bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying the Target Cell in Primary Simian Immunodeficiency Virus (SIV) Infection: Highly Activated Memory CD4+T Cells Are Rapidly Eliminated in Early SIV Infection In Vivo
Authors: Veazey Ronald S. , Tham Irene C. , Mansfield Keith G. , DeMaria MaryAnn , Forand Amy E. , Shvetz Daniel E. , Chalifoux Laura V. , Sehgal Prabhat K. , Lackner Andrew A. 
Published: April 2009

ABSTRACTIt has recently been shown that rapid and profound CD4+T-cell depletion occurs almost exclusively within the intestinal tract of simian immunodeficiency virus (SIV)-infected macaques within days of infection. Here we demonstrate (by three- and four-color flow cytometry) that this depletion is specific to a definable subset of CD4+T cells, namely, those having both a highly and/or acutely activated (CD69+CD38+HLA-DR+) and memory (CD45RA−Leu8−) phenotype. Moreover, we demonstrate that this subset of helper T cells is found primarily within the intestinal lamina propria. Viral tropism for this particular cell type (which has been previously suggested by various studies in vitro) could explain why profound CD4+T-cell depletion occurs in the intestine and not in peripheral lymphoid tissues in early SIV infection. Furthermore, we demonstrate that an acute loss of this specific subset of activated memory CD4+T cells may also be detected in peripheral blood and lymph nodes in early SIV infection. However, since this particular cell type is present in such small numbers in circulation, its loss does not significantly affect total CD4+T cell counts. This finding suggests that SIV and, presumably, human immunodeficiency virus specifically infect, replicate in, and eliminate definable subsets of CD4+T cells in vivo.
The
S2
Gene of Equine Infectious Anemia Virus Is a Highly Conserved Determinant of Viral Replication and Virulence Properties in Experimentally Infected Ponies
Authors: Li Feng , Leroux Caroline , Craigo Jodi K. , Cook Sheila J. , Issel Charles J. , Montelaro Ronald C. 
Published: April 2009

ABSTRACT

Equine infectious anemia virus (EIAV) is genetically one of the simplest lentiviruses in that the viral genome encodes only three accessory genes,
tat
,
rev
, and
S2
. Although serological analyses demonstrate the expression of the S2 protein in persistently infected horses, the role of this viral gene remains undefined. We recently reported that the
S2
gene is not essential for EIAV replication in primary equine macrophages, as EIAV mutants lacking the
S2
gene replicate to levels similar to those of the parental virus (F. Li, B. A. Puffer, and R. C. Montelaro, J. Virol. 72:8344–8348, 1998). We now describe in vivo studies that examine the evolution and role of the
S2
gene in ponies experimentally infected with EIAV. The results of these studies reveal for the first time that the
S2
gene is highly conserved during persistent infection and that deletion of the
S2
gene reduces viral virulence and virus replication levels compared to those of the parental virus containing a functional
S2
gene. These data indicate that the EIAV
S2
gene is in fact an important determinant of viral replication and pathogenic properties in vivo, despite the evident lack of
S2
influence on viral replication levels in vitro. Thus, these observations suggest in vivo functions of EIAV
S2
that are not adequately reflected in simple infections of cultured cells, including natural target macrophages.
Species Specificity of Macaque Rhadinovirus Glycoprotein B Sequences
Authors: Auerbach Marcy R. , Czajak Susan C. , Johnson Welkin E. , Desrosiers Ronald C. , Alexander Louis 
Published: April 2009

ABSTRACT

All members of the
Herpesviridae
family contain sequences for a highly conserved glycoprotein B (gB) gene. We investigated the phylogenetic relationships of gB sequences from eight independent rhadinovirus isolates obtained from three species: rhesus (
Macaca mulatta
), cynomologus (
Macaca fasicularis
), and pig-tailed (
Macaca nemestrina
) macaques. Samples were derived from monkeys housed at four separate facilities. Analysis of these eight independent gB sequences revealed five regions of heterogeneity within the 823- to 829-amino-acid polypeptides: residues 1 to 65, 120 to 185, 255 to 300, 352 to 393, and 412 to 457. The remaining regions of gB were highly conserved among the different macaque isolates. Overall divergence among these gene sequences ranged from 0.1 to 7.2% at the amino acid level. Phylogenetic trees constructed with our macaque rhadinovirus gB sequences and those derived from additional subfamilies or genera (alpha, beta, gamma-1, and gamma-2) revealed that the macaque gB sequences branched with other gamma-2 herpesvirus gB sequences and that within the gamma-2 genera, the macaque gB sequences clustered as a distinct branch. The eight macaque rhadinovirus gB sequences were all approximately equidistant from Kaposi sarcoma-associated herpesvirus (KSHV) gB sequences and had a shorter evolutionary distance to KSHV gB sequences than to any other herpesvirus, including the gamma-2 herpesvirus saimiri (HVS) of New World squirrel monkeys. The macaque gB sequences did not cluster according to the facility of origin, but did cluster according to the species of origin, displaying less intraspecies divergence (0.1 to 2.9%) than interspecies divergence (3.3 to 7.2%). These results demonstrate a close relatedness of rhadinovirus isolates from different macaque species.
Functional Interactions between C/EBP, Sp1, and COUP-TF Regulate Human Immunodeficiency Virus Type 1 Gene Transcription in Human Brain Cells
Authors: Schwartz Christian , Catez Philippe , Rohr Olivier , Lecestre Dominique , Aunis Dominique , Schaeffer Evelyne 
Published: April 2009

ABSTRACTHuman immunodeficiency virus type 1 (HIV-1) infects the central nervous system (CNS) and plays a direct role in the pathogenesis of AIDS dementia. However, mechanisms underlying HIV-1 gene expression in the CNS are poorly understood. The importance of CCAAT/enhancer binding proteins (C/EBP) for HIV-1 expression in cells of the immune system has been recently reported. In this study, we have examined the role and the molecular mechanisms by which proteins of the C/EBP family regulate HIV-1 gene transcription in human brain cells. We found that NF-IL6 acts as a potent activator of the long terminal repeat (LTR)-driven transcription in microglial and oligodendroglioma cells. In contrast, C/EBPγ inhibits NF-IL6-induced activation. Consistent with previous data, our transient expression results show cell-type-specific NF-IL6-mediated transactivation. In glial cells, full activation needs the presence of the C/EBP binding sites; however, NF-IL6 is still able to function via the minimal −40/+80 region. In microglial cells, C/EBP sites are not essential, since NF-IL6 acts through the −68/+80 LTR region, containing two binding sites for the transcription factor Sp1. Moreover, we show that functional interactions between NF-IL6 and Sp1 lead to synergistic transcriptional activation of the LTR in oligodendroglioma and to mutual repression in microglial cells. We further demonstrate that NF-IL6 physically interacts with the nuclear receptor chicken ovalbumin upstream promoter transcription factor (COUP-TF), via its DNA binding domain, in vitro and in cells, which results in mutual transcriptional repression. These findings reveal how the interplay of NF-IL6 and C/EBPγ, together with Sp1 and COUP-TF, regulates HIV-1 gene transcription in brain cells.
Respiratory Syncytial Virus That Lacks Open Reading Frame 2 of the M2 Gene (M2-2) Has Altered Growth Characteristics and Is Attenuated in Rodents
Authors: Jin Hong , Cheng Xing , Zhou Helen Z. Y. , Li Shengqiang , Seddiqui Adam 
Published: April 2009

ABSTRACT
The M2 gene of respiratory syncytial virus (RSV) encodes two putative proteins: M2-1 and M2-2; both are believed to be involved in the RNA transcription or replication process. To understand the function of the M2-2 protein in virus replication, we deleted the majority of the M2-2 open reading frame from an infectious cDNA clone derived from the human RSV A2 strain. Transfection of HEp-2 cells with the cDNA clone containing the M2-2 deletion, together with plasmids that encoded the RSV N, P, and L proteins, produced a recombinant RSV that lacked the M2-2 protein (rA2ΔM2-2). Recombinant virus rA2ΔM2-2 was recovered and characterized. The levels of viral mRNA expression for 10 RSV genes examined were unchanged in cells infected with rA2ΔM2-2, except that a shorter M2 mRNA was detected. However, the ratio of viral genomic or antigenomic RNA to mRNA was reduced in rA2ΔM2-2-infected cells. By use of an antibody directed against the bacterially expressed M2-2 protein, the putative M2-2 protein was detected in cells infected with wild-type RSV but not in cells infected with rA2ΔM2-2. rA2ΔM2-2 displayed a small-plaque morphology and grew much more slowly than wild-type RSV in HEp-2 cells. In infected Vero cells, rA2ΔM2-2 exhibited very large syncytium formation compared to that of wild-type recombinant RSV. rA2ΔM2-2 appeared to be a host range mutant, since it replicated poorly in HEp-2, HeLa, and MRC5 cells but replicated efficiently in Vero and LLC-MK2 cells. Replication of rA2ΔM2-2 in the upper and lower respiratory tracts of mice and cotton rats was highly restricted. Despite its attenuated replication in rodents, rA2ΔM2-2 was able to provide protection against challenge with wild-type RSV A2. The genotype and phenotype of the M2-2 deletion mutant were stably maintained after extensive in vitro passages. The attenuated phenotype of rA2ΔM2-2 suggested that rA2ΔM2-2 may be a potential candidate for use as a live attenuated vaccine.
The Disappearance of Cyclins A and B and the Increase in Activity of the G
2
/M-Phase Cellular Kinase cdc2 in Herpes Simplex Virus 1-Infected Cells Require Expression of the α22/U
S
1.5 and U
L
13 Viral Genes
Authors: Advani S. J. , Brandimarti R. , Weichselbaum R. R. , Roizman B. 
Published: April 2009

ABSTRACT

In uninfected cells the G
2
/M transition is regulated by cyclin kinase complex containing cdc2 and, initially, cyclin A, followed by cyclin B. cdc2 is downregulated through phosphorylation by wee-1 and myt-1 and upregulated by cdc-25C phosphatase. We have examined the accumulation and activities of these proteins in cells infected with wild type and mutants of herpes simplex virus 1. The results were as follows. (i) Cyclin A and B levels were reduced beginning 4 h after infection and were undetectable at 12 to 16 h after infection. (ii) cdc2 protein also decreased in amount but was detectable at all times after infection. In addition, a fraction of cdc2 protein from infected cells exhibited altered electrophoretic mobility in denaturing gels. (iii) The levels of cdk7 or myt-1 proteins remained relatively constant throughout infection, whereas the level of wee-1 was significantly decreased. (iv) cdc-25C formed novel bands characterized by slower electrophoretic mobility that disappeared after treatment with phosphatase. In addition, one phosphatase-sensitive band reacted with MPM-2 antibody that recognizes a phosphoepitope phosphorylated exclusively in M phase. (v) cdc2 accumulating in infected cells exhibited kinase activity. The activity of cdc2 was higher in infected cell lysates than those of corresponding proteins present in lysates of mock-infected cells even though cyclins A and B were not detectable in lysates of infected cells. (vi) The decrease in the levels of cyclins A and B, the increase in activity of cdc2, and the hyperphosphorylation of cdc-25C were mediated by U
L
13 and α22/U
S
1.5 gene products. In light of its normal functions, the activated cdc2 kinase may play a role in the changes in the morphology of the infected cell. These results are consistent with the accruing evidence that herpes simplex virus scavenges the cell for useful cell cycle proteins and subverts them for its own use.
Different Regions of Hepatitis B Virus X Protein Are Required for Enhancement of bZip-Mediated Transactivation versus Transrepression
Authors: Barnabas Sangeeta , Andrisani Ourania M. 
Published: April 2009

ABSTRACT

The hepatitis B virus X protein (pX) interacts directly with the bZip transactivator CREB and the bZip repressors ICERIIγ and ATF3, increasing their DNA-binding affinity in vitro and their transcriptional efficacy in vivo. However, the mechanism of bZip-pX interaction and of the pX-mediated increase in the bZip transcriptional efficacy remains to be understood. In this study with deletion mutants of pX, we delineated a 67-amino-acid region spanning residues 49 to 115 required for direct CREB, ATF3, and ICER IIγ interaction in vitro and in vivo and increased bZip/CRE binding in vitro. Transient transfections of the pX deletion mutants in AML12 hepatocytes demonstrate that pX
49–115
is as effective as the full-length pX in enhancing the ATF3- and ICERIIγ-mediated transrepression. However, this pX region is inactive in increasing the transactivation efficacy of CREB; additional amino acid residues present in pX
49–140
are required to mediate the increased transactivation efficacy of CREB in vivo. This requirement for different regions of pX in affecting CREB transactivation suggests that amino acid residues 115 to 140 integrate additional events in effecting pX-mediated transactivation, such as concomitant interactions with select components of the basal transcriptional apparatus.
The Phosphoprotein of Rabies Virus Is Phosphorylated by a Unique Cellular Protein Kinase and Specific Isomers of Protein Kinase C
Authors: Gupta Ashim K. , Blondel Danielle , Choudhary Suresh , Banerjee Amiya K. 
Published: April 2009

ABSTRACT

The phosphoprotein (P) gene of rabies virus (CVS strain) was cloned and expressed in bacteria. The purified protein was used as the substrate for phosphorylation by the protein kinase(s) present in cell extract prepared from rat brain. Two distinct types of protein kinases, staurosporin sensitive and heparin sensitive, were found to phosphorylate the P protein in vitro by the cell extract. Interestingly, the heparin-sensitive kinase was not the ubiquitous casein kinase II present in a variety of cell types. Further purification of the cell fractions revealed that the protein kinase C (PKC) isomers constitute the staurosporin-sensitive kinases α, β, γ, and ζ, with the PKCγ isomer being the most effective in phosphorylating the P protein. A unique heparin-sensitive kinase was characterized as a 71-kDa protein with biochemical properties not demonstrated by any known protein kinases stored in the protein data bank. This protein kinase, designated RVPK (rabies virus protein kinase), phosphorylates P protein (36 kDa) and alters its mobility in gel to migrate at 40 kDa. In contrast, the PKC isoforms do not change the mobility of unphosphorylated P protein. RVPK appears to be packaged in the purified virions, to display biochemical characteristics similar to those of the cell-purified RVPK, and to similarly alter the mobility of endogenous P protein upon phosphorylation. By site-directed mutagenesis, the sites of phosphorylation of RVPK were mapped at S
63
and S
64
, whereas PKC isomers phosphorylated at S
162
, S
210
, and S
271
. Involvement of a unique protein kinase in phosphorylating rabies virus P protein indicates its important role in the structure and function of the protein and consequently in the life cycle of the virus.
Alteration of Hepatitis A Virus (HAV) Particles by a Soluble Form of HAV Cellular Receptor 1 Containing the Immunoglobulin- and Mucin-Like Regions
Authors: Silberstein Erica , Xing Li , van de Beek Willem , Lu Jinhua , Cheng Holland , Kaplan Gerardo G. 
Published: April 2009

ABSTRACT
Hepatitis A virus (HAV) infects African green monkey kidney cells via HAV cellular receptor 1 (havcr-1). The ectodomain of havcr-1 contains an N-terminal cysteine-rich immunoglobulin-like region (D1), followed by a mucin-like region that extends D1 well above the cell surface. D1 is required for binding of HAV, and a soluble construct containing D1 fused to the hinge and Fc portions of human immunoglobulin G1 (IgG1), D1-Fc, bound and neutralized HAV inefficiently. However, D1-Fc did not alter the virions. To determine whether additional regions of havcr-1 are required to trigger uncoating of HAV, we constructed D1muc-Fc containing D1 and two-thirds of the mucin-like region fused to the Fc and hinge portions of human IgG1. D1muc-Fc neutralized 10 times more HAV than did D1-Fc. Sedimentation analysis in sucrose gradients showed that treatment of HAV with 20 to 200 nM D1muc-Fc disrupted the majority of the virions, whereas treatment with 2 nM D1muc-Fc had no effect on the sedimentation of the particles. Treatment of HAV with 100 nM D1muc-Fc resulted in low-level accumulation of 100- to 125S particles. Negative-stain electron microscopy analysis revealed that the 100- to 125S particles had the characteristics of disrupted virions, such as internal staining and diffuse edges. Quantitative PCR analysis showed that the 100- to 125S particles contained viral RNA. These results indicate that D1 and the mucin-like region of havcr-1 are required to induce conformational changes leading to HAV uncoating.
Time-Dependent Changes in Extreme-Precipitation Return-Period Amounts in the Continental United States
Authors: DeGaetano Arthur T. 
Published: April 2009

AbstractPartial-duration maximum precipitation series from Historical Climatology Network stations are used as a basis for assessing trends in extreme-precipitation recurrence-interval amounts. Two types of time series are analyzed: running series in which the generalized extreme-value (GEV) distribution is fit to separate overlapping 30-yr data series and lengthening series in which more recent years are iteratively added to a base series from the early part of the record. Resampling procedures are used to assess both trend and field significance. Across the United States, nearly two-thirds of the trends in the 2-, 5-, and 10-yr return-period rainfall amounts, as well as the GEV distribution location parameter, are positive. Significant positive trends in these values tend to cluster in the Northeast, western Great Lakes, and Pacific Northwest. Slopes are more pronounced in the 1960–2007 period when compared with the 1950–2007 interval. In the Northeast and western Great Lakes, the 2-yr return-period precipitation amount increases at a rate of approximately 2% per decade, whereas the change in the 100-yr storm amount is between 4% and 9% per decade. These changes result primarily from an increase in the location parameter of the fitted GEV distribution. Collectively, these increases result in a median 20% decrease in the expected recurrence interval, regardless of interval length. Thus, at stations across a large part of the eastern United States and Pacific Northwest, the 50-yr storm based on 1950–79 data can be expected to occur on average once every 40 yr, when data from the 1950–2007 period are considered.
Stochastic versus Dynamical Downscaling of Ensemble Precipitation Forecasts
Authors: Brussolo Elisa , von Hardenberg Jost , Rebora Nicola 
Published: April 2009

Abstract
The assessment of hydrometeorological risk in small basins requires the availability of skillful, high-resolution quantitative precipitation forecasts to predict the probability of occurrence of severe, localized precipitation events. Large-scale ensemble prediction systems (EPS) currently provide forecast scenarios down to a resolution of about 50 km. High-resolution, nonhydrostatic, limited-area ensemble prediction systems provide dynamically based forecasts by extending these scenarios to smaller scales, typically on the order of 10 km. This work explores an alternative approach to the use of limited-area ensemble prediction systems, by directly applying a stochastic downscaling technique to large-scale ensemble forecasts. The performances of these two different approaches for three well-predicted precipitation events in northwestern Italy during 2006 are compared. Ensemble forecasts provided by the ECMWF EPS, downscaled using the Rainfall Filtered Autoregressive Model (RainFARM) stochastic technique, and ensemble forecasts obtained from the Consortium for Small-Scale Modeling Limited-Area Ensemble Prediction System (COSMO-LEPS) are considered. A dense network of rain gauges is used for verification. It is found that the probabilistic forecast skill of stochastically downscaled ensembles may be comparable with that of dynamically downscaled ensembles, using a range of standard forecast skill measures. Stochastic downscaling is suggested as a tool for benchmarking the performance of dynamical ensemble downscaling systems.
A methodology for post-occupancy evaluation of ventilation rates in schools
Authors: Mumovic D. , Davies M. , Ridley I. , Altamirano-Medina H. , Oreszczyn T. 
Published: April 2009

The importance of maintaining adequate indoor air quality in schools is recognised as a contributing factor to pupils' learning performance. This paper describes a series of field measurements that investigating the ventilation rates in four recently built secondary schools in England. All schools were assessed for compliance with the recently adopted Building Bulletin 101, which defines the set of criteria in relation to the ventilation rates and indoor air quality in new school buildings. Using the obtained results a methodology has been suggested for post-occupancy evaluation of ventilation rates in schools. The suggested methodology draws particular attention to the dynamic nature of the interaction between the building and their occupants. Practical application: The new Building Bulletin 101 is quoted in Approved Document F as a means of compliance with Building Regulations for school buildings in the UK. This paper, based on four case studies, highlights some of the problems facing architects, mechanical engineers and building control officers associated with post-occupancy evaluation of ventilation rates in new school buildings. The methodology suggested in this paper, which differs radically from the current practice, takes into account the changing nature of the indoor environment in schools including occupancy level and occupant behaviour.
Prediction of flow-generated noise produced by an in-duct spoiler in a ventilation system using CIBSE Guide B5 methods
Authors: Mak CM , Ye C. , Wu J. , Yang J. 
Published: April 2009

Measurements of flow-generated noise produced by two different types of strip spoilers in the air duct and radiated from an open exhaust termination unit into a reverberation chamber have been made in 1/3 octave bands using sound power spectra. The measured values are compared with the predicted values using CIBSE Guide B5 method based on selected values of the constant C. It is found that the measured values agree well with the predicted values. The measured values are also compared with the predicted sound power levels using the generic equations given in the Appendix 5.A2 of the CIBSE Guide. It is found that the predicted values using the generic formulae and the single normalised spectrum given in the Appendix 5.A2 of CIBSE Guide do not agree well with the measured values, particularly at low frequencies. For very different in-duct elements, a single normalised spectrum for flow-generated noise may not be sufficient for all configurations of the in-duct elements. It is suggested that several representative normalised spectra for different types of in-duct elements should be given. Practical application: This study provides an evaluation of the accuracy of the CIBSE Guide B5 method and the CIBSE Appendix 5.A2 generic formulae for the prediction of flow-generated noise produced by in-duct spoilers in a ventilation system. It also gives comments on the method for improvements.