bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Absence of PspA or Presence of Antibody to PspA Facilitates the Complement-Dependent Phagocytosis of PneumococciIn Vitro
Authors: Ren Bing , Li Jie , Genschmer Kristopher , Hollingshead Susan K. , Briles David E. 
Published: August 2012

ABSTRACTPneumococcal surface protein A (PspA) is a surface molecule on pneumococci that is required for full virulence in mouse models of infection. PspA has been reported to inhibit complement deposition on the pneumococcal surface. It has been assumed that this decreased complement deposition results in the inefficient phagocytosis of wild-type pneumococci. However, an effect of PspA on phagocytosis had not been shown. Our present studies demonstrated that a loss of PspA by capsular type 3 strains WU2 and A66.1 led to enhanced complement-dependent phagocytosis of the pneumococci by the mouse macrophage cell line J774A.1. This observation was made using human complement as well as mouse complement. Since this enhanced phagocytosis could be blocked by antibody to complement receptor CR3 on J774A.1, it was concluded that PspA's effect on phagocytosis was due to its effect on the amount of deposited complement, which in turn helped opsonize the pneumococci for phagocytosis. Since these studies included new independent mutants lacking PspA, the results provide solid confirmation of the previously reported effects of PspA on pneumococcal virulence and complement deposition. Finally, we showed that antibody to PspA, which is also known to enhance complement deposition, also enhances the phagocytosis of pneumococci in a largely complement-dependent manner.
Dexamethasone Downregulates the Systemic Cytokine Response in Patients with Community-Acquired Pneumonia
Authors: Remmelts Hilde H. F. , Meijvis Sabine C. A. , Biesma Douwe H. , van Velzen-Blad Heleen , Voorn G. Paul , Grutters Jan C. , Bos Willem Jan W. , Rijkers Ger T. 
Published: August 2012

ABSTRACT

The influence of adjunctive corticosteroids on the cytokine response in community-acquired pneumonia (CAP) is largely unknown. In this study, we analyzed the effect of dexamethasone on the cytokine response in patients with CAP and evaluated whether this effect is dependent on the causative microorganism. We hypothesized that dexamethasone has a larger effect on the cytokine response in patients with pneumococcal pneumonia than in patients with pneumonia caused by an atypical bacterium. A total of 304 hospitalized, nonimmunocompromised patients with CAP were randomized to an adjunctive 4-day course of 5 mg dexamethasone once a day (
n
= 151) or a placebo (
n
= 153). Serum concentrations of interleukin-1 receptor antagonist (IL-1Ra), IL-6, IL-8, IL-10, IL-17, tumor necrosis factor alpha (TNF-α), gamma interferon (IFN-γ), macrophage inflammatory protein-1 alpha (MIP-1α), and monocyte chemotactic protein-1 (MCP-1) were measured on days 0, 1, 2, and 4 and at a control visit. Overall, the concentrations of IL-6 (
P
< 0.01), IL-8 (
P
< 0.01), MCP-1 (
P
< 0.01), and TNF-α (
P
< 0.01) were significantly lower on day 2 in the dexamethasone group than in the placebo group. In patients with pneumococcal pneumonia (
n
= 72), both treatment groups showed a rapid decrease of cytokine concentrations; only the concentration of TNF-α (
P
= 0.05) was significantly lower in the dexamethasone group on day 2. In patients with CAP caused by an atypical pathogen (
Legionella pneumophila
,
Chlamydophila
species,
Coxiella burnetii
, or
Mycoplasma pneumoniae
;
n
= 58), IL-1Ra (
P
< 0.01), IL-6 (
P
< 0.01), and MCP-1 (
P
= 0.03) decreased more rapidly in the dexamethasone group than in the placebo group. In conclusion, dexamethasone downregulates the cytokine response during CAP. This effect seems to be dependent on the causative microorganism. This study provides insight into which patients with CAP might benefit most from adjunctive dexamethasone.
Comparative Analysis of Two Broad-Range PCR Assays for Pathogen Detection in Positive-Blood-Culture Bottles: PCR–High-Resolution Melting Analysis versus PCR-Mass Spectrometry
Authors: Jeng Kevin , Gaydos Charlotte A. , Blyn Lawrence B. , Yang Samuel , Won Helen , Matthews Heather , Toleno Donna , Hsieh Yu-Hsiang , Carroll Karen C. , Hardick Justin , Masek Billy , Kecojevic Alexander , Sampath Rangarajan , Peterson Stephen , Rothman Richard E. 
Published: August 2012

ABSTRACT
Detection of pathogens in bloodstream infections is important for directing antimicrobial treatment, but current culture-based approaches can be problematic. Broad-range PCR assays which target conserved genomic motifs for postamplification amplicon analysis permit detection of sepsis-causing pathogens. Comparison of different broad-range assays is important for informing future implementation strategies. In this study, we compared positive-blood-culture bottles processed by PCR coupled to high-resolution melting curve analysis (PCR/HRMA) and PCR coupled to electrospray ionization-mass spectrometry (PCR/ESI-MS) to microbiology culture results. Genus-level concordance was 90% (confidence interval [CI], 80 to 96%) for PCR/HRMA and 94% (CI, 85 to 98%) for PCR/ESI-MS. Species-level concordance was 90% (CI, 80 to 96%) for PCR/HRMA and 86% (CI, 75 to 93%) for PCR/ESI-MS. Unlike PCR/HRMA, PCR/ESI-MS was able to resolve polymicrobial samples. Our results demonstrated that the two assays have similar overall concordance rates but may have different roles as potential adjunctive tests with standard blood culture, since each method has different capabilities, advantages, and disadvantages.
Isolation and Identification of Kroppenstedtia eburnea Isolates from Multiple Patient Samples
Authors: Barker Adam P. , Simmon Keith E. , Cohen Sam , Slechta E. Susan , Fisher Mark A. , Schlaberg Robert 
Published: August 2012

ABSTRACT

No clinical isolates have been reported for the recently described thermoactinomycete
Kroppenstedtia eburnea
. Between 2006 and 2011, we obtained 14 clinical isolates from patients in 9 U.S. states. Here we report growth characteristics, 16S rRNA gene sequencing, matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry-based identification, and antimicrobial susceptibility profiles of this recently described organism.
Aspergillus tanneri sp. nov., a New Pathogen That Causes Invasive Disease Refractory to Antifungal Therapy
Authors: Sugui Janyce A. , Peterson Stephen W. , Clark Lily P. , Nardone Glenn , Folio Les , Riedlinger Gregory , Zerbe Christa S. , Shea Yvonne , Henderson Christina M. , Zelazny Adrian M. , Holland Steven M. , Kwon-Chung Kyung J. 
Published: August 2012

ABSTRACT

The most common cause of invasive aspergillosis (IA) in patients with chronic granulomatous disease (CGD) is
Aspergillus fumigatus
followed by
A. nidulans
; other aspergilli rarely cause the disease. Here we review two clinical cases of fatal IA in CGD patients and describe a new etiologic agent of IA refractory to antifungal therapy. Unlike typical IA caused by
A. fumigatus
, the disease caused by the new species was chronic and spread from the lung to multiple adjacent organs. Mycological characteristics and the phylogenetic relationship with other aspergilli based on the sequence analysis of
Mcm7
,
RPB2
, and
Tsr1
indicated that the new species, which we named as
A. tanneri
, belongs to
Aspergillus
section
Circumdati
. The species has a higher amphotericin B, voriconazole, and itraconazole MIC and causes more chronic infection in CGD mice than
A. fumigatus
. This is the first report documenting IA in CGD patients caused by a species belonging to the
Aspergillus
section
Circumdati
that is inherently resistant to azoles and amphotericin B. Unlike the results seen with many members of
Aspergillus
section
Circumdati
, ochratoxin was not detected in filtrates of cultures grown in various media. Our phenotypic and genetic characterization of the new species and the case reports will assist future diagnosis of infection caused by
A. tanneri
and lead to more appropriate patient management.
Applying a Real-Time PCR Assay for Histoplasma capsulatum to Clinically Relevant Formalin-Fixed Paraffin-Embedded Human Tissue
Authors: Koepsell Scott A. , Hinrichs Steven H. , Iwen Peter C. 
Published: August 2012

ABSTRACT

A real-time PCR assay to detect
Histoplasma capsulatum
in formalin-fixed, paraffin-embedded (FFPE) tissue is described. The assay had an analytical sensitivity of 6 pg/μl of fungal DNA, analytical specificity of 100%, and clinical sensitivity of 88.9%. This proof-of-concept study may aid in the diagnosis of histoplasmosis from FFPE tissue.
Performance Assessment of the DR. TBDR/NTM IVD Kit for Direct Detection of Mycobacterium tuberculosis Isolates, Including Rifampin-Resistant Isolates, and Nontuberculous Mycobacteria
Authors: Lee Meng-Rui , Cheng Aristine , Huang Yu-Tsung , Liu Chia-Ying , Chung Kuei-Pin , Wang Hao-Chien , Liang Sheng-Kai , Liao Chun-Hsing , Yu Chong-Jen , Hsueh Po-Ren 
Published: August 2012

ABSTRACT

We evaluated the performance of the DR. TBDR/NTM IVD kit, which was designed to detect
Mycobacterium tuberculosis
, rifampin-resistant
M. tuberculosis
, and nontuberculous mycobacteria, for detecting 110 positive and 50 negative cultures in
Mycobacterium
Growth Indicator Tubes. The accuracy rate of this kit for identification of
Mycobacterium
species was 95.5% (105/110).
Detection and Serotyping of Lyophilized Nonculturable Pneumococcal Isolates
Authors: Modak Joyanta K. , Steinhoff Mark C. , Zaman K. , Islam Maksuda , El Arifeen Shams , Saha Samir K. 
Published: August 2012

ABSTRACT
One hundred fifty-two nonculturable lyophilized carriage pneumococcal isolates from a vaccine trial were subjected to PCR for serotyping, and 149 (98%) were successfully classified as vaccine or nonvaccine types, which were similar to viable isolates. The methodology will be useful for analysis of this and other studies where stored pneumococcal isolates fail to grow.
Human Endogenous Retrovirus K Gag Coassembles with HIV-1 Gag and Reduces the Release Efficiency and Infectivity of HIV-1
Authors: Monde Kazuaki , Contreras-Galindo Rafael , Kaplan Mark H. , Markovitz David M. , Ono Akira 
Published: August 2012

ABSTRACT

Human endogenous retroviruses (HERVs), which are remnants of ancestral retroviruses integrated into the human genome, are defective in viral replication. Because activation of HERV-K and coexpression of this virus with HIV-1 have been observed during HIV-1 infection, it is conceivable that HERV-K could affect HIV-1 replication, either by competition or by cooperation, in cells expressing both viruses. In this study, we found that the release efficiency of HIV-1 Gag was 3-fold reduced upon overexpression of HERV-K
CON
Gag. In addition, we observed that in cells expressing Gag proteins of both viruses, HERV-K
CON
Gag colocalized with HIV-1 Gag at the plasma membrane. Furthermore, HERV-K
CON
Gag was found to coassemble with HIV-1 Gag, as demonstrated by (i) processing of HERV-K
CON
Gag by HIV-1 protease in virions, (ii) coimmunoprecipitation of virion-associated HERV-K
CON
Gag with HIV-1 Gag, and (iii) rescue of a late-domain-defective HERV-K
CON
Gag by wild-type (WT) HIV-1 Gag. Myristylation-deficient HERV-K
CON
Gag localized to nuclei, suggesting cryptic nuclear trafficking of HERV-K Gag. Notably, unlike WT HERV-K
CON
Gag, HIV-1 Gag failed to rescue myristylation-deficient HERV-K
CON
Gag to the plasma membrane. Efficient colocalization and coassembly of HIV-1 Gag and HERV-K Gag also required nucleocapsid (NC). These results provide evidence that HIV-1 Gag heteromultimerizes with HERV-K Gag at the plasma membrane, presumably through NC-RNA interaction. Intriguingly, HERV-K Gag overexpression reduced not only HIV-1 release efficiency but also HIV-1 infectivity in a myristylation- and NC-dependent manner. Altogether, these results indicate that Gag proteins of endogenous retroviruses can coassemble with HIV-1 Gag and modulate the late phase of HIV-1 replication.
YB-1 Functions as a Porter To Lead Influenza Virus Ribonucleoprotein Complexes to Microtubules
Authors: Kawaguchi Atsushi , Matsumoto Ken , Nagata Kyosuke 
Published: August 2012

ABSTRACT

De novo
-synthesized RNAs are under the regulation of multiple posttranscriptional processes by a variety of RNA-binding proteins. The influenza virus genome consists of single-stranded RNAs and exists as viral ribonucleoprotein (vRNP) complexes. After the replication of vRNP in the nucleus, it is exported to the cytoplasm and then reaches the budding site beneath the cell surface in a process mediated by Rab11a-positive recycling endosomes along microtubules. However, the regulatory mechanisms of the postreplicational processes of vRNP are largely unknown. Here we identified, as a novel vRNP-interacting protein, Y-box-binding protein 1 (YB-1), a cellular protein that is involved in regulation of cellular transcription and translation. YB-1 translocated to the nucleus from the cytoplasm and accumulated in PML nuclear bodies in response to influenza virus infection. vRNP assembled into the exporting complexes with YB-1 at PML nuclear bodies. After nuclear export, using YB-1 knockdown cells and
in vitro
reconstituted systems, YB-1 was shown to be required for the interaction of vRNP exported from the nucleus with microtubules around the microtubule-organizing center (MTOC), where Rab11a-positive recycling endosomes were located. Further, we also found that YB-1 overexpression stimulates the production of progeny virions in an Rab11a-dependent manner. Taking these findings together, we propose that YB-1 is a porter that leads vRNP to microtubules from the nucleus and puts it into the vesicular trafficking system.
Identification of Transmembrane Protein 134 as a Novel LMP1-Binding Protein by Using Bimolecular Fluorescence Complementation and an Enhanced Retroviral Mutagen
Authors: Talaty Pooja , Emery Amanda , Holthusen Kirsten , Everly David N. 
Published: August 2012

ABSTRACT
Latent membrane protein 1 (LMP1) of Epstein-Barr virus induces constitutive signaling in infected cells. LMP1 signaling requires oligomerization of LMP1 via its transmembrane domain, localization to lipid rafts in the membrane, and association of the LMP1 cytoplasmic domain to adaptor proteins, such as the tumor necrosis factor receptor-associated factors (TRAFs). Protein complementation is a novel technique to examine protein-protein interaction through the assembly of functional fluorescent proteins or enzymes from inactive fragments. A previous study in our lab demonstrated the use of bimolecular fluorescence complementation (BiFC) to study the assembly of the LMP1 signaling complexes within the plasma membrane of mammalian cells. In the present study, LMP1 was used as bait in a genome-wide BiFC screen with an enhanced retroviral mutagen to identify new LMP1-binding proteins. Our screen identified a novel LMP1-binding protein, transmembrane protein 134 (Tmem134). Tmem134 is a candidate oncogene that is amplified in breast cancer cell lines. Binding, colocalization, and cofractionation between LMP1 and Tmem134 were confirmed. Finally, Tmem134 affected LMP1-induced NF-κB induction. Together, these data suggest that BiFC is a unique and novel platform to identify proteins recruited to the LMP1-signaling complex.
Hepatitis C Virus Induces Epidermal Growth Factor Receptor Activation via CD81 Binding for Viral Internalization and Entry
Authors: Diao Jingyu , Pantua Homer , Ngu Hai , Komuves Laszlo , Diehl Lauri , Schaefer Gabriele , Kapadia Sharookh B. 
Published: August 2012

ABSTRACT
While epidermal growth factor receptor (EGFR) has been shown to be important in the entry process for multiple viruses, including hepatitis C virus (HCV), the molecular mechanisms by which EGFR facilitates HCV entry are not well understood. Using the infectious cell culture HCV model (HCVcc), we demonstrate that the binding of HCVcc particles to human hepatocyte cells induces EGFR activation that is dependent on interactions between HCV and CD81 but not claudin 1. EGFR activation can also be induced by antibody mediated cross-linking of CD81. In addition, EGFR ligands that enhance the kinetics of HCV entry induce EGFR internalization and colocalization with CD81. While EGFR kinase inhibitors inhibit HCV infection primarily by preventing EGFR endocytosis, antibodies that block EGFR ligand binding or inhibitors of EGFR downstream signaling have no effect on HCV entry. These data demonstrate that EGFR internalization is critical for HCV entry and identify a hitherto-unknown association between CD81 and EGFR.
Incoming Influenza A Virus Evades Early Host Recognition, while Influenza B Virus Induces Interferon Expression Directly upon Entry
Authors: Österlund Pamela , Strengell Mari , Sarin L. Peter , Poranen Minna M. , Fagerlund Riku , Melén Krister , Julkunen Ilkka 
Published: August 2012

ABSTRACT
The activation of the interferon (IFN) system, which is triggered largely by the recognition of viral nucleic acids, is one of the most important host defense reactions against viral infections. Although influenza A and B viruses, which both have segmented negative-strand RNA genomes, share major structural similarities, they have evolutionarily diverged, with total genetic incompatibility. Here we compare antiviral-inducing mechanisms during infections with type A and B influenza viruses in human dendritic cells. We observed that IFN responses are induced significantly faster in cells infected with influenza B virus than in cells infected with type A influenza virus and that the early induction of antiviral gene expression is mediated by the activation of the transcription factor IFN regulatory factor 3 (IRF3). We further demonstrate that influenza A virus infection activates IFN responses only after viral RNA (vRNA) synthesis, whereas influenza B virus induces IFN responses even if its infectivity is destroyed by UV treatment. Thus, initial viral transcription, replication, and viral protein synthesis are dispensable for influenza B virus-induced antiviral responses. Moreover, vRNA molecules from both type A and B viruses are equally potent activators of IFN induction, but incoming influenza B virus structures are recognized directly in the cytosol, while influenza A virus is able to evade early recognition. Collectively, our data provide new evidence of a novel antiviral evasion strategy for influenza A virus without a contribution of the viral NS1 protein, and this opens up new insights into different influenza virus pathogenicities.
Hepatitis C Virus Envelope Glycoprotein Fitness Defines Virus Population Composition following Transmission to a New Host
Authors: Brown Richard J. P. , Hudson Natalia , Wilson Garrick , Rehman Shafiq Ur , Jabbari Sara , Hu Ke , Tarr Alexander W. , Borrow Persephone , Joyce Michael , Lewis Jamie , Zhu Lin Fu , Law Mansun , Kneteman Norman , Tyrrell D. Lorne , McKeating Jane A. , Ball Jonathan K. 
Published: August 2012

ABSTRACT
Genetic variability is a hallmark of RNA virus populations. However, transmission to a new host often results in a marked decrease in population diversity. This genetic bottlenecking is observed during hepatitis C virus (HCV) transmission and can arise via a selective sweep or through the founder effect. To model HCV transmission, we utilized chimeric SCID/Alb-uPA mice with transplanted human hepatocytes and infected them with a human serum HCV inoculum. E1E2 glycoprotein gene sequences in the donor inoculum and recipient mice were determined following single-genome amplification (SGA). In independent experiments, using mice with liver cells grafted from different sources, an E1E2 variant undetectable in the source inoculum was selected for during transmission. Bayesian coalescent analyses indicated that this variant arose in the inoculum pretransmission. Transmitted variants that established initial infection harbored key substitutions in E1E2 outside HVR1. Notably, all posttransmission E1E2s had lost a potential N-linked glycosylation site (PNGS) in E2. In lentiviral pseudoparticle assays, the major posttransmission E1E2 variant conferred an increased capacity for entry compared to the major variant present in the inoculum. Together, these data demonstrate that increased envelope glycoprotein fitness can drive selective outgrowth of minor variants posttransmission and that loss of a PNGS is integral to this improved phenotype. Mathematical modeling of the dynamics of competing HCV variants indicated that relatively modest differences in glycoprotein fitness can result in marked shifts in virus population composition. Overall, these data provide important insights into the dynamics and selection of HCV populations during transmission.
Membrane Interaction of the Portal Protein gp20 of Bacteriophage T4
Authors: Quinten Tobias A. , Kuhn Andreas 
Published: August 2012

ABSTRACT

Assembly of the bacteriophage T4 head structure occurs at the cytoplasmic face of the inner membrane of
Escherichia coli
with the formation of proheads. The proheads contain an internal scaffolding core that determines the size and the structure of the capsid. In a mutant where the major shell protein gp23 was compromised, core structures without a shell had been detected. Such core structures were also found in the mutant T4
am20am23
. Since the mutation in gene 20 is at the N terminus of gp20, it was assumed that these core structures assemble in the absence of gp20. However, sequencing showed that the mutation introduces a new ribosome binding site that leads to a restart at codon 15. Although the mutant protein gp20s lacks the very N-terminal sequence, we found that it still binds to the membrane of the host cell and can initiate prohead assembly. This explains its activity to allow the assembly of core structures and proheads at the membrane surface. With a cross-linking approach, we show here that gp20 and gp20s are escorted by the chaperones DnaK, trigger factor, and GroEL and dock on the membrane at the membrane protein YidC.
A Mutation Deleting Sequences Encoding the Amino Terminus of Human Cytomegalovirus UL84 Impairs Interaction with UL44 and Capsid Localization
Authors: Strang Blair L. , Bender Brian J. , Sharma Mayuri , Pesola Jean M. , Sanders Rebecca L. , Spector Deborah H. , Coen Donald M. 
Published: August 2012

ABSTRACT

Protein-protein interactions are required for many biological functions. Previous work has demonstrated an interaction between the human cytomegalovirus DNA polymerase subunit UL44 and the viral replication factor UL84. In this study, glutathione
S
-transferase pulldown assays indicated that residues 1 to 68 of UL84 are both necessary and sufficient for efficient interaction of UL84 with UL44
in vitro
. We created a mutant virus in which sequences encoding these residues were deleted. This mutant displayed decreased virus replication compared to wild-type virus. Immunoprecipitation assays showed that the mutation decreased but did not abrogate association of UL84 with UL44 in infected cell lysate, suggesting that the association in the infected cell can involve other protein-protein interactions. Further immunoprecipitation assays indicated that IRS1, TRS1, and nucleolin are candidates for such interactions in infected cells. Quantitative real-time PCR analysis of viral DNA indicated that the absence of the UL84 amino terminus does not notably affect viral DNA synthesis. Western blotting experiments and pulse labeling of infected cells with [
35
S]methionine demonstrated a rather modest downregulation of levels of multiple proteins and particularly decreased levels of the minor capsid protein UL85. Electron microscopy demonstrated that viral capsids assemble but are mislocalized in nuclei of cells infected with the mutant virus, with fewer cytoplasmic capsids detected. In sum, deletion of the sequences encoding the amino terminus of UL84 affects interaction with UL44 and virus replication unexpectedly, not viral DNA synthesis. Mislocalization of viral capsids in infected cell nuclei likely contributes to the observed decrease in virus replication.