Genes, rRNA: Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)rRNA Operon: Genetic loci which direct transcription of ribosomal RNA in bacterial operons. They are designated rrnB, rrnC, rrnD, etc. according to the structural position of the transcription unit in the DNA sequence.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.RNA, Ribosomal, 23S: Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.RNA, Ribosomal, 5S: Constituent of the 50S subunit of prokaryotic ribosomes containing about 120 nucleotides and 34 proteins. It is also a constituent of the 60S subunit of eukaryotic ribosomes. 5S rRNA is involved in initiation of polypeptide synthesis.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Bacterial Typing Techniques: Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.RNA, Ribosomal, 28S: Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Bacteria: One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Ribosomes: Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Seawater: The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Geologic Sediments: A mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)Fatty Acids: Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Ribosomal Proteins: Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.RNA Processing, Post-Transcriptional: Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.Cell Nucleolus: Within most types of eukaryotic CELL NUCLEUS, a distinct region, not delimited by a membrane, in which some species of rRNA (RNA, RIBOSOMAL) are synthesized and assembled into ribonucleoprotein subunits of ribosomes. In the nucleolus rRNA is transcribed from a nucleolar organizer, i.e., a group of tandemly repeated chromosomal genes which encode rRNA and which are transcribed by RNA polymerase I. (Singleton & Sainsbury, Dictionary of Microbiology & Molecular Biology, 2d ed)Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.Actinomycetales: An order of gram-positive, primarily aerobic BACTERIA that tend to form branching filaments.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Alphaproteobacteria: A class in the phylum PROTEOBACTERIA comprised mostly of two major phenotypes: purple non-sulfur bacteria and aerobic bacteriochlorophyll-containing bacteria.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.RNA, Fungal: Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.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.Fresh Water: Water containing no significant amounts of salts, such as water from RIVERS and LAKES.Polymorphism, Restriction Fragment Length: Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.RNA, Archaeal: Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.Bacteroidetes: A phylum of bacteria comprised of three classes: Bacteroides, Flavobacteria, and Sphingobacteria.RNA Polymerase I: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. The enzyme functions in the nucleolar structure and transcribes DNA into RNA. It has different requirements for cations and salts than RNA polymerase II and III and is not inhibited by alpha-amanitin. EC 188.8.131.52.DNA, Archaeal: Deoxyribonucleic acid that makes up the genetic material of archaea.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Ribosome Subunits, Small: The small ribonucleoprotein component of RIBOSOMES. It contains the MESSENGER RNA binding site and two TRANSFER RNA binding sites - one for the incoming AMINO ACYL TRNA (A site) and the other (P site) for the peptidyl tRNA carrying the elongating peptide chain.Biodiversity: The variety of all native living organisms and their various forms and interrelationships.Actinobacteria: Class of BACTERIA with diverse morphological properties. Strains of Actinobacteria show greater than 80% 16S rDNA/rRNA sequence similarity among each other and also the presence of certain signature nucleotides. (Stackebrandt E. et al, Int. J. Syst. Bacteriol. (1997) 47:479-491)Gammaproteobacteria: A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Korea: Former kingdom, located on Korea Peninsula between Sea of Japan and Yellow Sea on east coast of Asia. In 1948, the kingdom ceased and two independent countries were formed, divided by the 38th parallel.RNA, Transfer: The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.Quinones: Hydrocarbon rings which contain two ketone moieties in any position. They can be substituted in any position except at the ketone groups.RNA, Protozoan: Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.Methyltransferases: A subclass of enzymes of the transferase class that catalyze the transfer of a methyl group from one compound to another. (Dorland, 28th ed) EC 2.1.1.Vitamin K 2: A group of substances similar to VITAMIN K 1 which contains a ring of 2-methyl-1,4-naphthoquinione and an isoprenoid side chain of varying number of isoprene units. In vitamin K 2, each isoprene unit contains a double bond. They are produced by bacteria including the normal intestinal flora.Betaproteobacteria: A class in the phylum PROTEOBACTERIA comprised of chemoheterotrophs and chemoautotrophs which derive nutrients from decomposition of organic material.Sodium Chloride: A ubiquitous sodium salt that is commonly used to season food.Sewage: Refuse liquid or waste matter carried off by sewers.Proteobacteria: A phylum of bacteria consisting of the purple bacteria and their relatives which form a branch of the eubacterial tree. This group of predominantly gram-negative bacteria is classified based on homology of equivalent nucleotide sequences of 16S ribosomal RNA or by hybridization of ribosomal RNA or DNA with 16S and 23S ribosomal RNA.Ribosome Subunits, Small, Bacterial: The small subunit of eubacterial RIBOSOMES. It is composed of the 16S RIBOSOMAL RNA and about 23 different RIBOSOMAL PROTEINS.Endoribonucleases: A family of enzymes that catalyze the endonucleolytic cleavage of RNA. It includes EC 3.1.26.-, EC 3.1.27.-, EC 3.1.30.-, and EC 3.1.31.-.Ecosystem: A functional system which includes the organisms of a natural community together with their environment. (McGraw Hill Dictionary of Scientific and Technical Terms, 4th ed)Oligonucleotide Probes: Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.Deltaproteobacteria: A group of PROTEOBACTERIA represented by morphologically diverse, anaerobic sulfidogens. Some members of this group are considered bacterial predators, having bacteriolytic properties.Aerobiosis: Life or metabolic reactions occurring in an environment containing oxygen.Environmental Microbiology: The study of microorganisms living in a variety of environments (air, soil, water, etc.) and their pathogenic relationship to other organisms including man.Genetic Variation: Genotypic differences observed among individuals in a population.Hot Springs: Habitat of hot water naturally heated by underlying geologic processes. Surface hot springs have been used for BALNEOLOGY. Underwater hot springs are called HYDROTHERMAL VENTS.Pigments, Biological: Any normal or abnormal coloring matter in PLANTS; ANIMALS or micro-organisms.Bacterial Proteins: Proteins found in any species of bacterium.Operon: In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.RNA, Small Nucleolar: Small nuclear RNAs that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Bacillaceae: A family of bacteria which produce endospores. They are mostly saprophytes from soil, but a few are insect or animal parasites or pathogens.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Nocardia: A genus of gram-positive, aerobic bacteria whose species are widely distributed and are abundant in soil. Some strains are pathogenic opportunists for humans and animals.Pol1 Transcription Initiation Complex Proteins: Factors that form a preinitiation complex at promoters that are specifically transcribed by RNA POLYMERASE I.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.DNA Fingerprinting: A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.PseudouridineMethane: The simplest saturated hydrocarbon. It is a colorless, flammable gas, slightly soluble in water. It is one of the chief constituents of natural gas and is formed in the decomposition of organic matter. (Grant & Hackh's Chemical Dictionary, 5th ed)Anaerobiosis: The complete absence, or (loosely) the paucity, of gaseous or dissolved elemental oxygen in a given place or environment. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Nucleic Acid Precursors: Use for nucleic acid precursors in general or for which there is no specific heading.Flavobacteriaceae: A family of bacteria in the order Sphingobacteriales, class Sphingobacteria. They are gram-negative rods, mostly saprophytic in terrestrial and aquatic habitats.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Denaturing Gradient Gel Electrophoresis: Electrophoresis in which various denaturant gradients are used to induce nucleic acids to melt at various stages resulting in separation of molecules based on small sequence differences including SNPs. The denaturants used include heat, formamide, and urea.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Diaminopimelic AcidPlankton: Community of tiny aquatic PLANTS and ANIMALS, and photosynthetic BACTERIA, that are either free-floating or suspended in the water, with little or no power of locomotion. They are divided into PHYTOPLANKTON and ZOOPLANKTON.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Anti-Bacterial Agents: Substances that reduce the growth or reproduction of BACTERIA.Chloroflexi: Phylum of green nonsulfur bacteria including the family Chloroflexaceae, among others.Eukaryota: One of the three domains of life (the others being BACTERIA and ARCHAEA), also called Eukarya. These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.Rhodobacteraceae: A family in the order Rhodobacterales, class ALPHAPROTEOBACTERIA.Mycoplasma: A genus of gram-negative, mostly facultatively anaerobic bacteria in the family MYCOPLASMATACEAE. The cells are bounded by a PLASMA MEMBRANE and lack a true CELL WALL. Its organisms are pathogens found on the MUCOUS MEMBRANES of humans, ANIMALS, and BIRDS.DNA, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.Transcription Factor TFIIIA: One of several general transcription factors that are specific for RNA POLYMERASE III. It is a zinc finger (ZINC FINGERS) protein and is required for transcription of 5S ribosomal genes.Biodegradation, Environmental: Elimination of ENVIRONMENTAL POLLUTANTS; PESTICIDES and other waste using living organisms, usually involving intervention of environmental or sanitation engineers.DNA, Protozoan: Deoxyribonucleic acid that makes up the genetic material of protozoa.DNA Probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.Cytophaga: A genus of gram-negative gliding bacteria found in SOIL; HUMUS; and FRESHWATER and marine habitats.Gentian Violet: A dye that is a mixture of violet rosanilinis with antibacterial, antifungal, and anthelmintic properties.Microbial Consortia: A group of different species of microorganisms that act together as a community.In Situ Hybridization, Fluorescence: A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.Waste Disposal, Fluid: The discarding or destroying of liquid waste products or their transformation into something useful or innocuous.Mycobacterium: A genus of gram-positive, aerobic bacteria. Most species are free-living in soil and water, but the major habitat for some is the diseased tissue of warm-blooded hosts.Halobacteriaceae: A family of extremely halophilic archaea found in environments with high salt concentrations, such as salt lakes, evaporated brines, or salted fish. Halobacteriaceae are either obligate aerobes or facultative anaerobes and are divided into at least twenty-six genera including: HALOARCULA; HALOBACTERIUM; HALOCOCCUS; HALOFERAX; HALORUBRUM; NATRONOBACTERIUM; and NATRONOCOCCUS.Comamonadaceae: A family of gram-negative aerobic bacteria in the class BETA PROTEOBACTERIA, encompassing the acidovorans rRNA complex. Some species are pathogenic for PLANTS.China: A country spanning from central Asia to the Pacific Ocean.Bacteria, AnaerobicSymbiosis: The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.Ribosome Subunits, Large, Bacterial: The large subunit of the eubacterial 70s ribosome. It is composed of the 23S RIBOSOMAL RNA, the 5S RIBOSOMAL RNA, and about 37 different RIBOSOMAL PROTEINS.RNA Probes: RNA, usually prepared by transcription from cloned DNA, which complements a specific mRNA or DNA and is generally used for studies of virus genes, distribution of specific RNA in tissues and cells, integration of viral DNA into genomes, transcription, etc. Whereas DNA PROBES are preferred for use at a more macroscopic level for detection of the presence of DNA/RNA from specific species or subspecies, RNA probes are preferred for genetic studies. Conventional labels for the RNA probe include radioisotope labels 32P and 125I and the chemical label biotin. RNA probes may be further divided by category into plus-sense RNA probes, minus-sense RNA probes, and antisense RNA probes.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Aminoglycosides: Glycosylated compounds in which there is an amino substituent on the glycoside. Some of them are clinically important ANTIBIOTICS.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Feces: Excrement from the INTESTINES, containing unabsorbed solids, waste products, secretions, and BACTERIA of the DIGESTIVE SYSTEM.Ribosome Subunits, Small, Eukaryotic: The small subunit of the 80s ribosome of eukaryotes. It is composed of the 18S RIBOSOMAL RNA and 32 different RIBOSOMAL PROTEINS.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Helicobacter: A genus of gram-negative, spiral-shaped bacteria that has been isolated from the intestinal tract of mammals, including humans. It has been associated with PEPTIC ULCER.Sensitivity and Specificity: Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)Methylation: 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)PhenazinesGenes: 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.Flavobacterium: A genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in SOIL and WATER. Its organisms are also found in raw meats, MILK and other FOOD, hospital environments, and human clinical specimens. Some species are pathogenic in humans.Ribonucleoproteins, Small Nucleolar: Nucleolar RNA-protein complexes that function in pre-ribosomal RNA processing.Microbiota: The full collection of microbes (bacteria, fungi, virus, etc.) that naturally exist within a particular biological niche such as an organism, soil, a body of water, etc.Cytophagaceae: A family of gram-negative, gliding bacteria in the order Cytophagales, class Cytophagia. They are found in SOIL and SEA WATER.Gram-Positive Endospore-Forming Rods: Rod-shaped bacteria that form endospores and are gram-positive. Representative genera include BACILLUS and CLOSTRIDIUM.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Ribosome Subunits: The two dissimilar sized ribonucleoprotein complexes that comprise a RIBOSOME - the large ribosomal subunit and the small ribosomal subunit. The eukaryotic 80S ribosome is composed of a 60S large subunit and a 40S small subunit. The bacterial 70S ribosome is composed of a 50S large subunit and a 30S small subunit.Sphingomonadaceae: A family of gram-negative, asporogenous rods or ovoid cells, aerobic or facultative anaerobic chemoorganotrophs. They are commonly isolated from SOIL, activated sludge, or marine environments.Culture Media: Any liquid or solid preparation made specifically for the growth, storage, or transport of microorganisms or other types of cells. The variety of media that exist allow for the culturing of specific microorganisms and cell types, such as differential media, selective media, test media, and defined media. Solid media consist of liquid media that have been solidified with an agent such as AGAR or GELATIN.Drug Resistance, Bacterial: The ability of bacteria to resist or to become tolerant to chemotherapeutic agents, antimicrobial agents, or antibiotics. This resistance may be acquired through gene mutation or foreign DNA in transmissible plasmids (R FACTORS).Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Metagenomics: The genomic analysis of assemblages of organisms.Ribonuclease T1: An enzyme catalyzing the endonucleolytic cleavage of RNA at the 3'-position of a guanylate residue. EC 184.108.40.206.Gram-Positive Endospore-Forming Bacteria: Bacteria that form endospores and are gram-positive. Representative genera include BACILLUS; CLOSTRIDIUM; MICROMONOSPORA; SACCHAROPOLYSPORA; and STREPTOMYCES.Ribosome Inactivating Proteins: N-Glycosidases that remove adenines from RIBOSOMAL RNA, depurinating the conserved alpha-sarcin loop of 28S RIBOSOMAL RNA. They often consist of a toxic A subunit and a binding lectin B subunit. They may be considered as PROTEIN SYNTHESIS INHIBITORS. They are found in many PLANTS and have cytotoxic and antiviral activity.DNA-Directed RNA Polymerases: Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).Haloarcula marismortui: A species of halophilic archaea distinguished by its production of acid from sugar. This species was previously called Halobacterium marismortui.Bioreactors: Tools or devices for generating products using the synthetic or chemical conversion capacity of a biological system. They can be classical fermentors, cell culture perfusion systems, or enzyme bioreactors. For production of proteins or enzymes, recombinant microorganisms such as bacteria, mammalian cells, or insect or plant cells are usually chosen.Ribotyping: RESTRICTION FRAGMENT LENGTH POLYMORPHISM analysis of rRNA genes that is used for differentiating between species or strains.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Soil Pollutants: Substances which pollute the soil. Use for soil pollutants in general or for which there is no specific heading.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Soil: The unconsolidated mineral or organic matter on the surface of the earth that serves as a natural medium for the growth of land plants.Oligoribonucleotides: A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Bacillus: A genus of BACILLACEAE that are spore-forming, rod-shaped cells. Most species are saprophytic soil forms with only a few species being pathogenic.Prevotella: A genus of gram-negative, anaerobic, nonsporeforming, nonmotile rods. Organisms of this genus had originally been classified as members of the BACTEROIDES genus but overwhelming biochemical and chemical findings in 1990 indicated the need to separate them from other Bacteroides species, and hence, this new genus was established.Ribosome Subunits, Large: The largest ribonucleoprotein component of RIBOSOMES. It contains the domains which catalyze formation of the peptide bond and translocation of the ribosome along the MESSENGER RNA during GENETIC TRANSLATION.Bacteriological Techniques: Techniques used in studying bacteria.Gastrointestinal Tract: Generally refers to the digestive structures stretching from the MOUTH to ANUS, but does not include the accessory glandular organs (LIVER; BILIARY TRACT; PANCREAS).Exoribonucleases: A family of enzymes that catalyze the exonucleolytic cleavage of RNA. It includes EC 3.1.13.-, EC 3.1.14.-, EC 3.1.15.-, and EC 3.1.16.-. EC 3.1.-Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Peptidyl Transferases: Acyltransferases that use AMINO ACYL TRNA as the amino acid donor in formation of a peptide bond. There are ribosomal and non-ribosomal peptidyltransferases.DNA, Intergenic: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.Marine Biology: The study of the origin, structure, development, growth, function, genetics, and reproduction of organisms which inhabit the OCEANS AND SEAS.Ribonucleases: Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.Ciliophora: A phylum of EUKARYOTES characterized by the presence of cilia at some time during the life cycle. It comprises three classes: KINETOFRAGMINOPHOREA; OLIGOHYMENOPHOREA; and POLYMENOPHOREA.Gram-Positive Cocci: Coccus-shaped bacteria that retain the crystal violet stain when treated by Gram's method.Lactobacillus: A genus of gram-positive, microaerophilic, rod-shaped bacteria occurring widely in nature. Its species are also part of the many normal flora of the mouth, intestinal tract, and vagina of many mammals, including humans. Pathogenicity from this genus is rare.Genes, Archaeal: The functional genetic units of ARCHAEA.Locomotion: Movement or the ability to move from one place or another. It can refer to humans, vertebrate or invertebrate animals, and microorganisms.Genes, Fungal: The functional hereditary units of FUNGI.Porifera: The phylum of sponges which are sessile, suspension-feeding, multicellular animals that utilize flagellated cells called choanocytes to circulate water. Most are hermaphroditic. They are probably an early evolutionary side branch that gave rise to no other group of animals. Except for about 150 freshwater species, sponges are marine animals. They are a source of ALKALOIDS; STEROLS; and other complex molecules useful in medicine and biological research.Arctic Regions: The Arctic Ocean and the lands in it and adjacent to it. It includes Point Barrow, Alaska, most of the Franklin District in Canada, two thirds of Greenland, Svalbard, Franz Josef Land, Lapland, Novaya Zemlya, and Northern Siberia. (Webster's New Geographical Dictionary, 1988, p66)Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.Antarctic Regions: The continent lying around the South Pole and the southern waters of the Atlantic, Pacific, and Indian Oceans. It includes the Falkland Islands Dependencies. (From Webster's New Geographical Dictionary, 1988, p55)Chryseobacterium: A genus of aerobic, gram-negative bacteria in the family FLAVOBACTERIACEAE. Many of its species were formerly in the genus FLAVOBACTERIUM.Classification: The systematic arrangement of entities in any field into categories classes based on common characteristics such as properties, morphology, subject matter, etc.Plants: Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.Crenarchaeota: A kingdom in the domain ARCHAEA comprised of thermoacidophilic, sulfur-dependent organisms. The two orders are SULFOLOBALES and THERMOPROTEALES.Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.Fungi: A kingdom of eukaryotic, heterotrophic organisms that live parasitically as saprobes, including MUSHROOMS; YEASTS; smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi, commonly known as molds, refer to those that grow as multicellular colonies.Industrial Waste: Worthless, damaged, defective, superfluous or effluent material from industrial operations.Tetrahymena: A genus of ciliate protozoa commonly used in genetic, cytological, and other research.Gram-Negative Bacteria: Bacteria which lose crystal violet stain but are stained pink when treated by Gram's method.Alteromonadaceae: A family of marine, gram-negative PROTEOBACTERIA including the genera ALTEROMONAS; Colwellia; Idiomarina; MARINOBACTER; MORITELLA; PSEUDOALTEROMONAS; and SHEWANELLA.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Mediterranean SeaEscherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.tRNA Methyltransferases: Enzymes that catalyze the S-adenosyl-L-methionine-dependent methylation of ribonucleotide bases within a transfer RNA molecule. EC 2.1.1.Corynebacterium: A genus of asporogenous bacteria that is widely distributed in nature. Its organisms appear as straight to slightly curved rods and are known to be human and animal parasites and pathogens.Ricin: A protein phytotoxin from the seeds of Ricinus communis, the castor oil plant. It agglutinates cells, is proteolytic, and causes lethal inflammation and hemorrhage if taken internally.Heterotrophic Processes: The processes by which organisms utilize organic substances as their nutrient sources. Contrasts with AUTOTROPHIC PROCESSES which make use of simple inorganic substances as the nutrient supply source. Heterotrophs can be either chemoheterotrophs (or chemoorganotrophs) which also require organic substances such as glucose for their primary metabolic energy requirements, or photoheterotrophs (or photoorganotrophs) which derive their primary energy requirements from light. Depending on environmental conditions some organisms can switch between different nutritional modes (AUTOTROPHY; heterotrophy; chemotrophy; or PHOTOTROPHY) to utilize different sources to meet their nutrients and energy requirements.Bacteriochlorophyll A: A specific bacteriochlorophyll that is similar in structure to chlorophyll a.Colony Count, Microbial: Enumeration by direct count of viable, isolated bacterial, archaeal, or fungal CELLS or SPORES capable of growth on solid CULTURE MEDIA. The method is used routinely by environmental microbiologists for quantifying organisms in AIR; FOOD; and WATER; by clinicians for measuring patients' microbial load; and in antimicrobial drug testing.Streptococcaceae: A family of gram-positive non-sporing bacteria including many parasitic, pathogenic, and saprophytic forms.Bradyrhizobium: A genus of gram-negative, aerobic, rod-shaped bacteria usually containing granules of poly-beta-hydroxybutyrate. They characteristically invade the root hairs of leguminous plants and act as intracellular symbionts.RNA, Small Nuclear: Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.Rhizobiaceae: A family of gram-negative bacteria which are saprophytes, symbionts, or plant pathogens.UridineBlotting, Southern: A method (first developed by E.M. Southern) for detection of DNA 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.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Wetlands: Environments or habitats at the interface between truly terrestrial ecosystems and truly aquatic systems making them different from each yet highly dependent on both. Adaptations to low soil oxygen characterize many wetland species.Methylobacterium: A genus of gram-negative, aerobic, facultatively methylotrophic rods occurring singly or occasionally in rosettes. Members of this genus are usually motile and are isolated from soil, dust, fresh water, lake sediments, leaf surfaces, rice, air, and hospital environments. (From Bergey's Manual of Determinative Bacteriology, 9th ed)Hydrogen-Ion Concentration: The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
Base-specific fragmentation of amplified 16S rRNA genes and mass spectrometry analysis: A novel tool for rapid bacterial...Base-specific fragmentation of amplified 16S rRNA genes and mass spectrometry analysis: A novel tool for rapid bacterial ... Base-specific fragmentation of amplified 16S rRNA genes and mass spectrometry analysis: A novel tool for rapid bacterial ... Abstract: A rapid approach to the 16S rRNA gene (16S rDNA)-based bacterial identification has been developed that combines ...
Epigenetic regulation of TTF‐I‐mediated promoter-terminator interactions of rRNA genes | The EMBO JournalPromoter-terminator interactions of mammalian rRNA genes. In the present study, topological features of mouse rRNA genes were ... therefore correlating with inactive rRNA genes. The predominant association of histone H3 with inactive rRNA genes suggests a ... Analysis of the methylation status of the looped mouse rRNA genes showed that the majority of looped genes are devoid of DNA ... We could show that transcription factors of rRNA genes are associated with non‐methylated, active genes, whereas histone H3 and ...
Characterization of 16S rRNA genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing...Characterization of 16S rRNA genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing ... Characterization of 16S rRNA genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing ... Cloning and nucleotide sequencing experiments are performed on PCR-amplified 16S rRNA genes to characterize oil field microbial ...
Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of the gut microbiotaPCR amplification of 16S rRNA genes. DNA isolated from faecal material was used as a template in PCR amplification. PCR was ... The differentiated bands were excised and identified by sequencing the V3 region of the 16S rRNA genes. ... Sokol H, Lepage P, Seksik P, Dore J, Marteau P. Temperature gradient gel electrophoresis of fecal 16S rRNA reveals active ... Yu ZT, Morrison M. Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial ...
Different Types of Diatom-Derived Extracellular Polymeric Substances Drive Changes in Heterotrophic Bacterial Communities from...Microbial biomass increased ~4-6-fold over 9 days, and pyrosequencing of bacterial 16S rRNA genes revealed that the addition of ... The composition of the bacterial communities was assessed from 16S rRNA genes libraries constructed from the DNA extracts of ... Raw pyrosequences of amplified bacterial 16S rRNA genes from all the samples can be extracted from the European Nucleotide ... PCR amplification of bacterial 16S rRNA genes PCR amplifications were carried out using bacterial primers 341GC-F ( ...
Difference between revisions of "BISC209: Lab3" - OpenWetWareWhile the 16S rRNA genes from all of the bacterial species in your soil genomic isolate are being amplified in the thermal ... the amplified 16s rRNA genes in those pcr products. . Looking at the purity of your pcr amplification by agarose gel ... Before you leave today we will freeze away the remainder of the amplified 16s rRNA genes in those pcr products. Looking at the ... The sequencing facility is able to use conserved primer sites on our vector to be able to sequence the inserted 16S rRNA genes ...
General Biology/Genetics/Mutation - Wikibooks, open books for an open worldTandem clusters (rRNA genes; nucleolus). *Multigene families. *Single-copy genes (one copy per 1n) ... rearrangement of nucleotides and duplication of entire genes:. Inversion. Rearrangement. Gene/Exon Duplications[ ...
Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids [PeerJ Preprints]Summary of SSU rRNA genes in genome bins. DOI: 10.7287/peerj.preprints.2613v1/supp-2 ... A FASTA file containing 54 SSU rRNA genes with length ,300 base pairs extracted from the 98 genomes from metagenomes can be ...
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria |...16S rRNA genes. ACD20. 30x. Near Complete. 2,979,548. 33.5. 191. 33,361. 2,819. ND. ... 16S rRNA gene phylogeny. 16S rRNA gene sequences from MEL.A1, MEL.B1, and MEL.B2 were aligned using NAST (McDonald et al., 2012 ... 16S rRNA gene phylogeny of Melainabacteria and Cyanobacteria.. Trees were built using 16S rRNA gene sequences from MEL.A1, MEL. ... Then, the phylum assigned to majority of the four MEL-COG genes was assigned to the MEL-COG. If none of the MEL-COG genes ...
Molecular Epidemiology of Rickettsial Diseases | SpringerLinkAndersson SG, Zomorodipour A, Winkler HH, Kurland CG (1995). Unusual organization of the rRNA genes in Rickettsia prowazekii. J ... 2000). Phylogenetic analysis of the rompB genes of Rickettsia felis and Rickettsia prowazekii European-human and North American ... Stothard DR, Fuerst PA (1995). Evolutionary analysis of the spotted fever and typhus groups of Rickettsia using 16S rRNA gene ... 2012). A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of ...
Search Results - HKUST Institutional Repository1 16s Rrna Genes * 1 2-dimensional Crystals * 1 2-dimensional Gel Electrophoresis ...
4A part of the chromosome containing rrna genes.. Nucleotide. A subunit of dna or rna consisting of a nitrogenous base (adenine ... The study of variation in genes among a group of individuals.. Positional Cloning. A technique used to identify genes, usually ... A set of genes transcribed under the control of an operator gene.. Osteogenesis Imperfecta. A condition also known as brittle ... The natural process of breaking and rejoining dna strands to produce new combinations of genes and,. Regulatory Region Or ...
Genes | Free Full-Text | The Replication Fork: Understanding the Eukaryotic Replication Machinery and the Challenges to Genome...Little, R.D.; Platt, T.H.; Schildkraut, C.L. Initiation and termination of DNA replication in human rRNA genes. Mol. Cell. Biol ... The mating type switch-activating protein Sap1 is required for replication fork arrest at the rRNA genes of fission yeast. Mol ... Genes Dev. 1997, 11, 3375-3386. [Google Scholar] [CrossRef]. *Lee, K.Y.; Bang, S.W.; Yoon, S.W.; Lee, S.-H.; Yoon, J.-B.; Hwang ... Genes Dev. 2007, 21, 2288-2299. [Google Scholar] [CrossRef]. *Lou, H.; Komata, M.; Katou, Y.; Guan, Z.; Reis, C.C.; Budd, M.; ...
Difference between revisions of "BISC209: Lab5" - OpenWetWareLAB 5: Getting the 16S rRNA genes from the Soil Genomic DNA in the E. coli clones ready to send away for DNA sequencing. ... 1 LAB 5: Getting the 16S rRNA genes from the Soil Genomic DNA in the E. coli clones ready to send away for DNA sequencing ... LAB 5: Getting the 16S rRNA genes from the Soil Genomic DNA in the E. coli clones ready to send away for DNA sequencing) ... Preparing Over-night Cultures to send away for 16s rRNA gene sequencing 1. We need to keep track of which DNA sequences come ...
High-Pressure Transitions of Germanium and a New High-Pressure Form of Germanium.17158629 - The unique 16s rrna genes of piezophiles reflect both phylogeny and adaptation.. 18282059 - In situ high-pressure x- ...
MCB News | The School of Molecular and Cellular Biology | University of Illinois Urbana-ChampaignSeveral mechanisms ensure controlled transcriptional output from rRNA genes. Transcriptional repression of a subset of rRNA ... Supriya Prasanth's lab identifies a BEN domain-containing protein as a novel transcriptional repressor of rRNA genes, in PNAS. ... as a novel transcriptional repressor of rRNA genes. Prasanth and colleagues show that BEND3 directly binds to rDNA promoter in ... The genes encoding three proteins (named Pnkp1, Rnl, and Hen1) that constitute the putative new RNA repair system were then ...
Female viagra pills » Official Canadian Pharmacy ::: Canadian pharmacy support team.1: A speculatively rooted tree for rRNA genes. A rooted phylogenetic tree is a tree with a unique node corresponding to the ( ... mixed in with manifestation having an his role in male genital female viagra pills Watched it with happens to be idea of genes ...
ChlorarachniophytesPhylogeny of Nuclear and Nucleomorph Small Subunit rRNA Genes. Molecular Biology and Evolution 16(3):321-331 ... Genes encoded by the nucleomorph genome are mostly 'housekeeping genes', genes for maintaining its replication and expression ... The miniaturized nuclear genome of a eukaryotic endosymbiont contains genes that overlap, genes that are cotranscribed, and the ... These genes are arranged in the chromosomes in a highly compacted manner. However, the genes also contain numerous introns, ...
Physiological and genetic basis for self-aggregation of a thermophilic hydrogenotrophic methanogen, Methanothermobacter strain...Circle 4 shows the positions of tRNA genes (purple) and rRNA genes (brown). Circle 5 shows a plot of GC skew [(G − C)/(G + C); ... Table S4. Presence of formate transporter genes in sequenced methanogens.. Table S5. The predicted genes involved in ... Genes and their orientations are depicted with arrows. The formate utilizing genes (fdh) are shown as black. Grey lines ... The numbers of shared and unique genes are shown.. B. Comparison of the genomic location of formate dehydrogenase genes (fdhABC ...
Lean Breed Landrace Pigs Harbor Fecal Methanogens at Higher Diversity and Density than Obese Breed Erhualian PigsPrimers Met86F and Met1340R were used to amplify archaeal 16S rRNA genes . The amplification was initiated with a ... Sequence Analysis of the Two Archaeal 16S rRNA Gene Clone Libraries. A total of 381 cloned archaeal 16S rRNA gene amplicons, ... and screening of transformants using RFLP analysis of the cloned 16S rRNA genes by restriction digestion with endonucleases Hae ... The 16S rRNA gene library from Landrace pigs was comprised a total of 382 clones, consisting of 25 OTUs (Table 1). Most of ...
RNA18S2 Gene - GeneCards | RNA18S2 RNA GeneClones of human ribosomal DNA containing the complete 18 S-rRNA and 28 S-rRNA genes. Characterization, a detailed map of the ... Nucleolar organizer regions: genomic 'dark matter' requiring illumination. (PMID: 27474438) McStay B. (Genes Dev. 2016) 3 64 ... The 45S rDNA repeat unit encodes a 45S rRNA precursor, transcribed by RNA polymerase I, which is processed to form the 18S, 5.8 ... Phenotype-based relationships between genes and organs from Gene ORGANizer for RNA18S2 Gene ...
The ISME Journal - Strategies to improve reference databases for soil microbiomes... to RefSoil 16S rRNA genes; ring III (blue) indicates that these 16S rRNA genes shared similarity to sorted cells that were ... To evaluate the presence of RefSoil genomes in soil samples, EMP 16S rRNA gene amplicons and RefSoil 16S rRNA genes were ... Rinke et al., 2013). The 16S rRNA genes of these 14 SAGs, belonging to Proteobacteria, Actinobacteria, Nitrospirae, ... The 16S rRNA gene was successfully recovered from 109 of the 317 single amplified genomes (SAGs). This 34% 16S rRNA gene ...
Appl Environ Microbiol Volume 63(1); 1997 JanuaryPhylogenetic diversity of bacterial symbionts of Solemya hosts based on comparative sequence analysis of 16S rRNA genes. ... Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. ... Temporal Transcriptional Pattern of Three Melanin Biosynthesis Genes, PKS1, SCD1, and THR1, in Appressorium-Differentiating and ... phaseolicola based on phaseolotoxin-resistant ornithine carbamoyltransferase gene (argK) and 16S-23S rRNA intergenic spacer ...
The ISME Journal - Abstract of article: Diversity of active marine picoeukaryotes in the Eastern Mediterranean Sea unveiled...... several in situ molecular studies showed a broad genetic diversity of small eukaryotes by sequencing 18S rRNA genes. Compared ... Viral photosynthetic reaction center genes and transcripts in the marine environment. The ISME Journal Original Article ...
Prevalence and Risk Factors of Cryptosporidium Infection in Children Hospitalized for Diarrhea in Guangzhou, China | Open...PCR and sequencing of a fragment of the 18S rRNA genes were used for genotyping Cryptosporidium . Microscopic positive fecal ... DNA sequences of the 18S rRNA gene from infected children were 99.12% to 100% identical to sequences in the GenBank of C. ... Table 4: Comparison of 18S rRNA gene sequence of Cryptosporidium from children hospitalized for diarrhea in Guangzhou to highly ... 1999) Phylogenetic analysis of Cryptosporidium parasites based on the small-subunit rRNA gene locus. Appl Environ Microbiol 65 ...
Amplified Ribosomal DNA Restriction Analysis: Amplified rDNA (Ribosomal DNA) Restriction Analysis is the extension of the technique of RFLP (restriction fragment length polymorphism) to the gene encoding the small (16s) ribosomal subunit of bacteria. The technique involves an enzymatic amplification using primers directed at the conserved regions at the ends of the 16s gene, followed by digestion using tetracutter Restriction enzymes.MT-RNR2: Mitochondrially encoded 16S RNA (often abbreviated as 16S) is a mitochondrial ribosomal RNA (rRNA) that in humans is encoded by the MT-RNR2 gene. The MT-RNR2 gene also encodes the Humanin polypeptide that has been the target of Alzheimer's disease research.Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.Transfer-messenger RNA: Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex (tmRNP) together with Small Protein B (SmpB), Elongation Factor Tu (EF-Tu), and ribosomal protein S1.Coles PhillipsDNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).Symmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.Gemmatimonadetes: The Gemmatimonadetes are a family of bacteria, given their own phylum (Gemmatimonadetes). This bacterium makes up about 2% of soil bacterial communities and has been identified as one of the top nine phyla found in soils; yet, there are currently only six cultured isolates.Nucleic acid structure: Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar.Exogenous bacteria: Exogenous bacteria are microorganisms introduced to closed biological systems from the external world. They exist in aquatic and terrestrial environments, as well as the atmosphere.Internal ribosome entry site: An internal ribosome entry site, abbreviated IRES, is a nucleotide sequence that allows for translation initiation in the middle of a messenger RNA (mRNA) sequence as part of the greater process of protein synthesis. Usually, in eukaryotes, translation can be initiated only at the 5' end of the mRNA molecule, since 5' cap recognition is required for the assembly of the initiation complex.Deep chlorophyll maximum: A deep chlorophyll maximum (DCM) is a subsurface maximum in the concentration of chlorophyll in the ocean or a lake. A DCM is not always present--sometimes there is more chlorophyll at the surface than at any greater depth--but it is a common feature of most aquatic ecosystems.Thermal cyclerNankai Trough gas hydrate site: Nankai Methane Hydrate Site (or Japanese Methane Hydrate R&D Program at Nankai, Nankai Trough Methane Hydrate Site) is located in the Nankai Trough, Japan.Heptadecanoic acidRMF RNA motif: The rmf RNA motif is a conserved RNA structure that was originally detected using bioinformatics. rmf RNAs are consistently foundwithin species classified into the genus Pseudomonas, and is located potentially in the 5' untranslated regions (5' UTRs) of rmf genes.Nucleolus: The nucleolus (; plural nucleoli ) is the largest structure in the nucleus of eukaryotic cells, where it primarily serves as the site of ribosome synthesis and assembly. Nucleoli also have other important functions like assembly of signal recognition particles and playing a role in the cell's response to stress.Fecal coliform: A fecal coliform (British: faecal coliform) is a facultatively anaerobic, rod-shaped, gram-negative, non-sporulating bacterium. Coliform bacteria generally originate in the intestines of warm-blooded animals.Clavibacter michiganensis: Clavibacter michiganensis is an aerobic non-sporulating Gram-positive plant pathogenic actinomycete that currently constitutes the only species within the genus Clavibacter. The other former Clavibacter species have been reclassified to genera Leifsonia, Rathayibacter and Curtobacterium.Pelagibacter ubique: Pelagibacter, with the single species P. ubique, was isolated in 2002 and given a specific name, although it has not yet been validly published according to the bacteriological code.List of strains of Escherichia coli: Escherichia coli is a well studied bacterium that was first identified by Theodor Escherich, after whom it was later named.Bulloo-Bancannia drainage basin: The Bulloo-Bancannia drainage basin is a drainage basin that covers part of western Queensland and New South Wales. It is adjacent to the much larger Lake Eyre basin.Amplified fragment length polymorphismAlkaliflexus: Alkaliflexus is a genus in the phylum Bacteroidetes (Bacteria).Phenotype microarray: The phenotype microarray approach is a technology for high-throughput phenotyping of cells.Alliance for Zero Extinction: Formed in 2000 and launched globally in 2005, the Alliance for Zero Extinction (AZE) comprises 100 non-governmental biodiversity conservation organizations working to prevent species extinctions by identifying and safeguarding sites where species evaluated to be Endangered or Critically Endangered under International Union for Conservation of Nature (IUCN) criteria only exist at one location on earth."Zero Extinction - Home.Adlercreutzia: Adlercreutzia is a genus in the phylum Actinobacteria (Bacteria).Alkalimonas: Alkalimonas is a genus in the phylum Proteobacteria (Bacteria).Eukaryotic transcription: Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells.Yi Byeong-cheon: Yi Byeong-cheon (Hangeul: 이병천, also spelled Lee Byeong-chun, born January 5, 1965) is the veterinary professor at Seoul National University responsible for the ₩300 million KRW "Toppy" dog cloning program. Yi is a former aide to Hwang Woo-suk, a pioneer in the field with the "Snuppy" clone, who fell from grace after his stem cell research turned out to have been fabricated.T-box leaderIndole-5,6-quinoneO-methyltransferase: An O-methylated flavonoid (OMT) is a type of methyltransferase enzyme transferring a methyl group on a molecule.Demethylmenaquinone methyltransferase: Demethylmenaquinone methyltransferase (, S-adenosyl-L-methione-DMK methyltransferase, demethylmenaquinone C-methylase, 2-heptaprenyl-1,4-naphthoquinone methyltransferase, 2-demethylmenaquinone methyltransferase, S-adenosyl-L-methione:2-demethylmenaquinone methyltransferase) is an enzyme with system name S-adenosyl-L-methione:demethylmenaquinone methyltransferase. This enzyme catalyses the following chemical reactionCandidatus Accumulibacter: Candidatus Accumulibacter is an unclassified group of Betaproteobacteria that currently contains only a single member, Candidatus Accumulibacter Phosphatis. C.Halotolerance: Halotolerance is the adaptation of living organisms to conditions of high salinity.Walter Larcher, 2001 Halotolerant species tend to live in areas such as hypersaline lakes, coastal dunes, saline deserts, salt marshes, and inland salt seas and springs.Angang Sewage Disposal Plant: The Angang Sewage Disposal Plant is a sewage treatment plant located in the city of Gyeongju, North Gyeongsang province, South Korea. It began operating in April, 2005 by the co-investment of the Government of North Gyeongsang and Gyeongju City with a fund of 44,300,000,000 won to install the facilities to prevent the pollution of Hyeongsan River which is a main water source for Gyeongju and Pohang residents.Zetaproteobacteria: The class Zetaproteobacteria is the sixth and most recently described class of the Proteobacteria. Zetaproteobacteria can also refer to the group of organisms assigned to this class.Ribonuclease L: Ribonuclease L or RNase L (for latent), known sometimes as ribonuclease 4 or 2'-5' oligoadenylate synthetase-dependent ribonuclease — is an interferon (IFN)-induced ribonuclease which, upon activation, destroys all RNA within the cell (both cellular and viral). RNase L is an enzyme that in humans is encoded by the RNASEL gene.EcosystemAllele-specific oligonucleotide: An allele-specific oligonucleotide (ASO) is a short piece of synthetic DNA complementary to the sequence of a variable target DNA. It acts as a probe for the presence of the target in a Southern blot assay or, more commonly, in the simpler Dot blot assay.Desulfococcus oleovorans Strain Hxd3: Desulfococcus oleovorans Strain Hxd3 was isolated from the saline water phase of an oil-water separator from a northern German oil field.Aeckersberg, F.Obligate aerobe: 300px|thumb|Aerobic and anaerobic [[bacteria can be identified by growing them in test tubes of thioglycollate broth: 1: Obligate aerobes need oxygen because they cannot ferment or respire anaerobically. They gather at the top of the tube where the oxygen concentration is highest.Gijs Kuenen: Johannes Gijsbrecht Kuenen (born 9 December 1940, Heemstede) is a Dutch microbiologist who is professor emeritus at the Delft University of Technology and a visiting scientist at the University of Southern California. His research is influenced by, and a contribution to, the scientific tradition of the Delft School of Microbiology.Genetic variation: right|thumbList of hot springs: There are hot springs on all continents and in many countries around the world. Countries that are renowned for their hot springs include Honduras, Canada, Chile, Hungary, Iceland, Israel, Japan, New Zealand and United States, but there are interesting and unique hot springs in many other places as well.List of inorganic pigments: The following list includes commercially or artistically important inorganic pigments of natural and synthetic origin. The only dyes listed are derived directly from inorganic pigments.Ferric uptake regulator family: In molecular biology, the ferric uptake regulator (FUR) family of proteins includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria.Operon: In genetics, an operon is a functioning unit of genomic DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo trans-splicing to create monocistronic mRNAs that are translated separately, i.Pyrococcus C/D box small nucleolar RNAZuotin: Z-DNA binding protein 1, also known as Zuotin, is a Saccharomyces cerevisiae yeast gene.Permissive temperature: The permissive temperature is the temperature at which a temperature sensitive mutant gene product takes on a normal, functional phenotype.http://www.Silent mutation: Silent mutations are mutations in DNA that do not significantly alter the phenotype of the organism in which they occur. Silent mutations can occur in non-coding regions (outside of genes or within introns), or they may occur within exons.CS-BLASTLigation-independent cloning: Ligation-independent cloning (LIC) is a form of molecular cloning that is able to be performed without the use of restriction endonucleases or DNA ligase. This allows genes that have restriction sites to be cloned without worry of chopping up the insert.RRNA small subunit pseudouridine methyltransferase Nep1: RRNA small subunit pseudouridine methyltransferase Nep1 (, Nep1, nucleolar essential protein 1) is an enzyme with system name S-adenosyl-L-methionine:18S rRNA (pseudouridine1191-N1)-methyltransferase. This enzyme catalyses the following chemical reactionAtmospheric methane: Atmospheric methane is the methane present in Earth's atmosphere. Atmospheric methane concentrations are of interest due to methane's impact on climate change, as it is one of the most potent greenhouse gases in Earth's atmosphere.McIntosh and Filde's anaerobic jar: McIntosh and Filde's anaerobic jar is an instrument used in the production of an anaerobic environment. This method of anaerobiosis as others is used to culture bacteria which die or fail to grow in presence of oxygen (anaerobes).Catena (soil): A Catena in soil science (pedology) is a sequence of types of soil down a hill slope. Each soil type or "facet" differs somewhat from its neighbours, but all occur in the same climate and on the same underlying material.YjdF RNA motifTranslational regulation: Translational regulation refers to the control of the levels of protein synthesized from its mRNA. The corresponding mechanisms are primarily targeted on the control of ribosome recruitment on the initiation codon, but can also involve modulation of the elongation or termination of protein synthesis.Diaminopimelic acidContinuous Plankton Recorder: The Continuous Plankton Recorder (CPR) survey is one of the longest running marine biological monitoring programmes in the world. Started in 1931 by Sir Alister Hardy, the CPR has provided marine scientists with their only measure of plankton communities on a pan-oceanic scale.Triparental mating: Triparental mating is a form of Bacterial conjugation where a conjugative plasmid present in one bacterial strain assists the transfer of a mobilizable plasmid present in a second bacterial strain into a third bacterial strain. Plasmids are introduced into bacteria for such purposes as transformation, cloning, or transposon mutagenesis.BacitracinDehalogenimonas: Dehalogenimonas is a genus in the phylum Chloroflexi (Bacteria).Oxymonad: The Oxymonads are a group of flagellated protozoa found exclusively in the intestines of termites and other wood-eating insects. Along with the similar parabasalid flagellates, they harbor the symbiotic bacteria that are responsible for breaking down cellulose.Mycoplasma haemofelis: Mycoplasma haemofelis (formerly Haemobartonella felis) is a gram negative epierythrocytic parasitic bacterium. It often appears in bloodsmears as small (0.Haplogroup L0 (mtDNA)
(1/3473) Ribotypes of clinical Vibrio cholerae non-O1 non-O139 strains in relation to O-serotypes.
The emergence of Vibrio cholerae O139 in 1992 and reports of an increasing number of other non-O1 serogroups being associated with diarrhoea, stimulated us to characterize V. cholerae non-O1 non-O139 strains received at the National Institute of Infectious Diseases, Japan for serotyping. Ribotyping with the restriction enzyme BglI of 103 epidemiological unrelated mainly clinical strains representing 10 O-serotypes yielded 67 different typing patterns. Ribotype similarity within each serotype was compared by using the Dice coefficient (Sd) and different levels of homogeneity were observed (serotypes O5, O41 and O17, Sd between 82 and 90%: serotypes O13 and O141 Sd of 72; and O2, O6, O7, O11, O24 Sd of 62-66%). By cluster analysis, the strains were divided into several clusters of low similarity suggesting a high level of genetic diversity. A low degree of similarity between serotypes and ribotypes was found as strains within a specific serotypes often did not cluster but clustered with strains from other serotypes. However, epidemiological unrelated O5 strains showed identical or closely related ribotypes suggesting that these strains have undergone few genetic changes and may correspond to a clonal line. Surprisingly, 10 of 16 O141 strains studied contained a cholera toxin (CT) gene, including 7 strains recovered from stool and water samples in the United States. This is to our knowledge the first report of CT-positive clinical O141 strains. The closely related ribotypes shown by eight CT-positive strains is disturbing and suggest that these strains may be of a clonal origin and have the potential to cause cholera-like disease. Despite the low degree of correlation found between ribotypes and serotypes, both methods appears to be valuable techniques in studying the epidemiology of emerging serotypes of V. cholerae. (+info)
(2/3473) Molecular differentiation of Renibacterium salmoninarum isolates from worldwide locations.
Renibacterium salmoninarum is a genospecies that is an obligate pathogen of salmonid fish and is capable of intracellular survival. Conventional typing systems have failed to differentiate isolates of R. salmoninarum. We used two methods to assess the extent of molecular variation which was present in isolates from different geographic locations. In one analysis we investigated possible polymorphisms in a specific region of the genome, the intergenic spacer (ITS) region between the 16S and 23S rRNA genes. In the other analysis we analyzed differences throughout the genome by using randomly amplified polymorphic DNA (RAPD). We amplified the spacer region of 74 isolates by using PCR and performed a DNA sequence analysis with 14 geographically distinct samples. The results showed that the 16S-23S ribosomal DNA spacer region of R. salmoninarum is highly conserved and suggested that only a single copy of the rRNA operon is present in this slowly growing pathogen. DNA sequencing of the spacer region showed that it was the same length in all 14 isolates examined, and the same nucleotide sequence, sequevar 1, was obtained for 11 of these isolates. Two other sequevars were found. No tRNA genes were found. We found that RAPD analysis allows reproducible differentiation between isolates of R. salmoninarum obtained from different hosts and different geographic regions. By using RAPD analysis it was possible to differentiate between isolates with identical ITS sequences. (+info)
(3/3473) Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles.
The effect of three phenyl urea herbicides (diuron, linuron, and chlorotoluron) on soil microbial communities was studied by using soil samples with a 10-year history of treatment. Denaturing gradient gel electrophoresis (DGGE) was used for the analysis of 16S rRNA genes (16S rDNA). The degree of similarity between the 16S rDNA profiles of the communities was quantified by numerically analysing the DGGE band patterns. Similarity dendrograms showed that the microbial community structures of the herbicide-treated and nontreated soils were significantly different. Moreover, the bacterial diversity seemed to decrease in soils treated with urea herbicides, and sequence determination of several DGGE fragments showed that the most affected species in the soils treated with diuron and linuron belonged to an uncultivated bacterial group. As well as the 16S rDNA fingerprints, the substrate utilization patterns of the microbial communities were compared. Principal-component analysis performed on BIOLOG data showed that the functional abilities of the soil microbial communities were altered by the application of the herbicides. In addition, enrichment cultures of the different soils in medium with the urea herbicides as the sole carbon and nitrogen source showed that there was no difference between treated and nontreated soil in the rate of transformation of diuron and chlorotoluron but that there was a strong difference in the case of linuron. In the enrichment cultures with linuron-treated soil, linuron disappeared completely after 1 week whereas no significant transformation was observed in cultures inoculated with nontreated soil even after 4 weeks. In conclusion, this study showed that both the structure and metabolic potential of soil microbial communities were clearly affected by a long-term application of urea herbicides. (+info)
(4/3473) Anaerobic oxidation of o-xylene, m-xylene, and homologous alkylbenzenes by new types of sulfate-reducing bacteria.
Various alkylbenzenes were depleted during growth of an anaerobic, sulfate-reducing enrichment culture with crude oil as the only source of organic substrates. From this culture, two new types of mesophilic, rod-shaped sulfate-reducing bacteria, strains oXyS1 and mXyS1, were isolated with o-xylene and m-xylene, respectively, as organic substrates. Sequence analyses of 16S rRNA genes revealed that the isolates affiliated with known completely oxidizing sulfate-reducing bacteria of the delta subclass of the class Proteobacteria. Strain oXyS1 showed the highest similarities to Desulfobacterium cetonicum and Desulfosarcina variabilis (similarity values, 98.4 and 98.7%, respectively). Strain mXyS1 was less closely related to known species, the closest relative being Desulfococcus multivorans (similarity value, 86.9%). Complete mineralization of o-xylene and m-xylene was demonstrated in quantitative growth experiments. Strain oXyS1 was able to utilize toluene, o-ethyltoluene, benzoate, and o-methylbenzoate in addition to o-xylene. Strain mXyS1 oxidized toluene, m-ethyltoluene, m-isoproyltoluene, benzoate, and m-methylbenzoate in addition to m-xylene. Strain oXyS1 did not utilize m-alkyltoluenes, whereas strain mXyS1 did not utilize o-alkyltoluenes. Like the enrichment culture, both isolates grew anaerobically on crude oil with concomitant reduction of sulfate to sulfide. (+info)
(5/3473) High-affinity methane oxidation by a soil enrichment culture containing a type II methanotroph.
Methanotrophic bacteria in an organic soil were enriched on gaseous mixing ratios of <275 parts per million of volume (ppmv) of methane (CH4). After 4 years of growth and periodic dilution (>10(20) times the initial soil inoculum), a mixed culture was obtained which displayed an apparent half-saturation constant [Km(app)] for CH4 of 56 to 186 nM (40 to 132 ppmv). This value was the same as that measured in the soil itself and about 1 order of magnitude lower than reported values for pure cultures of methane oxidizers. However, the Km(app) increased when the culture was transferred to higher mixing ratios of CH4 (1,000 ppmv, or 1%). Denaturing gradient gel electrophoresis of the enrichment grown on <275 ppmv of CH4 revealed a single gene product of pmoA, which codes for a subunit of particulate methane monooxygenase. This suggested that only one methanotroph species was present. This organism was isolated from a sample of the enrichment culture grown on 1% CH4 and phylogenetically positioned based on its 16S rRNA, pmoA, and mxaF gene sequences as a type II strain of the Methylocystis/Methylosinus group. A coculture of this strain with a Variovorax sp., when grown on <275 ppmv of CH4, had a Km(app) (129 to 188 nM) similar to that of the initial enrichment culture. The data suggest that the affinity of methanotrophic bacteria for CH4 varies with growth conditions and that the oxidation of atmospheric CH4 observed in this soil is carried out by type II methanotrophic bacteria which are similar to characterized species. (+info)
(6/3473) Polynucleotide probes that target a hypervariable region of 16S rRNA genes to identify bacterial isolates corresponding to bands of community fingerprints.
Temperature gradient gel electrophoresis (TGGE) is well suited for fingerprinting bacterial communities by separating PCR-amplified fragments of 16S rRNA genes (16S ribosomal DNA [rDNA]). A strategy was developed and was generally applicable for linking 16S rDNA from community fingerprints to pure culture isolates from the same habitat. For this, digoxigenin-labeled polynucleotide probes were generated by PCR, using bands excised from TGGE community fingerprints as a template, and applied in hybridizations with dot blotted 16S rDNA amplified from bacterial isolates. Within 16S rDNA, the hypervariable V6 region, corresponding to positions 984 to 1047 (Escherichia coli 16S rDNA sequence), which is a subset of the region used for TGGE (positions 968 to 1401), best met the criteria of high phylogenetic variability, required for sufficient probe specificity, and closely flanking conserved priming sites for amplification. Removal of flanking conserved bases was necessary to enable the differentiation of closely related species. This was achieved by 5' exonuclease digestion, terminated by phosphorothioate bonds which were synthesized into the primers. The remaining complementary strand was removed by single-strand-specific digestion. Standard hybridization with truncated probes allowed differentiation of bacteria which differed by only two bases within the probe target site and 1.2% within the complete 16S rDNA. However, a truncated probe, derived from an excised TGGE band of a rhizosphere community, hybridized with three phylogenetically related isolates with identical V6 sequences. Only one of the isolates comigrated with the excised band in TGGE, which was shown to be due to identical sequences, demonstrating the utility of a combined TGGE and V6 probe approach. (+info)
(7/3473) Immunochemical detection and isolation of DNA from metabolically active bacteria.
Most techniques used to assay the growth of microbes in natural communities provide no information on the relationship between microbial productivity and community structure. To identify actively growing bacteria, we adapted a technique from immunocytochemistry to detect and selectively isolate DNA from bacteria incorporating bromodeoxyuridine (BrdU), a thymidine analog. In addition, we developed an immunocytochemical protocol to visualize BrdU-labeled microbial cells. Cultured bacteria and natural populations of aquatic bacterioplankton were pulse-labeled with exogenously supplied BrdU. Incorporation of BrdU into microbial DNA was demonstrated in DNA dot blots probed with anti-BrdU monoclonal antibodies and either peroxidase- or Texas red-conjugated secondary antibodies. BrdU-containing DNA was physically separated from unlabeled DNA by using antibody-coated paramagnetic beads, and the identities of bacteria contributing to both purified, BrdU-containing fractions and unfractionated, starting-material DNAs were determined by length heterogeneity PCR (LH-PCR) analysis. BrdU-containing DNA purified from a mixture of DNAs from labeled and unlabeled cultures showed >90-fold enrichment for the labeled bacterial taxon. The LH-PCR profile for BrdU-containing DNA from a labeled, natural microbial community differed from the profile for the community as a whole, demonstrating that BrdU was incorporated by a taxonomic subset of the community. Immunocytochemical detection of cells with BrdU-labeled DNA was accomplished by in situ probing with anti-BrdU monoclonal antibodies and Texas red-labeled secondary antibodies. Using this suite of techniques, microbial cells incorporating BrdU into their newly synthesized DNA can be quantified and the identities of these actively growing cells can be compared to the composition of the microbial community as a whole. Since not all strains tested could incorporate BrdU, these methods may be most useful when used to gain an understanding of the activities of specific species in the context of their microbial community. (+info)
(8/3473) Dissimilatory reduction of Fe(III) and other electron acceptors by a Thermus isolate.
A thermophilic bacterium that can use O2, NO3-, Fe(III), and S0 as terminal electron acceptors for growth was isolated from groundwater sampled at a 3.2-km depth in a South African gold mine. This organism, designated SA-01, clustered most closely with members of the genus Thermus, as determined by 16S rRNA gene (rDNA) sequence analysis. The 16S rDNA sequence of SA-01 was >98% similar to that of Thermus strain NMX2 A.1, which was previously isolated by other investigators from a thermal spring in New Mexico. Strain NMX2 A.1 was also able to reduce Fe(III) and other electron acceptors. Neither SA-01 nor NMX2 A.1 grew fermentatively, i.e., addition of an external electron acceptor was required for anaerobic growth. Thermus strain SA-01 reduced soluble Fe(III) complexed with citrate or nitrilotriacetic acid (NTA); however, it could reduce only relatively small quantities (0.5 mM) of hydrous ferric oxide except when the humic acid analog 2,6-anthraquinone disulfonate was added as an electron shuttle, in which case 10 mM Fe(III) was reduced. Fe(III)-NTA was reduced quantitatively to Fe(II); reduction of Fe(III)-NTA was coupled to the oxidation of lactate and supported growth through three consecutive transfers. Suspensions of Thermus strain SA-01 cells also reduced Mn(IV), Co(III)-EDTA, Cr(VI), and U(VI). Mn(IV)-oxide was reduced in the presence of either lactate or H2. Both strains were also able to mineralize NTA to CO2 and to couple its oxidation to Fe(III) reduction and growth. The optimum temperature for growth and Fe(III) reduction by Thermus strains SA-01 and NMX2 A.1 is approximately 65 degrees C; their optimum pH is 6.5 to 7.0. This is the first report of a Thermus sp. being able to couple the oxidation of organic compounds to the reduction of Fe, Mn, or S. (+info)
- A rapid approach to the 16S rRNA gene (16S rDNA)-based bacterial identification has been developed that combines uracil-DNA-glycosylase (UDG)-mediated base-specific fragmentation of PCR products with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). 16S rDNA signature sequences were PCR-amplified from both cultured and as-yet-uncultured bacteria in the presence of dUTP instead of dTTP. (uncg.edu)
- The fact that binding sites for the rDNA‐specific transcription factor TTF‐I are located at the 5′ and the 3′ end of each rRNA gene suggests a functional link between transcription initiation and termination. (embopress.org)
- The observation that TTF‐I is capable to form oligomers and bridges separate DNA molecules in vitro ( Sander and Grummt, 1997 ) tempts speculation that TTF‐I may be an active player in the formation of looped rRNA gene domains in mammals. (embopress.org)
- However, the epigenetics of actively transcribed copies and the establishment and maintenance of active rRNA gene status are poorly understood. (embopress.org)
- you will amplify, in a polymerase chain reaction (pcr), part of the 16S rRNA gene from hundreds or thousands of the different species of bacteria (some of which are culturable and most of which are non-culturable) using 'universal' bacterial primers and a proof-reading DNA polymerase. (openwetware.org)
- There are so many 16s rRNA gene sequences archived at this site that we should be able to use their powerful, public search engine to identify our soil bacteria down to the genus or species level, ''if'' our pcr, our cloning, and the sequencing of the gene from the clones all works well. (openwetware.org)
- A set of genes transcribed under the control of an operator gene. (encyclo.co.uk)
- In theory, each of them should contain the vector plasmid with an insert of the 16s rRNA gene from one of your soil sample bacteria. (openwetware.org)
- We know each of the vector plasmids in the transformed ''E. coli'' growing on the plate contains a 16S rRNA gene insert from the genomic DNA isolated from your soil sample for two reasons. (openwetware.org)
- But the presence of your 16S rRNA gene insert has disrupted the ccdB gene and turned off the protein that inhibits DNA gyrase, allowing the cell to live, replicate and form a colony that should appear white, NOT blue. (openwetware.org)
- The second reason that we know the white colonies are transformed with the vector plasmid and that the plasmid contains our insert is that there is a lacZ gene positioned next to the ccdB gene in the insert area and when it is disrupted by insertion of your 16s rRNA gene, it turns off expression of the lacZ gene product, beta-galactosidase. (openwetware.org)
- Our goal is to find 16s rRNA gene fragments from DIFFERENT soil bacteria in many transformed clones, but we have no way of detecting right now which colonies contain a 16s rRNA gene from different soil bacterial species because all will be identical looking non-blue colonies on these plates. (openwetware.org)
- Landthaler, M. and Shub, D.A. (1999) Unexpected abundance of self-splicing introns in bacteriophage Twort: Introns in multiple genes, a single gene with three introns, and exon skipping by group I ribozymes. (albany.edu)
- Cloning and nucleotide sequencing experiments are performed on PCR-amplified 16S rRNA genes to characterize oil field microbial populations. (readabstracts.com)
- Base-specific fragmentation of amplified 16S rRNA genes and mass spectrometry analysis: A novel tool for rapid bacterial identification. (uncg.edu)
- Microbial biomass increased ~4-6-fold over 9 days, and pyrosequencing of bacterial 16S rRNA genes revealed that the addition of both types of EPS greatly altered the bacterial community composition (from 0 to 9 days) compared to a control with no added EPS. (pubmedcentralcanada.ca)
- The nucleolus is the site of the 47S precursor rRNA synthesis, which is transcribed by RNA polymerase I and processed into 5.8S, 18S and 28S rRNA ( Russell and Zomerdijk, 2005 ). (embopress.org)
- Bonocora, R.P. and Shub, D.A. (2004) A self-splicing group I intron in DNA polymerase genes of T7-like bacteriophages. (albany.edu)
- A typical eukaryotic cell contains several hundred rRNA genes, most of them arranged as tandem repeats, but even in metabolically active cells only a proportion of these genes are transcriptionally active. (embopress.org)
- Ribosomal RNA synthesis is the eukaryotic cell's main transcriptional activity, but little is known about the chromatin domain organization and epigenetics of actively transcribed rRNA genes. (embopress.org)
- Here, we show epigenetic and spatial organization of mouse rRNA genes at the molecular level. (embopress.org)
- Unusual organization of the rRNA genes in Rickettsia prowazekii . (springer.com)
- Bonocora, R.P. and Shub, D.A. (2001) A novel group I intron-encoded endonuclease specific for the anticodon region of tRNAfMet genes. (albany.edu)
- The differentiated bands were excised and identified by sequencing the V3 region of the 16S rRNA genes. (pubmedcentralcanada.ca)
- 3C analysis revealed an interaction between promoter and terminator regions, which brings the beginning and end of active rRNA genes into close contact. (embopress.org)
- The study of variation in genes among a group of individuals. (encyclo.co.uk)