bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Shift from Oral to Blood pH Is a Stimulus for Adaptive Gene Expression of
Streptococcus gordonii
CH1 and Induces Protection against Oxidative Stress and Enhanced Bacterial Growth by Expression of
msrA
Authors: Vriesema Aldwin J. M. , Dankert Jacob , Zaat Sebastian A. J. 
Published: July 2002

ABSTRACT

Viridans group streptococci (VS) from the oral cavity entering the bloodstream may initiate infective endocarditis (IE). We aimed to identify genes expressed in response to a pH increase from slightly acidic (pH 6.2) to neutral (pH 7.3) as encountered by VS entering the bloodstream from the oral cavity. Using a recently developed promoter-screening vector, we isolated five promoter fragments from the genomic DNA of
Streptococcus gordonii
CH1 responding to this stimulus. No common regulatory sequences were identified in these promoter fragments that could account for the coordinate expression of the corresponding genes. One of the isolated fragments contained the promoter region and 5′ end of a gene highly homologous to the methionine sulfoxide reductase gene (
msrA
) of various bacterial and eukaryotic species. This gene has been found to be activated in
S. gordonii
strain V288 in a rabbit model of IE (A. O. Kiliç, M. C. Herzberg, M. W. Meyer, X. Zhao, and L. Tao, Plasmid 42:67–72, 1999). We isolated and characterized the
msrA
gene of
S. gordonii
CH1 and constructed a chromosomal insertion mutant. This mutant was more sensitive to hydrogen peroxide, suggesting a role for the streptococcal MsrA in protecting against oxidative stress. Moreover, MsrA appeared to be important for the growth of
S. gordonii
CH1 under aerobic and anaerobic conditions. Both these properties of MsrA may contribute to the ability of
S. gordonii
to cause IE.
Interleukin-1 Receptor Signaling Rather than That of Tumor Necrosis Factor Is Critical in Protecting the Host from the Severe Consequences of a Polymicrobe Anaerobic Infection
Authors: Graves Dana T. , Chen Chih-Ping , Douville Christopher , Jiang Yanling 
Published: July 2002

ABSTRACTInfection of the dental pulp leads to an osteolytic lesion that results from a polymicrobial infection consisting largely of pathogenic anaerobes. Infection causes significant morbidity and mortality mediated by bacterial factors and in some cases by the up-regulation of inflammatory cytokines. The inflammatory cytokines interleukin-1 (IL-1) and tumor necrosis factor (TNF), in particular, play a complex and central role in the responses to microbial pathogens. However, relatively little is known about the significance of these cytokines in protecting the host from focal polymicrobial anaerobic infections. To establish the relative importance of IL-1 and TNF in mediating the response to a mixed anaerobic infection, we inoculated the dental pulp of mice with six anaerobic pathogens containing functional deletions of receptors to IL-1 (IL-1R1−/−), TNF (TNFRp55−/−-p75−/−), or both (TNFRp55−/−-IL-1RI−/−). The results indicate that IL-1 receptor signaling and TNF receptor signaling both play similarly important roles in protecting the host from local tissue damage. However, IL-1 receptor signaling is considerably more important than TNF receptor signaling in preventing the spread of infection into surrounding fascial planes, since IL-1R1−/−but not TNFRp55−/−-p75−/−mice exhibited significantly higher morbidity and mortality. Moreover, all of the fatal infections occurred in male mice, suggesting the importance of gender differences in limiting the impact of these infections.
H
2
O
2
, Which Causes Macrophage-Related Stress, Triggers Induction of Expression of Virulence-Associated Plasmid Determinants in
Rhodococcus equi
Authors: Benoit Stephanie , Benachour Abdellah , Taouji Said , Auffray Yanick , Hartke Axel 
Published: July 2002

ABSTRACT

The response of the intracellular pathogen
Rhodococcus equi
to H
2
O
2
treatment, a situation potentially encountered after the oxidative burst of alveolar macrophages, was analyzed. Compared to other bacteria, including
Deinococcus radiodurans
,
R. equi
showed exceptionally high resistance to this stress. A proteomic approach showed that four polypeptides present in the wild-type strain (85F) are missing in the plasmid-cured strain 85F(P-), and by using a DNA macroarray, we identified two plasmid-encoded
vap
genes,
vapA
and
vapG
, whose expression was highly induced by H
2
O
2
treatment. Whereas the transcript size of
vapA
was compatible with a monocistronic mRNA, the transcript of
vapG
was considerably longer. Rapid amplification of cDNA ends PCRs showed that the transcriptional start sites of the two operons were 69 and 269 nucleotides (nt) upstream of the start codon, respectively. Analysis of these leader sequences revealed the presence of a small open reading frame named
podG
, which encodes a sequence of 55 amino acids preceded by a putative ribosome binding site sequence in the
vapG
transcript. Taking this result into account, the untranslated leader of the
podG
/
vapG
operon is 87 nt. Alignment of this sequence with the leader sequences of
vapA
and
vapD
, genes previously shown to be induced by acid, revealed significant homologies. Since our results showed that
vapA
,
vapD,
and
vapG
are genes highly induced by macrophage-related stresses, their gene products may, within the Vap protein family, play a dominant role inside these phagocytic cells and may be the most promising candidates for vaccination strategies.
Physical Map Location of the Multicopy Genes Coding for Ammonia Monooxygenase and Hydroxylamine Oxidoreductase in the Ammonia-Oxidizing Bacterium
Nitrosomonas
sp. Strain ENI-11
Authors: Hirota Ryuichi , Yamagata Akira , Kato Junichi , Kuroda Akio , Ikeda Tsukasa , Takiguchi Noboru , Ohtake Hisao 
Published: July 2002

ABSTRACT

Pulsed-field gel electrophoresis of
Pme
I digests of the
Nitrosomonas
sp. strain ENI-11 chromosome produced four bands ranging from 1,200 to 480 kb in size. Southern hybridizations suggested that a 487-kb
Pme
I fragment contained two copies of the
amoCAB
genes, coding for ammonia monooxygenase (designated

amoCAB
1

and

amoCAB
2

), and three copies of the
hao
gene, coding for hydroxylamine oxidoreductase (

hao
1

,

hao
2

, and

hao
3

). In this DNA fragment,

amoCAB
1

and

amoCAB
2

were about 390 kb apart, while

hao
1

,

hao
2

, and

hao
3

were separated by at least about 100 kb from each other. Interestingly,

hao
1

and

hao
2

were located relatively close to

amoCAB
1

and

amoCAB
2

, respectively. DNA sequence analysis revealed that

hao
1

and

hao
2

shared 160 identical nucleotides immediately upstream of each translation initiation codon. However,

hao
3

showed only 30% nucleotide identity in the 160-bp corresponding region.
Contributions of PBP 5 and
dd
-Carboxypeptidase Penicillin Binding Proteins to Maintenance of Cell Shape in
Escherichia coli
Authors: Nelson David E. , Young Kevin D. 
Published: July 2002

ABSTRACT

Escherichia coli
has 12 recognized penicillin binding proteins (PBPs), four of which (PBPs 4, 5, and 6 and DacD) have
dd
-carboxypeptidase activity. Although the enzymology of the
dd
-carboxypeptidases has been studied extensively, the in vivo functions of these proteins are poorly understood. To explain why
E. coli
maintains four independent loci encoding enzymes of considerable sequence identity and comparable in vitro activity, it has been proposed that the
dd
-carboxypeptidases may substitute for one another in vivo. We tested the validity of this equivalent substitution hypothesis by investigating the effects of these proteins on the aberrant morphology of Δ
dacA
mutants, which produce no PBP 5. Although cloned PBP 5 complemented the morphological phenotype of a Δ
dacA
mutant lacking a total of seven PBPs, controlled expression of PBP 4, PBP 6, or DacD did not. Also, a truncated PBP 5 protein lacking its amphipathic C-terminal membrane binding sequence did not reverse the morphological defects and was lethal at low levels of expression, implying that membrane anchoring is essential for the proper functioning of PBP 5. By examining a set of mutants from which multiple PBP genes were deleted, we found that significant morphological aberrations required the absence of at least three different PBPs. The greatest defects were observed in cells lacking, at minimum, PBPs 5 and 6 and one of the endopeptidases (either PBP 4 or PBP 7). The results further differentiate the roles of the low-molecular-weight PBPs, suggest a functional significance for the amphipathic membrane anchor of PBP 5 and, when combined with the recently determined crystal structure of PBP 5, suggest possible mechanisms by which these PBPs may contribute to maintenance of a uniform cell shape in
E. coli
.
Unusual Methyl-Branched α,β-Unsaturated Acyl Chain Substitutions in the Nod Factors of an Arctic Rhizobium,
Mesorhizobium
sp. Strain N33 (
Oxytropis arctobia
)
Authors: Poinsot Véréna , Bélanger Elaine , Laberge Serge , Yang Guo-Ping , Antoun Hani , Cloutier Jean , Treilhou Michel , Dénarié Jean , Promé Jean-Claude , Debellé Frédéric 
Published: July 2002

ABSTRACT

Mesorhizobium
sp. strain N33 (
Oxytropis arctobia
), a rhizobial strain isolated in arctic Canada, is able to fix nitrogen at very low temperatures in association with a few arctic legume species belonging to the genera
Astragalus, Onobrychis
, and
Oxytropis
. Using mass spectrometry and nuclear magnetic resonance spectroscopy, we have determined the structure of N33 Nod factors, which are major determinants of nodulation. They are pentameric lipochito-oligosaccharides 6-O sulfated at the reducing end and exhibit other original substitutions: 6-O acetylation of the glucosamine residue next to the nonreducing terminal glucosamine and N acylation of the nonreducing terminal glucosamine by methyl-branched acyl chains of the iso series, some of which are α,β unsaturated. These unusual substitutions may contribute to the peculiar host range of N33. Analysis of N33 whole-cell fatty acids indicated that synthesis of the methyl-branched fatty acids depended on the induction of bacteria by plant flavonoids, suggesting a specific role for these fatty acids in the signaling process between the plant and the bacteria. Synthesis of the methyl-branched α,β-unsaturated fatty acids required a functional
nodE
gene.
A Mutation in the 5′ Untranslated Region Increases Stability of
norA
mRNA, Encoding a Multidrug Resistance Transporter of
Staphylococcus aureus
Authors: Fournier Bénédicte , Truong-Bolduc Que Chi , Zhang Xiamei , Hooper David C. 
Published: July 2002

ABSTRACT

NorA, a multidrug efflux pump in
Staphylococcus aureus
, protects the cell from multiple drugs, including quinolones. The
flqB
mutation (T→G) in the 5′ untranslated region upstream of
norA
causes
norA
overexpression of 4.9-fold in
cis
, as measured in
norA
::
blaZ
fusions. The transcriptional initiation site of
norA
was unchanged in mutant and wild-type strains, but the half-life of
norA
mRNA was increased 4.8-fold in the
flqB
mutant compared to the wild-type strain. Computer-generated folding of the first 68 nucleotides of the
norA
transcript predicts an additional stem-loop and changes in a putative RNase III cleavage site in the
flqB
mutant.
High Genetic Variability of the
agr
Locus in
Staphylococcus
Species
Authors: Dufour Philippe , Jarraud Sophie , Vandenesch Francois , Greenland Timothy , Novick Richard P. , Bes Michele , Etienne Jerome , Lina Gerard 
Published: July 2002

ABSTRACT

The
agr
quorum-sensing and signal transduction system was initially described in
Staphylococcus aureus
, where four distinct allelic variants have been sequenced. Western blotting suggests the presence of homologous loci in many other staphylococci, and this has been confirmed for
S. epidermidis
and
S. lugdunensis
. In this study we isolated
agr
-like loci from a range of staphylococci by using PCR amplification from primers common to the six published
agr
sequences and bracketing the most variable region, associated with quorum-sensing specificity. Positive amplifications were obtained from 14 of 34 staphylococcal species or subspecies tested. Sequences of the amplicons identified 24 distinct variants which exhibited extensive sequence divergence with only 10% of the nucleotides absolutely conserved on multiple alignment. This variability involved all three open reading frames involved in quorum sensing and signal transduction. However, these variants retained several protein signatures, including the conserved cysteine residue of the autoinducing peptide, with the exception of
S. intermedius
of pigeon origin, which contained a serine in place of cysteine at this position. We discuss hypotheses on the mode of action and the molecular evolution of the
agr
locus based on comparisons between the newly determined sequences.
Xis Protein Binding to the Left Arm Stimulates Excision of Conjugative Transposon Tn916
Authors: Connolly Kevin M. , Iwahara Mizuho , Clubb Robert T. 
Published: July 2002

ABSTRACTTn916and related conjugative transposons are clinically significant vectors for the transfer of antibiotic resistance among human pathogens, and they excise from their donor organisms using the transposon-encoded integrase (Tn916Int) and excisionase (Tn916Xis) proteins. In this study, we have investigated the role of theTn916Xis protein in stimulating excisive recombination. The functional relevance ofTn916Xis binding sites on the arms of the transposon has been assessed in vivo using a transposon excision assay. Our results indicate that inEscherichia colithe stimulatory effect of theTn916Xis protein is mediated by sequence-specific binding to either of its two binding sites on the left arm of the transposon. These sites lie in between the core and arm sites recognized byTn916Int, suggesting that theTn916Xis protein enhances excision in a manner similar to the excisionase protein of bacteriophage λ, serving an architectural role in the stabilization of protein-nucleic acid structures required for strand synapsis. However, our finding that excision inE. coliis significantly enhanced by the host factor HU, but does not depend on the integration host factor or the factor for inversion stimulation, defines clear mechanistic differences between Tn916and bacteriophage λ recombination.
Efficient Extraction of Virus DNA by NucliSens Extractor Allows Sensitive Detection of Hepatitis B Virus by PCR
Authors: Gobbers Erik , Oosterlaken Tom A. M. , van Bussel Mario J. A. W. M. , Melsert Roel , Kroes Aloys C. M. , Claas Eric C. J. 
Published: July 2002

ABSTRACT
The NucliSens Extractor is an automated nucleic acid isolation system based on guanidinium thiocyanate (GuSCN)-silica extraction technology. The system has been validated for the isolation of human immunodeficiency virus (HIV) and hepatitis C virus (HCV) RNAs from human samples in combination with nucleic acid sequence-based amplification- and reverse transcription-PCR-based methods. We evaluated the extractor for hepatitis B virus (HBV) DNA extraction from human samples using a noncommercial HBV DNA PCR. Several sample pretreatment procedures in combination with the extractor were compared with the Qiagen extraction method, and the impact of the sample volume used in the extraction on the sensitivity was investigated. Heating of the lysed sample prior to extractor isolation and the use of a large sample volume resulted in highly sensitive detection of HBV DNA. Incubation of a 1-ml sample in GuSCN at 80°C (10 min) and at 37°C (30 min) allowed detection of 4 and 40 HBV genome equivalents/ml, respectively, in standard dilution panels. Sample lysis in GuSCN at room temperature and proteinase K treatment prior to use of the extractor were less efficient procedures. All clinical samples that were PCR positive after Qiagen extraction and/or that were HBsAg positive were also PCR positive after extractor isolation. HBV DNA, HCV RNA, and HIV type 1 RNA were efficiently coextracted from a single sample, allowing reliable detection of viral genomes.
Performance of the New Bayer VERSANT HCV RNA 3.0 Assay for Quantitation of Hepatitis C Virus RNA in Plasma and Serum: Conversion to International Units and Comparison with the Roche COBAS Amplicor HCV Monitor, Version 2.0, Assay
Authors: Beld Marcel , Sentjens Roel , Rebers Sjoerd , Weegink Christine , Weel Jan , Sol Cees , Boom René 
Published: July 2002

ABSTRACT

We have evaluated the VERSANT HCV RNA 3.0. Assay (HCV 3.0 bDNA assay) (Bayer Diagnostics, Berkeley, Calif.), which is an improved signal amplification procedure for the HCV 2.0 bDNA assay for the quantitation of hepatitis C virus (HCV) RNA in serum or plasma of HCV-infected individuals. The HCV 3.0 bDNA assay has a linear dynamic range of 2.5 × 10
3
to 4.0 × 10
7
HCV RNA copies per ml (c/ml). The performance of the HCV 3.0 bDNA assay was evaluated using three different test panels. An overall specificity of 96.8% relative to the detection limit of the HCV 3.0 bDNA assay was found. The intra- and interrun reproducibilities for both the dilution panel and the NAP (AcroMetrix, Benicia, Calif.) panel were consistent with coefficients of variation of less than 9%. Quantitation with the HCV 3.0 bDNA assay was linear over the entire range of both panels (ranges of 4.4 × 10
3
to 3.5 × 10
6
c/ml and 5 × 10
3
to 2 × 10
6
IU/ml, respectively), with correlation coefficients of 0.999, slopes close to one, and intercepts close to zero. The regression equation indicated that 1 IU corresponded to about 4.8 copies of HCV RNA. A correlation coefficient of 0.941 was found for HCV RNA values (in international units per milliliter) obtained from the HCV 3.0 bDNA assay and the HCV Monitor version 2.0 assay (HCV Monitor 2.0 assay) (Roche Diagnostic Systems, Branchburg, N.J.). Quantitative results obtained close to the lower limit of the HCV 3.0 bDNA assay might imply that its lower limit should be reconsidered and raised, if necessary. It appeared that quantitation values obtained from the HCV Monitor 2.0 assay of between 5 × 10
2
and 10
5
IU/ml were in general higher than those obtained from the HCV 3.0 bDNA assay, whereas values obtained from the HCV Monitor 2.0 assay were underestimated for samples with HCV RNA levels above 10
5
IU/ml.
Clinical Evaluation of a Frozen Commercially Prepared Microdilution Panel for Antifungal Susceptibility Testing of Seven Antifungal Agents, Including the New Triazoles Posaconazole, Ravuconazole, and Voriconazole
Authors: Pfaller M. A. , Diekema D. J. , Messer S. A. , Boyken L. , Huynh H. , Hollis R. J. 
Published: July 2002

ABSTRACT

A commercially prepared frozen broth microdilution panel (Trek Diagnostic Systems, Westlake, Ohio) was compared with a reference microdilution panel for antifungal susceptibility testing of two quality control (QC) strains and 99 clinical isolates of
Candida
spp. The antifungal agents tested included amphotericin B, flucytosine, fluconazole, itraconazole, posaconazole, ravuconazole, and voriconazole. Microdilution testing was performed according to NCCLS recommendations. MIC endpoints were read visually after 48 h of incubation and were assessed independently for each microdilution panel. The MICs for the QC strains were within published limits for both the reference and Trek microdilution panels. Discrepancies among MIC endpoints of no more than 2 dilutions were used to calculate the percent agreement. Acceptable levels of agreement between the Trek and reference panels were observed for all antifungal agents tested against the 99 clinical isolates. The overall agreement for each antifungal agent ranged from 96% for ravuconazole to 100% for amphotericin B. The Trek microdilution panel appears to be a viable alternative to frozen microdilution panels prepared in-house.
Use of Inhibitors To Evaluate Coreceptor Usage by Simian and Simian/Human Immunodeficiency Viruses and Human Immunodeficiency Virus Type 2 in Primary Cells
Authors: Zhang Yi-jun , Lou Bernard , Lal Renu B. , Gettie Agegnehu , Marx Preston A. , Moore John P. 
Published: July 2002

ABSTRACTWe have used coreceptor-targeted inhibitors to investigate which coreceptors are used by human immunodeficiency virus type 1 (HIV-1), simian immunodeficiency viruses (SIV), and human immunodeficiency virus type 2 (HIV-2) to enter peripheral blood mononuclear cells (PBMC). The inhibitors are TAK-779, which is specific for CCR5 and CCR2, aminooxypentane-RANTES, which blocks entry via CCR5 and CCR3, and AMD3100, which targets CXCR4. We found that for all the HIV-1 isolates and all but one of the HIV-2 isolates tested, the only relevant coreceptors were CCR5 and CXCR4. However, one HIV-2 isolate replicated in human PBMC even in the presence of TAK-779 and AMD3100, suggesting that it might use an undefined, alternative coreceptor that is expressed in the cells of some individuals. SIVmac239 and SIVmac251 (from macaques) were also able to use an alternative coreceptor to enter PBMC from some, but not all, human and macaque donors. The replication in human PBMC of SIVrcm(from a red-capped mangabey), a virus which uses CCR2 but not CCR5 for entry, was blocked by TAK-779, suggesting that CCR2 is indeed the paramount coreceptor for this virus in primary cells.
Potential Role for Luman, the Cellular Homologue of Herpes Simplex Virus VP16 (α Gene
trans
-Inducing Factor), in Herpesvirus Latency
Authors: Lu Rui , Misra Vikram 
Published: July 2002

ABSTRACT
The cascade of herpes simplex virus (HSV) gene expression that results in viral replication begins with the activation of viral immediate-early (IE) genes by the virion-associated protein VP16. VP16 on its own is inefficient at associating with complexes formed on IE gene promoters and depends upon the cellular factor HCF for its activity. In this respect VP16 mimics the host basic leucine zipper (bZIP) protein Luman, which also requires HCF for activating transcription. Our objective is to explore interactions between Luman and HCF and to determine if they play a role in the biology of herpesviruses. In this report we show that in cultured cells ectopically expressed Luman was retained in the cytoplasm, where it colocalized with Calnexin, a protein normally associated with the endoplasmic reticulum (ER). Retention of Luman in the ER depends on a hydrophobic segment of the protein that probably serves as a transmembrane domain. Deletion of this domain changed the intracellular location of Luman so that most of the mutant protein was in the nucleus of cells. While HCF was present in the nucleus of most cells, in cells expressing Luman it was retained in the cytoplasm where the two proteins colocalized. This cytoplasmic association of Luman and HCF could also be demonstrated in neurons in trigeminal ganglia removed from cattle soon after death. Cells in tissue culture that expressed Luman, but not a mutant form of the protein that fails to bind HCF, were resistant to a productive infection with HSV type 1 (HSV-1). We hypothesize that similar Luman-HCF interactions in sensory neurons in trigeminal ganglia result in the suppression of viral replication and the establishment of latency. Interestingly, Luman could activate the promoters of IE110 and LAT, two genes that are critical for reactivation of HSV-1 from latency. This suggests a role for Luman in the reactivation process as well.
Characterization of Human Immunodeficiency Virus Type 1 in Saliva and Blood Plasma by V3-Specific Heteroduplex Tracking Assay and Genotype Analyses
Authors: Freel Stephanie A. , Williams John M. , Nelson Julie A. E. , Patton Lauren L. , Fiscus Susan A. , Swanstrom Ronald , Shugars Diane C. 
Published: July 2002

ABSTRACTThe gp120 V3-encoding region of human immunodeficiency virus type 1 (HIV-1) RNA derived from the saliva and blood plasma of 11 individuals was characterized by heteroduplex tracking assay and sequence analyses. R5-like viral variants were identified in both fluids of all subjects. X4-like variants were detected in the plasma and/or saliva of three subjects, indicating that X4-like variants are not excluded from the saliva compartment. Viral subpopulations were similar in both fluids of most subjects, suggesting that HIV-1 in oral fluids and blood may stem from a common source. These findings raise the possibility of using saliva as a noninvasive fluid for evaluating and monitoring viral evolution in infected persons.