bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of ionic equilibria and electrowinning of indium from chloride solutions
Authors: Lee Man‐Seung , Oh Young‐Joo
Published: September 2004

The effects of variables on the current efficiency and cell voltage of indium electrowinning from chloride solution have been examined. Ionic equilibria for the InCl3–HCl–NaOH–H2O system at 25°C was analyzed and the experimentally measured pH values agreed well with those calculated from the analysis. The initial pH of electrolyte solution, reaction temperature and current density had negligible effect on the current efficiency and cell voltage increased linearly with increasing current density. In order to achieve current efficiency of 90% at the current density of 100 mA/cm2, the initial concentration of indium and NaCl should be higher than 50 g/L.
Phase equilibria in the ZnO‐rich area of the Fe–Zn–O system in air
Authors: Hansson Robert , Hayes Peter C. , Jak Evgueni
Published: September 2004

The phase equilibria in the Fe–Zn–O system in the range 900–1580°C in air have been experimentally studied using equilibration and quenching techniques. The compositions of the phases at equilibrium were determined using electron probe X‐ray microanalysis (EPMA). The ferrous and ferric bulk iron concentrations were measured with a wet chemical analysis using the ammonium metavanadate technique. X‐ray powder diffraction analysis (XRD) was used to characterise the phases. Iron oxide dissolved in zincite was found to be present principally in the ferric form. The XRD analysis and the composition measurements both indicate that zincite is the only phase stable in the ZnO‐rich area in the range of conditions investigated. The solubility of the iron oxide in zincite rapidly increases at temperatures above 1200°C; the morphology of the zincite crystals also sharply changes between 1200 and 1300°C from rounded to plate‐like crystals. The plate‐like zincite forms a refractory network—the type of microstructure beneficial to the Imperial Smelting Process (ISP) sinter performance. The software program FactSage with a thermodynamically optimised database was used to predict phase equilibria in the Fe–Zn–O system.
Preparation of high pure graphite by alkali digestion method
Authors: Bhima Rao R. , Patnaik Nivedita
Published: September 2004

This paper deals with a novel new technique: alkali digestion, followed by grinding and flotation, has been attempted for the first time on the Indian graphite ore. The novelty in this method is that the quartz mineral, SiO2, present in the flakes, releases during thermal shock treatment and dissolves partly with sodium hydroxide. Acid cleaning washes out the other soluble minerals. By this method, a product containing a maximum of up to 98% fixed carbon (FC) is achieved with 97% recovery from a graphite concentrate containing 85% FC. This process is environment‐friendly and the product achieved is suitable for most of the industries.
Viscosity of CaO–CrOx–SiO2 slags in a relatively high oxygen partial pressure atmosphere
Authors: Forsbacka Lasse , Holappa Lauri
Published: September 2004

Viscosities of eight CaO–SiO2–CrOx slags were measured by the rotating cylinder method up to a temperature of 1750°C. The compositions were selected in the composition range of 38–60 wt% SiO2, 53–37 wt% CaO and 0–9 wt% CrOx. The atmosphere was controlled by a CO2/CO gas mixture. Iida's viscosity model was applied and good consistency with the measured viscosity values was observed.
Analysis of asymptotic projectile motion with air resistance using the Lambert W function
Authors: Warburton R. D. H. , Wang J.
Published: September 2004

We calculate the range of a projectile experiencing air resistance in the asymptotic region of large velocities by introducing the Lambert W function. From the exact solution for the range in terms of the Lambert W function, we derive an approximation for the maximum range in the limit of large velocities. Analysis of the result confirms an independent numerical result observed in an introductory physics class that the angle at which the maximum range occurs, θmax, goes rapidly to zero for increasing initial firing speeds v0≫1. We show that θmax∼(ln v0)/v0.
Using an online homework system enhances students’ learning of physics concepts in an introductory physics course
Authors: Cheng K. Kelvin , Thacker Beth Ann , Cardenas Richard L. , Crouch Catherine
Published: September 2004

We report the results of a comparison of student understanding of physics concepts with and without online homework, as measured by the force concept inventory. We compared students in large introductory courses taught by interactive engagement and noninteractive engagement methods and with ungraded homework and with online homework. We also compared the understanding of students in different grade subgroups. The increase in the average force concept inventory normalized gain was statistically significant for all students taught with online homework, indicating that graded homework increases student understanding of physics concepts. The gain was significantly higher for those students taught with interactive engagement methods together with online homework. The C grade subgroup taught by interactive engagement methods benefited more from the implementation of online homework than the other subgroups.
Quantum mechanical description of linear optics
Authors: Skaar Johannes , Garcı́a Escartı́n Juan Carlos , Landro Harald
Published: September 2004

Linear optical networks with any number of modes are described quantum mechanically. We reformulate the conventional formal description based on input–output operator relations and obtain an intuitive description based on the possible paths taken by the photons. The effect of a linear optical network on localized photons is treated within the same formalism. The potential and limitations of linear optics for application in quantum information processing are briefly discussed.
Spin and statistics in classical mechanics
Authors: Morgan J. A.
Published: September 2004

The spin–statistics connection is obtained for classical particles. The connection holds within pseudomechanics, a theory of particle motion that extends classical physics to include anticommuting Grassmann variables, and that exhibits classical analogs of both spin and statistics. Classical realizations of Lie groups are constructed in a canonical formalism generalized to include Grassmann variables. The theory of irreducible canonical realizations of the Poincaré group is developed in this framework, with particular emphasis on the rotation subgroup. The behavior of irreducible realizations under time inversion and charge conjugation is obtained. The requirement that the Lagrangian retain its form under the combined operation of charge conjugation and time reversal leads directly to the spin–statistics connection by an adaptation of Schwinger’s 1951 proof to irreducible canonical realizations of the Poincaré group of spin j: Generalized spin coordinates and momenta satisfy fundamental Poisson bracket relations for 2j even, and fundamental Poisson antibracket relations for 2j odd.
Investigation of students’ reasoning regarding heat, work, and the first law of thermodynamics in an introductory calculus-based general physics course
Authors: Meltzer David E.
Published: September 2004

Students in an introductory university physics course were found to share many substantial difficulties related to learning fundamental topics in thermal physics. Responses to written questions by 653 students in three separate courses were consistent with the results of detailed individual interviews with 32 students in a fourth course. Although most students seemed to acquire a reasonable grasp of the state-function concept, it was found that there was a widespread and persistent tendency to improperly over-generalize this concept to apply to both work and heat. A large majority of interviewed students thought that net work done or net heat absorbed by a system undergoing a cyclic process must be zero, and only 20% or fewer were able to make effective use of the first law of thermodynamics even after instruction. Students’ difficulties seemed to stem in part from the fact that heat, work, and internal energy share the same units. The results were consistent with those of previously published studies of students in the U.S. and Europe, but portray a pervasiveness of confusion regarding process-dependent quantities that has been previously unreported. Significant enhancements of current standard instruction may be required for students to master basic thermodynamic concepts.
AJP Reviewers
Authors: Tobochnik Jan , Gould Harvey
Published: September 2004

Below is a listing of the 673 individuals who have reviewed manuscripts for the American Journal of Physics from July 1, 2003 to July 1, 2004. If you have reviewed for AJP during this time and are not on the list, we apologize and hope that you will let us know so that we can correct our records. If you are interested in reviewing for AJP and have not done so recently, please fill out the questionnaire at www.kzoo.edu/ajp/referees.html. The thoughtful and expert advice offered by the reviewers is essential for maintaining the quality of the journal. On behalf of all AJP authors and readers, we thank those listed below who have served as reviewers.
VP7 Mediates the Interaction of Rotaviruses with Integrin αvβ3 through a Novel Integrin-Binding Site
Authors: Zárate Selene , Romero Pedro , Espinosa Rafaela , Arias Carlos F. , López Susana
Published: September 2004

Rotavirus entry is a complex multistep process that depends on the trypsin cleavage of the virus spike protein VP4 into polypeptides VP5 and VP8 and on the interaction of these polypeptides and of VP7, the second viral surface protein, with several cell surface molecules, including integrin αvβ3. We characterized the effect of the trypsin cleavage of VP4 on the binding to MA104 cells of the sialic acid-dependent virus strain RRV and its sialic acid-independent variant, nar3. We found that, although the trypsin treatment did not affect the attachment of these viruses to the cell surface, their binding was qualitatively different. In contrast to the trypsin-treated viruses, which initially bound to the cell surface through VP4, the non-trypsin-treated variant nar3 bound to the cell through VP7. Amino acid sequence comparison of the surface proteins of rotavirus and hantavirus, both of which interact with integrin αvβ3 in an RGD-independent manner, identified a region shared by rotavirus VP7 and hantavirus G1G2 protein in which six of nine amino acids are identical. This region, which is highly conserved among the VP7 proteins of different rotavirus strains, mediates the binding of rotaviruses to integrin αvβ3 and probably represents a novel binding motif for this integrin.
cis
-Acting RNA Signals in the NS5B C-Terminal Coding Sequence of the Hepatitis C Virus Genome
Authors: Lee Haekyung , Shin Hyukwoo , Wimmer Eckard , Paul Aniko V.
Published: September 2004

The
cis
-replicating RNA elements in the 5′ and 3′ nontranslated regions (NTRs) of the hepatitis C virus (HCV) genome have been thoroughly studied before. However, no
cis
-replicating elements have been identified in the coding sequences of the HCV polyprotein until very recently. The existence of highly conserved and stable stem-loop structures in the RNA polymerase NS5B coding sequence, however, has been previously predicted (A. Tuplin, J. Wood, D. J. Evans, A. H. Patel, and P. Simmonds, RNA 8:824-841, 2002). We have selected for our studies a 249-nt-long RNA segment in the C-terminal NS5B coding region (NS5BCR), which is predicted to form four stable stem-loop structures (SL-IV to SL-VII). By deletion and mutational analyses of the RNA structures, we have determined that two of the stem-loops (SL-V and SL-VI) are essential for replication of the HCV subgenomic replicon in Huh-7 cells. Mutations in the loop and the top of the stem of these RNA elements abolished replicon RNA synthesis but had no effect on translation. In vitro gel shift and filter-binding assays revealed that purified NS5B specifically binds to SL-V. The NS5B-RNA complexes were specifically competed away by unlabeled homologous RNA, to a small extent by 3′ NTR RNA, and only poorly by 5′ NTR RNA. The other two stem-loops (SL-IV and SL-VII) of the NS5BCR domain were found to be important but not essential for colony formation by the subgenomic replicon. The precise function(s) of these
cis
-acting RNA elements is not known.
LMP2A Does Not Require Palmitoylation To Localize to Buoyant Complexes or for Function
Authors: Katzman Rebecca B. , Longnecker Richard
Published: September 2004

Epstein-Barr virus (EBV) latent membrane protein 2A (LMP2A) is expressed constitutively in lipid rafts in latently infected B lymphocytes. Lipid rafts are membrane microdomains enriched in cholesterol and sphingolipids selective for specific protein association. Lipid rafts have been shown to be necessary for B-cell receptor (BCR) signal transduction. LMP2A prevents BCR recruitment to lipid rafts, thereby abrogating BCR function. As LMP2A is palmitoylated, whether this fatty acid modification is necessary for LMP2A to localize to lipid rafts and for protein function was investigated. LMP2A palmitoylation was confirmed in latently infected B cells. LMP2A was found to be palmitoylated on multiple cysteines only by S acylation. An LMP2A mutant that was not palmitoylated was identified and functioned similar to wild-type LMP2A; unmodified LMP2A localized to lipid rafts, was tyrosine phosphorylated, was associated with LMP2A-associated proteins, was ubiquitinated, and was able to block calcium mobilization following BCR cross-linking. Therefore, palmitoylation of LMP2A is not required for LMP2A targeting to buoyant complexes or for function.
Early Bone Marrow Hematopoietic Defect in Simian/Human Immunodeficiency Virus C2/1-Infected Macaques and Relevance to Advance of Disease
Authors: Yamakami Kenji , Honda Mitsuo , Takei Masami , Ami Yasushi , Kitamura Noboru , Nishinarita Susumu , Sawada Shigemasa , Horie Takashi
Published: September 2004

To clarify hematological abnormalities following infection with human immunodeficiency virus (HIV), we examined the hematopoietic capability of bone marrow by using cynomolgus monkeys infected with pathogenic simian/human immunodeficiency virus (SHIV) strain C2/1, an animal model of HIV infection. The relationship between the progress of the infection and the CD4/CD8 ratio of T lymphocytes or the amount of SHIV C2/1 viral load in the peripheral blood was also investigated. A colony assay was performed to assess the hematopoietic capability of bone marrow stem cells during the early and advanced phases of the infection. Colonies of granulocytes-macrophages (GM) were examined by PCR for the presence of the SIVmac239
gag
region to reveal direct viral infection. There was a remarkable decrease in the CFU-GM growth on days 1 and 3 postinoculation, followed by recovery on day 56. During the more advanced stage, the CFU-GM growth decreased again. There was minimal evidence of direct viral infection of pooled cultured CFU-GM despite the continuously low CD4/CD8 ratios. These results indicate that the decrease in colony formation by bone marrow stem cells is reversible and fluctuates with the advance of the disease. This decrease was not due to direct viral infection of CFU-GM. Our data may support the concept that, in the early phase, production of inhibitory factors or deficiency of a stimulatory cytokine is responsible for some of the bone marrow defects described in the SHIV C2/1 model.
Phosphatidylserine Is Not the Cell Surface Receptor for Vesicular Stomatitis Virus
Authors: Coil David A. , Miller A. Dusty
Published: September 2004

The envelope protein from vesicular stomatitis virus (VSV) has become an important tool for gene transfer and gene therapy. It is widely used mainly because of its ability to mediate virus entry into all cell types tested to date. Consistent with the broad tropism of the virus, the receptor for VSV is thought to be a ubiquitous membrane lipid, phosphatidylserine (PS). However, the evidence for this hypothesis is indirect and incomplete. Here, we have examined the potential interaction of VSV and PS at the plasma membrane in more detail. Measurements of cell surface levels of PS show a wide range across cell types from different organisms. We demonstrate that there is no correlation between the cell surface PS levels and VSV infection or binding. We also demonstrate that an excess of annexin V, which binds specifically and tightly to PS, does not inhibit infection or binding by VSV. While the addition of PS to cells does allow increased virus entry, we show that this effect is not specific to the VSV envelope. We conclude that PS is not the cell surface receptor for VSV, although it may be involved in a postbinding step of virus entry.
mRNA Molecules Containing Murine Leukemia Virus Packaging Signals Are Encapsidated as Dimers
Authors: Hibbert Catherine S. , Mirro Jane , Rein Alan
Published: September 2004

Prior work by others has shown that insertion of ψ (i.e., leader) sequences from the Moloney murine leukemia virus (MLV) genome into the 3′ untranslated region of a nonviral mRNA leads to the specific encapsidation of this RNA in MLV particles. We now report that these RNAs are, like genomic RNAs, encapsidated as dimers. These dimers have the same thermostability as MLV genomic RNA dimers; like them, these dimers are more stable if isolated from mature virions than from immature virions. We characterized encapsidated mRNAs containing deletions or truncations of MLV ψ or with ψ sequences from MLV-related acute transforming viruses. The results indicate that the dimeric linkage in genomic RNA can be completely attributed to the ψ region of the genome. While this conclusion agrees with earlier electron microscopic studies on mature MLV dimers, it is the first evidence as to the site of the linkage in immature dimers for any retrovirus. Since the Ψ
+
mRNA is not encapsidated as well as genomic RNA, it is only present in a minority of virions. The fact that it is nevertheless dimeric argues strongly that two of these molecules are packaged into particles together. We also found that the kissing loop is unnecessary for this coencapsidation or for the stability of mature dimers but makes a major contribution to the stability of immature dimers. Our results are consistent with the hypothesis that the packaging signal involves a dimeric structure in which the RNAs are joined by intermolecular interactions between GACG loops.
The DNA Element Controlling Expression of the Varicella-Zoster Virus Open Reading Frame 28 and 29 Genes Consists of Two Divergent Unidirectional Promoters Which Have a Common USF Site
Authors: Yang Min , Hay John , Ruyechan William T.
Published: September 2004

The mechanism of the divergent expression of the varicella-zoster virus (VZV) ORF 28 and ORF 29 genes from a common intergenic DNA element, the ORF 28/29 promoter, is of interest based on the observation that both genes are expressed during VZV lytic infection but only the ORF 29 gene is expressed in latently infected neurons. In the work presented here, expression driven by the ORF 28/29 intergenic region was examined. We found that the promoter activity towards the ORF 29 direction is more responsive to activation by the major viral transactivator IE62 than that towards the ORF 28 direction in the context of our experimental system. Analysis of the functional DNA elements involved in IE62 activation of the bidirectional ORF 28/29 regulatory element revealed that in both transfected and VZV-superinfected cells it is a fusion of two unidirectional promoters overlapping an essential USF binding site but with distinct TATA elements. A single TATA element directs expression in the ORF 28 direction, whereas the two TATA elements directing ORF 29 gene expression are alternatively and differentially utilized for transcription initiation. We also identified an Sp1 site localized proximal to the ORF 28 gene which functions as an activator element for expression in both directions. These results indicate that the ORF 28 and ORF 29 genes can be expressed either coordinately or independently and that the observed expression of only the ORF 29 gene during VZV latency may involve neuron-specific cellular factors and/or structural aspects of the latent viral genome.
Influenza B Virus BM2 Protein Is a Crucial Component for Incorporation of Viral Ribonucleoprotein Complex into Virions during Virus Assembly
Authors: Imai Masaki , Watanabe Shinji , Ninomiya Ai , Obuchi Masatsugu , Odagiri Takato
Published: September 2004

Influenza B virus contains four integral membrane proteins in its envelope. Of these, BM2 has recently been found to have ion channel activity and is considered to be a functional counterpart to influenza A virus M2, but the role of BM2 in the life cycle of influenza B virus remains unclear. In an effort to explore its function, a number of BM2 mutant viruses were generated by using a reverse genetics technique. The BM2ΔATG mutant virus synthesized BM2 at markedly lower levels but exhibited similar growth to wild-type (wt) virus. In contrast, the BM2 knockout virus, which did not produce BM2, did not grow substantially but was able to grow normally when BM2 was supplemented in
trans
by host cells expressing BM2. These results indicate that BM2 is a required component for the production of infectious viruses. In the one-step growth cycle, the BM2 knockout virus produced progeny viruses lacking viral ribonucleoprotein complex (vRNP). The inhibited incorporation of vRNP was regained by
trans
-supplementation of BM2. An immunofluorescence study of virus-infected cells revealed that distribution of hemagglutinin, nucleoprotein, and matrix (M1) protein of the BM2 knockout virus at the apical membrane did not differ from that of wt virus, whereas the sucrose gradient flotation assay revealed that the membrane association of M1 was greatly affected in the absence of BM2, resulting in a decrease of vRNP in membrane fractions. These results strongly suggest that BM2 functions to capture the M1-vRNP complex at the virion budding site during virus assembly.
Anti-Vpr Activity of a Yeast Chaperone Protein
Authors: Benko Zsigmond , Liang Dong , Agbottah Emmanuel , Hou Jason , Chiu Karen , Yu Min , Innis Scott , Reed Patrick , Kabat William , Elder Robert T. , Di Marzio Paola , Taricani Lorena , Ratner Lee , Young Paul G. , Bukrinsky Michael , Zhao Richard Yuqi
Published: September 2004

Human immunodeficiency virus type 1 (HIV-1) viral protein R (Vpr) exerts multiple effects on viral and host cellular activities during viral infection, including nuclear transport of the proviral integration complex, induction of cell cycle G
2
arrest, and cell death. In this report, we show that a fission yeast chaperone protein Hsp16 inhibits HIV-1 by suppressing these Vpr activities. This protein was identified through three independent genome-wide screens for multicopy suppressors of each of the three Vpr activities. Consistent with the properties of a heat shock protein, heat shock-induced elevation or overproduction of Hsp16 suppressed Vpr activities through direct protein-protein interaction. Even though Hsp16 shows a stronger suppressive effect on Vpr in fission yeast than in mammalian cells, similar effects were also observed in human cells when fission yeast
hsp16
was expressed either in
vpr
-expressing cells or during HIV-1 infection, indicating a possible highly conserved Vpr suppressing activity. Furthermore, stable expression of
hsp16
prior to HIV-1 infection inhibits viral replication in a Vpr-dependent manner. Together, these data suggest that Hsp16 inhibits HIV-1 by suppressing Vpr-specific activities. This finding could potentially provide a new approach to studying the contribution of Vpr to viral pathogenesis and to reducing Vpr-mediated detrimental effects in HIV-infected patients.
Caspase Inhibition Protects against Reovirus-Induced Myocardial Injury In Vitro and In Vivo
Authors: DeBiasi Roberta L. , Robinson Bridget A. , Sherry Barbara , Bouchard Ron , Brown R. Dale , Rizeq Mona , Long Carlin , Tyler Kenneth L.
Published: September 2004

Viral myocarditis is a disease with a high morbidity and mortality. The pathogenesis of this disease remains poorly characterized, with components of both direct virus-mediated and secondary inflammatory and immune responses contributing to disease. Apoptosis has increasingly been viewed as an important mechanism of myocardial injury in noninfectious models of cardiac disease, including ischemia and failure. Using a reovirus murine model of viral myocarditis, we characterized and targeted apoptosis as a key mechanism of virus-associated myocardial injury in vitro and in vivo. We demonstrated caspase-3 activation, in conjunction with terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling and annexin binding, in cardiac myocytes after myocarditic viral infection in vitro. We also demonstrated a tight temporal and geographical correlation between caspase-3 activation, histologic injury, and viral load in cardiac tissue after myocarditic viral infection in vivo. Two pharmacologic agents that broadly inhibit caspase activity, Q-VD-OPH and Z-VAD(OMe)-FMK, effectively inhibited virus-induced cellular death in vitro. The inhibition of caspase activity in vivo by the use of pharmacologic agents as well as genetic manipulation reduced virus-induced myocardial injury by 40 to 60% and dramatically improved survival in infected caspase-3-deficient animals. This study indicates that apoptosis plays a critical role in mediating cardiac injury in the setting of viral myocarditis and is the first demonstration that caspase inhibition may serve as a novel therapeutic strategy for this devastating disease.
Identification of Differentially Expressed Genes in Scrapie-Infected Mouse Brains by Using Global Gene Expression Technology
Authors: Xiang Wei , Windl Otto , Wünsch Gerda , Dugas Martin , Kohlmann Alexander , Dierkes Nicola , Westner Ingo M. , Kretzschmar Hans A.
Published: September 2004

The pathogenesis of prion diseases, a class of transmissible fatal neurodegenerative diseases in humans and animals, is still unclear. The aim of this study was to identify the differentially regulated genes that correlate with the development of prion diseases for a better understanding of their pathological mechanisms. We employed Affymetrix Mouse Expression Arrays 430A containing >22,000 transcripts and compared the global gene expression profiles from brains of mice who were intracerebrally inoculated with scrapie strains ME7 and RML with those from brains of uninfected and mock-infected mice. The microarray data were analyzed by Significance Analysis of Microarrays, revealing 121 genes whose expression increased at least twofold in both ME7- and RML-infected mouse brains, with an estimated false discovery rate of ≤5%. These genes encode proteins involved in proteolysis, protease inhibition, cell growth and maintenance, the immune response, signal transduction, cell adhesion, and molecular metabolism. The time course of expression generally showed up-regulation of these genes from 120 days postinoculation (dpi) for ME7-inoculated mouse brains and from 90 dpi for RML-inoculated mouse brains. The onset of elevated expression correlated temporally with the onset of PrPScaccumulation and the activation of glia, which may have contributed to neuronal cell death. Among the differentially regulated genes reported in the present study, the emergence of genes for several cathepsins and S100 calcium binding proteins was conspicuous. These and other genes reported here may represent novel potential diagnostic and therapeutic targets for prion disease.
APOBEC3G
Genetic Variants and Their Influence on the Progression to AIDS
Authors: An Ping , Bleiber Gabriela , Duggal Priya , Nelson George , May Margaret , Mangeat Bastien , Alobwede Irene , Trono Didier , Vlahov David , Donfield Sharyne , Goedert James J. , Phair John , Buchbinder Susan , O'Brien Stephen J. , Telenti Amalio , Winkler Cheryl A.
Published: September 2004

The cytosine deaminase APOBEC3G, in the absence of the human immunodeficiency virus type 1 (HIV-1) accessory gene HIV-1 viral infectivity factor (
vif
), inhibits viral replication by introducing G→A hypermutation in the newly synthesized HIV-1 DNA negative strand. We tested the hypothesis that genetic variants of
APOBEC3G
may modify HIV-1 transmission and disease progression. Single nucleotide polymorphisms were identified in the promoter region (three), introns (two), and exons (two). Genotypes were determined for 3,073 study participants enrolled in six HIV-AIDS prospective cohorts. One codon-changing variant, H186R in exon 4, was polymorphic in African Americans (AA) (
f
= 37%) and rare in European Americans (
f
< 3%) or Europeans (
f
= 5%). For AA, the variant allele 186R was strongly associated with decline in CD4 T cells (CD4 slope on square root scale: −1.86,
P
= 0.009), The 186R allele was also associated with accelerated progression to AIDS-defining conditions in AA. The in vitro antiviral activity of the 186R enzyme was not inferior to that of the common H186 variant. These studies suggest that there may be a modifying role of variants of
APOBEC3G
on HIV-1 disease progression that warrants further investigation.
Repression of Human T-Cell Leukemia Virus Type 1 and Type 2 Replication by a Viral mRNA-Encoded Posttranscriptional Regulator
Authors: Younis Ihab , Khair Lyne , Dundr Miroslav , Lairmore Michael D. , Franchini Genoveffa , Green Patrick L.
Published: September 2004

Human T-cell leukemia virus type 1 (HTLV-1) and HTLV-2 are complex retroviruses that persist in the host, eventually causing leukemia and neurological disease in a small percentage of infected individuals. In addition to structural and enzymatic proteins, HTLV encodes regulatory (Tax and Rex) and accessory (open reading frame I and II) proteins. The viral Tax and Rex proteins positively regulate virus production. Tax activates viral and cellular transcription to promote T-cell growth and, ultimately, malignant transformation. Rex acts posttranscriptionally to facilitate cytoplasmic expression of viral mRNAs that encode the structural and enzymatic gene products, thus positively controlling virion expression. Here, we report that both HTLV-1 and HTLV-2 have evolved accessory genes to encode proteins that act as negative regulators of both Tax and Rex. HTLV-1 p30
II
and the related HTLV-2 p28
II
inhibit virion production by binding to and retaining
tax/rex
mRNA in the nucleus. Reduction of viral replication in a cell carrying the provirus may allow escape from immune recognition in an infected individual. These data are consistent with the critical role of these proteins in viral persistence and pathogenesis in animal models of HTLV-1 and HTLV-2 infection.
Avian Reovirus Temperature-Sensitive Mutant
tsA12
Has a Lesion in Major Core Protein σA and Is Defective in Assembly
Authors: Xu Wanhong , Patrick Megan K. , Hazelton Paul R. , Coombs Kevin M.
Published: September 2004

Members of our laboratory previously generated and described a set of avian reovirus (ARV) temperature-sensitive (
ts
) mutants and assigned 11 of them to 7 of the 10 expected recombination groups, named A through G (M. Patrick, R. Duncan, and K. M. Coombs, Virology
284:
113-122, 2001). This report presents a more detailed analysis of two of these mutants (
tsA12
and
tsA146
), which were previously assigned to recombination group A. The capacities of
tsA12
and
tsA146
to replicate at a variety of temperatures were determined. Morphological analyses indicated that cells infected with
tsA12
at a nonpermissive temperature produced ∼100-fold fewer particles than cells infected at a permissive temperature and accumulated core particles. Cells infected with
tsA146
at a nonpermissive temperature also produced ∼100-fold fewer particles, a larger proportion of which were intact virions. We crossed
tsA12
with ARV strain 176 to generate reassortant clones and used them to map the temperature-sensitive lesion in
tsA12
to the S2 gene. S2 encodes the major core protein σA. Sequence analysis of the
tsA12
S2 gene showed a single alteration, a cytosine-to-uracil transition, at nucleotide position 488. This alteration leads to a predicted amino acid change from proline to leucine at amino acid position 158 in the σA protein. An analysis of the core crystal structure of the closely related mammalian reovirus suggested that the Leu
158
substitution in ARV σA lies directly under the outer face of the σA protein. This may cause a perturbation in σA such that outer capsid proteins are incapable of condensing onto nascent cores. Thus, the ARV
tsA12
mutant represents a novel assembly-defective orthoreovirus clone that may prove useful for delineating virus assembly.
Multiple V1/V2
env
Variants Are Frequently Present during Primary Infection with Human Immunodeficiency Virus Type 1
Authors: Ritola Kimberly , Pilcher Christopher D. , Fiscus Susan A. , Hoffman Noah G. , Nelson Julie A. E. , Kitrinos Kathryn M. , Hicks Charles B. , Eron Joseph J. , Swanstrom Ronald
Published: September 2004

Human immunodeficiency virus type 1 (HIV-1) exists as a complex population of multiple genotypic variants in persons with chronic infection. However, acute HIV-1 infection via sexual transmission is a low-probability event in which there is thought to be low genetic complexity in the initial inoculum. In order to assess the viral complexity present during primary HIV-1 infection, the V1/V2 and V3 variable regions of the
env
gene were examined by using a heteroduplex tracking assay (HTA) capable of resolving these genotypic variants. Blood plasma samples from 26 primary HIV-1-infected subjects were analyzed for their level of diversity. Half of the subjects had more than one V1/V2 viral variant during primary infection, indicating the frequent transmission of multiple variants. This observation is inconsistent with the idea of infrequent transmission based on a small transmitting inoculum of cell-free virus. In chronically infected subjects, the complexity of the viral populations was even greater in both the V1/V2 and the V3 regions than in acutely infected subjects, indicating that in spite of the presence of multiple variants in acute infection, the virus does pass through a genetic bottleneck during transmission. We also examined how well the infecting virus penetrated different anatomical compartments by using the HTA. Viral variants detected in blood plasma were compared to those detected in seminal plasma and/or cerebral spinal fluid of six individuals. The virus in each of these compartments was to a large extent identical to virus in blood plasma, a finding consistent with rapid penetration of the infecting variant(s). The low-probability transmission of multiple variants could be the result of transient periods of hyperinfectiousness or hypersusceptibility. Alternatively, the inefficient transfer of a multiply infected cell could account for both the low probability of transmission and the transfer of multiple variants.
Evidence for Gene Expression by Unintegrated Human Immunodeficiency Virus Type 1 DNA Species
Authors: Brussel Audrey , Sonigo Pierre
Published: September 2004

The integrated form of human immunodeficiency virus type 1 (HIV-1) DNA is classically considered to be the sole template for viral gene expression. However, several studies have suggested that unintegrated viral DNA species could also support transcription. To determine the contribution of the different species of HIV-1 DNA to viral expression, we first monitored intracellular levels of various HIV-1 DNA and RNA species in a single-round infection assay. We observed that, in comparison to the precocity of HIV-1 DNA synthesis, viral expression was delayed, suggesting that only the HIV-1 DNA species that persist for a sufficient period of time would be transcribed efficiently. We next evaluated the transcriptional activity of the circular forms of HIV-1 DNA bearing two long terminal repeats, since these episomes were reported to exhibit an intrinsic molecular stability. Our results support the notion that these circular species of HIV-1 DNA are naturally transcribed during HIV-1 infection, thereby participating in virus replication.
Protective Efficacy of a DNA Influenza Virus Vaccine Is Markedly Increased by the Coadministration of a Schiff Base-Forming Drug
Authors: Charo Jehad , Lindencrona Jan Alvar , Carlson Lena-Maria , Hinkula Jorma , Kiessling Rolf
Published: September 2004

Effective vaccination against heterologous influenza virus infection remains elusive. Immunization with plasmid DNA (pDNA) expressing conserved genes from influenza virus is a promising approach to achieve cross-variant protection. However, despite having been described for more than a decade, pDNA vaccination still requires further optimization to be applied clinically as a standard vaccination approach. We have recently described a simple and efficient approach to enhance pDNA immunization, based on the use of tucaresol, a Schiff base-forming drug. In this report we have tested the ability of this drug to increase the protection conferred by pDNA vaccination against influenza virus infection. Our results demonstrate that a significant protection was achieved in two strains of mice by using the combination of pDNA and tucaresol. This protection was associated with an elevated humoral and cellular response and a switch in the type of the T helper cell (Th) immune response from type 2 to type 1. This vaccine combination represents a promising strategy for designing a clinical study for the protection from influenza and similar infections.
Transient Immunosuppression Stops Rejection of Virus-Transduced Enhanced Green Fluorescent Protein in Rabbit Retina
Authors: Doi Kentaro , Kong Jian , Hargitai Janos , Goff Stephen P. , Gouras Peter
Published: September 2004

The expression of lentivirus-transduced enhanced green fluorescent protein (EGFP) was detectable in rabbit retinal pigment epithelium (RPE) within 3 to 5 days after subretinal injection of the vector. Within 2 to 3 weeks, EGFP-expressing cells were eliminated by rejection. In the current experiments, we monitor serum antibody titers for EGFP before and after transduction and determine whether systemic immunosuppression prevents recognition of EGFP by the immune system. While all control rabbits developed antibodies against EFGP and showed signs of rejection, no such evidence was observed with animals which received immunosuppression. One month of systemic immunosuppression permanently prevented rejection of RPE with EGFP expression. Fluorescence has been maintained for more than a year. If a control eye was injected with the same virus after terminating immunosuppression, both eyes showed signs of rejection. The lack of rejection is not due to tolerance but to a failure of the animals to detect the foreign protein. Detection must depend upon a brief window of time after surgery needed to introduce the vector, perhaps related to a concurrent but transient inflammation. This strategy may be useful in managing other types of rejection in the retina.
Predicting the Impact of a Nonsterilizing Vaccine against Human Immunodeficiency Virus
Authors: Davenport Miles P. , Ribeiro Ruy M. , Chao Dennis L. , Perelson Alan S.
Published: September 2004

Studies of human immunodeficiency virus (HIV) vaccines in animal models suggest that it is difficult to induce complete protection from infection (sterilizing immunity) but that it is possible to reduce the viral load and to slow or prevent disease progression following infection. We have developed an age-structured epidemiological model of the effects of a disease-modifying HIV vaccine that incorporates the intrahost dynamics of infection, a transmission rate and host mortality that depend on the viral load, the possible evolution and transmission of vaccine escape mutant viruses, a finite duration of vaccine protection, and possible changes in sexual behavior. Using this model, we investigated the long-term outcome of a disease-modifying vaccine and utilized uncertainty analysis to quantify the effects of our lack of precise knowledge of various parameters. Our results suggest that the extent of viral load reduction in vaccinated infected individuals (compared to unvaccinated individuals) is the key predictor of vaccine efficacy. Reductions in viral load of about 1 log10copies ml−1would be sufficient to significantly reduce HIV-associated mortality in the first 20 years after the introduction of vaccination. Changes in sexual risk behavior also had a strong impact on the epidemic outcome. The impact of vaccination is dependent on the population in which it is used, with disease-modifying vaccines predicted to have the most impact in areas of low prevalence and rapid epidemic growth. Surprisingly, the extent to which vaccination alters disease progression, the rate of generation of escape mutants, and the transmission of escape mutants are predicted to have only a weak impact on the epidemic outcome over the first 25 years after the introduction of a vaccine.
Genomic and Proteomic Analysis of Thirty-Nine Structural Proteins of Shrimp White Spot Syndrome Virus
Authors: Tsai Jyh-Ming , Wang Han-Ching , Leu Jiann-Horng , Hsiao He-Hsuan , Wang Andrew H.-J. , Kou Guang-Hsiung , Lo Chu-Fang
Published: September 2004

White spot syndrome virus (WSSV) virions were purified from the hemolymph of experimentally infected crayfish
Procambarus clarkii
, and their proteins were separated by 8 to 18% gradient sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to give a protein profile. The visible bands were then excised from the gel, and following trypsin digestion of the reduced and alkylated WSSV proteins in the bands, the peptide sequence of each fragment was determined by liquid chromatography-nano-electrospray ionization tandem mass spectrometry (LC-nanoESI-MS/MS) using a quadrupole/time-of-flight mass spectrometer. Comparison of the resulting peptide sequence data against the nonredundant database at the National Center for Biotechnology Information identified 33 WSSV structural genes, 20 of which are reported here for the first time. Since there were six other known WSSV structural proteins that could not be identified from the SDS-PAGE bands, there must therefore be a total of at least 39 (33 + 6) WSSV structural protein genes. Only 61.5% of the WSSV structural genes have a polyadenylation signal, and preliminary analysis by 3′ rapid amplification of cDNA ends suggested that some structural protein genes produced mRNA without a poly(A) tail. Microarray analysis showed that gene expression started at 2, 6, 8, 12, 18, 24, and 36 hpi for 7, 1, 4, 12, 9, 5, and 1 of the genes, respectively. Based on similarities in their time course expression patterns, a clustering algorithm was used to group the WSSV structural genes into four clusters. Genes that putatively had common or similar roles in the viral infection cycle tended to appear in the same cluster.
Heterologous RNA Encapsidated in Pariacoto Virus-Like Particles Forms a Dodecahedral Cage Similar to Genomic RNA in Wild-Type Virions
Authors: Johnson Karyn N. , Tang Liang , Johnson John E. , Ball L. Andrew
Published: September 2004

The genome of some icosahedral RNA viruses plays an essential role in capsid assembly and structure. In T=3 particles of the nodavirus Pariacoto virus (PaV), a remarkable 35% of the single-stranded RNA genome is icosahedrally ordered. This ordered RNA can be visualized at high resolution by X-ray crystallography as a dodecahedral cage consisting of 30 24-nucleotide A-form RNA duplex segments that each underlie a twofold icosahedral axis of the virus particle and interact extensively with the basic N-terminal region of 60 subunits of the capsid protein. To examine whether the PaV genome is a specific determinant of the RNA structure, we produced virus-like particles (VLPs) by expressing the wild-type capsid protein open reading frame from a recombinant baculovirus. VLPs produced by this system encapsidated similar total amounts of RNA as authentic virus particles, but only about 6% of this RNA was PaV specific, the rest being of cellular or baculovirus origin. Examination of the VLPs by electron cryomicroscopy and image reconstruction at 15.4-Å resolution showed that the encapsidated RNA formed a dodecahedral cage similar to that of wild-type particles. These results demonstrate that the specific nucleotide sequence of the PaV genome is not required to form the dodecahedral cage of ordered RNA.
An N-Terminal Amphipathic Helix in Hepatitis C Virus (HCV) NS4B Mediates Membrane Association, Correct Localization of Replication Complex Proteins, and HCV RNA Replication
Authors: Elazar Menashe , Liu Ping , Rice Charles M. , Glenn Jeffrey S.
Published: September 2004

Like other positive-strand RNA viruses, hepatitis C virus (HCV) is believed to replicate its RNA in association with host cell cytoplasmic membranes. Because of its association with such membranes, NS4B, one of the virus's nonstructural proteins, may play an important role in this process, although the mechanistic details are not well understood. We identified a putative N-terminal amphipathic helix (AH) in NS4B that mediates membrane association. Introduction of site-directed mutations designed to disrupt the hydrophobic face of the AH abolishes the AH's ability to mediate membrane association. An AH in NS4B is conserved across HCV isolates. Completely disrupting the amphipathic nature of NS4B's N-terminal helix abolished HCV RNA replication, whereas partial disruption resulted in an intermediate level of replication. Finally, immunofluorescence studies revealed that HCV replication complex components were mislocalized in the AH-disrupted mutant. These results identify a key membrane-targeting domain which can form the basis for developing novel antiviral strategies.
Macaque Model for Severe Acute Respiratory Syndrome
Authors: Rowe Thomas , Gao Guangping , Hogan Robert J. , Crystal Ronald G. , Voss Thomas G. , Grant Rebecca L. , Bell Peter , Kobinger Gary P. , Wivel Nelson A. , Wilson James M.
Published: September 2004

Rhesus and cynomolgus macaques were challenged with 10
7
PFU of a clinical isolate of the severe acute respiratory syndrome (SARS) coronavirus. Some of the animals developed a mild self-limited respiratory infection very different from that observed in humans with SARS. The macaque model as it currently exists will have limited utility in the study of SARS and the evaluation of therapies.
Persistent Infection with Primate Foamy Virus Type 1 Increases Human Immunodeficiency Virus Type 1 Cell Binding via a Bet-Independent Mechanism
Authors: Schiffer Cecile , Lecellier Charles-Henri , Mannioui Abdelkrim , Felix Nathalie , Nelson Elisabeth , Lehmann-Che Jacqueline , Giron Marie-Louise , Gluckman Jean Claude , Saib Ali , Canque Bruno
Published: September 2004

We report that human T cells persistently infected with primate foamy virus type 1 (PFV-1) display an increased capacity to bind human immunodeficiency virus type 1 (HIV-1), resulting in increased cell permissiveness to HIV-1 infection and enhanced cell-to-cell virus transmission. This phenomenon is independent of HIV-1 receptor, CD4, and it is not related to PFV-1 Bet protein expression. Increased virus attachment is specifically inhibited by heparin, indicating that it should be mediated by interactions with heparan sulfate glycosaminoglycans expressed on the target cells. Given that both viruses infect similar animal species, the issue of whether coinfection with primate foamy viruses interferes with the natural course of lentivirus infections in nonhuman primates should be considered.