bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real‐Time Analysis of Enzymatic Surface‐Initiated Polymerization Using Surface Plasmon Resonance (SPR)
Authors: Kim Young‐Rok , Paik Hyun‐jong , Ober Christopher K. , Coates Geoffrey W. , Mark Sonny S. , Ryan Thomas E. , Batt Carl A. 
Published: January 2006

AbstractSummary: The kinetics of enzymatic surface‐initiated polymerization of PHB on gold surface has been examined by SPR and the resultant polymer layers characterized by AFM and FT‐IR spectrometry. The immobilized enzyme catalyzed surface‐initiated polymerization of 3HB‐CoA, resulting in the formation of a polymer brush on the surface. The rate of polymer growth from the surface was monitored by SPR in real‐time. Polymer growth as measured by the increase in the resonance angle showed no apparent lag phase during the polymerization reaction. SPR analysis also revealed that the thickness of the polymer film could be controlled by varying the initial enzyme density on the surface. The average thicknesses of the PHB film after polymerization reaction were 95, 45 and 15 nm for the surfaces that were treated with 0.5, 0.3 and 0.1*10−6 M of enzyme, respectively.The binding of PHA synthase at different concentration to the mixed SAMs and subsequent polymerization.magnified imageThe binding of PHA synthase at different concentration to the mixed SAMs and subsequent polymerization.
Global attractor for heat convection problem in a micropolar fluid
Authors: Tarasińska Agnieszka 
Published: January 2006

AbstractThe article is devoted to describe asymptotics in the heat convection problem for a micropolar fluid in two dimensions. We show the existence and the uniqueness of global in time solutions and then prove the existence of a global attractor for considered model. Next, the Hausdorff dimension of the global attractor is estimated. Copyright © 2006 John Wiley & Sons, Ltd.
Analysis of a novel preconditioner for a class of p‐level lower rank extracted systems
Authors: Salapaka S. , Peirce A. 
Published: January 2006

AbstractThis paper proposes and studies the performance of a preconditioner suitable for solving a class of symmetric positive definite systems, Âx=b, which we call p‐level lower rank extracted systems (p‐level LRES), by the preconditioned conjugate gradient method. The study of these systems is motivated by the numerical approximation of integral equations with convolution kernels defined on arbitrary p‐dimensional domains. This is in contrast to p‐level Toeplitz systems which only apply to rectangular domains. The coefficient matrix, Â, is a principal submatrix of a p‐level Toeplitz matrix, A, and the preconditioner for the preconditioned conjugate gradient algorithm is provided in terms of the inverse of a p‐level circulant matrix constructed from the elements of A. The preconditioner is shown to yield clustering in the spectrum of the preconditioned matrix which leads to a substantial reduction in the computational cost of solving LRE systems. Copyright © 2006 John Wiley & Sons, Ltd.
Poly(amide imide)s and poly(amide imide) composite membranes by interfacial polymerization
Authors: Buch Premang R , Mohan D Jagan , Reddy Alamuru VR 
Published: January 2006

AbstractNovel amic acid diamines (AADs) (2‐carboxyterephthalamido‐bis(alkyl or aryl amine)s, H2NXNH(O)CC6H3(COOH)C(O)NHXNH2, where X is
magnified image were synthesized by reacting trimellitic anhydride chloride with aromatic or aliphatic diamines in dimethylformamide at 5–10 °C. Poly(amide imide)s (PAIs) with an amide to imide ratio of three in the polymer chains were prepared by interfacial polycondensation of the AADs in aqueous alkaline solution with isophthaloyl chloride or terephthaloyl chloride in dichloromethane at ambient temperature to form poly(amide amic acid)s, followed by their subsequent thermal cycloimidization. All of the PAIs were soluble in polar aprotic solvents such as dimethylformamide, dimethylacetamide, dimethyl sulfoxide and N‐methylpyrrolidone, and have inherent viscosities in the range 0.15–0.48 dL g−1. The polymers were characterized by IR and NMR spectroscopy, TGA and DSC techniques. The PAIs have initial decomposition temperatures in the range 250–460 °C in air, and glass transition temperatures of 128–320 °C, depending upon the structures of the monomers. Composite membranes containing a poly(amide amic acid) and poly(amide imide) barrier layer on the top of a porous polyethersulfone support were prepared by in situ interfacial polymerization of the AADs in aqueous alkaline solution with trimesoyl chloride in hexane, and subsequent curing. The performances of these membranes were evaluated by using aqueous feed solutions containing 2000 ppm NaCl, Na2SO4 or CaCl2. Copyright © 2006 Society of Chemical Industry
Introduction of unusual properties into polymers by the use of liquid‐crystalline moieties
Authors: Palaprat G , Weyland M , Phou T , Binet C , Marty JD , Mingotaud AF , Mauzac M 
Published: January 2006

AbstractThe introduction of mesogenic substituents on polymer backbones facilitates the formation of materials with anisotropic properties. At the same time the polymer chains are connected each other through these substituents in a transient network. The properties of the polymer material, such as the mechanical response or conductivity, are modified by the presence of the liquid‐crystalline groups and can be tuned by changing the organisation of the mesogenic groups. Crosslinking the polymer in the liquid‐crystalline state induces the manifestation of some memory effect. These phenomena were used for improving the mechanisms of recognition in molecular imprinted materials. Copyright © 2006 Society of Chemical Industry
Ring‐opening polymerization of ε‐caprolactone initiated by rare earth alkoxides and borohydrides: a comparative study
Authors: Palard Isabelle , Schappacher Michèle , Soum Alain , Guillaume Sophie M 
Published: January 2006

AbstractThe polymerization of ε‐caprolactone initiated by trivalent rare earth (Ln) derivatives, namely the isopropoxide ‘Ln(OiPr)3’ opposed to the borohydride Ln(BH4)3(THF)3 (Ln = La, Nd, Sm) and (Cp*)2Sm(BH4)(THF) (Cp* = (η‐C5Me5)), has been evaluated. The comparison, based on the structure of the initiator and on the polymerization features (molar mass, molar mass distribution, side reactions) reveals some differences especially in the number of active polymer chains per metal and in the occurrence of some transfer reactions with Ln(BH4)3(THF)3. Polymerizations performed with borohydride derivatives lead to a gel as a result of van der Waals interactions, while the reaction medium remains fluid with the alkoxide species. A typical coordination‐insertion mechanism with oxygen‐acyl bond cleavage of the monomer prevails with both types of initiators. However, while the alkoxide complexes lead to α,ω‐hydroxyalkoxypoly(ε‐caprolactone), the borohydride compounds allow the synthesis of α,ω‐dihydroxypoly(ε‐caprolactone). Both polymerization processes are well controlled under specific conditions. Copyright © 2006 Society of Chemical Industry
Use of a fluorescent internal protein standard to achieve quantitative two‐dimensional gel electrophoresis
Authors: Wheelock Åsa M. , Morin Dexter , Bartosiewicz Matthew , Buckpitt Alan R. 
Published: January 2006

Abstract2‐DE is a powerful separation method for complex protein mixtures. However, large intergel variations in spot intensity limit its use for quantitative proteomics studies. To address this issue, we developed a fluorescent internal protein standard for use in 2‐DE analysis. Protein samples are spiked with an Alexa‐labeled internal standard (ALIS) prior to separation with 2‐DE. Due to the high extinction coefficient of the Alexa‐fluor, incorporation of 0.1% of total protein is sufficient to allow visualization of the internal standard yet low enough to avoid interference in subsequent quantification and identification steps. Following 2‐DE, total proteins are visualized with fluorescent postelectrophoretic stains spectrally separated from ALIS. Four protein stains, Deep Purple, Sulforhodamine G, ruthenium II‐tris(bathophenanthroline disulfonate) (RuTBS), and SYPRO Ruby, including improved purification and staining protocols for RuTBS and ten‐fold dilutions of SYPRO Ruby were evaluated. All staining protocols were compatible with the ALIS method and had similar LODs (1–4 ng) and dynamic ranges (103). ALIS is a powerful normalization method for quantitative 2‐DE which avoids potential problems associated with dual spot migration patterns observed in the DIGE method. Furthermore, ALIS provides significantly improved normality in the distribution of spot abundance‐variance compared to normalization through division by the total spot volume.
Proteomic and SAGE profiling of murine melanoma progression indicates the reduction of proteins responsible for ROS degradation
Authors: de Souza Gustavo A. , Godoy Lyris M. F. , Teixeira Veronica R. , Otake Andreia H. , Sabino Adão , Rosa José C. , Dinarte Anemari R. , Pinheiro Daniel G. , Silva Wilson A. , Eberlin Marcos N. , Chammas Roger , Greene Lewis J. 
Published: January 2006

AbstractUsing 2‐DE of total cell protein extracts, we compared soluble proteins from murine melanoma lines Tm1 and Tm5 with proteins from the nontumoral cell melan‐a from which they were derived. Seventy‐one of the 452 spots (average) detected with CBB were differentially accumulated, i.e., increased or decreased twofold. Forty‐four spots were identified by PMF/MALDI‐TOF, 15 with increased and 29 with decreased protein levels. SAGE showed that 17/34 (50%) of the differentially accumulated proteins, pI range 4–7, presented similar differences at the mRNA level. Major reductions in protein were observed in tumor cells of proteins that degrade reactive oxygen species (ROS). Decreases of ⋛ twofold in GST, superoxide dismutase, aldehyde dehydrogenase, thioredoxin, peroxiredoxin 2, and peroxiredoxin 6 protein were observed. SAGE indicated the reduction of other proteins involved in ROS degradation. As expected, the accumulation of exogenous peroxides was significantly higher in the tumor cells while the levels of glutathionylation were two times lower in the tumor cells compared to melan‐a. The differential accumulation of proteins involved in oncogene/tumor suppressor pathways was observed. Melanoma cells can favor survival pathways activated by ROS by inhibiting p53 pathways and activation of Ras and c‐myc pathways.
Human plasma proteome analysis by reversed sequence database search and molecular weight correlation based on a bacterial proteome analysis
Authors: Park Gun Wook , Kwon Kyung‐Hoon , Kim Jin Young , Lee Jeong Hwa , Yun Sung‐Ho , Kim Seung Il , Park Young Mok , Cho Sang Yun , Paik Young‐Ki , Yoo Jong Shin 
Published: January 2006

AbstractIn shotgun proteomics, proteins can be fractionated by 1‐D gel electrophoresis and digested into peptides, followed by liquid chromatography to separate the peptide mixture. Mass spectrometry generates hundreds of thousands of tandem mass spectra from these fractions, and proteins are identified by database searching. However, the search scores are usually not sufficient to distinguish the correct peptides. In this study, we propose a confident protein identification method for high‐throughput analysis of human proteome. To build a filtering protocol in database search, we chose Pseudomonas putida KT2440 as a reference because this bacterial proteome contains fewer modifications and is simpler than the human proteome. First, the P. putida KT2440 proteome was filtered by reversed sequence database search and correlated by the molecular weight in 1‐D‐gel band positions. The characterization protocol was then applied to determine the criteria for clustering of the human plasma proteome into three different groups. This protein filtering method, based on bacterial proteome data analysis, represents a rapid way to generate higher confidence protein list of the human proteome, which includes some of heavily modified and cleaved proteins.
Alteration of the glutamate and GABA transporters in the hippocampus of the Niemann‐Pick disease, type C mouse using proteomic analysis
Authors: Byun Kyunghee , Kim Jaewoo , Cho Sang‐Yun , Hutchinson Brian , Yang Se‐Ran , Kang Kyung‐Sun , Cho Moonjae , Hwang Kyukye , Michikawa Makoto , Jeon Young‐Wook , Paik Young‐Ki , Lee Bonghee 
Published: January 2006

AbstractNiemann‐Pick disease type C (NPC) is a fatal autosomal recessive cholesterol disorder characterized by severe progressive neurodegeneration. To unveil the mechanism of neurodegeneration, proteomic and morphological approaches were applied to the hippocampus in NPC –/– mouse. Two‐DE was utilized to resolve the hippocampal protein expression profiles of 4‐ and 8‐week‐old NPC +/+ and –/– mice. Differentially expressed protein spots were identified by MALDI‐TOF MS and database searching. At 4 weeks of age, there was no significant difference in protein profiles between NPC +/+ and –/– mice. However, at the age of 8 weeks, NPC +/+ and –/– mice showed marked difference in protein expressions. Among these, glutamate receptor 2 precursor was identified. The immunohistochemical study on neurotransporters showed that glial GABA transporter (GAT‐3) increased in both 4‐ and 8‐week‐old NPC –/– mouse and glutamic acid decarboxylase (GAD‐6) increased in 8‐week‐old NPC –/– mouse. Glial glutamate transporter, excitatory amino acids carrier‐1 (EAAC1), decreased in 8‐week‐old NPC –/– mouse. In conclusion, our data may provide insight into the understanding of the basic mechanism through perturbation of protein networks and neurotransporter systems in a single gene knockout model of NPC disease.
Is protein overlap in two‐dimensional gels a serious practical problem?
Authors: Hunsucker Stephen W. , Duncan Mark W. 
Published: January 2006

AbstractIn a recently published article, Campostrini et al. [Proteomics 2005, 5, 2385–2395] raised questions regarding the utility of 2‐D gels in proteomics research. We believe that the authors have overlooked several key issues including the dynamic range of protein expression and the sensitivity of the analytical methods used to explore a proteome. We argue that 2‐D gels have and will continue to provide meaningful quantitative data when applied to proteomic analysis and that the practical significance of spot overlap has been overstated.
Solvent effect on the heat of solution and partial molar volume of some non‐electrolytes and lithium perchlorate
Authors: Kiselev Vladimir D. , Kashaeva Elena A. , Iskhakova Gulnara G. , Potapova Lubov N. , Konovalov Alexander I. 
Published: January 2006

AbstractFor several non‐electrolytes and for lithium perchlorate the solvent effect on the heat of solution and partial molar volumes was studied. In the absence of the donor–acceptor and electrostatic interactions, clear proportionality can be seen only in the alkane solutions and these changes are defined by the non‐alkane component. For solutions of π‐acceptor (tetracyanoethylene) and ν‐acceptor (gallium chloride) in the presence of π,π‐, π,ν‐ and n,ν‐complexes, the relation between the changes of interaction energy and the values of the partial molar volumes can be seen. The maximum change in the value of partial molar volumes (up to 50 cm3 mol−1) was noted for lithium perchlorate in ten solvents. The volume change is proportional to the compressibility coefficients of the solvents and correlates less with the values of heat of solution and solvent permittivity. Copyright © 2006 John Wiley & Sons, Ltd.
Characterization of poly[(R)‐3‐hydroxybutyrate‐co‐ε‐caprolactone] copolymers by matrix‐assisted laser desorption/ionization time‐of‐flight and electrospray ionization mass spectrometry
Authors: Alicata Rossana , Barbuzzi Tony , Giuffrida Mario , Ballistreri Alberto 
Published: January 2006

AbstractMatrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) of narrowly dispersed molecular weight gel permeation chromatography (GPC) fractions was used to characterize random and microblock poly[(R)‐3‐hydroxybutyrate‐co‐ε‐caprolactone] [P(HB‐co‐CL)] copolymers obtained via the acid‐catalyzed transesterification of the corresponding homopolymers, poly([(R)‐3‐hydroxybutyrate] (PHB) and poly(ε‐caprolactone) (PCL). High‐quality mass spectra were obtained, which made it possible to establish the nature of the polymer end groups. Besides the carboxylic termination, two other moieties were found: alcoholic and tosyl end groups. MALDI mass spectra of CL‐rich samples possessed mostly tosyl end groups, while HB‐rich samples possessed mostly alcoholic end groups, showing that the tosyl moiety is linked prevalently to CL terminal units. The higher resolution of electrospray ionization (ESI) mass spectra of lower molecular weight GPC fractions permitted the identification of the different oligomer species hypothesized in the assignment of the corresponding MALDI mass spectra. Partial methanolysis of these copolymers was explored as a method of producing mixed HB‐CL oligomers to be utilized as new synthons, possessing a minor number of chiral centers from those obtained from hydrolysis of biotechnologically synthesized poly(hydroxyalkanoates) (PHAs). Copyright © 2006 John Wiley & Sons, Ltd.
Mild cognitive impairment: applicability of research criteria in a memory clinic and characterization of cognitive profile
Authors: ALLADI SUVARNA , ARNOLD ROBERT , MITCHELL JOANNA , NESTOR PETER J. , HODGES JOHN R. 
Published: January 2006

Background. We explored the applicability of recently proposed research criteria for mild cognitive impairment (MCI) in a memory clinic and changes in case definition related to which memory tests are used and the status of general cognitive function in MCI.Method. A total of 166 consecutive GP referrals to the Cambridge Memory Clinic underwent comprehensive neuropsychological and psychiatric evaluation.Results. Of 166 cases, 42 were excluded (significant depression 8, established dementia 29 and other disorders 5). Of 124 non-demented, non-depressed patients, 72 fulfilled Petersen's criteria for amnestic MCI based upon verbal memory performance [the Rey Auditory Verbal Learning Test (RAVLT)] and 90 met criteria if performance on verbal and/or non-verbal memory tests [the Rey figure recall or the Paired Associates Learning test (PAL)] was considered. Of the 90 broadly defined MCI cases, only 25 had pure amnesia: other subtle semantic and/or attention deficits were typically present. A further 12 were classed as non-amnestic MCI and 22 as ‘worried well’.Conclusions. Definition of MCI varies considerably dependent upon the tests used for case definition. The majority have other cognitive deficits despite normal performance on the Mini-mental State Examination (MMSE) and intact activities of daily living (ADL) and fit within multi-domain MCI. Pure amnesic MCI is rare.
MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition
Authors: Höglund Annette , Dönnes Pierre , Blum Torsten , Adolph Hans-Werner , Kohlbacher Oliver 
Published: January 2006

Abstract
Motivation: Functional annotation of unknown proteins is a major goal in proteomics. A key annotation is the prediction of a protein's subcellular localization. Numerous prediction techniques have been developed, typically focusing on a single underlying biological aspect or predicting a subset of all possible localizations. An important step is taken towards emulating the protein sorting process by capturing and bringing together biologically relevant information, and addressing the clear need to improve prediction accuracy and localization coverage.
Results: Here we present a novel SVM-based approach for predicting subcellular localization, which integrates N-terminal targeting sequences, amino acid composition and protein sequence motifs. We show how this approach improves the prediction based on N-terminal targeting sequences, by comparing our method TargetLoc against existing methods. Furthermore, MultiLoc performs considerably better than comparable methods predicting all major eukaryotic subcellular localizations, and shows better or comparable results to methods that are specialized on fewer localizations or for one organism.
Availability:
Contact: hoeglund@informatik.uni-tuebingen.de
Multiple Heme Oxygenase Family Members Contribute to the Biosynthesis of the Phytochrome Chromophore in Arabidopsis
Authors: Emborg Thomas J. , Walker Joseph M. , Noh Bosl , Vierstra Richard D. 
Published: January 2006

Abstract
The oxidative cleavage of heme by heme oxygenases (HOs) to form biliverdin IXα (BV) is the committed step in the biosynthesis of the phytochrome (phy) chromophore and thus essential for proper photomorphogenesis in plants. Arabidopsis (Arabidopsis thaliana) contains four possible HO genes (HY1, HO2–4). Genetic analysis of the HY1 locus showed previously that it is the major source of BV with hy1 mutant plants displaying long hypocotyls and decreased chlorophyll accumulation consistent with a substantial deficiency in photochemically active phys. More recent analysis of HO2 suggested that it also plays a role in phy assembly and photomorphogenesis but the ho2 mutant phenotype is more subtle than that of hy1 mutants. Here, we define the functions of HO3 and HO4 in Arabidopsis. Like HY1, the HO3 and HO4 proteins have the capacity to synthesize BV from heme. Through a phenotypic analysis of T-DNA insertion mutants affecting HO3 and HO4 in combination with mutants affecting HY1 or HO2, we demonstrate that both of the encoded proteins also have roles in photomorphogenesis, especially in the absence of HY1. Disruption of HO3 and HO4 in the hy1 background further desensitizes seedlings to red and far-red light and accelerates flowering time, with the triple mutant strongly resembling seedlings deficient in the synthesis of multiple phy apoproteins. The hy1/ho3/ho4 mutant can be rescued phenotypically and for the accumulation of holo-phy by feeding seedlings BV. Taken together, we conclude that multiple members of the Arabidopsis HO family are important for synthesizing the bilin chromophore used to assemble photochemically active phys.