bluuebunny/crossref_metadata_2025_split huggingface dataset:
The distribution of purse‐web Atypus spiders (Araneae: Mygalomorphae) in central Europe is constrained by microclimatic continentality and soil compactness
Authors: Řezáč Milan , Řezáčová Veronika , Pekár Stano 
Published: March 2007

AbstractAim  Three species of primitive spiders of the genus Atypus occur in European xerothermic habitats, where they live in burrows. The aim of this study is to explain their distribution by investigating environmental variables at sites where they occur in central Europe.Location  Over 50 sites in central Europe, Czech Republic.Methods  Data on climatic, edaphic and vegetational parameters were collected from more than 50 sites. Phytocenological data were processed using Ellenberg's indicator values.Results  Atypus muralis was found to occur almost exclusively in dry grassland (Festucion valesiacae), exposed to a continental microclimate. Atypus affinis usually occurred in dry sparse forests (Genisto germanicae–Quercion) that provide an Atlantic microclimate. Atypus piceus occurred in dry grassland (Bromion erecti) or forest fringes (Geranion sanguinei) characterized by an intermediate microclimate. Atypus piceus and A. muralis were restricted to agglutinate calcareous soils.Main conclusions  Our results show that Atypus species colonized sites with different continentality in central Europe. These differences correspond to differences among their probable glacial refugia. Atypus muralis and A. piceus occur in habitats with a markedly continental climate, and are restricted to calcareous agglutinate soils that more efficiently buffer temperature and humidity extremes. Habitats of A. muralis and A. piceus are threatened by overgrowth of vegetation after a recent decline in grazing and by the decalcification of the landscape. However, habitats of A. affinis are stable in the present central European climate.
Student dietitians’ attitudes towards research and audit: a comparison with registered dietitians
Authors: Whelan K. , Madden A. M. , Thomas J. E. 
Published: March 2007

AbstractBackgroundStudent dietitians’ attitudes towards research and audit are important as they are likely to influence their subsequent involvement in such activities once qualified. The aim of this study was to investigate the attitudes of student dietitians towards research and audit and to compare them with those of registered dietitians previously reported.MethodsA questionnaire survey of final‐year student dietitians’ attitudes towards research and audit was conducted. Students indicated their agreement with 12 statements relating to research and audit and the results were compared with those from an identical survey of registered dietitians.ResultsA total of 110 questionnaires were completed (87% response rate). In general, students had positive attitudes towards research and audit. The majority (91%) agreed that ‘all dietitians should be able to act on research’, whilst only a small minority agreed that research (6%) and audit (4%) was ‘not part of a dietitian's role’. In general, students had more positive attitudes towards research, and less positive attitudes towards audit, than dietitians from a previously published survey.DiscussionFinal year student dietitians have positive attitudes towards research and audit. These should be nurtured throughout the early years of their career in order to maximize on their research potential.
Changes in diet quality score, macro‐ and micronutrients intake following a nutrition education intervention in postmenopausal women
Authors: Manios Y. , Moschonis G. , Katsaroli I. , Grammatikaki E. , Tanagra S. 
Published: March 2007

AbstractIntroductionThe aim of the current study was to assess the effectiveness of a nutrition education programme on post‐menopausal women using self‐reported nutrient intake data as well as a qualitative data obtained by the Healthy Eating Index (HEI).Materials and methodsSeventy‐five women (55–65 years old) were randomized to a dietary intervention group (IG: n = 39), attending regular nutrition education sessions for 5 months and to a control group (CG: n = 36). The intervention scheme was based on a combined application of the Health Belief Model and the Social Cognitive Theory, aiming to increase nutritional knowledge and self‐efficacy of the subjects to adopt and maintain healthy dietary choices. Changes in self‐reported macro‐ and micronutrients’ intake as well as in the HEI total score and in its ten components were obtained.ResultsThe IG subjects reported increasing their milk (P < 0.001) and total fat (P = 0.01) HEI scores, decreasing total fat intake (P = 0.050) and increasing calcium and vitamin D intakes (P < 0.001 respectively) to a higher extent compared with the changes reported by the CG.ConclusionThe current nutrition education programme appears to have induced favourable changes for the IG in micronutrients’ intake primarily related to bone health and in total fat intake. These changes were reflected in the individual HEI indices but not in total HEI score.
Automatic thresholding of three‐dimensional microvascular structures from confocal microscopy images
Authors: SMITH CYNTHIA M. , COLE SMITH J. , WILLIAMS STUART K. , RODRIGUEZ JEFFREY J. , HOYING JAMES B. 
Published: March 2007

SummaryWe have combined confocal microscopy, image processing, and optimization techniques to obtain automated, accurate volumetric measurements of microvasculature. Initially, we made tissue phantoms containing 15‐μm FocalCheck™ microspheres suspended in type I collagen. Using these phantoms we obtained a stack of confocal images and examined the accuracy of various thresholding schemes. Thresholding algorithms from the literature that utilize a unimodal histogram, a bimodal histogram, or an intensity and edge‐based algorithm all significantly overestimated the volume of foreground structures in the image stack. Instead, we developed a heuristic technique to automatically determine good‐quality threshold values based on the depth, intensity, and (optionally) gradient of each voxel. This method analyzed intensity and gradient threshold methods for each individual image stack, taking into account the intensity attenuation that is seen in deeper images of the stack. Finally, we generated a microvascular construct comprised of rat fat microvessel fragments embedded in collagen I gels and obtained stacks of confocal images. Using our new thresholding scheme we were able to obtain automatic volume measurements of growing microvessel fragments.
Mechanisms of population differentiation in seabirds
Authors: FRIESEN V. L. , BURG T. M. , McCOY K. D. 
Published: March 2007

AbstractDespite recent advances in population genetic theory and empirical research, the extent of genetic differentiation among natural populations of animals remains difficult to predict. We reviewed studies of geographic variation in mitochondrial DNA in seabirds to test the importance of various factors in generating population genetic and phylogeographic structure. The extent of population genetic and phylogeographic structure varies extensively among species. Species fragmented by land or ice invariably exhibit population genetic structure and most also have phylogeographic structure. However, many populations (26 of 37) display genetic structure in the absence of land, suggesting that other barriers to gene flow exist. In these populations, the extent of genetic structure is best explained by nonbreeding distribution: almost all species with two or more population‐specific nonbreeding areas (or seasons) have phylogeographic structure, and all species that are resident at or near breeding colonies year‐round have population genetic structure. Geographic distance between colonies and foraging range appeared to have a weak influence on the extent of population genetic structure, but little evidence was found for an effect of colony dispersion or population bottlenecks. In two species (Galapagos petrel,Pterodroma phaeopygia, and Xantus's murrelet,Synthliboramphus hypoleucus), population genetic structure, and even phylogeographic structure, exist in the absence of any recognizable physical or nonphysical barrier, suggesting that other selective or behavioural processes such as philopatry may limit gene flow. Retained ancestral variation may be masking barriers to dispersal in some species, especially at high latitudes. Allopatric speciation undoubtedly occurs in this group, but reproductive isolation also appears to have evolved through founder‐induced speciation, and there is strong evidence that parapatric and sympatric speciation occur. While many questions remain unanswered, results of the present review should aid conservation efforts by enabling managers to predict the extent of population differentiation in species that have not yet been studied using molecular markers, and, thus, enable the identification of management units and evolutionary significant units for conservation.
Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites
Authors: Hendrickson Heather , Lawrence Jeffrey G. 
Published: March 2007

SummaryIn bacteria, Ter sites bound to Tus/Rtp proteins halt replication forks moving only in one direction, providing a convenient mechanism to terminate them once the chromosome had been replicated. Considering the importance of replication termination and its position as a checkpoint in cell division, the accumulated knowledge on these systems has not dispelled fundamental questions regarding its role in cell biology: why are there so many copies of Ter, why are they distributed over such a large portion of the chromosome, why is the tus gene not conserved among bacteria, and why do tus mutants lack measurable phenotypes? Here we examine bacterial genomes using bioinformatics techniques to identify the region(s) where DNA polymerase III‐mediated replication has historically been terminated. We find that in both Escherichia coli and Bacillus subtilis, changes in mutational bias patterns indicate that replication termination most likely occurs at or near the dif site. More importantly, there is no evidence from mutational bias signatures that replication forks originating at oriC have terminated at Ter sites. We propose that Ter sites participate in halting replication forks originating from DNA repair events, and not those originating at the chromosomal origin of replication.
Corynebacterium diphtheriae employs specific minor pilins to target human pharyngeal epithelial cells
Authors: Mandlik Anjali , Swierczynski Arlene , Das Asis , Ton‐That Hung 
Published: March 2007

SummaryAdherence to host tissues mediated by pili is pivotal in the establishment of infection by many bacterial pathogens. Corynebacterium diphtheriae assembles on its surface three distinct pilus structures. The function and the mechanism of how various pili mediate adherence, however, have remained poorly understood. Here we show that the SpaA‐type pilus is sufficient for the specific adherence of corynebacteria to human pharyngeal epithelial cells. The deletion of the spaA gene, which encodes the major pilin forming the pilus shaft, abolishes pilus assembly but not adherence to pharyngeal cells. In contrast, adherence is greatly diminished when either minor pilin SpaB or SpaC is absent. Antibodies directed against either SpaB or SpaC block bacterial adherence. Consistent with a direct role of the minor pilins, latex beads coated with SpaB or SpaC protein bind specifically to pharyngeal cells. Therefore, tissue tropism of corynebacteria for pharyngeal cells is governed by specific minor pilins. Importantly, immunoelectron microscopy and immunofluorescence studies reveal clusters of minor pilins that are anchored to cell surface in the absence of a pilus shaft. Thus, the minor pilins may also be cell wall anchored in addition to their incorporation into pilus structures that could facilitate tight binding to host cells during bacterial infection.
FtsK controls metastable recombination provoked by an extra Ter site in the Escherichia coli chromosome terminus
Authors: Louarn Jean‐Michel , Quentin Yves 
Published: March 2007

SummaryThe FtsK protein is required for septum formation in Escherichia coli and as a DNA translocase for chromosome processing while the septum closes. Its domain of action on the chromosome overlaps the replication terminus region, which lies between replication pause sites TerA and TerC. An extra Ter site, PsrA*, has been inserted at a position common to the FtsK and terminus domains. It is well tolerated, although it compels replication forks travelling clockwise from oriC to stall and await arrival of counter‐clockwise forks. Elevated recombination has been detected at the stalled fork. Analysis of PsrA*‐induced homologous recombination by an excision test revealed unique features. (i) rates of excision near PsrA* may fluctuate widely from clone to clone, a phenomenon we term whimsicality, (ii) excision rates are nevertheless conserved for many generations, a phenomenon we term memorization; their metastability at the clone level is explainable by frequent shifting between three cellular states – high, medium and low probability of excision, (iii) PsrA*‐induced excision is RecBC‐independent and is strongly counteracted by FtsK, which in addition is involved in its whimsicality and (iv) whimsicality disappears as the distance from the pause site increases. Action of FtsK at a replication fork was unexpected because the factor was thought to act on the chromosome only at septation, i.e. after replication is completed. Idiosyncrasy of PsrA*‐induced recombination is discussed with respect to possible intermingling of replication, repair and post‐replication steps of bacterial chromosome processing during the cell cycle.
Looking through the eyes of fungi: molecular genetics of photoreception
Authors: Herrera‐Estrella Alfredo , Horwitz Benjamin A. 
Published: March 2007

SummaryFilamentous fungi respond to a variety of environmental signals. One of them is light, providing critical information about orientation, or impending stress. Cells of filamentous fungi appear to sense blue light through a unique transcription factor that has a flavin chromophore and activates its targets in a light‐dependent manner, the white collar (WC) complex. Fungal photophysiology, though, predicted a greater complexity of responses to the whole visible spectrum. The rapidly growing fungal genome database provides candidates to explain how fungi see not only blue, but also near‐UV, green and red light. At the same time, there are surprises in the genomes, including photoreceptors for which there are no obvious photoresponses. Linking these genes and their functions will help understand how a list of only a few biological chromophores accounts for such a diversity of responses. At the same time, deeper mechanistic understanding of how the WC complex functions will lead to fundamental insights at the point where the environment impinges, in this case in the form of photons, on the transcriptional machinery of the cell.
Out on a limb: how the Caulobacter stalk can boost the study of bacterial cell shape
Authors: Wagner Jennifer K. , Brun Yves V. 
Published: March 2007

SummaryUnderstanding the mechanisms underlying the establishment of different bacterial cell shapes and the advantage that a particular shape imparts is one of the most fascinating and challenging areas of study in microbiology. One remarkable example of bacterial morphogenesis is the elaboration of long, tubular extensions of the cell envelope of certain aquatic bacteria. These appendages (also called prosthecae or stalks) possess features that make them particularly amenable models for experiments designed to uncover general principles of cell morphogenesis and of cell shape function. Recent evidence supports the hypothesis that stalk synthesis in Caulobacter crescentus is a specialized form of cell elongation that confers to the cell substantial advantages in nutrient uptake. Further insights into the mechanisms and function of stalk synthesis will require a multidisciplinary systems biology approach using principles and methodologies from ecology and evolutionary biology to biophysics and mathematical modelling.
Identification of an ospC operator critical for immune evasion of Borrelia burgdorferi
Authors: Xu Qilong , McShan Kristy , Liang Fang Ting 
Published: March 2007

SummaryTimely expression of the outer surface protein C (OspC) is crucial for the pathogenic strategy of the Lyme disease spirochete Borrelia burgdorferi. The pathogen abundantly expresses OspC during initial infection when the antigen is required, but downregulates when its presence poses a threat to the spirochetes once the anti‐OspC humoral response has developed. Here, we show that a large palindromic sequence immediately upstream of the ospC promoter is essential for the repression of ospC expression during murine infection and for the ability of B. burgdorferi to evade specific OspC humoral immunity. Deletion of the sequence completely diminished the ability of B. burgdorferi to avoid clearance by transferred OspC antibody in SCID mice. B. burgdorferi lacking the regulatory element was able to initiate infection but unable to persist in immunocompetent mice. Taken together, the regulatory element immediately upstream of the ospC promoter serves as an operator that may interact with an unidentified repressor(s) to negatively regulate ospC expression and is essential for the immune evasion of B. burgdorferi.
Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites: what's the Dif?
Authors: Higgins N. Patrick 
Published: March 2007

SummaryIn this issue of Molecular Microbiology, Hendrickson and Lawrence analyse the sequence of bacterial genomes to map the historical traffic pattern of chromosome replication. Their surprising conclusion is that most forks terminate at the dif site rather than at the Tus/Ter sites where most investigators have concluded termination occurs most frequently. What make this analysis novel are the methods and the revisionist hypotheses for how and why forks might stop at dif.
Antibiotic‐mediated recombination: ciprofloxacin stimulates SOS‐independent recombination of divergent sequences in Escherichia coli
Authors: López Elena , Elez Marina , Matic Ivan , Blázquez Jesús 
Published: March 2007

SummaryThe widespread use and abuse of antibiotics as therapeutic agents has produced a major challenge for bacteria, leading to the selection and spread of antibiotic resistant variants. However, antibiotics do not seem to be mere selectors of these variants. Here we show that the fluoroquinolone antibiotic ciprofloxacin, an inhibitor of type II DNA topoisomerases, stimulates intrachromosomal recombination of DNA sequences. The stimulation of recombination between divergent sequences occurs via either the RecBCD or RecFOR pathways and is, surprisingly, independent of SOS induction. Additionally, this stimulation also occurs in a hyperrecombinogenic mismatch repair mutS mutant. It is worth noting that ciprofloxacin also stimulates the conjugational recombination of an antibiotic resistance gene. Finally, we demonstrate that Escherichia coli is able to recover from treatments with recombination‐stimulating concentrations of the antibiotic. Thus, fluoroquinolones can increase genetic variation by the stimulation of the recombinogenic capability of treated bacteria (via an SOS‐independent mechanism) and consequently may favour the acquisition, evolution and spread of antibiotic resistance determinants.
A novel self‐capping mechanism controls aggregation of periplasmic chaperone Caf1M
Authors: Zavialov Anton V. , Knight Stefan D. 
Published: March 2007

SummaryThe chaperone Caf1M belongs to a family of ATP‐independent periplasmic chaperones that together with outer membrane ushers assemble and secrete filamentous adhesion organelles in Gram‐negative pathogens. It assists in folding and transport of Caf1 subunits of the F1 capsular antigen of Yersinia pestis, the microbe causing bubonic plague. In the periplasm, Caf1M prevents subunit aggregation by capping the extensive hydrophobic surface of activated Caf1. We found that subunit‐free Caf1M exists predominantly as a tetramer [Kd = (2–30) × 10−14 M3 in the 12–37°C interval]. A 2.9 Å resolution crystal structure of the Caf1M tetramer reveals that each of the four molecules contribute its subunit binding sequences (the A1 and G1 strands) to form an eight‐stranded hetero‐sandwich with a well‐packed phenylalanine‐rich hydrophobic core. Tetramerization protects chaperone molecules against enzymatic proteolysis. Deletions in the subunit binding motifs completely abolish tetramer assembly, suggesting that the hetero‐sandwich is the main structural feature holding the tetramer together. Arresting tetramer assembly by a deletion of the N‐terminal binding motif, while leaving the major subunit binding motif VGVFVQFAI (G1 strand) intact, results in accumulation of unspecific aggregates. Deletions in the VGVFVQFAI motif abolish both tetramer assembly and aggregation, consistent with the predicted high β‐aggregation propensity for this motif. These results suggest that the packing of the aggregation‐prone subunit binding sequences into the hetero‐domain is a novel molecular mechanism preventing unspecific aggregation of the free chaperone.
The quorum‐sensing transcription factor TraR decodes its DNA binding site by direct contacts with DNA bases and by detection of DNA flexibility
Authors: White Catharine E. , Winans Stephen C. 
Published: March 2007

SummaryTraR of Agrobacterium tumefaciens is a member of the LuxR family of transcriptional regulators, and binds to specific DNA sequences (tra boxes) at target promoters of the tumour‐inducing (Ti) plasmid. Each tra box has a pronounced dyad symmetry, and each subunit of a TraR dimer binds to one half of a tra box via a helix–turn–helix (HTH) DNA binding motif. Structural analysis has suggested that TraR makes extensive sequence‐specific contacts with tra box DNA. In this study, we tested these predictions using synthetic self‐complementary oligonucleotides containing variant tra box sequences. Some predictions made from structural analysis were confirmed, while others were shown to be incorrect. Unexpectedly, these experiments also showed that six nucleotides at the centre of the tra box that make no direct contact with TraR are nevertheless critical for high‐affinity binding and probably act by facilitating a previously described DNA bend. Variant tra boxes were also tested for transcription activity in vivo. Most transcription assays reflected in vitro binding assays. However, alterations of the outermost nucleotides had little effect on TraR binding but blocked transcription, probably by altering an overlapping −35 promoter motif.