bluuebunny/crossref_metadata_2025_split huggingface dataset:
Composition of the black crusts from the Saint Denis Basilica, France, as revealed by gas chromatography‐mass spectrometry
Authors: Gaviño Maria , Hermosin Bernardo , Vergès‐Belmin Véronique , Nowik Witold , Saiz‐Jimenez Cesareo 
Published: March 2004

AbstractThe organic fraction of black crusts from Saint Denis Basilica, France, is composed of a complex mixture of aliphatic and aromatic compounds. These compounds were studied by two different analytical approaches: tetramethyl ammonium hydroxide (TMAH) thermochemolysis in combination with gas chromatography‐mass spectrometry (GC‐MS), and solvent extraction, fractionation by silica column, and identification of the fraction components by GC‐MS. The first approach, feasible at the micro‐scale level, is able to supply fairly general information on a wide range of compounds. Using the second approach, we were able to separate the complex mixture of compounds into four fractions, enabling a better identification of the extractable compounds. These compounds belong to different classes: aliphatic hydrocarbons (n‐alkanes, n‐alkenes), aliphatic and aromatic carboxylic acids (n‐fatty acids, α,ω‐dicarboxylic acids, and benzenecarboxylic acids), polycyclic aromatic hydrocarbons (PAH), and molecular biomarkers (isoprenoid hydrocarbons, diterpenoids, and triterpenoids). With each approach, similar classes of compounds were identified, although TMAH thermochemolysis failed to identify compounds present at low concentrations in black crusts. The two proposed methodological approaches are complementary, particularly in the study of polar fractions.
Structural elucidation of catechin and epicatechin in sorrel leaf extracts using liquid‐chromatography coupled to diode array‐, fluorescence‐, and mass spectrometric detection
Authors: Stöggl W. M. , Huck C. W. , Bonn Günther K. 
Published: March 2004

AbstractFlavonoids are natural compounds in medicinal herbs and posses several biological activities important in plant drug design. Especially strong antioxidant effects play an important role against radical oxidative stress causing pathological processes, such as arteriosclerosis or cancer. The aim of this work was to investigate unknown analytes found in sorrel leaf (Rumex acetosa) extracts in order to discover new leading compounds to enable quality control in phytopharmaceuticals made thereof. Therefore compounds of interest were separated after methanolic extraction by reversed‐phase liquid chromatography (RP‐LC) employing silica‐C18 as stationary phase using gradient elution with water (10 mM H3PO4) and acetonitrile as mobile phase. Structural elucidation was carried out by diode array, fluorescence, and mass spectroscopic detection. Photodiode‐array detection allowed the extraction of UV‐absorbance spectra from the peaks of interest. Absorbance maxima were found at 203 and 279 nm with a shoulder at 230 nm. Additionally fluorescence emission and excitation spectra were recorded from the analytes using a fluorescence detector (FLD) after stop flow (λex = 279 nm, λem = 307 nm). The chromatographic reversed‐phase system was coupled to an ion‐trap mass spectrometer (LC‐MS) by using an electrospray ionization interface (ESI). After optimization processes the separation was carried out using an ammonium acetate buffer at pH 5.5. Mass spectrometric detection turned out to be more sensitive in negative mode. Collisionally induced dissociation (CID) was used to obtain fragment ions of structural relevance (LC‐MS/MS). Finally, compounds of interest coming from sorrel leaf (Rumex acetosa) eluting at low acetonitrile concentrations were confirmed to be catechin and epicatechin.
Studying the interactome with the yeast two‐hybrid system and mass spectrometry
Authors: Causier Barry 
Published: March 2004

Abstract

I.
Introduction
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II.
The Yeast Two‐Hybrid System
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A.  A Brief History
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1.  Basis of Yeast Two‐Hybrid System
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2.  Development of the System
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B.  Current Systems
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1.  The GAL4 and LexA Systems
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2.  The Sos Recruitment System
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3.  The Split‐Ubiquitin System
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4.  The Dual‐Bait System
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5.  Other Two‐Hybrid Systems
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6.  Variations on a Theme
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C.  Applications of Yeast Two‐Hybrid
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III.
Studying Protein Interactions by MS
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IV.
Genome‐Wide Analysis of Protein–Protein Interactions
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A.  Yeast Two‐Hybrid
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B.  Mass Spectrometry
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C.  Comparison of the Two Approaches
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D.  Placing Interactions in Context
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V.
Emerging Technologies
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VI.
Conclusions
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Acknowledgments
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Abbreviations
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References
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Protein interactions are crucial to the life of a cell. The analysis of such interactions is allowing biologists to determine the function of uncharacterized proteins and the genes that encode them. The yeast two‐hybrid system has become one of the most popular and powerful tools to study protein–protein interactions. With the advent of proteomics, the two‐hybrid system has found a niche in interactome mapping. However, it is clear that only by combining two‐hybrid data with that from complementary approaches such as mass spectrometry (MS) can the interactome be analyzed in full. This review introduces the yeast two‐hybrid system to those unfamiliar with the technique, and discusses how it can be used in combination with MS to unravel the network of protein interactions that occur in a cell. © 2004 Wiley Periodicals, Inc., Mass Spec Rev
Biaxial deformation of polyamide‐6: Assessment of orientation by means of infrared trichroism
Authors: Cole K. C. , Depecker C. , Jutigny M. , Lefebvre J.‐M. , Krawczak P. 
Published: March 2004

AbstractInfrared spectroscopy was used to study the evolution of structure in films of polyamide‐6 drawn on a Cellier tenter frame laboratory tester under conditions of simultaneous equibiaxial stretching and planar uniaxial stretching. The “tilted film” method was used to obtain trichroic spectra corresponding to the machine, transverse, and normal directions, as well the “structural factor” spectrum. From these it was possible to obtain information on the molecular orientation and the evolution of the crystalline structure. The starting films, prepared by melt casting from an extruder on a chilled roll, contained predominantly the mesomorphic β form. The structural factor spectra confirmed that strain‐induced transformation into the α form occurred upon drawing, and that the amount of α form increased with the extent of drawing. The trichroic spectra showed that the molecular orientation was localized mainly, but not exclusively, in the α form. Orientation functions could be determined for both the molecular chain axis and the normal to the hydrogen‐bonded sheets. For both the equibiaxial and planar uniaxial films, these sheets were found to be strongly oriented parallel to the plane of the film, with the degree of orientation increasing with overall draw ratio. For the biaxial samples, the molecular chain orientation was found to be equibiaxial, as expected. Mechanical test results indicated that the chains are evenly distributed in the film plane rather than showing a preference for the two orthogonal draw directions. For the planar uniaxial samples, the chain orientation was predominantly in the draw direction, but some degree of orientation in the transverse direction was also observed. The variation of orientation functions with draw ratio suggested that the α structure evolves in two stages, the first involving chain orientation in the draw direction and the second involving rotation of the sheets into the plane of the film.
Synthesis of unsaturated polyester‐clay nanocomposites using reactive organoclays
Authors: Fu Xiao‐An , Qutubuddin Syed 
Published: March 2004

AbstractTwo polymerizable cationic surfactants, vinylbenzyl n‐alkyldimethyl (n = 12 or 18) ammonium chlorides, were used for functionalization of montmorillonite (MMT) and preparation of unsaturated polyester (UP)‐clay nanocomposites. Polymerizable organophilic clays were prepared by exchanging the sodium ions of MMT with vinylbenzyldodecyldimethyl ammonium chloride (VDAC) or vinylbenzyloctadecyldimethyl ammonium chloride (VOAC) in an aqueous medium. The dispersion of organoclays in UP led to gel formation. UP/VDAC‐MMT resulted in intercalated nanocomposites while UP/VOAC‐MMT formed partially exfoliated nanocomposites. The nanocomposites exhibited higher dynamic modulus than pristine UP.
Curing and pyrolysis of cresol novolac epoxy resins containing [2‐(6‐oxido‐6H‐dibenz(c,e)(1,2)oxaphosphorin‐6‐yl)‐1,4‐naphthalenediol]
Authors: Rwei S.‐P. , Liu A.‐Y. , Liou G.‐S. , Cheng K.‐C. , Guo W. 
Published: March 2004

AbstractThis study investigates the curing kinetics, thermal properties and decomposition kinetics of cresol novolac epoxy (CNE) with two curing agents, 2‐(6‐oxido‐6H dibenz(c,e)(1,2) oxaphosphorin‐6‐yl)‐1,4‐benzenediol (ODOPN), and phenol novolac (PN). In comparison with the conventional PN system, introducing ODOPN, a phosphorus‐containing bulky pendant group, into CNE increases Tg by 33°C, char yield from 30% to 38%, and LOI from 22 to 31. The DSC curing study reveals that the Ea of the CNE/ODOPN epoxy can be obtained by Kissinger's method. The resulting Ea values indicate that the catalytic effect of EMI is insignificant on CNE/ODOPN but is marked on CNE/PN, whose Ea was reduced from 131.5 to 75.6 KJ/mole. This result may be caused by the fact that the symmetric diol attached to the 1 and 4 positions of the naphthalene ring in ODOPN sets up a steadily resonating structure and inhibits the catalytic action. Further investigating the conversion ratio with curing temperature yielded experimental data that agreed closely with Kaiser's model. The orders of the autocatalyzed reaction, m, and the crosslinking reaction, n, are close to 0.5 and 1.0, respectively, independently of the scan rate. Finally, the TGA decomposition study by Ozawa's method demonstrates that the mean Ea declines with the phosphorus content, because the easy decomposition of the phosphorus compound in the initiation stage facilitates the formation of an insulating layer. However, results in this study further reveal an increasing tendency for Ea with decomposition conversion for an ODOPN/PN mixture with the ODOPN content of over 50%, probably because of the retardation of gas diffusion by the insulating layer of phosphorus compound.
Intregrated analysis of the human cardiac transcriptome, proteome and phosphoproteome
Authors: Ruse Cristian I. , Tan Fen‐Lai , Kinter Michael , Bond Meredith 
Published: March 2004

AbstractAltered expression of different classes of genes has been shown to differentiate between failing and nonfailing human hearts. However, characterization of proteins and the post‐translational modifications that regulate their functions is required for understanding both the physiology of cardiac muscle and the mechanisms leading to pathological states associated with cardiac diseases. We present in this paper, an analysis of the human cardiac transcriptome, proteome and phosphoproteome. Data from two sources (i) experiments performed in our laboratory and (ii) bioinformatics searches of public databases (SWISS‐PROT, NCBI, Cardiac Gene Expression Knowledge Base, Gene Ontology Consortium and Affymetrix) are reported in a relational database that allows user‐designed specific queries. Microarray experiments were performed with Affymetrix Hu95Av2. Cardiac proteins were digested with trypsin. An 11 step cation exchange procedure produced fractions for analysis in separate reversed phase high‐performance liquid chromatography‐tandem mass spectrometry (MS/MS) experiments. Immobilized metal affinity chromatography was used to select the phosphopeptides from the same tryptic peptide mixture. They were then further investigated by MS/MS. Gel‐free approaches were used to detect 267 proteins and 47 phosphopeptides. Our human cardiac database contains 447 entries. We propose the use of this platform, built with data derived from nonfailing hearts, as a template for initiating the effort to characterize the human cardiac proteome and its associated post‐translational modifications.
A proteome reference map for Vibrio cholerae El Tor
Authors: Coelho Ana , de Oliveira Santos Eidy , da Hora Faria Mauro Luiz , de Carvalho Daniela Palermo , Soares Marcia Regina , von Kruger Wanda Maria Almeida , Bisch Paulo Mascarello 
Published: March 2004

AbstractA proteome reference map has been constructed for Vibrio cholerae El Tor, in the pI range of 4.0 to 7.0. The map is based on two‐dimensional gels (2‐D) and the identification, by peptide mass fingerprint, of proteins in 94 spots, corresponding to 80 abundant proteins. Two strains are compared, strain N16961 and a Latin American El Tor strain C3294. The consensus map contains 340 spots consistently seen with both strains grown in Luria‐Bertani broth (LB) or minimal M9 medium. The results were obtained from nine gels run with 18 cm immobilized pH gradient strips and precast gels. The 2‐D gels were anchored to real N16961 proteins identified by mass spectrometry. Various energy metabolism components and periplasmic ATP‐binding cassette (ABC) transporter proteins were identified among the abundant proteins. Two isoforms of OmpU were found. Five operons are proposed and seven hypothetical proteins were experimentally confirmed. Comparisons are made with protein 2‐D gels for a classical strain and to microarray analysis available for the N16961 El Tor strain. New results were obtained from the proteome analysis, indicating an abundance of periplasmic ABC transporter proteins not found in microarray studies.
A comprehensive approach for establishment of the platform to analyze functions of KIAA proteins: Generation and evaluation of anti‐mKIAA antibodies
Authors: Koga Hisashi , Shimada Kiyo , Hara Yasuhiro , Nagano Mihoko , Kohga Hiroshi , Yokoyama Ryo , Kimura Yayoi , Yuasa Sigeaki , Magae Junji , Inamoto Susumu , Okazaki Noriko , Ohara Osamu 
Published: March 2004

AbstractSince December 2001 we have been conducting a project to isolate and determine entire sequences of mouse KIAA cDNA clones which encode polypeptides corresponding to human KIAA proteins. The ultimate goal of this project is the elucidation of the functions of KIAA proteins. A critical step in this project is the generation of antibodies based on the cDNA sequence information. Although antibodies are the most optimal tools for biological analysis, the production and isolation of multiple recombinant proteins for an antigen is a rate‐limiting step in antibody production. To address this problem, we established a system utilizing the in vitro recombination‐assisted method and shotgun clones that were generated during the sequencing of mouse KIAA cDNAs (DNA Res. 2003, 10, 129–136). The authenticity of the expressed proteins was confirmed by matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry. Another critical step for antibody production is the evaluation of the antibodies. Thus, we also made efforts to develop a systematic approach for evaluation of the titer and the specificity of the antibodies. Using these systems, we have produced and evaluated more than 500 antibodies raised against mouse KIAA proteins to date. We are currently generating antibody arrays for analysis of protein expression profiles. We will verify protein‐protein interactions using immunoprecipitation and tandem mass spectrometry analysis.
Setting up standards and a reference map for the alkaline proteome of the Gram‐positive bacterium Lactococcus lactis
Authors: Drews Oliver , Reil Gerold , Parlar Harun , Görg Angelika 
Published: March 2004

AbstractDespite the fact that almost 39% of the theoretical expressed proteins of Lactococcus lactis have a predicted isoelectric point above 7, these proteins have not been studied in previous proteome analyses. In the present study, we set up a reference map of alkaline lactococcal proteins by using immobilized pH gradients (IPG) spanning pH 6 to 12 and 9 to 12, and protein identification by matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry (MALDI‐TOF MS). Different electrophoresis systems for isoelectric focusing were evaluated to optimize the first dimension. Best results were obtained by sample application using cup‐loading at the anodic side and increasing the final voltage up to 8000 V for IPGs, using N,N‐dimethylacrylamide as monomer. After two‐dimensional gel electrophoresis of extracts obtained from exponentially growing cells, about 200 protein spots were selected for identification by peptide mass fingerprinting. With MALDI‐TOF MS, 153 proteins were identified that were the products of 85 different genes. Their predicted isoelectric points range from as high as 11.31 to as low as 6.34. Ribosomal proteins, hypothetical proteins and proteins with unknown function represent the largest groups of identified proteins. For further classification, the codon adaptation index (CAI) and grand average of hydropathicity (GRAVY) for each lactococcal protein were calculated. The protein with the lowest CAI identified in this study is the manganese ABC transporter ATP‐binding protein. Less than 10% of the alkaline lactococcal proteins have a smaller CAI. The highest GRAVY for an identified protein is 0.26. The complete in silico data of Lactococcus lactis as well as clickable reference maps are available at www.wzw.tum.de/proteomik/lactis.
Web‐accessible proteome databases for microbial research
Authors: Pleißner Klaus‐Peter , Eifert Till , Buettner Sven , Schmidt Frank , Boehme Martina , Meyer Thomas F. , Kaufmann Stefan H. E. , Jungblut Peter R. 
Published: March 2004

AbstractThe analysis of proteomes of biological organisms represents a major challenge of the post‐genome era. Classical proteomics combines two‐dimensional electrophoresis (2‐DE) and mass spectrometry (MS) for the identification of proteins. Novel technologies such as isotope coded affinity tag (ICAT)‐liquid chromatography/mass spectrometry (LC/MS) open new insights into protein alterations. The vast amount and diverse types of proteomic data require adequate web‐accessible computational and database technologies for storage, integration, dissemination, analysis and visualization. A proteome database system (http://www.mpiib‐berlin.mpg.de/2D‐PAGE) for microbial research has been constructed which integrates 2‐DE/MS, ICAT‐LC/MS and functional classification data of proteins with genomic, metabolic and other biological knowledge sources. The two‐dimensional polyacrylamide gel electrophoresis database delivers experimental data on microbial proteins including mass spectra for the validation of protein identification. The ICAT‐LC/MS database comprises experimental data for protein alterations of mycobacterial strains BCG vs. H37Rv. By formulating complex queries within a functional protein classification database “FUNC_CLASS” for Mycobacterium tuberculosis and Helicobacter pylori the researcher can gather precise information on genes, proteins, protein classes and metabolic pathways. The use of the R language in the database architecture allows high‐level data analysis and visualization to be performed “on‐the‐fly”. The database system is centrally administrated, and investigators without specific bioinformatic competence in database construction can submit their data. The database system also serves as a template for a prototype of a European Proteome Database of Pathogenic Bacteria. Currently, the database system includes proteome information for six strains of microorganisms.
Proteomic investigation of natural variation between Arabidopsis ecotypes
Authors: Chevalier François , Martin Olivier , Rofidal Valérie , Devauchelle Anne‐Dominique , Barteau Samuel , Sommerer Nicolas , Rossignol Michel 
Published: March 2004

AbstractTwo‐dimensional (2‐D) gel electrophoresis and peptide mass fingerprinting were used to investigate the natural variation in the proteome among 8 Arabidopsis thaliana ecotypes, of which 3 were previously shown to display atypical responses to environmental stress. Comparison of 2‐D maps demonstrated that only one‐quarter of spots was shared by all accessions. On the other hand, only 15% of the 25 majors spots accounting for half the total protein amount could be classified as major spots in all ecotypes. Identification of these major spots demonstrated large differences between the major functions detected. Accordingly, the proteomes appeared to reveal important variations in terms of function between ecotypes. Hierarchical clustering of proteomes according to either the amount of all anonymous spots, that of the 25 major spots or the functions of these major spots identified the same classes of ecotypes, and grouped the three atypical ecotypes. It is proposed that proteome comparison has the capacity to evidence differences in the physiological status of ecotypes. Results are discussed with respect to the possibility to infer such differences from limited comparisons of major proteins. It is concluded that classical proteomics could constitute a powerful tool to mine the biodiversity between ecotypes of a single plant species.
Proteins associated with type II bone morphogenetic protein receptor (BMPR‐II) and identified by two‐dimensional gel electrophoresis and mass spectrometry
Authors: Hassel Sylke , Eichner Annegret , Yakymovych Mariya , Hellman Ulf , Knaus Petra , Souchelnytskyi Serhiy 
Published: March 2004

AbstractBone morphogenetic proteins (BMP) are polypeptide growth factors that regulate cell differentiation and proliferation. BMPs bind to type I and type II serine/threonine kinase receptors to initiate intracellular signalling. BMPR‐II is the type II receptor, its mutations lead to hereditary pulmonary hypertension, and knockout of Bmpr‐II results in early embryonic lethality. To identify novel interacting proteins and explore signalling pathways that can be initiated by BMPR‐II, we performed glutathione‐S‐transferase (GST) pull‐down assays with BMPR‐II protein constructs fused to GST and extracts of mouse myoblast C2C12 cells. We generated three constructs which contain different parts of the cytoplasmic region of BMPR‐II: full‐length cytoplasmic part of BMPR‐II, only the kinase domain, or only the C‐terminal tail of BMPR‐II. Proteins which formed complexes with these BMPR‐II constructs were analyzed by two‐dimensional gel electrophoresis (2‐D GE), and specifically interacting proteins were identified by matrix‐assisted laser desorption/ionization‐time of flight‐mass spectrometry (MALDI‐TOF‐MS). We identified 33 interacting proteins; 11 proteins interacted with the C‐terminal tail of BMPR‐II, 4 with full‐length BMPR‐II, and 18 with a short form of the receptor with a deleted tail. Fourteen proteins have assigned functions in various signalling processes, suggesting links of BMP signalling to regulation of MAP kinase pathway, apoptosis, transcription, PKCß, and PKA. Five of the identified proteins are components of the cytoskeleton, and four are enzymes involved in metabolism, e.g., processing of estrogens or lipids. We confirmed interaction of PKCβ and CtBP with BMPR‐II using immunodetection. We showed that the C‐terminal tail of BMPR‐II provides binding sites for a number of regulatory proteins that may initiate Smad‐independent signalling.