bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Protective Immune Response Is Generated in Rainbow Trout by an OmpH-Like Surface Antigen (P18) of
Flavobacterium psychrophilum
Authors: Dumetz Fabien , Duchaud Eric , LaPatra Scott E. , Le Marrec Claire , Claverol Stéphane , Urdaci Maria-C. , Le Hénaff Michel 
Published: July 2006

ABSTRACT

Investigations of the surface characteristics of
Flavobacterium psychrophilum
, an important pathogen of fish, assisted us in identifying a surface protein termed P18. In the current study, we developed a simple and efficient procedure for the purification of this protein by a two-step method. First, P18 was selectively released from flavobacteria by a heat-HEPES treatment of the cells and then subjected to anion-exchange high-performance liquid chromatography. De novo sequencing was used to generate a fragmented peptide spectrum from purified P18. Comparison of two obtained peptide sequences with a partial genome sequence of
F. psychrophilum
(INRA, Jouy-en-Josas, France) identified one gene encoding a 166-amino-acid OmpH-like protein that mostly likely undergoes N-terminal cleavage of the 23-residue signal peptide. The susceptibility of the OmpH-like protein to proteinase K treatment and the bacteriostatic/bactericidal activities of anti-OmpH-like protein antibodies indicated that this protein is actually exposed on the surface of
F. psychrophilum
. Vaccination trials showed that the OmpH-like protein can induce a high titer of anti-OmpH-like protein antibodies which are protective. Taken together, these results suggest that this surface protein produced by
F. psychrophilum
could be used in future vaccine development as a promising candidate antigen.
Facile Recovery of Individual High-Molecular-Weight, Low-Copy-Number Natural Plasmids for Genomic Sequencing
Authors: Williams Laura E. , Detter Chris , Barry Kerrie , Lapidus Alla , Summers Anne O. 
Published: July 2006

ABSTRACT

Sequencing of the large (>50 kb), low-copy-number (<5 per cell) plasmids that mediate horizontal gene transfer has been hindered by the difficulty and expense of isolating DNA from individual plasmids of this class. We report here that a kit method previously devised for purification of bacterial artificial chromosomes (BACs) can be adapted for effective preparation of individual plasmids up to 220 kb from wild gram-negative and gram-positive bacteria. Individual plasmid DNA recovered from less than 10 ml of
Escherichia coli
,
Staphylococcus
, and
Corynebacterium
cultures was of sufficient quantity and quality for construction of high-coverage libraries, as shown by sequencing five native plasmids ranging in size from 30 kb to 94 kb. We also report recommendations for vector screening to optimize plasmid sequence assembly, preliminary annotation of novel plasmid genomes, and insights on mobile genetic element biology derived from these sequences. Adaptation of this BAC method for large plasmid isolation removes one major technical hurdle to expanding our knowledge of the natural plasmid gene pool.
Old Yellow Enzymes Protect against Acrolein Toxicity in the Yeast
Saccharomyces cerevisiae
Authors: Trotter Eleanor W. , Collinson Emma J. , Dawes Ian W. , Grant Chris M. 
Published: July 2006

ABSTRACT

Acrolein is a ubiquitous reactive aldehyde which is formed as a product of lipid peroxidation in biological systems. In this present study, we screened the complete set of viable deletion strains in
Saccharomyces cerevisiae
for sensitivity to acrolein to identify cell functions involved in resistance to reactive aldehydes. We identified 128 mutants whose gene products are localized throughout the cell. Acrolein-sensitive mutants were distributed among most major biological processes but particularly affected gene expression, metabolism, and cellular signaling. Surprisingly, the screen did not identify any antioxidants or similar stress-protective molecules, indicating that acrolein toxicity may not be mediated via reactive oxygen species. Most strikingly, a mutant lacking an old yellow enzyme (
OYE2
) was identified as being acrolein sensitive. Old yellow enzymes are known to reduce α,β-unsaturated carbonyl compounds in vitro, but their physiological roles have remained uncertain. We show that mutants lacking
OYE2
, but not
OYE3
, are sensitive to acrolein, and overexpression of both isoenzymes increases acrolein tolerance. Our data indicate that
OYE2
is required for basal levels of tolerance, whereas
OYE3
expression is particularly induced following acrolein stress. Despite the range of α,β-unsaturated carbonyl compounds that have been identified as substrates of old yellow enzymes in vitro, we show that old yellow enzymes specifically mediate resistance to small α,β-unsaturated carbonyl compounds, such as acrolein, in vivo.
The
Caenorhabditis elegans
ABL-1 Tyrosine Kinase Is Required for
Shigella flexneri
Pathogenesis
Authors: Burton Elizabeth A. , Pendergast Ann Marie , Aballay Alejandro 
Published: July 2006

ABSTRACT

Shigellosis is a diarrheal disease caused by the gram-negative bacterium
Shigella flexneri
. Following ingestion of the bacterium,
S. flexneri
interferes with innate immunity, establishes an infection within the human colon, and initiates an inflammatory response that results in destruction of the tissue lining the gut. Examination of host cell factors required for
S. flexneri
pathogenesis in vivo has proven difficult due to limited host susceptibility. Here we report the development of a pathogenesis system that involves the use of
Caenorhabditis elegans
as a model organism to study
S. flexneri
virulence determinants and host molecules required for pathogenesis. We show that
S. flexneri-
mediated killing of
C. elegans
correlates with bacterial accumulation in the intestinal tract of the animal. The
S. flexneri
virulence plasmid, which encodes a type III secretory system as well as various virulence determinants crucial for pathogenesis in mammalian systems, was found to be required for maximal
C. elegans
killing. Additionally, we demonstrate that ABL-1, the
C. elegans
homolog of the mammalian c-Abl nonreceptor tyrosine kinase ABL1, is required for
S. flexneri
pathogenesis in nematodes. These data demonstrate the feasibility of using
C. elegans
to study
S. flexneri
pathogenesis in vivo and provide insight into host factors that contribute to
S. flexneri
pathogenesis.
Biofilm Formation by
Bacillus cereus
Is Influenced by PlcR, a Pleiotropic Regulator
Authors: Hsueh Yi-Huang , Somers Eileen B. , Lereclus Didier , Wong Amy C. Lee 
Published: July 2006

ABSTRACT

The Δ
plcR
mutant of
Bacillus cereus
strain ATCC 14579 developed significantly more biofilm than the wild type and produced increased amounts of biosurfactant. Biosurfactant production is required for biofilm formation and may be directly or indirectly repressed by PlcR, a pleiotropic regulator. Coating polystyrene plates with surfactin, a biosurfactant from
Bacillus subtilis
, rescued the deficiency in biofilm formation by the wild type.
Phage Display of an Intracellular Carboxylesterase of
Bacillus subtilis
: Comparison of Sec and Tat Pathway Export Capabilities
Authors: Dröge Melloney J. , Boersma Ykelien L. , Braun Peter G. , Buining Robbert Jan , Julsing Mattijs K. , Selles Karin G. A. , van Dijl Jan Maarten , Quax Wim J. 
Published: July 2006

ABSTRACT

Using the phage display technology, a protein can be displayed at the surface of bacteriophages as a fusion to one of the phage coat proteins. Here we describe development of this method for fusion of an intracellular carboxylesterase of
Bacillus subtilis
to the phage minor coat protein g3p. The carboxylesterase gene was cloned in the g3p-based phagemid pCANTAB 5E upstream of the sequence encoding phage g3p and downstream of a signal peptide-encoding sequence. The phage-bound carboxylesterase was correctly folded and fully enzymatically active, as determined from hydrolysis of the naproxen methyl ester with

K
m

values of 0.15 mM and 0.22 mM for the soluble and phage-displayed carboxylesterases, respectively. The signal peptide directs the encoded fusion protein to the cell membrane of
Escherichia coli
, where phage particles are assembled. In this study, we assessed the effects of several signal peptides, both Sec dependent and Tat dependent, on the translocation of the carboxylesterase in order to optimize the phage display of this enzyme normally restricted to the cytoplasm. Functional display of
Bacillus
carboxylesterase NA could be achieved when Sec-dependent signal peptides were used. Although a Tat-dependent signal peptide could direct carboxylesterase translocation across the inner membrane of
E. coli
, proper assembly into phage particles did not seem to occur.
Alteration of the Rugose Phenotype in
waaG
and
ddhC
Mutants of
Salmonella enterica
Serovar Typhimurium DT104 Is Associated with Inverse Production of Curli and Cellulose
Authors: Anriany Yuda , Sahu Surashri N. , Wessels Kimberly R. , McCann Lindsay M. , Joseph Sam W. 
Published: July 2006

ABSTRACT

The rugose (also known as wrinkled or rdar) phenotype in
Salmonella enterica
serovar Typhimurium DT104 Rv has been associated with cell aggregation and the ability, at low temperature under low-osmolarity conditions, to form pellicles and biofilms. Two Tn
5
insertion mutations in genes that are involved in lipopolysaccharide (LPS) synthesis,
ddhC
(A1-8) and
waaG
(A1-9), of Rv resulted in diminished expression of colony rugosity. Scanning electron micrographs revealed that the
ddhC
mutant showed reduced amounts of extracellular matrix, while there was relatively more, profuse matrix production in the
waaG
mutant, compared to Rv. Both mutants appeared to produce decreased levels of curli, as judged by Western blot assays probed with anti-AgfA (curli) antibodies but, surprisingly, were observed to have increased amounts of cellulose relative to Rv. Comparison with a non-curli-producing mutant suggested that the alteration in curli production may have engendered the increased presence of cellulose. While both mutants had impaired biofilm formation when grown in rich medium with low osmolarity, they constitutively formed larger amounts of biofilms when the growth medium was supplemented with either glucose or a combination of glucose and NaCl. These observations indicated that LPS alterations may have opposing effects on biofilm formation in these mutants, depending upon either the presence or the absence of these osmolytes. The phenotypes of the
waaG
mutant were further confirmed in a constructed, nonpolar deletion mutant of
S. enterica
serovar Typhimurium LT2, where restoration to the wild-type phenotypes was accomplished by complementation. These results highlight the importance of an integral LPS, at both the O-antigen and core polysaccharide levels, in the modulation of curli protein and cellulose production, as well as in biofilm formation, thereby adding another potential component to the complex regulatory system which governs multicellular behaviors in
S. enterica
serovar Typhimurium.
Recurrent Seasonal Variations in Abundance and Composition of Filamentous SOL Cluster Bacteria (
Saprospiraceae
,
Bacteroidetes
) in Oligomesotrophic Lake Mondsee (Austria)
Authors: Schauer Michael , Jiang Jing , Hahn Martin W. 
Published: July 2006

ABSTRACT
The spatial and temporal variation of SOL cluster bacteria was assessed in oligomesotrophic Lake Mondsee and adjacent lakes by fluorescence in situ hybridization over two annual cycles. The filamentous SOL bacteria were present in Lake Mondsee throughout the study period, and the seasonal dynamics of the SOL community were remarkably similar with respect to both abundance and composition in the two consecutive years. Only two of the three SOL subclusters were detected in Lake Mondsee and four connected lakes. These two populations significantly differed in size distribution and demonstrated pronounced but recurrent differences in seasonality and length of period of appearance in Lake Mondsee. Extensive sampling of the lakes in September 2003 revealed low horizontal variation in the composition of the SOL community within Lake Mondsee but marked variations with depth. Between connected habitats pronounced differences in the composition and abundance of the SOL community were detected. The interaction of SOL bacteria with bacterivorous protists, mesozooplankton, and phytoplankton was investigated in order to reveal variables controlling the structure and dynamics of SOL communities. No strong indication for a bottom-up influence of phytoplankton was found, while the estimated community grazing rates of mesozooplankton on SOL bacteria indicated a top-down control of SOL abundance during mesozooplankton peaks in spring and early autumn. Furthermore, species-specific differences in grazing of mesozooplankton on SOL bacteria were observed. In general, the overall composition of SOL communities was controlled by abiotic factors (water chemistry), while their dynamics seemed to be controlled by abiotic and biotic interactions.
Improved Serological Diagnosis Stresses the Major Role of
Campylobacter jejuni
in Triggering Guillain-Barré Syndrome
Authors: Schmidt-Ott Ruprecht , Schmidt Holger , Feldmann Sylvia , Brass Felicitas , Krone Bernd , Gross Uwe 
Published: July 2006

ABSTRACT

Guillain-Barré syndrome (GBS) is a postinfectious autoimmune polyradiculoneuropathy. The most frequent antecedent pathogen is
Campylobacter jejuni
, followed by cytomegalovirus. However, more than 40% of GBS cases currently cannot be attributed to triggering events. This might be due to the shortcomings of the serological assays used for diagnosing infections, in particular for
C. jejuni
. In our study investigating 36 patients with acute GBS, standard serological methods identified the triggering viral or bacterial etiology in only 25% of cases. However, using a highly specific enzyme-linked immunosorbent assay based on two recombinant outer antigens encoded by
C. jejuni
genes Cj0017 (P39) and Cj0113 (P18), we found serological evidence of a preceding
C. jejuni
infection in 80.6% of the patients but in only 3.5% of the controls. We conclude that the role of
C. jejuni
in triggering GBS has been greatly underestimated.
Diagnosis of First Case of
Balamuthia
Amoebic Encephalitis in Portugal by Immunofluorescence and PCR
Authors: Tavares Marta , Correia da Costa Jose M. , Carpenter S. Stirling , Santos L. A. , Afonso Caldas , Aguiar Álvaro , Pereira Josue , Cardoso Ana Isabel , Schuster Frederick L. , Yagi Shigeo , Sriram Rama , Visvesvara Govinda S. 
Published: July 2006

ABSTRACT

We report here the first Portuguese case of acute fatal granulomatous encephalitis attributed to
Balamuthia mandrillaris
, initially thought to be a brain tumor, which had a progressive and fatal outcome.
Balamuthia mandrillaris
is a free-living amoeba recognized as an uncommon agent of granulomatous encephalitis. Infections have been identified in immunocompromised hosts and in immunocompetent pediatric patients.
Balamuthia
infections are very rare, with only two reported cases in Europe. The case presented here occurred in a previously healthy boy who died 5 weeks after the onset of the symptoms. No evidence of immunological deficiency was noted, and testing for human immunodeficiency virus antibodies was negative. The symptoms were initially thought to be the result of a tumor, but histopathologic examination showed evidence of amoebic infection. Immunofluorescence staining of brain tissue identified
B. mandrillaris
as the infectious agent. The diagnosis was confirmed with PCR by detecting
Balamuthia
DNA in formalin-fixed brain tissue sections. Despite initiation of empirical antimicrobial therapy for balamuthiasis, the patient died 3 weeks after being admitted to the hospital. No source of infection was readily apparent.
Identification of Bacteria in Formalin-Fixed, Paraffin-Embedded Heart Valve Tissue via 16S rRNA Gene Nucleotide Sequencing
Authors: Imrit Kavita , Goldfischer Michael , Wang Jie , Green Jaime , Levine Jerome , Lombardo Joseph , Hong Tao 
Published: July 2006

ABSTRACT

We applied 16S rRNA gene sequencing to identify bacterial species present in formalin-fixed, paraffin-embedded heart valve tissue. In 40% (12/30) of the cases, we were able to identify the bacterium to the species-genus level. For more recent cases (≤4 years), the success rate was significantly improved, to 70% (
P
< 0.001).
Comparison of New Diagnostic Tools for Management of Pediatric Mediterranean Visceral Leishmaniasis
Authors: Cruz Israel , Chicharro Carmen , Nieto Javier , Bailo Begoña , Cañavate Carmen , Figueras María-Concepción , Alvar Jorge 
Published: July 2006

ABSTRACTNew techniques are available for diagnosing leishmaniasis, but their efficacy in the identification of pediatric visceral leishmaniasis (VL) has not been compared with that of traditional methods. Blood, bone marrow, and urine samples were taken from 25 children with VL during their first clinical episode, 22 days after the start of treatment with liposomal amphotericin B (3 mg/kg/day on 6 days over a 10-day period), and when a relapse was suspected during follow-up. The results obtained suggest that antibody detection techniques, the antigen detection in urine (KAtex kit), andLeishmanianested PCR (LnPCR) analysis of the blood could be used for diagnosis of the first clinical episode. After treatment, clinical improvement was associated with negativization of Novy-MacNeal-Nicolle culture and microscopy of bone marrow aspirate, KAtex test, and LnPCR blood analysis results. Interestingly, LnPCR analysis of the bone marrow aspirate showed that sterile cure was not achieved in eight patients, two of which suffered a relapse within 10 to 20 weeks. All of the new noninvasive techniques tested showed high diagnostic sensitivity. However, LnPCR analysis of the bone marrow was the most sensitive; this test was able to detect the persistence of parasites and predict potential relapses.
High Concordance of Results of Testing for Human Papillomavirus in Cervicovaginal Samples Collected by Two Methods, with Comparison of a Novel Self-Sampling Device to a Conventional Endocervical Brush
Authors: Brink Antoinette A. T. P. , Meijer Chris J. L. M. , Wiegerinck Maarten A. H. M. , Nieboer Thedoor E. , Kruitwagen Roy F. P. M. , van Kemenade Folkert , Fransen Daalmeijer Nathalie , Hesselink Albertus T. , Berkhof Johannes , Snijders Peter J. F. 
Published: July 2006

ABSTRACT

A user-friendly self-sampling method for collecting representative cervical cell material would lower the threshold for women to respond to the invitation for cervical screening. In the present article, we introduce such a device; we have evaluated its sensitivity and specificity to detect high-grade cervical intraepithelial neoplasia (CIN), via high-risk human papillomavirus (hrHPV) detection and liquid-based cytology (LBC), compared to endocervical brush samples obtained by gynecologists. Women who had a cervical smear reading of moderate dyskaryosis or worse or a repeat equivocal Pap smear result in the cervical screening program (
n
= 64) and healthy volunteers (
n
= 32) took a self-obtained sample at home prior to their visit to the gynecological outpatient department. At the outpatient department, an endocervical brush smear was taken, followed by colposcopy and biopsy whenever applicable. Both self-obtained samples and endocervical brush samples were immediately collected in Surepath preservation solution and used for LBC and hrHPV testing (by general primer-mediated GP5+/6+ PCR). hrHPV test results showed a good concordance between the two sample types (87%; κ = 0.71), with sensitivities for prevalent high-grade CIN that did not differ significantly (92% and 95%;
P
= 1.0). The hrHPV test on self-obtained samples proved to be at least as sensitive for high-grade CIN as cytology on endocervical brush samples (34/37 versus 31/37;
P
= 0.5). LBC showed a poor concordance between self-obtained and endocervical brush samples (60%; κ = 0.27). In conclusion, self-obtained samples taken by this novel device are highly representative of the hrHPV status of the cervix. In combination with hrHPV testing, the use of this device may have implications for increasing the attendance rate for cervical screening programs.
Illustration of a Common Framework for Relating Multiple Typing Methods by Application to Macrolide-Resistant
Streptococcus pyogenes
Authors: Carriço J. A. , Silva-Costa C. , Melo-Cristino J. , Pinto F. R. , de Lencastre H. , Almeida J. S. , Ramirez M. 
Published: July 2006

ABSTRACT

The studies that correlate the results obtained by different typing methodologies rely solely on qualitative comparisons of the groups defined by each methodology. We propose a framework of measures for the quantitative assessment of correspondences between different typing methods as a first step to the global mapping of type equivalences. A collection of 325 macrolide-resistant
Streptococcus pyogenes
isolates associated with pharyngitis cases in Portugal was used to benchmark the proposed measures. All isolates were characterized by macrolide resistance phenotyping, T serotyping,
emm
sequence typing, and pulsed-field gel electrophoresis (PFGE), using SmaI or Cfr9I and SfiI. A subset of 41 isolates, representing each PFGE cluster, was also characterized by multilocus sequence typing (MLST). The application of Adjusted Rand and Wallace indices allowed the evaluation of the strength and the directionality of the correspondences between the various typing methods and showed that if PFGE or MLST data are available one can confidently predict the
emm
type (Wallace coefficients of 0.952 for both methods). In contrast,
emm
typing was a poor predictor of PFGE cluster or MLST sequence type (Wallace coefficients of 0.803 and 0.655, respectively). This was confirmed by the analysis of the larger data set available from
http://spyogenes.mlst.net
and underscores the necessity of performing PFGE or MLST to unambiguously define clones in
S. pyogenes
.
Detection of
Chlamydia trachomatis
by Nucleic Acid Amplification Testing: Our Evaluation Suggests that CDC-Recommended Approaches for Confirmatory Testing Are Ill-Advised
Authors: Schachter Julius , Chow Joan M. , Howard Holly , Bolan Gail , Moncada Jeanne 
Published: July 2006

ABSTRACT

We evaluated three CDC-suggested approaches for confirming positive nucleic acid amplification tests (NAATs) for
Chlamydia trachomatis
: (i) repeat the original test on the original specimen, (ii) retest the original specimen with a different test, and (iii) perform a different test on a duplicate specimen. For approach 1, specimens (genital swabs or first-catch urine [FCU]) initially positive by the Abbott LCx Probe System
Chlamydia trachomatis
Assay (LCx; Abbott Laboratories), the APTIMA Combo 2 Assay (AC2; Gen-Probe Inc.), the Amplicor CT/NG Assay (PCR; Roche Diagnostics Corp.), or the BD ProbeTec ET System
C. trachomatis
amplified-DNA assay (SDA; Becton Dickinson Diagnostic Systems) were retested by the same NAAT. In several evaluations, multiple efforts were made to confirm the original positive result. For approach 2, specimens initially positive by SDA and the Hybrid Capture 2 CT-ID DNA Test (HC2; Digene Corp.) were retested by different NAATs (SDA, PCR, AC2, and the APTIMA assay for
C. trachomatis
[ACT]). For approach 3, duplicate male urethral or cervical swabs were tested by SDA or by both AC2 and ACT. FCU specimens were tested by all three tests. We found that 84 to 98% of SDA, LCx, PCR, and AC2 positive results were confirmed by a repeat test and that 89 to 99% of SDA and AC2 and 93% of HC2 positive results were confirmed by different NAATs, but that some NAATs cannot be used to confirm other NAATs. The use of repeat testing did not confirm 11% of
C. trachomatis
SDA positive results that could be confirmed by more extensive testing. Doing more testing confirms more positive results; >90% of all positive NAATs could be confirmed.