bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibodies against Immunodominant Antigens of
Mycobacterium tuberculosis
in Subjects with Suspected Tuberculosis in the United States Compared by HIV Status
Authors: Achkar Jacqueline M. , Jenny-Avital Elisabeth , Yu Xian , Burger Susanne , Leibert Eric , Bilder Patrick W. , Almo Steven C. , Casadevall Arturo , Laal Suman 
Published: January 2010

ABSTRACT

The immunodominance of
Mycobacterium tuberculosis
proteins malate synthase (MS) and MPT51 has been demonstrated in case-control studies with patients from countries in which tuberculosis (TB) is endemic. The value of these antigens for the serodiagnosis of TB now is evaluated in a cross-sectional study of pulmonary TB suspects in the United States diagnosed to have TB, HIV-associated TB, or other respiratory diseases (ORD). Serum antibody reactivity to recombinant purified MS and MPT51 was determined by enzyme-linked immunosorbent assays (ELISAs) of samples from TB suspects and well-characterized control groups. TB suspects were diagnosed with TB (
n
= 87; 49% sputum microscopy negative, 20% HIV
+
) or ORD (
n
= 63; 58% HIV
+
). Antibody reactivity to MS and MPT51 was significantly higher in U.S. HIV
+
/TB samples than in HIV
−
/TB samples (
P
< 0.001), and it was significantly higher in both TB groups than in control groups with latent TB infection (
P
< 0.001). Antibody reactivity to both antigens was higher in U.S. HIV
+
/TB samples than in HIV
+
/ORD samples (
P
= 0.052 for MS,
P
= 0.001 for MPT51) but not significantly different between HIV
−
/TB and HIV
−
/ORD. Among U.S. HIV
+
TB suspects, a positive anti-MPT51 antibody response was strongly and significantly associated with TB (odds ratio, 11.0; 95% confidence interval, 2.3 to 51.2;
P
= 0.002). These findings have implications for the adjunctive use of TB serodiagnosis with these antigens in HIV
+
subjects.
Phenotypic and Molecular Characterization of
Solobacterium moorei
Isolates from Patients with Wound Infection
Authors: Zheng Guili , Summanen Paula H. , Talan David , Bennion Robert , Rowlinson Marie-Claire , Finegold Sydney M. 
Published: January 2010

ABSTRACT

Though seldom reported,
Solobacterium moorei
, which was first described in 2000, has been identified in specimens from patients with root canals, periradicular lesions, periodontal disease, dentoalveolar abscesses, bacteremia, septic thrombophlebitis, and halitosis. In the present study, we describe 9 cases of mixed wound infection, from a pool of 400 surgical wound infections that we have studied, in which
S. moorei
was isolated or found in a clone library. All isolates of
S. moorei
were identified by 16S rRNA gene sequence analysis, and then six were examined for their physiological and biochemical characteristics and for antimicrobial susceptibility. The results of the present study indicate that
Solobacterium moorei
may be a significant component in some mixed surgical wound infections and that surgical management and antimicrobial therapy may be indicated when these bacteria are identified in significant situations.
Development of a Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for Detection of Pandemic (H1N1) 2009 Virus as a Novel Molecular Method for Diagnosis of Pandemic Influenza in Resource-Limited Settings
Authors: Kubo Toru , Agoh Masanobu , Mai Le Q. , Fukushima Kiyoyasu , Nishimura Hidekazu , Yamaguchi Akinori , Hirano Manabu , Yoshikawa Akira , Hasebe Futoshi , Kohno Shigeru , Morita Kouichi 
Published: January 2010

ABSTRACT
This paper reports on the development of a one-step, real-time reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay targeting the hemagglutinin (HA) gene for the rapid molecular-based detection of pandemic (H1N1) 2009 virus. The detection limit of the pandemic (H1N1) 2009 virus HA-specific RT-LAMP assay was same as that of the currently used real-time reverse transcription-PCR method. The assay detected the pandemic (H1N1) 2009 virus HA gene in 136 RNA samples extracted from nasopharyngeal swab specimens from Japanese and Vietnamese patients. No cross-reactive amplification with the RNA of other seasonal influenza viruses was observed, and the detection of specific viral genome targets in clinical specimens was achieved in less than 40 min. The sensitivity and specificity of the pandemic (H1N1) 2009 virus HA-specific RT-LAMP assay obtained in this study were 97.8% and 100%, respectively. Use of the (H1N1) 2009 virus HA-specific RT-LAMP assay will enable the faster and easier diagnosis of pandemic (H1N1) 2009 virus infection, especially in resource-limited situations in developing countries.
Fatal Infection Caused by
Cupriavidus gilardii
in a Child with Aplastic Anemia
Authors: Karafin Matthew , Romagnoli Mark , Fink Doran L. , Howard Tracy , Rau Rachel , Milstone Aaron M. , Carroll Karen C. 
Published: January 2010

ABSTRACT

Cupriavidus gilardii
is a Gram-negative bacterium that has rarely been associated with human infections. We report a fatal case of sepsis caused by
C. gilardii
in a previously healthy 12-year-old female.
Coexistence of Multiple Multilocus Variable-Number Tandem-Repeat Analysis Subtypes of
Clostridium difficile
PCR Ribotype 027 Strains within Fecal Specimens
Authors: Tanner Hannah E. , Hardy Katherine J. , Hawkey Peter M. 
Published: January 2010

ABSTRACT

We investigated whether multilocus variable-number tandem-repeat analysis (MLVA) typing could identify different subtypes of
Clostridium difficile
ribotype 027 within the same feces specimen. Five of 39 specimens yielded at least one isolate with an MLVA profile different (more than five summed tandem repeat differences) from that of other isolates in the same specimen, thereby potentially obscuring epidemiological links between
C. difficile
infection cases.
16S rRNA Gene Sequencing in Routine Identification of Anaerobic Bacteria Isolated from Blood Cultures
Authors: Justesen Ulrik Stenz , Skov Marianne Nielsine , Knudsen Elisa , Holt Hanne Marie , Søgaard Per , Justesen Tage 
Published: January 2010

ABSTRACTA comparison between conventional identification and 16S rRNA gene sequencing of anaerobic bacteria isolated from blood cultures in a routine setting was performed (n= 127). With sequencing, 89% were identified to the species level, versus 52% with conventional identification. The times for identification were 1.5 days and 2.8 days, respectively.
Identification of Novel Diagnostic Serum Biomarkers for Chagas' Disease in Asymptomatic Subjects by Mass Spectrometric Profiling
Authors: Ndao Momar , Spithill Terry W. , Caffrey Rebecca , Li Hongshan , Podust Vladimir N. , Perichon Regis , Santamaria Cynthia , Ache Alberto , Duncan Mark , Powell Malcolm R. , Ward Brian J. 
Published: January 2010

ABSTRACTMore than 10 million people are thought to be infected withTrypanosoma cruzi, primarily in the Americas. The clinical manifestations of Chagas' disease (CD) are variable, but most subjects remain asymptomatic for decades. Only 15 to 30% eventually develop terminal complications. All current diagnostic tests have limitations. New approaches are needed for blood bank screening as well as for improved diagnosis and prognosis. Sera from subjects with asymptomatic CD (n= 131) were compared to those from uninfected controls (n= 164) and subjects with other parasitic diseases (n= 140), using protein array mass spectrometry. To identify biomarkers associated with CD, sera were fractionated by anion-exchange chromatography and bound to two commercial ProteinChip array chemistries: WCX2 and IMAC3. Multiple candidate biomarkers were found in CD sera (3 to 75.4 kDa). Algorithms employing 3 to 5 of these biomarkers achieved up to 100% sensitivity and 98% specificity for CD. The biomarkers most useful for diagnosis were identified and validated. These included MIP1 alpha, C3a anaphylatoxin, and unusually truncated forms of fibronectin, apolipoprotein A1 (ApoA1), and C3. An antipeptide antiserum against the 28.9-kDa C terminus of the fibronectin fragment achieved good specificity (90%) for CD in a Western blot format. We identified full-length ApoA1 (28.1 kDa), the major structural and functional protein component of high-density lipoprotein (HDL), as an important negative biomarker for CD, and relatively little full-length ApoA1 was detected in CD sera. This work provides proof of principle that both platform-dependent (i.e., mass spectrometry-based) and platform-independent (i.e., Western blot) tests can be generated using high-throughput mass profiling.
Development of an Immunochromatographic Assay Specifically Detecting Pandemic H1N1 (2009) Influenza Virus
Authors: Miyoshi-Akiyama Tohru , Narahara Kenji , Mori Sunao , Kitajima Hirotake , Kase Tetsuo , Morikawa Saeko , Kirikae Teruo 
Published: January 2010

ABSTRACT
The pandemic caused by a new type of influenza virus, pandemic H1N1 (2009) influenza virus A (AH1pdm), has had a major worldwide impact. Since hemagglutinin (HA) genes are among the most specific genes in the influenza virus genome, AH1pdm can be definitively diagnosed by viral gene analysis targeting the HA genes. This type of analysis, however, cannot be easily performed in clinical settings. While commercially available rapid diagnosis kits (RDKs) based on immunochromatography can be used to detect nucleoproteins (NPs) of influenza A and B viruses in clinical samples, there are no such kits that are specific for AH1pdm. We show here that an RDK using a combination of monoclonal antibodies against NP can be used to specifically detect AH1pdm. The RDK recognized AH1pdm virus isolates but did not recognize seasonal H1N1 and H3N2 and influenza B viruses, indicating that the specificity of the RDK is 100%. A parallel comparison of RDK with a commercial influenza A/B virus kit revealed that both types of kits had equal sensitivities in detecting their respective viruses. Preliminary evaluation of clinical samples from 5 individuals with PCR-confirmed human AH1pdm infection showed that the RDK was positive for all samples, with the same detection intensity as that of a commercial influenza A/B virus kit. This RDK, together with a new vaccine and the stockpiling of anti-influenza drugs, will make aggressive measures to contain AH1pdm infections possible.
Preexisting Infection with Human T-Cell Lymphotropic Virus Type 2 neither Exacerbates nor Attenuates Simian Immunodeficiency Virus SIV
mac251
Infection in Macaques
Authors: Gordon Shari N. , Weissman Anna R. , Cecchinato Valentina , Fenizia Claudio , Ma Zhong-Min , Lee Tzong-Hae , Zaffiri Lorenzo , Andresen Vibeke , Parks Robyn Washington , Jones Kathryn S. , Heraud Jean Michel , Ferrari Maria Grazia , Chung Hye Kyung , Venzon David , Mahieux Renaud , Murphy Edward L. , Jacobson Steven , Miller Christopher J. , Ruscetti Francis W. , Franchini Genoveffa 
Published: January 2010

ABSTRACT

Coinfection with human T-cell lymphotropic virus type 2 (HTLV-2) and human immunodeficiency virus type 1 (HIV-1) has been reported to have either a slowed disease course or to have no effect on progression to AIDS. In this study, we generated a coinfection animal model and investigated whether HTLV-2 could persistently infect macaques, induce a T-cell response, and impact simian immunodeficiency virus SIV
mac251
-induced disease. We found that inoculation of irradiated HTLV-2-infected T cells into Indian rhesus macaques elicited humoral and T-cell responses to HTLV-2 antigens at both systemic and mucosal sites. Low levels of HTLV-2 provirus DNA were detected in the blood, lymphoid tissues, and gastrointestinal tracts of infected animals. Exposure of HTLV-2-infected or naïve macaques to SIV
mac251
demonstrated comparable levels of SIV
mac251
viral replication, similar rates of mucosal and peripheral CD4
+
T-cell loss, and increased T-cell proliferation. Additionally, neither the magnitude nor the functional capacity of the SIV-specific T-cell-mediated immune response was different in HTLV-2/SIV
mac251
coinfected animals versus SIV
mac251
singly infected controls. Thus, HTLV-2 targets mucosal sites, persists, and importantly does not exacerbate SIV
mac251
infection. These data provide the impetus for the development of an attenuated HTLV-2-based vectored vaccine for HIV-1; this approach could elicit persistent mucosal immunity that may prevent HIV-1/SIV
mac251
infection.
Human RNA Polymerase I-Driven Reverse Genetics for Influenza A Virus in Canine Cells
Authors: Suphaphiphat Pirada , Keiner Bjoern , Trusheim Heidi , Crotta Stefania , Tuccino Annunziata Barbara , Zhang Pu , Dormitzer Philip R. , Mason Peter W. , Franti Michael 
Published: January 2010

ABSTRACT
We have established a human RNA polymerase I (pol I)-driven influenza virus reverse genetics (RG) system in the Madin-Darby canine kidney 33016-PF cell line, which is approved for influenza vaccine manufacture. RNA pol I polymerases are generally active only in cells of species closely related to the species of origin of the polymerases. Nevertheless, we show that a nonendogenous RNA pol I promoter drives efficient rescue of influenza A viruses in a canine cell line. Application of this system allows efficient generation of virus strains and presents an alternative approach for influenza vaccine production.
Predominant Clonal Accumulation of CD8+T Cells with Moderate Avidity in the Central Nervous Systems of Theiler's Virus-Infected C57BL/6 Mice
Authors: Kang Hyun Seok , Kim Byung S. 
Published: January 2010

ABSTRACTInduction of antigen-specific CD8+T cells bearing a high-avidity T-cell receptor (TCR) is thought to be an important factor in antiviral and antitumor immune responses. However, the relationship between TCR diversity and functional avidity of epitope-specific CD8+T cells accumulating in the central nervous system (CNS) during viral infection is unknown. Hence, analysis of T-cell diversity at the clonal level is important to understand the fate and function of virus-specific CD8+T cells. In this study, we examined the Vβ diversity and avidity of CD8+T cells specific to the predominant epitope (VP2121-130) of Theiler's murine encephalomyelitis virus. We found that Vβ6+CD8+T cells, associated with epitope specificity, predominantly expanded in the CNS during viral infection. Further investigations of antigen-specific Vβ6+CD8+T cells by CDR3 spectratyping and sequencing indicated that distinct T-cell clonotypes are preferentially increased in the CNS compared to the periphery. Among the epitope-specific Vβ6+CD8+T cells, MGX-Jβ1.1 motif-bearing cells, which could be found at a high precursor frequency in naïve mice, were expanded in the CNS and tightly associated with gamma interferon production. These T cells displayed moderate avidity for the cognate epitope rather than the high avidity normally observed in memory/effector T cells. Therefore, our findings provide new insights into the CD8+T-cell repertoire during immune responses to viral infection in the CNS.
Meta-Analysis To Test the Association of HIV-1
nef
Amino Acid Differences and Deletions with Disease Progression
Authors: Pushker Ravindra , Jacqué Jean-Marc , Shields Denis C. 
Published: January 2010

ABSTRACT

Previous relatively small studies have associated particular amino acid replacements and deletions in the HIV-1
nef
gene with differences in the rate of HIV disease progression. We tested more rigorously whether particular
nef
amino acid differences and deletions are associated with HIV disease progression. Amino acid replacements and deletions in patients' consensus sequences were investigated for 153 progressor (P), 615 long-term nonprogressor (LTNP), and 2,311 unknown progressor sequences from 582 subtype B HIV-infected patients. LTNPs had more defective
nef
s (interrupted by frameshifts or stop codons), but on a per-patient basis there was no excess of LTNP patients with one or more defective
nef
sequences compared to the Ps (
P
= 0.47). The high frequency of amino acid replacement at residues S
8
, V
10
, I
11
, A
15
, V
85
, V
133
, N
157
, S
163
, V
168
, D
174
, R
178
, E
182
, and R
188
in LTNPs was also seen in permuted datasets, implying that these are simply rapidly evolving residues. Permutation testing revealed that residues showing the greatest excess over expectation (A
15
, V
85
, N
157
, S
163
, V
168
, D
174
, R
178
, and R
188
) were not significant (
P
= 0.77). Exploratory analysis suggested a hypothetical excess of frameshifting in the regions
9
SVIG and
118
QGYF among LTNPs. The regions V
10
and
152
KVEEA of
nef
were commonly deleted in LTNPs. However, permutation testing indicated that none of the regions displayed significantly excessive deletion in LTNPs. In conclusion, meta-analysis of HIV-1
nef
sequences provides no clear evidence of whether defective
nef
sequences or particular regions of the protein play a significant role in disease progression.
1a/1b Subtype Profiling of Nonnucleoside Polymerase Inhibitors of Hepatitis C Virus
Authors: Nyanguile Origène , Devogelaere Benoit , Vijgen Leen , Van den Broeck Walter , Pauwels Frederik , Cummings Maxwell D. , De Bondt Hendrik L. , Vos Ann M. , Berke Jan M. , Lenz Oliver , Vandercruyssen Geneviève , Vermeiren Katrien , Mostmans Wendy , Dehertogh Pascale , Delouvroy Frédéric , Vendeville Sandrine , VanDyck Koen , Dockx Koen , Cleiren Erna , Raboisson Pierre , Simmen Kenneth A. , Fanning Gregory C. 
Published: January 2010

ABSTRACTThe RNA-dependent RNA polymerase (NS5B) of hepatitis C virus (HCV) is an unusually attractive target for drug discovery since it contains five distinct drugable sites. The success of novel antiviral therapies will require nonnucleoside inhibitors to be active in at least patients infected with HCV of subtypes 1a and 1b. Therefore, the genotypic assessment of these agents against clinical isolates derived from genotype 1-infected patients is an important prerequisite for the selection of suitable candidates for clinical development. Here we report the 1a/1b subtype profiling of polymerase inhibitors that bind at each of the four known nonnucleoside binding sites. We show that inhibition of all of the clinical isolates tested is maintained, except for inhibitors that bind at the palm-1 binding site. Subtype coverage varies across chemotypes within this class of inhibitors, and inhibition of genotype 1a improves when hydrophobic contact with the polymerase is increased. We investigated if the polymorphism of the palm-1 binding site is the sole cause of the reduced susceptibility of subtype 1a to inhibition by 1,5-benzodiazepines by using reverse genetics, X-ray crystallography, and surface plasmon resonance studies. We showed Y415F to be a key determinant in conferring resistance on subtype 1a, with this effect being mediated through an inhibitor- and enzyme-bound water molecule. Binding studies revealed that the mechanism of subtype 1a resistance is faster dissociation of the inhibitor from the enzyme.
Epigenetic Regulation of Kaposi's Sarcoma-Associated Herpesvirus Latency by Virus-Encoded MicroRNAs That Target Rta and the Cellular Rbl2-DNMT Pathway
Authors: Lu Fang , Stedman William , Yousef Malik , Renne Rolf , Lieberman Paul M. 
Published: January 2010

ABSTRACT
Kaposi's sarcoma-associated herpesvirus (KSHV) encodes a cluster of 12 microRNAs (miRNAs) that are processed from a transcript that is embedded within the major latency control region. We have generated a deletion mutation that eliminates 10 of the 12 viral miRNAs from the KSHV bacmid by using recombineering methods. The KSHV miRNA deletion mutant (BAC36 ΔmiR) behaved similarly to wild-type (wt) BAC36 in viral production, latency gene transcription, and viral DNA copy number in 293 and dermal microvascular endothelial cells (DMVECs). However, BAC36 ΔmiR consistently expressed elevated levels of viral lytic genes, including the immediate-early transcriptional activator Rta (ORF50). At least one KSHV microRNA (miRK12-5) was capable of suppressing ORF50 mRNA, but poor seed sequence alignments suggest that these targets may be indirect. Comparison of epigenetic marks in ΔmiR KSHV genomes revealed decreases in histone H3 K9 methylation, increases in histone H3 acetylation, and a striking loss of DNA methylation throughout the viral and cellular genome. One viral miRNA, K12-4-5p, was found to have a sequence targeting retinoblastoma (Rb)-like protein 2 (Rbl2), which is a known repressor of DNA methyl transferase 3a and 3b mRNA transcription. We show that ectopic expression of miR-K12-4-5p reduces Rbl2 protein expression and increases DNMT1, -3a, and -3b mRNA levels relative to the levels for control cells. We conclude that KSHV miRNA targets multiple pathways to maintain the latent state of the KSHV genome, including repression of the viral immediate-early protein Rta and a cellular factor, Rbl2, that regulates global epigenetic reprogramming.
Murine Gammaherpesvirus 68 Has Evolved Gamma Interferon and Stat1-Repressible Promoters for the Lytic Switch Gene 50
Authors: Goodwin Megan M. , Canny Susan , Steed Ashley , Virgin Herbert W. 
Published: January 2010

ABSTRACT
Cytokines regulate viral gene expression with important consequences for viral replication and pathogenesis. Gamma interferon (IFN-γ) is a key regulator of chronic murine gammaherpesvirus 68 (γHV68) infection and a potent inhibitor of γHV68 reactivation from latency. Macrophages are the cell type that is responsive to the IFN-γ-mediated control of γHV68 reactivation; however, the molecular mechanism of this IFN-γ action is undefined. Here we report that IFN-γ inhibits lytic replication of γHV68 in primary bone marrow-derived macrophages and decreases transcript levels for the essential lytic switch gene 50. Interestingly, IFN-γ suppresses the activity of the two known gene 50 promoters, demonstrating that an inflammatory cytokine can directly regulate the promoters for the γHV68 lytic switch gene. Stat1, but not IFN-α/β signaling, is required for IFN-γ action. Moreover, Stat1 deficiency increases basal γHV68 replication, gene 50 expression, and promoter activity. Together, these data identify IFN-γ and Stat1 as being negative regulators of the γHV68 lytic cycle and raise the possibility that γHV68 maintains IFN-γ/Stat1-responsive gene 50 promoters to facilitate cell-extrinsic control over the interchange between the lytic and latent cycles.
NTPase and 5′ to 3′ RNA Duplex-Unwinding Activities of the Hepatitis E Virus Helicase Domain
Authors: Karpe Yogesh A. , Lole Kavita S. 
Published: January 2010

ABSTRACT

Hepatitis E virus (HEV) is a causative agent of acute hepatitis, and it is the sole member of the genus
Hepevirus
in the family
Hepeviridae
. The open reading frame 1 (ORF1) protein of HEV encodes nonstructural polyprotein with putative domains for methyltransferase, cysteine protease, helicase and RNA-dependent RNA polymerase. It is not yet known whether ORF1 functions as a single protein with multiple domains or is processed to form separate functional units. On the basis of amino acid conserved motifs, HEV helicase has been grouped into helicase superfamily 1 (SF-1). In order to examine the RNA helicase activity of the NTPase/helicase domain of HEV, the region (amino acids 960 to 1204) was cloned and expressed as histidine-tagged protein in
Escherichia coli
(HEV Hel) and purified. HEV Hel exhibited NTPase and RNA unwinding activities. Enzyme hydrolyzed all rNTPs efficiently, dATP and dCTP with moderate efficiency, while it showed less hydrolysis of dGTP and dTTP. Enzyme showed unwinding of only RNA duplexes with 5′ overhangs showing 5′-to-3′ polarity. We also expressed and purified two HEV Hel mutants. Helicase mutant I, with substitution in the nucleotide-binding motif I (GKS to GAS), showed 30% ATPase activity. Helicase mutant II, with substitutions in the Mg
2+
binding motif II (DEAP to AAAP), showed 50% ATPase activity. Both mutants completely lost ability to unwind RNA duplexes with 5′ overhangs. These findings represent the first report demonstrating NTPase/RNA helicase activity of the helicase domain of HEV ORF1.