bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy
Authors: Brownridge Philip , Holman Stephen W. , Gaskell Simon J. , Grant Christopher M. , Harman Victoria M. , Hubbard Simon J. , Lanthaler Karin , Lawless Craig , O'cualain Ronan , Sims Paul , Watkins Rachel , Beynon Robert J. 
Published: June 2011

AbstractIn this paper, we discuss the challenge of large‐scale quantification of a proteome, referring to our programme that aims to define the absolute quantity, in copies per cell, of at least 4000 proteins in the yeast Saccharomyces cerevisiae. We have based our strategy on the well‐established method of stable isotope dilution, generating isotopically labelled peptides using QconCAT technology, in which artificial genes, encoding concatenations of tryptic fragments as surrogate quantification standards, are designed, synthesised de novo and expressed in bacteria using stable isotopically enriched media. A known quantity of QconCAT is then co‐digested with analyte proteins and the heavy:light isotopologues are analysed by mass spectrometry to yield absolute quantification. This workflow brings issues of optimal selection of quantotypic peptides, their assembly into QconCATs, expression, purification and deployment.
Functional analysis of novel phosphorylation sites of CREB‐binding protein using mass spectrometry and mammalian two‐hybrid assays
Authors: Xia Zanxian , Guo Mingquan , Ma Hong 
Published: June 2011

AbstractIn the Wnt/β‐catenin pathway, p300/CBP (CREB‐binding protein) is recruited by nuclear β‐catenin to regulate a wide array of T‐cell factor (TCF)‐dependent gene expression. Previous studies have indicated that CBP/β‐catenin complex‐mediated transcription is critical for cell proliferation. Both CBP and β‐catenin are phosphoproteins. The interaction domain has been mapped to the N‐terminal region of CBP (amino acids 1–111) and the C‐terminal region of β‐catenin, but it is unclear whether phosphorylation on specific residues of these regions is required for the interaction. To address this unmet challenge, phosphoproteomic profile of the critical N‐terminus of CBP was determined by utilizing TiO2 affinity chromatography followed by LC‐MS/MS analysis. Two unique and novel phosphorylation sites Ser77 and Ser92 were identified. Further studies aided by site‐directed mutagenesis, immunoprecipitation and mammalian two‐hybrid assay have concluded that the phosphorylation of a Proline‐directed Ser92 residue modulates the selective binding ability of CBP with β‐catenin. The specific Mitogen‐activated protein kinase inhibitor PD98059, which promotes cell cycle G1 arrest, concomitantly inhibits the interaction, and the evidences suggest that the MEK/ERK (extracellular signal‐regulated kinase) cascade activation is the upstream signal required for Ser92 phosphorylation, leading to enhancement of the interaction of CBP with β‐catenin.
Atom transfer radical polymerization synthesis and photoresponsive solution behavior of spiropyran end‐functionalized polymers as simplistic molecular probes
Authors: Ventura Claudia , Byrne Robert , Audouin Fabrice , Heise Andreas 
Published: June 2011

AbstractPoly(methyl methacrylate)s (PMMAs) of two different molecular weights having a single photochromic benzospiropyran (BSP) end‐group were synthesized by atom transfer radical polymerization (ATRP). Polymer characterization by 1H NMR and matrix‐assisted laser desorption/ionitiation time of flight‐mass spectroscopy confirms that using an ATRP initiator equipped with BSP, a near quantitative functionalization of the PMMA with the BSP was achieved. Both polymers exhibit photochroism characterized by the UV‐induced transition from BSP to benzomerocyanine (BMC) in acetonitrile. However, a strong molecular weight dependence of the thermal relaxation kinetic of the BMC was found with a significantly faster temperature‐dependent transition for the higher molecular weight polymer. Thermodynamic analysis of the process revealed a higher gain in the entropy of activation ΔS± for the transition process in the higher molecular weight polymer. This suggests an energetically unfavorable nonpolar environment of the BMC group in the higher molecular weight polymers, although a higher solvation of the BMC in the lower molecular weight polymer contributes to its stabilization. The ability of the BMC polymer end‐groups to organize was shown in metal ion‐binding experiments forming bivalently linked complexes with Co ions. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Versatile synthesis of asymmetrical dendron‐like/dendron‐like poly(ε‐caprolactone)‐b‐poly(γ‐benzyl‐L‐glutamate) block copolymers
Authors: Liu Wei , Dong Chang‐Ming 
Published: June 2011

AbstractDendron‐like/dendron‐like poly(ε‐caprolactone)‐b‐poly(γ‐benzyl‐L‐glutamate) block copolymers with asymmetrical topology (PCL‐b‐PBLGn, both the subscript and the superscript denote the degree of polymerization and the branch number, respectively; n = 1, 2, and 4) were synthesized by combining ring‐opening polymerization (ROP) and click chemistry. The dendron‐like propargyl focal point PCL precursor with eight branches was synthesized from the controlled ROP of ε‐caprolactone, and then click conjugated with azido focal point poly(amido amine) dendrons to generate the PCL‐dendrons with multiple primary amine groups. The PCL‐dendrons were further used as macroinitiators for the ROP of γ‐benzyl‐L‐glutamate N‐carboxyanhydride to produce the targeted asymmetrical block copolymers. Their molecular structures and physicochemical properties were thoroughly characterized by means of FT‐IR, 1H NMR, gel permeation chromatography, differential scanning calorimetry, and wide angle X‐ray diffraction. Both the maximal melting temperature and the degree of crystallinity of PCL block within copolymers decreased with increasing the PBLG branches and/or the chain length, demonstrating that the crystallinity of PCL block was progressively suppressed by PBLG block. Meanwhile, the PBLG block within copolymers progressively transformed from β‐sheet to α‐helical conformation with increasing the PBLG chain length. Consequently, this provides a versatile strategy for the synthesis of biodegradable and biomimetic block copolymers with asymmetrical dendritic topology. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Liquid crystalline dendrimers containing photoactive cinnamate units
Authors: Viñuales Ana I. , Serrano Jose Luis , Giménez Raquel , Piñol Milagros , Tomczyk Jaroslaw , Stumpe Joachim 
Published: June 2011

AbstractCinnamate‐containing dendrimers have been prepared by peripheral functionalization of the amine groups of a poly(propyleneimine) dendrimer with 4‐methoxycinnamate‐ or 4‐(N,N‐dimethylamino)cinnamate‐derived units and/or 4‐cyanobiphenyl units in different proportions. The synthesis, full characterization in solution, thermal properties and optical properties of the novel monomers, homodendrimers and codendrimers are reported. The composition of the molecular structure of the codendrimers has been elucidated by matrix assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS). These liquid crystalline dendrimers display lamellar SmA mesophases. The codendrimers have been tailored in such a way that the photoactive units and the liquid crystal units absorb in different regions in order to allow better control over the processes induced by light. Linearly polarized UV light irradiation studies performed on thin films of the cinnamate codendrimers show that they are photoresponsive. A photoinduced anisotropy is generated with increasing exposure time, but in‐plane amplification of anisotropy by thermal annealing in the mesophase was not observed. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Synthesis of π‐conjugated copolymers composed of benzo[2,1,3]thiadiazole and thiophene units bearing various alkyl groups and their application to photovoltaic cells
Authors: Lee Kwang‐Hoi , Lee Ho‐Jin , Kuramoto Kouji , Tanaka Yohei , Morino Kazuhide , Sudo Atsushi , Okauchi Tatsuo , Tsuge Akihiko , Endo Takeshi 
Published: June 2011

Abstractπ‐Conjugated polymers, PTOTBT, PTEHTBT, and PTt‐BTBT, composed of benzothiadiazole as an electron accepting unit and terthiophene as an electron donating unit in the backbone were prepared. PTOTBT, PTEHTBT, and PTt‐BTBT contained side chain groups of n‐octyl, 2‐ethylhexyl, and t‐butyl groups, respectively. Solubility, optical and thermal properties of the polymers showed strong dependences on their side chain groups. PTEHTBT having 2‐ethylhexyl groups in the side chain exhibited absorption maximum (λmax) at longer wavelength (565 nm) than PTOTBT (534 nm) and PTt‐BTBT (495 nm). PTOTBT showed higher thermal stability than the others. The prepared polymers were employed to polymer solar cells (PSCs) with a configuration of ITO/PEDOT‐PSS/polymer: PC61BH/LiF/Al. Power conversion efficiency of the PSC‐based on PTEHTBT was 1.32%. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Synthesis and structure‐activity relationship of several aromatic ketone‐based two‐photon initiators
Authors: Li Zhiquan , Siklos Marton , Pucher Niklas , Cicha Klaus , Ajami Aliasghar , Husinsky Wolfgang , Rosspeintner Arnulf , Vauthey Eric , Gescheidt Georg , Stampfl Jürgen , Liska Robert 
Published: June 2011

AbstractSeveral novel aromatic ketone‐based two‐photon initiators containing triple bonds and dialkylamino groups were synthesized and the structure‐activity relationships were evaluated. Branched alkyl chains were used at the terminal donor groups to improve the solubility in the multifunctional monomers. Because of the long conjugation length and good coplanarity, the evaluated initiators showed large two‐photon cross section values, while their fluorescence lifetimes and quantum yields strongly depend on the solvent polarity. All novel initiators exhibited high activity in terms of two‐photon‐induced microfabrication. This is especially true for fluorenone‐based derivatives, which displayed much broader processing windows than well‐known highly active initiators from the literature and commercially available initiators. While the new photoinitiators gave high reactivity in two‐photon‐induced photopolymerization at concentration as low as 0.1% wt, these compounds are surprisingly stable under one photon condition and nearly no photo initiation activity was found in classical photo DSC experiment. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Molecular dynamics simulations of the effects of carbon dioxide on the interfacial bonding of polystyrene thin films
Authors: Alleman Coleman , Srivastava Anand , Ghosh Somnath 
Published: June 2011

AbstractFabrication of nanoscale polymer‐based devices, especially in biomedical applications, is a challenging process due to requirements of precise dimensions. Methods that involve elevated temperature or chemical adhesives are not practicable due to the fragility of the device components and associated deformation. To effectively fabricate devices for lab‐on‐a‐chip or drug delivery applications, a process is required that permits bonding at low temperatures. The use of carbon dioxide (CO2) to assist the bonding process shows promise in reaching this goal. It is now well established that CO2 can be used to depress the glass transition temperature (Tg) of a polymer, allowing bonding to occur at lower temperatures. Furthermore, it has been shown that CO2 can preferentially soften a polymer surface, which should allow for effective bonding at temperatures even below the bulk Tg. However, the impact of this effect on bonding has not been quantified, and the optimal bonding temperature and CO2 pressure conditions are unknown. In this study, a molecular dynamics model is used to examine the atomic scale behavior of polystyrene in an effort to develop understanding of the physical mechanisms of bonding and to quantify how the process is impacted by CO2. The final result is the identification of a range of CO2 pressure conditions which produce the strongest bonding between PS thin films at room temperature. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011
Identification of Ternary Phases in TiBC/a‐C Nanocomposite Thin Films: Influence on the Electrical and Optical Properties
Authors: Abad Manuel David , Sanjinés Rosendo , Endrino Jose Luis , Gago Raúl , Andersson Joakim , Sánchez‐López Juan Carlos 
Published: June 2011

AbstractThe local structure of TiBC and amorphous carbon (a‐C) nanocomposite films (TiBC/a‐C) was correlated with their optical and electrical properties. TiBC/a‐C films with increasing C content were deposited by magnetron co‐sputtering from TiC:TiB2 (60:40) and graphite targets. Chemical composition is determined by electron energy‐loss spectroscopy. Grazing incidence X‐ray diffraction reveals that the microstructure of the films is amorphous with small nanocrystallites emerging by increasing the C content that could be attributed to the formation of ternary (TiBxCy) or mixed binary (TiB2 and TiC) phases. Further information was then obtained by studying the chemical bonding by measuring the near‐edge fine structure (NES) by electron energy‐loss (B K‐, C K‐, and Ti L‐edges) and X‐ray absorption (B K‐ and Ti L‐edges) spectroscopies. The NES analysis indicates the formation of a nanocrystalline ternary TiBxCy compound concomitant with the segregation of an a‐C phase as the carbon content is increased. The optical properties were studied by spectroscopic ellipsometry and the electrical resistivity was measured by the Van der Pauw method between 20 and 300 K. The films continuously lose their metallic character in terms of optical constants and resistivity with increasing carbon content. Theoretical fitting of the electrical properties using the grain‐boundary scattering model supported the formation of a nanocomposite structure based on a ternary TiBxCy phase embedded in a matrix of a‐C. The electron transport properties are mainly limited by the high density of point defects, grain size, and transmission probability. magnified image
A designed redox‐controlled caspase
Authors: Witkowski Witold A. , Hardy Jeanne A. 
Published: June 2011

AbstractCaspases are a powerful class of cysteine proteases. Introduction of activated caspases in healthy or cancerous cells results in induction of apoptotic cell death. In this study, we have designed and characterized a version of caspase‐7 that can be inactivated under oxidizing extracellular conditions and then reactivated under reducing intracellular conditions. This version of caspase‐7 is allosterically inactivated when two of the substrate‐binding loops are locked together via an engineered disulfide. When this disulfide is reduced, the protein regains its full function. The inactive loop‐locked version of caspase‐7 can be readily observed by immunoblotting and mass spectrometry. The reduced and reactivated form of the enzyme observed crystallographically is the first caspase‐7 structure in which the substrate‐binding groove is properly ordered even in the absence of an active‐site ligand. In the reactivated structure, the catalytic‐dyad cysteine–histidine are positioned 3.5 Å apart in an orientation that is capable of supporting catalysis. This redox‐controlled version of caspase‐7 is particularly well suited for targeted cell death in concert with redox‐triggered delivery vehicles.
Integration of cell‐free protein coexpression with an enzyme‐linked immunosorbent assay enables rapid analysis of protein–protein interactions directly from DNA
Authors: Layton Curtis J. , Hellinga Homme W. 
Published: June 2011

AbstractAssays that integrate detection of binding with cell‐free protein expression directly from DNA can dramatically increase the pace at which protein–protein interactions (PPIs) can be analyzed by mutagenesis. In this study, we present a method that combines in vitro protein production with an enzyme‐linked immunosorbent assay (ELISA) to measure PPIs. This method uses readily available commodity instrumentation and generic antibody–affinity tag interactions. It is straightforward and rapid to execute, enabling many interactions to be assessed in parallel. In traditional ELISAs, reporter complexes are assembled stepwise with one layer at a time. In the method presented here, all the members of the reporter complex are present and assembled together. The signal strength is dependent on all the intercomponent interaction affinities and concentrations. Although this assay is straightforward to execute, establishing proper conditions and analysis of the results require a thorough understanding of the processes that determine the signal strength. The formation of the fully assembled reporter sandwich can be modeled as a competition between Langmuir adsorption isotherms for the immobilized components and binding equilibria of the solution components. We have shown that modeling this process provides semiquantitative understanding of the effects of affinity and concentration and can guide strategies for the development of experimental protocols. We tested the method experimentally using the interaction between a synthetic ankyrin repeat protein (Off7) and maltose‐binding protein. Measurements obtained for a collection of alanine mutations in the interface between these two proteins demonstrate that a range of affinities can be analyzed.
Comparative functional analysis of the human macrophage chitotriosidase
Authors: Vandevenne Marylène , Campisi Vincent , Freichels Astrid , Gillard Carole , Gaspard Gilles , Frère Jean‐Marie , Galleni Moreno , Filée Patrice 
Published: June 2011

AbstractThis work analyses the chitin‐binding and catalytic domains of the human macrophage chitotriosidase and investigates the physiological role of this glycoside hydrolase in a complex mechanism such as the innate immune system, especially its antifungal activity. Accordingly, we first analyzed the ability of its chitin‐binding domain to interact with chitin embedded in fungal cell walls using the β‐lactamase activity reporter system described in our previous work. The data showed that the chitin‐binding activity was related to the cell wall composition of the fungi strains and that their peptide‐N‐glycosidase/zymolyase treatments increased binding to fungal by increasing protein permeability. We also investigated the antifungal activity of the enzyme against Candida albicans. The antifungal properties of the complete chitotriosidase were analyzed and compared with those of the isolated chitin‐binding and catalytic domains. The isolated catalytic domain but not the chitin‐binding domain was sufficient to provide antifungal activity. Furthermore, to explain the lack of obvious pathologic phenotypes in humans homozygous for a widespread mutation that renders chitotriosidase inactive, we postulated that the absence of an active chitotriosidase might be compensated by the expression of another human hydrolytic enzyme such as lysozyme. The comparison of the antifungal properties of chitotriosidase and lysozyme indicated that surprisingly, both enzymes have similar in vitro antifungal properties. Furthermore, despite its more efficient hydrolytic activity on chitin, the observed antifungal activity of chitotriosidase was lower than that of lysozyme. Finally, this antifungal duality between chitotriosidase and lysozyme is discussed in the context of innate immunity.
High resolution at low beam energy in the SEM: resolution measurement of a monochromated SEM
Authors: Michael Joseph R. 
Published: June 2011

AbstractThe resolution of secondary electron low beam energy imaging of a scanning electron microscope equipped with a monochromator is quantitatively measured using the contrast transfer function (CTF) method. High‐resolution images, with sub‐nm resolutions, were produced using low beam energies. The use of a monochromator is shown to quantitatively improve the resolution of the SEM at low beam energies by limiting the chromatic aberration contribution to the electron probe size as demonstrated with calculations and images of suitable samples. Secondary electron image resolution at low beam energies is ultimately limited by noise in the images as shown by the CTFs. SCANNING 33: 147–154, 2011. © 2011 Wiley Periodicals, Inc.
Science, engineering, and technology in the policy process for mitigating natural–societal risk
Authors: Taylor Timothy R. B. , Ford David N. , Yvon‐Lewis Shari A. , Lindquist Eric 
Published: June 2011

AbstractIncreased societal risks due to the anthropogenic degradation of natural systems often require public policy action to mitigate. For example, increased skin cancer risks associated with anthropogenic stratospheric ozone depletion led to public policies limiting the emission of many ozone‐depleting substances. Natural–societal system interaction is complex and often requires expert knowledge and technology to develop effective and sustainable societal risk mitigation policies. However, available knowledge and technology are not always successful in increasing policy makers' attention to or understanding of these risks. The current work uses a system dynamics model of a feedback system that describes the stratospheric ozone depletion case to identify high leverage points for domain experts to influence policy makers in addressing risks posed by changes in a natural system. Model analysis suggests that the rate at which policy makers' attention to natural system risk is increased has a significant influence on the development of knowledge and technology and the ability of policy makers to mitigate societal risks. Copyright © 2011 System Dynamics Society.
High energy resolution Auger spectroscopy on a CMA instrument
Authors: Watson D. G. , Larson P. E. , Paul D. F. , Negri R. E. 
Published: June 2011

AbstractAn experimental method that increases the analyzer resolution of cylindrical mirror analyzer CMA‐based Auger spectrometers is described. By means of electrically biasing the sample, the effective energy resolution obtainable from the CMA instrument is improved from the native 0.5 to 0.1% or even better for higher kinetic energy Auger transitions. In addition, the maximum kinetic energy Auger transition observable by the CMA Auger instrument is increased from 3200 to 5700 eV, in the current realization. It is also shown that the sensitivity of the energy scale calibration to sample working distance with respect to the analyzer is simultaneously reduced, making the method suitable for chemical surface analysis. The biasing is accomplished using a special sample holder with electronics and software that can be added to an existing instrument. The overall capability of the Auger instrument for chemical analysis is, therefore, increased, while preserving all the analytical functionality and features of the CMA. Copyright © 2011 John Wiley & Sons, Ltd.