bluuebunny/crossref_metadata_2025 huggingface dataset:
Human Immunodeficiency Virus Type 1 Subtype B Ancestral Envelope Protein Is Functional and Elicits Neutralizing Antibodies in Rabbits Similar to Those Elicited by a Circulating Subtype B Envelope
Authors: Doria-Rose N. A. , Learn G. H. , Rodrigo A. G. , Nickle D. C. , Li F. , Mahalanabis M. , Hensel M. T. , McLaughlin S. , Edmonson P. F. , Montefiori D. , Barnett S. W. , Haigwood N. L. , Mullins J. I.
Published: August 2005

Human immunodeficiency virus type 1 (HIV-1) is a difficult target for vaccine development, in part because of its ever-expanding genetic diversity and attendant capacity to escape immunologic recognition. Vaccine efficacy might be improved by maximizing immunogen antigenic similarity to viruses likely to be encountered by vaccinees. To this end, we designed a prototype HIV-1 envelope vaccine using a deduced ancestral state for theenvgene. The ancestral state reconstruction method was shown to be >95% accurate by computer simulation and 99.8% accurate when estimating the known inoculum used in an experimental infection study in rhesus macaques. Furthermore, the deduced ancestor gene differed from the set of sequences used to derive the ancestor by an average of 12.3%, while these latter sequences were an average of 17.3% different from each other. A full-length ancestral subtype B HIV-1envgene was constructed and shown to produce a glycoprotein of 160 kDa that bound and fused with cells expressing the HIV-1 coreceptor CCR5. This Env was also functional in a virus pseudotype assay. When either gp160- or gp140-expressing plasmids and recombinant gp120 were used to immunize rabbits in a DNA prime-protein boost regimen, the artificial gene induced immunoglobulin G antibodies capable of weakly neutralizing heterologous primary HIV-1 strains. The results were similar for rabbits immunized in parallel with a natural isolate, HIV-1 SF162. Further design efforts to better present conserved neutralization determinants are warranted.
Broad Cross-Clade T-Cell Responses to Gag in Individuals Infected with Human Immunodeficiency Virus Type 1 Non-B Clades (A to G): Importance of HLA Anchor Residue Conservation
Authors: Geels Mark J. , Dubey Sheri A. , Anderson Kiersten , Baan Elly , Bakker Margreet , Pollakis Georgios , Paxton William A. , Shiver John W. , Goudsmit Jaap
Published: August 2005

We aimed to identify cross-clade human immunodeficiency virus type 1 (HIV-1) specific T-cell responses among 10 HLA-typed individuals who were infected with non-B HIV-1 strains (A, AG, C, D, G, or F) and to correlate these responses with genetic variation in documented T-cell epitopes. T-cell reactivity was tested against peptide pools spanning clade B Gag, Pol, Nef, Rev, and Tat consensus, with Gag and Nef providing the highest responses. Nine individuals who responded to clade B Gag demonstrated cross-reactive T-cell responses against clade A and C Gag pools, while six of seven responders to Nef-B reacted to clade A and C Nef pools. An inverse correlation between the height of the T-cell responses and the sequence divergence of the HLA class I-restricted epitopes was identified when we compared autologous Gag and Nef sequences with the reactive consensus pools. This could be explained for the Gag sequences through observed variations in the HLA anchor residues. Through mapping of 30 amino acid cross-clade-reactive regions using Gag-B pools, we were able to link 58% (14/24) of the T-cell responses to regions containing previously described HLA class I-restricted epitopes. Forty-two percent (10/24) of the responses were directed to regions containing new epitopes, for which predicted HLA class I motifs could be recognized in 70% (7/10) of individuals. We demonstrate here that cross-clade T-cell responses are frequently induced in individuals infected with distinct HIV-1 clades, suggesting that interclade variation outside of HLA anchor residues may have less impact on vaccine-induced T-cell reactivity than previously thought.
Are Ducks Contributing to the Endemicity of Highly Pathogenic H5N1 Influenza Virus in Asia?
Authors: Sturm-Ramirez K. M. , Hulse-Post D. J. , Govorkova E. A. , Humberd J. , Seiler P. , Puthavathana P. , Buranathai C. , Nguyen T. D. , Chaisingh A. , Long H. T. , Naipospos T. S. P. , Chen H. , Ellis T. M. , Guan Y. , Peiris J. S. M. , Webster R. G.
Published: August 2005

Wild waterfowl are the natural reservoir of all influenza A viruses, and these viruses are usually nonpathogenic in these birds. However, since late 2002, H5N1 outbreaks in Asia have resulted in mortality among waterfowl in recreational parks, domestic flocks, and wild migratory birds. The evolutionary stasis between influenza virus and its natural host may have been disrupted, prompting us to ask whether waterfowl are resistant to H5N1 influenza virus disease and whether they can still act as a reservoir for these viruses. To better understand the biology of H5N1 viruses in ducks and attempt to answer this question, we inoculated juvenile mallards with 23 different H5N1 influenza viruses isolated in Asia between 2003 and 2004. All virus isolates replicated efficiently in inoculated ducks, and 22 were transmitted to susceptible contacts. Viruses replicated to higher levels in the trachea than in the cloaca of both inoculated and contact birds, suggesting that the digestive tract is not the main site of H5N1 influenza virus replication in ducks and that the fecal-oral route may no longer be the main transmission path. The virus isolates' pathogenicities varied from completely nonpathogenic to highly lethal and were positively correlated with tracheal virus titers. Nevertheless, the eight virus isolates that were nonpathogenic in ducks replicated and transmitted efficiently to naïve contacts, suggesting that highly pathogenic H5N1 viruses causing minimal signs of disease in ducks can propagate silently and efficiently among domestic and wild ducks in Asia and that they represent a serious threat to human and veterinary public health.
Virulent Variants Emerging in Mice Infected with the Apathogenic Prototype Strain of the Parvovirus Minute Virus of Mice Exhibit a Capsid with Low Avidity for a Primary Receptor
Authors: Rubio Mari-Paz , López-Bueno Alberto , Almendral José M.
Published: August 2005

The mechanisms involved in the emergence of virulent mammalian viruses were investigated in the adult immunodeficient SCID mouse infected by the attenuated prototype strain of the parvovirus Minute Virus of Mice (MVMp). Cloned MVMp intravenously inoculated in mice consistently evolved during weeks of subclinical infection to variants showing altered plaque phenotypes. All the isolated large-plaque variants spread systemically from the oronasal cavity and replicated in major organs (brain, kidney, liver), in sharp contrast to the absolute inability of the MVMp and small-plaque variants to productively invade SCID organs by this natural route of infection. The virulent variants retained the MVMp capacity to infect mouse fibroblasts, consistent with the lack of genetic changes across the 220-to-335 amino acid sequence of VP2, a capsid domain containing main determinants of MVM tropism. However, the capsid of the virulent variants shared a lower affinity than the wild type for a primary receptor used in the cytotoxic infection. The capsid gene of a virulent variant engineered in the MVMp background endowed the recombinant virus with a large-plaque phenotype, lower affinity for the receptor, and productive invasiveness by the oronasal route in SCID mice, eventually leading to 100% mortality. In the analysis of virulence in mice, both MVMp and the recombinant virus similarly gained the bloodstream 1 to 2 days postoronasal inoculation and remained infectious when adsorbed to blood cells in vitro. However, the wild-type MVMp was cleared from circulation a few days afterwards, in contrast to the viremia of the recombinant virus, which was sustained for life. Significantly, attachment to an abundant receptor of primary mouse kidney epithelial cells by both viruses could be quantitatively competed by wild-type MVMp capsids, indicating that virulence is not due to an extended receptor usage in target tissues. We conclude that the selection of capsid-receptor interactions of low affinity, which favors systemic infection, is a major evolutionary process in the adaptation of parvoviruses to new hosts and in the cause of disease.
The UL7 Gene of Pseudorabies Virus Encodes a Nonessential Structural Protein Which Is Involved in Virion Formation and Egress
Authors: Fuchs Walter , Granzow Harald , Klopfleisch Robert , Klupp Barbara G. , Rosenkranz Daniela , Mettenleiter Thomas C.
Published: August 2005

Homologues of the UL7 gene of herpes simplex virus type 1 are conserved in alpha-, beta-, and gammaherpesviruses. However, little is known about their functions. Using a monospecific rabbit antiserum raised against a bacterial fusion protein, we identified the UL7 gene product of the neurotropic alphaherpesvirus pseudorabies virus (PrV). In Western blot analyses of infected cells and purified PrV particles the serum specifically detected a 29-kDa protein, which matches the calculated mass of the 266-amino-acid translation product of PrV UL7. For functional analysis, UL7 was deleted by mutagenesis of an infectious full-length clone of the PrV genome in
Escherichia coli
. The obtained recombinant PrV-ΔUL7F was replication competent in rabbit kidney cells, but maximum virus titers were decreased nearly 10-fold and plaque diameters were reduced by ca. 60% compared to wild-type PrV. Electron microscopy of infected cells revealed that in the absence of UL7, formation and nuclear egress of nucleocapsids were not affected, whereas secondary envelopment of cytoplasmic nucleocapsids appeared to be delayed and release of mature virions was less efficient. The observed replication defects were corrected by repair of the viral UL7 gene or by propagation of PrV-ΔUL7F in UL7-expressing cells. PrV-ΔUL7F was moderately attenuated in mice. Compared to wild-type virus, mean survival times were prolonged from 2 to 3 days after intranasal infection. However, neuroinvasion and transneuronal spread of PrV were not abolished in the absence of UL7. Thus, UL7 encodes a virion protein of PrV, which plays a role during virion maturation and egress both in vitro and in vivo.
Herpes Simplex Virus Type 1 Infection Leads to Loss of Serine-2 Phosphorylation on the Carboxyl-Terminal Domain of RNA Polymerase II
Authors: Fraser Kathryn A. , Rice Stephen A.
Published: August 2005

Previous studies have shown that herpes simplex virus type 1 (HSV-1) infection alters the phosphorylation of the carboxyl-terminal domain (CTD) of RNA polymerase II (RNAP II), creating a new form of the enzyme known as RNAP II
I
. However, the specific phosphorylation changes induced by HSV-1 have not been characterized. In this study, we used phospho-specific anti-CTD antibodies to probe the structure of the postinfection RNAP II. We find that RNAP II
I
is phosphorylated on serine-5 (Ser-5) of the CTD consensus repeat but generally lacks phosphorylation on serine-2 (Ser-2). Since Ser-2 phosphorylation is normally associated with efficient transcriptional elongation and the recruitment of pre-mRNA processing factors, our results suggest that RNAP II
I
may have altered elongation properties and decreased interactions with the mRNA processing machinery. The viral factors responsible for the reduction in Ser-2 CTD phosphorylation were studied. We found that viral immediate-early (IE) gene expression is required and sufficient, in the context of infection, for loss of Ser-2 phosphorylation. However, studies with viral mutants failed to implicate a single IE protein (among ICP0, ICP4, ICP22, and ICP27) in this process. Although most Ser-2-phosphorylated RNAP II is lost after infection, our immunofluorescence analyses identified a small subfraction that escapes loss and relocalizes to splicing antigen-rich nuclear speckles. A similar phenomenon is seen in uninfected cells after various treatments that inhibit RNAP II transcription. We hypothesize that the HSV-1-induced relocalization of residual Ser-2-phosphorylated RNAP II to nuclear speckles reflects a host response to the inhibition of cellular gene transcription.
Phylodynamic Analysis of Human Immunodeficiency Virus Type 1 in Distinct Brain Compartments Provides a Model for the Neuropathogenesis of AIDS
Authors: Salemi Marco , Lamers Susanna L. , Yu Stephanie , de Oliveira T. , Fitch Walter M. , McGrath Michael S.
Published: August 2005

“Phylodynamic” analysis combines various statistical procedures that can be used to correlate the epidemiological and evolutionary behavior of viral pathogens with the immune system of the host. We utilized this approach to examine human immunodeficiency virus type 1 (HIV-1) gp120 envelope DNA sequences (V1, V2, and V3) isolated from different brain compartments of a T-cell-depleted patient diagnosed with severe HIV-associated dementia at the time of death. In agreement with previous reports, phylogenetic analysis showed distinct virodemes but also revealed a significant amount of viral gene flow among different brain compartments. Local-molecular-clock analysis showed that HIV-1 meninges and temporal lobe subpopulations evolve about 30 and 100 times faster, respectively, than the other viral populations in the brain. However, maximum likelihood codon-based substitution models did not detect any site under significant positive selective pressure, and the main cause of HIV-1 genetic variation appeared to be random genetic drift. Therefore, the higher evolutionary rate in the meninges and temporal lobe could be due to an enhanced infection/expansion rate of macrophages as a consequence of the immune system failure. In conclusion, in this case study, viral infection in the brain progressed with a nonspecific genetic evolution, recurrent migration events, and an expansion of macrophage-tropic sequences. The data suggest that after immune failure newly produced viral variants, which would be rapidly cleared under normal conditions, begin to productively infect macrophages in a “self-amplifying” cycle of infection/inflammatory response that could be at the origin of HIV-associated dementia.
Hepatitis C Virus Core Protein Is a Dimeric Alpha-Helical Protein Exhibiting Membrane Protein Features
Authors: Boulant Steeve , Vanbelle Christophe , Ebel Christine , Penin François , Lavergne Jean-Pierre
Published: August 2005

The building block of hepatitis C virus (HCV) nucleocapsid, the core protein, together with viral RNA, is composed of different domains involved in RNA binding and homo-oligomerization. The HCV core protein 1-169 (C
HCV
169) and its N-terminal region from positions 1 to 117 (C
HCV
117) were expressed in
Escherichia coli
and purified to homogeneity suitable for biochemical and biophysical characterizations. The overall conformation and the oligomeric properties of the resulting proteins C
HCV
169 and C
HCV
117 were investigated by using analytical centrifugation, circular dichroism, intrinsic fluorescence measurements, and limited proteolysis. Altogether, our results show that core protein (C
HCV
169) behaves as a membranous protein and forms heterogeneous soluble micelle-like aggregates of high molecular weight in the absence of detergent. In contrast, it behaves, in the presence of mild detergent, as a soluble, well-folded, noncovalent dimer. Similar to findings observed for core proteins of HCV-related flaviviruses, the HCV core protein is essentially composed of α-helices (50%). In contrast, C
HCV
117 is soluble and monodispersed in the absence of detergent but is unfolded. It appears that the folding of the highly basic domain from positions 2 to 117 (2-117 domain) depends on the presence of the 117-169 hydrophobic domain, which contains the structural determinants ensuring the binding of core with cellular membranes. Finally, our findings provide valuable information for further investigations on isolated core protein, as well as for attempts to reconstitute nucleocapsid particles in vitro.
Adenovirus Type 5 E4orf3 Protein Targets the Mre11 Complex to Cytoplasmic Aggresomes
Authors: Araujo Felipe D. , Stracker Travis H. , Carson Christian T. , Lee Darwin V. , Weitzman Matthew D.
Published: August 2005

Virus infections have dramatic effects on structural and morphological characteristics of the host cell. The gene product of open reading frame 3 in the early region 4 (E4orf3) of adenovirus serotype 5 (Ad5) is involved in efficient replication and late protein synthesis. During infection with adenovirus mutants lacking the E4 region, the viral genomic DNA is joined into concatemers by cellular DNA repair factors, and this requires the Mre11/Rad50/Nbs1 complex. Concatemer formation can be prevented by the E4orf3 protein, which causes the cellular redistribution of the Mre11 complex. Here we show that E4orf3 colocalizes with components of the Mre11 complex in nuclear tracks and also in large cytoplasmic accumulations. Rearrangement of Mre11 and Rad50 by Ad5 E4orf3 is not dependent on interactions with Nbs1 or promyelocytic leukemia protein nuclear bodies. Late in infection the cytoplasmic inclusions appear as a distinct juxtanuclear accumulation at the centrosome and this requires an intact microtubule cytoskeleton. The large cytoplasmic accumulations meet the criteria defined for aggresomes, including γ-tubulin colocalization and formation of a surrounding vimentin cage. E4orf3 also appears to alter the solubility of the cellular Mre11 complex. These data suggest that E4orf3 can target the Mre11 complex to an aggresome and may explain how the cellular repair complex is inactivated during adenovirus infection.
Examination of the pRb-Dependent and pRb-Independent Functions of E7 In Vivo
Authors: Balsitis Scott , Dick Fred , Lee Denis , Farrell Linda , Hyde R. Katherine , Griep Anne E. , Dyson Nicholas , Lambert Paul F.
Published: August 2005

High-risk human papillomaviruses encode two oncogenes, E6 and E7, expressed in nearly all cervical cancers. Although E7 protein is best known for its ability to inactivate the retinoblastoma tumor suppressor protein, pRb, many other activities for E7 have been proposed in in vitro studies. Herein, we describe studies that allowed us to define unambiguously the pRb-dependent and -independent activities of E7 for the first time in vivo. In these studies, we crossed mice transgenic for human papillomavirus 16 E7 to knock-in mice genetically engineered to express a mutant form of pRb (pRb
ΔLXCXE
) that is selectively defective for binding E7. pRb inactivation was necessary for E7 to induce DNA synthesis and to overcome differentiation-dependent cell cycle withdrawal and DNA damage-induced cell cycle arrest. While most of E7's effects on epidermal differentiation were found to require pRb inactivation, a modest delay in terminal differentiation with resulting hyperplasia was observed in E7 mice on the
Rb

ΔLXCXE

mutant background. E7-induced p21 upregulation was also pRb dependent, and genetic
Rb
inactivation was sufficient to reproduce this effect. While E7-mediated p21 induction was partially p53 dependent, neither p53 nor p21 induction by E7 required p19
ARF
. These data show that E7 upregulates the expression of p53 and p21 via pRb-dependent mechanisms distinct from the proposed p19-Mdm2 pathway. These results extend our appreciation of the importance of pRb as a relevant target for high-risk E7 oncoproteins.
The Secreted Form of Dengue Virus Nonstructural Protein NS1 Is Endocytosed by Hepatocytes and Accumulates in Late Endosomes: Implications for Viral Infectivity
Authors: Alcon-LePoder Sophie , Drouet Marie-Thérèse , Roux Pascal , Frenkiel Marie-Pascale , Arborio Michel , Durand-Schneider Anne-Marie , Maurice Michèle , Le Blanc Isabelle , Gruenberg Jean , Flamand Marie
Published: August 2005

The flavivirus nonstructural protein NS1 is expressed as three discrete species in infected mammalian cells: an intracellular, membrane-associated form essential for viral replication, a cell surface-associated form that may be involved in signal transduction, and a secreted form (sNS1), the biological properties of which remain elusive. To determine the distribution of the dengue virus (DEN) sNS1 protein in vivo, we have analyzed by immunohistological means the tissue tropism of purified DEN sNS1 injected intravenously into adult mice. The sNS1 protein was found predominantly associated with the liver, where hepatocytes appeared to represent a major target cell. We further showed that sNS1 could be efficiently endocytosed by human Huh7 and HepG2 hepatocytes in vitro. After its internalization, the protein was detected intracellularly for at least 48 h without being substantially degraded. Colocalization studies of sNS1 with markers of the endolysosomal compartments revealed that the protein was specifically targeted to lysobisphosphatidic acid-rich structures reminiscent of late endosomes, as confirmed by electron microscopy. Intracellular accumulation of sNS1 in Huh7 cells enhanced the fluid phase uptake of rhodamine-labeled dextran. Furthermore, preincubation of Huh7 cells with sNS1 increased dengue virus production after infection with the homologous strain of DEN-1 virus. Our results demonstrate that the accumulation of DEN sNS1 in the late endosomal compartment of hepatocytes potentializes subsequent dengue virus infection in vitro, raising the possibility that sNS1 may contribute to viral propagation in vivo.
H5N2 Avian Influenza Outbreak in Texas in 2004: the First Highly Pathogenic Strain in the United States in 20 Years?
Authors: Lee Chang-Won , Swayne David E. , Linares Jose A. , Senne Dennis A. , Suarez David L.
Published: August 2005

In early 2004, an H5N2 avian influenza virus (AIV) that met the molecular criteria for classification as a highly pathogenic AIV was isolated from chickens in the state of Texas in the United States. However, clinical manifestations in the affected flock were consistent with avian influenza caused by a low-pathogenicity AIV and the representative virus (A/chicken/Texas/298313/04 [TX/04]) was not virulent for experimentally inoculated chickens. The hemagglutinin (HA) gene of the TX/04 isolate was similar in sequence to A/chicken/Texas/167280-4/02 (TX/02), a low-pathogenicity AIV isolate recovered from chickens in Texas in 2002. However, the TX/04 isolate had one additional basic amino acid at the HA cleavage site, which could be attributed to a single point mutation. The TX/04 isolate was similar in sequence to TX/02 isolate in several internal genes (NP, M, and NS), but some genes (PA, PB1, and PB2) had sequence of a clearly different origin. The TX/04 isolate also had a stalk deletion in the NA gene, characteristic of a chicken-adapted AIV. By analyzing viruses constructed by in vitro mutagenesis followed by reverse genetics, we found that the pathogenicity of the TX/04 virus could be increased in vitro and in vivo by the insertion of an additional basic amino acid at the HA cleavage site and not by the loss of a glycosylation site near the cleavage site. Our study provides the genetic and biologic characteristics of the TX/04 isolate, which highlight the complexity of the polygenic nature of the virulence of influenza viruses.
Human Immunodeficiency Virus Nef Induces Rapid Internalization of the T-Cell Coreceptor CD8αβ
Authors: Stove Veronique , Van de Walle Inge , Naessens Evelien , Coene Elisabeth , Stove Christophe , Plum Jean , Verhasselt Bruno
Published: August 2005

Human immunodeficiency virus (HIV) Nef is a membrane-associated protein decreasing surface expression of CD4, CD28, and major histocompatibility complex class I on infected cells. We report that Nef strongly down-modulates surface expression of the β-chain of the CD8αβ receptor by accelerated endocytosis, while CD8 α-chain expression is less affected. By mutational analysis of the cytoplasmic tail of the CD8 β-chain, an FMK amino acid motif was shown to be critical for Nef-induced endocytosis. Although independent of CD4, endocytosis of the CD8 β-chain was abrogated by the same mutations in Nef that affect CD4 down-regulation, suggesting common molecular interactions. The ability to down-regulate the human CD8 β-chain was conserved in HIV-1, HIV-2, and simian immunodeficiency virus SIVmac239 Nef and required an intact AP-2 complex. The Nef-mediated internalization of receptors, such as CD4, major histocompatibility complex class I, CD28, and CD8αβ, may contribute to the subversion of the host immune system and progression towards AIDS.
Large-Scale Analysis of Adeno-Associated Virus Vector Integration Sites in Normal Human Cells
Authors: Miller Daniel G. , Trobridge Grant D. , Petek Lisa M. , Jacobs Michael A. , Kaul Rajinder , Russell David W.
Published: August 2005

The integration sites of viral vectors used in human gene therapy can have important consequences for safety and efficacy. However, an extensive evaluation of adeno-associated virus (AAV) vector integration sites has not been completed, despite the ongoing use of AAV vectors in clinical trials. Here we have used a shuttle vector system to isolate and analyze 977 unique AAV vector-chromosome integration junctions from normal human fibroblasts and describe their genomic distribution. We found a significant preference for integrating within CpG islands and the first 1 kb of genes, but only a slight overall preference for transcribed sequences. Integration sites were clustered throughout the genome, including a major preference for integration in ribosomal DNA repeats, and 13 other hotspots that contained three or more proviruses within a 500-kb window. Both junctions were localized from 323 proviruses, allowing us to characterize the chromosomal deletions, insertions, and translocations associated with vector integration. These studies establish a profile of insertional mutagenesis for AAV vectors and provide unique insight into the chromosomal distribution of DNA strand breaks that may facilitate integration.
Radiation Leukemia Virus Common Integration at the
Kis2
Locus: Simultaneous Overexpression of a Novel Noncoding RNA and of the Proximal
Phf6
Gene
Authors: Landais Séverine , Quantin Renaud , Rassart Eric
Published: August 2005

Retroviral tagging has been used extensively and successfully to identify genes implicated in cancer pathways. In order to find oncogenes implicated in T-cell leukemia, we used the highly leukemogenic radiation leukemia retrovirus VL3 (RadLV/VL3). We applied the inverted PCR technique to isolate and analyze sequences flanking proviral integrations in RadLV/VL3-induced T lymphomas. We found retroviral integrations in c-
myc
and
Pim1
as already reported but we also identified for the first time
Notch1
as a RadLV common integration site. More interestingly, we found a new RadLV common integration site that is situated on mouse chromosome X (XA4 region, bp 45091000). This site has also been reported as an SL3-3 and Moloney murine leukemia virus integration site, which strengthens its implication in murine leukemia virus-induced T lymphomas. This locus, named
Kis2
(Kaplan Integration Site 2), was found rearranged in 11% of the tumors analyzed. In this article, we report not only the alteration of the
Kis2
gene located nearby in response to RadLV integration but also the induction of the expression of
Phf6
, situated about 250 kbp from the integration site. The
Kis2
gene encodes five different alternatively spliced noncoding RNAs and the
Phf6
gene codes for a 365-amino-acid protein which contains two plant homology domain fingers, recently implicated in the Börjeson-Forssman-Lehmann syndrome in humans. With the recent release of the mouse genome sequence, high-throughput retroviral tagging emerges as a powerful tool in the quest for oncogenes. It also allows the analysis of large DNA regions surrounding the integration locus.
Neuronal CXCL10 Directs CD8+T-Cell Recruitment and Control of West Nile Virus Encephalitis
Authors: Klein Robyn S. , Lin Eugene , Zhang Bo , Luster Andrew D. , Tollett Judy , Samuel Melanie A. , Engle Michael , Diamond Michael S.
Published: August 2005

The activation and entry of antigen-specific CD8+T cells into the central nervous system is an essential step towards clearance of West Nile virus (WNV) from infected neurons. The molecular signals responsible for the directed migration of virus-specific T cells and their cellular sources are presently unknown. Here we demonstrate that in response to WNV infection, neurons secrete the chemokine CXCL10, which recruits effector T cells via the chemokine receptor CXCR3. Neutralization or a genetic deficiency of CXCL10 leads to a decrease in CXCR3+CD8+T-cell trafficking, an increase in viral burden in the brain, and enhanced morbidity and mortality. These data support a new paradigm in chemokine neurobiology, as neurons are not generally considered to generate antiviral immune responses, and CXCL10 may represent a novel neuroprotective agent in response to WNV infection in the central nervous system.
The Severe Acute Respiratory Syndrome Coronavirus Nucleocapsid Protein Is Phosphorylated and Localizes in the Cytoplasm by 14-3-3-Mediated Translocation
Authors: Surjit Milan , Kumar Ravinder , Mishra Rabi N. , Reddy Malireddy K. , Chow Vincent T. K. , Lal Sunil K.
Published: August 2005

The severe acute respiratory syndrome coronavirus(SARS-CoV) nucleocapsid (N) protein is one of the four structural proteins of the virus and is predicted to be a 46-kDa phosphoprotein. Our in silico analysis predicted N to be heavily phosphorylated at multiple residues. Experimentally, we have shown in this report that the N protein of the SARS-CoV gets serine-phosphorylated by multiple kinases, in both the cytoplasm and the nucleus. The phosphoprotein is stable and localizes in the cytoplasm and coprecipitates with the membrane fraction. Also, using specific inhibitors of phosphorylation and an in vitro phosphorylation assay, we show that the nucleocapsid protein is a substrate of cyclin-dependent kinase (CDK), glycogen synthase kinase, mitogen-activated protein kinase, and casein kinase II. Further, we show that the phosphorylated protein is translocated to the cytoplasm by binding to 14-3-3 (tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein). 14-3-3 proteins are a family of highly conserved, ubiquitously expressed eukaryotic proteins that function primarily as adapters that modulate interactions between components of various cellular signaling and cell cycle regulatory pathways through phosphorylation-dependent protein-protein interactions. Coincidentally, the N protein was also found to downregulate the expression of the theta isoform of 14-3-3 (14-3-3θ), leading to the accumulation of phosphorylated N protein in the nucleus, in the absence of growth factors. Using short interfering RNA specific to 14-3-3θ we have inhibited its expression to show accumulation of phosphorylated N protein in the nucleus. Thus, the data presented here provide a possible mechanism for phosphorylation-dependent nucleocytoplasmic shuttling of the N protein. This 14-3-3-mediated transport of the phosphorylated N protein and its possible implications in interfering with the cellular machinery are discussed.
Replication of Varicella-Zoster Virus in Human Skin Organ Culture
Authors: Taylor Shannon L. , Moffat Jennifer F.
Published: August 2005

Varicella-zoster virus (VZV) infection is restricted to humans, which hinders studies of its pathogenesis in rodent models of disease. To facilitate the study of VZV skin tropism, we developed an ex vivo system using human fetal skin organ culture (SOC). VZV replication was analyzed by plaque assay, transmission electron microscopy, and histology. The yield of infectious VZV from SOC increased ∼100-fold over 6 days, virions were abundant, and lesions developed that contained VZV antigens and resembled varicella and zoster lesions. The SOC system for VZV replication has applications for testing virus mutants and antiviral drugs.
APOBEC3G/CEM15 (hA3G) mRNA Levels Associate Inversely with Human Immunodeficiency Virus Viremia
Authors: Jin Xia , Brooks Andy , Chen Huiyuan , Bennett Ryan , Reichman Richard , Smith Harold
Published: August 2005

APOBEC3G/CEM15 (hA3G) is a novel host factor that confers resistance to lentiviral infection under experimental conditions. Human immunodeficiency virus (HIV) type 1, however, produces viral infectivity factor (Vif) that targets hA3G for proteolysis, thereby escaping this defense system. To examine hA3G's contribution to the protection against HIV disease progression in humans, we quantified hA3G mRNA levels in peripheral blood mononuclear cells from 6 HIV-uninfected and 25 HIV-infected subjects; the latter group included 8 long-term nonprogressors (LTNPs) and 17 progressors. None of the HIV-infected subjects were receiving antiretroviral therapy. We found a striking inverse correlation between hA3G mRNA levels and HIV viral loads (
P
≤ 0.00009) and a highly significant positive correlation between hA3G mRNA levels and CD4 cell counts (
P
≤ 0.00012) in these patients. Furthermore, we discovered that the order of hA3G mRNA levels is LTNPs > HIV-uninfected subjects > progressors.
Human Immunodeficiency Virus Mutations during the First Month of Infection Are Preferentially Found in Known Cytotoxic T-Lymphocyte Epitopes
Authors: Bernardin Flavien , Kong Denice , Peddada Lorraine , Baxter-Lowe Lee Ann , Delwart Eric
Published: August 2005

The full protein coding region of human immunodeficiency virus (HIV) genomes were sequenced using plasma collected from nine African-Americans prior to seroconversion and 7 to 28 days later. HIV mutations emerged in seven of these subjects at a genomewide rate of 2% per year. The location of nonsynonymous (NS) HIV mutations within these subjects was compared to their potential HLA-A and B types restricted CTL epitopes reported in the Los Alamos National Laboratory HIV immunology database. A statistically significant (P< 0.005) number of the early NS mutations (13.5%) were found within previously reported CTL epitopes. A virus sequencing and reported CTL epitopes database analysis therefore support a model where a significant proportion of very early nonsynonymous HIV mutations are selected by CTL.
Reversion In Vivo after Inoculation of a Molecular Proviral DNA Clone of Simian Immunodeficiency Virus with a Cytotoxic-T-Lymphocyte Escape Mutation
Authors: Kobayashi Masahiro , Igarashi Hiroko , Takeda Akiko , Kato Moriaki , Matano Tetsuro
Published: August 2005

Vaccine-based control of the replication of a simian immunodeficiency virus (SIV), SIVmac239, in macaques has recently been shown. In the process of the control, a mutant virus escaping from epitope-specific cytotoxic-T-lymphocyte (CTL) responses was rapidly selected and contained. In this study, we show that the wild-type virus appeared and became predominant in the absence of the epitope-specific CTL after inoculation of naive macaques with a molecular clone DNA of the CTL escape mutant SIV. This is the first report describing reversion in vivo from an inoculated, molecular proviral DNA clone of immunodeficiency virus with a CTL escape mutation.
Long-Term Presence of Virus-Specific Plasma Cells in Sensory Ganglia and Spinal Cord following Intravaginal Inoculation of Herpes Simplex Virus Type 2
Authors: Milligan Gregg N. , Meador Michael G. , Chu Chin-Fun , Young Christal G. , Martin Talitha L. , Bourne Nigel
Published: August 2005

The tissue sites of long-term herpes simplex virus type 2 (HSV-2)-specific antibody production in mice and guinea pigs were identified. In addition to secondary lymphoid tissue and bone marrow, HSV-specific plasma cells were detected in spinal cords of mice up to 10 months after intravaginal inoculation with a thymidine kinase-deficient HSV-2 strain and in lumbosacral ganglia and spinal cords of guinea pigs inoculated with HSV-2 strain MS. The long-term retention of virus-specific plasma cells in the peripheral and central nervous systems following HSV infection may be important for resistance to reinfection of neuronal tissues or may play a role in modulation of reactivation from latency.
Importin 7 May Be Dispensable for Human Immunodeficiency Virus Type 1 and Simian Immunodeficiency Virus Infection of Primary Macrophages
Authors: Zielske Steven P. , Stevenson Mario
Published: August 2005

In an in vitro assay employing reconstituted nuclei, importin 7 (IPO7) has been implicated in nuclear translocation of human immunodeficiency virus type 1 (HIV-1) cDNA. Using RNA interference technology, we inhibited expression of IPO7 by 80 to 95% in primary macrophages and in HeLa cells and monitored their ability to support HIV-1 and simian immunodeficiency virus (SIV) cDNA synthesis, nuclear translocation, and infection efficiency. Marked IPO7 deficiency did not alter the rate or extent of HIV-1 or SIV cDNA synthesis or nuclear translocation. The infection efficiency of HIV-1 was similarly unaltered. Therefore, in natural, nondividing targets of HIV-1, IPO7 may be dispensable for infection.
REMARKS ON SUFFICIENT CONDITIONS FOR CONSERVATIVITY OF MINIMAL QUANTUM DYNAMICAL SEMIGROUPS
Authors: BAHN CHANGSOO , KO CHUL KI , PARK YONG MOON
Published: August 2005

We have obtained sufficient conditions for conservativity of minimal quantum dynamical semigroup by modifying and extending the method used in [1]. Our criterion for conservativity can be considered as a complement to Chebotarev and Fagnola's conditions [1]. In order to show that our conditions are useful, we apply our results to concrete examples (models of heavy ion collision and noncommutative elliptic operators).
MODELING OF ELECTRICAL BEHAVIOR OF La0.7Ca0.3MnO3 CERAMIC USING IMPEDANCE SPECTROSCOPY
Authors: KUMAR VINOD , THAKUR O. P. , PANDEY LAKSHMAN , GUIMARAES A. P. , GOEL ANUBHA , PARKASH OM , KUMAR DEVENDRA
Published: August 2005

The ceramic system La 0.7 Ca 0.3 MnO 3 was prepared by solid state method and impedance measurements were carried out as a function of frequency (100 Hz – 1 MHz) in the temperature range 303–529 K. An equivalent circuit model that represented the data well was arrived at by comparing the experimental plots with computer simulated complex immittance spectra of model circuits. It consisted of three parallel RC circuits connected in series indicating the presence of three processes present in the system. The resistances are found to follow the behavior R = R0 exp (E/kT). The values of activation energy E for these are obtained.
ON THE MICROSCOPIC BEHAVIOR OF HYDROGEN IN AMORPHOUS SILICON
Authors: TUTTLE BLAIR R.
Published: August 2005

Microscopic aspects of the behavior of hydrogen in amorphous silicon are reviewed in the context of density functional electronic structure calculations. The relative energetics of various hydrogen complexes are presented. Also, a hydrogen density of states picture is used to describe hydrogen-related phenomena including diffusion and defect formation. A microscopic theory for hydrogen-related metastability will be discussed in detail.
MULTI-COMPONENT SQUEEZED COHERENT STATE FOR N TRAPPED IONS IN ANY POSITION OF A STANDING WAVE
Authors: LUO FANG-FANG , YANG WEN-XING , LI JIAO-MEI , SHU HUA-LING , GUAN HUA , GAO KE-LIN
Published: August 2005

We proposed a scheme to generate a multi-component squeezed coherent states with arbitrary coefficients on a line in phase space for multiple trapped ions radiated by a single standing-wave laser whose carrier frequency is tuned to the ions transition. In the scheme each ion does not need to be exactly positioned at the node of the standing wave. Furthermore, our scheme may allow the generation of a multi-component squeezed coherent states with large mean phonon number in a fast way by choosing a suitable laser intensity, which is important in view of de-coherence processes.
MEASURE SYNCHRONIZATION IN A COUPLED HAMILTONIAN SYSTEM ASSOCIATED WITH NONLINEAR SCHRÖDINGER EQUATION
Authors: VINCENT U. E. , NJAH A. N. , AKINLADE O.
Published: August 2005

We present preliminary numerical findings concerning measure synchronization in a pair of coupled Nonlinear Hamiltonian Systems (NLHS) derived from a Nonlinear Schrödinger Equation (NLSE). The dynamics of the two coupled NLHS were found to exhibit a transition to coherent invariant measure; their orbits sharing the same phase space as the coupling strength is increased. Transitions from quasiperiodicity (QP) measure desynchronization to QP measure synchronization and QP measure desynchronization to chaotic (CH) measure synchronization were observed.
MONTE CARLO VIDEO TEXT SEGMENTATION
Authors: CHEN DATONG , ODOBEZ JEAN-MARC , THIRAN JEAN-PHILIPPE
Published: August 2005

This paper presents a probabilistic algorithm for segmenting and recognizing text embedded in video sequences based on adaptive thresholding using a Bayes filtering method. The algorithm approximates the posterior distribution of segmentation thresholds of video text by a set of weighted samples. The set of samples is initialized by applying a classical segmentation algorithm on the first video frame and further refined by random sampling under a temporal Bayesian framework. This framework allows us to evaluate a text image segmentor on the basis of recognition result instead of visual segmentation result, which is directly relevant to our character recognition task. Results on a database of 6944 images demonstrate the validity of the algorithm.
CONJUGATE AND NATURAL GRADIENT RULES FOR BYY HARMONY LEARNING ON GAUSSIAN MIXTURE WITH AUTOMATED MODEL SELECTION
Authors: MA JINWEN , GAO BIN , WANG YANG , CHENG QIANSHENG
Published: August 2005

Under the Bayesian Ying–Yang (BYY) harmony learning theory, a harmony function has been developed on a BI-directional architecture of the BYY system for Gaussian mixture with an important feature that, via its maximization through a general gradient rule, a model selection can be made automatically during parameter learning on a set of sample data from a Gaussian mixture. This paper further proposes the conjugate and natural gradient rules to efficiently implement the maximization of the harmony function, i.e. the BYY harmony learning, on Gaussian mixture. It is demonstrated by simulation experiments that these two new gradient rules not only work well, but also converge more quickly than the general gradient ones.
A NOVEL ROBUST REGRESSION APPROACH OF LIDAR SIGNAL BASED ON MODIFIED LEAST SQUARES SUPPORT VECTOR MACHINE
Authors: SUN BING-YU , HUANG DE-SHUANG , FANG HAI-TAO , YANG XING-MING
Published: August 2005

Lidar is an active remote sensing instrument, but its effective range is often limited by signal-to-noise (SNR) ratio. The reason is that noises or fluctuations always strongly affect the measured results. To resolve this problem, a novel approach of using least-squares support vector machine (LS-SVM) to reconstruct the Lidar signal is proposed in this paper. LS-SVM has been proven as robust to noisy data; the Lidar signal, which is strongly corrupted by noises or fluctuations, can be thought as a function of distance. So detecting Lidar signals from high noisy regime can be regarded as a robust regression procedure which involves estimating the underlying relationship from detected signal data set. To apply the LS-SVM on Lidar signal regression, firstly the noises in Lidar signal is analyzed and then the traditional LS-SVM algorithm is modified to incorporate the a priori knowledge of the Lidar signal in the training of LS-SVM. The experimental results demonstrate the effectiveness and efficiency of our approach.
MINIMAL CLASSIFICATION METHOD WITH ERROR-CORRECTING CODES FOR MULTICLASS RECOGNITION
Authors: SIVALINGAM DAYAN MANOHAR , PANDIAN NARENKUMAR , BEN-ARIE JEZEKIEL
Published: August 2005

In this work, we develop an efficient technique to transform a multiclass recognition problem into a minimal binary classification problem using the Minimal Classification Method (MCM). The MCM requires only log 2 N classifications whereas the other methods require much more. For the classification, we use Support Vector Machine (SVM) based binary classifiers since they have superior generalization performance. Unlike the prevalent one-versus-one strategy (the bottom-up one-versus-one strategy is called tournament method) that separates only two classes at each classification, the binary classifiers in our method have to separate two groups of multiple classes. As a result, the probability of generalization error increases. This problem is alleviated by utilizing error correcting codes, which results only in a marginal increase in the required number of classifications. However, in comparison to the tournament method, our method requires only 50% of the classifications and still similar performance can be attained. The proposed solution is tested with the Columbia Object Image Library (COIL). We also test the performance under conditions of noise and occlusion.
A WAVELET-BASED APPROACH TO RIDGE THINNING IN FINGERPRINT IMAGES
Authors: YOU XINGE , FANG BIN , TANG YUAN YAN , HE ZHENYU
Published: August 2005

As a global feature of fingerprints, the thinning of ridges, extraction of minutiae and computation of orientation field are very important for automatic fingerprint recognition. Many algorithms have been proposed for their computation and estimation, but their results are unsatisfactory, especially for poor quality fingerprint images. In this paper, a robust wavelet-based method to create thinned ridge map of fingerprint for automatic recognition is proposed. Properties of modulus minima based on the spline wavelet function are substantially investigated. Desirable characteristics show that this method is suitable to describe the skeleton of the ridge of the fingerprint image. A multi-scale thinning algorithm based on the modulus minima of wavelet transform is presented. The proposed algorithm is able to improve the skeleton representation of the ridge of the fingerprint without side-effects and limitations of the existing methods. The thinned ridge map can facilitate the extraction of the minutiae for matching in fingerprint recognition. Experiments have been conducted to validate the effectiveness and efficiency of the proposed method.
CHAOS IN NONAUTONOMOUS DIFFERENTIAL INCLUSIONS
Authors: FEČKAN MICHAL
Published: August 2005

The existence of a continuum of many chaotic solutions are shown for certain differential inclusions which are small nonautonomous multivalued perturbations of ordinary differential equations possessing homoclinic solutions to hyperbolic fixed points. Applications are given to dry friction problems.
THE DYNAMICS OF TWO PARAMETRICALLY EXCITED PENDULA WITH IMPACTS
Authors: DANE QUINN D.
Published: August 2005

We consider a parametrically excited vibro-impact system consisting of two colliding pendula supported on a moving base. Between the impacts the dynamics of the system are described by a nonlinear Mathieu equation, while impacts are represented by an appropriate jump in the state variables, dependent on the coefficient of restitution e. The method of averaging is applied to these equations and a reduced system is developed in which several nontrivial impacting states are identified, including synchronous oscillations, a symmetric impacting state, and a nonsymmetric impacting state. For the symmetric response (including both the synchronous and symmetric impacting states), a two-dimensional map is developed from the averaged equations and for a purely elastic collision (e = 1), a nonlinear Mathieu equation is obtained — the impacts play no role in the amplitude of the response. For inelastic collisions (e ≠ 1) the dissipation induced by the impacts can be combined with viscous damping into an overall dissipation parameter to determine the equilibrium points of the mapping. Finally, for more general nonsymmetric behavior, the existence of the stable nonsymmetric impacting state can be closely tied to the coexistence of the nontrivial state and the origin as stable states in the symmetric response.