bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effectiveness of dietary advice given by community dietitians to men with elevated blood cholesterol in a clinical setting: a pilot study
Authors: Drummond S. , Kirk T. , Jackson J. , Hendry J. , Panton S. , Gray F. 
Published: December 2004

AbstractObjective  To compare the effect of two types of dietary advice given by community dietitians on subsequent dietary intake in Scottish men, over 8 weeks.Design  A parallel design intervention study was employed. Twenty‐five men with elevated blood cholesterol levels were randomly assigned to Group 1 (advice to reduce dietary fat only) or Group 2 (advice to reduce dietary fat and sugar).Results  Neither group significantly reduced fat intakes, yet both groups self‐rated their fat intake as being lower at the end than at the start of the study. Group 2 reduced per cent energy from sugar and increased per cent energy from starch without significantly changing per cent energy from total carbohydrate. No significant change in blood cholesterol levels were observed.Conclusions  Advice to reduce dietary fat was not effective in this group of subjects. Advice to reduce both fat and sugar resulted in a decrease in sugar intake only. Both groups wrongly rated their fat intake to be lower at the end of the study. This may be a barrier to further dietary advice.
Distribution and diversity of rhizobia nodulating agroforestry legumes in soils from three continents in the tropics
Authors: Bala Abdullah , Murphy Phillip , Giller Ken E. 
Published: December 2004

AbstractThe natural rhizobial populations of Calliandra calothyrsus, Gliricidia sepium, Leucaena leucocephala and Sesbania sesban were assessed in soils from nine sites across tropical areas of three continents. The rhizobial population size varied from undetectable numbers to 1.8 × 104 cells/g of soil depending on the trap host and the soil. Calliandra calothyrsus was the most promiscuous legume, nodulating in eight soils, while S. sesban nodulated in only one of the soils. Polymerase chain reaction restriction fragment length polymorphism (PCR‐RFLP) analyses of the 16S rRNA gene and the internally transcribed spacer (ITS) region between the 16S and 23S rRNA genes were used to assess the diversity and relative abundance of rhizobia trapped from seven of the soils by C. calothyrsus, G. sepium and L. leucocephala. Representatives of the 16S rRNA RFLP groups were also subjected to sequence analysis of the first 950 base pairs of the 16S rRNA gene. Eighty ITS groups were obtained, with none of the ITS types being sampled in more than one soil. RFLP analysis of the 16S rRNA yielded 23 ‘species’ groups distributed among the Rhizobium, Mesorhizobium, Sinorhizobium and Agrobacterium branches of the rhizobial phylogenetic tree. The phylogeny of the isolates was independent of the site or host of isolation, with different rhizobial groups associated with each host across the soils from widely separated geographical regions. Although rhizobial populations in soils sampled from the centre of diversity of the host legumes were the most genetically diverse, soil acidity was highly correlated with the diversity of ITS types. Our results support the hypothesis that the success of these tree legumes in soils throughout the tropics is the result of their relative promiscuity (permissiveness) allowing nodulation with diverse indigenous rhizobial types.
Combining genetic markers and stable isotopes to reveal population connectivity and migration patterns in a Neotropical migrant, Wilson's warbler (Wilsonia pusilla)
Authors: Clegg Sonya M. , Kelly Jeffrey F. , Kimura Mari , Smith Thomas B. 
Published: December 2004

AbstractWe used results from the analysis of microsatellite DNA variation and hydrogen stable‐isotope ratios to characterize the population structure of a neotropical migrant passerine, the Wilson's warbler (Wilsonia pusilla). The resulting information was then used to infer migration patterns and population connectivity between breeding grounds in North America and overwintering areas in Mexico and Central America. The microsatellite data revealed genetic structure across the North American continent; populations in the west were found to significantly differ from the east. Minimal genetic structure was observed among western sites. The lack of isolation by distance and low variance inFSTvalues suggests that gene flow could play an ongoing role in limiting genetic differentiation among sites in the western part of the distribution. However, additional information including estimates of effective population size and the proximity of the population to equilibrium is required before the role of gene flow can be assessed fully. Analysis of isotope data showed a negative relationship between latitude and hydrogen isotope ratios in breeding ground individuals. There was a positive relationship between wintering ground latitude and hydrogen isotope ratios for individuals that were genetically western in origin. This is consistent with a leapfrog pattern of migration, in which genetically western birds from the northernmost breeding areas overwinter at the most southerly locations in Central America. Additionally, isotopic ratios of western birds suggest that coastal breeders overwinter in western Mexico, while western birds from further inland and at high elevations overwinter in eastern Mexico. Using information from both genetic an isotopic approaches will probably be useful for identifying patterns of migration and population connectivity between breeding and overwintering areas, both important issues for conservation efforts, and may also contribute to investigation of the evolution of migration.
Low and homogeneous copy number of plasmid‐borne symbiont genes affecting host nutrition in Buchnera aphidicola of the aphid Uroleucon ambrosiae
Authors: Plague Gordon R. , Dale Colin , Moran Nancy A. 
Published: December 2004

AbstractThe bacterial endosymbiont of aphids, Buchnera aphidicola, often provides amino acids to its hosts. Plasmid amplification of leucine (leuABCD) and tryptophan (trpEG) biosynthesis genes may be a mechanism by which some Buchnera over‐produce these nutrients. We used quantitative polymerase chain reaction to assess the leuABCD/trpEG copy variability within Uroleucon ambrosiae, an aphid with a wide diet breadth and range. Both leuABCD and trpEG abundances are: (i) similar for aphids across 15 populations, and (ii) low compared to Buchnera from other aphid species (particularly trpEG). Consequently, the plasmid location of trpEG combined with Buchnera's chromosomal polyploidy may functionally limit, rather than increase, tryptophan production within Uroleucon ambrosiae.
A test for deviation from island‐model population structure
Authors: Porter Adam H. 
Published: December 2004

AbstractThe neutral island model forms the basis for several estimation models that relate patterns of genetic structure to microevolutionary processes. Estimates of gene flow are often based on this model and may be biased when the model's assumptions are violated. An appropriate test for violations is to compare FST scores for individual loci to a null distribution based on the average FST taken over multiple loci. A parametric bootstrap method is described here based on Wright's β‐distribution to generate null distributions of FST for each locus. These null distributions account for error introduced by sampling populations, individuals and loci, and also biological sources of error, including variable alleles/locus and inbreeding. Confidence limits can be obtained directly from these distributions. Significant deviations from the island model may be the result of selection, deviations from the island model's migration pattern, nonequilibrium conditions, or other deviations from island‐model assumptions. Only strong biases are likely to be detected because of the inherently large sampling variation of FST. Nevertheless, a coefficient, Nb, describing bias in the spread of the β‐distribution in units comparable to the gene flow parameter, Nm, can be obtained for each locus. In samples from populations of the butterfly Coenonympha tullia, the loci Idh‐1, Mdh‐1, Pgi and Pgm showed significantly lower FST than expected.
Molecular phylogeography of the Amazonian Chagas disease vectors Rhodnius prolixus and R. robustus
Authors: Monteiro Fernando A. , Barrett Toby V. , Fitzpatrick Sinead , Cordon‐Rosales Celia , Feliciangeli Dora , Beard Charles B. 
Published: December 2004

AbstractThe phylogeographical structure of the closely related species Rhodnius prolixus and R. robustus is presented based on a 663‐base pair (bp) fragment of the mitochondrial cytochrome b gene. Twenty haplotypes were recovered from 84 samples examined, representing 26 populations from seven Latin American countries. The resulting phylogenetic tree is composed of five major reciprocally monophyletic clades, one representing R. prolixus and four representing R. robustus. While R. prolixus is a very homogeneous assemblage, R. robustus has deeper clades and is paraphyletic, with the clade comprising R. robustus from Venezuela (Orinoco region) more closely related to the R. prolixus clade than to the other R. robustus populations from the Amazon region. The R. robustus paraphyly was supported further by the analysis of a nuclear gene (D2 region of the 28S RNA) for a subset of specimens. The data support the view that R. robustus represents a species complex. Levels of sequence divergence between clades within each region are compatible with a Pleistocene origin. Nucleotide diversity (π) for all R. prolixus populations was extremely low (0.0008), suggesting that this species went through a recent bottleneck, and was subsequently dispersed by man.
Patterns of nuclear DNA degeneration over time — a case study in historic teeth samples
Authors: Wandeler P. , Smith S. , Morin P. A. , Pettifor R. A. , Funk S. M. 
Published: December 2004

AbstractThe amount of nuclear DNA extracted from teeth of 279 individual red fox Vulpes vulpes collected over a period spanning the last three decades was determined by quantitative polymerase chain reaction (PCR). Although teeth were autoclaved during initial collection, 73.8% of extracts contained sufficient DNA concentration (> 5 pg/µL) suitable for reliable microsatellite genotyping but the quantity of nuclear DNA decayed significantly over time in a nonlinear pattern. The success of PCR amplification across four examined canine microsatellites over time was dependent on fragment size. By including data from two different tests for human contamination and from frequencies of allelic dropout and false alleles, the methodological constraints of population genetic studies using microsatellite loci amplified from historic DNA are discussed.
Matrilineal genetic structure within and among populations of the cooperatively breeding common marmoset,Callithrix jacchus
Authors: Faulkes C. G. , Arruda M. F. , Monteiro Da Cruz M. A. O. 
Published: December 2004

AbstractCommon marmosets are members of the family Callitrichidae, South American primates characterized by highly social group living and cooperative breeding. In this study we analysed 1112 base pairs (bp) of the mitochondrial control region in 59Callithrix jacchusindividuals, sampled mainly from two geographically distinct field sites in N.E. Brazil. Analysis of molecular variation revealed a highly significant genetic structuring of haplotypes between social groups and between populations. Examination of matrilineal genetic structure within social groups revealed that seven of nine recorded breeding pairs were from different maternal lineages, indicating assortative mating and outbreeding. In addition to the breeders, at least six of 10 groups contained adult individuals from different matrilines, with five haplotypes present in one social group of nine animals. Groups of mixed lineages raise questions about potential reproductive conflicts of interest, and the extent of kin‐selected altruism in the evolution and maintenance of cooperative breeding in this species.
Clines and adaptive evolution in the methuselah gene region in Drosophila melanogaster
Authors: Duvernell David D. , Schmidt Paul S. , Eanes Walter F. 
Published: December 2004

AbstractIn an effort to characterize further the patterns of selection and adaptive evolution at the methuselah locus in Drosophila species, we extended an analysis of geographical variation to include single nucleotide polymorphisms (SNPs) in adjacent genes on either side of the mth locus, and examined the molecular variation in a neighbouring methuselah paralogue (mth2). An analysis of 13 SNPs spanning a region of nearly 19 kilobases surrounding the mth locus demonstrated that a clinal pattern associated with the most common mth haplotype does not extend to adjacent gene loci, providing compelling evidence that the clinal pattern results from selection on as yet unidentified sites associated with the functional mth locus. mth2 exhibited a significant pattern of adaptive divergence among D. melanogaster, D. simulans and D. yakuba similar to that seen at mth. However, Ka : Ks ratios indicate a difference in levels of functional constraint at the two methuselah, loci with mth2 exhibiting a five‐ to six‐fold reduction in levels of amino acid divergence relative to mth.
The distribution of the ancestral haplotype in finite stepping‐stone models with population expansion
Authors: Satta Y. , Takahata N. 
Published: December 2004

AbstractRecent extensive analyses of human DNA polymorphism reveal that the ancestral haplotype at various genetic loci occurs almost exclusively in African samples. We develop a coalescence‐based simulation method in stepping‐stone models with population expansion and examine the probability (PA) that the ancestral haplotype is found in African samples and the probability (QA) that the most recent common ancestor of sampled genes occurs in Africa. These probabilities and other summary statistics are used to infer the human demographic history. It is shown that the high observed PA value cannot be explained simply by sampling bias. Rather, it suggests that the African population has been more strongly subdivided and isolated from each other than the non‐African population and that there must have been some African populations which were not directly involved in the Out‐of‐Africa expansion in the late Pleistocene.
Genetic population structure of turbot (Scophthalmus maximus L.) supports the presence of multiple hybrid zones for marine fishes in the transition zone between the Baltic Sea and the North Sea
Authors: Nielsen Einar E. , Nielsen Peter H. , Meldrup Dorte , Hansen Michael M. 
Published: December 2004

AbstractGenetic population structure of turbot (Scophthalmus maximus L.) in the Northeast Atlantic was investigated using eight highly variable microsatellite loci. In total 706 individuals from eight locations with temporal replicates were assayed, covering an area from the French Bay of Biscay to the Aaland archipelago in the Baltic Sea. In contrast to previous genetic studies of turbot, we found significant genetic differentiation among samples with a maximum pairwise FST of 0.032. Limited or no genetic differentiation was found among samples within the Atlantic/North Sea area and within the Baltic Sea, suggesting high gene flow among populations in these areas. In contrast, there was a sharp cline in genetic differentiation going from the low saline Baltic Sea to the high saline North Sea. The data were explained best by two divergent populations connected by a hybrid zone; however, a mechanical mixing model could not be ruled out. A significant part of the genetic variance could be ascribed to variation among years within locality. Nevertheless, the population structure was relatively stable over time, suggesting that the observed pattern of genetic differentiation is biologically significant. This study suggests that hybrid zones are a common phenomenon for marine fishes in the transition area between the North Sea and the Baltic Sea and highlights the importance of using interspecific comparisons for inferring population structure in high gene flow species such as most marine fishes.
Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context
Authors: Yoder Anne D. , Yang Ziheng 
Published: December 2004

AbstractThe lemurs of Madagascar are a unique radiation of primates that show an extraordinary diversity of lifestyles, morphologies and behaviours. However, very little is known about the relative antiquity of lemuriform clades due to the lack of terrestrial fossils for the Tertiary of Madagascar. Here, we employ a Bayesian method to estimate divergence dates within the lemuriform radiation using several unlinked gene loci and multiple fossil calibrations outside the lemuriform clade. Two mitochondrial genes (cytochrome oxidase II and cytochromeb), two nuclear introns (transthyretin intron 1 and von Willebrand factor gene intron 11) and one nuclear exon (interphotoreceptor retinoid binding protein, exon 1) are used in separate and combined analyses. The genes differ in taxon sampling and evolutionary characteristics but produce congruent date estimates. Credibility intervals narrow considerably in combined analyses relative to separate analyses due to the increased amount of data. We also test the relative effects of multiple vs. single calibration points, finding that, when only single calibration points are employed, divergence dates are systematically underestimated. For the mitochondrial DNA data set, we investigate the effects of sampling density within the mouse lemur radiation (genusMicrocebus). When only two representative species are included, estimated dates throughout the phylogeny are more recent than with the complete‐species sample, with basal nodes less affected than recent nodes. The difference appears to be due to the manner in which priors on node ages are constructed in the two analyses. In nearly all analyses, the age of the lemuriform clade is estimated to be approximately 62–65 Ma, with initial radiation of mouse lemurs and true lemurs (genusEulemur) occurring approximately 8–12 Ma. The antiquity of the mouse lemur radiation is surprising given the near uniform morphology among species. Moreover, the observation that mouse lemurs and true lemurs are of similar ages suggests discrepancies in rates of morphological, behavioural and physiological evolution in the two clades, particularly with regard to characteristics of sexual signalling. These differences appear to correlate with the nocturnal vs. diurnal lifestyles, respectively, of these two primate groups.
Archaea: an archetype for replication initiation studies?
Authors: Kelman Lori M. , Kelman Zvi 
Published: December 2004

SummaryWhereas the process of DNA replication is fundamentally conserved in the three domains of life, the archaeal system is closer to that of eukarya than bacteria. In the time since the complete genome sequences of several members of the archaeal domain became available, there has been a burst of research on archaeal DNA replication. These studies have led to both expected and surprising findings. This review summarizes the search for origins of replication in archaea, and our current knowledge of initiation, the process by which replication origins are recognized, the DNA molecule is unwound and the replicative helicase is loaded onto the DNA in preparation for DNA synthesis. The similarities and differences of the initiation process in archea, bacteria and eukarya are also summarized.
Phase variation of the 987P‐like CS18 fimbriae of human enterotoxigenic Escherichia coli is regulated by site‐specific recombinases
Authors: Honarvar Shaya , Choi Byung‐Kwon , Schifferli Dieter M. 
Published: December 2004

SummaryThe gene cluster of the CS18 (PCFO20) fimbriae of human enterotoxigenic Escherichia coli (ETEC) was found to include seven genes (fotA to fotG) that are similar to each of the seven structural and export proteins of the 987P fimbriae. However, no analogous gene to the fasH regulatory gene, which is located at the 3′ end of the 987P gene cluster and encodes an AraC‐like activator of transcription, could be detected. Surprisingly, two novel genes (fotS and fotT) encoding proteins similar to the site‐specific recombinases of the type 1 fimbriae (FimB and FimE) were identified at the 5′ end of the fot gene cluster. These genes were shown to be required for the catalysis of a 312 bp‐inversion just upstream of fotA. The inversion determines CS18 fimbrial phase variation. FotS participates in inverting the 312 bp‐segment in both the ON and OFF orientation, whereas FotT has a bias for the OFF oriented recombination. Similar regulators of fimbriation by phase variation were described in uropathogenic and commensal Enterobacteriaceae. In contrast, only AraC‐like transcriptional activators were previously described as regulators of the intestinal colonization factors of human ETEC isolates. Thus, the CS18 and 987P gene clusters encode similar components for fimbrial biogenesis but different types of regulators for fimbriation. The combination of blocks of genes encoding similar structural products but different regulatory proteins underlines how modular DNA rearrangements can evolve by serving pathogen diversification. Acquisition of a phase variation module to regulate fimbrial genes is proposed to be beneficial for the adaptation and transmission of pathogens.
Efficient sporulation in Clostridium difficile requires disruption of the σK gene
Authors: Haraldsen Jeralyn D. , Sonenshein Abraham L. 
Published: December 2004

SummaryA 14.6 kb prophage‐like insertion, termed skinCd, was found to interrupt the sigK gene, which encodes an RNA polymerase sigma factor essential for sporulation, in six strains of Clostridium difficile. Until now, Bacillus subtilis was the only spore‐former shown to carry such an insertion, and the presence of the insertion is not required for efficient sporulation in this organism. The B. subtilis and C. difficile skin elements proved to be divergent in sequence, inserted at different sites within the sigK gene and in opposite orientations. The skinCd element was excised from the chromosome specifically during sporulation, forming a circular molecule. Two natural isolates of C. difficile lacked the skinCd element and were defective in sporulation. When a merodiploid strain was created that carries both interrupted and uninterrupted versions of the sigK gene, the cells became Spo–, showing that the uninterrupted gene is dominant and inhibits sporulation. C. difficile sigK genes, whether skinCd+ or skinCd–, lack the N‐terminal pro‐sequence found in all other sigK genes studied to date. Thus, regulated excision of skinCd appears to be a critical mechanism for achieving proper temporal activation of σK.