bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modulation of DNA Vaccine-Elicited CD8
+
T-Lymphocyte Epitope Immunodominance Hierarchies
Authors: Liu Jinyan , Ewald Bonnie A. , Lynch Diana M. , Nanda Anjali , Sumida Shawn M. , Barouch Dan H. 
Published: November 2006

ABSTRACT

Generating broad cellular immune responses against a diversity of viral epitopes is a major goal of current vaccine strategies for human immunodeficiency virus type 1 (HIV-1) and other pathogens. Virus-specific CD8
+
T-lymphocyte responses, however, are often highly focused on a very limited number of immunodominant epitopes. For an HIV-1 vaccine, the breadth of CD8
+
T-lymphocyte responses may prove to be critical as a result of the need to cover a wide diversity of viral isolates in the population and to limit viral escape from dominant epitope-specific T lymphocytes. Here we show that epitope modification strategies can alter CD8
+
T-lymphocyte epitope immunodominance hierarchies elicited by a DNA vaccine in mice. Mice immunized with a DNA vaccine expressing simian immunodeficiency virus Gag lacking the dominant D
b
-restricted AL11 epitope generated a marked and durable augmentation of responses specific for the subdominant D
b
-restricted KV9 epitope. Moreover, anatomic separation strategies and heterologous prime-boost regimens generated codominant responses against both epitopes. These data demonstrate that dominant epitopes can dramatically suppress the immunogenicity of subdominant epitopes in the context of gene-based vaccines and that epitope modification strategies can be utilized to enhance responses to subdominant epitopes.
Nonneutralizing Human Rhinovirus Serotype 2-Specific Monoclonal Antibody 2G2 Attaches to the Region That Undergoes the Most Dramatic Changes upon Release of the Viral RNA
Authors: Hewat Elizabeth A. , Blaas Dieter 
Published: November 2006

ABSTRACT
The monoclonal antibody 2G2 has been used extensively for detection and quantification of structural changes of human rhinovirus serotype 2 during infection. It recognizes exclusively A and B subviral particles, not native virus. We have elucidated the basis of this selectivity by determining the footprint of 2G2. Since viral escape mutants obviously cannot be obtained, the structures of complexes between Fab fragments of 2G2 and 80S subviral B particles were determined by cryoelectron microscopy. The footprint of the antibody corresponds to the capsid region that we predicted would undergo the most dramatic changes upon RNA release.
Spleen-Dependent Turnover of CD11b Peripheral Blood B Lymphocytes in Bovine Leukemia Virus-Infected Sheep
Authors: Florins Arnaud , Gillet Nicolas , Asquith Becca , Debacq Christophe , Jean Geneviève , Schwartz-Cornil Isabelle , Bonneau Michel , Burny Arsène , Reichert Michal , Kettmann Richard , Willems Luc 
Published: November 2006

ABSTRACTLymphocyte homeostasis is determined by a critical balance between cell proliferation and death, an equilibrium which is deregulated in bovine leukemia virus (BLV)-infected sheep. We have previously shown that an excess of proliferation occurs in lymphoid tissues and that the peripheral blood population is prone to increased cell death. To further understand the mechanisms involved, we evaluated the physiological role of the spleen in this accelerated turnover. To this end, B lymphocytes were labeled in vivo using a fluorescent marker (carboxyfluorescein diacetate succinimidyl ester), and the cell kinetic parameters (proliferation and death rates) of animals before and after splenectomy were compared. We show that the enhanced cell death observed in BLV-infected sheep is abrogated after splenectomy, revealing a key role of the spleen in B-lymphocyte dynamics.
Construction and Mutagenesis of an Artificial Bicistronic Tick-Borne Encephalitis Virus Genome Reveals an Essential Function of the Second Transmembrane Region of Protein E in Flavivirus Assembly
Authors: Orlinger Klaus K. , Hoenninger Verena M. , Kofler Regina M. , Mandl Christian W. 
Published: November 2006

ABSTRACT
Flaviviruses have a monopartite positive-stranded RNA genome, which serves as the sole mRNA for protein translation. Cap-dependent translation produces a polyprotein precursor that is co- and posttranslationally processed by proteases to yield the final protein products. In this study, using tick-borne encephalitis virus (TBEV), we constructed an artificial bicistronic flavivirus genome (TBEV-bc) in which the capsid protein and the nonstructural proteins were still encoded in the cap cistron but the coding region for the surface proteins prM and E was moved to a separate translation unit under the control of an internal ribosome entry site element inserted into the 3′ noncoding region. Mutant TBEV-bc was shown to produce particles that packaged the bicistronic RNA genome and were infectious for BHK-21 cells and mice. Compared to wild-type controls, however, TBEV-bc was less efficient in both RNA replication and infectious particle formation. We took advantage of the separate expression of the E protein in this system to investigate the role in viral assembly of the second transmembrane region of protein E (E-TM2), a second copy of which was retained in the cap cistron to fulfill its other role as an internal signal sequence in the polyprotein. Deletion analysis and replacement of the entire TBEV E-TM2 region with its counterpart from another flavivirus revealed that this element, apart from its role as a signal sequence, is important for virion formation.
Role of Ran Binding Protein 5 in Nuclear Import and Assembly of the Influenza Virus RNA Polymerase Complex
Authors: Deng Tao , Engelhardt Othmar G. , Thomas Benjamin , Akoulitchev Alexandre V. , Brownlee George G. , Fodor Ervin 
Published: November 2006

ABSTRACT
The influenza A virus RNA-dependent RNA polymerase is a heterotrimeric complex of polymerase basic protein 1 (PB1), PB2, and polymerase acidic protein (PA) subunits. It performs transcription and replication of the viral RNA genome in the nucleus of infected cells. We have identified a nuclear import factor, Ran binding protein 5 (RanBP5), also known as karyopherin β3, importin β3, or importin 5, as an interactor of the PB1 subunit. RanBP5 interacted with either PB1 alone or with a PB1-PA dimer but not with a PB1-PB2 dimer or the trimeric complex. The interaction between RanBP5 and PB1-PA was disrupted by RanGTP in vitro, allowing PB2 to bind to the PB1-PA dimer to form a functional trimeric RNA polymerase complex. We propose a model in which RanBP5 acts as an import factor for the newly synthesized polymerase by targeting the PB1-PA dimer to the nucleus. In agreement with this model, small interfering RNA (siRNA)-mediated knock-down of RanBP5 inhibited the nuclear accumulation of the PB1-PA dimer. Moreover, siRNA knock-down of RanBP5 resulted in the delayed accumulation of viral RNAs in infected cells, confirming that RanBP5 plays a biological role during the influenza virus life cycle.
Feline Model of Acute Nipah Virus Infection and Protection with a Soluble Glycoprotein-Based Subunit Vaccine
Authors: Mungall Bruce A. , Middleton Deborah , Crameri Gary , Bingham John , Halpin Kim , Russell Gail , Green Diane , McEachern Jennifer , Pritchard L. Ian , Eaton Bryan T. , Wang Lin-Fa , Bossart Katharine N. , Broder Christopher C. 
Published: November 2006

ABSTRACT

Nipah virus (NiV) and Hendra virus (HeV) are paramyxoviruses capable of causing considerable morbidity and mortality in a number of mammalian species, including humans. Case reports from outbreaks and previous challenge experiments have suggested that cats were highly susceptible to NiV infection, responding with a severe respiratory disease and systemic infection. Here we have assessed the cat as a model of experimental NiV infection and use it in the evaluation of a subunit vaccine comprised of soluble G glycoprotein (sG). Two groups of two adult cats each were inoculated subcutaneously with either 500 or 5,000 50% tissue culture infective dose(s) (TCID
50
) of NiV. Animals were monitored closely for disease onset, and extensive analysis was conducted on samples and tissues taken during infection and at necropsy to determine viral load and tissue tropism. All animals developed clinical disease 6 to 9 days postinfection, a finding consistent with previous observations. In a subsequent experiment, two cats were immunized with HeV sG and two were immunized with NiV sG. Homologous serum neutralizing titers were greater than 1:20,000, and heterologous titers were greater than 1:20,000 to 16-fold lower. Immunized animals and two additional naive controls were then challenged subcutaneously with 500 TCID
50
of NiV. Naive animals developed clinical disease 6 to 13 days postinfection, whereas none of the immunized animals showed any sign of disease. TaqMan PCR analysis of samples from naive animals revealed considerable levels of NiV genome in a wide range of tissues, whereas the genome was evident in only two immunized cats in only four samples and well below the limit of accurate detection. These results indicate that the cat provides a consistent model for acute NiV infection and associated pathogenesis and an effective subunit vaccine strategy appears achievable.
Activation of Microglia by Borna Disease Virus Infection: In Vitro Study
Authors: Ovanesov Mikhail V. , Sauder Christian , Rubin Steven A. , Richt Jürgen , Nath Avindra , Carbone Kathryn M. , Pletnikov Mikhail V. 
Published: November 2006

ABSTRACT
Neonatal Borna disease virus (BDV) infection of the rat brain is associated with microglial activation and damage to the certain neuronal populations. Since persistent BDV infection of neurons in vitro is noncytolytic and noncytopathic, activated microglia have been suggested to be responsible for neuronal cell death in vivo. However, the mechanisms of activation of microglia in neonatally BDV-infected rat brain have not been investigated. To address these issues, activation of primary rat microglial cells was studied following exposure to purified BDV or to persistently BDV-infected primary cortical neurons or after BDV infection of primary mixed neuron-glial cultures. Neither purified virus nor BDV-infected neurons alone activated primary microglia as assessed by the changes in cell shape or production of the proinflammatory cytokines. In contrast, in the BDV-infected primary mixed cultures, we observed proliferation of microglia cells that acquired the round morphology and expressed major histocompatibility complex molecules of classes I and II. These manifestations of microglia activation were observed in the absence of direct BDV infection of microglia or overt neuronal toxicity. In addition, compared to uninfected mixed cultures, activation of microglia in BDV-infected mixed cultures was associated with a significantly greater lipopolysaccharide-induced release of tumor necrosis factor alpha, interleukin 1β, and interleukin 10. Taken together, the present data are the first in vitro evidence that persistent BDV infection of neurons and astrocytes rather than direct exposure to the virus or dying neurons is critical for activating microglia.
CD4+T-Cell Responses Are Required for Clearance of West Nile Virus from the Central Nervous System
Authors: Sitati Elizabeth M. , Diamond Michael S. 
Published: November 2006

ABSTRACTAlthough studies have established that innate and adaptive immune responses are important in controlling West Nile virus (WNV) infection, the function of CD4+T lymphocytes in modulating viral pathogenesis is less well characterized. Using a mouse model, we examined the role of CD4+T cells in coordinating protection against WNV infection. A genetic or acquired deficiency of CD4+T cells resulted in a protracted WNV infection in the central nervous system (CNS) that culminated in uniform lethality by 50 days after infection. Mice surviving past day 10 had high-level persistent WNV infection in the CNS compared to wild-type mice, even 45 days following infection. The absence of CD4+T-cell help did not affect the kinetics of WNV infection in the spleen and serum, suggesting a role for CD4-independent clearance mechanisms in peripheral tissues. WNV-specific immunoglobulin M (IgM) levels were similar to those of wild-type mice in CD4-deficient mice early during infection but dropped ∼20-fold at day 15 postinfection, whereas IgG levels in CD4-deficient mice were ∼100- to 1,000-fold lower than in wild-type mice throughout the course of infection. WNV-specific CD8+T-cell activation and trafficking to the CNS were unaffected by the absence of CD4+T cells at day 9 postinfection but were markedly compromised at day 15. Our experiments suggest that the dominant protective role of CD4+T cells during primary WNV infection is to provide help for antibody responses and sustain WNV-specific CD8+T-cell responses in the CNS that enable viral clearance.
Visualization of α-Helices in a 6-Ångstrom Resolution Cryoelectron Microscopy Structure of Adenovirus Allows Refinement of Capsid Protein Assignments
Authors: Saban Susan D. , Silvestry Mariena , Nemerow Glen R. , Stewart Phoebe L. 
Published: November 2006

ABSTRACT
The structure of adenovirus was determined to a resolution of 6 Å by cryoelectron microscopy (cryoEM) single-particle image reconstruction. Docking of the hexon and penton base crystal structures into the cryoEM density established that α-helices of 10 or more residues are resolved as rods. A difference map was calculated by subtracting a pseudoatomic capsid from the cryoEM reconstruction. The resulting density was analyzed in terms of observed α-helices and secondary structure predictions for the additional capsid proteins that currently lack atomic resolution structures (proteins IIIa, VI, VIII, and IX). Protein IIIa, which is predicted to be highly α-helical, is assigned to a cluster of helices observed below the penton base on the inner capsid surface. Protein VI is present in ∼1.5 copies per hexon trimer and is predicted to have two long α-helices, one of which appears to lie inside the hexon cavity. Protein VIII is cleaved by the adenovirus protease into two fragments of 7.6 and 12.1 kDa, and the larger fragment is predicted to have one long α-helix, in agreement with the observed density for protein VIII on the inner capsid surface. Protein IX is predicted to have one long α-helix, which also has a strongly indicated propensity for coiled-coil formation. A region of density near the facet edge is now resolved as a four-helix bundle and is assigned to four copies of the C-terminal α-helix from protein IX.
Screening Random Peptide Libraries with Subacute Sclerosing PanencephalitisBrain-Derived Recombinant Antibodies Identifies Multiple Epitopes in the C-Terminal Region of the Measles Virus Nucleocapsid Protein
Authors: Owens Gregory P. , Shearer Andrew J. , Yu Xiaoli , Ritchie Alanna M. , Keays Kathryne M. , Bennett Jeffrey L. , Gilden Donald H. , Burgoon Mark P. 
Published: November 2006

ABSTRACTInfectious and inflammatory diseases of the CNS are often characterized by a robust B-cell response that manifests as increased intrathecal immunoglobulin G (IgG) synthesis and the presence of oligoclonal bands. We previously used laser capture microdissection and single-cell PCR to analyze the IgG variable regions of plasma cells from the brain of a patient with subacute sclerosing panencephalitis (SSPE). Five of eight human IgG1 recombinant antibodies (rAbs) derived from SSPE brain plasma cell clones recognized the measles virus (MV) nucleocapsid protein, confirming that the antibody response in SSPE targets primarily the agent causing disease. In this study, as part of our work on antigen identification, we used four rAbs to probe a random phage-displayed peptide library to determine if epitopes within the MV nucleocapsid protein could be identified with SSPE brain rAbs. All four of the SSPE rAbs enriched phage-displayed peptide sequences that reacted specifically to their panning rAb by enzyme-linked immunosorbent assay. BLASTP searches of the NCBI protein database revealed clear homologies in three peptides and different amino acid stretches within the 65 C-terminal amino acids of the MV nucleocapsid protein. The specificities of SSPE rAbs to these regions of the MV nucleocapsid protein were confirmed by binding to synthetic peptides or to short cDNA expression products. These results indicate the feasibility of using peptide screening for antigen discovery in central nervous system inflammatory diseases of unknown etiology, such as multiple sclerosis, neurosarcoidosis, or Behcet's syndrome.
Evidence for CDK-Dependent and CDK-Independent Functions of the Murine Gammaherpesvirus 68 v-Cyclin
Authors: Upton Jason W. , Speck Samuel H. 
Published: November 2006

ABSTRACT
Gamma-2 herpesviruses encode homologues of mammalian D-type cyclins
(v-cyclins), which likely function to manipulate the cell cycle,
thereby providing a cellular environment conducive to virus replication
and/or reactivation from latency. We have previously shown that the
v-cyclin of murine gammaherpesvirus 68 is an oncogene that binds and
activates cellular cyclin-dependent kinases (CDKs) and is required for
efficient reactivation from latency. To determine the contribution of
v-cyclin-mediated cell cycle regulation to the viral life cycle,
recombinant viruses in which specific point mutations (E133V or K104E)
were introduced into the v-cyclin open reading frame were generated,
resulting in the disruption of CDK binding and activation. While in
vitro growth of these mutant viruses was unaffected, lytic replication
in the lungs following low-dose intranasal inoculation was attenuated
for both mutants deficient in CDK binding as well as virus in which the
entire v-cyclin open reading frame was disrupted by the insertion of a
translation termination codon. This replication defect was not apparent
in spleens of mice following intraperitoneal inoculation, suggesting a
cell type- and/or route-specific dependence on v-cyclin-CDK
interactions during the acute phase of virus infection. Notably,
although a v-cyclin-null virus was highly attenuated for reactivation
from latency, the E133V v-cyclin CDK-binding mutant exhibited only a
modest defect in virus reactivation from splenocytes, and neither the
E133V nor K104E v-cyclin mutants were compromised in reactivation from
peritoneal exudate cells. Taken together, these data suggest that lytic
replication and reactivation in vivo are differentially regulated by
CDK-dependent and CDK-independent functions of v-cyclin,
respectively.
Mutation of YMYL in the Nipah Virus Matrix Protein Abrogates Budding and Alters Subcellular Localization
Authors: Ciancanelli Michael J. , Basler Christopher F. 
Published: November 2006

ABSTRACT
Matrix (M) proteins reportedly direct the budding of paramyxoviruses from infected cells. In order to begin to characterize the assembly process for the highly lethal, emerging paramyxovirus Nipah virus (NiV), we have examined the budding of NiV M. We demonstrated that expression of the NiV M protein is sufficient to produce budding virus-like particles (VLPs) that are physically and morphologically similar to NiV. We identified in NiV M a sequence, YMYL, with similarity to the YPDL late domain found in the equine infectious anemia virus Gag protein. When the YMYL within NiV M was mutated, VLP release was abolished and M was relocalized to the nucleus, but the mutant M proteins retained oligomerization activity. When YMYL was fused to a late-domain mutant of the Ebola virus VP40 matrix protein, VP40 budding was restored. These results suggest that the YMYL sequence may act as a trafficking signal and a late domain for NiV M.
Improving the Flotation Behavior of a Sulfide Ore by Controlling Electrochemical Interactions during Grinding
Authors: Grano Stephen , Huang Guozhi 
Published: November 2006

The effect of grinding media and purging gas during grinding, on the flotation behaviour of a complex copper-lead-zinc sulphide ore was investigated.	The optimum recoveries and grades of chalcopyrite were obtained with 21 % chromium medium combined with nitrogen purging. Mild steel medium may depress chalcopyrite flotation due to a high amount of oxidized iron species in the mill discharge.	Grinding media displayed an influence on the Eh and galvanic current between media and mineral electrodes. The more electrochemically active the grinding media and the more oxidizing the environment, the greater the amount of oxidised iron in the slurry. Mild steel and high chromium media are more electrochemically active than the examined sulphide minerals. A generic approach to optimizing grinding conditions to improve the flotation separation of sulphide minerals is suggested by the study.
Carbon Nanotube Field Effect Transistors for High Speed Electronics
Authors: Zhang Hong , Pesetski Aaron , Baumgardner James , Murduck James , Adam John , Przybysz John 
Published: November 2006

The frequency-independent performance of a carbon nanotube field effect transistor (CNT FET), at frequencies as high as 23 GHz, was demonstrated.	The FET was fabricated using a top- gated geometry on a quartz substrate. The high frequency measurement was performed on this FET using a novel measurement approach, and for the first time we demonstrated the CNT FET continues to operate at frequencies up to 23 GHz without loss of gain. This observed maximum operating frequency represents a significant breakthrough in the realization of carbon nanotube-based electronics for low-power, high frequency applications.
Materials and Processes for High k Gate Stacks: Results from the FEP Transition Center
Authors: Osburn Carl , Campbell Steve , Demkov Alex , Eisenbraun Eric , Garfunkel Eric , Gustafsson Torgny , Kingon Angus I. , Lee Jack , Lichtenwalner Dan , Lucovsky Gerry , Ma T.P. , Maria Jon-Paul , Misra Veena , Nemanich Robert , Parsons Greg , Schlom Darrell , Stemmer Susanne , Wallace Robert M. , Whitten Jerry 
Published: November 2006

A wide variety of materials and processes for high k dielectrics and metal gate electrodes have been studied as replacements for poly-Si/SiO2 or SiON in advanced CMOS devices.	Care must be taken with the interfacial layer to control not only the nitrogen content but its spatial location. Nanocrystallization of the high k dielectric and the corresponding formation of charge and trapping levels associated with defects in the dielectric present one of the current challenges. Control of the workfunction of the gate electrode is shown to depend on many variables, including oxygen content and the material used for the capping layer on the metal gate. The hafnium oxide family of materials, along with metal alloy gates, is seen to provide the best solution for equivalent oxide thicknesses (EOT's) < 0.7 nm, but higher k dielectrics and thinner interfacial layers are needed below 0.7 nm.
Performance Assessment of Ge-on-SOI-photodetector / Si-CMOS Receivers for High-Speed Optical Communications
Authors: Koester Steve , Schares Laurent , Schow Clint L. , Schaub Jeremy D. , Dehlinger Gabriel , Doany Fuad E. , John Richard A. , Chu Jack O. 
Published: November 2006

This paper provides an assessment of the performance capabilities of infrared detectors and receivers using Ge-on- silicon-on-insulator (Ge-on-SOI) photodiodes and CMOS ICs. An overview of our recent results on these detectors is given, and an estimate of their performance capabilities based upon an optimized layer structure design is described.	We also provide an overview of high-performance receivers that utilize Ge-on- SOI photodiodes paired with Si CMOS amplifier ICs, and describe the materials and integration challenges needed to be overcome in order to develop a full monolithically-integrated technology.