bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two Different Lantibiotic-Like Peptides Originate from the Ericin Gene Cluster of
Bacillus subtilis
A1/3
Authors: Stein Torsten , Borchert Stefan , Conrad Birgit , Feesche Jörg , Hofemeister Brigitte , Hofemeister Jürgen , Entian Karl-Dieter 
Published: July 2002

ABSTRACT

A lantibiotic gene cluster was identified in
Bacillus subtilis
A1/3 showing a high degree of homology to the subtilin gene cluster and occupying the same genetic locus as the
spa
genes in
B. subtilis
ATCC 6633. The gene cluster exhibits diversity with respect to duplication of two subtilin-like genes which are separated by a sequence similar to a portion of a
lanC
gene. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analyses of
B. subtilis
A1/3 culture extracts confirmed the presence of two lantibiotic-like peptides, ericin S (3,442 Da) and ericin A (2,986 Da). Disruption of the
lanB
-homologous gene
eriB
resulted in loss of production of both peptides, demonstrating that they are processed in an
eriB
-dependent manner. Although precursors of ericins S and A show only 75% of identity, the matured lantibiotic-like peptides reveal highly similar physical properties; separation was only achieved after multistep, reversed-phase high-performance liquid chromatography. Based on Edman and peptidase degradation in combination with MALDI-TOF MS, for ericin S a subtilin-like, lanthionine-bridging pattern is supposed. For ericin A two C-terminal rings are different from the lanthionine pattern of subtilin. Due to only four amino acid exchanges, ericin S and subtilin revealed similar antibiotic activities as well as similar properties in response to heat and protease treatment. For ericin A only minor antibiotic activity was found.
Malonyl-Coenzyme A Reductase from
Chloroflexus aurantiacus
, a Key Enzyme of the 3-Hydroxypropionate Cycle for Autotrophic CO
2
Fixation
Authors: Hügler Michael , Menendez Castor , Schägger Hermann , Fuchs Georg 
Published: July 2002

ABSTRACT

The 3-hydroxypropionate cycle is a new autotrophic CO
2
fixation pathway in
Chloroflexus aurantiacus
and some archaebacteria. The initial step is acetyl-coenzyme A (CoA) carboxylation to malonyl-CoA by acetyl-CoA carboxylase, followed by NADPH-dependent reduction of malonyl-CoA to 3-hydroxypropionate. This reduction step was studied in
Chloroflexus aurantiacus
. A new enzyme was purified, malonyl-CoA reductase, which catalyzed the two-step reduction malonyl-CoA + NADPH + H
+
→ malonate semialdehyde + NADP
+
+ CoA and malonate semialdehyde + NADPH + H
+
→ 3-hydroxypropionate + NADP
+
. The bifunctional enzyme (aldehyde dehydrogenase and alcohol dehydrogenase) had a native molecular mass of 300 kDa and consisted of a single large subunit of 145 kDa, suggesting an α
2
composition. The N-terminal amino acid sequence was determined, and the incomplete gene was identified in the genome database. Obviously, the enzyme consists of an N-terminal short-chain alcohol dehydrogenase domain and a C-terminal aldehyde dehydrogenase domain. No indication of the presence of a prosthetic group was obtained; Mg
2+
and Fe
2+
stimulated and EDTA inhibited activity. The enzyme was highly specific for its substrates, with apparent

K
m

values of 30 μM malonyl-CoA and 25 μM NADPH and a turnover number of 25 s
−1
subunit
−1
. The specific activity in autotrophically grown cells was 0.08 μmol of malonyl-CoA reduced min
−1
(mg of protein)
−1
, compared to 0.03 μmol min
−1
(mg of protein)
−1
in heterotrophically grown cells, indicating downregulation under heterotrophic conditions. Malonyl-CoA reductase is not required in any other known pathway and therefore can be taken as a characteristic enzyme of the 3-hydroxypropionate cycle. Furthermore, the enzyme may be useful for production of 3-hydroxypropionate and for a coupled spectrophotometric assay for activity screening of acetyl-CoA carboxylase, a target enzyme of potent herbicides.
The Superoxide Dismutase Gene
sodM
Is Unique to
Staphylococcus aureus
: Absence of
sodM
in Coagulase-Negative Staphylococci
Authors: Valderas Michelle Wright , Gatson Joshua W. , Wreyford Natalie , Hart Mark E. 
Published: July 2002

ABSTRACT

Superoxide dismutase (SOD) profiles of clinical isolates of
Staphylococcus aureus
and coagulase-negative staphylococci (CoNS) were determined by using whole-cell lysates and activity gels. All
S. aureus
clinical isolates exhibited three closely migrating bands of activity as previously determined for laboratory strains of
S. aureus
: SodM, SodA, and a hybrid composed of SodM and SodA (M. W. Valderas and M. E. Hart, J. Bacteriol. 183:3399-3407, 2001). In contrast, the CoNS produced only one SOD activity, which migrated similarly to SodA of
S. aureus
. Southern analysis of eight CoNS species identified only a single
sod
gene in each case. A full-length
sod
gene was cloned from
Staphylococcus epidermidis
and determined to be more similar to
sodA
than to
sodM
of
S. aureus
. Therefore, this gene was designated
sodA
. The deduced amino acid sequence of the
S. epidermidis sodA
was 92 and 76% identical to that of the SodA and SodM proteins of
S. aureus
, respectively. The
S. epidermidis sodA
gene expressed from a plasmid complemented a
sodA
mutation in
S. aureus
, and the protein formed a hybrid with SodM of
S. aureus
. Both hybrid SOD forms as well as the SodM and SodA proteins of
S. aureus
and the
S. epidermidis
SodA protein exist as dimers. These data indicate that
sodM
is found only in
S. aureus
and not in the CoNS, suggesting an important divergence in the evolution of this genus and a unique role for SodM in
S. aureus
.
Identification of Epidemic Strains of
Acinetobacter baumannii
by Integrase Gene PCR
Authors: Koeleman Johannes G. M. , Stoof Jeroen , Van Der Bijl Madelon W. , Vandenbroucke-Grauls Christina M. J. E. , Savelkoul Paul H. M. 
Published: July 2002

ABSTRACT

Forty-eight clinical
Acinetobacter
isolates with different epidemic behavior were investigated for the presence of integrons and plasmids and for antibiotic susceptibility. Integrons were demonstrated in 50% of the strains by an integrase gene PCR. Epidemic strains of
Acinetobacter baumannii
were found to contain significantly more integrons than nonepidemic strains. Also, the presence of integrons was significantly correlated with simultaneous resistance to several antibiotics. Plasmids were detected in 42% of the strains. However, there was no significant correlation between the numbers of plasmids and integrons in
Acinetobacter
species strains, no significant difference in the number of plasmids between epidemic and nonepidemic
A. baumannii
strains, and no significant correlation between the presence of plasmids and antibiotic resistance. Hence, it is likely that integrons play an important role in antibiotic resistance and thereby in the epidemic behavior of
A. baumannii
. Because the integrase gene PCR identified almost three-quarters of the epidemic
A. baumannii
isolates (17 of 23), this seems to be a rapid and simple technique for the routine screening and identification of clinical
A. baumannii
isolates with epidemic potential.
Relative Accuracy of Nucleic Acid Amplification Tests and Culture in Detecting
Chlamydia
in Asymptomatic Men
Authors: Cheng Hong , Macaluso Maurizio , Vermund Sten H. , Hook Edward W. 
Published: July 2002

ABSTRACT

Published estimates of the sensitivity and specificity of PCR and ligase chain reaction (LCR) for detecting
Chlamydia trachomatis
are potentially biased because of study design limitations (confirmation of test results was limited to subjects who were PCR or LCR positive but culture negative). Relative measures of test accuracy are less prone to bias in incomplete study designs. We estimated the relative sensitivity (
RSN
) and relative false-positive rate (
RFP
) for PCR and LCR versus cell culture among 1,138 asymptomatic men and evaluated the potential bias of
RSN
and
RFP
estimates. PCR and LCR testing in urine were compared to culture of urethral specimens. Discordant results (PCR or LCR positive, but culture negative) were confirmed by using a sequence including the other DNA amplification test, direct fluorescent antibody testing, and a DNA amplification test to detect chlamydial major outer membrane protein. The RSN estimates for PCR and LCR were 1.45 (95% confidence interval [CI] = 1.3 to 1.7) and 1.49 (95% CI = 1.3 to 1.7), respectively, indicating that both methods are more sensitive than culture. Very few false-positive results were found, indicating that the specificity levels of PCR, LCR, and culture are high. The potential bias in RSN and RFP estimates were <5 and <20%, respectively. The estimation of bias is based on the most likely and probably conservative parameter settings. If the sensitivity of culture is between 60 and 65%, then the true sensitivity of PCR and LCR is between 90 and 97%. Our findings indicate that PCR and LCR are significantly more sensitive than culture, while the three tests have similar specificities.
DNA Relatedness, Phenotypic Characteristics, and Antimicrobial Susceptibilities of
Globicatella sanguinis
Strains
Authors: Shewmaker P. Lynn , Steigerwalt Arnold G. , Shealey LaShondra , Weyant Robbin , Facklam Richard R. 
Published: July 2002

ABSTRACT

DNA-DNA reassociation was performed on 15 strains of
Globicatella sanguinis
to compare their taxonomic status with phenotypic characterization. All 15 strains selected for DNA-DNA reassociation readily met the criteria for species relatedness. The relative binding ratio was 81% or greater at the optimal temperature and 76% or greater at the stringent temperature, and the divergence was less than 3% for all strains hybridized with the type strain. These strains included nine strains from the Centers for Disease Control Streptococcus Laboratory culture collection that were previously included in comparative 16S rRNA gene sequencing studies as well as six additional phenotypically variant isolates. DNA-DNA relatedness was less than 18% at the optimal reassociation temperature to
Aerococcus viridans, Enterococcus avium
, and
Streptococcus uberis
, which are phenotypically similar to
G. sanguinis
. This study confirms these
Globicatella
strains were previously misidentified as
S. uberis
or
S. uberis
-like strains based on biochemical characteristics. The biochemical data from 28 strains was compiled to further define the phenotypic criteria for identification of this species. A revised description of the species should be variable reaction for pyrrolidonylarylamidase production (75% positive), positive reaction for the bile esculin test (100%), growth at 45°C (96%), variable reaction for acid production from arabinose (45% positive), and negative starch hydrolysis (0% positive). We also evaluated four rapid identification systems, the Biomerieux rapid ID32 STREP (ID32), the Crystal rapid gram-positive identification (Cry4), the BBL Crystal gram-positive identification (Cry24), and the Remel IDS RapID STR (IDS) systems for their ability to identify these strains.
Nucleic Acid Sequence-Based Amplification Assays for Rapid Detection of West Nile and St. Louis Encephalitis Viruses
Authors: Lanciotti Robert S. , Kerst Amy J. 
Published: July 2002

ABSTRACT
The development and application of nucleic acid sequence-based amplification (NASBA) assays for the detection of West Nile (WN) and St. Louis encephalitis (SLE) viruses are reported. Two unique detection formats were developed for the NASBA assays: a postamplification detection step with a virus-specific internal capture probe and electrochemiluminescence (NASBA-ECL assay) and a real-time assay with 6-carboxyfluorescein-labeled virus-specific molecular beacon probes (NASBA-beacon assay). The sensitivities and specificities of these NASBA assays were compared to those of a newly described standard reverse transcription (RT)-PCR and TaqMan assays for SLE virus and to a previously published TaqMan assay for WN virus. The NASBA assays demonstrated exceptional sensitivities and specificities compared to those of virus isolation, the TaqMan assays, and standard RT-PCR, with the NASBA-beacon assay yielding results in less than 1 h. These assays should be of utility in the diagnostic laboratory to complement existing diagnostic testing methodologies and as a tool in conducting flavivirus surveillance in the United States.
Evaluation of Two Enzyme Immunoassays for Detection of Human Rotaviruses in Fecal Specimens
Authors: Eing Bodo R. , May Guenter , Baumeister Horst G. , Kühn Joachim E. 
Published: July 2002

ABSTRACT
The two assays evaluated in this study (the Ridascreen rotavirus and the Pathfinder rotavirus) exhibited comparable sensitivities (100%) but highly divergent positive predictive values (93.74 and 57.7%, respectively) when compared on 393 specimens. This difference should be considered when using these tests on collectives with an unknown or low prevalence.
Association of the Urease Gene with Enterohemorrhagic
Escherichia coli
Strains Irrespective of Their Serogroups
Authors: Nakano Masayuki , Iida Tetsuya , Ohnishi Makoto , Kurokawa Ken , Takahashi Akira , Tsukamoto Teizo , Yasunaga Teruo , Hayashi Tetsuya , Honda Takeshi 
Published: July 2002

ABSTRACT

Among various diarrheagenic
Escherichia coli
strains from clinical sources, we found that the urease gene was specifically associated with enterohemorrhagic
E. coli
(EHEC) strains irrespective of their serogroups. The results suggest that the urease gene can be a useful genetic marker for the detection of EHEC strains and for the diagnosis of infections caused by EHEC strains in the clinical situation.
A Shared Noncapsular Antigen Is Responsible for False-Positive Reactions by
Staphylococcus epidermidis
in Commercial Agglutination Tests for
Staphylococcus aureus
Authors: Blake Janet E. , Metcalfe Mark A. 
Published: July 2002

ABSTRACT

Many of the commercial slide agglutination tests for
Staphylococcus aureus
incorporate antibodies against cell surface antigens associated with methicillin resistance, including capsular polysaccharides and an uncharacterized antigen, serotype 18. These tests are more sensitive than the first-generation agglutination procedures that detected only bound coagulase and protein A, but they suffer from false-positive reactions with some coagulase-negative staphylococci. The aim of this study was to elucidate the mechanism for false-positive agglutination by
S. epidermidis
in these tests. A group of methicillin-resistant
S. aureus
(MRSA) isolates, including a serotype 18 strain, that were not detectable in the first-generation tests were found to be of capsular polysaccharide type 8. All of these isolates were deficient in bound coagulase and/or protein A, and they possessed a heat-stable, proteinaceous antigen that was absent from a prototype capsule type 8 strain. Enzyme-linked immunosorbent assay and agarose gel immunodiffusion experiments demonstrated that this proteinaceous antigen was also present on both methicillin-sensitive and methicillin-resistant
S. epidermidis
clinical isolates.
S. epidermidis
strains that gave false-positive agglutination test results had a considerably higher level of this antigen than strains that gave the correct negative result. These findings reveal the importance of the careful selection of MRSA strains for raising anti-capsular type 8 antibodies for use in agglutination tests. Strains devoid of the antigen shared with
S. epidermidis
should be used to eliminate potential cross-reactions with this coagulase-negative coccus.
Direct Identification of
Mycobacterium avium
Complex and
Mycobacterium gordonae
from MB/BacT Bottles Using AccuProbe
Authors: Louro Ana Paula S. , Waites Ken B. , Georgescu Ecaterina , Benjamin William H. 
Published: July 2002

ABSTRACT

We evaluated the ability of the AccuProbe (Gen-Probe, San Diego, Calif.) to detect
Mycobacterium gordonae
and
Mycobacterium avium
complex directly in liquid medium flagged positive by the MB/BacT (Organon Teknika Corp., Durham, N.C.). Seventy-one bottles from clinical specimens containing
M. gordonae
and 34 containing
M. avium
, confirmed by culture, were tested by direct AccuProbe assay for both organisms after additional incubation for ≥48 h and centrifugation at 4,500 ×
g
for 15 min. Relative light unit (RLU) values were analyzed using the manufacturer's recommended cutoff of 30,000 RLU and a lower cutoff of 10,000 RLU. Using the 30,000 RLU cutoff, 55 of 71 (77.5%) specimens containing
M. gordonae
yielded positive results, whereas 28 of 34 (82.3%)
M. avium
complex specimens were correctly identified by direct probe. No specimens shown by culture to contain either
M. gordonae
or
M. avium
complex tested positive with the probe for the opposite organism (100% specificity). When the cutoff was lowered to 10,000 RLU, 67 of 71
M. gordonae
(94.4%) and 32 of 34
M. avium
complex (94.1%) specimens were correctly identified. This difference was significant for
M. gordonae
(
P
= 0.004) but not for
M. avium
complex (
P
= 0.26) compared to detection using the recommended RLU cutoff. Specificity was 100% for specimens containing
M. gordonae
that were tested with the
M. avium
complex probe using the 10,000 RLU cutoff, whereas specificity for specimens containing
M. avium
complex tested with the
M. gordonae
probe was 97%. Using a lower RLU cutoff for determining a positive result using the
M. gordonae
or
M. avium
complex probes when testing instrument-positive MB/BacT bottles directly will improve sensitivity without substantially compromising specificity.
Molecular Characterization of
fliD
Gene Encoding Flagellar Cap and Its Expression among
Clostridium difficile
Isolates from Different Serogroups
Authors: Tasteyre Albert , Karjalainen Tuomo , Avesani Véronique , Delmée Michel , Collignon Anne , Bourlioux Pierre , Barc Marie-Claude 
Published: July 2002

ABSTRACT

The
fliD
gene encoding the flagellar cap protein (FliD) of
Clostridium difficile
was studied in 46 isolates belonging to serogroups A, B, C, D, F, G, H, I, K, X, and S3, including 30 flagellated strains and 16 nonflagellated strains. In all but three isolates, amplification by PCR and reverse transcription-PCR demonstrated that the
fliD
gene is present and transcribed in both flagellated and nonflagellated strains. PCR-restriction fragment length polymorphism (RFLP) analysis of amplified
fliD
gene products revealed interstrain homogeneity, with one of two major patterns (a and b) found in all but one of the strains, which had pattern c. A polyclonal monospecific antiserum raised to the recombinant FliD protein reacted in immunoblots with crude flagellar preparations from 28 of 30 flagellated strains but did not recognize FliD from nonflagellated strains. The
fliD
genes from five strains representative of the three different RFLP groups were sequenced, and sequencing revealed 100% identity between the strains with the same pattern and 88% identity among strains with different patterns. Our results show that even though FliD is a structure exposed to the outer environment, the flagellar cap protein is very well conserved, and this high degree of conservation suggests that it has a very specific function in attachment to cell or mucus receptors.
Characterization of Lyme Borreliosis Isolates from Patients with Erythema Migrans and Neuroborreliosis in Southern Sweden
Authors: Ornstein Katharina , Berglund Johan , Nilsson Ingrid , Norrby Ragnar , Bergström Sven 
Published: July 2002

ABSTRACTSouthern Sweden is an area of Lyme borreliosis (LB) endemicity, with an incidence of 69 cases per 100,000 inhabitants. The most frequent clinical manifestations are erythema migrans (77%) and neuroborreliosis (16%). There was no record of humanBorreliastrains being isolated from patients in this region before the prospective study reported here.Borreliaspirochetes were isolated from skin and cerebrospinal fluid (CSF) from LB patients living in the region. A total of 39 strains were characterized by OspA serotype analysis, species-specific PCR, and signature nucleotide analysis of the 16S rRNA gene. Of 33 skin isolates, 31 (93.9%) wereBorrelia afzeliistrains and 2 (6.1%) wereBorrelia gariniistrains. Of six CSF isolates, five (83.3%) wereB. gariniiand one (16.7%) wasB. afzelii. NeitherBorrelia burgdorferisensu stricto strains nor multiple infections were observed. TheB. afzeliiisolates were of OspA serotype 2. ThreeB. gariniistrains were of OspA serotype 5, and the remaining four strains were of OspA serotype 6. All of theB. gariniistrains belonged to the same 16S ribosomal DNA ribotype class. Our findings agree with earlier findings from other geographic regions in Europe whereB. afzeliiandB. gariniihave been recovered predominately from skin and CSF cultures, respectively. To further study the possible presence in Sweden of the genotypeB. burgdorferisensu stricto, which is known to be present in Europe and to occur predominately in patients with Lyme arthritis, molecular detection ofBorrelia-specific DNA in synovial samples from Lyme arthritis patients should be performed.
New Tests for Syphilis: Rational Design of a PCR Method for Detection of
Treponema pallidum
in Clinical Specimens Using Unique Regions of the DNA Polymerase I Gene
Authors: Liu Hsi , Rodes Berta , Chen C.-Y. , Steiner Bret 
Published: July 2002

ABSTRACT

A sensitive and specific PCR method to detect
Treponema pallidum
in clinical specimens was developed. PCR primers were designed based on two unique features of the DNA polymerase I gene (
polA
). The first distinctive characteristic is that the region codes for a high cysteine content and has low homology with similar regions of DNA polymerase I gene from known microorganisms. The second unique feature is the presence of four insertions in the gene. PCR tests using primers designed on the basis these regions reacted with various pathogenic
T. pallidum
subspecies but did not react with nonpathogenic treponemal species or other spirochetes. An additional 59 species of bacteria and viruses, including those that cause genital ulcers, tested negative. This PCR method is extremely robust and sensitive. The detection limit is about 10 to 25 organisms when analyzed on gel. However, the analytic sensitivity can be increased by at least 1 log, to a detection limit of a single organism, when the ABI 310 Prism Genetic Analyzer is used to detect fluorescence-labeled amplicons. We further used this test in a clinical setting and compared the results with results from a previously reported multiplex-PCR test (for
T. pallidum, Haemophilus ducreyi
, and herpes simplex virus). We tested 112 genital ulcer specimens by the
polA
PCR, obtaining a sensitivity of 95.8% and a specificity of 95.7%. These results suggest that the
polA
PCR is applicable as a routine clinical diagnostic test for syphilis.