bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viral Determinants of Integration Site Preferences of Simian Immunodeficiency Virus-Based Vectors
Authors: Monse Hella , Laufs Stephanie , Kuate Seraphin , Zeller W. Jens , Fruehauf Stefan , Überla Klaus 
Published: July 2006

ABSTRACT

Preferential integration into transcriptionally active regions of genomes has been observed for retroviral vectors based on gamma-retroviruses and lentiviruses. However, differences in the integration site preferences were detected, which might be explained by differences in viral components of the preintegration complexes. Viral determinants of integration site preferences have not been defined. Therefore, integration sites of simian immunodeficiency virus (SIV)-based vectors produced in the absence of accessory genes or lacking promoter and enhancer elements were compared. Similar integration patterns for the different SIV vectors indicate that
vif
,
vpr
,
vpx
,
nef
,
env
, and promoter or enhancer elements are not required for preferential integration of SIV into transcriptionally active regions of genomes.
Altered Gag Polyprotein Cleavage Specificity of Feline Immunodeficiency Virus/Human Immunodeficiency Virus Mutant Proteases as Demonstrated in a Cell-Based Expression System
Authors: Lin Ying-Chuan , Brik Ashraf , de Parseval Aymeric , Tam Karen , Torbett Bruce E. , Wong Chi-Huey , Elder John H. 
Published: July 2006

ABSTRACT
We have used feline immunodeficiency virus (FIV) protease (PR) as a mutational system to study the molecular basis of substrate-inhibitor specificity for lentivirus PRs, with a focus on human immunodeficiency virus type 1 (HIV-1) PR. Our previous mutagenesis studies demonstrated that discrete substitutions in the active site of FIV PR with structurally equivalent residues of HIV-1 PR dramatically altered the specificity of the mutant PRs in in vitro analyses. Here, we have expanded these studies to analyze the specificity changes in each mutant FIV PR expressed in the context of the natural Gag-Pol polyprotein ex vivo. Expression mutants were prepared in which 4 to 12 HIV-1-equivalent substitutions were made in FIV PR, and cleavage of each Gag-Pol polyprotein was then assessed in pseudovirions from transduced cells. The findings demonstrated that, as with in vitro analyses, inhibitor specificities of the mutants showed increased HIV-1 PR character when analyzed against the natural substrate. In addition, all of the mutant PRs still processed the FIV polyprotein but the apparent order of processing was altered relative to that observed with wild-type FIV PR. Given the importance of the order in which Gag-Pol is processed, these findings likely explain the failure to produce infectious FIVs bearing these mutations.
Influenza A Virus PB1-F2 Protein Contributes to Viral Pathogenesis in Mice
Authors: Zamarin Dmitriy , Ortigoza Mila B. , Palese Peter 
Published: July 2006

ABSTRACTThe influenza virus PB1-F2 protein is a novel protein previously shown to be involved in induction of cell death. Here we characterize the expression and the function of the protein within the context of influenza viral infection in tissue culture and a mouse model. We show that the C-terminal region of the protein can be expressed from a downstream initiation codon and is capable of interaction with the full-length protein. Using this knowledge, we generated influenza viruses knocked out for the expression of PB1-F2 protein and its downstream truncation products. Knocking out the PB1-F2 protein had no effect on viral replication in tissue culture but diminished virus pathogenicity and mortality in mice. The viruses replicated to similar levels in mouse lungs by day 3 postinfection, suggesting that the knockout did not impair viral replication. However, while the PB1-F2 knockout viruses were cleared after day 5, the wild-type viruses were detectable in mouse lungs until day 7, implying that expression of PB1-F2 resulted in delayed clearance of the viruses by the host immune system. Based on our findings and on the fact that the PB1 genomic segment was always newly introduced into some pandemic influenza viruses of the last century, we speculate that the PB1-F2 protein plays an important role in pathogenesis of influenza virus infection and may be an important contributor to pathogenicity of pandemic influenza viruses.
Characterization of the Prototype Foamy Virus Envelope Glycoprotein Receptor-Binding Domain
Authors: Duda Anja , Lüftenegger Daniel , Pietschmann Thomas , Lindemann Dirk 
Published: July 2006

ABSTRACT

The
foamy virus (FV) glycoprotein precursor gp130
Env
undergoes a
highly unusual biosynthesis, resulting in the generation of three
particle-associated, mature subunits, leader peptide (LP), surface
(SU), and transmembrane (TM). Little structural and functional
information on the extracellular domains of FV Env is available. In
this study, we characterized the prototype FV (PFV) Env
receptor-binding domain (RBD) by flow cytometric analysis of
recombinant PFV Env immunoadhesin binding to target cells. The
extracellular domains of the C-terminal TM subunit as well as targeting
of the recombinant immunoadhesins by the cognate LP to the secretory
pathway were dispensable for target cell binding, suggesting that the
PFV Env RBD is contained within the SU subunit. N- and C-terminal
deletion analysis of the SU domain revealed a minimal continuous RBD
spanning amino acids (aa) 225 to 555; however, internal deletions
covering the region from aa 397 to 483, but not aa 262 to 300 or aa 342
to 396, were tolerated without significant influence on host cell
binding. Analysis of individual cysteine point mutants in PFV SU
revealed that only most of those located in the nonessential region
from aa 397 to 483 retained residual binding activity. Interestingly,
analysis of various N-glycosylation site mutants suggests an important
role of carbohydrate chain attachment to N
391
, either for
direct interaction with the receptor or for correct folding of the PFV
Env RBD. Taken together, these results suggest that a bipartite
sequence motif spanning aa 225 to 396 and aa 484 to 555 is essential
for formation of the PFV Env RBD, with N-glycosylation site at position
391 playing a crucial role for host cell
binding.
Crystal Structure of Nonstructural Protein 10 from the Severe Acute Respiratory Syndrome Coronavirus Reveals a Novel Fold with Two Zinc-Binding Motifs
Authors: Joseph Jeremiah S. , Saikatendu Kumar Singh , Subramanian Vanitha , Neuman Benjamin W. , Brooun Alexei , Griffith Mark , Moy Kin , Yadav Maneesh K. , Velasquez Jeffrey , Buchmeier Michael J. , Stevens Raymond C. , Kuhn Peter 
Published: July 2006

ABSTRACT

The severe acute respiratory syndrome coronavirus (SARS-CoV) possesses a large 29.7-kb positive-stranded RNA genome. The first open reading frame encodes replicase polyproteins 1a and 1ab, which are cleaved to generate 16 “nonstructural” proteins, nsp1 to nsp16, involved in viral replication and/or RNA processing. Among these, nsp10 plays a critical role in minus-strand RNA synthesis in a related coronavirus, murine hepatitis virus. Here, we report the crystal structure of SARS-CoV nsp10 at a resolution of 1.8 Å as determined by single-wavelength anomalous dispersion using phases derived from hexatantalum dodecabromide. nsp10 is a single domain protein consisting of a pair of antiparallel N-terminal helices stacked against an irregular β-sheet, a coil-rich C terminus, and two Zn fingers. nsp10 represents a novel fold and is the first structural representative of this family of Zn finger proteins found so far exclusively in coronaviruses. The first Zn finger coordinates a Zn
2+
ion in a unique conformation. The second Zn finger, with four cysteines, is a distant member of the “gag-knuckle fold group” of Zn
2+
-binding domains and appears to maintain the structural integrity of the C-terminal tail. A distinct clustering of basic residues on the protein surface suggests a nucleic acid-binding function. Gel shift assays indicate that in isolation, nsp10 binds single- and double-stranded RNA and DNA with high-micromolar affinity and without obvious sequence specificity. It is possible that nsp10 functions within a larger RNA-binding protein complex. However, its exact role within the replicase complex is still not clear.
Dodecamer Structure of Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein nsp10
Authors: Su Dan , Lou Zhiyong , Sun Fei , Zhai Yujia , Yang Haitao , Zhang Rongguang , Joachimiak Andrzej , Zhang Xuejun C. , Bartlam Mark , Rao Zihe 
Published: July 2006

ABSTRACT

The severe acute respiratory syndrome coronavirus (SARS-CoV) nonstructural proteins nsp1 to nsp16 have been implicated by genetic analysis in the assembly of a functional replication/transcription complex. We report the crystal structure of nsp10 from SARS-CoV at 2.1-Å resolution. The nsp10 structure has a novel fold, and 12 identical subunits assemble to form a unique spherical dodecameric architecture. Two zinc fingers have been identified from the nsp10 monomer structure with the sequence motifs C-(X)
2
-C-(X)
5
-H-(X)
6
-C and C-(X)
2
-C-(X)
7
-C-(X)-C. The nsp10 crystal structure is the first of a new class of zinc finger protein three-dimensional structures to be revealed experimentally. The zinc finger sequence motifs are conserved among all three coronavirus antigenic groups, implicating an essential function for nsp10 in all coronaviruses. Based on the structure, we propose that nsp10 is a transcription factor for coronavirus replication/transcription.
Relationships between Hepatitis C Virus Replication and CXCL-8 Production In Vitro
Authors: Koo Bon Chang A. , McPoland Paula , Wagoner Jessica P. , Kane Olivia J. , Lohmann Volker , Polyak Stephen J. 
Published: July 2006

ABSTRACTThe chemokine CXCL-8 (interleukin-8) is induced by many viruses, including hepatitis C virus (HCV). In the current study, we examined CXCL-8 levels in the context of acute and chronic HCV replication in vitro. Two different small interfering RNAs were used to silence CXCL-8 mRNA and protein expression in Huh7 and BB7 replicon cells. HCV RNA synthesis in BB7 cells was inhibited by CXCL-8 knockdown. Furthermore, antibody neutralization of endogenous CXCL-8 activity inhibited HCV replication, while addition of recombinant human CXCL-8 stimulated NS5A protein expression. Moreover, CXCL-8 protein levels correlated positively with HCV RNA levels in four independent subgenomic and genomic replicon lines (R= 0.41,P= 0.0013). However, CXCL-8 mRNA levels correlated inversely with CXCL-8 protein and HCV RNA levels in all replicon lines and in Huh7 cells. Transient replication assays with strongly permissive and weakly permissive Huh7 cells and three independent subgenomic replicons with various replicative capacities revealed that CXCL-8 protein levels were higher in weakly than in strongly permissive cells. The JFH-1 subgenomic replicon, which replicated to high levels in both strongly and weakly permissive Huh7 cells, induced CXCL-8 protein to high levels in both cell types. The data indicate that in the replicon system, CXCL-8 protein levels are positively associated with chronic HCV replication and that CXCL-8 removal inhibits HCV replication. During acute HCV replication, CXCL-8 production may be inhibitory to viruses with low replicative capacity. The data underscore the complex regulation of CXCL-8 mRNA and protein expression and further suggest that in addition to contributing to HCV pathology via proinflammatory actions, CXCL-8 may have opposing antiviral and proviral effects depending on the level of HCV replication, the cellular context, and whether the infection is acute or chronic.
Dissemination of Bovine Leukemia Virus-Infected Cells from a Newly Infected Sheep Lymph Node
Authors: Fulton B. E. , Portella M. , Radke K. 
Published: July 2006

ABSTRACT

To investigate the early establishment of bovine leukemia virus (BLV) infection, we injected BLV-infected or mock-infected allogeneic cells into the shoulder of sheep in which an efferent lymphatic duct of the draining prescapular lymph node had been cannulated. Rare mononuclear cells acting as centers of BLV infection in culture were present within 4 to 6 days in efferent lymph and within 6 to 10 days in blood. Soon after BLV injection, immunoglobulin M
+
(IgM
+
) and CD8
+
cells increased in efferent lymph and oscillated reciprocally in frequency. CD8
+
blasts increased on days 4 to 6, when infectious centers increased 100-fold in lymph. On days 6 and 7, both lymph and blood were enriched with CD8
+
cells that were labeled late on day 5 with an intravenous pulse of 5-bromo-2′-deoxyuridine (BrdU). Lymph, but not blood, was enriched with BrdU
+
B cells on day 7. Capsid-specific antibodies became detectable in efferent lymph on days 6 to 8 and surface glycoprotein-specific antibodies on day 9, preceding their detection in serum by 9 to 14 days. Systemic dissemination of BLV-infected cells was thus accompanied by an increase in proliferating CD8
+
cells and the onset of BLV-specific antibodies in lymph. Infectious centers reached maximum frequencies of 0.2% in lymph by days 11 to 13, and then their frequencies increased by 5- to 40-fold in blood cells, suggesting that many infected blood cells do not recirculate back into lymph. Beginning on days 10 to 13, a subpopulation of B cells having high levels of surface IgM increased sharply in peripheral blood. Such cells were not present in lymph. After a day 16 pulse of BrdU, recently proliferated cells that stained intensely for surface IgM appeared in blood within 15 h. Predominantly B lymphocytes contained the viral capsid protein when lymph and blood cells were cultured briefly to allow BLV expression. However, both early in lymph and later in blood, BrdU
+
B cells greatly exceeded productively infected cells, indicating that new BLV infections stimulate proliferation of two different populations of B cells.
Human CD4
+
CD25
high
Cells Suppress Proliferative Memory Lymphocyte Responses to Herpes Simplex Virus Type 2
Authors: Diaz George A. , Koelle David M. 
Published: July 2006

ABSTRACT

Lymphocytes with the regulatory CD4
+
CD25
+
phenotype frequently suppress memory T-cell responses. Murine herpes simplex virus type 1 (HSV-1) models have shown that CD4
+
CD25
+
cells can limit immunity-mediated corneal damage but slow viral clearance. We investigated the effect of CD4
+
CD25
+
cells from healthy HSV-2-infected humans on recall proliferative (CD4) responses to HSV-2. Depletion and reconstitution experiments were consistent with a suppressive effect of autologous blood-derived CD4
+
CD25
+
cells for whole HSV-2 antigen. Regulatory T cells may modulate human CD4 memory responses to HSV-2 and influence their antiviral and inflammatory functions.
Kaposi's Sarcoma-Associated Herpesvirus Latent Protein LANA Interacts with HIF-1α To Upregulate RTA Expression during Hypoxia: Latency Control under Low Oxygen Conditions
Authors: Cai Qiliang , Lan Ke , Verma Subhash C. , Si Huaxin , Lin Doug , Robertson Erle S. 
Published: July 2006

ABSTRACTHypoxia can induce lytic replication of Kaposi's sarcoma-associated herpesvirus (KSHV) in primary effusion lymphoma (PEL) cells. However, the molecular mechanism of lytic reactivation of KSHV by hypoxia remains unclear. Here we show that the latency-associated nuclear antigen (LANA), which plays a crucial role in modulating viral and cellular gene expression, directly associated with a low oxygen responder, hypoxia-inducible factor-1α (HIF-1α). LANA enhanced not only the transcriptional activities of HIF-1α but also its mRNA level. Coimmunoprecipitation and immunofluorescence studies documented a physical interaction between LANA and HIF-1α in transiently transfected 293T cells as well as in PEL cell lines during hypoxia. Through sequence analysis, several putative hypoxia response elements (HRE-1 to -6) were identified in the essential lytic geneRtapromoter. Reporter assays showed that HRE-2 (−1130 to −1123) and HRE-5 and HRE-6 (+234 to +241 and +812 to +820, respectively, within the intron sequence) were necessary and sufficient for the LANA-mediated HIF-1α response. Electrophoretic mobility shift assays showed HIF-1α-dependent binding of a LANA protein complex specifically to the HRE-2, -5, and -6 motifs within the promoter regulatory sequences. This study demonstrates that hypoxia-induced KSHV lytic replication is mediated at least in part through cooperation of HIF-1α with LANA bound to the HRE motifs of theRtapromoter.
Loss of Cell Membrane Integrity in Puumala Hantavirus-Infected PatientsCorrelates with Levels of Epithelial Cell Apoptosis and Perforin
Authors: Klingström Jonas , Hardestam Jonas , Stoltz Malin , Zuber Bartek , Lundkvist Åke , Linder Stig , Ahlm Clas 
Published: July 2006

ABSTRACTHemorrhagic fever with renal syndrome and hantavirus pulmonary syndrome are two diseases caused by hantaviruses. Capillary leakage is a hallmark of hantavirus infection. Pathogenic hantaviruses are not cytotoxic, but elevated levels of serum lactate dehydrogenase (LDH), indicative of cellular damage, are observed in patients. We report increased levels of serum perforin, granzyme B, and the epithelial cell apoptosis marker caspase-cleaved cytokeratin-18 during Puumala hantavirus infection. Significant correlation was observed between the levels of LDH and perforin and the levels of LDH and caspase-cleaved cytokeratin-18, suggesting that tissue damage is due to an immune reaction and that epithelial apoptosis contributed significantly to the damage.
Evidence for a Role of the Cellular ND10 Protein PML in Mediating Intrinsic Immunity against Human Cytomegalovirus Infections
Authors: Tavalai Nina , Papior Peer , Rechter Sabine , Leis Martina , Stamminger Thomas 
Published: July 2006

ABSTRACTSeveral viruses, including human cytomegalovirus (HCMV), encode proteins that colocalize with a cellular subnuclear structure known as ND10. Since only viral DNA deposited at ND10 initiates transcription, ND10 structures were hypothesized to be essential for viral replication. On the other hand, interferon treatment induces an up-regulation of ND10 structures and viruses have evolved polypeptides that disperse the dot-like accumulation of ND10 proteins, suggesting that ND10 could also be part of an intrinsic defense mechanism. In order to obtain evidence for either a proviral or an antiviral function of ND10, we generated primary human fibroblasts with a stable, short interfering RNA-mediated knockdown (kd) of PML. In these cells, other ND10-associated proteins like hDaxx showed a diffuse nuclear distribution. Interestingly, we observed that HCMV infection induced the de novo formation of ND10-like hDaxx and Sp100 accumulations that colocalized with IE2 and were disrupted, in the apparent absence of PML, in an IE1-dependent manner during the first hours after infection. Furthermore, infection of PML-kd cells with wild-type HCMV at a low multiplicity of infection resulted in enhanced replication. In particular, a significantly increased plaque formation was detected, suggesting that more cells are able to support initiation of replication in the absence of PML. While there was no difference in viral DNA uptake between PML-kd and control cells, we observed a considerable increase in the number of immediate-early (IE) protein-positive cells, indicating that the depletion of PML augments the initiation of viral IE gene expression. These results strongly suggest that PML functions as part of an intrinsic immune mechanism against cytomegalovirus infections.
The Self Primer of the Long Terminal Repeat Retrotransposon Tf1 Is Not Removed during Reverse Transcription
Authors: Atwood-Moore Angela , Yan Kenneth , Judson Robert L. , Levin Henry L. 
Published: July 2006

ABSTRACT

The long terminal repeat retrotransposon Tf1 of
Schizosaccharomyces pombe
uses a unique mechanism of self priming to initiate reverse transcription. Instead of using a tRNA, Tf1 primes minus-strand synthesis with an 11-nucleotide RNA removed from the 5′ end of its own transcript. We tested whether the self primer of Tf1 was similar to tRNA primers in being removed from the cDNA by RNase H. Our analysis of Tf1 cDNA extracted from virus-like particles revealed the surprising observation that the dominant species of cDNA retained the self primer. This suggests that integration of the cDNA relies on mechanisms other than reverse transcription to remove the primer.
From Placelessness to Place: An Ethnographer's Experience of Growing to Know Places at Sea
Authors: Tyrrell Martina 
Published: July 2006

AbstractHow do we come to know the places we inhabit? What do places mean to us? What associations do we make with them? As an ethnographer and outsider I have grown, in a small way, to know places at sea along the northwest coast of Hudson Bay. In this paper I explore my growth into that knowledge, and how the sea became transformed from a blank space to a place filled with memory and association. I compare my short experience with that of local Inuit, who make use of the sea on a daily basis. Where and how do Inuit learn about places at sea? And how important are those places in their use of and movement through their marine environment?
Water as Country on the Pitjantjatjara Yankunytjatjara Lands South Australia
Authors: Young Diana 
Published: July 2006

AbstractAnangu, Pitjantjatjara and Yankunytjatjara people living in the north-western areas of South Australia conceptualize changes in the surface of land as evincing the presence of ancestral power. Rain is one such catalyst of change, though it is by no means a certainty on the Pitjantjatjara Yankunytjatjara Lands. When it does appear, water does not stay long on the surface: it is shimmering and unstable. This paper examines the nature of various water sources in contemporary indigenous life, the spatial relationships between earth and sky and the dialectic between life and death that they mediate.
Integrated Tobacco Cessation Counseling in a Diabetes Self-management Training Program
Authors: Hokanson Jennifer M. , Anderson Robyn L. , Hennrikus Deborah J. , Lando Harry A. , Kendall David M. 
Published: July 2006

Purpose The purpose of this study was to evaluate the impact of a tobacco cessation intervention using motivational interviewing on smoking cessation rates during diabetes self-management training (DSMT). Methods A randomized controlled trial was conducted with subjects recruited from an ongoing type 2 diabetes adult education program at a large diabetes center. A total of 114 subjects were randomized to intervention (n = 57; face-to-face motivational interviewing plus telephone counseling and offering of medication) or standard care (n = 57). Outcome measures included tobacco cessation rates, mean number of cigarettes smoked, A1C, weight, blood pressure, and lipids. Results Intensive intervention using motivational interviewing integrated into a standard DSMT program resulted in a trend toward greater abstinence at 3 months of follow-up in those receiving the intervention. However, this same trend was not observed at 6 months. The addition of this structured smoking cessation intervention did not negatively affect either diabetes education or other measures of diabetes management, including A1C values.