bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Loop-Mediated Isothermal Amplification Assay for Rapid Detection of BK Virus
Authors: Bista Bipin Raj , Ishwad Chandra , Wadowsky Robert M. , Manna Pradip , Randhawa Parmjeet Singh , Gupta Gaurav , Adhikari Meena , Tyagi Rakhi , Gasper Gina , Vats Abhay 
Published: February 2007

ABSTRACT
Loop-mediated isothermal amplification (LAMP) is a novel method for rapid amplification of DNA. Its advantages include rapidity and minimal equipment requirement. The LAMP assay was developed for BK virus (BKV), which is a leading cause of morbidity in renal transplant recipients. The characteristics of the assay, including its specificity and sensitivity, were evaluated. BKV LAMP was performed using various incubation times with a variety of specimens, including unprocessed urine and plasma samples. A ladder pattern on gel electrophoresis, typical of successful LAMP reactions, was observed specifically only for BKV and not for other viruses. The sensitivity of the assay with 1 h of incubation was 100 copies/tube of a cloned BKV fragment. Additionally, a positive reaction was visually ascertained by a simple color reaction using SYBR green dye. BKV LAMP was also successful for urine and plasma specimens without the need for DNA extraction. Due to its simplicity and specificity, the LAMP assay can potentially be developed for “point of care” screening of BKV.
Development of Methods for Coordinate Measurement of Total Cell-Associated and Integrated Human Immunodeficiency Virus Type 1 (HIV-1) DNA Forms in Routine Clinical Samples: Levels Are Not Associated with Clinical Parameters, but Low Levels of Integrated HIV-1 DNA May Be Prognostic for Continued Successful Therapy
Authors: Carr J. M. , Cheney K. M. , Coolen C. , Davis A. , Shaw D. , Ferguson W. , Chang G. , Higgins G. , Burrell C. , Li P. 
Published: February 2007

ABSTRACT

We have adapted our established
Alu
PCR assay for proviral DNA and PCR for total cellular DNA to a real-time PCR format and applied these to human immunodeficiency virus (HIV)-positive specimens collected for routine determination of the plasma viral load (pVL). In a cohort of five patients, measurements of integrated viral load (iVL) and cell-associated viral load (cVL) in CD4
+
cells isolated by a single positive selection step were not indicative of HIV DNA levels in the circulation, and further analysis was performed on peripheral blood mononuclear cells (PBMC). In a cohort of 46 samples total cVL was quantitated in most samples, but iVL could be quantitated in only 47.8%, since in 26% iVL was undetectable and in 21.7% the results were invalid due to high levels of unintegrated HIV DNA. There was no correlation of cVL or iVL with pVL, CD4 count, or duration of successful antiretroviral treatment. Out of 26 patients with undetectable pVL, 4 patients failed therapy within the subsequent 12 months and had higher than average iVL, but this was not the case for cVL. Among nine patients with long-term undetectable pVL, no consistent decline in cVL or iVL was seen with time, and changes in cVL and iVL within a patient could be concordant or discordant. These results show that cVL and iVL can be coordinately measured in PBMC from clinical samples but do not correlate with pVL, CD4 counts, or length of suppressive antiretroviral therapy. Interestingly, a high iVL (but not a high cVL) in patients with undetectable pVL was associated with subsequent treatment failure.
Surveillance Cultures and Duration of Carriage of Multidrug-Resistant
Acinetobacter baumannii
Authors: Marchaim Dror , Navon-Venezia Shiri , Schwartz David , Tarabeia Jalal , Fefer Iris , Schwaber Mitchell J. , Carmeli Yehuda 
Published: February 2007

ABSTRACT

Isolating carriers of multidrug-resistant (MDR)
Acinetobacter baumannii
is the main measure to prevent its spread. Identification of carriers accompanied by contact precautions is essential. We aimed to determine the appropriate surveillance sampling sites and the duration of carriage of MDR
A. baumannii
. We studied prospectively two groups of patients from whom MDR
A. baumannii
was previously isolated: (i) those with recent clinical isolation (≤10 days) and (ii) those with remote clinical isolation (≥6 months). Screening for carriage was conducted from six sites: nostrils, pharynx, skin, rectum, wounds, and endotracheal aspirates. Strains recovered concurrently from different sites were genotyped using pulsed-field gel electrophoresis. Twelve of 22 with recent clinical isolation of MDR
A. baumannii
had ≥1 positive screening culture, resulting in a sensitivity of 55% when six body sites were sampled. Sensitivities of single sites ranged from 13.5% to 29%. Among 30 patients with remote clinical isolation, screening cultures were positive in 5 (17%), with a mean duration of 17.5 months from the last clinical culture. Remote carriers had positive screening cultures from the skin and pharynx but not from nose, rectum, wounds, or endotracheal aspirates. Eleven strains from five patients were genotyped. In all but one case, isolates from different sites in a given patient were clonal. Current methodology is suboptimal to detect MDR
A. baumannii
carriage. The sensitivity of surveillance cultures is low, even when six different body sites are sampled. The proportion of individuals with previous MDR
A. baumannii
isolation who remain carriers for prolonged periods is substantial. These data should be considered when designing measures to limit the spread of MDR
A. baumannii
.
False-Positive Culture Results from Patient Tissue Specimens Due to Contamination of RPMI Medium with
Cryptococcus albidus
Authors: Winston Lisa G. , Roemer Marguerite , Goodman Carol , Haller Barbara 
Published: February 2007

ABSTRACT

Cryptococcus albidus
, a rare opportunist, was isolated from biopsy specimens from three patients over 4 days. An investigation showed that the specimens had been contaminated by placement in RPMI medium. The importance of rapid communication between the microbiology laboratory, the infectious diseases/infection control division, and other involved parties in the event of unusual occurrences is highlighted.
Graphium basitruncatumFungemia in a Patient with Acute Leukemia
Authors: Kumar Deepali , Sigler Lynne , Gibas Connie Fe C. , Mohan Subhash , Schuh Andre , Medeiros Bruno C. , Peckham Kenneth , Humar Atul 
Published: February 2007

ABSTRACTWe report the first case of infection caused byGraphium basitruncatumin a man with acute leukemia who developed persistent fungemia and skin lesions.G. basitruncatum, a member of theMicroascaceae, is phylogenetically and morphologically distinct fromGraphium penicillioidesand the opportunistic pathogensScedosporium apiospermum(Pseudallescheria boydii) andScedosporium prolificans.
Clonal Distribution of Invasive
Neisseria meningitidis
Serogroup C Strains Circulating from 1976 to 2005 in Greater São Paulo, Brazil
Authors: de Lemos Ana Paula Silva , Yara Teresa Ykuko , Gorla Maria Cecília Outeiro , de Paiva Maria Vaneide , de Souza Adriana Lambert , Gonçalves Maria Inês Cappelletti , de Almeida Samanta Cristine Grassi , do Valle Gloria Regina Feitas , Sacchi Claudio Tavares 
Published: February 2007

ABSTRACT

Meningococcal disease is characterized by cyclic fluctuations in incidence, serogroup distribution, and antigenic profiles. In greater São Paulo, Brazil, there has been a constant increase in the incidence of serogroup C meningococcal disease since the late 1980s. To gain an understanding of changes in serogroup C meningococcal disease over three decades in greater São Paulo, Brazil, 1,059 invasive
Neisseria meningitidis
serogroup C isolates from 1976 and 2005 were analyzed. Three major clone complexes, sequence type (ST)-11, ST-8, and ST-103, were identified by multilocus sequence typing, and the isolates were characterized by serotyping and 16S rRNA typing. During the 30-year period, there were two major antigenic replacements: from 2a:P1.(5,2) to 2b:P1.3 and subsequently to 23:P1.14-6. All strains of clone ST-103 were characterized as serotype 23 and serosubtype P1.14-6. The origin of 23:P1.14-6 ST-103 complex strains is unknown, but efforts are needed to monitor its spread and define its virulence. The antigenic replacements we observed likely represent a mechanism to sustain meningococcal disease in the population as immunity to circulating strains accumulated.
Comparison of the Digene Hybrid Capture System Cytomegalovirus (CMV) DNA (Version 2.0), Roche CMV UL54 Analyte-Specific Reagent, and QIAGEN RealArt CMV LightCycler PCR Reagent Tests Using AcroMetrix OptiQuant CMV DNA Quantification Panels and Specimens from Allogeneic-Stem-Cell Transplant Recipients
Authors: Hanson Kimberly E. , Reller L. Barth , Kurtzberg Joanne , Horwitz Mitchell , Long Gwynn , Alexander Barbara D. 
Published: February 2007

ABSTRACT
The Digene Hybrid Capture system cytomegalovirus (CMV) DNA (version 2.0), Roche CMV UL54 analyte-specific reagent, and QIAGEN RealArt CMV LightCycler PCR reagent tests were compared using whole-virus standards and plasma specimens collected from allogeneic-stem-cell transplant recipients. PCR assays showed better speed, sensitivity, and specificity.
Simian Immunodeficiency Virus (SIV) Infection Influences the Level and Function of Regulatory T Cells in SIV-Infected Rhesus Macaques but Not SIV-Infected Sooty Mangabeys
Authors: Pereira L. E. , Villinger F. , Onlamoon N. , Bryan P. , Cardona A. , Pattanapanysat K. , Mori K. , Hagen S. , Picker L. , Ansari A. A. 
Published: February 2007

ABSTRACTDifferences in clinical outcome of simian immunodeficiency virus (SIV) infection in disease-resistant African sooty mangabeys (SM) and disease-susceptible Asian rhesus macaques (RM) prompted us to examine the role of regulatory T cells (Tregs) in these two animal models. Results from a cross-sectional study revealed maintenance of the frequency and absolute number of peripheral Tregs in chronically SIV-infected SM while a significant loss occurred in chronically SIV-infected RM compared to uninfected animals. A longitudinal study of experimentally SIV-infected animals revealed a transient increase in the frequency of Tregs from baseline values following acute infection in RM, but no change in the frequency of Tregs occurred in SM during this period. Further examination revealed a strong correlation between plasma viral load (VL) and the level of Tregs in SIV-infected RM but not SM. A correlation was also noted in SIV-infected RM that control VL spontaneously or in response to antiretroviral chemotherapy. In addition, immunofluorescent cell count assays showed that while Treg-depleted peripheral blood mononuclear cells from RM led to a significant enhancement of CD4+and CD8+T-cell responses to select pools of SIV peptides, there was no detectable T-cell response to the same pool of SIV peptides in Treg-depleted cells from SIV-infected SM. Our data collectively suggest that while Tregs do appear to play a role in the control of viremia and the magnitude of the SIV-specific immune response in RM, their role in disease resistance in SM remains unclear.
Extensive Intrasubtype Recombination in South African Human Immunodeficiency Virus Type 1 Subtype C Infections
Authors: Rousseau Christine M. , Learn Gerald H. , Bhattacharya Tanmoy , Nickle David C. , Heckerman David , Chetty Senica , Brander Christian , Goulder Philip J. R. , Walker Bruce D. , Kiepiela Photini , Korber Bette T. , Mullins James I. 
Published: February 2007

ABSTRACT
Recombinant human immunodeficiency virus type 1 (HIV-1) strains containing sequences from different viral genetic subtypes (intersubtype) and different lineages from within the same subtype (intrasubtype) have been observed. A consequence of recombination can be the distortion of the phylogenetic signal. Several intersubtype recombinants have been identified; however, less is known about the frequency of intrasubtype recombination. For this study, near-full-length HIV-1 subtype C genomes from 270 individuals were evaluated for the presence of intrasubtype recombination. A sliding window schema (window, 2 kb; step, 385 bp) was used to partition the aligned sequences. The Shimodaira-Hasegawa test detected significant topological incongruence in 99.6% of the comparisons of the maximum-likelihood trees generated from each sequence partition, a result that could be explained by recombination. Using RECOMBINE, we detected significant levels of recombination using five random subsets of the sequences. With a set of 23 topologically consistent sequences used as references, bootscanning followed by the interactive informative site test defined recombination breakpoints. Using two multiple-comparison correction methods, 47% of the sequences showed significant evidence of recombination in both analyses. Estimated evolutionary rates were revised from 0.51%/year (95% confidence interval [CI], 0.39 to 0.53%) with all sequences to 0.46%/year (95% CI, 0.38 to 0.48%) with the putative recombinants removed. The timing of the subtype C epidemic origin was revised from 1961 (95% CI, 1947 to 1962) with all sequences to 1958 (95% CI, 1949 to 1960) with the putative recombinants removed. Thus, intrasubtype recombinants are common within the subtype C epidemic and these impact analyses of HIV-1 evolution.
Analysis of Hepatitis C Virus Hypervariable Region 1 Sequence from Cryoglobulinemic Patients and Associated Controls
Authors: Bianchettin Gabriella , Bonaccini Claudia , Oliva Romina , Tramontano Anna , Cividini Agostino , Casato Milvia , Merlini Giampaolo , Silini Enrico , Mondelli Mario U. 
Published: February 2007

ABSTRACT

Chronic hepatitis C virus (HCV) infection is frequently associated with extrahepatic manifestations, including nonmalignant and malignant B-cell lymphoproliferative disorders. It has been reported that specific changes or recurring motifs in the amino acid sequence of the HCV hypervariable region 1 (HVR1) may be associated with cryoglobulinemia. We searched for specific insertions/deletions and/or amino acid motifs within HVR1 in samples from 80 symptomatic and asymptomatic patients with and 33 patients without detectable cryoglobulins, all with chronic HCV infection. At variance with the results of a previous study which reported a high frequency of insertions at position 385 of HVR1 from cryoglobulinemic patients, we found a 6.2% prevalence of insertions in samples from patients with and a 9.1% prevalence in those without cryoglobulinemia. Moreover, statistical and bioinformatics approaches including Fisher's exact test,
k
-means clustering, Tree determinant-residue identification, correlation of mutations, principal component analysis, and phylogenetic analysis failed to show statistically significant differences between sequences from cryoglobulin-negative and -positive patients. Our findings suggest that cryoglobulinemia may arise by virtue of as-yet-unidentified host- rather than virus-specific factors. Specific changes in HCV envelope sequence distribution are unlikely to be directly involved in the establishment of pathological B-cell monoclonal proliferation.
Relative Fitness and Replication Capacity of a Multinucleoside Analogue-Resistant Clinical Human Immunodeficiency Virus Type 1 Isolate with a Deletion of Codon 69 in the Reverse Transcriptase Coding Region
Authors: Villena Cristina , Prado Julia G. , Puertas Maria Carmen , Martínez Miguel Ángel , Clotet Bonaventura , Ruiz Lidia , Parkin Neil T. , Menéndez-Arias Luis , Martinez-Picado Javier 
Published: February 2007

ABSTRACTDeletions, insertions, and amino acid substitutions in the β3-β4 hairpin loop-coding region of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) have been associated with resistance to nucleoside RT inhibitors when appearing in combination with other mutations in the RT-coding region. In this work, we have measured the in vivo fitness of HIV-1 variants containing a deletion of 3 nucleotides affecting codon 69 (Δ69) of the viral RT as well as the replication capacity (RC) ex vivo of a series of recombinant HIV-1 variants carrying an RT bearing the Δ69 deletion or the T69A mutation in a multidrug-resistant (MDR) sequence background, including the Q151M complex and substitutions M184V, K103N, Y181C, and G190A. Patient-derived viral clones having RTs with Δ69 together with S163I showed increased RCs under drug pressure. These data were consistent with the viral population dynamics observed in a long-term-treated HIV-1-infected patient. In the absence of drugs, viral clones containing T69A replicated more efficiently than those having Δ69, but only when patient-derived sequences corresponding to RT residues 248 to 527 were present. These effects could be attributed to a functional interaction between the C-terminal domain of the p66 subunit (RNase H domain) and the DNA polymerase domain of the RT. Finally, recombinant HIV-1 clones bearing RTs with MDR-associated mutations, including deletions at codon 69, showed increased susceptibilities to protease inhibitors in phenotypic assays. These effects correlated with impaired Gag cleavage and could be attributed to delayed maturation and decreased production of active protease in those variants.
Involvement of the Oncoprotein c-Myc in Viral Telomerase RNA Gene Regulation during Marek's Disease Virus-Induced Lymphomagenesis
Authors: Shkreli Marina , Dambrine Ginette , Soubieux Denis , Kut Emmanuel , Rasschaert Denis 
Published: February 2007

ABSTRACTMarek's disease virus (MDV) is an alphaherpesvirus that induces a highly malignant T-lymphoma in chickens. The viral genome encodes two identical copies of a viral telomerase RNA subunit (vTR) that exhibits 88% sequence identity to its chicken ortholog chTR. The minimal telomerase ribonucleoprotein complex consists of a protein subunit with reverse transcriptase activity (TERT) and an RNA subunit (TR). The active complex compensates for the progressive telomere shortening that occurs during mitosis and is involved in the cell immortalization process. We show here that the upregulation of telomerase activity is associated with an increase in vTR gene expression in chickens infected with the highly oncogenic MDV strain RB-1B. A comparative functional analysis of the viral and chicken TR promoters, based on luciferase reporter assays, revealed that the vTR promoter was up to threefold more efficient than the chTR promoter in avian cells. We demonstrated, by directed mutagenesis of the vTR promoter region, that the stronger transcriptional activity of the vTR promoter resulted largely from an E-box located two nucleotides downstream from the transcriptional start site of the vTR gene. Furthermore, transactivation assays and chromatin immunoprecipitation assays demonstrated the involvement of the c-Myc oncoprotein in the transcriptional regulation of vTR. Finally, an Ets binding site was specifically implicated in the transcriptional regulation of vTR in the MDV-transformed lymphoblastoid cell line MSB-1.
Kaposi's Sarcoma-Associated Herpesvirus LANA Protein Downregulates Nuclear Glycogen Synthase Kinase 3 Activity and Consequently Blocks Differentiation
Authors: Liu Jianyong , Martin Heather , Shamay Meir , Woodard Crystal , Tang Qi-Qun , Hayward S. Diane 
Published: February 2007

ABSTRACT
The Kaposi's sarcoma-associated herpesvirus latency-associated nuclear antigen (LANA) protein interacts with glycogen synthase kinase 3 (GSK-3) and relocalizes GSK-3 in a manner that leads to stabilization of β-catenin and upregulation of β-catenin-responsive cell genes. The LANA-GSK-3 interaction was further examined to determine whether there were additional downstream consequences. In the present study, the nuclear GSK-3 bound to LANA in transfected cells and in BCBL1 primary effusion lymphoma cells was found to be enriched for the inactive serine 9-phosphorylated form of GSK-3. The mechanism of inactivation of nuclear GSK-3 involved LANA recruitment of the extracellular signal-regulated kinases 1 and 2 (ERK1/2) and the ribosomal S6 kinase 1 (RSK1). ERK1/2 and RSK1 coprecipitated with LANA, and LANA was a substrate for ERK1 in vitro. A model is proposed for the overall inactivation of nuclear GSK-3 that incorporates the previously described GSK-3 phosphorylation of LANA itself. Functional inactivation of nuclear GSK-3 was demonstrated by the ability of LANA to limit phosphorylation of the known GSK-3 substrates C/EBPβ and C/EBPα. The effect of LANA-mediated ablation of C/EBP phosphorylation on differentiation was modeled in the well-characterized 3T3L1 adipogenesis system. LANA-expressing 3T3L1 cells were impaired in their ability to undergo differentiation and adipogenesis. C/EBPβ induction followed the same time course as that seen in vector-transduced cells, but there was delayed and reduced induction of C/EBPβ transcriptional targets in LANA-expressing cells. We conclude that LANA inactivates nuclear GSK-3 and modifies the function of proteins that are GSK-3 substrates. In the case of C/EBPs, this translates into LANA-mediated inhibition of differentiation.
Primary CD4+T-Cell Responses Provide both Helper and Cytotoxic Functions during Epstein-Barr Virus Infection and Transformation of Fetal Cord Blood B Cells
Authors: MacArthur Georgina J. , Wilson A. Douglas , Birchall Martin A. , Morgan Andrew J. 
Published: February 2007

ABSTRACTMost humans carry Epstein-Barr virus (EBV) in circulating memory B cells as a latent infection that is controlled by an immune response. When infected by EBV, B lymphocytes in fetal cord blood are readily transformed to lymphoblastoid cell lines (LCL). It is frequently assumed that this high efficiency of transformation is due to the absence of a primary immune response. However, cord blood lymphocytes stimulated with autologous LCL yield CD4+T cells that can completely inhibit the growth of LCL by a major histocompatibility complex-restricted cytotoxic mechanism mediated by granulysin and granzyme B. Because EBV-transformed B cells maintain the phenotype of antigen-activated B-cell blasts, they can potentially receive inhibitory or helper functions from CD4+T cells. To assess these functions, the effect of EBV-specific CD4+T cells on the efficiency of virus transformation of autologous B cells was assayed. Paradoxically, although the cytotoxic CD4+T-cell lines reduced EBV B-cell transformation at a high effector/target ratio of 10:1, they caused a twofold increase in B-cell transformation at the lower effector/target ratio of 1:1. Th1-polarized CD4+T cells were more effective at inhibiting B-cell transformation, but Th2-polarized cell lines had reduced cytotoxic activity, were unable to inhibit LCL growth, and caused a 10-fold increase in transformation efficiency. Tonsil lymphoid follicles lacked NK cells and CD8+T cells but contained CD4+T cells. We propose that CD4+T cells provide helper or cytotoxic functions to EBV-transformed B cells and that the balance of these functions within tonsil compartments is critical in establishing asymptomatic primary EBV infection and maintaining a stable lifelong latent infection.