bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relevant Role of Fibronectin-Binding Proteins in
Staphylococcus aureus
Biofilm-Associated Foreign-Body Infections
Authors: Vergara-Irigaray Marta , Valle Jaione , Merino Nekane , Latasa Cristina , García Begoña , Ruiz de los Mozos Igor , Solano Cristina , Toledo-Arana Alejandro , Penadés José R. , Lasa Iñigo 
Published: July 2009

ABSTRACT

Staphylococcus aureus
can establish chronic infections on implanted medical devices due to its capacity to form biofilms. Analysis of the factors that assemble cells into a biofilm has revealed the occurrence of strains that produce either a polysaccharide intercellular adhesin/poly-
N
-acetylglucosamine (PIA/PNAG) exopolysaccharide- or a protein-dependent biofilm. Examination of the influence of matrix nature on the biofilm capacities of embedded bacteria has remained elusive, because a natural strain that readily converts between a polysaccharide- and a protein-based biofilm has not been studied. Here, we have investigated the clinical methicillin (meticillin)-resistant
Staphylococcus aureus
strain 132, which is able to alternate between a proteinaceous and an exopolysaccharidic biofilm matrix, depending on environmental conditions. Systematic disruption of each member of the LPXTG surface protein family identified fibronectin-binding proteins (FnBPs) as components of a proteinaceous biofilm formed in Trypticase soy broth-glucose, whereas a PIA/PNAG-dependent biofilm was produced under osmotic stress conditions. The induction of FnBP levels due to a spontaneous
agr
deficiency present in strain 132 and the activation of a LexA-dependent SOS response or FnBP overexpression from a multicopy plasmid enhanced biofilm development, suggesting a direct relationship between the FnBP levels and the strength of the multicellular phenotype. Scanning electron microscopy revealed that cells growing in the FnBP-mediated biofilm formed highly dense aggregates without any detectable extracellular matrix, whereas cells in a PIA/PNAG-dependent biofilm were embedded in an abundant extracellular material. Finally, studies of the contribution of each type of biofilm matrix to subcutaneous catheter colonization revealed that an FnBP mutant displayed a significantly lower capacity to develop biofilm on implanted catheters than the isogenic PIA/PNAG-deficient mutant.
The Electron Transfer System of Syntrophically Grown
Desulfovibrio vulgaris
Authors: Walker Christopher B. , He Zhili , Yang Zamin K. , Ringbauer Joseph A. , He Qiang , Zhou Jizhong , Voordouw Gerrit , Wall Judy D. , Arkin Adam P. , Hazen Terry C. , Stolyar Sergey , Stahl David A. 
Published: July 2009

ABSTRACT

Interspecies hydrogen transfer between organisms producing and consuming hydrogen promotes the decomposition of organic matter in most anoxic environments. Although syntrophic coupling between hydrogen producers and consumers is a major feature of the carbon cycle, mechanisms for energy recovery at the extremely low free energies of reactions typical of these anaerobic communities have not been established. In this study, comparative transcriptional analysis of a model sulfate-reducing microbe,
Desulfovibrio vulgaris
Hildenborough, suggested the use of alternative electron transfer systems dependent on growth modality. During syntrophic growth on lactate with a hydrogenotrophic methanogen, numerous genes involved in electron transfer and energy generation were upregulated in
D. vulgaris
compared with their expression in sulfate-limited monocultures. In particular, genes coding for the putative membrane-bound Coo hydrogenase, two periplasmic hydrogenases (Hyd and Hyn), and the well-characterized high-molecular-weight cytochrome (Hmc) were among the most highly expressed and upregulated genes. Additionally, a predicted operon containing genes involved in lactate transport and oxidation exhibited upregulation, further suggesting an alternative pathway for electrons derived from lactate oxidation during syntrophic growth. Mutations in a subset of genes coding for Coo, Hmc, Hyd, and Hyn impaired or severely limited syntrophic growth but had little effect on growth via sulfate respiration. These results demonstrate that syntrophic growth and sulfate respiration use largely independent energy generation pathways and imply that to understand microbial processes that sustain nutrient cycling, lifestyles not captured in pure culture must be considered.
Bifurcated Degradative Pathway of 3-Sulfolactate in
Roseovarius nubinhibens
ISM via Sulfoacetaldehyde Acetyltransferase and (
S
)-Cysteate Sulfolyase
Authors: Denger Karin , Mayer Jutta , Buhmann Matthias , Weinitschke Sonja , Smits Theo H. M. , Cook Alasdair M. 
Published: July 2009

ABSTRACT

Data from the genome sequence of the aerobic, marine bacterium
Roseovarius nubinhibens
ISM were interpreted such that 3-sulfolactate would be degraded as a sole source of carbon and energy for growth via a novel bifurcated pathway including two known desulfonative enzymes, sulfoacetaldehyde acetyltransferase (EC 2.3.3.15) (Xsc) and cysteate sulfo-lyase (EC 4.4.1.25) (CuyA). Strain ISM utilized sulfolactate quantitatively with stoichiometric excretion of the sulfonate sulfur as sulfate. A combination of enzyme assays, analytical chemistry, enzyme purification, peptide mass fingerprinting, and reverse transcription-PCR data supported the presence of an inducible, tripartite sulfolactate uptake system (SlcHFG), and a membrane-bound sulfolactate dehydrogenase (SlcD) which generated 3-sulfopyruvate, the point of bifurcation. 3-Sulfopyruvate was in part decarboxylated by 3-sulfopyruvate decarboxylase (EC 4.1.1.79) (ComDE), which was purified. The sulfoacetaldehyde that was formed was desulfonated by Xsc, which was identified, and the acetyl phosphate was converted to acetyl-coenzyme A by phosphate acetyltransferase (Pta). The other portion of the 3-sulfopyruvate was transaminated to (
S
)-cysteate, which was desulfonated by CuyA, which was identified. The sulfite that was formed was presumably exported by CuyZ (TC 9.B.7.1.1 in the transport classification system), and a periplasmic sulfite dehydrogenase is presumed. Bioinformatic analyses indicated that transporter SlcHFG is rare but that SlcD is involved in three different combinations of pathways, the bifurcated pathway shown here, via CuyA alone, and via Xsc alone. This novel pathway involves ComDE in biodegradation, whereas it was discovered in the biosynthesis of coenzyme M. The different pathways of desulfonation of sulfolactate presumably represent final steps in the biodegradation of sulfoquinovose (and exudates derived from it) in marine and aquatic environments.
An A257V Mutation in the
Bacillus subtilis
Response Regulator Spo0A Prevents Regulated Expression of Promoters with Low-Consensus Binding Sites
Authors: Seredick Steve D. , Seredick Barbara M. , Baker David , Spiegelman George B. 
Published: July 2009

ABSTRACT

In
Bacillus
species, the master regulator of sporulation is Spo0A. Spo0A functions by both activating and repressing transcription initiation from target promoters that contain 0A boxes, the binding sites for Spo0A. Several classes of
spo0A
mutants have been isolated, and the molecular basis for their phenotypes has been determined. However, the molecular basis of the Spo0A(A257V) substitution, representative of an unusual phenotypic class, is not understood. Spo0A(A257V) is unusual in that it abolishes sporulation; in vivo, it fails to activate transcription from key stage II promoters yet retains the ability to repress the
abrB
promoter. To determine how Spo0A(A257V) retains the ability to repress but not stimulate transcription, we performed a series of in vitro and in vivo assays. We found unexpectedly that the mutant protein both stimulated transcription from the
spoIIG
promoter and repressed transcription from the
abrB
promoter, albeit twofold less than the wild type. A DNA binding analysis of Spo0A(A257V) showed that the mutant protein was less able to tolerate alterations in the sequence and arrangement of its DNA binding sites than the wild-type protein. In addition, we found that Spo0A(A257V) could stimulate transcription of a mutant
spoIIG
promoter in vivo in which low-consensus binding sites were replaced by high-consensus binding sites. We conclude that Spo0A(A257V) is able to bind to and regulate the expression of only genes whose promoters contain high-consensus binding sites and that this effect is sufficient to explain the observed sporulation defect.
Short-Chain Chromate Ion Transporter Proteins from
Bacillus subtilis
Confer Chromate Resistance in
Escherichia coli
Authors: Díaz-Magaña Amada , Aguilar-Barajas Esther , Moreno-Sánchez Rafael , Ramírez-Díaz Martha I. , Riveros-Rosas Héctor , Vargas Eréndira , Cervantes Carlos 
Published: July 2009

ABSTRACT

Tandem paired genes encoding putative short-chain monodomain protein members of the chromate ion transporter (CHR) superfamily (
ywrB
and
ywrA
) were cloned from genomic DNA of
Bacillus subtilis
strain 168. The transcription of the paired genes, renamed
chr3N
and
chr3C
, respectively, was shown to occur via a bicistronic mRNA generated from a promoter upstream of the
chr3N
gene. The
chr3N
and
chr3C
genes conferred chromate resistance when expressed in
Escherichia coli
strain W3110. The cloned
chr3N
gene alone did not confer chromate resistance on
E. coli
, suggesting that both
chr3N
and
chr3C
genes are required for function.
E. coli
cells expressing paired
chr3N
and
chr3C
genes demonstrated diminished uptake of chromate compared to that by a vector-only control strain. These results suggest that short-chain CHR proteins form heterodimer transporters which efflux chromate ions from the cytoplasm.
Stability and Convergence Results Based on Fixed Point Theory for a Generalized Viscosity Iterative Scheme
Authors: De la Sen M. 
Published: July 2009

AbstractA generalization of Halpern's iteration is investigated on a compact convex subset of a smooth Banach space. The modified iteration process consists of a combination of a viscosity term, an external sequence, and a continuous nondecreasing function of a distance of points of an external sequence, which is not necessarily related to the solution of Halpern's iteration, a contractive mapping, and a nonexpansive one. The sum of the real coefficient sequences of four of the above terms is not required to be unity at each sample but it is assumed to converge asymptotically to unity. Halpern's iteration solution is proven to converge strongly to a unique fixed point of the asymptotically nonexpansive mapping.
New Names for Known Things: On the Association of Novel Word Forms with Existing Semantic Information
Authors: Dobel Christian , Junghöfer Markus , Breitenstein Caterina , Klauke Benedikt , Knecht Stefan , Pantev Christo , Zwitserlood Pienie 
Published: July 2009

AbstractThe plasticity of the adult memory network for integrating novel word forms (lexemes) was investigated with whole-head magnetoencephalography (MEG). We showed that spoken word forms of an (artificial) foreign language are integrated rapidly and successfully into existing lexical and conceptual memory networks. The new lexemes were learned in an untutored way, by pairing them frequently with one particular object (and thus meaning), and infrequently with 10 other objects (learned set). Other novel word forms were encountered just as often, but paired with many different objects (nonlearned set). Their impact on semantic memory was assessed with cross-modal priming, with novel word forms as primes and object pictures as targets. The MEG counterpart of the N400 (N400m) served as an indicator of a semantic (mis)match between words and pictures. Prior to learning, all novel words induced a pronounced N400m mismatch effect to the pictures. This component was strongly reduced after training for the learned novel lexemes only, and now closely resembled the brain's response to semantically related native-language words. This result cannot be explained by mere stimulus repetition or stimulus–stimulus association. Thus, learned novel words rapidly gained access to existing conceptual representations, as effectively as related native-language words. This association of novel lexemes and conceptual information happened fast and almost without effort. Neural networks mediating these integration processes were found within left temporal lobe, an area typically described as one of the main generators of the N400 response.
Lexical Competition in Nonnative Speech Comprehension
Authors: FitzPatrick Ian , Indefrey Peter 
Published: July 2009

AbstractElectrophysiological studies consistently find N400 effects of semantic incongruity in nonnative (L2) language comprehension. These N400 effects are often delayed compared with native (L1) comprehension, suggesting that semantic integration in one's second language occurs later than in one's first language. In this study, we investigated whether such a delay could be attributed to (1) intralingual lexical competition and/or (2) interlingual lexical competition. We recorded EEG from Dutch–English bilinguals who listened to English (L2) sentences in which the sentence-final word was (a) semantically fitting and (b) semantically incongruent or semantically incongruent but initially congruent due to sharing initial phonemes with (c) the most probable sentence completion within the L2 or (d) the L1 translation equivalent of the most probable sentence completion. We found an N400 effect in each of the semantically incongruent conditions. This N400 effect was significantly delayed to L2 words but not to L1 translation equivalents that were initially congruent with the sentence context. Taken together, these findings firstly demonstrate that semantic integration in nonnative listening can start based on word initial phonemes (i.e., before a single lexical candidate could have been selected based on the input) and secondly suggest that spuriously elicited L1 lexical candidates are not available for semantic integration in L2 speech comprehension.
Ketamine Modulates Theta and Gamma Oscillations
Authors: Lazarewicz Maciej T. , Ehrlichman Richard S. , Maxwell Christina R. , Gandal Michael J. , Finkel Leif H. , Siegel Steven J. 
Published: July 2009

Abstract
Ketamine, an N-methyl-d-aspartate (NMDA) receptor glutamatergic antagonist, has been studied as a model of schizophrenia when applied in subanesthetic doses. In EEG studies, ketamine affects sensory gating and alters the oscillatory characteristics of neuronal signals in a complex manner. We investigated the effects of ketamine on in vivo recordings from the CA3 region of mouse hippocampus referenced to the ipsilateral frontal sinus using a paired-click auditory gating paradigm. One issue of particular interest was elucidating the effect of ketamine on background network activity, poststimulus evoked and induced activity. We find that ketamine attenuates the theta frequency band in both background activity and in poststimulus evoked activity. Ketamine also disrupts a late, poststimulus theta power reduction seen in control recordings. In the gamma frequency range, ketamine enhances both background and evoked power, but decreases relative induced power. These findings support a role for NMDA receptors in mediating the balance between theta and gamma responses to sensory stimuli, with possible implications for dysfunction in schizophrenia.
Critique of the Mrkšić Trial Chamber (ICTY) Judgment: A Re-evaluation on Whether Soldiers Hors de Combat Are Entitled to Recognition as Victims of Crimes Against Humanity
Authors: Singh Hansdeep 
Published: July 2009

AbstractOn 27 September 2007, the Mrkšić Trial Chamber held that the unlawful killing of soldiers hors de combat ("out of the battle") did not entitle them to recognition as victims of crimes against humanity under Article 5 of the ICTY Statute. This article critically analyses the Court's mischaracterization of precedent, revealing both historical and contemporary support for a broader definition of "civilian population" under Article 5. Moreover, by looking at case law and statutes from Nuremberg, foreign countries, and international courts, a continuous pattern that encompasses soldiers hors de combat within the definition of "civilian population" begins to emerge. Ultimately, to validate the increasing role of international humanitarian and human rights law, international criminal law must provide greater protections for those most vulnerable, in this case, soldiers hors de combat.
The repertoire of G-protein-coupled receptors in Xenopus tropicalis
Authors: Ji Yanping , Zhang Zhen , Hu Yinghe 
Published: July 2009

AbstractBackgroundThe G-protein-coupled receptor (GPCR) superfamily represents the largest protein family in the human genome. These proteins have a variety of physiological functions that give them well recognized roles in clinical medicine. InXenopus tropicalis, a widely used animal model for physiology research, the repertoire of GPCRs may help link the GPCR evolutionary history in vertebrates from teleost fish to mammals.ResultsWe have identified 1452 GPCRs in theX. tropicalisgenome. Phylogenetic analyses classified these receptors into the following seven families:Glutamate,Rhodopsin,Adhesion,Frizzled,Secretin,Taste 2andVomeronasal 1. Nearly 70% ofX. tropicalisGPCRs are represented by the following three types of receptors thought to receive chemosensory information from the outside world: olfactory, vomeronasal 1 and vomeronasal 2 receptors.ConclusionX. tropicalisshares a more similar repertoire of GPCRs with mammals than it does with fish. An examination of the three major groups of receptors related to olfactory/pheromone detection shows that inX. tropicalis, these groups have undergone lineage specific expansion. A comparison of GPCRs inX. tropicalis, teleost fish and mammals reveals the GPCR evolutionary history in vertebrates.
Protein disorder in the human diseasome: unfoldomics of human genetic diseases
Authors: Midic Uros , Oldfield Christopher J , Dunker A Keith , Obradovic Zoran , Uversky Vladimir N 
Published: July 2009

AbstractBackgroundIntrinsically disordered proteins lack stable structure under physiological conditions, yet carry out many crucial biological functions, especially functions associated with regulation, recognition, signaling and control. Recently, human genetic diseases and related genes were organized into a bipartite graph (Goh KI, Cusick ME, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685–8690). This diseasome network revealed several significant features such as the common genetic origin of many diseases.Methods and findingsWe analyzed the abundance of intrinsic disorder in these diseasome network proteins by means of several prediction algorithms, and we analyzed the functional repertoires of these proteins based on prior studies relating disorder to function. Our analyses revealed that (i) Intrinsic disorder is common in proteins associated with many human genetic diseases; (ii) Different disease classes vary in the IDP contents of their associated proteins; (iii) Molecular recognition features, which are relatively short loosely structured protein regions within mostly disordered sequences and which gain structure upon binding to partners, are common in the diseasome, and their abundance correlates with the intrinsic disorder level; (iv) Some disease classes have a significant fraction of genes affected by alternative splicing, and the alternatively spliced regions in the corresponding proteins are predicted to be highly disordered; and (v) Correlations were found among the various diseasome graph-related properties and intrinsic disorder.ConclusionThese observations provide the basis for the construction of the human-genetic-disease-associated unfoldome.
Inactivation of murine norovirus by chemical biocides on stainless steel
Authors: Magulski Thomas , Paulmann Dajana , Bischoff Birte , Becker Britta , Steinmann Eike , Steinmann Jörg , Goroncy-Bermes Peter , Steinmann Jochen 
Published: July 2009

Abstract

Background
Human norovirus (NoV) causes more than 80% of nonbacterial gastroenteritis in Europe and the United States. NoV transmission via contaminated surfaces may be significant for the spread of viruses. Therefore, measures for prevention and control, such as surface disinfection, are necessary to interrupt the dissemination of human NoV. Murine norovirus (MNV) as a surrogate for human NoV was used to study the efficacy of active ingredients of chemical disinfectants for virus inactivation on inanimate surfaces.

Methods
The inactivating properties of different chemical biocides were tested in a quantitative carrier test with stainless steel discs without mechanical action. Vacuum-dried MNV was exposed to different concentrations of alcohols, peracetic acid (PAA) or glutaraldehyde (GDA) for 5 minutes exposure time. Detection of residual virus was determined by endpoint-titration on RAW 264.7 cells.

Results
PAA [1000 ppm], GDA [2500 ppm], ethanol [50% (v/v)] and 1-propanol [30% (v/v)] were able to inactivate MNV under clean conditions (0.03% BSA) on the carriers by ≥ 4 log10 within 5 minutes exposure time, whereas 2-propanol showed a reduced effectiveness even at 60% (v/v). Furthermore, there were no significant differences in virus reduction whatever interfering substances were used. When testing with ethanol, 1- and 2-propanol, results under clean conditions were nearly the same as in the presence of dirty conditions (0.3% BSA plus 0.3% erythrocytes).

Conclusion
Products based upon PAA, GDA, ethanol and 1-propanol should be used for NoV inactivation on inanimate surfaces. Our data provide valuable information for the development of strategies to control NoV transmission via surfaces.
Test-retest variability of high resolution positron emission tomography (PET) imaging of cortical serotonin (5HT2A) receptors in older, healthy adults
Authors: Chow Tiffany W , Mamo David C , Uchida Hiroyuki , Graff-Guerrero Ariel , Houle Sylvain , Smith Gwenn S , Pollock Bruce G , Mulsant Benoit H 
Published: July 2009

AbstractBackgroundPosition emission tomography (PET) imaging using [18F]-setoperone to quantify cortical 5-HT2Areceptors has the potential to inform pharmacological treatments for geriatric depression and dementia. Prior reports indicate a significant normal aging effect on serotonin 5HT2Areceptor (5HT2AR) binding potential. The purpose of this study was to assess the test-retest variability of [18F]-setoperone PET with a high resolution scanner (HRRT) for measuring 5HT2AR availability in subjects greater than 60 years old. Methods: Six healthy subjects (age range = 65–78 years) completed two [18F]-setoperone PET scans on two separate occasions 5–16 weeks apart.ResultsThe average difference in the binding potential (BPND) as measured on the two occasions in the frontal and temporal cortical regions ranged between 2 and 12%, with the lowest intraclass correlation coefficient in anterior cingulate regions.ConclusionWe conclude that the test-retest variability of [18F]-setoperone PET in elderly subjects is comparable to that of [18F]-setoperone and other 5HT2AR radiotracers in younger subject samples.
Ascending aortic aneurysm in a patient with bicuspid aortic valve, positive history of systemic autoimmune diseases and common genetic factors: a case report
Authors: Foffa Ilenia , Festa Pier Luigi , Ait-Ali Lamia , Mazzone Annamaria , Bevilacqua Stefano , Andreassi Maria Grazia 
Published: July 2009

Abstract
The bicuspid aortic valve (BAV) and specific systemic autoimmune diseases are associated with cardiovascular manifestation, including aortic aneurysm. We reported a case of 64 year-old patient with BAV and a history of ankylosing spondylitis (AS) and systemic lupus erythematosus (SLE), and who developed ascending thoracic aortic aneurysm. The patient presented also the homozygosity for genetic variants of MMP9, ACE, MTHFR and PAI-1 genes. Gene-environmental interactions may represent an additional pathogenetic dimension in the still challenging management of the abnormalities of the aortic wall, including dilatation, aneurysm and dissection.