bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phase variation has a role in Burkholderia ambifaria niche adaptation
Authors: Vial Ludovic , Groleau Marie-Christine , Lamarche Martin G , Filion Geneviève , Castonguay-Vanier Josée , Dekimpe Valérie , Daigle France , Charette Steve J , Déziel Eric 
Published: August 2009

Abstract
Members of the Burkholderia cepacia complex (Bcc), such as B. ambifaria, are effective biocontrol strains, for instance, as plant growth-promoting bacteria; however, Bcc isolates can also cause severe respiratory infections in people suffering from cystic fibrosis (CF). No distinction is known between isolates from environmental and human origins, suggesting that the natural environment is a potential source of infectious Bcc species. While investigating the presence and role of phase variation in B. ambifaria HSJ1, an isolate recovered from a CF patient, we identified stable variants that arose spontaneously irrespective of the culture conditions. Phenotypic and proteomic approaches revealed that the transition from wild-type to variant types affects the expression of several putative virulence factors. By using four different infection models (Drosophila melanogaster, Galleria mellonella, macrophages and Dictyostelium discoideum), we showed that the wild-type was more virulent than the variant. It may be noted that the variant showed reduced replication in a human monocyte cell line when compared with the wild-type. On the other hand, the variant of isolate HSJ1 was more competitive in colonizing plant roots than the wild-type. Furthermore, we observed that only clinical B. ambifaria isolates generated phase variants, and that these variants showed the same phenotypes as observed with the HSJ1 variant. Finally, we determined that environmental B. ambifaria isolates showed traits that were characteristic of variants derived from clinical isolates. Our study therefore suggest that B. ambifaria uses phase variation to adapt to drastically different environments: the lung of patients with CF or the rhizosphere.
Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
Authors: Hamady Micah , Lozupone Catherine , Knight Rob 
Published: August 2009

Abstract
Next-generation sequencing techniques, and PhyloChip, have made simultaneous phylogenetic analyses of hundreds of microbial communities possible. Insight into community structure has been limited by the inability to integrate and visualize such vast datasets. Fast UniFrac overcomes these issues, allowing integration of larger numbers of sequences and samples into a single analysis. Its new array-based implementation offers orders of magnitude improvements over the original version. New 3D visualization of principal coordinates analysis results, with the option to view multiple coordinate axes simultaneously, provides a powerful way to quickly identify patterns that relate vast numbers of microbial communities. We show the potential of Fast UniFrac using examples from three data types: Sanger-sequencing studies of diverse free-living and animal-associated bacterial assemblages and from the gut of obese humans as they diet, pyrosequencing data integrated from studies of the human hand and gut, and PhyloChip data from a study of citrus pathogens. We show that a Fast UniFrac analysis using a reference tree recaptures patterns that could not be detected without considering phylogenetic relationships and that Fast UniFrac, coupled with BLAST-based sequence assignment, can be used to quickly analyze pyrosequencing runs containing hundreds of thousands of sequences, showing patterns relating human and gut samples. Finally, we show that the application of Fast UniFrac to PhyloChip data could identify well-defined subcategories associated with infection. Together, these case studies point the way toward a broad range of applications and show some of the new features of Fast UniFrac.
Dense-shell glycodendrimers: UV/Vis and electron paramagnetic resonance study of metal ion complexation
Authors: Appelhans Dietmar , Oertel Ulrich , Mazzeo Roberto , Komber Hartmut , Hoffmann Jan , Weidner Steffen , Brutschy Bernhard , Voit Brigitte , Francesca Ottaviani Maria 
Published: August 2009

The development of dendritic metal ion carrier systems for use in a biological environment is a challenging task as the carrier system must possess multiple features (e.g. a protective shell for metal decomplexation, targeting functions, metal–intradendrimer complexes, etc.) to substitute for the function of metal proteins in processes such as copper metabolism. Thus, Cu(II) complexation by a series of poly(propyleneimine) glycodendrimers ranging up to the fifth generation that have either a dense maltose or maltotriose shell was investigated by UV/Vis spectroscopy and electron paramagnetic resonance (EPR). As a necessary step towards potential biological application, we elucidated the complexation capacity, location of the Cu(II)–dendrimer complexes and the Cu(II) coordination sphere in the dendritic environment. A generation-dependent Cu(II) complexation was found. Furthermore, analysis of the EPR spectra revealed that internal and external Cu(II) coordination and the symmetry (axial and rhombic) of the generated complexes depend on the oligosaccharide shell, dendrimer generation and the relative concentrations of Cu(II) and the dendrimers. Both axial and rhombic symmetries are generation dependent, but also distort with increasing generation number. External coordination of Cu(II) is supported by sugar groups and water molecules. Finally, a third-generation dendrimer with a maltose shell was used to explore the general complexation behaviour of the dendritic poly(propyleneimine) scaffold towards different metal ions [Cu(II), Ag(I), VO(IV), Ni(II), Eu(III) and UO2(VI)].
Most Water in the Tomato Truss Is Imported through the Xylem, Not the Phloem: A Nuclear Magnetic Resonance Flow Imaging Study
Authors: Windt Carel W. , Gerkema Edo , Van As Henk 
Published: August 2009

AbstractIn this study, we demonstrate nuclear magnetic resonance flow imaging of xylem and phloem transport toward a developing tomato (Solanum lycopersicum) truss. During an 8-week period of growth, we measured phloem and xylem fluxes in the truss stalk, aiming to distinguish the contributions of the two transport tissues and draw up a balance between influx and efflux. It is commonly estimated that about 90% of the water reaches the fruit by the phloem and the remaining 10% by the xylem. The xylem is thought to become dysfunctional at an early stage of fruit development. However, our results do not corroborate these findings. On the contrary, we found that xylem transport into the truss remained functional throughout the 8 weeks of growth. During that time, at least 75% of the net influx into the fruit occurred through the external xylem and about 25% via the perimedullary region, which contains both phloem and xylem. About one-half of the net influx was lost due to evaporation. Halfway through truss development, a xylem backflow appeared. As the truss matured, the percentage of xylem water that circulated into the truss and out again increased in comparison with the net uptake, but no net loss of water from the truss was observed. The circulation of xylem water continued even after the fruits and pedicels were removed. This indicates that neither of them was involved in generating or conducting the circulation of sap. Only when the main axis of the peduncle was cut back did the circulation stop.
Arabidopsis Putative Selenium-Binding Protein1 Expression Is Tightly Linked to Cellular Sulfur Demand and Can Reduce Sensitivity to Stresses Requiring Glutathione for Tolerance
Authors: Hugouvieux Véronique , Dutilleul Christelle , Jourdain Agnès , Reynaud Florie , Lopez Véronique , Bourguignon Jacques 
Published: August 2009

AbstractSelenium-Binding Protein1 (SBP1) gene expression was studied in Arabidopsis (Arabidopsis thaliana) seedlings challenged with several stresses, including cadmium (Cd), selenium {selenate [Se(VI)] and selenite [Se(IV)]}, copper (Cu), zinc (Zn), and hydrogen peroxide (H2O2) using transgenic lines expressing the luciferase (LUC) reporter gene under the control of the SBP1 promoter. In roots and shoots of SBP1∷LUC lines, LUC activity increased in response to Cd, Se(VI), Cu, and H2O2 but not in response to Se(IV) or Zn. The pattern of expression of SBP1 was similar to that of PRH43, which encodes the 5′-Adenylylphosphosulfate Reductase2, a marker for the induction of the sulfur assimilation pathway, suggesting that an enhanced sulfur demand triggers SBP1 up-regulation. Correlated to these results, SBP1 promoter showed enhanced activity in response to sulfur starvation. The sulfur starvation induction of SBP1 was abolished by feeding the plants with glutathione (GSH) and was enhanced when seedlings were treated simultaneously with buthionine sulfoxide, which inhibits GSH synthesis, indicating that GSH level participates in the regulation of SBP1 expression. Changes in total GSH level were observed in seedlings challenged with Cd, Se(VI), and H2O2. Accordingly, cad2-1 seedlings, affected in GSH synthesis, were more sensitive than wild-type plants to these three stresses. Moreover, wild-type and cad2-1 seedlings overexpressing SBP1 showed a significant enhanced tolerance to Se(VI) and H2O2 in addition to the previously described resistance to Cd, highlighting that SBP1 expression decreases sensitivity to stress requiring GSH for tolerance. These results are discussed with regard to the potential regulation and function of SBP1 in plants.
Sexuality and personal relationships for people with an intellectual disability. Part I: service‐user perspectives
Authors: Healy E. , McGuire B. E. , Evans D. S. , Carley S. N. 
Published: August 2009

AbstractBackground  Despite a recent ideological shift towards the recognition of sexual autonomy for people with an intellectual disability (ID), there are continuing social and cultural barriers to sexual expression. Part I of the current two‐part study assessed the sexual knowledge, experiences and aspirations of service users through focus groups and also examined their perceptions of impediments to achieving sexual autonomy.Method  Thirty‐two participants (20 male, 12 female) attending an ID service participated in focus groups delineated by gender and age group (13–17 years; 18–30 years; 31+ years).Results  Analysis of the focus groups showed that service users, especially those over the age of 18 years, had an understanding of their sexual rights but also identified a number of social and cultural barriers that they felt prevent them from achieving sexual autonomy. Those under the age of 18 years had only rudimentary knowledge of sexuality issues, for example pregnancy and sexual anatomy, but aspired to relationships and marriage similar to those over the age of 18 years. Family and staff attitudes appeared to be very influential in the views of respondents. All service users had received some form of sex education, although the benefits of such education appeared most enduring for those over 18 years.Conclusion  Service users had an understanding of their sexual rights and the social and environmental barriers that prevent them from fulfilling their rights. The provision of sex education training and promotion of positive attitudes towards appropriate sexual expression is critical to the realization of sexual autonomy for people with an ID.
A novel simple extracellular leucine‐rich repeat (eLRR) domain protein from rice (OsLRR1) enters the endosomal pathway and interacts with the hypersensitive‐induced reaction protein 1 (OsHIR1)
Authors: ZHOU LIANG , CHEUNG MING‐YAN , ZHANG QI , LEI CAI‐LIN , ZHANG SHI‐HONG , SUN SAMUEL SAI‐MING , LAM HON‐MING 
Published: August 2009

ABSTRACTReceptor‐like protein kinases (RLKs) containing an extracellular leucine‐rich repeat (eLRR) domain, a transmembrane domain and a cytoplasmic kinase domain play important roles in plant disease resistance. Simple eLRR domain proteins structurally resembling the extracellular portion of the RLKs may also participate in signalling transduction and plant defence response. Yet the molecular mechanisms and subcellular localization in regulating plant disease resistance of these simple eLRR domain proteins are still largely unclear. We provided the first experimental evidence to demonstrate the subcellular localization and trafficking of a novel simple eLRR domain protein (OsLRR1) in the endosomal pathway, using both confocal and electron microscopy. Yeast two‐hybrid and in vitro pull‐down assays show that OsLRR1 interacts with the rice hypersensitive‐induced response protein 1 (OsHIR1) which is localized on plasma membrane. The interaction between LRR1 and HIR1 homologs was shown to be highly conserved among different plant species, suggesting a close functional relationship between the two proteins. The function of OsLRR1 in plant defence response was examined by gain‐of‐function tests using transgenic Arabidopsis thaliana. The protective effects of OsLRR1 against bacterial pathogen infection were shown by the alleviating of disease symptoms, lowering of pathogen titres and higher expression of defence marker genes.
Co‐expression tools for plant biology: opportunities for hypothesis generation and caveats
Authors: USADEL BJÖRN , OBAYASHI TAKESHI , MUTWIL MAREK , GIORGI FEDERICO M. , BASSEL GEORGE W. , TANIMOTO MIMI , CHOW AMANDA , STEINHAUSER DIRK , PERSSON STAFFAN , PROVART NICHOLAS J. 
Published: August 2009

ABSTRACTGene co‐expression analysis has emerged in the past 5 years as a powerful tool for gene function prediction. In essence, co‐expression analysis asks the question ‘what are the genes that are co‐expressed, that is, those that show similar expression profiles across many experiments, with my gene of interest?’. Genes that are highly co‐expressed may be involved in the biological process or processes of the query gene. This review describes the tools that are available for performing such analyses, how each of these perform, and also discusses statistical issues including how normalization of gene expression data can influence co‐expression results, calculation of co‐expression scores andPvalues, and the influence of data sets used for co‐expression analysis. Finally, examples from the literature will be presented, wherein co‐expression has been used to corroborate and discover various aspects of plant biology.
Variations in the dorso‐ventral organization of leaf structure and Kranz anatomy coordinate the control of photosynthesis and associated signalling at the whole leaf level in monocotyledonous species
Authors: SOARES‐CORDEIRO ANA SOFIA , DRISCOLL SIMON P. , PELLNY TILL K. , OLMOS ENRIQUE , ARRABAÇA MARIA CELESTE , FOYER CHRISTINE H. 
Published: August 2009

ABSTRACTPhotosynthesis and associated signalling are influenced by the dorso‐ventral properties of leaves. The degree of adaxial/abaxial symmetry in stomatal numbers, photosynthetic regulation with respect to light orientation and the total section areas of the bundle sheath (BS) cells and the surrounding mesophyll (M) cells on the adaxial and abaxial sides of the vascular bundles were compared in two C4[Zea mays (maize) and Paspalum dilatatum] and one C3[Triticum turgidum (Durum wheat)] monocotyledonous species. The C3 leaves had a higher degree of dorso‐ventral symmetry than the C4 leaves. Photosynthetic regulation was the same on each side of the wheat leaves, as were stomatal numbers and the section area of the BS relative to that of the M cells (BS/M section area ratio). In contrast, photosynthetic regulation in maize and P. dilatatum leaves showed a marked surface‐specific response to light orientation. Compared to the adaxial sides of the C4 monocotyledonous leaves, the abaxial surfaces had more stomata and the BS/M section area ratio was significantly higher. Differences in dorso‐ventral structure, particularly in Kranz anatomy, serve not only to maximize photosynthetic capacity with respect light orientation in C4 monocotyledonous leaves but also allow adaxial and abaxial‐specific signalling from the respective M cells.
Persistence with asthma treatment is low in Germany especially for controller medication – a population based study of 483 051 patients
Authors: Hasford J. , Uricher J. , Tauscher M. , Bramlage P. , Virchow J. C. 
Published: August 2009

To cite this article: Hasford J, Uricher J, Tauscher M, Bramlage P, Virchow JC. Persistence with asthma treatment is low in Germany especially for controller medication – a population based study of 483 051 patients. Allergy 2010; 65: 347–354.AbstractBackground:  The objective of the present analysis was to evaluate treatment patterns and persistence with treatment of an unselected patient population with a diagnosis of asthma.Methods:  The database of the Bavarian statutory health insurance physician’s association (Kassenärztliche Vereinigung) covering 83% of the population was analyzed for an index period from April 2005 to March 2006. Defined daily doses (DDDs) were used to quantify treatment persistence. Results were compared with recent guidelines.Results:  The prevalence of physician diagnosed asthma in Bavaria was 4.8% in females and 4.5% in males; only 61.4% of these patients (of a total of n = 483 051) received any anti‐asthmatic pharmacotherapy; 68.3% received medical care from their general practitioner, and 8.3% from a pulmonologist alone. Most patients (65.1%) received no more than 90 DDDs of controller medication in the index period of 365 days, only about 1% received medication for the complete index period. Long‐ (40.1%) and short‐acting β2‐agonists (65.6%) were used more frequently than inhaled corticosteroids (ICS). 52.8% of asthma patients were treated in accordance with guidelines.Conclusions:  Persistence of asthma patients with medical treatment is low, especially for controller medication. The discrepancy between current knowledge, guidelines and clinical practice is substantial and may question the value of current guidelines for the treatment of patients with asthma in ambulatory care. In addition, the results of this study cast doubt on the impact of contemporary treatment on the decline of asthma mortality seen in recent years in Germany.
Hepatocellular MxA protein expression supports the differentiation of recurrent hepatitis C disease from acute cellular rejection after liver transplantation
Authors: MacQuillan Gerry C. , de Boer W. Bastiaan , Allan Jane E. , Platten Michael A. , Reed William D. , Jeffrey Gary P. 
Published: August 2009

MacQuillan GC, de Boer WB, Allan JE, Platten MA, Reed WD, Jeffrey GP. Hepatocellular MxA protein expression supports the differentiation of recurrent hepatitis C disease from acute cellular rejection after liver transplantation. Clin Transplant 2009 DOI: 10.1111/j.1399‐0012.2009.01068.x © 2009 John Wiley & Sons A/S.Abstract:  Differentiation of recurrent hepatitis C virus (HCV) disease from acute cellular rejection (ACR) following liver transplantation can be difficult. Previously, we have found that MxA protein, a specific and sensitive marker for type 1 interferon production, is strongly expressed in chronic HCV disease. Here, we investigate MxA expression as a marker for recurrent HCV disease in the livers of 14 adult HCV patients who underwent liver transplantation. Serial liver biopsies available for 12 of these patients were stained for MxA protein and scored using a semi‐quantitative approach. Hepatocellular MxA protein levels were significantly up‐regulated (p = 0.025) in recurrent HCV disease in comparison to ACR. In biopsies that showed histological changes consistent with recurrent HCV disease, strong hepatocellular MxA staining was present in 14/18 (78%). In the liver biopsies with histological evidence of ACR, strong MxA hepatocellular staining was present in only three of 10 (30%). Thus, assessment of hepatocellular MxA protein expression can contribute to the differential diagnosis of ACR and recurrent HCV disease following liver transplantation. In conclusion, analysis of intrahepatic MxA levels has the potential to reduce the inappropriate use with high‐dose pulsing of steroids post‐operatively.
The impact of invasive fungal diseases on survival after lung transplantation
Authors: Arthurs Supha K. , Eid Albert J. , Deziel Paul J. , Marshall William F. , Cassivi Stephen D. , Walker Randall C. , Razonable Raymund R. 
Published: August 2009

Arthurs SK, Eid AJ, Deziel PJ, Marshall WF, Cassivi SD, Walker RC, Razonable RR. The impact of invasive fungal diseases on survival after lung transplantation. Clin Transplant 2010: 24: 341–348. © 2009 John Wiley & Sons A/S.Abstract:  Background:  Recipients of lung transplants are at high risk of infectious complications. We investigated the epidemiology of infections after lung transplantation and determined their impact on survival.Methods:  We retrospectively reviewed the medical records of patients who underwent lung transplantation at Mayo Clinic (Rochester) during 1990–2005. Survival analyses were performed using Kaplan–Meier estimation and Cox proportional hazard modeling.Results:  Sixty‐nine lung transplants were performed during the 16‐yr study period. The mean (±SD) patient age was 50.5 ± 9.7 yr; 45% were male. During the mean (±SD) follow‐up period of 1188 (±1288) d, the cumulative percentage of patients with infections were: bacteria (52%), cytomegalovirus (CMV) (49%), other viruses (32%), fungi (19%), mycobacteria (7%), and Pneumocystis jiroveci (1%). The median survival time after lung transplantation was 5.02 yr. Kaplan–Meier estimation of one‐, three‐, and five‐yr survival was 80%, 61%, and 50%, respectively. Overall, 37 (54%) patients died due to graft rejection and failure (35%), invasive fungal diseases (16%), post‐transplant lymphoproliferative disorder and other malignancies (14%), cardiovascular diseases (5%), CMV disease (3%), bacterial infection (3%), or other causes (24%). Survival analysis using Kaplan–Meier estimation showed that invasive fungal disease (Aspergillus sp., n = 9, Candida sp., n = 2, Alternaria sp., n = 1, Rhizopus sp., n = 1, and/or Mucor sp., n = 1) was significantly associated with mortality (p = 0.0104). After adjusting for age and graft rejection, invasive fungal disease remains a significant predictor of mortality (p = 0.0262).Conclusion:  Invasive fungal disease is significantly associated with all‐cause mortality after lung transplantation. An aggressive antifungal preventive strategy may lead to improved survival after lung transplantation.
Autoimmune hepatitis in a demographically isolated area of Australia
Authors: Haider A. S. , Kaye G. , Thomson A. 
Published: August 2009

AbstractBackground: Previous studies describing autoimmune hepatitis (AIH) come from liver transplant centres in which a skewed distribution of cases may give a misleading picture of the incidence of AIH and its natural history. This series describes AIH in a stable and demographically discrete population of patients in the Australian Capital Territory (ACT) and the surrounding region.Methods: In 42 patients with type 1 AIH (point prevalence 8 per 100 000 population), clinical, laboratory and histological features at presentation, response to initial therapy, details of maintenance therapy and outcome were recorded.Results: Consistent with other publications, the male‐to‐female ratio was 1:3, mean age at presentation was 53 years and 24% had cirrhosis at diagnosis. Most patients (86%) responded to initial therapy and 67% went into long‐term remission. One patient died from liver failure and none required liver transplantation. Azathioprine was included in the treatment regimen in 74% of cases with doses generally <2 mg/kg. Azathioprine dose greater than or equal to 2 mg/kg was associated with better clinical outcome, but this did not reach statistical significance. A higher proportion of female patients had cirrhosis at presentation (9/10 vs 1/10; P= 0.24).Conclusion: In this Australian community‐based study, type 1 AIH was primarily a disease of later life, responded to conventional immunosuppressive therapy and generally has a good prognosis. Further study of the use of azathioprine is warranted to determine the optimal dose.