bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of Transferable Genetic Determinants on the Outcome of Typing Methods Commonly Used for
Enterococcus faecium
Authors: Werner Guido , Willems Rob J. L. , Hildebrandt Bianca , Klare Ingo , Witte Wolfgang 
Published: April 2003

ABSTRACT

A variety of methods is used for a molecular typing of
Enterococcus
spp. and related gram-positive bacteria including macrorestriction analysis using pulsed-field gel electrophoresis (PFGE), ribotyping, rapid amplification of polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP). To test the influence of transferable determinants on the outcome of different typing methods commonly used for enterococci, we established a homogenous strain collection of 24 transconjugants resulting from filter matings with antibiotic-resistant
Enterococcus faecium
. As expected, AFLP, RAPD, and PFGE all identified our model bacteria as strongly related. However, distinct differences in the resolving and discriminatory power of the tested methods could be clearly addressed. In PFGE, 22 of 24 transconjugants possessed less than a three-band difference to the recipient pattern and would be regarded as strongly related. Three different RAPD PCRs were tested; in two reactions, identical patterns for all transconjugants and the recipient were produced. One RAPD PCR produced an identical pattern for 18 transconjugants and the recipient and a clearly different pattern for the remaining 6 transconjugants due to a newly appearing fragment resulting from acquisition of the
tetL
gene. AFLP clusters all transconjugants into a group of major relatedness. Percent similarities were highly dependent on the method used for calculating the similarity coefficient (curve-based versus band-based similarity coefficient). Fragment patterns of digested plasmids showed the possession of nonidentical plasmids in most transconjugants. PFGE still could be recommended as the method of choice. Nevertheless, the more-modern AFLP approach produces patterns of comparable discriminatory power while possessing some advantages over PFGE (less-time-consuming internal standards). Plasmid fingerprints can be included to subdifferentiate enterococcal isolates possessing identical macrorestriction and PCR typing patterns.
Broadly Reactive and Highly Sensitive Assay for Norwalk-Like Viruses Based on Real-Time Quantitative Reverse Transcription-PCR
Authors: Kageyama Tsutomu , Kojima Shigeyuki , Shinohara Michiyo , Uchida Kazue , Fukushi Shuetsu , Hoshino Fuminori B. , Takeda Naokazu , Katayama Kazuhiko 
Published: April 2003

ABSTRACT
We have developed an assay for the detection of Norwalk-like viruses (NLVs) based on reverse transcription-PCR (RT-PCR) that is highly sensitive to a broad range of NLVs. We isolated virus from 71 NLV-positive stool specimens from 37 outbreaks of nonbacterial acute gastroenteritis and sequenced the open reading frame 1 (ORF1)-ORF2 junction region, the most conserved region of the NLV genome. The data were subjected to multiple-sequence alignment analysis and similarity plot analysis. We used the most conserved sequences that react with diverse NLVs to design primers and TaqMan probes for the respective genogroups of NLV, GI and GII, for use in a real-time quantitative RT-PCR assay. Our method detected NLV in 99% (80 of 81) of the stool specimens that were positive by electron microscopy, a better detection rate than with the two available RT-PCR methods. Furthermore, our new method also detected NLV in 20 of 28 stool specimens from the same NLV-related outbreaks that were negative for virus by electron microscopy. Our new assay is free from carryover DNA contamination and detects low copy numbers of NLV RNA. It can be used as a routine assay for diagnosis as well as for elucidation of the epidemiology of NLV infections.
PCR-Based Method To Differentiate the Subspecies of the
Mycobacterium tuberculosis
Complex on the Basis of Genomic Deletions
Authors: Huard Richard C. , de Oliveira Lazzarini Luiz Claudio , Butler W. Ray , van Soolingen Dick , Ho John L. 
Published: April 2003

ABSTRACT

The classical
Mycobacterium tuberculosis
complex (MtbC) subspecies include
Mycobacterium tuberculosis
,
Mycobacterium africanum
(subtypes I and II),
Mycobacterium bovis
(along with the attenuated
M. bovis
bacillus Calmette-Guérin [BCG]), and
Mycobacterium microti
; increasingly recognized MtbC groupings include
Mycobacterium bovis
subsp.
caprae
and “
Mycobacterium tuberculosis
subsp.
canettii
.” Previous investigations have documented each MtbC subspecies as a source of animal and/or human tuberculosis. However, study of these organisms is hindered by the lack of a single protocol that quickly and easily differentiates all of the MtbC groupings. Towards this end we have developed a rapid, simple, and reliable PCR-based MtbC typing method that makes use of MtbC chromosomal region-of-difference deletion loci. Here, seven primer pairs (which amplify within the loci
16S rRNA
, Rv0577, IS
1561
′, Rv1510, Rv1970, Rv3877/8, and Rv3120) were run in separate but simultaneous reactions. Each primer pair either specifically amplified a DNA fragment of a unique size or failed, depending upon the source mycobacterial DNA. The pattern of amplification products from all of the reactions, visualized by agarose gel electrophoresis, allowed immediate identification either as MtbC composed of
M. tuberculosis
(or
M. africanum
subtype II),
M. africanum
subtype I,
M. bovis
,
M. bovis
BCG,
M. caprae, M. microti
, or “
M. canettii
” or as a
Mycobacterium
other than MtbC (MOTT). This MtbC PCR typing panel provides an advanced approach to determine the subspecies of MtbC isolates and to differentiate them from clinically important MOTT species. It has proven beneficial in the management of
Mycobacterium
collections and may be applied for practical clinical and epidemiological use.
New Pathogenicity Marker Found in the Plasticity Region of theHelicobacter pyloriGenome
Authors: Santos Adriana , Queiroz Dulciene Maria Magalhães , Ménard Armelle , Marais Armelle , Rocha Gifone Aguiar , Oliveira Celso Affonso , Nogueira Ana Margarida Miguel Ferreira , Uzeda Milton , Mégraud Francis 
Published: April 2003

ABSTRACTComparison of gastric carcinoma and gastritis isolates showed the presence of genes, probably carcinoma associated (JHP947andJHP940), that are situated in aHelicobacter pylorigenome region (45 kb in J99 and 68 kb in 26695) called the “plasticity region.” This region presents a great variability of DNA sequences. We investigated, by PCR, the presence of theJHP940andJHP947genes, as well as the presence of a third gene which seems to be associated with gastritis (HP986), onH. pyloristrains isolated from 200 Brazilian patients, 79 of whom had gastric carcinomas and 53 of whom had duodenal ulcers, to confirm this association. Gastritis isolates (n= 68) were included as a control. We also evaluated if these genes were related to the virulence-associatedcagAgenotype. The present methodology did not permit definitive conclusions to be reached regarding the association between theJHP940gene and gastric carcinoma or between theHP986gene and gastritis. However, we showed that theJHP947gene might be implicated in the development of both duodenal ulcer and gastric carcinoma. The presence of theJHP947gene was associated with thecagA-positive genotype. TheJHP947gene is a novel virulence marker candidate ofH. pylori.
Heterogeneity of RNA Polymerase Gene (
rpoB
) Sequences of
Mycobacterium gordonae
Clinical Isolates Identified with a DNA Probe Kit and by Conventional Methods
Authors: Itoh Saotomo , Kazumi Yuko , Abe Chiyoji , Takahashi Mitsuyoshi 
Published: April 2003

ABSTRACT

In a previous study, we have evaluated genetic identification by using the
rpoB
gene, which was recently introduced by Kim et al. (J. Clin. Microbiol. 39:2102-2109, 2001; J. Clin. Microbiol. 37:1714-1720, 1999). In this process, we examined the
rpoB
gene heterogeneity of clinical isolates identified as
Mycobacterium gordonae
with the conventional biological and biochemical tests and/or a commercially available DNA probe kit. Sequencing of the
rpoB
gene of 34 clinical isolates revealed that
M. gordonae
clinical isolates were classified into four major clusters (A, B, C, and D). Interestingly, organisms belonging to cluster D (15 isolates) did not hybridize with
M. gordonae
ATCC 14470 and specifically possessed urease activity. Therefore, it could be considered to be a novel mycobacterium. The identification of
M. gordonae
is known to have ambiguous results sometimes. On the other hand, identification of clinical isolates seems to be inconvenient and unsuitable because of a more than 99% 16S rRNA gene similarity value between clusters. These findings suggest that the existence of
M. gordonae
-like mycobacteria that share similar biochemical and biological characteristics with the 16S rRNA gene of an
M. gordonae
type strain but less similarity at the genomic DNA level may have complicated the identification of
M. gordonae
in many laboratories. Furthermore, compared with
hsp65
PCR restriction analysis (PRA),
rpoB
PRA would have the advantage of producing no ambiguous results because of the intracluster homogeneity of the
rpoB
gene. In this case,
rpoB
would provide clearer results than
hsp65
, even if PRA analysis was used. We demonstrated that these
M. gordonae
-like mycobacteria were easily distinguished by PRA of the
rpoB
sequence. Additionally, the significance of this
M. gordonae
-like cluster may help to establish the comparison between the
M. gordonae
isolates from a clinical specimen and an infectious process in a given patient and to determine the true incidence of infection with this microorganism.
Tandem Tetramer-Based Microsatellite Fingerprinting for Typing of
Proteus mirabilis
Strains
Authors: Cieślikowski Tomasz , Gradecka Dobrosława , Mielczarek Magdalena , Kaca Wiesław 
Published: April 2003

ABSTRACT

Two microsatellite tandem repeated tetramers, (GACA)
4
and (CAAT)
4
, were used for
Proteus mirabilis
strain differentiation. The microsatellite-based PCR tests were applied for the examination of interstrain diversity for 87
P
.
mirabilis
strains. Forty-six of the investigated strains were clinical isolates (5 were hospital isolates and 39 were outpatient clinic isolates); 42 strains were derived from the Kauffmann-Perch collection of laboratory strains. Fingerprinting done with the tetramers had a high discrimination ability [0.992 and 0.940 for (GACA)
4
and (CAAT)
4
, respectively]. The distributions of clinical isolates among well-defined laboratory strains, determined by numerical analysis (unweighted pair-group method with arithmetic averages; Dice similarity coefficient), proved their genetic similarity to reference strains in the Kauffmann-Perch collection. This analysis also indicated that it is possible to estimate some phenotypic properties of
P
.
mirabilis
clinical isolates solely on the basis of microsatellite fingerprinting.
Detection of Hepatitis B Virus DNA in Sera from Patients with Chronic Hepatitis B Virus Infection by DNA Microarray Method
Authors: Kawaguchi Kazunori , Kaneko Shuichi , Honda Masao , Kawai Hiroshi F. , Shirota Yukihiro , Kobayashi Kenichi 
Published: April 2003

ABSTRACT

We have developed a sensitive and quantitative assay using a DNA microarray for the detection of hepatitis B virus (HBV) DNA in serum. Fluorescently labeled target cDNA prepared from cloned HBV DNA or serum HBV DNA was hybridized to capture DNA on a slide. A linear relationship was obtained between the intensities of the array spot and the amount of the cloned or serum HBV DNA, indicating the quantitative accuracy of this assay system. In addition, there was a significant correlation between the number of molecules of serum HBV DNA determined by the DNA microarray and that determined by a branched-DNA assay (
n
= 21,
r
= 0.89). Given these results, we conclude that the DNA microarray assay system may be useful as a diagnostic technique in the clinical laboratory.
Distinctiveness of
Mycobacterium tuberculosis
Genotypes from Human Immunodeficiency Virus Type 1-Seropositive and -Seronegative Patients in Lima, Peru
Authors: Ahmed Niyaz , Caviedes Luz , Alam Mahfooz , Rao K. Rajender , Sangal Vartul , Sheen Patricia , Gilman Robert H. , Hasnain Seyed E. 
Published: April 2003

ABSTRACT

Genotypic analysis of
Mycobacterium tuberculosis
isolates obtained from human immunodeficiency virus type 1 (HIV-1)-seropositive (
n
= 80) and -seronegative (
n
= 25) patients from Lima, Peru, revealed two distinct genotypes correlating with the host immune status. While the level of intrastrain diversity of DNA fingerprints of HIV-seropositive isolates was less pronounced, these isolates showed many clonal groupings.
Drug-Associated Resistance Mutations in Plasma and Peripheral Blood Mononuclear Cells of Human Immunodeficiency Virus Type 1-Infected Patients for Whom Highly Active Antiretroviral Therapy Is Failing
Authors: Sarmati Loredana , Nicastri Emanuele , Uccella Ilaria , d'Ettorre Gabriella , Parisi Saverio G. , Palmisano Lucia , Galluzzo Clementina , Concia Ercole , Vullo Vincenzo , Vella Stefano , Andreoni Massimo 
Published: April 2003

ABSTRACT

In 32 patients for whom highly active antiretroviral therapy was failing, a good agreement between drug resistance-associated mutations in plasma and peripheral blood mononuclear cells (PBMCs) was found (
k
= 0.85). The mutations with the lowest agreement were 20R, 63P, and 84V in the protease gene and 184V in the reverse transcriptase gene. In eight patients, primary drug resistance mutations were detected only in PBMCs.
Evaluation of a Fluorescence-Based PCR Method for Identification of Serogroup A Meningococci
Authors: Diggle M. A. , Smith K. , Girvan E. K. , Clarke S. C. 
Published: April 2003

ABSTRACT

Standard and fluorescence-based PCR assays were developed for the identification of serogroup A meningococci by detection of the
mynA
gene. This assay was evaluated using bacterial cultures but provides the sensitivity required for the detection of the
mynA
gene from bodily fluids during meningococcal disease.
Prenatal Diagnosis of Congenital Human Cytomegalovirus Infection in Amniotic Fluid by Nucleic Acid Sequence-Based Amplification Assay
Authors: Revello M. Grazia , Lilleri Daniele , Zavattoni Maurizio , Furione Milena , Middeldorp Jaap , Gerna Giuseppe 
Published: April 2003

ABSTRACT
Nucleic acid sequence-based amplification assays for detection of human cytomegalovirus (HCMV) immediate-early and pp67 mRNA in 65 amniotic fluid samples tested for prenatal diagnosis of congenital HCMV infection showed sensitivity, specificity, and negative and positive predictive values >90%.
Use of Equivocal Zone in Interpretation of Results of the Amplified Mycobacterium Tuberculosis Direct Test for Diagnosis of Tuberculosis
Authors: Kerleguer A. , Koeck J.-L. , Fabre M. , Gérôme P. , Teyssou R. , Hervé V. 
Published: April 2003

ABSTRACT
The sensitivity and specificity of the Amplified Mycobacterium Tuberculosis Direct (AMTD) test, evaluated with 1,363 respiratory samples (128 from tuberculous patients), were 92.97 and 98.7%, respectively. When an equivocal zone (30,000 to 1,000,000 relative light units [RLU]) was used instead of a 30,000-RLU cutoff, the sensitivity and specificity of the AMTD test were 92.97 and 100%, respectively.
BIBI, a Bioinformatics Bacterial Identification Tool
Authors: Devulder G. , Perrière G. , Baty F. , Flandrois J. P. 
Published: April 2003

ABSTRACT
BIBI was designed to automate DNA sequence analysis for bacterial identification in the clinical field. BIBI relies on the use of BLAST and CLUSTAL W programs applied to different subsets of sequences extracted from GenBank. These sequences are filtered and stored in a new database, which is adapted to bacterial identification.
Patterns of respiration in diving penguins: is the last gasp an inspired tactic?
Authors: Wilson Rory P. , Simeone Alejandro , Luna-Jorquera Guillermo , Steinfurth Antje , Jackson Sue , Fahlman Andreas 
Published: April 2003

SUMMARYHumboldt penguins Spheniscus humboldti in captivity and free-living Magellanic penguins S. magellanicus were fitted with loggers to determine beak angles during breathing. The Humboldt penguins were also fitted with masks for determining rates of air flow during breathing. During periods of higher gas exchange requirement, Humboldt penguins opened their beaks during inspiration, where tidal volume was linearly correlated with both change in beak angle and maximum beak angle, closed them slightly during the final stages of inspiration and finally closed them during expiration. Substantial differences were apparent between individuals. Contrary to the condition proposed for most birds, our data suggest that expiration is passive during periods of high respiratory tidal volumes, and that the increased resistance of the respiratory pathway serves to slow air flow so as to maximize gas exchange in the lungs. During foraging, Magellanic penguins at the surface between dives showed similar breathing patterns but maximum beak angles were much higher and breath cycle time shorter, as would be expected for animals attempting to maximize gas exchange. Both maximum beak angle per breath and breath frequency changed systematically over the surface pause; both were initially high, then decreased to a low before rising again to a maximum just before diving. Based on known changes in tidal volume with beak angle derived from Humboldt penguins, a simple model is proposed to examine rates of gas exchange over the surface pause. This indicates that the observed patterns do not maximize the rate of transfer of oxygen over the whole of the surface pause but are rather concerned with an initial rapid accumulation of oxygen in the tissues followed by effective carbon dioxide release.
Homozygous inactivation of NF1 gene in a patient with familial NF1 and disseminated neuroblastoma
Authors: Origone Paola , Defferrari Raffaella , Mazzocco Katia , Cunsolo Crocifissa Lo , Bernardi Bruno De , Tonini Gian Paolo 
Published: April 2003

AbstractNeurofibromatosis type 1 (NF1) patients are susceptible to tumor development. In the present study we describe a child with NF1 and disseminated neuroblastoma whose death resulted from disease progression. The mother had café‐au‐lait spots suggesting a familial NF1. Neuroblastoma cells showed MYCN amplification and chromosome 1p36 deletion, common features associated with tumor progression in this malignancy. The NF1 gene displayed a germline T → C transition of intron 14 in both the proband and mother DNA. This mutation, not yet previously described, occurs in a splicing donor site and produces a new mRNA variant observed together with normal NF1 mRNA. Furthermore, the SSCP analysis of the NF1 gene in tumor cells showed a somatic deletion encompassing the intron 26 and 27b of the paternal NF1 allele. Hence, neuroblastoma cells displayed both somatic and germline mutation of the NF1 gene. Our data suggest that, although rare, neuroblastoma in patients with NF1 may display homozygous gene inactivation. © 2003 Wiley‐Liss, Inc.
Evolution of a pigmentation gene, the melanocortin‐1 receptor, in primates
Authors: Mundy N.I. , Kelly J. 
Published: April 2003

AbstractThe melanocortin‐1 receptor (MC1R) forms a critical switch in the production of orange/red pheomelanin and black/brown eumelanin pigments during hair development in mammals. The molecular evolution of the melanocortin‐1 receptor gene was investigated in a broad range of primate species, including several groups with large differences in distribution of orange/red and black hairs. Primate MC1R has been subject to purifying selection throughout most of its evolution, with small changes in selective constraint being detected early in primate evolution. In contrast to the situation in humans and domestic mammals, many intraspecific and intrageneric differences in primate coat color cannot be attributed to changes in the MC1R coding sequence. Nevertheless, important changes in the biochemical function of MC1R are suggested by mutations in sites of known functional importance, particularly in New World monkeys and lemurs. The evolution of the MC1R in lion tamarins is anomalous, with a combination of a high nonsynonymous to synonymous substitution rate (dN/dS) ratio, deletions, and substitutions. Am J Phys Anthropol 121:000–000, 2003. © 2003 Wiley‐Liss, Inc.
Spacing system of the Mysore slender loris (Loris lydekkerianus lydekkerianus)
Authors: Nekaris K.A.I. 
Published: April 2003

AbstractLoris lydekkerianus lydekkerianus has been shown to have a promiscuous copulatory pattern, to maintain social networks via frequent loud calls, to interact socially throughout the night with all age classes, and to sleep socially. Though these behaviors point towards a multimale social system, no study of their spacing system has yet been provided to support this view. From October 1997–August 1998, I conducted a study of the Mysore slender loris in Ayyalur, India. During 1,400 field hours, data were collected on range use of 3 adult females, 3 adult males, 1 subadult female, and 1 subadult male. Lorises slept in groups averaging 4 individuals, composed of an adult female, her offspring, and 1–2 adult and subadult males. Sleeping sites for three groups were located within 1.9 ha in the center of the study area. The minimum convex polygon in hectares encompassing each animal's range was determined, as well as overlap among home ranges of individual lorises. Average home range sizes were: adult males, 3.6 ha ± 0.09; subadult/smaller males, 1.17 ha ± 0.26; and adult and subadult females, 1.59 ha ± 0.24. Male ranges overlapped with at least 2–3 other adult males (0.72 ha ± 0.23). Female ranges overlapped slightly with at least 2 other female ranges (0.22 ha ± 0.25). Male ranges overlapped those of at least 3 females (0.82 ha ± 0.51). Patterns of home range and sleeping site support previous suggestions of a multimale social system, similar to aye ayes and some galagos. Am J Phys Anthropol 121:000–000, 2003. © 2003 Wiley‐Liss, Inc.
Morphology and mechanical properties of polypropylene/high‐impact polystyrene blends from postconsumer plastic waste
Authors: Santana Ruth M. Campomanes , Manrich Sati 
Published: April 2003

AbstractThe compatibilizing effect of the triblock copolymer poly(styrene‐b‐ethylene‐co‐butylene‐b‐styrene) (SEBS) on the morphological and mechanical properties of virgin and recycled polypropylene (PP)/high‐impact polystyrene (HIPS) blends was studied, with the properties optimized for rigid composite films. The components of the blend were obtained from municipal plastic waste, PP being acquired from mineral water bottles (PPb) and HIPS from disposable cups. These materials were preground, washed only with water, dried with hot air, and ground again (PPb) or agglutinated (HIPS). Blends with three different weight ratios of PPb and HIPS (6:1, 6:2, and 6:3) were prepared, and three different concentrations of SEBS (5, 6, and 7 wt %) were used for investigations of its compatibilizing effect. Scanning electron microscopy showed that SEBS reduced the diameter of dispersed HIPS particles in the globular and fibril shapes and improved the adhesion between the disperse phase and the matrix. However, SEBS interactions with PPb and HIPS influenced the mechanical properties of the compatibilized PPb/HIPS/SEBS blends. An adequate composition of PP/HIPS, for both virgin and recycled blends, for applications in composite films with characteristics similar to those of synthetic paper was obtained with a minimal amount of SEBS and a maximal HIPS/PP ratio in the range of concentrations studied. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 88: 2861–2867, 2003