bluuebunny/crossref_metadata_2025_split huggingface dataset:
Colonic Immunopathogenesis of Clostridium difficile Infections
Authors: Darkoh Charles , Turnwald Bradley P. , Koo Hoonmo L. , Garey Kevin W. , Jiang Zhi-Dong , Aitken Samuel L. , DuPont Herbert L. 
Published: January 2014

ABSTRACT

There are major gaps in our understanding of the immunopathogenesis of
Clostridium difficile
infections (CDIs). In this study, 36 different biomarkers were examined in the stools of CDI and non-CDI patients using the Proteome Profiler human cytokine array assay and quantitative enzyme-linked immunosorbent assay. Diarrheal stools from patients with CDI (CDI-positive diarrheal stools) showed higher relative amounts of the following inflammatory markers than the diarrheal stools from CDI-negative patients (CDI-negative diarrheal stools): C5a, CD40L, granulocyte colony-stimulating factor, I-309, interleukin-13 (IL-13), IL-16, IL-27, monocyte chemoattractant protein 1, tumor necrosis factor alpha, and IL-8. IL-8 and IL-23 were present in a larger number of CDI-positive diarrheal stools than CDI-negative diarrheal stools. Th1 and Th2 cytokines were not significantly different between the CDI-positive and CDI-negative diarrheal stools. Lactoferrin and calprotectin concentrations were also higher in the CDI-positive diarrheal stools. Our results demonstrate that CDI elicits a proinflammatory host response, and we report for the first time that IL-23 is a major marker in CDI-positive diarrheal stools. IL-23 may explain the lack of a robust immunological response exhibited by a proportion of CDI patients and may relate to recurrence; the IL-23 levels induced during CDI in these patients may be inadequate to sustain the cellular immunity conferred by this cytokine in promoting the induction and proliferation of effector memory T cells.
Potential Impact of a Microarray-Based Nucleic Acid Assay for Rapid Detection of Gram-Negative Bacteria and Resistance Markers in Positive Blood Cultures
Authors: Mancini Nicasio , Infurnari Laura , Ghidoli Nadia , Valzano Grazia , Clementi Nicola , Burioni Roberto , Clementi Massimo 
Published: January 2014

ABSTRACT

We evaluated the Verigene Gram-negative blood culture (BC-GN) test, a microarray that detects Gram-negative bacteria and several resistance genes. A total of 102 positive blood cultures were tested, and the BC-GN test correctly identified 97.9% of the isolates within its panel. Resistance genes (CTX-M, KPC, VIM, and OXA genes) were detected in 29.8% of the isolates, with positive predictive values of 95.8% (95% confidence interval [CI], 87.7% to 98.9%) in
Enterobacteriaceae
and 100% (95% CI, 75.9% to 100%) in
Pseudomonas aeruginosa
and negative predictive values of 100% (95% CI, 93.9% to 100%) and 78.6% (95% CI, 51.0% to 93.6%), respectively.
De Novo
Meningitis Caused by Propionibacterium acnes in a Patient with Metastatic Melanoma
Authors: Burnham Jason P. , Thomas Benjamin S. , Trevino Sergio E. , McElvania TeKippe Erin , Burnham Carey-Ann D. , Kuhlmann F. Matthew 
Published: January 2014

ABSTRACT

Propionibacterium acnes
is a known cause of postneurosurgical meningitis; however, it is rarely implicated in
de novo
meningitis. Herein we report a case of a 49-year-old male with
de novo
meningitis caused by
P. acnes
with metastatic melanoma as the only identified risk factor for his infection.
A Multiplex Real-Time PCR Assay for Identification of Pneumocystis jirovecii, Histoplasma capsulatum, and Cryptococcus neoformans/Cryptococcus gattii in Samples from AIDS Patients with Opportunistic Pneumonia
Authors: Gago Sara , Esteban Cristina , Valero Clara , Zaragoza Óscar , Puig de la Bellacasa Jorge , Buitrago María José 
Published: January 2014

ABSTRACT

A molecular diagnostic technique based on real-time PCR was developed for the simultaneous detection of three of the most frequent causative agents of fungal opportunistic pneumonia in AIDS patients:
Pneumocystis jirovecii
,
Histoplasma capsulatum
, and
Cryptococcus neoformans
/
Cryptococcus gattii
. This technique was tested in cultured strains and in clinical samples from HIV-positive patients. The methodology used involved species-specific molecular beacon probes targeted to the internal transcribed spacer regions of the rDNA. An internal control was also included in each assay. The multiplex real-time PCR assay was tested in 24 clinical strains and 43 clinical samples from AIDS patients with proven fungal infection. The technique developed showed high reproducibility (
r
2
of >0.98) and specificity (100%). For
H. capsulatum
and
Cryptococcus
spp., the detection limits of the method were 20 and 2 fg of genomic DNA/20 μl reaction mixture, respectively, while for
P. jirovecii
the detection limit was 2.92 log
10
copies/20 μl reaction mixture. The sensitivity
in vitro
was 100% for clinical strains and 90.7% for clinical samples. The assay was positive for 92.5% of the patients. For one of the patients with proven histoplasmosis,
P. jirovecii
was also detected in a bronchoalveolar lavage sample. No PCR inhibition was detected. This multiplex real-time PCR technique is fast, sensitive, and specific and may have clinical applications.
Comparison of Two Assays for Molecular Determination of Rifampin Resistance in Clinical Samples from Patients with Buruli Ulcer Disease
Authors: Jansson Moritz , Beissner Marcus , Phillips Richard Odame , Badziklou Kossi , Piten Ebekalisai , Maman Issaka , Sarfo Fred Stephen , Huber Kristina Lydia , Rhomberg Agata , Symank Dominik , Wagner Magdalena , Wiedemann Franz , Nitschke Jörg , Banla Kere Abiba , Herbinger Karl-Heinz , Adjei Ohene , Löscher Thomas , Bretzel Gisela 
Published: January 2014

ABSTRACT

This study evaluates a novel assay for detecting rifampin resistance in clinical
Mycobacterium ulcerans
isolates. Although highly susceptible for PCR inhibitors in 50% of the samples tested, the assay was 100%
M. ulcerans
specific and yielded >98% analyzable sequences with a lower limit of detection of 100 to 200 copies of the target sequence.
Bacterial Lymphadenitis at a Major Referral Hospital in France from 2008 to 2012
Authors: Safont Marion , Angelakis Emmanouil , Richet Hervé , Lepidi Hubert , Fournier Pierre-Edouard , Drancourt Michel , Raoult Didier 
Published: January 2014

ABSTRACT

Lymph node enlargement is a common medical problem, and in a large number of patients, the causes of lymphadenopathy remain undiagnosed. We report a thorough microbiological analysis of 1,688 lymph node biopsy specimens collected in our bartonellosis reference center. We studied lymph node biopsy samples from patients with suspected regional infectious lymph node enlargement from January 2008 to December 2012. To evaluate a useful strategy for the diagnosis of infectious lymphadenitis, specimens were cultured and subjected to molecular assays. Histologic analysis was done when possible. A total of 642 (38%) biopsy specimens were infected with a bacterial agent, and quantitative PCR (qPCR) was significantly better than 16S rRNA gene PCR (
rrs
) for the detection of
Bartonella henselae
(
P
= 0.05),
Mycobacterium tuberculosis
(
P
= 0.05), and
Mycobacterium avium
(
P
= 0.007). Molecular assays were significantly better than bacterial cultures for the diagnosis of
Francisella tularensis
(
P
= 0.017) but were less effective for detecting
M. tuberculosis
(
P
= 0.004) and
M. avium
(
P
= 0.001). Histologic analysis was done for 412 lymph nodes, and 20% of these were compatible with an infectious lymphadenitis, whereas a neoplasm was found in 29% of these lymph nodes.
M. tuberculosis
was detected significantly more in female than in male patients (
P
= 0.01), and patients with cat scratch disease (CSD) were younger than patients with
M. tuberculosis
,
Tropheryma whipplei
, and
F. tularensis
. Negative
rrs
PCR does not exclude the diagnosis of infectious lymphadenitis. Histologic analysis of lymph node biopsy specimens is critical, as a diagnosis of infectious lymphadenitis does not preclude other concurrent diseases.
Prevalence of Mupirocin Resistance in Staphylococcus pseudintermedius
Authors: Godbeer Stacey M. , Gold Randi M. , Lawhon Sara D. 
Published: January 2014

ABSTRACT

In the United States, veterinary use of mupirocin is primarily limited to the treatment of canine pyoderma caused by methicillin-resistant
Staphylococcus pseudintermedius
(MRSP). In this study, only 1 of 581
S. pseudintermedius
isolates tested was resistant to mupirocin and carried the high-level mupirocin resistance gene,
ileS2
, on a plasmid.
Natural Single-Nucleotide Polymorphisms in the 3′ Region of the HIV-1
pol
Gene Modulate Viral Replication Ability
Authors: Nomaguchi Masako , Miyake Ariko , Doi Naoya , Fujiwara Sachi , Miyazaki Yasuyuki , Tsunetsugu-Yokota Yasuko , Yokoyama Masaru , Sato Hironori , Masuda Takao , Adachi Akio 
Published: January 2014

ABSTRACT

We previously showed that prototype macaque-tropic human immunodeficiency virus type 1 (HIV-1) acquired nonsynonymous growth-enhancing mutations within a narrow genomic region during the adaptation process in macaque cells. These adaptive mutations were clustered in the 3′ region of the
pol
gene, encoding a small portion of the C-terminal domain of integrase (IN). Mutations in HIV-1 IN have been reported to have pleiotropic effects on both the early and late phases in viral replication.
cis
-acting functions in the IN-coding sequence for viral gene expression have also been reported. We here demonstrated that the adaptive mutations promoted viral growth by increasing virion production with no positive effects on the early replication phase. Synonymous codon alterations in one of the adaptive mutations influenced virion production levels, which suggested nucleotide-dependent regulation. Indeed, when the single-nucleotide natural polymorphisms observed in the 3′ regions of 196 HIV-1/simian immunodeficiency virus (SIVcpz)
pol
genes (nucleotides [nt] 4895 to 4929 for HIV-1 NL4-3) were introduced into macaque- and human-tropic HIV-1 clones, more than half exhibited altered replication potentials. Moreover, single-nucleotide mutations caused parallel increases or decreases in the expression levels of viral late proteins and viral replication potentials. We also showed that the overall expression profiles of viral mRNAs were markedly changed by single-nucleotide mutations. These results demonstrate that the 3′ region of the HIV-1
pol
gene (nt 4895 to 4929) can alter viral replication potential by modulating the expression pattern of viral mRNAs in a nucleotide-dependent manner.

IMPORTANCE
Viruses have the plasticity to adapt themselves under various constraints. HIV-1 can mutate and evolve in growth-restrictive cells by acquiring adaptive changes in its genome. We have previously identified some growth-enhancing mutations in a narrow region of the IN-coding sequence, in which a number of
cis
-acting elements are located. We now focus on the virological significance of this
pol
gene region and the mechanistic basis underlying its effects on viral replication. We have found several naturally occurring synonymous mutations within this region that alter viral replication potentials. The effects caused by these natural single-nucleotide polymorphisms are linked to the definite expression patterns of viral mRNAs. We show here that the nucleotide sequence of the
pol
gene (nucleotides 4895 to 4929 for HIV-1 NL4-3) plays an important role in HIV-1 replication by modulating viral gene expression.
Human Papillomavirus E7 Oncoprotein Increases Production of the Anti-Inflammatory Interleukin-18 Binding Protein in Keratinocytes
Authors: Richards Kathryn H. , Doble Rosella , Wasson Christopher W. , Haider Mohammed , Blair G. Eric , Wittmann Miriam , Macdonald Andrew 
Published: January 2014

ABSTRACT
Human papillomavirus (HPV) can successfully evade the host immune response to establish a persistent infection. We show here that expression of the E7 oncoprotein in primary human keratinocytes results in increased production of interleukin-18 (IL-18) binding protein (IL-18BP). This anti-inflammatory cytokine binding protein is a natural antagonist of IL-18 and is necessary for skin homeostasis. We map increased IL-18BP production to the CR3 region of E7 and demonstrate that this ability is shared among E7 proteins from different HPV types. Furthermore, mutagenesis shows that increased IL-18BP production is mediated by a gamma-activated sequence (GAS) in the IL-18BP promoter. Importantly, the increased IL-18BP levels seen in E7-expressing keratinocytes are capable of diminishing IL-18-mediated CD4 lymphocyte activation. This study provides the first evidence for a virus protein that targets IL-18BP and further validates E7 as a key component of the HPV immune evasion armor.

IMPORTANCE
Infection with human papillomavirus is a leading cause of morbidity and mortality worldwide. This study demonstrates that the E7 protein increases production of the anti-inflammatory IL-18BP, a major regulator of epithelial homeostasis. A number of E7 proteins can increase IL-18BP production, and a region within the CR3 of E7 is necessary for mediating the increase. A consequence of increased IL-18BP production is a reduction in CD4-positive lymphocyte activation in response to IL-18 costimulation. These findings may shed light on the immune evasion abilities of HPV.
Recombinant Adeno-Associated Virus Utilizes Host Cell Nuclear Import Machinery To Enter the Nucleus
Authors: Nicolson Sarah C. , Samulski R. Jude 
Published: January 2014

ABSTRACT

Recombinant adeno-associated viral (rAAV) vectors have garnered much promise in gene therapy applications. However, widespread clinical use has been limited by transduction efficiency. Previous studies suggested that the majority of rAAV accumulates in the perinuclear region of cells, presumably unable to traffic into the nucleus. rAAV nuclear translocation remains ill-defined; therefore, we performed microscopy, genetic, and biochemical analyses
in vitro
in order to understand this mechanism. Lectin blockade of the nuclear pore complex (NPC) resulted in inhibition of nuclear rAAV2. Visualization of fluorescently labeled particles revealed that rAAV2 localized to importin-β-dense regions of cells in late trafficking steps. Additionally, small interfering RNA (siRNA) knockdown of importin-β partially inhibited rAAV2 nuclear translocation and inhibited transduction by 50 to 70%. Furthermore, coimmunopreciptation (co-IP) analysis revealed that capsid proteins from rAAV2 could interact with importin-β and that this interaction was sensitive to the small GTPase Ran. More importantly, mutations to key basic regions in the rAAV2 capsid severely inhibited interactions with importin-β. We tested several other serotypes and found that the extent of importin-β interaction varied, suggesting that different serotypes may utilize alternative import proteins for nuclear translocation. Co-IP and siRNA analyses were used to investigate the role of other karyopherins, and the results suggested that rAAV2 may utilize multiple import proteins for nuclear entry. Taken together, our results suggest that rAAV2 interacts with importin-β alone or in complex with other karyopherins and enters the nucleus via the NPC. These results may lend insight into the design of novel AAV vectors that have an enhanced nuclear entry capability and transduction potential.

IMPORTANCE
Use of recombinant adeno-associated viral (rAAV) vectors for gene therapy applications is limited by relatively low transduction efficiency, in part due to cellular barriers that hinder successful subcellular trafficking to the nucleus, where uncoating and subsequent gene expression occur. Nuclear translocation of rAAV has been regarded as a limiting step for successful transduction but it remains ill-defined. We explored potential nuclear entry mechanisms for rAAV2 and found that rAAV2 can utilize the classical nuclear import pathway, involving the nuclear pore complex, the small GTPase Ran, and cellular karyopherins. These results could lend insight into the rational design of novel rAAV vectors that can more efficiently translocate to the nucleus, which may lead to more efficient transduction.
Hijacking of RIG-I Signaling Proteins into Virus-Induced Cytoplasmic Structures Correlates with the Inhibition of Type I Interferon Responses
Authors: Santiago Felix W. , Covaleda Lina M. , Sanchez-Aparicio Maria T. , Silvas Jesus A. , Diaz-Vizarreta Ana C. , Patel Jenish R. , Popov Vsevolod , Yu Xue-jie , García-Sastre Adolfo , Aguilar Patricia V. 
Published: January 2014

ABSTRACT
Recognition of viral pathogens by the retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) family results in the activation of type I interferon (IFN) responses. To avoid this response, most viruses have evolved strategies that target different essential steps in the activation of host innate immunity. In this study, we report that the nonstructural protein NSs of the newly described severe fever with thrombocytopenia syndrome virus (SFTSV) is a potent inhibitor of IFN responses. The SFTSV NSs protein was found to inhibit the activation of the beta interferon (IFN-β) promoter induced by viral infection and by a RIG-I ligand. Astonishingly, we found that SFTSV NSs interacts with and relocalizes RIG-I, the E3 ubiquitin ligase TRIM25, and TANK-binding kinase 1 (TBK1) into SFTSV NSs-induced cytoplasmic structures. Interestingly, formation of these SFTSV NSs-induced structures occurred in the absence of the Atg7 gene, a gene essential for autophagy. Furthermore, confocal microscopy studies revealed that these SFTSV NSs-induced structures colocalize with Rab5 but not with Golgi apparatus or endoplasmic reticulum markers. Altogether, the data suggest that sequestration of RIG-I signaling molecules into endosome-like structures may be the mechanism used by SFTSV to inhibit IFN responses and point toward a novel mechanism for the suppression of IFN responses.

IMPORTANCE
The mechanism by which the newly described SFTSV inhibits host antiviral responses has not yet been fully characterized. In this study, we describe the redistribution of RIG-I signaling components into virus-induced cytoplasmic structures in cells infected with SFTSV. This redistribution correlates with the inhibition of host antiviral responses. Further characterization of the interplay between the viral protein and components of the IFN responses could potentially provide targets for the rational development of therapeutic interventions.
Functional Implications of the Binding Mode of a Human Conformation-Dependent V2 Monoclonal Antibody against HIV
Authors: Spurrier Brett , Sampson Jared , Gorny Miroslaw K. , Zolla-Pazner Susan , Kong Xiang-Peng 
Published: January 2014

ABSTRACTData from the RV144 HIV vaccine trial indicated that gp120 V2 antibodies were associated with a lower risk of infection; thus, the mapping of V2 epitopes can contribute to the design of an effective HIV vaccine. We solved the crystal structure of human monoclonal antibody (MAb) 2158, which targets a conformational V2 epitope overlapping the α4β7 integrin binding site, and constructed a full-length model of V1V2. Comparison of computational energy stability to experimental enzyme-linked immunosorbent assay (ELISA) results identified a hydrophobic core that stabilizes the V2 region for optimal 2158 binding, as well as residues that directly mediate side chain interactions with MAb 2158. These data define the binding surface recognized by MAb 2158 and offer a structural explanation for why a mismatched mutation at position 181 (I181X) in the V2 loop was associated with a higher vaccine efficiency in the RV144 clinical vaccine trial.IMPORTANCECorrelate analysis of the RV144 HIV-1 vaccine trial suggested that the presence of antibodies to the second variable region (V2) of HIV-1 gp120 was responsible for the modest protection observed in the trial. V2 is a highly variable and immunogenic region, and structural information on its antigenic landscape will be important for rational design of an effective HIV-1 vaccine. Using X-ray crystallography, computational design tools, and mutagenesis assays, we carried out a detailed and systematic investigation of the epitope recognition of human V2 MAb 2158 and demonstrated that its epitope region overlaps the integrin binding site within V2. In addition, we propose a structure-based mechanism for mismatching of the isoleucine at position 181 and the increased vaccine efficacy seen in the RV144 vaccine trial.
Novel Avian-Origin Influenza A (H7N9) Virus Attachment to the Respiratory Tract of Five Animal Models
Authors: Siegers Jurre Y. , Short Kirsty R. , Leijten Lonneke M. E. , de Graaf Miranda , Spronken Monique I. J. , Schrauwen Eefje J. A. , Marshall Nicolle , Lowen Anice C. , Gabriel Gülsah , Osterhaus Albert D. M. E. , Kuiken Thijs , van Riel Debby 
Published: January 2014

ABSTRACT
We determined the pattern of attachment of the avian-origin H7N9 influenza viruses A/Anhui/1/2013 and A/Shanghai/1/2013 to the respiratory tract in ferrets, macaques, mice, pigs, and guinea pigs and compared it to that in humans. The H7N9 attachment pattern in macaques, mice, and to a lesser extent pigs and guinea pigs resembled that in humans more closely than the attachment pattern in ferrets. This information contributes to our knowledge of the different animal models for influenza.
Chimeric Bovine/Human Parainfluenza Virus Type 3 Expressing Respiratory Syncytial Virus (RSV) F Glycoprotein: Effect of Insert Position on Expression, Replication, Immunogenicity, Stability, and Protection against RSV Infection
Authors: Liang Bo , Munir Shirin , Amaro-Carambot Emerito , Surman Sonja , Mackow Natalie , Yang Lijuan , Buchholz Ursula J. , Collins Peter L. , Schaap-Nutt Anne 
Published: January 2014

ABSTRACT

A recombinant chimeric bovine/human parainfluenza type 3 virus (rB/HPIV3) vector expressing the respiratory syncytial virus (RSV) fusion F glycoprotein previously exhibited disappointing levels of RSV F immunogenicity and genetic stability in children (D. Bernstein et al., Pediatr. Infect. Dis. J. 31:109–114, 2012; C.-F. Yang et al., Vaccine 31:2822–2827, 2013). To investigate parameters that might affect vaccine performance and stability, we constructed and characterized rB/HPIV3 viruses expressing RSV F from the first (pre-N), second (N-P), third (P-M), and sixth (HN-L) genome positions. There was a 30- to 69-fold gradient in RSV F expression from the first to the sixth position. The inserts moderately attenuated vector replication
in vitro
and in the upper and lower respiratory tracts of hamsters: this was not influenced by the level of RSV F expression and syncytium formation. Surprisingly, inserts in the second, third, and sixth positions conferred increased temperature sensitivity: this was greatest for the third position and was the most attenuating
in vivo
. Each rB/HPIV3 vector induced a high titer of neutralizing antibodies in hamsters against RSV and HPIV3. Protection against RSV challenge was greater for position 2 than for position 6. Evaluation of insert stability suggested that RSV F is under selective pressure to be silenced during vector replication
in vivo
, but this was not exacerbated by a high level of RSV F expression and generally involved a small percentage of recovered vector. Vector passaged
in vitro
accumulated mutations in the HN open reading frame, causing a dramatic increase in plaque size that may have implications for vaccine production and immunogenicity.

IMPORTANCE
The research findings presented here will be instrumental for improving the design of a bivalent pediatric vaccine for respiratory syncytial virus and parainfluenza virus type 3, two major causes of severe respiratory tract infection in infants and young children. Moreover, this knowledge has general application to the development and clinical evaluation of other mononegavirus vectors and vaccines.