bluuebunny/crossref_metadata_2025 huggingface dataset:
Ferric uptake regulator protein: Binding free energy calculations and per‐residue free energy decomposition
Authors: Ahmad Rafi , Brandsdal Bjørn Olav , Michaud‐Soret Isabelle , Willassen Nils‐Peder
Published: September 2008

Iron homeostasis is, in many bacterial species, mediated by the ferric uptake regulator (Fur). A regulatory site able to bind iron to activate Fur for DNA binding has been described, and a structural zinc site essential for the dimerization has also been proposed. They have been localized and named site 1 and site 2, respectively, from the crystal structure of a zinc‐substituted Pseudomonas aeruginosa Fur (PA‐Fur). Notwithstanding the studies on Fur proteins from various species, both the precise site of iron binding and the effect on DNA binding affinity are still controversial. These issues were investigated here by molecular dynamics simulations and free energy calculations. Simulations were performed for eight molecular systems represented by the three forms of Fur, that is, apo Fur, metal‐substituted Fur, and Fur complexed with DNA. Because of the lack of a Fur‐DNA complex crystal structure, the recently published model based on mass spectrometry experiments on Escherichia coli Fur (EC‐Fur), and the crystal structure of PA‐Fur, was used, after adjustment to adopt a symmetric conformation. The simulation results suggest that the formerly proposed site 2 is, in fact, the regulatory iron‐sensing site. The calculations also predict that Fe2+ at site 2 is hexacoordinated having an octahedral environment with only nitrogen and oxygen atoms, which is in accordance with previous spectroscopic characterizations. Energy decomposition pinpoints H87 as an additional amino acid that defines the regulatory metal site. Finally, free energy decomposition analysis reveals a number of amino acids potentially important in dimerization and in DNA binding. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Opening of the ADP‐bound active site in the ABC transporter ATPase dimer: Evidence for a constant contact, alternating sites model for the catalytic cycle
Authors: Jones Peter M. , George Anthony M.
Published: September 2008

ABC transporters are ubiquitous, ATP‐dependent transmembrane pumps. The mechanism by which ATP hydrolysis in the nucleotide‐binding domain (NBD) effects conformational changes in the transmembrane domain that lead to allocrite translocation remains largely unknown. A possible aspect of this mechanism was suggested by previous molecular dynamics simulations of the MJ0796 NBD dimer, which revealed a novel, nucleotide‐dependent intrasubunit conformational change involving the relative rotation of the helical and catalytic subdomains. Here, we find that in four of five simulations of the ADP/ATP‐bound dimer, the relative rotation of the helical and catalytic subdomains in the ADP‐bound monomer results in opening of the ADP‐bound active site, probably sufficient or close to sufficient to allow nucleotide exchange. We also observe that in all five simulations of the ADP/ATP‐bound dimer, the intimate contact of the LSGGQ signature sequence with the ATP γ‐phosphate is weakened by the intrasubunit conformational change within the ADP‐bound monomer. We discuss how these results support a constant contact model for the function of the NBD dimer in contrast to switch models, in which the NBDs are proposed to fully disassociate during the catalytic cycle. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Targeting the early steps of Aβ16–22 protofibril disassembly by N‐methylated inhibitors: A numerical study
Authors: Chebaro Yassmine , Derreumaux Philippe
Published: September 2008

Aggregation of the Aβ1–40/Aβ1–42 peptides is a key factor in Alzheimer's disease. Though the inhibitory effect of N‐methylated Aβ16–22 (mAβ16–22) peptides is well characterized in vitro, there is little information on how they disassemble full‐length Aβ fibrils or block fibril formation. Here, we report coarse‐grained implicit solvent molecular dynamics (MD) and replica exchange molecular dynamics (REMD) simulations on Aβ16–22 and mAβ16–22 monomers, and then a preformed six‐chain Aβ16–22 bilayer with either four copies of Aβ16–22 or four copies of mAβ16–22. Our simulations show that the effect of N‐methylation on mAβ16–22 monomer is to reduce the density of compact forms. While 100 ns MD trajectories do not reveal any significant differences between the two ten‐chain systems, the REMD simulations totaling 1 μs help understand the first steps of Aβ16–22 protofibril disassembly by N‐methylated inhibitors. Notably, we find that mAβ16–22 preferentially interacts with Aβ16–22 by blocking both β‐sheet extension and lateral association of layers, but also by intercalation of the inhibitors allowing sequestration of Aβ16–22 peptides. This third binding mode is particularly appealing for blocking Aβ fibrillogenesis. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Shape complementarity of protein–protein complexes at multiple resolutions
Authors: Zhang Qing , Sanner Michel , Olson Arthur J.
Published: September 2008

Biological complexes typically exhibit intermolecular interfaces of high shape complementarity. Many computational docking approaches use this surface complementarity as a guide in the search for predicting the structures of protein–protein complexes. Proteins often undergo conformational changes to create a highly complementary interface when associating. These conformational changes are a major cause of failure for automated docking procedures when predicting binding modes between proteins using their unbound conformations. Low resolution surfaces in which high frequency geometric details are omitted have been used to address this problem. These smoothed, or blurred, surfaces are expected to minimize the differences between free and bound structures, especially those that are due to side chain conformations or small backbone deviations. Despite the fact that this approach has been used in many docking protocols, there has yet to be a systematic study of the effects of such surface smoothing on the shape complementarity of the resulting interfaces. Here we investigate this question by computing shape complementarity of a set of 66 protein–protein complexes represented by multiresolution blurred surfaces. Complexed and unbound structures are available for these protein–protein complexes. They are a subset of complexes from a nonredundant docking benchmark selected for rigidity (i.e. the proteins undergo limited conformational changes between their bound and unbound states). In this work, we construct the surfaces by isocontouring a density map obtained by accumulating the densities of Gaussian functions placed at all atom centers of the molecule. The smoothness or resolution is specified by a Gaussian fall‐off coefficient, termed “blobbyness.” Shape complementarity is quantified using a histogram of the shortest distances between two proteins' surface mesh vertices for both the crystallographic complexes and the complexes built using the protein structures in their unbound conformation. The histograms calculated for the bound complex structures demonstrate that medium resolution smoothing (blobbyness = −0.9) can reproduce about 88% of the shape complementarity of atomic resolution surfaces. Complexes formed from the free component structures show a partial loss of shape complementarity (more overlaps and gaps) with the atomic resolution surfaces. For surfaces smoothed to low resolution (blobbyness = −0.3), we find more consistency of shape complementarity between the complexed and free cases. To further reduce bad contacts without significantly impacting the good contacts we introduce another blurred surface, in which the Gaussian densities of flexible atoms are reduced. From these results we discuss the use of shape complementarity in protein–protein docking. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Nonrandom distribution of intramolecular contacts in native single‐domain proteins
Authors: Mounce Bryan C. , Kurt Neşe , Ellison Paul A. , Cavagnero Silvia
Published: September 2008

The interplay of short‐ and long‐range interactions in protein structure and folding is poorly understood. This study focuses on the distribution of intramolecular contacts across different regions of the polypeptide chain in soluble single‐domain proteins. We show that while the average number of intramolecular interactions per residue is similar across all regions of the sequence, the interaction counterparts are distributed nonrandomly. Two types of proteins are observed. The first class comprises structures that have the majority of their intramolecular contacts linking amino acids within the same region of the sequence (i.e., N‐/C‐terminal or intermediate portion of the chain). A second smaller class includes proteins that have extensive contacts between the N and C termini. Such extensive interactions involve primarily distal β‐strands and are detected via the NCR parameter, a descriptor of the number of contacts with interaction counterparts in specific regions of the sequence. In summary, the majority of single‐domain proteins (first class) is dominated by short‐range interactions between contiguous elements of secondary structure and has only sparse contacts among the N and C termini. This finding defies the common assumption that the chain termini, often spatially close in folded proteins, have to participate in a large number of mutual interactions. Finally, our results suggest that the C‐terminal region of Class 2 proteins may be particularly effective at promoting folding upon completion of protein biosynthesis in the cell. Proteins 2009. © 2008 Wiley‐Liss, Inc.
The major toxin from the Australian Common Brown Snake is a hexamer with unusual gas‐phase dissociation properties
Authors: Aquilina J. Andrew
Published: September 2008

Asymmetric dissociation of multiply charged protein assemblies has been frequently reported. This phenomenon, which relies on the dissociation of one or more highly charged monomers, has been shown to provide insights into the structure and organization of large monodisperse and polydisperse assemblies. Here, the process of asymmetric dissociation is investigated using the multisubunit protein, textilotoxin, which has unusually high structural constraints on its monomers due to multiple disulfide linkages. Initially, it is shown that, contrary to previous reports, textilotoxin is made up of six, rather than five subunits. Furthermore, the hexamer exists as two isoforms, one of which is substantially more glycosylated. Gas‐phase dissociation studies on the hexamers reveal the subunit stoichiometry of each isoform to be (A/B)2C2D2a and (A/B)CD2aD2b, where A and B are subunits of very similar mass and D2a, D2b refer to differentially glycosylated dimers of the D subunit. The mechanism of dissociation was unusual, as rather than one subunit being largely removed before sequential dissociation of a second, the process was predominantly concurrent for the two smallest subunits. Furthermore, a small proportion of the dissociated species was observed to be a noncovalently associated dimer. A comparison of dissociation pathways for two neighboring charge states of the same textilotoxin isoform demonstrates that, in agreement with previous reports, variations in quaternary structure are responsible for the distinct charge states of a protein. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Computational determination of effects of electric fields upon “trigger linkages” of prototypical energetic molecules
Authors: Politzer Peter , Murray Jane S. , Lane Pat
Published: September 2008

For five prototypical energetic molecules (nitrobenzene, methyl azide, methyl nitrate, nitromethane, and dimethylnitramine), we examine computationally the effects of external electric fields upon their “trigger linkage” bonds, the breaking of which is believed to play a key role in detonation initiation. The bonds are, respectively, CNO2, NN2, ONO2, CNO2, and NNO2. The calculations are at the B3PW91/6–31G** level. We find that fields along these bonds that reinforce the molecules' intrinsic polarities also lower their energies and increase the bonds' stretching vibration frequencies. This suggests a strengthening of the bonds. Fields in the opposite direction do the reverse. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Density functional study of aurophilic interaction in Cl(AuPH3) and in its dimerization
Authors: Fang Hua , Wang Shu‐Guang , Zhang Xiao‐Gang
Published: September 2008

With the help of quantum mechanical calculations, the geometric structures and electronic structures of the closed‐shell systems Cl(AuPH3) and [Cl(AuPH3)]2 have been determined by DFT and MP2 methods. Experimental structure parameters of the title compounds were reproduced at Xα level. The Mulliken population and HOMO–LUMO gaps were examined. The intermolecular aurophilic interactions in [Cl(AuPH3)]2 were analyzed and decomposed. A positive BE value (no bonding) was calculated. When 2PC was added, each pair Au… Au interaction energy was about 83 kJ/mol. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Nonadditivity of methyl group in single‐electron hydrogen bond of methyl radical‐water complex
Authors: Li Qingzhong , Zhu Hongjie , An Xiulin , Gong Baoan , Cheng Jianbo
Published: September 2008

The nonadditivity of methyl group in the single‐electron hydrogen bond of the methyl radical‐water complex has been studied with quantum chemical calculations at the UMP2/6‐311++G(2df,2p) level. The bond lengths and interaction energies have been calculated in the four complexes: CH3H2O, CH3CH2H2O, (CH3)2CHH2O, and (CH3)3CH2O. With regard to the radicals, tert‐butyl radical forms the strongest hydrogen bond, followed by iso‐propyl radical and then ethyl radical; methyl radical forms the weakest hydrogen bond. These properties exhibit an indication of nonadditivity of the methyl group in the single‐electron hydrogen bond. The degree of nonadditivity of the methyl group is generally proportional to the number of methyl group in the radical. The shortening of the C···H distance and increase of the binding energy in the (CH3)2CHH2O and (CH3)3CH2O complexes are less two and three times as much as those in the CH3CH2H2O complex, respectively. The result suggests that the nonadditivity among methyl groups is negative. Natural bond orbital (NBO) and atom in molecules (AIM) analyses also support such conclusions. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Evaluation of molecular integral of Cartesian Gaussian type basis function with complex‐valued center coordinates and exponent via the McMurchie–Davidson recursion formula, and its application to electron dynamics
Authors: Kuchitsu T. , Okuda J. , Tachikawa M.
Published: September 2008

McMurchie–Davidson recursion formula is extended to derive the ab initio molecular integrals with higher angular quantum number complex Gaussian type basis function which has complex‐valued center coordinates and a complex‐valued exponent. Using the analytical recursion formulae, some calculations of electronic dynamics after beta decay of tritium hydride molecular ion HT+ are performed by a quantum wave packet method with thawed Gaussian basis functions of s‐ and p‐type. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Theoretical estimates of the IR spectrum of water intercalated into kaolinite
Authors: Campos Renan Borsoi , Wypych Fernando , Martins Filho Harley Paiva
Published: September 2008

Calculations at AM1, PM3, and HF/6‐31G levels of part of the IR spectrum of the water–kaolinite intercalated system based on a 96‐atom cluster of kaolinite with one water molecule are reported. Only the water molecule conformation is optimized. Frequencies and intensities for just the water vibrations and stretchings of four cluster hydroxyls were calculated through partial Hessian matrices and polar tensors obtained by numerical differentiation of energy gradients and dipole moment. The water molecule was found to attach to the cluster mainly through a double hydrogen bond to the siloxane inner surface, partially entering the siloxane ring hexagonal hole. Though the theoretical results predict that the water OH stretching frequencies decrease from the gas‐phase state to the intercalated state, they are still higher than expected with respect to the observed spectrum. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Theory of chemical bonds in metalloenzymes XI: Full geometry optimization and vibration analysis of porphyrin iron‐oxo species
Authors: Shoji Mitsuo , Isobe Hiroshi , Saito Toru , Kitagawa Yasutaka , Yamanaka Shusuke , Kawakami Takashi , Okumura Mitsutaka , Yamaguchi Kizashi
Published: September 2008

Physiochemical properties of compound I and II intermediate states for heme enzymes (catalase, peroxidase, P450) and inorganic models are investigated by hybrid density functional theory. Used theoretical models are composed of an oxoferryl porphyrin and an axial ligand, which are cresol, methylimidazole, methylthiol, and chloride for catalase, peroxidase, P450, and inorganic models, respectively. The oxoferryl bonds are characterized in terms of bond lengths and vibration frequencies. It is found that the oxoferryl bond lengths (the stretching frequency) are shorter (higher) than those of the X‐ray crystal structures of enzymes, on the other hand for inorganic models, they are comparable with the experimental values. Spin density distributions showed that radical state at the compound I can be classified into two types: (1) porphyrin radical state and (2) axial ligand radical state. Peroxidase and inorganic model are in the former case and Catalase and P450 are in the later case at the present calculation models. Magnetic interactions between oxoferryl and ligand radical moieties are analyzed by the natural orbital analysis and it is showed that the effective exchange integral (J) values are strongly related to the radical spin density distributions: axial ligand radical tends to increase the antiferromagnetic interaction. Mössbauer shift parameters are also evaluated and it is shown that iron charge states are similar for these models. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Comparison of polarization consistent and correlation consistent basis sets for noncovalent interactions
Authors: ElSohly Adel M. , Tschumper Gregory S.
Published: September 2008

The convergence of the polarization consistent family of basis sets to the MP2 complete basis set (CBS) limit has been examined for the dissociation energies of five weakly bound clusters: (HF)2, (HF)3, (H2O)2, (H2O)3, and (C2H2)2. MP2 results obtained with two series of polarization consistent basis sets and the analogous series of Dunning's correlation consistent basis sets are compared to the CBS limits obtained with the explicitly correlated MP2‐R12 method. Although the polarization consistent basis sets do converge systematically to the CBS limit, the correlation consistent basis sets with diffuse functions on nonhydrogen atoms (i.e., cc‐pVXZ for H and aug‐cc‐pVXZ otherwise) consistently produced the smallest errors. Counterpoise corrections for basis set superposition error did not improve the performance of either the polarization or correlation consistent basis sets. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Nature of science as depicted in Turkish biology textbooks
Authors: Irez Serhat
Published: September 2008

Given the impact of textbooks on learning, this study assesses the five most frequently used secondary school biology textbooks in Turkey to examine the nature and the quality of treatment given to the nature of science. A qualitative oriented approach was employed and ethnographic content analysis was used as the methodological framework for this particular research. Data were analyzed by means of cognitive maps. The investigation revealed a number of serious problems with the way nature of science is portrayed in the textbooks. Science was generally portrayed as collection of facts, not as a dynamic process of generating and testing alternative explanations about nature. The authors of the textbooks often appeared not to understand the processes well enough to explain them to students and therefore presented various misleading and inadequate descriptions regarding scientific enterprise, similar to those revealed by research on science teachers' and students' understandings of science. Furthermore, some important aspects of science were found to be neglected by textbooks. The study discusses the future success of scientific literacy movement in Turkey and has implications for science education, science curriculum, and science teacher education in Turkey and other developing countries. © 2008 Wiley Periodicals, Inc. Sci Ed 93: 422–447, 2009
Physical characteristics of Saccharomyces cerevisiae
Authors: Bui V. C. , Kim Y. U. , Choi S. S.
Published: September 2008

We examined the physical properties of the surrounding yeast cell walls by using atomic force microscopy (AFM). The yeast cells were prepared on a cleaned glass substrate for confocal microscopy (CM) observation and were mechanically trapped into a porous membrane for AFM measurement. The confocal image of the yeast cells was measured in air, meanwhile the AFM topography images of the cells were measured in both deionized (DI) water (pH = 6.9) and phosphate‐buffered saline (PBS) solution (pH = 7.4). No significant differences between the AFM topography images of the yeast cells measured in DI water and in PBS solution could be inferred. In order to get the quantitative information on the sample elasticity, the force curves between an AFM tip and the yeast cell have been measured. These curves were measured in both DI water and in PBS solution on the same yeast cell using the same AFM cantilever to get the reliable result. The contact region of the force curve in approach mode was then converted into force versus indentation curve, which would be fitted with Hertz–Sneddon model for the calculation of the elasticity. Analysis of the curves indicates that there is a difference of the Young's modulus values of the yeast cell in various environments. These data show that the salt buffer solution increases the rigidity of the biological system. Copyright © 2008 John Wiley & Sons, Ltd.
Differentiating calcium carbonate polymorphs by surface analysis techniques—an XPS and TOF‐SIMS study
Authors: Ni Ming , Ratner Buddy D.
Published: September 2008

Calcium carbonate has evoked interest owing to its use as a biomaterial, and for its potential in biomineralization. Three polymorphs of calcium carbonate, i.e. calcite, aragonite, and vaterite were synthesized. Three conventional bulk analysis techniques, Fourier transform infrared (FTIR), X‐ray diffraction (XRD), and SEM, were used to confirm the crystal phase of each polymorphic calcium carbonate. Two surface analysis techniques, X‐ray photoelectron spectroscopy (XPS) and time‐of‐flight secondary ion mass spectroscopy (TOF‐SIMS), were used to differentiate the surfaces of these three polymorphs of calcium carbonate. XPS results clearly demonstrate that the surfaces of these three polymorphs are different as seen in the Ca(2p) and O(1s) core‐level spectra. The different atomic arrangement in the crystal lattice, which provides for a different chemical environment, can explain this surface difference. Principal component analysis (PCA) was used to analyze the TOF‐SIMS data. Three polymorphs of calcium carbonate cluster into three different groups by PCA scores. This suggests that surface analysis techniques are as powerful as conventional bulk analysis to discriminate calcium carbonate polymorphs. Copyright © 2008 John Wiley & Sons, Ltd.
Efficiency enhancement of solid‐state dye sensitized solar cell by in situ deposition of CuI
Authors: Han Jing , Chen Jin Mao , Zhou Xiao Wen , Lin Yuan , Zhang Jing Bo , Jia Jian Guang , Sankapal Babasaheb Raghunath
Published: September 2008

Solid‐state dye‐sensitized solar cells based on nanocrystalline TiO2 thin film with the structures TiO2/dye/CuI/Pt and TiO2/dye/In situ CuI/CuI/Pt were developed in order to compare the use of In situ deposited CuI (In situ CuI). Porosity of the screen‐printed nanoporous TiO2 thin film was enhanced by the addition of polystyrene balls. Evidence of decrease in interfacial resistance was observed by electrochemical impedance measurement for the device with In situ deposited CuI as compared to that without In situ deposited CuI as hole conductor. This was attributed to good interfacial contacts and better charge transfer between CuI and dye‐sensitized TiO2 nanoparticles, which resulted in the enhancement of power conversion efficiency from 0.058 to 1.01%. Copyright © 2008 John Wiley & Sons, Ltd.
Einsparpotentiale bei Tragkonstruktionen von Offshore‐Windenergieanlagen
Authors: Scharff Rüdiger , Siems Michael , Ummenhofer Thomas
Published: September 2008

Aufgrund der hohen dynamischen Lastanteile aus Wind‐ und Wellenbeanspruchungen bei Offshore‐Windenergieanlagen erweist sich der Nachweis der Betriebsfestigkeit in vielen Fällen als bestimmender Faktor für die Auslegung der Tragstrukturen. Hierdurch wird in der aktuellen Bemessungspraxis insbesondere die Nutzung wirtschaftlicher Vorteile aus der Anwendung höherfester Stähle behindert. Gerade unter dem Aspekt der Serienfertigung ist jedoch die wirtschaftliche Optimierung der Bauteile für die Firmen ein wesentlicher Wettbewerbsvorteil. In diesem Beitrag werden verschiedene Möglichkeiten für Einsparungen bei Entwurf und Bemessung von Offshore‐Gründungsstrukturen aufgezeigt und am Beispiel der Übergangskonstruktion für eine Jacket‐Struktur dargestellt. Die Einsparpotentiale werden durch optimale Formgebung der Konstruktion, richtungsabhängige Last‐ermittlung, eine verfeinerte Nachweismethodik sowie durch moderne Verfahren der Schweißnahtnachbehandlung ermöglicht.
Bewertung der Ermüdungsfestigkeit von Baustrukturen in Offshore‐Windenergie‐Anlagen
Authors: Thöns Sebastian , Rohrmann Rolf G. , Rücker Werner , Faber Michael H.
Published: September 2008

Das Bauwerk einer Windenergieanlage dient der Sicherstellung der Energieproduktion. Eine entsprechende Zuverlässigkeit der Struktur und deren permanente Bewertung und Unterhaltung ist dazu notwendig. In diesem Beitrag werden Möglichkeiten der Bewertung des für die Struktur wichtigen Schädigungsmechanismus Ermüdung sowie dessen Überwachung in Zusammenhang mit Schädigungsindikatoren aufgezeigt. Dabei wird auf strukturmechanische, werkstoffmechanische und probabilistische Modelle sowie auf Messdaten eines Prototyps einer OWEA zurückgegriffen. Ausgehend von der gesamtdynamischen Berechnung wird die Zuverlässigkeit gemäß der Auslegung für den Schädigungsmechanismus Ermüdung durch ein Wöhlerlinienmodell berechnet. Damit werden ermüdungssensible Komponenten der Struktur identifiziert. Schädigungsindikatoren zur Überwachung der Ermüdungsfestigkeit werden auf Grundlage schädigungs‐äquivalenter Dehnungen vorgestellt.
Grout‐Verbindungen von Monopile‐Gründungsstrukturen – Trag‐ und Ermüdungsverhalten
Authors: Schaumann Peter , Wilke Fabian , Lochte‐Holtgreven Stephan
Published: September 2008

In dem Beitrag wird der aktuelle Stand der Technik für Grout‐Strukturen von Offshore‐Windenergieanlagen (OWEA) vorgestellt sowie über die Ergebnisse von experimentellen und numerischen Untersuchungen an klein‐ und großmaßstäblichen Grout‐Verbindungen berichtet, die im Rahmen des ForWind‐Projektes “TPV: Lebensdauerprognose für die Tragstruktur von Offshore‐Windenergieanlagen” am Institut für Stahlbau der Leibniz Universität Hannover durchgeführt wurden. Auf Grundlage der Erkenntnisse aus Versuch und Numerik werden anhand einer Referenzstruktur in der Ostsee mit einer Anlagengröße von 3MW repräsentative Berechnungen von Grouted‐Joint‐Verbindungen unter vorwiegender Biegebeanspruchung mit Hilfe von numerischen Modellen vorgestellt. Neben der Betrachtung von Grouted‐Joint‐Verbindungen mit glatten Stahlrohroberflächen werden die Möglichkeiten von Grout‐Strukturen unter Ansatz von versteifenden Schubrippen (Shear Keys) im Grenzzustand der Tragfähigkeit und Ermüdung vorgestellt. Neben der Betrachtung der Gesamtstruktur einer Grout‐Verbindung unter Ermüdungsbeanspruchungen werden lokale Konzepte für Degradationsberechnungen im Bereich der Shear Keys durchgeführt und eine Einstufung in Kerbfallklassen vorgenommen.
Temperature Related Structural Changes in Wheat and Corn Starch Granules and Their Effects on Gels and Dry Foam
Authors: Glenn Gregory M. , Klamczynski Artur , Chiou Bor‐Sen. , Orts William J. , Imam Syed H. , Wood Delilah F.
Published: September 2008

The effect of processing temperature on structural changes in wheat, corn, and high amylose corn starch granules was investigated and related to the mechanical properties of gels and microcellular foam (MCF). Scanning electron micrographs (SEM) showed that wheat starch granules form ghosts with thicker walls than dent corn granules. The granule wall was permeable to water and appeared to be at least partially permeable to the solubilized contents of the granule. The ghost walls became visibly porous after heating at 95ºC for 60 min and were completely solubilized by heating to 120ºC. High‐amylose corn starch (HACS) granules were completely dissolved by heating to 140ºC. Gels made with wheat starch had higher gel strength and dynamic modulus compared to dent corn starch gels. The density, compressive strength and modulus of MCF were lower in samples cooked for 60 min. The density of dent corn MCF was higher than that of wheat starch which may have accounted for higher compressive strength and modulus in the corn sample. MCF made from HACS had higher surface area and lower density, compressive strength, and modulus than the other starches tested. There were no significant differences in pore volume or surface area due to extended cooking times.
Influence of aroclor 1254 on benzo(a)pyrene‐induced DNA breakage, oxidative DNA damage, and cytochrome P4501A activity in human hepatoma cell line
Authors: Yuan Jing , Lu Wen‐Qing , Zou Ya‐Lin , Wei Wei , Zhang Chi , Xie Hong , Chen Xue‐Min
Published: September 2008

Both polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) are important environmental pollutants. They coexist widely in the environment at very low levels. Numerous studies indicated that aroclor1254 (one of PCBs mixture) is the inducer of cytochrome P450 1A enzyme acitivity. Benzo(a)pyrene (BaP) can cause a variety of toxicities in vitro, such as oxidative DNA damage and genotoxicity. In the present study, HepG2 cells were treated with either BaP (50 μM) or aroclor1254 at concentrations of 11.5 (low), 23.0 (medium), and 46.0 μM (high) alone, or pretreated the cells with aroclor1254 (11.5, 23.0, and 46.0 μM), followed by BaP (50 μM). It was found that 7‐ethoxyresorufin‐O‐deetylase (EROD) activities of HepG2 cells exposed to either BaP or aroclor 1254 increased. DNA damage measured by DNA migration and the formation of 8‐hydroxy‐2′‐deoxyguanosine (8‐OHdG) also increased in cells exposed to BaP, but not in cells exposed to aroclor1254. Under the Aroclor 1254 pretreatment condition, BaP‐induced EROD activities was enhanced in cells exposed to the medium and high concentrations of aroclor1254 (P < 0.01 for both), whereas in all pretreatment groups aroclor1254 significantly increased BaP‐induced DNA migration (P < 0.01 for all) and the 8‐OHdG formation (P < 0.05 for all). In addition, there was positive correlation between the EROD induction activity and Olive tail moment (r2 = 0.958, P < 0.01) or the levels of 8‐OHdG (r2 = 0.992, P < 0.01). The findings suggest that under the experimental conditions aroclor1254 may enhance BaP‐induced DNA migration and oxidative DNA damage in HepG2, due to inducing CYP1A enzyme activity. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2009.
Effect of short‐time exposures to nickel and lead on brain monoamine oxidase fromDanio rerioandPoecilia reticulata
Authors: Senatori Ornella , Setini Andrea , Scirocco Annunziata , Nicotra Antonietta
Published: September 2008

The aim of this work was to verify, in two small size freshwater teleostsDanio rerioandPoecilia reticulata, the effects of short‐time exposures (24 and 72 h) to a sublethal dose (500 μg/L) of nickel and lead, on brain monoamine oxidase (MAO), an important neural enzyme. The 24‐h treatment using both metals caused a strong reduction of MAO activity inD. reriobrain, whereas causing a slight MAO activity stimulation inP. reticulatabrain. The same treatment in both species did not affect the brain MAO mRNA production as showed by RT‐PCR. Extending the duration of treatment as far as 72 h, partly (D. rerio) or completely (P. reticulata) reversed the metal effects on brain MAO activity suggesting that mechanisms to neutralize the metals had been activated. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2009.
The value of stress protein 70 as an environmental biomarker of fish health under field conditions
Authors: Webb Diane , Gagnon Marthe Monique
Published: September 2008

Hsp70 protein in three tissue types (gill, liver, and muscle) from black bream (Acanthopagrus butcheri) collected in a highly variable estuarine environment was investigated to determine which tissue provides better intersite discrimination. The usefulness of hsp70 expression to identify anthropogenic stress under field conditions was evaluated. Intersite differences were detected in hsp70 levels in gill and white muscle of black bream while liver showed no spatial difference. There was high interfish variability in hsp70 levels in each tissue group. A post hoc power analysis of the datasets for each tissue found that in black bream, white muscle provided the best discriminatory power to elucidate spatial variability. Only 11 fish per site are required to identify significant intersite differences in white muscle whereas for gill and liver tissues 14 and 21 fish per site, respectively, would be required. Because of high intertissue and interindividual variability, field measurement of hsp70 should be complemented by evidence of changes in other biomarkers of fish health. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2009.
Combined repeated dose and reproductive/developmental toxicities of copper monochloride in rats
Authors: Chung Moon‐Koo , Baek Sung‐Soo , Lee Sang‐Hee , Kim Hyunmi , Choi Kyunghee , Kim Jong‐Choon
Published: September 2008

This study investigated the combined repeated dose and reproductive/developmental toxicity of copper monochloride in rats. The test substance was administered once daily by gavage at 0, 1.3, 5, 20, or 80 mg/kg/day. Male rats were dosed for a total of 30 days beginning 14 days before mating. Female rats were dosed from 2 weeks before mating to day 3 of lactation throughout the mating and gestation period. At 80 mg/kg/day, deaths were observed in 3 out of 12 females. There was a dose‐dependent increase in the incidence of clinical signs and a reduction in the food consumption. Hematological and serum biochemical investigations revealed a decrease in the red blood cell, hemoglobin, hematocrit, mean corpuscular volume, mean corpuscular hemoglobin (MCH), and serum total protein levels and an increase in the white blood cell and platelets in males, and a decrease in the MCH and an increase in the platelets in females. Histopathological examination showed an increased incidence of squamous cell hyperplasia of the stomach in both genders as well as increased hematopoiesis of the femur in males. There was an increase in the number of icteric and runt pups at birth. At 20 mg/kg/day, there was an increase in the incidence of clinical signs and squamous cell hyperplasia of the stomach in both genders. At 5 mg/kg/day, an increase in the incidence of squamous cell hyperplasia of the stomach was observed in females. There were no adverse effects in the lowest group in both genders. Based on these findings, the no‐observed‐adverse‐effect levels of copper monochloride were concluded to be 5 mg/kg/day in male rats and 1.3 mg/kg/day in female rats for general toxicity and 20 mg/kg/day for reproductive/developmental toxicity. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2009.
Activation of JNK and PAK2 is essential for citrinin‐induced apoptosis in a human osteoblast cell line
Authors: Huang Yu‐Ting , Lai Ching‐Yu , Lou Shyh‐Liang , Yeh Jui‐Ming , Chan Wen‐Hsiung
Published: September 2008

The mycotoxin citrinin (CTN), a natural contaminant in foodstuffs and animal feeds, exerts cytotoxic and genotoxic effects on various mammalian cells. CTN causes cell injury, including apoptosis. Previous studies by our group showed that CTN triggers apoptosis in mouse embryonic stem cells, as well as embryonic developmental injury. Here, we investigated the precise mechanisms governing this apoptotic effect in osteoblasts. CTN induced apoptotic biochemical changes in a human osteoblast cell line, including activation of c‐Jun N‐terminal kinase (JNK), loss of mitochondrial membrane potential, and caspase‐3 and p21‐activated protein kinase 2 (PAK2) activation. Experiments using a JNK‐specific inhibitor, SP600125, and antisense oligonucleotides against JNK reduced CTN‐induced activation of both JNK and caspase‐3 in osteoblasts, indicating that JNK is required for caspase activation in this apoptotic pathway. Experiments using caspase‐3 inhibitors and antisense oligonucleotides against PAK2 revealed that active caspase‐3 is essential for PAK2 activation. Moreover, both caspase‐3 and PAK2 require activation for CTN‐induced apoptosis of osteoblasts. Interestingly, CTN stimulates two‐stage activation of JNK in human osteoblasts. Early‐stage JNK activation is solely ROS‐dependent, whereas late‐stage activation is dependent on ROS‐mediated caspase activity, and regulated by caspase‐induced activation of PAK2. On the basis of these results, we propose a signaling cascade model for CTN‐induced apoptosis in human osteoblasts involving ROS, JNK, caspases, and PAK2. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2009.
Effect of 1‐butyl‐3‐methylimidazolium tetrafluoroborate on the wheat (Triticum aestivum L.) seedlings
Authors: Wang Lin‐Song , Wang Lin , Wang Li , Wang Ge , Li Zhao‐Hu , Wang Jian‐Ji
Published: September 2008

Although many studies describe ionic liquids (ILs) as potentially greener solvents, few studies address their relationship with the environment. Recent researches suggest that some ILs have toxicity. 1‐Butyl‐3‐methylimidazolium tetrafluoroborate ([C4mim][BF4]) was reported to have the lowest toxicity among ILs. In this work, we studied the toxicity of this IL on wheat seedlings. It was shown that wheat germination was reduced to 38.0% in the presence of 4.4 mmol/L [C4mim][BF4] compared with 100% germination for the control. Similarly, the root and shoot length of wheat seedlings decreased with increasing concentrations of [C4mim][BF4]. The activity of amylase increased in shoots and roots, but it decreased significantly in germinating seeds when the [C4mim][BF4] concentration exceeded 1.8 mmol/L. Peroxidase (POD) activity and soluble protein content in shoots treated with [C4mim][BF4] changed similarly, but chlorophyll content tended to decrease with increasing concentration of [C4mim][BF4], except for at 1.8 mmol/L. Thus, [C4mim][BF4] at the concentration of 0.9 mmol/L or more was toxic to wheat seedlings. Some remedial measures are suggested to deal with IL pollution in the environment. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2009.
Cost analysis and efficient radio bearer selection for multicasting over UMTS
Authors: Alexiou Antonios , Bouras Christos , Kokkinos Vasileios , Rekkas Evangelos
Published: September 2008

Along with the widespread deployment of the Third Generation (3G) cellular networks, the fast‐improving capabilities of the mobile devices, content, and service providers are increasingly interested in supporting multicast communications over wireless networks and in particular over Universal Mobile Telecommunications System (UMTS). To this direction, the Third Generation Partnership Project (3GPP) is currently standardizing the Multimedia Broadcast/Multicast Service (MBMS) framework of UMTS. In this paper, we present an overview of the MBMS multicast mode of UMTS. We analytically present the multicast mode of the MBMS and analyze its performance in terms of packet delivery cost under various network topologies, cell types, and multicast users' distributions. Furthermore, for the evaluation of the scheme, we consider different transport channels for the transmission of the multicast data over the UMTS Terrestrial Radio‐Access Network (UTRAN) interfaces. Finally, we propose a scheme for the efficient radio bearer selection that minimizes total packet delivery cost. Copyright © 2008 John Wiley & Sons, Ltd.
Synchrony in local population dynamics of stream‐dwelling Dolly Varden: do genetically similar groups show similar demography?
Authors: Koizumi Itsuro , Yamamoto Shoichiro , Nomoto Kazuhiro , Maekawa Koji
Published: September 2008

We investigated the relationship between genetic divergence and demographic dependence. Genetically related groups may consist of the same demographic unit or a single “population,” because high levels of dispersal may synchronize population dynamics. We examined this hypothesis by assessing the levels of synchrony in seven demographic parameters among locations supporting stream‐dwelling Dolly Varden. We analyzed synchrony using demographic data collected over 10 years in five neighboring tributary streams (<7 km) where little genetic divergence was observed. The overall synchrony was moderate for age‐0+ and ≥age‐1+ (average cross‐correlation coefficient), but the synchrony decreased at later life stages (mature adults,). No significant temporal co‐variation was observed for other demographic parameters (sex ratio and resident‐to‐migrant ratio,and 0.38, respectively). Therefore, it appears that demographic synchrony was more prevalent for early life stages, but less so for later life stages, suggesting the demography of each tributary is unique. Furthermore, since an isolated location showed high levels of synchrony with the other locations, the main driver of synchrony is likely correlated environmental influences on demography (Moran effect) rather than dispersal. Pairwise synchrony was not correlated with geographical distance, but negatively correlated with the degree of genetic differentiation (FST) in a few cases. Overall, however, we found little evidence that dispersal induces strong synchrony even among the neighboring tributaries where genetic analysis indicated considerable dispersal. Finally it is worth noting that the influences of dispersal may be different in terms of genetic and demographic contexts, and that density‐dependent processes may mask patterns of observed synchrony.
Re‐established mutualism in a seed‐dispersal system consisting of native and introduced birds and plants on the Bonin Islands, Japan
Authors: Kawakami Kazuto , Mizusawa Leiko , Higuchi Hiroyoshi
Published: September 2008

The disruption of plant–animal interactions such as seed dispersal is one of the most critical effects of biological invasions. To understand the role of introduced species in current seed‐dispersal systems, we conducted fecal analyses of the most common resident land birds on the Bonin Islands, Japan, and estimated their relative importance as seed‐dispersal agents. Two native birds, the brown‐eared bulbul and the Bonin Islands white‐eye, and the introduced Japanese white‐eye were the primary seed dispersers in secondary forest sites. Because the seed species composition in the feces of native and introduced white‐eyes was similar, the latter may be replacing the former as a seed‐dispersal agent. Introduced plants did not decrease the number of seed‐dispersal opportunities for native species through competition for seed dispersers. Because some bird species have already become extinct on the Bonin Islands, their ecological functions may also have been permanently lost; however, the introduced white‐eye may be compensating for this loss of function. In addition, new mutualistic relationships involving native and introduced birds and plants have already been established. In order to control introduced species while having the least impact on the native biota, interspecific interactions must be thoroughly understood before initiating control efforts.
Surface-Related States in Oxidized Silicon Nanocrystals Enhance Carrier Relaxation and Inhibit Auger Recombination
Authors: Othonos Andreas , Lioudakis Emmanouil , Nassiopoulou AG
Published: September 2008

We have studied ultrafast carrier dynamics in oxidized silicon nanocrystals (NCs) and the role that surface-related states play in the various relaxation mechanisms over a broad range of photon excitation energy corresponding to energy levels below and above the direct bandgap of the formed NCs. Transient photoinduced absorption techniques have been employed to investigate the effects of surface-related states on the relaxation dynamics of photogenerated carriers in 2.8 nm oxidized silicon NCs. Independent of the excitation photon energy, non-degenerate measurements reveal several distinct relaxation regions corresponding to relaxation of photoexcited carriers from the initial excited states, the lowest indirect states and the surface-related states. Furthermore, degenerate and non-degenerate measurements at difference excitation fluences reveal a linear dependence of the maximum of the photoinduced absorption (PA) signal and an identical decay, suggesting that Auger recombination does not play a significant role in these nanostructures even for fluence generating up to 20 carriers/NC.
Double Rashba Quantum Dots Ring as a Spin Filter
Authors: Chi Feng , Yuan Xiqiu , Zheng Jun
Published: September 2008

We theoretically propose a double quantum dots (QDs) ring to filter the electron spin that works due to the Rashba spin–orbit interaction (RSOI) existing inside the QDs, the spin-dependent inter-dot tunneling coupling and the magnetic flux penetrating through the ring. By varying the RSOI-induced phase factor, the magnetic flux and the strength of the spin-dependent inter-dot tunneling coupling, which arises from a constant magnetic field applied on the tunneling junction between the QDs, a 100% spin-polarized conductance can be obtained. We show that both the spin orientations and the magnitude of it can be controlled by adjusting the above-mentioned parameters. The spin filtering effect is robust even in the presence of strong intra-dot Coulomb interactions and arbitrary dot-lead coupling configurations.
Discrimination of Chain Positions in Mixed Short/Long‐Chain Glycerophosphocholines by NMR Chemical Shift Variations
Authors: D’Arrigo Paola , Mele Andrea , Rossi Cristina , Tessaro Davide , Servi Stefano
Published: September 2008

The synthesis of a series of (1,2‐) mixed short/long‐chain glycerophosphocholines has been performed. Starting from glycerophosphorylcholine (GPC), and using regioselective acylation in the presence of dibutyltin oxide, a set of high‐purity isomeric mixed‐chain phospholipids was obtained. This has allowed the development of a simple NMR method for the structural determination of the isomeric 1(2)‐short‐2(1)‐long‐diacylglycerophosphocholines. The method is based on the observation that selected protons in the two series of isomeric phospholipids undergo systematic chemical shift variations Δδ that can be ascribed to the acyl substituents on the glycerol backbone. The observed patterns can be exploited as a simple method for the discrimination of regioisomeric unsymmetrical 1,2‐diacylglycerophosphocholines.
CCN2 YAPs at cancer
Authors: Leask Andrew
Published: September 2008

The YAP transcription coactivator has been implicated as an oncogene and is amplified in human cancers. Previously, it has been shown that CCN2 (connective tissue growth factor, CTGF) is a target of the tumor promoting YAP and its transcription factor target TEAD. A recent report in Genes and Development by Zhao and colleagues (Genes Dev 22:1962–1971 2008) has extended these initial observations to show that CCN2 plays an important role in the growth‐promoting function of YAP. These data confirm the role of CCN2 as a key oncogenic mediator. This report briefly summarizes these findings.