bluuebunny/crossref_metadata_2025_split huggingface dataset:
Caulobacter crescentus
Synthesizes an S-Layer-Editing Metalloprotease Possessing a Domain Sharing Sequence Similarity with Its Paracrystalline S-Layer Protein
Authors: Umelo-Njaka Elizabeth , Bingle Wade H. , Borchani Faten , Le Khai D. , Awram Peter , Blake Theo , Nomellini John F. , Smit John 
Published: July 2002

ABSTRACT

Strains of
Caulobacter crescentus
elaborate an S-layer, a two-dimensional protein latticework which covers the cell surface. The S-layer protein (RsaA) is secreted by a type I mechanism (relying on a C-terminal signal) and is unusual among type I secreted proteins because high levels of protein are produced continuously. In efforts to adapt the S-layer for display of foreign peptides and proteins, we noted a proteolytic activity that affected S-layer monomers with foreign inserts. The cleavage was precise, resulting in fragments with an unambiguous N-terminal sequence. We developed an assay to screen for loss of this activity (i.e., presentation of foreign peptides without degradation), using transposon and traditional mutagenesis. A metalloprotease gene designated
sap
(S-layer-associated protease) was identified which could complement the protease-negative mutants. The N-terminal half of Sap possessed significant similarity to other type I secreted proteases (e.g., alkaline protease of
Pseudomonas aeruginosa
), including the characteristic RTX repeat sequences, but the C-terminal half which normally includes the type I secretion signal exhibited no such similarity. Instead, there was a region of significant similarity to the N-terminal region of RsaA. We hypothesize that Sap evolved by combining the catalytic portion of a type I secreted protease with an S-layer-like protein, perhaps to associate with nascent S-layer monomers to “scan” for modifications.
Characterization of
Streptococcus suis
Genes Encoding Proteins Homologous to Sortase of Gram-Positive Bacteria
Authors: Osaki Makoto , Takamatsu Daisuke , Shimoji Yoshihiro , Sekizaki Tsutomu 
Published: July 2002

ABSTRACT

Many surface proteins which are covalently linked to the cell wall of gram-positive bacteria have a consensus C-terminal motif, Leu-Pro-X-Thr-Gly (LPXTG). This sequence is cleaved, and the processed protein is attached to an amino group of a cross-bridge in the peptideglycan by a specific enzyme called sortase. Using the type strain of
Streptococcus suis
, NCTC 10234, we found five genes encoding proteins that were homologous to sortases of other bacteria and determined the nucleotide sequences of the genetic regions. One gene, designated
srtA
, was linked to
gyrA
, as were the sortase and sortase-like genes of other streptococci. Three genes, designated
srtB
,
srtC
, and
srtD
, were tandemly clustered in a different location, where there were three segments of directly repeated sequences of approximately 110 bp in close vicinity. The remaining gene, designated
srtE
, was located separately on the chromosome with a pseudogene which may encode a transposase. The deduced amino acid sequences of the five Srt proteins showed 18 to 31% identity with the sortases of
Streptococcus gordonii
and
Staphylococcus aureus
, except that SrtA of
S. suis
had 65% identity with that of
S. gordonii
. Isogenic mutants deficient for
srtA
,
srtBCD
, or
srtE
were generated by allelic exchanges. The protein fraction which was released from partially purified cell walls by digestion with
N
-acetylmuramidase was profiled by two-dimensional gel electrophoresis. More than 15 of the protein spots were missing in the profile of the
srtA
mutant compared with that of the parent strain, and this phenotype was completely complemented by
srtA
cloned from
S. suis
. Four genes encoding proteins corresponding to such spots were identified and sequenced. The deduced translational products of the four genes possessed the LPXTG motif in their C-terminal regions. On the other hand, the protein spots that were missing in the
srtA
mutant appeared in the profiles of the
srtBCD
and
srtE
mutants. These results provide evidence that the cell wall sorting system involving
srtA
is also present in
S. suis
.
VanT, a Homologue of
Vibrio harveyi
LuxR, Regulates Serine, Metalloprotease, Pigment, and Biofilm Production in
Vibrio anguillarum
Authors: Croxatto Antony , Chalker Victoria J. , Lauritz Johan , Jass Jana , Hardman Andrea , Williams Paul , Cámara Miguel , Milton Debra L. 
Published: July 2002

ABSTRACT

Vibrio anguillarum
possesses at least two
N
-acylhomoserine lactone (AHL) quorum-sensing circuits, one of which is related to the
luxMN
system of
Vibrio harveyi
. In this study, we have cloned an additional gene of this circuit,
vanT
, encoding a
V. harveyi
LuxR-like transcriptional regulator. A
V. anguillarum ΔvanT
null mutation resulted in a significant decrease in total protease activity due to loss of expression of the metalloprotease EmpA, but no changes in either AHL production or virulence. Additional genes positively regulated by VanT were identified from a plasmid-based gene library fused to a promoterless
lacZ
. Three
lacZ
fusions (
serA
::
lacZ
,
hpdA-hgdA
::
lacZ,
and
sat-vps73
::
lacZ)
were identified which exhibited decreased expression in the
ΔvanT
strain. SerA is similar to 3-phosphoglycerate dehydrogenases and catalyzes the first step in the serine-glycine biosynthesis pathway. HgdA has identity with homogentisate dioxygenases, and HpdA is homologous to 4-hydroxyphenylpyruvate dioxygenases (HPPDs) involved in pigment production.
V. anguillarum
strains require an active VanT to produce high levels of an
l
-tyrosine-induced brown color via HPPD, suggesting that VanT controls pigment production. Vps73 and Sat are related to
Vibrio cholerae
proteins encoded within a DNA locus required for biofilm formation. A
V. anguillarum ΔvanT
mutant and a mutant carrying a polar mutation in the
sat-vps73
DNA locus were shown to produce defective biofilms. Hence, a new member of the
V. harveyi
LuxR transcriptional activator family has been characterized in
V. anguillarum
that positively regulates serine, metalloprotease, pigment, and biofilm production.
Nitrite Reductase of
Nitrosomonas europaea
Is Not Essential for Production of Gaseous Nitrogen Oxides and Confers Tolerance to Nitrite
Authors: Beaumont Hubertus J. E. , Hommes Norman G. , Sayavedra-Soto Luis A. , Arp Daniel J. , Arciero David M. , Hooper Alan B. , Westerhoff Hans V. , van Spanning Rob J. M. 
Published: July 2002

ABSTRACT

A gene that encodes a periplasmic copper-type nitrite reductase (NirK) was identified in
Nitrosomonas europaea
. Disruption of this gene resulted in the disappearance of Nir activity in cell extracts. The nitrite tolerance of NirK-deficient cells was lower than that of wild-type cells. Unexpectedly, NirK-deficient cells still produced nitric oxide (NO) and nitrous oxide (N
2
O), the latter in greater amounts than that of wild-type cells. This demonstrates that NirK is not essential for the production of NO and N
2
O by
N. europaea
. Inactivation of the putative
fnr
gene showed that Fnr is not essential for the expression of
nirK
.
Rapid and Specific Genotyping System for Hepatitis B Virus Corresponding to Six Major Genotypes by PCR Using Type-Specific Primers
Authors: Naito Hideo , Hayashi Shigeki , Abe Kenji 
Published: July 2002

ABSTRACT
A simple and precise genotyping system based on PCR using type-specific primers was developed for the determination of genotypes A through F of hepatitis B virus (HBV). This assay system is considered to be a useful tool for the molecular diagnosis of HBV infection and for large-scale surveys.
Spoligotype Diversity of
Mycobacterium bovis
Strains Isolated in France from 1979 to 2000
Authors: Haddad N. , Ostyn A. , Karoui C. , Masselot M. , Thorel M. F. , Hughes S. L. , Inwald J. , Hewinson R. G. , Durand B. 
Published: July 2002

ABSTRACT

The molecular fingerprints of 1,349 isolates of
Mycobacterium bovis
received between 1979 and August 2000 at Agence Française de Sécurité Sanitaire des Aliments (Afssa) have been obtained by spoligotyping. The majority of the isolates (1,266) were obtained from cattle living in France. An apparently high level of heterogeneity was observed between isolates. One hundred sixty-one spoligotypes were observed in total, of which 153 were from French isolates. The two predominant spoligotypes, designated BCG-like and GB54, accounted for 26 and 12% of the isolates, respectively. In addition, 84% of the spoligotypes were found fewer than 10 times. Analysis of the results by clustering and parsimony-based algorithms revealed that the majority of the spoligotypes were closely related. The predominant spoligotype was identical to that of the vaccine strain
Mycobacterium bovis
BCG, which was isolated in France at the end of the 19th century. Some spoligotypes were closely associated with restricted geographical areas. Interestingly, some spoligotypes, which were frequently observed in France, were also observed in neighboring countries. Conversely, few spoligotypes were common to France and England, and those that were shared were observed at very different frequencies. This last point illustrates the potential role for an international data bank, which could help trace the spread of
M. bovis
across national borders.
Necessity of Quality-Controlled 16S rRNA Gene Sequence Databases: Identifying Nontuberculous
Mycobacterium
Species
Authors: Turenne Christine Y. , Tschetter Lorelee , Wolfe Joyce , Kabani Amin 
Published: July 2002

ABSTRACT
The use of the 16S rRNA gene for identification of nontuberculous mycobacteria (NTM) provides a faster and better ability to accurately identify them in addition to contributing significantly in the discovery of new species. Despite their associated problems, many rely on the use of public sequence databases for sequence comparisons. To best evaluate the taxonomic status of NTM species submitted to our reference laboratory, we have created a 16S rRNA sequence database by sequencing 121 American Type Culture Collection strains encompassing 92 species of mycobacteria, and have also included chosen unique mycobacterial sequences from public sequence repositories. In addition, the Ribosomal Differentiation of Medical Microorganisms (RIDOM) service has made freely available on the Internet mycobacterial identification by 16S rRNA analysis. We have evaluated 122 clinical NTM species using our database, comparing >1,400 bp of the 16S gene, and the RIDOM database, comparing ∼440 bp. The breakdown of analysis was as follows: 61 strains had a sequence with 100% similarity to the type strain of an established species, 19 strains showed a 1- to 5-bp divergence from an established species, 11 strains had sequences corresponding to uncharacterized strain sequences in public databases, and 31 strains represented unique sequences. Our experience with analysis of the 16S rRNA gene of patient strains has shown that clear-cut results are not the rule. As many clinical, research, and environmental laboratories currently employ 16S-based identification of bacteria, including mycobacteria, a freely available quality-controlled database such as that provided by RIDOM is essential to accurately identify species or detect true sequence variations leading to the discovery of new species.
Serotype-Specific Detection of Coxsackievirus A16 in Clinical Specimens by Reverse Transcription-Nested PCR
Authors: Bendig Justin W. A. , O'Brien Patrick S. , Muir Peter 
Published: July 2002

ABSTRACT
We describe the development of a coxsackievirus A16 (CVA16) serotype-specific PCR which correctly differentiated between CVA16 and other enterovirus serotypes of both laboratory isolates and clinical specimens. The assay will be useful for monitoring CVA16 outbreaks and studying the disease association, epidemiology, and evolution of this common enterovirus serotype.
Characterization of
Chlamydia trachomatis omp1
Genotypes among Sexually Transmitted Disease Patients in Sweden
Authors: Jurstrand Margaretha , Falk Lars , Fredlund Hans , Lindberg Margret , Olcén Per , Andersson Sören , Persson Kenneth , Albert Jan , Bäckman Anders 
Published: July 2002

ABSTRACT

A method for detection and genotyping of genital
Chlamydia trachomatis
infections based on
omp1
gene amplification and sequencing was developed. DNA was extracted from urogenital or urine samples using a Chelex-based method, and an approximately 1,100-bp-long fragment from the
omp1
gene was directly amplified and sequenced. Genotyping was performed by BLAST similarity search, and phylogenetic tree analysis was used to illustrate the evolutionary relationships between clinical isolates and reference strains. The method was used to determine the genotypes of
C. trachomatis
in 237 positive urogenital and/or urine specimens collected at a Swedish sexually transmitted disease clinic during 1 year. The most common genotypes corresponded to serotypes E (47%) and F (17%). The
omp1
gene was highly conserved for genotype E (106 of 112 samples without any mutation) and F (41 of 42 samples without any mutation) strains but appear slightly less conserved for genotypes G (
n
= 6) and H (
n
= 6), where the sequences displayed one to four nucleotide substitutions relative to the reference sequence. Genotyping of samples collected at the follow-up visit indicated that two patients had become reinfected, while three other patients suffered treatment failure or reinfection. One woman appeared to have a mixed infection with two different
C. trachomatis
strains. This
omp1
genotyping method had a high reproducibility and could be used for epidemiological characterization of sexually transmitted
Chlamydia
infections.
Transmission of
Borrelia garinii
OspA Serotype 4 to BALB/c Mice by
Ixodes ricinus
Ticks Collected in the Field
Authors: Hu C. M. , Wilske B. , Fingerle V. , Lobet Y. , Gern L. 
Published: July 2002

ABSTRACT

In Europe,
Borrelia garinii
OspA serotype 4 has been isolated from the cerebrospinal fluid of patients but, up to now, has never been identified among culture isolates from
Ixodes ricinus
ticks. This information raises the question of whether OspA serotype 4 is transmitted by
I. ricinus
in nature. In the present study,
I. ricinus
nymphs collected in an area of endemicity in southern Germany were allowed to feed on mice. Cultivation of ear biopsy specimens showed that six of seven
B. garinii
-infected mice were infected by OspA serotype 4. In contrast, very few
B. garinii
OspA serotype 4 organisms were isolated directly from the ticks which infected the mice; most isolates were
B. afzelii
. The infected mice transmitted mainly OspA serotype 4 to xenodiagnostic ticks, preferentially in combination with
B. afzelii
.
Phaeohyphomycosis Caused by
Alternaria infectoria
in a Renal Transplant Recipient
Authors: Halaby Teysir , Boots Hans , Vermeulen Anton , van der Ven André , Beguin Hugues , van Hooff Hans , Jacobs Jan 
Published: July 2002

ABSTRACT

We report on a case of phaeohyphomycosis caused by
Alternaria infectoria
in a renal transplant recipient with pulmonary infiltrates and multiple skin lesions. Diagnosis was based on microscopy and culture of the skin lesions. Treatment consisted of a combination of surgical excision and systemic antifungal therapy, first with itraconazole and subsequently with liposomal amphotericin B, for 39 days. At a 20-month follow-up visit, no recurrence of the skin lesions or the pulmonary infiltrates had occurred.
Phylogeny of
Pneumocystis carinii
from 18 Primate Species Confirms Host Specificity and Suggests Coevolution
Authors: Demanche Christine , Berthelemy Madeleine , Petit Thierry , Polack Bruno , Wakefield Ann E. , Dei-Cas Eduardo , Guillot Jacques 
Published: July 2002

ABSTRACT

Primates are regularly infected by fungal organisms identified as
Pneumocystis carinii
. They constitute a valuable population for the confirmation of
P. carinii
host specificity. In this study, the presence of
P. carinii
was assessed by direct examination and nested PCR at mitochondrial large subunit (mtLSU) rRNA and dihydropteroate synthetase (DHPS) genes in 98 lung tissue samples from captive or wild nonhuman primates. Fifty-nine air samples corresponding to the environment of different primate species in zoological parks were also examined. Cystic forms of
P. carinii
were detected in smears from 7 lung tissue samples corresponding to 5 New World primate species. Amplifications at the mtLSU rRNA gene were positive for 29 lung tissue samples representing 18 different primate species or subspecies and 2 air samples corresponding to the environment of two simian colonies. Amplifications at the DHPS gene were positive for 8 lung tissue samples representing 6 different primate species. Direct sequencing of nested PCR products demonstrated that a specific mtLSU rRNA and DHPS sequence could be attributed to each primate species or subspecies. No nonhuman primate harbored the human type of
P. carinii
(
P. carinii
f. sp.
hominis
). Genetic divergence in primate-derived
P. carinii
organisms varied in terms of the phylogenetic divergence existing among the corresponding host species, suggesting coevolution.
Sampling Variability in the Microbiological Evaluation of Expectorated Sputa and Endotracheal Aspirates
Authors: Nagendra Sanjai , Bourbeau Paul , Brecher Stephen , Dunne Michael , LaRocco Mark , Doern Gary 
Published: July 2002

ABSTRACT
A five-center study was conducted with the aim of determining how reproducibly expectorated sputa and tracheal aspirates could be sampled when preparing Gram-stained smears and inoculating cultures. With both specimen types, excessive variation was noted among Gram stain results obtained from replicate smears. Less variation was noted among culture results, especially with tracheal aspirates.
Reliable Detection of Respiratory Syncytial Virus Infection in Children for Adequate Hospital Infection Control Management
Authors: Abels Susanne , Nadal David , Stroehle Angelika , Bossart Walter 
Published: July 2002

ABSTRACTBy using a rapid test for respiratory syncytial virus (RSV) detection (Abbott TestPack RSV), a number of patients were observed, showing repeatedly positive results over a period of up to 10 weeks. A prospective study was initiated to compare the rapid test with an antigen capture enzyme immunoassay (EIA) and a nested reverse transcriptase PCR (RT-PCR) protocol for detection of RSV serotypes A and B. Only respiratory samples from children exhibiting the prolonged presence of RSV (≥5 days) as determined by the rapid test were considered. A total of 134 specimens from 24 children was investigated by antigen capture EIA and nested RT-PCR. Using RT-PCR as the reference method, we determined the RSV rapid test to have a specificity of 63% and a sensitivity of 66% and the antigen capture EIA to have a specificity of 96% and a sensitivity of 69% for acute-phase samples and the homologous virus serotype A. In 7 (29%) of 24 patients, the positive results of the RSV rapid test could not be confirmed by either nested RT-PCR or antigen capture EIA. In these seven patients a variety of other respiratory viruses were detected. For general screening the RSV rapid test was found to be a reasonable tool to get quick results. However, its lack of specificity in some patients requires confirmation by additional tests to rule out false-positive results and/or detection of other respiratory viruses.
Antibody Responses to Recombinant Epstein-Barr Virus Antigens in Nasopharyngeal Carcinoma Patients: Complementary Test of ZEBRA Protein and Early Antigens p54 and p138
Authors: Dardari R. , Hinderer W. , Lang D. , Benider A. , El Gueddari B. , Joab I. , Benslimane A. , Khyatti M. 
Published: July 2002

ABSTRACT
Serological tests based on the antibodies directed against the Epstein-Barr virus early antigen (EA) and viral capsid antigen (VCA), which have been recognized as tumor markers for nasopharyngeal carcinoma (NPC), are routinely used to help in the diagnosis of this malignancy. The detection of these antibodies reveals very low titers, found only in a small proportion of young compared with older NPC patients. This is a problem for the diagnosis of NPC, especially among Maghrebians, among whom young people are also affected, and emphasizes the necessity to search for more reliable markers. The present study reports results of immunoglobulin G (IgG) and IgA responses of NPC patients to recombinant EA antigens p54 (BMRF1) and p138 (BALF2), VCA complex antigens p18 (BFRF3) and p23 (BLRF2), and EBNA antigen p72 (BKRF1). Our results show that IgA-EA-p54 and -p138 (IgA-EA-p54+138) antibodies have a diagnostic value for detection of NPC (70%), compared with IgA-VCA-p18+23 and IgA-EBNA-p72, which have limited diagnostic value, especially in young patients. It is also noteworthy that IgA-EA-p54+138 can detect a high percentage (64%) of NPC cases negative by immunofluorescence. These results, however, clearly show that a single test cannot achieve the objective of detecting all NPC patients, and it seems advisable to combine different tests for the diagnosis of NPC. The combination of IgG-ZEBRA with IgA-EA-p54+138 improved the sensitivity of detection of NPC to 95% in the overall NPC population. The use of IgA-EA-p54+138 in combination with IgG-ZEBRA will facilitate detailed studies on the pattern of antibody response, which may result in the development of useful serological markers to guide the treatment of NPC.
Characterization of Chloramphenicol Resistance in Beta-Hemolytic
Escherichia coli
Associated with Diarrhea in Neonatal Swine
Authors: Bischoff Kenneth M. , White David G. , McDermott Patrick F. , Zhao Shaohua , Gaines Stuart , Maurer John J. , Nisbet David J. 
Published: July 2002

ABSTRACT

Ninety beta-hemolytic
Escherichia coli
isolates associated with diarrhea in neonatal pigs from multiple farms in Oklahoma were investigated for known associated disease serotypes, virulence factors, ribotypes, and antimicrobial susceptibility phenotypes. Fifteen different serotypes were observed, with 58% of isolates belonging to groups that produce one of three major enterotoxins: O149, O147, and O139. Thirty percent of the swine
E. coli
isolates possessed a combination of F4 fimbriae and the heat-labile toxin and heat-stable toxin B enterotoxins. Seventy-three percent of the
E. coli
isolates were resistant to five or more antibiotics. Interestingly, 53% of swine
E. coli
isolates exhibited resistance to chloramphenicol (CHL), an antibiotic whose use in food animals has been prohibited in the United States since the mid-1980s. The
cmlA
gene, which encodes a putative CHL efflux pump, was detected by PCR in 47 of the 48 CHL-resistant isolates, and 4 of these also possessed the
cat2
gene, which encodes a chloramphenicol acetyltransferase. The one CHL-resistant isolate that did not contain either
cmlA
or
cat-2
possessed the
flo
gene, which confers resistance to both florfenicol and CHL. To determine whether CHL-resistant swine
E. coli
isolates represented dissemination of a clonal strain, all 90 isolates were analyzed by ribotyping. Seventeen distinct
E. coli
ribogroups were identified, with CHL resistance observed among the isolates in all except one of the major ribogroups. The identification of the
cmlA
gene among diverse hemolytic enterotoxigenic
E
.
coli
strains demonstrates its broad dissemination in the swine production environment and its persistence even in the absence of CHL selection pressure.