bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic analysis of Candida magnoliae strains by two‐dimensional gel electrophoresis and mass spectrometry
Authors: Lee Do‐Yup , Park Yong‐Cheol , Kim Hyo‐Jin , Ryu Yeon‐Woo , Seo Jin‐Ho 
Published: December 2003

AbstractCandida magnoliae which has been newly isolated from honey comb is an osmotolerant yeast to produce erythritol as a major product. Erythritol is a noncariogenic, low calorie sweetener and safe for diabetics. Strain development by chemical mutation to obtain the improved erythritol yield and productivity relative to the parental strain made it necessary to elucidate the physiological differences between the wild and mutant strains. Proteomic analyses of C. magnoliae wild and mutant strains with two‐dimensional gel electrophoresis and nanoelectrospray mass spectrometry were carried out to identify intracellular proteins and to estimate the effects of newly characterized metabolic enzymes on the yeast cell growth and erythritol production. Most of the molecular mass of intracellular proteins were distributed in the range of pI 4–8 and molecular mass of ∼ 130 kDa. Six out of nine protein spots expressed at different levels between the wild and mutant strains were analyzed with nanoelectrospray tandem mass spectrometry and identified by comparing amino acid sequences with the National Center for Biotechnology Information and Saccharomyces Genome Databases. Except for Ygr086cp, these proteins were believed to be the metabolic enzymes involved in the citric acid cycle (citrate synthase, succinyl‐CoA ligase and fumarase) and the glycolysis pathway (pyruvate decarboxylase and enolase). Up‐regulated enzymes in the citric acid cycle could explain high growth of the C. magnoliae mutant strain owing to the increased NADH and ATP formation. Down‐regulated enolase and up‐regulated fumarase in the mutant strain seemed to play a role in the improved bioconversion of erythrose‐4‐phosphate to erythritol compared with the wild strain.
Comparative analysis of nuclear proteins of B cells in different developmental stages
Authors: Jin Sun Hee , Cho Eun Hye , Ko Jung Eun , Jung Eun Hee , Ahn Byungchan , Hahm Jong Ryeal , Kim Jae Won , Kim Choong Won , Kim Deok Ryong 
Published: December 2003

AbstractThe developmental stage‐specific regulation of V(D)J recombination, a gene rearrangement process of antigen receptor gene segments, is tightly controlled in cells. Here we screened proteins uniquely or differentially expressed among three developmentally distinguishable B cells (pro‐B, pre‐B and mature B cells) using two‐dimensional gel electrophoresis and mass spectrometry. Chromatin assembly factor 1 was uniquely expressed in pro‐B cells. Purine nucleotide phosphorylase, LCK, E2A and many other unidentified proteins were dominantly present in the nucleus at the early stage of B cell development where the V(D)J recombination process occurs. Also, few proteins including guanidine nucleotide binding proteins were exclusively expressed in pre‐B cell. Such findings can provide some information to help understand the developmental regulation of gene rearrangement occurring during B cell development.
Proteomic analysis of differentially expressed proteins induced by rice blast fungus and elicitor in suspension‐cultured rice cells
Authors: Kim Sun Tae , Cho Kyu Seong , Yu Seok , Kim Sang Gon , Hong Jong Chan , Han Chang‐deok , Bae Dong Won , Nam Myung Hee , Kang Kyu Young 
Published: December 2003

AbstractWe used two‐dimensional electrophoresis (2‐DE) and other proteomic approaches to identify proteins expressed in suspension‐cultured rice cells in response to the rice blast fungus, Magnaporthe grisea. Proteins were extracted from suspension‐cultured cells at 24 and 48 h after rice blast fungus inoculation or treatment with elicitor or other signal molecules such as jasmonic acid (JA), salicylic acid, and H2O2. The proteins were then polyethylene glycol fractionated before separation by 2‐DE. Fourteen protein spots were induced or increased by the treatments, which we analyzed by N‐terminal or internal amino acid sequencing. Twelve proteins from six different genes were identified. Rice pathogen‐related protein class 10 (OsPR‐10), isoflavone reductase like protein, β‐glucosidase, and putative receptor‐like protein kinase were among those induced by rice blast fungus; these have not previously been reported in suspension‐cultured rice cells. Six isoforms of probenazole‐inducible protein (PBZ1) and two isoforms of salt‐induced protein (SalT) that responded to blast fungus, elicitor, and JA were also resolved on a 2‐DE gel and identified by proteome analysis. The expression level of these induced proteins both in suspension‐cultured cells and in leaves of whole plants was analyzed by Western blot. PBZ1, OsPR‐10, and SalT proteins from incompatible reactions were induced earlier and to a greater extent than those in compatible reactions. Proteome analysis can thus distinguish differences in the timing and amount of protein expression induced by pathogens and other signal molecules in incompatible and compatible interactions.
A fluorescent natural product for ultra sensitive detection of proteins in one‐dimensional and two‐dimensional gel electrophoresis
Authors: Mackintosh James A. , Choi Hung‐Yoon , Bae Soo‐Han , Veal Duncan A. , Bell Philip J. , Ferrari Belinda C. , Van Dyk Derek D. , Verrills Nicole M. , Paik Young‐Ki , Karuso Peter 
Published: December 2003

AbstractLightning Fast is a sensitive fluorescence‐based stain for detecting proteins in one‐dimensional and two‐dimensional polyacrylamide electrophoresis gels. It contains the fluorophore epicocconone from the fungus Epicoccum nigrum that interacts noncovalently with sodium dodecyl sulfate and protein. Stained proteins can be excited optimally by near‐ultraviolet light of about 395 nm or with visible light of about 520 nm. The stain can be excited using a range of sources used in image analysis systems including UVA (ca. 365 nm) and UVB (ca. 302 nm) transilluminators; Xenon‐arc lamps; 488 nm and 457 nm Argon‐ion lasers; 473 nm and 532 nm neodymium: yttrium aluminum garnet (Nd:YAG) solid‐state lasers; 543 nm helium‐neon lasers, and emerging violet, blue and green diode lasers. Maximum fluorescence emission of the dye is at approximately 610 nm. The limit of detection in one‐dimensional gels stained with Lightning Fast protein gel stain is less than 100 pg of protein, rivaling the current limits of matrix‐assisted laser desorption/ionization‐mass spectrometry (MALDI‐MS). Lightning Fast was found to be considerably more sensitive than SYPRO Ruby, SYPRO Orange, silver and Coomassie Brilliant Blue G‐250 in matched experiments. Staining takes as little as 3.5 h and stained proteins displayed quantitative linearity over more than four orders of magnitude, thereby allowing visualization of entire proteomes. Lightning Fast protein gel staining is compatible with subsequent peptide mass fingerprinting using MALDI‐MS and Edman‐based sequencing chemistry.
Strategic shotgun proteomics approach for efficient construction of an expression map of targeted protein families in hepatoma cell lines
Authors: Lee Chih‐Lei , Hsiao He‐Hsuan , Lin Chia‐Wei , Wu Szu‐Pei , Huang Shiuan‐Yi , Wu Chi‐Yue , Wang Andrew H.‐J. , Khoo Kay‐Hooi 
Published: December 2003

AbstractAn expression map of the most abundant proteins in human hepatoma HepG2 cells was established by a combination of complementary shotgun proteomics approaches. Two‐dimensional liquid chromatography (LC)‐nano electrospray ionization (ESI) tandem mass spectrometry (MS/MS) as well as one‐dimensional LC‐matrix‐assisted laser desorption/ionization MS/MS were evaluated and shown that additional separation introduced at the peptide level was not as efficient as simple prefractionation of protein extracts in extending the range and total number of proteins identified. Direct LC‐nanoESI MS/MS analyses of peptides from total solubilized fraction and the excised gel bands from one‐dimensional sodium dodecyl sulfate‐polyacrylamide gel electrophoresis fractionated insolubilized fraction afforded the best combination in efficient construction of a nonredundant cell map. Compiling data from multiple variations of rapid shotgun proteomics analyses is nonetheless useful to increase sequence coverage and confidence of hits especially for those proteins identified primarily by a single or two peptide matches. While the returned hit score in general reflects the abundance of the respective proteins, it is not a reliable index for differential expression. Using another closely related hepatoma Hep3B as a comparative basis, 16 proteins with more than two‐fold difference in expression level as defined by spot intensity in two‐dimensional gel electrophoresis analysis were identified which notably include members of the heat shock protein (Hsp) and heterogeneous nuclear ribonucleoprotein (hnRPN) families. The observed higher expression level of hnRNP A2/B1 and Hsp90 in Hep3B led to a search for reported functional roles mediated in concert by both these multifunctional cellular chaperones. In agreement with the proposed model for telomerase and telomere bound proteins in promoting their interactions, data was obtained which demonstrated that the expression proteomics data could be correlated with longer telomeric length in tumorigenic Hep3B. This biological significance constitutes the basis for further delineation of the dynamic interactions and modifications of the two protein families and demonstrated how proteomic and biological investigation could be mutually substantiated in a productive cycle of hypothesis and pattern driven research.
Analysis of proteins expressed in rat plasma exposed to dioxin using 2‐dimensional gel electrophoresis
Authors: Son Won‐Kyu , Lee Do‐Youn , Lee Sung‐Han , Joo Won‐A. , Kim Chan‐Wha 
Published: December 2003

AbstractDioxins are a class of polyhalogenated aromatic hydrocarbons that induces a wide spectrum of toxic responses in animals. In this study, two groups of Sprague‐Dawley rats were exposed to 2,3,7,8‐tetrachlorobenzo‐p‐dioxin (TCDD); one group received short‐term exposure at a single dose of 1, 10, 20 or 50 μg/kg body weight and the other received long‐term exposure to a daily low dose of 0.01, 0.1, 1 or 2.5 μg/kg body weight for one month. Two‐dimensional electrophoresis was utilized to resolve the protein profile of rat plasma exposed to TCDD at different doses. One novel and three volume‐increased spots were identified and characterized by matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry and electrospray‐ionization on quadropole‐TOF2 mass spectrometry. The novel protein was identified as plasma glutathione peroxidase precursor and the volume‐increased proteins were cytokeratin 8 polypeptide, Ig lambda‐1 chain C region and Ig lambda‐2 chain C region. These proteins may be used as biomarkers to diagnose dioxin exposure and may help in understanding the toxic effects of dioxins.
Efficiency improvement of peptide identification for an organism without complete genome sequence, using expressed sequence tag database and tandem mass spectral data
Authors: Kwon Kyung‐Hoon , Kim Mioak , Kim Jin Young , Kim Kyung Wook , Kim Seung Il , Park Young Mok , Yoo Jong Shin 
Published: December 2003

AbstractWe compared peptide identification by database (DB) search methods with de novo sequencing results for proteomics study in an organism without genome sequence information. When the former was done by searching the Expressed Sequence Tag (EST) DB of the sample organism or the NCBI nonredundant (nr) protein DB of green plants using either the MASCOT or SEQUEST software program, it was confirmed that the former is as accurate as the latter. Peptides identified from EST DB were twice as many as those from the nr protein DB, in spite of the fact that the EST DB has less data (26 222 EST) than the NCBI nr protein DB (224 238). This study demonstrates that EST DB with tandem mass spectra can be used reliably for high‐throughput proteomics studies in an organism without genome information.
Proteomic profiling of heat shock protein 70 family members as biomarkers for hepatitis C virus‐related hepatocellular carcinoma
Authors: Takashima Motonari , Kuramitsu Yasuhiro , Yokoyama Yuuichiro , Iizuka Norio , Toda Toshifusa , Sakaida Isao , Okita Kiwamu , Oka Masaaki , Nakamura Kazuyuki 
Published: December 2003

AbstractTo identify proteins linked to the pathogenesis of hepatocellular carcinoma (HCC) associated with hepatitis C virus (HCV), we profiled protein expression levels in samples of HCC. To identify essential proteins, ten samples of HCV‐related HCC were analyzed by two‐dimensional gel electrophoresis and matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry. These experiments revealed increased levels of nine proteins in cancerous tissues compared to levels in corresponding noncancerous liver tissues. We focused on four members of the heat shock protein 70 family: 78 kDa glucose‐regulated protein (GRP78), heat shock cognate 71 kDa protein (HSC70), 75 kDa glucose‐regulated protein (GRP75), and heat shock 70 kDa protein 1 (HSP70.1). These results were confirmed by immunoblot analysis. In an additional 11 samples, the same expression patterns of these four proteins were observed. In total, 21 samples showed statistically significant up‐regulation of GRP78, GRP75 and HSP70.1 in cancerous tissues. HSC70 showed a tendency toward overexpression. There has been no report describing overexpression of these four proteins simultaneously in HBV‐related HCC as well as nonviral HCC. Our results suggest that these four proteins play important roles in the pathogenesis of HCV‐related HCC and could be molecular targets for diagnosis and treatment of this disease.
Proteomic and transcriptomic analysis of interleukin‐1ß treated lung carcinoma cell line
Authors: Kim Chang‐Hoon , Kim Do Kyun , Choi Seung Jin , Choi Kun Ho , Song Kyoung Seob , Chi Janghoon , Koo Ja Seok , Hwang Seung Yong , Yoon Joo‐Heon , Seong Je Kyung 
Published: December 2003

AbstractMucin hypersecretion is one of the main symptoms of inflammatory disease in the respiratory tract. We previously reported that the pleiotypic pro‐inflammatory cytokine, interleukin (IL)‐1β, plays a significant role in respiratory tract inflammation by inducing mucins. However, the molecular mechanism for mucin hypersecretion in the respiratory tract remains still unclear. In order to understand the mechanisms of mucin hypersecretion in the airway epithelium, the differentially expressed proteins and genes in the lung mucoepidermoid carcinoma cell line (NCI‐H292 cells), which were treated for 6 and 24 hours with IL‐1β (10 ng/mL) were identified using two‐dimensional polyacrylamide gel electrophoresis (2‐D PAGE) proteomics and cDNA microarray analysis (8.6K). In the 2‐D PAGE, eight differentially expressed proteins and 14 post‐translational modification proteins were identified at 6 and 24 hours after the IL‐1β‐treatment. Four hundred and thirteen genes (6.6%) and 115 genes (2.0%) were differentially expressed, respectively, at 6 and 24 hours after the IL‐1β‐treatment by microarray analysis. The differentially expressed genes and proteins that were regulated by the IL‐1β‐treatment were mostly in the metabolic pathway rather than in the regulatory pathway. These results clearly show that the transcript levels have little value in predicting the extent of protein expression.
Shape transition of medium‐sized neutral silicon clusters
Authors: Sieck A. , Frauenheim Th. , Jackson K. A. 
Published: December 2003

AbstractAddressing the shape transition of silicon clusters, indicated by mobility experiments on silicon cluster cations with 24 to 30 atoms, we investigate the structure of low energy neutral silicon clusters with 25, 29, and 35 atoms within a density‐functional based tight‐binding approach. Since there is strong evidence for several nearly degenerate low‐energy isomers for clusters of this size, we perform an extensive, but limited global search with Simulated Annealing and statistically analyze for each cluster size the 100 clusters with the lowest energy. We find different dominant shapes in the set of low energy clusters for each size. For neutral silicon clusters with 25 atoms, both prolate and spherical structures with low cohesive energies exist. For clusters containing 29 or 35 atoms, the low‐energy isomers exhibit a spherical shape. For each cluster size several stable isomers with similar shapes, and hence similar mobilities, but different bonding patterns exist. The most stable 25 atom cluster resulting from our global search has the lowest energy within DFT‐GGA known so far. Finally, we investigate the transition to diamond‐like bonding patterns expected for larger silicon clusters. Clusters with up to 239 atoms resemble amorphous silicon rather than the diamond structure and contain several highly coordinated atoms. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Metallic magnetoconductivity in copper gallium telluride
Authors: Essaleh L. , Galibert J. , Wasim S. M. , Marin G. 
Published: December 2003

AbstractLow‐temperature magnetoresistance measurements, in the metallic regime, on p‐type CuGaTe2 were performed. The magnetoresistance results were analyzed using localization and electron–electron theories taking into account the effect of strong spin–orbit coupling. The results were compared to those related to CuInSe2. Good agreement of the experimental data with theory was found over a wide range of magnetic fields up to 20 T. From the theoretical fit, both the inelastic and spin–orbit relaxation times were estimated. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Structural, thermodynamic and other associated properties of partially ordered Ag‐In alloy
Authors: Venkatesh R. , Mishra Raj Kumar , Gopala Rao R. V. 
Published: December 2003

AbstractExtensive computations have been performed using the Lebowitz solution of hard sphere mixtures as a reference system, and perturbed the hard sphere direct correlation function,COij(r), with square well attractive tail. We used mean spherical model to compute the total and partial direct correlation functions in the attractive and repulsive regions of the interacting potential of Ag–In alloy at different compositions. The potential parameters were those obtained for pure metals. With these potential parameters (the partial and total) structure factors were evaluated, and then Fourier transformed to get the partial and total radial distribution functions. Further the well‐known Bhatia–Thornton correlation functions namely the number‐number, concentration‐concentration, and number‐concentration correlation functions have been computed. We also obtained total and partial coordination numbers from partial and total pair correlation functions respectively. With the help of these pair correlation functions we give the distances between atoms namely Ag–Ag, In–In and Ag–In at different compositions of In in Ag–In alloy. It is found that these distances practically remain constant and are independent of composition, which has been attributed to the formation of segregated clusters of atomic dimensions. Using Kirkwood–Buff's equation, compressibillities have been calculated as a function of composition. The temperature derivative of diffusion coefficient for pure constituents has been formulated and the computed results were compared with the available experimental values. With this model the diffusion coefficients and the friction coefficients of the constituents have been obtained through the use of Helfand's trajectory principle with a reasonable success in the alloy as well. It is found that these metals of the alloy tend to segregate. The ratio of diffusion coefficients of the metals in the alloy is almost a constant and is equal to 0.9. This shows that the alloy forms a regular solution in spite of their tendency to segregate. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Many‐body and overlayer effects on surface optical properties
Authors: Bechstedt F. , Del Sole R. , Glutsch S. , Hahn P. H. , Pulci O. , Schmidt W. G. 
Published: December 2003

AbstractWe demonstrate the potential of recently developed total‐energy and electronic‐structure methods for the calculation of the optical properties of real surfaces. The many‐body effects are fully taken into account by a solution of the combined Dyson and Bethe‐Salpeter equations. We show that an initial‐value formulation of the polarization function allows an efficient numerical calculation of the optical susceptibility for large slabs consisting of many atoms. As examples we investigate GaP(001) and Si(001) surfaces covered by hydrogen. In the case of P‐rich GaP(001)2 × 2–H surfaces the low‐energy region of the reflectance anisotropy (RA) is dominated by electron–hole pair excitations in surface states. Surface‐induced modifications of bulk excitons near the E1 and E2 transitions are responsible for the RA of the monohydride Si(001)2 × 1–H surface. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The electronic Fermi surface e3 of aluminium under moderate compression
Authors: Bross Helmut 
Published: December 2003

AbstractBoth in LDA and in GGA the electronic structure of aluminium is evaluated by use of the MAPW selfconsistent scheme and with different exchange correlation functionals. Near and above the equilibrium lattice constant the electronic sheet of the Fermi surface, e3, is found to be quite similar to the model originally proposed by Ashcroft. However, even moderate compressions induce a drastic variation. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Combinatorial Oligocarbamate Collections: Synthesis by the Premix Method and Quality Control by HPLC‐MS
Authors: Warrass Ralf , Jung Günther , Wiesmüller Karl‐Heinz 
Published: December 2003

AbstractThe automated solid phase synthesis of 256 complex oligocarbamate collections by the premix method is described. The collections contain up to 1.9×106 compounds built up via synthons derived from 18 proteinogenic amino acids. The quality of the collections is investigated by comparing HPLC and electrospray ionization MS data of the products of the premix synthesis to those of a mixture of individually synthesized single compounds. The premix synthesis was found to yield compound mixtures in qualities sufficient for primary screening assays. For highly complex collections, where the determination of each single compound becomes impossible, the signal patterns of electrospray ionization mass spectrometry were compared to simulated mass distributions and good correlations between theoretical and measured data were observed. Therefore, highly diverse and complex oligocarbamate subcollections and individual compounds are conveniently accessible by optimized and reproducible protocols. The compounds are of particular value for lead finding due to their protease resistance and higher lipophilicity compared to peptides.
Prediction of Aqueous Solubility of Organic Compounds by Topological Descriptors
Authors: Yan Aixia , Gasteiger Johann 
Published: December 2003

AbstractTwo quantitative models for the prediction of aqueous solubility of 1293 organic compounds were generated by a Multilinear Regression (MLR) analysis, and a Backpropagation (BPG) neural network. The molecules were represented by 18 topological descriptors. The physicochemical relationship between solubility and the descriptors for different individual classes of monofunctional group compounds such as hydrocarbons, ethers, halocarbons, alcohols, aldehydes and ketones, acids, esters, and amines was investigated. The 1293 compounds were divided into a training set of 741 compounds and a test set of 552 compounds based on a Kohonen's self‐organizing neural network map. The models obtained show a good predictive power: for the test set, a correlation coefficient of 0.97 and a standard deviation of 0.52 were achieved by the backpropagation neural network approch.