Rna ribosomal 16s. Medical search

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)

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.

Ribonucleic acid that makes up the genetic material of viruses.

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).

The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.

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)

Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.

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).

Viruses whose genetic material is RNA.

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 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 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 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.

The processes of RNA tertiary structure formation.

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.

Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.

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.

A family of proteins that promote unwinding of RNA during splicing and translation.

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.

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.

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.

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 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 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.

The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.

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.

A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.

Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.

Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.

The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.

RNA present in neoplastic tissue.

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.

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.

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.

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.

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 molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.

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.

Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.

Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.

Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.

Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.

The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms.

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).

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)

Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.

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.

Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.

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)

The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.

Established cell cultures that have the potential to propagate indefinitely.

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.

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.

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.

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.

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.

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.

The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.

Small RNAs found in the cytoplasm usually complexed with proteins in scRNPs (RIBONUCLEOPROTEINS, SMALL CYTOPLASMIC).

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.

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.

Short RNA, about 200 base pairs in length or shorter, that does not code for protein.

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.

Complexes of RNA-binding proteins with ribonucleic acids (RNA).

Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.

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.

The complete genetic complement contained in a DNA or RNA molecule in a virus.

Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.

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).

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.

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.

The parts of a macromolecule that directly participate in its specific combination with another molecule.

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.

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)

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.

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.-.

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)

Ribonucleic acid in chloroplasts having regulatory and catalytic roles as well as involvement in protein synthesis.

Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.

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.

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.

The rate dynamics in chemical or physical systems.

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.

Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.

Ribonucleic acid in helminths having regulatory and catalytic roles as well as involvement in protein synthesis.

Viruses parasitic on plants higher than bacteria.

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.

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.

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.

Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.

A transfer RNA which is specific for carrying phenylalanine to sites on the ribosomes in preparation for protein synthesis.

A transfer RNA which is specific for carrying lysine to sites on the ribosomes in preparation for protein synthesis.

Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.

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.

Deoxyribonucleic acid that makes up the genetic material of viruses.

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.

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)

Interruption or suppression of the expression of a gene at transcriptional or translational levels.

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.

A transfer RNA which is specific for carrying tyrosine to sites on the ribosomes in preparation for protein synthesis.

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.

The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.

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.

The functional hereditary units of VIRUSES.

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.

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.

An enzyme catalyzing the endonucleolytic cleavage of RNA at the 3'-position of a guanylate residue. EC 3.1.27.3.

The sum of the weight of all the atoms in a molecule.

The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.

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)

The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.

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)

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.

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.

Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.

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.

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.

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.

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.

The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.

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.

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.

A transfer RNA which is specific for carrying alanine to sites on the ribosomes in preparation for protein synthesis.

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 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.

A plant genus of the family SOLANACEAE. Members contain NICOTINE and other biologically active chemicals; its dried leaves are used for SMOKING.

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.

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)

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)

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)

Viruses which produce a mottled appearance of the leaves of plants.

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.

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)

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).

The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.

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 in which a polyacrylamide gel is used as the diffusion medium.

A transfer RNA which is specific for carrying aspartic acid to sites on the ribosomes in preparation for protein synthesis.

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).

The relationships of groups of organisms as reflected by their genetic makeup.

A genus of tripartite plant viruses in the family BROMOVIRIDAE. Transmission is by beetles. Brome mosaic virus is the type species.

Proteins prepared by recombinant DNA technology.

A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.

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.

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.

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.

Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.

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)

A cell line derived from cultured tumor cells.

The outer protein protective shell of a virus, which protects the viral nucleic acid.

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.-

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.

Proteins found in any species of bacterium.

Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.

A transfer RNA which is specific for carrying glycine to sites on the ribosomes in preparation for protein synthesis.

A transfer RNA which is specific for carrying histidine to sites on the ribosomes in preparation for protein synthesis.

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.

A transfer RNA which is specific for carrying valine to sites on the ribosomes in preparation for protein synthesis.

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.

A family of RNA viruses infecting insects and fish. There are two genera: Alphanodavirus and Betanodavirus.

Use for nucleic acid precursors in general or for which there is no specific heading.

The assembly of VIRAL STRUCTURAL PROTEINS and nucleic acid (VIRAL DNA or VIRAL RNA) to form a VIRUS PARTICLE.

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.

Deletion of sequences of nucleic acids from the genetic material of an individual.

A transfer RNA which is specific for carrying arginine to sites on the ribosomes in preparation for protein synthesis.

Ribonucleic acid in algae having regulatory and catalytic roles as well as involvement in protein synthesis.

A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.

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.

Proteins obtained from ESCHERICHIA COLI.

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.

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.

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.

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).

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.

Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.

A transfer RNA which is specific for carrying tryptophan to sites on the ribosomes in preparation for protein synthesis.

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.

DNA sequences recognized as signals to end GENETIC TRANSCRIPTION.

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.

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.

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.

Elements of limited time intervals, contributing to particular results or situations.

Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.

Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.

A bacteriophage genus of the family LEVIVIRIDAE, whose viruses contain the short version of the genome and have a separate gene for cell lysis.

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.

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).

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.

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.

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.

Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.

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.

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)

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.

A transfer RNA which is specific for carrying leucine to sites on the ribosomes in preparation for protein synthesis.

The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.

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.

Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)

A new rapidly growing mycobacterial species, Mycobacterium murale sp. nov., isolated from the indoor walls of a children's day care centre. (1/13701)

Scotochromogenic mycobacterial isolates from water-damaged parts of indoor building materials of a children's day care centre represented a phenetically and genetically distinct group of strains. A 16S rDNA dendrogram (1243 bp) showed that the closest species to the new strain MA112/96T was Mycobacterium abscessus. Phylogenetic and phenetic analyses (100 characteristics) grouped the new isolates with M. abscessus, Mycobacterium vaccae, Mycobacterium aurum and Mycobacterium austroafricanum. Ribotyping with Pvull restriction distinguished the 5 isolates from the other 12 most closely related species by the major bands at 6.5-7 kb and 13-15 kb. The cell morphology of the new isolates was typical of mycobacteria, electron microscopy revealed a triple-layered cell wall with an irregular electron-dense outer layer. They grew at 10-37 degrees C, with no growth at 45 degrees C in 5 d. The gene encoding the secreted 32 kDa protein, specific to mycobacteria, was detected by PCR. The main whole-cell fatty acids were characterized by high tuberculostearic acid 10Me-C18:0 (17% at 28 degrees C), which increased with increasing growth temperature (22% at 37 degrees C). The other main fatty acids were C18:1 cis9 and C16:0 (21-20% each), followed by, C17:1 cis9 (14%), C16:1 cis10 (8%) and also a high amount of C20 alcohol (9%). alpha-Mycolic acids, keto-mycolates and wax esters were present (C60-C90), MK-9(H2) (90%) and MK-8(H2) were the main menaquinones. The cellular phospholipids were phosphatidylethanolamine, phosphatidylinositol, phosphatidyl inositolmannosides and diphosphatidylglycerol. Polyamine content was low. G+C content was 72.9 mol%. The new isolates are proposed as a new species, Mycobacterium murale sp. nov. The type strain is MA112/96T (= DSM 44340T). (+info)

Diversity of rhizobia associated with Amorpha fruticosa isolated from Chinese soils and description of Mesorhizobium amorphae sp. nov. (2/13701)

Fifty-five Chinese isolates from nodules of Amorpha fruticosa were characterized and compared with the type strains of the species and genera of bacteria which form nitrogen-fixing symbioses with leguminous host plants. A polyphasic approach, which included RFLP of PCR-amplified 16S rRNA genes, multilocus enzyme electrophoresis (MLEE), DNA-DNA hybridization, 16S rRNA gene sequencing, electrophoretic plasmid profiles, cross-nodulation and a phenotypic study, was used in the comparative analysis. The isolates originated from several different sites in China and they varied in their phenotypic and genetic characteristics. The majority of the isolates had moderate to slow growth rates, produced acid on YMA and harboured a 930 kb symbiotic plasmid (pSym). Five different RFLP patterns were identified among the 16S rRNA genes of all the isolates. Isolates grouped by PCR-RFLP of the 16S rRNA genes were also separated into groups by variation in MLEE profiles and by DNA-DNA hybridization. A representative isolate from each of these DNA homology groups had a separate position in a phylogenetic tree as determined from sequencing analysis of the 16S rRNA genes. A new species, Mesorhizobium amorphae, is proposed for the majority of the isolates, which belonged to a moderately slow- to slow-growing, acid-producing group based upon their distinct phylogenetic position, their unique electrophoretic type, their low DNA homology with reference strains representing the species within the genus Mesorhizobium and their distinct phenotypic features. Strain ACCC 19665 was chosen as the type strain for M. amorphae sp. nov. (+info)

Taxonomic relationships of the [Pasteurella] haemolytica complex as evaluated by DNA-DNA hybridizations and 16S rRNA sequencing with proposal of Mannheimia haemolytica gen. nov., comb. nov., Mannheimia granulomatis comb. nov., Mannheimia glucosida sp. nov., Mannheimia ruminalis sp. nov. and Mannheimia varigena sp. nov. (3/13701)

The present paper presents the conclusions of a polyphasic investigation of the taxonomy of the trehalose-negative [Pasteurella] haemolytica complex. Clusters previously identified by ribotyping and multilocus enzyme electrophoresis (MEE) have been evaluated by 16S rRNA sequencing and DNA-DNA hybridizations. Results obtained by the different techniques were highly related and indicated that the [P.] haemolytica complex contains distinct genetic and phenotypic groups. At least seven species were outlined, five of which were named. We refrained in formal naming of more groups until additional strains are characterized. Five 16S rRNA clusters were identified corresponding to distinct lineages previously outlined by MEE. Within 16S rRNA cluster I two distinct genotypic groups have been outlined in addition to [P.] haemolytica sensu stricto (biogroup 1). Each of the clusters II, III, IV and V represent at least one new species. The investigations underline that [P.] haemolytica sensu stricto only contains strains that do not ferment L-arabinose even though they are referred to as 'biotype A' of [P.] haemolytica. The five 16S rRNA clusters identified had a common root relative to the other species within the family Pasteurellaceae, and the overall sequence similarity among these five clusters was higher than what is observed within the existing genera of the family. The allocation of the trehalose-negative [P.] haemolytica complex to a new genus seems to be indicated. Based on the polyphasic investigation performed a new genus Mannheimia is proposed for the trehalose-negative [P.] haemolytica complex. At the present stage two previously named species are transferred to this new genus and three new species are described. [P.] haemolytica is reclassified as Mannheimia haemolytica comb. nov., whereas Pasteurella granulomatis, Bisgaard taxon 20 and [P.] haemolytica biovar 3J are reclassified and combined in the species Mannheimia granulomatis comb. nov. Mannheimia glucosida sp. nov. corresponds to [P.] haemolytica biogroups 3A-3H and the beta-glucosidase and meso-inositol-positive strains of [P.] haemolytica biogroup 9. All typable strains within M. glucosida belong to serotype 11. Mannheimia ruminalis sp. nov. consists of strains previously classified as Bisgaard taxon 18 and [P.] haemolytica biogroup 8D. Finally, Mannheimia varigena sp. nov. includes [P.] haemolytica biogroup 6 as well as Bisgaard taxon 15 and Bisgaard taxon 36. The type strains are NCTC 9380T (M. haemolytica), ATCC 49244T (M. granulomatis), CCUG 38457T = P925T (M. glucosida), CCUG 38470T = HPA92T (M. ruminalis) and CCUG 38462T = 177T (M. varigena). (+info)

Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA-DNA hybridization. (4/13701)

The phylogenetic relationships of 49 Acinetobacter strains, 46 of which have previously been classified into 18 genomic species by DNA-DNA hybridization studies, were investigated using the nucleotide sequence of gyrB, the structural gene for the DNA gyrase B subunit. The phylogenetic tree showed linkages between genomic species 1 (Acinetobacter calcoaceticus), 2 (Acinetobacter baumannii), 3 and TU13; genomic species 6, BJ15, BJ16 and BJ17; genomic species 5, BJ13 (synonym of TU14) and BJ14; genomic species 7 (Acinetobacter johnsonii), 10 and 11; and genomic species 8 and 9. The phylogenetic grouping of Acinetobacter strains based on gyrB genes was almost congruent with that based on DNA-DNA hybridization studies. Consequently, gyrB sequence comparison can be used to resolve the taxonomic positions of bacterial strains at the level of genomic species. However, minor discrepancies existed in the grouping of strains of genomic species 8, 9 and BJ17. The phylogenetic tree for these strains was reconstructed from the sequence of rpoD, the structural gene for the RNA polymerase sigma 70 factor. The latter tree was 100% congruent with the grouping based on DNA-DNA hybridization. The reliability of DNA-DNA hybridization may be superior to that of sequence comparison of a single protein-encoding gene in resolving closely related organisms since the former method measures the homologies between the nucleotide sequences of total genomic DNAs. Three strains that have not been characterized previously by DNA-DNA hybridization seem to belong to two new genomic species, one including strain ATCC 33308 and the other including strains ATCC 31012 and MBIC 1332. (+info)

Ignavigranum ruoffiae sp. nov., isolated from human clinical specimens. (5/13701)

Two strains of a hitherto undescribed Gram-positive catalase-negative, facultatively anaerobic coccus isolated from human sources were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies demonstrated the unknown strains were genealogically identical, and constitute a new line close to, but distinct from, the genera Facklamia and Globicatella. The unknown bacterium was readily distinguished from Facklamia species and Globicatella sanguinus by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence it is proposed that the unknown bacterium be classified as Ignavigranum ruoffiae gen. nov., sp. nov. The type strain of Ignavigranum ruoffiae is CCUG 37658T. (+info)

Application of temperature-gradient gel electrophoresis in taxonomy of coryneform bacteria. (6/13701)

Strains belonging to the Gram-positive coryneform soil bacteria were screened genotypically by temperature-gradient gel electrophoresis (TGGE). This method allows the sequence-specific separation of amplified fragments of 16S rRNA genes. A total of 115 reference strains representing the majority of the species of the genera Aeromicrobium, Agromyces, Arthrobacter, Aureobacterium, Cellulomonas, Curtobacterium, Nocardioides and Terrabacter were characterized. Depending on the genus investigated, the resolution limit of the technique appeared to be at the species or genus level or intermediate between the two. Aberrant TGGE profiles of strains within particular taxa revealed genomic heterogeneity and generic misclassification of nine strains studied. Beyond that, indications of 16S rRNA gene heterogeneity were found within the genomes of three Curtobacterium strains. The misclassifications revealed by TGGE were confirmed using whole-cell fatty acid methyl ester analysis and subsequent comparison with a database. TGGE has been demonstrated to be a useful tool in bacterial taxonomy. (+info)

RFLP of rRNA genes and sequencing of the 16S-23S rDNA intergenic spacer region of ammonia-oxidizing bacteria: a phylogenetic approach. (7/13701)

It has been established that 16S rRNA gene-based phylogeny gives a low resolution between members of the chemoautotrophic ammonia-oxidizing bacteria (AOB) belonging to the beta-subclass of the Proteobacteria. In this study, 12 isolates of AOB were ribotyped, and the sequences of the 16S-23S rDNA intergenic spacer region (ISR) were determined and used in a phylogenetic study. 16S and 23S rDNA ribotyping revealed that the AOB studied contain only one rrn operon per genome, in contrast to most bacteria, which have 5-10 copies of the rRNA genes per genome. It is likely that the presence of only one set of rRNA genes is related to the slow growth of the AOB. The 16S and 23S rRNA genes of the AOB were shown to be arranged in the classical way: a 16S rRNA gene, an ISR and a 23S rRNA gene. Despite the close phylogenetic relationship among the AOB, the relative location of the rRNA genes in the genome appears to vary considerably. The size of the ISR was approximately 400 bp in the Nitrosomonas isolates and 645-694 bp in the Nitrosospira isolates, suggesting a species-specific size difference in the ISR. The ISR contained two potential tRNA genes in the 5' end in all isolates studied. The similarity values between the ISR sequences of the AOB are low (42.9-96.2%) compared with the 16S rDNA sequence similarity values, and therefore the ISR sequences are valuable as a complementary phylogenetic tool in combination with 16S rRNA gene sequences. The phylogenetic analysis of the AOB based on ISR sequences confirms the 16S rRNA gene-based phylogeny but has the benefit of giving a higher resolution. (+info)

Proposal to transfer Halococcus turkmenicus, Halobacterium trapanicum JCM 9743 and strain GSL-11 to Haloterrigena turkmenica gen. nov., comb. nov. (8/13701)

The 16S rRNA gene sequences of Halococcus saccharolyticus and Halococcus salifodinae were closely related (94.5-94.7% similarity) to that of Halococcus morrhuae, the type species of the genus Halococcus. However, Halococcus turkmenicus was distinct from the other members of this genus, with low 16S rRNA similarities when compared to Halococcus morrhuae (88.7%). On the basis of phylogenetic tree reconstruction, detection of signature bases and DNA-DNA hybridization data, it is proposed to transfer Halococcus turkmenicus to a novel genus, Haloterrigena, as Haloterrigena turkmenica gen. nov., comb. nov., and to accommodate Halobacterium trapanicum JCM 9743 and strain GSL-11 in the same species. On the basis of morphological, cultural and 16S rRNA sequence data, it is also proposed that the culture collection strains of Halobacterium trapanicum NCIMB 767, ATCC 43102 and JCM 8979 should be renamed as Halococcus sp. (+info)

... (or 16S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome (SSU rRNA). It binds to the ... Bacterial Sequencing The Ribosomal Database Project Ribosomes and Ribosomal RNA: (rRNA) SILVA rRNA database Greengenes: 16S ... Multiple sequences of the 16S rRNA gene can exist within a single bacterium. Like the large (23S) ribosomal RNA, it has a ... Chakravorty S, Helb D, Burday M, Connell N, Alland D (May 2007). "A detailed analysis of 16S ribosomal RNA gene segments for ...

https://en.wikipedia.org/wiki/16S_ribosomal_RNA

"Natronoanaerobium salstagnum 16S ribosomal RNA". European Nucleotide Archive. Retrieved 2022-10-21. Gou M, Wang HZ, Yuan HW, ... "Natronoanaerobium halophilum 16S rRNA gene, isolate G-M14CH-4". European Nucleotide Archive. Retrieved 2022-10-21. Pagaling E, ... "Natronoanaerobium aggerbacterium 16S rRNA gene, isolate G-M16NWC-4". European Nucleotide Archive. Retrieved 2022-10-21. ...

https://en.wikipedia.org/wiki/Natronoanaerobium

All-Species Living Tree Project."16S rRNA-based LTP release 132". Silva Comprehensive Ribosomal RNA Database. Retrieved 2015-08 ...

https://en.wikipedia.org/wiki/Sulfolobus

LSU rRNA: the large subunit ribosomal ribonucleic acid. "Escherichia coli 16S ribosomal RNA". 13 June 2017. {{cite journal}}: ... "Arabidopsis thaliana 16S ribosomal RNA (chloroplast)". 26 September 2019. {{cite journal}}: Cite journal requires ,journal= ( ... "Halobacterium salinarum 16S ribosomal RNA". 7 August 1991. {{cite journal}}: Cite journal requires ,journal= (help) "Homo ... Small subunit ribosomal ribonucleic acid (SSU rRNA) is the smaller of the two major RNA components of the ribosome. Associated ...

https://en.wikipedia.org/wiki/SSU_rRNA

All-Species Living Tree Project."16S rRNA-based LTP release 132". Silva Comprehensive Ribosomal RNA Database. Retrieved 2015-08 ... Burggraf S; Huber H; Stetter KO (1997). "Reclassification of the crenarchael orders and families in accordance with 16S rRNA ... July 2015). "The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales". Biology Direct ...

https://en.wikipedia.org/wiki/Thermoproteaceae

All-Species Living Tree Project."16S rRNA-based LTP release 132". Silva Comprehensive Ribosomal RNA Database. Retrieved 2020-08 ... The 16S rRNA-based Greengenes taxonomy is used to supplement the taxonomy particularly in regions of the tree with no cultured ... and the phylogeny is based on 16S rRNA-based LTP release 132 by The All-Species Living Tree Project. National Center for ...

https://en.wikipedia.org/wiki/List_of_bacterial_orders

Noller HF, Woese CR (April 1981). "Secondary structure of 16S ribosomal RNA". Science. 212 (4493): 403-411. Bibcode:1981Sci... ... including RNA splicing, polyadenylation, and the maturation of ribosomal RNAs. The detailed three-dimensional structure of tRNA ... thereby implying that the sought-after activity might lie within ribosomal RNA rather than ribosomal proteins. Structural ... Analysis of ribosomal RNA sequences from a large number of organisms demonstrated that all extant forms of life on Earth share ...

https://en.wikipedia.org/wiki/History_of_RNA_biology

... results of 16S ribosomal RNA gene sequencing. To emphasize this difference, Woese, Otto Kandler and Mark Wheelis later proposed ... although there are many introns in their transfer RNA and ribosomal RNA genes, and introns may occur in a few protein-encoding ... Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular ... These classifications rely heavily on the use of the sequence of ribosomal RNA genes to reveal relationships among organisms ( ...

https://en.wikipedia.org/wiki/Archaea

16S, 23S and 5S. Bacterial 16S ribosomal RNA, 23S ribosomal RNA, and 5S rRNA genes are typically organized as a co-transcribed ... In prokaryotes a small 30S ribosomal subunit contains the 16S ribosomal RNA. The large 50S ribosomal subunit contains two rRNA ... 16S rRNA, BioMineWiki Ribosomal Database Project II Ribosomal+RNA at the US National Library of Medicine Medical Subject ... Ribosomal RNA is the predominant form of RNA found in most cells; it makes up about 80% of cellular RNA despite never being ...

https://en.wikipedia.org/wiki/Ribosomal_RNA

The All-Species Living Tree' Project."16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA ... and the phylogeny is based on 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project Yokota A, Tamura T, ...

https://en.wikipedia.org/wiki/Kineococcus

from the comparison of 16S + 23S ribosomal RNA sequences. Toni Gabaldón and Martijn Huynen (2003) reconstructed the proteome ( ...

https://en.wikipedia.org/wiki/Proto-mitochondrion

Woo, P.C.; Lau,Chan,Fung,Tang,Yuen (2005). "Clostridium bacteramia characterized by 16S ribosomal RNA gene sequencing". Journal ... Currently the standard to identify clostridial species such as C. cadaveris is via molecular techniques utilizing ribosomal RNA ...

https://en.wikipedia.org/wiki/Clostridium_cadaveris

Based on 16S ribosomal RNA sequences, Bala et al. renamed the species in 2004 Amycolatopsis rifamycinica. Rifamycins were first ... This is due to the high affinity of rifamycins for the prokaryotic RNA polymerase. The selectivity of the rifamycins depends on ... RifA through rifE encode a type I polyketide synthase module, with the loading module being a non-ribosomal peptide synthetase ... The rifamycins have a unique mechanism of action, selectively inhibiting bacterial DNA-dependent RNA polymerase, and show no ...

https://en.wikipedia.org/wiki/Rifamycin

The All-Species Living Tree' Project."16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA ... The currently accepted phylogeny is based on 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project Normand P ...

https://en.wikipedia.org/wiki/Geodermatophilaceae

All-Species Living Tree Project."16S rRNA-based LTP release 111 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database ... and the phylogeny is based on 16S rRNA-based LTP release 111 by The All-Species Living Tree Project Parte, A.C. "Brockia". LPSN ...

https://en.wikipedia.org/wiki/Thermoanaerobacteraceae

The All-Species Living Tree' Project."16S rRNA-based LTP release 111 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA ... and the phylogeny is based on 16S rRNA-based LTP release 111 by 'The All-Species Living Tree' Project Catacombs#Bacteria ...

https://en.wikipedia.org/wiki/Rubrobacter

"Classification of methanogenic bacteria by 16S ribosomal RNA characterization". Proceedings of the National Academy of Sciences ...

https://en.wikipedia.org/wiki/Ralph_Stoner_Wolfe

The All-Species Living Tree' Project."16S rRNA-based LTP release 106 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA ... and the phylogeny is based on 16S rRNA-based LTP release 106 by 'The All-Species Living Tree' Project Notes: Prokaryotes where ...

https://en.wikipedia.org/wiki/Campylobacterota

The All-Species Living Tree' Project."16S rRNA-based LTP release 106 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA ... "An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the ... names with Standing in Nomenclature and National Center for Biotechnology Information and the phylogeny is based on 16S rRNA- ...

https://en.wikipedia.org/wiki/Cryptosporangiaceae

"16S rRNA-based LTP release 106 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Archived from the original (PDF ... and the phylogeny is based on 16S rRNA-based LTP release 106 by The All-Species Living Tree Project Bacterial taxonomy ...

https://en.wikipedia.org/wiki/Demequina

All-Species Living Tree Project."16S rRNA-based LTP release 106 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database ... and the phylogeny is based on 16S rRNA-based LTP release 106 by The All-Species Living Tree Project: Zhi XY, Li WJ, ... Stackebrandt E. (2009). "An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class ...

https://en.wikipedia.org/wiki/Beutenbergiaceae

The species' 16S ribosomal RNA sequence has been determined. During the anammox process, it oxidizes acetate at the highest ...

https://en.wikipedia.org/wiki/Brocadia_fulgida

"16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20. Portal: ... The currently accepted phylogeny is based on 16S rRNA-based LTP release 123 by The All-Species Living Tree Project Tao TS, Yue ...

https://en.wikipedia.org/wiki/Nakamurella

https://en.wikipedia.org/wiki/Rarobacteraceae

Lau, S K P (1 March 2006). "Globicatella bacteraemia identified by 16S ribosomal RNA gene sequencing". Journal of Clinical ...

https://en.wikipedia.org/wiki/Globicatella_sulfidifaciens

https://en.wikipedia.org/wiki/Sporichthya

All-Species Living Tree Project."16S rRNA-based LTP release 111 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database ... or old releases of 16S rRNA-based tree from The All-Species Living Tree Project, may still include it. Pavan, María Elisa; ...

https://en.wikipedia.org/wiki/Thermodesulfobiaceae

https://en.wikipedia.org/wiki/Ruaniaceae

"16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20. J.P. ... October 2010). "Detection of WWE2-related Lentisphaerae by 16S rRNA gene sequencing and fluorescence in situ hybridization in ... "Detection of WWE2-related Lentisphaerae by 16S rRNA gene sequencing and fluorescence in situ hybridization in landfill leachate ...

https://en.wikipedia.org/wiki/Lentisphaerota

The All-Species Living Tree' Project."16S rRNA-based LTP release 106 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA ... Techniques such as 16S rRNA analysis and DNA-DNA hybridization have been major contributors to taxonomic classification in ... Wright, A-DG (2006). "Phylogenetic relationships within the order Halobacteriales inferred from 16S rRNA gene sequences". Int. ... and the phylogeny is based on 16S rRNA-based LTP release 106 by 'The All-Species Living Tree' Project. Notes: ♠ Strains found ...

https://en.wikipedia.org/wiki/Halobacteriaceae

"Psyllid endosymbionts exhibit patterns of co-speciation with hosts and destabilizing substitutions in ribosomal RNA". Insect ... identity for the 16S rDNA and 62% for orthologous genes was possible to shed light on the mechanism of genome miniaturization. ... The majority of RNA viruses lack an RNA proofreading facility, which limits their replication fidelity and hence their genome ... This has also been described as the "Eigen paradox". An exception to the rule of small genome sizes in RNA viruses is found in ...

https://en.wikipedia.org/wiki/Genome_size

... two ribosomal RNAs (12S and 16S), and 14 transfer RNAs (tRNAs). The light strand encodes one subunit, and 8 tRNAs. So, ... With the mitochondrial RNA processing, individual mRNA, rRNA, and tRNA sequences are released from the primary transcript. ... Measurement of the levels of the mtDNA-encoded RNAs in bovine tissues has shown that there are major differences in the ... Interestingly, while the expression of protein-encoding genes was stimulated by ACTH, the levels of the mitochondrial 16S rRNA ...

https://en.wikipedia.org/wiki/Mitochondrial_DNA

... nucleotides in 16S ribosomal RNA by binding to this RNA. Subsequent studies by Schroeder and Green began to plant the seed that ... Moazed, Danesh; Noller, Harry F. (June 1987). "Interaction of antibiotics with functional sites in 16S ribosomal RNA". Nature. ... Moazed, Danesh; Noller, Harry F. (June 1987). "Interaction of antibiotics with functional sites in 16S ribosomal RNA". Nature. ... end of the 16S RNA of E. coli taking advantage of RNA conformational changes. Green and coworkers further confirmed this idea, ...

https://en.wikipedia.org/wiki/RNA-targeting_small_molecule_drugs

... it is the eukaryotic nuclear homologue of the prokaryotic 23S and mitochondrial 16S ribosomal RNAs. The genes coding for 28S ... 28S ribosomal RNA is the structural ribosomal RNA (rRNA) for the large subunit (LSU) of eukaryotic cytoplasmic ribosomes, and ... the Ribosomal Database Project; SILVA, a ribosomal RNA gene database project. Lodish, Harvey F.; Darnell, James E. (1995-01-01 ... "Computational discovery of hidden breaks in 28S ribosomal RNAs across eukaryotes and consequences for RNA Integrity Numbers". ...

https://en.wikipedia.org/wiki/28S_ribosomal_RNA

A specimen from Asilomar, Monterey Bay has been sequenced for the 16S ribosomal RNA, Histone H3 and CO1 genes and several ... specimens from Puget Sound, Kitsap County, Washington have been sequenced for 16S and CO1. A. hudsoni is a translucent white ...

https://en.wikipedia.org/wiki/Acanthodoris_hudsoni

The earliest version of this analysis began with ribosomal RNA (rRNA) in microbes to better understand microbes that live in ... "Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects". PeerJ. 4: e1966. doi:10.7717/peerj.1966. PMC ... Circulating free DNA Exogenous DNA Extracellular RNA RNAs present in environmental samples Thomsen, Philip Francis; Sigsgaard, ... 2012). "The Protist Ribosomal Reference database (PR2): A catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with ...

https://en.wikipedia.org/wiki/Environmental_DNA

The two species are genetically very similar, and have identical 16S ribosomal RNA genes. However relative to M. marinum, M. ...

https://en.wikipedia.org/wiki/Mycobacterium_ulcerans

"Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences". ... Wisotzkey, J. D.; Jurtshuk, P.; Fox, G. E.; Deinhard, G.; Poralla, K. (1992-04-01). "Comparative Sequence Analyses on the 16S ...

https://en.wikipedia.org/wiki/Robertmurraya

... and culture independent DNA studies such as ribosomal RNA gene PCR and metagenomics. Building science Microbial biogeography ... "First microbiota assessments of children's paddling pool waters evaluated using 16S rRNA gene-based metagenome analysis". ...

https://en.wikipedia.org/wiki/Microbiomes_of_the_built_environment

For more information on the nomenclature, see Ribosomal protein § Table of ribosomal proteins.) MRPS1, MRPS2, MRPS3, MRPS4, ... Animal mitoribosomes only have two rRNAs, 12S (SSU) and 16S (LSU), both highly minimized compared to their larger homologues. ... Most eukaryotoes use 5S mitoribosomal RNA, animals, fungi, alveolates and euglenozoans being the exceptions. A variety of ... The mitochondrial ribosomal protein nomenclature generally follows that of bacteria, with extra numbers used for mitochondrion- ...

https://en.wikipedia.org/wiki/Mitochondrial_ribosome

Winker, S; Woese CR (1991). "A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA ... 2019 Analysis of their 16S rRNA gene sequences suggests that they are a deeply branching lineage that does not belong to the ... Hansmann, S; Martin W (2000). "Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is ... Keswani, J; Whitman WB (2001). "Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes". Int. J. Syst ...

https://en.wikipedia.org/wiki/Korarchaeota

https://en.wikipedia.org/wiki/Sutcliffiella

https://en.wikipedia.org/wiki/Weizmannia

Initially, Moran and Baumman used 16S ribosomal RNA sequencing to demonstrate that Buchnera aphidicola bacteria and their aphid ...

https://en.wikipedia.org/wiki/Nancy_A._Moran

16S ribosomal RNA sequencing, and DNA probes specific to the oxc (oxalyl-CoA decarboxylase) gene and frc (formyl-CoA ...

https://en.wikipedia.org/wiki/Oxalobacter_formigenes

A common phylogenetic marker for microbial community diversity studies is the 16S ribosomal RNA gene. Both MinION and PacBio's ... Transcriptomics is the study of the transcriptome, usually by characterizing the relative abundances of messenger RNA molecules ...

https://en.wikipedia.org/wiki/Third-generation_sequencing

... as well as 16S ribosomal RNA sequences. This branching pattern was also reflected in the Genome Taxonomy Database. There is one ... "Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences". ...

https://en.wikipedia.org/wiki/Litchfieldia

Runtime comparisons were also conducted by comparing the timings to align 16S ribosomal sequences. MAFFT performed the ... FSA is a multiple sequence alignment program for aligning many proteins or RNAs or long genomic DNA sequences. Along with ... FSA has been benchmarked against multiple alignment databases for protein (SABmark 1.65 and BAliBASE 3), RNA (BRAliBase 2.1 and ...

https://en.wikipedia.org/wiki/Fast_statistical_alignment

A cladogram based on sequences of mitochondrial 12S ribosomal RNA, 16S ribosomal RNA and cytochrome-c oxidase I (COI) genes ...

https://en.wikipedia.org/wiki/Patellogastropoda

Fourmy D, Recht MI, Blanchard SC, Puglisi JD (November 1996). "Structure of the A site of Escherichia coli 16S ribosomal RNA ... Microbiologists often rely on molecular biology tools such as DNA sequence based identification, for example the 16S rRNA gene ...

https://en.wikipedia.org/wiki/Microbiology

According to the molecular analyses of 18S ribosomal RNA, 28S ribosomal RNA, 16S ribosomal RNA, and cytochrome-c oxidase I (COI ...

https://en.wikipedia.org/wiki/Blanfordia

... marker sets are also used to cross-validate tree topologies including concatenated ribosomal proteins and ribosomal RNA genes. ... The 16S rRNA-based Greengenes taxonomy is used to supplement the taxonomy particularly in regions of the tree with no cultured ...

https://en.wikipedia.org/wiki/Branching_order_of_bacterial_phyla_(Genome_Taxonomy_Database,_2018)

Providencia rettgeri strain JVSP1 16S ribosomal RNA gene, partial sequence. GenBank: KR108920.1 ...

https://www.ncbi.nlm.nih.gov/nucleotide/KR108920.1?report=genbank&log$=nucltop&blast_rank=1&RID=55YB1VT6014

16S ribosomal RNA. Details. Name. 16S ribosomal RNA. Kind. nucleotide. Organism. Enteric bacteria and other eubacteria. Drug ...

https://go.drugbank.com/bio_entities/BE0004799

... structure and dynamics of microbial communities in seawater anaerobic bioreactors using 454 pyrosequencing of 16s ribosomal RNA ... structure and dynamics of microbial communities in seawater anaerobic bioreactors using 454 pyrosequencing of 16s ribosomal RNA ...

http://ites.upr.edu/content/characterization-structure-and-dynamics-microbial-communities-seawater-anaerobic-bioreactors

MD trajectories of the complex between the ribosomal protein S15 and RNA were also recorded in the presence and absence of Mg( ... The Mg(2+) ions are hexacoordinated by water and RNA oxygens. The coordination spheres mainly interact with the RNA ... the internal mobility of the RNA and of the protein increases at the interaction interface close to the RNA G-U/G-C motif as a ... On the other hand, several S15-RNA hydrogen bonds are reinforced, and water bridges appear between the three-way junction ...

https://hal-pasteur.archives-ouvertes.fr/pasteur-01570154

Complete nucleotide sequences were determined for two plasmids bearing rmtD group 16S rRNA methyltransferase genes. pKp64/11 ... Complete sequences of multidrug resistance plasmids bearing rmtD1 and rmtD2 16S ribosomal RNA methyltransferase genes. Authors: ... Complete nucleotide sequences were determined for two plasmids bearing rmtD group 16S rRNA methyltransferase genes. pKp64/11 ...

https://www.pacb.com/publications/complete-sequences-of-multidrug-resistance-plasmids-bearing-rmtd1-and-rmtd2-16s-ribosomal-rna-methyltransferase-genes/

Pharmacognosy Research (Pharmacogn Res.). [ISSN: Print -0976-4836, Online - 0974-8490] [http://www.phcogres.com], It provides peer-reviewed original research articles from the field of Natural Products. The journal serves an international audience of scientists and researchers in a variety of research and academia by quickly disseminating research findings related to Medicinal Plants and Natural Products.. It is a peer reviewed journal aiming to publish high quality original research articles, methods, techniques and evaluation reports, critical reviews, short communications, commentaries and editorials of all aspects of medicinal plant research. The journal is aimed at a broad readership, publishing articles on all aspects of pharmacognosy, and related fields. The journal aims to increase understanding of pharmacognosy as well as to direct and foster further research through the dissemination of scientific information by the publication of manuscripts. The submissions of original contributions ...

https://www.phcogres.com/tags/16s-ribosomal-rna

This rRNA sequence is 1,481 nucleotides long and is found in Sphingobium fuliginis. Annotated by 2 databases (ENA, RefSeq). Has a conserved secondary structure or a structured region. Matches 1 Rfam family (SSU_rRNA_bacteria, RF00177).

https://rnacentral.org/rna/URS000000E642/336203

Rapid identification of mycobacteria by gene amplification restriction analysis technique targeting 16S-23S ribosomal RNA ... Rapid identification of mycobacteria by gene amplification restriction analysis technique targeting 16S-23S ribosomal RNA ... METHODS: This system is based on the amplification of approximately 1.8 kb fragment encoding 16S-23S rRNA spacer region and ... region and flanking parts of the 16S as well as 23S rRNA gene. ... flanking parts of the 16S as well as 23S rRNA gene. This assay ...

https://imsear.searo.who.int/handle/123456789/18868

Concordance of urinary microbiota detected by 16S ribosomal RNA amplicon sequencing vs expanded quantitative urine culture. ... Concordance of urinary microbiota detected by 16S ribosomal RNA amplicon sequencing vs expanded quantitative urine culture. / ... Concordance of urinary microbiota detected by 16S ribosomal RNA amplicon sequencing vs expanded quantitative urine culture. In ... Concordance of urinary microbiota detected by 16S ribosomal RNA amplicon sequencing vs expanded quantitative urine culture. ...

https://ohsu.pure.elsevier.com/en/publications/concordance-of-urinary-microbiota-detected-by-16s-ribosomal-rna-a

PDB Description: structure of ribosomal proteins s15, s6, s18, and 16s ribosomal rna ... d1g1xa_ d.58.14.1 (A:) Ribosomal protein S6 {Thermus thermophilus} mrryevnivlnpnldqsqlalekeiiqralenygarvekveelglrrlaypiakdpqgyf ...

http://scop.berkeley.edu/sunid=39327&ver=1.61

... but not free unmethylated 16S rRNA, while the m5C MT functions reciprocally, using free rRNA b … ... We have partially purified two 16S rRNA-specific methyltransferases, one of which forms m2G966 (m2G MT), while the other one ... 200, 309-319). Our results show that the two ribosomal RNA MTs studied in this work are exquisitely sensitive to this small but ... Binding of ribosomal proteins S7, S9, and S19 to unmodified 16S rRNA individually and in all possible combinations showed that ...

https://pubmed.ncbi.nlm.nih.gov/1766869/

In this study, we determined the bacterial diversity profile of the Mexico City metro by massive sequencing of the 16S rRNA ... and then the best match confirmation against NCBIs type strains 16S ribosomal RNA database. Plant-derived sequences were ... Ribosomal Database Project: Data and tools for high throughput rRNA analysis. Nucleic Acids Res. 42, D633-D642 (2014). ... Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069-72 ( ...

https://www.nature.com/articles/s41598-020-65643-4?error=cookies_not_supported&code=77e9cd9c-81ba-4453-a93d-862ebd14167e

A comparison of culture vs 16S ribosomal RNA sequencing of chronic granulation tissue microbiota in cats and dogs, Page 1 of 1 ... fA comparison of culture vs 16S ribosomal RNA sequencing of chronic granulation tissue microbiota in cats and dogs. ... A comparison of culture vs 16S ribosomal RNA sequencing of chronic granulation tissue microbiota in cats and dogs ...

https://www.bsavalibrary.com/content/chapter/10.22233/9781910443446.ch69sec4

... amplified 16S ribosomal RNA genes (16S rRNA gene PCR-RFLP) was used to generate restriction profiles of reference strains of ... amplified 16S ribosomal RNA genes (16S rRNA gene PCR-RFLP) was used to generate restriction profiles of reference strains of ... amplified 16S ribosomal RNA genes (16S rRNA gene PCR-RFLP) was used to generate restriction profiles of reference strains of ... amplified 16S ribosomal RNA genes (16S rRNA gene PCR-RFLP) was used to generate restriction profiles of reference strains of ...

https://tohoku.pure.elsevier.com/en/publications/restriction-fragment-length-polymorphism-analysis-of-16s-ribosoma

SBV1 16S ribosomal RNA gene, partial sequence. Data. *Sep 2014. *. Marleen Otzen. ... It was identified by 16S rRNA gene sequencing as a strain of Variovorax paradoxus. Enzyme assays revealed an aminotransferase ...

https://www.researchgate.net/profile/Hein-Wijma

We sequenced partial nuclear 18S ribosomal RNA (18S rRNA; usually ~1300 bp), mitochondrial 16S ribosomal RNA (16S rRNA; ~470 bp ... based on mitochondrial and nuclear ribosomal RNA genes. Ann. Entomol. Soc. Am. 2004, 97, 903-912. [Google Scholar] [CrossRef][ ... Machida, R.J.; Knowlton, N. PCR Primers for metazoan nuclear 18S and 28S ribosomal DNA sequences. PLoS ONE 2012, 7, e46180. [ ... 5] using a combination of two nuclear (18S, H3) and two mitochondrial (16S, 12S) markers. The resulting phylogeny showed a ...

https://www.mdpi.com/2075-4450/11/1/51

Microbiota data were obtained using 16S ribosomal RNA sequencing. Untargeted metabolomics was conducted using a Q-Exactive ...

https://www.ars.usda.gov/research/publications/publication/?seqNo115=367059

... harbour two to three copies of 16S rRNA genes (rrsA, rrsB and rrsC) in their genomes. While rrsB and rrsC ... Dennis PP (1999) Expression of ribosomal RNA operons in halophilic archaea. In: Oren A (ed) Microbiology and biogeochemistry of ... 2017). We sequenced the 16S rRNA genes in each strain and estimated the Tmin, Topt and Tmax based on the PGC of the 16S rRNA ... Total RNA extraction and cDNA synthesis. We extracted total RNA from the pelleted cells by using a mirVana miRNA isolation kit ...

https://link.springer.com/article/10.1007/s10482-018-1144-3

GenBank M59100 Clostridium novyi 16S ribosomal RNA.. GenBank L37594 Clostridium novyi 16S ribosomal RNA (16S rRNA) gene. ...

https://www.atcc.org/products/17861

The Human Microbiome Project has identified more than 600 bacterial species in the oral cavity using 16S ribosomal (r)RNA ... Samples taken from the palate, buccal mucosa, tongue, and gingival crevice were subjected to 16S rRNA sequencing. The sequences ... stored in the Ribosomal Database Project, were compared to classify the microbes by biologic taxa. ...

http://www.medscape.com/viewarticle/753012

The composition of vaginal microbiota was characterised by 16S ribosomal RNA gene sequencing of the V3-V4 region. Results were ... The composition of vaginal microbiota was characterised by 16S ribosomal RNA gene sequencing of the V3-V4 region. Results were ... correlation analysis between the results of 16S ribosomal RNA gene sequencing and real-time qPCR. (a) In the discovery cohort, ... Richness and diversity indices of the vaginal microbiota were calculated from 16S ribosomal RNA gene sequencing of the V3-V4 ...

https://www.nature.com/articles/s41598-020-75534-3?error=cookies_not_supported&code=f736f39e-4c56-41ff-b033-d5007fbbb9bc

Process fluids were examined using culture, polymerase chain reaction, and 16S ribosomal RNA sequencing. RESULTS: Five ... Metalworking fluid primarily grew Pseudomonas pseudoalcaligenes and lacked mycobacterial DNA, but 16S analysis revealed more ... RNA; Ribonucleic acids; Humans; Men; Age groups; Air flow; Airway obstruction; Air samples; DNA; Deoxyribonucleic acids; ...

http://www2a.cdc.gov/nioshtic-2/BuildQyr.asp?s1=DNA+or+Deoxyribonucleic+acid&f1=TI&Startyear=&t1=1&s2=DNA+or+Deoxyribonucleic+acid&terms=3&Adv=1&ct=&B1=Search&f2=KW&Limit=500&Sort=DP+DESC&D1=10&EndYear=&PageNo=5&RecNo=45&View=f&

Phytoplasmas enclosed in at least sixteen different ribosomal groups infecting vegetable crops have been reported thus far ... Phytoplasmas enclosed in at least sixteen different ribosomal groups infecting vegetable crops have been reported thus far ... Candidatus Phytoplasma solani Clone Van 65 16S ribosomal RNA gene, Partial Sequence. GenBank Acc No. KT595210. ... 2004). Molecular characterization of 16S ribosomal DNA and phylogenetic analysis of two X-disease group phytoplasmas affecting ...

https://www.frontiersin.org/articles/10.3389/fmicb.2019.01349/full

16S ribosomal RNA methylation: emerging resistance mechanism against aminoglycosides. Clin Infect Dis. 2007;45:88-94. DOIPubMed ... or mutation of ribosomal proteins or rRNA. An additional mechanism, methylation of the aminoacyl site of 16S rRNA, confers high ... Wachino J, Yamane K, Shibayama K, Kurokawa H, Shibata N, Suzuki S, Novel plasmid-mediated 16S rRNA methylase, RmtC, found in a ... Wachino J, Yamane K, Kimura K, Shibata N, Suzuki S, Ike Y, Mode of transposition and expression of 16S rRNA methyltransferase ...

https://wwwnc.cdc.gov/eid/article/16/4/09-0736_article

Hippocampal amyloid-β (Aβ) assessment and the Morris water maze were used to evaluate AD-like changes, 16S ribosomal RNA ... Sequencing of the 16S ribosomal RNA gene in microbiota. 16S ribosomal RNA (rRNA) gene sequencing was performed as per our ... Hippocampal amyloid-β (Aβ) assessment and the Morris water maze were used to evaluate AD-like changes, 16S ribosomal RNA ... Distinct regions of 16S rRNA genes were amplified using specific primers (16S V4, 515F: GTGCCAGCMGCCGCGGTAA, 806R: ...

https://jneuroinflammation.biomedcentral.com/articles/10.1186/s12974-018-1223-4

16S Ribosomal RNA 31% * Prevotella 29% * rRNA Genes 29% * Metronidazole 29% * Genes 27% ...

https://portal.findresearcher.sdu.dk/en/persons/usjustesen/fingerprints/

CZERNILOFSKY, A.P.; KURLAND, C.G.; STÖFFLER, G.. 30S Ribosomal proteins associated with the 3′-terminus of 16S RNA. FEBS ... Taktiež ribozomálna RNA sa rozlišuje na základe sedimentácie; u prokaryotov poznáme 5S, 16S a 23S rRNA.[1] ... Veľká podjednotka sa skladá z 5S RNA (120 nukleotidov), 28S RNA (4700 nukleotidov), 5,8S RNA (160 nukleotidov) podjednotiek a ... 16S (1542 nukleotidov) 21 Eukaryotické ribozómy[upraviť , upraviť zdroj]. Eukaryotické 80S ribozómy sú umiestnené v cytoplazme ...

https://sk.wikipedia.org/wiki/Riboz%C3%B3m

Complete sequences of multidrug resistance plasmids bearing rmtD1 and rmtD2 16S ribosomal RNA methyltransferase genes. (pacb.com)
Complete nucleotide sequences were determined for two plasmids bearing rmtD group 16S rRNA methyltransferase genes. (pacb.com)
Before RFLP analysis, the 16S rRNA gene sequences were obtained from the GenBank database, and the analysis of the theoretical banding patterns for HpaII suggested good species discrimination. (elsevier.com)
16S rRNA gene sequences were amplified from isolated genomic DNA samples by PCR with spirochete-specific primers. (elsevier.com)
The sequences, stored in the Ribosomal Database Project, were compared to classify the microbes by biologic taxa. (medscape.com)
Prokaryotes harbour 16S rRNA genes encoding rRNA in the small subunit of the prokaryotic ribosome, and the sequences are highly conserved. (springer.com)
2017 ). A high percentage of prokaryotic genomes (83%) contain two or more copies of 16S rRNA genes, and the sequences are nearly identical among the copies of 16S rRNA genes (Sun et al. (springer.com)
2013 ). In particular, halophilic archaea of the genus Haloarcula have long been known to harbour significantly different sequences of 16S rRNA genes in their genomes (Mevarech et al. (springer.com)
For 16S rRNA gene sequences, rrsB and rrsC ( rrsBC ) show almost identical sequences, whereas rrsA shows different sequences (4-6%) from rrsBC (Mevarech et al. (springer.com)
2017 ). The different sequences of 16S rRNA genes were first reported in Haloarcula marismortui (Mevarech et al. (springer.com)
Phylogenetic tree generated by use of partial 16S rRNA gene sequences, indicating the relationship of 2 Eperythrozoon spp identified in swine and humans in the present study (asterisk) with other Eperythrozoon spp and Haemobartonella spp. (avma.org)
Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics Nature Chemistry. (nottingham.ac.uk)

In this study, restriction fragment-length polymorphism (RFLP) analysis of polymerase chain reaction (PCR)-amplified 16S ribosomal RNA genes (16S rRNA gene PCR-RFLP) was used to generate restriction profiles of reference strains of oral treponemes including Treponema denticola, Treponema socranskii, Treponema vincentii, Treponema pectinovorum and Treponema medium as well as for Treponema phagedenis and Treponema pallidum and five treponeme strains isolated from human periodontal pockets. (elsevier.com)
Sato, T & Kuramitsu, HK 1999, ' Restriction fragment-length polymorphism analysis of 16S ribosomal RNA genes amplified by polymerase chain reaction for rapid identification of cultivable oral treponemes ', Oral Microbiology and Immunology , vol. 14, no. 2, pp. 117-121. (elsevier.com)
Haloarcula strains, which are halophilic archaea, harbour two to three copies of 16S rRNA genes ( rrsA , rrsB and rrsC ) in their genomes. (springer.com)
Based on the strong correlation between the P GC of 16S rRNA genes and the growth temperatures of the prokaryotes, we hypothesised that high- P GC rrsA and low- P GC rrsBC are expressed at high and low temperatures, respectively. (springer.com)
Six types of 16S rRNA methyltransferase genes conferring resistance to these antimicrobial agents, armA , rmtA , rmtB , rmtC , rmtD , and npmA , have been identified ( 2 , 3 ). (cdc.gov)
Diversity of free-living and attached bacteria in offshore Western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA. (microbiologyresearch.org)
Bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes. (microbiologyresearch.org)

In this study, we determined the bacterial diversity profile of the Mexico City metro by massive sequencing of the 16S rRNA gene. (nature.com)
The Human Microbiome Project has identified more than 600 bacterial species in the oral cavity using 16S ribosomal (r)RNA sequencing. (medscape.com)
Metalworking fluid primarily grew Pseudomonas pseudoalcaligenes and lacked mycobacterial DNA , but 16S analysis revealed more complex bacterial communities. (cdc.gov)
They inhibit bacterial protein synthesis by binding irreversibly to the bacterial 16S ribosomal subunit, which thereby leads to cell death. (cdc.gov)
Results: Compared with control subjects, 16S ribosomal RNA amplicon concentrations (a proxy for bacterial burden) and bacterial diversity were significantly higher among asthmatic patients. (elsevier.com)
Sequence analysis of the 16S ribosomal RNA bacterial gene of some isolates, confirmed the phenotypic identification results. (worldfishcenter.org)
Tetracyclines inhibit protein synthesis and, therefore, bacterial growth by binding with 30S and possibly 50S ribosomal subunits of susceptible bacteria. (medscape.com)

To verify the hypothesis, we performed sequence analyses and expression surveys of each 16S rRNA gene in eight Haloarcula strains. (springer.com)
Molecular identification of the strains was carried out by analyzing the partial sequence of the 16S rRNA gene. (scielo.org.mx)
This subunit binds to the Shine-Dalgarno sequence of the bacteria and archaeal messenger RNA. (eurogentec.com)
The 16S rRNA is a highly conserved sequence between different species of bacteria and archaea. (eurogentec.com)

Samples taken from the palate, buccal mucosa, tongue, and gingival crevice were subjected to 16S rRNA sequencing. (medscape.com)
Rumen and fecal samples were collected on the day of diagnosis or matching and subjected to 16S rRNA profiling. (biomedcentral.com)

The composition of vaginal microbiota was characterised by 16S ribosomal RNA gene sequencing of the V3-V4 region. (nature.com)
Hippocampal amyloid-β (Aβ) assessment and the Morris water maze were used to evaluate AD-like changes, 16S ribosomal RNA sequencing analyses were used for intestinal flora measurements, and assessment of endothelial tight junctions and serum neurotransmitter and inflammatory mediator levels, as well as fecal microbiota transplant, was conducted to explore the underlying pathological mechanisms. (biomedcentral.com)
A combination of high-density 16S ribosomal RNA microarray and parallel clone library-sequencing analysis was used to profile the microbiota and examine relationships with clinical measurements. (elsevier.com)

16s and Shotgun tests identifies bacteria by their RNA and DNA. (microbiomeprescription.com)

Resistance to these antimicrobial agents usually results from production of aminoglycoside-modifying enzymes (such as acetyltransferases, phosphorylases, and adenyltransferases), reduced intracellular antimicrobial drug accumulation, or mutation of ribosomal proteins or rRNA. (cdc.gov)

We screened Salmonella and Escherichia coli isolates, collected 2004-2008 in the United Kingdom, for 16S rRNA methyltransferases. (cdc.gov)
In this study, 81,632 Salmonella and 10,700 Escherichia coli isolates obtained from the Health Protection Agency (HPA) Centre for Infections culture collection (isolated from January 2004 through December 2008) were screened for the presence of 16S rRNA methyltransferases. (cdc.gov)

Process fluids were examined using culture, polymerase chain reaction, and 16S ribosomal RNA sequencing. (cdc.gov)

16S rRNA (16S ribosomal RNA) is part of the 30S subunit of the prokaryotic ribosome. (eurogentec.com)

A prokaryotic initiation factor that plays a role in recycling of ribosomal subunits for a new round of translational initiation. (bvsalud.org)

The conformational landscape of the ribosomal protein S15 and its influence on the protein interaction with 16S RNA. (archives-ouvertes.fr)
The interaction between the ribosomal protein S15 and its binding sites in the 16S RNA was examined from two points of view. (archives-ouvertes.fr)
MD trajectories of the complex between the ribosomal protein S15 and RNA were also recorded in the presence and absence of Mg(2+) ions. (archives-ouvertes.fr)
When the Mg(2+) ions are removed, the internal mobility of the RNA and of the protein increases at the interaction interface close to the RNA G-U/G-C motif as a result of a gap between the phosphate groups in the UUCG capping tetraloop and of the disruption of S15-RNA hydrogen bonds in that region. (archives-ouvertes.fr)
RNA-binding protein;RNA degradosome binding protein [Ensembl]. (ntu.edu.sg)

16S rRNA gene PCR-RFLP using HpaII is a rapid and reliable method for differentiation of cultivable oral treponemes. (elsevier.com)

To better understand the microbial ecology of CRS, we generated a 16S rRNA gene sequencing profile of sinus mucus from CF-CRS patients. (umn.edu)
IMPACT: The metagenomics analysis will be a bridge to connect our current knowledge based on two existing datasets: 16S rRNA gene sequencing data (microbial profiles) and fecal and blood metabolomics (metabolite profiles). (elsevier.com)

It binds to 16S RIBOSOMAL RNA and stimulates the dissociation of vacant 70S ribosomes. (bvsalud.org)

This study was undertaken to develop a new rapid method to identify the mycobacterial isolates at species level by gene amplification restriction analysis using primers encoding 16S-23S rRNA internal transcribed spacer (ITS) region and flanking parts of the 16S as well as 23S rRNA gene. (who.int)

We previously obtained fecal and blood metabolomics and 16S rRNA gene sequencing datasets of the Phase 1 FMT trial. (elsevier.com)

Despite large surveys performed to identify 16S rRNA methyltransferases, the rmtC gene has been detected in only 2 Proteus mirabilis clinical isolates from Japan and Australia in 2006 and 2008, respectively ( 3 , 6 , 7 ). (cdc.gov)
Because 16S rRNA methyltransferases confer high-level resistance to amikacin, 13 S. enterica isolates were selected on the basis of ability to grow on Isosensitest agar containing 500 µg/mL amikacin, whereas none of the E. coli isolates grew under these conditions. (cdc.gov)

2000 ). Previous studies showed that variation of the salinity in the medium did not change the expression level of each 16S rRNA gene in Haloarcula strains (López-López et al. (springer.com)

METHODS: This system is based on the amplification of approximately 1.8 kb fragment encoding 16S-23S rRNA spacer region and flanking parts of the 16S as well as 23S rRNA gene. (who.int)

An additional mechanism, methylation of the aminoacyl site of 16S rRNA, confers high-level resistance to clinically important aminoglycosides such as amikacin, tobramycin, and gentamicin. (cdc.gov)

IMSEAR at SEARO: Rapid identification of mycobacteria by gene amplification restriction analysis technique targeting 16S-23S ribosomal RNA internal transcribed spacer & flanking region. (who.int)
Katoch VM, Parashar D, Chauhan DS, Singh D, Sharma VD, Ghosh S. Rapid identification of mycobacteria by gene amplification restriction analysis technique targeting 16S-23S ribosomal RNA internal transcribed spacer & flanking region. (who.int)

2017 ). Each rRNA operon contains a 5S rRNA gene, a 16S rRNA gene ( rrsA , rrsB or rrsC , respectively) and a 23S rRNA gene. (springer.com)

Our results show that the two ribosomal RNA MTs studied in this work are exquisitely sensitive to this small but nevertheless functionally important structural change. (nih.gov)
Our results suggest that the transcription of high- P GC rrsA and low- P GC rrsBC may be regulated in response to environmental temperature, and that 16S rRNAs transcribed from high- P GC rrsA function under high temperature conditions close to the maximum growth temperature. (springer.com)

RNA-DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA. (ndriresource.org)

On the other hand, several S15-RNA hydrogen bonds are reinforced, and water bridges appear between the three-way junction region and S15. (archives-ouvertes.fr)

S1 RNA binding domain, Ribonuclease E/G family, Polyribonucleotide phosphorylase C terminal [Interproscan]. (ntu.edu.sg)

en el control biológico de P . capsici en condiciones in vitro e in vivo . (scielo.org.mx)

Global epidemiology of non-influenza RNA respiratory viruses: data gaps and a growing need for surveillance. (cdc.gov)

Anatomy16

Organisms27

Diseases1

Chemicals and Drugs120

Analytical, Diagnostic and Therapeutic Techniques and Equipment23

Phenomena and Processes76

Information Science4

Health Care1

A new rapidly growing mycobacterial species, Mycobacterium murale sp. nov., isolated from the indoor walls of a children's day care centre. (1/13701)

Diversity of rhizobia associated with Amorpha fruticosa isolated from Chinese soils and description of Mesorhizobium amorphae sp. nov. (2/13701)

Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA-DNA hybridization. (4/13701)

Ignavigranum ruoffiae sp. nov., isolated from human clinical specimens. (5/13701)

Application of temperature-gradient gel electrophoresis in taxonomy of coryneform bacteria. (6/13701)

RFLP of rRNA genes and sequencing of the 16S-23S rDNA intergenic spacer region of ammonia-oxidizing bacteria: a phylogenetic approach. (7/13701)

Proposal to transfer Halococcus turkmenicus, Halobacterium trapanicum JCM 9743 and strain GSL-11 to Haloterrigena turkmenica gen. nov., comb. nov. (8/13701)

RNA

RNA, Small Interfering

RNA, Viral

RNA Editing

RNA Splicing

RNA, Ribosomal

RNA, Bacterial

DNA-Directed RNA Polymerases

RNA Viruses

RNA Interference

RNA, Messenger

RNA, Double-Stranded

RNA, Catalytic

RNA Folding

RNA Polymerase II

RNA, Fungal

RNA Stability

RNA Helicases

RNA, Antisense

RNA Processing, Post-Transcriptional

RNA, Transfer

RNA, Small Nuclear

RNA Precursors

RNA, Untranslated

Nucleic Acid Conformation

RNA Caps

Sequence Analysis, RNA

RNA, Plant

RNA, Protozoan

Base Sequence

RNA, Neoplasm

RNA Ligase (ATP)

DEAD-box RNA Helicases

RNA Polymerase III

Molecular Sequence Data

RNA Polymerase I

RNA, Nuclear

RNA, Guide

RNA, Ribosomal, 28S

RNA, Ribosomal, 18S

RNA-Binding Proteins

RNA, Ribosomal, 23S

RNA Transport

RNA, Spliced Leader

RNA, Satellite

RNA, Ribosomal, 16S

Amino Acid Sequence

RNA, Archaeal

Nucleic Acid Hybridization

Protein Biosynthesis

Cell Line

Virus Replication

Escherichia coli

RNA Cleavage

Mutation

Oligoribonucleotides

RNA, Heterogeneous Nuclear

Transcription, Genetic

RNA, Small Cytoplasmic

RNA 3' End Processing

Templates, Genetic

RNA, Small Untranslated

HeLa Cells

Ribonucleoproteins

Ribonucleases

Poly A

Genome, Viral

RNA, Ribosomal, 5.8S

DNA

RNA, Long Noncoding

RNA, Small Nucleolar

Binding Sites

RNA Virus Infections

Protein Binding

RNA, Complementary

Uridine

Promoter Regions, Genetic

Endoribonucleases

Cell Nucleus

RNA, Chloroplast