bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Immunologic Assays for Detecting Immune Responses in HIV Immunotherapeutic Studies: AIDS Clinical Trials Group Trial A5181
Authors: Macatangay Bernard J. C. , Zheng Lu , Rinaldo Charles R. , Landay Alan L. , Pollard Richard B. , Pahwa Savita , Lederman Michael M. , Bucy R. Pat 
Published: July 2010

ABSTRACT
This study was designed to evaluate which of several T-cell-specific, immune response assays are the most relevant in measuring the key characteristics of an effective immune response to HIV-1. Using 5 HIV-1 antigens as stimulants, we assessed lymphocyte proliferation, supernatant gamma interferon (IFN-γ) cytokine production (CP), single-cell IFN-γ production by enzyme-linked immunospot (ELISPOT) assay, with and without Epstein-Barr virus-transformed B-lymphoblastoid cell lines (B-LCLs), and intracellular cytokine production (ICC) for IFN-γ and interleukin 2 (IL-2) by flow cytometry. We used these to compare specimens from HIV-1-infected subjects who were virally suppressed with a stable antiretroviral therapy (ART) regimen (group A) with specimens from subjects not on ART but with HIV-1 viremia of <3,000 copies/ml (group B). The lymphocyte proliferation assay (LPA) did not significantly differentiate between the two groups. Using fresh peripheral blood mononuclear cells (PBMCs), the CP and ELISPOT assays for IFN-γ detected the greatest differences between the two groups, specific for three of the five HIV-1 antigens, whereas significant differences were seen only in response to one antigen when cryopreserved cells were used. The strongest correlations were seen between the CP and ELISPOT assays. The ELISPOT B-LCL assay showed a cell concentration-dependent increase in IFN-γ production compared to that shown by the standard ELISPOT assay but did not differentiate between the groups. In the ICC assay, greater numbers of IFN-γ-producing T cells were seen in group B, and little or no detectable IL-2 production was seen in both groups. These studies highlight complexities of immunologic monitoring of T-cell responses in multisite clinical trials in HIV infection and outline considerations for optimizing these efforts.
Infection during Infancy and Long Incubation Period of Leprosy Suggested in a Case of a Chimpanzee Used for Medical Research
Authors: Suzuki Koichi , Udono Toshifumi , Fujisawa Michiko , Tanigawa Kazunari , Idani Gen'ichi , Ishii Norihisa 
Published: July 2010

ABSTRACT

The length of the incubation period of leprosy following
Mycobacterium leprae
infection has never been conclusively determined, owing to the lack of a method to demonstrate the presence of an asymptomatic infection. We report a rare case of leprosy in a chimpanzee in which a 30-year incubation period was strongly suggested by single nucleotide polymorphism (SNP) analysis.
Evaluation of Pulsed-Field Gel Electrophoresis Profiles for Identification of
Salmonella
Serotypes
Authors: Zou Wen , Lin Wei-Jiun , Foley Steven L. , Chen Chun-Houh , Nayak Rajesh , Chen James J. 
Published: July 2010

ABSTRACT

Pulsed-field gel electrophoresis (PFGE) is a standard typing method for isolates from
Salmonella
outbreaks and epidemiological investigations. Eight hundred sixty-six
Salmonella enterica
isolates from eight serotypes, including Heidelberg (
n
= 323), Javiana (
n
= 200), Typhimurium (
n
= 163), Newport (
n
= 93), Enteritidis (
n
= 45), Dublin (
n
= 25), Pullorum (
n
= 9), and Choleraesuis (
n
= 8), were subjected to PFGE, and their profiles were analyzed by random forest classification and compared to conventional hierarchical cluster analysis to determine potential predictive relationships between PFGE banding patterns and particular serotypes. Cluster analysis displayed only the underlying similarities and relationships of the isolates from the eight serotypes. However, for serotype prediction of a nonserotyped
Salmonella
isolate from its PFGE pattern, random forest classification provided better accuracy than conventional cluster analysis. Discriminatory DNA band class markers were identified for distinguishing
Salmonella
serotype Heidelberg, Javiana, Typhimurium, and Newport isolates.
Rapid Identification of Bacterial Pathogens in Positive Blood Culture Bottles by Use of a Broad-Based PCR Assay Coupled with High-Resolution Melt Analysis
Authors: Won Helen , Rothman Richard , Ramachandran Padmini , Hsieh Yu-Hsiang , Kecojevic Aleksandar , Carroll Karen C. , Aird Deborah , Gaydos Charlotte , Yang Samuel 
Published: July 2010

ABSTRACT
We evaluated a broad-based PCR assay coupled with high-resolution melt analysis for rapid bacterial identification in patients with bacterial sepsis. With a reference library of 60 clinically relevant bacterial species, 52 positive blood culture samples were tested. Our assay identified 46/52 samples at the species level, with 100% concordance to culture findings.
Comparative Evaluation of the Vitek 2 Yeast Susceptibility Test and CLSI Broth Microdilution Reference Method for Testing Antifungal Susceptibility of Invasive Fungal Isolates in Italy: the GISIA3 Study
Authors: Borghi Elisa , Iatta Roberta , Sciota Rita , Biassoni Caterina , Cuna Teresa , Montagna Maria Teresa , Morace Giulia 
Published: July 2010

ABSTRACT

The newly available AST-YS01 Vitek 2 cards were evaluated, and the results were compared with those obtained by the CLSI M27-A2 microdilution reference method. Clinical fungal isolates, including 614 isolates of
Candida
spp., 10
Cryptococcus neoformans
isolates, 1
Geotrichum capitatum
isolate, and 2 quality control strains, were tested for their susceptibilities to amphotericin B, fluconazole, and voriconazole using both methods. The majority of fungal isolates were susceptible to all antifungal agents tested: the MIC
90
values determined by the Vitek 2 and CLSI methods were 0.5 and 1 μg/ml, respectively, for amphotericin B; 8 and 16 μg/ml, respectively, for fluconazole; and <0.12 and 0.25 μg/ml, respectively, for voriconazole. Overall there was excellent categorical agreement (CA) between the methods (99.5% for amphotericin B, 92% for fluconazole, 98.2% for voriconazole), but discrepancies were observed within species. The CAs for fluconazole were low for
Candida glabrata
and
Candida krusei
when the results of the CLSI method at 48 h were considered. Moreover, the fully automated commercial system did not detect the susceptibility of
Cryptococcus neoformans
to voriconazole. The Vitek 2 system can be considered a valid support for antifungal susceptibility testing of fungi, but testing of susceptibility to agents not included in the system (e.g., echinocandins and posaconazole) should be performed with other methods.
Characterization of RD-114 Virus Isolated from a Commercial Canine Vaccine Manufactured Using CRFK Cells
Authors: Yoshikawa Rokusuke , Sato Eiji , Igarashi Tatsuhiko , Miyazawa Takayuki 
Published: July 2010

ABSTRACT
Recently, we found that several commercial pet vaccines were contaminated with an infectious endogenous retrovirus, RD-114-related virus. Here, we determined the entire nucleotide sequences of RD-114-related viruses isolated from CRFK cells and a vaccine manufactured using CRFK cells. These RD-114-related viruses were nearly identical to the authentic RD-114 virus.
Recognition of Potentially Novel Human Disease-Associated Pathogens by Implementation of Systematic 16S rRNA Gene Sequencing in the Diagnostic Laboratory
Authors: Keller Peter M. , Rampini Silvana K. , Büchler Andrea C. , Eich Gerhard , Wanner Roger M. , Speck Roberto F. , Böttger Erik C. , Bloemberg Guido V. 
Published: July 2010

ABSTRACT
Clinical isolates that are difficult to identify by conventional means form a valuable source of novel human pathogens. We report on a 5-year study based on systematic 16S rRNA gene sequence analysis. We found 60 previously unknown 16S rRNA sequences corresponding to potentially novel bacterial taxa. For 30 of 60 isolates, clinical relevance was evaluated; 18 of the 30 isolates analyzed were considered to be associated with human disease.
Comparison of
Leishmania
OligoC-TesT PCR with Conventional and Real-Time PCR for Diagnosis of Canine
Leishmania
Infection
Authors: Carson Connor , Quinnell Rupert J. , Holden Jennifer , Garcez Lourdes M. , Deborggraeve Stijn , Courtenay Orin 
Published: July 2010

ABSTRACT

There is a need for standardization and simplification of the existing methods for molecular detection of
Leishmania infantum
in the canine reservoir host. The commercially available OligoC-TesT kit incorporates standardized PCR reagents with rapid oligochromatographic dipstick detection of PCR products and is highly sensitive for use in humans but not yet independently validated for use in dogs. Here we compare the sensitivity of OligoC-TesT with those of nested kinetoplast DNA (kDNA) PCR, nested internal transcribed spacer 1 (ITS-1) PCR, and a PCR-hybridization protocol, using longitudinal naturally infected canine bone marrow samples whose parasite burdens were measured by real-time quantitative PCR (qPCR). The sensitivity of OligoC-TesT for infected dogs was 70% (95% confidence interval [CI], 63 to 78%), similar to that of kDNA PCR (72%; 95% CI, 65 to 80%;
P
= 0.69) but significantly greater than those of PCR-hybridization (61%; 95% CI, 53 to 69%;
P =
0.007) and ITS-1 nested PCR (54%; 95% CI, 45 to 62%;
P
< 0.001); real-time qPCR had the highest sensitivity (91%; 95% CI, 85 to 95%;
P
< 0.001). OligoC-TesT sensitivity was greater for polysymptomatic and oligosymptomatic dogs than for asymptomatic dogs (93%, 74%, and 61%, respectively;
P
= 0.005), a trend also observed for the other qualitative PCR methods tested (
P
≤ 0.05). Test positivity increased with increasing parasite burdens, as measured by real-time qPCR: OligoC-TesT and kDNA PCR detected 100% and 99% of positive samples when parasite burdens exceeded 74 and 49 parasites/ml, respectively. OligoC-TesT has high sensitivity for detection of canine
Leishmania
infections; its ease of operation and ease of interpretation are further advantages for veterinary diagnostic laboratories and for large-scale survey work in developing countries.
Genetic Determinants of Mouse Hepatitis Virus Strain 1 Pneumovirulence
Authors: Leibowitz Julian L. , Srinivasa Rajiv , Williamson Shawn T. , Chua Ming Ming , Liu Mingfeng , Wu Samantha , Kang Hyojeung , Ma Xue-Zhong , Zhang Jianhua , Shalev Itay , Smith Robert , Phillips Melville J. , Levy Gary A. , Weiss Susan R. 
Published: July 2010

ABSTRACTWe report here investigation into the genetic basis of mouse hepatitis virus strain 1 (MHV-1) pneumovirulence. Sequencing of the 3′ one-third of the MHV-1 genome demonstrated that the genetic organization of MHV-1 was similar to that of other strains of MHV. The hemagglutinin esterase (HE) protein was truncated, and reverse transcription-PCR (RT-PCR) studies confirmed previous work that suggested that the MHV-1 HE is a pseudogene. Targeted recombination was used to select chimeric viruses containing either the MHV-1 S gene or genes encoding all of the MHV-1 structural proteins, on an MHV-A59 background. Challenge studies in mice demonstrated that expression of the MHV-1 S gene within the MHV-A59 background (rA59/SMHV-1) increased the pneumovirulence of MHV-A59, and mice infected with this recombinant virus developed pulmonary lesions that were similar to those observed with MHV-1, although rA59/SMHV-1was significantly less virulent. Chimeras containing all of the MHV-1 structural genes on an MHV-A59 background were able to reproduce the severe acute respiratory syndrome (SARS)-like pathology observed with MHV-1 and reproducibly increased pneumovirulence relative to rA59/SMHV-1, but were still much less virulent than MHV-1. These data suggest that important determinants of pneumopathogenicity are contained within the 3′ one-third of the MHV-1 genome, but additional important virulence factors must be encoded in the genome upstream of the S gene. The severity of the pulmonary lesions observed correlates better with elevated levels of inflammatory cytokines than with viral replication in the lungs, suggesting that pulmonary disease has an important immunological component.
Structure and Capsid Association of the Herpesvirus Large Tegument Protein UL36
Authors: Newcomb William W. , Brown Jay C. 
Published: July 2010

ABSTRACT
The tegument of all herpesviruses contains a high-molecular-weight protein homologous to herpes simplex virus (HSV) UL36. This large (3,164 amino acids), essential, and multifunctional polypeptide is located on the capsid surface and present at 100 to 150 copies per virion. We have been testing the idea that UL36 is important for the structural organization of the tegument. UL36 is proposed to bind directly to the capsid with other tegument proteins bound indirectly by way of UL36. Here we report the results of studies carried out with HSV type 1-derived structures containing the capsid but lacking a membrane and depleted of all tegument proteins except UL36 and a second high-molecular-weight protein, UL37. Electron microscopic analysis demonstrated that, compared to capsids lacking a tegument, these capsids (called T36 capsids) had tufts of protein located at the vertices. Projecting from the tufts were thin, variably curved strands with lengths (15 to 70 nm) in some cases sufficient to extend across the entire thickness of the tegument (∼50 nm). Strands were sensitive to removal from the capsid by brief sonication, which also removed UL36 and UL37. The findings are interpreted to indicate that UL36 and UL37 are the components of the tufts and of the thin strands that extend from them. The strand lengths support the view that they could serve as organizing features for the tegument, as they have the potential to reach all parts of the tegument. The variably curved structure of the strands suggests they may be flexible, a property that could contribute to the deformable nature of the tegument.
Assessing the Viral Fitness of Oseltamivir-Resistant Influenza Viruses in Ferrets, Using a Competitive-Mixtures Model
Authors: Hurt Aeron C. , Nor'e Siti Sarah , McCaw James M. , Fryer Helen R. , Mosse Jennifer , McLean Angela R. , Barr Ian G. 
Published: July 2010

ABSTRACT

To determine the relative fitness of oseltamivir-resistant strains compared to susceptible wild-type viruses, we combined mathematical modeling and statistical techniques with a novel
in vivo
“competitive-mixtures” experimental model. Ferrets were coinfected with either pure populations (100% susceptible wild-type or 100% oseltamivir-resistant mutant virus) or mixed populations of wild-type and oseltamivir-resistant influenza viruses (80%:20%, 50%:50%, and 20%:80%) at equivalent infectivity titers, and the changes in the relative proportions of those two viruses were monitored over the course of the infection during within-host and over host-to-host transmission events in a ferret contact model. Coinfection of ferrets with mixtures of an oseltamivir-resistant R292K mutant A(H3N2) virus and a R292 oseltamivir-susceptible wild-type virus demonstrated that the R292K mutant virus was rapidly outgrown by the R292 wild-type virus in artificially infected donor ferrets and did not transmit to any of the recipient ferrets. The competitive-mixtures model was also used to investigate the fitness of the seasonal A(H1N1) oseltamivir-resistant H274Y mutant and showed that within infected ferrets the H274Y mutant virus was marginally outgrown by the wild-type strain but demonstrated equivalent transmissibility between ferrets. This novel
in vivo
experimental method and accompanying mathematical analysis provide greater insight into the relative fitness, both within the host and between hosts, of two different influenza virus strains compared to more traditional methods that infect ferrets with only pure populations of viruses. Our statistical inferences are essential for the development of the next generation of mathematical models of the emergence and spread of oseltamivir-resistant influenza in human populations.
The Transmission Efficiency of
Tomato Yellow Leaf Curl Virus
by the Whitefly
Bemisia tabaci
Is Correlated with the Presence of a Specific Symbiotic Bacterium Species
Authors: Gottlieb Yuval , Zchori-Fein Einat , Mozes-Daube Netta , Kontsedalov Svetlana , Skaljac Marisa , Brumin Marina , Sobol Iris , Czosnek Henryk , Vavre Fabrice , Fleury Frédéric , Ghanim Murad 
Published: July 2010

ABSTRACT

Tomato yellow leaf curl virus
(TYLCV) (
Geminiviridae
:
Begomovirus
) is exclusively vectored by the whitefly
Bemisia tabaci
(Gennadius) (Hemiptera: Aleyrodidae). TYLCV transmission depends upon a 63-kDa GroEL protein produced by the vector's endosymbiotic bacteria.
B. tabaci
is a species complex comprising several genetically distinct biotypes that show different secondary-symbiont fauna. In Israel, the B biotype harbors
Hamiltonella
, and the Q biotype harbors
Wolbachia
and
Arsenophonus.
Both biotypes harbor
Rickettsia
and
Portiera
(the obligatory primary symbionts). The aim of this study was to determine which
B. tabaci
symbionts are involved in TYLCV transmission using
B. tabaci
populations collected in Israel. Virus transmission assays by
B. tabaci
showed that the B biotype efficiently transmits the virus, while the Q biotype scarcely transmits it. Yeast two-hybrid and protein pulldown assays showed that while the GroEL protein produced by
Hamiltonella
interacts with TYLCV coat protein, GroEL produced by
Rickettsia
and
Portiera
does not. To assess the role of
Wolbachia
and
Arsenophonus
GroEL proteins (GroELs), we used an immune capture PCR (IC-PCR) assay, employing
in vivo
- and
in vitro
-synthesized GroEL proteins from all symbionts and whitefly artificial feeding through membranes. Interaction between GroEL and TYLCV was found to occur in the B biotype, but not in the Q biotype. This assay further showed that release of virions protected by GroEL occurs adjacent to the primary salivary glands. Taken together, the GroEL protein produced by
Hamiltonella
(present in the B biotype, but absent in the Q biotype) facilitates TYLCV transmission. The other symbionts from both biotypes do not seem to be involved in transmission of this virus.
Epstein-Barr Virus LF2 Protein Regulates Viral Replication by Altering Rta Subcellular Localization
Authors: Heilmann Andreas M. F. , Calderwood Michael A. , Johannsen Eric 
Published: July 2010

ABSTRACT
The switch from Epstein-Barr virus (EBV) latent infection to lytic replication is governed by two viral transactivators, Zta and Rta. We previously reported that the EBV protein LF2 binds Rta, inhibits Rta promoter activation, and blocks EBV replication in cells. In addition, LF2 induces SUMO2/3 modification of Rta. We now show that this modification occurs at four lysines within the Rta activation domain (426, 446, 517, and 530) and that sumoylation of Rta is not essential for its repression. Coexpression studies demonstrated that Rta is sequestered to the extranuclear cytoskeleton in the presence of LF2. We mapped the LF2 binding site to Rta amino acids (aa) 476 to 519 and showed that LF2 binding is critical for Rta relocalization and repression. The core of this binding site, Rta aa 500 to 526, confers LF2-mediated relocalization and repression onto the artificial transcription factor GAL4-VP16. Mutational analysis of LF2 provided further evidence that Rta redistribution is essential for repression. Rta localization changes during replication of the LF2-positive P3HR1 genome, but not during replication of the LF2-negative B95-8 genome. BLRF2 protein expression was decreased and delayed in P3HR1 cells compared with B95-8 cells, consistent with reduced Rta activity. By contrast, BMRF1 expression, regulated primarily by Zta, did not differ significantly between the two cell lines. Our results support a model in which LF2 regulates EBV replication by binding to Rta and redistributing it out of the nucleus.
Different Rotavirus Strains Enter MA104 Cells through Different Endocytic Pathways: the Role of Clathrin-Mediated Endocytosis
Authors: Gutiérrez Michelle , Isa Pavel , Sánchez-San Martin Claudia , Pérez-Vargas Jimena , Espinosa Rafaela , Arias Carlos F. , López Susana 
Published: July 2010

ABSTRACT
Rotaviruses, the single most important agents of acute severe gastroenteritis in children, are nonenveloped viruses formed by a three-layered capsid that encloses a genome formed by 11 segments of double-stranded RNA. The mechanism of entry of these viruses into the host cell is not well understood. The best-studied strain, RRV, which is sensitive to neuraminidase (NA) treatment of the cells, uses integrins α2β1 and αvβ3 and the heat shock protein hsc70 as receptors and enters MA104 cells through a non-clathrin-, non-caveolin-mediated pathway that depends on a functional dynamin and on the presence of cholesterol on the cell surface. In this work, using a combination of pharmacological, biochemical, and genetic approaches, we compared the entry characteristics of four rotavirus strains known to have different receptor requirements. We chose four rotavirus strains that represent all phenotypic combinations of NA resistance or sensitivity and integrin dependence or independence. We found that even though all the strains share their requirements for hsc70, dynamin, and cholesterol, three of them differ from the simian strain RRV in the endocytic pathway used. The human strain Wa, porcine strain TFR-41, and bovine strain UK seem to enter the cell through clathrin-mediated endocytosis, since treatments that inhibit this pathway block their infectivity; consistent with this entry route, these strains were sensitive to changes in the endosomal pH. The inhibition of other endocytic mechanisms, such as macropinocytosis or caveola-mediated uptake, had no effect on the internalization of the rotavirus strains tested here.
TLR4 Ligands Augment Antigen-Specific CD8
+
T Lymphocyte Responses Elicited by a Viral Vaccine Vector
Authors: Rhee Elizabeth G. , Kelley R. Phelps , Agarwal Isha , Lynch Diana M. , La Porte Annalena , Simmons Nathaniel L. , Clark Sarah L. , Barouch Dan H. 
Published: July 2010

ABSTRACT

Toll-like receptor (TLR) ligands are critical activators of innate immunity and are being developed as vaccine adjuvants. However, their utility in conjunction with viral vector-based vaccines remains unclear. In this study, we evaluated the impact of a variety of TLR ligands on antigen-specific CD8
+
T lymphocyte responses elicited by a recombinant adenovirus serotype 26 (rAd26) vector expressing simian immunodeficiency virus Gag in mice. The TLR3 ligand poly(I:C) suppressed Gag-specific cellular immune responses, whereas the TLR4 ligands lipopolysaccharide and monophosphoryl lipid A substantially augmented the magnitude and functionality of these responses by a MyD88- and TRIF-dependent mechanism. These data demonstrate that TLR ligands can modulate the immunogenicity of viral vaccine vectors both positively and negatively. Moreover, these findings suggest the potential utility of TLR4 ligands as adjuvants for rAd vector-based vaccines.