bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limited Genetic Diversity of
Brucella
spp
Authors: Gándara Benjamı́n , Merino Ahidé López , Rogel Marco Antonio , Martı́nez-Romero Esperanza 
Published: July 2002

ABSTRACT

Multilocus enzyme electrophoresis (MLEE) of 99
Brucella
isolates, including the type strains from all recognized species, revealed a very limited genetic diversity and supports the proposal of a monospecific genus. In MLEE-derived dendrograms,
Brucella abortus
and a marine
Brucella
sp. grouped into a single electrophoretic type related to
Brucella neotomae
and
Brucella ovis. Brucella suis
and
Brucella canis
formed another cluster linked to
Brucella melitensis
and related to
Rhizobium tropici
. The
Brucella
strains tested that were representatives of the six electrophoretic types had the same rRNA gene restriction fragment length polymorphism patterns and identical ribotypes. All 99 isolates had similar chromosome profiles as revealed by the Eckhardt procedure.
Rapid Detection of Smear-Negative
Mycobacterium tuberculosis
by PCR and Sequencing for Rifampin Resistance with DNA Extracted Directly from Slides
Authors: Patnaik Madhumita , Liegmann Karsten , Peter James B. 
Published: July 2002

ABSTRACT

Conventional methods for identification of
Mycobacterium tuberculosis
from culture can take 6 weeks. To facilitate the rapid detection of
M. tuberculosis
and to assess the risks of drug resistance, we developed a technique of eluting DNA directly from sputum slides and performing PCR for the detection of
M. tuberculosis
DNA, followed by sequencing the
rpoB
gene to detect rifampin resistance. This entire process requires only 48 h. Forty-seven sputum specimens submitted for microscopy for detection of acid-fast bacilli (AFB) and for mycobacterial culture and susceptibility testing were assessed after elution from the slides and extraction.
M. tuberculosis
-specific DNA was amplified in a nested PCR with previously described primers (primers rpo95-rpo293 and rpo105-rpo273), followed by analysis on a 4% agarose gel for a 168-bp product. Automated sequencing was performed, and the sequences were aligned against a database for detection of anomalies in the
rpoB
gene (codons 511 to 533) which indicate rifampin resistance. Of the 47 sputum specimens tested, 51% (24 of 47) were culture positive (time to positive culture, 2 to 6 weeks). Smears for AFB were positive for 58% (14 of 24) of the specimens and were negative for 42% (10 of 24) of the specimens. All 24 culture-positive sputum specimens (14 microscopy-positive and 10 microscopy-negative sputum specimens) were positive by PCR with eluates from the smears. Forty-nine percent (23 of 47) of the sputum specimens were negative for
M. tuberculosis
by smear, culture, and PCR. Of the isolates from the culture-positive samples, five were rifampin resistant by sequencing; all five were also rifampin resistant by in vitro susceptibility testing. Of these rifampin-resistant
M. tuberculosis
isolates, two were microscopy negative for AFB. Patients who are negative for AFB and culture positive for
M. tuberculosis
can now be identified within a day, allowing institution of therapy and reducing isolation time and medical costs.
Qualitative Plasma PCR Assay (AMPLICOR CMV Test) versus pp65 Antigenemia Assay for Monitoring Cytomegalovirus Viremia and Guiding Preemptive Ganciclovir Therapy in Allogeneic Stem Cell Transplantation
Authors: Solano Carlos , Muñoz Isabel , Gutiérrez Antonio , Farga Amparo , Prósper Felipe , Garcı́a-Conde Javier , Navarro David , Gimeno Concepción 
Published: July 2002

ABSTRACT

The performances of a commercially available qualitative plasma PCR assay (AMPLICOR CMV test; Roche Diagnostics) and the pp65 antigenemia assay (AG) were evaluated for the monitoring of cytomegalovirus (CMV) viremia in 43 allogeneic stem cell transplant recipients. In addition, the suitabilities of both assays for triggering the initiation of preemptive ganciclovir therapy were assessed. A total of 37 CMV viremic episodes were detected in 28 patients. Positivity of plasma PCR testing in one or more consecutive specimens was the only marker of CMV viremia in 18 of the 37 episodes (PCR positive and AG negative,
n
= 50 specimens). Five episodes were diagnosed on the basis of a single positive AG result (AG positive and PCR negative,
n
= 5 specimens); both assays were eventually positive (PCR positive and AG positive,
n
= 27 specimens) for 14 viremic episodes; for these episodes, conversion of the PCR assay result to a positive result occurred an average of 1 week before conversion of the AG result. Overall, the concordance between the two methods was 90%, and the sensitivities of the plasma PCR assay and AG for the detection of CMV viremic episodes were 86.5 and 51.3%, respectively. Two patients who tested positive by both assays simultaneously progressed to CMV end-stage organ disease, despite the initiation of preemptive ganciclovir therapy. Conversion of the AG result to a negative result upon administration of preemptive ganciclovir therapy occurred a median of 7.5 days earlier than conversion of the plasma PCR assay result. Nineteen of the 28 patients with CMV viremia received AG-guided preemptive ganciclovir therapy; had the positivity of the plasma PCR assay triggered the initiation of preemptive therapy, 9 additional patients would have been unnecessarily treated since none of them developed CMV end-stage organ disease. Although the AMPLICOR CMV assay is more sensitive than AG, the latter appears to be more suitable both for guiding the initiation of preemptive therapy and for monitoring a patient's response to antiviral therapy.
Unusual Occurrence of M Type 77, Antibiotic-Resistant Group A Streptococci in Southern Sweden
Authors: Jasir A. , Tanna A. , Efstratiou A. , Schalén C. 
Published: July 2002

ABSTRACT

For many years group A streptococci of T type 28 (T28) have been common in southern Sweden; however, since 1995 resistance to both macrolide-lincosamide-streptogramin B (MLS) antibiotics and tetracycline was observed among T28 isolates, which prompted the present studies on clonal relatedness of antibiotic-resistant T28 strains. By extended T typing, 95 of 100 examined tetracycline-resistant strains showed the combination T9-T13-T28; of these, 94 belonged to M type 77 (M77) and one belonged to M73. Three strains were T28-M28 and two were T28-M nontypeable. The serological M77 was confirmed by PCR capture enzyme-linked immunosorbent assay,
emm
amplicon restriction profiling, and
emm
sequence typing. Fifty strains were examined for superantigen genes:
speA
was detected in three blood isolates only, whereas all isolates harbored
speB
, and only two of the strains were negative for
speC
. Eighty-nine of the 100 strains were also macrolide resistant, of which 59 were inducibly MLS resistant (IR) and 21 were constitutively MLS resistant (CR), 6 were noninducibly resistant (NI), and 3 had novel subphenotypes recently reported by our group. Resistance genes were determined by PCR and hybridization methods. Eighty-four of the 100 strains harbored
tetM. ermB
was detected in all CR and IR strains, and
mefA
was found in all NI strains; both
ermB
and
mefA
were identified in two strains with novel subphenotypes. Pulsed-field gel electrophoresis showed that these antibiotic-resistant M77 strains belonged to at least five different clones.
Chronic Melioidosis in a Patient with Cystic Fibrosis
Authors: Schülin Tanja , Steinmetz Ivo 
Published: July 2002

ABSTRACT

Burkholderia pseudomallei
, the causative agent of melioidosis, is endemic in Southeast Asia and northern Australia, where it can be found in soil and surface water. We report a case of chronic pulmonary melioidosis in a patient with cystic fibrosis who had traveled to an area where
B. pseudomallei
is endemic.
Persistence of Two Invasive
Streptococcus pneumoniae
Clones of Serotypes 1 and 5 in Comparison to That of Multiple Clones of Serotypes 6B and 23F among Children in Southern Israel
Authors: Porat Nurith , Trefler Ronit , Dagan Ron 
Published: July 2002

ABSTRACT
We conducted a study to examine the clonal distribution of invasive serotype 1 and 5 isolates as representatives of serotypes that are rarely carried by healthy individuals compared to that of invasive serotype 6B and 23F isolates as representatives of serotypes often carried by young children for prolonged periods. All invasive serotype 1, 5, 6B, and 23F isolates recovered from blood cultures during January 1995 to May 1999 were analyzed; these included 66 serotype 1, 30 serotype 5, 11 serotype 6B, and 15 serotype 23F isolates. One hundred thirty-three nasopharyngeal (NP) isolates of the indicated four serotypes from healthy children were also studied. The strains were characterized using serotyping, antimicrobial susceptibility testing, and pulsed-field gel electrophoresis profiling. We found that both invasive and NP serotype 1 and 5 isolates were susceptible to penicillin and that each serotype showed only one clonal type. In contrast, serotype 6B and 23F strains showed different phenotypic characteristics as well as multiple clonal types; 10 clones were identified among 6B isolates, and 11 clones were identified among 23F isolates.
Variable Oncogene Promoter Activity of Human Papillomavirus Type 16 Cervical Cancer Isolates from Australia
Authors: Watts Kylie J. , Thompson Carol H. , Cossart Yvonne E. , Rose Barbara R. 
Published: July 2002

ABSTRACT
The functional significance of sequence variation within the upstream regulatory region (URR) of six human papillomavirus type 16 (HPV16) cervical cancer isolates from Australia was investigated. Specific changes in transcription factor binding sites leading to increased promoter activity may explain the transforming ability of some episomal HPV16 isolates.
Performance of the Chromogenic Medium CHROMagar Staph Aureus and the Staphychrom Coagulase Test in the Detection and Identification of
Staphylococcus aureus
in Clinical Specimens
Authors: Carricajo Anne , Treny Axel , Fonsale Nathalie , Bes Michele , Reverdy Marie Elisabeth , Gille Yves , Aubert Gerald , Freydiere Anne Marie 
Published: July 2002

ABSTRACT

CHROMagar Staph aureus (CSAM) (CHROMagar Microbiology, Paris, France) is a new chromogenic medium designed to enable detection of colonies of
Staphylococcus aureus
by their pink color. A total of 775 specimens were cultured in parallel on CHROMagar Staph aureus and conventional media. Among the 267
S. aureus
strains recovered on at least one medium, 263 were isolated on CSAM medium (sensitivity, 98.5%), and 245 (sensitivity, 91.8%) were isolated on conventional media. The specificity of presumptive identification of
S. aureus
on the basis of pink colony color on CSAM medium was 97% (493 of 508). This specificity increased to 100% when coagulase detection with the Staphychrom coagulase test was added and to 98.8% when
S. aureus
surface components were detected by agglutination in the Pastorex Staph Plus test. Susceptibility testing of 67
S. aureus
strains, performed in parallel on pink CSAM colonies and on colonies grown on blood agar, gave similar results. Thus, rapid and accurate recognition and identification of
S. aureus
isolates were achieved with CSAM as the primary isolation medium, followed by the staphylocoagulase Staphychrom test. Antimicrobial susceptibility testing (disk-diffusion method or ATB STAPH System) can be performed directly on pink CSAM colonies.
Comparison of Digene Hybrid Capture 2 and Conventional Culture for Detection of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
in Cervical Specimens
Authors: Darwin Ling H. , Cullen Allison P. , Arthur Patrick M. , Long Carole D. , Smith Kim R. , Girdner Jennifer L. , Hook Edward W. , Quinn Thomas C. , Lorincz Attila T. 
Published: July 2002

ABSTRACT

Digene's Hybrid Capture 2 (HC2) CT/GC, CT-ID, and GC-ID DNA tests were evaluated by comparison to traditional culture methods for detecting
Chlamydia trachomatis
and
Neisseria gonorrhoeae
infections in 669 cervical specimens from high-risk female populations attending two sexually transmitted disease clinics. For detection of either or both infections, the HC2 CT/GC test algorithm had 93.8% sensitivity and 95.9% specificity compared to those of culture. After resolution of discrepant results by direct fluorescent-antibody (DFA) staining or PCR assay, the relative sensitivity and specificity of the HC2 CT/GC test algorithm increased to 94.8 and 99.8%, while the values for culture were 83.6% (McNemar's
P
value, 0.0062) and 100%, respectively. For detection of the individual pathogens, the relative sensitivities for the HC2 CT-ID and GC-ID tests were 97.2 and 92.2% and the specificities were greater than 99% compared to culture adjucated by DFA staining and PCR. Test performance varied at the two clinics: the HC2 CT/GC algorithm, CT-ID, and GC-ID tests had significantly higher sensitivities (McNemar's
P
value, <0.05) than that of culture for the population at one clinic as well as for the combined populations. At the other clinic, the HC2 tests performed as well as culture.
Genetic Variation of Capsid Protein VP7 in Genotype G4 Human Rotavirus Strains: Simultaneous Emergence and Spread of Different Lineages in Argentina
Authors: Bok Karin , Matson David O. , Gomez Jorge A. 
Published: July 2002

ABSTRACT
Rotavirus is the most-common cause of severe diarrhea in young children. Complete rotavirus characterization includes determination of the antigenic type of the two outer capsid proteins, VP7 and VP4, designated G and P types, respectively. During a nationwide rotavirus surveillance study, genotype G4 frequency increased during the second year. To evaluate further the mechanism of emergence and the relationship among G4 strains, the genetic diversity of VP7 capsid protein in these samples was studied in detail. Overall nucleotide sequence divergence ranged from less than 0.1 to 19.5%, a higher divergence than that observed for other rotavirus G types (0.1 to 9%). Sequences were classified into two major lineages (designated I and II) based on their nucleotide distances. The most heterogeneous lineage was further subdivided into four sublineages (designated Ia to Id). Most Argentine sequences were of sublineages Ib and Ic, which were confirmed to be independent sequence clusters by parsimony analysis. This study describes different lineages and sublineages within G4 strains and shows that Argentine strains are distantly related to reference strain ST3. The appearance of at least two G4 genotype (sub)lineages during 1998 demonstrates that the increased frequency of these strains was due to the synchronized emergence of different groups of strains.
Characterization of a Baculovirus Alkaline Nuclease
Authors: Li Lulin , Rohrmann George F. 
Published: July 2002

ABSTRACT

All baculovirus genomes sequenced to date encode a homolog of an alkaline nuclease that has been characterized in the
Herpesviridae
. In this report we describe the characterization of the alkaline nuclease (AN) homolog of the
Autographa californica
multinucleocapsid nucleopolyhedrovirus (Ac
M
NPV) (open reading frame 133). His-tagged AN constructs were expressed in recombinant baculoviruses and affinity purified, and then their enzymatic activity was characterized. AN was found to degrade linear DNA at alkaline pH, preferred Mg
2+
over Mn
2+
, had optimal activity at 35°C, and did not appear to have a salt requirement. To rule out contamination by the endogenous baculovirus gene product or a cellular enzyme, point mutations were introduced into a highly conserved domain of the gene. These mutations were found to markedly reduce or eliminate most of the activity of the affinity-purified enzyme. An antibody generated against the protein was used to analyze its expression by Western blot analysis. AN was found to be expressed at low levels by 12 h postinfection, with maximal expression at 24 h postinfection. Attempts to generate a virus with this gene inactivated were unsuccessful, suggesting that AN may be encoded by an essential gene.
Enhanced Infectivity of an R5-Tropic Simian/Human Immunodeficiency Virus Carrying Human Immunodeficiency Virus Type 1 Subtype C Envelope after Serial Passages in Pig-Tailed Macaques (
Macaca nemestrina
)
Authors: Chen Zhiwei , Huang Yaoxing , Zhao Xiuqing , Skulsky Eva , Lin Dorothy , Ip James , Gettie Agegnehu , Ho David D. 
Published: July 2002

ABSTRACT

The increasing prevalence of human immunodeficiency virus type 1 (HIV-1) subtype C infection worldwide calls for efforts to develop a relevant animal model for evaluating strategies against the transmission of the virus. A chimeric simian/human immunodeficiency virus (SHIV), SHIV
CHN19
, was generated with a primary, non-syncytium-inducing HIV-1 subtype C envelope from a Chinese strain in the background of SHIV
33
. Unlike R5-tropic SHIV
162
, SHIV
CHN19
was not found to replicate in rhesus CD4
+
T lymphocytes. SHIV
CHN19
does, however, replicate in CD4
+
T lymphocytes of pig-tailed macaques (
Macaca nemestrina
). The observed replication competence of SHIV
CHN19
requires the full
tat/rev
genes and partial gp41 region derived from SHIV
33
. To evaluate in vivo infectivity, SHIV
CHN19
was intravenously inoculated, at first, into two pig-tailed and two rhesus macaques. Although all four animals became infected, the virus replicated preferentially in pig-tailed macaques with an earlier plasma viral peak and a faster seroconversion. To determine whether in vivo adaptation would enhance the infectivity of SHIV
CHN19
, passages were carried out serially in three groups of two pig-tailed macaques each, via intravenous blood-bone marrow transfusion. The passages greatly enhanced the infectivity of the virus as shown by the increasingly elevated viral loads during acute infection in animals with each passage. Moreover, the doubling time of plasma virus during acute infection became much shorter in passage 4 (P4) animals (0.2 day) in comparison to P1 animals (1 to 2 days). P2 to P4 animals all became seropositive around 2 to 3 weeks postinoculation and had a decline in CD4/CD8 T-cell ratio during the early phase of infection. In P4 animals, a profound depletion of CD4 T cells in the lamina propria of the jejunum was observed. Persistent plasma viremia has been found in most of the infected animals with sustained viral loads ranging from 10
3
to 10
5
per ml up to 6 months postinfection. Serial passages did not change the viral phenotype as confirmed by the persistence of the R5 tropism of SHIV
CHN19
isolated from P4 animals. In addition, the infectivity of SHIV
CHN19
in rhesus peripheral blood mononuclear cells was also increased after in vivo passages. Our data indicate that SHIV
CHN19
has adapted well to grow in macaque cells. This established R5-tropic SHIV
CHN19
/macaque model would be very useful for HIV-1 subtype C vaccine and pathogenesis studies.
Human Immunodeficiency Virus Type 1 Vpr Contains Two Leucine-Rich Helices That Mediate Glucocorticoid Receptor Coactivation Independently of Its Effects on G
2
Cell Cycle Arrest
Authors: Sherman Michael P. , de Noronha Carlos M. C. , Pearce David , Greene Warner C. 
Published: July 2002

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) Vpr participates in nuclear targeting of the viral preintegration complex in nondividing cells and induces G
2
cell cycle arrest in proliferating cells, which creates an intracellular milieu favorable for viral replication. Vpr also activates the transcription of several promoters and enhancers by a poorly understood mechanism. Vpr enhances glucocorticoid receptor (GR) signaling and may mediate the effects of steroids on HIV replication. More specifically, recombinant Vpr can potentiate virion production from U937 cells, downregulate NF-κB induction, and enhance programmed cell death, all effects also mediated by glucocorticoids. Vpr has been proposed to act as a GR coactivator, although other studies suggest that these enhancing effects are merely a consequence of G
2
cell cycle arrest. We now demonstrate that Vpr functions as a GR coactivator and that this activity is independent of cell cycle arrest. In addition, we show that the Vpr-induced coactivation requires an intact glucocorticoid response element, that it is dependent on the presence of hormone and the corresponding receptor, and that it is mediated by the two highly conserved leucine-rich domains within Vpr that resemble the GR coactivator signature motif.
Granulocyte-Macrophage Colony-Stimulating Factor Priming plus Papillomavirus E6 DNA Vaccination: Effects on Papilloma Formation and Regression in the Cottontail Rabbit Papillomavirus-Rabbit Model
Authors: Leachman Sancy A. , Tigelaar Robert E. , Shlyankevich Mark , Slade Martin D. , Irwin Michele , Chang Ed , Wu T. C. , Xiao Wei , Pazhani Sundaram , Zelterman Daniel , Brandsma Janet L. 
Published: July 2002

ABSTRACTA cottontail rabbit papillomavirus (CRPV) E6 DNA vaccine that induces significant protection against CRPV challenge was used in a superior vaccination regimen in which the cutaneous sites of vaccination were primed with an expression vector encoding granulocyte-macrophage colony-stimulating factor (GM-CSF), a cytokine that induces differentiation and local recruitment of professional antigen-presenting cells. This treatment induced a massive influx of major histocompatibility complex class II-positive cells. In a vaccination-challenge experiment, rabbit groups were treated by E6 DNA vaccination, GM-CSF DNA inoculation, or a combination of both treatments. After two immunizations, rabbits were challenged with CRPV at low, moderate, and high stringencies and monitored for papilloma formation. As expected, all clinical outcomes were monotonically related to the stringency of the viral challenge. The results demonstrate that GM-CSF priming greatly augmented the effects of CRPV E6 vaccination. First, challenge sites in control rabbits (at the moderate challenge stringency) had a 0% probability of remaining disease free, versus a 50% probability in E6-vaccinated rabbits, and whereas GM-CSF alone had no effect, the interaction between GM-CSF priming and E6 vaccination increased disease-free survival to 67%. Second, the incubation period before papilloma onset was lengthened by E6 DNA vaccination alone or to some extent by GM-CSF DNA inoculation alone, and the combination of treatments induced additive effects. Third, the rate of papilloma growth was reduced by E6 vaccination and, to a lesser extent, by GM-CSF treatment. In addition, the interaction between the E6 and GM-CSF treatments was synergistic and yielded more than a 99% reduction in papilloma volume. Finally, regression occurred among the papillomas that formed in rabbits treated with the E6 vaccine and/or with GM-CSF, with the highest regression frequency occurring in rabbits that received the combination treatment.
Leader Proteinase of the Beet Yellows Closterovirus: Mutation Analysis of the Function in Genome Amplification
Authors: Peng Chih-Wen , Dolja Valerian V. 
Published: July 2002

ABSTRACT
The beet yellows closterovirus leader proteinase (L-Pro) possesses a C-terminal proteinase domain and a nonproteolytic N-terminal domain. It was found that although L-Pro is not essential for basal-level replication, deletion of its N-terminal domain resulted in a 1,000-fold reduction in RNA accumulation. Mutagenic analysis of the N-terminal domain revealed its structural flexibility except for the 54-codon-long, 5′-terminal element in the corresponding open reading frame that is critical for efficient RNA amplification at both RNA and protein levels.