sup 2}H and {sup 13}C labeling in NMR analysis of solution protein structure and dynamics

Energy Technology Data Exchange (ETDEWEB)

LeMaster, D.M. [Northwestern Univ., Evanston, IL (United States)

1994-12-01

Preparation of samples bearing combined isotope enrichment patterns has played a central role in the recent advances in NMR analysis of proteins in solution. In particular, uniform {sup 13}C, {sup 15}N enrichment has made it possible to apply heteronuclear multidimensional correlation experiments for the mainchain assignments of proteins larger than 30 KDa. In contrast, selective labeling approaches can offer advantages in terms of the directedness of the information provided, such as chirality and residue type assignments, as well as through enhancements in resolution and sensitivity that result from editing the spectral complexity, the relaxation pathways and the scalar coupling networks. In addition, the combination of selective {sup 13}C and {sup 2}H enrichment can greatly facilitate the determination of heteronuclear relaxation behavior.

The application of high-resolution IR spectroscopy and isotope labeling for detailed investigation of TiO2/gas interface reactions

Czech Academy of Sciences Publication Activity Database

Civiš, Svatopluk; Ferus, Martin; Zukalová, Markéta; Kavan, Ladislav; Zelinger, Zdeněk

2013-01-01

Roč. 36, č. 1 (2013), s. 159-162 ISSN 0925-3467 R&D Projects: GA ČR GAP208/10/2302; GA ČR GA13-07724S Institutional support: RVO:61388955 Keywords : isotope exchange * titania * isotope labeling Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.075, year: 2013

In vivo labelling of proteins associated with folded chromosomes of yeast

International Nuclear Information System (INIS)

Litske Petersen, J.G.; Pinon, R.

1980-01-01

Proteins associated with the pre-replicative (g 1 ) and post-replicative (g 2 ) folded chromosomes of Saccharomyces cerevisiae can be labelled in vivo by growing cells in acetate vegetative medium containing [ 35 S]methionine. In both sporulating (MATa/MATα) and non-sporulating (MATa/MATa, MATα/MATα) diploids proteins associated with the resting stage genome (g 0 ) can be labelled with [ 35 S]methionine during nitrogen starvation and in sporulation medium. In addition, in MATa/MATα diploids proteins associated with the meiotic replication form (r) can also be labelled. SDS-polyacrylamide gel electrophoresis and autoradiography of the labelled proteins from the various folded genome forms showed that the g 1 and g 2 patterns are, with the exception of one polypeptide band, essentially identical. Several differences distinguished the r and g 0 patterns from those of the g 1 and g 2 structures. At least four polypeptide bands distinguish the r and g 0 patterns. No significant differences were observed between the g 0 proteins of sporulating and non-sporulating diploids. (author)

Label swapper device for spectral amplitude coded optical packet networks monolithically integrated on InP

NARCIS (Netherlands)

Muñoz, P.; García-Olcina, R.; Habib, C.; Chen, L.R.; Leijtens, X.J.M.; Vries, de T.; Robbins, D.J.; Capmany, J.

2011-01-01

In this paper the design, fabrication and experimental characterization of an spectral amplitude coded (SAC) optical label swapper monolithically integrated on Indium Phosphide (InP) is presented. The device has a footprint of 4.8x1.5 mm2 and is able to perform label swapping operations required in

Label swapper device for spectral amplitude coded optical packet networks monolithically integrated on InP.

Science.gov (United States)

Muñoz, P; García-Olcina, R; Habib, C; Chen, L R; Leijtens, X J M; de Vries, T; Robbins, D; Capmany, J

2011-07-04

In this paper the design, fabrication and experimental characterization of an spectral amplitude coded (SAC) optical label swapper monolithically integrated on Indium Phosphide (InP) is presented. The device has a footprint of 4.8x1.5 mm2 and is able to perform label swapping operations required in SAC at a speed of 155 Mbps. The device was manufactured in InP using a multiple purpose generic integration scheme. Compared to previous SAC label swapper demonstrations, using discrete component assembly, this label swapper chip operates two order of magnitudes faster.

[INVITED] Luminescent QR codes for smart labelling and sensing

Science.gov (United States)

Ramalho, João F. C. B.; António, L. C. F.; Correia, S. F. H.; Fu, L. S.; Pinho, A. S.; Brites, C. D. S.; Carlos, L. D.; André, P. S.; Ferreira, R. A. S.

2018-05-01

QR (Quick Response) codes are two-dimensional barcodes composed of special geometric patterns of black modules in a white square background that can encode different types of information with high density and robustness, correct errors and physical damages, thus keeping the stored information protected. Recently, these codes have gained increased attention as they offer a simple physical tool for quick access to Web sites for advertising and social interaction. Challenges encompass the increase of the storage capacity limit, even though they can store approximately 350 times more information than common barcodes, and encode different types of characters (e.g., numeric, alphanumeric, kanji and kana). In this work, we fabricate luminescent QR codes based on a poly(methyl methacrylate) substrate coated with organic-inorganic hybrid materials doped with trivalent terbium (Tb3+) and europium (Eu3+) ions, demonstrating the increase of storage capacity per unit area by a factor of two by using the colour multiplexing, when compared to conventional QR codes. A novel methodology to decode the multiplexed QR codes is developed based on a colour separation threshold where a decision level is calculated through a maximum-likelihood criteria to minimize the error probability of the demultiplexed modules, maximizing the foreseen total storage capacity. Moreover, the thermal dependence of the emission colour coordinates of the Eu3+/Tb3+-based hybrids enables the simultaneously QR code colour-multiplexing and may be used to sense temperature (reproducibility higher than 93%), opening new fields of applications for QR codes as smart labels for sensing.

Constellation labeling optimization for bit-interleaved coded APSK

Science.gov (United States)

Xiang, Xingyu; Mo, Zijian; Wang, Zhonghai; Pham, Khanh; Blasch, Erik; Chen, Genshe

2016-05-01

This paper investigates the constellation and mapping optimization for amplitude phase shift keying (APSK) modulation, which is deployed in Digital Video Broadcasting Satellite - Second Generation (DVB-S2) and Digital Video Broadcasting - Satellite services to Handhelds (DVB-SH) broadcasting standards due to its merits of power and spectral efficiency together with the robustness against nonlinear distortion. The mapping optimization is performed for 32-APSK according to combined cost functions related to Euclidean distance and mutual information. A Binary switching algorithm and its modified version are used to minimize the cost function and the estimated error between the original and received data. The optimized constellation mapping is tested by combining DVB-S2 standard Low-Density Parity-Check (LDPC) codes in both Bit-Interleaved Coded Modulation (BICM) and BICM with iterative decoding (BICM-ID) systems. The simulated results validate the proposed constellation labeling optimization scheme which yields better performance against conventional 32-APSK constellation defined in DVB-S2 standard.

Validation of 13CO2 breath analysis as a measurement of demethylation of stable isotope labeled aminopyrine in man

International Nuclear Information System (INIS)

Schneider, J.F.; Schoeller, D.A.; Nemchausky, B.; Bayer, J.L.; Klein, P.

1978-01-01

Interval sampling of expired breath as a simple, non-invasive assessment of the effect of liver disease upon hepatic microsomal drug metabolism, has been demonstrated with [ 14 C] dimethylaminoantipyrine (aminopyrine). In order to eliminate radiation risk the authors have validated the use of aminopyrine labeled with the stable, non-radioactive isotope 13 C. Simultaneous oral administration of both [ 14 C]- and [ 13 C] aminopyrine to five adult subjects without liver disease as well as five patients with known liver disease, resulted in the excretion of label at nearly identical rates in both individual time collections (r=0.94) as well as cumulative excretion for three hours (r=0.97). An oral dose of 2-mg/kg of [ 13 C) aminopyrine resulted in rates of production of 13 CO 2 significantly greater than baseline variations in 13 CO 2 production in the fasting, resting subject. Measurements of a single peak value at one half hour correlated closely with the determination of cumulative appearance over three hours (r=0.96). A consistent reproducible increase in the peak production of 13 CO 2 was observed when five patients received phenobarbital. Stable isotope labeled aminopyrine may be used to detect the effects of disease and treatment upon hepatic N-demethylation activity in human subjects without incurring any risk from radiation. Furthermore, the availability of another isotopic carbon label should make possible the study of direct drug-drug interaction utilizing CO 2 analysis. (Auth.)

Aptamer-mediated indirect quantum dot labeling and fluorescent imaging of target proteins in living cells

International Nuclear Information System (INIS)

Liu, Jianbo; Zhang, Pengfei; Yang, Xiaohai; Wang, Kemin; Guo, Qiuping; Huang, Jin; Li, Wei

2014-01-01

Protein labeling for dynamic living cell imaging plays a significant role in basic biological research, as well as in clinical diagnostics and therapeutics. We have developed a novel strategy in which the dynamic visualization of proteins within living cells is achieved by using aptamers as mediators for indirect protein labeling of quantum dots (QDs). With this strategy, the target protein angiogenin was successfully labeled with fluorescent QDs in a minor intactness model, which was mediated by the aptamer AL6-B. Subsequent living cell imaging analyses indicated that the QDs nanoprobes were selectively bound to human umbilical vein endothelial cells, gradually internalized into the cytoplasm, and mostly localized in the lysosome organelle, indicating that the labeled protein retained high activity. Compared with traditional direct protein labeling methods, the proposed aptamer-mediated strategy is simple, inexpensive, and provides a highly selective, stable, and intact labeling platform that has shown great promise for future biomedical labeling and intracellular protein dynamic analyses. (paper)

Demonstration of de novo synthesis of enzymes by density labelling with stable isotopes

International Nuclear Information System (INIS)

Huebner, G.; Hirschberg, K.

1977-01-01

The technique of in vivo density labelling of proteins with H 2 18 O and 2 H 2 O has been used to investigate hormonal regulation and developmental expression of enzymes in plant cells. Buoyant density data obtained from isopycnic equilibrium centrifugation demonstrated that the cytokinine-induced nitrate reductase activity and the gibberellic acid-induced phosphatase activity in isolated embryos of Agrostemma githago are activities of enzymes synthesized de novo. The increase in alanine-specific aminopeptidase in germinating A. githago seeds is not due to de novo synthesis but to the release of preformed enzyme. On the basis of this result it is possible to apply the enzyme aminopeptidase as an internal density standard in equilibrium centrifugation. Density labelling experiments on proteins in pea cotyledons have been used to study the change in the activity of acid phosphatase, alanine-specific aminopeptidase, and peroxidase during germination. The activities of these enzymes increase in cotyledons of Pisum sativum. Density labelling by 18 O and 2 H demonstrates de novo synthesis of these three enzymes. The differential time course of enzyme induction shows the advantage of using H 2 18 O as labelling substance in cases when the enzyme was synthesized immediately at the beginning of germination. At this stage of development the amino-acid pool available for synthesis is formed principally by means of hydrolysis of storage proteins. The incorporation of 2 H into the new proteins takes place in a measurable amount at a stage of growth in which the amino acids are also synthesized de novo. The enzyme acid phosphatase of pea cotyledons was chosen to demonstrate the possibility of using the density labelling technique to detect protein turnover. (author)

A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins

International Nuclear Information System (INIS)

Plevin, Michael J.; Hamelin, Olivier; Boisbouvier, Jérôme; Gans, Pierre

2011-01-01

A new method for stereospecific assignment of prochiral methyl groups in proteins is presented in which protein samples are produced using U-[ 13 C]glucose and subsaturating amounts of 2-[ 13 C]methyl-acetolactate. The resulting non-uniform labeling pattern allows proR and proS methyl groups to be easily distinguished by their different phases in a constant-time two-dimensional 1 H- 13 C correlation spectra. Protein samples are conveniently prepared using the same media composition as the main uniformly-labeled sample and contain higher levels of isotope-enrichment than fractional labeling approaches. This new strategy thus represents an economically-attractive, robust alternative for obtaining isotopically-encoded stereospecific NMR assignments of prochiral methyl groups.

Perdeuteration and methyl-selective 1H, 13C-labeling by using a Kluyveromyces lactis expression system

International Nuclear Information System (INIS)

Miyazawa-Onami, Mayumi; Takeuchi, Koh; Takano, Toshiaki; Sugiki, Toshihiko; Shimada, Ichio; Takahashi, Hideo

2013-01-01

The production of stable isotope-labeled proteins is critical in structural analyses of large molecular weight proteins using NMR. Although prokaryotic expression systems using Escherichia coli have been widely used for this purpose, yeast strains have also been useful for the expression of functional eukaryotic proteins. Recently, we reported a cost-effective stable isotope-labeled protein expression using the hemiascomycete yeast Kluyveromyces lactis (K. lactis), which allow us to express exogenous proteins at costs comparable to prokaryotic expression systems. Here, we report the successful production of highly deuterated (>90 %) protein in the K. lactis system. We also examined the methyl-selective 1 H, 13 C-labeling of Ile, Leu, and Val residues using commonly used amino acid precursors. The efficiency of 1 H- 13 C-incorporation varied significantly based on the amino acid. Although a high level of 1 H- 13 C-incorporation was observed for the Ile δ1 position, 1 H, 13 C-labeling rates of Val and Leu methyl groups were limited due to the mitochondrial localization of enzymes involved in amino acid biosynthesis and the lack of transporters for α-ketoisovalerate in the mitochondrial membrane. In line with this notion, the co-expression with branched-chain-amino-acid aminotransferase in the cytosol significantly improved the incorporation rates of amino acid precursors. Although it would be less cost-effective, addition of 13 C-labeled valine can circumvent problems associated with precursors and achieve high level 1 H, 13 C-labeling of Val and Leu. Taken together, the K. lactis system would be a good alternative for expressing large eukaryotic proteins that need deuteration and/or the methyl-selective 1 H, 13 C-labeling for the sensitive detection of NMR resonances

Yeast-expressed human membrane protein aquaporin-1 yields excellent resolution of solid-state MAS NMR spectra

International Nuclear Information System (INIS)

Emami, Sanaz; Fan Ying; Munro, Rachel; Ladizhansky, Vladimir; Brown, Leonid S.

2013-01-01

One of the biggest challenges in solid-state NMR studies of membrane proteins is to obtain a homogeneous natively folded sample giving high spectral resolution sufficient for structural studies. Eukaryotic membrane proteins are especially difficult and expensive targets in this respect. Methylotrophic yeast Pichia pastoris is a reliable producer of eukaryotic membrane proteins for crystallography and a promising economical source of isotopically labeled proteins for NMR. We show that eukaryotic membrane protein human aquaporin 1 can be doubly ( 13 C/ 15 N) isotopically labeled in this system and functionally reconstituted into phospholipids, giving excellent resolution of solid-state magic angle spinning NMR spectra.

Correlated optical and isotopic nanoscopy

Science.gov (United States)

Saka, Sinem K.; Vogts, Angela; Kröhnert, Katharina; Hillion, François; Rizzoli, Silvio O.; Wessels, Johannes T.

2014-04-01

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.

Deproteinization assessment using isotopically enriched compounds to trace the coprecipitation of low-molecular-weight selenium species with proteins.

Science.gov (United States)

Godin, Simon; Bouzas-Ramos, Diego; Fontagné-Dicharry, Stéphanie; Bouyssière, Brice; Bueno, Maïté

2017-08-01

Studies have shown that information related to the presence of low-molecular-weight metabolites is frequently lost after deproteinization of complex matrices, such as blood and plasma, during sample preparation. Therefore, the effect of several deproteinization reagents on low-molecular-weight selenium species has been compared by species-specific isotope labeling. Two isotopically enriched selenium tracers were used to mimic models of small inorganic anionic ( 77 Se-selenite) and organic zwitterionic ( 76 Se-selenomethionine) species. The results presented here show that the use of a methanol-acetonitrile-acetone (1:1:1 v/v/v) mixture provided approximately two times less tracer loss from plasma samples in comparison with the classic procedure using acetonitrile, which may not be optimal as it leads to important losses of low-molecular-weight selenium species. In addition, the possible interactions between selenium tracers and proteins were investigated, revealing that both coprecipitation phenomena and association with proteins were potentially responsible for selenite tracer losses during protein precipitation in blood samples. However, coprecipitation phenomena were found to be fully responsible for losses of both tracers observed in plasma samples and of the selenomethionine tracer in blood samples. This successfully applied strategy is anticipated to be useful for more extensive future studies in selenometabolomics. Copyright © 2017 Elsevier Inc. All rights reserved.

New stable isotope method to measure protein digestibility and response to pancreatic enzyme intake in cystic fibrosis.

Science.gov (United States)

Engelen, M P K J; Com, G; Anderson, P J; Deutz, N E P

2014-12-01

Adequate protein intake and digestion are necessary to prevent muscle wasting in cystic fibrosis (CF). Accurate and easy-to-use methodology to quantify protein maldigestion is lacking in CF. To measure protein digestibility and the response to pancreatic enzyme intake in CF by using a new stable isotope methodology. In 19 CF and 8 healthy subjects, protein digestibility was quantified during continuous (sip) feeding for 6 h by adding (15)N-labeled spirulina protein and L-[ring-(2)H5]phenylalanine (PHE) to the nutrition and measuring plasma ratio [(15)N]PHE to [(2)H5]PHE. Pancreatic enzymes were ingested after 2 h in CF and the response in protein digestibility was assessed. To exclude difference in mucosal function, postabsorptive whole-body citrulline (CIT) production rate was measured by L-[5-(13)C-5,5-(2)H2]-CIT pulse and blood samples were taken to analyze tracer-tracee ratios. Protein digestibility was severely reduced in the CF group (47% of healthy subjects; P digestibility in CF until 90% of values obtained by healthy subjects. Maximal digestibility was reached at 100 min and maintained for 80 min. Stratification into CF children (n = 10) and adults showed comparable values for protein digestibility and similar kinetic responses to pancreatic enzyme intake. Whole-body citrulline production was elevated in CF indicating preserved mucosal function. Protein digestibility is severely compromised in patients with CF as measured by this novel and easy-to-use stable isotope approach. Pancreatic enzymes are able to normalize protein digestibility in CF, albeit with a severe delay. Registration ClinicalTrials.gov = NCT01494909. Copyright © 2013 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

Lacan - a global simulation code for laser isotope separation

International Nuclear Information System (INIS)

Goldstein, S.; Quaegebeur, J.P.

1990-01-01

Dimensioning a Laser Isotope Separation (LIS) plant means calculating the values of a large number of parameters in order to optimize some objective function. In such algorithms the calculation of the objective function must be repeated thousands of times, therefore each elementary calculation must consume little time. LACAN uses simple models to describe the elementary physical processes: evaporation, vapour expansion, interaction between photons and atoms, ion extraction etc ... These simple models are derived from refined modeling codes or are empirical. As an example the optimization of the separative work of an uranium facility is discussed

Study of multiplication factor sensitivity to the spread of WWER spent fuel isotopics calculated by different codes

International Nuclear Information System (INIS)

Markova, L.

2001-01-01

As a sensitivity study the impact on the system reactivity was studied in the case that different calculational methodologies of spent fuel isotopic concentrations were used for WWER spent fuel inventory computations. The sets of isotopic concentrations obtained by calculations with different codes and libraries as a result of the CB2 international benchmark focused on WWER-440 burnup credit were used to show the spread of the calculated spent fuel system reactivity. Using the MCNP 4B code and changing the isotopics input data, the multiplication factor of an infinite array of the WWER-440 fuel pin cells was calculated. The evaluation of the results shows the sensitivity of the calculated reactivity to different calculational methodologies used for the spent fuel inventory computation. In the studied cases of the CB2 benchmark, the spread of the reference k-results relative to the mean was found less or about ±1% in spite of the fact that the data of isotopic concentrations were spread much more. (author)

Preparation of H3-labelled methyl ethers of saturated fatty acids by heterogeneous catalytic isotope exchange in solution with gaseous tritium

International Nuclear Information System (INIS)

Shevchenko, V.P.; Myasoedov, N.F.

1980-01-01

A simple method of preparing 3 H-labelled methyl ethers of saturated fatty acids in the dioxane solution using the method of isotopic heterogenous catalytic exchange with gaseous tritium, is suggested. 3 H-labelled natural fatty acids (C 12 -C 18 ) are prepared by alkaline hydrolysis [ru

Effect of reagent charge on the labeling of erythrocyte membrane proteins by photoactivated reagents

International Nuclear Information System (INIS)

Schaeffer, J.C.; Hakimian, R.; Shimer, M.L.

1986-01-01

Leaky erythrocyte ghosts were labeled with 3 H-[2-(4-azido-2-nitroanilino)ethyl]trimethylammonium iodide (cationic label) or 3 H-N-(4-azido-2-nitrophenyl)-β-alanine (anionic label). After the membranes were thoroughly washed, seven times as much cationic label was associated with the membranes as anionic label at 5 μM, whereas at 50 μM the cationic label was favored 15-fold. The distribution of label in the membrane proteins was ascertain by SDS-gel electrophoresis followed by autoradiography. At 50 μM cationic label, erythrocyte membrane protein bands 1,2,3,4.2, and 5 were intensely labeled, while band 6 was labeled weakly. At 5 μM cationic label, bands 1 and 4.2 were heavily labeled, while 2,3 and 5 were labeled less well. At both 50 μM and 5 μM anionic label, bands 1 and 6 were most prominently labeled. Bands 2,3,4.2 and 5 were labeled also at 50 μM, but they were labeled only very weakly at 5 μM. Band 4.1 was labeled very poorly if at all by either reagent. A mixture of the reagents gave an additive pattern. Thus, the charge and concentration of these reagents appear to play a major role in their ability to label membrane proteins indiscriminately. Because these reagents contain the same chromophore, 4-azido-2-nitroaniline, and differ mainly only in their charge, they may prove useful in assessing the location of charged sites on proteins in supramolecular complexes

Development of high-performance chemical isotope labeling LC-MS for profiling the human fecal metabolome.

Science.gov (United States)

Xu, Wei; Chen, Deying; Wang, Nan; Zhang, Ting; Zhou, Ruokun; Huan, Tao; Lu, Yingfeng; Su, Xiaoling; Xie, Qing; Li, Liang; Li, Lanjuan

2015-01-20

Human fecal samples contain endogenous human metabolites, gut microbiota metabolites, and other compounds. Profiling the fecal metabolome can produce metabolic information that may be used not only for disease biomarker discovery, but also for providing an insight about the relationship of the gut microbiome and human health. In this work, we report a chemical isotope labeling liquid chromatography-mass spectrometry (LC-MS) method for comprehensive and quantitative analysis of the amine- and phenol-containing metabolites in fecal samples. Differential (13)C2/(12)C2-dansyl labeling of the amines and phenols was used to improve LC separation efficiency and MS detection sensitivity. Water, methanol, and acetonitrile were examined as an extraction solvent, and a sequential water-acetonitrile extraction method was found to be optimal. A step-gradient LC-UV setup and a fast LC-MS method were evaluated for measuring the total concentration of dansyl labeled metabolites that could be used for normalizing the sample amounts of individual samples for quantitative metabolomics. Knowing the total concentration was also useful for optimizing the sample injection amount into LC-MS to maximize the number of metabolites detectable while avoiding sample overloading. For the first time, dansylation isotope labeling LC-MS was performed in a simple time-of-flight mass spectrometer, instead of high-end equipment, demonstrating the feasibility of using a low-cost instrument for chemical isotope labeling metabolomics. The developed method was applied for profiling the amine/phenol submetabolome of fecal samples collected from three families. An average of 1785 peak pairs or putative metabolites were found from a 30 min LC-MS run. From 243 LC-MS runs of all the fecal samples, a total of 6200 peak pairs were detected. Among them, 67 could be positively identified based on the mass and retention time match to a dansyl standard library, while 581 and 3197 peak pairs could be putatively

Selective Labeling of Proteins on Living Cell Membranes Using Fluorescent Nanodiamond Probes

Directory of Open Access Journals (Sweden)

Shingo Sotoma

2016-03-01

Full Text Available The impeccable photostability of fluorescent nanodiamonds (FNDs is an ideal property for use in fluorescence imaging of proteins in living cells. However, such an application requires highly specific labeling of the target proteins with FNDs. Furthermore, the surface of unmodified FNDs tends to adsorb biomolecules nonspecifically, which hinders the reliable targeting of proteins with FNDs. Here, we combined hyperbranched polyglycerol modification of FNDs with the β-lactamase-tag system to develop a strategy for selective imaging of the protein of interest in cells. The combination of these techniques enabled site-specific labeling of Interleukin-18 receptor alpha chain, a membrane receptor, with FNDs, which eventually enabled tracking of the diffusion trajectory of FND-labeled proteins on the membrane surface.

Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics.

Science.gov (United States)

Mosbæk, Freya; Kjeldal, Henrik; Mulat, Daniel G; Albertsen, Mads; Ward, Alastair J; Feilberg, Anders; Nielsen, Jeppe L

2016-10-01

Inhibition of anaerobic digestion through accumulation of volatile fatty acids occasionally occurs as the result of unbalanced growth between acidogenic bacteria and methanogens. A fast recovery is a prerequisite for establishing an economical production of biogas. However, very little is known about the microorganisms facilitating this recovery. In this study, we investigated the organisms involved by a novel approach of mapping protein-stable isotope probing (protein-SIP) onto a binned metagenome. Under simulation of acetate accumulation conditions, formations of (13)C-labeled CO2 and CH4 were detected immediately following incubation with [U-(13)C]acetate, indicating high turnover rate of acetate. The identified (13)C-labeled peptides were mapped onto a binned metagenome for improved identification of the organisms involved. The results revealed that Methanosarcina and Methanoculleus were actively involved in acetate turnover, as were five subspecies of Clostridia. The acetate-consuming organisms affiliating with Clostridia all contained the FTFHS gene for formyltetrahydrofolate synthetase, a key enzyme for reductive acetogenesis, indicating that these organisms are possible syntrophic acetate-oxidizing (SAO) bacteria that can facilitate acetate consumption via SAO, coupled with hydrogenotrophic methanogenesis (SAO-HM). This study represents the first study applying protein-SIP for analysis of complex biogas samples, a promising method for identifying key microorganisms utilizing specific pathways.

Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics

Science.gov (United States)

Mosbæk, Freya; Kjeldal, Henrik; Mulat, Daniel G; Albertsen, Mads; Ward, Alastair J; Feilberg, Anders; Nielsen, Jeppe L

2016-01-01

Inhibition of anaerobic digestion through accumulation of volatile fatty acids occasionally occurs as the result of unbalanced growth between acidogenic bacteria and methanogens. A fast recovery is a prerequisite for establishing an economical production of biogas. However, very little is known about the microorganisms facilitating this recovery. In this study, we investigated the organisms involved by a novel approach of mapping protein-stable isotope probing (protein-SIP) onto a binned metagenome. Under simulation of acetate accumulation conditions, formations of 13C-labeled CO2 and CH4 were detected immediately following incubation with [U-13C]acetate, indicating high turnover rate of acetate. The identified 13C-labeled peptides were mapped onto a binned metagenome for improved identification of the organisms involved. The results revealed that Methanosarcina and Methanoculleus were actively involved in acetate turnover, as were five subspecies of Clostridia. The acetate-consuming organisms affiliating with Clostridia all contained the FTFHS gene for formyltetrahydrofolate synthetase, a key enzyme for reductive acetogenesis, indicating that these organisms are possible syntrophic acetate-oxidizing (SAO) bacteria that can facilitate acetate consumption via SAO, coupled with hydrogenotrophic methanogenesis (SAO-HM). This study represents the first study applying protein-SIP for analysis of complex biogas samples, a promising method for identifying key microorganisms utilizing specific pathways. PMID:27128991

Technological advances in site-directed spin labeling of proteins.

Science.gov (United States)

Hubbell, Wayne L; López, Carlos J; Altenbach, Christian; Yang, Zhongyu

2013-10-01

Molecular flexibility over a wide time range is of central importance to the function of many proteins, both soluble and membrane. Revealing the modes of flexibility, their amplitudes, and time scales under physiological conditions is the challenge for spectroscopic methods, one of which is site-directed spin labeling EPR (SDSL-EPR). Here we provide an overview of some recent technological advances in SDSL-EPR related to investigation of structure, structural heterogeneity, and dynamics of proteins. These include new classes of spin labels, advances in measurement of long range distances and distance distributions, methods for identifying backbone and conformational fluctuations, and new strategies for determining the kinetics of protein motion. Copyright © 2013 Elsevier Ltd. All rights reserved.

Association of protein C23 with rapidly labeled nucleolar RNA

International Nuclear Information System (INIS)

Herrera, A.H.; Olson, M.O.

1986-01-01

The association of nucleolar phosphoprotein C23 with preribosomal ribonucleoprotein (RNP) particles was examined in Novikoff hepatoma nucleoli. RNA was labeled with [ 3 H]uridine for various times in cell suspensions, and RNP particles were extracted from isolated nucleoli and fractionated by sucrose gradient ultracentrifugation. The majority of protein C23 cosedimented with fractions containing rapidly labeled RNA (RL fraction). To determine whether there was a direct association of RNA with protein C23, the RL fraction was exposed to ultraviolet (UV) light (254 nm) for short periods of time. After 2 min of exposure there was a 50% decrease in C23 as measured by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analyses, with no significant further decrease at longer times. When UV-treated fractions were subjected to phenol/chloroform extractions, as much as 30% of the labeled RNA was found in the phenol (protein) layer, indicating that RNA became cross-linked to protein. Similarly, there was an increase in protein C23 extracted into the water layer after irradiation. By SDS-PAGE analyses the cross-linked species migrated more slowly than protein C23, appearing as a smear detected either by [ 3 H]uridine radioactivity or by anti-C23 antibody. With anti-C23 antibodies, up to 25% of the labeled RNA was precipitated from the RL fraction. Dot-blot hybridizations, using cloned rDNA fragments as probes, indicated that the RNA in the RL fraction and the immunoprecipitated RNA contained sequences from 18S and 28S ribosomal RNA

Stable isotope labeling by amino acids in cell culture (SILAC) and quantitative comparison of the membrane proteomes of self-renewing and differentiating human embryonic stem cells

DEFF Research Database (Denmark)

Prokhorova, Tatyana A; Rigbolt, Kristoffer T G; Johansen, Pia T

2009-01-01

Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful quantitative proteomics platform for comprehensive characterization of complex biological systems. However, the potential of SILAC-based approaches has not been fully utilized in human embryonic stem cell (hESC) research...... embryonic stem cell lines. Of the 811 identified membrane proteins, six displayed significantly higher expression levels in the undifferentiated state compared with differentiating cells. This group includes the established marker CD133/Prominin-1 as well as novel candidates for hESC surface markers......: Glypican-4, Neuroligin-4, ErbB2, receptor-type tyrosine-protein phosphatase zeta (PTPRZ), and Glycoprotein M6B. Our study also revealed 17 potential markers of hESC differentiation as their corresponding protein expression levels displayed a dramatic increase in differentiated embryonic stem cell...

Measurement of protein digestibility in humans by a dual-tracer method.

Science.gov (United States)

Devi, Sarita; Varkey, Aneesia; Sheshshayee, M S; Preston, Thomas; Kurpad, Anura V

2018-06-01

Recent evaluations of the risk of dietary protein deficiency have indicated that protein digestibility may be a key limiting factor in the provision of indispensable amino acids (IAAs), particularly for vulnerable populations living in challenging environments where intestinal dysfunction may exist. Since the digestion of protein occurs only in the small intestine, and the metabolic activity of colonic bacteria confounds measurements at the fecal level, there is a need to develop noninvasive protein digestibility measurements at the ileal level. We used a dual-tracer method with stable isotopes to characterize the digestibility of uniformly labeled [13C]-spirulina protein as a standard protein, in comparison to a mixture of 2H-labeled crystalline amino acids, and then demonstrated the use of this standard protein to measure the digestibility of selected legumes (chick pea and mung bean) through the use of proteins that were intrinsically labeled with 2H. The digestibility of uniformly labeled [13C]-spirulina was first measured in 6 healthy volunteers (3 males and 3 females) by feeding it along with a standard mixture of 2H-labeled amino acids, in a dual-tracer, plateau-fed test meal approach. Next, intrinsically labeled legume protein digestibility was studied with a similar dual-tracer approach, with uniformly labeled [13C]-spirulina as the standard, when processed differently before consumption. The average digestibility of IAA in spirulina protein was 85.2%. The average IAA digestibility of intrinsically 2H-labeled chick pea and mung bean protein was 56.6% and 57.7%, respectively. Dehulling of mung bean before ingestion increased the average IAA digestibility by 9.9% in comparison to whole mung bean digestibility. An innovative, minimally invasive "dual-stable-isotope" method was developed to measure protein digestibility, in which the ingestion of an intrinsically 2H-labeled test protein along with a 13C-labeled standard protein of known digestibility allows

Chemical method of labelling proteins with the radionuclides of technetium at physiological condition

International Nuclear Information System (INIS)

Wong, D.W.

1983-01-01

A novel rapid chemical method of labeling plasma proteins, other compounds and/or substances containing protein with radionuclides of technetium such as sup(95m)Tc, sup(99m)Tc or sup(99)Tc at physiologic pH 7.4 condition, producing a sterile non-pyrogenic radioactive tracer material suitable for biological and medical uses. These radiolabeled protein substances are not denatured by the labeling process but retain their natural physiological and immunological properties. This novel labeling technique provides a simple and rapid means of labeling plasma proteins such as human serum albumin, fibrinogen, antibodies, hormones and enzymes with sup(95m)Tc or sup(99m)Tc for scintigraphic imaging which may allow visualization of thrombi, emboli, myocardial infarcts, infectious lesions or tumors

Semi-supervised sparse coding

KAUST Repository

Wang, Jim Jing-Yan; Gao, Xin

2014-01-01

Sparse coding approximates the data sample as a sparse linear combination of some basic codewords and uses the sparse codes as new presentations. In this paper, we investigate learning discriminative sparse codes by sparse coding in a semi-supervised manner, where only a few training samples are labeled. By using the manifold structure spanned by the data set of both labeled and unlabeled samples and the constraints provided by the labels of the labeled samples, we learn the variable class labels for all the samples. Furthermore, to improve the discriminative ability of the learned sparse codes, we assume that the class labels could be predicted from the sparse codes directly using a linear classifier. By solving the codebook, sparse codes, class labels and classifier parameters simultaneously in a unified objective function, we develop a semi-supervised sparse coding algorithm. Experiments on two real-world pattern recognition problems demonstrate the advantage of the proposed methods over supervised sparse coding methods on partially labeled data sets.

Semi-supervised sparse coding

KAUST Repository

Wang, Jim Jing-Yan

2014-07-06

Sparse coding approximates the data sample as a sparse linear combination of some basic codewords and uses the sparse codes as new presentations. In this paper, we investigate learning discriminative sparse codes by sparse coding in a semi-supervised manner, where only a few training samples are labeled. By using the manifold structure spanned by the data set of both labeled and unlabeled samples and the constraints provided by the labels of the labeled samples, we learn the variable class labels for all the samples. Furthermore, to improve the discriminative ability of the learned sparse codes, we assume that the class labels could be predicted from the sparse codes directly using a linear classifier. By solving the codebook, sparse codes, class labels and classifier parameters simultaneously in a unified objective function, we develop a semi-supervised sparse coding algorithm. Experiments on two real-world pattern recognition problems demonstrate the advantage of the proposed methods over supervised sparse coding methods on partially labeled data sets.

Trends in the use of stable isotopes in biochemistry and pharmacology

International Nuclear Information System (INIS)

Matwiyoff, N.A.; Walker, T.E.

1977-01-01

Recent trends in the use of the stable isotopes 13 C, 15 N and 18 O in biochemistry and pharmacology are reviewed with emphasis on the studies that have employed nuclear magnetic resonance (nmr) spectroscopy and mass spectrometry as analytical techniques. Pharmacological studies with drugs and other compounds labelled with stable isotopes have developed in parallel with the rapid progress in the enhancement of sensitivity and selectivity of gas chromatography - mass spectrometric analyses, and have been directed largely to an evaluation of pharmako-kinetics and drug metabolic pathways. In these studies, illustrated with selected samples, isotopically labelled compounds have been used to advantage as internal standards for the mass spectrometric analyses and as in vivo tracers for metabolites. In the broader discipline of biochemistry, stable isotopes and isotopically labelled compounds have been used increasingly in conjuction with both nmr spectroscopy and mass spectrometry in tracer and structural studies. The more recent trends in the use of stable isotopes in these biochemical studies are discussed in the context of the improvements in analytical techniques. Specific examples will be drawn from investigations of the biosynthesis of natural products by micro-organisms; the protein, fat and carbohydrate fluxes in humans; and the structure and function of enzymes, membranes and other macro-molecular assemblages. The potential for the future development of stable isotopes in biochemistry and pharmacology are considered briefly, together with some of the problems that must be solved if their considerable potential is to be realized. (author)

Backbone dynamics of a model membrane protein: measurement of individual amide hydrogen-exchange rates in detergent-solubilized M13 coat protein using 13C NMR hydrogen/deuterium isotope shifts

International Nuclear Information System (INIS)

Henry, G.D.; Weiner, J.H.; Sykes, B.D.

1987-01-01

Hydrogen-exchange rates have been measured for individual assigned amide protons in M13 coat protein, a 50-residue integral membrane protein, using a 13 C nuclear magnetic resonance (NMR) equilibrium isotope shift technique. The locations of the more rapidly exchanging amides have been determined. In D 2 O solutions, a peptide carbonyl resonance undergoes a small upfield isotope shift (0.08-0.09 ppm) from its position in H 2 O solutions; in 1:1 H 2 O/D 2 O mixtures, the carbonyl line shape is determined by the exchange rate at the adjacent nitrogen atom. M13 coat protein was labeled biosynthetically with 13 C at the peptide carbonyls of alanine, glycine, phenylalanine, proline, and lysine, and the exchange rates of 12 assigned amide protons in the hydrophilic regions were measured as a function of pH by using the isotope shift method. This equilibrium technique is sensitive to the more rapidly exchanging protons which are difficult to measure by classical exchange-out experiments. In proteins, structural factors, notably H bonding, can decrease the exchange rate of an amide proton by many orders of magnitude from that observed in the freely exposed amides of model peptides such as poly(DL-alanine). With corrections for sequence-related inductive effects, the retardation of amide exchange in sodium dodecyl sulfate solubilized coat protein has been calculated with respect to poly(DL-alanine). The most rapidly exchanging protons, which are retarded very little or not at all, are shown to occur at the N- and C-termini of the molecule. A model of the detergent-solubilized coat protein is constructed from these H-exchange data which is consistent with circular dichroism and other NMR results

Secretion of 35SO4-labeled proteins from isolated rat hepatocytes

International Nuclear Information System (INIS)

von Wuertemberg, M.M.F.; Fries, E.

1989-01-01

Sulfation is a Golgi-specific modification of secretory proteins. We have characterized the proteins that are labeled with 35 SO 4 in cultures of rat hepatocytes and studied their transport to the medium. Analysis by polyacrylamide gel electrophoresis showed that of the five most heavily labeled proteins, four had well-defined mobilities--apparent molecular masses of 188, 142, 125, and 82 kDa--whereas one was electrophoretically heterogeneous--apparent molecular mass of 35-45 kDa. Judging by their relatively high resistance to acid treatment, the sulfate residues in the 125- and 35-45-kDa proteins were linked to carbohydrate. Some of the secreted proteins were sialylated. In samples of pulse-labeled cells, there appeared to be no unsialylated forms, indicating that sulfation occurred after sialylation, presumably in the trans Golgi. Kinetic experiments showed that the cellular half-life was the same for all the sulfated proteins--about 8 min--consistent with the idea that transport from the Golgi complex to the cell surface occurs by liquid bulk flow

Nitrogen 15 abundance in protein fractions of beans fertilized with ({sup 15}NH{sub 4}){sub 2}SO{sub 4}

Energy Technology Data Exchange (ETDEWEB)

Chaud, Saula Goulart; Oliveira, Admar Costa de [Universidade Estadual de Campinas, SP (Brazil). Faculdade de Estudos Agricolas. Dept. de Planejamento Alimentar e Nutricao; Trivelin, Paulo Cesar Ocheuze [Centro de Energia Nuclear na Agricultura (CENA), Piracicaba, SP (Brazil). Lab. de Isotopos Estaveis]. E-mail: admarco@fea.unicamp.br

2002-12-01

Studies evaluating the protein nutritive value of beans labelled with 15 N, using nitrogen balance and the quantitation of faecal and urinary endogenous nitrogen, determined by isotopic dilution, have been extensively used. The objective of this research was to verify if the isotopic labelling of raw, freeze dried beans (Phaseolus vulgaris L., cultivar Pirata 1) with 1.394 atoms % 15 N, resulted in the same abundance of the whole flour and of the protein fractions extracted from the beans with 0.5 mol L{sup -1} NaCl. The isotopic abundance found in the whole bean flour, in the protein extract, in the globulin and albumin fractions were respectively: 1.394 +- 0.011; 1.403 +- 0.012; 1.399 +- 0.007 and 1.399 +- 0.028 atoms % of 15 N, presenting no difference (P > 0.05). However, a difference was found (P < 0.05) between the above mentioned abundances and the isotopic abundance found in the nitrogen of the proteins in the extraction residue, which was 0.969 +- 0.084. Since the abundances did not differ, the protein nutritive indexes, such as digestibility and biological value, determined from the nitrogen balance and corrected for isotopic dilution, would not be affected by extracting the proteins from the beans with 0.5 mol L 1 NaCl. If working with the nitrogen balance of the residual proteins after extraction and even with the whole flours, these indexes could present incorrect values, since the isotopic labelling of the residual proteins was less than that of the protein fractions. (author)

The synthesis of tritium, carbon-14 and stable isotope labelled selective estrogen receptor degraders.

Science.gov (United States)

Bragg, Ryan A; Bushby, Nick; Ericsson, Cecilia; Kingston, Lee P; Ji, Hailong; Elmore, Charles S

2016-09-01

As part of a Medicinal Chemistry program aimed at developing an orally bioavailable selective estrogen receptor degrader, a number of tritium, carbon-14, and stable isotope labelled (E)-3-[4-(2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indol-1-yl)phenyl]prop-2-enoic acids were required. This paper discusses 5 synthetic approaches to this compound class. Copyright © 2016 John Wiley & Sons, Ltd.

Photoaffinity labelling of a small protein component of a purified (Na+-K+)ATPase

International Nuclear Information System (INIS)

Rogers, T.B.; Lazdunski, M.

1979-01-01

Studies have been carried out on the photoaffinity labelling of the (Na + -K + )ATPase from the electric organ of Electrophorus electricus. The aims were to see if different photoaffinity labels of the ouabain binding site, are capable of labelling a small protein component and to know if there is a small protein component, in addition to the major protein chains with molecular weights in the regions of 100 000 and 50 000, which is present in other purified (Na + -K + )ATPase preparations. (Auth.)

Bioorthogonal fluorescent labeling of functional G-protein-coupled receptors

DEFF Research Database (Denmark)

Tian, He; Naganathan, Saranga; Kazmi, Manija A

2014-01-01

Novel methods are required for site-specific, quantitative fluorescent labeling of G-protein-coupled receptors (GPCRs) and other difficult-to-express membrane proteins. Ideally, fluorescent probes should perturb the native structure and function as little as possible. We evaluated bioorthogonal...

Labelling of proteins with radioiodine and their application

International Nuclear Information System (INIS)

Franek, M.; Hampl, J.; Rodak, L.; Hruska, K.; Prochazka, Z.

1975-01-01

Various techniques of labelling proteins and peptides with radioactive iodine are reviewed. Particular attention is focused on the mechanism of iodination of tyrosine used as a model substance for radioiodination of proteins. Particular consideration is given to recent techniques attaining high specific radioactivity without side effects on the protein molecule and to factors affecting the rate of iodination and its character (buffers, polarity of the reaction environment, molecule type, etc.). The suitability is shown of radioiodinated proteins in the studies of protein metabolism and in the radioimmunoanalytical determination of substances of both the protein and non-protein nature. The possibility of further application of radioiodinated protein is discussed. (author)

HaloTag protein-mediated specific labeling of living cells with quantum dots

International Nuclear Information System (INIS)

So, Min-kyung; Yao Hequan; Rao Jianghong

2008-01-01

Quantum dots emerge as an attractive alternative to small molecule fluorophores as fluorescent tags for in vivo cell labeling and imaging. This communication presents a method for specific labeling of live cells using quantum dots. The labeling is mediated by HaloTag protein expressed at the cell surface which forms a stable covalent adduct with its ligand (HaloTag ligand). The labeling can be performed in one single step with quantum dot conjugates that are functionalized with HaloTag ligand, or in two steps with biotinylated HaloTag ligand first and followed by streptavidin coated quantum dots. Live cell fluorescence imaging indicates that the labeling is specific and takes place at the cell surface. This HaloTag protein-mediated cell labeling method should facilitate the application of quantum dots for live cell imaging

Problems and prospects in future applications of stable isotopes in the life sciences and medicine

International Nuclear Information System (INIS)

Matwiyoff, N.A.; Unkefer, C.J.; Walker, T.E.

1982-01-01

In the last decade, there has been a resurgence of interest in the use of stable isotopes of carbon, oxygen, and nitrogen in the life sciences and medicine fueled by the increased availability of the isotopes and isotopically labeled compounds and of instruments for their detection. Accelerated development of 13 C, 15 N, and 17 18 O can be expected in the future for studies of drug bioavailability, nutrition and body protein economy, viability of organs for transplant, and for non-invasive tests of metabolic diseases and dysfunctions. These accelerated developments depend on continued improvements in nmr and ms instrumentation and in methods for the synthesis of isotopically labeled compounds. The main part of this paper explores the possibilities of biosynthesis for the selective enrichment of natural products, especially amino acids, with 13 C

Labelling of eggs of Ceratitis capitata (Wiedmann) through radioactive sperm ( 32p)

International Nuclear Information System (INIS)

Wiendl, F.M.; Pacheco, J.M.

1975-06-01

The labelling of Med-fly eggs, using the sperm in the transmission of radioisotope 32 P is described. A hundred hatched couples were used, the males fed on a diet made of 5 g sugar and 1.66g of hydrolized protein. This diet was labelled with a solution of Na 2 HPO 4 , in which the atom of phosphorus was labelled with 32 P isotope. It showed an activity calculated at 343,9 μCi. Statistical treatment of the data indicated that the eggs became labelled and remained labelled until the 5th day after mating, even on eggs laid by female who mated with untreated males

ISOTOPE METHODS IN HOMOGENEOUS CATALYSIS.

Energy Technology Data Exchange (ETDEWEB)

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.

Amino acid code of protein secondary structure.

Science.gov (United States)

Shestopalov, B V

2003-01-01

The calculation of protein three-dimensional structure from the amino acid sequence is a fundamental problem to be solved. This paper presents principles of the code theory of protein secondary structure, and their consequence--the amino acid code of protein secondary structure. The doublet code model of protein secondary structure, developed earlier by the author (Shestopalov, 1990), is part of this theory. The theory basis are: 1) the name secondary structure is assigned to the conformation, stabilized only by the nearest (intraresidual) and middle-range (at a distance no more than that between residues i and i + 5) interactions; 2) the secondary structure consists of regular (alpha-helical and beta-structural) and irregular (coil) segments; 3) the alpha-helices, beta-strands and coil segments are encoded, respectively, by residue pairs (i, i + 4), (i, i + 2), (i, i = 1), according to the numbers of residues per period, 3.6, 2, 1; 4) all such pairs in the amino acid sequence are codons for elementary structural elements, or structurons; 5) the codons are divided into 21 types depending on their strength, i.e. their encoding capability; 6) overlappings of structurons of one and the same structure generate the longer segments of this structure; 7) overlapping of structurons of different structures is forbidden, and therefore selection of codons is required, the codon selection is hierarchic; 8) the code theory of protein secondary structure generates six variants of the amino acid code of protein secondary structure. There are two possible kinds of model construction based on the theory: the physical one using physical properties of amino acid residues, and the statistical one using results of statistical analysis of a great body of structural data. Some evident consequences of the theory are: a) the theory can be used for calculating the secondary structure from the amino acid sequence as a partial solution of the problem of calculation of protein three

Studies of phosphorus-containing fertilizer uptake in soils by 32P isotope labelling

International Nuclear Information System (INIS)

Fueleky, Gyoergy; Osztoics, Andrasne; Papne Kranitz, Erzsebet

1983-01-01

Breeding experiments were carried out with rye-grass (Lolium perenne L.) on two soil types to determine the plant uptake of phosphorus from naturally occuring element and from that added to the soil by superphosphate fertilizers. 32 P isotope labelling and radiometric measuring method were applied. In addition to the determination of phosphorus uptake, the phosphorus contents of the soil from its natural stock and from the fertilizer for both soil types can be determined by this method. (A.L.)

Effect of thyroid hormone on the protein turnover rate of mouse pancreas

International Nuclear Information System (INIS)

He Xinjun; Zhou Hui; Wang Shizhen; Zhou Zhonming; Li Liangxue; Wei Huaiwei; Sun Xiaomiao; Wang Yanli

1986-01-01

The effects of thyroid hormone on the protein turnover of pancreas in mice were studied using labelled amino acid incorporation, double isotopic and labelled protein decay methods. After injection of L-thyroxine (100 μ g/mouse) for 5 days, the amino acid incorporation into pancreatic proteins of mice was profoundly decreased, the ratio of 3 H/ 14 C in labelled proteins and the fractional turnover rate of pancreatic proteins were also decreased, the protein half-lives being consequently prolonged. These findings suggest that large doses of thyroid hormone may reduce the trunover rate of pancreatic proteins, by inhibiting not only the synthesis but also the degradation

Survey of surface proteins from the pathogenic Mycoplasma hyopneumoniae strain 7448 using a biotin cell surface labeling approach.

Science.gov (United States)

Reolon, Luciano Antonio; Martello, Carolina Lumertz; Schrank, Irene Silveira; Ferreira, Henrique Bunselmeyer

2014-01-01

The characterization of the repertoire of proteins exposed on the cell surface by Mycoplasma hyopneumoniae (M. hyopneumoniae), the etiological agent of enzootic pneumonia in pigs, is critical to understand physiological processes associated with bacterial infection capacity, survival and pathogenesis. Previous in silico studies predicted that about a third of the genes in the M. hyopneumoniae genome code for surface proteins, but so far, just a few of them have experimental confirmation of their expression and surface localization. In this work, M. hyopneumoniae surface proteins were labeled in intact cells with biotin, and affinity-captured biotin-labeled proteins were identified by a gel-based liquid chromatography-tandem mass spectrometry approach. A total of 20 gel slices were separately analyzed by mass spectrometry, resulting in 165 protein identifications corresponding to 59 different protein species. The identified surface exposed proteins better defined the set of M. hyopneumoniae proteins exposed to the host and added confidence to in silico predictions. Several proteins potentially related to pathogenesis, were identified, including known adhesins and also hypothetical proteins with adhesin-like topologies, consisting of a transmembrane helix and a large tail exposed at the cell surface. The results provided a better picture of the M. hyopneumoniae cell surface that will help in the understanding of processes important for bacterial pathogenesis. Considering the experimental demonstration of surface exposure, adhesion-like topology predictions and absence of orthologs in the closely related, non-pathogenic species Mycoplasma flocculare, several proteins could be proposed as potential targets for the development of drugs, vaccines and/or immunodiagnostic tests for enzootic pneumonia.

Survey of surface proteins from the pathogenic Mycoplasma hyopneumoniae strain 7448 using a biotin cell surface labeling approach.

Directory of Open Access Journals (Sweden)

Luciano Antonio Reolon

Full Text Available The characterization of the repertoire of proteins exposed on the cell surface by Mycoplasma hyopneumoniae (M. hyopneumoniae, the etiological agent of enzootic pneumonia in pigs, is critical to understand physiological processes associated with bacterial infection capacity, survival and pathogenesis. Previous in silico studies predicted that about a third of the genes in the M. hyopneumoniae genome code for surface proteins, but so far, just a few of them have experimental confirmation of their expression and surface localization. In this work, M. hyopneumoniae surface proteins were labeled in intact cells with biotin, and affinity-captured biotin-labeled proteins were identified by a gel-based liquid chromatography-tandem mass spectrometry approach. A total of 20 gel slices were separately analyzed by mass spectrometry, resulting in 165 protein identifications corresponding to 59 different protein species. The identified surface exposed proteins better defined the set of M. hyopneumoniae proteins exposed to the host and added confidence to in silico predictions. Several proteins potentially related to pathogenesis, were identified, including known adhesins and also hypothetical proteins with adhesin-like topologies, consisting of a transmembrane helix and a large tail exposed at the cell surface. The results provided a better picture of the M. hyopneumoniae cell surface that will help in the understanding of processes important for bacterial pathogenesis. Considering the experimental demonstration of surface exposure, adhesion-like topology predictions and absence of orthologs in the closely related, non-pathogenic species Mycoplasma flocculare, several proteins could be proposed as potential targets for the development of drugs, vaccines and/or immunodiagnostic tests for enzootic pneumonia.

Discovery of Proteomic Code with mRNA Assisted Protein Folding

Directory of Open Access Journals (Sweden)

Jan C. Biro

2008-12-01

Full Text Available The 3x redundancy of the Genetic Code is usually explained as a necessity to increase the mutation-resistance of the genetic information. However recent bioinformatical observations indicate that the redundant Genetic Code contains more biological information than previously known and which is additional to the 64/20 definition of amino acids. It might define the physico-chemical and structural properties of amino acids, the codon boundaries, the amino acid co-locations (interactions in the coded proteins and the free folding energy of mRNAs. This additional information, which seems to be necessary to determine the 3D structure of coding nucleic acids as well as the coded proteins, is known as the Proteomic Code and mRNA Assisted Protein Folding.

Increased Protein Structural Resolution from Diethylpyrocarbonate-based Covalent Labeling and Mass Spectrometric Detection

Science.gov (United States)

Zhou, Yuping; Vachet, Richard W.

2012-04-01

Covalent labeling and mass spectrometry are seeing increased use together as a way to obtain insight into the 3-dimensional structure of proteins and protein complexes. Several amino acid specific (e.g., diethylpyrocarbonate) and non-specific (e.g., hydroxyl radicals) labeling reagents are available for this purpose. Diethylpyrocarbonate (DEPC) is a promising labeling reagent because it can potentially probe up to 30% of the residues in the average protein and gives only one reaction product, thereby facilitating mass spectrometric analysis. It was recently reported, though, that DEPC modifications are labile for some amino acids. Here, we show that label loss is more significant and widespread than previously thought, especially for Ser, Thr, Tyr, and His residues, when relatively long protein digestion times are used. Such label loss ultimately decreases the amount of protein structural information that is obtainable with this reagent. We find, however, that the number of DEPC modified residues and, thus, protein structural information, can be significantly increased by decreasing the time between the covalent labeling reaction and the mass spectrometric analysis. This is most effectively accomplished using short (e.g., 2 h) proteolytic digestions with enzymes such as immobilized chymotrypsin or Glu-C rather than using methods (e.g., microwave or ultrasonic irradiation) that accelerate proteolysis in other ways. Using short digestion times, we show that the percentage of solvent accessible residues that can be modified by DEPC increases from 44% to 67% for cytochrome c, 35% to 81% for myoglobin, and 76% to 95% for β-2-microglobulin. In effect, these increased numbers of modified residues improve the protein structural resolution available from this covalent labeling method. Compared with typical overnight digestion conditions, the short digestion times decrease the average distance between modified residues from 11 to 7 Å for myoglobin, 13 to 10 Å for

Aqueous Oxidative Heck Reaction as a Protein-Labeling Strategy

NARCIS (Netherlands)

Ourailidou, Marilena; van der Meer, Jan-Ytzen; Baas, Bert-Jan; Jeronimus-Stratingh, Catherine; Gottumukkala, Aditya L.; Poelarends, Gerrit J.; Minnaard, Adriaan J.; Dekker, Frans

2014-01-01

An increasing number of chemical reactions are being employed for bio-orthogonal ligation of detection labels to protein-bound functional groups. Several of these strategies, however, are limited in their application to pure proteins and are ineffective in complex biological samples such as cell

Indirect Radiohalogenation of Targeting Proteins: Labelling Chemistry and Biological Characterisation

Energy Technology Data Exchange (ETDEWEB)

Orlova, Anna

2003-03-01

In about half of all newly diagnosed cancer cases, conventional treatment is not adequately curative, mainly due to the failure of conventional techniques to find and kill residual cells and metastases, which might consist of only a few malignant cells, without causing unacceptable complications to healthy tissue. To solve the problem a more selective delivery of cytotoxic substances to tumour cells is needed. The approach applied here is called 'tumour targeting' and implies the use of biomolecules that recognise specific molecular structures on the malignant cell surface. Such molecules are then used for a selective transport of toxic agents to the cancer cells. The use of radionuclides as cytotoxic substances has a number of advantages: 1) radiation does not cause severe resistance; 2) there is a cross-fire effect and 3) smaller amounts of nuclides are required than other cytotoxic substances to cause the same damage. Such an approach is called radionuclide tumour therapy. Several factors are important for the success of radionuclide therapy, such as the pharmacokinetics of the radiolabelled substance and its radiocatabolites, as well as the physical and chemical properties of the radiolabel used. Nuclear properties of the label should be consistent with the problem to be solved: primary diagnostics; quantification of pharmacokinetics and dose planning; or therapy. From this point of view, radiohalogens are an attractive group of radiolabels. Halogens have nuclides with a variety of physical properties while the chemical and biological properties of halogens are very similar. The same labelling procedures can be used for all heavy halogens, i.e. bromine, iodine and astatine. It has been demonstrated that the biodistribution of proteins labelled with different heavy halogens is quite similar. The main goal of the study was to develop protein radiohalogenation methods that provide a stable halogen-protein bond, convenient labelling chemistry that

Uniform and selective deuteration in two-dimensional NMR of proteins

International Nuclear Information System (INIS)

LeMaster, D.M.

1990-01-01

This paper reports on the practicality of isotopic labeling, particularly deuteration, that has received considerable impetus from advances in molecular biology, which have allowed ready production of NMR quantities of labeled proteins. Protein expression in Escherichia coli allows use of the considerable metabolic genetics known for the organism in shaping the biosynthetic process to meet the labeling demands of the NMR experiments. In addition to deuteration's common use in spectral assignment problems, it also offers considerable potential for enhancing the quality of the nuclear Overhauser effect (NOE) distance and dihedral angle constraints used for solution structural analysis of proteins. Recent reviews emphasize the sample preparation and spectral benefits of protein deuteration

A label-free internal standard method for the differential analysis of bioactive lupin proteins using nano HPLC-Chip coupled with Ion Trap mass spectrometry.

Science.gov (United States)

Brambilla, Francesca; Resta, Donatella; Isak, Ilena; Zanotti, Marco; Arnoldi, Anna

2009-01-01

Quantitative proteomics based on MS is useful for pointing out the differences in some food proteomes relevant to human nutrition. Stable isotope label-free (SIF) techniques are suitable for comparing an unlimited number of samples by the use of relatively simple experimental workflows. We have developed an internal standard label-free method based on the intensities of peptide precursor ions from MS/MS spectra, collected in data dependent runs, for the simultaneous qualitative characterization and relative quantification of storage proteins of Lupinus albus seeds in protein extracts of four lupin cultivars (cv Adam, Arés, Lucky, Multitalia). The use of an innovative microfluidic system, the HPLC-Chip, coupled with a classical IT mass spectrometer, has allowed a complete qualitative characterization of all proteins. In particular, the homology search mode has permitted to identify single amino acid substitutions in the sequences of vicilins (beta-conglutin precursor and vicilin-like protein). The MS/MS sequencing of substituted peptides confirms the high heterogeneity of vicilins according to the peculiar characteristics of the vicilin-encoding gene family. Two suitable bioinformatics parameters were optimized for the differential analyses of the main bioactive proteins: the "normalized protein average of common reproducible peptides" (N-ACRP) for gamma-conglutin, which is a homogeneous protein, and the "normalized protein mean peptide spectral intensity" (N-MEAN) for the highly heterogenous class of the vicilins.

Isotope labelling study of CO oxidation-assisted epoxidation of propene. Implications for oxygen activation on Au catalysts.

Science.gov (United States)

Jiang, Jian; Oxford, Sean M; Fu, Baosong; Kung, Mayfair C; Kung, Harold H; Ma, Jiantai

2010-06-07

(18)O isotope labelling studies of the CO oxidation-assisted epoxidation of propene, catalyzed by a mixture of Au/TiO(2) and TS-1, using a methanol-H(2)O solvent showed the O in the epoxide was exclusively from O(2) and not H(2)O or methanol.

Direct application of radioiodinated aminoacyl tRNA for radiolabeling nascent proteins

International Nuclear Information System (INIS)

Scherberg, N.H.; Barokas, K.; Murata, Y.; Refetoff, S.

1985-01-01

A two-step procedure to incorporate 125 I-iodotyrosine into protein synthesized in a reticulocyte lysate is described. In the first step, the iodination of tyrosyl tRNA was catalyzed by a solid-state glycouril compound. More than one-third of 200 microCi of radioiodine became bound to 70 micrograms of aminoacyl tRNA after 15 min at 0 degrees C. The isotope was distributed in a three-to-one ratio of monoiodotyrosine to di-iodotyrosine. In the second step, the soluble product of the radioiodination was transferred directly into a nuclease-treated reticulocyte lysate coded with RNA isolated from the human hepatoma cell line Hep G2. Fractional recovery of radioiodine in nascent protein was maximally 7.6%. Reaction of the product of translation with antibody against alpha-antitrypsin separated an 125 I-containing protein having a molecular weight estimated as 47,000. The synthesis of unprocessed alpha-antitrypsin was confirmed by cleavage of the labeled protein with leader peptidase and by its displacement from immunocomplex formation with purified alpha-antitrypsin. The amount of 125 I incorporated into alpha-antitrypsin was proportionate to iodinated tRNA additions up to a concentration of 70 micrograms/ml. The synthesis of alpha-antitrypsin as detected in radioautograms after gel electrophoresis was more than twice as sensitive using radioiodinated aminoacyl tRNA as compared with [ 35 S]methionine. Iodine labeling of thyroxine-binding globulin was also demonstrated in the translation product of Hep G2 RNA. Since the specific activity of the radioiodine is high and the means for detection of the isotope efficient, the method described can facilitate the demonstration of quantitatively minor translation products

Efficient cellular solid-state NMR of membrane proteins by targeted protein labeling

Energy Technology Data Exchange (ETDEWEB)

Baker, Lindsay A. [University of Oxford, Oxford Particle Imaging Centre, The Wellcome Trust Centre for Human Genetics, Division of Structural Biology, Nuffield Department of Medicine (United Kingdom); Daniëls, Mark; Cruijsen, Elwin A. W. van der; Folkers, Gert E.; Baldus, Marc, E-mail: m.baldus@uu.nl [Utrecht University, NMR Spectroscopy, Department of Chemistry, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands)

2015-06-15

Solid-state NMR spectroscopy (ssNMR) has made significant progress towards the study of membrane proteins in their native cellular membranes. However, reduced spectroscopic sensitivity and high background signal levels can complicate these experiments. Here, we describe a method for ssNMR to specifically label a single protein by repressing endogenous protein expression with rifampicin. Our results demonstrate that treatment of E. coli with rifampicin during induction of recombinant membrane protein expression reduces background signals for different expression levels and improves sensitivity in cellular membrane samples. Further, the method reduces the amount of time and resources needed to produce membrane protein samples, enabling new strategies for studying challenging membrane proteins by ssNMR.

Efficient cellular solid-state NMR of membrane proteins by targeted protein labeling

International Nuclear Information System (INIS)

Baker, Lindsay A.; Daniëls, Mark; Cruijsen, Elwin A. W. van der; Folkers, Gert E.; Baldus, Marc

2015-01-01

Solid-state NMR spectroscopy (ssNMR) has made significant progress towards the study of membrane proteins in their native cellular membranes. However, reduced spectroscopic sensitivity and high background signal levels can complicate these experiments. Here, we describe a method for ssNMR to specifically label a single protein by repressing endogenous protein expression with rifampicin. Our results demonstrate that treatment of E. coli with rifampicin during induction of recombinant membrane protein expression reduces background signals for different expression levels and improves sensitivity in cellular membrane samples. Further, the method reduces the amount of time and resources needed to produce membrane protein samples, enabling new strategies for studying challenging membrane proteins by ssNMR

Synthesis of {sup 15}N isotope labeled alanine; Sintese da alanina enriquecida com {sup 15}N

Energy Technology Data Exchange (ETDEWEB)

Oliveira, Claudineia R. de; Bendassolli, Jose Albertino; Sant' Ana, Carlos Roberto; Tagliassachi, Romulo Barbieri; Maximo, Everaldo; Prestes, Clelber Vieira [Centro de Energia Nuclear na Agricultura (CENA), Piracicaba, SP (Brazil). Dept. de Isotopos Estaveis]. E-mail: crolivei@cena.usp.br

2005-07-01

The application of light chemical elements and their stable isotopes in biological studies have been increased over the last years. The use of {sup 15}N labeled amino acids is an important tool for elucidation of peptides structures. This paper describe a method for the synthesis of {sup 15}N isotope labeled alanine at lower costs than international ones, as well as the details of the recovery system of the nitrogen residues. In the present work an amination of {alpha}-haloacids, with the bromopropionic carboxylic acid and labeled aqua ammonia ({sup 15}NH{sub 3} aq) was carried out. In order to avoid eventually losses of {sup 15}NH{sub 3}, special cares were adopted, since the production cost is high. Although the acquisition cost of the {sup 13}N (radioactive) labeled compounds is lower, the obtained stable tracer will allow the accomplishment of important studies of the nitrogen cycling in living things, less occupational and environment hazards, and the time limitation problems in field studies. The tests took place in triplicates with NH{sub 3} (aq) being employed. With the establishment of the system for {sup 15}NH{sub 3} recovery, an average of 94 % of the ammonia employed in the synthesis process was recovered. The purity of the amino acid was state determined by TLC (Thin Layer Chromatography) and HPLC (High-Performance Liquid Chromatography) with a fluorescence detector. The Rf and the retention time of the synthesized sample were similar the sigma standard. Finally, regarding the established conditions, it was possible to obtain the alanine with a production cost about 40 % lower than the international price. (author)

Historical and contemporary stable isotope tracer approaches to studying mammalian protein metabolism

Science.gov (United States)

2016-01-01

Over a century ago, Frederick Soddy provided the first evidence for the existence of isotopes; elements that occupy the same position in the periodic table are essentially chemically identical but differ in mass due to a different number of neutrons within the atomic nucleus. Allied to the discovery of isotopes was the development of some of the first forms of mass spectrometers, driven forward by the Nobel laureates JJ Thomson and FW Aston, enabling the accurate separation, identification, and quantification of the relative abundance of these isotopes. As a result, within a few years, the number of known isotopes both stable and radioactive had greatly increased and there are now over 300 stable or radioisotopes presently known. Unknown at the time, however, was the potential utility of these isotopes within biological disciplines, it was soon discovered that these stable isotopes, particularly those of carbon (13C), nitrogen (15N), oxygen (18O), and hydrogen (2H) could be chemically introduced into organic compounds, such as fatty acids, amino acids, and sugars, and used to “trace” the metabolic fate of these compounds within biological systems. From this important breakthrough, the age of the isotope tracer was born. Over the following 80 yrs, stable isotopes would become a vital tool in not only the biological sciences, but also areas as diverse as forensics, geology, and art. This progress has been almost exclusively driven through the development of new and innovative mass spectrometry equipment from IRMS to GC‐MS to LC‐MS, which has allowed for the accurate quantitation of isotopic abundance within samples of complex matrices. This historical review details the development of stable isotope tracers as metabolic tools, with particular reference to their use in monitoring protein metabolism, highlighting the unique array of tools that are now available for the investigation of protein metabolism in vivo at a whole body down to a single protein level

Recycling of an amino acid label with prolonged isotope infusion: Implications for kinetic studies

International Nuclear Information System (INIS)

Schwenk, W.F.; Tsalikian, E.; Beaufrere, B.; Haymond, M.W.

1985-01-01

To investigate whether recycling of a labeled amino acid would occur after 24 h of infusion, two groups of normal volunteers were infused with [ 3 H]leucine and alpha-[ 14 C]-ketoisocaproate for 4 h and [ 2 H 3 ]leucine for either 4 or 24 h (groups I and II, respectively). Entry of [ 2 H 3 ]leucine at steady state into the plasma space was indistinguishable from its infusion rate for group I but 30% higher (P less than 0.001) than this rate for group II, demonstrating significant recycling of label. After discontinuation of the infusions, isotope disappearance from the plasma space was followed for 2 h. The 3 H and 14 C decay data for both groups suggest that plasma leucine and alpha- ketoisocaproate are derived from a single intracellular pool in the postabsorptive state. In group I, the 3 H and 2 H labels decayed identically; whereas, in group II, the decay of [ 2 H 3 ]-leucine and alpha- [ 2 H 3 ]ketoisocaproate was slower (P less than 0.01) than the decay of [ 3 H]leucine and alpha-[ 3 H]ketoisocaproate, confirming re-entry of label after a 24-h infusion. Therefore kinetic values calculated from models assuming no recycling of labeled amino acids are most likely not quantitative and must be interpreted with care when flux does not change or decreases

Small Molecule-Photoactive Yellow Protein Labeling Technology in Live Cell Imaging

Directory of Open Access Journals (Sweden)

Feng Gao

2016-08-01

Full Text Available Characterization of the chemical environment, movement, trafficking and interactions of proteins in live cells is essential to understanding their functions. Labeling protein with functional molecules is a widely used approach in protein research to elucidate the protein location and functions both in vitro and in live cells or in vivo. A peptide or a protein tag fused to the protein of interest and provides the opportunities for an attachment of small molecule probes or other fluorophore to image the dynamics of protein localization. Here we reviewed the recent development of no-wash small molecular probes for photoactive yellow protein (PYP-tag, by the means of utilizing a quenching mechanism based on the intramolecular interactions, or an environmental-sensitive fluorophore. Several fluorogenic probes have been developed, with fast labeling kinetics and cell permeability. This technology allows quick live-cell imaging of cell-surface and intracellular proteins without a wash-out procedure.

iMS2Flux – a high–throughput processing tool for stable isotope labeled mass spectrometric data used for metabolic flux analysis

Directory of Open Access Journals (Sweden)

Poskar C Hart

2012-11-01

Full Text Available Abstract Background Metabolic flux analysis has become an established method in systems biology and functional genomics. The most common approach for determining intracellular metabolic fluxes is to utilize mass spectrometry in combination with stable isotope labeling experiments. However, before the mass spectrometric data can be used it has to be corrected for biases caused by naturally occurring stable isotopes, by the analytical technique(s employed, or by the biological sample itself. Finally the MS data and the labeling information it contains have to be assembled into a data format usable by flux analysis software (of which several dedicated packages exist. Currently the processing of mass spectrometric data is time-consuming and error-prone requiring peak by peak cut-and-paste analysis and manual curation. In order to facilitate high-throughput metabolic flux analysis, the automation of multiple steps in the analytical workflow is necessary. Results Here we describe iMS2Flux, software developed to automate, standardize and connect the data flow between mass spectrometric measurements and flux analysis programs. This tool streamlines the transfer of data from extraction via correction tools to 13C-Flux software by processing MS data from stable isotope labeling experiments. It allows the correction of large and heterogeneous MS datasets for the presence of naturally occurring stable isotopes, initial biomass and several mass spectrometry effects. Before and after data correction, several checks can be performed to ensure accurate data. The corrected data may be returned in a variety of formats including those used by metabolic flux analysis software such as 13CFLUX, OpenFLUX and 13CFLUX2. Conclusion iMS2Flux is a versatile, easy to use tool for the automated processing of mass spectrometric data containing isotope labeling information. It represents the core framework for a standardized workflow and data processing. Due to its flexibility

Determination of symbiotic nitrogen fixation by labelling the soil atmosphere with sup(15)N sub(2) at low isotope enrichment

International Nuclear Information System (INIS)

Trivelin, P.C.O.

1982-01-01

A direct method to determine the total symbiotic nitrogen fixation during the leguminous plants cycles has been, developed, by labelling the soil atmosphere with sup(15)N sub(2) at low isotope enrichment, of about 1 atom % excess. The soil explored by the root system of leguminous plants was confined by means of a chamber in the field and by sealed pots in greenhouse experiments in order to maintain the soil air labelled with sup(15)N sub(2). The average sup(15)N concentration in the soil atmosphere, necessary to calculate dinitrogen fixation, was obtained by integration of the exponential functions of isotope dilution. Those functions were obtained by periodic sampling and analysis of the N sub(2) in the soil atmosphere. The field experiment with labelled atmosphere was carried out from the 22 sup(nd) to the 31 sup(st) day of the bean crop cycle and 5.5 mg N/plant (24% of total plant N) was derived from fixation. In pot experiments, under greenhouse conditions, integrated determination of fixation was made in Phaseolus beans (from the 19 sup(th) to the 67 sup(th) day from planting) and in soybeans (from the 24 sup(th) to the 70 sup(th) day from planting). The soil atmosphere was labelled with sup(15)N sub(2) in both cases. Average fixation obtained for Phaseolus beans was 80 mg N/plant (65% of total plant N) and for soybeans 265 mg N/plant (71% of total plant N). Evaluation of the basic concept of the isotope dilution method to determine nitrogen fixation in pots experiments, as proposed by Fried and Middelboe (1977) has also been made in the present paper. Simultaneous determinations of fixation in soybeans, using the isotope dilution method of Fried and Middelboe, natural variation of the sup(15)N/ sup(14)N ratios, and total-N differences, indicated the same results for pot experiments, harvested at the end of the plant cycle. (author)

Peptides and proteins

Energy Technology Data Exchange (ETDEWEB)

Bachovchin, W.W.; Unkefer, C.J.

1994-12-01

Advances in magnetic resonance and vibrational spectroscopy make it possible to derive detailed structural information about biomolecular structures in solution. These techniques are critically dependent on the availability of labeled compounds. For example, NMR techniques used today to derive peptide and protein structures require uniformity {sup 13}C-and {sup 15}N-labeled samples that are derived biosynthetically from (U-6-{sup 13}C) glucose. These experiments are possible now because, during the 1970s, the National Stable Isotope Resource developed algal methods for producing (U-6-{sup 13}C) glucose. If NMR techniques are to be used to study larger proteins, we will need sophisticated labelling patterns in amino acids that employ a combination of {sup 2}H, {sup 13}C, and {sup 15}N labeling. The availability of these specifically labeled amino acids requires a renewed investment in new methods for chemical synthesis of labeled amino acids. The development of new magnetic resonance or vibrational techniques to elucidate biomolecular structure will be seriously impeded if we do not see rapid progress in labeling technology. Investment in labeling chemistry is as important as investment in the development of advanced spectroscopic tools.

Algal autolysate medium to label proteins for NMR in mammalian cells.

Science.gov (United States)

Fuccio, Carmelo; Luchinat, Enrico; Barbieri, Letizia; Neri, Sara; Fragai, Marco

2016-04-01

In-cell NMR provides structural and functional information on proteins directly inside living cells. At present, the high costs of the labeled media for mammalian cells represent a limiting factor for the development of this methodology. Here we report a protocol to prepare a homemade growth medium from Spirulina platensis autolysate, suitable to express uniformly labeled proteins inside mammalian cells at a reduced cost-per-sample. The human proteins SOD1 and Mia40 were overexpressed in human cells grown in (15)N-enriched S. platensis algal-derived medium, and high quality in-cell NMR spectra were obtained.

Algal autolysate medium to label proteins for NMR in mammalian cells

Energy Technology Data Exchange (ETDEWEB)

Fuccio, Carmelo; Luchinat, Enrico; Barbieri, Letizia [University of Florence, Magnetic Resonance Center (CERM) (Italy); Neri, Sara [Giotto Biotech S.R.L. (Italy); Fragai, Marco, E-mail: fragai@cerm.unifi.it [University of Florence, Magnetic Resonance Center (CERM) (Italy)

2016-04-15

In-cell NMR provides structural and functional information on proteins directly inside living cells. At present, the high costs of the labeled media for mammalian cells represent a limiting factor for the development of this methodology. Here we report a protocol to prepare a homemade growth medium from Spirulina platensis autolysate, suitable to express uniformly labeled proteins inside mammalian cells at a reduced cost-per-sample. The human proteins SOD1 and Mia40 were overexpressed in human cells grown in {sup 15}N-enriched S. platensis algal-derived medium, and high quality in-cell NMR spectra were obtained.

Closing the gap between T-cell life span estimates from stable isotope-labeling studies in mice and humans

NARCIS (Netherlands)

Westera, Liset; Drylewicz, Julia; den Braber, Ineke; Mugwagwa, Tendai; van der Maas, Iris; Kwast, Lydia; Volman, Thomas; van de Weg-Schrijver, Elise H. R.; Bartha, István; Spierenburg, Gerrit; Gaiser, Koos; Ackermans, Mariëtte T.; Asquith, Becca; de Boer, Rob J.; Tesselaar, Kiki; Borghans, José A. M.

2013-01-01

Quantitative knowledge of the turnover of different leukocyte populations is a key to our understanding of immune function in health and disease. Much progress has been made thanks to the introduction of stable isotope labeling, the state-of-the-art technique for in vivo quantification of cellular

Neutron scattering with deuterium labeling reveals the nature of complexes formed by Ca{sup 2+}-binding proteins and their regulatory targets

Energy Technology Data Exchange (ETDEWEB)

Trewhella, J. [Los Alamos National Laboratory, NM (United States)

1994-12-01

Small-angle neutron scattering with deuterium labeling is extremely useful for studying the structures of complex biomolecular assemblies in solution. The different neutron scattering properties of their isotopes of hydrogen combines with the ability to uniformly label biomolecules with deuterium allow one to characterize the structures and relative dispositions of the individual components of an assembly using methods of {open_quotes}contrast variation.{close_quotes} We have applied these techniques to studies of the evolutionarily related dumbbell-shaped Ca{sup 2+}-binding proteins calmodulin and troponin C and their interactions with the target proteins whose activities they regulate. Ca{sup 2+} is one of the simplest of nature`s messengers used in the communication pathways between physiological stimulus and cellular response. The signaling mechanism generally involves Ca{sup 2+} binding to a protein and inducing a conformational change that transmits a signal to modify the activity of a specific target protein. Ca{sup 2+} is thus important in the regulation of a diverse array of intracellular responses, including neurotransmitter release, muscle contraction, the degradation of glycogen to glucose to generate energy, microtubule assembly, membrane phosphorylation, etc. It is the conformational language of the Ca{sup 2+} induced signal transduction that we have sought to understand because of its central importance to biochemical regulation and, hence, to healthy cellular function.

Isotopic labeling as a tool to establish intramolecular vibrational coupling: The reaction of 2-propanol on Mo(110)

International Nuclear Information System (INIS)

Uvdal, P.; Wiegand, B.C.; Serafin, J.G.; Friend, C.M.

1992-01-01

The reactions of 2-propanol on Mo(110) were investigated using temperature programmed reaction, high resolution electron energy loss, and x-ray photoelectron spectroscopies. 2-Propanol forms 2-propoxide upon adsorption at 120 K on Mo(110). The 2-propoxide intermediate deoxygenates via selective γ C--H bond scission to eliminate propene as well as C--O bond hydrogenolysis to form trace amounts of propane. The C--O bond of 2-propoxide is estimated to be nearly perpendicular to the surface. Selective isotopic labeling was used to establish the coupling between the C--O stretch and modes associated with the hydrocarbon framework. The degree of coupling was strongly affected by bonding to the surface, primarily due to weakening of the C--O bond when 2-propoxide is bound to Mo(110). Selective isotopic labeling was, therefore, essential in making vibrational assignments and in identifying key reaction steps. Only a small kinetic isotope effect was observed during reaction of (CD 3 )(CH 3 )CHOH, consistent with a substantial component of C--O bond breaking in the transition state for propene elimination. Coupling of the C--O stretch to motion of the methyl group is also suggested to be important in the transition state for propene elimination

Mapping Protein-Protein Interactions by Quantitative Proteomics

DEFF Research Database (Denmark)

Dengjel, Joern; Kratchmarova, Irina; Blagoev, Blagoy

2010-01-01

spectrometry (MS)-based proteomics in combination with affinity purification protocols has become the method of choice to map and track the dynamic changes in protein-protein interactions, including the ones occurring during cellular signaling events. Different quantitative MS strategies have been used...... to characterize protein interaction networks. In this chapter we describe in detail the use of stable isotope labeling by amino acids in cell culture (SILAC) for the quantitative analysis of stimulus-dependent dynamic protein interactions.......Proteins exert their function inside a cell generally in multiprotein complexes. These complexes are highly dynamic structures changing their composition over time and cell state. The same protein may thereby fulfill different functions depending on its binding partners. Quantitative mass...

An isotope approach based on C-13 pulse-chase labelling vs. the root trenching method to separate heterotrophic and autotrophic respiration in cultivated peatlands

Energy Technology Data Exchange (ETDEWEB)

Biasi, C.; Pitkamaki, A. S.; Tavi, N. M.; Koponen, H. T.; Martikainen, P. J. [Univ.of Eastern Finland, Kuopio (Finland). Dept. of Environmental Science], e-mail: christina.biasi@uef.fi

2012-11-01

We tested an isotope method based on C-13 pulse-chase labelling for determining the fractional contribution of soil microbial respiration to overall soil respiration in an organic soil (cutaway peatland, eastern Finland), cultivated with the bioenergy crop, reed canary grass. The plants were exposed to CO{sub 2}-13 for five hours and the label was thereafter determined in CO{sub 2} derived from the soil-root system. A two-pool isotope mixing model was used to separate sources of respiration. The isotopic approach showed that a minimum of 50% of the total CO{sub 2} originated from soil-microbial respiration. Even though the method uses undisturbed soil-plant systems, it has limitations concerning the experimental determination of the true isotopic signal of all components contributing to autotrophic respiration. A trenching experiment which was comparatively conducted resulted in a 71% fractional contribution of soil-microbial respiration. This value was likely overestimated. Further studies are needed to evaluate critically the output from these two partitioning approaches. (orig.)

Autodegradation of 125I-labeled human epidermal cell surface proteins

International Nuclear Information System (INIS)

Hashimoto, K.; Singer, K.H.; Lazarus, G.S.

1982-01-01

Triton X-100 extracts of cultured human epidermal cells exhibited proteolytic activity as measured by the hydrolysis of [ 3 H]-casein at neutral pH. The majority of endogenous proteolytic activity was inhibited by parahydroxy mercuribenzoate and by mersalyl acid, indicating the enzyme(s) was a thiol class proteinase(s). Crude Triton X-100 extracts were prepared from epidermal cells following labeling of proteins with 125 I. Autodegradation of labeled proteins at 37 degrees C was detected as early as 1 hr and reached a plateau level by 4 hr. Degradation was inhibited by thiol class proteinase inhibitors. Among the detergent-solubilized radiolabeled proteins a polypeptide chain of Mr 155,000 was particularly sensitive to degradation by endogenous thiol proteinase(s)

Protein aggregation and degradation during iodine labeling and its consequences for protein adsorption to biomaterials

DEFF Research Database (Denmark)

Holmberg, Maria; Jensen, Karin Bagger Stibius; Ndoni, Sokol

2007-01-01

Protein adsorption on modified and unmodified polymer surfaces investigated through radiolabeling experiments showed a tendency for higher than expected albumin and immunoglobulin G (IgG) adsorption. Possible enhanced protein aggregation and degradation caused by the iodine labeling method used w...

Comparative study of label and label-free techniques using shotgun proteomics for relative protein quantification.

Science.gov (United States)

Sjödin, Marcus O D; Wetterhall, Magnus; Kultima, Kim; Artemenko, Konstantin

2013-06-01

The analytical performance of three different strategies, iTRAQ (isobaric tag for relative and absolute quantification), dimethyl labeling (DML) and label free (LF) for relative protein quantification using shotgun proteomics have been evaluated. The methods have been explored using samples containing (i) Bovine proteins in known ratios and (ii) Bovine proteins in known ratios spiked into Escherichia coli. The latter case mimics the actual conditions in a typical biological sample with a few differentially expressed proteins and a bulk of proteins with unchanged ratios. Additionally, the evaluation was performed on both QStar and LTQ-FTICR mass spectrometers. LF LTQ-FTICR was found to have the highest proteome coverage while the highest accuracy based on the artificially regulated proteins was found for DML LTQ-FTICR (54%). A varying linearity (k: 0.55-1.16, r(2): 0.61-0.96) was shown for all methods within selected dynamic ranges. All methods were found to consistently underestimate Bovine protein ratios when matrix proteins were added. However, LF LTQ-FTICR was more tolerant toward a compression effect. A single peptide was demonstrated to be sufficient for a reliable quantification using iTRAQ. A ranking system utilizing several parameters important for quantitative proteomics demonstrated that the overall performance of the five different methods was; DML LTQ-FTICR>iTRAQ QStar>LF LTQ-FTICR>DML QStar>LF QStar. Copyright © 2013 Elsevier B.V. All rights reserved.

InP monolithically integrated label swapper device for spectral amplitude coded optical packet networks

NARCIS (Netherlands)

Muñoz, P.; García-Olcina, R.; Doménech, J.D.; Rius, M.; Sancho, J.C.; Capmany, J.; Chen, L.R.; Habib, C.; Leijtens, X.J.M.; Vries, de T.; Heck, M.J.R.; Augustin, L.M.; Nötzel, R.; Robbins, D.J.

2010-01-01

In this paper a label swapping device, for spectral amplitude coded optical packet networks, fully integrated using InP technology is presented. Compared to previous demonstrations using discrete component assembly, the device footprint is reduced by a factor of 105 and the operation speed is

Scrambling free combinatorial labeling of alanine-β, isoleucine-δ1, leucine-proS and valine-proS methyl groups for the detection of long range NOEs

Energy Technology Data Exchange (ETDEWEB)

Kerfah, Rime [NMR-Bio, IBS/CEA (France); Plevin, Michael J. [University of York, Department of Biology (United Kingdom); Pessey, Ombeline [Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS) (France); Hamelin, Olivier [CNRS (France); Gans, Pierre; Boisbouvier, Jerome, E-mail: jerome.boisbouvier@ibs.fr [Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS) (France)

2015-01-15

Specific isotopic labeling of methyl groups in proteins has greatly extended the applicability of solution NMR spectroscopy. Simultaneous labeling of the methyl groups of several different amino acid types can offer a larger number of useful probes that can be used for structural characterisations of challenging proteins. Herein, we propose an improved AILV methyl-labeling protocol in which L and V are stereo-specifically labeled. We show that 2-ketobutyrate cannot be combined with Ala and 2-acetolactate (for the stereo-specific labeling of L and V) as this results in co-incorporation incompatibility and isotopic scrambling. Thus, we developed a robust and cost-effective enzymatic synthesis of the isoleucine precursor, 2-hydroxy-2-(1′-[{sup 2}H{sub 2}], 2′-[{sup 13}C])ethyl-3-keto-4-[{sup 2}H{sub 3}]butanoic acid, as well as an incorporation protocol that eliminates metabolic leakage. We show that application of this labeling scheme to a large 82 kDa protein permits the detection of long-range {sup 1}H–{sup 1}H NOE cross-peaks between methyl probes separated by up to 10 Å.

Surface-Enhanced Raman Scattering Nanoparticles as Optical Labels for Imaging Cell Surface Proteins

Science.gov (United States)

MacLaughlin, Christina M.

Assaying the expression of cell surface proteins has widespread application for characterizing cell type, developmental stage, and monitoring disease transformation. Immunophenotyping is conducted by treating cells with labelled targeting moieties that have high affinity for relevant surface protein(s). The sensitivity and specificity of immunophenotyping is defined by the choice of contrast agent and therefore, the number of resolvable signals that can be used to simultaneously label cells. Narrow band width surface-enhanced Raman scattering (SERS) nanoparticles are proposed as optical labels for multiplexed immunophenotying. Two types of surface coatings were investigated to passivate the gold nanoparticles, incorporate SERS functionality, and to facilitate attachment of targeting antibodies. Thiolated poly(ethylene glycol) forms dative bonds with the gold surface and is compatible with multiple physisorbed Raman-active reporter molecules. Ternary lipid bilayers are used to encapsulate the gold nanoparticles particles, and incorporate three different classes of Raman reporters. TEM, UV-Visible absorbance spectroscopy, DLS, and electrophoretic light scattering were used characterize the particle coating. Colourimetric protein assay, and secondary antibody labelling were used to quantify the antibody conjugation. Three different in vitromodels were used to investigate the binding efficacy and specificity of SERS labels for their biomarker targets. Primary human CLL cells, LY10 B lymphoma, and A549 adenocarcinoma lines were targeted. Dark field imaging was used to visualize the colocalization of SERS labels with cells, and evidence of receptor clustering was obtained based on colour shifts of the particles' Rayleigh scattering. Widefield, and spatially-resolved Raman spectra were used to detect labels singly, and in combination from labelled cells. Fluorescence flow cytometry was used to test the particles' binding specificity, and SERS from labelled cells was also

Lifetimes of organic photovoltaics: Using TOF-SIMS and ¹⁸O₂ isotopic labelling to characterise chemical degradation mechanisms

DEFF Research Database (Denmark)

Norrman, K.; Krebs, Frederik C

2006-01-01

The lifetimes of organic photovoltaic cells based on conjugated polymer materials were studied. The device geometry was glass:ITO:PEDOT:PSS:C-12-PSV:C-60:aluminium. To characterise and elucidate the parts of the degradation mechanisms induced by molecular oxygen, 1802 isotopic labelling was emplo......The lifetimes of organic photovoltaic cells based on conjugated polymer materials were studied. The device geometry was glass:ITO:PEDOT:PSS:C-12-PSV:C-60:aluminium. To characterise and elucidate the parts of the degradation mechanisms induced by molecular oxygen, 1802 isotopic labelling...

The labelling of Nanocoll[reg] with [111In] for dual-isotope scanning

International Nuclear Information System (INIS)

Mitterhauser, Markus; Wadsak, Wolfgang; Key Mien, Leonhard-; Eidherr, Harald; Roka, Sebastian; Zettinig, Georg; Angelberger, Peter; Viernstein, Helmut; Kletter, Kurt; Dudczak, Robert

2003-01-01

Visualization and biopsy of sentinel lymph nodes play an important role in planning and controlling the therapy of breast cancer. Hitherto two methods--scintigraphy or gamma probe detection after injection of [ 99m Tc]-nanocolloids and visual detection after injection of patent blue dye--are used routinely. There are no conclusive publications elucidating such important parameters as injection site, injection method and colloidal parameters. The present work aims to label Nanocoll[reg] with [ 111 In] to provide an alternative method, a simultaneous one-compound dual-isotope application. Methods: [ 111 In]-Indiumchloride was buffered with acetate and transferred to the nanocolloid. The colloid labelling reaction was complete after 30 min and filtrated through 100 nm Nuclepore[reg] filters. Results: Incorporation yield of [ 111 In]-Indium into the nanocolloid was nearly quantitative, the step associated with the major loss of activity was the particle sizing with a mean yield of 55%. Conclusion: The presented method allows for the routine supply of [ 111 In]-nanocolloids. Size-filtered [ 111 In]-Nanocoll[reg] shows the same particle size range as [ 99m Tc]-Nanocoll[reg

Development of chemical isotope labeling liquid chromatography mass spectrometry for silkworm hemolymph metabolomics

International Nuclear Information System (INIS)

Shen, Weifeng; Han, Wei; Li, Yunong; Meng, Zhiqi; Cai, Leiming; Li, Liang

2016-01-01

Silkworm (Bombyx mori) is a very useful target insect for evaluation of endocrine disruptor chemicals (EDCs) due to mature breeding techniques, complete endocrine system and broad basic knowledge on developmental biology. Comparative metabolomics of silkworms with and without EDC exposure offers another dimension of studying EDCs. In this work, we report a workflow on metabolomic profiling of silkworm hemolymph based on high-performance chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS) and demonstrate its application in studying the metabolic changes associated with the pesticide dichlorodiphenyltrichloroethane (DDT) exposure in silkworm. Hemolymph samples were taken from mature silkworms after growing on diet that contained DDT at four different concentrations (1, 0.1, 0.01, 0.001 ppm) as well as on diet without DDT as controls. They were subjected to differential "1"2C-/"1"3C-dansyl labeling of the amine/phenol submetabolome, LC-UV quantification of the total amount of labeled metabolites for sample normalization, and LC-MS detection and relative quantification of individual metabolites in comparative samples. The total concentration of labeled metabolites did not show any significant change between four DDT-treatment groups and one control group. Multivariate statistical analysis of the metabolome data set showed that there was a distinct metabolomic separation between the five groups. Out of the 2044 detected peak pairs, 338 and 1471 metabolites have been putatively identified against the HMDB database and the EML library, respectively. 65 metabolites were identified by the dansyl library searching based on the accurate mass and retention time. Among the 65 identified metabolites, 33 positive metabolites had changes of greater than 1.20-fold or less than 0.83-fold in one or more groups with p-value of smaller than 0.05. Several useful biomarkers including serine, methionine, tryptophan, asymmetric dimethylarginine, N

Development of chemical isotope labeling liquid chromatography mass spectrometry for silkworm hemolymph metabolomics

Energy Technology Data Exchange (ETDEWEB)

Shen, Weifeng [Key Laboratory of Detection for Pesticide Residues, Ministry of Agriculture (China); Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou (China); Han, Wei; Li, Yunong [Department of Chemistry, University of Alberta, Edmonton, Alberta (Canada); Meng, Zhiqi [Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou (China); Cai, Leiming, E-mail: cailm@mail.zaas.ac.cn [Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou (China); Li, Liang, E-mail: Liang.Li@ualberta.ca [Department of Chemistry, University of Alberta, Edmonton, Alberta (Canada)

2016-10-26

Silkworm (Bombyx mori) is a very useful target insect for evaluation of endocrine disruptor chemicals (EDCs) due to mature breeding techniques, complete endocrine system and broad basic knowledge on developmental biology. Comparative metabolomics of silkworms with and without EDC exposure offers another dimension of studying EDCs. In this work, we report a workflow on metabolomic profiling of silkworm hemolymph based on high-performance chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS) and demonstrate its application in studying the metabolic changes associated with the pesticide dichlorodiphenyltrichloroethane (DDT) exposure in silkworm. Hemolymph samples were taken from mature silkworms after growing on diet that contained DDT at four different concentrations (1, 0.1, 0.01, 0.001 ppm) as well as on diet without DDT as controls. They were subjected to differential {sup 12}C-/{sup 13}C-dansyl labeling of the amine/phenol submetabolome, LC-UV quantification of the total amount of labeled metabolites for sample normalization, and LC-MS detection and relative quantification of individual metabolites in comparative samples. The total concentration of labeled metabolites did not show any significant change between four DDT-treatment groups and one control group. Multivariate statistical analysis of the metabolome data set showed that there was a distinct metabolomic separation between the five groups. Out of the 2044 detected peak pairs, 338 and 1471 metabolites have been putatively identified against the HMDB database and the EML library, respectively. 65 metabolites were identified by the dansyl library searching based on the accurate mass and retention time. Among the 65 identified metabolites, 33 positive metabolites had changes of greater than 1.20-fold or less than 0.83-fold in one or more groups with p-value of smaller than 0.05. Several useful biomarkers including serine, methionine, tryptophan, asymmetric dimethylarginine, N

High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast

DEFF Research Database (Denmark)

Gnad, Florian; de Godoy, Lyris M F; Cox, Jürgen

2009-01-01

Protein phosphorylation is a fundamental regulatory mechanism that affects many cell signaling processes. Using high-accuracy MS and stable isotope labeling in cell culture-labeling, we provide a global view of the Saccharomyces cerevisiae phosphoproteome, containing 3620 phosphorylation sites ma...

Influence of diet on the incorporation of labelled amino acids in muscles of calves

International Nuclear Information System (INIS)

Kumar, P.; Hansen, R.J.; Black, A.L.

1974-01-01

Experiments were conducted to study the influence of diet on the incorporation of labelled amino acids into the semitendinosus and biceps femoris muscles of calves after 48 h administration of isotope through jugular vein. 14 C or 3 H-labelled tyrosine and 14 C or 3 H-histidine were used as tracers. The results suggest that the incorporation into myofibrillar protein fraction of both the muscles was at least two fold greater on good diets as compared to all forage ration. Similar trend was also recorded with the plasma protein fraction at both 24 and 48 h after injection. (author)

Influence of diet on the incorporation of labelled amino acids in muscles of calves

Energy Technology Data Exchange (ETDEWEB)

Kumar, P; Hansen, R J; Black, A L [California Univ., Davis (USA). Dept. of Physiological Sciences

1974-12-01

Experiments were conducted to study the influence of diet on the incorporation of labeled amino acids into the semitendinosus and biceps femoris muscles of calves after 48 h administration of isotope through jugular vein. /sup 14/C or /sup 3/H-labelled tyrosine and /sup 14/C or /sup 3/H-histidine were used as tracers. The results suggest that the incorporation into myofibrillar protein fraction of both the muscles was at least two fold greater on good diets as compared to all forage ration. Similar trend was also recorded with the plasma protein fraction at both 24 and 48 h after injection.

iLoc-Animal: a multi-label learning classifier for predicting subcellular localization of animal proteins.

Science.gov (United States)

Lin, Wei-Zhong; Fang, Jian-An; Xiao, Xuan; Chou, Kuo-Chen

2013-04-05

Predicting protein subcellular localization is a challenging problem, particularly when query proteins have multi-label features meaning that they may simultaneously exist at, or move between, two or more different subcellular location sites. Most of the existing methods can only be used to deal with the single-label proteins. Actually, multi-label proteins should not be ignored because they usually bear some special function worthy of in-depth studies. By introducing the "multi-label learning" approach, a new predictor, called iLoc-Animal, has been developed that can be used to deal with the systems containing both single- and multi-label animal (metazoan except human) proteins. Meanwhile, to measure the prediction quality of a multi-label system in a rigorous way, five indices were introduced; they are "Absolute-True", "Absolute-False" (or Hamming-Loss"), "Accuracy", "Precision", and "Recall". As a demonstration, the jackknife cross-validation was performed with iLoc-Animal on a benchmark dataset of animal proteins classified into the following 20 location sites: (1) acrosome, (2) cell membrane, (3) centriole, (4) centrosome, (5) cell cortex, (6) cytoplasm, (7) cytoskeleton, (8) endoplasmic reticulum, (9) endosome, (10) extracellular, (11) Golgi apparatus, (12) lysosome, (13) mitochondrion, (14) melanosome, (15) microsome, (16) nucleus, (17) peroxisome, (18) plasma membrane, (19) spindle, and (20) synapse, where many proteins belong to two or more locations. For such a complicated system, the outcomes achieved by iLoc-Animal for all the aforementioned five indices were quite encouraging, indicating that the predictor may become a useful tool in this area. It has not escaped our notice that the multi-label approach and the rigorous measurement metrics can also be used to investigate many other multi-label problems in molecular biology. As a user-friendly web-server, iLoc-Animal is freely accessible to the public at the web-site .

Assessing of distribution, mobility and bioavailability of exogenous Pb in agricultural soils using isotopic labeling method coupled with BCR approach

International Nuclear Information System (INIS)

Huang, Zhi-Yong; Xie, Hong; Cao, Ying-Lan; Cai, Chao; Zhang, Zhi

2014-01-01

Highlights: • Large amounts of exogenous Pb were found to distribute in reducible fractions. • Very few of exogenous Pb were found to distribute in acid-extractable fractions. • More than 60% of exogenous Pb in rhizosphere soils lost after planting. • Isotopic labeling method and SEP enable to explore Pb bioavailability in soil. -- Abstract: The contamination of Pb in agricultural soils is one of the most important ecological problems, which potentially results in serious health risk on human health through food chain. Hence, the fate of exogenous Pb contaminated in agricultural soils is needed to be deeply explored. By spiking soils with the stable enriched isotopes of 206 Pb, the contamination of exogenous Pb 2+ ions in three agricultural soils sampled from the estuary areas of Jiulong River, China was simulated in the present study, and the distribution, mobility and bioavailability of exogenous Pb in the soils were investigated using the isotopic labeling method coupled with a four-stage BCR (European Community Bureau of Reference) sequential extraction procedure. Results showed that about 60–85% of exogenous Pb was found to distribute in reducible fractions, while the exogenous Pb in acid-extractable fractions was less than 1.0%. After planting, the amounts of exogenous Pb presenting in acid-extractable, reducible and oxidizable fractions in rhizospheric soils decreased by 60–66%, in which partial exogenous Pb was assimilated by plants while most of the metal might transfer downward due to daily watering and applying fertilizer. The results show that the isotopic labeling technique coupled with sequential extraction procedures enables us to explore the distribution, mobility and bioavailability of exogenous Pb contaminated in soils, which may be useful for the further soil remediation

Assessing of distribution, mobility and bioavailability of exogenous Pb in agricultural soils using isotopic labeling method coupled with BCR approach

Energy Technology Data Exchange (ETDEWEB)

Huang, Zhi-Yong, E-mail: zhyhuang@jmu.edu.cn [College of Bioengineering, Jimei University, Xiamen 361021 (China); Xie, Hong [College of Bioengineering, Jimei University, Xiamen 361021 (China); Shandong Vocational Animal Science and Veterinary College, Weifang 261061 (China); Cao, Ying-Lan [College of Bioengineering, Jimei University, Xiamen 361021 (China); Cai, Chao [Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021 (China); Zhang, Zhi [College of Bioengineering, Jimei University, Xiamen 361021 (China)

2014-02-15

Highlights: • Large amounts of exogenous Pb were found to distribute in reducible fractions. • Very few of exogenous Pb were found to distribute in acid-extractable fractions. • More than 60% of exogenous Pb in rhizosphere soils lost after planting. • Isotopic labeling method and SEP enable to explore Pb bioavailability in soil. -- Abstract: The contamination of Pb in agricultural soils is one of the most important ecological problems, which potentially results in serious health risk on human health through food chain. Hence, the fate of exogenous Pb contaminated in agricultural soils is needed to be deeply explored. By spiking soils with the stable enriched isotopes of {sup 206}Pb, the contamination of exogenous Pb{sup 2+} ions in three agricultural soils sampled from the estuary areas of Jiulong River, China was simulated in the present study, and the distribution, mobility and bioavailability of exogenous Pb in the soils were investigated using the isotopic labeling method coupled with a four-stage BCR (European Community Bureau of Reference) sequential extraction procedure. Results showed that about 60–85% of exogenous Pb was found to distribute in reducible fractions, while the exogenous Pb in acid-extractable fractions was less than 1.0%. After planting, the amounts of exogenous Pb presenting in acid-extractable, reducible and oxidizable fractions in rhizospheric soils decreased by 60–66%, in which partial exogenous Pb was assimilated by plants while most of the metal might transfer downward due to daily watering and applying fertilizer. The results show that the isotopic labeling technique coupled with sequential extraction procedures enables us to explore the distribution, mobility and bioavailability of exogenous Pb contaminated in soils, which may be useful for the further soil remediation.

Dansylation isotope labeling liquid chromatography mass spectrometry for parallel profiling of human urinary and fecal submetabolomes

Energy Technology Data Exchange (ETDEWEB)

Su, Xiaoling [State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003 (China); Wang, Nan [State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003 (China); Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2 (Canada); Chen, Deying [State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003 (China); Li, Yunong [Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2 (Canada); Lu, Yingfeng [State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003 (China); Huan, Tao [Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2 (Canada); Xu, Wei [State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003 (China); Li, Liang, E-mail: Liang.Li@ualberta.ca [State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003 (China); Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2 (Canada); Li, Lanjuan, E-mail: ljli@zju.edu.cn [State Key Laboratory and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003 (China)

2016-01-15

Human urine and feces can be non-invasively collected for metabolomics-based disease biomarker discovery research. Because urinary and fecal metabolomes are thought to be different, analysis of both biospecimens may generate a more comprehensive metabolomic profile that can be better related to the health state of an individual. Herein we describe a method of using differential chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS) for parallel metabolomic profiling of urine and feces. Dansylation labeling was used to quantify the amine/phenol submetabolome changes among different samples based on {sup 12}C-labeling of individual samples and {sup 13}C-labeling of a pooled urine or pooled feces and subsequent analysis of the {sup 13}C-/{sup 12}C-labeled mixture by LC-MS. The pooled urine and pooled feces are further differentially labeled, mixed and then analyzed by LC-MS in order to relate the metabolite concentrations of the common metabolites found in both biospecimens. This method offers a means of direct comparison of urinary and fecal submetabolomes. We evaluated the analytical performance and demonstrated the utility of this method in the analysis of urine and feces collected daily from three healthy individuals for 7 days. On average, 2534 ± 113 (n = 126) peak pairs or metabolites could be detected from a urine sample, while 2507 ± 77 (n = 63) peak pairs were detected from a fecal sample. In total, 5372 unique peak pairs were detected from all the samples combined; 3089 and 3012 pairs were found in urine and feces, respectively. These results reveal that the urine and fecal metabolomes are very different, thereby justifying the consideration of using both biospecimens to increase the probability of finding specific biomarkers of diseases. Furthermore, the CIL LC-MS method described can be used to perform parallel quantitative analysis of urine and feces, resulting in more complete coverage of the human metabolome

Dansylation isotope labeling liquid chromatography mass spectrometry for parallel profiling of human urinary and fecal submetabolomes

International Nuclear Information System (INIS)

Su, Xiaoling; Wang, Nan; Chen, Deying; Li, Yunong; Lu, Yingfeng; Huan, Tao; Xu, Wei; Li, Liang; Li, Lanjuan

2016-01-01

Human urine and feces can be non-invasively collected for metabolomics-based disease biomarker discovery research. Because urinary and fecal metabolomes are thought to be different, analysis of both biospecimens may generate a more comprehensive metabolomic profile that can be better related to the health state of an individual. Herein we describe a method of using differential chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS) for parallel metabolomic profiling of urine and feces. Dansylation labeling was used to quantify the amine/phenol submetabolome changes among different samples based on "1"2C-labeling of individual samples and "1"3C-labeling of a pooled urine or pooled feces and subsequent analysis of the "1"3C-/"1"2C-labeled mixture by LC-MS. The pooled urine and pooled feces are further differentially labeled, mixed and then analyzed by LC-MS in order to relate the metabolite concentrations of the common metabolites found in both biospecimens. This method offers a means of direct comparison of urinary and fecal submetabolomes. We evaluated the analytical performance and demonstrated the utility of this method in the analysis of urine and feces collected daily from three healthy individuals for 7 days. On average, 2534 ± 113 (n = 126) peak pairs or metabolites could be detected from a urine sample, while 2507 ± 77 (n = 63) peak pairs were detected from a fecal sample. In total, 5372 unique peak pairs were detected from all the samples combined; 3089 and 3012 pairs were found in urine and feces, respectively. These results reveal that the urine and fecal metabolomes are very different, thereby justifying the consideration of using both biospecimens to increase the probability of finding specific biomarkers of diseases. Furthermore, the CIL LC-MS method described can be used to perform parallel quantitative analysis of urine and feces, resulting in more complete coverage of the human metabolome. - Highlights: • A

Methyl labeling and TROSY NMR spectroscopy of proteins expressed in the eukaryote Pichia pastoris

International Nuclear Information System (INIS)

Clark, Lindsay; Zahm, Jacob A.; Ali, Rustam; Kukula, Maciej; Bian, Liangqiao; Patrie, Steven M.; Gardner, Kevin H.; Rosen, Michael K.; Rosenbaum, Daniel M.

2015-01-01

13 C Methyl TROSY NMR spectroscopy has emerged as a powerful method for studying the dynamics of large systems such as macromolecular assemblies and membrane proteins. Specific 13 C labeling of aliphatic methyl groups and perdeuteration has been limited primarily to proteins expressed in E. coli, preventing studies of many eukaryotic proteins of physiological and biomedical significance. We demonstrate the feasibility of efficient 13 C isoleucine δ1-methyl labeling in a deuterated background in an established eukaryotic expression host, Pichia pastoris, and show that this method can be used to label the eukaryotic protein actin, which cannot be expressed in bacteria. This approach will enable NMR studies of previously intractable targets

Synthesizing labeled compounds

International Nuclear Information System (INIS)

London, R.E.; Matwiyoff, N.A.; Unkefer, C.J.; Walker, T.E.

1983-01-01

A metabolic study is presented of the chemical reactions provided by isotopic labeling and NMR spectroscopy. Synthesis of 13 C-labeled D-glucose, a 6-carbon sugar, involves adding a labeled nitrile group to the 5-carbon sugar D-arabinose by reaction with labeled hydrogen cyanide. The product of this reaction is then reduced and hydrolyzed to a mixture of the labeled sugars. The two sugars are separated by absorption chromotography. The synthesis of 13 C-labeled L-tyrosine, an amino acid, is also presented

The Snf1 Protein Kinase in the Yeast Saccharomyces cerevisiae

DEFF Research Database (Denmark)

Usaite, Renata

2008-01-01

4 on the regulation of glucose and galactose metabolism, I physiologically characterized Δsnf1, Δsnf4, and Δsnf1Δsnf4 CEN.PK background yeast strains in glucose and glucose-galactose mixture batch cultivations (chapter 2). The results of this study showed that delayed induction of galactose...... that the stable isotope labeling approach is highly reproducible among biological replicates when complex protein mixtures containing small expression changes were analyzed. Where poor correlation between stable isotope labeling and spectral counting was found, the major reason behind the discrepancy was the lack...

In Vivo Isotopic Labeling of Symbiotic Bacteria Involved in Cellulose Degradation and Nitrogen Recycling within the Gut of the Forest Cockchafer (Melolontha hippocastani).

Science.gov (United States)

Alonso-Pernas, Pol; Bartram, Stefan; Arias-Cordero, Erika M; Novoselov, Alexey L; Halty-deLeon, Lorena; Shao, Yongqi; Boland, Wilhelm

2017-01-01

The guts of insects harbor symbiotic bacterial communities. However, due to their complexity, it is challenging to relate a specific symbiotic phylotype to its corresponding function. In the present study, we focused on the forest cockchafer ( Melolontha hippocastani ), a phytophagous insect with a dual life cycle, consisting of a root-feeding larval stage and a leaf-feeding adult stage. By combining in vivo stable isotope probing (SIP) with 13 C cellulose and 15 N urea as trophic links, with Illumina MiSeq (Illumina-SIP), we unraveled bacterial networks processing recalcitrant dietary components and recycling nitrogenous waste. The bacterial communities behind these processes change between larval and adult stages. In 13 C cellulose-fed insects, the bacterial families Lachnospiraceae and Enterobacteriaceae were isotopically labeled in larvae and adults, respectively. In 15 N urea-fed insects, the genera Burkholderia and Parabacteroides were isotopically labeled in larvae and adults, respectively. Additionally, the PICRUSt-predicted metagenome suggested a possible ability to degrade hemicellulose and to produce amino acids of, respectively, 13 C cellulose- and 15 N urea labeled bacteria. The incorporation of 15 N from ingested urea back into the insect body was confirmed, in larvae and adults, by isotope ratio mass spectrometry (IRMS). Besides highlighting key bacterial symbionts of the gut of M. hippocastani , this study provides example on how Illumina-SIP with multiple trophic links can be used to target microorganisms embracing different roles within an environment.

In Vivo Isotopic Labeling of Symbiotic Bacteria Involved in Cellulose Degradation and Nitrogen Recycling within the Gut of the Forest Cockchafer (Melolontha hippocastani

Directory of Open Access Journals (Sweden)

Pol Alonso-Pernas

2017-10-01

Full Text Available The guts of insects harbor symbiotic bacterial communities. However, due to their complexity, it is challenging to relate a specific symbiotic phylotype to its corresponding function. In the present study, we focused on the forest cockchafer (Melolontha hippocastani, a phytophagous insect with a dual life cycle, consisting of a root-feeding larval stage and a leaf-feeding adult stage. By combining in vivo stable isotope probing (SIP with 13C cellulose and 15N urea as trophic links, with Illumina MiSeq (Illumina-SIP, we unraveled bacterial networks processing recalcitrant dietary components and recycling nitrogenous waste. The bacterial communities behind these processes change between larval and adult stages. In 13C cellulose-fed insects, the bacterial families Lachnospiraceae and Enterobacteriaceae were isotopically labeled in larvae and adults, respectively. In 15N urea-fed insects, the genera Burkholderia and Parabacteroides were isotopically labeled in larvae and adults, respectively. Additionally, the PICRUSt-predicted metagenome suggested a possible ability to degrade hemicellulose and to produce amino acids of, respectively, 13C cellulose- and 15N urea labeled bacteria. The incorporation of 15N from ingested urea back into the insect body was confirmed, in larvae and adults, by isotope ratio mass spectrometry (IRMS. Besides highlighting key bacterial symbionts of the gut of M. hippocastani, this study provides example on how Illumina-SIP with multiple trophic links can be used to target microorganisms embracing different roles within an environment.

Analysis of carbon and nitrogen co-metabolism in yeast by ultrahigh-resolution mass spectrometry applying 13C- and 15N-labeled substrates simultaneously

International Nuclear Information System (INIS)

Blank, Lars M.; Desphande, Rahul R.; Schmid, Andreas; Hayen, Heiko

2012-01-01

Alternative metabolic pathways inside a cell can be deduced using stable isotopically labeled substrates. One prerequisite is accurate measurement of the labeling pattern of targeted metabolites. Experiments are generally limited to the use of single-element isotopes, mainly 13 C. Here, we demonstrate the application of direct infusion nanospray, ultrahigh-resolution Fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) for metabolic studies using differently labeled elemental isotopes simultaneously - i.e., 13 C and 15 N - in amino acids of a total protein hydrolysate. The optimized strategy for the analysis of metabolism by a hybrid linear ion trap-FTICR-MS comprises the collection of multiple adjacent selected ion monitoring scans. By limiting both the width of the mass range and the number of ions entering the ICR cell with automated gain control, sensitive measurements of isotopologue distribution were possible without compromising mass accuracy and isotope intensity mapping. The required mass-resolving power of more than 60,000 is only achievable on a routine basis by FTICR and Orbitrap mass spectrometers. Evaluation of the method was carried out by comparison of the experimental data to the natural isotope abundances of selected amino acids and by comparison to GC/MS results obtained from a labeling experiment with 13 C-labeled glucose. The developed method was used to shed light on the complexity of the yeast Saccharomyces cerevisiae carbon-nitrogen co-metabolism by administering both 13 C-labeled glucose and 15 N-labeled alanine. The results indicate that not only glutamate but also alanine acts as an amino donor during alanine and valine synthesis. Metabolic studies using FTICR-MS can exploit new possibilities by the use of multiple-labeled elemental isotopes. (orig.)

Simple method for identification of plasmid-coded proteins

International Nuclear Information System (INIS)

Sancar, A.; Hack, A.M.; Rupp, W.D.

1979-01-01

Proteins encoded by plasmid DNA are specifically labeled in uv-irradiated cells of Escherichia coli carrying recA and uvrA mutations because extensive degradation of the chromosome DNA occurs concurrently with amplification of plasmid DNA

Identification and quantification of protein S-nitrosation by nitrite in the mouse heart during ischemia.

Science.gov (United States)

Chouchani, Edward T; James, Andrew M; Methner, Carmen; Pell, Victoria R; Prime, Tracy A; Erickson, Brian K; Forkink, Marleen; Lau, Gigi Y; Bright, Thomas P; Menger, Katja E; Fearnley, Ian M; Krieg, Thomas; Murphy, Michael P

2017-09-01

Nitrate (NO 3 - ) and nitrite (NO 2 - ) are known to be cardioprotective and to alter energy metabolism in vivo NO 3 - action results from its conversion to NO 2 - by salivary bacteria, but the mechanism(s) by which NO 2 - affects metabolism remains obscure. NO 2 - may act by S -nitrosating protein thiols, thereby altering protein activity. But how this occurs, and the functional importance of S -nitrosation sites across the mammalian proteome, remain largely uncharacterized. Here we analyzed protein thiols within mouse hearts in vivo using quantitative proteomics to determine S -nitrosation site occupancy. We extended the thiol-redox proteomic technique, isotope-coded affinity tag labeling, to quantify the extent of NO 2 - -dependent S -nitrosation of proteins thiols in vivo Using this approach, called SNOxICAT ( S -nitrosothiol redox isotope-coded affinity tag), we found that exposure to NO 2 - under normoxic conditions or exposure to ischemia alone results in minimal S -nitrosation of protein thiols. However, exposure to NO 2 - in conjunction with ischemia led to extensive S -nitrosation of protein thiols across all cellular compartments. Several mitochondrial protein thiols exposed to the mitochondrial matrix were selectively S -nitrosated under these conditions, potentially contributing to the beneficial effects of NO 2 - on mitochondrial metabolism. The permeability of the mitochondrial inner membrane to HNO 2 , but not to NO 2 - , combined with the lack of S -nitrosation during anoxia alone or by NO 2 - during normoxia places constraints on how S -nitrosation occurs in vivo and on its mechanisms of cardioprotection and modulation of energy metabolism. Quantifying S -nitrosated protein thiols now allows determination of modified cysteines across the proteome and identification of those most likely responsible for the functional consequences of NO 2 - exposure. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Introducing AAA-MS, a rapid and sensitive method for amino acid analysis using isotope dilution and high-resolution mass spectrometry.

Science.gov (United States)

Louwagie, Mathilde; Kieffer-Jaquinod, Sylvie; Dupierris, Véronique; Couté, Yohann; Bruley, Christophe; Garin, Jérôme; Dupuis, Alain; Jaquinod, Michel; Brun, Virginie

2012-07-06

Accurate quantification of pure peptides and proteins is essential for biotechnology, clinical chemistry, proteomics, and systems biology. The reference method to quantify peptides and proteins is amino acid analysis (AAA). This consists of an acidic hydrolysis followed by chromatographic separation and spectrophotometric detection of amino acids. Although widely used, this method displays some limitations, in particular the need for large amounts of starting material. Driven by the need to quantify isotope-dilution standards used for absolute quantitative proteomics, particularly stable isotope-labeled (SIL) peptides and PSAQ proteins, we developed a new AAA assay (AAA-MS). This method requires neither derivatization nor chromatographic separation of amino acids. It is based on rapid microwave-assisted acidic hydrolysis followed by high-resolution mass spectrometry analysis of amino acids. Quantification is performed by comparing MS signals from labeled amino acids (SIL peptide- and PSAQ-derived) with those of unlabeled amino acids originating from co-hydrolyzed NIST standard reference materials. For both SIL peptides and PSAQ standards, AAA-MS quantification results were consistent with classical AAA measurements. Compared to AAA assay, AAA-MS was much faster and was 100-fold more sensitive for peptide and protein quantification. Finally, thanks to the development of a labeled protein standard, we also extended AAA-MS analysis to the quantification of unlabeled proteins.

Promoter Analysis Reveals Globally Differential Regulation of Human Long Non-Coding RNA and Protein-Coding Genes

KAUST Repository

Alam, Tanvir

2014-10-02

Transcriptional regulation of protein-coding genes is increasingly well-understood on a global scale, yet no comparable information exists for long non-coding RNA (lncRNA) genes, which were recently recognized to be as numerous as protein-coding genes in mammalian genomes. We performed a genome-wide comparative analysis of the promoters of human lncRNA and protein-coding genes, finding global differences in specific genetic and epigenetic features relevant to transcriptional regulation. These two groups of genes are hence subject to separate transcriptional regulatory programs, including distinct transcription factor (TF) proteins that significantly favor lncRNA, rather than coding-gene, promoters. We report a specific signature of promoter-proximal transcriptional regulation of lncRNA genes, including several distinct transcription factor binding sites (TFBS). Experimental DNase I hypersensitive site profiles are consistent with active configurations of these lncRNA TFBS sets in diverse human cell types. TFBS ChIP-seq datasets confirm the binding events that we predicted using computational approaches for a subset of factors. For several TFs known to be directly regulated by lncRNAs, we find that their putative TFBSs are enriched at lncRNA promoters, suggesting that the TFs and the lncRNAs may participate in a bidirectional feedback loop regulatory network. Accordingly, cells may be able to modulate lncRNA expression levels independently of mRNA levels via distinct regulatory pathways. Our results also raise the possibility that, given the historical reliance on protein-coding gene catalogs to define the chromatin states of active promoters, a revision of these chromatin signature profiles to incorporate expressed lncRNA genes is warranted in the future.