bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple Copies of the 16S rRNA Gene in
Nocardia nova
Isolates and Implications for Sequence-Based Identification Procedures
Authors: Conville Patricia S. , Witebsky Frank G. 
Published: June 2005

ABSTRACT

Molecular investigation of two
Nocardia
patient isolates showed unusual restriction fragment length polymorphism patterns with restriction endonuclease assays (REA) using an amplified portion of the 16S rRNA gene. Patterns typical of
Nocardia nova
were obtained with REA of an amplified portion of the 65-kDa heat shock protein gene. Subsequent sequence analysis of the 16S rRNA gene regions of these isolates showed the presence of ambiguous bases within an expected restriction endonuclease recognition site which were not able to be resolved on repeat testing. Cloning of amplified regions of the 16S rRNA genes and subsequent sequencing of the resulting clones from the two patient isolates showed three different 16S rRNA gene sequences which corresponded to sequences found in
N. nova
, a molecular variant of
N. nova
, and a previously undescribed sequence. Hybridization studies using a DNA probe corresponding to an 89-bp conserved region of the 16S rRNA gene confirmed the presence of at least two copies of the 16S rRNA gene in the
N. nova
type strain, in a patient isolate identical to the molecular variant of
N. nova
, and in the two other patient isolates. All isolates were found to belong to the species
N. nova
as determined by DNA-DNA hybridization. Because minimal variation has been found in the 16S rRNA gene sequences of different species of
Nocardia
, those laboratories employing molecular methods for identification of these species must be aware of the potential identification complications that may be caused by the presence of differing 16S rRNA genes in the same isolate.
Rapid Detection and Differentiation of Dengue Virus Serotypes by a Real-Time Reverse Transcription-Loop-Mediated Isothermal Amplification Assay
Authors: Parida Manmohan , Horioke Kouhei , Ishida Hiroyuki , Dash Paban Kumar , Saxena Parag , Jana Asha Mukul , Islam Mohammed Alimul , Inoue Shingo , Hosaka Norimitsu , Morita Kouichi 
Published: June 2005

ABSTRACT

The development and validation of a one-step, real-time, and quantitative dengue virus serotype-specific reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay targeting the 3′ noncoding region for the rapid detection and differentiation of dengue virus serotypes are reported. The RT-LAMP assay is very simple and rapid, wherein the amplification can be obtained in 30 min under isothermal conditions at 63°C by employing a set of four serotype-specific primer mixtures through real-time monitoring in an inexpensive turbidimeter. The evaluation of the RT-LAMP assay for use for clinical diagnosis with a limited number of patient serum samples, confirmed to be infected with each serotype, revealed a higher sensitivity by picking up 100% samples as positive, whereas 87% and 81% of the samples were positive by reverse transcription-PCR and virus isolation, respectively. The sensitivity and specificity of the RT-LAMP assay for the detection of viral RNA in patient serum samples with reference to virus isolation were 100% and 93%, respectively. The optimal assay conditions with zero background and no cross-reaction with other closely related members of the
Flavivirus
family (Japanese encephalitis, West Nile, and St. Louis encephalitis viruses) as well as within the four serotypes of dengue virus were established. None of the serum samples from healthy individuals screened in this study showed any cross-reaction with the four dengue virus serotype-specific RT-LAMP assay primers. These findings demonstrate that RT-LAMP assay has the potential clinical application for detection and differentiation of dengue virus serotypes, especially in developing countries.
Enteropathogenic
Escherichia coli
Strains Carrying Genes Encoding the PER-2 and TEM-116 Extended-Spectrum β-Lactamases Isolated from Children with Diarrhea in Uruguay
Authors: Vignoli Rafael , Varela Gustavo , Mota María Inés , Cordeiro Nicolas F. , Power Pablo , Ingold Elizabet , Gadea Pilar , Sirok Alfredo , Schelotto Felipe , Ayala Juan A. , Gutkind Gabriel 
Published: June 2005

ABSTRACT

We studied 13 extended-spectrum β-lactamase (ESBL)-producing enteropathogenic
Escherichia coli
isolates from children suffering acute diarrhea in Uruguay. ESBL characterization in crude extracts showed a single band at pI 5.4. PCR amplification and sequencing data allowed identification of
bla
PER-2
and
bla
TEM-116
. Retrospective analysis suggests that these strains were disseminated in the community, even if unnoticed, prior to their access to the hospital environment more than a decade ago.
Multiplex PCR for Direct Detection of Shiga Toxigenic
Escherichia coli
Strains Producing the Novel Subtilase Cytotoxin
Authors: Paton Adrienne W. , Paton James C. 
Published: June 2005

ABSTRACT

We have recently described a novel AB
5
subtilase cytotoxin produced by certain Shiga toxigenic
Escherichia coli
(STEC) strains. This potentially lethal toxin may contribute to severe gastrointestinal and systemic disease in humans. In this study we have developed a trivalent PCR assay for the detection of the novel toxin A subunit gene
subA
, as well as
stx
1
and
stx
2
. The three primer pairs used in the assay do not interfere with each other and generate amplification products of 556, 180, and 255 bp, respectively. The assay can be used for determining the toxin genotype of STEC isolates, as well as for direct detection of toxin genes in primary fecal culture extracts.
Gene Mutations Responsible for Overexpression of AmpC β-Lactamase in Some Clinical Isolates ofEnterobacter cloacae
Authors: Kaneko Kenichi , Okamoto Ryoichi , Nakano Ryuichi , Kawakami Sayoko , Inoue Matsuhisa 
Published: June 2005

ABSTRACTAmpC regulatory genes in 21 ceftazidime-resistant clinical isolates ofEnterobacter cloacae(MICs of ≥16 μg/ml) were characterized. All isolates exhibited AmpC overproduction due to AmpD mutation. Additionally, we found two AmpR mutants among the isolates. This is the first report of chromosomalampRmutation in clinical isolates ofE. cloacae.
Quinolone-Resistant Uropathogenic
Escherichia coli
Strains from Phylogenetic Group B2 Have Fewer Virulence Factors than Their Susceptible Counterparts
Authors: Horcajada Juan P. , Soto Sara , Gajewski Abby , Smithson Alex , Jiménez de Anta M. Teresa , Mensa Josep , Vila Jordi , Johnson James R. 
Published: June 2005

ABSTRACT

The prevalence of 31 virulence factors was analyzed among nalidixic acid-susceptible and -resistant
Escherichia coli
strains from phylogenetic group B2. Hemolysin, cytotoxic necrotizing factor 1, and S and F1C fimbriae genes were less prevalent among nalidixic acid-resistant
E. coli
strains. Quinolone resistance may be associated with a decrease in the presence of some virulence factors.
Occurrence of
hlyA
and
sheA
Genes in Extraintestinal
Escherichia coli
Strains
Authors: Kerényi Monika , Allison Heather E. , Bátai István , Sonnevend Ágnes , Emödy Levente , Plaveczky Nóra , Pál Tibor 
Published: June 2005

ABSTRACT

The association of a hemolytic phenotype with the carriage of the α-hemolysin gene (
hlyA
) and/or the silent hemolysin gene (
sheA
or
clyA
) among 540 extraintestinal clinical isolates of
Escherichia coli
and 110 fecal isolates from healthy individuals was investigated. Though HlyA is an important virulence factor in extraintestinal
E. coli
infection, the role of SheA is not completely clarified. Two hemolytic
sheA
+
E. coli
strains that lacked
hlyA
and possessed no other hemolysin genes were identified. No
hlyA
+
sheA
+
strains were identified, suggesting that there is possible incompatibility between
hlyA
and
sheA
in the chromosome of
E. coli
.
Demonstration of a High Level of Parasite Population Homology by Quantification of
Plasmodium falciparum
Alleles in Matched Peripheral, Placental, and Umbilical Cord Blood Samples
Authors: Jafari-Guemouri Sayeh , Ndam Nicaise Tuikue , Bertin Gwladys , Renart Emily , Sow Sokhna , Le Hesran Jean-Yves , Deloron Philippe 
Published: June 2005

ABSTRACT

Plasmodium falciparum msp-1
and
msp-2
genes were quantified by fragment analysis in matched placental, peripheral, and cord blood samples. In the three compartments, the multiplicity of infection values were similar, and parasite populations only partially overlapped, as reported. However, identical alleles represented 80 to 95% of the overall parasite populations of each compartment, demonstrating much more homogenous parasite populations than previously thought.
Cryptococcal Antigen Test Revisited: Significance for Cryptococcal Meningitis Therapy Monitoring in a Tertiary Chinese Hospital
Authors: Lu Hongzhou , Zhou Yingjie , Yin Youkuan , Pan Xiaozhang , Weng Xinhua 
Published: June 2005

ABSTRACT
For a total of 29 non-human immunodeficiency virus 1 cryptococcal meningitis cases, titer changes in the latex agglutination test before and after therapy were reviewed along with clinical manifestations, laboratory findings, and therapy regimens. The cryptococcal antigen titer decreased for every case after therapy and was correlated to fungal clearance as defined by fungus smear and/or culture. However, cryptococcal antigen can remain at low titers for long periods of time after therapy, even when fungus smears and/or cultures become negative.
Extraction of
Mycobacterium tuberculosis
DNA: a Question of Containment
Authors: Somerville Wendy , Thibert Louise , Schwartzman Kevin , Behr Marcel A. 
Published: June 2005

ABSTRACT

DNA fingerprinting of
Mycobacterium tuberculosis
by IS
6110
restriction fragment length polymorphism analysis requires substantial high-quality DNA. We demonstrated that, despite extraction treatments that might be expected to inactivate this organism,
M. tuberculosis
remained viable during this process. These data suggest that the extraction of
M. tuberculosis
DNA should be performed within containment until complete.
Inability To Make a Premortem Diagnosis ofAcanthamoebaSpecies Infection in a Patient with Fatal Granulomatous Amebic Encephalitis
Authors: Bloch Karen C. , Schuster Frederick L. 
Published: June 2005

ABSTRACTGranulomatous amebic encephalitis (GAE), an infection of immunocompromised hosts, is almost uniformly fatal. A case of GAE in a patient who failed to mount a serologic response toAcanthamoeba polyphagais presented. AlthoughAcanthamoeba polyphagathat is sensitive to multiple antimicrobials grew from brain tissue, an inability to make a premortem diagnosis precluded therapy.
Infection by
Chlamydophilia avium
in an Elderly Couple Working in a Pet Shop
Authors: Saito Takashi , Ohnishi Jitsuko , Mori Yoshihiro , Iinuma Yoshitsugu , Ichiyama Satoshi , Kohi Fumikazu 
Published: June 2005

ABSTRACT

Psittacosis infection is usually reported in adults aged around 30 to 60 years. We report here two cases of psittacosis in an elderly couple (76 and 77 years old) who jointly ran a pet shop. Psittacosis was diagnosed from a history of exposure to birds and from serological testing for
Chlamydophilia avium
.
First Reported Case of Endocarditis Caused by
Candida dubliniensis
Authors: Carr Michael J. , Clarke Susan , O'Connell Finbar , Sullivan Derek J. , Coleman David C. , O'Connell Brian 
Published: June 2005

ABSTRACT

Candida dubliniensis
is an uncommon cause of bloodstream infection. We describe the first reported case of endocarditis caused by
C. dubliniensis
and the use of a rapid and novel real-time PCR assay based on the internal transcribed spacer 2 variable region of the rRNA operon that was used to identify this organism.
Junctional Adhesion Molecule A Serves as a Receptor for Prototype and Field-Isolate Strains of Mammalian Reovirus
Authors: Campbell Jacquelyn A. , Schelling Pierre , Wetzel J. Denise , Johnson Elizabeth M. , Forrest J. Craig , Wilson Greame A. R. , Aurrand-Lions Michel , Imhof Beat A. , Stehle Thilo , Dermody Terence S. 
Published: June 2005

ABSTRACTReovirus infections are initiated by the binding of viral attachment protein σ1 to receptors on the surface of host cells. The σ1 protein is an elongated fiber comprised of an N-terminal tail that inserts into the virion and a C-terminal head that extends from the virion surface. The prototype reovirus strains type 1 Lang/53 (T1L/53) and type 3 Dearing/55 (T3D/55) use junctional adhesion molecule A (JAM-A) as a receptor. The C-terminal half of the T3D/55 σ1 protein interacts directly with JAM-A, but the determinants of receptor-binding specificity have not been identified. In this study, we investigated whether JAM-A also mediates the attachment of the prototype reovirus strain type 2 Jones/55 (T2J/55) and a panel of field-isolate strains representing each of the three serotypes. Antibodies specific for JAM-A were capable of inhibiting infections of HeLa cells by T1L/53, T2J/55, and T3D/55, demonstrating that strains of all three serotypes use JAM-A as a receptor. To corroborate these findings, we introduced JAM-A or the structurally related JAM family members JAM-B and JAM-C into Chinese hamster ovary cells, which are poorly permissive for reovirus infection. Both prototype and field-isolate reovirus strains were capable of infecting cells transfected with JAM-A but not those transfected with JAM-B or JAM-C. A sequence analysis of the σ1-encoding S1 gene segment of the strains chosen for study revealed little conservation in the deduced σ1 amino acid sequences among the three serotypes. This contrasts markedly with the observed sequence variability within each serotype, which is confined to a small number of amino acids. Mapping of these residues onto the crystal structure of σ1 identified regions of conservation and variability, suggesting a likely mode of JAM-A binding via a conserved surface at the base of the σ1 head domain.
Enhanced Breadth of CD4 T-Cell Immunity by DNA Prime and Adenovirus Boost Immunization to Human Immunodeficiency Virus Env and Gag Immunogens
Authors: Wu Lan , Kong Wing-pui , Nabel Gary J. 
Published: June 2005

ABSTRACTA variety of gene-based vaccination approaches have been used to enhance the immune response to viral pathogens. Among them, the ability to perform heterologous immunization by priming with DNA and boosting with replication-defective adenoviral (ADV) vectors encoding foreign antigens has proven particularly effective in eliciting enhanced cellular and humoral immunity compared to either agent alone. Because adenoviral vector immunization alone can elicit substantial cellular and humoral immune responses in a shorter period of time, we asked whether the immune response induced by the prime-boost immunization was different from adenoviral vaccines with respect to the potency and breadth of T-cell recognition. While DNA/ADV immunization stimulated the CD8 response, it was directed to the same epitopes in Gag and Env immunogens of human immunodeficiency virus as DNA or ADV alone. In contrast, the CD4 response to these immunogens diversified after DNA/ADV immunization compared to each vector alone. These findings suggest that the diversity of the CD4 immune response is increased by DNA/ADV prime-boost vaccination and that these components work synergistically to enhance T-cell epitope recognition.
Investigation by Atomic Force Microscopy of the Structure of Ty3 Retrotransposon Particles
Authors: Kuznetsov Yurii G. , Zhang Min , Menees Thomas M. , McPherson Alexander , Sandmeyer Suzanne 
Published: June 2005

ABSTRACT

Ty3, a member of the
Metaviridiae
family of long-terminal-repeat retrotransposons found in
Saccharomyces cerevisiae
, encodes homologs of retroviral Gag and Gag-Pol proteins, which, together with genomic RNA, assemble into virus-like particles (VLPs) that undergo processing and reverse transcription. The Ty3 structural proteins, capsid and nucleocapsid, contain major homology and nucleocapsid motifs similar to retrovirus capsid and nucleocapsid proteins, but Ty3 lacks a matrix-like structural domain amino terminal to capsid. Mass spectrometry analysis of Ty3 Gag3 processing products defined an acetylated Ser residue as the amino terminus of Gag3/p34, p27, and CA/p24 species and supported a model where p34 and p27 occur in phosphorylated forms. Using atomic force microscopy, VLPs were imaged from cells producing wild-type and protease and reverse transcriptase mutant Ty3. Wild-type VLPs were found to have a broad range of diameters, but the majority, if not all of the particles, exhibited arrangements of capsomeres on their surfaces which were consistent with icosahedral symmetry. Wild-type particles were in the range of 25 to 52 nm in diameter, with particles in the 42- to 52-nm diameter range consistent with T=7 symmetry. Both classes of mutant VLPs fell into a narrower range of 44 to 53 nm in diameter and appeared to be consistent with T=7 icosahedral symmetry. The smaller particles in the wild-type population likely correspond to VLPs that have progressed to reverse transcription or later stages, which do not occur in the protease and reverse transcriptase mutants. Ty3 VLPs did not undergo major external rearrangements during proteolytic maturation.
Effects of a Temperature Sensitivity Mutation in the J1R Protein Component of a Complex Required for Vaccinia Virus Assembly
Authors: Chiu Wen-Ling , Szajner Patricia , Moss Bernard , Chang Wen 
Published: June 2005

ABSTRACT

Vaccinia virus J1R protein is required for virion morphogenesis (W. L. Chiu and W. Chang, J. Virol.
76:
9575-9587, 2002). In this work, we further characterized the J1R protein of wild-type vaccinia virus and compared it with the protein encoded by the temperature-sensitive mutant virus C
ts
45. The mutant C
ts
45 was found to contain a Pro-to-Ser substitution at residue 132 of the J1R open reading frame, which is responsible for a loss-of-function phenotype. The half-life of the J1R-P132S mutant protein was comparable at both 31 and 39°C, indicating that the P132S mutation did not affect the stability of the J1R protein. We also showed that the J1R protein interacts with itself in the virus-infected cells. The N-terminal region of the J1R protein, amino acids (aa) 1 to 77, interacted with the C-terminal region, aa 84 to 153, and the P132 mutation did not abolish this interaction, as determined by two-hybrid analysis. Furthermore, we demonstrated that J1R protein is part of a viral complex containing the A30L, G7L, and F10L proteins in virus-infected cells. In immunofluorescence analyses, wild-type J1R protein colocalized with the A30L, G7L, and F10L proteins in virus-infected cells but the loss-of-function P132 mutant did not. Furthermore, without a functional J1R protein, rapid degradation of A30L and the 15-kDa forms of the G7L and F10L proteins was observed in cells infected with C
ts
45 at 39°C. This study thus demonstrated the importance of the J1R protein in the formation of a viral assembly complex required for morphogenesis.
Gene 5 of the Avian Coronavirus Infectious Bronchitis Virus Is Not Essential for Replication
Authors: Casais Rosa , Davies Marc , Cavanagh David , Britton Paul 
Published: June 2005

ABSTRACT

The avian coronavirus
Infectious bronchitis virus
(IBV), like other coronaviruses, expresses several small nonstructural (ns) proteins in addition to those from gene 1 (replicase) and the structural proteins. These coronavirus ns genes differ both in number and in amino acid similarity between the coronavirus groups but show some concordance within a group or subgroup. The functions and requirements of the small ns gene products remain to be elucidated. With the advent of reverse genetics for coronaviruses, the first steps in elucidating their role can be investigated. We have used our reverse genetics system for IBV (R. Casais, V. Thiel, S. G. Siddell, D. Cavanagh, and P. Britton, J. Virol. 75:12359-12369, 2001) to investigate the requirement of IBV gene 5 for replication in vivo, in ovo, and ex vivo. We produced a series of recombinant viruses, with an isogenic background, in which complete expression of gene 5 products was prevented by the inactivation of gene 5 following scrambling of the transcription-associated sequence, thereby preventing the expression of IBV subgenomic mRNA 5, or scrambling either separately or together of the translation initiation codons for the two gene 5 products. As all of the recombinant viruses replicated very similarly to the wild-type virus, Beau-R, we conclude that the IBV gene 5 products are not essential for IBV replication per se and that they are accessory proteins.
Effect of CD8
+
Lymphocyte Depletion on Virus Containment after Simian Immunodeficiency Virus SIVmac251 Challenge of Live Attenuated SIVmac239Δ3-Vaccinated Rhesus Macaques
Authors: Schmitz Jörn E. , Johnson R. Paul , McClure Harold M. , Manson Kelledy H. , Wyand Michael S. , Kuroda Marcelo J. , Lifton Michelle A. , Khunkhun Rajinder S. , McEvers Kimberly J. , Gillis Jacqueline , Piatak Michael , Lifson Jeffrey D. , Grosschupff Gudrun , Racz Paul , Tenner-Racz Klara , Rieber E. Peter , Kuus-Reichel Kristine , Gelman Rebecca S. , Letvin Norman L. , Montefiori David C. , Ruprecht Ruth M. , Desrosiers Ronald C. , Reimann Keith A. 
Published: June 2005

ABSTRACT

Although live attenuated vaccines can provide potent protection against simian immunodeficiency virus (SIV) and simian-human immunodeficiency virus challenges, the specific immune responses that confer this protection have not been determined. To test whether cellular immune responses mediated by CD8
+
lymphocytes contribute to this vaccine-induced protection, we depleted rhesus macaques vaccinated with the live attenuated virus SIVmac239Δ3 of CD8
+
lymphocytes and then challenged them with SIVmac251 by the intravenous route. While vaccination did not prevent infection with the pathogenic challenge virus, the postchallenge levels of virus in the plasmas of vaccinated control animals were significantly lower than those for unvaccinated animals. The depletion of CD8
+
lymphocytes at the time of challenge resulted in virus levels in the plasma that were intermediate between those of the vaccinated and unvaccinated controls, suggesting that CD8
+
cell-mediated immune responses contributed to protection. Interestingly, at the time of challenge, animals expressing the Mamu-A*01 major histocompatibility complex class I allele showed significantly higher frequencies of SIV-specific CD8
+
T-cell responses and lower neutralizing antibody titers than those in
Mamu-A*01
−
animals. Consistent with these findings, the depletion of CD8
+
lymphocytes abrogated vaccine-induced protection, as judged by the peak postchallenge viremia, to a greater extent in
Mamu-A*01
+
than in
Mamu-A*01
−
animals. The partial control of postchallenge viremia after CD8
+
lymphocyte depletion suggests that both humoral and cellular immune responses induced by live attenuated SIV vaccines can contribute to protection against a pathogenic challenge and that the relative contribution of each of these responses to protection may be genetically determined.