bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic and Kinetic Diversity of Aerobic Vinyl Chloride-Assimilating Bacteria from Contaminated Sites
Authors: Coleman Nicholas V. , Mattes Timothy E. , Gossett James M. , Spain Jim C. 
Published: November 2002

ABSTRACT

Aerobic bacteria that grow on vinyl chloride (VC) have been isolated previously, but their diversity and distribution are largely unknown. It is also unclear whether such bacteria contribute to the natural attenuation of VC at chlorinated-ethene-contaminated sites. We detected aerobic VC biodegradation in 23 of 37 microcosms and enrichments inoculated with samples from various sites. Twelve different bacteria (11
Mycobacterium
strains and 1
Nocardioides
strain) capable of growth on VC as the sole carbon source were isolated, and 5 representative strains were examined further. All the isolates grew on ethene in addition to VC and contained VC-inducible ethene monooxygenase activity. The
Mycobacterium
strains (JS60, JS61, JS616, and JS617) all had similar growth yields (5.4 to 6.6 g of protein/mol), maximum specific growth rates (0.17 to 0.23 day
−1
), and maximum specific substrate utilization rates (9 to 16 nmol/min/mg of protein) with VC. The
Nocardioides
strain (JS614) had a higher growth yield (10.3 g of protein/mol), growth rate (0.71 day
−1
), and substrate utilization rate (43 nmol/min/mg of protein) with VC but was much more sensitive to VC starvation. Half-velocity constant (

K
s

) values for VC were between 0.5 and 3.2 μM, while

K
s

values for oxygen ranged from 0.03 to 0.3 mg/liter. Our results indicate that aerobic VC-degrading microorganisms (predominantly
Mycobacterium
strains) are widely distributed at sites contaminated with chlorinated solvents and are likely to be responsible for the natural attenuation of VC.
Identification and Characterization of Novel Surface Proteins in
Lactobacillus johnsonii
and
Lactobacillus gasseri
Authors: Ventura Marco , Jankovic Ivana , Walker D. Carey , Pridmore R. David , Zink Ralf 
Published: November 2002

ABSTRACT

We have identified and sequenced the genes encoding the aggregation-promoting factor (APF) protein from six different strains of
Lactobacillus johnsonii
and
Lactobacillus gasseri
. Both species harbor two
apf
genes,
apf1
and
apf2
, which are in the same orientation and encode proteins of 257 to 326 amino acids. Multiple alignments of the deduced amino acid sequences of these
apf
genes demonstrate a very strong sequence conservation of all of the genes with the exception of their central regions. Northern blot analysis showed that both genes are transcribed, reaching their maximum expression during the exponential phase. Primer extension analysis revealed that
apf1
and
apf2
harbor a putative promoter sequence that is conserved in all of the genes. Western blot analysis of the LiCl cell extracts showed that APF proteins are located on the cell surface. Intact cells of
L. johnsonii
revealed the typical cell wall architecture of S-layer-carrying gram-positive eubacteria, which could be selectively removed with LiCl treatment. In addition, the amino acid composition, physical properties, and genetic organization were found to be quite similar to those of S-layer proteins. These results suggest that APF is a novel surface protein of the
Lactobacillus acidophilus
B-homology group which might belong to an S-layer-like family.
Response of Ants to a Deterrent Factor(s) Produced by the Symbiotic Bacteria of Entomopathogenic Nematodes
Authors: Zhou Xinsheng , Kaya Harry K. , Heungens Kurt , Goodrich-Blair Heidi 
Published: November 2002

ABSTRACT

The production of an ant-deterrent factor(s) (ADF) by
Xenorhabdus nematophila
and
Photorhabdus luminescens
, the symbiotic bacteria of the nematodes
Steinernema carpocapsae
and
Heterorhabditis bacteriophora
, respectively, was examined. In addition to an in vivo assay in which bacteria were tested for their ability to produce ADF within insect cadavers (M.E. Baur, H. K. Kaya, and D. R. Strong, Biol. Control 12:231-236, 1998), an in vitro microtiter dish assay was developed to monitor ADF activity produced by bacteria grown in cultures. Using these methods, we show that ADF activity is present in the supernatants of bacterial cultures, is filterable, heat stable, and acid sensitive, and passes through a 10-kDa-pore-size membrane. Thus, ADF appears to be comprised of a small, extracellular, and possibly nonproteinaceous compound(s). The amount of ADF repellency detected depends on the ant species being tested, the sucrose concentration (in vitro assays), and the strain, form, and age of the ADF-producing bacteria. These findings demonstrate that the symbiotic bacteria of some species of entomopathogenic nematodes produce a compound(s) that deters scavengers such as ants and thus could protect nematodes from being eaten during reproduction within insect cadavers.
Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry of Lipopeptide Biosurfactants in Whole Cells and Culture Filtrates of
Bacillus subtilis
C-1 Isolated from Petroleum Sludge
Authors: Vater Joachim , Kablitz Bärbel , Wilde Christopher , Franke Peter , Mehta Neena , Cameotra Swaranjit Singh 
Published: November 2002

ABSTRACT

An innovative method was developed for rapid sensitive detection and efficient structural characterization of lipopeptide biosurfactants by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry by using whole microbial cells and crude culture filtrates as targets in combination with surface tension measurements. This was done for a bacterial strain that was isolated from petroleum sludge and efficiently produces biosurfactants. This organism was identified by using biochemical, physiological, and genetic parameters as a
Bacillus subtilis
strain, designated
B. subtilis
C-1. This assignment was supported by a mass spectrometric investigation of the secondary metabolite spectrum determined by whole-cell MALDI-TOF mass spectrometry, which revealed three lipopeptide complexes, the surfactins, the iturins, and the fengycins, which are well-known biosurfactants produced by
B. subtilis
strains. These compounds were structurally characterized by in situ structure analysis by using postsource decay MALDI-TOF mass spectrometry. The isoforms were separated by miniaturized high-resolution reversed-phase high-performance liquid chromatography for mass spectrometric characterization. Iturin compounds which contain unusual fatty acid components were detected.
Coexistence of Multiple Proteobacterial Endosymbionts in the Gills of the Wood-Boring Bivalve
Lyrodus pedicellatus
(Bivalvia: Teredinidae)
Authors: Distel Daniel L. , Beaudoin David J. , Morrill Wendy 
Published: November 2002

ABSTRACT

Wood-boring bivalves of the family Teredinidae (commonly called shipworms) are known to harbor dense populations of gram-negative bacteria within specialized cells (bacteriocytes) in their gills. These symbionts are thought to provide enzymes, e.g., cellulase and dinitrogenase, which assist the host in utilizing wood as a primary food source. A cellulolytic, dinitrogen-fixing bacterium,
Teredinibacter turnerae
, has been isolated from the gill tissues of numerous teredinid bivalves and has been proposed to constitute the sole or predominant symbiont of this bivalve family. Here we demonstrate that one teredinid species,
Lyrodus pedicellatus
, contains at least four distinct bacterial 16S rRNA types within its gill bacteriocytes, one of which is identical to that of
T. turnerae
. Phylogenetic analyses indicate that the three newly detected ribotypes are derived from gamma proteobacteria that are related to but distinct (>6.5% sequence divergence) from
T. turnerae.
In situ hybridizations with 16S rRNA-directed probes demonstrated that the pattern of occurrence of symbiont ribotypes within bacteriocytes was predictable and specific, with some bacteriocytes containing two symbiont ribotypes. However, only two of the six possible pairwise combinations of the four ribotypes were observed to cooccur within the same host cells. The results presented here are consistent with the existence of a complex multiple symbiosis in this shipworm species.
A Whole-Genome Shotgun Optical Map of
Yersinia pestis
Strain KIM
Authors: Zhou Shiguo , Deng Wen , Anantharaman Thomas S. , Lim Alex , Dimalanta Eileen T. , Wang Jun , Wu Tian , Chunhong Tao , Creighton Robert , Kile Andrew , Kvikstad Erika , Bechner Michael , Yen Galex , Garic-Stankovic Ana , Severin Jessica , Forrest Dan , Runnheim Rod , Churas Chris , Lamers Casey , Perna Nicole T. , Burland Valerie , Blattner Frederick R. , Mishra Bhubaneswar , Schwartz David C. 
Published: November 2002

ABSTRACT

Yersinia pestis
is the causative agent of the bubonic, septicemic, and pneumonic plagues (also known as black death) and has been responsible for recurrent devastating pandemics throughout history. To further understand this virulent bacterium and to accelerate an ongoing sequencing project, two whole-genome restriction maps (
Xho
I and
Pvu
II) of
Y. pestis
strain KIM were constructed using shotgun optical mapping. This approach constructs ordered restriction maps from randomly sheared individual DNA molecules directly extracted from cells. The two maps served different purposes; the
Xho
I map facilitated sequence assembly by providing a scaffold for high-resolution alignment, while the
Pvu
II map verified genome sequence assembly. Our results show that such maps facilitated the closure of sequence gaps and, most importantly, provided a purely independent means for sequence validation. Given the recent advancements to the optical mapping system, increased resolution and throughput are enabling such maps to guide sequence assembly at a very early stage of a microbial sequencing project.
AbiA, a Lactococcal Abortive Infection Mechanism Functioning in
Streptococcus thermophilus
Authors: Tangney Mark , Fitzgerald Gerald F. 
Published: November 2002

ABSTRACT

The lactococcal abortive infection mechanisms AbiA and AbiG were introduced into
Streptococcus thermophilus
4035, and a range of phages capable of infecting this host were examined for sensitivity to these mechanisms. AbiA proved effective against six phages when examined at a growth temperature of 30°C but had no effect on any of the phages when tested at 37 or 42°C. AbiG failed to affect any of the
S. thermophilus
phages at 30, 37, or 42°C.
The Environmental Pathogen
Mycobacterium ulcerans
Grows in Amphibian Cells at Low Temperatures
Authors: Drancourt Michel , Jarlier Vincent , Raoult Didier 
Published: November 2002

ABSTRACT

Mycobacterium ulcerans
, the etiological agent of Buruli ulcers, is an environmental pathogen. We cultivated it in an amphibian (XTC-2) cell line that grows at 28°C. By counting of Ziehl-Neelsen-stained mycobacteria and by quantitative PCR analysis, we found that
M. ulcerans
multiplies rapidly in association with XTC-2 cells. Transmission electron microscopy demonstrated the presence of intracellular
M. ulcerans
microorganisms. These data suggest an intracellular environmental niche, and we propose use of XTC-2 cells for isolation of
M. ulcerans
from environmental sources.
Phylogenetic Analysis of Acute Bee Paralysis Virus Strains
Authors: Bakonyi Tamás , Grabensteiner Elvira , Kolodziejek Jolanta , Rusvai Miklós , Topolska Gražyna , Ritter Wolfgang , Nowotny Norbert 
Published: November 2002

ABSTRACT

Reverse transcription-PCR assays have been established for a quick, sensitive, and specific diagnosis of acute bee paralysis virus (ABPV), a common virus of the honeybee (
Apis mellifera
), directly from clinical samples. A 3,071-nucleotide fragment of the ABPV genome, which includes the entire capsid polyprotein gene, was amplified from Austrian, German, Polish, and Hungarian ABPV samples and sequenced, and the sequences were compared. The alignment of a smaller fragment with ABPV sequences from the United States and the United Kingdom revealed nucleotide identity rates between 89 and 96%, respectively. Phylogenetic trees which display the molecular relationship between the viruses of different geographic origin were constructed.
Reliability of Nested PCR for Detection of
Chlamydia pneumoniae
DNA in Atheromas: Results from a Multicenter Study Applying Standardized Protocols
Authors: Apfalter Petra , Assadian Ojan , Blasi Francesco , Boman Jens , Gaydos Charlotte A. , Kundi Michael , Makristathis Athanasios , Nehr Marion , Rotter Manfred L. , Hirschl Alexander M. 
Published: November 2002

ABSTRACT

The present multicenter study was designed to find explanations for the discrepancies in the reported rates of detection of
Chlamydia pneumoniae
DNA in endarterectomy specimens. Coded identical sets of (i) a
C. pneumoniae
DNA dilution series (panel 1;
n
= 10), (ii) spiked control tissue specimens (panel 2;
n
= 10 specimens, including 5 negative controls), and (iii) endarterectomy specimens (panel 3; 15 atheromas, 5 negative controls) were analyzed at four laboratories by three standardized DNA extraction methods in each laboratory and a nested touchdown PCR protocol targeting the
ompA
gene of
C. pneumoniae
. Panel 1 samples were correctly identified as positive to levels of 0.3 inclusion-forming units (IFU)/PCR mixture (100%) and 0.03 IFU/PCR mixture (50%). All negative controls were correctly reported as negative. Panel 2 samples were identified as
C. pneumoniae
positive to levels of 0.01 IFU/PCR mixture (100%) and 0.005 IFU/PCR mixture (91%), independent of the DNA extraction method used, and only one false-positive result was reported. For panel 3 samples, 5 of 240 (2%) analyses (in which DNA extractions and PCR were performed at the same laboratory) were positive; the positive specimens were from three endarterectomy specimens and two negative controls. After exchange of DNA extracts between laboratories, 13 of 15 atheroma samples were
C. pneumoniae
DNA positive in at least 1 of a series of 48 analyses per atheroma sample; however, the overall positivity rate did not exceed 5% (33 of 720 analyses) and therefore was lower than that for the negative controls (8%; 19 of 240 analyses). Not a single positive result could be achieved when all panel 3 extracts (
n
= 240 analyses) were reamplified by a 16S rRNA PCR followed by hybridization with a
C. pneumoniae
-specific probe. Statistical analyses demonstrated that positive results did not occur in an independent and random fashion and could most likely be explained by amplicon carryover at the nested PCR level as well as amplicon introduction during DNA extraction, but not by the patterns of distribution of very low target levels or a certain DNA extraction protocol. The results of studies by nested PCR for detection of the prevalence of
C. pneumoniae
will always be questionable.
Microevolution of the Direct Repeat Region of
Mycobacterium tuberculosis
: Implications for Interpretation of Spoligotyping Data
Authors: Warren R. M. , Streicher E. M. , Sampson S. L. , van der Spuy G. D. , Richardson M. , Nguyen D. , Behr M. A. , Victor T. C. , van Helden P. D. 
Published: November 2002

ABSTRACT

The direct repeat (DR) region has been determined to be an important chromosomal domain for studying the evolution of
Mycobacterium tuberculosis
. Despite this, very little is known about microevolutionary events associated with clonal expansion and how such events influence the interpretation of both restriction fragment length polymorphism (RFLP) and spoligotype data. This study examined the structure of the DR region in three independently evolving lineages of
M. tuberculosis
with a combination of DR-RFLP, spoligotyping, and partial DNA sequencing. The results show that the duplication of direct variable repeat (DVR) sequences and single-nucleotide polymorphisms is rare; conversely, the deletion of DVR sequences and IS
6110
-mediated mutation is observed frequently. Deletion of either single or contiguous DVR sequences was observed. The deletion of adjacent DVR sequences occurred in a dependent manner rather than as an accumulation of independent events. Insertion of IS
6110
into either the direct repeat or spacer sequences influenced the spoligotype pattern, resulting in apparent deletion of DVR sequences. Homologous recombination between adjacent IS
6110
elements led to extensive deletion in the DR region, again demonstrating a dependent evolutionary mechanism. Different isolates from the same strain family and isolates from different strain families were observed to converge to the same spoligotype pattern. In conclusion, the binary data of the spoligotype are unable to provide sufficient information to accurately establish genotypic relationships between certain clinical isolates of
M. tuberculosis
. This has important implications for molecular epidemiologic strain tracking and for the application of spoligotype data to phylogenetic analysis of
M. tuberculosis
isolates.
M Types of Group A Streptococcal Isolates Submitted to the National Centre for Streptococcus (Canada) from 1993 to 1999
Authors: Tyrrell Gregory J. , Lovgren Marguerite , Forwick Betty , Hoe Nancy P. , Musser James M. , Talbot James A. 
Published: November 2002

ABSTRACTThe National Centre for Streptococcus (NCS) (Canada) determined the group A streptococcal (GAS) M types of 4,760 Canadian isolates submitted between 1993 and 1999 by classic serotyping. The 10 most frequently identified M types were M1 (26.4%), M12 (9.8%), M28 (8.9%), M3 (6.8%), M4 (6.2%), M11 (4.8%), M89 (3.1%), M6 (3.0%), M2 (2.6%), and M77 (1.9%). Nontypeable isolates accounted for 15.4% of the collection. The province of Ontario submitted 51.1% of the isolates, followed by Quebec (21.2%) and Alberta (13.9%). Together, these three provinces constituted 71.3% of the Canadian population in 1996. The numbers of M types M1, M12, M28, and M3 occurred most frequently in subjects whose ages were <1 to 15 years and 25 to 45 years, as well as in the elderly (60 to 90 years). Further analysis found that the four most frequently identified M types from blood, brain, and cerebrospinal fluid were M1 (28.2%), M28 (9.2%), M12 (9.1%), and M3 (8.2%), with 13.4% of isolates being nontypeable. The four isolates from throats most frequently identified were M1 (19.5%), M12 (15.3%), M3 (8.6%), and M28 (5%) with 19.4% of isolates being nontypeable. Thesicgene of a subset of M1 strains (9.5% of the M1 collection) was sequenced. Of 36 sic types identified, the four most common were sic1.01 (22.8%), sic1.02 (14.9%), sic1.135 (10.5%), and sic1.178 (9.6%). Together these four sic types further characterized nearly 60% of the M1 strains sequenced. In summary, from the years 1993 to 1999, the NCS detected 54 M types, of which 10 different M types constituted 73.5% of the collection. M1 was the most common GAS M type circulating in the Canadian population, responsible for more than a quarter of the isolates typed. The most common throat isolates differed in M-type and proportion from those of invasive isolates. Sequencing thesicgene further characterized the most common M-type serotype 1 in a fashion that may be useful for epidemiologic investigations.
Genetic Diversity of Intimin Genes of Attaching and EffacingEscherichia coliStrains
Authors: Zhang W. L. , Köhler B. , Oswald E. , Beutin L. , Karch H. , Morabito S. , Caprioli A. , Suerbaum S. , Schmidt H. 
Published: November 2002

ABSTRACTIn this study, we determined the sequences of four intimin variant genes detected in attaching and effacingEscherichia coliisolates of human origin. Three of them were novel and were designatedeae-η (eta),eae-ι (iota), andeae-κ (kappa). The fourth was identical to the recently describedeae-ζ (zeta), isolated from a bovineE. coliO84:NM isolate. We compared these sequences with those of published intimin-α, intimin-β, intimin-γ1, intimin-γ2, intimin-ε, and intimin-θ alleles. Sequence analysis of these 10 intimin alleles confirmed extensive genetic diversity within the intimin gene family inE. coli.The genetic diversity was more prominent in the 3′ region (starting at bp 2112), which encodes the binding domain of intimin. Phylogenetic analyses revealed four groups of closely related intimin genes: α and ζ; β and κ; γ1 and γ2/θ; and ε and η. Calculation of homoplasy ratios of sequences of the 5′ region ofeae(positions 1 to 2111) revealed evidence for intragenic recombination. Split decomposition analysis also indicates that recombination events have played a role in the evolutionary history ofeae.In conclusion, we recommend aneaenomenclature system based on the Greek alphabet and provide an updated PCR scheme for amplification and typing ofE. coli eae.
Sequence Diversity of
Neisseria meningitidis
16S rRNA Genes and Use of 16S rRNA Gene Sequencing as a Molecular Subtyping Tool
Authors: Sacchi Claudio T. , Whitney Anne M. , Reeves Michael W. , Mayer Leonard W. , Popovic Tanja 
Published: November 2002

ABSTRACT

We investigated the diversity of the primary sequences of 16S rRNA genes among
Neisseria meningitidis
strains (Men) and evaluated the use of this approach as a molecular subtyping tool. We aligned and compared a 1,417-bp fragment of the 16S rRNA gene from 264 Men strains of serogroups A, B, C, and Y (MenA, MenB, MenC, and MenY, respectively) isolated throughout the world over a 30-year period. Thirty-one positions of difference were found among 49 16S types: differences between types ranged from 1 to 14 positions (0.07 to 0.95%). 16S types and serogroups were highly associated; only 3 out 49 16S types were shared by two or more serogroups. We have identified 16S types that are exclusively associated with strains of certain hypervirulent clones: 16S type 5 with MenA subgroup III, 16S type 4 with the MenB electrophoretic type 5 (ET-5) complex, and 16S types 12 and 13 with MenC of the ET-37 complex. For MenC strains, 16S sequencing provided the highest sensitivity and specificity and the best overall association with the outbreak-related versus sporadic isolates when compared with pulsed-field gel electrophoresis, multilocus enzyme electrophoresis, and multilocus sequence typing. We demonstrated for the first time an unexpected diversity among 16S rRNA genes of Men strains, identified 16S types associated with well-defined hypervirulent clones, and showed the potential of this approach to rapidly identify virulent strains associated with outbreaks and/or an increased incidence of sporadic disease.
Direct and Rapid Identification and Genogrouping of Meningococci andporAAmplification by LightCycler PCR
Authors: Mölling Paula , Jacobsson Susanne , Bäckman Anders , Olcén Per 
Published: November 2002

ABSTRACTInvasive meningococcal infections are usually diagnosed by culture. This approach is far from optimal due to, e.g., treatment with precollection antibiotics. Molecular-genetics methods are therefore recognized as important tools for optimal laboratory confirmation of meningococcal infections as well as characterization of meningococci (Mc). The aims of the present study were to develop real-time PCRs for identification and genogrouping (A, B, C, Y, and W-135) of Mc andporAamplification that further can be used for subsequent genosubtyping. In a first run Mc were identified. In a second run they were genogrouped andporAgenes were amplified. All the Mc isolates (n= 71) but one and cerebrospinal fluid samples (n= 11) tested gave the expected positive results. The specificity, inter- and intra-assay variations, and effects of different amounts of DNA on the melting temperatures were also explored. The LightCycler PCR system was found to effectively detect and characterize Mc in a few hours. This testing, including the DNA sequencing of theporAgene to reveal the genosubtype, does not take more than a working day, and the results can be compared to those from culturing with phenotypic analysis, which takes at least a few days.