bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ground‐ and excited‐state properties of DNA base molecules from plane‐wave calculations using ultrasoft pseudopotentials
Authors: Preuss M. , Schmidt W. G. , Seino K. , Furthmüller J. , Bechstedt F. 
Published: June 2004

AbstractWe present equilibrium geometries, vibrational modes, dipole moments, ionization energies, electron affinities, and optical absorption spectra of the DNA base molecules adenine, thymine, guanine, and cytosine calculated from first principles. The comparison of our results with experimental data and results obtained by using quantum chemistry methods show that in specific cases gradient‐corrected density‐functional theory (DFT‐GGA) calculations using ultrasoft pseudopotentials and a plane‐wave basis may be a numerically efficient and accurate alternative to methods employing localized orbitals for the expansion of the electron wave functions. © 2003 Wiley Periodicals, Inc. J Comput Chem 1: 112–122, 2004
A comparative molecular field analysis (CoMFA) study using semiempirical, density functional, ab initio methods and pharmacophore derivation using DISCOtech on sigma 1 ligands
Authors: Jung Dawoon , Floyd Jie , Gund Tamara M. 
Published: June 2004

AbstractThe Comparative Molecular Field Analysis (CoMFA) was developed to investigate a three‐dimensional quantitative structure activity relationship (3D‐QSAR) model of ligands for the sigma 1 receptor. The starting geometry of sigma‐1 receptor ligands was obtained from the Tripos force field minimizations and conformations were decided from DISCOtech using the SYBYL 6.8. program. The structures of 48 molecules were fully optimized at the ab initio HF/3‐21G* and semiempirical AM1 calculations using GAUSSIAN 98. The electrostatic charges were calculated using several methods such as semiempirical AM1, density functional B3LYP/3‐21G*, and ab initio HF/3‐21G*, MP2/3‐21G* calculations within GAUSSIAN 98. Using the optimized geometries, the CoMFA results derived from the HF/3‐21G method were better than those from AM1. The best CoMFA was obtained from HF/3‐21G* optimized geometry and charges (R2 = 0.977). Using the optimized geometries, the CoMFA results derived from the HF/3‐21G methods were better than those from AM1 calculations. The training set of 43 molecules gave higher R2 (0.989–0.977) from HF/3‐21G* optimized geometries than R2 (0.966–0.911) values from AM1 optimized geometries. The test set of five molecules also suggested that HF/3‐21G* optimized geometries produced good CoMFA models to predict bioactivity of sigma 1 receptor ligands but AM1 optimized geometries failed to predict reasonable bioactivity of sigma 1 receptor ligands using different calculations for atomic charges. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1385–1399, 2004
An evaluation of the radial part of numerical integration commonly used in DFT
Authors: El‐Sherbiny Aisha , Poirier Raymond A. 
Published: June 2004

AbstractRecently, Gill and Chien introduced a new radial quadrature for multiexponential integrands (MultiExp grid) to deal with the radial part of the numerical integration. In this article, the MultiExp grid is studied and used to integrate the charge density. The MultiExp grid, along with an optimal pruning scheme, performed very well both in terms of accuracy and efficiency compared to other radial mappings commonly used in Density Functional Theory. © 2004 Wiley Periodicals, Inc. J Comput Chem 11: 1378–1384, 2004
Wavelet algorithm for solving integral equations of molecular liquids. A test for the reference interaction site model
Authors: Chuev Gennady N. , Fedorov Maxim V. 
Published: June 2004

AbstractA new efficient method is developed for solving integral equations based on the reference interaction site model (RISM) of molecular liquids. The method proposes the expansion of site–site correlation functions into the wavelet series and further calculations of the approximating coefficients. To solve the integral equations we have applied the hybrid scheme in which the coarse part of the solution is calculated by wavelets with the use of the Newton–Raphson procedure, while the fine part is evaluated by the direct iterations. The Coifman 2 basis set is employed for the wavelet treatment of the coarse solution. This wavelet basis set provides compact and accurate approximation of site–site correlation functions so that the number of basis functions and the amplitude of the fine part of solution decrease sufficiently with respect to those obtained by the conventional scheme. The efficiency of the method is tested by calculations of SPC/E model of water. The results indicated that the total CPU time to obtain solution by the proposed procedure reduces to 20% of that required for the conventional hybrid method. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1369–1377, 2004
Co‐operation of Gsα and Gβγ in maintaining G2 arrest in xenopus oocytes
Authors: Sheng Yinglun , Montplaisir Véronique , Johné Liu X. 
Published: June 2004

AbstractProgesterone‐induced oocyte maturation is thought to involve the inhibition of an oocyte adenylyl cyclase and reduction of intracellular cAMP. Our previous studies demonstrated that injection of inhibitors of G protein βγ complex induces hormone‐independent oocyte maturation. In contrast, over‐expression of Xenopus Gβ1 (xGβ1), alone or together with bovine Gγ2, elevates oocyte cAMP and inhibits progesterone‐induced oocyte maturation. To further investigate the mechanism of Gβγ‐induced oocyte maturation, we generated a mutant xGβ1, substituting Asp‐228 for Gly (D228G). An equivalent mutation in the mammalian Gβ1 results in the loss of its ability to activate adenylyl cyclases. Indeed, co‐injection of xGβ1D228G with Gγ2 failed to increase oocyte cAMP or inhibit progesterone‐induced oocyte maturation. To directly demonstrate that oocytes contained a Gβγ‐regulated adenylyl cyclase, we analyzed cAMP formation in vitro by using oocyte membrane preparations. Purified brain Gβγ complexes significantly activated membrane‐bound adenylyl cyclase activities. Multiple adenylyl cyclase isoforms were identified in frog oocytes by PCR using degenerate primers corresponding to highly conserved catalytic amino acid sequences. Among these we identified a partial Xenopus adenylyl cyclase 7 (xAC7) that was 65% identical in amino acid sequence to human AC7. A dominant‐negative mutant of xAC7 induced hormone‐independent oocyte maturation and accelerated progesterone‐induced oocyte maturation. Theses findings suggest that xAC7 is a major component of the G2 arrest mechanism in Xenopus oocytes. © 2005 Wiley‐Liss, Inc.
Multiple signaling conduits regulate global differentiation‐specific gene expression in PC12 cells
Authors: Marek Lindsay , Levresse Valerie , Amura Claudia , Zentrich Eve , Putten Vicki Van , Nemenoff Raphael A. , Heasley Lynn E. 
Published: June 2004

AbstractPC12 cells serve as a model for exploring nerve growth factor (NGF)‐stimulated signal pathways that mediate neural differentiation. We previously demonstrated that neurofilament light chain (NFLC) gene induction by NGF requires collaborative extracellular signal‐regulated kinase (ERK) and c‐Jun N‐terminal kinase (JNK) signaling. Herein, we investigate the broader requirement for integrated ERK and JNK signaling in NGF‐stimulated gene expression. NGF stimulates differentiation as well as maintenance of cell viability while insulin‐like growth factor‐1 (IGF‐1) stimulates only trophic actions in PC12 cells. Affymetrix Genechips were used to identify genes whose expression specifically increased in response to NGF, but not IGF‐1. From the set of NGF‐specific genes, the induction by NGF of ten genes with diverse predicted cellular functions was tested for ERK and JNK pathway requirements using the protein kinase inhibitors, PD98059 and SP600125, respectively. Like NFLC, induction of urokinase plasminogen activator (uPAR), transin/matrix metalloproteinase 3 (MMP3), Fra‐1 and transforming growth factor β1 (TGFβ1) required collaborative ERK and JNK signaling while the increased expression of cortexin, rat collapsin response mediator protein 4 (rCRMP4), rat growth and transformation‐dependent protein (RGT), and synapsin II required neither mitogen‐activated protein kinase (MAPK) pathway. NGF‐induction of the bradykinin B2 receptor and c‐Ret mRNAs was partially inhibited by SP600125, but not PD98059. Reporter constructs containing the promoters for ERK/JNK‐dependent genes (NFLC, transin, uPAR) as well as an ERK/JNK‐independent gene (synapsin II) revealed that both sets of genes required functional Ras signaling for activation by NGF. Integrated signaling through the ERK and JNK MAPKs, therefore, represents a general conduit for NGF‐dependent gene expression, but additional Ras‐dependent signaling pathways distinct from the ERKs and JNKs must contribute as well. Thus, multiple signaling conduits control global differentiation‐specific gene expression in PC12 cells. © 2004 Wiley‐Liss, Inc.
FGF6 mediated expansion of a resident subset of cells with SP phenotype in the C2C12 myogenic line
Authors: Israeli David , Benchaouir Rachid , Ziaei Simindokht , Rameau Philippe , Gruszczynski Carole , Peltekian Elise , Danos Olivier , Garcia Luis 
Published: June 2004

AbstractFibroblast growth factor 6 (FGF6) is selectively expressed during muscle development and regeneration. We examined its effect on muscle precursor cells (mpc) by forcing stable FGF6 expression in C2C12 cells in vitro. FGF6 produced in genetically engineered mpc was active, inducing strong morphological changes, altering cell adhesion and compromising their ability to differentiate into myotubes. Expression of MyoD and myogenin, but not of Myf5, was abrogated in FGF6 engineered mpc. These effects were reversed by FGF inhibitors. Ectopic expression of MyoD also restored fiber formation indicating that FGF6 interferes with the myogenic differentiation pathway upstream of MyoD. We also report that in the presence of FGF6, the minor (0.5–2%) subpopulation of cells actively excluding Hoechst 33342 in a verapamil‐dependent manner (SP phenotype) was increased to 15–20% and the expression of the mdr1a gene (but not mdr1b) was upregulated by 400‐fold. Our data establish a previously undescribed link between FGF6—a muscle specific growth factor—and a multidrug resistance gene expressed in stem cells, and suggest a role for FGF6 in the maintenance of a reserve pool of progenitor cells in the skeletal muscle. © 2004 Wiley‐Liss, Inc.
Regulation of inward rectifier K+ channels by shift of intracellular pH dependence
Authors: Collins Anthony , Larson Maureen 
Published: June 2004

AbstractThe mechanistic link between mitochondrial metabolism and inward rectifier K+ channel activity was investigated by studying the effects of a mitochondrial inhibitor, carbonyl cyanide p‐trifluoromethoxyphenylhydrazone (FCCP) on inward rectifiers of the Kir2 subfamily expressed in Xenopus oocytes, using two‐electrode voltage‐clamp, patch‐clamp, and intracellular pH recording. FCCP inhibited Kir2.2 and Kir2.3 currents and decreased intracellular pH, but the pH change was too small to account for the inhibitory effect by itself. However, pre‐incubation of oocytes with imidazole prevented both the pH decrease and the inhibition of Kir2.2 and Kir2.3 currents by FCCP. The pH dependence of Kir2.2 was shifted to higher pH in membrane patches from FCCP‐treated oocytes compared to control oocytes. Therefore, the inhibition of Kir2.2 by FCCP may involve a combination of intracellular acidification and a shift in the intracellular pH dependence of these channels. To investigate the sensitivity of heteromeric channels to FCCP, we studied its effect on currents expressed by heteromeric tandem dimer constructs. While Kir2.1 homomeric channels were insensitive to FCCP, both Kir2.1‐Kir2.2 and Kir2.1‐Kir2.3 heterotetrameric channels were inhibited. These data support the notion that mitochondrial dysfunction causes inhibition of heteromeric inward rectifier K+ channels. The reduction of inward rectifier K+ channel activity observed in heart failure and ischemia may result from the mitochondrial dysfunction that occurs in these conditions. © 2005 Wiley‐Liss, Inc.
FGF2‐mediated upregulation of urokinase‐type plasminogen activator expression requires a MAP‐kinase dependent activation of poly(ADP‐ribose) polymerase
Authors: Caldini Riccardo , Barletta Emanuela , Del Rosso Mario , Giovannelli Lisa , Chevanne Marta 
Published: June 2004

AbstractPoly(ADP‐ribosyl)ation is a post‐translational modification of protein occurring in the nucleus by poly(ADP‐ribose) polymerase enzyme activity. The main role of poly(ADP‐ribose) polymerase system as “nick sensor” and DNA breaks repair is based on its activation via DNA strand breaks. Furthermore, poly(ADP‐ribose) polymerase modifies the binding to DNA of several transcriptional factors by poly(ADP‐ribosyl)ation, thereby regulating also transcriptional gene expression. We have analyzed whether poly(ADP‐ribose) polymerase activity is involved in basic fibroblast growth factor (FGF2)‐mediated upregulation of urokinase‐type plasminogen activator (uPA) mRNA. We demonstrated that specific inhibition of poly(ADP‐ribose) polymerase activity via 3‐aminobenzamide (3ABA) or NAD+ deprivation prevents FGF2‐mediated uPA mRNA over‐expression and cell‐associated plasminogen activator (PA) production in GM7373 endothelial cell line. We verified that FGF2 stimulates poly(ADP‐ribose) polymerase activity by a DNA strand breaks‐independent manner which involves a mitogen‐activated protein kinases (MAPK)‐dependent pathway, as confirmed by using PD98059 inhibitor and anisomycin stimulation. Poly(ADP‐ribose) polymerase involved in this mechanism is mainly the 60 kDa molecular mass isoform, that presents an increase in serine phosphorylation in the presence of FGF2. © 2005 Wiley‐Liss, Inc.
Interleukin 11 signaling in 3T3‐L1 adipocytes
Authors: Tenney Raleigh , Stansfield Karrie , Pekala Phillip H. 
Published: June 2004

AbstractInterleukin 11 (IL‐11) is an anti‐inflammatory cytokine with receptors located on most cell types and tissues throughout the body. Its anti‐inflammatory properties are mediated through suppression of cytokine synthesis, in large part by prevention of NF‐κB activation. As adipose tissue synthesizes and secretes cytokines involved in establishing insulin resistance and due to the ability of IL‐11 to suppress cytokine synthesis, we initiated an investigation to determine the signal transduction pathways initiated by IL‐11 in adipose tissue. Using the 3T3‐L1 adipocyte cell culture model we demonstrate the rapid activation of the p44/42MAP kinase, PI3‐kinase, and STATs 1 and 3. Activation of MAP kinase is demonstrated to lead to the downstream activation of p90 RSK (ribosomal S6 kinase) as well as ATF‐1 and CREB. PI3‐kinase appears to activate the downstream target of p70 S6 kinase resulting in phosphorylation of ribosomal protein S6. STAT phosphorylation appears to be initiated through PI3‐kinase and to a lesser degree through p44/42 MAP kinase. These studies demonstrate the activation of three major signaling pathways and support a role for IL‐11 in the regulation of both transcription and protein synthesis in fully differentiated adipocytes. © 2005 Wiley‐Liss, Inc.
A Gβγ stimulated adenylyl cyclase is involved in xenopus laevis oocyte maturation
Authors: Guzmán Leonardo , Romo Ximena , Grandy Rodrigo , Soto Ximena , Montecino Martín , Hinrichs Maríavictoria , Olate Juan 
Published: June 2004

AbstractXenopus laevis oocyte maturation is induced by the steroid hormone progesterone through a nongenomic mechanism that implicates the inhibition of the effector system adenylyl cyclase (AC). Recently, it has been shown that the G protein βγ heterodimer is involved in oocyte maturation arrest. Since AC is the proposed target for Gβγ action, we considered of importance to identify and characterize the Gβγ regulated AC isoform(s) that are expressed in the Xenopus oocyte. Through biochemical studies, we found that stage VI plasma membrane oocyte AC activity showed attributes of an AC2 isoform. Furthermore, exogenous Gβγ was capable to activate oocyte AC only in the presence of the activated form of Gαs (Gαs‐GTPγS), which is in agreement with the Gγβ conditional activation reported for the mammalian AC2 and AC4 isotypes. In order to study the functional role of AC in oocyte maturation we cloned from a Xenopus oocyte cDNA library a gene encoding an AC with high identity to AC7 (xAC7). Based on this sequence, we constructed a minigene encoding the AC‐Gβγ interacting region (xAC7pep) to block, within the oocyte, this interaction. We found that microinjection of the xAC7pep potentiated progesterone‐induced maturation, as did the AC2 minigene. From these results we can conclude that a Gβγ‐activated AC is playing an important role in Xenopus oocyte meiotic arrest in a Gαs‐GTP dependent manner. © 2005 Wiley‐Liss, Inc.
Survival Capacity of Haploid‐Diploid Goldfish Chimeras
Authors: Tanaka Minoru , Yamaha Etsuro , Arai Katsutoshi 
Published: June 2004

AbstractIn teleosts, haploidy has been considered to be inviable due to the expression of abnormalities during embryogenesis, but the recent report of live haploid‐diploid mosaic fish suggests the probable improvement of survival capacity by adding diploid cells or tissues to haploid embryos. In order to examine such possibilities, two types of haploid‐diploid goldfish chimeric embryos were produced by transplantation of blastoderm between the normally fertilized diploid and the artificially induced gynogenetic haploid: the haploid‐base chimera with the diploid upper half on the haploid lower half blastoderm and the diploid‐base chimera with the haploid upper half on the diploid lower half blastoderm. Fluorescent detection of FITC‐labeled cells, subsequent histochemical detection of biotin‐labeled haploid cells and flow‐cytometrical detection of both haploid and diploid cells proved successful induction of the haploid‐diploid chimera. Both types of chimeric embryos demonstrated much better survival capacity than pure haploid individuals, but all the haploid‐base chimeras died before 10 days after fertilization due to the expression of edema, whereas several diploid‐base chimeras survived until 16 months after fertilization when the experiment was ended. This concluded diploid‐base chimeras became viable by adding diploid cells to haploid embryos. However, the proportion of transplanted haploid cells was reduced and the distribution of these cells was limited to certain organs because survivors exhibited haploid cells only in brain, eye and/or skin. These results suggest possible elimination of haploid cells from the organs originated from ectoderm. J. Exp. Zool. 301A:491–501, 2004. © 2004 Wiley‐Liss, Inc.
Clonal diploid sperm of the diploid‐triploid mosaic loach, Misgurnus anguillicaudatus (Teleostei:Cobitidae)
Authors: Morishima Kagayaki , Oshima Kouzou , Horie Shin , Fujimoto Takafumi , Yamaha Etsuro , Arai Katsutoshi 
Published: June 2004

AbstractThe loach Misgurnus anguillicaudatus comprises diploid, triploid and diploid‐triploid mosaic individuals in a wild population of the Hokkaido island, Japan. Previous studies revealed the presence of a cryptic clonal lineage among diploid loaches, which is maintained by uniparental reproduction of genetically identical diploid eggs. In the present study, we analyzed distribution and genetic status of diploid and triploid cells in infrequent mosaic males. Flow cytometry, microsatellite genotyping and DNA fingerprinting verified that mosaic males consisted of diploid cells with genotypes identical to the natural clone and triploid cells with diploid genomes of the clonal lineage plus haploid genome from sperm nucleus of the father. Thus, the occurrence of diploid‐triploid mosaicism might be caused by accidental fertilization of a diploid blastomere nucleus with haploid sperm after the initiation of clonal development of unreduced eggs. Such mosaic males produced fertile sperm with diploid DNA content. The experimental cross between normal diploid female and diploid‐triploid mosaic male gave rise to the appearance of triploid progeny which exhibited two microsatellite alleles identical to the clonal genotype and one allele derived from the normal female. In DNA fingerprinting, such triploid progeny gave not only all the DNA fragments from the clone, but also other fragments from the normal female. Induced androgenesis using UV irradiated eggs and sperm of the mosaic male gave rise to the occurrence of diploid individuals with paternally derived microsatellite genotypes and DNA fingerprints, absolutely identical to the natural clonal lineage. These results conclude that the diploid‐triploid mosaic male produced unreduced diploid sperm with genetically identical genotypes. The spermatogenesis in the clonal diploid cells under the mosaic condition suggests that triploid male somatic cells might transform genetically all‐female germ cells to differentiate into functionally male gametes. The discovery of the mosaic male producing unreduced sperm suggests the theoretical occurrence of triploids and other polyploids by the syngamy of such paternally derived diploid gametes. J. Exp. Zool. 301A:502–511, 2004. © 2004 Wiley‐Liss, Inc.
Molecular cloning of a putative membrane form guanylyl cyclase from the crayfish Procambarus clarkii
Authors: Liu Hui‐Fen , Lai Chi‐Yung , Watson R. Douglas , Lee Chi‐Ying 
Published: June 2004

AbstractAvailable data indicate that crustacean hyperglycemic hormone (CHH) stimulates membrane‐bound guanylyl cyclase (GC), producing cyclic guanosine 3′,5′–monophosphate, which in turn mediates the effect of CHH on carbohydrate metabolism. In the present study, we report the cloning of a cDNA (PcGC‐M2) encoding a putative membrane form GC from the muscle of the crayfish, Procambarus clarkii. Analysis of the deduced amino acid sequence shows that PcGC‐M2 contains the signature domains characteristic of membrane form GCs, including an extracellular ligand‐binding domain, a single transmembrane, and intracellular kinase‐like and cyclase catalytic domains. In addition, a C‐terminal domain of 247 residues is present following the cyclase catalytic domain. PcGC‐M2 is most closely related (33% identity) to a Drosophila membrane form GC (DrGC–1), and an Anopheles gambiae membrane form GC (AgaGC); the three GCs also share a similar distribution pattern of conserved cysteine residues in the extracellular domain. The PcGC‐M2 transcript is expressed in several CHH target tissues, including muscle, hepatopancreas, heart, ovary, testis, and gill, suggesting that PcGC‐M2 may participate in the signaling cascade activated by CHH. J. Exp. Zool. 301A:512–520, 2004. © 2004 Wiley‐Liss, Inc.
Progesterone determination in Iberian red deer by time‐resolved fluorometry: An alternative method to RIA
Authors: Parra María Dolores , García Andrés José , Bernal Luis Jesús , Landete‐Castillejos Tomás , Cerón José Joaquín 
Published: June 2004

AbstractThe validation for Iberian red deer of a commercially available Time‐resolved fluoroimmunoassay (TR‐FIA) designed for analysis of progesterone in human beings was carried out. Intra‐assay coefficients of variation ranged from 3.6% to 7.4%, while inter‐assay coefficients of variation varied from 5.2% to 15.5%. Accuracy, evaluated by comparing results yielded by TR‐FIA with those obtained from a validated radioimmunoassay (RIA) in the measurement of 14 samples, provided a high regression coefficient (R2= 0.93). Different progesterone concentrations added to pool plasma showed percentages of recovery that ranged between 102.6% and 82.48%. The limit of detection was 0.102 nmol/L. The results obtained indicate that the present method is suitable for the measurement of progesterone in female Iberian red deer. J. Exp. Zool. 301A:472–476, 2004. © 2004 Wiley‐Liss, Inc.