bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential relationships between transaminase abnormality and valproic acid clearance or serum carnitine concentrations in Japanese epileptic patients
Authors: Goto Shuji , Seo Takayuki , Hagiwara Takashi , Ueda Kentaro , Yamauchi Tsuyuko , Nagata Shiro , Ando Yukio , Ishitsu Takateru , Nakagawa Kazuko
Published: January 2008

This study tested the hypothesis that the determinants of mild liver injury are prerequisites for more severe idiosyncratic hepatotoxicity. This study verified whether the possible risk factors for rare idiosyncratic valproic acid (VPA)-induced hepatotoxicity, VPA clearance and/or serum carnitine concentrations are common to those for a mild elevation in transaminases in VPA-treated patients. VPA clearance was calculated in 172 Japanese patients with epilepsy, using a non-linear mixed-effects regression program. Carnitine concentrations were determined in a subset of 60 patients. The relationships between VPA clearance, carnitine concentration and levels of transaminases and ammonia were evaluated by Pearson's correlation coefficients. The final model of VPA apparent clearance (CL/F) was as follows: CL/F (L h−1) = 0.012 × (BW/40)0.34 × dose0.55 × 0.90gender × 1.32PHT × 1.11CBZ × 1.12PB, where BW = total body weight (kg); gender = 1 if female, 0 if male; PHT/CBZ/PB = 1 if phenytoin, carbamazepine, or phenobarbital, respectively, is coadministrated, otherwise 0. Either a higher VPA clearance or acyl/free carnitine ratio and a lower total and/or free carnitine concentration, but not VPA concentration, were associated with the mild elevation in transaminases or ammonia. These results support the initial hypothesis, while also helping to clarify the mechanism of severe idiosyncratic hepatotoxicity with VPA.
A methodology for modelling the effects of nitriding on fatigue life
Authors: Hyde T. R. , Leen S. B. , McColl I R.
Published: January 2008

A methodology is presented for modelling the effects of nitriding for fatigue life prediction. The method is illustrated by application to tooth bending fatigue failure in notch conditions representative of the fillet regions in spline teeth. The methodology first involves the prediction of nitrided layer stress distributions which take account of the graduation in material stress—strain curve through the nitrided layer and the effects of residual stresses. Second, the life prediction aspect requires that the effects of the graded material properties and residual stresses on mean stress levels and thus on fatigue constants be accounted for. Comparisons between predicted and experimentally-determined lives show that the methodology significantly improves the predictions for nitrided specimens.
Adsorption of Aqueous Mercury(II) Species by Commercial Activated Carbon Fibres with and without Surface Modification
Authors: Nabais João M. Valente , Carrott Peter J.M. , Carrott Manuela Ribeiro , Silvestre Sara , Durán-Valle Carlos J.
Published: January 2008

The adsorption of HgCl2, [HgCl4]2– and Hg2+ onto a series of activated carbon fibres was studied. These included the as-received commercial activated carbon fibre (K), that obtained after modification via by sulphuric acid oxidation (KAC) and that obtained after modification by reaction with pentaethylenehexamine (KBAS). The effects of concentration (10–1500 mg/l), solution pH (1–10) and temperature (25°C, 35°C and 45°C) were studied. The mercury(II) adsorption isotherms followed the Langmuir model with maximum adsorption capacities of 361.0, 142.2 and 300.3 mg/g for HgCl2, [HgCl4]2– and Hg2+, respectively. Fibre K proved to have the highest adsorption capacity towards HgCl2 but the best results for the adsorption of [HgCl4]2– and Hg2+ were obtained with the fibre KAC. The performance of fibre KBAS was always worse than those of the other two fibres tested. The negative values obtained for ΔH0 and ΔG0 indicate that the adsorption was an exothermic and spontaneous process and also demonstrated that the adsorption of Hg(II) is a feasible process.
Reference Intervals for Serum Creatinine Concentrations: Assessment of Available Data for Global Application
Authors: Ceriotti Ferruccio , Boyd James C , Klein Gerhard , Henny Joseph , Queraltó Josep , Kairisto Veli , Panteghini Mauro ,   the IFCC Committee on Reference Intervals and Decision Limits (C-RIDL)
Published: January 2008

Background: Reference intervals for serum creatinine remain relevant despite the current emphasis on the use of the estimated glomerular filtration rate for assessing renal function. Many studies on creatinine reference values have been published in the last 20 years. Using criteria derived from published IFCC documents, we sought to identify universally applicable reference intervals for creatinine via a systematic review of the literature.

Methods: Studies were selected for inclusion in the systematic review only if the following criteria were met: (a) reference individuals were selected using an “a priori” selection scheme, (b) preanalytical conditions were adequately described; (c) traceability of the produced results to the isotope dilution–mass spectrometry (IDMS) reference method was demonstrated experimentally, and (d) the collected data received adequate statistical treatment.

Results: Of 37 reports dealing specifically with serum creatinine reference values, only 1 report with pediatric data and 5 reports with adult data met these criteria. The primary reason for exclusion of most papers was an inadequate demonstration of measurement traceability. Based on the data of the selected studies, we have collated recommended reference intervals for white adults and children.

Conclusion: Laboratories using methods producing traceable results to IDMS can apply the selected reference intervals for serum creatinine in evaluating white individuals.
Hook‐Ups and Train Wrecks: Contextual Parameters and the Coordination of Jazz Interactions
Authors: Dempsey Nicholas P.
Published: January 2008

This article discusses the importance of several parameters of context integral to jazz musicians' ability to hear musical signs as meaningful, such as performers' individual backgrounds and the various other styles of music available in the aural landscape, and how those parameters influence what the musicians play. Several examples from an ongoing ethnography of jazz jam sessions suggest that context is constituted by several variables, that different variables may become salient at different times, and that different interactants vary in their ability to attend to these variables. This study thus extends and elaborates frame analysis by showing that, while an interaction frame of the sort described by Goffman (1974) may perdure, it is subject to change, and the nature of the context it provides for interactions can change whenever a new interaction is initiated.
Human Fertility Increases With Marital Radius
Authors: Labouriau Rodrigo , Amorim António
Published: January 2008

We report a positive association between marital radius (distance between mates' birthplaces) and fertility detected in a large population. Spurious association due to socioeconomic factors is discarded by a conditional analysis involving income, education, and urbanicity. Strong evidence of consanguinity's deleterious effects affecting an entire human population is provided.
Genetic Design and Statistical Power of Nested Association Mapping in Maize
Authors: Yu Jianming , Holland James B , McMullen Michael D , Buckler Edward S
Published: January 2008

We investigated the genetic and statistical properties of the nested association mapping (NAM) design currently being implemented in maize (26 diverse founders and 5000 distinct immortal genotypes) to dissect the genetic basis of complex quantitative traits. The NAM design simultaneously exploits the advantages of both linkage analysis and association mapping. We demonstrated the power of NAM for high-power cost-effective genome scans through computer simulations based on empirical marker data and simulated traits with different complexities. With common-parent-specific (CPS) markers genotyped for the founders and the progenies, the inheritance of chromosome segments nested within two adjacent CPS markers was inferred through linkage. Genotyping the founders with additional high-density markers enabled the projection of genetic information, capturing linkage disequilibrium information, from founders to progenies. With 5000 genotypes, 30–79% of the simulated quantitative trait loci (QTL) were precisely identified. By integrating genetic design, natural diversity, and genomics technologies, this new complex trait dissection strategy should greatly facilitate endeavors to link molecular variation with phenotypic variation for various complex traits.
Hitchhiking Mapping Reveals a Candidate Genomic Region for Natural Selection in Three-Spined Stickleback Chromosome VIII
Authors: Mäkinen Hannu S , Shikano Takahito , Cano José Manuel , Merilä Juha
Published: January 2008

Identification of genes and genomic regions under directional natural selection has become one of the major goals in evolutionary genetics, but relatively little work to this end has been done by applying hitchhiking mapping to wild populations. Hitchhiking mapping starts from a genome scan using a randomly spaced set of molecular markers followed by a fine-scale analysis in the flanking regions of the candidate regions under selection. We used the hitchhiking mapping approach to narrow down a selective sweep in the genomic region flanking a candidate locus (Stn90) in chromosome VIII in the three-spined stickleback (Gasterosteus aculeatus). Twenty-four microsatellite markers were screened in an ∼800-kb region around the candidate locus in three marine and four freshwater populations. The patterns of genetic diversity and differentiation in the candidate region were compared to those of a putatively neutral set of markers. The Bayesian FST-test indicated an elevated genetic differentiation, deviating significantly from neutral expectations, at a continuous region of ∼20 kb upstream from the candidate locus. Furthermore, a method developed for an array of microsatellite markers rejected neutrality in a region of ∼90 kb flanking the candidate locus supporting the selective sweep hypothesis. Likewise, the genomewide pattern of genetic diversity differed from the candidate region in a bottleneck analysis suggesting that selection, rather than demography, explains the reduced genetic diversity at the candidate interval. The neutrality tests suggest that the selective sweep had occurred mainly in the Lake Pulmanki population, but the results from bottleneck analyses indicate that selection might have operated in other populations as well. These results suggest that the narrow interval around locus Stn90 has likely been under directional selection, but the region contains several predicted genes, each of which can be the actual targets of selection. Understanding of the functional significance of this genomic region in an ecological context will require a more detailed sequence analysis.
Investigations of CHD1 Function in Transcription and Development of Drosophila melanogaster
Authors: McDaniel Ivy E , Lee Jennifer M , Berger Matthew S , Hanagami Cori K , Armstrong Jennifer A
Published: January 2008

In this report we describe chd1 mutant alleles and show that the CHD1 chromatin-remodeling factor is important for wing development and fertility. While CHD1 colocalizes with elongating RNA polymerase II (Pol II) on polytene chromosomes, elongating Pol II can persist on chromatin in the absence of CHD1. These results clarify the roles of chromatin remodelers in transcription and provide novel insights into CHD1 function.
Mitochondrial DNA Transfer to the Nucleus Generates Extensive Insertion Site Variation in Maize
Authors: Lough Ashley N , Roark Leah M , Kato Akio , Ream Thomas S , Lamb Jonathan C , Birchler James A , Newton Kathleen J
Published: January 2008

Mitochondrial DNA (mtDNA) insertions into nuclear chromosomes have been documented in a number of eukaryotes. We used fluorescence in situ hybridization (FISH) to examine the variation of mtDNA insertions in maize. Twenty overlapping cosmids, representing the 570-kb maize mitochondrial genome, were individually labeled and hybridized to root tip metaphase chromosomes from the B73 inbred line. A minimum of 15 mtDNA insertion sites on nine chromosomes were detectable using this method. One site near the centromere on chromosome arm 9L was identified by a majority of the cosmids. To examine variation in nuclear mitochondrial DNA sequences (NUMTs), a mixture of labeled cosmids was applied to chromosome spreads of ten diverse inbred lines: A188, A632, B37, B73, BMS, KYS, Mo17, Oh43, W22, and W23. The number of detectable NUMTs varied dramatically among the lines. None of the tested inbred lines other than B73 showed the strong hybridization signal on 9L, suggesting that there is a recent mtDNA insertion at this site in B73. Different sources of B73 and W23 were examined for NUMT variation within inbred lines. Differences were detectable, suggesting either that mtDNA is being incorporated or lost from the maize nuclear genome continuously. The results indicate that mtDNA insertions represent a major source of nuclear chromosomal variation.
Testing for Archaic Hominin Admixture on the X Chromosome: Model Likelihoods for the Modern Human RRM2P4 Region From Summaries of Genealogical Topology Under the Structured Coalescent
Authors: Cox Murray P , Mendez Fernando L , Karafet Tatiana M , Pilkington Maya Metni , Kingan Sarah B , Destro-Bisol Giovanni , Strassmann Beverly I , Hammer Michael F
Published: January 2008

A 2.4-kb stretch within the RRM2P4 region of the X chromosome, previously sequenced in a sample of 41 globally distributed humans, displayed both an ancient time to the most recent common ancestor (e.g., a TMRCA of ∼2 million years) and a basal clade composed entirely of Asian sequences. This pattern was interpreted to reflect a history of introgressive hybridization from archaic hominins (most likely Asian Homo erectus) into the anatomically modern human genome. Here, we address this hypothesis by resequencing the 2.4-kb RRM2P4 region in 131 African and 122 non-African individuals and by extending the length of sequence in a window of 16.5 kb encompassing the RRM2P4 pseudogene in a subset of 90 individuals. We find that both the ancient TMRCA and the skew in non-African representation in one of the basal clades are essentially limited to the central 2.4-kb region. We define a new summary statistic called the minimum clade proportion (pmc), which quantifies the proportion of individuals from a specified geographic region in each of the two basal clades of a binary gene tree, and then employ coalescent simulations to assess the likelihood of the observed central RRM2P4 genealogy under two alternative views of human evolutionary history: recent African replacement (RAR) and archaic admixture (AA). A molecular-clock-based TMRCA estimate of 2.33 million years is a statistical outlier under the RAR model; however, the large variance associated with this estimate makes it difficult to distinguish the predictions of the human origins models tested here. The pmc summary statistic, which has improved power with larger samples of chromosomes, yields values that are significantly unlikely under the RAR model and fit expectations better under a range of archaic admixture scenarios.
The Fixation of Locally Beneficial Alleles in a Metapopulation
Authors: Vuilleumier Séverine , Yearsley Jon M , Perrin Nicolas
Published: January 2008

Extinction, recolonization, and local adaption are common in natural spatially structured populations. Understanding their effect upon genetic variation is important for systems such as genetically modified organism management or avoidance of drug resistance. Theoretical studies on the effect of extinction and recolonization upon genetic variance started appearing in the 1970s, but the role of local adaption still has no good theoretical basis. Here we develop a model of a haploid species in a metapopulation in which a locally adapted beneficial allele is introduced. We study the effect of different spatial patterns of local adaption, and different metapopulation dynamics, upon the fixation probability of the beneficial allele. Controlling for the average selection pressure, we find that a small area of positive selection can significantly increase the global probability of fixation. However, local adaption becomes less important as extinction rate increases. Deme extinction and recolonization have a spatial smoothing effect that effectively reduces spatial variation in fitness.
Identification of Novel Activation Mechanisms for FLO11 Regulation in Saccharomyces cerevisiae
Authors: Barrales Ramón R , Jimenez Juan , Ibeas José I
Published: January 2008

Adhesins play a central role in the cellular response of eukaryotic microorganisms to their host environment. In pathogens such as Candida spp. and other fungi, adhesins are responsible for adherence to mammalian tissues, and in Saccharomyces spp. yeasts also confer adherence to solid surfaces and to other yeast cells. The analysis of FLO11, the main adhesin identified in Saccharomyces cerevisiae, has revealed complex mechanisms, involving both genetic and epigenetic regulation, governing the expression of this critical gene. We designed a genomewide screen to identify new regulators of this pivotal adhesin in budding yeasts. We took advantage of a specific FLO11 allele that confers very high levels of FLO11 expression to wild “flor” strains of S. cerevisiae. We screened for mutants that abrogated the increased FLO11 expression of this allele using the loss of the characteristic fluffy-colony phenotype and a reporter plasmid containing GFP controlled by the same FLO11 promoter. Using this approach, we isolated several genes whose function was essential to maintain the expression of FLO11. In addition to previously characterized activators, we identified a number of novel FLO11 activators, which reveal the pH response pathway and chromatin-remodeling complexes as central elements involved in FLO11 activation.
Few Mendelian Genes Underlie the Quantitative Response of a Forest Tree, Eucalyptus globulus, to a Natural Fungal Epidemic
Authors: Freeman Jules S , Potts Brad M , Vaillancourt René E
Published: January 2008

Foliar fungal pathogens from the genus Mycosphaerella affect eucalypts in natural forests and plantations worldwide. QTL analysis was conducted to dissect the genetic control of resistance in Eucalyptus globulus to a natural infection by Mycosphaerella leaf disease, using a clonally replicated outbred F2 family (112 genotypes) planted in a field trial. Two major QTL, with high LOD support (20.2 and 10.9) and high genomewide significance, explained a large proportion (52%) of the phenotypic variance in the severity of damage by Mycosphaerella cryptica, which may be indicative of oligogenic control. Both QTL were validated in a second F2 family and one was validated in a third F2 family. The mean values of different genotype classes at both major QTL argue for Mendelian inheritance with resistance dominant over susceptibility. There were strong correlations between the levels of Mycosphaerella damage in related genetic material planted in three widely separated locations in Tasmania. These findings together provide evidence that the genes controlling resistance to Mycosphaerella damage are stable in different genetic backgrounds and across different environments.
Empirical Tests of the Reliability of Phylogenetic Trees Constructed With Microsatellite DNA
Authors: Takezaki Naoko , Nei Masatoshi
Published: January 2008

Microsatellite DNA loci or short tandem repeats (STRs) are abundant in eukaryotic genomes and are often used for constructing phylogenetic trees of closely related populations or species. These phylogenetic trees are usually constructed by using some genetic distance measure based on allele frequency data, and there are many distance measures that have been proposed for this purpose. In the past the efficiencies of these distance measures in constructing phylogenetic trees have been studied mathematically or by computer simulations. Recently, however, allele frequencies of 783 STR loci have been compiled from various human populations. We have therefore used these empirical data to investigate the relative efficiencies of different distance measures in constructing phylogenetic trees. The results showed that (1) the probability of obtaining the correct branching pattern of a tree (PC) is generally highest for DA distance; (2) FST*, standard genetic distance (DS), and $\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(F_{\mathrm{ST}}/(1{-}F_{\mathrm{ST}})\) \end{document}$ give similar PC-values, FST* being slightly better than the other two; and (3) (δμ)2 shows PC-values much lower than the other distance measures. To have reasonably high PC-values for trees similar to ours, at least 30 loci with a minimum of 15 individuals are required when DA distance is used.
A Bayesian Method for Simultaneously Detecting Mendelian and Imprinted Quantitative Trait Loci in Experimental Crosses of Outbred Species
Authors: Hayashi Takeshi , Awata Takashi
Published: January 2008

Genomic imprinting is interpreted as a phenomenon, in which some genes inherited from one parent are not completely expressed due to modification of the genome caused during gametogenesis. Subsequently, the expression level of an allele at the imprinted gene is changed dependent on the parental origin, which is referred to as the parent-of-origin effect. In livestock, some QTL for reproductive performance and meat productivity have been reported to be imprinted. So far, methods detecting imprinted QTL have been proposed on the basis of interval mapping, where only a single QTL was tested at a time. In this study, we developed a Bayesian method for simultaneously mapping multiple QTL, allowing the inference about expression modes of QTL in an outbred F2 family. The inference about whether a QTL is Mendelian or imprinted was made using Markov chain Monte Carlo estimation by comparing the goodness-of-fits between models, assuming the presence and the absence of parent-of-origin effect at a QTL. We showed by the analyses of simulated data sets that the Bayesian method can effectively detect both Mendelian QTL and imprinted QTL.
Population Genetics of Speciation in Two Closely Related Wild Tomatoes (Solanum Section Lycopersicon)
Authors: Städler Thomas , Arunyawat Uraiwan , Stephan Wolfgang
Published: January 2008

We present a multilocus sequencing study to assess patterns of polymorphism and divergence in the closely related wild tomato species, Solanum peruvianum and S. chilense (Solanum section Lycopersicon, Solanaceae). The data set comprises seven mapped nuclear loci (≈9.3 kb of analyzed sequence across loci) and four local population samples per species that cover much of the species' range (between 80 and 88 sequenced alleles across both species). We employ the analytical framework of divergence population genetics (DPG) in evaluating the utility of the “isolation” model of speciation to explain observed patterns of polymorphism and divergence. Whereas the isolation model is not rejected by goodness-of-fit criteria established via coalescent simulations, patterns of intragenic linkage disequilibrium provide evidence for postdivergence gene flow at two of the seven loci. These results suggest that speciation occurred under residual gene flow, implying that natural selection is one of the evolutionary forces driving the divergence of these tomato species. This inference is fully consistent with their recent divergence, conservatively estimated to be ≤0.55 million years. We discuss possible biases in the demographic parameter estimates due to the current restriction of DPG algorithms to panmictic species.
Dual Involvement of CbrAB and NtrBC in the Regulation of Histidine Utilization inPseudomonas fluorescensSBW25
Authors: Zhang Xue-Xian , Rainey Paul B
Published: January 2008

Pseudomonas fluorescens SBW25 is capable of growing on histidine as a sole source of carbon and/or nitrogen. Previous work showed that the two-component regulatory system CbrAB is required for expression of the histidine utilization (hut) locus when histidine is the sole source of carbon and nitrogen. Here, using mutational analysis and transcriptional assays, we demonstrate involvement of a second two-component system, NtrBC. When histidine is the sole carbon source, transcription of the hutU operon is initiated from a σ54-type promoter and requires CbrB (an enhancer binding protein for σ54-recruitment). However, when histidine is the sole nitrogen source, the hutU operon is transcribed from a σ70-type promoter and requires either CbrB or the nitrogen regulator, NtrC. No role was found for the SBW25 homolog of the nitrogen assimilation control protein (NAC). Biolog phenotypic microarray analysis of the ability of the three mutants (ΔcbrB, ΔntrC, and ΔcbrB ΔntrC) to utilize 190 carbon and 95 nitrogen substrates confirmed the central regulatory roles of CbrAB and NtrBC in cellular carbon and nitrogen catabolism: deletion of cbrB abolished growth on 20 carbon substrates; deletion of ntrC eliminated growth on 28 nitrogen substrates. A double cbrB–ntrC mutant was unable to utilize a further 14 nitrogen substrates (including histidine, proline, leucine, isoleucine, and valine). Our data show that CbrAB plays a role in regulation of both carbon and nitrogen catabolism and maintains activity of catabolic pathways under different C:N ratios.
Chromatin-Associated Genes Protect the Yeast Genome From Ty1 Insertional Mutagenesis
Authors: Nyswaner Katherine M , Checkley Mary Ann , Yi Ming , Stephens Robert M , Garfinkel David J
Published: January 2008

Chromosomal genes modulate Ty retrotransposon movement in the genome of Saccharomyces cerevisiae. We have screened a collection of 4739 deletion mutants to identify those that increase Ty1 mobility (Ty1 restriction genes). Among the 91 identified mutants, 80% encode products involved in nuclear processes such as chromatin structure and function, DNA repair and recombination, and transcription. However, bioinformatic analyses encompassing additional Ty1 and Ty3 screens indicate that 264 unique genes involved in a variety of biological processes affect Ty mobility in yeast. Further characterization of 33 of the mutants identified here show that Ty1 RNA levels increase in 5 mutants and the rest affect mobility post-transcriptionally. RNA and cDNA levels remain unchanged in mutants defective in transcription elongation, including ckb2Δ and elf1Δ, suggesting that Ty1 integration may be more efficient in these strains. Insertion-site preference at the CAN1 locus requires Ty1 restriction genes involved in histone H2B ubiquitination by Paf complex subunit genes, as well as BRE1 and RAD6, histone H3 acetylation by RTT109 and ASF1, and transcription elongation by SPT5. Our results indicate that multiple pathways restrict Ty1 mobility and histone modifications may protect coding regions from insertional mutagenesis.
The Telotype Defines the Telomere State inSaccharomyces cerevisiaeand Is Inherited as a Dominant Non-Mendelian Characteristic in Cells Lacking Telomerase
Authors: Makovets Svetlana , Williams Tanya L , Blackburn Elizabeth H
Published: January 2008

Telomeres are an unusual component of the genome because they do not encode genes, but their structure and cellular maintenance machinery (which we define as “telotype”) are essential for chromosome stability. Cells can switch between different phenotypic states. One such example is when they switch from maintenance mediated by telomerase (TERT telotype) to one of the two alternative mechanisms of telomere preservation (ALT I and ALT II telotype). The nature of this switch is largely unknown. Reintroduction of telomerase into ALT II, but not ALT I, yeast led to the loss of their ability to survive a second round of telomerase withdrawal. Mating-based genetic analysis of ALT I and II revealed that both types of telomerase-independent telomere maintenance are inherited as a non-Mendelian trait dominant over senescence (SEN telotype). Additionally, inheritance of ALT I and ALT II did not depend on either the mitochondrial genome or a prion-based mechanism. Type I, but not type II, survivor cells exhibited impaired gene silencing, potentially connecting the switch to the ALT telotype epigenetic changes. These data provide evidence that nonprion epigenetic-like mechanisms confer flexibility on cells as a population to adjust to the life-threatening situation of telomerase loss, allowing cells to switch from TERT to ALT telotypes that can sustain viable populations.
Molecular Population Genetics of Drosophila Subtelomeric DNA
Authors: Anderson Jennifer A , Song Yun S , Langley Charles H
Published: January 2008

DNA sequence surveys in yeast and humans suggest that the forces shaping telomeric polymorphism and divergence are distinctly more dynamic than those in the euchromatic, gene-rich regions of the chromosomes. However, the generality of this pattern across outbreeding, multicellular eukaryotes has not been determined. To characterize the structure and evolution of Drosophila telomeres, we collected and analyzed molecular population genetics data from the X chromosome subtelomere in 58 lines of North American Drosophila melanogaster and 29 lines of African D. melanogaster. We found that Drosophila subtelomeres exhibit high levels of both structural and substitutional polymorphism relative to linked euchromatic regions. We also observed strikingly different patterns of variation in the North American and African samples. Moreover, our analyses of the polymorphism data identify a localized hotspot of recombination in the most-distal portion of the X subtelomere. While the levels of polymorphism decline sharply and in parallel with rates of crossing over per physical length over the distal first euchromatic megabase pairs of the X chromosome, our data suggest that they rise again sharply in the subtelomeric region (≈80 kbp). These patterns of historical recombination and geographic differentiation indicate that, similar to yeast and humans, Drosophila subtelomeric DNA is evolving very differently from euchromatic DNA.
Inhibition of Transcription by the Caenorhabditis elegans Germline Protein PIE-1: Genetic Evidence for Distinct Mechanisms Targeting Initiation and Elongation
Authors: Ghosh Dolan , Seydoux Geraldine
Published: January 2008

In Caenorhabditis elegans embryos, specification of the germ lineage depends on PIE-1, a maternal protein that blocks mRNA transcription in germline blastomeres. Studies in mammalian cell culture have suggested that PIE-1 inhibits P-TEFb, a kinase that phosphorylates serine 2 in the carboxyl-terminal domain (CTD) repeats of RNA polymerase II during transcriptional elongation. We have tested this hypothesis using an in vivo complementation assay for PIE-1 function. Our results support the view that PIE-1 inhibits P-TEFb using the CTD-like motif YAPMAPT. This activity is required to block serine 2 phosphorylation in germline blastomeres, but unexpectedly is not essential for transcriptional repression or specification of the germline. We find that sequences outside of the YAPMAPT are required to inhibit serine 5 phosphorylation, and that this second inhibitory mechanism is essential for transcriptional repression and specification of the germ lineage. Our results suggest that PIE-1 uses partially redundant mechanisms to block transcription by targeting both the initiation and elongation phases of the transcription cycle.
SiRNA technology, the gene therapy of the future?
Authors: Rácz Zsuzsanna , Hamar Péter
Published: January 2008

A genetikában új korszak kezdődött 17 éve, amikor a petúniában felfedezték a koszuppressziót. Később a koszuppressziót azonosították a növényekben és alacsonyabb rendű eukariótákban megfigyelt RNS-interferenciával (RNSi). Bár a növényekben ez ősi vírusellenes gazdaszervezeti védekezőmechanizmus, emlősökben az RNSi élettani szerepe még nincs teljesen tisztázva. Az RNSi-t rövid kettős szálú interferáló RNS-ek (short interfering RNA, siRNS) irányítják. A jelen cikkben összefoglaljuk az RNSi történetét és mechanizmusát, az siRNS-ek szerkezete és hatékonysága közötti összefüggéseket, a célsejtbe való bejuttatás virális és nem virális módjait. Az siRNS-ek klinikai alkalmazásának legfontosabb akadálya azin vivoalkalmazás. Bár a hidrodinamikus kezelés állatokban hatékony, embereknél nem alkalmazható. Lehetőséget jelent viszont a szervspecifikus katéterezés. A szintetizált siRNS-ek ismert mellékhatásait szintén tárgyaljuk. Bár a génterápia ezen új területén számos problémával kell szembenézni, a sikeresin vitroésin vivokísérletek reményt jelentenek emberi betegségek siRNS-sel történő kezelésére.
Nature Is Not What It Used to Be… New Cosmological Orders in Contemporary, Western Astrology
Authors: Munk Kirstine
Published: January 2008

How does astrology work? This is a question that has concerned practitioners of astrology for as long as astrology has existed. Since astrology is perceived to be a part of the laws of nature, major changes in the perception of nature is also reflected in the ways astrology is perceived to work. During the more recent revival of astrology in the twentieth century, more holistic notions have superseded the idea of planetary influence. However, the Newtonian language persists in astrologers’ writings and in the astrological consultations. This article explores why.
Astrology as Religion
Authors: Laishley Lilan
Published: January 2008

Astrology can be understood as religious in both its principles and practices. A standard definition of religion is used to track astrology’s theoretical, practical, and sociological components. Theoretically, astrology’s Western foundations come from Plato and his story of creation, Timaeus. In establishing a relationship between the larger world of God (macrocosm) and the smaller world of humankind (microcosm), astrology illustrates the Greek concept of an interconnected cosmos. The practice of astrology as a nature religion arises from astrology’s literal, metaphorical, symbolic, and perceptual links to nature. The intersection of time and place at each person’s birth establishes an ‘axis of placement’ connecting each person to the natural world. Astrological practices include tracking the movement of the sun, moon, and planets; ritual participation in the cycles of nature; and honoring nature as sacred. Sociologically, astrology has an amorphous organizational structure, lack of a clear doctrine, and few identifiable institutional partnerships.
New Testament Astral Portents
Authors: Cooper Michael T.
Published: January 2008

Christianity's relationship with astrology is complex. Astrology has been seen as demonic as well as has been utilized for guidance. This complex relationship continues in the twenty-first century. With two important New Testament texts in mind, the article argues that a first century BCE–CE astrological ‘hermeneutic’ illumines Christianity’s understanding of astrology. The article begins with a discussion of the tenacity of astrology in Western culture and then moves to Christianity's relationship with it by looking at some biblical texts and early Christian writings. After the discussion of two New Testament texts, the article concludes with implications for Christianity and astrology.
Grounding the Stars
Authors: Curry Patrick
Published: January 2008

In this paper I seek to outline a conception of astrology in which nature—not a modernist Cartesian nature but the living and sensuous natural world—is central. This involves contextualizing astrology as, in effect, a divinatory practice in which the Earth and its animist apprehension is indispensable. Such a move runs counter to much discourse, both by hostile critics (religious and scientific) and astrologers themselves, which is viewed in Weberian and neo-Weberian terms as part of an attempt, damaging if ultimately unsuccessful, to rationalize and thus disenchant astrology. The positive implications for an openly animist and pluralist astrology are then briefly explored.
The Hero’s Journey
Authors: Pannone Silvia
Published: January 2008

The intention of this paper is to ascertain whether the search for one’s highest and true being is inherent in humanity, how it can best be accomplished, and with what possible results. To this end, I have tried to identify common themes in psychology, myth, and astrology. This article begins with an exploration of the tenets of the main exponents of growth-oriented psychologies. I will then look at the role of mythology and its symbolic language. Consequently, I will analyse current developments within astrology and what the influence of psychology has been. Looking then for possible correlations between psychology and astrology, I will use, as my principal example, the archetype of the Self and the symbolism of the astrological sun. I will suggest that the theme most deeply-rooted in the human psyche is that of the hero’s journey and I will examine what this means in the different disciplines.
Astrology in England in the Twenty-First Century
Authors: Eccles Bernard
Published: January 2008

This paper examines the state of astrology in England at the opening of the twenty-first century. It compares the present state of astrology to a previous assessment published in 1986, and finds that astrology’s long-term survival is not as assured as was assumed at that time. Criteria for the continuance of astrology are suggested, and various options for the future are examined, most of which fail to meet these criteria. In the end, the most promising direction for astrology to take, supported by both external and internal indications, appears to be in association with ecological and neo-pagan movements.
Postscript
Authors: York Michael
Published: January 2008

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On Historical Pragmatics and Peircean Pragmatism
Authors: Pietarinen Ahti-Veikko
Published: January 2008

Historical pragmatics constitutes both the subject matter and methodology. In this paper, the scientific methodology of historical pragmatics is discussed and related to the opinions shared by some 19th-century linguists and philosophers. In particular, Charles S. Peirce’s (1839–1914) semiotics and pragmatism is related to studies on meaning and its change, and his opinions on hypothesis selection in historical research to historical pragmatics. The conclusion is that historical pragmatics is hermeneutic, but that economic and evolutionary considerations square it from the hermeneutic circle.
Exploring Codeswitching in Systemic Functional Linguistics
Authors: Vail Peter
Published: January 2008

Codeswitching is a phenomenon well-studied in several branches of linguistics and anthropology, but one which has not been well integrated into a systemic-functional (SFL) approach. This paper aims to provide an empirical account of codeswitching with an SFL metafunctional framework based on ethnographic field research among Thai and Lao speakers in Northeastern Thailand. Codeswitching was found to have textual functions involving the organization and cohesion of oral texts produced in conversational interaction among multilingual speakers. Codeswitching was also found to produce interpersonal meaning, both within and above the level of the clause. Such meanings were produced through, among other things, the choice of pronouns and politeness markers. Less clear are codeswitching functions in ideation; because the transitivity systems of Thai and Lao are so similar, ideational functions are found more at the level of discourse. The ideational differences between Thai and Lao are argued to be connected to literacy, since Lao as used in Thailand lacks a literate mode and, consequently, the discourse types associated with it. Codeswitching was used to appropriate literate discourses of Thai into Lao through a strategy of simultaneity, and thereby validate Lao as a politically efficacious language.
Discursive Practices in Disciplinary and Professional Contexts
Authors: Bhatia Vijay K.
Published: January 2008

Analysis of professional discourse, which often forms the basis of English for Specific Purposes (ESP) theory and practice, has often been constrained by its focus on textual characteristics, paying little attention to professional practices in specific disciplinary, institutional, or organizational contexts within which these discourses are embedded. This has led to a divide between discourse and genre analysts, on the one hand, and organizational analysts and professional communication theorists, on the other, even though all of them seem to pursue similar objectives. One of the consequences of such mutually exclusive perspectives is that they often take only a partial view of discursive, professional, institutional, and organizational practices. Just as professional communication scholars pay less attention to language use, similarly ESP practitioners do not view professional practices critically. Organizational theorists, in a similar fashion, tend to ignore discursive practices to focus entirely on text-external factors for the study of organizational behaviour. This paper argues that discursive practices within specific professional cultures have multiple perspectives and hence their analysis requires integration of discursive practices with disciplinary, professional, organizational and institutional practices, which are often realized through specialized discourses. The main purpose of the paper therefore is to review recent work in some of these diverse to propose an integration of text-internal as well as text-external perspectives on the analysis of professional discourses, so that we can have a more informed and comprehensive view of the discursive realities of disciplinary and professional practices.
Size Distributions of Different Orders of Kernels within the Oat Spikelet
Authors: Doehlert Douglas C. , Jannink Jean‐Luc , McMullen Michael S.
Published: January 2008

Oat kernel size uniformity is of interest to the oat milling industry because kernel size is important in the dehulling process. Previous studies indicated that oat kernel size distributions are bimodal. In this study oat spikelets were dissected into primary, secondary, and tertiary kernels and kernel size distributions were determined for each of these kernel orders by digital image analysis. Spikelets with two kernels are the most abundant, and their primary and secondary kernels have distinctly different size distributions. These two kernel spikelets appear to be responsible for the bimodal distribution observed among oat kernels. Primary kernels from single kernel spikelets and primary, secondary, and tertiary kernels from triple kernel spikelets all had different mean sizes and distributions. These kernels appeared to contribute to deviations from bimodal distributions. Thus, data presented provide direct definitive evidence that the non‐Gaussian distributions observed for oat kernel sizes are derived from the combination of subpopulations from each of the different orders of kernels from within the spikelet. Sieving analysis of kernel types indicated that for the samples analyzed here, secondary kernels from two kernel spikelets and tertiary kernels from three kernel spikelets appear to contribute equally to undersized kernels under 2 mm in width. Thus, from a kernel size prospective, no advantage can be attributed to the elimination of three kernel spikelets by selective breeding.
Community Resources and Strategies for Association Mapping in Sorghum
Authors: Casa Alexandra M. , Pressoir Gael , Brown Patrick J. , Mitchell Sharon E. , Rooney William L. , Tuinstra Mitchell R. , Franks Cleve D. , Kresovich Stephen
Published: January 2008

Association mapping is a powerful strategy for identifying genes underlying quantitative traits in plants. We have assembled and characterized genetic and phenotypic diversity of a sorghum [Sorghum bicolor (L.) Moench] panel suitable for association mapping, comprised of 377 accessions representing all major cultivated races (tropical lines from diverse geographic and climatic regions), and important U.S. breeding lines and their progenitors. Accessions were phenotyped for eight traits, and levels of population structure and familial relatedness were assessed with 47 simple sequence repeat (SSR) loci. The panel exhibited substantial morphological variation and little genotypic differentiation was observed between the converted tropical and breeding lines. The phenotypic and genotypic data were used to evaluate the performance of several association models in controlling for spurious associations. Our analysis indicated that association models that accounted for both population structure and kinship performed better than those that did not. In addition, we found that the optimal number of subpopulations used to correct for population structure was trait dependent. Although augmentation of the genotypic data with additional SSR loci may be necessary, the association models, genotypic data, and germplasm panel described here provide a starting point for sorghum researchers to begin association studies of traits and markers or candidate genes of interest.
Genetic and Physiological Analysis of an Irradiated Bloomless Mutant (Epicuticular Wax Mutant) of Sorghum
Authors: Burow G. B. , Franks C. D. , Xin Z.
Published: January 2008

An irradiation‐induced bloomless mutant of sorghum [Sorghum bicolor (L.) Moench.], KFS2021, which visually exhibits an absence of white fluffy epicuticular wax in leaf and sheath, was characterized using a combination of genetic and physiological approaches. Study of the phenotypic segregation for the bloomless trait in F2 and F2:3 populations from a cross between KFS2021 and BTx623 (a cultivar with bloom showing profuse deposition of white epicuticular wax) suggests that bloomless is controlled by a single nuclear recessive gene. The bloomless parent (KFS2021) and F2 individuals had lower frequency of guttation, leakier epidermal layer (based on percentage of chlorophyll leaching), and higher rate of seedling water loss than the BTx623 and F2 bloom individuals. Bloomless F2 individuals showed 3‐ to 6‐fold higher nighttime transpiration rates relative to F2 bloom individuals based on nighttime conductance. Correlation analysis showed significant negative associations between leaf epicuticular wax load with epidermal permeability and nighttime conductance, which indicate the important role of epicuticular wax in these traits. These results suggest that epicuticular wax may enhance water use efficiency of sorghum by regulating nighttime water loss.
Divergent Selection for Phosphorus Concentration in Reed Canarygrass
Authors: Casler M. D. , Undersander D. J. , Jokela W. E.
Published: January 2008

Phosphorus is a vital nonrenewable natural resource that is essential for plant and animal growth. Grass swards and buffer strips can be used to reduce P losses that occur by soil erosion, surface runoff, or leaching. The objective of this study was to conduct one cycle of divergent selection for P concentration in reed canarygrass (Phalaris arundinacea L.) and to evaluate the effects of selection on P concentration, forage yield, and P uptake (the product of P concentration and forage yield). Divergent selections and original populations were evaluated in sward plots, harvested three times per year for 2 yr at three locations. Selection responses indicated that P concentration is a heritable trait in reed canarygrass; that genetic gains were highly repeatable across harvests, locations, and years; and that there is a negative genetic correlation between P concentration and sward‐plot forage yield. Future selection efforts must be based on genotypic selection methods, in which half‐sib families are evaluated for forage yield, P concentration, and P uptake in sward plots.