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We propose that mvRNAs act as the main agonists of RIG-I during influenza virus infection. Aberrant mini viral RNAs, which are produced by erroneous RNA polymerase activity during the replication of the viral RNA genome, act as the main agonists of RIG-I during influenza virus infection.
s/Significance These findings suggested that influenza A virus may acquire an RNA polymerase adapted to different body temperatures of the host by reassortment of the RNA polymerase genes.
Influenza virus is thus unique among nononcogenic RNA viruses in synthesizing its mRNA in the nucleus.
Taken together, these data suggest that HA and the viral RNA polymerase complex are critical determinants of Spanish influenza pathogenesis, but only HA, and not the viral RNA polymerase complex and NP, is responsible for extreme host responses observed in mice infected with the 1918 influenza virus.
Influenza virus is a negative strand RNA virus and is one of the rare RNA viruses to replicate in the nucleus.
We demonstrate that, in the presence of preexisting viral RNA polymerase and nucleoprotein (NP), influenza A virus synthesizes both mRNA (transcription) and cRNA (replication) early in infection.
Along with previous reports, our data propose that influenza A virus uses a redundant and plastic network of RNA-RNA and potentially RNA-nucleoprotein interactions to coordinately incorporate its segmented genome into virions.
In this study we hypothesise that a cloned DI influenza A virus RNA may prevent infection of human respiratory epithelial cells with infection by influenza A.
Here, we show that short interfering RNAs (siRNAs) specific for conserved regions of influenza virus genes can prevent and treat influenza virus infection in mice.
Open accessJournal ArticleDOI
Frank T. Vreede, Ervin Fodor 
01 Sep 2010-Virulence
45 Citations
These findings extend our understanding of how influenza virus counteracts antiviral host responses and underpin studies into the mechanisms by which the RNA polymerase determines virulence.

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What is TE exonization ?
5 answers
TE exonization refers to the process where transposable elements (TEs) inserted into intronic regions of genes provide splice sites, leading to the creation of alternatively spliced cassette exons. This event enriches transcriptomes and proteomes by generating diverse RNA transcripts and protein isoforms. TE exonization can contribute significantly to the complexity of transcriptomes, with up to 71% of exonized transcripts being potential targets for the nonsense-mediated decay pathway. The incorporation of TE-derived sequences into coding regions of genes can expand the proteome diversity by offering new protein isoforms. Additionally, TE exonization can be regulated by epigenetic mechanisms, such as histone modifications, to control the expression of TE-derived coding sequences in different cell types.
What ins rna sequencing?
4 answers
RNA sequencing, also known as RNA-Seq, is a powerful technology that enables the detection of qualitative and quantitative changes in RNA expression across the genome in clinical samples. This revolutionary method allows for the identification and quantification of ribonucleic acid (RNA) in a given sample, aiding in the detection of changes in gene expression. RNA sequencing has transformed next-generation sequencing technology by providing a precise measure of gene expression without the need for gene probes, allowing for a wider range of gene expression analysis and storage of transcriptome data in accessible databases. By automating the construction of highly complex RNA libraries from various sample types, including fresh frozen and FFPE samples, RNA sequencing has overcome limitations related to sample integrity, heterogeneity, and analytical factors, ultimately improving molecular diagnostic rates achieved by other sequencing methods.
What is the advantage in adding salt in the production of virus or viral vectors?
5 answers
Adding salt, specifically sodium chloride (NaCl) and potassium chloride (KCl), during the production of adeno-associated virus (AAV) vectors and retroviral particles has shown significant advantages. The presence of NaCl and KCl has been found to dramatically increase the yield and quality of AAV vectors, resulting in up to a 10-fold increase in production. Similarly, adjusting salt concentration in the medium has led to high-titer production of multiple AAV serotypes and transgenes in suspension cells. Moreover, the use of salts in retroviral particle production has been associated with enhanced stability and efficient generation of particles. These findings highlight the crucial role of salt in optimizing the production process of viruses and viral vectors, ultimately improving their yield and quality.
What alterations in transcription and translation accompany hypoxia?
10 answers
Hypoxia triggers a complex array of cellular adaptations at both the transcriptional and translational levels to maintain homeostasis in low-oxygen environments. At the transcriptional level, the hypoxia signaling pathway, primarily mediated by hypoxia-inducible factors (HIFs), activates to induce the expression of hypoxia-regulated genes, which are crucial for cellular adaptation to decreased oxygen availability. This process involves not only the stabilization and activation of HIFs but also a range of post-translational modifications that affect HIF localization, stability, and activity. Furthermore, hypoxia leads to significant changes in RNA synthesis rates, which are the major determinant of changes in RNA levels, alongside contributions from RNA degradation processes. This results in a reduction of overall mRNA stability and total RNA content per cell, affecting fundamental global responses such as the inhibition of translation. At the translational level, cells adapt by downregulating energy-consuming processes like translation. This is evidenced by the alternative splicing and retention of introns in key regulatory genes under hypoxia, which can lead to the production of truncated protein isoforms that inhibit global translation. Additionally, chronic hypoxia exposure alters the translational machinery, with specific translational repressors and activators modulating the synthesis of proteins like HIF1α, suggesting a major regulatory role in the pulmonary hypoxic response. The rate of canonical protein synthesis pathways is significantly slowed due to limited ATP availability, necessitating alternative mechanisms for protein synthesis. Moreover, fetal hypoxia affects the transcriptomes of neonatal brains in a cell-specific and sex-dependent manner, indicating that the impact of hypoxia on transcription and translation extends to developmental stages. Oxygen and glucose deprivation during conditions like ischemia lead to a reprogramming of initiation and elongation rates in translation, affecting a wide array of genes. Finally, the preferential translation of HIF1α mRNA in hypoxic conditions is crucial for the full activation of the HIF1-dependent hypoxic response, highlighting the importance of translational control mechanisms in adapting to hypoxia. Together, these studies illustrate that hypoxia induces profound alterations in both transcription and translation, involving a wide range of mechanisms from HIF-mediated gene expression to the modulation of translation through alternative splicing and the preferential translation of specific mRNAs.
What is known about the role of hypoxia in mRNA regulation in breast cancer?
8 answers
Hypoxia, a common feature in the tumor microenvironment of breast cancer, significantly influences mRNA regulation, affecting cancer progression and patient survival. The transcription factor CCAAT/enhancer binding protein-α (C/EBPα), known for its role in cell differentiation and proliferation, is down-regulated under hypoxic conditions in T-47D breast cancer cells. This down-regulation involves both transcriptional repression and decreased mRNA stability, mediated by hypoxia-inducible factor (HIF)-1α. Furthermore, hypoxia impairs the type I interferon (IFN) pathway, crucial for immune response against tumors, by suppressing mRNA and protein expressions of key components in this pathway, including sensors, adaptors, and transcription factors, in a manner that is independent of HIF1/2α. The expression of hypoxia-inducible factors (HIFs), particularly HIF-1, is pivotal in adapting solid tumors to hypoxic conditions, influencing the expression of genes involved in cancer progression. RNA sequencing studies reveal that hypoxia leads to differential expression of genes related to glycolysis, proliferation, growth, and migration in T47D breast cancer cells. Hypoxia also appears to modulate the expression of APOBEC3A and APOBEC3B, enzymes involved in mutation and tumor progression, suggesting a complex interaction between hypoxia and genetic variability within tumors. Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) are also regulated by hypoxia, playing roles in tumorigenesis and cancer progression. NDRG1-OT1, a hypoxia-induced lncRNA, is upregulated under hypoxic conditions and promotes tumor growth and migration, acting as a miRNA sponge. Similarly, hypoxia-related circRNAs are involved in the progression, angiogenesis, metabolic reprogramming, and stemness maintenance of breast cancer. Single-cell and bulk sequencing data have been utilized to construct hypoxia-related prognostic signatures, highlighting the importance of hypoxia in breast cancer prognosis. The role of hypoxia-associated lncRNAs in breast cancer underscores their potential as diagnostic and prognostic tools, further emphasizing the critical impact of hypoxia on mRNA regulation in breast cancer.
How transcriptome data sets leads to identifying novel prophages?
4 answers
Transcriptome data sets play a crucial role in identifying novel prophages by enriching for highly expressed features within bacterial cells, particularly accessory loci that encode beneficial functions. These accessory loci are often challenging to detect solely through DNA sequence analysis. By examining the transcriptional landscapes of bacterial genomes hosting prophages, researchers can heuristically identify functionally important prophage features that are actively expressed. This approach has been demonstrated in the discovery of a novel antisense RNA species, STnc6030, in prophage BTP1, which mediates superinfection exclusion and immunity to related phages. Utilizing bacterial RNA-seq data provides a powerful tool to explore the molecular biology of temperate phages and uncover previously unknown prophage elements within bacterial genomes.
What evidence is available on garlic in influenza prevention or treatment of symptoms?
5 answers
Garlic has shown promising antiviral activity against influenza. Studies have highlighted its potential in inhibiting virus penetration and proliferation. Garlic extract demonstrated significant antiviral effects on influenza infection, as evidenced by hemagglutination, cytotoxicity assays, and RT-PCR. Traditional medicine involving garlic has been explored due to the lack of effective drugs and vaccines for influenza, emphasizing its importance in preventing the spread of this infectious agent. The use of garlic in treating respiratory infections, including flu symptoms like cough and headache, has been documented, suggesting its role as a complementary approach for managing mild virus-infected respiratory diseases. Overall, garlic's antiviral properties make it a potential candidate for influenza prevention and symptom management.
Does the mRNA vaccine cause permanent mutations?
5 answers
mRNA vaccines have raised concerns about potential genome alterations. Studies suggest that mRNA vaccines could theoretically integrate into genomes through L1 retroelements, raising uncertainties about insertional mutagenesis safety. However, mRNA vaccines are primarily designed to trigger an immune response without entering the cell nucleus where DNA is housed, reducing the likelihood of permanent mutations. While mRNA vaccines show promise in cancer therapy by targeting specific mutations, concerns persist regarding their impact on genome integrity. The rapid development and adaptability of mRNA vaccines in response to viral mutations are advantageous in combating evolving viruses like SARS-CoV-2. Despite claims of adverse effects, including on vital organs and genome integrity, further research is needed to comprehensively assess the long-term safety of mRNA vaccines.
Amino acid that act as active site in NS3 helicase for dengue with protein Id
5 answers
In the NS3 helicase of dengue virus, the amino acids D290 and R538 play crucial roles as active sites. These amino acids interact specifically with G2 and G5 bases of the RNA, leading to enhanced ATPase activity when these bases are present. D290, located near the DEXH motif, acts as a molecular switch that activates the ATPase site upon RNA binding. Disruption of the D290-R387 interaction increases basal ATPase activity, indicating the importance of this interaction in regulating enzyme activity. Additionally, R538 is essential for RNA interactions and affects the translocation of viral RNA through dynamic interactions with specific bases, particularly at positions 4 and 5 of the single-stranded RNA. The protein ID for this NS3 helicase is PDB ID: 2FOM.
How are used self-amplyfing RNA in animal health? Animal health meaning swine, poultry, ruminant or pets?
5 answers
Self-amplifying RNA (saRNA) vaccines have shown promise in animal health applications. These vaccines, administered in two doses, have demonstrated acceptable safety profiles in rats, with considerations for delivery systems, antigen-encoding sequences, and RNA amplification. SaRNA technology offers advantages over conventional mRNA vaccines, including lower dosage requirements, fewer side effects, and longer-lasting effects, making it a potential tool for managing health disorders in animals. In the context of animal health, saRNA vaccines could be beneficial for swine, poultry, ruminants, and pets by potentially providing enhanced immune responses against infectious diseases. Further research is needed to explore the full potential of saRNA vaccines in improving animal health outcomes.
Amino acid that act as active site in NS3 helicase for dengue
5 answers
The amino acids that act as active sites in the NS3 helicase for dengue virus are D290 and R538. These amino acids play crucial roles in the catalytic activity of the NS3 helicase. Specifically, D290 interacts with R387, forming a molecular switch that activates the ATPase site upon RNA binding, thereby stimulating ATPase activity. On the other hand, R538 is involved in critical RNA interactions that affect the translocation of viral RNA by dynamically interacting with bases in the single-stranded RNA, particularly at positions 4 and 5. Disruption of these interactions can impact the functionality of the NS3 helicase, highlighting the significance of these active site amino acids in the viral replication process.