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1

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

SciTech Connect

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

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

2012-04-02

2

Efficient isotopic tryptophan labeling of membrane proteins by an indole controlled process conduct.  

PubMed

A protocol for the efficient isotopic labeling of large G protein-coupled receptors with tryptophan in Escherichia coli as expression host was developed that sufficiently suppressed the naturally occurring L-tryptophan indole lyase, which cleaves tryptophan into indole, pyruvate, and ammonia resulting in scrambling of the isotopic label in the protein. Indole produced by the tryptophanase is naturally used as messenger for cell-cell communication. Detailed analysis of different process conducts led to the optimal expression strategy, which mimicked cell-cell communication by the addition of indole during expression. Discrete concentrations of indole and (15) N2 -L-tryptophan at dedicated time points in the fermentation drastically increased the isotopic labeling efficiency. Isotope scrambling was only observed in glutamine, asparagine, and arginine side chains but not in the backbone. This strategy allows producing specifically tryptophan labeled membrane proteins at high concentrations avoiding the disadvantages of the often low yields of auxotrophic E. coli strains. In the fermentation process carried out according to this protocol, we produced ?15?mg of tryptophan labeled neuropeptide Y receptor type 2 per liter medium. PMID:23297054

Berger, Christian; Berndt, Sandra; Pichert, Annelie; Theisgen, Stephan; Huster, Daniel

2013-06-01

3

Quantification of stable isotope label in metabolites via mass spectrometry.  

PubMed

Isotope labelling experiments with stable or radioactive isotopes have long been an integral part of biological and medical research. Labelling experiments led to the discovery of new metabolic pathways and made it possible to calculate the fluxes responsible for a metabolic phenotype, i.e., the qualitative and quantitative composition of metabolites in a biological system. Prerequisite for efficient isotope labelling experiments is a reliable and precise method to analyze the redistribution of isotope label in a metabolic network. Here we describe the use of the CORRECTOR program, which utilizes matrix calculations to correct mass spectral data from stable isotope labelling experiments for the distorting effect of naturally occurring stable isotopes (NOIs). CORRECTOR facilitates and speeds up the routine quantification of experimentally introduced isotope label from multiple mass spectral readouts, which are generated by routine metabolite profiling when combined with stable isotope labelling experiments. PMID:24306876

Huege, Jan; Goetze, Jan; Dethloff, Frederik; Junker, Bjoern; Kopka, Joachim

2014-01-01

4

Efficient stable isotope labeling and purification of vitamin D receptor from inclusion bodies  

PubMed Central

Vitamin D receptor (VDR) plays a crucial role in many cellular processes including calcium and phosphate homeostasis. Previous purification methods from prokaryotic and eukaryotic expression systems were challenged by low protein solubility accompanied by multi purification steps resulting in poor protein recovery. The full-length VDR and its ligand binding domain (LBD) were mostly (>90%) insoluble even when expressed at low temperatures in the bacterial system. We describe a one-step procedure that results in the purification of rat VDR and LBD proteins in high-yield from E. coli inclusion bodies. The heterologously expressed protein constructs retain full function as demonstrated by ligand binding and DNA binding assays. Furthermore, we describe an efficient strategy for labeling these proteins with, 13C, and 15N for structural and functional studies by nuclear magnetic resonance (NMR) spectroscopy. This efficient production system will facilitate future studies on the mechanism of vitamin D action including characterization of the large number of synthetic vitamin D analogs that have been developed. PMID:22750673

Zhu, Jinge; Rao, Hongyu; Tonelli, Marco; Westler, Milo; Singarapu, Kiran K.; Markley, John L.; DeLuca, Hector F.; Assadi-Porter, Fariba M.

2012-01-01

5

Stable isotopic labeling in proteomics.  

PubMed

Labeling of proteins and peptides with stable heavy isotopes (deuterium, carbon-13, nitrogen-15, and oxygen-18) is widely used in quantitative proteomics. These are either incorporated metabolically in cells and small organisms, or postmetabolically in proteins and peptides by chemical or enzymatic reactions. Only upon measurement with mass spectrometers holding sufficient resolution, light, and heavy labeled peptide ions or reporter peptide fragment ions segregate and their intensity values are subsequently used for quantification. Targeted use of these labels or mass tags further leads to specific monitoring of diverse aspects of dynamic proteomes. In this review article, commonly used isotope labeling strategies are described, both for quantitative differential protein profiling and for targeted analysis of protein modifications. PMID:19003869

Gevaert, Kris; Impens, Francis; Ghesquière, Bart; Van Damme, Petra; Lambrechts, Anja; Vandekerckhove, Joël

2008-12-01

6

Isotope-coded protein label.  

PubMed

A great variety of technologies using stable isotope labeling in combination with mass spectrometry have been described being tools to identify and relatively quantify proteins within complex mixtures. Here, we present a method, termed isotope-coded protein label (ICPL), which is capable of high-throughput quantitative proteome profiling on a global scale. Since ICPL is based on tagging stable isotope derivatives at the free amino groups of intact proteins, the method is applicable to any protein sample, including extracts from tissues or body fluids. All separation methods currently employed in proteome studies can be used to reduce complexity on the protein level. After enzymatic cleavage of the protein fractions, the ratios of peptides from different proteome states can be calculated by simple MS-based mass spectrometric analyses. Only peptides representing different expression levels in the different proteomic states are further analyzed by tandem-mass spectrometry to identify respective proteins. For quantification of proteins from multiplexed ICPL experiments, ICPLQuant was developed, a software package especially designed to cover the whole ICPL workflow. The ICPL method results in accurate and reproducible quantification of proteins and high sequence coverage, indispensable for a comprehensive detection of posttranslational modifications and discrimination of protein isoforms. PMID:22665300

Kellermann, Josef; Lottspeich, Friedrich

2012-01-01

7

Synthesis of isotopically labeled epothilones  

PubMed Central

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

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

2014-01-01

8

Carbon isotope labelling in graphene research  

NASA Astrophysics Data System (ADS)

The large scale production of graphene for any potential application relies on catalytic chemical vapour deposition (CVD). Despite much effort put into the graphene CVD research, there are still many challenges to be solved, not only concerning the growth itself, but also the subsequent treatment, i.e. transfer from the catalyst to a desired substrate. The need for fast progress naturally necessitates easy-to-use, versatile and efficient characterization methods. This perspective reviews the recent advances and potential of probably the most prospective one - Raman spectroscopy in connection with carbon isotope labelling of the CVD grown graphene layers. We discuss its use for the explanation and optimization of the growth process, followed by examples of employing isotope engineering in the studies of fundamental properties of graphene, not only by Raman spectroscopy.

Frank, O.; Kavan, L.; Kalbac, M.

2014-05-01

9

Tailoring of a TiO2 nanotube array-integrated portable microdevice for efficient on-chip enrichment and isotope labeling of serum phosphopeptides.  

PubMed

Herein we present a gravity-driven microdevice furnished with tunable TiO2 nanotube arrays (TNAs) inside as the separation medium for consecutive on-chip enrichment and isotope labeling of serum phosphopeptides. The 3D tubular architectures of TNAs dramatically enhanced the affinity towards phosphate-containing molecules and also provided a spacious microenvironment for isotope dimethyl labeling reactions. To maximize the efficiency and capacity of the phosphopeptide enrichment, nanoscale tailoring and microscale fabrication were employed for adjusting the TNAs' pore sizes and the channel patterns. The S-shaped microdevice equipped with interior TNAs anodized at 25 V was utilised for consecutive serum processing, and further differential expression analysis of endogenous phosphopeptides between ovarian cancer patients and healthy women. The phosphorylated fibrinogen peptide A (FPA, AD[pS]GEGDFLAEGGGVR) was found to be down-regulated by about 4 times while its isoform (D[pS]GEGDFLAEGGGV) was 2.4-fold up-regulated in the patient specimens. In principle, this nanostructure-embedded model introduced tailor-made bioseparation materials into the microdevice, undoubtedly facilitating the workflow of sample pretreatment and thus assisting the analysis of disease-associated biomolecules in biomedical research. PMID:23907452

Min, Qianhao; Chen, Xueqin; Zhang, Xiaoxia; Zhu, Jun-Jie

2013-10-01

10

Simple, rapid method for the preparation of isotopically labeled formaldehyde  

DOEpatents

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.

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

2011-10-04

11

Stereospecific multiple isotopic labeling of benzyl alcohol.  

PubMed

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

Roston, Daniel; Kohen, Amnon

2014-02-01

12

Synthesis of isotopically labeled phosphoenolpyruvic acid  

SciTech Connect

Phosphoenolypyruvic acid isotopically labeled at C/sub 1/ and C/sub 2/ as well as at the bridging oxygen of the phosphate was synthesized in eleven steps with an overall yield of 15-20%. The cornerstone of this synthesis was the use of 1,3-dithiane as an acyl anion equivalent. The anion derived from this compound was alkylated with isotopically labeled methyl iodide and carboxylated with isotopically labeled carbon dioxide. After protection of the carbonyl group as the benzyl ester, the carbonyl group was unmasked with N-bromosuccinimide. The oxygen of the carbonyl group was exchanged with /sup 18/O water and the benzyl group was removed via hydrogenolysis. The labeled pyruvic acid thus formed was converted to phosphoenolypyruvic acid with a modification of the Perkow reaction. This was accomplished in four steps with a 50% overall yield using dimethyl trimethylsilyl phosphite as the phosphorylating agent. The last four steps were accomplished without isolation of intermediates. The extent of isotopic enrichment was determined using /sup 31/P NMR.

Caldwell, W.S.

1986-01-01

13

Weaving a two-dimensional fishing net from titanoniobate nanosheets embedded with Fe3O4 nanocrystals for highly efficient capture and isotope labeling of phosphopeptides.  

PubMed

Qualitative and quantitative characterization of phosphopeptides by means of mass spectrometry (MS) is the main goal of MS-based phosphoproteomics, but suffers from their low abundance in the large haystack of various biological molecules. Herein, we introduce two-dimensional (2D) metal oxides to tackle this biological separation issue. A nanocomposite composed of titanoniobate nanosheets embedded with Fe3O4 nanocrystals (Fe3O4-TiNbNS) is constructed via a facile cation-exchange approach, and adopted for the capture and isotope labeling of phosphopeptides. In this nanoarchitecture, the 2D titanoniobate nanosheets offer enlarged surface area and a spacious microenvironment for capturing phosphopeptides, while the Fe3O4 nanocrystals not only incorporate a magnetic response into the composite but, more importantly, also disrupt the restacking process between the titanoniobate nanosheets and thus preserve a greater specific surface for binding phosphopeptides. Owing to the extended active surface, abundant Lewis acid sites and excellent magnetic controllability, Fe3O4-TiNbNS demonstrates superior sensitivity, selectivity and capacity over homogeneous bulk metal oxides, layered oxides, and even restacked nanosheets in phosphopeptide enrichment, and further allows in situ isotope labeling to quantify aberrantly-regulated phosphopeptides from sera of leukemia patients. This composite nanosheet greatly contributes to the MS analysis of phosphopeptides and gives inspiration in the pursuit of 2D structured materials for separation of other biological molecules of interests. PMID:25757497

Chen, Xueqin; Li, Siyuan; Zhang, Xiaoxia; Min, Qianhao; Zhu, Jun-Jie

2015-03-19

14

Weaving a two-dimensional fishing net from titanoniobate nanosheets embedded with Fe3O4 nanocrystals for highly efficient capture and isotope labeling of phosphopeptides  

NASA Astrophysics Data System (ADS)

Qualitative and quantitative characterization of phosphopeptides by means of mass spectrometry (MS) is the main goal of MS-based phosphoproteomics, but suffers from their low abundance in the large haystack of various biological molecules. Herein, we introduce two-dimensional (2D) metal oxides to tackle this biological separation issue. A nanocomposite composed of titanoniobate nanosheets embedded with Fe3O4 nanocrystals (Fe3O4-TiNbNS) is constructed via a facile cation-exchange approach, and adopted for the capture and isotope labeling of phosphopeptides. In this nanoarchitecture, the 2D titanoniobate nanosheets offer enlarged surface area and a spacious microenvironment for capturing phosphopeptides, while the Fe3O4 nanocrystals not only incorporate a magnetic response into the composite but, more importantly, also disrupt the restacking process between the titanoniobate nanosheets and thus preserve a greater specific surface for binding phosphopeptides. Owing to the extended active surface, abundant Lewis acid sites and excellent magnetic controllability, Fe3O4-TiNbNS demonstrates superior sensitivity, selectivity and capacity over homogeneous bulk metal oxides, layered oxides, and even restacked nanosheets in phosphopeptide enrichment, and further allows in situ isotope labeling to quantify aberrantly-regulated phosphopeptides from sera of leukemia patients. This composite nanosheet greatly contributes to the MS analysis of phosphopeptides and gives inspiration in the pursuit of 2D structured materials for separation of other biological molecules of interests.Qualitative and quantitative characterization of phosphopeptides by means of mass spectrometry (MS) is the main goal of MS-based phosphoproteomics, but suffers from their low abundance in the large haystack of various biological molecules. Herein, we introduce two-dimensional (2D) metal oxides to tackle this biological separation issue. A nanocomposite composed of titanoniobate nanosheets embedded with Fe3O4 nanocrystals (Fe3O4-TiNbNS) is constructed via a facile cation-exchange approach, and adopted for the capture and isotope labeling of phosphopeptides. In this nanoarchitecture, the 2D titanoniobate nanosheets offer enlarged surface area and a spacious microenvironment for capturing phosphopeptides, while the Fe3O4 nanocrystals not only incorporate a magnetic response into the composite but, more importantly, also disrupt the restacking process between the titanoniobate nanosheets and thus preserve a greater specific surface for binding phosphopeptides. Owing to the extended active surface, abundant Lewis acid sites and excellent magnetic controllability, Fe3O4-TiNbNS demonstrates superior sensitivity, selectivity and capacity over homogeneous bulk metal oxides, layered oxides, and even restacked nanosheets in phosphopeptide enrichment, and further allows in situ isotope labeling to quantify aberrantly-regulated phosphopeptides from sera of leukemia patients. This composite nanosheet greatly contributes to the MS analysis of phosphopeptides and gives inspiration in the pursuit of 2D structured materials for separation of other biological molecules of interests. Electronic supplementary information (ESI) available: Sequence of phosphopeptides from the digests of ?- and ?-casein percentages of the 4 methylated products from peptide ?1 at different labeling reaction times; sequence of serum phosphopeptides; XPS spectra of Nb 3d and Ti 2p in layered oxides and H+-stacked nanosheets; phosphopeptide enrichment sensitivity of bulk oxides, layered oxides and H+-stacked nanosheets; AFM image of TiNbNS; saturated adsorption isotherm for pNPP adsorbed on bulk oxides, layered oxides and H+-stacked nanosheets; XPS spectra of Fe3O4-TiNbNS nitrogen adsorption-desorption isotherms and pore size distribution curves for the Fe3O4 nanocrystals; phosphopeptide enrichment sensitivity, capacity and selectivity of the Fe3O4-TiNbNS composites; MS/MS spectra of phosphopeptides enriched from serum; linear relationship between the logarithms of peak area ratio and loading volume rat

Chen, Xueqin; Li, Siyuan; Zhang, Xiaoxia; Min, Qianhao; Zhu, Jun-Jie

2015-03-01

15

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

PubMed Central

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

Basu, Sankha S; Blair, Ian A

2013-01-01

16

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

PubMed

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

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

2015-04-01

17

Isotopic labeling of heterologous proteins in the yeast Pichia pastoris and Kluyveromyces lactis.  

PubMed

Several protein expression systems are available for the preparation of stable isotope-labeled recombinant proteins for NMR studies. Yeast expression systems have several advantages over prokaryotic systems, such as the widely used Escherichia coli expression system. Protein expression using the methylotrophic yeast Pichia pastoris is commonly employed for the preparation of isotope-labeled proteins. Recently, the hemiascomycete yeast Kluyveromyces lactis expression system was reported as being useful for preparing proteins for NMR studies. Since each yeast expression system has different features, their applications have increased in number. In this chapter, we describe procedures for the efficient production of uniformly isotope-labeled proteins using the P. pastoris and the K. lactis yeast expression systems. PMID:22167666

Sugiki, Toshihiko; Ichikawa, Osamu; Miyazawa-Onami, Mayumi; Shimada, Ichio; Takahashi, Hideo

2012-01-01

18

Quantitative Analysis of Snake Venoms Using Soluble Polymer-based Isotope Labeling*S?  

PubMed Central

We present the design and synthesis of a new quantitative strategy termed soluble polymer-based isotope labeling (SoPIL) and its application as a novel and inclusive method for the identification and relative quantification of individual proteins in complex snake venoms. The SoPIL reagent selectively captures and isolates cysteine-containing peptides, and the subsequent tagged peptides are released and analyzed using nanoflow liquid chromatography-tandem mass spectrometry. The SoPIL strategy was used to quantify venom proteins from two pairs of venomous snakes: Crotalus scutulatus scutulatus type A, C. scutulatus scutulatus type B, Crotalus oreganus helleri, and Bothrops colombiensis. The hemorrhagic, hemolytic, clotting ability, and fibrinogenolytic activities of crude venoms were measured and correlated with difference in protein abundance determined by the SoPIL analysis. The SoPIL approach could provide an efficient and widely applicable tool for quantitative proteomics. PMID:18089550

Galan, Jacob A.; Guo, Minjie; Sanchez, Elda E.; Cantu, Esteban; Rodriguez-Acosta, Alexis; Perez, John C.; Tao, W. Andy

2008-01-01

19

Isotopic labelling of photosystem II in Thermosynechococcus elongatus  

Microsoft Academic Search

This report describes a protocol to incorporate isotopically labelled aromatic amino acids into the proteins of the thermophilic\\u000a cyanobacterium Thermosynechoccus elongatus. By using the EPR signal of the two redox active tyrosines of Photosystem II, TyrD• and TyrZ•, as spectroscopic probes it is shown that labelled tyrosines can be incorporated with a high yield in this cyanobacterium.\\u000a The production of

Alain Boussac; Jean-Marc Verbavatz; Miwa Sugiura

2008-01-01

20

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

Microsoft Academic Search

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

Fluor Daniel Hanford

1997-01-01

21

Isotope labeling experiments in metabolomics and fluxomics.  

PubMed

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

Klein, Sebastian; Heinzle, Elmar

2012-01-01

22

Profiling of RNA modifications by multiplexed stable isotope labelling.  

PubMed

The combination of (15)N/(13)C stable isotope labelling (SIL) and LC-MS/MS revealed a total of 52 modifications in RNA from E. coli and yeast, including 10 previously undescribed modifications. Two modifications, N-ribosylnicotinamide and 2-methylthioadenosine, were newly detected in species hitherto thought not to contain these modifications. PMID:24567952

Kellner, Stefanie; Neumann, Jennifer; Rosenkranz, David; Lebedeva, Svetlana; Ketting, René F; Zischler, Hans; Schneider, Dirk; Helm, Mark

2014-04-01

23

Isotopic labeling-assisted metabolomics using LC-MS.  

PubMed

Metabolomics has emerged as the latest of the so-called "omics" disciplines and has great potential to provide deeper understanding of fundamental biochemical processes at the biological system level. Among recent technological developments, LC-HRMS enables determination of hundreds to thousands of metabolites over a wide range of concentrations and has developed into one of the most powerful techniques in non-targeted metabolomics. The analysis of mixtures of in-vivo-stable isotopic-labeled samples or reference substances with un-labeled samples leads to specific LC-MS data patterns which can be systematically exploited in practically all data-processing steps. This includes recognition of true metabolite-derived analytical features in highly complex LC-MS data and characterization of the global biochemical composition of biological samples. In addition, stable-isotopic labeling can be used for more accurate quantification (via internal standardization) and identification of compounds in different organisms. PMID:23010843

Bueschl, C; Krska, R; Kluger, B; Schuhmacher, R

2013-01-01

24

Correction of MS data for naturally occurring isotopes in isotope labelling experiments.  

PubMed

Mass spectrometry (MS) in combination with isotope labelling experiments is widely used for investigations of metabolism and other biological processes. Quantitative applications-e.g., (13)C metabolic flux analysis-require correction of raw MS data (isotopic clusters) for the contribution of all naturally abundant isotopes. This chapter describes how to perform such correction using the software IsoCor. This flexible, user-friendly software can be used to exploit any isotopic tracer, from well-known ((13)C, (15)N, (18)O, etc.) to unusual ((57)Fe, (77)Se, etc.) isotopes. It also provides options-e.g., correction for the isotopic purity of the tracer-to improve the accuracy of quantitative isotopic studies, and allows automated correction of large datasets that can be collected with modern MS methods. PMID:25178792

Millard, Pierre; Letisse, Fabien; Sokol, Serguei; Portais, Jean-Charles

2014-01-01

25

A novel strategy for quantitative proteomics using isotope-coded protein labels.  

PubMed

Stable isotope labelling in combination with mass spectrometry has emerged as a powerful tool to identify and relatively quantify thousands of proteins within complex protein mixtures. Here we describe a novel method, termed isotope-coded protein label (ICPL), which is capable of high-throughput quantitative proteome profiling on a global scale. Since ICPL is based on stable isotope tagging at the frequent free amino groups of isolated intact proteins, it is applicable to any protein sample, including extracts from tissues or body fluids, and compatible to all separation methods currently employed in proteome studies. The method showed highly accurate and reproducible quantification of proteins and yielded high sequence coverage, indispensable for the detection of post-translational modifications and protein isoforms. The efficiency (e.g. accuracy, dynamic range, sensitivity, speed) of the approach is demonstrated by comparative analysis of two differentially spiked proteomes. PMID:15602776

Schmidt, Alexander; Kellermann, Josef; Lottspeich, Friedrich

2005-01-01

26

Plant SILAC: Stable-Isotope Labelling with Amino Acids of Arabidopsis Seedlings for Quantitative Proteomics  

PubMed Central

Stable Isotope Labelling by Amino acids in Cell culture (SILAC) is a powerful technique for comparative quantitative proteomics, which has recently been applied to a number of different eukaryotic organisms. Inefficient incorporation of labelled amino acids in cell cultures of Arabidopsis thaliana has led to very limited use of SILAC in plant systems. We present a method allowing, for the first time, efficient labelling with stable isotope-containing arginine and lysine of whole Arabidopsis seedlings. To illustrate the utility of this method, we have combined the high labelling efficiency (>95%) with quantitative proteomics analyses of seedlings exposed to increased salt concentration. In plants treated for 7 days with 80 mM NaCl, a relatively mild salt stress, 215 proteins were identified whose expression levels changed significantly compared to untreated seedling controls. The 92 up-regulated proteins included proteins involved in abiotic stress responses and photosynthesis, while the 123 down-regulated proteins were enriched in proteins involved in reduction of oxidative stress and other stress responses, respectively. Efficient labelling of whole Arabidopsis seedlings by this modified SILAC method opens new opportunities to exploit the genetic resources of Arabidopsis and analyse the impact of mutations on quantitative protein dynamics in vivo. PMID:23977254

Lewandowska, Dominika; ten Have, Sara; Hodge, Kelly; Tillemans, Vinciane; Lamond, Angus I.; Brown, John W. S.

2013-01-01

27

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

PubMed

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

Preston, Tom

2014-01-01

28

Optimal isotope labelling for NMR protein structure determinations  

Microsoft Academic Search

Nuclear-magnetic-resonance spectroscopy can determine the three-dimensional structure of proteins in solution. However, its potential has been limited by the difficulty of interpreting NMR spectra in the presence of broadened and overlapping resonance lines and low signal-to-noise ratios. Here we present stereo-array isotope labelling (SAIL), a technique that can overcome many of these problems by applying a complete stereospecific and regiospecific

Masatsune Kainosho; Takuya Torizawa; Yuki Iwashita; Tsutomu Terauchi; Akira Mei Ono; Peter Güntert

2006-01-01

29

Isotopic Labeling of Red Cabbage Anthocyanins with Atmospheric 13-CO2  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

30

Growth and isotopic labelling of adherent cells in small volumes of medium.  

PubMed

The in vivo labelling of viral or cellular components is usually conducted through the addition of radioactively labelled precursors to the culture medium. A limiting factor for isotope use is often the cost of isotope purchase and disposal. Therefore, significant savings can be achieved if the smallest possible volume of medium is employed. However, in the case of adherent cells growing in tissue culture dishes or multi-well plates, surface tension causes a very uneven distribution of the liquid due to the formation of a meniscus at the edge of the petri. This prevents the use of very small volumes of medium for cell growth and labelling because the cells at the center of the petri dish would dry out and die, especially after longer incubation periods. In this communication, we describe a technique whereby cells are grown in an area surrounded by a hydrophobic ring of Teflon, which greatly improves the distribution of the medium by eliminating the concave meniscus. This translates into a dramatic improvement in the condition of the cells, as well as the efficiency of labelling of phosphoproteins, such as the Simian Virus 40 large tumor antigen with 32P-orthophosphate or labelling of the cellular DNA with 3[H]thymidine. The technique is useful for any application where growth of cells in small volumes of medium is required. PMID:11849699

Vultur, Adina; Keiski, Carrie Lynn; Maynard, Mindy; Grammatikakis, Nicholas; Raptis, Leda

2002-03-01

31

Efficient Thread Labeling for Monitoring Programs with Nested Parallelism  

NASA Astrophysics Data System (ADS)

It is difficult and cumbersome to detect data races occurred in an execution of parallel programs. Any on-the-fly race detection techniques using Lamport's happened-before relation needs a thread labeling scheme for generating unique identifiers which maintain logical concurrency information for the parallel threads. NR labeling is an efficient thread labeling scheme for the fork-join program model with nested parallelism, because its efficiency depends only on the nesting depth for every fork and join operation. This paper presents an improved NR labeling, called e-NR labeling, in which every thread generates its label by inheriting the pointer to its ancestor list from the parent threads or by updating the pointer in a constant amount of time and space. This labeling is more efficient than the NR labeling, because its efficiency does not depend on the nesting depth for every fork and join operation. Some experiments were performed with OpenMP programs having nesting depths of three or four and maximum parallelisms varying from 10,000 to 1,000,000. The results show that e-NR is 5 times faster than NR labeling and 4.3 times faster than OS labeling in the average time for creating and maintaining the thread labels. In average space required for labeling, it is 3.5 times smaller than NR labeling and 3 times smaller than OS labeling.

Ha, Ok-Kyoon; Kim, Sun-Sook; Jun, Yong-Kee

32

Quantitating isotopic molecular labels with accelerator mass spectrometry.  

PubMed

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

Vogel, John S; Love, Adam H

2005-01-01

33

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

PubMed

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

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

2014-01-01

34

Design and Operation of a Continuous 13C and 15N Labeling Chamber for Uniform or Differential, Metabolic and Structural, Plant Isotope Labeling  

PubMed Central

Tracing rare stable isotopes from plant material through the ecosystem provides the most sensitive information about ecosystem processes; from CO2 fluxes and soil organic matter formation to small-scale stable-isotope biomarker probing. Coupling multiple stable isotopes such as 13C with 15N, 18O or 2H has the potential to reveal even more information about complex stoichiometric relationships during biogeochemical transformations. Isotope labeled plant material has been used in various studies of litter decomposition and soil organic matter formation1-4. From these and other studies, however, it has become apparent that structural components of plant material behave differently than metabolic components (i.e. leachable low molecular weight compounds) in terms of microbial utilization and long-term carbon storage5-7. The ability to study structural and metabolic components separately provides a powerful new tool for advancing the forefront of ecosystem biogeochemical studies. Here we describe a method for producing 13C and 15N labeled plant material that is either uniformly labeled throughout the plant or differentially labeled in structural and metabolic plant components. Here, we present the construction and operation of a continuous 13C and 15N labeling chamber that can be modified to meet various research needs. Uniformly labeled plant material is produced by continuous labeling from seedling to harvest, while differential labeling is achieved by removing the growing plants from the chamber weeks prior to harvest. Representative results from growing Andropogon gerardii Kaw demonstrate the system's ability to efficiently label plant material at the targeted levels. Through this method we have produced plant material with a 4.4 atom%13C and 6.7 atom%15N uniform plant label, or material that is differentially labeled by up to 1.29 atom%13C and 0.56 atom%15N in its metabolic and structural components (hot water extractable and hot water residual components, respectively). Challenges lie in maintaining proper temperature, humidity, CO2 concentration, and light levels in an airtight 13C-CO2 atmosphere for successful plant production. This chamber description represents a useful research tool to effectively produce uniformly or differentially multi-isotope labeled plant material for use in experiments on ecosystem biogeochemical cycling. PMID:24457314

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

2014-01-01

35

Production of isotopically-labeled standards from a uniformly labeled precursor for quantitative volatile metabolomic studies  

PubMed Central

Optimal accuracy and precision in small molecule profiling by mass spectrometry generally requires isotopically labeled standards chemically representative of all compounds of interest. However, preparation of mixed standards from commercially available pure compounds is often prohibitively expensive and time consuming, and many labeled compounds are not available in pure form. We used a single prototype uniformly labeled [U-13C]-compound to generate [U-13C]-volatile standards for use in subsequent experimental profiling studies. [U-13C]-?-linolenic acid (C18:3n-3, ALA) was thermally oxidized to produce labeled lipid degradation volatiles which were subsequently characterized qualitatively and quantitatively. Twenty-five [U-13C]-labeled volatiles were identified by headspace solid-phase microextraction-gas chromatography-time of flight-mass spectrometry (HS-SPME-GC-TOF-MS) by comparison of spectra with unlabeled volatiles. Using 250 ?L starting sample, labeled volatiles were quantified by a reverse isotope dilution procedure. Using the [U-13C]-labeled standards, limits of detection comparable to or better than previous HS-SPME reports were achieved, 0.010–1.04 ng/g. The performance of the [U-13C]-volatile standards was evaluated using a commodity soybean oil (CSO) oxidized at 60°C from 0 to 15 d. Relative responses of n-decane, an unlabeled internal standard otherwise absent from the mixture, and [U-13C]-oxidation products changed by up to 8-fold as the CSO matrix was oxidized, demonstrating that reliance on a single standard in volatile profiling studies yields inaccurate results due to changing matrix effects. The [U-13C]-standard mixture was used to quantify 25 volatiles in oxidized CSO and low-ALA soybean oil with an average relative standard deviation of 8.5%. Extension of this approach to other labeled substrates, e.g., [U-13C]-sugars and amino acids, for profiling studies should be feasible and can dramatically improve quantitative results compared to use of a single standard. PMID:22662968

Gómez-Cortés, Pilar; Brenna, J. Thomas; Sacks, Gavin L.

2012-01-01

36

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

PubMed Central

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

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

2011-01-01

37

Multiple segmental and selective isotope labeling of large RNA for NMR structural studies  

PubMed Central

Multiple segmental and selective isotope labeling of RNA with three segments has been demonstrated by introducing an RNA segment, selectively labeled with 13C9/15N2/2H(1?, 3?, 4?, 5?, 5??)-labeled uridine residues, into the central position of the 20 kDa ?-RNA of Duck Hepatitis B Virus. The RNA molecules were produced via two efficient protocols: a two-step protocol, which uses T4 DNA ligase and T4 RNA ligase 1, and a one-pot protocol, which uses T4 RNA ligase 1 alone. With T4 RNA ligase 1 all not-to-be-ligated termini are usually protected to prevent formation of side products. We show that such labor-intensive protection of termini is not required, provided segmentation sites can be chosen such that the segments fold into the target structure or target-like structures and thus are not trapped into stable alternate structures. These sites can be reliably predicted via DINAMelt. The simplified NMR spectrum provided evidence for the presence of a U28 H3-imino resonance, previously obscured in the fully labeled sample, and thus of the non-canonical base pair U28:C37. The demonstrated multiple segmental labeling protocols are generally applicable to large RNA molecules and can be extended to more than three segments. PMID:18583361

Nelissen, Frank H. T.; van Gammeren, Adriaan J.; Tessari, Marco; Girard, Frederic C.; Heus, Hans A.; Wijmenga, Sybren S.

2008-01-01

38

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

DOEpatents

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

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

2014-12-09

39

Optimal isotope labelling for NMR protein structure determinations.  

PubMed

Nuclear-magnetic-resonance spectroscopy can determine the three-dimensional structure of proteins in solution. However, its potential has been limited by the difficulty of interpreting NMR spectra in the presence of broadened and overlapping resonance lines and low signal-to-noise ratios. Here we present stereo-array isotope labelling (SAIL), a technique that can overcome many of these problems by applying a complete stereospecific and regiospecific pattern of stable isotopes that is optimal with regard to the quality and information content of the resulting NMR spectra. SAIL uses exclusively chemically and enzymatically synthesized amino acids for cell-free protein expression. We demonstrate for the 17-kDa protein calmodulin and the 41-kDa maltodextrin-binding protein that SAIL offers sharpened lines, spectral simplification without loss of information, and the ability to rapidly collect the structural restraints required to solve a high-quality solution structure for proteins twice as large as commonly solved by NMR. It thus makes a large class of proteins newly accessible to detailed solution structure determination. PMID:16511487

Kainosho, Masatsune; Torizawa, Takuya; Iwashita, Yuki; Terauchi, Tsutomu; Mei Ono, Akira; Güntert, Peter

2006-03-01

40

Hydrolysis of adenosine 5'-triphosphate: an isotope-labeling study  

SciTech Connect

A combination of /sup 18/O-labeling experiments and kinetic studies to clarify the nonenzymatic hydrolytic pathways of adenosine 5'-triphosphate (ATP) at pH values ranging from 0 to 8.3 has been used in this experiment. In 1 N and 0.1 N HCl, the data are consistent with the hypothesis that hydrolysis occurs by addition-elimination, with initial attack 93% ..gamma.. and 7% ..beta..; both lead only to ADP + P/sub i/. In the subsequent hydrolysis of the ADP to AMP + P/sub i/, attack is 83% ..beta.. and 17% ..cap alpha... At pH 8.3, the data are consistent with the hypothesis that hydrolsysis occurs by elimination-addition. Over the entire pH range studied, no oxygen exchange between water and ATP, ADP, or P/sub i/ was detected. Nonenzymatic hydrolysis and isotopic analysis of the resultant P/sub i/ comprise a preferred means of assaying the isotopic enrichment of (..gamma..-/sup 18/O)ATP to be used in studies of enzymatic processes.

Meyerson, S. (Standard Oil Co. (Indiana), Naperville, IL); Kuh, E.S.; Ramirez, F.; Marecek, J.F.

1982-12-15

41

Uniform stable-isotope labeling in mammalian cells: formulation of a cost-effective culture medium  

Microsoft Academic Search

Uniform stable-isotope labeling of mammalian cells is achieved via a novel formulation of a serum-free cell culture medium\\u000a that is based on stable-isotope-labeled autolysates and lipid extracts of various microbiological origin. Yeast autolysates\\u000a allow complete replacement of individual amino acids and organic acids in a chemically defined medium (DMEM\\/F12), enabling\\u000a a cost-effective formulation of a stable-isotope-labeled culture medium for mammalian

Tatiana A. Egorova-Zachernyuk; Giel J. C. G. M. Bosman; Willem J. DeGrip

2011-01-01

42

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

SciTech Connect

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

Jewett, J.R., Fluor Daniel Hanford

1997-02-24

43

Determination of the enrichment of isotopically labelled molecules by mass spectrometry.  

PubMed

A general method for the determination of the enrichment of isotopically labelled molecules by mass spectrometry (MS) is described. In contrast to other published procedures, the method described here takes into account and corrects for measurement errors such as the contribution at M?-?1 due to loss of hydrogen or lack of spectral resolution and provides an uncertainty value for the determined enrichment. The general procedure requires the following steps: (1) evaluation of linearity in the mass spectrometer by injecting the natural abundance compound at different concentration levels, (2) determination of the purity of the mass cluster using the natural abundance analogue, (3) calculation of the theoretical isotope composition of the labelled compound using different tentative isotope enrichments, (4) calculation of 'convoluted' isotope distributions for the labelled compound taking into account the purity of the mass cluster determined with the natural abundance analogue and (5) comparison of the isotope distributions measured for the labelled compound with those calculated for different isotope enrichments using linear regression. The method was applied to a series of commercially available (13)C- and (2)H-labelled compounds and to a suite of singly (13)C-labelled ?2-agonist prepared in-house both by gas chromatography (GC)-MS, GC-tandem MS (MS/MS) and liquid chromatography-MS/MS with satisfactory results. It was observed that the main uncertainty source for the isotope enrichment was the uncertainty in the purity of the measured cluster as determined with the natural abundance compound. PMID:25044895

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

2014-08-01

44

Fluorination of isotopically labeled turbostratic and Bernal stacked bilayer graphene.  

PubMed

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

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

2015-01-12

45

Convenient synthesis of stable deuterium-labeled alkylpyrazines for use in stable isotope dilution assays.  

PubMed

Stable isotope dilution assays (SIDA) provide for accurate and precise quantitation of aroma components, such as alkylpyrazines, which are often present in low concentrations in complex food matrices. The unavailability of labeled standards is the main limitation to the widespread use of SIDA. This study describes the chlorination of several alkylpyrazines to form the corresponding chloroalkylpyrazine compounds, which are efficient starting materials for the synthesis of deuterium-labeled alkylpyrazines, namely [²H?]-2-methylpyrazine (d-1), [²H?]-2-ethylpyrazine (d-2), [²H?]-2,3(or 6)-dimethylpyrazine (d-3A, d-3B), [²H?]-2,[²H?]-6-dimethylpyrazine (d-3C), [²H?]-2,[²H?]-6-diethylpyrazine (d-4), [²H?]-2-ethyl-3(or 6)-methylpyrazine (d-5A, d-5B), 2,[²H?]-3,5-trimethylpyrazine (d-6), [²H?]-2-ethyl-3,6-dimethylpyrazine (d-7), [²H?]-2-ethyl-3,5-dimethylpyrazine (d-8), and 2,3-diethyl-[²H?]-5-methylpyrazine (d-9), which were obtained in good yields (57-100%) and high purities (86-98%). These stable isotopes were used as internal standards in SIDA to accurately and precisely determine selected alkylpyrazines in commercial peanut butter, cocoa powder, and instant coffee. 2,3-Diethyl-5-methylpyrazine (p-9) and 2-ethyl-3,5-dimethylpyrazine (p-8), despite their low abundance, had the highest odor-active values among the 13 pyrazines quantified in all products due to their very low odor thresholds. PMID:23528050

Fang, Mingchih; Cadwallader, Keith R

2013-04-17

46

A Novel Method for Relative Quantitation of N-Glycans by Isotopic Labeling Using 18O-Water  

PubMed Central

Quantitation is an essential aspect of comprehensive glycomics study. Here, a novel isotopic-labeling method is described for N-glycan quantitation using 18O-water. The incorporation of the 18O-labeling into the reducing end of N-glycans is simply and efficiently achieved during peptide-N4-(N-acetyl-?-glucosaminyl) asparagine amidase F release. This process provides a 2-Da mass difference compared with the N-glycans released in 16O-water. A mathematical calculation method was also developed to determine the 18O/16O ratios from isotopic peaks. Application of this method to several standard glycoprotein mixtures and human serum demonstrated that this method can facilitate the relative quantitation of N-glycans over a linear dynamic range of two orders, with high accuracy and reproducibility. PMID:25365792

Tao, Shujuan; Orlando, Ron

2014-01-01

47

A novel method for relative quantitation of N-glycans by isotopic labeling using (18)o-water.  

PubMed

Quantitation is an essential aspect of comprehensive glycomics study. Here, a novel isotopic-labeling method is described for N-glycan quantitation using (18)O-water. The incorporation of the (18)O-labeling into the reducing end of N-glycans is simply and efficiently achieved during peptide-N4-(N-acetyl-?-glucosaminyl) asparagine amidase F release. This process provides a 2-Da mass difference compared with the N-glycans released in (16)O-water. A mathematical calculation method was also developed to determine the (18)O/(16)O ratios from isotopic peaks. Application of this method to several standard glycoprotein mixtures and human serum demonstrated that this method can facilitate the relative quantitation of N-glycans over a linear dynamic range of two orders, with high accuracy and reproducibility. PMID:25365792

Tao, Shujuan; Orlando, Ron

2014-12-01

48

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

PubMed Central

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

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

2014-01-01

49

Nature of vibrational coupling in helical peptides: an isotopic labeling study.  

PubMed

Infrared (IR) and vibrational circular dichroism (VCD) spectra were measured for a series of isotopically ((13)C on two or more amide Cdouble bond]O) labeled, 25 residue, alpha-helical peptides of the sequence Ac-(AAAAK)(4)AAAAY-NH(2) that were also studied in the previous paper. Theoretical IR and VCD simulations were performed for correspondingly isotopically labeled Ac-A(24)-NHCH(3) constrained to an alpha-helical conformation by use of property tensor transfer from density functional theory (DFT) calculations on Ac-A(10)-NHCH(3). The simulations predicted and experiments confirmed that the vibrational coupling constants between i, i + 1 and i, i + 2 residues differ in sign, thus leading to a reversal of the (13)C VCD pattern and explaining the large shift in the (13)C amide I frequency as reported in the previous paper. The sign of the coupling constant remained consistent for larger label separation (with the exception of i, i + 4) and for more labels with uniform separation. Such effects confirm that the isotopically labeled group vibrations are essentially only coupled to each other and are effectively uncoupled from those of the unlabeled groups. This development confirms the utility of isotopic labels for site-specific structural studies with vibrational spectra. Observed spectral effects cannot be explained by considering only transition dipole coupling (TDC) between amide oscillators, particularly for smaller label separations, but the TDC and ab initio predicted couplings roughly converge at large separation. PMID:14982438

Huang, Rong; Kubelka, Jan; Barber-Armstrong, Wendy; Silva, R A G D; Decatur, Sean M; Keiderling, Timothy A

2004-03-01

50

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

PubMed

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

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

2012-10-01

51

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

PubMed Central

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

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

2013-01-01

52

Stable isotope-labelled feed nutrients to assess nutrient-specific feed passage kinetics in ruminants.  

PubMed

Knowledge of digesta passage kinetics in ruminants is essential to predict nutrient supply to the animal in relation to optimal animal performance, environmental pollution and animal health. Fractional passage rates (FPR) of feed are widely used in modern feed evaluation systems and mechanistic rumen models, but data on nutrient-specific FPR are scarce. Such models generally rely on conventional external marker techniques, which do not always describe digesta passage kinetics in a satisfactory manner. Here the use of stable isotope-labelled dietary nutrients as a promising novel tool to assess nutrient-specific passage kinetics is discussed. Some major limitations of this technique include a potential marker migration, a poor isotope distribution in the labelled feed and a differential disappearance rate of isotopes upon microbial fermentation in non-steady state conditions. Such limitations can often be circumvented by using intrinsically stable isotope-labelled plant material. Data are limited but indicate that external particulate markers overestimate rumen FPR of plant fibre compared with the internal stable isotope markers. Stable isotopes undergo the same digestive mechanism as the labelled feed components and are thus of particular interest to specifically measure passage kinetics of digestible dietary nutrients. PMID:24114801

Warner, Daniel; Dijkstra, Jan; Hendriks, Wouter H; Pellikaan, Wilbert F

2014-03-30

53

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

PubMed

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

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

2015-03-01

54

Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities.  

PubMed

Soil microbial diversity represents the largest global reservoir of novel microorganisms and enzymes. In this study, we coupled functional metagenomics and DNA stable-isotope probing (DNA-SIP) using multiple plant-derived carbon substrates and diverse soils to characterize active soil bacterial communities and their glycoside hydrolase genes, which have value for industrial applications. We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon ((12)C) or stable-isotope-labeled ((13)C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates. Among characterized taxa, Actinomycetales (Salinibacterium), Rhizobiales (Devosia), Rhodospirillales (Telmatospirillum), and Caulobacterales (Phenylobacterium and Asticcacaulis) were bacterial indicator species for the heavy substrates and soils tested. Both Actinomycetales and Caulobacterales (Phenylobacterium) were associated with metabolism of cellulose, and Alphaproteobacteria were associated with the metabolism of arabinose; members of the order Rhizobiales were strongly associated with the metabolism of xylose. Annotated metagenomic data suggested diverse glycoside hydrolase gene representation within the pooled heavy DNA. By screening 2,876 cloned fragments derived from the (13)C-labeled DNA isolated from soils incubated with cellulose, we demonstrate the power of combining DNA-SIP, multiple-displacement amplification (MDA), and functional metagenomics by efficiently isolating multiple clones with activity on carboxymethyl cellulose and fluorogenic proxy substrates for carbohydrate-active enzymes. Importance: The ability to identify genes based on function, instead of sequence homology, allows the discovery of genes that would not be identified through sequence alone. This is arguably the most powerful application of metagenomics for the recovery of novel genes and a natural partner of the stable-isotope-probing approach for targeting active-yet-uncultured microorganisms. We expanded on previous efforts to combine stable-isotope probing and metagenomics, enriching microorganisms from multiple soils that were active in degrading plant-derived carbohydrates, followed by construction of a cellulose-based metagenomic library and recovery of glycoside hydrolases through functional metagenomics. The major advance of our study was the discovery of active-yet-uncultivated soil microorganisms and enrichment of their glycoside hydrolases. We recovered positive cosmid clones in a higher frequency than would be expected with direct metagenomic analysis of soil DNA. This study has generated an invaluable metagenomic resource that future research will exploit for genetic and enzymatic potential. PMID:25028422

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

2014-01-01

55

Metabolic pathway of inorganic and organic selenocompounds labeled with stable isotope in Japanese quail.  

PubMed

The distribution and metabolism of an inorganic selenium (Se) compound and a selenoamino acid in quails were evaluated by speciation with inductively coupled plasma mass spectrometry (ICP-MS) and a stable isotope. Quails were orally administered stable isotope [(77)Se]-labeled selenite and selenomethionine (SeMet) at the nutritional dose of 10 ?g Se/bird. Then, the quails were dissected 3, 9, and 24 h after the administration to examine the metabolic pathway and the time-dependent change of Se. The concentrations of exogenous Se in all the organs and tissues of the SeMet-administered group were significantly higher than those of the selenite-administered group 3 h after the administration. This suggested that SeMet was more rapidly and/or efficiently incorporated into the quail body than selenite. A Se-containing protein in the serum was detected only in the SeMet-administered quails, but not in the selenite-administered quails. The major urinary Se metabolite, i.e., Se-methylseleno-N-acetyl-galactosamine (selenosugar), was detected in the quail serum after the administration of both selenite and SeMet. The endogenous amount of Se-methylated selenosugar (MeSeSug) in the serum of quails seemed to be larger than that of the rodents. We conclude that the metabolic pathway of Se in quails was the same as that in rodents, but the metabolic capacity for Se seemed to be larger in quails than in rodents. PMID:25326891

Anan, Yasumi; Ohbo, Ai; Tani, Yuta; Ogra, Yasumitsu

2014-12-01

56

Radioactive Labeling of Antibody: A Simple and Efficient Method  

Microsoft Academic Search

A simple and efficient method of covalently coupling the strong chelator diethylenetriaminepentaacetic acid to proteins was developed for radiolabeling immunoglobulin G antibodies. After being coupled and labeled with indium-111, a monoclonal antibody to carcinoembryonic antigen retained its ability to bind to its antigen in vitro and in vivo. In nude mice with a human colorectal xenograft, 41 percent of the

D. J. Hnatowich; W. W. Layne; R. L. Childs; D. Lanteigne; M. A. Davis; T. W. Griffin; P. W. Doherty

1983-01-01

57

Radioactive labeling of antibody: a simple and efficient method  

Microsoft Academic Search

A simple and efficient method of covalently coupling the strong chelator diethylenetriaminepentaacetic acid to proteins was developed for radiolabeling immunoglobulin G antibodies. After being coupled and labeled with indium-111, a monoclonal antibody to carcinoembryonic antigen retained its ability to bind to its antigen in vitro and in vivo. In nude mice with a human colorectal xenograft, 41 percent of the

D. J. Hnatowich; W. W. Layne; R. L. Childs; D. Lanteigne; M. A. Davis; T. W. Griffin; P. W. Doherty

1983-01-01

58

Isotope Labeling for Solution and Solid-State NMR Spectroscopy of Membrane Proteins  

PubMed Central

In this chapter, we summarize the isotopic labeling strategies used to obtain high-quality solution and solid-state NMR spectra of biological samples, with emphasis on integral membrane proteins (IMPs). While solution NMR is used to study IMPs under fast tumbling conditions, such as in the presence of detergent micelles or isotropic bicelles, solid-state NMR is used to study the structure and orientation of IMPs in lipid vesicles and bilayers. In spite of the tremendous progress in biomolecular NMR spectroscopy, the homogeneity and overall quality of the sample is still a substantial obstacle to overcome. Isotopic labeling is a major avenue to simplify overlapped spectra by either diluting the NMR active nuclei or allowing the resonances to be separated in multiple dimensions. In the following we will discuss isotopic labeling approaches that have been successfully used in the study of IMPs by solution and solid-state NMR spectroscopy. PMID:23076578

Verardi, Raffaello; Traaseth, Nathaniel J.; Masterson, Larry R.; Vostrikov, Vitaly V.; Veglia, Gianluigi

2013-01-01

59

Sample-efficient learning with auxiliary class-label information  

PubMed Central

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

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

2011-01-01

60

Turnover of Leaf Waxes in Florida Slash Pine: Results of an Isotopic Labeling Experiment  

NASA Astrophysics Data System (ADS)

Isotopic discrimination of terrestrial photosynthesis, atmospheric CO2 concentration, and ?13CO2 are important parameters in global carbon models that are employed to estimate global carbon sources and sinks. Yet, terrestrial isotopic discrimination can be highly variable over space and time, yielding large uncertainties of terrestrial fluxes. The isotopic composition of plant wax aerosols in continental air masses can be used as an indirect measure of the spatial and temporal patterns of photosynthetic discrimination integrated over large (subcontinental) spatial scales. However, the temporal offset between wax biosynthesis and the wax aerosol isotopic signal of photosynthetic discrimination is not well constrained. To further our understanding of this temporal lag, this study sought to determine the turnover time of conifer leaf waxes by performing an isotopic labeling experiment. Four clonal pine saplings were placed in a tent and labeled with enriched 13CO2 for one year, while another four control saplings were grown under ambient CO2. At the end of the year long enrichment, the labeled saplings were removed from the tent and placed in ambient air, such that the wax turnover rate could be determined by analyzing the resultant isotopic and molecular changes. The results of this experiment indicated that after 80 days of sequestering ambient CO2, the wax (and soluble sugar) isotopic composition of the labeled saplings varied minimally. The molecular composition of the waxes, however, did change over time. From these results we concluded that waxes are turning over, but rather than being synthesized de novo from recently fixed carbon precursors they are synthesized using carbon from stored (labeled) carbon pools. Therefore, the ?13C of conifer leaf waxes in aerosols may not reflect recent photosynthetic discrimination, but instead represents photosynthetic discrimination integrated over a longer period of time. The implications of these findings are focused on interpreting the wax aerosol ?13C as an integrative measure of past photosynthetic discrimination in global carbon cycling models, and also provide new insights on internal cycling among plant carbon pools.

Crumsey, J.; Conte, M. H.; Weber, J. C.; Mortazavi, B.; Smith, M.; Chanton, J.

2006-12-01

61

X13CMS: global tracking of isotopic labels in untargeted metabolomics.  

PubMed

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

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

2014-02-01

62

Structural determination of larger proteins using stable isotope labeling and NMR spectroscopy  

SciTech Connect

The project sought to employ stable isotope labeling and NMR spectroscopy to study protein structures and provide insight into important biochemical problems. A methylotrophic bacterial expression system has been developed for uniform deuterium and carbon-13 labeling of proteins for structural studies. These organisms grow using methanol as the sole source of carbon and energy. Because isotopically labeled methanol is relatively inexpensive, the methylotrophs are ideal for expressing proteins labeled uniformly with deuterium and/or carbon-13. This expression system has been employed to prepare deuterated troponin C. NMR spectroscopy measurements have been made on the inhibitory peptide from troponin I (residues 96--115), both as the free peptide and the peptide complexed with deuterated troponin C. Proton-NMR spectroscopy resonance-signal assignments have been made for the free peptide.

Unkefer, C.; Hernandez, G.; Springer, P.; Trewhella, J. [Los Alamos National Lab., NM (United States); Blumenthal, D. [Univ. of Utah, Salt Lake City, UT (United States); Lidstrom, M. [California Inst. of Tech., Pasadena, CA (United States)

1996-04-01

63

Fully automated isotopic dimethyl labeling and phosphopeptide enrichment using a microfluidic HPLC phosphochip.  

PubMed

Quantitative detection of phosphorylation levels is challenging and requires an expertise in both stable isotope labeling as well as enrichment of phosphorylated peptides. Recently, a microfluidic device incorporating a nanoliter flow rate reversed phase column as well as a titania (TiO(2)) enrichment column was released. This HPLC phosphochip allows excellent recovery and separation of phosphorylated peptides in a robust and reproducible manner with little user intervention. In this work, we have extended the abilities of this chip by defining the conditions required for on-chip stable isotope dimethyl labeling allowing for automated quantitation. The resulting approach will make quantitative phosphoproteomics more accessible. PMID:22975804

Polat, Ayse Nur; Kraiczek, Karsten; Heck, Albert J R; Raijmakers, Reinout; Mohammed, Shabaz

2012-11-01

64

On a criterion efficiency for multi-isotope mixtures separation  

SciTech Connect

The criterion for efficiency for separation of binary isotopic mixtures is the well-known value function. However, in the case of multi-isotope separation, this value function does not exist. In this paper the authors develop a criterion to define the efficiency for separation of multi-isotope mixtures. It is based o the concept of the match-abundance ratio cascade (MARC) originally introduced by De La Garza for a ternary isotope mixture. The criterion has the property that, when applied to binary mixtures, it is the same as the value function. This approach has demonstrated that for obtaining the optimal parameters of a single stage in the cascade it is necessary to minimize the linear combination of the inverse values of partial separative powers for all mixture components. A numerical example using this efficiency criterion is presented using the separation of chromium isotopes by a single gas centrifuge.

Wood, H.G. [Univ. of Virginia, Charlottesville, VA (United States). Dept. of Mechanical, Aerospace and Nuclear Engineering] [Univ. of Virginia, Charlottesville, VA (United States). Dept. of Mechanical, Aerospace and Nuclear Engineering; Borisevich, V.D.; Sulaberidze, G.A. [Moscow State Engineering Physics Inst. (Russian Federation)] [Moscow State Engineering Physics Inst. (Russian Federation)

1999-02-01

65

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

EPA Science Inventory

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...

66

Stable isotope labeling of oligosaccharide cell surface antigens  

SciTech Connect

The overall goal of this Laboratory Directed Research and Development (LDRD) project was to develop new methods for synthesis of {sup 13}C-labeled oligosaccharides that are required for nuclear magnetic resonance (NMR) studies of their solution conformation. Oligosaccharides are components of the cell`s outer surface and are involved in important processes such as cell-cell recognition and adhesion. Recently, Danishefsky and coworkers at Slone-Kettering Cancer Center developed a method for the solid-phase chemical synthesis of oligosaccharides. The specific goal of this LDRD project was to prepare uniform {sup 13}C-labeled aldohexose precursors required for the solid-phase synthesis of the Lewis blood-group antigenic determinants. We report the synthesis of {sup 13}C-labeled D-glucal, D-galactal and Fucosyl precursors. We have been collaborating with the Danishefsky group on the synthesis of the Lewis oligosaccharides and the NMR analysis of their solution conformation.

Unkefer, C.J.; Silks, L.A. III; Martinez, R.A. [and others

1998-12-31

67

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

68

Ion-Surface Reactions Involving Isotopically Labeled Langmuir-Blodgett Films  

E-print Network

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

Wysocki, Vicki H.

69

Analysis of Isotopic Labeling in Peptide Fragments by Tandem Mass Spectrometry  

PubMed Central

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

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

2014-01-01

70

Analysis of isotopic labeling in peptide fragments by tandem mass spectrometry.  

PubMed

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

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

2014-01-01

71

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

E-print Network

of phosphate, enzyme-labeled fluorescence, and turnover times Karen McLaughlin,1 Jill A. Sohm,2 Gregory A alkaline phosphatase (AP) activity as measured by enzyme-labeling fluorescence are also used. In surface: Investigation using the oxygen isotopic composition of phosphate, enzyme-labeled fluorescence, and turnover

Paytan, Adina

72

Utilization of organophosphate:phosphate antiporter for isotope-labeling experiments in E. coli.  

PubMed

The transport of organophosphates across the cytoplasma membrane is mediated by organophosphate:phosphate antiporter proteins. In this work, we present the application of a recombinant phosphoenolpyruvate:phosphate antiporter for isotopic labeling experiments in E. coli strains. The antiporters UhpT, UhpT-D388C, and PgtP were investigated regarding transport activity and growth on phosphoenolpyruvate as sole carbon source. The expression of the protein variant UhpT-D388C in a shikimic acid producing E. coli strain was used to show the successful isotopic labeling of shikimic acid from extracellular phosphoenolpyruvate. The results demonstrate the possibility of a direct incorporation of exogenously applicated glycolysis intermediates into E. coli cells for (13) C-labeling experiments. PMID:25273627

Albermann, Christoph; Weiner, Michael; Tröndle, Julia; Weuster-Botz, Dirk; Sprenger, Georg A

2014-10-01

73

Hydrolysis of adenosine 5'-triphosphate: an isotope-labeling study  

Microsoft Academic Search

A combination of ¹⁸O-labeling experiments and kinetic studies to clarify the nonenzymatic hydrolytic pathways of adenosine 5'-triphosphate (ATP) at pH values ranging from 0 to 8.3 has been used in this experiment. In 1 N and 0.1 N HCl, the data are consistent with the hypothesis that hydrolysis occurs by addition-elimination, with initial attack 93% ..gamma.. and 7% ..beta..; both

Seymour Meyerson; E. S. Kuh; Fausto Ramirez; James F. Marecek

1982-01-01

74

Use of (13)C stable isotope labelling for pathway and metabolic flux analysis in Leishmania parasites.  

PubMed

This protocol describes the combined use of metabolite profiling and stable isotope labelling to define pathways of central carbon metabolism in the protozoa parasite, Leishmania mexicana. Parasite stages are cultivated in standard or completely defined media and then rapidly transferred to chemically equivalent media containing a single (13)C-labelled nutrient. The incorporation of label can be followed over time or after establishment of isotopic equilibrium by harvesting parasites with rapid metabolic quenching. (13)C enrichment of multiple intracellular polar and apolar (lipidic) metabolites can be quantified using gas chromatography-mass spectrometry (GC-MS), while the uptake and secretion of (13)C-labelled metabolites can be measured by (13)C-NMR. Analysis of the mass isotopomer distribution of key metabolites provides information on pathway structure, while analysis of labelling kinetics can be used to infer metabolic fluxes. This protocol is exemplified using L. mexicana labelled with (13)C-U-glucose. The method can be used to measure perturbations in parasite metabolism induced by drug inhibition or genetic manipulation of enzyme levels and is broadly applicable to any cultured parasite stages. PMID:25388122

Saunders, Eleanor C; de Souza, David P; Chambers, Jennifer M; Ng, Milica; Pyke, James; McConville, Malcolm J

2015-01-01

75

Raman spectroscopic investigation of polycrystalline structures of CVD-grown graphene by isotope labeling  

NASA Astrophysics Data System (ADS)

Topological defects, such as point defects, dislocations and grain boundaries, have a dramatic influence on the chemical and physical properties of large-scale graphene grown by chemical vapor deposition (CVD) method. Here we demonstrate the Raman visualization of polycrystalline structures in an isotopically modified CVD graphene. By means of the reversible reaction of methane on a copper catalyst, the etching of 12C-lattice and surface deposition of 13C-atoms occur in CVD graphene by sequentially introducing hydrogen and isotopic methane after standard growth of graphene with full monolayer coverage. Spatial Raman spectroscopic mapping on labeled graphene reveals pronounced network-like 13C-rich regions, which are further identified to exist along the grain boundaries of graphene by low-energy electron microscopy. The structural defects inside the graphene grains are also targeted in the isotope labeling process. Our work opens a new way to investigate multiple grain structures in CVD graphene with a simple spectroscopic technique.Topological defects, such as point defects, dislocations and grain boundaries, have a dramatic influence on the chemical and physical properties of large-scale graphene grown by chemical vapor deposition (CVD) method. Here we demonstrate the Raman visualization of polycrystalline structures in an isotopically modified CVD graphene. By means of the reversible reaction of methane on a copper catalyst, the etching of 12C-lattice and surface deposition of 13C-atoms occur in CVD graphene by sequentially introducing hydrogen and isotopic methane after standard growth of graphene with full monolayer coverage. Spatial Raman spectroscopic mapping on labeled graphene reveals pronounced network-like 13C-rich regions, which are further identified to exist along the grain boundaries of graphene by low-energy electron microscopy. The structural defects inside the graphene grains are also targeted in the isotope labeling process. Our work opens a new way to investigate multiple grain structures in CVD graphene with a simple spectroscopic technique. Electronic supplementary information (ESI) available: Fig. S1, experimental scheme; Fig. S2-3, scanning electron microscopy analysis and optical images; Fig. S4-5, additional LEEM analysis of labeled graphene and hydrogen-etched graphene; Fig. S6-10, additional Raman spectra of labeled graphene. See DOI: 10.1039/c4nr03824j

Wang, Shengnan; Suzuki, Satoru; Hibino, Hiroki

2014-10-01

76

Use of oxygen-18 isotopic labeling to assay photorespiration in terrestrial plants and algae  

SciTech Connect

A new method was devised to quantify photorespiration. The assay utilized {sup 18}O{sub 2} to isotopically label intermediates of the glycolate pathway, specifically glycolate, glycine, and serine, for various time periods. The pathway intermediates were isolated and analyzed on a mass spectrometer to determine molecular percent {sup 18}O-enrichment. Rates of glycolate synthesis were determined from: {sup 18}O-labeling kinetics of the intermediates, derived rate equations, and non-linear regression techniques. The method was adapted to measure photorespiratory rates in both terrestrial plants and algae. Test plants are Triticum aestivum, Zea mays L., Pavlova lutheri and Chlorella pyrenoidosa.

de Veau, E.J.

1988-01-01

77

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

SciTech Connect

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.

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

78

Design, synthesis, and evaluation of an isotopic labeling strategy for studying fatty acid-protein binding by NMR.  

PubMed

Here we describe the synthesis and evaluation of a new isotopic labeling strategy for fatty acids to be used as probes for studying ligand binding by NMR. We synthesized palmitic acid with carbons C-3 through C-16 perdeuterated, C-1 and C-2 with 13C atoms and hydrogens at C-2. Our strategy began with commercially available perdeuterated myristic acid and built up to palmitic acid using a Horner-Wadsworth-Emmons reaction. To evaluate the power of this isotopic enrichment strategy, we evaluated ligand binding to a prototypical member of the intracellular lipid binding protein family, FABP2. This small 15 kDa protein is well known to bind fatty acids with high affinity, and we used this system to illustrate the spectral filtering abilities of our described labeling strategy. Herein we show how having two vicinal 13C-enriched carbons, two hydrogens at the alpha-position, and a perdeuterated aliphatic tail allows the efficient use of multidimensional NMR experiments to effectively filter all background resonances from the protein and facilitate the study of ligand binding. PMID:18493652

Han, Yong; Alexander, Timothy E; Tochtrop, Gregory P

2008-06-01

79

Mass-related inversion symmetry breaking and phonon self-energy renormalization in isotopically labeled AB-stacked bilayer graphene  

E-print Network

A mass-related symmetry breaking in isotopically labeled bilayer graphene (2LG) was investigated during in-situ electrochemical charging of AB stacked (AB-2LG) and turbostratic (t-2LG) layers. The overlap of the two ...

Araujo, Paulo Antonio Trinidade

80

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

E-print Network

FTIR Difference Spectroscopy in Combination with Isotope Labeling for Identification infrared (FTIR) difference spectra have been obtained using photosystem I (PS I) particles from) FTIR difference spectrum, even with ;50% proton exchange. This indicates that the P700 binding site

Hastings, Gary

81

Microwave-assisted deuterium exchange: the convenient preparation of isotopically labelled analogues for stable isotope dilution analysis of volatile wine phenols.  

PubMed

This study reports the convenient, low cost, one-step synthesis of labelled analogues of six volatile phenols, guaiacol, 4-methylguaiacol, 4-ethylguaiacol, 4-ethylphenol, eugenol and vanillin, using microwave-assisted deuterium exchange, for use as internal standards for stable isotope dilution analysis. The current method improves on previous strategies in that it enables incorporation of deuterium atoms on the aromatic ring, thereby ensuring retention of the isotope label during mass spectrometry fragmentation. When used as standards for SIDA, these labelled volatile phenols will improve the accuracy and reproducibility of quantitative food and beverage analysis. PMID:24874385

Crump, Anna M; Sefton, Mark A; Wilkinson, Kerry L

2014-11-01

82

Ligands of glutamate and dopamine receptors evenly labeled with hydrogen isotopes  

Microsoft Academic Search

Abstact  A reaction of high-temperature solid-phase catalytic isotope exchange (HSCIE) was studied for the preparation of tritium-\\u000a and deuterium-labeled ligands of glutamate and dopamine receptors. Tritium-labeled (5S,10R)-(+)-5-methyl-10,11-dihydro-5H-dibenzo[a,d]cyclopenten-5,1-imine ([G-3H]MK-801) and R(+)-7-hydroxy-N,N-di-n-propyl-2-aminotetraline ([G-3H]-7-OH-DPAT) were obtained with a specific activity of 210 and 120 Ci\\/mol, respectively. The isotopomeric distribution of\\u000a deuterium-labeled ligands was studied using time-of-flight mass-spectrometer MX 5310 (ESI-o-TOF) with electrospray and orthogonal

Yu. A. Zolotarev; Yu. Yu. Firsova; A. Abaimov; A. K. Dadayan; V. S. Kosik; A. V. Novikov; N. V. Krasnov; B. V. Vaskovskii; I. V. Nazimov; G. I. Kovalev; N. F. Myasoedov

2009-01-01

83

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

PubMed

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

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

2014-01-01

84

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

85

Efficient excitation of media for laser isotope separation  

Microsoft Academic Search

A theoretical investigation is made of the photoionisation of a three-level medium intended for laser isotope separation. The results show that the highest ionisation efficiency can be achieved by dividing the process into two stages: coherent population inversion and photoionisation. A study is made of the possibility of inversion of three-level systems for various detunings of the laser frequencies from

S. K. Borisov; M A Kuzmina; V. A. Mishin

1995-01-01

86

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics  

E-print Network

The abbreviations used are: SILAC: Stable isotope labeling by amino acids in cell culture, 2DE: two dimensional (isoelectric focusing/SDS-PAGE) gel electrophoresis: ICATTM: isotope-coded affinity tag; MS: mass spectrometry; MALDI-TOF: matrix assisted laser desorption ionization-time of flight; PMF

Shao-en Ong; Blagoy Blagoev; Irina Kratchmarova; Dan Bach Kristensen; Akhilesh P; Matthias Mann

2002-01-01

87

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

Microsoft Academic Search

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

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

2002-01-01

88

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

NASA Astrophysics Data System (ADS)

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

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

2015-04-01

89

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

PubMed

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

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

2015-04-01

90

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

NASA Astrophysics Data System (ADS)

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

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

2015-01-01

91

Raman spectroscopic investigation of polycrystalline structures of CVD-grown graphene by isotope labeling.  

PubMed

Topological defects, such as point defects, dislocations and grain boundaries, have a dramatic influence on the chemical and physical properties of large-scale graphene grown by chemical vapor deposition (CVD) method. Here we demonstrate the Raman visualization of polycrystalline structures in an isotopically modified CVD graphene. By means of the reversible reaction of methane on a copper catalyst, the etching of (12)C-lattice and surface deposition of (13)C-atoms occur in CVD graphene by sequentially introducing hydrogen and isotopic methane after standard growth of graphene with full monolayer coverage. Spatial Raman spectroscopic mapping on labeled graphene reveals pronounced network-like (13)C-rich regions, which are further identified to exist along the grain boundaries of graphene by low-energy electron microscopy. The structural defects inside the graphene grains are also targeted in the isotope labeling process. Our work opens a new way to investigate multiple grain structures in CVD graphene with a simple spectroscopic technique. PMID:25303722

Wang, Shengnan; Suzuki, Satoru; Hibino, Hiroki

2014-11-21

92

Tracing bioavailability of ZnO nanoparticles using stable isotope labeling.  

PubMed

Zinc oxide nanoparticles (ZnO NPs) are widely used in commercial products and knowledge of their environmental fate is a priority for ecological protection. Here we synthesized model ZnO NPs that were made from and thus labeled with the stable isotope (68)Zn and this enables highly sensitive and selective detection of labeled components against high natural Zn background levels. We combine high precision stable isotope measurements and novel bioimaging techniques to characterize parallel water-borne exposures of the common mudshrimp Corophium volutator to (68)ZnO NPs, bulk (68)ZnO, and soluble (68)ZnCl(2) in the presence of sediment. C. volutator is an important component of coastal ecosystems where river-borne NPs will accumulate and is used on a routine basis for toxicity assessments. Our results demonstrate that ionic Zn from ZnO NPs is bioavailable to C. volutator and that Zn uptake is active. Bioavailability appears to be governed primarily by the dissolved Zn content of the water, whereby Zn uptake occurs via the aqueous phase and/or the ingestion of sediment particles with adsorbed Zn from dissolution of ZnO particles. The high sorption capacity of sediments for Zn thus enhances the potential for trophic transfer of Zn derived from readily soluble ZnO NPs. The uncertainties of our isotopic data are too large, however, to conclusively rule out any additional direct uptake route of ZnO NPs by C. volutator. PMID:23050854

Larner, Fiona; Dogra, Yuktee; Dybowska, Agnieszka; Fabrega, Julia; Stolpe, Björn; Bridgestock, Luke J; Goodhead, Rhys; Weiss, Dominik J; Moger, Julian; Lead, Jamie R; Valsami-Jones, Eugenia; Tyler, Charles R; Galloway, Tamara S; Rehkämper, Mark

2012-11-01

93

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

SciTech Connect

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

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

2006-04-10

94

METHOD TO TEST ISOTOPIC SEPARATION EFFICIENCY OF PALLADIUM PACKED COLUMNS  

SciTech Connect

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

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

2007-06-27

95

Identification of ejaculated proteins in the house mouse (Mus domesticus) via isotopic labeling  

PubMed Central

Background Seminal fluid plays an important role in successful fertilization, but knowledge of the full suite of proteins transferred from males to females during copulation is incomplete. The list of ejaculated proteins remains particularly scant in one of the best-studied mammalian systems, the house mouse (Mus domesticus), where artificial ejaculation techniques have proven inadequate. Here we investigate an alternative method for identifying ejaculated proteins, by isotopically labeling females with 15N and then mating them to unlabeled, vasectomized males. Proteins were then isolated from mated females and identified using mass spectrometry. In addition to gaining insights into possible functions and fates of ejaculated proteins, our study serves as proof of concept that isotopic labeling is a powerful means to study reproductive proteins. Results We identified 69 male-derived proteins from the female reproductive tract following copulation. More than a third of all spectra detected mapped to just seven genes known to be structurally important in the formation of the copulatory plug, a hard coagulum that forms shortly after mating. Seminal fluid is significantly enriched for proteins that function in protection from oxidative stress and endopeptidase inhibition. Females, on the other hand, produce endopeptidases in response to mating. The 69 ejaculated proteins evolve significantly more rapidly than other proteins that we previously identified directly from dissection of the male reproductive tract. Conclusion Our study attempts to comprehensively identify the proteins transferred from males to females during mating, expanding the application of isotopic labeling to mammalian reproductive genomics. This technique opens the way to the targeted monitoring of the fate of ejaculated proteins as they incubate in the female reproductive tract. PMID:21663664

2011-01-01

96

Study of neurotrophin 3 signaling in primary cultured neurons using multiplex stable isotope labeling with amino acids in cell culture  

PubMed Central

Conventional stable isotope labeling with amino acids in cell culture (SILAC) requires extensive metabolic labeling of proteins, and therefore is difficult to apply to cells that do not divide or are unstable in SILAC culture. Using two different sets of heavy amino acids for labeling allows for straightforward SILAC quantitation using partially labeled cells because the two cell populations are always equally labeled. Here we report the application of this labeling strategy to primary cultured neurons. We demonstrated that protein quantitation was not compromised by incomplete labeling of the neuronal proteins. We used this method to study neurotrophin-3 (NT-3) signaling in primary cultured neurons. Surprisingly our results indicate TrkB signaling is a major component of the signaling network induced by NT-3 in cortical neurons. In addition, involvement of proteins such as VAMP2, Scamp1 and Scamp3 suggest NT-3 may lead to enhanced exocytosis of synaptic vesicles. PMID:21370927

Zhang, Guoan; Deinhardt, Katrin; Chao, Moses V.; Neubert, Thomas A.

2011-01-01

97

Preferential isotopic labeling of lattice oxygen positions on the SnO 2(110) surface  

NASA Astrophysics Data System (ADS)

The stoichiometric SnO 2(110) surface exposes two crystallographically inequivalent forms of lattice oxygen. One form occupies top atomic layer bridging sites between sixfold-coordinated second-layer tin cations, and the second form occupies "in-plane" positions in the second atomic layer. The oxygen anions occupying the bridging positions are quite labile and can be removed by heating to ? 700 K in vacuum [D.F. Cox, T.B. Fryberger and S. Semancik, Phys. Rev. B 38 (1988) 2072]. Ion scattering spectroscopy has been used to demonstrate the feasibility of preferentially labeling the bridging positions ( > 70%) with 18O while maintaining a relatively small amount of isotopic scrambling (< 15%) in the second layer in-plane positions. This labeling procedure provides a means of studying the role of crystallographically inequivalent forms of lattice oxygen in the oxidation chemistry of tin oxide surfaces via thermal desorption spectroscopy.

Cox, David F.; Fryberger, Teresa B.

1990-03-01

98

Multiplexed analysis of cage and cage free chicken egg fatty acids using stable isotope labeling and mass spectrometry.  

PubMed

Binary stable isotope labeling couple with LC-ESI-MS has been used as a powerful non-targeted approach for the relative quantification of lipids, amino acids, and many other important metabolite classes. A multiplexed approach using three or more isotopic labeling reagents greatly reduces analytical run-time while maintaining excellent sensitivity and reproducibility. Three isotopic cholamine labeling reagents have been developed to take advantage of the pre-ionized character of cholamine, for ESI, and the ease by which stable isotopes can be incorporated into the cholamine structure. These three cholamine labeling reagents have been used to relatively quantify three fatty acid samples simultaneously. The quantification resulted in the observation of 12 fatty acids that had an average absolute error of 0.9% and an average coefficient of variation of 6.1%. Caged versus cage-free isotope labeling experiments showed that cage-free eggs have an increased level of omega-3 fatty acids as compared to caged eggs. This multiplexed fatty acid analysis provides an inexpensive and expedited tool for broad-based lipid profiling that will further aid discoveries in the mechanisms of fatty acid action in cells. PMID:24317525

Torde, Richard G; Therrien, Andrew J; Shortreed, Michael R; Smith, Lloyd M; Lamos, Shane M

2013-01-01

99

Stable Carbon Isotopes As Indicators of Plant Water Use Efficiency  

Microsoft Academic Search

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

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

2007-01-01

100

mzMatch–ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data  

PubMed Central

Motivation: Stable isotope-labelling experiments have recently gained increasing popularity in metabolomics studies, providing unique insights into the dynamics of metabolic fluxes, beyond the steady-state information gathered by routine mass spectrometry. However, most liquid chromatography–mass spectrometry data analysis software lacks features that enable automated annotation and relative quantification of labelled metabolite peaks. Here, we describe mzMatch–ISO, a new extension to the metabolomics analysis pipeline mzMatch.R. Results: Targeted and untargeted isotope profiling using mzMatch–ISO provides a convenient visual summary of the quality and quantity of labelling for every metabolite through four types of diagnostic plots that show (i) the chromatograms of the isotope peaks of each compound in each sample group; (ii) the ratio of mono-isotopic and labelled peaks indicating the fraction of labelling; (iii) the average peak area of mono-isotopic and labelled peaks in each sample group; and (iv) the trend in the relative amount of labelling in a predetermined isotopomer. To aid further statistical analyses, the values used for generating these plots are also provided as a tab-delimited file. We demonstrate the power and versatility of mzMatch–ISO by analysing a 13C-labelled metabolome dataset from trypanosomal parasites. Availability: mzMatch.R and mzMatch–ISO are available free of charge from http://mzmatch.sourceforge.net and can be used on Linux and Windows platforms running the latest version of R. Contact: rainer.breitling@manchester.ac.uk . Supplementary information: Supplementary data are available at Bioinformatics online PMID:23162054

Chokkathukalam, Achuthanunni; Jankevics, Andris; Creek, Darren J.; Achcar, Fiona; Barrett, Michael P.; Breitling, Rainer

2013-01-01

101

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

NASA Astrophysics Data System (ADS)

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

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

2010-12-01

102

Accurate quantitation of MHC-bound peptides by application of isotopically labeled peptide MHC complexes.  

PubMed

Knowledge of the accurate copy number of HLA class I presented ligands is important in fundamental and clinical immunology. Currently, the best copy number determinations are based on mass spectrometry, employing single reaction monitoring (SRM) in combination with a known amount of isotopically labeled peptide. The major drawback of this approach is that the losses during sample pretreatment, i.e. immunopurification and filtration steps, are not well defined and must, therefore, be estimated. In addition, such losses can vary for individual peptides. Therefore, we developed a new approach in which isotopically labeled peptide-MHC monomers (hpMHC) are prepared and added directly after cell lysis, i.e. before the usual sample processing. Using this approach, all losses during sample processing can be accounted for and allows accurate determination of specific MHC class I-presented ligands. Our study pinpoints the immunopurification step as the origin of the rather extreme losses during sample pretreatment and offers a solution to account for these losses. Obviously, this has important implications for accurate HLA-ligand quantitation. The strategy presented here can be used to obtain a reliable view of epitope copy number and thus allows improvement of vaccine design and strategies for immunotherapy. PMID:25050860

Hassan, Chopie; Kester, Michel G D; Oudgenoeg, Gideon; de Ru, Arnoud H; Janssen, George M C; Drijfhout, Jan W; Spaapen, Robbert M; Jiménez, Connie R; Heemskerk, Mirjam H M; Falkenburg, J H Frederik; van Veelen, Peter A

2014-09-23

103

Determination of protein conformation by isotopically labelled cross-linking and dedicated software  

NASA Astrophysics Data System (ADS)

Chemical cross-linking in conjunction with mass spectrometry (MS) can be used for sensitive and rapid investigation of the three-dimensional structure of proteins at low resolution. However, the resulting data are very complex, and on the bioinformatic side, there still exists an urgent need for improving computer software for (semi-) automated cross-linking data analysis. In this study, we have developed dedicated software for rapid and confident identification and validation of cross-linked species using an isotopic labelled cross-linker approach in combination with MS. Deuterated (+4 Da) and non-deuterated (+0 Da) bis(sulfosuccinimidyl)suberate, BS3, was used as homobifunctional cross-linker to tag the cross-linked regions. Peptides generated from proteolysis were separated using high performance liquid chromatography, and peptide mass fingerprinting was obtained for the individual fractions using matrix-assisted laser-desorption ionisation time-of-flight (MALDI TOF) MS. The resulting peptide mass lists were combined and transferred to the program, ProteinXXX, which generated the theoretical mass values of all combinations of cross-linked peptides and dead-end cross-links and compared this to the obtained mass lists. In addition, screening for 4 Da-separated signals aided the identification of potential cross-linked species. Sequence information of these candidates was then obtained using MALDI TOF TOF. The cross-linked peptides could then be validated based on the match of the fragmentation pattern and the theoretical values produced by ProteinXXX. This semi-automated interpretation provided a high analysis speed of cross-linking data, with efficient and confident identification of cross-linked species. Four experiments using different conditions showed a high degree of reproducibility as only 1 and 2 cross-links out of 36 identified was not observed in two experiments. The method was tested using human placenta calreticulin (CRT). Based on the identified cross-links, a few corrections to a model of calreticulin obtained by homology modelling using calnexin as template can be suggested. Furthermore, the cross-links show that the C-terminal of the protein continues along the core region opposite the P-domain for at least 11 residues beyond the known structure. In addition, it was observed that the conformation of CRT does not change significantly in the presence or absence of the divalent ions, Ca2+ and Zn2+.

Nielsen, Tina; Thaysen-Andersen, Morten; Larsen, Nanna; Jørgensen, Flemming S.; Houen, Gunnar; Højrup, Peter

2007-12-01

104

Isotope labeling studies on the electron impact mass spectral fragmentation patterns of chloropropanol acetates.  

PubMed

Chloropropanol (CP) esters are part of an emerging group of process-induced toxicants that are considered as potential health hazards particularly in palm oil. Mass spectrometry-based methodologies for identification of CP esters in food are critical in overcoming the challenges associated with direct detection methods. In the present study, a convenient strategy was employed to generate all possible CP acetates through reacting acetic anhydride with either glycerol in the presence of a chloride source or the corresponding CPs, such as 3-chloro-, 1,3-dichloro-, 2-chloro-, and 1,2-dichloropropanols, allowing for the identification of the individual CP acetates and assignment of their mass spectral fragmentations. Mass spectral fragmentations were confirmed through the use of the isotopic signature of chlorine in addition to the isotope labeling experiments performed using isotopically labeled precursors, such as [¹³C-U?] glycerol, [¹³C-U?] acetic anhydride, [¹³C-2,2'] acetic anhydride, and [d?] 3-monochloropropane-1,2-diol (3-MCPD) as reactants. Such studies have indicated that all CP esters can undergo two general fragmentations under electron impact (EI) conditions, one generating the acylium ion at m/z 45 and the other generating a chlorinated cyclic acyloxonium ion at m/z 135.6. Considering the fact that such ions can also be generated from any fatty acid containing CP esters after undergoing McLafferty rearrangement, the ion at m/z 135.6 can therefore be considered as a universal marker for the presence of CP esters undergoing EI fragmentation. Furthermore, these studies have also indicated the formation of ions characteristic of CP diesters, monoesters, and dichloro esters. PMID:23964824

Rahn, Anja K K; Yaylayan, Varoujan A

2013-09-18

105

Identification of Biologically-Produced Organic Matter in an Aquifer System using Stable Isotope Labeling  

NASA Astrophysics Data System (ADS)

The carbon cycle in aquifer systems is poorly understood. In particular, the role of prokaryotic and eukaryotic microbes in the cycling of organic matter (OM) has not been well documented. The goal of this work was to utilize stable isotopes in combination with geochemical and microbial methods to study microbially-mediated OM transformations in aquifers and aquifer sediments. A laboratory flow-through column experiment was conducted with sediment collected from a pristine, shallow, coastal plain aquifer. The groundwater medium was amended with low levels of an isotopically labeled nutrient, 13C-acetate. At pre-determined time points, organic matter (OM) was isolated from the sediment and groundwater. OM components were analyzed by isotope-ratio GC-MS and electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The incorporation of 13C was examined for both the aqueous phase and sediment bound OM. Analyzing both dissolved and adsorbed fractions enabled us to determine the relative importance of each on microbe-mediated OM transformations. The incorporation of 13C allowed us to estimate residence times of different organic matter fractions and to answer fundamental questions about organic matter lability in the subsurface environment.

Kujawinski, E. B.; Mailloux, B. J.; Morrison, L.

2004-12-01

106

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

NASA Astrophysics Data System (ADS)

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.

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

1999-01-01

107

Cost-effective production of 13C, 15N stable isotope-labelled biomass from phototrophic microalgae for various biotechnological applications.  

PubMed

The present study outlines a process for the cost-effective production of 13C/15N-labelled biomass of microalgae on a commercial scale. The core of the process is a bubble column photobioreactor with exhaust gas recirculation by means of a low-pressure compressor. To avoid accumulation of dissolved oxygen in the culture, the exhaust gas is bubbled through a sodium sulphite solution prior to its return to the reactor. The engineered system can be used for the production of 13C, 15N, and 13C-15N stable isotope-labelled biomass as required. To produce 13C-labelled biomass, 13CO2 is injected on demand for pH control and carbon supply, whereas for 15N-labelled biomass Na15NO3 is supplied as nitrogen source at the stochiometric concentration. The reactor is operated in semicontinuous mode at different biomass concentrations, yielding a maximum mean biomass productivity of 0.3 gL(-1) day(-1). In order to maximize the uptake efficiency of the labelled substrates, the inorganic carbon is recovered from the supernatant by acidification/desorption processes, while the nitrate is delivered at stochiometric concentration and the harvesting of biomass is performed when the 15NO3- is depleted. In these conditions, elemental analysis of both biomass and supernatant shows that 89.2% of the injected carbon is assimilated into the biomass and 6.9% remains in the supernatant. Based on elemental analysis, 97.8% of the supplied nitrogen is assimilated into the biomass and 1.3% remains in the supernatant. Stable isotope-labelling enrichment has been analysed by GC-MS results showing that the biomass is highly labelled. All the fatty acids are labelled; more than 96% of the carbon present in these fatty acids is 13C. The engineered system was stably operated for 3 months, producing over 160 g of 13C and/or 15N-labelled biomass. The engineered bioreactor can be applied for the labelling of various microalgae. PMID:16257578

Acién Fernández, F G; Fernández Sevilla, J M; Egorova-Zachernyuk, T A; Molina Grima, E

2005-12-01

108

Stable Carbon Isotopes As Indicators of Plant Water Use Efficiency  

NASA Astrophysics Data System (ADS)

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

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

2007-12-01

109

Labeling  

MedlinePLUS

... Vaccines, Blood & Biologics Animal & Veterinary Cosmetics Tobacco Products Cosmetics Print this page Share this page E-mail this page Home Cosmetics Labeling Labeling The following are resources on cosmetic ...

110

Convenient procedures for the biosynthesis, isolation, and isotope labeling of cytochalasins.  

PubMed Central

Efforts to improve small-scale yields of useful cytochalasins by fermentation resulted in selection of an enriched aflatoxin medium which increased yields by fivefold over those reported in the literature. With Helminthosporium dematoideum and Zygosporium masonii in stationary culture for 3 weeks, cytochalasins B and D were obtained in quantities approaching 700 and 500 mg/liter, respectively. It appears that the critical component in this growth medium is factors associated with whole wheat. By using these procedures, coupled with improvements in isolation, supplementation with two radioactive phenylalanine species readily produced [14C]- or [3H]cytochalasin B. Oxidation of carrier-free radioactive cytochalasin B to cytochasasin A readily provided this labeled congener as well. The isotopic ocnversion of precursor to crystalline products that met analytical criteria ranged from 2 to 4% of the administered radioactivity. PMID:571262

Zabel, R A; Miller, C A; Tanenbaum, S W

1979-01-01

111

Glycoproteomics of Trypanosoma cruzi trypomastigotes using subcellular fractionation, lectin affinity, and stable isotope labeling.  

PubMed

Herein we detail the first glycoproteomic analysis of a human pathogen. We describe an approach that enables the identification of organelle and cell surface N-linked glycoproteins from Trypanosoma cruzi, the causative agent of Chagas' disease. This approach is based on a subcellular fractionation protocol to produce fractions enriched in either organelle or plasma membrane/cytoplasmic proteins. Through lectin affinity capture of the glycopeptides from each subcellular fraction and stable isotope labeling of the glycan attachment sites with H(2)18O, we unambiguously identified 36 glycosylation sites on 35 glycopeptides which mapped to 29 glycoproteins. We also present the first expression evidence for 11 T. cruzi specific glycoproteins and provide experimental data indicating that the mucin associated surface protein family (MASP) and dispersed gene family (DGF-1) are post-translationally modified by N-linked glycans. PMID:17137339

Atwood, James A; Minning, Todd; Ludolf, Fernanda; Nuccio, Arthur; Weatherly, Daniel B; Alvarez-Manilla, Gerardo; Tarleton, Rick; Orlando, Ron

2006-12-01

112

Negative ion ESI-MS analysis of natural yellow dye flavonoids--An isotopic labelling study  

NASA Astrophysics Data System (ADS)

Flavonoids are amongst the most commonly used natural yellow colourants in paintings, as lakes, and in historical textiles as mordant dyes. In this paper, evidence from isotopically labelled substrates is used to propose negative ion electrospray collision induced decomposition mechanisms of flavones, flavonols and an isoflavone. These mechanisms include a retro-Diels-Alder fragmentation (observed for flavones and flavonols) and an M-122 fragmentation (characteristic of 3',4'-dihydroxyflavonols). In addition, the presence of a m/z 125 fragment ion is shown to be characteristic of 2'-hydroxyflavonols and an ion at m/z 149 is shown to be characteristic of 4'-hydroxyflavones. Applications of these methods are exemplified by the identification of a minor component of Dyer's camomile (Anthemis tinctoria L.) and the identification of the dye source in green threads sampled from an 18th Century Scottish tartan fragment.

McNab, Hamish; Ferreira, Ester S. B.; Hulme, Alison N.; Quye, Anita

2009-07-01

113

Facile preparation of deuterium-labeled N-acylhomoserine lactones as internal standards for isotope dilution mass spectrometry.  

PubMed

N-Acylhomoserine lactones (AHLs) are widely conserved signal molecules that mediate quorum sensing in Gram-negative bacteria. In this study, deuterium-labeled AHLs were prepared for use as internal standards for isotope dilution mass spectrometry. Their utility in the sensitive and precise quantification of AHLs in culture supernatants of bacteria by GC/MS was demonstrated. PMID:20471840

Kai, Kenji; Tani, Ayaka; Hayashi, Hideo

2010-06-01

114

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

NASA Astrophysics Data System (ADS)

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

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

2011-03-01

115

Carbon isotope labeling in boreal forests to assess roles of fungal species in decomposition  

NASA Astrophysics Data System (ADS)

We used 14C and 13C labeling to assess the in situ respiration of alanine-, starch-, and lignocellulose-derived carbon from the sporocarps of particular fungal species fruiting in a boreal forest in Alaska. By measuring isotopically-labeled respiration of sporocarps, which can be identified to species, we were able to attribute turnover of carbon compounds to specific fungal groups. Moreover, collection of sporocarp respiration is non-destructive, so we could return to the same sporocarps to collect a time series of measurements that spanned hours to days. We tested the hypotheses that alanine and starch turn over more quickly than lignocellulose, and that saprotrophic fungi would use starch-C and lignocellulose-C but ectomycorrhizal fungi would not. Small amounts of 14C-labeled alanine (about 100,000 permil) were dispensed into the soil within three meters of sporocarps of the ectomycorrhizal fungus Lactarius alnicola. ?14CO2 values of sporocarp respiration climbed from 75.8 +/- 6.3 permil to 7855 +/- 3940 permil within one hour of additions, indicating that the fungus quickly acquired, transported, and transformed the alanine-C. In a separate approach, a mixture of 13C-labeled starch (about 15,000 permil) and 14C-labeled lignocellulose (about 36,000 permil) was applied in 9 m2 plots containing sporocarps of the ectomycorrhizal genera Phellodon and Sarcodon and the saprotrophic genera Lycoperdon and Polyporus. An unlabeled control plot was also established. We observed no detectable increase in 14CO2 or 13CO2 over a 144 hour period, suggesting that neither ectomycorrhizal nor saprotrophic fungi significantly broke down starch or lignocellulose during this time. The alanine experiment is one of the first to indicate that ectomycorrhizal fungi can influence the spatial distribution and storage of soil carbon over short time scales. This influence may be restricted to carbon of organic compounds like amino acids. In contrast, starch was not transformed quickly even by saprotrophic fungi, which may be due to an absence or lack of activity of starch-degrading fungal species during the study period. Potential activity of the starch-metabolizing enzyme alpha-glucosidase was only 0.59 +/- 0.17 ìmol h-1 g dry soil-1, which was 7 times less than activity of beta-glucosidase, which breaks down cellulose. The slow turnover of lignocellulose-C was consistent with slow decomposition rates of plant litter in this biome.

Treseder, K. K.; Czimczik, C. I.; Trumbore, S. E.; Allison, S. D.

2006-12-01

116

A Method for Sporulating Budding Yeast Cells That Allows for Unbiased Identification of Kinase Substrates Using Stable Isotope Labeling by Amino Acids in Cell Culture  

PubMed Central

Quantitative proteomics has been widely used to elucidate many cellular processes. In particular, stable isotope labeling by amino acids in cell culture (SILAC) has been instrumental in improving the quality of data generated from quantitative high-throughput proteomic studies. SILAC uses the cell’s natural metabolic pathways to label proteins with isotopically heavy amino acids. Incorporation of these heavy amino acids effectively labels a cell’s proteome, allowing the comparison of cell cultures treated under different conditions. SILAC has been successfully applied to a variety of model organisms including yeast, fruit flies, plants, and mice to look for kinase substrates as well as protein–protein interactions. In budding yeast, several kinases are known to play critical roles in different aspects of meiosis. Therefore, the use of SILAC to identify potential kinase substrates would be helpful in the understanding the specific mechanisms by which these kinases act. Previously, it has not been possible to use SILAC to quantitatively study the phosphoproteome of meiotic Saccharomyces cerevisiae cells, because yeast cells sporulate inefficiently after pregrowth in standard synthetic medium. In this study we report the development of a synthetic, SILAC-compatible, pre-sporulation medium (RPS) that allows for efficient sporulation of S. cerevisiae SK1 diploids. Pre-growth in RPS supplemented with heavy amino acids efficiently labels the proteome, after which cells proceed relatively synchronously through meiosis, producing highly viable spores. As proof of principle, SILAC experiments were able to identify known targets of the meiosis-specific kinase Mek1. PMID:25168012

Suhandynata, Ray; Liang, Jason; Albuquerque, Claudio. P.; Zhou, Huilin; Hollingsworth, Nancy M.

2014-01-01

117

Efficient and Accurate Label Propagation on Large Graphs and Label Sets Michele Covell and Shumeet Baluja  

E-print Network

nodes, starting from partial information and a weighted- connection graph. In their work on video propagation across weighted graphs of nodes [1,2,3,4,5,6]. These applications share the characteristics of having a limited amount of label data, often of uneven quality, associated with a large graph of weighted

Tomkins, Andrew

118

An Isotope Release Cytotoxicity Assay Applicable to Human Tumors: the Use of 111Indium  

Microsoft Academic Search

We have demonstrated that human tumors can be labelled efficiently with the 111indium-oxine chelate. Subsequently, this isotope can be released by cytotoxic lymphoid cells. Both natural and induced cytotoxicity can be demonstrated utilizing this isotope release method. Because of the slow spontaneous release of 111indium and its efficient labelling of human tumor cells, this isotope release assay can be utilized

P. Frost; R. Wiltrout; Z. Maciorowski; N. R. Rose

1977-01-01

119

CTA coronary labeling through efficient geodesics between trees using anatomy priors.  

PubMed

We present an efficient realization of recent work on unique geodesic paths between tree shapes for the application of matching coronary arteries to a standard model of coronary anatomy in order to label the coronary arteries. Automatically labeled coronary arteries would speed reporting for physicians. The efficiency of the approach and the quality of the results are enhanced using the relative position of detected cardiac structures. We explain how to efficiently compute the geodesic paths between tree shapes using Dijkstra's algorithm and we present a methodology to account for missing side branches during matching. For nearly all labels our approach shows promise compared with recent work and we results for 8 additional labels. PMID:25485419

Gülsün, Mehmet A; Funka-Lea, Gareth; Zheng, Yefeng; Eckert, Matthias

2014-01-01

120

Labeled trees and the efficient computation of derivations  

NASA Technical Reports Server (NTRS)

The effective parallel symbolic computation of operators under composition is discussed. Examples include differential operators under composition and vector fields under the Lie bracket. Data structures consisting of formal linear combinations of rooted labeled trees are discussed. A multiplication on rooted labeled trees is defined, thereby making the set of these data structures into an associative algebra. An algebra homomorphism is defined from the original algebra of operators into this algebra of trees. An algebra homomorphism from the algebra of trees into the algebra of differential operators is then described. The cancellation which occurs when noncommuting operators are expressed in terms of commuting ones occurs naturally when the operators are represented using this data structure. This leads to an algorithm which, for operators which are derivations, speeds up the computation exponentially in the degree of the operator. It is shown that the algebra of trees leads naturally to a parallel version of the algorithm.

Grossman, Robert; Larson, Richard G.

1989-01-01

121

Imaging complex protein metabolism in live organisms by stimulated Raman scattering microscopy with isotope labeling.  

PubMed

Protein metabolism, consisting of both synthesis and degradation, is highly complex, playing an indispensable regulatory role throughout physiological and pathological processes. Over recent decades, extensive efforts, using approaches such as autoradiography, mass spectrometry, and fluorescence microscopy, have been devoted to the study of protein metabolism. However, noninvasive and global visualization of protein metabolism has proven to be highly challenging, especially in live systems. Recently, stimulated Raman scattering (SRS) microscopy coupled with metabolic labeling of deuterated amino acids (D-AAs) was demonstrated for use in imaging newly synthesized proteins in cultured cell lines. Herein, we significantly generalize this notion to develop a comprehensive labeling and imaging platform for live visualization of complex protein metabolism, including synthesis, degradation, and pulse-chase analysis of two temporally defined populations. First, the deuterium labeling efficiency was optimized, allowing time-lapse imaging of protein synthesis dynamics within individual live cells with high spatial-temporal resolution. Second, by tracking the methyl group (CH3) distribution attributed to pre-existing proteins, this platform also enables us to map protein degradation inside live cells. Third, using two subsets of structurally and spectroscopically distinct D-AAs, we achieved two-color pulse-chase imaging, as demonstrated by observing aggregate formation of mutant hungtingtin proteins. Finally, going beyond simple cell lines, we demonstrated the imaging ability of protein synthesis in brain tissues, zebrafish, and mice in vivo. Hence, the presented labeling and imaging platform would be a valuable tool to study complex protein metabolism with high sensitivity, resolution, and biocompatibility for a broad spectrum of systems ranging from cells to model animals and possibly to humans. PMID:25560305

Wei, Lu; Shen, Yihui; Xu, Fang; Hu, Fanghao; Harrington, Jamie K; Targoff, Kimara L; Min, Wei

2015-03-20

122

Efficient excitation of media for laser isotope separation  

SciTech Connect

A theoretical investigation is made of the photoionisation of a three-level medium intended for laser isotope separation. The results show that the highest ionisation efficiency can be achieved by dividing the process into two stages: coherent population inversion and photoionisation. A study is made of the possibility of inversion of three-level systems for various detunings of the laser frequencies from the radiative transition frequencies. It is shown that there are detunings for which the population of the third level is maximal for any a priori selected parameters of the medium and field. Such detunings lie near a two-photon resonance and depend on the energy density and duration of the laser pulses, and also on the dipole moments of the transitions. The suitability of this method in the case of inhomogeneously broadend optically dense media is considered. It is shown that the method is most efficient in the case of counterpropagating laser pulses. The efficiency of the method is demonstrated for ytterbium. 6 refs., 5 figs.

Borisov, S.K.; Kuz`mina, M.A.; Mishin, V.A.

1995-07-01

123

Development of a New Extended Motor Product Label for Industrial Energy Efficiency  

E-print Network

Development of a New Extended Motor Product Label for Industrial Energy Efficiency Ethan A. Rogers, Senior Program Manager, Industry Robert Boteler, Visiting Fellow R. Neal Elliott, Associate Director for Research 2014 Industrial Energy Technology... transformation • Extended Motor Product Label Initiative • Who, what, when, and why • Goals and progress to date ESL-IE-14-05-11 Proceedings of the Thrity-Sixth Industrial Energy Technology Conference New Orleans, LA. May 20-23, 2014 Typology of IEEPs Program...

Rogers, E.; Boteler, R.; Elliot, R. N.

2014-01-01

124

Measuring supply chain carbon efficiency : a carbon label framework  

E-print Network

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

Craig, Anthony (Anthony J.)

2012-01-01

125

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

NASA Astrophysics Data System (ADS)

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

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

2014-06-01

126

Investigation of bn-44 peptide fragments using high resolution mass spectrometry and isotope labeling.  

PubMed

An N-terminal deuterohemin-containing hexapeptide (DhHP-6) was designed as a short peptide cytochrome c (Cyt c) mimetic to study the effect of N-terminal charge on peptide fragmentation pathways. This peptide gave different dissociation patterns than normal tryptic peptides. Upon collision-induced dissociation (CID) with an ion trap mass spectrometer, the singly charged peptide ion containing no added proton generated abundant and characteristic bn-44 ions instead of bn-28 (an) ions. Studies by high resolution mass spectrometry (HRMS) and isotope labeling indicate that elimination of 44 Da fragments from b ions occurs via two different pathways: (1) loss of CH3CHO (44.0262) from a Thr side chain; (2) loss of CO2 (43.9898) from the oxazolone structure in the C-terminus. A series of analogues were designed and analyzed. The experimental results combined with Density Functional Theory (DFT) calculations on the proton affinity of the deuteroporphyrin demonstrate that the production of these novel bn-44 ions is related to the N-terminal charge via a charge-remote rather than radical-directed fragmentation pathway. PMID:25280401

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

2014-12-01

127

Isotope Coded Protein Labeling analysis of plasma specimens from acute severe dengue fever patients  

PubMed Central

Background Dengue fever is the most important arthropod born viral disease of public health significance. Although most patients suffer only from flu-like symptoms, a small group of patient experiences more severe forms of the disease. To contribute to a better understanding of its pathogenesis this study aims to identify proteins differentially expressed in a pool of five viremic plasma from severe dengue patients relative to a pool of five non-severe dengue patients. Results The use of Isotope Coded Protein Labeling (ICPLTM) to analyze plasma depleted of twenty high-abundance proteins allowed for the identification of 51 differentially expressed proteins, which were characterized by mass spectrometry. Using quantitative ELISA, three of these proteins (Leucine-rich glycoprotein 1, Vitamin D binding-protein and Ferritin) were confirmed as having an increased expression in a panel of severe dengue plasma. The proteins identified as overexpressed by ICPLTM in severe dengue plasma involve in clear up action after cell injury, tissue coherence and immune defense. Conclusion This ICPLTM study evaluating differences between acute severe dengue plasmas and acute non-severe dengue plasmas suggests that the three proteins identified are overexpressed early in the course of the disease. Their possible use as biomarkers for the prognostic of disease severity is discussed. PMID:23101585

2012-01-01

128

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

NASA Technical Reports Server (NTRS)

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

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

2004-01-01

129

Tracking down sulphate-reducing microorganisms by molecular and isotope-labelling techniques  

NASA Astrophysics Data System (ADS)

Sulphate-reducing microorganisms (SRM) are of great ecological importance for carbon compound degradation and sulphur cycling in many anoxic ecosystems, including marine sediments, peatlands, and oil reservoirs. However, the activity of SRM can result in oil souring and pipeline corrosion and thus is also an economic burden for the oil industry. Molecular diversity surveys based on rRNA genes and dsrAB, genes that encode major subunits of the dissimilatory sulfite reductase, indicate that our view of the natural diversity of SRM (as we know it from cultivation) is far from being complete. This enormous phylogenetic diversity complicates unbiased identification and quantification of SRM by molecular methods such as fluorescence in situ hybridization, real-time PCR or DNA microarrays. Combining these 16S rRNA and dsrAB-based molecular methods with substrate-mediated isotope labelling techniques is a potential solution for identification and functional characterization of yet uncultivated SRM. Using SRM in peatlands as an example, the problems and opportunities of these techniques for diagnosing and monitoring SRM in the environment will be discussed in this talk.

Loy, Alexander

2010-05-01

130

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

131

Evaluation of isotopically labeled internal standards and methods of derivatization for quantitative determination of cocaine and related compounds  

Microsoft Academic Search

Gas chromatography-mass spectrometry (GCMS) is the preferred method for the analysis of drugs\\/metabolites in biological specimens\\u000a with use of isotopically labeled analogs of the analytes as internal standards (ISs). An important aspect of the chemical\\u000a derivatization (CD) for GC-MS analysis is that the CD products derived from the analyte and the selected IS must generate\\u000a ions suitable for designating the

Sheng-Meng Wang; Meng-Yen Wu; Ray H. Liu; Russell J. Lewis; Dennis V. Canfield

2006-01-01

132

Systematic studies on the determination of Hg-labelled proteins using laser ablation-ICPMS and isotope dilution analysis.  

PubMed

A method was developed for the precise and accurate determination of ovalbumin labelled with p-hydroxy-mercuribenzoic acid (pHMB) using polyacrylamide gel electrophoresis with ns-laser ablation-inductively coupled plasma mass spectrometry. Following systematic optimisation of the ablation process in terms of detection sensitivity, two different quantification strategies were applied: external calibration using standards of the derivatized protein after (13)C(+) normalization and, as a proof of concept, label-specific isotope dilution analysis (IDA) using pHMB enriched in the isotope (199)Hg. Due to the inhomogeneous distribution of the protein within the gel bands, it could be demonstrated that the IDA approach was superior in terms of precision and accuracy. Furthermore, it permits a reliable quantification, if more complex separation protocols are applied, as typically occurring analyte loss and degradation can be compensated for as soon as complete mixture of spike and sample is achieved. The estimated limit of detection was 160 fmol in the case of ovalbumin. In contrast to earlier studies using metals naturally present in proteins, no loss of mercury was observed during separation under denaturing conditions and other sample preparation steps. Using label-specific IDA, the measured isotope ratios in the gel corresponded to recoveries between 95% and 103%. PMID:21773737

Kutscher, Daniel J; Fricker, Mattias B; Hattendorf, Bodo; Bettmer, Jörg; Günther, Detlef

2011-11-01

133

Stable isotope labeling tandem mass spectrometry (SILT): Integration with peptide identification and extension to data-dependent scans  

PubMed Central

Quantitation of relative or absolute amounts of proteins by mass spectrometry can be prone to large errors. The use of MS/MS ion intensities and stable isotope labeling, which we term stable isotope labeling tandem mass spectrometry (SILT), decreases the effects of contamination from unrelated compounds. We present a software package (SILTmass) that automates protein identification and quantification by the SILT method. SILTmass has the ability to analyze the kinetics of protein turnover, in addition to relative and absolute protein quantitation. Instead of extracting chromatograms to find elution peaks, SILTmass uses only scans in which a peptide is identified and that meet an ion intensity threshold. Using only scans with identified peptides, the accuracy and precision of SILT is shown to be superior to precursor ion intensities, particularly at high or low dilutions of the isotope labeled compounds or with low amounts of protein. Using example scans, we demonstrate likely reasons for the improvements in quantitation by SILT. The appropriate use of variable modifications in peptide identification is described for measurement of protein turnover kinetics. The combination of identification with SILT facilitates quantitation without peak detection and helps to ensure the appropriate use of variable modifications for kinetics experiments. PMID:18774841

Elbert, Donald L.; Mawuenyega, Kwasi G.; Scott, Evan A.; Wildsmith, Kristin R.; Bateman, Randall J.

2009-01-01

134

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

PubMed Central

Background In the context of a Sterile Insect Technique programme, the occurrence of multiple insemination in the malaria mosquito Anopheles arabiensis Patton was studied using a novel labelling system with the stable isotopes 15N and 13C. The incidence of multiple insemination in the absence of radiation, and when males were irradiated in the pupal stage and competed against un-irradiated males were assessed. Males used in the experiments were labelled with either 15N or 13C and the label was applied to the larval rearing water. Males with either label and virgin females were caged at a 1:1:1 ratio. Males used in the radiation treatments were irradiated in the pupal stage with a partially or fully-sterilizing dose of 70 or 120 Gy, respectively. After mating, females were dissected and inseminated spermathecae analysed using mass spectrometry. Results The data indicate that about 25% of inseminated females had been inseminated multiply. The presence of irradiated males in the experiments did not affect the incidence of multiple insemination. In line with previous research, irradiated males were generally less competitive than un-irradiated males. Conclusion The implications of these findings for the Sterile Insect Technique are discussed, and further experiments recommended. The dual-labelling system used to determine paternity gave good results for 13C, however, for 15N it is recommended to increase the amount of label in future studies. PMID:18402666

Helinski, Michelle EH; Hood, Rebecca C; Knols, Bart GJ

2008-01-01

135

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

PubMed Central

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

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

2015-01-01

136

An efficient technique for primer development and application that integrates fluorescent labeling and multiplex PCR1  

PubMed Central

• Premise of the study: Development of genetic markers can be costly and time-consuming, especially when multiple primer pairs are fluorescently labeled. This step was streamlined by combining two techniques in the same PCR reaction: (1) custom-labeling of primers by the investigator and (2) multiplexing multiple primers together in the same reaction. • Methods and Results: This technique was successfully used to develop microsatellite markers in several plant species. Microsatellites amplified with this multiplexing process were identical to those generated from PCR using individual primer pairs and with traditional methods using a priori labeled fluorescent primers. Tests of PCR cycling programs revealed that conditions recommended for the commercial kit generated stronger fragment peaks than the previously recommended cycling protocol. • Conclusions: This technique is an efficient and economical way to fluorescently label multiple microsatellite primers in the same reaction. It is also applicable to other markers used in PCR amplification of genetic material. PMID:25202486

Culley, Theresa M.; Stamper, Trevor I.; Stokes, Richard L.; Brzyski, Jessica R.; Hardiman, Nicole A.; Klooster, Matthew R.; Merritt, Benjamin J.

2013-01-01

137

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

SciTech Connect

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

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

2002-05-16

138

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

PubMed Central

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

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

2013-01-01

139

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

PubMed

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

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

2013-01-01

140

In Vivo Calibration of Microdialysis Using Infusion of Stable-Isotope Labeled Neurotransmitters  

PubMed Central

In vivo calibration of microdialysis probes is required for interpreting measured concentrations. The most popular method of in vivo calibration is no-net-flux (NNF), which requires infusing several concentrations of neurotransmitters to determine in vivo recoveries (extraction fraction or Ed) and extracellular concentrations. A new method for in vivo calibration of microdialysis of neurotransmitters using glutamate (GLU) and dopamine (DA) as model analytes is reported. 13C6-DA and 13C5-GLU were perfused through microdialysis probes as internal calibrators. Using liquid chromatography with mass spectrometry, it was possible to distinguish the 13C-forms from the endogenous forms of each neurotransmitter. Ed was directly calculated by measuring the loss of the 13C-forms during infusion. The measured endogenous 12C forms of the neurotransmitters could be corrected for Ed to give calibrated extracellular concentrations in vivo. Retrodialysis of stable-isotope-labeled (SIL) neurotransmitters gave Ed and extracellular concentrations of 13C5-GLU and 13C6-DA that matched no-net-flux measurements; however, the values were obtained in a fraction of time because no added measurements were required to obtain the calibration. Ed was reduced during uptake inhibition for GLU and DA when measured by SIL retrodialysis. Because Ed is directly measured at each microdialysis fraction, it was possible to monitor changes in Ed under transient conditions created by systemic injection of uptake inhibitors. The results show that DA and GLU concentrations are underestimated by as much as 50% if not corrected for Ed during uptake inhibition. SIL retrodialysis provides equivalent information to NNF at much reduced time and animal use. PMID:23374073

2013-01-01

141

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

PubMed Central

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

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

2011-01-01

142

Latest developments in sample treatment for 18O-isotopic labeling for proteomics mass spectrometry-based approaches: A critical review  

Microsoft Academic Search

Nowadays isotopic 18O-labeling of peptides has recalled the attention of researchers due to its simplicity of application and high versatility for proteomics studies. Protein quantification, differential peptide mass mapping, studies regarding proteins overexpressed or underexpressed, or the searching of biomarkers can be accomplished by using 18O-labeling. In this critical review we comment on the different ways in which 18O-labeling can

J. L. Capelo; R. J. Carreira; L. Fernandes; C. Lodeiro; H. M. Santos; J. Simal-Gandara

2010-01-01

143

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

SciTech Connect

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

McMahon, James E.; Wiel, Stephen

2001-02-16

144

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

PubMed Central

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

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

2015-01-01

145

Stable isotopic labelling-assisted untargeted metabolic profiling reveals novel conjugates of the mycotoxin deoxynivalenol in wheat.  

PubMed

An untargeted screening strategy for the detection of biotransformation products of xenobiotics using stable isotopic labelling (SIL) and liquid chromatography-high resolution mass spectrometry (LC-HRMS) is reported. The organism of interest is treated with a mixture of labelled and non-labelled precursor and samples are analysed by LC-HRMS. Raw data are processed with the recently developed MetExtract software for the automated extraction of corresponding peak pairs. The SIL-assisted approach is exemplified by the metabolisation of the Fusarium mycotoxin deoxynivalenol (DON) in planta. Flowering ears were inoculated with 100 ?g of a 1 + 1 (v/v) mixture of non-labelled and fully labelled DON. Subsequent sample preparation, LC-HRMS measurements and data processing revealed a total of 57 corresponding peak pairs, which originated from ten metabolites. Besides the known DON and DON-3-glucoside, which were confirmed by measurement of authentic standards, eight further DON-biotransformation products were found by the untargeted screening approach. Based on a mass deviation of less than ±5 ppm and MS/MS measurements, one of these products was annotated as DON-glutathione (GSH) conjugate, which is described here for the first time for wheat. Our data further suggest that two DON-GSH-related metabolites, the processing products DON-S-cysteine and DON-S-cysteinyl-glycine and five unknown DON conjugates were formed in planta. Future MS/MS measurements shall reveal the molecular structures of the detected conjugates in more detail. PMID:23086087

Kluger, Bernhard; Bueschl, Christoph; Lemmens, Marc; Berthiller, Franz; Häubl, Georg; Jaunecker, Günther; Adam, Gerhard; Krska, Rudolf; Schuhmacher, Rainer

2013-06-01

146

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

SciTech Connect

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

Mark E. Fuller; Tullis C. Onstott

2003-12-17

147

Integration of High Accuracy N-Terminus Identification in Peptide Sequencing and Comparative Protein Analysis Via Isothiocyanate-Based Isotope Labeling Reagent with ESI Ion-trap TOF MS  

NASA Astrophysics Data System (ADS)

A multifunctional isothiocyanate-based isotope labeling reagent, [ d 0]-/[ d 6]-4,6-dimethoxy pyrimidine-2-isothiocyanate (DMPITC), has been developed for accurate N-terminus identification in peptide sequencing and comparative protein analysis by ESI Ion-trap TOF mass spectrometry. In contrast with the conventional labeling reagent phenyl isothiocyanate (PITC), DMPITC showed more desirable properties such as rapid labeling, sensitivity enhancement, and facilitating peptide sequencing. More significantly, DMPITC-based labeling strategy possessed the capacity of higher reliable N-terminus identification owning to the high-yield b1 ion combined with the isotope validation of 6 Da. Meanwhile, it also showed potential in differentiating isomeric residues of leucine and isoleucine at N-terminus on the basis of the relative abundance ratios between the fragment ions of their respective b1 ions. The strategy not only allows accurate interpretation for peptide but also ensures rapid and sensitive comparative analysis for protein by direct MS analysis. Using trypsin-digested bovine serum albumin (BSA), both peptide N-terminus identification and quantitative analysis were accomplished with high accuracy, efficiency, and reproducibility. The application of DMPITC-based labeling strategy is expected to serve as a promising tool for proteome research.

Leng, Jiapeng; Wang, Haoyang; Zhang, Li; Zhang, Jing; Wang, Hang; Cai, Tingting; Yao, Jinting; Guo, Yinlong

2011-07-01

148

Fast and Balanced: Efficient Label Tree Learning for Large Scale Object Recognition  

E-print Network

Fast and Balanced: Efficient Label Tree Learning for Large Scale Object Recognition Jia Deng1 balanced trees. Experiments are performed on large scale image classification with 10184 classes and 9,2 , Sanjeev Satheesh1 , Alexander C. Berg3 , Li Fei-Fei1 Computer Science Department, Stanford University1

Li, Fei-Fei

149

Human serum albumin coated iron oxide nanoparticles for efficient cell labeling†  

PubMed Central

A novel dopamine-plus-HSA (human serum albumin) approach was developed to functionalize iron oxide nanoparticles (IONPs), yielding nanoconjugates that are highly efficient in labeling various types of cell lines, which was demonstrated by in vivo MR imaging on xenograft and focal cerebral ischemia models. PMID:20066316

Xie, Jin; Wang, Jinhua; Niu, Gang; Huang, Jing; Chen, Kai; Li, Xingguo

2013-01-01

150

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

PubMed Central

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

Schwender, Jörg; Ohlrogge, John B.

2002-01-01

151

Status of China's Energy Efficiency Standards and Labels for Appliances and International Collaboration  

SciTech Connect

China first adopted minimum energy performance standards (MEPS) in 1989. Today, there are standards for a wide range of domestic, commercial and selected industrial equipment. In 1999, China launched a voluntary endorsement label, which has grown to cover over 40 products including water-saving products (See Figure 1). Further, in 2005, China started a mandatory energy information label (also referred to as the 'Energy Label'). Today, the Energy Label is applied to four products including: air conditioners; household refrigerators; clothes washers; and unitary air conditioners (See Figure 2). MEPS and the voluntary endorsement labeling specifications have been updated and revised in order to reflect technology improvements to those products in the market. These programs have had an important impact in reducing energy consumption of appliances in China. Indeed, China has built up a strong infrastructure to develop and implement product standards. Historically, however, the government's primary focus has been on the technical requirements for efficiency performance. Less attention has been paid to monitoring and enforcement with a minimal commitment of resources and little expansion of administrative capacity in this area. Thus, market compliance with both mandatory standards and labeling programs has been questionable and actual energy savings may have been undermined as a result. The establishment of a regularized monitoring system for tracking compliance with the mandatory standard and energy information label in China is a major area for program improvement. Over the years, the Collaborative Labeling and Appliance Standards Program (CLASP) has partnered with several Chinese institutions to promote energy-efficient products in China. CLASP, together with its implementing partner Lawrence Berkeley National Laboratory (LBNL), has assisted China in developing and updating the above-mentioned standards and labeling programs. Because of the increasing need for the development of a monitoring system to track compliance with standards and labeling, CLASP, with support from Japan's Ministry of Economy, Trade and Industry (METI), has expanded its ongoing collaboration with the China National Institute of Standards (CNIS) to include enforcement and monitoring. CNIS has already begun working on the issue of compliance. CNIS has conducted modest sample testing in 2006 for refrigerators, freezers and room air-conditioners, and repeated the same task in 2007 with a similar sample size for three products (refrigerators, freezers, air-conditioners and clothes washers). And, CNIS, with technical support from LBNL, has analyzed the data collected through testing. At the same time, parallel effort has also been paid to look at the potential impact of the label to 2020. In conjunction with CNIS, CLASP technical experts reviewed the standards development timeline of the four products currently subject to the mandatory energy information label. CLASP, with the support of METI/IEEJ, collaborated with CNIS to develop the efficiency grades, providing: technical input to the process; comment and advice on particular technical issues; as well as evaluation of the results. In addition, in order to effectively evaluate the impact of the label on China's market, CLASP further provided assistance to CNIS to collect data on both the efficiency distribution and product volume distribution of refrigerators on the market. This short report summarizes the status of Standards and Labeling program, current enforcement and monitoring mechanism in China, and states the importance of international collaborations.

Zhou, Nan

2008-03-01

152

Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT): A Novel Glycan-Relative Quantification Strategy  

NASA Astrophysics Data System (ADS)

The Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT) strategy for the sample preparation, data analysis, and relative quantification of N-linked glycans is presented. Glycans are derivatized with either natural (L) or stable-isotope labeled (H) hydrazide reagents and analyzed using reversed phase liquid chromatography coupled online to a Q Exactive mass spectrometer. A simple glycan ladder, maltodextrin, is first used to demonstrate the relative quantification strategy in samples with negligible analytical and biological variability. It is shown that after a molecular weight correction attributable to isotopic overlap and a post-acquisition normalization of the data to account for any systematic bias, a plot of the experimental H:L ratio versus the calculated H:L ratio exhibits a correlation of unity for maltodextrin samples mixed in different ratios. We also demonstrate that the INLIGHT approach can quantify species over four orders of magnitude in ion abundance. The INLIGHT strategy is further demonstrated in pooled human plasma, where it is shown that the post-acquisition normalization is more effective than using a single spiked-in internal standard. Finally, changes in glycosylation are able to be detected in complex biological matrices, when spiked with a glycoprotein. The ability to spike in a glycoprotein and detect change at the glycan level validates both the sample preparation and data analysis strategy, making INLIGHT an invaluable relative quantification strategy for the field of glycomics.

Walker, S. Hunter; Taylor, Amber D.; Muddiman, David C.

2013-09-01

153

Cadmium absorption in women fed processed edible sunflower kernels labeled with a stable isotope of cadmium, (113)Cd.  

PubMed

The apparent fractional absorption of cadmium (Cd) from sunflower kernels (SFK) was determined in women volunteers by using kernels labeled with a stable isotope of Cd ((113)Cd) by injecting it into the flowering head. Fourteen women who were between the ages of 30 and 70 years, who did not use tobacco products, who were in good health, and who had been consuming a self-selected diet low in Cd content participated in the study. The volunteers were fed a breakfast composed primarily of cereal, milk, and fruit juice. The breakfast also contained a portion of (113)Cd-labeled SFK processed into a buttery spread. Each volunteer collected individual stool samples for 21 days beginning immediately after they had consumed the labeled kernels. The total amounts of Cd and (113)Cd excreted in each stool were determined by isotope dilution inductively coupled plasma mass spectrometry. Mean fecal Cd excretion was 14.1+/-4.1 microg/day and mean (113)Cd absorption was 10.6+/-4.4%. In agreement with previous studies, no significant (P>0.3) correlation between Cd absorption and serum ferritin concentrations was found in women whose serum ferritin concentrations were >25 ng/mL. These data suggest that the availability of Cd from highly processed sunflower kernels to humans is similar to that reported for other types of food. PMID:11683590

Vanderpool, R A; Reeves, P G

2001-10-01

154

CK-LPA: Efficient community detection algorithm based on label propagation with community kernel  

NASA Astrophysics Data System (ADS)

With the rapid development of Web 2.0 and the rise of online social networks, finding community structures from user data has become a hot topic in network analysis. Although research achievements are numerous at present, most of these achievements cannot be adopted in large-scale social networks because of heavy computation. Previous studies have shown that label propagation is an efficient means to detect communities in social networks and is easy to implement; however, some drawbacks, such as low accuracy, high randomness, and the formation of a “monster” community, have been found. In this study, we propose an efficient community detection method based on the label propagation algorithm (LPA) with community kernel (CK-LPA). We assign a corresponding weight to each node according to node importance in the whole network and update node labels in sequence based on weight. Then, we discuss the composition of weights, the label updating strategy, the label propagation strategy, and the convergence conditions. Compared with the primitive LPA, existing drawbacks are solved by CK-LPA. Experiments and benchmarks reveal that our proposed method sustains nearly linear time complexity and exhibits significant improvements in the quality aspect of static community detection. Hence, the algorithm can be applied in large-scale social networks.

Lin, Zhen; Zheng, Xiaolin; Xin, Nan; Chen, Deren

2014-12-01

155

Phosphorus use efficiency by cotton measured through 32P isotope technique  

NASA Astrophysics Data System (ADS)

Deficiency of phosphorus (P) is the major limitation to agricultural production in the Brazilian Savannah (Cerrado), which is naturally poor in this nutrient. Most of the P applied by fertilizer in Cerrado soils are converted into low solubility forms and can not be easily absorbed by plants. This occurs for characteristics of adsorption, conditioned by the predominance of low pH and aluminum and iron oxides in the clay fraction. The development of genotypes and cultivars with greater capacity to grow up in soils with low P availability ('phosphorus efficiency') is interesting to improve the agriculture in these areas in a sustainable way. Cotton (Gossypium spp.) is the main product for the fibers used nationally and globally in the textile chain. This study aim was to evaluate the efficiency of absorption and utilization of P by cotton cultivars/genotypes grown in Cerrado soil by the isotopic dilution technique. The soil classified as Ultisols, was labeled with the radioisotope 32P.The experiment was conducted in a greenhouse in a completely randomized design factorial 2 x 17. Factors were considered two levels of P (insufficient = 20 mg kg-1 and sufficient = 120 mg kg-1) and 17 genetic materials of cotton recommended for Cerrado region. Phosphorus levels influenced significantly the shoots dry matter production, the P content and accumulation, the 32P specific activity, the L value and L value less seed cotton P by cultivars and genotypes. The hierarchical clustering analysis used to verify the similarities between the cultivars and genotypes of cotton, classified them into internally homogeneous groups and heterogeneous between different groups. Cultivars FMT 523, FM 910 and CNPA GO 2043 were the most responsive to phosphate fertilizer in sufficient level of P, while the genotype Barbadense 01 and cultivars FM 966LL, IPR Jataí, BRS Aroeira and BRS Buriti were most efficient absorbing P in soils with insufficient level.

Marcante, N. C.; Muraoka, T.; Camacho, M. A.; César, F. R. C. F.; Bruno, I. P.

2012-04-01

156

Efficient isotope separation by single-photon atomic sorting  

SciTech Connect

We propose a general and scalable approach to isotope separation. The method is based on an irreversible change of the mass-to-magnetic moment ratio of a particular isotope in an atomic beam, followed by a magnetic multipole whose gradients deflect and guide the atoms. The underlying mechanism is a reduction of the entropy of the beam by the information of a single scattered photon for each atom that is separated. We numerically simulate isotope separation for a range of examples, which demonstrate this technique's general applicability to almost the entire periodic table. The practical importance of the proposed method is that large-scale isotope separation should be possible, using ordinary inexpensive magnets and the existing technologies of supersonic beams and lasers.

Jerkins, M.; Chavez, I.; Raizen, M. G. [Center for Nonlinear Dynamics and Department of Physics, University of Texas at Austin, Austin, Texas 78712 (United States); Even, U. [Sackler School of Chemistry, Tel-Aviv University, Tel-Aviv (Israel)

2010-09-15

157

Biosynthesis of 15N3-labeled enniatins and beauvericin and their application to stable isotope dilution assays.  

PubMed

The first stable isotope dilution assay for the determination of enniatins A, A1, B, and B1 and beauvericin was developed. The (15)N(3)-labeled enniatins and beauvericin were biosynthesized by feeding two Fusarium strains Na(15)NO(3) and subsequently isolated from the fungal culture. The chemical structures of the biosynthesized products were characterized by LC-MS/MS and (1)H NMR. Standard solutions of (15)N(3)-labeled beauvericin, enniatin A, and enniatin A1 were accurately quantitated by quantitative NMR. On the basis of the use of the labeled products as internal standards, stable isotope dilution assays were developed and applied to various food samples using LC-MS/MS. The sample extracts were directly injected without any tedious cleanup procedures. The limits of detection were 3.9, 2.6, 3.7, 1.9, and 4.4 ?g/kg for enniatins A, A1, B, and B1 and beauvericin, respectively. Limits of quantitation were 11.5 (enniatin A), 7.6 (enniatin A1), 10.9 (enniatin B), 5.8 (enniatin B1), and 13.1 ?g/kg (beauvericin). Recoveries were within the range between 90 and 120%, and good intraday and interday precisions with coefficients of variation between 1.35 and 8.61% were obtained. Thus, the stable isotope dilution assay presented here is similarly sensitive and precise but more accurate than assays reported before. Analyses of cereals and cereal products revealed frequent contaminations of barley, wheat, rye, and oats with enniatins B and B1, whereas beauvericin was not quantifiable. PMID:22734473

Hu, Ling; Rychlik, Michael

2012-07-25

158

An isotope-coded fluorogenic cross-linker for high-performance target identification based on photoaffinity labeling.  

PubMed

A photoaffinity labeling (PAL)-based method for the rapid identification of target proteins is presented in which a high-performance chemical tag, an isotope-coded fluorescent tag (IsoFT), can be attached to the interacting site by irradiation. Labeled peptides can be easily distinguished among numerous proteolytic digests by sequential detection with highly sensitive fluorescence spectroscopy and mass spectrometry. Subsequent MS/MS analysis provides amino acid sequence information with a higher depth of coverage. The combination of PAL and heterogeneous target-selecting techniques significantly reduces the amount of time and protein required for identification. An additional photocleavable moiety successfully accelerated proteomic analysis using cell lysate. This method is a widely applicable approach for the rapid and accurate identification of interacting proteins. PMID:25382598

Tomohiro, Takenori; Morimoto, Shota; Shima, Toshiya; Chiba, Junya; Hatanaka, Yasumaru

2014-12-01

159

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

EPA Science Inventory

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

160

Innovative method for carbon dioxide determination in human postmortem cardiac gas samples using headspace-gas chromatography-mass spectrometry and stable labeled isotope as internal standard.  

PubMed

A novel approach to measure carbon dioxide (CO2) in gaseous samples, based on a precise and accurate quantification by (13)CO2 internal standard generated in situ is presented. The main goal of this study was to provide an innovative headspace-gas chromatography-mass spectrometry (HS-GC-MS) method applicable in the routine determination of CO2. The main drawback of the GC methods discussed in the literature for CO2 measurement is the lack of a specific internal standard necessary to perform quantification. CO2 measurement is still quantified by external calibration without taking into account analytical problems which can often occur considering gaseous samples. To avoid the manipulation of a stable isotope-labeled gas, we have chosen to generate in situ an internal labeled standard gas ((13)CO2) on the basis of the stoichiometric formation of CO2 by the reaction of hydrochloric acid (HCl) with sodium hydrogen carbonate (NaH(13)CO3). This method allows a precise measurement of CO2 concentration and was validated on various human postmortem gas samples in order to study its efficiency. PMID:23746406

Varlet, V; Smith, F; de Froidmont, S; Dominguez, A; Rinaldi, A; Augsburger, M; Mangin, P; Grabherr, S

2013-06-19

161

Status of the Local Enforcement of Energy Efficiency Standards and Labeling Program in China  

SciTech Connect

As part of its commitment to promoting and improving the local enforcement of appliance energy efficiency standards and labeling, the China National Institute of Standardization (CNIS) launched the National and Local Enforcement of Energy Efficiency Standards and Labeling project on August 14, 2009. The project’s short-term goal is to expand the effort to improve enforcement of standards and labeling requirements to the entire country within three years, with a long-term goal of perfecting overall enforcement. For this project, Jiangsu, Shandong, Sichuan and Shanghai were selected as pilot locations. This report provides information on the local enforcement project’s recent background, activities and results as well as comparison to previous rounds of check-testing in 2006 and 2007. In addition, the report also offers evaluation on the achievement and weaknesses in the local enforcement scheme and recommendations. The results demonstrate both improvement and some backsliding. Enforcement schemes are in place in all target cities and applicable national standards and regulations were followed as the basis for local check testing. Check testing results show in general high labeling compliance across regions with 100% compliance for five products, including full compliance for all three products tested in Jiangsu province and two out of three products tested in Shandong province. Program results also identified key weaknesses in labeling compliance in Sichuan as well as in the efficiency standards compliance levels for small and medium three-phase asynchronous motors and self-ballasted fluorescent lamps. For example, compliance for the same product ranged from as low as 40% to 100% with mixed results for products that had been tested in previous rounds. For refrigerators, in particular, the efficiency standards compliance rate exhibited a wider range of 50% to 100%, and the average rate across all tested models also dropped from 96% in 2007 to 63%, possibly due to the implementation of newly strengthened efficiency standards in 2009. Areas for improvement include: Greater awareness at the local level to ensure that all manufacturers register their products with the label certification project and to minimize their resistance to inspections; improvement of the product sampling methodology to include representative testing of both large and small manufacturers and greater standardization of testing tools and procedures; and continued improvement in local enforcement efforts.

Zhou, Nan; Zheng, Nina; Fino-Chen, Cecilia; Fridley, David; Ning, Cao

2011-09-26

162

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

PubMed

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

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

2014-12-01

163

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

PubMed Central

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

2014-01-01

164

Research recommendations for applying vitamin A-labelled isotope dilution techniques to improve human vitamin A nutrition.  

PubMed

The current use of serum retinol concentrations as a measurement of subclinical vitamin A deficiency is unsatisfactory for many reasons. The best technique available for vitamin A status assessment in humans is the measurement of total body pool size. Pool size is measured by the administration of retinol labelled with stable isotopes of carbon or hydrogen that are safe for human subjects, with subsequent measurement of the dilution of the labelled retinol within the body pool. However, the isotope techniques are time-consuming, technically challenging, and relatively expensive. There is also a need to assess different types of tracers and doses, and to establish clear guidelines for the use and interpretation of this method in different populations. Field-friendly improvements are desirable to encourage the application of this technique in developing countries where the need is greatest for monitoring the risk of vitamin A deficiency, the effectiveness of public health interventions, and the potential of hypervitaminosis due to combined supplement and fortification programs. These techniques should be applied to validate other less technical methods of assessing vitamin A deficiency. Another area of public health relevance for this technique is to understand the bioconversion of ?-carotene to vitamin A, and its relation to existing vitamin A status, for future dietary diversification programs. PMID:25537106

Tanumihardjo, Sherry A; Kurpad, Anura V; Hunt, Janet R

2014-01-01

165

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

SciTech Connect

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

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

2012-09-21

166

Synthesis of isotopically labeled R- or S-[.sup.13C, .sup.2H] glycerols  

DOEpatents

The present invention is directed to asymmetric chiral labeled glycerols including at least one chiral atom, from one to two .sup.13C atoms and from zero to four deuterium atoms bonded directly to a carbon atom, e.g., (2S) [1,2-.sup.13C.sub.2]glycerol and (2R) [1,2-.sup.13C.sub.2]glycerol, and to the use of such chiral glycerols in the preparation of labeled amino acids.

Martinez, Rodolfo A. (Santa Fe, NM); Unkefer, Clifford J. (Los Alamos, NM); Alvarez, Marc A. (Santa Fe, NM)

2008-01-22

167

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

PubMed Central

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

2014-01-01

168

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

PubMed

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

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

2014-08-01

169

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

PubMed

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

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

2015-03-01

170

Histone H4 acetylation dynamics determined by stable isotope labeling with amino acids in cell culture and mass spectrometry.  

PubMed

This paper describes an integrated approach that couples stable isotope labeling with amino acids in cell culture to acetic acid-urea polyacrylamide gel electrophoresis (AU-PAGE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the quantitation and dynamics of histone H4 acetylation. The 697 acute lymphoblastic cell lines were grown in regular medium and in medium in which lysine was substituted with deuterium-labeled lysine. Histone deacetylase (HDAC) activity was inhibited by addition of the HDAC inhibitor depsipeptide to the culture medium for different exposure times. Histones were extracted from cells pooled from unlabeled, untreated cells and from labeled, treated cells, followed by AU-PAGE separation. Gel bands corresponding to different acetylation states of H4 were excised, in-gel digested with trypsin, and analyzed by MALDI-TOF MS. Detailed information was obtained for both the change of histone H4 acetylation specific to the N terminus and the global transformation of H4 from one acetylation state to another following treatment with the HDAC inhibitor depsipeptide. The kinetics of H4 acetylation was also assessed. This study provides a quantitative basis for developing potential therapies by using epigenetic regulation and the developed methodology can be applied to quantitation of change for other histone modifications induced by external stimuli. PMID:17286952

Su, Xiaodan; Zhang, Liwen; Lucas, David M; Davis, Melanie E; Knapp, Amy R; Green-Church, Kari B; Marcucci, Guido; Parthun, Mark R; Byrd, John C; Freitas, Michael A

2007-04-01

171

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

PubMed Central

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

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

2015-01-01

172

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

PubMed Central

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

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

2012-01-01

173

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

PubMed Central

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

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

2013-01-01

174

Efficient, highly selective laser isotope separation of carbon-13  

Microsoft Academic Search

We recently demonstrated an original approach to highly selective laser isotope separation of carbon-13 that employs vibrational overtone pre-excitation of CF3H together with infrared multiphoton dissociation [O.V. Boyarkin, M. Kowalczyk, T.R. Rizzo, J. Chem. Phys. 118, 93 (2003)]. The practical implementation of this approach was complicated by the long absorption path length needed for the overtone excitation laser beam. In

M. N. Polianski; T. R. Rizzo; O. V. Boyarkin

2006-01-01

175

Quantitative analysis of the yeast proteome by incorporation of isotopically labeled leucine.  

PubMed

Quantitative comparison of protein expression levels in 2D gels is complicated by the variables associated with protein separation and mass spectrometric responses. Metabolic labeling allows cells from different experiments to be mixed prior to analysis. This approach has been reported for prokaryotic cells. Here, we demonstrate that metabolic labeling can also be successfully applied to the eukaryote Saccharormyces cerevisiae. Yeast leucine auxotrophs grown on synthetic complete media containing natural abundance Leu or D10-Leu were mixed prior to 2D gel separation and MALDI analysis of the digested proteins. D10-Leu labeling provided an effective internal calibrant for peptide MS analysis, and the number of Leu residues yielded an additional parameter for peptide identification at low mass resolution (1000). Metabolic incorporation of D10-Leu into yeast proteins was found to be quantitative since the intensities of the peptide peaks corresponded to those expected on the basis of the percent label in the media. Thus, D10-Leu labeling should provide reliable data for comparing proteomes both quantitatively and qualitatively from wild-type and nonessential-gene-null-mutant strains of S. cerevisiae. Given the central role played by yeast in our understanding of eukaryotic gene and protein expression, it is anticipated that the quantitative expressional proteomic method outlined here will have widespread applications. PMID:12645890

Jiang, Heng; English, Ann M

2002-01-01

176

Isotopically labeled sulfur compounds and synthetic selenium and tellurium analogues to study sulfur metabolism in marine bacteria  

PubMed Central

Summary Members of the marine Roseobacter clade can degrade dimethylsulfoniopropionate (DMSP) via competing pathways releasing either methanethiol (MeSH) or dimethyl sulfide (DMS). Deuterium-labeled [2H6]DMSP and the synthetic DMSP analogue dimethyltelluriopropionate (DMTeP) were used in feeding experiments with the Roseobacter clade members Phaeobacter gallaeciensis DSM 17395 and Ruegeria pomeroyi DSS-3, and their volatile metabolites were analyzed by closed-loop stripping and solid-phase microextraction coupled to GC–MS. Feeding experiments with [2H6]DMSP resulted in the incorporation of a deuterium label into MeSH and DMS. Knockout of relevant genes from the known DMSP demethylation pathway to MeSH showed in both species a residual production of [2H3]MeSH, suggesting that a second demethylation pathway is active. The role of DMSP degradation pathways for MeSH and DMS formation was further investigated by using the synthetic analogue DMTeP as a probe in feeding experiments with the wild-type strain and knockout mutants. Feeding of DMTeP to the R. pomeroyi knockout mutant resulted in a diminished, but not abolished production of demethylation pathway products. These results further corroborated the proposed second demethylation activity in R. pomeroyi. Isotopically labeled [2H3]methionine and 34SO4 2?, synthesized from elemental 34S8, were tested to identify alternative sulfur sources besides DMSP for the MeSH production in P. gallaeciensis. Methionine proved to be a viable sulfur source for the MeSH volatiles, whereas incorporation of labeling from sulfate was not observed. Moreover, the utilization of selenite and selenate salts by marine alphaproteobacteria for the production of methylated selenium volatiles was explored and resulted in the production of numerous methaneselenol-derived volatiles via reduction and methylation. The pathway of selenate/selenite reduction, however, proved to be strictly separated from sulfate reduction. PMID:23766810

Brock, Nelson L; Citron, Christian A; Zell, Claudia; Berger, Martine; Wagner-Döbler, Irene; Petersen, Jörn; Brinkhoff, Thorsten; Simon, Meinhard

2013-01-01

177

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

NASA Astrophysics Data System (ADS)

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

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

2012-04-01

178

Stable-Isotope-Based Labeling of Styrene-Degrading Microorganisms in Biofilters†  

PubMed Central

Deuterated styrene ([2H8]styrene) was used as a tracer in combination with phospholipid fatty acid (PLFA) analysis for characterization of styrene-degrading microbial populations of biofilters used for treatment of waste gases. Deuterated fatty acids were detected and quantified by gas chromatography-mass spectrometry. The method was evaluated with pure cultures of styrene-degrading bacteria and defined mixed cultures of styrene degraders and non-styrene-degrading organisms. Incubation of styrene degraders for 3 days with [2H8]styrene led to fatty acids consisting of up to 90% deuterated molecules. Mixed-culture experiments showed that specific labeling of styrene-degrading strains and only weak labeling of fatty acids of non-styrene-degrading organisms occurred after incubation with [2H8]styrene for up to 7 days. Analysis of actively degrading filter material from an experimental biofilter and a full-scale biofilter by this method showed that there were differences in the patterns of labeled fatty acids. For the experimental biofilter the fatty acids with largest amounts of labeled molecules were palmitic acid (16:0), 9,10-methylenehexadecanoic acid (17:0 cyclo9-10), and vaccenic acid (18:1 cis11). These lipid markers indicated that styrene was degraded by organisms with a Pseudomonas-like fatty acid profile. In contrast, the most intensively labeled fatty acids of the full-scale biofilter sample were palmitic acid and cis-11-hexadecenoic acid (16:1 cis11), indicating that an unknown styrene-degrading taxon was present. Iso-, anteiso-, and 10-methyl-branched fatty acids showed no or weak labeling. Therefore, we found no indication that styrene was degraded by organisms with methyl-branched fatty fatty acids, such as Xanthomonas, Bacillus, Streptomyces, or Gordonia spp. PMID:11571187

Alexandrino, Maria; Knief, Claudia; Lipski, André

2001-01-01

179

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

E-print Network

deposition (CVD). During the synthesis, carbon from 2 C- and 3 C-methane was deposited on, and dissolved in by this cold-wall CVD approach has a quality as high as highly oriented pyrolytic graphite (HOPG). The results, graphene Introduction Carbon has two stable isotopes, 2 C and 3 C, with natural abundances of 98

180

Efficient calculation of exact fine structure isotope patterns via the multidimensional Fourier transform.  

PubMed

The isotope patterns of unknown analytes provide information that can be of great value in their identification as part of a mass spectrometry experiment. Determining the range of compounds that are consistent with an empirically observed isotope pattern requires, as an initial step, the calculation of the theoretical isotope patterns of all feasible candidate formulas, and this is not a trivial mathematical task. While algorithms based on the Fourier transform have been used for almost two decades to perform such calculation efficiently, they have hitherto not been able to provide the exact sets of masses and abundances that constitute the fundamental isotope pattern. This article presents a new approach to the treatment of such calculations, which involves arranging and manipulating the isotope patterns of distinct elements as multidimensional data structures. This enables the use of the multidimensional Fourier transform to calculate isotope patterns with an accuracy that is limited only by the errors of floating point arithmetic. The algorithm is both highly efficient and very easy to implement in many programming environments. An open-source implementation of the algorithm in the R programming language will be made publicly available and is also available upon request. PMID:24841326

Ipsen, Andreas

2014-06-01

181

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

ERIC Educational Resources Information Center

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

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

2004-01-01

182

Characterization of volatile nylon 6.6 thermal-oxidative degradation products by selective isotopic labeling and cryo-GC/MS.  

PubMed

Aged materials, such as polymers, can exhibit modifications to their chemical structure and physical properties, which may render the material ineffective for its intended purpose. Isotopic labeling was used to characterize low-molecular weight volatile thermal-oxidative degradation products of nylon 6.6 in an effort to better understand and predict changes in the aged polymer. Headspace gas from aged (up to 243 d at 138 °C) nylon 6.6 monomers (adipic acid and 1,6-hexanediamine) and polymer were preconcentrated, separated, and detected using cryofocusing gas chromatography mass spectrometry (cryo-GC/MS). Observations regarding the relative concentrations observed in each chromatographic peak with respect to aging time were used in conjunction with mass spectra for samples aged under ambient air to determine the presence and identity of 18 degradation products. A comparison of the National Institute of Standards and Technology (NIST) library, unlabeled, and isotopically labeled mass spectra (C-13 or N-15) and expected fragmentation pathways of each degradation product were used to identify the location of isotopically labeled atoms within the product's chemical structure, which can later be used to determine the exact origin of the species. In addition, observations for unlabeled nylon 6.6 aged in an O-18 enriched atmosphere were used to determine if the source of oxygen in the applicable degradation products was from the gaseous environment or the polymer. Approximations for relative isotopic ratios of unlabeled to labeled products are reported, where appropriate. PMID:22711515

Smith, Jonell N; White, Gregory V; White, Michael I; Bernstein, Robert; Hochrein, James M

2012-09-01

183

Phosphoric acid functionalized mesoporous organo-silica (EPO) as the adsorbent for in situ enrichment and isotope labeling of endogenous phosphopeptides.  

PubMed

Ti(4+)-EPO nanoparticles were adopted as the adsorbent for in situ solid phase enrichment and isotope labeling of endogenous phosphopeptides, which has great potential application in high-throughput analyses of biological samples for screening and discovery of disease-specific biomarkers. PMID:22051540

Qin, Hongqiang; Wang, Fangjun; Wang, Peiyuan; Zhao, Liang; Zhu, Jun; Yang, Qihua; Wu, Ren'an; Ye, Mingliang; Zou, Hanfa

2012-01-25

184

Characterization of Volatile Nylon 6.6 Thermal-Oxidative Degradation Products by Selective Isotopic Labeling and Cryo-GC/MS  

NASA Astrophysics Data System (ADS)

Aged materials, such as polymers, can exhibit modifications to their chemical structure and physical properties, which may render the material ineffective for its intended purpose. Isotopic labeling was used to characterize low-molecular weight volatile thermal-oxidative degradation products of nylon 6.6 in an effort to better understand and predict changes in the aged polymer. Headspace gas from aged (up to 243 d at 138 °C) nylon 6.6 monomers (adipic acid and 1,6-hexanediamine) and polymer were preconcentrated, separated, and detected using cryofocusing gas chromatography mass spectrometry (cryo-GC/MS). Observations regarding the relative concentrations observed in each chromatographic peak with respect to aging time were used in conjunction with mass spectra for samples aged under ambient air to determine the presence and identity of 18 degradation products. A comparison of the National Institute of Standards and Technology (NIST) library, unlabeled, and isotopically labeled mass spectra (C-13 or N-15) and expected fragmentation pathways of each degradation product were used to identify the location of isotopically labeled atoms within the product's chemical structure, which can later be used to determine the exact origin of the species. In addition, observations for unlabeled nylon 6.6 aged in an O-18 enriched atmosphere were used to determine if the source of oxygen in the applicable degradation products was from the gaseous environment or the polymer. Approximations for relative isotopic ratios of unlabeled to labeled products are reported, where appropriate.

Smith, Jonell N.; V. White, Gregory; White, Michael I.; Bernstein, Robert; Hochrein, James M.

2012-09-01

185

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

E-print Network

isotope labeling; expressed protein ligation; intein; structural biology; hnRNP A1; UP1; RRM; NMR; inter-functional protein involved in many aspects of nucleic- acid processing such as alternative splicing, micro of hnRNP A1, also named unwinding protein 1 (UP1), is composed of two closely related RNA recogni- tion

Paris-Sud XI, Université de

186

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

PubMed Central

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

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

2008-01-01

187

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

PubMed

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. PMID:19154813

Ocaña, Mireia Fernández; Fraser, Paul D; Patel, Raj K P; Halket, John M; Bramley, Peter M

2009-02-16

188

Unraveling the photocatalytic mechanisms on TiO2 surfaces using the oxygen-18 isotopic label technique.  

PubMed

During the last several decades TiO2 photocatalytic oxidation using the molecular oxygen in air has emerged as a promising method for the degradation of recalcitrant organic pollutants and selective transformations of valuable organic chemicals. Despite extensive studies, the mechanisms of these photocatalytic reactions are still poorly understood due to their complexity. In this review, we will highlight how the oxygen-18 isotope labeling technique can be a powerful tool to elucidate complicated photocatalytic mechanisms taking place on the TiO2 surface. To this end, the application of the oxygen-18 isotopic-labeling method to three representative photocatalytic reactions is discussed: (1) the photocatalytic hydroxylation of aromatics; (2) oxidative cleavage of aryl rings on the TiO2 surface; and (3) photocatalytic decarboxylation of saturated carboxylic acids. The results show that the oxygen atoms of molecular oxygen can incorporate into the corresponding products in aqueous solution in all three of these reactions, but the detailed incorporation pathways are completely different in each case. For the hydroxylation process, the O atom in O2 is shown to be incorporated through activation of O2 by conduction band electrons. In the cleavage of aryl rings, O atoms are inserted into the aryl ring through the site-dependent coordination of reactants on the TiO2 surface. A new pathway for the decarboxylation of saturated carboxylic acids with pyruvic acid as an intermediate is identified, and the O2 is incorporated into the products through the further oxidation of pyruvic acid by active species from the activation of O2 by conduction band electrons. PMID:25310153

Pang, Xibin; Chen, Chuncheng; Ji, Hongwei; Che, Yanke; Ma, Wanhong; Zhao, Jincai

2014-01-01

189

Deciphering systemic wound responses of the pumpkin extrafascicular phloem by metabolomics and stable isotope-coded protein labeling.  

PubMed

In cucurbits, phloem latex exudes from cut sieve tubes of the extrafascicular phloem (EFP), serving in defense against herbivores. We analyzed inducible defense mechanisms in the EFP of pumpkin (Cucurbita maxima) after leaf damage. As an early systemic response, wounding elicited transient accumulation of jasmonates and a decrease in exudation probably due to partial sieve tube occlusion by callose. The energy status of the EFP was enhanced as indicated by increased levels of ATP, phosphate, and intermediates of the citric acid cycle. Gas chromatography coupled to mass spectrometry also revealed that sucrose transport, gluconeogenesis/glycolysis, and amino acid metabolism were up-regulated after wounding. Combining ProteoMiner technology for the enrichment of low-abundance proteins with stable isotope-coded protein labeling, we identified 51 wound-regulated phloem proteins. Two Sucrose-Nonfermenting1-related protein kinases and a 32-kD 14-3-3 protein are candidate central regulators of stress metabolism in the EFP. Other proteins, such as the Silverleaf Whitefly-Induced Protein1, Mitogen Activated Protein Kinase6, and Heat Shock Protein81, have known defensive functions. Isotope-coded protein labeling and western-blot analyses indicated that Cyclophilin18 is a reliable marker for stress responses of the EFP. As a hint toward the induction of redox signaling, we have observed delayed oxidation-triggered polymerization of the major Phloem Protein1 (PP1) and PP2, which correlated with a decline in carbonylation of PP2. In sum, wounding triggered transient sieve tube occlusion, enhanced energy metabolism, and accumulation of defense-related proteins in the pumpkin EFP. The systemic wound response was mediated by jasmonate and redox signaling. PMID:23085839

Gaupels, Frank; Sarioglu, Hakan; Beckmann, Manfred; Hause, Bettina; Spannagl, Manuel; Draper, John; Lindermayr, Christian; Durner, Jörg

2012-12-01

190

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

PubMed Central

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

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

2012-01-01

191

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

SciTech Connect

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

Zhou, Nan; Zheng, Nina; Fridley, David

2012-02-28

192

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

NASA Astrophysics Data System (ADS)

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

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

2014-11-01

193

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

PubMed Central

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

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

2013-01-01

194

Quantitation of glutathione and its oxidation products in erythrocytes by multiple-label stable-isotope dilution.  

PubMed

A multiple-label stable isotope dilution assay for quantifying glutathione (GSH), glutathione disulfide (GSSG), and glutathione sulfonic acid in erythrocytes was developed. As the internal standards, [(13)C3,(15)N]glutathione, [(13)C4,(15)N2]glutathione disulfide, and [(13)C3,(15)N]glutathione sulfonic acid were used. Analytes and internal standards were detected by LC-MS/MS after derivatization of GSH with iodoacetic acid and dansylation of all compounds under study. The calibration functions for all analytes relative to their respective isotopologic standards revealed slopes close to 1.0 and negligible intercepts. As various labelings of the standards for GSH and GSSG were used, their simultaneous quantitation was possible, although GSH was partly oxidized to its disulfide during analysis. The degree of this artifact formation of GSSG was calculated from the abundance of the mixed disulfide formed from unlabeled GSH and its respective standard. Thus, the detected GSSG amount could be corrected for the artifact amount. In this way, the amount of GSSG in erythrocytes was found to be less than 0.5% of the GSH concentration. Similar to GSSG, the detected amount of glutathione sulfonic acid was found to be formed at least in part during the analytical process, but the degree could not be quantified. PMID:24120409

Reinbold, Julia; Koehler, Peter; Rychlik, Michael

2014-01-15

195

Human lactation: maternal transfer of dietary triglycerides labeled with stable isotopes  

Microsoft Academic Search

A stable isotope tracer method was utilized to measure quantitatively the secretion of diet-derived fatty acids (FA) into human milk. A mixture of (²H6)tripalmitin, (²H18)-triolein, and (²H12)trilinolein was administered to three healthy, lactating women 22 to 30 years of age. Milk and blood samples were collected sequentially for 72 hr. The FA composition and concentration of total plasma, lipoprotein, and

David L. Hachey; M. Rita Thomas; Edward A. Emken; C. Garza; L. Brown-Booth; R. O. Adlof; P. D. Klein

1987-01-01

196

Field-scale isotopic labeling of phospholipid fatty acids from acetate-degrading sulfate-reducing bacteria.  

PubMed

Isotopic labeling of biomarker molecules is a technique applied to link microbial community structure with activity. Previously, we successfully labeled phospholipid fatty acids (PLFA) of suspended nitrate-reducing bacteria in an aquifer. However, the application of the method to low energy-yielding processes such as sulfate reduction, and extension of the analysis to attached communities remained to be studied. To test the feasibility of the latter application, an anoxic test solution of 500 l of groundwater with addition of 0.5 mM Br- as a conservative tracer, 1.1 mM SO4(2-), and 2.0 mM [2-13C]acetate was injected in the transition zone of a petroleum hydrocarbon-contaminated aquifer where sulfate-reducing and methanogenic conditions prevailed. Thousand liters of test solution/groundwater mixture were extracted in a stepwise fashion after 2-46 h incubation. Computed apparent first-order rate coefficients were 0.31+/-0.04 day(-1) for acetate and 0.34+/-0.05 day(-1) for SO4(2-) consumption. The delta13C increased from -71.03 per thousand to +3352.50 per thousand in CH4 and from -16.15 per thousand to +32.13 per thousand in dissolved inorganic carbon (DIC). A mass balance suggested that 43% of the acetate-derived (13)C appeared in DIC and 57% appeared in CH4. Thus, acetate oxidation coupled to sulfate reduction and acetoclastic methanogenesis occurred simultaneously. The delta13C of PLFA increased on average by 27 per thousand in groundwater samples and 4 per thousand in sediment samples. Hence, both suspended and attached communities actively degraded acetate. The PLFA labeling patterns and fluorescent in situ hybridization (FISH) analyses of sediment and groundwater samples suggested that the main sulfate-reducing bacteria degrading the acetate were Desulfotomaculum acetoxidans and Desulfobacter sp. in groundwater, and D. acetoxidans in sediment. PMID:16329868

Pombo, Silvina A; Kleikemper, Jutta; Schroth, Martin H; Zeyer, Josef

2005-01-01

197

Direct biosynthetic cyclization of a distorted paracyclophane highlighted by double isotopic labelling of l-tyrosine.  

PubMed

The biosynthesis of pyrrocidines, fungal PK-NRP compounds featuring a strained [9]paracyclophane, was investigated in Acremonium zeae. We used a synthetic l-tyrosine probe, labelled with oxygen 18 as a reporter of phenol reactivity and carbon 13 as a tracer of incorporation of this exogenous precursor. The ((18)O)phenolic oxygen was incorporated, suggesting that phenol behaves as a nucleophile during the formation of the bent aryl ether. PMID:25675395

Ear, Alexandre; Amand, Séverine; Blanchard, Florent; Blond, Alain; Dubost, Lionel; Buisson, Didier; Nay, Bastien

2015-03-11

198

LASER APPLICATIONS AND OTHER TOPICS IN QUANTUM ELECTRONICS: Efficient excitation of media for laser isotope separation  

Microsoft Academic Search

A theoretical investigation is made of the photoionisation of a three-level medium intended for laser isotope separation. The results show that the highest ionisation efficiency can be achieved by dividing the process into two stages: coherent population inversion and photoionisation. A study is made of the possibility of inversion of three-level systems for various detunings of the laser frequencies from

S. K. Borisov; M. A. Kuz'mina; V. A. Mishin

1995-01-01

199

The efficiency of consuming rare isotopes in a PIG ion source  

Microsoft Academic Search

The efficiency of consuming a working substance in the cyclotron arc ion source during operation at the LNR JINR cyclotrons is analyzed in comparison with the results obtained for the ECR ion source of GANIL and the Berkeley cyclotrons. The experimental results described have been obtained during the acceleration of rare isotopes ion beams (Mg-Ge) at the U-400 and U-300

V. B. Kutner; S. L. Bogomolov; A. A. Efremov; A. S. Pasyuk; Yu. P. Tretyakov

1990-01-01

200

Efficient Analysis of Mass Spectrometry Data Using the Isotope Wavelet  

NASA Astrophysics Data System (ADS)

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

Hussong, Rene; Tholey, Andreas; Hildebrandt, Andreas

2007-09-01

201

Efficient Analysis of Mass Spectrometry Data Using the Isotope Wavelet  

SciTech Connect

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

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

2007-09-18

202

Competition for phosphorus: differential uptake from dual-isotope--labeled soil interspaces between shrub and grass.  

PubMed

Two species of Agropyron grass differed strikingly in their capacity to compete for phosphate in soil interspaces shared with a common competitor, the sagebrush Artemisia tridentata. Of the total phosphorus-32 and -33 absorbed by Artemisia, 86 percent was from the interspace shared with Agropyron spicatum and only 14 percent from that shared with Agropyron desertorum. Actively absorbing mycorrhizal roots of Agropyron and Artemisia were present in both interspaces, where competition for the labeled phosphate occurred. The results have important implications about the way in which plants compete for resources below ground in both natural plant communities and agricultural intercropping systems. PMID:17795898

Caldwell, M M; Eissenstat, D M; Richards, J H; Allen, M F

1985-07-26

203

Competition for phosphorus: differential uptake from dual-isotope-labeled soil interspaces between shrub and grass  

SciTech Connect

Two species of Agropyron grass differed strikingly in their capacity to compete for phosphate in soil interspaces shared with a common competitor, the sagebrush Artemisia tridentata. Of the total phosphorus-32 and -33 absorbed by Artemisia, 86% was from the interspace shared with Agropyron spicatum and only 14% from that shared with Agropyron desertorum. Actively absorbing mycorrhizal roots of Agropyron and Artemisia were present in both interspaces, where competition for the labeled phosphate occurred. The results have important implications about the way in which plants compete for resources below ground in both natural plant communities and agricultural intercropping systems.

Caldwell, M.M.; Eissenstat, D.M.; Richards, J.H.; Allen, M.F.

1985-07-26

204

Radiolabeling of MAG3-morpholino oligomers with 188Re at high labeling efficiency and specific radioactivity for tumor pretargeting  

PubMed Central

We are investigating a novel pretargeting approach involving an initial IV injection of antitumor antibody conjugated with a phosphorodiamidate morpholino oligomer (MORF, a DNA analog) and the subsequent IV injection of the radiolabeled complement oligomer (cMORF). In this paper, the cMORF was labeled with 188Re using MAG3 as chelator for therapeutic applications. Since (c)MORFs are unstable in acidic condition, an optimal labeling pH was first selected and the other labeling factors were then examined. A labeling efficiency of greater than 90% can be achieved even at a concentration of MAG3–cMORF as low as 0.8 ?M. The labeled cMORF is stable and capable of hybridizing to its complement. PMID:16730997

Liu, Guozheng; Dou, Shuping; He, Jiang; Yin, Dongguang; Gupta, Suresh; Zhang, Surong; Wang, Yi; Rusckowski, Mary; Hnatowich, Donald J.

2006-01-01

205

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

206

Human lactation: maternal transfer of dietary triglycerides labeled with stable isotopes  

SciTech Connect

A stable isotope tracer method was utilized to measure quantitatively the secretion of diet-derived fatty acids (FA) into human milk. A mixture of (/sup 2/H6)tripalmitin, (/sup 2/H18)-triolein, and (/sup 2/H12)trilinolein was administered to three healthy, lactating women 22 to 30 years of age. Milk and blood samples were collected sequentially for 72 hr. The FA composition and concentration of total plasma, lipoprotein, and milk triglycerides were determined by gas-liquid chromatography (GLC) and the isotopic enrichment was determined by gas-liquid chromatography-mass spectrometry (GLC-MS). There were no statistically significant differences in mammary secretion of the individual fats, either by a single individual or between subjects. The mean secretion of fat by one breast was 5.11 +/- 1.26% of the dose (CV = 25%). There was a significant 6.0-hr delay between peak occurrence of the tracer in plasma and its occurrence in milk. The lipids are transported to the mammary gland primarily by the chylomicron and very low density lipoprotein triglycerides.

Hachey, D.L.; Thomas, M.R.; Emken, E.A.; Garza, C.; Brown-Booth, L.; Adlof, R.O.; Klein, P.D.

1987-10-01

207

Identification of metabolites of honokiol in rat urine using 13C stable isotope labeling and liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry.  

PubMed

A general approach based on stable isotope labeling and UPLC/Q-TOF-MS analysis of in vivo novel metabolites of honokiol has been developed in our study. In this method, urine samples were collected after intravenous administration of mixture of regular and [(13)C6]-labeled honokiol at 1:1 ratio to healthy rats. The metabolites could be easily recognized by the determination of a chromatographically co-eluted pair of isotopomers (MS doublet peaks) with similar peak intensities and mass difference corresponding to that between isotope-labeled and non-isotope-labeled honokiol. A total of 51 metabolites were detected, 37 of which were tentatively identified based on mass accuracy (<5 ppm). Among them, 33 of honokiol metabolites were first reported with 5 metabolites belonging to phase I and other 32 metabolites belonging to phase II metabolites. Our results highlighted that the main phase I metabolic pathways of honokiol in rats were oxidation, and the phase II metabolic pathways were sulfation, glucuronidation, acetylation as well as amino acids conjugation. This was the first research focused on the biotransformation of honokiol in rats, and the identification of these metabolites might provide us essential information for further pharmacological and clinical studies of honokiol. PMID:23618226

Liu, Juan; Tang, Minghai; Lai, Huijun; Dong, Yinfeng; Xie, Caifeng; Ye, Haoyu; Ma, Liang; Qiu, Neng; Li, Yanfang; Cai, Lulu; Chen, Lijuan

2013-06-21

208

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

PubMed Central

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

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

2010-01-01

209

Separation efficiency of the MASHA facility for short-lived mercury isotopes  

NASA Astrophysics Data System (ADS)

The mass-separator MASHA built to identify Super Heavy Elements by their mass-to-charge ratios is described. The results of the off- and on-line measurements of its separation efficiency are presented. In the former case four calibrated leaks of noble gases were used. In the latter the efficiency was measured via 284 MeV Ar beam and with using the hot catcher. The ECR ion source was used in both cases. The -radioactive isotopes of mercury produced in the complete fusion reaction Ar+SmHg+xn were detected at the mass-separator focal plane. The half-lives and the separation efficiency for the short-lived mercury isotopes were measured. Potentialities of the MEDIPIX detector system have been demonstrated for future use at the mass-separator MASHA.

Rodin, A. M.; Belozerov, A. V.; Chernysheva, E. V.; Dmitriev, S. N.; Gulyaev, A. V.; Gulyaeva, A. V.; Itkis, M. G.; Kliman, J.; Kondratiev, N. A.; Krupa, L.; Novoselov, A. S.; Oganessian, Yu. Ts.; Podshibyakin, A. V.; Salamatin, V. S.; Sivá?ek, I.; Stepantsov, S. V.; Vanin, D. V.; Vedeneev, V. Yu.; Yukhimchuk, S. A.; Granja, C.; Pospisil, S.

2014-06-01

210

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

PubMed Central

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 it facilitates the inclusion of different experimental datasets and thus can contribute to the expansion of flux analysis applications. PMID:23146204

2012-01-01

211

Isolation, In111 labeling, and abscess detection efficiency of rabbit polymorphonuclear leukocytes (PMN) from blood and peritoneal fluid  

Microsoft Academic Search

In-111 labeled blood and peritoneal exudate PMN were compared for labeling efficiency and ability to migrate to sites of experimental abscesses using both direct sampling and visual imaging techniques. Blood PMN were prepared by combining heparinized blood with 6% Hetastarch for 1 hour and layering the plasma over a double density Ficoll-Hy-paque gradient (S.G. 1.076 over 1.141). The PMN layer

K. M. Bettin; M. K. Elson; D. N. Gerding; D. M. Bamberger; L. A. Forstrom; R. B. Shafer

1984-01-01

212

An Efficient Method to Calculate the Aggregated Isotopic Distribution and Exact Center-Masses  

NASA Astrophysics Data System (ADS)

In this article, we present a computation- and memory-efficient method to calculate the probabilities of occurrence and exact center-masses of the aggregated isotopic distribution of a molecule. The method uses fundamental mathematical properties of polynomials given by the Newton-Girard theorem and Viete's formulae. The calculation is based on the atomic composition of the molecule and the natural abundances of the elemental isotopes in normal terrestrial matter. To evaluate the performance of the proposed method, which we named BRAIN, we compare it with the results obtained from five existing software packages ( IsoPro, Mercury, Emass, NeutronCluster, and IsoDalton) for 10 biomolecules. Additionally, we compare the computed mass centers with the results obtained by calculating, and subsequently aggregating, the fine isotopic distribution for two of the exemplary biomolecules. The algorithm will be made available as a Bioconductor package in R, and is also available upon request.

Claesen, Jürgen; Dittwald, Piotr; Burzykowski, Tomasz; Valkenborg, Dirk

2012-04-01

213

Enzymatic synthesis of isotopically labelled serine and tryptophan for application in peptide synthesis.  

PubMed

L-[1.2-13C2, 15N]Serine was prepared from [1,2-13C2, 15N]glycine on a gram scale by the use of the enzyme serine hydroxymethyltransferase. The reaction was monitored by 13C-NMR spectroscopy. This is the first simultaneously 13C- and 15N-labelled serine isotopomer so far reported. Part of the product was directly converted by tryptophan synthase to L-[1,2-13C2, 15N]tryptophan which could conveniently be purified and isolated as Boc-derivative in a yield of 71%. Most of the serine was isolated similarly but to remove remaining starting material in this case purification by column chromatography was required. PMID:9391911

Malthouse, J P; Fitzpatrick, T B; Milne, J J; Grehn, L; Ragnarsson, U

1997-01-01

214

Microscale synthesis of isotopically labeled R-[6- xH] N 5, N 10-methylene-5,6,7,8-tetrahydrofolate as a cofactor for thymidylate synthase  

Microsoft Academic Search

A one-pot synthesis of isotopically labeled R-[6-xH]N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2H4F) is presented, where x=1, 2, or 3 represents hydrogen, deuterium, or tritium, respectively. The current procedure offers high-yield, high-purity, and microscale-quantity synthesis. In this procedure, two enzymes were used simultaneously in the reaction mixture. The first was Thermoanaerobium brockii alcohol dehydrogenase, which stereospecifically catalyzed a hydride transfer from C-2-labeled isopropanol to the

Nitish Agrawal; Cornelia Mihai; Amnon Kohen

2004-01-01

215

A coding method for efficient subgraph querying on vertex- and edge-labeled graphs.  

PubMed

Labeled graphs are widely used to model complex data in many domains, so subgraph querying has been attracting more and more attention from researchers around the world. Unfortunately, subgraph querying is very time consuming since it involves subgraph isomorphism testing that is known to be an NP-complete problem. In this paper, we propose a novel coding method for subgraph querying that is based on Laplacian spectrum and the number of walks. Our method follows the filtering-and-verification framework and works well on graph databases with frequent updates. We also propose novel two-step filtering conditions that can filter out most false positives and prove that the two-step filtering conditions satisfy the no-false-negative requirement (no dismissal in answers). Extensive experiments on both real and synthetic graphs show that, compared with six existing counterpart methods, our method can effectively improve the efficiency of subgraph querying. PMID:24853266

Zhu, Lei; Song, Qinbao; Guo, Yuchen; Du, Lei; Zhu, Xiaoyan; Wang, Guangtao

2014-01-01

216

Expression of human chorionic gonadotropin uniformly labeled with NMR isotopes in Chinese hamster ovary cells: an advance toward rapid determination of glycoprotein structures.  

PubMed

Most secreted eukaryotic proteins are modified by glycosylation, and it has been difficult to solve their structures by crystallographic or NMR techniques because of problems posed by the presence of the carbohydrate. The structure of a chemically deglycosylated form of the human pregnancy hormone, human chorionic gonadotropin (hCG), has been solved by crystallographic methods. Since chemical deglycosylation may have induced changes in the structure, and since it is known that deglycosylated hCG is biologically inactive, the crystallographic structure confirmation by NMR techniques. Also, it has not been possible to determine the structures of the isolated subunits, nor the nature of interactions between the carbohydrate side chains and the protein backbone by crystallographic methods. Structural information via NMR techniques can be obtained from proteins in solution if they can be uniformly labeled with 13C and 15N isotopes. We report the first such uniform labeling of a glycoprotein using a universal 13C- and 15N-labeling medium to express 13C, 15N-labeled hCG, suitable for solving the structure in solution of the native, biologically active form of hCG as well as that of its free subunits. The 13C, 15N-labeled recombinant hCG and its separated subunits are shown to be nearly identical to urinary hCG reference preparations on the basis of protein chemical studies, immunochemistry, biological activity, and the capability of isolated hormone subunits to recombine to form biologically active hormone. Mass spectrometric analysis and preliminary NMR studies indicate that the isotopic labeling is uniform and greater than 90% after only two growth passages in the labeling media. One unexpected finding during subunit purification was that lyophilization of glycoproteins from trifluoroacetic acid HPLC buffers may result in the loss of a significant portion of sialic acid. PMID:8765736

Lustbader, J W; Birken, S; Pollak, S; Pound, A; Chait, B T; Mirza, U A; Ramnarain, S; Canfield, R E; Brown, J M

1996-06-01

217

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

PubMed Central

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

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

2015-01-01

218

Amyloid-beta Isoform Metabolism Quantitation by Stable Isotope Labeled Kinetics  

PubMed Central

Abundant evidence suggests a central role for the amyloid-? (A?) peptide in Alzheimer’s disease (AD) pathogenesis. Production and clearance of different A? isoforms have been established as targets of proposed disease-modifying therapeutic treatments of AD. However, previous studies used multiple sequential purification steps to isolate the isoforms individually and quantitate them based on a common mid-domain peptide. We created a method to simultaneously purify A? isoforms and quantitate them by the specific C-terminal peptides in order to investigate A? isoform physiology in the central nervous system. By using standards generated from in vitro metabolic labeling, the relative quantitation of four peptides representing total amount of A? (A?-Tot), A?38, A?40 and A?42 were achieved, both in cell culture and human CSF. Standard curves for each isoform demonstrated good sensitivity with very low limits of detection and high accuracy. Because the assay does not require antibody development for each A? isoform peptide, significant improvements in the throughput and accuracy of isoform quantitation were achieved. PMID:23714261

Mawuenyega, Kwasi G.; Kasten, Tom; Sigurdson, Wendy; Bateman, Randall J.

2013-01-01

219

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

SciTech Connect

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

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

2007-04-15

220

Metabolic cartography: experimental quantification of metabolic fluxes from isotopic labelling studies  

SciTech Connect

For the past decade, flux maps have provided researchers with an in-depth perspective on plant metabolism. As a rapidly developing field, significant headway has been made recently in computation, experimentation, and overall understanding of metabolic flux analysis. These advances are particularly applicable to the study of plant metabolism. New dynamic computational methods such as non-stationary metabolic flux analysis are finding their place in the toolbox of metabolic engineering, allowing more organisms to be studied and decreasing the time necessary for experimentation, thereby opening new avenues by which to explore the vast diversity of plant metabolism. Also, improved methods of metabolite detection and measurement have been developed, enabling increasingly greater resolution of flux measurements and the analysis of a greater number of the multitude of plant metabolic pathways. Methods to deconvolute organelle-specific metabolism are employed with increasing effectiveness, elucidating the compartmental specificity inherent in plant metabolism. Advances in metabolite measurements have also enabled new types of experiments, such as the calculation of metabolic fluxes based on {sup 13}CO{sub 2} dynamic labelling data, and will continue to direct plant metabolic engineering. Newly calculated metabolic flux maps reveal surprising and useful information about plant metabolism, guiding future genetic engineering of crops to higher yields. Due to the significant level of complexity in plants, these methods in combination with other systems biology measurements are necessary to guide plant metabolic engineering in the future.

O'Grady J.; Schwender J.; Shachar-Hill, Y.; Morgan, J. A.

2012-03-01

221

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

222

Tracing Nitrogenous Disinfection Byproducts after Medium Pressure UV Water Treatment by Stable Isotope Labeling and High Resolution Mass Spectrometry.  

PubMed

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

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

2015-04-01

223

Quantitative analysis of global phosphorylation changes with high-resolution tandem mass spectrometry and stable isotopic labeling  

PubMed Central

Quantitative measurement of specific protein phosphorylation sites is a primary interest of biologists, as site-specific phosphorylation information provides insights into cell signaling networks and cellular dynamics at a system level. Over the last decade, selective phosphopeptide enrichment methods including IMAC and metal oxides (TiO2 and ZrO2) have been developed and greatly facilitate large scale phosphoproteome analysis of various cells, tissues and living organisms, in combination with modern mass spectrometers featuring high mass accuracy and high mass resolution. Various quantification strategies have been applied to detecting relative changes in expression of proteins, peptides, and specific modifications between samples. The combination of mass spectrometry-based phosphoproteome analysis with quantification strategies provides a straightforward and unbiased method to identify and quantify site-specific phosphorylation. We describe common strategies for mass spectrometric analysis of stable isotope labeled samples, as well as two widely applied phosphopeptide enrichment methods based on IMAC(NTA-Fe3+) and metal oxide (ZrO2). Instrumental configurations for on-line LC-tandem mass spectrometric analysis and parameters of conventional bioinformatic analysis of large data sets are also considered for confident identification, localization, and reliable quantification of site-specific phosphorylation. PMID:23611819

Kweon, Hye Kyong; Andrews, Philip C.

2013-01-01

224

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

PubMed

The automated chemical shift assignment algorithm FLYA has been extended for use with stereo-array isotope labeled (SAIL) proteins to determine the sequence-specific resonance assignments of large proteins. Here we present the assignment of the backbone and sidechain chemical shifts of the 21kDa thioldisulfide oxidoreductase DsbA from Escherichia coli that were determined with the SAIL-FLYA algorithm in conjunction with automated peak picking. No manual corrections of peak lists or assignments were applied. The assignments agreed with manually determined reference assignments in 95.4% of the cases if 16 input spectra were used, 94.1% if only 3D (13)C/(15)N-resolved NOESY, CBCA(CO)NH, and 2D [(13)C/(15)N,(1)H]-HSQC were used, and 86.8% if exclusively 3D (13)C/(15)N-resolved NOESY spectra were used. Considering only the assignments that are classified as reliable by the SAIL-FLYA algorithm, the degrees of agreement increased to 97.5%, 96.5%, and 94.2%, respectively. With our approach it is thus possible to automatically obtain almost complete and correct assignments of proteins larger than 20kDa. PMID:25462951

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

2014-10-17

225

Systematic characterization of nuclear proteome during apoptosis: a quantitative proteomic study by differential extraction and stable isotope labeling.  

PubMed

Identification and characterization of the nuclear proteome is important for detailed understanding of multiple signaling events in eukaryotic cells. Toward this goal, we extensively characterized the nuclear proteome of human T leukemia cells by sequential extraction of nuclear proteins with different physicochemical properties using three buffer conditions. This large scale proteomic study also tested the feasibility and technical challenges associated with stable isotope labeling by amino acids in cell culture (SILAC) to uncover quantitative changes during apoptosis. Analyzing proteins from three nuclear fractions extracted from naive and apoptotic cells generated 780,530 MS/MS spectra that were used for database searching using the SEQUEST algorithm. This analysis resulted in the identification and quantification of 1,174 putative nuclear proteins. A number of known nuclear proteins involved in apoptosis as well as novel proteins not known to be part of the nuclear apoptotic machinery were identified and quantified. Consistent with SILAC-based quantifications, immunofluorescence staining of nucleus, mitochondria, and some associated proteins from both organelles revealed a dynamic recruitment of mitochondria into nuclear invaginations during apoptosis. PMID:16540461

Hwang, Sun-Il; Lundgren, Deborah H; Mayya, Viveka; Rezaul, Karim; Cowan, Ann E; Eng, Jimmy K; Han, David K

2006-06-01

226

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

227

Using carbon isotope fractionation for an improved quantification of CH4 oxidation efficiency in Arctic peatlands  

NASA Astrophysics Data System (ADS)

Much research effort is focused on identifying global CH4 sources and sinks to estimate their current and potential strength in response to land-use change and global warming. Aerobic CH4 oxidation is regarded as the key process reducing the strength of CH4 emissions in wetlands, but is hitherto difficult to quantify. Recent studies quantify the efficiency of CH4 oxidation based on CH4 stable isotope signatures. The approach utilizes the fact that a significant isotope fractionation occurs when CH4 is oxidized. Moreover, it also considers isotope fractionation by diffusion. For field applications the 'open-system equation' is applied to determine the CH4 oxidation efficiency: fox = (?E - ?P)/ (?ox - ?trans) where fox is the fraction of CH4 oxidized; ?E is ?13C of emitted CH4; ?P is ?13C of produced CH4; ?ox is the isotopic fractionation factor of oxidation; ?trans is the isotopic fractionation factor of transport. We quantified CH4 oxidation in polygonal tundra soils of Russia's Lena River Delta analyzing depth profiles of CH4 concentrations and stable isotope signatures. Therefore, both fractionation factors ?ox and ?trans were determined for three polygon centers with differing water table positions and a polygon rim. While most previous studies on landfill cover soils have assumed a gas transport dominated by advection (?trans = 1), other CH4 transport mechanisms as diffusion have to be considered in peatlands and ?trans exceeds a value of 1. At our study we determined ?trans = 1.013 ± 0.003 for CH4 when diffusion is the predominant transport mechanism. Furthermore, results showed that ?ox differs widely between sites and horizons (?ox = 1.013 ± 0.012) and has to be determined for each case. The impact of both fractionation factors on the quantification of CH4 oxidation was estimated by considering both the potential diffusion rate at different water contents and potential oxidation rates. Calculations for a water saturated tundra soil indicated a CH4 oxidation efficiency of 88% in the upper horizon. Using carbon isotope fractionation improves the in situ quantification of CH4 oxidation in wetlands and thus the assessment of current and potential CH4 sources and sinks in these ecosystems.

Preuss, I.; Knoblauch, C.; Gebert, J.; Pfeiffer, E.-M.

2012-04-01

228

In-depth Qualitative and Quantitative Profiling of Tyrosine Phosphorylation Using a Combination of Phosphopeptide Immunoaffinity Purification and Stable Isotope Dimethyl Labeling*  

PubMed Central

Several mass spectrometry-based assays have emerged for the quantitative profiling of cellular tyrosine phosphorylation. Ideally, these methods should reveal the exact sites of tyrosine phosphorylation, be quantitative, and not be cost-prohibitive. The latter is often an issue as typically several milligrams of (stable isotope-labeled) starting protein material are required to enable the detection of low abundance phosphotyrosine peptides. Here, we adopted and refined a peptidecentric immunoaffinity purification approach for the quantitative analysis of tyrosine phosphorylation by combining it with a cost-effective stable isotope dimethyl labeling method. We were able to identify by mass spectrometry, using just two LC-MS/MS runs, more than 1100 unique non-redundant phosphopeptides in HeLa cells from about 4 mg of starting material without requiring any further affinity enrichment as close to 80% of the identified peptides were tyrosine phosphorylated peptides. Stable isotope dimethyl labeling could be incorporated prior to the immunoaffinity purification, even for the large quantities (mg) of peptide material used, enabling the quantification of differences in tyrosine phosphorylation upon pervanadate treatment or epidermal growth factor stimulation. Analysis of the epidermal growth factor-stimulated HeLa cells, a frequently used model system for tyrosine phosphorylation, resulted in the quantification of 73 regulated unique phosphotyrosine peptides. The quantitative data were found to be exceptionally consistent with the literature, evidencing that such a targeted quantitative phosphoproteomics approach can provide reproducible results. In general, the combination of immunoaffinity purification of tyrosine phosphorylated peptides with large scale stable isotope dimethyl labeling provides a cost-effective approach that can alleviate variation in sample preparation and analysis as samples can be combined early on. Using this approach, a rather complete qualitative and quantitative picture of tyrosine phosphorylation signaling events can be generated. PMID:19770167

Boersema, Paul J.; Foong, Leong Yan; Ding, Vanessa M. Y.; Lemeer, Simone; van Breukelen, Bas; Philp, Robin; Boekhorst, Jos; Snel, Berend; den Hertog, Jeroen; Choo, Andre B. H.; Heck, Albert J. R.

2010-01-01

229

Simultaneous determination of glucose turnover, alanine turnover, and gluconeogenesis in human using a double stable-isotope-labeled tracer infusion and gas chromatography-mass spectrometry analysis  

SciTech Connect

We have developed and validated a new method to measure simultaneously glucose turnover, alanine turnover, and gluconeogenesis in human, in steady and non-steady states, using a double stable-isotope-labeled tracer infusion and GC-MS analysis. The method is based on the concomitant infusion and dilution of D-(2,3,4,6,6-2H5)glucose and L-(1,2,3-13C3)alanine. The choice of the tracers was done on the basis of a minimal overlap between the ions of interest and those arising from natural isotopic abundances. Alanine was chosen as the gluconeogenic substrate because it is the major gluconeogenic amino acid extracted by the liver and, with lactate, constitutes the bulk of the gluconeogenic precursors. The method was validated by comparing the results obtained during simultaneous infusion of trace amounts of both stable isotope labeled compounds with the radioactive tracers (D-(3-3H)glucose and L-(1,2,3-14C3)alanine) in a normal and a diabetic subject; the radiolabeled tracers were used as the accepted reference procedure. A slight overestimation of glucose turnover (7.3 versus 6.8 in normal and 10.8 versus 9.2 mumol/kg min in diabetic subject) was noticed when the stable isotope-labeled tracers were used. For the basal turnover rate of alanine, similar values were obtained with both methods (6.2 mumol/kg min). For gluconeogenesis, higher values were observed in the basal state with the stable isotopes (0.42 versus 0.21 mumol/kg min); however, these differences disappeared in the postprandial period after the ingestion of a mixed meal. Despite those minor differences, the overall correlation with the reference method was excellent for glucose turnover (r = 0.87) and gluconeogenesis (r = 0.86).

Martineau, A.; Lecavalier, L.; Falardeau, P.; Chiasson, J.L.

1985-12-01

230

Efficient estimators for quantum instanton evaluation of the kinetic isotope effects: Application to the intramolecular hydrogen transfer  

E-print Network

instanton approximation is used to compute kinetic isotope effects for intramolecular hydrogen transferEfficient estimators for quantum instanton evaluation of the kinetic isotope effects: Application to the intramolecular hydrogen transfer in pentadiene Jií Vaníceka Kenneth S. Pitzer Center for Theoretical Chemistry

Miller, William H.

231

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

PubMed

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

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

2015-01-01

232

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

PubMed Central

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

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

2015-01-01

233

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

PubMed

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

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

2014-07-01

234

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

SciTech Connect

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

Wiel, Stephen; McMahon, James E.

2005-04-28

235

Improved quantification of microbial CH4 oxidation efficiency in arctic wetland soils using carbon isotope fractionation  

NASA Astrophysics Data System (ADS)

Permafrost-affected tundra soils are significant sources of the climate-relevant trace gas methane (CH4). The observed accelerated warming of the arctic will cause deeper permafrost thawing, followed by increased carbon mineralization and CH4 formation in water-saturated tundra soils, thus creating a positive feedback to climate change. Aerobic CH4 oxidation is regarded as the key process reducing CH4 emissions from wetlands, but quantification of turnover rates has remained difficult so far. The application of carbon stable isotope fractionation enables the in situ quantification of CH4 oxidation efficiency in arctic wetland soils. The aim of the current study is to quantify CH4 oxidation efficiency in permafrost-affected tundra soils in Russia's Lena River delta based on stable isotope signatures of CH4. Therefore, depth profiles of CH4 concentrations and ?13CH4 signatures were measured and the fractionation factors for the processes of oxidation (?ox) and diffusion (?diff) were determined. Most previous studies employing stable isotope fractionation for the quantification of CH4 oxidation in soils of other habitats (such as landfill cover soils) have assumed a gas transport dominated by advection (?trans = 1). In tundra soils, however, diffusion is the main gas transport mechanism and diffusive stable isotope fractionation should be considered alongside oxidative fractionation. For the first time, the stable isotope fractionation of CH4 diffusion through water-saturated soils was determined with an ?diff = 1.001 ± 0.000 (n = 3). CH4 stable isotope fractionation during diffusion through air-filled pores of the investigated polygonal tundra soils was ?diff = 1.013 ± 0.003 (n = 18). Furthermore, it was found that ?ox differs widely between sites and horizons (mean ?ox = 1.017 ± 0.009) and needs to be determined on a case by case basis. The impact of both fractionation factors on the quantification of CH4 oxidation was analyzed by considering both the potential diffusion rate under saturated and unsaturated conditions and potential oxidation rates. For a submerged, organic-rich soil, the data indicate a CH4 oxidation efficiency of 50% at the anaerobic-aerobic interface in the upper horizon. The improved in situ quantification of CH4 oxidation in wetlands enables a better assessment of current and potential CH4 sources and sinks in permafrost-affected ecosystems and their potential strengths in response to global warming.

Preuss, I.; Knoblauch, C.; Gebert, J.; Pfeiffer, E.-M.

2013-04-01

236

Improved quantification of microbial CH4 oxidation efficiency in Arctic wetland soils using carbon isotope fractionation  

NASA Astrophysics Data System (ADS)

Permafrost-affected tundra soils are significant sources of the climate-relevant trace gas methane (CH4). The observed accelerated warming of the Arctic will cause a deeper permafrost thawing followed by increased carbon mineralization and CH4 formation in water saturated tundra soils which might cause a positive feedback to climate change. Aerobic CH4 oxidation is regarded as the key process reducing CH4 emissions from wetlands, but quantification of turnover rates has remained difficult so far. The application of carbon stable isotope fractionation enables the in situ quantification of CH4 oxidation efficiency in arctic wetland soils. The aim of the current study is to quantify CH4 oxidation efficiency in permafrost-affected tundra soils in Russia's Lena River Delta based on stable isotope signatures of CH4. Therefore, depth profiles of CH4 concentrations and ?13CH4-signatures were measured and the fractionation factors for the processes of oxidation (?ox) and diffusion (?diff) were determined. Most previous studies employing stable isotope fractionation for the quantification of CH4 oxidation in soils of other habitats (e.g. landfill cover soils) have assumed a gas transport dominated by advection (?trans = 1). In tundra soils, however, diffusion is the main gas transport mechanism, aside from ebullition. Hence, diffusive stable isotope fractionation has to be considered. For the first time, the stable isotope fractionation of CH4 diffusion through water-saturated soils was determined with an ?diff = 1.001 ± 0.000 (n = 3). CH4 stable isotope fractionation during diffusion through air-filled pores of the investigated polygonal tundra soils was ?diff = 1.013 ± 0.003 (n = 18). Furthermore, it was found that ?ox differs widely between sites and horizons (mean ?ox, = 1.017 ± 0.009) and needs to be determined individually. The impact of both fractionation factors on the quantification of CH4 oxidation was analyzed by considering both the potential diffusion rate under saturated and unsaturated conditions and potential oxidation rates. For a submerged organic rich soil, the data indicate a CH4 oxidation efficiency of 50% at the anaerobic-aerobic interface in the upper horizon. The improved in situ quantification of CH4 oxidation in wetlands enables a better assessment of current and potential CH4 sources and sinks in permafrost affected ecosystems and their potential strengths in response to global warming.

Preuss, I.; Knoblauch, C.; Gebert, J.; Pfeiffer, E.-M.

2012-12-01

237

Quantitative determination of free and total bisphenol A in human urine using labeled BPA glucuronide and isotope dilution mass spectrometry.  

PubMed

Bisphenol A (BPA) is a widely used industrial chemical in the manufacturing of polycarbonate plastic bottles, food and beverage can linings, thermal receipts, and dental sealants. Animal and human studies suggest that BPA may disrupt normal hormonal function and hence, potentially, have negative effects on the human health. While total BPA is frequently reported, it is recognized that free BPA is the biologically active form and is rarely reported in the literature. The objective of this study was to develop a sensitive and improved method for the measurement of free and total BPA in human urine. Use of a labeled conjugated BPA (bisphenol A-d6 ?-D-glucuronide) allowed for the optimization of the enzymatic reaction and permitted an accurate determination of the conjugated BPA concentration in urine samples. In addition, a (13)C12-BPA internal standard was used to account for the analytical recoveries and performance of the isotope dilution method. Solid-phase extraction (SPE) combined with derivatization and analysis using a triple quadrupole GC-EI/MS/MS system achieved very low method detection limit of 0.027 ng/mL. BPA concentrations were measured in urine samples collected during the second and third trimesters of pregnancy in 36 Canadian women. Total maternal BPA concentrations in urine samples ranged from not detected to 9.40 ng/mL (median, 1.21 ng/mL), and free BPA concentrations ranged from not detected to 0.950 ng/mL (median, 0.185 ng/mL). Eighty-six percent of the women had detectable levels of conjugated BPA, whereas only 22 % had detectable levels of free BPA in their urine. BPA levels measured in this study agreed well with data reported internationally. PMID:24817354

Kubwabo, Cariton; Kosarac, Ivana; Lalonde, Kaela; Foster, Warren G

2014-07-01

238

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

E-print Network

of phosphate, enzyme-labeled fluorescence, and turnover times Karen McLaughlin,1 Jill A. Sohm,2 Gregory A) activity as measured by enzyme-labeling fluorescence are also used. In surface waters, d18 OPO4 values were of phosphate, enzyme-labeled fluorescence, and turnover times, Global Biogeochem. Cycles, 27, doi:10.1002/gbc

Paytan, Adina

239

High-yield expression and purification of isotopically labeled cytochrome P450 monooxygenases for solid-state NMR spectroscopy  

PubMed Central

Cytochrome P450 monooxygenases (P450s), which represent the major group of drug metabolizing enzymes in humans, also catalyze important synthetic and detoxicative reactions in insects, plants and many microbes. Flexibilities in their catalytic sites and membrane associations are thought to play central roles in substrate binding and catalytic specificity. To date, E. coli expression strategies for structural analysis of eukaryotic membrane-bound P450s by X-ray crystallography have necessitated full or partial removal of their N-terminal signal anchor domain (SAD) and, often, replacement of residues more peripherally associated with the membrane (such as the F-G loop region). Even with these modifications, investigations of P450 structural flexibility remain challenging with multiple single crystal conditions needed to identify spatial variations between substrate-free and different substrate-bound forms. To overcome these limitations, we have developed methods for the efficient expression of 13C- and 15N-labeled P450s and analysis of their structures by magic-angle spinning solid-state NMR (SSNMR) spectroscopy. In the presence of co-expressed GroEL and GroES chaperones, full-length (53 kDa) Arabidopsis 13C,15N-labeled CYP98A3 is expressed at yields of 2–4 mg per liter of minimal media without the necessity of generating side chain modifications or N-terminal deletions. Precipitated CYP98A3 generates high quality SSNMR spectra consistent with a homogeneous, folded protein. These data highlight the potential of these methodologies to contribute to the structural analysis of membrane-bound proteins. PMID:18005930

Rupasinghe, Sanjeewa G.; Duan, Hui; Frericks Schmidt, Heather L.; Berthold, Deborah A.; Rienstra, Chad M.; Schuler, Mary A.

2008-01-01

240

Adaptation of a commonly used, chemically defined medium for human embryonic stem cells to stable isotope labeling with amino acids in cell culture.  

PubMed

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 rarely employed in the context of complex culturing conditions as those required for human embryonic stem cells (hESCs). Classic hESC culture is based on the use of mouse embryonic fibroblasts (MEFs) as a feeder layer, and as a result, possible xenogeneic contamination, contribution of unlabeled amino acids by the feeders, interlaboratory variability of MEF preparation, and the overall complexity of the culture system are all of concern in conjunction with SILAC. We demonstrate a feeder-free SILAC culture system based on a customized version of a commonly used, chemically defined hESC medium developed by Ludwig et al. and commercially available as mTeSR1 [mTeSR1 is a trade mark of WiCell (Madison, WI) licensed to STEMCELL Technologies (Vancouver, Canada)]. This medium, together with adjustments to the culturing protocol, facilitates reproducible labeling that is easily scalable to the protein amounts required by proteomic work flows. It greatly enhances the usability of quantitative proteomics as a tool for the study of mechanisms underlying hESCs differentiation and self-renewal. Associated data have been deposited to the ProteomeXchange with the identifier PXD000151. PMID:23734825

Liberski, Albert R; Al-Noubi, Muna N; Rahman, Zahra H; Halabi, Najeeb M; Dib, Shaima S; Al-Mismar, Rasha; Billing, Anja M; Krishnankutty, Roopesh; Ahmad, Faizzan S; Raynaud, Christophe M; Rafii, Arash; Engholm-Keller, Kasper; Graumann, Johannes

2013-07-01

241

Characterization of the strongly coupled, low-frequency vibrational modes of the special pair of photosynthetic reaction centers via isotopic labeling of the cofactors  

SciTech Connect

Low-frequency (50-425-cm{sup -1}), near-infrared-excitation resonance Raman (RR) spectra are reported for bacterial photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides in which the bacteriochlorophyll (BChl) and bacteriopheophytin (BPh) cofactors are labeled with {sup 15}N or {sup 26}Mg. The focus of the study is the identification of the very low-frequency modes of the dimer of BChls (P) which are strongly coupled to the P{sup *} electronic transition which initiates the primary charge separation process in RCs. In order to gain a complete picture of the vibrational characteristics, the low-frequency RR spectra of the accessory BChls and the BPhs were examined in addition to those of P. The RR spectra of the isotopically labeled cofactors in the RCs were compared with one another and with the spectra obtained for solid-film samples of isolated, isotopically labeled BChl and BPh. Based on these comparisons and the predictions of semiempirical normal coordinate calculations, a self-consistent set of assignments has been developed for all the RR active modes of the different BChl and BPh cofactors in the RC which are observed in the very low-frequency regime (50-250 cm{sup -1}). The assignments indicate that the strongly coupled, low-frequency modes of P all involve either deformations localized on pyrrole ring I or the macrocycle core. 45 refs., 10 figs., 3 tabs.

Czarnecki, K.; Diers, J.R.; Bocian, D.F. [Univ. of California, Riverside, CA (United States)] [Univ. of California, Riverside, CA (United States); Chynwat, V.; Erickson, J.P.; Frank, H.A. [Univ. of Connecticut, Storrs, CT (United States)] [Univ. of Connecticut, Storrs, CT (United States)

1997-01-15

242

Quantitative isomer-specific N-glycan fingerprinting using isotope coded labeling and high performance liquid chromatography-electrospray ionization-mass spectrometry with graphitic carbon stationary phase.  

PubMed

Glycan reductive isotope labeling (GRIL) using (12)C6-/(13)C6-aniline as labeling reagent is reported with the aim of quantitative N-glycan fingerprinting. Porous graphitized carbon (PGC) as stationary phase in capillary scale HPLC coupled to electrospray mass spectrometry with time of flight analyzer was applied for the determination of labeled N-glycans released from glycoproteins. The main benefit of using stable isotope-coding in the context of comparative glycomics lies in the improved accuracy and precision of the quantitative analysis in combined samples and in the potential of correcting for structure-dependent incomplete enzymatic release of oligosaccharides when comparing identical target proteins. The method was validated with respect to mobile phase parameters, reproducibility, accuracy, linearity and limit of detection/quantification (LOD/LOQ) using test glycoproteins. It is shown that the developed method is capable of determining relative amounts of N-glycans (including isomers) comparing two samples in one single HPLC-MS run. The analytical potential and usefulness of GRIL in combination with PGC-ESI-TOF-MS is demonstrated comparing glycosylation in human monoclonal antibodies produced in Chinese hamster ovary cells (CHO) and hybridoma cell lines. PMID:25638265

Michael, Claudia; Rizzi, Andreas M

2015-02-27

243

A Set of Engineered Escherichia coli Expression Strains for Selective Isotope and Reactivity Labeling of Amino Acid Side Chains and Flavin Cofactors  

PubMed Central

Biological reactions are facilitated by delicate molecular interactions between proteins, cofactors and substrates. To study and understand their dynamic interactions researchers have to take great care not to influence or distort the object of study. As a non-invasive alternative to a site-directed mutagenesis approach, selective isotope labeling in combination with vibrational spectroscopy may be employed to directly identify structural transitions in wild type proteins. Here we present a set of customized Escherichia coli expression strains, suitable for replacing both the flavin cofactor and/or selective amino acids with isotope enriched or chemically modified substrates. For flavin labeling we report optimized auxotrophic strains with significantly enhanced flavin uptake properties. Labeled protein biosynthesis using these strains was achieved in optimized cultivation procedures using high cell density fermentation. Finally, we demonstrate how this approach is used for a clear assignment of vibrational spectroscopic difference signals of apoprotein and cofactor of a flavin containing photoreceptor of the BLUF (Blue Light receptors Using FAD) family. PMID:24223875

Mehlhorn, Jennifer; Steinocher, Helena; Beck, Sebastian; Kennis, John T. M.; Hegemann, Peter; Mathes, Tilo

2013-01-01

244

Transpiration efficiency over an annual cycle, leaf gas exchange and wood carbon isotope ratio of three tropical tree species  

E-print Network

Transpiration efficiency over an annual cycle, leaf gas exchange and wood carbon isotope ratio; published online August 6, 2009 Summary Variation in transpiration efficiency (TE) and its relationship. Cumulative transpiration was determined by repeatedly weighing the pots with a pallet truck scale. Dry matter

Bermingham, Eldredge

245

Insights into nitrogen allocation and recycling from nitrogen elemental analysis and 15N isotope labelling in 14 genotypes of willow.  

PubMed

Minimizing nitrogen (N) fertilization inputs during cultivation is essential for sustainable production of bioenergy and biofuels. The biomass crop willow (Salix spp.) is considered to have low N fertilizer requirements due to efficient recycling of nutrients during the perennial cycle. To investigate how successfully different willow genotypes assimilate and allocate N during growth, and remobilize and consequently recycle N before the onset of winter dormancy, N allocation and N remobilization (to and between different organs) were examined in 14 genotypes of a genetic family using elemental analysis and (15)N as a label. Cuttings were established in pots in April and sampled in June, August and at onset of senescence in October. Biomass yield of the trees correlated well with yields recorded in the field. Genotype-specific variation was observed for all traits measured and general trends spanning these sampling points were identified when trees were grouped by biomass yield. Nitrogen reserves in the cutting fuelled the entirety of the canopy establishment, yet earlier cessation of this dependency was linked to higher biomass yields. The stem was found to be the major N reserve by autumn, which constitutes a major source of N loss at harvest, typically every 2-3 years. These data contribute to understanding N remobilization in short rotation coppice willow and to the identification of traits that could potentially be selected for in breeding programmes to further improve the sustainability of biomass production. PMID:24186940

Brereton, Nicholas J B; Pitre, Frederic E; Shield, Ian; Hanley, Steven J; Ray, Michael J; Murphy, Richard J; Karp, Angela

2014-11-01

246

A spectral correlation function for efficient sequential NMR assignments of uniformly (15)N-labeled proteins.  

PubMed

A new computer-based approach is described for efficient sequence-specific assignment of uniformly (15)N-labeled proteins. For this purpose three-dimensional (15)N-correlated [(1)H, (1)H]-NOESY spectra are divided up into two-dimensional (1)H-(1)H strips which extend over the entire spectral width along one dimension and have a width of ca. 100 Hz, centered about the amide proton chemical shifts along the other dimension. A spectral correlation function enables sorting of these strips according to proximity of the corresponding residues in the amino acid sequence. Thereby, starting from a given strip in the spectrum, the probability of its corresponding to the C-terminal neighboring residue is calculated for all other strips from the similarity of their peak patterns with a pattern predicted for the sequentially adjoining residue, as manifested in the scalar product of the vectors representing the predicted and measured peak patterns. Tests with five different proteins containing both ?-helices and ?-sheets, and ranging in size from 58 to 165 amino acid residues show that the discrimination achieved between the sequentially neighboring residue and all other residues compares well with that obtained with an unguided interactive search of pairs of sequentially neighboring strips, with important savings in the time needed for complete analysis of 3D (15)N-correlated [(1)H, (1)H]-NOESY spectra. The integration of this routine into the program package XEASY ensures that remaining ambiguities can be resolved by visual inspection of the strips, combined with reference to the amino acid sequence and information on spin-system types obtained from additional NMR spectra. PMID:22911386

Bartels, C; Wüthrich, K

1994-11-01

247

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

PubMed Central

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

Straus, Suzana K

2004-01-01

248

Isotopic distributions.  

PubMed

Isotopic information determined by mass spectrometry can be used in a wide variety of applications. Broadly speaking these could be classified as "passive" applications, meaning that they use naturally occurring isotopic information, and "active" applications, meaning that the isotopic distributions are manipulated in some way. The classic passive application is the determination of chemical composition by comparing observed isotopic patterns of molecules to theoretically calculated isotopic patterns. Active applications include isotope exchange experiments of a variety of types, as well as isotope labeling in tracing studies and to provide references for quantitation. Regardless of the type of application considered, the problem of theoretical calculation of isotopic patterns almost invariably arises. This paper reviews a number of application examples and computational approaches for isotopic studies in mass spectrometry. PMID:23666722

Rockwood, Alan L; Palmblad, Magnus

2013-01-01

249

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

E-print Network

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

Tan, Kwan Chong

2009-01-01

250

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

E-print Network

,10 This technique11 provides a determination of the isotope depth distributions with an accuracy 0.4­0.5 nm isotopic enrich- ment 98%, water concentration less than 2 ppm . Although the samples were transferred by target masses, the incident energy and the scattering angle. In addition, since protons lose energy while

Gustafsson, Torgny

251

Isolation, In-111 labeling, and abscess detection efficiency of rabbit polymorphonuclear leukocytes (PMN) from blood and peritoneal fluid  

SciTech Connect

In-111 labeled blood and peritoneal exudate PMN were compared for labeling efficiency and ability to migrate to sites of experimental abscesses using both direct sampling and visual imaging techniques. Blood PMN were prepared by combining heparinized blood with 6% Hetastarch for 1 hour and layering the plasma over a double density Ficoll-Hy-paque gradient (S.G. 1.076 over 1.141). The PMN layer (90-99% PMN) at the interface yielded 10/sup 6/-10/sup 7/ PMN from 80-120 ml of blood. Peritoneal PMN were obtained by infusion of 0.1% glycogen, followed by infusion of saline after 4 or 18 hours. The exudate yielded 10/sup 7/-10/sup 8/ PMN (80-99% PMN). PMN suspensions were labeled for 30 minutes by addition of 100 ..mu..Ci of In-111-oxine, then washed twice. Percent cell-associated radioactivity of the labeled blood, 4 hour, and 18 hour peritoneal PMN was 89%, 88%, and 86%. The labeled PMN were injected intravenously into rabbits which had two of three abdominal capsules (table tennis balls drilled with 250 1.5 mm holes) inoculated with Staphylococcus aureus 4 hours earlier. Peak venous recovery of circulating labeled PMN, for blood, 4 hour and 18 hour peritoneal PMN was 60%, 43%, and 19%. Gamma camera images 24 hours after infusion into infected rabbits were superior with 4 hour peritoneal PMN. The peritoneal PMN harvested 4 hours after glycogen stimulation are simple to prepare, are obtainable in greater numbers than blood PMN, and result in better abscess visualization.

Bettin, K.M.; Elson, M.K.; Gerding, D.N.; Bamberger, D.M.; Forstrom, L.A.; Shafer, R.B.

1984-01-01

252

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

PubMed

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

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

2013-01-01

253

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

SciTech Connect

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

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

2006-06-27

254

Validation of methane measurement using headspace-GC-MS and quantification by a stable isotope-labeled internal standard generated in situ.  

PubMed

A previous study has shown the possibility to identify methane (CH4 ) using headspace-GC-MS and quantify it with a stable isotope as internal standard. The main drawback of the GC-MS methods discussed in literature for CH4 measurement is the absence of a specific internal standard necessary to perform quantification. However, it becomes essential to develop a safer method to limit the manipulation of gaseous CH4 and to precisely control the injected amount of gas for spiking and calibration by comparison with external calibration. To avoid the manipulation of a stable isotope-labeled gas, we have chosen to generate a labeled gas as an internal standard in a vial on the basis of the formation of CH4 by the reaction of Grignard reagent methylmagnesium chloride with deuterated water. This method allows precise measurement of CH4 concentrations in gaseous sample as well as in a solid or a liquid sample after a thermodesorption step in a headspace vial. A full accuracy profile validation of this method is then presented. PMID:23585415

Varlet, Vincent; Smith, Fiona; Augsburger, Marc

2013-06-01

255

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

NASA Astrophysics Data System (ADS)

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

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

2012-05-01

256

Phosphorylcholine-coated semiconducting polymer nanoparticles as rapid and efficient labeling agents for in vivo cell tracking.  

PubMed

Despite the pressing need to noninvasively monitor transplanted cells in vivo with fluorescence imaging, desirable fluorescent agents with rapid labeling capability, durable brightness, and ideal biocompatibility remain lacking. Here, phosphorylcholine-coated near-infrared (NIR) fluorescent semiconducting polymer nanoparticles (SPNs) are reported as a new class of rapid, efficient, and cytocompatible labeling nanoagents for in vivo cell tracking. The phosphorylcholine coating results in efficient and rapid endocytosis and allows the SPN to enter cells within 0.5 h in complete culture medium apparently independent of the cell type, while its NIR fluorescence leads to a tissue penetration depth of 0.5 cm. In comparison to quantum dots and Cy5.5, the SPN is tolerant to physiologically ubiquitous reactive oxygen species (ROS), resulting in durable fluorescence both in vitro and in vivo. These desirable physical and physiological properties of the SPN permit cell tracking of human renal cell carcinoma (RCC) cells in living mice at a lower limit of detection of 10 000 cells with no obvious alteration of cell phenotype after 12 d. SPNs thus can provide unique opportunities for optimizing cellular therapy and deciphering pathological processes as a cell tracking label. PMID:24668903

Pu, Kanyi; Shuhendler, Adam J; Valta, Maija P; Cui, Lina; Saar, Matthias; Peehl, Donna M; Rao, Jianghong

2014-08-01

257

Efficient Access to 3?-Terminal Azide-Modified RNA for Inverse Click-Labeling Patterns  

PubMed Central

Labeled RNA becomes increasingly important for molecular diagnostics and biophysical studies on RNA with its diverse interaction partners, which range from small metabolites to large macromolecular assemblies, such as the ribosome. Here, we introduce a fast synthesis path to 3?-terminal 2?-O-(2-azidoethyl) modified oligoribonucleotides for subsequent bioconjugation, as exemplified by fluorescent labeling via Click chemistry for an siRNA targeting the brain acid-soluble protein 1 gene (BASP1). Importantly, the functional group pattern is inverse to commonly encountered alkyne-functionalized “click”-able RNA and offers increased flexibility with respect to multiple and stepwise labeling of the same RNA molecule. Additionally, our route opens up a minimal step synthesis of 2?-O-(2-aminoethyl) modified pyrimidine nucleoside phosphoramidites which are of widespread use to generate amino-modified RNA for N-hydroxysuccinimide (NHS) ester-based conjugations. PMID:24358989

2013-01-01

258

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

E-print Network

. Keywords: quantitation · variation · SILAC · mass spectrometry · proteomics · sample preparation protein quantitation by mass spectrometry. The high quantitative accuracy of SILAC allowsEvaluation of the Variation in Sample Preparation for Comparative Proteomics Using Stable Isotope

Chait, Brian T.

259

The Isotope Array, a New Tool That Employs Substrate-Mediated Labeling of rRNA for Determination of Microbial Community Structure and Function  

PubMed Central

A new microarray method, the isotope array approach, for identifying microorganisms which consume a 14C-labeled substrate within complex microbial communities was developed. Experiments were performed with a small microarray consisting of oligonucleotide probes targeting the 16S rRNA of ammonia-oxidizing bacteria (AOB). Total RNA was extracted from a pure culture of Nitrosomonas eutropha grown in the presence of [14C]bicarbonate. After fluorescence labeling of the RNA and microarray hybridization, scanning of all probe spots for fluorescence and radioactivity revealed that specific signals were obtained and that the incorporation of 14C into rRNA could be detected unambiguously. Subsequently, we were able to demonstrate the suitability of the isotope array approach for monitoring community composition and CO2 fixation activity of AOB in two nitrifying activated-sludge samples which were incubated with [14C]bicarbonate for up to 26 h. AOB community structure in the activated-sludge samples, as predicted by the microarray hybridization pattern, was confirmed by quantitative fluorescence in situ hybridization (FISH) and comparative amoA sequence analyses. CO2 fixation activities of the AOB populations within the complex activated-sludge communities were detectable on the microarray by 14C incorporation and were confirmed independently by combining FISH and microautoradiography. AOB rRNA from activated sludge incubated with radioactive bicarbonate in the presence of allylthiourea as an inhibitor of AOB activity showed no incorporation of 14C and thus was not detectable on the radioactivity scans of the microarray. These results suggest that the isotope array can be used in a PCR-independent manner to exploit the high parallelism and discriminatory power of microarrays for the direct identification of microorganisms which consume a specific substrate in the environment. PMID:14602652

Adamczyk, Justyna; Hesselsoe, Martin; Iversen, Niels; Horn, Matthias; Lehner, Angelika; Nielsen, Per Halkjaer; Schloter, Michael; Roslev, Peter; Wagner, Michael

2003-01-01

260

A low-toxic artificial fluorescent glycoprotein can serve as an efficient cytoplasmic labeling in living cell.  

PubMed

To maintain the virtue of good optical property and discard the dross of conventional fluorescent staining dyes, we provide a strategy for designing new fluorescent scaffolds. In this study, a novel fluorescent labeling glycoprotein (chitosan-poly-L-cysteine, CPC) was synthesized through graft copolymerization. CPC gives emission peak at 465-470 nm when excited at 386 nm. The submicro-scale CPC microspheres could be localized and persisted specifically in the cytoplasm of living cells, with strong blue fluorescence. Moreover, CPC was highly resistant to photo bleaching, the fluorescence was remained stable for up to 72 h as the cells grew and developed. The glycoprotein CPC was bio-compatible and in zero grade cytotoxicity as quantified by MTT assay. The fluorescent labeling process with our newly designed glycoprotein CPC is exceptionally efficient. PMID:25498627

Si, Jiangju; Liang, Dawei; Kong, Dan; Wu, Sufang; Yuan, Lan; Xiang, Yan; Jiang, Lei

2015-03-01

261

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

PubMed Central

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

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

2015-01-01

262

Relative quantitation of glycosylation variants by stable isotope labeling of enzymatically released N-glycans using [12C]/[13C] aniline and ZIC-HILIC-ESI-TOF-MS.  

PubMed

Glycan reductive isotope labeling (GRIL) using [(12)C]- and [(13)C]-coded aniline was used for relative quantitation of N-glycans. In a first step, the labeling method by reductive amination was optimized for this reagent. It could be demonstrated that selecting aniline as limiting reactant and using the reductant in excess is critical for achieving high derivatization yields (over 95 %) and good reproducibility (relative standard deviations ?1-5 % for major and ?5-10 % for minor N-glycans). In a second step, zwitterionic-hydrophilic interaction liquid chromatography in capillary columns coupled to electrospray mass spectrometry with time-of-flight analyzer (?ZIC-HILIC-ESI-TOF-MS) was applied for the analysis of labeled N-glycans released from intact glycoproteins. Ovalbumin, bovine ?1-acid-glycoprotein and bovine fetuin were used as test glycoproteins to establish and evaluate the methodology. Excellent separation of isomeric N-glycans and reproducible quantitation via the extracted ion chromatograms indicate a great potential of the proposed methodology for glycoproteomic analysis and for reliable relative quantitation of glycosylation variants in biological samples. PMID:23846592

Giménez, Estela; Sanz-Nebot, Victòria; Rizzi, Andreas

2013-09-01

263

Efficient approximate and dynamic matching of patterns using a labeling paradigm  

SciTech Connect

A key approach in string processing algorithmics has been the labeling paradigm [KMR72], which is based on assigning labels to some of the substrings of a given string. If these labels are chosen consistently, they can enable fast comparisons of substrings. Until the first optimal parallel algorithm for suffix tree construction was given in [SV94], the labeling paradigm was considered not to be competitive with other approaches. In this paper we show that, this general method is also useful for several central problems in the area of string processing: (1) Approximate String Matching, (2) Dynamic Dictionary Matching, (3) Dynamic Text Indexing. The approximate string matching problem deals with finding all substrings of a text which match a pattern {open_quotes}approximately{close_quotes}, i.e., with at most m differences. The differences can be in the form of inserted, deleted, or replaced characters. The text indexing problem deals with finding all occurrences of a pattern in a text, after the text is preprocessed. In the dynamic text indexing problem, updates to the text in the form of insertions and deletions of substrings are permitted. The dictionary matching problem deals with finding all occurrences of each pattern out of a set of patterns in a text, after the pattern set is preprocessed. In the dynamic dictionary matching problem, insertions and deletions of patterns to the pattern set are permitted.

Cenk Sahinalp, S. [Univ. of Maryland, College Park, MD (United States); [Bell Labs., Murray Hill, NJ (United States); Vishkin, U. [Univ. of Maryland, College Park, MD (United States); [Tel Aviv Univ. (Israel)

1996-12-31

264

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

NASA Astrophysics Data System (ADS)

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

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

2009-08-01

265

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

NASA Astrophysics Data System (ADS)

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

Guo, Kevin; Bamforth, Fiona; Li, Liang

2011-02-01

266

Realistic Fasting Does Not Affect Stable Isotope Levels of a Metabolically Efficient Salamander  

EPA Science Inventory

Stable isotopes are commonly used to examine various aspects of animal ecology. The use of stable isotopes generally proceeds under the implicit assumption that resource use is the only factor driving variation in stable isotope levels; however, a wealth of studies demonstrate a...

267

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

PubMed

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

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

2004-05-01

268

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

PubMed

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

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

2015-03-01

269

Spatially tracking 13C labeled substrate (bicarbonate) accumulation in microbial communities using laser ablation isotope ratio mass spectrometry  

SciTech Connect

This is a manuscript we would like to submit for publication in Environmental Microbiology Reports. This manuscript contains a description of a laser ablation isotope ratio mass spectrometry methodology developed at PNNL and applied to a microbial system at a PNNL project location – Hot Lake, Washington. I will submit a word document containing the entire manuscript with this Erica input request form.

Moran, James J.; Doll, Charles G.; Bernstein, Hans C.; Renslow, Ryan S.; Cory, Alexandra B.; Hutchison, Janine R.; Lindemann, Stephen R.; Fredrickson, Jim K.

2014-08-25

270

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

271

Biosynthesis of seven carbon-13 labeled Alternaria toxins including altertoxins, alternariol, and alternariol methyl ether, and their application to a multiple stable isotope dilution assay.  

PubMed

An unprecedented stable isotope dilution assay for the genotoxic altertoxins along with exposure data of consumers is presented to enable a first risk assessment of these Alternaria toxins in foods. Altertoxins were produced as the most abundant Alternaria toxins in a modified Czapek-Dox medium with a low level of glucose as the carbon source and ammonium sulfate as the sole nitrogen source. Labeled altertoxins were synthesized in the same way using [(13)C6]glucose. Moreover, labeled alternariol, alternariol methyl ether, altenuene, and alternuisol were biosynthesized in another modified medium containing [(13)C6]glucose and sodium [(13)C2]acetate. A stable isotope dilution LC-MS/MS method was developed and used for food analysis. For altertoxin I, altertoxin II, alterperylenol, alternariol, and alternariol methyl ether, the limits of detection ranged from 0.09 to 0.53 ?g kg(-1). The inter-/intra-day (n?=?3?×?6) relative standard deviations of the method were below 13 %, and the recoveries ranged between 96 and 109 %. Among the various commercial food samples, some of the organic whole grains revealed low-level contamination with altertoxin I and alterperylenol, and paprika powder, which was heavily loaded with alternariol, alternariol methyl ether, and tentoxin, showed higher contamination level of altertoxin I and alterperylenol. Altertoxin II and III and stemphyltoxin III were not detectable. In addition, if the food was contaminated with altertoxins, it was likely to be co-contaminated with the other Alternaria toxins, but not necessarily vice versa. Maximum concentrations of altertoxin I and alterperylenol were detected in sorghum feed samples containing 43 and 58 ?g kg(-1), respectively. This was significantly higher than that in the measured food samples. PMID:25577349

Liu, Yang; Rychlik, Michael

2015-02-01

272

Deciphering Systemic Wound Responses of the Pumpkin Extrafascicular Phloem by Metabolomics and Stable Isotope-Coded Protein Labeling1[C][W  

PubMed Central

In cucurbits, phloem latex exudes from cut sieve tubes of the extrafascicular phloem (EFP), serving in defense against herbivores. We analyzed inducible defense mechanisms in the EFP of pumpkin (Cucurbita maxima) after leaf damage. As an early systemic response, wounding elicited transient accumulation of jasmonates and a decrease in exudation probably due to partial sieve tube occlusion by callose. The energy status of the EFP was enhanced as indicated by increased levels of ATP, phosphate, and intermediates of the citric acid cycle. Gas chromatography coupled to mass spectrometry also revealed that sucrose transport, gluconeogenesis/glycolysis, and amino acid metabolism were up-regulated after wounding. Combining ProteoMiner technology for the enrichment of low-abundance proteins with stable isotope-coded protein labeling, we identified 51 wound-regulated phloem proteins. Two Sucrose-Nonfermenting1-related protein kinases and a 32-kD 14-3-3 protein are candidate central regulators of stress metabolism in the EFP. Other proteins, such as the Silverleaf Whitefly-Induced Protein1, Mitogen Activated Protein Kinase6, and Heat Shock Protein81, have known defensive functions. Isotope-coded protein labeling and western-blot analyses indicated that Cyclophilin18 is a reliable marker for stress responses of the EFP. As a hint toward the induction of redox signaling, we have observed delayed oxidation-triggered polymerization of the major Phloem Protein1 (PP1) and PP2, which correlated with a decline in carbonylation of PP2. In sum, wounding triggered transient sieve tube occlusion, enhanced energy metabolism, and accumulation of defense-related proteins in the pumpkin EFP. The systemic wound response was mediated by jasmonate and redox signaling. PMID:23085839

Gaupels, Frank; Sarioglu, Hakan; Beckmann, Manfred; Hause, Bettina; Spannagl, Manuel; Draper, John; Lindermayr, Christian; Durner, Jörg

2012-01-01

273

Use of Differential Isotopic Labeling and Mass Spectrometry To Analyze Capacitation-Associated Changes in the Phosphorylation Status of Mouse Sperm Proteins  

PubMed Central

Mammalian sperm need to reside in the female reproductive tract for a finite period of time before acquiring fertilizing competence. The biochemical changes associated with this process are collectively known as “capacitation”. With the use of the mouse as an experimental model, we have previously demonstrated that capacitation is associated with a cAMP-dependent increase in protein tyrosine phosphorylation. However, little is known about the identity and function of the protein targets of this phosphorylation cascade. In the present work, we have used differential isotopic labeling coupled with immobilized metal affinity chromatography (IMAC)-based phosphopeptide enrichment and analysis on a hybrid linear ion trap/FT-ICR mass spectrometer to measure the changes in protein phosphorylation resulting from the capacitation process. As no kinase activators and/or phosphatase inhibitors were used in the preparation of the sperm samples, phosphorylated residues identified in this study represent in vivo sites of phosphorylation. Also, in contrast to other methods which rely on the incorporation of isotopically labeled amino acids at the protein level (e.g., SILAC), the present technique is based on the Fisher esterification of protein digests, allowing for the comparison of phosphorylation status in the absence of protein synthesis. This approach resulted in the identification of 55 unique, in vivo sites of phosphorylation and permitted the relative extent of phosphorylation, as a consequence of capacitation, to be calculated for 42 different phosphopeptides. This work represents the first effort to determine which specific protein phosphorylation sites change their phosphorylation status in vivo as a result of the mammalian capacitation process. PMID:19186949

Platt, Mark D.; Salicioni, Ana M.; Hunt, Donald F.; Visconti, Pablo E.

2010-01-01

274

Using stable isotopes to reconcile differences in nitrogen uptake efficiency relative to late season fertilization of northern red oak seedlings in Wisconsin bare-root nurseries  

NASA Astrophysics Data System (ADS)

Cultural applications (e.g., timing, amount) of nitrogen (N) fertilizer in bareroot tree nurseries have been assessed for some time. However, the use of different metrologies to quantify the efficient use of fertilizer N and its allocation within biomass has confounded comparisons between fertilization regimes. This inconsistency is especially problematic when quantifying N fertilizer uptake efficiency (NFUE) of late season N fertilization in northern red oak (Quercus rubra L.) (NRO) seedlings characterized by episodic flushes in growth and N storage in perennial tissue to support spring growth. The use of isotopic tracers could help elucidate these differences. We therefore hypothesized that: 1) calculations of NFUE using isotopically enriched fertilizer would yield lower, more precise estimates of NFUE relative to traditional methods due to differences in the accounting of mineralized and reabsorbed N, and 2) a significant fraction of leaf N in older leaves (early flushes) would be reabsorbed into root and shoot tissue before abscission relative to leaves produced toward the end of the growing season (late flushes). To test these hypotheses, we conducted an experiment in two-year old NRO seedlings at two bare-root nurseries in Wisconsin. We applied a total of 147 mg N seedling-1 in pulses from early July after the seedlings completed their second leaf flush until late August. The treatments consisted of three replicated plots of 15N enriched (1.000 atom%) ammonium sulfate, three non-enriched plots, and three unfertilized plots (controls) at each nursery. Subsequent changes in plant N uptake and N allocation were quantified from destructively harvested samples taken at 40, 60, and 120 days after the fertilization began. We evaluated three common methods currently used to estimate NFUE (total N without control, total N with control, and isotopic difference). The total N without control method overestimated mean NFUE by 3.2 times relative to the isotope method, because mineralized N uptake and reabsorption of leaf N was unaccounted for. The total N with control method also overestimated mean NFUE, but only by 20% relative to the isotope method; variation associated with the effects of N fertilization on mineralization and immobilization was large enough to preclude significant difference between these methods. The difference of non-labeled N between day 60 and day 120 revealed that the roots and shoots absorbed 95% and 5%, respectively, of initial leaf N. However, isotopic mass balance between day 60 and day 120 indicated that the NRO seedlings did not reabsorb leaf fertilized N from the youngest leaves before abscission. This study shows that using stable isotopes to understand plant-soil interactions in response to fertilization will help elucidate the contribution of additional N fluxes (e.g., N reabsorption) within perennial plants and thus improve fertility management of production systems.

Fujinuma, R.; Balster, N. J.

2009-12-01

275

In folio respiratory fluxomics revealed by 13C isotopic labeling and H/D isotope effects highlight the noncyclic nature of the tricarboxylic acid "cycle" in illuminated leaves.  

PubMed

While the possible importance of the tricarboxylic acid (TCA) cycle reactions for leaf photosynthesis operation has been recognized, many uncertainties remain on whether TCA cycle biochemistry is similar in the light compared with the dark. It is widely accepted that leaf day respiration and the metabolic commitment to TCA decarboxylation are down-regulated in illuminated leaves. However, the metabolic basis (i.e. the limiting steps involved in such a down-regulation) is not well known. Here, we investigated the in vivo metabolic fluxes of individual reactions of the TCA cycle by developing two isotopic methods, (13)C tracing and fluxomics and the use of H/D isotope effects, with Xanthium strumarium leaves. We provide evidence that the TCA "cycle" does not work in the forward direction like a proper cycle but, rather, operates in both the reverse and forward directions to produce fumarate and glutamate, respectively. Such a functional division of the cycle plausibly reflects the compromise between two contrasted forces: (1) the feedback inhibition by NADH and ATP on TCA enzymes in the light, and (2) the need to provide pH-buffering organic acids and carbon skeletons for nitrate absorption and assimilation. PMID:19675152

Tcherkez, Guillaume; Mahé, Aline; Gauthier, Paul; Mauve, Caroline; Gout, Elizabeth; Bligny, Richard; Cornic, Gabriel; Hodges, Michael

2009-10-01

276

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

NASA Astrophysics Data System (ADS)

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

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

2015-03-01

277

Production of recombinant isotopically labelled peptide by fusion to an insoluble partner protein: generation of integrin ?v?6 binding peptides for NMR.  

PubMed

The integrin ?v?6 is up-regulated in several cancers and has clinical potential for both tumour imaging and therapy. Peptide ligands have been developed which show good binding specificity for ?v?6 and provide an opportunity to study the interaction in more detail by NMR. Such studies ideally require (15)N and (13)C labelled peptides, and recombinant expression within E. coli provides a cost effective way of generating isotopically labelled proteins and peptides. In this study we have used an insoluble fusion partner (ketosteroid isomerase) to produce high yields of recombinant peptide. The insoluble nature of the fusion allowed simple product recovery by cell lysis and centrifugation, and thorough washing of the insoluble pellet to remove contaminating proteins avoided the need for nickel-affinity chromatography in denaturing conditions which is the standard procedure. The protocol described here is convenient to scale-up and requires only one chromatography step (reverse-phase HPLC) which is comparable to solid-phase synthesis. PMID:20953501

Wagstaff, Jane L; Howard, Mark J; Williamson, Richard A

2010-12-01

278

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

Microsoft Academic Search

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

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

2003-01-01

279

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

PubMed

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

Li, Ying-Qin; Tang, Ying; Fu, Rao; Meng, Qiu-Hua; Zhou, Xue; Ling, Ze-Min; Cheng, Xiao; Tian, Su-Wei; Wang, Guo-Jie; Liu, Xue-Guo; Zhou, Li-Hua

2015-07-01

280

Identification of Cargo Proteins Specific for Importin-? with Importin-? Applying a Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)-based in Vitro Transport System*  

PubMed Central

The human importin (Imp)-? family consists of 21 nucleocytoplasmic transport carrier proteins, which transport thousands of proteins (cargoes) across the nuclear envelope through nuclear pores in specific directions. To understand the nucleocytoplasmic transport in a physiological context, the specificity of cargoes for their cognate carriers should be determined; however, only a limited number of nuclear proteins have been linked to specific carriers. To address this biological question, we recently developed a novel method to identify carrier-specific cargoes. This method includes the following three steps: (i) the cells are labeled by stable isotope labeling by amino acids in cell culture (SILAC); (ii) the labeled cells are permeabilized, and proteins in the unlabeled cell extracts are transported into the nuclei of the permeabilized cells by a particular carrier; and (iii) the proteins in the nuclei are quantitatively identified by LC-MS/MS. The effectiveness of this method was demonstrated by the identification of transportin (Trn)-specific cargoes. Here, we applied this method to identify cargo proteins specific for Imp-?, which is a predominant carrier that exclusively utilizes Imp-? as an adapter for cargo binding. We identified candidate cargoes, which included previously reported and potentially novel Imp-? cargoes. In in vitro binding assays, most of the candidate cargoes bound to Imp-? in one of three binding modes: directly, via Imp-?, or via other cargoes. Thus, our method is effective for identifying a variety of Imp-? cargoes. The identified Imp-? and Trn cargoes were compared, ensuring the carrier specificity of the method and illustrating the complexity of these transport pathways. PMID:23846694

Kimura, Makoto; Okumura, Nobuaki; Kose, Shingo; Takao, Toshifumi; Imamoto, Naoko

2013-01-01

281

Probing the electronic structure of tyrosine radical Y Drad in photosystem II by EPR spectroscopy using site specific isotope labelling in Spirodela oligorrhiza  

NASA Astrophysics Data System (ADS)

Tyrosine (Y D) in the D2 reaction centre polypeptide of photosystem II (PSII) is redox-active and, under illumination, forms a dark-stable radical Y Drad . The origin of its stability and the functional role of Y Drad are not well understood. For understanding the electronic structure and reactivity of Y Drad , it is crucial to unambiguosly establish its hyperfine structure. There is considerable variation in the hyperfine data of Y Drad and their interpretation in literature. In the present study, the hyperfine structure of tyrosine radical Y Drad in PSII was probed by EPR in conjunction with carefully designed site specific isotope labelling. A comprehensive series of different selectively 2H-, 13C- or 17O-labeled tyrosine were synthesized and incorporated in Spirodela oligorrhiza with more than 95% enrichment. The 13C- and 17O-hyperfine interactions were obtained from spectral simulations. From the anisotropy of the hyperfine interactions the spin densities at all phenoxyl ring positions were precisely obtained. Comparison of the absolute differences in individual spin densities between Y Drad and neutral tyrosine radical in vitro with those of computationally calculated spin densities yield excellent agreement for a well ordered hydrogen bond between Y Drad and the surrounding protein matrix with a bond length of 1.5 Å. Enantioselective labeling confirms that the ?-methylene hydrogens of Y Drad in S. oligorrhiza are oriented in a highly constrained specific position making Y Drad strongly immobilized, thereby ensuring a firm hydrogen bond of the phenoxyl oxygen to the protein matrix.

Alia; Hulsebosch, Bob; van Gorkom, Hans J.; Raap, Jan; Lugtenburg, Johan; Matysik, Jörg; de Groot, Huub J. M.; Gast, Peter

2003-11-01

282

Efficient (18)F-labeling of large 37-amino-acid pHLIP peptide analogues and their biological evaluation.  

PubMed

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

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

2012-08-15

283

Isotopic composition of H2 from wood burning: Dependency on combustion efficiency, moisture content, and ?D of local precipitation  

NASA Astrophysics Data System (ADS)

Differences in isotopic composition between the various sources of H2 are large, but only a few measurements have been carried out to constrain them. Two conflicting values have been published for H2 from biomass burning. Both rely on the assumption that the isotopic composition of H2 should scale with the isotopic composition of the precipitation at the location where the biomass grew. Here we test this hypothesis using 18 wood samples collected from various locations around the globe. The sample locations cover a range of ?D content of H2 in precipitation, from below -120‰ in Siberia and Canada to -15‰ in Zimbabwe. The results confirm the predicted dependence of the H2 isotopic composition on the precipitation in the sampling region. The water content itself is found to at most slightly affect the results. Furthermore, ?D of H2 depends strongly on combustion efficiency. Thus, the isotopic composition of H2 from biomass burning shows a strong variability around the globe and between different stages of a fire. It is suggested that, rather than a global bulk number, global models that attempt to reproduce the spatial and temporal distribution of ?D in H2 should incorporate explicitly the variability of ?D(H2) from biomass burning on ?D in precipitation.

RöCkmann, Thomas; Gómez ÁLvarez, Catalina X.; Walter, Sylvia; van der Veen, Carina; Wollny, Adam G.; Gunthe, Sachin S.; Helas, Günther; PöSchl, Ulrich; Keppler, Frank; Greule, Markus; Brand, Willi A.

2010-09-01

284

Water use efficiency and carbon isotope composition of plants in a cold desert environment.  

PubMed

The effects of the availabilities of water and nitrogen on water use efficiency (WUE) of plants were investigated in a sagebrush steppe. The four species studied wereArtemisia tridentata (shrub),Ceratoides lanata (suffrutescent shrub),Elymus lanceolatus (rhizomatous grass), andElymus elymoides (tussock grass). Water and nitrogen levels were manipulated in a two-by-two factorial design resulting in four treatments: control (no additions), added water, added nitrogen, and added water and nitrogen. One instantaneous and two long-term indicators of WUE were used to testa priori predictions of the ranking of WUE among treatments. The short-term indicator was the instantaneous ratio of assimilation to transpiration (A/E). The long-term measures were 1) the slope of the relationship between conductance to water vapor and maximum assimilation and 2) the carbon isotope composition (?(13)C) of plant material. Additional water decreased WUE, whereas additional nitrogen increased WUE. For both A/E and ?(13)C, the mean for added nitrogen alone was significantly greater than the mean for added water alone, and means for the control and added water and nitrogen fell in between. This ranking of WUE supported the hypothesis that both water and nitrogen limit plant gas exchange in this semiarid environment. The short- and long-term indicators were in agreement, providing evidence in support of theoretical models concerning the water cost of carbon assimilation. PMID:23494339

Toft, N L; Anderson, J E; Nowak, R S

1989-03-01

285

Highly efficient click labeling using 2-[18F]fluoroethyl azide and synthesis of an 18F N-hydroxysuccinimide ester as conjugation agent  

PubMed Central

Introduction Click labeling using 2-[18F]fluoroethyl azide has been proven to be promising methods of radiolabeling small molecules and peptides, some of which are undergoing clinical evaluations. However, the previously reported method afforded low yield, poor purities and under desirable reproducibility. Methods A vacuum distillation method was used to isolate 2-[18F]fluoroethyl azide, and the solvent effect of acetonitrile (ACN) and dimethylformamide (DMF) on the click labeling using Cu(I) from copper sulfate/sodium ascorbate was studied. The labeling conditions were optimized to radiosynthesize a hydroxysuccinimide ester (NHS). Results 2-[18F]fluoroethyl azide was isolated by the vacuum distillation method with > 80% yield within 10 min in a “pure” and click-ready form. It was found that the amount of DMF was critical for maintaining high levels of Cu(I) from copper sulfate/sodium ascorbate in order to rapidly complete the click labeling reaction. The addition of bathophenanthrolinedisulfonic acid disodium salt (BPDS) to the mixture of copper sulfate/sodium ascorbate also greatly improved the click labeling efficiency. Through exploiting these optimizations, a base-labile N-hydroxysuccinimide (NHS) ester was rapidly radiosynthesized in 90% isolated yield with good chemical and radiochemical purities. Conclusions We have developed a general method to click-label small molecules efficiently using [18F]2 for research and clinical use. This NHS ester can be used for conjugation chemistry to label antibodies, peptides and small molecules as PET tracers. PMID:22770647

Zhou, Dong; Chu, Wenhua; Dence, Carmen S.; Mach, Robert H.; Welch, Michael J.

2012-01-01

286

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

PubMed Central

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

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

2014-01-01

287

Water-Use Efficiency and Stable Carbon Isotopes: Accounting for Photosynthetic Refixation  

NASA Astrophysics Data System (ADS)

Three processes are performed by every green plant tissue: photosynthesis, respiration and refixation. Each of these affects the ratio of stable isotopes, 12C and 13C. Refixation allows plants to fix a portion of the CO2 produced via respiration prior to releasing the remaining CO2 back into the atmosphere. The process begins with a pool of CO2 already depleted in 13C and subsequently depletes it further, resulting in two simultaneous effects: enrichment of CO2 released into the atmosphere and depletion of biomass that is formed. Recently, considerable research has concentrated on identifying processes that determine the isotopic composition of a given plant tissue. A convincing explanation for the observed enrichment of stems versus leaves has still not been derived. We advocate that refixation can explain currently inexplicable patterns. We hypothesized that leaves re-fix carbon during their entire lifespan when light intensity is below the light compensation point and above total darkness. We grew Idaho hybrid poplars under controlled conditions in a growth chamber. Light intensity was regulated to create three different treatments: (1) Light (PAR=270 ?mol/m2s), (2) Shade (PAR=89 ?mol/m2s) and (3) Dark (PAR=0 ?mol/m2s). For each treatment we modified respiration values by regulating the light environment between total darkness and the light compensation point. For the light treatment group, leaf respired CO2 was collected at 5% (PAR=14) and 22% (PAR=59) of the light growing environment. For the shade treatment group, leaf respired CO2 was collected at 22% (PAR=20) of the light growing environment. We estimated the amount of refixation as (Ddark- Dlight)/Ddark, where Ddark represents dark respiration (?mol/gs) and Dlight respiration during light periods (?mol/gs). Light treatments plants exhibited a maximum refixation level of 53% at PAR=59, with an associated enrichment of leaf respired C isotopic composition (?13CLR) of 3.3‰. At PAR=14, refixation rate for Light plants decreased to 10% and the observed enrichment on ?13CLR was 1‰. Correspondingly, Shade plants showed a 37% level of refixation and 3.6‰ enrichment at PAR=20. Our findings support the hypothesis that leaves re-fix carbon under low-light intensity environments. The degree of refixation is proportional to light intensity, with higher refixation rates associated with higher light intensities and more depleted leaf biomass. The continuous refixation of the internal leaf carbon pool during leaf expansion together with diurnal refixation periods in mature leaves adds depleted biomass into the leaf that is likely to account for the patterns described in the literature (i.e. 2‰ depletion of leaf versus stem biomass). This can influence the interpretation of ?13C leaf biomass data of previous studies and can compromise the utility of ?13C from leaf tissue as a precise meter of water-use efficiency.

Ubierna Lopez, N.; Marshall, J. D.

2007-12-01

288

99mTc-Labeled HYNIC-DAPI Causes Plasmid DNA Damage with High Efficiency  

PubMed Central

99mTc is the standard radionuclide used for nuclear medicine imaging. In addition to gamma irradiation, 99mTc emits low-energy Auger and conversion electrons that deposit their energy within nanometers of the decay site. To study the potential for DNA damage, direct DNA binding is required. Plasmid DNA enables the investigation of the unprotected interactions between molecules and DNA that result in single-strand breaks (SSBs) or double-strand breaks (DSBs); the resulting DNA fragments can be separated by gel electrophoresis and quantified by fluorescent staining. This study aimed to compare the plasmid DNA damage potential of a 99mTc-labeled HYNIC-DAPI compound with that of 99mTc pertechnetate (99mTcO4?). pUC19 plasmid DNA was irradiated for 2 or 24 hours. Direct and radical-induced DNA damage were evaluated in the presence or absence of the radical scavenger DMSO. For both compounds, an increase in applied activity enhanced plasmid DNA damage, which was evidenced by an increase in the open circular and linear DNA fractions and a reduction in the supercoiled DNA fraction. The number of SSBs elicited by 99mTc-HYNIC-DAPI (1.03) was twice that caused by 99mTcO4? (0.51), and the number of DSBs increased fivefold in the 99mTc-HYNIC-DAPI-treated sample compared with the 99mTcO4? treated sample (0.02 to 0.10). In the presence of DMSO, the numbers of SSBs and DSBs decreased to 0.03 and 0.00, respectively, in the 99mTcO4– treated samples, whereas the numbers of SSBs and DSBs were slightly reduced to 0.95 and 0.06, respectively, in the 99mTc-HYNIC-DAPI-treated samples. These results indicated that 99mTc-HYNIC-DAPI induced SSBs and DSBs via a direct interaction of the 99mTc-labeled compound with DNA. In contrast to these results, 99mTcO4? induced SSBs via radical formation, and DSBs were formed by two nearby SSBs. The biological effectiveness of 99mTc-HYNIC-DAPI increased by approximately 4-fold in terms of inducing SSBs and by approximately 10-fold in terms of inducing DSBs. PMID:25098953

Kotzerke, Joerg; Punzet, Robert; Runge, Roswitha; Ferl, Sandra; Oehme, Liane; Wunderlich, Gerd; Freudenberg, Robert

2014-01-01

289

Metabolically stable isotope labeling prior to electrophoretic protein separation reveals differences in fractional synthesis rates between mitochondrial aldehyde dehydrogenase isoforms.  

PubMed

Living mice were subjected to whole body labeling by intravenous infusion of [(13)C]glucose as the sole carbon source. After 10 h infusion the mice were sacrificed, and liver proteins were separated by two-dimensional polyacrylamide gel electrophoresis. Five spots were found to contain mitochondrial aldehyde dehydrogenase (ALDH2) by matrix assisted time of flight mass spectrometry protein identification. By measuring the isotopologue mass distributions of peptide ions, and modeling the (13)C content of the precursor amino acid pool, the fractional synthesis rate of ALDH2 molecules synthesized during the labeling period was determined. One of the five spots was observed to have a five-fold higher fraction of (13)C-containing newly synthesized ALDH2 than the spot with the highest ALDH2 content, and contained more than 60% of newly synthesized ALDH2 although it accounted for less than 20% of the total ALDH2 detected. The total range in the fraction of (13)C-containing proteins between different ALDH2 spots approached 50-fold. The ability to quantitatively characterize different protein isoforms of biological origin for ALDH2 and other proteins from living animals provides new avenues for the exploration of protein function. PMID:17466314

Cahill, Michael A; Vogt, Josef A; Servos, Jörg; Wozny, Wojciech; Schwall, Gerhard P; Groebe, Karlfried; Schrattenholz, André; Stegmann, Werner

2007-08-17

290

ACCESSING OVERSEAS MARKETS ENERGY EFFICIENCY STANDARDS AND APPLIANCE LABELING IN ASIA AND LATIN AMERICA  

EPA Science Inventory

The purpose of the project is to reduce pollution and environmental degradation by increasing the efficiency of energy end-uses in the industrial and household sectors of key Asian and Latin American countries. This will be accomplished by encouraging the adoption and harmo...

291

Porous Polymersomes with Encapsulated Gd-labeled Dendrimers as Highly Efficient MRI Contrast Agents**  

PubMed Central

The use of nanovesicles with encapsulated Gd as MR contrast agents has largely been ignored due to the detrimental effects of the slow water exchange rate through the vesicle bilayer on the relaxivity of encapsulated Gd. Here, we describe the facile synthesis of a composite MR contrast platform, consisting of dendrimer conjugates encapsulated in porous polymersomes. These nanoparticles exhibit improved permeability to water flux and a large capacity to store chelated Gd within the aqueous lumen, resulting in enhanced longitudinal relaxivity. The porous polymersomes, ~130 nm in diameter, were produced through the aqueous assembly of the polymers, polyethylene oxide-b-polybutadiene (PBdEO), and polyethylene oxide-b-polycaprolactone (PEOCL). Subsequent hydrolysis of the caprolactone (CL) block resulted in a highly permeable outer membrane. To prevent the leakage of small Gd-chelate through the pores, Gd was conjugated to PAMAM dendrimer via diethylenetriaminepentaacetic acid dianhydride (DTPA dianhydride) prior to encapsulation. As a result of the slower rotational correlation time of Gd-labeled dendrimers, the porous outer membrane of the nanovesicle, and the high Gd payload, these functional nanoparticles were found to exhibit a relaxivity (R1) of 292,109 mM?1 s?1 per particle. The polymersomes were also found to exhibit unique pharmacokinetics with a circulation half-life of >3.5 hrs and predominantly renal clearance. PMID:23293575

Cheng, Zhiliang; Thorek, Daniel L.J.; Tsourkas, Andrew

2012-01-01

292

Characterization of a three-component coupling reaction on proteins by isotopic labeling and nuclear magnetic resonance spectroscopy.  

PubMed

A three-component Mannich-type electrophilic aromatic substitution reaction was previously developed to target the phenolic side chain of tyrosine residues on proteins. This reaction proceeds under mild conditions and provides a convenient alternative to lysine-targeting strategies. However, the use of reactive aldehydes, such as formaldehyde, warrants careful inspection of the reaction products to ensure that other modifications have not occurred. Through the use of isotopically enriched reagents, nuclear magnetic resonance (NMR)-based studies were used to obtain structural confirmation of the tyrosine-modification products. These experiments also revealed the formation of a reaction byproduct arising from the indole ring of tryptophan residues. Cysteine residues were shown to not participate in the reaction, except in the case of a reduced disulfide, which formed a dithioacetal. We anticipate that this analysis method will prove useful for the detailed study of a number of bioconjugation reactions. PMID:18498164

McFarland, Jesse M; Joshi, Neel S; Francis, Matthew B

2008-06-18

293

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

PubMed

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

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

2014-09-01

294

Insulin-dependent interactions of proteins with GLUT4 revealed through stable isotope labeling by amino acids in cell culture (SILAC).  

PubMed

The insulin-regulated glucose transporter (GLUT4) translocates to the plasma membrane in response to insulin in order to facilitate the postprandial uptake of glucose into fat and muscle cells. While early insulin receptor signaling steps leading to this translocation are well defined, the integration of signaling and regulation of GLUT4 traffic remains elusive. Several lines of evidence suggest an important role for the actin cytoskeleton and for protein-protein interactions in regulating GLUT4 localization by insulin. Here, we applied stable isotope labeling by amino acids in cell culture (SILAC) to identify proteins that interact with GLUT4 in an insulin-regulated manner. Myc-tagged GLUT4 (GLUT4myc) stably expressed in L6 myotubes was immunoprecipitated via the myc epitope from total membranes isolated from basal and insulin-stimulated cells grown in medium containing normal isotopic abundance leucine or deuterated leucine, respectively. Proteins coprecipitating with GLUT4myc were analyzed by liquid chromatography/ tandem mass spectrometry. Of 603 proteins quantified, 36 displayed an insulin-dependent change of their interaction with GLUT4myc of more than 1.5-fold in either direction. Several cytoskeleton-related proteins were elevated in immunoprecipates from insulin-treated cells, whereas components of the ubiquitin-proteasome degradation system were generally reduced. Proteins participating in vesicle traffic also displayed insulin-regulated association. Of cytoskeleton-related proteins, alpha-actinin-4 recovery in GLUT4 immunoprecipitates rose in response to insulin 2.1 +/- 0.5-fold by SILAC and 2.9 +/- 0.8-fold by immunoblotting. Insulin caused GLUT4 and alpha-actinin-4 co-localization as revealed by confocal immunofluorescence microscopy. We conclude that insulin elicits changes in interactions between diverse proteins and GLUT4, and that cytoskeletal proteins, notably alpha-actinin-4, associate with the transporter, potentially to facilitate its routing to the plasma membrane. PMID:16396496

Foster, Leonard J; Rudich, Assaf; Talior, Ilana; Patel, Nish; Huang, Xudong; Furtado, L Michelle; Bilan, Philip J; Mann, Matthias; Klip, Amira

2006-01-01

295

Antibody labeling and elemental mass spectrometry (inductively coupled plasma-mass spectrometry) using isotope dilution for highly sensitive ferritin determination and iron-ferritin ratio measurements.  

PubMed

Ferritin, an iron storage protein, is a sensitive clinical biomarker for iron metabolic disorders. It is mainly accumulated in the liver hepatocytes and is present in human plasma at trace levels (picomolar or nanograms per milliliter). Therefore, highly sensitive analytical methods are required to perform ferritin quantification in plasma with high precision and accuracy. For this purpose, we present a mass spectrometry-based analytical strategy (inductively coupled plasma-mass spectrometry, ICP-MS) combined with antibody labeling in a sandwich assay format for ferritin determination. The developed methodology involves two ferritin monoclonal antibodies, one of them biotinylated and the other one labeled with a ruthenium chelate [Ru(bpy)3](2+). The complex formed in solution between ferritin and the two antibodies is then captured using streptavidin-coated magnetic microparticles and directly introduced into ICP-MS for Ru monitoring. Since the Ru complex also allows one to obtain electrogenerated chemiluminescence (ECL), the combination of both sets of data (ICP-MS and ECL) will permit the establishment of the ferritin:Ru stoichiometry. This serves as a basis for further quantification studies using flow injection analysis with isotopically enriched (99)Ru as a carrier with ICP-MS detection. Such strategy permits absolute ferritin determination at a picomolar level with good precision (below 5%) and accuracy (85-109% recovery in the existing ferritin reference material, NIBSC code 94/572). Furthermore, the development of a new strategy to address ferritin:iron-ferritin ratios by ICP-MS opens the door also to address the potential of such ratios as a new clinical biomarker for Fe metabolic disorders. PMID:23889701

Konz, Tobias; Añón Alvarez, Elena; Montes-Bayon, Maria; Sanz-Medel, A

2013-09-01

296

Alzheimer's disease biomarkers detection in human samples by efficient capturing through porous magnetic microspheres and labelling with electrocatalytic gold nanoparticles.  

PubMed

A nanobiosensor based on the use of porous magnetic microspheres (PMM) as efficient capturing/pre-concentrating platform is presented for detection of Alzheimer's disease (AD) biomarkers. These PMMs prepared by a multistep swelling polymerization combined with iron oxide precipitation afford carboxyl functional groups suitable for immobilization of antibodies on the particle surface allowing an enhanced efficiency in the capturing of AD biomarkers from human serum samples. The AD biomarkers signaling is produced by gold nanoparticle (AuNP) tags monitored through their electrocatalytic effect towards hydrogen evolution reaction (HER). Novel properties of PMMs in terms of high functionality and high active area available for enhanced catalytic activity of the captured AuNPs electrocatalytic tags are exploited for the first time. A thorough characterization by scanning transmission electron microscope in high angle annular dark field mode (STEM-HAADF) demonstrates the enhanced ability of PMMs to capture a higher quantity of analyte and consequently of electrocatalytic label, when compared with commercially available microspheres. The optimized and characterized PMMs are also applied for the first time for the detection of beta amyloid and ApoE at clinical relevant levels in cerebrospinal fluid (CSF), serum and plasma samples of patients suffering from AD. PMID:25153932

de la Escosura-Muñiz, Alfredo; Plichta, Zden?k; Horák, Daniel; Merkoçi, Arben

2015-05-15

297

Stable-isotope-labeled histone peptide library for histone post-translational modification and variant quantification by mass spectrometry.  

PubMed

To facilitate accurate histone variant and post-translational modification (PTM) quantification via mass spectrometry, we present a library of 93 synthetic peptides using Protein-Aqua™ technology. The library contains 55 peptides representing different modified forms from histone H3 peptides, 23 peptides representing H4 peptides, 5 peptides representing canonical H2A peptides, 8 peptides representing H2A.Z peptides, and peptides for both macroH2A and H2A.X. The PTMs on these peptides include lysine mono- (me1), di- (me2), and tri-methylation (me3); lysine acetylation; arginine me1; serine/threonine phosphorylation; and N-terminal acetylation. The library was subjected to chemical derivatization with propionic anhydride, a widely employed protocol for histone peptide quantification. Subsequently, the detection efficiencies were quantified using mass spectrometry extracted ion chromatograms. The library yields a wide spectrum of detection efficiencies, with more than 1700-fold difference between the peptides with the lowest and highest efficiencies. In this paper, we describe the impact of different modifications on peptide detection efficiencies and provide a resource to correct for detection biases among the 93 histone peptides. In brief, there is no correlation between detection efficiency and molecular weight, hydrophobicity, basicity, or modification type. The same types of modifications may have very different effects on detection efficiencies depending on their positions within a peptide. We also observed antagonistic effects between modifications. In a study of mouse trophoblast stem cells, we utilized the detection efficiencies of the peptide library to correct for histone PTM/variant quantification. For most histone peptides examined, the corrected data did not change the biological conclusions but did alter the relative abundance of these peptides. For a low-abundant histone H2A variant, macroH2A, the corrected data led to a different conclusion than the uncorrected data. The peptide library and detection efficiencies presented here may serve as a resource to facilitate studies in the epigenetics and proteomics fields. PMID:25000943

Lin, Shu; Wein, Samuel; Gonzales-Cope, Michelle; Otte, Gabriel L; Yuan, Zuo-Fei; Afjehi-Sadat, Leila; Maile, Tobias; Berger, Shelley L; Rush, John; Lill, Jennie R; Arnott, David; Garcia, Benjamin A

2014-09-01

298

Acetylation and glycation of fibrinogen in vitro occur at specific lysine residues in a concentration dependent manner: A mass spectrometric and isotope labeling study  

SciTech Connect

Highlights: Black-Right-Pointing-Pointer Fibrinogen was incubated in vitro with glucose or aspirin. Black-Right-Pointing-Pointer Acetylations and glycations were found at twelve lysine sites by mass spectrometry. Black-Right-Pointing-Pointer The labeling by aspirin and glucose occurred dose-dependently. Black-Right-Pointing-Pointer No competition between glucose and aspirin for binding to fibrinogen was found. -- Abstract: Aspirin may exert part of its antithrombotic effects through platelet-independent mechanisms. Diabetes is a condition in which the beneficial effects of aspirin are less prominent or absent - a phenomenon called 'aspirin resistance'. We investigated whether acetylation and glycation occur at specific sites in fibrinogen and if competition between glucose and aspirin in binding to fibrinogen occurs. Our hypothesis was that such competition might be one explanation to 'aspirin resistance' in diabetes. After incubation of fibrinogen in vitro with aspirin (0.8 mM, 24 h) or glucose (100 mM, 5-10 days), we found 12 modified sites with mass spectrometric techniques. Acetylations in the {alpha}-chain: {alpha}K191, {alpha}K208, {alpha}K224, {alpha}K429, {alpha}K457, {alpha}K539, {alpha}K562, in the {beta}-chain: {beta}K233, and in the {gamma}-chain: {gamma}K170 and {gamma}K273. Glycations were found at {beta}K133 and {gamma}K75, alternatively {gamma}K85. Notably, the lysine 539 is a site involved in FXIII-mediated cross-linking of fibrin. With isotope labeling in vitro, using [{sup 14}C-acetyl]salicylic acid and [{sup 14}C]glucose, a labeling of 0.013-0.084 and 0.12-0.5 mol of acetylated and glycated adduct/mol fibrinogen, respectively, was found for clinically (12.9-100 {mu}M aspirin) and physiologically (2-8 mM glucose) relevant plasma concentrations. No competition between acetylation and glycation could be demonstrated. Thus, fibrinogen is acetylated at several lysine residues, some of which are involved in the cross-linking of fibrinogen. This may mechanistically explain why aspirin facilitates fibrin degradation. We find no support for the idea that glycation of fibrin(ogen) interferes with acetylation of fibrinogen.

Svensson, Jan, E-mail: jan.svensson@ki.se [Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital (Solna), SE-171 76 Stockholm (Sweden) [Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital (Solna), SE-171 76 Stockholm (Sweden); Karolinska Institutet, Department of Clinical Sciences, Danderyd Hospital, SE-182 88 Stockholm (Sweden); Bergman, Ann-Charlotte [Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital (Solna), SE-171 76 Stockholm (Sweden)] [Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital (Solna), SE-171 76 Stockholm (Sweden); Adamson, Ulf [Karolinska Institutet, Department of Clinical Sciences, Danderyd Hospital, SE-182 88 Stockholm (Sweden)] [Karolinska Institutet, Department of Clinical Sciences, Danderyd Hospital, SE-182 88 Stockholm (Sweden); Blombaeck, Margareta [Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital (Solna), SE-171 76 Stockholm (Sweden)] [Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital (Solna), SE-171 76 Stockholm (Sweden); Wallen, Hakan; Joerneskog, Gun [Karolinska Institutet, Department of Clinical Sciences, Danderyd Hospital, SE-182 88 Stockholm (Sweden)] [Karolinska Institutet, Department of Clinical Sciences, Danderyd Hospital, SE-182 88 Stockholm (Sweden)

2012-05-04

299

Stable isotope-labeled tracers for metabolic pathway elucidation by GC-MS and FT-MS.  

PubMed

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

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

2014-01-01

300

Promotion of expression of interferon-stimulated genes in U937 monocytic cells by HIV RNAs, measured using stable isotope labeling with amino acids in cell culture (SILAC).  

PubMed

Type I interferon (IFN) exerts strong antiviral activity, particularly against human immunodeficiency virus (HIV), and although several viral proteins have been shown to deregulate IFN induction, little is known about the induction of type I IFNs by HIV RNAs. In the present study, we used the stable isotope labeling with amino acids in cell culture (SILAC) method to determine the proteomic profile in U937 monocytic cells after transfection with viral RNA of HIV. We then used a western blot assay to validate the proteomic results. It was revealed by the SILAC method that there were 1624 non-redundant peptides with quantitative information and 281 proteins with quantitative information in the HIV-RNA-transfected U937 cells when compared to cells transfected with control RNA. In particular, 6, 8 or 12 hours post-transfection, HIV RNA transfection promoted the expression of such interferon stimulated genes (ISGs) as interferon-induced proteins with tetratricopeptide repeats (IFITs), interferon-induced transmembrane proteins (IFITMs), interferon-induced gene 15 protein (ISG15), myxovirus (influenza virus) resistance protein 1 (MX1), and interferon-induced guanylate-binding protein 1 (GBP1), and this was confirmed by western blot assay. In conclusion, HIV RNA is a strong stimulator of IFNs, promoting the expression of such ISGs as IFITs, IFITMs, ISG15, MX1 and GBP1. PMID:25772570

Li, Yulan; Wen, Bin; Chen, Ran; Jiang, Feng; Zhao, Xiaofang; Deng, Xin

2015-05-01

301

Identifying Natural Substrates for Dipeptidyl Peptidases 8 and 9 Using Terminal Amine Isotopic Labeling of Substrates (TAILS) Reveals in Vivo Roles in Cellular Homeostasis and Energy Metabolism*?  

PubMed Central

Dipeptidyl peptidases (DP) 8 and 9 are homologous, cytoplasmic N-terminal post-proline-cleaving enzymes that are anti-targets for the development of DP4 (DPPIV/CD26) inhibitors for treating type II diabetes. To date, DP8 and DP9 have been implicated in immune responses and cancer biology, but their pathophysiological functions and substrate repertoire remain unknown. This study utilizes terminal amine isotopic labeling of substrates (TAILS), an N-terminal positional proteomic approach, for the discovery of in vivo DP8 and DP9 substrates. In vivo roles for DP8 and DP9 in cellular metabolism and homeostasis were revealed via the identification of more than 29 candidate natural substrates and pathways affected by DP8/DP9 overexpression. Cleavage of 14 substrates was investigated in vitro; 9/14 substrates for both DP8 and DP9 were confirmed by MALDI-TOF MS, including two of high confidence, calreticulin and adenylate kinase 2. Adenylate kinase 2 plays key roles in cellular energy and nucleotide homeostasis. These results demonstrate remarkable in vivo substrate overlap between DP8/DP9, suggesting compensatory roles for these enzymes. This work provides the first global investigation into DP8 and DP9 substrates, providing a number of leads for future investigations into the biological roles and significance of DP8 and DP9 in human health and disease. PMID:23519473

Wilson, Claire H.; Indarto, Dono; Doucet, Alain; Pogson, Lisa D.; Pitman, Melissa R.; McNicholas, Kym; Menz, R. Ian; Overall, Christopher M.; Abbott, Catherine A.

2013-01-01

302

Pulsed Stable Isotope Labeling of Amino Acids in Cell Culture Uncovers the Dynamic Interactions between HIV-1 and the Monocyte-Derived Macrophage  

PubMed Central

Dynamic interactions between human immunodeficiency virus-1 (HIV-1) and the macrophage govern the tempo of viral dissemination and replication in its human host. HIV-1 affects macrophage phenotype, and the macrophage, in turn, can modulate the viral life cycle. While these processes are linked to host–cell function and survival, the precise intracellular pathways involved are incompletely understood. To elucidate such dynamic virus–cell events, we employed pulsed stable isotope labeling of amino acids in cell culture. Alterations in de novo protein synthesis of HIV-1 infected human monocyte-derived macrophages (MDM) were examined after 3, 5, and 7 days of viral infection. Synthesis rates of cellular metabolic, regulatory, and DNA packaging activities were decreased, whereas, those affecting antigen presentation (major histocompatibility complex I and II) and interferon-induced antiviral activities were increased. Interestingly, enrichment of proteins linked to chromatin assembly or disassembly, DNA packaging, and nucleosome assembly were identified that paralleled virus-induced cytopathology and replication. We conclude that HIV-1 regulates a range of host MDM proteins that affect its survival and abilities to contain infection. PMID:21500866

2011-01-01

303

Analysis of the Membrane Proteome of Ciprofloxacin-Resistant Macrophages by Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC)  

PubMed Central

Overexpression of multidrug transporters is a well-established mechanism of resistance to chemotherapy, but other changes may be co-selected upon exposure to drugs that contribute to resistance. Using a model of J774 macrophages made resistant to the fluoroquinolone antibiotic ciprofloxacin and comparing it with the wild-type parent cell line, we performed a quantitative proteomic analysis using the stable isotope labeling with amino acids in cell culture technology coupled with liquid chromatography electrospray ionization Fourier transform tandem mass spectrometry (LC-ESI-FT-MS/MS) on 2 samples enriched in membrane proteins (fractions F1 and F2 collected from discontinuous sucrose gradient). Nine hundred proteins were identified with at least 3 unique peptides in these 2 pooled fractions among which 61 (F1) and 69 (F2) showed a significantly modified abundance among the 2 cell lines. The multidrug resistance associated protein Abcc4, known as the ciprofloxacin efflux transporter in these cells, was the most upregulated, together with Dnajc3, a protein encoded by a gene located downstream of Abcc4. The other modulated proteins are involved in transport functions, cell adhesion and cytoskeleton organization, immune response, signal transduction, and metabolism. This indicates that the antibiotic ciprofloxacin is able to trigger a pleiotropic adaptative response in macrophages that includes the overexpression of its efflux transporter. PMID:23505477

Marquez, Béatrice; Mingeot-Leclercq, Marie-Paule; Tulkens, Paul M.; Devreese, Bart; Van Bambeke, Françoise

2013-01-01

304

Comprehensive and highly sensitive urinary steroid hormone profiling method based on stable isotope-labeling liquid chromatography-mass spectrometry.  

PubMed

Steroid hormones are crucial substances that mediate a wide range of vital physiological functions of the body. Determination of the levels of steroid hormones plays an important role in understanding the mechanism of the steroid hormone-related diseases. In this study, we present a novel targeted metabolic profiling method based on the introduction of an easily protonated stable isotope tag to a hydroxyl-containing steroid hormone with a synthesized derivatization reagent, deuterium 4-(dimethylamino)-benzoic acid (d(4)-DMBA), and liquid chromatography-mass spectrometry (LC-MS). Different from other reported derivatization reagents that have been used to enhance the sensitivities for estrogens or androgens, our method is comprehensive with the capability of covering hydroxyl-containing androgens, estrogens, corticoids, and progestogens. Furthermore, the nonderivatized steroid hormones (e.g., 17?-hydroxyprogesterone, progesterone, and androstenedione) were not destroyed during the derivatization process, and their levels could still be obtained in one LC-MS run. We were able to detect 24 steroid hormones at subng/mL levels (the lower limit of detection could reach 5 pg/mL for estrone and 16?-hydroxy estrone, which is equivalent to 0.1 pg on column) with maximum sensitivity enhancement factors of more than 10(3)- to 10(4)-fold after derivatization. The method was successfully applied to the measurement of free (unconjugated) steroid hormones in urine samples of males, females, and pregnant women. Because the significant role the steroid hormone pathway plays in humans, a comprehensive, sensitive, specific, and accurate method for profiling the steroid hormone metabolome shall offer new insights into hormone-related diseases. PMID:23110480

Dai, Weidong; Huang, Qiang; Yin, Peiyuan; Li, Jia; Zhou, Jia; Kong, Hongwei; Zhao, Chunxia; Lu, Xin; Xu, Guowang

2012-12-01

305

Novel tracer method to measure isotopic labeled gas-phase nitrous acid (HO15NO) in biogeochemical studies.  

PubMed

Gaseous nitrous acid (HONO), the protonated form of nitrite, contributes up to ?60% to the primary formation of hydroxyl radical (OH), which is a key oxidant in the degradation of most air pollutants. Field measurements and modeling studies indicate a large unknown source of HONO during daytime. Here, we developed a new tracer method based on gas-phase stripping-derivatization coupled to liquid chromatography-mass spectrometry (LC-MS) to measure the 15N relative exceedance, ?(15N), of HONO in the gas-phase. Gaseous HONO is quantitatively collected and transferred to an azo dye, purified by solid phase extraction (SPE), and analyzed using high performance liquid chromatography coupled to mass spectrometry (HPLC-MS). In the optimal working range of ?(15N)=0.2-0.5, the relative standard deviation of ?(15N) is <4%. The optimum pH and solvents for extraction by SPE and potential interferences are discussed. The method was applied to measure HO15NO emissions from soil in a dynamic chamber with and without spiking 15) labeled urea. The identification of HO15NO from soil with 15N urea addition confirmed biogenic emissions of HONO from soil. The method enables a new approach of studying the formation pathways of HONO and its role for atmospheric chemistry (e.g., ozone formation) and environmental tracer studies on the formation and conversion of gaseous HONO or aqueous NO2- as part of the biogeochemical nitrogen cycle, e.g., in the investigation of fertilization effects on soil HONO emissions and microbiological conversion of NO2- in the hydrosphere. PMID:24954648

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

2014-07-15

306

Cytotoxicity, cytocompatibility, cell-labeling efficiency, and in vitro cellular magnetic resonance imaging of gadolinium-catalyzed single-walled carbon nanotubes  

PubMed Central

Cell tracking by magnetic resonance imaging (MRI) is an emerging technique that typically requires the use of MRI contrast agents (CAs). A MRI CA for cellular imaging should label cells efficiently at potentially safe concentrations, have high relaxivity, and not affect the cellular machinery. In this article, we report the cytotoxicity, cytocompatibility, and cell labeling efficiency in NIH/3T3 fibroblasts of novel, single-walled carbon nanotubes synthesized using gadolinium nano-particles as catalysts (Gd-SWCNTs). Cells incubated with the Gd-SWCNT showed a dose- (50–100 ?g/mL nanotube concentration) and time- (12–48 h) dependent decrease in viability. 30% cell death was observed for cells incubated with Gd-SWCNTs at the maximum dose of 100 ?g/mL for 48 h. Cells incubated with the Gd-SWCNTs at concentrations between 1–10 ?g/mL for 48 h showed no change in viability or proliferation compared to untreated controls. Additionally, at these potentially safe concentrations, up to 48 h, the cells showed no phosphatidyl serine externalization (pre-apoptotic condition), caspase-3 activity (point of no return for apoptosis), genetic damage, or changes in their division cycle. Localization of Gd-SWCNTs within the cells was confirmed by transmission electron microscopy (TEM) and Raman microscopy, and these results show 100% cell labeling efficiency. Elemental analysis also indicates significant uptake of Gd-SWCNTs by the cells (108–109 Gd3+ ions per cell). Finally, T1-weighted MRI at 3 T of Gd-SWCNT-labelled cells show up to a four-fold increase in MR signal intensities as compared to untreated cells. These results indicate that Gd-SWCNTs label cells efficiently at potentially safe concentrations, and enhance MRI contrast without any structural damage to the cells. PMID:23686792

Avti, Pramod K.; Caparelli, Elisabeth D.; Sitharaman, Balaji

2013-01-01

307

High-throughput quantitation of amino acids in rat and mouse biological matrices using stable isotope labeling and UPLC-MS/MS analysis.  

PubMed

Quantifying amino acids in biological matrices is typically performed using liquid chromatography (LC) coupled with fluorescent detection (FLD), requiring both derivatization and complete baseline separation of all amino acids. Due to its high specificity and sensitivity, the use of UPLC-MS/MS eliminates the derivatization step and allows for overlapping amino acid retention times thereby shortening the analysis time. Furthermore, combining UPLC-MS/MS with stable isotope labeling (e.g., isobaric tag for relative and absolute quantitation, i.e., iTRAQ) of amino acids enables quantitation while maintaining sensitivity, selectivity and speed of analysis. In this study, we report combining UPLC-MS/MS analysis with iTRAQ labeling of amino acids resulting in the elution and quantitation of 44 amino acids within 5 min demonstrating the speed and convenience of this assay over established approaches. This chromatographic analysis time represented a 5-fold improvement over the conventional HPLC-MS/MS method developed in our laboratory. In addition, the UPLC-MS/MS method demonstrated improvements in both specificity and sensitivity without loss of precision. In comparing UPLC-MS/MS and HPLC-MS/MS results of 32 detected amino acids, only 2 amino acids exhibited imprecision (RSD) >15% using UPLC-MS/MS, while 9 amino acids exhibited RSD >15% using HPLC-MS/MS. Evaluating intra- and inter-assay precision over 3 days, the quantitation range for 32 detected amino acids in rat plasma was 0.90-497 ?M, with overall mean intra-day precision of less than 15% and mean inter-day precision of 12%. This UPLC-MS/MS assay was successfully implemented for the quantitative analysis of amino acids in rat and mouse plasma, along with mouse urine and tissue samples, resulting in the following concentration ranges: 0.98-431 ?M in mouse plasma for 32 detected amino acids; 0.62-443 ?M in rat plasma for 32 detected amino acids; 0.44-8590?M in mouse liver for 33 detected amino acids; 0.61-1241 ?M in mouse kidney for 37 detected amino acids; and 1.39-1,681 ?M in rat urine for 34 detected amino acids. The utility of the assay was further demonstrated by measuring and comparing plasma amino acid levels between pre-diabetic Zucker diabetic fatty rats (ZDF/Gmi fa/fa) and their lean littermates (ZDF/Gmi fa/?). Significant differences (P<0.001) in 9 amino acid concentrations were observed, with the majority ranging from a 2- to 5-fold increase in pre-diabetic ZDF rats on comparison with ZDF lean rats, consistent with previous literature reports. PMID:24842860

Takach, Edward; O'Shea, Thomas; Liu, Hanlan

2014-08-01

308

Determination of an Angiotensin II-regulated Proteome in Primary Human Kidney Cells by Stable Isotope Labeling of Amino Acids in Cell Culture (SILAC)  

PubMed Central

Angiotensin II (AngII), the major effector of the renin-angiotensin system, mediates kidney disease progression by signaling through the AT-1 receptor (AT-1R), but there are no specific measures of renal AngII activity. Accordingly, we sought to define an AngII-regulated proteome in primary human proximal tubular cells (PTEC) to identify potential AngII activity markers in the kidney. We utilized stable isotope labeling with amino acids (SILAC) in PTECs to compare proteomes of AngII-treated and control cells. Of the 4618 quantified proteins, 83 were differentially regulated. SILAC ratios for 18 candidates were confirmed by a different mass spectrometry technique called selected reaction monitoring. Both SILAC and selected reaction monitoring revealed heme oxygenase-1 (HO-1) as the most significantly up-regulated protein in response to AngII stimulation. AngII-dependent regulation of the HO-1 gene and protein was further verified in PTECs. To extend these in vitro observations, we overlaid a network of significantly enriched gene ontology terms from our AngII-regulated proteins with a dataset of differentially expressed kidney genes from AngII-treated wild type mice and AT-1R knock-out mice. Five gene ontology terms were enriched in both datasets and included HO-1. Furthermore, HO-1 kidney expression and urinary excretion were reduced in AngII-treated mice with PTEC-specific AT-1R deletion compared with AngII-treated wild-type mice, thus confirming AT-1R-mediated regulation of HO-1. Our in vitro approach identified novel molecular markers of AngII activity, and the animal studies demonstrated that these markers are relevant in vivo. These interesting proteins hold promise as specific markers of renal AngII activity in patients and in experimental models. PMID:23846697

Konvalinka, Ana; Zhou, Joyce; Dimitromanolakis, Apostolos; Drabovich, Andrei P.; Fang, Fei; Gurley, Susan; Coffman, Thomas; John, Rohan; Zhang, Shao-Ling; Diamandis, Eleftherios P.; Scholey, James W.

2013-01-01

309

An isotope-labeled chemical derivatization method for the quantitation of short-chain fatty acids in human feces by liquid chromatography-tandem mass spectrometry.  

PubMed

Short-chain fatty acids (SCFAs) are produced by anaerobic gut microbiota in the large bowel. Qualitative and quantitative measurements of SCFAs in the intestinal tract and the fecal samples are important to understand the complex interplay between diet, gut microbiota and host metabolism homeostasis. To develop a new LC-MS/MS method for sensitive and reliable analysis of SCFAs in human fecal samples, 3-nitrophenylhydrazine (3NPH) was employed for pre-analytical derivatization to convert ten C2-C6 SCFAs to their 3-nitrophenylhydrazones under a single set of optimized reaction conditions and without the need of reaction quenching. The derivatives showed excellent in-solution chemical stability. They were separated on a reversed-phase C18 column and quantitated by negative-ion electrospray ionization - multiple-reaction monitoring (MRM)/MS. To achieve accurate quantitation, the stable isotope-labeled versions of the derivatives were synthesized in a single reaction vessel from (13)C6-3NPH, and were used as internal standard to compensate for the matrix effects in ESI. Method validation showed on-column limits of detection and quantitation over the range from low to high femtomoles for the ten SCFAs, and the intra-day and inter-day precision for determination of nine of the ten SCFAs in human fecal samples was ?8.8% (n=6). The quantitation accuracy ranged from 93.1% to 108.4% (CVs?4.6%, n=6). This method was used to determine the SCFA concentrations and compositions in six human fecal samples. One of the six samples, which was collected from a clinically diagnosed type 2 diabetes patient showed a significantly high molar ratio of branch-chain SCFAs to straight-chain SCFAs than the others. In summary, this work provides a new LC-MS/MS method for precise and accurate quantitation of SCFAs in human feces. PMID:25479871

Han, Jun; Lin, Karen; Sequeira, Carita; Borchers, Christoph H

2015-01-01

310

Osmium isotopes suggest fast and efficient mixing in the oceanic upper mantle.  

NASA Astrophysics Data System (ADS)

The depleted upper mantle (DUM; the source of MORB) is thought to represent the complementary reservoir of continental crust extraction. Previous studies have calculated the "average" DUM composition based on the geochemistry of MORB. However the Nd isotope compositions of abyssal peridotites have been shown to extend to more depleted compositions than associated MORB. While this argues for the presence of both relatively depleted and enriched material within the upper mantle, the extent of compositional variability, length scales of heterogeneity and timescales of mixing in the upper mantle are not well constrained. Model calculations show that 2Ga is a reasonable mean age of depletion for DUM while Hf - Nd isotopes show the persistence of a depleted terrestrial reservoir by the early Archean (3.5-3.8Ga). U/Pb zircon ages of crustal rocks show three distinct peaks at 1.2, 1.9, and 2.7Ga and these are thought to represent the ages of three major crustal growth events. A fundamental question therefore is whether the present day upper mantle retains a memory of multiple ancient depletion events, or has been effectively homogenized. This has important implications for the nature of convection and time scales of survival of heterogeneities in the upper mantle. Here we compare published Os isotope data from abyssal peridotites and ophiolitic Os-Ir alloys with new data from Hawaiian spinel peridotite xenoliths. The Re-Os isotope system has been shown to yield useful depletion age information in peridotites, so we use it here to investigate the distribution of Re-depletion ages (TRD) in these mantle samples as a proxy for the variability of DUM. The probability density functions (PDF) of TRD from osmiridiums, abyssal and Hawaiian peridotites are all remarkably similar and show a distinct peak at 1.2-1.3 Ga (errors for TRD are set at 0.2Ga to suppress statistically spurious age peaks). The Hawaiian peridotites further show a distinct peak at 1.9-2Ga, but no oceanic mantle samples with TRD older than 2Ga have been reported. The TRD age peaks overlap with two major crustal building events recorded in the U/Pb crustal zircon ages. Therefore, peridotites from the convecting upper mantle can retain some memory of ancient depletion events, and these depletions are perhaps linked to major crustal building or large-scale mantle melting events. In the case of the Hawaiian peridotites, an ancient depletion event is further supported by some extremely radiogenic Hf isotope compositions. However, the vast majority of oceanic mantle samples show a narrow rage of Os isotope compositions (187Os/188Os = 0.123-0.126) with TRDs at 300-600 Ma. If the upper mantle has been produced continuously (or episodically) since at least the early Archean, it is then surprising that almost all oceanic mantle samples record such young depletion ages. We suggest that convective mixing in the mantle is rigorous enough that effectively re-homogenizes and resets the Os isotope composition of previously depleted peridotites within short time scales (<500Ma). Similarly recent ages have been derived from modeling the Sr, Nd, Hf, Pb isotopic composition of MORBs. This resetting and homogenization can be due to re-equilibration of depleted mantle with enriched components, e.g. recycled basaltic crust or more fertile mantle. Ancient depletion events are only effectively preserved in the sublithospheric mantle samples (e.g. Kaapval, Slave, Wyoming cratons) because they remain isolated from the convective mantle.

Bizimis, Michael; Salters, Vincent

2010-05-01

311

Uptake and Distribution of Soil Applied Zinc by Citrus Trees-Addressing Fertilizer Use Efficiency with 68Zn Labeling.  

PubMed

The zinc (Zn) supply increases the fruit yield of Citrus trees that are grown, especially in the highly weathered soils of the tropics due to the inherently low nutrient availability in the soil solution. Leaf sprays containing micronutrients are commonly applied to orchards, even though the nutrient supply via soil could be of practical value. This study aimed to evaluate the effect of Zn fertilizers that are applied to the soil surface on absorption and partitioning of the nutrient by citrus trees. A greenhouse experiment was conducted with one-year-old sweet orange trees. The plants were grown in soils with different textures (18.1 or 64.4% clay) that received 1.8 g Zn per plant, in the form of either ZnO or ZnSO4 enriched with the stable isotope 68Zn. Zinc fertilization increased the availability of the nutrient in the soil and the content in the orange trees. Greater responses were obtained when ZnSO4 was applied to the sandy loam soil due to its lower specific metal adsorption compared to that of the clay soil. The trunk and branches accumulated the most fertilizer-derived Zn (Zndff) and thus represent the major reserve organ for this nutrient in the plant. The trees recovered up to 4% of the applied Zndff. Despite this relative low recovery, the Zn requirement of the trees was met with the selected treatment based on the total leaf nutrient content and increased Cu/Zn-SOD activity in the leaves. We conclude that the efficiency of Zn fertilizers depends on the fertilizer source and the soil texture, which must be taken into account by guidelines for fruit crop fertilization via soil, in substitution or complementation of traditional foliar sprays. PMID:25751056

Hippler, Franz Walter Rieger; Boaretto, Rodrigo Marcelli; Quaggio, José Antônio; Boaretto, Antonio Enedi; Abreu-Junior, Cassio Hamilton; Mattos, Dirceu

2015-01-01

312

Uptake and Distribution of Soil Applied Zinc by Citrus Trees—Addressing Fertilizer Use Efficiency with 68Zn Labeling  

PubMed Central

The zinc (Zn) supply increases the fruit yield of Citrus trees that are grown, especially in the highly weathered soils of the tropics due to the inherently low nutrient availability in the soil solution. Leaf sprays containing micronutrients are commonly applied to orchards, even though the nutrient supply via soil could be of practical value. This study aimed to evaluate the effect of Zn fertilizers that are applied to the soil surface on absorption and partitioning of the nutrient by citrus trees. A greenhouse experiment was conducted with one-year-old sweet orange trees. The plants were grown in soils with different textures (18.1 or 64.4% clay) that received 1.8 g Zn per plant, in the form of either ZnO or ZnSO4 enriched with the stable isotope 68Zn. Zinc fertilization increased the availability of the nutrient in the soil and the content in the orange trees. Greater responses were obtained when ZnSO4 was applied to the sandy loam soil due to its lower specific metal adsorption compared to that of the clay soil. The trunk and branches accumulated the most fertilizer-derived Zn (Zndff) and thus represent the major reserve organ for this nutrient in the plant. The trees recovered up to 4% of the applied Zndff. Despite this relative low recovery, the Zn requirement of the trees was met with the selected treatment based on the total leaf nutrient content and increased Cu/Zn-SOD activity in the leaves. We conclude that the efficiency of Zn fertilizers depends on the fertilizer source and the soil texture, which must be taken into account by guidelines for fruit crop fertilization via soil, in substitution or complementation of traditional foliar sprays. PMID:25751056

Hippler, Franz Walter Rieger; Boaretto, Rodrigo Marcelli; Quaggio, José Antônio; Boaretto, Antonio Enedi; Abreu-Junior, Cassio Hamilton; Mattos, Dirceu

2015-01-01

313

The semiquinone at the Qi site of the bc1 complex explored using HYSCORE spectroscopy and specific isotopic labeling of ubiquinone in Rhodobacter sphaeroides via (13)C methionine and construction of a methionine auxotroph.  

PubMed

Specific isotopic labeling at the residue or substituent level extends the scope of different spectroscopic approaches to the atomistic level. Here we describe (13)C isotopic labeling of the methyl and methoxy ring substituents of ubiquinone, achieved through construction of a methionine auxotroph in Rhodobacter sphaeroides strain BC17 supplemented with l-methionine with the side chain methyl group (13)C-labeled. Two-dimensional electron spin echo envelope modulation (HYSCORE) was applied to study the (13)C methyl and methoxy hyperfine couplings in the semiquinone generated in situ at the Qi site of the bc1 complex in its membrane environment. The data were used to characterize the distribution of unpaired spin density and the conformations of the methoxy substituents based on density functional theory calculations of (13)C hyperfine tensors in the semiquinone of the geometry-optimized X-ray structure of the bc1 complex (Protein Data Bank entry 1PP9 ) with the highest available resolution. Comparison with other proteins indicates individual orientations of the methoxy groups in each particular case are always different from the methoxy conformations in the anion radical prepared in a frozen alcohol solution. The protocol used in the generation of the methionine auxotroph is more generally applicable and, because it introduces a gene deletion using a suicide plasmid, can be applied repeatedly. PMID:25184535

Hong, Sangjin; de Almeida, Wagner B; Taguchi, Alexander T; Samoilova, Rimma I; Gennis, Robert B; O'Malley, Patrick J; Dikanov, Sergei A; Crofts, Antony R

2014-09-30

314

Absolute quantification of UGT1A1 in various tissues and cell lines using isotope label-free UPLC-MS/MS method determines its turnover number and correlates with its glucuronidation activities.  

PubMed

Uridine 5'-diphosphate-glucuronosyltransferase (UGT)1A1 is a major phase II metabolism enzyme responsible for glucuronidation of drugs and endogenous compounds. The purpose of this study was to determine the expression level of UGT1A1 in human liver microsomes and human cell lines by using an isotope label-free LC-MS/MS method. A Waters Ultra performance liquid chromatography (UPLC) system coupled with an API 5500Qtrap mass spectrometer was used for the analysis. Two signature peptides (Pep-1, and Pep-2) were employed to quantify UGT1A1 by multiple reaction monitoring (MRM) approach. Standard addition method was used to validate the assay to account for the matrix effect. 17?-Estradiol was used as the marker substrate to determine UGT1A1 activities. The validated method has a linear range of 200-0.0195nM for both signature peptides. The precision, accuracy, and matrix effect were in acceptable ranges. UGT1A1 expression levels were then determined using 8 individual human liver microsomes, a pooled human liver microsomes, three UGT1A1 genotyped human liver microsomes, and four cell lines (Caco-2, MCF-7, Hela, and HepG2). The correlations study showed that the UGT1A1 protein levels were strongly correlated with its glucuronidation activities in human liver microsomes (R(2)=0.85) and in microsomes prepared from cell lines (R(2)=0.95). Isotope-labeled peptides were not necessary for LC-MS/MS quantitation of proteins. The isotope label-free absolute quantification method used here had good accuracy, sensitivity, linear range, and reproducibility, and were used successfully for the accurate determination of UGT1A1 from tissues and cell lines. PMID:24055854

Xu, Beibei; Gao, Song; Wu, Baojian; Yin, Taijun; Hu, Ming

2014-01-01

315

Passage of stable isotope-labeled grass silage fiber and fiber-bound protein through the gastrointestinal tract of dairy cows.  

PubMed

Fractional passage rates are required to predict nutrient absorption in ruminants but data on nutrient-specific passage kinetics are largely lacking. With the use of the stable isotope ratio (?) as an internal marker, we assessed passage kinetics of fiber and fiber-bound nitrogen (N) of intrinsically labeled grass silage from fecal and omasal excretion patterns of ?(13)C and ?(15)N. In a 6×6 Latin square, lactating dairy cows received grass silages [455 g/kg of total diet dry matter (DM) ] in a 2×3 factorial arrangement from ryegrass swards fertilized at low (45 kg of N/ha) or high (90 kg of N/ha) levels of N and harvested at 3 maturity stages. Feed intake (16.7±0.48 kg of DM/d; mean ± standard error of the mean) and milk yield (26.7±0.92 kg/d) increased at the high level of N fertilization and at decreasing maturity. Nutrient digestibility decreased with increasing plant maturity, particularly at the high level of N fertilization, essentially reflecting dietary treatment effects on the nutritional composition of the grass silage. Fractional rumen passage rates (K1) were highest and total mean retention time in the gastrointestinal tract (TMRT) was lowest when based on the external marker chromium mordanted fiber (Cr-NDF; 0.047/h and 38.0 h, respectively). Fecal ?(13)C in the acid detergent fiber fraction ((13)CADF) provided the lowest K1 (0.023/h) and the highest TMRT (61.1 h) and highest peak concentration time (PCT; 24.3h) among markers. In comparison, fecal fiber-bound N ((15)NADF) had a considerably higher K1 (0.032/h) and lower TMRT (46.4 h) than (13)CADF. Total N (measured with (15)NDM) had a comparable K1 (0.034/h) to that of (15)NADF but provided the highest fractional passage rates from the proximal colon-cecum (K2; 0.37/h) and lowest PCT (17.4 h) among markers. A literature review indicated unclear effects of grass silage maturity on K1 and unknown effects of N fertilization on K1. Our study indicated no effect of advancing maturity on fecal K1 and a trend for K1 to increase with the high level of N fertilization. Parameter K2 increased, whereas PCT and TMRT generally decreased with the high level of N fertilization. Omasal digesta sampling largely confirmed results based on fecal sampling. Results indicate that the use of ?(13)C and ?(15)N can describe fiber-specific passage kinetics of forage. PMID:24119806

Warner, D; Dijkstra, J; Hendriks, W H; Pellikaan, W F

2013-12-01

316

Fate of isotopically labeled zinc oxide nanoparticles in sediment and effects on two endobenthic species, the clam Scrobicularia plana and the ragworm Hediste diversicolor.  

PubMed

Although it is reported that metal and metal oxide nanoparticles, which are among the most rapidly commercialized materials, can cause toxicity to organisms, their fate in the environment and toxicity to marine organisms are not well understood. In this study, we used a stable isotope labelling approach to trace the fate of nanoparticles (NPs) in sediments and also investigated bio-uptake in two estuarine intra-sedimentary invertebrates Scrobicularia plana and Nereis diversicolor. We selected exposure to 3 mg kg(-1) sediment ZnO NPs since this level is a realistic prediction of the environmental concentration in sediments. 67ZnO NPs (DLS: 21-34 nm, positively charged: 31.3 mV) suspensions were synthesised in diethylene glycol (DEG). We explored the fate of 67ZnO NPs in sediment, 67Zn bioaccumulation and the biochemical (biomarkers of defence and damage) and behavioural (burrowing kinetics and feeding rates) biomarkers in both species to 67ZnO NPs and DEG on its own during a 16 d laboratory exposure. After exposure, 67Zn concentrations in sediment showed higher levels in the upper section (1cm: 2.59 mg kg(-1)) decreasing progressively (2 cm: 1.63 mg kg(-1), 3 cm: 0.90 mg kg(-1), 4 cm: 0.67 mg kg(-1)) to a minimum value at the bottom (5 cm: 0.31 mg kg(-1)). 67Zn bioaccumulation was observed in both organisms exposed to 67ZnO NPs in DEG but no major inter-species differences were found. At the biochemical level, 67ZnO NPs exposure significantly induced increased glutathione-S-transferase activity in worms and catalase activity in clams whereas superoxide dismutase activity and thiobarbituric acid reactive substance levels were not affected in any species. Exposure to DEG on its own leads to a significant increase of metallothionein-like protein levels in clams compared with those exposed to 67ZnO NPs or controls. Burrowing behaviour as well as feeding rate were significantly impaired in both species exposed to 67ZnO NPs. Concerning exposure to DEG on its own, burrowing behaviour impairments were also shown in both species and feeding rate was impaired in bivalves. At environmentally realistic concentration of 67ZnO NPs in sediment, there is no strong evidence for a severe nanoparticle effect since most effects were also observed in the presence of DEG alone. PMID:22858103

Buffet, Pierre-Emmanuel; Amiard-Triquet, Claude; Dybowska, Agnieszka; Risso-de Faverney, Christine; Guibbolini, Marielle; Valsami-Jones, Eugénia; Mouneyrac, Catherine

2012-10-01

317

Preparation of 13C and 15N labelled RNAs for heteronuclear multi-dimensional NMR studies.  

PubMed Central

A procedure is described for the efficient preparation of isotopically enriched RNAs of defined sequence. Uniformly labelled nucleotide 5'triphosphates (NTPs) were prepared from E.coli grown on 13C and/or 15N isotopically enriched media. These procedures routinely yield 180 mumoles of labelled NTPs per gram of 13C enriched glucose. The labelled NTPs were then used to synthesize RNA oligomers by in vitro transcription. Several 13C and/or 15N labelled RNAs have been synthesized for the sequence r(GGCGCUUGCGUC). Under conditions of high salt or low salt, this RNA forms either a symmetrical duplex with two U.U base pairs or a hairpin containing a CUUG loop respectively. These procedures were used to synthesize uniformly labelled RNAs and a RNA labelled only on the G and C residues. The ability to generate milligram quantities of isotopically labelled RNAs allows application of multi-dimensional heteronuclear magnetic resonance experiments that enormously simplify the resonance assignment and solution structure determination of RNAs. Examples of several such heteronuclear NMR experiments are shown. PMID:1383927

Nikonowicz, E P; Sirr, A; Legault, P; Jucker, F M; Baer, L M; Pardi, A

1992-01-01

318

Elevated CO2 increases tree-level intrinsic water use efficiency: insights from carbon and oxygen isotope analyses in tree rings  

E-print Network

Elevated CO2 increases tree-level intrinsic water use efficiency: insights from carbon and oxygen of trees to increased atmo- spheric CO2 concentration is relatively well understood, there is still isotope analyses in tree rings across three forest FACE sites Giovanna Battipaglia1,2 , Matthias Saurer3

319

Fluorescence energy transfer efficiency in labeled yeast cytochrome c: a rapid screen for ion biocompatibility in aqueous ionic liquids  

SciTech Connect

A fluorescence energy transfer de-quenching assay was implemented to follow the equilibrium unfolding behaviour of site-specific tetramethylrhodamine-labelled yeast cytochrome c in aqueous ionic liquid solutions; additionally, this approach offers the prospect of naked eye screening for biocompatible ion combinations in hydrated ionic liquids.

Baker, Sheila N [ORNL; Zhao, Hua [Savannah State University; Pandey, Siddharth [Indian Institute of Technology, Delhi; Heller, William T [ORNL; Bright, Frank [University of Buffalo, The State University of New York; Baker, Gary A [ORNL

2011-01-01

320

Mechanisms of trichloramine removal with activated carbon: stoichiometric analysis with isotopically labeled trichloramine and theoretical analysis with a diffusion-reaction model.  

PubMed

This study investigated the mechanism by which activated carbon removes trichloramine, a byproduct of water treatment that has a strongly offensive chlorinous odor. A stoichiometrical mass balance for ¹?N before and after activated carbon treatment of laboratory-prepared ¹?N-labeled trichloramine solutions clearly revealed that the mechanism of trichloramine removal with activated carbon was not adsorption but rather reductive decomposition to nitrogen gas. There was a weak positive correlation between the surface decomposition rate constant of trichloramine and the concentration of basic functional groups on the surface of the carbon particles, the suggestion being that the trichloramine may have been reduced by sulfhydryl groups (-SH) on the activated carbon surface. Efficient decomposition of trichloramine was achieved with super powdered activated carbon (SPAC), which was prepared by pulverization of commercially available PAC into very fine particles less than 1 ?m in diameter. SPAC could decompose trichloramine selectively, even when trichloramine and free chlorine were present simultaneously in water, the indication being that the strong disinfection capability of residual free chlorine could be retained even after trichloramine was effectively decomposed. The residual ratio of trichloramine after carbon contact increased somewhat at low water temperatures of 1-5 °C. At these low temperatures, biological treatment, the traditional method for control of a major trichloramine precursor (ammonium nitrogen), is inefficient. Even at these low temperatures, SPAC could reduce the trichloramine concentration to an acceptable level. A theoretical analysis with a diffusion-reaction model developed in the present study revealed that the increase in the trichloramine residual with decreasing water temperature was attributable to the temperature dependence of the rate of the reductive reaction rather than to the temperature dependence of the diffusive mass transfer rate. PMID:25466640

Sakuma, Miki; Matsushita, Taku; Matsui, Yoshihiko; Aki, Tomoko; Isaka, Masahito; Shirasaki, Nobutaka

2015-01-01

321

Silicon isotopes indicate enhanced carbon export efficiency in the North Atlantic during deglaciation.  

PubMed

Today's Sargasso Sea is nutrient starved, except for episodic upwelling events caused by wind-driven winter mixing and eddies. Enhanced diatom opal burial in Sargasso Sea sediments indicates that silicic acid, a limiting nutrient today, may have been more available in subsurface waters during Heinrich Stadials, millennial-scale climate perturbations of the last glacial and deglaciation. Here we use the geochemistry of opal-forming organisms from different water depths to demonstrate changes in silicic acid supply and utilization during the most recent Heinrich Stadial. We suggest that during the early phase (17.5-18 ka), wind-driven upwelling replenished silicic acid to the subsurface, resulting in low Si utilization. By 17 ka, stratification reduced the surface silicic acid supply leading to increased Si utilization efficiency. This abrupt shift in Si cycling would have contributed to high regional carbon export efficiency during the recent Heinrich Stadial, despite being a period of increasing atmospheric CO2. PMID:24452197

Hendry, Katharine R; Robinson, Laura F; McManus, Jerry F; Hays, James D

2014-01-01

322

Carbon transfer from photosynthesis to below ground fine root/hyphae respiration in Quercus serrata using stable carbon isotope pulse labeling  

NASA Astrophysics Data System (ADS)

Studying carbon allocation in trees is a key to better understand belowground carbon cycle and its response to climate change. Tracing 13C in tree and soil compartments after pulse labeling is one of powerful tool to study the fate of carbon in forest ecosystems. This experiment was conducted in Yamashiro experimental forest, Kyoto, Japan. Annual mean temperature and precipitation from 1994 to 2009 are 15.5 ° C and 1,388 mm respectively. The branch pulse labeling were done 7 times in 2011 using same branch of Quercus serrata (H:11.7 m, DBH; 33.7 cm) to see seasonal variations of carbon velocity. Whole crown labeling of Quercus serrata (H:9 m, DBH; 13.7 cm) was done in 2012 to study carbon allocation and to especially focus on belowground carbon flux until to the hyphae respiration. Pure 13CO2 (99.9%) was injected to the labeling chamber which was set to branch or crown. Then, after one hour of branch labeling and 3.5 hour for crown labeling, the chamber was opened. Trunk respiration chambers, fine root chambers and hyphae chambers were set to the target tree to trace labeled carbon in the CO2 efflux. 41 ?m mesh was used to exclude ingrowth of roots into hyphae chambers. The results show that the velocity of carbon through the tree varied seasonally, with higher velocity in summer than autumn, averaging 0.47 m h-1. Half-lives of labeled carbon in autotrophic respiration were similar above and below ground during the growing season, but they were twice longer in trunk than in root in autumn. From the whole crown labeling done end of growing season, the 13CO2 signal was observed 25 hours after labeling in trunk chamber and 34-37.7 hours after labeling in fine root and hyphae respiration almost simultaneously. Half-lives of 13 was longer in trunk than below ground. Trunk respiration was still using labelled carbon during winter suggesting that winter trunk respiration is partly fueled by carbon stored in the trunk at the end of the growing season.

Dannoura, M.; Kominami, Y.; Takanashi, S.; Takahashi, K.

2013-12-01

323

Water use efficiency and carbon isotope composition of plants in a cold desert environment  

Microsoft Academic Search

The effects of the availabilities of water and nitrogen on water use efficiency (WUE) of plants were investigated in a sagebrush steppe. The four species studied wereArtemisia tridentata (shrub),Ceratoides lanata (suffrutescent shrub),Elymus lanceolatus (rhizomatous grass), andElymus elymoides (tussock grass). Water and nitrogen levels were manipulated in a two-by-two factorial design resulting in four treatments: control (no additions), added water, added

Nancee L. Toft; Jay E. Anderson; Robert S. Nowak

1989-01-01

324

Nutritional efficiency of alpha-ketoisocaproate relative to leucine, assessed isotopically  

SciTech Connect

The efficiency of alpha-ketoisocaproate as a dietary substitute for leucine was assessed in rats by two techniques: first, the minimal dose of alpha-ketoisocaproate required, as a supplement to a leucine-free diet, to achieve a growth rate as great as animals receiving leucine was found to be between 2.2 and 4.4 times larger. Therefore the nutritional efficiency of alpha-ketoisocaproate lies between 0.23 and 0.46. Second, alpha-(1- UC)-ketoisocaproate and (TH)leucine were administered orally and the ratio of UC/TH incorporated into the leucine of whole-body protein and fibrin was measured. This ratio, divided by the ratio UC/TH injected, was the same in fibrin as in whole-body protein and averaged 0.39. Thus both techniques yield the same value, within the error of measurement, for the relative nutritional efficiency of alpha-ketoisocaproate. The authors also found that alpha-ketoisocaproate feeding at varying dosage did not alter this ratio in whole-body protein, suggesting that neither wide variations in growth rate nor exposure for 10 days to alpha-ketoisocaproate alters the relative rates of utilization (or oxidation) of alpha-ketoisocaproate vs. leucine.

Kang, C.W.; Walser, M.

1985-10-01

325

High-efficiency preparative-scale reversed-phase high-performance liquid chromatographic purification of 14C-labelled antibiotics.  

PubMed

The 14C-labelled antibiotics [2-14C]mupirocin, and [thienyl-3-14C]temocillin cannot be satisfactorily purified on a small scale by conventional methods of chromatography or recrystallisation. Their purification was successfully achieved by high-efficiency preparative-scale reversed-phase high-performance liquid chromatography. The purifications employed 250 mm X 10 mm I.D. or 22 mm I.D. stainless-steel columns packed with Merck LiChrosorb RP-18 (10 microns) stationary phase which were eluted with aqueous buffer solutions at flow-rates of 10-25 ml min-1 using conventional analytical instrumentation. PMID:3106386

Morecombe, D J

1987-03-13

326

Quantitative analysis of N-glycans from human alfa-acid-glycoprotein using stable isotope labeling and zwitterionic hydrophilic interaction capillary liquid chromatography electrospray mass spectrometry as tool for pancreatic disease diagnosis.  

PubMed

In this work we demonstrate the potential of glycan reductive isotope labeling (GRIL) using [(12)C]- and [(13)C]-coded aniline and zwitterionic hydrophilic interaction capillary liquid chromatography electrospray mass spectrometry (?ZIC-HILIC-ESI-MS) for relative quantitation of glycosylation variants in selected glycoproteins present in samples from cancer patients. Human ?1-acid-glycoprotein (hAGP) is an acute phase serum glycoprotein whose glycosylation has been described to be altered in cancer and chronic inflammation. However, it is not clear yet whether some particular glycans in hAGP can be used as biomarker for differentiating between these two pathologies. In this work, hAGP was isolated by immunoaffinity chromatography (IAC) from serum samples of healthy individuals and from those suffering chronic pancreatitis and different stages of pancreatic cancer, respectively. After de-N-glycosylation, relative quantitation of the hAGP glycans was carried out using stable isotope labeling and ?ZIC-HILIC-ESI-MS analysis. First, protein denaturing conditions prior to PNGase F digestion were optimized to achieve quantitative digestion yields, and the reproducibility of the established methodology was evaluated with standard hAGP. Then, the proposed method was applied to the analysis of the clinical samples (control vs. pathological). Pancreatic cancer samples clearly showed an increase in the abundance of fucosylated glycans as the stage of the disease increases and this was unlike to samples from chronic pancreatitis. The results gained here indicate the mentioned glycan in hAGP as a candidate structure worth to be corroborated by an extended study including more clinical cases; especially those with chronic pancreatitis and initial stages of pancreatic cancer. Importantly, the results demonstrate that the presented methodology combining an enrichment of a target protein by IAC with isotope coded relative quantitation of N-glycans can be successfully used for targeted glycomics studies. The methodology is assumed being suitable as well for other such studies aimed at finding novel cancer associated glycoprotein biomarkers. PMID:25732693

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

2015-03-25

327

Ingestion and assimilation efficiency of Aeshna brevistyla and Hemicordulia australiae larvae (Odonata)  

Microsoft Academic Search

In a laboratory study of the ingestion and assimilation efficiency of larvae of Aeshna brevistyla Rambur and Hemicordulia australiae Rambur, ingestion was determined using Cerenkov radiation techniques and assimilation efficiency by a double?labelled isotope technique. Of each prey item (Daphnia carinata), 30% was not ingested but lost as body fluids and as material within the alimentary canal of the prey.

R. A. Prestidge

1979-01-01

328

Antibodies labeled with 199Au: potential of 199Au for radioimmunotherapy.  

PubMed

We have investigated the direct labeling of antibodies with gold isotopes as an alternative to iodine and chelated metals for antibody guided therapy. Both 199Au and 195Au complex anions in citrate-buffered solutions (pH 3.8-7.2) are rapidly bound to sheep polyclonal anti-CEA with high efficiency. After purification by gel filtration, the antibody retained 80% of the bound gold for upto 6 days at 4 degrees C and was reactive with its target antigen in a solid phase assay. Incubation with the gold binding substance D-penicillamine reduced labeling efficiency and stability. PMID:3384677

Anderson, P; Vaughan, A T; Varley, N R

1988-01-01

329

Food labeling  

MedlinePLUS

Nutrition labeling ... made, those nutrients must be listed on the nutrition label. Percent daily value: The amounts of vitamins ... listed as a Percent Daily Value on the nutrition label. The Percent Daily Value for vitamins and ...

330

Transpiration efficiency over an annual cycle, leaf gas exchange and wood carbon isotope ratio of three tropical tree species.  

PubMed

Variation in transpiration efficiency (TE) and its relationship with the stable carbon isotope ratio of wood was investigated in the saplings of three tropical tree species. Five individuals each of Platymiscium pinnatum (Jacq.) Dugand, Swietenia macrophylla King and Tectona grandis Linn. f. were grown individually in large (760 l) pots over 16 months in the Republic of Panama. Cumulative transpiration was determined by repeatedly weighing the pots with a pallet truck scale. Dry matter production was determined by destructive harvest. The TE, expressed as experiment-long dry matter production divided by cumulative water use, averaged 4.1, 4.3 and 2.9 g dry matter kg(-1) water for P. pinnatum, S. macrophylla and T. grandis, respectively. The TE of T. grandis was significantly lower than that of the other two species. Instantaneous measurements of the ratio of intercellular to ambient CO(2) partial pressures (c(i)/c(a)), taken near the end of the experiment, explained 66% of variation in TE. Stomatal conductance was lower in S. macrophylla than in T. grandis, whereas P. pinnatum had similar stomatal conductance to T. grandis, but with a higher photosynthetic rate. Thus, c(i)/c(a) and TE appeared to vary in response to both stomatal conductance and photosynthetic capacity. Stem-wood delta(13)C varied over a relatively narrow range of just 2.2 per thousand, but still explained 28% of variation in TE. The results suggest that leaf-level processes largely determined variation among the three tropical tree species in whole-plant water-use efficiency integrated over a full annual cycle. PMID:19661136

Cernusak, Lucas A; Winter, Klaus; Aranda, Jorge; Virgo, Aurelio; Garcia, Milton

2009-09-01

331

The physiological basis for genetic variation in water use efficiency and carbon isotope composition in Arabidopsis thaliana.  

PubMed

Ecologists and physiologists have documented extensive variation in water use efficiency (WUE) in Arabidopsis thaliana, as well as association of WUE with climatic variation. Here, we demonstrate correlations of whole-plant transpiration efficiency and carbon isotope composition (?(13)C) among life history classes of A. thaliana. We also use a whole-plant cuvette to examine patterns of co-variation in component traits of WUE and ?(13)C. We find that stomatal conductance (g s) explains more variation in WUE than does A. Overall, there was a strong genetic correlation between A and g s, consistent with selection acting on the ratio of these traits. At a more detailed level, genetic variation in A was due to underlying variation in both maximal rate of carboxylation (V cmax) and maximum electron transport rate (Jmax). We also found strong effects of leaf anatomy, where lines with lower WUE had higher leaf water content (LWC) and specific leaf area (SLA), suggesting a role for mesophyll conductance (g m) in variation of WUE. We hypothesize that this is due to an effect through g m, and test this hypothesis using the abi4 mutant. We show that mutants of ABI4 have higher SLA, LWC, and g m than wild-type, consistent with variation in leaf anatomy causing variation in g m and ?(13)C. These functional data also add further support to the central, integrative role of ABI4 in simultaneously altering ABA sensitivity, sugar signaling, and CO2 assimilation. Together our results highlight the need for a more holistic approach in functional studies, both for more accurate annotation of gene function and to understand co-limitations to plant growth and productivity. PMID:23893317

Easlon, Hsien Ming; Nemali, Krishna S; Richards, James H; Hanson, David T; Juenger, Thomas E; McKay, John K

2014-02-01

332

Simultaneous detection of stable isotope-labeled and unlabeled L-tryptophan and of its main metabolites, L-kynurenine, serotonin and quinolinic acid, by gas chromatography/negative ion chemical ionization mass spectrometry.  

PubMed

A method for the detection of unlabeled and (15)N2 -labeled L-tryptophan (L-Trp), L-kynurenine (L-Kyn), serotonin (5-HT) and quinolinic acid (QA) in human and rat plasma by GC/MS is described. Labeled and unlabeled versions of these four products were analyzed as their acyl substitution derivatives using pentafluoropropionic anhydride and 2,2,3,3,3-pentafluoro-1-propanol. Products were then separated by GC and analyzed by selected ion monitoring using negative ion chemical ionization mass spectrometry. L-[(13)C11, (15)N2]-Trp, methyl-serotonin and 3,5-pyridinedicarboxylic acid were used as internal standards for this method. The coefficients of variation for inter-assay repeatability were found to be approximately 5.2% for L-Trp and (15)N2-Trp, 17.1% for L-Kyn, 16.9% for 5-HT and 5.8% for QA (n?=?2). We used this method to determine isotope enrichments in plasma L-Trp over the course of a continuous, intravenous infusion of L-[(15) N2 ]Trp in pregnant rat in the fasting state. Plasma (15)N2-Trp enrichment reached a plateau at 120?min. The free Trp appearance rate (Ra) into plasma was 49.5?±?3.35?µmol/kg/h. The GC/MS method was applied to determine the enrichment of (15)N-labeled L-Trp, L-Kyn, 5-HT and QA concurrently with the concentration of non-labeled L-Trp, L-Kyn, 5-HT and QA in plasma. This method may help improve our understanding on L-Trp metabolism in vivo in animals and humans and potentially reveal the relative contribution of the four pathways of L-Trp metabolism. PMID:24677305

Sano, Mitsue; Ferchaud-Roucher, Véronique; Nael, Charlotte; Aguesse, Audrey; Poupeau, Guillaume; Castellano, Blandine; Darmaun, Dominique

2014-02-01

333

Efficient Blind Spectral Unmixing of Fluorescently Labeled Samples Using Multi-Layer Non-Negative Matrix Factorization  

PubMed Central

The ample variety of labeling dyes and staining methods available in fluorescence microscopy has enabled biologists to advance in the understanding of living organisms at cellular and molecular level. When two or more fluorescent dyes are used in the same preparation, or one dye is used in the presence of autofluorescence, the separation of the fluorescent emissions can become problematic. Various approaches have been recently proposed to solve this problem. Among them, blind non-negative matrix factorization is gaining interest since it requires little assumptions about the spectra and concentration of the fluorochromes. In this paper, we propose a novel algorithm for blind spectral separation that addresses some of the shortcomings of existing solutions: namely, their dependency on the initialization and their slow convergence. We apply this new algorithm to two relevant problems in fluorescence microscopy: autofluorescence elimination and spectral unmixing of multi-labeled samples. Our results show that our new algorithm performs well when compared with the state-of-the-art approaches for a much faster implementation. PMID:24260120

Zudaire, Isabel; Ortiz-de-Solorzano, Carlos

2013-01-01

334

Isotope effect in BEDT-TTF based organic superconductors  

SciTech Connect

The results of the comprehensive isotope effect studies, in which seven different isotopically labeled (involving {sup 13}C, {sup 34}S and {sup 2}H labeling) BEDT-TTF derivatives and isotopically labeled anion [Cu({sup 15}N{sup 13}CS){sub 2}]{sup {minus}} were utilized, are summarized. For the first time, convincing evidence for a genuine BCS-like mass isotope effect in an organic superconductor is revealed in these studies.

Kini, A.M.; Carlson, K.D.; Dudek, J.D.; Geiser, U.; Wang, H.H.; Williams, J.M.

1996-10-01

335

Estradiol-17 beta determined in plasma by gas chromatography-mass spectrometry with selected ion monitoring of mixed silyl ether-perfluoroacyl ester derivatives and use of various stable-isotope-labeled internal standards  

SciTech Connect

A highly specific method is described for measuring estradiol-17 beta (E2) in plasma by gas chromatography-mass spectrometry (GC-MS) associated with stable isotope dilution. A mixed derivative, E2-3-trimethylsilyl ether-17-heptafluorobutyrate (E2-3-TMS-17-HFB), was found to have excellent analytical properties. The specificity of the derivatization procedure exploits a unique feature of estrogens: the selective exchange of a phenolic perfluoroacyl ester for a trialkylsilyl ether. No significant differences in E2 concentration could be ascribed to the use of /sup 2/H- or /sup 13/C-labeled analogs, thus ruling out interferences from possible isotope exchange commonly attributed to deuterated compounds. Precision is closely similar to that for methods in which the more common E2-3, 17-bis(trimethylsilyl) ether and E2-3, 17-bis(heptafluorobutyrate) derivatives are used. Sensitivity and specificity of the mixed 3-TMS-17-HFB derivative allow adequate determinations of E2, even in plasma from males, in 2-mL samples. Interlaboratory mean concentrations of E2 obtained by routine immunoassays were consistently higher than the target values estimated by GC-MS, particularly at concentrations less than 100 pmol/L.

Dehennin, L.

1989-04-01

336

Strategy combining separation of isotope-labeled unfolded proteins and matrix-assisted laser desorption/ionization mass spectrometry analysis enables quantification of a wide range of serum proteins.  

PubMed

A novel strategy for the quantitative profiling of serum proteome is described. It includes an ammonium sulfate depletion of the serum, an affordable stable isotope labeling chemistry for samples with a large amount of protein, separation of the unfolded proteins, and relative quantification by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS). Labeling of unfolded proteins was performed using normal (D(0)) acrylamide and deuterated (D(3)) acrylamide. The workflow for separating the unfolded proteins includes whole gel elution and ion exchange liquid chromatography, and it combines electrophoretic separation based on the protein molecular weight followed by chromatographic separation in the presence of 8M urea based on protein charge. This was followed by trypsinolysis and MALDI MS analysis, leading to the quantification of a large number of serum proteins, including those with an abundance of 10(-5) less than albumin. This robust and inexpensive workflow is suitable for the quantitative profiling of protein changes in serum associated with preanalytical variables. PMID:18384735

Liao, Wei-Li; Turko, Illarion V

2008-06-01

337

Estimation of the efficiency of hydrocarbon mineralization in soil by measuring CO2-emission and variations in the isotope composition of carbon dioxide  

NASA Astrophysics Data System (ADS)

Estimation of the efficiency of hydrocarbon mineralization in soil by measuring CO2-emission and variations in the isotope composition of carbon dioxide E. Dubrovskaya1, O. Turkovskaya1, A. Tiunov2, N. Pozdnyakova1, A. Muratova1 1 - Institute of Biochemistry and Physiology of Plants and Microorganisms, RAS, Saratov, 2 - A.N. Severtsov Institute of Ecology and Evolution, RAS, Moscow, Russian Federation Hydrocarbon mineralization in soil undergoing phytoremediation was investigated in a laboratory experiment by estimating the variation in the 13?/12? ratio in the respired ??2. Hexadecane (HD) was used as a model hydrocarbon pollutant. The polluted soil was planted with winter rye (Secale cereale) inoculated with Azospirillum brasilense strain SR80, which combines the abilities to promote plant growth and to degrade oil hydrocarbon. Each vegetated treatment was accompanied with a corresponding nonvegetated one, and uncontaminated treatments were used as controls. Emission of carbon dioxide, its isotopic composition, and the residual concentration of HD in the soil were examined after two and four weeks. At the beginning of the experiment, the CO2-emission level was higher in the uncontaminated than in the contaminated soil. After two weeks, the quantity of emitted carbon dioxide decreased by about three times and did not change significantly in all uncontaminated treatments. The presence of HD in the soil initially increased CO2 emission, but later the respiration was reduced. During the first two weeks, nonvegetated soil had the highest CO2-emission level. Subsequently, the maximum increase in respiration was recorded in the vegetated contaminated treatments. The isotope composition of plant material determines the isotope composition of soil. The soil used in our experiment had an isotopic signature typical of soils formed by C3 plants (?13C,-22.4‰). Generally, there was no significant fractionation of the carbon isotopes of the substrates metabolized by the soil microbiota. The plants and microorganisms used had the isotopic signatures similar to that of the soil, whereas the ?13C of HD was -47.9‰. The HD mineralization level was assessed by determining the difference between the isotopic compositions of soil CO2 immediately after pollution and during remediation. In the unvegetated soil, about 13% of initially added HD was mineralized, the phytoremediation increased the total decomposition of the contaminant to 19%, and an additional plant inoculation with strain SR80 raised it to 33%. The GC analysis of soil demonstrated that contaminant loss in the plant treatments and in the inoculated plant treatment was 71 and 72%, respectively, whereas in the nonvegetated treatments, it was 64 and 66%, respectively. Thus, the elimination of the contaminant resulted from its total mineralization (CO2 emission) and partial chemical transformation.

Dubrovskaya, Ekaterina; Turkovskaya, Olga

2010-05-01

338

Proteins with High Turnover Rate in Barley Leaves Estimated by Proteome Analysis Combined with in Planta Isotope Labeling1[W][OPEN  

PubMed Central

Protein turnover is a key component in cellular homeostasis; however, there is little quantitative information on degradation kinetics for individual plant proteins. We have used 15N labeling of barley (Hordeum vulgare) plants and gas chromatography-mass spectrometry analysis of free amino acids and liquid chromatography-mass spectrometry analysis of proteins to track the enrichment of 15N into the amino acid pools in barley leaves and then into tryptic peptides derived from newly synthesized proteins. Using information on the rate of growth of barley leaves combined with the rate of degradation of 14N-labeled proteins, we calculate the turnover rates of 508 different proteins in barley and show that they vary by more than 100-fold. There was approximately a 9-h lag from label application until 15N incorporation could be reliably quantified in extracted peptides. Using this information and assuming constant translation rates for proteins during the time course, we were able to quantify degradation rates for several proteins that exhibit half-lives on the order of hours. Our workflow, involving a stringent series of mass spectrometry filtering steps, demonstrates that 15N labeling can be used for large-scale liquid chromatography-mass spectrometry studies of protein turnover in plants. We identify a series of abundant proteins in photosynthesis, photorespiration, and specific subunits of chlorophyll biosynthesis that turn over significantly more rapidly than the average protein involved in these processes. We also highlight a series of proteins that turn over as rapidly as the well-known D1 subunit of photosystem II. While these proteins need further verification for rapid degradation in vivo, they cluster in chlorophyll and thiamine biosynthesis. PMID:25082890

Nelson, Clark J.; Alexova, Ralitza; Jacoby, Richard P.; Millar, A. Harvey

2014-01-01

339

Dissection of Hydrogen Bond Interaction Network around an Iron-sulfur Cluster by Site-specific Isotope Labeling of Hyperthermophilic Archaeal Rieske-type Ferredoxin  

PubMed Central

The electronic structure and geometry of redox-active metal cofactors in proteins are tuned by the pattern of hydrogen bonding with the backbone peptide matrix. In this study we developed a method for selective amino acid labeling of a hyper-thermophilic archaeal metalloprotein with engineered Escherichia coli auxotroph strains, and applied this to resolve the hydrogen bond interactions with the reduced Rieske-type [2Fe-2S] cluster by two-dimensional pulsed electron spin resonance (EPR) technique. Because deep electron spin-echo envelope modulation of two histidine 14N? ligands of the cluster decreased non-coordinating 15N signal intensities via the cross-suppression effect, an inverse labeling strategy was employed in which 14N amino acid-labeled archaeal Rieske-type ferredoxin samples were examined in an 15N-protein background. This has directly identified Lys45 N? as providing the major pathway for the transfer of unpaired electron spin density from the reduced cluster by a “through-bond” mechanism. All other backbone peptide nitrogens interact more weakly with the reduced cluster. The extension of this approach will allow visualizing the three-dimensional landscape of preferred pathways for the transfer of unpaired spin density from a paramagnetic metal center onto the protein frame, and will discriminate specific interactions by a “through-bond” mechanism from interactions which are “through-space” in various metalloproteins. PMID:23145461

Iwasaki, Toshio; Fukazawa, Risako; Miyajima-Nakano, Yoshiharu; Baldansuren, Amgalanbaatar; Matsushita, Shinichi; Lin, Myat T.; Gennis, Robert B.; Hasegawa, Kazuya; Kumasaka, Takashi; Dikanov, Sergei A.

2012-01-01

340

Protected Amine Labels: A Versatile Molecular Scaffold for Multiplexed Nominal Mass and Sub-Da Isotopologue Quantitative Proteomic Reagents  

NASA Astrophysics Data System (ADS)

We assemble a versatile molecular scaffold from simple building blocks to create binary and multiplexed stable isotope reagents for quantitative mass spectrometry. Termed Protected Amine Labels (PAL), these reagents offer multiple analytical figures of merit including, (1) robust targeting of peptide N-termini and lysyl side chains, (2) optimal mass spectrometry ionization efficiency through regeneration of primary amines on labeled peptides, (3) an amino acid-based mass tag that incorporates heavy isotopes of carbon, nitrogen, and oxygen to ensure matched physicochemical and MS/MS fragmentation behavior among labeled peptides, and (4) a molecularly efficient architecture, in which the majority of hetero-atom centers can be used to synthesize a variety of nominal mass and sub-Da isotopologue stable isotope reagents. We demonstrate the performance of these reagents in well-established strategies whereby up to four channels of peptide isotopomers, each separated by 4 Da, are quantified in MS-level scans with accuracies comparable to current commercial reagents. In addition, we utilize the PAL scaffold to create isotopologue reagents in which labeled peptide analogs differ in mass based on the binding energy in carbon and nitrogen nuclei, thereby allowing quantification based on MS or MS/MS spectra. We demonstrate accurate quantification for reagents that support 6-plex labeling and propose extension of this scheme to 9-channels based on a similar PAL scaffold. Finally, we provide exemplar data that extend the application of isotopologe-based quantification reagents to medium resolution, quadrupole time-of-flight mass spectrometers.

Ficarro, Scott B.; Biagi, Jessica M.; Wang, Jinhua; Scotcher, Jenna; Koleva, Rositsa I.; Card, Joseph D.; Adelmant, Guillaume; He, Huan; Askenazi, Manor; Marshall, Alan G.; Young, Nicolas L.; Gray, Nathanael S.; Marto, Jarrod A.

2014-04-01

341

Efficient Estimators for Quantum Instanton Evaluation of theKinetic Isotope Effects: Application to the Intramolecular HydrogenTransfer in Pentadiene  

SciTech Connect

The quantum instanton approximation is used to compute kinetic isotope effects for intramolecular hydrogen transfer in cis-1,3-pentadiene. Due to the importance of skeleton motions, this system with 13 atoms is a simple prototype for hydrogen transfer in enzymatic reactions. The calculation is carried out using thermodynamic integration with respect to the mass of the isotopes and a path integral Monte Carlo evaluation of relevant thermodynamic quantities. Efficient 'virial' estimators are derived for the logarithmic derivatives of the partition function and the delta-delta correlation functions. These estimators require significantly fewer Monte Carlo samples since their statistical error does not increase with the number of discrete time slices in the path integral. The calculation treats all 39 degrees of freedom quantum-mechanically and uses an empirical valence bond potential based on a modified general AMBER force field.

Vanicek, Jiri; Miller, William H.

2007-06-13

342

An Efficient and Compact Difference-Frequency-Generation Spectrometer and Its Application to 12CH3D/12CH4 Isotope Ratio Measurements  

PubMed Central

We have developed an efficient and compact 3.4 ?m difference-frequency-generation spectrometer using a 1.55 ?m distributed feedback (DFB) laser diode, a 1.06 ?m DFB laser diode, and a ridge-waveguide periodically poled lithium niobate. It is continuously tunable in the 30 cm?1 span and is applied to 12CH3D/12CH4 isotope ratio measurements. The suitable pair of 12CH3D ?4 pP(7,6) and 12CH4 ? 2+?4 R(6) F1(1) lines enabled us to determine their isotope ratio with a precision repeatability of 0.8‰ using a sample and a working standard of pure methane with an effective signal averaging time of 100 ms. PMID:22163569

Tsuji, Kiyoshi; Teshima, Hiroaki; Sasada, Hiroyuki; Yoshida, Naohiro

2010-01-01

343

ISOTOPE METHODS IN HOMOGENEOUS CATALYSIS.  

SciTech Connect

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.

BULLOCK,R.M.; BENDER,B.R.

2000-12-01

344

Direct Detection and Characterization of Chloride in the Active Site of the Low-pH Form of Sulfite Oxidase Using ESEEM Spectroscopy, Isotopic Labeling, and DFT Calculations  

PubMed Central

Electron spin echo envelope modulation (ESEEM) investigations were carried out on samples of the low-pH (lpH) form of vertebrate sulfite oxidase (SO) prepared with 35Cl- and 37Cl-enriched buffers as well as with buffer containing the natural abundance of Cl isotopes. The isotope-related changes observed in the ESEEM spectra provide direct and unequivocal evidence that Cl? is located in close proximity to the Mo(V) center of lpH SO. The measured isotropic hyperfine interaction constant of about 4 MHz (35Cl) suggests that the Cl? ion is either weakly coordinated to Mo(V) at its otherwise vacant axial position, trans to the oxo ligand, or is hydrogen-bonded to the equatorial exchangeable OH ligand. Scalar relativistic all-electron density functional theory (DFT) calculations of the hyperfine and nuclear quadrupole interaction parameters, along with steric and energetic arguments, strongly support the possibility that Cl? is hydrogen-bonded to the equatorial OH ligand rather than being directly coordinated to the Mo(V). PMID:19402624

Klein, Eric L.; Astashkin, Andrei V.; Ganyushin, Dmitry; Riplinger, Christoph; Johnson-Winters, Kayunta; Neese, Frank; Enemark, John H.

2009-01-01

345

International Isotope Society  

NSDL National Science Digital Library

The international isotope society (IIS) "aims to encourage the synthesis and applications of isotopes and isotopically labeled compounds to benefit of all." Visitors can find information about upcoming international conferences as well as summaries of past symposiums. The website provides copies of the presentation speeches discussing the activities of award winning scientists. Researchers can find out about the society's low level radioactive waste committee's activities to create a positive public image of the use of radioisotopes in research. An online technical report educates students and teachers about photomultipliers and their applications.

346

Determination of betaine metabolites and dimethylsulfoniopropionate in coral tissues using liquid chromatography-time-of-flight mass spectrometry and stable isotope-labeled internal standards.  

PubMed

A convenient procedure for determination of seven betaine analogs and dimethylsulfoniopropionate (DMSP) in extracts of coral tissues using LC-MS stable isotope dilution is described. Extraction procedures were optimized for selective extraction of polar metabolites from coral tissues. The LC-MS protocol employed a pentafluorophenylpropyl (PFPP) column for HPLC separation, with chromatographic resolution of isobaric and isomeric zwitterionic metabolites optimized by adjusting the acidity of the mobile phase. A ternary gradient was used to exploit the unusual retention characteristics of cationic metabolites on the PFPP column, with incorporation of ammonium acetate in a later gradient stage promoting elution of more hydrophobic betaines which are retained at high organic content in the absence of ammonium acetate. We demonstrate that the new LC-MS based method provides accurate measurements from nanomolar to high micromolar concentrations, and can be applied for profiling of betaine metabolites and DMSP in corals or other aquatic organisms. PMID:20627732

Li, Chao; Hill, Richard W; Jones, A Daniel

2010-07-01

347

Synthesis of deuterium-labeled prochlorperazine  

Microsoft Academic Search

The propylpiperazine side chain of prochlorperazine was labeled with two, four, or six deuterium atoms by lithium aluminum deuteride reduction of the appropriate amide. The isotopic purity of the products after correcting for chlorine isotopes was greater than 95.7%.

Edward M. Hawes; Trevor S. Gurnsey; H. Umesha Shetty; Kamal K. Midha

1983-01-01

348

Synthesis of deuterium-labeled prochlorperazine  

SciTech Connect

The propylpiperazine side chain of prochlorperazine was labeled with two, four, or six deuterium atoms by lithium aluminum deuteride reduction of the appropriate amide. The isotopic purity of the products after correcting for chlorine isotopes was greater than 95.7%.

Hawes, E.M.; Gurnsey, T.S.; Shetty, H.U.; Midha, K.K.

1983-06-01

349

Isotopes in day to day life  

NASA Astrophysics Data System (ADS)

Developments are reported in the use of isotopic labeling and isotope irradiation in agriculture, medical science, hydrology, geochemistry, geophysics, environment pollution detection, and industries. Radioisotope instruments are described as well as techniques for gamma radiography, neutron radiography, and autoradiography. Isotope dating in geology and archaeology is covered. Basic scientific research topics in various areas are listed.

1984-06-01

350

Hydrogen isotope fractionation during H2\\/CO2 acetogenesis: hydrogen utilization efficiency and the origin of lipid-bound hydrogen  

Microsoft Academic Search

Hydrogen metabolism was studied in the anaerobic bacterium, Sporomusa sp. strain DMG 58, by measuring natural abundance levels of deuterium in H 2 , H 2 O, and individual fatty acids during acetogenic growth on H 2 \\/ CO 2 . Four cultures were grown, each in medium with a distinct hydrogen-isotopic composition ( ? D-H 2 O). The ?

D. L. VALENTINE; A. L. SESSIONS; S. C. TYLER; A. CHIDTHAISONG

2004-01-01

351

A comparative study of the selectivity and efficiency of target tissue uptake of five tritium-labeled androgens in the rat.  

PubMed

A comparative study of the tissue distribution of five tritium-labeled androgens was done in rats to determine the efficiency and selectivity of their uptake by target tissue. Testosterone (T), 5 alpha-dihydrotestosterone (DHT), 19-nortestosterone (nor-T), mibolerone (Mib) and methyltrienolone (R1881) all showed selective uptake by the ventral prostate in one-day castrated rats (250 g) that was 61-90% displaceable by co-injection of an excess of unlabeled steroid. The greatest uptake was with R1881 (0.69% injected dose per gram prostate tissue (%ID/g) at 1 h), and Mib (0.56% ID/g); the other three showed lower uptake (approx. 0.4% ID/g). The target tissue activity remained high for all compounds up to 4 h after injection, and at 2-4 h the prostate to blood ratio for Mib and R1881 exceeded 10 and 20, respectively. The uptake efficiency and selectivity of these five androgens appear to be related to their affinity for the androgen receptor and their resistance to metabolism. Mib and R1881 have substantial affinity for other steroid receptors, which might account for some of their prostate uptake. However, co-administration of triamcinolone acetonide, which has high affinity for progesterone and corticosteroid receptors but not for the androgen receptor, failed to block their uptake significantly, whereas co-administration of DHT, the most selective ligand for the androgen receptor, blocked their uptake as completely as the unlabeled tracer itself. The prostate uptake of Mib and R1881 in intact animals was significantly lower than in castrated animals, but treatment of the intact animals with diethylstilbestrol restored their uptake nearly to the level seen in castrated animals. These uptake patterns are consistent with earlier studies of in vivo androgen uptake and with known changes in androgen receptor content and occupancy as a result of castration or diethylstilbestrol treatment. They further suggest that high affinity androgens labeled with suitable radionuclides--particularly derivatives of mibolerone (Mib) or methyltrienolone (R1881)--may be effective receptor-based imaging agents for androgen target tissues and tumors, even when patients are already receiving hormonal therapy. PMID:2214772

Carlson, K E; Katzenellenbogen, J A

1990-08-28

352

Labeling Theory  

Microsoft Academic Search

Labeling theory provides a distinctively sociological approach that focuses on the role of social labeling in the development\\u000a of crime and deviance. The theory assumes that although deviant behavior can initially stem from various causes and conditions,\\u000a once individuals have been labeled or defined as deviants, they often face new problems that stem from the reactions of self\\u000a and others

Jón Gunnar Bernburg

353

An Enhanced In Vivo Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) Model for Quantification of Drug Metabolism Enzymes*  

PubMed Central

Many of the enzymes involved in xenobiotic metabolism are maintained at a low basal level and are only synthesized in response to activation of upstream sensor/effector proteins. This induction can have implications in a variety of contexts, particularly during the study of the pharmacokinetics, pharmacodynamics, and drug–drug interaction profile of a candidate therapeutic compound. Previously, we combined in vivo SILAC material with a targeted high resolution single ion monitoring (tHR/SIM) LC-MS/MS approach for quantification of 197 peptide pairs, representing 51 drug metabolism enzymes (DME), in mouse liver. However, as important enzymes (for example, cytochromes P450 (Cyp) of the 1a and 2b subfamilies) are maintained at low or undetectable levels in the liver of unstimulated metabolically labeled mice, quantification of these proteins was unreliable. In the present study, we induced DME expression in labeled mice through synchronous ligand-mediated activation of multiple upstream nuclear receptors, thereby enhancing signals for proteins including Cyps 1a, 2a, 2b, 2c, and 3a. With this enhancement, 115 unique, lysine-containing, Cyp-derived peptides were detected in the liver of a single animal, as opposed to 56 in a pooled sample from three uninduced animals. A total of 386 peptide pairs were quantified by tHR/SIM, representing 68 Phase I, 30 Phase II, and eight control proteins. This method was employed to quantify changes in DME expression in the hepatic cytochrome P450 reductase null (HRN) mouse. We observed compensatory induction of several enzymes, including Cyps 2b10, 2c29, 2c37, 2c54, 2c55, 2e1, 3a11, and 3a13, carboxylesterase (Ces) 2a, and glutathione S-transferases (Gst) m2 and m3, along with down-regulation of hydroxysteroid dehydrogenases (Hsd) 11b1 and 17b6. Using DME-enhanced in vivo SILAC material with tHR/SIM, therefore, permits the robust analysis of multiple DME of importance to xenobiotic metabolism, with improved utility for the study of drug pharmacokinetics, pharmacodynamics, and of chemically treated and genetically modified mouse models. PMID:25561501

MacLeod, A. Kenneth; Fallon, Padraic G.; Sharp, Sheila; Henderson, Colin J.; Wolf, C. Roland; Huang, Jeffrey T.-J.

2015-01-01

354

CAESAR—A high-efficiency CsI(Na) scintillator array for in-beam ?-ray spectroscopy with fast rare-isotope beams  

NASA Astrophysics Data System (ADS)

We report on the construction and commissioning of the high-efficiency CAESium-iodide scintillator ARray CAESAR, a device designed for in-beam ?-ray spectroscopy experiments utilizing fast beams of rare isotopes at the National Superconducting Cyclotron Laboratory (NSCL) at Michigan State University (MSU). CAESAR consists of 192 CsI(Na) crystals, totaling 290 kg of active scintillator material. For 1 MeV ? rays, a full-energy-peak efficiency of 35% is achieved at an in-beam energy resolution of better than 10% FWHM after event-by-event Doppler reconstruction of the ? rays emitted by nuclei moving with velocities of v/c˜0.3-0.4. The spectral quality of the array allows for the identification of ?-ray transitions with intensities of several 10 counts in the full-energy peak and thus opens new avenues for the study of the most exotic nuclei available at the NSCL for in-beam spectroscopy.

Weisshaar, D.; Gade, A.; Glasmacher, T.; Grinyer, G. F.; Bazin, D.; Adrich, P.; Baugher, T.; Cook, J. M.; Diget, C. Aa.; McDaniel, S.; Ratkiewicz, A.; Siwek, K. P.; Walsh, K. A.

2010-12-01

355

Assessment of effects of the rising atmospheric nitrogen deposition on nitrogen uptake and long-term water-use efficiency of plants using nitrogen and carbon stable isotopes.  

PubMed

This study assesses the effects of the atmospheric nitrogen (N) deposition on the N uptake and the long-term water-use efficiency of two C(3) plants (Agropyron cristatum and Leymus chinensis) and two C(4) plants (Amaranthus retroflexus and Setaria viridis) using N and C stable isotopes. In addition, this study explores the potential correlation between leaf N isotope (?(15)N) values and leaf C isotope (?(13)C) values. This experiment shows that the atmospheric N deposition has significant effects on the N uptake, ?(15)N and leaf N content (N(m)) of C(3) plants. As the atmospheric N deposition rises, the proportion and the amount of N absorbed from the simulated atmospheric deposition become higher, and the ?(15)N and N(m) of the two C(3) plants both also increase, suggesting that the rising atmospheric N deposition is beneficial for C(3) plants. However, C(4) plants display different patterns in their N uptake and in their variations of ?(15)N and N(m) from those of C(3) plants. C(4) plants absorb less N from the atmospheric deposition, and the leaf N(m) does not change with the elevated atmospheric N deposition. Photosynthetic pathways may account for the differences between C(3) and C(4) plants. This study also shows that atmospheric N deposition does not play a role in determining the ?(13)C and in the long-term water-use efficiency of C(3) and C(4) plants, suggesting that the long-term water-use pattern of the plants does not change with the atmospheric N input. In addition, this study does not observe any relationship between leaf ?(15)N and leaf ?(13)C in both C(3) and C(4) plants. PMID:21638358

Yao, F Y; Wang, G A; Liu, X J; Song, L

2011-07-15

356

Nutrition Labeling  

NASA Astrophysics Data System (ADS)

Nutrition labeling regulations differ in countries around the world. The focus of this chapter is on nutrition labeling regulations in the USA, as specified by the Food and Drug Administration (FDA) and the Food Safety and Inspection Service (FSIS) of the United States Department of Agriculture (USDA). A major reason for analyzing the chemical components of foods in the USA is nutrition labeling regulations. Nutrition label information is not only legally required in many countries, but also is of increasing importance to consumers as they focus more on health and wellness.

Metzger, Lloyd E.

357

Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fish.  

PubMed

The developing vertebrate nervous system contains a remarkable array of neural cells organized into complex, evolutionarily conserved structures. The labeling of living cells in these structures is key for the understanding of brain development and function, yet the generation of stable lines expressing reporter genes in specific spatio-temporal patterns remains a limiting step. In this study we present a fast and reliable pipeline to efficiently generate a set of stable lines expressing a reporter gene in multiple neuronal structures in the developing nervous system in medaka. The pipeline combines both the accurate computational genome-wide prediction of neuronal specific cis-regulatory modules (CRMs) and a newly developed experimental setup to rapidly obtain transgenic lines in a cost-effective and highly reproducible manner. 95% of the CRMs tested in our experimental setup show enhancer activity in various and numerous neuronal structures belonging to all major brain subdivisions. This pipeline represents a significant step towards the dissection of embryonic neuronal development in vertebrates. PMID:21637758

Mongin, Emmanuel; Auer, Thomas O; Bourrat, Franck; Gruhl, Franziska; Dewar, Ken; Blanchette, Mathieu; Wittbrodt, Joachim; Ettwiller, Laurence

2011-01-01

358

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

NASA Astrophysics Data System (ADS)

Chemical cross-linking of proteins followed by proteolysis and mass spectrometric analysis of the resulting cross-linked peptides provides powerful insight into the quaternary structure of protein complexes. Mixed-isotope cross-linking (a method for distinguishing intermolecular cross-links) was coupled with liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS) to provide an additional separation dimension to the traditional cross-linking approach. This method produced multiplet m/z peaks that are aligned in the IMS drift time dimension and serve as signatures of intermolecular cross-linked peptides. We developed an informatics tool to use the amino acid sequence information inherent in the multiplet spacing for accurate identification of the cross-linked peptides. Because of the separation of cross-linked and non-cross-linked peptides in drift time, our LC-IMS-MS approach was able to confidently detect more intermolecular cross-linked peptides than LC-MS alone.

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

2013-03-01

359

Isotopic labeling experiments that elucidate the mechanism of DNA strand cleavage by the hypoxia-selective antitumor agent 1,2,4-benzotriazine 1,4-di-N-oxide.  

PubMed

The 1,2,4-benzotriazine 1,4-dioxides are an important class of potential anticancer drugs that selectively kill the low-oxygen (hypoxic) cells found in solid tumors. These compounds undergo intracellular one-electron enzymatic reduction to yield an oxygen-sensitive drug radical intermediate that partitions forward, under hypoxic conditions, to generate a highly reactive secondary radical that causes cell killing DNA damage. Here, we characterized bioreductively activated, hypoxia-selective DNA-strand cleavage by 1,2,4-benzotriazine 1,4-dioxide. We found that one-electron enzymatic activation of 1,2,4-benzotriazine 1,4-dioxide under hypoxic conditions in the presence of the deuterium atom donor methanol-d4 produced nondeuterated mono-N-oxide metabolites. This and the results of other isotopic labeling studies provided evidence against the generation of atom-abstracting drug radical intermediates and are consistent with a DNA-damage mechanism involving the release of hydroxyl radical from enzymatically activated 1,2,4-benzotriazine 1,4-dioxides. PMID:24328261

Shen, Xiulong; Rajapakse, Anuruddha; Gallazzi, Fabio; Junnotula, Venkatraman; Fuchs-Knotts, Tarra; Glaser, Rainer; Gates, Kent S

2014-01-21

360

Isotopic labeling experiments that elucidate the mechanism of DNA strand cleavage by the hypoxia-selective antitumor agent 1,2,4-benzotriazine 1,4-di-N-oxide  

PubMed Central

The 1,2,4-benzotriazine 1,4-dioxides are an important class of potential anticancer drugs that selectively kill the low-oxygen (hypoxic) cells found in solid tumors. These compounds undergo intracellular one-electron enzymatic reduction to yield an oxygen-sensitive drug radical intermediate that partitions forward, under hypoxic conditions, to generate a highly reactive secondary radical that causes cell killing DNA damage. Here we characterized bioreductively-activated, hypoxia-selective DNA-strand cleavage by 1,2,4-benzotriazine 1,4-dioxide. We found that one-electron enzymatic activation of 1,2,4-benzotriazine 1,4-dioxide under hypoxic conditions in the presence of the deuterium atom donor methanol-d4 produced non-deuterated mono-N-oxide metabolites. This and the results of other isotopic labeling studies provided evidence against the generation of atom-abstracting drug radical intermediates and are consistent with a DNA-damage mechanism involving release of hydroxyl radical from enzymatically-activated 1,2,4-benzotriazine 1,4-dioxides. PMID:24328261

Shen, Xiulong; Rajapakse, Anuruddha; Gallazzi, Fabio; Junnotula, Venkatraman; Fuchs-Knotts, Tarra; Glaser, Rainer; Gates, Kent S.

2014-01-01

361

Phosphoprotein Isotope-Coded Solid-Phase Tag Approach for Enrichment and Quantitative Analysis of Phosphopeptides from Complex Mixtures  

SciTech Connect

Many cellular processes are regulated by reversible protein phosphorylation and the ability to identify and quantify phosphoproteins from proteomes is essential for gaining a better understanding of these dynamic cellular processes. However, a sensitive, efficient and global method capable of addressing the phosphoproteome has yet to be developed. Here we describe an improved stable-isotope labeling method using a Phosphoprotein Isotope-coded Solid-phase Tag (PhIST) for isolating and measuring the relative abundance of phosphorylated peptides from complex peptide mixtures resulting from the enzymatic digestion of extracted proteins. The PhIST approach is an extension of the previously reported Phosphoprotein Isotope-coded Affinity Tag (PhIAT)approach developed by our laboratory1-2, where the O-phosphate moiety on phosphoseryl or phosphothreonyl residues were derivatized by hydroxide ion-medated B-elimination followed by the addition of 1,2-ethanedithiol (EDT). Instead of using the biotin affinity tag, peptides containing the EDT moiety were captured and labeled in one step using isotope-coded solid-phase reagents containing either light (12C6, 14N) or heavy (13C6, 15N) stable isotopes. The captured peptides labeled with the isotope-coded tags were released from the solid-phase support by UV photocleavage and analyzed by capillary LC-MS/MS. The efficiency and sensitivity of the PhIST labeling approach for identification of phosphopeptides from mixtures was demonstrated using casein phosphoproteins. Its utility for proteomic applications is demonstrated by the labeling of soluble proteins from human breast cancer cell line.

Qian, Weijun (BATTELLE (PACIFIC NW LAB)) [BATTELLE (PACIFIC NW LAB); Goshe, Michael B.(North Carolina State University) [North Carolina State University; Camp, David G.(BATTELLE (PACIFIC NW LAB)) [BATTELLE (PACIFIC NW LAB); Yu, Li-Rong (BATTELLE (PACIFIC NW LAB)) [BATTELLE (PACIFIC NW LAB); Tang, Keqi (BATTELLE (PACIFIC NW LAB)) [BATTELLE (PACIFIC NW LAB); Smith, Richard D.(BATTELLE (PACIFIC NW LAB)) [BATTELLE (PACIFIC NW LAB)

2003-10-15

362

Biomolecular tracing using long-lived isotopes  

SciTech Connect

Accelerator mass spectrometry (AMS) was developed over the past 15 years as an essential tool for detecting long-lived, cosmogenic radio-isotopes in the earth and space sciences. We apply this technology to the measurement of chemical kinetics, primarily in biomedical systems, which had heretofore employed short-lived isotopes and/or long counting times to quantify radio-isotopic labels. AMS provides detection efficiencies of {approx} 1%, 10{sup 3} to 10{sup 6} better than decay-counting. Long-lived isotopes are used and detected with AMS at concentrations which reduce sample size, chemical dose, radiation safety hazards and radiolysis. We measure {sup 3}H, {sup 7,1O}Be, {sup 14}C, {sup 26}Al, {sup 36}CI, {sup 41}Ca and {sup 129}I, but most of our current program uses {sup 14}C. Initial experiments involved research on the genotoxicity of mutagens in cooked foods and reversible binding of compounds to antibodies. Through collaborations, we apply AMS detection to research in carcinogenesis, pharmacokinetics of toxins, elemental metabolism, distribution of topical medications and nutrition.

Vogel, J.S.; Turteltaub, K.W.; Frantz, C.E.; Keating, G.; Felton, J.S.; Southon, J.R.; Roberts, M.R.; Gledhill, B.L.

1992-06-03

363

18O-Labeled Proteome Reference as Global Internal Standards for Targeted Quantification by Selected Reaction Monitoring-Mass Spectrometry  

SciTech Connect

Selected reaction monitoring-mass spectrometry (SRM-MS) is an emerging technology for high throughput targeted protein quantification and verification in biological and biomarker discovery studies; however, the cost associated with the use of stable isotope labeled synthetic peptides as internal standards is prohibitive for quantitatively screening large numbers of candidate proteins as often required in the pre-verification phase of biomarker discovery. Herein we present the proof-of-concept experiments of using an 18O-labeled 'universal' reference as comprehensive internal standards for quantitative SRM-MS analysis. With an 18O-labeled whole proteome sample as reference, every peptide of interest will have its own corresponding heavy isotope labeled internal standard, thus providing an ideal approach for quantitative screening of a large number of candidates using SRM-MS. Our results showed that the 18O incorporation efficiency using a recently improved protocol was >99.5% for most peptides investigated, a level comparable to 13C/15N labeled synthetic peptides in terms of heavy isotope incorporation. The accuracy, reproducibility, and linear dynamic range of quantification were further assessed based on known ratios of standard proteins spiked into mouse plasma with an 18O-labeled mouse plasma reference. A dynamic range of four orders of magnitude in relative concentration was obtained with high reproducibility (i.e., coefficient of variance <10%) based on the 16O/18O peak area ratios. Absolute and relative quantification of C-reactive protein and prostate-specific antigen were demonstrated by coupling an 18O-labeled reference with standard additions of protein standards. Collectively, our results demonstrated that the use of 18O-labeled reference provides a convenient and effective strategy for quantitative SRM screening of large number of candidate proteins.

Kim, Jong Seo; Fillmore, Thomas L.; Liu, Tao; Robinson, Errol W.; Hossain, Mahmud; Champion, Boyd L.; Moore, Ronald J.; Camp, David G.; Smith, Richard D.; Qian, Weijun

2011-10-11

364

Estimates of precipitation efficiency and evaporation of falling precipitation in the tropics and subtropics based on measurements of the stable isotope ratio from satellite  

NASA Astrophysics Data System (ADS)

The humidity of the tropics and subtropics plays a disproportionate role in the radiative balance of the planet, and understanding the response of the tropical humidity to climate forcing is critical for determining climate sensitivity. Correctly modeling the complex set of processes that control the humidity requires consideration of large-scale transport, turbulence processes and cloud microphysical processes. While these are all included in general circulation models, many of the aspects associated with clouds are treated by parameterizations which represents a significant challenge. Previous modeling work has highlighted the importance of rain production, which is often modeled using a simplified treatment of autoconversion of cloud condensate. This quantity directly influences the fraction of total water lofted at the cloud based which is ultimately detrained by clouds to moisten the environment. Similarly, the degree to which falling condensate evaporates and moistening the lower troposphere is generally not well understood and not well observed over wide spatial scales. Consequently, evaporation of falling precipitation is parameterized simply in most climate models. Here we analyze results from a simple model of the humidity and isotope ratio profiles in the tropics. The model includes many of the features included in climate models such as detrainment, precipitation formation by autoconversion, large-scale subsidence, evaporation of falling condensate and export of water by horizontal eddies. Sensitivity tests show that the selection of parameters associated with precipitation efficiency and the evaporation of falling precipitation are the critical controls on the profile of isotope ratios. Making use of this sensitivity, profile observations of the D/H isotope ratio from NASA Tropospheric Emission Spectrometer are used to provide an optimal parameter estimate. The solutions provide an observational target for climate models. We discuss the limitations of the modeling framework and the need to balance the microphysical controls against influences of large-scale moisture transport.

Noone, D. C.

2012-12-01

365

Highly efficient one-pot labeling of new phosphonium cations with fluorine-18 as potential PET agents for myocardial perfusion imaging.  

PubMed

Lipophilic cations such as phosphonium salts can accumulate in mitochondria of heart in response to the negative inner-transmembrane potentials. Two phosphonium salts [(18)F]FMBTP and [(18)F]mFMBTP were prepared and evaluated as potential myocardial perfusion imaging (MPI) agents in this study. The cations were radiolabeled via a simplified one-pot method starting from [(18)F]fluoride and followed by physicochemical property tests, in vitro cellular uptake assay, ex vivo mouse biodistribution, and in vivo rat microPET imaging. The total radiosynthesis time was less than 60 min including HPLC purification. The [(18)F] labeled compounds were obtained in high radiolabeling yield (?50%) and good radiochemical purity (>99%). Both compounds were electropositive, and their log P values at pH 7.4 were 1.16 ± 0.003 (n = 3) and 1.05 ± 0.01 (n = 3), respectively. Both [(18)F]FMBTP and [(18)F]mFMBTP had high heart uptake (25.24 ± 2.97% ID/g and 31.02 ± 0.33% ID/g at 5 min postinjection (p.i.)) in mice with good retention (28.99 ± 3.54% ID/g and 26.82 ± 3.46% ID/g at 120 min p.i.). From the PET images in rats, the cations exhibited high myocardium uptake and fast clearance from liver and small intestine to give high-contrast images across all time points. These phosphonium cations were radiosynthesized via a highly efficient one-pot procedure for potential MPI offering high heart accumulation and rapid nontarget clearance. PMID:24852080

Zhao, Zuoquan; Yu, Qian; Mou, Tiantian; Liu, Chang; Yang, Wenjiang; Fang, Wei; Peng, Cheng; Lu, Jie; Liu, Yu; Zhang, Xianzhong

2014-11-01

366

Rapid and efficient localization of depth electrodes and cortical labeling using free and open source medical software in epilepsy surgery candidates  

PubMed Central

Depth intracranial electrodes (IEs) placement is one of the most used procedures to identify the epileptogenic zone (EZ) in surgical treatment of drug resistant epilepsy patients, about 20–30% of this population. IEs localization is therefore a critical issue defining the EZ and its relation with eloquent functional areas. That information is then used to target the resective surgery and has great potential to affect outcome. We designed a methodological procedure intended to avoid the need for highly specialized medical resources and reduce time to identify the anatomical location of IEs, during the first instances of intracranial EEG recordings. This workflow is based on established open source software; 3D Slicer and Freesurfer that uses MRI and Post-implant CT fusion for the localization of IEs and its relation with automatic labeled surrounding cortex. To test this hypothesis we assessed the time elapsed between the surgical implantation process and the final anatomical localization of IEs by means of our proposed method compared against traditional visual analysis of raw post-implant imaging in two groups of patients. All IEs were identified in the first 24 H (6–24 H) of implantation using our method in 4 patients of the first group. For the control group; all IEs were identified by experts with an overall time range of 36 h to 3 days using traditional visual analysis. It included (7 patients), 3 patients implanted with IEs and the same 4 patients from the first group. Time to localization was restrained in this group by the specialized personnel and the image quality available. To validate our method; we trained two inexperienced operators to assess the position of IEs contacts on four patients (5 IEs) using the proposed method. We quantified the discrepancies between operators and we also assessed the efficiency of our method to define the EZ comparing the findings against the results of traditional analysis. PMID:24427112

Princich, Juan Pablo; Wassermann, Demian; Latini, Facundo; Oddo, Silvia; Blenkmann, Alejandro Omar; Seifer, Gustavo; Kochen, Silvia

2013-01-01

367

Tree-ring stable isotopes reveal twentieth-century increases in water-use efficiency of Fagus sylvatica and Nothofagus spp. in Italian and Chilean mountains.  

PubMed

Changes in intrinsic water use efficiency (iWUE) were investigated in Fagus sylvatica and Nothofagus spp. over the last century. We combined dendrochronological methods with dual-isotope analysis to investigate whether atmospheric changes enhanced iWUE of Fagus and Nothofagus and tree growth (basal area increment, BAI) along latitudinal gradients in Italy and Chile. Post-maturation phases of the trees presented different patterns in ?13C, ?13C, ?18O, Ci (internal CO2 concentration), iWUE, and BAI. A continuous enhancement in isotope-derived iWUE was observed throughout the twentieth century, which was common to all sites and related to changes in Ca (ambient CO2 concentration) and secondarily to increases in temperature. In contrast to other studies, we observed a general increasing trend of BAI, with the exception of F. sylvatica in Aspromonte. Both iWUE and BAI were uncoupled with the estimated drought index, which is in agreement with the absence of enduring decline in tree growth. In general, ?13C and ?18O showed a weak relationship, suggesting the major influence of photosynthetic rate on Ci and ?13C, and the minor contribution of the regulation of stomatal conductance to iWUE. The substantial warming observed during the twentieth century did not result in a clear pattern of increased drought stress along these latitudinal transects, because of the variability in temporal trends of precipitation and in specific responses of populations. PMID:25398040

Tognetti, Roberto; Lombardi, Fabio; Lasserre, Bruno; Cherubini, Paolo; Marchetti, Marco

2014-01-01

368

Monte Carlo simulation of a PhosWatch detector using Geant4 for xenon isotope beta-gamma coincidence spectrum profile and detection efficiency calculations.  

PubMed

A simulation tool has been developed using the Geant4 Toolkit to simulate a PhosWatch single channel beta-gamma coincidence detection system consisting of a CsI(Tl)/BC404 Phoswich well detector and pulse shape analysis algorithms implemented digital signal processor. The tool can be used to simulate the detector's response for all the gamma rays and beta particles emitted from (135)Xe, (133m)Xe, (133)Xe, (131m)Xe and (214)Pb. Two- and three-dimensional beta-gamma coincidence spectra from the PhosWatch detector can be produced using the simulation tool. The accurately simulated spectra could be used to calculate system coincidence detection efficiency for each xenon isotope, the corrections for the interference from the various spectral components from radon and xenon isotopes, and system gain calibration. Also, it can generate two- and three-dimensional xenon reference spectra to test beta-gamma coincidence spectral deconvolution analysis software. PMID:19647444

Mekarski, P; Zhang, W; Ungar, K; Bean, M; Korpach, E

2009-10-01

369

Elevated CO2 increases tree-level intrinsic water use efficiency: insights from carbon and oxygen isotope analyses in tree rings across three forest FACE sites  

SciTech Connect

Elevated CO2 increases intrinsic water use efficiency (WUEi) of forests, but the magnitude of this effect and its interaction with climate is still poorly understood. We combined tree ring analysis with isotope measurements at three Free Air CO2 Enrichment (FACE, POP-EUROFACE, in Italy; Duke FACE in North Carolina and ORNL in Tennessee, USA) sites, to cover the entire life of the trees. We used 13C to assess carbon isotope discrimination ( 13C ci/ca) and changes in WUEi, while direct CO2 effects on stomatal conductance were explored using 18O as a proxy. Across all the sites, elevated CO2 increased 13C-derived WUEi on average by 73% for Liquidambar styraciflua, 77% for Pinus taeda and 75% for Populus sp., but through different ecophysiological mechanisms. Our findings provide a robust means of predicting WUEi responses from a variety of tree species exposed to variable environmental conditions over time, and species-specific relationships that can help modeling elevated CO2 and climate impacts on forest productivity, carbon and water balances.

Battipaglia, Giovanna [Second University of Naples; Saurer, Matthias [Paul Scherrer Institut, Villigen, Switzerland; Cherubini, Paulo [WSL Swiss Federal Institute for Forest, Snow and Landscape Research; Califapietra, Carlo [University of Tuscia; McCarthy, Heather R [Duke University; Norby, Richard J [ORNL; Cotrufo, M. Francesca [Colorado State University, Fort Collins

2013-01-01

370

Tree-Ring Stable Isotopes Reveal Twentieth-Century Increases in Water-Use Efficiency of Fagus sylvatica and Nothofagus spp. in Italian and Chilean Mountains  

PubMed Central

Changes in intrinsic water use efficiency (iWUE) were investigated in Fagus sylvatica and Nothofagus spp. over the last century. We combined dendrochronological methods with dual-isotope analysis to investigate whether atmospheric changes enhanced iWUE of Fagus and Nothofagus and tree growth (basal area increment, BAI) along latitudinal gradients in Italy and Chile. Post-maturation phases of the trees presented different patterns in ?13C, ?13C, ?18O, Ci (internal CO2 concentration), iWUE, and BAI. A continuous enhancement in isotope-derived iWUE was observed throughout the twentieth century, which was common to all sites and related to changes in Ca (ambient CO2 concentration) and secondarily to increases in temperature. In contrast to other studies, we observed a general increasing trend of BAI, with the exception of F. sylvatica in Aspromonte. Both iWUE and BAI were uncoupled with the estimated drought index, which is in agreement with the absence of enduring decline in tree growth. In general, ?13C and ?18O showed a weak relationship, suggesting the major influence of photosynthetic rate on Ci and ?13C, and the minor contribution of the regulation of stomatal conductance to iWUE. The substantial warming observed during the twentieth century did not result in a clear pattern of increased drought stress along these latitudinal transects, because of the variability in temporal trends of precipitation and in specific responses of populations. PMID:25398040

Tognetti, Roberto; Lombardi, Fabio; Lasserre, Bruno; Cherubini, Paolo; Marchetti, Marco

2014-01-01

371

Stable isotope coded derivatizing reagents as internal standards in metabolite profiling.  

PubMed

Gas chromatography (GC) and liquid chromatography (LC) coupled to mass spectrometric (MS) detection have become the two main techniques for the analysis of metabolite pools (i.e. Metabolomics). These technologies are especially suited for Metabolite Profiling analysis of various metabolite groups due to high separation capabilities of the chromatographs and high sensitivity of the mass analysers. The trend in quantitative Metabolite Profiling is to add more metabolites and metabolite groups in a single method. This should not be done by compromising the analytical precision. Mass spectrometric detection comes with certain limitations, especially in the quantitative aspects as standards are needed for conversion of ion abundance to concentration and ionization efficiencies are directly dependent on eluent conditions. This calls for novel strategies to counteract all variables that can influence the quantitative precision. Usually, internal standards are used to correct any technical variation. For quantitation of single or just a few analytes this can be executed with spiking isotopically labeled standards. However, for more comprehensive analytical tasks, e.g. profiling tens or hundreds of analytes simultaneously, this strategy becomes expensive and in many cases isotopically labeled standards are not available. An alternative is to introduce a derivatizing step where the sample is derivatized with naturally labeled reagent, while a standard solution is separately derivatized with isotopically labeled reagent and spiked into the sample solution prior to analysis. This strategy, named isotope coded derivatization - ICD, is attractive in the emerging field of quantitative Metabolite Profiling where current protocols can easily comprise over hundred metabolites. This review provides an overview of isotopically labeled derivatizing reagents that have been developed for important metabolite groups with the aim to improve analytical performance and precision. PMID:23628173

Bruheim, Per; Kvitvang, Hans Fredrik Nyvold; Villas-Boas, Silas G

2013-06-28

372

Quantitative Proteomics Using Stable Isotope Labeling with Amino Acids in Cell Culture Reveals Changes in the Cytoplasmic, Nuclear, and Nucleolar Proteomes in Vero Cells Infected with the Coronavirus Infectious Bronchitis Virus*  

PubMed Central

Virus-host interactions involve complex interplay between viral and host factors, rendering them an ideal target for proteomic analysis. Here we detail a high throughput quantitative proteomics analysis of Vero cells infected with the coronavirus infectious bronchitis virus (IBV), a positive strand RNA virus that replicates in the cytoplasm. Stable isotope labeling with amino acids in cell culture (SILAC) was used in conjunction with LC-MS/MS to identify and quantify 1830 cellular and two viral proteins from IBV-infected cells. Fractionation of cells into cytoplasmic, nuclear, and nucleolar extracts was used to reduce sample complexity and provide information on the trafficking of proteins between the different compartments. Each fraction showed a proportion of proteins exhibiting ?2-fold changes in abundance. Ingenuity Pathway Analysis revealed that proteins that changed in response to infection could be grouped into different functional categories. These included proteins regulated by NF-?B- and AP-1-dependent pathways and proteins involved in the cytoskeleton and molecular motors. A luciferase-based reporter gene assay was used to validate the up-regulation of AP-1- and NF-?B-dependent transcription in IBV-infected cells and confirmed using immunofluorescence. Immunofluorescence was used to validate changes in the subcellular localization of vimentin and myosin VI in IBV-infected cells. The proteomics analysis also confirmed the presence of the viral nucleocapsid protein as localizing in the cytoplasm, nucleus, and nucleolus and the viral membrane protein in the cytoplasmic fraction. This research is the first application of SILAC to study total host cell proteome changes in response to positive sense RNA virus infection and illustrates the versatility of this technique as applied to infectious disease research. PMID:20467043

Emmott, Edward; Rodgers, Mark A.; Macdonald, Andrew; McCrory, Sarah; Ajuh, Paul; Hiscox, Julian A.

2010-01-01

373

An efficient and expedient method for the synthesis of 11C-labeled ?-aminoisobutyric acid: a tumor imaging agent potentially useful for cancer diagnosis.  

PubMed

We describe the synthesis of (11)C-labeled ?-aminoisobutyric acid 2 from iodo[(11)C]methane and methyl N-(diphenylmethylen)-d,l-alaniate (5). The tetrabutylammonium fluoride (TBAF)-promoted ?-[(11)C]methylation of sterically hindered analog 5 was a key step in our synthesis process. Total radiochemical conversion of 2 was high and a remote-controlled synthesis was carried out. A comparative tumor positron emission tomography (PET) imaging study using the same model mouse showed higher uptake of 2 than with (11)C-labeled methionine and [(18)F] fluorodeoxyglucose (FDG). PMID:21392981

Kato, Koichi; Tsuji, Atsushi B; Saga, Tsuneo; Zhang, Ming-Rong

2011-04-15

374

Uranium Isotopic Analysis with the FRAM Isotopic Analysis Code  

SciTech Connect

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.

Duc T. Vo; Thomas E. Sampson

1999-05-01

375

Variation in the carbon and oxygen isotope composition of plant biomass and its relationship to water-use efficiency at the leaf- and ecosystem-scales in a northern Great Plains grassland.  

PubMed

Measurements of the carbon (?(13) Cm ) and oxygen (?(18) Om ) isotope composition of C3 plant tissue provide important insights into controls on water-use efficiency. We investigated the causes of seasonal and inter-annual variability in water-use efficiency in a grassland near Lethbridge, Canada using stable isotope (leaf-scale) and eddy covariance measurements (ecosystem-scale). The positive relationship between ?(13) Cm and ?(18) Om values for samples collected during 1998-2001 indicated that variation in stomatal conductance and water stress-induced changes in the degree of stomatal limitation of net photosynthesis were the major controls on variation in ?(13) Cm and biomass production during this time. By comparison, the lack of a significant relationship between ?(13) Cm and ?(18) Om values during 2002, 2003 and 2006 demonstrated that water stress was not a significant limitation on photosynthesis and biomass production in these years. Water-use efficiency was higher in 2000 than 1999, consistent with expectations because of greater stomatal limitation of photosynthesis and lower leaf ci /ca during the drier conditions of 2000. Calculated values of leaf-scale water-use efficiency were 2-3 times higher than ecosystem-scale water-use efficiency, a difference that was likely due to carbon lost in root respiration and water lost during soil evaporation that was not accounted for by the stable isotope measurements. PMID:23862667

Flanagan, Lawrence B; Farquhar, Graham D

2014-02-01

376

Multiple tag labeling method for DNA sequencing  

DOEpatents

A DNA sequencing method described which uses single lane or channel electrophoresis. Sequencing fragments are separated in said lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radio-isotope labels.

Mathies, Richard A. (Contra Costa County, CA); Huang, Xiaohua C. (Mt. View, CA); Quesada, Mark A. (San Francisco, CA)

1995-01-01

377

Isotope-labeled immunoassays without radiation waste  

E-print Network

in the laboratory environment. Furthermore, the short half-life of the radioisotopes translates into short shelf organic ligands. 14 C and 3 H are incorporated seamlessly into organics, but have decay detec- tion limits in areas such as environmental monitoring and food analysis. Accelerator mass spectrometry (AMS) developed

Hammock, Bruce D.

378

Proteomic response to 5,6-dimethylxanthenone 4-acetic acid (DMXAA, vadimezan) in human non-small cell lung cancer A549 cells determined by the stable-isotope labeling by amino acids in cell culture (SILAC) approach  

PubMed Central

5,6-Dimethylxanthenone 4-acetic acid (DMXAA), also known as ASA404 and vadimezan, is a potent tumor blood vessel-disrupting agent and cytokine inducer used alone or in combination with other cytotoxic agents for the treatment of non-small cell lung cancer (NSCLC) and other cancers. However, the latest Phase III clinical trial has shown frustrating outcomes in the treatment of NSCLC, since the therapeutic targets and underlying mechanism for the anticancer effect of DMXAA are not yet fully understood. This study aimed to examine the proteomic response to DMXAA and unveil the global molecular targets and possible mechanisms for the anticancer effect of DMXAA in NSCLC A549 cells using a stable-isotope labeling by amino acids in cell culture (SILAC) approach. The proteomic data showed that treatment with DMXAA modulated the expression of 588 protein molecules in A549 cells, with 281 protein molecules being up regulated and 306 protein molecules being downregulated. Ingenuity pathway analysis (IPA) identified 256 signaling pathways and 184 cellular functional proteins that were regulated by DMXAA in A549 cells. These targeted molecules and signaling pathways were mostly involved in cell proliferation and survival, redox homeostasis, sugar, amino acid and nucleic acid metabolism, cell migration, and invasion and programed cell death. Subsequently, the effects of DMXAA on cell cycle distribution, apoptosis, autophagy, and reactive oxygen species (ROS) generation were experimentally verified. Flow cytometric analysis showed that DMXAA significantly induced G1 phase arrest in A549 cells. Western blotting assays demonstrated that DMXAA induced apoptosis via a mitochondria-dependent pathway and promoted autophagy, as indicated by the increased level of cytosolic cytochrome c, activation of caspase 3, and enhanced expression of beclin 1 and microtubule-associated protein 1A/1B-light chain 3 (LC3-II) in A549 cells. Moreover, DMXAA significantly promoted intracellular ROS generation in A549 cells. Collectively, this SILAC study quantitatively evaluates the proteomic response to treatment with DMXAA that helps to globally identify the potential molecular targets and elucidate the underlying mechanism of DMXAA in the treatment of NSCLC. PMID:25733813

Pan, Shu-Ting; Zhou, Zhi-Wei; He, Zhi-Xu; Zhang, Xueji; Yang, Tianxin; Yang, Yin-Xue; Wang, Dong; Qiu, Jia-Xuan; Zhou, Shu-Feng

2015-01-01

379

A Prime Number Labeling Scheme for Dynamic Ordered XML Trees  

Microsoft Academic Search

Efficient evaluation of XML queries requires the determination of whether a relationship exists between two elements. A number of labeling schemes have been designed to label the element nodes such that the relationships between nodes can be easily determined by comparing their labels. With the increased popularity of XML on the Web, finding a labeling scheme that is able to

Xiaodong Wu; Mong-li Lee; Wynne Hsu

2004-01-01

380

Isotopic Biogeochemistry  

NASA Technical Reports Server (NTRS)

An overview is provided of the biogeochemical research. The funding, productivity, personnel and facilities are reviewed. Some of the technical areas covered are: carbon isotopic records; isotopic studies of banded iron formations; isotope effects in microbial systems; studies of organic compounds in ancient sediments; and development in isotopic geochemistry and analysis.

Hayes, J. M.

1985-01-01