bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of an Algorithmic Approach in Comparison with the Illumigene Assay for Laboratory Diagnosis of Clostridium difficile Infection
Authors: Walkty A. , Lagacé-Wiens P. R. S. , Manickam K. , Adam H. , Pieroni P. , Hoban D. , Karlowsky J. A. , Alfa M. 
Published: January 2013

ABSTRACT

The following three diagnostic algorithms were evaluated in comparison with the Illumigene assay as a stand-alone test for
Clostridium difficile
detection: glutamate dehydrogenase antigen screen (GDH) followed by toxin A/B antigen testing (Tox A/B) with the cell cytotoxicity assay for discordant specimens (algorithm 1), GDH followed by the Illumigene (algorithm 2), and GDH followed by Tox A/B with the Illumigene for discordant specimens (algorithm 3). A total of 428 stool specimens submitted to three clinical microbiology laboratories in Manitoba, Canada, for
C. difficile
detection between June 2011 and April 2012 were included in the study. The prevalence of
C. difficile
in the stool specimens was 14.7% (63/428) based on toxigenic culture (microbiologic reference standard). The sensitivity and specificity of the Illumigene for
C. difficile
detection were 73.0% and 99.7%, respectively. The corresponding sensitivities and specificities were 65.1% and 100.0% for algorithm 1, 68.3% and 100.0% for algorithm 2, and 69.8% and 100.0% for algorithm 3. Using algorithm 1, a cell cytotoxicity assay was required for toxin detection in 37% of positive tests, prolonging turnaround time. However, the predictive value of a positive test based on a clinical reference standard (all tests positive or cytotoxigenic culture positive and clinical disease on chart review) was slightly higher with algorithm 1 than with the Illumigene assay as a stand-alone test or as part of an algorithm (algorithms 2 and 3). Based on a reduction in turnaround time, simplicity, and acceptable sensitivity and specificity, we recommend algorithm 2 (screening with the GDH antigen test and confirmatory testing with the Illumigene).
Ciprofloxacin-Resistant Aeromonas hydrophila Cellulitis following Leech Therapy
Authors: Giltner Carmen L. , Bobenchik April M. , Uslan Daniel Z. , Deville Jaime G. , Humphries Romney M. 
Published: January 2013

ABSTRACT

We report a case of surgical site infection with ciprofloxacin-resistant
Aeromonas hydrophila
following leech therapy. Antimicrobial and genetic analyses of leech and patient isolates demonstrated that the resistant isolates originated from the leech gut microbiota. These data suggest that ciprofloxacin monotherapy as a prophylaxis regimen prior to leech therapy may not be effective in preventing infection.
Two Cases of Ruminococcus gnavus Bacteremia Associated with Diverticulitis
Authors: Hansen Sanne G. K. , Skov Marianne N. , Justesen Ulrik S. 
Published: January 2013

ABSTRACT

We report two cases of bacteremia with the anaerobic bacterium
Ruminococcus gnavus
. In both cases, the bacteremia was associated with diverticular disease. Preliminary conventional identification suggested peptostreptococci, and matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) analysis did not produce scores high enough for species identification. Finally, the bacteria were identified by 16S rRNA gene sequencing.
The Human Papillomavirus Type 8 E6 Protein Interferes with NOTCH Activation during Keratinocyte Differentiation
Authors: Meyers Jordan M. , Spangle Jennifer M. , Munger Karl 
Published: January 2013

ABSTRACT
Cutaneous β-human papillomavirus (β-HPV) E6 proteins inhibit NOTCH signaling by associating with the transcriptional coactivator MAML1. NOTCH has tumor suppressor activities in epithelial cells and is activated during keratinocyte differentiation. Here we report that HPV type 8 (HPV8) E6 subverts NOTCH activation during keratinocyte differentiation by inhibiting RBPJ/MAML1 transcriptional activator complexes at NOTCH target DNA. NOTCH inhibition impairs epithelial differentiation and may thus contribute to β-HPV replication and viral oncogenesis.
Infection of the Upper Respiratory Tract with Seasonal Influenza A(H3N2) Virus Induces Protective Immunity in Ferrets against Infection with A(H1N1)pdm09 Virus after Intranasal, but Not Intratracheal, Inoculation
Authors: Bodewes Rogier , Kreijtz Joost H. C. M. , van Amerongen Geert , Hillaire Marine L. B. , Vogelzang-van Trierum Stella E. , Nieuwkoop Nella J. , van Run Peter , Kuiken Thijs , Fouchier Ron A. M. , Osterhaus Albert D. M. E. , Rimmelzwaan Guus F. 
Published: January 2013

ABSTRACTThe clinical symptoms caused by infection with influenza A virus vary widely and depend on the strain causing the infection, the dose and route of inoculation, and the presence of preexisting immunity. In most cases, seasonal influenza A viruses cause relatively mild upper respiratory tract disease, while sometimes patients develop an acute severe pneumonia. Heterosubtypic immunity induced by previous infections with influenza A viruses may dampen the development of clinical symptoms caused by infection with influenza A viruses of another subtype, as is the case during influenza pandemics. Here we show that ferrets acquire protective immunity after infection of the upper respiratory tract with a seasonal influenza A(H3N2) virus against subsequent infection with influenza A(H1N1)pdm09 virus inoculated by the intranasal route. However, protective heterosubtypic immunity was afforded locally, since the prior infection with the A(H3N2) virus did not provide protection against the development of pneumonia induced after intratracheal inoculation with the A(H1N1)pdm09 virus. Interestingly, some of these animals developed more severe disease than that observed in naïve control animals. These findings are of interest in light of the development of so-called universal influenza vaccines that aim at the induction of cross-reactive T cell responses.
Structural Basis of Substrate Specificity and Protease Inhibition in Norwalk Virus
Authors: Muhaxhiri Zana , Deng Lisheng , Shanker Sreejesh , Sankaran Banumathi , Estes Mary K. , Palzkill Timothy , Song Yongcheng , Prasad B. V. Venkataram 
Published: January 2013

ABSTRACT
Norwalk virus (NV), the prototype human calicivirus, is the leading cause of nonbacterial acute gastroenteritis. The NV protease cleaves the polyprotein encoded by open reading frame 1 of the viral genome at five nonhomologous sites, releasing six nonstructural proteins that are essential for viral replication. The structural details of how NV protease recognizes multiple substrates are unclear. In our X-ray structure of an NV protease construct, we observed that the C-terminal tail, representing the native substrate positions P5 to P1, is inserted into the active site cleft of the neighboring protease molecule, providing atomic details of how NV protease recognizes a substrate. The crystallographic structure of NV protease with the C-terminal tail redesigned to mimic P4 to P1 of another substrate site provided further structural details on how the active site accommodates sequence variations in the substrates. Based on these structural analyses, substrate-based aldehyde inhibitors were synthesized and screened for inhibition potency. Crystallographic structures of the protease in complex with each of the three most potent inhibitors were determined. These structures showed concerted conformational changes in the S4 and S2 pockets of the protease to accommodate variations in the P4 and P2 residues of the substrate/inhibitor, which could be a mechanism for how the NV protease recognizes multiple sites in the polyprotein with differential affinities during virus replication. These structures further indicate that the mechanism of inhibition by these inhibitors involves covalent bond formation with the side chain of the conserved cysteine in the active site by nucleophilic addition, and such substrate-based aldehydes could be effective protease inhibitors.
Inhibition of the Host Translation Shutoff Response by Herpes Simplex Virus 1 Triggers Nuclear Envelope-Derived Autophagy
Authors: Radtke Kerstin , English Luc , Rondeau Christiane , Leib David , Lippé Roger , Desjardins Michel 
Published: January 2013

ABSTRACT
Macroautophagy is a cellular pathway that degrades intracellular pathogens and contributes to antigen presentation. Herpes simplex virus 1 (HSV-1) infection triggers both macroautophagy and an additional form of autophagy that uses the nuclear envelope as a source of membrane. The present study constitutes the first in-depth analysis of nuclear envelope-derived autophagy (NEDA). We established LC3a as a marker that allowed us to distinguish between NEDA and macroautophagy in both immunofluorescence and flow cytometry. NEDA was observed in many different cell types, indicating that it is a general response to HSV-1 infection. This autophagic pathway is known to depend on the viral protein γ34.5, which can inhibit macroautophagy via binding to beclin-1. Using mutant viruses, we were able to show that binding of beclin-1 by γ34.5 had no effect on NEDA, demonstrating that NEDA is regulated differently than macroautophagy. Instead, NEDA was triggered in response to γ34.5 binding to protein phosphatase 1α, an interaction used by the virus to prevent host cells from shutting off protein translation. NEDA was not triggered when late viral protein production was inhibited with acyclovir or hippuristanol, indicating that the accumulation of these proteins might stress infected cells. Interestingly, expression of the late viral protein gH was sufficient to rescue NEDA in the context of infection with a virus that otherwise does not support strong late viral protein expression. We argue that NEDA is a cellular stress response triggered late during HSV-1 infection and might compensate for the viral alteration of the macroautophagic response.
Structural and Functional Analysis of Coxsackievirus A9 Integrin α
v
β
6
Binding and Uncoating
Authors: Shakeel Shabih , Seitsonen Jani J. T. , Kajander Tommi , Laurinmäki Pasi , Hyypiä Timo , Susi Petri , Butcher Sarah J. 
Published: January 2013

ABSTRACT

Coxsackievirus A9 (CVA9) is an important pathogen of the
Picornaviridae
family. It utilizes cellular receptors from the integrin α
v
family for binding to its host cells prior to entry and genome release. Among the integrins tested, it has the highest affinity for α
v
β
6
, which recognizes the arginine-glycine-aspartic acid (RGD) loop present on the C terminus of viral capsid protein, VP1. As the atomic model of CVA9 lacks the RGD loop, we used surface plasmon resonance, electron cryo-microscopy, and image reconstruction to characterize the capsid-integrin interactions and the conformational changes on genome release. We show that the integrin binds to the capsid with nanomolar affinity and that the binding of integrin to the virion does not induce uncoating, thereby implying that further steps are required for release of the genome. Electron cryo-tomography and single-particle image reconstruction revealed variation in the number and conformation of the integrins bound to the capsid, with the integrin footprint mapping close to the predicted site for the exposed RGD loop on VP1. Comparison of empty and RNA-filled capsid reconstructions showed that the capsid undergoes conformational changes when the genome is released, so that the RNA-capsid interactions in the N termini of VP1 and VP4 are lost, VP4 is removed, and the capsid becomes more porous, as has been reported for poliovirus 1, human rhinovirus 2, enterovirus 71, and coxsackievirus A7. These results are important for understanding the structural basis of integrin binding to CVA9 and the molecular events leading to CVA9 cell entry and uncoating.
Ribosomal Protein P0 Promotes
Potato Virus A
Infection and Functions in Viral Translation Together with VPg and eIF(iso)4E
Authors: Hafrén Anders , Eskelin Katri , Mäkinen Kristiina 
Published: January 2013

ABSTRACT

We report here that the acidic ribosomal protein P0 is a component of the membrane-associated
Potato virus A
(PVA) ribonucleoprotein complex. As a constituent of the ribosomal stalk, P0 functions in translation. Although the ribosomal stalk proteins P0, P1, P2, and P3 are all important for PVA infection, P0 appears to have a distinct role from those of the other stalk proteins in infection. Our results indicate that P0 also regulates viral RNA functions as an extraribosomal protein. We reported previously that PVA RNA can be targeted by VPg to a specific gene expression pathway that protects the viral RNA from degradation and facilitates its translation. Here, we show that P0 is essential for this activity of VPg, similar to eIF4E/eIF(iso)4E. We also demonstrate that VPg, P0, and eIF(iso)4E synergistically enhance viral translation. Interestingly, the positive effects of VPg and P0 on viral translation were negatively correlated with the cell-to-cell spread of infection, suggesting that these processes may compete for viral RNA.
ComprehensiveIn VitroAnalysis of Simian Retrovirus Type 4 Susceptibility to Antiretroviral Agents
Authors: Togami Hiroaki , Shimura Kazuya , Okamoto Munehiro , Yoshikawa Rokusuke , Miyazawa Takayuki , Matsuoka Masao 
Published: January 2013

ABSTRACTSimian retrovirus type 4 (SRV-4), a simian type D retrovirus, naturally infects cynomolgus monkeys, usually without apparent symptoms. However, some infected monkeys presented with an immunosuppressive syndrome resembling that induced by simian immunodeficiency virus infection. Antiretrovirals with inhibitory activity against SRV-4 are considered to be promising agents to combat SRV-4 infection. However, although some antiretrovirals have been reported to have inhibitory activity against SRV-1 and SRV-2, inhibitors with anti-SRV-4 activity have not yet been studied. In this study, we identified antiretroviral agents with anti-SRV-4 activity from a panel of anti-human immunodeficiency virus (HIV) drugs using a robustin vitroluciferase reporter assay. Among these, two HIV reverse transcriptase inhibitors, zidovudine (AZT) and tenofovir disoproxil fumarate (TDF), potently inhibited SRV-4 infection within a submicromolar to nanomolar range, which was similar to or higher than the activities against HIV-1, Moloney murine leukemia virus, and feline immunodeficiency virus. In contrast, nonnucleoside reverse transcriptase inhibitors and protease inhibitors did not exhibit any activities against SRV-4. Although both AZT and TDF effectively inhibited cell-free SRV-4 transmission, they exhibited only partial inhibitory activities against cell-to-cell transmission. Importantly, one HIV integrase strand transfer inhibitor, raltegravir (RAL), potently inhibited single-round infection as well as cell-free and cell-to-cell SRV-4 transmission. These findings indicate that viral expansion routes impact the inhibitory activity of antiretrovirals against SRV-4, while only RAL is effective in suppressing both the initial SRV-4 infection and subsequent SRV-4 replication.
RNA Transfer from Poliovirus 135S Particles across Membranes Is Mediated by Long Umbilical Connectors
Authors: Strauss Mike , Levy Hazel C. , Bostina Mihnea , Filman David J. , Hogle James M. 
Published: January 2013

ABSTRACT
During infection, the binding of poliovirus to its cell surface receptor at 37°C triggers an expansion of the virus in which internal polypeptides that bind to membranes are externalized. Subsequently, in a poorly understood process, the viral RNA genome is transferred directly across an endosomal membrane, and into the host cell cytoplasm, to initiate infection. Here, cryoelectron tomography demonstrates the results of 37°C warming of a poliovirus-receptor-liposome model complex that was produced using Ni-nitrilotriacetic acid lipids and His-tagged receptor ectodomains. In total, 651 subtomographic volumes were aligned, classified, and averaged to obtain detailed pictures, showing both the conversion of virus into its expanded form and the passage of RNA into intact liposomes. Unexpectedly, the virus and membrane surfaces were located ∼50 Å apart, with the 5-fold axis tilted away from the perpendicular, and the solvent spaces between them were spanned by either one or two long “umbilical” density features that lie at an angle to the virus and membrane. The thinner connector, which sometimes appears alone, is 28 to 30 Å in diameter and has a footprint on the virus surface located close to either a 5-fold or a 3-fold axis. The broader connector has a footprint near the quasi-3-fold hole that opens upon virus expansion and is hypothesized to include RNA, shielded from enzymatic degradation by polypeptides that include the N-terminal extension of VP1 and capsid protein VP4. The implications of these observations for the mechanism of RNase-protected RNA transfer in picornaviruses are discussed.
An Antiviral Role for Antimicrobial Peptides during the Arthropod Response to Alphavirus Replication
Authors: Huang Zhijing , Kingsolver Megan B. , Avadhanula Vasanthi , Hardy Richard W. 
Published: January 2013

ABSTRACT

Alphaviruses establish a persistent infection in arthropod vectors which is essential for the effective transmission of the virus to vertebrate hosts. The development of persistence in insects is not well understood, although it is thought to involve the innate immune response. Using a transgenic fly system expressing a self-replicating viral RNA genome analog, we have previously demonstrated antiviral roles of the
Drosophila
Imd (immune deficiency) and Jak-STAT innate immunity pathways in response to alphavirus replication. In the present study, comparative microarray analysis of flies harboring an alphavirus replicon and control green fluorescent protein flies identified 95 SINrep-sensitive genes. Furthermore, a subset of these genes is regulated by Rel or STAT transcription factors of the Imd and Jak-STAT pathways, respectively. We identified two antimicrobial peptide genes,
attC
and
dptB
, which are SINrep sensitive and regulated by STAT and Rel, respectively. SINrep flies heterozygous for
attC
had an increased viral RNA level, while knocking down
dptB
in SINrep flies resulted in impaired development. When injected with whole virus, the double-stranded RNA knockdowns of either
attC
or
dptB
showed a significant increase in virus titers. Our data demonstrate an antiviral response involving the Imd and Jak-STAT mediated expression of
dptB
and
attC
.
Chromatin Immunoprecipitation and Microarray Analysis Suggest Functional Cooperation between Kaposi's Sarcoma-Associated Herpesvirus ORF57 and K-bZIP
Authors: Hunter Olga V. , Sei Emi , Richardson R. Blake , Conrad Nicholas K. 
Published: January 2013

ABSTRACT

The Kaposi's sarcoma-associated herpesvirus (KSHV) open reading frame 57 (ORF57)-encoded protein (Mta) is a multifunctional regulator of viral gene expression. ORF57 is essential for viral replication, so elucidation of its molecular mechanisms is important for understanding KSHV infection. ORF57 has been implicated in nearly every aspect of viral gene expression, including transcription, RNA stability, splicing, export, and translation. Here we demonstrate that ORF57 interacts with the KSHV K-bZIP protein
in vitro
and in cell extracts from lytically reactivated infected cells. To further test the biological relevance of the interaction, we performed a chromatin immunoprecipitation and microarray (ChIP-chip) analysis using anti-ORF57 antibodies and a KSHV tiling array. The results revealed four specific areas of enrichment, including the ORF4 and K8 (K-bZIP) promoters, as well as oriLyt, all of which interact with K-bZIP. In addition, ORF57 associated with DNA corresponding to the PAN RNA transcribed region, a known posttranscriptional target of ORF57. All of the peaks were RNase insensitive, demonstrating that ORF57 association with the viral genome is unlikely to be mediated exclusively by an RNA tether. Our data demonstrate that ORF57 associates with the viral genome by using at least two modes of recruitment, and they suggest that ORF57 and K-bZIP coregulate viral gene expression during lytic infection.
Structural and Thermodynamic Basis of Amprenavir/Darunavir and Atazanavir Resistance in HIV-1 Protease with Mutations at Residue 50
Authors: Mittal Seema , Bandaranayake Rajinthna M. , King Nancy M. , Prabu-Jeyabalan Moses , Nalam Madhavi N. L. , Nalivaika Ellen A. , Kurt Yilmaz Nese , Schiffer Celia A. 
Published: January 2013

ABSTRACT
Drug resistance occurs through a series of subtle changes that maintain substrate recognition but no longer permit inhibitor binding. In HIV-1 protease, mutations at I50 are associated with such subtle changes that confer differential resistance to specific inhibitors. Residue I50 is located at the protease flap tips, closing the active site upon ligand binding. Under selective drug pressure, I50V/L substitutions emerge in patients, compromising drug susceptibility and leading to treatment failure. The I50V substitution is often associated with amprenavir (APV) and darunavir (DRV) resistance, while the I50L substitution is observed in patients failing atazanavir (ATV) therapy. To explain how APV, DRV, and ATV susceptibility are influenced by mutations at residue 50 in HIV-1 protease, structural and binding thermodynamics studies were carried out on I50V/L-substituted protease variants in the compensatory mutation A71V background. Reduced affinity to both I50V/A71V and I50L/A71V double mutants is largely due to decreased binding entropy, which is compensated for by enhanced enthalpy for ATV binding to I50V variants and APV binding to I50L variants, leading to hypersusceptibility in these two cases. Analysis of the crystal structures showed that the substitutions at residue 50 affect how APV, DRV, and ATV bind the protease with altered van der Waals interactions and that the selection of I50V versus I50L is greatly influenced by the chemical moieties at the P1 position for APV/DRV and the P2 position for ATV. Thus, the varied inhibitor susceptibilities of I50V/L protease variants are largely a direct consequence of the interdependent changes in protease inhibitor interactions.
The Myeloid Transcription Factor GATA-2 Regulates the Viral UL144 Gene during Human Cytomegalovirus Latency in an Isolate-Specific Manner
Authors: Poole Emma , Walther Anett , Raven Kathy , Benedict Christopher A. , Mason Gavin M. , Sinclair John 
Published: January 2013

ABSTRACTIt is generally accepted that, following primary infection, human cytomegalovirus (HCMV) establishes lifelong latency in CD34+progenitor cells and other derivative cells of the myeloid lineage. In this study, we show that the viral UL144 gene is expressed during latent infection in two cell types of the myeloid lineage, CD34+and CD14+monocytes, and that the UL144 protein is functional in latently infected monocytes. However, this latency-associated expression of UL144 occurs only in certain isolates of HCMV and depends on the presence of functional GATA-2 transcription factor binding sites in theUL144promoter, in contrast to the viral latency-associated geneLUNA, which we also show is regulated by GATA-2 but expressed uniformly during latent infection independent of the virus isolate. Taken together, these data suggest that the HCMV latency-associated transcriptome may be virus isolate specific and dependent on the repertoire of transcription factor binding sites in the promoters of latency-associated genes.