bluuebunny/crossref_metadata_2025 huggingface dataset:
Organotin concentrations in the Rivers Bure and Yare, Norfolk Broads, England
Authors: Waite M E , Evans K E , Thain J E , Waldock M J
Published: January 2005

Butyltin concentrations have been measured at eight freshwater sites (rivers and lakes) in the Norfolk Broads, UK, during 1986 and 1987. Tributyltin (TBT) was found in water samples from seven of the sites. Wherever TBT was present, dibutyltin and (usually) monobutyltin occurred. Levels of TBT exceeded 100 ng dm−3 in open stretches of both the Rivers Bure and Yare in 1986 and 1987. The highest concentration of TBT recorded for Wroxham Broad (a shallow lake) was 898 ng dm−3. Values of up to 3.26 μg dm−3 were measured in water samples taken from a marina. A depth profile for Wroxham Broad showed TBT to be uniformly distributed throughout the shallow water column. The results are discussed in relation to toxicity of TBT to freshwater organisms. Laboratory measurements of the degradation of TBT in freshwater from a marina gave a half‐life of six days at 20°C in the light.
Determination of arsenic compounds by high‐pressure liquid chromatography–graphite furnace atomic absorption spectrometry and thermospray mass spectrometry
Authors: Cullen William R , Dodd Matthew
Published: January 2005

Biologically important arsenic species such as arsenobetaine, arsenocholine iodide, tetramethylarsonium iodide, methylarsonic acid, and dimethylarsinic acid can be separated and quantitated by HPLC. The pH‐sensitive separations on a weak anion‐exchange column are described, as well as separations on a reverse‐phase column with the aid of tetrabutylammonium nitrate or heptanesulfonic acid as ion‐pairing agents. The thermospray mass spectra of these arsenicals in addition to those of sodium arsenate and an arsenosugar derivative are described. This technique is suitable for HPLC MS studies.
Complexes in polymers III: Addition reactions of trans‐Ir(PPh3)2(CO)Cl embedded in polystyrene with hydrogen, oxygen, sulfur dioxide, carbon monoxide and gaseous iodine and of (η‐C5H5)Ru(η4‐1,5‐cyclooctadiene)Cl in polystyrene with carbon monoxide
Authors: Shaver Alan , Gao Jian Ping , Butler Ian S
Published: January 2005

The addition rections of trans‐Ir(PPh3)2(CO)Cl embedded in films of polystyrene (PS) with hydrogen, oxygen, sulfur dioxide, carbon monoxide and gaseous iodine were monitored by infrared spectroscopy and found to be similar to those occurring in toluene. While the reaction with iodine was rapid at the surface of the film as determined by attenuated‐total‐reflectance infrared spectroscopy, the reaction was much slower in the body of the film, as shown by transmission infrared spectroscopy. No such difference was observed for oxygen. The complex CpRu(COD)Cl (Cp = η‐C5H5, COD = 1,5‐cyclooctadiene) in PS readily undergoes ligand substitution by carbon monoxide (CO and 13CO) to give CpRu(CO)2Cl and CpRu(13CO)2Cl embedded in PS, respectively.
Organotin biocides XV: Modelling the interactions of triorganotins with cell membranes
Authors: Heywood B R , Molloy K C , Waterfield P C
Published: January 2005

The interaction of triorganotins with cell membranes has been examined using synthetic phospholipid membranes (vesicles). Electron microscopy and NMR methods indicate that the organotin is in a five‐coordinate environment at the membrane surface, and is associated weakly with the phosphate headgroups of the vesicle components. Both trimethyl‐ and tributyl‐tin cause extensive modifications to the vesicles including fusion, aggregation, blebbing and total rupture, these effects being initiated at concentrations as low as 25 μmol dm−3.
Carbon–oxygen bond cleavage in allylic esters promoted by low‐valent transition‐metal hydride complexes
Authors: Srivastava R S
Published: January 2005

CoH(N2)(PPh3)3 promotes carbon–oxygen (CO) bond cleavage in allylic carboxylates to give the corresponding olefins at room temperature. On the other hand, RuH2(PPh3)4 and RhH(PPh3)4 are mainly active for CO bond cleavage at elevated temperature. Reaction proceeds through a mechanism involving predissociation of one of the tertiary phosphines from the RuH2(PPh3)4 and RhH(PPh3)4 and competitive coordination of allylic carboxylates and PPh3 to the vacant site on ruthenium and rhodium. A new six‐membered metallocyclic complex, Co(OCOCH2COCH3)(PPh3)2, has been isolated.
Synthesis and spectroscopic studies on organotin(IV) complexes of some pyrazoles and pyrazol‐5‐ones and their antibacterial activity
Authors: Al‐Allaf Talal A K , Al‐Bayati Redha H , Khalaf Subhi H
Published: January 2005

A series of organotin(IV) complexes of the general formula RxSnCl4−x.L (where R=Me, n−Bu, Ph; x = 2 or 3; L = pyrazole or pyrazol‐5‐one) have been prepared and characterized by elemental analyses, IR and NMR spectroscopy. The ligands used were found to coordinate with R3SnCl species as monodentate ligands via the more reactive nitrogen atom, to give pentacoordinate tin complexes, whilst they may coordinate with R2SnCl2 species as bidentate ligands through the N–N linkage to give hexacoordinate tin complexes. These were demonstrated mainly by spectroscopic data. The tautomeric behaviour of organotin complexes of pyrazol‐5‐one ligands in inert (CDCl3) and donor (DMSO‐d6) solvents were also studied. The complexes were screened against six species of bacteria.
Reduction of clay surface‐sorbed organometallics during measurement of X‐ray photoelectron spectra (XPS)
Authors: Claire Ashcroft R. , Abid Khalid Y. , McWhinnie William R. , Saied Sayah O.
Published: January 2005

Some organometallic compounds, e.g. Ph3SnCl, react on the surface of the smectite clay, laponite. Other compounds, e.g. Br3TeC6H4CH=NCH2CH2N=CHC6H4TeBr3, are sorbed onto the organophilic surface of cetylpyridinium‐ion‐exchanged Wyoming bentonite. X‐ray photoelectron spectroscopy (XPS) is an appropriate technique with which to examine the nature of the surface‐sorbed species; however, it is demonstrated that decomposition of the organometallic can occur when the clay surface is exposed over a period of time to energetic X‐rays. Thus, care must be taken with the interpretation of data of which some features may be the result of the XPS experiment.
Structure–Activity relationships of effect of aryltin compounds onCeratocystis ulmi
Authors: Eng George , Zhang Ying Zhi , Whalen Deborah , Ramsammy Roger , Khoo Lian Ee , Derosa Michael
Published: January 2005

The effect of aryltin compounds (Ar4Sn and Ar3SnCl) on the growth ofCeratocystis ulmi, the causative agent of Dutch elm disease, was studied in shake culture. In all cases, the triaryltins were more effective than the tetra‐aryltins as inhibitors ofC. ulmi in vitro.Furthermore, substitution on the phenyl ring at themeta‐ andpara‐ positions in the triaryltins did not have a major effect on the biocidal activity for the substituted triaryltins. Quantitative structure–activity relationships (QSARs) gave support to the idea that the species responsible for the inhibition of the fungus is the triaryltin cation. The QSARs further suggest that the interaction of the triaryltin cation with the fungal cell wall ofC. ulmiis by a non‐specific mechanism.
Application of whole cell NMR techniques to study the interaction of arsenic compounds with catharanthus roseus cell suspension cultures
Authors: Cullen William R. , Hettipathirana Deepthi I.
Published: January 2005

1H spin–echo NMR spectroscopy of intact cells of C. roseus facilitates monitoring changes inside the cells on treatment with arsenicals. This in situ detection method is non‐invasive and non‐destructive in comparison to other available biochemical methods. Short term uptake of the arsinicals, methylarsinate MMA and dimethylarsenate DMA, by C. roseus cells that have reached stationary phase in 1‐B5 medium, is followed by using NMR spectroscopy, and in particular, the Carr–Purcell–Meiboom–Gill pulse sequence. An increase in the peak height of the methylarsenic resonance over a period of 11 h is indicative of uptake of each arsenical. However, there is no evidence of any biotransformation products in the 1H NMR spectra. The accumulation site of DMA is probably the vacuole as is seen from the change in the chemical shift of DMA as it moves into a compartment of lower pH. Biochemical changes associated with the presence of arsenicals are evident in the 1H NMR spectra of C. roseus cells isolated at different stages in the growth cycle. Although uptake has been demonstrated by other analytical techniques, the resonances corresponding to both MMA and DMA are not observed in the 1H NMR spectra of cells growing in media containing each arsenical. The association of these arsenicals with large biomolecules in the cell may account for these absences. In this event, the spins–spin relaxation time of the arsenic species would shorten and the signals would not be seen in the spin–echo NMR spectrum. In cells growing in the presence of MMA, a new resonance is observed at a chemical shift position 2.2 ppm after 15 days of growth. The shift in position of the resonance, from 1.75 ppm expected at physiological pH, may indicate an altered environment around the arsenic species such as high intracellular acidity.
The anti‐inflammatory activity of metal complexes and salts of amine carboxyboranes
Authors: Hall Iris H. , Rajendran K. G. , Chen S. Y. , Norwood V. N. , Morse K. W. , Sood A. , Spielvogel B. F.
Published: January 2005

The metal complexes and salts of amine carboxyboranes were shown to be potent anti‐inflammatory agents in rodents at 8 mg kg−1. They were effective in blocking induced edema, pleurisy and endotoxic shock while blocking both local and central pain processes. The ability of the agents to function as anti‐inflammatory agents is multi‐fold. First, lysosomal enzymes of specific cells, e.g. macrophages, were inhibited with IC50 values in the range of 10−6 M. Collagenase I and II activities were inhibited with IC50 values approximately equal to 10−4 M. The anti‐inflammatory activity of these agents at the molecular levels appears to be due to inhibition of the release of TNFα and Il‐1 from macrophages which indirectly control chemotaxic migration of white blood cells as indicated by the suppression of PMN and macrophage invasion into sponges implanted subcutaneously (SC) in mice. Furthermore, in these invading cells, the agents' blockage of TNFα and Il‐1 or Il‐2 release down‐regulates prostaglandin and leukotriene enzymatic synthetic rates and, consequently, their release, resulting in a reduction of the inflammation process.
From crystalline boryl‐substituted and boryl‐coupled 2,2,4,4,6,6‐hexamethyl‐cyclotrisilazanes to β‐SiC and BN
Authors: Schaible Sabine , Riedel Ralf , Boese R. , Werner E. , Klingebiel Uwe , Nieger Martin
Published: January 2005

[Me2SiNBFN(SiMe3)2]3 (1) is synthesized in the reaction of trilithiated hexamethylcyclotrisilazane with F2BN(SiMe3)2. The mono‐ and dilithium derivatives of the six‐membered ring (Me2SiNH)2 Me2SiNSiFMe2 react with the F2B‐substituted cyclotrisilazane F2B(NSiMe2)3(SiFMe2)2 in the molar ratio 1:1 or 1:2 to give the BF‐coupled rings 2 and 3. The crystal structure analysis of 1 and 3 and pyrolysis of 1 and 3 with formation of silicon boron carbonitride and its crystallisation to composite powders at very high temperatures are reported.
In‐vitro prenatal toxicity of trimethylarsine, trimethylarsine oxide and trimethylarsine sulfide
Authors: Rick Irvin T. , Irgolic Kurt J.
Published: January 2005

The embryolethality and the embryotoxicity of trimethylarsine, trimethylarsine oxide and trimethylarsine sulfide were investigated employing Sprague–Dawley rat embryos with intact yolk sacs. The embryos were removed on day 11 of gestation and grown in a culture medium (Way‐mouth's 725/1) spiked with the arsenic compounds to concentrations in the range 4–100 mM in the presence or absence of rat liver (S‐9) homogenate. After 24 h the yolk‐sac circulation and heart beat were monitored (indicator of embryolethality), the crown‐to‐rump lengths were measured, the neural structures (somites) counted, and the development of the limb buds evaluated (indicators of embryotoxicity). At a trimethylarsine concentration of 18.7 mM 78% of the embryos were dead when no S‐9 was present. In the presence of S‐9 all embryos survived but were necrotic and malformed. Signs of embryotoxicity were observed at concentrations of 18.7 and 9.3 mM. At the 4.7 mM concentration the embryos grew as well as the control embryos. Trimethylarsine oxide v as lethal at 100 mM and severely embryotoxic at 50 and 25 mM. At all but the lowest concentration (4.5 mM) the embryos looked sick, and were frequently necrotic, deformed and underdeveloped. Trimethylarsine sulfide exhibited severe embryotoxicity at 50 mM concentration in the absence and in the presence of S‐9. Signs of acute toxicity were observable at 9 mM concentrations of trimethylarsine and trimethylarsine oxide. Compared with other environmental toxicants that show effects at concentrations orders of magnitude smaller, these arsenic compounds cannot be classified as very toxic.
A palladium(O)–samarium(II) system for the preparation of allenes from propargylic acetates: Application to the synthesis of 2,3‐naphthoquinodimethanes
Authors: Sugimoto Yuichi , Hanamoto Takeshi , Inanaga Junji
Published: January 2005

The selective conversion of 1,2‐bis(1′‐acetoxy‐2′‐ propynyl)benzene derivatives to the corresponding 1,2‐diallenylbenzenes with the aid of a palladium(O)–samarium(II) reduction system leads to a new route to fairly reactive o‐naphthoquinodimethane derivatives under mild conditions. The reactions of these naphthoquinodimethanes were found to follow different paths depending on the nature of the substituents on the terminal acetylenic carbon atoms. They undergo intermolecular Diels–Alder reactions with various dienophiles, intramolecular [2+2] cycloadditions, or intramolecular [1,5]‐sigmatropic hydrogen shifts.
Lanthanoid‐Metal‐Mediated organic reactions of acyltrialkylsilanes
Authors: Taniguchi Yuki , Fujii Nobuto , Takaki Ken , Fujiwara Yuzo
Published: January 2005

Aromatic acylsilanes such as benzoyltrimethylsilane react with ytterbium (Yb) metal to give the corresponding Yb‐oxametallacycle of the aromatic acylsilane. The Yb‐oxametallacycle thereby formed reacts with another aroylsilane to afford the symmetrical 1,2‐diarylacetylene in good yield. These nucleophilic Yb‐oxametallacycles have been found to react with a variety of electrophiles affording α‐silyl alcohol derivatives. In contrast, aliphatic acylsilanes are reduced with lanthanoid reagents such as Yb metal and samarium(II) iodide (SmI2) to give α‐silyl alcohols, and the corresponding aliphatic acetylene was not obtained.
Cerium in organic reactions: Construction of 2‐isoxazoline ring mediated by ammonium cerium nitrate
Authors: Sugiyama Takashi
Published: January 2005

Direct construction of the 2‐isoxazoline ring directly from an alkene, or from an alkene and primary nitroalkane, was achieved in the presence of ammonium cerium nitrates. It has been found that (1) a carboxylic acid such as formic acid is required to promote the reaction, (2) an appropriate additive is required, when ammonium cerium(IV) nitrate is employed, but the additive is not necessary when ammonium cerium(III) nitrate is employed, (3) both ammonium cerium nitrates are converted into cerium(III) formate before the reaction takes place, and, (4) the cerium ion acts as a carrier of NOx as well as the activator of the nitro compound, and nitrate anion is the source of the NOx as well as the promoter of the reaction. A plausible reaction scheme has been proposed.
Unusual cerium(III) chloride‐promoted reactions of alkenyl grignard reagents or alkenyl‐lithiums with 1,3‐diphenyl‐2‐propanone: Formation and trapping of diorganometallic species
Authors: Imamoto Tsuneo , Hatajima Toshihiko , Ogata Koreharu , Nishiura Masayoshi
Published: January 2005

Treatment of vinylmagnesium chloride with anhydrous cerium(III) chloride in tetrahydrofuran at −20°C, followed by reaction with 1,3‐diphenyl‐2‐propanone, afforded (Z)‐2,7‐dibenzyl 1,8‐diphenyl‐4‐octene‐2,7‐diol and (Z)‐2,7‐dibenzyl‐1,8‐diphenyl‐4,6‐octadien‐2‐ol in 19% and 9% yield, respectively. Isopropenyl‐magnesium bromide underwent trimerization on treatment with cerium chloride at 20°C, and the subsequent reaction with the same ketone provided (Z,Z)‐2,9‐dibenzyl‐4,5,7‐trimethyl‐1,10‐diphenyl‐4,6‐decadiene‐2, 9‐diol in 22% yield. Under similar conditions, the reaction of 2‐methyl‐1‐propenylmagnesium bromide provided (Z)‐2,6‐dibenzyl‐4‐methyl‐1,7‐diphenyl‐3,5‐heptadien‐2‐ol in 7% yield. Vinyl‐lithium and isopropenyl‐lithium were also subjected to dimerization by the action of cerium chloride, and the generated diorganometallic species were trapped by 1,3‐diphenyl‐2‐propanone.
Yb/TMSBr promoted homocoupling reactions of aliphatic ketones, α,β‐unsaturated ketones and aliphatic imines
Authors: Taniguchi Yuki , Kuno Tatsuhiro , Nakahashi Manabu , Takaki Ken , Fujiwara Yuzo
Published: January 2005

A powerful reducing reagent, ytterbium dibromide (YbBr2), was synthesized by a new method using ytterbium metal and trimethylsilyl bromide (TMSBr) in tetrahydrofuran‐hexamethylphosphoramide (THF–HMPA). YbBr2, thus formed in situ, causes coupling reactions of aliphatic ketones, α,β‐unsaturated ketones and aliphatic aldimines to give bis‐silylated 1,2‐diols, 1,6‐diketones and 1,2‐diamines, respectively, in good yields. In the case of aliphatic ketimines, the corresponding reduced and silylated amines are obtained. In this solvent system, the trialkylsilyl moiety of trialkylsilyl bromide is converted to trialkylsilanes quantitatively. These results show that the Yb/TMSBr reagent generates YbBr2 in situ and the YbBr2 thus formed acts as a single‐electron reductant for these coupling reactions.
Development and application of a model for chitosan hydrolysis by a family 18 chitinase
Authors: Sikorski Pawel , Stokke Bjørn T. , Sørbotten Audun , Vårum Kjell M. , Horn Svein J. , Eijsink Vincent G. H.
Published: January 2005

Hydrolysis of partially deacetylated chitosans by ChitinaseB (ChiB) from Serratia marcescens results in mixtures of oligosaccharides typically between 2 and 20 sugar residues. The amounts of different oligomer fractions depend on the degree of acetylation of the starting chitosans. We have used experimentally determined distributions of hydrolysis products to develop a model for chitosan hydrolysis by ChiB. Important elements of the model include interaction parameters for acetylated/deacetylated units in each of the six subsites in the active cleft and degree of processivity (multiple attack). The hydrolysis reaction is described as a chemical reaction with an activation barrier that depends on the substrate sequence presented to the enzyme subsites. Using a Monte Carlo approach, the interaction parameters were refined by minimizing the difference between observed and predicted amounts of hydrolysis products obtained upon degradation of chitosan with a degree of acetylation of 65%. The final model can accurately predict complex patterns of oligosaccharides produced in the hydrolysis of chitosans with various degrees of acetylation, as well as patterns observed during reactions with chito‐oligosaccharides. The behavior of a ChiB mutant with a mutation in subsite +2 (Gly188Asp), which reduces the affinity for an acetylated sugar, could be predicted correctly by introducing one single change in the model parameters (the interaction energy for an acetylated unit in the +2 subsite). The proposed model may be used to explore degradation products for different enzyme–substrates combinations and to optimize conditions for preparation of specific oligosaccharides. In addition, the model provides insight into subsite interaction parameters and the degree of processivity, which complements previous experimental studies on the mode of action of ChiB. © 2005 Wiley Periodicals, Inc. Biopolymers 77: 273–285, 2005
The effect of temperature on DNA structural transitions under the action of Cu2+ and Ca2+ ions in aqueous solutions
Authors: Hackl Elene V. , Blagoi Yurij P.
Published: January 2005

The work examines the structural transitions of DNA under the action of Cu2+ and Ca2+ ions in aqueous solution at temperatures of 29 and 45°C by ir spectroscopy. Upon binding to the divalent ions studied, DNA transits into the compact state both at 29 and 45°C. In the compact state DNA remains in B‐form limits. The compaction process is of high positive cooperativity. As temperature increases the divalent metal ion concentration required to induce DNA compaction decreases in the case of Cu2+‐induced compaction and increases in the case of Ca2+‐induced compaction. It is suggested that the mechanism of the temperature effect on DNA compaction in the presence of Cu2+ ions possessing higher affinity for DNA bases differs from that of the temperature influence on Ca2+‐induced DNA compaction. In the case of copper ions the determining factor is the increase of binding constants of the Cu2+ ions interacting with the denatured parts formed on DNA while in the case of calcium ions it is the decreased screening action of counterions upon the increase of their hydration with temperature. The efficiency of divalent metal ions studied in inducing DNA compaction depends on hydration of counterions. DNA compaction occurs in a narrow interval of Cu2+ concentrations. As the Cu2+ ion concentration increases, DNA compaction is replaced with Cu2+‐induced DNA aggregation. At elevated temperatures Cu2+‐induced DNA compaction could acquire a phase transition character. © 2005 Wiley Periodicals, Inc. Biopolymers 77: 315–324, 2005
Workshop—predicting the structure of biological molecules
Authors: Counsell Damian
Published: January 2005

This April, in Cambridge (UK), principal investigators from the Mathematical Biology Group of the Medical Research Council's National Institute of Medical Research organized a workshop in structural bioinformatics at the Centre for Mathematical Sciences. Bioinformatics researchers of several nationalities from labs around the country presented and discussed their computational work in biomolecular structure prediction and analysis, and in protein evolution. The meeting was intensive and lively and gave attendees an overview of the healthy state of protein bioinformatics in the UK. Copyright © 2004 John Wiley & Sons, Ltd.
The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature
Authors: Yamamoto Satoko , Asanuma Takao , Takagi Toshihisa , Fukuda Ken Ichiro
Published: January 2005

In general, it is not easy to specify a single sequence identity for each molecule name that appears in a pathway in the scientific literature. A molecule name may stand for concepts of various granularities, from concrete objects such as H‐Ras and ERK1 to abstract concepts or categories such as Ras and MAPK. Typically, the relations among molecule names derive a hierarchical structure; without a proper way to handle this knowledge, it becomes ever more difficult to develop a reliable pathway database. This paper describes an ontology that is designed to annotate molecules in the scientific literature on signal transduction pathways. Copyright © 2004 John Wiley & Sons, Ltd.
Obol: integrating language and meaning in bio‐ontologies
Authors: Mungall Christopher J.
Published: January 2005

Ontologies are intended to capture and formalize a domain of knowledge. The ontologies comprising the Open Biological Ontologies (OBO) project, which includes the Gene Ontology (GO), are formalizations of various domains of biological knowledge. Ontologies within OBO typically lack computable definitions that serve to differentiate a term from other similar terms. The computer is unable to determine the meaning of a term, which presents problems for tools such as automated reasoners. Reasoners can be of enormous benefit in managing a complex ontology. OBO term names frequently implicitly encode the kind of definitions that can be used by computational tools, such as automated reasoners. The definitions encoded in the names are not easily amenable to computation, because the names are ostensibly natural language phrases designed for human users. These names are highly regular in their grammar, and can thus be treated as valid sentences in some formal or computable language. With a description of the rules underlying this formal language, term names can be parsed to derive computable definitions, which can then be reasoned over. This paper describes the effort to elucidate that language, called Obol, and the attempts to reason over the resulting definitions. The current implementation finds unique non‐trivial definitions for around half of the terms in the GO, and has been used to find 223 missing relationships, which have since been added to the ontology. Obol has utility as an ontology maintenance tool, and as a means of generating computable definitions for a whole ontology.

The software is available under an open‐source license from: http://www.fruitfly.org/∼cjm/obol. Supplementary material for this article can be found at: http://www.interscience.wiley.com/jpages/1531‐6912/suppmat. Copyright © 2004 John Wiley & Sons, Ltd.
Ontology for genome comparison and genomic rearrangements
Authors: Flanagan Keith , Stevens Robert , Pocock Matthew , Lee Pete , Wipat Anil
Published: January 2005

We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation. Copyright © 2004 John Wiley & Sons, Ltd.
Characterization of multilocus linkage disequilibrium
Authors: Rinaldo Alessandro , Bacanu Silviu‐Alin , Devlin B. , Sonpar Vibhor , Wasserman Larry , Roeder Kathryn
Published: January 2005

Linkage disequilibrium (LD) in the human genome, often measured as pairwise correlation between adjacent markers, shows substantial spatial heterogeneity. Congruent with these results, studies have found that certain regions of the genome have far less haplotype diversity than expected if the alleles at multiple markers were independent, while other sets of adjacent markers behave almost independently. Regions with limited haplotype diversity have been described as “blocked” or “haplotype blocks.” In this article, we propose a new method that aims to distinguish between blocked and unblocked regions in the genome. Like some other approaches, the method analyses haplotype diversity. Unlike other methods, it allows for adjacent, distinct blocks and also multiple, independent single nucleotide polymorphisms (SNPs) separating blocks. Based on an approximate likelihood model and a parsimony criterion to penalize for model complexity, the method partitions a genomic region into blocks relatively quickly, and simulations suggest that its partitions are accurate. We also propose a new, efficient method to select SNPs for association analysis, namely tag SNPs. These methods compare favorably to similar blocking and tagging methods using simulations. Genet. Epidemiol. © 2005 Wiley‐Liss, Inc.
Involvement of glial cell line‐derived neurotrophic factor in activation processes of rodent macrophages
Authors: Hashimoto Manabu , Nitta Atsumi , Fukumitsu Hidefumi , Nomoto Hiroshi , Shen Liya , Furukawa Shoei
Published: January 2005

The physiological roles of glial cell line‐derived neurotrophic factor (GDNF) expressed in the microglia/macrophages of the injured spinal cord have not yet been clarified. mRNA expression of chemokines, including monocyte chemoattractant protein (MCP)‐1, was evoked within 1 hr after transection of the spinal cord, and GDNF mRNA expression was similarly up‐regulated. Immunohistochemical analysis showed that GDNF was coexpressed with MCP‐1 in the CD11b‐positive cells. Therefore, we examined further the effects of GDNF on cultured rat peritoneal macrophages. GDNF enhanced the phagocytic activity of the macrophages via GFRα‐1, glycosylphosphatidylinositol‐anchored specific binding site of GDNF, in a c‐Ret‐independent manner. The influence of autocrine and/or paracrine GDNF synthesis was evaluated by performing activation experiments using macrophages cultured from heterozygous (+/−) GDNF gene‐deficient mice or wild‐type (+/+) mice. There were no morphological differences dependent on genetic types or stimulators. However, the GDNF mRNA level, but not the MCP‐1 or GFRα‐1 mRNA level, was substantially lower in the mutant macrophages than in the +/+ cells irrespective of stimulation with MCP‐1 or lipopolysaccharide (LPS). The phagocytic activity enhanced by MCP‐1 or LPS was significantly lower in the mutant cells (+/−) than in the +/+ ones, demonstrating the involvement of endogenous GDNF in the activation processes of macrophages in vitro and suggesting that not only neuroprotective function but also activation of macrophages is effected by the GDNF produced after a spinal cord injury. © 2005 Wiley‐Liss, Inc.
Schwann cell‐autonomous role of neuropilin‐2
Authors: Ara J. , Bannerman P. , Shaheen F. , Pleasure D.E.
Published: January 2005

Neuropilins and group A plexins are components of receptor complexes for class 3 semaphorins, gradients of which help to guide migration of neural progenitor cells and axonal growth cones during development. We demonstrated previously that neuropilins and class 3 semaphorins are induced in sciatic nerve by crush or transection. We now report that in cultured rat Schwann cells, expression of mRNA encoding neuropilin‐2 (NRP2) and plexin‐A3 (PlexA3), proteins involved in semaphorin‐3F (Sema3F) signal transduction, is diminished markedly by forskolin, an adenylate cyclase activator that, like axonal contact, induces Schwann cell synthesis of myelin lipids and proteins. Interestingly, Schwann cell expression of mRNA encoding NRP1, which participates in Sema3A signaling, is not downregulated by forskolin. Antibodies that recognize ectodomains of NRP2 but not control antibodies prevented cultured Schwann cells from aligning in parallel and forming columns. These results are consistent with the view that in nerves undergoing Wallerian degeneration, Schwann cell NRP2 facilitates assembly of Schwann cells into the tubular aggregates (bands of Büngner) that guide regenerating axons. © 2005 Wiley‐Liss, Inc.
Mercury compounds disrupt neuronal glutamate transport in cultured mouse cerebellar granule cells
Authors: Fonfría Elena , Vilaró M. Teresa , Babot Zoila , Rodríguez‐Farré Eduard , Suñol Cristina
Published: January 2005

Cerebellar granule cells are targeted selectively by mercury compounds in vivo. Despite the affinity of mercury for thiol groups present in all cells, the molecular determinant(s) of selective cerebellar degeneration remain to be elucidated fully. We studied the effect of mercury compounds on neuronal glutamate transport in primary cultures of mouse cerebellar granule cells. Immunoblots probed with an antibody against the excitatory amino acid transporter (EAAT) neuronal glutamate transporter, EAAT3, revealed the presence of a specific band in control and mercury‐treated cultures. Micromolar concentrations of both methylmercury and mercuric chloride increased the release of endogenous glutamate, inhibited glutamate uptake, reduced mitochondrial activity, and decreased ATP levels. All these effects were completely prevented by the nonpermeant reducing agent Tris‐(2‐carboxyethyl)phosphine (TCEP). Reduction of mitochondrial activity by mercuric chloride, but not by methylmercury, was inhibited significantly by 4,4′‐diisothiocyanato‐stilbene‐2,2′‐disulfonic acid (DIDS) and by reduced extracellular Cl− ion concentration. In addition, DIDS and low extracellular Cl− completely inhibited the release of glutamate induced by mercuric chloride, and produced a partial although significant reduction of that induced by methylmercury. We suggest that a direct inhibition of glutamate uptake triggers an imbalance in cell homeostasis, leading to neuronal failure and Cl−‐regulated cellular glutamate efflux. Our results demonstrate that neuronal glutamate transport is a novel target to be taken into account when assessing mercury‐induced neurotoxicity. © 2005 Wiley‐Liss, Inc.
The reactions of atomic hydrogen and active nitrogen with hydrogen azide
Authors: Le Bras G. , Combourieu J.
Published: January 2005

Detection of atoms by mass spectrometry has been used to study the reactions of hydrogen azide, HN3, with H atoms and active nitrogen, in a fast flow reactor at pressures of about 1 torr. Stoichiometry and products of the H + HN3 reaction have been determined and the rate constant of the initial step, assumed to be H + HN3 → NH2 + N2, was found to be 2.54 × 10−11 exp (−4600/RT) cm3 molecule−1 s−1, in the temperature range of 300–460K. The formation of NH3 and H2 products has been discussed from the different secondary steps which may occur in the mechanism. For the reaction of active nitrogen with HN3, evidence has been found for the participation of excited nitrogen molecules produced by a microwave discharge through molecular nitrogen. The influence of excited nitrogen molecules has been reduced by lowering the gas flow velocity. It was then possible to study the N + HN3 reaction for which the rate constant of the initial step was found to be 4.9 × 10−15 cm3 molecule−1 s−1 at room temperature. Finally, the occurrence of these elementary reactions has been discussed in the mechanism of the decomposition flame of HN3.
Are HO radicals produced in the reaction of O(3P) with 1‐C4H8?
Authors: Luria Menachem , Simonaitis R. , Heicklen Julian
Published: January 2005

The reaction of O(3P) with 1‐C4H8 was examined in the presence of CO which scavenges HO radicals to produce CO2. From the CO2 quantum yield, an upper limit to the efficiency of HO production in the reaction of O(3P) with 1‐C4H8 was found to be 0.02 at both 298° and 473°K.
Methyl‐radical association studied by time‐resolved mass spectroscopy
Authors: Truby Frank K. , Rice James K.
Published: January 2005

Time‐resolved mass spectroscopy has been utilized to study the kinetics of methylradical association. The rate coefficient for the association process was determined by following the time dependence of ethane formation after flash photolysis of CH3I in the presence of N2. The net rate coefficient for the process 2CH3 (+M) → C2H6(+M) has a high‐pressure limit of (4.0 ± 0.3) × 10−11 cm3 molecule−1 sec−1 at 313°K. This rate coefficient has found to be insensitive to the third‐body number densities for pressures ranging from 13 Torr down to below 0.5 Torr, indicating that the lifetime for dissociation of the intermediate C2H6* species is greater than 2 × 10−7 sec at 313°K for a gas pressure of 0.5 Torr.
Vibrational energy transfer in near resonance due to dipole–dipole interactions
Authors: Lev‐on Miriam , Palke William E. , Millikan Roger C.
Published: January 2005

The contribution of long‐range forces to the observed rates of V → V energy transfer processes has been studied. The theoretical model uses the first order perturbation approximation to generate a probability function, with the dipole–dipole perturbing potential as given by Margenau: Vif = [(1/6)1/2μ1 · μ2]R−3. The probability function derived is shown to be a strong function of the energy mismatch between the IR bands of the colliding molecules. The calculation emphasizes the importance of rotational state population effects, the most important J states being those which minimize the energy mismatch. A complete analysis of energy transfer between CO(v) and COS(000) where v = 1,2, ⃛ 13 is presented. The calculation reveals the importance of combination bands in the energy transfer mechanism of polyatomics. The temperature dependence for near‐resonant processes is also studied and the importance of the V → R energy transfer leads to the classification of ω0 (band‐center energy mismatch) into three categories small, medium, and large, according to the temperature dependence that the corresponding processes exhibit. The predictions of the theoretical model are compared to experimental data for the same system.
Electronically excited oxygen atoms, O(21D2). A time‐resolved study of the collisional quenching by the gases H2, D2, CH4, NO, NO2, N2O, and C3O2 using atomic absorption spectroscopy in the vacuum ultraviolet
Authors: Heidner R. F. , Husain D.
Published: January 2005

Time‐resolved atomic absorption spectroscopy in the vacuum ultraviolet has been employed to monitor electronically excited oxygen atoms, O(21D2), following their genera‐tion by the flash photolysis of ozone in the Hartley band region. We report the first values for the absolute second‐order rate constants describing the removal of the excited atom on collision with the molecules H2, D2, CH4, NO, NO2, N2O, and C3O2. Where possible, these data are considered within the context of restrictions arising from spin and orbital symmetry and are further discussed in tems of previously reported relative rate data derived from indirect measurements. Consideration is given to the importance of these rate con‐stants in discussing processes taking place in the earth's atmosphere and in systems giving rise to chemical laser action.
A flash photolysis–resonance fluorescence kinetics study of the reactions of ground‐state sulfur atoms. V. Rate parameters for the reaction of S(3P)with cis‐2‐butene and tetramethylethylene
Authors: Davis D. D. , Klemm R. B.
Published: January 2005

Rate parameters for the reaction of ground‐state atomic sulfur, S(3P), with the olefins cis‐2‐butene and tetramethylethylene have been determined over a temperature range of ∽280°K. A major finding of this study was that the rate constants for both reactions showed negative temperature dependencies. When k is expressed in the form of an Arrhenius equation, this necessarily leads to negative activation energies: k1 = (4.68 ± 0.70) × 10−12 exp (+0.23 ± 0.09 kcal/mole)/RT (219°‐500°K) k2 = (4.68 ± 1.70) × 10−12 exp (+1.29 ± 0.23 kcal/mole)/RT (252°‐500°K) Units are cm3 molec−1s−1. When a threshold energy of 0.0 kcal/mole is assumed for reaction (2), the temperature dependence of the preexponential term has a value of T−2. Making the usual simplifying assumptions, neither collision theory nor transition state theory leads to a preexponential factor with a strong enough negative temperature dependence. A comparison of these results with those derived from studies of the reactions of atomic oxygen, O(3P), with the same olefins shows that in both studies simple bimolecular processes were being examined. Also discussed are the possible experimental and theoretical ramifications of these new results.
Chemical lasers produced from O(3P) atom reactions. III. 5‐μm CO laser emission from the O + CH reaction
Authors: Lin M. C.
Published: January 2005

Very strong laser emission at 5 μm was detected when SO2 and CHBr3 were flash photolyzed in the vacuum ultraviolet (λ ≥ 165 nm) in the presence of a large amount of diluent (SF6, He, or Ar). About 110 vibration–rotation transitions ranging from Δv = 18 → 17 to 3 → 2, except 16 → 15, were identified. The primary reactions leading to the CO stimulated emission are as follows:

equation image

The product analysis results and the variation of laser intensity with flash energy and SO concentration indicate that the following side reactions

equation image

are also occurring. Addition of a small amount of O2 enhances the laser output by both eliminating these side reactions and simultaneously producing vibrationally excited CO via reaction (8),

equation image

which has been previously shown to generate CO stimulated emission. The effects of various reactive (NO and H2) and inert (He, Ar, SF6, CO, N2, N2O, and CO2) gases have been examined. All additives (P ≤ 20 torr), except NO and H2, increase the total laser output. N2O enhances the power most efficiently, whereas CO, N2, and CO2 are less effective and have similar efficiencies. The enhancement of the laser intensity by these near‐resonant gases is ascribed to the depletion of CO population at lower levels which thus increases the rates cascading from higher levels. NO and H2 quench the laser output by chemically reducing the concentration of the CH radical.
Reactions of halogens with hydrogen halides. Studies in the Cl2 + HBr system
Authors: Wen Walter Y. , Noyes Richard M.
Published: January 2005

The following net processes occur in a system containing chlorine and hydrogen bromide:

equation image

These reactions have been followed spectrophotometrically in a gas phase stopped flow apparatus. The first two reactions are strongly surface catalyzed on untreated glass or quartz, but are much slower if the cell surface has been covered with silicone and photochlorinated. Rates in such systems are first order in each reactant, and comparable limiting rate constants have been obtained in cells with different methods of preparing the surfaces and with different surface‐to‐volume ratios. These experimental rate constants must be equal to or greater than those of the homogeneous bimolecular reactions. Then limiting rate constants at 35°C in liters per mole per second are k1 ≤ 0.8, k 2 ≤ 15, and k3 ≤ 0.04. Reactions of HI with Cl2, Br2, and ICl are all much faster than reaction (2). These observations and those of other diatomic molecule reactions can be rationalized if halogen and hydrogen halide molecules react through a transition state in which the hydrogen atom is near the center of a triangle of three halogen atoms.
Flash Photolysis of 2,4,6‐Trinitrotoluene Solutions
Authors: Suryanarayanan K. , Capellos C.
Published: January 2005

Flash photolysis of 2,4,6‐trinitrotoluene solutions (TNT) indicates a photochemically induced isomerization leading to the aci‐quinoid isomer magnified image with an absorption maximum at 460 nm in nonpolar solvents, or the conjugate base magnified image of the aci‐quinoid isomer with absorption maxima at 500, 540, and 630 nm in polar solvents. Both species, the quinoid isomer and the conjugate base, have transient existence and their identification was based on detailed spectroscopic and kinetic studies presented here. The magnitude of the negative charge on the transient conjugate base was determined with salt effect experiments and found to be equal to unity.
Kinetic and mechanistic study of the reactions of palladium(II) chlorocomplexes with ethylenediamine in aqueous acid medium
Authors: De Waal D. J. A. , Robb W.
Published: January 2005

The complexes PdCl42−, PdCl3(H2O)−, and PdCl3(Ac)2−, in rapid equilibrium with each other under the adopted experimental conditions, react with ethylenediamine according to the experimental rate law

A reaction scheme is proposed involving the reaction of enH+ with each of the above species, and the specific rate constants are computed. The activation parameters are given.
Initiation process in the system Fe3+ + H2O2
Authors: Kozlov Yu. N. , Nadezhdin A. D. , Pourmal A. P.
Published: January 2005

An inhibitor method for measuring the initiation rate is proposed for the system Fe3+ + H2O2. C(NO2)4 was used as inhibitor. The number of chains terminated by one C(NO2)4 molecule was estimated in specific photochemical experiments and found to be unity. The initiation appeared to involve two processes. The first is proportional to the first power of ferric ion concentration, and the second to the second power. The rate constants and activation energies of these processes are determined. Allowance for the second initiation process permitted qualitative and quantitative description of various reported data on H2O2 decomposition rates over a wide range of Fe3+, H2O2, and H+ concentrations.
Addition–substitution competition in liquid‐phase chlorinations
Authors: Coppens G. , Martens G. J. , Godfroid M. , Delvaux J. , Verbeyst J.
Published: January 2005

The rate constants of liquid‐phase hydrogen abstraction by chlorine atoms from 1,2‐C2H4Cl2 relative to those of addition to C2HCl3 and to C2Cl4 and to that of hydrogen abstraction from cyclohexane have been measured between 250 and 345°K. Assuming a zero activation energy for the addition reactions permits one to calculate the corresponding values for the liquid‐phase hydrogen abstraction from the chlorinated ethanes. These values are discussed and compared with the gas‐phase data.
Arrhenius parameters for reactions of oxygen atoms with the fluorinated ethylenes
Authors: Jones D. S. , Moss S. J.
Published: January 2005

Competitive studies of the reactions of ground‐state oxygen atoms, generated by mercury‐photosensitized decomposition of nitrous oxide, have been carried out with ethylene and all the fluoroethylenes using 2‐(trifluoromethyl)‐propene as reference compound. From measurements at 25°C and 150°C relative rate constants have been determined and used to calculate the Arrhenius parameters shown in the following table:

Olefin

ΔERef

ΔE

CH2CH2
1.10
−1.18
(1.0)
(0)

CH2CHF
1.03
0.84
0.94
2.02

CH2CF2
0.71
1.49
0.65
2.67

CHFCHF (cis‐)
1.23
1.92
1.12
3.10

CHFCHF (trans‐)
1.40
0.79
1.27
1.97

CF2CHF
1.06
0.00
0.96
1.22

CF2CF2
0.86
−3.22
0.78
−2.04

ΔERef = Eolefin − E2TFMP and ΔE = Eolefin − E. Units are kJ/mole.

The results are compared with corresponding data for other atoms and radicals, and discussed in terms of the electronic changes produced in the double bond by fluorine substitution, and in relation to the nature of the transition state.
Rate constants for the bimolecular self‐reactions of ethyl, isopropyl, and tert‐butyl radicals in solution. A direct comparison
Authors: Griller D. , Ingold K. U.
Published: January 2005

A competitive method involving the direct measurement of radical concentrations by EPR spectroscopy has been used to show that in solution at 25°C the rate constants for the bimolecular self‐reactions of ethyl, isopropyl, tert‐butyl, cyclopentyl, and trichloromethyl are all approximately equal, as had been indicated previously by direct measurement of the rate constants for decay of these radicals.
The kinetics of nucleophilic substitution processes in the alkyl halides. Part A—theory
Authors: German E. D. , Dogonadze R. R.
Published: January 2005

Activation energies for substitution reactions of the type AC + B → A + CB, occurring in polar media and characterized by an abrupt change of the term along two coordinates have been calculated within the framework of the quantum‐mechanical theory of chemical reactions. In the case of nonadiabatic processes, the transmission coefficient and activation energy for these reactions are expressed in terms of characteristic parameters of the medium (reorganization energy, effective frequency of solvent fluctuation polarization) and the potential energy curves for intermolecular interactions between the reactants (AC and B) and between the products (A and BC).
The ferric ion catalyzed decomposition of hydrogen peroxide in perchloric acid solution
Authors: Walling Cheves , Weil Tomas
Published: January 2005

Predictions of the “redox” and “complex” schemes for the Fe3+ catalyzed decomposition of H2O2 have been compared with published and new experimental data by numerical integratior of the appropriate complete sets of differential equations. Apparent discrepancies for the redox scheme at high Fe3+/H2O2 ratios are shown to disappear in the complete treatment, and inconsistencies of the complex scheme with both kinetic data and spectroscopic measurements are pointed out.