Stable isotope labelling methods in mass spectrometry-based quantitative proteomics.

PubMed

Chahrour, Osama; Cobice, Diego; Malone, John

2015-09-10

Mass-spectrometry based proteomics has evolved as a promising technology over the last decade and is undergoing a dramatic development in a number of different areas, such as; mass spectrometric instrumentation, peptide identification algorithms and bioinformatic computational data analysis. The improved methodology allows quantitative measurement of relative or absolute protein amounts, which is essential for gaining insights into their functions and dynamics in biological systems. Several different strategies involving stable isotopes label (ICAT, ICPL, IDBEST, iTRAQ, TMT, IPTL, SILAC), label-free statistical assessment approaches (MRM, SWATH) and absolute quantification methods (AQUA) are possible, each having specific strengths and weaknesses. Inductively coupled plasma mass spectrometry (ICP-MS), which is still widely recognised as elemental detector, has recently emerged as a complementary technique to the previous methods. The new application area for ICP-MS is targeting the fast growing field of proteomics related research, allowing absolute protein quantification using suitable elemental based tags. This document describes the different stable isotope labelling methods which incorporate metabolic labelling in live cells, ICP-MS based detection and post-harvest chemical label tagging for protein quantification, in addition to summarising their pros and cons. Copyright © 2015 Elsevier B.V. All rights reserved.

A dual isotope approach to isolate soil carbon pools of different turnover times

DOE PAGES

Torn, M. S.; Kleber, M.; Zavaleta, E. S.; ...

2013-12-10

Soils are globally significant sources and sinks of atmospheric CO 2. Increasing the resolution of soil carbon turnover estimates is important for predicting the response of soil carbon cycling to environmental change. We show that soil carbon turnover times can be more finely resolved using a dual isotope label like the one provided by elevated CO 2 experiments that use fossil CO 2. We modeled each soil physical fraction as two pools with different turnover times using the atmospheric 14C bomb spike in combination with the label in 14C and 13C provided by an elevated CO 2 experiment in amore » California annual grassland. In sandstone and serpentine soils, the light fraction carbon was 21–54% fast cycling with 2–9 yr turnover, and 36–79% slow cycling with turnover slower than 100 yr. This validates model treatment of the light fraction as active and intermediate cycling carbon. The dense, mineral-associated fraction also had a very dynamic component, consisting of ~7% fast-cycling carbon and ~93% very slow cycling carbon. Similarly, half the microbial biomass carbon in the sandstone soil was more than 5 yr old, and 40% of the carbon respired by microbes had been fixed more than 5 yr ago. Resolving each density fraction into two pools revealed that only a small component of total soil carbon is responsible for most CO 2 efflux from these soils. In the sandstone soil, 11% of soil carbon contributes more than 90% of the annual CO 2 efflux. The fact that soil physical fractions, designed to isolate organic material of roughly homogeneous physico-chemical state, contain material of dramatically different turnover times is consistent with recent observations of rapid isotope incorporation into seemingly stable fractions and with emerging evidence for hot spots or micro-site variation of decomposition within the soil matrix. Predictions of soil carbon storage using a turnover time estimated with the assumption of a single pool per density fraction would greatly

Contrasting dual (C, Cl) isotope fractionation offers potential to distinguish reductive chloroethene transformation from breakdown by permanganate.

PubMed

Doğan-Subaşı, Eylem; Elsner, Martin; Qiu, Shiran; Cretnik, Stefan; Atashgahi, Siavash; Shouakar-Stash, Orfan; Boon, Nico; Dejonghe, Winnie; Bastiaens, Leen

2017-10-15

cis-1,2-Dichloroethene (cis-DCE) and trichloroethene (TCE) are persistent, toxic and mobile pollutants in groundwater systems. They are both conducive to reductive dehalogenation and to oxidation by permanganate. In this study, the potential of dual element (C, Cl) compound specific isotope analyses (CSIA) for distinguishing between chemical oxidation and anaerobic reductive dechlorination of cis-DCE and TCE was investigated. Well-controlled cis-DCE degradation batch tests gave similar carbon isotope enrichment factors ε C (‰), but starkly contrasting dual element isotope slopes Δδ 13 C/Δδ 37 Cl for permanganate oxidation (ε C =-26‰±6‰, Δδ 13 C/Δδ 37 Cl≈-125±47) compared to reductive dechlorination (ε C =-18‰±4‰, Δδ 13 C/Δδ 37 Cl≈4.5±3.4). The difference can be tracked down to distinctly different chlorine isotope fractionation: an inverse isotope effect during chemical oxidation (ε Cl =+0.2‰±0.1‰) compared to a large normal isotope effect in reductive dechlorination (ε Cl =-3.3‰±0.9‰) (p≪0.05). A similar trend was observed for TCE. The dual isotope approach was evaluated in the field before and up to 443days after a pilot scale permanganate injection in the subsurface. Our study indicates, for the first time, the potential of the dual element isotope approach for distinguishing cis-DCE (and TCE) concentration drops caused by dilution, oxidation by permanganate and reductive dechlorination both at laboratory and field scale. Copyright © 2017. Published by Elsevier B.V.

Isotope-Labeled Composition B for Tracing Detonation Signatures

NASA Astrophysics Data System (ADS)

Manner, Virginia; Podlesak, David; Huber, Rachel; Amato, Ronald; Giambra, Anna; Bowden, Patrick; Hartline, Ernest; Dattelbaum, Dana

2017-06-01

To better understand how solid carbon forms and evolves during detonation, we have prepared Composition B with 13 C and 15 N-labeled 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) and 2,4,6-trinitrotoluene (TNT) in order to trace the formation of soot from the carbon and nitrogen atoms in these explosives. Isotope-labeling of explosives has been performed in the recent past for a variety of reasons, including environmental remediation and reaction mechanism studies. Because it is expensive and time consuming to prepare these materials, and our detection equipment only requires trace amounts of isotopes, we have prepared fully-labeled materials and substituted them into unlabeled RDX and TNT at less than the 1% level. We will discuss the preparation and full characterization of this labeled Composition B, the detonation tests performed, along with the results of the post-detonation soot analysis. Various detonation models predict differing amounts and forms of carbon and nitrogen; these isotopically-labeled precursors have allowed these models to be tested.

[Progress in stable isotope labeled quantitative proteomics methods].

PubMed

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

2013-06-01

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

Stable isotope dimethyl labelling for quantitative proteomics and beyond

PubMed Central

Hsu, Jue-Liang; Chen, Shu-Hui

2016-01-01

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

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

PubMed

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

2018-06-01

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

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

PubMed

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

2012-06-19

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-(13)C]compound to generate [U-(13)C]-labeled volatile standards for use in subsequent experimental profiling studies. [U-(13)C]-α-Linolenic acid (18:3n-3, ALA) was thermally oxidized to produce labeled lipid degradation volatiles which were subsequently characterized qualitatively and quantitatively. Twenty-five [U-(13)C]-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. Labeled volatiles were quantified by a reverse isotope dilution procedure. Using the [U-(13)C]-labeled standards, limits of detection comparable to or better than those of previous HS-SPME reports were achieved, 0.010-1.04 ng/g. The performance of the [U-(13)C]-labeled 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-(13)C]-labeled 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-(13)C]-labeled 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-(13)C]-labeled sugars and amino acids, for profiling studies should be feasible and can dramatically improve

Use of dual carbon-chlorine isotope analysis to assess the degradation pathways of 1,1,1-trichloroethane in groundwater.

PubMed

Palau, Jordi; Jamin, Pierre; Badin, Alice; Vanhecke, Nicolas; Haerens, Bruno; Brouyère, Serge; Hunkeler, Daniel

2016-04-01

Compound-specific isotope analysis (CSIA) is a powerful tool to track contaminant fate in groundwater. However, the application of CSIA to chlorinated ethanes has received little attention so far. These compounds are toxic and prevalent groundwater contaminants of environmental concern. The high susceptibility of chlorinated ethanes like 1,1,1-trichloroethane (1,1,1-TCA) to be transformed via different competing pathways (biotic and abiotic) complicates the assessment of their fate in the subsurface. In this study, the use of a dual C-Cl isotope approach to identify the active degradation pathways of 1,1,1-TCA is evaluated for the first time in an aerobic aquifer impacted by 1,1,1-TCA and trichloroethylene (TCE) with concentrations of up to 20 mg/L and 3.4 mg/L, respectively. The reaction-specific dual carbon-chlorine (C-Cl) isotope trends determined in a recent laboratory study illustrated the potential of a dual isotope approach to identify contaminant degradation pathways of 1,1,1-TCA. Compared to the dual isotope slopes (Δδ(13)C/Δδ(37)Cl) previously determined in the laboratory for dehydrohalogenation/hydrolysis (DH/HY, 0.33 ± 0.04) and oxidation by persulfate (∞), the slope determined from field samples (0.6 ± 0.2, r(2) = 0.75) is closer to the one observed for DH/HY, pointing to DH/HY as the predominant degradation pathway of 1,1,1-TCA in the aquifer. The observed deviation could be explained by a minor contribution of additional degradation processes. This result, along with the little degradation of TCE determined from isotope measurements, confirmed that 1,1,1-TCA is the main source of the 1,1-dichlorethylene (1,1-DCE) detected in the aquifer with concentrations of up to 10 mg/L. This study demonstrates that a dual C-Cl isotope approach can strongly improve the qualitative and quantitative assessment of 1,1,1-TCA degradation processes in the field. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed

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

2006-01-01

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

IsoCor: correcting MS data in isotope labeling experiments.

PubMed

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

2012-05-01

Mass spectrometry (MS) is widely used for isotopic labeling studies of metabolism and other biological processes. Quantitative applications-e.g. metabolic flux analysis-require tools to correct the raw MS data for the contribution of all naturally abundant isotopes. IsoCor is a software that allows such correction to be applied to any chemical species. Hence it 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 new features-e.g. correction for the isotopic purity of the tracer-to improve the accuracy of quantitative isotopic studies, and implements an efficient algorithm to process large datasets. Its user-friendly interface makes isotope labeling experiments more accessible to a wider biological community. IsoCor is distributed under OpenSource license at http://metasys.insa-toulouse.fr/software/isocor/

Nitrate source apportionment using a combined dual isotope, chemical and bacterial property, and Bayesian model approach in river systems

NASA Astrophysics Data System (ADS)

Xia, Yongqiu; Li, Yuefei; Zhang, Xinyu; Yan, Xiaoyuan

2017-01-01

Nitrate (NO3-) pollution is a serious problem worldwide, particularly in countries with intensive agricultural and population activities. Previous studies have used δ15N-NO3- and δ18O-NO3- to determine the NO3- sources in rivers. However, this approach is subject to substantial uncertainties and limitations because of the numerous NO3- sources, the wide isotopic ranges, and the existing isotopic fractionations. In this study, we outline a combined procedure for improving the determination of NO3- sources in a paddy agriculture-urban gradient watershed in eastern China. First, the main sources of NO3- in the Qinhuai River were examined by the dual-isotope biplot approach, in which we narrowed the isotope ranges using site-specific isotopic results. Next, the bacterial groups and chemical properties of the river water were analyzed to verify these sources. Finally, we introduced a Bayesian model to apportion the spatiotemporal variations of the NO3- sources. Denitrification was first incorporated into the Bayesian model because denitrification plays an important role in the nitrogen pathway. The results showed that fertilizer contributed large amounts of NO3- to the surface water in traditional agricultural regions, whereas manure effluents were the dominant NO3- source in intensified agricultural regions, especially during the wet seasons. Sewage effluents were important in all three land uses and exhibited great differences between the dry season and the wet season. This combined analysis quantitatively delineates the proportion of NO3- sources from paddy agriculture to urban river water for both dry and wet seasons and incorporates isotopic fractionation and uncertainties in the source compositions.

INCORPORATING CONCENTRATION DEPENDENCE IN STABLE ISOTOPE MIXING MODELS

EPA Science Inventory

Stable isotopes are often used as natural labels to quantify the contributions of multiple sources to a mixture. For example, C and N isotopic signatures can be used to determine the fraction of three food sources in a consumer's diet. The standard dual isotope, three source li...

Carbon-11 radiolabeling of iron-oxide nanoparticles for dual-modality PET/MR imaging

NASA Astrophysics Data System (ADS)

Sharma, Ramesh; Xu, Youwen; Kim, Sung Won; Schueller, Michael J.; Alexoff, David; Smith, S. David; Wang, Wei; Schlyer, David

2013-07-01

Dual-modality imaging, using Magnetic Resonance Imaging (MRI) and Positron Emission Tomography (PET) simultaneously, is a powerful tool to gain valuable information correlating structure with function in biomedicine. The advantage of this dual approach is that the strengths of one modality can balance the weaknesses of the other. However, success of this technique requires developing imaging probes suitable for both. Here, we report on the development of a nanoparticle labeling procedure via covalent bonding with carbon-11 PET isotope. Carbon-11 in the form of [11C]methyl iodide was used as a methylation agent to react with carboxylic acid (-COOH) and amine (-NH2) functional groups of ligands bound to the nanoparticles (NPs). The surface coating ligands present on superparamagnetic iron-oxide nanoparticles (SPIO NPs) were radiolabeled to achieve dual-modality PET/MR imaging capabilities. The proof-of-concept dual-modality PET/MR imaging using the radiolabeled SPIO NPs was demonstrated in an in vivo experiment.Dual-modality imaging, using Magnetic Resonance Imaging (MRI) and Positron Emission Tomography (PET) simultaneously, is a powerful tool to gain valuable information correlating structure with function in biomedicine. The advantage of this dual approach is that the strengths of one modality can balance the weaknesses of the other. However, success of this technique requires developing imaging probes suitable for both. Here, we report on the development of a nanoparticle labeling procedure via covalent bonding with carbon-11 PET isotope. Carbon-11 in the form of [11C]methyl iodide was used as a methylation agent to react with carboxylic acid (-COOH) and amine (-NH2) functional groups of ligands bound to the nanoparticles (NPs). The surface coating ligands present on superparamagnetic iron-oxide nanoparticles (SPIO NPs) were radiolabeled to achieve dual-modality PET/MR imaging capabilities. The proof-of-concept dual-modality PET/MR imaging using the radiolabeled

Determination of the origin of groundwater nitrate at an air weapons range using the dual isotope approach.

PubMed

Bordeleau, Geneviève; Savard, Martine M; Martel, Richard; Ampleman, Guy; Thiboutot, Sonia

2008-06-06

Nitrate is one of the most common contaminants in shallow groundwater, and many sources may contribute to the nitrate load within an aquifer. Groundwater nitrate plumes have been detected at several ammunition production sites. However, the presence of multiple potential sources and the lack of existing isotopic data concerning explosive degradation-induced nitrate constitute a limitation when it comes to linking both types of contaminants. On military training ranges, high nitrate concentrations in groundwater were reported for the first time as part of the hydrogeological characterization of the Cold Lake Air Weapons Range (CLAWR), Alberta, Canada. Explosives degradation is thought to be the main source of nitrate contamination at CLAWR, as no other major source is present. Isotopic analyses of N and O in nitrate were performed on groundwater samples from the unconfined and confined aquifers; the dual isotopic analysis approach was used in order to increase the chances of identifying the source of nitrate. The isotopic ratios for the groundwater samples with low nitrate concentration suggested a natural origin with a strong contribution of anthropogenic atmospheric NOx. For the samples with nitrate concentration above the expected background level the isotopic ratios did not correspond to any source documented in the literature. Dissolved RDX samples were degraded in the laboratory and results showed that all reproduced degradation processes released nitrate with a strong fractionation. Laboratory isotopic values for RDX-derived NO(3)(-) produced a trend of high delta(18)O-low delta(15)N to low delta(18)O-high delta(15)N, and groundwater samples with nitrate concentrations above the expected background level appeared along this trend. Our results thus point toward a characteristic field of isotopic ratios for nitrate being derived from the degradation of RDX.

Stable isotope labeling by essential nutrients in cell culture for preparation of labeled coenzyme A and its thioesters.

PubMed

Basu, Sankha S; Mesaros, Clementina; Gelhaus, Stacy L; Blair, Ian A

2011-02-15

Stable isotope dilution mass spectrometry (MS) represents the gold standard for quantification of endogenously formed cellular metabolites. Although coenzyme A (CoA) and acyl-CoA thioester derivatives are central players in numerous metabolic pathways, the lack of a commercially available isotopically labeled CoA limits the development of rigorous MS-based methods. In this study, we adapted stable isotope labeling by amino acids in cell culture (SILAC) methodology to biosynthetically generate stable isotope labeled CoA and thioester analogues for use as internal standards in liquid chromatography/multiple reaction monitoring mass spectrometry (LC/MRM-MS) assays. This was accomplished by incubating murine hepatocytes (Hepa 1c1c7) in media in which pantothenate (a precursor of CoA) was replaced with [(13)C(3)(15)N(1)]-pantothenate. Efficient incorporation into various CoA species was optimized to >99% [(13)C(3)(15)N(1)]-pantothenate after three passages of the murine cells in culture. Charcoal-dextran-stripped fetal bovine serum (FBS) was found to be more efficient for serum supplementation than dialyzed or undialyzed FBS, due to lower contaminating unlabeled pantothenate content. Stable isotope labeled CoA species were extracted and utilized as internal standards for CoA thioester analysis in cell culture models. This methodology of stable isotope labeling by essential nutrients in cell culture (SILEC) can serve as a paradigm for using vitamins and other essential nutrients to generate stable isotope standards that cannot be readily synthesized.

Water and light improvement after thinning at a xeric site: Which weights the most? A dual isotope approach

NASA Astrophysics Data System (ADS)

Giuggiola, Arnaud; Ogée, Jérôme; Gessler, Arthur; Rigling, Andreas; Bugmann, Harald; Treydte, Kerstin

2015-04-01

Reductions in stand density foster individual tree growth due to increases of resources such as water, light and nutrients. Detailed knowledge of the short- to long-term physiological response underlying the growth response to thinning is crucial for the management of forests already suffering from recurrent drought-induced dieback. We applied a dual isotope approach together with mechanistic isotope models such as MuSICA to study the physiological processes underlying growth enhancement in a long-term thinning experiment in a xeric Pinus sylvestris forest in Switzerland. This approach allowed for identifying and disentangling changes in stomatal conductance and assimilation rate. Our results indicate that an increase in stomatal conductance outweighs an increase in assimilation, meaning that the observed growth releases in heavy thinned trees at our xeric site are primarily driven by enhanced water availability rather than by the increase in light availability. We conclude that in areas with isohydric species (drought avoiders) that tend to grow close to their physiological limits, thinning is highly recommended to maintain a less negative water balance and thus foster tree growth, and ultimately the survival rate of individual trees and forests.

Gluconeogenesis from labeled carbon: estimating isotope dilution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kelleher, J.K.

1986-03-01

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

Simple, rapid method for the preparation of isotopically labeled formaldehyde

DOEpatents

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

2011-10-04

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

Metabolomics of Early Stage Plant Cell–Microbe Interaction Using Stable Isotope Labeling

PubMed Central

Pang, Qiuying; Zhang, Tong; Wang, Yang; Kong, Wenwen; Guan, Qijie; Yan, Xiufeng; Chen, Sixue

2018-01-01

Metabolomics has been used in unraveling metabolites that play essential roles in plant–microbe (including pathogen) interactions. However, the problem of profiling a plant metabolome with potential contaminating metabolites from the coexisting microbes has been largely ignored. To address this problem, we implemented an effective stable isotope labeling approach, where the metabolome of a plant bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000 was labeled with heavy isotopes. The labeled bacterial cells were incubated with Arabidopsis thaliana epidermal peels (EPs) with guard cells, and excessive bacterial cells were subsequently removed from the plant tissues by washing. The plant metabolites were characterized by liquid chromatography mass spectrometry using multiple reactions monitoring, which can differentiate plant and bacterial metabolites. Targeted metabolomic analysis suggested that Pst DC3000 infection may modulate stomatal movement by reprograming plant signaling and primary metabolic pathways. This proof-of-concept study demonstrates the utility of this strategy in differentiation of the plant and microbe metabolomes, and it has broad applications in studying metabolic interactions between microbes and other organisms. PMID:29922325

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

PubMed Central

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

2011-01-01

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

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

PubMed

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

2017-08-18

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

An optimized method for measuring fatty acids and cholesterol in stable isotope-labeled cells

PubMed Central

Argus, Joseph P.; Yu, Amy K.; Wang, Eric S.; Williams, Kevin J.; Bensinger, Steven J.

2017-01-01

Stable isotope labeling has become an important methodology for determining lipid metabolic parameters of normal and neoplastic cells. Conventional methods for fatty acid and cholesterol analysis have one or more issues that limit their utility for in vitro stable isotope-labeling studies. To address this, we developed a method optimized for measuring both fatty acids and cholesterol from small numbers of stable isotope-labeled cultured cells. We demonstrate quantitative derivatization and extraction of fatty acids from a wide range of lipid classes using this approach. Importantly, cholesterol is also recovered, albeit at a modestly lower yield, affording the opportunity to quantitate both cholesterol and fatty acids from the same sample. Although we find that background contamination can interfere with quantitation of certain fatty acids in low amounts of starting material, our data indicate that this optimized method can be used to accurately measure mass isotopomer distributions for cholesterol and many fatty acids isolated from small numbers of cultured cells. Application of this method will facilitate acquisition of lipid parameters required for quantifying flux and provide a better understanding of how lipid metabolism influences cellular function. PMID:27974366

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

PubMed

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

2017-02-01

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

Relative and accurate measurement of protein abundance using 15N stable isotope labeling in Arabidopsis (SILIA).

PubMed

Guo, Guangyu; Li, Ning

2011-07-01

In the quantitative proteomic studies, numerous in vitro and in vivo peptide labeling strategies have been successfully applied to measure differentially regulated protein and peptide abundance. These approaches have been proven to be versatile and repeatable in biological discoveries. (15)N metabolic labeling is one of these widely adopted and economical methods. However, due to the differential incorporation rates of (15)N or (14)N, the labeling results produce imperfectly matched isotopic envelopes between the heavy and light nitrogen-labeled peptides. In the present study, we have modified the solid Arabidopsis growth medium to standardize the (15)N supply, which led to a uniform incorporation of (15)N into the whole plant protein complement. The incorporation rate (97.43±0.11%) of (15)N into (15)N-coded peptides was determined by correlating the intensities of peptide ions with the labeling efficiencies according to Gaussian distribution. The resulting actual incorporation rate (97.44%) and natural abundance of (15)N/(14)N-coded peptides are used to re-calculate the intensities of isotopic envelopes of differentially labeled peptides, respectively. A modified (15)N/(14)N stable isotope labeling strategy, SILIA, is assessed and the results demonstrate that this approach is able to differentiate the fold change in protein abundance down to 10%. The machine dynamic range limitation and purification step will make the precursor ion ratio deriving from the actual ratio fold change. It is suggested that the differentially mixed (15)N-coded and (14)N-coded plant protein samples that are used to establish the protein abundance standard curve should be prepared following a similar protein isolation protocol used to isolate the proteins to be quantitated. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

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

PubMed

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

2013-11-27

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

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

PubMed Central

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

2013-01-01

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

Isotopic labeling of milk disialogangliosides (GD3).

PubMed

Reis, Mariza Gomes; Bibiloni, Rodrigo; McJarrow, Paul; MacGibbon, Alastair; Fong, Bertram; Bassett, Shalome; Roy, Nicole; Dos Reis, Marlon Martins

2016-10-01

The most abundant ganglioside group in both human milk and bovine milk during the first postnatal week is ganglioside GD3. This group of disialogangliosides forms up to 80% of the total ganglioside content of colostrum. Although dietary gangliosides have shown biological activity such as improvement of cognitive development, gastrointestinal health, and immune function, there is still a gap in our understanding of the molecular mechanisms governing its uptake and the metabolic processes affecting its bioavailability. The use of isotopically labeled ganglioside to track the bioavailability, absorption, distribution, and metabolism of gangliosides may provide key information to bridge this gap. However, isotope labeled GD3 is not commercially available and its preparation has not been described. We report for the first time the preparation of labeled GD3 with stable isotopes. Using alkaline hydrolysis, we were able to selectively remove both acetyl groups from the tetrasaccharide portion of GD3 without promoting significant hydrolysis of the ceramide portion of the molecule to generate N-deacetyl-GD3 (Neu5α2-8Neu5-GD3). The N-deacetyl-GD3 was then chemoselectively re-acetylated in aqueous medium using deuterated acetic anhydride in the presence of Triton X 100 to produce 2 H 6 -GD3 {GD3[(Neu5Ac-11- 2 H 3 )-(Neu5Ac-11- 2 H 3 )]}. This method provided 2 H 6 -GD3 with approximately 60% yield. This compound was characterized by proton nuclear magnetic resonance ( 1 H NMR) and liquid chromatography mass spectrometry (LC-MS). The oral absorption of the 2 H 6 -GD3 was demonstrated using a Sprague-Dawley weaning rats. Our results indicate that some ingested labeled milk gangliosides are absorbed and transported into the bloodstream without modification. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Advances in stable isotope assisted labeling strategies with information science.

PubMed

Kigawa, Takanori

2017-08-15

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

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

PubMed

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

2015-01-01

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

Monitoring Microbial Mineralization Using Reverse Stable Isotope Labeling Analysis by Mid-Infrared Laser Spectroscopy

PubMed Central

2017-01-01

Assessing the biodegradation of organic compounds is a frequent question in environmental science. Here, we present a sensitive, inexpensive, and simple approach to monitor microbial mineralization using reverse stable isotope labeling analysis (RIL) of dissolved inorganic carbon (DIC). The medium for the biodegradation assay contains regular organic compounds and 13C-labeled DIC with 13C atom fractions (x(13C)DIC) higher than natural abundance (typically 2–50%). The produced CO2 (x(13C) ≈ 1.11%) gradually dilutes the initial x(13C)DIC allowing to quantify microbial mineralization using mass-balance calculations. For 13C-enriched CO2 samples, a newly developed isotope ratio mid-infrared spectrometer was introduced with a precision of x(13C) < 0.006%. As an example for extremely difficult and slowly degradable compounds, CO2 production was close to the theoretical stoichiometry for anaerobic naphthalene degradation by a sulfate-reducing enrichment culture. Furthermore, we could measure the aerobic degradation of dissolved organic carbon (DOC) adsorbed to granular activated carbon in a drinking water production plant, which cannot be labeled with 13C. Thus, the RIL approach can be applied to sensitively monitor biodegradation of various organic compounds under anoxic or oxic conditions. PMID:28903553

Improvement of water and light availability after thinning at a xeric site: which matters more? A dual isotope approach.

PubMed

Giuggiola, Arnaud; Ogée, Jérôme; Rigling, Andreas; Gessler, Arthur; Bugmann, Harald; Treydte, Kerstin

2016-04-01

Thinning fosters individual tree growth by increasing the availability of water, light and nutrients. At sites where water rather than light is limiting, thinning also enhances soil evaporation and might not be beneficial. Detailed knowledge of the short- to long-term physiological response underlying the growth responses to thinning is crucial for the management of forests already suffering from recurrent drought-induced dieback. We applied a dual isotope approach together with mechanistic isotope models to study the physiological processes underlying long-term growth enhancement of heavily thinned Pinus sylvestris in a xeric forest in Switzerland. This approach allowed us to identify and disentangle thinning-induced changes in stomatal conductance and assimilation rate. At our xeric study site, the increase in stomatal conductance far outweighed the increase in assimilation, implying that growth release in heavily thinned trees is primarily driven by enhanced water availability rather than increased light availability. We conclude that in forests with relatively isohydric species (drought avoiders) that are growing close to their physiological limits, thinning is recommended to maintain a less negative water balance and thus foster tree growth, and ultimately the survival of forest trees under drought. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Multiplexed MRM-Based Protein Quantitation Using Two Different Stable Isotope-Labeled Peptide Isotopologues for Calibration.

PubMed

LeBlanc, André; Michaud, Sarah A; Percy, Andrew J; Hardie, Darryl B; Yang, Juncong; Sinclair, Nicholas J; Proudfoot, Jillaine I; Pistawka, Adam; Smith, Derek S; Borchers, Christoph H

2017-07-07

When quantifying endogenous plasma proteins for fundamental and biomedical research - as well as for clinical applications - precise, reproducible, and robust assays are required. Targeted detection of peptides in a bottom-up strategy is the most common and precise mass spectrometry-based quantitation approach when combined with the use of stable isotope-labeled peptides. However, when measuring protein in plasma, the unknown endogenous levels prevent the implementation of the best calibration strategies, since no blank matrix is available. Consequently, several alternative calibration strategies are employed by different laboratories. In this study, these methods were compared to a new approach using two different stable isotope-labeled standard (SIS) peptide isotopologues for each endogenous peptide to be quantified, enabling an external calibration curve as well as the quality control samples to be prepared in pooled human plasma without interference from endogenous peptides. This strategy improves the analytical performance of the assay and enables the accuracy of the assay to be monitored, which can also facilitate method development and validation.

Dual-Quantum-Dots-Labeled Lateral Flow Strip Rapidly Quantifies Procalcitonin and C-reactive Protein

NASA Astrophysics Data System (ADS)

Qi, XiaoPing; Huang, YunYe; Lin, ZhongShi; Xu, Liang; Yu, Hao

2016-03-01

In the article, a dual-quantum-dots-labeled (dual-QDs-labeled) lateral flow strip (LFS) method was developed for the simultaneous and rapid quantitative detection of procalcitonin (PCT) and C-reactive protein (CRP) in the blood. Two QD-antibody conjugates with different fluorescence emission spectra were produced and sprayed on the LFS to capture PCT and CRP in the blood. Furthermore, a double antibody sandwich method for PCT and, meanwhile, a competitive inhibition method for CRP were employed in the LFS. For PCT and CRP in serum assayed by the dual-QDs-labeled LFS, their detection sensitivities reached 0.1 and 1 ng/mL, respectively, and their linear quantitative detection ranges were from 0.3 to 200 ng/mL and from 50 to 250 μg/mL, respectively. There was little evidence that the PCT and CRP assays would be interfered with each other. The correlations for testing CRP and PCT in clinical samples were 99.75 and 97.02 %, respectively, between the dual-QDs-labeled LFS we developed and commercial methods. The rapid quantification of PCT and CRP on dual-QDs-labeled LFS is of great clinical value to distinguish inflammation, bacterial infection, or viral infection and to provide guidance for the use of antibiotics or other medicines.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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

Simulation of dual carbon-bromine stable isotope fractionation during 1,2-dibromoethane degradation.

PubMed

Jin, Biao; Nijenhuis, Ivonne; Rolle, Massimo

2018-06-01

We performed a model-based investigation to simultaneously predict the evolution of concentration, as well as stable carbon and bromine isotope fractionation during 1,2-dibromoethane (EDB, ethylene dibromide) transformation in a closed system. The modelling approach considers bond-cleavage mechanisms during different reactions and allows evaluating dual carbon-bromine isotopic signals for chemical and biotic reactions, including aerobic and anaerobic biological transformation, dibromoelimination by Zn(0) and alkaline hydrolysis. The proposed model allowed us to accurately simulate the evolution of concentrations and isotope data observed in a previous laboratory study and to successfully identify different reaction pathways. Furthermore, we illustrated the model capabilities in degradation scenarios involving complex reaction systems. Specifically, we examined (i) the case of sequential multistep transformation of EDB and the isotopic evolution of the parent compound, the intermediate and the reaction product and (ii) the case of parallel competing abiotic pathways of EDB transformation in alkaline solution.

Dual-isotope method for determination of human zinc absorption: the use of a test meal of turkey meat

DOE Office of Scientific and Technical Information (OSTI.GOV)

Flanagan, P.R.; Cluett, J.; Chamberlain, M.J.

The percentage of /sup 65/Zn taken up (absorbed) from extrinsically labeled turkey meat was calculated from the amounts of /sup 65/Zn and a nonabsorbed /sup 51/Cr marker present in the body or in a single stool specimen after 1-2 d. /sup 51/CrCl/sub 3/ proved to be a suitable marker for unabsorbed /sup 65/Zn and so the early determination of /sup 65/Zn absorption was possible. With stool counting, /sup 65/Zn absorption data from first stool samples after 1-2 d were accurate as judged by correlation with the amount of /sup 65/Zn in the body 7-10 d later (retention); results from subsequentmore » stools gave lower absorption values due to the early excretion of some absorbed /sup 65/Zn. The dual-isotope method gave reproducible results when four successive tests of zinc absorption were carried out in a group of six subjects. The average (mean +/- SD) /sup 65/Zn absorption from turkey meals containing 31 mumol (2 mg) and 46 mumol (3 mg) of zinc was 39 +/- 8% and 29 +/- 6%, respectively, measured by stool counting; /sup 65/Zn absorption and retention correlated well in both studies. A series of different beverages was given in place of water with the turkey meal. Orange juice significantly reduced /sup 65/Zn absorption and milk also showed this tendency, but tea, whiskey, wine or beer had no significant effect on the absorption of /sup 65/Zn from the turkey meal. In groups of subjects the mean ratio of /sup 65/Zn absorption from extrinsically labeled turkey meat on two occasions (1.06) was not significantly different from that of the absorption of extrinsic to intrinsic /sup 65/Zn labels (1.16). The dual-isotope technique with either stool or body counting is suitable for the rapid determination of /sup 65/Zn absorption from extrinsically labeled turkey within 2 d.« less

Escherichia coli cell-free protein synthesis and isotope labeling of mammalian proteins.

PubMed

Terada, Takaho; Yokoyama, Shigeyuki

2015-01-01

This chapter describes the cell-free protein synthesis method, using an Escherichia coli cell extract. This is a cost-effective method for milligram-scale protein production and is particularly useful for the production of mammalian proteins, protein complexes, and membrane proteins that are difficult to synthesize by recombinant expression methods, using E. coli and eukaryotic cells. By adjusting the conditions of the cell-free method, zinc-binding proteins, disulfide-bonded proteins, ligand-bound proteins, etc., may also be produced. Stable isotope labeling of proteins can be accomplished by the cell-free method, simply by using stable isotope-labeled amino acid(s) in the cell-free reaction. Moreover, the cell-free protein synthesis method facilitates the avoidance of stable isotope scrambling and dilution over the recombinant expression methods and is therefore advantageous for amino acid-selective stable isotope labeling. Site-specific stable isotope labeling is also possible with a tRNA molecule specific to the UAG codon. By the cell-free protein synthesis method, coupled transcription-translation is performed from a plasmid vector or a PCR-amplified DNA fragment encoding the protein. A milligram quantity of protein can be produced with a milliliter-scale reaction solution in the dialysis mode. More than a thousand solution structures have been determined by NMR spectroscopy for uniformly labeled samples of human and mouse functional domain proteins, produced by the cell-free method. Here, we describe the practical aspects of mammalian protein production by the cell-free method for NMR spectroscopy. © 2015 Elsevier Inc. All rights reserved.

Flow-through SIP - A novel stable isotope probing approach limiting cross-feeding

NASA Astrophysics Data System (ADS)

Mooshammer, Maria; Kitzinger, Katharina; Schintlmeister, Arno; Kjedal, Henrik; Nielsen, Jeppe Lund; Nielsen, Per; Wagner, Michael

2017-04-01

Stable isotope probing (SIP) is a widely applied tool to link specific microbial populations to metabolic processes in the environment without the prerequisite of cultivation, which has greatly advanced our understanding of the role of microorganisms in biogeochemical cycling. SIP relies on tracing specific isotopically labeled substrates (e.g., 13C, 15N, 18O) into cellular biomarkers, such as DNA, RNA or phospholipid fatty acids, and is considered to be a robust technique to identify microbial populations that assimilate the labeled substrate. However, cross-feeding can occur when labeled metabolites are released from a primary consumer and then used by other microorganisms. This leads to erroneous identification of organisms that are not directly responsible for the process of interest, but are rather connected to primary consumers via a microbial food web. Here, we introduce a new approach that has the potential to eliminate the effect of cross-feeding in SIP studies and can thus also be used to distinguish primary consumers from other members of microbial food webs. In this approach, a monolayer of microbial cells are placed on a filter membrane, and labeled substrates are supplied by a continuous flow. By means of flow-through, labeled metabolites and degradation products are constantly removed, preventing secondary consumption of the substrate. We present results from a proof-of-concept experiment using nitrifiers from activated sludge as model system, in which we used fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes for identification of nitrifiers in combination with nanoscale secondary ion mass spectrometry (NanoSIMS) for visualization of isotope incorporation at the single-cell level. Our results show that flow-through SIP is a promising approach to significantly reduce cross-feeding and secondary substrate consumption in SIP experiments.

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

PubMed

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

2014-03-30

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. © 2013 Society of Chemical Industry.

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

PubMed

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

2016-05-01

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

Chemo-enzymatic synthesis of isotopically labeled nicotinamide riboside.

PubMed

Tran, Ai; Yokose, Ryota; Cen, Yana

2018-05-15

As a cofactor for numerous reactions, NAD+ is found widely dispersed across many maps of cellular metabolism. This core redox role alone makes the biosynthesis of NAD+ of great interest. Recent studies have revealed new biological roles for NAD+ as a substrate for diverse enzymes that regulate a broad spectrum of key cellular tasks. These NAD+-consuming enzymes further highlight the importance of understanding NAD+ biosynthetic pathways. In this study, we developed a chemo-enzymatic synthesis of isotopically labeled NAD+ precursor, nicotinamide riboside (NR). The synthesis of NR isotopomers allowed us to unambiguously determine that NR is efficiently converted to NAD+ in the cellular environment independent of degradation to nicotinamide, and it is incorporated into NAD+ in its intact form. The versatile synthetic method along with the isotopically labeled NRs will provide powerful tools to further decipher the important yet complicated NAD+ metabolism.

In Vivo Isotopic Labeling of Symbiotic Bacteria Involved in Cellulose Degradation and Nitrogen Recycling within the Gut of the Forest Cockchafer (Melolontha hippocastani).

PubMed

Alonso-Pernas, Pol; Bartram, Stefan; Arias-Cordero, Erika M; Novoselov, Alexey L; Halty-deLeon, Lorena; Shao, Yongqi; Boland, Wilhelm

2017-01-01

The guts of insects harbor symbiotic bacterial communities. However, due to their complexity, it is challenging to relate a specific symbiotic phylotype to its corresponding function. In the present study, we focused on the forest cockchafer ( Melolontha hippocastani ), a phytophagous insect with a dual life cycle, consisting of a root-feeding larval stage and a leaf-feeding adult stage. By combining in vivo stable isotope probing (SIP) with 13 C cellulose and 15 N urea as trophic links, with Illumina MiSeq (Illumina-SIP), we unraveled bacterial networks processing recalcitrant dietary components and recycling nitrogenous waste. The bacterial communities behind these processes change between larval and adult stages. In 13 C cellulose-fed insects, the bacterial families Lachnospiraceae and Enterobacteriaceae were isotopically labeled in larvae and adults, respectively. In 15 N urea-fed insects, the genera Burkholderia and Parabacteroides were isotopically labeled in larvae and adults, respectively. Additionally, the PICRUSt-predicted metagenome suggested a possible ability to degrade hemicellulose and to produce amino acids of, respectively, 13 C cellulose- and 15 N urea labeled bacteria. The incorporation of 15 N from ingested urea back into the insect body was confirmed, in larvae and adults, by isotope ratio mass spectrometry (IRMS). Besides highlighting key bacterial symbionts of the gut of M. hippocastani , this study provides example on how Illumina-SIP with multiple trophic links can be used to target microorganisms embracing different roles within an environment.

Highly enriched multiply-labeled stable isotopic compounds as atmospheric tracers

DOEpatents

Goldblatt, M.; McInteer, B.B.

1974-01-29

Compounds multiply-labeled with stable isotopes and highly enriched in these isotopes are readily capable of detection in tracer experiments involving high dilutions. Thus, for example, /sup 13/C/sup 18/O/sub 2/ provides a useful tracer for following atmospheric pol lution produced as a result of fossil fuel burning. (Official Gazette)

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

PubMed Central

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

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

An Isotopic Labelling Strategy to Study Cytochrome P450 Oxidations of Terpenes.

PubMed

Rinkel, Jan; Litzenburger, Martin; Bernhardt, Rita; Dickschat, Jeroen Sidney

2018-04-26

The cytochrome P450 monooxygenase CYP267B1 from Sorangium cellulosum was applied for enzymatic oxidation of the sesquiterpene alcohols T-muurolol and isodauc-8-en-11-ol. Various isotopically labelled geranyl and farnesyl diphosphates were used for product identification from micro-scale reactions, for determination of the absolute configurations of unknown compounds, to follow the stereochemical course of a cytochrome P450-catalysed hydroxylation step, and to investigate kinetic isotope effects. Overall, this study demonstrates that isotopically labelled terpene precursors are highly useful to follow cytochrome P450 dependent oxidations of terpenes. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

NASA Astrophysics Data System (ADS)

Chandra, Subhash

2004-06-01

Ion microscopy is a potentially powerful technique for localization of isotopically labeled molecules. In this study, L-arginine and phenylalanine amino acids labeled with stable isotopes 13C and 15N were localized in cultured cells with the ion microscope at 500 nm spatial resolution. Cells were exposed to the labeled amino acids and cryogenically prepared. SIMS analyses were made in fractured freeze-dried cells. A dynamic distribution was observed from labeled arginine-treated LLC-PK 1 kidney cells at mass 28 ( 13C15N) in negative secondaries, revealing cell-to-cell heterogeneity and preferential accumulation of the amino acid (or its metabolite) in the nucleus and nucleolus of some cells. The smaller nucleolus inside the nucleus was clearly resolved in SIMS images and confirmed by correlative light microscopy. The distribution of labeled phenylalanine contrasted with arginine as it was rather homogeneously distributed in T98G human glioblastoma cells. Images of 39K, 23Na and 40Ca were also recorded to confirm the reliability of sample preparation and authenticity of the observed amino acid distributions. These observations indicate that SIMS techniques can provide a valuable technology for subcellular localization of nitrogen-containing molecules in proteomics since nitrogen does not have a radionuclide tracer isotope. Amino acids labeled with stable isotopes can be used as tracers for studying their transport and metabolism in distinct subcellular compartments with SIMS. Further studies of phenylalanine uptake in human glioblastoma cells may have special significance in boron neutron capture therapy (BNCT) as a boron analogue of phenylalanine, boronophenylalanine is a clinically approved compound for the treatment of brain tumors.

A Modular Dual-Labeling Scaffold That Retains Agonistic Properties for Somatostatin Receptor Targeting

PubMed Central

Ghosh, Sukhen C.; Rodriguez, Melissa; Carmon, Kendra S.; Voss, Julie; Wilganowski, Nathaniel L.; Schonbrunn, Agnes

2017-01-01

Fluorescence-guided surgery is an emerging imaging technique that can enhance the ability of surgeons to detect tumors when compared with visual observation. To facilitate characterization, fluorescently labeled probes have been dual-labeled with a radionuclide to enable cross-validation with nuclear imaging. In this study, we selected the somatostatin receptor imaging agent DOTATOC as the foundation for developing a dual-labeled analog. We hypothesized that a customized dual-labeling approach with a multimodality chelation (MMC) scaffold would minimize steric effects of dye conjugation and retain agonist properties. Methods: An MMC conjugate (MMC-TOC) was synthesized on solid-phase and compared with an analog prepared using conventional methods (DA-TOC). Both analogs were conjugated to IRDye 800 using copper-free click chemistry. The resulting compounds, MMC(IR800)-TOC and DA(IR800)-TOC, were labeled with Cu and 64Cu and tested in vitro in somatostatin receptor subtype 2–overexpressing HEK-293 cells to assess agonist properties, and in AR42J rat pancreatic cancer cells to determine receptor binding characteristics. Multimodality imaging was performed in AR42J xenografts. Results: Cu-MMC(IR800)-TOC demonstrated higher potency for cyclic adenosine monophosphate inhibition (half maximal effective concentration [EC50]: 0.21 ± 0.18 vs. 1.38 ± 0.54 nM) and receptor internalization (EC50: 41.9 ± 29.8 vs. 455 ± 299 nM) than Cu-DA(IR800)-TOC. Radioactive uptake studies showed that blocking with octreotide caused a dose-dependent reduction in 64Cu-MMC(IR800)-TOC uptake whereas 64Cu-DA(IR800)-TOC was not affected. In vivo studies revealed higher tumor uptake for 64Cu-MMC(IR800)-TOC than 64Cu-DA(IR800)-TOC (5.2 ± 0.2 vs. 3.6 ± 0.4 percentage injected dose per gram). In vivo blocking studies with octreotide reduced tumor uptake of 64Cu-MMC(IR800)-TOC by 66%. Excretion of 64Cu-MMC(IR800)-TOC was primarily through the liver and spleen whereas 64Cu-DA(IR800)-TOC was

Single-larger-portion-size and dual-column nutrition labeling may help consumers make more healthful food choices.

PubMed

Lando, Amy M; Lo, Serena C

2013-02-01

The Food and Drug Administration is considering changes to the Nutrition Facts label to help consumers make more healthful choices. To examine the effects of modifications to the Nutrition Facts label on foods that can be listed as having 1 or 2 servings per container, but are reasonably consumed at a single eating occasion. Participants were randomly assigned to study conditions that varied on label format, product, and nutrition profile. Data were collected via an online consumer panel. Adults aged 18 years and older were recruited from Synovate's online household panel. Data were collected during August 2011. A total of 32,897 invitations were sent for a final sample of 9,493 interviews. Participants were randomly assigned to one of 10 label formats classified into three groups: listing 2 servings per container with a single column, listing 2 servings per container with a dual column, and listing a single serving per container. Within these groups there were versions that enlarged the font size for "calories," removed "calories from fat," and changed the wording for serving size declaration. The single product task measured product healthfulness, the amount of calories and various nutrients per serving and per container, and label perceptions. The product comparison task measured ability to identify the healthier product and the product with fewer calories per container and per serving. Analysis of covariance models with Tukey-Kramer tests were used. Covariates included general label use, age, sex, level of education, and race/ethnicity. Single-serving and dual-column formats performed better and scored higher on most outcome measures. For products that contain 2 servings but are customarily consumed at a single eating occasion, using a single-serving or dual-column labeling approach may help consumers make healthier food choices. Published by Elsevier Inc.

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

PubMed Central

2014-01-01

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

Radionuclide and Fluorescence Imaging of Clear Cell Renal Cell Carcinoma Using Dual Labeled Anti-Carbonic Anhydrase IX Antibody G250.

PubMed

Muselaers, Constantijn H J; Rijpkema, Mark; Bos, Desirée L; Langenhuijsen, Johan F; Oyen, Wim J G; Mulders, Peter F A; Oosterwijk, Egbert; Boerman, Otto C

2015-08-01

Tumor targeted optical imaging using antibodies labeled with near infrared fluorophores is a sensitive imaging modality that might be used during surgery to assure complete removal of malignant tissue. We evaluated the feasibility of dual modality imaging and image guided surgery with the dual labeled anti-carbonic anhydrase IX antibody preparation (111)In-DTPA-G250-IRDye800CW in mice with intraperitoneal clear cell renal cell carcinoma. BALB/c nu/nu mice with intraperitoneal SK-RC-52 lesions received 10 μg DTPA-G250-IRDye800CW labeled with 15 MBq (111)In or 10 μg of the dual labeled irrelevant control antibody NUH-82 (20 mice each). To evaluate when tumors could be detected, 4 mice per group were imaged weekly during 5 weeks with single photon emission computerized tomography/computerized tomography and the fluorescence imaging followed by ex vivo biodistribution studies. As early as 1 week after tumor cell inoculation single photon emission computerized tomography and fluorescence images showed clear delineation of intraperitoneal clear cell renal cell carcinoma with good concordance between single photon emission computerized tomography/computerized tomography and fluorescence images. The high and specific accumulation of the dual labeled antibody conjugate in tumors was confirmed in the biodistribution studies. Maximum tumor uptake was observed 1 week after inoculation (mean ± SD 58.5% ± 18.7% vs 5.6% ± 2.3% injected dose per gm for DTPA-G250-IRDye800CW vs NUH-82, respectively). High tumor uptake was also observed at other time points. This study demonstrates the feasibility of dual modality imaging with dual labeled antibody (111)In-DTPA-G250-IRDye800CW in a clear cell renal cell carcinoma model. Results indicate that preoperative and intraoperative detection of carbonic anhydrase IX expressing tumors, positive resection margins and metastasis might be feasible with this approach. Copyright © 2015 American Urological Association Education and Research

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

PubMed

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

2014-11-01

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. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2006-12-01

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

Overcoming interference with the detection of a stable isotopically labeled microtracer in the evaluation of beclabuvir absolute bioavailability using a concomitant microtracer approach.

PubMed

Jiang, Hao; Titsch, Craig; Zeng, Jianing; Jones, Barry; Joyce, Philip; Gandhi, Yash; Turley, Wesley; Burrell, Richard; Aubry, Anne F; Arnold, Mark E

2017-09-05

The oral absolute bioavailability of beclabuvir in healthy subjects was determined using a microdose (100μg) of the stable isotopically labeled tracer via intravenous (IV) infusion started after oral dosing of beclabuvir (150mg). To simultaneously analyze the concentrations of the IV microtracer ([ 13 C 6 ]beclabuvir) and beclabuvir in plasma samples, a liquid chromatography-triple quadrupole mass spectrometry (LC-MS/MS) method was initially developed. Surprisingly beclabuvir significantly interfered with the IV microtracer detection when using the selected reaction monitoring (SRM) in the assay. An interfering component from the drug substance was observed using a high resolution mass spectrometer (HRMS). The mass-to-charge (m/z) of the interfering component was -32ppm different from the nominal value for the IV microtracer and thus could not be differentiated in the SRM assay by the unit mass resolution. To overcome this interference, we evaluated two approaches by either monitoring an alternative product ion using the SRM assay or isolating the interfering component using the parallel reaction monitoring (PRM) assay on the HRMS. This case study has demonstrated two practical approaches for overcoming interferences with the detection of stable isotopically labeled IV microtracers in the evaluation of absolute bioavailability, which provides users the flexibility in using either LC-MS/MS or HRMS to mitigate unpredicted interferences in the assay to support microtracer absolute bioavailability studies. Copyright © 2017 Elsevier B.V. All rights reserved.

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...

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

PubMed

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

2014-05-20

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

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

PubMed

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

2016-09-01

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

The topology of metabolic isotope labeling networks.

PubMed

Weitzel, Michael; Wiechert, Wolfgang; Nöh, Katharina

2007-08-29

Metabolic Flux Analysis (MFA) based on isotope labeling experiments (ILEs) is a widely established tool for determining fluxes in metabolic pathways. Isotope labeling networks (ILNs) contain all essential information required to describe the flow of labeled material in an ILE. Whereas recent experimental progress paves the way for high-throughput MFA, large network investigations and exact statistical methods, these developments are still limited by the poor performance of computational routines used for the evaluation and design of ILEs. In this context, the global analysis of ILN topology turns out to be a clue for realizing large speedup factors in all required computational procedures. With a strong focus on the speedup of algorithms the topology of ILNs is investigated using graph theoretic concepts and algorithms. A rigorous determination of all cyclic and isomorphic subnetworks, accompanied by the global analysis of ILN connectivity is performed. Particularly, it is proven that ILNs always brake up into a large number of small strongly connected components (SCCs) and, moreover, there are natural isomorphisms between many of these SCCs. All presented techniques are universal, i.e. they do not require special assumptions on the network structure, bidirectionality of fluxes, measurement configuration, or label input. The general results are exemplified with a practically relevant metabolic network which describes the central metabolism of E. coli comprising 10390 isotopomer pools. Exploiting the topological features of ILNs leads to a significant speedup of all universal algorithms for ILE evaluation. It is proven in theory and exemplified with the E. coli example that a speedup factor of about 1000 compared to standard algorithms is achieved. This widely opens the door for new high performance algorithms suitable for high throughput applications and large ILNs. Moreover, for the first time the global topological analysis of ILNs allows to comprehensively

Dual-tracer background subtraction approach for fluorescent molecular tomography

PubMed Central

Holt, Robert W.; El-Ghussein, Fadi; Davis, Scott C.; Samkoe, Kimberley S.; Gunn, Jason R.; Leblond, Frederic

2013-01-01

Abstract. Diffuse fluorescence tomography requires high contrast-to-background ratios to accurately reconstruct inclusions of interest. This is a problem when imaging the uptake of fluorescently labeled molecularly targeted tracers in tissue, which can result in high levels of heterogeneously distributed background uptake. We present a dual-tracer background subtraction approach, wherein signal from the uptake of an untargeted tracer is subtracted from targeted tracer signal prior to image reconstruction, resulting in maps of targeted tracer binding. The approach is demonstrated in simulations, a phantom study, and in a mouse glioma imaging study, demonstrating substantial improvement over conventional and homogenous background subtraction image reconstruction approaches. PMID:23292612

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

DOEpatents

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

2014-12-09

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

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

PubMed

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

2005-03-01

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

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

PubMed

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

2016-12-01

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

Dual-Labeled Near-Infrared/99mTc Imaging Probes Using PAMAM-Coated Silica Nanoparticles for the Imaging of HER2-Expressing Cancer Cells

PubMed Central

Yamaguchi, Haruka; Tsuchimochi, Makoto; Hayama, Kazuhide; Kawase, Tomoyuki; Tsubokawa, Norio

2016-01-01

We sought to develop dual-modality imaging probes using functionalized silica nanoparticles to target human epidermal growth factor receptor 2 (HER2)-overexpressing breast cancer cells and achieve efficient target imaging of HER2-expressing tumors. Polyamidoamine-based functionalized silica nanoparticles (PCSNs) for multimodal imaging were synthesized with near-infrared (NIR) fluorescence (indocyanine green (ICG)) and technetium-99m (99mTc) radioactivity. Anti-HER2 antibodies were bound to the labeled PCSNs. These dual-imaging probes were tested to image HER2-overexpressing breast carcinoma cells. In vivo imaging was also examined in breast tumor xenograft models in mice. SK-BR3 (HER2 positive) cells were imaged with stronger NIR fluorescent signals than that in MDA-MB231 (HER2 negative) cells. The increased radioactivity of the SK-BR3 cells was also confirmed by phosphor imaging. NIR images showed strong fluorescent signals in the SK-BR3 tumor model compared to muscle tissues and the MDA-MB231 tumor model. Automatic well counting results showed increased radioactivity in the SK-BR3 xenograft tumors. We developed functionalized silica nanoparticles loaded with 99mTc and ICG for the targeting and imaging of HER2-expressing cells. The dual-imaging probes efficiently imaged HER2-overexpressing cells. Although further studies are needed to produce efficient isotope labeling, the results suggest that the multifunctional silica nanoparticles are a promising vehicle for imaging specific components of the cell membrane in a dual-modality manner. PMID:27399687

Dual-Labeled Near-Infrared/(99m)Tc Imaging Probes Using PAMAM-Coated Silica Nanoparticles for the Imaging of HER2-Expressing Cancer Cells.

PubMed

Yamaguchi, Haruka; Tsuchimochi, Makoto; Hayama, Kazuhide; Kawase, Tomoyuki; Tsubokawa, Norio

2016-07-07

We sought to develop dual-modality imaging probes using functionalized silica nanoparticles to target human epidermal growth factor receptor 2 (HER2)-overexpressing breast cancer cells and achieve efficient target imaging of HER2-expressing tumors. Polyamidoamine-based functionalized silica nanoparticles (PCSNs) for multimodal imaging were synthesized with near-infrared (NIR) fluorescence (indocyanine green (ICG)) and technetium-99m ((99m)Tc) radioactivity. Anti-HER2 antibodies were bound to the labeled PCSNs. These dual-imaging probes were tested to image HER2-overexpressing breast carcinoma cells. In vivo imaging was also examined in breast tumor xenograft models in mice. SK-BR3 (HER2 positive) cells were imaged with stronger NIR fluorescent signals than that in MDA-MB231 (HER2 negative) cells. The increased radioactivity of the SK-BR3 cells was also confirmed by phosphor imaging. NIR images showed strong fluorescent signals in the SK-BR3 tumor model compared to muscle tissues and the MDA-MB231 tumor model. Automatic well counting results showed increased radioactivity in the SK-BR3 xenograft tumors. We developed functionalized silica nanoparticles loaded with (99m)Tc and ICG for the targeting and imaging of HER2-expressing cells. The dual-imaging probes efficiently imaged HER2-overexpressing cells. Although further studies are needed to produce efficient isotope labeling, the results suggest that the multifunctional silica nanoparticles are a promising vehicle for imaging specific components of the cell membrane in a dual-modality manner.

Dual-process theory and consumer response to front-of-package nutrition label formats.

PubMed

Sanjari, S Setareh; Jahn, Steffen; Boztug, Yasemin

2017-11-01

Nutrition labeling literature yields fragmented results about the effect of front-of-package (FOP) nutrition label formats on healthy food choice. Specifically, it is unclear which type of nutrition label format is effective across different shopping situations. To address this gap, the present review investigates the available nutrition labeling literature through the prism of dual-process theory, which posits that decisions are made either quickly and automatically (system 1) or slowly and deliberately (system 2). A systematically performed review of nutrition labeling literature returned 59 papers that provide findings that can be explained according to dual-process theory. The findings of these studies suggest that the effectiveness of nutrition label formats is influenced by the consumer's dominant processing system, which is a function of specific contexts and personal variables (eg, motivation, nutrition knowledge, time pressure, and depletion). Examination of reported findings through a situational processing perspective reveals that consumers might prefer different FOP nutrition label formats in different situations and can exhibit varying responses to the same label format across situations. This review offers several suggestions for policy makers and researchers to help improve current FOP nutrition label formats. © The Author(s) 2017. Published by Oxford University Press on behalf of the International Life Sciences Institute. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Dual isotopic approach for determining groundwater origin and water-rock interactions in over exploited watershed in India

NASA Astrophysics Data System (ADS)

Negrel, Philippe; Pauwels, Hélène; Millot, Romain; Roy, Stéphane; Guerrot, Catherine

2010-05-01

Groundwater flow and storage in hard rock areas is becoming a matter of great interest and importance to researchers and water managers either with regards to the quantity, quality of water as well as delimitation of resources and aquifers. Degradation of groundwater resources by abstraction, contamination, ... has been increasing in many areas and is of growing concern for few decades. In terms of hydrogeology, hard rocks represent a quite heterogeneous and anisotropic media with irregular distribution of pathways of groundwater flow, typically consisting of three vertical zones, upper weathered, middle fractured and lower massive bedrock. Aim of this work is dual and the Maheshwaram watershed (53 km2, Andhra Pradesh, India) representative of watersheds in southern India in terms of geology, overpumping of its hard-rock aquifer (more than 700 classical open end wells in use), its cropping pattern (rice dominating), and its rural socio-economy mainly based on traditional agriculture is investigated through stable isotopes of the water molecule and lead isotopes in groundwater. The overall objective is to incorporate isotopic- and chemical-tracing data and constraints into methods for evaluating groundwater circulation. It divides into fingerprinting the groundwater recharge processes (e.g. the input by the monsoon) and the water use in such agricultural watershed, which is of primary importance in such semi-arid context and investigating the processes of water-rock interactions (e.g. granite-water interaction). In the frame of delimitation of resources and aquifers and long-term sustainability, we monitored the input from monsoon-precipitation over 2 years, and measured spatial and temporal variations in δ18O and δ2H in the groundwater and in precipitation. Individual recharge from the two monsoon periods was identified. This led to identification of periods during which evaporation affects groundwater quality through a higher concentration of salts and stable

Intact stable isotope labeled plasma proteins from the SILAC-labeled HepG2 secretome.

PubMed

Mangrum, John B; Martin, Erika J; Brophy, Donald F; Hawkridge, Adam M

2015-09-01

The plasma proteome remains an attractive biospecimen for MS-based biomarker discovery studies. The success of these efforts relies on the continued development of quantitative MS-based proteomics approaches. Herein we report the use of the SILAC-labeled HepG2 secretome as a source for stable isotope labeled plasma proteins for quantitative LC-MS/MS measurements. The HepG2 liver cancer cell line secretes the major plasma proteins including serum albumin, apolipoproteins, protease inhibitors, coagulation factors, and transporters that represent some of the most abundant proteins in plasma. The SILAC-labeled HepG2 secretome was collected, spiked into human plasma (1:1 total protein), and then processed for LC-MS/MS analysis. A total of 62 and 56 plasma proteins were quantified (heavy:light (H/L) peptide pairs) from undepleted and depleted (serum albumin and IgG), respectively, with log2 H/L = ± 6. Major plasma proteins quantified included albumin, apolipoproteins (e.g., APOA1, APOA2, APOA4, APOB, APOC3, APOE, APOH, and APOM), protease inhibitors (e.g., A2M and SERPINs), coagulation factors (e.g., Factor V, Factor X, fibrinogen), and transport proteins (e.g., TTR). The average log2 H/L values for shared plasma proteins in both undepleted and depleted plasma samples were 0.43 and 0.44, respectively. This work further expands the SILAC strategy into MS-based biomarker discovery of clinical biospecimens. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The impact of carbon-13 and deuterium on relative quantification of proteins using stable isotope diethyl labeling.

PubMed

Koehler, Christian J; Arntzen, Magnus Ø; Thiede, Bernd

2015-05-15

Stable isotopic labeling techniques are useful for quantitative proteomics. A cost-effective and convenient method for diethylation by reductive amination was established. The impact using either carbon-13 or deuterium on quantification accuracy and precision was investigated using diethylation. We established an effective approach for stable isotope labeling by diethylation of amino groups of peptides. The approach was validated using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and nanospray liquid chromatography/electrospray ionization (nanoLC/ESI)-ion trap/orbitrap for mass spectrometric analysis as well as MaxQuant for quantitative data analysis. Reaction conditions with low reagent costs, high yields and minor side reactions were established for diethylation. Furthermore, we showed that diethylation can be applied to up to sixplex labeling. For duplex experiments, we compared diethylation in the analysis of the proteome of HeLa cells using acetaldehyde-(13) C(2)/(12) C(2) and acetaldehyde-(2) H(4)/(1) H(4). Equal numbers of proteins could be identified and quantified; however, (13) C(4)/(12) C(4) -diethylation revealed a lower variance of quantitative peptide ratios within proteins resulting in a higher precision of quantified proteins and less falsely regulated proteins. The results were compared with dimethylation showing minor effects because of the lower number of deuteriums. The described approach for diethylation of primary amines is a cost-effective and accurate method for up to sixplex relative quantification of proteomes. (13) C(4)/(12) C(4) -diethylation enables duplex quantification based on chemical labeling without using deuterium which reduces identification of false-negatives and increases the quality of the quantification results. Copyright © 2015 John Wiley & Sons, Ltd.

Formation of nonextractable soil residues: A stable isotope approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richnow, H.H.; Eschenback, A.; Mahro, B.

1999-11-01

Stable carbon isotopic measurements were employed to characterize the transformation of a {sup 13}C-labeled polycyclic aromatic hydrocarbon (PAH), anthracene, in a closed soil bioreactor system. The {sup 13}C-label was used to calculate a carbon mass balance including mineralization and the formation of nonextractable soil-bound residues. Similar results were obtained from {sup 13}C-labeled carbon and {sup 14}C-labeled carbon mass balance calculations for separate batch experiments with labeled anthracene. In concentration ranges typical for real PAH-contaminated sites, the sensitivity of the {sup 13}C tracer method meets the requirements of classical radiotracer experiments. Therefore, the authors balancing method based on stable isotope-labeled chemicalsmore » may supplement or substitute radiotracer experiments under many circumstances. One major advantage of using stable isotope-labeled tracers is the possible application in transformation studies where the use of radioactive substances is of environmental concern. The transformation of {sup 13}C-labeled PAH into nonextractable residues clearly depends on the metabolic activity of the soil microflora and occurs during an early phase of biodegradation. Successive contamination of the soil by anthracene leads to a progressive adaptation of the microflora to a complete mineralization of anthracene in the soil. The extent of residue formation is controlled by the capability of the microflora to degrade the contaminant. Results of long-term experiments indicate that nonextractable residues are relatively stable over time.« less

UNiquant, a program for quantitative proteomics analysis using stable isotope labeling.

PubMed

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

2011-03-04

Stable isotope labeling (SIL) methods coupled with nanoscale liquid chromatography and high resolution tandem mass spectrometry are increasingly useful for elucidation of the proteome-wide differences between multiple biological samples. Development of more effective programs for the sensitive identification of peptide pairs and accurate measurement of the relative peptide/protein abundance are essential for quantitative proteomic analysis. We developed and evaluated the performance of a new program, termed UNiquant, for analyzing quantitative proteomics data using stable isotope labeling. UNiquant was compared with two other programs, MaxQuant and Mascot Distiller, using SILAC-labeled complex proteome mixtures having either known or unknown heavy/light ratios. For the SILAC-labeled Jeko-1 cell proteome digests with known heavy/light ratios (H/L = 1:1, 1:5, and 1:10), UNiquant quantified a similar number of peptide pairs as MaxQuant for the H/L = 1:1 and 1:5 mixtures. In addition, UNiquant quantified significantly more peptides than MaxQuant and Mascot Distiller in the H/L = 1:10 mixtures. UNiquant accurately measured relative peptide/protein abundance without the need for postmeasurement normalization of peptide ratios, which is required by the other programs.

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

PubMed Central

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

2011-01-01

Stable isotope labeling (SIL) methods coupled with nanoscale liquid chromatography and high resolution tandem mass spectrometry are increasingly useful for elucidation of the proteome-wide differences between multiple biological samples. Development of more effective programs for the sensitive identification of peptide pairs and accurate measurement of the relative peptide/protein abundance are essential for quantitative proteomic analysis. We developed and evaluated the performance of a new program, termed UNiquant, for analyzing quantitative proteomics data using stable isotope labeling. UNiquant was compared with two other programs, MaxQuant and Mascot Distiller, using SILAC-labeled complex proteome mixtures having either known or unknown heavy/light ratios. For the SILAC-labeled Jeko-1 cell proteome digests with known heavy/light ratios (H/L = 1:1, 1:5, and 1:10), UNiquant quantified a similar number of peptide pairs as MaxQuant for the H/L = 1:1 and 1:5 mixtures. In addition, UNiquant quantified significantly more peptides than MaxQuant and Mascot Distiller in the H/L = 1:10 mixtures. UNiquant accurately measured relative peptide/protein abundance without the need for post-measurement normalization of peptide ratios, which is required by the other programs. PMID:21158445

Time-resolved Analysis of Proteome Dynamics by Tandem Mass Tags and Stable Isotope Labeling in Cell Culture (TMT-SILAC) Hyperplexing*

PubMed Central

Welle, Kevin A.; Zhang, Tian; Hryhorenko, Jennifer R.; Shen, Shichen; Qu, Jun; Ghaemmaghami, Sina

2016-01-01

Recent advances in mass spectrometry have enabled system-wide analyses of protein turnover. By globally quantifying the kinetics of protein clearance and synthesis, these methodologies can provide important insights into the regulation of the proteome under varying cellular and environmental conditions. To facilitate such analyses, we have employed a methodology that combines metabolic isotopic labeling (Stable Isotope Labeling in Cell Culture - SILAC) with isobaric tagging (Tandem Mass Tags - TMT) for analysis of multiplexed samples. The fractional labeling of multiple time-points can be measured in a single mass spectrometry run, providing temporally resolved measurements of protein turnover kinetics. To demonstrate the feasibility of the approach, we simultaneously measured the kinetics of protein clearance and accumulation for more than 3000 proteins in dividing and quiescent human fibroblasts and verified the accuracy of the measurements by comparison to established non-multiplexed approaches. The results indicate that upon reaching quiescence, fibroblasts compensate for lack of cellular growth by globally downregulating protein synthesis and upregulating protein degradation. The described methodology significantly reduces the cost and complexity of temporally-resolved dynamic proteomic experiments and improves the precision of proteome-wide turnover data. PMID:27765818

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

PubMed

Keiderling, Timothy A

2017-12-01

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

High-coverage quantitative proteomics using amine-specific isotopic labeling.

PubMed

Melanson, Jeremy E; Avery, Steven L; Pinto, Devanand M

2006-08-01

Peptide dimethylation with isotopically coded formaldehydes was evaluated as a potential alternative to techniques such as the iTRAQ method for comparative proteomics. The isotopic labeling strategy and custom-designed protein quantitation software were tested using protein standards and then applied to measure proteins levels associated with Alzheimer's disease (AD). The method provided high accuracy (10% error), precision (14% RSD) and coverage (70%) when applied to the analysis of a standard solution of BSA by LC-MS/MS. The technique was then applied to measure protein abundance levels in brain tissue afflicted with AD relative to normal brain tissue. 2-D LC-MS analysis identified 548 unique proteins (p<0.05). Of these, 349 were quantified with two or more peptides that met the statistical criteria used in this study. Several classes of proteins exhibited significant changes in abundance. For example, elevated levels of antioxidant proteins and decreased levels of mitochondrial electron transport proteins were observed. The results demonstrate the utility of the labeling method for high-throughput quantitative analysis.

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

A dual stable-isotope approach to analyse the linkages between tree water fluxes and soil water pools in a Mediterranean mountain catchment

NASA Astrophysics Data System (ADS)

Llorens, Pilar; Cayuela, Carles; Sánchez-Costa, Elisenda; Gallart, Francesc; Latron, Jérôme

2017-04-01

This work uses a dual isotope-based approach (18O, 2H) to examine the mixing of water in the soil and the linkages between tree water fluxes and soil water pools in a Mediterranean mountain catchment (Vallcebre Research Catchments, NE Spain, 42° 12'N, 1° 49'E). Since May 2015, water-isotopes have been monitored in rainfall, throughfall and stemflow below a Scots pine stand and in stream water at the Can Vila (0.56 km2) catchment outlet. Moreover, fortnightly (From May to December 2015) soil samples (10, 20, 30, 50 and 100 cm), xylem samples (3 Scots pines) and mobile soil water samples in low-suction lysimeters (20, 50 and 100 cm) and in a piezometer (150-300 cm deep) were collected at the same stand. Water from soil and xylem samples was extracted by cryogenic vacuum distillation and isotope analyses were obtained by infrared spectroscopy. All this information has been combined with continuous measurement of meteorological, soil moisture and water potential, piezometric levels and hydrological variables at the stand and catchment scales. Stable isotopes ratios of bound soil water fell below the local meteoric water line (LMWL), with more evaporative enrichment in the shallow horizons. On the contrary, mobile soil water (low suction lysimeters) and groundwater fell along the LMWL, well mixed with stream water. The differences observed between these two water pools remained similar during the whole study period. Stable isotopes ratios indicate that Scots pine trees use shallow bound soil water during the whole study period. No marked changes in depth of water uptake were observed, presumably due to the availability of water in the shallow horizons, even during the summer months.

Dye bias correction in dual-labeled cDNA microarray gene expression measurements.

PubMed Central

Rosenzweig, Barry A; Pine, P Scott; Domon, Olen E; Morris, Suzanne M; Chen, James J; Sistare, Frank D

2004-01-01

A significant limitation to the analytical accuracy and precision of dual-labeled spotted cDNA microarrays is the signal error due to dye bias. Transcript-dependent dye bias may be due to gene-specific differences of incorporation of two distinctly different chemical dyes and the resultant differential hybridization efficiencies of these two chemically different targets for the same probe. Several approaches were used to assess and minimize the effects of dye bias on fluorescent hybridization signals and maximize the experimental design efficiency of a cell culture experiment. Dye bias was measured at the individual transcript level within each batch of simultaneously processed arrays by replicate dual-labeled split-control sample hybridizations and accounted for a significant component of fluorescent signal differences. This transcript-dependent dye bias alone could introduce unacceptably high numbers of both false-positive and false-negative signals. We found that within a given set of concurrently processed hybridizations, the bias is remarkably consistent and therefore measurable and correctable. The additional microarrays and reagents required for paired technical replicate dye-swap corrections commonly performed to control for dye bias could be costly to end users. Incorporating split-control microarrays within a set of concurrently processed hybridizations to specifically measure dye bias can eliminate the need for technical dye swap replicates and reduce microarray and reagent costs while maintaining experimental accuracy and technical precision. These data support a practical and more efficient experimental design to measure and mathematically correct for dye bias. PMID:15033598

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

PubMed

Preston, Tom

2014-01-01

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

Recent advances in stable isotope labeling based techniques for proteome relative quantification.

PubMed

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

2014-10-24

The large scale relative quantification of all proteins expressed in biological samples under different states is of great importance for discovering proteins with important biological functions, as well as screening disease related biomarkers and drug targets. Therefore, the accurate quantification of proteins at proteome level has become one of the key issues in protein science. Herein, the recent advances in stable isotope labeling based techniques for proteome relative quantification were reviewed, from the aspects of metabolic labeling, chemical labeling and enzyme-catalyzed labeling. Furthermore, the future research direction in this field was prospected. Copyright © 2014 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Dual isotope notch observer for isotope identification, assay and imaging with mono-energetic gamma-ray sources

DOEpatents

Barty, Christopher P.J.

2013-02-05

A dual isotope notch observer for isotope identification, assay and imaging with mono-energetic gamma-ray sources includes a detector arrangement consists of three detectors downstream from the object under observation. The latter detector, which operates as a beam monitor, is an integrating detector that monitors the total beam power arriving at its surface. The first detector and the middle detector each include an integrating detector surrounding a foil. The foils of these two detectors are made of the same atomic material, but each foil is a different isotope, e.g., the first foil may comprise U235 and second foil may comprise U238. The integrating detectors surrounding these pieces of foil measure the total power scattered from the foil and can be similar in composition to the final beam monitor. Non-resonant photons will, after calibration, scatter equally from both foils.

Quantifying the effect of plant growth on litter decomposition using a novel, triple-isotope label approach

NASA Astrophysics Data System (ADS)

Ernakovich, J. G.; Baldock, J.; Carter, T.; Davis, R. A.; Kalbitz, K.; Sanderman, J.; Farrell, M.

2017-12-01

Microbial degradation of plant detritus is now accepted as a major stabilizing process of organic matter in soils. Most of our understanding of the dynamics of decomposition come from laboratory litter decay studies in the absence of plants, despite the fact that litter decays in the presence of plants in many native and managed systems. There is growing evidence that living plants significantly impact the degradation and stabilization of litter carbon (C) due to changes in the chemical and physical nature of soils in the rhizosphere. For example, mechanistic studies have observed stimulatory effects of root exudates on litter decomposition, and greenhouse studies have shown that living plants accelerate detrital decay. Despite this, we lack a quantitative understanding of the contribution of living plants to litter decomposition and how interactions of these two sources of C build soil organic matter (SOM). We used a novel triple-isotope approach to determine the effect of living plants on litter decomposition and C cycling. In the first stage of the experiment, we grew a temperate grass commonly used for forage, Poa labillardieri, in a continuously-labelled atmosphere of 14CO2 fertilized with K15NO3, such that the grass biomass was uniformly labelled with 14C and 15N. In the second stage, we constructed litter decomposition mescososms with and without a living plant to test for the effect of a growing plant on litter decomposition. The 14C/15N litter was decomposed in a sandy clay loam while a temperate forage grass, Lolium perenne, grew in an atmosphere of enriched 13CO2. The fate of the litter-14C/15N and plant-13C was traced into soil mineral fractions and dissolved organic matter (DOM) over the course of nine weeks using four destructive harvests of the mesocosms. Our preliminary results suggest that living plants play a major role in the degradation of plant litter, as litter decomposition was greater, both in rate and absolute amount, for soil mesocosms

Evaluation of stereo-array isotope labeling (SAIL) patterns for automated structural analysis of proteins with CYANA.

PubMed

Ikeya, Teppei; Terauchi, Tsutomu; Güntert, Peter; Kainosho, Masatsune

2006-07-01

Recently we have developed the stereo-array isotope labeling (SAIL) technique to overcome the conventional molecular size limitation in NMR protein structure determination by employing complete stereo- and regiospecific patterns of stable isotopes. SAIL sharpens signals and simplifies spectra without the loss of requisite structural information, thus making large classes of proteins newly accessible to detailed solution structure determination. The automated structure calculation program CYANA can efficiently analyze SAIL-NOESY spectra and calculate structures without manual analysis. Nevertheless, the original SAIL method might not be capable of determining the structures of proteins larger than 50 kDa or membrane proteins, for which the spectra are characterized by many broadened and overlapped peaks. Here we have carried out simulations of new SAIL patterns optimized for minimal relaxation and overlap, to evaluate the combined use of SAIL and CYANA for solving the structures of larger proteins and membrane proteins. The modified approach reduces the number of peaks to nearly half of that observed with uniform labeling, while still yielding well-defined structures and is expected to enable NMR structure determinations of these challenging systems.

Individual-specific transgenerational marking of fish populations based on a barium dual-isotope procedure.

PubMed

Huelga-Suarez, Gonzalo; Moldovan, Mariella; Garcia-Valiente, America; Garcia-Vazquez, Eva; Alonso, J Ignacio Garcia

2012-01-03

The present study focuses on the development and evaluation of an individual-specific transgenerational marking procedure using two enriched barium isotopes, (135)Ba and (137)Ba, mixed at a given and selectable molar ratio. The method is based on the deconvolution of the isotope patterns found in the sample into four molar contribution factors: natural xenon (Xe nat), natural barium (Ba nat), Ba135, and Ba137. The ratio of molar contributions between Ba137 and Ba135 is constant and independent of the contribution of natural barium in the sample. This procedure was tested in brown trout ( Salmo trutta ) kept in captivity. Trout were injected with three different Ba137/Ba135 isotopic signatures ca. 7 months and 7 days before spawning to compare the efficiency of the marking procedure at long and short term, respectively. The barium isotopic profiles were measured in the offspring by means of inductively coupled plasma mass spectrometry. Each of the three different isotopic signatures was unequivocally identified in the offspring in both whole eggs and larvae. For 9 month old offspring, the characteristic barium isotope signatures could also be detected in the otoliths even in the presence of a high and variable amount of barium of natural isotope abundance. In conclusion, it can be stated that the proposed dual-isotope marking is inheritable and can be detected after both long-term and short-term marking. Furthermore, the dual-isotope marking can be made individual-specific, so that it allows identification of offspring from a single individual or a group of individuals within a given fish group. © 2011 American Chemical Society

Preparation of ⁶⁸Ga-labelled DOTA-peptides using a manual labelling approach for small-animal PET imaging.

PubMed

Romero, Eduardo; Martínez, Alfonso; Oteo, Marta; García, Angel; Morcillo, Miguel Angel

2016-01-01

(68)Ga-DOTA-peptides are a promising PET radiotracers used in the detection of different tumours types due to their ability for binding specifically receptors overexpressed in these. Furthermore, (68)Ga can be produced by a (68)Ge/(68)Ga generator on site which is a very good alternative to cyclotron-based PET isotopes. Here, we describe a manual labelling approach for the synthesis of (68)Ga-labelled DOTA-peptides based on concentration and purification of the commercial (68)Ga/(68)Ga generator eluate using an anion exchange-cartridge. (68)Ga-DOTA-TATE was used to image a pheochromocytoma xenograft mouse model by a microPET/CT scanner. The method described provides satisfactory results, allowing the subsequent (68)Ga use to label DOTA-peptides. The simplicity of the method along with its implementation reduced cost, makes it useful in preclinical PET studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Real-time dual-loop electric current measurement for label-free nanofluidic preconcentration chip.

PubMed

Chung, Pei-Shan; Fan, Yu-Jui; Sheen, Horn-Jiunn; Tian, Wei-Cheng

2015-01-07

An electrokinetic trapping (EKT)-based nanofluidic preconcentration device with the capability of label-free monitoring trapped biomolecules through real-time dual-loop electric current measurement was demonstrated. Universal current-voltage (I-V) curves of EKT-based preconcentration devices, consisting of two microchannels connected by ion-selective channels, are presented for functional validation and optimal operation; universal onset current curves indicating the appearance of the EKT mechanism serve as a confirmation of the concentrating action. The EKT mechanism and the dissimilarity in the current curves related to the volume flow rate (Q), diffusion coefficient (D), and diffusion layer (DL) thickness were explained by a control volume model with a five-stage preconcentration process. Different behaviors of the trapped molecular plug were categorized based on four modes associated with different degrees of electroosmotic instability (EOI). A label-free approach to preconcentrating (bio)molecules and monitoring the multibehavior molecular plug was demonstrated through real-time electric current monitoring, rather than through the use of microscope images.

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

PubMed

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

2011-09-22

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

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

PubMed

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

2015-04-21

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

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

PubMed

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

2014-02-15

The contamination of Pb in agricultural soils is one of the most important ecological problems, which potentially results in serious health risk on human health through food chain. Hence, the fate of exogenous Pb contaminated in agricultural soils is needed to be deeply explored. By spiking soils with the stable enriched isotopes of (206)Pb, the contamination of exogenous Pb(2+) ions in three agricultural soils sampled from the estuary areas of Jiulong River, China was simulated in the present study, and the distribution, mobility and bioavailability of exogenous Pb in the soils were investigated using the isotopic labeling method coupled with a four-stage BCR (European Community Bureau of Reference) sequential extraction procedure. Results showed that about 60-85% of exogenous Pb was found to distribute in reducible fractions, while the exogenous Pb in acid-extractable fractions was less than 1.0%. After planting, the amounts of exogenous Pb presenting in acid-extractable, reducible and oxidizable fractions in rhizospheric soils decreased by 60-66%, in which partial exogenous Pb was assimilated by plants while most of the metal might transfer downward due to daily watering and applying fertilizer. The results show that the isotopic labeling technique coupled with sequential extraction procedures enables us to explore the distribution, mobility and bioavailability of exogenous Pb contaminated in soils, which may be useful for the further soil remediation. Copyright © 2014 Elsevier B.V. All rights reserved.

Distinct Dual C-Cl Isotope Fractionation Patterns during Anaerobic Biodegradation of 1,2-Dichloroethane: Potential To Characterize Microbial Degradation in the Field.

PubMed

Palau, J; Yu, R; Hatijah Mortan, S; Shouakar-Stash, O; Rosell, M; Freedman, D L; Sbarbati, C; Fiorenza, S; Aravena, R; Marco-Urrea, E; Elsner, M; Soler, A; Hunkeler, D

2017-03-07

This study investigates, for the first time, dual C-Cl isotope fractionation during anaerobic biodegradation of 1,2-dichloroethane (1,2-DCA) via dihaloelimination by Dehalococcoides and Dehalogenimonas-containing enrichment cultures. Isotopic fractionation of 1,2-DCA (ε bulk C and ε bulk Cl ) for Dehalococcoides (-33.0 ± 0.4‰ and -5.1 ± 0.1‰) and Dehalogenimonas-containing microcosms (-23 ± 2‰ and -12.0 ± 0.8‰) resulted in distinctly different dual element C-Cl isotope correlations (Λ = Δδ 13 C/Δδ 37 Cl ≈ ε bulk C /ε bulk Cl ), 6.8 ± 0.2 and 1.89 ± 0.02, respectively. Determined isotope effects and detected products suggest that the difference on the obtained Λ values for biodihaloelimination could be associated with a different mode of concerted bond cleavage rather than two different reaction pathways (i.e., stepwise vs concerted). Λ values of 1,2-DCA were, for the first time, determined in two field sites under reducing conditions (2.1 ± 0.1 and 2.2 ± 2.9). They were similar to the one obtained for the Dehalogenimonas-containing microcosms (1.89 ± 0.02) and very different from those reported for aerobic degradation pathways in a previous laboratory study (7.6 ± 0.1 and 0.78 ± 0.03). Thus, this study illustrates the potential of a dual isotope analysis to differentiate between aerobic and anaerobic biodegradation pathways of 1,2-DCA in the field and suggests that this approach might also be used to characterize dihaloelimination of 1,2-DCA by different bacteria, which needs to be confirmed in future studies.

Less label, more free: approaches in label-free quantitative mass spectrometry.

PubMed

Neilson, Karlie A; Ali, Naveid A; Muralidharan, Sridevi; Mirzaei, Mehdi; Mariani, Michael; Assadourian, Gariné; Lee, Albert; van Sluyter, Steven C; Haynes, Paul A

2011-02-01

In this review we examine techniques, software, and statistical analyses used in label-free quantitative proteomics studies for area under the curve and spectral counting approaches. Recent advances in the field are discussed in an order that reflects a logical workflow design. Examples of studies that follow this design are presented to highlight the requirement for statistical assessment and further experiments to validate results from label-free quantitation. Limitations of label-free approaches are considered, label-free approaches are compared with labelling techniques, and forward-looking applications for label-free quantitative data are presented. We conclude that label-free quantitative proteomics is a reliable, versatile, and cost-effective alternative to labelled quantitation. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Estimating pathway-specific contributions to biodegradation in aquifers based on dual isotope analysis: theoretical analysis and reactive transport simulations.

PubMed

Centler, Florian; Heße, Falk; Thullner, Martin

2013-09-01

At field sites with varying redox conditions, different redox-specific microbial degradation pathways contribute to total contaminant degradation. The identification of pathway-specific contributions to total contaminant removal is of high practical relevance, yet difficult to achieve with current methods. Current stable-isotope-fractionation-based techniques focus on the identification of dominant biodegradation pathways under constant environmental conditions. We present an approach based on dual stable isotope data to estimate the individual contributions of two redox-specific pathways. We apply this approach to carbon and hydrogen isotope data obtained from reactive transport simulations of an organic contaminant plume in a two-dimensional aquifer cross section to test the applicability of the method. To take aspects typically encountered at field sites into account, additional simulations addressed the effects of transverse mixing, diffusion-induced stable-isotope fractionation, heterogeneities in the flow field, and mixing in sampling wells on isotope-based estimates for aerobic and anaerobic pathway contributions to total contaminant biodegradation. Results confirm the general applicability of the presented estimation method which is most accurate along the plume core and less accurate towards the fringe where flow paths receive contaminant mass and associated isotope signatures from the core by transverse dispersion. The presented method complements the stable-isotope-fractionation-based analysis toolbox. At field sites with varying redox conditions, it provides a means to identify the relative importance of individual, redox-specific degradation pathways. © 2013.

Analysis of Hydrogen Isotopic Exchange: Lava Creek Tuff Ash and Isotopically Labeled Water

NASA Astrophysics Data System (ADS)

Ross, A. M.; Seligman, A. N.; Bindeman, I. N.; Nolan, G. S.

2015-12-01

Nolan and Bindeman (2013) placed secondarily hydrated ash from the 7.7 ka eruption of Mt. Mazama (δD=-149‰, 2.3wt% H2Ot) in isotopically labeled water (+650 ‰ δD, +56 ‰ δ18O) and observed that the H2Ot and δ18O values remained constant, but the δD values of ash increased with the surrounding water at 20, 40 and 70 °C. We expand on this work by conducting a similar experiment with ash from the 640 ka Lava Creek Tuff (LCT, δD of -128 ‰; 2.1 wt.% H2Ot) eruption of Yellowstone to see if significantly older glass (with a hypothesized gel layer on the surface shielding the interior from alteration) produces the same results. We have experiments running at 70, 24, and 5 °C, and periodically remove ~1.5 mg of glass to measure the δD (‰) and H2Ot (wt.%) of water extracted from the glass on a TC/EA MAT 253 continuous flow system. After 600 hours, the δD of the samples left at 5 and 24 °C remains at -128 ‰, but increased 8‰ for the 70 °C run series. However, there is no measurable change in wt.% of H2Ot, indicating that hydrogen exchange is not dictated by the addition of water. We are measuring and will report further progress of isotope exchange. We also plan to analyze the water in the LCT glass for δ18O (‰) to see if, as is the case for the Mt. Mazama glass, the δ18O (‰) remains constant. We also analyzed Mt. Mazama glass from the Nolan and Bindeman (2013) experiments that have now been sitting in isotopically labeled water at room temperature for ~5 years. The water concentration is still unchanged (2.3 wt.% H2Ot), and the δD of the water in the glass is now -111 ‰, causing an increase of 38 ‰. Our preliminary results show that exchange of hydrogen isotopes of hydrated glass is not limited by the age of the glass, and that the testing of hydrogen isotopes of secondarily hydrated glass, regardless of age, may not be a reliable paleoclimate indicator.

Use of a multi-isotope and multi-tracer approach including organic matter isotopes for quantifying nutrient contributions from agricultural vs wastewater sources

NASA Astrophysics Data System (ADS)

Kendall, C.; Silva, S. R.; Young, M. B.

2013-12-01

While nutrient isotopes are a well-established tool for quantifying nutrients inputs from agricultural vs wastewater treatment plant (WWTP) sources, we have found that combining nutrient isotopes with the C, N, and S isotopic compositions of dissolved and particulate organic matter, as part of a comprehensive multi-isotope and multi-tracer approach, is a much more diagnostic approach. The main reasons why organic matter C-N-S isotopes are a useful adjunct to studies of nutrient sources and biogeochemical processes are that the dissolved and particulate organic matter associated with (1) different kinds of animals (e.g., humans vs cows) often have distinctive isotopic compositions reflecting the different diets of the animals, and (2) the different processes associated with the different land uses (e.g., in the WWTP or associated with different crop types) often result in significant differences in the isotopic compositions of the organics. The analysis of the δ34S of particulate organic matter (POM) and dissolved organic matter (DOM) has been found to be especially useful for distinguishing and quantifying water, nutrient, and organic contributions from different land uses in aquatic systems where much of the organic matter is aquatic in origin. In such environments, the bacteria and algae incorporate S from sulfate and sulfide that is isotopically labeled by the different processes associated with different land uses. We have found that there is ~35 permil range in δ34S of POM along the river-estuary continuum in the San Joaquin/Sacramento River basin, with low values associated with sulfate reduction in the upstream wetlands and high values associated with tidal inputs of marine water into the estuary. Furthermore, rice agriculture results in relatively low δ34S values whereas WWTP effluent in the Sacramento River produces distinctly higher values than upstream of the WWTP, presumably because SO2 is used to treat chlorinated effluent. The fish living

Integrated carbon and chlorine isotope modeling: applications to chlorinated aliphatic hydrocarbons dechlorination.

PubMed

Jin, Biao; Haderlein, Stefan B; Rolle, Massimo

2013-02-05

We propose a self-consistent method to predict the evolution of carbon and chlorine isotope ratios during degradation of chlorinated hydrocarbons. The method treats explicitly the cleavage of isotopically different C-Cl bonds and thus considers, simultaneously, combined carbon-chlorine isotopologues. To illustrate the proposed modeling approach we focus on the reductive dehalogenation of chlorinated ethenes. We compare our method with the currently available approach, in which carbon and chlorine isotopologues are treated separately. The new approach provides an accurate description of dual-isotope effects regardless of the extent of the isotope fractionation and physical characteristics of the experimental system. We successfully applied the new approach to published experimental results on dehalogenation of chlorinated ethenes both in well-mixed systems and in situations where mass-transfer limitations control the overall rate of biodegradation. The advantages of our self-consistent dual isotope modeling approach proved to be most evident when isotope fractionation factors of carbon and chlorine differed significantly and for systems with mass-transfer limitations, where both physical and (bio)chemical transformation processes affect the observed isotopic values.

Preparation of stable isotope-labeled peripheral cannabinoid receptor CB2 by bacterial fermentation

PubMed Central

Berger, Christian; Ho, Jenny T.C.; Kimura, Tomohiro; Hess, Sonja; Gawrisch, Klaus; Yeliseev, Alexei

2010-01-01

We developed a bacterial fermentation protocol for production of a stable isotope-labeled cannabinoid receptor CB2 for subsequent structural studies of this protein by nuclear magnetic resonance spectroscopy. The human peripheral cannabinoid receptor was expressed in Escherichia coli as a fusion with maltose binding protein and two affinity tags. The fermentation was performed in defined media comprised of mineral salts, glucose and 15N2-L-tryptophan to afford incorporation of the labeled amino acid into the protein. Medium, growth and expression conditions were optimized so that the fermentation process produced about 2 mg of purified, labeled CB2 per liter of culture medium. By performing a mass spectroscopic characterization of the purified CB2, we determined that one of the two 15N atoms in tryptophan was incorporated into the recombinant protein. NMR analysis of 15N chemical shifts strongly suggests that the 15N atoms are located in Trp-indole rings. Importantly, analysis of the peptides derived from the CNBr cleavage of the purified protein confirmed a minimum of 95% incorporation of the labeled tryptophan into the CB2 sequence. The labeled CB2, purified and reconstituted into liposomes at a protein-to-lipid molar ratio of 1:500, was functional as confirmed by activation of cognate G proteins in an in vitro coupled assay. To our knowledge, this is the first reported production of a biologically active, stable isotope-labeled G protein-coupled receptor by bacterial fermentation. PMID:20044006

Parallel labeling experiments and metabolic flux analysis: Past, present and future methodologies.

PubMed

Crown, Scott B; Antoniewicz, Maciek R

2013-03-01

Radioactive and stable isotopes have been applied for decades to elucidate metabolic pathways and quantify carbon flow in cellular systems using mass and isotope balancing approaches. Isotope-labeling experiments can be conducted as a single tracer experiment, or as parallel labeling experiments. In the latter case, several experiments are performed under identical conditions except for the choice of substrate labeling. In this review, we highlight robust approaches for probing metabolism and addressing metabolically related questions though parallel labeling experiments. In the first part, we provide a brief historical perspective on parallel labeling experiments, from the early metabolic studies when radioisotopes were predominant to present-day applications based on stable-isotopes. We also elaborate on important technical and theoretical advances that have facilitated the transition from radioisotopes to stable-isotopes. In the second part of the review, we focus on parallel labeling experiments for (13)C-metabolic flux analysis ((13)C-MFA). Parallel experiments offer several advantages that include: tailoring experiments to resolve specific fluxes with high precision; reducing the length of labeling experiments by introducing multiple entry-points of isotopes; validating biochemical network models; and improving the performance of (13)C-MFA in systems where the number of measurements is limited. We conclude by discussing some challenges facing the use of parallel labeling experiments for (13)C-MFA and highlight the need to address issues related to biological variability, data integration, and rational tracer selection. Copyright © 2012 Elsevier Inc. All rights reserved.

Anaerobic reductive dechlorination of tetrachloroethene: how can dual Carbon-Chlorine isotopic measurements help elucidating the underlying reaction mechanism?

NASA Astrophysics Data System (ADS)

Badin, Alice; Buttet, Géraldine; Maillard, Julien; Holliger, Christof; Hunkeler, Daniel

2014-05-01

Chlorinated ethenes (CEs) such as tetrachloroethene (PCE) are common persistent groundwater contaminants. Among clean-up strategies applied to sites affected by such pollution, bioremediation has been considered with a growing interest as it represents a cost-effective, environmental friendly approach. This technique however sometimes leads to an incomplete and slow biodegradation of CEs resulting in an accumulation of toxic metabolites. Understanding the reaction mechanisms underlying anaerobic reductive dechlorination would thus help assessing PCE biodegradation in polluted sites. Stable isotope analysis can provide insight into reaction mechanisms. For chlorinated hydrocarbons, carbon (C) and chlorine (Cl) isotope data (δ13C and δ37Cl) tend to show a linear correlation with a slope (m ≡ ɛC/ɛCl) characteristic of the reaction mechanism [1]. This study hence aims at exploring the potential of a dual C-Cl isotope approach in the determination of the reaction mechanisms involved in PCE reductive dechlorination. C and Cl isotope fractionation were investigated during anaerobic PCE dechlorination by two bacterial consortia containing members of the Sulfurospirillum genus. The specificity in these consortia resides in the fact that they each conduct PCE reductive dechlorination catalysed by one different reductive dehalogenase, i.e. PceADCE which yields trichloroethene (TCE) and cis-dichloroethene (cDCE), and PceATCE which yields TCE only. The bulk C isotope enrichment factors were -3.6±0.3 o for PceATCE and -0.7±0.1o for PceADCE. The bulk Cl isotope enrichment factors were -1.3±0.2 o for PceATCE and -0.9±0.1 o for PceADCE. When applying the dual isotope approach, two m values of 2.7±0.1 and 0.7±0.2 were obtained for the reductive dehalogenases PceATCE and PceADCE, respectively. These results suggest that PCE can be degraded according to two different mechanisms. Furthermore, despite their highly similar protein sequences, each reductive dehalogenase seems

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

PubMed Central

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

2012-01-01

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

Identification of core components and transient interactors of the peroxisomal importomer by dual-track stable isotope labeling with amino acids in cell culture analysis.

PubMed

Oeljeklaus, Silke; Reinartz, Benedikt S; Wolf, Janina; Wiese, Sebastian; Tonillo, Jason; Podwojski, Katharina; Kuhlmann, Katja; Stephan, Christian; Meyer, Helmut E; Schliebs, Wolfgang; Brocard, Cécile; Erdmann, Ralf; Warscheid, Bettina

2012-04-06

The importomer complex plays an essential role in the biogenesis of peroxisomes by mediating the translocation of matrix proteins across the organellar membrane. A central part of this highly dynamic import machinery is the docking complex consisting of Pex14p, Pex13p, and Pex17p that is linked to the RING finger complex (Pex2p, Pex10p, Pex12p) via Pex8p. To gain detailed knowledge on the molecular players governing peroxisomal matrix protein import and, thus, the integrity and functionality of peroxisomes, we aimed at a most comprehensive investigation of stable and transient interaction partners of Pex14p, the central component of the importomer. To this end, we performed a thorough quantitative proteomics study based on epitope tagging of Pex14p combined with dual-track stable isotope labeling with amino acids in cell culture-mass spectrometry (SILAC-MS) analysis of affinity-purified Pex14p complexes and statistics. The results led to the establishment of the so far most extensive Pex14p interactome, comprising 9 core and further 12 transient components. We confirmed virtually all known Pex14p interaction partners including the core constituents of the importomer as well as Pex5p, Pex11p, Pex15p, and Dyn2p. More importantly, we identified new transient interaction partners (Pex25p, Hrr25p, Esl2p, prohibitin) that provide a valuable resource for future investigations on the functionality, dynamics, and regulation of the peroxisomal importomer.

The value and throughput of rest Thallium-201/stress Technetium -99m sestamibi dual-isotope myocardial SPECT.

PubMed

Okudan, Berna; Smitherman, Thomas C

2004-06-01

Myocardial perfusion scintigraphy is an established method in cardiology for the diagnosis and evaluation of coronary artery disease (CAD). Thallium-201 and Tc-99m sestamibi myocardial perfusion imaging has been widely accepted as non-invasive diagnostic procedure for detection of CAD, risk stratification and myocardial viability assessment. But, standard Tl-201 redistribution and same day or 2-day rest/stress Tc-99m sestamibi protocols are time-consuming. Hence, the dual isotope rest thallium-201/stress technetium-99m sestamibi gated single-photon emission tomography protocol has gained increasing popularity for these applications. Combining the use of thallium-201 with technetium-99m agents permits optimal image resolution and simultaneous assessment of viability. Dual-isotope imaging may be separate or simultaneous acquisition set-up. The more rapid completion of these studies is appreciated as an advantage by patients, technologists, interpreting and referring physicians, nurses and hospital management. Simultaneous imaging has the potential advantages of precise pixel registration and artifacts, if present, are identical in both thallium and sestamibi, and require only one set of imaging. Also, there are some disadvantages of spillover of activity from the Tc-99m to the Tl-201 window. Fortunately, despite this problem it can be overcome. Separate acquisition dual isotope also has some disadvantages. Difference in defect resolution in attenuation and scatter between T-201 and Tc-99m sestamibi potentially results in interpretation problems. But, studies about cost-effectiveness of dual isotope imaging showed that some selective elimination of the rest studies may decrease the cost of the nuclear procedures and should be considered in the current care health system.

Novel Approach for High-Throughput Metabolic Screening of Whole Plants by Stable Isotopes

PubMed Central

Beckers, Veronique; Kiep, Katina; Becker, Horst; Bläsing, Oliver Ernst; Fuchs, Regine

2016-01-01

Here, we demonstrate whole-plant metabolic profiling by stable isotope labeling and combustion isotope-ratio mass spectrometry for precise quantification of assimilation, translocation, and molecular reallocation of 13CO2 and 15NH4NO3. The technology was applied to rice (Oryza sativa) plants at different growth stages. For adult plants, 13CO2 labeling revealed enhanced carbon assimilation of the flag leaf from flowering to late grain-filling stage, linked to efficient translocation into the panicle. Simultaneous 13CO2 and 15NH4NO3 labeling with hydroponically grown seedlings was used to quantify the relative distribution of carbon and nitrogen. Two hours after labeling, assimilated carbon was mainly retained in the shoot (69%), whereas 7% entered the root and 24% was respired. Nitrogen, taken up via the root, was largely translocated into the shoot (85%). Salt-stressed seedlings showed decreased uptake and translocation of nitrogen (69%), whereas carbon metabolism was unaffected. Coupled to a gas chromatograph, labeling analysis provided enrichment of proteinogenic amino acids. This revealed significant protein synthesis in the panicle of adult plants, whereas protein biosynthesis in adult leaves was 8-fold lower than that in seedling shoots. Generally, amino acid enrichment was similar among biosynthetic families and allowed us to infer labeling dynamics of their precursors. On this basis, early and strong 13C enrichment of Embden-Meyerhof-Parnas pathway and pentose phosphate pathway intermediates indicated high activity of these routes. Applied to mode-of-action analysis of herbicides, the approach showed severe disturbance in the synthesis of branched-chain amino acids upon treatment with imazapyr. The established technology displays a breakthrough for quantitative high-throughput plant metabolic phenotyping. PMID:26966172

Heavy atom labeled nucleotides for measurement of kinetic isotope effects.

PubMed

Weissman, Benjamin P; Li, Nan-Sheng; York, Darrin; Harris, Michael; Piccirilli, Joseph A

2015-11-01

Experimental analysis of kinetic isotope effects represents an extremely powerful approach for gaining information about the transition state structure of complex reactions not available through other methodologies. The implementation of this approach to the study of nucleic acid chemistry requires the synthesis of nucleobases and nucleotides enriched for heavy isotopes at specific positions. In this review, we highlight current approaches to the synthesis of nucleic acids enriched site specifically for heavy oxygen and nitrogen and their application in heavy atom isotope effect studies. This article is part of a special issue titled: Enzyme Transition States from Theory and Experiment. Copyright © 2015 Elsevier B.V. All rights reserved.

Simultaneous determination of the intravenous and oral pharmacokinetic parameters of D,L-verapamil using stable isotope-labelled verapamil.

PubMed

Eichelbaum, M; Somogyi, A; von Unruh, G E; Dengler, H J

1981-01-01

Following i.v. administration, the plasma concentration-time curve of verapamil could best be described by either a mono- or biexponential equation. Total plasma clearance (1.26 1/min) approached liver blood flow (1.51/min), so it can be concluded that its clearance is liver blood flow-dependent. Although absorption was almost complete after oral administration, absolute bioavailability (20%) was low, due to extensive hepatic first-pass metabolism. The approach using stable isotope-labelled and unlabelled drug permits simultaneous administration by the intravascular and extravascular routes, thus allowing determination of absolute bioavailability in a single experiment.

Human neutrophil kinetics: modeling of stable isotope labeling data supports short blood neutrophil half-lives.

PubMed

Lahoz-Beneytez, Julio; Elemans, Marjet; Zhang, Yan; Ahmed, Raya; Salam, Arafa; Block, Michael; Niederalt, Christoph; Asquith, Becca; Macallan, Derek

2016-06-30

Human neutrophils have traditionally been thought to have a short half-life in blood; estimates vary from 4 to 18 hours. This dogma was recently challenged by stable isotope labeling studies with heavy water, which yielded estimates in excess of 3 days. To investigate this disparity, we generated new stable isotope labeling data in healthy adult subjects using both heavy water (n = 4) and deuterium-labeled glucose (n = 9), a compound with more rapid labeling kinetics. To interpret results, we developed a novel mechanistic model and applied it to previously published (n = 5) and newly generated data. We initially constrained the ratio of the blood neutrophil pool to the marrow precursor pool (ratio = 0.26; from published values). Analysis of heavy water data sets yielded turnover rates consistent with a short blood half-life, but parameters, particularly marrow transit time, were poorly defined. Analysis of glucose-labeling data yielded more precise estimates of half-life (0.79 ± 0.25 days; 19 hours) and marrow transit time (5.80 ± 0.42 days). Substitution of this marrow transit time in the heavy water analysis gave a better-defined blood half-life of 0.77 ± 0.14 days (18.5 hours), close to glucose-derived values. Allowing the ratio of blood neutrophils to mitotic neutrophil precursors (R) to vary yielded a best-fit value of 0.19. Reanalysis of the previously published model and data also revealed the origin of their long estimates for neutrophil half-life: an implicit assumption that R is very large, which is physiologically untenable. We conclude that stable isotope labeling in healthy humans is consistent with a blood neutrophil half-life of less than 1 day. © 2016 by The American Society of Hematology.

Dual Labeling Biotin Switch Assay to Reduce Bias Derived From Different Cysteine Subpopulations: A Method to Maximize S-Nitrosylation Detection.

PubMed

Chung, Heaseung Sophia; Murray, Christopher I; Venkatraman, Vidya; Crowgey, Erin L; Rainer, Peter P; Cole, Robert N; Bomgarden, Ryan D; Rogers, John C; Balkan, Wayne; Hare, Joshua M; Kass, David A; Van Eyk, Jennifer E

2015-10-23

S-nitrosylation (SNO), an oxidative post-translational modification of cysteine residues, responds to changes in the cardiac redox-environment. Classic biotin-switch assay and its derivatives are the most common methods used for detecting SNO. In this approach, the labile SNO group is selectively replaced with a single stable tag. To date, a variety of thiol-reactive tags have been introduced. However, these methods have not produced a consistent data set, which suggests an incomplete capture by a single tag and potentially the presence of different cysteine subpopulations. To investigate potential labeling bias in the existing methods with a single tag to detect SNO, explore if there are distinct cysteine subpopulations, and then, develop a strategy to maximize the coverage of SNO proteome. We obtained SNO-modified cysteine data sets for wild-type and S-nitrosoglutathione reductase knockout mouse hearts (S-nitrosoglutathione reductase is a negative regulator of S-nitrosoglutathione production) and nitric oxide-induced human embryonic kidney cell using 2 labeling reagents: the cysteine-reactive pyridyldithiol and iodoacetyl based tandem mass tags. Comparison revealed that <30% of the SNO-modified residues were detected by both tags, whereas the remaining SNO sites were only labeled by 1 reagent. Characterization of the 2 distinct subpopulations of SNO residues indicated that pyridyldithiol reagent preferentially labels cysteine residues that are more basic and hydrophobic. On the basis of this observation, we proposed a parallel dual-labeling strategy followed by an optimized proteomics workflow. This enabled the profiling of 493 SNO sites in S-nitrosoglutathione reductase knockout hearts. Using a protocol comprising 2 tags for dual-labeling maximizes overall detection of SNO by reducing the previously unrecognized labeling bias derived from different cysteine subpopulations. © 2015 American Heart Association, Inc.

Fast methodology for the reliable determination of nonylphenol in water samples by minimal labeling isotope dilution mass spectrometry.

PubMed

Fabregat-Cabello, Neus; Castillo, Ángel; Sancho, Juan V; González, Florenci V; Roig-Navarro, Antoni Francesc

2013-08-02

In this work we have developed and validated an accurate and fast methodology for the determination of 4-nonylphenol (technical mixture) in complex matrix water samples by UHPLC-ESI-MS/MS. The procedure is based on isotope dilution mass spectrometry (IDMS) in combination with isotope pattern deconvolution (IPD), which provides the concentration of the analyte directly from the spiked sample without requiring any methodological calibration graph. To avoid any possible isotopic effect during the analytical procedure the in-house synthesized (13)C1-4-(3,6-dimethyl-3-heptyl)phenol was used as labeled compound. This proposed surrogate was able to compensate the matrix effect even from wastewater samples. A SPE pre-concentration step together with exhaustive efforts to avoid contamination were included to reach the signal-to-noise ratio necessary to detect the endogenous concentrations present in environmental samples. Calculations were performed acquiring only three transitions, achieving limits of detection lower than 100ng/g for all water matrix assayed. Recoveries within 83-108% and coefficients of variation ranging from 1.5% to 9% were obtained. On the contrary a considerable overestimation was obtained with the most usual classical calibration procedure using 4-n-nonylphenol as internal standard, demonstrating the suitability of the minimal labeling approach. Copyright © 2013 Elsevier B.V. All rights reserved.

Detection of transgenerational barium dual-isotope marks in salmon otoliths by means of LA-ICP-MS.

PubMed

Huelga-Suarez, Gonzalo; Fernández, Beatriz; Moldovan, Mariella; García Alonso, J Ignacio

2013-03-01

The present study evaluates the use of an individual-specific transgenerational barium dual-isotope procedure and its application to salmon specimens from the Sella River (Asturias, Spain). For such a purpose, the use of laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) in combination with multiple linear regression for the determination of the isotopic mark in the otoliths of the specimens is presented. In this sense, a solution in which two barium-enriched isotopes ((137)Ba and (135)Ba) were mixed at a molar ratio of ca. 1:3 (N Ba137/N Ba135) was administered to eight returning females caught during the spawning period. After injection, these females, as well as their offspring, were reared in a governmental hatchery located in the council of Cangas de Onís (Asturias, Spain). For comparison purposes, as well as for a time-monitoring control, egg and larva data obtained by solution analysis ICP-MS are also given. Otoliths (9-month-old juveniles) of marked offspring were analysed by LA-ICP-MS demonstrating a 100 % marking efficacy of this methodology. The capabilities of the molar fraction approach for 2D imaging of fish otoliths are also addressed.

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

USDA-ARS?s Scientific Manuscript database

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...

A dual-labeled knottin peptide for PET and near-infrared fluorescence imaging of integrin expression in living subjects

PubMed Central

Kimura, Richard H.; Miao, Zheng; Cheng, Zhen; Gambhir, Sanjiv S.; Cochran, Jennifer R.

2010-01-01

Previously, we used directed evolution to engineer mutants of the Ecballium elaterium trypsin inhibitor (EETI-II) knottin that bind to αvβ3 and αvβ5 integrin receptors with low nanomolar affinity, and showed that Cy5.5- or 64Cu-DOTA-labeled knottin peptides could be used to image integrin expression in mouse tumor models using near-infrared fluorescence (NIRF) imaging or positron emission tomography (PET). Here, we report the development of a dual-labeled knottin peptide conjugated to both NIRF and PET imaging agents for multimodality imaging in living subjects. We created an orthogonally-protected peptide-based linker for stoichiometric coupling of 64Cu-DOTA and Cy5.5 onto the knottin N-terminus, and confirmed that conjugation did not affect binding to αvβ3 and αvβ5 integrins. NIRF and PET imaging studies in tumor xenograft models showed that Cy5.5 conjugation significantly increased kidney uptake and retention compared to the knottin peptide labeled with 64Cu-DOTA alone. In the tumor, the dual-labeled 64Cu-DOTA/Cy5.5 knottin probe showed decreased wash-out leading to significantly better retention (p < 0.05) compared to the 64Cu-DOTA-labeled knottin probe. Tumor uptake was significantly reduced (p < 0.05) when the dual-labeled probe was co-injected with an excess of unlabeled competitor and when tested in a tumor model with lower levels of integrin expression. Finally, plots of tumor-to-background tissue ratios for Cy5.5 versus 64Cu uptake were well correlated over several time points post injection, demonstrating pharmacokinetic cross validation of imaging labels. This dual-modality NIRF/PET imaging agent is promising for further development in clinical applications where high sensitivity and high-resolution are desired, such as detection of tumors located deep within the body and image-guided surgical resection. PMID:20131753

IDAWG: Metabolic incorporation of stable isotope labels for quantitative glycomics of cultured cells

PubMed Central

Orlando, Ron; Lim, Jae-Min; Atwood, James A.; Angel, Peggi M.; Fang, Meng; Aoki, Kazuhiro; Alvarez-Manilla, Gerardo; Moremen, Kelley W.; York, William S.; Tiemeyer, Michael; Pierce, Michael; Dalton, Stephen; Wells, Lance

2012-01-01

Robust quantification is an essential component of comparative –omic strategies. In this regard, glycomics lags behind proteomics. Although various isotope-tagging and direct quantification methods have recently enhanced comparative glycan analysis, a cell culture labeling strategy, that could provide for glycomics the advantages that SILAC provides for proteomics, has not been described. Here we report the development of IDAWG, Isotopic Detection of Aminosugars With Glutamine, for the incorporation of differential mass tags into the glycans of cultured cells. In this method, culture media containing amide-15N-Gln is used to metabolically label cellular aminosugars with heavy nitrogen. Because the amide side chain of Gln is the sole source of nitrogen for the biosynthesis of GlcNAc, GalNAc, and sialic acid, we demonstrate that culturing mouse embryonic stems cells for 72 hours in the presence of amide-15N-Gln media results in nearly complete incorporation of 15N into N-linked and O-linked glycans. The isotopically heavy monosaccharide residues provide additional information for interpreting glycan fragmentation and also allow quantification in both full MS and MS/MS modes. Thus, IDAWG is a simple to implement, yet powerful quantitative tool for the glycomics toolbox. PMID:19449840

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

PubMed

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

2012-12-01

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

Independent valine and leucine isotope labeling in Escherichia coli protein overexpression systems.

PubMed

Lichtenecker, Roman J; Weinhäupl, Katharina; Reuther, Lukas; Schörghuber, Julia; Schmid, Walther; Konrat, Robert

2013-11-01

The addition of labeled α-ketoisovalerate to the growth medium of a protein-expressing host organism has evolved into a versatile tool to achieve concomitant incorporation of specific isotopes into valine- and leucine- residues. The resulting target proteins represent excellent probes for protein NMR analysis. However, as the sidechain resonances of these residues emerge in a narrow spectral range, signal overlap represents a severe limitation in the case of high-molecular-weight NMR probes. We present a protocol to eliminate leucine labeling by supplying the medium with unlabeled α-ketoisocaproate. The resulting spectra of a model protein exclusively feature valine signals of increased intensity, confirming the method to be a first example of independent valine and leucine labeling employing α-ketoacid precursor compounds.

Novel Approach for High-Throughput Metabolic Screening of Whole Plants by Stable Isotopes.

PubMed

Dersch, Lisa Maria; Beckers, Veronique; Rasch, Detlev; Melzer, Guido; Bolten, Christoph; Kiep, Katina; Becker, Horst; Bläsing, Oliver Ernst; Fuchs, Regine; Ehrhardt, Thomas; Wittmann, Christoph

2016-05-01

Here, we demonstrate whole-plant metabolic profiling by stable isotope labeling and combustion isotope-ratio mass spectrometry for precise quantification of assimilation, translocation, and molecular reallocation of (13)CO2 and (15)NH4NO3 The technology was applied to rice (Oryza sativa) plants at different growth stages. For adult plants, (13)CO2 labeling revealed enhanced carbon assimilation of the flag leaf from flowering to late grain-filling stage, linked to efficient translocation into the panicle. Simultaneous (13)CO2 and (15)NH4NO3 labeling with hydroponically grown seedlings was used to quantify the relative distribution of carbon and nitrogen. Two hours after labeling, assimilated carbon was mainly retained in the shoot (69%), whereas 7% entered the root and 24% was respired. Nitrogen, taken up via the root, was largely translocated into the shoot (85%). Salt-stressed seedlings showed decreased uptake and translocation of nitrogen (69%), whereas carbon metabolism was unaffected. Coupled to a gas chromatograph, labeling analysis provided enrichment of proteinogenic amino acids. This revealed significant protein synthesis in the panicle of adult plants, whereas protein biosynthesis in adult leaves was 8-fold lower than that in seedling shoots. Generally, amino acid enrichment was similar among biosynthetic families and allowed us to infer labeling dynamics of their precursors. On this basis, early and strong (13)C enrichment of Embden-Meyerhof-Parnas pathway and pentose phosphate pathway intermediates indicated high activity of these routes. Applied to mode-of-action analysis of herbicides, the approach showed severe disturbance in the synthesis of branched-chain amino acids upon treatment with imazapyr. The established technology displays a breakthrough for quantitative high-throughput plant metabolic phenotyping. © 2016 American Society of Plant Biologists. All Rights Reserved.

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

NASA Astrophysics Data System (ADS)

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

2015-01-01

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

Stable isotope labeling-solid phase extraction-mass spectrometry analysis for profiling of thiols and aldehydes in beer.

PubMed

Zheng, Shu-Jian; Wang, Ya-Lan; Liu, Ping; Zhang, Zheng; Yu, Lei; Yuan, Bi-Feng; Feng, Yu-Qi

2017-12-15

In this study, we developed a strategy for profiling of thiols and aldehydes in beer samples by stable isotope labeling-solid phase extraction-liquid chromatography-double precursor ion scan/double neutral loss scan-mass spectrometry analysis (SIL-SPE-LC-DPIS/DNLS-MS). A pair of isotope reagents (ω-bromoacetonylquinolinium bromide, BQB; ω-bromoacetonylquinolinium-d 7 bromide, BQB-d 7 ) were used to label thiols; while for the aldehydes, a pair of isotope reagents (4-(2-(trimethylammonio) ethoxy) benzenaminium halide, 4-APC; 4-(2-(trimethylammonio) ethoxy) benzenaminium halide-d 4 , 4-APC-d 4 ) were used. The labeled thiols and aldehydes were extracted and purified with solid-phase extraction, respectively, followed by LC-MS analysis. Using the proposed SIL-SPE-LC-DPIS/DNLS-MS methods, 76 thiol and 25 aldehyde candidates were found in beer. Furthermore, we established SIL-SPE-LC-MRM-MS methods for the relative quantitation of thiols and aldehydes in different beer samples. The results showed that the contents of thiols and aldehydes are closely related to the brands and origins of beers. Copyright © 2017 Elsevier Ltd. All rights reserved.

Moving toward focal therapy in prostate cancer: dual-isotope permanent seed implants as a possible solution.

PubMed

Todor, Dorin A; Barani, Igor J; Lin, Peck-Sun; Anscher, Mitchell S

2011-09-01

To compare the ability of single- and dual-isotope prostate seed implants to escalate biologically effective dose (BED) to foci of disease while reducing prescription dose to the prostate. Nine plans, using 125I, 103Pd, and 131Cs alone and in combination were created retrospectively for 2 patients. Ultrasound and MRI/MRS datasets were used for treatment planning. Voxel-by-voxel BED was calculated for single- and dual-isotope plans. Equivalent uniform BED (EUBED) was used to compare plans. The MRS-positive planning target volumes (PTVi) were delineated along with PTV (prostate+5 mm), rectum, and urethra. Single-isotope implants, prescribed to conventional doses, were generated to achieve good PTV coverage. The PTVi were prospectively used to generate implants using mixtures of isotopes. For mixed-radioisotope implants, we also explored the impact on EUBED of lowering prescription doses by 15%. The EUBED of PTVi in the setting of primary 125I implant increased 20-66% when 103Pd and 131Cs were used compared with 125I boost. Decreasing prescription dose by 15% in mixed-isotope implants results in a potential 10% reduction in urethral EUBED with preservation of PTV coverage while still boosting PTVi (up to 80%). When radiobiologic parameters corresponding to more-aggressive disease are assigned to foci, faster-decaying isotopes used in mixed implants have the potential to preserve the equivalent biological effect of mono-isotope implants considering less-aggressive disease distributed in the entire prostate. This is a hypothesis-generating study proposing a treatment paradigm that could be the middle ground between whole-gland irradiation and focal-only treatment. The use of two isotopes concurrent with decreasing the minimal peripheral dose is shown to increase EUBED of selected subvolumes while preserving the therapeutic effect at the level of the gland. Copyright © 2011 Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

1999-01-01

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

VEGF-Iron Oxide Conjugate for Dual MR and PET Imaging of Breast Cancer Angiogenesis

DTIC Science & Technology

2007-09-01

with both VEGF121 and PET isotope 64Cu (t1/2 = 12.7 h) and test the dual probe in vitro. Aim 2: To test the PET and mMRI efficacy of the dual...iron oxide nanoparticles conjugated with macrocyclic chelating agent DOTA for 64Cu -labeling and cyclic RGD peptide for integrin alpha(v)beta(3...radionuclide 64Cu without loss of receptor affinity and functional activity of the protein. 64Cu -VEGF is also able to delineate small tumors that are

Shifts in rotifer life history in response to stable isotope enrichment: testing theories of isotope effects on organismal growth

PubMed Central

2017-01-01

In ecology, stable isotope labelling is commonly used for tracing material transfer in trophic interactions, nutrient budgets and biogeochemical processes. The main assumption in this approach is that the enrichment with a heavy isotope has no effect on the organism growth and metabolism. This assumption is, however, challenged by theoretical considerations and experimental studies on kinetic isotope effects in vivo. Here, I demonstrate profound changes in life histories of the rotifer Brachionus plicatilis fed 15N-enriched algae (0.4–5.0 at%); i.e. at the enrichment levels commonly used in ecological studies. These findings support theoretically predicted effects of heavy isotope enrichment on growth, metabolism and ageing in biological systems and underline the importance of accounting for such effects when using stable isotope labelling in experimental studies. PMID:28405367

TRITIUM-LABELED COMPOUNDS VII. ISOTOPE EFFECTS IN THE OXIDATION OF d- MANNITOLS-C$sup 14$ AND d-MANNITOLS-t TO d-FRUCTOSES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sniegoski, L.T.; Frush, H.L.; Isbell, H.S.

1961-09-01

D-Mannitols, labeled either with carbon-14 at C1, C2, or C3, or with tritium attached to C1, C2, or C3, were prepared. After oxidation by Acetobacter suboxydans, the distribution of radioactivity in each of the resulting labeled D- fructoses was determined. Labeled D-mannitol is unique among the hexitols in that it may be oxidized by A. suboxydans in either the labeled or the unlabeled part of the molecule. Except in the oxidation of D-mannitol-2-t, the competing reactions result in the formation of a mixture of D-fructoses, each having radioactivity in one of two different positions. Hence, the isotope effect, k*/ k,more » (where k* and k are, respectively, the rate constants for oxidation in the labeled and in the unlabeled part of the labeled emannitol molecule) is the ratio of the activities at the two positions of the product, D-fructose. The following isotope effects were found for the bacterial oxidation of labeled D-mannitols: for D-mannitol-2-C/sup 14/, k*/k = 0.93; for Dmannitol-2-t, k*/k = 0.23; and for D-mannitol-3-t, k*/k = 0.70. For D-mannitols labeled at other positions, no isotope effect was detected, since k*/k was unity. The large isotope effect for D-mannitol-2-t is indicative of rupture of the C2-H bond in the rate determining process. It is suggested that the secondary isotope effect for tritium at C3 indicates hyperconjugation of the C3 hydrogen atom in the activated enzyme-- substrate complex; the lack of such effect for tritium at C1 may be due to unfavorable steric conditions for hyperconjugation of the C1 hydrogen atoms in the complex. The following substances were prepared and their isotopic distributions determined: D-fructose1,6-C/sup 14/ and D-fructose-1,6-t (from 1- labeled D-mannitols); D-fructose-2,5-C/sup 14/ and D-fructose-5-t (from 2-labeled e-mannitols); and D-fructose-3,4-C/sup 14/ and D-fructose-3,4-t (from 3-labeled D- mannitols). A procedure, employing D-fructose-1,6-C/sup 14/ as an internal standard, was devised for the

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

PubMed

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

2011-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2012-09-01

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.

On structural identifiability analysis of the cascaded linear dynamic systems in isotopically non-stationary 13C labelling experiments.

PubMed

Lin, Weilu; Wang, Zejian; Huang, Mingzhi; Zhuang, Yingping; Zhang, Siliang

2018-06-01

The isotopically non-stationary 13C labelling experiments, as an emerging experimental technique, can estimate the intracellular fluxes of the cell culture under an isotopic transient period. However, to the best of our knowledge, the issue of the structural identifiability analysis of non-stationary isotope experiments is not well addressed in the literature. In this work, the local structural identifiability analysis for non-stationary cumomer balance equations is conducted based on the Taylor series approach. The numerical rank of the Jacobian matrices of the finite extended time derivatives of the measured fractions with respect to the free parameters is taken as the criterion. It turns out that only one single time point is necessary to achieve the structural identifiability analysis of the cascaded linear dynamic system of non-stationary isotope experiments. The equivalence between the local structural identifiability of the cascaded linear dynamic systems and the local optimum condition of the nonlinear least squares problem is elucidated in the work. Optimal measurements sets can then be determined for the metabolic network. Two simulated metabolic networks are adopted to demonstrate the utility of the proposed method. Copyright © 2018 Elsevier Inc. All rights reserved.

Dynamic dual-isotope molecular imaging elucidates principles for optimizing intrathecal drug delivery

PubMed Central

Wolf, Daniel A.; Hesterman, Jacob Y.; Sullivan, Jenna M.; Orcutt, Kelly D.; Silva, Matthew D.; Lobo, Merryl; Wellman, Tyler; Hoppin, Jack

2016-01-01

The intrathecal (IT) dosing route offers a seemingly obvious solution for delivering drugs directly to the central nervous system. However, gaps in understanding drug molecule behavior within the anatomically and kinetically unique environment of the mammalian IT space have impeded the establishment of pharmacokinetic principles for optimizing regional drug exposure along the neuraxis. Here, we have utilized high-resolution single-photon emission tomography with X-ray computed tomography to study the behavior of multiple molecular imaging tracers following an IT bolus injection, with supporting histology, autoradiography, block-face tomography, and MRI. Using simultaneous dual-isotope imaging, we demonstrate that the regional CNS tissue exposure of molecules with varying chemical properties is affected by IT space anatomy, cerebrospinal fluid (CSF) dynamics, CSF clearance routes, and the location and volume of the injected bolus. These imaging approaches can be used across species to optimize the safety and efficacy of IT drug therapy for neurological disorders. PMID:27699254

Nitric Oxide Isotopic Analyzer Based on a Compact Dual-Modulation Faraday Rotation Spectrometer

PubMed Central

Zhang, Eric; Huang, Stacey; Ji, Qixing; Silvernagel, Michael; Wang, Yin; Ward, Bess; Sigman, Daniel; Wysocki, Gerard

2015-01-01

We have developed a transportable spectroscopic nitrogen isotopic analyzer. The spectrometer is based on dual-modulation Faraday rotation spectroscopy of nitric oxide isotopologues with near shot-noise limited performance and baseline-free operation. Noise analysis indicates minor isotope (15NO) detection sensitivity of 0.36 ppbv·Hz−1/2, corresponding to noise-equivalent Faraday rotation angle (NEA) of 1.31 × 10−8 rad·Hz−1/2 and noise-equivalent absorbance (αL)min of 6.27 × 10−8 Hz−1/2. White-noise limited performance at 2.8× the shot-noise limit is observed up to ~1000 s, allowing reliable calibration and sample measurement within the drift-free interval of the spectrometer. Integration with wet-chemistry based on acidic vanadium(III) enables conversion of aqueous nitrate/nitrite samples to gaseous NO for total nitrogen isotope analysis. Isotopic ratiometry is accomplished via time-multiplexed measurements of two NO isotope transitions. For 5 μmol potassium nitrate samples, the instrument consistently yields ratiometric precision below 0.3‰, thus demonstrating potential as an in situ diagnostic tool for environmental nitrogen cycle studies. PMID:26473876

Nitric oxide isotopic analyzer based on a compact dual-modulation Faraday rotation spectrometer.

PubMed

Zhang, Eric; Huang, Stacey; Ji, Qixing; Silvernagel, Michael; Wang, Yin; Ward, Bess; Sigman, Daniel; Wysocki, Gerard

2015-10-14

We have developed a transportable spectroscopic nitrogen isotopic analyzer. The spectrometer is based on dual-modulation Faraday rotation spectroscopy of nitric oxide isotopologues with near shot-noise limited performance and baseline-free operation. Noise analysis indicates minor isotope ((15)NO) detection sensitivity of 0.36 ppbv·Hz(-1/2), corresponding to noise-equivalent Faraday rotation angle (NEA) of 1.31 × 10(-8) rad·Hz(-1/2) and noise-equivalent absorbance (αL)min of 6.27 × 10(-8) Hz(-1/2). White-noise limited performance at 2.8× the shot-noise limit is observed up to ~1000 s, allowing reliable calibration and sample measurement within the drift-free interval of the spectrometer. Integration with wet-chemistry based on acidic vanadium(III) enables conversion of aqueous nitrate/nitrite samples to gaseous NO for total nitrogen isotope analysis. Isotopic ratiometry is accomplished via time-multiplexed measurements of two NO isotope transitions. For 5 μmol potassium nitrate samples, the instrument consistently yields ratiometric precision below 0.3‰, thus demonstrating potential as an in situ diagnostic tool for environmental nitrogen cycle studies.

Simultaneous detection of imidacloprid and parathion by the dual-labeled time-resolved fluoroimmunoassay.

PubMed

Shi, Haiyan; Sheng, Enze; Feng, Lu; Zhou, Liangliang; Hua, Xiude; Wang, Minghua

2015-10-01

A highly sensitive direct dual-labeled time-resolved fluoroimmunoassay (TRFIA) to detect parathion and imidacloprid simultaneously in food and environmental matrices was developed. Europium (Eu(3+)) and samarium (Sm(3+)) were used as fluorescent labels by coupling separately with L1-Ab and A1P1-Ab. Under optimal assay conditions, the half-maximal inhibition concentration (IC50) and limit of detection (LOD, IC10) were 10.87 and 0.025 μg/L for parathion and 7.08 and 0.028 μg/L for imidacloprid, respectively. The cross-reactivities (CR) were negligible except for methyl-parathion (42.4 %) and imidaclothiz (103.4 %). The average recoveries of imidacloprid ranged from 78.9 to 104.2 % in water, soil, rice, tomato, and Chinese cabbage with a relative standard deviation (RSD) of 2.4 to 11.6 %, and those of parathion were from 81.5 to 110.9 % with the RSD of 3.2 to 10.5 %. The results of TRFIA for the authentic samples were validated by comparison with gas chromatography (GC) analyses, and satisfactory correlations (parathion: R (2) = 0.9918; imidacloprid: R (2) = 0.9908) were obtained. The results indicate that the dual-labeled TRFIA is convenient and reliable to detect parathion and imidacloprid simultaneously in food and environmental matrices.

Psychosocial approaches to dual diagnosis.

PubMed

Drake, R E; Mueser, K T

2000-01-01

Recent research elucidates many aspects of the problem of co-occurring substance use disorder (SUD) in patients with severe mental illness, which is often termed dual diagnosis. This paper provides a brief overview of current research on the epidemiology, adverse consequences, and phenomenology of dual diagnosis, followed by a more extensive review of current approaches to services, assessment, and treatment. Accumulating evidence shows that comorbid SUD is quite common among individuals with severe mental illness and that these individuals suffer serious adverse consequences of SUD. The research further suggests that traditional, separate services for individuals with dual disorders are ineffective, and that integrated treatment programs, which combine mental health and substance abuse interventions, offer more promise. In addition to a comprehensive integration of services, successful programs include assessment, assertive case management, motivational interventions for patients who do not recognize the need for substance abuse treatment, behavioral interventions for those who are trying to attain or maintain abstinence, family interventions, housing, rehabilitation, and psychopharmacology. Further research is needed on the organization and financing of dual-diagnosis services and on specific components of the integrated treatment model, such as group treatments, family interventions, and housing approaches.

From position-specific isotope labeling towards soil fluxomics: a novel toolbox to assess the microbial impact on biogeochemical cycles

NASA Astrophysics Data System (ADS)

Apostel, C.; Dippold, M. A.; Kuzyakov, Y.

2015-12-01

Understanding the microbial impact on C and nutrient cycles is one of the most important challenges in terrestrial biogeochemistry. Transformation of low molecular weight organic substances (LMWOS) is a key step in all biogeochemical cycles because 1) all high molecular substances pass the LMWOS pool during their degradation and 2) only LMWOS can be taken up by microorganisms intact. Thus, the transformations of LMWOS are dominated by biochemical pathways of the soil microorganisms. Thus, understanding fluxes and transformations in soils requires a detailed knowledge on the microbial metabolic network and its control mechanism. Tracing C fate in soil by isotopes became on of the most applied and promising biogeochemistry tools but studies were nearly exclusively based on uniformly labeled substances. However, such tracers do not allow the differentiation of the intact use of the initial substances from its transformation to metabolites. The novel tool of position-specific labeling enables to trace molecule atoms separately and thus to determine the cleavage of molecules - a prerequisite for metabolic tracing. Position-specific labeling of basic metabolites and quantification of isotope incorporation in CO2 and bulk soil enabled following the basic metabolic pathways of microorganisms. However, the combination of position-specific 13C labeling with compound-specific isotope analysis of microbial biomarkers and metabolites like phospholipid fatty acids (PLFA) or amino sugars revealed new insights into the soil fluxome: First, it enables tracing specific anabolic pathways in diverse microbial communities in soils e.g. carbon starvation pathways versus pathways reflecting microbial growth. Second, it allows identification of specific pathways of individual functional microbial groups in soils in situ. Tracing metabolic pathways and understanding their regulating factors are crucial for soil C fluxomics i.e. the unravaling of the complex network of C transformations

Isotopic studies of metabolic systems by mass spectrometry: using Pascal's triangle to produce biological standards with fully controlled labeling patterns.

PubMed

Millard, Pierre; Massou, Stéphane; Portais, Jean-Charles; Létisse, Fabien

2014-10-21

Mass spectrometry (MS) is widely used for isotopic studies of metabolism in which detailed information about biochemical processes is obtained from the analysis of isotope incorporation into metabolites. The biological value of such experiments is dependent on the accuracy of the isotopic measurements. Using MS, isotopologue distributions are measured from the quantitative analysis of isotopic clusters. These measurements are prone to various biases, which can occur during the experimental workflow and/or MS analysis. The lack of relevant standards limits investigations of the quality of the measured isotopologue distributions. To meet that need, we developed a complete theoretical and experimental framework for the biological production of metabolites with fully controlled and predictable labeling patterns. This strategy is valid for different isotopes and different types of metabolisms and organisms, and was applied to two model microorganisms, Pichia augusta and Escherichia coli, cultivated on (13)C-labeled methanol and acetate as sole carbon source, respectively. The isotopic composition of the substrates was designed to obtain samples in which the isotopologue distribution of all the metabolites should give the binomial coefficients found in Pascal's triangle. The strategy was validated on a liquid chromatography-tandem mass spectrometry (LC-MS/MS) platform by quantifying the complete isotopologue distributions of different intracellular metabolites, which were in close agreement with predictions. This strategy can be used to evaluate entire experimental workflows (from sampling to data processing) or different analytical platforms in the context of isotope labeling experiments.

Robust surface coating for a fast, facile fluorine-18 labeling of iron oxide nanoparticles for PET/MR dual-modality imaging

DOE PAGES

Sun, Ziyan; Cheng, Kai; Wu, Fengyu; ...

2016-10-31

Grafting a robust organic shell around inorganic nanoparticles can optimize their colloidal features to dramatically improve their physicochemical properties. Here, we have developed a polymer coating procedure for providing colloidal stability to the nanoparticles and, more importantly, for applying a fast, facile fluorine-18 labeling of iron oxide nanoparticles (IONPs) for positron emission tomography (PET)/magnetic resonance (MR) dual-modality imaging. The structure of the amphiphilic polymer is based on a backbone of polyacrylic acid, conjugated with multiple oleylamines to form a comb-like branched structure. The dense polymer shell provides high colloidal stability to the IONPs against harsh conditions such as high temperature,more » low pH value, and high ion strength. By incorporating a 1,4,7-triazacyclononane (NOTA) chelator to the comb-like amphiphilic polymer for the chelation of aluminum fluoride ions, we applied a one-step radiolabeling approach for a fast, facile radiofluorination of magnetic nanoparticles. The new strategy can significantly reduce the procedure time and radiation exposure. In conclusion, the PET/MR dual modality imaging was successfully achieved in living subjects by using 18F labeled magnetic nanoparticles.« less

Robust surface coating for a fast, facile fluorine-18 labeling of iron oxide nanoparticles for PET/MR dual-modality imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Ziyan; Cheng, Kai; Wu, Fengyu

Grafting a robust organic shell around inorganic nanoparticles can optimize their colloidal features to dramatically improve their physicochemical properties. Here, we have developed a polymer coating procedure for providing colloidal stability to the nanoparticles and, more importantly, for applying a fast, facile fluorine-18 labeling of iron oxide nanoparticles (IONPs) for positron emission tomography (PET)/magnetic resonance (MR) dual-modality imaging. The structure of the amphiphilic polymer is based on a backbone of polyacrylic acid, conjugated with multiple oleylamines to form a comb-like branched structure. The dense polymer shell provides high colloidal stability to the IONPs against harsh conditions such as high temperature,more » low pH value, and high ion strength. By incorporating a 1,4,7-triazacyclononane (NOTA) chelator to the comb-like amphiphilic polymer for the chelation of aluminum fluoride ions, we applied a one-step radiolabeling approach for a fast, facile radiofluorination of magnetic nanoparticles. The new strategy can significantly reduce the procedure time and radiation exposure. In conclusion, the PET/MR dual modality imaging was successfully achieved in living subjects by using 18F labeled magnetic nanoparticles.« less

Dual, differential isotope labeling shows the preferential movement of labile plant constituents into mineral-bonded soil organic matter.

PubMed

Haddix, Michelle L; Paul, Eldor A; Cotrufo, M Francesca

2016-06-01

The formation and stabilization of soil organic matter (SOM) are major concerns in the context of global change for carbon sequestration and soil health. It is presently believed that lignin is not selectively preserved in soil and that chemically labile compounds bonding to minerals comprise a large fraction of the SOM. Labile plant inputs have been suggested to be the main precursor of the mineral-bonded SOM. Litter decomposition and SOM formation are expected to have temperature sensitivity varying with the lability of plant inputs. We tested this framework using dual (13) C and (15) N differentially labeled plant material to distinguish the metabolic and structural components within a single plant material. Big Bluestem (Andropogon gerardii) seedlings were grown in an enriched (13) C and (15) N environment and then prior to harvest, removed from the enriched environment and allowed to incorporate natural abundance (13) C-CO2 and (15) N fertilizer into the metabolic plant components. This enabled us to achieve a greater than one atom % difference in (13) C between the metabolic and structural components within the plant litter. This differentially labeled litter was incubated in soil at 15 and 35 °C, for 386 days with CO2 measured throughout the incubation. After 14, 28, 147, and 386 days of incubation, the soil was subsequently fractionated. There was no difference in temperature sensitivity of the metabolic and structural components with regard to how much was respired or in the amount of litter biomass stabilized. Only the metabolic litter component was found in the sand, silt, or clay fraction while the structural component was exclusively found in the light fraction. These results support the stabilization framework that labile plant components are the main precursor of mineral-associated organic matter. © 2016 John Wiley & Sons Ltd.

Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Zhou; Adams, Rachel M; Chourey, Karuna

2012-01-01

A variety of quantitative proteomics methods have been developed, including label-free, metabolic labeling, and isobaric chemical labeling using iTRAQ or TMT. Here, these methods were compared in terms of the depth of proteome coverage, quantification accuracy, precision, and reproducibility using a high-performance hybrid mass spectrometer, LTQ Orbitrap Velos. Our results show that (1) the spectral counting method provides the deepest proteome coverage for identification, but its quantification performance is worse than labeling-based approaches, especially the quantification reproducibility; (2) metabolic labeling and isobaric chemical labeling are capable of accurate, precise, and reproducible quantification and provide deep proteome coverage for quantification. Isobaricmore » chemical labeling surpasses metabolic labeling in terms of quantification precision and reproducibility; (3) iTRAQ and TMT perform similarly in all aspects compared in the current study using a CID-HCD dual scan configuration. Based on the unique advantages of each method, we provide guidance for selection of the appropriate method for a quantitative proteomics study.« less

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

NASA Astrophysics Data System (ADS)

Dippold, Michaela; Kuzyakov, Yakov

2015-04-01

Understanding the soil organic matter (SOM) dynamics is one of the most important challenges in soil science. Transformation of low molecular weight organic substances (LMWOS) is a key step in biogeochemical cycles because 1) all high molecular substances pass this stage during their decomposition and 2) only LMWOS will be taken up by microorganisms. Previous studies on LMWOS were focused on determining net fluxes through the LMWOS pool, but they rarely identified transformations. As LMWOS are the preferred C and energy source for microorganisms, the transformations of LMWOS are dominated by biochemical pathways of the soil microorganisms. Thus, understanding fluxes and transformations in soils requires a detailed knowledge on the biochemical pathways and its controlling factors. Tracing C fate in soil by isotopes became on of the most applied and promising biogeochemistry tools. Up to now, studies on LMWOS were nearly exclusively based on uniformly labeled organic substances i.e. all C atoms in the molecules were labeled with 13C or 14C. However, this classical approach did not allow the differentiation between use of intact initial substances in any process, or whether they were transformed to metabolites. The novel tool of position-specific labeling enables to trace molecule atoms separately and thus to determine the cleavage of molecules - a prerequisite for metabolic tracing. Position-specific labeling of LMWOS and quantification of 13CO2 and 13C in bulk soil enabled following the basic metabolic pathways of soil microorganisms. However, only the combination of position-specific 13C labeling with compound-specific isotope analysis of microbial biomarkers and metabolites allowed 1) tracing specific anabolic pathways in diverse microbial communities in soils and 2) identification of specific pathways of individual functional microbial groups. So, these are the prerequisites for soil fluxomics. Our studies combining position-specific labeled glucose with amino

Hydrogen Isotope Fractionation during the Biodegradation of 1,2-Dichloroethane: Potential for Pathway Identification Using a Multi-element (C, Cl, and H) Isotope Approach.

PubMed

Palau, Jordi; Shouakar-Stash, Orfan; Hatijah Mortan, Siti; Yu, Rong; Rosell, Monica; Marco-Urrea, Ernest; Freedman, David L; Aravena, Ramon; Soler, Albert; Hunkeler, Daniel

2017-09-19

Even though multi-element isotope fractionation patterns provide crucial information with which to identify contaminant degradation pathways in the field, those involving hydrogen are still lacking for many halogenated groundwater contaminants and degradation pathways. This study investigates for the first time hydrogen isotope fractionation during both aerobic and anaerobic biodegradation of 1,2-dichloroethane (1,2-DCA) using five microbial cultures. Transformation-associated isotope fractionation values (ε bulk H ) were -115 ± 18‰ (aerobic C-H bond oxidation), -34 ± 4‰ and -38 ± 4‰ (aerobic C-Cl bond cleavage via hydrolytic dehalogenation), and -57 ± 3‰ and -77 ± 9‰ (anaerobic C-Cl bond cleavage via reductive dihaloelimination). The dual-element C-H isotope approach (Λ C-H = Δδ 2 H/Δδ 13 C ≈ ε bulk H /ε bulk C , where Δδ 2 H and Δδ 13 C are changes in isotope ratios during degradation) resulted in clearly different Λ C-H values: 28 ± 4 (oxidation), 0.7 ± 0.1 and 0.9 ± 0.1 (hydrolytic dehalogenation), and 1.76 ± 0.05 and 3.5 ± 0.1 (dihaloelimination). This result highlights the potential of this approach to identify 1,2-DCA degradation pathways in the field. In addition, distinct trends were also observed in a multi- (i.e., Δδ 2 H versus Δδ 37 Cl versus Δδ 13 C) isotope plot, which opens further possibilities for pathway identification in future field studies. This is crucial information to understand the mechanisms controlling natural attenuation of 1,2-DCA and to design appropriate strategies to enhance biodegradation.

Moving Toward Focal Therapy in Prostate Cancer: Dual-Isotope Permanent Seed Implants as a Possible Solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Todor, Dorin A., E-mail: dtodor@mcvh-vcu.edu; Barani, Igor J.; Lin, Peck-Sun

2011-09-01

Purpose: To compare the ability of single- and dual-isotope prostate seed implants to escalate biologically effective dose (BED) to foci of disease while reducing prescription dose to the prostate. Methods and Materials: Nine plans, using {sup 125}I, {sup 103}Pd, and {sup 131}Cs alone and in combination were created retrospectively for 2 patients. Ultrasound and MRI/MRS datasets were used for treatment planning. Voxel-by-voxel BED was calculated for single- and dual-isotope plans. Equivalent uniform BED (EUBED) was used to compare plans. The MRS-positive planning target volumes (PTV{sub i}) were delineated along with PTV (prostate + 5 mm), rectum, and urethra. Single-isotope implants,more » prescribed to conventional doses, were generated to achieve good PTV coverage. The PTV{sub i} were prospectively used to generate implants using mixtures of isotopes. For mixed-radioisotope implants, we also explored the impact on EUBED of lowering prescription doses by 15%. Results: The EUBED of PTV{sub i} in the setting of primary {sup 125}I implant increased 20-66% when {sup 103}Pd and {sup 131}Cs were used compared with {sup 125}I boost. Decreasing prescription dose by 15% in mixed-isotope implants results in a potential 10% reduction in urethral EUBED with preservation of PTV coverage while still boosting PTV{sub i} (up to 80%). When radiobiologic parameters corresponding to more-aggressive disease are assigned to foci, faster-decaying isotopes used in mixed implants have the potential to preserve the equivalent biological effect of mono-isotope implants considering less-aggressive disease distributed in the entire prostate. Conclusions: This is a hypothesis-generating study proposing a treatment paradigm that could be the middle ground between whole-gland irradiation and focal-only treatment. The use of two isotopes concurrent with decreasing the minimal peripheral dose is shown to increase EUBED of selected subvolumes while preserving the therapeutic effect at the level

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mark E. Fuller; Tullis C. Onstott

2003-12-17

This report summarizes the results of a research project conducted to develop new methods to label bacterial cells so that they could be tracked and enumerated as they move in the subsurface after they are introduced into the groundwater (i.e., during bioaugmentation). Labeling methods based on stable isotopes of carbon (13C) and vital fluorescent stains were developed. Both approaches proved successful with regards to the ability to effectively label bacterial cells. Several methods for enumeration of fluorescently-labeled cells were developed and validated, including near-real time microplate spectrofluorometry that could be performed in the field. However, the development of a novelmore » 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).« less

Dual isotope Schilling test for measuring absorption of food-bound and free vitamin B12 simultaneously

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doscherholmen, A.; Silvis, S.; McMahon, J.

1983-10-01

A prototype food-bound vitamin B12 (food-B12) absorption test has been developed in which /sup 57/Co-B12 was incorporated in vitro into egg yolk (yolk-B12) and served to volunteers in 50-g cooked portions together with toast and coffee for breakfast. Six hours later, 1 mg nonlabeled B12 was given intramuscularly and 24-hour urine was collected for radioactivity measurement. In separate tests, the absorption of yolk-B12 and crystalline /sup 57/Co-B12 was equally poor in patients with pernicious anemia. However, in patients with simple gastric achlorhydria and those who had undergone gastric surgery, the assimilation of yolk-B12 was impaired greatly, whereas the absorption ofmore » crystalline radio-B12 was normal. Egg yolk labeled with /sup 58/Co-B12 was administered together with crystalline /sup 57/Co-B12 in a dual isotope test with results similar to those obtained when the tests were prepared separately. This yolk-/sup 58/Co-B12 test with its ability to detect malabsorption of food-B12 may be considered as an addition to the first part of the Schilling test.« less

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

PubMed

Terzi, F; Cambridge, S

2017-01-01

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

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

PubMed Central

Tao, Shujuan; Orlando, Ron

2014-01-01

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-β-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

Reconciling Estimates of Cell Proliferation from Stable Isotope Labeling Experiments

PubMed Central

Drylewicz, Julia; Elemans, Marjet; Zhang, Yan; Kelly, Elizabeth; Reljic, Rajko; Tesselaar, Kiki; de Boer, Rob J.; Macallan, Derek C.; Borghans, José A. M.; Asquith, Becca

2015-01-01

Stable isotope labeling is the state of the art technique for in vivo quantification of lymphocyte kinetics in humans. It has been central to a number of seminal studies, particularly in the context of HIV-1 and leukemia. However, there is a significant discrepancy between lymphocyte proliferation rates estimated in different studies. Notably, deuterated 2H2-glucose (D2-glucose) labeling studies consistently yield higher estimates of proliferation than deuterated water (D2O) labeling studies. This hampers our understanding of immune function and undermines our confidence in this important technique. Whether these differences are caused by fundamental biochemical differences between the two compounds and/or by methodological differences in the studies is unknown. D2-glucose and D2O labeling experiments have never been performed by the same group under the same experimental conditions; consequently a direct comparison of these two techniques has not been possible. We sought to address this problem. We performed both in vitro and murine in vivo labeling experiments using identical protocols with both D2-glucose and D2O. This showed that intrinsic differences between the two compounds do not cause differences in the proliferation rate estimates, but that estimates made using D2-glucose in vivo were susceptible to difficulties in normalization due to highly variable blood glucose enrichment. Analysis of three published human studies made using D2-glucose and D2O confirmed this problem, particularly in the case of short term D2-glucose labeling. Correcting for these inaccuracies in normalization decreased proliferation rate estimates made using D2-glucose and slightly increased estimates made using D2O; thus bringing the estimates from the two methods significantly closer and highlighting the importance of reliable normalization when using this technique. PMID:26437372

Shielded dual-loop resonator for arterial spin labeling at the neck.

PubMed

Hetzer, Stefan; Mildner, Toralf; Driesel, Wolfgang; Weder, Manfred; Möller, Harald E

2009-06-01

To construct a dual-loop coil for continuous arterial spin labeling (CASL) at the human neck and characterize it using computer simulations and magnetic resonance experiments. The labeling coil was designed as a perpendicular pair of shielded-loop resonators made from coaxial cable to obtain balanced circular loops with minimal electrical interaction with the lossy tissue. Three different excitation modes depending on the phase shift, Deltapsi, of the currents driving the two circular loops were investigated including a "Maxwell mode" (Deltapsi = 0 degrees ; ie, opposite current directions in both loops), a "quadrature mode" (Deltapsi = 90 degrees ), and a "Helmholtz mode" (Deltapsi = 180 degrees ; ie, identical current directions in both loops). Simulations of the radiofrequency field distribution indicated a high inversion efficiency at the locations of the carotid and vertebral arteries. With a 7-mm-thick polypropylene insulation, a sufficient distance from tissue was achieved to guarantee robust performance at a local specific absorption rate (SAR) well below legal safety limits. Application in healthy volunteers at 3 T yielded quantitative maps of gray matter perfusion with low intersubject variability. The coil permits robust labeling with low SAR and minimal sensitivity to different loading conditions.

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

PubMed

Yarita, Takashi; Aoyagi, Yoshie; Otake, Takamitsu

2015-05-29

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

Combining Solvent Isotope Effects with Substrate Isotope Effects in Mechanistic Studies of Alcohol and Amine Oxidation by Enzymes*

PubMed Central

Fitzpatrick, Paul F.

2014-01-01

Oxidation of alcohols and amines is catalyzed by multiple families of flavin-and pyridine nucleotide-dependent enzymes. Measurement of solvent isotope effects provides a unique mechanistic probe of the timing of the cleavage of the OH and NH bonds, necessary information for a complete description of the catalytic mechanism. The inherent ambiguities in interpretation of solvent isotope effects can be significantly decreased if isotope effects arising from isotopically labeled substrates are measured in combination with solvent isotope effects. The application of combined solvent and substrate (mainly deuterium) isotope effects to multiple enzymes is described here to illustrate the range of mechanistic insights that such an approach can provide. PMID:25448013

Quantitative detection of codeine in human plasma using surface-enhanced Raman scattering via adaptation of the isotopic labelling principle.

PubMed

Subaihi, Abdu; Muhamadali, Howbeer; Mutter, Shaun T; Blanch, Ewan; Ellis, David I; Goodacre, Royston

2017-03-27

In this study surface enhanced Raman scattering (SERS) combined with the isotopic labelling (IL) principle has been used for the quantification of codeine spiked into both water and human plasma. Multivariate statistical approaches were employed for the analysis of these SERS spectral data, particularly partial least squares regression (PLSR) which was used to generate models using the full SERS spectral data for quantification of codeine with, and without, an internal isotopic labelled standard. The PLSR models provided accurate codeine quantification in water and human plasma with high prediction accuracy (Q 2 ). In addition, the employment of codeine-d 6 as the internal standard further improved the accuracy of the model, by increasing the Q 2 from 0.89 to 0.94 and decreasing the low root-mean-square error of predictions (RMSEP) from 11.36 to 8.44. Using the peak area at 1281 cm -1 assigned to C-N stretching, C-H wagging and ring breathing, the limit of detection was calculated in both water and human plasma to be 0.7 μM (209.55 ng mL -1 ) and 1.39 μM (416.12 ng mL -1 ), respectively. Due to a lack of definitive codeine vibrational assignments, density functional theory (DFT) calculations have also been used to assign the spectral bands with their corresponding vibrational modes, which were in excellent agreement with our experimental Raman and SERS findings. Thus, we have successfully demonstrated the application of SERS with isotope labelling for the absolute quantification of codeine in human plasma for the first time with a high degree of accuracy and reproducibility. The use of the IL principle which employs an isotopolog (that is to say, a molecule which is only different by the substitution of atoms by isotopes) improves quantification and reproducibility because the competition of the codeine and codeine-d 6 for the metal surface used for SERS is equal and this will offset any difference in the number of particles under analysis or any fluctuations in

Dual isotope plots reflect transformation pathways of pesticides: Potential to assess pesticide fate and elucidate transformation mechanisms

NASA Astrophysics Data System (ADS)

Meyer, Armin; Penning, Holger; Sorensen, Sebastian; Aamand, Jens; Elsner, Martin

2010-05-01

The degradation of pesticides in deeper soil layers and groundwater is of growing interest, because they have repeatedly been found in drinking water supply wells and may pose a risk to future water resources. Current assessment schemes face a common problem, however: natural degradation often cannot be reliably assessed by concentration measurements alone, since mass balances are difficult to establish and transformation cannot be distinguished from sorption or dilution. Even detection of metabolites may only give an incomplete picture. When several transformation pathways occur, some metabolites may be degraded or form bound residues so that the associated pathways may be missed. Our research shows that dual isotope plots derived from compound specific isotope analysis offer a novel approach to give additional, complementary insight into the natural degradation of pesticides. Detection of metabolites is not required, since the isotope fractionation can be fully observed in the pesticide itself. Specifically, different initial biotransformation reactions of the phenylurea herbicide isoproturon (3-(4-isopropylphenyl)-1,1-dimethylurea) in pure culture experiments with bacterial and fungal strains showed strongly pathway-dependent isotope fractionation. When analyzing isotopic changes in different parts of the isoproturon molecule, hydroxylation of the isopropyl group by fungi was found to be associated with C and H isotope fractionation. In contrast, hydrolysis by Arthrobacter globiformis D47 caused strong C and N isotope fractionation, albeit in a different manner than abiotic hydrolysis so that isotope measurements can distinguish between both modes of transformation. Likewise, we observed highly pathway-dependent C and N isotope fractionation of atrazine (1-chloro-3-ethylamino-5-isopropylamino-2,4,6-triazine). Desalkylation of atrazine by Rhodococcus sp. strain NI86/21 resulted in enrichment of both 13-C and 15-N in atrazine, whereas hydrolysis to hydroxyatrazine

Isotope Label-Aided Mass Spectrometry Reveals the Influence of Environmental Factors on Metabolism in Single Eggs of Fruit Fly

PubMed Central

Tseng, Te-Wei; Wu, June-Tai; Chen, Yu-Chie; Urban, Pawel L.

2012-01-01

In order to investigate the influence of light/dark cycle on the biosynthesis of metabolites during oogenesis, here we demonstrate a simple experimental protocol which combines in-vivo isotopic labeling of primary metabolites with mass spectrometric analysis of single eggs of fruit fly (Drosophila melanogaster). First, fruit flies were adapted to light/dark cycle using artificial white light. Second, female flies were incubated with an isotopically labeled sugar (13C6-glucose) for 12 h – either during the circadian day or the circadian night, at light or at dark. Third, eggs were obtained from the incubated female flies, and analyzed individually by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS): this yielded information about the extent of labeling with carbon-13. Since the incorporation of carbon-13 to uridine diphosphate glucose (UDP-glucose) in fruit fly eggs is very fast, the labeling of this metabolite was used as an indicator of the biosynthesis of metabolites flies/eggs during 12-h periods, which correspond to circadian day or circadian night. The results reveal that once the flies adapted to the 12-h-light/12-h-dark cycle, the incorporation of carbon-13 to UDP-glucose present in fruit fly eggs was not markedly altered by an acute perturbation to this cycle. This effect may be due to a relationship between biosynthesis of primary metabolites in developing eggs and an alteration to the intake of the labeled substrate – possibly related to the change of the feeding habit. Overall, the study shows the possibility of using MALDI-MS in conjunction with isotopic labeling of small metazoans to unravel the influence of environmental cues on primary metabolism. PMID:23185587

Application of stable isotope tools for evaluating natural and stimulated biodegradation of organic pollutants in field studies.

PubMed

Fischer, Anko; Manefield, Mike; Bombach, Petra

2016-10-01

Stable isotope tools are increasingly applied for in-depth evaluation of biodegradation of organic pollutants at contaminated field sites. They can be divided into three methods i) determination of changes in natural abundance of stable isotopes using compound-specific stable isotope analysis (CSIA), ii) detection of incorporation of stable-isotope label from a stable-isotope labelled target compound into degradation and/or mineralisation products and iii) determination of stable-isotope label incorporation into biomarkers using stable isotope probing (SIP). Stable isotope tools have been applied as key monitoring tools for multiple-line-of-evidence-approaches (MLEA) for sensitive evaluation of pollutant biodegradation. This review highlights the application of CSIA, SIP and MLEA including stable isotope tools for assessing natural and stimulated biodegradation of organic pollutants in field studies dealing with soil and groundwater contaminations. Copyright © 2016 Elsevier Ltd. All rights reserved.

High Yield Production and Radiochemical Isolation of Isotopically Pure Arsenic-72 and Novel Radioarsenic Labeling Strategies for the Development of Theranostic Radiopharmaceuticals.

PubMed

Ellison, Paul A; Barnhart, Todd E; Chen, Feng; Hong, Hao; Zhang, Yin; Theuer, Charles P; Cai, Weibo; Nickles, Robert J; DeJesus, Onofre T

2016-01-20

Radioisotopes of arsenic are of considerable interest to the field of nuclear medicine with unique nuclear and chemical properties making them well-suited for use in novel theranostic radiopharmaceuticals. However, progress must still be made in the production of isotopically pure radioarsenic and in its stable conjugation to biological targeting vectors. This work presents the production and irradiation of isotopically enriched (72)Ge(m) discs in an irrigation-cooled target system allowing for the production of isotopically pure (72)As with capability on the order of 10 GBq. A radiochemical separation procedure isolated the reactive trivalent radioarsenic in a small volume buffered aqueous solution, while reclaiming (72)Ge target material. The direct thiol-labeling of a monoclonal antibody resulted in a conjugate exhibiting exceptionally poor in vivo stability in a mouse model. This prompted further investigations to alternative radioarsenic labeling strategies, including the labeling of the dithiol-containing chelator dihydrolipoic acid, and thiol-modified mesoporous silica nanoparticles (MSN-SH). Radioarsenic-labeled MSN-SH showed exceptional in vivo stability toward dearsenylation.

High Yield Production and Radiochemical Isolation of Isotopically Pure Arsenic-72 and Novel Radioarsenic Labeling Strategies for the Development of Theranostic Radiopharmaceuticals

PubMed Central

Ellison, Paul A.; Barnhart, Todd E.; Chen, Feng; Hong, Hao; Zhang, Yin; Theuer, Charles P.; Cai, Weibo; Nickles, Robert J.; DeJesus, Onofre T.

2016-01-01

Radioisotopes of arsenic are of considerable interest to the field of nuclear medicine with unique nuclear and chemical properties making them well-suited for use in novel theranostic radiopharmaceuticals. However, progress must still be made in the production of isotopically pure radioarsenic and in its stable conjugation to biological targeting vectors. This work presents the production and irradiation of isotopically enriched 72Ge(m) discs in an irrigation-cooled target system allowing for the production of isotopically pure 72As with capability on the order of 10 GBq. A radiochemical separation procedure isolated the reactive trivalent radioarsenic in a small volume buffered aqueous solution, while reclaiming 72Ge target material. The direct thiol-labeling of a monoclonal antibody resulted in a conjugate exhibiting exceptionally poor in vivo stability in a mouse model. This prompted further investigations to alternative radioarsenic labeling strategies, including the labeling of the dithiol-containing chelator dihydrolipoic acid, and thiol-modified mesoporous silica nanoparticles (MSN-SH). Radioarsenic-labeled MSN-SH showed exceptional in vivo stability toward dearsenylation. PMID:26646989

Secretory overexpression and isotopic labeling of the chimeric relaxin family peptide R3/I5 in Pichia pastoris.

PubMed

Guo, Yu-Qi; Wu, Qing-Ping; Shao, Xiao-Xia; Shen, Ting; Liu, Ya-Li; Xu, Zeng-Guang; Guo, Zhan-Yun

2015-06-01

Relaxin family peptides are a group of peptide hormones with divergent biological functions. Mature relaxin family peptides are typically composed of two polypeptide chains with three disulfide linkages, rendering their preparation a challenging task. In the present study, we established an efficient approach for preparation of the chimeric relaxin family peptide R3/I5 through secretory overexpression in Pichia pastoris and in vitro enzymatic maturation. A designed single-chain R3/I5 precursor containing the B-chain of human relaxin-3 and the A-chain of human INSL5 was overexpressed in PichiaPink strain 1 by high-density fermentation in a two-liter fermenter, and approximately 200 mg of purified precursor was obtained from one liter of the fermentation supernatant. We also developed an economical approach for preparation of the uniformly (15)N-labeled R3/I5 precursor by culturing in shaking flasks, and approximately 15 mg of purified (15)N-labeled precursor was obtained from one liter of the culture supernatant. After purification by cation ion-exchange chromatography and reverse-phase high performance liquid chromatography, the R3/I5 precursor was converted to the mature two-chain form by sequential treatment with endoproteinase Lys-C and carboxypeptidase B. The mature R3/I5 peptide had an α-helix-dominated conformation and retained full receptor-binding and receptor activation activities. Thus, Pichia overexpression was an efficient approach for sample preparation and isotopic labeling of the chimeric R3/I5 peptide. This approach could also be extended to the preparation of other relaxin family peptides in future studies.

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities

PubMed Central

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

2014-01-01

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

Microbial detection in microfluidic devices through dual staining of quantum dots-labeled immunoassay and RNA hybridization.

PubMed

Zhang, Qing; Zhu, Liang; Feng, Hanhua; Ang, Simon; Chau, Fook Siong; Liu, Wen-Tso

2006-01-18

This paper reported the development of a microfludic device for the rapid detection of viable and nonviable microbial cells through dual labeling by fluorescent in situ hybridization (FISH) and quantum dots (QDs)-labeled immunofluorescent assay (IFA). The coin sized device consists of a microchannel and filtering pillars (gap=1-2 microm) and was demonstrated to effectively trap and concentrate microbial cells (i.e. Giardia lamblia). After sample injection, FISH probe solution and QDs-labeled antibody solution were sequentially pumped into the device to accelerate the fluorescent labeling reactions at optimized flow rates (i.e. 1 and 20 microL/min, respectively). After 2 min washing for each assay, the whole process could be finished within 30 min, with minimum consumption of labeling reagents and superior fluorescent signal intensity. The choice of QDs 525 for IFA resulted in bright and stable fluorescent signal, with minimum interference with the Cy3 signal from FISH detection.

Simulating Stable Isotope Ratios in Plumes of Groundwater Pollutants with BIOSCREEN-AT-ISO.

PubMed

Höhener, Patrick; Li, Zhi M; Julien, Maxime; Nun, Pierrick; Robins, Richard J; Remaud, Gérald S

2017-03-01

BIOSCREEN is a well-known simple tool for evaluating the transport of dissolved contaminants in groundwater, ideal for rapid screening and teaching. This work extends the BIOSCREEN model for the calculation of stable isotope ratios in contaminants. A three-dimensional exact solution of the reactive transport from a patch source, accounting for fractionation by first-order decay and/or sorption, is used. The results match those from a previously published isotope model but are much simpler to obtain. Two different isotopes may be computed, and dual isotope plots can be viewed. The dual isotope assessment is a rapidly emerging new approach for identifying process mechanisms in aquifers. Furthermore, deviations of isotope ratios at specific reactive positions with respect to "bulk" ratios in the whole compound can be simulated. This model is named BIOSCREEN-AT-ISO and will be downloadable from the journal homepage. © 2016, National Ground Water Association.

NMR studies of two spliced leader RNAs using isotope labeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lapham, J.; Crothers, D.M.

1994-12-01

Spliced leader RNAs are a class of RNA molecules (<200 nts) involved in the trans splicing of messenger RNA found in trypanosomes, nematodes, and other lower eukaryotes. The spliced leader RNA from the trypanosome Leptomonas Collosoma exists in two alternate structural forms with similar thermal stabilities. The 54 nucleotides on the 5{prime} end of the SL molecule is structurally independent from the 3{prime} half of the RNA, and displays the two structural forms. Furthermore, the favored of the two structures was shown to contain anomalous nuclease sensitivity and thermal stability features, which suggests that there may be tertiary interactions betweenmore » the splice site and other nucleotides in the 5{prime} end. Multidimensional NMR studies are underway to elucidate the structural elements present in the SL RNAs that give rise to their physical properties. Two spliced leader sequences have been studied. The first, the 54 nucleotides on the 5{prime} end of the L. Collosoma sequence, was selected because of earlier studies in our laboratory. The second sequence is the 5{prime} end of the trypanosome Crithidia Fasciculata, which was chosen because of its greater sequence homology to other SL sequences. Given the complexity of the NMR spectra for RNA molecules of this size, we have incorporated {sup 15}N/{sup 13}C-labeled nucleotides into the RNA. One of the techniques we have developed to simplify the spectra of these RNA molecules is isotope labeling of specific regions of the RNA. This has been especially helpful in assigning the secondary structure of molecules that may be able to adopt multiple conformations. Using this technique one can examine a part of the molecule without spectral interference from the unlabeled portion. We hope this approach will promote an avenue for studying the structure of larger RNAs in their native surroundings.« less

Application of the Stable Isotope Label Approach in Clinical Development-Supporting Dissolution Specifications for a Commercial Tablet Product with Tafenoquine, a Long Half-life Compound.

PubMed

Goyal, Navin; Mohamed, Khadeeja; Rolfe, Katie; Sahota, Satty; Ernest, Terry; Duparc, Stephan; Taylor, Maxine; Casillas, Linda; Koh, Gavin C K W

2018-06-04

Bioavailability/bioequivalence studies supporting clinical drug development or commercial supply of drug formulations are often time, cost, and resource intensive. The drug's pharmacokinetic (PK) variability, systemic half-life, and safety issues may pose additional challenges. The stable isotope label (SIL) approach provides a useful tool to significantly reduce the study size in clinical PK studies. Tafenoquine (TQ) is an 8-aminoquinoline under development for preventing Plasmodium vivax malaria relapse. This SIL study assessed the impact of differences in the in vitro dissolution profiles on in vivo exposure of TQ tablets. Fourteen healthy volunteers received a single dose of 300 mg TQ Intermediate Aged or 300 mg TQ Control formulations in this single-center, two-arm, randomized, open-label, parallel-group study. Endpoints included the geometric means ratio of the area under the concentration-time curve (AUC (0-t) and AUC (0-∞) ; primary endpoint) and maximum plasma concentration (C max ) for Intermediate Aged versus Control TQ; correlation of PK parameters for venous versus peripheral (via microsample) blood samples; and safety and tolerability endpoints. Geometric mean ratios for PK parameters (AUC and C max ) and their 90% confidence intervals fell well within standard bioequivalence limits (0.80-1.25). Only one mild adverse event (skin abrasion) was reported. In summary, this SIL methodology-based study demonstrates that the observed differences in the in vitro dissolution profiles between the Control and Intermediate Aged TQ tablets have no clinically relevant effect on systemic TQ exposure. The SIL approach was successfully implemented to enable the setting of a clinically relevant dissolution specification. This study (GSK study number 201780) is registered at clinicaltrials.gov with identifier NCT02751294.

A preliminary feasibility study of simultaneous dual-isotope imaging with a solid-state dedicated cardiac camera for evaluating myocardial perfusion and fatty acid metabolism.

PubMed

Ko, Toshiyuki; Utanohara, Yuko; Suzuki, Yasuhiro; Kurihara, Makiko; Iguchi, Nobuo; Umemura, Jun; Sumiyoshi, Tetsuya; Tomoike, Hitonobu

2016-01-01

Simultaneous dual-isotope SPECT imaging with 201Tl and (123)I-β-methyl-p-iodophenylpentadecanoic acid (BMIPP) is used to study the perfusion-metabolism mismatch. It predicts post-ischemic functional recovery by detecting stunned myocardium. On the other hand, (99m)Tc-MIBI is another radioisotope widely used in myocardial perfusion imaging because of its better image quality and lower radiation exposure than 201Tl. However, since the photopeak energies of (99m)Tc and (123)I are very similar, crosstalk hampers the simultaneous use of these two radioisotopes. To overcome this problem, we conducted simultaneous dual-isotope imaging study using the D-SPECT scanner (Spectrum-Dynamics, Israel) which has a novel detector design and excellent energy resolution. We first conducted a basic experiment using cardiac phantom to simulate the condition of normal perfusion and impaired fatty acid metabolism. Subsequently, we prospectively recruited 30 consecutive patients who underwent successful percutaneous coronary intervention for acute myocardial infarction, and performed (99m)Tc-MIBI/(123)I-BMIPP dual-isotope imaging within 5 days after reperfusion. Images were interpreted by two experienced cardiovascular radiologists to identify the infarcted and stunned areas based on the coronary artery territories. As a result, cardiac phantom experiment revealed no significant crosstalk between (99m)Tc and (123)I. In the subsequent clinical study, (99m)Tc-MIBI/(123)I-BMIPP dual-isotope imaging in all participant yielded excellent image quality and detected infarcted and stunned areas correctly when compared with coronary angiographic findings. Furthermore, we were able to reduce radiation exposure to significantly approximately one-eighth. In conclusion, we successfully demonstrated the practical application of simultaneous assessment of myocardial perfusion and fatty acid metabolism by (99m)Tc-MIBI and (123)I-BMIPP using a D-SPECT cardiac scanner. Compared with conventional (201)Tl

Heavy isotope labeling study of the turnover of forskolin-stimulated adenylate cyclase in BC/sup 3/H1 cell line

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bouhelal, R.; Bockaert, J.; Mermet-Bouvier, R.

1987-06-25

We have used the method of heavy isotope labeling to study the metabolic turnover of adenylate cyclase in a nonfusing muscle cell line, the BC/sup 3/H1 cells. These cells contains an adenylate cyclase coupled to beta-adrenergic receptors and highly stimulated by forskolin, a potent activator of the enzyme. After transfer of the cells from normal medium to heavy medium (a medium containing heavy labeled amino acids, /sup 3/H, /sup 13/C, /sup 15/N), heavy isotope-labeled adenylate cyclase molecules progressively replace pre-existing light molecules. In sucrose gradient differential sedimentation, after a 5-day switch in heavy medium, the enzyme exhibited a higher massmore » (s = 8.40 +/- 0.03 S, n = 13) compared to the control enzyme. Indeed, the increase in the sedimentation coefficient of the heavy molecules was due to the synthesis of new molecules of adenylate cyclase labeled with heavy isotope amino acids since in the presence of cycloheximide, an inhibitor of protein synthesis, no change in the sedimentation pattern of the forskolin-stimulated adenylate cyclase occurred. After incorporation of heavy isotope amino acids in the adenylate cyclase molecules, the kinetics parameters of the enzyme did not change. However, adenylate cyclase from cells incubated with heavy medium exhibits an activity about 2-fold lower than control. After switching the cells to the heavy medium, the decrease of the activity of the enzyme occurred during the first 24 h and thereafter remained at a steady state for at least 4 days. In contrast, 24 h after the switch, the sedimentation coefficient of forskolin-stimulated adenylate cyclase was progressively shifted to a higher value.« less

Synthesis of two potent glucocorticoid receptor agonists labeled with carbon-14 and stable isotopes.

PubMed

Latli, Bachir; Reeves, Jonathan T; Tan, Zhulin; Hrapchak, Matt; Song, Jinhua J; Busacca, Carl B; Senanayake, Chris H

2015-01-01

Two potent glucocorticoid receptor agonists were prepared labeled with carbon-14 and with stable isotopes to perform drug metabolism, pharmacokinetics, and bioanalytical studies. Carbon-14 labeled (1) was obtained from an enantiopure alkyne (5) via a Sonogashira coupling to a previously reported 5-amino-4-iodo-[2-(14)C]pyrimidine [(14)C]-(6), followed by a base-mediated cyclization (1) in 72% overall radiochemical yield. Carbon-14 labeled (2) was prepared in five steps employing a key benzoic acid intermediate [(14)C]-(13), which was synthesized in one pot from enolization of trifluoromethylketone (12), followed by bromine-magnesium exchange and then electrophile trapping reaction with [(14)C]-carbon dioxide. A chiral auxiliary (S)-1-(4-methoxyphenyl)ethylamine was then coupled to this acid to give [(14)C]-(15). Propargylation and separation of diastereoisomers by crystallizations gave the desired diastereomer [(14)C]-(17) in 34% yield. Sonogashira coupling to iodopyridine (10) followed by cyclization to the azaindole [(14)C]-(18) and finally removal of the chiral auxiliary gave [(14)C]-(2) in 7% overall yield. For stable isotope syntheses, [(13)C6]-(1) was obtained in three steps using [(13)C4]-(6) and trimethylsilylacetylene-[(13)C2] in 26% yield, while [(2)H5]-(2) was obtained by first preparing the iodopyridine [(2)H5]-(10) in five steps. Then, Sonogashira coupling to chiral alkyne (24) and cyclization gave [(2)H5]-(2) in 42% overall yield. Copyright © 2015 John Wiley & Sons, Ltd.

p16(INK4a) /Ki-67 dual labelling as a marker for the presence of high-grade cancer cells or disease progression in urinary cytopathology.

PubMed

Piaton, E; Advenier, A S; Carré, C; Decaussin-Petrucci, M; Mege-Lechevallier, F; Ruffion, A

2013-10-01

Overexpression of p16(INK4a) independent of the presence of E6-E7 oncoproteins of high-risk papillomaviruses has been identified in bladder carcinoma in situ lesions with or without concurrent papillary or invasive high-grade (HG) urothelial carcinoma. As p16(INK4a) and Ki-67 co-expression clearly indicates deregulation of the cell cycle, the aim of this study was to investigate the frequency of p16(INK4a) /Ki-67 dual labelling in urinary cytology samples. Immunolabelling was performed in demounted, destained Papanicolaou slides after ThinPrep(®) processing. A total of 84 urinary cytology samples (18 negative, 10 low grade, 19 atypical urothelial cells and 37 high grade) were analysed for p16(INK4a) /Ki-67 co-expression. We assessed underlying urothelial malignancy with cystoscopy, histopathology and follow-up data in every case. Compared with raw histopathological results, p16 (INK4a) /Ki-67 dual labelling was observed in 48 out of 55 (87.3%) HG lesions and in 11 out of 29 (37.9%) negative, papillary urothelial neoplasia of low malignant potential or low-grade carcinomas (P = 0.05). All cases with high-grade/malignant cytology were dual labelled. Sixteen out of 17 (94.1%) carcinoma in situ cases and eight out of 14 (57.1%) cases with atypical urothelial cells matching with HG lesions were dual labelled. Extended follow-up allowed three cases of progression to be diagnosed in dual-labelled cases with negative/low-grade cytology results after a 9- to 11-months delay. The data show that p16(INK4a) /Ki-67 co-expression allows most HG cancer cells to be detected initially and in the follow-up period. Additional studies are needed in order to determine whether dual labelling can be used as a triage tool for atypical urothelial cells in the urine. © 2012 John Wiley & Sons Ltd.

A transversal approach for patch-based label fusion via matrix completion

PubMed Central

Sanroma, Gerard; Wu, Guorong; Gao, Yaozong; Thung, Kim-Han; Guo, Yanrong; Shen, Dinggang

2015-01-01

Recently, multi-atlas patch-based label fusion has received an increasing interest in the medical image segmentation field. After warping the anatomical labels from the atlas images to the target image by registration, label fusion is the key step to determine the latent label for each target image point. Two popular types of patch-based label fusion approaches are (1) reconstruction-based approaches that compute the target labels as a weighted average of atlas labels, where the weights are derived by reconstructing the target image patch using the atlas image patches; and (2) classification-based approaches that determine the target label as a mapping of the target image patch, where the mapping function is often learned using the atlas image patches and their corresponding labels. Both approaches have their advantages and limitations. In this paper, we propose a novel patch-based label fusion method to combine the above two types of approaches via matrix completion (and hence, we call it transversal). As we will show, our method overcomes the individual limitations of both reconstruction-based and classification-based approaches. Since the labeling confidences may vary across the target image points, we further propose a sequential labeling framework that first labels the highly confident points and then gradually labels more challenging points in an iterative manner, guided by the label information determined in the previous iterations. We demonstrate the performance of our novel label fusion method in segmenting the hippocampus in the ADNI dataset, subcortical and limbic structures in the LONI dataset, and mid-brain structures in the SATA dataset. We achieve more accurate segmentation results than both reconstruction-based and classification-based approaches. Our label fusion method is also ranked 1st in the online SATA Multi-Atlas Segmentation Challenge. PMID:26160394

Assimilation efficiency for sediment-sorbed benzo(a)pyrene by Diporeia spp.

USGS Publications Warehouse

Lydy, M.J.; Landrum, P.F.

1993-01-01

Two methods are currently available for determining contaminant assimilation efficiencies (AE) from ingested material in benthic invertebrates. These methods were compared using the Great Lakes amphipod Diporeia spp. and [14C]benzo(a)pyrene (BaP) sorbed to Florissant sediment (< 63 µm). The first approach, the direct measurement method, uses total organic carbon as a tracer and yielded AE values ranging from 45.9~50.4%. The second approach, the dual-labeled method, uses 51Cr as a non-assimilated tracer and did not yield AE values for our data. The inability of the dual-labeled approach to estimate AEs was due, in part, to the selective feeding by Diporeia resulting in a failure of the non-assimilated tracer (51Cr) to track with the assimilated tracer ([14C]BaP). The failure of the dual-labeled approach was not a result of an uneven distribution of the labels among particle size classes, but more likely resulted from differential sorption of the two isotopically labeled materials to particles of differing composition. The [14C]BaP apparently sorbs to organic particles that are selectively ingested, while the 51Cr apparently sorbs to particles which are selectively excluded by Diporeia. The dual-labeled approach would be a viable and easier experimental approach for determining AE values if the characteristics that govern selective feeding can be determined.

Isotope-labeled cross-linkers and Fourier transform ion cyclotron resonance mass spectrometry for structural analysis of a protein/peptide complex.

PubMed

Ihling, Christian; Schmidt, Andreas; Kalkhof, Stefan; Schulz, Daniela M; Stingl, Christoph; Mechtler, Karl; Haack, Michael; Beck-Sickinger, Annette G; Cooper, Dermot M F; Sinz, Andrea

2006-08-01

For structural studies of proteins and their complexes, chemical cross-linking combined with mass spectrometry presents a promising strategy to obtain structural data of protein interfaces from low quantities of proteins within a short time. We explore the use of isotope-labeled cross-linkers in combination with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry for a more efficient identification of cross-linker containing species. For our studies, we chose the calcium-independent complex between calmodulin and a 25-amino acid peptide from the C-terminal region of adenylyl cyclase 8 containing an "IQ-like motif." Cross-linking reactions between calmodulin and the peptide were performed in the absence of calcium using the amine-reactive, isotope-labeled (d0 and d4) cross-linkers BS3 (bis[sulfosuccinimidyl]suberate) and BS2G (bis[sulfosuccinimidyl]glutarate). Tryptic in-gel digestion of excised gel bands from covalently cross-linked complexes resulted in complicated peptide mixtures, which were analyzed by nano-HPLC/nano-ESI-FTICR mass spectrometry. In cases where more than one reactive functional group, e.g., amine groups of lysine residues, is present in a sequence stretch, MS/MS analysis is a prerequisite for unambiguously identifying the modified residues. MS/MS experiments revealed two lysine residues in the central alpha-helix of calmodulin as well as three lysine residues both in the C-terminal and N-terminal lobes of calmodulin to be cross-linked with one single lysine residue of the adenylyl cyclase 8 peptide. Further cross-linking studies will have to be conducted to propose a structural model for the calmodulin/peptide complex, which is formed in the absence of calcium. The combination of using isotope-labeled cross-linkers, determining the accurate mass of intact cross-linked products, and verifying the amino acid sequences of cross-linked species by MS/MS presents a convenient approach that offers the perspective to obtain structural

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

PubMed

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

2015-01-20

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

An improved stable isotope N-terminal labeling approach with light/heavy TMPP to automate proteogenomics data validation: dN-TOP.

PubMed

Bertaccini, Diego; Vaca, Sebastian; Carapito, Christine; Arsène-Ploetze, Florence; Van Dorsselaer, Alain; Schaeffer-Reiss, Christine

2013-06-07

In silico gene prediction has proven to be prone to errors, especially regarding precise localization of start codons that spread in subsequent biological studies. Therefore, the high throughput characterization of protein N-termini is becoming an emerging challenge in the proteomics and especially proteogenomics fields. The trimethoxyphenyl phosphonium (TMPP) labeling approach (N-TOP) is an efficient N-terminomic approach that allows the characterization of both N-terminal and internal peptides in a single experiment. Due to its permanent positive charge, TMPP labeling strongly affects MS/MS fragmentation resulting in unadapted scoring of TMPP-derivatized peptide spectra by classical search engines. This behavior has led to difficulties in validating TMPP-derivatized peptide identifications with usual score filtering and thus to low/underestimated numbers of identified N-termini. We present herein a new strategy (dN-TOP) that overwhelmed the previous limitation allowing a confident and automated N-terminal peptide validation thanks to a combined labeling with light and heavy TMPP reagents. We show how this double labeling allows increasing the number of validated N-terminal peptides. This strategy represents a considerable improvement to the well-established N-TOP method with an enhanced and accelerated data processing making it now fully compatible with high-throughput proteogenomics studies.

A modified TEW approach to scatter correction for In-111 and Tc-99m dual-isotope small-animal SPECT.

PubMed

Prior, Paul; Timmins, Rachel; Petryk, Julia; Strydhorst, Jared; Duan, Yin; Wei, Lihui; Glenn Wells, R

2016-10-01

In dual-isotope (Tc-99m/In-111) small-animal single-photon emission computed tomography (SPECT), quantitative accuracy of Tc-99m activity measurements is degraded due to the detection of Compton-scattered photons in the Tc-99m photopeak window, which originate from the In-111 emissions (cross talk) and from the Tc-99m emission (self-scatter). The standard triple-energy window (TEW) estimates the total scatter (self-scatter and cross talk) using one scatter window on either side of the Tc-99m photopeak window, but the estimate is biased due to the presence of unscattered photons in the scatter windows. The authors present a modified TEW method to correct for total scatter that compensates for this bias and evaluate the method in phantoms and in vivo. The number of unscattered Tc-99m and In-111 photons present in each scatter-window projection is estimated based on the number of photons detected in the photopeak of each isotope, using the isotope-dependent energy resolution of the detector. The camera-head-specific energy resolutions for the 140 keV Tc-99m and 171 keV In-111 emissions were determined experimentally by separately sampling the energy spectra of each isotope. Each sampled spectrum was fit with a Linear + Gaussian function. The fitted Gaussian functions were integrated across each energy window to determine the proportion of unscattered photons from each emission detected in the scatter windows. The method was first tested and compared to the standard TEW in phantoms containing Tc-99m:In-111 activity ratios between 0.15 and 6.90. True activities were determined using a dose calibrator, and SPECT activities were estimated from CT-attenuation-corrected images with and without scatter-correction. The method was then tested in vivo in six rats using In-111-liposome and Tc-99m-tetrofosmin to generate cross talk in the area of the myocardium. The myocardium was manually segmented using the SPECT and CT images, and partial-volume correction was performed using

Identifying nitrate sources and transformations in surface water by combining dual isotopes of nitrate and stable isotope mixing model in a watershed with different land uses and multi-tributaries

NASA Astrophysics Data System (ADS)

Wang, Meng; Lu, Baohong

2017-04-01

Nitrate is essential for the growth and survival of plants, animals and humans. However, excess nitrate in drinking water is regarded as a health hazard as it is linked to infant methemoglobinemia and esophageal cancer. Revealing nitrate characteristics and identifying its sources are fundamental for making effective water management strategies, but nitrate sources in multi-tributaries and mixed land covered watersheds remain unclear. It is difficult to determine the predominant NO3- sources using conventional water quality monitoring techniques. In our study, based on 20 surface water sampling sites for more than two years' monitoring from April 2012 to December 2014, water chemical and dual isotopic approaches (δ15N-NO3- and δ18O-NO3-) were integrated for the first time to evaluate nitrate characteristics and sources in the Huashan watershed, Jianghuai hilly region, East China. The results demonstrated that nitrate content in surface water was relatively low in the downstream (<10 mg/L), but spatial heterogeneities were remarkable among different sub-watersheds. Extremely high nitrate was observed at the source of the river in one of the sub-watersheds, which exhibited an exponential decline along the stream due to dilution, absorption by aquatic plants, and high forest cover. Although dramatically decline of nitrate occurred along the stream, denitrification was not found in surface water by analyzing δ15N-NO3- and δ18O-NO3- relationship. Proportional contributions of five potential nitrate sources (i.e., precipitation; manure and sewage; soil nitrogen; nitrate fertilizer; nitrate derived from ammonia fertilizer and rainfall) were estimated using a Bayesian isotope mixing model. Model results indicated nitrate sources varied significantly among different rainfall conditions, land use types, as well as anthropologic activities. In summary, coupling dual isotopes of nitrate (δ15N-NO3- and δ18O-NO3-, simultaneously) with a Bayesian isotope mixing model offers

Enzyme-antibody dual labeled gold nanoparticles probe for ultrasensitive detection of κ-casein in bovine milk samples.

PubMed

Li, Y S; Zhou, Y; Meng, X Y; Zhang, Y Y; Liu, J Q; Zhang, Y; Wang, N N; Hu, P; Lu, S Y; Ren, H L; Liu, Z S

2014-11-15

A dual labeled probe was synthesized by coating gold nanoparticles (AuNPs) with anti-κ-CN monoclonal antibody (McAb) and horseradish peroxidase (HRP) enzyme on their surface. The McAb was used as detector and HRP was used as label for signal amplification catalytically oxidize the substrate. AuNPs were used as bridges between the McAb and HRP. Based on the probe, an immunoassay was developed for ultrasensitive detection of κ-CN in bovine milk samples. The assay has a linear response range within 4.2-560 ng mL(-1). The limit of detection (LOD) was 4.2 ng mL(-1) which was 10 times lower than that of traditional McAb-HRP based ELISA. The recoveries of κ-CN from three brand bovine milk samples were from 95.8% to 111.0% that had a good correlation (R(2)=0.998) with those obtained by official standard Kjeldahl method. For higher sensitivity and as simple as the traditional ELISA, the developed immunoassay could provide an alternative approach for ultrasensitive detection of κ-CN in bovine milk sample. Copyright © 2014 Elsevier B.V. All rights reserved.

Quantification of spatial and seasonal variations in the proportional contribution of nitrate sources using a multi-isotope approach and Bayesian isotope mixing model.

PubMed

Meghdadi, Aminreza; Javar, Narmin

2018-04-01

Spatial and seasonal variations in nitrate contamination are a globally concern. While numerous studies have used δ 15 N-NO 3 and δ 18 O-NO 3 to elucidate the dominant sources of nitrate in groundwater, this approach has significant limitations due to the overlap of nitrate isotopic ranges and the occurrence of nitrate isotopic fractionation. This study quantitatively assessed the spatial and seasonal variations in the proportional contributions of nitrate sources from different land uses in the Tarom watershed in North-West Iran. To achieve this aim, orthogonal projection of the hydrochemical and isotopic dataset of the principal component analysis (PCA) as well as correlation coefficient matrix (Corr-PCA) were evaluated to reduce the dimensionality of the inter-correlated dataset. Next, a nitrate isotopic biplot accompanied with a Bayesian isotope mixing model (SIAR) were applied to specify the spatial and seasonal trends in the proportional contribution of three dominant sources of nitrate (fertilizers, animal manure and residential waste) in the watershed. Finally, in order to provide a sensitive framework for nitrate source appointment and overcome the associated limitations of dual nitrate isotope application, the integration of boron isotope (δ 11 B) and strontium isotopic ratio ( 87 Sr/ 86 Sr) was introduced. The results revealed that the mean contribution of residential sewage increased (17%-27.5%), while the mean contribution of fertilizers decreased (28.3%-19%), from late spring to early autumn. Also, fertilizer was the highest contributor (42.1% ± 3.2) during late spring, especially in regions with more than 75% agricultural land. Meanwhile, the mean contribution of sewage was highest in early autumn (32.1% ± 2.8) in the areas with more than 20% residential land. These results were confirmed by coupled application of δ 11 B and 87 Sr/ 86 Sr. This study provides a useful insight for environmental managers to verify groundwater pollution

A Global Approach for Quantitative Super Resolution and Electron Microscopy on Cryo and Epoxy Sections Using Self-labeling Protein Tags.

PubMed

Müller, Andreas; Neukam, Martin; Ivanova, Anna; Sönmez, Anke; Münster, Carla; Kretschmar, Susanne; Kalaidzidis, Yannis; Kurth, Thomas; Verbavatz, Jean-Marc; Solimena, Michele

2017-02-02

Correlative light and electron microscopy (CLEM) is a powerful approach to investigate the molecular ultrastructure of labeled cell compartments. However, quantitative CLEM studies are rare, mainly due to small sample sizes and the sensitivity of fluorescent proteins to strong fixatives and contrasting reagents for EM. Here, we show that fusion of a self-labeling protein to insulin allows for the quantification of age-distinct insulin granule pools in pancreatic beta cells by a combination of super resolution and transmission electron microscopy on Tokuyasu cryosections. In contrast to fluorescent proteins like GFP organic dyes covalently bound to self-labeling proteins retain their fluorescence also in epoxy resin following high pressure freezing and freeze substitution, or remarkably even after strong chemical fixation. This enables for the assessment of age-defined granule morphology and degradation. Finally, we demonstrate that this CLEM protocol is highly versatile, being suitable for single and dual fluorescent labeling and detection of different proteins with optimal ultrastructure preservation and contrast.

Dual pressure-dual temperature isotope exchange process

DOEpatents

Babcock, D.F.

1974-02-12

A liquid and a gas stream, each containing a desired isotope, flow countercurrently through two liquid-gas contacting towers maintained at different temperatures and pressures. The liquid is enriched in the isotope in one tower while the gas is enriched within the other and a portion of at least one of the enriched streams is withdrawn from the system for use or further enrichment. The tower operated at the lower temperature is also maintained at the lower pressure to prevent formation of solid solvates. Gas flow between the towers passes through an expander-compressor apparatas to recover work from the expansion of gas to the lower pressure and thereby compress the gas returning to the tower of higher pressure. (Official Gazette)

Ionization enhancement in atmospheric pressure chemical ionization and suppression in electrospray ionization between target drugs and stable-isotope-labeled internal standards in quantitative liquid chromatography/tandem mass spectrometry.

PubMed

Liang, H R; Foltz, R L; Meng, M; Bennett, P

2003-01-01

The phenomena of ionization suppression in electrospray ionization (ESI) and enhancement in atmospheric pressure chemical ionization (APCI) were investigated in selected-ion monitoring and selected-reaction monitoring modes for nine drugs and their corresponding stable-isotope-labeled internal standards (IS). The results showed that all investigated target drugs and their co-eluting isotope-labeled IS suppress each other's ionization responses in ESI. The factors affecting the extent of suppression in ESI were investigated, including structures and concentrations of drugs, matrix effects, and flow rate. In contrast to the ESI results, APCI caused seven of the nine investigated target drugs and their co-eluting isotope-labeled IS to enhance each other's ionization responses. The mutual ionization suppression or enhancement between drugs and their isotope-labeled IS could possibly influence assay sensitivity, reproducibility, accuracy and linearity in quantitative liquid chromatography/mass spectrometry (LC/MS) and liquid chromatography/tandem mass spectrometry (LC/MS/MS). However, calibration curves were linear if an appropriate IS concentration was selected for a desired calibration range to keep the response factors constant. Copyright 2003 John Wiley & Sons, Ltd.

A retrospective, dual-isotope approach reveals individual predispositions to winter-drought induced tree dieback in the southernmost distribution limit of Scots pine.

PubMed

Voltas, Jordi; Camarero, Jesús Julio; Carulla, David; Aguilera, Mònica; Ortiz, Araceli; Ferrio, Juan Pedro

2013-08-01

Winter-drought induced forest diebacks in the low-latitude margins of species' distribution ranges can provide new insights into the mechanisms (carbon starvation, hydraulic failure) underlying contrasting tree reactions. We analysed a winter-drought induced dieback at the Scots pine's southern edge through a dual-isotope approach (Δ(13) C and δ(18) O in tree-ring cellulose). We hypothesized that a differential long-term performance, mediated by the interaction between CO(2) and climate, determined the fates of individuals during dieback. Declining trees showed a stronger coupling between climate, growth and intrinsic water-use efficiency (WUEi) than non-declining individuals that was noticeable for 25 years prior to dieback. The rising stomatal control of water losses with time in declining trees, indicated by negative Δ(13) C-δ(18) O relationships, was likely associated with their native aptitude to grow more and take up more water (suggested by larger tracheid lumen widths) than non-declining trees and, therefore, to exhibit a greater cavitation risk. Freeze-thaw episodes occurring in winter 2001 unveiled such physiological differences by triggering dieback in those trees more vulnerable to hydraulic failure. Thus, WUEi tightly modulated growth responses to long-term warming in declining trees, indicating that co-occurring individuals were differentially predisposed to winter-drought mortality. These different performances were unconnected to the depletion of stored carbohydrates. © 2013 John Wiley & Sons Ltd.

Segmental isotopic labeling of HIV-1 capsid protein assemblies for solid state NMR.

PubMed

Gupta, Sebanti; Tycko, Robert

2018-02-01

Recent studies of noncrystalline HIV-1 capsid protein (CA) assemblies by our laboratory and by Polenova and coworkers (Protein Sci 19:716-730, 2010; J Mol Biol 426:1109-1127, 2014; J Biol Chem 291:13098-13112, 2016; J Am Chem Soc 138:8538-8546, 2016; J Am Chem Soc 138:12029-12032, 2016; J Am Chem Soc 134:6455-6466, 2012; J Am Chem Soc 132:1976-1987, 2010; J Am Chem Soc 135:17793-17803, 2013; Proc Natl Acad Sci USA 112:14617-14622, 2015; J Am Chem Soc 138:14066-14075, 2016) have established the capability of solid state nuclear magnetic resonance (NMR) measurements to provide site-specific structural and dynamical information that is not available from other types of measurements. Nonetheless, the relatively high molecular weight of HIV-1 CA leads to congestion of solid state NMR spectra of fully isotopically labeled assemblies that has been an impediment to further progress. Here we describe an efficient protocol for production of segmentally labeled HIV-1 CA samples in which either the N-terminal domain (NTD) or the C-terminal domain (CTD) is uniformly 15 N, 13 C-labeled. Segmental labeling is achieved by trans-splicing, using the DnaE split intein. Comparisons of two-dimensional solid state NMR spectra of fully labeled and segmentally labeled tubular CA assemblies show substantial improvements in spectral resolution. The molecular structure of HIV-1 assemblies is not significantly perturbed by the single Ser-to-Cys substitution that we introduce between NTD and CTD segments, as required for trans-splicing.

Stable isotope labeling tandem mass spectrometry (SILT) to quantify protein production and clearance rates

PubMed Central

Bateman, Randall J.; Munsell, Ling Y.; Chen, Xianghong; Holtzman, David M.; Yarasheski, Kevin E.

2007-01-01

In all biological systems, protein amount is a function of the rate of production and clearance. The speed of a response to a disturbance in protein homeostasis is determined by turnover rate. Quantifying alterations in protein synthesis and clearance rates is vital to understanding disease pathogenesis (e.g., aging, inflammation). No methods exist for quantifying production and clearance rates of low abundance (femtomole) proteins in vivo. We describe a novel, mass spectrometry-based method for quantitating low abundance protein synthesis and clearance rates in vitro and in vivo in animals and humans. The utility of this method is demonstrated with amyloid-beta (Aß), an important low abundance protein involved in Alzheimer's disease pathogenesis. We used in vivo stable isotope labeling, immunoprecipitation of Aß from cerebrospinal fluid, and quantitative liquid chromatography electrospray-ionization tandem mass spectrometry (LC-ESI-tandem MS) to quantify human Aß protein production and clearance rates. The method is sensitive and specific for stable isotope labeled amino acid incorporation into CNS (± 1% accuracy). This in vivo method can be used to identify pathophysiologic changes in protein metabolism; and may serve as a biomarker for monitoring disease risk, progression, or response to novel therapeutic agents. The technique is adaptable to other macromolecules, such as carbohydrates or lipids. PMID:17383190

Kinetic 15N-isotope effects on algal growth

NASA Astrophysics Data System (ADS)

Andriukonis, Eivydas; Gorokhova, Elena

2017-03-01

Stable isotope labeling is a standard technique for tracing material transfer in molecular, ecological and biogeochemical studies. The main assumption in this approach is that the enrichment with a heavy isotope has no effect on the organism metabolism and growth, which is not consistent with current theoretical and empirical knowledge on kinetic isotope effects. Here, we demonstrate profound changes in growth dynamics of the green alga Raphidocelis subcapitata grown in 15N-enriched media. With increasing 15N concentration (0.37 to 50 at%), the lag phase increased, whereas maximal growth rate and total yield decreased; moreover, there was a negative relationship between the growth and the lag phase across the treatments. The latter suggests that a trade-off between growth rate and the ability to adapt to the high 15N environment may exist. Remarkably, the lag-phase response at 3.5 at% 15N was the shortest and deviated from the overall trend, thus providing partial support to the recently proposed Isotopic Resonance hypothesis, which predicts that certain isotopic composition is particularly favorable for living organisms. These findings confirm the occurrence of KIE in isotopically enriched algae and underline the importance of considering these effects when using stable isotope labeling in field and experimental studies.

Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach

PubMed Central

Bennett, Bryson D; Yuan, Jie; Kimball, Elizabeth H; Rabinowitz, Joshua D

2009-01-01

This protocol provides a method for quantitating the intracellular concentrations of endogenous metabolites in cultured cells. The cells are grown in stable isotope-labeled media to near-complete isotopic enrichment and then extracted in organic solvent containing unlabeled internal standards in known concentrations. The ratio of endogenous metabolite to internal standard in the extract is determined using mass spectrometry (MS). The product of this ratio and the unlabeled standard amount equals the amount of endogenous metabolite present in the cells. The cellular concentration of the metabolite can then be calculated on the basis of intracellular volume of the extracted cells. The protocol is exemplified using Escherichia coli and primary human fibroblasts fed uniformly with 13C-labeled carbon sources, with detection of 13C-assimilation by liquid chromatography–tandem MS. It enables absolute quantitation of several dozen metabolites over ~1 week of work. PMID:18714298

Dynamic PET and Optical Imaging and Compartment Modeling using a Dual-labeled Cyclic RGD Peptide Probe

PubMed Central

Zhu, Lei; Guo, Ning; Li, Quanzheng; Ma, Ying; Jacboson, Orit; Lee, Seulki; Choi, Hak Soo; Mansfield, James R.; Niu, Gang; Chen, Xiaoyuan

2012-01-01

Purpose: The aim of this study is to determine if dynamic optical imaging could provide comparable kinetic parameters to that of dynamic PET imaging by a near-infrared dye/64Cu dual-labeled cyclic RGD peptide. Methods: The integrin αvβ3 binding RGD peptide was conjugated with a macrocyclic chelator 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) for copper labeling and PET imaging and a near-infrared dye ZW-1 for optical imaging. The in vitro biological activity of RGD-C(DOTA)-ZW-1 was characterized by cell staining and receptor binding assay. Sixty-min dynamic PET and optical imaging were acquired on a MDA-MB-435 tumor model. Singular value decomposition (SVD) method was applied to compute the dynamic optical signal from the two-dimensional optical projection images. Compartment models were used to quantitatively analyze and compare the dynamic optical and PET data. Results: The dual-labeled probe 64Cu-RGD-C(DOTA)-ZW-1 showed integrin specific binding in vitro and in vivo. The binding potential (Bp) derived from dynamic optical imaging (1.762 ± 0.020) is comparable to that from dynamic PET (1.752 ± 0.026). Conclusion: The signal un-mixing process using SVD improved the accuracy of kinetic modeling of 2D dynamic optical data. Our results demonstrate that 2D dynamic optical imaging with SVD analysis could achieve comparable quantitative results as dynamic PET imaging in preclinical xenograft models. PMID:22916074

Dynamic PET and Optical Imaging and Compartment Modeling using a Dual-labeled Cyclic RGD Peptide Probe.

PubMed

Zhu, Lei; Guo, Ning; Li, Quanzheng; Ma, Ying; Jacboson, Orit; Lee, Seulki; Choi, Hak Soo; Mansfield, James R; Niu, Gang; Chen, Xiaoyuan

2012-01-01

The aim of this study is to determine if dynamic optical imaging could provide comparable kinetic parameters to that of dynamic PET imaging by a near-infrared dye/(64)Cu dual-labeled cyclic RGD peptide. The integrin α(v)β(3) binding RGD peptide was conjugated with a macrocyclic chelator 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) for copper labeling and PET imaging and a near-infrared dye ZW-1 for optical imaging. The in vitro biological activity of RGD-C(DOTA)-ZW-1 was characterized by cell staining and receptor binding assay. Sixty-min dynamic PET and optical imaging were acquired on a MDA-MB-435 tumor model. Singular value decomposition (SVD) method was applied to compute the dynamic optical signal from the two-dimensional optical projection images. Compartment models were used to quantitatively analyze and compare the dynamic optical and PET data. The dual-labeled probe (64)Cu-RGD-C(DOTA)-ZW-1 showed integrin specific binding in vitro and in vivo. The binding potential (Bp) derived from dynamic optical imaging (1.762 ± 0.020) is comparable to that from dynamic PET (1.752 ± 0.026). The signal un-mixing process using SVD improved the accuracy of kinetic modeling of 2D dynamic optical data. Our results demonstrate that 2D dynamic optical imaging with SVD analysis could achieve comparable quantitative results as dynamic PET imaging in preclinical xenograft models.

Dual-Mode SERS-Fluorescence Immunoassay Using Graphene Quantum Dot Labeling on One-Dimensional Aligned Magnetoplasmonic Nanoparticles.

PubMed

Zou, Fengming; Zhou, Hongjian; Tan, Tran Van; Kim, Jeonghyo; Koh, Kwangnak; Lee, Jaebeom

2015-06-10

A novel dual-mode immunoassay based on surface-enhanced Raman scattering (SERS) and fluorescence was designed using graphene quantum dot (GQD) labels to detect a tuberculosis (TB) antigen, CFP-10, via a newly developed sensing platform of linearly aligned magnetoplasmonic (MagPlas) nanoparticles (NPs). The GQDs were excellent bilabeling materials for simultaneous Raman scattering and photoluminescence (PL). The one-dimensional (1D) alignment of MagPlas NPs simplified the immunoassay process and enabled fast, enhanced signal transduction. With a sandwich-type immunoassay using dual-mode nanoprobes, both SERS signals and fluorescence images were recognized in a highly sensitive and selective manner with a detection limit of 0.0511 pg mL(-1).

Specific detection of Mycobacterium sp. genomic DNA using dual labeled gold nanoparticle based electrochemical biosensor.

PubMed

Thiruppathiraja, Chinnasamy; Kamatchiammal, Senthilkumar; Adaikkappan, Periyakaruppan; Santhosh, Devakirubakaran Jayakar; Alagar, Muthukaruppan

2011-10-01

The present study was aimed at the development and evaluation of a DNA electrochemical biosensor for Mycobacterium sp. genomic DNA detection in a clinical specimen using a signal amplifier as dual-labeled AuNPs. The DNA electrochemical biosensors were fabricated using a sandwich detection strategy involving two kinds of DNA probes specific to Mycobacterium sp. genomic DNA. The probes of enzyme ALP and the detector probe both conjugated on the AuNPs and subsequently hybridized with target DNA immobilized in a SAM/ITO electrode followed by characterization with CV, EIS, and DPV analysis using the electroactive species para-nitrophenol generated by ALP through hydrolysis of para-nitrophenol phosphate. The effect of enhanced sensitivity was obtained due to the AuNPs carrying numerous ALPs per hybridization and a detection limit of 1.25 ng/ml genomic DNA was determined under optimized conditions. The dual-labeled AuNP-facilitated electrochemical sensor was also evaluated by clinical sputum samples, showing a higher sensitivity and specificity and the outcome was in agreement with the PCR analysis. In conclusion, the developed electrochemical sensor demonstrated unique sensitivity and specificity for both genomic DNA and sputum samples and can be employed as a regular diagnostics tool for Mycobacterium sp. monitoring in clinical samples. Copyright © 2011 Elsevier Inc. All rights reserved.

Global combined precursor isotopic labeling and isobaric tagging (cPILOT) approach with selective MS(3) acquisition.

PubMed

Evans, Adam R; Robinson, Renã A S

2013-11-01

Recently, we reported a novel proteomics quantitation scheme termed "combined precursor isotopic labeling and isobaric tagging (cPILOT)" that allows for the identification and quantitation of nitrated peptides in as many as 12-16 samples in a single experiment. cPILOT offers enhanced multiplexing and posttranslational modification specificity, however excludes global quantitation for all peptides present in a mixture and underestimates reporter ion ratios similar to other isobaric tagging methods due to precursor co-isolation. Here, we present a novel chemical workflow for cPILOT that can be used for global tagging of all peptides in a mixture. Specifically, through low pH precursor dimethylation of tryptic or LysC peptides followed by high pH tandem mass tags, the same reporter ion can be used twice in a single experiment. Also, to improve triple-stage mass spectrometry (MS(3) ) data acquisition, a selective MS(3) method that focuses on product selection of the y1 fragment of lysine-terminated peptides is incorporated into the workflow. This novel cPILOT workflow has potential for global peptide quantitation that could lead to enhanced sample multiplexing and increase the number of quantifiable spectra obtained from MS(3) acquisition methods. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Dual Reporter Iodinated Labeling Reagent for Cancer Positron Emission Tomography Imaging and Fluorescence-Guided Surgery

PubMed Central

2018-01-01

The combination of early diagnosis and complete surgical resection offers the greatest prospect of curative cancer treatment. An iodine-124/fluorescein-based dual-modality labeling reagent, 124I-Green, constitutes a generic tool for one-step installation of a positron emission tomography (PET) and a fluorescent reporter to any cancer-specific antibody. The resulting antibody conjugate would allow both cancer PET imaging and intraoperative fluorescence-guided surgery. 124I-Green was synthesized in excellent radiochemical yields of 92 ± 5% (n = 4) determined by HPLC with an improved one-pot three-component radioiodination reaction. The A5B7 carcinoembryonic antigen (CEA)-specific antibody was conjugated to 124I-Green. High tumor uptake of the dual-labeled A5B7 of 20.21 ± 2.70, 13.31 ± 0.73, and 10.64 ± 1.86%ID/g was observed in CEA-expressing SW1222 xenograft mouse model (n = 3) at 24, 48, and 72 h post intravenous injection, respectively. The xenografts were clearly visualized by both PET/CT and ex vivo fluorescence imaging. These encouraging results warrant the further translational development of 124I-Green for cancer PET imaging and fluorescence-guided surgery. PMID:29388770

Iron physiological requirements in Chinese adults assessed by the stable isotope labeling technique.

PubMed

Cai, Jie; Ren, Tongxiang; Zhang, Yuhui; Wang, Zhilin; Gou, Lingyan; Huang, Zhengwu; Wang, Jun; Piao, Jianhua; Yang, Xiaoguang; Yang, Lichen

2018-01-01

Iron is a kind of essential trace mineral in the human body, while the studies on its physiological requirement are very limited recently, especially in China. And most studies were performed with the radioisotope tracer technique, which was harmful to health. This study aimed to first get the value of iron physiological requirements in Chinese adults assessed by the stable isotope labeling technique. Forty-four eligible young Chinese healthy adults were randomly recruited from the Bethune Military Medical College (Shijiazhuang, Hebei, China) between January 2010 and March 2011, and 19 subjects were included in the final data analysis. After adaptive diets and observation, subjects received 58 Fe intravenously. The baseline venous blood sample and general information were collected on day 0. Venous blood samples were also collected on day 14, 30, 60, 100, 120, 150, 240, 330, 425, 515, 605, 767, 1155, respectively. The blood samples were acid digested by a Microwave Digestion System and then analyzed by the MC-ICP-MS and Atomic Absorption Spectroscopy to get the abundance of Fe isotopes and the total iron concentration respectively. The circulation rate (the proportion of blood iron to whole body iron) could be calculated by the intake amount, background content and the peak isotope content. When the abundance changed stably, the iron physiological requirement could be calculated by the iron loss in a period of time. The abundance of 58 Fe reached its peak on day 14, and changed stably from day 425. The average circulation rate was 84%, with no significance difference between the 2 genders. The mean iron requirement in females was 1101.68 μg/d, and the mean requirement adjusted by body weight was 20.69 μg/kg.d. For males, the mean iron requirement was 959.9 μg/d, and the requirement adjusted by body weight was 14.04 μg/kg.d. Our study has obtained the data about the iron physiological requirements of Chinese adults using stable isotope labeling technique

Isotope labeling of proteins in insect cells.

PubMed

Skora, Lukasz; Shrestha, Binesh; Gossert, Alvar D

2015-01-01

Protein targets of contemporary research are often membrane proteins, multiprotein complexes, secreted proteins, or other proteins of human origin. These are difficult to express in the standard expression host used for most nuclear magnetic resonance (NMR) studies, Escherichia coli. Insect cells represent an attractive alternative, since they have become a well-established expression system and simple solutions have been developed for generation of viruses to efficiently introduce the target protein DNA into cells. Insect cells enable production of a larger fraction of the human proteome in a properly folded way than bacteria, as insect cells have a very similar set of cytosolic chaperones and a closely related secretory pathway. Here, the limited and defined glycosylation pattern that insect cells produce is an advantage for structural biology studies. For these reasons, insect cells have been established as the most widely used eukaryotic expression host for crystallographic studies. In the past decade, significant advancements have enabled amino acid type-specific as well as uniform isotope labeling of proteins in insect cells, turning them into an attractive expression host for NMR studies. © 2015 Elsevier Inc. All rights reserved.

Isotopic signals of denitrification in a northern hardwood forested catchment

NASA Astrophysics Data System (ADS)

Wexler, Sarah; Goodale, Christine

2013-04-01

Water samples from streams, groundwater and precipitation were collected during summer from the hydrologic reference watershed (W3) at Hubbard Brook Experimental Forest in the White Mountains, New Hampshire, and analysed for d15N-NO3 and d18O-NO3. Despite very low nitrate concentrations (<0.5 to 8.8 uM NO3-) dual-isotopic signals of sources and processes were clearly distinguishable. The isotopic composition of nitrate from shallow groundwater showed evidence of dual isotopic fractionation in line with denitrification, with a positive relationship between nitrogen and oxygen isotopic composition, a regression line slope of 0.76 (r2 = 0.68), and an empirical isotope enrichment factor of ɛP-S 15N-NO3 -12.7%. The isotopic composition of riparian groundwater nitrate from time-series samples showed variation in processes over a small spatial scale. The expected isotopic composition of nitrate sources in the watershed was used to distinguish nitrate in rain and nitrate from nitrification of both rainfall ammonium and ammonium from mineralised soil organic nitrogen. Evidence of oxygen exchange with water during nitrification was seen in the isotopic composition of stream and shallow groundwater nitrate. The isotopic composition of streamwater nitrate following a period of storms indicated that 25% of nitrate in the streamwater was of atmospheric origin. This suggests rapid infiltration of rainfall via vertical bypass flow to the saturated zone, enabling transport of atmospheric nitrate to the stream channels. Across the Hubbard Brook basin, the isotopic composition of nitrate from paired samples from watersheds 4-7 indicated a switch between a nitrification and assimilation dominated system, to a system influenced by rainfall nitrogen inputs and denitrification. The dual isotope approach has revealed evidence of denitrification of nitrate from different sources at low concentrations at Hubbard Brook during summer. This isotopic evidence deepens our understanding of the

Application of isotopic labeling, and gas chromatography mass spectrometry, to understanding degradation products and pathways in the thermal-oxidative aging of Nylon 6.6

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Gregory Von; Clough, Roger L.; Hochrein, James M.

2013-12-01

Nylon 6.6 containing 13C isotopic labels at specific positions along the macromolecular backbone has been subjected to extensive thermal-oxidative aging at 138 °C for time periods up to 243 days. In complementary experiments, unlabeled Nylon 6.6 was subjected to the same aging conditions under an atmosphere of 18O 2. Volatile organic degradation products were analyzed by cryofocusing gas chromatography mass spectrometry (cryo-GC/MS) to identify the isotopic labeling. The labeling results, combined with basic considerations of free radical reaction chemistry, provided insights to the origin of degradation species, with respect to the macromolecular structure. A number of inferences on chemical mechanismsmore » were drawn, based on 1) the presence (or absence) of the isotopic labels in the various products, 2) the location of the isotope within the product molecule, and 3) the relative abundance of products as indicated by large differences in peak intensities in the gas chromatogram. The overall degradation results can be understood in terms of free radical pathways originating from initial attacks on three different positions along the nylon chain which include hydrogen abstraction from: the (CH 2) group adjacent to the nitrogen atom, at the (CH 2) adjacent the carbonyl group, and direct radical attack on the carbonyl. Understanding the pathways which lead to Nylon 6.6 degradation ultimately provides new insight into changes that can be leveraged to detect and reduce early aging and minimize problems associated with material degradation.« less

Abstracts of the 24th international isotope society (UK group) symposium: synthesis and applications of labelled compounds 2015.

PubMed

Aigbirhio, F I; Allwein, S; Anwar, A; Atzrodt, J; Audisio, D; Badman, G; Bakale, R; Berthon, F; Bragg, R; Brindle, K M; Bushby, N; Campos, S; Cant, A A; Chan, M Y T; Colbon, P; Cornelissen, B; Czarny, B; Derdau, V; Dive, V; Dunscombe, M; Eggleston, I; Ellis-Sawyer, K; Elmore, C S; Engstrom, P; Ericsson, C; Fairlamb, I J S; Georgin, D; Godfrey, S P; He, L; Hickey, M J; Huscroft, I T; Kerr, W J; Lashford, A; Lenz, E; Lewinton, S; L'Hermite, M M; Lindelöf, Å; Little, G; Lockley, W J S; Loreau, O; Maddocks, S; Marguerit, M; Mirabello, V; Mudd, R J; Nilsson, G N; Owens, P K; Pascu, S I; Patriarche, G; Pimlott, S L; Pinault, M; Plastow, G; Racys, D T; Reif, J; Rossi, J; Ruan, J; Sarpaki, S; Sephton, S M; Simonsson, R; Speed, D J; Sumal, K; Sutherland, A; Taran, F; Thuleau, A; Wang, Y; Waring, M; Watters, W H; Wu, J; Xiao, J

2016-04-01

The 24th annual symposium of the International Isotope Society's United Kingdom Group took place at the Møller Centre, Churchill College, Cambridge, UK on Friday 6th November 2015. The meeting was attended by 77 delegates from academia and industry, the life sciences, chemical, radiochemical and scientific instrument suppliers. Delegates were welcomed by Dr Ken Lawrie (GlaxoSmithKline, UK, chair of the IIS UK group). The subsequent scientific programme consisted of oral presentations, short 'flash' presentations in association with particular posters and poster presentations. The scientific areas covered included isotopic synthesis, regulatory issues, applications of labelled compounds in imaging, isotopic separation and novel chemistry with potential implications for isotopic synthesis. Both short-lived and long-lived isotopes were represented, as were stable isotopes. The symposium was divided into a morning session chaired by Dr Rebekka Hueting (University of Oxford, UK) and afternoon sessions chaired by Dr Sofia Pascu (University of Bath, UK) and by Dr Alan Dowling (Syngenta, UK). The UK meeting concluded with remarks from Dr Ken Lawrie (GlaxoSmithKline, UK). Copyright © 2016 John Wiley & Sons, Ltd.

Metabolomics relative quantitation with mass spectrometry using chemical derivatization and isotope labeling

DOE PAGES

O'Maille, Grace; Go, Eden P.; Hoang, Linh; ...

2008-01-01

Comprehensive detection and quantitation of metabolites from a biological source constitute the major challenges of current metabolomics research. Two chemical derivatization methodologies, butylation and amination, were applied to human serum for ionization enhancement of a broad spectrum of metabolite classes, including steroids and amino acids. LC-ESI-MS analysis of the derivatized serum samples provided a significant signal elevation across the total ion chromatogram to over a 100-fold increase in ionization efficiency. It was also demonstrated that derivatization combined with isotopically labeled reagents facilitated the relative quantitation of derivatized metabolites from individual as well as pooled samples.

Reliability of the dual-isotope Schilling test for the diagnosis of pernicious anemia or malabsorption syndrome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Domstad, P.A.; Choy, Y.C.; Kim, E.E.

1981-05-01

To evaluate the dual-isotope Schilling test for the diagnosis of pernicious anemia or malabsorption syndrome, 65 studies were selected for clinical correlation. Criteria for pernicious anemia included mean corpuscular volume greater than 100 cu micrometer, serum B12 greater than 100 ng/l, megaloblastic marrow, achlorhydria, reticulocytes greater than 5% on B12 therapy, atrophic gastritis, and elevated serum antibodies to parietal cells or intrinsic factor. Criteria for malabsorption syndrome included: decreased serum B12, folate, and carotene; increased fecal fat; abnormal D-xylose absorption; abnormal radiographic and biopsy findings. /sup 58/Co-cyanocobalamin and /sup 57/Co-cyanocobalamin bound to intrinsic factor were given orally to fasting patients;more » 1 mg of nonradioactive B12 was injected intramuscularly within two hours. Aliquots of 24-hour urine samples were counted. If the excretion of /sup 58/Co was less than 7% and the /sup 57/Co//sup 58/Co ratio was greater than 1.7, the test indicated pernicious anemia; a ratio less than 1.7 indicated malabsorption syndrome. Sensitivity, specificity, and accuracy of the dual-isotope Schilling test were 83%, 98%, and 94% for pernicious anemia, and 67%, 90%, and 86% for malabsorption syndrome, respectively.« less

Compound-specific isotope analysis as a tool to characterize biodegradation of ethylbenzene.

PubMed

Dorer, Conrad; Vogt, Carsten; Kleinsteuber, Sabine; Stams, Alfons J M; Richnow, Hans-Hermann

2014-08-19

This study applied one- and two-dimensional compound-specific isotope analysis (CSIA) for the elements carbon and hydrogen to assess different means of microbial ethylbenzene activation. Cultures incubated under nitrate-reducing conditions showed significant carbon and highly pronounced hydrogen isotope fractionation of comparable magnitudes, leading to nearly identical slopes in dual-isotope plots. The results imply that Georgfuchsia toluolica G5G6 and an enrichment culture dominated by an Azoarcus species activate ethylbenzene by anaerobic hydroxylation catalyzed by ethylbenzene dehydrogenase, similar to Aromatoleum aromaticum EbN1. The isotope enrichment pattern in dual plots from two strictly anaerobic enrichment cultures differed considerably from those for benzylic hydroxylation, indicating an alternative anaerobic activation step, most likely fumarate addition. Large hydrogen fractionation was quantified using a recently developed Rayleigh-based approach considering hydrogen atoms at reactive sites. Data from nine investigated microbial cultures clearly suggest that two-dimensional CSIA in combination with the magnitude of hydrogen isotope fractionation is a valuable tool to distinguish ethylbenzene degradation and may be of practical use for monitoring natural or technological remediation processes at field sites.

Potential of isotope analysis (C, Cl) to identify dechlorination mechanisms

NASA Astrophysics Data System (ADS)

Cretnik, Stefan; Thoreson, Kristen; Bernstein, Anat; Ebert, Karin; Buchner, Daniel; Laskov, Christine; Haderlein, Stefan; Shouakar-Stash, Orfan; Kliegman, Sarah; McNeill, Kristopher; Elsner, Martin

2013-04-01

Chloroethenes are commonly used in industrial applications, and detected as carcinogenic contaminants in the environment. Their dehalogenation is of environmental importance in remediation processes. However, a detailed understanding frequently accounted problem is the accumulation of toxic degradation products such as cis-dichloroethylene (cis-DCE) at contaminated sites. Several studies have addressed the reductive dehalogenation reactions using biotic and abiotic model systems, but a crucial question in this context has remained open: Do environmental transformations occur by the same mechanism as in their corresponding in vitro model systems? The presented study shows the potential to close this research gap using the latest developments in compound specific chlorine isotope analysis, which make it possible to routinely measure chlorine isotope fractionation of chloroethenes in environmental samples and complex reaction mixtures.1,2 In particular, such chlorine isotope analysis enables the measurement of isotope fractionation for two elements (i.e., C and Cl) in chloroethenes. When isotope values of both elements are plotted against each other, different slopes reflect different underlying mechanisms and are remarkably insensitive towards masking. Our results suggest that different microbial strains (G. lovleyi strain SZ, D. hafniense Y51) and the isolated cofactor cobalamin employ similar mechanisms of reductive dechlorination of TCE. In contrast, evidence for a different mechanism was obtained with cobaloxime cautioning its use as a model for biodegradation. The study shows the potential of the dual isotope approach as a tool to directly compare transformation mechanisms of environmental scenarios, biotic transformations, and their putative chemical lab scale systems. Furthermore, it serves as an essential reference when using the dual isotope approach to assess the fate of chlorinated compounds in the environment.

Correlated optical and isotopic nanoscopy

NASA Astrophysics Data System (ADS)

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

2014-04-01

The isotopic composition of different materials can be imaged by secondary ion mass spectrometry. In biology, this method is mainly used to study cellular metabolism and turnover, by pulsing the cells with marker molecules such as amino acids labelled with stable isotopes (15N, 13C). The incorporation of the markers is then imaged with a lateral resolution that can surpass 100 nm. However, secondary ion mass spectrometry cannot identify specific subcellular structures like organelles, and needs to be correlated with a second technique, such as fluorescence imaging. Here, we present a method based on stimulated emission depletion microscopy that provides correlated optical and isotopic nanoscopy (COIN) images. We use this approach to study the protein turnover in different organelles from cultured hippocampal neurons. Correlated optical and isotopic nanoscopy can be applied to a variety of biological samples, and should therefore enable the investigation of the isotopic composition of many organelles and subcellular structures.

Random Matrix Approach for Primal-Dual Portfolio Optimization Problems

NASA Astrophysics Data System (ADS)

Tada, Daichi; Yamamoto, Hisashi; Shinzato, Takashi

2017-12-01

In this paper, we revisit the portfolio optimization problems of the minimization/maximization of investment risk under constraints of budget and investment concentration (primal problem) and the maximization/minimization of investment concentration under constraints of budget and investment risk (dual problem) for the case that the variances of the return rates of the assets are identical. We analyze both optimization problems by the Lagrange multiplier method and the random matrix approach. Thereafter, we compare the results obtained from our proposed approach with the results obtained in previous work. Moreover, we use numerical experiments to validate the results obtained from the replica approach and the random matrix approach as methods for analyzing both the primal and dual portfolio optimization problems.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merkley, Eric D.; Baker, Erin S.; Crowell, Kevin L.

2013-02-20

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

A dual marker label free electrochemical assay for Flavivirus dengue diagnosis.

PubMed

Santos, Adriano; Bueno, Paulo R; Davis, Jason J

2018-02-15

Dengue is a RNA viral illness of the genus Flavivirus which can cause, depending on the pervasiveness of the infection, hemorrhagic dengue fever or dengue shock syndrome. Herein we present an electrochemical label free approach enabling the rapid sensitive quantification of NS1 and IgG (supporting an ability to distinguish primary and secondary infections). Using a bifunctional SAM containing PEG moieties and a tethered redox thiol, both markers are detectable across clinically relevant levels by label free impedance derived redox capacitance. A subsequent frequency specific immittance function approach enables assaying (within seconds) with no impairment of analytical quality (linearity, sensitivity and variance). Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed

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

2013-10-01

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

PSMA-11-Derived Dual-Labeled PSMA Inhibitors for Preoperative PET Imaging and Precise Fluorescence-Guided Surgery of Prostate Cancer.

PubMed

Baranski, Ann-Christin; Schäfer, Martin; Bauder-Wüst, Ulrike; Roscher, Mareike; Schmidt, Jana; Stenau, Esther; Simpfendörfer, Tobias; Teber, Dogu; Maier-Hein, Lena; Hadaschik, Boris; Haberkorn, Uwe; Eder, Matthias; Kopka, Klaus

2018-04-01

Resection of tumors using targeted dual-modality probes combining preoperative imaging with intraoperative guidance is of high clinical relevance and might considerably affect the outcome of prostate cancer therapy. This work aimed at the development of dual-labeled prostate-specific membrane antigen (PSMA) inhibitors derived from the established N,N' -bis[2-hydroxy-5-(carboxyethyl)benzyl]ethylenediamine- N,N' -diacetic acid (HBED-CC)-based PET tracer 68 Ga-Glu-urea-Lys(Ahx)-HBED-CC ( 68 Ga-PSMA-11) to allow accurate intraoperative detection of PSMA-positive tumors. Methods: A series of novel PSMA-targeting fluorescent dye conjugates of Glu-urea-Lys-HBED-CC was synthesized, and their biologic properties were determined in cell-based assays and confocal microscopy. As a preclinical proof of concept, specific tumor uptake, pharmacokinetics, and feasibility for intraoperative fluorescence guidance were investigated in tumor-bearing mice and healthy pigs. Results: The designed dual-labeled PSMA inhibitors exhibited high binding affinity and PSMA-specific effective internalization. Conjugation of fluorescein isothiocyanate (10.86 ± 0.94 percentage injected dose [%ID]/g), IRDye800CW (13.66 ± 3.73 %ID/g), and DyLight800 (15.62 ± 5.52 %ID/g) resulted in a significantly increased specific tumor uptake, whereas 68 Ga-Glu-urea-Lys-HBED-CC-AlexaFluor488 (9.12 ± 5.47 %ID/g) revealed a tumor uptake similar to that of 68 Ga-PSMA-11 (4.89 ± 1.34 %ID/g). The first proof-of-concept studies with the clinically relevant candidate 68 Ga-Glu-urea-Lys-HBED-CC-IRDye800CW reinforced a fast, specific enrichment in PSMA-positive tumors, with rapid background clearance. With regard to intraoperative navigation, a specific fluorescence signal was detected in PSMA-expressing tissue. Conclusion: This study demonstrated that PSMA-11-derived dual-labeled dye conjugates are feasible for providing PSMA-specific pre-, intra-, and postoperative detection of prostate cancer lesions and have high

Identification and characterization of isomeric N-glycans of human alfa-acid-glycoprotein by stable isotope labelling and ZIC-HILIC-MS in combination with exoglycosidase digestion.

PubMed

Mancera-Arteu, Montserrat; Giménez, Estela; Barbosa, José; Sanz-Nebot, Victòria

2016-10-12

In this study, a ZIC-HILIC-MS methodology for the analysis of N-glycan isomers was optimized to obtain greater detection sensitivity and thus identify more glycan structures in hAGP. In a second step, this method was combined with glycan reductive isotope labelling (GRIL) through [(12)C6]/[(13)C6]-aniline and exoglycosidase digestion to characterize the different glycan isomers. The GRIL method allows the peak areas resulting from two different labelled samples to be compared, since neither retention time shifts nor variations in the ionization of glycans between these samples are obtained. First, sialic acid linkage assignations were performed for most hAGP glycan isomers with α2-3 sialidase digestion. Bi-, tri- and tetraantennary glycan isomers with different terminal sialic acid linkages to galactose (α2-3 or α2-6) were assigned, and the potential of this technique for the structural characterization of isobaric isomers was therefore demonstrated. Furthermore, fucose linkage isomers of hAGP glycans were also characterized using this isotope-labelling approach in combination with α1-3,4 fucosidase and β1-4 galactosidase digestion. α1-3 antennary fucoses and α1-6 core fucosylation were detected in hAGP fucosylated glycans. These established methodologies can be extremely useful for patho-glycomic studies to characterize glycoproteins of biomedical interest and find novel glycan isomers that could be used as biomarkers in cancer research. Copyright © 2016 Elsevier B.V. All rights reserved.

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

PubMed Central

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

2013-01-01

The 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 due to isotopic overlap and a post-acquisition normalization of the data to account for both the systematic variability, a plot of the experimental H:L ratio vs. 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. PMID:23860851

Natural isotope correction of MS/MS measurements for metabolomics and (13)C fluxomics.

PubMed

Niedenführ, Sebastian; ten Pierick, Angela; van Dam, Patricia T N; Suarez-Mendez, Camilo A; Nöh, Katharina; Wahl, S Aljoscha

2016-05-01

Fluxomics and metabolomics are crucial tools for metabolic engineering and biomedical analysis to determine the in vivo cellular state. Especially, the application of (13)C isotopes allows comprehensive insights into the functional operation of cellular metabolism. Compared to single MS, tandem mass spectrometry (MS/MS) provides more detailed and accurate measurements of the metabolite enrichment patterns (tandem mass isotopomers), increasing the accuracy of metabolite concentration measurements and metabolic flux estimation. MS-type data from isotope labeling experiments is biased by naturally occurring stable isotopes (C, H, N, O, etc.). In particular, GC-MS(/MS) requires derivatization for the usually non-volatile intracellular metabolites introducing additional natural isotopes leading to measurements that do not directly represent the carbon labeling distribution. To make full use of LC- and GC-MS/MS mass isotopomer measurements, the influence of natural isotopes has to be eliminated (corrected). Our correction approach is analyzed for the two most common applications; (13)C fluxomics and isotope dilution mass spectrometry (IDMS) based metabolomics. Natural isotopes can have an impact on the calculated flux distribution which strongly depends on the substrate labeling and the actual flux distribution. Second, we show that in IDMS based metabolomics natural isotopes lead to underestimated concentrations that can and should be corrected with a nonlinear calibration. Our simulations indicate that the correction for natural abundance in isotope based fluxomics and quantitative metabolomics is essential for correct data interpretation. © 2015 Wiley Periodicals, Inc.

Some approaches to optimal cluster labeling of aerospace imagery

NASA Technical Reports Server (NTRS)

Chittineni, C. B.

1980-01-01

Some approaches are presented to the problem of labeling clusters using information from a given set of labeled and unlabeled aerospace imagery patterns. The assignment of class labels to the clusters is formulated as the determination of the best assignment over all possible ones with respect to some criterion. Cluster labeling is also viewed as the probability of correct labeling with a maximization of likelihood function. Results of the application of these techniques in the processing of remotely sensed multispectral scanner imagery data are presented.

Assessing the dietary bioavailability of metals associated with natural particles: Extending the use of the reverse labeling approach to zinc

USGS Publications Warehouse

Croteau, Marie-Noele; Cain, Daniel J.; Fuller, Christopher C.

2017-01-01

We extend the use of a novel tracing technique to quantify the bioavailability of zinc (Zn) associated with natural particles using snails enriched with a less common Zn stable isotope. Lymnaea stagnalis is a model species that has relatively fast Zn uptake rates from the dissolved phase, enabling their rapid enrichment in 67Zn during the initial phase of labeling. Isotopically enriched snails were subsequently exposed to algae mixed with increasing amounts of metal-rich particles collected from two acid mine drainage impacted rivers. Zinc bioavailability from the natural particles was inferred from calculations of 66Zn assimilation into the snail’s soft tissues. Zinc assimilation efficiency (AE) varied from 28% for the Animas River particles to 45% for the Snake River particles, indicating that particle-bound, or sorbed Zn, was bioavailable from acid mine drainage wastes. The relative binding strength of Zn sorption to the natural particles was inversely related to Zn bioavailability; a finding that would not have been possible without using the reverse labeling approach. Differences in the chemical composition of the particles suggest that their geochemical properties may influence the extent of Zn bioavailability.

Assessing the Dietary Bioavailability of Metals Associated with Natural Particles: Extending the Use of the Reverse Labeling Approach to Zinc.

PubMed

Croteau, Marie-Noële; Cain, Daniel J; Fuller, Christopher C

2017-03-07

We extend the use of a novel tracing technique to quantify the bioavailability of zinc (Zn) associated with natural particles using snails enriched with a less common Zn stable isotope. Lymnaea stagnalis is a model species that has relatively fast Zn uptake rates from the dissolved phase, enabling their rapid enrichment in 67 Zn during the initial phase of labeling. Isotopically enriched snails were subsequently exposed to algae mixed with increasing amounts of metal-rich particles collected from two acid mine drainage impacted rivers. Zinc bioavailability from the natural particles was inferred from calculations of 66 Zn assimilation into the snail's soft tissues. Zinc assimilation efficiency (AE) varied from 28% for the Animas River particles to 45% for the Snake River particles, indicating that particle-bound, or sorbed Zn, was bioavailable from acid mine drainage wastes. The relative binding strength of Zn sorption to the natural particles was inversely related to Zn bioavailability; a finding that would not have been possible without using the reverse labeling approach. Differences in the chemical composition of the particles suggest that their geochemical properties may influence the extent of Zn bioavailability.

Metrology for stable isotope reference materials: 13C/12C and 18O/16O isotope ratio value assignment of pure carbon dioxide gas samples on the Vienna PeeDee Belemnite-CO2 scale using dual-inlet mass spectrometry.

PubMed

Srivastava, Abneesh; Michael Verkouteren, R

2018-07-01

Isotope ratio measurements have been conducted on a series of isotopically distinct pure CO 2 gas samples using the technique of dual-inlet isotope ratio mass spectrometry (DI-IRMS). The influence of instrumental parameters, data normalization schemes on the metrological traceability and uncertainty of the sample isotope composition have been characterized. Traceability to the Vienna PeeDee Belemnite(VPDB)-CO 2 scale was realized using the pure CO 2 isotope reference materials(IRMs) 8562, 8563, and 8564. The uncertainty analyses include contributions associated with the values of iRMs and the repeatability and reproducibility of our measurements. Our DI-IRMS measurement system is demonstrated to have high long-term stability, approaching a precision of 0.001 parts-per-thousand for the 45/44 and 46/44 ion signal ratios. The single- and two-point normalization bias for the iRMs were found to be within their published standard uncertainty values. The values of 13 C/ 12 C and 18 O/ 16 O isotope ratios are expressed relative to VPDB-CO 2 using the [Formula: see text] and [Formula: see text] notation, respectively, in parts-per-thousand (‰ or per mil). For the samples, value assignments between (-25 to +2) ‰ and (-33 to -1) ‰ with nominal combined standard uncertainties of (0.05, 0.3) ‰ for [Formula: see text] and [Formula: see text], respectively were obtained. These samples are used as laboratory reference to provide anchor points for value assignment of isotope ratios (with VPDB traceability) to pure CO 2 samples. Additionally, they serve as potential parent isotopic source material required for the development of gravimetric based iRMs of CO 2 in CO 2 -free dry air in high pressure gas cylinder packages at desired abundance levels and isotopic composition values. Graphical abstract CO 2 gas isotope ratio metrology.

Tracing Fasting Glucose Fluxes with Unstressed Catheter Approach in Streptozotocin Induced Diabetic Rats

PubMed Central

Wu, Hui; Xu, Xiao; Meng, Ying; Xia, Fangzhen; Zhai, Hualing; Lu, Yingli

2014-01-01

Objective. Blood glucose concentrations of type 1 diabetic rats are vulnerable, especially to stress and trauma. The present study aimed to investigate the fasting endogenous glucose production and skeletal muscle glucose uptake of Streptozotocin induced type 1 diabetic rats using an unstressed vein and artery implantation of catheters at the tails of the rats as a platform. Research Design and Methods. Streptozotocin (65 mg·kg−1) was administered to induce type 1 diabetic state. The unstressed approach of catheters of vein and artery at the tails of the rats was established before the isotope tracer injection. Dynamic measurement of fasting endogenous glucose production was assessed by continuously infusing stable isotope [6, 6-2H2] glucose, while skeletal muscle glucose uptake by bolus injecting radioactively labeled [1-14C]-2-deoxy-glucose. Results. Streptozotocin induced type 1 diabetic rats displayed polydipsia, polyphagia, and polyuria along with overt hyperglycemia and hypoinsulinemia. They also had enhanced fasting endogenous glucose production and reduced glucose uptake in skeletal muscle compared to nondiabetic rats. Conclusions. The dual catheters implantation at the tails of the rats together with isotope tracers injection is a save time, unstressed, and feasible approach to explore the glucose metabolism in animal models in vivo. PMID:24772449

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

NASA Astrophysics Data System (ADS)

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

2006-12-01

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. Δ14CO2 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

A Test of Carbon and Oxygen Stable Isotope Ratio Process Models in Tree Rings.

NASA Astrophysics Data System (ADS)

Roden, J. S.; Farquhar, G. D.

2008-12-01

Stable isotopes ratios of carbon and oxygen in tree ring cellulose have been used to infer environmental change. Process-based models have been developed to clarify the potential of historic tree ring records for meaningful paleoclimatic reconstructions. However, isotopic variation can be influenced by multiple environmental factors making simplistic interpretations problematic. Recently, the dual isotope approach, where the variation in one stable isotope ratio (e.g. oxygen) is used to constrain the interpretation of variation in another (e.g. carbon), has been shown to have the potential to de-convolute isotopic analysis. However, this approach requires further testing to determine its applicability for paleo-reconstructions using tree-ring time series. We present a study where the information needed to parameterize mechanistic models for both carbon and oxygen stable isotope ratios were collected in controlled environment chambers for two species (Pinus radiata and Eucalyptus globulus). The seedlings were exposed to treatments designed to modify leaf temperature, transpiration rates, stomatal conductance and photosynthetic capacity. Both species were grown for over 100 days under two humidity regimes that differed by 20%. Stomatal conductance was significantly different between species and for seedlings under drought conditions but not between other treatments or humidity regimes. The treatments produced large differences in transpiration rate and photosynthesis. Treatments that effected photosynthetic rates but not stomatal conductance influenced carbon isotope discrimination more than those that influenced primarily conductance. The various treatments produced a range in oxygen isotope ratios of 7 ‰. Process models predicted greater oxygen isotope enrichment in tree ring cellulose than observed. The oxygen isotope ratios of bulk leaf water were reasonably well predicted by current steady-state models. However, the fractional difference between models that

The Labelling Approach to Deviance.

ERIC Educational Resources Information Center

Rains, Prudence M.; Kitsuse, John L.; Duster, Troy; Freidson, Eliot

2003-01-01

This reprint of one chapter from the 1975 text, "Issues in the Classification of Children" by Nicholas Hobbs and others, addresses the theoretical, methodological, and empirical issues involved in the "labeling" approach to the sociology of deviance. It examines the social process of classification, the use of classification in social agencies,…

Rate-dependent carbon and nitrogen kinetic isotope fractionation in hydrolysis of isoproturon.

PubMed

Penning, Holger; Cramer, Christopher J; Elsner, Martin

2008-11-01

Stable isotope fractionation permits quantifying contaminant degradation in the field when the transformation reaction is associated with a consistent isotope enrichment factor epsilon. When interpreted in conjunction with dual isotope plots, isotope fractionation is also particularly useful for elucidating reaction mechanisms. To assess the consistency of epsilon and dual isotope slopes in a two-step reaction, we investigated the abiotic hydrolysis of the herbicide isoproturon (3-(4-isopropylphenyl)-1,1-dimethylurea) using a fragmentation method that allows measuring isotope ratios in different parts of the molecule. Carbon and nitrogen position-specific isotope fractionation, as well as slopes in dual isotope plots, varied linearly with rate constants k(obs) depending on the presence of buffers that mediate the initial zwitterion formation. The correlation can be explained by two consecutive reaction steps (zwitterion formation followed by dimethylamine elimination) each of which has a different kinetic isotope effect and may be rate-limiting. Intrinsic isotope effects for both steps, extracted from our kinetic data using a novel theoretical treatment, agree well with values computed from density functional calculations. Our study therefore demonstrates that more variable isotope fractionation may be observed in simple chemical reactions than commonly thought, but that consistent epsilon or dual isotope slopes may nonetheless be encountered in certain molecular fragments.

Metabolic De-Isotoping for Improved LC-MS Characterization of Modified RNAs

NASA Astrophysics Data System (ADS)

Wetzel, Collin; Li, Siwei; Limbach, Patrick A.

2014-07-01

Mapping, sequencing, and quantifying individual noncoding ribonucleic acids (ncRNAs), including post-transcriptionally modified nucleosides, by mass spectrometry is a challenge that often requires rigorous sample preparation prior to analysis. Previously, we have described a simplified method for the comparative analysis of RNA digests (CARD) that is applicable to relatively complex mixtures of ncRNAs. In the CARD approach for transfer RNA (tRNA) analysis, two complete sets of digestion products from total tRNA are compared using the enzymatic incorporation of 16O/18O isotopic labels. This approach allows one to rapidly screen total tRNAs from gene deletion mutants or comparatively sequence total tRNA from two related bacterial organisms. However, data analysis can be challenging because of convoluted mass spectra arising from the natural 13C and 15 N isotopes present in the ribonuclease-digested tRNA samples. Here, we demonstrate that culturing in 12C-enriched/13C-depleted media significantly reduces the isotope patterns that must be interpreted during the CARD experiment. Improvements in data quality yield a 35 % improvement in detection of tRNA digestion products that can be uniquely assigned to particular tRNAs. These mass spectral improvements lead to a significant reduction in data processing attributable to the ease of spectral identification of labeled digestion products and will enable improvements in the relative quantification of modified RNAs by the 16O/18O differential labeling approach.

Apparatus and process for separating hydrogen isotopes

DOEpatents

Heung, Leung K; Sessions, Henry T; Xiao, Xin

2013-06-25

The apparatus and process for separating hydrogen isotopes is provided using dual columns, each column having an opposite hydrogen isotopic effect such that when a hydrogen isotope mixture feedstock is cycled between the two respective columns, two different hydrogen isotopes are separated from the feedstock.

Determination of chemical purity and isotopic composition of natural and carbon-13-labeled arsenobetaine bromide standards by quantitative(1)H-NMR.

PubMed

Le, Phuong-Mai; Ding, Jianfu; Leek, Donald M; Mester, Zoltan; Robertson, Gilles; Windust, Anthony; Meija, Juris

2016-10-01

In this study, we report the characterization of three arsenobetaine-certified reference materials by quantitative NMR. We have synthesized an arsenobetaine bromide high-purity standard of natural isotopic composition (ABET-1) and two carbon-13-labeled isotopic standards (BBET-1 and CBET-1). Assignments of the chemical purity and isotopic composition are not trivial in the case of arsenobetaine, and in this study we utilized quantitative(1)H-NMR techniques for the determination of the mass fractions (chemical purity). The isotopic purity of all three standards was also assessed by NMR from the carbon-13 satellite signals. The standards are non-hygroscopic, high-purity (ca. 0.99 g/g), and the carbon-13 enrichment for both isotopic standards is x((13)C)≈0.99. These standards are designed for use as primary calibrators for mass spectrometric determination of arsenobetaine in environmental samples.

Radiogenic isotopic approaches for quantifying radionuclide transport (Invited)

NASA Astrophysics Data System (ADS)

Maher, K.; Depaolo, D. J.; Singleton, M. J.; Christensen, J. N.; Conrad, M. E.

2009-12-01

Naturally occurring variations in the isotopic compositions of U and Sr provide unique opportunities for assessing the fate and transport of radionuclides at field-scale conditions. When coupled with reactive transport models, U and Sr isotopes may also provide additional constraints on the rates of sediment-fluid or sediment-waste interactions. Such isotopic approaches can be useful for sites where subsurface characterization is complicated by a lack of accessibility or the presence of substantial heterogeneity. In addition, a variety of quantitative modeling approaches of different complexity can be used to evaluate experimentally determined parameters for radionuclide mobility at the field-scale. At the Hanford Site in eastern Washington, 87Sr/86Sr and 234U/238U ratios have been used to quantify the residence time of Sr and U in the unsaturated zone, the long-term background infiltration rate through the unsaturated zone, and to assess the influence of enhanced wastewater discharge on the regional unconfined aquifer. As a result of different processing techniques or due to interactions between caustic waste and the natural sediment, waste plumes may also inherit isotopic fingerprints (e.g. 234U/238U, 235U/238U, 236U/238U; δ15N & δ18O of nitrate) that can be used to resolve multiple sources of contamination. Finally, enriched isotopic tracers can be applied to experimental manipulations to assess the retardation of a variety of contaminants. Collectively this isotopic data contributes unique perspectives on both the hydrologic conditions across the site and the mobility of key radionuclides. Predicting the long-term fate and transport of radionuclides in the environment is often challenging due to natural heterogeneity and incomplete characterization of the subsurface, however detailed analysis of isotopic variations can provide one additional means of characterizing the subsurface.

Reliable LC-MS quantitative glycomics using iGlycoMab stable isotope labeled glycans as internal standards.

PubMed

Zhou, Shiyue; Tello, Nadia; Harvey, Alex; Boyes, Barry; Orlando, Ron; Mechref, Yehia

2016-06-01

Glycans have numerous functions in various biological processes and participate in the progress of diseases. Reliable quantitative glycomic profiling techniques could contribute to the understanding of the biological functions of glycans, and lead to the discovery of potential glycan biomarkers for diseases. Although LC-MS is a powerful analytical tool for quantitative glycomics, the variation of ionization efficiency and MS intensity bias are influencing quantitation reliability. Internal standards can be utilized for glycomic quantitation by MS-based methods to reduce variability. In this study, we used stable isotope labeled IgG2b monoclonal antibody, iGlycoMab, as an internal standard to reduce potential for errors and to reduce variabililty due to sample digestion, derivatization, and fluctuation of nanoESI efficiency in the LC-MS analysis of permethylated N-glycans released from model glycoproteins, human blood serum, and breast cancer cell line. We observed an unanticipated degradation of isotope labeled glycans, tracked a source of such degradation, and optimized a sample preparation protocol to minimize degradation of the internal standard glycans. All results indicated the effectiveness of using iGlycoMab to minimize errors originating from sample handling and instruments. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The effects of isotope-labeled analogs on the LC-IDMS measurement by comparison of ESI responses and matrix effect of melamine, 13C3-melamine, 13C3+15N3-melamine, and 15N3-melamine.

PubMed

Li, Xiu Qin; Zhang, Qing He; Yang, Zong; Li, Hong Mei; Huang, Dong Feng

2017-05-01

In this paper, the effect of isotope-labeled analogs on the liquid chromatography-isotope dilution mass spectrometry (LC-IDMS) measurement was evaluated based on the comparison research of electrospray ionization responses (ESI) and matrix effect of melamine, 13 C 3 -melamine, 13 C 3 + 15 N 3 -melamine, and 15 N 3 -melamine. The isotope-labeled melamines had similar ionization efficiency with melamine in the electrospray ionization source, but the intensity of corresponding quantitative fragment ions had distinctive differences. Based on the density functional theory at the B3LYP/6-311+G** level, this phenomenon was explained very well. The rare cleavage pathways of melamine, which just could be exactly identified by 15 N-labeled melamines, resulted in the difference of quantitative fragment ions between 15 N-labeled melamines and melamine. The interaction of ESI response between melamine and isotope-labeled melamines was investigated using MRM monitor mode. 15 N-labeled melamine had significant ion inter-suppression effect on melamine, while 13 C-labeled melamine had little influence on melamine. Finally, the influence of different isotope-labeled melamines on the LC-IDMS result was evaluated using the IDMS correction factor (θ). Taking the determination of melamine in milk powder as an example, the matrix effects of different isotope-labeled melamines and melamine had notable difference and the impact of this difference on the measurement results depended on the concentrations of analyte and matrix solution. It was worth noting that 15 N 3 -melamine exhibited significant ion suppression to melamine in matrix solution. The deviation of the results from IDMS method might reach 59% using 15 N 3 -melamine as internal standard in special matrix solution. Graphical Abstract The comparison of ESI responses of melamine, 13 C 3 -melamine, 13 C 3 + 15 N 3 -melamine and 15 N 3 -melamine.

Dual-labeling method for electron microscopy to characterize synaptic connectivity using genetically encoded fluorescent reporters in Drosophila

PubMed Central

Tanaka, Nobuaki K.; Dye, Louis; Stopfer, Mark

2010-01-01

Light and electron microscopy (LM and EM) both offer important advantages for characterizing neuronal circuitry in intact brains: LM can reveal the general patterns neurons trace between brain areas, and EM can confirm synaptic connections between identified neurons within a small area. In a few species, genetic labeling with fluorescent proteins has been used with LM to visualize many kinds of neurons and to analyze their morphologies and projection patterns. However, combining these large-scale patterns with the fine detail available in EM analysis has been a technical challenge. To analyze the synaptic connectivity of neurons expressing fluorescent markers with EM, we developed a dual-labeling method for use with pre-embedded brains. In Drosophila expressing genetic labels and also injected with markers we visualized synaptic connections among two populations of neurons in the AL, one of which has been shown to mediate a specific function, odor evoked neural oscillation. PMID:21074556

A new dimethyl labeling-based SID-MRM-MS method and its application to three proteases involved in insulin maturation.

PubMed

Cheng, Dongwan; Zheng, Li; Hou, Junjie; Wang, Jifeng; Xue, Peng; Yang, Fuquan; Xu, Tao

2015-01-01

The absolute quantification of target proteins in proteomics involves stable isotope dilution coupled with multiple reactions monitoring mass spectrometry (SID-MRM-MS). The successful preparation of stable isotope-labeled internal standard peptides is an important prerequisite for the SID-MRM absolute quantification methods. Dimethyl labeling has been widely used in relative quantitative proteomics and it is fast, simple, reliable, cost-effective, and applicable to any protein sample, making it an ideal candidate method for the preparation of stable isotope-labeled internal standards. MRM mass spectrometry is of high sensitivity, specificity, and throughput characteristics and can quantify multiple proteins simultaneously, including low-abundance proteins in precious samples such as pancreatic islets. In this study, a new method for the absolute quantification of three proteases involved in insulin maturation, namely PC1/3, PC2 and CPE, was developed by coupling a stable isotope dimethyl labeling strategy for internal standard peptide preparation with SID-MRM-MS quantitative technology. This method offers a new and effective approach for deep understanding of the functional status of pancreatic β cells and pathogenesis in diabetes.

In vivo characterization of the novel CD44v6-targeting Fab fragment AbD15179 for molecular imaging of squamous cell carcinoma: a dual-isotope study

PubMed Central

2014-01-01

Background Patients with squamous cell carcinoma in the head and neck region (HNSCC) offer a diagnostic challenge due to difficulties to detect small tumours and metastases. Imaging methods available are not sufficient, and radio-immunodiagnostics could increase specificity and sensitivity of diagnostics. The objective of this study was to evaluate, for the first time, the in vivo properties of the radiolabelled CD44v6-targeting fragment AbD15179 and to assess its utility as a targeting agent for radio-immunodiagnostics of CD44v6-expressing tumours. Methods The fully human CD44v6-targeting Fab fragment AbD15179 was labelled with 111In or 125I, as models for radionuclides suitable for imaging with SPECT or PET. Species specificity, antigen specificity and internalization properties were first assessed in vitro. In vivo specificity and biodistribution were then evaluated in tumour-bearing mice using a dual-tumour and dual-isotope setup. Results Both species-specific and antigen-specific binding of the conjugates were demonstrated in vitro, with no detectable internalization. The in vivo studies demonstrated specific tumour binding and favourable tumour targeting properties for both conjugates, albeit with higher tumour uptake, slower tumour dissociation, higher tumour-to-blood ratio and higher CD44v6 sensitivity for the 111In-labelled fragment. In contrast, the 125I-Fab demonstrated more favourable tumour-to-organ ratios for liver, spleen and kidneys. Conclusions We conclude that AbD15179 efficiently targets CD44v6-expressing squamous cell carcinoma xenografts, and particularly, the 111In-Fab displayed high and specific tumour uptake. CD44v6 emerges as a suitable target for radio-immunodiagnostics, and a fully human antibody fragment such as AbD15179 can enable further clinical imaging studies. PMID:24598405

Envelope: interactive software for modeling and fitting complex isotope distributions.

PubMed

Sykes, Michael T; Williamson, James R

2008-10-20

An important aspect of proteomic mass spectrometry involves quantifying and interpreting the isotope distributions arising from mixtures of macromolecules with different isotope labeling patterns. These patterns can be quite complex, in particular with in vivo metabolic labeling experiments producing fractional atomic labeling or fractional residue labeling of peptides or other macromolecules. In general, it can be difficult to distinguish the contributions of species with different labeling patterns to an experimental spectrum and difficult to calculate a theoretical isotope distribution to fit such data. There is a need for interactive and user-friendly software that can calculate and fit the entire isotope distribution of a complex mixture while comparing these calculations with experimental data and extracting the contributions from the differently labeled species. Envelope has been developed to be user-friendly while still being as flexible and powerful as possible. Envelope can simultaneously calculate the isotope distributions for any number of different labeling patterns for a given peptide or oligonucleotide, while automatically summing these into a single overall isotope distribution. Envelope can handle fractional or complete atom or residue-based labeling, and the contribution from each different user-defined labeling pattern is clearly illustrated in the interactive display and is individually adjustable. At present, Envelope supports labeling with 2H, 13C, and 15N, and supports adjustments for baseline correction, an instrument accuracy offset in the m/z domain, and peak width. Furthermore, Envelope can display experimental data superimposed on calculated isotope distributions, and calculate a least-squares goodness of fit between the two. All of this information is displayed on the screen in a single graphical user interface. Envelope supports high-quality output of experimental and calculated distributions in PNG or PDF format. Beyond simply

Isotopic measurements (C,N,O) of detonation soot produced from labeled and unlabeled Composition B-3 indicate source of solid carbon residues

NASA Astrophysics Data System (ADS)

Podlesak, David; Manner, Virginia; Amato, Ronald; Dattelbaum, Dana; Gusavsen, Richard; Huber, Rachel

2017-06-01

Detonation of HE is an exothermic process whereby metastable complex molecules are converted to simple stable molecules such as H2 O, N2, CO, CO2, and solid carbon. The solid carbon contains various allotropes such as detonation nanodiamonds, graphite, and amorphous carbon. It is well known that certain HE formulations such as Composition B (60% RDX, 40% TNT) produce greater amounts of solid carbon than other more oxygen-balanced formulations. To develop a greater understanding of how formulation and environment influence solid carbon formation, we synthesized TNT and RDX with 13 C and 15 N at levels slightly above natural abundance levels. Synthesized RDX and TNT were mixed at a ratio of 60:40 to form Composition B and solid carbon residues were collected from detonations of isotopically-labeled as well as un-labelled Composition B. The raw HE and detonation residues were analyzed isotopically for C, N, O isotopic compositions. We will discuss differences between treatments groups as a function of formulation and environment. LA-UR - 17-21266.

Insights on the marine microbial nitrogen cycle from isotopic approaches to nitrification

PubMed Central

Casciotti, Karen L.; Buchwald, Carolyn

2012-01-01

The microbial nitrogen (N) cycle involves a variety of redox processes that control the availability and speciation of N in the environment and that are involved with the production of nitrous oxide (N2O), a climatically important greenhouse gas. Isotopic measurements of ammonium (NH+4), nitrite (NO−2), nitrate (NO−3), and N2O can now be used to track the cycling of these compounds and to infer their sources and sinks, which has lead to new and exciting discoveries. For example, dual isotope measurements of NO−3 and NO−2 have shown that there is NO−3 regeneration in the ocean's euphotic zone, as well as in and around oxygen deficient zones (ODZs), indicating that nitrification may play more roles in the ocean's N cycle than generally thought. Likewise, the inverse isotope effect associated with NO−2 oxidation yields unique information about the role of this process in NO−2 cycling in the primary and secondary NO−2 maxima. Finally, isotopic measurements of N2O in the ocean are indicative of an important role for nitrification in its production. These interpretations rely on knowledge of the isotope effects for the underlying microbial processes, in particular ammonia oxidation and nitrite oxidation. Here we review the isotope effects involved with the nitrification process and the insights provided by this information, then provide a prospectus for future work in this area. PMID:23091468

Insights on the marine microbial nitrogen cycle from isotopic approaches to nitrification.

PubMed

Casciotti, Karen L; Buchwald, Carolyn

2012-01-01

The microbial nitrogen (N) cycle involves a variety of redox processes that control the availability and speciation of N in the environment and that are involved with the production of nitrous oxide (N(2)O), a climatically important greenhouse gas. Isotopic measurements of ammonium (NH(+) (4)), nitrite (NO(-) (2)), nitrate (NO(-) (3)), and N(2)O can now be used to track the cycling of these compounds and to infer their sources and sinks, which has lead to new and exciting discoveries. For example, dual isotope measurements of NO(-) (3) and NO(-) (2) have shown that there is NO(-) (3) regeneration in the ocean's euphotic zone, as well as in and around oxygen deficient zones (ODZs), indicating that nitrification may play more roles in the ocean's N cycle than generally thought. Likewise, the inverse isotope effect associated with NO(-) (2) oxidation yields unique information about the role of this process in NO(-) (2) cycling in the primary and secondary NO(-) (2) maxima. Finally, isotopic measurements of N(2)O in the ocean are indicative of an important role for nitrification in its production. These interpretations rely on knowledge of the isotope effects for the underlying microbial processes, in particular ammonia oxidation and nitrite oxidation. Here we review the isotope effects involved with the nitrification process and the insights provided by this information, then provide a prospectus for future work in this area.

Dual-isotope Cryo-imaging Quantitative Autoradiography (CIQA): Anvestigating Antibody-Drug Conjugate Distribution And Payload Delivery Through Imaging.

PubMed

Ilovich, Ohad; Qutaish, Mohammed; Hesterman, Jacob; Orcutt, Kelly; Hoppin, Jack; Polyak, Ildiko; Seaman, Marc; Abu-Yousif, Adnan; Cvet, Donna; Bradley, Daniel

2018-05-04

In vitro properties of antibody drug conjugates (ADCs) such as binding, internalization, and cytotoxicity are often well characterized prior to in vivo studies. Interpretation of in vivo studies could significantly be enhanced by molecular imaging tools. We present here a dual-isotope cryo-imaging quantitative autoradiography (CIQA) methodology combined with advanced 3D imaging and analysis allowing for the simultaneous study of both antibody and payload distribution in tissues of interest. in a pre-clinical setting. Methods: TAK-264, an investigational anti-guanylyl cyclase C (GCC) targeting ADC was synthesized utilizing tritiated Monomethyl auristatin E (MMAE). The tritiated ADC was then conjugated to DTPA, labeled with indium-111 and evaluated in vivo in GCC-positive and GCC-negative tumor-bearing animals. Results: Cryo-imaging Quantitative Autoradiography (CIQA) reveals the time course of drug release from ADC and its distribution into various tumor regions seemingly impenetrablethat are less accessible to the antibody. For GCC-positive tumors, a representative section obtained 96 hours post tracer injection showed only 0.8% of the voxels have co-localized signal versus over 15% of the voxels for a GCC-negative tumor section., suggesting successful and specific cleaving of the toxin in the antigen positive lesions. Conclusion: The combination of a veteran established autoradiography technology with advanced image analysis methodologies affords an experimental tool that can support detailed characterization of ADC tumor penetration and pharmacokinetics. Copyright © 2018 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Expression and purification of isotopically labeled peptide inhibitors and substrates of cAMP-dependant protein kinase A for NMR analysis.

PubMed

Masterson, Larry R; Bortone, Nadia; Yu, Tao; Ha, Kim N; Gaffarogullari, Ece C; Nguyen, Oanh; Veglia, Gianluigi

2009-04-01

Extensive X-ray crystallographic studies carried out on the catalytic-subunit of protein kinase A (PKA-C) enabled the atomic characterization of inhibitor and/or substrate peptide analogues trapped at its active site. Yet, the structural and dynamic transitions of these peptides from the free to the bound state are missing. These conformational transitions are central to understanding molecular recognition and the enzymatic cycle. NMR spectroscopy allows one to study these phenomena under functionally relevant conditions. However, the amounts of isotopically labeled peptides required for this technique present prohibitive costs for solid-phase peptide synthesis. To enable NMR studies, we have optimized both expression and purification of isotopically enriched substrate/inhibitor peptides using a recombinant fusion protein system. Three of these peptides correspond to the cytoplasmic regions of the wild-type and lethal mutants of the membrane protein phospholamban, while the fourth peptide correspond to the binding epitope of the heat-stable protein kinase inhibitor (PKI(5-24)). The target peptides were fused to the maltose binding protein (MBP), which is further purified using a His(6) tag approach. This convenient protocol allows for the purification of milligram amounts of peptides necessary for NMR analysis.

Analysis of the differentially expressed low molecular weight peptides in human serum via an N-terminal isotope labeling technique combining nano-liquid chromatography/matrix-assisted laser desorption/ionization mass spectrometry.

PubMed

Leng, Jiapeng; Zhu, Dong; Wu, Duojiao; Zhu, Tongyu; Zhao, Ningwei; Guo, Yinlong

2012-11-15

Peptidomics analysis of human serum is challenging due to the low abundance of serum peptides and interference from the complex matrix. This study analyzed the differentially expressed (DE) low molecular weight peptides in human serum integrating a DMPITC-based N-terminal isotope labeling technique with nano-liquid chromatography and matrix-assisted laser desorption/ionization mass spectrometry (nano-LC/MALDI-MS). The workflow introduced a [d(6)]-4,6-dimethoxypyrimidine-2-isothiocyanate (DMPITC)-labeled mixture of aliquots from test samples as the internal standard. The spiked [d(0)]-DMPITC-labeled samples were separated by nano-LC then spotted on the MALDI target. Both quantitative and qualitative studies for serum peptides were achieved based on the isotope-labeled peaks. The DMPITC labeling technique combined with nano-LC/MALDI-MS not only minimized the errors in peptide quantitation, but also allowed convenient recognition of the labeled peptides due to the 6 Da mass difference. The data showed that the entire research procedure as well as the subsequent data analysis method were effective, reproducible, and sensitive for the analysis of DE serum peptides. This study successfully established a research model for DE serum peptides using DMPITC-based N-terminal isotope labeling and nano-LC/MALDI-MS. Application of the DMPITC-based N-terminal labeling technique is expected to provide a promising tool for the investigation of peptides in vivo, especially for the analysis of DE peptides under different biological conditions. Copyright © 2012 John Wiley & Sons, Ltd.

Cross-Course Collaboration in the Undergraduate Chemistry Curriculum: Isotopic Labeling with Sodium Borodeuteride in the Introductory Organic Chemistry Laboratory

ERIC Educational Resources Information Center

Kjonaas, Richard A.; Fitch, Richard W.; Noll, Robert J.

2017-01-01

A microscale isotopic labeling experiment is described for the introductory organic chemistry laboratory course wherein half of the students use sodium borohydride (NaBH[subscript 4]) and the other half use sodium borodeuteride (NaBD[subscript 4]) to reduce acetophenone to 1-phenylethanol and then compare spectral data. The cost is reasonable, and…

Protein-based stable isotope probing.

PubMed

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

2010-12-01

We describe a stable isotope probing (SIP) technique that was developed to link microbe-specific metabolic function to phylogenetic information. Carbon ((13)C)- or nitrogen ((15)N)-labeled substrates (typically with >98% heavy label) were used in cultivation experiments and the heavy isotope incorporation into proteins (protein-SIP) on growth was determined. The amount of incorporation provides a measure for assimilation of a substrate, and the sequence information from peptide analysis obtained by mass spectrometry delivers phylogenetic information about the microorganisms responsible for the metabolism of the particular substrate. In this article, we provide guidelines for incubating microbial cultures with labeled substrates and a protocol for protein-SIP. The protocol guides readers through the proteomics pipeline, including protein extraction, gel-free and gel-based protein separation, the subsequent mass spectrometric analysis of peptides and the calculation of the incorporation of stable isotopes into peptides. Extraction of proteins and the mass fingerprint measurements of unlabeled and labeled fractions can be performed in 2-3 d.

Sauna, sweat and science - quantifying the proportion of condensation water versus sweat using a stable water isotope ((2)H/(1)H and (18)O/(16)O) tracer experiment.

PubMed

Zech, Michael; Bösel, Stefanie; Tuthorn, Mario; Benesch, Marianne; Dubbert, Maren; Cuntz, Matthias; Glaser, Bruno

2015-01-01

Most visitors of a sauna appreciate the heat pulse that is perceived when water is poured on the stones of a sauna stove. However, probably only few bathers are aware that this pleasant heat pulse is caused by latent heat being released onto our skin due to condensation of water vapour. In order to quantify the proportion of condensation water versus sweat to dripping water of test persons we conducted sauna experiments using isotopically labelled (δ(18)O and δ(2)H) thrown water as tracer. This allows differentiating between 'pure sweat' and 'condensation water'. Two ways of isotope mass balance calculations were applied and yielded similar results for both water isotopes. Accordingly, condensation contributed considerably to dripping water with mean proportions of 52 ± 12 and 54 ± 7% in a sauna experiment in winter semester 2011/12 and 30 ± 13 and 33 ± 6% in a sauna experiment in winter semester 2012/13, respectively, depending on the way of calculating the isotope mass balance. It can be concluded from the results of our dual isotope labelling sauna experiment that it is not all about sweat in the sauna.

Stable Isotope Labeling, in Vivo, of d- and l-Tryptophan Pools in Lemna gibba and the Low Incorporation of Label into Indole-3-Acetic Acid 1

PubMed Central

Baldi, Bruce G.; Maher, Barbara R.; Slovin, Janet Pernise; Cohen, Jerry D.

1991-01-01

We present evidence that the role of tryptophan and other potential intermediates in the pathways that could lead to indole derivatives needs to be reexamined. Two lines of Lemna gibba were tested for uptake of [15N-indole]-labeled tryptophan isomers and incorporation of that label into free indole-3-acetic acid (IAA). Both lines required levels of l-[15N]tryptophan 2 to 3 orders of magnitude over endogenous levels in order to obtain measurable incorporation of label into IAA. Labeled l-tryptophan was extractable from plant tissue after feeding and showed no measurable isomerization into d-tryptophan. d-[15N]tryptophan supplied to Lemna at rates of approximately 400 times excess of endogenous d-tryptophan levels (to yield an isotopic enrichment equal to that which allowed detection of the incorporation of l-tryptophan into IAA), did not result in measurable incorporation of label into free IAA. These results demonstrate that l-tryptophan is a more direct precursor to IAA than the d isomer and suggest (a) that the availability of tryptophan in vivo is not a limiting factor in the biosynthesis of IAA, thus implying that other regulatory mechanisms are in operation and (b) that l-tryptophan also may not be a primary precursor to IAA in plants. PMID:16668112

Extrinsic labeling method may not accurately measure Fe absorption from cooked pinto beans (Phaseolus vulgaris): comparison of extrinsic and intrinsic labeling of beans.

PubMed

Jin, Fuxia; Cheng, Zhiqiang; Rutzke, Michael A; Welch, Ross M; Glahn, Raymond P

2008-08-27

Isotopic labeling of food has been widely used for the measurement of Fe absorption in determining requirements and evaluating the factors involved in Fe bioavailability. An extrinsic labeling technique will not accurately predict the total Fe absorption from foods unless complete isotopic exchange takes place between an extrinsically added isotope label and the intrinsic Fe of the food. We examined isotopic exchange in the case of both white beans and colored beans (Phaseolus vulgaris) with an in vitro digestion model. There are significant differences in (58)Fe/(56)Fe ratios between the sample digest supernatant and the pellet of extrinsically labeled pinto bean. The white bean digest shows significantly better equilibration of the extrinsic (58)Fe with the intrinsic (56)Fe. In contrast to the extrinsically labeled samples, both white and red beans labeled intrinsically with (58)Fe demonstrated consistent ratios of (58)Fe/(56)Fe in the bean meal, digest, supernatant, and pellet. It is possible that the polyphenolics in the bean seed coat may bind Fe and thus interfere with extrinsic labeling of the bean meals. These observations raise questions on the accuracy of studies that used extrinsic tags to measure Fe absorption from beans. Intrinsic labeling appears necessary to accurately measure Fe bioavailability from beans.

Calculation and mitigation of isotopic interferences in liquid chromatography-mass spectrometry/mass spectrometry assays and its application in supporting microdose absolute bioavailability studies.

PubMed

Gu, Huidong; Wang, Jian; Aubry, Anne-Françoise; Jiang, Hao; Zeng, Jianing; Easter, John; Wang, Jun-sheng; Dockens, Randy; Bifano, Marc; Burrell, Richard; Arnold, Mark E

2012-06-05

A methodology for the accurate calculation and mitigation of isotopic interferences in liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) assays and its application in supporting microdose absolute bioavailability studies are reported for the first time. For simplicity, this calculation methodology and the strategy to minimize the isotopic interference are demonstrated using a simple molecule entity, then applied to actual development drugs. The exact isotopic interferences calculated with this methodology were often much less than the traditionally used, overestimated isotopic interferences simply based on the molecular isotope abundance. One application of the methodology is the selection of a stable isotopically labeled internal standard (SIL-IS) for an LC-MS/MS bioanalytical assay. The second application is the selection of an SIL analogue for use in intravenous (i.v.) microdosing for the determination of absolute bioavailability. In the case of microdosing, the traditional approach of calculating isotopic interferences can result in selecting a labeling scheme that overlabels the i.v.-dosed drug or leads to incorrect conclusions on the feasibility of using an SIL drug and analysis by LC-MS/MS. The methodology presented here can guide the synthesis by accurately calculating the isotopic interferences when labeling at different positions, using different selective reaction monitoring (SRM) transitions or adding more labeling positions. This methodology has been successfully applied to the selection of the labeled i.v.-dosed drugs for use in two microdose absolute bioavailability studies, before initiating the chemical synthesis. With this methodology, significant time and cost saving can be achieved in supporting microdose absolute bioavailability studies with stable labeled drugs.

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

PubMed Central

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

2008-01-01

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

Incorporation of {sup 13}C-labeled intermediates into developing lignin revealed by analytical pyrolysis and CuO oxidation in combination with IRM-GC-MS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eglinton, T.I.; Goni, M.A.; Boon, J.J.

1995-12-31

Tissue samples from Ginkgo shoots (Ginkgo biloba L.) and Rice grass (Oryzasitiva sp.) incubated in the presence of {sup 13}C-labeled substrates such as coniferin (postulated to be biosynthetic intermediates in lignin biosynthesis) were studied using thermal and chemical dissociation methods in combination with molecular-level isotopic measurements. The aim of the study was (1) to investigate dissociation mechanisms, and (2) to examine and quantify the proportions of labeled material incorporated within each sample. Isotopic analysis of specific dissociation products revealed the presence of the label in its original positions, and only within lignin-derived (phenolic) products. Moreover, the distribution and isotopic compositionmore » of the dissociation products strongly suggest an origin from newly-formed lignin. These results clearly indicate that there is no {open_quotes}scrambling{close_quotes} of carbon atoms as a result of the dissociation process, thereby lending support to this analytical approach. In addition, the data provide confidence in the selective labeling approach for elucidation of the structure and biosynthesis of lignin.« less

Development of High-Performance Chemical Isotope Labeling LC-MS for Profiling the Carbonyl Submetabolome.

PubMed

Zhao, Shuang; Dawe, Margot; Guo, Kevin; Li, Liang

2017-06-20

Metabolites containing a carbonyl group represent several important classes of molecules including various forms of ketones and aldehydes such as steroids and sugars. We report a high-performance chemical isotope labeling (CIL) LC-MS method for profiling the carbonyl submetabolome with high coverage and high accuracy and precision of relative quantification. This method is based on the use of dansylhydrazine (DnsHz) labeling of carbonyl metabolites to change their chemical and physical properties to such an extent that the labeled metabolites can be efficiently separated by reversed phase LC and ionized by electrospray ionization MS. In the analysis of six standards representing different carbonyl classes, acetaldehyde could be ionized only after labeling and MS signals were significantly increased for other 5 standards with an enhancement factor ranging from ∼15-fold for androsterone to ∼940-fold for 2-butanone. Differential 12 C- and 13 C-DnsHz labeling was developed for quantifying metabolic differences in comparative samples where individual samples were separately labeled with 12 C-labeling and spiked with a 13 C-labeled pooled sample, followed by LC-MS analysis, peak pair picking, and peak intensity ratio measurement. In the replicate analysis of a 1:1 12 C-/ 13 C-labeled human urine mixture (n = 6), an average of 2030 ± 39 pairs per run were detected with 1737 pairs in common, indicating the possibility of detecting a large number of carbonyl metabolites as well as high reproducibility of peak pair detection. The average RSD of the peak pair ratios was 7.6%, and 95.6% of the pairs had a RSD value of less than 20%, demonstrating high precision for peak ratio measurement. In addition, the ratios of most peak pairs were close to the expected value of 1.0 (e.g., 95.5% of them had ratios of between 0.67 and 1.5), showing the high accuracy of the method. For metabolite identification, a library of DnsHz-labeled standards was constructed, including 78 carbonyl

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

PubMed

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

2013-10-09

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

Novel diagnostics of metabolic dysfunction detected in breath and plasma by selective isotope-assisted labeling.

PubMed

Haviland, Julia A; Tonelli, Marco; Haughey, Dermot T; Porter, Warren P; Assadi-Porter, Fariba M

2012-08-01

Metabolomics is the study of a unique fingerprint of small molecules present in biological systems under healthy and disease conditions. One of the major challenges in metabolomics is validation of fingerprint molecules to identify specifically perturbed pathways in metabolic aberrations. This step is crucial to the understanding of budding metabolic pathologies and the ability to identify early indicators of common diseases such as obesity, type 2 diabetes mellitus, metabolic syndrome, polycystic ovary syndrome, and cancer. We present a novel approach to diagnosing aberrations in glucose utilization including metabolic pathway switching in a disease state. We used a well-defined prenatally exposed glucocorticoid mouse model that results in adult females with metabolic dysfunction. We applied the complementary technologies of nuclear magnetic resonance spectroscopy and cavity ring-down spectroscopy to analyze serial plasma samples and real-time breath measurements following selective (13)C-isotope-assisted labeling. These platforms allowed us to trace metabolic markers in whole animals and identify key metabolic pathway switching in prenatally glucocorticoid-treated animals. Total glucose flux is significantly proportionally increased through the major oxidative pathways of glycolysis and the pentose phosphate pathway in the prenatally glucocorticoid-treated animals relative to the control animals. This novel diagnostics approach is fast, noninvasive, and sensitive for determining specific pathway utilization, and provides a direct translational application in the health care field. Copyright © 2012 Elsevier Inc. All rights reserved.

Variability of 13C-labeling in plant leaves.

PubMed

Nguyen Tu, Thanh Thuy; Biron, Philippe; Maseyk, Kadmiel; Richard, Patricia; Zeller, Bernd; Quénéa, Katell; Alexis, Marie; Bardoux, Gérard; Vaury, Véronique; Girardin, Cyril; Pouteau, Valérie; Billiou, Daniel; Bariac, Thierry

2013-09-15

Plant tissues artificially labeled with (13)C are increasingly used in environmental studies to unravel biogeochemical and ecophysiological processes. However, the variability of (13)C-content in labeled tissues has never been carefully investigated. Hence, this study aimed at documenting the variability of (13)C-content in artificially labeled leaves. European beech and Italian ryegrass were subjected to long-term (13)C-labeling in a controlled-environment growth chamber. The (13)C-content of the leaves obtained after several months labeling was determined by isotope ratio mass spectrometry. The (13)C-content of the labeled leaves exhibited inter- and intra-leaf variability much higher than those naturally occurring in unlabeled plants, which do not exceed a few per mil. This variability was correlated with labeling intensity: the isotope composition of leaves varied in ranges of ca 60‰ and 90‰ for experiments that led to average leaf (13)C-content of ca +15‰ and +450‰, respectively. The reported variability of isotope composition in (13)C-enriched leaves is critical, and should be taken into account in subsequent experimental investigations of environmental processes using (13)C-labeled plant tissues. Copyright © 2013 John Wiley & Sons, Ltd.

Propagation of human corneal endothelial cells: a novel dual media approach.

PubMed

Peh, Gary S L; Chng, Zhenzhi; Ang, Heng-Pei; Cheng, Terence Y D; Adnan, Khadijah; Seah, Xin-Yi; George, Benjamin L; Toh, Kah-Peng; Tan, Donald T; Yam, Gary H F; Colman, Alan; Mehta, Jodhbir S

2015-01-01

Corneal endothelium-associated corneal blindness is the most common indication for corneal transplantation. Restorative corneal transplant surgery is the only option to reverse the blindness, but a global shortage of donor material remains an issue. There are immense clinical interests in the development of alternative treatment strategies to alleviate current reliance on donor materials. For such endeavors, ex vivo propagation of human corneal endothelial cells (hCECs) is required, but current methodology lacks consistency, with expanded hCECs losing cellular morphology to a mesenchymal-like transformation. In this study, we describe a novel dual media culture approach for the in vitro expansion of primary hCECs. Initial characterization included analysis of growth dynamics of hCECs grown in either proliferative (M4) or maintenance (M5) medium. Subsequent comparisons were performed on isolated hCECs cultured in M4 alone against cells expanded using the dual media approach. Further characterizations were performed using immunocytochemistry, quantitative real-time PCR, and gene expression microarray. At the third passage, results showed that hCECs propagated using the dual media approach were homogeneous in appearance, retained their unique polygonal cellular morphology, and expressed higher levels of corneal endothelium-associated markers in comparison to hCECs cultured in M4 alone, which were heterogeneous and fibroblastic in appearance. Finally, for hCECs cultured using the dual media approach, global gene expression and pathway analysis between confluent hCECs before and after 7-day exposure to M5 exhibited differential gene expression associated predominately with cell proliferation and wound healing. These findings showed that the propagation of primary hCECs using the novel dual media approach presented in this study is a consistent method to obtain bona fide hCECs. This, in turn, will elicit greater confidence in facilitating downstream development of

Molecular imaging needles: dual-modality optical coherence tomography and fluorescence imaging of labeled antibodies deep in tissue

PubMed Central

Scolaro, Loretta; Lorenser, Dirk; Madore, Wendy-Julie; Kirk, Rodney W.; Kramer, Anne S.; Yeoh, George C.; Godbout, Nicolas; Sampson, David D.; Boudoux, Caroline; McLaughlin, Robert A.

2015-01-01

Molecular imaging using optical techniques provides insight into disease at the cellular level. In this paper, we report on a novel dual-modality probe capable of performing molecular imaging by combining simultaneous three-dimensional optical coherence tomography (OCT) and two-dimensional fluorescence imaging in a hypodermic needle. The probe, referred to as a molecular imaging (MI) needle, may be inserted tens of millimeters into tissue. The MI needle utilizes double-clad fiber to carry both imaging modalities, and is interfaced to a 1310-nm OCT system and a fluorescence imaging subsystem using an asymmetrical double-clad fiber coupler customized to achieve high fluorescence collection efficiency. We present, to the best of our knowledge, the first dual-modality OCT and fluorescence needle probe with sufficient sensitivity to image fluorescently labeled antibodies. Such probes enable high-resolution molecular imaging deep within tissue. PMID:26137379

pH-regulated formation of side products in the reductive amination approach for differential labeling of peptides in relative quantitative experiments.

PubMed

Levi Mortera, Stefano; Dioni, Ilaria; Greco, Viviana; Neri, Cristina; Rovero, Paolo; Urbani, Andrea

2014-05-01

Among the most common stable-isotope labeling strategies, the reaction of formaldehyde with peptides in the presence of NaCNBH₃ features many attractive aspects that are conducive to its employment in quantitation experiments in proteomics. Reductive amination, with formaldehyde and d(2)-formaldehyde, is reported to be a fast, easy, and specific reaction, undoubtedly inexpensive if compared with commercially available kits for differential isotope coding. Acetaldehyde and d(4)-acetaldehyde could be employed as well without a substantial increase in terms of cost, and should provide a wider spacing between the differentially tagged peptides in the mass spectrum. Nevertheless, only a single paper reports about a diethylation approach for quantitation. We undertook a systematic analytical investigation on the reductive amination of some standard peptides pointing out the occasional occurrence of side reactions in dependence of pH or reagents order of addition, particularly observing the formation of cyclic adducts ascribable to rearrangements involving the generated Schiff-base and all the nucleophilic sites of its chemical environment. We also tried to evaluate how much this side-products amount may impair isotope coded relative quantitation.

The calibration of the intramolecular nitrogen isotope distribution in nitrous oxide measured by isotope ratio mass spectrometry.

PubMed

Westley, Marian B; Popp, Brian N; Rust, Terri M

2007-01-01

Two alternative approaches for the calibration of the intramolecular nitrogen isotope distribution in nitrous oxide using isotope ratio mass spectrometry have yielded a difference in the 15N site preference (defined as the difference between the delta15N of the central and end position nitrogen in NNO) of tropospheric N2O of almost 30 per thousand. One approach is based on adding small amounts of labeled 15N2O to the N2O reference gas and tracking the subsequent changes in m/z 30, 31, 44, 45 and 46, and this yields a 15N site preference of 46.3 +/- 1.4 per thousand for tropospheric N2O. The other involves the synthesis of N2O by thermal decomposition of isotopically characterized ammonium nitrate and yields a 15N site preference of 18.7 +/- 2.2 per thousand for tropospheric N2O. Both approaches neglect to fully account for isotope effects associated with the formation of NO+ fragment ions from the different isotopic species of N2O in the ion source of a mass spectrometer. These effects vary with conditions in the ion source and make it impossible to reproduce a calibration based on the addition of isotopically enriched N2O on mass spectrometers with different ion source configurations. These effects have a much smaller impact on the comparison of a laboratory reference gas with N2O synthesized from isotopically characterized ammonium nitrate. This second approach was successfully replicated and leads us to advocate the acceptance of the site preference value 18.7 +/- 2.2 per thousand for tropospheric N2O as the provisional community standard until further independent calibrations are developed and validated. We present a technique for evaluating the isotope effects associated with fragment ion formation and revised equations for converting ion signal ratios into isotopomer ratios. Copyright 2007 John Wiley & Sons, Ltd.

Isotope-labelled urea to test colon drug delivery devices in vivo: principles, calculations and interpretations.

PubMed

Maurer, Marina J M; Schellekens, Reinout C A; Wutzke, Klaus D; Stellaard, Frans

2013-01-01

This paper describes various methodological aspects that were encountered during the development of a system to monitor the in vivo behaviour of a newly developed colon delivery device that enables oral drug treatment of inflammatory bowel diseases. [(13)C]urea was chosen as the marker substance. Release of [(13)C]urea in the ileocolonic region is proven by the exhalation of (13)CO2 in breath due to bacterial fermentation of [(13)C]urea. The (13)CO2 exhalation kinetics allows the calculation of a lag time as marker for delay of release, a pulse time as marker for the speed of drug release and the fraction of the dose that is fermented. To determine the total bioavailability, also the fraction of the dose absorbed from the intestine must be quantified. Initially, this was done by calculating the time-dependent [(13)C]urea appearance in the body urea pool via measurement of (13)C abundance and concentration of plasma urea. Thereafter, a new methodology was successfully developed to obtain the bioavailability data by measurement of the urinary excretion rate of [(13)C]urea. These techniques required two experimental days, one to test the coated device, another to test the uncoated device to obtain reference values for the situation that 100 % of [(13)C]urea is absorbed. This is hampered by large day-to-day variations in urea metabolism. Finally, a completely non-invasive, one-day test was worked out based on a dual isotope approach applying a simultaneous administration of [(13)C]urea in a coated device and [(15)N2]urea in an uncoated device. All aspects of isotope-related analytical methodologies and required calculation and correction systems are described.

Performance comparison of single and dual metal dielectrically modulated TFETs for the application of label free biosensor

NASA Astrophysics Data System (ADS)

Verma, Madhulika; Sharma, Dheeraj; Pandey, Sunil; Nigam, Kaushal; Kondekar, P. N.

2017-01-01

In this work, we perform a comparative analysis between single and dual metal dielectrically modulated tunnel field-effect transistors (DMTFETs) for the application of label free biosensor. For this purpose, two different gate material with work-function as ϕM 1 and ϕM 2 are used in short-gate DMTFET, where ϕM 1 represents the work-function of gate M1 near to the drain end, while ϕM 2 denotes the work-function of gate M2 near to the source end. A nanogap cavity in the gate dielectric is formed by removing the selected portion of gate oxide for sensing the biomolecules. To investigate the sensitivity of these biosensors, dielectric constant and charge density within the cavity region are considered as governing parameters. The work-function of gate M2 is optimized and considered less than M1 to achieve abruptness at the source/channel junction, which results in better tunneling and improved ON-state current. The ATLAS device simulations show that dual metal SG-DMTFETs attains higher ON-state current and drain current sensitivity as compared to its counterpart device. Finally, a dual metal short-gate (DSG) biosensor is compared with the single metal short-gate (SG), single metal full-gate (FG), and dual metal full-gate (DFG) biosensors to analyse structurally enhanced conjugation effect on gate-channel coupling.

Chloroformate derivatization for tracing the fate of Amino acids in cells and tissues by multiple stable isotope resolved metabolomics (mSIRM).

PubMed

Yang, Ye; Fan, Teresa W-M; Lane, Andrew N; Higashi, Richard M

2017-07-11

Amino acids have crucial roles in central metabolism, both anabolic and catabolic. To elucidate these roles, steady-state concentrations of amino acids alone are insufficient, as each amino acid participates in multiple pathways and functions in a complex network, which can also be compartmentalized. Stable Isotope-Resolved Metabolomics (SIRM) is an approach that uses atom-resolved tracking of metabolites through biochemical transformations in cells, tissues, or whole organisms. Using different elemental stable isotopes to label multiple metabolite precursors makes it possible to resolve simultaneously the utilization of these precursors in a single experiment. Conversely, a single precursor labeled with two (or more) different elemental isotopes can trace the allocation of e.g. C and N atoms through the network. Such dual-label experiments however challenge the resolution of conventional mass spectrometers, which must distinguish the neutron mass differences among different elemental isotopes. This requires ultrahigh resolution Fourier transform mass spectrometry (UHR-FTMS). When combined with direct infusion nano-electrospray ion source (nano-ESI), UHR-FTMS can provide rapid, global, and quantitative analysis of all possible mass isotopologues of metabolites. Unfortunately, very low mass polar metabolites such as amino acids can be difficult to analyze by current models of UHR-FTMS, plus the high salt content present in typical cell or tissue polar extracts may cause unacceptable ion suppression for sources such as nano-ESI. Here we describe a modified method of ethyl chloroformate (ECF) derivatization of amino acids to enable rapid quantitative analysis of stable isotope labeled amino acids using nano-ESI UHR-FTMS. This method showed excellent linearity with quantifiable limits in the low nanomolar range represented in microgram quantities of biological specimens, which results in extracts with total analyte abundances in the low to sub-femtomole range. We have

Combination of diOlistic labeling with retrograde tract tracing and immunohistochemistry.

PubMed

Neely, M Diana; Stanwood, Gregg D; Deutch, Ariel Y

2009-11-15

Neuronal staining techniques have played a crucial role in the analysis of neuronal function. Several different staining techniques have been developed to allow morphological analyses of neurons. DiOlistic labeling, in which beads are coated with a lipophilic dye and then ballistically ejected onto brain tissue, has recently been introduced as a useful and simple means to label neurons and glia in their entirety. Although diOlistic labeling provides detailed information on the morphology of neurons, combining this approach with other staining methods is a significant advance. We have developed protocols that result in high quality diOlistically- and retrogradely-labeled or diOlistically-immunohistochemically labeled neurons. These dual-label methods require modification of fixation parameters and the restricted use of detergents for tissue permeabilization, and are readily applicable to a wide range of tracers and antibodies.

Combination of DiOlistic Labeling with Retrograde Tract Tracing and Immunohistochemistry

PubMed Central

Diana Neely, M.; Stanwood, Gregg D; Deutch, Ariel Y.

2009-01-01

Neuronal staining techniques have played a crucial role in the analysis of neuronal function. Several different staining techniques have been developed to allow morphological analyses of neurons. Recently diOlistic labeling, in which beads are coated with a lipophilic dye and then ballistically ejected onto brain tissue, has been developed as a useful and simple means to label neurons and glia in their entirety. Although diOlistic labeling provides detailed information on the morphology of neurons, combining this approach with other staining methods is a significant advance. We have developed protocols that result in high quality diOlistically- and retrogradely-labeled or diOlistically-immunohistochemically labeled neurons. These dual-label methods require modification of fixation parameters and the use of detergents for tissue permeabilization, and are readily applicable to a wide range of tracers and antibodies. PMID:19712695

Ratiometric fluorescent sensing of pH values in living cells by dual-fluorophore-labeled i-motif nanoprobes.

PubMed

Huang, Jin; Ying, Le; Yang, Xiaohai; Yang, Yanjing; Quan, Ke; Wang, He; Xie, Nuli; Ou, Min; Zhou, Qifeng; Wang, Kemin

2015-09-01

We designed a new ratiometric fluorescent nanoprobe for sensing pH values in living cells. Briefly, the nanoprobe consists of a gold nanoparticle (AuNP), short single-stranded oligonucleotides, and dual-fluorophore-labeled i-motif sequences. The short oligonucleotides are designed to bind with the i-motif sequences and immobilized on the AuNP surface via Au-S bond. At neutral pH, the dual fluorophores are separated, resulting in very low fluorescence resonance energy transfer (FRET) efficiency. At acidic pH, the i-motif strands fold into a quadruplex structure and leave the AuNP, bringing the dual fluorophores into close proximity, resulting in high FRET efficiency, which could be used as a signal for pH sensing. The nanoprobe possesses abilities of cellular transfection, enzymatic protection, fast response and quantitative pH detection. The in vitro and intracellular applications of the nanoprobe were demonstrated, which showed excellent response in the physiological pH range. Furthermore, our experimental results suggested that the nanoprobe showed excellent spatial and temporal resolution in living cells. We think that the ratiometric sensing strategy could potentially be applied to create a variety of new multicolor sensors for intracellular detection.

Tracking nitrate sources in the Chaohu Lake, China, using the nitrogen and oxygen isotopic approach.

PubMed

Yu, Qibiao; Wang, Fang; Li, Xinyan; Yan, Weijin; Li, Yanqiang; Lv, Shucong

2018-05-07

The Chaohu Lake is highly polluted and suffers from severe eutrophication. Nitrate is a key form of nitrogen that can cause water quality degradation. In this study, hydrochemical and dual isotopic approaches were utilized to identify the seasonal variation of nitrate sources in the Chaohu Lake and its inflowing rivers. The average nitrate concentrations ([NO 3 - ]) of the lake and its inflowing rivers were 89.9 and 140.8 μmol L -1 , respectively. The isotopic values of δ 15 N-NO 3 - and δ 18 O-NO 3 - in the lake ranged from - 1.01 to + 16.67‰ and from - 4.39 to + 22.20‰, respectively. The two major rivers had distinct isotopic compositions, with average δ 15 N-NO 3 - values of + 17.52 and + 3.51‰, and average δ 18 O-NO 3 - values of + 2.71 and + 7.47‰ for the Nanfei River and Hangbu River, respectively. The results show that soil organic ammonium and urban wastewater discharge were the main sources of nitrate in the Chaohu Lake, and nitrate assimilation was an important process affected [NO 3 - ] and isotopic compositions, especially in the western Chaohu Lake. The elevated [NO 3 - ] and δ 15 N-NO 3 - values in the western Chaohu Lake indicate the high influence of human activities. Urban wastewater discharge was the primary nitrate source in the Nanfei River and soil organic ammonium was the main source in the Hangbu River. Although nitrate from direct atmospheric deposition was low, its strong flushing effect can substantially improve riverine [NO 3 - ] and nitrate loading from terrestrial ecosystem. The relatively high nitrate fluxes from the Hangbu River indicate that nitrogen loading from agricultural watershed is unneglectable in watershed nitrogen sources reduction strategies.

Intrinsically 89Zr-labeled Gd2O2S:Eu nanophosphors with high in vivo stability for dual-modality imaging

PubMed Central

Ai, Fanrong; Goel, Shreya; Zhan, Yonghua; Valdovinos, Hector F; Chen, Feng; Barnhart, Todd E; Cai, Weibo

2016-01-01

Radioluminescence imaging (RLI) employs high energy particles from radioisotope decay for in situ excitation of selected nanophosphors. Co-injection of radiopharmaceuticals and nanophosphors suffers from suboptimal RL efficiency owing to the large separation between the source and the emitter. In addition, vastly different pharmacokinetic profiles of the two further impede the practical applications of this approach. To overcome the above challenges, chelator-free radiolabeled nanophosphors with excellent RL efficiency and dual-modality imaging capabilities have been proposed. Abundant O2- donors on Gd2O2S:Eu could intrinsically chelate oxophilic radionuclide 89Zr with ~80 % labeling yield. Positron emission tomography demonstrated superb long-term radiostability of [89Zr]Gd2O2S:Eu@PEG nanoparticles in vivo, and a conventional optical imaging system was used to study radiouminescence properties of [89Zr]Gd2O2S:Eu@PEG nanoparticles in vitro and in vivo. PMID:28078029

Sensitive electrochemical immunosensor for α-synuclein based on dual signal amplification using PAMAM dendrimer-encapsulated Au and enhanced gold nanoparticle labels.

PubMed

An, Yarui; Jiang, Xiaoli; Bi, Wenji; Chen, Hua; Jin, Litong; Zhang, Shengping; Wang, Chuangui; Zhang, Wen

2012-02-15

A novel electrochemical immunosensor for sensitive detection of α-synuclein (α-SYN), a very important neuronal protein, has been developed based on dual signal amplification strategy. Herein, G4-polyamidoamine dendrimer-encapsulated Au nanoparticles (PAMAM-Au nanocomposites) were covalently bound on the poly-o-aminobenzoic acid (poly-o-ABA), which was initially electropolymerized on the electrode surface to perform abundant carboxyl groups. The formed immunosensor platform, PAMAM-Au, was proved to provide numerous amino groups to allow highly dense immobilization of antigen, and facilitate the improvement of electrochemical responses as well. Subsequently, the enhanced gold nanoparticle labels ({HRP-Ab(2)-GNPs}) were fabricated by immobilizing horseradish peroxidase-secondary antibody (HRP-Ab(2)) on the surface of gold nanoparticles (GNPs). After an immunoassay process, the {HRP-Ab(2)-GNPs} labels were introduced onto the electrode surface, and produced an electrocatalytic response by reduction of hydrogen peroxide (H(2)O(2)) in the presence of enzymatically oxidized thionine. On the basis of the dual signal amplification of PAMAM-Au and {HRP-Ab(2)-GNPs} labels, the designed immunosensor displayed an excellent analytical performance with high sensitivity and stability. This developed strategy was successfully proved as a simple, cost-effective method, and could be easily extended to other protein analysis schemes. Copyright © 2011 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2006-12-01

Tree-ring density and widths have been successfully used to reconstruct summer temperatures in high- northern latitudes, although a discrepancy between tree-growth and temperature has been found for recent decades. The so-called "reduced sensitivity" of tree rings to summer temperatures has been observed especially strongly in northern Siberia (Briffa et al., 1998) and drought stress (increased water use efficiency) arose from global warming and/or increasing CO2 are suggested as causes (Barber et al. 2000, Saurer et al. 2004). By using carbon isotope ratio as an indicator of drought stress and ring-width/density as indicators of growth, we can clarify how drought stress caused by recent global warming affects wood formation of Siberian trees. However, isotope dendroclimatology is still in its infancy and our understanding of basic physiological processes of isotope signal transfer from leaves to tree rings is insufficient. In order to understand translocation, storage, and allocation of photoassimilate to different organs of trees, we pulse- labeled ten L. gmelinii growing in a continuous permafrost zone with stable 13CO2. We studied seasonal course of carbon allocation patterns of photoassimilate among needles, branches, stem and roots and also how spring, summer, and autumn photoassimilate is later used for both earlywood and latewood formation. About half of the carbon in new needles was derived from stored material. The starch pool in non- needle parts, which can be used for xylem formation, drew about 43 percent of its carbon from previous year's photoassimilate, suggesting that carbon storage is the key mechanism behind autocorrelation in (isotope) dendroclimatology. Analysis of intra-annual 13C of the tree rings formed after the labeling revealed that earlywood contained photoassimilate from the previous summer and autumn as well as from the current spring. Latewood was mainly composed of photoassimilate from the current year's summer/autumn, although it

Quantifying nitrous oxide production pathways in wastewater treatment systems using isotope technology - A critical review.

PubMed

Duan, Haoran; Ye, Liu; Erler, Dirk; Ni, Bing-Jie; Yuan, Zhiguo

2017-10-01

Nitrous oxide (N 2 O) is an important greenhouse gas and an ozone-depleting substance which can be emitted from wastewater treatment systems (WWTS) causing significant environmental impacts. Understanding the N 2 O production pathways and their contribution to total emissions is the key to effective mitigation. Isotope technology is a promising method that has been applied to WWTS for quantifying the N 2 O production pathways. Within the scope of WWTS, this article reviews the current status of different isotope approaches, including both natural abundance and labelled isotope approaches, to N 2 O production pathways quantification. It identifies the limitations and potential problems with these approaches, as well as improvement opportunities. We conclude that, while the capabilities of isotope technology have been largely recognized, the quantification of N 2 O production pathways with isotope technology in WWTS require further improvement, particularly in relation to its accuracy and reliability. Copyright © 2017 Elsevier Ltd. All rights reserved.

Measurement of Enzyme Isotope Effects.

PubMed

Kholodar, Svetlana A; Ghosh, Ananda K; Kohen, Amnon

2017-01-01

Enzyme isotope effects, or the kinetic effects of "heavy" enzymes, refer to the effect of isotopically labeled protein residues on the enzyme's activity or physical properties. These effects are increasingly employed in the examination of the possible contributions of protein dynamics to enzyme catalysis. One hypothesis assumed that isotopic substitution of all 12 C, 14 N, and nonexchangeable 1 H by 13 C, 15 N, and 2 H, would slow down protein picosecond to femtosecond dynamics without any effect on the system's electrostatics following the Born-Oppenheimer approximation. It was suggested that reduced reaction rates reported for several "heavy" enzymes accords with that hypothesis. However, numerous deviations from the predictions of that hypothesis were also reported. Current studies also attempt to test the role of individual residues by site-specific labeling or by labeling a pattern of residues on activity. It appears that in several systems the protein's fast dynamics are indeed reduced in "heavy" enzymes in a way that reduces the probability of barrier crossing of its chemical step. Other observations, however, indicated that slower protein dynamics are electrostatically altered in isotopically labeled enzymes. Interestingly, these effects appear to be system dependent, thus it might be premature to suggest a general role of "heavy" enzymes' effect on catalysis. © 2017 Elsevier Inc. All rights reserved.

The Novel Approach to Enhance Seed Security: Dual Anti-Counterfeiting Methods Applied on Tobacco Pelleted Seeds

PubMed Central

Guan, Yajing; Wang, Jianchen; Tian, Yixin; Hu, Weimin; Zhu, Liwei; Zhu, Shuijin; Hu, Jin

2013-01-01

Seed security is of prime importance for agriculture. To protect true seeds from being faked, more secure dual anti-counterfeiting technologies for tobacco (Nicotiana tabacum L.) pelleted seed were developed in this paper. Fluorescein (FR), rhodamine B (RB), and magnetic powder (MP) were used as anti-counterfeiting labels. According to their different properties and the special seed pelleting process, four dual-labeling treatments were conducted for two tobacco varieties, MS Yunyan85 (MSYY85) and Honghua Dajinyuan (HHDJY). Then the seed germination and seedling growth status were investigated, and the fluorescence in cracked pellets and developing seedlings was observed under different excitation lights. The results showed that FR, RB, and MP had no negative effects on the germination, seedling growth, and MDA content of the pelleted seeds, and even some treatments significantly enhanced seedling dry weight, vigor index, and shoot height in MS YY85, and increased SOD activity and chlorophyll content in HHDJY as compared to the control. In addition, the cotyledon tip of seedlings treated with FR and MP together represented bright green fluorescence under illumination of blue light (478 nm). And the seedling cotyledon vein treated with RB and MP together showed red fluorescence under green light (546 nm). All seeds pelleted with magnetic powder of proper concentration could be attracted by a magnet. Thus, it indicated that those new dual-labeling methods that fluorescent compound and magnetic powder simultaneously applied in the same seed pellets definitely improved anti-counterfeiting technology and enhanced the seed security. This technology will ensure that high quality seed will be used in the crop production. PMID:23468953

Selected reaction monitoring (SRM) mass spectrometry without isotope labeling can be used for rapid protein quantification

PubMed Central

Zhi, Wenbo; Wang, Meiyao

2014-01-01

The validation of putative biomarker candidates has become the major bottle-neck in protein biomarker development. Conventional immunoaffinity methods are limited by the availability of antibodies and kits. Here we demonstrated the feasibility of using the selected reaction monitoring (SRM) without isotope labeling to achieve fast and reproducible quantification of serum proteins. The SRM/MRM assays for three standard serum proteins, including ceruloplasmin (CP), serum aymloid A (SAA) and sex hormone binding globulin (SHBG) have good linear ranges, generally 103 – 104. There are almost perfect correlations between SRM intensities and the loaded peptide amounts (R2 is usually ~0.99). Our data suggest that SRM/MRM is able to quantify proteins at 0.2 – 2 fmol level, which are comparable to the commercial ELISA/LUMINEX kits for these proteins. Excellent correlations between SRM/MRM and ELISA/LUMINEX assays were observed for SAA and SHBG (R2 = 0.928 and 0.851 respectively). The correlation between SRM/MRM and ELISA for CP is less desirable (R2 = 0.565). The reproducibility for SRM/MRM assays is generally very good but may depend on the proteins/peptides (R2 = 0.931 and 0.882 for SAA and SHBG, and 0.723 for CP). SRM/MRM assay without isotope labeling is a rapid and useful method for protein biomarker validation in a modest number of samples and is especially useful when other assays such as ELISA or Luminex beads are not available. PMID:21594933

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

PubMed

Huan, Tao; Li, Liang

2015-07-21

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

INCORPORATING CONCENTRATION DEPENDENCE IN STABLE ISOTOPE MIXING MODELS

EPA Science Inventory

Stable isotopes are frequently used to quantify the contributions of multiple sources to a mixture; e.g., C and N isotopic signatures can be used to determine the fraction of three food sources in a consumer's diet. The standard dual isotope, three source linear mixing model ass...

Data-driven Approaches to Teaching Stable Isotopes in Hydrology and Environmental Geochemistry

NASA Astrophysics Data System (ADS)

Jefferson, A.; Merchant, W. R.; Dees, D.; Griffith, E. M.; Ortiz, J. D.

2016-12-01

Stable isotopes have revolutionized our understanding of watershed hydrology and other earth science processes. However, students may struggle to correctly interpret isotope ratios and few students understand how isotope measurements are made. New laser-based technologies lower the barrier to entry for giving students hands on experience with isotope measurements and data analysis. We hypothesizedthat integrating such activities into the curriculum would increase student content knowledge, perceptions, and motivation to learn. This project assessed the impact that different pedagogical approaches have on student learning of stable isotope concepts in upper-division geoscience courses. An isotope hydrograph separation module was developed and taught for a Watershed Hydrology course, and a Rayleigh distillation activity was developed and deployed for Environmental Geochemistry and Sedimentology/Stratigraphy classes. Groups of students were exposed to this content via (1) a lecture-only format; (2) a paper-based data analysis activity; and (3) hands-on data collection, sometimes including spectrometer analysis. Pre- and post-tests measured gains in content knowledge while approaches to learning and motivational questionnaires instruments were used to identify the effects of the classroom environment on learning approaches and motivation. Focus group interviews were also conducted to verify the quantitative data. All instructional styles appear to be equally effective at increasing student content knowledge of stable isotopes in the geosciences, but future studies need to move beyond "exam question" style assessment of learning. Our results may reflect that hands-on experiences are not new to upper-level geosciences students, because this is the way that many classes are taught in the geosciences (labs, field trips). Thus, active learning approaches may not have had the impact they would with other groups. The "messiness" of hands-on activities and authentic research

Nitrogen sources and cycling revealed by dual isotopes of nitrate in a complex urbanized environment.

PubMed

Archana, Anand; Thibodeau, Benoit; Geeraert, Naomi; Xu, Min Nina; Kao, Shuh-Ji; Baker, David M

2018-06-05

Elevated nutrient inputs have led to increased eutrophication in coastal marine ecosystems worldwide. An understanding of the relative contribution of different nutrient sources is imperative for effective water quality management. Stable isotope values of nitrate (δ 15 N NO3- , δ 18 O NO3- ) can complement conventional water quality monitoring programs to help differentiate natural sources of NO 3 - from anthropogenic inputs and estimate the processes involved in N cycling within an ecosystem. We measured nutrient concentrations, δ 15 N NO3- , and δ 18 O NO3- in 76 locations along a salinity gradient from the lower end of the Pearl River Estuary, one of China's largest rivers discharging into the South China Sea, towards the open ocean. NO 3 - concentrations decreased with increasing salinity, indicative of conservative mixing of eutrophic freshwater and oligotrophic seawater. However, our data did not follow conservative mixing patterns. At salinities <20 psu, samples exhibited decreasing NO 3 - concentrations with almost unchanged NO 3 - isotope values, indicating simple dilution. At salinities >20 psu, NO 3 - concentrations decreased, while dual NO 3 - isotopes increased, suggesting mixing and/or other transformation processes. Our analysis yielded mean estimates for isotope enrichment factors ( 15 ε = -2.02‰ and 18 ε = -3.37‰), Δ(15,18) = -5.5‰ and δ 15 N NO3- - δ 15 N NO2-  = 12.3‰. After consideration of potential alternative sources (sewage, atmospheric deposition and groundwater) we concluded that there are three plausible interpretations for deviations from conservative mixing behaviour (1) NO 3 - uptake by assimilation (2) in situ NO 3 - production (from fixation-derived nitrogen and nitrification of sewage-derived effluents) and (3) input of groundwater nitrate carrying a denitrification signal. Through this study, we propose a simple workflow that incorporates a synthesis of numerous isotope-based studies to constrain

Novel and non-traditional use of stable isotope tracers to study metal bioavailability from natural particles

USGS Publications Warehouse

Croteau, Marie-Noële; Cain, Daniel J.; Fuller, Christopher C.

2013-01-01

We devised a novel tracing approach that involves enriching test organisms with a stable metal isotope of low natural abundance prior to characterizing metal bioavailability from natural inorganic particles. In addition to circumventing uncertainties associated with labeling natural particles and distinguishing background metals, the proposed "reverse labeling" technique overcomes many drawbacks inherent to using radioisotope tracers. Specifically, we chronically exposed freshwater snails (Lymnaea stagnalis) to synthetic water spiked with Cu that was 99.4% 65Cu to increase the relative abundance of 65Cu in the snail’s tissues from 32% to >80%. The isotopically enriched snails were then exposed to benthic algae mixed with Cu-bearing Fe–Al particles collected from the Animas River (Colorado), an acid mine drainage impacted river. We used 63Cu to trace Cu uptake from the natural particles and inferred their bioavailability from calculation of Cu assimilation into tissues. Cu assimilation from these particles was 44%, indicating that 44% of the particulate Cu was absorbed by the invertebrate. This demonstrates that inorganic particulate Cu can be bioavailable. The reverse labeling approach shows great potential in various scientific areas such as environmental contamination and nutrition for addressing questions involving uptake of an element that naturally has multiple isotopes.

Isotope labeling to determine the dynamics of metabolic response in CHO cell perfusion bioreactors using MALDI-TOF-MS.

PubMed

Karst, Daniel J; Steinhoff, Robert F; Kopp, Marie R G; Soos, Miroslav; Zenobi, Renato; Morbidelli, Massimo

2017-11-01

The steady-state operation of Chinese hamster ovary (CHO) cells in perfusion bioreactors requires the equilibration of reactor dynamics and cell metabolism. Accordingly, in this work we investigate the transient cellular response to changes in its environment and their interactions with the bioreactor hydrodynamics. This is done in a benchtop perfusion bioreactor using MALDI-TOF MS through isotope labeling of complex intracellular nucleotides (ATP, UTP) and nucleotide sugars (UDP-Hex, UDP-HexNAc). By switching to a 13 C 6 glucose containing feed media during constant operation at 20 × 10 6 cells and a perfusion rate of 1 reactor volume per day, isotopic steady state was studied. A step change to the 13 C 6 glucose medium in spin tubes allowed the determination of characteristic times for the intracellular turnover of unlabeled metabolites pools, τST (≤0.56 days), which were confirmed in the bioreactor. On the other hand, it is shown that the reactor residence time τR (1 day) and characteristic time for glucose uptake τGlc (0.33 days), representative of the bioreactor dynamics, delayed the consumption of 13 C 6 glucose in the bioreactor and thus the intracellular 13 C enrichment. The proposed experimental approach allowed the decoupling of bioreactor hydrodynamics and intrinsic dynamics of cell metabolism in response to a change in the cell culture environment. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1630-1639, 2017. © 2017 American Institute of Chemical Engineers.

Dual-Responsive Metabolic Precursor and Light-Up AIEgen for Cancer Cell Bio-orthogonal Labeling and Precise Ablation.

PubMed

Hu, Fang; Yuan, Youyong; Wu, Wenbo; Mao, Duo; Liu, Bin

2018-06-05

Metabolic glycoengineering of unnatural glycans with bio-orthogonal chemical groups and a subsequent click reaction with fluorescent probes have been widely used in monitoring various bioprocesses. Herein, we developed a dual-responsive metabolic precursor that could specifically generate unnatural glycans with azide groups on the membrane of targeted cancer cells with high selectivity. Moreover, a water-soluble fluorescent light-up probe with aggregation-induced emission (AIE) was synthesized, which turned its fluorescence on upon a click reaction with azide groups on the cancer cell surface, enabling special cancer cell imaging with low background signal. Furthermore, the probe can generate 1 O 2 upon light irradiation, fulfilling its dual role as an imaging and therapeutic agent for cancer cells. Therefore, the concepts of the cancer-cell-specific metabolic precursor cRGD-S-Ac 3 ManNAz and the AIE light-up probe are promising in bio-orthogonal labeling and cancer-specific imaging and therapy.

An in-advance stable isotope labeling strategy for relative analysis of multiple acidic plant hormones in sub-milligram Arabidopsis thaliana seedling and a single seed.

PubMed

Sun, Xiaohong; Ouyang, Yue; Chu, Jinfang; Yan, Jing; Yu, Yan; Li, Xiaoqiang; Yang, Jun; Yan, Cunyu

2014-04-18

A sensitive and reliable in-advance stable isotope labeling strategy was developed for simultaneous relative quantification of 8 acidic plant hormones in sub-milligram amount of plant materials. Bromocholine bromide (BETA) and its deuterated counterpart D9-BETA were used to in-advance derivatize control and sample extracts individually, which were then combined and subjected to solid-phase extraction (SPE) purification followed by UPLC-MS/MS analysis. Relative quantification of target compounds was obtained by calculation of the peak area ratios of BETA/D9-BETA labeled plant hormones. The in-advance stable isotope labeling strategy realized internal standard-based relative quantification of multiple kinds of plant hormones independent of availability of internal standard of every analyte with enhanced sensitivity of 1-3 orders of magnitude. Meanwhile, the in-advance labeling contributes to higher sample throughput and more reliability. The method was successfully applied to determine 8 plant hormones in 0.8mg DW (dry weight) of seedlings and 4 plant hormones from single seed of Arabidopsis thaliana. The results show the potential of the method in relative quantification of multiple plant hormones in tiny plant tissues or organs, which will advance the knowledge of the crosstalk mechanism of plant hormones. Copyright © 2014 Elsevier B.V. All rights reserved.

EM reconstruction of dual isotope PET using staggered injections and prompt gamma positron emitters

PubMed Central

Andreyev, Andriy; Sitek, Arkadiusz; Celler, Anna

2014-01-01

Purpose: The aim of dual isotope positron emission tomography (DIPET) is to create two separate images of two coinjected PET radiotracers. DIPET shortens the duration of the study, reduces patient discomfort, and produces perfectly coregistered images compared to the case when two radiotracers would be imaged independently (sequential PET studies). Reconstruction of data from such simultaneous acquisition of two PET radiotracers is difficult because positron decay of any isotope creates only 511 keV photons; therefore, the isotopes cannot be differentiated based on the detected energy. Methods: Recently, the authors have proposed a DIPET technique that uses a combination of radiotracer A which is a pure positron emitter (such as 18F or 11C) and radiotracer B in which positron decay is accompanied by the emission of a high-energy (HE) prompt gamma (such as 38K or 60Cu). Events that are detected as triple coincidences of HE gammas with the corresponding two 511 keV photons allow the authors to identify the lines-of-response (LORs) of isotope B. These LORs are used to separate the two intertwined distributions, using a dedicated image reconstruction algorithm. In this work the authors propose a new version of the DIPET EM-based reconstruction algorithm that allows the authors to include an additional, independent estimate of radiotracer A distribution which may be obtained if radioisotopes are administered using a staggered injections method. In this work the method is tested on simple simulations of static PET acquisitions. Results: The authors’ experiments performed using Monte-Carlo simulations with static acquisitions demonstrate that the combined method provides better results (crosstalk errors decrease by up to 50%) than the positron-gamma DIPET method or staggered injections alone. Conclusions: The authors demonstrate that the authors’ new EM algorithm which combines information from triple coincidences with prompt gammas and staggered injections improves

EM reconstruction of dual isotope PET using staggered injections and prompt gamma positron emitters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andreyev, Andriy, E-mail: andriy.andreyev-1@philips.com; Sitek, Arkadiusz; Celler, Anna

2014-02-15

Purpose: The aim of dual isotope positron emission tomography (DIPET) is to create two separate images of two coinjected PET radiotracers. DIPET shortens the duration of the study, reduces patient discomfort, and produces perfectly coregistered images compared to the case when two radiotracers would be imaged independently (sequential PET studies). Reconstruction of data from such simultaneous acquisition of two PET radiotracers is difficult because positron decay of any isotope creates only 511 keV photons; therefore, the isotopes cannot be differentiated based on the detected energy. Methods: Recently, the authors have proposed a DIPET technique that uses a combination of radiotracermore » A which is a pure positron emitter (such as{sup 18}F or {sup 11}C) and radiotracer B in which positron decay is accompanied by the emission of a high-energy (HE) prompt gamma (such as {sup 38}K or {sup 60}Cu). Events that are detected as triple coincidences of HE gammas with the corresponding two 511 keV photons allow the authors to identify the lines-of-response (LORs) of isotope B. These LORs are used to separate the two intertwined distributions, using a dedicated image reconstruction algorithm. In this work the authors propose a new version of the DIPET EM-based reconstruction algorithm that allows the authors to include an additional, independent estimate of radiotracer A distribution which may be obtained if radioisotopes are administered using a staggered injections method. In this work the method is tested on simple simulations of static PET acquisitions. Results: The authors’ experiments performed using Monte-Carlo simulations with static acquisitions demonstrate that the combined method provides better results (crosstalk errors decrease by up to 50%) than the positron-gamma DIPET method or staggered injections alone. Conclusions: The authors demonstrate that the authors’ new EM algorithm which combines information from triple coincidences with prompt gammas and

Copper-doped titanium dioxide nanoparticles as dual-functional labels for fabrication of electrochemical immunosensors.

PubMed

Zhang, Sen; Ma, Hongmin; Yan, Liangguo; Cao, Wei; Yan, Tao; Wei, Qin; Du, Bin

2014-09-15

Constructions of versatile electroactive labels are key issues in the development of electrochemical immunosensors. In this study, copper-doped titanium dioxide nanoparticle (Cu@TiO2) was synthesized and used as labels for fabrication of sandwich-type electrochemical immunosensors on glassy carbon electrode (GCE). Due to the presence of copper ions, Cu@TiO2 shows a strong response current when coupled to an electrode. The prepared nanocomposite also shows high electrocatalytic activity towards reduction of hydrogen peroxide (H2O2). The dual functionality of Cu@TiO2 enables the fabrication of immunosensor using different detection modes, that is, square wave voltammetry (SWV) or chronoamperometry (CA). While Cu@TiO2 was used as labels of secondary antibodies (Ab2), carboxyl functionalized graphene oxide (CFGO) was used as electrode materials to immobilize primary antibodies (Ab1). Using human immunoglobulin G (IgG) as a model analyte, the immunosensor shows high sensitivity, acceptable stability and good reproducibility for both detection modes. Under optimal conditions, a linear range from 0.1 pg/mL to 100 ng/mL with a detection limit of 0.052 pg/mL was obtained for SWV analysis. For CA analysis, a wider linear range from 0.01 pg/mL to 100 ng/mL and a lower detection limit of 0.0043 pg/mL were obtained. The proposed metal ion-based enzyme-free and noble metal-free immunosensor may have promising applications in clinical diagnoses and many other fields. Copyright © 2014 Elsevier B.V. All rights reserved.

Detection and tracking of dual-labeled HIV particles using wide-field live cell imaging to follow viral core integrity

PubMed Central

Mamede, Joao I.; Hope, Thomas J.

2016-01-01

Summary Live cell imaging is a valuable technique that allows the characterization of the dynamic processes of the HIV-1 life-cycle. Here, we present a method of production and imaging of dual-labeled HIV viral particles that allows the visualization of two events. Varying release of the intravirion fluid phase marker reveals virion fusion and the loss of the integrity of HIV viral cores with the use of live wide-field fluorescent microscopy. PMID:26714704

A stable isotope-based approach to tropical dendroclimatology

NASA Astrophysics Data System (ADS)

Evans, Michael N.; Schrag, Daniel P.

2004-08-01

We describe a strategy for development of chronological control in tropical trees lacking demonstrably annual ring formation, using high resolution δ 18O measurements in tropical wood. The approach applies existing models of the oxygen isotopic composition of alpha-cellulose (Roden et al., 2000), a rapid method for cellulose extraction from raw wood (Brendel et al., 2000), and continuous flow isotope ratio mass spectrometry (Brenna et al., 1998) to develop proxy chronological, rainfall and growth rate estimates from tropical trees lacking visible annual ring structure. Consistent with model predictions, pilot datasets from the temperate US and Costa Rica having independent chronological control suggest that observed cyclic isotopic signatures of several permil (SMOW) represent the annual cycle of local rainfall and relative humidity. Additional data from a plantation tree of known age from ENSO-sensitive northwestern coastal Peru suggests that the 1997-8 ENSO warm phase event was recorded as an 8‰ anomaly in the δ 18O of α-cellulose. The results demonstrate reproducibility of the stable isotopic chronometer over decades, two different climatic zones, and three tropical tree genera, and point to future applications in paleoclimatology.

Reductive methods for isotopic labeling of antibiotics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Champney, W.S.

1989-08-15

Methods for the reductive methylation of the amino groups of eight different antibiotics using {sup 3}HCOH or H{sup 14}COH are presented. The reductive labeling of an additional seven antibiotics by NaB{sub 3}H{sub 4} is also described. The specific activity of the methyl-labeled drugs was determined by a phosphocellulose paper binding assay. Two quantitative assays for these compounds based on the reactivity of the antibiotic amino groups with fluorescamine and of the aldehyde and ketone groups with 2,4-dinitrophenylhydrazine are also presented. Data on the cellular uptake and ribosome binding of these labeled compounds are also presented.

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

Michael, Claudia; Rizzi, Andreas M

2015-02-27

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. Copyright © 2015 Elsevier B.V. All rights reserved.

Single-Cell Growth Rates in Photoautotrophic Populations Measured by Stable Isotope Probing and Resonance Raman Microspectrometry

PubMed Central

Taylor, Gordon T.; Suter, Elizabeth A.; Li, Zhuo Q.; Chow, Stephanie; Stinton, Dallyce; Zaliznyak, Tatiana; Beaupré, Steven R.

2017-01-01

A new method to measure growth rates of individual photoautotrophic cells by combining stable isotope probing (SIP) and single-cell resonance Raman microspectrometry is introduced. This report explores optimal experimental design and the theoretical underpinnings for quantitative responses of Raman spectra to cellular isotopic composition. Resonance Raman spectra of isogenic cultures of the cyanobacterium, Synechococcus sp., grown in 13C-bicarbonate revealed linear covariance between wavenumber (cm−1) shifts in dominant carotenoid Raman peaks and a broad range of cellular 13C fractional isotopic abundance. Single-cell growth rates were calculated from spectra-derived isotopic content and empirical relationships. Growth rates among any 25 cells in a sample varied considerably; mean coefficient of variation, CV, was 29 ± 3% (σ/x¯), of which only ~2% was propagated analytical error. Instantaneous population growth rates measured independently by in vivo fluorescence also varied daily (CV ≈ 53%) and were statistically indistinguishable from single-cell growth rates at all but the lowest levels of cell labeling. SCRR censuses of mixtures prepared from Synechococcus sp. and T. pseudonana (a diatom) populations with varying 13C-content and growth rates closely approximated predicted spectral responses and fractional labeling of cells added to the sample. This approach enables direct microspectrometric interrogation of isotopically- and phylogenetically-labeled cells and detects as little as 3% changes in cellular fractional labeling. This is the first description of a non-destructive technique to measure single-cell photoautotrophic growth rates based on Raman spectroscopy and well-constrained assumptions, while requiring few ancillary measurements. PMID:28824580

Target analyte quantification by isotope dilution LC-MS/MS directly referring to internal standard concentrations--validation for serum cortisol measurement.

PubMed

Maier, Barbara; Vogeser, Michael

2013-04-01

Isotope dilution LC-MS/MS methods used in the clinical laboratory typically involve multi-point external calibration in each analytical series. Our aim was to test the hypothesis that determination of target analyte concentrations directly derived from the relation of the target analyte peak area to the peak area of a corresponding stable isotope labelled internal standard compound [direct isotope dilution analysis (DIDA)] may be not inferior to conventional external calibration with respect to accuracy and reproducibility. Quality control samples and human serum pools were analysed in a comparative validation protocol for cortisol as an exemplary analyte by LC-MS/MS. Accuracy and reproducibility were compared between quantification either involving a six-point external calibration function, or a result calculation merely based on peak area ratios of unlabelled and labelled analyte. Both quantification approaches resulted in similar accuracy and reproducibility. For specified analytes, reliable analyte quantification directly derived from the ratio of peak areas of labelled and unlabelled analyte without the need for a time consuming multi-point calibration series is possible. This DIDA approach is of considerable practical importance for the application of LC-MS/MS in the clinical laboratory where short turnaround times often have high priority.

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

NASA Astrophysics Data System (ADS)

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

2014-06-01

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

Nitrogen isotope and mass balance approach in the Elbe Estuary

NASA Astrophysics Data System (ADS)

Sanders, Tina; Wankel, Scott D.; Dähnke, Kirstin

2017-04-01

The supply of bioavailable nitrogen is crucial to primary production in the world's oceans. Especially in estuaries, which act as a nutrient filter for coastal waters, microbial nitrogen turnover and removal has a particular significance. Nitrification as well as other nitrogen-based processes changes the natural abundance of the stable isotope, which can be used as proxies for sources and sinks as well as for process identification. The eutrophic Elbe estuary in northern Germany is loaded with fertilizer-derived nitrogen, but management efforts have started to reduce this load effectively. However, an internal nitrate source in turn gained in importance and the estuary changed from a sink to a source of dissolved inorganic nitrogen: Nitrification is responsible for significant estuarine nutrient regeneration, especially in the Hamburg Port. In our study, we aimed to quantify sources and sinks of nitrogen based on a mass and stable isotope budget in the Elbe estuary. A model was developed reproduce internal N-cycling and associated isotope changes. For that approach we measured dissolved inorganic nitrogen (DIN), particulate nitrogen and their stable isotopes in a case study in July 2013. We found an almost closed mass balance of nitrogen, with only low lost or gains which we attribute to sediment resuspension. The isotope values of different DIN components and the model approach both support a high fractionation of up to -25‰ during nitrification. However, the nitrogen balance and nitrogen stable isotopes suggest that most important processes are remineralization of organic matter to ammonium and further on the oxidation to nitrate. Denitrification and nitrate assimilation play a subordinate role in the Elbe Estuary.

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)

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

2015-03-01

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 Fe3

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

PubMed Central

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

2011-01-01

Isoindoline nitroxides are potentially useful probes for viable biological systems, exhibiting low cytotoxicity, moderate rates of biological reduction and favorable Electron Paramagnetic Resonance (EPR) characteristics. We have evaluated the anionic (5-carboxy-1,1,3,3-tetramethylisoindolin-2-yloxyl; CTMIO), cationic (5-(N,N,N-trimethylammonio)-1,1,3,3-tetramethylisoindolin-2-yloxyl iodide, QATMIO) and neutral (1,1,3,3-tetramethylisoindolin-2-yloxyl; TMIO) nitroxides and their isotopically labeled analogues (2H12- and/or 2H12-15N-labeled) as potential EPR oximetry probes. An active ester analogue of CTMIO, designed to localize intracellularly, and the azaphenalene nitroxide 1,1,3,3-tetramethyl-2,3-dihydro-2-azaphenalen-2-yloxyl (TMAO) were also studied. While the EPR spectra of the unlabeled nitroxides exhibit high sensitivity to O2 concentration, deuteration resulted in a loss of superhyperfine features and a subsequent reduction in O2 sensitivity. Labeling the nitroxides with 15N increased the signal intensity and this may be useful in decreasing the detection limits for in vivo measurements. The active ester nitroxide showed approximately 6% intracellular localization and low cytotoxicity. The EPR spectra of TMAO nitroxide indicated an increased rigidity in the nitroxide ring, due to dibenzo-annulation. PMID:21665499

Using nitrate dual isotopic composition (δ15N and δ18O) as a tool for exploring sources and cycling of nitrate in an estuarine system: Elkhorn Slough, California

USGS Publications Warehouse

Wankel, Scott D.; Kendall, Carol; Paytan, Adina

2009-01-01

Nitrate (NO-3 concentrations and dual isotopic composition (??15N and ??18O) were measured during various seasons and tidal conditions in Elkhorn Slough to evaluate mixing of sources of NO-3 within this California estuary. We found the isotopic composition of NO-3 was influenced most heavily by mixing of two primary sources with unique isotopic signatures, a marine (Monterey Bay) and terrestrial agricultural runoff source (Old Salinas River). However, our attempt to use a simple two end-member mixing model to calculate the relative contribution of these two NO-3 sources to the Slough was complicated by periods of nonconservative behavior and/or the presence of additional sources, particularly during the dry season when NO-3 concentrations were low. Although multiple linear regression generally yielded good fits to the observed data, deviations from conservative mixing were still evident. After consideration of potential alternative sources, we concluded that deviations from two end-member mixing were most likely derived from interactions with marsh sediments in regions of the Slough where high rates of NO-3 uptake and nitrification result in NO-3 with low ?? 15N and high ??18O values. A simple steady state dual isotope model is used to illustrate the impact of cycling processes in an estuarine setting which may play a primary role in controlling NO -3 isotopic composition when and where cycling rates and water residence times are high. This work expands our understanding of nitrogen and oxygen isotopes as biogeochemical tools for investigating NO -3 sources and cycling in estuaries, emphasizing the role that cycling processes may play in altering isotopic composition. Copyright 2009 by the American Geophysical Union.

Glacial/interglacial wetland, biomass burning, and geologic methane emissions constrained by dual stable isotopic CH4 ice core records.

PubMed

Bock, Michael; Schmitt, Jochen; Beck, Jonas; Seth, Barbara; Chappellaz, Jérôme; Fischer, Hubertus

2017-07-18

Atmospheric methane (CH 4 ) records reconstructed from polar ice cores represent an integrated view on processes predominantly taking place in the terrestrial biogeosphere. Here, we present dual stable isotopic methane records [δ 13 CH 4 and δD(CH 4 )] from four Antarctic ice cores, which provide improved constraints on past changes in natural methane sources. Our isotope data show that tropical wetlands and seasonally inundated floodplains are most likely the controlling sources of atmospheric methane variations for the current and two older interglacials and their preceding glacial maxima. The changes in these sources are steered by variations in temperature, precipitation, and the water table as modulated by insolation, (local) sea level, and monsoon intensity. Based on our δD(CH 4 ) constraint, it seems that geologic emissions of methane may play a steady but only minor role in atmospheric CH 4 changes and that the glacial budget is not dominated by these sources. Superimposed on the glacial/interglacial variations is a marked difference in both isotope records, with systematically higher values during the last 25,000 y compared with older time periods. This shift cannot be explained by climatic changes. Rather, our isotopic methane budget points to a marked increase in fire activity, possibly caused by biome changes and accumulation of fuel related to the late Pleistocene megafauna extinction, which took place in the course of the last glacial.

Glacial/interglacial wetland, biomass burning, and geologic methane emissions constrained by dual stable isotopic CH4 ice core records

NASA Astrophysics Data System (ADS)

Bock, Michael; Schmitt, Jochen; Beck, Jonas; Seth, Barbara; Chappellaz, Jérôme; Fischer, Hubertus

2017-07-01

Atmospheric methane (CH4) records reconstructed from polar ice cores represent an integrated view on processes predominantly taking place in the terrestrial biogeosphere. Here, we present dual stable isotopic methane records [δ13CH4 and δD(CH4)] from four Antarctic ice cores, which provide improved constraints on past changes in natural methane sources. Our isotope data show that tropical wetlands and seasonally inundated floodplains are most likely the controlling sources of atmospheric methane variations for the current and two older interglacials and their preceding glacial maxima. The changes in these sources are steered by variations in temperature, precipitation, and the water table as modulated by insolation, (local) sea level, and monsoon intensity. Based on our δD(CH4) constraint, it seems that geologic emissions of methane may play a steady but only minor role in atmospheric CH4 changes and that the glacial budget is not dominated by these sources. Superimposed on the glacial/interglacial variations is a marked difference in both isotope records, with systematically higher values during the last 25,000 y compared with older time periods. This shift cannot be explained by climatic changes. Rather, our isotopic methane budget points to a marked increase in fire activity, possibly caused by biome changes and accumulation of fuel related to the late Pleistocene megafauna extinction, which took place in the course of the last glacial.

Capillary electrophoretic separation-based approach to determine the labeling kinetics of oligodeoxynucleotides

PubMed Central

Kanavarioti, Anastassia; Greenman, Kevin L.; Hamalainen, Mark; Jain, Aakriti; Johns, Adam M.; Melville, Chris R.; Kemmish, Kent; Andregg, William

2014-01-01

With the recent advances in electron microscopy (EM), computation, and nanofabrication, the original idea of reading DNA sequence directly from an image can now be tested. One approach is to develop heavy atom labels that can provide the contrast required for EM imaging. While evaluating tentative labels for the respective nucleobases in synthetic oligodeoxynucleotides (oligos), we developed a streamlined capillary electrophoresis (CE) protocol to assess the label stability, reactivity, and selectivity. We report our protocol using osmium tetroxide 2,2′-bipyridine (Osbipy) as a thymidine (T) specific label. The observed rates show that the labeling process is kinetically independent of both the oligo length, and the base composition. The conditions, i.e. temperature, optimal Osbipy concentration, and molar ratio of reagents, to promote 100% conversion of the starting oligo to labeled product were established. Hence the optimized conditions developed with the oligos could be leveraged to allow osmylation of effectively all Ts in single-stranded (ss) DNA, while achieving minimal mislabeling. In addition, the approach and methods employed here may be adapted to the evaluation of other prospective contrasting agents/labels to facilitate next-generation DNA sequencing by EM. PMID:23147698

Vitamin B12 effects on chlorinated methanes-degrading microcosms: Dual isotope and metabolically active microbial populations assessment.

PubMed

Rodríguez-Fernández, Diana; Torrentó, Clara; Guivernau, Miriam; Viñas, Marc; Hunkeler, Daniel; Soler, Albert; Domènech, Cristina; Rosell, Mònica

2018-04-15

Field-derived anoxic microcosms were used to characterize chloroform (CF) and carbon tetrachloride (CT) natural attenuation to compare it with biostimulation scenarios in which vitamin B 12 was added (B 12 /pollutant ratio of 0.01 and 0.1) by means of by-products, carbon and chlorine compound-specific stable-isotope analysis, and the active microbial community through 16S rRNA MiSeq high-throughput sequencing. Autoclaved slurry controls discarded abiotic degradation processes. B 12 catalyzed CF and CT biodegradation without the accumulation of dichloromethane, carbon disulphide, or CF. The carbon isotopic fractionation value of CF (ƐC CF ) with B 12 was -14±4‰, and the value for chlorine (ƐCl CF ) was -2.4±0.4‰. The carbon isotopic fractionation values of CT (ƐC CT ) were -16±6 with B 12 , and -13±2‰ without B 12 ; and the chlorine isotopic fractionation values of CT (ƐCl CT ) were -6±3 and -4±2‰, respectively. Acidovorax, Ancylobacter, and Pseudomonas were the most metabolically active genera, whereas Dehalobacter and Desulfitobacterium were below 0.1% of relative abundance. The dual C-Cl element isotope slope (Λ=Δδ 13 C/Δδ 37 Cl) for CF biodegradation (only detected with B 12 , 7±1) was similar to that reported for CF reduction by Fe(0) (8±2). Several reductive pathways might be competing in the tested CT scenarios, as evidenced by the lack of CF accumulation when B 12 was added, which might be linked to a major activity of Pseudomonas stutzeri; by different chlorine apparent kinetic isotope effect values and Λ which was statistically different with and without B 12 (5±1 vs 6.1±0.5), respectively. Thus, positive B 12 effects such as CT and CF degradation catalyst were quantified for the first time in isotopic terms, and confirmed with the major activity of species potentially capable of their degradation. Moreover, the indirect benefits of B 12 on the degradation of chlorinated ethenes were proved, creating a basis for remediation

Chemical Isotope Labeling LC-MS for High Coverage and Quantitative Profiling of the Hydroxyl Submetabolome in Metabolomics.

PubMed

Zhao, Shuang; Luo, Xian; Li, Liang

2016-11-01

A key step in metabolomics is to perform accurate relative quantification of the metabolomes in comparative samples with high coverage. Hydroxyl-containing metabolites are an important class of the metabolome with diverse structures and physical/chemical properties; however, many of them are difficult to detect with high sensitivity. We present a high-performance chemical isotope labeling liquid chromatography mass spectrometry (LC-MS) technique for in-depth profiling of the hydroxyl submetabolome, which involves the use of acidic liquid-liquid extraction to enrich hydroxyl metabolites into ethyl acetate from an aqueous sample. After drying and then redissolving in acetonitrile, the metabolite extract is labeled using a base-activated 12 C- or 13 C-dansylation reaction. A fast step-gradient LC-UV method is used to determine the total concentration of labeled metabolites. On the basis of the concentration information, a 12 C-labeled individual sample is mixed with an equal mole amount of a 13 C-labeled pool or control for relative metabolite quantification. The 12 C-/ 13 C-labeled mixtures are individually analyzed by LC-MS, and the resultant peak pairs of labeled metabolites in MS are measured for relative quantification and metabolite identification. A standard library of 85 hydroxyl compounds containing MS, retention time, and MS/MS information was constructed for positive metabolite identification based on matches of two or all three of these parameters with those of an unknown. Using human urine as an example, we analyzed samples of 1:1 12 C-/ 13 C-labeled urine in triplicate with triplicate runs per sample and detected an average of 3759 ± 45 peak pairs or metabolites per run and 3538 ± 71 pairs per sample with 3093 pairs in common (n = 9). Out of the 3093 peak pairs, 2304 pairs (75%) could be positively or putatively identified based on metabolome database searches, including 20 pairs positively identified using the dansylated hydroxyl standards library

Optimization of a simultaneous dual-isotope 201Tl/123I-MIBG myocardial SPECT imaging protocol with a CZT camera for trigger zone assessment after myocardial infarction for routine clinical settings: Are delayed acquisition and scatter correction necessary?

PubMed

D'estanque, Emmanuel; Hedon, Christophe; Lattuca, Benoît; Bourdon, Aurélie; Benkiran, Meriem; Verd, Aurélie; Roubille, François; Mariano-Goulart, Denis

2017-08-01

Dual-isotope 201 Tl/ 123 I-MIBG SPECT can assess trigger zones (dysfunctions in the autonomic nervous system located in areas of viable myocardium) that are substrate for ventricular arrhythmias after STEMI. This study evaluated the necessity of delayed acquisition and scatter correction for dual-isotope 201 Tl/ 123 I-MIBG SPECT studies with a CZT camera to identify trigger zones after revascularization in patients with STEMI in routine clinical settings. Sixty-nine patients were prospectively enrolled after revascularization to undergo 201 Tl/ 123 I-MIBG SPECT using a CZT camera (Discovery NM 530c, GE). The first acquisition was a single thallium study (before MIBG administration); the second and the third were early and late dual-isotope studies. We compared the scatter-uncorrected and scatter-corrected (TEW method) thallium studies with the results of magnetic resonance imaging or transthoracic echography (reference standard) to diagnose myocardial necrosis. Summed rest scores (SRS) were significantly higher in the delayed MIBG studies than the early MIBG studies. SRS and necrosis surface were significantly higher in the delayed thallium studies with scatter correction than without scatter correction, leading to less trigger zone diagnosis for the scatter-corrected studies. Compared with the scatter-uncorrected studies, the late thallium scatter-corrected studies provided the best diagnostic values for myocardial necrosis assessment. Delayed acquisitions and scatter-corrected dual-isotope 201 Tl/ 123 I-MIBG SPECT acquisitions provide an improved evaluation of trigger zones in routine clinical settings after revascularization for STEMI.

Stable isotope tracer dilution for quantifying very low-density lipoprotein-triacylglycerol kinetics in man.

PubMed

Sidossis, Labros S; Magkos, Faidon; Mittendorfer, Bettina; Wolfe, Robert R

2004-08-01

A number of approaches have been employed in the past to measure very low-density lipoprotein (VLDL) triacylglycerol (TG) kinetics in humans in vivo, varying in the selection of tracer and mode of administration. All, however, make use of labeled TG precursors and more or less complicated mathematical models to derive the kinetic parameters of interest. The aim of the present study was to develop a conceptually straightforward method, based on the traditional tracer infusion technique, for quantifying VLDL-TG production rates in man using stable isotopes. Our approach involves ingestion of [U-13C3]glycerol to endogenously label the glycerol in VLDL-TG, plasmapheresis, isolation of the newly 13C-labeled VLDL from plasma, and administration within the next 2-3 days via a primed constant autologous reinfusion. This procedure produces enough tracer for a priming dose plus 2-3 h of infusion. In the physiological conditions examined (basal and hyperglycemic states, fat- and carbohydrate-rich diets), with almost 3-fold ranging VLDL-TG pool sizes, a steady state in plasma VLDL-TG glycerol tracer-to-tracee ratio was readily achieved within 2 h. Consequently, calculations are made according to the isotope dilution principle, thus avoiding assumptions implicit in more complicated models. The stable isotope VLDL-TG tracer dilution method offers an alternative and reliable tool for the determination of endogenous VLDL-TG kinetics in man under a variety of metabolic states. Copyright 2003 Elsevier Ltd.

Multiple isotope effects with alternative dinucleotide substrates as a probe of the malic enzyme reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weiss, P.M.; Urbauer, J.L.; Cleland, W.W.

1991-06-11

Deuterium isotope effects and {sup 13}C isotope effects with deuterium- and protium-labeled malate have been obtained for both NAD- and NADP-malic enzymes by using a variety of alternative dinucleotide substrates. With nicotinamide-containing dinucleotides as the oxidizing substrate, the {sup 13}C effect decreases when deuterated malate is the substrate compared to the value obtained with protium-labeled malate. These data are consistent with a stepwise chemical mechanism in which hydride transfer precedes decarboxylation of the oxalacetate intermediate as previously proposed. When dinucleotide substrates such as thio-NAD, 3-nicotinamide rings are used, the {sup 13}C effect increases when deuterated malate is the substrate comparedmore » to the value obtained with protium-labeled malate. These data, at face value, are consistent with a change in mechanism from stepwise to concerted for the oxidative decarboxylation portion of the mechanism. However, the increase in the deuterium isotope effect from 1.5 to 3 with a concomitant decrease in the {sup 13}C isotope effect from 1.034 to 1.003 as the dinucleotide substrate is changed suggests that the reaction may still be stepwise with the non-nicotinamide dinucleotides. A more likely explanation is that a {beta}-secondary {sup 13}C isotope effect accompanies hydride transfer as a result of hyperconjugation of the {beta}-carboxyl of malate as the transition state for the hydride transfer step is approached.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Jordan Ned; Tyrrell, Kimberly J.; Hansen, Joshua R.

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

Identification of degradation routes of metamitron in soil microcosms using 13C-isotope labeling.

PubMed

Wang, Shizong; Miltner, Anja; Nowak, Karolina M

2017-01-01

Metamitron is one of the most commonly used herbicide in sugar beet and flower bulb cultures. Numerous laboratory and field studies on sorption and degradation of metamitron were performed. Detailed biodegradation studies in soil using 13 C-isotope labeling are still missing. Therefore, we aimed at providing a detailed turnover mass balance of 13 C 6 -metamitron in soil microcosms over 80 days. In the biotic system, metamitron mineralized rapidly, and 13 CO 2 finally constituted 60% of the initial 13 C 6 -metamitron equivalents. In abiotic control experiments CO 2 rose to only 7.4% of the initial 13 C 6 -metamitron equivalents. The 13 C label from 13 C 6 -metamitron was incorporated into microbial amino acids that were ultimately stabilized in the soil organic matter forming presumably harmless biogenic residues. Finally, 13 C label from 13 C 6 -metamitron was distributed between the 13 CO 2 and the 13 C-biogenic residues indicating nearly complete biodegradation. The parallel increase of 13 C-alanine, 13 C-glutamate and 13 CO 2 indicates that metamitron was initially biodegraded via the desamino-metamitron route suggesting its relevance in the growth metabolism. In later phases of biodegradation, the "Rhodococcus route" was indicated by the low 13 CO 2 evolution and the high relevance of the pyruvate pathway, which aims at biomolecule synthesis and seems to be related to starvation. This is a first report on the detailed degradation route of metamitron in soil. Copyright © 2016 Elsevier Ltd. All rights reserved.

Position-specific isotope modeling of organic micropollutants transformations through different reaction pathways

NASA Astrophysics Data System (ADS)

Jin, Biao; Rolle, Massimo

2016-04-01

Organic compounds are produced in vast quantities for industrial and agricultural use, as well as for human and animal healthcare [1]. These chemicals and their metabolites are frequently detected at trace levels in fresh water environments where they undergo degradation via different reaction pathways. Compound specific stable isotope analysis (CSIA) is a valuable tool to identify such degradation pathways in different environmental systems. Recent advances in analytical techniques have promoted the fast development and implementation of multi-element CSIA. However, quantitative frameworks to evaluate multi-element stable isotope data and incorporating mechanistic information on the degradation processes [2,3] are still lacking. In this study we propose a mechanism-based modeling approach to simultaneously evaluate concentration as well as bulk and position-specific multi-element isotope evolution during the transformation of organic micropollutants. The model explicitly simulates position-specific isotopologues for those atoms that experience isotope effects and, thereby, provides a mechanistic description of isotope fractionation occurring at different molecular positions. We validate the proposed approach with the concentration and multi-element isotope data of three selected organic micropollutants: dichlorobenzamide (BAM), isoproturon (IPU) and diclofenac (DCF). The model precisely captures the dual element isotope trends characteristic of different reaction pathways and their range of variation consistent with observed multi-element (C, N) bulk isotope fractionation. The proposed approach can also be used as a tool to explore transformation pathways in scenarios for which position-specific isotope data are not yet available. [1] Schwarzenbach, R.P., Egli, T., Hofstetter, T.B., von Gunten, U., Wehrli, B., 2010. Global Water Pollution and Human Health. Annu. Rev. Environ. Resour. doi:10.1146/annurev-environ-100809-125342. [2] Jin, B., Haderlein, S.B., Rolle, M

Combination of Mass Signal Amplification and Isotope-Labeled Alkanethiols for the Multiplexed Detection of miRNAs.

PubMed

Kang, Hyunook; Hong, Seol-Hye; Sung, Jiha; Yeo, Woon-Seok

2017-08-04

We report a fast and sensitive method for the multiplexed detection of miRNAs by combining mass signal amplification and isotope-labeled signal reporter molecules. In our strategy, target miRNAs are captured specifically by immobilized DNAs on gold nanoparticles (AuNPs), which carry a large number of small molecules, called amplification tags (Am-tags), as the reporter for the detection of target miRNAs. For multiplexed detection, we designed and synthesized four Am-tags containing 0, 4, 8, 12 isotopes so that they had same molecular properties but different molecular weights. By observing the mass signals of the Am-tags on AuNPs decorated along with different probe DNAs, four types of miRNAs in a sample could be easily discriminated, and the relative amounts of these miRNAs could be quantified. The practicability of our strategy was further verified by measuring the expression levels of two miRNAs in HUVECs in response to different CuSO 4 concentrations. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative Proteomics by Metabolic Labeling of Model Organisms*

PubMed Central

Gouw, Joost W.; Krijgsveld, Jeroen; Heck, Albert J. R.

2010-01-01

In the biological sciences, model organisms have been used for many decades and have enabled the gathering of a large proportion of our present day knowledge of basic biological processes and their derailments in disease. Although in many of these studies using model organisms, the focus has primarily been on genetics and genomics approaches, it is important that methods become available to extend this to the relevant protein level. Mass spectrometry-based proteomics is increasingly becoming the standard to comprehensively analyze proteomes. An important transition has been made recently by moving from charting static proteomes to monitoring their dynamics by simultaneously quantifying multiple proteins obtained from differently treated samples. Especially the labeling with stable isotopes has proved an effective means to accurately determine differential expression levels of proteins. Among these, metabolic incorporation of stable isotopes in vivo in whole organisms is one of the favored strategies. In this perspective, we will focus on methodologies to stable isotope label a variety of model organisms in vivo, ranging from relatively simple organisms such as bacteria and yeast to Caenorhabditis elegans, Drosophila, and Arabidopsis up to mammals such as rats and mice. We also summarize how this has opened up ways to investigate biological processes at the protein level in health and disease, revealing conservation and variation across the evolutionary tree of life. PMID:19955089

Quantitative Peptidomics with Five-plex Reductive Methylation labels

NASA Astrophysics Data System (ADS)

Tashima, Alexandre K.; Fricker, Lloyd D.

2017-12-01

Quantitative peptidomics and proteomics often use chemical tags to covalently modify peptides with reagents that differ in the number of stable isotopes, allowing for quantitation of the relative peptide levels in the original sample based on the peak height of each isotopic form. Different chemical reagents have been used as tags for quantitative peptidomics and proteomics, and all have strengths and weaknesses. One of the simplest approaches uses formaldehyde and sodium cyanoborohydride to methylate amines, converting primary and secondary amines into tertiary amines. Up to five different isotopic forms can be generated, depending on the isotopic forms of formaldehyde and cyanoborohydride reagents, allowing for five-plex quantitation. However, the mass difference between each of these forms is only 1 Da per methyl group incorporated into the peptide, and for many peptides there is substantial overlap from the natural abundance of 13C and other isotopes. In this study, we calculated the contribution from the natural isotopes for 26 native peptides and derived equations to correct the peak intensities. These equations were applied to data from a study using human embryonic kidney HEK293T cells in which five replicates were treated with 100 nM vinblastine for 3 h and compared with five replicates of cells treated with control medium. The correction equations brought the replicates to the expected 1:1 ratios and revealed significant decreases in levels of 21 peptides upon vinblastine treatment. These equations enable accurate quantitation of small changes in peptide levels using the reductive methylation labeling approach. [Figure not available: see fulltext.

Quantitative Peptidomics with Five-plex Reductive Methylation labels

NASA Astrophysics Data System (ADS)

Tashima, Alexandre K.; Fricker, Lloyd D.

2018-05-01

Quantitative peptidomics and proteomics often use chemical tags to covalently modify peptides with reagents that differ in the number of stable isotopes, allowing for quantitation of the relative peptide levels in the original sample based on the peak height of each isotopic form. Different chemical reagents have been used as tags for quantitative peptidomics and proteomics, and all have strengths and weaknesses. One of the simplest approaches uses formaldehyde and sodium cyanoborohydride to methylate amines, converting primary and secondary amines into tertiary amines. Up to five different isotopic forms can be generated, depending on the isotopic forms of formaldehyde and cyanoborohydride reagents, allowing for five-plex quantitation. However, the mass difference between each of these forms is only 1 Da per methyl group incorporated into the peptide, and for many peptides there is substantial overlap from the natural abundance of 13C and other isotopes. In this study, we calculated the contribution from the natural isotopes for 26 native peptides and derived equations to correct the peak intensities. These equations were applied to data from a study using human embryonic kidney HEK293T cells in which five replicates were treated with 100 nM vinblastine for 3 h and compared with five replicates of cells treated with control medium. The correction equations brought the replicates to the expected 1:1 ratios and revealed significant decreases in levels of 21 peptides upon vinblastine treatment. These equations enable accurate quantitation of small changes in peptide levels using the reductive methylation labeling approach. [Figure not available: see fulltext.

Synthesis of carbon-14 and stable isotope labeled Avagacestat: a novel gamma secretase inhibitor for the treatment of Alzheimer's disease.

PubMed

Burrell, Richard C; Easter, John A; Cassidy, Michael P; Gillman, Kevin W; Olson, Richard E; Bonacorsi, Samuel J

2014-08-01

Bristol-Myers Squibb and others are developing drugs that target novel mechanisms to combat Alzheimer's disease. γ-Secretase inhibitors are one class of potential therapies that have received considerable attention. (R)-2-(4-Chloro-N-(2-fluoro-4-(1,2,4-oxadiazol-3-yl)benzyl)phenylsulfonamido)-5,5,5-trifluoropentanamide (Avagacestat) is a γ-secretase-inhibiting drug that has been investigated by Bristol-Myers Squibb in preclinical and clinical studies. An important step in the development process was the synthesis of a carbon-14-labeled analog for use in a human absorption, distribution, metabolism, and excretion study and a stable isotope labeled analog for use as a standard in bioanalytical assays to accurately quantify the concentration of the drug in biological samples. Carbon-14 labeled Avagacestat was synthesized in seven steps in a 33% overall yield from carbon-14 labeled potassium cyanide. A total of 5.95 mCi was prepared with a specific activity of 0.81 μCi/mg and a radiochemical purity of 99.9%. (13) C6 -Labeled Avagacestat was synthesized in three steps in a 15% overall yield from 4-chloro[(13) C6 ]aniline. A total of 585 mg was prepared with a ultraviolet purity of 99.9%. Copyright © 2014 John Wiley & Sons, Ltd.

Dehydrogenation and dehalogenation of amines in MALDI-TOF MS investigated by isotopic labeling.

PubMed

Kang, Chuanqing; Zhou, Yihan; Du, Zhijun; Bian, Zheng; Wang, Jianwei; Qiu, Xuepeng; Gao, Lianxun; Sun, Yuequan

2013-12-01

Secondary and tertiary amines have been reported to form [M-H](+) that correspond to dehydrogenation in matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). In this investigation, we studied the dehydrogenation of amines in MALDI-TOF MS by isotopic labeling. Aliphatic amines were labeled with deuterium on the methylene of an N-benzyl group, which resulted in the formation of [M-D](+) and [M-H](+) ions by dedeuteration and dehydrogenation, respectively. This method revealed the proton that was removed. The spectra of most tertiary amines with an N-benzyl group showed high-intensity [M-D](+) and [M-H](+) ion peaks, whereas those of secondary amines showed low-intensity ion peaks. Ratios between the peak intensities of [M-D](+) and [M-H](+) greater than 1 suggested chemoselective dehydrogenation at the N-benzyl groups. The presence of an electron donor group on the N-benzyl groups enhanced the selectivity. The dehalogenation of amines with an N-(4-halobenzyl) group was also observed alongside dehydrogenation. The amino ions from dehalogenation can undergo second dehydrogenation. These results provide the first direct evidence about the position at which dehydrogenation of an amine occurs and the first example of dehalogenation of haloaromatic compounds in MALDI-TOF MS. These results should be helpful in the structural identification and elucidation of synthetic and natural molecules. Copyright © 2013 John Wiley & Sons, Ltd.

Detection of Cancer Metastases with a Dual-labeled Near-Infrared/Positron Emission Tomography Imaging Agent12

PubMed Central

Sampath, Lakshmi; Kwon, Sunkuk; Hall, Mary A; Price, Roger E; Sevick-Muraca, Eva M

2010-01-01

By dual labeling a targeting moiety with both nuclear and optical probes, the ability for noninvasive imaging and intraoperative guidance may be possible. Herein, the ability to detect metastasis in an immunocompetent animal model of human epidermal growth factor receptor 2 (HER-2)-positive cancer metastases using positron emission tomography (PET) and near-infrared (NIR) fluorescence imaging is demonstrated. METHODS: (64Cu-DOTA)n-trastuzumab-(IRDye800)m was synthesized, characterized, and administered to female Balb/c mice subcutaneously inoculated with highly metastatic 4T1.2neu/R breast cancer cells. (64Cu-DOTA)n-trastuzumab-(IRDye800)m (150 µg, 150 µCi, m = 2, n = 2) was administered through the tail vein at weeks 2 and 6 after implantation, and PET/computed tomography and NIR fluorescence imaging were performed 24 hours later. Results were compared with the detection capabilities of F-18 fluorodeoxyglucose (18FDG-PET). RESULTS: Primary tumors were visualized with 18FDG and (64Cu-DOTA)n-trastuzumab-(IRDye800)m, but resulting metastases were identified only with the dual-labeled imaging agent. 64Cu-PET imaging detected lung metastases, whereas ex vivo NIR fluorescence showed uptake in regions of lung, skin, skeletal muscle, and lymph nodes, which corresponded with the presence of cancer cells as confirmed by histologic hematoxylin and eosin stains. In addition to detecting the agent in lymph nodes, the high signal-to-noise ratio from NIR fluorescence imaging enabled visualization of channels between the primary tumor and the axillary lymph nodes, suggesting a lymphatic route for trafficking cancer cells. Because antibody clearance occurs through the liver, we could not distinguish between nonspecific uptake and liver metastases. CONCLUSION: (64Cu-DOTA)n-trastuzumab-(IRDye800)m may be an effective diagnostic imaging agent for staging HER-2-positive breast cancer patients and intraoperative resection. PMID:20885893

Isotopically Nonstationary Metabolic Flux Analysis (INST-MFA) of Photosynthesis and Photorespiration in Plants.

PubMed

Ma, Fangfang; Jazmin, Lara J; Young, Jamey D; Allen, Doug K

2017-01-01

Photorespiration is a central component of photosynthesis; however to better understand its role it should be viewed in the context of an integrated metabolic network rather than a series of individual reactions that operate independently. Isotopically nonstationary 13 C metabolic flux analysis (INST-MFA), which is based on transient labeling studies at metabolic steady state, offers a comprehensive platform to quantify plant central metabolism. In this chapter, we describe the application of INST-MFA to investigate metabolism in leaves. Leaves are an autotrophic tissue, assimilating CO 2 over a diurnal period implying that the metabolic steady state is limited to less than 12 h and thus requiring an INST-MFA approach. This strategy results in a comprehensive unified description of photorespiration, Calvin cycle, sucrose and starch synthesis, tricarboxylic acid (TCA) cycle, and amino acid biosynthetic fluxes. We present protocols of the experimental aspects for labeling studies: transient 13 CO 2 labeling of leaf tissue, sample quenching and extraction, mass spectrometry (MS) analysis of isotopic labeling data, measurement of sucrose and amino acids in vascular exudates, and provide details on the computational flux estimation using INST-MFA.

Evaluating abdominal oedema during experimental sepsis using an isotope technique.

PubMed

Lattuada, Marco; Maripuu, Enn; Segerstad, Carl Hard af; Lundqvist, Hans; Hedenstierna, Göran

2012-05-01

Abdominal oedema is common in sepsis. A technique for the study of such oedema may guide in the fluid regime of these patients. We modified a double-isotope technique to evaluate abdominal organ oedema and fluid extravasation in 24 healthy or endotoxin-exposed ('septic') piglets. Two different markers were used: red blood cells (RBC) labelled with Technetium-99m ((99m)Tc) and Transferrin labelled with Indium111 ((111)In). Images were acquired on a dual-head gamma camera. Microscopic evaluation of tissue biopsies was performed to compare data with the isotope technique. No (99m)Tc activity was measured in the plasma fraction in blood sampled after labelling. Similarly, after molecular size gel chromatography, (111)In activity was exclusively found in the high molecular fraction of the plasma. Extravasation of transferrin, indicating the degree of abdominal oedema, was 4·06 times higher in the LPS group compared to the healthy controls (P<0·0001). Abdominal free fluid, studied in 3 animals, had as high (111)In activity as in plasma, but no (99m)Tc activity. Intestinal lymphatic vessel size was higher in LPS (3·7 ± 1·1 μm) compared to control animals (0·6 + 0·2 μm; P<0·001) and oedema correlated to villus diameter (R(2) = 0·918) and lymphatic diameter (R(2) = 0·758). A correlation between a normalized index of oedema formation (NI) and intra-abdominal pressure (IAP) was also found: NI = 0·46*IAP-3·3 (R(2) = 0·56). The technique enables almost continuous recording of abdominal oedema formation and may be a valuable tool in experimental research, with the potential to be applied in the clinic. © 2011 The Authors. Clinical Physiology and Functional Imaging © 2011 Scandinavian Society of Clinical Physiology and Nuclear Medicine.

Uranium disequilibrium in groundwater: An isotope dilution approach in hydrologic investigations

USGS Publications Warehouse

Osmond, J.K.; Rydell, H.S.; Kaufman, M.I.

1968-01-01

The distribution and environmental disequilibrium patterns of naturally occurring uranium isotopes (U234 and U238) in waters of the Floridan aquifer suggest that variations in the ratios of isotopic activity and concentrations can be used quantitatively to evaluate mixing proportions of waters from differing sources. Uranium is probably unique in its potential for this approach, which seems to have general usefulness in hydrologic investigations.

Metabolically Generated Stable Isotope-Labeled Deoxynucleoside Code for Tracing DNA N6-Methyladenine in Human Cells.

PubMed

Liu, Baodong; Liu, Xiaoling; Lai, Weiyi; Wang, Hailin

2017-06-06

DNA N 6 -methyl-2'-deoxyadenosine (6mdA) is an epigenetic modification in both eukaryotes and bacteria. Here we exploited stable isotope-labeled deoxynucleoside [ 15 N 5 ]-2'-deoxyadenosine ([ 15 N 5 ]-dA) as an initiation tracer and for the first time developed a metabolically differential tracing code for monitoring DNA 6mdA in human cells. We demonstrate that the initiation tracer [ 15 N 5 ]-dA undergoes a specific and efficient adenine deamination reaction leading to the loss the exocyclic amine 15 N, and further utilizes the purine salvage pathway to generate mainly both [ 15 N 4 ]-dA and [ 15 N 4 ]-2'-deoxyguanosine ([ 15 N 4 ]-dG) in mammalian genomes. However, [ 15 N 5 ]-dA is largely retained in the genomes of mycoplasmas, which are often found in cultured cells and experimental animals. Consequently, the methylation of dA generates 6mdA with a consistent coding pattern, with a predominance of [ 15 N 4 ]-6mdA. Therefore, mammalian DNA 6mdA can be potentially discriminated from that generated by infecting mycoplasmas. Collectively, we show a promising approach for identification of authentic DNA 6mdA in human cells and determine if the human cells are contaminated with mycoplasmas.

Glacial/interglacial wetland, biomass burning, and geologic methane emissions constrained by dual stable isotopic CH4 ice core records

PubMed Central

Beck, Jonas; Seth, Barbara; Chappellaz, Jérôme

2017-01-01

Atmospheric methane (CH4) records reconstructed from polar ice cores represent an integrated view on processes predominantly taking place in the terrestrial biogeosphere. Here, we present dual stable isotopic methane records [δ13CH4 and δD(CH4)] from four Antarctic ice cores, which provide improved constraints on past changes in natural methane sources. Our isotope data show that tropical wetlands and seasonally inundated floodplains are most likely the controlling sources of atmospheric methane variations for the current and two older interglacials and their preceding glacial maxima. The changes in these sources are steered by variations in temperature, precipitation, and the water table as modulated by insolation, (local) sea level, and monsoon intensity. Based on our δD(CH4) constraint, it seems that geologic emissions of methane may play a steady but only minor role in atmospheric CH4 changes and that the glacial budget is not dominated by these sources. Superimposed on the glacial/interglacial variations is a marked difference in both isotope records, with systematically higher values during the last 25,000 y compared with older time periods. This shift cannot be explained by climatic changes. Rather, our isotopic methane budget points to a marked increase in fire activity, possibly caused by biome changes and accumulation of fuel related to the late Pleistocene megafauna extinction, which took place in the course of the last glacial. PMID:28673973

Sulphur tracer experiments in laboratory animals using 34S-labelled yeast.

PubMed

Martínez-Sierra, J Giner; Moreno Sanz, F; Herrero Espílez, P; Marchante Gayón, J M; Rodríguez Fernández, J; García Alonso, J I

2013-03-01

We have evaluated the use of (34)S-labelled yeast to perform sulphur metabolic tracer experiments in laboratory animals. The proof of principle work included the selection of the culture conditions for the preparation of sulphur labelled yeast, the study of the suitability of this labelled yeast as sulphur source for tracer studies using in vitro gastrointestinal digestion and the administration of the (34)S-labelled yeast to laboratory animals to follow the fate and distribution of (34)S in the organism. For in vitro gastrointestinal digestion, the combination of sodium dodecyl sulphate-polyacrylamide gel electrophoresis and high-performance liquid chromatography and inductively coupled plasma mass spectrometry (HPLC-ICP-MS) showed that labelled methionine, cysteine and other low molecular weight sulphur-containing biomolecules were the major components in the digested extracts of the labelled yeast. Next, in vivo kinetic experiments were performed in healthy Wistar rats after the oral administration of (34)S-labelled yeast. The isotopic composition of total sulphur in tissues, urine and faeces was measured by double-focusing inductively coupled plasma mass spectrometry after microwave digestion. It was observed that measurable isotopic enrichments were detected in all samples. Finally, initial investigations on sulphur isotopic composition of serum and urine samples by HPLC-ICP-MS have been carried out. For serum samples, no conclusive data were obtained. Interestingly, chromatographic analysis of urine samples showed differential isotope enrichment for several sulphur-containing biomolecules.

Dual-mode fluorophore-doped nickel nitrilotriacetic acid-modified silica nanoparticles combine histidine-tagged protein purification with site-specific fluorophore labeling.

PubMed

Kim, Sung Hoon; Jeyakumar, M; Katzenellenbogen, John A

2007-10-31

We present the first example of a fluorophore-doped nickel chelate surface-modified silica nanoparticle that functions in a dual mode, combining histidine-tagged protein purification with site-specific fluorophore labeling. Tetramethylrhodamine (TMR)-doped silica nanoparticles, estimated to contain 700-900 TMRs per ca. 23 nm particle, were surface modified with nitrilotriacetic acid (NTA), producing TMR-SiO2-NTA-Ni2+. Silica-embedded TMR retains very high quantum yield, is resistant to quenching by buffer components, and is modestly quenched and only to a certain depth (ca. 2 nm) by surface-attached Ni2+. When exposed to a bacterial lysate containing estrogen receptor alpha ligand binding domain (ERalpha) as a minor component, these beads showed very high specificity binding, enabling protein purification in one step. The capacity and specificity of these beads for binding a his-tagged protein were characterized by electrophoresis, radiometric counting, and MALDI-TOF MS. ERalpha, bound to TMR-SiO2-NTA-Ni++ beads in a site-specific manner, exhibited good activity for ligand binding and for ligand-induced binding to coactivators in solution FRET experiments and protein microarray fluorometric and FRET assays. This dual-mode type TMR-SiO2-NTA-Ni2+ system represents a powerful combination of one-step histidine-tagged protein purification and site-specific labeling with multiple fluorophore species.

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

PubMed Central

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

2015-01-01

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

The Cannon: A data-driven approach to Stellar Label Determination

NASA Astrophysics Data System (ADS)

Ness, M.; Hogg, David W.; Rix, H.-W.; Ho, Anna. Y. Q.; Zasowski, G.

2015-07-01

New spectroscopic surveys offer the promise of stellar parameters and abundances (“stellar labels”) for hundreds of thousands of stars; this poses a formidable spectral modeling challenge. In many cases, there is a subset of reference objects for which the stellar labels are known with high(er) fidelity. We take advantage of this with The Cannon, a new data-driven approach for determining stellar labels from spectroscopic data. The Cannon learns from the “known” labels of reference stars how the continuum-normalized spectra depend on these labels by fitting a flexible model at each wavelength; then, The Cannon uses this model to derive labels for the remaining survey stars. We illustrate The Cannon by training the model on only 542 stars in 19 clusters as reference objects, with {T}{eff}, {log} g, and [{Fe}/{{H}}] as the labels, and then applying it to the spectra of 55,000 stars from APOGEE DR10. The Cannon is very accurate. Its stellar labels compare well to the stars for which APOGEE pipeline (ASPCAP) labels are provided in DR10, with rms differences that are basically identical to the stated ASPCAP uncertainties. Beyond the reference labels, The Cannon makes no use of stellar models nor any line-list, but needs a set of reference objects that span label-space. The Cannon performs well at lower signal-to-noise, as it delivers comparably good labels even at one-ninth the APOGEE observing time. We discuss the limitations of The Cannon and its future potential, particularly, to bring different spectroscopic surveys onto a consistent scale of stellar labels.

Synthesis of l-cysteine derivatives containing stable sulfur isotopes and application of this synthesis to reactive sulfur metabolome.

PubMed

Ono, Katsuhiko; Jung, Minkyung; Zhang, Tianli; Tsutsuki, Hiroyasu; Sezaki, Hiroshi; Ihara, Hideshi; Wei, Fan-Yan; Tomizawa, Kazuhito; Akaike, Takaaki; Sawa, Tomohiro

2017-05-01

Cysteine persulfide is an L-cysteine derivative having one additional sulfur atom bound to a cysteinyl thiol group, and it serves as a reactive sulfur species that regulates redox homeostasis in cells. Here, we describe a rapid and efficient method of synthesis of L-cysteine derivatives containing isotopic sulfur atoms and application of this method to a reactive sulfur metabolome. We used bacterial cysteine syntheses to incorporate isotopic sulfur atoms into the sulfhydryl moiety of L-cysteine. We cloned three cysteine synthases-CysE, CysK, and CysM-from the Gram-negative bacterium Salmonella enterica serovar Typhimurium LT2, and we generated their recombinant enzymes. We synthesized 34 S-labeled L-cysteine from O-acetyl-L-serine and 34 S-labeled sodium sulfide as substrates for the CysK or CysM reactions. Isotopic labeling of L-cysteine at both sulfur ( 34 S) and nitrogen ( 15 N) atoms was also achieved by performing enzyme reactions with 15 N-labeled L-serine, acetyl-CoA, and 34 S-labeled sodium sulfide in the presence of CysE and CysK. The present enzyme systems can be applied to syntheses of a series of L-cysteine derivatives including L-cystine, L-cystine persulfide, S-sulfo-L-cysteine, L-cysteine sulfonate, and L-selenocystine. We also prepared 34 S-labeled N-acetyl-L-cysteine (NAC) by incubating 34 S-labeled L-cysteine with acetyl coenzyme A in test tubes. Tandem mass spectrometric identification of low-molecular-weight thiols after monobromobimane derivatization revealed the endogenous occurrence of NAC in the cultured mammalian cells such as HeLa cells and J774.1 cells. Furthermore, we successfully demonstrated, by using 34 S-labeled NAC, metabolic conversion of NAC to glutathione and its persulfide, via intermediate formation of L-cysteine, in the cells. The approach using isotopic sulfur labeling combined with mass spectrometry may thus contribute to greater understanding of reactive sulfur metabolome and redox biology. Copyright © 2017 Elsevier Inc

Capture and detection of Staphylococcus aureus with dual labeled aptamers to cell surface components.

PubMed

Ramlal, Shylaja; Mondal, Bhairab; Lavu, Padma Sudharani; N, Bhavanashri; Kingston, Joseph

2018-01-16

In the present study, a high throughput whole cell SELEX method has been applied successfully in selecting specific aptamers against whole cells of Staphylococcus aureus, a potent food poisoning bacterium. A total ten rounds of SELEX and three rounds of intermittent counter SELEX, was performed to obtain specific aptamers. Obtained oligonucleotide pool were cloned, sequenced and then grouped into different families based on their primary sequence homology and secondary structure similarity. FITC labeled sequences from different families were selected for further characterization via flow cytometry analysis. The dissociation constant (K d ) values of specific and higher binders ranged from 34 to 128nM. Binding assays to assess the selectivity of aptamer RAB10, RAB 20, RAB 28 and RAB 35 demonstrated high affinity against S. aureus and low binding affinity for other bacteria. To demonstrate the potential use of the aptamer a sensitive dual labeled sandwich detection system was developed using aptamer RAB10 and RAB 35 with a detection limit of 10 2 CFU/mL. Furthermore detection from mixed cell population and spiked sample emphasized the robustness as well as applicability of the developed method. Altogether, the established assay could be a reliable detection tool for the routine investigation of Staphylococcus aureus in samples from food and clinical sources. Copyright © 2017. Published by Elsevier B.V.

Developing a Dual-Level Capabilities Approach: Using Constructivist Grounded Theory and Feminist Ethnography to Enhance the Capabilities Approaches

ERIC Educational Resources Information Center

Hall, Kia M. Q.

2014-01-01

In this study, a dual-level capabilities approach to development is introduced. This approach intends to improve upon individual-focused capabilities approaches developed by Amartya Sen and Martha Nussbaum. Based upon seven months of ethnographic research in the Afro-descendant, autochthonous Garifuna community of Honduras, constructivist grounded…

Investigating CH4 production in an oxic plant-soil system -a new approach combining isotopic labelling (13C) and inhibitors

NASA Astrophysics Data System (ADS)

Lenhart, Katharina; Keppler, Frank

2017-04-01

Typically, aerated soil are net sinks of atmospheric methane (CH4), being highest in native ecosystems (pristine forests > managed forests > grasslands > crop fields). However, this does not exclude a simultaneous endogenic CH4 production in the plant-soil system, which cannot be detected simply via CH4 flux measurements. Methanogenic archaea producing CH4 under anoxic conditions were thought to be the only biotic source of CH4 in the soil. However, until recently a non-archaeal pathway of CH4 formation is known where CH4 is produced under oxic conditions in plants (Keppler et al. 2006) and fungi (Lenhart et al. 2012). Additionally, abiotic formation of CH4 from soil organic matter was reported (Jugold et al. 2012) and may be ubiquitous in terrestrial ecosystems. The major goal of this project was to determine soil endogenic CH4 sources and to estimate their contribution to the endogenic CH4 production. Especially the effect of plants and fungi on soil CH4 production was investigated. Therefore, a series of experiments was carried out on field fresh soil collected in a grassland and a forest ecosystem under controlled laboratory conditions. By combining selective inhibitors and 13C labelling, CH4 production rates of several CH4 sources were quantified. The major difficulty was to detect the comparatively small flux of CH4 production against the background of the high CH4 consumption rates due to methanotrophic bacteria. Therefore, we supplemented bare soil and soil with vegetation with selective inhibitors and 13C labelled substrates in a closed chamber system. In a first step, CH4 production was determined by the inhibition of CH4 oxidizing bacteria with Difluoromethane (DFM, 2ml l-1). In the following, a 13C labelled substrate (either CO2, Acetate, or Methionine -S-CH3 labelled) was added in combination with a specific inhibitor -either for archaeal methanogenesis (Bromoethanesulfonate), bacteria (Streptomycin), or fungi (Captan, Cycloheximide). Gas samples were

Practical strategies when using a stable isotope labeled microtracer for absolute bioavailability assessment: A case study of a high oral dose clinical candidate GDC-0810.

PubMed

Chen, Buyun; Lu, Pingping; Freeman, Dugan; Gao, Yang; Choo, Edna; DeMent, Kevin; Savage, Scott; Zhang, Kelly; Milanwoski, Dennis; Liu, Lichuan; Dean, Brian; Deng, Yuzhong

2018-05-30

The pH labile metabolite, hydrophobicity, high oral dose and systematic exposure of GDC-0810 posed tremendous challenges to develop a LC-MS method for a stable isotope labeled aBA study. In this study, we explored practical solutions to balance stability and sensitivity and to cope with the impact of high C p.o. to C i.v. ratio on the labeling selection and assay dynamic range. A [ 13 C 9 ] GDC-0810 was synthesized to minimize the isotopic interference between PO dose, internal standard and I.V. microtracer. A highly sensitive LC-MS assay was validated for quantitation of [ 13 C 9 ] GDC-0810 from 5 to 1250 pg/mL. The optimized method was applied to a proof of concept cynomolgus monkey aBA study and the bioavailability calculated using microtracer dosing and regular dosing were similar to each other. Copyright © 2018 Elsevier B.V. All rights reserved.

Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients.

PubMed

Lueders, Tillmann; Manefield, Mike; Friedrich, Michael W

2004-01-01

Stable isotope probing (SIP) of nucleic acids allows the detection and identification of active members of natural microbial populations that are involved in the assimilation of an isotopically labelled compound into nucleic acids. SIP is based on the separation of isotopically labelled DNA or rRNA by isopycnic density gradient centrifugation. We have developed a highly sensitive protocol for the detection of 'light' and 'heavy' nucleic acids in fractions of centrifugation gradients. It involves the fluorometric quantification of total DNA or rRNA, and the quantification of either 16S rRNA genes or 16S rRNA in gradient fractions by real-time PCR with domain-specific primers. Using this approach, we found that fully 13C-labelled DNA or rRNA of Methylobacterium extorquens was quantitatively resolved from unlabelled DNA or rRNA of Methanosarcina barkeri by cesium chloride or cesium trifluoroacetate density gradient centrifugation respectively. However, a constant low background of unspecific nucleic acids was detected in all DNA or rRNA gradient fractions, which is important for the interpretation of environmental SIP results. Consequently, quantitative analysis of gradient fractions provides a higher precision and finer resolution for retrieval of isotopically enriched nucleic acids than possible using ethidium bromide or gradient fractionation combined with fingerprinting analyses. This is a prerequisite for the fine-scale tracing of microbial populations metabolizing 13C-labelled compounds in natural ecosystems.

Mass spectrometric measurements of norepinephrine synthesis in man from infusion of stable isotope-labelled L-threo-3,4-dihydroxyphenylserine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suzuki, T.; Sakoda, S.; Ueji, M.

The kinetics of stable isotope-labelled L-threo-3,4-dihydroxyphenylserine (L-threo-DOPS), an immediate precursor of (-)-norepinephrine, was studied to investigate the pharmacologic mechanism of its therapeutic effect on orthostatic hypotension in familial amyloid polyneuropathy (FAP) and on akinesia and freezing in parkinsonism. (/sup 13/C,D)-L-threo-DOPS was synthesized, and 100 mg of the compound was infused for 2 h into two normal subjects, two FAP patients and two patients with the degenerative diseases of the central nervous system. Labelled and endogenous norepinephrine in urine and plasma was assayed simultaneously by gas chromatography/mass spectrometry. The results indicate that the increase in norepinephrine in biological fluids after administrationmore » of L-threo-DOPS is attributable mostly to norepinephrine derived from L-threo-DOPS, not to pre-formed endogenous norepinephrine released by L-threo-DOPS.« less

Co-Labeling for Multi-View Weakly Labeled Learning.

PubMed

Xu, Xinxing; Li, Wen; Xu, Dong; Tsang, Ivor W

2016-06-01

It is often expensive and time consuming to collect labeled training samples in many real-world applications. To reduce human effort on annotating training samples, many machine learning techniques (e.g., semi-supervised learning (SSL), multi-instance learning (MIL), etc.) have been studied to exploit weakly labeled training samples. Meanwhile, when the training data is represented with multiple types of features, many multi-view learning methods have shown that classifiers trained on different views can help each other to better utilize the unlabeled training samples for the SSL task. In this paper, we study a new learning problem called multi-view weakly labeled learning, in which we aim to develop a unified approach to learn robust classifiers by effectively utilizing different types of weakly labeled multi-view data from a broad range of tasks including SSL, MIL and relative outlier detection (ROD). We propose an effective approach called co-labeling to solve the multi-view weakly labeled learning problem. Specifically, we model the learning problem on each view as a weakly labeled learning problem, which aims to learn an optimal classifier from a set of pseudo-label vectors generated by using the classifiers trained from other views. Unlike traditional co-training approaches using a single pseudo-label vector for training each classifier, our co-labeling approach explores different strategies to utilize the predictions from different views, biases and iterations for generating the pseudo-label vectors, making our approach more robust for real-world applications. Moreover, to further improve the weakly labeled learning on each view, we also exploit the inherent group structure in the pseudo-label vectors generated from different strategies, which leads to a new multi-layer multiple kernel learning problem. Promising results for text-based image retrieval on the NUS-WIDE dataset as well as news classification and text categorization on several real-world multi

Using Power Spectrum Analysis to Evaluate 18O-Water Labeling Data Acquired from Low Resolution Mass Spectrometers

PubMed Central

Sadygov, Rovshan G.; Zhao, Yingxin; Haidacher, Sigmund J.; Starkey, Jonathan M.; Tilton, Ronald G.; Denner, Larry

2010-01-01

We describe a method for ratio estimations in 18O-water labeling experiments acquired from low resolution isotopically resolved data. The method is implemented in a software package specifically designed for use in experiments making use of zoom-scan mode data acquisition. Zoom-scan mode data allows commonly used ion trap mass spectrometers to attain isotopic resolution, which make them amenable to use in labeling schemes such as 18O-water labeling, but algorithms and software developed for high resolution instruments may not be appropriate for the lower resolution data acquired in zoom-scan mode. The use of power spectrum analysis is proposed as a general approach which may be uniquely suited to these data types. The software implementation uses power spectrum to remove high-frequency noise, and band-filter contributions from co-eluting species of differing charge states. From the elemental composition of a peptide sequence we generate theoretical isotope envelopes of heavy-light peptide pairs in five different ratios; these theoretical envelopes are correlated with the filtered experimental zoom scans. To automate peptide quantification in high-throughput experiments, we have implemented our approach in a computer program, MassXplorer. We demonstrate the application of MassXplorer to two model mixtures of known proteins, and to a complex mixture of mouse kidney cortical extract. Comparison with another algorithm for ratio estimations demonstrates the increased precision and automation of MassXplorer. PMID:20568695

The metabolic fate of doubly stable isotope labelled heat-killed Lactobacillus johnsonii in humans.

PubMed

Wutzke, K D; Berg, D; Haffner, D

2008-02-01

In this study, heat-killed Lactobacillus johnsonii (La1), doubly labelled with (13)C and (15)N (hk-dlLa1), was used to follow the metabolic fate after oral administration in humans. Experimental study. University of Rostock, Children's Hospital, Research Laboratory. Ten healthy adults aged 23-26 years. The subjects received 74.6 mg/kg body weight hk-dlLa1 and 10 g alpha-D-raffinose together with breakfast. A sample of venous blood was taken after 2 h. Expired air samples were taken over 14 h, whereas urine and faeces were collected over a period of 48 h. (13)C- and (15)N-enrichments were measured by isotope ratio mass spectrometry. Hydrogen concentrations were measured by electrochemical detection. The orocaecal transit time (OCTT) was reached after 3.4 h. After 2 h, (13)C- and (15)N-enrichment of fibrinogen amounted to 2 and 25 p.p.m. excess, respectively. The (13)CO(2)-exhalation amounted to 9.2% of the ingested dose. The urinary excretion of (13)C and (15)N was 2.1 and 10.4% of the ingested dose, respectively, whereas the faecal excretion was 47.9 and 43.7% of the ingested dose, respectively. In comparison to OCTT of 3.4 h, both stable isotopes appear after 30 min in breath and urine, indicating that hk-dlLa1 is rapidly digested in the small bowel before reaching the caecum. This is confirmed by (13)C-and (15)N-enrichments of blood plasma fractions. The ingestion of hk-dlLa1 led to a (13)C- and (15)N-excretion of 59.2 and 54.1% of the ingested dose, respectively, of both stable isotopes.

Chemical biology-based approaches on fluorescent labeling of proteins in live cells.

PubMed

Jung, Deokho; Min, Kyoungmi; Jung, Juyeon; Jang, Wonhee; Kwon, Youngeun

2013-05-01

Recently, significant advances have been made in live cell imaging owing to the rapid development of selective labeling of proteins in vivo. Green fluorescent protein (GFP) was the first example of fluorescent reporters genetically introduced to protein of interest (POI). While GFP and various types of engineered fluorescent proteins (FPs) have been actively used for live cell imaging for many years, the size and the limited windows of fluorescent spectra of GFP and its variants set limits on possible applications. In order to complement FP-based labeling methods, alternative approaches that allow incorporation of synthetic fluorescent probes to target POIs were developed. Synthetic fluorescent probes are smaller than fluorescent proteins, often have improved photochemical properties, and offer a larger variety of colors. These synthetic probes can be introduced to POIs selectively by numerous approaches that can be largely categorized into chemical recognition-based labeling, which utilizes metal-chelating peptide tags and fluorophore-carrying metal complexes, and biological recognition-based labeling, such as (1) specific non-covalent binding between an enzyme tag and its fluorophore-carrying substrate, (2) self-modification of protein tags using substrate variants conjugated to fluorophores, (3) enzymatic reaction to generate a covalent binding between a small molecule substrate and a peptide tag, and (4) split-intein-based C-terminal labeling of target proteins. The chemical recognition-based labeling reaction often suffers from compromised selectivity of metal-ligand interaction in the cytosolic environment, consequently producing high background signals. Use of protein-substrate interactions or enzyme-mediated reactions generally shows improved specificity but each method has its limitations. Some examples are the presence of large linker protein, restriction on the choice of introducible probes due to the substrate specificity of enzymes, and competitive

Development of isotope labeling liquid chromatography mass spectrometry for mouse urine metabolomics: quantitative metabolomic study of transgenic mice related to Alzheimer's disease.

PubMed

Peng, Jun; Guo, Kevin; Xia, Jianguo; Zhou, Jianjun; Yang, Jing; Westaway, David; Wishart, David S; Li, Liang

2014-10-03

Because of a limited volume of urine that can be collected from a mouse, it is very difficult to apply the common strategy of using multiple analytical techniques to analyze the metabolites to increase the metabolome coverage for mouse urine metabolomics. We report an enabling method based on differential isotope labeling liquid chromatography mass spectrometry (LC-MS) for relative quantification of over 950 putative metabolites using 20 μL of urine as the starting material. The workflow involves aliquoting 10 μL of an individual urine sample for ¹²C-dansylation labeling that target amines and phenols. Another 10 μL of aliquot was taken from each sample to generate a pooled sample that was subjected to ¹³C-dansylation labeling. The ¹²C-labeled individual sample was mixed with an equal volume of the ¹³C-labeled pooled sample. The mixture was then analyzed by LC-MS to generate information on metabolite concentration differences among different individual samples. The interday repeatability for the LC-MS runs was assessed, and the median relative standard deviation over 4 days was 5.0%. This workflow was then applied to a metabolomic biomarker discovery study using urine samples obtained from the TgCRND8 mouse model of early onset familial Alzheimer's disease (FAD) throughout the course of their pathological deposition of beta amyloid (Aβ). It was showed that there was a distinct metabolomic separation between the AD prone mice and the wild type (control) group. As early as 15-17 weeks of age (presymptomatic), metabolomic differences were observed between the two groups, and after the age of 25 weeks the metabolomic alterations became more pronounced. The metabolomic changes at different ages corroborated well with the phenotype changes in this transgenic mice model. Several useful candidate biomarkers including methionine, desaminotyrosine, taurine, N1-acetylspermidine, and 5-hydroxyindoleacetic acid were identified. Some of them were found in previous

Revisiting streamside trees that do not use stream water: can the two water worlds hypothesis and snowpack isotopic effects explain a missing water source?: Riparian tree water sources

DOE PAGES

Bowling, David R.; Schulze, Emily S.; Hall, Steven J.

2016-10-14

We revisit a classic ecohydrological study that showed streamside riparian trees in a semiarid mountain catchment did not use perennial stream water. The original study suggested that mature individuals of Acer negundo, Acer grandidentatum, and other species were dependent on water from “deeper strata,” possibly groundwater. We used a dual stable isotope approach (δ 18O and δ 2H) to further examine the water sources of these trees. We tested the hypothesis that groundwater was the main tree water source, but found that neither groundwater nor stream water matched the isotope composition of xylem water during two growing seasons. Soil watermore » (0–1 m depth) was closest to and periodically overlapped with xylem water isotope composition, but overall, xylem water was isotopically enriched compared to all measured water sources. The “two water worlds” hypothesis postulates that soil water comprises isotopically distinct mobile and less mobile pools that do not mix, potentially explaining this disparity. We further hypothesized that isotopic effects during snowpack metamorphosis impart a distinct isotope signature to the less mobile soil water that supplies summer transpiration. Depth trends in water isotopes following snowmelt were consistent with the two water worlds hypothesis, but snow metamorphic isotope effects could not explain the highly enriched xylem water. Thus, the dual isotope approach did not unambiguously determine the water source(s) of these riparian trees. Further exploration of physical, geochemical, and biological mechanisms of water isotope fractionation and partitioning is necessary to resolve these data, highlighting critical challenges in the isotopic determination of plant water sources.« less

Revisiting streamside trees that do not use stream water: can the two water worlds hypothesis and snowpack isotopic effects explain a missing water source?: Riparian tree water sources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bowling, David R.; Schulze, Emily S.; Hall, Steven J.

We revisit a classic ecohydrological study that showed streamside riparian trees in a semiarid mountain catchment did not use perennial stream water. The original study suggested that mature individuals of Acer negundo, Acer grandidentatum, and other species were dependent on water from “deeper strata,” possibly groundwater. We used a dual stable isotope approach (δ 18O and δ 2H) to further examine the water sources of these trees. We tested the hypothesis that groundwater was the main tree water source, but found that neither groundwater nor stream water matched the isotope composition of xylem water during two growing seasons. Soil watermore » (0–1 m depth) was closest to and periodically overlapped with xylem water isotope composition, but overall, xylem water was isotopically enriched compared to all measured water sources. The “two water worlds” hypothesis postulates that soil water comprises isotopically distinct mobile and less mobile pools that do not mix, potentially explaining this disparity. We further hypothesized that isotopic effects during snowpack metamorphosis impart a distinct isotope signature to the less mobile soil water that supplies summer transpiration. Depth trends in water isotopes following snowmelt were consistent with the two water worlds hypothesis, but snow metamorphic isotope effects could not explain the highly enriched xylem water. Thus, the dual isotope approach did not unambiguously determine the water source(s) of these riparian trees. Further exploration of physical, geochemical, and biological mechanisms of water isotope fractionation and partitioning is necessary to resolve these data, highlighting critical challenges in the isotopic determination of plant water sources.« less

A Simplified Micromechanical Modeling Approach to Predict the Tensile Flow Curve Behavior of Dual-Phase Steels

NASA Astrophysics Data System (ADS)

Nanda, Tarun; Kumar, B. Ravi; Singh, Vishal

2017-11-01

Micromechanical modeling is used to predict material's tensile flow curve behavior based on microstructural characteristics. This research develops a simplified micromechanical modeling approach for predicting flow curve behavior of dual-phase steels. The existing literature reports on two broad approaches for determining tensile flow curve of these steels. The modeling approach developed in this work attempts to overcome specific limitations of the existing two approaches. This approach combines dislocation-based strain-hardening method with rule of mixtures. In the first step of modeling, `dislocation-based strain-hardening method' was employed to predict tensile behavior of individual phases of ferrite and martensite. In the second step, the individual flow curves were combined using `rule of mixtures,' to obtain the composite dual-phase flow behavior. To check accuracy of proposed model, four distinct dual-phase microstructures comprising of different ferrite grain size, martensite fraction, and carbon content in martensite were processed by annealing experiments. The true stress-strain curves for various microstructures were predicted with the newly developed micromechanical model. The results of micromechanical model matched closely with those of actual tensile tests. Thus, this micromechanical modeling approach can be used to predict and optimize the tensile flow behavior of dual-phase steels.

Dual-comb spectroscopy of laser-induced plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bergevin, Jenna; Wu, Tsung-Han; Yeak, Jeremy

Dual-comb spectroscopy has become a powerful spectroscopic technique in applications that rely on its broad spectral coverage combined with high frequency resolution capabilities. Experiments to date have primarily focused on detection and analysis of multiple gas species under semi-static conditions, with applications ranging from environmental monitoring of greenhouse gases to high resolution molecular spectroscopy. Here, we utilize dual-comb spectroscopy to demonstrate broadband, high-resolution, and time-resolved measurements in a laser induced plasma for the first time. As a first demonstration, we simultaneously detect trace amounts of Rb and K in solid samples with a single laser ablation shot, with transitions separatedmore » by over 6 THz (13 nm) and spectral resolution sufficient to resolve isotopic and ground state hyperfine splittings of the Rb D2 line. This new spectroscopic approach offers the broad spectral coverage found in the powerful techniques of laser-induced breakdown spectroscopy (LIBS) while providing the high-resolution and accuracy of cw laser-based spectroscopies.« less

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

NASA Astrophysics Data System (ADS)

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

2009-07-01

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.

Highly efficient preparation of selectively isotope cluster-labeled long chain fatty acids via two consecutive C(sp3)-C(sp3) cross-coupling reactions.

PubMed

Lethu, Sébastien; Matsuoka, Shigeru; Murata, Michio

2014-02-07

An efficient synthesis involving two copper-catalyzed alkyl-alkyl coupling reactions has been designed to easily access doubly isotope-labeled fatty acids. Such NMR- and IR-active compounds were obtained in excellent overall yields and will be further used for determining the conformation of an alkyl chain of lipidic biomolecules upon interaction with proteins.

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

Dual Si and O Isotope Measurement of Lunar Samples Using IRMS

NASA Astrophysics Data System (ADS)

Banerjee, N.; Hill, P. J. A.; Osinski, G. R.

2016-12-01

The use of isotopic systems and their associated theoretical models have become an increasingly sophisticated tool for investigating the origin of planetary bodies in the solar system. It was originally hypothesized that evidence for the impact origin of Moon would manifest itself as an isotopic heterogeneity between lunar and terrestrial samples; however, most isotope systems show no difference between the bulk Earth and Moon. The stable isotopes of both silicon (Si) and oxygen (O) have been essential in further understanding planetary processes including core formation. Historically the analysis of the Si and O isotope ratios in terrestrial and extraterrestrial material has primarily been measured independent of each other through three main techniques: isotope ratio mass spectrometry (IRMS), secondary ion mass spectrometry (SIMS), and multi-collector inductively coupled plasma mass-spectrometry (MC-ICPMS). Each technique has its own strength and weakness in regards to resolution and precision; however, one of the main limiting factors in all three of these techniques rests on the requirement of multiple aliquots. As most literature focuses on the measurement of oxygen or silicon isotopes, this unique line allows for the precise analysis of Si and O isotopes from the same aliquot of bulk sample, which cannot be done with SIMS or ICP-MS analysis. To deal with this problem a unique laser line system has been developed in the Laboratory for Stable Isotope Science at Western University, Canada, that simultaneously extracts SiF4 and O2 from the same 1-2 mg aliquot. We present the application of analyzing both isotopic systems from the sample aliquot to Apollo, meteoritic, and terrestrial samples and its implication for the formation of the Moon. Preliminary results from this line suggest that although the O isotopes ratios are consistent with a homogenous Moon-Earth system, a difference is observed in Si isotopes between Apollo and terrestrial samples compared to

Effects of climatic seasonality on the isotopic composition of evaporating soil waters

NASA Astrophysics Data System (ADS)

Benettin, Paolo; Volkmann, Till H. M.; von Freyberg, Jana; Frentress, Jay; Penna, Daniele; Dawson, Todd E.; Kirchner, James W.

2018-05-01

Stable water isotopes are widely used in ecohydrology to trace the transport, storage, and mixing of water on its journey through landscapes and ecosystems. Evaporation leaves a characteristic signature on the isotopic composition of the water that is left behind, such that in dual-isotope space, evaporated waters plot below the local meteoric water line (LMWL) that characterizes precipitation. Soil and xylem water samples can often plot below the LMWL as well, suggesting that they have also been influenced by evaporation. These soil and xylem water samples frequently plot along linear trends in dual-isotope space. These trend lines are often termed "evaporation lines" and their intersection with the LMWL is often interpreted as the isotopic composition of the precipitation source water. Here we use numerical experiments based on established isotope fractionation theory to show that these trend lines are often by-products of the seasonality in evaporative fractionation and in the isotopic composition of precipitation. Thus, they are often not true evaporation lines, and, if interpreted as such, can yield highly biased estimates of the isotopic composition of the source water.

Syntheses of halogen derivatives of L-tryptophan, L-tyrosine and L-phenylalanine labeled with hydrogen isotopes.

PubMed

Pająk, Małgorzata; Pałka, Katarzyna; Winnicka, Elżbieta; Kańska, Marianna

2016-01-01

Halogenated, labeled with tritium and doubly with deuterium and tritium, derivatives of L-tryptophan, i.e. 5'-bromo-[2-(3)H]-, 5'-bromo-[2-(2)H/(3)H]-, 5'-fluoro-[2-(3)H]-5'-fluoro-[2-(2)H/(3)H]-, 6'-fluoro-[2-(3)H]-, 6'-fluoro-[2-(2)H/(3)H]-L-tryptophan, as well as, L-tyrosine, i.e. 3'-fluoro-[2-(3)H]-, 3'-fluoro-[2-(2)H/(3)H]-, 3'-chloro-[2-(3)H]-, and 3'-chloro-[2-(2)H/(3)H]-L-tyrosine, and also L-phenylalanine, i.e. 2'-fluoro-[(3S)-(3)H]-, 2'-fluoro-[(3S)-(2)H/(3) H]-, 2'-chloro-[(3S)-(3)H]-, 2'-chloro-[(3S)-(2)H/(3)H]-, 4'-chloro-[(3S)-(3)H]-, and 4'-chloro-[(3S)-(2)H/(3)H]-L-phenylalanine were synthesized using enzymatic methods. Isotopomers of L-tryptophan were synthesized by coupling of halogenated indoles with S-methyl-L-cysteine carried out in deuteriated or tritiated incubation media. Labeled halogenated derivatives of L-tyrosine were obtained by the enzymatically supported exchange between halogenated L-tyrosine and isotopic water. Labeled halogenated isotopologues of L-Phe were synthesized by the enzymatic addition of ammonia to halogenated cinnamic acid. As a source of hydrogen tritiated water (HTO) and heavy water (D2O) with addition of HTO were used. Copyright © 2015 John Wiley & Sons, Ltd.

Stable isotope methodology in the pharmacokinetic studies of androgenic steroids in humans.

PubMed

Shinohara, Y; Baba, S

1990-04-01

The use of stable isotopically labeled steroids combined with gas chromatography/mass spectrometry (GC/MS) has found a broad application in pharmacologic studies. Initially, stable isotopically labeled steroids served as the ideal analytic internal standard for GC/MS analysis; however, their in vivo use has expanded and has proven to be a powerful pharmacokinetic tool. We have successfully used stable isotope methodology to study the pharmacokinetic/bioavailability of androgens. The primary advantage of the technique is that endogenous and exogenous steroids with the same basic structure can be differentiated by using stable isotopically labeled analogs. The method was used to examine the pharmacokinetics of testosterone and testosterone propionate, and to clarify the influence of endogenous testosterone. Another advantage of the isotope methods is that steroidal drugs can be administered concomitantly in two formulations (e.g., solution and solid dosage). A single set of blood samples serves to describe the time course of the formulations being compared. This stable isotope coadministration technique was used to estimate the relative bioavailability of 17 alpha-methyltestosterone.

NeuCode Labeling in Nematodes: Proteomic and Phosphoproteomic Impact of Ascaroside Treatment in Caenorhabditis elegans*

PubMed Central

Rhoads, Timothy W.; Prasad, Aman; Kwiecien, Nicholas W.; Merrill, Anna E.; Zawack, Kelson; Westphall, Michael S.; Schroeder, Frank C.; Kimble, Judith; Coon, Joshua J.

2015-01-01

The nematode Caenorhabditis elegans is an important model organism for biomedical research. We previously described NeuCode stable isotope labeling by amino acids in cell culture (SILAC), a method for accurate proteome quantification with potential for multiplexing beyond the limits of traditional stable isotope labeling by amino acids in cell culture. Here we apply NeuCode SILAC to profile the proteomic and phosphoproteomic response of C. elegans to two potent members of the ascaroside family of nematode pheromones. By consuming labeled E. coli as part of their diet, C. elegans nematodes quickly and easily incorporate the NeuCode heavy lysine isotopologues by the young adult stage. Using this approach, we report, at high confidence, one of the largest proteomic and phosphoproteomic data sets to date in C. elegans: 6596 proteins at a false discovery rate ≤ 1% and 6620 phosphorylation isoforms with localization probability ≥75%. Our data reveal a post-translational signature of pheromone sensing that includes many conserved proteins implicated in longevity and response to stress. PMID:26392051

Highly Efficient Quantum Sieving in Porous Graphene-like Carbon Nitride for Light Isotopes Separation

NASA Astrophysics Data System (ADS)

Qu, Yuanyuan; Li, Feng; Zhou, Hongcai; Zhao, Mingwen

2016-01-01

Light isotopes separation, such as 3He/4He, H2/D2, H2/T2, etc., is crucial for various advanced technologies including isotope labeling, nuclear weapons, cryogenics and power generation. However, their nearly identical chemical properties made the separation challenging. The low productivity of the present isotopes separation approaches hinders the relevant applications. An efficient membrane with high performance for isotopes separation is quite appealing. Based on first-principles calculations, we theoretically demonstrated that highly efficient light isotopes separation, such as 3He/4He, can be reached in a porous graphene-like carbon nitride material via quantum sieving effect. Under moderate tensile strain, the quantum sieving of the carbon nitride membrane can be effectively tuned in a continuous way, leading to a temperature window with high 3He/4He selectivity and permeance acceptable for efficient isotopes harvest in industrial application. This mechanism also holds for separation of other light isotopes, such as H2/D2, H2/T2. Such tunable quantum sieving opens a promising avenue for light isotopes separation for industrial application.

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

PubMed

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

2015-03-01

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

Correction for isotopic interferences between analyte and internal standard in quantitative mass spectrometry by a nonlinear calibration function.

PubMed

Rule, Geoffrey S; Clark, Zlatuse D; Yue, Bingfang; Rockwood, Alan L

2013-04-16

Stable isotope-labeled internal standards are of great utility in providing accurate quantitation in mass spectrometry (MS). An implicit assumption has been that there is no "cross talk" between signals of the internal standard and the target analyte. In some cases, however, naturally occurring isotopes of the analyte do contribute to the signal of the internal standard. This phenomenon becomes more pronounced for isotopically rich compounds, such as those containing sulfur, chlorine, or bromine, higher molecular weight compounds, and those at high analyte/internal standard concentration ratio. This can create nonlinear calibration behavior that may bias quantitative results. Here, we propose the use of a nonlinear but more accurate fitting of data for these situations that incorporates one or two constants determined experimentally for each analyte/internal standard combination and an adjustable calibration parameter. This fitting provides more accurate quantitation in MS-based assays where contributions from analyte to stable labeled internal standard signal exist. It can also correct for the reverse situation where an analyte is present in the internal standard as an impurity. The practical utility of this approach is described, and by using experimental data, the approach is compared to alternative fits.

Optimal tracers for parallel labeling experiments and 13C metabolic flux analysis: A new precision and synergy scoring system.

PubMed

Crown, Scott B; Long, Christopher P; Antoniewicz, Maciek R

2016-11-01

13 C-Metabolic flux analysis ( 13 C-MFA) is a widely used approach in metabolic engineering for quantifying intracellular metabolic fluxes. The precision of fluxes determined by 13 C-MFA depends largely on the choice of isotopic tracers and the specific set of labeling measurements. A recent advance in the field is the use of parallel labeling experiments for improved flux precision and accuracy. However, as of today, no systemic methods exist for identifying optimal tracers for parallel labeling experiments. In this contribution, we have addressed this problem by introducing a new scoring system and evaluating thousands of different isotopic tracer schemes. Based on this extensive analysis we have identified optimal tracers for 13 C-MFA. The best single tracers were doubly 13 C-labeled glucose tracers, including [1,6- 13 C]glucose, [5,6- 13 C]glucose and [1,2- 13 C]glucose, which consistently produced the highest flux precision independent of the metabolic flux map (here, 100 random flux maps were evaluated). Moreover, we demonstrate that pure glucose tracers perform better overall than mixtures of glucose tracers. For parallel labeling experiments the optimal isotopic tracers were [1,6- 13 C]glucose and [1,2- 13 C]glucose. Combined analysis of [1,6- 13 C]glucose and [1,2- 13 C]glucose labeling data improved the flux precision score by nearly 20-fold compared to widely use tracer mixture 80% [1- 13 C]glucose +20% [U- 13 C]glucose. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

D and 18O enrichment measurements in biological fluids in a continuous-flow elemental analyser with an isotope-ratio mass spectrometer using two configurations.

PubMed

Ripoche, N; Ferchaud-Roucher, V; Krempf, M; Ritz, P

2006-09-01

In doubly labelled water studies, biological sample enrichments are mainly measured using off-line techniques (equilibration followed by dual-inlet introduction) or high-temperature elemental analysis (HT-EA), coupled with an isotope-ratio mass spectrometer (IRMS). Here another continuous-flow method, (CF-EA/IRMS), initially dedicated to water, is tested for plasma and urine analyses. The elemental analyser configuration is adapted for each stable isotope: chromium tube for deuterium reduction and glassy carbon reactor for 18O pyrolysis. Before on-line conversion of water into gas, each matrix is submitted to a short and easy treatment, which is the same for the analysis of the two isotopes. Plasma is passed through centrifugal filters. Urine is cleaned with black carbon and filtered (0.45 microm diameter). Tested between 150 and 300 ppm in these fluids, the D/H ratio response is linear with good repeatability (SD<0.2 ppm) and reproducibility (SD<0.5 ppm). For 18O/16O ratios (from 2000 to 2200 ppm), the same repeatability is obtained with a between-day precision lower than 1.4 ppm. The accuracy on biological samples is validated by comparison to classical dual-inlet methods: 18O analyses give more accurate results. The data show that enriched physiological fluids can be successfully analysed in CF-EA/IRMS. Copyright (c) 2006 John Wiley & Sons, Ltd.

Efficient enzymatic synthesis and dual-colour fluorescent labelling of DNA probes using long chain azido-dUTP and BCN dyes

PubMed Central

Ren, Xiaomei; El-Sagheer, Afaf H.; Brown, Tom

2016-01-01

A sterically undemanding azide analogue of dTTP (AHP dUTP) with an alkyl chain and ethynyl attachment to the nucleobase was designed and incorporated into DNA by primer extension, reverse transcription and polymerase chain reaction (PCR). An azide-modified 523 bp PCR amplicon with all 335 thymidines replaced by AHP dU was shown to be a perfect copy of the template from which it was amplified. Replacement of thymidine with AHP dU increases duplex stability, accounting in part for the high incorporation efficiency of the azide-modified triphosphate. Single-stranded azide-labelled DNA was conveniently prepared from PCR products by λ-exonuclease digestion and streptavidin magnetic bead isolation. Efficient fluorescent labelling of single and double-stranded DNA was carried out using dyes functionalized with bicyclo[6.1.0]non-4-yne (BCN) via the strain-promoted alkyne-azide cycloaddition (SPAAC) reaction. This revealed that the degree of labelling must be carefully controlled to achieve optimum fluorescence and avoid fluorescence quenching. Dual-coloured probes were obtained in a single tube fluorescent labelling reaction; and varying the ratios of the two dyes provides a simple method to prepare DNA probes with unique fluorescent signatures. AHP dUTP is a versatile clickable nucleotide with potentially wide applications in biology and nanotechnology including single molecule studies and synthesis of modified aptamer libraries via SELEX. PMID:26819406

Visualization and Analysis of Microtubule Dynamics Using Dual Color-Coded Display of Plus-End Labels

PubMed Central

Garrison, Amy K.; Xia, Caihong; Wang, Zheng; Ma, Le

2012-01-01

Investigating spatial and temporal control of microtubule dynamics in live cells is critical to understanding cell morphogenesis in development and disease. Tracking fluorescently labeled plus-end-tracking proteins over time has become a widely used method to study microtubule assembly. Here, we report a complementary approach that uses only two images of these labels to visualize and analyze microtubule dynamics at any given time. Using a simple color-coding scheme, labeled plus-ends from two sequential images are pseudocolored with different colors and then merged to display color-coded ends. Based on object recognition algorithms, these colored ends can be identified and segregated into dynamic groups corresponding to four events, including growth, rescue, catastrophe, and pause. Further analysis yields not only their spatial distribution throughout the cell but also provides measurements such as growth rate and direction for each labeled end. We have validated the method by comparing our results with ground-truth data derived from manual analysis as well as with data obtained using the tracking method. In addition, we have confirmed color-coded representation of different dynamic events by analyzing their history and fate. Finally, we have demonstrated the use of the method to investigate microtubule assembly in cells and provided guidance in selecting optimal image acquisition conditions. Thus, this simple computer vision method offers a unique and quantitative approach to study spatial regulation of microtubule dynamics in cells. PMID:23226282

Application of isotope labeling experiments and (13)C flux analysis to enable rational pathway engineering.

PubMed

McAtee, Allison G; Jazmin, Lara J; Young, Jamey D

2015-12-01

Isotope labeling experiments (ILEs) and (13)C flux analysis provide actionable information for metabolic engineers to identify knockout, overexpression, and/or media optimization targets. ILEs have been used in both academic and industrial labs to increase product formation, discover novel metabolic functions in previously uncharacterized organisms, and enhance the metabolic efficiency of host cell factories. This review highlights specific examples of how ILEs have been used in conjunction with enzyme or metabolic engineering to elucidate host cell metabolism and improve product titer, rate, or yield in a directed manner. We discuss recent progress and future opportunities involving the use of ILEs and (13)C flux analysis to characterize non-model host organisms and to identify and subsequently eliminate wasteful byproduct pathways or metabolic bottlenecks. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evidencing 98 secondary metabolites of Penicillium verrucosum using substrate isotopic labeling and high-resolution mass spectrometry.

PubMed

Hautbergue, Thaïs; Puel, Olivier; Tadrist, Souria; Meneghetti, Lauriane; Péan, Michel; Delaforge, Marcel; Debrauwer, Laurent; Oswald, Isabelle P; Jamin, Emilien L

2017-12-15

Industrial applications of fungal compounds, coupled with the emergence of fungal threats to natural ecosystems and public health, have increased interest in filamentous fungi. Among all pathogenic fungi, Penicillium verrucosum is one of the most common mold-infecting stored cereals in temperate regions. However, it is estimated that 80% of fungal secondary metabolites remain unknown. To detect new P. verrucosum compounds, an untargeted metabolomic approach was applied to fungus grown on wheat grains labeled with stable isotopes: (i) natural grains (99% 12 C); (ii) grains enriched with 97% of 13 C; and (iii) grains enriched with 53% of 13 C and 97% of 15 N. Analyses performed by high-performance liquid chromatography coupled with high-resolution mass spectrometry (HPLC-HRMS) enabled the specific detection of fungal metabolites, and the unambiguous characterization of their chemical formulas. In this way, 98 secondary metabolites were detected and their chemical formulas were determined. Of these, only 18 identifications could be made based on databases, the literature and mass spectrometry fragmentation experiments, with the result that 80 were totally unknown. Molecular networks were generated to analyze these results, leading to the characterization by MS n experiments of a new fungisporin produced by P. verrucosum. More generally, this article provides precise mass spectrometric data about all these compounds for further studies of the Penicillium metabolome. Copyright © 2017 Elsevier B.V. All rights reserved.

Seeking excellence: An evaluation of 235 international laboratories conducting water isotope analyses by isotope-ratio and laser-absorption spectrometry.

PubMed

Wassenaar, L I; Terzer-Wassmuth, S; Douence, C; Araguas-Araguas, L; Aggarwal, P K; Coplen, T B

2018-03-15

Water stable isotope ratios (δ 2 H and δ 18 O values) are widely used tracers in environmental studies; hence, accurate and precise assays are required for providing sound scientific information. We tested the analytical performance of 235 international laboratories conducting water isotope analyses using dual-inlet and continuous-flow isotope ratio mass spectrometers and laser spectrometers through a water isotope inter-comparison test. Eight test water samples were distributed by the IAEA to international stable isotope laboratories. These consisted of a core set of five samples spanning the common δ-range of natural waters, and three optional samples (highly depleted, enriched, and saline). The fifth core sample contained unrevealed trace methanol to assess analyst vigilance to the impact of organic contamination on water isotopic measurements made by all instrument technologies. For the core and optional samples ~73 % of laboratories gave acceptable results within 0.2 ‰ and 1.5 ‰ of the reference values for δ 18 O and δ 2 H, respectively; ~27 % produced unacceptable results. Top performance for δ 18 O values was dominated by dual-inlet IRMS laboratories; top performance for δ 2 H values was led by laser spectrometer laboratories. Continuous-flow instruments yielded comparatively intermediate results. Trace methanol contamination of water resulted in extreme outlier δ-values for laser instruments, but also affected reactor-based continuous-flow IRMS systems; however, dual-inlet IRMS δ-values were unaffected. Analysis of the laboratory results and their metadata suggested inaccurate or imprecise performance stemmed mainly from skill- and knowledge-based errors including: calculation mistakes, inappropriate or compromised laboratory calibration standards, poorly performing instrumentation, lack of vigilance to contamination, or inattention to unreasonable isotopic outcomes. To counteract common errors, we recommend that laboratories include 1-2 'known

Seeking excellence: An evaluation of 235 international laboratories conducting water isotope analyses by isotope-ratio and laser-absorption spectrometry

USGS Publications Warehouse

Wassenaar, L. I.; Terzer-Wassmuth, S.; Douence, C.; Araguas-Araguas, L.; Aggarwal, P. K.; Coplen, Tyler B.

2018-01-01

RationaleWater stable isotope ratios (δ2H and δ18O values) are widely used tracers in environmental studies; hence, accurate and precise assays are required for providing sound scientific information. We tested the analytical performance of 235 international laboratories conducting water isotope analyses using dual-inlet and continuous-flow isotope ratio mass spectrometers and laser spectrometers through a water isotope inter-comparison test.MethodsEight test water samples were distributed by the IAEA to international stable isotope laboratories. These consisted of a core set of five samples spanning the common δ-range of natural waters, and three optional samples (highly depleted, enriched, and saline). The fifth core sample contained unrevealed trace methanol to assess analyst vigilance to the impact of organic contamination on water isotopic measurements made by all instrument technologies.ResultsFor the core and optional samples ~73 % of laboratories gave acceptable results within 0.2 ‰ and 1.5 ‰ of the reference values for δ18O and δ2H, respectively; ~27 % produced unacceptable results. Top performance for δ18O values was dominated by dual-inlet IRMS laboratories; top performance for δ2H values was led by laser spectrometer laboratories. Continuous-flow instruments yielded comparatively intermediate results. Trace methanol contamination of water resulted in extreme outlier δ-values for laser instruments, but also affected reactor-based continuous-flow IRMS systems; however, dual-inlet IRMS δ-values were unaffected.ConclusionsAnalysis of the laboratory results and their metadata suggested inaccurate or imprecise performance stemmed mainly from skill- and knowledge-based errors including: calculation mistakes, inappropriate or compromised laboratory calibration standards, poorly performing instrumentation, lack of vigilance to contamination, or inattention to unreasonable isotopic outcomes. To counteract common errors, we recommend that

Follow the Carbon: Isotopic Labeling Studies of Early Earth Aerosol.

PubMed

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

2016-11-01

Despite the faint young Sun, early Earth might have been kept warm by an atmosphere containing the greenhouse gases CH 4 and CO 2 in mixing ratios higher than those found on Earth today. Laboratory and modeling studies suggest that an atmosphere containing these trace gases could lead to the formation of organic aerosol haze due to UV photochemistry. Chemical mechanisms proposed to explain haze formation rely on CH 4 as the source of carbon and treat CO 2 as a source of oxygen only, but this has not previously been verified experimentally. In the present work, we use isotopically labeled precursor gases and unit-mass resolution (UMR) and high-resolution (HR) aerosol mass spectrometry to examine the sources of carbon and oxygen to photochemical aerosol formed in a CH 4 /CO 2 /N 2 atmosphere. UMR results suggest that CH 4 contributes 70-100% of carbon in the aerosol, while HR results constrain the value from 94% to 100%. We also confirm that CO 2 contributes approximately 10% of the total mass to the aerosol as oxygen. These results have implications for the geochemical interpretations of inclusions found in Archean rocks on Earth and for the astrobiological potential of other planetary atmospheres. Key Words: Atmosphere-Early Earth-Planetary atmospheres-Carbon dioxide-Methane. Astrobiology 16, 822-830.

Improved Discrimination for Brassica Vegetables Treated with Agricultural Fertilizers Using a Combined Chemometric Approach.

PubMed

Yuan, Yuwei; Hu, Guixian; Chen, Tianjin; Zhao, Ming; Zhang, Yongzhi; Li, Yong; Xu, Xiahong; Shao, Shengzhi; Zhu, Jiahong; Wang, Qiang; Rogers, Karyne M

2016-07-20

Multielement and stable isotope (δ(13)C, δ(15)N, δ(2)H, δ(18)O, (207)Pb/(206)Pb, and (208)Pb/(206)Pb) analyses were combined to provide a new chemometric approach to improve the discrimination between organic and conventional Brassica vegetable production. Different combinations of organic and conventional fertilizer treatments were used to demonstrate this authentication approach using Brassica chinensis planted in experimental test pots. Stable isotope analyses (δ(15)N and δ(13)C) of B. chinensis using elemental analyzer-isotope ratio mass spectrometry easily distinguished organic and chemical fertilizer treatments. However, for low-level application fertilizer treatments, this dual isotope approach became indistinguishable over time. Using a chemometric approach (combined isotope and elemental approach), organic and chemical fertilizer mixes and low-level applications of synthetic and organic fertilizers were detectable in B. chinensis and their associated soils, improving the detection limit beyond the capacity of individual isotopes or elemental characterization. LDA shows strong promise as an improved method to discriminate genuine organic Brassica vegetables from produce treated with chemical fertilizers and could be used as a robust test for organic produce authentication.

Sulfur and oxygen isotope fractionation during benzene, toluene, ethyl benzene, and xylene degradation by sulfate-reducing bacteria.

PubMed

Knöller, Kay; Vogt, Carsten; Richnow, Hans-Herrmann; Weise, Stephan M

2006-06-15

We examined the oxygen and sulfur isotope fractionation of sulfate during anaerobic degradation of toluene by sulfate-reducing bacteria in culture experiments with Desulfobacula toluolica as a type strain and with an enrichment culture Zz5-7 obtained from a benzene, toluene, ethylbenzene, and xylene (BTEX)-contaminated aquifer. Sulfur isotope fractionation can show considerable variation upon sulfate reduction and may react extremely sensitively to changes in environmental conditions. In contrast, oxygen isotope fractionation seems to be less sensitive to environmental changes. Our results clearly indicate that oxygen isotope fractionation is dominated by isotope exchange with ambient water. To verify our experimental results and to test the applicability of oxygen and sulfur isotope investigations under realistic field conditions, we evaluated isotope data from two BTEX-contaminated aquifers presented in the recent literature. On a field scale, bacterial sulfate reduction may be superimposed by processes such as dispersion, adsorption, reoxidation, or mixing. The dual isotope approach enables the identification of such sulfur transformation processes. This identification is vital for a general qualitative evaluation of the natural attenuation potential of the contaminated aquifer.

Non-Animal Testing Approach to EPA Labeling for Eye Irritation

EPA Pesticide Factsheets

This document is an update to EPA’s 2013 published alternative testing approach (using in vitro/ex vivo assays) for determination of eye irritation potential in the pesticide program under EPA's classification and labeling system.

Parallel labeling experiments for pathway elucidation and (13)C metabolic flux analysis.

PubMed

Antoniewicz, Maciek R

2015-12-01

Metabolic pathway models provide the foundation for quantitative studies of cellular physiology through the measurement of intracellular metabolic fluxes. For model organisms metabolic models are well established, with many manually curated genome-scale model reconstructions, gene knockout studies and stable-isotope tracing studies. However, for non-model organisms a similar level of knowledge is often lacking. Compartmentation of cellular metabolism in eukaryotic systems also presents significant challenges for quantitative (13)C-metabolic flux analysis ((13)C-MFA). Recently, innovative (13)C-MFA approaches have been developed based on parallel labeling experiments, the use of multiple isotopic tracers and integrated data analysis, that allow more rigorous validation of pathway models and improved quantification of metabolic fluxes. Applications of these approaches open new research directions in metabolic engineering, biotechnology and medicine. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

PubMed

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

2016-10-26

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

The Doubly Labeled Water Method for Measuring Human Energy Expenditure: Adaptations for Spaceflight

NASA Technical Reports Server (NTRS)

Schulz, Leslie O.

1991-01-01

It is essential to determine human energy requirements in space, and the doubly labeled water method has been identified as the most appropriate means of indirect calorimetry to meet this need. The method employs naturally occurring, stable isotopes of hydrogen (H-2, deuterium) and oxygen (O-18) which, after dosing, mix with body water. The deuterium is lost from the body as water while the O-18 is eliminated as both water and CO2. The difference between the two isotope elimination rates is therefore a measure of CO2 production and hence energy expenditure. Spaceflight will present a unique challenge to the application of the doubly labeled water method. Specifically, interpretation of doubly labeled water results assumes that the natural abundance or 'background' levels of the isotopes remain constant during the measurement interval. To address this issue, an equilibration model will be developed in an ongoing ground-based study. As energy requirements of women matched to counterparts in the Astronauts Corps are being determined by doubly labeled water, the baseline isotope concentration will be changed by consumption of 'simulated Shuttle water' which is artificially enriched. One group of subjects will be equilibrated on simulated Shuttle water prior to energy determinations by doubly labeled water while the others will consume simulated Shuttle water after dosing. This process will allow us to derive a prediction equation to mathematically model the effect of changing background isotope concentrations.

Snap-, CLIP- and Halo-Tag Labelling of Budding Yeast Cells

PubMed Central

Stagge, Franziska; Mitronova, Gyuzel Y.; Belov, Vladimir N.; Wurm, Christian A.; Jakobs, Stefan

2013-01-01

Fluorescence microscopy of the localization and the spatial and temporal dynamics of specifically labelled proteins is an indispensable tool in cell biology. Besides fluorescent proteins as tags, tag-mediated labelling utilizing self-labelling proteins as the SNAP-, CLIP-, or the Halo-tag are widely used, flexible labelling systems relying on exogenously supplied fluorophores. Unfortunately, labelling of live budding yeast cells proved to be challenging with these approaches because of the limited accessibility of the cell interior to the dyes. In this study we developed a fast and reliable electroporation-based labelling protocol for living budding yeast cells expressing SNAP-, CLIP-, or Halo-tagged fusion proteins. For the Halo-tag, we demonstrate that it is crucial to use the 6′-carboxy isomers and not the 5′-carboxy isomers of important dyes to ensure cell viability. We report on a simple rule for the analysis of 1H NMR spectra to discriminate between 6′- and 5′-carboxy isomers of fluorescein and rhodamine derivatives. We demonstrate the usability of the labelling protocol by imaging yeast cells with STED super-resolution microscopy and dual colour live cell microscopy. The large number of available fluorophores for these self-labelling proteins and the simplicity of the protocol described here expands the available toolbox for the model organism Saccharomyces cerevisiae. PMID:24205303

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

PubMed

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

2011-01-07

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

Soil Moisture Flow and Nitrate Movement Simulation through Deep and Heterogeneous Vadose Zone using Dual-porosity Approach

NASA Astrophysics Data System (ADS)

Yadav, B. K.; Tomar, J.; Harter, T.

2014-12-01

We investigate nitrate movement from non-point sources in deep, heterogeneous vadose zones, using multi-dimensional variably saturated flow and transport simulations. We hypothesize that porous media heterogeneity causes saturation variability that leads to preferential flow systems such that a significant portion of the vadose zone does not significantly contribute to flow. We solve Richards' equation and the advection-dispersion equation to simulate soil moisture and nitrate transport regimes in plot-scale experiments conducted in the San Joaquin Valley, California. We compare equilibrium against non-equilibrium (dual-porosity) approaches. In the equilibrium approach we consider each soil layer to have unique hydraulic properties as a whole, while in the dual-porosity approach we assume that large fractions of the porous flow domain are immobile. However we consider exchange of water and solute between mobile and immobile zone using the appropriate mass transfer terms. The results indicate that flow and transport in a nearly 16 m deep stratified vadose zone comprised of eight layers of unconsolidated alluvium experiences highly non-uniform, localized preferential flow and transport patterns leading to accelerated nitrate transfer. The equilibrium approach largely under-predicted the leaching of nitrate to groundwater while the dual-porosity approach showed higher rates of nitrate leaching, consistent with field observations. The dual-porosity approach slightly over-predicted nitrogen storage in the vadose zone, which may be the result of limited matrix flow or denitrification not accounted for in the model. Results of this study may be helpful to better predict fertilizer and pesticide retention times in deep vadose zone, prior to recharge into the groundwater flow system. Keywords: Nitrate, Preferential flow, Heterogeneous vadose zone, Dual-porosity approach

Dual-color two-photon fluorescence correlation spectroscopy

NASA Astrophysics Data System (ADS)

Berland, Keith M.

2001-04-01

Fluorescence correlation spectroscopy (FCS) is rapidly growing in popularity as a research tool in biological and biophysical research. Under favorable conditions, FCS measurements can produce an accurate characterization of the chemical, physical, and kinetic properties of a biological system. However, interpretation of FCS data quickly becomes complicated as the heterogeneity of a molecular system increases, as well as when there is significant non-stationery fluorescence background (e.g. intracellular autofluorescence). Use of multi-parameter correlation measurements is one promising approach that can improve the fidelity of FCS measurements in complex systems. In particular, the use of dual-color fluorescence assays, in which different interacting molecular species are labeled with unique fluorescent indicators, can "tune" the sensitivity of FCS measurements in favor of particular molecular species of interest, while simultaneously minimizing the contribution of other molecular species to the overall fluorescence correlation signal. Here we introduce the combined application of two-photon fluorescence excitation and dual-color cross-correlation analysis for detecting molecular interactions in solution. The use of two-photon excitation is particularly advantageous for dual-color FCS applications due to the uncomplicated optical alignment and the superior capabilities for intracellular applications. The theory of two-photon dual-color FCS is introduced, and initial results quantifying hybridization reactions between three independent single stranded DNA molecules are presented.

Flavin-mediated dual oxidation controls an enzymatic Favorskii-type rearrangement

PubMed Central

Louie, Gordon; Noel, Joseph P.; Baran, Phil S.; Palfey, Bruce; Moore, Bradley S.

2013-01-01

Flavoproteins catalyze a diversity of fundamental redox reactions and are one of the most studied enzyme families1,2. As monooxygenases, they are universally thought to control oxygenation by means of a peroxyflavin species that transfers a single atom of molecular oxygen to an organic substrate1,3,4. Here we report that the bacterial flavoenzyme EncM5,6 catalyzes the peroxyflavin-independent oxygenation-dehydrogenation dual oxidation of a highly reactive poly(β-carbonyl). The crystal structure of EncM with bound substrate mimics coupled with isotope labeling studies reveal previously unknown flavin redox biochemistry. We show that EncM maintains an unanticipated stable flavin oxygenating species, proposed to be a flavin-N5-oxide, to promote substrate oxidation and trigger a rare Favorskii-type rearrangement that is central to the biosynthesis of the antibiotic enterocin. This work provides new insight into the fine-tuning of the flavin cofactor in offsetting the innate reactivity of a polyketide substrate to direct its efficient electrocyclization. PMID:24162851

Monitoring of protease catalyzed reactions by quantitative MALDI MS using metal labeling.

PubMed

Gregorius, Barbara; Jakoby, Thomas; Schaumlöffel, Dirk; Tholey, Andreas

2013-05-21

Quantitative mass spectrometry is a powerful tool for the determination of enzyme activities as it does not require labeled substrates and simultaneously allows for the identification of reaction products. However, major restrictions are the limited number of samples which can be measured in parallel due to the need for isotope labeled internal standards. Here we describe the use of metal labeling of peptides for the setup of multiplexed enzyme activity assays. After proteolytic reaction, using the protease trypsin, remaining substrates and peptide products formed in the reaction were labeled with metal chelators complexing rare earth metal ions. Labeled peptides were quantified with high accuracy and over a wide dynamic range (at least 2 orders of magnitude) using MALDI MS in case of simple peptide mixtures or by LC-MALDI MS for complex substrate mixtures and used for the monitoring of time-dependent product formation and substrate consumption. Due to multiplexing capabilities and accuracy, the presented approach will be useful for the determination of enzyme activities with a wide range of biochemical and biotechnological applications.

Dual fermionic variables and renormalization group approach to junctions of strongly interacting quantum wires

NASA Astrophysics Data System (ADS)

Giuliano, Domenico; Nava, Andrea

2015-09-01

Making a combined use of bosonization and fermionization techniques, we build nonlocal transformations between dual fermion operators, describing junctions of strongly interacting spinful one-dimensional quantum wires. Our approach allows for trading strongly interacting (in the original coordinates) fermionic Hamiltonians for weakly interacting (in the dual coordinates) ones. It enables us to generalize to the strongly interacting regime the fermionic renormalization group approach to weakly interacting junctions. As a result, on one hand, we are able to pertinently complement the information about the phase diagram of the junction obtained within the bosonization approach; on the other hand, we map out the full crossover of the conductance tensors between any two fixed points in the phase diagram connected by a renormalization group trajectory.

ICT: isotope correction toolbox.

PubMed

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

2016-01-01

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

Dual-primer self-generation SERS signal amplification assay for PDGF-BB using label-free aptamer.

PubMed

Ye, SuJuan; Zhai, XiaoMo; Wu, YanYing; Kuang, ShaoPing

2016-05-15

Highly sensitive detection of proteins, especially those associated with cancers, is essential to biomedical research as well as clinical diagnosis. In this work, a simple and novel one-two-three signal amplification surface-enhanced Raman scattering (SERS) method for the detection of protein is fabricated by using label-free aptamer and dual-primer self-generation. Platelet-derived growth factor B-chain (PDGF-BB) is selected as the model protein. The one-two-three cascade DNA amplification means one target-aptamer binding event, two hairpin DNA switches and three DNA amplification reactions. This strategy possesses some remarkable features compared to conventional signal amplification methods: (i) A smart probe including a label-free aptamer is fabricated, for suitable hybridization without hindering the affinity of the aptamer toward its target. (ii) Using the unique structure switch of the aptamer and cooperator, a one-two-three working mode is developed to amplify the SERS signal. The amplification efficiency is enhanced. Given the unique and attractive characteristics, a simple and universal strategy is designed to accomplish ultrasensitive detection of proteins. The detection limit of PDGF-BB via SERS detection is 0.42 pM, with the linear range from 1.0×10(-12)M to 10(-8)M. It is potentially universal because the aptamer can be easily designed for biomolecules whose aptamers undergo similar conformational changes. Copyright © 2015 Elsevier B.V. All rights reserved.

Determining the Composition and Stability of Protein Complexes Using an Integrated Label-Free and Stable Isotope Labeling Strategy

PubMed Central

Greco, Todd M.; Guise, Amanda J.; Cristea, Ileana M.

2016-01-01

In biological systems, proteins catalyze the fundamental reactions that underlie all cellular functions, including metabolic processes and cell survival and death pathways. These biochemical reactions are rarely accomplished alone. Rather, they involve a concerted effect from many proteins that may operate in a directed signaling pathway and/or may physically associate in a complex to achieve a specific enzymatic activity. Therefore, defining the composition and regulation of protein complexes is critical for understanding cellular functions. In this chapter, we describe an approach that uses quantitative mass spectrometry (MS) to assess the specificity and the relative stability of protein interactions. Isolation of protein complexes from mammalian cells is performed by rapid immunoaffinity purification, and followed by in-solution digestion and high-resolution mass spectrometry analysis. We employ complementary quantitative MS workflows to assess the specificity of protein interactions using label-free MS and statistical analysis, and the relative stability of the interactions using a metabolic labeling technique. For each candidate protein interaction, scores from the two workflows can be correlated to minimize nonspecific background and profile protein complex composition and relative stability. PMID:26867737

Stable isotope labeling-mass spectrometry analysis of methyl- and pyridyloxobutyl-guanine adducts of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone in p53-derived DNA sequences.

PubMed

Rajesh, Mathur; Wang, Gang; Jones, Roger; Tretyakova, Natalia

2005-02-15

The p53 tumor suppressor gene is a primary target in smoking-induced lung cancer. Interestingly, p53 mutations observed in lung tumors of smokers are concentrated at guanine bases within endogenously methylated (Me)CG dinucleotides, e.g., codons 157, 158, 245, 248, and 273 ((Me)C = 5-methylcytosine). One possible mechanism for the increased mutagenesis at these sites involves targeted binding of metabolically activated tobacco carcinogens to (Me)CG sequences. In the present work, a stable isotope labeling HPLC-ESI(+)-MS/MS approach was employed to analyze the formation of guanine lesions induced by the tobacco-specific lung carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) within DNA duplexes representing p53 mutational "hot spots" and surrounding sequences. Synthetic DNA duplexes containing p53 codons 153-159, 243-250, and 269-275 were prepared, where (Me)C was incorporated at all physiologically methylated CG sites. In each duplex, one of the guanine bases was replaced with [1,7,NH(2)-(15)N(3)-2-(13)C]-guanine, which served as an isotope "tag" to enable specific quantification of guanine lesions originating from that position. After incubation with NNK diazohydroxides, HPLC-ESI(+)-MS/MS analysis was used to determine the yields of NNK adducts at the isotopically labeled guanine and at unlabeled guanine bases elsewhere in the sequence. We found that N7-methyl-2'-deoxyguanosine and N7-[4-oxo-4-(3-pyridyl)but-1-yl]guanine lesions were overproduced at the 3'-guanine bases within polypurine runs, while the formation of O(6)-methyl-2'-deoxyguanosine and O(6)-[4-oxo-4-(3-pyridyl)but-1-yl]-2'-deoxyguanosine adducts was specifically preferred at the 3'-guanine base of 5'-GG and 5'-GGG sequences. In contrast, the presence of 5'-neighboring (Me)C inhibited O(6)-guanine adduct formation. These results indicate that the N7- and O(6)-guanine adducts of NNK are not overproduced at the endogenously methylated CG dinucleotides within the p53 tumor suppressor gene

DNA stable-isotope probing (DNA-SIP).

PubMed

Dunford, Eric A; Neufeld, Josh D

2010-08-02

DNA stable-isotope probing (DNA-SIP) is a powerful technique for identifying active microorganisms that assimilate particular carbon substrates and nutrients into cellular biomass. As such, this cultivation-independent technique has been an important methodology for assigning metabolic function to the diverse communities inhabiting a wide range of terrestrial and aquatic environments. Following the incubation of an environmental sample with stable-isotope labelled compounds, extracted nucleic acid is subjected to density gradient ultracentrifugation and subsequent gradient fractionation to separate nucleic acids of differing densities. Purification of DNA from cesium chloride retrieves labelled and unlabelled DNA for subsequent molecular characterization (e.g. fingerprinting, microarrays, clone libraries, metagenomics). This JoVE video protocol provides visual step-by-step explanations of the protocol for density gradient ultracentrifugation, gradient fractionation and recovery of labelled DNA. The protocol also includes sample SIP data and highlights important tips and cautions that must be considered to ensure a successful DNA-SIP analysis.

On Anticipatory Development of Dual Education Based on the Systemic Approach

ERIC Educational Resources Information Center

Alshynbayeva, Zhuldyz; Sarbassova, Karlygash; Galiyeva, Temir; Kaltayeva, Gulnara; Bekmagambetov, Aidos

2016-01-01

The article addresses separate theoretical and methodical aspects of the anticipatory development of dual education in the Republic of Kazakhstan based on the systemic approach. It states the need to develop orientating basis of prospective professional activities in students. We define the concepts of anticipatory cognition and anticipatory…

In vivo evaluation of (64)Cu-labeled magnetic nanoparticles as a dual-modality PET/MR imaging agent.

PubMed

Glaus, Charles; Rossin, Raffaella; Welch, Michael J; Bao, Gang

2010-04-21

A novel nanoparticle-based dual-modality positron emission tomograph/magnetic resonance imaging (PET/MRI) contrast agent was developed. The probe consisted of a superparamagnetic iron oxide (SPIO) core coated with PEGylated phospholipids. The chelator 1,4,7,10-tetraazacyclo-dodecane-1,4,7,10-tetraacetic acid (DOTA) was conjugated to PEG termini to allow labeling with positron-emitting (64)Cu. Radiolabeling with (64)Cu at high yield and high purity was readily achieved. The (64)Cu-SPIO probes produced strong MR and PET signals and were stable in mouse serum for 24 h at 37 degrees C. Biodistribution and in vivo PET/CT imaging studies of the probes showed a circulation half-life of 143 min and high initial blood retention with moderate liver uptake, making them an attractive contrast agent for disease studies.

Estimating ground-water inflow to lakes in central Florida using the isotope mass-balance approach

USGS Publications Warehouse

Sacks, Laura A.

2002-01-01

The isotope mass-balance approach was used to estimate ground-water inflow to 81 lakes in the central highlands and coastal lowlands of central Florida. The study area is characterized by a subtropical climate and numerous lakes in a mantled karst terrain. Ground-water inflow was computed using both steady-state and transient formulations of the isotope mass-balance equation. More detailed data were collected from two study lakes, including climatic, hydrologic, and isotopic (hydrogen and oxygen isotope ratio) data. For one of these lakes (Lake Starr), ground-water inflow was independently computed from a water-budget study. Climatic and isotopic data collected from the two lakes were similar even though they were in different physiographic settings about 60 miles apart. Isotopic data from all of the study lakes plotted on an evaporation trend line, which had a very similar slope to the theoretical slope computed for Lake Starr. These similarities suggest that data collected from the detailed study lakes can be extrapolated to the rest of the study area. Ground-water inflow computed using the isotope mass-balance approach ranged from 0 to more than 260 inches per year (or 0 to more than 80 percent of total inflows). Steady-state and transient estimates of ground-water inflow were very similar. Computed ground-water inflow was most sensitive to uncertainty in variables used to calculate the isotopic composition of lake evaporate (isotopic compositions of lake water and atmospheric moisture and climatic variables). Transient results were particularly sensitive to changes in the isotopic composition of lake water. Uncertainty in ground-water inflow results is considerably less for lakes with higher ground-water inflow than for lakes with lower ground-water inflow. Because of these uncertainties, the isotope mass-balance approach is better used to distinguish whether ground-water inflow quantities fall within certain ranges of values, rather than for precise

An LC-MRM method for measuring intestinal triglyceride assembly using an oral stable isotope-labeled fat challenge.

PubMed

Li, Xiaofang; Parks, Elizabeth J; McLaren, David G; Lambert, Jennifer E; Cardasis, Helene L; Chappell, Derek L; McAvoy, Thomas; Salituro, Gino; Alon, Achilles; Dennie, Justin; Chakravarthy, Manu; Shankar, Sudha S; Laterza, Omar F; Lassman, Michael E

2016-06-01

A traditional oral fatty acid challenge assesses absorption of triacylglycerol (TG) into the periphery through the intestines, but cannot distinguish the composition or source of fatty acid in the TG. Stable isotope-labeled tracers combined with LC-MRM can be used to identify and distinguish TG synthesized with dietary and stored fatty acids. Concentrations of three abundant TGs (52:2, 54:3 and 54:4) were monitored for incorporation of one or two (2)H11-oleate molecules per TG. This method was subjected to routine assay validation and meets typical requirements for an assay to be used to support clinical studies. Calculations for the fractional appearance rate of TG in plasma are presented along with the intracellular enterocyte precursor pool for 12 study participants.

Image segmentation for uranium isotopic analysis by SIMS: Combined adaptive thresholding and marker controlled watershed approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Willingham, David G.; Naes, Benjamin E.; Heasler, Patrick G.

A novel approach to particle identification and particle isotope ratio determination has been developed for nuclear safeguard applications. This particle search approach combines an adaptive thresholding algorithm and marker-controlled watershed segmentation (MCWS) transform, which improves the secondary ion mass spectrometry (SIMS) isotopic analysis of uranium containing particle populations for nuclear safeguards applications. The Niblack assisted MCWS approach (a.k.a. SEEKER) developed for this work has improved the identification of isotopically unique uranium particles under conditions that have historically presented significant challenges for SIMS image data processing techniques. Particles obtained from five NIST uranium certified reference materials (CRM U129A, U015, U150, U500more » and U850) were successfully identified in regions of SIMS image data 1) where a high variability in image intensity existed, 2) where particles were touching or were in close proximity to one another and/or 3) where the magnitude of ion signal for a given region was count limited. Analysis of the isotopic distributions of uranium containing particles identified by SEEKER showed four distinct, accurately identified 235U enrichment distributions, corresponding to the NIST certified 235U/238U isotope ratios for CRM U129A/U015 (not statistically differentiated), U150, U500 and U850. Additionally, comparison of the minor uranium isotope (234U, 235U and 236U) atom percent values verified that, even in the absence of high precision isotope ratio measurements, SEEKER could be used to segment isotopically unique uranium particles from SIMS image data. Although demonstrated specifically for SIMS analysis of uranium containing particles for nuclear safeguards, SEEKER has application in addressing a broad set of image processing challenges.« less

Palladium-catalyzed double carbonylation using near stoichiometric carbon monoxide: expedient access to substituted 13C2-labeled phenethylamines.

PubMed

Nielsen, Dennis U; Neumann, Karoline; Taaning, Rolf H; Lindhardt, Anders T; Modvig, Amalie; Skrydstrup, Troels

2012-07-20

A novel and general approach for (13)C(2)- and (2)H-labeled phenethylamine derivatives has been developed, based on a highly convergent single-step assembly of the carbon skeleton. The efficient incorporation of two carbon-13 isotopes into phenethylamines was accomplished using a palladium-catalyzed double carbonylation of aryl iodides with near stoichiometric carbon monoxide.

Dual-Chamber/Dual-Anode Proportional Counter Incorporating an Intervening Thin-Foil Solid Neutron Converter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boatner, Lynn A; Neal, John S; Blackston, Matthew A

2012-01-01

A dual-chamber/dual-anode gas proportional counter utilizing thin solid 6LiF or 10B neutron converters coated on a 2-micon-thick Mylar film that is positioned between the two counter chambers and anodes has been designed, fabricated, and tested using a variety of fill gases including naturally abundant helium. In this device, neutron conversion products emitted from both sides of the coated converter foil are detected rather than having half of the products absorbed in the wall of a conventional tube type counter where the solid neutron converter is deposited on the tube wall. Geant4-based radiation transport calculations were used to determine the optimummore » neutron converter coating thickness for both isotopes. Solution methods for applying these optimized-thickness coatings on a Mylar film were developed that were carried out at room temperature without any specialized equipment and that can be adapted to standard coating methods such as silk screen or ink jet printing. The performance characteristics of the dual-chamber/dual-anode neutron detector were determined for both types of isotopically enriched converters. The experimental performance of the 6LiF converter-based detector was described well by modeling results from Geant4. Additional modeling studies of multiple-foil/multiple-chamber/anode configurations addressed the basic issue of the relatively longer absorption range of neutrons versus the shorter range of the conversion products for 6LiF and 10B. Combined with the experimental results, these simulations indicate that a high-performance neutron detector can be realized in a single device through the application of these multiple-foil/solid converter, multiple-chamber detector concepts.« less

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

PubMed

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

2009-08-01

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

Variable dual carbon-bromine stable isotope fractionation during enzyme-catalyzed reductive dehalogenation of brominated ethenes.

PubMed

Woods, Angela; Kuntze, Kevin; Gelman, Faina; Halicz, Ludwik; Nijenhuis, Ivonne

2018-01-01

The potential of compound-specific stable isotope analysis (CSIA) to characterize biotransformation of brominated organic compounds (BOCs) was assessed and compared to chlorinated analogues. Sulfurospirillum multivorans and Desulfitobacterium hafniense PCE-S catalyzed the dehalogenation of tribromoethene (TBE) to either vinyl bromide (VB) or ethene, respectively. Significantly lower isotope fractionation was observed for TBE dehalogenation by S. multivorans (ε C  = -1.3 ± 0.2‰) compared to D. hafniense (ε C  = -7.7 ± 1.5‰). However, higher fractionation was observed for dibromoethene (DBE) dehalogenation by S. multivorans (ε C  = -16.8 ± 1.8‰ and -21.2 ± 1.6‰ for trans- and cis-1,2- (DBE) respectively), compared to D. hafniense PCE-S (ε C  = -9.5 ± 1.2‰ and -14.5 ± 0.7‰ for trans-1,2-DBE and cis-1,2-DBE, respectively). Significant, but similar, bromine fractionation was observed for for S. multivorans (ε Br  = -0.53 ± 0.15‰, -1.03 ± 0.26‰, and -1.18 ± 0.13‰ for trans-1,2-DBE, cis-1,2-DBE and TBE, respectively) and D. hafniense PCE-S (ε Br  = -0.97 ± 0.28‰, -1.16 ± 0.36‰, and -1.34 ± 0.32‰ for cis-1,2-DBE, TBE and trans-1,2-DBE, respectively). Variable CBr dual-element slopes were estimated at Λ (ε C /ε Br ) = 1.03 ± 0.2, 17.9 ± 5.8, and 29.9 ± 11.0 for S. multivorans debrominating TBE, cis-1,2-DBE and trans-1,2-DBE, respectively, and at 7.14 ± 1.6, 8.27 ± 3.7, and 8.92 ± 2.4 for D. hafniense PCE-S debrominating trans-1,2-DBE, TBE and cis-1,2-DBE, respectively. A high variability in isotope fractionation, which was substrate property related, was observed for S. multivorans but not D. hafniense, similar as observed for chlorinated ethenes, and may be due to rate-limiting steps preceding the bond-cleavage or differences in the reaction mechanism. Overall, significant isotope fractionation was observed and, therefore, CSIA can be applied to monitor the

Monitoring CO[subscript 2] Fixation Using GC-MS Detection of a [superscript 13]C-Label

ERIC Educational Resources Information Center

Hammond, Daniel G.; Bridgham, April; Reichert, Kara; Magers, Martin

2010-01-01

Much of our understanding of metabolic pathways has resulted from the use of chemical and isotopic labels. In this experiment, a heavy isotope of carbon, [superscript 13]C, is used to label the product of the well-known RuBisCO enzymatic reaction. This is a key reaction in photosynthesis that converts inorganic carbon to organic carbon; a process…

Dual stable isotopes of CH 4 from Yellowstone hot-springs suggest hydrothermal processes involving magmatic CO 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moran, James J.; Whitmore, Laura M.; Jay, Zackary J.

Volcanism and post-magmatism contribute both significant annual CH 4 fluxes to the atmosphere (on par with other natural sources such as forest fire and wild animal emissions) and have been implicated in past climate-change events. The Yellowstone hot spot is one of the largest volcanic systems on Earth and is known to emit methane in addition to other greenhouse gases (e.g. carbon dioxide) but the ultimate source of this methane flux has not been elucidated. Here we use dual stable isotope analysis (δ 2H and δ 13C) of CH 4(g) sampled from ten high-temperature geothermal pools in Yellowstone National Parkmore » to show that the predominant flux of CH4(g) is abiotic. The average δ 13C and δ 2H values of CH 4(g) emitted from hot springs (-26.7 (±2.4) and -236.9 (±12.0) ‰, respectively) are not consistent with biotic (microbial or thermogenic) methane sources, but are within previously reported ranges for abiotic methane production. Correlation between δ 13C CH4 and δ 13C-dissolved inorganic C (DIC) also suggests that CO 2 is a parent C source for the observed CH 4(g). Moreover, CH 4-CO 2 isotopic geothermometry was used to estimate CH 4(g) formation temperatures ranging from ~ 250 - 350°C, which is just below the temperature estimated for the hydrothermal reservoir and consistent with the hypothesis that subsurface, rock-water interactions are responsible for large methane fluxes from this volcanic system. An understanding of conditions leading to the abiotic production of methane and associated isotopic signatures are central to understanding the evolutionary history of deep carbon sources on Earth.« less

Calibration strategies for the determination of stable carbon absolute isotope ratios in a glycine candidate reference material by elemental analyser-isotope ratio mass spectrometry.

PubMed

Dunn, Philip J H; Malinovsky, Dmitry; Goenaga-Infante, Heidi

2015-04-01

We report a methodology for the determination of the stable carbon absolute isotope ratio of a glycine candidate reference material with natural carbon isotopic composition using EA-IRMS. For the first time, stable carbon absolute isotope ratios have been reported using continuous flow rather than dual inlet isotope ratio mass spectrometry. Also for the first time, a calibration strategy based on the use of synthetic mixtures gravimetrically prepared from well characterised, highly (13)C-enriched and (13)C-depleted glycines was developed for EA-IRMS calibration and generation of absolute carbon isotope ratio values traceable to the SI through calibration standards of known purity. A second calibration strategy based on converting the more typically determined delta values on the Vienna PeeDee Belemnite (VPDB) scale using literature values for the absolute carbon isotope ratio of VPDB itself was used for comparison. Both calibration approaches provided results consistent with those previously reported for the same natural glycine using MC-ICP-MS; absolute carbon ratios of 10,649 × 10(-6) with an expanded uncertainty (k = 2) of 24 × 10(-6) and 10,646 × 10(-6) with an expanded uncertainty (k = 2) of 88 × 10(-6) were obtained, respectively. The absolute carbon isotope ratio of the VPDB standard was found to be 11,115 × 10(-6) with an expanded uncertainty (k = 2) of 27 × 10(-6), which is in excellent agreement with previously published values.

High-efficiency dual labeling of influenza virus for single-virus imaging.

PubMed

Liu, Shu-Lin; Tian, Zhi-Quan; Zhang, Zhi-Ling; Wu, Qiu-Mei; Zhao, Hai-Su; Ren, Bin; Pang, Dai-Wen

2012-11-01

Many viruses invade host cells by entering the cells and releasing their genome for replication, which are remarkable incidents for viral infection. Therefore, the viral internal and external components should be simultaneously labeled and dynamically tracked at single-virus level for further understanding viral infection mechanisms. However, most of the previously reported methods have very low labeling efficiency and require considerable time and effort, which is laborious and inconvenient for researchers. In this work, we report a general strategy to high-efficiently label viral envelope and genome for single-virus imaging with quantum dots (QDs) and Syto 82, respectively. It was found that nearly all viral envelopes could be labeled with QDs with superior stability, which makes it possible to realize global and long-term tracking of single virus in individual cells. Effectively labeling their genome with Syto 82, about 90% of QDs-labeled viruses could be used to monitor the viral genome signal, which may provide valuable information for deeply studying viral genome transport. This is very important and meaningful to investigate the viral infection mechanism. Our labeling strategy has advantage in commonality, convenience and efficiency, which is expected to be widely used in biological research. Copyright © 2012 Elsevier Ltd. All rights reserved.

Positron Emission Tomography and Near-Infrared Fluorescence Imaging of Vascular Endothelial Growth Factor with Dual-Labeled Bevacizumab.

PubMed

Zhang, Yin; Hong, Hao; Engle, Jonathan W; Yang, Yunan; Barnhart, Todd E; Cai, Weibo

2012-01-01

The pivotal role of vascular endothelial growth factor (VEGF) in cancer is underscored by the approval of bevacizumab (Bev, a humanized anti-VEGF monoclonal antibody) for first line treatment of cancer patients. The aim of this study was to develop a dual-labeled Bev for both positron emission tomography (PET) and near-infrared fluorescence (NIRF) imaging of VEGF. Bev was conjugated to a NIRF dye (i.e. 800CW) and 2-S-(4-isothiocyanatobenzyl)-1,4,7-triazacyclononane-1,4,7-triacetic acid (p-SCN-Bn-NOTA) before (64)Cu-labeling. Flow cytometry analysis of U87MG human glioblastoma cells revealed no difference in VEGF binding affinity/specificity between Bev and NOTA-Bev-800CW. (64)Cu-labeling of NOTA-Bev-800CW was achieved with high yield. Serial PET imaging of U87MG tumor-bearing female nude mice revealed that tumor uptake of (64)Cu-NOTA-Bev-800CW was 4.6 ± 0.7, 16.3 ± 1.6, 18.1 ± 1.4 and 20.7 ± 3.7 %ID/g at 4, 24, 48 and 72 h post-injection respectively (n = 4), corroborated by in vivo/ex vivo NIRF imaging and biodistribution studies. Tumor uptake as measured by ex vivo NIRF imaging had a good linear correlation with the %ID/g values obtained from PET (R(2) = 0.93). Blocking experiments and histology both confirmed the VEGF specificity of (64)Cu-NOTA-Bev-800CW. The persistent, prominent, and VEGF-specific uptake of (64)Cu-NOTA-Bev-800CW in the tumor, observed by both PET and NIRF imaging, warrants further investigation and future clinical translation of such Bev-based imaging agents.

Multiple tag labeling method for DNA sequencing

DOEpatents

Mathies, Richard A.; Huang, Xiaohua C.; Quesada, Mark A.

1995-01-01

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.

Compensation of matrix effects in gas chromatography-mass spectrometry analysis of pesticides using a combination of matrix matching and multiple isotopically labeled internal standards.

PubMed

Tsuchiyama, Tomoyuki; Katsuhara, Miki; Nakajima, Masahiro

2017-11-17

In the multi-residue analysis of pesticides using GC-MS, the quantitative results are adversely affected by a phenomenon known as the matrix effect. Although the use of matrix-matched standards is considered to be one of the most practical solutions to this problem, complete removal of the matrix effect is difficult in complex food matrices owing to their inconsistency. As a result, residual matrix effects can introduce analytical errors. To compensate for residual matrix effects, we have developed a novel method that employs multiple isotopically labeled internal standards (ILIS). The matrix effects of ILIS and pesticides were evaluated in spiked matrix extracts of various agricultural commodities, and the obtained data were subjected to simple statistical analysis. Based on the similarities between the patterns of variation in the analytical response, a total of 32 isotopically labeled compounds were assigned to 338 pesticides as internal standards. It was found that by utilizing multiple ILIS, residual matrix effects could be effectively compensated. The developed method exhibited superior quantitative performance compared with the common single-internal-standard method. The proposed method is more feasible for regulatory purposes than that using only predetermined correction factors and is considered to be promising for practical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

An Example-Based Multi-Atlas Approach to Automatic Labeling of White Matter Tracts

PubMed Central

Yoo, Sang Wook; Guevara, Pamela; Jeong, Yong; Yoo, Kwangsun; Shin, Joseph S.; Mangin, Jean-Francois; Seong, Joon-Kyung

2015-01-01

We present an example-based multi-atlas approach for classifying white matter (WM) tracts into anatomic bundles. Our approach exploits expert-provided example data to automatically classify the WM tracts of a subject. Multiple atlases are constructed to model the example data from multiple subjects in order to reflect the individual variability of bundle shapes and trajectories over subjects. For each example subject, an atlas is maintained to allow the example data of a subject to be added or deleted flexibly. A voting scheme is proposed to facilitate the multi-atlas exploitation of example data. For conceptual simplicity, we adopt the same metrics in both example data construction and WM tract labeling. Due to the huge number of WM tracts in a subject, it is time-consuming to label each WM tract individually. Thus, the WM tracts are grouped according to their shape similarity, and WM tracts within each group are labeled simultaneously. To further enhance the computational efficiency, we implemented our approach on the graphics processing unit (GPU). Through nested cross-validation we demonstrated that our approach yielded high classification performance. The average sensitivities for bundles in the left and right hemispheres were 89.5% and 91.0%, respectively, and their average false discovery rates were 14.9% and 14.2%, respectively. PMID:26225419

An Example-Based Multi-Atlas Approach to Automatic Labeling of White Matter Tracts.

PubMed

Yoo, Sang Wook; Guevara, Pamela; Jeong, Yong; Yoo, Kwangsun; Shin, Joseph S; Mangin, Jean-Francois; Seong, Joon-Kyung

2015-01-01

We present an example-based multi-atlas approach for classifying white matter (WM) tracts into anatomic bundles. Our approach exploits expert-provided example data to automatically classify the WM tracts of a subject. Multiple atlases are constructed to model the example data from multiple subjects in order to reflect the individual variability of bundle shapes and trajectories over subjects. For each example subject, an atlas is maintained to allow the example data of a subject to be added or deleted flexibly. A voting scheme is proposed to facilitate the multi-atlas exploitation of example data. For conceptual simplicity, we adopt the same metrics in both example data construction and WM tract labeling. Due to the huge number of WM tracts in a subject, it is time-consuming to label each WM tract individually. Thus, the WM tracts are grouped according to their shape similarity, and WM tracts within each group are labeled simultaneously. To further enhance the computational efficiency, we implemented our approach on the graphics processing unit (GPU). Through nested cross-validation we demonstrated that our approach yielded high classification performance. The average sensitivities for bundles in the left and right hemispheres were 89.5% and 91.0%, respectively, and their average false discovery rates were 14.9% and 14.2%, respectively.

A Learner-Centered Spiral Knowledge Approach to Teaching Isotope Geology

NASA Astrophysics Data System (ADS)

Reid, M. R.

2006-12-01

Aided by the insights I gained by participation in the Arizona Board of Regents Tri-University Collaboration on Learner-Centered Practice, I made major changes to a graduate course in isotope geology (GLG617), including: 1) implementation of a spiral knowledge approach (e.g., Bruner, 1990; Dyar et al., 2004); 2) incorporation of more learner-centered in-class activities; and 3) more explicit emphasis on skills that I regarded as important for success in geochemistry. In the geosciences, the field of isotope geology is now an essential area of inquiry with implications for geologic timescales, climate information, tracing geochemical processes, and biological evolution, to name a few. The traditional approach to teaching isotope geology suffers from the fact that learning tends to be compartmentalized by technique/approach and one subfield (e.g., stable or radiogenic isotopes) is usually favored by appearing earlier in semester. To make learning more integrated, I employed a simplified spiral learning approach so that common principles could be revisited several times over the course of the semester and, in so doing, students' grasp of the fundamental principles could be scaffolded into greater understanding. Other learner-centered changes to the course included more explicit emphasis on helping students become comfortable with interpreting data displayed graphically and explicit emphasis on helping students give and evaluate oral presentations that rely on isotope data. I also developed a detailed grading rubric for the final paper and allowed students to have a draft of their final papers evaluated and graded (guided by Huba and Freed, 2000) A number of cooperative learning activities developed specifically for this course (19 in all) enabled me to gain a better appreciation for students' learning. Activities included pair share, round-robin, small group explorations of techniques and case studies (sometimes as introduction to, sometimes as review of material

Quantification of dynamic soil - vegetation feedbacks following an isotopically labelled precipitation pulse

NASA Astrophysics Data System (ADS)

Piayda, Arndt; Dubbert, Maren; Siegwolf, Rolf; Cuntz, Matthias; Werner, Christiane

2017-04-01

The presence of vegetation alters hydrological cycles of ecosystems. Complex plant-soil interactions govern the fate of precipitation input and water transitions through ecosystem compartments. Disentangling these interactions is a major challenge in the field of ecohydrology and pivotal foundation for understanding the carbon cycle of semi-arid ecosystems. Stable water isotopes can be used in this context as tracer to quantify water movement through soil-vegetation-atmosphere interfaces. The aim of this study is to disentangle vegetation effects on soil water infiltration and distribution as well as dynamics of soil evaporation and grassland water-use in a Mediterranean cork-oak woodland during dry conditions. An irrigation experiment using δ18O-labeled water was carried out in order to quantify distinct effects of tree and herbaceous vegetation on infiltration and distribution of event water in the soil profile. Dynamic responses of soil and herbaceous vegetation fluxes to precipitation regarding event water-use, water uptake depth plasticity and contribution to ecosystem evapotranspiration were quantified. Total water loss to the atmosphere from bare soil was as high as from vegetated soil, utilizing large amounts of unproductive water loss for biomass production, carbon sequestration and nitrogen fixation. During the experiment no adjustments of main root water uptake depth to changes of water availability could be observed, rendering light to medium precipitation events under dry conditions useless. This forces understory plants to compete with adjacent trees for soil water in deeper soil layers. Thus understory plants are faster subject to chronic drought, leading to premature senescence at the onset of drought. Despite this water competition, the presence of Cork oak trees fosters infiltration to large degrees. That reduces drought stress, caused by evapotranspiration, due to favourable micro climatic conditions under tree crown shading. This study

Quantification of dynamic soil-vegetation feedbacks following an isotopically labelled precipitation pulse

NASA Astrophysics Data System (ADS)

Piayda, Arndt; Dubbert, Maren; Siegwolf, Rolf; Cuntz, Matthias; Werner, Christiane

2017-05-01

The presence of vegetation alters hydrological cycles of ecosystems. Complex plant-soil interactions govern the fate of precipitation input and water transitions through ecosystem compartments. Disentangling these interactions is a major challenge in the field of ecohydrology and a pivotal foundation for understanding the carbon cycle of semi-arid ecosystems. Stable water isotopes can be used in this context as tracer to quantify water movement through soil-vegetation-atmosphere interfaces. The aim of this study is to disentangle vegetation effects on soil water infiltration and distribution as well as dynamics of soil evaporation and grassland water use in a Mediterranean cork oak woodland during dry conditions. An irrigation experiment using δ18O labelled water was carried out in order to quantify distinct effects of tree and herbaceous vegetation on the infiltration and distribution of event water in the soil profile. Dynamic responses of soil and herbaceous vegetation fluxes to precipitation regarding event water use, water uptake depth plasticity, and contribution to ecosystem soil evaporation and transpiration were quantified. Total water loss to the atmosphere from bare soil was as high as from vegetated soil, utilizing large amounts of unproductive evaporation for transpiration, but infiltration rates decreased. No adjustments of main root water uptake depth to changes in water availability could be observed during the experiment. This forces understorey plants to compete with adjacent trees for water in deeper soil layers at the onset of summer. Thus, understorey plants are subjected to chronic water deficits faster, leading to premature senescence at the onset of drought. Despite this water competition, the presence of cork oak trees fosters infiltration and reduces evapotranspirative water losses from the understorey and the soil, both due to altered microclimatic conditions under crown shading. This study highlights complex soil-plant-atmosphere and

Quantification of in Situ Biodegradation Rate Constants Using a Novel Combined Isotope Approach

NASA Astrophysics Data System (ADS)

Blum, P.; Sültenfuß, J.; Martus, P.

2014-12-01

Numerous studies have shown the enormous potential of the compound-specific isotope analysis (CSIA) for studying the biodegradation of organic compounds such as monoaromatic hydrocarbons (BTEX), polyaromatic hydrocarbons (PAH), chlorinated solvents and other organic contaminants and environmental transformation mechanisms in groundwater. In addition, two-dimensional isotope analysis such as carbon and hydrogen have been successfully studied indicating the potential to also investigate site-specific reaction mechanisms. The main objective of the current study however is to quantify real effective in situ biodegradation rate constants in a coal-tar contaminated aquifer by combining compound-specific isotope analysis (CSIA) and tracer-based (3H-3He) ground-water dating (TGD). Hence, groundwater samples are used to determine groundwater residence times, and carbon and hydrogen stable isotopes are analyzed for selected BTEX and PAH. The results of the hydrogen stable isotopes surprisingly indicate no isotope fractionation and therefore no biodegradation. In contrast, for stable carbon isotopes of selected BTEX such as o-xylene and toluene, isotope shifts are detected indicating active biodegradation under sulfate-reducing conditions. These and previous results of stable carbon isotopes show that only for o-xylene a clear evidence for biodegradation is possible for the studied site. Nevertheless, in combining these results with the groundwater residence times, which range between 1 year for the shallow wells (20 m below surface) and 41 years for the deeper wells (40 m below surface), it is feasible to effectively determine in situ biodegradation rate constants for o-xylene. Conversely, the outcome also evidently demonstrate the major limitations of the novel combined isotope approach for a successful implementation of monitored natural attenuation (MNA) at such field sites.

Isotope-Encoded Carboxyl Group Footprinting for Mass Spectrometry-Based Protein Conformational Studies

NASA Astrophysics Data System (ADS)

Zhang, Hao; Liu, Haijun; Blankenship, Robert E.; Gross, Michael L.

2016-01-01

We report an isotope-encoding method coupled with carboxyl-group footprinting to monitor protein conformational changes. The carboxyl groups of aspartic/glutamic acids and of the C-terminus of proteins can serve as reporters for protein conformational changes when labeled with glycine ethyl ester (GEE) mediated by carbodiimide. In the new development, isotope-encoded "heavy" and "light" GEE are used to label separately the two states of the orange carotenoid protein (OCP) from cyanobacteria. Two samples are mixed (1:1 ratio) and analyzed by a single LC-MS/MS experiment. The differences in labeling extent between the two states are represented by the ratio of the "heavy" and "light" peptides, providing information about protein conformational changes. Combining isotope-encoded MS quantitative analysis and carboxyl-group footprinting reduces the time of MS analysis and improves the sensitivity of GEE and other footprinting.

Determination of the Isotopic Enrichment of 13C- and 2H-Labeled Tracers of Glucose Using High-Resolution Mass Spectrometry: Application to Dual- and Triple-Tracer Studies.

PubMed

Trötzmüller, Martin; Triebl, Alexander; Ajsic, Amra; Hartler, Jürgen; Köfeler, Harald; Regittnig, Werner

2017-11-21

Multiple-tracer approaches for investigating glucose metabolism in humans usually involve the administration of stable and radioactive glucose tracers and the subsequent determination of tracer enrichments in sampled blood. When using conventional, low-resolution mass spectrometry (LRMS), the number of spectral interferences rises rapidly with the number of stable tracers employed. Thus, in LRMS, both computational effort and statistical uncertainties associated with the correction for spectral interferences limit the number of stable tracers that can be simultaneously employed (usually two). Here we show that these limitations can be overcome by applying high-resolution mass spectrometry (HRMS). The HRMS method presented is based on the use of an Orbitrap mass spectrometer operated at a mass resolution of 100 000 to allow electrospray-generated ions of the deprotonated glucose molecules to be monitored at their exact masses. The tracer enrichment determination in blood plasma is demonstrated for several triple combinations of 13 C- and 2 H-labeled glucose tracers (e.g., [1- 2 H 1 ]-, [6,6- 2 H 2 ]-, [1,6- 13 C 2 ]glucose). For each combination it is shown that ions arising from 2 H-labeled tracers are completely differentiated from those arising from 13 C-labeled tracers, thereby allowing the enrichment of a tracer to be simply calculated from the observed ion intensities using a standard curve with curve parameters unaffected by the presence of other tracers. For each tracer, the HRMS method exhibits low limits of detection and good repeatability in the tested 0.1-15.0% enrichment range. Additionally, due to short sample preparation and analysis times, the method is well-suited for high-throughput determination of multiple glucose tracer enrichments in plasma samples.