bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multicenter Performance Evaluation of a New TaqMan PCR Assay for Monitoring Human Immunodeficiency Virus RNA Load
Authors: Perrin L. , Pawlotsky J. M. , Bouvier-Alias M. , Sarrazin C. , Zeuzem S. , Colucci G. 
Published: December 2006

ABSTRACT

A TaqMan real-time PCR assay, the COBAS TaqMan human immunodeficiency virus (HIV) (HPS-CTMHIV) PCR assay, recently developed for the quantification of HIV type 1 RNA in plasma, was evaluated in comparison with the licensed COBAS AMPLICOR HIV-1 MONITOR (CAHIM) assay. In this study, we have analyzed the tests' sensitivities, precisions, and linearities using multiple replicates of a standard panel of HIV RNA covering a 7-logarithm range of concentrations, as well as serial threefold dilutions of high-titer clinical samples. The subtype inclusivity was also investigated, using a panel of subtypes A to H, while a collection of 160 clinical samples was analyzed to assess the tests' specificities and the systems' similarities. The results of these experiments showed that the HPS-CTMHIV assay has a sensitivity of 53 copies/ml (95% hit rate), 100% specificity, and good intra- and interassay precision. The results of the HPS-CTMHIV assay were linear in the 50- to 10
7
-copies/ml range, with a correlation coefficient (
R
) for expected versus observed results of 0.98. Compared to the CAHIM assay, the HPS-CTMHIV assay showed a high correlation (
R
= 0.99) across the dynamic range of RNA concentrations that, for the CAHIM assay, requires two different sample preparations. Equivalent performances were also observed for the two systems in the detection and quantification of HIV subtypes A to H. These data indicate that the HPS-CTMHIV assay may be one of the tests of choice for monitoring viral load throughout the course of HIV infection and during highly active antiretroviral therapy.
Interlaboratory Study of Quality Control Isolates for a Broth Microdilution Method (Modified CLSI M38-A) for Testing Susceptibilities of Dermatophytes to Antifungals
Authors: Ghannoum M. A. , Arthington-Skaggs B. , Chaturvedi V. , Espinel-Ingroff A. , Pfaller M. A. , Rennie R. , Rinaldi M. G. , Walsh T. J. 
Published: December 2006

ABSTRACT

The Clinical and Laboratory Standards Institute (CLSI; formerly National Committee for Clinical Laboratory Standards, or NCCLS) M38-A standard for the susceptibility testing of filamentous fungi does not specifically address the testing of dermatophytes. In 2003, a multicenter study investigated the reproducibility of the microdilution method developed at the Center for Medical Mycology, Cleveland, Ohio, for testing the susceptibility of dermatophytes. Data from that study supported the introduction of this method for testing dermatophytes in the future version of the CLSI M38-A standard. In order for the method to be accepted by CLSI, appropriate quality control isolates needed to be identified. To that end, an interlaboratory study, involving the original six laboratories plus two additional sites, was conducted to evaluate potential candidates for quality control isolates. These candidate strains included five
Trichophyton rubrum
strains known to have elevated MICs to terbinafine and five
Trichophyton mentagrophytes
strains. Antifungal agents tested included ciclopirox, fluconazole, griseofulvin, itraconazole, posaconazole, terbinafine, and voriconazole. Based on the data generated, two quality control isolates, one
T. rubrum
isolate and one
T. mentagrophytes
isolate, were identified and submitted to the American Type Culture Collection (ATCC) for inclusion as reference strains. Ranges encompassing 95.2 to 97.9% of all data points for all seven drugs were established.
Borrelia burgdorferi
Genetic Markers and Disseminated Disease in Patients with Early Lyme Disease
Authors: Jones Kathryn L. , Glickstein Lisa J. , Damle Nitin , Sikand Vijay K. , McHugh Gail , Steere Allen C. 
Published: December 2006

ABSTRACT

Three genetic markers of
Borrelia burgdorferi
have been associated with disseminated disease: the OspC type, the 16S-23S rRNA intergenic spacer type (RST), and
vlsE
. Here, we modified previous methods so as to identify the three markers by PCR and restriction fragment length polymorphism in parallel, analyzed
B. burgdorferi
isolates from erythema migrans (EM) skin lesions in 91 patients, and correlated the results with evidence of dissemination. OspC type A was found approximately twice as frequently in patients with disseminated disease, whereas type K was identified approximately twice as often in those without evidence of dissemination, but these trends were not statistically significant. The remaining seven types identified were found nearly equally in patients with or without evidence of dissemination. RST 1 strains were significantly associated with dissemination (
P
= 0.03), whereas RST 2 and RST 3 strains tended to have an inverse association with this outcome. The
vlsE
gene was identified in all 91 cases, using primer sets specific for an N-terminal sequence of
B. burgdorferi
strain B31 (
vlsE
B31
) or strain 297 (
vlsE
297
), but neither marker was associated with dissemination. Specific combinations of the three genetic markers usually occurred together. OspC type A was always found with RST 1 and
vlsE
B31
, type K was always identified with RST 2 and more often with
vlsE
297
, and types E and I were almost always found with RST 3 and equally often with
vlsE
B31
and
vlsE
297
. We conclude that
B. burgdorferi
strains vary in their capacity to disseminate, but almost all strains isolated from EM lesions sometimes caused disseminated disease.
Quantification of Genital Human Immunodeficiency Virus Type 1 (HIV-1) DNA in Specimens from Women with Low Plasma HIV-1 RNA Levels Typical of HIV-1 Nontransmitters
Authors: Benki Sarah , McClelland R. Scott , Emery Sandra , Baeten Jared M. , Richardson Barbra A. , Lavreys Ludo , Mandaliya Kishorchandra , Overbaugh Julie 
Published: December 2006

ABSTRACTStudies of human immunodeficiency virus type 1 (HIV-1) transmission suggest that genital HIV-1 RNA and DNA may both be determinants of HIV-1 infectivity. Despite its potential role in HIV-1 transmission, there are limited quantitative data on genital HIV-1 DNA. Here we validated an in-house real-time PCR method for quantification of HIV-1 DNA in genital specimens. In reactions with 100 genomes to 1 genome isolated from a cell line containing one HIV-1 provirus/cell, this real-time PCR assay is linear and agrees closely with a commercially available real-time PCR assay specific for a cellular housekeeping gene. In mock genital samples spiked with low numbers of HIV-1-infected cells such that the expected HIV-1 DNA copy number/reaction was 100, 10, or 5, the average copy number/reaction was 80.2 (standard deviation [SD], 28.3), 9.1 (SD, 5.4), or 3.1 (SD, 2.1), respectively. We used this method to examine genital HIV-1 DNA levels in specimens from women whose low plasma HIV-1 RNA levels are typical of HIV-1 nontransmitters. The median HIV-1 DNA copy number in endocervical secretions from these women (1.8 HIV-1 DNA copies/10,000 cells) was lower than that for women with higher plasma HIV-1 RNA levels (16.6 HIV-1 DNA copies/10,000 cells) (P= 0.04), as was the median HIV-1 DNA copy number in vaginal secretions (undetectable versus 1.0 HIV-1 DNA copies/10,000 cells). These data suggest that women with low plasma HIV-1 RNA and thus a predicted low risk of HIV-1 transmission have low levels of genital HIV-1 cell-associated virus. The assay described here can be utilized in future efforts to examine the role of cell-associated HIV-1 in transmission.
Presence of the
exoU
Gene of
Pseudomonas aeruginosa
Is Correlated with Cytotoxicity in MDCK Cells but Not with Colonization in BALB/c Mice
Authors: Lin Hsi-Hsun , Huang Shiao-ping , Teng Hsiu-Chen , Ji Dar-Der , Chen Yao-Shen , Chen Ya-Lei 
Published: December 2006

ABSTRACT

A total of 141 independent strains of
Pseudomonas aeruginosa
with different heterogeneities in the
exo
gene (
exoS
,
exoT
,
exoU
, and
exoY
) background were examined for their pathogenic roles. Results indicated that the
exoU
gene is the major contributor to cytotoxicity in Madin-Darby canine kidney cells but is not related to bacterial colonization in mice.
Antimicrobial Susceptibility Patterns and Staphylococcal Cassette Chromosome
mec
Types of, as Well as Panton-Valentine Leukocidin Occurrence among, Methicillin-Resistant
Staphylococcus aureus
Isolates from Children and Adults in Middle Tennessee
Authors: Kilic Abdullah , Li Haijing , Stratton Charles W. , Tang Yi-Wei 
Published: December 2006

ABSTRACT

Antimicrobial susceptibility patterns, Panton-Valentine leukocidin (PVL) occurrence, and staphylococcal cassette chromosome
mec
(SCC
mec
) types in methicillin-resistant
Staphylococcus aureus
(MRSA) strains isolated from children and adults at Vanderbilt University Medical Center during a 12-month period were evaluated. A total of 1,315 MRSA isolates were collected, of which 748 (36.7%) were recovered from children. Among all isolates, 448 (34.1%) were SCC
mec
-II, and 847 (64.4%) were SCC
mec
-IV. More SCC
mec
-IV isolates were recovered from children than SCC
mec
-II isolates (424 [50.1%] versus 50 [11.2%]; odds ration [OR] = 7.98;
P
< 0.000001). The PVL gene was detected in 93.6% of SCC
mec
-IV isolates, in contrast to 0.2% in SCC
mec
-II isolates. Within SCC
mec
-IV isolates, a statistically higher PVL occurrence was noticed in children (98.1%) than in adults (89.1%) (OR = 6.34;
P
< 0.000001). Overall, SCC
mec
-II strains showed greater resistance than SCC
mec
-IV strains to clindamycin, erythromycin, levofloxacin, gentamicin, rifampin, minocycline, and trimethoprim-sulfamethoxazole. Both SCC
mec
-II and SCC
mec
-IV strains recovered from adults were more resistant to these antibiotics than those recovered from children. SCC
mec
-II strains were predominantly recovered from the respiratory tract, whereas SCC
mec
-IV strains were predominantly recovered from skin, soft tissue, abscesses, and surgical wounds. These data indicate that SCC
mec
-IV MRSA isolates frequently infect children in middle Tennessee and are likely to harbor the PVL gene.
Determination of MICs of Aminocandin for
Candida
spp. and Filamentous Fungi
Authors: Isham N. , Ghannoum M. A. 
Published: December 2006

ABSTRACT

Candida
and As
pergillus
spp., as well as other filamentous molds, have increasingly been reported as the causes of severe invasive fungal infections. We evaluated the new echinocandin aminocandin (AMN) for its antifungal activities against a range of fungal pathogens by determination of the MICs for the organisms. The MICs of the comparator drugs amphotericin B, caspofungin, micafungin, and voriconazole were also determined. The MICs of AMN for 25 strains each of non-
Candida albicans Candida
spp. (including
Candida parapsilosis
,
Candida krusei
,
Candida guilliermondii
, and
Candida tropicalis
),
Aspergillus fumigatus
,
Scedosporium
spp.,
Fusarium
spp., and zygomycetes (including
Absidia
,
Mucor
, and
Rhizopus
spp.) were determined by using the Clinical and Laboratory Standards Institute M27-A2 and M38-A methodologies for yeasts and filamentous molds, respectively. The MIC ranges of AMN for all yeasts were similar (0.03 to 4.0 μg/ml), while the MIC ranges of AMN for filamentous fungi were species specific. AMN demonstrated potent antifungal activity against
A. fumigatus
, limited activity against
Scedosporium
spp., and no activity against zygomycetes or
Fusarium
spp. Our data showed that AMN demonstrated potent antifungal activities against all of the yeasts and
Aspergillus
isolates tested, suggesting that AMN could be an important addition to our arsenal of antifungals for the treatment of invasive fungal disease.
A Protein Encoded by the Bovine Herpesvirus 1 Latency-Related Gene Interacts with Specific Cellular Regulatory Proteins, Including CCAAT Enhancer Binding Protein Alpha
Authors: Meyer Florencia , Perez Sandra , Geiser Vicki , Sintek Mark , Inman Melissa , Jones Clinton 
Published: December 2006

ABSTRACT
Following acute infection, bovine herpesvirus 1 establishes latency in sensory neurons of trigeminal ganglia (TG). Reactivation from latency occurs periodically, resulting in the shedding of infectious virus. The latency-related (LR) RNA is abundantly expressed in TG of latently infected calves, and the expression of LR proteins is necessary for dexamethasone-induced reactivation from latency. Previously published studies also identified an alternatively spliced LR transcript which is abundantly expressed in TG at 7 days after infection and has the potential to encode a novel LR fusion protein. Seven days after infection is when extensive viral gene expression is extinguished in TG and latency is established, suggesting that LR gene products influence the establishment of latency. In this study, we used a bacterial two-hybrid assay to identify cellular proteins that interact with the novel LR fusion protein. The LR fusion protein interacts with two proteins that can induce apoptosis (Bid and Cdc42) and with CCAAT enhancer binding protein alpha (C/EBP-α). Additional studies confirmed that the LR fusion protein interacts with human or insect C/EBP-α. C/EBP-α protein expression is induced in TG neurons of infected calves and after dexamethasone-induced reactivation from latency. Wild-type C/EBP-α, but not a DNA binding mutant of C/EBP-α, enhances plaque formation in bovine cells. We hypothesize that interactions between the LR fusion protein and C/EBP-α promote the establishment of latency.
Rapid Reversion of Sequence Polymorphisms Dominates Early Human Immunodeficiency Virus Type 1 Evolution
Authors: Li Bin , Gladden Adrianne D. , Altfeld Marcus , Kaldor John M. , Cooper David A. , Kelleher Anthony D. , Allen Todd M. 
Published: December 2006

ABSTRACT

The error-prone replication of human immunodeficiency virus type 1 (HIV-1) enables it to continuously evade host CD8
+
T-cell responses. The observed transmission, and potential accumulation, of CD8
+
T-cell escape mutations in the population may suggest a gradual adaptation of HIV-1 to immune pressures. Recent reports, however, have highlighted the propensity of some escape mutations to revert upon transmission to a new host in order to restore efficient replication capacity. To more specifically address the role of reversions in early HIV-1 evolution, we examined sequence polymorphisms arising across the HIV-1 genome in seven subjects followed longitudinally 1 year from primary infection. As expected, numerous nonsynonymous mutations were associated with described CD8
+
T-cell epitopes, supporting a prominent role for cellular immune responses in driving early HIV-1 evolution. Strikingly, however, a substantial proportion of substitutions (42%) reverted toward the clade B consensus sequence, with nearly one-quarter of them located within defined CD8 epitopes not restricted by the contemporary host's HLA. More importantly, these reversions arose significantly faster than forward mutations, with the most rapidly reverting mutations preferentially arising within structurally conserved residues. These data suggest that many transmitted mutations likely incur a fitness cost that is recovered through retrieval of an optimal, or ancestral, form of the virus. The propensity of mutations to revert may limit the accumulation of immune pressure-driven mutations in the population, thus preserving critical CD8
+
T-cell epitopes as vaccine targets, and argue against an unremitting adaptation of HIV-1 to host immune pressures.
Examination of a Fusogenic Hexameric Core from Human Metapneumovirus and Identification of a Potent Synthetic Peptide Inhibitor from the Heptad Repeat 1 Region
Authors: Miller Scott A. , Tollefson Sharon , Crowe James E. , Williams John V. , Wright David W. 
Published: December 2006

ABSTRACT
Paramyxoviruses are a leading cause of childhood illness worldwide. A recently discovered paramyxovirus, human metapneumovirus (hMPV), has been studied by our group in order to determine the structural relevance of its fusion (F) protein to other well-characterized viruses utilizing type I integral membrane proteins as fusion aids. Sequence analysis and homology models suggested the presence of requisite heptad repeat (HR) regions. Synthetic peptides from HR regions 1 and 2 (HR-1 and -2, respectively) were induced to form a thermostable (melting temperature, ∼90°C) helical structure consistent in mass with a hexameric coiled coil. Inhibitory studies of hMPV HR-1 and -2 indicated that the synthetic HR-1 peptide was a significant fusion inhibitor with a 50% inhibitory concentration and a 50% effective concentration of ∼50 nM. Many viral fusion proteins are type I integral membrane proteins utilizing the formation of a hexameric coiled coil of HR peptides as a major driving force for fusion. Our studies provide evidence that hMPV also uses a coiled-coil structure as a major player in the fusion process. Additionally, viral HR-1 peptide sequences may need further investigation as potent fusion inhibitors.
Contributions of Two Nuclear Localization Signals of Influenza A Virus Nucleoprotein to Viral Replication
Authors: Ozawa Makoto , Fujii Ken , Muramoto Yukiko , Yamada Shinya , Yamayoshi Seiya , Takada Ayato , Goto Hideo , Horimoto Taisuke , Kawaoka Yoshihiro 
Published: December 2006

ABSTRACT
The RNA genome of influenza A virus, which forms viral ribonucleoprotein complexes (vRNPs) with viral polymerase subunit proteins (PA, PB1, and PB2) and nucleoprotein (NP), is transcribed and replicated in the nucleus. NP, the major component of vRNPs, has at least two amino acid sequences that serve as nuclear localization signals (NLSs): an unconventional NLS (residues 3 to 13; NLS1) and a bipartite NLS (residues 198 to 216; NLS2). Although both NLSs are known to play a role in nuclear transport, their relative contributions to viral replication are poorly understood. We therefore investigated their contributions to NP subcellular/subnuclear localization, viral RNA (vRNA) transcription, and viral replication. Abolishing the unconventional NLS caused NP to localize predominantly to the cytoplasm and affected its activity in vRNA transcription. However, we were able to create a virus whose NP contained amino acid substitutions in NLS1 known to abolish its nuclear localization function, although this virus was highly attenuated. These results indicate that while the unconventional NLS is not essential for viral replication, it is necessary for efficient viral mRNA synthesis. On the other hand, the bipartite NLS, whose contribution to the nuclear transport of NP is limited, was essential for vRNA transcription and NP's nucleolar accumulation. A virus with nonfunctional NLS2 could not be generated. Thus, the bipartite NLS, but not the unconventional NLS, of NP is essential for influenza A virus replication.
Impact of Natural Polymorphism within the gp41 Cytoplasmic Tail of Human Immunodeficiency Virus Type 1 on the Intracellular Distribution of Envelope Glycoproteins and Viral Assembly
Authors: Lambelé Marie , Labrosse Béatrice , Roch Emmanuelle , Moreau Alain , Verrier Bernard , Barin Francis , Roingeard Philippe , Mammano Fabrizio , Brand Denys 
Published: December 2006

ABSTRACTThe motifs involved in the various functions of the human immunodeficiency virus type 1 (HIV-1) gp41 cytoplasmic tail (CT), particularly those related to the intracellular trafficking and assembly of envelope glycoproteins (Env) onto core particles, have generally been assessed with a restricted panel of T-cell laboratory-adapted virus strains. Here, we investigated gp41 CT sequences derived from individuals infected with HIV-1 viruses of various subtypes. We identified four patients harboring HIV variants with a natural polymorphism in the membrane-proximal tyrosine-based signal Y712SPL or the Y802W803diaromatic motif, which are two major determinants of Env intracellular trafficking. Confocal microscopy showed that the intracellular distribution of Env with a mutation in the tyrosine or diaromatic motif differed from that of Env with no mutation in these motifs. Surprisingly, the gp41 CTs of the primary viruses also had differential effects on the intracellular distribution of Env, independently of mutations in the tyrosine or diaromatic motifs, suggesting the involvement of additional determinants. Furthermore, analyses of virus replication kinetics indicated that the effects of mutations in the tyrosine or diaromatic motifs on viral replication depended on the gp41 CT context. These effects were at least partly due to differences in the efficiency of Env incorporation into virions. Thus, polymorphisms in primary HIV-1 gp41 CTs at the quasispecies or subtype level can influence the intracellular distribution of Env, its incorporation into virions, and viral replication capacity.
Effects of streptozotocin-induced diabetes mellitus on some bone turnover markers in the vertebrae of ovary-intact and ovariectomized adult rats
Authors: Gopalakrishnan V. , Arunakaran J. , Aruldhas M. M. , Srinivasan N. 
Published: December 2006

Diabetes mellitus and estrogen deficit are known causes of osteopenia in animal models as well as in humans. In the present work, the combined effect of ovariectomy and diabetes was investigated. Diabetes was induced in ovary-intact and ovariectomized female Wistar rats with a single injection (50 mg/kg body weight, i.p.) of streptozotocin. The rats were administered insulin (I) daily or 17-β estradiol (E2) on alternate days for a period of 35 days and sacrificed. Serum calcium (Ca2+), phosphorus (P), alkaline phosphatase (ALP), tartrate-resistant acid phosphatase (TRAP), vertebral ALP, collagen, and glycosaminoglycans were estimated. The levels of serum Ca2+and P increased in diabetic rats, but decreased after I or E2treatments. Serum ALP and TRAP activity increased in the ovary-intact and ovariectomized diabetic rats. Vertebral ALP activity increased in ovariectomized diabetic rats, but decreased in diabetic rats, which were treated with I or E2. In the vertebrae, TRAP activity was elevated as a result of diabetes, but this was prevented by insulin or estradiol. Diabetes induced a decrease in total collagen in the vertebrae, while I or E2treatment induced an increase. The levels of chondroitin sulphate and heparan sulphate decreased significantly in the vertebrae of both ovary-intact and ovariectomized diabetic rats, while hyaluronic acid increased. In conclusion, diabetes and ovariectomy each seem to affect the process of matrix formation and mineralization in the bone, and this is aggravated by the combination of diabetes and ovariectomy. The effects of I and E2were similar, and both hormones reversed the changes brought about by diabetes.