bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of GBF1 as a Cellular Factor Required for Hepatitis C Virus RNA Replication
Authors: Goueslain Lucie , Alsaleh Khaled , Horellou Pauline , Roingeard Philippe , Descamps Véronique , Duverlie Gilles , Ciczora Yann , Wychowski Czeslaw , Dubuisson Jean , Rouillé Yves 
Published: November 2009

ABSTRACT
In infected cells, hepatitis C virus (HCV) induces the formation of membrane alterations referred to as membranous webs, which are sites of RNA replication. In addition, HCV RNA replication also occurs in smaller membrane structures that are associated with the endoplasmic reticulum. However, cellular mechanisms involved in the formation of HCV replication complexes remain largely unknown. Here, we used brefeldin A (BFA) to investigate cellular mechanisms involved in HCV infection. BFA acts on cell membranes by interfering with the activation of several members of the family of ADP-ribosylation factors (ARF), which can lead to a wide range of inhibitory actions on membrane-associated mechanisms of the secretory and endocytic pathways. Our data show that HCV RNA replication is highly sensitive to BFA. Individual knockdown of the cellular targets of BFA using RNA interference and the use of a specific pharmacological inhibitor identified GBF1, a guanine nucleotide exchange factor for small GTPases of the ARF family, as a host factor critically involved in HCV replication. Furthermore, overexpression of a BFA-resistant GBF1 mutant rescued HCV replication in BFA-treated cells, indicating that GBF1 is the BFA-sensitive factor required for HCV replication. Finally, immunofluorescence and electron microscopy analyses indicated that BFA does not block the formation of membranous web-like structures induced by expression of HCV proteins in a nonreplicative context, suggesting that GBF1 is probably involved not in the formation of HCV replication complexes but, rather, in their activity. Altogether, our results highlight a functional connection between the early secretory pathway and HCV RNA replication.
The Full-Length Isoform of Human Papillomavirus 16 E6 and Its Splice Variant E6* Bind to Different Sites on the Procaspase 8 Death Effector Domain
Authors: Tungteakkhun Sandy S. , Filippova Maria , Fodor Nadja , Duerksen-Hughes Penelope J. 
Published: November 2009

ABSTRACT

Human papillomavirus 16 is a causative agent of most cases of cervical cancer and has also been implicated in the development of some head and neck cancers. The early viral E6 gene codes for two alternatively spliced isoforms, E6
large
and E6*. We have previously demonstrated the differential effects of E6
large
and E6* binding on the expression and stability of procaspase 8, a key mediator of the apoptotic pathway. Additionally, we have reported that E6 binds to the FADD death effector domain (DED) at a novel E6 binding domain. Sequence similarities between the FADD and procaspase 8 DEDs suggested a specific region for E6
large
/procaspase 8 binding, which was subsequently confirmed by mutational analysis as well as by the ability of peptides capable of blocking E6/FADD binding to also block E6
large
/caspase 8 binding. However, the binding of the smaller isoform, E6*, to procaspase 8 occurs at a different region, as deletion and point mutations that disrupt E6
large
/caspase 8 DED binding do not disrupt E6*/caspase 8 DED binding. In addition, peptide inhibitors that can block E6
large
/procaspase 8 binding do not affect the binding of E6* to procaspase 8. These results demonstrate that the residues that mediate E6*/procaspase 8 DED binding localize to a different region on the protein and employ a separate binding motif. This provides a molecular explanation for our initial findings that the two E6 isoforms affect procaspase 8 stability in an opposing manner.
Extrachromosomal Histone H2B Mediates Innate Antiviral Immune Responses Induced by Intracellular Double-Stranded DNA
Authors: Kobiyama Kouji , Takeshita Fumihiko , Jounai Nao , Sakaue-Sawano Asako , Miyawaki Atsushi , Ishii Ken J. , Kawai Taro , Sasaki Shin , Hirano Hisashi , Ishii Norihisa , Okuda Kenji , Suzuki Koichi 
Published: November 2009

ABSTRACT

Fragments of double-stranded DNA (dsDNA) forming a right-handed helical structure (B-DNA) stimulate cells to produce type I interferons (IFNs). While an adaptor molecule, IFN-β promoter stimulator 1 (IPS-1), mediates dsDNA-induced cellular signaling in human cells, the underlying molecular mechanism is not fully understood. Here, we demonstrate that the extrachromosomal histone H2B mediates innate antiviral immune responses in human cells. H2B physically interacts with IPS-1 through the association with a newly identified adaptor, CIAO (
C
OOH-terminal
i
mportin 9-related
a
daptor
o
rganizing histone H2B and IPS-1), to transmit the cellular signaling for dsDNA but not immunostimulatory RNA. Extrachromosomal histone H2B was biologically crucial for cell-autonomous responses to protect against multiplication of DNA viruses but not an RNA virus. Thus, the present findings provide evidence indicating that the extrachromosomal histone H2B is engaged in the signaling pathway initiated by dsDNA to trigger antiviral innate immune responses.
Herpes Simplex Virus Type 1 (HSV-1)-Induced Apoptosis in Human Dendritic Cells as a Result of Downregulation of Cellular FLICE-Inhibitory Protein and Reduced Expression of HSV-1 Antiapoptotic Latency-Associated Transcript Sequences
Authors: Kather Angela , Raftery Martin J. , Devi-Rao Gayathri , Lippmann Juliane , Giese Thomas , Sandri-Goldin Rozanne M. , Schönrich Günther 
Published: November 2009

ABSTRACTHerpes simplex virus type 1 (HSV-1) is one of the most frequent and successful human pathogens. It targets immature dendritic cells (iDCs) to interfere with the antiviral immune response. The mechanisms underlying apoptosis of HSV-1-infected iDCs are not fully understood. Previously, we have shown that HSV-1-induced apoptosis of iDCs is associated with downregulation of the cellular FLICE-inhibitory protein (c-FLIP), a potent inhibitor of caspase-8-mediated apoptosis. In this study, we prove that HSV-1 induces degradation of c-FLIP in a proteasome-independent manner. In addition, by using c-FLIP-specific small interfering RNA (siRNA) we show for the first time that downregulation of c-FLIP expression is sufficient to drive uninfected iDCs into apoptosis, underlining the importance of this molecule for iDC survival. Surprisingly, we also observed virus-induced c-FLIP downregulation in epithelial cells and many other cell types that do not undergo apoptosis after HSV-1 infection. Microarray analyses revealed that HSV-1-encoded latency-associated transcript (LAT) sequences, which can substitute for c-FLIP as an inhibitor of caspase-8-mediated apoptosis, are much less abundant in iDCs as compared to epithelial cells. Finally, iDCs infected with an HSV-1 LAT knockout mutant showed increased apoptosis when compared to iDCs infected with the corresponding wild-type HSV-1. Taken together, our results demonstrate that apoptosis of HSV-1-infected iDCs requires both c-FLIP downregulation and diminished expression of viral LAT.
Hepatitis C Virus (HCV) Sequence Variation Induces an HCV-Specific T-Cell Phenotype Analogous to Spontaneous Resolution
Authors: Kasprowicz Victoria , Kang Yu-Hoi , Lucas Michaela , Schulze zur Wiesch Julian , Kuntzen Thomas , Fleming Vicki , Nolan Brian E. , Longworth Steven , Berical Andrew , Bengsch Bertram , Thimme Robert , Lewis-Ximenez Lia , Allen Todd M. , Kim Arthur Y. , Klenerman Paul , Lauer Georg M. 
Published: November 2009

ABSTRACT

Hepatitis C virus (HCV)-specific CD8
+
T cells in persistent HCV infection are low in frequency and paradoxically show a phenotype associated with controlled infections, expressing the memory marker CD127. We addressed to what extent this phenotype is dependent on the presence of cognate antigen. We analyzed virus-specific responses in acute and chronic HCV infections and sequenced autologous virus. We show that CD127 expression is associated with decreased antigenic stimulation after either viral clearance or viral variation. Our data indicate that most CD8 T-cell responses in chronic HCV infection do not target the circulating virus and that the appearance of HCV-specific CD127
+
T cells is driven by viral variation.
Identification of the Cellular Prohibitin 1/Prohibitin 2 Heterodimer as an Interaction Partner of the C-Terminal Cytoplasmic Domain of the HIV-1 Glycoprotein
Authors: Emerson Vanessa , Holtkotte Denise , Pfeiffer Tanya , Wang I-Hsuan , Schnölzer Martina , Kempf Tore , Bosch Valerie 
Published: November 2009

ABSTRACTOur studies aim to elucidate the functions carried out by the very long, and in its length highly conserved, C-terminal cytoplasmic domain (Env-CT) of the HIV-1 glycoprotein. Mass spectrometric analysis of cellular proteins bound to a tagged version of the HIV Env-CT led to the identification of the prohibitin 1 and 2 proteins (Phb1 and Phb2). These ubiquitously expressed proteins, which exist as stable heterodimers, have been shown to have multiple functions within cells and to localize to multiple cellular and extracellular compartments. The specificity of binding of the Phb1/Phb2 complex to the Env-CT was confirmed in various manners, including coimmunoprecipitation with authentic provirally encoded, full-length Env. Strong binding was dependent on Env residues 790 to 800 and could be severely inhibited by the double mutation L799R/L800Q but not by mutation of these amino acids individually. Analysis of the respective mutant virions revealed that their different abilities to bind Phb1/Phb2 correlated with their replicative properties. Thus, mutated virions with single mutations [HIV-Env-(L799R) and HIV-Env-(L800Q)] replicated similarly to wild-type HIV, but HIV-Env-(L799R/L800Q) virions, which cannot bind Phb1/Phb2, exhibited a cell-dependent replicative phenotype similar to that of HIV-Env-Tr712, lacking the entire Env-CT domain. Thus, replicative spread was achieved, although somewhat delayed, in “permissive” MT-4 cells but failed to occur in “nonpermissive” H9 T cells. These results point to binding of the Phb1/Phb2 complex to the Env-CT as being of importance for replicative spread in nonpermissive cells, possibly by modulating critical Phb-dependent cellular process(es).
Envelope Vaccination Shapes Viral Envelope Evolution following Simian Immunodeficiency Virus Infection in Rhesus Monkeys
Authors: Basavapathruni Aravind , Yeh Wendy W. , Coffey Rory T. , Whitney James B. , Hraber Peter T. , Giri Ayush , Korber Bette T. , Rao Srinivas S. , Nabel Gary J. , Mascola John R. , Seaman Michael S. , Letvin Norman L. 
Published: November 2009

ABSTRACT

The evolution of envelope mutations by replicating primate immunodeficiency viruses allows these viruses to escape from the immune pressure mediated by neutralizing antibodies. Vaccine-induced anti-envelope antibody responses may accelerate and/or alter the specificity of the antibodies, thus shaping the evolution of envelope mutations in the replicating virus. To explore this possibility, we studied the neutralizing antibody response and the envelope sequences in rhesus monkeys vaccinated with either
gag
-
pol
-
nef
immunogens or
gag
-
pol
-
nef
immunogens in combination with
env
and then infected with simian immunodeficiency virus (SIV). Using a pseudovirion neutralization assay, we demonstrate that envelope vaccination primed for an accelerated neutralizing antibody response following virus challenge. To monitor viral envelope evolution in these two cohorts of monkeys, full-length envelopes from plasma virus isolated at weeks 37 and 62 postchallenge were sequenced by single genome amplification to identify sites of envelope mutations. We show that
env
vaccination was associated with a change in the pattern of envelope mutations. Prevalent mutations in sequences from
gag
-
pol
-
nef
vaccinees included deletions in both variable regions 1 and 4 (V1 and V4), whereas deletions in the
env
vaccinees occurred only in V1. These data show that
env
vaccination altered the focus of the antibody-mediated selection pressure on the evolution of envelope following SIV challenge.
Attenuation of Vesicular Stomatitis Virus Encephalitis through MicroRNA Targeting
Authors: Kelly Elizabeth J. , Nace Rebecca , Barber Glen N. , Russell Stephen J. 
Published: November 2009

ABSTRACT
Vesicular stomatitis virus (VSV) has long been regarded as a promising recombinant vaccine platform and oncolytic agent but has not yet been tested in humans because it causes encephalomyelitis in rodents and primates. Recent studies have shown that specific tropisms of several viruses could be eliminated by engineering microRNA target sequences into their genomes, thereby inhibiting spread in tissues expressing cognate microRNAs. We therefore sought to determine whether microRNA targets could be engineered into VSV to ameliorate its neuropathogenicity. Using a panel of recombinant VSVs incorporating microRNA target sequences corresponding to neuron-specific or control microRNAs (in forward and reverse orientations), we tested viral replication kinetics in cell lines treated with microRNA mimics, neurotoxicity after direct intracerebral inoculation in mice, and antitumor efficacy. Compared to picornaviruses and adenoviruses, the engineered VSVs were relatively resistant to microRNA-mediated inhibition, but neurotoxicity could nevertheless be ameliorated significantly using this approach, without compromise to antitumor efficacy. Neurotoxicity was most profoundly reduced in a virus carrying four tandem copies of a neuronal mir125 target sequence inserted in the 3′-untranslated region of the viral polymerase (L) gene.
Sequential Recruitment of the Endoplasmic Reticulum and Chloroplasts for Plant Potyvirus Replication
Authors: Wei Taiyun , Huang Tyng-Shyan , McNeil Jamie , Laliberté Jean-François , Hong Jian , Nelson Richard S. , Wang Aiming 
Published: November 2009

ABSTRACT
The replication of positive-strand RNA viruses occurs in cytoplasmic membrane-bound virus replication complexes (VRCs). Depending on the virus, distinct cellular organelles such as the endoplasmic reticulum (ER), chloroplast, mitochondrion, endosome, and peroxisome are recruited for the formation of VRC-associated membranous structures. Previously, the 6,000-molecular-weight protein (6K) of plant potyviruses was shown to be an integral membrane protein that induces the formation of 6K-containing membranous vesicles at endoplasmic reticulum (ER) exit sites for potyvirus genome replication. Here, we present evidence that the 6K-induced vesicles predominantly target chloroplasts, where they amalgamate and induce chloroplast membrane invaginations. The vesicular transport pathway and actomyosin motility system are involved in the trafficking of the 6K vesicles from the ER to chloroplasts. Viral RNA, double-stranded RNA, and viral replicase components are concentrated at the 6K vesicles that associate with chloroplasts in infected cells, suggesting that these chloroplast-bound 6K vesicles are the site for potyvirus replication. Taken together, these results suggest that plant potyviruses sequentially recruit the ER and chloroplasts for their genome replication.
Residues in the Heptad Repeat A Region of the Fusion Protein Modulate the Virulence of Sendai Virus in Mice
Authors: Luque Laura E. , Bridges Olga A. , Mason John N. , Boyd Kelli L. , Portner Allen , Russell Charles J. 
Published: November 2009

ABSTRACTWhile the molecular basis of fusion (F) protein refolding during membrane fusion has been studied extensively in vitro, little is known about the biological significance of membrane fusion activity in parainfluenza virus replication and pathogenesis in vivo. Two recombinant Sendai viruses, F-L179V and F-K180Q, were generated that contain F protein mutations in the heptad repeat A region of the ectodomain, a region of the protein known to regulate F protein activation. In vitro, the F-L179V virus caused increased syncytium formation (cell-cell membrane fusion) yet had a rate of replication and levels of F protein expression and cleavage similar to wild-type virus. The F-K180Q virus had a reduced replication rate along with reduced levels of F protein expression, cleavage, and fusogenicity. In DBA/2 mice, the hyperfusogenic F-L179V virus induced greater morbidity and mortality than wild-type virus, while the attenuated F-K180Q virus was much less pathogenic. During the first week of infection, virus replication and inflammation in the lungs were similar for wild-type and F-L179V viruses. After approximately 1 week of infection, the clearance of F-L179V virus was delayed, and more extensive interstitial inflammation and necrosis were observed in the lungs, affecting entire lobes of the lungs and having significantly greater numbers of syncytial cell masses in alveolar spaces on day 10. On the other hand, the slower-growing F-K180Q virus caused much less extensive inflammation than wild-type virus, presumably due to its reduced replication rate, and did not cause observable syncytium formation in the lungs. Overall, the results show that residues in the heptad repeat A region of the F protein modulate the virulence of Sendai virus in mice by influencing both the spread and clearance of the virus and the extent and severity of inflammation. An understanding of how the F protein contributes to infection and inflammation in vivo may assist in the development of antiviral therapies against respiratory paramyxoviruses.
ARGOS — A VIDEO SURVEILLANCE SYSTEM FOR BOAT TRAFFIC MONITORING IN VENICE
Authors: BLOISI DOMENICO , IOCCHI LUCA 
Published: November 2009

Visual surveillance in dynamic scenes is currently one of the most active research topics in computer vision, many existing applications are available. However, difficulties in realizing effective video surveillance systems that are robust to the many different conditions that arise in real environments, make the actual deployment of such systems very challenging. In this article, we present a real, unique and pioneer video surveillance system for boat traffic monitoring, ARGOS. The system runs continuously 24 hours a day, 7 days a week, day and night in the city of Venice (Italy) since 2007 and it is able to build a reliable background model of the water channel and to track the boats navigating the channel with good accuracy in real-time. A significant experimental evaluation, reported in this article, has been performed in order to assess the real performance of the system.
STOCHASTIC GALERKIN DISCRETIZATION OF THE LOG-NORMAL ISOTROPIC DIFFUSION PROBLEM
Authors: GITTELSON C. J. 
Published: November 2009

The stochastic Galerkin method is developed for the isotropic diffusion equation with an unbounded random diffusion coefficient. The logarithm of the diffusion coefficient is assumed to be an infinite series of Gaussian random variables. Well-posed weak formulations of the model problem are derived on standard Bochner–Lebesgue spaces. The Galerkin solution is shown to be almost quasi-optimal in the sense that the error of the Galerkin projection can be estimated by a best approximation error in a slightly stronger norm. As a result, convergence analysis of the stochastic Galerkin method is reduced to the problem of approximating the Hermite coefficients of the exact solution by standard finite elements.
Intraoperative Evaluation of Breast Tumor Margins with Optical Coherence Tomography
Authors: Nguyen Freddy T. , Zysk Adam M. , Chaney Eric J. , Kotynek Jan G. , Oliphant Uretz J. , Bellafiore Frank J. , Rowland Kendrith M. , Johnson Patricia A. , Boppart Stephen A. 
Published: November 2009

Abstract
As breast cancer screening rates increase, smaller and more numerous lesions are being identified earlier, leading to more breast-conserving surgical procedures. Achieving a clean surgical margin represents a technical challenge with important clinical implications. Optical coherence tomography (OCT) is introduced as an intraoperative high-resolution imaging technique that assesses surgical breast tumor margins by providing real-time microscopic images up to 2 mm beneath the tissue surface. In a study of 37 patients split between training and study groups, OCT images covering 1 cm2 regions were acquired from surgical margins of lumpectomy specimens, registered with ink, and correlated with corresponding histologic sections. A 17-patient training set used to establish standard imaging protocols and OCT evaluation criteria showed that areas of higher scattering tissue with a heterogeneous pattern were indicative of tumor cells and tumor tissue in contrast to lower scattering adipocytes found in normal breast tissue. The remaining 20 patients were enrolled into the feasibility study. Of these lumpectomy specimens, 11 were identified with a positive or close surgical margin and 9 were identified with a negative margin under OCT. Based on histologic findings, 9 true positives, 9 true negatives, 2 false positives, and 0 false negatives were found, yielding a sensitivity of 100% and specificity of 82%. These results show the potential of OCT as a real-time method for intraoperative margin assessment in breast-conserving surgeries. [Cancer Res 2009;69(22):8790–6]
Length Scales of the Neutral Wind Profile over Homogeneous Terrain
Authors: Peña Alfredo , Gryning Sven-Erik , Mann Jakob , Hasager Charlotte B. 
Published: November 2009

AbstractThe wind speed profile for the neutral boundary layer is derived for a number of mixing-length parameterizations, which account for the height of the boundary layer. The wind speed profiles show good agreement with the reanalysis of the Leipzig wind profile (950 m high) and with combined cup–sonic anemometer and lidar measurements (300 m high) performed over flat and homogeneous terrain at Høvsøre, Denmark. In the surface layer, the mixing-length parameterizations agree well with the traditional surface-layer theory, but the wind speed profile is underestimated when the surface-layer scaling is extended to the entire boundary layer, demonstrating the importance of the boundary layer height as a scaling parameter. The turbulence measurements, performed up to 160-m height only at the Høvsøre site, provide the opportunity to derive the spectral-length scales from two spectral models. Good agreement is found between the behaviors of the mixing- and spectral-length scales.
Quantifying Interagency Differences in Tropical Cyclone Best-Track Wind Speed Estimates
Authors: Knapp Kenneth R. , Kruk Michael C. 
Published: November 2009

Abstract
Numerous agencies around the world perform postseason analysis of tropical cyclone position and intensity, a process described as “best tracking.” However, this process is temporally and spatially inhomogeneous because data availability, operational techniques, and knowledge have changed over time and differ among agencies. The net result is that positions and intensities often vary for any given storm for different agencies. In light of these differences, it is imperative to analyze and document the interagency differences in tropical cyclone intensities. To that end, maximum sustained winds from different agencies were compared using data from the International Best Track Archive for Climate Stewardship (IBTrACS) global tropical cyclone dataset. Comparisons were made for a recent 5-yr period to investigate the current differences, where linear systematic differences were evident. Time series of the comparisons also showed temporal changes in the systematic differences, which suggest changes in operational procedures. Initial attempts were made to normalize maximum sustained winds by correcting for known changes in operational procedures. The result was mixed, in that the adjustments removed some but not all of the systematic differences. This suggests that more details on operational procedures are needed and that a complete reanalysis of tropical cyclone intensities should be performed.