bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for Distinct
l
-Methionine Catabolic Pathways in the Yeast
Geotrichum candidum
and the Bacterium
Brevibacterium linens
Authors: Arfi Kenza , Landaud Sophie , Bonnarme Pascal 
Published: March 2006

ABSTRACT

Tracing experiments were carried out to identify volatile and nonvolatile
l
-methionine degradation intermediates and end products in the yeast
Geotrichum candidum
and in the bacterium
Brevibacterium linens
, both of which are present in the surface flora of certain soft cheeses and contribute to the ripening reactions. Since the acid-sensitive bacterium
B. linens
is known to produce larger amounts and a greater variety of volatile sulfur compounds (VSCs) than the yeast
G. candidum
produces, we examined whether the
l
-methionine degradation routes of these microorganisms differ. In both microorganisms, methanethiol and α-ketobutyrate are generated; the former compound is the precursor of other VSCs, and the latter is subsequently degraded to 2,3-pentanedione, which has not been described previously as an end product of
l
-methionine catabolism. However, the
l
-methionine degradation pathways differ in the first steps of
l
-methionine degradation.
l
-Methionine degradation is initiated by a one-step degradation process in the bacterium
B. linens
, whereas a two-step degradation pathway with 4-methylthio-2-oxobutyric acid (MOBA) and 4-methylthio-2-hydroxybutyric acid (MHBA) as intermediates is used in the yeast
G. candidum
. Since
G. candidum
develops earlier than
B. linens
during the ripening process, MOBA and MHBA generated by
G.candidum
could also be used as precursors for VSC production by
B. linens
.
Heterologous Expression of BetL, a Betaine Uptake System, Enhances the Stress Tolerance ofLactobacillus salivariusUCC118
Authors: Sheehan Vivien M. , Sleator Roy D. , Fitzgerald Gerald F. , Hill Colin 
Published: March 2006

ABSTRACTGiven the increasing commercial and clinical relevance of probiotic cultures, improving the technological robustness of what are often process-sensitive cultures is an important biological goal. The nisin-controlled expression system was used to direct the heterologous expression of the listerial betaine uptake system BetL in the probiotic strainLactobacillus salivariusUCC118. Following nisin induction, strains expressingbetLexhibited a significant increase in resistance to several stresses, including elevated osmo-, cryo-, baro-, and chill tolerance, as well as increased resistance to spray- and freeze-drying. The ability to confer additional stress tolerance on a probiotic culture may be an important step in delivering viable cultures for maximal efficacy.
Inactivation of Single-Celled
Ascaris suum
Eggs by Low-Pressure UV Radiation
Authors: Brownell Sarah A. , Nelson Kara L. 
Published: March 2006

ABSTRACT

Intact and decorticated single-celled
Ascaris suum
eggs were exposed to UV radiation from low-pressure, germicidal lamps at fluences (doses) ranging from 0 to 8,000 J/m
2
for intact eggs and from 0 to 500 J/m
2
for decorticated eggs. With a UV fluence of 500 J/m
2
, 0.44- ± 0.20-log inactivation (mean ± 95% confidence interval) (63.7%) of intact eggs was observed, while a fluence of 4,000 J/m
2
resulted in 2.23- ± 0.49-log inactivation (99.4%). (The maximum quantifiable inactivation was 2.5 log units.) Thus, according to the methods used here,
Ascaris
eggs are the most UV-resistant water-related pathogen identified to date. For the range of fluences recommended for disinfecting drinking water and wastewater (200 to 2,000 J/m
2
), from 0- to 1.5-log inactivation can be expected, although at typical fluences (less than 1,000 J/m
2
), the inactivation may be less than 1 log. When the eggs were decorticated (the outer egg shell layers were removed with sodium hypochlorite, leaving only the lipoprotein ascaroside layer) before exposure to UV, 1.80- ± 0.32-log reduction (98.4%) was achieved with a fluence of 500 J/m
2
, suggesting that the outer eggshell layers protected
A. suum
eggs from inactivation by UV radiation. This protection may have been due to UV absorption by proteins in the outer layers of the 3- to 4-μm-thick eggshell. Stirring alone (without UV exposure) also inactivated some of the
Ascaris
eggs (∼20% after 75 min), which complicated determination of the inactivation caused by UV radiation alone.
Effect of Transport at Ambient Temperature on Detection and Isolation of
Vibrio cholerae
from Environmental Samples
Authors: Alam Munirul , Sadique Abdus , Nur-A-Hasan  , Bhuiyan Nurul A. , Nair G. Balakrish , Siddique A. K. , Sack David A. , Ahsan Sunjukta , Huq Anwar , Sack R. Bradley , Colwell Rita R. 
Published: March 2006

ABSTRACT

It has long been assumed that prolonged holding of environmental samples at the ambient air temperature prior to bacteriological analysis is detrimental to isolation and detection of
Vibrio cholerae
, the causative agent of pandemic cholera. The present study was aimed at understanding the effect of transporting environmental samples at the ambient air temperature on isolation and enumeration of
V. cholerae
. For water and plankton samples held at ambient temperatures ranging from 31°C to 35°C for 20 h, the total counts did not increase significantly but the number of culturable
V. cholerae
increased significantly compared to samples processed within 1 h of collection, as measured by culture, acridine orange direct count, direct fluorescent-antibody-direct viable count (DFA-DVC), and multiplex PCR analyses. For total coliform counts, total bacterial counts, and DFA-DVC counts, the numbers did not increase significantly, but the culturable plate counts for
V. cholerae
increased significantly after samples were held at the ambient temperature during transport to the laboratory for analysis. An increase in the recovery of
V. cholerae
O1 and improved detection of
V. cholerae
O1
rfb
and
ctxA
also occurred when samples were enriched after they were kept for 20 h at the ambient temperature during transport. Improved detection and isolation of toxigenic
V. cholerae
from freshwater ecosystems can be achieved by holding samples at the ambient temperature, an observation that has significant implications for tracking this pathogen in diverse aquatic environments.
Generation of Novel-Substrate-Accepting Biphenyl Dioxygenases through Segmental Random Mutagenesis and Identification of Residues Involved in Enzyme Specificity
Authors: Zielinski Marco , Kahl Silke , Standfuß-Gabisch Christine , Cámara Beatriz , Seeger Michael , Hofer Bernd 
Published: March 2006

ABSTRACT

Aryl-hydroxylating dioxygenases are of interest for the degradation of persistant aromatic pollutants, such as polychlorobiphenyls (PCBs), or as catalysts for the functionalization of aromatic scaffolds. In order to achieve dioxygenation of technical mixtures of PCBs, enzymes with broadened or altered substrate ranges are essential. To alter the substrate specificity of the biphenyl dioxygenase (BphA) of
Burkholderia xenovorans
LB400, we applied a directed evolution approach that used structure-function relationship data to target random mutageneses to specific segments of the enzyme. The limitation of random amino acid (AA) substitutions to regions that are critical for substrate binding and the exclusion of AA exchanges from positions that are essential for catalytic activity yielded enzyme variants of interest at comparatively high frequencies. After only a single mutagenic cycle, 10 beneficial variants were detected in a library of fewer than 1,000 active enzymes. Compared to the parental BphA, they showed between 5- and 200-fold increased turnover of chlorinated biphenyls, with substituent patterns that rendered them largely recalcitrant to attack by BphA-LB400. Determination of their sequences identified AAs that prevent the acceptance of specific PCBs by the wild-type enzyme, such as Pro334 and Phe384. The results suggest prime targets for subsequent cycles of BphA modification. Correlations with a three-dimensional model of the enzyme indicated that most of the exchanges with major influence on substrate turnover do not involve pocket-lining residues and had not been predictable through structural modeling.
Evaluation of 23S rRNA PCR Primers for Use in Phylogenetic Studies of Bacterial Diversity
Authors: Hunt Dana E. , Klepac-Ceraj Vanja , Acinas Silvia G. , Gautier Clement , Bertilsson Stefan , Polz Martin F. 
Published: March 2006

ABSTRACT
The availability of a diverse set of 23S rRNA gene sequences enabled evaluation of the specificity of 39 previously published and 4 newly designed primers specific for bacteria. An extensive clone library constructed using an optimized primer pair resulted in similar gene richness but slightly differing coverage of some phylogenetic groups, compared to a 16S rRNA gene library from the same environmental sample.
In Situ Gene Expression by
Vibrio vulnificus
Authors: Smith Ben , Oliver James D. 
Published: March 2006

ABSTRACT

Strains of
Vibrio vulnificus
incubated in situ in natural estuarine waters during warm months continued to express
katG
(periplasmic catalase),
rpoS
(stress sigma factor),
tufA
(elongation factor),
wza
, and
wzb
(capsule synthesis).
vvhA
(hemolysin) was differentially expressed between environmental and clinical isolates. These results paralleled our in vitro findings.
Resistance Determinants of a Highly Arsenic-Resistant Strain of
Leptospirillum ferriphilum
Isolated from a Commercial Biooxidation Tank
Authors: Tuffin I. Marla , Hector Stanton B. , Deane Shelly M. , Rawlings Douglas E. 
Published: March 2006

ABSTRACT

Two sets of arsenic resistance genes were isolated from the highly arsenic-resistant
Leptospirillum ferriphilum
Fairview strain. One set is located on a transposon, Tn
LfArs
, and is related to the previously identified Tn
AtcArs
from
Acidithiobacillus caldus
isolated from the same arsenopyrite biooxidation tank as
L. ferriphilum
. Tn
LfArs
conferred resistance to arsenite and arsenate and was transpositionally active in
Escherichia coli
. Tn
LfArs
and Tn
AtcArs
were sufficiently different for them not to have been transferred from one type of bacterium to the other in the biooxidation tank. The second set of arsenic resistance genes conferred very low levels of resistance in
E. coli
and appeared to be poorly expressed in both
L. ferriphilum
and
E. coli
.
Thermophilic Lifestyle for an Uncultured Archaeon from Hydrothermal Vents: Evidence from Environmental Genomics
Authors: Moussard Hélène , Henneke Ghislaine , Moreira David , Jouffe Vincent , López-García Purificacion , Jeanthon Christian 
Published: March 2006

ABSTRACT

We present a comparative analysis of two genome fragments isolated from a diverse and widely distributed group of uncultured euryarchaea from deep-sea hydrothermal vents. The optimal activity and thermostability of a DNA polymerase predicted in one fragment were close to that of the thermophilic archaeon
Thermoplasma acidophilum
, providing evidence for a thermophilic way of life of this group of uncultured archaea.
Recovery of
Escherichia coli
from Soil after Addition of Sterile Organic Wastes
Authors: Unc Adrian , Gardner Julie , Springthorpe Susan 
Published: March 2006

ABSTRACT

Laboratory batch tests indicate that addition of sterile municipal sewage biosolids to clay soil from four depths increases the numbers of
Escherichia coli
isolates recoverable in EC-MUG broth (EC broth with 4-methylumbelliferyl-β-glucuronide). This effect was most marked for the deeper soil layers, with increases of about 2.6 orders of magnitude in
E. coli
most probable number.
Transformation of Rhizobia with Broad-Host-Range Plasmids by Using a Freeze-Thaw Method
Authors: Vincze Eva , Bowra Steve 
Published: March 2006

ABSTRACT

Several species of rhizobia were successfully transformed with broad-host-range plasmids of different replicons by using a modified freeze-thaw method. A generic binary vector (pPZP211) was maintained in
Mesorhizobium loti
without selection and stably inherited during nodulation. The method could extend the potential of rhizobia as a vehicle for plant transformation.
Novel Technique of Quantitative Nested Real-Time PCR Assay for
Mycobacterium tuberculosis
DNA
Authors: Takahashi Teruyuki , Nakayama Tomohiro 
Published: March 2006

ABSTRACT

The diagnosis of tuberculous meningitis (TBM) remains a complex issue because the most widely used conventional diagnostic tools, such as culture and PCR assay for cerebrospinal fluid (CSF) samples, are unable to rapidly detect
Mycoba
ct
erium tuberculosis
with sufficient sensitivity in the acute phase of TBM. Based on TaqMan PCR, we designed a novel technique consisting of an internally controlled quantitative nested real-time (QNRT) PCR assay that provided a marked improvement in detection sensitivity and quantification. We applied this novel technique to quantitatively detect
M. tuberculosis
DNA in CSF samples from patients with suspected TBM. For use as the internal control in the measurement of the
M. tuberculosis
DNA copy numbers in the QNRT-PCR assay, the original mutation (M) plasmid, which included an artificial random 22-nucleotide sequence within an inserted DNA fragment of the MPB64 gene of
M. tuberculosis
, was prepared. The QNRT-PCR assay showed high sensitivity and specificity that were approximately equivalent to those of the conventional nested PCR assay. Moreover, the QNRT-PCR assay made it possible to precisely and quantitatively detect the initial copy number of
M. tuberculosis
DNA in CSF samples. Therefore, compared to the conventional PCR assay, the QNRT-PCR assay can be considered a more useful and advanced technique for the rapid and accurate diagnosis of TBM. To establish the superiority of this novel technique in TBM diagnosis, it will be necessary to accumulate data from a larger number of patients with suspected TBM.
Use of Oligoarrays for Characterization of Community-Onset Methicillin-Resistant
Staphylococcus aureus
Authors: Koessler Thibaud , Francois Patrice , Charbonnier Yvan , Huyghe Antoine , Bento Manuela , Dharan Sasi , Renzi Gesuele , Lew Daniel , Harbarth Stephan , Pittet Didier , Schrenzel Jacques 
Published: March 2006

ABSTRACT

Until recently, methicillin-resistant
Staphylococcus aureus
(MRSA) was considered the prototype of a hospital-acquired bacterial pathogen. However, recent reports have shown that MRSA has now emerged in the community. Characterization of specific markers for distinguishing the origin of isolates could contribute to improved knowledge of MRSA epidemiology. The release of whole-genome sequences of hospital- and community-acquired
S. aureus
strains allowed the development of whole-genome content analysis techniques, including microarrays. We developed a microarray composed of 8,191 open reading frame-specific oligonucleotides covering >99% of the four sequenced
S. aureus
genomes (N315, Mu50, MW2, and COL) to evaluate gene contents of hospital- and community-onset
S. aureus
strains. In parallel, pulsed-field gel electrophoresis, variable number of tandem repeats, antibiogram, staphylococcal cassette chromosome-
mec
element typing, and presence of the Panton-Valentine leukocidin gene were evaluated in a collection of 15 clinical isolates. Clusters obtained with microarrays showed a high degree of similarity with those obtained by pulsed-field gel electrophoresis or variable number of tandem repeats. Clusters clearly segregated hospital-onset strains from community-onset strains. Moreover, the microarray approach allowed definition of novel marker genes and chromosomal regions specific for given groups of isolates, thus providing better discrimination and additional information compared to pulsed-field gel electrophoresis and variable number of tandem repeats. Finally, the comparative genome hybridization approach unraveled the occurrence of multiple horizontal transfer events leading to community-onset MRSA as well as the need for a specific genetic background in recipient strains for both the acquisition and the stability of the
mec
element.
High-Level Ciprofloxacin Resistance from Point Mutations in
gyrA
and
parC
Confined to Global Hospital-Adapted Clonal Lineage CC17 of
Enterococcus faecium
Authors: Leavis Helen L. , Willems Rob J. L. , Top Janetta , Bonten Marc J. M. 
Published: March 2006

ABSTRACT

To substantiate a common genetic background of ciprofloxacin-resistant
Enterococcus faecium
, 32 ciprofloxacin-resistant (Cip
r
) and 31 ciprofloxacin-susceptible (Cip
s
) isolates from outbreaks, clinical infections, surveillances, and animals from 10 different countries were genotyped by multilocus sequence typing. Additionally, susceptibilities to ampicillin and vancomycin and the presence of
esp
were determined and the quinolone resistance-determining regions of
parC
,
gyrA
,
parB
, and
gyrE
were sequenced. High-level Cip
r
(MIC ≥ 64 μg/ml) due to point mutations in the quinolone resistance-determining region was unique to a distinct hospital-adapted genetic complex in
E. faecium
, previously designated CC17. Low-level Cip
r
(MIC = 4 μg/ml) in non-CC17 strains is not attributable to point mutations in any subunit of the topoisomerase genes, and the mechanism of resistance remains unclear. Acquisition of mutations in
parC
and
gyrA
, leading to high-level Cip
r
, is, in addition to ampicillin resistance and the presence of a putative pathogenicity island, another cumulative step in hospital adaptation of CC17.
Molecular Subtyping of Poultry-Associated Type AClostridium perfringensIsolates by Repetitive-Element PCR
Authors: Siragusa G. R. , Danyluk M. D. , Hiett K. L. , Wise M. G. , Craven S. E. 
Published: March 2006

ABSTRACTClostridium perfringensstrains (type A) isolated from an integrated poultry operation were subtyped using repetitive-element PCR with Dt primers. Isolates were obtained from fecal, egg shell, fluff, and carcass rinse samples as part of a previously reported temporally linked epidemiological survey. A total of 48 isolates ofC. perfringenswere obtained from different stages of the broiler chicken production chain from two separate breeder farms that supplied a single hatchery that in turn provided chicks to a single grow-out farm whose flocks were processed at a single plant. All 48 isolates were typeable (100% typeability) by repetitive-element PCR with Dt primers. This subtyping method was highly reproducible and discriminatory. By repetitive-element PCR with Dt primers, isolates were classified into four major branches with 12 subgroups or clades. The Simpson's index of discrimination was calculated to be 0.96 for groupings of >95% correlation. Toxin gene profiles of the isolates indicated that all of the isolates wereC. perfringensalpha-toxin gene positive and 46 of 48 isolates were beta2-toxin gene positive. All strains were negative for beta- and epsilon-toxin genes. Repetitive sequence-based PCR was found to be a technically practical and reproducible means of subtypingC. perfringenslibraries from specific epidemiological or production environment settings.
Molecular Diagnosis of
Bordetella pertussis
Infection by Evaluation of Formalin-Fixed Tissue Specimens
Authors: Tatti Kathleen M. , Wu Kai-Hui , Sanden Gary N. , Greer Patricia , Sumner John , Guarner Jeannette , Paddock Christopher D. , Zaki Sherif R. 
Published: March 2006

ABSTRACT

Formalin-fixed lung or trachea tissue specimens from four infants and one adolescent who died of respiratory illness were tested for
Bordetella pertussis
by conventional and real-time PCR assays.
B. pertussis
was confirmed in all cases. PCR can be an invaluable retrospective diagnostic tool for evaluating archival tissues from patients with suspected fatal pertussis.
Insertion Sequence IS
900
Revisited
Authors: Semret Makeda , Turenne Christine Y. , Behr Marcel A. 
Published: March 2006

ABSTRACT

Many studies investigating
Mycobacterium avium
subsp.
paratuberculosis
in Crohn's disease have used molecular detection of IS
900
in clinical samples, but some have described polymorphisms in IS
900
as variants of this organism. Analysis of 23
M. avium
subsp.
paratuberculosis
isolates revealed that IS
900
is highly conserved, with only two sequevars distinguishing sheep and cattle lineages. Amplification of IS
900
-like sequences is not sufficient as a proxy for
M. avium
subsp.
paratuberculosis
.
PCR as a Confirmatory Technique for Laboratory Diagnosis of Malaria
Authors: Johnston Stephanie P. , Pieniazek Norman J. , Xayavong Maniphet V. , Slemenda Susan B. , Wilkins Patricia P. , da Silva Alexandre J. 
Published: March 2006

ABSTRACT

We compared a nested PCR assay and microscopic examination of Giemsa-stained blood films for detection and identification of
Plasmodium
spp. in blood specimens. PCR was more sensitive than microscopy and capable of identifying malaria parasites at the species level when microscopy was equivocal.
Establishment of ST30 as the Predominant Clonal Type among Community-Associated Methicillin-Resistant
Staphylococcus aureus
Isolates in Singapore
Authors: Hsu Li-Yang , Koh Yin-Ling , Chlebicka Nidhi Loomba , Tan Thean-Yen , Krishnan Prabha , Lin Raymond Tzer-Pin , Tee Nancy , Barkham Timothy , Koh Tse-Hsien 
Published: March 2006

ABSTRACT

The number of infections attributable to community-associated methicillin-resistant
Staphylococcus aureus
(CA-MRSA) in Singapore is progressively increasing. Most cases in the past 2 years were caused by Panton-Valentine leukocidin-positive isolates belonging to sequence type 30, according to multilocus sequence typing. This has clearly become the predominant sequence type among CA-MRSA isolates in Singapore.
Sensitive Line Probe Assay That Simultaneously Detects Mutations Conveying Resistance to Lamivudine and Adefovir
Authors: Hussain Munira , Fung Scott , Libbrecht Evelien , Sablon Erwin , Cursaro Carmela , Andreone Pietro , Lok Anna S. F. 
Published: March 2006

ABSTRACT
The INNO-LiPA HBV DR v2 assay is designed to detect hepatitis B virus mutations conveying resistance to lamivudine and adefovir. Our study confirms that this assay can simultaneously detect the presence of lamivudine and adefovir resistance mutations in clinical samples, has a high degree of concordance with sequencing, and can detect mutants earlier.
Respiratory Syncytial Virus Detection by Remel Xpect, Binax Now RSV, Direct Immunofluorescent Staining, and Tissue Culture
Authors: Borek Anita P. , Clemens Susan H. , Gaskins Valerie K. , Aird Deborah Z. , Valsamakis Alexandra 
Published: March 2006

ABSTRACT

The performance characteristics of Xpect RSV (XP) and Binax Now RSV (BN) were compared to those of direct fluorescent-antibody staining and/or tissue culture for detection of respiratory syncytial virus (RSV) in nasopharyngeal aspirate and wash samples from children (
n
= 110) and adults (
n
= 66). The sensitivity, specificity, positive predictive value, and negative predictive value of XP were 75%, 98%, 95%, and 90%, respectively; and those of BN were 74%, 100%, 100%, and 90%, respectively. The performances of the assays were similar within a given age group and specimen type (nasopharyngeal aspirate or wash specimen). XP and BN are useful for screening for RSV in respiratory specimens when large volumes are tested or low levels of staffing occur.
Candida krusei
Transmission among Hematology Patients Resolved by Adapted Antifungal Prophylaxis and Infection Control Measures
Authors: Vos Margreet C. , Endtz Hubert P. , Horst-Kreft Deborah , Doorduijn Jeanette , Lugtenburg Elly , Verbrugh Henri A. , Löwenberg Bob , de Marie Siem , van Pelt Cindy , van Belkum Alex 
Published: March 2006

ABSTRACT

A sudden increase in neutropenic hematology patients with
Candida krusei
colonization and bacteremia prompted a longitudinal epidemiological investigation. We identified 39 patients; 13 developed candidemia, and three died; 25 patients carried the same genotype. We intervened by changing antifungal prophylaxis and implementing strict infection control measures. The incidence dropped immediately.