bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Crystal Structure of Zn(II)-Free
Treponema pallidum
TroA, a Periplasmic Metal-Binding Protein, Reveals a Closed Conformation
Authors: Lee Yong-Hwan , Dorwart Michael R. , Hazlett Karsten R. O. , Deka Ranjit K. , Norgard Michael V. , Radolf Justin D. , Hasemann Charles A. 
Published: July 2002

ABSTRACT

We previously demonstrated that
Treponema pallidum
TroA is a periplasmic metal-binding protein (MBP) with a distinctive alpha-helical backbone. To better understand the mechanisms of metal binding and release by TroA, we determined the crystal structure of the apoprotein at a resolution of 2.5 Å and compared it to that of the Zn(II)-bound form (Protein Data Bank accession code 1toa). apo-TroA shows a conformation even more closed than that of its Zn(II)-bound counterpart due to a 4° tilt of the C-terminal domain (residues 190 through 308) about an axis parallel to the poorly flexible backbone helix. This domain tilting pushes two loops (residues 248 through 253 and 277 through 286) towards the metal-binding site by more than 1 Å, resulting in an unfavorable interaction of I251 with D66. To avoid this contact, D66 shifts towards H68, one of the four Zn(II)-coordinating residues. The approach of this negative charge coincides with the flipping of the imidazole side chain of H68, resulting in the formation of a new hydrogen bond. The conformational change of H68, along with a slight rearrangement of D279, a C-terminal domain Zn(II)-coordinating residue, distorts the metal-binding site geometry, presumably causing the release of the bound metal ion. Ligand binding and release by TroA, and presumably by other members of the MBP cluster, differs from the “Venus flytrap” mechanism utilized by bacterial nonmetal solute-binding receptors.
Characterization of Plasmid pRT1 from
Pyrococcus
sp. Strain JT1
Authors: Ward Donald E. , Revet Ingrid M. , Nandakumar Renu , Tuttle Jon H. , de Vos Willem M. , van der Oost John , DiRuggiero Jocelyne 
Published: July 2002

ABSTRACT

We discovered a 3,373-bp plasmid (pRT1) in the hyperthermophilic archaeon
Pyrococcus
sp. strain JT1. Two major open reading frames were identified, and analysis of the sequence revealed some resemblance to motifs typically found in plasmids that replicate via a rolling-circle mechanism. The presence of single-stranded DNA replication intermediates of pRT1 was detected, confirming this mode of replication.
Molecular Analysis of
Malassezia
Microflora on the Skin of Atopic Dermatitis Patients and Healthy Subjects
Authors: Sugita Takashi , Suto Hajime , Unno Tetsushi , Tsuboi Ryoji , Ogawa Hideoki , Shinoda Takako , Nishikawa Akemi 
Published: July 2002

ABSTRACT

Members of the genus
Malassezia
, lipophilic yeasts, are considered to be one of the exacerbating factors in atopic dermatitis (AD). We examined variation in cutaneous colonization by
Malassezia
species in AD patients and compared it with variation in healthy subjects. Samples were collected by applying transparent dressings to the skin lesions of AD patients. DNA was extracted directly from the dressings and amplified in a specific nested PCR assay.
Malassezia
-specific DNA was detected in all samples obtained from 32 AD patients. In particular,
Malassezia globosa
and
M. restricta
were detected in approximately 90% of the AD patients and
M. furfur
and
M. sympodialis
were detected in approximately 40% of the cases. The detection rate was not dependent on the type of skin lesion. In healthy subjects,
Malassezia
DNA was detected in 78% of the samples, among which
M. globosa
,
M. restricta
, and
M. sympodialis
were detected at frequencies ranging from 44 to 61%, with
M. furfur
at 11%. The diversity of
Malassezia
species found in AD patients was greater (2.7 species detected in each individual) than that found in healthy subjects (1.8 species per individual). Our results suggest that
M. furfur
,
M. globosa
,
M. restricta
, and
M. sympodialis
are common inhabitants of the skin of both AD patients and healthy subjects, while the skin microflora of AD patients shows more diversity than that of healthy subjects. To our knowledge, this is the first report of the use of a nested PCR as an alternative to fungal culture for analysis of the distribution of cutaneous
Malassezia
spp.
Removal of PCR Inhibitors by Silica Membranes: Evaluating the Amplicor
Mycobacterium tuberculosis
Kit
Authors: Böddinghaus Boris , Wichelhaus Thomas A. , Brade Volker , Bittner Thomas 
Published: July 2002

ABSTRACT

The effectiveness of PCR inhibitor removal by silica membranes in combination with the Amplicor
Mycobacterium tuberculosis
kit was analyzed for 655 respiratory and nonrespiratory specimens. The overall inhibition rate was reduced from 12.5%, when applying the Amplicor kit alone, to 1.1% with the addition of silica membrane DNA purification.
Phenotypic Identification of
Actinomyces
and Related Species Isolated from Human Sources
Authors: Sarkonen Nanna , Könönen Eija , Summanen Paula , Könönen Mauno , Jousimies-Somer Hannele 
Published: July 2002

ABSTRACT

Recent advancements in chemotaxonomic and molecular biology-based identification methods have clarified the taxonomy of the genus
Actinomyces
and have led to the recognition of several new
Actinomyces
and related species.
Actinomyces
-like gram-positive rods have increasingly been isolated from various clinical specimens. Thus, an easily accessible scheme for reliable differentiation at the species level is needed in clinical and oral microbiology laboratories, where bacterial identification is mainly based on conventional biochemical methods. In the present study we designed a two-step protocol that consists of a flowchart that describes rapid, cost-efficient tests for preliminary identification of
Actinomyces
and closely related species and an updated more comprehensive scheme that also uses fermentation reactions for accurate differentiation of
Actinomyces
and closely related species.
Bacterial Genetic Fingerprint: a Reliable Factor in the Study of the Epidemiology of Human
Campylobacter
Enteritis?
Authors: Steinbrueckner B. , Ruberg F. , Kist M. 
Published: July 2002

ABSTRACT

The rate of human intestinal infections with more than a single
Campylobacter
strain was determined and the genetic variabilities of
Campylobacter
strains throughout an infection episode were investigated by means of pulsed-field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR). For 48 and 49 of 50 patients, all isolates from one sample showed identical patterns by PFGE and ERIC-PCR, respectively. Throughout an infection episode in 47 of 52 patients, the PFGE fingerprints of the isolates remained stable, while in 1 patient two different species were observed and in 4 patients different patterns were observed. Therefore, ERIC-PCR proved less discriminative than PFGE. These findings suggest that human infection with more than one
Campylobacter
strain is rare and should not significantly impair epidemiologic analyses. However, changes in the genetic fingerprint throughout an infection should be considered in the assessment of epidemiologic studies of
Campylobacter
spp.
Comparison of DNA Sequencing and a Line Probe Assay for Detection of Human Immunodeficiency Virus Type 1 Drug Resistance Mutations in Patients Failing Highly Active Antiretroviral Therapy
Authors: Servais Jean , Lambert Christine , Fontaine Elodie , Plesséria Jean-Marc , Robert Isabelle , Arendt Vic , Staub Thérèse , Schneider François , Hemmer Robert , Burtonboy Guy , Schmit Jean-Claude 
Published: July 2002

ABSTRACT

The resistance of human immunodeficiency virus type 1 (HIV-1) to drugs is a major cause of antiretroviral treatment failure. We have compared direct sequencing to a line probe assay (LiPA) for the detection of drug resistance-related mutations in 197 clinical samples, and we have investigated the sequential appearance of mutations under drug pressure. For 26 patients with virological failure despite the use of two nucleoside analogues and one protease inhibitor (indinavir [
n
= 6], ritonavir [
n
= 10], and saquinavir [
n
= 10]), genotypic resistance assays were carried out retrospectively every 3 months for up to 2 years by using direct sequencing (TruGene; Visible Genetics) and a LiPA for detection of mutations in the reverse transcriptase (INNO-LiPA HIV-1 RT; Innogenetics) and the protease (INNO-LiPA HIV Protease, prototype version; Innogenetics) genes. Comparison of the results from both assays found rare major discrepancies (<1% of codons analyzed). INNO-LiPA detected more wild-type–mutant mixtures than sequencing but suffered from a high rate of codon hybridization failures for the reverse transcriptase. LiPA detected earlier and more frequently than sequencing the transient mixed virus population that contained I84V, which appears before V82A in the protease sequence. Mutations M461, G48V, and L90M were often transient and drug pressure related. In conclusion, direct sequencing and LiPAs give concordant results for most clinical isolates. LiPAs are more sensitive for the detection of mixed virus populations. Mutation I84V appears in minor populations in the early steps of the pathways of resistance to indinavir and ritonavir. The fact that some mutations can be found only transiently and in minor virus populations highlights the importance of a low detection limit for resistance assays.
Multicenter Comparison Trial of DNA Extraction Methods and PCR Assays for Detection of
Chlamydia pneumoniae
in Endarterectomy Specimens
Authors: Apfalter Petra , Blasi Francesco , Boman Jens , Gaydos Charlotte A. , Kundi Michael , Maass Matthias , Makristathis Athanasios , Meijer Adam , Nadrchal Reinhard , Persson Kenneth , Rotter Manfred L. , Tong C. Y. William , Stanek Gerold , Hirschl Alexander M. 
Published: July 2002

ABSTRACT

The reported rate of detection of
Chlamydia pneumoniae
DNA within atherosclerotic lesions by PCR varies between 0 and 100%. In this study, identical sets of coded experimental atheroma samples (
n
= 15) and spiked controls (
n
= 5) were analyzed by 16 test methods in nine centers by means of PCR. The positive controls were correctly identified to levels of 1, 0.1, and 0.01 inclusion bodies of
C. pneumoniae
/ml of tissue homogenate by 16 (100%), 11 (69%), and 3 (19%) of the test methods, respectively. Three out of 16 negative controls (19%) were rated positive. Positivity rates for atheroma samples varied between 0 and 60% for the different test methods, with the maximum concordant result for positivity being only 25% for one carotid artery sample. There was no consistent pattern of positive results among the various laboratories, and there was no correlation between the detection rates and the sensitivity of the assay used.
Use of a LightCycler
gyrA
Mutation Assay for Rapid Identification of Mutations Conferring Decreased Susceptibility to Ciprofloxacin in Multiresistant
Salmonella enterica
Serotype Typhimurium DT104 Isolates
Authors: Walker R. A. , Saunders N. , Lawson A. J. , Lindsay E. A. , Dassama M. , Ward L. R. , Woodward M. J. , Davies R. H. , Liebana E. , Threlfall E. J. 
Published: July 2002

ABSTRACT

A LightCycler-based PCR-hybridization
gyrA
mutation assay (GAMA) was developed to rapidly detect
gyrA
point mutations in multiresistant (MR)
Salmonella enterica
serotype Typhimurium DT104 with decreased susceptibility to ciprofloxacin (MIC, 0.25 to 1.0 mg/liter). Ninety-two isolates (49 human, 43 animal) were tested with three individual oligonucleotide probes directed against an Asp-87-to-Asn (GAC→AAC) mutation, an Asp-87-to-Gly (GAC→GGC) mutation, and a Ser-83-to-Phe (TCC→TTC) mutation. Strains homologous to the probes could be distinguished from strains that had different mutations by their probe-target melting temperatures. Thirty-seven human and 30 animal isolates had an Asp-87-to-Asn substitution, 6 human and 6 animal isolates had a Ser-83-to-Phe substitution, and 5 human and 2 animal isolates had an Asp-87-to-Gly substitution. The remaining six strains all had mismatches with the three probes and therefore different
gyrA
mutations. The sequencing of
gyrA
from these six isolates showed that one human strain and two animal strains had an Asp-87-to-Tyr (GAC→TAC) substitution and two animal strains had a Ser-83-to-Tyr (TCC→TAC) substitution. One animal strain had no
gyrA
mutation, suggesting that this isolate had a different mechanism of resistance. Fifty-eight of the strains tested were indistinguishable by several different typing methods including antibiograms, pulsed-field gel gel electrophoresis, and plasmid profiling, although they could be further subdivided according to
gyrA
mutation. This study confirmed that MR DT104 with decreased susceptibility to ciprofloxacin from humans and food animals in England and Wales may have arisen independently against a background of clonal spread of MR DT104.
Coexistence of SHV-4- and TEM-24-Producing
Enterobacter aerogenes
Strains before a Large Outbreak of TEM-24-Producing Strains in a French Hospital
Authors: Mammeri H. , Laurans G. , Eveillard M. , Castelain S. , Eb F. 
Published: July 2002

ABSTRACT

In 1996, a monitoring program was initiated at the teaching hospital of Amiens, France, and carried out for 3 years. All extended-spectrum β-lactamase (ESBL)-producing
Enterobacter aerogenes
isolates recovered from clinical specimens were collected for investigation of their epidemiological relatedness by pulsed-field gel electrophoresis and enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) and determination of the type of ESBL harbored by isoelectric focusing and DNA sequencing. Molecular typing revealed the endemic coexistence, during the first 2 years, of two clones expressing, respectively, SHV-4 and TEM-24 ESBLs, while an outbreak of the TEM-24-producing strain raged in the hospital during the third year, causing the infection or colonization of 165 patients. Furthermore, this strain was identified as the prevalent clone responsible for outbreaks in many French hospitals since 1996. This study shows that TEM-24-producing
E. aerogenes
is an epidemic clone that is well established in the hospital's ecology and able to spread throughout wards. The management of the outbreak at the teaching hospital of Amiens, which included the reinforcement of infection control measures, failed to obtain complete eradication of the clone, which has become an endemic pathogen.
Truncated Hantavirus Nucleocapsid Proteins for Serotyping Hantaan, Seoul, and Dobrava Hantavirus Infections
Authors: Araki Koichi , Yoshimatsu Kumiko , Ogino Michiko , Ebihara Hideki , Lundkvist Åke , Kariwa Hiroaki , Takashima Ikuo , Arikawa Jiro 
Published: July 2002

ABSTRACT
Truncated recombinant nucleocapsid proteins (rNPs) of Hantaan virus (HTNV), Seoul virus (SEOV), and Dobrava virus (DOBV) were expressed by a baculovirus system. The truncated rNPs, which lacked 49 (rNP50) or 154 (rNP155) N-terminal amino acids of the NPs of HTNV, SEOV, and DOBV, were able to differentiate HTNV-, SEOV-, and DOBV-specific immune sera. Recombinant NP50s retained higher reactivities than rNP155s and were proven useful for enzyme-linked immunosorbent assay (ELISA). The ELISAs based on the rNP50s of HTNV, SEOV, and DOBV successfully differentiated three groups of patient sera, previously defined by neutralization tests: 17 with HTNV infection, 12 with SEOV infection, and 20 with DOBV infection. The entire rNP of Puumala virus (PUUV) distinguished PUUV infection from the other types of hantavirus infection. Serotyping with these rNP50s can be recommended as a rapid and efficient system for hantavirus diagnosis.
Waldenström's Disease Complicated by Recurrent Meningococcal Arthritis
Authors: Singwe-Ngandeu Madeleine , Buchs Nicolas , Rohner Peter , Gabay Cem 
Published: July 2002

ABSTRACT
Meningococcal arthritis is rare. We report a patient in whom a first episode of meningococcal arthritis revealed Waldenström's disease and who experienced a second episode of meningococcal arthritis 8 years later. We suggest that an impaired immune response secondary to Waldenström's disease favored the recurrence of meningococcal arthritis.
Biofilm Formation by
Candida dubliniensis
Authors: Ramage Gordon , Vande Walle Kacy , Wickes Brian L. , López-Ribot José L. 
Published: July 2002

ABSTRACT

Candida dubliniensis
is an opportunistic yeast closely related to
Candida albicans
that has been recently implicated in oropharyngeal candidiasis in human immunodeficiency virus-infected patients. Most manifestations of candidiasis are associated with biofilm formation, with cells in biofilms displaying properties dramatically different from free-living cells grown under normal laboratory conditions. Here, we report on the development of in vitro models of
C. dubliniensis
biofilms on the surfaces of biomaterials (polystyrene and acrylic) and on the characteristics associated with biofilm formation by this newly described species. Time course analysis using a formazan salt reduction assay to monitor metabolic activities of cells within the biofilm, together with microscopy studies, revealed that biofilm formation by
C. dubliniensis
occurred after initial focal adherence, followed by growth, proliferation, and maturation over 24 to 48 h. Serum and saliva preconditioning films enhanced the initial attachment of
C. dubliniensis
and subsequent biofilm formation. Scanning electron microscopy and confocal scanning laser microscopy were used to further characterize
C. dubliniensis
biofilms. Mature
C. dubliniensis
biofilms consisted of a dense network of yeasts cells and hyphal elements embedded within exopolymeric material.
C. dubliniensis
biofilms displayed spatial heterogeneity and an architecture showing microcolonies with ramifying water channels. Antifungal susceptibility testing demonstrated the increased resistance of sessile
C. dubliniensis
cells, including the type strain and eight different clinical isolates, against fluconazole and amphotericin B compared to their planktonic counterparts.
C. dubliniensis
biofilm formation may allow this species to maintain its ecological niche as a commensal and during infection with important clinical repercussions.
Application of PCR to Distinguish Common Species of Dermatophytes
Authors: Faggi Elisabetta , Pini Gabriella , Campisi Enza , Bertellini Chiara , Difonzo Elisa , Mancianti Francesca 
Published: July 2002

ABSTRACT

This report describes the application of PCR fingerprinting for the identification of species and varieties of common dermatophytes and related fungi utilizing as a single primer the simple repetitive oligonucleotide (GACA)
4
. The primer was able to amplify all the strains, producing species-specific profiles for
Microsporum canis
,
Microsporum gypseum
,
Trichophyton rubrum
,
Trichophyton ajelloi
, and
Epidermophyton floccosum.
Intraspecific variability was not observed for these species. Instead, three different profiles were observed in the
Trichophyton mentagrophytes
group.
The
ica
Operon and Biofilm Production in Coagulase-Negative Staphylococci Associated with Carriage and Disease in a Neonatal Intensive Care Unit
Authors: de Silva G. D. I. , Kantzanou M. , Justice A. , Massey R. C. , Wilkinson A. R. , Day N. P. J. , Peacock S. J. 
Published: July 2002

ABSTRACT

Coagulase-negative staphylococci (CoNS) are a major cause of sepsis in the neonatal intensive care unit (NICU). We evaluated the hypothesis that the
ica
operon and biofilm production are associated with CoNS disease in this setting. CoNS associated with bacteremia or blood culture contamination and from the skin of infants with CoNS bacteremia or healthy controls were obtained during a prospective case-control study on a busy NICU. A total of 180 strains were identified, of which 122 (68%) were
Staphylococcus epidermidis
and the remainder were
S. capitis
(
n
= 29),
S. haemolyticus
(
n
= 11),
S. hominis
(
n
= 9),
S. warneri
(
n
= 8), and
S. auricularis
(
n
= 1). The presence of the genes
icaA, icaB, icaC
, and
icaD
was determined by PCR, and biofilm production was examined using qualitative (Congo red agar [CRA]) and quantitative (microtiter plate) techniques. There were no significant differences in the presence of the
ica
operon or CRA positivity among the four groups of strains. However, quantitative biofilm production was significantly greater in strains isolated from either the blood or the skin of neonates with
S. epidermidis
bacteremia. We conclude that the quantity of biofilm produced may be associated with the ability to cause CoNS infection. This conclusion suggests that the regulation of biofilm expression may play a central role in the disease process.
Discrimination of Single-Copy IS6110DNA Fingerprints ofMycobacterium tuberculosisIsolates by High-Resolution Minisatellite-Based Typing
Authors: Lee Ann S. G. , Tang Lynn L. H. , Lim Irene H. K. , Bellamy Richard , Wong Sin-Yew 
Published: July 2002

ABSTRACTSeven isoniazid-resistant isolates with mutations in the NADH dehydrogenase (ndh) gene were molecularly typed by IS6110-based restriction fragment length polymorphism analysis. All seven isolates with the R268H mutation had identical 1.4-kb IS6110fingerprints. High-resolution minisatellite-based typing discriminated five of these isolates; two isolates were identical.
In Vitro Activities of Broad-Spectrum Cephalosporins against Nonmeningeal Isolates of
Streptococcus pneumoniae
: MIC Interpretation Using NCCLS M100-S12 Recommendations
Authors: Sahm Daniel F. , Thornsberry Clyde , Mayfield David C. , Jones Mark E. , Karlowsky James A. 
Published: July 2002

ABSTRACT

Publication of the NCCLS M100-S12 document in January 2002 introduced ceftriaxone and cefotaxime MIC interpretative breakpoints of ≤1 μg/ml (susceptible), 2 μg/ml (intermediate), and ≥4 μg/ml (resistant) for nonmeningeal isolates of
Streptococcus pneumoniae
. To estimate the effect of these breakpoint changes on clinical laboratory susceptibility testing results, nonmeningeal pneumococcal isolate (blood and respiratory) data from The Surveillance Network Database-USA, an electronic surveillance database, for the years 1996 to 2000 were collated and studied. Of 9,863 nonmeningeal isolates tested against ceftriaxone, 82.7% were susceptible, 13.2% were intermediate, and 4.1% were resistant by the M100-S11 NCCLS breakpoints (2001); by M100-S12 breakpoints, 95.9% of the isolates were susceptible, 3.1% were intermediate, and 1.0% were resistant. Of 10,777 nonmeningeal isolates tested against cefotaxime, 79.2% were susceptible, 14.3% were intermediate, and 6.5% were resistant by M100-S11 breakpoints; by M100-S12 breakpoints, 93.5% were susceptible, 4.2% were intermediate, and 2.3% were resistant. Overall, the new M100-S12 ceftriaxone and cefotaxime interpretative breakpoints for nonmeningeal isolates of
S. pneumoniae
decreased the number of isolates interpreted as intermediate by 10% and as resistant by 3 to 4%.
Pulmonary Colonization by
Chrysosporium zonatum
Associated with Allergic Inflammation in an Immunocompetent Subject
Authors: Hayashi Shinichiro , Naitoh Keiko , Matsubara Shinichi , Nakahara Yoshiaki , Nagasawa Zenzo , Tanabe Ichiro , Kusaba Kohzi , Tadano Jutaro , Nishimura Kazuko , Sigler Lynne 
Published: July 2002

ABSTRACT

We report a case of noninvasive pulmonary disease due to
Chrysosporium zonatum
in an immunocompetent male. The fungus colonized an existing tuberculous cavity and was isolated from transbronchial lavage fluid and from a percutaneous aspiration specimen. The disease was accompanied by the unusual feature of an allergic reaction. The fungus ball was successfully treated by intracavitary administration of amphotericin B.
C. zonatum
is the anamorph of the heterothallic ascomycete
Uncinocarpus orissi
, and the identity of the case isolate was verified by formation of ascospores in mating tests with reference isolates.