bluuebunny/crossref_metadata_2025_split huggingface dataset:
The steady-state mechanism of cytochrome c oxidase: redox interactions between metal centres
Authors: Mason Maria G. , Nicholls Peter , Cooper Chris E. 
Published: June 2009

The steady-state behaviour of isolated mammalian cytochrome c oxidase was examined by increasing the rate of reduction of cytochrome c. Under these conditions the enzyme's 605 (haem a), 655 (haem a3/CuB) and 830 (CuA) nm spectral features behaved as if they were at near equilibrium with cytochrome c (550 nm). This has implications for non-invasive tissue measurements using visible (550, 605 and 655 nm) and near-IR (830 nm) light. The oxidized species represented by the 655 nm band is bleached by the presence of oxygen intermediates P and F (where P is characterized by an absorbance spectrum at 607 nm relative to the oxidized enzyme and F is characterized by an absorbance spectrum at 580 nm relative to the oxidized enzyme) or by reduction of haem a3 or CuB. However, at these ambient oxygen levels (far above the enzyme Km), the populations of reduced haem a3 and the oxygen intermediates were very low (&lt;10%). We therefore interpret 655 nm changes as reduction of the otherwise spectrally invisible CuB centre. We present a model where small anti-cooperative redox interactions occur between haem a–CuA–CuB (steady-state potential ranges: CuA, 212–258 mV; haem a, 254–281 mV; CuB, 227–272 mV). Contrary to static equilibrium measurements, in the catalytic steady state there are no high potential redox centres (&gt;300 mV). We find that the overall reaction is correctly described by the classical model in which the Michaelis intermediate is a ferrocytochrome c–enzyme complex. However, the oxidation of ferrocytochrome c in this complex is not the sole rate-determining step. Turnover is instead dependent upon electron transfer from haem a to haem a3, but the haem a potential closely matches cytochrome c at all times.
Inhibitory effects of kynurenic acid, a tryptophan metabolite, and its derivatives on cytosolic sulfotransferases
Authors: Senggunprai Laddawan , Yoshinari Kouichi , Yamazoe Yasushi 
Published: June 2009

KYNA (kynurenic acid) is an endogenous metabolite of tryptophan in the kynurenine pathway and has been characterized as an antagonist of ionotropic glutamate receptors. In addition, we have reported this endogenous compound as a potent inhibitor of SULTs (cytosolic sulfotransferases). In the present study we characterized the inhibitory effects of KYNA on several human (h) and mouse (m) recombinant SULTs. No sulfate metabolite of KYNA was detected with mouse and human SULTs examined under the conditions used, suggesting that it is a bona fide inhibitor of SULTs. Among the mouse enzymes examined, KYNA exhibited selective inhibitory effects on Sult1b1-mediated sulfation of various compounds with IC50 values in the low micromolar range (2.9–4.9 μM). KYNA also exerted an inhibitory activity towards hSULT1A1 and hSULT1B1. The inhibitory potency of KYNA for mSult1b1 was stronger than that of 2,6-dichloro-4-nitrophenol, a known non-specific SULT inhibitor, whereas the potencies of these two inhibitors for hSULT1B1 were comparable. The inhibitory characteristics of KYNA were clearly distinct from those of mefenamic acid, a selective inhibitor of SULT1A enzymes. The KYNA derivatives 5,7-dichlorokynurenic acid and L689,560 exhibited preferential inhibitory effects on hSULT1A1 and hSULT1B1 respectively. Interestingly, gavestinel, another KYNA derivative, was found to be an extremely potent inhibitor of hSULT1B1. Finally, we have demonstrated that the mechanism underlying the KYNA inhibition varied depending on the enzyme and substrate involved. Taken together, the present results unveil another distinct aspect of KYNA and its derivatives as an inhibitor of SULTs.
Crystal structure of Glycine max glutathione transferase in complex with glutathione: investigation of the mechanism operating by the Tau class glutathione transferases
Authors: Axarli Irene , Dhavala Prathusha , Papageorgiou Anastassios C. , Labrou Nikolaos E. 
Published: June 2009

Cytosolic GSTs (glutathione transferases) are a multifunctional group of enzymes widely distributed in Nature and involved in cellular detoxification processes. The three-dimensional structure of GmGSTU4-4 (Glycine max GST Tau 4-4) complexed with GSH was determined by the molecular replacement method at 2.7 Å (1 Å=0.1 nm) resolution. The bound GSH is located in a region formed by the beginning of α-helices H1, H2 and H3 in the N-terminal domain of the enzyme. Significant differences in the G-site (GSH-binding site) as compared with the structure determined in complex with Nb-GSH [S-(p-nitrobenzyl)-glutathione] were found. These differences were identified in the hydrogen-bonding and electrostatic interaction pattern and, consequently, GSH was found bound in two different conformations. In one subunit, the enzyme forms a complex with the ionized form of GSH, whereas in the other subunit it can form a complex with the non-ionized form. However, only the ionized form of GSH may form a productive and catalytically competent complex. Furthermore, a comparison of the GSH-bound structure with the Nb-GSH-bound structure shows a significant movement of the upper part of α-helix H4 and the C-terminal. This indicates an intrasubunit modulation between the G-site and the H-site (electrophile-binding site), suggesting that the enzyme recognizes the xenobiotic substrates by an induced-fit mechanism. The reorganization of Arg111 and Tyr107 upon xenobiotic substrate binding appears to govern the intrasubunit structural communication between the G- and H-site and the binding of GSH. The structural observations were further verified by steady-state kinetic analysis and site-directed mutagenesis studies.
Human haem oxygenase-1 induction by nitro-linoleic acid is mediated by cAMP, AP-1 and E-box response element interactions
Authors: WRIGHT Marcienne M. , KIM Junghyun , HOCK Thomas D. , LEITINGER Norbert , FREEMAN Bruce A. , AGARWAL Anupam 
Published: June 2009

Nitro-fatty acid products of oxidative inflammatory reactions mediate anti-inflammatory cell signalling responses. LNO2 (nitrolinoleic acid) induces expression of HO-1 (haem oxygenase-1), an enzyme that catabolizes haem into products exhibiting potent anti-inflammatory properties. In the present manuscript, the molecular mechanisms underlying HO-1 induction by LNO2 were examined in HAEC (human aortic endothelial cells), HEK-293 (human embryonic kidney 293) cells, and in transcription factor-deficient MEF (mouse embryonic fibroblasts). LNO2 induced HO-1 expression in Nrf2 [NF-E2 (nuclear factor-erythroid 2)-related factor 2]-deficient MEF and in HEK-293 cells transfected with Nrf2-specific shRNA (small-hairpin RNA), supporting the fact that LNO2-mediated HO-1 induction can be regulated by Nrf2-independent mechanisms. LNO2 activated expression of a −4.5 kb human HO-1 promoter construct, whereas a −4.0 kb construct with deletion of 500 bp from the 5′ region was unresponsive. Site-directed mutagenesis of a CRE (cAMP-response element) or of a downstream NF-E2/AP-1 (activating protein-1) element, individually, within this 500 bp region modestly reduced activation of the HO-1 promoter by LNO2. Mutations of both the CRE and the NF-E2/AP-1 site also attenuated LNO2-mediated HO-1 promoter expression, whereas the addition of a third mutation in the proximal E-box sequence completely abolished LNO2-induced HO-1 expression. Chromatin immunoprecipitation assays confirmed CREB (CRE-binding protein)-1 binding to the CRE (located at −4.0 kb) and E-box regions (located at −44 bp) of the human HO-1 promoter. A 3C (Chromosome Conformation Capture) assay of intact cells showed LNO2-induced interactions between the CRE- and E-box- containing regions. These observations indicate that regulation of human HO-1 expression by LNO2 requires synergy between CRE, AP-1 and E-box sequences and involves the participation of CREB-1.
Human Ccr4–Not complexes contain variable deadenylase subunits
Authors: Lau Nga-Chi , Kolkman Annemieke , van Schaik Frederik M. A. , Mulder Klaas W. , Pijnappel W. W. M. Pim , Heck Albert J. R. , Timmers H. Th. Marc 
Published: June 2009

The Ccr4–Not complex is evolutionarily conserved and important for regulation of mRNA synthesis and decay. The composition of the yeast complex has been well described. Orthologues of the yeast Ccr4–Not components have been identified in human cells including multiple subunits with mRNA deadenylase activity. In the present study, we examine the composition of the human Ccr4–Not complex in an in-depth proteomic approach using stable cell lines expressing tagged CNOT proteins. We find at least four different variants of the human complex, consisting of seven stable core proteins and mutually exclusive associated mRNA deadenylase subunits. Interestingly, human CNOT4 is in a separate ~200 kDa complex. Furthermore, analyses of associated proteins indicate involvement of Ccr4–Not complexes in splicing, transport and localization of RNA molecules. Taken together, human Ccr4–Not complexes are heterogeneous in composition owing to differences in their deadenylase subunits, which may reflect the multi-functionality of these complexes in cellular processes.
Two novel phosphatidylinositol-4-phosphate 5-kinase type Iγ splice variants expressed in human cells display distinctive cellular targeting
Authors: Schill Nicholas J. , Anderson Richard A. 
Published: June 2009

The generation of various phosphoinositide messenger molecules at distinct locations within the cell is mediated via the specific targeting of different isoforms and splice variants of phosphoinositide kinases. The lipid messenger PtdIns(4,5)P2 is generated by several of these enzymes when targeted to distinct cellular compartments. Several splice variants of the type Iγ isoform of PIPK (PtdIns4P 5-kinase), which generate PtdIns(4,5)P2, have been identified, and each splice variant is thought to serve a unique functional role within cells. Here, we have identified two novel C-terminal splice variants of PIPKIγ in human cells consisting of 700 and 707 amino acids. These two splice variants are expressed in multiple tissue types and display PIPK activity in vitro. Interestingly, both of these novel splice variants display distinct subcellular targeting. With the addition of these two new splice isoforms, there are minimally five PIPKIγ splice variants that have been identified in mammals. Therefore, we propose the use of the HUGO (Human Genome Organization) nomenclature in the naming of the splice isoforms. PIPKIγ_i4 (700 amino acids) is present in the nucleus, a targeting pattern that has not been previously observed in any PIPKIγ splice variant. PIPKIγ_i5 (707 amino acids) is targeted to intracellular vesicle-like structures, where it co-localizes with markers of several types of endosomal compartments. As occurs with other PIPKIγ splice variants, the distinctive C-terminal sequences of PIPKIγ_i4 and PIPKIγ_i5 may facilitate association with unique protein targeting factors, thereby localizing the kinases to their appropriate cellular subdomains for the site-specific generation of PtdIns(4,5)P2.
Recombinant production of eight human cytosolic aminotransferases and assessment of their potential involvement in glyoxylate metabolism
Authors: Donini Stefano , Ferrari Manuela , Fedeli Chiara , Faini Marco , Lamberto Ilaria , Marletta Ada Serena , Mellini Lara , Panini Michela , Percudani Riccardo , Pollegioni Loredano , Caldinelli Laura , Petrucco Stefania , Peracchi Alessio 
Published: June 2009

PH1 (primary hyperoxaluria type 1) is a severe inborn disorder of glyoxylate metabolism caused by a functional deficiency of the peroxisomal enzyme AGXT (alanine-glyoxylate aminotransferase), which converts glyoxylate into glycine using L-alanine as the amino-group donor. Even though pre-genomic studies indicate that other human transaminases can convert glyoxylate into glycine, in PH1 patients these enzymes are apparently unable to compensate for the lack of AGXT, perhaps due to their limited levels of expression, their localization in an inappropriate cell compartment or the scarcity of the required amino-group donor. In the present paper, we describe the cloning of eight human cytosolic aminotransferases, their recombinant expression as His6-tagged proteins and a comparative study on their ability to transaminate glyoxylate, using any standard amino acid as an amino-group donor. To selectively quantify the glycine formed, we have developed and validated an assay based on bacterial GO (glycine oxidase); this assay allows the detection of enzymes that produce glycine by transamination in the presence of mixtures of potential amino-group donors and without separation of the product from the substrates. We show that among the eight enzymes tested, only GPT (alanine transaminase) and PSAT1 (phosphoserine aminotransferase 1) can transaminate glyoxylate with good efficiency, using L-glutamate (and, for GPT, also L-alanine) as the best amino-group donor. These findings confirm that glyoxylate transamination can occur in the cytosol, in direct competition with the conversion of glyoxylate into oxalate. The potential implications for the treatment of primary hyperoxaluria are discussed.
Identification and functional characterization of legumain in amphioxus Branchiostoma belcheri
Authors: Teng Lei , Wada Hiroshi , Zhang Shicui 
Published: June 2009

Legumain has been reported from diverse sources such as plants, parasites (animals) and mammals, but little is known in the lower chordates. The present study reports the first characterization of legumain cDNA from the protochordate Branchiostoma belcheri. The deduced 435-amino-acid-long protein is structurally characterized by the presence of a putative N-terminal signal peptide, a peptidase_C13 superfamily domain with the conserved Lys123-Gly124-Asp125 motif and catalytic dyad His153 and Cys195 and two potential Asn-glycosylation sites at Asn85 and Asn270. Phylogenetic analysis demonstrates that B. belcheri legumain forms an independent cluster together with ascidian legumain, and is positioned at the base of vertebrate legumains, suggesting that B. belcheri legumain gene may represent the archetype of vertebrate legumain genes. Both recombinant legumain expressed in yeast and endogenous legumain are able to be converted into active protein of ~37 kDa via a C-terminal autocleavage at acid pH values. The recombinant legumain efficiently degrades the legumain-specific substrate Z-Ala-Ala-Asn-MCA (benzyloxycarbonyl-L-alanyl-L-alanyl-L-asparagine-4-methylcoumaryl-7-amide) at optimum pH 5.5; and the enzymatic activity is inhibited potently by iodoacetamide and N-ethylmaleimide, partially by hen's-egg white cystatin, but not by E-64 [trans-epoxysuccinyl-L-leucylamido-(4-guanidino)butane], PMSF and pepstatin A. In addition, legumain is expressed in vivo in a tissue-specific manner, with main expression in the hepatic caecum and hind-gut of B. belcheri. Altogether, these results suggest that B. belcheri legumain plays a role in the degradation of macromolecules in food.
Comparison of Acoustic and Kinematic Approaches to Measuring Utterance-Level Speech Variability
Authors: Howell Peter , Anderson Andrew J. , Bartrip Jon , Bailey Eleanor 
Published: June 2009

PurposeThe spatiotemporal index (STI) is one measure of variability. As currently implemented, kinematic data are used, requiring equipment that cannot be used with some patient groups or in scanners. An experiment is reported that addressed whether STI can be extended to an audio measure of sound pressure of the speech envelope over time that did not need specialized equipment.MethodSTI indices of variability were obtained from lip track (L-STI) and amplitude envelope (E-STI) signals. These measures were made concurrent while either fluent speakers or speakers who stutter repeated “Buy Bobby a puppy” 20 times.ResultsL-STI and E-STI correlated significantly. STI decreased with age for both L-STI and E-STI. E-STI scores and L-STI scores discriminated successfully between fluent speakers and speakers who stutter.ConclusionThe amplitude-envelope-over-time signal can be used to obtain an STI score. This STI score can be used in situations where lip movement STI scores are precluded.
Development and Perceptual Evaluation of Amplitude-Based F0 Control in Electrolarynx Speech
Authors: Saikachi Yoko , Stevens Kenneth N. , Hillman Robert E. 
Published: June 2009

PurposeCurrent electrolarynx (EL) devices produce a mechanical speech quality that has been largely attributed to the lack of natural fundamental frequency (F0) variation. In order to improve the quality of EL speech, in the present study the authors aimed to develop and evaluate an automatic F0 control scheme, in which F0 was modulated based on variations in the root-mean-square (RMS) amplitude of the EL speech signal.MethodRecordings of declarative sentences produced by 2 male participants before and after total laryngectomy were used to develop procedures for calculating F0 contours for EL speech. Specifically, the positive linear relationship between F0 and RMS amplitude observed in pre-laryngectomy speech was used as the basis for generating an F0 contour based on the amplitude variation of EL speech. An analysis-by-synthesis approach was used to modify the F0 contour, and a perceptual experiment was conducted to examine its impact on the quality of the EL speech.ResultsThe results of perceptual experiments showed that modulating the F0 of EL speech using a linear relationship between amplitude and frequency made it significantly more natural sounding than EL speech with constant F0.ConclusionsThe current study provides preliminary support for amplitude-based control of F0 in EL speech.
Directional Effects on Infants and Young Children in Real Life: Implications for Amplification
Authors: Ching Teresa Y. C. , O’Brien Anna , Dillon Harvey , Chalupper Josef , Hartley Lisa , Hartley David , Raicevich George , Hain Jens 
Published: June 2009

PurposeThis study examined the head orientation of young children in naturalistic settings and the acoustics of their everyday environments for quantifying the potential effects of directionality.MethodTwenty-seven children (11 with normal hearing, 16 with impaired hearing) between 11 and 78 months of age were video recorded in naturalistic settings for analyses of head orientation. Reports on daily activities were obtained from caregivers. The effect of directionality in different environments was quantified by measuring the Speech Transmission Index (STI; H. J. M. Steeneken & T. Houtgast, 1980).ResultsAveraged across 4 scenarios, children looked in the direction of a talker for 40% of the time when speech was present. Head orientation was not affected by age or hearing status. The STI measurements revealed a directional advantage of 3 dB when a child looked at a talker but a deficit of 2.8 dB when the talker was sideways or behind the child. The overall directional effect in real life was between −0.4 and 0.2 dB.ConclusionsThe findings suggest that directional microphones in personal hearing devices for young children are not detrimental and have much potential for benefits in real life. The benefits may be enhanced by fitting directionality early and by counseling caregivers on ways to maximize benefits in everyday situations.
Surgical versus medical treatment for secondary post‐partum hemorrhage
Authors: FEIGENBERG TOMER , EITAN YAEL , SELA HEN Y. , ELCHALAL URIEL , BEN‐MEIR ASSAF , ROJANSKY NATHAN 
Published: June 2009

AbstractBackground. Secondary post‐partum hemorrhage (PPH) is defined as any abnormal bleeding from the birth canal occurring between 24 hours and 12 weeks postnatally. Treatment usually falls into one of the two categories: surgical evacuation of the uterus or medical treatment. Objective. To compare the two different clinical approaches and the implications on future fertility. Study design. A retrospective study. Setting. From 1990 to 2002, 168 women diagnosed with late PPH were admitted to the Hadassah Medical Centers in Jerusalem. The cases were divided into two groups according to the planned initial treatment: primary surgical treatment vs. primary medical treatment. Results. Primary surgical treatment was associated with significantly more primary negative events (p = 0.01). After the primary event, primary surgical treatment was associated with fewer future deliveries (p = 0.04) and resulted in increased rate of secondary infertility of borderline significance (p = 0.06). Conclusions. Our results show that secondary PPH is related to high rates of immediate and long‐term complications. It is possible that a conservative medical approach for secondary PPH may be superior to surgical treatment.
French National Program for Prevention of Healthcare-Associated Infections and Antimicrobial Resistance, 1992–2008: Positive Trends, But Perseverance Needed
Authors: Carlet Jean , Astagneau Pascal , Brun-Buisson Christian , Coignard Bruno , Salomon Valérie , Tran Béatrice , Desenclos Jean-Claude , Jarlier Vincent , Schlemmer Benoît , Parneix Pierre , Regnier Bernard , Fabry Jacques ,   French National Program for Prevention of Healthcare-Associated Infections and Antimicrobial Resistance
Published: June 2009

Objective.To describe the French program for the prevention of healthcare-associated infections and antibiotic resistance and provide results for some of the indicators available to evaluate the program. In addition to structures and process indicators, the 2 outcome indicators selected were the rate of surgical site infection and the proportion of methicillin-resistant Staphylococcus aureus (MRSA) isolates among the S. aureus isolates recovered.Design.Descriptive study of the evolution of the national structures for control of healthcare-associated infections since 1992. Through national surveillance networks, process indicators were available from 1993 to 2006, surgical site infection rates were available from 1999 to 2005, and prevalence rates for MRSA infection were available from 2001 to 2007.Results.A comprehensive national program has gradually been set up in France during the period from 1993 to 2004, which included strengthening of organized infection control activities at the local, regional, and national levels and developing large networks for surveillance of specific infections and antibiotic resistance. These achievements were complemented by instituting mandatory notification for unusual nosocomial events, especially outbreaks. The second phase of the program involved the implementation of 5 national quality indicators with public reporting. Surgical site infection rates decreased by 25% over a 6-year period. In France, the median proportion of MRSA among S. aureus isolates recovered from patients with bacteremia decreased from 33.4% to 25.7% during the period from 2001 to 2007, whereas this proportion increased in many other European countries.Conclusions.Very few national programs have been evaluated since the Study on the Efficacy of Nosocomial Infection Control. Although continuing efforts are required, the French program appears to have been effective at reducing infection rates.
Biophysical annotation and representation of CellML models
Authors: Wimalaratne S. M. , Halstead M. D. B. , Lloyd C. M. , Crampin E. J. , Nielsen P. F. 
Published: June 2009

Abstract
Motivation: CellML is an implementation-independent model description language for specifying and exchanging biological processes. The focus of CellML is the representation of mathematical formulations of biological processes. The language captures the mathematical and model building constructs well, but does not lend itself to capturing the biology these models represent.
Results: This article describes the development of an ontological framework for annotating CellML models with biophysical concepts. We demonstrate that, by using these ontological mappings, in combination with a set of graph reduction rules, it is possible to represent the underlying biological process described in a CellML model.
Contact: sarala.dissanayake@auckland.ac.nz
Supplementary information: Supplementary data are available at Bioinformatics online.