bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome‐wide analysis of the effects of heat shock on a Saccharomyces cerevisiae mutant with a constitutively activated cAMP‐dependent pathway
Authors: Jones Dawn L. , Petty June , Hoyle David C. , Hayes Andrew , Oliver Stephen G. , Riba‐Garcia Isabel , Gaskell Simon J. , Stateva Lubomira 
Published: August 2004

AbstractWe have used DNA microarray technology and 2‐D gel electrophoresis combined with mass spectrometry to investigate the effects of a drastic heat shock from 30 °C to 50 °C on a genome‐wide scale. This experimental condition is used to differentiate between wild‐type cells and those with a constitutively active cAMP‐dependent pathway in Saccharomyces cerevisiae. Whilst more than 50% of the former survive this shock, almost all of the latter lose viability. We compared the transcriptomes of the wild‐type and a mutant strain deleted for the gene PDE2, encoding the high‐affinity cAMP phosphodiesterase before and after heat shock treatment. We also compared the two heat‐shocked samples with one another, allowing us to determine the changes that occur in the pde2Δ mutant which cause such a dramatic loss of viability after heat shock. Several genes involved in ergosterol biosynthesis and carbon source utilization had altered expression levels, suggesting that these processes might be potential factors in heat shock survival. These predictions and also the effect of the different phases of the cell cycle were confirmed by biochemical and phenotypic analyses. 146 genes of previously unknown function were identified amongst the genes with altered expression levels and deletion mutants in 13 of these genes were found to be highly sensitive to heat shock. Differences in response to heat shock were also observed at the level of the proteome, with a higher level of protein degradation in the mutant, as revealed by comparing 2‐D gels of wild‐type and mutant heat‐shocked samples and mass spectrometry analysis of the differentially produced proteins. Copyright © 2004 John Wiley & Sons, Ltd.
A case study on choosing normalization methods and test statistics for two‐channel microarray data
Authors: Xie Yang , Jeong Kyeong S. , Pan Wei , Khodursky Arkady , Carlin Bradley P. 
Published: August 2004

AbstractDNA microarray analysis is a biological technology which permits the whole genome to be monitored simultaneously on a single slide. Microarray technology not only opens an exciting research area for biologists, but also provides significant new challenges to statisticians. Two very common questions in the analysis of microarray data are, first, should we normalize arrays to remove potential systematic biases, and if so, what normalization method should we use? Second, how should we then implement tests of statistical significance? Straightforward and uniform answers to these questions remain elusive. In this paper, we use a real data example to illustrate a practical approach to addressing these questions. Our data is taken from a DNA–protein binding microarray experiment aimed at furthering our understanding of transcription regulation mechanisms, one of the most important issues in biology. For the purpose of preprocessing data, we suggest looking at descriptive plots first to decide whether we need preliminary normalization and, if so, how this should be accomplished. For subsequent comparative inference, we recommend use of an empirical Bayes method (the B statistic), since it performs much better than traditional methods, such as the sample mean (M statistic) and Student's t statistic, and it is also relatively easy to compute and explain compared to the others. The false discovery rate (FDR) is used to evaluate the different methods, and our comparative results lend support to our above suggestions. Copyright © 2004 John Wiley & Sons, Ltd.
Comparative analysis of the testis and ovary transcriptomes in zebrafish by combining experimental and computational tools
Authors: Li Yang , Chia Jer Ming , Bartfai Richard , Christoffels Alan , Yue Gen Hua , Ding Ke , Ho Mei Yin , Hill James A. , Stupka Elia , Orban Laszlo 
Published: August 2004

AbstractStudies on the zebrafish model have contributed to our understanding of several important developmental processes, especially those that can be easily studied in the embryo. However, our knowledge on late events such as gonad differentiation in the zebrafish is still limited. Here we provide an analysis on the gene sets expressed in the adult zebrafish testis and ovary in an attempt to identify genes with potential role in (zebra)fish gonad development and function. We produced 10 533 expressed sequence tags (ESTs) from zebrafish testis or ovary and downloaded an additional 23 642 gonad‐derived sequences from the zebrafish EST database. We clustered these sequences together with over 13 000 kidney‐derived zebrafish ESTs to study partial transcriptomes for these three organs. We searched for genes with gonad‐specific expression by screening macroarrays containing at least 2600 unique cDNA inserts with testis‐, ovary‐ and kidney‐derived cDNA probes. Clones hybridizing to only one of the two gonad probes were selected, and subsequently screened with computational tools to identify 72 genes with potentially testis‐specific and 97 genes with potentially ovary‐specific expression, respectively. PCR‐amplification confirmed gonad‐specificity for 21 of the 45 clones tested (all without known function). Our study, which involves over 47 000 EST sequences and specialized cDNA arrays, is the first analysis of adult organ transcriptomes of zebrafish at such a scale. The study of genes expressed in adult zebrafish testis and ovary will provide useful information on regulation of gene expression in teleost gonads and might also contribute to our understanding of the development and differentiation of reproductive organs in vertebrates. Copyright © 2004 John Wiley & Sons, Ltd.
A “Single‐Sample Concept” (SSC): A New Approach to the Combinatorial Chemistry of Inorganic Materials
Authors: Hulliger Jürg , Aslam Awan Muhammad 
Published: August 2004

AbstractCombinatorial estimations show that, within an unreacted ceramic sample prepared by mixing N different starting materials MxOy with average particle size ∼1 μm, there are about 1012 grains per cubic centimeter, sufficient for local reactions to occur that may produce a larger number of product oxides than presently accessible by 2D plate techniques. The “single‐sample concept” (SSC) is proposed for performing property‐directed syntheses for the preparation of ferri‐/ferromagnetic or superconducting compounds. Because of the magnetic properties of the products, libraries of product grains can be sorted by means of magnetic separation techniques. For materials with a large magnetization, the separation efficiency is so high that traces of products can be isolated. The SSC concept was tested experimentally to prepare Fe‐based oxides (N=17, 24, 30). The large yields (<75 wt %, N=17) of product grains agree with the literature data, which indicate that 3d metal magnetic oxide phases (Tc>300 K) are most probably Fe oxides. In combination with magnetic separation techniques, SSC seems particularly adapted for exploring the solid‐state chemistry of metallic lead elements that form ferri‐/ferromagnetic or superconducting oxide phases difficult to detect systematically within the large phase space of theoretically existing compounds.
Conformational Analysis of Bis(L‐N,N‐dimethylvalinato)copper(II) and Bis(L‐N,N‐dimethylleucinato)copper(II) in Different Solvents by EPR Spectroscopy and a Molecular Mechanics Study
Authors: Mirosavljević Krunoslav , Sabolović Jasmina , Noethig‐Laslo Vesna 
Published: August 2004

AbstractAn EPR study on the Brownian motion of bis(L‐N,N‐dimethylvalinato)copper(II), Cu(L‐Me2Val)2 and bis(L‐N,N‐dimethylleucinato)copper(II), Cu(L‐Me2Leu)2, dissolved in different solvents (CD3OD, CH3CH2OH, CDCl3) as a function of temperature is presented. The theoretical fits of the EPR spectra revealed different EPR behaviour for the two copper(II) complexes in hydrogen bond making solvents. In order to examine whether the different behaviour could be explained on conformational (steric) grounds, a conformational analysis of the copper(II) complexes with L‐N,N‐dimethylated amino acids was performed with a molecular mechanics force field. The ability of the most stable conformations to bind a water molecule in the copper(II) first coordination sphere was also examined using the force field. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Structure Comparison of Early and Late Lanthanide(III) Homodinuclear Macrocyclic Complexes with the Polyamine Polycarboxylic Ligand H8OHEC
Authors: Böttger Ulrike A. , O’Sullivan Brendon , Ziemer Burkhard , Schumann Herbert , Mügge Clemens , Weißhoff Hardy 
Published: August 2004

AbstractThe solid‐state structures of two new homodinuclear chelate complexes with the late lanthanide(III) ions Yb and Lu, [Na2(Yb2OHEC)].14.5H2O (1), and [Na2(Lu2OHEC)].14.5H2O (2) (H8OHEC = 1,4,7,10,14,17,20,23‐octaazacyclohexacosane‐ 1,4,7,10,14,17,20,23‐octaacetic acid), have been determined by X‐ray crystal structure analysis. Each lanthanide(III) ion is coordinated by eight donor atoms of the ligand and the geometry of the coordination polyhedron approaches a bicapped trigonal prism. These structures are compared with those of the homodinuclear chelate complexes with the same ligand and the mid to early lanthanide(III) ions Gd, Eu, La and also Y. A distinctive structural change occurs across the lanthanide series. The centrosymmetric mid to early lanthanide(III) complexes are all ninefold‐coordinated in a capped square antiprismatic arrangement with a water molecule coordinated in a prismatic position. This structure is maintained in aqueous solution, together with an asymmetric minor isomer. The late lanthanide(III) OHEC complexes not only lack the inner‐sphere water, but the change of coordination sphere also results in a loss of symmetry of the whole complex molecule. The observed change of coordination mode and number of the lanthanide ion may offer a geometric model for the isomerization process in eight‐ and ninefold‐coordinated complex species that are isomers in a possible coordination equilibrium observed by NMR in aqueous solution. This model may also explain the intramolecular rearrangements necessary during water exchange in the inner coordination sphere of the complex [(Gd2OHEC)(H2O)2]2− through a slow dissociative mechanism. Protonation constants of the H8OHEC ligand and complex formation constants of this ligand with GdIII, CaII, CuII and ZnII have been determined by solution thermodynamic studies. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Boranophosphate Salts as an Excellent Mimic of Phosphate Salts: Preparation, Characterization, and Properties
Authors: Nahum Victoria , Fischer Bilha 
Published: August 2004

AbstractWe report on the preparation of boranophosphate salts, BPi (2), and the exploration of their properties with a view to developing a new mimic of the parent phosphate. BPi salts were easily prepared in excellent yield in a one‐pot two‐step reaction from tris(trimethylsilyl) phosphite, and were characterized by X‐ray crystallography and IR, 1H and 31P NMR spectroscopy. We evaluated the acid/base character of BPi by determining its acidity constants. Likewise, we evaluated the stability of BPi at various pH values, and calculated the decomposition‐rate constants at highly acidic pH. We also monitored the H‐bonded clustering of BPi in organic solvents, including MeOH. Finally, we explored the chemical behavior of BPi with respect to various organic and inorganic reagents. BPi is stable under the following conditions: both basic and acidic pH (pH > 2), in the presence of amines, and in the presence of Mg2+ ions. However, a P−B bond cleavage is observed upon the reaction of BPi with carbodiimides or upon catalytic hydrogenation. The reducing nature of the BH3 moiety is drastically decreased in BPi. Likewise, the nucleophilicity of BPi’s oxygen atom is lower than in phosphate, Pi, salts. Based on its water solubility, acid‐base character, and H‐bonding properties, BPi appears as a perfect mimic of Pi and is an attractive alternative to the known phosphate isosters. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Dinuclear ZnII Complexes of Polydentate Polyamines as Minimalist Models of Hydrolytic Reactions
Authors: Aguilar Juan , Bencini Andrea , Berni Emanuela , Bianchi Antonio , García‐España Enrique , Gil Laura , Mendoza Angel , Ruiz‐Ramírez Lena , Soriano Conxa 
Published: August 2004

AbstractThe synthesis of the novel macrocycle 2,6,9,12,16‐pentaaza[17](2,9)(1,10)phenanthrolinophane (L3) is reported. Speciation studies on the systems ZnII−L3 and ZnII−L2 (L2 =2,6,10,13,17,21‐hexaaza[22]metacyclophane) performed in aqueous solution show the formation of mono‐ and dinuclear ZnII complexes. In the two systems, the dinuclear complexes readily hydroxylate, with the hydroxo species being the main ones in solution at relatively low pH values. This feature makes these complexes promising hydrolytic agents for carboxy and phosphate esters. The hydrolytic ability of the L1−L3 dinuclear complexes toward the carboxy and phosphate ester bond was tested by addition of p‐nitrophenyl acetate (NA) and bis(p‐nitrophenyl)phosphate (BNP). While in the case of NA the cleavage takes place through a simple bimolecular mechanism and the hydrolysis rate depends on the nucleophilicity of the ZnII−OH functions, in the case of BNP the hydrolytic mechanism involves substrate interaction with the metal ions and nucleophilic attack of a ZnII‐bound hydroxide ion at the phosphorus atom. The L3 complex gives rise to the highest hydrolysis rate constant {k = 62 × 10−5 M−1·s−1 vs. k = 8 × 10−5 and 4 × 10−5 M−1·s−1 for [Zn2L2(OH)2]2+ and [Zn2L1(OH)2]2+, respectively}. This may be related to a stronger interaction with the substrate due to the synergetic role in BNP binding played by the phenanthroline unit, which can give π‐stacking and hydrophobic interactions with the aromatic units of the substrate, and by the two ZnII ions, which can act cooperatively in BNP coordination. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Formation of Thermotropic and Lyotropic Liquid Crystals of Bis(N‐alkylethylenediamine)silver(I) Nitrate
Authors: Iida Masayasu , Inoue Michiko , Tanase Tomoaki , Takeuchi Takae , Sugibayashi Makiko , Ohta Kazuchika 
Published: August 2004

AbstractWe have synthesized bis(N‐hexylethylenediamine)silver(I) nitrate ([Ag(hex‐en)2]NO3), bis(N‐octylethylenediamine)silver(I) nitrate ([Ag(oct‐en)2]NO3), and bis(N‐dodecylethylenediamine)silver(I) nitrate ([Ag(dod‐en)2]NO3) and investigated the aggregation behavior of [Ag(dod‐en)2]NO3 and [Ag(oct‐en)2]NO3 in the liquid state. An X‐ray crystallographic analysis revealed that [Ag(dod‐en)2]NO3 has a dinuclear structure in the crystalline state — the molecular composition unit is [Ag2(dod‐en)4](NO3)2, where the two dod‐en ligands bridge two silver ions that are coordinated by four nitrogen atoms. The dinuclear complex is appreciably dissociated into a mononuclear complex in solution. It was found that [Ag(oct‐en)2]NO3 and [Ag(dod‐en)2]NO3 form thermotropic liquid crystals in the temperature ranges 48−67 °C and 59−96 °C, respectively, and a lyotropic liquid crystal was also observed for [Ag(dod‐en)2]NO3 in n‐heptane at around room temperature in the presence of a small amount of water. The structures of the thermotropic and lyotropic liquid crystals of [Ag(dod‐en)2]NO3 were identified as a typical smectic A (SA) type and a nematic one, respectively. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
A Cationic Tetranuclear [NiII4(MeOH)2(pko)6]2+ Cluster Showing Antiferro‐ and Ferromagnetic Features
Authors: Alexiou Maria , Dendrinou‐Samara Catherine , Raptopoulou Catherine P. , Terzis Aris , Tangoulis Vassilis , Kessissoglou Dimitris P. 
Published: August 2004

AbstractThe majority of reported nickel tetranuclear clusters have a dicubane‐like structural core. The compound presented here is the second example possessing an Ni4O2 core based on a chair or butterfly “out‐of‐face” topology. This compound also belongs to the family of compounds characterized as metallacrowns with an [Ni−N−O−]n linkage and is the only example with three Ni−O−N−Ni strands bridging the nickel atoms. The values obtained from the fitting procedure are J1 = 55.8 cm−1, J2 = −67.2 cm−1, g = 2.2, ρ = 1.1%. These values suggest the presence of both ferromagnetic and antiferromagnetic interactions, while a small paramagnetic impurity is also present. This magnetic behaviour with antiferromagnetic internal coupling and ferromagnetic spin‐alignment is the second example in the literature and the first in the metallacrown family. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Synthesis and Electrochemistry of the Monolacunary Dawson‐Type Tungstoarsenate [H4AsW17O61]11− and Some First‐Row Transition‐Metal Ion Derivatives
Authors: Mbomekalle Israel‐Martyr , Keita Bineta , Lu Yu Wei , Nadjo Louis , Contant Roland , Belai Nebebech , Pope Michael T. 
Published: August 2004

AbstractThe novel family of the Dawson‐type tungstomonoarsenate [H4AsW18O62]7− has been extended by preparing for the first time its monolacunary species and its first‐row transition‐metal ion substituted derivatives. All compounds were characterized by elemental analysis, IR and UV/Vis spectroscopy and representative examples by 183W NMR spectroscopy. Several lines of experimental evidence converge to indicate that the substitution occurs in the α2 position. The lacunary species, unlike its phosphorus analogue, was sufficiently stable for a few voltammetric runs. Therefore, the cyclic voltammetric properties of substituted compounds were studied as a function of pH and systematically compared with those of the lacunary precursor rather than with those of their analogues derived from the symmetrical species [As2W18O62]6−. The electrocatalytic properties of all compounds were illustrated by the reduction of nitrite by reduced [H4AsW18O62]7− and of nitrate by reduced α2‐[(H2O)Cu(H4AsW17O61)]9−. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Sequence‐Specific Oxidative Degradation of Tripeptides by a Cobalt(III) Complex Containing a Terpyridine Ligand
Authors: Jitsukawa Koichiro , Takahashi Hiroshi , Hyuga Ryoji , Arii Hidekazu , Masuda Hideki 
Published: August 2004

AbstractA sequence‐specific oxidative degradation of an oligopeptide consisting of aliphatic amino acids was performed with a ternary cobalt(III) complex. Under aerobic conditions the reaction of [Co(CO3)(OH)(terpy)] and an equimolar amount of tripeptide at 40 °C at pH 8.5 gave two fraction bands (a and b) with water and then two bands (c and d) with NaCl solution, respectively, after column separation. In the case of gly‐gly‐leu (ggl, 1), [Co(gg′l)(terpy)] [1a, gg′l = glycyl(2‐oxoglycyl)leucine], [Co(g′l)(terpy)] [1b, g′l = N‐(2‐oxoglycyl)leucine], [Co(ggl)(terpy)]+ (1c), and [Co(terpy)2]3+ (1d) were obtained. The crystal structure of 1c, which was the main product, revealed that the starting ggl ligand was cleaved to give a bis‐amide compound, g′l, which might be generated by loss of N‐terminal glycine and carbonylation of the α‐carbon of the N‐2 glycine residue. Although the source of the oxygen of the newly generated carbonyl group is not clear, gg′l is supposed to be an intermediate for g′l on the basis of time‐dependent HPLC analyses. NMR investigation of other tripeptides [βala‐gly‐leu (2), gly‐gly‐phe (3), and gly‐gly‐ala (4)] containing a bulky C‐terminal aliphatic side chain indicated the formation of the corresponding oxidation complexes. On the other hand, peptides containing a C‐terminal glycine residue [gly‐gly‐gly (5) and phe‐gly‐gly (6)] or an N‐2 β‐alanine residue [gly‐βala‐leu (7)] did not give such a transformation product. The crystal structure of [Co(fgg)(terpy)] (6c) revealed that the tripeptide is coordinated to cobalt with a tridentate N‐terminal N‐N‐N geometry. Such sequence specificity demonstrated in the reaction of the aliphatic tripeptide complexes is interpreted by the interligand interaction between the side chain of the C‐terminal amino acid residue and terpy. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Anion Binding of 1,1′‐Bis(dialkylboryl)cobaltocenium Complexes − Structures of [Co{C5H4(BMe2)}2]PF6, Co[C5H4(BMe2)][C5H4(BMe2Cl)], Co[C5H4(BiPr2)]2(µ‐F) and NMe4[Co{C5H4(BiPr2F)}2]
Authors: Herberich Gerhard E. , Englert Ulli , Fischer Andreas , Wiebelhaus Dag 
Published: August 2004

AbstractThe cobaltocenium salts [Co{C5H4(BiPr2)}2]PF6 [(1a)PF6] and [Co{C5H4(BMe2)}2]PF6 [(1b)PF6] are strong Lewis acids. With pyridine (1a)PF6 forms a mono‐adduct 2 and a di‐adduct 3 which show NMR spectra in the low‐temperature regime of pyridine exchange. With chloride from PPh4Cl the adduct formed is dynamic; quite remarkably, the formation of an anionic di‐adduct is also observed. The mono‐adducts (1a)X (X = F, Cl, Br, I, OH, and NH2) and (1b)X (X = F, Cl, and OH) as well as the di‐adduct salts NMe4[(1a)F2] (5) and K[(1a)(OH)2] (6) are made by treating the salts (1a,b)PF6 in CH2Cl2 or MeNO2 with salts PPh4X, NMe4F, or powders of NaNH2 or KOH in the appropriate ratios. X‐ray single‐crystal structures of the salt [Co{C5H4(BMe)2}2]PF6 [(1b)PF6], the semi‐quaternized mono‐adduct Co[C5H4(BMe2)][C5H4(BMe2Cl)] (4bd) [B−Cl = 1.969(2) Å], the inverse chelate Co[C5H4(BiPr2)]2(µ‐F) (4ac) with the very rare feature of fluorine bridging two boron centers [C2 symmetric; B−F = 1.641(4) Å, B−F−B′ = 148.4(3)°], and the doubly quaternized di‐adduct NMe4[Co{C5H4(BiPr2F)}2] (5) [exactly centrosymmetric; B−F = 1.477(4) Å] are given. Solution structures of the 1:1 products greatly depend on the nature of the anion, displaying i) exclusively ionic structures for (1a)PF6 and (1b)PF6, ii) semi‐quaternized structures for the heavier halides (1a)Br (4ae) and (1a)I (4af) with some noticeable ionic dissociation, iii) semi‐quaternized structures in equilibrium with minor amounts of inverse chelate isomers for (1a)F (4ac), (1b)Cl (4bd), and very likely for (1a)Cl (4ad), and iv) stable inverse chelate structures for Co[C5H4(BiPr2)]2(µ‐NH2) (4aa) (static in variable temperature NMR spectra, with diastereotopic Me groups), Co[C5H4(BR2)]2(µ‐OH) [4ab: R = iPr; 4bb: R = Me; dynamic; for 4ab Tc = 95 ± 5 °C, ΔG≠368 = 75(1) kJ·mol−1 for interchange of the diastereotopic Me groups], and Co[C5H4(BMe2)]2(µ‐F) (4bc). The stability of the inverse chelates decreases in the order amide (4aa) > hydroxides (4ab and 4bb) > fluorides (4ac and 4bc) > chlorides (4ad and 4bd), and also in the order BMe2 > BiPr2 (specifically 4bc > 4ac, and 4bd > 4ad). Variable temperature NMR spectra of solutions of 4bd (CD2Cl2, 173−243 K) show that i) the ring‐opening of the chelated chloride (ΔG≠368 ≈︁ 45 kJ·mol−1) is energetically easier than for the chelated hydroxide 4ab, ii) the predominance of the semi‐quaternized isomer over the inverse chelate (ΔRH = 2.5 ± 1.1 kJ·mol−1, ΔRS = 37.6 ± 5.4 kJ·mol−1·K−1) in the equilibrium is entropic in nature, and iii) the semi‐quaternized isomer still undergoes fast chloride‐exchange in the low‐temperature regime of this equilibrium, proving the existence of an independent, intermolecular chloride‐exchange mechanism. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)