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At least 1,189 records · Page 66Linked to original sources
PubMed2003

Tumor necrosis factor alpha inhibition of hepatitis B virus replication involves disruption of capsid Integrity through activation of NF-kappaB.

Chronic infection by hepatitis B virus results from an inability to clear the virus, which is associated with liver disease and liver cancer. Tumor necrosis factor alpha (TNF-alpha) is associated with noncytopathic clearance of hepatitis B virus in animal models. Here we demonstrate that the nuclear factor kappaB (NF-kappaB) signaling pathway is a central mediator of inhibition of hepatitis B virus by TNF-alpha and we describe the molecular mechanism. TNF-alpha is shown to suppress hepatitis B virus DNA replication without cell killing by disrupting the formation or stability of cytoplasmic viral capsids through a pathway requiring the NF-kappaB-activating inhibitor of kappaB kinase complex IKK-alpha/beta and active transcription factor NF-kappaB. Hepatitis B virus replication could also be inhibited and viral capsid formation could be disrupted in the absence of TNF-alpha solely by overexpression of IKK-alpha/beta or strong activation of NF-kappaB. In contrast, inhibition of NF-kappaB signaling stimulated viral replication, demonstrating that HBV replication is both positively and negatively regulated by the level of activity of the NF-kappaB pathway. Studies are presented that exclude the possibility that HBV inhibition by NF-kappaB is carried out by secondary production of gamma interferon or alpha/beta interferon. These results identify a novel mechanism for noncytopathic suppression of hepatitis B virus replication that is mediated by the NF-kappaB signaling pathway and activated by TNF-alpha.

Animals↗
PubMed2001

A method to maintain introduced DNA sequences stably and safely on the bacterial chromosome: application of prophage integration and subsequent designed excision.

By application of prophage integration and subsequent intended excision, a method to maintain an introduced DNA sequence stably onto a bacterial chromosome has been proposed. Recently-constructed integration plasmids using Campbell-type prophage integration system in Lactobacillus casei strain Shirota and its temperate phage phi FSW was modified for this purpose and a chloramphenicol (Cm)-resistance gene was used as a model passenger DNA. On the integration plasmid having an erythromycin (Em)-resistance gene as a selection marker, N- and C-terminally-truncated Cm-resistance genes were inserted into both sides of the attP of phi FSW, within which the site-specific recombination took place with the attB of phi FSW on the recipient chromosome through the phi FSW integrase. Primary integrants of the modified plasmid (integration-excision vector) exhibiting Em-resistant and Cm-sensitive phenotype generated Em-sensitive and Cm-resistant derivatives under the nonselective conditions. Sequence analyses showed that one copy of the complete Cm-resistance gene resided at the attachment site on the host chromosome and the other vector-derived sequences were excised probably by endogenous homologous recombination in the host cells to derive final integrants. The Cm-resistant phenotype of the final integrants was stable for more than 50 generations under non-selective conditions. Frequency of the homologous recombination suggests that negative selection is also adoptable. Thus, this method using the integration-excision vector gives a stable and safe derivatives of the strain and is likely to be applicable to various bacteria, since Campbell-type prophage integration system and homologous recombination are prevalent among bacteria.

Bacteriophages↗
PubMed1998

Characterization of the lysogenic bacteriophage MAV1 from Mycoplasma arthritidis.

The lysogenic bacteriophage MAV1, which is associated with the arthritogenicity of Mycoplasma arthritidis, was characterized. Several strains of M. arthritidis were examined for their ability to support growth of MAV1. A PFU assay was developed, and the sensitivity of phage to various chemical treatments was assayed. The most notable result was the resistance of MAV1 to proteinase K. The MAV1 genome is a double-stranded, linear DNA molecule of about 16 kb. The site of MAV1 DNA integration in the host chromosome was investigated. The ends of MAV1 DNA were cloned from three independent lysogens shown to have MAV1 DNA inserted at different sites in the host. The nucleotide sequences of the ends of the MAV1 genome and of the MAV1 DNA-chromosomal DNA junctions from each of three lysogens were determined. Sequences flanking the integrated prophage and the ends of native MAV1 DNA were determined, allowing the identification of the phage DNA (attP) and bacterial DNA (attB) recombination sites. Analysis of the left MAV1 DNA-chromosomal DNA junction sites showed a single-base heterogeneity located within MAV1 DNA sequences immediately adjacent to the attB sequence. A model for MAV1 integration-excision is proposed.

Bacteriophages↗
PubMed2006

Role of secondary attachment sites in changing the specificity of site-specific recombination.

We previously proposed that lambdoid phages change their insertion specificity by adapting their integrases to sequences found in secondary attachment sites. To test this model, we quantified recombination between partners that carried sequences from secondary attachment sites catalyzed by wild-type and by mutant integrases with altered specificities. The results are consistent with the model, and indicate differential core site usage in excision and integration.

Attachment Sites, Microbiological↗
PubMed1980

Tandem integration of avian retroviruses in double-infected cells.

Chicken embryo fibroblasts were chronically infected by both RAV-1 and SR-E, and established SR-E-transformed quail cells were superinfected with RAV-1. About 75 and 50% of double-infected and superinfected cells, respectively, produced both parental viruses. The DNA purified from these cells contained infectious provirus of both parents and no detectable recombinant provirus. In assays using agar overlay, about 5% of the transformed foci that were induced by the DNA of double-infected, but not superinfected, cells were found to contain the progeny of both parents. This observation suggests that in double infections with avian retroviruses, DNA of both parent viruses may integrate into the host genome either in tandem or in close proximity.

Animals↗
PubMed1994

Lentivirus infection of macrophages.

The ovine and caprine lentiviruses infect monocytes, and the viral DNA is integrated into the cellular DNA. The provirus remains silent until the monocyte matures into a macrophage. Intrinsic to this maturation is the induction of a class of immediate early genes in the monocyte that includes the transcription factors JUN and FOS. These transcription factors are thought to couple short-term signals in the cell to long-term cellular differentiation by regulation of specific cellular genes. Thus, JUN and FOS bind to the AP-1 site in the promoters of cellular genes and activate their transcription, resulting in maturation of the monocyte into a macrophage. In addition, these cellular factors activate the same AP-1 sequence in the visna virus LTR, leading to transcriptional activation, full viral gene expression, and production of progeny virus. The expression of viral antigens in the context of MHC class II on the macrophage leads to the production of cytokines and a lymphoproliferative response that causes the lesions in specific target organs in an infected animal. We still understand only the framework of these events. The specific mechanisms by which viral genes alter macrophage gene expression and the molecular basis of different viral tropism for specific tissue macrophages, i.e. microglia, remain to be determined.

Animals↗
PubMed1994

Integrase mutants of human immunodeficiency virus type 1 with a specific defect in integration.

A previous genetic analysis of the human immunodeficiency virus type 1 integrase protein failed to identify single amino acid substitutions that only block the integration of viral DNA (C.-G. Shin, B. Taddeo, W.A. Haseltine, and C.M. Farnet, J. Virol. 68:1633-1642, 1994). Additional substitutions of amino acids that are highly conserved among retroviral integrases were constructed in human immunodeficiency virus type 1 and analyzed for their effects on viral protein synthesis and processing, virion morphology, and viral DNA synthesis and integration in an attempt to identify mutants with a specific defect in integration. Four single amino acid substitutions resulted in replication defective viruses. Conservative, single amino acid substitutions of the two invariant aspartic acid residues found in all retroviral integrases prevented the integration of viral DNA and had no detectable effect on the other stages in the viral replication cycle, indicating that these mutants exhibited a specific defect in integration. Mutations at two positions, S-81 and P-109, blocked the integration of viral DNA but also resulted in the production of viral particles that exhibited reduced reverse transcriptase activity, suggesting additional defects in viral replication. Substitution of the highly conserved amino acid T66 had no effect on viral replication in a CD4+ human T-cell line. This analysis extends the range of possible phenotypes that may be produced by single amino acid substitutions in conserved residues of the integrase protein.

Animals↗
PubMed1993

Carcinogen-induced amplification of SV40 DNA inserted at 9q12-21.1 associated with chromosome breakage, deletions, and translocations in human uroepithelial cell transformation in vitro.

The fate of integrated SV40 viral genome in SV40-immortalized human uroepithelial cells (SV-HUC) during multistep chemical transformation in vitro was studied. We previously reported that exposure of SV-HUC at passage (P) 15 to the chemical carcinogens 3-methylcholanthrene (MCA), 4-aminobiphenyl (ABP), or the N-hydroxy metabolites of ABP causes tumorigenic transformation and/or neoplastic progression. We report now that these same chemical carcinogens induce amplification of SV40 DNA in SV-HUC. We used fluorescence in situ hybridization (FISH) to show that this amplification occurs at the SV40 integration site, which was mapped near a common fragile site at 9q12-21.1 on the der(9)t(8;9) chromosome that is present in all SV-HUC at the earliest passage studied. Karyotypic analysis, along with FISH, also revealed that all carcinogen-induced tumors (T-SV-HUCs) had breaks at 9q12-21.1, deletions of 9q12-21.1-->pter, and new derivative chromosomes containing SV40 in the segment 9q12-21.1-->9q34::8q22-->8qter. Southern blot analysis, along with FISH, confirmed SV40 genome rearrangements in T-SV-HUCs. In contrast, no 9q12-21.1 breaks were observed in control SV-HUC. Thus, these results associate 9q12-21.1-->pter alterations with HUC tumorigenic transformation. In addition, these results indicate for the first time that (carcinogen-induced) amplification of chromosome-integrated viral genes may create sites that are prone to breakage, deletions, and translocations. These results suggest a new mechanism by which chemical carcinogens in synergy with a DNA tumor virus could initiate a cascade of events that contribute to the genomic instability associated with tumorigenesis.

Carcinogens↗
PubMed2003

Cell-free HIV type 1 infection is restricted in the human trophoblast choriocarcinoma BeWo cell line, even with expression of CD4, CXCR4 and CCR5.

The restriction of cell-free HIV-1 infection has been demonstrated in placental trophoblast choriocarcinoma BeWo cells. We tried to determine the level of the viral replication cycle at which this restriction occurs. BeWo cells produce infectious viruses after transfection with HIV-1 plasmids, independently of viral tropism. CCR5 and CXCR4, but not the CD4 molecule, were detected at the cell surface. We therefore derived CD4-expressing clones from transfected BeWo cells. Cell-free virus infection of these clones resulted in neither virus production nor viral sequence integration, indicating that the restriction occurs before integration of the virus. If we used luciferase reporter viruses pseudotyped with HIV-1 Env R5 and X4 for infection, no luciferase activity was detected, even in the BeWo-CD4+ clone, in contrast to what was observed in VSV-G pseudotyped virus infection. Our results show that infection of trophoblast-derived cells with cell-free virus is at least restricted at the level of entry. Thus, BeWo is an interesting human placental cell line that is resistant to HIV-1, even if CD4, CXCR4, and CCR5 are expressed.

CD4 Antigens↗
PubMed1981

Mechanism of enteroviral inactivation by ozone.

The mechanism of enteroviral inactivation by ozone was investigated with poliovirus 1 (Mahoney) as the model virus. Ozone was observed to alter two of the four polypeptide chains present in the viral protein coat of poliovirus 1. However, the alteration of the protein coat did not significantly impair virus adsorption or alter the integrity of the virus particle. Damage to the viral RNA after exposure to ozone was demonstrated by velocity sedimentation analysis. It was concluded that the damage to the viral nucleic acid is the major cause of poliovirus 1 inactivation by ozone.

Ozone↗
PubMed1971

Proteins of a polyhedral cytoplasmic deoxyvirus. 3. Structure of frog virus 3 and location ov virus-associated adenosine triphosphate phosphohydrolase.

The adenosine triphosphatase associated with frog virus 3 shows high specificity for ATP or deoxyadenosine triphosphate and appears to be distinct from the corresponding activity in host cells, poxvirus, or reovirus. The enzyme activity is probably integrated into virus particles since it is firmly associated with subviral particles produced when approximately 50 to 60% of the outer viral protein is removed by detergent treatment. The occurrence of adenosine triphosphatase activity within three unrelated viruses suggests that adenosine tryphosphatase might be a necessary function for most viruses that replicate in the cell cytoplasm.

Adenosine Triphosphatases↗
PubMed1990

Nucleotide sequence analysis of the 3' half of the genome of bovine leukaemia virus grown in FLK cells.

The DNA sequence of the env and px (tat) regions of bovine leukaemia virus cloned from integrated proviral DNA of the virus producing FLK cell line was determined and compared with published sequences cloned from bovine leukaemia virus-induced tumours of cattle. The homology of 97% between a Belgian tumour clone and the FLK clone was significantly lower than that between a Japanese tumour clone and the FLK clone, where less than 1% nucleotide exchanges were observed. The sequences of cDNAs synthesized from purified virus RNA material which had been grown in different FLK sublines were found completely identical with one another as well as with the equivalent FLK proviral DNA sequences.

Base Sequence↗
PubMed2006

Integrated reverse transcription polymerase chain reaction systems for virus detection.

The current study reports on an integrated microreverse transcription polymerase chain reaction (RT-PCR) system for molecular diagnosis of microorganisms automatically. By using antibodies-conjugated superparamagnetic beads, the developed system can detect viruses with higher sensitivity and specificity when compared with traditional biological diagnosis methods using a ribonucleic acid (RNA) extraction kit. The target viruses were first captured by the conjugated antibodies on the magnetic beads, and were enriched using a magnetic field generated by micro-electromagnets or permanent magnets. With this approach, the virus can be purified and concentrated first, then the virus RNA was extracted and transcripted to complementary deoxyribonucleic acid (cDNA), followed by a nucleic acid amplification process using a micro-RT-PCR module. The integrated microfluidic chip can perform the whole process automatically with the aid of integrated micropumps and microvalves. This study successfully performs the specific detection of two different types of viruses, Dengue virus serotype 2 and enterovirus (EV) 71 using this developed integrated system. Comparable to a large-scale apparatus, the integrated microsystem can perform mixing, incubation, purification, transportation, and nucleic acid amplification of virus, possibly making it a crucial platform for future diagnosis applications.

Magnetics↗
PubMed2026

Dual-dimensional profiling of host genomic variations and HPV integration in PD-L1-stratified cervical cancer via Oxford Nanopore Technology.

BACKGROUND: The integration of human papillomavirus (HPV) DNA into the host genome is a key step in the development of HPV-associated cervical cancer (CC). However, the genomic characteristics of host genomic variations and HPV integration within the context of programmed death-ligand 1 (PD-L1) expression stratification have not been systematically investigated. METHODS: Whole-genome sequencing was performed using Oxford Nanopore Technology (ONT) on six samples (three from the high PD-L1 expression group and three from the low PD-L1 expression group). The characteristics of host genomic variations under different PD-L1 expression stratifications were explored, including structural variations (SV), copy number variations (CNV), single nucleotide polymorphisms (SNP), and insertion-deletions (Indel). Subsequently, the distribution features of HPV integration sites were analyzed, different integration types were identified, and pathway analysis was conducted. RESULTS: Whole-genome SV analysis revealed that the total number of SVs and the composition of mutation types were similar between the high and low PD-L1 expression groups, with insertions (INS) and deletions (DEL) predominating in both. These variations were primarily enriched in intergenic regions and introns. In the low PD-L1 expression group, integration events were observed at multiple chromosomal loci, with the most frequent integration occurring in the KLF5 gene region on chromosome 13. No frequently integrated loci were identified in the high PD-L1 expression group. Additionally, four distinct HPV integration breakpoint patterns were preliminarily identified and analyzed. CONCLUSION: PD-L1 expression stratification did not significantly alter the overall genomic instability of the host. However, differences were observed in the distribution patterns of HPV integration sites. These findings provide new insights into the genomic heterogeneity of CC under different PD-L1 expression backgrounds and may lay the groundwork for future research exploring stratified immunotherapy based on HPV integration features.

Humans↗
PubMed1991

The sequence of human immunodeficiency virus type 2 circle junction suggests that integration protein cleaves the ends of linear DNA asymmetrically.

The sequence of the human immunodeficiency virus type 2 circle junction was determined. The most common sequence found between the conserved CA and TG dinucleotides at the ends of the integrated provirus was five bases long (GGTAC). This suggests that the integration of human immunodeficiency virus type 2 DNA is accompanied by the asymmetric loss of two and three bases, respectively, from the U3 and U5 ends of the linear double-stranded DNA prior to integration.

Base Sequence↗