bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a Locus Under Complex Positive Selection in Drosophila simulans by Haplotype Mapping and Composite-Likelihood Estimation
Authors: Meiklejohn Colin D , Kim Yuseob , Hartl Daniel L , Parsch John 
Published: September 2004

AbstractThe recent action of positive selection is expected to influence patterns of intraspecific DNA sequence variation in chromosomal regions linked to the selected locus. These effects include decreased polymorphism, increased linkage disequilibrium, and an increased frequency of derived variants. These effects are all expected to dissipate with distance from the selected locus due to recombination. Therefore, in regions of high recombination, it should be possible to localize a target of selection to a relatively small interval. Previously described patterns of intraspecific variation in three tandemly arranged, testes-expressed genes (janusA, janusB, and ocnus) in Drosophila simulans included all three of these features. Here we expand the original sample and also survey nucleotide polymorphism at three neighboring loci. On the basis of recombination events between derived and ancestral alleles, we localize the target of selection to a 1.5-kb region surrounding janusB. A composite-likelihood-ratio test based on the spatial distribution and frequency of derived polymorphic variants corroborates this result and provides an estimate of the strength of selection. However, the data are difficult to reconcile with the simplest model of positive selection, whereas a new composite-likelihood method suggests that the data are better described by a model in which the selected allele has not yet gone to fixation.
Linkage Disequilibrium Mapping of Yield and Yield Stability in Modern Spring Barley Cultivars
Authors: Kraakman Arnold T W , Niks Rients E , Van den Berg Petra M M M , Stam Piet , Van Eeuwijk Fred A 
Published: September 2004

AbstractAssociations between markers and complex quantitative traits were investigated in a collection of 146 modern two-row spring barley cultivars, representing the current commercial germ plasm in Europe. Using 236 AFLP markers, associations between markers were found for markers as far apart as 10 cM. Subsequently, for the 146 cultivars the complex traits mean yield, adaptability (Finlay-Wilkinson slope), and stability (deviations from regression) were estimated from the analysis of variety trial data. Regression of those traits on individual marker data disclosed marker-trait associations for mean yield and yield stability. Support for identified associations was obtained from association profiles, i.e., from plots of P-values against chromosome positions. In addition, many of the associated markers were located in regions where earlier QTL were found for yield and yield components. To study the oligogenic genetic base of the traits in more detail, multiple linear regression of the traits on markers was carried out, using stepwise selection. By this procedure, 18–20 markers that accounted for 40–58% of the variation were selected. Our results indicate that association mapping approaches can be a viable alternative to classical QTL approaches based on crosses between inbred lines, especially for complex traits with costly measurements.
Abortive Transposition by a Group II Intron in Yeast Mitochondria
Authors: Dickson Lorna , Connell Stuart , Huang Hon-Ren , Henke R Michael , Liu Lu , Perlman Philip S 
Published: September 2004

AbstractGroup II intron homing in yeast mitochondria is initiated at active target sites by activities of intron-encoded ribonucleoprotein (RNP) particles, but is completed by competing recombination and repair mechanisms. Intron aI1 transposes in haploid cells at low frequency to target sites in mtDNA that resemble the exon 1-exon 2 (E1/E2) homing site. This study investigates a system in which aI1 can transpose in crosses (i.e., in trans). Surprisingly, replacing an inefficient transposition site with an active E1/E2 site supports &lt;1% transposition of aI1. Instead, the ectopic site was mainly converted to the related sequence in donor mtDNA in a process we call “abortive transposition.” Efficient abortive events depend on sequences in both E1 and E2, suggesting that most events result from cleavage of the target site by the intron RNP particles, gapping, and recombinational repair using homologous sequences in donor mtDNA. A donor strain that lacks RT activity carries out little abortive transposition, indicating that cDNA synthesis actually promotes abortive events. We also infer that some intermediates abort by ejecting the intron RNA from the DNA target by forward splicing. These experiments provide new insights to group II intron transposition and homing mechanisms in yeast mitochondria.
An AFLP-Based Interspecific Linkage Map of Sympatric, Hybridizing Colias Butterflies
Authors: Wang Baiqing , Porter Adam H 
Published: September 2004

AbstractColias eurytheme and C. philodice are sister species with broad sympatry in North America. They hybridize frequently and likely share a significant portion of their genomes through introgression. Both taxa have been ecologically well characterized and exploited to address a broad spectrum of evolutionary issues. Using AFLP markers, we constructed the first linkage map of Colias butterflies. The map is composed of 452 markers spanning 2541.7 cM distributed over 51 linkage groups (40 major groups and 11 small groups with 2–4 markers). Statistical tests indicate that these AFLP markers tend to cluster over the map, with the coefficient of variation of interval sizes being 1.236 (95% C.I. is 1.234–1.240). This nonrandom marker distribution can account for the nonequivalence between the number of linkage groups and the actual haploid chromosome number (N = 31). This study presents the initial step for further marker-assisted research on Colias butterflies, including QTL and introgression analyses. Further investigation of the genomes will help us understand better the roles of introgression and natural selection in the evolution of hybridizing species and devise more appropriate strategies to control these pests.
Simultaneous Estimation of Haplotype Frequencies and Quantitative Trait Parameters
Authors: Shibata Kyoko , Ito Toshikazu , Kitamura Yutaka , Iwasaki Naoko , Tanaka Hiroshi , Kamatani Naoyuki 
Published: September 2004

Abstract
The analysis of the haplotype-phenotype relationship has become more and more important. We have developed an algorithm, using individual genotypes at linked loci as well as their quantitative phenotypes, to estimate the parameters of the distribution of the phenotypes for subjects with and without a particular haplotype by an expectation-maximization (EM) algorithm. We assumed that the phenotype for a diplotype configuration follows a normal distribution. The algorithm simultaneously calculates the maximum likelihood (L0max) under the null hypothesis (i.e., nonassociation between the haplotype and phenotype), and the maximum likelihood (Lmax) under the alternative hypothesis (i.e., association between the haplotype and phenotype). Then we tested the association between the haplotype and the phenotype using a test statistic, −2 log(L0max/Lmax). The above algorithm along with some extensions for different modes of inheritance was implemented as a computer program, QTLHAPLO. Simulation studies using single-nucleotide polymorphism (SNP) genotypes have clarified that the estimation was very accurate when the linkage disequilibrium between linked loci was rather high. Empirical power using the simulated data was high enough. We applied QTLHAPLO for the analysis of the real data of the genotypes at the calpain 10 gene obtained from diabetic and control subjects in various laboratories.
Co-infection Weakens Selection Against Epistatic Mutations in RNA Viruses
Authors: Froissart Rémy , Wilke Claus O , Montville Rebecca , Remold Susanna K , Chao Lin , Turner Paul E 
Published: September 2004

Abstract
Co-infection may be beneficial in large populations of viruses because it permits sexual exchange between viruses that is useful in combating the mutational load. This advantage of sex should be especially substantial when mutations interact through negative epistasis. In contrast, co-infection may be detrimental because it allows virus complementation, where inferior genotypes profit from superior virus products available within the cell. The RNA bacteriophage φ6 features a genome divided into three segments. Co-infection by multiple φ6 genotypes produces hybrids containing reassorted mixtures of the parental segments. We imposed a mutational load on φ6 populations by mixing the wild-type virus with three single mutants, each harboring a deleterious mutation on a different one of the three virus segments. We then contrasted the speed at which these epistatic mutations were removed from virus populations in the presence and absence of co-infection. If sex is a stronger force, we predicted that the load should be purged faster in the presence of co-infection. In contrast, if complementation is more important we hypothesized that mutations would be eliminated faster in the absence of co-infection. We found that the load was purged faster in the absence of co-infection, which suggests that the disadvantages of complementation can outweigh the benefits of sex, even in the presence of negative epistasis. We discuss our results in light of virus disease management and the evolutionary advantage of haploidy in biological populations.
Dose-Sensitive Autosomal Modifiers Identify Candidate Genes for Tissue Autonomous and Tissue Nonautonomous Regulation by the Drosophila Nuclear Zinc-Finger Protein, Hindsight
Authors: Wilk Ronit , Pickup Amanda T , Hamilton Jill K , Reed Bruce H , Lipshitz Howard D 
Published: September 2004

Abstract
The nuclear zinc-finger protein encoded by the hindsight (hnt) locus regulates several cellular processes in Drosophila epithelia, including the Jun N-terminal kinase (JNK) signaling pathway and actin polymerization. Defects in these molecular pathways may underlie the abnormal cellular interactions, loss of epithelial integrity, and apoptosis that occurs in hnt mutants, in turn causing failure of morphogenetic processes such as germ band retraction and dorsal closure in the embryo. To define the genetic pathways regulated by hnt, 124 deficiencies on the second and third chromosomes and 14 duplications on the second chromosome were assayed for dose-sensitive modification of a temperature-sensitive rough eye phenotype caused by the viable allele, hntpeb; 29 interacting regions were identified. Subsequently, 438 P-element-induced lethal mutations mapping to these regions and 12 candidate genes were tested for genetic interaction, leading to identification of 63 dominant modifier loci. A subset of the identified mutants also dominantly modify hnt308-induced embryonic lethality and thus represent general rather than tissue-specific interactors. General interactors include loci encoding transcription factors, actin-binding proteins, signal transduction proteins, and components of the extracellular matrix. Expression of several interactors was assessed in hnt mutant tissue. Five genes—apontic (apt), Delta (Dl), decapentaplegic (dpp), karst (kst), and puckered (puc)—are regulated tissue autonomously and, thus, may be direct transcriptional targets of HNT. Three of these genes—apt, Dl, and dpp—are also regulated nonautonomously in adjacent non-HNT-expressing tissues. The expression of several additional interactors—viking (vkg), Cg25, and laminin-α (LanA)—is affected only in a nonautonomous manner.
FDA/PI flow cytometry assay of complement‐mediated cytotoxicity of antibodies generated during xenotransplantation
Authors: Díaz Tomas M. , Pértega Sonia , Ortega Dolores , López Eduardo , Centeno Alberto , Mañez Rafael , Doménech Nieves 
Published: September 2004

AbstractBackgroundA flow cytometry complement‐mediated cytotoxicity assay (FCCA) using fluorescein diacetate (FDA) and propidium iodide (PI) to measure antibody‐dependent toxicity is useful to determine the success of xenotransplant organs. We evaluated the validity of different mathematical models as a measure of cytotoxicity in FCCA.MethodsSera from untreated baboons (n = 7) and from immunosuppressed animals (n = 5) undergoing different xenotransplantation protocols with pig organs were tested by endogenous FCCA and a similar assay also using exogenous complement, and the results were compared with those of a complement‐dependent hemolytic assay to detect anti‐pig antibodies (APHA). The influence of PI/FDA staining and the use of several mathematical models were analyzed.ResultsFor both groups of animals, we observed high correlations between the endogenous and exogenous FCCA pathways and between calculations based on PI and FDA staining. Of the four mathematical models tested—the Von Krogh equation, two exponential models, and area under the curve—the Von Krogh equation was the most appropriate in terms of goodness of fit and concordance with APHA.ConclusionsFDA/PI FCCA is useful to measure endogenous and exogenous complement‐mediated cytotoxicities, and it has advantages related to identification of potential new xenoantibodies. Although all four mathematical models produced acceptable solutions, the Von Krogh equation was the best option. © 2004 Wiley‐Liss, Inc.
Small Cyclic Disulfide Peptides: Synthesis in Preparative Amounts and Characterization by Means of NMR and FT‐IR Spectroscopy
Authors: Kolano Christoph , Gomann Klaus , Sander Wolfram 
Published: September 2004

AbstractTwo cyclic disulfide‐bridged tetrapeptides [cyclo(Boc−Cys−Pro−Aib−Cys−OMe) and cyclo(Boc−Cys−Pro−Phe−Cys−OMe)] were prepared in high yield and purity. The use of double‐walled reaction flasks, which were attached to an external cryostat, gave perfect temperature control of the reaction. The acetamidomethyl and trityl group were used for the protection of the thiol groups of Cys. Disulfide bond formation was obtained by cleavage of the protection groups and subsequent oxidation of the free thiols with iodine under high dilution conditions in one step. The obtained cyclic peptides were checked for purity by analytical HPLC, and identified by NMR spectroscopy and a variety of standard analytical methods (IR, m. p., FAB‐MS, ELA, TLC). Conformational properties of the peptides were derived from one‐ and two‐dimensional NMR experiments. Temperature‐dependent NMR and FT‐IR experiments allowed for the determination of the degree of inter‐ and intramolecular hydrogen bonding of the cyclic tetrapeptides. The results from the temperature‐dependent NMR experiments are in good agreement with the observed dynamics of the peptides in the amide I and II region, which were determined by means of temperature‐dependent FT‐IR spectroscopy using the ATR technique. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Preparation of Chiral 2‐Stannyloxazolidines and First Considerations on the Transacetalisation Reaction Mechanism
Authors: Cintrat Jean‐Christophe , Léat‐Crest Véronique , Parrain Jean‐Luc , Le Grognec Erwan , Beaudet Isabelle , Quintard Jean‐Paul 
Published: September 2004

AbstractN‐Protected 2‐tributylstannyl‐1,3‐oxazolidines derived from N‐monoprotected chiral β‐amino alcohols were obtained through transacetalisation of (diethoxymethyl)tributylstannane under acidic conditions. In the case of 4‐substituted 2‐tributylstannyl‐1,3‐oxazolidines, the kinetic product of the reaction was shown to be the trans isomer whatever the nature of the protective group, while the thermodynamic product was the cis isomer in the N‐Ts series and the trans isomer in N‐CO2R compounds. Aspects of the transacetalisation reaction are discussed along with those concerning the isomerisation of the products, allowing an interpretation of the obtained results. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
[2+2]‐Cycloaddition of Chlorosulfonyl Isocyanate to (Z)‐Propenyl Ethers Bound to Polystyrene Resins by Alkylsulfonyl Linkers
Authors: Łysek Robert , Grzeszczyk Barbara , Furman Bartłomiej , Chmielewski Marek 
Published: September 2004

AbstractThe 3‐O‐ and 5‐O‐(Z)‐propenyl ethers derived from 1,2‐O‐isopropylidene‐α‐D‐xylo‐ and glucofuranoses, respectively, were attached to the Merrifield, MPPC and NCPSC resins using alkylsulfonyl linkers. The [2+2]‐cycloaddition of chlorosulfonyl isocyanate to the polymer‐bound vinyl ethers followed by the intramolecular alkylation of the β‐lactam nitrogen led to the formation of mixtures of the corresponding diastereomeric oxacephams or clavams with a low stereoselectivity. In the case of Merrifield and MPP resins, the β‐lactams were accompanied by the corresponding oxetanes or oxiranes. Reactions performed using soluble polymer proceeded similarly to those carried out in solution. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Four New Derivatives of Trihomononactic Acids from Streptomyces globisporus
Authors: Řezanka Tomáš , Spížek Jaroslav , Přikrylová Věra , Dembitsky Valery M. 
Published: September 2004

AbstractNew compounds, namely a homolog of nonactic acid (trihomononactic acid), its lactone and dilactones were isolated from a strain of Streptomyces globisporus. Their structures, including the absolute configurations of the hydroxy and methyl groups, were determined by spectroscopic techniques such as UV, IR, MS, 1D and 2D NMR spectroscopy. All compounds were highly active against Gram‐positive bacteria and brine shrimp. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Dithiocarbamates, Thiocarbamic Esters, Dithiocarboimidates, Guanidines, Thioureas, Isothioureas, and Tetraazathiapentalene Derived from 2‐Aminobenzothiazole
Authors: Téllez Fabiola , Cruz Alejandro , López‐Sandoval Horacio , Ramos‐García Iris , Gayosso Martha , Castillo‐Sierra R. Nely , Paz‐Michel Brenda , Nöth Heinrich , Flores‐Parra Angelina , Contreras Rosalinda 
Published: September 2004

AbstractReactions between CS2 and the exocyclic amino groups of 2‐aminobenzothiazoles gave series of molecules bearing thiourea, isothiourea, dithiocarbamate, dithiocarboimine, dimethyldithiocarbamate, methyldithiocarbamate, S‐CH3 and O‐alkyl thiocarbamic ester, and guanidine groups. Preferred tautomers and conformers were determined. Most compounds present coordinative bonds between the endocyclic sulfur atom, which behaves as a Lewis acid, and oxygen, nitrogen, and sulfur acting as bases. A new dibenzothiazolyltetraazathiapentalene containing a T‐shaped hypervalent sulfur atom and displaying “single bond‐no bond resonance” is discussed. X‐ray structures of eleven compounds are reported. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Chiral Poly(aromatic amide ester) Dendrimers Bearing an Amino Acid Derived C3‐Symmetric Core − Synthesis and Properties
Authors: Romagnoli Barbara , van Baal Ingrid , Price David W. , Harwood Laurence M. , Hayes Wayne 
Published: September 2004

AbstractThe effect of hyperbranched macromolecular architectures (dendrimers) upon chirality has received significant attention in recent years in the light of the proposal of amplification of chirality. In particular, several studies have been carried out on the chiroptical properties of dendrimers that contain a chiral core and achiral branches in order to determine if the chirality of the central core can be transmitted to the distal region of the macromolecule. In addition to interest of a pure academic nature, the presence of such chiral conformational order would be extremely useful in the development of asymmetric catalysts. In this paper, a novel class of chiral dendrimers is described − these perfect hyperbranched macromolecules have been prepared by a convergent route by the coupling of a chiral central core based upon tris(2‐aminoethyl)amine and poly(aromatic amide ester) dendritic branches. The chiral properties of these dendrimers have been investigated by detailed optical rotation studies and circular dichroism analysis; the results of these studies are described herein. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Cover Picture: Synthesis of a Novel Enantiopure Spiro‐B‐norestradiol Analogue by Multiple Pd‐Catalyzed Transformations (Eur. J. Org. Chem. 20/2004)
Authors: Tietze Lutz F. , Wiegand J. Matthias , Vock Carsten A. 
Published: September 2004

AbstractThe cover picture shows the unexpected formation of an unusual enantiopure spiro‐B‐norsteroid instead of the corresponding annulated compound by a twofold palladium‐catalyzed transformation of a hydrindane−boronic ester and an ortho‐bromobenzyl chloride. Details are discussed in the article by L. F. Tietze et al. on p. 4107 ff.
Assembly of Glucose Oxidase and Different Polyelectrolytes by Means of Electrostatic Layer‐by‐Layer Adsorption on Thiolated Gold Surface
Authors: Rodríguez Marcela C. , Rivas Gustavo A. 
Published: September 2004

AbstractA rational strategy for the construction of a bioelectrocatalytic architecture by means of alternate electrostatic adsorption is described. Multilayer films containing glucose oxidase (GOx) and different polyelectrolytes were assembled onto a thiolated‐gold surface and the resulting bioelectrode was used for glucose biosensing. The supramolecular multistructure was prepared by assembling polyethylenimine and Nafion (as anti‐interference barrier), followed by the adsorption of polyethylenimine and DNA (as stabilizing film) and finally by the alternate deposition of polyethylenimine and glucose oxidase (as a biocatalytic layer). The influence of the deposition time and concentration of polyelectrolytes, organization and number of layers on the sensitivity and selectivity of the bioelectrode is discussed. The resulting enzymatic biorecognition layer exhibits very good analytical performance with a fast, sensitive (3.3±0.1)×104 nA M−1 and highly selective (0% interference for 6.0 mg % uric acid and 2.0×10−4 M ascorbic acid) response to glucose, demonstrating that the alternate electrostatic adsorption of conveniently selected polyelectrolytes allow a large improvement in the selectivity and sensitivity of a biosensor.
Ormosil Encapsulated Pyrroloquinoline Quinone‐Modified Electrochemical Sensor for Thiols
Authors: Joshi Kanchan A. , Pandey Prem C. , Chen Wilfred , Mulchandani Ashok 
Published: September 2004

AbstractAn organically modified sol‐gel glass (ORMOSIL) encapsulating pyrroloquinoline quinone (PQQ)‐modified electrode for the rapid, sensitive and simple determination of thiol‐containing compounds such as cysteine and glutathione is reported. The effect of applied potential, nature of thiol compound and pH on the response of the sensor was examined and optimum conditions were determined. The electrochemical responses and detection limits were found to be sensitive to the nature of thiols and pH. The electrochemical responses for cysteine and glutathione at an applied potential of −0.2 V (vs. Ag/AgCl) were found to be linear with detection limits of 18 nM for cysteine and 36 nM for glutathione at pH 3.5, whereas the detection limits at pH 8.5 were 0.5 μM for cysteine and 1 μM for glutathione. The electrode retained 95% of the original response for 7 days when stored at 4 °C. The ORMOSIL‐encapsulated PQQ was also characterized by spectrophotometry. The absorbance measurement using 5,5′‐dithiobis(2‐nitrobenzoic acid) at 412 nm justify the PQQ‐mediated oxidation of glutathione whereas fluorescence measurements (excitation wavelength=380 nm; emission wavelength=480 nm) justify the successful encapsulation of PQQ in ORMOSIL matrix.