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

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)

Obtaining full-length 16S rRNA gene sequences is important for generating accurate taxonomy assignments of bacteria, which normally is realized via clone library construction. However, the application of clone library has been hindered due to its limitations in sample throughput and in capturing minor populations (<1 % of total microorganisms). To overcome these limitations, a new strategy, two-step denaturing gradient gel electrophoresis (2S-DGGE), is developed to obtain full-length 16S rRNA gene sequences. 2S-DGGE can compare microbial communities based on its first-round DGGE profiles and generate partial 16S rRNA gene sequences (8-534 bp, Escherichia coli numbering). Then, strain-specific primers can be designed based on sequence information of bacteria of interest to PCR amplify their remaining 16S rRNA gene sequences (515-1541 bps, E. coli numbering). The second-round DGGE can confirm DNA sequence purity of these PCR products. Finally, the full-length 16S rRNA gene sequences can be ...
Two Gram-stain-positive, aerobic, pink, curved, rod-shaped, non-motile bacterial strains, designated MI-28T and SKY-11, were isolated from freshwater samples taken from a river and fish pond, respectively. Based on characterization using a polyphasic approach, the two strains showed highly similar phenotypic, physiological and genetic profiles. They demonstrated 99.9 % 16S rRNA gene sequence similarity and a 93-95 % DNA-DNA relatedness value, suggesting that they represent a single genomic species. Phylogenetic analyses, based on 16S rRNA gene sequences, showed that strains MI-28T and SKY-11 form a distinct lineage with respect to closely related genera within the family Microbacteriaceae of the class Actinobacteria , which is most closely related to Rhodoluna and Pontimonas, and levels of 16S rRNA gene sequence similarity with the type species of related genera were less than 95 %. Cell-wall analysis showed that the peptidoglycan contained 2,4-diaminobutyric acid, alanine, glycine and glutamic acid.
A novel Ferrimonas species is described on the basis of phenotypic, chemotaxonomic and phylogenetic studies. Four halophilic organisms were isolated from marine sand and marine macroalgae samples by using high-pH marine agar 2216. An analysis of the nearly complete 16S rRNA gene sequences of these new isolates indicated that they were phylogenetically close (16S rRNA gene sequence similarity |99·5 %, gyrB gene sequence similarity |97·8 %), and were most closely related to Ferrimonas balearica (16S rRNA gene sequence similarity 97·1-97·3 %, gyrB gene sequence similarity 84·4-85·0 %). Chemotaxonomic data (major menaquinone MK7; major fatty acids C16 : 0 and C18 : 1 ω9c) supported the affiliation of the new isolates to the genus Ferrimonas. The results of physiological and biochemical tests allowed phenotypic differentiation of the isolates from F. balearica. It is therefore proposed that the new isolates represent a novel species with the name Ferrimonas marina sp. nov. and type strain A4D-4T (
A Gram-stain-positive, aerobic, non-motile, rod-shaped bacterium, strain 0704C9-2T, was isolated from hydrothermal sediment of the Indian Ocean. The organism grew with 0-5 % (w/v) NaCl and at 10-37 °C, with optimal growth occurring with 1 % NaCl and at 28-30 °C. Comparative 16S rRNA gene sequence analysis revealed that strain 0704C9-2T belonged to the genus Microbacterium . It exhibited highest 16S rRNA gene sequence similarity with Microbacterium testaceum DSM 20166T (98.4 %). Levels of similarity with the type strains of all other recognized species of the genus Microbacterium were less than 98.0 %. DNA-DNA hybridization experiments with strain 0704C9-2T and its closest relative, M. testaceum DSM 20166T, revealed a low reassociation value of 42.9 %. The DNA G+C content of strain 0704C9-2T was 73.3 mol%. The cell-wall peptidoglycan contained ornithine and the acyl type was glycolyl. The major whole-cell sugars were mannose, galactose, rhamnose and glucose. The major cellular fatty acids were
A polyphasic study was carried out to clarify the taxonomic position of two Gram-positive bacteria isolated from soil samples of the Grotta dei Cervi (Italy), a relatively unexplored hypogean environment. The strains, 20-5T and 23-23T, showed phenotypic and phylogenetic characteristics that were consistent with their classification in the genus Agromyces. 16S rRNA gene sequence comparisons revealed that the two strains formed distinct phyletic lines within the genus Agromyces. Based on 16S rRNA gene sequence similarity, chemotaxonomic data and the results of DNA-DNA relatedness studies, it is proposed that the two isolates represent two novel species of the genus Agromyces. Pronounced differences in a broad range of phenotypic characteristics and DNA G+C content distinguished the two strains from each other and from previously described species of the genus Agromyces. Two novel species are proposed: Agromyces salentinus sp. nov. (type strain, 20-5T=HKI 0320T=DSM 16198T=NCIMB 13990T) and Agromyces
Over a period of ten months a total of 5618 cord blood units (CBU) were screened for microbial contamination under routine conditions. The antibiotic resistance profile for all isolates was also examined using ATB strips. The detection rate for culture positive units was 7.5%, corresponding to 422 samples.16S rRNA sequence analysis and identification with API test system were used to identify the culturable aerobic, microaerophilic and anaerobic bacteria from CBUs. From these samples we recovered 485 isolates (84 operational taxonomic units, OTUs) assigned to the classes Bacteroidia, Actinobacteria, Clostridia, Bacilli, Betaproteobacteria and primarily to the Gammaproteobacteria. Sixty-nine OTUs, corresponding to 447 isolates, showed 16S rRNA sequence similarities above 99.0% with known cultured bacteria. However, 14 OTUs had 16S rRNA sequence similarities between 95 and 99% in support of genus level identification and one OTU with 16S rRNA sequence similarity of 90.3% supporting a family level
INTRODUCTION. The genus Bacillus is a phenotypically large, diverse collection of Gram-positive or Gram-variable staining, endospore-forming, aerobic or facultatively anaerobic, rod-shaped bacteria that have undergone considerable reclassification as advances in molecular biology have revealed a high phylogenetic heterogeneity (5, 21). The genus Bacillus and related genera are distributed widely in nature and include thermophilic, psychrophilic, acidophilic, alkalophilic and halophilic bacteria that utilize a wide range of carbon sources for heterotrophic growth or grow autotrophically.. The investigations on phylogenetic divergence of the genus Bacillus and its mesophilic and thermophilic members indicated the need for further and extensive studies to place some of these bacilli in appropriate taxonomic levels (1, 23, 21). With the accumulation of further 16S rRNA gene sequence data, Bacillus has been divided into more manageable and better-defined groups (16). According to Ludwig et al. (2007) ...
Background. 16S rRNA gene sequences are routinely assigned to operational taxonomic units (OTUs) that are then used to analyze complex microbial communities. A number of methods have been employed to carry out the assignment of 16S rRNA gene sequences to OTUs leading to confusion over which method is the most rigorous. A recent study suggested that a clustering method should be selected based on its ability to generate stable OTU assignments that do not change as additional sequences are added to the dataset. In contrast, we contend that the ability of the method to properly represent the distances between the sequences is more important. Methods. Our analysis implemented five de novo clustering algorithms including the single linkage, complete linkage, average linkage, abundance-based greedy clustering, distance-based greedy clustering, and the open and closed-reference methods. Using two previously published datasets we used the Matthews Correlation Coefficient (MCC) to assess the stability and
The recent development of methods applying next-generation sequencing to microbial community characterization has led to the proliferation of these studies in a wide variety of sample types. Yet, variation in the physical properties of environmental samples demands that optimal DNA extraction techniques be explored for each new environment. The microbiota associated with many species of insects offer an extraction challenge as they are frequently surrounded by an armored exoskeleton, inhibiting disruption of the tissues within. In this study, we examine the efficacy of several commonly used protocols for extracting bacterial DNA from ants. While bacterial community composition recovered using Illumina 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. These results indicate that the concentration necessary for dependable sequencing is around 10,000 copies of ...
A bacterial strain, B5-2(T), was isolated from an ice core drilled from Muztagh Glacier, China. Strain B5-2(T) was a Gram-stainnegative, short rod-shaped, motile by polar flagella, aerobic bacterium. The major fatty acids of strain B5-2(T) were summed feature 8 (C-18 : 1 omega 7c and/ or C-18 : 1 omega 6c) and iso-C-13 : 0. The G+C content of the DNA from strain B5-2(T) was 69.3 mol%. The predominant isoprenoid quinone of strain B5-2(T) was Q-10. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, an unidentified phospholipid and sulfoquinovosyldiacylglycerol. Comparative 16S rRNA gene sequence analysis revealed that the novel strain B5-2(T) shared highest similarity (96.7 %) with Aureimonas altamirensis S21B(T). On the basis of the results of this polyphasic study, strain B5-2(T) represents a novel species of the genus Aureimonas, for which the name Aureimonas glaciei sp. nov. is ...
Community Structure, Diversity, and Vertical Distribution of Archaea Revealed by 16S rRNA Gene Analysis in the Deep Sea Sediment of the Ulleung Basin, East Sea - archaeal diversity;16S rRNA gene;marine group;Ulleung Basin;East Sea;
In a recent study, rich clinical assessment and longitudinal study design are combined with host gene expression and microbial sequencing analyses to develop a framework for exploring disease etiology and outcomes in the context of human inflammatory disease. See related article: http://dx.doi.org/10.1186/s13059-015-0637-x
An obligately aerobic, chemoheterotrophic, mesophilic prosthecate bacterium, designated strain CGM1-3ENT, was isolated from the enrichment cultures of forest soil from Cheonggyesan Mountain, Republic of Korea. Cells were Gram-reaction-negative, motile rods (1.3–2.4 µm long by 0.30–0.75 µm wide) with single flagella. The strain grew at 10–37 °C (optimum 25–30 °C) and at pH 4.5–9.5 (optimum 5.0–7.0). The major cellular fatty acids were C16 : 0, C18 : 1ω7c 11-methyl, C12 : 1 3-OH and summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c). The genomic DNA G+C content of strain CGM1-3ENT was 63.7 mol%. The closest phylogenetic neighbour to strain CGM1-3ENT was identified as Asticcacaulis biprosthecium DSM 4723T (97.2 % 16S rRNA gene sequence similarity) and the DNA–DNA hybridization value between strain CGM1-3ENT and A. biprosthecium DSM 4723T was less than 24.5 %. Strain ...
16S rRNA amplicon analysis and shotgun metagenome sequencing are two main culture-independent strategies to explore the genetic landscape of various microbial communities. Recently, numerous studies have employed these two approaches together, but downstream data analyses were performed separately, which always generated incongruent or conflict signals on both taxonomic and functional classifications. Here we propose a novel approach, RiboFR-Seq (Ribosomal RNA gene flanking region sequencing), for capturing both ribosomal RNA variable regions and their flanking protein-coding genes simultaneously. Through extensive testing on clonal bacterial strain, salivary microbiome and bacterial epibionts of marine kelp, we demonstrated that RiboFR-Seq could detect the vast majority of bacteria not only in well-studied microbiomes but also in novel communities with limited reference genomes. Combined with classical amplicon sequencing and shotgun metagenome sequencing, RiboFR-Seq can link the annotations of 16S
The PyroTRF-ID bioinformatics methodology (http://bbcf.epfl.ch/PyroTRF-ID/) was developed to combine pyrosequencing and T-RFLP for describing microbial communities and identifying T-RFs by comparison of experimental and digital T-RFLP profiles obtained from the same biological samples. DNA extracts were subjected to amplification of the 16S rRNA gene pool, T-RFLP with the HaeIII restriction enzyme, 454 tag encoded FLX amplicon pyrosequencing, and PyroTRF-ID analysis. Digital T-RFLP profiles were generated from the denoised pyrosequencing datasets. Sequences contributing to each digital T-RF were classified to taxonomic bins using the Greengenes reference database. The method was tested on bacterial communities found in chloroethene-contaminated groundwater samples and in granular biofilms from lab-scale wastewater treatment systems. PyroTRF-ID was efficient for high-throughput mapping and digital T-RFLP profiling of pyrosequencing datasets. After denoising, multiple datasets comprising ca. ...
The appeal of using MinION for 16S rRNA sequencing is the portability, the potential to get near full-length 16S rRNA reads, and the ability for rapid (same day) sequence data. The capital costs are also low (a laptop), which is a step forward in the democratization of sequencing. While there are many potential applications, some may include sample screening prior to sequencing on another platform, sequencing in the field, or sequencing in the clinic for patient monitoring. The obvious challenge is the error rate.. To initially evaluate the potential of this technology, we sequenced 16S rRNA sequences from pure-culture E. coli and P. fluorescens, as well as a low-diversity sample from hydraulic fracturing produced water that we had previously analyzed using Illumina sequencing. We actually evaluated many more samples, but were forced to exclude them due to sample carryover between washes, which I discuss below.. We attempted to cluster the pure-culture reads into Operational Taxonomic Units ...
Bacterial community composition, as revealed by deep 16S sequence analyses, is argued to contribute to diverse human health and disease states (10). While the microbial community structure has been shown to influence susceptibility to infection in models of gastrointestinal disease (2, 4, 5, 34), the application of this concept to the female urinary tract has not been pursued. To define the existence and compositions of bladder bacterial communities in human females without the confounding factor of possible vulvo-vaginal contamination, we carefully sampled urine directly from female bladders using TUC and SPA. Deep 16S rRNA gene sequencing of these samples revealed that bacterial bladder communities of different types do exist in women, although not in all individuals. These data confirm and extend results of earlier studies (17, 21-23), clearly showing that urine specimens reported to clinicians as "culture-negative" or "insignificant growth" can contain varied bacterial communities that can ...
Widdel 1981) Kuever 2006 may be the type and only species of the genus and the order GEBAproject. class represents a separate lineage within the which is only distantly related to most other members of this class. The closest relatives based on 16S rRNA gene sequence similarity values are the type strains of (87.6% sequence identity) and (87.2%) both belonging to the family within the order [9]. The most similar cloned 16S rRNA gene EUB-42 [10] shared only 95.5% sequence similarity with and was retrieved from anaerobic sludge. Strain 2st14T WYE-354 represents the only stress of this varieties obtainable from a tradition collection so far. Available data from cultivation 3rd party studies (environmental testing and genomic studies) didnt surpass 86% series similarity indicating that people of this varieties are limited to specific habitats which are undersampled generally in most conditions or are in low great quantity (status Oct 2010). The solitary genomic 16S rRNA series of stress 2st14T was ...
Bacillus tusciae Bonjour & Aragno 1994 is a hydrogen-oxidizing, thermoacidophilic spore former that lives as a facultative chemolithoautotroph in solfataras. Although 16S rRNA gene sequencing was well established at the time of the initial description of the organism, 16S sequence data were not available and the strain was placed into the genus Bacillus based on limited chemotaxonomic information. Despite the now obvious misplacement of strain T2(T) as a member of the genus Bacillus in 16S rRNA-based phylogenetic trees, the misclassification remained uncorrected for many years, which was likely due to the extremely difficult, analysis-hampering cultivation conditions and poor growth rate of the strain. Here we provide a taxonomic re-evaluation of strain T2(T) (= DSM 2912 = NBRC 15312) and propose its reclassification as the type strain of a new species, Kyrpidia tusciae, and the type species of the new genus Kyrpidia, which is a sister-group of Alicyclobacillus. The family Alicyclobacillaceae da ...
Plant roots associate with a wide diversity of bacteria and archaea across the root-soil spectrum. The rhizosphere microbiota, the communities of microbes in the soil adjacent to the root, can contain up to 10 billion bacterial cells per gram of soil (Raynaud and Nunan, 2014) and can play important roles for the fitness of the host plant. Subsets of the rhizospheric microbiota can colonize the root surface (rhizoplane) and the root interior (endosphere), forming an intimate relationship with the host plant. Compositional analysis of these communities is important to develop tools in order to manipulate root-associated microbiota for increased crop productivity. Due to the reduced cost and increasing throughput of next-generation sequencing, major advances in deciphering these communities have recently been achieved, mainly through the use of amplicon sequencing of the 16S rRNA gene. Here we first present a protocol for dissecting the microbiota from various root compartments, developed using rice as a
An international consortium of scientists has proposed a new, updated method for assigning scientific names to uncultivated bacteria and archaea.
This module is in beta. Its interface or its results may change in a future update.. Bio::DB::Taxonomy::greengenes is an implementation of Bio::DB::Taxonomy which stores and accesses the Greengenes taxonomy of Bacteria and Archaea. Internally, it keeps the taxonomy into memory by using Bio::DB::Taxonomy::list. As a consequence, note that the IDs assigned to the taxonomy nodes, e.g. gg123, are arbitrary, contrary to the pre-defined IDs that NCBI assigns to taxons.. The latest release of the Greengene taxonomy (2011) contains about 4,600 taxa and occupies about 4MB of memory once parsed into a Bio::DB::Taxonomy::greengenes object. The taxonomy files taxonomy_16S_all_gg_2011_1.txt and taxonomy_16S_candiv_gg_2011_1.txt that this module can use are available from http://www.secondgenome.com/go/2011-greengenes-taxonomy/.. ...
TY - JOUR. T1 - PCR primers and probes for the 16S rRNA gene of most species of pathogenic bacteria, including bacteria found in cerebrospinal fluid. AU - Greisen, K.. AU - Loeffelholz, M.. AU - Purohit, A.. AU - Leong, D.. PY - 1994/1/1. Y1 - 1994/1/1. N2 - A set of broad-range PCR primers for the 16S rRNA gene in bacteria were tested, along with three series of oligonucleotide probes to detect the PCR product. The first series of probes is broad in range and consists of a universal bacterial probe, a gram-positive probe, a Bacteroides- Flavobacterium probe, and two probes for other gram-negative species. The second series was designed to detect PCR products from seven major bacterial species or groups frequently causing meningitis: Neisseria meningitidis, Haemophilus influenzae, Streptococcus pneumoniae, S. agalactiae, Escherichia coli and other enteric bacteria, Listeria monocytogenes, and Staphylococcus aureus. The third series was designed for the detection of DNA from species or genera ...
Perspectives. (i) Recommendation for future experiments.Our experiments demonstrated the need to include many different kinds of controls, at different steps, in order to avoid data misinterpretation. In particular, alien positive controls are important for establishing threshold values for OTU positivity. These alien positive controls should include taxa that are distant enough from those of potential pathogens to avoid potential confusion between sequences of alien controls and sequences that result from actual infection of rodent samples. Ideally, one should choose alien positive controls from bacterial genera which are not able to infect the studys host species. In our study, the use of Mycoplasma and Borrelia species as alien positive controls was not ideal because both genera are potential rodent pathogens. Thankfully, the species used as alien controls could be easily distinguished from the species found in rodents on the basis of the phylogenetic analyses of the V4 sequences. However, ...
Aerobic and anaerobic cultivation techniques, 16S rDNA-based phylogeny, and fluorescent in situ hybridization were used to describe the phylogenetic diversity and physiological versatility of lotic microbial aggregates (river snow) obtained from the river Elbe. In the course of the year the river snow community changed. It was characterized by a great bacterial diversity in spring, the predominant occurrence of algae in summer and reduction of the total bacterial cell count in autumn and winter. In all river snow samples, more than 70% of the bacteria counted with the general DNA stain DAPI also hybridized with the Bacteria-specific probe EUB338. In situ analysis of the bacterial river snow community with a comprehensive suite of specific rRNA-targeted probes revealed population dynamics to be governed by seasonal factors. During all seasons, beta-Proteobacteria constituted the numerically most important bacterial group forming up to 54% of the total cell counts. In contrast to this, the ...
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A denitrifying bacterium, designated strain FS(T), was isolated from anoxic digested sludge on oestradiol [17beta-oestra-1,3,5(10)-triene-3,17-diol] or testosterone (17beta-hydroxyandrost-4-en-3-one) as the sole source of carbon and energy with nitrate as the electron acceptor. Strain FS(T) represents the first known bacterium to grow anaerobically on both oestradiol (C-18) and testosterone (C-19). Steroidal hormones were degraded completely by nitrate reduction to dinitrogen monoxide, which was further reduced to dinitrogen in stationary-phase cultures. Gram-negative cells were slightly curved rods, 0.3-0.5 x 0.6-1.6 microm in size, motile, non-fermentative, non-spore-forming and catalase- and oxidase-positive, showing optimal growth at pH 7.0, 28 degrees C and 0.1% (w/v) NaCl. Beside steroidal hormones, the bacterium utilized only a narrow range of organic substrates with nitrate as the electron acceptor, including several fatty acids and glutamate. No aerobic or anaerobic growth occurred on ...
The resolution of the OFRG analysis was evaluated by examining the nucleotide sequences of the clones in six clusters distributed throughout the UPGMA tree (Fig. 3A, clusters 1 and 4 to 8). Clusters 2 and 3 (Fig. 3A) were not used for this analysis because only two clones from these groups were fully sequenced. For each cluster, pairwise sequence analysis showed that clones with an average sequence identity of 97% were grouped in the same cluster. The range of identities was 92.7 to 100%, and 79% of the values were between 96 and 98%. Thus, this OFRG analysis approximated species level resolution because DNA-DNA reassociation experiments have been used to show that bacterial rDNA with sequence identities of 97% or more are likely to come from the same species (25). In general, the resolution of OFRG depends on probe set properties, such as the number of probes, their discriminatory power, and the suitability of the set for a specific environment. Further refinements of probe selection algorithms ...
Estimating the diversity of life is a persistent challenge in biology. In microbiology, the task is complicated by the fact that the subjects of the census are not visible to the naked eye or easily differentiated morphologically, and they are estimated to number over 1030 individual bacteria worldwide (30). The properties of microorganisms necessitate the use of indirect analysis, involving culturing or 16S rRNA gene sequence analysis, to conduct a census of prokaryotes. Previous estimates of the number of bacterial species in the world range from 107 to 109 (6, 7). Although it is well accepted that the number of prokaryotic species in the world is immense and that our efforts to sample them have been inadequate, there has been no systematic analysis to assess how well we have sampled the bacterial world.. Estimating microbial phylogenetic diversity is intrinsically interesting to many microbiologists, but it also plays a crucial role in the functional analysis of microbial communities. ...
Estimating the diversity of life is a persistent challenge in biology. In microbiology, the task is complicated by the fact that the subjects of the census are not visible to the naked eye or easily differentiated morphologically, and they are estimated to number over 1030 individual bacteria worldwide (30). The properties of microorganisms necessitate the use of indirect analysis, involving culturing or 16S rRNA gene sequence analysis, to conduct a census of prokaryotes. Previous estimates of the number of bacterial species in the world range from 107 to 109 (6, 7). Although it is well accepted that the number of prokaryotic species in the world is immense and that our efforts to sample them have been inadequate, there has been no systematic analysis to assess how well we have sampled the bacterial world.. Estimating microbial phylogenetic diversity is intrinsically interesting to many microbiologists, but it also plays a crucial role in the functional analysis of microbial communities. ...
If your groups gene sequencing didnt work well, omit the exercise described in this paragraph.)If your soil samples 16s rRNA gene sequencing yielded enough data, prepare draft table/figure(s) on the information gleaned from your RDP data base analysis of the DNA sequence information on your cultured isolates. This analysis should identify your cultured soil community members. Do these bacteria belong to the genus or family you expected from the morphologic and metabolic information you have gathered? You can use Wellesleys electronic version of The Procaryotes found at [1] and/or Bergeys Manualfound at [2] to look up the bacteria identified by 16s rDNA sequencing. It would be interesting to compare the characteristics described in these reference books to the characteristics you noted in your analyses of your isolates.Do you have evidence for phylogenetic diversity as different form of richness in the community? Create a phylogenetic tree of your community members and selected non-members ...
The five most frequent keywords within the labels of environmental samples which yielded hits were microbi (9.4%), hypersalin (9.1%), http://www.selleckchem.com/products/pazopanib.html mat (8.6%), len, miniprim, new, view, world (8.5%) and food (3.4%). The single most frequent keyword within the labels of environmental samples which yielded hits of a higher score than the highest scoring species was hypersalin, len, mat, microbi, miniprim, new, view, world (12.5%). These key words are in line with the ecology and the niche from where strains of H. praevalens have been isolated. Figure 1 shows the phylogenetic neighborhood of H. praevalens GSLT in a 16S rRNA gene based tree.. The sequences of the four 16S rRNA gene copies in the genome differ from each other by up to five nucleotides, and differ by up to five nucleotides from the previously published 16S rRNA gene sequence ("type":"entrez-nucleotide","attrs":"text":"AB022034″,"term_id":"4127263″,"term_text":"AB022034″AB022034). ...
Dish one containing the swabbed doorknob bacteria grew three distinctive colonies. A dark yellow colony that was a rougher outside circle, a lighter yellow colony with a smooth outside circle, and finally a white colony which was round and smooth. Dish two containing the swabbed phone before sterilization grew the same colonies as dish one. Dish three containing the swabbed phone after sterilization grew four distinctive colonies. A dark yellow colony that was a rougher outside circle, a lighter yellow colony with a smooth outside circle, a white colony which was round and smooth, and finally a red colony that was a smooth circle that resided directly inside of the dark yellow colony ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
The SeqRank project aims are to develop approaches for automatic selection of high-quality molecular sequences for microbial strains, through the use of modern ranking techniques. Currently, the SeqRank algorithm can automate the process of selecting a high-quality 16S rRNA gene sequence for any given prokaryotic strain, based on a series of quality statistics, the latest status of taxonomy and the latest sequence information from the INSDC databases. The extended SeqRank workflow applies SeqRank to all type strains of a given prokaryotic genus or family, adds an automatically chosen outgroup sequence, and infers a phylogenetic tree from the resulting list of sequences.. Contact: [email protected] or the StrainInfo team (see contact). ...
Lineage: cellular organisms; Bacteria; Terrabacteria group; Firmicutes; Clostridia; Clostridiales; Ruminococcaceae; Ruminiclostridium; Ruminiclostridium ...
In order for the development of antibiotics and vaccines to be successful, the lifecycle and infection pattern of a pathogen must be studied well. In this paper, we study the rate of replication and the pattern of infection in a homogeneous population, which may or may not have an effective immunity or immunization program against the pathogen. We utilize three functions: one will determine the rate with which the pathogen replicates; the second will show the result of an infection by a single individual of a susceptible population without a removal rate; and the third will include the removal rate and its dependent factor, intensity.
Singleton, D.R., M. Hunt, S.M. Powell, R. Frontera-Suau and M.D. Aitken. (2007) Stable isotope probing with multiple growth substrates to determine substrate specificity of uncultivated bacteria. Journal of Microbiological Methods: 69:180-187 ...
Lineage: cellular organisms; Bacteria; Terrabacteria group; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; Alkaliphilus; Alkaliphilus ...
Gene sequencing is the process of identifying the base nucleotides in an organisms DNA. Practical applications of gene sequencing...
Check specificity/coverage. Use these options to reveal the in silico specificity (i.e. number of matching rRNA sequences outside the target taxon) and coverage (i.e. percentage of matching rRNA sequences within the target taxon) of an oligonucleotide against the most recent SSU and LSU rRNA sequence databases.. ...
Our understanding of thermophile diversity is based predominantly on PCR studies of community DNA. Universal and domain-specific rRNA gene PCR primers have historically been used for the assessment of microbial diversity ...
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COMPARISON OF THE POTENCY OF POLYVALENT ANTIMENINGOCOCCUS SERUM PRODUCED WITH FOUR AND SIX REPRESENTATIVE STRAINS AND THAT PRODUCED WITH SIXTY STRAINS, AS DETERMINED BY THE AGGLUTINATION ...
Thermobaculum terrenum ATCC ® BAA-798D-5™ Designation: Genomic DNA from Thermobaculum terrenum strain YNP1 (ATCC ® BAA-798™) TypeStrain=False Application:
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Parablechnum roraimense and P. paucipinna spp. nov. (Blechnaceae: Polypodiopsida), lectotypification of P. stuebelii , and citation corrections in the family
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"16S rRNA-based LTP release 111 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20.. ... "16S rRNA-based LTP release 111 (full tree)". Silva Comprehensive Ribosomal RNA Database [3]. Retrieved 2013-03-20. ... and the phylogeny is based on 16S rRNA-based LTP release 111 by 'The All-Species Living Tree' Project.[6] ...
"16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20.. ... The phylogeny is based on 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project.[3] ...
"16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20.. ... The currently accepted phylogeny is based on 16S rRNA-based LTP release 123 by The All-Species Living Tree Project.[7] ...
The All-Species Living Tree' Project."16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA ... The CSIs found in DNA-directed RNA polymerase subunit beta and DNA topoisomerase I in Thermales species may be involved in ... CSIs have also been found specific for Truepera radiovictrix . The phylogeny is based on 16S rRNA-based LTP release 123 by 'The ... Zhang G, Campbell EA, Minakhin L, Richter C, Severinov K, Darst SA (1999). "Crystal structure of Thermus aquaticus core RNA ...
"Escherichia coli 16S ribosomal RNA". "Halobacterium salinarum 18S ribosomal RNA". "Homo sapiens 18S ribosomal RNA (nuclear)". ... "Arabidopsis thaliana 16S ribosomal RNA (chloroplast)". Woese, Carl R.; Kandler, O; Wheelis, M (1990). "Towards a natural system ... Small subunit ribosomal ribonucleic acid (SSU rRNA) is the smallest of the two major RNA components of the ribosome. Associated ... LSU rRNA: the large subunit ribosomal ribonucleic acid. " ... with a number of ribosomal proteins, the SSU rRNA forms the ...
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 See the List of Prokaryotic ...
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 Notes: Strains found at ...
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. Stackebrandt E, Rainey ...
The All-Species Living Tree' Project."16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA ... and the 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project. Class "Chitinispirillia" ♠ Sorokin et al. 2016 ...
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. See the NCBI webpage on ...
The All-Species Living Tree' Project."16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA ... divided Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences and grouped the genera Chloroflexus, ... 16S identity, meaning that they could fall in different families or even orders. Recent phylogenetic analysis of the ... and the phylogeny is based on 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project. Notes: ♠ Strains found ...
"16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20. J.P. ... In the 16S rRNA trees, the Thermotogae have been observed to branch with the Aquificae (another phylum comprising ... Many of these CSIs in important housekeeping proteins such as Pol1, RecA, and TrpRS, and ribosomal proteins L4, L7/L12, S8, S9 ... 1999). "RNA polymerase of Aquifex pyrophilus: Implications for the evolution of the bacterial rpoBC operon and extremely ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20. J.P. Euzéby. "Thermoleophilia". List of Prokaryotic names ... The phylogeny is based on 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project. The currently accepted ... 2014 List of bacterial orders 'The All-Species Living Tree' Project."16S rRNA-based LTP release 123 (full tree)" (PDF). ...
"16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20. J.P. ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2011-11-17. J.P. Euzéby (June 13, 2011). "Geodermatophilaceae". List of ... 2013 ♠ Strains found at the NCBI, but not listed in the LSPN 'The All-Species Living Tree' Project."16S rRNA-based LTP release ... The currently accepted phylogeny is based on 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project The ...
The All-Species Living Tree' Project."16S rRNA-based LTP release 106 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA ... However, several studies disagree,. Furthermore, it has been found that the GC-content of ribosomal RNA, the traditional ... and the phylogeny is based on 16S rRNA-based LTP release 106 by 'The All-Species Living Tree' Project Notes: ♠ Strains found at ... members of the Holosporales have a much higher ribosomal GC-content than members of the Pelagibacterales and Rickettsiales, ...
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". www. ...
The All-Species Living Tree' Project."16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA ... The phylogeny is based on 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project. The currently accepted ...
"16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20. J.P. ... The currently accepted phylogeny is based on 16S rRNA-based LTP release 123 by The All-Species Living Tree Project The ...
Silva Comprehensive Ribosomal RNA Database [3]. Retrieved 2011-11-17. External link in ,publisher= (help) NCBI Taxonomy Browser ... External link in ,publisher= (help) 'The All-Species Living Tree' Project."16S rRNA-based LTP release 106 (full tree)" (PDF). ... and the phylogeny is based on 16S rRNA-based LTP release 106 by 'The All-Species Living Tree' Project The recently described ...
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 J.P. Euzéby. " ...
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 ...
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 "Jiella". www.uniprot.org. ...
2009 'The All-Species Living Tree' Project."16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal ... RNA Database. Retrieved 2016-03-20. J.P. Euzéby. "Nitriliruptoria". List of Prokaryotic names with Standing in Nomenclature ( ... The phylogeny is based on 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project. The currently accepted ...
1991 'The All-Species Living Tree' Project."16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal ... RNA Database. Retrieved 2016-11-11. J.P. Euzéby. "Glycomycetaceae". List of Prokaryotic names with Standing in Nomenclature. ... The currently accepted phylogeny is based on 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project The ...
... results of 16S ribosomal RNA gene sequencing. To emphasize this difference, Woese, Otto Kandler and Mark Wheelis later proposed ... Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular RNA ... although there are many introns in their transfer RNA and ribosomal RNA genes,[146] and introns may occur in a few protein- ... Fox based on the sequences of ribosomal RNA (rRNA) genes.[10] These two groups were originally named the Archaebacteria and ...
16S ribosomal RNA BSU_rRNA_4 rrnA-16S; 16S ribosomal RNA BSU_rRNA_6 rrnJ-16S; 16S ribosomal RNA BSU_rRNA_22 rrnD-16S; 16S ... 16S ribosomal RNA BSU_rRNA_30 rrnE-16S; 16S ribosomal RNA BSU_rRNA_19 rrnB-16S; 16S ribosomal RNA BSU_rRNA_23 rrnI-16S; 16S ... 16S ribosomal RNA BSU_rRNA_4 rrnA-16S; 16S ribosomal RNA BSU_rRNA_6 rrnJ-16S; 16S ribosomal RNA BSU_rRNA_22 rrnD-16S; 16S ... 16S ribosomal RNA BSU_rRNA_30 rrnE-16S; 16S ribosomal RNA BSU_rRNA_19 rrnB-16S; 16S ribosomal RNA BSU_rRNA_23 rrnI-16S; 16S ...
16S ribosomal RNA (or 16S rRNA) is the component of the 30S small subunit of a prokaryotic ribosome that binds to the Shine- ... Bacterial Sequencing The Ribosomal Database Project Ribosomes and Ribosomal RNA: (rRNA) SILVA rRNA database Greengenes: 16S ... Chakravorty S, Helb D, Burday M, Connell N, Alland D (May 2007). "A detailed analysis of 16S ribosomal RNA gene segments for ... Coenye T, Vandamme P (November 2003). "Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced ...
Classification of methanogenic bacteria by 16S ribosomal RNA characterization. George E. Fox, Linda J. Magrum, William E. Balch ... Classification of methanogenic bacteria by 16S ribosomal RNA characterization. George E. Fox, Linda J. Magrum, William E. Balch ... The 16S ribosomal RNAs from 10 species of methanogenic bacteria have been characterized in terms of the oligonucleotides ... Classification of methanogenic bacteria by 16S ribosomal RNA characterization. George E. Fox, Linda J. Magrum, William E. Balch ...
Entomoplasma melaleucae 16S ribosomal RNA gene, partial sequence Entomoplasma melaleucae 16S ribosomal RNA gene, partial ... Ribosomal Database Project II [Ribosomal Database Project II] Ribosomal Database Project II ...
Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin ... Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin ... Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin ... Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses Message Subject (Your Name) has sent you a message ...
SM9_1439 16S ribosomal RNA gene, partial sequence Pseudomonas sp. SM9_1439 16S ribosomal RNA gene, partial sequence. gi, ... Ribosomal Database Project II [Ribosomal Database Project II] Ribosomal Database Project II ...
16S ribosomal RNA. Details. Name. 16S ribosomal RNA. Kind. nucleotide. Organism. Enteric bacteria and other eubacteria. Drug ...
Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. ... STRUCTURE OF 16S RIBOSOMAL RNA, NMR, MINIMIZED AVERAGE STRUCTURE. *DOI: 10.2210/pdb1pbr/pdb ...
Ribosomal, 16S" by people in Harvard Catalyst Profiles by year, and whether "RNA, Ribosomal, 16S" was a major or minor topic of ... "RNA, Ribosomal, 16S" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical ... Utility of Histologic and Histochemical Screening for 16S Ribosomal RNA Gene Sequencing of Formalin-Fixed, Paraffin-Embedded ... RNA, Ribosomal, 16S*RNA, Ribosomal, 16S. *16S Ribosomal RNA. *RNA, 16S Ribosomal ...
Conformational changes in 16S ribosomal RNA induced by 30S ribosomal subunit proteins from Escherichia coli ... Conformational changes in 16S ribosomal RNA induced by 30S ribosomal subunit proteins from Escherichia coli ... Conformational changes in 16S ribosomal RNA induced by 30S ribosomal subunit proteins from Escherichia coli ... Conformational changes in 16S ribosomal RNA induced by 30S ribosomal subunit proteins from Escherichia coli ...
Structure of the A Site of Escherichia coli 16S Ribosomal RNA Complexed with an Aminoglycoside Antibiotic ... Aminoglycoside antibiotics that bind to 30S ribosomal A-site RNA cause misreading of the genetic code and inhibit translocation ... Structure of the A Site of Escherichia coli 16S Ribosomal RNA Complexed with an Aminoglycoside Antibiotic ... Structure of the A Site of Escherichia coli 16S Ribosomal RNA Complexed with an Aminoglycoside Antibiotic ...
Group G Beta-Hemolytic Streptococcal Bacteremia Characterized by 16S Ribosomal RNA Gene Sequencing. Patrick C. Y. Woo, Ami M. Y ... Identification by 16S ribosomal RNA gene sequencing of an Enterobacteriaceae species from a bone marrow transplant recipient. ... Identification by 16S ribosomal RNA gene sequencing of an Enterobacteriaceae species with ambiguous biochemical profile from a ... Group G Beta-Hemolytic Streptococcal Bacteremia Characterized by 16S Ribosomal RNA Gene Sequencing ...
... an uncommon 16S ribosomal methyltransferase gene, in an aminoglycoside- and cephalosporin-resistant Escherichia coli sequence ... Chromosomal 16S Ribosomal RNA Methyltransferase RmtE1 in Escherichia coli Sequence Type 448 On This Page ... Li B, Pacey MP, Doi Y. Chromosomal 16S Ribosomal RNA Methyltransferase RmtE1 in Escherichia coli Sequence Type 448. Emerging ... Li B, Pacey MP, Doi Y. Chromosomal 16S Ribosomal RNA Methyltransferase RmtE1 in Escherichia coli Sequence Type 448. Emerg ...
Structural changes in ribosomal RNA can be facilitated by the presence of modified nucleotides. Helix 31 of bacterial 16S ... ribosomal RNA harbors two modified nucleotides, m2G966 and m5C967, that are highly conserved among bacteria, though the degree ... Contacts between helix 31 and the P-site tRNA, initiation factors, and ribosomal proteins highlight the importance of this ... and were also shown to bind 30S ribosomal subunits. These peptides also inhibited protein synthesis in cell-free translation ...
The sequence of the 16S ribosomal RNA (rRNA) from the archaebacterium Halobacterium volcanii has been determined by DNA ... Sequence of the 16S ribosomal RNA from Halobacterium volcanii, an archaebacterium. Author and Affiliation:. Gupta, R.. ( ... The sequence of the 16S ribosomal RNA (rRNA) from the archaebacterium Halobacterium volcanii has been determined by DNA ... Although it is closer in sequence to the eubacterial 16S rRNA than to the eukaryotic 16S-like rRNA, the H. volcanii sequence ...
... study we developed a simple method using restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal RNA ... streptococci by restriction fragment length polymorphism analysis of polymerase chain reaction-amplified 16S ribosomal RNA ... We amplified 16S rRNA gene sequences from genomic DNA samples by PCR using universal primers and digested the PCR products with ... Therefore, 16S rRNA genes PCR-RFLP, using HpaII and HaeIII, could be an alternative method for the identification of mutans ...
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An analysis of Sargasso Sea bacterioplankton diversity using 16S ribosomal RNA Public Deposited ... The objective of this project was to use ribosomal RNA genes, cloned from natural populations of Sargasso Sea bacterioplankton ... The method described here for analyzing natural bacterial communities circumvents this problem by utilizing ribosomal RNA, ... Two different clone libraries of eubacterial 16S rRNA genes amplified from a natural population of Sargasso Sea picoplankton by ...
The 16S rDNA for two strains of toxic M. aeruginosa were sequenced and compared to available cyanobacterial, bacterial, and ... chloroplast 16S rRNA gene information. Phylogeny and the validity of a molecular taxonomy for the genus Microcystis is ... 16S ribosomal RNA gene sequence and phylogeny of toxic Microcystis sp. (cyanobacteria).. @article{Neilan199416SRR, title={16S ... ribosomal RNA gene sequence and phylogeny of toxic Microcystis sp. (cyanobacteria).}, author={Brett A Neilan and Philip T. Cox ...
Part of the mitochondrial (mt) 16S ribosomal (r) RNA gene was amplified by PCR from 582 ticks collected from southern Canada, ... There is considerable genetic variation in the mt 16S rRNA gene of I. scapularis. There is some evidence to support the ... From: Genetic variation in the mitochondrial 16S ribosomal RNA gene of Ixodes scapularis (Acari: Ixodidae) ...
Burton, MJ; Holland, MJ; Jeffries, D; Mabey, DC; Bailey, RL; (2006) Conjunctival chlamydial 16S ribosomal RNA expression in ... We measured chlamydial 16S ribosomal RNA (rRNA) expression, a marker of chlamydial metabolic activity, in comparison with the ... Conjunctival chlamydial 16S ribosomal RNA expression in trachoma: is chlamydial metabolic activity required for disease to ... The expression of 16S rRNA was strongly associated with the presence of clinical signs of active trachoma. CONCLUSIONS: The use ...
Evaluation of Real-time Polymerase Chain Reaction for Detection of the 16S Ribosomal RNA Gene of Mycobacterium tuberculosis and ... Evaluation of Real-time Polymerase Chain Reaction for Detection of the 16S Ribosomal RNA Gene of Mycobacterium tuberculosis and ... Evaluation of Real-time Polymerase Chain Reaction for Detection of the 16S Ribosomal RNA Gene of Mycobacterium tuberculosis and ...
Selection of peptides targeting helix 31 of bacterial 16S ribosomal RNA by screening M13 phage-display libraries.Molecules 16, ... Selection of peptides targeting helix 31 of bacterial 16S ribosomal RNA by screening M13 phage-display libraries.. [2011]. ... Selection of peptides targeting helix 31 of bacterial 16S ribosomal RNA by screening M13 phage-display libraries.. Molecules 16 ...
16s synonyms, 16s pronunciation, 16s translation, English dictionary definition of 16s. n. Abbr. rRNA The RNA that is a ... n biochem a type of RNA thought to be transcribed from DNA in the nucleoli of cell... ... ribosomal RNA. (redirected from 16s). Also found in: Medical. ribosomal RNA. n. Abbr. rRNA. The RNA that is a permanent ... ribosomal RNA. n (Biochemistry) biochem a type of RNA thought to be transcribed from DNA in the nucleoli of cell nuclei, ...
Part of the mitochondrial (mt) 16S ribosomal (r) RNA gene was amplified by PCR from 582 ticks collected from southern Canada, ... There is considerable genetic variation in the mt 16S rRNA gene of I. scapularis. There is some evidence to support the ... Genetic variation in the mitochondrial 16S ribosomal RNA gene of Ixodes scapularis (Acari: Ixodidae). *Chantel N Krakowetz1. , ... Krakowetz, C.N., Lindsay, L.R. & Chilton, N.B. Genetic variation in the mitochondrial 16S ribosomal RNA gene of Ixodes ...
  • Binding is dependent on the presence of a highly conserved purine-rich internal loop in the RNA, whereas removal of the loop minimally affects binding of the classical intercalators ethidium bromide and methidiumpropyl-EDTA·Fe (MPE·Fe). (elsevier.com)
  • [ 20 ] [ 21 ] Coa chegada a moitos laboratorios de técnicas de secuenciación de terceira xeración , é posible a identificación simultánea de miles de secuencias de ARNr 16S en cuestión de horas, o que permite facer estudos metaxenómicos , como por exemplo da flora intestinal . (wikipedia.org)
  • Conjunctival samples were tested for the presence of C. trachomatis DNA using a quantitative real-time polymerase chain reaction (PCR) assay for the omp1 gene and for the expression of C. trachomatis 16S rRNA using a 1-step, real-time reverse-transcriptase PCR assay. (lshtm.ac.uk)