pinecone/core-2020-05-10-deduplication huggingface dataset:
Synergistic Interactions of Antibodies in Rate of Virus Neutralization

AbstractAntibodies and antibody combinations are often evaluated only by their potency in inactivating a known quantity of virus in dose–effect assays. However, a crucial additional parameter is the rate at which neutralization takes place, or kinetics. Synergism of certain antibody combinations in dose–effect assays has been previously demonstrated. In the present report, using a battery of murine monoclonal antibodies to herpes simplex virus (HSV), we investigated whether antiviral antibodies can also synergize in neutralization kinetics. To determine whether synergism in dose–effect assays can predict synergism in neutralization rate, the ability of neutralizing antibodies to synergize in neutralization rate (kinetics) was compared to their ability to synergize in dose–effect assays (potency) in cell-free assays. Although certain antibody combinations synergized in both neutralization rate and potency, combinations that did not clearly synergize in potency could still significantly synergize in neutralization rate. Weak neutralizing antibodies could also greatly increase the neutralization rate of more potent antibodies. These results suggest that evaluating antibody combinations in dose–effect assays but not in neutralization kinetics provides a partial picture of neutralizing antibody dynamic interactions and may prevent the identification of certain favorable antibody combinations. These findings also support the importance of establishing defined antibody cocktails for prophylactic and therapeutic purposes. A simple strategy to evaluate antibody interactions in neutralization kinetics is proposed in which a quantitative prediction of additivity is made on the basis of the neutralization rate constants of the individual antibodies in the combination
Interactions of HIV-1 Nef with the μ Subunits of Adaptor Protein Complexes 1, 2, and 3: Role of the Dileucine-Based Sorting Motif

AbstractHIV-1 Nef interacts with cellular adaptor protein (AP) complexes and their medium (μ) subunits. However, the role of the dileucine-based sorting motif within Nef in these interactions has been incompletely characterized. Here, yeast two-hybrid assays indicated that HIV-1 Nef interacted not only with the μ subunits of AP-1 and AP-2, but also with that of AP-3. The interactions with μ1 and μ3 were markedly stronger than the interaction with μ2. Leucine residues of the sorting motif were required for the interactions with μ3 and μ2 and contributed to the interaction with μ1. Confocal immunofluorescence microscopy indicated that Nef, AP-1, and AP-3 (but not AP-2) were concentrated in a juxtanuclear region near the cell center, potentially facilitating interaction between Nef and the μ1 and μ3 subunits. However, leucine residues of the sorting motif were not required for this subcellular localization of Nef. These data suggest that the dileucine motif, required for optimal viral replication, functions through interactions with a variety of AP complexes, including AP-3, potentially by recruiting adaptor complexes to subcellular locations specified by additional determinants in the Nef protein
Electron Microscopy of the Human Respiratory Syncytial Virus Fusion Protein and Complexes That It Forms with Monoclonal Antibodies

AbstractFull-length fusion (F) glycoprotein of human respiratory syncytial virus (HRSV) and a truncated anchorless mutant lacking the C-terminal 50 amino acids were expressed from vaccinia recombinants and purified by immunoaffinity chromatography and sucrose gradient centrifugation. Electron microscopy of full-length F protein in the absence of detergents revealed micelles, (i.e., rosettes) containing two distinct types of protein rods, one cone-shaped and the other lollipop-shaped. Analysis of membrane anchorless F molecules indicated that they were similar to the cone-shaped rods and that rosettes, which they formed on storage, were made up of lollipop-shaped rods. The two forms of F protein may represent different structures that the molecule may adopt before and after activation for its role in membrane fusion. Studies of complexes of these structures with monoclonal antibodies of known specificity provide information on the three-dimensional organization of antigenic sites on the F protein and confirm the oligomeric structure, possibly trimeric, of both full-length F and membrane anchorless F
Temperature Dependence of Fusion by Sendai Virus

AbstractStudies of the temperature dependence of liposome fusion by Sendai virus indicate that fusion occurs maximally at 55°C. The fusion capacity of the virus is also inactivated maximally by preincubation at this temperature and, under the same conditions, the F glycoprotein becomes resistant to proteolysis. By analogy with the activation at elevated temperatures of fusion by influenza virus our results suggest that temperature is also a variable in the activation of fusion by paramyxoviruses and possibly in the activation of other members of the group of viruses that includes myxo-, paramyxo-, retro-, and filoviruses, which all contain cleaved, trimeric fusion glycoproteins
Detection and Characterization of Functional T-Cell Epitopes on the Structural Proteins VP2, VP3, and VP4 of Foot and Mouth Disease Virus O1 Campos

AbstractFoot and mouth disease virus (FMDV) is the cause of a widespread infectious disease affecting cloven-hoofed animals. It is controlled by vaccination with immune-inactivated virus grown in tissue culture. However, peptide vaccines represent a safer alternative to the current virus-inactivated immunogens. Their design requires the identification and evaluation of the sequences recognized by T- and B-lymphocytes. Four structural proteins, VP1, VP2, VP3, and VP4, comprise the viral capsid of the FMDV, but only VP1 has been extensively studied regarding the existence of relevant T-cell epitopes. Here, we utilize a murine model to present a functional T-cell epitope mapping on the complete sequences of VP2, VP3, and VP4 of FMDV O1 Campos. We used two in vitro assays to describe 13 amino acid sequences, each one of them including at least one T-cell epitope. The in vivo T-cell helper function of these sequences was studied in an adoptive cell-transfer assay in mice. Immunization experiments with a fusion peptide containing one of the sequences characterized were also done comparing the helper activity of this sequence with other T-cell epitopes included in the major immunogenic region of VP1
Retinoic Acid Resistance at Late Stages of Human Papillomavirus Type 16-Mediated Transformation of Human Keratinocytes Arises Despite Intact Retinoid Signaling and Is Due to a Loss of Sensitivity to Transforming Growth Factor-β

AbstractIn our in vitro model of human cell carcinogenesis, normal human foreskin keratinocytes (HKc) transfected with human papillomavirus type 16 DNA (HKc/HPV16) progress toward malignancy through several phenotypically defined and reproducible “steps” that include immortalization, growth factor independence (HKc/GFI), differentiation resistance (HKc/DR), and ultimately malignant conversion. While HKc/HPV16 are very sensitive to growth inhibition by all-trans-retinoic acid (RA) at early passages, they lose their sensitivity to RA during progression in culture. However, gel mobility shift assays using the retinoid response elements DR1 and DR5 showed no changes in binding activity of nuclear extracts obtained from HKc/HPV16 at different stages of in vitro progression. Similarly, Western blot analyses for retinoic acid receptor γ-1 and the retinoid X receptors failed to reveal any decreases in the levels of these retinoid receptors throughout progression. In addition, luciferase activity driven by the SV40 promoter with a DR5 enhancer element was activated following RA treatment of HKc/DR that were resistant to growth inhibition by RA. Since RA induces transforming growth factor-β2 (TGF-β2) in normal HKc and HKc/HPV16, we investigated whether this response changed during progression. Again, RA induced TGF-β2 mRNA in early and late passage HKc/HPV16, HKc/GFI, and HKc/DR approximately to the same extent, confirming that the RA signaling pathways remained intact during in vitro progression despite the fact that the cells become resistant to growth inhibition by RA. We then investigated the sensitivity of HKc/HPV16 to growth inhibition by TGF-β. While early passage HKc/HPV16 were as sensitive as normal HKc to growth inhibition by TGF-β1 and TGF-β2, the cells became increasingly resistant to both TGF-β isotypes during in vitro progression. In addition, while both RA and TGF-β produced a decrease in the levels of mRNA for the HPV16 oncogenes E6 and E7 in early passage HKc/HPV16, this effect was also lost at later stages of progression. Finally, blocking anti-TGF-β antibodies partially prevented RA inhibition of growth and E6/E7 expression in early passage HKc/HPV16. Taken together, these data strongly suggest that inhibition of growth and HPV16 early gene expression in HKc/HPV16 by RA is mediated by TGF-β and that a loss of RA sensitivity is linked to TGF-β resistance rather than alterations in RA signaling
Loss of Transforming Growth Factor-β (TGF-β) Receptor Type I Mediates TGF-β Resistance in Human Papillomavirus Type 16-Transformed Human Keratinocytes at Late Stages of in Vitro Progression

AbstractHuman keratinocytes (HKc) immortalized by human papillomavirus type 16 DNA (HKc/HPV16) progress toward malignancy through growth factor-independent (HKc/GFI) and differentiation-resistant stages (HKc/DR). This progression is associated with a loss of sensitivity to growth inhibition by both all-trans-retinoic acid (RA) and transforming growth factor-β (TGF-β). In the accompanying article (Borger et al., 2000, Virology 270, 397–407), we demonstrate that RA resistance in HKc/HPV16 arises despite functional nuclear retinoid receptors and that TGF-β mediates growth inhibition by RA. To investigate the basis for the loss of TGF-β sensitivity during in vitro progression of HKc/HPV16, we explored the expression of TGF-β receptors type I and type II in independently derived HKc/HPV16 lines and their corresponding HKc/GFI and HKc/DR derivatives. While TGF-β receptor type II mRNA levels were unchanged during progression, mRNA levels for TGF-β receptor type I decreased dramatically as the cells became TGF-β resistant. At the HKc/DR stage, loss of TGF-β receptor type I mRNA, compared to low-passage cells, ranged from 55 to 87% in four HKc/HPV16 lines examined. Immunohistochemistry, using anti-TGF-β receptor type I antibodies, confirmed a loss of TGF-β receptor type I expression in HKc/DR. Reintroduction of the TGF-β-receptor type I into TGF-β-resistant HKc/DR completely restored growth inhibition by TGF-β. Southern blot analysis of DNA extracted from normal HKc, HKc/HPV16, and HKc/DR ruled out any gross changes in the TGF-β receptor type I gene. The activity of the TGF-β receptor type I promoter, cloned upstream of a luciferase reporter gene, was decreased in HKc/DR, to an extent comparable to the decrease in mRNA levels for the TGF-β receptor type I. Thus, TGF-β resistance at late stages of HPV16-mediated transformation of HKc is the result of a loss of expression of TGF-β receptor type I
Isolation, Cloning, and Complete Nucleotide Sequence of a Phenotypically Distinct Brazilian Isolate of Human T-Lymphotropic Virus Type II (HTLV-II)

AbstractAnalysis of human T-lymphotropic virus type II (HTLV-II) isolates from North America and Europe have demonstrated the existence of two molecular subtypes of the virus, HTLV-IIa and HTLV-IIb. Recently, studies on HTLV-II infections in Brazil have revealed isolates that are related phylogenetically to the HTLV-IIa subtype but have a HTLV-IIb phenotype with respect to the transactivating protein, tax. To more clearly define this relationship, HTLV-II was isolated from peripheral blood of an IVDA from Sao Paulo, Brazil (SP-WV), and the complete provirus was cloned and sequenced. Comparison of HTLV-IISP-WV nucleotide sequences to other available complete HTLV-II proviral sequences revealed that HTLV-IISP-WV is most closely related to HTLV-IIMo, the prototypic HTLV-IIa subtype sequence. Phylogenetic analysis of LTR, env, and tax regions unequivocally demonstrated that HTLV-IISP-WV and all other Brazilian sequences examined are members of the IIa subtype. The predicted amino acid sequences of the major coding regions of HTLV-IISP-WV are also most closely related to HTLV-IIMo, with the important exception of tax. The tax protein encoded by HTLV-IISP-WV is 96–99% identical to the tax of IIb isolates and is similar in that it has an additional 25 amino acids at the carboxy-terminus compared to the HTLV-IIMo tax with which it shares 91% identity. Analysis of tax stop codon usage of a number of HTLV-IIa isolates from North American, Europe, and Brazil demonstrated that isolates from the last region appear to be unique in their extended tax phenotype. It could be demonstrated that the extended tax proteins in the HTLV-IIb and Brazilian isolates had equivalent ability to transactivate the viral LTR, and studies with deletion mutants indicated that the extended C-terminus is not essential for transactivation. In contrast, the HTLV-IIa tax was found to have a greatly diminished ability to transactivate the viral LTR, which appeared to be a consequence of reduced expression of the protein. The studies show that although the Brazilian strains do not represent an entirely new subtype based on nucleotide sequence analysis they are a phenotypically unique molecular variant within the HTLV-IIa subtype
Protection against Measles Virus-Induced Encephalitis by Anti-mimotope Antibodies: The Role of Antibody Affinity

AbstractSynthetic peptides mimicking a conformational B-cell epitope (M2) of the measles virus fusion protein (MVF) were used for the immunization of BALB/c mice and the anti-peptide and anti-virus antibody titers induced were compared. Of the panel of tested peptides, a chimeric peptide consisting of two copies of a T-helper epitope (residues 288–302 of MVF) and one copy of the mimotope M2 (TTM2) and a multiple antigen peptide with eight copies of M2 (MAP-M2) induced the highest titers of anti-M2 and anti-MV antibodies. Furthermore, peptides TTM2 and MAP-M2 induced antibodies with highest affinity for the mimotope and highest avidity for measles virus. Immunization with the MAP-M2 construct induced high titers of high-affinity anti-M2 antibody despite the absence of a T-helper epitope, and lymphocyte proliferation data suggest that the addition of M2 to the MAP resulted in the generation of a structure capable of stimulating T-cell help. Sera with anti-M2 reactivity were pooled according to affinity values for binding to M2, and high- and low-affinity pools were tested for their ability to prevent MV-induced encephalitis in a mouse model. The high-affinity serum pool conferred protection in 100% of mice, whereas the lower affinity pool conferred protection to only 50% of animals. These results indicate the potential of mimotopes for use as synthetic peptide immunogens and highlight the importance of designing vaccines to induce antibodies of high affinity
Oligomerization, Secretion, and Biological Function of an Anchor-Free Parainfluenza Virus Type 2 (PI2) Fusion Protein

AbstractA number of studies indicate that the transmembrane domain, the cytoplasmic domain, or both regions of viral surface glycoproteins are involved in quaternary structure formation. In this report, the transmembrane domain and cytoplasmic tail coding sequence of the fusion (F) glycoprotein gene from parainfluenza type 2 virus was truncated by PCR and the resulting gene (PI2F′) was expressed in HeLa-T4 cells by using the vaccinia virus-T7 transient expression system. Pulse–chase experiments indicated that the anchor-free PI2F′ was expressed and processed into F1 and F2 subunits. Both the processed and the unprocessed anchor-free PI2F′ proteins were found to be efficiently secreted into the culture medium. Examination of the oligomeric form of the anchor-free PI2F′ by chemical cross-linking demonstrated that it assembles posttranslationally into dimers and trimers with a pattern similar to that of the wild-type PI2F protein. In an effort to better understand the biological properties of the truncated form of PI2F′, we anchored PI2F′ by a glycosyl-phosphatidylinositol (GPI) linkage. The GPI-anchored PI2F′ protein, when coexpressed with PI2HN, did not induce cell fusion seen as syncytium formation, but was found to initiate lipid mixing (hemifusion) as observed by transfer of R-18 rhodamine from red blood cells to the GPI-PI2F′/PI2HN cotransfected cells. The results therefore indicate that the extracellular domain of the PI2 fusion protein contains not only the structural information sufficient to direct assembly into higher oligomers, but also is competent to initiate membrane fusion, suggesting that the anchor-free PI2F′ may be useful for further structural studies
Cleavage of Hepatitis C Virus Nonstructural Protein 5A by a Caspase-like Protease(s) in Mammalian Cells

AbstractNonstructural 5A protein (NS5A) of hepatitis C virus (HCV) is localized in the cytoplasm although it has a functional nuclear localization signal. To clarify the determinant of NS5A cytoplasmic localization, various N- or C-terminal deleted NS5A mutants were generated and their subcellular localization was analyzed in cell lines after transient expression. N-terminal deleted forms of NS5A were localized in the nucleus, and the sequence of the N-terminal 27 amino acids of NS5A had sufficient function to cause retention of a normally nuclear protein in the cytoplasm. These observations indicated that cytoplasmic localization of NS5A is determined primarily by the N-terminal region of the molecule. In addition, we found proteolytic processing of NS5A in transiently expressing cells. In these cells, cleavage occurred at a few sites located in the N- and C-terminal regions of NS5A. This cleavage in cells was enhanced by apoptotic stimuli and was inhibited by the caspase inhibitor Z-VAD-FMK, suggesting that a caspase-like protease(s) contributes to the cleavages of NS5A. Based on the results of mutational analysis of NS5A, we predicted one cleaved form, which had lost both the N- and the C-terminal portions of NS5A, to be composed of amino acid residues 155 to 389. Peptide containing the same amino acid sequence as this cleaved product was localized in the nucleus. Furthermore, we found that a fusion protein consisting of Gal4 DNA-binding domain fused with this cleaved form showed transcriptional activity only when the α-catalytic subunit of protein kinase A (PKA) was coproduced, suggesting that the transcriptional activity of this product was regulated by PKA. These results suggested that the cleavage product of NS5A by a caspase-like protease(s) plays a role in transcriptional regulation of the host cell gene(s) in HCV-infected cells
Sequencing of Peach Latent Mosaic Viroid Variants from Nine North American Peach Cultivars Shows that This RNA Folds into a Complex Secondary Structure

AbstractWe sequenced 34 new peach latent mosaic viroid (PLMVd) variants isolated from nine different peach cultivars. This study provides the widest view of PLMVd diversity reported to date and includes the original characterization of North American variants, which cannot be differentiated from European sequences. PLMVd appears as a species in which each isolate is a complex mixture of RNAs. Analysis of base-pair covariations supports the hypothesis that PLMVd folds into a complex branched structure with the potential of including three new pseudoknots. The resulting “globular-like” structure is in contrast to the rod-like one adopted by most other viroids
Re-emergence of Vesicular Stomatitis in the Western United States Is Associated with Distinct Viral Genetic Lineages

AbstractPhylogenetic analysis of partial phosphoprotein and glycoprotein gene sequences showed that a single genetic lineage of vesicular stomatitis virus (VSV) serotype New Jersey (NJ) caused the 1995 and 1997 outbreaks of vesicular stomatitis (VS) in the western United States. While distinct from VSV-NJ strains causing previous outbreaks in the western United States and those circulating in feral swine in the southeastern United States, this lineage was closely related to viral lineages circulating in the Mexican states of Guerrero, Veracruz, and Oaxaca in 1996, 1989, and 1984 respectively. In 1997 and 1998, VSV serotype Indiana 1 (IN1) re-emerged in the western United States after 30 years. Viruses causing these outbreaks grouped within a single genetic lineage distinct from VSV-IN1 isolates causing outbreaks in the western United States in 1929 and 1956 but closely related to a strain circulating in the state of Colima in central Mexico in 1997. Our data showed that sporadic VS outbreaks in the western United States are caused by genetically distinct viral lineages closer to those circulating in enzootic areas of central and southern Mexico than to those causing previous outbreaks in the United States. The genetic evidence and temporal distribution of outbreaks are not consistent with a pattern of long-term maintenance of VSV in the western United States
Role of Type I IFNs in the in Vitro Attenuation of Live, Temperature-Sensitive Vaccine Strains of Human Respiratory Syncytial Virus

AbstractThe contributions of type I interferons (IFNs) to the in vitro attenuation of three temperature-sensitive (Ts) subgroup A and one subgroup B deletion mutant RSV strains were evaluated. The ability of these vaccine viruses to induce IFNs at their permissive and restrictive temperatures and their sensitivity to the antiviral effects of exogenous I IFNs were tested in human lung epithelial A549 cells. Our results show that the highly attenuated and immunogenic subgroup A vaccine strain Ts1C produced higher levels of IFN-β than its parent RSS-2 or two related strains, Ts1A and Ts1B, at their permissive temperature. Growth of RSV-infected A549 cultures at restrictive temperatures or prior UV inactivation of the virus abolished the observed induction of IFN-β, suggesting a strict requirement of viral replication for cellular IFN induction. The enhanced induction of IFN-β by the highly immunogenic Ts1C at permissive temperature may be an advantageous characteristic of a live intranasal vaccine candidate. The subgroup B strain RSV B1 and its mutant cp-52 (with SH and G gene deletions) both induced similar but low levels of IFN-β. Hence the observed overattenuation of cp-52 in human infants is probably not due to enhanced IFN induction during its replication in the host. The ability of cp-52, which does not express the SH and G proteins, to induce IFN-β levels similar to those of its parent strain suggests that these viral proteins may not have a role in the induction of IFN-β in the host. In addition, both subgroup A and B mutants and their respective parent strains were similarly resistant to the antiviral effects of exogenous IFN-α or -β. Therefore, increased sensitivity of the mutants to IFNs does not seem to contribute to their attenuation