A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.
Ribonucleic acid that makes up the genetic material of viruses.
A process that changes the nucleotide sequence of mRNA from that of the DNA template encoding it. Some major classes of RNA editing are as follows: 1, the conversion of cytosine to uracil in mRNA; 2, the addition of variable number of guanines at pre-determined sites; and 3, the addition and deletion of uracils, templated by guide-RNAs (RNA, GUIDE).
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).
Viruses whose genetic material is RNA.
A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. Most of the double-stranded segments are formed from transcription of DNA by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. Some double-stranded segments of RNA are normal in all organisms.
RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.
The processes of RNA tertiary structure formation.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6.
Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.
The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.
A family of proteins that promote unwinding of RNA during splicing and translation.
RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.
Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.
RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.
RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
Nucleic acid structures found on the 5' end of eukaryotic cellular and viral messenger RNA and some heterogeneous nuclear RNAs. These structures, which are positively charged, protect the above specified RNAs at their termini against attack by phosphatases and other nucleases and promote mRNA function at the level of initiation of translation. Analogs of the RNA caps (RNA CAP ANALOGS), which lack the positive charge, inhibit the initiation of protein synthesis.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.
Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
RNA present in neoplastic tissue.
An enzyme that catalyzes the conversion of linear RNA to a circular form by the transfer of the 5'-phosphate to the 3'-hydroxyl terminus. It also catalyzes the covalent joining of two polyribonucleotides in phosphodiester linkage. EC 6.5.1.3.
A large family of RNA helicases that share a common protein motif with the single letter amino acid sequence D-E-A-D (Asp-Glu-Ala-Asp). In addition to RNA helicase activity, members of the DEAD-box family participate in other aspects of RNA metabolism and regulation of RNA function.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure where it transcribes DNA into RNA. It has specific requirements for cations and salt and has shown an intermediate sensitivity to alpha-amanitin in comparison to RNA polymerase I and II. EC 2.7.7.6.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. The enzyme functions in the nucleolar structure and transcribes DNA into RNA. It has different requirements for cations and salts than RNA polymerase II and III and is not inhibited by alpha-amanitin. EC 2.7.7.6.
RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.
Small kinetoplastid mitochondrial RNA that plays a major role in RNA EDITING. These molecules form perfect hybrids with edited mRNA sequences and possess nucleotide sequences at their 5'-ends that are complementary to the sequences of the mRNA's immediately downstream of the pre-edited regions.
Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.
The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms.
The small RNAs which provide spliced leader sequences, SL1, SL2, SL3, SL4 and SL5 (short sequences which are joined to the 5' ends of pre-mRNAs by TRANS-SPLICING). They are found primarily in primitive eukaryotes (protozoans and nematodes).
Small, linear single-stranded RNA molecules functionally acting as molecular parasites of certain RNA plant viruses. Satellite RNAs exhibit four characteristic traits: (1) they require helper viruses to replicate; (2) they are unnecessary for the replication of helper viruses; (3) they are encapsidated in the coat protein of the helper virus; (4) they have no extensive sequence homology to the helper virus. Thus they differ from SATELLITE VIRUSES which encode their own coat protein, and from the genomic RNA; (=RNA, VIRAL); of satellite viruses. (From Maramorosch, Viroids and Satellites, 1991, p143)
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
Established cell cultures that have the potential to propagate indefinitely.
The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
A reaction that severs one of the sugar-phosphate linkages of the phosphodiester backbone of RNA. It is catalyzed enzymatically, chemically, or by radiation. Cleavage may be exonucleolytic, or endonucleolytic.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
Nuclear nonribosomal RNA larger than about 1000 nucleotides, the mass of which is rapidly synthesized and degraded within the cell nucleus. Some heterogeneous nuclear RNA may be a precursor to mRNA. However, the great bulk of total hnRNA hybridizes with nuclear DNA rather than with mRNA.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
Small RNAs found in the cytoplasm usually complexed with proteins in scRNPs (RIBONUCLEOPROTEINS, SMALL CYTOPLASMIC).
The steps that generate the 3' ends of mature RNA molecules. For most mRNAs (RNA, MESSENGER), 3' end processing referred to as POLYADENYLATION includes the addition of POLY A.
Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.
Short RNA, about 200 base pairs in length or shorter, that does not code for protein.
The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.
Complexes of RNA-binding proteins with ribonucleic acids (RNA).
Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.
A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
A class of untranslated RNA molecules that are typically greater than 200 nucleotides in length and do not code for proteins. Members of this class have been found to play roles in transcriptional regulation, post-transcriptional processing, CHROMATIN REMODELING, and in the epigenetic control of chromatin.
Small nuclear RNAs that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
Synthetic transcripts of a specific DNA molecule or fragment, made by an in vitro transcription system. This cRNA can be labeled with radioactive uracil and then used as a probe. (King & Stansfield, A Dictionary of Genetics, 4th ed)
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
A family of enzymes that catalyze the endonucleolytic cleavage of RNA. It includes EC 3.1.26.-, EC 3.1.27.-, EC 3.1.30.-, and EC 3.1.31.-.
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Ribonucleic acid in chloroplasts having regulatory and catalytic roles as well as involvement in protein synthesis.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
The rate dynamics in chemical or physical systems.
Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
Ribonucleic acid in helminths having regulatory and catalytic roles as well as involvement in protein synthesis.
Viruses parasitic on plants higher than bacteria.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
A transfer RNA which is specific for carrying phenylalanine to sites on the ribosomes in preparation for protein synthesis.
A transfer RNA which is specific for carrying lysine to sites on the ribosomes in preparation for protein synthesis.
Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.
Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
Deoxyribonucleic acid that makes up the genetic material of viruses.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)
Interruption or suppression of the expression of a gene at transcriptional or translational levels.
The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.
A transfer RNA which is specific for carrying tyrosine to sites on the ribosomes in preparation for protein synthesis.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.
Cyclic peptides extracted from carpophores of various mushroom species. They are potent inhibitors of RNA polymerases in most eukaryotic species, blocking the production of mRNA and protein synthesis. These peptides are important in the study of transcription. Alpha-amanitin is the main toxin from the species Amanitia phalloides, poisonous if ingested by humans or animals.
The functional hereditary units of VIRUSES.
Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.
An enzyme catalyzing the endonucleolytic cleavage of RNA at the 3'-position of a guanylate residue. EC 3.1.27.3.
The sum of the weight of all the atoms in a molecule.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Within most types of eukaryotic CELL NUCLEUS, a distinct region, not delimited by a membrane, in which some species of rRNA (RNA, RIBOSOMAL) are synthesized and assembled into ribonucleoprotein subunits of ribosomes. In the nucleolus rRNA is transcribed from a nucleolar organizer, i.e., a group of tandemly repeated chromosomal genes which encode rRNA and which are transcribed by RNA polymerase I. (Singleton & Sainsbury, Dictionary of Microbiology & Molecular Biology, 2d ed)
The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.
A fractionated cell extract that maintains a biological function. A subcellular fraction isolated by ultracentrifugation or other separation techniques must first be isolated so that a process can be studied free from all of the complex side reactions that occur in a cell. The cell-free system is therefore widely used in cell biology. (From Alberts et al., Molecular Biology of the Cell, 2d ed, p166)
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
Proteins encoded by a VIRAL GENOME that are produced in the organisms they infect, but not packaged into the VIRUS PARTICLES. Some of these proteins may play roles within the infected cell during VIRUS REPLICATION or act in regulation of virus replication or VIRUS ASSEMBLY.
Intermediates in protein biosynthesis. The compounds are formed from amino acids, ATP and transfer RNA, a reaction catalyzed by aminoacyl tRNA synthetase. They are key compounds in the genetic translation process.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
Nucleotide sequences located at the ends of EXONS and recognized in pre-messenger RNA by SPLICEOSOMES. They are joined during the RNA SPLICING reaction, forming the junctions between exons.
A transfer RNA which is specific for carrying alanine to sites on the ribosomes in preparation for protein synthesis.
A species of ENTEROVIRUS which is the causal agent of POLIOMYELITIS in humans. Three serotypes (strains) exist. Transmission is by the fecal-oral route, pharyngeal secretions, or mechanical vector (flies). Vaccines with both inactivated and live attenuated virus have proven effective in immunizing against the infection.
Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.
A plant genus of the family SOLANACEAE. Members contain NICOTINE and other biologically active chemicals; its dried leaves are used for SMOKING.
An RNA-containing enzyme that plays an essential role in tRNA processing by catalyzing the endonucleolytic cleavage of TRANSFER RNA precursors. It removes the extra 5'-nucleotides from tRNA precursors to generate mature tRNA molecules.
Separation of particles according to density by employing a gradient of varying densities. At equilibrium each particle settles in the gradient at a point equal to its density. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
The part of a cell that contains the CYTOSOL and small structures excluding the CELL NUCLEUS; MITOCHONDRIA; and large VACUOLES. (Glick, Glossary of Biochemistry and Molecular Biology, 1990)
The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
Viruses which produce a mottled appearance of the leaves of plants.
An enzyme that synthesizes DNA on an RNA template. It is encoded by the pol gene of retroviruses and by certain retrovirus-like elements. EC 2.7.7.49.
A compound composed of a two CYCLIC PEPTIDES attached to a phenoxazine that is derived from STREPTOMYCES parvullus. It binds to DNA and inhibits RNA synthesis (transcription), with chain elongation more sensitive than initiation, termination, or release. As a result of impaired mRNA production, protein synthesis also declines after dactinomycin therapy. (From AMA Drug Evaluations Annual, 1993, p2015)
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
A genus of FLAVIVIRIDAE causing parenterally-transmitted HEPATITIS C which is associated with transfusions and drug abuse. Hepatitis C virus is the type species.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
A transfer RNA which is specific for carrying aspartic acid to sites on the ribosomes in preparation for protein synthesis.
A transfer RNA which is specific for carrying methionine to sites on the ribosomes. During initiation of protein synthesis, tRNA(f)Met in prokaryotic cells and tRNA(i)Met in eukaryotic cells binds to the start codon (CODON, INITIATOR).
The relationships of groups of organisms as reflected by their genetic makeup.
A genus of tripartite plant viruses in the family BROMOVIRIDAE. Transmission is by beetles. Brome mosaic virus is the type species.
Proteins prepared by recombinant DNA technology.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
A ribonuclease that specifically cleaves the RNA moiety of RNA:DNA hybrids. It has been isolated from a wide variety of prokaryotic and eukaryotic organisms as well as RETROVIRUSES.
Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.
A multiribosomal structure representing a linear array of RIBOSOMES held together by messenger RNA; (RNA, MESSENGER); They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
A cell line derived from cultured tumor cells.
The outer protein protective shell of a virus, which protects the viral nucleic acid.
A family of enzymes that catalyze the exonucleolytic cleavage of RNA. It includes EC 3.1.13.-, EC 3.1.14.-, EC 3.1.15.-, and EC 3.1.16.-. EC 3.1.-
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
Proteins found in any species of bacterium.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
A transfer RNA which is specific for carrying glycine to sites on the ribosomes in preparation for protein synthesis.
A transfer RNA which is specific for carrying histidine to sites on the ribosomes in preparation for protein synthesis.
Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.
A transfer RNA which is specific for carrying valine to sites on the ribosomes in preparation for protein synthesis.
A group of uridine ribonucleotides in which the phosphate residues of each uridine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
A family of RNA viruses infecting insects and fish. There are two genera: Alphanodavirus and Betanodavirus.
Use for nucleic acid precursors in general or for which there is no specific heading.
The assembly of VIRAL STRUCTURAL PROTEINS and nucleic acid (VIRAL DNA or VIRAL RNA) to form a VIRUS PARTICLE.
Viruses which lack a complete genome so that they cannot completely replicate or cannot form a protein coat. Some are host-dependent defectives, meaning they can replicate only in cell systems which provide the particular genetic function which they lack. Others, called SATELLITE VIRUSES, are able to replicate only when their genetic defect is complemented by a helper virus.
Deletion of sequences of nucleic acids from the genetic material of an individual.
A transfer RNA which is specific for carrying arginine to sites on the ribosomes in preparation for protein synthesis.
Ribonucleic acid in algae having regulatory and catalytic roles as well as involvement in protein synthesis.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
A family of ribonucleoproteins that were originally found as proteins bound to nascent RNA transcripts in the form of ribonucleoprotein particles. Although considered ribonucleoproteins they are primarily classified by their protein component. They are involved in a variety of processes such as packaging of RNA and RNA TRANSPORT within the nucleus. A subset of heterogeneous-nuclear ribonucleoproteins are involved in additional functions such as nucleocytoplasmic transport (ACTIVE TRANSPORT, CELL NUCLEUS) of RNA and mRNA stability in the CYTOPLASM.
Proteins obtained from ESCHERICHIA COLI.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
The infective system of a virus, composed of the viral genome, a protein core, and a protein coat called a capsid, which may be naked or enclosed in a lipoprotein envelope called the peplos.
Highly conserved nuclear RNA-protein complexes that function in RNA processing in the nucleus, including pre-mRNA splicing and pre-mRNA 3'-end processing in the nucleoplasm, and pre-rRNA processing in the nucleolus (see RIBONUCLEOPROTEINS, SMALL NUCLEOLAR).
A defective virus, containing particles of RNA nucleoprotein in virion-like form, present in patients with acute hepatitis B and chronic hepatitis. It requires the presence of a hepadnavirus for full replication. This is the lone species in the genus Deltavirus.
Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.
A transfer RNA which is specific for carrying tryptophan to sites on the ribosomes in preparation for protein synthesis.
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.
DNA sequences recognized as signals to end GENETIC TRANSCRIPTION.
Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
Elements of limited time intervals, contributing to particular results or situations.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
A bacteriophage genus of the family LEVIVIRIDAE, whose viruses contain the short version of the genome and have a separate gene for cell lysis.
Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.
A hemoflagellate subspecies of parasitic protozoa that causes nagana in domestic and game animals in Africa. It apparently does not infect humans. It is transmitted by bites of tsetse flies (Glossina).
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
A genus of plant viruses that infects ANGIOSPERMS. Transmission occurs mechanically and through soil, with one species transmitted via a fungal vector. The type species is Tomato bushy stunt virus.
A purine nucleoside that has guanine linked by its N9 nitrogen to the C1 carbon of ribose. It is a component of ribonucleic acid and its nucleotides play important roles in metabolism. (From Dorland, 28th ed)
The addition of a tail of polyadenylic acid (POLY A) to the 3' end of mRNA (RNA, MESSENGER). Polyadenylation involves recognizing the processing site signal, (AAUAAA), and cleaving of the mRNA to create a 3' OH terminal end to which poly A polymerase (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) adds 60-200 adenylate residues. The 3' end processing of some messenger RNAs, such as histone mRNA, is carried out by a different process that does not include the addition of poly A as described here.
A transfer RNA which is specific for carrying leucine to sites on the ribosomes in preparation for protein synthesis.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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-positive, motile, round to ellipsoidal, endospore-forming, rod-shaped bacterial strain, SF-57T, was isolated from a marine solar saltern in Korea. This organism grew between 4 and 39 °C, with optimum growth at 30 °C. Strain SF-57T grew in the presence of 0·5-15·0 % NaCl, with optimum growth at 2-3 % NaCl. The peptidoglycan type of strain SF-57T was A1α linked directly through l-Lys. In strain SF-57T, menaquinone-7 (MK-7) was the predominant isoprenoid quinone and anteiso-C15 : 0 was the major fatty acid. The DNA G+C content was 41·8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SF-57T formed a coherent cluster with Marinibacillus marinus, with a bootstrap resampling value of 100 %. The level of 16S rRNA gene sequence similarity between strain SF-57T and M. marinus DSM 1297T was 98·9 %. The mean DNA-DNA relatedness level between strain SF-57T and the type strain of M. marinus was 20·6 %. Based on phenotypic properties, phylogenetic analyses and genomic
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
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
1), metal-rich acid mine drainage habitats in the Richmond Mine at Iron Mountain, Calif., we detected 16S rRNA gene sequences of a novel bacterial group belonging to the order Rickettsiales in the Alphaproteobacteria. The closest known relatives of this group (92% 16S rRNA gene sequence identity) are endosymbionts of the protist Acanthamoeba. Oligonucleotide 16S rRNA probes were designed and used to observe members of this group within acidophilic protists. To improve visualization of eukaryotic populations in the acid mine drainage samples, broad-specificity probes for eukaryotes were redesigned and combined to highlight this component of the acid mine drainage community. Approximately 4% of protists in the acid mine drainage samples contained endosymbionts. Measurements of internal pH of the protists showed that their cytosol is close to neutral, indicating that the endosymbionts may be neutrophilic. The endosymbionts had a conserved 273-nucleotide intervening sequence (IVS) in variable region ...
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. ...
Objectives Dysbiosis of the intestinal microbiota is associated with Crohns disease (CD). Functional evidence for a causal role of bacteria in the development of chronic small intestinal inflammation is lacking. Similar to human pathology, TNFdeltaARE mice develop a tumour necrosis factor (TNF)-driven CD-like transmural inflammation with predominant ileal involvement. Design Heterozygous TNFdeltaARE mice and wildtype (WT) littermates were housed under conventional (CONV), specific pathogen-free (SPF) and germ-free (GF) conditions. Microbial communities were analysed by high-throughput 16S ribosomal RNA gene sequencing. Metaproteomes were measured using LC-MS. Temporal and spatial resolution of disease development was followed after antibiotic treatment and transfer of microbial communities into GF mice. Granulocyte infiltration and Paneth cell function was assessed by immunofluorescence and gene expression analysis. Results GF-TNFdeltaARE mice were free of inflammation in the gut and antibiotic ...
View more ,A new extremely halophilic chemoorganotrophic bacterium (strain H200T [T = type strain]) was isolated from the hypersaline sediments of Retba Lake in Senegal. This organism was a sluggishly motile, rod-shaped, non-spore-forming, gram-negative, obligate anaerobe that grew optimally at 40 degrees C in the presence of 180 to 200 g of NaCl per liter. The DNA base composition was 32 mol% guanine plus cytosine. The fermentation products from glucose were ethanol, acetate, H2, and CO2. Yeast extract was required for growth. The fermentable substrates included D-fructose, galactose, D-xylose, cellobiose, lactose, maltose, sucrose, starch, D-mannitol, glycerol, and Casamino Acids. On the basis of the results of a 16S rRNA sequence analysis, strain H200T was found to be related to Haloanaerobium species. The 16S rRNA sequence of strain H200T differed from the sequences of the three previously described Haloanaerobium species, and strain H200T also differed from these organisms in its NaCl range ...
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 ...
Strains VIM M 10366(T), YIM M 10378(T) and YIM M 10400(T) were isolated from marine sediments collected from the Xisha Islands in the South China Sea. All three isolates were able to grow optimally at pH 7.0, 28-37 degrees C and 0-3% (w/v) NaCl. Comparison of 16S rRNA gene sequences showed that these strains are members of the genus Streptomyces, exhibiting moderately high 16S rRNA gene sequence similarities of 97.0-98.8% to members of the most closely related Streptomyces species. Morphological characteristics, physiological characteristics and compositions of whole-cell sugars and phospholipids are consistent with the diagnostic characteristics of the genus Streptomyces, but still allowed differentiation amongst the three strains and their neighbours. Based on 16S rRNA gene sequence analysis, DNA DNA relatedness, phenotypic characteristics and chemotaxonomic data, strains VIM M 10366(T), VIM M 10378(T) and VIM M 10400(T) were identified as members of three novel species of the genus ...
A Gram-stain-positive, aerobic, non-spore-forming, atrichous and short rod-shaped endophytic actinomycete, designated strain BGMRC 2075 , was isolated from the leaves of Kandelia candel, and was subjected to polyphasic characterization to unravel its taxonomic position. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BGMRC 2075 belongs to the genus Nocardioides ,showing the highest 16S rRNA gene sequence similarity to Nocardioides aestuarii JC2056 (96.1 %), Nocardioides agariphilus MSL-28 (95.1 %) andNocardioides islandiensis MSL-26 (95.1 %). The predominant cellular fatty acids of strain BGMRC 2075 were iso-C16 : 0, C17 : 1ω8c and C17 : 0. The major menaquinone was MK-8(H4). The diagnostic diamino acid in the cell-wall peptidoglycan was ll-2,6-diaminopimelic acid. The predominant cell-wall sugars were composed of ribose and glucose. The polar lipid pattern contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine, ...
A Gram-staining-positive, cocci, halotolerant bacterial strain, designated as SV-16T, was isolated from marine sediment and subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genus Salinicoccus. Growth occurs at temperatures in the range between 25-37 °C (optimum 30 °C), pH 7.0-11.0 (optimum 8.0) and at NaCl concentrations up to 25 .0 % (optimum 15.0 %). The highest level of 16S rRNA gene sequence similarity was with Salinicoccus carnicancri CrmT (98.6 %) followed by Salinicoccus halodurans W24T (96.6 %). The predominant polar lipids are diphosphatidylglycerol (DPG), phosphatidylinositol (PI) and phosphatidylglycerol (PG). The major cellular fatty acids are iso-C15: 0, anteiso-C15: 0, iso-C17: 0 and anteiso C17: 0. The draft genome of strain SV-16T consisted of 2,591,284 bp with G+C content of 48.7 mol %. On the basis of the phenotypic characteristics and genotypic ...
Background Next-generation sequencing platforms have revolutionised our ability to investigate the microbiota composition of complex environments, frequently through 16S rRNA gene sequencing of the bacterial component of the community. Numerous factors, including DNA extraction method, primer sequences and sequencing platform employed, can affect the accuracy of the results achieved. The aim of this study was to determine the impact of these three factors on 16S rRNA gene sequencing results, using mock communities and mock community DNA. Results The use of different primer sequences (V4-V5, V1-V2 and V1-V2 degenerate primers) resulted in differences in the genera and species detected. The V4-V5 primers gave the most comparable results across platforms. The three Ion PGM primer sets detected more of the 20 mock community species than the equivalent MiSeq primer sets. Data generated from DNA extracted using the 2 extraction methods were very similar. Conclusions Microbiota compositional data ...
article{7225551, abstract = {A Gram-stain-positive, ovoid, lactic acid bacterium, strain LMG 27676(T), was isolated from a spoiled sous-vide-cooked rutabaga. 16S rRNA gene sequence analysis indicated that the novel strain belongs to the genus Leuconostoc, with Leuconostoc kimchii and Leuconostoc miyukkimchii as the nearest neighbours (99.1 and 98.8\% 16S rRNA gene sequence similarity towards the type strain, respectively). Phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of the pheS, rpoA and atpA genes, and biochemical and genotypic characteristics allowed differentiation of strain LMG 27676(T) from all established species of the genus Leuconostoc. Strain LMG 27676(T) (=R-50029(T)=MHB 277(T)=DSM 27776(T)) therefore represents the type strain of a novel species, for which the name Leuconostoc rapi sp. nov. is proposed.}, author = {Lyhs, Ulrike and Snauwaert, Isabel and Pihlajaviita, Seija and De Vuyst, Luc and Vandamme, Peter}, issn = {1466-5026}, journal = {INTERNATIONAL ...
Globally, marine surface sediments constitute a habitat for estimated 1.7 × 1028 prokaryotes. For benthic microbial community analysis, usually, several grams of sediment are processed. In this study, we made the step from bulk sediments to single sand grains to address the microbial community directly in its micro-habitat: the individual bacterial diversity on 17 sand grains was analyzed by 16S ribosomal RNA gene sequencing and visualized on sand grains using catalyzed reporter deposition fluorescence in situ hybridization. In all, 104-105 cells were present on grains from 202 to 635 μm diameter. Colonization was patchy, with exposed areas largely devoid of any epi-growth (mean cell-cell distance 4.5±5.9 μm) and protected areas more densely populated (0.5±0.7 μm). Mean cell-cell distances were 100-fold shorter compared with the water column. In general, growth occurred in monolayers. Each sand grain harbors a highly diverse bacterial community as shown by several thousand species-level
Multiyear comparisons of bacterioplankton succession reveal that environmental conditions drive community shifts with repeatable patterns between years. However, corresponding insight into bacterioplankton dynamics at a temporal resolution relevant for detailed examination of variation and characteristics of specific populations within years is essentially lacking. During 1 year, we collected 46 samples in the Baltic Sea for assessing bacterial community composition by 16S rRNA gene pyrosequencing (nearly twice weekly during productive season). Beta-diversity analysis showed distinct clustering of samples, attributable to seemingly synchronous temporal transitions among populations (populations defined by 97% 16S rRNA gene sequence identity). A wide spectrum of bacterioplankton dynamics was evident, where divergent temporal patterns resulted both from pronounced differences in relative abundance and presence/absence of populations. Rates of change in relative abundance calculated for individual ...
Terminal restriction fragment length polymorphism (TRFLP or sometimes T-RFLP) is a molecular biology technique for profiling of microbial communities based on the position of a restriction site closest to a labelled end of an amplified gene. The method is based on digesting a mixture of PCR amplified variants of a single gene using one or more restriction enzymes and detecting the size of each of the individual resulting terminal fragments using a DNA sequencer. The result is a graph image where the x-axis represents the sizes of the fragment and the y-axis represents their fluorescence intensity. TRFLP is one of several molecular methods aimed to generate a fingerprint of an unknown microbial community. Other similar methods include DGGE, TGGE, ARISA, ARDRA, PLFA, etc. These relatively high throughput methods were developed in order to reduce the cost and effort in analyzing microbial communities using a clone library. The method was first described by Liu and colleagues in 1997 which employed ...
A polyphasic taxonomic approach including analysis of phenotypic, physiological and genotypic characteristics, 16S rRNA gene sequence and DNA-DNA hybridization analysis was used to determine the most consistent affiliation of Pseudomonas pictorum. Pseudomonas pictorum ATCC 23328 T exhibited phenotypic traits of members of the genus Stenotrophomonas including cellular fatty acid composition, quinone and limited range of substrates that could be used. Antibiotic susceptibility and physiological characteristics were determined. The DNA G+C content was 65.7 mol%. Phylogenetic analysis revealed that the type strains of Stenotrophomonas terrae, Stenotrophomonas humi, Stenotrophomonas nitritireducens and Stenotrophomonas acidaminiphila were the nearest relatives (16S rRNA gene sequence similarity of 98.0 to 98.8 %). All the other type strains of species of the genus Stenotrophomonas showed high 16S rRNA gene sequence similarities (96.8 to 97.2 %). DNA-DNA hybridizations revealed 31.0, 32.0, 43.3 and 43.6 %
A Gram-positive, spore-forming, aerobic, rod-shaped, xylanolytic bacterium designated strain CC-Alfalfa-35T was isolated from the rhizosphere of Medicago sativa L. in Taiwan. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain CC-Alfalfa-35T was affiliated to the genus Cohnella. Strain CC-Alfalfa-35T shared 95.3 % pairwise 16S rRNA gene sequence similarity to the type strain of the type species of the genus Cohnella (Cohnella thermotolerans DSM 17683T) besides showing a similarity of 97.4-93.6 % with other recognized species of the genus Cohnella. The DNA-DNA hybridization value between CC-Alfalfa-35T and Cohnella thailandensis KCTC 22296T was 37.7 %±1.7 % (reciprocal value, 55.7 %±3.0 %). Predominant cellular fatty acids were iso-C16 : 0 and anteiso-C15 : 0. The polar lipid profile constituted diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, lysyl-phosphatidylglycerol, three unidentified phospholipids and three unidentified aminophospholipids. The ...
Abstract: A group-specific PCR-based denaturing gradient gel electrophoresis (DGGE) method was developed and combined with group-specific clone library analysis to investigate the diversity of the Clostridium leptum subgroup in human feces. PCR products (length, 239 bp) were amplified using C. leptum cluster-specific primers and were well separated by DGGE. The DGGE patterns of fecal amplicons from 11 human individuals revealed host-specific profiles; the patterns for fecal samples collected from a child for 3 years demonstrated the structural succession of the population in the first 2 years and its stability in the third year. A clone library was constructed with 100 clones consisting of 1,143-bp inserts of 16S rRNA gene fragments that were amplified from one adult fecal DNA with one forward universal bacterial primer and one reverse group-specific primer. Eighty-six of the clones produced the 239-bp C. leptum cluster-specific amplicons, and the remaining 14 clones did not produce these ...
Background Assessment of the biodiversity of communities of small organisms is most readily done using PCR-based analysis of environmental samples consisting of mixtures of individuals. Known as metagenetics, this approach has transformed understanding of microbial communities and is beginning to be applied to metazoans as well. Unlike microbial studies, where analysis of the 16S ribosomal DNA sequence is standard, the best gene for metazoan metagenetics is less clear. In this study we designed a set of PCR primers for the mitochondrial 12S ribosomal DNA sequence based on 64 complete mitochondrial genomes and then tested their efficacy. Methodology/Principal Findings A total of the 64 complete mitochondrial genome sequences representing all metazoan classes available in GenBank were downloaded using the NCBI Taxonomy Browser. Alignment of sequences was performed for the excised mitochondrial 12S ribosomal DNA sequences, and conserved regions were identified for all 64 mitochondrial genomes. These
The 2,030 isolates analyzed in the present study comprised 1,235 isolates from stool samples from hospital patients, 395 isolates from stool samples referred via community practitioners, 150 isolates from the hospital environment, 27 isolates from veterinary sources, 89 isolates from the general environment, 1 isolate from an extraintestinal human site, and 133 reference strains held in the National Collection of Type Cultures, the American Type Culture Collection and the Culture Collection, University of Göteborg, and in the personal collections of C. difficile types held by Delmee and others (6, 16) and other members of the International Study Group on C. difficile (3).. PCR ribotyping was performed in duplicate, with slight modifications to a method described previously (13). Briefly, bacteria were harvested from overnight anaerobic cultures on Fastidious Anaerobe Agar (LabM, Bury, United Kingdom) supplemented with 6% horse blood. Crude template nucleic acid was prepared by resuspension of ...
Résumé: Transfer of Pseudomonas pictorum Gray and Thornton 1928 to genus Stenotrophomonas as Stenotrophomonas pictorum comb. nov., and emended description of the genus Stenotrophomonas Abstract A polyphasic taxonomic approach including analysis of phenotypic, physiological and genotypic characteristics, 16S rRNA gene sequence and DNA-DNA hybridization analysis was used to determine the most consistent affiliation of Pseudomonas pictorum. Pseudomonas pictorum ATCC 23328 T exhibited phenotypic traits of members of the genus Stenotrophomonas including cellular fatty acid composition, quinone and limited range of substrates that could be used. Antibiotic susceptibility and physiological characteristics were determined. The DNA G+C content was 65.7 mol%. Phylogenetic analysis revealed that the type strains of Stenotrophomonas terrae, Stenotrophomonas humi, Stenotrophomonas nitritireducens and Stenotrophomonas acidaminiphila were the nearest relatives (16S rRNA gene sequence similarity of 98.0 to ...
Abstract Environmental enteric dysfunction (EED) is often measured with a dual sugar absorption test and implicated as a causative factor in childhood stunting. Disturbances in the gut microbiota are hypothesized to be a mechanism by which EED is exacerbated, although this supposition lacks support. We performed 16S ribosomal RNA gene sequencing of fecal samples from 81 rural Malawian children with varying degrees of EED to determine which bacterial taxa were associated with EED. At the phyla level, Proteobacteria abundance is reduced with severe EED. Among bacterial genera, Megasphaera, Mitsuokella, and Sutterella were higher in EED and Succinivibrio, Klebsiella, and Clostridium_XI were lower in EED. Bacterial diversity did not vary with the extent of EED. Though EED is a condition that is typically believed to affect the proximal small bowel, and our focus was on stool, our data do suggest that there are intraluminal microbial differences that reflect, or plausibly lead to, EED.
During a study of bacterial diversity of soil, a novel strain, CA-15 , was isolated from Kyonggi University forest soil. Cells were aerobic, Gram-stain-negative, motile, non-spore-forming, rod-shaped, oxidase-positive and catalase- negative. Tyrosine was not oxidized but produced red pigmentation on an agar palte. Strain CA-15 hydrolysed Tween 60 and DNA. It grew at 15-35 C (optimum, 25-30 C), pH 6.0-10.0 (optimum, 7.0-9.0) and at 1.5 % (w/v) NaCl concentration. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain CA-15 formed a lineage within the family Caulobacteraceae of the class Alphaproteobacteria that was distinct from various species of the genus Brevundimonas. Brevundimonas bullata DSM 7126 was the closest member of strain CA-15 on the basis of 16S rRNA gene sequence similarity (98.48 %). Q-10 was only an isoprenoid quinone detected for strain CA-15 . The major polar lipids were 1,2-di-O-acyl-3-O-[d-glucopyranosyl-(1→4)-αd-glucopyranuronosyl]glycerol, ...
A novel halophilic actinomycete, strain H32T,was isolated froma Saharan soil sample collected in El-Oued province, south Algeria. The isolate was characterized by means of polyphasic taxonomy. Optimal growth was determined to occur at 28-32°C, pH 6.0-7.0 and in the presence of 15-25 %(w/v) NaCl. The strain was observed to produce abundant aerial mycelium, which formed long chains of rod-shaped spores at maturity, and fragmented substrate mycelium. The cell wall was determined to contain meso-diaminopimelic acid and the characteristic whole-cell sugars were arabinose and galactose. The predominant menaquinoneswere found to beMK-10(H4) andMK-9(H4). The predominant cellular fatty acids were determined to be anteiso C17:0, iso-C15:0 and iso-C16:0. The diagnostic phospholipid detected was phosphatidylcholine. Phylogenetic analyses based on the 16S rRNA gene sequence showed that this strain formed a distinct phyletic line within the radiation of the genus Actinopolyspora. The 16S rRNAgene sequence ...
Haemophilus segnis is a bacterium. H. segnis can be cultured on chocolate agar. Kilian, M. (1976). A Taxonomic Study of the Genus Haemophilus, with the Proposal of a New Species. Journal of General Microbiology. 93 (1): 9-62. doi:10.1099/00221287-93-1-9. ISSN 0022-1287. Kar-Pui Lau, Susanna; Chiu-Yat Woo, Patrick; Yin-Leung Chan, Benedict; Mei-Yuk Fung, Ami; Que, Tak-Lun; Yuen, Kwok-Yung (August 2002). Haemophilus Segnis Polymicrobial and Monomicrobial Bacteraemia Identified by 16S Ribosomal RNA Gene Sequencing. Journal of Medical Microbiology. 51 (8): 635-640. doi:10.1099/0022-1317-51-8-635. Retrieved 28 October 2014 ...
Chronic wounds affect millions of people and cost billions of dollars in the United States each year. These wounds harbor polymicrobial biofilm communities, which can be difficult to elucidate using culturing methods. Clinical molecular microbiological methods are increasingly being employed to investigate the microbiota of chronic infections, including wounds, as part of standard patient care. However, molecular testing is more sensitive than culturing, which results in markedly different results being reported to clinicians. This study compares the results of aerobic culturing and molecular testing (culture-free 16S ribosomal DNA sequencing), and it examines the relative abundance score that is generated by the molecular test and the usefulness of the relative abundance score in predicting the likelihood that the same organism would be detected by culture. Parallel samples from 51 chronic wounds were studied using aerobic culturing and 16S DNA sequencing for the identification of bacteria. One hundred
Four novel strains of saprophytic bacteria were isolated from the soil samples collected in the moist subtropics region (the Black Sea coast of the Caucasus) and studied using methods of polyphasic taxonomic analysis. Microorganisms were Gram-negative, oxidase positive, aerobic, rod-shaped motile bacteria that produced antibiotic named batumin with high and selective activity against staphylococci; its total formula was С 30Н48N2O7. Phylogenetic analysis of 16S rRNA gene sequences (1376 bp, accession number in Genbank - JF306642) indicated that the isolates belonged to the γ-Proteobacteria, formed a separate branch within the genus Pseudomonas and had 98% 16S rRNA gene sequence similarity with Pseudomonas gingeri. The latter essentially differed from the studied strains in its phenotypic characteristics ...
Experimental designs that take advantage of high-throughput sequencing to generate datasets include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), sequencing of 16S rRNA gene fragments, metagenomic analysis and selective growth experiments. In each case the underlying data are similar and are composed of counts of sequencing reads mapped to a large number of features in each sample. Despite this underlying similarity, the data analysis methods used for these experimental designs are all different, and do not translate across experiments. Alternative methods have been developed in the physical and geological sciences that treat similar data as compositions. Compositional data analysis methods transform the data to relative abundances with the result that the analyses are more robust and reproducible. Data from an in vitro selective growth experiment, an RNA-seq experiment and the Human Microbiome Project 16S rRNA gene abundance dataset were examined by ALDEx2, a
Two halophilic archaea, designated strains WSM-64(T) and WSM-66, were isolated from a sample taken from a borehole in the currently unexploited Barycz mining area belonging to the Wieliczka Salt Mine Company, in Poland. Strains are red pigmented and form non-motile cocci that stain Gram-negative. Strains WSM-64(T) and WSM-66 showed optimum growth at 40 °C, in 20% NaCl and at pH 6.5-7.5. The strains were facultative anaerobes. The major polar lipids of the two strains were phosphatidylglycerol (PG2), phosphatidylglycerol phosphate methyl ester (PGP-Me) and sulfated diglycosyl diether (S-DGD). Menaquinone MK-8 was the major respiratory quinone. The DNA G+C content of strain WSM-64(T) was 61.2 mol% by HPLC method; 61.0 mol% by genome sequencing. Analysis of the almost complete 16S rRNA gene sequence indicated that the strains WSM-64(T) and WSM-66 (99.7% identity) represented a member of the genus Halorhabdus in the family Halobacteriaceae. Both strains formed a distinct cluster and were most ...
Massively parallel high throughput sequencing technologies allow us to interrogate the microbial composition of biological samples at unprecedented resolution. The typical approach is to perform high-throughout sequencing of 16S rRNA genes, which are then taxonomically classified based on similarity to known sequences in existing databases. Current technologies cause a predicament though, because although they enable deep coverage of samples, they are limited in the length of sequence they can produce. As a result, high-throughout studies of microbial communities often do not sequence the entire 16S rRNA gene. The challenge is to obtain reliable representation of bacterial communities through taxonomic classification of short 16S rRNA gene sequences. In this study we explored properties of different study designs and developed specific recommendations for effective use of short-read sequencing technologies for the purpose of interrogating bacterial communities, with a focus on classification using
Members of phylum Acanthocephala are parasites of vertebrates and arthropods and are distributed worldwide. The phylum has traditionally been divided into three classes, Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala; a fourth class, Polyacanthocephala, has been recently proposed. However, erection of this new class, based on morphological characters, has been controversial. We sequenced the near complete 18S rRNA gene of Polyacanthorhynchus caballeroi (Polyacanthocephala) and Rhadinorhynchus sp. (Palaeacanthocephala); these sequences were aligned with another 21 sequences of acanthocephalans representing the three widely recognized classes of the phylum and with 16 sequences from outgroup taxa. Phylogenetic relationships inferred by maximum-likelihood and maximum-parsimony analyses showed Archiacanthocephala as the most basal group within the phylum, whereas classes Polyacanthocephala + Eoacanthocephala formed a monophyletic clade, with Palaeacanthocephala as its sister group. ...
A bacterial strain (CCUG 44693T) was recovered during an industrial hygiene control. Phylogenetic analyses using the 16S rRNA gene sequence of the isolate indicated that it represents a new lineage in the α-1 subclass of the Proteobacteria, with the highest sequence similarity of 93.3% to the type strain of Muricoccus roseus. In the polyamine pattern spermidine was the predominant compound. The polar lipid profile consisted of the major lipids phosphatidyl ethanolamine, phosphatidyl dimethylethanolamine, phosphatidyl glycerol, phosphatidyl cholin and an unknown amino lipid. The major respiratory quinone was a ubiquinone Q-10 and the major whole cell fatty acids were 19:0 cyclo ω8c and 18:1 ω7c. The isolate also contained 18:1 2-OH and other fatty acids typical for members of the α-1 subclass of the Proteobacteria in addition to 10:0 2-OH in low amounts, not detected in members of closely related genera. The strain grew heterotrophically and strictly aerobically and formed red-colored ...
A Gram-negative, heterotrophic, marine bacterium, designated strain SW-11(T), was isolated from the reef-building coral Isopora palifera in Kenting, Taiwan. Cells were rods and were motile by a single polar flagellum. The strain grew at 10-45 degrees C (optimum, 30-35 degrees C), at pH 7.0-8.0 (optimum, pH 7.5) and with 2.0-4.0% NaCl (optimum, 2.5-3.0%). The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, diphosphatidylglycerol and four unknown phospholipids. Isoprenoid quinones consisted of ubiquinone 9 (78.8%) and ubiquinone 8(21.1%). Major cellular fatty acids were summed feature 3 (C(16:1)omega 7c and/or C(16:1)omega 6c; 22.3%), C(17:1)omega 8c (13.4%), summed feature 8 (C(18:1)omega 6c and/or C(18:1)omega 7c; 13.1%), C(16:0) (10.3%) and anteiso-C(17:1)omega 9c (10.0%). The DNA G+C content was 51.6 mol%. 165 rRNA gene sequence analysis indicated that strain SW-11(T) belongs to the class Gammaproteobacteria and is a member of the order ...
The 16S rRNA gene sequence analysis of Bifidobacterium species reveals high interspecies sequence similarity in the range of 87.7-99.5%. This study illustrated the extent of superiority of a multigenic approach, involving protein-coding genes, in comparison to the 16S rRNA gene, to precisely delineate presumptive Bifidobacterium isolates obtained from probiotic milk beverages, culture collections and pharmaceutical probiotic preparations. Oligonucleotide pairs PurF-rev/PurF-uni; RpoCuni/ RpoC-rev; DnaB-uni/DnaB-rev; DnaG-uni/DnaG-rev; and ClpC-uni/ClpC-rev amplified housekeeping genes while 27F/ 1492R amplified the 16S rRNA gene of the presumptive bifidobacteria in a polymerase chain reaction. Sequences of 16S rRNA gene and some protein-coding genes effectively identified the isolates. Phylogenetic analysis together with concatenation showed that clpC, purF and dnaG genes had over 8-fold better discriminatory power than the 16S rRNA gene in discriminating between Bifidobacterium isolates. ...
The structure of microbial communities was examined as a function of community composition and the relative abundance of specific microbial groups to examine the effects that plant community composition and land-use history have on microbial communities in the soil. The sites sampled were part of the Long Term Ecological Research (LTER) project in agricultural ecology at the W.K. Kellogg Biological Station of Michigan State University (Hickory Corners, MI) and included both active and abandoned agricultural fields as well as nearby fields that had never been cultivated. Microbial community structure was assessed by extracting total RNA from soil samples and using 16S rRNA-targeted oligonucleotide probes to quantify the abundance of rRNA from the alpha, beta, and gamma Proteobacteria, the Actinobacteria (Gram positive bacteria with a high mol % G+C genome), the Bacteria, and the Eukarya. In addition, soil microbial communities were characterized by examining fluorescently tagged terminal ...
Chen, H.,Lim, C.K.,Lee, Y.K.,Chan, Y.N. (2000). Comparative analysis of the genes encoding 23S-5S rRNA intergenic spacer regions of Lactobacillus casei-related strains. International Journal of Systematic and Evolutionary Microbiology 50 (2) : 471-478. [email protected] Repository ...
A novel Gram-negative, slightly halophilic, catalase-positive, oxidase-negative, obligately aerobic, non-sporulating rod-shaped bacterium, designated strain JSM 078169(T), was isolated from a sea urchin (Hemicentrotus pulcherrimus) collected from the South China Sea. Growth occurred with 1-20 % (w/v) total salts (optimum, 3-5 %), at pH 6.0-10.5 (optimum, pH 7.5) and at 4-40 degrees C (optimum, 25-30 degrees C). The major cellular fatty acids were C-18: 1 omega 7c, C-16:0 and C-12:0 3-OH. The predominant respiratory quinone was Q-9 and the genomic DNA G + C content was 55.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 078169(T) should be assigned to the genus Halomonas. The sequence similarities between the isolate and the type strains of members of the genus Halomonas were in the range 92.4-97.0%. The combination of phylogenetic analysis, DNA-DNA relatedness, phenotypic characteristics and chemotaxonomic data supported the view that strain JSM 078169(T) ...
Investigation of the initial and spoilage microbial diversity of iced stored sea bream was carried out. Culture dependent methods were used for bacterial enumeration and phenotypic identification of bacterial isolates, while culture independent methods, using bacterial 16S rRNA gene amplification, cloning and sequencing of DNA extracted directly from the flesh were also employed. The culture dependent approach revealed that the initial microbiota was dominated by Acinetobacter, Shewanella, Pseudomonas and Flavobacterium, while at the end of shelf-life determined by sensory analysis (16 days), the predominant microbiota was Pseudomonas and Shewanella. Culture independent approach showed that initially the sea bream flesh was strongly dominated by Acinetobacter, while Pseudomonas, Aeromonas salmonicida and Shewanella were the predominant phylotypes at the end of shelf-life. Initial and spoilage microbiota comprised of phylotypes previously identified by others using traditional or molecular ...
TY - JOUR. T1 - Diversity of Haloquadratum and other haloarchaea in three, geographically distant, Australian saltern crystallizer ponds. AU - Oh, Dickson. AU - Porter, Kate. AU - Russ, Brendan. AU - Burns, David. AU - Dyall-Smith, Mike. PY - 2010/3. Y1 - 2010/3. N2 - Haloquadratum walsbyi is frequently a dominant member of the microbial communities in hypersaline waters. 16S rRNA gene sequences indicate that divergence within this species is very low but relatively few sites have been examined, particularly in the southern hemisphere. The diversity of Haloquadratum was examined in three coastal, but geographically distant saltern crystallizer ponds in Australia, using both culture-independent and culture-dependent methods. Two 97%-OTU, comprising Haloquadratum- and Halorubrum-related sequences, were shared by all three sites, with the former OTU representing about 40% of the sequences recovered at each site. Sequences 99.5% identical to that of Hqr. walsbyi C23T were present at all three sites ...
PubMed journal article: Use of 16S rRNA gene sequencing for rapid identification and differentiation of Burkholderia pseudomallei and B. mallei. Download Prime PubMed App to iPhone, iPad, or Android
Staphylococcus aureus is an important human and animal pathogen, and is regarded as an important cause of intramammary infection (IMI) in ruminants. Staphylococcus aureus genetic variability and virulence factors have been well studied in veterinary medicine, especially in cows as support for control and management of IMI. The aim of the present study was to genotype 71 Staph. aureus isolates from the bulk tank and foremilk of water buffaloes (n. = 40) and from udder tissue (n. = 7) and foremilk (n. = 24) from small ruminants. The method used was previously applied to bovine Staph. aureus and is based on the amplification of the 16S-23S rRNA intergenic spacer region. The technique applied was able to identify different Staph. aureus genotypes isolated from dairy species other than the bovine species, and cluster the genotypes according to species and herds. Virulence gene distribution was consistent with genotype differentiation. The isolates were also characterized through determination of the ...
The bacterial communities of aphids were investigated by terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis analysis of 16S rRNA gene fragments generated by PCR with general eubacterial primers. By both methods, the -proteobacterium Buchnera was detected in laboratory cultures of six parthenogenetic lines of the pea aphid Acyrthosiphon pisum and one line of the black bean aphid Aphis fabae, and one or more of four previously described bacterial taxa were also detected in all aphid lines except one of A. pisum. These latter bacteria, collectively known as secondary symbionts or accessory bacteria, comprised three taxa of -proteobacteria (R-type [PASS], T-type [PABS], and U-type [PAUS]) and a rickettsia (S-type [PAR]). Complementary analysis of aphids from natural populations of four aphid species (A. pisum [n 74], Amphorophora rubi [n 109], Aphis sarothamni [n 42], and Microlophium carnosum [n 101]) from a single geographical location revealed Buchnera ...
Looking for online definition of DNA-DNA hybridization in the Medical Dictionary? DNA-DNA hybridization explanation free. What is DNA-DNA hybridization? Meaning of DNA-DNA hybridization medical term. What does DNA-DNA hybridization mean?
Evaluating the composition of the human gut microbiota greatly facilitates studies on its role in human pathophysiology, and is heavily reliant on culture-independent molecular methods. A microarray designated the Human Gut Chip (HuGChip) was developed to analyze and compare human gut microbiota samples. The PhylArray software was used to design specific and sensitive probes. The DNA chip was composed of 4,441 probes (2,442 specific and 1,919 explorative probes) targeting 66 bacterial families. A mock community composed of 16S rRNA gene sequences from intestinal species was used to define the threshold criteria to be used to analyze complex samples. This was then experimentally verified with three human faecal samples and results were compared (i) with pyrosequencing of the V4 hypervariable region of the 16S rRNA gene, (ii) metagenomic data, and (iii) qPCR analysis of three phyla. When compared at both the phylum and the family level, high Pearsons correlation coefficients were obtained between ...
The Hallman et al. [8] definition of endophytic bacteria requires surface-disinfested plant tissue or extraction from the plant. Disinfestation by killing all the epiphytic bacteria may be effective when culture-dependent protocols are used, but is not appropriate in culture-independent protocols, such as the present one, since the DNA or RNA of dead epiphytes, if not removed, would still be amplified by bacteria-specific PCR. For those organs, like tubers, whose outer layers can be easily peeled off, endophytic bacteria can be isolated from inside of the plants unambiguously. However, peeling the epidermis off leaves, while possible, is not practical for a study like the present one. Therefore, to study leaf endophytic bacterial communities, it is critical to dislodge epiphytic bacteria from the leaf surfaces as far as possible. We have dislodged epiphytes using methods similar to those reported by others [13, 26-28]. Since we did not test the rinse water for rDNA amplicons, we cannot be ...
Oceanospirillales merupakan ordo yang beraneka ragam jika dilihat dari sisi morfologi dan metabolismenya. Beberapa dapat tumbuh di tengah-tengah oksigen, sementara yang lain membutuhkan lingkungan yang anaerob.[2] Most Oceanospirillales are prefer or require high salt concentrations to grow.[2] Mereka ada di berbagai macam relung, tetapi Oceanospirillales memperoleh energi dengan mengolah berbagai produk organik. Semua bakteri Oceanospirillales bersifat motil kecuali untuk anggota genus Alcanivorax.[2] ...
The aim of this work was to determine the effect of light crude oil on bacterial communities during an experimental oil spill in the North Sea and in mesocosms (simulating a heavy, enclosed oil spill), and to isolate and characterize hydrocarbon-degrading bacteria from the water column. No oil-induced changes in bacterial community (3 m below the sea surface) were observed 32 h after the experimental spill at sea. In contrast, there was a decrease in the dominant SAR11 phylotype and an increase in Pseudoalteromonas spp. in the oiled mesocosms (investigated by 16S rRNA gene analysis using denaturing gradient gel electrophoresis), as a consequence of the longer incubation, closer proximity of the samples to oil, and the lack of replenishment with seawater. A total of 216 strains were isolated from hydrocarbon enrichment cultures, predominantly belonging to the genus Pseudoaltero monas; most strains grew on PAHs, branched and straight-chain alkanes, as well as many other carbon sources. No obligate ...
Automated Ribosomal Intergenic Spacer Analysis (ARISA) - Science Exchange Lets You Compare Quotes From Leading Service Providers.
16S rRNA sequencing data on human skin microbiome samples collected before and after swimming in the ocean. This dataset contains raw sequencing data contained in fasta and qual files produced from an Ion Torrent PGM sequencer. There were 2 sampling occurrences (041218 and 092718) and each occurrence has an associated fasta and qual file. This dataset contains the 092718 sampling data only due to storage restrictions. The other dataset is published separately. Our research has shown that the human skin microbiome is altered after swimming in the ocean. Normal commensals were washed off and simultaneously, exogenous bacteria were deposited on the skin. QIIME was used for initial analysis and indicated that the abundance and diversity of microbial communities on the skin increased after swimming and these changes persisted for more than 24 hours. Downstream analysis using PICRUSt to predict functional metagenomics indicated that there was an increase in antibiotic resistance genes, antibiotic biosynthesis
As the importance of beneficial bacteria is better recognized, understanding the dynamics of symbioses becomes increasingly crucial. In many gut symbioses, it is essential to understand whether changes in host diet play a role in the persistence of the bacterial gut community. In this study, termites were fed six dietary sources and the microbial community was monitored over a 49-day period using 16S rRNA gene sequencing. A deep backpropagation artificial neural network (ANN) was used to learn how the six different lignocellulose food sources affected the temporal composition of the hindgut microbiota of the termite as well as taxon-taxon and taxon-substrate interactions. Shifts in the termite gut microbiota after diet change in each colony were observed using 16S rRNA gene sequencing and beta diversity analyses. The artificial neural network accurately predicted the relative abundances of taxa at random points in the temporal study and showed that low-abundant taxa maintain community driving
Microbial biodiversity is difficult to measure in extreme environments due to the inability to culture many of the species, especially from hypersaline environments. Great Salt Lake (GSL), Utah, USA offers a unique ecology to study microbial diversity across a salt gradient. GSL has increasing salt from South to North that varies from marine salt concentrations to saturation, respectively. We used three methods to examine the biodiversity of the GSL-traditional cultivation on solid media, 16s rRNA gene sequencing, multiplexed 16s rRNA gene hybridization to the phylochip, and DNA hybridization to the Geochip for metabolic diversity estimates. Over 40 isolates from the North Arm were obtained, while six were selected for identification. Isolates included gammaproteobacteria, bacilli, and actinobacteria. Sequencing the 16S rRNA genes for identification yielded 350 clones. Refraction curves indicated that this did not represent the bacterial diversity of the GSL, while estimation of the diversity with the
Two bacterial species were isolated from a salt marsh located on privately owned land in Russell County, Kansas. Water samples from the saIt marsh were streaked for isolation on tryptic soy agar supplemented with 12 % NaCI. Visual scanning of the plates revealed two prominent colony types. The two colony types were subcultured repeatedly until axenic cultures were obtained. 80th of these organisms were shown to be moderately halophilic. The organisms were characterized partially by fatty acid methyl ester analysis, 16S rRNA sequencing, and scanning electron microscopy. These studies revealed that the bacteria previously were unreported members of genera Marinococcus and Halomonas.
Black Band Disease (BBD), the destructive microbial consortium dominated by the cyanobacterium Roseofilum reptotaenium, affects corals worldwide. While the taxonomic composition of BBD consortia has been well-characterized, substantially less is known about its functional repertoire. We sequenced the metagenomes of Caribbean and Pacific black band mats and cultured Roseofilum and obtained five metagenome-assembled genomes (MAGs) of Roseofilum, nine of Proteobacteria, and 12 of Bacteroidetes. Genomic content analysis suggests that Roseofilum is a source of organic carbon and nitrogen, as well as natural products that may influence interactions between microbes. Proteobacteria and Bacteroidetes members of the disease consortium are suited to the degradation of amino acids, proteins, and carbohydrates. The accumulation of sulfide underneath the black band mat, in part due to a lack of sulfur oxidizers, contributes to the lethality of the disease. The presence of sulfide:quinone oxidoreductase genes in all
In the present study, we investigated the bacterial diversity of aMasi, a traditional South African fermented milk product, by 16S rRNA clone library and Denaturing Gradient Gel Electrophoresis (DGGE) analysis. Two hundred and eighty two clones from clone library were isolated and identified from aMasi, prepared from the milk of four cows from one herd in the EkuPindiseni Community, North West of Hluhluwe-iMfolozi Park in KwaZulu-Natal Province. The majority of the identified sequences corresponded to lactic acid bacteria (LAB), with the genus Lactococcus as major representative. The species Lactococcus lactis accounted for 179 of the identified clones. In addition, several species of Lactobacillus, Leuconostoc and Enterococcus were detected. Furthermore, several clones belonging to Acinetobacter, Aeromonas and genera within the Enterobacteriaceae were detected. It is important to note that human pathogens such as Klebsiella pneumoniae were identified in aMasi in the present study. Conversely, ...
The screening of bacteria isolated from soil, water and sediment samples of the Gavkhooni Wetland in Iran led to the isolation of about 161 moderately halophilic and halotolerant bacteria which were able to accumulate intracellular lipid inclusions under conditions of nitrogen limitation. Primary studies showed that most of the isolates were able to produce these inclusions but that only a Gram-negative, rod-shaped halotolerant bacterium, designated as strain GK1(IBRC-M10197), showed high-capacity production in a wide range of culture conditions. Gas chromatography and Fourier transform infrared spectroscopy studies revealed that the inclusions were poly-β-hydroxybutyrate (PHB). Phenotypic characterization and phylogenetic analysis based on 16S rRNA gene sequence comparison showed that this strain is a member of the genus Oceanimonas. The genome sequence study of this bacterium revealed the presence of genes involved in the PHB synthesis pathway, which was supported by results of the ...
Three strictly anaerobic, Gram-positive, non-spore-forming, rod-shaped, motile bacteria, designated strains ACB1(T), ACB7(T) and ACB8, were isolated from human subgingival dental plaque. All strains required yeast extract for growth. Strains ACB1(T) and ACB8 were able to grow on glucose, lactose, maltose, maltodextrin and raffinose; strain ACB7(T) grew weakly on sucrose only. The growth temperature range was 30-42 °C with optimum growth at 37 °C. Major metabolic fermentation end products of strain ACB1(T) were acetate and lactate; the only product of strains ACB7(T) and ACB8 was acetate. Major fatty acids of strain ACB1(T) were C(14 : 0), C(16 : 0), C(16 : 1)ω7c dimethyl aldehyde (DMA) and C(18 : 1)ω7c DMA. Major fatty acids of strain ACB7(T) were C(12 : 0), C(14 : 0), C(16 : 0), C(16 : 1)ω7c and C(16 : 1)ω7c DMA. The hydrolysate of the peptidoglycan contained meso-diaminopimelic acid, indicating peptidoglycan type A1γ. Genomic DNA G+C content varied from 42 to 43.3% between strains. ...
Symbiotic relationships with subcuticular bacteria (SCB) have been identified and studied in numerous echinoderms, but have not been examined using current sequencing technologies in the brooding brittle star, Amphipholis squamata. Previously, A. squamata SCB were placed in the genus Vibrio (γ-Proteobacteria), but recent evidence suggests the SCB is primarily composed of α-Proteobacteria. The present study clarifies the taxonomic composition of SCB associated with A. squamata from the Northwest Atlantic. Isolated gDNA was amplified using 16S rRNA gene-targeted PCR and sequenced on an Illumina HiSeq at the UNH Genomics Center. Results suggest the presence of a single dominant bacterial type within the family Rhodobacteraceae, which composes 70-80% of the A. squamata microbiome. The majority of sequences within Rhodobacteraceae were identified as members of the genus Octadecabacter (97% similarity). By comparison, adjacent seawater and sediment support significantly more diverse bacterial communities,
TY - JOUR. T1 - Some Observations on the Taxonomy of the Genus Microbacterium. II. Cell Wall Analysis, Gel Electrophoresis and Serology. AU - Robinson, K.. PY - 1966/12. Y1 - 1966/12. N2 - Summary. The chemical composition of the cell wall mucopeptide, the esterases and catalases of the cell free extracts, and the serology of the 25 species of microbacteria whose morphological and cultural characteristics had been investigated previously, were examined. Suggestions are made about the relationships of the species within the genus Microbacterium and with other genera.. AB - Summary. The chemical composition of the cell wall mucopeptide, the esterases and catalases of the cell free extracts, and the serology of the 25 species of microbacteria whose morphological and cultural characteristics had been investigated previously, were examined. Suggestions are made about the relationships of the species within the genus Microbacterium and with other genera.. UR - ...
Volatile fatty acid intoxication (acidosis), a common process failure recorded in anaerobic reactors, leads to drastic losses in methane production. Unfortunately, little is known about the microbial mechanisms underlining acidosis and the potential to recover the process. In this study, triplicate mesophilic anaerobic reactors of 100 L were exposed to acidosis resulting from an excessive feeding with sugar beet pulp and were compared to a steady-state reactor. Stable operational conditions at the beginning of the experiment initially led to similar microbial populations in the four reactors, as revealed by 16S rRNA gene T-RFLP and high-throughput amplicon sequencing. Bacteroidetes and Firmicutes were the two dominant phyla, and although they were represented by a high number of operational taxonomic units, only a few were dominant. Once the environment became deterministic (selective pressure from an increased substrate feeding), microbial populations started to diverge between the overfed reactors.
The marine bacterium Halomonas titanicae strain BH1 was isolated from a sample of rusticles, which are formed in part by a consortium of microorganisms, collected from the RMS Titanic wreck site (1). This bacterium was previously characterized as a new species of the genus Halomonas, which includes a large number of species isolated predominantly from marine, hypersaline, or alkaline habitats (saline lakes, salterns, salted food, etc.). Although these species are easily isolated from saline and hypersaline environments, genome data are currently available only from the type species of the genus Halomonas, H. elongata (2). Halomonas titanicae is a Gram-negative, heterotrophic, aerobic rod, motile by peritrichous flagella. Phylogenetically this organism belongs to the Gammaproteobacteria within the family Halomonadaceae (3, 4). This halophilic organism has a respiratory metabolism, being able to grow in media with 0.5 to 25% NaCl (optimal growth at 2 to 8% NaCl); no growth occurs in the absence of ...
"Escherichia coli 16S ribosomal RNA". "Halobacterium salinarum 16S ribosomal RNA". "Homo sapiens 18S ribosomal RNA (nuclear)". ... "Arabidopsis thaliana 16S ribosomal RNA (chloroplast)". Woese CR, Kandler O, Wheelis ML (June 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 ...
... results of 16S ribosomal RNA gene sequencing. To emphasize this difference, Woese, Otto Kandler and Mark Wheelis later proposed ... although there are many introns in their transfer RNA and ribosomal RNA genes, and introns may occur in a few protein-encoding ... Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular ... These classifications rely heavily on the use of the sequence of ribosomal RNA genes to reveal relationships among organisms ( ...
"16S rRNA-based LTP release 132 (full tree)". All-Species Living Tree Project. Silva Comprehensive Ribosomal RNA Database. ... 16S ribosomal RNA identity, meaning that they could fall in different families or even orders. Recent phylogenetic analysis of ... divided Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences and grouped the genera Chloroflexus, ... The phylogeny is based on 16S rRNA-based LTP release 132 by The All-Species Living Tree Project Notes: ♠ Strains found at the ...
"16S rRNA-based LTP release 132 (full tree)". All-Species Living Tree Project. Silva Comprehensive Ribosomal RNA Database. ... A phylogeny by Annotree and GTDB release 05-RS95 (17th July 2020). This second phylogeny is based on 16S rRNA-based LTP release ...
"16S rRNA-based LTP release 132 (full tree)". All-Species Living Tree Project. Silva Comprehensive Ribosomal RNA Database. ... and the phylogeny is based on 16S rRNA-based LTP release 132 by 'The All-Species Living Tree' Project. Note: * Strains found at ...
"16S rRNA-based LTP release 132 (full tree)". All-Species Living Tree Project. Silva Comprehensive Ribosomal RNA Database. ... The phylogeny is based on 16S rRNA-based LTP release 132 by The All-Species Living Tree Project, with the currently accepted ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20. CS1 maint: discouraged parameter (link) Biology portal v t e ... CS1 maint: discouraged parameter (link) All-Species Living Tree Project."16S rRNA-based LTP release 111 (full tree)" (PDF). ... and the phylogeny is based on 16S rRNA-based LTP release 111 by The All-Species Living Tree Project See the List of Prokaryotic ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-06-05. CS1 maint: discouraged parameter (link) Kineococcus at ... CS1 maint: discouraged parameter (link) 'The All-Species Living Tree' Project."16S rRNA-based LTP release 123 (full tree)" (PDF ... 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 ...
Woo, P.C.; Lau,Chan,Fung,Tang,Yuen (2005). "Clostridium bacteramia characterized by 16S ribosomal RNA gene sequencing". Journal ... Currently the standard to identify clostridial species such as C. cadaveris is via molecular techniques utilizing ribosomal RNA ...
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. The Thermoanaerobacterales ...
"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). ...
Based on 16S ribosomal RNA sequences, Bala et al. renamed the species in 2004 Amycolatopsis rifamycinica. Rifamycins were first ... This is due to the high affinity of rifamycins for the prokaryotic RNA polymerase. The selectivity of the rifamycins depends on ... RifA through rifE encode a type I polyketide synthase module, with the loading module being a non-ribosomal peptide synthetase ... The rifamycins have a unique mechanism of action, selectively inhibiting bacterial DNA-dependent RNA polymerase, and show no ...
The All-Species Living Tree' Project."16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA ... The currently accepted phylogeny is based on 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project The ...
The All-Species Living Tree' Project."16S rRNA-based LTP release 106 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA ... Furthermore, it has been found that the GC-content of ribosomal RNA (the traditional phylogenetic marker for prokaryotes) ... A newer tree based on 16S and 23S rRNA (and other data) is given by Ferla et al. (2013) as follows: An updated phylogeny of the ... One example of this atypical decorrelation of ribosomal GC-content with phylogeny is that members of the Holosporales have a ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20. CS1 maint: discouraged parameter (link). ... CS1 maint: discouraged parameter (link) All-Species Living Tree Project."16S rRNA-based LTP release 111 (full tree)" (PDF). ... and the phylogeny is based on 16S rRNA-based LTP release 111 by The All-Species Living Tree Project Parte, A.C. "Brockia". LPSN ...
"16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20. CS1 maint ... 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 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 ♠ Strains found at the ...
"Classification of methanogenic bacteria by 16S ribosomal RNA characterization". Proceedings of the National Academy of Sciences ...
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 The recently described ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20. CS1 maint: discouraged parameter (link) J.P. Euzéby. " ... The phylogeny is based on 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project. The currently accepted ... CS1 maint: discouraged parameter (link) 'The All-Species Living Tree' Project."16S rRNA-based LTP release 123 (full tree)" (PDF ...
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. Euzéby JP. "Rhizobium". ...
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. ...
"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] ...
... 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 ...
... divided bacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences:[5][6] ... All modern ideas start with the sequence analysis of DNA and RNA. In 1987, Carl Woese, the forerunner of the molecular ...
Coenye T, Vandamme P (November 2003). "Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced ... O ARNr 16S, é dicir, ácido ribonucleico ribosómico 16S (en inglés 16S rRNA) é o compoñente da subunidade menor de 30S (S son as ... "Next-generation sequencing of 16S ribosomal RNA gene amplicons". J Vis Exp (90). PMC 4828026. PMID 25226019. doi:10.3791/51709. ... "A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria". Journal of Microbiological ...
... a basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids". Environ. Microbiol. 9 (4): 1001-16 ... Werner F (2007). "Structure and function of archaeal RNA polymerases". Mol. Microbiol. 65 (6): 1395-404. PMID 17697097. doi: ... baseado en datos de secuencias xenéticas de ARNr 16S. Prema en cada filo para ir á súa páxina. ... "A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, ...
Winker, S; Woese CR (1991). "A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA ... Analysis of their 16S rRNA gene sequences suggests that they are a deeply branching lineage that does not belong to the main ... Hansmann, S; Martin W (2000). "Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is ... Keswani, J; Whitman WB (2001). "Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes". Int. J. Syst ...
Professor of environmental health engineering best known for the use of 16S ribosomal RNA-targeted techniques and community- ...
ஆர்க்கீயாவின் ரைபோசோமிய ஆர்.என்.ஏ (ribosomal RNA) மற்றும் நகர் ரைபோகருக்காடிகள் பாக்டீரியாவில் உள்ளதை விட வேறான கட்டுமானம் ... இதில் குறிப்பாக மெய்க்கருவிலிகளுக்கு 16S rRNA மற்றும் மெய்க்கருவுயிரிகளுக்கு 18S rRNA மரபணுத் தொடரின் மூலமும் வகைப்படுத்தப் ... 1983), Archaebacteria and eukaryotes possess DNA-dependent RNA polymerases of a common type, The EMBO Journal, 2(8): 1291-1294. ... 1977ல் இல்லினியாசு பல்கலைக்கழகத்தைச் சேர்ந்த கார்ல் வூசே (Carl Woese) என்பவரால் ...
... end of the 16S region of the smaller (30S) ribosomal subunit. Upon encountering the Shine-Dalgarno sequence, the ASD of the ... 9] Sequences within ribosome binding site affecting messenger RNA translatability and method to direct ribosomes to single ... A ribosome binding site, or ribosomal binding site (RBS), is a sequence of nucleotides upstream of the start codon of an mRNA ... "Ribosomal Binding Site Sequence Requirements". www.thermofisher.com. Retrieved 2015-10-16.. ...
An interesting fact that gas chromatography-mass spectrometry, 16S ribosomal RNA analysis, omics, and other advanced ... For example, humans can make neither RNA replicases nor reverse transcriptase, and the presence of these enzymes are ...
"16S rDNA", the sequence of DNA which encodes the ribosomal RNA molecule).[47] Since ribosomes are present in all living ... The 16S rDNA gene contains both slowly evolving regions and fast evolving regions; the former can be used to design broad ... RNA and protein-based approachesEdit. Metatranscriptomics studies have been performed to study the gene expression of microbial ... A common marker for human microbiome studies is the gene for bacterial 16S rRNA (i.e. " ...
"16S rRNA-based LTP release 132 (full tree)". All-Species Living Tree Project. Silva Comprehensive Ribosomal RNA Database. ... divided Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences and grouped the genera Chloroflexus, ... 16S ribosomal RNA identity, meaning that they could fall in different families or even orders.[9] ... The phylogeny is based on 16S rRNA-based LTP release 132 by The All-Species Living Tree Project[13] ...
16S and 23S) rRNA genes.[15] Crystallographic studies indicate that 5S rRNA-binding proteins and other proteins of the central ... The 5S ribosomal RNA (5S rRNA) is an approximately 120 nucleotide-long ribosomal RNA molecule with a mass of 40 kDa. It is a ... "Interaction of the RNA binding fingers of Xenopus transcription factor IIIA with specific regions of 5 S ribosomal RNA". ... Sun, FJ; Caetano-Anollés, G (Nov 2009). "The evolutionary history of the structure of 5S ribosomal RNA". Journal of Molecular ...
... as a set of 16S ribosomal RNA sequences with less than 85% similarity to already-described phyla.[32] More recently an even ... divided Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences:[12][14] ... Atomic structure of the 30S ribosomal Subunit from Thermus thermophilus of which 16S makes up a part. Proteins are shown in ... "ARB-Silva: comprehensive ribosomal RNA database". The ARB development Team. Retrieved January 2, 2016.. ...
and Other Lactic Acid Bacteria in the Human Intestine as Determined by Specific Amplification of 16S Ribosomal DNA. Appl ... DNA dan RNA) bakteri melayang-layang di daerah sitoplasma yang bernama nukleoid.[17] Salah satu struktur bakteri yang penting ...
Rappe MS et al, Chromophyte plastid 16S ribosomal RNA genes found in a clone library from Atlantic Ocean seawater, in Journal ...
Based on 16S ribosomal RNA phylogenetic studies of the late microbiologist Carl Woese and collaborators and colleagues at the ... Based on molecular studies of the 16S sequences, Woese recognised twelve bacterial phyla. Two of these were gram-positive and ...
"16S rRNA-based LTP release 106 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Consultado o 2011-11-17.. ... e a filoxenia está baseada en datos do ARNr 16S do LTP 106 do Proxecto The All-Species Living Tree.[7] ...
CZERNILOFSKY, A.P.; KURLAND, C.G.; STÖFFLER, G.. 30S Ribosomal proteins associated with the 3′-terminus of 16S RNA. FEBS ... Taktiež ribozomálna RNA sa rozlišuje na základe sedimentácie; u prokaryotov poznáme 5S, 16S a 23S rRNA.[1] ... Veľká podjednotka sa skladá z 5S RNA (120 nukleotidov), 28S RNA (4700 nukleotidov), 5,8S RNA (160 nukleotidov) podjednotiek a ... 16S (1542 nukleotidov) 21 Eukaryotické ribozómyUpraviť. Eukaryotické 80S ribozómy sú umiestnené v cytoplazme, každý pozostáva z ...
In 1987 Carl Woese divided the Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences, which with several ... Hori, H.; Osawa, S. (1987). "Origin and evolution of organisms as deduced from 5S ribosomal RNA sequences". Molecular Biology ... "The ribosomal RNA database project". Nucleic Acids Research. 19 Suppl: 2017-2021. doi:10.1093/nar/19.suppl.2017. PMC 331344. ... namely either Ribosomal Database Project[2], which align the sequence to other 16S sequences using infernal, a secondary ...
... also includes DNA:RNA hybrid triplex formation.[27] References[edit]. *^ Fischer J, Ganellin CR (2006). Analogue-based ... Mehta R, Champney WS (September 2003). "Neomycin and paromomycin inhibit 30S ribosomal subunit assembly in Staphylococcus ... the binding of neomycin-class aminoglycosides to the A site of 16S rRNA". Biochemistry. 41 (24): 7695-706. doi:10.1021/ ... Aminoglycosides such as neomycin are known for their ability to bind to duplex RNA with high affinity.[24] The association ...
March 2007). "Suitability of partial 16S ribosomal RNA gene sequence analysis for the identification of dangerous bacterial ...
An example can be seen in bacteria: Escherichia coli has seven operons encoding various Ribosomal RNA. For each of these genes ... When the 2 species are compared together however, the sequence divergence of the 16S rRNA gene between them is 5.90%.[1] ... Haemophilus influenzae its six ribosomal RNA operons are entirely identical. ...
Winker, S; Woese CR (1991). "A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA ... 2011). "16S rRNA phylogenetic analysis and quantification of Korarchaeota indigenous to the hot springs of Kamchatka, Russia". ... Achenbach-Richter, L; Woese CR (1988). "The ribosomal gene spacer region in archaebacteria". Syst. Appl. Microbiol. 10: 211-214 ... Foron descubertas a partir de mostras de secuencias xenómicas de ARNr de 16S recollidas en ambientes naturais e non se puideron ...
Molekylær analyse baseret på 16S rRNA sekventiering viser GFAJ-1 til at være tæt beslægtede til andre moderat halofile ("salt- ... Fylogeni af GFAJ-1 og tæt beslægtede bakterier baserede på ribosomal DNA sekventering.[12] ... såvel som dets DNA og RNA. [3][4] Øjeblikkeligt efter offentliggørelsen, udtrykte andre mikrobiologer og biokemikere tvivl om ...
"16S rRNA-based LTP release 106 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Consultado o 30 xuño 2012.. ... Klenk, H. P., Meier, T. D., Durovic, P. and others (1999) RNA polymerase of Aquifex pyrophilus: Implications for the evolution ...
16S ribosomal RNA - an intensively studied nucleic acid that has been useful in phylogenetics ...
However 16S ribosomal RNA research finds that while common, these species make up only 5% of skin bacteria.[5] However, skin ... The estimate of the number of species present on skin bacteria has been radically changed by the use of 16S ribosomal RNA to ... These samples then were analyzed using 16S rDNA libraries so that strains that did not grow well in cultures could be ...
"16S rRNA-based LTP release 106 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Consultado o 6 xullo 2012.. ...
16S ribosomal RNA (or 16S rRNA) is the RNA component of the 30S small subunit of a prokaryotic ribosome (SSU rRNA). It binds to ... 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 ... Czernilofsky, A. P.; Kurland, C. G.; Stöffler, G. (1975). "30S Ribosomal proteins associated with the 3′-terminus of 16S RNA". ...
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 ...
Evaluation of 16S rRNA Gene-Based PCR Assays for Genus-Level Identification of Helicobacter Species H. Moyaert, F. Pasmans, R. ... 16S rRNA Gene Sequencing in Routine Identification of Anaerobic Bacteria Isolated from Blood Cultures Ulrik Stenz Justesen, ... Simultaneous Sequence Analysis of the 16S rRNA and rpoB Genes by Use of RipSeq Software To Identify Mycobacterium Species Keith ... Analysis of Mixed Sequencing Chromatograms and Its Application in Direct 16S rRNA Gene Sequencing of Polymicrobial Samples ...
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 ...
Maize chloroplast 16S rDNA shows strong sequence homology with E. coli 16S rRNA13. Sequence analysis of a total spacer in E. ... 16S-23S-5S-3′ (ref. 9). Total chloroplast tRNA hybridizes to fragments of rDNA9 and it was suggested that the 16S-23S spacer ... Flanking sequences, coding for the 3′-terminal region of 16S rRNA and for the 5′-terminal region of 23S rRNA have also been ... We have therefore analysed E. gracilis strain Z 16S-23S spacer DNA at the nucleotide level, hoping this would allow ...
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 ...
Oligonucleotide sequences selected from the 16S rRNA genes of various species of ammonia-oxidizing bacteria were evaluated as ... Amplification of 16S ribosomal RNA genes of autotrophic ammonia-oxidizing bacteria demonstrates the ubiquity of nitrosospiras ... Oligonucleotide sequences selected from the 16S rRNA genes of various species of ammonia-oxidizing bacteria were evaluated as ... were found to contain DNA from both Nitrosospira and Nitrosomonas as determined by nested PCR amplification and probing of 16S ...
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 ...
Fish, Steven Anthony and Shepherd, Thomas J. and McGenity, Terry J. and Grant, William D. (2002) Recovery of 16S ribosomal RNA ... Fragments of 16S ribosomal RNA genes were detected by polymerase chain reaction amplification of DNA extracted from halite ... yielded only bacterial 16S rDNA amplicons. Terminal restriction fragment length polymorphism analyses indicate complex and ... samples ranging in age from 11 to 425 Myr (millions of years). Haloarchaeal 16S rDNA amplicons were present in one sample (11- ...
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) ...
There is thus the need for computational methods to design optimal bacterial 16S primers able to take into account the ... Results confirm the predicted efficiency and the ability to maximize the number of different bacterial 16S sequences matched by ... minimizes the differences in the number of primers matching each bacterial 16S sequence. Our algorithm can be applied to any ... specificity and sensitivity in the amplification of the different bacterial 16S sequences contained in a sample. ...
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 ...
The results demonstrate that it is possible to distinguish and classify the methylotrophic bacteria using 16S rRNA sequence ... The secondary structures of the 16S rRNA sequences of Methylocystis parvus strain OBBP, Methylosinus trichosporium strain ... are similar in 16S rRNA sequence to bacteria in the β-subdivision. The methane-utilizing, obligate group I methanotrophs, ... Methylobacterium organophilum strain XX and Methylobacterium extorquens strain AM1 are clearly distinguishable by their 16S ...
  • The 16S rRNA in bulk cellular RNA preparations is selectively targeted for dideoxynucleotide-terminated sequencing by using reverse transcriptase and synthetic oligodeoxynucleotide primers complementary to universally conserved 16S rRNA sequences. (pnas.org)
  • The genes coding for it are referred to as 16S rRNA gene and are used in reconstructing phylogenies, due to the slow rates of evolution of this region of the gene. (wikipedia.org)
  • The rRNA genes are located within three tandemly repeated DNA regions of approximately 5.6 kilobase pairs each 6-8 and the arrangement of the structural genes within each repeat follows the prokaryotic pattern, being 5′-16S-23S-5S-3′ (ref. 9). (nature.com)
  • We have therefore analysed E. gracilis strain Z 16S-23S spacer DNA at the nucleotide level, hoping this would allow identification of tRNA genes together with the processing sites of the respective primary transcripts. (nature.com)
  • Flanking sequences, coding for the 3′-terminal region of 16S rRNA and for the 5′-terminal region of 23S rRNA have also been sequenced, to compare the drift rates between the spacer and its adjacent structural genes. (nature.com)
  • Sequencing of the 16S rRNA genes of the group G beta-hemolytic streptococci showed that all 75 isolates were Streptococcus dysgalactiae subspecies equisimilis . (asm.org)
  • Several other 16S RMTase genes, such as rmtB , rmtC , and rmtF , have been found on the chromosome of gram-negative bacteria ( 7 , 8 ). (cdc.gov)
  • Oligonucleotide sequences selected from the 16S rRNA genes of various species of ammonia-oxidizing bacteria were evaluated as specific PCR amplification primers and probes. (nih.gov)
  • Enrichments of lakewater and sediment samples, incubated for two weeks in the presence of ammonium, produced nitrite and were found to contain DNA from both Nitrosospira and Nitrosomonas as determined by nested PCR amplification and probing of 16S rRNA genes. (nih.gov)
  • Therefore, in this study we developed a simple method using restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal RNA genes (16S rRNA genes PCR-RFLP) for the identification of seven different species included in the group of mutans streptococci. (nih.gov)
  • Therefore, 16S rRNA genes PCR-RFLP, using HpaII and HaeIII, could be an alternative method for the identification of mutans streptococci, and may be applicable for large-scale studies on the cariogenicity of mutans streptococci. (nih.gov)
  • Fragments of 16S ribosomal RNA genes were detected by polymerase chain reaction amplification of DNA extracted from halite samples ranging in age from 11 to 425 Myr (millions of years). (lancs.ac.uk)
  • The objective of this project was to use ribosomal RNA genes, cloned from natural populations of Sargasso Sea bacterioplankton, as markers for picoplankton diversity. (oregonstate.edu)
  • Two different clone libraries of eubacterial 16S rRNA genes amplified from a natural population of Sargasso Sea picoplankton by the polymerase chain reaction (11) have been phylogenetically analysed. (oregonstate.edu)
  • A) Total RNA samples isolated from cultured spirochetes were converted into cDNA and amplification cycles (cycle threshold or Ct value) of various L . interrogans target genes are assessed in qRT-PCR assays in the presence (gray bars) or absence (black bars) of hamster cDNA. (cdc.gov)
  • a form of RNA transcribed from DNA in the NUCLEOLI of EUKARYOTE cells or clustered ribosomal genes in PROKARYOTES , that complexes with various proteins (r proteins) to form the RIBOSOME . (thefreedictionary.com)
  • Sequencing and analysis: Sequencing of the PCR product of 16S rDNA and blaNDM-1 genes of the representative samples was carried out commercially through Macrogen, South Korea. (thefreedictionary.com)
  • Based on the structural complexity of ribosomes, 16S rRNA genes are considered species-specific and hence used for bacterial phylogenetic analysis. (nature.com)
  • The location of the variable regions, and implicitly the conserved parts flanking them, has been based on some multiple alignment of more or less full-length 16S genes. (biomedcentral.com)
  • This development could provide an efficient, high throughput tool to test engineered essential genes, such as the 16S rRNA. (synbiobeta.com)
  • abstract = "Aims: Next-generation sequencing of 16S ribosomal RNA genes (rDNA) and ribosomal RNA (rRNA) was used to characterize water and biofilm microbiome collected from a drinking water distribution system of an office building after its first year of operation. (aalto.fi)
  • However, contradictory data has emerged concerning the diagnostic accuracy of the most popular PCR assays that target either the 16S ribosomal RNA (rrs) or the subsurface lipoprotein (LipL32) genes. (unibo.it)
  • To investigate the frequency of heterogeneity among the multiple 16S rRNA genes within a single microorganism, we determined directly the 120-bp nucleotide sequences containing the hypervariable α region of the 16S rRNA gene from 475 Streptomyces strains. (asm.org)
  • From these characteristics, the DNA sequences of the 16S rRNA genes (rDNA) have become powerful tools in modern prokaryotic taxonomy with the increasing use of PCR technology ( 21 , 25 , 26 ). (asm.org)
  • this would be important not only for estimation of the consistency of the risk frequency with the phylogenetic relationship reconstructed by using cloned 16S rRNA genes but also for evaluating the mechanism introducing breaks into the rRNA homogeneity fixed by hypothetical concerted evolution. (asm.org)
  • To address this need, an extensive study was conducted with a partial sequence containing the most variable α region ( 25 ) of the 16S rRNA genes from 475 standard type strains belonging to the genus Streptomyces . (asm.org)
  • This is the first study to estimate the extent of heterogeneity in the 16S rRNA genes within a single microorganism. (asm.org)
  • Our diagnostic test using spiked human blood was at least 100-fold more sensitive than corresponding leptospiral DNA-based quantitative PCR assays, targeting the same 16S nucleotide sequence in the RNA and DNA molecules. (cdc.gov)
  • Characterization of a ribosomal RNA gene cluster from Clostridium tyrobutyricum: phylogenetic positioning based on the 16S and 23S nucleotide sequences. (unil.ch)
  • Comparative analysis of the nucleotide base sequence of a 16S rdna fragment amplified from the infected liver tissue revealed that it was identical to a C piliforme 16S rdna sequence. (biomedsearch.com)
  • In addition to highly conserved primer binding sites, 16S rRNA gene sequences contain hypervariable regions that can provide species-specific signature sequences useful for identification of bacteria. (wikipedia.org)
  • Although it was originally used to identify bacteria, 16S sequencing was subsequently found to be capable of reclassifying bacteria into completely new species, or even genera. (wikipedia.org)
  • While 16S hypervariable regions can vary dramatically between bacteria, the 16S gene as a whole maintains greater length homogeneity than its eukaryotic counterpart (18S ribosomal RNA), which can make alignments easier. (wikipedia.org)
  • The 16S ribosomal RNAs from 10 species of methanogenic bacteria have been characterized in terms of the oligonucleotides produced by T 1 RNase digestion. (pnas.org)
  • Helix 31 of bacterial 16S ribosomal RNA harbors two modified nucleotides, m 2 G966 and m 5 C967, that are highly conserved among bacteria, though the degree and nature of the modifications in this region are different in eukaryotes. (mdpi.com)
  • Many of the current bacterial 16S primers have been designed from sequence data obtained from in vitro cultured species, even though environmental microbiologists estimate that less than 2% of bacteria can be cultured in the laboratory. (biomedcentral.com)
  • 16S ribosomal RNAs (rRNA) of 12 methylotrophic bacteria have been almost completely sequenced to establish their phylogenetic relationships. (microbiologyresearch.org)
  • The group I methylotrophs, Methylophilus methylotrophus strain AS1 and methylotrophic species DM11, which do not utilize methane, are similar in 16S rRNA sequence to bacteria in the β -subdivision. (microbiologyresearch.org)
  • The results demonstrate that it is possible to distinguish and classify the methylotrophic bacteria using 16S rRNA sequence analysis. (microbiologyresearch.org)
  • These idiosyncratic mutations gradually shaped the species-specificity of the gene, which became the basis of the use of 16S rRNA gene sequence for the phylogenetic classification of bacteria-indeed all living organisms on earth-based on the small subunit of rRNA 11 , 12 (Fig. 1A ). (nature.com)
  • The 16S rRNA gene is composed of highly conserved, specie-specific sequences between different species of bacteria and the application of restriction endonucleases on the amplified 16S rRNA gene is a novel diagnostic tool in molecular characterization of bacterial isolates. (ijcmas.com)
  • Along the 16S gene there are regions with more or less variation across the kingdom of bacteria. (biomedcentral.com)
  • The 16S small ribosomal subunit gene (16S rRNA) is today considered the gold standard for phylogenetic studies of microbial communities and for assigning taxonomic names to bacteria [ 3 - 5 ]. (biomedcentral.com)
  • Bacteria contain a simple RNA polymerase consisting of four polypeptides. (britannica.com)
  • Therefore, the archaeal RNA polymerases more closely resemble RNA polymerases of eukaryotes rather than those of bacteria. (britannica.com)
  • A prominent difference is that bacteria have an initiator tRNA (transfer RNA) that has a modified methionine , whereas eukaryotes and archaea have an initiator tRNA with an unmodified methionine. (britannica.com)
  • In this study, we surveyed wards where drug-resistant bacteria had been isolated and compared conventional culture methods with 16S rRNA gene sequencing methods. (biomedcentral.com)
  • Samples for 16S rRNA sequence analysis have been expanded from the bacteria in environments such as the oceans and soils to clinical settings. (biomedcentral.com)
  • To address these shortcomings, we developed a 16S rRNA gene PCR with a next-generation sequencing (NGS) approach to detect tick-borne bacteria in whole blood. (cdc.gov)
  • As 16S ribosomal RNA (rRNA)-targeted sequencing can detect DNA from non-viable bacteria , it can be used to identify pathogens from clinical samples even in patients pretreated with antibiotics . (bvsalud.org)
  • 16S rRNA -targeted sequencing in conjunction with culture could be useful for identifying bacteria in NSBF samples, especially when patients have been pretreated with antibiotics and when anaerobic infection is suspected. (bvsalud.org)
  • This pilot study explored the etiology of this disparity using culture-independent analyses to identify bacterial species associated with oral disease.Bacteria in subgingival plaque samples from twelve participants in two independent West Virginia dental-related studies were characterized using 16S rRNA gene sequencing and Human Oral Microbe Identification Microarray (HOMIM) analysis. (duke.edu)
  • To describe the midgut microbial diversity and the candidate bacteria for the genetic manipulation for the generation of transgenic mosquitoes refractory to transmission of diseases, the microbiota of wild Culex quinquefasciatus mosquito midgut was studied using a conventional culture technique and analysis of a 16S ribosomal RNA (rRNA) gene sequence library. (ajtmh.org)
  • The 16S rRNA gene library was composed of 46% unidentified and uncultured bacteria, 41% Acinetobacter spp. (ajtmh.org)
  • Selected faecal bacteria were investigated using viable counting procedures, 16S ribosomal RNA (rRNA) abundance measurements, and the occurrence of specific signature fatty acids in whole community fatty acid methyl ester profiles. (bmj.com)
  • Although it was a considerably less sensitive diagnostic tool, cellular fatty acid analysis correlated with viable bacterial counts and 16S rRNA measurements in a number of bacteria, including bacteroides. (bmj.com)
  • Second, 16S ribosomal protein is found only in bacteria and mitochondria plasts, so they might not be what you are looking for. (biology-online.org)
  • Nunha soa bacteria poden existir múltiples secuencias do xene de ARNr 16S. (wikipedia.org)
  • The method is evaluated with respect to accuracy, sensitivity to modified nucleotides in the template RNA, and phylogenetic usefulness, by examination of several 16S rRNAs whose gene sequences are known. (pnas.org)
  • The relative simplicity of this approach should facilitate a rapid expansion of the 16S rRNA sequence collection available for phylogenetic analyses. (pnas.org)
  • The implemented phylogenetic analysis of ribosomal RNA 16S gene allowed us to identify Pasteurella strains isolated in 2010-2015 as P. multocida subspecies multocida . (springer.com)
  • Phylogenetic trees constructed using 16S rRNA gene sequencing revealed that Clostridiales were repeated colonizers in plaque associated with high oral disease, providing evidence that the oral environment is somehow influencing the bacterial signature linked to disease.Culture-independent analyses identified an atypical bacterial signature associated with high oral disease in West Virginians and provided evidence that the oral environment influenced this signature. (duke.edu)
  • The phylogenetic classification of prokaryotes with 16S rDNA sequences is based on the assumption that the differences in sequences reflect the evolution of the organisms that they have been extracted from. (asm.org)
  • The results presented here may provide important information concerning the application of 16S rDNA sequences for phylogenetic analyses and the evolutionary mechanisms of the redundant multigenes on a single genome. (asm.org)
  • 1997. Phylogenetic relationships of filamentous cyanobacterial taxa inferred from 16S rRNA sequence divergence. (tolweb.org)
  • A 12-dimensional vector extracted from CHC, as a numerical characterization of CHC, was applied to analyze phylogenetic relationships of 11 species, 74 ribosomal RNAs, 48 Hepatitis E viruses, and 18 eutherian mammals, respectively. (hindawi.com)
  • It has several functions: Like the large (23S) ribosomal RNA, it has a structural role, acting as a scaffold defining the positions of the ribosomal proteins. (wikipedia.org)
  • Chloroplasts of the unicellular flagellate eukaryote Euglena gracilis contain several copies of a circular 135-140-kilobase pair DNA 1 which codes for chloroplast-specific stable RNAs (16S, 23S (refs 2, 3), 5S rRNAs 4 and tRNAs 5 ) and for an unknown number of chloroplast-specific proteins. (nature.com)
  • Proteins that interact strongly with the 16S RNA early in subunit assembly stabilize the RNA chain against unfolding in 1 mM Mg2+ and actually promote the formation of a more compact teriary structure in 20 mM Mg2+. (sciencemag.org)
  • A vital function of these proteins may therfore consist in altering the configuration of the RNA so that further assembly reactions can take place. (sciencemag.org)
  • Contacts between helix 31 and the P-site tRNA, initiation factors, and ribosomal proteins highlight the importance of this region in translation. (mdpi.com)
  • However, it remains unknown whether ribosomal components, i.e., rRNAs and r-proteins, also have such high modularity and interoperability. (nature.com)
  • Associated with a number of ribosomal proteins, the SSU rRNA forms the small subunit of the ribosome. (wikipedia.org)
  • Proteins are shown in blue and RNA in orange. (newworldencyclopedia.org)
  • The formation of proteins by rRNA, mRNA, and tRNA is remarkably complex, involving transcription of the various RNAs from DNA, the movement of RNA within a cell, different types of rRNA, and the process of assembling the amino acids in a precise order. (newworldencyclopedia.org)
  • It is at the site of the ribosome that messenger RNA's (mRNA) code for linking amino acids together to form new proteins and where transfer RNAs (tRNA) transfer specific amino acids to the growing polypeptide chain during the translation of the mRNA into a protein. (newworldencyclopedia.org)
  • abstract = "Helix-threading peptides (HTPs) constitute a new class of small molecules that bind selectively to duplex RNA structures adjacent to helix defects and project peptlde functionality into the dissimilar duplex grooves. (elsevier.com)
  • Although the applicability of small subunit ribosomal RNA (16S rRNA) sequences for bacterial classification is now well accepted, the general use of these molecules has been hindered by the technical difficulty of obtaining their sequences. (pnas.org)
  • 1995. The phylogeny of plastids: a review based on comparisons of small-subunit ribosomal RNA coding regions. (tolweb.org)
  • Small subunit ribosomal ribonucleic acid (SSU rRNA) is the smallest of the two major RNA components of the ribosome. (wikipedia.org)
  • LSU rRNA: the large subunit ribosomal ribonucleic acid. (wikipedia.org)
  • LOCUS CRECPCPRG 4153 bp DNA PLN 01-JUN-1995 DEFINITION Chlamydomonas pallidostigmatica chloroplast small subunit ribosomal RNA gene, partial CDS. (bio.net)
  • small subunit ribosomal RNA. (bio.net)
  • Small subunit ribosomal RNA, 5' domain taken from the Rfam database. (newworldencyclopedia.org)
  • Some thermophilic archaea (e.g. order Thermoproteales) contain 16S rRNA gene introns that are located in highly conserved regions and can impact the annealing of "universal" primers. (wikipedia.org)
  • Additionally, the 16S gene contains highly conserved sequences between hypervariable regions, enabling the design of universal primers that can reliably produce the same sections of the 16S sequence across different taxa. (wikipedia.org)
  • We amplified 16S rRNA gene sequences from genomic DNA samples by PCR using universal primers and digested the PCR products with the restriction endonucleases, HpaII and HaeIII. (nih.gov)
  • There is thus the need for computational methods to design optimal bacterial 16S primers able to take into account the knowledge provided by the new sequencing technologies. (biomedcentral.com)
  • 3) minimizes the differences in the number of primers matching each bacterial 16S sequence. (biomedcentral.com)
  • Results confirm the predicted efficiency and the ability to maximize the number of different bacterial 16S sequences matched by primers. (biomedcentral.com)
  • There is thus the need for automated methods that leverage such newly available information in the design and update of bacterial 16S primers. (biomedcentral.com)
  • Since the 16S gene sequence is similar but not identical in different organisms, degenerate primers are used for 16S rRNA sequencing. (biomedcentral.com)
  • L . interrogans 16S rRNA primers offered highest analytical sensitivity. (cdc.gov)
  • B) 16S rRNA primers display a high PCR efficiency. (cdc.gov)
  • L . interrogans cDNA in RNase-free water (320 ng/μL) was serially diluted to tenfold (10 −1 to 10 −9 ) and subjected to qRT-PCR assays using 16S-1 primers. (cdc.gov)
  • Specific primers for 16S rDNA of full-length 1.6kb gene were used (Bukhari and Shakoori, 2010). (thefreedictionary.com)
  • About 425 bp 16S rDNA fragments were purified using QIAquick PCR purification kit (QIAGEN, Valencia, CA, USA) according to the manufacturer's instructions and sequenced with the same primers using the sequencer (Gene analyzer 3121) by Macrogen co. (thefreedictionary.com)
  • This study was undertaken to develop a new rapid method to identify the mycobacterial isolates at species level by gene amplification restriction analysis using primers encoding 16S- 23S rRNA internal transcribed spacer (ITS) region and flanking parts of the 16S as well as 23S rRNA gene . (bvsalud.org)
  • A workflow was optimized by comparing combinations of two extraction platforms and two primer sets, ultimately pursuing DNA extraction from blood with the MagNA Pure 96 and PCR amplification using dual-priming oligonucleotide primers specific to the V1-V3 region of the 16S rRNA gene. (cdc.gov)
  • All of the mentioned isolates were positive for coa, nuc , and 16S rDNA primers. (hindawi.com)
  • Polymorphisms present on the internal transcribed spacer 2 (ITS2) of ribosomal DNA allowed the development of 10 primers that combined with an universal forward primer lead to a simple and sensitive multiplex allele-specific polymerase chain reaction (AS-PCR). (ajtmh.org)
  • As non-coding RNA, rRNA itself is not translated into a protein, but it does provide a mechanism for decoding messenger RNA ( mRNA ) into amino acids and interacting with the transfer RNAs ( tRNAs ) during translation by providing peptidyl transferase activity. (newworldencyclopedia.org)
  • As a result, 16S rRNA gene sequencing has become prevalent in medical microbiology as a rapid and cheap alternative to phenotypic methods of bacterial identification. (wikipedia.org)
  • With third-generation sequencing coming to many labs, simultaneous identification of thousands of 16S rRNA sequences is possible within hours, allowing metagenomic studies, for example of gut flora. (wikipedia.org)
  • Utility of Histologic and Histochemical Screening for 16S Ribosomal RNA Gene Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue for Bacterial Endocarditis. (harvard.edu)
  • The sequence of the 16S ribosomal RNA (rRNA) from the archaebacterium Halobacterium volcanii has been determined by DNA sequencing methods. (nasa.gov)
  • Targeted amplicon sequencing of the 16S ribosomal RNA gene is one of the key tools for studying microbial diversity. (biomedcentral.com)
  • The accuracy of 16S rRNA sequencing strongly depends on the choice of the primer pairs. (biomedcentral.com)
  • haemolytica was confirmed by complete sequencing of the 16S rDNA gene with 99% identity in all analyzed isolates. (thefreedictionary.com)
  • Disseminated subcutaneous nocardiosis caused by Nocardia farcinica diagnosed by FNA biopsy and 16S ribosomal gene sequencing. (biomedsearch.com)
  • This was confirmed by 16S ribosomal gene sequencing. (biomedsearch.com)
  • Microbial communities were analysed by high-throughput 16S ribosomal RNA gene sequencing. (bmj.com)
  • The samples were then analyzed using high-throughput sequencing of 16S rRNA V3 + V4 amplicons. (springer.com)
  • Sequencing of the 16S ribosomal RNA (16S rRNA) gene is recognized to be effective for bacterial identification. (biomedcentral.com)
  • In contrast, 16S rRNA gene sequencing analysis detected Acinetobacter sp. (biomedcentral.com)
  • was isolated from bathrooms of the southern ward and was detected from four of seven samples using the culture method in comparison with six of seven samples by 16S rRNA gene sequencing analysis. (biomedcentral.com)
  • Our results suggest that 16S rRNA gene sequencing analysis is useful to identify range of contamination which were not found in conventional culture method. (biomedcentral.com)
  • The amplified product underwent modified Illumina 16S metagenomics sequencing library preparation and sequencing on a MiSeq V2 Nano flow cell, with data analysis using Pathogenomix RipSeq NGS software. (cdc.gov)
  • We compared the results of 16S rRNA -targeted sequencing and culture for identifying bacterial species in normally sterile body fluid (NSBF) cerebrospinal, pericardial, peritoneal and pleural fluids. (bvsalud.org)
  • Over a 10-year period, a total of 312 NSBF samples were evaluated simultaneously using 16S rRNA -targeted sequencing and culture . (bvsalud.org)
  • 0.001) were identified in subgingival plaque of individuals with low or high oral disease in West Virginia based on 16S rRNA gene sequencing. (duke.edu)
  • The remaining whole-transcriptome RiboMinus™ RNA is suitable for direct sequencing using any next-generation sequencing platforms or microarray analysis. (thermofisher.com)
  • Several recent studies using rDNA sequencing have reported the existence of divergent 16S rRNA sequences within a single organism in the eubacterial actinomycete Thermobispora bispora ( 26 ), the archaebacterium Halobacterium marismortui ( 15 ), and phytoplasma ( 14 ). (asm.org)
  • Subsequent partial 16S ribosomal RNA (rRNA) gene sequencing identified a Veillonella sp. (cdc.gov)
  • When metagenomic analysis first became common practice, bacterial diversity was studied using 16S rDNA clone libraries and automated Sanger sequencing. (thefreelibrary.com)
  • Global Targeted DNA/RNA Sequencing Market is expected to reach USD 15.9 billion by 2025. (express-press-release.net)
  • The Targeted DNA/RNA Sequencing Market is estimated to grow at a significant CAGR over the future period as the scope and its applications are rising enormously across the globe. (express-press-release.net)
  • Amplicon generation and target enrichment are the two important methods used for Targeted DNA/RNA Sequencing that could be explored in forecast period. (express-press-release.net)
  • AnRNA-based Targeted Sequencing and DNA-based Targeted Sequencing are the types of Targeted DNA/RNA Sequencing that could be explored in the foremost period. (express-press-release.net)
  • RNA-based Targeted Sequencing is a technique for sequencing and selecting specific pathways or transcripts of interest of gene expression microarray. (express-press-release.net)
  • Pharma & biotech entities, academic research, hospitals & clinics, and other end users could be explored in Targeted DNA/RNA Sequencing in the future period. (express-press-release.net)
  • Globally, North America accounted for the largest market share of Targeted DNA/RNA Sequencing and is estimated to lead the overall market in the coming years. (express-press-release.net)
  • The United States is a major consumer of Targeted DNA/RNA Sequencing in the coming years. (express-press-release.net)
  • The developing countries like China, Japan, and India are the major consumers of Targeted DNA/RNA Sequencing in the region. (express-press-release.net)
  • Total chloroplast tRNA hybridizes to fragments of rDNA 9 and it was suggested that the 16S-23S spacer region contains tRNA coding sequences as is observed in Escherichia coli 10,11 and in spinach chloroplast 12 rDNA. (nature.com)
  • We present DNA sequence data from four mitochondrial (cytochrome b, 12S rRNA, Valine tRNA, and 16S rRNA), and three nuclear loci (intron 7 of _-fibrinogen, intron 5 of alcohol dehydrogenase-I, and introns 3 through 5 of glyceraldehyde-3-phosphate dehydrogenase) to test previous hypotheses of interfamilial relationships within Grues, with particular attention to the enigmatic family Heliornithidae. (treebase.org)
  • Maize chloroplast 16S rDNA shows strong sequence homology with E. coli 16S rRNA 13 . (nature.com)
  • Here we present the synthesis and characterization of helix-threading peptides that bind selectively to helix 22 of E. coli 16S RNA. (elsevier.com)
  • M59073 Campylobacter coli 16S ribosomal RNA. (atcc.org)
  • We identified rmtE1 , an uncommon 16S ribosomal methyltransferase gene, in an aminoglycoside- and cephalosporin-resistant Escherichia coli sequence type 448 clinical strain co-harboring bla CMY-2 . (cdc.gov)
  • The bacterial 16S gene contains nine hypervariable regions (V1-V9), ranging from about 30 to 100 base pairs long, that are involved in the secondary structure of the small ribosomal subunit. (wikipedia.org)
  • This purine-rich 5' UTR sequence is complementary to the UCCU core sequence of the 3'-end of 16S rRNA (located within the 30S small ribosomal subunit). (thermofisher.com)
  • 16S ribosomal RNA (or 16S rRNA) is the RNA component of the 30S small subunit of a prokaryotic ribosome (SSU rRNA). (wikipedia.org)
  • The RNA that is a permanent structural part of a ribosome. (thefreedictionary.com)
  • See Ribosome, RNA . (thefreedictionary.com)
  • In the past, these components-especially in 16S rRNA and 23S rRNA, localized at the centre of the ribosome-were not considered to harbour these characteristics due to their elaborate structural integrity within the supramolecule. (nature.com)
  • ribosome (16S refers to the rate of sedimentation, in Svedberg units, of the RNA molecule in a centrifugal field). (britannica.com)
  • In addition, the S15-16S RNA interaction is important for the ordered assembly of the bacterial ribosome. (elsevier.com)
  • Our data demonstrate that in contrast to the E. coli ribosome, which preferentially recognizes the Shine-Dalgarno sequence, eukaryotic ribosomes (such as those found in retic lysate used in in vitro translation systems) can efficiently use either the Shine-Dalgarno or the Kozak ribosomal binding sites. (thermofisher.com)
  • The protein manufacturing unit of all living cells, the ribosome , is composed of ribosomal RNA and protein . (newworldencyclopedia.org)
  • More than half the weight of a ribosome is RNA (Alberts et al. (newworldencyclopedia.org)
  • Haloarchaeal 16S rDNA amplicons were present in one sample (11-16 Myr), whereas other samples (65-425 Myr) yielded only bacterial 16S rDNA amplicons. (lancs.ac.uk)
  • The accuracy of this approach strongly depends on the choice of primer pairs and, in particular, on the balance between efficiency, specificity and sensitivity in the amplification of the different bacterial 16S sequences contained in a sample. (biomedcentral.com)
  • A primer pair is composed of a forward and a reverse primer: the former is meant to match the sense sequence of the bacterial 16S, while the latter should match the antisense sequence [ 1 ]. (biomedcentral.com)
  • The 16S rRNA gene is present in all prokaryotes and contains both fast-evolving regions, which can be used to classify organisms at different taxonomic levels, and slowly-evolving regions, which are relatively conserved throughout different species. (biomedcentral.com)
  • The 16S/23S ribosomal RNA (rRNA) intergenic space (IGS) regions from pathogenic and non-pathogenic species (spp. (uleth.ca)
  • Based on 16S rRNA gene analysis, Moritella marina shows nearly identical similarities with other Moritella species (97-99% identity with other species) (Fig. 1). (kenyon.edu)
  • We performed a comparative analysis of the bacteriomes in three populations of B. yothersi and three additional Tetranychoidea species using sequences from V4-fragment of 16S DNA. (mdpi.com)
  • The phylogeny is based on 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project . (wikipedia.org)
  • Enrichment of whole transcriptome RNA by depleting ribosomal RNA (rRNA) species using our RiboMinus™ technology has the potential to enhance discovery using gene expression microarrays, RNA-Seq, and other methods. (thermofisher.com)
  • 2010). The 16S rDNA gene is highly conserved in prokaryotes, but the sequence is hypervariable between species, allowing it to be used as a marker of evolutionary relatedness by comparing sequence polymorphisms. (thefreelibrary.com)
  • I searched 18s RNA in NCBI and realized that the sequence lengths for different species are different, what should I do with them? (biology-online.org)
  • Several of the peptides exhibited moderate affinity (in the high nM to low µM range) to modified helix 31 in biophysical assays, including surface plasmon resonance (SPR), and were also shown to bind 30S ribosomal subunits. (mdpi.com)
  • While the ribosomal subunits are quite similar between prokaryotes and eukaryotes, the 70S ribosomes contain proportionally more RNA than protein, while the 80S ribosomes are composed of less RNA than protein. (newworldencyclopedia.org)
  • We examined con-served bridge interactions between the two ribosomal subunits, giving anindication of which contacts are more significant. (slideshare.net)
  • 1999. Detection of seven major evolutionary lineages in cyanobacteria based on the 16S rRNA gene sequence analysis with new sequences of five marine Synechococcus strains. (tolweb.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)
  • transcription within all types of organisms is performed by an enzyme called RNA polymerase, which copies a DNA template into an RNA product. (britannica.com)
  • The RNA polymerases of eukaryotes also consist of a high number of polypeptides (10-12), with the relative sizes of the polypeptides being similar to that of hyperthermophilic archaeal RNA polymerase. (britannica.com)
  • The expression of 16S rRNA was strongly associated with the presence of clinical signs of active trachoma. (lshtm.ac.uk)
  • The investigators amplified the V4 region of the 16S ribosomal RNA. (medscape.com)
  • Multiple sequences of the 16S rRNA gene can exist within a single bacterium. (wikipedia.org)
  • LOCUS CREMTRGU1 115 bp DNA PLN 20-JUN-1995 DEFINITION Chlamydomonas reinhardtii mitochondrial 16S-like small subunit S-1 ribosomal DNA. (bio.net)
  • LOCUS CREMTRGU2 217 bp DNA PLN 20-JUN-1995 DEFINITION Chlamydomonas reinhardtii mitochondrial 16S-like small subunit S-2 ribosomal DNA. (bio.net)
  • Ribosomal RNA (rRNA) is a type of non-coding ribonucleic acid (RNA) that is a primary and permanent component of ribosomes , the small, cellular particles that form the site of protein synthesis in all living cells . (newworldencyclopedia.org)
  • However, both archaea and eukaryotes have multiple RNA polymerases that contain multiple polypeptides. (britannica.com)
  • For eukaryotes, it is usually 18S ribosomal sequences that are used. (biology-online.org)
  • Drosophila 28S ribosomal RNA is processed into 2 fragments that migrate in a similar manner to the 18S rRNA. (thermofisher.com)
  • The 16S rRNA is by far the most common genomic marker used for prokaryotic classification, and has been used extensively in metagenomic studies over recent years. (biomedcentral.com)
  • When classifying genera the site selection algorithm needed around 80% of the sites in the 16S gene before the classification error reached a minimum. (biomedcentral.com)
  • 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)
  • Furthermore, the RFLP patterns predicted from the 16S rRNA gene sequences in the GenBank database agreed with the actual RFLP patterns produced in the present study. (nih.gov)
  • To further explore and develop the capabilities of the HTP design for binding RNA selectively, we identified helix 22 of the prokaryotic ribosomal RNA 16S as a target. (elsevier.com)
  • Rapid identification of mycobacteria by gene amplification restriction analysis technique targeting 16S-23S ribosomal RNA internal transcribed spacer & flanking region. (bvsalud.org)
  • This system is based on the amplification of approximately 1.8 kb fragment encoding 16S- 23S rRNA spacer region and flanking parts of the 16S as well as 23S rRNA gene . (bvsalud.org)
  • The Ambion® WT Expression Kit for RNA amplification prior to microarray analysis circumvents the need to deplete rRNA by selectively eliminating rRNA from reverse transcription in the amplification process. (thermofisher.com)
  • C. trachomatis was detected in 19.8% and 6.8% of subjects by the omp1 and 16S rRNA assays, respectively. (lshtm.ac.uk)
  • In protein synthesis a sequence near the 3′-end of the 16S rRNA interacts with the SHINE-DALGARNO sequence to initiate TRANSLATION . (thefreedictionary.com)
  • O ARNr 16S , é dicir, ácido ribonucleico ribosómico 16S (en inglés 16S rRNA ) é o compoñente da subunidade menor de 30S (S son as unidades svedberg ) do ribosoma procariota , o cal se une á secuencia Shine-Dalgarno . (wikipedia.org)
  • Three particularly useful priming sites, which provide access to the three major 16S rRNA structural domains, routinely yield 800-1000 nucleotides of 16S rRNA sequence. (pnas.org)
  • Structural changes in ribosomal RNA can be facilitated by the presence of modified nucleotides. (mdpi.com)
  • Our RiboMinus™ technology utilizes specific locked nucleic acid (LNA®) capture probes to bind ribosomal RNA and subsequently remove it from the sample via binding to streptavidin-coated Dynabeads® magnetic beads. (thermofisher.com)
  • The 16S rDNA for two strains of toxic M. aeruginosa were sequenced and compared to available cyanobacterial, bacterial, and chloroplast 16S rRNA gene information. (semanticscholar.org)
  • Strains that produce 16S-RMTase are frequently multidrug-resistant or even extensively drug-resistant. (fujita-hu.ac.jp)
  • Carl Woese and George E. Fox were two of the people who pioneered the use of 16S rRNA in phylogenetics in 1977. (wikipedia.org)
  • Carl Woese (1977) pioneered this use of 16S rRNA. (wikipedia.org)
  • [ 2 ] Carl Woese e George E. Fox foron os dous investigadores pioneiros no uso do ARNr 16S en filoxenética en 1977. (wikipedia.org)
  • 16S rRNA gene sequence analyses were compared conventional culture methods. (biomedcentral.com)
  • Use of 16S ribosomal RNA gene analyses to characterize the bacterial signature associated with poor oral health in West Virginia. (duke.edu)
  • Such a cell would need to construct ten million copies of each type of ribosomal RNA molecule. (newworldencyclopedia.org)
  • Aminoglycosides primarily act by binding to 16S ribosomal RNA within the 30S ribosomal subunit. (medscape.com)
  • Aminoglycosides inhibit protein synthesis by irreversibly binding to the 30S ribosomal subunit. (medscape.com)
  • and 23S ribosomal RNA gene, partial sequence. (atcc.org)
  • 16S analysis and metaproteomics revealed specific compositional and functional alterations of bacterial communities in inflamed mice. (bmj.com)
  • 16S rDNA-based metagenomic analysis of bacterial diversity associated with two populations of the Kleptoplastic sea slug Elysia chlorotica and its algal prey Vaucheria litorea. (thefreelibrary.com)
  • An amplified fragment of 222bp from 16S rDNA , 424bp from XCF/XCR and 500bp from XACF/XACR was observed from all collected citrus cultivars. (thefreedictionary.com)
  • High sequence diversity of Alteromonas macleodii-related cloned and cellular 16S rDNAs from a Mediterranean seawater mesocosm experiment. (kenyon.edu)
  • Aminoglycoside-producing Actinobacteria are known to protect themselves from their own aminoglycoside metabolites by producing 16S ribosomal RNA methyltransferase (16S-RMTase), which prevents them from binding to the 16S rRNA targets. (fujita-hu.ac.jp)
  • Specific interactions occur between aminoglycoside chemical groups important for antibiotic activity and conserved nucleotides in the RNA. (sciencemag.org)
  • Although it is closer in sequence to the eubacterial 16S rRNA than to the eukaryotic 16S-like rRNA, the H. volcanii sequence also shows certain points of specific similarity to its eukaryotic counterpart. (nasa.gov)
  • It is suggested that 16S rRNA gene can be used as a reliable molecular clock because 16S rRNA sequences from distantly related bacterial lineages are shown to have similar functionalities. (wikipedia.org)
  • [ 2 ] Suxeriuse que o xene do ARNr 16S pode utilizarse como un reloxo molecular fiable porque as súas secuencias en distintas liñaxes bacterianas relacionadas distantemente teñen funcionalidades similares. (wikipedia.org)
  • Here we show the genetic interoperability and promiscuity of 16S rRNA in the ribosomes of an extremely thermophilic bacterium, Thermus thermophilus . (nature.com)
  • [ 6 ] Carl Woese foi o pioneiro neste uso do ARNr 16S. (wikipedia.org)