bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Natural Variants of the Human Immunodeficiency Virus Type 1
gag-pol
Frameshift Stem-Loop Structure
Authors: Telenti Amalio , Martinez Raquel , Munoz Miguel , Bleiber Gabriela , Greub Gilbert , Sanglard Dominique , Peters Solange 
Published: July 2002

ABSTRACT

Human immunodeficiency virus type 1 uses ribosomal frameshifting for translation of the Gag-Pol polyprotein. Frameshift activities are thought to be tightly regulated. Analysis of
gag p1
sequences from 270 plasma virions identified in 64% of the samples the occurrence of polymorphism that could lead to changes in thermodynamic stability of the stem-loop. Expression in
Saccharomyces cerevisiae
of p1-β-galactosidase fusion proteins from 10 representative natural stem-loop variants and three laboratory mutant constructs (predicted the thermodynamic stability [Δ
G
°] ranging from −23.0 to −4.3 kcal/mol) identified a reduction in frameshift activity of 13 to 67% compared with constructs with the wild-type stem-loop (Δ
G
°, −23.5 kcal/mol). Viruses carrying stem-loops associated with greater than 60% reductions in frameshift activity presented profound defects in viral replication. In contrast, viruses with stem-loop structures associated with 16 to 42% reductions in frameshift efficiency displayed no significant viral replication deficit.
Rapid Progression to Simian AIDS Can Be Accompanied by Selection of CD4-Independent gp120 Variants with Impaired Ability To Bind CD4
Authors: Ryzhova Elena , Whitbeck J. Charles , Canziani Gabriela , Westmoreland Susan V. , Cohen Gary H. , Eisenberg Roselyn J. , Lackner Andrew , González-Scarano Francisco 
Published: July 2002

ABSTRACT

Aspartate 368 on human immunodeficiency virus type 1 (HIV-1) gp120 forms multiple contacts with CD4; in mutagenesis studies, its replacement by asparagine and corresponding changes in simian immunodeficiency virus SIVmac (D385N) reduced binding with CD4. Nevertheless, simian immunodeficiency virus envelopes with D385N were prevalent in several studies. Extending these observations, we also found D385N to be dominant among
env
clones from two rhesus macaques that progressed rapidly to simian AIDS. These envelopes showed a CD4-independent phenotype as well as reduced affinity to CD4. Moreover, an adjacent change, G383R, which was frequently coselected with D385N, further decreased binding. An optical biosensor study demonstrated that the SIVmac239 gp120 bound to CD4 with kinetics similar to those of HIV-1. However, the gp120s with D385N and G383R showed a 40-fold reduction in affinity, with a drastic increase in dissociation rate, indicating an inherently unstable complex. This finding showed that rapid progression to simian AIDS may be accompanied by the selection of CD4-independent gp120 variants with impaired CD4 binding ability.
Bovine Leukemia Virus SU Protein Interacts with Zinc, and Mutations within Two Interacting Regions Differently Affect Viral Fusion and Infectivity In Vivo
Authors: Gatot Jean-Stéphane , Callebaut Isabelle , Van Lint Carine , Demonté Dominique , Kerkhofs Pierre , Portetelle Daniel , Burny Arsène , Willems Luc , Kettmann Richard 
Published: July 2002

ABSTRACTBovine leukemia virus (BLV) and human T-cell lymphotropic virus type 1 (HTLV-1) belong to the genus of deltaretroviruses. Their entry into the host cell is supposed to be mediated by interactions of the extracellular (SU) envelope glycoproteins with cellular receptors. To gain insight into the mechanisms governing this process, we investigated the ability of SU proteins to interact with specific ligands. In particular, by affinity chromatography, we have shown that BLV SU protein specifically interacted with zinc ions. To identify the protein domains involved in binding, 16 peptides distributed along the sequence were tested. Two of them appeared to be able to interact with zinc. To unravel the role of these SU regions in the biology of the virus, mutations were introduced into theenvgene of a BLV molecular clone in order to modify residues potentially interacting with zinc. The fusogenic capacity of envelope mutated within the first zinc-binding region (104 to 123) was completely abolished. Furthermore, the integrity of this domain was also required for in vivo infectivity. In contrast, mutations within the second zinc-binding region (218 to 237) did not hamper the fusogenic capacity; indeed, the syncytia were even larger. In sheep, mutations in region 218 to 237 did not alter infectivity or viral spread. Finally, we demonstrated that the envelope of the related HTLV-1 was also able to bind zinc. Interestingly, zinc ions were found to be associated with the receptor-binding domain (RBD) of Friend murine leukemia virus (Fr-MLV) SU glycoprotein, further supporting their relevance in SU structure. Based on the sequence similarities shared with the Fr-MLV RBD, whose three-dimensional structure has been experimentally determined, we located the BLV zinc-binding peptide 104-123 on the opposite side of the potential receptor-binding surface. This observation supports the hypothesis that zinc ions could mediate interactions of the SU RBD either with the C-terminal part of SU, thereby contributing to the SU structural integrity, or with a partner(s) different from the receptor.
Multiple Transmembrane Amino Acid Requirements Suggest a Highly Specific Interaction between the Bovine Papillomavirus E5 Oncoprotein and the Platelet-Derived Growth Factor Beta Receptor
Authors: Nappi Valerie M. , Petti Lisa M. 
Published: July 2002

ABSTRACT
The bovine papillomavirus E5 protein activates the cellular platelet-derived growth factor β receptor (PDGFβR) tyrosine kinase in a ligand-independent manner. Evidence suggests that the small transmembrane E5 protein homodimerizes and physically interacts with the transmembrane domain of the PDGFβR, thereby inducing constitutive dimerization and activation of this receptor. Amino acids in the receptor previously found to be required for the PDGFβR-E5 interaction are a transmembrane Thr513 and a juxtamembrane Lys499. Here, we sought to determine if these are the only two receptor amino acids required for an interaction with the E5 protein. Substitution of large portions of the PDGFβR transmembrane domain indicated that additional amino acids in both the amino and carboxyl halves of the receptor transmembrane domain are required for a productive interaction with the E5 protein. Indeed, individual amino acid substitutions in the receptor transmembrane domain identified roles for the extracellular proximal transmembrane residues in the interaction. These data suggest that multiple amino acids within the transmembrane domain of the PDGFβR are required for a stable interaction with the E5 protein. These may be involved in direct protein-protein contacts or may support the proper transmembrane alpha-helical conformation for optimal positioning of the primary amino acid requirements.
A Novel Herpes Simplex Virus Type 1 Transcript (AL-RNA) Antisense to the 5′ End of the Latency-Associated Transcript Produces a Protein in Infected Rabbits
Authors: Perng Guey-Chuen , Maguen Barak , Jin Ling , Mott Kevin R. , Kurylo John , BenMohamed Lbachir , Yukht Ada , Osorio Nelson , Nesburn Anthony B. , Henderson Gail , Inman Melissa , Jones Clinton , Wechsler Steven L. 
Published: July 2002

ABSTRACT

Following primary ocular infection, herpes simplex virus type 1 (HSV-1) establishes a lifelong latent infection in sensory neurons of the trigeminal ganglia. Latency-associated transcript (LAT), the only known viral gene abundantly transcribed during HSV-1 neuronal latency, is required for high levels of reactivation. Recently we showed that three different mutants that do not alter the LAT promoter but contain deletions within the 5′ end of the primary LAT transcript affect viral virulence (G. C. Perng et al., J. Virol. 75:9018-9028, 2001). In contrast, in LAT-null mutants viral virulence appears unaltered (T. M. Block et al., Virology 192:618-630, 1993; D. C. Bloom et al., J. Virol. 68:1283-1292, 1994; J. M. Hill et al., Virology 174:117-125, 1990; G. C. Perng et al., J. Virol. 68:8045-8055, 1994; F. Sedarati, K. M. Izumi, E. K. Wagner, and J. G. Stevens, J. Virol. 63:4455-4458, 1989). We therefore hypothesized that the 5′ end of LAT and/or an as yet unidentified gene that overlaps part of this region is involved in viral virulence. We report here on the discovery and initial characterization of a novel HSV-1 RNA consistent with such a putative gene. The novel RNA was antisense to the 5′ end of LAT and was designated AL-RNA (anti-LAT sense RNA). The AL-RNA overlapped the core LAT promoter and the first 158 nucleotides of the 5′ end of the primary LAT transcript. AL-RNA was detected in extracts from neuron-like cells (PC-12) infected with wild-type HSV-1 but not in cells infected with a mutant with the AL region deleted. The deletions in each of the above three mutants with altered virulence encompass the 5′ end of the AL-RNA, and these mutants cannot transcribe AL. This supports the hypothesis that the AL gene may play a role in viral virulence. Based on comparison to the corresponding genomic sequence, the AL-RNA did not appear to be spliced. The AL-RNA was polyadenylated and contained an open reading frame capable of encoding a protein 56 amino acids in length with a predicted molecular mass of 6.8 kDa. Sera from three of three rabbits infected with wild-type HSV-1 but not sera from any of three rabbits infected with a mutant with the AL-RNA region deleted recognized the
Escherichia coli
recombinantly expressed AL open reading frame on Western blots. In addition, four of six rabbits infected with wild-type virus developed enzyme-linked immunosorbent assay titers against one or more AL synthetic peptides. These results suggest that an AL protein is produced in vivo.
The Lytic Cycle of Epstein-Barr Virus Is Associated with Decreased Expression of Cell Surface Major Histocompatibility Complex Class I and Class II Molecules
Authors: Keating Sinéad , Prince Stuart , Jones Matthew , Rowe Martin 
Published: July 2002

ABSTRACTHuman herpesviruses utilize an impressive range of strategies to evade the immune system during their lytic replicative cycle, including reducing the expression of cell surface major histocompatibility complex (MHC) and immunostimulatory molecules required for recognition and lysis by virus-specific cytotoxic T cells. Study of possible immune evasion strategies by Epstein-Barr virus (EBV) in lytically infected cells has been hampered by the lack of an appropriate permissive culture model. Using two-color immunofluorescence staining of cell surface antigens and EBV-encoded lytic cycle antigens, we examined EBV-transformed B-cell lines in which a small subpopulation of cells had spontaneously entered the lytic cycle. Cells in the lytic cycle showed a four- to fivefold decrease in cell surface expression of MHC class I molecules relative to that in latently infected cells. Expression of MHC class II molecules, CD40, and CD54 was reduced by 40 to 50% on cells in the lytic cycle, while no decrease was observed in cell surface expression of CD19, CD80, and CD86. Downregulation of MHC class I expression was found to be an early-lytic-cycle event, since it was observed when progress through late lytic cycle was blocked by treatment with acyclovir. The immediate-early transactivator of the EBV lytic cycle, BZLF1, did not directly affect expression of MHC class I molecules. However, BZLF1 completely inhibited the upregulation of MHC class I expression mediated by the EBV cell-transforming protein, LMP1. This novel function of BZLF1 elucidates the paradox of how MHC class I expression can be downregulated when LMP1, which upregulates MHC class I expression in latent infection, remains expressed in the lytic cycle.
Physical Interaction between Envelope Glycoproteins E and M of Pseudorabies Virus and the Major Tegument Protein UL49
Authors: Fuchs Walter , Klupp Barbara G. , Granzow Harald , Hengartner Christoph , Brack Alexandra , Mundt Alice , Enquist Lynn W. , Mettenleiter Thomas C. 
Published: July 2002

ABSTRACT

Envelope glycoprotein M (gM) and the complex formed by glycoproteins E (gE) and I (gI) are involved in the secondary envelopment of pseudorabies virus (PrV) particles in the cytoplasm of infected cells. In the absence of the gE-gI complex and gM, envelopment is blocked and capsids surrounded by tegument proteins accumulate in the cytoplasm (A. R. Brack, J. Dijkstra, H. Granzow, B. G. Klupp, and T. C. Mettenleiter, J. Virol.
73:
5364-5372, 1999). Here we demonstrate by yeast two-hybrid analyses that the cytoplasmic domains of gE and gM specifically interact with the C-terminal part of the UL49 gene product of PrV, which represents a major tegument protein and which is homologous to VP22 of herpes simplex virus type 1. However, deletion of the UL49 gene from PrV had only minor effects on viral replication, and ultrastructural analyses of infected cells confirmed that virus maturation and egress, including secondary envelopment in the cytoplasm, were not detectably affected by the absence of UL49. Moreover, the UL49 gene product was shown to be dispensable for virion localization of gE and gM, and mutants lacking either gE or gM incorporated the UL49 protein efficiently into virus particles. In contrast, a PrV mutant with deletions of gE-gI and gM failed to incorporate the UL49 protein despite apparently unaltered intracytoplasmic UL49 expression. In summary, we describe specific interactions between herpesvirus envelope and tegument proteins which may play a role in secondary envelopment during herpesvirus virion maturation.
Mammalian Reovirus Nonstructural Protein μNS Forms Large Inclusions and Colocalizes with Reovirus Microtubule-Associated Protein μ2 in Transfected Cells
Authors: Broering Teresa J. , Parker John S. L. , Joyce Patricia L. , Kim Jonghwa , Nibert Max L. 
Published: July 2002

ABSTRACT

Cells infected with mammalian orthoreoviruses contain large cytoplasmic phase-dense inclusions believed to be the sites of viral replication and assembly, but the morphogenesis, structure, and specific functions of these “viral factories” are poorly understood. Using immunofluorescence microscopy, we found that reovirus nonstructural protein μNS expressed in transfected cells forms inclusions that resemble the globular viral factories formed in cells infected with reovirus strain type 3 Dearing from our laboratory (T3D
N
). In the transfected cells, the formation of μNS large globular perinuclear inclusions was dependent on the microtubule network, as demonstrated by the appearance of many smaller μNS globular inclusions dispersed throughout the cytoplasm after treatment with the microtubule-depolymerizing drug nocodazole. Coexpression of μNS and reovirus protein μ2 from a different strain, type 1 Lang (T1L), which forms filamentous viral factories, altered the distributions of both proteins. In cotransfected cells, the two proteins colocalized in thick filamentous structures. After nocodazole treatment, many small dispersed globular inclusions containing μNS and μ2 were seen, demonstrating that the microtubule network is required for the formation of the filamentous structures. When coexpressed, the μ2 protein from T3D
N
also colocalized with μNS, but in globular inclusions rather than filamentous structures. The morphology difference between the globular inclusions containing μNS and μ2 protein from T3D
N
and the filamentous structures containing μNS and μ2 protein from T1L in cotransfected cells mimicked the morphology difference between globular and filamentous factories in reovirus-infected cells, which is determined by the μ2-encoding M1 genome segment. We found that the first 40 amino acids of μNS are required for colocalization with μ2 but not for inclusion formation. Similarly, a fusion of μNS amino acids 1 to 41 to green fluorescent protein was sufficient for colocalization with the μ2 protein from T1L but not for inclusion formation. These observations suggest a functional difference between μNS and μNSC, a smaller form of the protein that is present in infected cells and that is missing amino acids from the amino terminus of μNS. The capacity of μNS to form inclusions and to colocalize with μ2 in transfected cells suggests a key role for μNS in forming viral factories in reovirus-infected cells.
Nef Enhances Human Immunodeficiency Virus Type 1 Infectivity and Replication Independently of Viral Coreceptor Tropism
Authors: Papkalla Armin , Münch Jan , Otto Claas , Kirchhoff Frank 
Published: July 2002

ABSTRACTWe investigated the infectivities and replicative capacities of a large panel of variants of the molecular human immunodeficiency virus type 1 (HIV-1) NL4-3 clone that differ exclusively in the V3 region of the viral envelope glycoprotein and thenefgene. Our results demonstrate that Nef enhances virion infectivity and HIV-1 replication independently of the viral coreceptor tropism.
Glycoprotein I of Varicella-Zoster Virus Is Required for Viral Replication in Skin and T Cells
Authors: Moffat Jennifer , Ito Hideki , Sommer Marvin , Taylor Shannon , Arvin Ann M. 
Published: July 2002

ABSTRACT
Varicella-zoster virus (VZV) glycoprotein I (gI) is dispensable in cell culture; the SCIDhu model of VZV pathogenesis was used to determine whether gI is necessary in vivo. The parental and repaired viruses grew in human skin and thymus/liver implants, but the gI deletion mutant was not infectious. Thus, gI is essential for VZV infectivity in skin and T cells.
Overtime work, insufficient sleep, and risk of non-fatal acute myocardial infarction in Japanese men
Authors: Liu Y , Tanaka H 
Published: July 2002

Objectives:To examine the relation between working hours and hours of sleep and the risk of acute myocardial infarction (AMI), with special reference to the joint effect of these two factors.Method:Case-control study in Japan. Cases were 260 men aged 40–79 admitted to hospitals with AMI during 1996–8. Controls were 445 men free from AMI matched for age and residence who were recruited from the resident registers. Odds ratios of AMI relative to mean weekly working hours and daily hours of sleep in the past year or in the recent past were calculated.Results:Weekly working hours were related to progressively increased odds ratios of AMI in the past year as well as in the past month, with a twofold increased risk for overtime work (weekly working hours ≥61) compared with working hours ≤40. Short time sleep (daily hours of sleep ≤5) and frequent lack of sleep (2 or more days/week with <5 hours of sleep) were also associated with a two to threefold increased risk. Frequent lack of sleep and few days off in the recent past showed greater odds ratios than those in the past year.Conclusions:Overtime work and insufficient sleep may be related to increased risk of AMI.
Comparison of two different approaches for the analysis of data from a prospective cohort study: an application to work related risk factors for low back pain
Authors: Hoogendoorn W E , Bongers P M , de Vet H C W , Twisk J W R , van Mechelen W , Bouter L M 
Published: July 2002

Aims:To compare the results of a traditional approach using standard regression for the analysis of data from a prospective cohort study with the results of generalised estimating equations (GEE) analysis.Methods:The research was part of a three year prospective cohort study on work related risk factors for low back pain. The study population consisted of a cohort of 1192 workers with no low back pain at baseline. Information on work related physical and psychosocial factors and the occurrence of low back pain was obtained by means of questionnaires at baseline and at the three annual follow up measurements. In a traditional standard logistic regression model, physical and psychosocial risk factors at baseline were related to the cumulative incidence of low back pain during the three year follow up period. In a GEE logistic model, repeated measurements of the physical and psychosocial risk factors were related to low back pain reported at one measurement point later.Results:The traditional standard regression model showed a significant effect of flexion and/or rotation of the upper part of the body (OR = 1.8; 95% CI: 1.2 to 3.0), but not of moving heavy loads (OR = 1.4; 95% CI: 0.7 to 3.1). The GEE model showed a significant effect of both flexion and/or rotation of the upper part of the body (OR = 2.2; 95% CI: 1.5 to 3.3) and moving heavy loads (OR = 1.5; 95% CI: 1.0 to 2.4). No significant associations with low back pain were found for the psychosocial work characteristics with either method, but the GEE model showed weaker odds ratios for these variables than the traditional standard regression model.Conclusions:Results show that there are differences between the two analytical approaches in both the magnitude and the precision of the observed odds ratios.
The prevalence of occupational dermatitis in the UK printing industry
Authors: Livesley E J , Rushton L , English J S , Williams H C 
Published: July 2002

Aims:To quantify occupational ill health resulting from dermatitis in the UK printing industry and to explore links with particular processes and activities.Methods:Approximately 2600 members of the Graphical, Paper and Media Union living in Nottinghamshire were sent a self completion questionnaire. A sample of respondents, both those who reported current skin problems and those who did not, were invited for a short dermatological examination.Results:The overall response rate was 62%. A total of 1189 respondents were directly involved in the printing industry and categorised according to work in pre-press (25%), printing (46%), or finishing (42%) processes. A total of 490 respondents (41%) self reported having a skin complaint at some time. Prevalence was highest in males (43%) and those working in printing (49%), in particular those who cleaned rollers and cylinders or who came into contact with substances containing isocyanates on a daily basis. The most commonly affected areas reported were the fingers and webs between the fingers. Twenty six per cent of the 490 reported a current problem on the hand. Reported symptoms included itching (61%), rash (58%), and dry skin (56%). Although certain printing industry substances were thought by respondents to aggravate their condition, constant washing and friction was most often cited. Reported use of protective equipment and cleansing products was generally high, particularly by printers. Clinical examination confirmed the high self reported prevalence and also identified a substantial proportion of mild cases which were not reported. The overall prevalence of occupationally related skin complaints is estimated to be 40%.Conclusions:A much higher prevalence of dermatitis has been identified than from routine surveillance schemes. The use of good quality records from unions with high membership facilitated access to workers across a range of company sites and printing processes. Validation of self reported symptoms through clinical examination was shown to be essential. The importance of non-chemical causes of dermatitis was highlighted. The findings point towards the need for the development of effective and acceptable risk reduction strategies, in particular to reduce water contact and friction.