bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bdellovibrio
Predation in the Presence of Decoys: Three-Way Bacterial Interactions Revealed by Mathematical and Experimental Analyses
Authors: Hobley Laura , King John R. , Sockett R. Elizabeth 
Published: October 2006

ABSTRACT

Bdellovibrio bacteriovorus
is a small, gram-negative, motile bacterium that preys upon other gram-negative bacteria, including several known human pathogens. Its predation efficiency is usually studied in pure cultures containing solely
B. bacteriovorus
and a suitable prey. However, in natural environments, as well as in any possible biomedical uses as an antimicrobial,
Bdellovibrio
is predatory in the presence of diverse decoys, including live nonsusceptible bacteria, eukaryotic cells, and cell debris. Here we gathered and mathematically modeled data from three-member cultures containing predator, prey, and nonsusceptible bacterial decoys. Specifically, we studied the rate of predation of planktonic late-log-phase
Escherichia coli
S17-1 prey by
B. bacteriovorus
HD100, both in the presence and in the absence of
Bacillus subtilis
nonsporulating strain 671, which acted as a live bacterial decoy. Interestingly, we found that although addition of the live
Bacillus
decoy did decrease the rate of
Bdellovibrio
predation in liquid cultures, this addition also resulted in a partially compensatory enhancement of the availability of prey for predation. This effect resulted in a higher final yield of
Bdellovibrio
than would be predicted for a simple inert decoy. Our mathematical model accounts for both negative and positive effects of predator-prey-decoy interactions in the closed batch environment. In addition, it informs considerations for predator dosing in any future therapeutic applications and sheds some light on considerations for modeling the massively complex interactions of real mixed bacterial populations in nature.
Generation of Useful Insertionally Blocked Sterol Degradation Pathway Mutants of Fast-Growing Mycobacteria and Cloning, Characterization, and Expression of the Terminal Oxygenase of the 3-Ketosteroid 9α-Hydroxylase in
Mycobacterium smegmatis
mc
2
155
Authors: Andor Attila , Jekkel Antónia , Hopwood David A. , Jeanplong Ferenc , Ilkőy Éva , Kónya Attila , Kurucz István , Ambrus Gábor 
Published: October 2006

ABSTRACT

Integration of the pCG79 temperature-sensitive plasmid carrying Tn
611
was used to generate libraries of mutants with blocked sterol-transforming ability of the sterol-utilizing strains
Mycobacterium smegmatis
mc
2
155 and
Mycobacterium phlei
M51-Ept. Of the 10,000 insertional mutants screened from each library, 4 strains with altered activity of the sterol-degrading enzymes were identified. A blocked 4-androstene-3,17-dione-producing
M. phlei
mutant transformed sitosterol to 23,24-dinorcholane derivatives that are useful starting materials for corticosteroid syntheses. A recombinant plasmid, pFJ92, was constructed from the genomic DNA of one of the insertional mutants of
M. smegmatis
, 10A12, which was blocked in 3-ketosteroid 9α-hydroxylation and carrying the transposon insertion and flanking DNA sequences, and used to isolate a chromosomal fragment encoding the 9α-hydroxylase. The open reading frame encodes the 383-amino-acid terminal oxygenase of 3-ketosteroid 9α-hydroxylase in
M. smegmatis
mc
2
155 and has domains typically conserved in class IA terminal oxygenases.
Escherichia coli
containing the gene could hydroxylate the steroid ring at the 9α position.
Occurrence of
sep
Insecticidal Toxin Complex Genes in
Serratia
spp. and
Yersinia frederiksenii
Authors: Dodd Steven J. , Hurst Mark R. H. , Glare Travis R. , O'Callaghan Maureen , Ronson Clive W. 
Published: October 2006

ABSTRACT

Some strains of
Serratia entomophila
and
S. proteamaculans
cause amber disease of the grass grub
Costelytra zealandica
(Coleoptera: Scarabaeidae). Three genes required for virulence,
sepABC
, are located on a large plasmid, pADAP. Sequence analysis suggests that the
sepABC
gene cluster may be part of a horizontally mobile region. This study presents evidence for the putative mobility of the
sep
genes of pADAP. Southern blot analysis showed that orthologues of the
sep
genes reside on plasmids within
S. entomophila
,
S. liquefaciens
,
S. proteamaculans
, and a plasmid from
Yersinia frederiksenii
. Three plasmids hybridized to the pADAP
sep
virulence-associated region but not the pADAP replication and conjugation regions. Subsequent DNA sequence analysis of the
Y. frederiksenii sep
-like genes, designated
tcYF1
and
tcYF2
, showed that they had 88% and 87% DNA identity to
sepA
and
sepB
, respectively. These results indicate that the
sep
genes are part of a discrete horizontally mobile region.
Natural Genetic Transformation: a Novel Tool for Efficient Genetic Engineering of the Dairy BacteriumStreptococcus thermophilus
Authors: Blomqvist Trinelise , Steinmoen Hilde , Håvarstein Leiv Sigve 
Published: October 2006

ABSTRACTStreptococcus thermophilusis widely used for the manufacture of yoghurt and Swiss or Italian-type cheeses. These products have a market value of approximately $40 billion per year, makingS. thermophilusa species that has major economic importance. Even though the fermentation properties of this bacterium have been gradually improved by classical methods, there is great potential for further improvement through genetic engineering. Due to the recent publication of three complete genome sequences, it is now possible to use a rational approach for designingS. thermophilusstarter strains with improved properties. Progress in this field, however, is hampered by a lack of genetic tools. Therefore, we developed a system, based on natural transformation, which makes genetic manipulations inS. thermophiluseasy, rapid, and highly efficient. The efficiency of this novel tool should make it possible to construct food-grade mutants ofS. thermophilus, opening up exciting new possibilities that should benefit consumers as well as the dairy industry.
Immunoquantitative Real-Time PCR for Detection and Quantification of
Staphylococcus aureus
Enterotoxin B in Foods
Authors: Rajkovic Andreja , Moualij Benaissa El , Uyttendaele Mieke , Brolet Philippe , Zorzi Willy , Heinen Ernst , Foubert Ellen , Debevere Johan 
Published: October 2006

ABSTRACT

A real-time immunoquantitative PCR (iqPCR) method for detection of
Staphylococcus aureus
enterotoxin B (SEB) was developed and evaluated using both pure cultures and foods. The assay consisted of immunocapture of SEB and real-time PCR amplification of the DNA probe linked to the detection antibody. iqPCR was compared to an in-house enzyme-linked immunosorbent assay (ELISA) using the same couple of capture-detection antibodies and to commercial kits for detection of
S. aureus
enterotoxins (SE). The iqPCR was approximately 1,000 times more sensitive (<10 pg ml
−1
) than the in-house ELISA and had a dynamic range of approximately 10 pg ml
−1
to approximately 30,000 pg ml
−1
. iqPCR was not inhibited by any of the foods tested and was able to detect SEB present in these foods. No cross-reactivity with SE other than SEB was observed. Application of iqPCR for detection of SEB in cultures of
S. aureus
revealed the onset of SEB production after 4 h of incubation at 22, 37, and 42°C, which was in the first half of the exponential growth phase. The total amounts of SEB produced by the two strains tested were larger at 42°C than at 37°C and were strain dependent.
Use of a Multiantigen Detection Algorithm for Diagnosis of Kaposi's Sarcoma-Associated Herpesvirus Infection
Authors: Laney A. Scott , Peters Jonathan S. , Manzi Susan M. , Kingsley Lawrence A. , Chang Yuan , Moore Patrick S. 
Published: October 2006

ABSTRACT

The ability to readily and accurately diagnose Kaposi's sarcoma-associated herpesvirus (KSHV, or human herpesvirus 8) infection in individuals remains a demanding task. Among the available diagnostic methods, sensitivities and specificities range widely, and many are inadequate for large-scale screening studies. We examined a serological algorithm for detecting KSHV in human sera having high sensitivity and specificity. This method uses previously described open reading frame (ORF) K8.1 and ORF65 peptide-based enzyme-linked immunosorbent assays and a novel purified recombinant full-length LANA1 protein. We generated two multiantigen algorithms: one that maximized sensitivity and one that maximized specificity. These serological algorithms were then used to evaluate seroprevalence rates among populations of clinical and epidemiological importance. The serological algorithms yielded sensitivities of 96% and 93% and specificities of 94% and 98% for the more sensitive and specific algorithms, respectively. Among kidney donors, seroprevalence was low, 4.0% (2/50), and similar to that of blood donors (
P
= 0.46; odds ratio [OR], 1.4; confidence interval [CI], 0.14 to 7.9) using the highly specific algorithm. Using the sensitive algorithm, 8.0% (4/50) were infected compared to 6.4% (16/250) observed among blood donors (OR, 1.3; CI, 0.41 to 4.0;
P
= 0.43). Among subjects requiring bone marrow transplantation, seroprevalence rates were not elevated compared to those of blood donors (OR, 2.0; 95% CI, 0.10 to 122.9;
P
= 0.50). Because the need for high-quality KSHV detection methods are warranted and because questions remain about the optimal methods for assessing KSHV infection in individuals, we propose a systematic approach to standardize and optimize the assessment of KSHV infection rates using a combination of established and novel serological assays and methods.
Common Virulence Factors and Genetic Relationships between O18:K1:H7
Escherichia coli
Isolates of Human and Avian Origin
Authors: Moulin-Schouleur Maryvonne , Schouler Catherine , Tailliez Patrick , Kao Mu-Rong , Brée Annie , Germon Pierre , Oswald Eric , Mainil Jacques , Blanco Miguel , Blanco Jorge 
Published: October 2006

ABSTRACT

Extraintestinal pathogenic (ExPEC)
Escherichia coli
strains of serotype O18:K1:H7 are mainly responsible for neonatal meningitis and sepsis in humans and belong to a limited number of closely related clones. The same serotype is also frequently isolated from the extraintestinal lesions of colibacillosis in poultry, but it is not well known to what extent human and avian strains of this particular serotype are related. Twenty-two ExPEC isolates of human origin and 33 isolates of avian origin were compared on the basis of their virulence determinants, lethality for chicks, pulsed-field gel electrophoresis (PFGE) patterns, and classification in the main phylogenetic groups. Both avian and human isolates were lethal for chicks and harbored similar virulence genotypes. A major virulence pattern, identified in 75% of the isolates, was characterized by the presence of F1 variant fimbriae; S fimbriae; IbeA; the aerobactin system; and genomic fragments A9, A12, D1, D7, D10, and D11 and by the absence of P fimbriae, F1C fimbriae, Afa adhesin, and CNF1. All but one of the avian and human isolates also belonged to major phylogenetic group B2. However, various subclonal populations could be distinguished by PFGE in relation to animal species and geographical origin. These results demonstrate that very closely related clones can be recovered from extraintestinal infections in humans and chickens and suggest that avian pathogenic
E. coli
isolates of serotype O18:K1:H7 are potential human pathogens.
Occurrence of Carbapenem-Resistant
Acinetobacter baumannii
Clones at Multiple Hospitals in London and Southeast England
Authors: Coelho Juliana M. , Turton Jane F. , Kaufmann Mary E. , Glover Judith , Woodford Neil , Warner Marina , Palepou Marie-France , Pike Rachel , Pitt Tyrone L. , Patel Bharat C. , Livermore David M. 
Published: October 2006

ABSTRACT

From late 2003 to the end of 2005, the Health Protection Agency's national reference laboratories received approximately 1,600 referrals of
Acinetobacter
spp., including 419 and 58 examples, respectively, of two carbapenem-resistant
Acinetobacter baumannii
lineages, designated OXA-23 clones 1 and 2. Representatives of these clones were obtained from 40 and 8 hospitals, respectively, in London or elsewhere in Southeast England. Both clones had
bla
OXA-23
-like genes, as well as the intrinsic (but downregulated)
bla
OXA-51
-like carbapenemase genes typical of
A. baumannii
. Both were highly multiresistant: only colistin and tigecycline remained active versus OXA-23 clone 1 isolates; OXA-23 clone 2 isolates were also susceptible to amikacin and minocycline. These lineages increase the burden created by the southeast (SE) clone, a previously reported
A. baumannii
lineage with variable carbapenem resistance contingent on upregulation of the
bla
OXA-51
-like gene. Known since 2000, the SE clone had been referred from over 40 hospitals by the end of 2005, with 627 representatives received by the reference laboratories. The OXA-23 clone 2 is now in decline, but OXA-23 clone 1 continues to be referred from new sites, as does the SE clone. Their spread is forcing the use of unorthodox therapies, principally colistin and tigecycline, although the optimal regimens remain uncertain.
Expertise of Laboratories in Viral Load Quantification, Genotyping, and Precore Mutant Determination for Hepatitis B Virus in a Multicenter Study
Authors: Laperche Syria , Thibault Vincent , Bouchardeau Françoise , Alain Sophie , Castelain Sandrine , Gassin Michelle , Gueudin Marie , Halfon Philippe , Larrat Sylvie , Lunel Françoise , Martinot-Peignoux Michèle , Mercier Bernard , Pawlotsky Jean-Michel , Pozzetto Bruno , Roque-Afonso Anne-Marie , Roudot-Thoraval Françoise , Sauné Karine , Lefrère Jean-Jacques 
Published: October 2006

ABSTRACTA national evaluation study was performed in 14 specialized laboratories with the objective of assessing their capacities to provide (i) hepatitis B virus (HBV) viral loads (VL), (ii) HBV genotypes, and(iii) identification of precore/core mutants. The panel consisted of 12 HBV DNA-positive samples with VLs from 2.8 to 9.1 log10copies/ml, different HBV genotypes (A to F), and 3 mutant and 9 wild-type samples at nucleotide 1896. The coefficients of variation of the mean VLs ranged from 2.4% to 10.4% with the Cobas HBV Monitor assay, from 1.8% to 5.5% with the CobasTaqMan 48, from 1.5 to 26.2% with RealArt HBV PCR, and from 0 to 7% with branched DNA (bDNA). The Cobas Monitor assay underestimated the VLs of genotype F samples, with differences ranging from 1.4 to 2.4 log10copies/ml. The accuracies of genotype determinations ranged from 33% to 100%, and those of precore mutant determinations ranged from 25 to 100%. This study showed some drawbacks of two widely used assays: (i) Cobas Monitor has a narrow dynamic range and underestimates genotype F sample VLs and (ii) bDNA shows poor sensitivity and may fail to identify patients with low VLs. With higher performance in terms of analytical sensitivity combined with a larger dynamic range and an ability to quantify the main genotypes equally, real-time PCR methods appear more appropriate for accurate monitoring of HBV DNA quantification. Furthermore, the clinical implications of HBV genotyping and the determination of precore/core mutants need to be clearly stated to justify the standardization of these methods.
Genotyping of Measles Virus in Clinical Specimens on the Basis of Oligonucleotide Microarray Hybridization Patterns
Authors: Neverov Alexander A. , Riddell Michaela A. , Moss William J. , Volokhov Dmitriy V. , Rota Paul A. , Lowe Luis E. , Chibo Doris , Smit Sheilagh B. , Griffin Diane E. , Chumakov Konstantin M. , Chizhikov Vladimir E. 
Published: October 2006

ABSTRACT
An oligonucleotide microarray hybridization method for identification of most known measles virus (MV) genotypes was developed. Like the conventional genotyping method, the microarray relied on detecting sequence differences in the 450-nucleotide region coding for the COOH-terminal 150 amino acids of the nucleoprotein (N). This region was amplified using PCR primers binding to all known MV genotypes. The microarray included 71 pairs of oligonucleotide probes (oligoprobes) immobilized on glass slides. Each pair consisted of a genotype-specific oligoprobe, which matched the sequence of only one target genotype, and a control oligoprobe, which contained mismatches at the nucleotide positions unique to this genotype. A pattern recognition algorithm based on cluster analysis of the ratios of hybridization signals from specific and control oligoprobes was used to identify the specific MV genotype. Following the initial validation, the method was used for rapid genotyping of two panels of coded samples. The results of this study showed good sensitivity (90.7%), specificity (100%), and genotype agreement (91.8%) for the new method compared to the results of genotyping conducted using phylogenetic analysis of viral sequences of the C terminus of the N gene. In addition, the microarray demonstrated the ability to identify potential new genotypes of MV based on the similarity of their hybridization patterns with those of known MV genotypes.
Genetic Background and Antibiotic Resistance ofStaphylococcus aureusStrains Isolated in the Republic of Georgia
Authors: Revazishvili Tamara , Bakanidze Lela , Gomelauri Tsaro , Zhgenti Ekaterine , Chanturia Gvantsa , Kekelidze Merab , Rajanna Chythanya , Kreger Arnold , Sulakvelidze Alexander 
Published: October 2006

ABSTRACTThe genetic composition and antibiotic sensitivities of 50 clinical isolates ofStaphylococcus aureusobtained from various clinics in the Republic of Georgia were characterized.S. aureusstrains ATCC 700699 and ATCC 29737 were included as reference standards in all analyses. All 52 strains had identical 16S rRNA profiles. In contrast, pulsed-field gel electrophoresis (PFGE) identified 20 distinct PFGE types among the 52 strains examined, which indicates that PFGE is more discriminating than is 16S rRNA sequence analysis for differentiatingS. aureusstrains. The results of our PFGE typing also suggest that multiple genetic subpopulations (related at the ca. 85% similarity level, based on their SmaI PFGE patterns) exist among the GeorgianS. aureusstrains. Twenty-two of the 50 Georgian strains were methicillin resistant and PCR positive formecA, and 5 strains were methicillin sensitive even though they possessedmecA. None of the strains were vancomycin resistant or containedvanA. The nucleotide sequences ofmecAfragments obtained from allmecA-containing strains were identical. Our data indicate that the population ofS. aureusstrains in Georgia is fairly homogeneous and that the prevalence of methicillin-resistant,mecA-positive strains is relatively high in that country.
Age Dependence of Adenovirus-Specific Neutralizing Antibody Titers in Individuals from Sub-Saharan Africa
Authors: Thorner Anna R. , Vogels Ronald , Kaspers Jorn , Weverling Gerrit J. , Holterman Lennart , Lemckert Angelique A. C. , Dilraj Athmanundh , McNally Lisa M. , Jeena Prakash M. , Jepsen Soren , Abbink Peter , Nanda Anjali , Swanson Patricia E. , Bates Andrew T. , O'Brien Kara L. , Havenga Menzo J. E. , Goudsmit Jaap , Barouch Dan H. 
Published: October 2006

ABSTRACT
We assessed neutralizing antibody titers to adenovirus serotype 5 (Ad5) and six rare adenovirus serotypes, serotypes 11, 35, 50, 26, 48, and 49, in pediatric populations in sub-Saharan Africa. We observed a clear age dependence of Ad5-specific neutralizing antibody titers. These data will help to guide the development of Ad vector-based vaccines for human immunodeficiency virus type 1 and other pathogens.
Comparative Study of Surgical Instruments from Sterile-Service Departments for Presence of Residual Gram-Negative Endotoxin and Proteinaceous Deposits
Authors: Lipscomb I. P. , Sihota A. K. , Keevil C. W. 
Published: October 2006

ABSTRACT

The ineffective cleaning of surgical instruments may be a vector for the transmission of hospital-acquired infections. The aim of this research was to investigate whether further decontamination procedures need to be instigated in sterile-service departments (SSDs) to reduce the risk of nosocomial illnesses, such as endotoxemia, sepsis, or iatrogenic Creutzfeldt-Jakob disease (to date, 1,147 cases of confirmed Creutzfeldt-Jakob disease deaths in the United Kingdom since 1990 have been reported). Instrument sets were obtained from nine anonymous United Kingdom National Health Service (NHS) primary care trust SSDs. The investigation implemented an advanced light microscopy technique, episcopic differential interference contrast microscopy with the sensitive fluorescent reagents SYPRO Ruby and 4′,6-diamidino-2-phenylindole dihydrochloride (DAPI), to detect proteinaceous and microbial contamination levels. Gram-negative lipopolysaccharide (LPS) endotoxin was monitored using a dansylated polymyxin B fluorochrome agent. None of the 260 instruments examined displayed signs of microbial colonization or LPS endotoxin contamination. However, over 60 percent of the instruments showed a high degree of protein soiling (0.4 to 4.2 μg protein/mm
2
). Some instruments appeared soiled with crystalline deposits that may consist of a potentially hazardous material contributing to inflammation and/or surgical shock. It is clear that the overall standard for cleaning must be raised in order to fulfill the imminent introduction of new European standards and to reduce the risk of cross-patient contamination and iatrogenic transmission.
Patched homologue 1 mutations in four Japanese families with basal cell nevus syndrome
Authors: Matsuzawa N , Nagao T , Shimozato K , Niikawa N , Yoshiura K-i 
Published: October 2006

Aim:To search for patched homologue 1 (PTCH1) mutations in four families with basal cell nevus syndrome (BCNS).Methods:Mutation analysis ofPTCH1in unrelated Japanese families affected with BCNS was carried out by direct sequencing.Results:Six novelPTCH1mutations, 833G→A in exon 6, 1415C→A and 1451G→T in exon 10, 2798delC in exon 17, 2918–2925dupAGTTCCCT in exon 18 and 3956C→A in exon 23, were identified.Conclusions:Among the sixPTCH1mutations, two frameshift mutations (2798delC and 2918–2925dupAGTTCCCT) and one nonsense mutation (833G→A) are predicted to lead to premature termination ofPTCH1protein translation. Three simultaneous mutations, 1415C→A (A472D) and 1451G→T (G484V) in exon 10, and 3956G→A (R1319H) in exon 23, were found on one allele in only affected members in one family and none of them were found among 90 unrelated healthy Japanese. The three mutations on one chromosome may have resulted from errors in the recombinational repair process and this is the first report on thePTCH1mutations due to such a mechanism.
Expression of c-kit in human osteosarcoma and its relevance as a prognostic marker
Authors: Sulzbacher Irene , Birner Peter , Toma Cyril , Wick Nikolaus , Mazal Peter R 
Published: October 2006

Aims:To examine the prognostic relevance of c-kit expression in human osteosarcomas and to evaluate the mutation status in exon 9 and exon 11 of the c-kit gene.Methods:c-kit expression was examined in 100 human osteosarcomas by immunohistochemistry using paraffin embedded tumour tissues, and capillary sequencing of genomic DNA was performed to search for mutations in exons 9 and 11 of the c-kit gene.Results:20 osteosarcomas showed c-kit expression ranging from 5% to 90% (mean 5.9%; SD 16.74%). Furthermore, DNA sequences of exon 9 and exon 11 of the c-kit gene were not altered in these tumours. Overall and disease free survival analysis did not reveal any differences between patients with osteosarcoma with c-kit expression and those with c-kit negative tumours.Conclusions:C-kit expression is not a prognostic marker in patients with osteosarcoma. The protein expression is not linked to mutations in exon 9 or exon 11 of the c-kit gene. Therefore, these exons may not function as targets for treatment modalities based on the suppression of c-kit tyrosine kinase activity.