bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bhc‐cNMPs as either Water‐Soluble or Membrane‐Permeant Photoreleasable Cyclic Nucleotides for both One‐ and Two‐Photon Excitation
Authors: Furuta Toshiaki , Takeuchi Hiroko , Isozaki Masahiro , Takahashi Yasuhiro , Kanehara Makoto , Sugimoto Masazumi , Watanabe Takayoshi , Noguchi Kousei , Dore Timothy M. , Kurahashi Takashi , Iwamura Michiko , Tsien Roger Y. 
Published: August 2004

AbstractCyclic nucleoside monophosphates (cNMPs) play key roles in many cellular regulatory processes, such as growth, differentiation, motility, and gene expression. Caged derivatives that can be activated by irradiation could be powerful tools for studying such diverse functions of intracellular second messengers, since the spatiotemporal dynamics of these molecules can be controlled by irradiation with appropriately focused light. Here we report the synthesis, photochemistry, and biological testing of 6‐bromo‐7‐hydroxycoumarin‐4‐ylmethyl esters of cNMP (Bhc‐cNMP) and their acetyl derivatives (Bhc‐cNMP/Ac) as new caged second messengers. Irradiation of Bhc‐cNMPs quantitatively produced the parent cNMPs with one‐photon uncaging efficiencies (Φε) of up to one order of magnitude better than those of 2‐nitrophenethyl (NPE) cNMPs. In addition, two‐photon induced photochemical release of cNMP from Bhc‐cNMPs (7and8) can be observed with the two‐photon uncaging action cross‐sections (δu) of up to 2.28 GM (1 GM=10−50cm4 s photon−1), which is the largest value among those of the reported Bhc‐caged compounds. The wavelength dependence of the δuvalues of7revealed that the peak wavelength was twice that of the one‐photon absorption maximum. Bhc‐cNMPs showed practically useful water solubility (nearly 500 μM), whereas 7‐acetylated derivatives (Bhc‐cNMPs/Ac) were expected to have a certain membrane permeability. Their advantages were demonstrated in two types of biological systems: the opening of cAMP‐mediated transduction channels in newt olfactory receptor cells and cAMP‐mediated motility responses in epidermal melanophores in scales from medaka fish. Both examples showed that Bhc and Bhc/Ac caged compounds have great potential for use in many cell biological applications.
Dendritic Polyamines: Simple Access to New Materials with Defined Treelike Structures for Application in Nonviral Gene Delivery
Authors: Krämer Michael , Stumbé Jean‐François , Grimm Günther , Kaufmann Brigitte , Krüger Ute , Weber Martin , Haag Rainer 
Published: August 2004

AbstractPolycationic dendrimers are interesting nonviral vectors for in vitro DNA delivery. We describe a simple approach to the synthesis of dendritic polyamines with different molecular weights and adjustable flexibility (degrees of branching; DB). Both parameters influence the transfection efficiency and the cell toxicity of the polymer. Functionalization of hyperbranched polyethylenimine (PEI) by a two‐step procedure generated fully branched pseudodendrimers (analogues of polypropylenimine (PPI) and polyamidoamine (PAMAM) dendrimers). The DNA transfection efficiencies observed for these polymers depended on the cell line investigated. The highest efficiencies were observed for polymers whose unfunctionalized PEI cores had molecular weights in the range Mw=6000–25 000 g mol−1. The cytotoxicity of the dendrimers generally rises with increasing core size. The data collected for NIH/3T3 and COS‐7 cells indicate a maximum transfection efficiency at around 60 % branching for the PPI analogues, and at a PEI‐core molecular weight of Mw=25 000 g mol−1. PAMAM functionalization of PEI (Mw=5000 and 21 000 g mol−1) leads to polymers with little or no cytotoxity in the cell lines investigated.
Preliminary Characterization of Light Harvesting in E. coli DNA Photolyase
Authors: Henry Allison A. , Jimenez Ralph , Hanway Denise , Romesberg Floyd E. 
Published: August 2004

AbstractE. coli DNA photolyase is a monomeric light‐harvesting enzyme that utilizes a methenyltetrahydrofolate (MTHF) antenna cofactor to harvest light energy for the repair of thymine dimers in DNA. For this purpose, the enzyme evolved to bind the cofactor and red‐shift its absorption maximum by 25 nm. Using the crystal structure as a guide, we mutated each protein residue that contacts the cofactor in an effort to identify the interactions responsible for this selective stabilization of the cofactor's excited state. Hydrogen bonding, packing, and electrostatic interactions were examined. Remarkably, a single residue, Glu109, appears to play an important, if not exclusive, role in inducing the observed red‐shift. Thus, this protein, the simplest light‐harvesting system known, appears to have evolved a remarkably simple mechanism to tune the photophysical properties of the antenna cofactor appropriately for biological function.
Cell‐free Protein Synthesis through Solubilisate Exchange in Water/Oil Emulsion Compartments
Authors: Pietrini Adriana V. , Luisi Pier Luigi 
Published: August 2004

AbstractThis work is aimed at finding conditions under which synthetic compartments used as cell models can fuse with each other and allow reagents contained in the different compartments to react. This goal seems to be best achieved by the use of water in oil emulsions (w/o) with dimensions in the range of 30–60 μm. In particular, cell‐free EGFP (enhanced green fluorescent protein) synthesis takes place in Tween 80/Span 80 w/o emulsions, and the extent of the reaction can be monitored directly by fluorescence. The medium is mineral oil, containing 0.5 % v/v aqueous solution. Different premixing configurations of the components (plasmid, amino acids, E. Coli extract) are used and compared. The in vitro synthesis of EGFP in emulsion droplets proceeds for 1 h, and the yield is 7.5 ng μL−1 protein. EGFP synthesis in aqueous solution takes place for at least 5 h. The yield is 10.5 ng μL−1 protein after 1 h and 15.8 ng μL−1 protein after 5 h. The results with the w/o emulsions show that solubilisate exchange takes place among the different water droplets, but it is not possible to demonstrate clearly that a true fusion takes place.
A Metal‐Coordinating DNA Hairpin Mimic
Authors: Bianké Gapian , Häner Robert 
Published: August 2004

AbstractA self‐complementary oligodeoxynucleotide containing a 6,6′′‐substituted terpyridine was found to adopt a highly stable, hairpin‐like structure. In addition to serving as a hairpin‐loop mimic, the terpyridine can act as a coordination site for metals. Thus, the binding of several divalent transition metals (Zn2+, Co2+, Ni2+, Cu2+ and Pd2+) to the terpyridine hairpin mimic was investigated. The terpyridine‐modified hairpin mimic forms a stable secondary structure in the presence of these metals. The stability of the metal‐coordinated hairpin mimic was found to be lower than in the absence of metal. Furthermore, the Tm of the metallohairpin is strongly influenced by the type of the bound metal, with Tm's increasing in the order Co2+∼Ni2+<Zn2+<Cu2+<Pd2+. Model considerations suggest that a conformational change of the terpyridine ligand is required to allow coordination of the metal.
The Identification of an Adenovirus Receptor by Using Affinity Capture and Mass Spectrometry
Authors: Trauger Sunia A. , Wu Eugene , Bark Steve J. , Nemerow Glen R. , Siuzdak Gary 
Published: August 2004

AbstractA tandem mass spectrometry‐based approach is demonstrated for detecting a receptor for Ad37, one of the causative agents for epidemic keratoconjunctivitis. Partial purification of membrane glycoproteins was performed by using lectin‐affinity chromatography and SDS‐PAGE. Gel bands that were shown to bind Ad37 by using Viral Overlay Protein Blot Assay (VOPBA) were excised, proteolyzed and analyzed by using nanoLC‐MS/MS to identify putative receptors contained in a mixture of proteins. Four candidate receptors were identified among approximately 50 proteins based on a search against a protein database. Inhibition of gene delivery mediated by an Ad37 vector, with antibodies against the glycoproteins identified by tandem mass spectrometry, strongly indicated that Membrane Cofactor Protein (MCP), a member of the complement regulatory family of proteins, is the receptor. This rapid and sensitive MS/MS‐based strategy is perceived to have wide potential applications for the detection of viral receptors.
Conformationally Gated Electrochemical Gene Detection
Authors: Immoos Chad E. , Lee Stephen J. , Grinstaff Mark W. 
Published: August 2004

AbstractThe synthesis and characterization of a 26‐base DNA hairpin containing both a redox‐active reporter (ferrocene) and terminal thiol functionality for electrochemical gene detection is described. This electrochemical DNA sensor exploits electron‐transfer dynamics that alter as a consequence of a large structural rearrangement (hairpin‐to‐duplex) induced by hybridization of the target DNA sequence. Melting temperature and circular dichroism studies confirm that the 26‐mer DNA forms a hairpin structure in the absence of target DNA. The loop region of the DNA hairpin is shown to form a stable duplex in the presence of complementary single‐stranded DNA. Atomic force microscopy and ellipsometry experiments of immobilized self‐assembled DNA monolayers suggest that hybridization with complementary DNA affords a conformational change that alters the electrochemical response.
A High‐Throughput Screen for Porphyrin Metal Chelatases: Application to the Directed Evolution of Ferrochelatases for Metalloporphyrin Biosynthesis
Authors: Kwon Seok Joon , Petri Ralf , deBoer Arjo L. , Schmidt‐Dannert Claudia 
Published: August 2004

AbstractPorphyrins are of particular interest in a variety of applications ranging from biocatalysis and chemical synthesis to biosensor and electronic technologies as well as cancer treatment. Recently, we have developed a versatile system for the high‐level production of porphyrins in engineered E. coli cells with the aim of diversifying substitution patterns and accessing porphyrin systems not readily available through chemical synthesis. However, this approach failed to produce significant amounts of the metalloporphyrin in vivo from overproduced protoporphyrin due to insufficient metal insertion. Therefore, we systematically assessed the activity of the B. subtilis ferrochelatase in vivo and in vitro. A true high‐throughput‐screening approach based on catalytic in vivo ferrochelatase activity was developed by using fluorescence‐activated cell sorting (FACS). This assay was used to screen a library of 2.4×106 ferrochelatase mutants expressed in protoporphyrin‐overproducing recombinant E. coli cells. Several selected protein variants were purified, and their improved catalytic activity was confirmed in vitro. In addition to ferrochelatase activity, metal transport into E. coli was identified as another limitation for in vivo heme overproduction. Overexpression of the metal transporter zupT as part of the assembled pathway increased the overall metalloporphyrin production twofold. This report represents the most exhaustive in vitro evolution study of a ferrochelatase and demonstrates the effectiveness of our novel high‐throughput‐screening system for directed evolution of ferrochelatases based on their catalytic activity.
Exploring Hoogsteen and Reversed‐Hoogsteen Duplex and Triplex Formation with Tricyclo‐DNA Purine Sequences
Authors: Renneberg Dorte , Leumann Christian J. 
Published: August 2004

AbstractThe duplex‐ and triplex‐formation properties of the tricyclo‐DNA purine decamer 5′p‐gagaaggaaa‐3′ as a single strand or as part of a hairpin duplex with corresponding parallel and antiparallel pyrimidine DNA and RNA complements, as well as with antiparallel purine DNA and RNA complements, were investigated by UV melting curve analysis, circular dichroism spectroscopy, and gel mobility shift experiments. It was found that tricyclo‐DNA forms very stable duplexes with the pyrimidine RNA and DNA complements not only in the Watson–Crick pairing mode, but also in the Hoogsteen one. Below pH 6.0, the tc‐DNA/DNA and tc‐DNA/RNA Hoogsteen duplexes were found to be more stable than the corresponding Watson–Crick DNA duplexes. Triplexes of the hairpin structure with parallel pyrimidine complements revealed even stronger Hoogsteen pairing relative to the duplexes, presumably due to structural preorganization phenomena. Triplex formation with antiparallel pyrimidine and purine third strands (reversed‐Hoogsteen motif) could not be observed and seem to be unstable.
Factors Affecting Chemical Remediation of Oil Contaminated Water‐Wetted Soil
Authors: Amro M.M. 
Published: August 2004

AbstractThe removal of hydrocarbons from contaminated soil is an essential practice because of environmental concerns, and in order to avoid surface and groundwater contamination. There are different methods applied to remove the hydrocarbons from the soil environment. However, the efficiency of soil remediation depends on several factors, such as the penetration depth of the oil into the soil, the type of oil and polluted soil and the age and degree of contamination. Chemical extraction is one of the approaches employed in handling contaminated sites. Many operations in the petroleum exploration, production and transportation have the potential to affect the environment in different degrees. Leakages from pipelines and stranded oil spills are the major sources of oil‐contamination. If hydrocarbon contamination occurs in the soil, the affected portion of soil must be treated to prevent subsequent pollution of groundwater. In this study, a laboratory investigation of factors affecting the chemical extraction using different solvents was conducted to remove the hydrocarbon from artificially contaminated soil samples in presence of water. Moreover, two different types of crude oil were used to study the effect of oil composition on the removal process. The results have identified large variation in the removal efficiency of the applied solvents, depending mainly on the solvent and the type of oil. The main factors affecting the removal process are presented and investigated. In addition, these results were compared with those of dry soil samples.
Experimental Investigation and Simulation of a Gas‐agitated Sieve Plate Column
Authors: Lü S. , Mi Z. , Wang Y. , Wang L. 
Published: August 2004

AbstractThe extraction of hydrogen peroxide by means of deionized water from anthraquinone working solution via anthraquinone process was carried out in a gas‐agitated sieve plate extraction column. The effects of the superficial velocity of air, dispersed phase and continuous phase on the overall plate extraction efficiency have been investigated. The corrections for the prediction of the overall plate extraction efficiency were presented. The correction proposed to predict the overall plate extraction efficiency in the air, water, anthraquinone working solution three‐phase system agreed satisfactory with experimental data with a maximum absolute deviation of 5.6 %. A new design method for gas‐liquid‐liquid three‐phase extractors is developed based on the multistage countercurrent extraction model. The calculated data by the model agreed well with experimental data and the average relative deviation was less than 10 %. Moreover, the model was used to predict a gas‐agitated sieve plate extraction column for industrial production of hydrogen peroxide. The results show that the plate numbers of gas‐agitated sieve plate extraction column are 30–40 % less than that of liquid‐liquid sieve plate column.
Compatibilization of Polymer Blends from Poly(butadiene‐g‐poly(styrene‐co‐acrylonitrile)) and Polycarbonate through Oxazoline‐ and Benzoxazole‐Modification of ABS
Authors: Becker H.G. , Schmidt‐Naake G. 
Published: August 2004

AbstractBlends of poly(butadiene‐g‐poly(styrene‐co‐acrylonitrile) (ABS) with polycarbonate (PC) are some of the most successful multiphase materials, with applications in the automotive and electronics industries. The mechanical properties of the complete incompatible blends are mainly determined by the interaction between the poly(styrene‐co‐acrylonitrile) (S/AN) component of the ABS and the PC as well as through the dispersion of the elastomeric component poly(butadiene) in the thermoplastic S/AN‐matrix.The aim of our work is to optimize the modification process by the use of new substituted amino alcohols and amino phenols, as well as the use of a more efficient catalyst. Both reactive and non reactive compatibilization of polymer blends should be performed with the new ABS‐modifications.
Heat Dispersion Effects on the Functional Characteristics of Industrial‐scale Adiabatic Membrane Reactors
Authors: Vogiatzis E. , Koukou M.K. , Papayannakos N. , Markatos N.C. 
Published: August 2004

AbstractThe influence of heat dispersion on the performance of adiabatic industrial‐scale membrane reactors is studied in this work. The results presented are from the application of the model to a membrane reactor that is introduced in an IGCC plant, to control carbon dioxide emissions. The performance of this reactor equipped with highly selective membranes is studied in detail. The thermal phenomena that take place in the interior of the membrane reactor have a considerable influence on the operation of the reactor thus the assumption of isothermal operation is not valid. The omission of thermal dispersion results on the underestimation of the system operation and the total gaseous fluxes that permeate through the membrane. The temperature distribution in the membrane reactor differs significantly from the calculated distribution predicted from the model that ignores thermal dispersion effects.
Liquid‐Phase Catalytic Hydrogenation of p‐Chlorobenzophenone to p‐Chlorobenzhydrol over a 5 % Pd/C Catalyst
Authors: Bawane S.P. , Sawant S.B. 
Published: August 2004

AbstractThe kinetics of the liquid‐phase catalytic hydrogenation of p‐chlorobenzophenone have been investigated over a 5 % Pd/C catalyst. The effects of hydrogen partial pressure (800–2200 kPa), catalyst loading (0.4–1.6 gm dm–3), p‐chlorobenzophenone concentration (0.37–1.5 mol dm–3), and temperature (303–313 K) were studied. A stirring speed > 20 rps has no effect on the initial rate of reaction. Effects of various catalysts (Pd/C, Pd/BaSO4, Pd/CaCO3, Pt/C, Raney nickel) and solvents (2‐propanol, methanol, dimethylformamide, toluene, xylene, hexane) on the hydrogenation of p‐chlorobenzophenone were also investigated. The reaction was found to be first order with respect to hydrogen partial pressure and catalyst loading, and zero order with respect to p‐chlorobenzophenone concentration. Several Langmuir‐Hinshelwood type models were considered and the experimental data fitted to a model involving reaction between adsorbed p‐chlorobenzophenone and hydrogen in the liquid phase.
A Critical Study of Decentralized Controllers for a Multivariable System
Authors: Viknesh R. , Sivakumaran N. , Chandra J.S. , Radhakrishnan T.K. 
Published: August 2004

AbstractIndustrial processes are naturally multivariable in nature. A comparison of multivariable decentralized controllers has been performed and a multivariable four interconnected water tank system, which exhibits a RHP (Right Half Plane) zero is considered for decentralized control. The characteristics of a four‐tank system are discussed and a decentralized PI (Proportional‐Integral) controller is designed for the system based on various control algorithms. The algorithms are simulated using MATLAB and the performances are compared for reference tracking, disturbance rejection and model uncertainty cases. The comparison of the results show that the controllers based on Gershgorin band and Ideal relay method are suitable for the control of a four‐tank system.
Axial Dispersion and Wall Effects in Narrow Fixed Bed Reactors: A Comparative Study Based on RTD and NMR Measurements
Authors: Tang D. , Jess A. , Ren X. , Bluemich B. , Stapf S. 
Published: August 2004

AbstractAxial dispersion and wall effects in narrow fixed beds with aspect ratios < 10 were investigated, both by classical methods and by NMR imaging. The residence time distribution (RTD) in the center and at the wall was measured, system water/NaCl‐solution as tracer, and subsequently compared with radial velocity profiles based on NMR imaging. The influence of the aspect ratio and Rep on dispersion and on the degree of non‐uniformity of the velocity profile was studied. The NMR results are consistent with the RTD and also with literature data of numerical simulations. For low aspect ratios, dispersion/wall effects have a strong influence on the reactor behavior, above all, in cases where a low effluent concentration is essential, as proven by breakthrough experiments with the reaction of H2S with ZnO.
Iridium–Imine and –Amine Complexes Relevant to the (S)‐Metolachlor Process: Structures, Exchange Kinetics, and CH Activation by IrI Causing Racemization
Authors: Dorta Romano , Broggini Diego , Kissner Reinhard , Togni Antonio 
Published: August 2004

AbstractIridium complexes of DMA‐imine [2,6‐dimethylphenyl‐1′‐methyl‐2′‐methoxyethylimine, 1 a) and (R)‐DMA‐amine [(1′R)‐2,6‐dimethylphenyl‐1′‐methyl‐2′‐methoxyethylamine, 2 a] that are relevant to the catalytic imine hydrogenation step of the Syngenta (S)‐Metolachlor process were synthesized: metathetical exchange of [Ir2Cl2(cod)2] (cod=1,5‐cyclooctadiene) with [Ag(1 a)2]BF4 and [Ag((R)‐2 a)2]BF4 afforded [Ir(cod)(κ2‐‐1 a)]BF4 (11) and [Ir(cod)(κ2‐(R)‐2 a)]BF4 ((R)‐19)), respectively. These complexes were then used in stopped‐flow experiments to study the displacement of amine 2 a from complex 19 by imine 1 a to form the imine complex 11, thus modeling the product/substrate exchange step in the catalytic cycle. The data suggest a two‐step associative mechanism characterized by k1=(2.6±0.3)×102 M−1 s−1 and k2=(4.3±0.6)×10−2 s−1 with the respective activation energies EA1=(7.5±0.6) kJ mol−1 and EA2=(37±3) kJ mol−1. Furthermore, complex 11 reacted with H2O to afford the hydrolysis product [Ir(cod)(η6‐‐2,6‐dimethylaniline)]BF4 (12), and with I2 to liberate quantitatively the DMA‐iminium salt 14. On the other hand, the chiral amine complex (R)‐19 formed the optically inactive η6‐bound compound [Ir(cod)(η6‐rac‐2 a)]BF4 (rac‐18) upon dissolution in THF at room temperature, presumably via intramolecular CH activation. This racemization was found to be a two‐step event with k′1=9.0×10−4 s−1 and k2=2.89×10−5 s−1, featuring an optically active intermediate prior to sp3 CH activation. Compounds 11, 12, rac‐18, and (R)‐19 were structurally characterized by single‐crystal X‐ray analyses.