bluuebunny/crossref_metadata_2025_split huggingface dataset:
BOX Elements Modulate Gene Expression inStreptococcus pneumoniae: Impact on the Fine-Tuning of Competence Development
Authors: Knutsen Eivind , Johnsborg Ola , Quentin Yves , Claverys Jean-Pierre , Håvarstein Leiv Sigve 
Published: November 2006

ABSTRACTMore than 100 BOX elements are randomly distributed in intergenic regions of the pneumococcal genome. Here we demonstrate that these elements can affect expression of neighboring genes and present evidence that they are mobile. Together, our findings show that BOX elements enhance genetic diversity and genomic plasticity inStreptococcus pneumoniae.
Revised Model for
Enterococcus faecalis fsr
Quorum-Sensing System: the Small Open Reading Frame
fsrD
Encodes the Gelatinase Biosynthesis-Activating Pheromone Propeptide Corresponding to Staphylococcal AgrD
Authors: Nakayama Jiro , Chen Shengmin , Oyama Nozomi , Nishiguchi Kenzo , Azab Essam A. , Tanaka Emi , Kariyama Reiko , Sonomoto Kenji 
Published: November 2006

ABSTRACT

Gelatinase biosynthesis-activating pheromone (GBAP) is an autoinducing peptide involved in
Enterococcus faecalis fsr
quorum sensing, and its 11-amino-acid sequence has been identified in the C-terminal region of the 242-residue deduced
fsrB
product (J. Nakayama et al., Mol. Microbiol. 41:145-154, 2001). In this study, however, we demonstrated the existence of
fsrD
, encoding the GBAP propeptide, which is in frame with
fsrB
but is translated independently of
fsrB
. It was also demonstrated that FsrB′, an FsrD segment-truncated FsrB, functions as a cysteine protease-like processing enzyme to generate GBAP from FsrD. This revised model is consistent with the staphylococcal
agr
system.
Role of Bacteriocin Immunity Proteins in the Antimicrobial Sensitivity of
Streptococcus mutans
Authors: Matsumoto-Nakano Michiyo , Kuramitsu Howard K. 
Published: November 2006

ABSTRACT

Bacteria utilize quorum-sensing systems to modulate environmental stress responses. The quorum-sensing system of
Streptococcus mutans
is mediated by the competence-stimulating peptide (CSP), whose precursor is encoded by the
comC
gene. A
comC
mutant of strain GS5 exhibited enhanced antimicrobial sensitivity to a wide variety of different agents. Since the addition of exogenous CSP did not complement this phenotype, it was determined that the increased tetracycline, penicillin, and triclosan sensitivities resulted from repression of the putative bacteriocin immunity protein gene,
bip
, which is located immediately upstream from
comC
. We further demonstrated that the inactivation of
bip
or
smbG
, another bacteriocin immunity protein gene present within the
smb
operon in
S. mutans
GS5, affected sensitivity to a variety of antimicrobial agents. Furthermore, both the
bip
and
smbG
genes were upregulated in the presence of low concentrations of antibiotics and were induced during biofilm formation relative to in planktonic cells. These results suggest, for the first time, that the antimicrobial sensitivity of a bacterium can be modulated by some of the putative bacteriocin immunity proteins expressed by the organism. The implications of these observations for the evolution of bacteriocin immunity protein genes as well as for potential new chemotherapeutic strategies are discussed.
Analysis ofPseudomonas aeruginosaConditional Psl Variants Reveals Roles for the Psl Polysaccharide in Adhesion and Maintaining Biofilm Structure Postattachment
Authors: Ma Luyan , Jackson Kara D. , Landry Rebecca M. , Parsek Matthew R. , Wozniak Daniel J. 
Published: November 2006

ABSTRACTThe ability to form biofilms in the airways of people suffering from cystic fibrosis is a critical element ofPseudomonas aeruginosapathogenesis. The 15-genepsloperon encodes a putative polysaccharide that plays an important role in biofilm initiation in nonmucoidP. aeruginosastrains. Biofilm initiation by aP. aeruginosaPAO1 strain with disruption ofpslAandpslB(ΔpslAB) was severely compromised, indicating thatpslhas a role in cell-surface interactions. In this study, we investigated the adherence properties of this ΔpslABmutant using biotic surfaces (epithelial cells and mucin-coated surfaces) and abiotic surfaces. Our results showed thatpslis required for attachment to a variety of surfaces, independent of the carbon source. To study the potential roles of Psl apart from attachment, we generated apsl-inducibleP. aeruginosastrain (Δpsl/pBAD-psl) by replacing thepslpromoter region witharaC-pBAD, so that expression ofpslcould be controlled by addition of arabinose. Analysis of biofilms formed by the Δpsl/pBAD-pslstrain indicated that expression of thepsloperon is required to maintain the biofilm structure at steps postattachment. Overproduction of the Psl polysaccharide led to enhanced cell-surface and intercellular adhesion ofP. aeruginosa. This translated into significant changes in the architecture of the biofilm. We propose that Psl has an important role inP. aeruginosaadhesion, which is critical for initiation and maintenance of the biofilm structure.
IS1301Fingerprint Analysis ofNeisseria meningitidisStrains Belonging to the ET-15 Clone
Authors: Elias Johannes , Vogel Ulrich 
Published: November 2006

ABSTRACTMeningococci of the ET-15 clone frequently cause clusters of invasive meningococcal disease (IMD) and are associated with a high case-fatality ratio. Timely typing of strains from outbreaks of IMD caused by this clone is hampered by the low variability of its surface antigens. We present a new Southern blot-based typing method for ET-15 meningococci based on the insertion element IS1301, which was present in all 70 ET-15 strains tested. Fingerprints were stable in vitro over a period of 100 days of cultivation on agar plates. The discriminatory power of IS1301fingerprinting exceeded that of typing by serogrouping and antigen sequencing of the outer membrane proteins PorA and FetA, as determined by the analysis of 52 epidemiologically unrelated strains. In addition, the method provided conclusive results with regard to the comparison of strains from clusters of IMD. The investigation of insertion sites of IS1301revealed several new intragenic insertions, among others, into open reading frames homologous tomafBandtspB. A previously described insertion innadAwas present in more than two-thirds of the strains analyzed, suggesting that NadA is probably an unreliable vaccine candidate for the prevention of ET-15 disease.
Rapid Detection and Identification of Metallo-β-Lactamase-Encoding Genes by Multiplex Real-Time PCR Assay and Melt Curve Analysis
Authors: Mendes Rodrigo E. , Kiyota Katia A. , Monteiro Jussimara , Castanheira Mariana , Andrade Soraya S. , Gales Ana C. , Pignatari Antonio C. C. , Tufik Sergio 
Published: November 2006

ABSTRACT

Metallo-β-lactamase enzymes (MβL) are encoded by transferable genes, which appear to spread rapidly among gram-negative bacteria. The objective of this study was to develop a multiplex real-time PCR assay followed by a melt curve step for rapid detection and identification of genes encoding MβL-type enzymes based on the amplicon melting peak. The reference sequences of all genes encoding IMP and VIM types, SPM-1, GIM-1, and SIM-1 were downloaded from GenBank, and primers were designed to obtain amplicons showing different sizes and melting peak temperatures (

T
m

). The real-time PCR assay was able to detect all MβL-harboring clinical isolates, and the

T
m

-assigned genotypes were 100% coincident with previous sequencing results. This assay could be suitable for identification of MβL-producing gram-negative bacteria by molecular diagnostic laboratories.
Quality Control Limits for Posaconazole Disk Susceptibility Tests on Mueller-Hinton Agar with Glucose and Methylene Blue
Authors: Brown S. , Traczewski M. 
Published: November 2006

ABSTRACT

A multilaboratory collaborative study was performed in order to propose quality control limits for posaconazole disk diffusion susceptibility tests on Mueller-Hinton agar supplemented with 2% glucose and 0.5 μg of methylene blue per ml. Replicate tests were performed on three lots of prepared media using 5-μg posaconazole disks in each of eight laboratories to generate data to propose quality control zone diameter ranges for tests of
Candida albicans
ATCC 90028 (24 to 34 mm),
C. parapsilosis
ATCC 22019 (25 to 36 mm),
C. tropicalis
ATCC 750 (23 to 33 mm), and
C. krusei
ATCC 6258 (23 to 31 mm).
A Hypervariable Region within the 3′
cis
-Acting Element of the Murine Coronavirus Genome Is Nonessential for RNA Synthesis but Affects Pathogenesis
Authors: Goebel Scott J. , Miller Timothy B. , Bennett Corey J. , Bernard Kristen A. , Masters Paul S. 
Published: November 2006

ABSTRACT

The 3′
cis
-acting element for mouse hepatitis virus (MHV) RNA synthesis resides entirely within the 301-nucleotide 3′ untranslated region (3′ UTR) of the viral genome and consists of three regions. Encompassing the upstream end of the 3′ UTR are a bulged stem-loop and an overlapping RNA pseudoknot, both of which are essential to MHV and common to all group 2 coronaviruses. At the downstream end of the genome is the minimal signal for initiation of negative-strand RNA synthesis. Between these two ends is a hypervariable region (HVR) that is only poorly conserved between MHV and other group 2 coronaviruses. Paradoxically, buried within the HVR is an octanucleotide motif (oct), 5′-GGAAGAGC-3′, which is almost universally conserved in coronaviruses and is therefore assumed to have a critical biological function. We conducted an extensive mutational analysis of the HVR. Surprisingly, this region tolerated numerous deletions, rearrangements, and point mutations. Most striking, a mutant deleted of the entire HVR was only minimally impaired in tissue culture relative to the wild type. By contrast, the HVR deletion mutant was highly attenuated in mice, causing no signs of clinical disease and minimal weight loss compared to wild-type virus. Correspondingly, replication of the HVR deletion mutant in the brains of mice was greatly reduced compared to that of the wild type. Our results show that neither the HVR nor oct is essential for the basic mechanism of MHV RNA synthesis in tissue culture. However, the HVR appears to play a significant role in viral pathogenesis.
GLUT1 Is Not the Primary Binding Receptor but Is Associated with Cell-to-Cell Transmission of Human T-Cell Leukemia Virus Type 1
Authors: Takenouchi Norihiro , Jones Kathryn S. , Lisinski Ivonne , Fugo Kazunori , Yao Karen , Cushman Samuel W. , Ruscetti Francis W. , Jacobson Steven 
Published: November 2006

ABSTRACT

GLUT1 has recently been suggested to be a binding receptor for human T-cell leukemia virus type 1 (HTLV-1). We used a novel, short-term assay to define the role of GLUT1 in cell-to-cell transmission. Although increasing cell surface levels of GLUT1 enhanced HTLV-I transfer, efficient virus spread correlated largely with heparan sulfate proteoglycan (HSPG) expression on target cells. Moreover, since activated CD4
+
T cells and cord blood lymphocytes that are susceptible to HTLV-1 infection expressed undetectable levels of surface GLUT1, these results indicate that GLUT1 and HSPGs are important for efficient cell-to-cell transmission of HTLV-1 but raise concerns on the role of GLUT1 as the HTLV-1 primary binding receptor.
Genetic Studies of the β-Hairpin Loop of Rous Sarcoma Virus Capsid Protein
Authors: Spidel Jared L. , Wilson Carol B. , Craven Rebecca C. , Wills John W. 
Published: November 2006

ABSTRACT
The first few residues of the Rous sarcoma virus (RSV) CA protein comprise a structurally dynamic region that forms part of a Gag-Gag interface in immature virus particles. Dissociation of this interaction during maturation allows refolding and formation of a β-hairpin structure important for assembly of CA monomers into the mature capsid shell. A consensus binding site for the cellular Ubc9 protein was previously identified within this region, suggesting that binding of Ubc9 and subsequent small ubiquitin-like modifier protein 1 (SUMO-1) modification of CA may play a role either in regulating the assembly activity of CA in immature particles or mature cores or in controlling postentry function(s) during the establishment of infection. In the present study, mutations designed to eliminate the consensus binding site were used to dissect the potentially overlapping functions of these residues. The resulting replication defects could not be traced to a failure to form particles of normal composition but, rather, to a deficit in genome replication. Genetic suppressors of two detrimental β-hairpin mutations improved infectivity without restoring the consensus site or creating a novel one elsewhere. Optimal restoration of infectivity to a Lys-to-Arg mutant required a combination of secondary changes, one on the surface of each domain of CA. Rather than arguing for a critical role of Ubc9 and SUMO in RSV replication, these findings provide strong support for a structural role of the N-terminal residues and a particularly striking example of long-range interactions between regions of CA in achieving a functional core competent for genome replication.
Severe Acute Respiratory Syndrome Coronavirus Open Reading Frame (ORF) 3b, ORF 6, and Nucleocapsid Proteins Function as Interferon Antagonists
Authors: Kopecky-Bromberg Sarah A. , Martínez-Sobrido Luis , Frieman Matthew , Baric Ralph A. , Palese Peter 
Published: November 2006

ABSTRACTThe severe acute respiratory syndrome coronavirus (SARS-CoV) is highly pathogenic in humans, with a death rate near 10%. This high pathogenicity suggests that SARS-CoV has developed mechanisms to overcome the host innate immune response. It has now been determined that SARS-CoV open reading frame (ORF) 3b, ORF 6, and N proteins antagonize interferon, a key component of the innate immune response. All three proteins inhibit the expression of beta interferon (IFN-β), and further examination revealed that these SARS-CoV proteins inhibit a key protein necessary for the expression of IFN-β, IRF-3. N protein dramatically inhibited expression from an NF-κB-responsive promoter. All three proteins were able to inhibit expression from an interferon-stimulated response element (ISRE) promoter after infection with Sendai virus, while only ORF 3b and ORF 6 proteins were able to inhibit expression from the ISRE promoter after treatment with interferon. This indicates that N protein inhibits only the synthesis of interferon, while ORF 3b and ORF 6 proteins inhibit both interferon synthesis and signaling. ORF 6 protein, but not ORF 3b or N protein, inhibited nuclear translocation but not phosphorylation of STAT1. Thus, it appears that these three interferon antagonists of SARS-CoV inhibit the interferon response by different mechanisms.
Synthesis and Structure Assignment of 2-(4-Methoxybenzyl)cyclohexyl β-D-Glucopyranoside Enantiomers
Authors: Šaman David , Kratina Pavel , Moravcová Jitka , Wimmerová Martina , Wimmer Zdeněk 
Published: November 2006

Glucosylation of the cis- and trans-isomers of 2-(4-methoxybenzyl)cyclohexan-1-ol (1a/1b, 2a/2b, 1a or 2a) was performed to prepare the corresponding alkyl β-D-glucopyranosides, mainly to get analytical data of pure enantiomers of the glucosides (3a-6b), required for subsequent investigations of related compounds with biological activity. One of the employed modifications of the Koenigs-Knorr synthesis resulted in achieving 85-95% yields of pure β-anomers 3a/3b, 4a/4b, 3a or 4a of protected intermediates, with several promoters and toluene as solvent, yielding finally the deprotected products 5a/5b, 6a/6b, 5a or 6a as pure β-anomers. To obtain enantiomerically pure β-anomers of the target structure (3a, 4a, 5a and 6a) for unambiguous structure assignment, an enzymic reduction of 2-(4-methoxybenzyl)cyclohexan-1-one by Saccharomyces cerevisiae whole cells was performed to get (1S,2S)- and (1S,2R)-enantiomers (1a and 2a) of 2-(4-methoxybenzyl)cyclohexan-1-ol. The opposite enantiomers of alkyl β-D-glucopyranosides (5b and 6b) were obtained by separation of the diastereoisomeric mixtures 5a/5b and 6a/6b by chiral HPLC. All stereoisomers of the products (3a-6b) were subjected to a detailed 1H NMR and 13C NMR analysis.
Short-term lifestyle modification alters circulating biomarkers of endothelial health in sedentary, overweight adults
Authors: Rector R. Scott , Turk James R. , Sun Grace Y. , Guilford Brianne L. , Toedebusch Brian W. , McClanahan Matt W. , Thomas Tom R. 
Published: November 2006

Obesity and inactivity are associated with endothelial dysfunction that may contribute to the development of atherosclerosis. We examined the effects of a short-term lifestyle intervention on circulating biomarkers of endothelial health. Nineteen overweight or obese (mean body mass index (BMI): 28.9 ± 0.7 kg/m2) men and women underwent 6 weeks of body mass reduction induced by moderate energy restriction (~750 kcal/d; 1 kcal = 4.184 kJ) and aerobic training (~400 kcal/d). Fasting serum samples were collected at baseline and after reduction in body mass (week 6) to assess concentrations of nitrotyrosine (NT), secretory phospholipase A2 (sPLA2), and soluble intracellular adhesion molecule-1 (sICAM-1). Body mass was significantly reduced from 81.3 ± 2.8 to 77.3 ± 2.6 kg (p < 0.05). Circulating concentrations of NT and sICAM-1 were significantly reduced with treatment (~25% and ~10%, respectively), whereas sPLA2 levels were significantly elevated (~45%). Elevations in sPLA2 were negatively correlated with changes in NT (r = –0.58, p = 0.047); reductions in NT did not correlate significantly with reductions in sICAM-1. It appears that circulating markers of endothelial health are susceptible to short-term exercise interventions with modest reduction in body mass, and such a lifestyle modification may improve endothelial health by reducing protein nitration products and cellular adhesion.
Classical simulation of quantum fields II
Authors: Hirayama T , Holdom B , Koniuk R , Yavin T 
Published: November 2006

We consider the classical time evolution of a real scalar field in two-dimensional Minkowski space with a [Formula: see text] interaction. We compute the spatial and temporal two-point correlation functions and extract the renormalized mass of the interacting theory. We find our results are consistent with the one- and two-loop quantum computation. We also perform Monte Carlo simulations of the quantum theory and conclude that the classical scheme is able to produce more accurate results with a fraction of the CPU time. PACS Nos.: 03.70.+k, 03.50.–z, 11.15.Tk
Classical simulation of quantum fields I
Authors: Hirayama T , Holdom B 
Published: November 2006

We study classical field theories in a background field configuration where all modes of the theory are excited, matching the zero-point energy spectrum of quantum field theory. Our construction involves elements of a theory of classical electrodynamics by Wheeler–Feynman and the theory of stochastic electrodynamics of Boyer. The nonperturbative effects of interactions in these theories can be very efficiently studied on the lattice. In [Formula: see text] theory in 1 + 1 dimensions, we find results, in particular, for mass renormalization and the critical coupling for symmetry breaking that are in agreement with their quantum counterparts. We then study the perturbative expansion of the n-point Green's functions and find a loop expansion very similar to that of quantum field theory. When compared to the usual Feynman rules, we find some differences associated with particular combinations of internal lines going on-shell simultaneously. PACS Nos.: 03.70.+k, 03.50.–z, 11.15.Tk
Mass Spectrometry–Based Metabolic Profiling Reveals Different Metabolite Patterns in Invasive Ovarian Carcinomas and Ovarian Borderline Tumors
Authors: Denkert Carsten , Budczies Jan , Kind Tobias , Weichert Wilko , Tablack Peter , Sehouli Jalid , Niesporek Silvia , Könsgen Dominique , Dietel Manfred , Fiehn Oliver 
Published: November 2006

Abstract
Metabolites are the end products of cellular regulatory processes, and their levels can be regarded as the ultimate response of biological systems to genetic or environmental changes. We have used a metabolite profiling approach to test the hypothesis that quantitative signatures of primary metabolites can be used to characterize molecular changes in ovarian tumor tissues. Sixty-six invasive ovarian carcinomas and nine borderline tumors of the ovary were analyzed by gas chromatography/time-of-flight mass spectrometry (GC-TOF MS) using a novel contamination-free injector system. After automated mass spectral deconvolution, 291 metabolites were detected, of which 114 (39.1%) were annotated as known compounds. By t test statistics with P &lt; 0.01, 51 metabolites were significantly different between borderline tumors and carcinomas, with a false discovery rate of 7.8%, estimated with repeated permutation analysis. Principal component analysis (PCA) revealed four principal components that were significantly different between both groups, with the highest significance found for the second component (P = 0.00000009). PCA as well as additional supervised predictive models allowed a separation of 88% of the borderline tumors from the carcinomas. Our study shows for the first time that large-scale metabolic profiling using GC-TOF MS is suitable for analysis of fresh frozen human tumor samples, and that there is a consistent and significant change in primary metabolism of ovarian tumors, which can be detected using multivariate statistical approaches. We conclude that metabolomics is a promising high-throughput, automated approach in addition to functional genomics and proteomics for analyses of molecular changes in malignant tumors. (Cancer Res 2006; 66(22): 10795-804)
A Mechanism-Based Combination Therapy Reduces Local Tumor Growth and Metastasis in an Orthotopic Model of Prostate Cancer
Authors: Kosharskyy Boleslav , Solban Nicolas , Chang Sung K. , Rizvi Imran , Chang Yuchiao , Hasan Tayyaba 
Published: November 2006

Abstract
Therapy-induced stimulation of angiogenic molecules can promote tumor angiogenesis leading to enhanced tumor growth and cancer metastasis. Several standard and emerging therapies, such as radiation and photodynamic therapy (PDT), can induce angiogenic molecules, thus limiting their effectiveness. PDT is approved for the treatment of several cancers; however, its induction of vascular endothelial growth factor (VEGF) creates conditions favorable to enhanced tumor growth and metastasis, therefore mitigating its cytotoxic and antivascular effects. This is the first report showing that subcurative PDT in an orthotopic model of prostate cancer (LNCaP) increases not only VEGF secretion (2.1-fold) but also the fraction of animals with lymph node metastases. PDT followed by administration of an antiangiogenic agent, TNP-470, abolished this increase and reduced local tumor growth. On the other hand, administration of TNP-470 before PDT was less effective at local tumor control. In addition, animals in all groups, except in the PDT + TNP-470 group, had a weight loss of &gt;3 g at the time of sacrifice; the weight of the animals in the PDT + TNP-470 group did not change. The significant reduction (P &lt; 0.05) in tumor weight and volume observed between the PDT + TNP-470 group and the control group suggests that the combination of PDT and antiangiogenic treatment administered in the appropriate sequence was not only more effective at controlling local tumor growth and metastases but also reduced disease-related toxicities. Such molecular response-based combinations merit further investigations as they enhance both monotherapies and lead to improved treatment outcomes. (Cancer Res 2006; 66(22): 10953-8)