bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple stressors and regime shifts in shallow aquatic ecosystems in antipodean landscapes
Authors: DAVIS JENNY , SIM LIEN , CHAMBERS JANE 
Published: January 2010

Summary1. Changes in land management (land use and land cover) and water management (including extraction of ground water and diversion of surface waters for irrigation) driven by increases in agricultural production and urban expansion (and fundamentally by population growth) have created multiple stressors on global freshwater ecosystems that we can no longer ignore.2. The development and testing of conceptual ecological models that examine the impact of stressors on aquatic ecosystems, and recognise that responses may be nonlinear, is now essential for identifying critical processes and predicting changes, particularly the possibility of catastrophic regime shifts or ‘ecological surprises’.3. Models depicting gradual ecological change and three types of regime shift (simple thresholds, hysteresis and irreversible changes) were examined in the context of shallow inland aquatic ecosystems (wetlands, shallow lakes and temporary river pools) in southwestern Australia subject to multiple anthropogenic impacts (hydrological change, eutrophication, salinisation and acidification).4. Changes in hydrological processes, particularly the balance between groundwater‐dominated versus surface water‐dominated inputs and a change from seasonal to permanent water regimes appeared to be the major drivers influencing ecological regime change and the impacts of eutrophication and acidification (in urban systems) and salinisation and acidification (in agricultural systems).5. In the absence of hydrological change, urban wetlands undergoing eutrophication and agricultural wetlands experiencing salinisation appeared to fit threshold models. Models encompassing alternative regimes and hysteresis appeared to be applicable where a change from a seasonal to permanent hydrological regime had occurred.6. Irreversible ecological change has potentially occurred in agricultural landscapes because the external economic driver, agricultural productivity, persists independently of the impact on aquatic ecosystems.7. Thematic implications: multiple stressors can create multiple thresholds that may act in a hierarchical fashion in shallow, lentic systems. The resulting regime shifts may follow different models and trajectories of recovery. Challenges for ecosystem managers and researchers include determining how close a system may be to critical thresholds and which processes are essential to maintaining or restoring the system. This requires an understanding of both external drivers and internal ecosystem dynamics, and the interactions between them, at appropriate spatial and temporal scales.
The distribution of microsatellites in theNasoniaparasitoid wasp genome
Authors: Pannebakker B. A. , Niehuis O. , Hedley A. , Gadau J. , Shuker D. M. 
Published: January 2010

AbstractMicrosatellites are important molecular markers used in numerous genetic contexts. Despite this widespread use, the evolutionary processes governing microsatellite distribution and diversity remain controversial. Here, we present results on the distribution of microsatellites of three species in the parasitic wasp genusNasoniagenerated by anin silicodata‐mining approach. Our results show that the overall microsatellite density inNasoniais comparable to that of the honey bee, but much higher than in eight non‐Hymenopteran arthropods. Across theNasonia vitripennisgenome, microsatellite density varied both within and amongst chromosomes. In contrast to other taxa, dinucleotides are the most abundant repeat type in all four species of Hymenoptera studied. Whether the differences between the Hymenoptera and other taxa are of functional significance remains to be determined.
Comparative analysis of nuclear tRNA genes of Nasonia vitripennis and other arthropods, and relationships to codon usage bias
Authors: Behura S. K. , Stanke M. , Desjardins C. A. , Werren J. H. , Severson D. W. 
Published: January 2010

AbstractUsing bioinformatics methods, we identified a total of 221 and 199 tRNA genes in the nuclear genomes of Nasonia vitripennis and honey bee (Apis mellifera), respectively. We performed comparative analyses of Nasonia tRNA genes with honey bee and other selected insects to understand genomic distribution, sequence evolution and relationship of tRNA copy number with codon usage patterns. Many tRNA genes are located physically close to each other in the form of small clusters in the Nasonia genome. However, the number of clusters and the tRNA genes that form such clusters vary from species to species. In particular, the Ala‐, Pro‐, Tyr‐ and His‐tRNA genes tend to accumulate in clusters in Nasonia but not in honey bee, whereas the bee contains a long cluster of 15 tRNA genes (of which 13 are Gln‐tRNAs) that is absent in Nasonia. Though tRNA genes are highly conserved, contrasting patterns of nucleotide diversity are observed among the arm and loop regions of tRNAs between Nasonia and honey bee. Also, the sequence convergence between the reconstructed ancestral tRNAs and the present day tRNAs suggests a common ancestral origin of Nasonia and honey bee tRNAs. Furthermore, we also present evidence that the copy number of isoacceptor tRNAs (those having a different anticodon but charge the same amino acid) is correlated with codon usage patterns of highly expressed genes in Nasonia.
Characteristics of the genome of Arsenophonus nasoniae, son‐killer bacterium of the wasp Nasonia
Authors: Darby A. C. , Choi J.‐H. , Wilkes T. , Hughes M. A. , Werren J. H. , Hurst G. D. D. , Colbourne J. K. 
Published: January 2010

AbstractWe report the properties of a draft genome sequence of the bacterium Arsenophonus nasoniae, son‐killer bacterium of Nasonia vitripennis. The genome sequence data from this study are the first for a male‐killing bacterium, and represent a microorganism that is unusual compared with other sequenced symbionts, in having routine vertical and horizontal transmission, two alternating hosts, and being culturable on cell‐free media. The resulting sequence totals c. 3.5 Mbp and is annotated to contain 3332 predicted open reading frames (ORFs). Therefore, Arsenophonus represents a relatively large genome for an insect symbiont. The annotated ORF set suggests that the microbe is capable of a broad array of metabolic functions, well beyond those found for reproductive parasite genomes sequenced to date and more akin to horizontally transmitted and secondary symbionts. We also find evidence of genetic transfer from Wolbachia symbionts, and phage exchange with other gammaproteobacterial symbionts. These findings reflect the complex biology of a bacterium that is able to live, invade and survive multiple host environments while resisting immune responses.
The SciZ protein anchors the enteroaggregative Escherichia coli Type VI secretion system to the cell wall
Authors: Aschtgen Marie‐Stéphanie , Gavioli Marthe , Dessen Andrea , Lloubès Roland , Cascales Eric 
Published: January 2010

SummaryType VI secretion systems (T6SS) are multi‐component machines encoded within the genomes of most Gram‐negative bacteria that associate with plant, animal and/or human cells, and therefore are considered as potential virulence factors. We recently launched a study on the Sci‐1 T6SS of enteroaggregative Escherichia coli (EAEC). The Sci‐1 T6SS is composed of all or a subset of the 21 gene products encoded within the cluster, 13 of which are shared by all T6SS identified so far. In the present work, we focussed our attention on the SciZ protein. We first showed that SciZ is required for the release of the Hcp protein in the culture supernatant and for efficient biofilm formation, demonstrating that SciZ is necessary for EAEC T6SS function. Indeed, SciZ forms a complex with SciP, SciS and SciN, three core components of the transport apparatus. Fractionation and topology studies showed that SciZ is a polytopic inner membrane protein with three trans‐membrane segments. Computer analyses identified a motif shared by peptidoglycan binding proteins of the OmpA family in the SciZ periplasmic domain. Using in vivo and in vitro binding assays, we showed that this motif anchors the SciZ protein to the cell wall and is required for T6SS function.
Peptidoglycan metabolism is controlled by the WalRK (YycFG) and PhoPR two‐component systems in phosphate‐limited Bacillus subtilis cells
Authors: Bisicchia Paola , Lioliou Efthimia , Noone David , Salzberg Letal I. , Botella Eric , Hübner Sebastian , Devine Kevin M. 
Published: January 2010

SummaryIn Bacillus subtilis, the WalRK (YycFG) two‐component system controls peptidoglycan metabolism in exponentially growing cells while PhoPR controls the response to phosphate limitation. Here we examine the roles of WalRK and PhoPR in peptidoglycan metabolism in phosphate‐limited cells. We show that B. subtilis cells remain viable in a phosphate‐limited state for an extended period and resume growth rapidly upon phosphate addition, even in the absence of a PhoPR‐mediated response. Peptidoglycan synthesis occurs in phosphate‐limited wild‐type cells at ∼27% the rate of exponentially growing cells, and at ∼18% the rate of exponentially growing cells in the absence of PhoPR. In phosphate‐limited cells, the WalRK regulon genes yocH, cwlO(yvcE), lytE and ydjM are expressed in a manner that is dependent on the WalR recognition sequence and deleting these genes individually reduces the rate of peptidoglycan synthesis. We show that ydjM expression can be activated by PhoP∼P in vitro and that PhoP occupies its promoter in phosphate‐limited cells. However, iseA(yoeB) expression cannot be repressed by PhoP∼P in vitro, but can be repressed by non‐phosphorylated WalR in vitro. Therefore, we conclude that peptidoglycan metabolism is controlled by both WalRK and PhoPR in phosphate‐limited B. subtilis cells.
Thermal acclimation of photosynthesis: a comparison of boreal and temperate tree species along a latitudinal transect
Authors: DILLAWAY DYLAN N. , KRUGER ERIC L. 
Published: January 2010

ABSTRACTCommon gardens were established along a ∼900 km latitudinal transect to examine factors limiting geographical distributions of boreal and temperate tree species in eastern North America. Boreal representatives were trembling aspen (Populus tremuloides Michx.) and paper birch (Betula papyrifera Marsh.), while temperate species were eastern cottonwood (Populus deltoides Bartr ex. Marsh var. deltoides) and sweetgum (Liquidambar styraciflua L.). The species were compared with respect to adjustments of leaf photosynthetic metabolism along the transect, with emphasis on temperature sensitivities of the maximum rate of ribulose bisphosphate (RuBP) carboxylation (EV) and regeneration (EJ). During leaf development, the average air temperature (Tgrowth) differed between the coolest and warmest gardens by 12 °C. Evidence of photosynthetic thermal acclimation (metabolic shifts compensating for differences in Tgrowth) was generally lacking in all species. Namely, neither EV nor EJ was positively related to Tgrowth. Correspondingly, the optimum temperature (Topt) of ambient photosynthesis (Asat) did not vary significantly with Tgrowth. Modest variation in Topt was explained by the combination of EV plus the slope and curvature of the parabolic temperature response of mesophyll conductance (gm). All in all, species differed little in photosynthetic responses to climate. Furthermore, the adaptive importance of photosynthetic thermal acclimation was overshadowed by gm's influence on Asat's temperature response.
On the 13C/12C isotopic signal of day and night respiration at the mesocosm level
Authors: TCHERKEZ GUILLAUME , SCHÄUFELE RUDI , NOGUÉS SALVADOR , PIEL CLÉMENT , BOOM ARNOUD , LANIGAN GARY , BARBAROUX CÉCILE , MATA CATARINA , ELHANI SLIMAN , HEMMING DEBBIE , MAGUAS CHRISTINA , YAKIR DAN , BADECK FRANZ W. , GRIFFITHS HOWARD , SCHNYDER HANS , GHASHGHAIE JALEH 
Published: January 2010

ABSTRACTWhile there is currently intense effort to examine the 13C signal of CO2 evolved in the dark, less is known on the isotope composition of day‐respired CO2. This lack of knowledge stems from technical difficulties to measure the pure respiratory isotopic signal: day respiration is mixed up with photorespiration, and there is no obvious way to separate photosynthetic fractionation (pure ci/ca effect) from respiratory effect (production of CO2 with a different δ13C value from that of net‐fixed CO2) at the ecosystem level. Here, we took advantage of new simple equations, and applied them to sunflower canopies grown under low and high [CO2]. We show that whole mesocosm‐respired CO2 is slightly 13C depleted in the light at the mesocosm level (by 0.2–0.8‰), while it is slightly 13C enriched in darkness (by 1.5–3.2‰). The turnover of the respiratory carbon pool after labelling appears similar in the light and in the dark, and accordingly, a hierarchical clustering analysis shows a close correlation between the 13C abundance in day‐ and night‐evolved CO2. We conclude that the carbon source for respiration is similar in the dark and in the light, but the metabolic pathways associated with CO2 production may change, thereby explaining the different 12C/13C respiratory fractionations in the light and in the dark.
H2O2 and cytosolic Ca2+ signals triggered by the PM H+‐coupled transport system mediate K+/Na+ homeostasis in NaCl‐stressed Populus euphratica cells
Authors: SUN JIAN , WANG MEI‐JUAN , DING MING‐QUAN , DENG SHU‐RONG , LIU MEI‐QIN , LU CUN‐FU , ZHOU XIAO‐YANG , SHEN XIN , ZHENG XIAO‐JIANG , ZHANG ZENG‐KAI , SONG JIN , HU ZAN‐MIN , XU YUE , CHEN SHAO‐LIANG 
Published: January 2010

ABSTRACTUsing confocal microscopy, X‐ray microanalysis and the scanning ion‐selective electrode technique, we investigated the signalling of H2O2, cytosolic Ca2+ ([Ca2+]cyt) and the PM H+‐coupled transport system in K+/Na+ homeostasis control in NaCl‐stressed calluses of Populus euphratica. An obvious Na+/H+ antiport was seen in salinized cells; however, NaCl stress caused a net K+ efflux, because of the salt‐induced membrane depolarization. H2O2 levels, regulated upwards by salinity, contributed to ionic homeostasis, because H2O2 restrictions by DPI or DMTU caused enhanced K+ efflux and decreased Na+/H+ antiport activity. NaCl induced a net Ca2+ influx and a subsequent rise of [Ca2+]cyt, which is involved in H2O2‐mediated K+/Na+ homeostasis in salinized P. euphratica cells. When callus cells were pretreated with inhibitors of the Na+/H+ antiport system, the NaCl‐induced elevation of H2O2 and [Ca2+]cyt was correspondingly restricted, leading to a greater K+ efflux and a more pronounced reduction in Na+/H+ antiport activity. Results suggest that the PM H+‐coupled transport system mediates H+ translocation and triggers the stress signalling of H2O2 and Ca2+, which results in a K+/Na+ homeostasis via mediations of K+ channels and the Na+/H+ antiport system in the PM of NaCl‐stressed cells. Accordingly, a salt stress signalling pathway of P. euphratica cells is proposed.
Investigations of prostate epithelial stem cells and prostate cancer stem cells
Authors: Miki Jun 
Published: January 2010

AbstractAlthough both prostate epithelial stem cells and prostate cancer stem cells are implicated in the differentiation of the normal prostate gland and carcinogenesis of prostate cancer, there has, until recently, been little information regarding their biology. This review summarizes the recent advancements in cell biological research including various in vitro culture systems that have offered the characterization and isolation of prostate epithelial stem cells and prostate cancer stem cells. In addition, the stromal niche or microenvironment of stem cells plays an essential role in proliferation and differentiation of normal stem cells. Stroma surrounding cancer cells, which also provide another unique niche, may involve the initiation and development of cancer stem cells. Investigation of stem cells and their microenvironments in the prostate should lead to the elucidation of biological features and the development of novel treatments for prostate cancer.
NON‐SYMMETRICAL CORRESPONDENCE ANALYSIS WITH CONCATENATION AND LINEAR CONSTRAINTS
Authors: Beh Eric J. , D'Ambra Luigi 
Published: January 2010

SummaryCorrespondence analysis is a popular statistical technique used to identify graphically the presence, and structure, of association between two or more cross‐classified categorical variables. Such a procedure is very useful when it is known that there is a symmetric (two‐way) relationship between the variables. When such a relationship is known not to exist, non‐symmetrical correspondence analysis is more appropriate as a method of establishing the source of association. This paper highlights some tools that can be used to explore the behaviour of asymmetric categorical variables. These tools consist of confidence regions, the link between non‐symmetrical correspondence analysis and the analysis of variance of categorical variables, and the effect of imposing linear constraints. We also explore the application of non‐symmetrical correspondence analysis to three‐way contingency tables.
“Whom should We Help First?” Transnational Helping Practices in Ecuadorian Migration
Authors: Boccagni Paolo 
Published: January 2010

AbstractCollective remittances, in the framework of migrant transnationalism, have been recently dealt with in some empirical research, especially on the Mexican‐US migration system. Far less studied is their significance in different migration flows, including their real contribution – as desirable as this may be – to local development. The article is concerned with a bottom up analysis of a migration flow where collective remittances – as the only way for emigrants to keep helping their local communities, well beyond their own families – are still in their infancy. It explores, through a translocal ethnography of Ecuadorian migration to Italy, the underlying attitudes, personal meanings and expectations – as well as the structural opportunities and constraints – accounting for helping practices at a distance. Charitable transfers to communities of origin are reconstructed as to their motivations, their main aims and beneficiaries, their embeddedness in mutual networks among immigrant co‐nationals. How is it that some of them decide to help “people in need” in their own communities overseas, or in their home towns, or in both? Is this an expression of communal belonging, or a matter of social status maintenance, or something else?Further reflections on the dilemmas inherent in transnational helping practices are then developed. Concluding remarks emphasize the relatively poor scope for such initiatives, in a recent and first‐generation flow over a long distance. While co‐ethnic solidarity overseas is a precondition for transnational helping practices, the latter are also affected by the developments of public policies in the countries of origin and of destination. Overall, an effective integration overseas is necessary for collective remittances to have some currency and impact.
Using Group‐Based Parent Training Interventions with Parents of Children with Disabilities: A Description of Process, Content and Outcomes in Clinical Practice
Authors: Todd Samantha , Bromley Jo , Ioannou Korina , Harrison James , Mellor Christine , Taylor Eric , Crabtree Elizabeth 
Published: January 2010

Background:  There is a need for further development and evaluation of group‐based parent‐ training interventions for parents of children with disabilities. This paper describes interventions delivered in two areas of Greater Manchester.Method:  The process and content of an approach designed for parents of children with learning disabilities and autistic spectrum disorders is described.Results:  Clinical outcome data for 22 parents/carers are presented. Client feedback about the course is also reported.Conclusions:  The data suggest that this intervention is effective in reducing the frequency and impact of children’s challenging behaviours, and improving parental psychological well‐being. More rigorous and extensive evaluation is required.
Effects of spironolactone on atrial structural remodelling in a canine model of atrial fibrillation produced by prolonged atrial pacing
Authors: Zhao J , Li J , Li W , Li Y , Shan H , Gong Y , Yang B 
Published: January 2010

Background and purpose:  Suppression of the renin‐angiotensin‐aldosterone system can prevent atrial fibrillation (AF) by attenuating atrial structural remodelling but the role of aldosterone in AF prevention has not been investigated thoroughly. We explored whether the aldosterone antagonist, spironolactone, could improve atrial structural remodelling in long‐term rapid pacing‐induced AF.Experimental approach:  Three groups of dogs were used, sham‐operated, control and spironolactone‐treated groups. Dogs in the control and spironolactone groups had right atrial pacing for 6 weeks. The spironolactone group was given spironolactone 1 week before and during the atrial pacing. After 6 weeks of pacing, atrial structural and functional changes were assessed by echocardiography, haemodynamic parameters by cardiac catheterization, histopathological changes by light and electron microscopy and cardiomyocyte apoptosis by TUNEL. Caspase‐3, Bcl‐2, bax, calpain I, calpastatin, matrix metalloproteinase (MMP)‐9 and tissue inhibitors of metalloproteinase (TIMP)‐1 were analysed by immunohistochemistry and Western blotting. The inducibility and duration of AF were measured by atrial burst pacing.Key results:  After atrial pacing, the proportion of TUNEL positive cells, myolysis, atrial fibrosis and dilatation were all significantly increased and these changes were inhibited by spironolactone. Spironolactone treatment reversed the increased expression of caspase‐3, bax, calpain I and MMP‐9 and the decreased level of Bcl‐2, calpastatin and TIMP‐1, induced by chronic atrial pacing. Also spironolactone prevented the increased inducibility and duration of AF, induced by tachypacing.Conclusions and implications:  Treatment with spironolactone prevented myocardial apoptosis, myolysis, atrial fibrosis and dilatation, suggesting a possible beneficial effect of aldosterone antagonism on atrial structural remodelling in AF.This article is commented on by Lendeckel et al., pp. 1581–1583 of this issue. To view this commentary visit http://dx.doi.org/10.1111/j.1476‐5381.2010.00675.x