bluuebunny/crossref_metadata_2025 huggingface dataset:
Silica induces cell cycle changes through PI‐3K/AP‐1 pathway in human embryo lung fibroblast cells
Authors: Jia Xiaowei , Liu Bingci , Ye Meng , Liu Haifeng , Shi Xianglin
Published: October 2010

Exposure to silica is associated with progressive pulmonary inflammation and fibrosis. Our previous study had demonstrated silica exposure could cause cell cycle alternation and activator protein‐1 (AP‐1) activation. This study showed that silica exposure induced phosphorylation of p70S6 kinase (p70S6K) and Akt in human embryo lung fibroblasts (HELFs). These changes were blocked by overexpression of dominant‐negative mutants of phosphatidylinositol‐3 kinase (Δp85) or Akt (DN‐Akt), respectively. Moreover, pretreatment of cells with rapamycin, a specific p70S6K inhibitor, could inhibit silica‐induced cell cycle alteration, AP‐1 activation, and phosphorylation of p70S6K, but had no effect on Akt phosphorylation. This suggested that phosphatidylinositol‐3 kinase (PI‐3K)/AP‐1 pathway was likely responsible for cell cycle changes. Furthermore, we observed the effect of the pathway on cell cycle regulatory proteins. Our results indicated that inactivation of PI‐3K, Akt, or p70S6K could inhibit silica‐induced overexpression of cyclin D1 and cyclin‐dependent kinase 4 (CDK4) and decreased expression of E2F‐4. Taken together, silica could induce cell cycle changes through PI‐3K/ AP‐1 pathway in HELFs. Copyright © 2010 John Wiley & Sons, Ltd.
Atomic‐Scale Observation of the Ni Activation Process for Partial Oxidation of Methane Using In Situ Environmental TEM
Authors: Chenna Santhosh , Banerjee Ritubarna , Crozier Peter A.
Published: October 2010

In situ environmental transmission electron microscopy (ETEM) studies on nanostructures, in parallel with conversion and selectivity measurements, have been carried out on Ni/SiO2 catalysts for partial oxidation of methane, in order to elucidate structure–property relationships. In situ ETEM experiments under different gas conditions are carried out to simulate the various gas atmospheres that exist in the reactor. During ramp‐up in CH4 and O2, Ni metal particles transform to void‐like NiO particles at temperatures above 300 °C due to preferential migration of Ni cations along grain boundaries and extended defects. As the temperature increases, the gas environment becomes more reducing, transforming NiO back to Ni and favoring syngas formation. The NiO reduction mechanism also involves diffusion of Ni cations along grain boundaries and extended defects. This transformation pathway suppresses the formation Ni metal crystallites on the catalyst surface during the early stage in NiO reduction. Syngas formation only takes place during the later stages of NiO reduction, when Ni metal nanoparticles have broken through the NiO shell.
Expression ofSlitandRobogenes in the developing mouse heart
Authors: Medioni Caroline , Bertrand Nicolas , Mesbah Karim , Hudry Bruno , Dupays Laurent , Wolstein Orit , Washkowitz Andrew J. , Papaioannou Virginia E. , Mohun Timothy J. , Harvey Richard P. , Zaffran Stéphane
Published: October 2010

Development of the mammalian heart is mediated by complex interactions between myocardial, endocardial, and neural crest‐derived cells. Studies inDrosophilahave shown that the Slit‐Robo signaling pathway controls cardiac cell shape changes and lumen formation of the heart tube. Here, we demonstrate by in situ hybridization that multiple Slit ligands and Robo receptors are expressed in the developing mouse heart.Slit3is the predominant ligand transcribed in the early mouse heart and is expressed in the ventral wall of the linear heart tube and subsequently in chamber but not in atrioventricular canal myocardium. Furthermore, we identify that the homeobox geneNkx2‐5is required for early ventral restriction ofSlit3and that the T‐box transcription factor Tbx2 mediates repression ofSlit3in nonchamber myocardium. Our results suggest that patterned Slit‐Robo signaling may contribute to the control of oriented cell growth during chamber morphogenesis of the mammalian heart. Developmental Dynamics 239:3303–3311, 2010. © 2010 Wiley‐Liss, Inc.
Characterization of a novel type I keratin gene and generation of transgenic lines with fluorescent reporter genes driven by its promoter/enhancer in Xenopus laevis
Authors: Suzuki Ken‐ichi T. , Kashiwagi Keiko , Ujihara Motomu , Marukane Takuzo , Tazaki Akira , Watanabe Kenji , Mizuno Nobuhiko , Ueda Yoko , Kondoh Hisato , Kashiwagi Akihiko , Mochii Makoto
Published: October 2010

We investigated the characteristics of a novel type I keratin gene in Xenopus laevis during ontogenesis. The transcript was first detected in the posterior region at the late neurula stage, and then restricted to the fin and external gill during embryogenesis. To examine the transcriptional regulation of the keratin gene in vivo, we generated transgenic lines with fluorescent reporter genes driven by its 4.2‐kb upstream sequence. The promoter/enhancer activity recapitulated the endogenous gene expression during embryogenesis. Sequential deletion analyses revealed that the regions proximal to the promoter were essential for fin‐specific expression. Reporter expression was detected in various organs, including the fin and gill. In particular, robust expression was observed in the developing limbs and gill. The reporter fluorescence rapidly decreased with internal gill resorption during metamorphosis. The transgenic lines carrying the promoter/enhancer should represent valuable tools for elucidating the formation, development and resorption of various organs, especially the gill. Developmental Dynamics 239:3172–3181, 2010. © 2010 Wiley‐Liss, Inc.
Epoxidation of Alkenes with H2O2 Catalyzed by Dititanium‐Containing 19‐Tungstodiarsenate(III): Experimental and Theoretical Studies
Authors: Donoeva Baira G. , Trubitsina Tatiana A. , Antonova Nadya S. , Carbó Jorge J. , Poblet Josep M. , Al‐Kadamany Ghada , Kortz Ulrich , Kholdeeva Oxana A.
Published: October 2010

Epoxidation of a range of alkenes with aqueous H2O2 easily proceeds in the presence of the dititanium‐containing 19‐tungstodiarsenate(III) [Ti2(OH)2As2W19O67(H2O)]8– (1), which contains five‐coordinate Ti atoms. The results of product and kinetics studies support a mechanism that involves a reversible interaction between H2O2 and the Ti–OH group of 1 to produce a titanium hydroperoxo complex followed by electrophilic oxygen atom transfer from the hydroperoxo ligand to the alkene substrate in the rate‐limiting step. The effect of the alkene substrate nature has been investigated at the DFT level. A clear correlation between the energy of πC=C orbitals in the alkene and the turnover frequency values has been found, thereby indicating that the higher nucleophilicity of the alkene, the higher the reactivity. ONIOM (ONIOM = our own n‐layered integrated molecular orbital and molecular mechanics) calculations have been employed to evaluate the role of steric effects of alkene substituents. The calculations show that the steric bulk can play a secondary role and tunes the activity in specific cases such as trans‐stilbene.
Direct Access to Cumbersome Aminated Quaternary Centers by Hyperbaric Aza‐Michael Additions
Authors: Rulev Alexander Yu. , Azad Saleha , Kotsuki Hiyoshizo , Maddaluno Jacques
Published: October 2010

The aza‐Michael addition of secondary amines to α,β‐ or β,β‐disubstituted α,β‐unsaturated esters was efficiently achieved under high pressure (10–16 kbar) in protic solvents in the absence of any catalyst. The expected cumbersome β‐aminoesters bearing a tertiary amine directly connected to a quaternary carbon atom could be isolated in fair to good yields. By using α,β,δ,γ‐unsaturated esters (alkyl sorbate), the addition took place regioselectively in a 1,6 manner and afforded the β,γ‐unsaturated δ‐aminoesters.
Cognitive processes in implicit attitude tasks: An experimental validation of the Trip Model
Authors: Nadarevic Lena , Erdfelder Edgar
Published: October 2010

Implicit attitude tasks have become very popular in various areas of psychology. However, little is known about the cognitive processes they involve. To address this issue, we investigated the underlying processes of the Go/No‐go Association Task (GNAT), a go/no‐go variant of the well‐known Implicit Association Test (IAT). More precisely, we tested two alternative multinomial processing tree (MPT) models of GNAT performance, the Trip Model and the generalized Quad Model. Both models assume that GNAT performance is influenced not only by automatic associations but also by response biases and a controlled discrimination process. However, the two models differ with respect to an additional overcoming bias process. In contrast to the Quad Model, the Trip Model assumes that overcoming bias does not play a major role in GNAT performance. Instead, the Trip Model emphasizes the role of response biases. We report three experiments that demonstrate the validity of the Trip Model for GNAT data. Copyright © 2010 John Wiley & Sons, Ltd.
Textile‐based Electrochemical Sensing: Effect of Fabric Substrate and Detection of Nitroaromatic Explosives
Authors: Chuang Min‐Chieh , Windmiller Joshua Ray , Santhosh Padmanabhan , Ramírez Gabriela Valdés , Galik Michal , Chou Tzu‐Yang , Wang Joseph
Published: October 2010

This study examines the influence of textile substrates upon the behavior of wearable screen‐printed electrodes and demonstrates the attractive sensing properties of these sensors towards the detection of nitroaromatic explosives. Compared to electrodes printed on common cotton or polyester substrates, GORE‐TEX‐based electrochemical sensors display reproducible background cyclic voltammograms, reflecting the excellent water‐repellant properties of the GORE‐TEX fabric. The wetting properties of different printed textile electrodes are elucidated using contact angle measurements. The influence of laundry washing and mechanical stress is explored. The GORE‐TEX‐based printed electrodes exhibit favorable detection of 2,4‐dinitrotoluene (DNT) and 2,4,6‐trinitrotoluene (TNT) explosives, including rapid detection of DNT vapor.
An Electrochemical Approach for the Cucurbit[7]uril/Carbendazim Supramolecular Inclusion Complex. Application to Carbendazim Determination in Apples
Authors: del Pozo María , Alonso Marina , Hernández Lucas , Quintana Carmen
Published: October 2010

This work presents the electrochemical behaviour of the supramolecular complex formed between the macrocyclic receptor cucurbit[7]uril and the fungicide carbendazim. Moreover, this host molecule is used to develop a selective and sensitive differential pulse voltammetric method for the determination of carbendazim through its cucurbit[7]uril inclusion complex, allowing the detection of the analyte at 4.25×10−9 M. The method was applied to the determination of the fungicide in untreated apple peel samples after a matrix solid‐phase dispersion sample preparation procedure. The detection limit calculated for this real sample was 0.17 mg kg−1, which is below the legally allowed limit of 0.20 mg kg−1.
Uncertainty matters: impact of stimulus ambiguity on infant social referencing
Authors: Kim Geunyoung , Kwak Keumjoo
Published: October 2010

Most infant social referencing studies have assumed that infants would be more likely to engage in social looking and be influenced by adults' message when a context is ambiguous. The present study empirically tested the effect of stimulus ambiguity on infants' referencing behaviours, with three different stimuli (positive, ambiguous, and negative), two different messages (happy and fearful), two different message providers (mother and stranger), and in two age groups (12 and 16 month olds). A typical social referencing paradigm was used and infants' social looking and regulation were measured. Infants looked at adults more frequently and faster during ambiguous situations than during unambiguous situations. They also tended to regulate their affect and behaviour based on adults' message only towards ambiguous toys. Older infants tended to look at adults faster, and showed stronger reactions towards ambiguous stimuli than younger infants, suggesting that infants' social development may moderate the effect of stimulus ambiguity on social referencing. Overall, results indicated that the ambiguity postulate is a legitimate assumption for infant social referencing. Copyright © 2010 John Wiley & Sons, Ltd.
Binary quantile regression: a Bayesian approach based on the asymmetric Laplace distribution
Authors: Benoit Dries F. , Van den Poel Dirk
Published: October 2010

This paper develops a Bayesian method for quantile regression for dichotomous response data. The frequentist approach to this type of regression has proven problematic in both optimizing the objective function and making inferences on the parameters. By accepting additional distributional assumptions on the error terms, the Bayesian method proposed sets the problem in a parametric framework in which these problems are avoided. To test the applicability of the method, we ran two Monte Carlo experiments and applied it to Horowitz's (1993) often studied work‐trip mode choice dataset. Compared to previous estimates for the latter dataset, the method proposed leads to a different economic interpretation. Copyright © 2010 John Wiley & Sons, Ltd.
Generation of Kekulé valence structures and the corresponding valence bond wave function
Authors: Rashid Zahid , van Lenthe Joop H.
Published: October 2010

A new scheme, called “list of nonredundant bonds”, is presented to record the number of bonds and their positions for the atoms involved in Kekulé valence structures of (poly)cyclic conjugated systems. Based on this scheme, a recursive algorithm for generating Kekulé valence structures has been developed and implemented. The method is general and applicable for all kinds of (poly)cyclic conjugated systems including fullerenes. The application of the algorithm in generating Valence Bond (VB) wave functions, in terms of Kekulé valence structures, is discussed and illustrated in actual VB calculations. Two types of VBSCF calculations, one involving Kekulé valence structures only and the second one involving all covalent VB structures, were performed for benzene, pentalene, benzocyclobutadiene, and naphthalene. Both strictly local and delocalised p‐orbitals were used in these calculations. Our results show that, when the orbitals are restricted to their own atoms, other VB structures (Dewar structures) also have a significant contribution in the VB wave function. When removing this restriction, the other VB structures (Dewar and also the ionic structures) are accommodated in the Kekulé valence structures, automatically. Therefore, at VBSCF delocal level, the ground states of these systems can be described almost quantitatively by considering Kekulé valence structures only at a considerable saving of time. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010.
Using correlated parameters for improved ranking of protein–protein docking decoys
Authors: Mitra Pralay , Pal Debnath
Published: October 2010

A successful protein–protein docking study culminates in identification of decoys at top ranks with near‐native quaternary structures. However, this task remains enigmatic because no generalized scoring functions exist that effectively infer decoys according to the similarity to near‐native quaternary structures. Difficulties arise because of the highly irregular nature of the protein surface and the significant variation of the nonbonding and solvation energies based on the chemical composition of the protein–protein interface. In this work, we describe a novel method combining an interface‐size filter, a regression model for geometric compatibility (based on two correlated surface and packing parameters), and normalized interaction energy (calculated from correlated nonbonded and solvation energies), to effectively rank decoys from a set of 10,000 decoys. Tests on 30 unbound binary protein–protein complexes show that in 16 cases we can identify at least one decoy in top three ranks having ≤10 Å backbone root mean square deviation from true binding geometry. Comparisons with other state‐of‐art methods confirm the improved ranking power of our method without the use of any experiment‐guided restraints, evolutionary information, statistical propensities, or modified interaction energy equations. Tests on 118 less‐difficult bound binary protein–protein complexes with ≤35% sequence redundancy at the interface showed that in 77% cases, at least 1 in 10,000 decoys were identified with ≤5Å backbone root mean square deviation from true geometry at first rank. The work will promote the use of new concepts where correlations among parameters provide more robust scoring models. It will facilitate studies involving molecular interactions, including modeling of large macromolecular assemblies and protein structure prediction. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.
Intermolecular potential energy surface for CS2 dimer
Authors: Farrokhpour Hossein , Mombeini Zainab , Namazian Mansoor , Coote Michelle L.
Published: October 2010

A new four‐dimensional intermolecular potential energy surface for CS2 dimer is obtained by ab initio calculation of the interaction energies for a range of configurations and center‐of‐mass separation distances for the first time. The calculations were performed using the supermolecular approach at the Møller–Plesset second‐order perturbation (MP2) level of theory with the augmented correlation consistent basis sets (aug‐cc‐pVxZ, x = D, T) and corrected for the basis‐set superposition error using the full counterpoise correction method. A two‐point extrapolation method was used to extrapolate the calculated energy points to the complete basis set limit. The effect of using the higher levels of theory, quadratic configuration interaction containing single, double, and perturbative triple excitations QCISD(T) and coupled cluster singles, doubles and perturbative triples excitations CCSD(T), on the shape of potential energy surface was investigated. It is shown that the MP2 level of theory apparently performs extremely poorly for describing the intermolecular potential energy surface, overestimating the total energy by a factor of nearly 1.73 in comparison with the QCISD(T) and CCSD(T) values. The value of isotropic dipole–dipole dispersion coefficient (C6) of CS2 fluid was obtained from the extrapolated MP2 potential energy surface. The MP2 extrapolated energy points were fitted to well‐known analytical potential functions using two different methods to represent the potential energy surface analytically. The most stable configuration of the dimer was determined at R = 6.23 au, α = 90°, β = 90°, and γ = 90°, with a well depth of 3.980 kcal mol−1 at the MP2 level of theory. Finally, the calculated second virial coefficients were compared with experimental values to test the quality of the presented potential energy surface. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.
Electrostatic solvation free energy of amino acid side chain analogs: Implications for the validity of electrostatic linear response in water
Authors: Lin Bin , Pettitt B. Montgomery
Published: October 2010

Electrostatic free energies of solvation for 15 neutral amino acid side chain analogs are computed. We compare three methods of varying computational complexity and accuracy for three force fields: free energy simulations, Poisson‐Boltzmann (PB), and linear response approximation (LRA) using AMBER, CHARMM, and OPLS‐AA force fields. We find that deviations from simulation start at low charges for solutes. The approximate PB and LRA produce an overestimation of electrostatic solvation free energies for most of molecules studied here. These deviations are remarkably systematic. The variations among force fields are almost as large as the variations found among methods. Our study confirms that success of the approximate methods for electrostatic solvation free energies comes from their ability to evaluate free energy differences accurately. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.
Looking for high energy density compounds applicable for propellant among the derivatives of dpo with n3, ono2, and nno2 groups
Authors: Wang Gui‐Xiang , Gong Xue‐Dong , Liu Yan , Du Hong‐Chen , Xu Xiao‐Juan , Xiao He‐Ming
Published: October 2010

The derivatives of DPO (2,5‐dipicryl‐1,3,4‐oxadiazole) are optimized to obtain their molecular geometries and electronic structures at the DFT‐B3LYP/6‐31G* level. The bond length is focused to primarily predict thermal stability and the pyrolysis mechanism of the title compounds. Detonation properties are evaluated using the modified Kamlet‐Jacobs equations based on the calculated densities and heats of formation. It is found that there are good linear relationships between density, detonation velocity, detonation pressure, and the number of azido, nitrate, and nitramine groups. According to the largest exothermic principle, the relative specific impulse is investigated by calculating the enthalpy of combustion (ΔHcomb) and the total heat capacity (Cp,gases). It is found that the introduction of N3, ONO2, and NNO2 groups could increase the specific impulses and II‐4, II‐5, and III‐5 are potential candidates for High Energy Density Materials (HEDMs). The effect of the azido, nitrate, and nitramine groups on the structure and the properties is discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.
Numerical modelling of bit–rock fracture mechanisms in percussive drilling with a continuum approach
Authors: Saksala Timo
Published: October 2010

This paper presents a numerical method for continuum modelling of the dynamic bit–rock interaction process in percussive drilling. The method includes a constitutive model based on a combination of the recent viscoplastic consistency model, the isotropic damage concept and a parabolic compression cap. The interaction between the drill bit and rock is modelled using contact mechanics by treating the bit as a rigid body. As the bit–rock interaction in percussive drilling is a transient event, the method is implemented in explicit dynamics FEM. The rock strength heterogeneity is characterized at the mesoscopic level statistically using the Weibull distribution. The bit–rock interaction is simulated under axisymmetric conditions using cylindrical and hemispherical buttons. The choice of the quite complex constitutive model accounting, e.g. for plastic compaction, viscoplastic shear and tensile failure along with induced damage and rate dependency is justified by numerical simulations. Moreover, the quasi‐static and dynamic cases are compared in plane strain simulations. Finally, some results clarifying the discrepancy of opinions found in the literature concerning the side (lateral) crack formation are obtained. Copyright © 2010 John Wiley & Sons, Ltd.
Diffuse failure in geomaterials: Experiments, theory and modelling
Authors: Daouadji A. , Darve F. , Al Gali H. , Hicher P. Y. , Laouafa F. , Lignon S. , Nicot F. , Nova R. , Pinheiro M. , Prunier F. , Sibille L. , Wan R.
Published: October 2010

This paper presents a synthesis of the works performed by various teams from France, Italy and Canada around the question of second‐order work criterion. Because of the non‐associative character of geomaterials plastic strains, it is now recognized that a whole bifurcation domain exists in the stress space with various possible modes of failure. In a first part these failure modes are observed in lab experimental tests and in discrete element modelling. Then a theoretical study of second‐order work allows to establish a link with the kinetic energy, giving a basis to explain the transition from a prefailure (quasi)static regime to a postfailure dynamic regime. Eventually the main features of geomaterials failure are obtained by applying second‐order work criterion to five different constitutive rate‐independent models—three being phenomenological and two micromechanical. As a whole this paper tries to gather together all the elements for a proper understanding and use of second‐order work criterion in geomechanics. Copyright © 2010 John Wiley & Sons, Ltd.
Warpage and countermeasure for injection‐molded in‐mold labeling parts
Authors: Larpsuriyakul Patcharee , Fritz Hans‐Gerhard
Published: October 2010

Decades ago, the production of packaging with the injection in‐mold labeling (IML) has been established. With this manufacturing technique, label and packaging, both are of the same polymeric material, become inseparably connected during the injection molding process. Because thermal conductivity of the polymeric label material is clearly smaller than that of the metal mold wall, thermal‐induced warpage of injected IML parts or part surface deformation could occur. In this study, structure and warpage behavior of IML parts, which are different from those of conventional molded parts without labels were intensively investigated. It was found that it is the volume contraction difference between label and substrate that forces IML parts to warp to the opposite side of the label. In addition, IML part warpage problem can be coped by varying the mold temperature on the stationary and moving mold platen. By increasing the mold temperature on the label side, the degree of IML part warpage can be reduced with acceptable reduction in mechanical properties. The optimum mold temperature range for particular substrate material, however, was found to be more decisive in maintaining the modulus of elasticity of IML parts than the magnitude of mold temperature difference. POLYM. ENG. SCI., 2011. © 2010 Society of Plastics Engineers
Telechelic polynorbornenes with hydrogen bonding moieties by direct end capping of living chains
Authors: Kurzhals Steffen , Binder Wolfgang H.
Published: October 2010

We present two novel symmetric olefins bearing hydrogen bonding moieties for the direct capping of living ring opening metathesis polymerization‐chains using Grubbs catalyst 1st‐ and 3rd‐generation. The symmetric olefins are generated via homo metathesis of the corresponding α‐olefins under aid of microwave irradiation and are used to prepare polynorbornene‐chains (Mn = 4,000–10,000 g/mol, Mw/Mn = 1.1–1.4) bearing barbiturate and thymine‐moieties. A qualitative and quantitative analysis of the generated polymers is done via MALDI‐TOF MS proving the introduction of hydrogen‐bonding moieties into the polymer chain and revealing the strong dependence of the desorption on the chemical structure of the different polymer species and high efficiencies for the end group introduction (90–99%). The efficiency of this process depends strongly on the reaction time and the equivalents of terminating agent with respect to the living end. The best results for the end group introduction are achieved by reacting the living chains with an excess of the terminating agent (5–20 equiv) for 100 h. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010
Reconstructing the pipeline by introducing multiplexed multiple reaction monitoring mass spectrometry for cancer biomarker verification: An NCI‐CPTC initiative perspective
Authors: Rodriguez Henry , Rivers Robert , Kinsinger Christopher , Mesri Mehdi , Hiltke Tara , Rahbar Amir , Boja Emily
Published: October 2010

Proteomics holds great promise in personalized medicine for cancer in the post‐genomic era. In the past decade, clinical proteomics has significantly evolved in terms of technology development, optimization and standardization, as well as in advanced bioinformatics data integration and analysis. Great strides have been made for characterizing a large number of proteins qualitatively and quantitatively in a proteome, including the use of sample fractionation, protein microarrays and MS. It is believed that differential proteomic analysis of high‐quality clinical biospecimen (tissue and biofluids) can potentially reveal protein/peptide biomarkers responsible for cancer by means of their altered levels of expression and/or PTMs. Multiple reaction monitoring, a multiplexed platform using stable isotope dilution‐MS with sensitivity and reproducibility approaching that of traditional ELISAs commonly used in the clinical setting, has emerged as a potentially promising technique for next‐generation high‐throughput protein biomarker measurements for diagnostics and therapeutics.
Methionyl‐tRNA synthetase from Caenorhabditis elegans: A specific multidomain organization for convergent functional evolution
Authors: Havrylenko Svitlana , Legouis Renaud , Negrutskii Boris , Mirande Marc
Published: October 2010

Methionyl‐tRNA synthetase (MetRS) is a multidomain protein that specifically binds tRNAMet and catalyzes the synthesis of methionyl‐tRNAMet. The minimal, core enzyme found in Aquifex aeolicus is made of a catalytic domain, which catalyzes the aminoacylation reaction, and an anticodon‐binding domain, which promotes tRNA–protein association. In eukaryotes, additional domains are appended in cis or in trans to the core enzyme and increase the stability of the tRNA–protein complexes. Eventually, as observed for MetRS from Homo sapiens, the C‐terminal appended domain causes a slow release of aminoacyl‐tRNA and establishes a limiting step in the global aminoacylation reaction. Here, we report that MetRS from the nematode Caenorhabditis elegans displays a new type of structural organization. Its very C‐terminal appended domain is related to the oligonucleotide binding‐fold‐based tRNA‐binding domain (tRBD) recovered at the C‐terminus of MetRS from plant, but, in the nematode enzyme, this domain is separated from the core enzyme by an insertion domain. Gel retardation and tRNA aminoacylation experiments show that MetRS from nematode is functionally related to human MetRS despite the fact that their appended tRBDs have distinct structural folds, and are not orthologs. Thus, functional convergence of human and nematode MetRS is the result of parallel and convergent evolution that might have been triggered by the selective pressure to invent processivity of tRNA handling in translation in higher eukaryotes.
Insights into Mycoplasma genitalium metabolism revealed by the structure of MG289, an extracytoplasmic thiamine binding lipoprotein
Authors: Sippel Katherine H. , Venkatakrishnan Balasubramanian , Boehlein Susan K. , Sankaran Banumathi , Quirit Jeanne G. , Govindasamy Lakshamanan , Agbandje‐McKenna Mavis , Goodison Steve , Rosser Charles J. , McKenna Robert
Published: October 2010

Mycoplasma genitalium is one of the smallest organisms capable of self‐replication and its sequence is considered a starting point for understanding the minimal genome required for life. MG289, a putative phosphonate substrate binding protein, is considered to be one of these essential genes. The crystal structure of MG289 has been solved at 1.95 Å resolution. The structurally identified thiamine binding region reveals possible mechanisms for ligand promiscuity. MG289 was determined to be an extracytoplasmic thiamine binding lipoprotein. Computational analysis, size exclusion chromatography, and small angle X‐ray scattering indicates that MG289 homodimerizes in a concentration‐dependant manner. Comparisons to the thiamine pyrophosphate binding homolog Cypl reveal insights into the metabolic differences between mycoplasmal species including identifying possible kinases for cofactor phosphorylation and describing the mechanism of thiamine transport into the cell. These results provide a baseline to build our understanding of the minimal metabolic requirements of a living organism. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Distinct second extracellular loop structures of the brain cannabinoid CB1 receptor: Implication in ligand binding and receptor function
Authors: Shim Joong‐Youn , Rudd James , Ding Tomas T.
Published: October 2010

The G‐protein‐coupled receptor (GPCR) second extracellular loop (E2) is known to play an important role in receptor structure and function. The brain cannabinoid (CB1) receptor is unique in that it lacks the interloop E2 disulfide linkage to the transmembrane (TM) helical bundle, a characteristic of many GPCRs. Recent mutation studies of the CB1 receptor, however, suggest the presence of an alternative intraloop disulfide bond between two E2 Cys residues. Considering the oxidation state of these Cys residues, we determine the molecular structures of the 17‐residue E2 in the dithiol form (E2dithiol) and in the disulfide form (E2disulfide) of the CB1 receptor in a fully hydrated 1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐3‐phosphocholine bilayer, using a combination of simulated annealing and molecular dynamics simulation approaches. We characterize the CB1 receptor models with these two E2 forms, CB1(E2dithiol) and CB1(E2disulfide), by analyzing interaction energy, contact number, core crevice, and cross correlation. The results show that the distinct E2 structures interact differently with the TM helical bundle and uniquely modify the TM helical topology, suggesting that E2 of the CB1 receptor plays a critical role in stabilizing receptor structure, regulating ligand binding, and ultimately modulating receptor activation. Further studies on the role of E2 of the CB1 receptor are warranted, particularly comparisons of the ligand‐bound form with the present ligand‐free form. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Structural and functional analysis of substrate recognition by the 250s loop in amylomaltase from Thermus brockianus
Authors: Jung Jong‐Hyun , Jung Tae‐Yang , Seo Dong‐Ho , Yoon Sei‐Mee , Choi Hyun‐Chang , Park Byoung Chul , Park Cheon‐Seok , Woo Eui‐Jeon
Published: October 2010

Amylomaltase, or 4‐α‐glucanotransferase (EC 2.4.1.25), is involved in glycogen and maltooligosaccharide metabolism in microorganisms, catalyzing both the hydrolysis and transfer of an α‐1,4‐oligosacchraride to other sugar molecules. In this study, we determined the crystal structure of amylomaltase from Thermus brockianus at a resolution of 2.3 Å and conducted a biochemical study to understand the detailed mechanism for its activity. Careful comparison with previous amylomaltase structures showed a pattern of conformational flexibility in the 250s loop with higher B‐factor. Amylomaltase from T. brockianus exhibited a high transglycosylation factor for glucose and a lower value for maltose. Mutation of Gln256 resulted in increased Km for maltotriose and a sharp decrease of the transglycosylation factor for maltose, suggesting the involvement of Gln 256 in substrate binding between subsites +1 and +2. Mutation of Phe251 resulted in significantly lower glucose production but increased maltose production from maltopentose substrates, showing an altered substrate‐binding affinity. The mutational data suggest the conformational flexibility of the loop may be involved in substrate binding in the GH77 family. Here, we present an action model of the 250s loop providing the molecular basis for the involvement of residues Phe251, Gln256, and Trp258 in the hydrolysis and transglycosylation activities in amylomaltase. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Structure of the Mycobacterium tuberculosis OmpATb protein: A model of an oligomeric channel in the mycobacterial cell wall
Authors: Yang Yinshan , Auguin Daniel , Delbecq Stéphane , Dumas Emilie , Molle Gérard , Molle Virginie , Roumestand Christian , Saint Nathalie
Published: October 2010

The pore‐forming outer membrane protein OmpATb from Mycobacterium tuberculosis is a virulence factor required for acid resistance in host phagosomes. In this study, we determined the 3D structure of OmpATb by NMR in solution. We found that OmpATb is composed of two independent domains separated by a proline‐rich hinge region. As expected, the high‐resolution structure of the C‐terminal domain (OmpATb198–326) revealed a module structurally related to other OmpA‐like proteins from Gram‐negative bacteria. The N‐terminal domain of OmpATb (73–204), which is sufficient to form channels in planar lipid bilayers, exhibits a fold, which belongs to the α+β sandwich class fold. Its peculiarity is to be composed of two overlapping subdomains linked via a BON (Bacterial OsmY and Nodulation) domain initially identified in bacterial proteins predicted to interact with phospholipids. Although OmpATb73–204 is highly water soluble, current–voltage measurements demonstrate that it is able to form conducting pores in model membranes. A HADDOCK modeling of the NMR data gathered on the major monomeric form and on the minor oligomeric populations of OmpATb73–204 suggest that OmpATb73–204 can form oligomeric rings able to insert into phospholipid membrane, similar to related proteins from the Type III secretion systems, which form multisubunits membrane‐associated rings at the basal body of the secretion machinery. Proteins 2011. © 2010 Wiley‐Liss, Inc.
On the high temperature transport properties of thermoelectric oxides
Authors: Dragoe Nita , Berardan David , Byl Celine
Published: October 2010

Thermoelectric modules have been the subject of recent scientific interest, in part due to their remarkable potential applications, such as waste heat recovery systems for automotive applications, industrial thermal power stations, etc. Based on their superior thermal stability in air, oxides have been considered the material of choice for these high temperature applications, even though they display reduced efficiency compared to semimetals. Here we show that oxides are rather unstable at high temperature and that severe changes can occur even during measurement of their physical properties. We propose that cycling measurements should be done when reporting high temperature transport properties of materials.
Resonant Raman scattering on carbon nanotubes covalently functionalized with lithium decyne
Authors: Müller M. , Meinke R. , Maultzsch J. , Gebhardt B. , Hauke F. , Hirsch A. , Thomsen C.
Published: October 2010

We present resonant Raman measurements on single‐walled carbon nanotubes covalently functionalized with lithium decyne. We study the influence of the functional moieties on the optical transitions of the nanotubes. From the extracted resonance profiles of the radial breathing modes the chiral indices of the corresponding tubes are assigned. Slight red shifts of the optical transitions are observed, which implies only a little charge transfer due to the chemical reaction. The reaction shows a pronounced diameter dependence as previously observed for comparable reactions with different addends.

Carbon nanotubes covalently functionalized with decyne moieties.

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Temperature dependent band gap behavior and excitons in metallic carbon nanotubes
Authors: May Patrick , Telg Hagen , Thomsen Christian , Maultzsch Janina
Published: October 2010

Resonant Raman spectroscopy is used to investigate the temperature dependence of the optical transitions of metallic and semiconducting nanotubes. While the semiconducting nanotubes show an approximately linear temperature dependence as known for bulk semiconductors, the metallic nanotubes show a different temperature dependent behavior with a non‐monotonic dependence of the transition energy on the temperature. This result can be attributed to dissociation of bound electron–hole pairs (excitons), leading to a quasi band‐to‐band transition.

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First optical transition $E_{11}^{{\rm M}} $ of metallic nanotubes and sketch of a metallic (13,1) tube.
The Applications of ‘active packaging and chlorine dioxide’ for extended shelf life of fresh strawberries
Authors: Aday Mehmet Seckin , Caner Cengiz
Published: October 2010

Fresh strawberries are highly perishable because of their high respiration rates. Three alternative packaging approaches were investigated to maintain the high quality and to extend the shelf life of strawberries. These were active packaging using chlorine dioxide (ClO2) and ethylene‐moisture sachets. The quality properties of four groups of samples were measured over 3 weeks at 4°C. The groups were: control, active packaging without ClO2 treatment, active packaging with low‐dose (5 ppm) ClO2 treatment and active packaging with high‐dose (10 ppm) ClO2 treatment. Measured properties were weight loss, gas concentration, pH, titratable acidity (TA), soluble solids content, texture profile and colour. Active packaging with low‐dose (5 ppm) ClO2 treatment was found to be the most effective for TA retention and for maintaining (L) brightness values. The control group showed the largest total soluble solids reduction from 7.60 to 6.57. Active packaging without ClO2 treatment showed the lowest weight loss (0.33%), while the control group showed the highest (1.86%) at the end of the storage.

Active packaging with high‐dose ClO2 treatment showed the highest preference value in global appearance, colour and firmness properties. The low‐ and high‐dose active packaging groups had greater firmness, gumminess and chewiness than that of all other treatments. The results from this study showed that active packaging treatment with ClO2 and the ethylene‐moisture sachets had a beneficial effect on the quality of strawberries and could be used commercially. Copyright © 2010 John Wiley & Sons, Ltd.
Idealized modelling of landfalling cold fronts
Authors: Muir Les C. , Reeder Michael J.
Published: October 2010

The effects of land surfaces, sea surfaces and coastlines on the dynamics of cold fronts are examined in an idealised two‐dimensional confluent deformation model of frontogenesis. When the deformation field is stationary, increasing the surface roughness weakens the fronts, while increasing the cross‐front ageostrophic wind and frontal updraughts. The frontogenetic effect of deformation balances the frontolytic effect of turbulent mixing, resulting in near‐steady‐state fronts. In steady state, the surface fronts are located near the point at which the cross‐front flow vanishes. This equilibrium point moves towards the warm air as the surface roughness is increased because the cross‐front ageostophic wind also increases with increasing surface roughness. Surface sensible heating weakens and slows the fronts during the day, whereas surface sensible cooling strengthens and accelerates them at night. Adding a coastline to the model results in very strong gravity‐current‐like fronts in the afternoon with a relative flow of cool air towards their leading edge. Above the boundary layer, the synoptic fronts remain unaffected by the coastline. As the turbulent mixing weakens in the late afternoon, the coastal fronts surge inland, advancing faster than the wind speed in the boundary layer. When the deformation field is allowed to translate, the fronts advance across the ocean towards land. If the fronts reach the coastline between mid‐morning and late afternoon, the daytime heating over the land opposes the onshore advection of cold air, retarding the fronts at the coastline. If the fronts reach the coastline in the evening or early morning, they advance onshore relatively unimpeded. Hence, the fronts arrive onshore preferentially in the late afternoon or evening. Copyright © 2010 Royal Meteorological Society
Recent progress in chiral photonic band‐gap liquid crystals for laser applications
Authors: Furumi Seiichi
Published: October 2010

This article describes a brief review of recent research advances in chiral liquid crystals (CLCs) for laser applications. The CLC molecules have an intrinsic capability to spontaneously organize supramolecular helical assemblages consisting of liquid crystalline layers through their helical twisting power. Such CLC supramolecular helical structures can be regarded as one‐dimensional photonic crystals (PhCs). Owing to their supramolecular helical structures, the CLCs show negative birefringence along the helical axis. Selective reflection of circularly polarized light is the most unique and important optical property in order to generate internal distributed feedback effect for optically‐excited laser emission. When a fluorescent dye is embedded in the CLC medium, optical excitation gives rise to stimulated laser emission peak(s) at the band edge(s) and/or within the CLC selective reflection. Furthermore, the optically‐excited laser emission peaks can be controlled by external stimuli through the self‐organization of CLC molecules. This review introduces the research background of CLCs carried out on the PhC realm, and highlights intriguing precedents of various CLC materials for laser applications. It would be greatly advantageous to fabricate active CLC laser devices by controlling the supramolecular helical structures. Taking account of the peculiar features, we can envisage that a wide variety of supramolecular helical structures of CLC materials will play leading roles in next‐generation optoelectronic molecular devices. © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.201000013
Dual–systems and the development of reasoning: competence–procedural systems
Authors: Overton Willis F. , Ricco Robert B.
Published: October 2010

Dual‐system, dual‐process, accounts of adult cognitive processing are examined in the context of a self‐organizing relational developmental systems approaches to cognitive growth. Contemporary adult dual‐process accounts describe a linear architecture of mind entailing two split‐off, but interacting systems; a domain general, content‐free ‘analytic’ system (system 2) and a domain specific highly contextualized ‘heuristic’ system (system 1). In the developmental literature on deductive reasoning, a similar distinction has been made between a domain general competence (reflective, algorithmic) system and a domain specific procedural system. In contrast to the linear accounts offered by empiricist, nativist, and/or evolutionary explanations, the dual competence–procedural developmental perspective argues that the mature systems emerge through developmental transformations as differentiations and intercoordinations of an early relatively undifferentiated action matrix. This development, whose microscopic mechanism is action‐in‐the‐world, is characterized as being embodied, nonlinear, and epigenetic. WIREs Cogni Sci 2011 2 231–237 DOI: 10.1002/wcs.120

This article is categorized under:

Psychology > Development and Aging
Psychology of auditory perception
Authors: Lotto Andrew , Holt Lori
Published: October 2010

Audition is often treated as a ‘secondary’ sensory system behind vision in the study of cognitive science. In this review, we focus on three seemingly simple perceptual tasks to demonstrate the complexity of perceptual–cognitive processing involved in everyday audition. After providing a short overview of the characteristics of sound and their neural encoding, we present a description of the perceptual task of segregating multiple sound events that are mixed together in the signal reaching the ears. Then, we discuss the ability to localize the sound source in the environment. Finally, we provide some data and theory on how listeners categorize complex sounds, such as speech. In particular, we present research on how listeners weigh multiple acoustic cues in making a categorization decision. One conclusion of this review is that it is time for auditory cognitive science to be developed to match what has been done in vision in order for us to better understand how humans communicate with speech and music. WIREs Cogni Sci 2011 2 479–489 DOI: 10.1002/wcs.123

This article is categorized under:

Psychology > Perception and Psychophysics