bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of selective logging on inbreeding and gene dispersal in an Amazonian tree population of Carapa guianensis Aubl.
Authors: CLOUTIER D. , KANASHIRO M. , CIAMPI A. Y. , SCHOEN D. J. 
Published: November 2006

AbstractSelective logging may impact patterns of genetic diversity within populations of harvested forest tree species by increasing distances separating conspecific trees, and modifying physical and biotic features of the forest habitat. We measured levels of gene diversity, inbreeding, pollen dispersal and spatial genetic structure (SGS) of an Amazonian insect‐pollinated Carapa guianensis population before and after commercial selective logging. Similar levels of gene diversity and allelic richness were found before and after logging in both the adult and the seed generations. Pre‐ and post‐harvest outcrossing rates were high, and not significantly different from one another. We found no significant levels of biparental inbreeding either before or after logging. Low levels of pollen pool differentiation were found, and the pre‐ vs. post‐harvest difference was not significant. Pollen dispersal distance estimates averaged between 75 m and 265 m before logging, and between 76 m and 268 m after logging, depending on the value of tree density and the dispersal model used. There were weak and similar levels of differentiation of allele frequencies in the adults and in the pollen pool, before and after logging occurred, as well as weak and similar pre‐ and post‐harvest levels of SGS among adult trees. The large neighbourhood sizes estimated suggest high historical levels of gene flow. Overall our results indicate that there is no clear short‐term genetic impact of selective logging on this population of C. guianensis.
Hybridization between multiple fence lizard lineages in an ecotone: locally discordant variation in mitochondrial DNA, chromosomes, and morphology
Authors: LEACHÉ ADAM D. , COLE CHARLES J. 
Published: November 2006

AbstractWe investigated a hybrid zone between two major lineages of fence lizards (Sceloporus cowlesiandSceloporus tristichus) in theSceloporus undulatusspecies complex in eastern Arizona. This zone occurs in an ecotone between Great Basin Grassland and Conifer Woodland habitats. We analysed spatial variation in mtDNA (N = 401; 969 bp), chromosomes (N = 217), and morphology (N = 312; 11 characters) to characterize the hybrid zone and assess species limits. A fine‐scale population level phylogenetic analysis refined the boundaries between these species and indicated that four nonsister mtDNA clades (three belonging toS. tristichusand one toS. cowlesi) are sympatric at the centre of the zone. Estimates of cytonuclear disequilibria in the population closest to the centre of the hybrid zone suggest that theS. tristichusclades are randomly mating, but that theS. cowlesihaplotype has a significant nonrandom association with nuclear alleles. Maximum‐likelihood cline‐fitting analyses suggest that the karyotype, morphology, and dorsal colour pattern clines are all coincident, but the mtDNA cline is skewed significantly to the south. A temporal comparison of cline centres utilizing karyotype data collected in the early 1970s and in 2002 suggests that the cline may have shifted by approximately 1.5 km to the north over a 30‐year period. The recent northward expansion of juniper trees into the Little Colorado River Basin resulting from intense cattle overgrazing provides a plausible mechanism for a shifting hybrid zone and the introgression of the mtDNA haplotypes, which appear to be selectively neutral. It is clear that complex interactions are operating simultaneously in this contact zone, including the formation of hybrids between populations withinS. tristichushaving diagnostic mtDNA, morphology, karyotypes, and dorsal colour patterns, and secondary contact between these and a distantly related yet morphologically cryptic mtDNA lineage (S. cowlesi).
Ribonucleotide reductase and the regulation of DNA replication: an old story and an ancient heritage
Authors: Herrick John , Sclavi Bianca 
Published: November 2006

SummaryAll organisms that synthesize their own DNA have evolved mechanisms for maintaining a constant DNA/cell mass ratio independent of growth rate. The DNA/cell mass ratio is a central parameter in the processes controlling the cell cycle. The co‐ordination of DNA replication with cell growth involves multiple levels of regulation. DNA synthesis is initiated at specific sites on the chromosome termed origins of replication, and proceeds bidirectionally to elongate and duplicate the chromosome. These two processes, initiation and elongation, therefore determine the total rate of DNA synthesis in the cell. In Escherichia coli, initiation depends on the DnaA protein while elongation depends on a multiprotein replication factory that incorporates deoxyribonucleotides (dNTPs) into the growing DNA chain. The enzyme ribonucleotide reductase (RNR) is universally responsible for synthesizing the necessary dNTPs. In this review we examine the role RNR plays in regulating the total rate of DNA synthesis in E. coli and, hence, in maintaining constant DNA/cell mass ratios during normal growth and under conditions of DNA stress.
Reduced action of polypeptide release factors induces mRNA cleavage and tmRNA tagging at stop codons in Escherichia coli
Authors: Li Xia , Yokota Teruaki , Ito Koichi , Nakamura Yoshikazu , Aiba Hiroji 
Published: November 2006

SummaryCertain C‐terminal sequences of nascent peptide cause an efficient protein tagging by tmRNA system at stop codons in Escherichia coli. Here, we demonstrate that both mRNA cleavage and tmRNA tagging occur at UAG stop codon recognized specifically by polypeptide release factor 1 (RF‐1) when the activity of RF‐1 is reduced by a mutation in the prfA gene without requirement of particular C‐terminal sequences of nascent peptide. The tmRNA tagging and mRNA cleavage in the prfA mutant were eliminated when the wild‐type RF‐1 but not RF‐2 was supplied from plasmid. In addition, depletion of either RF‐1 or RF‐2 induces endonucleolytic cleavage and tmRNA tagging at UAG or UGA stop codons respectively. We conclude that ribosome stalling at the cognate stop codon caused by reduced activity or expression of RF‐1 or RF‐2 is responsible for mRNA cleavage. The present data along with our previous studies strongly suggest that ribosome stalling leads to endonucleolytic cleavage of mRNA in general resulting in non‐stop mRNA and that the 3′ end of non‐stop mRNA is probably only target for the tmRNA system.
In vivo contextual requirements for UAG translation as pyrrolysine
Authors: Longstaff David Gordon , Blight Sherry Kathleen , Zhang Liwen , Green‐Church Kari B. , Krzycki Joseph Adrian 
Published: November 2006

SummaryPyrrolysine and selenocysteine have infiltrated natural genetic codes via the translation of canonical stop codons. UGA translation as selenocysteine is absolutely dependent on message context. Here we describe the first experimental examination of contextual requirements for UAG translation as pyrrolysine. A hexahistidine‐tagged Methanosarcina barkeri mtmB1 gene, encoding monomethylamine methyltransferase MtmB1, was introduced into Methanosarcina acetivorans. Host mtmB expression was minimized by growth on methanol and recombinant mtmB1 products monitored by anti‐MtmB and anti‐hexahistidine immunoblotting. UAG translation was not compromised, as recombinant MtmB1 was 1% of cellular protein with only trace UAG‐terminated mtmB1 product detectable. Untranslated regions flanking mtmB1 were not required for UAG translation, but loss of a downstream pyrrolysine insertion sequence (PYLIS) significantly increased the UAG‐termination product of mtmB1 and decreased the UAG‐translation product, which nonetheless contained pyrrolysine. An in‐frame UAG within a bacterial uidA transcript was translated in the methanogen as pyrrolysine with 20% efficiency, suggesting UAG translation in the absence of evolved context. However, predominant UAG‐directed termination with enhancement of UAG translation by the PYLIS appears analogous to cis‐acting elements for UGA translation as selenocysteine, although different mechanisms may underlie these recoding events.
Haem recognition by a Staphylococcus aureus NEAT domain
Authors: Grigg Jason C. , Vermeiren Christie L. , Heinrichs David E. , Murphy Michael E. P. 
Published: November 2006

SummarySuccessful pathogenic organisms have developed mechanisms to thrive under extreme levels of iron restriction. Haem‐iron represents the largest iron reservoir in the human body and is a significant source of iron for some bacterial pathogens. NEAT (NEAr Transporter) domains are found exclusively in a family of cell surface proteins in Gram‐positive bacteria. Many NEAT domain‐containing proteins, including IsdA in Staphylococcus aureus, are implicated in haem binding. Here, we show that overexpression of IsdA in S. aureus enhances growth and an inactivation mutant of IsdA has a growth defect, compared with wild type, when grown in media containing haem as the sole iron source. Furthermore, the haem‐binding property of IsdA is contained within the NEAT domain. Crystal structures of the apo‐IsdA NEAT domain and in complex with haem were solved and reveal a clathrin adapter‐like β‐sandwich fold with a large hydrophobic haem‐binding pocket. Haem is bound with the propionate groups directed at the molecular surface and the iron is co‐ordinated solely by Tyr166. The phenol groups of Tyr166 and Tyr170 form an H‐bond that may function in regulating haem binding and release. An analysis of IsdA structure‐sequence alignments indicate that conservation of Tyr166 is a predictor of haem binding by NEAT domains.
Genome‐wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus
Authors: MORCUENDE ROSA , BARI RAJENDRA , GIBON YVES , ZHENG WENMING , PANT BIKRAM DATT , BLÄSING OLIVER , USADEL BJÖRN , CZECHOWSKI TOMASZ , UDVARDI MICHAEL K. , STITT MARK , SCHEIBLE WOLF‐RÜDIGER 
Published: November 2006

ABSTRACTAffymetrix ATH1 arrays, large‐scale real‐time reverse transcription PCR of ∼ 2200 transcription factor genes and other gene families, and analyses of metabolites and enzyme activities were used to investigate the response of Arabidopsis to phosphate (Pi) deprivation and re‐supply. Transcript data were analysed with MapMan software to identify coordinated, system‐wide changes in metabolism and other cellular processes. Phosphorus (P) deprivation led to induction or repression of > 1000 genes involved in many processes. A subset, including the induction of genes involved in P uptake, the mobilization of organic Pi, the conversion of phosphorylated glycolytic intermediates to carbohydrates and organic acids, the replacement of P‐containing phospholipids with galactolipids and the repression of genes involved in nucleotide/nucleic acid synthesis, was reversed within 3 h after Pi re‐supply. Analyses of 22 enzyme activities revealed that changes in transcript levels often, but not always, led to changes in the activities of the encoded enzymes in P‐deprived plants. Analyses of metabolites confirmed that P deprivation leads to a shift towards the accumulation of carbohydrates, organic acids and amino acids, and that Pi re‐supply leads to use of the latter. P‐deprived plants also showed large changes in the expression of many genes involved in, for example, secondary metabolism and photosynthesis. These changes were not reversed rapidly upon Pi re‐supply and were probably secondary in origin. Differentially expressed and highly P‐specific putative regulator genes were identified that presumably play central roles in coordinating the complex responses of plants to changes in P nutrition. The specific responses to Pi differ markedly from those found for nitrate, whereas the long‐term responses during P and N deprivation share common and non‐specific features.
Assessing environmental and physiological controls over water relations in a Scots pine (Pinus sylvestris L.) stand through analyses of stable isotope composition of water and organic matter
Authors: BRANDES ELKE , WENNINGER JOCHEN , KOENIGER PAUL , SCHINDLER DIRK , RENNENBERG HEINZ , LEIBUNDGUT CHRISTIAN , MAYER HELMUT , GESSLER ARTHUR 
Published: November 2006

ABSTRACTThis study investigated the influence of meteorological, pedospheric and physiological factors on the water relations of Scots pine, as characterized by the origin of water taken up, by xylem transport as well as by carbon isotope discrimination (Δ13C) and oxygen isotope enrichment (Δ18O) of newly assimilated organic matter. For more than 1 year, we quantified δ2H and δ18O of potential water sources and xylem water as well as Δ13C and Δ18O in twig and trunk phloem organic matter biweekly, and related these values to continuously measured or modelled meteorological parameters, soil water content, stand transpiration (ST) and canopy stomatal conductance (Gs). During the growing season, δ18O and δ2H of xylem water were generally in a range comparable to soil water from a depth of 2–20 cm. Long residence time of water in the tracheids uncoupled the isotopic signals of xylem and soil water in winter. Δ18O but not Δ13C in phloem organic matter was directly indicative of recent environmental conditions during the whole year. Δ18O could be described applying a model that included 18O fractionation associated with water exchange between leaf and atmosphere, and with the production of organic matter as well as the influence of transpiration. Phloem Δ13C was assumed to be concertedly influenced by Gs and photosynthetically active radiation (PAR) (as a proxy for photosynthetic capacity). We conclude that isotope signatures can be used as effective tools (1) to characterize the seasonal dynamics in source and xylem water, and (2) to assess environmental effects on transpiration and Gs of Scots pine, thus helping to understand and predict potential impacts of climate change on trees and forest ecosystems.
Physiological girdling of pine trees via phloem chilling: proof of concept
Authors: JOHNSEN KURT , MAIER CHRIS , SANCHEZ FELIPE , ANDERSON PETER , BUTNOR JOHN , WARING RICHARD , LINDER SUNE 
Published: November 2006

ABSTRACTQuantifying below‐ground carbon (C) allocation is particularly difficult as methods usually disturb the root–mycorrhizal–soil continuum. We reduced C allocation below ground of loblolly pine trees by: (1) physically girdling trees and (2) physiologically girdling pine trees by chilling the phloem. Chilling reduced cambium temperatures by approximately 18 °C. Both methods rapidly reduced soil CO2efflux, and after approximately 10 days decreased net photosynthesis (Pn), the latter indicating feedback inhibition. Chilling decreased soil‐soluble C, indicating that decreased soil CO2efflux may have been mediated by a decrease in root C exudation that was rapidly respired by microbes. These effects were only observed in late summer/early autumn when above‐ground growth was minimal, and not in the spring when above‐ground growth was rapid. All of the effects were rapidly reversed when chilling was ceased. In fertilized plots, both chilling and physical girdling methods reduced soil CO2efflux by approximately 8%. Physical girdling reduced soil CO2efflux by 26% in non‐fertilized plots. This work demonstrates that phloem chilling provides a non‐destructive alternative to reducing the movement of recent photosynthate below the point of chilling to estimate C allocation below ground on large trees.
Interaction of Cholera Toxin with Three Life‐cycle Stages of Schistosoma mansoni: Adult Worm, Egg and Cercaria
Authors: Akhiani A. A. , Deelder A. M. , Månsson J.‐E. , Nilsson L.‐Å. 
Published: November 2006

AbstractWe have previously reported that there is an immunological cross‐reactivity between Schistosoma mansoni and cholera toxin (CT). In this study, using an immunofluorescence technique with anti‐CT antibody, we provide further evidence for this cross‐reactivity by demonstrating an antigen, localized in the tegument of S. mansoni adult worms which is cross‐reactive with a CT antigen. Anti‐CT antibodies also reacted with structures in S. mansoni cercariae and eggs. Additionally, CT itself was found to bind strongly to the gut of the adult worm, gut cells of cercaria and the egg shell. The binding of CT to the parasite was blocked when parasite sections were incubated with CT which had been incubated with the ganglioside GM1. Lipid extraction and isolation of gangliosides demonstrated the presence of GM1 in adult worms. For further analysis of CT‐binding structures, the possible interaction of CT with two major schistosome gut antigens, circulating cathodic antigen (CCA) and circulating anodic antigen (CAA), was studied. We found that CT blocked the binding of anti‐CCA antibody to the gut of adult worms and that anti‐CCA blocked the binding of CT to the worm gut. These findings indicate that CT binds to CCA present in the gut of the parasite and thus has, in addition to GM1, a second binding specificity.
Inflammatory Cytokines in Relation to Adrenal Response Following Total Hip Replacement
Authors: Bjornsson G. L. , Thorsteinsson L. , Gudmundsson K. O. , Jonsson H. , Gudmundsson S. , Gudbjornsson B. 
Published: November 2006

AbstractOur objective was to investigate the initiation and course of pro‐ and anti‐inflammatory cytokines in early inflammatory response and to elucidate the cytokine system in relation to the adrenal response caused by stress. Seven blood samples were collected, pre‐ and postoperatively (0–72 h) after total hip replacement (THR) due to osteoarthritis. The following cytokines were measured using Cytometric Bead Array: interleukin‐1β (IL‐1β), IL‐6, tumour necrosis factor‐α, IL‐8, IL‐12 and IL‐10 (B&D). Thirteen patients took part in the study (67 ± 9 years). C‐reactive protein increased from <6 to over 200 mg/l on the second post‐op day. The concentration of IL‐6 increased 10‐fold just 3 h post‐op (4–47 pg/ml) and reached its maximum value 6 h post‐op (77 pg/ml; Wilcoxon test P < 0.01) Repeated measurements were also significant (Friedman P < 0.05). The concentration of IL‐8 doubled the day of surgery but did not reach a significant level (Friedman test =0.069). None of the other cytokines showed any significant changes. The diurnal cortisol rhythm was interrupted after the surgery and there was a significant correlation between the cortisol secretion and IL‐6 response. This study demonstrates an isolated elevation in IL‐6 levels with only a minor elevation in IL‐8 following THR. This pro‐inflammatory response seemed to decline without activation of anti‐inflammatory cytokines (IL‐10), but cortisol seemed to play a complicated role in halting the acute inflammatory response.
The Late Jurassic Tithonian, a greenhouse phase in the Middle Jurassic–Early Cretaceous ‘cool’ mode: evidence from the cyclic Adriatic Platform, Croatia
Authors: HUSINEC ANTUN , FRED READ J. 
Published: November 2006

AbstractWell‐exposed Mesozoic sections of the Bahama‐like Adriatic Platform along the Dalmatian coast (southern Croatia) reveal the detailed stacking patterns of cyclic facies within the rapidly subsiding Late Jurassic (Tithonian) shallow platform‐interior (over 750 m thick, ca 5–6 Myr duration). Facies within parasequences include dasyclad‐oncoid mudstone‐wackestone‐floatstone and skeletal‐peloid wackestone‐packstone (shallow lagoon), intraclast‐peloid packstone and grainstone (shoal), radial‐ooid grainstone (hypersaline shallow subtidal/intertidal shoals and ponds), lime mudstone (restricted lagoon), fenestral carbonates and microbial laminites (tidal flat). Parasequences in the overall transgressive Lower Tithonian sections are 1–4·5 m thick, and dominated by subtidal facies, some of which are capped by very shallow‐water grainstone‐packstone or restricted lime mudstone; laminated tidal caps become common only towards the interior of the platform. Parasequences in the regressive Upper Tithonian are dominated by peritidal facies with distinctive basal oolite units and well‐developed laminate caps. Maximum water depths of facies within parasequences (estimated from stratigraphic distance of the facies to the base of the tidal flat units capping parasequences) were generally <4 m, and facies show strongly overlapping depth ranges suggesting facies mosaics. Parasequences were formed by precessional (20 kyr) orbital forcing and form parasequence sets of 100 and 400 kyr eccentricity bundles. Parasequences are arranged in third‐order sequences that lack significant bounding disconformities, and are evident on accommodation (Fischer) plots of cumulative departure from average cycle thickness plotted against cycle number or stratigraphic position. Modelling suggests that precessional sea‐level changes were small (several metres) as were eccentricity sea‐level changes (or precessional sea‐level changes modulated by eccentricity), supporting a global, hot greenhouse climate for the Late Jurassic (Tithonian) within the overall ‘cool’ mode of the Middle Jurassic to Early Cretaceous.
The glauconite–Fe‐illite–Fe‐smectite problem: a critical review
Authors: Meunier Alain , El Albani Abderrazak 
Published: November 2006

AbstractIron silicate minerals are a significant component of sedimentary systems but their modes of formation remain controversial. Our analysis of published data identifies end‐member compositions and mixtures and allows us to recognize controls of formation of different mineral species. The compositional fields of glaucony, Fe‐illite, Fe–Al smectites are determined in the M+/4Si vs. Fe/Sum of octahedral cations (M+ = interlayer charge). Solid solutions could exist between these phases. The Fe–Al and Fe‐rich clay minerals form two distinct solid solutions. The earliest phases to be formed are Fe–Al smectites or berthierine depending on the sedimentation rate. Reductive microsystems appear in the vicinity of organic debris in unconsolidated sediments. The Fe is incorporated first in pyrite and then in silicates after oxidation. Potassium ions diffuse from the sea‐water–sediment interface. If not interrupted, the diffusion process is active until reaction completion is reached, i.e. formation of Fe‐illite or glauconite or a mineral assemblage (berthierine–nontronite) according to the available Al ion amounts in the microsystem. Mixed‐layer minerals are formed when the diffusion process is interrupted because of sedimentation, compaction or cementation. Despite the common belief of their value as palaeoenvironment indicators, these minerals can form in a variety of environments and over a period of millions of years during sediment burial.