bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein abundance quantification in embryonic stem cells using incomplete metabolic labelling with 15N amino acids, matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry, and analysis of relative isotopologue abundances of peptides
Authors: Vogt Josef A. , Schroer Klaus , Hölzer Kerstin , Hunzinger Christian , Klemm Martina , Biefang‐Arndt Katja , Schillo Simone , Cahill Michael A. , Schrattenholz André , Matthies Helmut , Stegmann Werner 
Published: June 2003

AbstractAn isotope dilution method for protein quantification is presented in the context of matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry (MALDI‐TOFMS) and mass fingerprinting experiments, revealing an unappreciated high reproducibility and accuracy of relative peak intensity measurements. Labelled proteins were generated by growing cells in a medium containing 15N‐enriched amino acids, and were mixed with proteins of natural isotopic composition from control cells in ratios of approximately 0:1, 1:7, 1:2, 2:1, 7:1, and 1:0 (labelled/unlabelled). Mixtures were separated by two‐dimensional gel electrophoresis and analysed by MALDI‐TOFMS using typical experimental conditions. A linear relationship is demonstrated between the relative isotopologue abundances (RIA values) for particular peaks in the isotopic distribution of tryptic peptide fragments of the proteins, and the mole fractions of labelled proteins in the mixture. Analysis of RIA values (ARIA quantification) for peptides of six typical silver‐stained protein spots for the various mixtures could reproduce the experimentally contrived ratios with approximate errors between 4% (2:1 mixture) and about 18% (1:7 mixture). A consideration of error and its propagation is discussed. ARIA does not require complete separation of the isotope patterns of labelled and unlabelled peptides, and is therefore advantageous in combination with all kinds of labelling experiments in biological systems, because it is compatible with minimal metabolic incorporation of labelling reagent. Simulations indicate that the minimum required 15N enrichment of the total amino acid pool sufficient for ARIA is less than 4%. In an accompanying paper in this issue, we apply ARIA to proteins differentially labelled with isotope‐coded alkylation reagents. Copyright © 2003 John Wiley & Sons, Ltd.
Analysis of relative isotopologue abundances for quantitative profiling of complex protein mixtures labelled with the acrylamide/D3‐acrylamide alkylation tag system
Authors: Cahill Michael A. , Wozny Wojciech , Schwall Gerhard , Schroer Klaus , Hölzer Kerstin , Poznanovic Slobodan , Hunzinger Christian , Vogt Josef A. , Stegmann Werner , Matthies Helmut , Schrattenholz André 
Published: June 2003

AbstractThe new method of analysis of relative isotopologue abundances (ARIA) applied here is based on the evaluation of total isotope patterns of tryptic protein fragments measured by matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry (MALDI‐TOFMS) to calculate the mixing ratios of composites consisting of stable isotope labelled and isotopically natural (unlabelled) proteins, as described in an accompanying paper in this issue. Recently, Sechi (Rapid Commun. Mass Spectrom. 2002; 16: 1416–1424) and Gehanne et al. (Rapid Commun. Mass Spectrom. 2002; 16: 1692–1698) introduced the use of differential quantitative mass analysis by MALDI‐TOFMS using mixtures of standard proteins alkylated prior to two‐dimensional polyacrylamide gel electrophoresis (2D‐PAGE) with either acrylamide (AA) or deuterium‐labelled [2,3,3′‐D3]‐acrylamide (D3AA). In the present study we validate the AA/D3AA system, firstly by measuring the yield of proteins alkylated with AA, and secondly by using differential radioactive labels (125I and 131I) to quantitatively establish that non‐comigration in 2D‐PAGE is negligible. ARIA is then applied to quantitatively estimate the relative proportions of peptides labelled with AA or D3AA in the validated system, using typical silver‐stained 2D‐PAGE protein spots from 2D gels loaded with 150 μg of total liver protein. The precision and limitations of ARIA quantification of peptides differentially alkylated with isotopomeric reagents are discussed. Copyright © 2003 John Wiley & Sons, Ltd.
Preliminary study of the stability of calix[4]arene crown compounds under radiolysis
Authors: Jankowski C. K. , Allain F. , Dozol J. F. , Virelizier H. , Tabet J. C. , Moulin C. , Lamouroux C. 
Published: June 2003

AbstractThe extraction of 135Cs from high activity waste arising from reprocessing of spent fuel can be achieved by using calix[4]arene crown compounds. The radiolytic degradation of calix[4]arene crowns as well as their solvent, o‐nitrophenyloctyl ether (NPOE), was studied using electrospray ionization mass spectrometry (ESI‐MS) (that formed Cs+ or Na+ adducts) in nitric acid, as well as by chemical ionization tandem mass spectrometry (MS/MS) experiments. The structures of major degradation products were identified with MS and specifically labelled nitric acid. Although NPOE and calix[4]arene crowns alone are relatively stable, under simulated conditions resembling the real industrial processes involving radiolysis in the presence of nitric acid, several products resulting from nitration and oxidation were observed. Copyright © 2003 John Wiley & Sons, Ltd.
Nano‐high‐performance liquid chromatography in combination with nano‐electrospray ionization Fourier transform ion‐cyclotron resonance mass spectrometry for proteome analysis
Authors: Ihling Christian , Berger Kerstin , Höfliger Martin M. , Führer Dagmar , Beck‐Sickinger Annette G. , Sinz Andrea 
Published: June 2003

AbstractFourier transform ion‐cyclotron resonance (FTICR) mass spectrometry offers several advantages for the analysis of biological samples, including excellent mass resolution, ultra‐high mass measurement accuracy, high sensitivity, and wide mass range. We report the application of a nano‐HPLC system coupled to an FTICR mass spectrometer equipped with nanoelectrospray source (nano‐HPLC/nano‐ESI‐FTICRMS) for proteome analysis. Protein identification in proteomics is usually conducted by accurately determining peptide masses resulting from enzymatic protein digests and comparing them with theoretically digested protein sequences from databases. A tryptic in‐solution digest of bovine serum albumin was used to optimize experimental conditions and data processing. Spots from Coomassie Blue and silver‐stained two‐dimensional (2D) gels of human thyroid tissue were excised, in‐gel digested with trypsin, and subsequently analyzed by nano‐HPLC/nano‐ESI‐FTICRMS. Additionally, we analyzed 1D‐gel bands of membrane preparations of COS‐6 cells from African green monkey kidney as an example of more complex protein mixtures. Nano‐HPLC was performed using 1‐mm reverse‐phase C‐18 columns for pre‐concentration of the samples and reverse‐phase C‐18 capillary columns for separation, applying water/acetonitrile gradient elution conditions at flow rates of 200 nL/min. Mass measurement accuracies smaller than 3 ppm were routinely obtained. Different methods for processing the raw data were compared in order to identify a maximum number of peptides with the highest possible degree of automation. Parallel identification of proteins from complex mixtures down to low‐femtomole levels makes nano‐HPLC/nano‐ESI‐FTICRMS an attractive approach for proteome analysis. Copyright © 2003 John Wiley & Sons, Ltd.
Identification of phytoestrogens in bovine milk using liquid chromatography/electrospray tandem mass spectrometry
Authors: Antignac Jean‐Philippe , Cariou Ronan , Le Bizec Bruno , Cravedi Jean‐Pierre , Andre François 
Published: June 2003

AbstractIn an international context of promoting scientific research on food safety, the interest in molecules having potential hormonal disrupting effects is growing. While industrial endocrine disruptors (phthalates, alkylphenols, PCBs, etc.) have been studied for several years, natural compounds like phytoestrogens remain less investigated. Accordingly, a research project was initiated with its main objectives to develop efficient analytical methods for a wide range of phytoestrogens in various food matrices, and to evaluate their occurrence in food products. Electrospray ionization with tandem mass spectrometric (MS/MS) analysis of isoflavones (genistein, daidzein, equol, formononetin, biochanin A), lignans (enterolactone, enterodiol), and coumestans (coumestrol) was investigated. This study revealed the formation of a large number of fragment ions in both positive and negative modes, corresponding to specific cleavages of the hydroxyl, carbonyl, and/or methoxy groups, and to Retro‐Diels‐Alder reactions. An LC/ESI‐MS/MS method was developed consistent with the 2002/657/EC European decision criteria. An extraction and clean‐up method was developed for milk samples. The identification limit for the proposed method appears to be under 1 ng/mL. The developed methodology was applied to various milk samples, and the occurrence of isoflavones (particularly equol) was demonstrated in the concentration range 1–30 ng/mL. The efficiency of the proposed analytical method permitted evaluation of a new and promising approach to a global risk assessment of natural estrogenic active substances including phytoestrogens and their metabolites. Copyright © 2003 John Wiley & Sons, Ltd.
ESI‐MS/MS analysis of underivatised amino acids: a new tool for the diagnosis of inherited disorders of amino acid metabolism. Fragmentation study of 79 molecules of biological interest in positive and negative ionisation mode
Authors: Piraud Monique , Vianey‐Saban Christine , Petritis Konstantinos , Elfakir Claire , Steghens Jean‐Paul , Morla Aymeric , Bouchu Denis 
Published: June 2003

AbstractThe diagnosis of inherited disorders of amino acids (AA) metabolism is usually performed on automated analysers by ion‐exchange chromatography and quantification after ninhydrin derivatisation of about 50 different AA. A single run liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for these molecules can be an alternative to this time‐consuming technique. The first step of this development is the infusion study of the fragmentation of 79 molecules of biological interest in electrospray ionisation tandem mass spectrometry (ESI‐MS/MS), in positive and in negative ionisation mode. Among them, three molecules can be detected only in negative ionisation mode, 38 only in positive mode and 38 in the two modes. All the most abundant fragmentations are presented, with optimisation of the MS/MS parameters. The positive ionisation mode was retained for the simultaneous analysis of 76 molecules. One sensitive and/or specific transition is proposed for the monitoring of each molecule. Improvement in sensitivity of detection was obtained with the use of an acidic mobile phase. Flow injection analysis studies led us to highlight a number of interferences—due to isobaric molecules, to in‐source collision‐induced dissociation, or to natural isotopic distribution of the elements—which are listed. For a reliable quantification method, these molecules have to be separated by LC before analysis in the tandem mass spectrometer. Ion‐pairing reversed‐phase liquid chromatography (RPLC) using perfluorinated carboxylic acids as ion‐pairing agents has already been found suitable for analysis of AA in MS/MS positive ionisation mode and is under development. Copyright © 2003 John Wiley & Sons, Ltd.
Fast high‐precision on‐line determination of hydrogen isotope ratios of water or ice by continuous‐flow isotope ratio mass spectrometry
Authors: Huber C. , Leuenberger M. 
Published: June 2003

AbstractA new fast high‐precision on‐line technique is described for the determination of hydrogen isotope ratios of water by continuous‐flow mass spectrometry. For the first time H2/H2O‐equilibration using a platinum catalyst has been used in a fully continuous process. A significant reduction in the H2/H2O‐equilibration time is achieved by a complete vaporization of the water and by increasing the exchange temperature to 100°C. The analysis time is only ∼5 min/sample which includes equilibration and processing. Measurement precision and accuracy are better than 1‰ and sample consumption is only ∼5 μL. This new technique allows the measurement of a wide range of aqueous samples either in a semi‐continuous way (discrete samples are injected one after another) or in a fully continuous way. This allows us, for the first time, to make continuous measurements of ice cores. Copyright © 2003 John Wiley & Sons, Ltd.
Wave theory of x‐ray scattering in capillary structures
Authors: Dabagov S. B. 
Published: June 2003

AbstractRecently, several coherent phenomena associated with the propagation of x‐rays in capillary optical elements (polycapillary lenses and systems of capillaries) have been observed. In order to describe these effects, a quantum‐wave theory of channeling was developed. In this paper, a theoretical analysis of scattering of x‐rays in capillary micro‐ and nanostructures within the frame of the wave approach is presented. Copyright © 2003 John Wiley & Sons, Ltd.
Review of capillary x‐ray optics from the 2nd International Capillary Optics Meeting
Authors: Bilderback Donald H. 
Published: June 2003

AbstractThe 2nd International Capillary Optics Meeting (ICOM2001) took place at the University of Antwerp, 17–21 June 2001. One of the meeting aims was to provide a forum to review the progress in x‐ray optics made from monocapillaries, polycapillaries and waveguides. These optics are often employed to better match the properties of a tube or synchrotron x‐ray source to x‐ray applications such as diffraction, fluorescence, spectroscopy, etc. Many of the applications involve small beams on the size scale from 30 nm to 50µm. The focus on the initial capillary optics meeting 5 years ago at Cornell University was on how to make and characterize optics. At this meeting, however, the highlights were more centered on how to use optics in interesting applications. Steady progress has been made in the manufacture of higher performance optics and this improvement in technical performance is continuing to drive the interest in commercialization and utilization of these novel forms of x‐ray optics in many areas of science and technology. This paper gives a brief overview of the meeting presentations and also describes some of the recent progress in capillary optics manufacture and application at CHESS at Cornell University. Copyright © 2003 John Wiley & Sons, Ltd.
Examination of poly‐capillary lenses for their use in micro‐XRF spectrometers
Authors: Haschke M. , Haller M. 
Published: June 2003

AbstractThe availability of poly‐capillary lenses opens up a wide variety of possibilities for the analysis of small sample areas because a large part of the tube radiation can captured and focused on the sample. Propagation in the glass capillaries is achieved by external total reflection on their internal surface. At first the intensity gain of the lenses and their spot size were the most interesting parameters. However, by using these lenses in commercial instruments, other parameters became more important for characterizing their performance for spectroscopic use, e.g. the energy dependence of the spot size and of the transmission efficiency and their influence to the tube spectrum. In this paper, the examination of various lenses from different manufacturers is described. It is shown that for the main parameters spot size and intensity gain, the differences are negligible. However, other parameters can be influenced by the change in geometric parameters of the lens such as the diameter of the single capillaries and bending radius of the lenses. These changes need high perfection in lens manufacturing. It seems that at present only one of the manufacturers is able to control the process in this way. However, there is also another requirement for the implementation of lenses for commercial instruments, namely the uniformity of the outer dimensions. Only in this case can these components be used without special adaptation in a routine instrument. This also requires the complete control of the manufacturing process. Because the use of poly‐capillary lenses is in its early stages, it seems necessary to define more exactly the parameters that characterize the x‐ray optical components. Only in this case will it be possible to define the performance of the optics with high precision and compare lenses from different manufacturers. Copyright © 2003 John Wiley & Sons, Ltd.
Metal capillary optics: novel fabrication methods and characterization
Authors: Hirsch Gregory 
Published: June 2003

AbstractA method for manufacturing metal monocapillary optics is described. The fabrication process begins by withdrawing an initially uniform wire from an etchant bath at a variable rate using a computer‐controlled translation stage. This generates a precise taper profile on the wire that corresponds to the bore of a capillary that will be produced in subsequent steps. Paraboloidal, ellipsoidal or other capillary figures can be programmed into the motion controller. Two different methods are discussed for generating the completed optic from the etched wire. In both of these techniques, the wire functions as an expendable mandrel. In the first method, the wire is first coated with a radiation‐reflecting material and then bonded to a rigid substrate. The wire is then dissolved using a chemical process to produce the hollow capillary optic. In the second method, a purely mechanical process imprints the wire figure into a softer material to create the capillary optic. Both manufacturing processes permit the production of capillaries that are accurately figured, extremely straight and have very low surface roughness. Wide latitude is possible in the selection of reflective materials that coat the internal surface of the optics. Experimental measurements using the optics with synchrotron radiation have demonstrated 5–10 µm diameter beams having flux‐density gains near 100. Potential improvements to the capillaries for achieving higher gains and smaller sizes are discussed. In addition to synchrotron radiation experiments, applications with small laboratory instruments are considered. The ultimate limitations of the optics and their comparison with glass capillaries are discussed. Copyright © 2003 John Wiley & Sons, Ltd.
Involvement of FGF‐2 in the action of Emdogain® on normal human osteoblastic activity
Authors: Mizutani S , Tsuboi T , Tazoe M , Koshihara Y , Goto S , Togari A 
Published: June 2003

Objective: The present study was designed to evaluate the pharmacological characteristics of Emdogain (EMD) on cell growth and cell activity in human osteoblasts.Methods: Cell proliferation as well as several gene and protein expressions were examined using reverse transcription‐polymerase chain reaction (RT‐PCR) and enzyme‐linked immunosorbent assay (ELISA) procedures in human osteoblastic cells (SaM‐1) treated with EMD (30 μg ml−1).Results: Treatment of osteoblasts with EMD significantly stimulated cell proliferation and fibroblast growth factor (FGF)‐2 expression but decreased alkaline phosphatase expression. In addition, increases in cyclooxygenase (COX)‐2 expression and decreases in matrix metalloproteinases (MMP)‐1 expression were observed in osteoblasts treated with EMD. The effects of EMD on FGF‐2 and MMP‐1 expressions were not observed in osteoblasts treated with NS‐398, an inhibitor of COX‐2. The decrease in MMP‐1 mRNA by EMD was prevented by treatment with antisense oligodeoxynucleotide (AS‐ODN) for FGF‐2.Conclusion: Emdogain showing both stimulation of cell proliferation and inhibition of cell differentiation has been shown to increase FGF‐2 expression in the mediation of prostaglandin E2 and to decrease MMP‐1 mRNA expression through the activation of FGF‐2. FGF‐2 may underlie in the action of EMD on osteoblasts during periodontal regeneration.
Drug effects on salivary glands: dry mouth
Authors: Scully CBE C 
Published: June 2003

Objective: To identify drugs associated with the complaint of dry mouth.Materials and Methods: MEDLINE was searched for papers 1980–2002 using keywords, oral, mouth, salivary, drugs, dry mouth and xerostomia, and relevant secondary references were hand‐searched.Results: Evidence was forthcoming for a number of xerogenic drugs, especially antimuscarinic agents, some sympathomimetic agents, and agents affecting serotonin and noradrenaline uptake, as well as a miscellany of other drugs such as appetite suppressants, protease inhibitors and cytokines.Conclusion: Dry mouth has a variety of possible causes but drugs – especially those with anticholinergic activity against the M3 muscarinic receptor – are the most common cause of reduced salivation.
Thromboprophylaxis in laparoscopic abdominal surgery
Authors: Meshikhes Abdul‐Wahed N. 
Published: June 2003

Background:  Since the introduction of laparoscopic cholecystectomy, there has been a great concern regarding the increased risk of thromboembolism following laparoscopic surgery. However, in the absence of clear guidelines, the use of thromboprophylaxis in laparoscopic abdominal surgery is controversial.Methods:  The evidence for and against routine and selective thromboprophylaxis in patients undergoing laparoscopic abdominal procedures was reviewed based mainly on published British and Danish surveys, together with the author's own survey. An attempt was made to come up with a generally‐accepted protocol for thromboprophylaxis in laparoscopic surgery.Results:  Less thromboembolic events were encountered by laparoscopic surgeons who adopt routine thromboprophylaxis. More thromboembolic events following laparoscopic abdominal surgery were encountered by surgeons adopting selective thromboprophylaxis policy.Conclusion:  Routine thromboprophylaxis seems to be more effective in protection against thromboembolism. However, this warrants further confirmation by prospective randomized trials.
The rice blast pathosystem as a case study for the development of new tools and raw materials for genome analysis of fungal plant pathogens
Authors: K. Mitchell Thomas , Thon Michael R. , Jeong Jun–Seop , Brown Doug , Deng Jixin , Dean Ralph A. 
Published: June 2003

SummaryFungi have an astounding and diverse impact on this planet. While they are agents of human diseases and the cause of allergic reactions, factories for the conversion of carbon in environmental and industrially adapted systems, and potential biological weapons, their importance as plant pathogens is unparalleled. In plants alone, fungi cause tens of thousands of different diseases and are responsible for massive losses of food, fiber and forestry at an estimated annual cost of hundreds of billions of dollars. These losses are not only realized in the incomes of individual farmers and state economies, but contribute significantly to world hunger problems and issues relating to safeguarding a global food supply. Our collective understanding of how fungi, particularly plant pathogens, grow, reproduce, identify a host and cause disease is still at a formative stage. There is an equal lack of detailed knowledge about how a plant recognizes that it is being attacked and then mounts an adequate defense response. The advent of genomic technologies has given researchers an unprecedented opportunity to address these mysteries in a powerful and more holistic manner. Where the genetic revolution of only a few years ago allowed for the characterization of single genes, today's genomic technologies are facilitating the evaluation of the entire complement of genes in an organism and the discovery of the suites of genes that act during any one time or particular condition. This review will describe the recent development of tools for whole or partial genome analysis and multigenome comparisons. Th discussion focuses on the rice blast pathosystem as a case study.