bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Particle Agglutination Method with Soluble Virus Receptor for Identification of Poliovirus
Authors: Arita Minetaro , Masujima Souji , Wakita Takaji , Shimizu Hiroyuki 
Published: June 2010

ABSTRACT

In the Global Polio Eradication Initiative, laboratory diagnosis plays a critical role by isolating and identifying poliovirus (PV) from the stool samples of patients with acute flaccid paralysis (AFP). In this study, we developed a particle agglutination (PA) method with a soluble human PV receptor (hPVR) in the form of an immunoadhesin (PVR-IgG2a) for the simple and rapid identification of PV. Sensitized gelatin particles with PVR-IgG2a showed specific agglutination with the culture fluid of PV-infected cells within 2 h of reaction in a one-step procedure. Detection limits for type 1, 2, and 3 PV(Sabin) strains were 1.5 × 10
6
50% cell culture infectious doses (CCID
50
), 5.3 × 10
5
CCID
50
, and 9.1 × 10
5
CCID
50
, respectively. Wild-type PVs and PV isolates from acute flaccid paralysis cases examined were identified correctly with this PA method, except for some samples with a mixture of different serotypes of PVs, where a minor population of PV failed to be detected. These results suggest that this PA method is useful for the simple and rapid identification of PV, although the sensitivity was not high enough to detect a minor population of PV (<1/10 of the major population) among mixed PVs.
Three-Hour Molecular Detection of
Campylobacter
,
Salmonella
,
Yersinia
, and
Shigella
Species in Feces with Accuracy as High as That of Culture
Authors: Cunningham Scott A. , Sloan Lynne M. , Nyre Lisa M. , Vetter Emily A. , Mandrekar Jayawant , Patel Robin 
Published: June 2010

ABSTRACT

Campylobacter jejuni
and
Salmonella
,
Shigella
, and
Yersinia
species (along with Shiga toxin-producing
Escherichia coli
) are the most common causes of acute bacterial diarrheal disease in the United States. Current detection techniques are time-consuming, limiting usefulness for patient care. We developed and validated a panel of rapid PCR assays for the detection and identification of
C. jejuni
,
C. coli
,
Salmonella
, and
Yersinia
species and
Shigella
and enteroinvasive
E. coli
in stool samples. A total of 392 archived stool specimens, previously cultured for enteric pathogens, were evaluated by PCR. Overall, 104 stool specimens had been culture positive (
C. jejuni
/
coli
[
n
= 51],
Salmonella
species [
n
= 42],
Shigella
species [
n
= 6], and
Yersinia
species [
n
= 5]). Compared to culture, the overall sensitivity and specificity of PCR detection of these organisms were 92 and 98% (96/104 and 283/288), respectively, from fresh or Cary Blair stool (
P
= 0.41); 87 and 98% (41/47 and 242/246), respectively, from fresh stool (
P
= 0.53); and 96 and 98% (55/57 and 41/42), respectively, from Cary Blair stool (
P
= 0.56). For individual genera, PCR was as sensitive as the culture method, with the exception of
Salmonella
culture using selenite enrichment for which PCR was less sensitive than culture from fresh, but not Cary Blair (
P
= 0.03 and 1.00, respectively) stools. This PCR assay panel for the rapid diagnosis of acute infectious bacterial diarrheal pathogens has a sensitivity and specificity equivalent to that of culture for stools in Cary Blair transport medium. Paired with reflexive culture of stools testing positive, this should provide an improvement in care for patients with acute infectious diarrheal disease.
Unusual Distribution of
Burkholderia cepacia
Complex Species in Danish Cystic Fibrosis Clinics May Stem from Restricted Transmission between Patients
Authors: Nørskov-Lauritsen Niels , Johansen Helle Krogh , Fenger Mette G. , Nielsen Xiaohui C. , Pressler Tacjana , Olesen Hanne V. , Høiby Niels 
Published: June 2010

ABSTRACT

Forty-four of 48
Burkholderia cepacia
complex strains cultured from Danish cystic fibrosis patients were
Burkholderia multivorans
, a distribution of species that has not been reported before. Although cases of cross infections were demonstrated, no major epidemic clone was found. The species distribution may represent the sporadic acquisition of bacteria from the environment.
Immediate Incubation Reduces Indeterminate Results for QuantiFERON-TB Gold In-Tube Assay
Authors: Herrera Victor , Yeh Ellen , Murphy Kelly , Parsonnet Julie , Banaei Niaz 
Published: June 2010

ABSTRACT

In vitro
gamma interferon release assays (IGRAs) are increasingly used as an alternative to the traditional tuberculin skin test for the diagnosis of latent
Mycobacterium tuberculosis
infection. Evaluation of the QuantiFERON-TB Gold in-tube assay (QFT-IT) prior to large-scale implementation at the Stanford Hospital and Clinics for a health care worker screening program revealed a critical preanalytical factor affecting the results. We found that incubation delay significantly increased the frequency of indeterminate results. In this study, QFT-IT was performed with samples from healthy volunteers, and replicate tubes were incubated at 37°C either immediately or after a delay at room temperature for 6 and 12 h. No indeterminate results (0/41) were seen when the assay was performed with immediate incubation. Incubation delays of 6 and 12 h yielded indeterminate results at rates of 10% (2/20) (
P
= 0.10) and 17.1% (7/41) (
P
= 0.01), respectively. The increased rate of indeterminate results was due to a decrease in the mean values for the mitogen-nil tubes when incubation was delayed for 6 h (
P
= 0.004) and 12 h (
P
< 0.001). The rates of concordance of positive or negative results obtained following immediate incubation and following 6- and 12-h delays were 77.8% (14/18) and 79.4% (27/34), respectively. Subsequent implementation of the immediate incubation procedure in our screening program for 14,830 health care workers yielded an indeterminate result rate of 0.36% over a period of 12 months, a significant improvement over the reported rates of 5 to 40% for QFT-IT. We conclude that immediate incubation of QFT-IT tubes is an effective way to minimize indeterminate results. The effect of incubation delay on the accuracy of QFT-IT remains to be determined.
Monoclonal Antibody Kit for Identification of the Novel 2009 H1N1 Influenza A Virus
Authors: Higgins Angela D. , Shaw Carl J. , Johnson Jennifer G. , Navarro Adriana , Chapman Nathan A. , Ewers Steven D. , Stockwell James W. , Carpenter Julie M. , Olivo Paul D. , Miao Lynn Yihong 
Published: June 2010

ABSTRACT

To develop an immunofluorescence assay for identification of the 2009 H1N1 influenza A virus, we generated a number of monoclonal antibodies (MAbs) by using inactivated H1N1 2009 virus (A/California/07/2009) as the immunogen. Two MAbs that target two different epitopes of the 2009 H1N1 hemagglutinin (HA) were selected to make the D
3
Ultra 2009 H1N1 Influenza A ID kit (2009 H1N1 ID kit; Diagnostic Hybrids, Inc., Athens, OH), which is intended for the identification of the 2009 H1N1 virus by indirect immunofluorescence assay (IFA). The kit does not detect any of 14 seasonal H1N1 or H3N2 prototype influenza virus strains and is also not reactive with seven other major respiratory viruses. Clinical respiratory specimens were evaluated using both the 2009 H1N1 ID kit and the CDC human influenza virus real-time reverse transcription-PCR swine flu panel (CDC rRT-PCR) and showed 100% agreement between the two assays. Four of these clinical specimens, however, were positive by the 2009 H1N1 ID kit but were identified as presumptively positive by the CDC rRT-PCR by virtue of showing threshold cycle (

C
T

) values only with universal InfA and swInfA primers, not with swH1 primers. Sequence analysis of the HA genes of these four specimens revealed point mutations in both the primer and probe regions. In addition, unlike the CDC rRT-PCR, the 2009 H1N1 ID kit can differentiate the 2009 H1N1 virus from a swine-derived H1 influenza A virus (A/New Jersey/8/76). The 2009 H1N1 ID kit offers clinical laboratories an alternative to RT-PCR for the identification of the 2009 H1N1 influenza A virus.
Detection of Large Numbers of Pneumococcal Virulence Genes in Streptococci of the Mitis Group
Authors: Johnston Calum , Hinds Jason , Smith Andrew , van der Linden Mark , Van Eldere Johan , Mitchell Tim J. 
Published: June 2010

ABSTRACT

Seven streptococcal isolates from the mitis group were analyzed for the presence of pneumococcal gene homologues by comparative genomic hybridization studies with microarrays based on open reading frames from the genomes of
Streptococcus pneumoniae
TIGR4 and R6. The diversity of pneumolysin (
ply
) and neuraminidase A (
nanA
) gene sequences was explored in more detail in a collection of 14
S. pseudopneumoniae
and 29 mitis group isolates, respectively. The mitis group isolates used in the microarray experiments included a type strain (NCTC 12261), two
S. mitis
isolates from the nasopharynxes of children, one
S. mitis
isolate from a case of infective endocarditis, one
S. mitis
isolate from a dental abscess, and one
S. oralis
isolate and one
S. pseudopneumoniae
isolate from the nasopharynxes of children. The results of the microarray study showed that the 5
S. mitis
isolates had homologues to between 67 and 82% of pneumococcal virulence genes,
S. oralis
hybridized to 83% of pneumococcal virulence genes, and
S. pseudopneumoniae
hybridized to 92% of identified pneumococcal virulence genes. Comparison of the pneumolysin, mitilysin (
mly
), and newly identified pseudopneumolysin (
pply
) gene sequences revealed that
mly
and
pply
genes are more closely related to each other than either is to
ply
. In contrast, the
nanA
gene sequences in the pneumococcus and streptococci from the mitis group are closely clustered together, sharing 99.4 to 99.7% sequence identity with pneumococcal
nanA
alleles.
Evaluation of Multiple-Locus Variable-Number Tandem-Repeat Analysis for Typing a Polyclonal Hospital-Acquired Methicillin-Resistant
Staphylococcus aureus
Population in an Area Where Such Infections Are Endemic
Authors: Rivero-Pérez Belinda , Pérez-Roth Eduardo , Méndez-Álvarez Sebastián 
Published: June 2010

ABSTRACT

Multiple-locus variable-number tandem-repeat analysis (MLVA) was performed with 292 methicillin-resistant
Staphylococcus aureus
(MRSA) isolates previously characterized by pulsed-field gel electrophoresis, multilocus sequence typing, and staphylococcal cassette chromosome
mec
typing. Quantitative correspondence analyses showed the best correlation between data when an ≥80% cutoff was applied to MLVA. We confirmed the validity of MLVA for identification of related strains in a polyclonal MRSA population.
Babesia lengausp. nov., a NovelBabesiaSpecies in Cheetah (Acinonyx jubatus, Schreber, 1775) Populations in South Africa
Authors: Bosman Anna-Mari , Oosthuizen Marinda C. , Peirce Michael A. , Venter Estelle H. , Penzhorn Barend L. 
Published: June 2010

ABSTRACTIn a previous paper, we reported on a large number of cheetah blood specimens that gave positive signals only forBabesiaand/orTheileriagenus-specific probes on the reverse line blot (RLB) assay, indicating the presence of a novel species or variant of an existing species. Some of these specimens were investigated further by microscopic, serological, sequencing, and phylogenetic analyses. The near-full-length 18S rRNA genes of 13 samples, as well as the second internal transcribed spacer (ITS2) region, were amplified, cloned, and sequenced. A species-specific RLB probe, designed to target the hypervariable V4 region of the 18S rRNA gene for detection of the novelBabesiasp., was used to screen an additional 137 cheetah blood specimens for the presence of the species. The prevalence of infection was 28.5%. Here we describe the morphology and phylogenetic relationships of the novel species, which we have namedBabesia lengausp. nov.
Specificity of Baculovirus P6.9 Basic DNA-Binding Proteins and Critical Role of the C Terminus in Virion Formation
Authors: Wang Manli , Tuladhar Era , Shen Shu , Wang Hualin , van Oers Monique M. , Vlak Just M. , Westenberg Marcel 
Published: June 2010

ABSTRACT

The majority of double-stranded DNA (dsDNA) viruses infecting eukaryotic organisms use host- or virus-expressed histones or protamine-like proteins to condense their genomes. In contrast, members of the
Baculoviridae
family use a protamine-like protein named P6.9. The dephosphorylated form of P6.9 binds to DNA in a non-sequence-specific manner. By using a
p6.9
-null mutant of
Autographa californica
multiple nucleopolyhedrovirus (
Ac
MNPV), we demonstrate that P6.9 is not required for viral DNA replication but is essential for the production of infectious virus. Virion production was rescued by P6.9 homologs from a number of
Alpha
baculovirus
species and one
Gammabaculovirus
species but not from the genus
Betabaculovirus
, comprising the granuloviruses, or by the P6.9 homolog VP15 from the unrelated white spot syndrome virus of shrimp. Mutational analyses demonstrated that
Ac
MNPV P6.9 with a conserved 11-residue deletion of the C terminus was not capable of rescuing
p6.9
-null
Ac
MNPV, while a chimeric
Betabaculovirus
P6.9 containing the P6.9 C-terminal region of an
Alphabaculovirus
strain was able to do so. This implies that the C terminus of baculovirus P6.9 contains sequence elements essential for virion formation. Such elements may possibly interact with species- or genus-specific domains of other nucleocapsid proteins during virus assembly.
Multiple ASF/SF2 Sites in the Human Papillomavirus Type 16 (HPV-16) E4-Coding Region Promote Splicing to the Most Commonly Used 3′-Splice Site on the HPV-16 Genome
Authors: Somberg Monika , Schwartz Stefan 
Published: June 2010

ABSTRACT
Our results presented here demonstrate that the most abundant human papillomavirus type 16 (HPV-16) mRNAs expressing the viral oncogenes E6 and E7 are regulated by cellular ASF/SF2, itself defined as a proto-oncogene and overexpressed in cervical cancer cells. We show that the most frequently used 3′-splice site on the HPV-16 genome, site SA3358, which is used to produce primarily E4, E6, and E7 mRNAs, is regulated by ASF/SF2. Splice site SA3358 is immediately followed by 15 potential binding sites for the splicing factor ASF/SF2. Recombinant ASF/SF2 binds to the cluster of ASF/SF2 sites. Mutational inactivation of all 15 sites abolished splicing to SA3358 and redirected splicing to the downstream-located, late 3′-splice site SA5639. Overexpression of a mutant ASF/SF2 protein that lacks the RS domain, also totally inhibited the usage of SA3358 and redirected splicing to the late 3′-splice site SA5639. The 15 ASF/SF2 binding sites could be replaced by an ASF/SF2-dependent, HIV-1-derived splicing enhancer named GAR. This enhancer was also inhibited by the mutant ASF/SF2 protein that lacks the RS domain. Finally, silencer RNA (siRNA)-mediated knockdown of ASF/SF2 caused a reduction in spliced HPV-16 mRNA levels. Taken together, our results demonstrate that the major HPV-16 3′-splice site SA3358 is dependent on ASF/SF2. SA3358 is used by the most abundantly expressed HPV-16 mRNAs, including those encoding E6 and E7. High levels of ASF/SF2 may therefore be a requirement for progression to cervical cancer. This is supported by our earlier findings that ASF/SF2 is overexpressed in high-grade cervical lesions and cervical cancer.
A Quantitative and Kinetic Fusion Protein-Triggering Assay Can Discern Distinct Steps in the Nipah Virus Membrane Fusion Cascade
Authors: Aguilar Hector C. , Aspericueta Vanessa , Robinson Lindsey R. , Aanensen Karen E. , Lee Benhur 
Published: June 2010

ABSTRACTThe deadly paramyxovirus Nipah virus (NiV) contains a fusion glycoprotein (F) with canonical structural and functional features common to its class. Receptor binding to the NiV attachment glycoprotein (G) triggers F to undergo a two-phase conformational cascade: the first phase progresses from a metastable prefusion state to a prehairpin intermediate (PHI), while the second phase is marked by transition from the PHI to the six-helix-bundle hairpin. The PHI can be captured with peptides that mimic F's heptad repeat regions, and here we utilized a NiV heptad repeat peptide to quantify PHI formation and the half-lives (t1/2) of the first and second fusion cascade phases. We found that ephrinB2 receptor binding to G triggered ∼2-fold more F than that triggered by ephrinB3, consistent with the increased rate and extent of fusion observed with ephrinB2- versus ephrinB3-expressing cells. In addition, for a series of hyper- and hypofusogenic F mutants, we quantified F-triggering capacities and measured the kinetics of their fusion cascade phases. Hyper- and hypofusogenicity can each be manifested through distinct stages of the fusion cascade, giving rise to vastly different half-lives for the first (t1/2, 1.9 to 7.5 min) or second (t1/2, 1.5 to 15.6 min) phase. While three mutants had a shorter first phase and a longer second phase than the wild-type protein, one mutant had the opposite phenotype. Thus, our results reveal multiple critical parameters that govern the paramyxovirus fusion cascade, and our assays should help efforts to elucidate other class I membrane fusion processes.
Cell-Based Quantification of Chronic Wasting Disease Prions
Authors: Bian Jifeng , Napier Dana , Khaychuck Vadim , Angers Rachel , Graham Catherine , Telling Glenn 
Published: June 2010

ABSTRACT
Cell-based measurement of prion infectivity is currently restricted to experimental strains of mouse-adapted scrapie. Having isolated cell cultures with susceptibility to prions from diseased elk, we describe a modification of the scrapie cell assay allowing evaluation of prions causing chronic wasting disease, a naturally occurring transmissible spongiform encephalopathy. We compare this cervid prion cell assay to bioassays in transgenic mice, the only other existing method for quantification, and show this assay to be a relatively economical and expedient alternative that will likely facilitate studies of this important prion disease.
Clonal Expansion of Normal-Appearing Human Hepatocytes during Chronic Hepatitis B Virus Infection
Authors: Mason William S. , Liu Chen , Aldrich Carol E. , Litwin Samuel , Yeh Matthew M. 
Published: June 2010

ABSTRACTChronic hepatitis B virus (HBV) infections are associated with persistent immune killing of infected hepatocytes. Hepatocytes constitute a largely self-renewing population. Thus, immune killing may exert selective pressure on the population, leading it to evolve in order to survive. A gradual course of hepatocyte evolution toward an HBV-resistant state is suggested by the substantial decline in the fraction of infected hepatocytes that occurs during the course of chronic infections. Consistent with hepatocyte evolution, clones of >1,000 hepatocytes develop postinfection in the noncirrhotic livers of chimpanzees chronically infected with HBV and of woodchucks infected with woodchuck hepatitis virus (W. S. Mason, A. R. Jilbert, and J. Summers, Proc. Natl. Acad. Sci. U. S. A.102:1139-1144, 2005; W. S. Mason et al., J. Virol.83:8396-8408, 2009). The present study was carried out to determine (i) if extensive clonal expansion of hepatocytes also occurred in human HBV carriers, particularly in the noncirrhotic liver, and (ii) if clonal expansion included normal-appearing hepatocytes, not just hepatocytes that appear premalignant. Host DNA extracted from fragments of noncancerous liver, collected during surgical resection of hepatocellular carcinoma (HCC), was analyzed by inverse PCR for randomly integrated HBV DNA as a marker of expanding hepatocyte lineages. This analysis detected extensive clonal expansion of hepatocytes, as previously found in chronically infected chimpanzees and woodchucks. Tissue sections were stained with hematoxylin and eosin (H&E), and DNA was extracted from the adjacent section for inverse PCR to detect integrated HBV DNA. This analysis revealed that clonal expansion can occur among normal-appearing human hepatocytes.
Transcription Factor YY1 Interacts with Retroviral Integrases and Facilitates Integration of Moloney Murine Leukemia Virus cDNA into the Host Chromosomes
Authors: Inayoshi Yujin , Okino Yuuki , Miyake Katsuhide , Mizutani Akifumi , Yamamoto-Kishikawa Junko , Kinoshita Yuya , Morimoto Yusuke , Imamura Kazuhito , Morshed Mahboob , Kono Ken , Itoh Toshinari , Nishijima Ken-ichi , Iijima Shinji 
Published: June 2010

ABSTRACT

Retroviral integrases associate during the early viral life cycle with preintegration complexes that catalyze the integration of reverse-transcribed viral cDNA into the host chromosomes. Several cellular and viral proteins have been reported to be incorporated in the preintegration complex. This study demonstrates that transcription factor Yin Yang 1 binds to Moloney murine leukemia virus, human immunodeficiency virus type 1, and avian sarcoma virus integrases. The results of coimmunoprecipitation and
in vitro
pulldown assays revealed that Yin Yang 1 interacted with the catalytic core and C-terminal domains of Moloney murine leukemia virus and human immunodeficiency virus type 1 integrases, while the transcriptional repression and DNA-binding domains of the Yin Yang 1 molecule interacted with Moloney murine leukemia virus integrase. Immunoprecipitation of the cytoplasmic fraction of virus-infected cells followed by Southern blotting and chromatin immunoprecipitation demonstrated that Yin Yang 1 associated with Moloney murine leukemia virus cDNA in virus-infected cells. Yin Yang 1 enhanced the
in vitro
integrase activity of Moloney murine leukemia virus, human immunodeficiency virus type 1, and avian sarcoma virus integrases. Furthermore, knockdown of Yin Yang 1 in host cells by small interfering RNA reduced Moloney murine leukemia virus cDNA integration
in vivo
, although viral cDNA synthesis was increased, suggesting that Yin Yang 1 facilitates integration events
in vivo
. Taking these results together, Yin Yang 1 appears to be involved in integration events during the early viral life cycle, possibly as an enhancer of integration.
Respiratory Syncytial Virus-Neutralizing Monoclonal Antibodies Motavizumab and Palivizumab Inhibit Fusion
Authors: Huang Kelly , Incognito Len , Cheng Xing , Ulbrandt Nancy D. , Wu Herren 
Published: June 2010

ABSTRACT
Respiratory syncytial virus (RSV) is a major cause of virus-induced respiratory disease and hospitalization in infants. Palivizumab, an RSV-neutralizing monoclonal antibody, is used clinically to prevent serious RSV-related respiratory disease in high-risk infants. Motavizumab, an affinity-optimized version of palivizumab, was developed to improve protection against RSV. These antibodies bind RSV F protein, which plays a role in virus attachment and mediates fusion. Determining how these antibodies neutralize RSV is important to help guide development of new antibody drugs against RSV and, potentially, other viruses. This study aims to uncover the mechanism(s) by which palivizumab and motavizumab neutralize RSV. Assays were developed to test the effects of these antibodies at distinct steps during RSV replication. Pretreatment of virus with palivizumab or motavizumab did not inhibit virus attachment or the ability of F protein to interact with the target cell membrane. However, pretreatment of virus with either of these antibodies resulted in the absence of detectable viral transcription. These results show that palivizumab and motavizumab act at a point after F protein initiates interaction with the cell membrane and before virus transcription. Palivizumab and motavizumab also inhibited F protein-mediated cell-to-cell fusion. Therefore, these results strongly suggest that these antibodies block both cell-to-cell and virus-to-cell fusion, since these processes are likely similar. Finally, palivizumab and motavizumab did not reduce viral budding. Based on models developed from numerous studies of viral fusion proteins, our results indicate that these antibodies may prevent conformational changes in F protein required for the fusion process.