bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Single Amino Acid Change in the Newcastle Disease Virus Fusion Protein Alters the Requirement for HN Protein in Fusion
Authors: Sergel Theresa A. , McGinnes Lori W. , Morrison Trudy G. 
Published: July 2002

ABSTRACT

The role of a leucine heptad repeat motif between amino acids 268 and 289 in the structure and function of the Newcastle disease virus (NDV) F protein was explored by introducing single point mutations into the F gene cDNA. The mutations affected either folding of the protein or the fusion activity of the protein. Two mutations, L275A and L282A, likely interfered with folding of the molecule since these proteins were not proteolytically cleaved, were minimally expressed at the cell surface, and formed aggregates. L268A mutant protein was cleaved and expressed at the cell surface although the protein migrated slightly slower than wild type on polyacrylamide gels, suggesting an alteration in conformation or processing. L268A protein was fusion inactive in the presence or absence of HN protein expression. Mutant L289A protein was expressed at the cell surface and proteolytically cleaved at better than wild-type levels. Most importantly, this protein mediated syncytium formation in the absence of HN protein expression although HN protein enhanced fusion activity. These results show that a single amino acid change in the F
1
portion of the NDV F protein can alter the stringent requirement for HN protein expression in syncytium formation.
Mov34 Protein from Mouse Brain Interacts with the 3′ Noncoding Region of Japanese Encephalitis Virus
Authors: Ta Malancha , Vrati Sudhanshu 
Published: July 2002

ABSTRACT

The plus-sense RNA genome of Japanese encephalitis virus (JEV) contains noncoding regions (NCRs) of 95 and 585 bases at its 5′ and 3′ ends, respectively. The last 83 nucleotides of the 3′-NCR are predicted to form stable stem-loop (SL) structures. The shape of this 3′-SL structure is highly conserved among divergent flaviviruses even though only small stretches of nucleotide sequence contained within these structures are conserved. These SL structures have been predicted to function as
cis
-acting signals for RNA replication and as such may bind to viral and cellular proteins that may be involved in viral replication. We have studied the interaction of the JEV 3′-NCR RNA with host proteins using gel retardation assays. We show that the JEV 3′-SL structure RNA forms three complexes with proteins from the S100 cytoplasmic extract prepared from the neonatal mouse brain. These complexes could be obtained in the presence of 200 mM KCl, indicating that the RNA-protein interaction may be physiologically relevant. UV-induced cross-linking and Northwestern blotting analyses detected three proteins with apparent molecular masses of 32, 35, and 50 kDa that bound to the JEV 3′-SL structure RNA. Screening of the neonatal mouse brain cDNA library with the JEV 3′-SL structure RNA identified a 36-kDa Mov34 protein interacting with it. Competition experiments using the RNA extracted from JEV virions established that the 36-kDa Mov34 protein indeed bound to the JEV genome. Murine Mov34 belongs to a family of proteins whose members have been shown to be involved in RNA transcription and translation. It is, therefore, likely that the murine Mov34 interaction with JEV 3′-NCR has a role in RNA replication.
Mutational Analysis of the Rubella Virus Nonstructural Polyprotein and Its Cleavage Products in Virus Replication and RNA Synthesis
Authors: Liang Yuying , Gillam Shirley 
Published: July 2002

ABSTRACT
Rubella virus nonstructural proteins, translated from input genomic RNA as a p200 polyprotein and subsequently processed into p150 and p90 by an intrinsic papain-like thiol protease, are responsible for virus replication. To examine the effect of p200 processing on virus replication and to study the roles of nonstructural proteins in viral RNA synthesis, we introduced into a rubella virus infectious cDNA clone a panel of mutations that had variable defective effects on p200 processing. The virus yield and viral RNA synthesis of these mutants were examined. Mutations that completely abolished (C1152S and G1301S) or largely abolished (G1301A) cleavage of p200 resulted in noninfectious virus. Mutations that partially impaired cleavage of p200 (R1299A and G1300A) decreased virus replication. An RNase protection assay revealed that all of the mutants synthesized negative-strand RNA as efficiently as the wild type does but produced lower levels of positive-strand RNA. Our results demonstrated that processing of rubella virus nonstructural protein is crucial for virus replication and that uncleaved p200 could function in negative-strand RNA synthesis, whereas the cleavage products p150 and p90 are required for efficient positive-strand RNA synthesis.
Influenza A Viruses Lacking Sialidase Activity Can Undergo Multiple Cycles of Replication in Cell Culture, Eggs, or Mice
Authors: Hughes Mark T. , Matrosovich Mikhail , Rodgers M. Elizabeth , McGregor Martha , Kawaoka Yoshihiro 
Published: July 2002

ABSTRACT
Influenza A viruses possess both hemagglutinin (HA), which is responsible for binding to the terminal sialic acid of sialyloligosaccharides on the cell surface, and neuraminidase (NA), which contains sialidase activity that removes sialic acid from sialyloligosaccharides. Interplay between HA receptor-binding and NA receptor-destroying sialidase activity appears to be important for replication of the virus. Previous studies by others have shown that influenza A viruses lacking sialidase activity can undergo multiple cycles of replication if sialidase activity is provided exogenously. To investigate the sialidase requirement of influenza viruses further, we generated a series of sialidase-deficient mutants. Although their growth was less efficient than that of the parental NA-dependent virus, these viruses underwent multiple cycles of replication in cell culture, eggs, and mice. To understand the molecular basis of this viral growth adaptation in the absence of sialidase activity, we investigated changes in the HA receptor-binding affinity of the sialidase-deficient mutants. The results show that mutations around the HA receptor-binding pocket reduce the virus's affinity for cellular receptors, compensating for the loss of sialidase. Thus, sialidase activity is not absolutely required in the influenza A virus life cycle but appears to be necessary for efficient virus replication.
Chimeric Retroviral Helper Virus and Picornavirus IRES Sequence To Eliminate DNA Methylation for Improved Retroviral Packaging Cells
Authors: Young Won-Bin , Link Charles J. 
Published: July 2002

ABSTRACT

Most retroviral packaging cell lines were established by a helper virus plasmid cotransfected with a separate plasmid encoding a selection marker. Since this selection marker coexisted in
trans
with the helper virus sequence, helper virus gene expression could be inactivated by host DNA methylation despite selection for the cotransfected selection marker. We have reported that DNA methylation could occur in the long terminal repeat (LTR) region of helper virus in vector producer cells (VPC) in up to 2% of the population per day (W. B. Young, G. L. Lindberg, and C. J. Link, Jr., J. Virol. 74:3177–3187, 2000). To overcome host cell DNA methylation that suppresses viral gene expression, we constructed a chimeric retroviral helper virus, pAM3-IRES-Zeo, that contains Moloney murine leukemia virus as a helper virus and a picornavirus internal ribosome entry site (IRES) sequence followed by a Zeocin selection marker at the 3′ end of the
env
sequence. This pAM3-IRES-Zeo permitted selection for intact and functional helper virus in transfected cells without subcloning. By selection with Zeocin, a mixed population of pAM3-IRES-Zeo-transfected NIH3T3 cells (AMIZ cells) was maintained with little or no DNA methylation of the helper virus 5′ LTR. The high level of pAM3-IRES-Zeo gene expression resulted in no detectable vector superinfection and in high vector titers (2 × 10
6
to 1.5 × 10
7
CFU/ml) after introduction of a retroviral vector. When Zeocin selection was withdrawn from AMIZ cells, methylation of the 5′ LTR increased from 17 to 36% of the population during 67 days of continuous culture and the cells became susceptible to superinfection. During this period, gene expression of pAM3-IRES-Zeo decreased and vector titer production was reduced to 2 × 10
4
CFU/ml. These data demonstrate an important role of DNA methylation in the genetic instability of VPC. The chimeric helper virus allows the establishment of a mixed population of packaging cells capable of high-level and sustained vector production without cloning procedures.
HLA-B57-Restricted Cytotoxic T-Lymphocyte Activity in a Single Infected Subject toward Two Optimal Epitopes, One of Which Is Entirely Contained within the Other
Authors: Goulder Philip J. R. , Tang Yanhua , Pelton Stephen I. , Walker Bruce D. 
Published: July 2002

ABSTRACTViral peptides are recognized by cytotoxic T lymphocytes (CTL) as a complex with major histocompatibility complex (MHC) class I molecules, but the extent to which a single HLA allele can accommodate epitope peptides of different length and sequence is not well characterized. Here we report the identification of clonal CTL responses from the same donor that independently recognize one of two HLA-B57-restricted epitopes, KAFSPEVIPMF (KF11; p24Gagresidues 30 to 40) and KAFSPEVI (KF8; p24Gagresidues 30 to 37). Although lysis studies indicated that the KF11 peptide stabilized the HLA-B57-peptide complex more efficiently than the KI8 peptide, strong clonal responses were directed at each epitope. In samples from a second donor, the same phenomenon was observed, in which distinct CTL clones recognized peptide epitopes presented by the same HLA class I allele (in this case, HLA-A3) which were entirely overlapping. These data are relevant to the accurate characterization of CTL responses, which is fundamental to a detailed understanding of MHC class I-restricted immunity. In addition, these studies demonstrate marked differences in the length of peptides presented by HLA-B57, an allele which is associated with nonprogressive human immunodeficiency virus infection.
Mutation of a Conserved Residue (D123) Required for Oligomerization of Human Immunodeficiency Virus Type 1 Nef Protein Abolishes Interaction with Human Thioesterase and Results in Impairment of Nef Biological Functions
Authors: Liu Lang Xia , Heveker Nikolaus , Fackler Oliver T. , Arold Stefan , Le Gall Sylvie , Janvier Katy , Peterlin B. Matija , Dumas Christian , Schwartz Olivier , Benichou Serge , Benarous Richard 
Published: July 2002

ABSTRACT
Nef is a myristoylated protein of 27 to 35 kDa that is conserved in primate lentiviruses. In vivo, Nef is required for high viral load and full pathological effects. In vitro, Nef has at least four activities: induction of CD4 and major histocompatibility complex (MHC) class I downregulation, enhancement of viral infectivity, and alteration of T-cell activation pathways. We previously reported that the Nef protein from human immunodeficiency virus type 1 interacts with a novel human thioesterase (hTE). In the present study, by mutational analysis, we identified a region of the Nef core, extending from the residues D108 to W124, that is involved both in Nef-hTE interaction and in Nef-induced CD4 downregulation. This region of Nef is located on the oligomer interface and is in close proximity to the putative CD4 binding site. One of the mutants carrying a mutation in this region, targeted to the conserved residue D123, was also found to be defective in two other functions of Nef, MHC class I downmodulation and enhancement of viral infectivity. Furthermore, mutation of this residue affected the ability of Nef to form dimers, suggesting that the oligomerization of Nef may be critical for its multiple functions.
Mutational Definition of Functional Domains within the Rev Homolog Encoded by Human Endogenous Retrovirus K
Authors: Bogerd Hal P. , Wiegand Heather L. , Yang Jin , Cullen Bryan R. 
Published: July 2002

ABSTRACT

Nuclear export of the incompletely spliced mRNAs encoded by several complex retroviruses, including human immunodeficiency virus type 1 (HIV-1), is dependent on a virally encoded adapter protein, termed Rev in HIV-1, that directly binds both to a
cis
-acting viral RNA target site and to the cellular Crm1 export factor. Human endogenous retrovirus K, a family of ancient endogenous retroviruses that is not related to the exogenous retrovirus HIV-1, was recently shown to also encode a Crm1-dependent nuclear RNA export factor, termed K-Rev. Although HIV-1 Rev and K-Rev display little sequence identity, they share the ability not only to bind to Crm1 and to RNA but also to form homomultimers and shuttle between nucleus and cytoplasm. We have used mutational analysis to identify sequences in the 105-amino-acid K-Rev protein required for each of these distinct biological activities. While mutations in K-Rev that inactivate any one of these properties also blocked K-Rev-dependent nuclear RNA export, several K-Rev mutants were comparable to wild type when assayed for any of these individual activities yet nevertheless defective for RNA export. Although several nonfunctional K-Rev mutants acted as dominant negative inhibitors of K-Rev-, but not HIV-1 Rev-, dependent RNA export, these were not defined by their inability to bind to Crm1, as is seen with HIV-1 Rev. In total, this analysis suggests a functional architecture for K-Rev that is similar to, but distinct from, that described for HIV-1 Rev and raises the possibility that viral RNA export mediated by the ∼25 million-year-old K-Rev protein may require an additional cellular cofactor that is not required for HIV-1 Rev function.
Determination of Essential Amino Acids Involved in the CD4-Independent Tropism of the X4 Human Immunodeficiency Virus Type 1 m7NDK Isolate: Role of Potential N Glycosylations in the C2 and V3 Regions of gp120
Authors: Dumonceaux Julie , Goujon Caroline , Joliot Veronique , Briand Pascale , Hazan Uriel 
Published: July 2002

ABSTRACT
Seven mutations in the C2, V3, and C3 regions of gp120 are implicated in the tropism of the first CD4-independent human immunodeficiency virus type 1 isolate, m7NDK. Site-directed mutagenesis revealed that three amino acids are essential to maintain this tropism, one in the C2 region and two in the V3 loop. Two mutations implied N glycosylation modifications.
Structural Flexibility and Functional Valence of CD4-IgG2 (PRO 542): Potential for Cross-Linking Human Immunodeficiency Virus Type 1 Envelope Spikes
Authors: Zhu Ping , Olson William C. , Roux Kenneth H. 
Published: July 2002

ABSTRACT
CD4-immunoglobulin G2 (CD4-IgG2) incorporates four copies of the D1D2 domains of CD4 into an antibody-like molecule that potently neutralizes primary human immunodeficiency virus type 1. Here electron microscopy was used to explore the structure and functional valence of CD4-IgG2 in complex with gp120. CD4-γ2, a divalent CD4-immunoglobulin fusion protein, was evaluated in parallel. Whereas CD4-γ2–gp120 complexes adopted a simple Y-shaped structure, CD4-IgG2–gp120 complexes consisted of four gp120s arrayed about a central CD4-IgG2 molecule, a structure more reminiscent of complement C1q. Molecular modeling corroborated the electron microscopy data and further indicated that CD4-IgG2 but not CD4-γ2 has significant potential to cross-link gp120-gp41 trimers on the virion surface, suggesting a mechanism for the heightened antiviral activity of CD4-IgG2.
Protection against Woodchuck Hepatitis Virus (WHV) Infection by Gene Gun Coimmunization with WHV Core and Interleukin-12
Authors: Garcı́a-Navarro R. , Blanco-Urgoiti B. , Berraondo P. , Sánchez de la Rosa R. , Vales A. , Hervás-Stubbs S. , Lasarte J. J. , Borrás F. , Ruiz J. , Prieto J. 
Published: July 2002

ABSTRACTWoodchuck hepatitis virus (WHV) and hepatitis B virus (HBV) are closely similar with respect to genomic organization, host antiviral responses, and pathobiology of the infection. T-cell immunity against viral nucleocapsid (HBcAg or WHcAg) has been shown to play a critical role in viral clearance and protection against infection. Here we show that vaccination of healthy woodchucks by gene gun bombardment with a plasmid coding for WHcAg (pCw) stimulates proliferation of WHcAg-specific T cells but that these cells do not produce significant levels of gamma interferon (IFN-γ) upon antigen stimulation. In addition, animals vaccinated with pCw alone were not protected against WHV inoculation. In order to induce a Th1 cytokine response, another group of woodchucks was immunized with pCw together with another plasmid coding for woodchuck interleukin-12 (IL-12). These animals exhibited WHcAg-specific T-cell proliferation with high IFN-γ production and were protected against challenge with WHV, showing no viremia or low-level transient viremia after WHV inoculation. In conclusion, gene gun immunization with WHV core generates a non-Th1 type of response which does not protect against experimental infection. However, steering the immune response to a Th1 cytokine profile by IL-12 coadministration achieves protective immunity. These data demonstrate a crucial role of Th1 responses in the control of hepadnavirus replication and suggest new approaches to inducing protection against HBV infection.
THE STOCHASTIC BURGERS EQUATION: FINITE MOMENTS AND SMOOTHNESS OF THE DENSITY
Authors: LEÓN JORGE A. , NUALART D. , PETTERSSON ROGER 
Published: July 2002

We apply a stochastic version of the Hopf–Cole transformation to the solution of the stochastic Burgers equation with Dirichlet boundary conditions driven by a space–time Gaussian white noise. As a consequence, we deduce that the solution of the Burgers equation has moments of all orders. Using the techniques of the Malliavin calculus we show that if the dispersion is state-independent, then the solution of the stochastic Burgers equation has a smooth density at any point (t, x), with t>0 and x ∈(0,1).
ENVIRONMENTAL ASSESSMENT IN SRI LANKA: ITS STATUS AND THE POTENTIAL FOR THE INTRODUCTION OF STRATEGIC ENVIRONMENTAL ASSESSMENT
Authors: MACKEE JAMIE , OBBARD JEFFREY , BRIFFETT CLIVE 
Published: July 2002

Sri Lanka is an island republic situated off the southern tip of the Indian subcontinent. It has a long and continuous recorded history dating back approximately 2,500 years, and claims to have one of the oldest nature reserves in the world. However, Environmental Assessment (EA) in the country has a much shorter history. This can be traced back to the early eighties and the dramatic change in economic policies when initial legislation was enacted. The final three amendments to this legislation making EAs mandatory came into force in 1993, although there were some EIAs predating this legislation that were voluntary and prepared for large infrastructure projects. Since then, a number of EAs and Initial Environmental Examinations (IEEs) have been prepared for a wide variety of projects with varying degrees of success. Despite this, the natural environment is still undergoing rapid deterioration, while proper implementation of good EIA practice is still needed. The research presented in this paper, which is part of a larger study on implementation of EA and Strategic Environmental Assessment (SEA) in Asia, discusses the current status of environmental assessment in Sri Lanka based on information collected from field visits and interviews, as well as published and unpublished data. EA practices are discussed in the context of investigating the potential for introducing the process of SEA in Sri Lanka. Two case studies demonstrate the consideration of environmental issues in the development of strategic sectoral policies programmes and plans. These case studies highlight the potential benefits of an effective SEA strategy in Sri Lanka, as well as identifying some of the weaknesses in the current EA system within the country. Findings from the study suggest that rapid industrialisation combined with poor monitoring, a dearth of technically skilled personnel, the lack of baseline information and the continuing protracted civil war are key factors restricting the successful implementation of the EA process. It is from this perspective that the paper looks at the possible role that SEA may play in overcoming the failings of EA.
High-level programming features for improving the efficiency of a relational database system
Authors: Van de Riet Reind P. , Kersten Martin L. , de Jonge Wiebren , Wasserman Anthony I. 
Published: July 2002

This paper discusses some high-level language programming constructs that can be used to manipulate the relations of a relational database system efficiently. Three different constructs are described: (1) tuple identifiers that directly reference tuples of a relation; (2) cursors that may iterate over the tuples of a relation; and (3) markings, a form of temporary relation consisting of a set of tuple identifiers. In each case, attention is given to syntactic, semantic, and implementation considerations.
The use of these features is first presented within the context of the programming language PLAIN, and it is then shown how these features could be used more generally to provide database manipulation capabilities in a high-level programming language. Consideration is also given to issues of programming methodology, with an important goal being the achievement of a balance between the enforcement of good programming practices and the ability to write efficient programs.
Tree queries
Authors: Goodman Nathan , Shmueli Oded 
Published: July 2002

One can partition the class of relational database schemas into tree schemas and cyclic schemas. (These are called acyclic hypergraphs and cyclic hypergraphs elsewhere in the literature.) This partition has interesting implications in query processing, dependency theory, and graph theory.
The tree/cyclic partitioning of database schemas originated with a similar partition of equijoin queries. Given an arbitrary equijoin query one can obtain an equivalent query that calculates the natural join of all relations in (an efficiently) derived database; such a query is called a natural join (NJ) query. If the derived database is a tree schema the original query is said to be a tree query, and otherwise a cyclic query.
In this paper we analyze query processing consequences of the tree/cyclic partitioning. We are able to argue, qualitatively, that queries which imply a tree schema are easier to process than those implying a cyclic schema. Our results also extend the study of the semijoin operator.