bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhibitory effect of salvinorin A, fromSalvia divinorum, on ileitis‐induced hypermotility: cross‐talk between κ‐opioid and cannabinoid CB1receptors
Authors: Capasso R , Borrelli F , Cascio M G , Aviello G , Huben K , Zjawiony J K , Marini P , Romano B , Di Marzo V , Capasso F , Izzo A A 
Published: July 2008

Background and purpose:Salvinorin A, the active component of the hallucinogenic herbSalvia divinorum, inhibits intestinal motility through activation of κ‐opioid receptors (KORs). However, this compound may have target(s) other than the KORs in the inflamed gut. Because intestinal inflammation upregulates cannabinoid receptors and endogenous cannabinoids, in the present study we investigated the possible involvement of the endogenous cannabinoid system in salvinorin A‐induced delay in motility in the inflamed gut.Experimental approach:Motilityin vivowas measured by evaluating the distribution of a fluorescent marker along the small intestine; intestinal inflammation was induced by the irritant croton oil; direct or indirect activity at cannabinoid receptors was evaluated by means of binding, enzymic and cellular uptake assays.Key results:Salvinorin A as well as the KOR agonist U‐50488 reduced motility in croton oil treated mice. The inhibitory effect of both salvinorin A and U‐50488 was counteracted by the KOR antagonist nor‐binaltorphimine and by the cannabinoid CB1receptor antagonist rimonabant. Rimonabant, however, did not counteract the inhibitory effect of salvinorin A on motility in control mice. Binding experiments showed very weak affinity of salvinorin A for cannabinoid CB1and CB2and no inhibitory effect on 2‐arachidonoylglycerol and anandamide hydrolysis and cellular uptake.Conclusions and implications:The inhibitory effect of salvinorin A on motility reveals a functional interaction between cannabinoid CB1receptors and KORs in the inflamed—but not in the normal—gutin vivo.British Journal of Pharmacology(2008)155, 681–689; doi:10.1038/bjp.2008.294; published online 14 July 2008
Chop‐deficient Mice Showed Increased Adiposity But No Glucose Intolerance
Authors: Ariyama Yasuyo , Shimizu Hiroyuki , Satoh Tetsurou , Tsuchiya Takafumi , Okada Shuichi , Oyadomari Seiichi , Mori Masataka , Mori Masatomo 
Published: July 2008

AbstractObjective: CCAAT/enhancer binding protein (C/EBP) homologous protein (CHOP)‐10/growth arrest and DNA damage 153 is a dominant‐negative member of the C/EBP transcription family and inhibits adipogenesis in vitro. The study was undertaken to determine the role of CHOP in obesity in vivo.Research Methods and Procedures: Changes in daily food consumption and body weight were measured. The weight of white and brown adipose tissue was compared between Chop(+/+) and (−/−) mice fed normal chow or a high‐fat diet. Glucose and insulin tolerance tests were done, and serum adipocytokine was measured to determine their metabolic state. Fat cell size of subcutaneous and mesenteric adipose tissue was microscopically observed. C/EBP expression in white adipose tissue was examined by Western blot.Results: Female Chop(−/−) mice had significantly greater body weight and adiposity than Chop(+/+) mice, although daily food intake and rectal temperature did not differ. In comparison with Chop(+/+) mice, glucose tolerance and insulin sensitivity did not differ in female Chop(−/−) mice, but levels of plasma leptin and adiponectin were higher. High‐fat diet feeding resulted in obesity in female Chop(+/−) and (−/−) mice, although caloric intake did not differ from that of Chop(+/+) mice. Fat cell area was larger in mesenteric fat but not in subcutaneous fat in Chop(−/−) mice fed a high‐fat diet. C/EBPβ and the 30‐kDa form of C/EBPα expressions were increased in parametrial fat of Chop(−/−) mice, but the 42‐kDa form of C/EBPα expression was lower than in Chop(+/+) mice.Discussion: CHOP deficiency causes obesity in female animals without severe metabolic disorders, and C/EBP's expression may be considered to participate in the process.
A novel neuronal calcium sensor family protein, calaxin, is a potential Ca2+‐dependent regulator for the outer arm dynein of metazoan cilia and flagella
Authors: Mizuno Katsutoshi , Padma Potturi , Konno Aru , Satouh Yuhkoh , Ogawa Kazuo , Inaba Kazuo 
Published: July 2008

Background information. Spermatozoa show several changes in flagellar waveform, such as upon fertilization. Ca2+ has been shown to play critical roles in modulating the waveforms of sperm flagella. However, a Ca2+‐binding protein in sperm flagella that regulates axonemal dyneins has not been fully characterized.Results. We identified a novel neuronal calcium sensor family protein, named calaxin (Ca2+‐binding axonemal protein), in sperm flagella of the ascidian Ciona intestinalis. Calaxin has three EF‐hand Ca2+‐binding motifs, and its orthologues are present in metazoan species, but not in yeast, green algae or plant. Immunolocalization revealed that calaxin is localized near the outer arm of the sperm flagellar axonemes. Moreover, it is distributed in adult tissues bearing epithelial cilia. An in vitro binding experiment indicated that calaxin binds to outer arm dynein. A cross‐linking experiment showed that calaxin binds to β‐tubulin in situ. Overlay experiments further indicated that calaxin binds the β‐dynein heavy chain of outer arm dynein in the presence of Ca2+.Conclusions. These results suggest that calaxin is a potential Ca2+‐dependent modulator of outer arm dynein in metazoan cilia and flagella.
Implementation of an Industrial Systems-Engineering Approach to Reduce the Incidence of Methicillin-ResistantStaphylococcus aureusInfection
Authors: Muder Robert R. , Cunningham Candace , McCray Ellesha , Squier Cheryl , Perreiah Peter , Jain Rajiv , Sinkowitz-Cochran Ronda L. , Jernigan John A. 
Published: July 2008

Objective.To measure the effectiveness of an industrial systems-engineering approach to a methicillin-resistantStaphylococcus aureus(MRSA) prevention program.Design.Before-after intervention studySetting.An intensive care unit (ICU) and a surgical unit that was not an ICU in the Pittsburgh Veterans Administration hospitalPatients.Allpatientsadmittedtothe study unitsIntervention.We implemented an MRSA infection control program that consisted of the following 4 elements: (1) the use of standard precautions for all patient contact, with emphasis on hand hygiene; (2) the use of contact precautions for interactions with patients known to be infected or colonized with MRSA; (3) the use of active surveillance cultures to identify patients who were asymptomatically colonized with MRSA; and (4) use of an industrial systems-engineering approach, the Toyota Production System, to facilitate consistent and reliable adherence to the infection control program.Results.The rate of healthcare-associated MRSA infection in the surgical unit decreased from 1.56 infections per 1,000 patient-days in the 2 years before the intervention to 0.63 infections per 1,000 patient-days in the 4 years after the intervention (a 60% reduction;P= .003). The rate of healthcare-associated MRSA infection in the ICU decreased from 5.45 infections per 1,000 patient-days in the 2 years before to the intervention to 1.35 infections per 1,000 patient-days in the 3 years after the intervention (a 75% reduction;P= .001). The combined estimate for reduction in the incidence of infection after the intervention in the 2 units was 68% (95% confidence interval, 50%-79%;P< .001).Conclusions.Sustained reduction in the incidence of MRSA infection is possible in a setting where this pathogen is endemic. An industrial systems-engineering approach can be adapted to facilitate consistent and reliable adherence to MRSA infection prevention practices in healthcare facilities.
Variation in Mortality Rates Among Long-Term Care Facilities for Residents With Lower Respiratory Tract Infection
Authors: Nicolle L. E. , Mubareka S. , Simor A. , Liu B. , McNeil S. , Lewis D. , Duckworth H. , Cheang M. , Loeb M. 
Published: July 2008

Objective.To identify variables contributing to interfacility differences in mortality among residents of long-term care facilities who have lower respiratory tract infection.Design.Multicenter, prospective, 1 -year observational study.Setting.Twenty-one long-term care facilities in 4 geographic areas of Canada.Participants.Residents of long-term care facilities prescribed antimicrobials for treatment of lower respiratory tract infection.Methods.Mortality rates were calculated for 3 definitions of lower respiratory tract infection: episodes with a clinical or radiographic diagnosis and treated with antimicrobials (definition 1); episodes with a physician diagnosis of pneumonia (definition 2); and episodes with chest radiography findings consistent with pneumonia (definition 3). Multilevel modeling was used to evaluate variables describing premorbid resident status, clinical presentation, management, and facility characteristics. Multivariable models were developed to identify independent predictors of mortality and determine whether facility-level variables remained independently associated with mortality rate after incorporation of individual-level variables.Results.Facility mortality rates varied from 0% to 17.8% for definition 1, from 0% to 47.1% for definition 2, and from 0% to 37.5% for definition 3. There were significant differences in mortality rate depending on which definition was used; for definitions 1 and 2, there were significant differences in mortality rate across facilities. Poorer premorbid resident status and a more severe presentation remained independent predictors of mortality in the multivariable analysis. There were also significantly increased mortality rates for episodes in which a fluoroquinolone was prescribed for initial treatment. For definitions 1 and 3, facility-level variables remained independently associated with mortality rate in the final multivariable model.Conclusions.Rates of mortality due to lower respiratory tract infection varied among long-term care facilities and differed within a facility, depending on the definition applied. Variables describing premorbid resident status, severity of presentation, and management did not fully explain the variation in mortality rate. Some facility-level variables remained independent predictors of mortality.
Classification with reject option in gene expression data
Authors: Hanczar Blaise , Dougherty Edward R. 
Published: July 2008

Abstract
Motivation: The classification methods typically used in bioinformatics classify all examples, even if the classification is ambiguous, for instance, when the example is close to the separating hyperplane in linear classification. For medical applications, it may be better to classify an example only when there is a sufficiently high degree of accuracy, rather than classify all examples with decent accuracy. Moreover, when all examples are classified, the classification rule has no control over the accuracy of the classifier; the algorithm just aims to produce a classifier with the smallest error rate possible. In our approach, we fix the accuracy of the classifier and thereby choose a desired risk of error.
Results: Our method consists of defining a rejection region in the feature space. This region contains the examples for which classification is ambiguous. These are rejected by the classifier. The accuracy of the classifier becomes a user-defined parameter of the classification rule. The task of the classification rule is to minimize the rejection region with the constraint that the error rate of the classifier be bounded by the chosen target error. This approach is also used in the feature-selection step. The results computed on both synthetic and real data show that classifier accuracy is significantly improved.
Availability: Companion Website. http://gsp.tamu.edu/Publications/rejectoption/
Contact: edward@ece.tamu.edu, hanczar_blaise@yahoo.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Integrating metabolic, transcriptional regulatory and signal transduction models inEscherichia coli
Authors: Covert Markus W. , Xiao Nan , Chen Tiffany J. , Karr Jonathan R. 
Published: July 2008

AbstractMotivation: The effort to build a whole-cell model requires the development of new modeling approaches, and in particular, the integration of models for different types of processes, each of which may be best described using different representation. Flux-balance analysis (FBA) has been useful for large-scale analysis of metabolic networks, and methods have been developed to incorporate transcriptional regulation (regulatory FBA, or rFBA). Of current interest is the integration of these approaches with detailed models based on ordinary differential equations (ODEs).Results: We developed an approach to modeling the dynamic behavior of metabolic, regulatory and signaling networks by combining FBA with regulatory Boolean logic, and ordinary differential equations. We use this approach (called integrated FBA, or iFBA) to create an integrated model of Escherichia coli which combines a flux-balance-based, central carbon metabolic and transcriptional regulatory model with an ODE-based, detailed model of carbohydrate uptake control. We compare the predicted Escherichia coli wild-type and single gene perturbation phenotypes for diauxic growth on glucose/lactose and glucose/glucose-6-phosphate with that of the individual models. We find that iFBA encapsulates the dynamics of three internal metabolites and three transporters inadequately predicted by rFBA. Furthermore, we find that iFBA predicts different and more accurate phenotypes than the ODE model for 85 of 334 single gene perturbation simulations, as well for the wild-type simulations. We conclude that iFBA is a significant improvement over the individual rFBA and ODE modeling paradigms.Availability: All MATLAB files used in this study are available at http://www.simtk.org/home/ifba/.Contact: covert@stanford.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Combination of Novel Green Fluorescent Protein Mutant TSapphire and DsRed Variant mOrange to Set Up a Versatile in Planta FRET-FLIM Assay
Authors: Bayle Vincent , Nussaume Laurent , Bhat Riyaz A. 
Published: July 2008

AbstractFörster resonance energy transfer (FRET) measurements based on fluorescence lifetime imaging microscopy (FLIM) are increasingly being used to assess molecular conformations and associations in living systems. Reduction in the excited-state lifetime of the donor fluorophore in the presence of an appropriately positioned acceptor is taken as strong evidence of FRET. Traditionally, cyan fluorescent protein has been widely used as a donor fluorophore in FRET experiments. However, given its photolabile nature, low quantum yield, and multiexponential lifetime, cyan fluorescent protein is far from an ideal donor in FRET imaging. Here, we report the application and use of the TSapphire mutant of green fluorescent protein as an efficient donor to mOrange in FLIM-based FRET imaging in intact plant cells. Using time-correlated single photon counting-FLIM, we show that TSapphire expressed in living plant cells decays with lifetime of 2.93 ± 0.09 ns. Chimerically linked TSapphire and mOrange (with 16-amino acid linker in between) exhibit substantial energy transfer based on the reduction in the lifetime of TSapphire in the presence of the acceptor mOrange. Experiments performed with various genetically and/or biochemically known interacting plant proteins demonstrate the versatility of the FRET-FLIM system presented here in different subcellular compartments tested (cytosol, nucleus, and at plasma membrane). The better spectral overlap with red monomers, higher photostability, and monoexponential lifetime of TSapphire makes it an ideal FRET-FLIM donor to study protein-protein interactions in diverse eukaryotic systems overcoming, in particular, many technical challenges encountered (like autofluorescence of cell walls and fluorescence of pigments associated with photosynthetic apparatus) while studying plant protein dynamics and interactions.
A Novel RNA-Binding Protein Associated with Cell Plate Formation
Authors: Ma Lian , Xie Bo , Hong Zonglie , Verma Desh Pal S. , Zhang Zhongming 
Published: July 2008

Abstract
Building a cell plate during cytokinesis in plant cells requires the participation of a number of proteins in a multistep process. We previously identified phragmoplastin as a cell plate-specific protein involved in creating a tubulovesicular network at the cell plate. We report here the identification and characterization of a phragmoplastin-interacting protein, PHIP1, in Arabidopsis (Arabidopsis thaliana). It contains multiple functional motifs, including a lysine-rich domain, two RNA recognition motifs, and three CCHC-type zinc fingers. Polypeptides with similar motif structures were found only in plant protein databases, but not in the sequenced prokaryotic, fungal, and animal genomes, suggesting that PHIP1 represents a plant-specific RNA-binding protein. In addition to phragmoplastin, two Arabidopsis small GTP-binding proteins, Rop1 and Ran2, are also found to interact with PHIP1. The zinc fingers of PHIP1 were not required for its interaction with Rop1 and phragmoplastin, but they may participate in its binding with the Ran2 mRNA. Immunofluorescence, in situ RNA hybridization, and green fluorescent protein tagging experiments showed the association of PHIP1 with the forming cell plate during cytokinesis. Taken together, our data suggest that PHIP1 is a novel RNA-binding protein and may play a unique role in the polarized mRNA transport to the vicinity of the cell plate.
The Omp85-Related Chloroplast Outer Envelope Protein OEP80 Is Essential for Viability in Arabidopsis
Authors: Patel Ramesh , Hsu Shih-Chi , Bédard Jocelyn , Inoue Kentaro , Jarvis Paul 
Published: July 2008

Abstractβ-Barrel proteins of the Omp85 (Outer membrane protein, 85 kD) superfamily exist in the outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts. Prominent Omp85 proteins in bacteria and mitochondria mediate biogenesis of other β-barrel proteins and are indispensable for viability. In Arabidopsis (Arabidopsis thaliana) chloroplasts, there are two distinct types of Omp85-related protein: Toc75 (Translocon at the outer envelope membrane of chloroplasts, 75 kD) and OEP80 (Outer Envelope Protein, 80 kD). Toc75 functions as a preprotein translocation channel during chloroplast import, but the role of OEP80 remains elusive. We characterized three T-DNA mutants of the Arabidopsis OEP80 (AtOEP80) gene. Selectable markers associated with the oep80-1 and oep80-2 insertions segregated abnormally, suggesting embryo lethality of the homozygous genotypes. Indeed, no homozygotes were identified among &gt;100 individuals, and heterozygotes of both mutants produced approximately 25% aborted seeds upon self-pollination. Embryo arrest occurred at a relatively late stage (globular embryo proper) as revealed by analysis using Nomarski optics microscopy. This is substantially later than arrest caused by loss of the principal Toc75 isoform, atToc75-III (two-cell stage), suggesting a more specialized role for AtOEP80. Surprisingly, the oep80-3 T-DNA (located in exon 1 between the first and second ATG codons of the open reading frame) did not cause any detectable developmental defects or affect the size of the AtOEP80 protein in chloroplasts. This indicates that the N-terminal region of AtOEP80 is not essential for the targeting, biogenesis, or functionality of the protein, in contrast with atToc75-III, which requires a bipartite targeting sequence.
Molecular and Functional Analyses Support a Role of Ornithine-δ-Aminotransferase in the Provision of Glutamate for Glutamine Biosynthesis during Pine Germination
Authors: Cañas Rafael A. , Villalobos David P. , Díaz-Moreno Sara M. , Cánovas Francisco M. , Cantón Francisco R. 
Published: July 2008

AbstractWe report the molecular characterization and functional analysis of a gene (PsδOAT) from Scots pine (Pinus sylvestris) encoding Orn-δ-aminotransferase (δ-OAT; EC 2.6.1.13), an enzyme of arginine metabolism. The deduced amino acid sequence contains a putative N-terminal signal peptide for mitochondrial targeting. The polypeptide is similar to other δ-OATs from plants, yeast, and mammals and encoded by a single-copy gene in pine. PsδOAT encodes a functional δ-OAT as determined by expression of the recombinant protein in Escherichia coli and analysis of the active enzyme. The expression of PsδOAT was undetectable in the embryo, but highly induced at early stages of germination and seedling development in all different organs. Transcript levels decreased in later developmental stages, although an increase was observed in lignified stems of 90-d-old plants. An increase of δ-OAT activity was observed in germinating embryos and seedlings and appears to mirror the observed alterations in PsδOAT transcript levels. Similar expression patterns were also observed for genes encoding arginase and isocitrate dehydrogenase. Transcripts of PsδOAT and the arginase gene were found widely distributed in different cell types of pine organs. Consistent with these results a metabolic pathway is proposed for the nitrogen flow from the megagametophyte to the developing seedling, which is also supported by the relative abundance of free amino acids in embryos and seedlings. Taken together, our data support that δ-OAT plays an important role in this process providing glutamate for glutamine biosynthesis during early pine growth.
Identification of the Wax Ester Synthase/Acyl-Coenzyme A:Diacylglycerol Acyltransferase WSD1 Required for Stem Wax Ester Biosynthesis in Arabidopsis
Authors: Li Fengling , Wu Xuemin , Lam Patricia , Bird David , Zheng Huanquan , Samuels Lacey , Jetter Reinhard , Kunst Ljerka 
Published: July 2008

AbstractWax esters are neutral lipids composed of aliphatic alcohols and acids, with both moieties usually long-chain (C16 and C18) or very-long-chain (C20 and longer) carbon structures. They have diverse biological functions in bacteria, insects, mammals, and terrestrial plants and are also important substrates for a variety of industrial applications. In plants, wax esters are mostly found in the cuticles coating the primary shoot surfaces, but they also accumulate to high concentrations in the seed oils of a few plant species, including jojoba (Simmondsia chinensis), a desert shrub that is the major commercial source of these compounds. Here, we report the identification and characterization of WSD1, a member of the bifunctional wax ester synthase/diacylglycerol acyltransferase gene family, which plays a key role in wax ester synthesis in Arabidopsis (Arabidopsis thaliana) stems, as first evidenced by severely reduced wax ester levels of in the stem wax of wsd1 mutants. In vitro assays using protein extracts from Escherichia coli expressing WSD1 showed that this enzyme has a high level of wax synthase activity and approximately 10-fold lower level of diacylglycerol acyltransferase activity. Expression of the WSD1 gene in Saccharomyces cerevisiae resulted in the accumulation of wax esters, but not triacylglycerol, indicating that WSD1 predominantly functions as a wax synthase. Analyses of WSD1 expression revealed that this gene is transcribed in flowers, top parts of stems, and leaves. Fully functional yellow fluorescent protein-tagged WSD1 protein was localized to the endoplasmic reticulum, demonstrating that biosynthesis of wax esters, the final products of the alcohol-forming pathway, occurs in this subcellular compartment.