bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cloning and Characterization of the
pnb
Genes, Encoding Enzymes for 4-Nitrobenzoate Catabolism in
Pseudomonas putida
TW3
Authors: Hughes Michelle A. , Williams Peter A. 
Published: July 2002

ABSTRACT

Pseudomonas putida
strain TW3 is able to metabolize 4-nitrotoluene via 4-nitrobenzoate (4NBen) and 3, 4-dihydroxybenzoic acid (protocatechuate [PCA]) to central metabolites. We have cloned, sequenced, and characterized a 6-kbp fragment of TW3 DNA which contains five genes, two of which encode the enzymes involved in the catabolism of 4NBen to PCA. In order, they encode a 4NBen reductase (PnbA) which is responsible for catalyzing the direct reduction of 4NBen to 4-hydroxylaminobenzoate with the oxidation of 2 mol of NADH per mol of 4NBen, a reductase-like enzyme (Orf1) which appears to have no function in the pathway, a regulator protein (PnbR) of the LysR family, a 4-hydroxylaminobenzoate lyase (PnbB) which catalyzes the conversion of 4-hydroxylaminobenzoate to PCA and ammonium, and a second lyase-like enzyme (Orf2) which is closely associated with
pnbB
but appears to have no function in the pathway. The central
pnbR
gene is transcribed in the opposite direction to the other four genes. These genes complete the characterization of the whole pathway of 4-nitrotoluene catabolism to the ring cleavage substrate PCA in
P. putida
strain TW3.
In Vivo and In Vitro Effects of Integration Host Factor at the DmpR-Regulated ς
54
-Dependent Po Promoter
Authors: Sze Chun Chau , Laurie Andrew D. , Shingler Victoria 
Published: July 2002

ABSTRACT

Transcription from the
Pseudomonas
CF600-derived ς
54
-dependent promoter Po is controlled by the aromatic-responsive activator DmpR. Here we examine the mechanism(s) by which integration host factor (IHF) stimulates DmpR-activated transcriptional output of the Po promoter both in vivo and in vitro. In vivo, the Po promoter exhibits characteristics that typify many ς
54
-dependent promoters, namely, a phasing-dependent tolerance with respect to the distance from the regulator binding sites to the distally located RNA polymerase binding site, and a strong dependence on IHF for optimal promoter output. IHF is shown to affect transcription via structural repercussions mediated through binding to a single DNA signature located between the regulator and RNA polymerase binding sites. In vitro, using DNA templates that lack the regulator binding sites and thus bypass a role of IHF in facilitating physical interaction between the regulator and the transcriptional apparatus, IHF still mediates a DNA binding-dependent stimulation of Po transcription. This stimulatory effect is shown to be independent of previously described mechanisms for the effects of IHF at ς
54
promoters such as aiding binding of the regulator or recruitment of ς
54
-RNA polymerase via UP element-like DNA. The effect of IHF could be traced to promotion and/or stabilization of open complexes within the nucleoprotein complex that may involve an A+T-rich region of the IHF binding site and promoter-upstream DNA. Mechanistic implications are discussed in the context of a model in which IHF binding results in transduction of DNA instability from an A+T-rich region to the melt region of the promoter.
Proteome and Transcriptome Analysis of the Virulence Genes Regulated by the VirR/VirS System in
Clostridium perfringens
Authors: Shimizu Takeshi , Shima Kensuke , Yoshino Ken-ichi , Yonezawa Kazuyoshi , Shimizu Tohru , Hayashi Hideo 
Published: July 2002

ABSTRACT

The proteins under the control of the two-component system VirR/VirS in
Clostridium perfringens
were analyzed by using two-dimensional gel electrophoresis of the culture supernatant from the wild type and the
virR
mutant. Based on matrix-assisted laser desorption ionization-time of flight/mass spectrometry, seven positively regulated proteins and eight negatively regulated proteins were identified. Transcriptome analysis confirmed that 7 of the 15 proteins were regulated by the VirR/VirS system at the transcriptional level, but the remaining proteins were modified with a VirR/VirS-directed protease at the posttranslation and secretion levels. We purified and characterized the VirR/VirS-directed protease from the culture supernatant and identified it as a kind of clostripain. Because this proteolytic activity was strongly inhibited by leupeptin and antipain, it was concluded that this protease was a member of the family of cysteine proteases of
C. perfringens
.
Genome-Wide Dynamic Transcriptional Profiling of the Light-to-Dark Transition inSynechocystissp. Strain PCC 6803
Authors: Gill Ryan T. , Katsoulakis Eva , Schmitt William , Taroncher-Oldenburg Gaspar , Misra Jatin , Stephanopoulos Gregory 
Published: July 2002

ABSTRACTWe report the results of whole-genome transcriptional profiling of the light-to-dark transition with the model photosynthetic prokaryoteSynechocystissp. strain PCC 6803 (Synechocystis). Experiments were conducted by growingSynechocystiscultures to mid-exponential phase and then exposing them to two cycles of light/dark conditions, during which RNA samples were obtained. These samples were probed with a full-genome DNA microarray (3,169 genes, 20 samples) as well as a partial-genome microarray (88 genes, 29 samples). We concluded that (i) 30-min sampling intervals accurately captured transcriptional dynamics throughout the light/dark transition, (ii) 25% of theSynechocystisgenes (783 genes) responded positively to the presence of light, and (iii) the response dynamics varied greatly for individual genes, with a delay of up to 120 to 150 min for some genes. Four classes of genes were identified on the basis of their dynamic gene expression profiles: class I (108 genes, 30-min response time), class II (279 genes, 60 to 90 min), class III (258 genes, 120 to 150 min), and class IV (138 genes, 180 min). The dynamics of several transcripts from genes involved in photosynthesis and primary energy generation are discussed. Finally, we applied Fisher discriminant analysis to better visualize the progression of the overall transcriptional program throughout the light/dark transition and to determine those genes most indicative of the lighting conditions during growth.
The Extracellular Transport Signal of the
Vibrio cholerae
Endochitinase (ChiA) Is a Structural Motif Located between Amino Acids 75 and 555
Authors: Folster Jason P. , Connell Terry D. 
Published: July 2002

ABSTRACT

ChiA, an 88-kDa endochitinase encoded by the
chiA
gene of the gram-negative enteropathogen
Vibrio cholerae,
is secreted via the
eps
-encoded main terminal branch of the general secretory pathway (GSP), a mechanism which also transports cholera toxin. To localize the extracellular transport signal of ChiA that initiates transport of the protein through the GSP, a chimera comprised of ChiA fused at the N terminus with the maltose-binding protein (MalE) of
Escherichia coli
and fused at the C terminus with a 13-amino-acid epitope tag (E-tag) was expressed in strain 569B(
chiA
::Kan
r
), a
chiA
-deficient but secretion-competent mutant of
V. cholerae
. Fractionation studies revealed that blockage of the natural N terminus and C terminus of ChiA did not prevent secretion of the MalE-ChiA-E-tag chimera. To locate the amino acid sequences which encoded the transport signal, a series of truncations of ChiA were engineered. Secretion of the mutant polypeptides was curtailed only when ChiA was deleted from the N terminus beyond amino acid position 75 or from the C terminus beyond amino acid 555. A mutant ChiA comprised of only those amino acids was secreted by wild-type
V. cholerae
but not by an
epsD
mutant, establishing that amino acids 75 to 555 independently harbored sufficient structural information to promote secretion by the GSP of
V. cholerae
. Cys77 and Cys537, two cysteines located just within the termini of ChiA(75-555), were not required for secretion, indicating that those residues were not essential for maintaining the functional activity of the ChiA extracellular transport signal.
Validity of Earlier Positivity of Central Venous Blood Cultures in Comparison with Peripheral Blood Cultures for Diagnosing Catheter-Related Bacteremia in Cancer Patients
Authors: Malgrange Véronique Bussy , Escande Marie Christine , Theobald Serge 
Published: July 2002

ABSTRACT

We carried out a prospective study in two French Comprehensive Cancer Centers (95 and 184 beds, respectively) to assess the validity of a test based on the earlier positivity of central venous blood cultures in comparison with peripheral blood cultures for predicting catheter-related bacteremia. The differences between the times to positivity for the 21 patients with clinical catheter-related bacteremia and the differences between the times to positivity for the nine patients with bacteremia due to another source were compared by the median test. The difference between the median values was significant (
P
= 0.0003). A receiver operating characteristic curve was constructed to determine the optimum threshold of the test, which appeared to be at the cutoff point of ≥+3 h, with 100% specificity and 81% sensitivity. The positive and negative predictive values obtained with this cutoff point confirmed the efficacy of the test for predicting the presence or absence of catheter-related bacteremia in cancer patients. The cutoff point was then used to post-classify the 68 episodes of bacteremia from an unknown source. The characteristics and clinical course of both the positive and negative post-classified episodes did not show that the test was clearly useful for a large number of clinical presentations. We therefore suggest restricting it to febrile neutropenic cancer patients for whom clinical signs of infection are slight or absent and when the test is positive.
First Report of Methicillin-Resistant
Staphylococcus aureus
with Reduced Susceptibility to Vancomycin in Thailand
Authors: Trakulsomboon Suwanna , Danchaivijitr Somwang , Rongrungruang Yong , Dhiraputra Chertsak , Susaemgrat Wattanachai , Ito Teruyo , Hiramatsu Keiichi 
Published: July 2002

ABSTRACT

To investigate whether there are methicillin-resistant
Staphylococcus aureus
(MRSA) strains with reduced susceptibility to vancomycin in Thailand, a total of 155 MRSA strains isolated from patients hospitalized between 1988 and 1999 in university hospitals in Thailand were tested for glycopeptide susceptibility. All the strains were classified as susceptible to vancomycin and teicoplanin when judged by NCCLS criteria for glycopeptide susceptibility using the agar dilution MIC determination. Vancomycin MICs at which 50 and 90% of the isolates tested were inhibited (MIC
50
and MIC
90
, respectively) were 0.5 and 1 μg/ml, respectively, with a range of 0.25 to 2 μg/ml. For teicoplanin, MIC
50
and MIC
90
were 2 μg/ml, with a range of 0.5 to 4 μg/ml. However, one-point population analysis identified three MRSA strains, MR135, MR187, and MR209, which contained subpopulations of cells that could grow in 4 μg of vancomycin per ml. The proportions of the subpopulations were 2 × 10
−4
, 1.5 × 10
−6
, and 4 × 10
−7
, respectively. The subsequent performance of a complete population analysis and testing for the emergence of mutants with reduced susceptibility to vancomycin (MIC ≥ 8 μg/ml) confirmed that these strains were heterogeneously resistant to vancomycin. Two of these strains caused infection that was refractory to vancomycin therapy. Pulsed-field gel electrophoresis showed that the two strains had identical
Sma
I macrorestriction patterns and that they were one of the common types of MRSA isolated in the hospital. This is the first report of heterogeneous resistance to vancomycin in Thailand and an early warning for the possible emergence of vancomycin resistance in
S. aureus
in Southeast Asia.
Validation of the String Test for the Recovery of
Helicobacter pylori
from Gastric Secretions and Correlation of Its Results with Urea Breath Test Results, Serology, and Gastric pH Levels
Authors: Torres Javier , Camorlinga Margarita , Pérez-Peréz Guillermo , Gonzalez Gerardo , Muñoz Onofre 
Published: July 2002

ABSTRACT

The efficacy of the string culture test to isolate
Helicobacter pylori
from gastric secretions of 28 volunteers was studied. With the urea breath test (UBT) as the “gold standard,” the string culture test showed a sensitivity of 75% and a specificity of 100%. The results of string culture did not correlate with the UBT results, with serum antibody levels, or with the pH levels of gastric secretions.
High Prevalence of TT Virus (TTV) and TTV-Like Minivirus in Cervical Swabs
Authors: Fornai Claudia , Maggi Fabrizio , Vatteroni Maria Linda , Pistello Mauro , Bendinelli Mauro 
Published: July 2002

ABSTRACT
Genomes of TT virus (TTV) and TTV-like minivirus DNA were detected in 80% and 61% of cervical swabs from healthy women, respectively, regardless of concurrent human papillomavirus infection. These results show that the potential exists for sexual transmission of TTV and related viruses.
Relevance of the Number of Positive Bottles in Determining Clinical Significance of Coagulase-Negative Staphylococci in Blood Cultures
Authors: Mirrett Stanley , Weinstein Melvin P. , Reimer Larry G. , Wilson Michael L. , Reller L. Barth 
Published: July 2002

ABSTRACT
Coagulase-negative staphylococci (CNS) are the most commonly isolated contaminants from blood cultures, yet they frequently cause true infections. Determining the clinical significance of CNS is difficult, and clinicians often consider the number of positive bottles within a set of blood culture bottles in their assessment. Therefore, in three separate studies, we counted the number of positive bottles within blood culture sets comprising two, three, or four bottles in order to predict whether or not CNS were clinically significant isolates (CSI) in adult patients with suspected sepsis. Each culture was evaluated by independent, published clinical criteria to determine its clinical importance. Of 486 positive sets that included two adequately filled bottles, 127 (26%) CNS were CSI, 329 (67%) were contaminants, and 30 (6%) were indeterminate as a cause of sepsis. Among CSI, 39 and 61% were isolated from one and two bottles, respectively. The positive predictive value for sepsis was 18% when one bottle was positive and 37% when both bottles were positive. Of 235 positive sets that included three adequately filled bottles, 81 (34%) were CSI, 109 (46%) were contaminants, and 45 (19%) were indeterminate as a cause of sepsis. Of CSI, 43, 38, and 19% were found in one, two, and three bottles, respectively. The positive predictive value for sepsis was 28, 52, and 30% when one, two and three bottles were positive. Of 303 positive blood culture sets that included four adequately filled bottles, 64 (21%) were considered CSI, 197 (65%) were contaminants, and 42 (14%) were indeterminate as a cause of sepsis. Of CSI, 27, 28, 19, and 27% were found in one, two, three, and four bottles, respectively. The positive predictive value for sepsis was 11, 30, 34, and 37% when one, two, three, and four bottles were positive. We conclude that the number of culture bottles positive in a given culture set cannot reliably predict the clinical significance of the CNS isolated and, therefore, should not be used as a criterion for determining whether or not an isolate represents true infection or contamination.
Molecular Characterization of Group A Streptococcus Strains Isolated during a Scarlet Fever Outbreak
Authors: Perea-Mejía Luis M. , Inzunza-Montiel Alma E. , Cravioto Alejandro 
Published: July 2002

ABSTRACT

Forty group A streptococcus (GAS) isolates, recovered during a scarlet fever outbreak, were grouped based on their
Dde
I restriction profiles from
emm
amplicons. Twenty-seven isolates were identified by sequencing as
emm2
. The
emm2
isolates showed the
speA1
,
speB1
, and
speC1
alleles. Isolation of this GAS type from scarlet fever outbreaks is uncommon.
The VP5 Domain of VP4 Can Mediate Attachment of Rotaviruses to Cells
Authors: Zárate Selene , Espinosa Rafaela , Romero Pedro , Méndez Ernesto , Arias Carlos F. , López Susana 
Published: July 2002

ABSTRACT

Some animal rotaviruses require the presence of sialic acid (SA) on the cell surface to infect the cell. We have isolated variants of rhesus rotavirus (RRV) whose infectivity no longer depends on SA. Both the SA-dependent and -independent interactions of these viruses with the cell are mediated by the virus spike protein VP4, which is cleaved by trypsin into two domains, VP5 and VP8. In this work we have compared the binding characteristics of wild-type RRV and its variant nar3 to MA104 cells. In a direct nonradioactive binding assay, both viruses bound to the cells in a saturable and specific manner. When neutralizing monoclonal antibodies directed to both the VP8 and VP5 domains of VP4 were used to block virus binding, antibodies to VP8 blocked the cell attachment of wild-type RRV but not that of the variant nar3. Conversely, an antibody to VP5 inhibited the binding of nar3 but not that of RRV. These results suggest that while RRV binds to the cell through VP8, the variant does so through the VP5 domain of VP4. This observation was further sustained by the fact that recombinant VP8 and VP5 proteins, produced in bacteria as fusion products with glutathione
S
-transferase, were found to bind to MA104 cells in a specific and saturable manner and, when preincubated with the cell, were capable of inhibiting the binding of wild-type and variant viruses, respectively. In addition, the VP5 and VP8 recombinant proteins inhibited the infectivity of nar3 and RRV, respectively, confirming the results obtained in the binding assays. Interestingly, when the infectivity assay was performed on neuraminidase-treated cells, the VP5 fusion protein was also found to inhibit the infectivity of RRV, suggesting that RRV could bind to the cell through two sequential steps mediated by the interaction of VP8 and VP5 with SA-containing and SA-independent cell surface receptors, respectively.
A Recent Outbreak of Human Immunodeficiency Virus Type 1 Infection in Southern China Was Initiated by Two Highly Homogeneous, Geographically Separated Strains, Circulating Recombinant Form AE and a Novel BC Recombinant
Authors: Piyasirisilp Sucheep , McCutchan Francine E. , Carr Jean K. , Sanders-Buell Eric , Liu Wei , Chen Jie , Wagner Ralf , Wolf Hans , Shao Yiming , Lai Shenghan , Beyrer Chris , Yu Xiao-Fang 
Published: July 2002

ABSTRACT

New outbreaks of human immunodeficiency virus type 1 (HIV-1) among injecting drug users (IDUs) are spreading in China along heroin trafficking routes. Recently, two separate HIV-1 epidemics among IDUs were reported in Guangxi, Southern China, where partial sequencing of the
env
gene showed subtype C and circulating recombinant form (CRF) AE. We evaluated five virtually full-length HIV-1 genome sequences from IDUs in Guangxi to determine the genetic diversity and the presence of intersubtype recombinants. Sequence analysis showed two geographically separated, highly homogeneous HIV-1 strains. B/C intersubtype recombinants were found in three IDUs from Baise City, in a mountainous region near the Yunnan-Guangxi border. These were mostly subtype C, with portions of the capsid and reverse transcriptase (RT) genes from subtype B. The subtype B portion of the capsid was located in the N-terminal domain, which has been shown to influence virus core maturation, virus infectivity, and binding to cyclophilin A, whereas the subtype B portion of RT was located in the palm subdomain, which is the active site of the enzyme. These BC recombinants differed from a BC recombinant found in Xinjiang Province in northwestern China. CRF AE strains were found in IDUs from Nanning, the capital of Guangxi, and in IDUs from Pingxiang City near the China-Vietnam border. The AE and BC recombinants were both remarkable for their low interpatient diversity, less than 1% for the full genome. Rapid spread of HIV-1 among IDUs may foster the emergence of highly homogeneous strains, including novel recombinants in regions with multiple subtypes.
Mutations in Herpes Simplex Virus Glycoprotein D Distinguish Entry of Free Virus from Cell-Cell Spread
Authors: Rauch Daniel A. , Rodriguez Nilda , Roller Richard J. 
Published: July 2002

ABSTRACT

Herpes simplex virus type 1 (HSV-1) glycoprotein D (gD) is an essential component of the entry apparatus that is responsible for viral penetration and subsequent cell-cell spread. To test the hypothesis that gD may serve distinguishable functions in entry of free virus and cell-cell spread, mutants were selected for growth on U
S
11cl19.3 cells, which are resistant to both processes due to the lack of a functional gD receptor, and then tested for their ability to enter as free virus and to spread from cell to cell. Unlike their wild-type parent, HSV-1(F), the variants that emerged from this selection, which were named SP mutants, are all capable of forming macroscopic plaques on the resistant cells. This ability is caused by a marked increase in cell-cell spread without a concomitant increase in efficiency of entry of free virus. gD substitutions that arose within these mutants are sufficient to mediate cell-cell spread in U
S
11cl19.3 cells but are insufficient to overcome the restriction to entry of free virions. These results suggest that mutations in gD (i) are sufficient but not necessary to overcome the block to cell-cell spread exhibited by U
S
11cl19.3 cells and (ii) are insufficient to mediate entry of free virus in the same cells.
Species-Specific TT Viruses and Cross-Species Infection in Nonhuman Primates
Authors: Okamoto Hiroaki , Fukuda Masako , Tawara Akio , Nishizawa Tsutomu , Itoh Yukio , Hayasaka Ikuo , Tsuda Fumio , Tanaka Takeshi , Miyakawa Yuzo , Mayumi Makoto 
Published: July 2002

ABSTRACT

Viruses resembling human TT virus (TTV) were searched for in sera from nonhuman primates by PCR with primers deduced from well-conserved areas in the untranslated region. TTV DNA was detected in 102 (98%) of 104 chimpanzees, 9 (90%) of 10 Japanese macaques, 4 (100%) of 4 red-bellied tamarins, 5 (83%) of 6 cotton-top tamarins, and 5 (100%) of 5 douroucoulis tested. Analysis of the amplification products of 90 to 106 nucleotides revealed TTV DNA sequences specific for each species, with a decreasing similarity to human TTV in the order of chimpanzee, Japanese macaque, and tamarin/douroucouli TTVs. Full-length viral sequences were amplified by PCR with inverted nested primers deduced from the untranslated region of TTV DNA from each species. All animal TTVs were found to be circular with a genomic length at 3.5 to 3.8 kb, which was comparable to or slightly shorter than human TTV. Sequences closely similar to human TTV were determined by PCR with primers deduced from a coding region (N22 region) and were detected in 49 (47%) of the 104 chimpanzees; they were not found in any animals of the other species. Sequence analysis of the N22 region (222 to 225 nucleotides) of chimpanzee TTV DNAs disclosed four genetic groups that differed by 36.1 to 50.2% from one another; they were 35.0 to 52.8% divergent from any of the 16 genotypes of human TTV. Of the 104 chimpanzees, only 1 was viremic with human TTV of genotype 1a. It was among the 53 chimpanzees which had been used in transmission experiments with human hepatitis viruses. Antibody to TTV of genotype 1a was detected significantly more frequently in the chimpanzees that had been used in transmission experiments than in those that had not (8 of 28 [29%] and 3 of 35 [9%], respectively;
P = 0.038).
These results indicate that species-specific TTVs are prevalent in nonhuman primates and that human TTV can cross-infect chimpanzees.