bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lake depth and geographical position modify lake fish assemblages of the European ‘Central Plains’ ecoregion
Authors: MEHNER THOMAS , HOLMGREN KERSTIN , LAURIDSEN TORBEN L. , JEPPESEN ERIK , DIEKMANN MARKUS 
Published: July 2007

Summary1. Classification of European lake fish assemblages can be based on fish‐assemblage structure or morphological, geographical, physical and chemical lake attributes. However, substantial gaps in knowledge exist with respect to the correspondence between both classification approaches.2. Here, we compiled fish assemblage data from 165 lakes situated in the European ‘Central Plains’ ecoregion. Cluster analysis of fish abundances was performed to compare fish assemblage types of the entire ecoregion with those from previous country‐specific studies. Nonparametric group comparisons, classification trees and partial canonical ordinations were used to infer the correspondence between fish assemblage types and morphology, geographical position and nutrient concentration of the lakes.3. Three distinct fish assemblages were revealed: vendace (Coregonus albula), ruffe (Gymnocephalus cernuus) and roach (Rutilus rutilus) lake types. Both latitude and lake depth were the best determinants of lake type, but total phosphorus (TP) concentrations were also important. Vendace lakes were deep and had low TP concentrations, whereas the shallower ruffe and roach lakes had higher TP values. Roach lakes were more frequent in the north‐west area of the ecoregion, whereas ruffe lakes were more often found south of the Baltic Sea.4. Controlling for the influence of nutrient concentration showed that lake morphology and geographical position were important determinants of fish assemblages. However, the variance explained was low (<20%), implying that biological interactions may also be important in forming the lake‐specific fish assemblages.5. The results suggest that fish assemblages differ between deep and shallow lakes, and between the north‐west and south‐east locations within the Central Plains ecoregion. Accordingly, establishment of depth‐related lake morphotypes is needed, and the European ecoregions recommended to be used in evaluation systems according to the Water Framework Directive seem to be too coarse to reflect the subtle differences of fish species richness along geographical gradients.
How does elevated carbon dioxide (CO2) affect plant–herbivore interactions? A field experiment and meta‐analysis of CO2‐mediated changes on plant chemistry and herbivore performance
Authors: STILING PETER , CORNELISSEN TATIANA 
Published: July 2007

AbstractFirst, we report the results of the longest‐known field study (9 years) to examine the effects of elevated carbon dioxide (CO2) on leaf miner densities in a scrub‐oak community at Kennedy Space Center, Florida. Here, the densities of all leaf miner species (6) on all host species (3) were lower in every year in elevated CO2 than they were in ambient CO2. Second, meta‐analyses were used to review the effects of elevated CO2 on both plants (n=59 studies) and herbivores (n=75 studies). The log of the response ratio was chosen as the metric to calculate effect sizes. Results showed that elevated CO2 significantly decreased herbivore abundance (−21.6%), increased relative consumption rates (+16.5%), development time (+3.87%) and total consumption (+9.2%), and significantly decreased relative growth rate (−8.3%), conversion efficiency (−19.9%) and pupal weight (−5.03%). No significant differences were observed among herbivore guilds. Host plants growing under enriched CO2 environments exhibited significantly larger biomass (+38.4%), increased C/N ratio (+26.57%), and decreased nitrogen concentration (−16.4%), as well as increased concentrations of tannins (+29.9%) and other phenolics. Effects of changes on plant primary and secondary chemistry due to elevated CO2 and consequences for herbivore growth and development are discussed.
Sequence analysis and molecular characterization of larval midgut cDNA transcripts encoding peptidases from the yellow mealworm, Tenebrio molitor L.
Authors: Prabhakar S. , Chen M.‐S. , Elpidina E. N. , Vinokurov K. S. , Smith C. M. , Marshall J. , Oppert B. 
Published: July 2007

AbstractPeptidase sequences were analysed in randomly picked clones from cDNA libraries of the anterior or posterior midgut or whole larvae of the yellow mealworm, Tenebrio molitor Linnaeus. Of a total of 1528 sequences, 92 encoded potential peptidases, from which 50 full‐length cDNA sequences were obtained, including serine and cysteine proteinases and metallopeptidases. Serine proteinase transcripts were predominant in the posterior midgut, whereas transcripts encoding cysteine and metallopeptidases were mainly found in the anterior midgut. Alignments with other proteinases indicated that 40% of the serine proteinase sequences were serine proteinase homologues, and the remaining ones were identified as either trypsin, chymotrypsin or other serine proteinases. Cysteine proteinase sequences included cathepsin B‐ and L‐like proteinases, and metallopeptidase transcripts were similar to carboxypeptidase A. Northern blot analysis of representative sequences demonstrated the differential expression profile of selected transcripts across five developmental stages of Te. molitor. These sequences provide insights into peptidases in coleopteran insects as a basis to study the response of coleopteran larvae to external stimuli and to evaluate regulatory features of the response.
Biochemical and Functional Characterization of Salp20, an Ixodes scapularis Tick Salivary Protein that Inhibits the Complement Pathway
Authors: Tyson K. , Elkins C. , Patterson H. , Fikrig E. , De Silva A. 
Published: July 2007

Abstract Ixodes ticks are vectors of several pathogens including Borrelia burgdorferi. Tick saliva contains numerous molecules that facilitate blood feeding without host immune recognition and rejection. We have expressed, purified, and characterized Ixodes scapularis salivary protein 20 (Salp20), a potential inhibitor of the alternative complement pathway that shares homology with the Isac protein family. When analysed by SDS‐PAGE and size exclusion chromatography, Salp20 was approximately 48 kDa, more than double its predicted mass, primarily due N‐ and O‐linked glycosylations. Recombinant Salp20 inhibited the alternative complement pathway by dissociating the C3 convertase, and partially protected a serum sensitive species of Borrelia from lysis by normal human serum. We propose that Salp20 facilitates tick feeding and possibly protects tick‐borne pathogens from complement components.
Comprehensive characterization of serum clinical chemistry parameters and the identification of urinary superoxide dismutase in a carbon tetrachloride‐induced model of hepatic fibrosis in the female Hanover Wistar rat
Authors: Smyth Rosemary , Munday Michael R. , York Malcolm J. , Clarke Christopher J. , Dare Theo , Turton John A. 
Published: July 2007

SummaryCarbon tetrachloride (CCl4) was used to induce liver fibrosis in the rat. Using this model, we have identified changes in serum and urinary clinical chemistry parameters, and characterized histopathological lesions in the liver. Two experiments were conducted. In Experiment 1, rats were dosed at six levels of CCl4 (0.06–0.36 ml/kg) twice weekly for 6 weeks, followed by a 6‐week non‐dosing recovery period (week 12). Livers were removed for histology at 6 and 12 weeks and serum parameters analysed. In Experiment 2, rats were given seven dose levels of CCl4 (0.4–1.0 ml/kg) twice weekly for 6 weeks, followed by a 6‐week recovery period (week 12); urine samples were analysed at 3, 6, 9 and 12 weeks using one‐dimensional sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS–PAGE). Liver fibrosis was evident at 6 weeks in Experiments 1 and 2, and the activity of serum enzymes (including alanine aminotransferase, aspartate aminotransferase and glutamate dehydrogenase) was increased. Sodium dodecyl sulphate–polyacrylamide gel electrophoresis analysis (Experiment 2) revealed a protein band at 18.4 kDa in urine from rats treated with CCl4, not present in control urine, which was identified as copper/zinc superoxide dismutase (Cu/Zn SOD). Western blotting revealed that SOD was increased in urine from rats treated with CCl4 at 3 and 6 weeks, but not at 9 and 12 weeks. We conclude that Cu/Zn SOD is a urinary marker of hepatic necrosis, but not hepatic fibrosis.
Laser capture microdissection reveals dose–response of gene expression in situ consequent to asbestos exposure
Authors: Yin Qi , Brody Arnold R. , Sullivan Deborah E. 
Published: July 2007

SummaryThe genes that mediate fibroproliferative lung disease remain to be defined. Prior studies from our laboratory showed by in situ hybridization and immunohistochemistry that the genes coding for tumour necrosis factor alpha, transforming growth factor beta, the platelet‐derived growth factor A and B isoforms, and alpha‐1 pro‐collagen are expressed in fibroproliferative lesions that develop quickly after asbestos inhalation. These five genes, along with matrix metalloproteinase 9, a collagenase found to be increased in several lung diseases, are known to control matrix production and cell proliferation in humans and animals. Here we show by laser capture microdissection that (i) The six genes are expressed at significantly higher levels in the asbestos‐exposed mice when comparing the same anatomic regions ‘captured’ in unexposed mice. (ii) The bronchiolar‐alveolar duct (BAD) junctions, where the greatest number of fibres initially deposit, were always significantly higher than the other anatomic regions for each gene. The first alveolar duct bifurcation (ADB) generally was higher than the second ADB, the ADBs were always significantly higher than the airway walls and pleura, and the airway walls and pleura were generally higher than the unexposed tissues. (iii) Animals exposed for 3 days always exhibited significantly higher levels of gene expression at the BAD junctions and ADBs than animals exposed for 2 days. To our knowledge, this is the first demonstration of a dose–response to a toxic particle in situ, and this response appears to be dependent on the number of fibres that deposits at the individual anatomic site.
Lysosomal acid lipase over‐expression disrupts lamellar body genesis and alveolar structure in the lung
Authors: Li Yuan , Qin Yulin , Li Huimin , Wu Renliang , Yan Cong , Du Hong 
Published: July 2007

SummaryThe functional role of neutral lipids in the lung is poorly understood. Lysosomal acid lipase (LAL) is a critical enzyme in hydrolysis of cholesteryl esters and triglycerides to generate free fatty acids and cholesterol in lysosomes. Human LAL was over‐expressed in a doxycycline‐controlled system in mouse respiratory epithelial cells to accelerate intracellular neutral lipid degradation and perturb the surfactant homeostasis in the lung. In this animal system, neutral lipid concentrations of pulmonary surfactant were reduced in bronchoalveolar lavage fluid (BALF) in association with decrease of surfactant protein C (SP‐C) gene expression. The size and the number of lamellar bodies in alveolar type II epithelial cells (AT II cells) were significantly reduced accordingly. The number of macrophages required for surfactant recycling in BALF was also significantly reduced. As a result of these combinatory effects, emphysema of the alveolar structure was observed. Taken together, neutral lipid homeostasis is essential for maintenance of lamellar body genesis and the alveolar structure in the lung.
Women's satisfaction with intrapartum care – a pattern approach
Authors: Rudman Ann , El‐Khouri Bassam , Waldenström Ulla 
Published: July 2007

AbstractTitle.  Women's satisfaction with intrapartum care – a pattern approach Aim.  This paper is a report of a study to investigate women's satisfaction with intrapartum care along three distinct dimensions simultaneously (interpersonal care, information and involvement in decision‐making and physical birth environment) and to describe the characteristics of women with different patterns of satisfaction.Background.  Patient satisfaction is an important outcome in the evaluation and development of healthcare services. Studies of satisfaction have often used single global ratings but such ratings may not capture the multidimensionality of care during childbirth.Method.  A cluster analytic technique was used to establish a finite set of response patterns. Data were obtained from a longitudinal population‐based Swedish survey including 2605 women who completed questionnaires in early pregnancy, and 2 months and 1 year after the birth. Data collection commenced in March 1999 and was completed in April 2002.Results.  Nine different clusters, or patterns of satisfaction/dissatisfaction, were found. Nearly half of the women (47%) were in clusters that were satisfied or very satisfied with at least one dimension of care, 20% in clusters that were fairly satisfied (average), and 33% in less than satisfied clusters. Fifteen per cent were mainly dissatisfied with the physical environment, 8% mainly with interpersonal care, 7% only with information and decision‐making and 3% with all dimensions. Women in the different clusters differed statistically significantly in psychological health in early pregnancy, emotional reactions during labour and in labour outcomes, but not in background characteristics.Conclusion.  Looking at different dimensions of care instead of a single global measure gave a richer, more diverse, and also a more negative picture of women's experiences of intrapartum care.
User participation in mental health nurse decision‐making: a co‐operative enquiry
Authors: Tee Steve , Lathlean Judith , Herbert Lesley , Coldham Tina , East Bella , Johnson Tammy‐Jo 
Published: July 2007

AbstractTitle.  User participation in mental health nurse decision‐making: a co‐operative enquiry Aim.  This paper is a report of a study to encourage participants to work together to identify strategies for increasing user participation in clinical decisions and to evaluate the value of co‐operative inquiry as a vehicle for supporting learning in practice.Background.  Service user participation in the clinical practice decisions of mental health nurses is considered essential for good practice. Methods need to be found which enable opportunities for shared learning, facilitate practice development and empower service users.Method.  A co‐operative inquiry design engaged all participants (n = 17) as co‐researchers and involved repeated cycles of action and reflection, using multiple data collection methods. The research was conducted over a two year period in 2004–2005, with mental health nursing students collaborating with service users.Findings.  Factors inhibiting participation included stigmatizing and paternalistic approaches, where clinical judgments were made solely on the basis of diagnosis. Enhancing factors were a respectful culture which recognized users’‘expertise’ and communicated belief in individual potential. Inquiry benefits included insight into service users’ perspectives, enhanced confidence in decision‐making, appreciation of power issues in helping relationships and deconstruction of decision‐making within a safe learning environment.Conclusion.  Learning from novel approaches which enable nursing students to develop their reflective and reflexive ability is essential to avoid practice which disempowers and potentially harms service users’ recovery. Co‐operative inquiry is a valuable vehicle for developing professional practice in higher education and practice environments.
The lived experiences of newly qualified nurses on clinical placement during the first six months following registration in the Republic of Ireland
Authors: O'Shea Maria , Kelly Billy 
Published: July 2007

Aim.  To explore the lived experiences of newly qualified nurses on clinical placement, during the first six months following registration, in the Republic of Ireland.Background.  The subject of the experiences of newly qualified nurses is not generally well researched, although anecdotal articles are plentiful. In particular, the lived experiences of newly qualified diploma nurses in the Republic of Ireland are not reflected in the research literature. However, available literature on the subject clearly demonstrates that being a newly qualified staff nurse is particularly stressful and many nurses feel unprepared for the staff nurse role.Design.  A phenomenological, Heideggerian, hermeneutic approach was used for this study.Methods.  Ten diplomate staff nurses were interviewed and the data were analysed using a thematic analysis framework.Results.  Newly qualified nurses in the Republic of Ireland describe their initial experiences of being on the ward as stressful. This stress is primarily related to the multi‐dimensional responsibilities associated with the new role and to managerial/organizational/clinical skills deficits. The allocation of students and dealing with situations that they felt unprepared for added to their anxieties. However, diplomate nurses were willing to acknowledge these limitations and seek help when appropriate. Feeling valued, making a difference and financial reward were cited as being the positive aspects of the new role.Relevance to clinical practice.  The preregistration nurse education curriculum needs to be developed further to help alleviate the problems associated with the initial transition to the staff nurse role. In addition, effective supportive systems need to be introduced for newly qualified nurses to help ensure that they are prepared for and supported in their professional role.
Cobalt chloride, a hypoxia‐mimicking agent, targets sterol synthesis in the pathogenic fungus Cryptococcus neoformans
Authors: Lee Hyeseung , Bien Clara M. , Hughes Adam L. , Espenshade Peter J. , Kwon‐Chung Kyung J. , Chang Yun C. 
Published: July 2007

SummaryWe investigated the effects of the hypoxia‐mimetic CoCl2 in the pathogenic fungus Cryptococcus neoformans and demonstrated that CoCl2 leads to defects in several enzymatic steps in ergosterol biosynthesis. Sterol defects were amplified in cells lacking components of the Sre1p‐mediated oxygen‐sensing pathway. Consequently, Sre1p and its binding partner Scp1p were essential for growth in the presence of CoCl2. Interestingly, high copies of a single gene involved in ergosterol biosynthesis, ERG25, rescued this growth defect. We show that the inhibitory effect of CoCl2 on scp1Δ and sre1Δ cells likely resulted from either an accumulation of non‐viable methylated sterols or a decrease in the amount of ergosterol. Similar findings were also observed in the ascomycetous yeast, Schizosaccharomyces pombe, suggesting that the effects of CoCl2 on the Sre1p‐mediated response are conserved in fungi. In addition, gene expression analysis revealed limited overlap between Sre1p‐dependant gene activation in the presence of CoCl2 and low oxygen. The majority of genes similarly affected by both CoCl2 and low oxygen were involved in ergosterol synthesis and in iron/copper transport. This article identifies the Sre1p pathway as a common mechanism by which yeast cells sense and adapt to changes in both CoCl2 concentrations and oxygen levels.
HobA – a novel protein involved in initiation of chromosomal replication in Helicobacter pylori
Authors: Zawilak‐Pawlik Anna , Kois Agnieszka , Stingl Kerstin , Boneca Ivo G. , Skrobuk Paulina , Piotr Jakimowicz , Lurz Rudi , Zakrzewska‐Czerwińska Jolanta , Labigne Agnés 
Published: July 2007

SummaryReplication of the bacterial chromosome is initiated by the binding of the DnaA protein to a unique DNA region, called oriC. Many regulatory factors in numerous species act by controlling the ability of DnaA to bind and unwind DNA, but the Helicobacter pylori genome does not contain homologues to any of these factors. Here, we describe HobA, a novel protein essential for initiation of H. pylori chromosome replication, which is conserved among, and unique to, epsilon proteobacteria. We demonstrate that HobA interacts specifically via DnaA with the oriC–DnaA complex. We postulate that HobA is essential for correct formation and stabilization of the orisome by facilitating the spatial positioning of DnaA at oriC. Consistent with its function, overexpression of hobA had no effect on growth of H. pylori, whereas depletion of HobA led to growth arrest and failure to initiate replication. In conclusion, HobA may be the first identified of a new group of initiation factors common to epsilon proteobacteria.
Continuous periplasm in a filamentous, heterocyst‐forming cyanobacterium
Authors: Mariscal Vicente , Herrero Antonia , Flores Enrique 
Published: July 2007

SummaryThe cyanobacteria bear a Gram‐negative type of cell wall that includes a peptidoglycan layer and an outer membrane outside of the cytoplasmic membrane. In filamentous cyanobacteria, the outer membrane appears to be continuous along the filament of cells. In the heterocyst‐forming cyanobacteria, two cell types contribute specialized functions for growth: vegetative cells provide reduced carbon to heterocysts, which provide N2‐derived fixed nitrogen to vegetative cells. The promoter of the patS gene, which is active specifically in developing proheterocysts and heterocysts of Anabaena sp. PCC 7120, was used to direct the expression of altered versions of the gfp gene. An engineered green fluorescent protein (GFP) that was exported to the periplasm of the proheterocysts through the twin‐arginine translocation system was observed also in the periphery of neighbouring vegetative cells. However, if the GFP was anchored to the cytoplasmic membrane, it was observed in the periphery of the producing proheterocysts or heterocysts but not in adjacent vegetative cells. These results show that there is no cytoplasmic membrane continuity between heterocysts and vegetative cells and that the GFP protein can move along the filament in the periplasm, which is functionally continuous and so provides a conduit that can be used for chemical communication between cells.
A tridecameric c ring of the adenosine triphosphate (ATP) synthase from the thermoalkaliphilic Bacillus sp. strain TA2.A1 facilitates ATP synthesis at low electrochemical proton potential
Authors: Meier Thomas , Morgner Nina , Matthies Doreen , Pogoryelov Denys , Keis Stefanie , Cook Gregory M. , Dimroth Peter , Brutschy Bernhard 
Published: July 2007

SummaryDespite the thermodynamic problem imposed on alkaliphilic bacteria of synthesizing adenosine triphosphate (ATP) against a large inverted pH gradient and consequently a low electrochemical proton potential, these bacteria still utilize a proton‐coupled F1Fo‐ATP synthase to synthesize ATP. One potential solution to this apparent thermodynamic problem would be the operation of a larger oligomeric c ring, which would raise the ion to ATP ratio, thus facilitating the conversion of a low electrochemical potential into a significant phosphorylation potential. To address this hypothesis, we have purified the oligomeric c ring from the thermoalkaliphilic bacterium Bacillus sp. strain TA2.A1 and determined the number of c‐subunits using a novel mass spectrometry method, termed ‘laser‐induced liquid bead ion desorption’ (LILBID). This technique allows the mass determination of non‐covalently assembled, detergent‐solubilized membrane protein complexes, and hence enables an accurate determination of c ring stoichiometries. We show that the Bacillus sp. strain TA2.A1 ATP synthase harbours a tridecameric c ring. The operation of a c ring with 13 subunits renders the thermodynamic problem of ATP synthesis at alkaline pH less severe and may represent a strategy for ATP synthesis at low electrochemical potential.