bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reactivity of nitric oxide with the [4Fe–4S] cluster of dihydroxyacid dehydratase fromEscherichia coli
Authors: Duan Xuewu , Yang Juanjuan , Ren Binbin , Tan Guoqiang , Ding Huangen 
Published: October 2008

Although the NO (nitric oxide)-mediated modification of iron–sulfur proteins has been well-documented in bacteria and mammalian cells, specific reactivity of NO with iron–sulfur proteins still remains elusive. In the present study, we report the first kinetic characterization of the reaction between NO and iron–sulfur clusters in protein using the Escherichia coli IlvD (dihydroxyacid dehydratase) [4Fe–4S] cluster as an example. Combining a sensitive NO electrode with EPR (electron paramagnetic resonance) spectroscopy and an enzyme activity assay, we demonstrate that NO is rapidly consumed by the IlvD [4Fe–4S] cluster with the concomitant formation of the IlvD-bound DNIC (dinitrosyl–iron complex) and inactivation of the enzyme activity under anaerobic conditions. The rate constant for the initial reaction between NO and the IlvD [4Fe–4S] cluster is estimated to be (7.0±2.0)×106 M−2·s−1 at 25 °C, which is approx. 2–3 times faster than that of the NO autoxidation by O2 in aqueous solution. Addition of GSH failed to prevent the NO-mediated modification of the IlvD [4Fe–4S] cluster regardless of the presence of O2 in the medium, further suggesting that NO is more reactive with the IlvD [4Fe–4S] cluster than with GSH or O2. Purified aconitase B [4Fe–4S] cluster from E. coli has an almost identical NO reactivity as the IlvD [4Fe–4S] cluster. However, the reaction between NO and the endonuclease III [4Fe–4S] cluster is relatively slow, apparently because the [4Fe–4S] cluster in endonuclease III is less accessible to solvent than those in IlvD and aconitase B. When E. coli cells containing recombinant IlvD, aconitase B or endonuclease III are exposed to NO using the Silastic tubing NO delivery system under aerobic and anaerobic conditions, the [4Fe–4S] clusters in IlvD and aconitase B, but not in endonuclease III, are efficiently modified forming the protein-bound DNICs, confirming that NO has a higher reactivity with the [4Fe–4S] clusters in IlvD and aconitase B than with O2 or GSH. The results suggest that the iron–sulfur clusters in proteins such as IlvD and aconitase B may constitute the primary targets of the NO cytotoxicity under both aerobic and anaerobic conditions.
Muscle acylcarnitines during short-term fasting in lean healthy men
Authors: Soeters Maarten R. , Sauerwein Hans P. , Duran Marinus , Wanders Ronald J. , Ackermans Mariëtte T. , Fliers Eric , Houten Sander M. , Serlie Mireille J. 
Published: October 2008

The transition from the fed to the fasted resting state is characterized by, among other things, changes in lipid metabolism and peripheral insulin resistance. Acylcarnitines have been suggested to play a role in insulin resistance, as well as other long-chain fatty acid metabolites. Plasma levels of long-chain acylcarnitines increase during fasting, but this is unknown for muscle long-chain acylcarnitines. In the present study we investigated whether muscle long-chain acylcarnitines increase during fasting and we investigated their relationship with glucose/fat oxidation and insulin sensitivity in lean healthy humans. After 14 h and 62 h of fasting, glucose fluxes, substrate oxidation, and plasma and muscle acylcarnitines were measured before and during a hyperinsulinaemic–euglycaemic clamp. Hyperinsulinaemia decreased long-chain muscle acylcarnitines after 14 h of fasting, but not after 62 h of fasting. In both the basal state and during the clamp, glucose oxidation was lower and fatty acid oxidation was higher after 62 h compared with 14 h of fasting. Absolute changes in glucose and fatty acid oxidation in the basal compared with hyperinsulinaemic state were not different. Muscle long-chain acylcarnitines did not correlate with glucose oxidation, fatty acid oxidation or insulin-mediated peripheral glucose uptake. After 62 h of fasting, the suppression of muscle long-chain acylcarnitines by insulin was attenuated compared with 14 h of fasting. Muscle long-chain acylcarnitines do not unconditionally reflect fatty acid oxidation. The higher fatty acid oxidation during hyperinsulinaemia after 62 h compared with 14 h of fasting, although the absolute decrease in fatty acid oxidation was not different, suggests a different set point.
Natural history of cervical intraepithelial neoplasia during pregnancy
Authors: SERATI MAURIZIO , UCCELLA STEFANO , LATERZA ROSA M. , SALVATORE STEFANO , BERETTA PAOLO , RIVA CRISTINA , BOLIS PIER FRANCESCO 
Published: October 2008

AbstractObjective. It is uncertain whether pregnancy influences the natural history of cervical intraepithelial neoplasia (CIN). Our aim was to evaluate the evolution of CIN in pregnant women. Design. Prospective study. Setting. Department of Obstetrics and Gynaecology, University of Insubria, Italy. Population. Women with histological CIN during pregnancy. Methods and main outcome measures. Between 2003 and 2007, women with an abnormal Pap‐smear during pregnancy underwent colposcopy. Patients with histological CIN were followed during pregnancy with colposcopy every 8 weeks and post‐partum evaluation was scheduled 3–6 months after delivery. Women with post‐partum histological diagnosis of CIN 2–3 underwent conization. To understand the impact of pregnancy on the evolution of CIN, women with CIN 1 discovered during pregnancy were compared to a group of non‐pregnant fertile patients with first diagnosis of CIN 1. Results. A total of 78 women were included: 36 (46.2%) with CIN 2–3 and 42 (53.8%) with CIN 1. In women with CIN 2–3, no invasion was suspected during pregnancy and at post‐partum evaluation, no invasive or microinvasive cancer, and 19 (52.7%) persistent CIN 2–3, and 17 (47.3%) regressions were diagnosed. In the group of CIN 1, we recorded six (14.3%) progressions to CIN 2–3, seven (16.6%) persistent CIN 1 and 29 (69%) regressions. The control group of non‐pregnant women had a lower regression rate (37/76: 48.7%) in comparison to pregnant women (p = 0.03). Conclusions. Expectant management for CIN 2–3 diagnosed during gestation is safe. When discovered during pregnancy, CIN 1 has a significantly higher tendency to spontaneous regression in comparison to non‐pregnant condition.
Testing for 22q11 microdeletion in 146 fetuses with nuchal translucency above the 99th percentile and a normal karyotype
Authors: LAUTRUP CHARLOTTE KVIST , KJAERGAARD SUSANNE , BRØNDUM‐NIELSEN KAREN , FAGERBERG CHRISTINA , HERTZ JENS MICHAEL , PETERSEN OLAV BENNIKKE BJØRN , JØRGENSEN METTE WARMING , VOGEL IDA 
Published: October 2008

AbstractThe aim of this study was to examine the value of testing for a 22q11 microdeletion in fetuses with nuchal translucency (NT) above the 99th percentile (>3.5 mm). A 22q11 microdeletion results in the development of 22q11 deletion syndrome, a spectrum of disorders also known as DiGeorge/Velocardiofacial syndrome. A total of 146 pregnancies met the inclusion criteria of NT >3.5 mm between 11+2 and 13+6 weeks’ gestation, no structural malformation and normal karyotype. Chorionic villi samples were tested with either multiplex ligation‐dependent probe amplification (MLPA) or fluorescent in situ hybridization (FISH) analysis for 22q11 microdeletion. None were diagnosed with the microdeletion. The estimated prevalence of 22q11 microdeletion in these otherwise normal fetuses with increased NT is below 2.7%.
History of cesarean before 32 weeks’ gestation and trial of labor: What is the risk of uterine rupture?
Authors: ESTRADE SONIA , SCHMITZ THOMAS , CABROL DOMINIQUE , HUCHON CYRILLE , GOFFINET FRANÇOIS 
Published: October 2008

AbstractObjectives. To estimate the risk of uterine rupture in women with a previous cesarean delivery before 32 weeks’ gestation and a trial of labor. Design. Retrospective case control study. Setting. Level III maternity center. Methods. Among women with trial of labor, the case and control groups were women with previous cesarean section before and after 32 weeks, respectively. The main outcome was uterine rupture, defined as rupture of the three layers of the uterine wall. Results. The study compared 108 trials of labor in patients with a previous cesarean delivery at a mean gestation of 29.8 weeks±2.0 SD and 137 trials of labor in patients with a previous cesarean delivery at a mean gestation of 39.2 weeks±2.3 SD. Mode of delivery did not differ between groups. Two uterine ruptures (1.9%, 95% CI: 0.0–4.4) occurred in the case group and none in the control group (p = 0.16). Uterine ruptures caused no serious maternal or neonatal complications. The condition of the neonates was similar in the two groups. Conclusion. In view of the small number of uterine ruptures and the absence of severe maternal and fetal consequences over an 8‐year period, a trial of labor may be proposed to women with a history of cesarean delivery before 32 weeks, when obstetrical conditions are optimal.
Antimicrobial-Resistant Pathogens Associated With Healthcare-Associated Infections: Annual Summary of Data Reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2006–2007
Authors: Hidron Alicia I. , Edwards Jonathan R. , Patel Jean , Horan Teresa C. , Sievert Dawn M. , Pollock Daniel A. , Fridkin Scott K. ,   National Healthcare Safety Network Team and Participating National Healthcare Safety Network Facilities
Published: October 2008

Objective.To describe the frequency of selected antimicrobial resistance patterns among pathogens causing device-associated and procedure-associated healthcare-associated infections (HAIs) reported by hospitals in the National Healthcare Safety Network (NHSN).Methods.Data are included on HAIs (ie, central line-associated bloodstream infections, catheter-associated urinary tract infections, ventilator-associated pneumonia, and surgical site infections) reported to the Patient Safety Component of the NHSN between January 2006 and October 2007. The results of antimicrobial susceptibility testing of up to 3 pathogenic isolates per HAI by a hospital were evaluated to define antimicrobial-resistance in the pathogenic isolates. The pooled mean proportions of pathogenic isolates interpreted as resistant to selected antimicrobial agents were calculated by type of HAI and overall. The incidence rates of specific device-associated infections were calculated for selected antimicrobial-resistant pathogens according to type of patient care area; the variability in the reported rates is described.Results.Overall, 463 hospitals reported 1 or more HAIs: 412 (89%) were general acute care hospitals, and 309 (67%) had 200-1,000 beds. There were 28,502 HAIs reported among 25,384 patients. The 10 most common pathogens (accounting for 84% of any HAIs) were coagulase-negative staphylococci (15%), Staphylococcus aureus (15%), Enterococcus species (12%), Candida species (11%), Escherichia coli (10%), Pseudomonas aeruginosa (8%), Klebsiella pneumoniae (6%), Enterobacter species (5%), Acinetobacter baumannii (3%), and Klebsiella oxytoca (2%). The pooled mean proportion of pathogenic isolates resistant to antimicrobial agents varied significantly across types of HAI for some pathogen-antimicrobial combinations. As many as 16% of all HAIs were associated with the following multidrug-resistant pathogens: methicillin-resistant S. aureus (8% of HAIs), vancomycin-resistant Enterococcus faecium (4%), carbapenem-resistant P. aeruginosa (2%), extended-spectrum cephalosporin-resistant K. pneumoniae (1%), extended-spectrum cephalosporin-resistant E. coli (0.5%), and carbapenem-resistant A. baumannii, K. pneumoniae, K. oxytoca, and E. coli (0.5%). Nationwide, the majority of units reported no HAIs due to these antimicrobial-resistant pathogens.
CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data
Authors: Cesaroni Matteo , Cittaro Davide , Brozzi Alessandro , Pelicci Pier Giuseppe , Luzi Lucilla 
Published: October 2008

AbstractSummary: CARPET (collection of automated routine programs for easy tiling) is a set of Perl, Python and R scripts, integrated on the Galaxy2 web-based platform, for the analysis of ChIP-chip and expression tiling data, both for standard and custom chip designs. CARPET allows rapid experimental data entry, simple quality control, normalization, easy identification and annotation of enriched ChIP-chip regions, detection of the absolute or relative transcriptional status of genes assessed by expression tiling experiments and, more importantly, it allows the integration of ChIP-chip and expression data. Results can be visualized instantly in a genomic context within the UCSC genome browser as graph-based custom tracks through Galaxy2. All generated and uploaded data can be stored within sessions and are easily shared with other users.Availability: http://bio.ifom-ieo-campus.it/galaxyContacts: matteo.cesaroni@ifom-ieo-campus.it; lucilla.luzi@ifom-ieo-campus.it
Integrated search and alignment of protein structures
Authors: Sacan Ahmet , Toroslu I. Hakki , Ferhatosmanoglu Hakan 
Published: October 2008

Abstract
Motivation: Identification and comparison of similar three-dimensional (3D) protein structures has become an even greater challenge in the face of the rapidly growing structure databases. Here, we introduce Vorometric, a new method that provides efficient search and alignment of a query protein against a database of protein structures. Voronoi contacts of the protein residues are enriched with the secondary structure information and a metric substitution matrix is developed to allow efficient indexing. The contact hits obtained from a distance-based indexing method are extended to obtain high-scoring segment pairs, which are then used to generate structural alignments.
Results: Vorometric is the first to address both search and alignment problems in the protein structure databases. The experimental results show that Vorometric is simultaneously effective in retrieving similar protein structures, producing high-quality structure alignments, and identifying cross-fold similarities. Vorometric outperforms current structure retrieval methods in search accuracy, while requiring com-parable running times. Furthermore, the structural superpositions produced are shown to have better quality and coverage, when compared with those of the popular structure alignment tools.
Availability: Vorometric is available as a web service at http://bio.cse.ohio-state.edu/Vorometric
Contact: sacan@cse.ohio-state.edu
SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology
Authors: Viklund Håkan , Bernsel Andreas , Skwark Marcin , Elofsson Arne 
Published: October 2008

Abstract
Summary: SPOCTOPUS is a method for combined prediction of signal peptides and membrane protein topology, suitable for genome-scale studies. Its objective is to minimize false predictions of transmembrane regions as signal peptides and vice versa. We provide a description of the SPOCTOPUS algorithm together with a performance evaluation where SPOCTOPUS compares favorably with state-of-the-art methods for signal peptide and topology predictions.
Availability: SPOCTOPUS is available as a web server and both the source code and benchmark data are available for download at http://octopus.cbr.su.se/
Contact: arne@bioinfo.se
Supplementary information: Supplementary data are available at Bioinformatics online.
Transcriptional Modulation of Ethylene Response Factor Protein JERF3 in the Oxidative Stress Response Enhances Tolerance of Tobacco Seedlings to Salt, Drought, and Freezing
Authors: Wu Lijun , Zhang Zhijin , Zhang Haiwen , Wang Xue-Chen , Huang Rongfeng 
Published: October 2008

Abstract
Abiotic stresses such as drought, cold, and salinity affect normal growth and development in plants. The production and accumulation of reactive oxygen species (ROS) cause oxidative stress under these abiotic conditions. Recent research has elucidated the significant role of ethylene response factor (ERF) proteins in plant adaptation to abiotic stresses. Our earlier functional analysis of an ERF protein, JERF3, indicated that JERF3-expressing tobacco (Nicotiana tabacum) adapts better to salinity in vitro. This article extends that study by showing that transcriptional regulation of JERF3 in the oxidative stress response modulates the increased tolerance to abiotic stresses. First, we confirm that JERF3-expressing tobacco enhances adaptation to drought, freezing, and osmotic stress during germination and seedling development. Then we demonstrate that JERF3-expressing tobacco imparts not only higher expression of osmotic stress genes compared to wild-type tobacco, but also the activation of photosynthetic carbon assimilation/metabolism and oxidative genes. More importantly, this regulation of the expression of oxidative genes subsequently enhances the activities of superoxide dismutase but reduces the content of ROS in tobacco under drought, cold, salt, and abscisic acid treatments. This indicates that JERF3 also modulates the abiotic stress response via the regulation of the oxidative stress response. Further assays indicate that JERF3 activates the expression of reporter genes driven by the osmotic-responsive GCC box, DRE, and CE1 and by oxidative-responsive as-1 in transient assays, suggesting the transcriptional activation of JERF3 in the expression of genes involved in response to oxidative and osmotic stress. Our results therefore establish that JERF3 activates the expression of such genes through transcription, resulting in decreased accumulation of ROS and, in turn, enhanced adaptation to drought, freezing, and salt in tobacco.
Arabidopsis Casein Kinase 1-Like 6 Contains a Microtubule-Binding Domain and Affects the Organization of Cortical Microtubules
Authors: Ben-Nissan Gili , Cui Weier , Kim Dong-Jin , Yang Yaodong , Yoo Byung-Chun , Lee Jung-Youn 
Published: October 2008

AbstractMembers of the casein kinase 1 (CK1) family are evolutionarily conserved eukaryotic protein kinases that are involved in various cellular, physiological, and developmental processes in yeast and metazoans, but the biological roles of CK1 members in plants are not well understood. Here, we report that an Arabidopsis (Arabidopsis thaliana) CK1 member named casein kinase 1-like 6 (CKL6) associates with cortical microtubules in vivo and phosphorylates tubulins in vitro. The unique C-terminal domain of CKL6 was shown to contain the signal that allows localization of CKL6 to the cortical microtubules. This domain on its own was sufficient to associate with microtubules in vivo and to bind tubulins in vitro. CKL6 was able to phosphorylate soluble tubulins as well as microtubule polymers, and its endogenous activity was found to associate with a tubulin-enriched subcellular fraction. Two major in vitro phosphorylation sites were mapped to serine-413 and serine-420 of tubulin β. Ectopic expression of wild-type CKL6 or a kinase-inactive mutant form induced alterations in cortical microtubule organization and anisotropic cell expansion. Collectively, these results demonstrate that CKL6 is a protein kinase containing a novel tubulin-binding domain and plays a role in anisotropic cell growth and shape formation in Arabidopsis through the regulation of microtubule organization, possibly through the phosphorylation of tubulins.
Metabolome Phenotyping of Inorganic Carbon Limitation in Cells of the Wild Type and Photorespiratory Mutants of the CyanobacteriumSynechocystissp. Strain PCC 6803
Authors: Eisenhut Marion , Huege Jan , Schwarz Doreen , Bauwe Hermann , Kopka Joachim , Hagemann Martin 
Published: October 2008

AbstractThe amount of inorganic carbon represents one of the main environmental factors determining productivity of photoautotrophic organisms. Using the model cyanobacterium Synechocystis sp. PCC 6803, we performed a first metabolome study with cyanobacterial cells shifted from high CO2 (5% in air) into conditions of low CO2 (LC; ambient air with 0.035% CO2). Using gas chromatography-mass spectrometry, 74 metabolites were reproducibly identified under different growth conditions. Shifting wild-type cells into LC conditions resulted in a global metabolic reprogramming and involved increases of, for example, 2-oxoglutarate (2OG) and phosphoenolpyruvate, and reductions of, for example, sucrose and fructose-1,6-bisphosphate. A decrease in Calvin-Benson cycle activity and increased usage of associated carbon cycling routes, including photorespiratory metabolism, was indicated by synergistic accumulation of the fumarate, malate, and 2-phosphoglycolate pools and a transient increase of 3-phosphoglycerate. The unexpected accumulation of 2OG with a concomitant decrease of glutamine pointed toward reduced nitrogen availability when cells are confronted with LC. Despite the increase in 2OG and low amino acid pools, we found a complete dephosphorylation of the PII regulatory protein at LC characteristic for nitrogen-replete conditions. Moreover, mutants with defined blocks in the photorespiratory metabolism leading to the accumulation of glycolate and glycine, respectively, exhibited features of LC-treated wild-type cells such as the changed 2OG to glutamine ratio and PII phosphorylation state already under high CO2 conditions. Thus, metabolome profiling demonstrated that acclimation to LC involves coordinated changes of carbon and interacting nitrogen metabolism. We hypothesize that Synechocystis has a temporal lag of acclimating carbon versus nitrogen metabolism with carbon leading.
A Novel 2-Oxoacid-Dependent Dioxygenase Involved in the Formation of the Goiterogenic 2-Hydroxybut-3-enyl Glucosinolate and Generalist Insect Resistance in Arabidopsis
Authors: Hansen Bjarne G. , Kerwin Rachel E. , Ober James A. , Lambrix Virginia M. , Mitchell-Olds Thomas , Gershenzon Jonathan , Halkier Barbara A. , Kliebenstein Daniel J. 
Published: October 2008

Abstract
Glucosinolates are secondary metabolites found almost exclusively in the order Brassicales. They are synthesized from a variety of amino acids and can have numerous side chain modifications that control biological function. We investigated the biosynthesis of 2-hydroxybut-3-enyl glucosinolate, which has biological activities including toxicity to Caenorhabditis elegans, inhibition of seed germination, induction of goiter disease in mammals, and production of bitter flavors in Brassica vegetable crops. Arabidopsis (Arabidopsis thaliana) accessions contain three different patterns of 2-hydroxybut-3-enyl glucosinolate accumulation (present in leaves and seeds, seeds only, or absent) corresponding to three different alleles at a single locus, GSL-OH. Fine-scale mapping of the GSL-OH locus identified a 2-oxoacid-dependent dioxygenase encoded by At2g25450 required for the formation of both 2R- and 2S-2-hydroxybut-3-enyl glucosinolate from the precursor 3-butenyl glucosinolate precursor. Naturally occurring null mutations and T-DNA insertional mutations in At2g25450 exhibit a complete absence of 2-hydroxybut-3-enyl glucosinolate accumulation. Analysis of herbivory by the generalist lepidopteran Trichoplusia ni showed that production of 2-hydroxybut-3-enyl glucosinolate provides increased resistance. These results show that At2g25450 is necessary for the hydroxylation of but-3-enyl glucosinolate to 2-hydroxybut-3-enyl glucosinolate in planta and that this metabolite increases resistance to generalist herbivory.