RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)RNA, Small Interfering: Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.RNA Editing: A process that changes the nucleotide sequence of mRNA from that of the DNA template encoding it. Some major classes of RNA editing are as follows: 1, the conversion of cytosine to uracil in mRNA; 2, the addition of variable number of guanines at pre-determined sites; and 3, the addition and deletion of uracils, templated by guide-RNAs (RNA, GUIDE).RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.DNA-Directed RNA Polymerases: Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).RNA Viruses: Viruses whose genetic material is RNA.RNA Interference: A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.RNA, Double-Stranded: RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. Most of the double-stranded segments are formed from transcription of DNA by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. Some double-stranded segments of RNA are normal in all organisms.RNA, Catalytic: RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.RNA Folding: The processes of RNA tertiary structure formation.RNA Polymerase II: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6.RNA, Fungal: Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.RNA Stability: The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.RNA Helicases: A family of proteins that promote unwinding of RNA during splicing and translation.RNA, Antisense: RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.RNA Processing, Post-Transcriptional: Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.RNA, Transfer: The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.RNA, Small Nuclear: Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.RNA Precursors: RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.RNA, Untranslated: RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.RNA Caps: Nucleic acid structures found on the 5' end of eukaryotic cellular and viral messenger RNA and some heterogeneous nuclear RNAs. These structures, which are positively charged, protect the above specified RNAs at their termini against attack by phosphatases and other nucleases and promote mRNA function at the level of initiation of translation. Analogs of the RNA caps (RNA CAP ANALOGS), which lack the positive charge, inhibit the initiation of protein synthesis.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.RNA, Protozoan: Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.RNA, Neoplasm: RNA present in neoplastic tissue.RNA Ligase (ATP): An enzyme that catalyzes the conversion of linear RNA to a circular form by the transfer of the 5'-phosphate to the 3'-hydroxyl terminus. It also catalyzes the covalent joining of two polyribonucleotides in phosphodiester linkage. EC 6.5.1.3.DEAD-box RNA Helicases: A large family of RNA helicases that share a common protein motif with the single letter amino acid sequence D-E-A-D (Asp-Glu-Ala-Asp). In addition to RNA helicase activity, members of the DEAD-box family participate in other aspects of RNA metabolism and regulation of RNA function.RNA Polymerase III: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure where it transcribes DNA into RNA. It has specific requirements for cations and salt and has shown an intermediate sensitivity to alpha-amanitin in comparison to RNA polymerase I and II. EC 2.7.7.6.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.RNA Polymerase I: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. The enzyme functions in the nucleolar structure and transcribes DNA into RNA. It has different requirements for cations and salts than RNA polymerase II and III and is not inhibited by alpha-amanitin. EC 2.7.7.6.RNA, Nuclear: RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.RNA, Guide: Small kinetoplastid mitochondrial RNA that plays a major role in RNA EDITING. These molecules form perfect hybrids with edited mRNA sequences and possess nucleotide sequences at their 5'-ends that are complementary to the sequences of the mRNA's immediately downstream of the pre-edited regions.RNA, Ribosomal, 28S: Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.RNA, Ribosomal, 18S: Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.RNA, Ribosomal, 23S: Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.RNA Transport: The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms.RNA, Spliced Leader: The small RNAs which provide spliced leader sequences, SL1, SL2, SL3, SL4 and SL5 (short sequences which are joined to the 5' ends of pre-mRNAs by TRANS-SPLICING). They are found primarily in primitive eukaryotes (protozoans and nematodes).RNA, Satellite: Small, linear single-stranded RNA molecules functionally acting as molecular parasites of certain RNA plant viruses. Satellite RNAs exhibit four characteristic traits: (1) they require helper viruses to replicate; (2) they are unnecessary for the replication of helper viruses; (3) they are encapsidated in the coat protein of the helper virus; (4) they have no extensive sequence homology to the helper virus. Thus they differ from SATELLITE VIRUSES which encode their own coat protein, and from the genomic RNA; (=RNA, VIRAL); of satellite viruses. (From Maramorosch, Viroids and Satellites, 1991, p143)RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.RNA, Archaeal: Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Virus Replication: The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.RNA Cleavage: A reaction that severs one of the sugar-phosphate linkages of the phosphodiester backbone of RNA. It is catalyzed enzymatically, chemically, or by radiation. Cleavage may be exonucleolytic, or endonucleolytic.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Oligoribonucleotides: A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.RNA, Heterogeneous Nuclear: Nuclear nonribosomal RNA larger than about 1000 nucleotides, the mass of which is rapidly synthesized and degraded within the cell nucleus. Some heterogeneous nuclear RNA may be a precursor to mRNA. However, the great bulk of total hnRNA hybridizes with nuclear DNA rather than with mRNA.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.RNA, Small Cytoplasmic: Small RNAs found in the cytoplasm usually complexed with proteins in scRNPs (RIBONUCLEOPROTEINS, SMALL CYTOPLASMIC).RNA 3' End Processing: The steps that generate the 3' ends of mature RNA molecules. For most mRNAs (RNA, MESSENGER), 3' end processing referred to as POLYADENYLATION includes the addition of POLY A.Templates, Genetic: Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.RNA, Small Untranslated: Short RNA, about 200 base pairs in length or shorter, that does not code for protein.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.Ribonucleoproteins: Complexes of RNA-binding proteins with ribonucleic acids (RNA).Ribonucleases: Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.Poly A: A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.RNA, Ribosomal, 5.8S: Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).RNA, Long Noncoding: A class of untranslated RNA molecules that are typically greater than 200 nucleotides in length and do not code for proteins. Members of this class have been found to play roles in transcriptional regulation, post-transcriptional processing, CHROMATIN REMODELING, and in the epigenetic control of chromatin.RNA, Small Nucleolar: Small nuclear RNAs that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.RNA Virus InfectionsProtein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.RNA, Complementary: Synthetic transcripts of a specific DNA molecule or fragment, made by an in vitro transcription system. This cRNA can be labeled with radioactive uracil and then used as a probe. (King & Stansfield, A Dictionary of Genetics, 4th ed)UridinePromoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Endoribonucleases: A family of enzymes that catalyze the endonucleolytic cleavage of RNA. It includes EC 3.1.26.-, EC 3.1.27.-, EC 3.1.30.-, and EC 3.1.31.-.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)RNA, Chloroplast: Ribonucleic acid in chloroplasts having regulatory and catalytic roles as well as involvement in protein synthesis.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Kinetics: The rate dynamics in chemical or physical systems.Single-Strand Specific DNA and RNA Endonucleases: Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.RNA, Helminth: Ribonucleic acid in helminths having regulatory and catalytic roles as well as involvement in protein synthesis.Plant Viruses: Viruses parasitic on plants higher than bacteria.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.RNA, Transfer, Phe: A transfer RNA which is specific for carrying phenylalanine to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, Lys: A transfer RNA which is specific for carrying lysine to sites on the ribosomes in preparation for protein synthesis.Ribosomes: Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.Blotting, Northern: Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.5' Untranslated Regions: The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.RNA, Transfer, Tyr: A transfer RNA which is specific for carrying tyrosine to sites on the ribosomes in preparation for protein synthesis.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.3' Untranslated Regions: The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.Amanitins: Cyclic peptides extracted from carpophores of various mushroom species. They are potent inhibitors of RNA polymerases in most eukaryotic species, blocking the production of mRNA and protein synthesis. These peptides are important in the study of transcription. Alpha-amanitin is the main toxin from the species Amanitia phalloides, poisonous if ingested by humans or animals.Genes, Viral: The functional hereditary units of VIRUSES.Nucleic Acid Denaturation: Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.Ribonuclease T1: An enzyme catalyzing the endonucleolytic cleavage of RNA at the 3'-position of a guanylate residue. EC 3.1.27.3.Molecular Weight: The sum of the weight of all the atoms in a molecule.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Cell Nucleolus: Within most types of eukaryotic CELL NUCLEUS, a distinct region, not delimited by a membrane, in which some species of rRNA (RNA, RIBOSOMAL) are synthesized and assembled into ribonucleoprotein subunits of ribosomes. In the nucleolus rRNA is transcribed from a nucleolar organizer, i.e., a group of tandemly repeated chromosomal genes which encode rRNA and which are transcribed by RNA polymerase I. (Singleton & Sainsbury, Dictionary of Microbiology & Molecular Biology, 2d ed)HIV-1: The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.Cell-Free System: A fractionated cell extract that maintains a biological function. A subcellular fraction isolated by ultracentrifugation or other separation techniques must first be isolated so that a process can be studied free from all of the complex side reactions that occur in a cell. The cell-free system is therefore widely used in cell biology. (From Alberts et al., Molecular Biology of the Cell, 2d ed, p166)Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Viral Nonstructural Proteins: Proteins encoded by a VIRAL GENOME that are produced in the organisms they infect, but not packaged into the VIRUS PARTICLES. Some of these proteins may play roles within the infected cell during VIRUS REPLICATION or act in regulation of virus replication or VIRUS ASSEMBLY.RNA, Transfer, Amino Acyl: Intermediates in protein biosynthesis. The compounds are formed from amino acids, ATP and transfer RNA, a reaction catalyzed by aminoacyl tRNA synthetase. They are key compounds in the genetic translation process.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.RNA Splice Sites: Nucleotide sequences located at the ends of EXONS and recognized in pre-messenger RNA by SPLICEOSOMES. They are joined during the RNA SPLICING reaction, forming the junctions between exons.RNA, Transfer, Ala: A transfer RNA which is specific for carrying alanine to sites on the ribosomes in preparation for protein synthesis.Poliovirus: A species of ENTEROVIRUS which is the causal agent of POLIOMYELITIS in humans. Three serotypes (strains) exist. Transmission is by the fecal-oral route, pharyngeal secretions, or mechanical vector (flies). Vaccines with both inactivated and live attenuated virus have proven effective in immunizing against the infection.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Tobacco: A plant genus of the family SOLANACEAE. Members contain NICOTINE and other biologically active chemicals; its dried leaves are used for SMOKING.Ribonuclease P: An RNA-containing enzyme that plays an essential role in tRNA processing by catalyzing the endonucleolytic cleavage of TRANSFER RNA precursors. It removes the extra 5'-nucleotides from tRNA precursors to generate mature tRNA molecules.Centrifugation, Density Gradient: Separation of particles according to density by employing a gradient of varying densities. At equilibrium each particle settles in the gradient at a point equal to its density. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Cytoplasm: The part of a cell that contains the CYTOSOL and small structures excluding the CELL NUCLEUS; MITOCHONDRIA; and large VACUOLES. (Glick, Glossary of Biochemistry and Molecular Biology, 1990)Nucleotides: The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)Mosaic Viruses: Viruses which produce a mottled appearance of the leaves of plants.RNA-Directed DNA Polymerase: An enzyme that synthesizes DNA on an RNA template. It is encoded by the pol gene of retroviruses and by certain retrovirus-like elements. EC 2.7.7.49.Dactinomycin: A compound composed of a two CYCLIC PEPTIDES attached to a phenoxazine that is derived from STREPTOMYCES parvullus. It binds to DNA and inhibits RNA synthesis (transcription), with chain elongation more sensitive than initiation, termination, or release. As a result of impaired mRNA production, protein synthesis also declines after dactinomycin therapy. (From AMA Drug Evaluations Annual, 1993, p2015)Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Hepacivirus: A genus of FLAVIVIRIDAE causing parenterally-transmitted HEPATITIS C which is associated with transfusions and drug abuse. Hepatitis C virus is the type species.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.RNA, Transfer, Asp: A transfer RNA which is specific for carrying aspartic acid to sites on the ribosomes in preparation for protein synthesis.TritiumRNA, Transfer, Met: A transfer RNA which is specific for carrying methionine to sites on the ribosomes. During initiation of protein synthesis, tRNA(f)Met in prokaryotic cells and tRNA(i)Met in eukaryotic cells binds to the start codon (CODON, INITIATOR).Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Bromovirus: A genus of tripartite plant viruses in the family BROMOVIRIDAE. Transmission is by beetles. Brome mosaic virus is the type species.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Ribonuclease H: A ribonuclease that specifically cleaves the RNA moiety of RNA:DNA hybrids. It has been isolated from a wide variety of prokaryotic and eukaryotic organisms as well as RETROVIRUSES.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Regulatory Sequences, Ribonucleic Acid: Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.Polyribosomes: A multiribosomal structure representing a linear array of RIBOSOMES held together by messenger RNA; (RNA, MESSENGER); They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Cell Line, Tumor: A cell line derived from cultured tumor cells.Capsid: The outer protein protective shell of a virus, which protects the viral nucleic acid.Exoribonucleases: A family of enzymes that catalyze the exonucleolytic cleavage of RNA. It includes EC 3.1.13.-, EC 3.1.14.-, EC 3.1.15.-, and EC 3.1.16.-. EC 3.1.-Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Bacterial Proteins: Proteins found in any species of bacterium.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.RNA, Transfer, Gly: A transfer RNA which is specific for carrying glycine to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, His: A transfer RNA which is specific for carrying histidine to sites on the ribosomes in preparation for protein synthesis.Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.RNA, Transfer, Val: A transfer RNA which is specific for carrying valine to sites on the ribosomes in preparation for protein synthesis.Poly U: A group of uridine ribonucleotides in which the phosphate residues of each uridine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Nodaviridae: A family of RNA viruses infecting insects and fish. There are two genera: Alphanodavirus and Betanodavirus.Nucleic Acid Precursors: Use for nucleic acid precursors in general or for which there is no specific heading.Virus Assembly: The assembly of VIRAL STRUCTURAL PROTEINS and nucleic acid (VIRAL DNA or VIRAL RNA) to form a VIRUS PARTICLE.Defective Viruses: Viruses which lack a complete genome so that they cannot completely replicate or cannot form a protein coat. Some are host-dependent defectives, meaning they can replicate only in cell systems which provide the particular genetic function which they lack. Others, called SATELLITE VIRUSES, are able to replicate only when their genetic defect is complemented by a helper virus.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.RNA, Transfer, Arg: A transfer RNA which is specific for carrying arginine to sites on the ribosomes in preparation for protein synthesis.RNA, Algal: Ribonucleic acid in algae having regulatory and catalytic roles as well as involvement in protein synthesis.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Heterogeneous-Nuclear Ribonucleoproteins: A family of ribonucleoproteins that were originally found as proteins bound to nascent RNA transcripts in the form of ribonucleoprotein particles. Although considered ribonucleoproteins they are primarily classified by their protein component. They are involved in a variety of processes such as packaging of RNA and RNA TRANSPORT within the nucleus. A subset of heterogeneous-nuclear ribonucleoproteins are involved in additional functions such as nucleocytoplasmic transport (ACTIVE TRANSPORT, CELL NUCLEUS) of RNA and mRNA stability in the CYTOPLASM.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.Virion: The infective system of a virus, composed of the viral genome, a protein core, and a protein coat called a capsid, which may be naked or enclosed in a lipoprotein envelope called the peplos.Ribonucleoproteins, Small Nuclear: Highly conserved nuclear RNA-protein complexes that function in RNA processing in the nucleus, including pre-mRNA splicing and pre-mRNA 3'-end processing in the nucleoplasm, and pre-rRNA processing in the nucleolus (see RIBONUCLEOPROTEINS, SMALL NUCLEOLAR).Hepatitis Delta Virus: A defective virus, containing particles of RNA nucleoprotein in virion-like form, present in patients with acute hepatitis B and chronic hepatitis. It requires the presence of a hepadnavirus for full replication. This is the lone species in the genus Deltavirus.Ribosomal Proteins: Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.RNA, Transfer, Trp: A transfer RNA which is specific for carrying tryptophan to sites on the ribosomes in preparation for protein synthesis.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.Terminator Regions, Genetic: DNA sequences recognized as signals to end GENETIC TRANSCRIPTION.Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Macromolecular Substances: Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.Plants: Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Levivirus: A bacteriophage genus of the family LEVIVIRIDAE, whose viruses contain the short version of the genome and have a separate gene for cell lysis.Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.PolynucleotidesTrypanosoma brucei brucei: A hemoflagellate subspecies of parasitic protozoa that causes nagana in domestic and game animals in Africa. It apparently does not infect humans. It is transmitted by bites of tsetse flies (Glossina).DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Tombusvirus: A genus of plant viruses that infects ANGIOSPERMS. Transmission occurs mechanically and through soil, with one species transmitted via a fungal vector. The type species is Tomato bushy stunt virus.Guanosine: A purine nucleoside that has guanine linked by its N9 nitrogen to the C1 carbon of ribose. It is a component of ribonucleic acid and its nucleotides play important roles in metabolism. (From Dorland, 28th ed)Polyadenylation: The addition of a tail of polyadenylic acid (POLY A) to the 3' end of mRNA (RNA, MESSENGER). Polyadenylation involves recognizing the processing site signal, (AAUAAA), and cleaving of the mRNA to create a 3' OH terminal end to which poly A polymerase (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) adds 60-200 adenylate residues. The 3' end processing of some messenger RNAs, such as histone mRNA, is carried out by a different process that does not include the addition of poly A as described here.RNA, Transfer, Leu: A transfer RNA which is specific for carrying leucine to sites on the ribosomes in preparation for protein synthesis.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Structure-Activity Relationship: The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.

Gene silencing: plants and viruses fight it out. (1/25126)

Plants can become 'immune' to attack by viruses by degrading specific viral RNA, but some plant viruses have evolved the general capacity to suppress this resistance mechanism.  (+info)

Structural basis for the specificity of the initiation of HIV-1 reverse transcription. (2/25126)

Initiation of human immunodeficiency virus type 1 (HIV-1) reverse transcription requires specific recognition of the viral genome, tRNA3Lys, which acts as primer, and reverse transcriptase (RT). The specificity of this ternary complex is mediated by intricate interactions between HIV-1 RNA and tRNA3Lys, but remains poorly understood at the three-dimensional level. We used chemical probing to gain insight into the three-dimensional structure of the viral RNA-tRNA3Lys complex, and enzymatic footprinting to delineate regions interacting with RT. These and previous experimental data were used to derive a three-dimensional model of the initiation complex. The viral RNA and tRNA3Lys form a compact structure in which the two RNAs fold into distinct structural domains. The extended interactions between these molecules are not directly recognized by RT. Rather, they favor RT binding by preventing steric clashes between the nucleic acids and the polymerase and inducing a viral RNA-tRNA3Lys conformation which fits perfectly into the nucleic acid binding cleft of RT. Recognition of the 3' end of tRNA3Lys and of the first template nucleotides by RT is favored by a kink in the template strand promoted by the short junctions present in the previously established secondary structure.  (+info)

A premature termination codon interferes with the nuclear function of an exon splicing enhancer in an open reading frame-dependent manner. (3/25126)

Premature translation termination codon (PTC)-mediated effects on nuclear RNA processing have been shown to be associated with a number of human genetic diseases; however, how these PTCs mediate such effects in the nucleus is unclear. A PTC at nucleotide (nt) 2018 that lies adjacent to the 5' element of a bipartite exon splicing enhancer within the NS2-specific exon of minute virus of mice P4 promoter-generated pre-mRNA caused a decrease in the accumulated levels of P4-generated R2 mRNA relative to P4-generated R1 mRNA, although the total accumulated levels of P4 product remained the same. This effect was seen in nuclear RNA and was independent of RNA stability. The 5' and 3' elements of the bipartite NS2-specific exon enhancer are redundant in function, and when the 2018 PTC was combined with a deletion of the 3' enhancer element, the exon was skipped in the majority of the viral P4-generated product. Such exon skipping in response to a PTC, but not a missense mutation at nt 2018, could be suppressed by frame shift mutations in either exon of NS2 which reopened the NS2 open reading frame, as well as by improvement of the upstream intron 3' splice site. These results suggest that a PTC can interfere with the function of an exon splicing enhancer in an open reading frame-dependent manner and that the PTC is recognized in the nucleus.  (+info)

High level inhibition of HIV replication with combination RNA decoys expressed from an HIV-Tat inducible vector. (4/25126)

Intracellular immunization, an antiviral gene therapy approach based on the introduction of DNA into cells to stably express molecules for the inhibition of viral gene expression and replication, has been suggested for inhibition of HIV infection. Since the Tat and Rev proteins play a critical role in HIV regulation, RNA decoys and ribozymes of these sequences have potential as therapeutic molecular inhibitors. In the present study, we have generated several anti-HIV molecules; a tat-ribozyme, RRE, RWZ6 and TAR decoys and combinations of decoys, and tested them for inhibition of HIV-1 replication in vitro. We used T cell specific CD2 gene elements and regulatory the HIV inducible promoter to direct high level expression and a 3' UTR sequence for mRNA stabilization. We show that HIV replication was most strongly inhibited with the combination TAR + RRE decoy when compared with the single decoys or the tat-ribozyme. We also show that the Tat-inducible HIV promoter directs a higher level of steady-state transcription of decoys and inhibitors and that higher levels of expression directly relate to increased levels of inhibition of HIV infection. Furthermore, a stabilization of the 3' end of TAR + RRE inhibitor transcripts using a beta-globin 3' UTR sequence leads to an additional 15-fold increase in steady-state RNA levels. This cassette when used to express the best combination decoy inhibitor TAR + RRE, yields high level HIV inhibition for greater than 3 weeks. Taken together, both optimization for high level expression of molecular inhibitors and use of combinations of inhibitors suggest better therapeutic application in limiting the spread of HIV.  (+info)

Reverse transcription-nested polymerase chain reaction for detecting p40 RNA of Borna disease virus, without risk of plasmid contamination. (5/25126)

Several methods for the detection of Borna disease virus (BDV) RNA have been reported, one being the reverse transcription-nested polymerase chain reaction (RT-nested PCR) method. However, due to the possibility of contamination of the cloned DNA in a reaction tube, false-positive results might be obtained by RT-nested PCR. To detect only BDV RNA without anxiety of contamination, we developed an RT-nested PCR system using "mRNA selective PCR kit". Using this system, cDNA of BDV p40 in the plasmid (up to 5 x 10(7) molecules) was not amplified. BDV specific sequence was amplified from total RNA (more than 50 pg) of MDCK/BDV cells, which were persistently infected with BDV. These results indicate that this mRNA selective RT-nested PCR system can specifically amplify target RNA as distinguished from plasmid contaminated.  (+info)

Enteroviral RNA replication in the myocardium of patients with left ventricular dysfunction and clinically suspected myocarditis. (6/25126)

BACKGROUND: Previous studies dealing with the detection of enteroviral RNA in human endomyocardial biopsies have not differentiated between latent persistence of the enteroviral genome and active viral replication. Enteroviruses that are considered important factors for the development of myocarditis have a single-strand RNA genome of positive polarity that is transcribed by a virus-encoded RNA polymerase into a minus-strand mRNA during active viral replication. The synthesis of multiple copies of minus-strand enteroviral RNA therefore occurs only at sites of active viral replication but not in tissues with mere persistence of the viral genome. METHODS AND RESULTS: We investigated enteroviral RNA replication versus enteroviral RNA persistence in endomyocardial biopsies of 45 patients with left ventricular dysfunction and clinically suspected myocarditis. Using reverse-transcriptase polymerase chain reaction in conjunction with Southern blot hybridization, we established a highly sensitive assay to specifically detect plus-strand versus minus-strand enteroviral RNA in the biopsies. Plus-strand enteroviral RNA was detected in endomyocardial biopsies of 18 (40%) of 45 patients, whereas minus-strand RNA as an indication of active enteroviral RNA replication was detected in only 10 (56%) of these 18 plus-strand-positive patients. Enteroviral RNA was not found in biopsies of the control group (n=26). CONCLUSIONS: These data demonstrate that a significant fraction of patients with left ventricular dysfunction and clinically suspected myocarditis had active enteroviral RNA replication in their myocardium (22%). Differentiation between patients with active viral replication and latent viral persistence should be particularly important in future studies evaluating different therapeutic strategies. In addition, molecular genetic detection of enteroviral genome and differentiation between replicating versus persistent viruses is possible in a single endomyocardial biopsy.  (+info)

HIV-associated nephropathy is a late, not early, manifestation of HIV-1 infection. (7/25126)

BACKGROUND: Human immunodeficiency virus-associated nephropathy (HIVAN) can be the initial presentation of HIV-1 infection. As a result, many have assumed that HIVAN can occur at any point in the infection. This issue has important implications for appropriate therapy and, perhaps, for pathogenesis. Since the development of new case definitions for acquired immunodeficiency syndrome (AIDS) and better tools to assess infection, the relationship of HIVAN to the time of AIDS infection has not been addressed. In this study, we reassessed the stage of infection at the time of HIVAN diagnosis in 10 patients, and we reviewed all previously published cases applying the new case definitions to assess stage of infection. METHODS: HIVAN was confirmed by kidney biopsy in HIV seropositive patients with azotemia and/or proteinuria. CD4+ cell count and plasma HIV-1 RNA copy number were measured. We also reviewed all published cases of HIVAN to determine if AIDS-defining conditions, by current Centers for Disease Control definitions, were present in patients with biopsy-proven HIVAN. RESULTS: Twenty HIV-1 seropositive patients with proteinuria and an elevated creatinine concentration were biopsied. HIVAN was the single most common cause of renal disease. CD4+ cell count was below 200/mm3 in all patients with HIVAN, fulfilling Centers for Disease Control criteria for an AIDS-defining condition. HIV-1 plasma RNA was detectable in all patients with HIVAN. In reviewing previous reports, an AIDS-defining condition was present in virtually all patients with HIVAN. CONCLUSION: HIVAN develops late, not early, in the course of HIV-1 infection following the development of AIDS. This likely accounts for the poor prognosis noted in previous publications and has implications for pathogenesis. In addition, given the detectable viral RNA levels, highly active antiretroviral therapy is indicated in HIVAN. Highly active antiretroviral therapy may improve survival as well as alter the natural history of HIVAN.  (+info)

A multistate, foodborne outbreak of hepatitis A. National Hepatitis A Investigation Team. (8/25126)

BACKGROUND: We investigated a large, foodborne outbreak of hepatitis A that occurred in February and March 1997 in Michigan and then extended the investigation to determine whether it was related to sporadic cases reported in other states among persons who had consumed frozen strawberries, the food suspected of causing the outbreak. METHODS: The cases of hepatitis A were serologically confirmed. Epidemiologic studies were conducted in the two states with sufficient numbers of cases, Michigan and Maine. Hepatitis A virus RNA detected in clinical specimens was sequenced to determine the relatedness of the virus from outbreak-related cases and other cases. RESULTS: A total of 213 cases of hepatitis A were reported from 23 schools in Michigan and 29 cases from 13 schools in Maine, with the median rate of attack ranging from 0.2 to 14 percent. Hepatitis A was associated with the consumption of frozen strawberries in a case-control study (odds ratio for the disease, 8.3; 95 percent confidence interval, 2.1 to 33) and a cohort study (relative risk of infection, 7.5; 95 percent confidence interval, 1.1 to 53) in Michigan and in a case-control study in Maine (odds ratio for infection, 3.4; 95 percent confidence interval, 1.0 to 14). The genetic sequences of viruses from 126 patients in Michigan and Maine were identical to one another and to those from 5 patients in Wisconsin and 7 patients in Arizona, all of whom attended schools where frozen strawberries from the same processor had been served, and to those in 2 patients from Louisiana, both of whom had consumed commercially prepared products containing frozen strawberries from the same processor. CONCLUSIONS: We describe a large outbreak of hepatitis A in Michigan that was associated with the consumption of frozen strawberries. We found apparently sporadic cases in other states that could be linked to the same source by viral genetic analysis.  (+info)

The group of Negative-Stranded RNA Viruses (NSVs) includes many human pathogens, like the influenza, measles, mumps, respiratory syncytial or Ebola viruses, which produce frequent epidemics of disease and occasional, high mortality outbreaks by transmission from animal reservoirs. The genome of NSVs consists of one to several single-stranded, negative-polarity RNA molecules that are always assembled into mega Dalton-sized complexes by association to many nucleoprotein monomers. These RNA-protein complexes or ribonucleoproteins function as templates for transcription and replication by action of the viral RNA polymerase and accessory proteins. Here we review our knowledge on these large RNA-synthesis machines, including the structure of their components, the interactions among them and their enzymatic activities, and we discuss models showing how they perform the virus transcription and replication programmes. - Highlights: • Overall organisation of NSV RNA synthesis machines. • Structure and ...
TY - JOUR. T1 - Detection of negative-stranded hepatitis C virus RNA using a novel strand-specific reverse transcription-polymerase chain reaction. AU - Mizutani, Tetsuya. AU - Ikeda, Masanori. AU - Saito, Satoru. AU - Sugiyama, Kazuo. AU - Shimotohno, Kunitada. AU - Kato, Nobuyuki. PY - 1998/2/1. Y1 - 1998/2/1. N2 - We developed a novel single-tube reverse transcription-polymerase chain reaction (RT-PCR) for the specific detection of negative-stranded hepatitis C virus (HCV) RNA. By using in vitro synthesized positive- and negative-stranded HCV RNAs, it was demonstrated that as few as 50 copies of negative-stranded HCV RNA could be specifically detected with a set of primers that amplify a 232-base pair sequence unique to the 5-non-coding region of HCV RNA, while 108 copies of positive-stranded HCV RNA were not detected. In addition, we demonstrated that this method allows the detection as few as 100 copies of negative-stranded HCV RNA even with the coexistence of a 100-fold excess of ...
387440791 - EP 0832191 A4 2000-11-15 - RECOMBINANT VIRAL NUCLEIC ACIDS - [origin: WO9640867A1] The present invention relates to a recombinant viral nucleic acid selected from a (+) sense, single stranded RNA virus possessing a native subgenomic promoter encoding for a first viral subgenomic promoter, a nucleic acid sequence that codes for a viral coat protein whose transcription is regulated by the first viral subgenomic promoter, a second viral subgenomic promoter and a second nucleic acid sequence whose transcription is regulated by the second viral subgenomic promoter. The first and second viral subgenomic promoters of the recombinant viral nucleic acid do not have homologous sequences relative to each other. The recombinant viral nucleic acid provides the particular advantage that it systematically transcribes the second nucleic acid in the host. Host organisms encompassed by the present invention include procaryotes and eucaryotes, particularly animals and plants. The present invention also relates
Two copies of unspliced human immunodeficiency virus (HIV)-1 genomic RNA (gRNA) are preferentially selected for packaging by the group-specific antigen (Gag) polyprotein into progeny virions as a dimer during the late stages of the viral lifecycle. Elucidating the RNA features responsible for selective recognition of the full-length gRNA in the presence of an abundance of other cellular RNAs and spliced viral RNAs remains an area of intense research. The recent nuclear magnetic resonance (NMR) structure by Keane et al. [1] expands upon previous efforts to determine the conformation of the HIV-1 RNA packaging signal. The data support a secondary structure wherein sequences that constitute the major splice donor site are sequestered through base pairing, and a tertiary structure that adopts a tandem 3-way junction motif that exposes the dimerization initiation site and unpaired guanosines for specific recognition by Gag. While it remains to be established whether this structure is conserved in the context
Polivirüsün hücresel yaşam döngüsü (1) CD155 reseptörüne bağlanmasıyla başlar. Virüs endositozla alınır, ve viral RNA serbest kalır (2). Translation of the viral RNA occurs by an IRES-mediated mechanism (3). The polyprotein is cleaved, yielding mature viral proteins (4). The positive-sense RNA serves as template for complementary negative-strand synthesis, producing double-stranded replicative form (RF) RNA(5). Many positive strand RNA copies are produced from the single negative strand (6). The newly synthesized positive-sense RNA molecules can serve as templates for translation of more viral proteins (7) or can be enclosed in a capsid (8), which ultimately generates progeny virions. Lysis of the infected cell results in release of infectious progeny virions (9).[2] ...
This review is centered on the major strategies used by plant RNA viruses to produce the proteins required for virus multiplication. The strategies at the level of transcription presented here are synthesis of mRNA or subgenomic RNAs from viral RNA templates, and cap-snatching. At the level of translation, several strategies have been evolved by viruses at the steps of initiation, elongation and termination. At the initiation step, the classical scanning mode is the most frequent strategy employed by viruses; however in a vast number of cases, leaky scanning of the initiation complex allows expression of more than one protein from the same RNA sequence. During elongation, frameshift allows the formation of two proteins differing in their carboxy terminus. At the termination step, suppression of termination produces a protein with an elongated carboxy terminus. The last strategy that will be described is co- and/or post-translational cleavage of a polyprotein precursor by virally encoded ...
Upon entry, the host cell senses an invasion. Recent evidence suggests that structured viral RNAs can act as Pathogen Associated Molecular Patterns (PAMPs) that are recognized by host Pattern Recognition Receptors (PRR) to activate cell signaling. An immediate goal of the laboratory is to understand how specific viral RNA-protein interactions influence the viral life cycle and the host immune response. The triphosphate group found at the 5 end of some viral RNA transcripts (5 3P) has been described recently as an important determinant of "self versus non-self" that allows cells to distinguish between viral and cellular RNAs. Our results suggest that the 5 3P cannot be the only determinant because some RNAs with a 5 3P are potent activators, while others cause no activation of innate immune signaling. We have identified a non-structured region in the hepatitis C virus (HCV) 3 untranslated region RNA that activates innate immune signaling by interacting with the RNA helicase RIG-I. We ...
The extra length that dimer RNA provides is critical in encouraging PKR to pair up and function properly. "The length needed for one PKR to bind to RNA is fifteen base pairs," said Philip Bevilacqua, professor of chemistry, Penn State, one of the lead scientists on the project along with James Cole, associate professor, University of Connecticut. "To get two PKRs to bind and dimerize, you need an RNA strand that is twice as long." Coles laboratory provided evidence of dimerization of RNA and PKR. In their experiments at Penn State, the scientists found the dimer RNA activated PKR from 9 to 118 times more than the single strand RNA, depending on the RNA type. TAR RNA dimerization activated the most PKR when the TAR did not exhibit structural defects. The researchers report their findings in a recent issue of the Journal of Molecular Biology. "Adding these defects decreases the number of places where PKR can bind to the RNA," Heinicke explained. RNAs that showed the greatest degree of symmetry ...
The genomes of RNA viruses often contain RNA structures that are crucial for translation and RNA replication and may play additional, uncharacterized roles during the viral replication cycle. RNA structure with single-nucleotide resolution. In combination with orthogonal evolutionary analyses, we uncover several conserved RNA structures in the open reading frame of the viral genome. The…
Id like to determine viral RNA level changes in virus producing cell culture transfected with as-DNA. Can anybody provide me with a protocol and anything to be noted in the operation? Thanks in advance.. ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Patients are stratified by screening plasma viral RNA results (50,000 copies/ml or below vs above 50,000 copies/ml) and randomized to 1 of 2 treatment arms. Group 1 receives IDV 3 times daily plus d4T/3TC twice daily. Group 2 receives IDV/NFV/d4T/3TC twice daily. Patients remain on study medications for 24 weeks and are seen at the clinic once every 4 weeks after entering the study. At each clinic visit, blood samples are taken to evaluate CD4 cell count and plasma HIV RNA levels ...
Dear All, I am looking for a reliable method for the quantitation of in vitro transcribed RNA. If its quick and cheap alls the better. Also does anyone else have problems with the Ambion capped RNA making kit, Ithink they call it the mMESSAGE mMACHINE. We seem t get such variable results in term of yield its untrue, even when we make RNA from the same sample of linearised DNA (But on different days) Robert R. Woodward Email rw200 at cus.cam.ac.uk d ...
The one-step RT-ddPCR kit for probes, introduced by Bio-Rad Laboratories, Inc., provides researchers with the ability to measure target RNA molecules with precision and sensitivity for applications such as gene expression analysis, miRNA analysis, and viral load quantitation.
... The genome of HIV is diploid, composed of 2 identical single stranded positive sense RNA copies. In association with viral RNA is the reverse transcriptase enzyme which is the characteristic
... The genome of HIV is diploid, composed of 2 identical single stranded positive sense RNA copies. In association with viral RNA is the reverse transcriptase enzyme which is the characteristic
[The episode starts with tons of virus organisms on Gumballs fur, then one of them stands on a hill-like lump of fur] Virus: Brothers, weve mutated many times over for this moment, but now we are ready. Today, we take this body; tomorrow, the REST OF THE WORLD! [The virus army starts cheering...
STDcheck.com offers the only HIV RNA early detection test that can give results as soon as 9 to 11 days post exposure to HIV. Know your HIV status sooner!
Tusq X Plus-ன் பயன்பாடுகள், மருந்தளவு, பக்க விளைவுகள், நன்மைகள், தொடர்புகள் மற்றும் எச்சரிக்கைகள் ஆகியவற்றை கண்டுபிடியுங்கள்.
Summary of Facts and Submissions. I. European patent No. 0 846 181 with the title cDNA corresponding to the antigenome of nonsegmented negative strand RNA viruses, and process for the production of such viruses encoding additional antigenically active proteins was granted on European patent application No. 96928446.2 (published as WO 97/06270). The patent was granted with 21 claims.. II. Claim 1 of the patent as granted read as follows:. 1. A method for the production of an infectious non-segmented negative-strand RNA virus of the family Paramyxoviridae comprising. (a) introducing a cDNA molecule contained in a plasmid, wherein said cDNA molecule comprises the entire (+)-strand sequence of said negative- strand RNA virus operatively linked to an expression control sequence, which allows the synthesis of anti-genomic RNA transcripts bearing the authentic 3 -termini, and wherein said cDNA molecule consists of an integral multiple of six nucleotides, into a helper cell expressing an ...
A positive-sense single-stranded RNA virus (or (+)ssRNA virus) is a virus that uses positive sense, single-stranded RNA as its genetic material. Single stranded RNA viruses are classified as positive or negative depending on the sense or polarity of the RNA. The positive-sense viral RNA genome can also serve as messenger RNA and can be translated into protein in the host cell. Positive-sense ssRNA viruses belong to Group IV in the Baltimore classification. Positive-sense RNA viruses account for a large fraction of known viruses, including many pathogens such as the hepatitis C virus, West Nile virus, dengue virus, and SARS and MERS coronaviruses, as well as less clinically serious pathogens such as the rhinoviruses that cause the common cold. Positive-sense ssRNA viruses have genetic material that can function both as a genome and as messenger RNA; it can be directly translated into protein in the host cell by host ribosomes. The first proteins to be expressed after infection serve genome ...
In this study we developed a novel highly adapted HCV replicon that harbors two synergistic mutations in NS3 and one in NS5A. The ECF of this RNA was ∼5 × 105 CFU per μg of RNA, which is ∼20-fold higher than that of the best-adapted replicon we described recently (29). By analyzing this and several other HCV RNAs that differed with respect to their levels of cell culture adaptation, we found a clear correlation between the ECF and RNA replication as determined by two different transient-transfection assays. These results demonstrate that cell culture-adaptive mutations increase RNA replication. They also provide an explanation of how adaptive replicons are generated. As shown with the parental replicon carrying the luciferase gene, this nonadapted RNA replicated only transiently and at a low level in transfected cells. During this time, mutations must have been generated by the viral RNA polymerase that in a few instances were adaptive. By increasing the level of RNA replication, cells ...
A negative-sense single-stranded RNA virus (or (-)ssRNA virus) is a virus that uses negative sense, single-stranded RNA as its genetic material. Single stranded RNA viruses are classified as positive or negative depending on the sense or polarity of the RNA. The negative viral RNA is complementary to the mRNA and must be converted to a positive RNA by RNA polymerase before translation. Therefore, the purified RNA of a negative sense virus is not infectious by itself, as it needs to be converted to a positive sense RNA for replication. These viruses belong to Group V on the Baltimore classification. In addition, negative-sense single-stranded RNA viruses have complex genomic sequences, cell cycles, and replication habits that use various protein complexes to arrange in specific conformations and carry out necessary processes for survival and reproduction of their genomic sequences. The complexity of negative-sense single-stranded RNA viruses carries into its ability to suppress the innate immune ...
Both genomic and subgenomic replicative intermediates (RIs) and replicative-form (RF) structures were found in 17CL1 mouse cells that had been infected with the A59 strain of mouse hepatitis virus (MHV), a prototypic coronavirus. Seven species of RNase-resistant RF RNAs, whose sizes were consistent with the fact that each was derived from an RI that was engaged in the synthesis of one of the seven MHV positive-strand RNAs, were produced by treatment with RNase A. Because the radiolabeling of the seven RF RNAs was proportional to that of the corresponding seven positive-strand RNAs, the relative rate of synthesis of each of the MHV positive-strand RNAs may be controlled by the relative number of each of the size classes of RIs that are produced. In contrast to alphavirus, which produced its subgenome-length RF RNAs from genome-length RIs, MHV RF RNAs were derived from genome- and subgenome-length RIs. Only the three largest MHV RF RNAs (RFI, RFII, and RFIII) were derived from the RIs that ...
Poliovirus RNA replicates in membrane-associated replication complexes in the cytoplasm of infected cells. By using a reversible inhibitor of poliovirus RNA replication, it is possible to synchronize viral RNA replication. The processing of the viral polyprotein results in the formation of the individual viral proteins along with stable intermediates in the processing pathway. To expand the utility of the in vitro complementation assay, experiments were designed to determine if all of the viral replication proteins could be provided in trans to support the replication of mutant RNA templates. The authors engineered two transcript RNAs (DJB2 and DJB15) that contained large out-of-frame deletions in the polyprotein coding sequence. The results to date using the in vitro complementation assay indicate that the 5 cloverleaf, the 3 nontranslated region (NTR), and the poly(A) tail are the minimum sequences required for negative-strand synthesis. Previous studies have shown that the 5 cloverleaf plays an
Figure 2 shows the genome organization of GRV; those of other umbraviruses are very similar. For each RNA, there is at the 5′ end a very short non-coding region preceding ORF1, which encodes a putative product of 31-37 kDa. ORF2, which slightly overlaps the end of ORF1, could encode a product of 63-65 kDa but lacks an AUG initiation codon near its 5′ end. However, immediately before the stop codon of ORF1 there is a 7 nt sequence that is associated with frameshifting in several plant and animal viruses, and it seems probable that ORF1 and ORF2 are translated as a single polypeptide of 94-98 kDa by a mechanism involving a −1 frameshift. The predicted product contains, in the ORF2 region, sequence motifs characteristic of viral RdRp. A short untranslated region separates ORF2 from ORF3 and ORF4, which overlap each other almost completely in different reading frames and each yield a putative product of 26-29 kDa. The ORF4 product contains sequences characteristic of plant virus MPs. The ORF3 ...
TY - JOUR. T1 - Molecular cloning of full-length HIV-1 genomes directly from plasma viral RNA. AU - Fang, Guowei. AU - Weiser, Barbara. AU - Visosky, Aloise A.. AU - Townsend, Laura. AU - Burger, Harold. PY - 1996. Y1 - 1996. N2 - Human immunodeficiency virus type 1 (HIV-1) in plasma reflects the replicating virus population at any point in time in vivo. Studies of the relationship of the complete HIV-1 genome to pathogenesis therefore need to focus on plasma virions. Since dual infections and recombination can occur in vivo, cloning an intact plasma virus genome as a single full-length molecule is desirable. For these reasons, we developed an efficient method to clone full-length HIV-1 genomes directly from plasma viral RNA. This method used reverse transcription and long polymerase chain reaction (PCR) amplification. Virion-associated RNA was isolated from plasma samples and then reverse- transcribed to make cDNA for PCR amplification. Two different strategies were employed to amplify the ...
Shop RNA replication protein ELISA Kit, Recombinant Protein and RNA replication protein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.
Hepatitis C trojan (HCV) is an enveloped, positive strand RNA computer virus of about 9. attributable to inherently different properties of low density particles, to association of these particles with factors stimulating fusion, or to co-floatation of factors enhancing fusion activity in genus of the Flaviviridae family (1). Based on sequence comparison, patient isolates are classified into seven genotypes, differing in their nucleotide sequence by 30C35% (2C5). The two viral surface proteins, E1 (residues 192C383) and E2 (residues 384C746), are processed by transmission peptidases of the endoplasmic reticulum from a 3,000-amino acid-long polyprotein encoded by the HCV genome (examined in Ref. 2). The E1 (31 kDa) and E2 (70 kDa) proteins are glycosylated in their large amino-terminal ectodomains (6) and are anchored in the viral membrane by their carboxyl-terminal transmembrane domains. E1 and E2 form a heterodimer stabilized by noncovalent interactions. This oligomer is usually thought to be ...
Early biochemical experiments established that the minimal RNA synthesis machinery of NNS RNA viruses comprises the N encased genomic RNA associated with the viral polymerase, an L-P complex (Emerson and Yu, 1975; Mellon and Emerson, 1978). The atomic structure of N‐RNA complexes from VSV and rabies virus provided evidence that the RNA must somehow be dissociated from N for copying by the polymerase (Albertini et al, 2006; Green et al, 2006). The co‐crystal structure of the PCTD of VSV with the N‐RNA complex led to a model in which P brings L to the RNA template by binding directly between N molecules, and this interaction is perhaps also required to keep L associated with the N‐RNA during copying (Green and Luo, 2009). By now providing the first direct evidence that L can actually use RNA in the absence of the N and P, we have defined the minimal RNA synthesis components as L and RNA. We conclude that while N and P play important roles in viral RNA synthesis they are not essential for ...
Hepatitis C virus (HCV) is a single-stranded plus-sense RNA virus that is transmitted by blood-to-blood contact, and infects the human liver. HCV has a unique dependence on the liver-specific microRNA miR-122, where miR-122 binds the 5´ un-translated region of the viral RNA at two tandem sites and increases viral RNA abundance. The mechanisms of augmentation are not yet fully understood, but the interaction is known to stabilize the viral RNA, increase translation from the viral internal ribosomal entry site (IRES), and result in increased viral yield. In an attempt to create a small animal model for HCV, we added miR-122 to mouse cell lines previously thought non-permissive to HCV, which rendered these cells permissive to the virus, additionally showing that miR-122 is one of the major determinants of HCV hepatotropism. We found that some wild-type and knockout mouse cell lines - NCoA6 and PKR knockout embryonic fibroblasts - could be rendered permissive to transient HCV sub-genomic, but not ...
Hepatitis C Virus Translation Preferentially Depends on Active RNA Replication. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
The HCV replication complex. After clathrin-mediated endocytosis, fusion of HCV with cellular membranes, and uncoating the viral nucleocapsid, the single-stranded positive-sense RNA genome of the virus of approximately 9600 nucleotides is released into the cytoplasm to serve as a messenger RNA for the HCV polyprotein precursor. The HCV genome contains a single large open reading frame encoding for a polyprotein of approximately 3100 amino acids. The translated section of the HCV genome is flanked by the strongly conserved HCV 3′ and 5′ untranslated regions (UTR). The 5′ UTR is comprised of four highly structured domains forming the internal ribosome entry site (IRES), which is a virus-specific structure to initiate HCV mRNA translation. From the initially translated polyprotein, the structural HCV protein core (C) and envelope 1 and 2 (E1, E2); p7; and the six nonstructural HCV proteins NS2, NS3, NS4A, NS4B, NS5A and NS5B, are processed by both viral and host proteases. The core protein ...
The overall goal of our research is to understand the structure and function of RNA molecules. Most of our early work focused on ribosomal RNA (rRNA), characterizing the role of the RNA in protein synthesis (Vila et al 1994, Thompson et al 2001). More recently, we have turned our attention to understanding the structure and function of viral RNA molecules, particularly enteroviral genomic RNA. We have conducted studies to learn the structure of the internal ribosome entry site (IRES) RNA found in picornaviruses (Kim et al., 2005, Bailey and Tapprich 2007) and we have determined virulence determinants in picornal genomic RNA (Prusa et al. 2014). In our initial studies we have used chemical modification and primer extension to deduce the structure of the IRES elements in coxsackievirus B3. This analysis has been completed for virulent wild type viruses, attenuated mutant viruses and avirulent viruses. We have shown localized structural changes in the IRES RNA that correlate with virulence. These ...
Coronaviruses are positive-strand RNA viruses that are important infectious agents of both animals and humans. A common feature among positive-strand RNA viruses is their assembly of replication-transcription complexes in association with cytoplasmic membranes. Upon infection, coronaviruses extensively rearrange cellular membranes into organelle-like replicative structures that consist of double-membrane vesicles and convoluted membranes to which the nonstructural proteins involved in RNA synthesis localize. Double-stranded RNA, presumably functioning as replicative intermediate during viral RNA synthesis, has been detected at the double-membrane vesicle interior. Recent studies have provided new insights into the assembly and functioning of the coronavirus replicative structures. This review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the replication-transcription complexes, and the location of viral RNA synthesis, with particular
Once transcribed, the nascent full-length RNA of HIV-1 must travel to the appropriate host cell sites to be translated or to find a partner RNA for copackaging to form newly generated viruses. In this report, we sought to delineate the location where HIV-1 RNA initiates dimerization and the influence of the RNA transport pathway used by the virus on downstream events essential to viral replication. Using a cell-fusion-dependent recombination assay, we demonstrate that the two RNAs destined for copackaging into the same virion select each other mostly within the cytoplasm. Moreover, by manipulating the RNA export element in the viral genome, we show that the export pathway taken is important for the ability of RNA molecules derived from two viruses to interact and be copackaged. These results further illustrate that at the point of dimerization the two main cellular export pathways are partially distinct. Lastly, by providing Gag in trans, we have demonstrated that Gag is able to package RNA from either
This observation argues that RNPs are not randomly incorporated into virions, and is consistent with the presence of specific signals in each RNA segment that enable the RNPs to be packaged as a complete set. The mechanisms by which these signals are recognized, and how they ensure incorporation of one copy of each RNA segment into the particle, are not known.. There is clear evidence for a selective mechanism during the packaging of the bacteriophage ψ6 genome. Viral particles contain one copy each of a S, M, and L dsRNA segment. All particles contain a complete complement of genome segments, as indicated by the fact that every virus particle is infectious. Only the S RNA segment can enter newly formed particles; once that segment is packaged, then the M RNA can enter. The L RNA can only enter particles that contain both the S and M segments. Precise packaging is therefore the result of a serial dependence of packaging of the RNA segments.. Muramoto, Y., Takada, A., Fujii, K., Noda, T., ...
Viral RNA-dependent RNA Polymerase Assay. The Viral RNA-dependent RNA Polymerase Assay is developed using a RNA polymerase in the Flaviviridae,. a family of positive, single-stranded, enveloped RNA viruses. The assay is based on measurement of the. RNA molecules synthesized by the RNA polymerase using RNA as a template in the presence of NTPs.. The assay can be performed in a 384-well or 96-well plate format for tests of theenzyme activities of RNA. polymerases in the Flaviviridae family and high throughput screening of inhibitors. ...
My group uses X-ray crystallography as a central technique to study the structure-function relationships of complexes involving RNA of various kinds in eukaryotic cells. This includes the transcription/replication machinery of segmented negative strand RNA viruses (e.g. influenza), complexes involved in sorting of Pol II transcripts into their appropriate processing pathways and innate immune system pattern recognition receptors, notably the response to viral RNA via Rig-I like helicases.. Keywords: Protein-RNA recognition / aminoacyl tRNA synthetases / RNA metabolism / virus structure / influenza virus polymerase / innate immunity / Rig-I like helicases / X-ray crystallography. Subject area(s): Microbiology, Virology & Pathogens , RNA , Structural Biology & Biophysics. ...
Although changing therapies is a common strategy in the treatment of HIV disease, guidelines are needed to help clinicians and patients decide when a change in antiretroviral therapy is indicated. The technology of measuring HIV RNA in plasma has been suggested as a tool for monitoring clinical drug efficacy. However, uncertainty remains about whether aggressive antiretroviral treatment to lower HIV RNA and maintain low levels for as long as possible will confer clinical benefit in comparison with management based on monitoring CD4 counts and HIV-related symptoms.. Patients are randomized to a decision making strategy for initiating or changing therapy based on current clinical practice alone vs. decision making based on plasma HIV RNA quantitation in addition to current clinical practice in patients with ,= 300 CD4+ cells/mm3. All patients in the RNA arm as well as a subset (n = 183) of those in the CCP arm will have a plasma HIV RNA quantitation drawn every 4 months. The results of these ...
The bunyavirus genome is monomeric and consists of three segments of linear negative-sense (or ambisense, depending on the genus) RNA. The terminal sequences of each segment are base-paired. Because of this, the RNAs form non-covalently closed circles. The nucleotide sequences at the 3-terminus and the 5-terminus are complimentary, forming panhandle structures. The 5-terminus is not capped. The complete genome is 10500-22700 nucleotides long. The three segments of the genome are labeled L, M, and S. The L segment is 6300-12000 nucleotides long and encodes the viral RNA polymerase. The M segment is 3500-6000 nucleotides long and encodes two glycoproteins as a single gene product that is usually co-translationally cleaved. The S segments is 1000-2200 nucleotides long and encodes the coat protein. (sources: Descriptions of Plant Viruses, ICTVdB) ...
Genome RNA replication of all (+)RNA viruses takes place in close association with rearranged intracellular membranes. We are only beginning to understand the biogenesis and ultrastructure of these virus-induced membrane structures. In collaboration with the virology groups of LUMC (Prof. Dr. Eric Snijder) and the University of Utrecht (Prof. Dr. Frank van Kuppeveld), EM and tomography approaches will be used to gain more insight into the architecture of the rearranged membranes, the localization of the viral replication enzymes, and the localization of host factors that are hijacked by picornavirus to facilitate replication of their RNA genome.. Host institute ...
The multiscale model of hepatitis C virus (HCV) dynamics, which includes intracellular viral RNA (vRNA) replication, has been formulated in recent years in order to provide a new conceptual framework for understanding the mechanism of action of a variety of agents for the treatment of HCV. We present a robust and efficient numerical method that belongs to the family of adaptive stepsize methods and is implicit, a Rosenbrock type method that is highly suited to solve this problem. We provide a Graphical User Interface that applies this method and is useful for simulating viral dynamics during treatment with anti-HCV agents that act against HCV on the molecular level.
Recent studies have shown that replication of hepatitis C virus (HCV) is dependent on miR-122 expression.[20] miR-122 regulates HCV by binding directly to two adjacent sites close to the 5 end of HCV RNA.[21] Although these experiments were conducted using genotype 1a and 1b HCV RNA, the miR-122 binding sites are highly conserved across different genotypes, and miR-122 is also required for replication of infectious type 2a HCV.[22] As miRNAs generally function to repress gene expression by binding to 3UTR sites, this positive regulation of viral replication via a 5UTR represents a novel function for miR-122. The mechanism of regulation is not yet clear. miR-122 stimulates translation of HCV RNA, but not to a sufficient extent to explain its effects on viral replication, indicating that a second stage of the viral replication cycle must also be regulated.[23][24] HCV RNA synthesis is not affected by miR-122, suggesting that regulation of other processes such as RNA stability may occur.[25][26] ...
Hiv rna pcr test - What is the window period for p42 antigen/ antibody dual 4th gen HIV test? And the window period for HIV RNA PCR test? When can it be conclusive? See below. Please consult this site for a detailed answer. Nucleic acid tests are conclusive about a month after acquiring infection. Http://www. Sfaf. Org/hiv-info/testing/hiv-test-window-periods. Html
TheBody.com fills you in on the topic, how accurate is the hiv rna test, with a wealth of fact sheets, expert advice, community perspective, the latest news/research, and much more.
Plays an essential role in viral RNA transcription and replication by forming the heterotrimeric polymerase complex together with PB1 and PB2 subunits. The complex transcribes viral mRNAs by using a unique mechanism called cap-snatching. It consists in the hijacking and cleavage of host capped pre-mRNAs. These short capped RNAs are then used as primers for viral mRNAs. The PB2 subunit is responsible for the binding of the 5 cap of cellular pre-mRNAs which are subsequently cleaved after 10-13 nucleotides by the PA subunit that carries the endonuclease activity.
Single-stranded RNA viruses have evolved to survive extremely high mutation rates.The ubiquity and effect of ssRNA viral diseases makes an understanding of the theoretical and mechanical underpinnings of rapid viral evolution vital to our ability to control them. In this body of work, we explore some of the ways in which ssRNA viruses can uncouple the rate at which variation is generated (mutation rate) from the rate at which variation is observed (measured rate of molecular evolution).. ...
Description: An enzyme that catalyses RNA-template-directed extension of the 3- end of an RNA strand by one nucleotide at a time, and can initiate a chain de novo. (Enzyme Nomenclature, 1992, p293 ...
Order the hepatitis C viral RNA, quantitative, real-time PCR lab test online from the convenience of your home and without visiting a doctor!
Ilkka Julkunen, Department of Virology, University of Turku and Virology Unit, National Institute for Health and Welfare (THL), Helsinki, Finland, will give a seminar on Mechanisms of activation of innate immune responses in viral RNA and virus infection stimulated human cells Host: Malin Flodström Tullberg
In a landmark finding published in Science, Hyde et al. have demonstrated that a hairpin RNA structure adjacent to the 5 cap of alphavirus genomic RNA confers the ability of these viruses to evade restriction by the interferon-induced host protein IFIT1 ...
A single virus particle (virion) cannot replicate or express genetic material (DNA, RNA) without a host cell. Viral infection and virus replication involves six…
RNA is chemically better suited to carry out certain tasks than is DNA. There are also other reasons RNA, not DNA, is used for these tasks. First, it is desirable to keep DNA available for replication and not tied up with other functions. Second, the small number of DNA molecules in the cell is often insufficient. Creating many identical RNA molecules that are copies of a single segment of DNA provides the necessary numbers. Third, RNA can be differentially degraded when it is no longer needed, providing an important regulatory mechanism that would be unavailable if there were only one type of nucleic acid. ...
Ampliqon produces innovative solutions supplementing DNA and RNA extraction. We have recently launched a brand new product, named G2 DNA/RNA Enhancer. G2 DNA/RNA Enhancer increases the DNA yield from difficult samples such as clay dramatically. G2 DNA/RNA Enhancer must be used either in combination with commercial extraction kits or as part of the extraction method of interest.. ...
RNA extraction with TRIZOL (Invitrogen product name) or the equivalent TRI (Sigma-Aldrich product name) is a common method of total RNA extraction from cells. It takes slightly longer than column-based methods like RNAeasy but it has higher capacity and can yield more RNA. ...
Nucleic acids from ATCC can save you the time and expense of isolating DNA yourself. Viral nucleic acids in the form of RNA and DNA from infected cells or allantoic fluid are available for use in a variety of applications.
Lets work together to get you started with PrimeFlow RNA Assay! Complete the form below to tell us about your next project or experiment or let us know the challenges youre currently facing, and one of our product experts will contact you to help ensure you get the help you need.. ...
Passive transfer of DENV2 E85-VRP-immune serum or adoptive transfer of DENV2 E85-VRP-immune B cells can increase the viral RNA levels in the liver upon infectio
Sequence analysis of the 3′ termini of RSV antigenome and genome RNA isolated from RSV infected cells.(A) Putative structures formed by the terminal sequences
if Im not mistaken, the heating is needed to "melt" all the secondary structures and to anneal the primers (Hexa or oligoT) or at least to give them a better chance to interact with RNA. In the standard Invitrogen kit they usually recommended to heat the mix of RNA, primers and dNTPs at 65 C for 5 min before the reaction. However, in general the reaction can work well without heating as well if your target RNA does not have strong self-complementary sites. Before using Invitrogen I was using the home-made reverse transcriptase and never did the heating step, but all was working quite well. The point is that some enzymes can loose their activity after heating, so I think that if you decide to heat - do it before the revertase addition. Anyway, if the protocol says that there is no need for heating, than it seems like you can abandom it (:. ...
You dont indicate why the test was obtained, but likely represents chronic infection with HCV. That viral load level is a little higher than the average. Other tests will need to be performed to...
Anchored protein C (ancC) binds the host cell membrane and gathers the viral RNA genome to form the core of the mature viral particles. During viral entry into the host cell, the protein may induce genome penetration into host cytoplasm. Furthermore, ancC can migrate to the nucleus to modulate host functions ...
There are two views, that RNA came first and that Protien came first. Due to the evidence given forth in my class Im siding as of now with the Protein side. Protein acts as cell machinery (the hard ware) and RNA the soft ware. The first cells were formed by spontenously formed proteins envoloped by a chemical enveolope, very likely sulfur bubbles relseased form the earth. These proto-cells could reproduce but not replicate (they could grow large enough from the protein machinery inside that the simple membrane splits into two organisms. Spontaneously created RNA eventually was enveloped. RNA became the method of replication, hijacking the machinery to reproduce itself. RNA existed as early proto life and lived parasitically using the cell to replicate. The existing form of this early process are what we call viruses. All life as we know it arose from the interaction between viruses and protein machinery. Over a very long time these two processes of replication and reproduction became ...
DNA and RNA are both made up of nucleotides and carry molecules from one end of a cell to another monomers of protein molecules that provide stru...
Hep C Virus RNA Quant PCR (copies/m was 26340.. I dont know what the difference of these two are but I am very relieved. My last test in December was 85078 and 170156, so it is working.. Thanks! Thanks! Thanks! You are helping so many people, I am spreading the word and handing out your books.. Thanks ...
DNA and RNA are both nucleic acids that work together in living cells. They interact to transcribe a cells genetic information...
Hepatitis C virus RNA replication requires not only the viral replicase but also the host cytoskeletons, membrane structures, and cellular factors. Several hnRNPs, such as polypyrimidin-tract-binding protein (PTB) and La autoantigen were found to regulate both HCV RNA replication and translation. Another hnRNP, SYNCRIP (synaptotamin-Binding, Cytoplasmic RNA-Interacting Protein, or NSAP-1), was found to regulate HCV-IRES dependent translation. In my first part of dissertation, we identified SYNCRIP as a positive regulator of HCV RNA replication.; With a growing number of "dual-function" proteins which are able to regulate HCV RNA translation and replication, it is interesting to investigate how the two important steps in HCV life cycle are temporally and spatially regulated. Therefore, we initiated a series of experiments to examine if HCV RNA translation is dependent on its replication. The colocalization of newly-synthesized viral RNA and peptide were detected in live cell and under ...
The particle-bound RNA polymerase activity of vesicular stomatitis virus (VSV) can be demonstrated in vivo. Linear synthesis of viral RNA persists for 5 to 6 hours at 34°C in infected monolayers of chick embryo cells treated with cycloheximide and actinomycin D to block synthesis of protein and cell-specific RNA. At least 55 percent of the RNA made under these conditions is complementary to virion RNA. RNA synthesis mediated by VSV polymerase activity is inhibited in cells first treated with chick-derived interferon or polyriboinosinate• polyribocytidylate, but not by mouse interferon. The RNA product of VSV polymerase activity is present throughout the cytoplasm, and its synthesis is inhibited by the interferon system, as judged by autoradiographs that show the physical distribution, in cells, of RNA produced by virion polymerase in the absence of translation-a demonstration of the transcription product of the viral genome. ...
TY - JOUR. T1 - Terminal structures of West Nile virus genomic RNA and their interactions with viral NS5 protein. AU - Dong, Hongping. AU - Zhang, Bo. AU - Shi, Pei-Yong. PY - 2008/11/10. Y1 - 2008/11/10. N2 - Genome cyclization is essential for flavivirus replication. We used RNases to probe the structures formed by the 5′-terminal 190 nucleotides and the 3′-terminal 111 nucleotides of the West Nile virus (WNV) genomic RNA. When analyzed individually, the two RNAs adopt stem-loop structures as predicted by the thermodynamic-folding program. However, when mixed together, the two RNAs form a duplex that is mediated through base-pairings of two sets of RNA elements (5′CS/3′CSI and 5′UAR/3′UAR). Formation of the RNA duplex facilitates a conformational change that leaves the 3′-terminal nucleotides of the genome (position - 8 to - 16) to be single-stranded. Viral NS5 binds specifically to the 5′-terminal stem-loop (SL1) of the genomic RNA. The 5′SL1 RNA structure is essential for ...
HCV RNA viral load is an important predictor of sustained virological response and, recently, a significant correlation with liver fibrosis was described. We investigated on possible influence of clinical and viro-immunological variables on HCV viral load in HIV-HCV co-infected patients over a study time of three years (2009-2012). We retrospectively enrolled 98 adult patients with a diagnosis of chronic HIV infection in 2009, a diagnosis of chronic HCV infection with a detectable plasma HCV RNA in 2009 and 2012, HCV therapy-naïve or with failed and stopped antiviral treatment before June 2008. The following variables were recorded: age, gender, HCV genotype, IL28B rs12979860 CC genotype, HCV treatment status, advanced liver fibrosis diagnosis, antiretroviral therapy, CD4+ cell count, HCV viral load, HIV RNA (plasma HIV-1 RNA levels were measured from blood samples every three months at least). The correlation was established using linear regression analysis, analysis of variance and Fishers exact
Genome replication in picornaviruses is catalyzed by a virally encoded RNA-dependent RNA polymerase, termed 3D. These viruses also use a small protein primer, named VPg, to initiate RNA replication. The recent explosion of structural information on picornaviral 3D polymerases has provided insights into the initiation of RNA synthesis and chain elongation. Comparing these data with results from previous structural analyses of viral RNA-dependent RNA polymerases that catalyze de novo RNA synthesis sheds light on the different strategies that these viruses use to initiate replication. © 2006 Elsevier Ltd. All rights reserved ...
The genomic RNA of all members of the family has a similar organization and is the viral mRNA found in infected cells. It contains a single long open reading frame (ORF) flanked by 5′- and 3′-terminal non-coding regions (NCRs) that form specific secondary structures required for genome replication and translation. Members of the genus Flavivirus, but not pestiviruses, hepaciviruses or pegiviruses produce a unique, subgenomic, small (0.3-0.5 kb) non-coding RNA that is derived from the 3′-NCR of genomic RNA (Lin et al., 2004) but which is essential for virus replication in cells and modulates pathogenicity in animals. Translation-initiation of genomic RNA is cap-dependent for members of the genus Flavivirus, whereas IRES elements are present in viruses of the other genera. Viral proteins are synthesized as part of a polyprotein that is co- and post-translationally cleaved by viral and cellular proteases. The structural proteins are contained in the N-proximal portion of this polyprotein and ...
The nucleoprotein of negative-strand RNA viruses forms a major component of the ribonucleoprotein complex that is responsible for viral transcription and replication. However, the precise role of nucleoprotein in viral RNA transcription and replication is not clear. Here we show that nucleoprotein of influenza A virus is entirely dispensable for replication and transcription of short viral RNA-like templates in vivo, suggesting that nucleoprotein represents an elongation factor for the viral RNA polymerase. We also find that the recruitment of nucleoprotein to nascent ribonucleoprotein complexes during replication of full-length viral genes is mediated through nucleoprotein-nucleoprotein homo-oligomerization in a tail loop-first orientation and is independent of RNA binding. This work demonstrates that nucleoprotein does not regulate the initiation and termination of transcription and replication by the viral polymerase in vivo, and provides new mechanistic insights into the assembly and regulation of
Borna disease virus (BDV) is a non-segmented, negative-strand RNA virus that replicates and transcribes its genome in the nucleus of infected cells. It uses the cellular splicing machinery to generate a set of alternatively spliced mRNAs from the 2.8 and 7.1 kb primary transcripts, each harbouring two introns. To determine whether splicing of these transcripts is regulated by viral factors, the extent of splicing was studied in infected cells and COS-7 cells transiently transfected with plasmids encoding the 2.8 kb RNA of BDV. Unspliced RNA was found to be the most abundant RNA species in infected cells, whereas viral transcripts lacking both introns were only found in minute amounts. In sharp contrast, plasmid-derived 2.8 kb RNA was predominantly intron 1-spliced and double-spliced. Co-expression of the BDV proteins P, N and X did not influence splicing of plasmid-expressed 2.8 kb RNA. Furthermore, the splicing pattern did not change when the 2.8 kb RNA was expressed in BDV-infected cells. Based on
TY - BOOK. T1 - Viral genome replication. AU - Cameron, Craig Eugene. AU - Raney, Kevin D.. AU - Götte, Matthias. PY - 2009/1/1. Y1 - 2009/1/1. N2 - Provides the first comprehensive review of viral genome replication strategies, emphasizing not only pathways and regulation but also the structure-function, mechanism, and inhibition of proteins and enzymes required for this process Currently, there is no single source that permits comparison of the factors, elements, enzymes and/or mechanisms employed by different classes of viruses for genome replication. As a result, we (and our students) often restrict our focus to our particular system, missing out on the opportunity to define unifying themes in viral genome replication or benefit from the advances in other systems. For example, extraordinary biological and experimental paradigms that have been established over the past five years for the DNA replication systems of bacteriophage T4 and T7 will likely be of great value to anyone interested in ...
During assembly of the human immunodeficiency virus type 1 (HIV-1), two copies of the intact, unspliced viral RNA genome are efficiently incorporated into virions, whereas host RNAs and spliced viral RNAs are excluded. Packaging is mediated by interactions between the nucleocapsid (NC) domain of the viral Gag polyproteins and the packaging segments located in the highly conserved 5-untranslated region (5-UTR) of the RNA genome. Current understanding of the structural determinants of the diploid genome selection and packaging by HIV-1 remains limited, in part due to the lack of high-resolution structural information about the 5-UTR. We hypothesized that diploid genome selection is mediated by a dimerization-dependent RNA structural switch mechanism, in which the NC binding sites are sequestered in the monomeric RNA, and become exposed upon dimerization. In our efforts to test this hypothesis, we found that RNA dimerization through the dimer-promoting hairpin (DIS) per se does not alter the RNA ...
Viruses depend on their host cell for the production of their progeny. The genetic information that is required to regulate this process is contained in the viral genome. In the case of plus-stranded RNA viruses, like nidoviruses, the RNA genome is directly involved in translation (resulting in the synthesis of viral enzymes), replication, transcription and encapsidation into progeny virions. The multifunctional nature of these viral RNA genomes requires the tight control of all these processes for which they are equipped with RNA sequence motifs and higher order RNA structures. At 25-32 kilobases, nidoviruses possess the largest known RNA genomes. One characteristic of nidoviruses is that in infected cells they produce a nested set of subgenomic (sg) mRNAs. The sg mRNAs of two nidovirus families, arteri- and coronaviruses, consist of two RNA stretches that are noncontiguous in the genome. It was demonstrated that primary and higher order RNA structures play a crucial role during the synthesis ...
Overall, only 68% of patients who achieved an optimally defined EVR (2 log10 unit decline in HCV RNA) had an SVR. For several reasons, this definition of an EVR does not guarantee eradication of virus. First, not surprisingly, the positive predictive value decreases as the definition of EVR is made less rigorous. This simply reflects the fact that patients who have a less pronounced decrease in virus (e.g., a 2 log10 unit decline only) have a lower chance of a sustained response. Indeed, SVRs were achieved in 80% of patients who were HCV RNA negative at week 12 of treatment, but in only 40% in those who had a 2 log10 unit decline in HCV RNA level while remaining HCV RNA positive (data not shown). Fortunately, the majority of subjects with an EVR (greater than a 2 log10 unit decrease) at 12 weeks were HCV RNA negative (89%). At issue is whether the 11% of patients who achieve an EVR by 12 weeks but are still HCV RNA positive should be retested at 24 weeks to assess continued positivity and ...
Quantification of the 5 noncoding region of the genomic and antigenomic HCV RNA strands was done using a strand-specific real-time RT-PCR, with use of the thermostable enzyme Tth for the synthesis of cDNA at a high temperature. Thus, for the amplification of the genomic HCV RNA strand, cDNA was generated in 20 L of reaction mixture that contained the total RNA extracted from 200 uL of serum or 0.5 ug of total RNA from liver specimens or PBMC samples, 50 pmol/L antisense primer UTRLC2 (5-CAAGCACCCTATCAGGCAGT-3), 1 mmol/L MnCl2, 200 umol/L each deoxynucleotide triphosphate, 1X RT buffer (Applied Biosystems), and 5 U of Tth (Applied Biosystems). After 20 min at 65 C, the RT activity was inactivated by Mn2+ chelation with 8 uL of the 10X chelating buffer (Applied Biosystems), followed by heating at 95 C for 30 min. For amplification of antigenomic HCV RNA, cDNA was synthesized under the same conditions by the addition of 50 pmol/L sense primer UTRLC1 (5-CTTCACGCAGAAAGCGTCTA-3). Real-time PCR was ...
An in situ molecular hybridization system which will detect retrovirus RNA in the cytoplasm of individual virus-infected cells has been developed. The technique was applied to cells infected with simian sarcoma-leukemia virus, where the virus-specific RNA was detected by hybridization to simian sarcoma-leukemia virus 3H-labeled complementary DNA. The system is useful for detecting viral RNA-containing cells in the presence of an excess of virus-negative cells and for determining which type of cell in a heterogenous population is expressing viral RNA.
RNA-dependent RNA polymerase which is responsible for replication and transcription of virus RNA segments. The transcription of viral mRNAs occurs by a unique mechanism called cap-snatching. 5 methylated caps of cellular mRNAs are cleaved after 10-13 nucleotides by PA. In turn, these short capped RNAs are used as primers by PB1 for transcription of viral mRNAs. During virus replication, PB1 initiates RNA synthesis and copy vRNA into complementary RNA (cRNA) which in turn serves as a template for the production of more vRNAs.
All viruses utilize host cell machinery to synthesize their own genetic materials. Upon entry into cells, the virus has to initiate replication and gene expression. Paramyxoviruses use a unique strategy for replication and gene expression. The active template for paramyxovirus replication is not the naked RNA genome but the protein and RNA complex. Viral genomic RNA is completely encapsidated by the nucleocapsid (N) protein to form an N-RNA complex. During RNA synthesis, the N-RNA template is recognized by viral RNA-dependent RNA polymerase (RdRp) that carries out two distinct processes: (i) transcription to yield 6-10 capped, methylated and polyadenylated messenger RNAs and (ii) replication to yield full-length antigenomic and subsequently genomic RNA.. Our lab uses hMPV and aMPV as models to understand the mechanisms by which the RdRp controls these two processes: replication and transcription. We will focus on the two major components of RdRp, the large protein catalytic subunit (L) and the ...
Alphaviruses have a positive-stranded RNA genome that can serve as the mRNA for translation of the polyprotein precursor that is autocatalytically processed to the four non-structural viral proteins by the virus-encoded protease in nsP2. The non-structural proteins form the transcription/replication complex. The nsP1 protein is implicated in capping of viral RNAs. The nsP2 gene encodes a putative helicase and a protease , which presents a unique fold distantly related to that of known cysteine proteases. This protease domain is linked to the downstream domain of degenerated O-methyltransferase fold that may regulate transcription/replication through RNA binding. The nsP3 protein is required for RNA replication. Its N-terminal sequence reveals a macro domain, the crystal structures of which have recently been determined (Malet et al., 2009). The nsP4 protein carries the viral RNA dependant RNA Polymerase (RdRP), the key activity for the viral replication/transcription. Unlike the RdRP of ...
TY - JOUR. T1 - In vitro activation of HIV RNA expression in peripheral blood lymphocytes as a marker to predict the stability of non-progressive status in long-term survivors. AU - Garbuglia, Anna R.. AU - Salvi, Roberto. AU - Di Caro, Antonino. AU - Cappiello, Giuseppina. AU - Montella, Francesco. AU - Di Sora, Fiorella. AU - Recchia, Olga. AU - Lauria, Filippo. AU - Benedetto, Arrigo. PY - 1996. Y1 - 1996. N2 - Objectives: We investigated a selected group of 11 non-progressor, HIV-infected individuals 20 months prior to this study and found that they all had undetectable levels of viral RNA expression in their peripheral blood lymphocytes (PBL). Phorbol 12-myristate 13-acetate (PMA) and phytohaemagglutinin (PHA) stimulation of PBL produced easily detectable amounts of HIV RNA in only two out of five of these patients. Here we report the results of the virological and clinical follow-up of nine non-progressors from this group. We verified the stability of their non-progressive status and ...
1) If the HCV antibody test is positive, or in immunocompromised people, send a blood sample for HCV RNA to check if HCV infection is active and a genotype analysis.. 2) If the HCV RNA test is positive, send a repeat sample for confirmation. A positive HCV RNA result means the person has current infection with active hepatitis C. 3) If the HCV RNA result is negative, repeat the test after a period of 6 months. If the negative result is confirmed, this means the person has a previously resolved HCV infection, but they are not immune to future HCV infection. 4) Chronic infection is confirmed if HCV RNA is positive 6 months after the first positive test. ...
Registrations are now being accepted for the *VIZIER / SPINE2 Workshop on Structural Virology* taking place from 14th - 16th July 2008, in Vienna, Austria This workshop will cover recent advances in our understanding of viral entry, assembly, replication and pathogenesis principally, but not exclusively, based upon information derived from structural studies. The planned sessions are on viral assembly, double-stranded RNA viruses, the flavivirus replication machinery, the coronavirus replication machinery, virus/host interactions including aspects of viral entry, negative strand RNA viruses and viruses of prokaryotes and archea. In addition to the invited speakers, oral presentations will be selected from the submitted abstracts. The sessions are not exclusive and any topic relevant to the structural biology of viruses will be considered for a poster or oral presentation. For this reason early registration and abstract submission is strongly encouraged. The workshop is part of the training and ...
The regional metabolism of high-molecular-weight RNA in the developing female rat brain was investigated after the intracranial injection of [32P]P1. The synthesis of polyadenylated RNA relative to high-molecular-weight RNA was determined after oligo(dT)-cellulose chromatography of total cellular high-molecular-weight RNA labelled after 4h. In both hypothalamus and cortex this synthesis was significantly higher during the first 10 days post partum than at subsequent ages. In both regions apparently more mRNA is synthesized in the young. The ratio of the specific radioactivity of cytoplasmic high-molecular-weight RNA relative to that of the nucleus, measured after a 48 h period of labelling, was considered to be an index of the nucleocytoplasmic transport of newly synthesized RNA [Berthold & Lim (1976) Biochem. J. 154, 529-539]. In the cortex, nucleo-cytoplasmic RNA transport in rats aged up to 20 days was significantly higher than in older rats, with the maximal value being attained between 16 ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Epstein-Barr virus (EBV) associated cancers have traditionally been thought to harbor the viral genomes as nuclear plasmids in all or nearly all of a patients tumor cells as determined by in situ hybridization (ISH). We discovered EBV in 4 out of 7 standard multiple myeloma (MM) cell lines. In these positive cell lines, EBV was found in only a subpopulation of cells. For example, in MM.1S (a MM cell line) less than 1% of the cells harbored viral DNA as determined by limiting dilution PCR. These rare infected cells carried approximately 20 EBV copies. Fluorescence in situ hybridization (FISH) confirmed the presence of multiple copies of the EBV genome in rare cells. Immunofluorescence similarly detected the presence of viral genomes expressing EBV nuclear antigen (EBNA) - 1 and 2 in rare cells. Reverse transcriptase PCR confirmed EBNA1 and EBNA2 viral RNA expression. The cells that harbor virus are phenotypically distinct CD19+CD138− B cells. The phenotype overlaps with that identified as a MM ...
Authors response : This has been revised throughout the text. However, we find the genome arrangement to be strikingly different from most circoviruses, thus have retained Figure1.. Reviewers report 2: Dr. Mart Krupovic (nominated by Dr. Patrick Forterre) (Institut Pasteur, France): Diemer and Stedman report on characterization of a putative viral genome, which has been obtained in the course of a metagenomic analysis of virome samples collected at the Boiling Springs Lake. The putative viral genome (BSL-RDHV) encodes four proteins, two of which share sequence similarity with proteins from previously characterized viruses. One of these proteins is related to typical superfamily II rolling circle replication initiation proteins that are abundantly found in DNA viruses and plasmids. Strikingly, the other one is most similar to capsid proteins of eukaryotic icosahedral positive-sense RNA viruses. The observation that genes for two key viral functions- virion formation and genome replication-are ...
When a virus infects a cell, its goal is to make more virus particles. To do this, a virus takes over the cells protein making machinery (the ribosome), so that the cell essentially becomes a viral protein factory. It does this by using an internal ribosome entry site (IRES); which shuts down and bypasses the normal mechanisms that regulate binding of messenger RNAs to ribosomes. While many viral messenger RNAs are known to possess an IRES, few normal cellular RNAs do. Abnormal IRES regulation has been correlated with two human diseases- multiple myeloma and Charcot-Marie-Tooth disease. This is the first time that scientists have demonstrated that normal nerve cells can use an IRES to produce large quantities of protein under physiological conditions ...
TY - JOUR. T1 - Analysis of the CIS-acting elements of coronavirus transcription. AU - Joo, M.. AU - Makino, Shinji. PY - 1994. Y1 - 1994. UR - http://www.scopus.com/inward/record.url?scp=0028326927&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=0028326927&partnerID=8YFLogxK. M3 - Article. VL - 342. SP - 91. EP - 97. JO - Advances in Experimental Medicine and Biology. JF - Advances in Experimental Medicine and Biology. SN - 0065-2598. ER - ...
This is the place of all things RNA related. RNA Analysis workflow products include RNA purification systems, RNasin protection, fluorescent RNA quantitation dyes and fluorometers, as well as all-inclusive kits for RT-PCR. Youll also find Riboprobe and other in vitro transcription kits in this product category.
This is an application for renewal of a grant to study picornavirus genome replication. All positive-strand RNA viruses hijack and/or remodel host membranes to...
This chapter will take up two types of bipolar items in Japanese to identify various factors that contribute to polarity sensitivity. It has been well known since Fauconnier (1975) that scalar semantics is closely related to licensing of negative polarity items. There are indeed languages like Dutch and Hindi that have negative polarity items overtly marked with a scalar focus particle. The chapter show that there are other morphological characteristics that play important roles in polarity sensitivity. Furthermore, the chapter suggest that the relation between negative concord and negative polarity must be taken into account when concord items and polarity items are morphologically very similar.
In con-trast to HBV, HDV infec-tion induces pro-found innate immune response which is medi-at-ed by pat-tern recog-ni-tion recep-tor MDA5 (Zhang, et al. 2018. J Hepa-tol. 69:25-35). MDA5 is a cytosol sen-sor usu-al-ly rec-og-niz-ing long dou-ble strand RNA (dsR-NA). How-ev-er, unlike oth-er RNA virus-es, HDV repli-cates its RNA in the nucle-us via a unique dou-ble-rolling-cycle mech-a-nism with-out pro-duc-ing long dsR-NA. Inves-ti-gat-ing the innate immune acti-va-tion dur-ing HDV repli-ca-tion will pro-vide impor-tant insights for under-stand-ing MDA5 medi-at-ed innate immune sens-ing of viral RNA. To this aim, we plan to: (i) iden-ti-fy the HDV RNA lig-and rec-og-nized by MDA5; (ii) deter-mine the sub-cel-lu-lar loca-tion of MDA5-HDV RNA inter-ac-tion; and (iii) elu-ci-date the roles of host fac-tors (LGP2, ADAR1, etc.) and viral fac-tors (HDAg and HBV enve-lope pro-teins) in the process of innate immu-ni-ty acti-va-tion.. Long term per-sis-tence of HBV and HDV makes it chal-leng-ing to ...
SLAMseq can differentiate between newly synthesized (nascent) RNA and existing RNA, while standard RNA-Seq measures total steady-state RNA levels only.. Compared to standard RNA-Seq the SLAMseq protocol adds only two extra steps: labeling of the RNA by adding one compound to the culture medium and pre-processing the total RNA before continuing with a standard RNA-Seq protocol.. SLAMseq. ...
TY - JOUR. T1 - Hepatitis C virus RNA quantification in right and left lobes of the liver in patients with chronic hepatitis C. AU - Idrovo, V.. AU - Dailey, P. J.. AU - Jeffers, Lennox J. AU - Coelho-Little, E.. AU - Bernstein, D.. AU - Bartholomew, M.. AU - Alvarez, L.. AU - Urdea, M. S.. AU - Collins, M. L.. AU - Schiff, Eugene R. PY - 1996/9/1. Y1 - 1996/9/1. N2 - Quantification of hepatitis C virus RNA in liver tissue is likely to be useful in the study of the natural history, pathogenesis, progression and treatment of hepatitis C virus-associated liver disease. Quantitative measurements of hepatitis C virus RNA in liver biopsy samples using the branched DNA (bDNA) signal amplification assay were carried out. The aims of this study were threefold: first, to assess the level of hepatitis C virus RNA in biopsy samples from the right and left lobes of the liver; second, to evaluate the correlation between hepatitis C virus RNA levels in serum and liver; and third, to investigate the ...
Plant Dicer-like (DCL) enzymes exhibit a GC-preference during anti-viral post-transcriptional gene silencing (PTGS), delivering an evolutionary selection pressure resulting in plant viruses with GC-poor genomes. However, some viruses, e.g. Turnip Yellow Mosaic Virus (TYMV, genus Tymovirus) have GC-rich genomes, raising the question as to whether or not DCL derived selection pressure affects these viruses. In this study we analyzed the virus-derived small interfering RNAs from TYMV-infected leaves of Brassica juncea showed that the TYMV population accumulated a mutational bias with AU replacing GC (GC-AU), demonstrating PTGS pressure. Interestingly, at the highly polymorphic sites the GC-AU bias was no longer observed. This suggests the presence of an unknown mechanism preventing mutational drift of the viral population and maintaining viral genome stability, despite the host PTGS pressure.. ...
Satellite tobacco necrosis virus. Computer illustration showing the surface structure of a tobacco necrosis satellivirus particle (virion) rendered with wireframes. Satellite viruses are subviral agents consisting of a nucleic acid core surrounded by a protein coat (shown here). They cannot infect host cells without a helper virus, which in this case is the tobacco necrosis virus. - Stock Image C035/7834
We have investigated the usefulness of serum hepatitis delta virus (HDV) RNA detection using a slot hybridization analysis of serum samples from ten patients with acute hepatitis and delta markers (group I), from 28 patients with chronic delta hepatitis (group II) and from seven liver graft recipients with hepatitis B virus (HBV) and HDV related cirrhosis or fulminant hepatitis (group III). The slot-blots were hybridized with both HDV-complementary DNA and single-stranded RNA probes. With the single-stranded RNA probe, HDV RNA was detected in the first serum sample available in 9/10 of the patients with acute hepatitis (group I). In addition, HDV RNA was detected in 8/9 and 7/8 of the samples obtained within and after 1 month of the onset of hepatitis. Five of the ten patients scored positive for HDV RNA and negative for hepatitis delta antigen (HDAg) while one was negative for HDV RNA and positive for HDAg. The same RNA probe enabled the detection of serum HDV RNA in 21/28 chronic hepatitis ...
Avian encephalomyelitis virus (AEV) is a picornavirus that affects young chickens, quails, pheasants and turkeys. Translation initiation on picornavirus mRNA is cap independent and occurs through a mechanism known as internal initiation, which depends on Internal Ribosome Entry Site (IRES) element within the 5 untranslated region (UTR) of the viral RNA. AEV has been assigned within the Hepatovirus genus and shares protein sequence similarity with hepatitis A virus (HAV). I have demonstrated that the 494 nucleotide 5 UTR of the AEV genome contains an internal ribosome entry site (IRES) element. However, in contrast to the HAV IRES, the AEV IRES functions efficiently in the presence of cleaved eEF4G, suggesting functional differences exist. Characterization of the AEV IRES element revealed that there are remarkable structural and functional similarities between the AEV, flavivirus [especially hepatitis C virus (HCV)] and newly discovered type 4 picornaviras IRES elements, including porcine ...
BACKGROUND Hepatitis delta virus is a unique human pathogen responsible for some 20 million infections globally. This virus is dependent on hepatitis B virus for transmission and propagation. Currently, at least three genotypes of hepatitis delta virus with different geographic distribution and clinical manifestations are described. METHODS In this study, hepatitis delta virus RNA of 35 patients sera were analyzed by RT- semi-nested polymerase chain reaction. Based on genomic differences of hepatitis delta antigen coding region of hepatitis delta virus RNA among hepatitis delta virus RNA-positive sera, the polymerase chain reaction products were digested with restriction enzymes and studied by restriction fragment length polymorphism. RESULTS Out of 35 samples, 13 (38.46%) were positive for hepatitis delta virus RNA by RT- semi-nested polymerase chain reaction. All polymorphisms were shown to be genotype I. Out of 13 hepatitis delta virus RNA-positive (13/35), eight were HBeAg negative.
Hepatitis C is a common cause of chronic liver disease but is rarely associated with acute hepatitis. The majority of patients have no clinical symptoms and jaundice in this phase of acute viral hepatitis C. Clinical symptoms are not difference with other types of hepatitis [2]. It is necesseray to treat acute hepatitis C infection. HCV infection becomes chronic in about 85 % of individuals as demonstrated by the persistence of HCV. HCV is the major cause of cirrhosis and hepatocellular carcinoma [2]. Interferon-α is effective in improving biochemical outcomes and achieving sustained virologic clearance in patients with acute hepatitis C [3]. If acute infection is confirmed (with or without acute hepatitis), recent data suggest that early treatment of acute HCV infection with interferon-α may be highly effective in preventing chronic HCV infection [1]. These data underscore the importance of identifying persons with acute HCV infection and promptly referring them to experienced clinicians who ...
They promote viral RNA destruction. MicroRNA attach to viral-RNA because they are complementary. Then the complex is recognised ... Micro-RNA[edit]. MicroRNA are small RNA fragments produced in the host cells thanks to a specific enzymatic mechanism. ... Viral replication is nuclear. DNA-templated transcription is the method of transcription. The virus exits the host cell by ... Wasps perhaps use microRNA to control the viral genes they carry.. *PolyDNAvirus can also use PTGS to interfere with the host's ...
Positive stranded RNA virus transcription is the method of transcription. Translation takes place by viral initiation, and ... "Viral Zone". ExPASy. Retrieved 15 June 2015. Kanamori, Y; Nakashima N (2001). "A tertiary structure model of the internal ... Many of the Dicistroviridae genomes contains structured RNA elements. For example, the Cripaviruses have an internal ribosome ... Replication follows the positive stranded RNA virus replication model. ...
Viral genomes, which are usually RNA, take over the cell machinery and make both new viral RNA and the protein coat of the ... They are transfer RNA (tRNA) and ribosomal RNA (rRNA). tRNA[change , change source]. Transfer RNA (tRNA) is a short molecule of ... RNA is physically different from DNA: DNA contains two intercoiled strands, but RNA only contains one single strand. RNA also ... Protein synthesis RNAs[change , change source]. Messenger RNA[change , change source]. The structure of a mature eukaryotic ...
Rev-directed export of viral RNAs is similar to the mechanism by which snRNAs and the 5s rRNAs are exported, as opposed to the ... Binding of Rev to viral RNAs containing the RRE allows for mRNA export out of the nucleus and into the cytoplasm by a mechanism ... Hope, TJ (May 1997). "Viral RNA export". Chemistry and Biology Journal. 4 (5): 335-344. doi:10.1016/s1074-5521(97)90124-1. PMID ... HIV-1 genes are expressed from either completely spliced RNA or from intron-containing RNA. The export of fully spliced mRNAs ( ...
Replication follows the positive stranded RNA virus replication model. Positive stranded rna virus transcription is the method ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Viralzone: ...
Positive stranded RNA virus transcription is the method of transcription. Translation takes place by leaky scanning, and RNA ... Viral replication is cytoplasmic. Entry into the host cell is achieved by attachment to host receptors, which mediates ... Feline calicivirus "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. ... They are positive-sense, single stranded RNA which is non-segmented. There are currently seven species in this family, divided ...
Replication follows the positive stranded RNA virus replication model. Positive stranded rna virus transcription is the method ... Viral replication is cytoplasmic. Entry into the host cell is achieved by attachment of the virus to host receptors, which ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Jones, MS.; Lukashov ... Translation takes place by -1 ribosomal frameshifting, viral initiation, and ribosomal skipping. The virus exits the host cell ...
Positive stranded rna virus transcription is the method of transcription. The virus exits the host cell by tubule-guided viral ... Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. Replication follows ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. ICTV Taxonomy ... the positive stranded RNA virus replication model. ...
Replication follows the positive stranded RNA virus replication model. Positive stranded RNA virus transcription is the method ... Viral replication is cytoplasmic. Entry into the host cell is achieved by attachment of the virus to host receptors, which ... "Viral meningitis in Kansas City-area babies probed". The Kansas City Star. The Associated Press. August 13, 2014. Viralzone: ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Shakeel, Shabih; ...
Viral replication is cytoplasmic. Entry into the host cell is achieved by attachment of the viral G glycoproteins to host ... Replication follows the negative stranded RNA virus replication model. Negative stranded rna virus transcription, using ... The virus exits the host cell by budding, and tubule-guided viral movement. Plants serve as the natural host. The virus is ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Afonso, Claudio L.; ...
Viral replication is nuclear. Entry into the host cell is achieved by attachment of the viral GP glycoproteins to host ... Replication follows the negative stranded RNA virus replication model. Negative stranded RNA virus transcription, using ... The viral family is named after the city of Borna in Saxony, Germany, which is where a large number of animals were lost to the ... "Viral Zone". ExPASy. Retrieved 12 June 2015. Amarasinghe, Gaya K.; Bào, Yīmíng; Basler, Christopher F.; Bavari, Sina; Beer, ...
Replication follows the positive stranded RNA virus replication model. Positive stranded RNA virus transcription is the method ... Viral replication is cytoplasmic. Entry into the host cell is achieved by attachment of the virus to host receptors, which ... "Viral Zone". ExPASy. Retrieved 13 August 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 13 August 2015. Viralzone: ...
Replication follows the positive stranded RNA virus replication model. Positive stranded rna virus transcription is the method ... ". "Viral Zone". ExPASy. Retrieved 15 June 2015. Kelly AG, Netzler NE, White PA (2016) Ancient recombination events and the ...
Viral replication is cytoplasmic. Replication follows the double-stranded RNA virus replication model. Double-stranded RNA ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Peever, Tobin; Liu, ... "Hypovirulence of Chestnut Blight Fungus Conferred by an Infectious Viral cDNA". Science. 257: 800-803. doi:10.1126/science. ...
Replication follows the positive stranded RNA virus replication model. Positive stranded rna virus transcription is the method ... Viral replication is cytoplasmic, and is lysogenic. Entry into the host cell is achieved by penetration into the host cell. ... The virus exits the host cell by tripartite non-tubule guided viral movement. Plants serve as the natural host. Transmission ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Viralzone: ...
Positive stranded RNA virus transcription, using the premature termination model of subgenomic RNA transcription is the method ... Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. Replication follows ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Wu, J. X.; Wang, Q; ... The virus exits the host cell by tubule-guided viral movement. Plants serve as the natural host. Transmission routes are ...
"Tentative identification of RNA-dependent RNA polymerases of dsRNA viruses and their relationship to positive strand RNA viral ... ribosomal RNA (rRNA), transfer RNA (tRNA), or other enzymatic RNA molecules called ribozymes.[1] Overall, RNA helps synthesize ... RNA synthesis by RNA polymerase was established in vitro by several laboratories by 1965; however, the RNA synthesized by these ... RNA sugar-phosphate backbone forms with assistance from RNA polymerase to form an RNA strand. ...
Viral replication is cytoplasmic. Replication follows the double-stranded RNA virus replication model. Double-stranded rna ... They were able to identify viral plaques from this and then subsequently sequence their genomes. "ICTV Report Cystoviridae". " ... "Viral Zone". ExPASy. Retrieved 15 June 2015. "NCBI Taxonomy Browser: Cystoviridae". NCBI. Retrieved 19 June 2016. Silander OK, ... "Intermediates in the assembly pathway of the double-stranded RNA virus phi6". EMBO J. 16 (14): 4477-87. doi:10.1093/emboj/16.14 ...
Positive stranded RNA virus transcription is the method of transcription. Fungi serve as the natural host. "Viral Zone". ExPASy ... Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. Replication follows ... the positive stranded RNA virus replication model. ...
Viral replication is cytoplasmic. Replication follows the positive stranded RNA virus replication model. Positive stranded RNA ... There are currently only two species in this genus including the type species Saccharomyces 20S RNA narnavirus. Genomes are ... "Viral Zone". ExPASy. Retrieved 15 June 2015. Viralzone: Narnavirus ICTV. ...
Replication follows the double-stranded RNA virus replication model. Double-stranded rna virus transcription is the method of ... Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Viralzone: ...
4th step: Minus- strand RNAs are synthesized.. *5th step: Plus- strand RNAs and viral proteins are synthesized. Virions ... RNA 2 and RNA 3) and a subgenomic RNA (RNA 4) which is obtained by transcription of the negative- sense strand of RNA 3. RNA 1 ... RNA 4 encodes the capsid. Beside encapsidation and its role in movement the viral coat protein also plays a role in the ... Tenllado F.; Bol J. (2000). "Genetic dissection of the multiple functions of alfalfa mosaic virus coat protein in viral RNA ...
... interaction with host RNA 3. APOBEC3G interaction with viral RNA 4. Interaction of APOBEC3G with HIV-1 Gag proteins. ... It is predicted that reverse transcription is also negatively affected by APOBEC3G binding to viral RNA and causing steric ... thus leading to aberrant viral 3' long terminal repeat (LTR) DNA ends. These viral DNA ends are inefficient substrates for ... CD1 is catalytically inactive, but very important for binding to DNA and RNA and is key to defining the 5'->3' processivity of ...
Viral escape from antisense RNA. Mol. Microbiol. 28:835-846. Hibma, A. M., S. A. Jassim, and M. W. Griffiths. 1997. Infection ... Viral escape from Merril, C. R., B. Biswas, R. Carlton, N. C. Jensen, G. J. Creed, S. Zullo, and S. Adhya. 1996. Long- ... Evolvability of an RNA virus is determined by its mutational neighbourhood. Nature 406:625-628. Wichman, H. A., L. A. Scott, C ... Altered 3'-terminal RNA structure in phage Q_ adapted to host factor-less Escherichia coli. Proc. Natl. Acad. Sci. USA 94:10239 ...
Viral replication is cytoplasmic. Replication follows the double-stranded RNA virus replication model. Double-stranded rna ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Dolja, Valerian V ( ... 2001). "Capsid-Less RNA Viruses". eLS. doi:10.1002/9780470015902.a0023269. ICTVdB Management (2006). 00.108.0.01. Endornavirus ...
6. Late genes are now transcribed by the host's RNA polymerase. 7. Synthesis of the new virons Viral protein C binds to ... Replication of the viral genome Viral protein A cleaves replicative form I DNA strand at the origin of replication (ori) and ... Unlike protein A it is capable of cleaving the phi X viral DNA in the presence of single-stranded binding protein of the host. ... There are a number of steps in the life cycle 1. Adsorption to the host via specific receptor(s) 2. Movement of the viral DNA ...
Xin-Cheng Qin et al.: A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors, in: ... 3 RNA-Viren *3.1 Doppelsträngige RNA-Viren (dsRNA, double stranded RNA). *3.2 Einzelstrang-RNA-Viren mit negativer Polarität ( ... ss(−)RNA: negative single-stranded RNA). *3.3 Einzelstrang-RNA-Viren mit positiver Polarität (ss(+)RNA: positive single ... Einzelstrang-RNA-Viren mit negativer Polarität (ss(−)RNA: negative single-stranded RNA)[Bearbeiten , Quelltext bearbeiten]. ...
RNA editing APOBEC3G Viral infectivity factor Michael Wentzel (12 January 2004). "UR Invests in Anti-HIV Startup". Rochester ... The company is also researching drugs that protect A3G from Viral infectivity factor (ViF). ViF is a protein created by HIV ... James H Miller; Vlad Presnyak; Harold C Smith (27 July 2007). "The dimerization domain of HIV-1 viral infectivity factor Vif is ... A3G combats HIV infection by interacting with and mutating the virus' RNA. The mutations genetically damage the virus protein ...
ABSTRACT: Betanodaviruses, the causative agents of viral nervous necrosis in marine fish, have bipartite positive-sense RNA ... although the primary structures of the viral RNAs and encoded proteins are similar among the viruses. We have previously ... KEY WORDS: Betanodavirus · Host specificity · Viral nervous necrosis · Chimeric virus · RNA2 · T4 region · SJNNV · RGNNV ...
The endoribonucleolytic cleavage of viral RNA is important not only for viral RNA degradation but for RNA recombination as well ... RNA degradation, together with RNA synthesis, controls the steady-state level of viral RNAs in infected cells. ... Viruses change rapidly due to genetic mutations, and viral RNA recombination in RNA viruses can lead to the emergence of drug- ... Role of RNase MRP in viral RNA degradation and RNA recombination.. Jaag HM, Lu Q, Schmitt ME, Nagy PD. ...
Sardanyés J. (2014) Viral RNA Replication Modes: Evolutionary and Dynamical Implications. In: Corral Á., Deluca A., Font-Clos F ... J. Sardanyés, F. Martínez, J.A. Daròs, S.F. Elena, Dynamics of alternative modes of RNA replication for positive-sense RNA ... L. Chao, C.U. Rang, L.E. Wong, Distribution of spontaneous mutants and inferences about the replication mode of the RNA ... F. Martínez, J. Sardanyés, J.A. Daròs, S.F. Elena, Dynamics of a plant RNA virus intracellular accumulation: stamping machine ...
These modifications -- chemical tags known as methyl groups -- influence viral replication and the human immune response. ... of California San Diego School of Medicine have discovered that Zika virus infection leads to modifications of both viral and ... the researchers removed the human enzymes responsible for adding methyl groups to viral RNA. Without m6A, the viral RNA was ... the cell modifies viral RNA with m6A as a means to get rid of the infection. RNA tagged with m6A is a beacon for human enzymes ...
Replicon RNA vectors have also been subjected to clinical trials. Overall, immunization with self-replicating RNA viruses ... Immunization of mice, chicken, pigs and primates with virus-like particles, naked RNA or layered DNA/RNA plasmids has provided ... Administration of replicon RNA vectors has resulted in strong immune responses and generation of neutralizing antibodies in ... Moreover, recombinant particles and replicon RNAs have been encapsulated by liposomes to improve delivery and targeting. ...
Many RNA viruses are known to be associated with gastroenteritis; however, the enteric RNA viral community present in healthy ... and viral RNA was extracted and cloned into shotgun viral cDNA libraries for sequencing analysis. The vast majority of the ... RNA viral community in human feces: prevalence of plant pathogenic viruses.. Zhang T1, Breitbart M, Lee WH, Run JQ, Wei CL, Soh ... C) RNA viruses were directly detected by RT-PCR from the total RNA of fecal sample 2: PMMV (lane 1), MCMV (lane 2), PBV, ...
Bevilacqua »HIV-1 genome »Molecular Biology »PKR »RNA »RNA dimers »TAR »double-stranded RNAs »genetic material »human cells » ... Further reports about: , Bevilacqua , HIV-1 genome , Molecular Biology , PKR , RNA , RNA dimers , TAR , double-stranded RNAs , ... One way for this to happen is for the viral RNA to first form linked pairs called dimers. These RNA dimers then allow separate ... Link uncovered between viral RNA and human immune response. 06.08.2009. In its fight against an intruding virus, an enzyme in ...
A) Viral RNA and viral replication protein (3A, 3Dpol) subcellular distribution in early stages of CVB3 RNA replication.. (B) ... Viral RNA and viral replication protein (3A, 3Dpol) subcellular distribution at peak stages of CVB3 RNA replication. See also . ... J and K) PI4KIIIβ activity regulates viral RNA synthesis. Cell-free PV RNA translation (J) and synthesis (K) assays performed ... Viral reorganization of the secretory pathway generates distinct organelles for RNA replication.. Hsu NY1, Ilnytska O, Belov G ...
Abstract RNA interference (RNAi) is a powerful gene silencing mechanism that if properly harnessed has the potential to ... Delivery of inhibitory RNAs to target tissues needs to be safe, efficient, and for many diseases, long-lasting, in order to ... Viral vector systems, based on adeno-associated viruses and lentiviruses, are ideally suited to mediate RNAi because they can ... Abstract RNA interference (RNAi) is a powerful gene silencing mechanism that if properly harnessed has the potential to ...
quantitative viral RNA assay - (Jun/08/2001 ). Id like to determine viral RNA level changes in virus producing cell culture ...
The PureLink Viral Mini Kit is specifically designed to isolate high-q ... The PureLink Viral RNA/DNA Mini Kit provides a rapid and efficient method to simultaneously purify viral RNA/DNA from fresh or ... The PureLink® Viral RNA/DNA Mini Kit provides a rapid and efficient method to simultaneously purify viral RNA/DNA from fresh or ... The PureLink® Viral RNA/DNA Mini Kit contains enough reagents for 50 reactions.. Kit Contents:. • 32 ml Viral Lysis buffer (L22 ...
The nucleotide sequence of the gene from which messenger RNA mole- cules are transcribed is in a form that can be translated by ... The Interactions of Viral Proteins with Rous Sarcoma Virus RNA and Possible Control of Reverse Transcription, Translation and ... The Interaction between Viral Messenger RNA and Eukaryotic Initiation Factor 2, a Protein Involved in Translational Control ... This volume is devoted to current studies in the field of cellular and viral messenger RNA. The studies presented provide an ...
RNA-Seq) offers an unbiased approach for analyzing and quantifying bacterial, viral, and other microbial transcripts. ... RNA-Seq for Microbial Transcript Analysis. Bacterial, viral, and other microbial RNA-Seq experiments enable annotation and ... Note: If using the TruSeq RNA library prep kit, you will NOT need to extract RNA and transcribe to cDNA. If you use an RNA ... Next-generation RNA sequencing (RNA-Seq) of bacteria, viruses, and other microbes has become a standard method for analyzing ...
A Viral RNA Structural Element Alters Host Recognition of Nonself RNA Message Subject. (Your Name) has forwarded a page to you ... A Viral RNA Structural Element Alters Host Recognition of Nonself RNA. By Jennifer L. Hyde, Christina L. Gardner, Taishi Kimura ... A Viral RNA Structural Element Alters Host Recognition of Nonself RNA. By Jennifer L. Hyde, Christina L. Gardner, Taishi Kimura ... As an example, 2-O methylation of the 5′ cap of viral RNA subverts mammalian antiviral responses by evading restriction of ...
Thermo Scientific MagJET Viral DNA and RNA Kit For 96 preparations Life Sciences:Biochemicals and Reagents:DNA Extraction and ... Thermo Scientific MagJET Viral DNA and RNA Kit Purifies viral nucleic acids from human and animal samples, including plasma, ... Quality Control:The MagJET Viral DNA and RNA Kit has been tested by isolating DNA and RNA from 200 µL of human plasma spiked ... The Thermo Scientific MagJET Viral DNA and RNA Kit is designed for fast and efficient purification of viral nucleic acids from ...
A new study by University of Kentucky researchers shows promise for developing ultrastable RNA nanoparticles that may help ... treat cancer and viral infections by regulating cell function and binding to cancers without harming surrounding tissue. ... Their RNA nanoparticles can include small interfering RNA for silencing genes, micro-RNA for regulating gene expression, ... New study shows promise in using RNA nanotechnology to treat cancers and viral infections. University of Kentucky ...
Buy Nuclear Export of Viral RNAs by Joachim Hauber, P. K. Vogt from Waterstones today! Click and Collect from your local ... Nuclear Export of Viral RNAs - Current Topics in Microbiology and Immunology 259 (Paperback). Joachim Hauber (editor), P. K. ... CRM I appears to be involved in the nucleocytoplasmic translocation of the vast majority of viral and cellular proteins that ...
Viral RNA and DNA capture, purification and qRT-PCR and qPCR analyses; featuring PureLink™, RNA UltraSense™, & Dynabeads® ... Specific Capture of Viral RNA/DNA Target a specific viral RNA or DNA sequence and capture only that specific nucleic acid ... Dynabeads® SILANE Viral RNA/DNA Sensitive and highly consistent isolation of viral RNA and DNA from cell-free samples. These ... Viral RNA/DNA purification Both spin-column and 96-well plate kits are designed for fast and easy isolation of viral RNA or DNA ...
RNA interference (RNAi) is a highly conserved post-transcriptional gene silencing process triggered by double-stranded RNA ( ... The aim of this thesis is to evaluate the efficacy of viral vector-mediated RNAi in the retina using recombinant adeno- ... The efficient gene silencing achieved by these short hairpin RNA (shRNA) molecules and the cumulative understanding of the RNAi ... A detailed assessment of the utility and extend of RNAi in the retina using different viral vectors and hairpin designs is ...
We conclude that viral replicating RNA constitutes the majority of the viral immunostimulatory RNA associated with RIG-I. In ... purified SeV-C RNA, total RNA from SeV-C-infected cells, and poly(I:C) were used in various experiments. Viral RNA was isolated ... or trailer RNA. Comparison of relative abundances of DI RNA and genome RNA/L mRNA between total RNA from infected cells, RIG-I ... Analysis of RIG-I-Associated RNA at Early Times of SeV Infection.. We next determined whether the same or different viral RNA ...
Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution. ... Description: RNA pseudoknot rna , Length: 28 This entity is NOT a polypeptide entity and therefore cannot be considered for the ...
Notes from the Field: Investigation of Patients Testing Positive for Yellow Fever Viral RNA After Vaccination During a Mass ... Thus, the detection of yellow fever viral RNA by RT-PCR testing before postvaccination day 3 or after day 13 could represent ... Notes from the Field: Investigation of Patients Testing Positive for Yellow Fever Viral RNA After Vaccination During a Mass ... Eighteen (56%) received positive test results for yellow fever viral RNA after postvaccination day 13, and 11 (34%) received ...
... extracts total RNA and captures target PAN RNA with oligonucleotide probes. Subsequently, she uses state-of-the-art RNA-centric ... Inside COSAM Labs - Joanna Sztuba-Solinska - Elucidating the Mystery of Viral Long Non-Coding RNAs. Published: 02/05/2019 ... "Research is new on viral non-coding RNAs structure and functions," Sztuba-Solinska stated when asked why she chose this field ... The most abundant KSHV-encoded lncRNA is polyadenylated nuclear (PAN) RNA, which acts as a major switch during viral lytic ...
Using RNA as a therapeutic modality brings to bear an entirely new approach, which not only allows for the construction of ... New research demonstrates that multifunctional RNA nanoparticles with a nanoring design allow the use of different types of ... but also permits the use of all the different types of functionalities that are inherent in natural RNAs. ... There is a significant need for new therapeutic approaches to combat diseases such as cancer and viral infections. ...
Mutational analysis of a viral RNA element that counteracts rapid RNA decay by interaction with the polyadenylate tail. ... Mutational analysis of a viral RNA element that counteracts rapid RNA decay by interaction with the polyadenylate tail ... Mutational analysis of a viral RNA element that counteracts rapid RNA decay by interaction with the polyadenylate tail ... Mutational analysis of a viral RNA element that counteracts rapid RNA decay by interaction with the polyadenylate tail ...
  • Commercially available HIV-1 RNA assays do not detect HIV-2 viral load. (nih.gov)
  • The identified protein regions involved in packaging viral RNAs bind random cellular RNA with high affinity and standard methods of identifying RNA-protein interactions such as gel shift mobility assays will be unable to discriminate between specific and unspecific binding. (uwaterloo.ca)
  • Comparison of the results of five kinds of assays of HCV antibodies and HCV RNA. (annals.org)
  • Discrepancies in viral load (VL) measurements obtained in different plasma collection tubes have underscored the importance of specimen collection and handling in the determination of accurate results in HIV viral load assays. (asm.org)
  • Elevated HIV-1 viral loads in plasma specimens collected and frozen in PPTs and quantified in the standard and ultrasensitive Roche COBAS Amplicor HIV-1 Monitor assays ( 2 , 4 , 13 ) have led investigators to believe that it may have an impact on therapeutic management of HIV-infected patients ( 1 , 8 ). (asm.org)
  • The large differences are due to different blip definitions and viral load assays. (biomedcentral.com)
  • Here, we present an international collaboration of 4,221 paired blood plasma viral load (pVL) results from four commercial assays, emphasizing the data with low pVL. (uzh.ch)
  • Correlation and concordance between the viral load assays were lower at a low pVL. (uzh.ch)
  • Due to the difficulty in differentiating between specific and unspecific binding a new method for studying RNA-protein interactions was developed using a surface based detection approach. (uwaterloo.ca)
  • The high-affinity and specificity of the Rev-RRE binding has been well characterized and was used as a model system to gauge the sensitivity of the surface based detection system, which can be further used to characterize various RNA-protein interactions. (uwaterloo.ca)
  • Using the RNA sequence information of DI RNA, we designed several short complementary DNA probes to capture single DI RNA molecules for detection with single molecule fluorescence microscopy. (illinois.edu)
  • However, traditional viral detection methods rely on prior sequence or antigen knowledge. (pubmedcentralcanada.ca)
  • In general, a strong association was observed between two different viral DNA/RNA extraction kits and detection frequency of targets ( P = 0.017). (iwaponline.com)
  • Moreover, detection of viral RNA packaged in CsCl purified human adenovirus (HAdV) -5 virions indicates that the viral RNA packaging might be a common phenomenon in members of Adenoviridae family. (biomedcentral.com)
  • Different RMs are expected to produce different evolutionary and dynamical outcomes in viral quasi-species due to differences in the mutations accumulation rate. (springer.com)
  • Mutations within the 5′-UTR affecting RNA structural elements enabled restriction by or antagonism of Ifit1 in vitro and in vivo. (sciencemag.org)
  • 3 Except for the NSW03 and NSW01 isolates, viral mutations are located at the stem loop-II (s2m) motif, an extremely conserved RNA element in the 3' untranslated region (Figure 1A). (mja.com.au)
  • The first analysis included 29 patients receiving either monotherapy or combination therapy with the protease inhibitor ritonavir whose plasma HIV RNA levels rebounded from the point of greatest decline with mutations associated with resistance to ritonavir. (ovid.com)
  • Conclusion: In this multiethnic cohort of 488 untreated individuals with CHB, factors associated with serum HBV RNA level were HBeAg status, serum ALT, HBV genotype, and presence of basal core promotor mutations. (eur.nl)
  • The studies presented provide an insight into molecular and genetic aspects of messenger RNA. (springer.com)
  • Molecular model of the p19 protein (yellow) from a Tombusvirus, suppressing a double-stranded, small interfering RNA (siRNA) molecule (red and blue). (sciencephoto.com)
  • We provide a Graphical User Interface that applies this method and is useful for simulating viral dynamics during treatment with anti-HCV agents that act against HCV on the molecular level. (frontiersin.org)
  • This has important implications for our understanding of the fundamental molecular biology of Picornavirales,and opens the door to novel research and therapeutic applications in the field of custom RNA packaging and delivery technologies. (jic.ac.uk)
  • In this work, we tried to elucidate molecular machinery underlying RNA recognition by RLRs and physiological significance of RLR-mediated signaling. (nii.ac.jp)
  • Molecular Dynamics studies, focusing on the area surrounding the ligation site, have indicated multiple opportunities for recombination between model RNAs. (jbsdonline.com)
  • Publications] Tetsuya Toyoda: 'Molecular dissection of the influenza virus RNA polymerase : PB1 alone is able to catalyze RNA. (nii.ac.jp)
  • Publications] Tetsuya Toyoda: 'Molecular assembly of the influenza virus RNA polymerase : Determination of the subunit-subnit contact sites. (nii.ac.jp)
  • We conducted comprehensive free energy calculations on various nucleotide insertions for viral T7 RNAP employing all-atom molecular dynamics simulations. (escholarship.org)
  • Dynamical experimental quantification of Turnip mosaic virus RNA strands, together with a nonlinear mathematical model, indicated the SMR model for this pathogen. (springer.com)
  • Single strands of these RNAs did not activate PKR. (innovations-report.com)
  • Both spin-column and 96-well plate kits are designed for fast and easy isolation of viral RNA or DNA from cell-free samples such as serum, plasma, cerebrospinal fluid, and cell culture supernatant. (thermofisher.com)
  • Sensitive and highly consistent isolation of viral RNA and DNA from cell-free samples. (thermofisher.com)
  • Mag-Bind® Viral DNA/RNA Kit is designed for the rapid and reliable isolation of viral RNA and viral DNA from whole blood, serum, plasma, saliva and other body fluids. (omegabiotek.com)
  • In this study, two commercially available kits were compared to assess their performance, the MO BIO PowerViral Environmental DNA/RNA Isolation kit and the Qiagen QIAamp Viral RNA Mini kit. (iwaponline.com)
  • After isolation of cytoplasmic RNA from either infected or transfected cells and extraction of virus particle-associated RNA, specific RNA levels present in both fractions are determined. (bio-protocol.org)
  • Add fresh medium to the transfected or infected cells and place them in the incubator until cytoplasmic RNA isolation. (bio-protocol.org)
  • 300 IU/mL, then Hepatitis C Viral RNA Genotype, LIPA(R) will be performed at an additional charge (CPT code(s): 87902). (specialtylabs.com)
  • Target a specific viral RNA or DNA sequence and capture only that specific nucleic acid sequence directly from crude lysates or other biological fluids. (thermofisher.com)
  • Additionally, 5′ppp containing RNAs rich in U residues have been found to act as more potent inducers of RIG-I, indicating that sequence composition might play a role in activation ( 22 ). (pnas.org)
  • The translational increase depends on the nucleotide composition and 5' positioning of the ER-targeting sequence coding regions and is facilitated by the RNA-binding domain of NS1, which can associate with ER membranes. (diva-portal.org)
  • The Ebola virus VP35 protein binds viral immunostimulatory and host RNAs identified through deep sequencing. (jcvi.org)
  • The Partnership for Research on Ebola Virus in Liberia (PREVAIL), a U.S.-Liberia joint Clinical Research Partnership has announced the opening of PREVAIL IV, a treatment trial for men who have survived Ebola virus disease (EVD) but continue to have evidence of Ebola virus genetic material, RNA, in their semen. (technologynetworks.com)
  • The six-month study will enroll 60 to 120 EVD survivors whose semen has evidence of Ebola virus RNA prior to their enrollment. (technologynetworks.com)
  • Investigators will test the semen samples to see if Ebola viral RNA can continue to be detected. (technologynetworks.com)
  • Dried blood spots have been used successfully for DNA and RNA polymerase chain reaction (PCR) to diagnose infant HIV( 3 ) and to determine HIV RNA concentration( 4 ) under laboratory conditions. (ucsf.edu)
  • Both a 142 nucleotide (nt) amplicon of the M segment, encoding a portion of the G2 transmembrane glycoprotein, and a 751 nt amplicon of the S segment, encoding part of the nucleocapsid protein, were cloned and sequenced from 19 deer mice and from one brush mouse ( P. boylii ), S RNA but not M RNA from one deer mouse, and M RNA but not S RNA from another deer mouse. (biomedcentral.com)
  • It is activated by long stretches of double-stranded RNA. (innovations-report.com)
  • Double-stranded RNAs (dsRNAs) are widespread in plant pathogenic fungi, but their functions in fungal hosts remain mostly unclear, with a few exceptions. (apsnet.org)
  • The synthetic R N A substrate mimics the 21-nt double-stranded siRNAs that occur in the double-strand RNA-induced RNAi silencing pathway. (proteopedia.org)
  • Delivery of inhibitory RNAs to target tissues needs to be safe, efficient, and for many diseases, long-lasting, in order to exploit this endogenous mechanism for therapeutic purposes. (omicsonline.org)
  • Using the RNA nanotechnology pioneered by Guo, the researchers constructed ultrastable X-shaped RNA nanoparticles using re-engineered RNA fragments to carry up to four therapeutic and diagnostic modules. (eurekalert.org)
  • We have addressed these issues, and now it is possible to produce RNA nanoparticles that are highly stable both chemically and thermodynamically in the test tube or in the body with great potential as therapeutic reagents. (eurekalert.org)
  • Using RNA as a therapeutic modality brings to bear an entirely new approach, which not only allows for the construction of uniform scaffolds for attachment of functional entities, but also permits the use of all the different types of functionalities that are inherent in natural RNAs. (nanowerk.com)
  • To assess relative utility of viral load testing in determining therapeutic choice by the surrogate marker of CD4 cell counts after 48 weeks of therapy. (clinicaltrials.gov)
  • It is hypothesized that among HIV-infected patients whose baseline CD4 count is in the range of 300 to 750 cells/mm3, those patients who incorporate initial and periodic viral RNA measurements in their therapeutic decisions will have higher CD4 counts after 48 weeks than patients whose therapeutic decisions do not incorporate initial and periodic viral RNA measurements. (clinicaltrials.gov)
  • Elevated HIV-1 viral load (VL) observed in specimens frozen in situ in plasma preparation tubes (PPTs) compared to EDTA plasma specimens may affect therapeutic monitoring of HIV-infected patients. (asm.org)
  • Many HIV-1-infected patients on suppressive antiretroviral therapy (ART) have transiently elevated HIV RNA levels. (biomedcentral.com)
  • To determine whether splicing of these transcripts is regulated by viral factors, the extent of splicing was studied in infected cells and COS-7 cells transiently transfected with plasmids encoding the 2.8 kb RNA of BDV. (columbia.edu)
  • The PureLink® Viral RNA/DNA Mini Kit provides a rapid and efficient method to simultaneously purify viral RNA/DNA from fresh or frozen cell-free biological fluids (plasma, serum, cerebrospinal fluid) and cell culture supernatants. (thermofisher.com)
  • Purifies viral nucleic acids from human and animal samples, including plasma, serum, saliva, and urine, using magnetic bead technology amenable to high-throughput operations. (fishersci.com)
  • The Thermo Scientific MagJET Viral DNA and RNA Kit is designed for fast and efficient purification of viral nucleic acids from various human and animal liquid samples such as plasma, serum, saliva and urine, as well as from nasal, buccal and urogenital swabs and blood. (fishersci.com)
  • and chemically stable, which makes the nanoparticles resistant to RNase (an enzyme, which cleaves RNA) digestion in the blood serum. (eurekalert.org)
  • Most of these appear to represent false-positive results because HCV RNA is usually absent from the serum. (annals.org)
  • Viral reactivation was seen in scid mice treated with hyperimmune serum or a low dose of monoclonal antibody to the E2 envelope glycoprotein, but not in mice treated with a high dose of monoclonal antibody to E2. (asm.org)
  • For its proper use, it is essential to identify factors influencing serum HBV RNA level. (eur.nl)
  • For the future use of serum HBV RNA as a clinical marker, it seems mandatory to take these factors into consideration. (eur.nl)
  • Moreover, recombinant particles and replicon RNAs have been encapsulated by liposomes to improve delivery and targeting. (mdpi.com)
  • Nonpermissive cells infected with {varphi}X174 gene D amber mutants synthesized some sixfold less viral RNA than permissive cells. (caltech.edu)
  • The surface based system monitors real-time binding, whereby specific and unspecific RNA-protein interactions will be distinguished through comparison of relative association rates for each binding interaction. (uwaterloo.ca)
  • A well studied RNA-protein interaction, the HIV-1 Rev-RRE, was used to develop the methodology for the surface based system. (uwaterloo.ca)
  • These RNA dimers then allow separate sets of PKR to bind with themselves, also forming dimers, a state where the paired PKR is most effective against a viral onslaught. (innovations-report.com)
  • The length needed for one PKR to bind to RNA is fifteen base pairs," said Philip Bevilacqua, professor of chemistry, Penn State, one of the lead scientists on the project along with James Cole, associate professor, University of Connecticut. (innovations-report.com)
  • To get two PKRs to bind and dimerize, you need an RNA strand that is twice as long. (innovations-report.com)
  • Adding these defects decreases the number of places where PKR can bind to the RNA," Heinicke explained. (innovations-report.com)
  • To demonstrate the combinatorial nature of the scaffolds, the scientists functionalized their nanorings with up to six RNA aptamers (see the top right ring in Figure 1) selected to bind the malachite green (MG) dye and significantly increase its emission, which is otherwise undetectable in aqueous solutions. (nanowerk.com)
  • Viral nucleic acid was isolated with Omega Bio-tek's Mag-Bind® Viral DNA/RNA Kit and with a comparable kit from Company A according to recommended protocols. (omegabiotek.com)
  • 1 The key goal of ART is to achieve and maintain durable viral suppression. (nih.gov)
  • If viral suppression is not possible, repeat viral load every 3 months or more frequently if indicated (AIII) . (nih.gov)
  • Can extend to every 6 months for patients with consistent viral suppression for ≥2 years (AIII) . (nih.gov)
  • Taken together, our data support the formation of the proposed ENE secondary structure in vivo and argue that the specific ENE structure inhibits rapid RNA decay in cis by engaging in a limited set of base-pairing interactions with the polyA tail. (pnas.org)
  • We conclude that Tsg101, through selective interactions with its partners including Hrs and Alix, may link receptor sorting and lysosome targeting to the back-fusion process involved in viral capsid release. (ovid.com)
  • Several conserved serine and threonine residues in p19 mediate key interactions with 2'-hydroxyls specifying RNA as the substrate, rather than DNA. (proteopedia.org)
  • This view only shows part of the network of interactions with the ribose sugar 2'-hydroxyls of the RNA. (proteopedia.org)
  • Each 'reading' helix is connected to the structured core of p19 by a short flexible loop and several side-chain interactions this presumably allows some flexibility in the positioning of the RNA end-capping tryptophan residues. (proteopedia.org)
  • Previously, we reported that the viral envelope fuses preferentially with the membrane of vesicles present within multivesicular endosomes. (ovid.com)
  • Strikingly, an analysis of host RNAs bound by wild-type, but not mutant, VP35 revealed that select host RNAs are preferentially bound by VP35 in cell culture. (jcvi.org)
  • We show that pathogenic alphaviruses use secondary structural motifs within the 5′-untranslated region (UTR) of their RNA to alter Ifit1 binding and function. (sciencemag.org)
  • As such, this knowledge may also influence future strategies for the prevention and treatment of pathogenic viral diseases. (jbsdonline.com)
  • These Dynabeads® have an optimized surface chemistry for viral nucleic acid purification and provide efficient kinetics and a high sensitivity. (thermofisher.com)
  • Notably, the first age-based multiscale mathematical model for HCV kinetics has been developed [ 25 , 40 , 41 ] providing a more comprehensive understanding of viral treatment response kinetics observed in patients treated with IFN, HCV protease inhibitors (telaprevir and danoprevir), or the HCV NS5A inhibitor daclatasvir as well as modes of action of these drugs. (frontiersin.org)
  • We analyzed the viral RNA load kinetics of SARS-CoV-2 in various clinical specimens in children with COVID-19. (cdc.gov)
  • An elongation cycle of a transcribing RNA polymerase (RNAP) usually consists of multiple kinetics steps, so there exist multiple kinetic checkpoints where non-cognate nucleotides can be selected against. (escholarship.org)
  • Viral analysis of biological and environmental samples requires the use of advanced technologies to assure assay effectiveness. (thermofisher.com)
  • We extracted RNA from clinical specimens and detected SARS-CoV-2 by using the Allplex 2019-nCoV Assay kit (Seegene, http://www.seegene.com ). (cdc.gov)
  • Rather, a nuclear run-on assay indicated that, in the absence of pUL79, RNAP II failed to elongate and stalled on the viral DNA. (diagenode.com)
  • Pre-treatment viral load level is also an important factor in the selection of an initial ARV regimen because several currently approved ARV drugs or regimens have been associated with poorer responses in patients with high baseline viral load (see What to Start ). (nih.gov)
  • To evaluate, in HIV-infected patients whose baseline CD4 count is 300 to 750 cells/mm3, whether an antiretroviral treatment regimen based upon clinical evaluation and CD4 counts plus HIV RNA viral load is more effective than a treatment regimen based upon clinical evaluation and CD4 counts without the use of HIV RNA viral load information. (clinicaltrials.gov)
  • The baseline RNA level was the first DBS RNA measurement at 40 days or less and the follow-up level was the second DBS measurement taken between 41 and 80 days. (ucsf.edu)
  • In the first analysis, durability of response was analyzed with respect to baseline HIV RNA, HIV RNA at the nadir, and the drop in HIV RNA from baseline to the nadir. (ovid.com)
  • In the second analysis, time to rebound was examined using Kaplan-Meier analysis, stratifying by either baseline HIV RNA or HIV RNA at the nadir. (ovid.com)
  • In both analyses, the durability of response was not highly associated with either baseline RNA or the magnitude of RNA decline from baseline. (ovid.com)
  • Blips were associated with high baseline viral load and an increased risk of subsequent virological failure. (biomedcentral.com)
  • Most people with declines of more than 1 log 10 had undetectable HBV RNA at baseline. (infohep.org)
  • The nested PCR amplified integrated proviral DNA in nucleic acid extracted from plasma in PPT and EDTA specimens with high viral load values. (asm.org)
  • Cells can chemically modify RNA to influence protein production. (eurekalert.org)
  • She grows infected cells, extracts total RNA and captures target PAN RNA with oligonucleotide probes. (auburn.edu)
  • She has published one of only two papers that used SHAPE-MaP, a new method that allows researchers to probe the structure of any RNA of interest inside the living cells or within viral particle. (auburn.edu)
  • Computationally designed RNA and RNA-DNA based nanorings presented in this work have multiple advantages in diagnostics and delivery of functional moieties to diseased cells,' Shapiro tells Nanowerk. (nanowerk.com)
  • The Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear (PAN) RNA ( nut-1 , T1.1) accumulates to unusually high levels (≈2.5 × 10 5 ) in the nucleus of lytically infected human cells ( 21 - 23 ). (pnas.org)
  • Utilizing a biological system of virally infected mammalian cells, the substrate targeted in the study are viral RNA-protein complexes. (illinois.edu)
  • yet, there are no data that identify viral immunostimulatory RNAs (isRNA) or host RNAs bound to VP35 in cells. (jcvi.org)
  • The existence of these vast quantities of non-coding RNAs in cells implies the significance of these differential RNA species in the regulation of biological processes ( 1 , 4 ). (pubmedcentralcanada.ca)
  • RNA was made from these constructs and used to transfect HeLa cells. (caltech.edu)
  • The team adapted a technique that attaches fluorescent chemical probes to RNA in cells. (technewslit.com)
  • Unspliced RNA was found to be the most abundant RNA species in infected cells, whereas viral transcripts lacking both introns were only found in minute amounts. (columbia.edu)
  • Furthermore, the splicing pattern did not change when the 2.8 kb RNA was expressed in BDV-infected cells. (columbia.edu)
  • they made very little viral protein, they did not inhibit host cell translation, and they synthesized a significant amount of viral RNA, although with some delay compared with wild type. (caltech.edu)
  • In the past, clinical practice, which was supported by treatment guidelines, was generally to monitor both CD4 cell count and viral load concurrently. (nih.gov)
  • Several systematic reviews of data from clinical trials involving thousands of participants have established that decreases in viral load following initiation of ART are associated with reduced risk of progression to AIDS or death. (nih.gov)
  • The clinical significance of these viral blips is uncertain. (biomedcentral.com)
  • We are a leading supplier of the most successful tools used for viral RNA and DNA capture, purification, and qRT-PCR and qPCR analyses. (thermofisher.com)
  • The findings were extended to a group of singly spliced viral mRNAs that produce Env in the following biochemical analyses. (nii.ac.jp)