bluuebunny/crossref_metadata_2025_split huggingface dataset:
Directed Evolution of Proteins In Vitro Using Compartmentalization in Emulsions
Authors: Davidson Eric A. , Dlugosz Paulina J. , Levy Matthew , Ellington Andrew D. 
Published: July 2009

AbstractThis unit describes a protocol for the directed evolution of proteins utilizing in vitro compartmentalization. This method uses a large number of independent in vitro transcription and translation (IVTT) reactions in water droplets suspended in an oil emulsion to enable selection of proteins that bind a target molecule. Protein variants that bind the target also bind to and allow recovery of the genes that encoded them. This protocol serves as a basis for carrying out selections in emulsions, and can potentially be modified to select for other functionalities, including catalysis. This selection method is advantageous compared to alternative selection protocols due to the ability to screen through very large‐size libraries and the ability to express and screen or select for functions that would otherwise be toxic or inaccessible to in vivo selections and screens. Curr. Protoc. Mol. Biol. 87:24.6.1‐24.6.12. © 2009 by John Wiley & Sons, Inc.
Laser Microdissection‐Mediated Isolation and In Vitro Transcriptional Amplification of Plant RNA
Authors: Scanlon Michael J. , Ohtsu Kazuhiro , Timmermans Marja C.P. , Schnable Patrick S. 
Published: July 2009

AbstractProtocols for laser microdissection and linear amplification of RNA from fixed, sectioned plant tissues are described. When combined with quantitative RT‐PCR, microarray analysis, or RNA‐sequencing, these procedures enable quantitative analyses of transcript accumulation from microscopic quantities of specific plant organs, tissues, or single cells. Curr. Protoc. Mol. Biol. 87:25A.3.1‐25A.3.15 © 2009 by John Wiley & Sons, Inc.
Pathway Modulators and Inhibitors
Authors: Smith John A. 
Published: July 2009

AbstractInhibitors of specific cellular pathways are useful for investigating the roles of proteins of unknown function, and for selectively inhibiting a protein in complex pathways to uncover its relationships to other proteins in this and other interacting pathways. This appendix provides links to Web sites that describe cellular processes and pathways along with the various classes of inhibitors, numerous references, downloadable diagrams, and technical tips. Curr. Protoc. Mol. Biol. 87:A.6.1‐A.6.5. © 2009 by John Wiley & Sons, Inc.
Lasers for Flow Cytometry
Authors: Shapiro Howard M. , Telford William G. 
Published: July 2009

AbstractLasers are the principal light sources for flow cytometers. Most modern benchtop instruments feature air‐cooled lasers emitting 10 to 25 mW of light at 488 nm. This unit covers the various types of lasers available and the qualities that make them suitable or unsuitable for use in flow cytometers. Also included is a discussion of future directions, particularly in the development of solid‐state devices. Curr. Protoc. Cytom. 49:1.9.1‐1.9.17. © 2009 by John Wiley & Sons, Inc.
Calibration of Flow Cytometry for Quantitative Quantum Dot Measurements
Authors: Mittal Rowena , Bruchez Marcel P. 
Published: July 2009

AbstractObservations of quantum dot (QD)–labeled cells in biomedical research are mainly qualitative in nature, which limits the ability of researchers to compare results experiment to experiment and laboratory to laboratory. Labeled cells are useful in a range of in vitro and in vivo assays where tracking behavior of administered cells is integral for answering research questions in areas such as tissue engineering and stem cell therapy. Before the full potential of QD‐based toolsets can be realized, uptake of QDs by cells must be quantified and standardized. This unit describes a novel, simple method to assess the number of QDs per cell using flow cytometry and commercially available standards. This quick and easy method can be used to calibrate flow cytometry instruments and settings, and quantify QD uptake by cells for in vitro and in vivo experimentation for comparable results across QD conjugate types, cell types, research groups, lots of commercial QDs, and homemade QDs. Curr. Protoc. Cytom. 49:6.26.1‐6.26.7. © 2009 by John Wiley & Sons, Inc.
Highly Efficient Asymmetric Epoxidation of Electron‐Deficient α,β‐Enones and Related Applications to Organic Synthesis
Authors: Zheng Changwu , Li Yawen , Yang Yingquan , Wang Haifeng , Cui Haifeng , Zhang Junkang , Zhao Gang 
Published: July 2009

AbstractThe asymmetric epoxidation of electron‐deficient olefins has been achieved using inexpensive and readily available prolinols as catalysts with good to excellent yields and enantioselectivities. The utility of the resulting chiral epoxides was illustrated by elaboration to several synthetically useful compounds featuring a concise synthesis of (−)‐(5R,6S)‐balasubramide.
Efficient Copper‐Catalyzed Synthesis of N‐Alkylanthranilic Acids via an ortho‐Substituent Effect of the Carboxyl Group of 2‐Halobenzoic Acids at Room Temperature
Authors: Zeng Liang , Fu Hua , Qiao Renzhong , Jiang Yuyang , Zhao Yufen 
Published: July 2009

AbstractWe have developed an efficient copper‐catalyzed method for the synthesis of N‐alkylanthranilic acids. The protocol uses inexpensive copper(I) iodide/racemic 1,1′‐binaphthyl‐2,2′‐diol (rac‐BINOL) as the catalyst/ligand system, readily available 2‐halobenzoic acids and aliphatic amines as the starting materials, the coupling reactions were performed at room temperature, and various functionalities in the substrates were tolerated.
Gold‐Catalyzed Intermolecular Reactions of (Z)‐Enynols with Indoles for the Construction of Dihydrocyclohepta[b]indole Skeletons through a Cascade Friedel–Crafts/Hydroarylation Sequence
Authors: Lu Yuhua , Du Xiangwei , Jia Xueshun , Liu Yuanhong 
Published: July 2009

AbstractAn efficient domino approach for the synthesis of indole‐fused carbocycles and their analogues from the reactions of suitably substituted (Z)‐enynols with indoles or pyrroles under mild reaction conditions was developed. This methodology is realized by a tandem reaction using Au/Ag catalysts, which could catalyze both of the Friedel–Crafts and the hydroarylation reaction in the same vessel.
Regioselective Synthesis of Phenols and Halophenols from Arylboronic Acids Using Solid Poly(N‐vinylpyrrolidone)/ Hydrogen Peroxide and Poly(4‐vinylpyridine)/Hydrogen Peroxide Complexes
Authors: Prakash G. K. Surya , Chacko Sujith , Panja Chiradeep , Thomas Tisa Elizabeth , Gurung Laxman , Rasul Golam , Mathew Thomas , Olah George A. 
Published: July 2009

AbstractSolid hydrogen peroxide complexes based on poly(N‐vinylpyrrolidone) and poly(4‐vinylpyridine) were prepared and used as solid hydroxylating reagents. These solid hydrogen peroxide equivalents are found to be much safer, convenient and efficient reagent systems for the ipso‐hydroxylation of arylboronic acids to the corresponding phenols in high yields at a faster rate. The versatility of the reagents has been further expanded for the one‐pot synthesis of halophenols. Density functional theory calculations were carried out on hydrogen peroxide complexes of N‐ethylpyrrolidone and 4‐ethylpyridine as models to get a better understanding of structure and behavior of hydrogen peroxide complexes of the polymers poly(N‐vinylpyrrolidone) and poly(4‐vinylpyridine) compared to aqueous hydrogen peroxide.
Modular Furanoside Phosphite‐Phosphoroamidites, a Readily Available Ligand Library for Asymmetric Palladium‐Catalyzed Allylic Substitution Reactions. Origin of Enantioselectivity
Authors: Raluy Eva , Pàmies Oscar , Diéguez Montserrat 
Published: July 2009

AbstractA library of furanoside phosphite‐phosphoroamidite ligands has been synthesized and screened in the palladium‐catalyzed allylic substitution reactions of several substrate types. These series of ligands can be prepared efficiently from easily accessible D‐xylose and D‐glucose. Their modular nature enables the position of the phosphoroamidite group, configuration of C‐3 of the furanoside backbone and the substituents/configurations in the biaryl phosphite/phosphoroamidite moieties to be easily and systematically varied. By carefully selecting the ligand components, therefore, high regio‐ and enantioselectivities (ees up to 98%) and good activities have been achieved in a broad range of mono‐ and disubstituted hindered and unhindered linear and cyclic substrates. The NMR studies on the palladium‐π‐allyl intermediates provide a deeper understanding about the effect of the ligand parameters on the origin of enantioselectivity. They also indicate that the nucleophilic attack takes place predominantly at the allylic terminal carbon atom located trans to the phosphoroamidite moiety.
Micellar Effects in Olefin Hydroformylation Catalysed by Neutral, Calix[4]arene‐Diphosphite Rhodium Complexes
Authors: Monnereau Laure , Sémeril David , Matt Dominique , Toupet Loïc 
Published: July 2009

AbstractThe combination of calixarene‐derived surfactants and neutral rhodium complexes containing a hemispherical “1,3‐calix‐diphosphite” ligand led to efficient catalysts for the hydroformylation of octene and other olefins in water. While the surfactants allowed the formation of micelles that dissolve both the catalyst and the alkene, thereby resulting in high olefin:rhodium ratios, the diphosphite provided a tight envelope about the catalytic centre able to drive the reaction towards the linear aldehydes. Best results in the hydroformylation of 1‐octene were obtained when using [tetra(p‐sulfonato)]‐(tetra‐n‐butoxy)‐calix[4]arene as surfactant. With this additive remarkable linear to branched aldehyde ratios of up to 62 were obtained, the corresponding activities being higher than those observed when operating in an organic solvent [turnover frequencies (TOFs) up to 630 mol(converted 1‐octene)⋅ mol(Rh)−1⋅h−1].
Cationic Ruthenium‐Cyclopentadienyl‐Diphosphine Complexes as Catalysts for the Allylation of Phenols with Allyl Alcohol; Relation between Structure and Catalytic Performance in O‐ vs. C‐Allylation
Authors: van Rijn Jimmy A. , Lutz Martin , von Chrzanowski Lars S. , Spek Anthony L. , Bouwman Elisabeth , Drent Eite 
Published: July 2009

AbstractA new catalytic method has been investigated to obtain either O‐ or C‐allylated phenolic products using allyl alcohol or diallyl ether as the allyl donor. With the use of new cationic ruthenium(II) complexes as catalyst, both reactions can be performed with good selectivity. Active cationic Ru(II) complexes, having cyclopentadienyl and bidentate phosphine ligands are generated from the corresponding Ru(II) chloride complexes with a silver salt. The structures of three novel (diphosphine)Ru(II)CpCl catalyst precursor complexes are reported. It appears that the structure of the bidentate ligand has a major influence on catalytic activity as well as chemoselectivity. In addition, a strong cocatalytic effect of small amounts of acid is revealed. Model experiments are described that have been used to build a reaction network that explains the origin and evolution in time of both O‐allylated and C‐allylated phenolic products. Some mechanistic implications of the observed structure vs. performance relation of the [(diphosphine)RuCp]+ complexes and the cocatalytic role of added protons are discussed.
Construction of Recombinant Escherichia coli Catalysts which Simultaneously Express an (S)‐Oxynitrilase and Different Nitrilase Variants for the Synthesis of (S)‐Mandelic Acid and (S)‐Mandelic Amide from Benzaldehyde and Cyanide
Authors: Sosedov Olga , Matzer Kathrin , Bürger Sibylle , Kiziak Christoph , Baum Stefanie , Altenbuchner Josef , Chmura Andrzej , van Rantwijk Fred , Stolz Andreas 
Published: July 2009

AbstractRecombinant Escherichia coli strains were constructed which simultaneously expressed the genes encoding the (S)‐oxynitrilase from cassava (Manihot esculenta) together with the wild‐type or a mutant variant of the arylacetonitrilase from Pseudomonas fluorescens EBC191 in a single organism under the control of a rhamnose‐inducible promoter. The whole cell catalysts obtained converted benzaldehyde and potassium cyanide in aqueous media at pH 5.2 mainly to (S)‐mandelic acid and/or (S)‐mandelic amide and synthesized only low amounts of the corresponding (R)‐enantiomers. The conversion of benzaldehyde and potassium cyanide (KCN) by a whole‐cell catalyst simultaneously expressing the (S)‐oxynitrilase and the wild‐type nitrilase resulted in a ratio of (S)‐mandelic acid to (S)‐mandelic amide of about 4:3. This could be explained by the strong nitrile hydratase activity of the wild‐type nitrilase with (S)‐mandelonitrile as substrate. The relative proportion of (S)‐mandelic amide formed in this system was significantly increased by coexpressing the (S)‐oxynitrilase with a carboxy‐terminally truncated variant of the nitrilase. This whole‐cell catalyst converted benzaldehyde and KCN to mandelic amide and mandelic acid in a ratio of about 9:1. The ee of the (S)‐mandelic amide formed was calculated to be >95%.
Iron‐Catalyzed Ligand‐Free Carbon‐Selenium (or Tellurium) Coupling of Arylboronic Acids with Diselenides and Ditellurides
Authors: Wang Min , Ren Kai , Wang Lei 
Published: July 2009

AbstractCarbon‐selenium and carbon‐tellurium cross‐couplings of arylboronic acids with diselenides and ditellurides have been catalyzed by iron(0), iron(II) chloride or iron(III) chloride without any ligand and additive in the air. The method yields the corresponding unsymmetrical diorgano monoselenides and monotellurides in good to excellent yields, displays a broad substrate scope, and is simple, convenient, effective, economical and environmentally friendly.
Selective Oxidation of Acetophenones Bearing Various Functional Groups to Benzoic Acid Derivatives with Molecular Oxygen
Authors: Nakamura Ryota , Obora Yasushi , Ishii Yasutaka 
Published: July 2009

AbstractAcetophenones substituted by alkyl, alkoxy, acetoxy, and halogen groups were selectively oxidized with molecular oxygen to the corresponding benzoic acids by using the N,N′,N′′‐trihydroxyisocyanuric acid (THICA)/cobalt(II) acetate [Co(OAc)2] and THICA/Co(OAc)2/manganese(II) acetate [Mn(OAc)2]. For example, 4‐methylacetophenone was selectively oxidized with molecular oxygen to 4‐acetylbenzoic acid (85%) by THICA/Co(OAc)2 and to 4‐methylbenzoic acid (93%) by Mn(OAc)2, while terephthalic acid was obtained in 93% with the THICA/Co(OAc)2/Mn(OAc)2 catalytic system. It is interesting that the acetyl group on the aromatic ring is efficiently converted by a very small amount of Mn(OAc)2 to the corresponding carboxylic acid, and that the present method provides a versatile route to acetylbenzoic acids which are difficult to prepare by conventional methods.
Electrocatalytic Recycling of CO2 and Small Organic Molecules
Authors: Lee Jaeyoung , Kwon Youngkook , Machunda Revocatus L. , Lee Hye Jin 
Published: July 2009

AbstractAs global warming directly affects the ecosystems and humankind in the 21st century, attention and efforts are continuously being made to reduce the emission of greenhouse gases, especially carbon dioxide (CO2). In addition, there have been numerous efforts to electrochemically convert CO2 gas to small organic molecules (SOMs) and vice versa. Herein, we highlight recent advances made in the electrocatalytic recycling of CO2 and SOMs including (i) the overall trend of research activities made in this area, (ii) the relations between reduction conditions and products in the aqueous phase, (iii) the challenges in the use of gas diffusion electrodes for the continuous gas phase CO2 reduction, as well as (iv) the development of state of the art hybrid techniques for industrial applications. Perspectives geared to fully exploit the potential of zero‐gap cells for CO2 reduction in the gaseous phase and the high applicability on a large scale are also presented. We envision that the hybrid system for CO2 reduction supported by sustainable solar, wind, and geothermal energies and waste heat will provide a long term reduction of greenhouse gas emissions and will allow for continued use of the abundant fossil fuels by industries and/or power plants but with zero emissions.
Calixarene Dimers as Host Molecules for Biologically Important Di‐ and Oligophosphates
Authors: Zadmard Reza , Taghvaei‐Ganjali Saeed , Gorji Banafsheh , Schrader Thomas 
Published: July 2009

AbstractA dimeric calixarene, with an aliphatic C6‐bridge and six anilinium head groups at its upper rim, preferably complexes diphosphates and oligonucleotides with more than 10 bonds between both anionic moieties. Free binding energies correlate with the length of the aliphatic bridge in a roughly linear fashion. The binding event, which is monitored by fluorescence titrations and competition experiments, relies on Coulomb interactions, as opposed to a nonpolar variant with tert‐butyl instead of ammonium groups; here, hydrophobic forces prevail, rendering the calixarene dimer selective for less polar cofactors such as FAD. The best guest for the hexaanilinium dimer is found in ssDNA, which carries multiple copies of the optimal trinucleotide for maximum attraction towards the extended cationic host. The recognition event is also observed in the environment of a lipid monolayer, and provides a means to quantify dimer diphosphate interactions by measuring p/A shifts.
Ester Hydrolysis by a Cyclodextrin Dimer Catalyst with a Tridentate N,N′,N′′‐Zinc Linking Group
Authors: Tang Si‐Ping , Zhou Ying‐Hua , Chen Huo‐Yan , Zhao Cun‐Yuan , Mao Zong‐Wan , Ji Liang‐Nian 
Published: July 2009

AbstractA new β‐cyclodextrin dimer, 2,6‐dimethylpyridine‐bridged‐bis(6‐monoammonio‐β‐cyclodextrin) (pyridyl BisCD, L), is synthesized. Its zinc complex (ZnL) is prepared, characterized, and applied as a catalyst for diester hydrolysis. The formation constant (log KML=7.31±0.04) of the complex and deprotonation constant (pKa1=8.14±0.03, pKa2=9.24±0.01) of the coordinated water molecule were determined by a potentiometric pH titration at (25±0.1)°C, indicating a tridentate N,N′,N′′‐zinc coordination. Hydrolysis kinetics of carboxylic acid esters were determined with bis(4‐nitrophenyl)carbonate (BNPC) and 4‐nitrophenyl acetate (NA) as the substrates. The resulting hydrolysis rate constants show that ZnL has a very high rate of catalysis for BNPC hydrolysis, yielding an 8.98×103‐fold rate enhancement over uncatalyzed hydrolysis at pH 7.00, compared to only a 71.76‐fold rate enhancement for NA hydrolysis. Hydrolysis kinetics of phosphate esters catalyzed by ZnL are also investigated using bis(4‐nitrophenyl)phosphate (BNPP) and disodium 4‐nitrophenyl phosphate (NPP) as the substrates. The initial first‐order rate constant of catalytic hydrolysis for BNPP was 1.29×10−7 s−1 at pH 8.5, 35 °C and 0.1 mM catalyst concentration, about 1600‐fold acceleration over uncatalyzed hydrolysis. The pH dependence of the BNPP cleavage in aqueous buffer was shown as a sigmoidal curve with an inflection point around pH 8.25, which is nearly identical to the pKa value of the catalyst from the potentiometric titration. The kBNPP of BNPP hydrolysis promoted by ZnL is found to be 1.68×10−3 M−1 s−1, higher than that of NPP, and comparatively higher than those promoted by its other tridentate N,N′,N′′‐zinc analogues.
A simple and robust algorithm for microarray data clustering based on gene population‐variance ratio metric
Authors: Chatterjee Soumyadeep , Bhattacharjee Kasturi , Konar Amit 
Published: July 2009

AbstractWith the advent of the microarray technology, the field of life science has been greatly revolutionized, since this technique allows the simultaneous monitoring of the expression levels of thousands of genes in a particular organism. However, the statistical analysis of expression data has its own challenges, primarily because of the huge amount of data that is to be dealt with, and also because of the presence of noise, which is almost an inherent characteristic of microarray data. Clustering is one tool used to mine meaningful patterns from microarray data. In this paper, we present a novel method of clustering yeast microarray data, which is robust and yet simple to implement. It identifies the best clusters from a given dataset on the basis of the population of the clusters as well as the variance of the feature values of the members from the cluster‐center. It has been found to yield satisfactory results even in the presence of noisy data.
Characterisation of a Recombinant NADP‐Dependent Glycerol Dehydrogenase from Gluconobacter oxydans and its Application in the Production of L‐Glyceraldehyde
Authors: Richter Nina , Neumann Markus , Liese Andreas , Wohlgemuth Roland , Eggert Thorsten , Hummel Werner 
Published: July 2009

AbstractThe acetic acid bacterium Gluconobacter oxydans has a high potential for oxidoreductases with a variety of different catalytic abilities. One putative oxidoreductase gene codes for an enzyme with a high similarity to the NADP+‐dependent glycerol dehydrogenase (GlyDH) from Hypocrea jecorina. Due to this homology, the GlyDH (Gox1615) has been cloned, over‐expressed in Escherichia coli, purified and characterised. Gox1615 shows an apparent native molecular mass of 39 kDa, which corresponds well to the mass of 37.213 kDa calculated from the primary structure. From HPLC measurements, a monomeric structure can be deduced. Kinetic parameters and the dependence of the activity on temperature and pH were determined. The enzyme shows a broad substrate spectrum in the reduction of different aliphatic, branched and aromatic aldehydes. Additionally, the enzyme has been shown to oxidize a variety of different alcohols. The highest activities were observed for the conversion of D‐glyceraldehyde in the reductive and L‐arabitol in the oxidative direction. Since high enantioselectivities were observed for the reduction of glyceraldehyde, the kinetic resolution of glyceraldehyde was investigated and found to yield enantiopure L‐glyceraldehyde on preparative scale.
Magnetism in Nanoparticles: Beyond the Effect of Particle Size
Authors: Peddis Davide , Cannas Carla , Musinu Anna , Piccaluga Giorgio 
Published: July 2009

AbstractA set of investigations on selected samples of nanosized cobalt ferrite are reviewed, aimed at studying the various factors affecting the magnetic properties of nanoparticles. Specifically, the effects of inter‐particle interactions, of structural and magnetic order, both in the core and on the surface of the particle, have been examined. All factors render the control of the magnetic properties of nanosystems quite difficult, but, at the same time, they also offer the opportunity of tuning them properly, so that materials for specific applications may be created.
New Mechanistic Aspects of the Fenton Reaction
Authors: Rachmilovich‐Calis Sandra , Masarwa Alexandra , Meyerstein Naomi , Meyerstein Dan , van Eldik Rudi 
Published: July 2009

AbstractThe kinetics of the Fenton reaction was studied in detail. A second reaction step in the presence of excess H2O2 is attributed to formation of the complex FeIII(−O2H)aq. Therefore, the reaction of Fe(H2O)62+ with FeIII(−O2H)aq in the presence of FeII to form FeIIIaq (k=(7.7±1.5)×105 M−1 s−1) may contribute to the overall Fenton reaction, and could account for some of the debate in the literature concerning its detailed mechanism. If this is correct for LFeIII(−O2H)aq also, then it might be of significant biological importance. The activation parameters ΔH≠, ΔS≠, and ΔV≠ for the Fenton reaction were measured under various experimental conditions, and are used in the mechanistic interpretation.