bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of Sindbis/Eastern Equine Encephalitis Chimeric Viruses in Plaque Reduction Neutralization Tests for Arboviral Disease Diagnostics
Authors: Johnson B. W. , Kosoy O. , Wang E. , Delorey M. , Russell B. , Bowen R. A. , Weaver S. C.
Published: July 2011

Eastern equine encephalitis virus (EEEV) is a highly virulent, mosquito-borne alphavirus that causes severe and often fatal neurological disease in humans and horses in eastern North American, the Caribbean, and Mexico and throughout Central and South America. EEEV infection is diagnosed serologically by anti-EEEV-specific IgM detection, with confirmation by the plaque reduction neutralization test (PRNT), which is highly specific for alphaviruses. Live virus is used in the PRNT procedure, which currently requires biosafety level 3 containment facilities and select agent security in the case of EEEV. These requirements restrict the ability of public health laboratories to conduct PRNTs. Sindbis virus (SINV)/EEEV recombinant constructs have been engineered to express the immunogenic structural proteins from 2 wild-type EEEV strains in an attenuated form. These SINV/EEEVs, which are not classified as select agents, were evaluated as alternative diagnostic reagents in a PRNT using human, equine, and murine sera. The results indicate that the chimeric viruses exhibit specificity comparable to that of wild-type EEEV, with only a slight reduction in sensitivity. Considering their benefits in increased safety and reduced regulatory requirements, these chimeric viruses should be highly useful in diagnostic laboratories throughout the Americas.
Use of a Recombinant Burkholderia Intracellular Motility A Protein for Immunodiagnosis of Glanders
Authors: Kumar Subodh , Malik Praveen , Verma Shailendra Kumar , Pal Vijai , Gautam Vandana , Mukhopadhyay Chiranjay , Rai Ganga Prasad
Published: July 2011

Glanders, caused by the Gram-negative, nonmotile bacteriumBurkholderia mallei, is a contagious and highly fatal disease of equines. During the last decade, the number of glanders outbreaks has increased steadily. The disease also has high zoonotic significance andB. malleiis listed biological warfare agent. The complement fixation test (CFT) is a routinely used and internationally recognized test to screen equine sera for the glanders. However, discrepant results have been observed using the CFT. The low sensitivity and specificity of the CFT and enzyme-linked immunosorbent assay (ELISA) have been linked to the use of crude test antigens. We expressed a novel recombinantBurkholderiaintracellular motility A (rBimA) protein inEscherichia colifor the diagnosis of equine glanders. Purified rBimA was used in an indirect ELISA format. All of the 21 true-positive serum samples used in the study tested positive, whereas only 17 of the 1,524 potentially negative sera tested positive by indirect ELISA, thus exhibiting 100% sensitivity and 98.88% specificity. Also, rBimA protein did not react with melioidosis patient and normal healthy human serum samples, showing its high specificity. The developed assay can be used as a simple and rapid tool for diagnosis of glanders in equine serum samples. An Indian patent (1328/DEL/2010) has been filed for the reagent.
Phoenix 100 versus Vitek 2 in the Identification of Gram-Positive and Gram-Negative Bacteria: a Comprehensive Meta-Analysis
Authors: Chatzigeorgiou Kalliopi-Stavroula , Sergentanis Theodoros N. , Tsiodras Sotirios , Hamodrakas Stavros J. , Bagos Pantelis G.
Published: July 2011

Phoenix 100 and Vitek 2 (operating with the current colorimetric cards) are commonly used in hospital laboratories for rapid identification of microorganisms. The present meta-analysis aims to evaluate and compare their performance on Gram-positive and Gram-negative bacteria. The MEDLINE database was searched up to October 2010 for the retrieval of relevant articles. Pooled correct identification rates were derived from random-effects models, using the arcsine transformation. Separate analyses were conducted at the genus and species levels; subanalyses and meta-regression were undertaken to reveal meaningful system- and study-related modifiers. A total of 29 (6,635 isolates) and 19 (4,363 isolates) articles were eligible for Phoenix and colorimetric Vitek 2, respectively. No significant differences were observed between Phoenix and Vitek 2 either at the genus (97.70% versus 97.59%,
P
= 0.919) or the species (92.51% versus 88.77%,
P
= 0.149) level. Studies conducted with conventional comparator methods tended to report significantly better results compared to those using molecular reference techniques. Speciation of
Staphylococcus aureus
was significantly more accurate in comparison to coagulase-negative staphylococci by both Phoenix (99.78% versus 88.42%,
P
< 0.00001) and Vitek 2 (98.22% versus 91.89%,
P
= 0.043). Vitek 2 also reached higher correct identification rates for Gram-negative fermenters versus nonfermenters at the genus (99.60% versus 95.90%,
P
= 0.004) and the species (97.42% versus 84.85%,
P
= 0.003) level. In conclusion, the accuracy of both systems seems modified by underlying sample- and comparator method-related parameters. Future simultaneous assessment of the instruments against molecular comparator procedures may facilitate interpretation of the current observations.
Limitations of Spoligotyping and Variable-Number Tandem-Repeat Typing for Molecular Tracing of Mycobacterium bovis in a High-Diversity Setting
Authors: Rodriguez-Campos Sabrina , Aranaz Alicia , de Juan Lucía , Sáez-Llorente José Luis , Romero Beatriz , Bezos Javier , Jiménez Antonio , Mateos Ana , Domínguez Lucas
Published: July 2011

This study describes the attempt to trace the first
Mycobacterium bovis
outbreak in alpacas (
Lama pacos
) in Spain by spoligotyping and variable-number tandem-repeat (VNTR) analysis. Due to high genotype diversity, no matching source was identified, but local expansion of a clonal group was found and its significance for molecular tracing is discussed.
Reidentification of Streptococcus bovis Isolates Causing Bacteremia According to the New Taxonomy Criteria: Still an Issue?
Authors: Romero Beatriz , Morosini María-Isabel , Loza Elena , Rodríguez-Baños Mercedes , Navas Enrique , Cantón Rafael , Campo Rosa del
Published: July 2011

All
Streptococcus bovis
blood culture isolates recovered from January 2003 to January 2010 (
n
= 52) at the Hospital Universitario Ramón y Cajal were reidentified on the basis of their genetic traits using new taxonomic criteria. Initial identification was performed by the semiautomatic Wider system (Fco. Soria-Melguizo, Spain) and the API 20 Strep system (bioMérieux, France). All isolates were reidentified by PCR amplification and sequencing of both the 16S rRNA and
sodA
genes and by mass spectrometry using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS; Bruker, Germany). Results of 16S rRNA/
sod
A
gene sequencing were as follows:
Streptococcus gallolyticus
subsp.
gallolyticus
, 14/14 (number of isolates identified by 16S rRNA/number of isolates identified by
sodA
gene sequencing);
Streptococcus gallolyticus
subsp.
pasteurianus
, 24/24;
Streptococcus
spp., 7/0;
Streptococcus infantarius
subsp.
infantarius
, 0/2;
Streptococcus lutetiensis
, 0/5;
Leuconostoc mesenteroides
, 4/0; and
Lactococcus lactis
, 3/3. MALDI-TOF MS identified 27
S. gallolyticus
isolates but not at the subspecies level, 4
L. mesenteroides
isolates, 3
L. lactis
isolates, and 6
S. lutetiensis
isolates, whereas 12 isolates rendered a nonreliable identification result. Pulsed-field gel electrophoresis grouped all
S. gallolyticus
subsp.
gallolyticus
isolates into 3 major clusters clearly different from those of the
S. gallolyticus
subsp.
pasteurianus
isolates, which, in turn, exhibited no clonal relationship. The percentages of resistance to the tested antimicrobials were 38% for erythromycin, 23% for fosfomycin, 10% for levofloxacin, 6% for tetracycline, and 4% for co-trimoxazole. The most frequent underlying diseases were hepatobiliary disorders (53%), endocarditis (17%), and malignancies (12%). We conclude that sequencing of the
sod
A
gene was the most discriminatory method and that
S. gallolyticus
subsp.
pasteurianus
appears to have a higher genetic diversity than
S. gallolyticus
subsp.
gallolyticus
.
Detection of Blastomyces dermatitidis and Histoplasma capsulatum from Culture Isolates and Clinical Specimens by Use of Real-Time PCR
Authors: Babady N. Esther , Buckwalter Seanne P. , Hall Leslie , Le Febre Kara M. , Binnicker Matthew J. , Wengenack Nancy L.
Published: July 2011

Blastomyces dermatitidis
and
Histoplasma capsulatum
are dimorphic fungi that often cause self-limited respiratory infections. However, they may also cause severe disseminated disease, depending on the level of the exposure to the organism and the host immune status. In addition, patients with infections caused by these fungi may have very similar clinical presentations. Although microbiologic culture is a standard method for detecting these pathogens, their recovery may require days to weeks, and the manipulation of cultures presents a significant safety hazard to laboratory personnel. Therefore, the goal of this study was to design a rapid, real-time PCR assay to detect and differentiate
B. dermatitidis
and
H. capsulatum
from culture isolates and directly from clinical specimens. Primers and fluorescence resonance energy transfer hybridization probes were designed to target the histidine kinase and glyceraldehyde-3-phosphate dehydrogenase genes of
B. dermatitidis
and
H. capsulatum
, respectively. The analytical sensitivity of the assay was determined to be 100 copies/μl for both fungi. From culture isolates, the assay demonstrated 100% specificity and 100% sensitivity for
B. dermatitidis
and 100% specificity and 94% sensitivity for
H. capsulatum
. Detection directly from 797 clinical specimens demonstrated specificities and sensitivities of 99% and 86% for
B. dermatitidis
and 100% and 73% for
H. capsulatum
compared with the results for culture. This real-time PCR assay provides a rapid method for the detection of
B. dermatitidis
and
H. capsulatum
from culture isolates and directly from clinical specimens.
Molecular Epidemiology of a Hepatitis C Virus Outbreak in a Leprosy Sanatorium in Japan
Authors: Teramoto Hidemi , Shiogama Kazuya , Mizutani Yasuyoshi , Inada Ken-ichi , Kamahora Toshio , Makino Masanao , Tsutsumi Yutaka
Published: July 2011

The hepatitis C virus (HCV) outbreak that occurred between 1940 and 1999 in a closed leprosy sanatorium located on a small island in Japan was analyzed. The analysis of 318 nucleotides in the NS5B region of HCV allowed us to establish the existence of at least three different HCV strains in this sanatorium.
First Case of Segniliparus rotundus Pneumonia in a Patient with Bronchiectasis
Authors: Koh Won-Jung , Choi Go-Eun , Lee Seung-Heon , Park Young Kil , Lee Nam Yong , Shin Sung Jae
Published: July 2011

We report the first case of
Segniliparus rotundus
pneumonia in an adult with non-cystic fibrosis bronchiectasis. All isolates were identified as
S. rotundus
by 16S rRNA gene sequencing and
rpoB
PCR-restriction analysis. Antibiotic therapy with clarithromycin and ciprofloxacin for 2 months improved the patient's condition and achieved successful sputum conversion.
Stability of Hepatitis C Virus, HIV, and Hepatitis B Virus Nucleic Acids in Plasma Samples after Long-Term Storage at −20
o
C and −70
o
C
Authors: Baleriola Cristina , Johal Harpreet , Jacka Brendan , Chaverot Sandra , Bowden Scott , Lacey Sara , Rawlinson William
Published: July 2011

The storage of biological samples may affect detection of viral nucleic acid, yet the stability of viral nucleic acid at standard laboratory storage temperatures (−70°C and −20°C) has not been comprehensively assessed. Deterioration of viral RNA and DNA during storage may affect the detection of viruses, thus leading to an increased likelihood of false-negative results on diagnostic testing. The viral loads of 99 hepatitis C virus (HCV), 41 HIV, and 101 hepatitis B virus (HBV) patient samples were measured before and after storage at −20°C and −70°C for up to 9.1 years using Versant branched DNA assays, Cobas Monitor assays, and/or AmpliPrep/AmpliScreen assays. Clinical samples stored at −20°C for up to 1.2 years and at −70°C for up to 9 years showed a statistically significant difference from baseline with respect to HCV RNA titer, although this difference was not greater than 0.5 log
10
unit. The concentration of HIV RNA in clinical samples stored at −20°C for 2.3 years and at −70°C for up to 9.1 years did not differ significantly from the baseline viral load. HBV DNA-positive clinical samples stored at −20°C for up to 5 years and at −70°C for up to 4 years differed significantly in viral load. In all studies, however, the loss of viral load of HCV, HIV, or HBV in clinical samples tested after storage at −20°C and −70°C for up to 9 years ranged from 0.01 to 0.35 log
10
IU/ml and did not exceed 0.5 log
10
, which is the estimated intra-assay variation for molecular tests. Hence, the loss was considered of minimal clinical impact and adequate for the detection of HCV, HIV-1, and HBV nucleic acids using nucleic acid assays for the assessment of the infectious risk of cell, blood, and tissue donors.
APOBEC3G Complexes Decrease Human Immunodeficiency Virus Type 1 Production
Authors: Martin Kenneth L. , Johnson Megan , D'Aquila Richard T.
Published: July 2011

APOBEC3G (A3G) is packaged into human immunodeficiency virus type 1 (HIV-1) virions unless HIV-1 virion infectivity factor (Vif) counteracts it. Virion A3G restricts HIV-1 reverse transcription and integration in target cells. Some A3G in producer cells colocalizes with specific cytoplasmic structures, in what are called “A3G complexes” here. Functional effects of producer cell A3G complexes on HIV-1 replication were studied. HeLa cells were cotransfected with HIV-1 constructs producing pseudoviruses, as well as either wild-type (WT) A3G or a mutant A3G (C97A, Y124A, W127A, or D128K A3G). Pseudovirus particle production was decreased from cells expressing any of the A3Gs that formed complexes by 24 h after transfection, relative to cells with C97A A3G that did not form detectable A3G complexes by 24 h or A3G-negative cells. The intracellular HIV-1 Gag half-life was shorter in cells containing A3G complexes than in those lacking complexes. HIV-1 virion output was decreased in a single round of replication from a T cell line containing A3G complexes (CEM cells) after infection with Vif-negative HIV-1, compared to Vif-positive HIV-1 that depleted A3G. Levels of production of Vif-negative and Vif-positive virus were similar from cells not containing A3G (CEM-SS cells). Knockdown of the mRNA processing body (P-body) component RCK/p54, eliminated A3G complex formation, and increased HIV-1 production. We conclude that endogenous A3G complexes in producer cells decrease HIV-1 production if not degraded by Vif.
Epigenetic and Transcriptional Changes Which Follow Epstein-Barr Virus Infection of Germinal Center B Cells and Their Relevance to the Pathogenesis of Hodgkin's Lymphoma
Authors: Leonard Sarah , Wei Wenbin , Anderton Jennifer , Vockerodt Martina , Rowe Martin , Murray Paul G. , Woodman Ciaran B.
Published: July 2011

Although Epstein-Barr virus (EBV) usually establishes an asymptomatic lifelong infection, it is also implicated in the development of germinal center (GC) B-cell-derived malignancies, including Hodgkin's lymphoma (HL). Following primary infection, EBV remains latent in the memory B-cell population, where host-driven methylation of viral DNA contributes to the repression of viral gene expression. However, it is still unclear how EBV harnesses the cell's methylation machinery in B cells, how this contributes to viral persistence, and what impact this has on the methylation of cellular genes. We show that EBV infection of GC B cells is followed by upregulation of the DNA methyltransferase DNMT3A and downregulation of DNMT3B and DNMT1. We show that the EBV latent membrane protein 1 (LMP1) oncogene downregulates DNMT1 and that DNMT3A binds to the viral promoter Wp. Genome-wide promoter arrays performed with these cells showed that EBV-associated methylation changes in cellular genes were not randomly distributed across the genome but clustered at chromosomal locations, consistent with an instructive pattern of methylation, and were in part determined by promoter CpG content. Both DNMT3B and DNMT1 were downregulated and DNMT3A was upregulated in HL cell lines, recapitulating the pattern of expression observed following EBV infection of GC B cells. We also found, by using gene expression profiling, that genes differentially expressed following EBV infection of GC B cells were significantly enriched for those reported to be differentially expressed in HL. These observations suggest that EBV-infected GC B cells are a useful model for studying virus-associated changes contributing to the pathogenesis of HL.
The Leader Protein of Cardioviruses Inhibits Stress Granule Assembly
Authors: Borghese Fabian , Michiels Thomas
Published: July 2011

Stress granules (SG) are cytoplasmic aggregates of stalled translation preinitiation complexes that form in cells exposed to various environmental stresses. Here, we show that stress granules assemble in cells infected with Theiler's murine encephalomyelitis virus (TMEV) mutants carrying alterations in the leader (L) protein, but not in cells infected with wild-type TMEV. Stress granules also formed in STAT1-deficient cells, suggesting that SG formation was not a consequence of increased type I interferon (IFN) production when cells were infected with the mutant virus. Ectopic expression of the wild-type L protein was sufficient to inhibit stress granule formation induced by sodium arsenite or thapsigargin treatment. In conclusion, TMEV infection induces stress granule assembly, but this process is inhibited by the L protein. Unlike poliovirus-induced stress granules, TMEV-induced stress granules did not contain the nuclear protein Sam68 but contained polypyrimidine tract binding protein (PTB), an internal ribosome entry site (IRES)-interacting protein. Moreover, G3BP was not degraded and was found in SG after TMEV infection, suggesting that SG content could be virus specific. Despite the colocalization of PTB with SG and the known interaction of PTB with viral RNA,
in situ
hybridization and immunofluorescence assays failed to detect viral RNA trapped in infection-induced SG. Recombinant Theiler's viruses expressing the L protein of Saffold virus 2 (SAFV-2), a closely related human theilovirus, or the L protein of mengovirus, an encephalomyocarditis virus (EMCV) strain, also inhibited infection-induced stress granule assembly, suggesting that stress granule antagonism is a common feature of cardiovirus L proteins.
The HIV-1 Tat Protein Has a Versatile Role in Activating Viral Transcription
Authors: Das Atze T. , Harwig Alex , Berkhout Ben
Published: July 2011

It is generally acknowledged that the Tat protein has a pivotal role in HIV-1 replication because it stimulates transcription from the viral long terminal repeat (LTR) promoter by binding to the TAR hairpin in the nascent RNA transcript. However, a multitude of additional Tat functions have been suggested. The importance of these functions is difficult to assess in replication studies with Tat-mutated HIV-1 variants because of the dominant negative effect on viral gene expression. We therefore used an HIV-1 construct that does not depend on the Tat-TAR interaction for transcription to reevaluate whether or not Tat has a second essential function in HIV-1 replication. This HIV-rtTA variant uses the incorporated Tet-On gene expression system for activation of transcription and replicates efficiently upon complete TAR deletion. Here we demonstrated that Tat inactivation does nevertheless severely inhibit replication. Upon long-term culturing, the Tat-minus HIV-rtTA variant acquired mutations in the U3 region that improved promoter activity and reestablished replication. We showed that in the absence of a functional TAR, Tat remains important for viral transcription via Sp1 sequence elements in the U3 promoter region. Substitution of these U3 sequences with nonrelated promoter elements created a virus that replicates efficiently without Tat in SupT1 T cells. These results indicate that Tat has a versatile role in transcription via TAR and U3 elements. The results also imply that Tat has no other essential function in viral replication in cultured T cells.
Hepatitis C Virus Infection Is Blocked by HMGB1 Released from Virus-Infected Cells
Authors: Jung Jong Ha , Park Ji Hoon , Jee Min Hyeok , Keum Sun Ju , Cho Min-Sun , Yoon Seung Kew , Jang Sung Key
Published: July 2011

High-mobility group box 1 (HMGB1), an abundant nuclear protein that triggers host immune responses, is an endogenous danger signal involved in the pathogenesis of various infectious agents. However, its role in hepatitis C virus (HCV) infection is not known. Here, we show that HMGB1 protein is translocated from the nucleus to cytoplasm and subsequently is released into the extracellular milieu by HCV infection. Secreted HMGB1 triggers antiviral responses and blocks HCV infection, a mechanism that may limit HCV propagation in HCV patients. Secreted HMGB1 also may have a role in liver cirrhosis, which is a common comorbidity in HCV patients. Further investigations into the roles of HMGB1 in the diseases caused by HCV infection will shed light on and potentially help prevent these serious and prevalent HCV-related diseases.
Role of Calpain in the Formation of Human Papillomavirus Type 16 E1^E4 Amyloid Fibers and Reorganization of the Keratin Network
Authors: Khan Jameela , Davy Clare E. , McIntosh Pauline B. , Jackson Deborah J. , Hinz Steven , Wang Qian , Doorbar John
Published: July 2011

The human papillomavirus (HPV) type 16 E1^E4 (16E1^E4) protein is expressed in the middle to upper layers of infected epithelium and has several roles within the virus life cycle. It is apparent that within the epithelium there are multiple species of 16E1^E4 that differ in length and/or degree of phosphorylation and that some or all of these can associate with the cellular keratin networks, leading to network disruption. We show here that the cellular cysteine protease calpain cleaves the 16E1^E4 protein after amino acid 17 to generate species that lack the N terminus. These C-terminal fragments are able to multimerize and form amyloid-like fibers. This can lead to accumulation of 16E1^E4 and disruption of the normal dynamics of the keratin networks. The cleavage of E1^E4 proteins by calpain may be a common strategy used by α-group viruses, since we show that cleavage of type 18 E1^E4 in raft culture is also dependent on calpain. Interestingly, the cleavage of 16E1^E4 by calpain appears to be highly regulated as differentiation of HPV genome-containing cells by methylcellulose is insufficient to induce cleavage. We hypothesize that this is important since it ensures that the formation of the amyloid fibers is not prematurely triggered in the lower layers and is restricted to the upper layers, where calpain is active and where disruption of the keratin networks may aid virus release.
A High Level of Mutation Tolerance in the Multifunctional Sequence Encoding the RNA Encapsidation Signal of an Avian Hepatitis B Virus and Slow Evolution Rate Revealed by
In Vivo
Infection
Authors: Schmid Bernadette , Rösler Christine , Nassal Michael
Published: July 2011

In all hepadnaviruses, protein-primed reverse transcription of the pregenomic RNA (pgRNA) is initiated by binding of the viral polymerase, P protein, to the ε RNA element. Universally, ε consists of a lower stem and an upper stem, separated by a bulge, and an apical loop. Complex formation triggers pgRNA encapsidation and the ε-templated synthesis of a DNA oligonucleotide (priming) that serves to generate minus-strand DNA.
In vitro
systems for duck hepatitis B virus (DHBV) yielded important insights into the priming mechanism, yet their relevance in infection is largely unexplored. Moreover, additional functions encoded in the DHBV ε (Dε) sequence could affect
in vivo
fitness. We therefore assessed the
in vivo
performances of five recombinant DHBVs bearing multiple mutations in the upper Dε stem. Three variants with only modestly reduced
in vitro
replication competence established chronic infection in ducks. From one variant but not another, three adapted new variants emerged upon passaging, as demonstrated by increased relative fitness in coinfections with wild-type DHBV. All three showed enhanced priming and replication competence
in vitro
, and in one, DHBV e antigen (DHBeAg) production was restored. Pronounced impacts on other Dε functions were not detected; however, gradual, synergistic contributions to overall performance are suggested by the fact of none of the variants reaching the
in vivo
fitness of wild-type virus. These data shed more light on the P-Dε interaction, define important criteria for the design of future
in vivo
evolution experiments, and suggest that the upper Dε stem sequences provided an evolutionary playground for DHBV to optimize
in vivo
fitness.
The Structure of Barmah Forest Virus as Revealed by Cryo-Electron Microscopy at a 6-Angstrom Resolution Has Detailed Transmembrane Protein Architecture and Interactions
Authors: Kostyuchenko Victor A. , Jakana Joanita , Liu Xiangan , Haddow Andrew D. , Aung Myint , Weaver Scott C. , Chiu Wah , Lok Shee-Mei
Published: July 2011

Barmah Forest virus (BFV) is a mosquito-borne alphavirus that infects humans. A 6-Å-resolution cryo-electron microscopy three-dimensional structure of BFV exhibits a typical alphavirus organization, with RNA-containing nucleocapsid surrounded by a bilipid membrane anchored with the surface proteins E1 and E2. The map allows details of the transmembrane regions of E1 and E2 to be seen. The C-terminal end of the E2 transmembrane helix binds to the capsid protein. Following the E2 transmembrane helix, a short α-helical endodomain lies on the inner surface of the lipid envelope. The E2 endodomain interacts with E1 transmembrane helix from a neighboring E1-E2 trimeric spike, thereby acting as a spacer and a linker between spikes. In agreement with previous mutagenesis studies, the endodomain plays an important role in recruiting other E1-E2 spikes to the budding site during virus assembly. The E2 endodomain may thus serve as a target for antiviral drug design.
Human Immunodeficiency Virus Rev-Binding Protein Is Essential for Influenza A Virus Replication and Promotes Genome Trafficking in Late-Stage Infection
Authors: Eisfeld Amie J. , Neumann Gabriele , Kawaoka Yoshihiro
Published: July 2011

Influenza A virus uses cellular protein transport systems (e.g., CRM1-mediated nuclear export and Rab11-dependent recycling endosomes) for genome trafficking from the nucleus to the plasma membrane, where new virions are assembled. However, the detailed mechanisms of these events have not been completely resolved, and additional cellular factors are probably required. Here, we investigated the role of the cellular human immunodeficiency virus (HIV) Rev-binding protein (HRB), which interacts with influenza virus nuclear export protein (NEP), during the influenza virus life cycle. By using small interfering RNAs (siRNAs) and overexpression of a dominant negative HRB protein fragment, we show that cells lacking functional HRB have significantly reduced production of influenza virus progeny and that this defect results from impaired viral ribonucleoprotein (vRNP) delivery to the plasma membrane in late-stage infection. Since HRB colocalizes with influenza vRNPs early after their delivery to the cytoplasm, it may mediate a connection between the nucleocytoplasmic transport machinery and the endosomal system, thus facilitating the transfer of vRNPs from nuclear export to cytoplasmic trafficking complexes. We also found an association between NEP and HRB in the perinuclear region, suggesting that NEP may contribute to this process. Our results identify HRB as a second endosomal factor with a crucial role in influenza virus genome trafficking, suggest cooperation between unique endosomal compartments in the late steps of the influenza virus life cycle, and provide a common link between the cytoplasmic trafficking mechanisms of influenza virus and HIV.
Cell-Type-Specific Type I Interferon Antagonism Influences Organ Tropism of Murine Coronavirus
Authors: Zhao Ling , Rose Kristine M. , Elliott Ruth , Van Rooijen Nico , Weiss Susan R.
Published: July 2011

Previous studies have demonstrated that mouse hepatitis virus (MHV) hepatotropism is determined largely by postentry events rather than by availability of the viral receptor. In addition, mutation of MHV nonstructural protein 2 (ns2) abrogates the ability of the virus to replicate in the liver and induce hepatitis but does not affect replication in the central nervous system (CNS). Here we show that replication of ns2 mutant viruses is attenuated in bone marrow-derived macrophages (BMM) generated from wild-type (wt) mice but not in L2 fibroblasts, primary astrocytes, or BMM generated from type I interferon receptor-deficient (IFNAR−/−) mice. In addition, ns2 mutants are more sensitive than wt virus to pretreatment of BMM, but not L2 fibroblasts or primary astrocytes, with alpha/beta interferon (IFN-α/β). The ns2 mutants induced similar levels of IFN-α/β in wt and IFNAR−/−BMM, indicating that ns2 expression has no effect on the induction of IFN but rather that it antagonizes a later step in IFN signaling. Consistent with thesein vitrodata, the virulence of ns2 mutants increased to near that of wt virus after depletion of macrophagesin vivo. These data imply that the ability of MHV to replicate in macrophages is a prerequisite for replication in the liver and induction of hepatitis but not for replication or disease in the CNS, underscoring the importance of IFN signaling in macrophagesin vivofor protection of the host from hepatitis. Our results further support the notion that viral tissue tropism is determined in part by postentry events, including the early type I interferon response.
Antagonistic Effects of Cellular Poly(C) Binding Proteins on Vesicular Stomatitis Virus Gene Expression
Authors: Dinh Phat X. , Beura Lalit K. , Panda Debasis , Das Anshuman , Pattnaik Asit K.
Published: July 2011

Immunoprecipitation and subsequent mass spectrometry analysis of the cellular proteins from cells expressing the vesicular stomatitis virus (VSV) P protein identified the poly(C) binding protein 2 (PCBP2) as one of the P protein-interacting proteins. To investigate the role of PCBP2 in the viral life cycle, we examined the effects of depletion or overexpression of this protein on VSV growth. Small interfering RNA-mediated silencing of PCBP2 promoted VSV replication. Conversely, overexpression of PCBP2 in transfected cells suppressed VSV growth. Further studies revealed that PCBP2 negatively regulates overall viral mRNA accumulation and subsequent genome replication. Coimmunoprecipitation and immunofluorescence microscopic studies showed that PCBP2 interacts and colocalizes with VSV P protein in virus-infected cells. The P-PCBP2 interaction did not result in reduced levels of protein complex formation with the viral N and L proteins, nor did it induce degradation of the P protein. In addition, PCBP1, another member of the poly(C) binding protein family with homology to PCBP2, was also found to interact with the P protein and inhibit the viral mRNA synthesis at the level of primary transcription without affecting secondary transcription or genome replication. The inhibitory effects of PCBP1 on VSV replication were less pronounced than those of PCBP2. Overall, the results presented here suggest that cellular PCBP2 and PCBP1 antagonize VSV growth by affecting viral gene expression and highlight the importance of these two cellular proteins in restricting virus infections.
Isocitrate dehydrogenase mutations in diffuse gliomas: clinical and aetiological implications
Authors: Gupta R , Webb-Myers R , Flanagan S , Buckland M E
Published: July 2011

The discovery of isocitrate dehydrogenase (IDH) mutations in gliomas is one example of the large impact that next-generation sequencing is having on the understanding of tumour biology and human disease in general.IDHmutations are early and common events in the development of astrocytomas, oligodendrogliomas and oligoastrocytomas.IDHmutations are also found in some myeloid malignancies and soft tissue tumours, but are rare in other malignancies.IDHmutation detection can be incorporated into routine pathology practice via immunohistochemistry and/or standard sequencing techniques and has great diagnostic value. An emerging theme is thatIDHmutation status in gliomas is of great prognostic relevance, and there are proposals to includeIDHmutation status in the next iteration of the WHO classification of gliomas. The mechanisms of action(s) of mutant IDH are not fully understood, but the understanding is progressing rapidly, and may provide a mechanism to link diverse proneoplastic processes such as oxidative damage and epigenetic dysregulation. There are exciting prospects of novel therapies for glioma patients emerging from the elucidation of these mechanisms. Given the diagnostic and prognostic implications ofIDHmutation, and the potential for new therapies, all gliomas should be assessed forIDHmutation status in the future.
Malignant ovarian germ cell tumours in gonadal Y chromosome mosaicism
Authors: Shahsiah Reza , Jahanbin Behnaz , Rabiei Reza , Ardalan Farid Azmoudeh , Sarhadi Behnaz , Izadi-Mood Narges
Published: July 2011

Aims

Previous studies have shown that two partially overlapping mechanisms are responsible for the development of malignant ovarian germ cell tumours (MOGCT): either spontaneous mutations, mostly in KIT gene, or the presence of Y chromosome material, in dysgenetic gonads. While unilateral oophorectomy and preservation of fertility is favourable in most cases, presence of whole or part of Y chromosome in dysgenetic ovaries is associated with a risk of bilateral germ cell tumour development. The aim of this study was to evaluate the frequency of Y chromosome material in these tumours.

Methods

A total of 47 cases with histopathologic diagnosis of malignant germ cell tumour were selected in a period of 9 years. A relative quantitative PCR (RQ-PCR) method was designed and validated to detect testis-specific protein Y-encoded (TSPY) gene on Y chromosome. After DNA extraction, TSPY gene was sought as a surrogate of Y chromosome.

Results

Significant amounts of TSPY gene were found in seven cases, two of which had gonadoblastoma and one had cytogenetic proof of Y chromosome presence.

Conclusions

Some MOGCTs develop on the background of gonadal mosaicism and gonadal dysgenesis. Bilateral oophorectomy may be indicated in patients with these disorders because they are at risk of developing an MOGCT on the contralateral gonad. Moreover, this chromosomal abnormality is hardly found by routine methods, and the abnormality is more easily sought in MOGCT cells by means of RQ-PCR.
Young adult smokers' perceptions of plain packaging: a pilot naturalistic study
Authors: Moodie Crawford , Mackintosh Anne Marie , Hastings Gerard , Ford Allison
Published: July 2011

Aims

To explore the impact, if any, that using plain (non-branded) cigarette packs in real-life settings has on young adult smokers.

Methods

Naturalistic-type research was employed, where smokers used brown ‘plain’ packs for 2 weeks and their regular packs for 2 weeks, in real-life settings. Participants were recruited in Glasgow, Scotland. Of the 140 smokers aged 18–35 years who participated in the naturalistic study, 48 correctly completed and returned all questionnaires. Over the 4-week study period, participants completed a questionnaire twice a week assessing pack perceptions and feelings, feelings about smoking, salience of health warnings and smoking-related behaviours. A subsample of 18 participated in a post-study interview, which employed a semistructured topic guide to assess perceptions and experiences of using plain packs.

Results

Trends in the data show that in comparison with branded packaging, plain packaging increased negative perceptions and feelings about the pack and about smoking. Plain packaging also increased avoidant behaviour (hiding the pack, covering the pack), certain smoking cessation behaviours, such as smoking less around others and forgoing cigarettes, and thinking about quitting. Almost half (n=8) of those in the post-study interview, predominantly women (n=6), reported that the use of plain packs had either increased avoidant behaviour or reduced consumption.

Conclusions

This pilot naturalistic study suggests that plain packaging could potentially help reduce tobacco consumption among some young adult smokers, and women in particular. Employing an innovative research methodology, the findings of this study are consistent with, and indeed support, past plain packaging research.
Smokers' self-reported responses to the introduction of reduced ignition propensity (RIP) cigarettes: Table 1
Authors: Seidenberg Andrew B , Rees Vaughan W , Alpert Hillel R , O'Connor Richard J , Giovino Gary A , Hyland Andrew , Connolly Gregory N
Published: July 2011

Background

Changes in cigarette design to meet mandated fire safety standards may have unintended effects on smoker responses by diminishing the consumer's perceptions of product acceptability, smoking and increasing fire-risk behaviours. To address these concerns, population-level data are needed from a jurisdiction where reduced ignition propensity (RIP) cigarettes have been introduced.

Methods

A cohort of adult smokers was recruited in Massachusetts, USA using a random-digit-dialled telephone survey. The cohort was contacted prior to, and 8 months following, the state-mandated introduction of RIP cigarettes on 1 January 2008. Changes in self-reported subjective cigarette characteristics, smoking topography, fire-risk behaviours, fire events and quitting intentions were assessed.

Results

A total of 620 Massachusetts smokers completed the baseline survey conducted prior to implementation of the law, and 353 (57%) completed the follow-up survey conducted after implementation. No significant changes were found in self-reported fire-risk behaviour or quitting intentions. In addition, smokers were less likely to report smoking greater than 20 cigarettes per day and inhaling deeply into the chest after the law.

Conclusions

The introduction of RIP cigarettes in Massachusetts yielded little change, and no adverse effect, on self-reported smoker response, among a sample of mostly Caucasian smokers.
PIECEWISE FUNCTION FEEDBACK STRATEGY IN INTELLIGENT TRAFFIC SYSTEMS WITH A SPEED LIMIT BOTTLENECK
Authors: CHEN BOKUI , SUN XIAOYAN , WEI HUA , DONG CHUANFEI , WANG BINGHONG
Published: July 2011

The road capacity can be greatly improved if an appropriate and effective information feedback strategy is adopted in the traffic system. In this paper, a strategy called piecewise function feedback strategy (PFFS) is introduced and applied into an asymmetrical two-route scenario with a speed limit bottleneck in which the dynamic information can be generated and displayed on the information board to guide road users to make a choice. Meanwhile, the velocity-dependent randomization (VDR) mechanism is adopted which can better reflect the dynamic behavior of vehicles in the system than NS mechanism. Simulation results adopting PFFS have demonstrated high efficiency in controlling spatial distribution of traffic patterns compared with the previous strategies.
PHANTOM ACCRETION BY FIVE-DIMENSIONAL CHARGED BLACK HOLE
Authors: SHARIF M. , ABBAS G.
Published: July 2011

This paper deals with the dynamical behavior of phantom field near five-dimensional charged black hole. We formulate equations of motion for steady-state spherically symmetric flow of phantom fluids. It is found that phantom energy accretes onto black holes for u < 0. Further, the location of critical point of accretion are evaluated that leads to mass to charge ratio for 5D charged black hole. This ratio implies that accretion cannot transform a black hole into a naked singularity. We would like to mention here that this work is an irreducible extension of 4D charged black hole.
DIFFERENTIAL STRUCTURE ON κ-MINKOWSKI SPACE, AND κ-POINCARÉ ALGEBRA
Authors: MELJANAC STJEPAN , KREŠIĆ-JURIĆ SAŠA
Published: July 2011

We construct realizations of the generators of the κ-Minkowski space and κ-Poincaré algebra as formal power series in the h-adic extension of the Weyl algebra. The Hopf algebra structure of the κ-Poincaré algebra related to different realizations is given. We construct realizations of the exterior derivative and one-forms, and define a differential calculus on κ-Minkowski space which is compatible with the action of the Lorentz algebra. In contrast to the conventional bicovariant calculus, the space of one-forms has the same dimension as the κ-Minkowski space.
CONTROLLED RANDOMNESS AND FRUSTRATION OF THE MANY-BODY INTERACTIONS
Authors: HASHIZUME YOICHIRO , SUZUKI MASUO
Published: July 2011

On the Ising spin systems constructed with four-body interactions, there appears the "spin-pair ordered phase" or "spin-pair glass phase" in a certain temperature. Especially, the random four-body models include the frustration and the spin-pair glass phase appears in those models. This frustration may play an important role of spin-pair glass transitions, similarly to the case of ordinary spin-glass transitions. In this study, we clarify the way to discriminate quantitatively "frustrated unit cells" from "nonfrustrated ones" on the random four-body models. Then we introduce a parameter to control the frustration in the Ising spin systems with random four-body interactions. This parameter enables us to analyze the frustration continuously in many-body models. Thus we have analyzed the phase transitions and obtained phase diagrams using the frustration parameter. These interesting phase diagrams show that there appear the spin-pair ordered phases even on the completely frustrated models. This result is essentially different from the random two-body models, namely spin-glass models (there appears no ferromagnetic phase in the fully frustrated spin-glass models, which correspond to the Villain models).
SIGNATURE OF PRE-EQUILIBRIUM-EMISSION IN FORWARD-TO-BACKWARD YIELD RATIO MEASUREMENT
Authors: YADAV ABHISHEK , SINGH PUSHPENDRA P. , SHARMA VIJAY R. , GUPTA UNNATI , SINGH DEVENDRA P. , SHARMA MANOJ K. , SINGH B. P. , PRASAD R. , KUMAR R. , SINGH R. P. , MURALITHAR S. , BHOWMIK R. K.
Published: July 2011

In this paper, pre-equilibrium-emission has been investigated using particle-γ coincidence technique. Forward-to-backward yield ratios of different reaction products have been measured in 16 O +169 Tm system at 5.6 MeV /nucleon. Coincidences between prompt-γ-rays and charged particles emitted in various angular zones have been recorded to identify different reaction products. Several gating conditions have been projected onto the energy spectra to achieve the information about mode of reaction. Yield profiles of fusion/fusion-like channels identified from forward/backward/sideways particle (Z = 1, 2)-gated-spectra have been measured. High yield in forward cone has been observed from the experimentally measured forward-to-backward yield ratios. The enhanced forward cone yield has been attributed to the pre-equilibrium-emission. The maximum observed spin [Formula: see text] is found to be decreased with the number of proton emitted from the composite nucleus during the equilibrium and/or pre-equilibrium decay.
LEARNING AN ADAPTIVE DICTIONARY USING A PROJECTED GRADIENT METHOD AND ITS APPLICATION ON IMAGE DE-NOISING
Authors: CAI ZEMIN , LAI JIANHUANG , TAN CHAOQIANG , YAN JINGWEN
Published: July 2011

In recent years, considerable efforts have been made in the research of sparse representation for signals over overcomplete dictionaries. The dictionaries can be either pre-specified transforms or designed by learning from a set of training signals. In the paper, the dictionary learning problem was extended into a quadratic programming framework. A projected gradient with line search method was presented for solving this large-scale box-constrained quadratic program. The non-negative dictionary learned using this method was applied to image de-noising. Experimental results demonstrated that this learning-based method had better performance than the wavelet-based, the variation-based and the K-SVD methods.
OPERATOR-ADAPTED WAVELETS: CONNECTION WITH THE STRANG–FIX CONDITIONS
Authors: ZAKHAROV VICTOR G.
Published: July 2011

In this paper, we present an explicit method to construct directly in the x-domain compactly supported scaling functions corresponding to the wavelets adapted to a sum of differential operators with constant coefficients. Here the adaptation to an operator is taken to mean that the wavelets give a diagonal form of the operator matrix. We show that the biorthogonal compactly supported wavelets adapted to a sum of differential operators with constant coefficients are closely connected with the representation of the null-space of the adjoint operator by the corresponding scaling functions. We consider the necessary and sufficient conditions (actually the Strang–Fix conditions) on integer shifts of a compactly supported function (distribution) f ∈ S'(ℝ) to represent exactly any function from the null-space of a sum of differential operators with constant coefficients.
ORTHONORMAL MRA WAVELETS: SPECTRAL FORMULAS AND ALGORITHMS
Authors: GÓMEZ-CUBILLO F. , SUCHANECKI Z. , VILLULLAS S.
Published: July 2011

Spectral decompositions of translation and dilation operators are built in terms of suitable orthonormal bases of L2(ℝ), leading to spectral formulas for scaling functions and orthonormal wavelets associated with multiresolution analysis (MRA). The spectral formulas are useful to compute compactly supported scaling functions and wavelets. It is illustrated with a particular choice of the orthonormal bases, the so-called Haar bases, which yield a new algorithm related to the infinite product matrix representation of Daubechies and Lagarias.
BALANCED MULTIWAVELETS ON THE INTERVAL [0,1] WITH ARBITRARY INTEGER DILATION FACTOR a
Authors: HUANG YONGDONG , ZHAO YINGMIN
Published: July 2011

In this paper, orthogonal multiwavelets on interval [0, 1] with arbitrary compact support γ and integer dilation factor a are studied. Firstly, the concept of multiwavelets on the interval [0, 1] is generalized to the arbitrary integer dilation factor a, a ≥ 2, a ∈ ℤ, and an algorithm for constructing orthogonal multiscaling function and multiwavelets on interval [0, 1] with dilation factor a is presented. Secondly, the decomposition and reconstruction formulas of multiwavelets on interval [0, 1] are deduced. Finally, the "balancing" concept of multiwavelets on the interval [0, 1] with dilation factor a is defined, and the algorithm of balancing the unbalanced multiwavelets on the interval [0, 1] is also given.
INTELLECTUAL PROPERTY MANAGEMENT MODEL IN ENTERPRISES: A TECHNOLOGY LIFE CYCLE PERSPECTIVE
Authors: CAO YONG , ZHAO LI
Published: July 2011

The cyclicality, fluctuation, and periodicity of the technology requires the dynamic management of the intellectual property (IP) in enterprises. Unfortunately, companies do not connect the management of their IP to the underlying technology life cycle (TLC), and companies do not change the management of IP in different stages of the TLC. Anyway, most companies use one-size-fits-all method to manage all kinds of IP and different technologies. The purpose of this research is to arouse the attention on TLC characteristics of IP management research in academic and business fields. An IP management model is proposed to deal with the one-size-fits-all issue from the perspective of TLC which manifests the importance of phase characteristics of the technology in IP management. This paper indicates that the IP management strategy should vary with the periods of TLC. Likewise, the results from a case study about Motorola's IP management on global system for mobile (GSM) communications have primarily tested the feasibility and validity of IP management model.