bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using biotechnology in the laboratory: Using an immobilized‐laccase reactor‐system to learn about wastewater treatment
Authors: Genç Rukan , Rodríguez‐Couto Susana 
Published: May 2009

AbstractThis article includes a practical guide, which was used to teach the phenomenon of immobilization of enzymes and their subsequent use for discoloration of dyes to under‐graduate students of Biotechnology at the Rovira i Virgili University (Tarragona, Spain). Alginate was selected as a support for the immobilization of laccase. Remazol Brilliant Blue R (RBBR) was used as a substrate for laccase because it is easy to see the color change from dark blue to light blue or no color depending on the discoloration ability of the enzyme. Colorimetric methods to determine the amount of encapsulated enzyme, the effect of the immobilization, and the rate of the discoloration were also pursued by the students.
Automatic rigging for animation characters with 3D silhouette
Authors: Pan JunJun , Yang Xiaosong , Xie Xin , Willis Philip , Zhang Jian J 
Published: May 2009

AbstractAnimating an articulated 3D character requires the specification of its interior skeleton structure which defines how the skin surface is deformed during animation. Currently this task is to a large extent accomplished manually, which consumes a large amount of animators' time. This paper presents an automatic rigging method making use of a new geometry entity called the 3D silhouette. The first step is to extract a coarse 3D curve skeleton and some skeletal joints of a character. This curve skeleton is then refined with a perpendicular silhouette. According to the connectivity of the skeletal joints, the hierarchical animation skeleton is finally constructed. By avoiding complicated computation such as voxelization and pruning, this method is simple and efficient, much faster than existing methods. It proves very useful for quick animation production, with applications including games design and prototype graphical systems. Copyright © 2009 John Wiley & Sons, Ltd.
Age associated high level of major vault protein is p53 dependent
Authors: An Hong‐Joo , Ryu Sung‐Jin , Kim Sung‐Young , Choi Hae‐Ri , Chung Jun‐Ho , Park Sang‐Chul 
Published: May 2009

AbstractMajor vault protein (MVP) represents the main component of vaults and has been linked to multi‐drug resistance (MDR) in cancer cells. We previously reported that MVP plays an important role in the resistance of senescent human diploid fibroblasts (HDFs) to apoptosis and also that MVP expression is markedly reduced in young HDFs but not in senescent HDFs. In this study, designed to elucidate the regulation of MVP in young and senescent HDFs, we examined the levels of transcriptional factors for the MVP gene, which revealed that among the putative transcriptional factors, p53 decreased only in young HDFs, but not in senescent HDFs in response to H2O2 treatment in the same mode as the expression of MVP. Moreover, the phosphorylation status of p53 increased only in senescent HDFs but not in young HDFs in response to H2O2 treatment. Therefore, we tested the possibility of MVP regulation by p53 status. MVP is upregulated in p53 over‐expressing young HDFs, while MVP is downregulated in p53‐specific small interfering RNA (siRNA)‐transfected senescent HDFs, which suggests that the expression of MVP would be p53 dependent. Furthermore, using chromatin immunoprecipitation (ChIP) assay, we observed that p53 binds directly to the MVP promoter. Taken together, these results suggest that p53 would be a major transcriptional factor for MVP gene expression. Copyright © 2009 John Wiley & Sons, Ltd.
Genotyping of five single nucleotide polymorphisms in the OCA2 and HERC2 genes associated with blue‐brown eye color in the Japanese population
Authors: Iida Reiko , Ueki Misuzu , Takeshita Haruo , Fujihara Junko , Nakajima Tamiko , Kominato Yoshihiko , Nagao Masataka , Yasuda Toshihiro 
Published: May 2009

AbstractHuman eye color is a polymorphic phenotype influenced by multiple genes. It has recently been reported that three single nucleotide polymorphisms (SNPs) within intron 1 of the OCA2 gene (rs7495174, rs4778241, rs4778138) and two SNPs in intron 86 (rs12913832) and the 3′ UTR region (rs1129038) of the HERC2 gene—located in the upstream of the OCA2 locus —have a high statistical association with human eye color. The present study is the first to examine in detail the genotype and haplotype frequencies for these five SNPs in an Asian (Japanese) population (n = 523) comprising solely brown‐eyed individuals. Comparison of the genotype and haplotype distributions in Japanese with those in African and European subjects revealed significant differences between Japanese and other populations. Analysis of haplotypes consisting of four SNPs at the HERC2‐OCA2 locus (rs12913832/rs7495174/rs4778241/rs4778138) showed that the most frequent haplotype in the Japanese population is A‐GAG (0.568), while the frequency of this haplotype is rather low in the European population, even in the brown‐eyed group (0.167). The haplotype distribution in the Japanese population was significantly different from that in the brown‐eyed European group (FST = 0.18915). Copyright © 2009 John Wiley & Sons, Ltd.
Evolution of Nacre: Biochemistry and Proteomics of the Shell Organic Matrix of the Cephalopod Nautilus macromphalus
Authors: Marie Benjamin , Marin Frédéric , Marie Arul , Bédouet Laurent , Dubost Lionel , Alcaraz Gérard , Milet Christian , Luquet Gilles 
Published: May 2009

AbstractMatrix evolutions: We have biochemically characterized the nacre matrix of the cephalopod Nautilus macromphalus, in part by a proteomic approach applied to the acetic acid‐soluble and ‐insoluble shell matrices, as well as to spots obtained after 2D gel electrophoresis. Strikingly, most of the obtained partial sequences are entirely new, whereas a few correspond only partly with bivalvian nacre proteins. Our findings shed new light on the macroevolution of nacre matrix proteins. magnified imageIn mollusks, one of the most widely studied shell textures is nacre, the lustrous aragonitic layer that constitutes the internal components of the shells of several bivalves, a few gastropods, and one cephalopod: the nautilus. Nacre contains a minor organic fraction, which displays a wide range of functions in relation to the biomineralization process. Here, we have biochemically characterized the nacre matrix of the cephalopod Nautilus macromphalus. The acid‐soluble matrix contains a mixture of polydisperse and discrete proteins and glycoproteins, which interact with the formation of calcite crystals. In addition, a few bind calcium ions. Furthermore, we have used a proteomic approach, which was applied to the acetic acid‐soluble and ‐insoluble shell matrices, as well as to spots obtained after 2D gel electrophoresis. Our data demonstrate that the insoluble and soluble matrices, although different in their bulk monosaccharide and amino acid compositions, contain numerous shared peptides. Strikingly, most of the obtained partial sequences are entirely new. A few only partly match with bivalvian nacre proteins. Our findings have implications for knowledge of the long‐term evolution of molluskan nacre matrices.
Ribosomal Synthesis of Cyclic Peptides with a Fluorogenic Oxidative Coupling Reaction
Authors: Yamagishi Yusuke , Ashigai Hiroshi , Goto Yuki , Murakami Hiroshi , Suga Hiroaki 
Published: May 2009

AbstractRing around the peptides: We demonstrate a new method for the cyclization of peptides that involves the oxidative coupling of 5‐hydroxyindole and benzylamine. After two nonproteinogenic amino acids were incorporated into peptides by reprogramming the genetic code, cyclization took place rapidly upon the addition of K3Fe(CN)6 and generated a conjugated, fluorescent, heterocyclic structure.magnified image
Identification of OxyE as an Ancillary Oxygenase during Tetracycline Biosynthesis
Authors: Wang Peng , Zhang Wenjun , Zhan Jixun , Tang Yi 
Published: May 2009

AbstractAncillary oxygenase: OxyE is identified as a likely ancillary C‐4 hydroxylase used during oxytetracycline biosynthesis in Streptomyces rimosus. The synergistic actions of oxygenases OxyE and OxyL ensure complete oxidative tailoring and prevent irreversible shunt modifications of the biosynthetic intermediate.magnified imageThe double hydroxylation of 6‐pretetramid to 4‐keto‐anhydrotetracycline is a key tailoring reaction during the biosynthesis of the broad‐spectrum antibiotic tetracyclines. It has been shown previously by heterologous reconstitution that OxyL is a dioxygenase and is the only enzyme required to catalyze the insertion of oxygen atoms at the C‐12a and C‐4 positions. We report here that OxyE, a flavin adenine dinucleotide (FAD)‐dependent hydroxylase homologue, is an ancillary mono‐oxygenase for OxyL during oxytetracycline biosynthesis in Streptomyces rimosus. By using both gene disruption and heterologous reconstitution approaches, we demonstrated that OxyE plays a nonessential, but important role in oxytetracycline biosynthesis by serving as a more efficient C‐4 hydroxylase. In addition, we demonstrated that partially oxidized biosynthetic intermediates can undergo various glycosylation modifications in S. rimosus. Our results indicate that the synergistic actions of OxyE and OxyL in the double hydroxylation step prevent accumulation of shunt products during oxytetracycline biosynthesis in S. rimosus.
Periodic Mesoporous Organosilica in Confined Environments
Authors: Keilbach Andreas , Döblinger Markus , Köhn Ralf , Amenitsch Heinz , Bein Thomas 
Published: May 2009

AbstractConfined tubes: Periodic mesoporous organosilica (PMO) mesophases were synthesized within the confined tubular environment of anodic alumina membrane (AAM) channels, resulting in the formation of either the hexagonal circular or the cubic mesophase.magnified imagePeriodic mesoporous organosilica (PMO) mesophases based on bis(triethoxysilyl)ethane (BTSE) were synthesized within the confined tubular environment of anodic alumina membrane (AAM) channels. The resulting mesophases were investigated by transmission small angle X‐ray scattering (SAXS), nuclear magnetic resonance (NMR), nitrogen sorption, and transmission electron microscopy (TEM). Two different surfactants—nonionic Brij 56 and ionic cetyltrimethylammonium bromide (CTAB)—were used in an acid‐catalyzed evaporation‐induced self‐assembly (EISA) process. Brij 56 as the structure‐directing agent (SDA) resulted in the formation of either the hexagonal circular or the cubic mesophase. While the hexagonal circular mesophase is common for such kinds of composites, the cubic mesophase has never been reported before. The template could be removed from the mesophases by template extraction and calcination after annealing the samples. When using CTAB as the SDA during EISA, the only mesophase observed was the hexagonal circular structure. This is in contrast to previous experiments and reports on pure silica mesophases, where the only mesophase formed with CTAB is hexagonal columnar.
Unusual Optical Properties of Mn‐doped ZnO: The Search for a New Red Pigment—A Combined Experimental and Theoretical Study
Authors: Saal Hilkka , Binnewies Michael , Schrader Marius , Börger Alexander , Becker Klaus‐Dieter , Tikhomirov Viatcheslav A. , Jug Karl 
Published: May 2009

AbstractA pigment of your imagination: A range of polycrystalline solid solutions of a zinc‐rich Znx−1MnxO system (see figure) have been prepared and studied in terms of their colour, diffuse reflectance spectra, Mn valence state and electronic structure. The intense optical absorption arises from Mn2+ doping and is thought to be due to forbidden or partially forbidden transitions between the valence and the conduction band.magnified imageWe report an investigation of zinc‐rich polycrystalline solid solutions of the Zn1−xMnxO system concerning the colour, the diffuse reflectance spectra, the valence state of manganese and the electronic structure. Samples were prepared by a chemical‐vapour‐transport‐assisted route and optimized with respect to colour strength. In agreement with previous experimental results, EPR studies showed that manganese is in the divalent charge state. The nature of the very intense optical absorption, which is caused by Mn2+ doping and determines the colour of the material, is discussed. It is argued that the Mn2+‐induced optical absorption is due to forbidden or partially forbidden transitions between the valence and the conduction band that involve Mn admixed states. This assignment is also confirmed by quantum chemical calculations using the semiempirical molecular orbital method MSINDO.
Synthesis and Properties of Salen–Aluminum Complexes as a Novel Class of Color‐Tunable Luminophores
Authors: Hwang Kyu Young , Kim Hyoseok , Lee Yoon Sup , Lee Min Hyung , Do Youngkyu 
Published: May 2009

AbstractShowing their true colors? Full emission color tuning in the visible region can be achieved with salen–aluminum complexes that are electronically modulated at C5 of the phenoxide ring in the salen moiety. Emission spectra for various substituents R5 are shown (EWG: electron‐withdrawing group, EDG: electron‐donating group).magnified imageA series of salen–aluminum complexes, [{(R5)2‐salen(3‐tBu)2}Al(OC6H4‐p‐C6H5)] (salen=N,N′‐bis(salicylidene)ethylenediamine; R5=H (1), tBu (2), Br (3), Ph (4), OMe (5), NMe2 (6)) and [{5,5′‐(NMe3)2‐salen(3‐tBu)2}Al(OC6H4‐p‐C6H5)][OTf]2 (7; OTf=CF3SO3) that are electronically modulated directly at C5 of the phenoxide ring in the salen moiety has been prepared. The crystal structures of 1, 4, 6, and 7 determined by X‐ray diffraction reveal distorted square‐pyramidal geometries around the Al atoms. Complexes 1–7 are all air‐stable in both the solid and solution states and have high thermal stability (decomp 313–338 °C). Differential scanning calorimetric analyses show that they can form amorphous glasses with glass transition temperatures of 95–132 °C depending on the C5 substituent. UV/Vis absorption spectra of the complexes exhibit major bands at λ=338–413 nm assignable to salen‐centered π–π* transitions with a gradual red shift of the absorption maximum wavelengths as the substituent is varied from an electron‐withdrawing (NMe3) to an electron‐donating group (NMe2). The maxima in the emission spectra of 1–7 occur over the entire visible region, ranging from λ=438 nm for 7 to λ=599 nm for 6, with high fluorescence quantum efficiencies of up to Φ=0.40 for 4 in solution. DFT calculations suggest that the low‐energy electronic transitions in 1–7 are characterized by HOMO−i–LUMO+1 (i=1 for 1–6 or i=4 for 7) transitions localized on the salen moiety, with much involvement of the C5 position in the HOMO−i. Thus, the electronic alteration at the C5 position of the phenoxide ring, which mainly affects the HOMO−i energy levels of salen–Al luminophores, is responsible for the observed emission color‐tuning properties over the entire visible region.
Ti‐Substituted Boranes as Hydrogen Storage Materials: A Computational Quest for the Ideal Combination of Stable Electronic Structure and Optimal Hydrogen Uptake
Authors: Zhang Cheng‐Gen , Zhang Renwu , Wang Zhi‐Xiang , Zhou Zhen , Zhang Shengbai B. , Chen Zhongfang 
Published: May 2009

AbstractHydrogen storage: A family of Ti‐substituted boranes (see figure) having optimum electronic structures and the ability to absorb hydrogen has been designed computationally. Substantial binding energies and gravimetric densities of hydrogen storage show their potential as hydrogen storage materials. The computational study invites experimental synthesis of the novel borane family and offers a guide to searching for new hydrogen storage materials.magnified imageBased on the Wade–Mingos n+1 rule for the closo‐boranes (BnHn2−), a family of Ti‐substituted closo‐boranes has been designed computationally. Due to the isolobal relation of Ti to a BH2− group, these Ti‐substituted boranes have n+1 pairs of skeletal electrons to fulfill the bonding requirement for such stable cages. The reported representatives, B4H4Ti2H2 in particular, not only have stable electronic structures but also superior capability to adsorb hydrogen. The optimal binding energies and high gravimetric densities of hydrogen storage indicate their potential to store hydrogen for practical applications. Simultaneously achieving electronic stability and optimal hydrogen uptake may provide a way of overcoming the issue of aggregation in designing transition‐metal‐decorated hydrogen storage materials. This study invites experimental realization of novel boranes and provides new ideas for searching for hydrogen storage materials.
Lys314 is a Nucleophile in Non‐Classical Reactions of Orotidine‐5′‐Monophosphate Decarboxylase
Authors: Heinrich Daniel , Diederichsen Ulf , Rudolph Markus Georg 
Published: May 2009

AbstractMolecular versatility: Unusual reactivities such as hydrolysis, nucleophilic aromatic substitution, and addition reactions of human orotidine‐5′‐monophosphate decarboxylase are explained by crystal structures and involve a nucleophilic lysine residue that normally is expected to act solely as a general base (RP=phosphoribosyl, R=CO2H, CN, acetyl, N3, I; R′=OH, SH, acetyl, hydroxymethyl).magnified imageOrotidine‐5′‐monophosphate decarboxylase (OMPD) catalyzes the decarboxylation of orotidine‐5′‐monophosphate (OMP) to uridine‐5′‐monophosphate (UMP) in an extremely proficient manner. The reaction does not require any cofactors and proceeds by an unknown mechanism. In addition to decarboxylation, OMPD is able to catalyze other reactions. We show that several C6‐substituted UMP derivatives undergo hydrolysis or substitution reactions that depend on a lysine residue (Lys314) in the OMPD active site. 6‐Cyano‐UMP is converted to UMP, and UMP derivatives with good leaving groups inhibit OMPD by a suicide mechanism in which Lys314 covalently binds to the substrate. These non‐classical reactivities of human OMPD were characterized by cocrystallization and freeze‐trapping experiments with wild‐type OMPD and two active‐site mutants by using substrate and inhibitor nucleotides. The structures show that the C6‐substituents are not coplanar with the pyrimidine ring. The extent of this substrate distortion is a function of the substituent geometry. Structure‐based mechanisms for the reaction of 6‐substituted UMP derivatives are extracted in accordance with results from mutagenesis, mass spectrometry, and OMPD enzyme activity. The Lys314‐based mechanisms explain the chemodiversity of OMPD, and offer a strategy to design mechanism‐based inhibitors that could be used for antineoplastic purposes for example.
A Cholesterol‐Based Tether for Creating Photopatterned Lipid Membrane Arrays on both a Silica and Gold Surface
Authors: Han Xiaojun , Achalkumar Ammathnadu S. , Bushby Richard J. , Evans Stephen D. 
Published: May 2009

AbstractSurfing gold and silica! A new cholesterol‐based tether was attached to both amine‐functionalised silica and gold surfaces. The resultant self‐assembled monolayers, which can be deep‐UV‐patterned, were used in attaching essentially equivalent patterned supported lipid bilayers both on silica for fluorescence studies (left figure) and on gold for impedance studies (right figure).magnified imageWe report a new cholesterol‐based self‐assembled monolayer (SAM) for use in attaching lipid membranes to both gold and silica surfaces that can be patterned by deep UV (254 nm) photolysis. It allows essentially equivalent patterned supported bilayers to be created both on gold for impedance studies and on silica for fluorescence studies. On either surface an amine‐functionalised SAM is reacted with an N‐hydroxysuccinimidylcarbonyl‐functionalised EO3‐cholesteryl derivative. The formation of the amine‐functionalised SAM and its reaction with the EO3‐cholesteryl derivative were followed by contact‐angle measurements, ellipsometry and X‐ray photoelectron spectroscopy. The resultant layer of cholesterol tethers was patterned by deep UV photolysis, which regenerates the original SiO2 surface in exposed regions on a silica substrate and oxidises thiol groups on a gold substrate. This patterned surface containing hydrophilic SiO2 (or ‐OH groups) and hydrophobic cholesterol tether regions can be converted to a surface patterned with supported lipid bi‐ and monolayers (respectively) by immersing in a solution of small unilamellar vesicles of egg yolk phosphatidycholine. The formation of the lipid bi‐ and monolayer regions on the silica surface was evidenced by fluorescence microscopy. Crucially the bilayer regions remain fully fluid yielding lipid mobilities comparable to those found in physisorbed bilayers. Furthermore charged fluorescent lipids are shown to migrate in an applied field thus providing a platform for the studying the electrophoresis (potentially) for a wide range of charged membrane components, such as membrane proteins. The formation of the patterned lipid membrane on the gold surface was confirmed by electrochemical impedance measurements.
Unique Twisted Ribbons Generated by Self‐Assembly of Oligo(p‐phenylene ethylene) Bearing Dimeric Bile Acid Pendant Groups
Authors: Li Yan , Li Guangtao , Wang Xinyan , Li Weina , Su Zhixiang , Zhang Yihe , Ju Yong 
Published: May 2009

AbstractLet's twist again! Remarkable broad and twisted ribbons were generated from the self‐assembly of oligo(p‐ phenylene ethylene) (OPE) bearing dimeric deoxycholic acid pendant groups (see graphic). Varying the bile acid led to nanostructures with drastically different morphologies. The distinctive aggregate shapes of these steroid–OPE conjugates are attributed to the subtle differences in their molecular structures.magnified imageA series of novel oligo(p‐phenylene ethynylene) (OPE) derivatives bearing dimeric cholic acid (OPE1), deoxycholic acid (OPE2) and lithocholic acid (OPE3) was synthesized. The self‐assembly behavior of these derivatives were systematically studied and compared in a THF/water solvent mixture. The addition of water to THF can induce the helical stacking of oligo(p‐phenylene ethylene) bearing dimeric deoxycholic acid end groups, which leads to highly interesting twisted assemblies. Variation of the bile acid group led to nanostructures with drastically different morphologies. The application of spectroscopy in combination with X‐ray diffraction techniques provided a reasonable view of the final self‐assembled structures. The observed distinctive aggregate shapes and the preference in the type of molecular packing of these steroid–OPE conjugates are attributed to the subtle differences in their molecular features.
The Supramolecular Association of Polyelectrolytes to Complementary Charged Surfactants and Protein Assemblies
Authors: Perico Angelo , Ciferri Alberto 
Published: May 2009

AbstractCohesion matters! The correlation between the conformational rigidity of the polyelectrolyte and the size and stability of the globular assembly is discussed in this review article. Some examples of models for the association of polyelectrolytes to globular assemblies are shown here.magnified imageSupramolecular complexes of strong polyelectrolytes and oppositely charged ionic micelles or protein assemblies derive their main stabilization from electrostatic interactions that include the counterion condensation/release mechanism and from hydrophobic interactions distributed along apolar sections of the components. The predicted and the experimental behavior of selected complexes differing in the flexibility of the polyelectrolyte and in the cohesion of the complementary assembly is reviewed and analyzed. Depending upon the rigidity of the polyelectrolyte, globular surfactant clusters persist in the final structure or are transformed into elongated assemblies. On the other hand, even the rather rigid DNA molecule is forced to bend by strongly associated cationic protein complexes such as the histone octamers. A general framework should allow the prediction of these structures in terms of the interplay between the persistence length of the polyelectrolyte and the association constant of the protein or the surfactant assembly.