bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of theBacillus subtilis furandperRGenes by PerR: Not All Members of the PerR Regulon Are Peroxide Inducible
Authors: Fuangthong Mayuree , Herbig Andrew F. , Bsat Nada , Helmann John D. 
Published: July 2002

ABSTRACTPerR is a ferric uptake repressor (Fur) homolog that functions as the central regulator of the inducible peroxide stress response inBacillus subtilis. PerR has been previously demonstrated to regulate themrgA,katA,ahpCF,hemAXCDBL, andzosAgenes. We now demonstrate that PerR also mediates both the repression of its own gene and that offur. Whereas PerR-mediated repression of most target genes can be elicited by either manganese or iron, repression ofperRandfuris selective for manganese. Genetic studies indicate that repression of PerR regulon genes by either manganese or iron requires PerR and is generally independent of Fur. Indeed, in afurmutant, iron-mediated repression is enhanced. Unexpectedly, repression of thefurgene by manganese appears to require both PerR and Fur, but only PerR binds to thefurregulatory region in vitro. Thefurmutation appears to act indirectly by affecting cellular metal ion pools and thereby affecting PerR-mediated repression. While many components of theperRregulon are strongly induced by hydrogen peroxide, little, if any, induction offurandperRcould be demonstrated. Thus, not all components of the PerR regulon are components of the peroxide stimulon. We suggest that PerR exists in distinct metallated forms that differ in DNA target selectivity and in sensitivity to oxidation. This model is supported by the observation that the metal ion composition of the growth medium can greatly influence the transcriptional response of the various PerR regulon genes to hydrogen peroxide.
Catabolite Repression of
Escherichia coli
Biofilm Formation
Authors: Jackson Debra W. , Simecka Jerry W. , Romeo Tony 
Published: July 2002

ABSTRACT

Biofilm formation was repressed by glucose in several species of
Enterobacteriaceae
. In
Escherichia coli
, this effect was mediated at least in part by cyclic AMP (cAMP)-cAMP receptor protein. A temporal role for cAMP in biofilm development was indicated by the finding that glucose addition after ∼24 h failed to repress and generally activated biofilm formation.
ccfA
, the Genetic Determinant for the cCF10 Peptide Pheromone in
Enterococcus faecalis
OG1RF
Authors: Antiporta Michelle H. , Dunny Gary M. 
Published: July 2002

ABSTRACT

The nosocomial pathogen
Enterococcus faecalis
has a unique pheromone-inducible conjugative mating system. Conjugative transfer of the
E. faecalis
plasmid pCF10 is specifically induced by the cCF10 peptide pheromone (LVTLVFV). Genomic sequence information has recently allowed the identification of putative structural genes coding for the various enterococcal pheromones (D. B. Clewell et al., Mol. Microbiol. 35:246-247, 2000). The cCF10 pheromone sequence LVTLVFV was found within an open reading frame designated
ccfA
, encoding a putative lipoprotein precursor. Several other pheromone sequences were found in similar locations within other predicted lipoproteins. CcfA shows significant sequence relatedness to the
Escherichia coli
protein YidC, an inner membrane protein translocase, as well as to a large number of homologs identified in gram-positive and in gram-negative bacteria. Analysis of the deduced CcfA amino acid sequence suggested that mature cCF10 peptide could be formed from the proteolytic degradation of its signal peptide. Expression of the cloned
ccfA
gene with an inducible expression vector dramatically increased cCF10 production by
E. faecalis
and also resulted in cCF10 production by
Lactococcus lactis
, a non-pheromone producer. Site-directed mutagenesis of the
ccfA
sequence encoding the cCF10 peptide confirmed that
ccfA
was a functional genetic determinant for cCF10.
Demonstration that
fbiC
Is Required by
Mycobacterium bovis
BCG for Coenzyme F
420
and FO Biosynthesis
Authors: Choi Kwang-Pil , Kendrick Nathan , Daniels Lacy 
Published: July 2002

ABSTRACT

Using the nitroimidazopyran-based antituberculosis drug PA-824 as a selective agent, transposon-generated
Mycobacterium bovis
strain BCG (
M. bovis
) mutants that could not make coenzyme F
420
were identified. Four independent mutants that could not make F
420
or the biosynthesis intermediate FO were examined more closely. These mutants contained transposons inserted in the
M. bovis
homologue of the
Mycobacterium tuberculosis
gene Rv1173, which we have named
fbiC
. Complementation of an
M. bovis
FbiC
−
mutant with
fbiC
restored the F
420
phenotype. These data demonstrate that
fbiC
is essential for F
420
production and that FbiC participates in a portion of the F
420
biosynthetic pathway between pyrimidinedione and FO. Homologues of
fbiC
were found in all 11 microorganisms that have been fully sequenced and that are known to make F
420
. Four of these homologues (all from members of the aerobic actinomycetes) coded for proteins homologous over the entire length of the
M. bovis
FbiC, but in seven microorganisms two separate genes were found to code for proteins homologous with either the N-terminal or C-terminal portions of the
M. bovis
FbiC. Histidine-tagged FbiC overexpressed in
Escherichia coli
produced a fusion protein of the molecular mass predicted from the
M. bovis
BCG sequence (∼95,000 Da), as well as three other histidine-tagged proteins of significantly smaller size, which are thought to be proteolysis products of the FbiC fusion protein.
Identification of an Akinete Marker Gene in
Anabaena variabilis
Authors: Zhou Ruanbao , Wolk C. Peter 
Published: July 2002

ABSTRACT
Cyanobacteria that form akinetes as well as heterocysts present a rare opportunity to investigate the relationships between alternative differentiation processes and pattern formation processes in a single bacterium. Because no akinete marker gene has been identified, akinete formation has been little studied genetically. We report the first identification of an akinete marker gene.
Multilocus Sequence Typing System for
Campylobacter jejuni
Authors: Dingle K. E. , Colles F. M. , Wareing D. R. A. , Ure R. , Fox A. J. , Bolton F. E. , Bootsma H. J. , Willems R. J. L. , Urwin R. , Maiden M. C. J. 
Published: July 2002

ABSTRACT

The gram-negative bacterium
Campylobacter jejuni
has extensive reservoirs in livestock and the environment and is a frequent cause of gastroenteritis in humans. To date, the lack of (i) methods suitable for population genetic analysis and (ii) a universally accepted nomenclature has hindered studies of the epidemiology and population biology of this organism. Here, a multilocus sequence typing (MLST) system for this organism is described, which exploits the genetic variation present in seven housekeeping loci to determine the genetic relationships among isolates. The MLST system was established using 194
C. jejuni
isolates of diverse origins, from humans, animals, and the environment. The allelic profiles, or sequence types (STs), of these isolates were deposited on the Internet (
http://mlst.zoo.ox.ac.uk
), forming a virtual isolate collection which could be continually expanded. These data indicated that
C. jejuni
is genetically diverse, with a weakly clonal population structure, and that intra- and interspecies horizontal genetic exchange was common. Of the 155 STs observed, 51 (26% of the isolate collection) were unique, with the remainder of the collection being categorized into 11 lineages or clonal complexes of related STs with between 2 and 56 members. In some cases membership in a given lineage or ST correlated with the possession of a particular Penner HS serotype. Application of this approach to further isolate collections will enable an integrated global picture of
C. jejuni
epidemiology to be established and will permit more detailed studies of the population genetics of this organism.
Epidemiology and Infection Control Implications of
Acinetobacter
spp. in Hong Kong
Authors: Houang Elizabeth T. S. , Chu Y. W. , Leung C. M. , Chu K. Y. , Berlau J. , Ng K. C. , Cheng A. F. B. 
Published: July 2002

ABSTRACT

In a previous study, we showed that
Acinetobacter
genomic DNA group 3 was the most common species among blood culture isolates and was commonly found on superficial carriage sites of the healthy and the sick, which are different findings from those reported in Europe and North America. We used amplified ribosomal DNA restriction analysis and pulsed-field gel electrophoresis to study further the molecular epidemiology of acinetobacters in our region. Over a study period of 6 weeks with 136 consecutive routine clinical isolates (1.33% of all specimens), genomic DNA groups 2 (
Acinetobacter baumannii
), 3, and 13TU were obtained from 59 of 69 positive patients. There is a significant difference in the specimen sources of the three genomic DNA groups, with group 13TU being significantly associated with the respiratory tract (chi-square exact test,
P
= 0.0064). Settle plates showed a significantly heavier environmental load from the intensive care unit (ICU) than from the four surgical wards examined (22 of 70 versus 76 of 120 plates with <5 colonies; chi-square test,
P <
0.0001). Genomic group 3 accounted for 6 of 12 clusters of possibly related strains among patients, between patients and the ICU environment, and in the ICU environment. Genomic groups 2 and 3 accounted for 21% of the 132 genomically identified isolates recovered from 21 of 41 local vegetables, 53 of 74 fish and meat samples, and 22 of 60 soil samples. Group 13TU was present only in patients' immediate surroundings. The role played by the environment and by human carriage should be evaluated in order to devise a cost-effective infection control program pertinent to our situation of acinetobacter endemicity.
Evaluation of the Triage Micro Parasite Panel for Detection of
Giardia lamblia
,
Entamoeba histolytica/Entamoeba dispar
, and
Cryptosporidium parvum
in Patient Stool Specimens
Authors: Sharp Susan E. , Suarez Clarisa A. , Duran Yolanda , Poppiti Robert J. 
Published: July 2002

ABSTRACT

A study comparing the Triage Micro Parasite Panel (Biosite Diagnostics, Inc., San Diego, Calif.) to conventional O&P examination (O&P) was performed using patient fecal specimens. Five hundred twenty-three stool samples were compared. Nineteen specimens were found to be positive by Triage, and 29 were found to be positive by O&P. Seven specimens were positive for
Giardia lamblia
, four were positive for
Entamoeba histolytica/E. dispar
, and three were positive for
Cryptosporidium parvum
as determined by both methods. There was one false positive by Triage (
C. parvum
) and four false negatives by O&P (two
G. lamblia
, one
E. histolytica/E. dispar
, and one
C. parvum
). The Triage test accurately detected all 18 specimens that contained one of the three organisms that it was designed to detect. The Triage test is a rapid, easy-to-use enzyme immunoassay for the detection of
G. lamblia
,
E. histolytica/E. dispar
, and
C. parvum
in fresh or fresh-frozen fecal specimens. These data suggest that the Triage test can be used as a screen for the immediate testing of stool specimens for these three pathogenic parasites. If Triage test results are negative, O&P can be performed if parasitic infections other than
G. lamblia
,
E. histolytica/E. dispar
, or
C. parvum
are suspected.
Automated High-Throughput Genotyping for Study of Global Epidemiology of
Mycobacterium tuberculosis
Based on Mycobacterial Interspersed Repetitive Units
Authors: Supply Philip , Lesjean Sarah , Savine Evgueni , Kremer Kristin , van Soolingen Dick , Locht Camille 
Published: July 2002

ABSTRACT

Large-scale genotyping of
Mycobacterium tuberculosis
is especially challenging, as the current typing methods are labor-intensive and the results are difficult to compare among laboratories. Here, automated typing based on variable-number tandem repeats (VNTRs) of genetic elements named mycobacterial interspersed repetitive units (MIRUs) in 12 mammalian minisatellite-like loci of
M. tuberculosis
is presented. This system combines analysis of multiplex PCRs on a fluorescence-based DNA analyzer with computerized automation of the genotyping. Analysis of a blinded reference set of 90 strains from 38 countries (K. Kremer et al., J. Clin. Microbiol. 37:2607–2618, 1999) demonstrated that it is 100% reproducible, sensitive, and specific for
M. tuberculosis
complex isolates, a performance that has not been achieved by any other typing method tested in the same conditions. MIRU-VNTRs can be used for analysis of the global genetic diversity of
M. tuberculosis
complex strains at different levels of evolutionary divergence. To fully exploit the portability of this typing system, a website was set up for the analysis of
M. tuberculosis
MIRU-VNTR genotypes via the Internet. This opens the way for global epidemiological surveillance of tuberculosis and should lead to novel insights into the evolutionary and population genetics of this major pathogen.
PCR Fingerprinting of
Candida albicans
Associated with Chronic Hyperplastic Candidosis and Other Oral Conditions
Authors: Bartie Kerry L. , Williams David W. , Wilson Melanie J. , Potts A. John C. , Lewis Michael A. O. 
Published: July 2002

ABSTRACT

The purpose of this study was to genotype strains of
Candida albicans
to determine whether specific types were associated with chronic hyperplastic candidosis (CHC). A total of 67 candidal isolates from CHC patients (
n
= 17) and from patients with other oral conditions (
n
= 21) were genotyped by PCR fingerprinting employing two interrepeat primer combinations (1245 and 1246 primers or 1251 primer) and a single minisatellite-specific M13 primer. The most suitable primer for fingerprint analysis was found to be primer 1251, yielding well-resolved banding patterns. For the 67 isolates tested, PCR fingerprinting delineated 25 (1245 and 1246 primers), 27 (1251 primer), and 25 (M13 primer) profiles. The majority of
C. albicans
isolates from multiple sites within the mouth produced identical profiles (six out of nine subjects examined). For patients for whom a series of longitudinal isolates was available, strain persistence for up to 7 years was evident for five out of eight individuals, despite episodes of antifungal therapy. Computer-assisted comparison of the interrepeat PCR fingerprints identified seven distinct profiles that were shared among isolates from different individuals. However, no association was evident among isolates of
C. albicans
from specific clinical conditions. Eight isolates that were initially identified as
C. albicans
but having atypical PCR profiles were later confirmed as
Candida dubliniensis
. In conclusion, the genotypic data do not indicate clonal restriction of
C. albicans
with respect to CHC. Furthermore, these results have demonstrated that in the majority of individuals, colonizing populations of
C. albicans
are clonal in nature and exhibit strain persistence.
Human Babesiosis in Japan: Epizootiologic Survey of Rodent Reservoir and Isolation of New Type of
Babesia microti
-Like Parasite
Authors: Tsuji Masayoshi , Wei Qiang , Zamoto Aya , Morita Chiharu , Arai Satoru , Shiota Tsunezo , Fujimagari Masato , Itagaki Asao , Fujita Hiromi , Ishihara Chiaki 
Published: July 2002

ABSTRACT

We have carried out epizootiologic surveys at various sites in Japan to investigate wild animals that serve as reservoirs for the agents of human babesiosis in the country. Small mammals comprising six species,
Apodemus speciosus
,
Apodemus argenteus
,
Clethrionomys rufocanus
,
Eothenomys smithii
,
Crocidura dsinezumi
, and
Sorex unguiculatus
, were trapped at various places, including Hokkaido, Chiba, Shiga, Hyogo, Shimane, and Tokushima Prefectures. Animals harboring
Babesia microti
-like parasites were detected in all six prefectures. Inoculation of their blood samples into hamsters gave rise to a total of 20 parasite isolates; 19 were from
A. speciosus
, and the other 1 was from
C. rufocanus
. Sequencing of the parasite small-subunit rRNA gene (rDNA) sequence revealed that 2 of the 20 isolates were classified as Kobe type because their rDNAs were identical to that of the Kobe strain (the strain from the Japanese index case). The other 18 isolates were classified as a new type, designated the Hobetsu type, because they all shared an identical rDNA sequence which differed significantly from both that of Kobe-type isolates and that of northeastern United States
B. microti
(U.S. type). The parasites with Kobe-, Hobetsu- and U.S.-type rDNAs were phylogenetically closely related to each other but clearly different from each other antigenically. The isolates from rodents were demonstrated to be infective for human erythrocytes by inoculation into SCID mice whose erythrocytes had been replaced with human erythrocytes. The results suggest that a new type of
B. microti
-like parasite, namely, the Hobetsu type, is the major one which is prevalent among Japanese wild rodents, that
A. speciosus
serves as a major reservoir for both Kobe- and Hobetsu-type
B. microti
-like parasites, and that
C. rufocanus
may also be an additional reservoir on Hokkaido Island.
European Proficiency Testing Program for Molecular Detection and Quantitation of Hepatitis B Virus DNA
Authors: Valentine-Thon Elizabeth , van Loon Anton M. , Schirm Jurjen , Reid Jim , Klapper Paul E. , Cleator Graham M. 
Published: July 2002

ABSTRACT

External quality control of hepatitis B virus (HBV) DNA detection remains an important issue. This study reports and compares the results obtained from two different proficiency panels for both the qualitative and quantitative assessment of HBV DNA. The panels were designed by the European Union Quality Control Concerted Action, prepared by Boston Biomedica, Inc., and distributed in May 1999 (panel 1) and February 2000 (panel 2). Each contained two negative samples and six positive samples with 10
3
to 10
7
copies/ml (panel 1) or 10
3
to 2 × 10
6
copies of HBV DNA per ml (panel 2). For panel 1, 42 laboratories submitted 20 qualitative (all in-house PCRs) and 37 quantitative (87% commercial assays) data sets. For panel 2, 51 laboratories submitted 25 qualitative (all in-house PCRs) and 47 quantitative (94% commercial assays) data sets. Five data sets (8.8%) in panel 1 and two data sets (2.8%) in panel 2 contained totals of six and two false-positives, respectively, corresponding to false-positive result rates of 5.3% for panel 1 and 1.4% for panel 2. The false-negative result rates of 10.5% for panel 1 and 17.4% for panel 2 were dependent on the detection levels of the assays employed as well as panel composition. In the qualitative analysis of all data sets, 47.4% (panel 1) and 51.4% (panel 2) had all samples correct. An adequate or better score (all correct or only the weak-positive sample missed) was obtained with 77.2% of the panel 1 samples and 68.1% of the panel 2 samples. In the quantitative analysis, 57.1% (panel 1) and 42.6% (panel 2) of the data sets achieved an adequate or better score (positive results within the acceptable range of the geometric mean ± 0.5 log
10
of all positive results). These results demonstrate that while the qualitative performance of HBV detection has considerably improved compared to that of a previously published HBV proficiency study, the detection levels of many commercial quantitative assays are still too high to allow adequate quantitation of all relevant clinical samples.
PCR-Based Diagnosis of
Helicobacter pylori
Infection and Real-Time Determination of Clarithromycin Resistance Directly from Human Gastric Biopsy Samples
Authors: Chisholm Stephanie A. , Owen Robert J. , Teare E. Louise , Saverymuttu Seth 
Published: July 2002

ABSTRACT

A novel PCR detection assay that amplifies the
Helicobacter pylori
-specific vacuolating cytotoxin gene (
vacA
) and thus enables rapid diagnosis of infection is described. Additionally, a real-time probe hybridization melting point analysis assay to detect all three mutations in the 23S rRNA gene associated with clarithromycin resistance was applied directly to antral gastric biopsy samples. Comparison with culture and an alternative PCR assay targeting the 16S
rrn
gene showed that the
vacA
assay was sensitive and specific when tested on biopsy samples from 121 patients. Clarithromycin susceptibilities could be determined in the majority (92.3%) of culture-positive gastric biopsy samples analyzed, four of which generated melting peaks indicative of clarithromycin resistance by either an A→G or A→C mutation. The presence of the mutations correlated with the clarithromycin disk diffusion sensitivities of matched cultures. This PCR-based system was simple to perform and could be completed in 3 to 4 h, thereby overcoming the delays associated with conventional culture methods for
H. pylori
identification and susceptibility testing.
Evaluation of PCR Methods for Rapid Identification and Differentiation of
Streptococcus uberis
and
Streptococcus parauberis
Authors: Hassan A. A. , Khan I. U. , Abdulmawjood A. , Lämmler C. 
Published: July 2002

ABSTRACT

Streptococcus uberis
and
Streptococcus parauberis
reference strains and isolates obtained from routine diagnostics were investigated by PCR with oligonucleotide primers designed according to species-specific parts of the 16S rRNA gene, the 23S rRNA gene, and the 16S-23S rRNA intergenic spacer region of both species. All three primer pairs allowed an identification of 67 isolates as
S. uberis
and 4 isolates as
S. parauberis
.
Characterization of AfaE Adhesins Produced by Extraintestinal and Intestinal Human
Escherichia coli
Isolates: PCR Assays for Detection of Afa Adhesins That Do or Do Not Recognize Dr Blood Group Antigens
Authors: Le Bouguénec Chantal , Lalioui Lila , du Merle Laurence , Jouve Mabel , Courcoux Pascale , Bouzari Saeid , Selvarangan Rangaraj , Nowicki Bogdan J. , Germani Yves , Andremont Antoine , Gounon Pierre , Garcia Marie-Isabelle 
Published: July 2002

ABSTRACT

Operons of the
afa
family are expressed by pathogenic
Escherichia coli
strains associated with intestinal and extraintestinal infections in humans and animals. The recently demonstrated heterogeneity of these operons (L. Lalioui, M. Jouve, P. Gounon, and C. Le Bouguénec, Infect. Immun. 67:5048–5059, 1999) was used to develop a new PCR assay for detecting all the operons of the
afa
family with a single genetic tool. This PCR approach was validated by investigating three collections of human
E. coli
isolates originating from the stools of infants with diarrhea (88 strains), the urine of patients with pyelonephritis (97 strains), and the blood of cancer patients (115 strains). The results obtained with this single test and those previously obtained with several PCR assays were closely correlated. The AfaE adhesins encoded by the
afa
operons are variable, particularly with respect to the primary sequence encoded by the
afaE
gene. The receptor binding specificities have not been determined for all of these adhesins; some recognize the Dr blood group antigen (Afa/Dr
+
adhesins) on the human decay-accelerating factor (DAF) as a receptor, and others (Afa/Dr
−
adhesins) do not. Thus, the
afa
operons detected in this study were characterized by subtyping the
afaE
gene using specific PCRs. In addition, the DAF-binding capacities of as-yet-uncharacterized AfaE adhesins were tested by various cellular approaches. The
afaE8
subtype (Afa/Dr
−
adhesin) was found to predominate in
afa
-positive isolates from sepsis patients (75%); it was frequent in
afa
-positive pyelonephritis
E. coli
(55.5%) and absent from diarrhea-associated strains. In contrast, Afa/Dr
+
strains (regardless of the
afaE
subtype) were associated with both diarrhea (100%) and extraintestinal infections (44 and 25% in
afa
-positive pyelonephritis and sepsis strains, respectively). These data suggest that there is an association between the subtype of AfaE adhesin and the physiological site of the infection caused by
afa
-positive strains.