bluuebunny/crossref_metadata_2025_split huggingface dataset:
ASIAN: a website for network inference
Authors: Aburatani Sachiyo , Goto Kousuke , Saito Shigeru , Fumoto Masaki , Imaizumi Akira , Sugaya Nobuyoshi , Murakami Hiroo , Sato Makihiko , Toh Hiroyuki , Horimoto Katsuhisa 
Published: May 2004

Abstract
Summary: We constructed a website for inferring a network by applying the graphical Gaussian model, from a large amount of data, including redundant information. The available tools on the website are based on a system, named ASIAN (Automatic System for Inferring A Network), in combination with the two methods in our previous papers, which were designed to analyze gene expression profiles on a genomic scale. One of the remarkable features of the website is its ability to infer a network, concomitant with hierarchical clustering and the following estimation of cluster boundaries.
Availability: http://eureka.ims.u-tokyo.ac.jp/asian
Carbon monoxide improves cardiac energetics and safeguards the heart during reperfusion after cardiopulmonary bypass in pigs
Authors: Lavitrano Marialuisa , Smolenski Ryszard T. , Musumeci Antonino , Maccherini Massimo , Slominska Ewa , di Florio Ernesto , Bracco Adele , Mancini Antonio , Stassi Giorgio , Patti Mariella , Giovannoni Roberto , Froio Alberto , Simeone Felicetta , Forni Monica , Bacci Maria Laura , D'Alise Giuseppe , Cozzi Emanuele , Otterbein Leo E. , Yacoub Magdi H. , Bach Fritz H. , Calise Fulvio 
Published: May 2004

ABSTRACTIschemia‐reperfusion injury, a clinical problem during cardiac surgery, involves worsened adenosine trisphosphate (ATP) generation and damage to the heart. We studied carbon monoxide (CO) pretreatment, proven valuable in rodents but not previously tested in large animals, for its effects on pig hearts subjected to cardiopulmonary bypass with cardioplegic arrest. Hearts of CO‐treated pigs showed significantly higher ATP and phosphocreatine levels, less interstitial edema, and apoptosis of cardiomyocytes and required fewer defibrillations after bypass. We conclude that treatment with CO improves the energy status, prevents edema formation and apoptosis, and facilitates recovery in a clinically relevant model of cardiopulmonary bypass surgery.
Cardiac myocyte‐specific HIF‐1α deletion alters vascularization, energy availability, calcium flux, and contractility in the normoxic heart
Authors: Huang Yan , Hickey Reed P. , Yeh Jennifer L. , Liu Dinggang , Dadak Agnes , Young Lawrence H. , Johnson Randall S. , Giordano Frank J. 
Published: May 2004

ABSTRACTAt a resting pulse rate the heart consumes almost twice‐as much oxygen per gram tissue as the brain and more than 43 times more than resting skeletal muscle (1). Unlike skeletal muscle, cardiac muscle cannot sustain anaerobic metabolism. Balancing oxygen demand with availability is crucial to cardiac function and survival, and regulated gene expression is a critical element of maintaining this balance. We investigated the role of the hypoxia‐inducible transcription factor HIF‐1α in maintaining this balance under normoxic conditions. Cardiac myocyte‐specific HIF‐ 1α gene deletion in the hearts of genetically engineered mice caused reductions in contractility, vascularization, high‐energy phosphate content, and lactate production. This was accompanied by altered calcium flux and altered expression of genes involved in calcium handling, angiogenesis, and glucose metabolism. These findings support a central role for HIF‐1α in coordinating energy availability and utilization in the heart and have implications for disease states in which cardiac oxygen delivery is impaired.Heart muscle requires a constant supply of oxygen. When oxygen supply does not match myocardial demand cardiac contractile dysfunction occurs, and prolongation of this mismatch leads to apoptosis and necrosis. Coordination of oxygen supply and myocardial demand involves immediate adaptations, such as coronary vasodilatation, and longer‐term adaptations that include altered patterns of gene expression (2–4). How the expression of multiple genes is coordinated with oxygen availability in the heart and the impact of oxygen‐dependent gene expression on cardiac function are insufficiently understood. Further elucidating these relationships may help clarify the molecular pathology of various cardiovascular disease states, including ischemic cardiomyopathy and myocardial hibernation (5, 6).
Structure of a novel c7‐type three‐heme cytochrome domain from a multidomain cytochrome c polymer
Authors: Pokkuluri P. Raj , Londer Yuri Y. , Duke Norma E.C. , Erickson Jill , Pessanha Miguel , Salgueiro Carlos A. , Schiffer Marianne 
Published: May 2004

AbstractThe structure of a novel c7‐type cytochrome domain that has two bishistidine coordinated hemes and one heme with histidine, methionine coordination (where the sixth ligand is a methionine residue) was determined at 1.7 Å resolution. This domain is a representative of domains that form three polymers encoded by the Geobacter sulfurreducens genome. Two of these polymers consist of four and one protein of nine c7‐type domains with a total of 12 and 27 hemes, respectively. Four individual domains (termed A, B, C, and D) from one such multiheme cytochrome c (ORF03300) were cloned and expressed in Escherichia coli. The domain C produced diffraction quality crystals from 2.4 M sodium malonate (pH 7). The structure was solved by MAD method and refined to an R‐factor of 19.5% and R‐free of 21.8%. Unlike the two c7 molecules with known structures, one from G. sulfurreducens (PpcA) and one from Desulfuromonas acetoxidans where all three hemes are bishistidine coordinated, this domain contains a heme which is coordinated by a methionine and a histidine residue. As a result, the corresponding heme could have a higher potential than the other two hemes. The apparent midpoint reduction potential, Eapp, of domain C is −105 mV, 50 mV higher than that of PpcA.
Two‐promoter vector is highly efficient for overproduction of protein complexes
Authors: Kim Kyung‐Jin , Kim Han‐Eol , Lee Kwang‐Hoon , Han Wondeok , Yi Min‐Ju , Jeong Jinseok , Oh Byung‐Ha 
Published: May 2004

AbstractThe use of bicistronic vectors, which contain two target genes under one promoter, has been the most common practice for the heterologous production of binary protein complexes. The major problem of this method is the much lower expression of the second gene compared with that of the first gene next to the promoter. We tested a simple idea of whether inclusion of an additional promoter in front of the second gene may remove the problem. Compared with bicistronic vectors, corresponding two‐promoter vectors yielded four to nine times larger amounts of the complexes between BCL‐2 family proteins, BCL‐XL:BAD, BCL‐XL:BIM‐S, and CED‐9:EGL‐1 in bacterial cells as a result of significantly increased expression of the second genes in a manner independent of the order of the target genes. With the two‐promoter system, we produced two other complexes in large quantity suitable for extensive crystallization trial. The method does not accompany any technical disadvantages, and represents a significant improvement from the conventional method, which should enjoy wide application for the coexpression of binary or higher order protein complexes by extension.
What can dependence theories tell us about assessing the emergence of tobacco dependence?
Authors: Tiffany Stephen T. , Conklin Cynthia A. , Shiffman Saul , Clayton Richard R. 
Published: May 2004

ABSTRACTLittle is known about the processes that underlie changes in smoking that occur between the first use of a cigarette, subsequent regular use and eventual addictive use. At present, assessments of those critical processes are poorly developed and not strongly informed by contemporary models of drug dependence. The preceding three papers in this special issue address explicitly how modern drug‐dependence theories describe the emergence of drug dependence and the implications of those theories for assessment. The papers covered three domains of theories: negative reinforcement, positive reinforcement, and cognitive and social learning. In this paper, we summarize these reviews and extract general themes and issues that emerge across all the articles. These include: (1) the importance of learning processes; (2) limitations of self‐report measures; (3) the view of dependence as a process and not a state; (4) the conception of dependence on a continuum in contrast to the conventional perspective of tobacco dependence as a natural category; (5) the ontological status of the dependence concept; (6) limitations of backward extrapolations from adult assessments; (7) the possibility of multiple dimensions or forms of dependence; and (8) the value of a transdisciplinary approach when studying the emergence of tobacco dependence.
Measuring the emergence of tobacco dependence: the contribution of negative reinforcement models
Authors: Eissenberg Thomas 
Published: May 2004

ABSTRACTThis review of negative reinforcement models of drug dependence is part of a series that takes the position that a complete understanding of current concepts of dependence will facilitate the development of reliable and valid measures of the emergence of tobacco dependence. Other reviews within the series consider models that emphasize positive reinforcement and social learning/cognitive models. This review summarizes negative reinforcement in general and then presents four current negative reinforcement models that emphasize withdrawal, classical conditioning, self‐medication and opponent‐processes. For each model, the paper outlines central aspects of dependence, conceptualization of dependence development and influences that the model might have on current and future measures of dependence. Understanding how drug dependence develops will be an important part of future successful tobacco dependence measurement, prevention and treatment strategies.
Measures and models of nicotine dependence: positive reinforcement
Authors: Glautier Steven 
Published: May 2004

ABSTRACTThis paper addresses the problem of assessing nicotine dependence. The main objective is to develop theory‐led suggestions for measures that will be relevant in the early phases of tobacco use, as well as in established smokers. Theoretical models of addiction falling into the general class of ‘positive reinforcement theories’ were identified and reviewed. From this review a number of drug effects and patterns of behaviour were distilled and categorized as either vulnerability or dependence indicators. A comparison of those features with the International Classification of Diseases (ICD‐10) and Diagnostic and Statistical Manual (DSM‐IV) diagnostic systems shows that neither system includes detailed assessment of vulnerability indicators. It is argued that measurement of vulnerability indicators, in addition to dependence indicators, may add to the predictive validity of assessments carried out in early career tobacco users, especially where there is limited evidence of established dependence. In addition, it is suggested that examination of measures that differentiate a subgroup of early career smokers termed ‘rapid accelerators’ may prove profitable and enable identification of the key parameters of nicotine reinforcement.
Cognitive and social learning models of drug dependence: implications for the assessment of tobacco dependence in adolescents
Authors: Brandon Thomas H. , Herzog Thaddeus A. , Irvin Jennifer E. , Gwaltney Chad J. 
Published: May 2004

ABSTRACTThis paper is part of a series that has the goal of identifying potential approaches toward developing new instruments for assessing tobacco dependence among adolescents. The fundamental assumption underlying the series is that contemporary theories of drug dependence offer a rich source of opportunities for the development of theoretically based assessment tools. The present paper focuses on cognitive and social‐learning models of drug dependence and the implications of these models for novel assessment instruments. In particular, the paper focuses on Mark Goldman's model of drug expectancies, Albert Bandura's model of self‐efficacy, Thomas Wills's model of stress and coping and Stephen Tiffany's cognitive‐processing model of drug urges and cravings. In addition to traditional self‐report measures, naturalistic and laboratory‐based assessments are identified that may yield information relevant to multi‐dimensional measurement of tobacco dependence.
Structural tolerance of bacterial autotransporters for folded passenger protein domains
Authors: Veiga Esteban , De Lorenzo Víctor , Fernández Luis Angel 
Published: May 2004

SummaryIn this report we investigate the capacity of bacterial autotransporters (AT) to translocate folded protein domains across the outer membrane (OM). Polypeptides belonging to the AT family contain a C‐terminal domain that supports the secretion of the N‐domain (the passenger) across the OM of Gram‐negative bacteria. Despite some controversial data, it has been widely accepted that N‐passenger domains of AT must be unfolded and devoid of disulphide bonds for efficient translocation. To address whether or not AT are able to translocate folded protein domains across the OM, we employed several types of recombinant antibodies as heterologous N‐passengers of the transporter C‐domain of IgA protease (C‐IgAP) of Neisseria gonorroheae. The N‐domains used were single chain Fv fragments (scFv) and variable mono‐domains derived from camel antibodies (VHH) selected on the basis of their distinct and defined folding properties (i.e. enhanced solubility, stability and presence or not of disulphide bonds). Expression of these hybrids in Escherichia coli shows that stable scFv and VHH domains are efficiently (>99%) translocated towards the bacterial surface regardless of the presence or not of disulphide bonds on their structure. Antigen‐binding assays demonstrate that surface‐exposed scFv and VHH domains are correctly folded and thus able to bind their cognate antigens. Expression of scFv‐ or VHH‐C‐IgAP hybrids in E. coli dsbA or fkpA mutant cells reveals that these periplasmic protein chaperones fold these N‐domains before their translocation across the OM. Furthermore, large N‐passengers composed of strings of VHH domains were secreted in a folded state by AT with no loss of efficacy (>99%) despite having multiple disulphide bonds. Thus AT can efficiently translocate toward the cell surface folded N‐passengers composed of one, two or three immunoglobulin (Ig) domains, each with a folded diameter between ∼2 nm and having disulphide bonds. This tolerance for folded protein domains of ∼2 nm fits with the diameter of the central hydrophilic channel proposed for the ring‐like oligomeric complex assembled by C‐IgAP in the OM.
Fur functions as an activator and as a repressor of putative virulence genes in Neisseria meningitidis
Authors: Delany Isabel , Rappuoli Rino , Scarlato Vincenzo 
Published: May 2004

SummaryFur is a well‐known iron‐responsive repressor of gene transcription, which is used by many bacteria to respond to the low‐iron environment that pathogens encounter during infection. Four promoters of Neisseria meningitidis predicted to have Fur‐binding boxes were selected to study the molecular interactions between Fur and the promoter regions of genes expected to play a central role in survival and pathogenesis. We demonstrate that Fur acts not only as a repressor, but also as an activator of gene expression both in vivo and in vitro. We report that Fur binds to operators located upstream of three promoters that are positively regulated in vivo by Fur and iron, whereas Fur binds to an operator overlapping the classically iron‐repressed tbp promoter. Deletion of the upstream operator in the norB promoter abolished activation of transcription in vivo in response to iron and in vitro in response to Fur. The role of such a dual mechanism of Fur regulation during infection is discussed.
The Bacillus subtilisσW anti‐sigma factor RsiW is degraded by intramembrane proteolysis through YluC
Authors: Schöbel Susanne , Zellmeier Stephan , Schumann Wolfgang , Wiegert Thomas 
Published: May 2004

SummaryThe Bacillus subtilisσW regulon is induced by different stresses such as alkaline shock, salt shock, phage infection and certain antibiotics that affect cell wall biosynthesis. The activity of the alternative, extracytoplasmic function (ECF) sigma factor σW is modulated by a specific anti‐sigma factor (RsiW or YbbM) encoded by the rsiW (ybbM) gene located immediately downstream of sigW. The RsiW membrane topology was determined, and a specific reporter system for RsiW function was constructed. Experiments using the yeast two‐hybrid system suggested a direct interaction of σW with the cytoplasmic part of RsiW. Analysis of truncated forms of the RsiW protein revealed that σW induction by alkaline shock is dependent on both the transmembrane and the extracytoplasmic domain of RsiW. Western blot and pulse–chase experiments demonstrated degradation of RsiW after an alkaline shock. A B. subtilis mutant strain deleted for the Escherichia coli yaeL orthologue yluC, encoding a transmembrane protease, was defective in inducing a σW‐controlled promoter after alkaline shock and accumulated a membrane‐bound truncated form of RsiW, suggesting that the activity of σW is controlled by the proteolysis of RsiW by at least two different proteolytic steps.
Characterization of an inducible vancomycin resistance system in Streptomyces coelicolor reveals a novel gene (vanK) required for drug resistance
Authors: Hong Hee‐Jeon , Hutchings Matthew I. , Neu John M. , Wright Gerard D. , Paget Mark S. B. , Buttner Mark J. 
Published: May 2004

SummaryVancomycin is the front‐line therapy for treating problematic infections caused by methicillin‐resistant Staphylococcus aureus (MRSA), and the spread of vancomycin resistance is an acute problem. Vancomycin blocks cross‐linking between peptidoglycan intermediates by binding to the d‐Ala‐d‐Ala termini of bacterial cell wall precursors, which are the substrate of transglycosylase/transpeptidase. We have characterized a cluster of seven genes (vanSRJKHAX) in Streptomyces coelicolor that confers inducible, high‐level vancomycin resistance. vanHAX are orthologous to genes found in vancomycin‐resistant enterococci that encode enzymes predicted to reprogramme peptidoglycan biosynthesis such that cell wall precursors terminate in d‐Ala‐d‐Lac rather than d‐Ala‐d‐Ala. vanR and vanS encode a two‐component signal transduction system that mediates transcriptional induction of the seven van genes. vanJ and vanK are novel genes that have no counterpart in previously characterized vancomycin resistance clusters from pathogens. VanK is a member of the Fem family of enzymes that add the cross‐bridge amino acids to the stem pentapeptide of cell wall precursors, and vanK is essential for vancomycin resistance. The van genes are organized into four transcription units, vanRS, vanJ, vanK and vanHAX, and these transcripts are induced by vancomycin in a vanR‐dependent manner. To develop a sensitive bioassay for inducers of the vancomycin resistance system, the promoter of vanJ was fused to a reporter gene conferring resistance to kanamycin. All the inducers identified were glycopeptide antibiotics, but teicoplanin, a membrane‐anchored glycopeptide, failed to act as an inducer. Analysis of mutants defective in the vanRS and cseBC cell envelope signal transduction systems revealed significant cross‐talk between the two pathways.
Differential recognition of members of the carcinoembryonic antigen family by Afa/Dr adhesins of diffusely adhering Escherichia coli (Afa/Dr DAEC)
Authors: Berger Cedric N. , Billker Oliver , Meyer Thomas F. , Servin Alain L. , Kansau Imad 
Published: May 2004

SummaryLittle is known about the molecular bases underlying the virulence of diffusely adhering Escherichia coli (DAEC) harbouring the Afa/Dr family of adhesins. These adhesins recognize as receptors the GPI‐anchored proteins CD55 (decay‐accelerating factor, DAF) and CD66e (carcinoembryonic antigen, CEA). CD66e is a member of the CEA‐related cell adhesion molecules (CEACAM) family, comprising seven members. We analysed the interactions of Afa/Dr DAEC with the CEACAMs using CEACAM‐expressing CHO and HeLa cells. The results demonstrate that only E. coli expressing a subfamily of Afa/Dr adhesins, named here Afa/Dr‐I, including Dr, F1845 and AfaE‐III adhesins, bound onto CHO cells expressing CEACAM1, CEA or CEACAM6. Whereas all the Afa/Dr adhesins elicit recruitment of CD55 around adhering bacteria, only the Afa/Dr‐I subfamily elicits the recruitment of CEACAM1, CEA and CEACAM6. In addition, although CEACAM3 is not recognized as a receptor by the subfamily of Afa/Dr adhesins, it is recruited around bacteria in HeLa cells. The recruited CEACAM1, CEA and CEACAM6 around adhering bacteria resist totally or in part a detergent extraction, whereas the recruited CEACAM3 does not. Finally, the results show that recognition of CEA and CEACAM6, but not CEACAM1, is accompanied by tight attachment to bacteria of cell surface microvilli‐like extensions, which are elongated. Moreover, recognition of CEA is accompanied by an activation of the Rho GTPase Cdc42 and by a phosphorylation of ERM, which in turn elicit the observed cell surface microvilli‐like extensions.
Analysis of the 5S rRNA gene promoter from Acanthamoeba castellanii
Authors: Peng Zhihua , Bateman Erik 
Published: May 2004

SummaryThe promoter region of the Acanthamoeba 5S rRNA gene was analysed by in vitro transcription of several 5′ and 3′ deletion and substitution mutants, as well as a series of linker scanning mutants. The promoter consists of three sequence regions contained entirely within the gene; two of these correspond to the A and C boxes that bind TFIIIA, found in the genes from other genera. In addition, a region immediately 3′ to the transcription start site has a strong effect on initiation efficiency. No strict requirement was found for specific sequences 5′ to the transcription start site. Substitution of a consensus TATA box at −29 had only a modest effect on transcription, and deletion or substitution of sequences between −15 and −10 as well as −34 and −21 was only modestly more active than the wild‐type template. Analysis of 3′ deletions sets the 3′ end‐point of the promoter between +79 and +97, and demonstrates the importance of a T‐rich region in transcription termination. Taken together, these results suggest that promoter elements within the Acanthamoeba 5S RNA gene are somewhat redundant, with the exception of a sequence between +50 and +60, which functions in binding TFIIIA. Remarkably, polymerase chain reaction product templates containing only non‐specific 5′ ends between −6 and +1 relative to the transcription start site are fully functional, demonstrating that no external DNA scaffold is needed for TFIIIB and RNA polymerase III binding, and that productive initiation can be mediated solely by protein–DNA interactions within the coding region of the 5S gene.