bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competition favours reduced cost of plasmids to host bacteria
Authors: Haft Rembrandt J F , Mittler John E , Traxler Beth 
Published: April 2009

Abstract
Conjugative plasmids of Gram-negative bacteria have both vertical and horizontal modes of transmission: they are segregated to daughter cells during division, and transferred between hosts by plasmid-encoded conjugative machinery. Despite maintaining horizontal mobility, many plasmids carry fertility inhibition (fin) systems that repress their own conjugative transfer. To assess the ecological basis of self-transfer repression, we compared the invasion of bacterial populations by fin+ and fin− variants of the plasmid R1 using a computational model and co-culture competitions. We observed that the fin+ variant had a modest cost to the host (measured by reduction in growth rate), while the fin− variant incurred a larger cost. In simulations and empirical competitions the fin− plasmid invaded cultures quickly, but was subsequently displaced by the fin+ plasmid. This indicated a competitive advantage to reducing horizontal transmission and allowing increased host replication. Computational simulations predicted that the advantage associated with reduced cost to the host would be maintained over a wide range of environmental conditions and plasmid costs. We infer that vertical transmission in concert with competitive exclusion favour decreased horizontal mobility of plasmids. Similar dynamics may exert evolutionary pressure on parasites, such as temperate bacteriophages and vertically transmitted animal viruses, to limit their rates of horizontal transfer.
Arabidopsis Protein Kinases GRIK1 and GRIK2 Specifically Activate SnRK1 by Phosphorylating Its Activation Loop
Authors: Shen Wei , Reyes Maria Ines , Hanley-Bowdoin Linda 
Published: April 2009

AbstractSNF1-related kinases (SnRK1s) play central roles in coordinating energy balance and nutrient metabolism in plants. SNF1 and AMPK, the SnRK1 homologs in budding yeast (Saccharomyces cerevisiae) and mammals, are activated by phosphorylation of conserved threonine residues in their activation loops. Arabidopsis (Arabidopsis thaliana) GRIK1 and GRIK2, which were first characterized as geminivirus Rep interacting kinases, are phylogenetically related to SNF1 and AMPK activating kinases. In this study, we used recombinant proteins produced in bacteria to show that both GRIKs specifically bind to the SnRK1 catalytic subunit and phosphorylate the equivalent threonine residue in its activation loop in vitro. GRIK-mediated phosphorylation increased SnRK1 kinase activity in autophosphorylation and peptide substrate assays. These data, together with earlier observations that GRIKs could complement yeast mutants lacking SNF1 activation activities, established that the GRIKs are SnRK1 activating kinases. Given that the GRIK proteins only accumulate in young tissues and geminivirus-infected mature leaves, the GRIK-SnRK1 cascade may function in a developmentally regulated fashion and coordinate the unique metabolic requirements of rapidly growing cells and geminivirus-infected cells that have been induced to reenter the cell cycle.
Broken gears in the avian molecular clock: new phylogenetic analyses support stem galliform status forGallinuloides wyomingensisand rallid affinities forAmitabha urbsinterdictensis
Authors: Ksepka Daniel T. 
Published: April 2009

AbstractGalliformes (landfowl) have been the focus of numerous divergence dating studies that seek a refined understanding of the early radiation of living birds. The Eocene fossil birdsAmitabha urbsinterdictensis(Bridger Formation) andGallinuloides wyomingensis(Green River Formation) have been used extensively in studies dealing with the timing of evolution in crown Galliformes. Divergence estimates from studies incorporating these fossils as calibration points suggest that multiple galliform lineages radiated in the Cretaceous and survived the Cretaceous–Tertiary mass extinction. However, the phylogenetic position of both fossils has been disputed, particularly with regard to crown or stem status. In order to resolve this debate, a new study ofA. urbsinterdictensisandG. wyomingensiswas undertaken. Further preparation and re‐examination of theA. urbsinterdictensisholotype indicates this fossil falls outside both crown and stem Galliformes, and reveals evidence for a relationship with Rallidae (rails). In order to reassess the status ofG. wyomingensis, a matrix of 120 morphological characters was constructed by revising and expanding on previous studies. Phylogenetic analyses using this matrix placeG. wyomingensisbasal to all crown Galliformes. Stem placement ofG. wyomingensisis retained and resolution is improved in combined analyses incorporating sequence data from cytochromeb, NADH dehydrogenase subunit 2, mitochondrial control region, 12S rDNA, and nuclear ovomucoid intron G. All evidence indicates thatA. urbsinterdictensisandG. wyomingensisare inappropriate internal calibration points for Galliformes and may have contributed to overestimation of divergence event ages. Though stem galliforms existed in the Cretaceous, the divergence of crown lineages in the Cretaceous remains inconclusively demonstrated. Because few galliform fossils have been evaluated phylogenetically, further investigations into the tempo of galliform evolution must await identification of proper fossil calibration points. © The Willi Hennig Society 2009.
Correlated morphological and colour differences among females of the damselflyIschnura elegans
Authors: ABBOTT JESSICA K. , GOSDEN THOMAS P. 
Published: April 2009

Abstract1. The female‐limited colour polymorphic damselflyIschnura eleganshas proven to be an interesting study organism both as an example of female sexual polymorphism, and in the context of the evolution of colour polymorphism, as a model of speciation processes.2. Previous research suggests the existence of correlations between colour morph and other phenotypic traits, and the different female morphs inI. elegansmay be pursuing alternative phenotypically integrated strategies. However, previous research on morphological differences in southern Swedish individuals of this species was only carried out on laboratory‐raised offspring from a single population, leaving open the question of how widespread such differences are.3. The present study therefore analysed multi‐generational data from 12 populations, investigating morphological differences between the female morphs in the field, differences in the pattern of phenotypic integration between morphs, and quantified selection on morphological traits.4. It was found that consistent morphological differences indeed existed between the morphs across populations, confirming that the previously observed differences were not simply a laboratory artefact. It was also found, somewhat surprisingly, that despite the existence of sexual dimorphism in body size and shape, patterns of phenotypic integration differed most between the morphs and not between the sexes. Finally, linear selection gradients showed that female morphology affected fecundity differently between the morphs.5. We discuss the relevance of these results to the male mimicry hypothesis and to the existence of potential ecological differences between the morphs.
Rainfall in arid zones: possible effects of climate change on the population ecology of blue cranes
Authors: Altwegg Res , Anderson Mark D. 
Published: April 2009

Summary 1. Understanding the demographic mechanisms through which climate affects population dynamics is critical for predicting climate change impacts on biodiversity. In arid habitats, rainfall is the most important forcing climatic factor. Rainfall in arid zones is typically variable and unpredictable, and we therefore hypothesise that its seasonality and variability may be as important for the population ecology of arid zone animals as its total amount. 2. Here we examine the effect of these aspects of rainfall on reproduction and age specific survival of blue cranes (Anthropoides paradiseus Lichtenstein) in the semi‐arid eastern Nama Karoo, South Africa. We then use our results to predict the effect of changes in rainfall at the population level. 3. Using combined capture‐mark‐resighting and dead‐recovery models, we estimated average survival of cranes to be 0·53 in their first year, 0·73 in their second and third year, and 0·96 for older birds. 4. We distinguished between three seasons, based on the blue cranes’ breeding phenology: early breeding season, late breeding season and nonbreeding season. Cranes survived better with increasing rainfall during the late but not early breeding season. Based on road counts and success of monitored nests, reproduction was positively associated with rainfall during the early but not late breeding season. 5. A matrix population model predicted that population growth rate would increase with increasing rainfall. A stochastic analysis showed that variation in early breeding season rainfall increased population growth slightly due to the nonlinear relationship between rainfall and reproduction. This effect was opposed by the effect of variation in late breeding season rainfall on survival and overall, variation in rainfall had a negligible effect on population growth. 6. Our results allow predictions to be made for a range of climate‐change scenarios. For example, a shift in seasonality with drier springs but wetter summers would likely decrease reproduction but increase survival, with little overall effect on population growth.
Causal diagrams for encoding and evaluation of information bias
Authors: Shahar Eyal 
Published: April 2009

AbstractBackground  Epidemiologists and clinical researchers usually classify bias into three main categories: confounding, selection bias and information bias. Previous authors have described the first two categories in the logic and notation of causal diagrams, formally known as directed acyclic graphs (DAG).Methods  I examine common types of information bias – disease‐related and exposure‐related – from the perspective of causal diagrams.Results  Disease or exposure information bias always involves the use of an effect of the variable of interest – specifically, an effect of true disease status or an effect of true exposure status. The bias typically arises from a causal or an associational path of no interest to the researchers. In certain situations, it may be possible to prevent or remove some of the bias.Conclusions  Common types of information bias, just like confounding and selection bias, have a clear and helpful representation within the framework of causal diagrams.
Satisfaction of osteoarthritis patients with provided care is not related to the disease‐specific quality of life
Authors: Rosemann Thomas , Wensing Michel , Szecsenyi Joachim , Grol Richard 
Published: April 2009

AbstractBackground  Osteoarthritis (OA) has a high prevalence in primary care. Patient satisfaction is an important indicator for the quality of care provided to OA patients. Little is known about satisfaction of patients with this condition in a primary care setting in Germany. The aim of the study was to assess current satisfaction of patients and reveal possible disease and quality of life related predictors.Methods/Design  Seventy‐five German GPs approached 1250 patients with OA consecutively. Sociodemographics, OA‐specific quality of life (GERMAN‐AIMS2‐SF), co‐morbidities and depression (using PHQ‐9) were assessed. Patient satisfaction was measured by means of the European Task Force on Patient Evaluations of General Practice (EUROPEP) instrument. A stepwise linear regression analysis with the EUROPEP score as dependent variable controlled for the amount of GP visits was performed to assess predictors of satisfaction.Results  A total of 1021 OA patients returned the questionnaire. The adjusted R2 of the final model was 0.270 (P < 0.001). The main predictors were the PHQ‐9 score (beta = −0.372; P < 0.001), age (beta = −0.185; P < 0.001), living alone (beta = −0.209; P < 0.001) and number of co‐morbidities (beta = −0.152; P < 0.001). The only disease‐related factor which remained as predictor of patient satisfaction was duration of OA (beta = −0.105; P = 0.008).Discussion  The finding that depression and social factors are more important for patient satisfaction with provided care than disease‐related aspects suggests that these factors need to be considered carefully in treatment. This represents a big challenge within an increasingly specialized health care system. The General Practitioner as the regular and first‐choice provider of health care seems to be the most appropriate instance who can accomplish this.
Morphological characterization of the tunic in the edible ascidian, Halocynthia roretzi (Drasche), with remarks on ‘soft tunic syndrome’ in aquaculture
Authors: Hirose E , Ohtake S‐I , Azumi K 
Published: April 2009

Abstract‘Soft tunic syndrome’ is a serious problem in the aquaculture of the edible ascidian, Halocynthia roretzi (Drasche), and often leads to mass mortality. Here, we describe the tunic morphology of intact and diseased ascidians to reveal structural differences between them. Morphologically, diseased tunics are not very different from intact tunics, although the former are thinner and softer than the latter. While several types of cells are distributed in the tunic, the cell types and their cytomorphologies were almost identical in both groups. As bacterial/protozoan cells were not found in either intact or diseased tunics, they are not the direct cause of soft tunic syndrome. The most remarkable difference was in the bundles of tunic fibres that compose the tunic matrix; in intact tunics, the thick bundles interlace to form a firm matrix, whereas in soft tunics, the tunic fibres do not form thick bundles. Furthermore, areas of low fibre density were found in diseased tunics. Therefore, soft tunic syndrome probably causes inhibition of bundle formation and degradation of tunic bundles, creating areas of low fibre density, although the causes remain unknown.
Decoupling the influence of leaf and root hydraulic conductances on stomatal conductance and its sensitivity to vapour pressure deficit as soil dries in a drained loblolly pine plantation
Authors: DOMEC JEAN‐CHRISTOPHE , NOORMETS ASKO , KING JOHN S. , SUN GE , MCNULTY STEVEN G. , GAVAZZI MICHAEL J. , BOGGS JOHNNY L. , TREASURE EMRYS A. 
Published: April 2009

ABSTRACTThe study examined the relationships between whole tree hydraulic conductance (Ktree) and the conductance in roots (Kroot) and leaves (Kleaf) in loblolly pine trees. In addition, the role of seasonal variations inKrootandKleafin mediating stomatal control of transpiration and its response to vapour pressure deficit (D) as soil‐dried was studied. Compared to trunk and branches, roots and leaves had the highest loss of conductivity and contributed to more than 75% of the total tree hydraulic resistance. Drought altered the partitioning of the resistance between roots and leaves. As soil moisture dropped below 50%, relative extractable water (REW),Krootdeclined faster thanKleaf. AlthoughKtreedepended on soil moisture, its dynamics was tempered by the elongation of current‐year needles that significantly increasedKleafwhen REW was below 50%. After accounting for the effect ofDongs, the seasonal decline inKtreecaused a 35% decrease ingsand in its sensitivity toD, responses that were mainly driven byKleafunder high REW and byKrootunder low REW. We conclude that not only water stress but also leaf phenology affects the coordination betweenKtreeandgsand the acclimation of trees to changing environmental conditions.
Role of corticular photosynthesis following defoliation in Eucalyptus globulus
Authors: EYLES ALIETA , PINKARD ELIZABETH A. , O'GRADY ANTHONY P. , WORLEDGE DALE , WARREN CHARLES R. 
Published: April 2009

ABSTRACTDefoliation can reduce net fixation of atmospheric CO2 by the canopy, but increase the intensity and duration of photosynthetically active radiation on stems. Stem CO2 flux and leaf gas exchange in young Eucalyptus globulus seedlings were measured to assess the impact of defoliation on these processes and to determine the potential contribution of re‐fixation by photosynthetic inner bark in offsetting the effects of defoliation in a woody species. Pot and field trials examined how artificial defoliation of the canopy affected the photosynthetic characteristics of main stems of young Eucalyptus globulus seedlings. Defoliated potted seedlings were characterized by transient increases in foliar photosynthetic rates and concomitant decreases in stem CO2 fluxes (both in the dark and light). Defoliated field‐grown seedlings showed similar stem CO2 flux responses, but of reduced magnitude. Despite demonstrating increased re‐fixation capability, defoliated potted‐seedlings had slowed stem growth. The green stem of seedlings exhibited largely shade‐adapted characteristics. Defoliation reduced stem chlorophyll a/b ratio and increased carotenoid concentration. An increased capacity to re‐fix internally respired CO2 (up to 96%) suggested that stem re‐fixation represents a previously unexplored mechanism to minimize the impact of foliar loss by maximizing the contribution of all photosynthetic tissues, particularly for young seedlings.
Evidence for allergen‐specific IgE of maternal origin in human placenta
Authors: Joerink M. , Rindsjö E. , Stenius F. , Alm J. , Lilja G. , Grönlund H. , Scheynius A. 
Published: April 2009

Background:  Immunoglobulin E (IgE) has been identified on macrophage‐like cells in the villi of human placenta, irrespective of the serum IgE levels or allergy status of the mother. The origin of placental IgE is debated and it is not known if it is spontaneously produced, so‐called ‘natural IgE’, or if it has any specificity for certain allergens. The aim of this study was to investigate if placental IgE originates from mother or child and to analyse its specificity.Methods:  Immunoglobulin E was eluted from placenta by lowering the pH. Total and allergen‐specific IgEs were measured in placenta eluate, maternal and cord blood plasma by means of ImmunoCAP (Phadia AB). The levels of natural antibodies were determined with an anti‐phosphorylcholine (PC) enzyme‐linked immunosorbent assay, as natural IgE has been shown in one previous publication with this assay.Results:  Detectable amounts of IgE were eluted from 11/12 full‐term placentas. Natural (anti‐PC) IgE antibodies were detected in low amounts in maternal plasma but not in the placental eluate or in cord blood plasma. There was a significant correlation between the amount of total IgE eluted from placenta and the levels of total IgE in maternal plasma; however, not between maternal and cord blood plasma. Allergen‐specific IgE was only found in placental eluates from mothers with specific IgE towards these allergens. Furthermore, there was a significant correlation between the amount of allergen‐specific IgE eluted from placenta and the levels of allergen‐specific IgE in maternal plasma. Allergen‐specific IgE could not be detected in cord blood.Conclusion:  These results suggest a maternal origin of placental IgE, which can be allergen‐specific.
Genome sequence of Vibrio splendidus: an abundant planctonic marine species with a large genotypic diversity
Authors: Le Roux Frédérique , Zouine Mohamed , Chakroun Nesrine , Binesse Johan , Saulnier Denis , Bouchier Christiane , Zidane Nora , Ma Laurence , Rusniok Christophe , Lajus Aurélie , Buchrieser Carmen , Médigue Claudine , Polz Martin F. , Mazel Didier 
Published: April 2009

Summary Vibrio splendidus is a dominant Vibrio species in seawater presenting a remarkable genetic diversity; several strains have been linked to invertebrate's mortality. We report the complete genome sequence of V. splendidus LGP32, an oyster pathogen, and its comparison with partial genome sequences from related strains. As is typical for the genus, V. splendidus LGP32 contains two chromosomes (3.29 and 1.67 Mb) and most essential cellular processes are encoded by chromosome 1. Comparison with two other V. splendidus partial genome sequences (strains 12B01 and Med222) confirms the previously suggested high genotypic diversity within this species and led to the identification of numerous strain‐specific regions that could frequently not be assigned to a specific mechanisms of recombination. Surprisingly, the chromosomal integron, the most variable genetic element in all other Vibrio species analysed to date, is absent from 12B01 and inactivated by a mobile element in Med222, while in LGP32 it only contains a limited number of cassettes. Finally, we found that the LGP32 integron contains a new dfrA cassette, related to those found in resistance integrons of Gram‐negative clinical isolates. Those results suggest that marine Vibrio can be a source of antibiotic resistance genes.
Use of myocutaneous flaps for perineal closure following abdominoperineal excision of the rectum for adenocarcinoma
Authors: Chan S. , Miller M. , Ng R. , Ross D. , Roblin P. , Carapeti E. , Williams A. B. , George M. L. 
Published: April 2009

AbstractIntroduction  Abdominoperineal excision (APE) following radiotherapy is associated with a high rate of perineal wound complications. The use of myocutaneous flaps may improve wound healing. We present our experience using myocutaneous flaps for immediate reconstruction.Method  Prospective data were collected on patients undergoing APE from October 2003 to December 2008. Patient demographics, operating time, wound complications and length of stay were recorded.Results  Fifty‐one patients underwent APE for rectal adenocarcinoma, 21 had primary closure and 30 had myocutaneous flap closure (24 VRAM, 6 gracilis). The proportion of patients undergoing preoperative radiotherapy in each group were 62% and 93% respectively (P = 0.011). There were no major complications following primary closure of the unirradiated perineum. Major perineal wound complications requiring reoperation or debridement were seen in three (14%) patients following primary closure and five (17%) patients with flap closure. After radiotherapy, closure with a flap reduced the length of stay from 20 to 15 days, but this difference was not statistically significant (P = 0.36).Conclusion  The use of flap closure in irradiated patients is associated with fewer perineal complications and a shorter hospital stay.
ASYMMETRIC MULTIPRODUCT FIRMS, PROFITABILITY AND WELFARE
Authors: Symeonidis George 
Published: April 2009

ABSTRACTIn a differentiated multiproduct Cournot duopoly with linear demand, industry profit usually falls (even though concentration rises) when the distribution of products across firms becomes more asymmetric, if the products are not very differentiated or the total number of products is large. Consumer surplus and overall welfare always fall as the degree of asymmetry increases. These results contrast with the conventional wisdom on the effects of firm heterogeneity and the links between concentration and industry profits.