Project description:Giant viruses infecting amoebae are notable for their substantial particle sizes and expansive genomes. In this study, we collected water samples from 44 distinct locations along a river within Brazil's Pantanal biome. These samples were processed and subsequently inoculated into Vermamoeba vermiformis cultures. Observation of cytopathic effects led to the isolation of a novel virus, designated Naiavirus, distinguished by its unprecedented virion morphology and genomic organization. To elucidate the protein composition of Naiavirus particles, large-scale infections were conducted using 20 T175 flasks, each containing 10 million amoebae. Post-infection, viral particles were purified through two successive sucrose gradient centrifugations to achieve high purity. Proteomic analysis of these purified particles identified 254 associated viral proteins, a count exceeding those reported for all known giant viruses except for pandoraviruses. This dataset encompasses the raw mass spectrometry data, identification files, and associated metadata, offering valuable insights into the structural proteome of this unique giant virus.
Project description:There is a growing need for novel antiviral therapies that are broad-spectrum, effective, and not subject to resistance due to viral mutations. Using high-throughput screening methods, including computational docking studies and an ISG54-luciferase reporter assay, we identified a class of isoflavone compounds that act as specific agonists of innate immune signaling pathways and cause activation of the IRF-3 transcription factor. The objective of the microarray study was to examine the biological pathways associated with global gene expression changes following agonist treatment. Total RNA isolation and mRNA amplification were performed on equal masses of total RNA from MRC5 cells treated with either DMSO (negative control; n=3), or 10μM of the isoflavone agonist KIN 101 (n=3) at 20 hours post treatment. As a positive control for response to an RNA virus, total RNA isolation and mRNA amplification was performed on equal masses of total RNA from MRC5 cells infected with Sendai virus (n=3) at 20 hours post infection.
Project description:Innate antiviral immune responses are driven by virus-induced changes in host gene expression. In this study, RNA-sequencing of mock-infected and Sendai virus-infected cells was performed to characterize the virus-inducible transcriptome and identify novel virus-inducible RNAs in human cells.
Project description:We report the differences in innate immune activation in the comparison of wild type and mutant Mouse Hepatitis Virus Strain A59 infection of bone marrow derived macrophages. We infected BMDMs and harvested RNA at 3, 6, 9, and 12 hpi while comparing changes in host gene expression compared to mock infected cells. Here, using a transcriptomics approach, we compared the scope and kinetics of the host response to the wild type, DUBmut, and EndoUmut viruses in infected macrophages. We found that the EndoUmut virus activates a focused response, predominantly involving type I interferons and a subset of interferon-responsive genes, within 12 hours after infection. In contrast, the wild type and DUBmut viruses stimulate the upregulation of over 2,800 genes, including the activation of unfolded protein response (UPR) pathways and a proinflammatory response associated with viral pathogenesis. This study highlights the role of viral interferon antagonists in modulating the kinetics and magnitude of the host response during virus infection and demonstrates that inactivation of a dominant viral antagonist, the coronavirus endoribonuclease, dramatically alters the host response in macrophages and the disease process.
Project description:Porcine cytomegalovirus (PCMV; genus Cytomegalovirus, subfamily Betaherpesvirinae, family Herpesviridae) is an immunosuppressive virus that mainly inhibits the immune function of T lymphocytes and macrophages, which has caused great distress to the farming industry. In this study, we obtained the miRNA expression profiles of PCMV-infected and control porcine macrophages, PCMV-infected and control porcine tissues via high-throughput sequencing. The comprehensive analysis of miRNA profiles showed that 306 miRNA database annotated and 295 novel pig-encoded miRNAs were detected. Gene Ontology (GO) analysis of the target genes of miRNAs in PCMV infected porcine macrophages showed that the differentially expressed miRNAs are mainly involved in immune and metabolic process. This is the first report of the miRNA transcriptome in PCMV infected porcine macrophages and PCMV infected tissues and the analysis of the miRNA regulatory mechanism during PCMV infection. Further research into the regulatory mechanisms of miRNAs during immunosuppressive viral infections will contribute to the treatment and prevention of immunosuppressive viruses.
Project description:Diagnosis of acute respiratory viral infection is currently based on clinical symptoms and pathogen detection. Use of host peripheral blood gene expression data to classify individuals with viral respiratory infection represents a novel means of infection diagnosis. We used microarrays to capture peripheral blood gene expression at baseline and time of peak symptoms in healthy volunteers infected intranasally with influenza A H3N2, respiratory syncytial virus or rhinovirus. We determined groups of coexpressed genes that accurately classified symptomatic versus asymptomatic individuals. We experimentally inoculated healthy volunteers with intranasal influenza, respiratory syncytial virus or rhinovirus. Symptoms were documented and peripheral blood samples drawn into PAXgene tubes for RNA isolation.
Project description:Nucleocytoviricota viruses (NCVs) belong to a newly established phylum originally grouped as Nucleocytoplasmic large DNA viruses. NCVs are unique because of their large and complicated genomes that contain cellular genes with homologs from all kingdoms of life, raising intensive debates on their evolutional origins. Many NCVs pack their genomes inside massive icosahedral capsids assembled from thousands of proteins. Studying the assembly mechanism of such capsids has been challenging until breakthroughs from structural studies. Subsequently, several models of the capsid assembly were proposed, which provided some interesting insights on this elaborate process. In this review, we discuss three of the most recent assembly models as well as supporting experimental observations. Furthermore, we propose a new model that combines research developments from multiple sources. Investigation of the assembly process of these vast NCV capsids will facilitate future deciphering of the molecular mechanisms driving the formation of similar supramolecular complexes.