bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mass spectrometry‐based metabolomics oriented by correlation analysis for wound‐induced molecule discovery: identification of a novel jasmonate glucoside
Authors: Glauser Gaetan , Boccard Julien , Rudaz Serge , Wolfender Jean‐Luc 
Published: September 2009

AbstractIntroduction − Jasmonates are members of the oxylipin family involved in various plant regulatory processes, particularly in the response to biotic and abiotic stresses. They are present in very low amounts in wounded plants, which complicates their detection within complex plant extracts. Therefore, advanced analytical methods are needed for the profiling and characterisation of novel jasmonate derivatives.Objective – To use metabolomics to search for original wound‐induced metabolites belonging to the jasmonate family.Methodology – Numerous Arabidopsis specimens harvested at various time points after wounding were analysed by ultra‐high pressure liquid chromatography coupled to time‐of‐flight mass spectrometry (UHPLC/TOFMS). A correlation analysis based on kinetic profile similarities with known jasmonates was applied to find wound‐induced molecules having a potential role in defence signalling. Their characterisation was performed by tandem mass spectrometry and capillary nuclear magnetic resonance spectroscopy.Results – The statistical data treatment highlighted several previously reported jasmonates as well as a new glucoside derivative of the jasmonate 3‐oxo‐2‐(2Z‐pentenyl) cyclopentane‐1‐butyric acid (OPC‐4). The monitoring of its kinetics in response to wounding revealed a delayed accumulation compared to the profile of OPC‐4. This suggests an inactivation or elimination of OPC‐4 through the formation of a polar glucosylated metabolite.Conclusion – The metabolomic approach developed has proved useful in the discovery of original jasmonates synthesised in response to plant wounding. Copyright © 2009 John Wiley & Sons, Ltd.
Metabolomic analysis of Echinacea spp. by 1H nuclear magnetic resonance spectrometry and multivariate data analysis technique
Authors: Frédérich Michel , Jansen Céline , de Tullio Pascal , Tits Monique , Demoulin Vincent , Angenot Luc 
Published: September 2009

AbstractIntroduction – The genus Echinacea (Asteraceae) comprises about 10 species originally distributed in North America. Three species are very well known as they are used worldwide as medicinal plants: Echinacea purpurea, E. pallida, E. angustifolia.Objective – To discriminate between these three Echinacea species and E. simulata by 1H NMR‐based metabolomics.Methodology – 1H NMR and multivariate analysis techniques were applied to diverse Echinacea plants including roots and aerial parts, authentic plants, commercial plants and commercial dry extracts.Results – Using the 1H NMR metabolomics, it was possible, without previous evaporation or separation steps, to obtain a metabolic fingerprint to distinguish between species.Conclusion – A clear distinction between the three pharmaceutical species was possible and some useful metabolites were identified. Copyright © 2009 John Wiley & Sons, Ltd.
Proteomic, functional and motif‐based analysis of C‐terminal Src kinase‐interacting proteins
Authors: Yang Guang , Li Qingrun , Ren Siyuan , Lu Xuefeng , Fang Longhou , Zhou Wenchao , Zhang Fan , Xu Feilai , Zhang Zhe , Zeng Rong , Lottspeich Friedrich , Chen Zhengjun 
Published: September 2009

AbstractC‐terminal Src kinase (Csk) that functions as an essential negative regulator of Src family tyrosine kinases (SFKs) interacts with tyrosine‐phosphorylated molecules through its Src homology 2 (SH2) domain, allowing it targeting to the sites of SFKs and concomitantly enhancing its kinase activity. Identification of additional Csk‐interacting proteins is expected to reveal potential signaling targets and previously undescribed functions of Csk. In this study, using a direct proteomic approach, we identified 151 novel potential Csk‐binding partners, which are associated with a wide range of biological functions. Bioinformatics analysis showed that the majority of identified proteins contain one or several Csk‐SH2 domain‐binding motifs, indicating a potentially direct interaction with Csk. The interactions of Csk with four proteins (partitioning defective 3 (Par3), DDR1, SYK and protein kinase C iota) were confirmed using biochemical approaches and phosphotyrosine 1127 of Par3 C‐terminus was proved to directly bind to Csk‐SH2 domain, which was consistent with predictions from in silico analysis. Finally, immunofluorescence experiments revealed co‐localization of Csk with Par3 in tight junction (TJ) in a tyrosine phosphorylation‐dependent manner and overexpression of Csk, but not its SH2‐domain mutant lacking binding to phosphotyrosine, promoted the TJ assembly in Madin‐Darby canine kidney cells, implying the involvement of Csk‐SH2 domain in regulating cellular TJs. In conclusion, the newly identified potential interacting partners of Csk provided new insights into its functional diversity in regulation of numerous cellular events, in addition to controlling the SFK activity.
Shotgun proteome profile of Populus developing xylem
Authors: Kalluri Udaya C. , Hurst Gregory B. , Lankford Patricia K. , Ranjan Priya , Pelletier Dale A. 
Published: September 2009

AbstractUnderstanding the molecular pathways of plant cell wall biosynthesis and remodeling is central to interpreting biological mechanisms underlying plant growth and adaptation as well as leveraging that knowledge towards development of improved bioenergy feedstocks. Here, we report the application of shotgun MS/MS profiling to the proteome of Populus developing xylem. Nearly 6000 different proteins were identified from the xylem proteome. To identify low‐abundance DNA‐regulatory proteins from the developing xylem, a selective nuclear proteome profiling method was developed. Several putative transcription factors and chromatin remodeling proteins were identified using this method, such as NAC domain, CtCP‐like and CHB3‐SWI/SNF‐related proteins. Public databases were mined to obtain information in support of subcellular localization, transcript‐level expression and functional categorization of identified proteins. In addition to finding protein‐level evidence of candidate cell wall biosynthesis genes from xylem (wood) tissue such as cellulose synthase, sucrose synthase and polygalacturonase, several other potentially new candidate genes in the cell wall biosynthesis pathway were discovered. Further application of such proteomics methods will aid in plant systems biology modeling efforts by enhancing the understanding not only of cell wall biosynthesis but also of other plant developmental and physiological pathways.
Nanozeolite‐driven approach for enrichment of secretory proteins in human hepatocellular carcinoma cells
Authors: Cao Jing , Hu Yuanyuan , Shen Chengpin , Yao Jun , Wei Liming , Yang Fengying , Nie Aiying , Wang Hong , Shen Huali , Liu Yinkun , Zhang Yahong , Tang Yi , Yang Pengyuan 
Published: September 2009

AbstractGiven the importance of secreted proteins as a source for early detection and diagnosis of disease, secreted proteins have been arousing considerable attention. However, the analysis of secreted proteins represents a challenge for current proteomic techniques. One of the difficulties in secretomic study is to concentrate proteins from large volume of growth media, particularly, the low abundant and low molecular weight proteins (molecular weight <30 kDa). Herein, we describe a novel strategy for harvesting secretory proteins. In this approach, proteins secreted from the human hepatocellular carcinoma cell line were enriched by zeolite LTL nanocrystals, followed by 1‐D SDS‐PAGE for protein fractionation and then by LC‐ESI‐MS/MS for protein identification. In total, 1474 unique proteins were confidently identified, including 505 low molecular weight proteins, and covered a broad range of pI and molecular weight. Furthermore, this study not only offered an efficient and powerful method for the enrichment of secretory proteins but also allowed in‐depth study of secretome of hepatocellular carcinoma cells. The reported work is expected to represent one of the most comprehensive secretomic analyses so far.
Proteolysis during long‐term glucose starvation in Staphylococcus aureus COL
Authors: Michalik Stephan , Liebeke Manuel , Zühlke Daniela , Lalk Michael , Bernhardt Jörg , Gerth Ulf , Hecker Michael 
Published: September 2009

AbstractA combination of pulse‐chase experiments and 2‐D PAGE revealed that protein degradation appears to play a crucial role for the cell physiology of Staphylococcus aureus COL during extended periods of glucose starvation. The synthesis rate of virtually all cytosolic and radioactively labeled proteins from growing cells seemed dramatically reduced in the first 3.5 h of glucose starvation. The stability of proteins synthesized in growing cells was monitored by a pulse‐chase approach on a proteome wide scale. Especially, enzymes involved in nucleic acid and amino acid biosyntheses, energy metabolism and biosynthesis of cofactors were found rather rapidly degraded within the onset of the stationary phase, whereas the majority of glycolytic and tricarboxylic acid cycle enzymes remained more stable. Furthermore, single enzymes of biosynthetic pathways were differentially degraded. A metabolite analysis revealed that glucose completely depleted from the medium in the transient phase, and amino acids such as alanine and glycine were taken up by the cells in the stationary phase. We suggest that vegetative proteins no longer required in non‐growing cells and thus no longer protected by integration into functional complexes were degraded. Proteolysis of putative non‐substrate‐bound or “unemployed” proteins appears to be a characteristic feature of S. aureus in order to access nutrients as an important survival strategy under starvation conditions.
Interaction networks: Lessons from large‐scale studies in yeast
Authors: Cagney Gerard 
Published: September 2009

AbstractSaccharomyces cerevisiae is the simplest eukaryotic model organism and has made countless contributions to cell biology. The ease with which it can be genetically manipulated has made it a favourite organism among technologists for developing methods for large‐scale analysis based on reverse genetics. Consequently, more genomewide datasets describing aspects of gene and protein biology are available for yeast than for any other organism. This has led to the pioneering of many computational analysis techniques using yeast data. Here, we make a brief survey of yeast physical and genetic interaction networks, highlighting major experimental and computational achievements first described in this organism.
Modification‐specific proteomics: Strategies for characterization of post‐translational modifications using enrichment techniques
Authors: Zhao Yingming , Jensen Ole N. 
Published: September 2009

AbstractMore than 300 different types of protein post‐translational modifications (PTMs) have been described, many of which are known to have pivotal roles in cellular physiology and disease. Nevertheless, only a handful of PTMs have been extensively investigated at the proteome level. Knowledge of protein substrates and their PTM sites is key to dissection of PTM‐mediated cellular processes. The past several years have seen a tremendous progress in developing MS‐based proteomics technologies for global PTM analysis, including numerous studies of yeast and other microbes. Modification‐specific enrichment techniques combined with advanced MS/MS methods and computational data analysis have revealed a surprisingly large extent of PTMs in proteins, including multi‐site, cooperative modifications in individual proteins. We review some of the current strategies employed for enrichment and detection of PTMs in modification‐specific proteomics.
Nucleophilic reactivity of thiolate, hydroxide, and phenolate ions toward a model O2‐arylated diazeniumdiolate prodrug in aqueous and cationic surfactant media
Authors: Ning Matthew S. , Price Stacy E. , Ta Jackie , Davies Keith M. 
Published: September 2009

AbstractThe kinetics of aromatic nucleophilic substitution of the nitric oxide‐generating diazeniumdiolate ion, DEA/NO, by thiols (L‐glutathione, L‐cysteine, DL‐homocysteine, 1‐propanethiol, 2‐mercaptoethanol, and sodium thioglycolate) from the prodrug, DNP‐DEA/NO, has been examined in aqueous solution and in solutions of cationic DOTAP vesicles. Second‐order rate constants in buffered aqueous solutions (kRS‐ = 3.48–30.9 M−1 s−1; 30 °C) gave a linear Brønsted plot (βnuc = 0.414 ± 0.068) consistent with the rate‐limiting SNAr nucleophilic attack by thiolate ions. Cationic DOTAP vesicles catalyze the thiolysis reactions with rate enhancements between 11 and 486‐fold in Tris‐HCl buffered solutions at pH 7.4. The maximum rate increase was obtained with thioglycolate ion. Thiolysis data are compared to data for nucleophilic displacement by phenolate (kPhO‐ = 0.114 M−1 s−1) and hydroxide (kOH‐ = 1.82 × 10−2 M−1 s−1, 37 °C) ions. The base hydrolysis reaction is accelerated by CTAB micelles and DODAC vesicles, with the vesicles being ca 3‐fold more effective as catalysts. Analysis of the data using pseudo‐phase ion‐exchange (PIE) formalism implies that the rate enhancement of the thiolysis and base hydrolysis reactions is primarily due to reactant concentration in the surfactant pseudo‐phase. Copyright © 2009 John Wiley & Sons, Ltd.
Covalently Bound Biomimetic Layers on Plasma Polymers with Graded Metallic Interfaces for in vivo Implants
Authors: Yin Yongbai , Fisher Keith , Nosworthy Neil J. , Bax Daniel , Rubanov Sergey , Gong Bill , Weiss Anthony S. , McKenzie David R. , Bilek Marcela M. M. 
Published: September 2009

AbstractSurfaces capable of covalently immobilizing a dense layer of bioactive protein may be used to stimulate desired cellular responses at the surface of an implant. Pulse biased plasma polymerization onto metallic substrates is studied with the aim of producing surfaces suitable for such biomimetic in vivo implants. Plasma polymers were formed that are graded from stainless steel to a pure plasma polymer to provide the exceptionally strong adhesion necessary for in vivo applications, such as in cardiovascular stents. We show that the use of pulsed bias during deposition enhances the density of free radicals and improves the covalent protein binding capacity of the surface, indicating that the free radicals are responsible for the direct covalent attachment of protein observed after incubation in protein‐containing buffer solution. The radical density and degree of covalent binding was found to increase with the magnitude of the pulsing voltage. Aging in air reduced the radical density in the plasma polymer surfaces for all deposition conditions examined but substantially more radicals remained for the surfaces deposited with pulsed bias. Annealing in vacuum recovered the density of the radicals in the polymers subjected to pulsed bias while those prepared without pulsed bias showed a reduction in radical density upon annealing. The degree of covalent attachment increased linearly with the thickness of the polymer layer and showed a saturation at a thickness at which the total number of free radicals was equal to the number required to bind a full monolayer of the protein.magnified image
Development of DBD‐Plasmas Across Fibre Rovings
Authors: Ermel Vladimir , Kurrat Michael 
Published: September 2009

AbstractDevelopment of dielectric barrier discharge (DBD) plasmas across a 3D‐microporous medium as a glass fibre fabric is introduced in this paper. The barrier plasma is produced on the high field blade‐to‐plate arrangement with the lateral air flow at atmospheric pressure as a background gas. A uniformly distributed production of discharges over the substrate surface is obtained by the generation of a high inhomogeneous field along the blade electrode. The redistribution of the field due to insertion of the microporous medium in the plasma region is also investigated. The simulation results showed that the microdischarge develops in cavity of the roving as a streamer. Electron density decays due to the rising impact on the wall of orifice. The field shift in the neighbour cells causes avalanche‐like plasma ignition through the roving during the DBD development.
Fabrication of Tunable Band Pass Filters for CWDM Applications
Authors: Meister Stefan , Franke Bülent A. , Scharfenorth Chris , Eichler Hans J. 
Published: September 2009

AbstractThe paper describes a method to fabricate tunable band pass filters. The thin film optical filters are based on a Fabry‐Perot structure with laterally varying layer thickness. This leads to a variation of the transmission band along the substrate. The filter can be tuned by lateral translation of the filters through an optical beam path. A linear variation of the layer thickness and, therefore, of the transmission band along a 75 mm long substrate could be achieved by choosing proper geometries in the coating chamber. Filters are designed for a centre wavelength of 1300 nm with a −3 dB transmission bandwidth of 2.0 nm. A tuning range of more than 150 nm could be achieved with constant filter losses of ≈0.9 dB. So, the filters are well suited for side band suppression in CWDM applications.
Thermal Stability of TaN‐Based Thin Layers for Cu Metallization
Authors: Nazon Julien , Berger Marie‐Hélène , Sarradin Joël , Tedenac Jean‐Claude , Fréty Nicole 
Published: September 2009

AbstractThe diffusion of Cu through TaN‐based thin layers into a Si substrate has been studied. The barrier efficiency of TaN/Ta/TaN multilayer barrier of 50 nm:50 nm:50 nm in thickness has been investigated and is compared with that of TaN single layers. Thermal stabilities of these TaN‐based thin layers were determined from glancing incidence angle X‐ray diffraction and transmission electron microscopy, conducted in the temperature range of 773–973 K. The TaN/Ta/TaN barrier appeared to be more efficient than the TaN single layer in preventing Cu diffusion.
Ellipsometric study of electronic excitations in triglycine sulphate and triglycine selenate crystals
Authors: Andriyevsky Bohdan , Patryn Aleksy , Cobet Christoph , Mytsyk Bogdan , Esser Norbert 
Published: September 2009

AbstractThe real and imaginary parts of the pseudo‐dielectric susceptibility, 〈χ1〉(E) and 〈χ2〉(E), of triglycine sulphate (TGS) and triglycine selenate (TGSe) ferroelectric crystals have been obtained in the range 4–9.8 eV by spectroscopic ellipsometry using the Berlin Electron Storage Ring for synchrotron radiation source. A first maximum in 〈χ2〉(E) was found at E = 7.3 eV for both crystals and is attributed to the excitation of p‐electrons of oxygen. The spectra were measured at different temperatures in the range comprising the ferroelectric phase transition temperatures, 49 °C (TGS) and 22 °C (TGSe). Of note is the peak‐like behaviour in 〈χ1〉(T) and 〈χ2〉(T) near the phase transition temperature and a considerable decrease (about 50%) of the reflected light intensity IR in the range below the phase transition temperature (T < TC). The latter is probably caused by light scattering on the ferroelectric domain walls.
Positron preferential annihilation in Bi–Sb alloys
Authors: Dryzek Jerzy 
Published: September 2009

AbstractWe report the measurements of the positron annihilation characteristics, i.e., positron lifetime and coincidence Doppler broadening spectra performed on five Bi–Sb alloys having a Bi content between 12.5 and 81 at.%. The strong effect of the preferential annihilation of positrons with the electrons of the Bi atoms has been revealed in these alloys.
Enhancement of ferroelectricity in nanocones
Authors: Bykov Pavel I. , Suchaneck Gunnar , Jastrabik Lubomir , Gerlach Gerald 
Published: September 2009

AbstractIn this work, for the very first time a calculation of the ferroelectric size effect of cone‐shaped nanoparticles (nanocones) was performed. To solve the appropriate Euler–Lagrange equations, a direct variational method was used. An approximate analytical expression for the phase transition temperature dependence on the nanocone volume was derived. We have shown that the transition temperature might be higher by up to a factor of 2.5 compared to bulk materials.
2D and 3D‐QSPR Models for the Fluorophilicity of Organic Compounds in Consideration of Chirality
Authors: Hu Gui‐Xiang , Zou Jian‐Wei , Zeng Min , Pan Shan‐Fei , Yu Qing‐Sen 
Published: September 2009

AbstractFluorous biphase system (FBS) exhibits significant prospect in synthesis and catalysis fields. With the development of FBS, the design and prediction on the fluorophilicity of compounds show major importance. QSPR models are established by using three‐dimensional structural descriptors derived from VolSurf program and two‐dimensional topological descriptors derived from Tsar program. Good results are received and the training set model has satisfactory predictive capability for the test set. MLR method is applicative for Tsar descriptors and the equation shows that more number of F atoms in the compound will result in higher fluorophilicity. PLS analysis is suitable for VolSurf descriptors. Analysis on VolSurf descriptors demonstrates that large hydrophilic regions at medium energy level are beneficial to the fluorophilicity. The capacity factor is negative correlation with the fluorophilicity, so do the best local interaction energy minimum and its distance. High hydrophobic descriptor values and large hydrogen bond acceptor regions at medium energy levels are favorable elements. High anionic regions, low POL value and high MW are advantageous to the fluorophilicity. 3D‐VolSurf descriptors (R2=0.976, Q2=0.966) are more satisfying and suitable to build the QSPR model for the fluorophilicity than other descriptors. In addition, chirality has different extent influence on the calculated result for the different chiral molecules or with the different modeling methods. Using single configuration to compute for chiral molecules will be hopeful to bring about more accurate and credible result.