bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensitive Determination of Microbial Growth by Nucleic Acid Staining in Aqueous Suspension
Authors: Martens-Habbena Willm , Sass Henrik 
Published: January 2006

ABSTRACT

The determination of cell numbers or biomass in laboratory cultures or environmental samples is usually based on turbidity measurements, viable counts, biochemical determinations (e.g., protein and lipid measurements), microscopic counting, or recently, flow cytometric analysis. In the present study, we developed a novel procedure for the sensitive quantification of microbial cells in cultures and most-probable-number series. The assay combines fluorescent nucleic acid staining and subsequent fluorescence measurement in suspension. Six different fluorescent dyes (acridine orange, DAPI [4′,6′-diamidino-2-phenylindole], ethidium bromide, PicoGreen, and SYBR green I and II) were evaluated. SYBR green I was found to be the most sensitive dye and allowed the quantification of 50,000 to up to 1.5 × 10
8
Escherichia coli
cells per ml sample. The rapid staining procedure was robust against interference from rRNA, sample fixation by the addition of glutaric dialdehyde, and reducing agents such as sodium dithionite, sodium sulfide, and ferrous sulfide. It worked well with phylogenetically distant bacterial and archaeal strains. Excellent agreement with optical density measurements of cell increases was achieved during growth experiments performed with aerobic and sulfate-reducing bacteria. The assay offers a time-saving, more sensitive alternative to epifluorescence microscopy analysis of most-probable-number dilution series. This method simplifies the quantification of microbial cells in pure cultures as well as enrichments and is particularly suited for low cell densities.
Heat Resistance and Mechanism of Heat Inactivation in Thermophilic Campylobacters
Authors: Nguyen Hong T. T. , Corry Janet E. L. , Miles Christopher A. 
Published: January 2006

ABSTRACT

The heat resistance of
Campylobacter jejuni
strains AR6 and L51 and the heat resistance of
Campylobacter coli
strains DR4 and L6 were measured over the temperature range from 50 to 60°C by two methods. Isothermal measurements yielded
D
55
values in the range from 4.6 to 6.6 min and
z
values in the range from 5.5 to 6.3°C. Dynamic measurements using differential scanning calorimetry (DSC) during heating at a rate of 10°C/min yielded
D
55
values of 2.5 min and 3.4 min and
z
values of 6.3°C and 6.5°C for AR6 and DR4, respectively. Both dynamic and isothermal methods yielded mean
D
55
values that were substantially greater than those reported previously (0.75 to 0.95 min). DSC analysis of each strain during heating at a rate of 10°C/min yielded a complex series of overlapping endothermic peaks, which were assigned to cell wall lipids, ribosomes, and DNA. Measurement of the decline in the numbers of CFU in calorimetric samples as they were heated showed that the maximum rate of cell death occurred at 56 to 57°C, which is close to the value predicted mathematically from the isothermal measurements of
D
and
z
(61°C). Both estimates were very close to the peak
m
1
values, 60 to 62°C, which were tentatively identified with unfolding of the 30S ribosome subunit, showing that cell death in
C. jejuni
and
C. coli
coincided with unfolding of the most thermally labile regions of the ribosome. Other measurements indicated that several essential proteins, including the α and β subunits of RNA polymerase, might also unfold at the same time and contribute to cell death.
Sequential Multiplex PCR Approach for Determining Capsular Serotypes of
Streptococcus pneumoniae
Isolates
Authors: Pai Rekha , Gertz Robert E. , Beall Bernard 
Published: January 2006

ABSTRACT

Accurate serotyping is essential to monitor the changes in the seroepidemiology of
Streptococcus pneumoniae
. We devised a simple and schematic sequence-based system of seven multiplex PCRs, in a sequence order based upon Active Bacterial Core surveillance (ABCs) serotype distribution during 2002 to 2003, to reliably deduce specific pneumococcal serotypes. A total of 421 isolates from ABCs were randomly chosen to evaluate this system. Two hundred twenty-nine of the isolates (54.3%) were specifically assigned 1 of 17 serotypes by the multiplex PCR system, with the results in complete concordance with conventional serotyping. One hundred seventy-two additional isolates (40.9%) were assigned to 11 specific sets of 2 to 4 serotypes that with one exception (serotypes 6A and 6B) consisted of the single frequently occurring targeted serotype and 1 to 3 additional rare serotypes primarily within the same serogroup as the targeted serotype. Only 20 isolates (4.8%) could not be assigned specific serotypes or serotype sets, since they were either of rare serotypes not included in the assay design or were nonserotypeable. Overall, we found this system to be highly reliable, with the potential to greatly reduce our reliance upon conventional serotyping. Especially important is the capability of this system to give serotype-determining potential to any facility that lacks the expensive typing sera and expertise needed for conventional serotyping yet has the modest equipment necessary for DNA amplification and electrophoresis.
Molecular Characterization of
Haemophilus ducreyi
Isolates from Different Geographical Locations
Authors: Mbwana J. , Bölin I. , Lyamuya E. , Mhalu F. , Lagergård T. 
Published: January 2006

ABSTRACT

The technique of random amplified polymorphic DNA (RAPD) was adapted and optimized to study
Haemophilus ducreyi
isolates. A panel of 43 strains isolated from chancroid patients from different countries in Africa, Europe, North America, and Asia were characterized. The strains were also studied with respect to lipooligosaccharide (LOS) migration and immunoblotting patterns and the presence of cytolethal distending toxin genes. The RAPD method with the OPJ20 primer generated nine banding patterns (1 to 9). The majority of the isolates were clustered into two major profiles, 14 and 13 strains into profiles 1 and 2, respectively, and just a few strains revealed patterns 3 and 4. The isolates from Thailand were exceptional in that they showed greater diversity and were represented by six different RAPD patterns, i.e., patterns 3 and 5 to 9. The LOS migration and immunoblotting analyses revealed two different patterns, which indicated long and short forms of LOS; the former was found in 20/23 tested strains. Two strains that expressed the short form of LOS were grouped into RAPD pattern 4. The absence of
cdtABC
genes was observed in only 4/23 strains, and three of these isolates were assigned to RAPD pattern 4. Our results showed limited genotypic and phenotypic variations among
H. ducreyi
strains, as supported by the conserved RAPD and LOS profiles shared by the majority of the studied strains. However, the RAPD method identified differences between strains, including those from different geographic areas, which indicate the potential of RAPD as an epidemiological tool for the typing of
H. ducreyi
isolates in countries where chancroid is endemic.
Evolution and Molecular Characterization of Methicillin-Resistant
Staphylococcus aureus
Epidemic and Sporadic Clones in Cordoba, Argentina
Authors: Sola Claudia , Cortes Paulo , Saka Hector A. , Vindel Ana , Bocco José Luis 
Published: January 2006

ABSTRACT

Since 1999, a new, epidemic, methicillin-resistant
Staphylococcus aureus
(MRSA) strain, named the “Cordobes clone,” has emerged in Argentina and coexists with the pandemic Brazilian clone. The purpose of this study was to determine the stability over time of the new clone and to investigate its evolutionary relationship with epidemic international MRSA lineages and with other MRSA and methicillin-susceptible
S. aureus
(MSSA) major clones distributed in this region. One hundred three MRSA isolates recovered in 2001 from Cordoba, Argentina, hospitals and 31 MSSA strains collected from 1999 to 2002 were analyzed by their antibiotic resistance patterns, phage typing, and pulsed-field gel electrophoresis. Additionally, representative members of most MRSA defined genotypes (A, B, C, E, K, and I) were characterized by multilocus sequence typing (MLST) and
spaA
and SCC
mec
typing. The most prevalent MSSA pulsotypes were also analyzed by MLST. Our results support the displacement of the Brazilian clone (sequence type [ST] 239,
spaA
type WGKAOMQ, SCC
mec
type IIIA) by the Cordobes clone (ST5,
spaA
type TIMEMDMGMGMK, SCC
mec
type I) in the hospital environment. MRSA and MSSA isolates shared only ST5. The data support the origin of the Cordobes clone as a member of a lineage that includes the pediatric and New York/Japan international clones and that is genetically related to the British EMRSA-3 strain. Interestingly, the pediatric clone, isolated from most community-acquired infections in Cordoba, was characterized by ST100, a single-locus variant of ST5 and a new variant of SCC
mec
type related to SCC
mec
type IVc.
Community-Associated Methicillin-Resistant
Staphylococcus aureus
Epidemic Clone USA300 in Isolates from Florida and Washington
Authors: Roberts Jill C. , Krueger Robin L. , Peak K. Kealy , Veguilla William , Cannons Andrew C. , Amuso Philip T. , Cattani Jacqueline 
Published: January 2006

ABSTRACT

We examined 299 methicillin-resistant, community-associated
Staphylococcus aureus
isolates from Florida and Washington State for the presence of the USA300 epidemic clone. Pulsed-field gel electrophoresis demonstrated the epidemic clone in 43% of our
S. aureus
strains and in isolates from both states. The majority of the USA300 isolates (88%) were from wound infections.
Novel PCR-Restriction Fragment Length Polymorphism Analysis for Rapid Typing of Staphylococcal Cassette Chromosome
mec
Elements
Authors: Yang Jin Ah , Park Dae Won , Sohn Jang Wook , Kim Min Ja 
Published: January 2006

ABSTRACT

We developed a novel PCR-restriction fragment length polymorphism test for the
ccrB
gene by using HinfI and BsmI for rapid typing of staphylococcal cassette chromosome
mec
(SCC
mec
). When tested with reference strains and methicillin-resistant
Staphylococcus aureus
isolates, the method proved to be valid and useful for rapid identification of four SCC
mec
types, especially type IV.
Serological Evidence for Increased Human Exposure to
Burkholderia pseudomallei
following the Tsunami in Southern Thailand
Authors: Wuthiekanun Vanaporn , Chierakul Wirongrong , Rattanalertnavee Jurairat , Langa Sayan , Sirodom Damrong , Wattanawaitunechai Charnkij , Winothai Wut , White Nicholas J. , Day Nicholas , Peacock Sharon J. 
Published: January 2006

ABSTRACT

A serological study was performed to determine recent human exposure to
Burkholderia pseudomallei
(the cause of melioidosis) in residents of southern Thailand affected by the tsunami of 26 December 2004. The findings were suggestive of increased recent exposure in both tsunami survivors and uninjured bystanders. Survivors of the Thailand tsunami may be at increased risk of melioidosis.
Use of Variations in Staphylococcal Interspersed Repeat Units for Molecular Typing of Methicillin-Resistant
Staphylococcus aureus
Strains
Authors: Hardy Katherine J. , Oppenheim Beryl A. , Gossain Savita , Gao Fang , Hawkey Peter M. 
Published: January 2006

ABSTRACT

Staphylococcal interspersed repeat unit typing has previously been shown to have the ability to discriminate between epidemic methicillin-resistant
Staphylococcus aureus
strains in the United Kingdom. The current study illustrates its ability to distinguish between strains within an endemic setting thereby providing a rapid transportable typing method for the identification of transmission events.
Molecular Analysis of Human and Bovine Tubercle Bacilli from a Local Setting in Nigeria
Authors: Cadmus Simeon , Palmer Si , Okker Melissa , Dale James , Gover Karen , Smith Noel , Jahans Keith , Hewinson R. Glyn , Gordon Stephen V. 
Published: January 2006

ABSTRACT

To establish a molecular epidemiological baseline for the strains causing tuberculosis in Nigeria, a survey of isolates from humans and cattle was carried out. Spoligotyping and variable-number tandem-repeat analysis revealed that the majority of tuberculosis disease in humans in Ibadan, southwestern Nigeria, is caused by a single, closely related group of
Mycobacterium tuberculosis
strains. Using deletion typing, we show that approximately 13% of the disease in humans in this sample was caused by strains of
Mycobacterium africanum
and
Mycobacterium bovis
rather than
M. tuberculosis
. Molecular analysis of strains of
M. bovis
recovered from Nigerian cattle show that they form a group of closely related strains that show similarity to strains from neighboring Cameroon. Surprisingly, the strains of
M. bovis
recovered from humans do not match the molecular type of the cattle strains, and possible reasons for this are discussed. This is the first molecular analysis of
M. tuberculosis
complex strains circulating among humans and cattle in Nigeria, the results of which have significant implications for disease control.
Development and Evaluation of a Real-Time PCR Assay Targeting the Type III Secretion System of
Burkholderia pseudomallei
Authors: Novak Ryan T. , Glass Mindy B. , Gee Jay E. , Gal Daniel , Mayo Mark J. , Currie Bart J. , Wilkins Patricia P. 
Published: January 2006

ABSTRACT

Here we report on the development of a discriminatory real-time assay for the rapid identification of
Burkholderia pseudomallei
isolates and the evaluation of this assay for sensitivity against related species and detection in spiked human blood samples. The assay targets a 115-base-pair region within
orf2
of the
B. pseudomallei
type III secretion system gene cluster and distinguishes
B. pseudomallei
from other microbial species. Assay performance was evaluated with 224 geographically, temporally, and clinically diverse
B. pseudomallei
isolates from the Centers for Disease Control and Prevention strain collection. This represents the first real-time PCR for rapid and sensitive identification of
B. pseudomallei
that has been tested for cross-reactivity with 23
Burkholderia mallei
, 5
Burkholderia thailandensis
, and 35
Burkholderia
and 76 non
-Burkholderia
organisms which have historically presented diagnostic challenges. The assay performed with 100% specificity. The limit of detection was found to be 76 femtograms of DNA (equivalent to 5.2 × 10
3
genome equivalents per ml) in a single PCR. In spiked human blood, the assay could detect as few as 8.4 × 10
3
CFU per ml. This rapid assay is a valuable tool for identification of
B. pseudomallei
and may improve diagnosis in regions endemic for melioidosis.
PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change
Authors: Fourment Mathieu , Gibbs Mark J 
Published: January 2006

Abstract

Background
Phylogenies are commonly used to analyse the differences between genes, genomes and species. Patristic distances calculated from tree branch lengths describe the amount of genetic change represented by a tree and are commonly compared with other measures of mutation to investigate the substitutional processes or the goodness of fit of a tree to the raw data. Up until now no universal tool has been available for calculating patristic distances and correlating them with other genetic distance measures.

Results
PATRISTICv1.0 is a java program that calculates patristic distances from large trees in a range of file formats and allows graphical and statistical interpretation of distance matrices calculated by other programs.

Conclusion
The software overcomes some logistic barriers to analysing signals in sequences. In additional to calculating patristic distances, it provides plots for any combination of matrices, calculates commonly used statistics, allows data such as isolation dates to be entered and reorders matrices with matching species or gene labels. It will be used to analyse rates of mutation and substitutional saturation and the evolution of viruses. It is available at http://biojanus.anu.edu.au/programs/ and requires the Java runtime environment.
Which strategy is better for linkage analysis: single-nucleotide polymorphisms or microsatellites? Evaluation by identity-by-state – identity-by-descent transformation affected sib-pair method on GAW14 data
Authors: Yue Qingqi , Apprey Victor , Bonney George E 
Published: January 2006

Abstract
The central issue for Genetic Analysis Workshop 14 (GAW14) is the question, which is the better strategy for linkage analysis, the use of single-nucleotide polymorphisms (SNPs) or microsatellite markers? To answer this question we analyzed the simulated data using Duffy's SIB-PAIR program, which can incorporate parental genotypes, and our identity-by-state – identity-by-descent (IBS-IBD) transformation method of affected sib-pair linkage analysis which uses the matrix transformation between IBS and IBD. The advantages of our method are as follows: the assumption of Hardy-Weinberg equilibrium is not necessary; the parental genotype information maybe all unknown; both IBS and its related IBD transformation can be used in the linkage analysis; the determinant of the IBS-IBD transformation matrix provides a quantitative measure of the quality of the marker in linkage analysis. With the originally distributed simulated data, we found that 1) for microsatellite markers there are virtually no differences in types I and II error rates when parental genotypes were or were not used; 2) on average, a microsatellite marker has more power than a SNP marker does in linkage detection; 3) if parental genotype information is used, SNP markers show lower type I error rates than microsatellite markers; and 4) if parental genotypes are not available, SNP markers show considerable variation in type I error rates for different methods.
Linkage analysis of alcohol dependence using MOD scores
Authors: Strauch Konstantin , Fürst Robert , Rüschendorf Franz , Windemuth Christine , Dietter Johannes , Flaquer Antonia , Baur Max P , Wienker Thomas F 
Published: January 2006

Abstract
Alcohol dependence is a typical example of a complex trait that is governed by several genes and for which the mode of inheritance is unknown. We analyzed the microsatellite markers and the Affymetrix single-nucleotide polymorphisms (SNPs) for a subset of the Collaborative Study on the Genetics of Alcoholism family sample, 93 pedigrees of Caucasian ancestry comprising 919 persons, 390 of whom are affected according to DSM III-R and Feighner criteria. In particular, we performed parametric single-marker linkage analysis using MLINK of the LINKAGE package (for the microsatellite data), as well as multipoint MOD-score analysis with GENEHUNTER-MODSCORE (for the microsatellite and SNP data). By use of two liability classes, different penetrances were assigned to males and females. In order to investigate parent-of-origin effects, we calculated MOD scores under trait models with and without imprinting. In addition, for the microsatellite data, the MOD-score analysis was performed with sex-averaged as well as sex-specific maps. The highest linkage peaks were obtained on chromosomes 1, 2, 7, 10, 12, 13, 15, and 21. There was evidence for paternal imprinting at the loci on chromosomes 2, 10, 12, 13, 15, and 21. A tendency to maternal imprinting was observed at two loci on chromosome 7. Our findings underscore the fact that an adequate modeling of the genotype-phenotype relation is crucial for the genetic mapping of a complex trait.
A genome-wide linkage analysis of alcoholism on microsatellite and single-nucleotide polymorphism data, using alcohol dependence phenotypes and electroencephalogram measures
Authors: Zhang Chun , Cawley Simon , Liu Guoying , Cao Manqiu , Gorrell Harley , Kennedy Giulia C 
Published: January 2006

Abstract
The Collaborative Study on the Genetics of Alcoholism (COGA) is a large-scale family study designed to identify genes that affect the risk for alcoholism and alcohol-related phenotypes. We performed genome-wide linkage analyses on the COGA data made available to participants in the Genetic Analysis Workshop 14 (GAW 14). The dataset comprised 1,350 participants from 143 families. The samples were analyzed on three technologies: microsatellites spaced at 10 cM, Affymetrix GeneChip® Human Mapping 10 K Array (HMA10K) and Illumina SNP-based Linkage III Panel. We used ALDX1 and ALDX2, the COGA definitions of alcohol dependence, as well as electrophysiological measures TTTH1 and ECB21 to detect alcoholism susceptibility loci. Many chromosomal regions were found to be significant for each of the phenotypes at a p-value of 0.05. The most significant region for ALDX1 is on chromosome 7, with a maximum LOD score of 2.25 for Affymetrix SNPs, 1.97 for Illumina SNPs, and 1.72 for microsatellites. The same regions on chromosome 7 (96–106 cM) and 10 (149–176 cM) were found to be significant for both ALDX1 and ALDX2. A region on chromosome 7 (112–153 cM) and a region on chromosome 6 (169–185 cM) were identified as the most significant regions for TTTH1 and ECB21, respectively. We also performed linkage analysis on denser maps of markers by combining the SNPs datasets from Affymetrix and Illumina. Adding the microsatellite data to the combined SNP dataset improved the results only marginally. The results indicated that SNPs outperform microsatellites with the densest marker sets performing the best.
Linkage mapping of a complex trait in the New York population of the GAW14 simulated dataset: a multivariate phenotype approach
Authors: Ghosh Saurabh , Bhattacharjee Samsiddhi , Basu Gourab , Pal Sandip , Majumder Partha P 
Published: January 2006

Abstract
Multivariate phenotypes underlie complex traits. Thus, instead of using the end-point trait, it may be statistically more powerful to use a multivariate phenotype correlated to the end-point trait for detecting linkage. In this study, we develop a reverse regression method to analyze linkage of Kofendrerd Personality Disorder affection status in the New York population of the Genetic Analysis Workshop 14 (GAW14) simulated dataset. When we used the multivariate phenotype, we obtained significant evidence of linkage near four of the six putative loci in at least 25% of the replicates. On the other hand, the linkage analysis based on Kofendrerd Personality Disorder status as a phenotype produced significant findings only near two of the loci and in a smaller proportion of replicates.