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 2.7.7.6.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 3.1.27.3.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)

*  Data from: Phylogenetic relatedness determined between antibiotic resistance...
The phylogeny of ABC transporter gene was correlated to 16S rRNA genes mainly above the ... based on 16S rRNA genes or five housekeeping genes was observed for both the erm genes ... The type of erm resistance gene sequences was influenced by linkage to 16S rRNA gene ... actinobacteria, 16S rRNA diversity, resistance genes, thin layer chromatography, ......
http://datadryad.org/resource/doi:10.5061/dryad.td742
*  African Journal of Biotechnology - bacterial species identification getting...
... sequence analysis of the 16S rRNA gene, matrix-assisted laser desorption/ionization time- ... sequence analysis of the 16S rRNA gene, matrix-assisted laser desorption/ionization time- ......
http://academicjournals.org/journal/AJB/article-abstract/D0EE3FE30501
*  Plus it
... with the gene on the negative strand. The gene was predicted to contain six exons spliced ... Primer pair sequences were as follows: CCC CTC GAT GCT CTT AGC TGA GTG T (18S-rRNA- ... The UGT2A3 gene was located within a large cluster of other genes encoding all known ... UGT2A3 Gene Encodes a Polymorphic Enzyme. Approximately 10% of amplified UGT2A3 cDNA ......
http://molpharm.aspetjournals.org/content/74/3/744
*  CiNii 論文 - Geographic Variation in the Body...
Based on the Mitochondrial COl and Nuclear 28S rRNA Genes(Animal Diversity and Evolution ... and evolution of the Japanese Carabinae ground beetles based on mitochodrial ND5 gene ......
http://ci.nii.ac.jp/naid/110003374671
*  PCR amplification and DNA sequencing of Demodex injai from otic secretions of a...
PCR扩增从耳部样本取得的长体蠕形螨rRNA DNA, 约为330bp,与从犬背部皮肤的injai蠕形螨形态学鉴定相同。此外,这个检查出的螨虫与任何已报道的蠕形螨基因都没有任何显 ... the examined mite did not have any significant homology to any of the reported genes from ... La amplificación por PCR del rRNA a partir del DNA del ácaro de cuerpo largo obtenido de ... Para identificar el ácaro Demodex se extrajo DNA y se amplificó el gen 16S rRNA mediante ......
http://onlinelibrary.wiley.com/doi/10.1111/vde.12010/abstract
*  Progressive genomic convergence of two Helicobacter pylori strains during mixed...
... the 23S-rRNA genes) in South African isolates of Helicobacter pylori. Ann Trop Med ... Genes involved in recombination. The recombination events we found were mapped onto the ... Characterisation of the genes encoding resistance to metronidazole (rdxA and frxA) and ... RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; ......
http://gut.bmj.com/content/64/4/554
*  Antievolution.org - Antievolution.org Discussion Board -Topic::Evolution of...
Comparative sequence analysis of the 16S rRNA gene confirmed that the isolate is a member ... Based on the genes of the lcrD family we developed gene probes for Gram-negative human, ... Originally posted by Mike Gene:. Nic: Hey, I'm just following the peer-reviewed lit., man ... As Mike Gene states, as far as pores go, not any old pore would do. The logic of this is ......
http://antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=50aaad593e244ecc
*  Draft Genome Sequence of Pseudoalteromonas sp. Strain PAB 2.2 Isolated from...
... and Moritella using genes coding for small-subunit rRNA sequences and division of the ... and 126 genes for motility and chemotaxis, including operons fli, flg, and flh and genes ... Analyzing the genes predicted by RAST, it was possible to observe 95 genes involved in ... The absence of genes encoding for lateral flagellum indicates that even though this ......
http://pubmedcentralcanada.ca/pmcc/articles/PMC5347232/
*  Everything About Wood: Impact of Lowland Rainforest Transformation on Diversity...
Bioinformatic Analysis of 16S rRNA Gene Sequences. The resulting 16S rRNA gene sequences ... The 16S rRNA gene amplicons were generated as described by Schneider et al. (2013). In ... The 16S rRNA gene sequences were deposited in the National Center for Biotechnology ... The hypervariable regions V3 to V5 of the 16S rRNA gene were targeted in this study. ......
http://woodethic.blogspot.com/2016/10/impact-of-lowland-rainforest.html
*  Freezing fecal samples prior to DNA extraction affects the Firmicutes to...
In seven out of nine cases the Firmicutes to Bacteroidetes 16S rRNA gene ratio was ... performed on all DNA samples using six different primer pairs targeting 16S rRNA genes of ......
http://orbit.dtu.dk/en/publications/freezing-fecal-samples-prior-to-dna-extraction-affects-the-firmicutes-to-bacteroidetes-ratio-determined-by-downstream-quantitative-pcr-analysis
*  RRNA endonuclease
... alpha sarcin is an enzyme this enzyme catalyses the following chemical reaction hydrolysis of the phosphodiester linkage between guanosine and adenosine residues at one specific position in s rrna from rat ribosome s this enzyme also acts on bacterial rrna references external links category ec...
https://en.wikipedia.org/wiki/RRNA_endonuclease
*  Composition of Acridid gut bacterial communities as revealed by 16S rRNA gene analysis - Opus
... Study. Faculties Departments. Business. Site Search. Publications. Browse by author. Browse by department. Browse by funder. Browse by year. Search. Policy. Authors' corner. Contact. Login. Composition of Acridid gut bacterial communities as revealed by 16S rRNA gene analysis. Reference: Dillon, R. J , Webster, G. , Weightman, A. J , Dillon, V. M , Blanford, S. and Charnley, A. Composition of Acridid gut bacterial communities as revealed by 16S rRNA gene analysis. Contact Author Official URL: http://dx.doi.org/10.1016/j.jip.2007.09.010 Abstract The gut bacterial community from four species of feral locusts and grasshoppers was determined by denaturing gradient gel electrophoresis DGGE analysis of bacterial 16S rRNA gene fragments. The study revealed an effect of phase polymorphism on gut bacterial diversity in brown locusts from South Africa. A single bacterial phylotype, consistent with Citrobacter sp. dominated the gut microbiota of two sympatric populations of Moroccan and Italian locusts in Spain. Th...
http://opus.bath.ac.uk/3449/
*  Mutational Analysis | Applications & Technologies | Bio-Rad
Different Types of Mutations Mutation Detection Methods Denaturing Gradient Gel Electrophoresis Constant Denaturing Gel Electrophoresis CDGE Temporal Temperature Gradient Gel Electrophoresis TTGE Single-Strand Conformation Polymorphism Protein Truncation Test PTT High Resolution Melt Further Reading Related Content. Over the past couple of decades, mutation detection techniques, such as denaturing gradient gel electrophoresis DGGE, constant denaturing gel electrophoresis CDGE, temporal temperature gradient gel electrophoresis TTGE, single-strand conformation polymorphism SSCP, and protein truncation test PTT, have assisted researchers with analyzing mutations. Lane 1 contains the mutant fragment; lane 2 contains the wild-type fragment; lane 3 contains both the mutant and wild-type fragments. In CDGE, the denaturant concentration that gives optimal resolution from a parallel or perpendicular DGGE gel is held constant. The optimal concentration of denaturant to use for a CDGE is determined from the maximum spli...
http://bio-rad.com/en-us/applications-technologies/mutational-analysis
*  So-Jung Kang, Korea Research Institute of Bioscience and Biotechnology KRIBB, Biological Resource Ce
... nter - ResearchGate. For full functionality of ResearchGate it is necessary to enable JavaScript. Here are the instructions how to enable JavaScript in your web browser. So-Jung Kang. Korea Research Institute of Bioscience and Biotechnology KRIBB, Anzan, Gyeonggi Province, South Korea. Are you So-Jung Kang. Claim your profile. Publications 119 297.2 Total impact. Article:. Bizionia hallyeonensis sp. nov., isolated from seawater in an oyster farm. Jung-Hoon Yoon. Chul-Hyung Kang. Yong-Taek Jung So-Jung Kang. ABSTRACT: A Gram-staining-negative, non-spore-forming, aerobic, non-flagellated, non-gliding, rod-shaped bacterial strain, T-y7T, was isolated from seawater of an oyster farm in the South Sea, Korea, and subjected to a polyphasic study. Strain T-y7T grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2 % w/v NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain T-y7T fell within the clade comprising Bizionia species, forming a coherent cluster with the type strains...
http://researchgate.net/researcher/39666287_So-Jung_Kang
*  BISC209/S11: Lab6 - OpenWetWare
... BISC209/S11: Lab6 From OpenWetWare. Jump to: navigation, search. Wellesley College-BISC 209 Microbiology -Spring 2011. Welcome To Microbiology Lab. Read Me: Lab Safety. Calendar/Weekly Planner. Resources. OWW Basics. LABS 1-12: Soil Communities Diversity Project. Graded Assignments. Protocols. Contents. 1 LAB 6: Finishing the Culture-Independent Identification of Bacteria by 16s rRNA Gene Sequence Analysis 2 Culture-Dependent Isolate Characterizations: 3 Assessing Bacterial Morphology and Characteristic Arrangement and Cell Wall Composition by Gram Stain 4 The Gram Stain 5 Use of the Compound Light Microscope 6 Gram Reaction Confirmation by use of Selective/Differential Media 7 Cultured Bacterial Isolates: Examples of Competition and Co-operation in a Soil Community 8 CLEAN UP 9 Assignment 10 Links to Labs. LAB 6: Finishing the Culture-Independent Identification of Bacteria by 16s rRNA Gene Sequence Analysis. To summarize our culture-independent work, you have extracted genomic DNA from a soil sample, am...
http://openwetware.org/wiki/BISC209/S11:_Lab6
*  Chthonomonas calidirosea
... 'Chthonomonas calidirosea' is a Gram-negative bacterium and also the first representative of the new class 'Chthonomonadetes' within the phylum 'Armatimonadetes'. OP10 was composed solely of environmental 16S rRNA gene clone sequences prior to 'C. calidirosea's' relative, 'Armatimonas rosea's' discovery. Discovery Relatives Characteristics References. The environmental 16S rRNA gene sequences, belonging to the phylum 'Armatimonadetes' are currently sorted into six groups. Groups 2, 5, and 6 consist solely of sequences. Group 1 contains 'Armatimonadetes rosea', Group 3 contains 'Chthonomonadetes calidirosea', and Group 4 conatins 'Fimbriimonas ginsengisoli'. {{Clade |1={{clade |1=' Fimbriimonas ginsengisoli ' Im et al. }} 'Armatimonas rosea' an aerobic, Gram-negative, pink pigmented, nonmotile, ovoid/rod shaped bacterium, was isolated from the rhizoplane of an aquatic plan Phragmites australis in Japan. It is the first representative of the phylum 'Armatimonadetes'. 'Fimbriimonas ginsengisoli', an aerobic...
https://en.wikipedia.org/wiki/Chthonomonas_calidirosea
*  Nope. Had Everclear a few times (Reply #49) - Democratic Underground
Nope. Had Everclear a few times Reply #49 - Democratic Underground. Help. Log in Site search Web search. Advanced search. Home Latest Threads Greatest Threads Forums Groups My Subscriptions My Posts. DU Home. Latest Threads. Forums Groups. Main. The DU Lounge Forum. Anyone Here Ever Drink Mo... Reply #49. In the discussion thread: Anyone Here Ever Drink Moonshine and Lived to Tell About It. Response to Yavin4 Original post Wed Nov 7, 2012, 05:06 PM hifiguy 27,764 posts. Nope. Had Everclear a few times. Stuff smelled and tasted like lighter fluid/rocket fuel and it was about 160 proof. Sufficiently nasty that I only managed a small shot and I can drink pretty much anything. Reply to this post Back to OP Alert abuse Link to post in-thread. Always highlight: 10 newest replies. Replies posted after I mark a forum Replies to this discussion thread 62 replies Author Time Post. Anyone Here Ever Drink Moonshine and Lived to Tell About It. Yavin4 Nov 2012 OP. Nasty like drinking rubbing alcohol. doc03 Nov 2012 #1. Oh ...
http://democraticunderground.com/?com=view_post&forum=1018&pid=229764
*  Image-Line Sound Design Contest (CLOSED) (Topic) • Image-Line
Nov 14, 2010 22:34. SoundCloud proile. Nov 15, 2010 6:01. SoundCloud proile. Last edited by Scott on Mon Nov 22, 2010 6:15 am, edited 2 times in total. Nov 15, 2010 6:04. SoundCloud proile. My entry. Last edited by GeorgeZ on Sat Nov 20, 2010 9:33 pm, edited 8 times in total. Nov 15, 2010 6:56. Last edited by laffik on Mon Nov 15, 2010 1:19 pm, edited 1 time in total. Nov 15, 2010 7:59. Last edited by groffi2k on Tue Nov 16, 2010 10:17 am, edited 4 times in total. Last edited by Philip313 on Wed Nov 17, 2010 2:41 pm, edited 2 times in total. Last edited by MoZZe on Mon Nov 15, 2010 11:42 pm, edited 1 time in total. Last edited by ruckus on Mon Nov 15, 2010 10:19 pm, edited 2 times in total. Last edited by Hoffmeister on Tue Nov 23, 2010 4:38 am, edited 2 times in total. Last edited by KaCeTheProducer on Tue Nov 16, 2010 6:12 am, edited 5 times in total. Last edited by spectroman on Tue Nov 16, 2010 2:03 pm, edited 1 time in total. Last edited by 9 Toes on Tue Nov 16, 2010 8:13 pm, edited 1 time in total. Last...
http://forum.image-line.com/viewtopic.php?t=62827
*  The Vinyl District | thevinyldistrict.com: TVD's Parting Shots
January 2. Jan 02 1. Jan 01 1. Dec 31 2. Dec 24 1. Dec 23 2. Dec 22 2. Dec 21 2. Dec 20 3. Dec 17 3. Dec 16 2. Dec 15 3. Dec 14 2. Dec 13 2. Dec 10 4. Dec 09 3. Dec 08 4. Dec 07 2. Dec 06 3. Dec 03 3. Dec 02 4. Dec 01 3. Nov 30 2. Nov 29 3. Nov 24 2. Nov 23 3. Nov 22 3. Nov 19 3. Nov 18 2. Nov 17 3. Nov 16 4. Nov 15 4. Nov 12 4. Nov 11 2. Nov 10 4. Nov 09 3. Nov 08 2. Nov 05 4. Nov 04 4. Nov 03 4. Nov 02 3. Nov 01 2. Oct 29 4. Oct 28 3. Oct 27 3. Oct 26 1. Oct 25 3. Oct 22 2. Oct 21 2. Oct 20 2. Oct 19 2. Oct 18 3. Oct 15 5. Oct 14 3. Oct 13 4. Oct 12 4. Oct 11 4. Oct 09 1. Oct 08 4. Oct 07 3. Oct 06 3. Oct 05 2. Oct 04 2. Oct 01 4. September 70. Sep 30 4. Sep 29 4. Sep 28 4. Sep 27 2. Sep 26 1. Sep 24 3. Sep 23 4. Sep 22 4. Sep 21 4. Sep 20 4. Sep 18 1. Sep 17 3. Sep 16 4. Sep 15 3....
http://vinyldistrict.blogspot.com/2009/09/tvds-parting-shots_18.html
*  Mavic Cosmic Carbone SLRs - Weight Weenies
Mavic Cosmic Carbone SLRs. Joined: Sat Oct 06, 2012 6:18 pm Posts: 5 Has anyone tried the mavic cosmic carbone SLRs, and if so would you reccommend them for all-around racing. Zen Cyclery Post subject: Re: Mavic Cosmic Carbone SLRs Posted: Sat Nov 10, 2012 3:42 am. Weenie Post subject: Re: Mavic Cosmic Carbone SLRs Posted: Sat Nov 10, 2012 3:42 am. kevhogaz Post subject: Re: Mavic Cosmic Carbone SLRs Posted: Sat Nov 10, 2012 3:58 am. SpinnerTim Post subject: Re: Mavic Cosmic Carbone SLRs Posted: Sat Nov 10, 2012 4:24 am. poppiholla Post subject: Re: Mavic Cosmic Carbone SLRs Posted: Sat Nov 10, 2012 8:47 am. MajorMantra Post subject: Re: Mavic Cosmic Carbone SLRs Posted: Sat Nov 10, 2012 9:39 am. Omiar Post subject: Re: Mavic Cosmic Carbone SLRs Posted: Sat Nov 10, 2012 12:29 pm. Joined: Wed Dec 14, 2011 8:20 pm Posts: 205 I really would like to see an Enve/Smart custom build coming to the price range of carbon spoked SLR or metal spoked SLR WTS wheelset. ENVE 45 Clincher Front DT Swiss Hub wheelset is 2500 e...
http://weightweenies.starbike.com/forum/viewtopic.php?p=933100
*  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. Patterns obtained from several restriction enzymes can be used to phylogenetically characterize cultured isolates and 16s genes obtained through cloning from community DNA. Evaluating amplified rDNA restriction analysis assay for identification of bacterial communities. Identification of Mycobacterium species with amplified rDNA restriction analysis. who used the method to characterize Mycobacterium species, the method has been used by many more for similar characterization of other bacterial species Vaneechoutte, M., L. Identification of Acinetobacter Genomic Species by Amplified Ribosomal DNA Restriction Analysis. A restriction enzyme having a recognition site of more than 4bp would be irrelevant with respect to a gene of approximately 1500bp such as that coding for the 16s ribosomal subunit. For the sake...
https://en.wikipedia.org/wiki/Amplified_Ribosomal_DNA_Restriction_Analysis
*  Ramaria
... The genus 'Ramaria' comprises approximately 200 species of coral fungi. Petersen RH, Scates C. Vernally fruiting taxa of 'Ramaria' from the Pacific Northwest. 'Mycotaxon' 33:101-144. Several, such as ' Ramaria flava ', are edible and picked in Europe, though they are easily confused with several mildly poisonous species capable of causing nausea, vomiting and diarrhoea; these include ' R. formosa ' and ' R. pallida '. Etymology Description Classification Species References External links. Etymology. The genus name is derived from Latin 'rāmus' meaning 'branch'. 1 Description. Basidiocarp s may range in color from bright yellow, red, or orange, to purple, white, and shades of tan. Color changes after bruising occur in some species. The spore s of 'Ramaria' species are yellow-brown to rusty-brown in mass deposit and range from smooth to warted to echinulate or striate ; spore size may range considerably, and ornamentation, when present, is cyanophilous. Classification. Hjomsköld was the first to introduce ...
https://en.wikipedia.org/wiki/Ramaria
*  GO:0000182 rDNA binding
... Services. Research. Training. Industry. About us. QuickGO A fast browser for Gene Ontology terms and annotations. EBI Databases QuickGO GO:0000182 rDNA binding. Search for terms by keyword or ID: apoptosis GO:0006915 Search for proteins by name or accession: tropomyosin P06727. Web Services. Dataset. Term Basket. Term Information ID GO:0000182. Name rDNA binding. Ontology Molecular Function. Definition Interacting selectively and non-covalently with DNA sequences encoding ribosomal RNA. GONUTS GO:0000182 Wiki Page. Synonyms. Synonyms are alternative words or phrases closely related in meaning to the term name, with indication of the relationship between the name and synonym given by the synonym scope. Click on the icon for more details. Type Synonym. exact ribosomal DNA binding. Annotation Guidance Usage of this term is subject to the following annotation guidelines: Annotation Guidelines. Binding term considerations Link. Considerations when annotating from ChiP assay results Link. Ancestor Chart This c...
http://ebi.ac.uk/QuickGO/GTerm?id=GO:0000182
*  23S ribosomal RNA
s ribosomal rna s ribosomal rna infobox rfam name pseudoknot of the domain g g of s ribosomal rna image pk g rrna secondary structure jpg width caption predicted secondary structure and sequence conservation of pk g rrna symbol pk g rrna altsymbols rfam rf mirbase mirbase family rna type gene rrna tax domain bacteria go so cas number entrezgene hgncid omim pdb refseq chromosome arm band locussupplementarydata image pdb c w ebi png thumb px right a d representation of the ribosome this is a view of the d arrangement of the s and s rrna in the escherichia coli s ribosomal subunit based on a cryo electron microscopic reconstruction thumb px left a d representation of the ribosome the s rrna is a nt long in e coli component of the large subunit s of the bacterial ribosome the ribosomal peptidyl transferase activity resides in domain v of this rrna and this domain is the most common binding site for antibiotics that inhibit translation a well known member of this antibiotic class chloramphenicol acts by inhibiting...
https://en.wikipedia.org/wiki/23S_ribosomal_RNA
*  The 3' end of large ribosomal subunit RNA from mosquito mitochondria: homogeneity of transcribed moi
The 3 end of large ribosomal subunit RNA from mosquito mitochondria: homogeneity of transcribed moieties. BioMedSearch. Advanced Search. Search Tutorial. Document Detail. The 3' end of large ribosomal subunit RNA from mosquito mitochondria: homogeneity of transcribed moieties. MedLine Citation:. PMID: 2408289 Owner: NLM Status: MEDLINE. Abstract/OtherAbstract:. 3' Terminal sequences of mosquito mitochondrial 16 S ribosomal RNA, which is post-transcriptionally polyadenylated, have been examined with the aim of determining the degree of homogeneity of transcribed moieties. 3' End-labeled samples were subjected to oligonucleotide fingerprint analysis and to ladder gel analysis after primary and secondary nuclease digestion; and products of reverse transcriptase reactions were characterized using 16 S RNA as template and selected oligodeoxynucleotides as primers. The results indicated a remarkable degree of homogeneity compared to homologous mammalian mitochondrial systems, and suggested differences in modes of e...
http://biomedsearch.com/nih/3-end-large-ribosomal-subunit/2408289.html
*  30S
s s image atomic structure of the s subunit from thermus thermophilus proteins are shown in blue and the single rna strand in orange s is the smaller subunit of the s ribosome of prokaryote s it is a complex of ribosomal rna and ribonucleoproteins that functions in mrna translation it includes the s ribosomal rna it has about basic proteins the s subunit is the site of inhibition for antibiotics such as tetracycline and aminoglycosides see also s ribosomal rna s is the larger subunit of the s ribosome of prokaryotes in the cell it is the site of inhibition for antibiotics such as macrolides chloramphenicol clindamycin and the pleuromutilin s it includes the s ribosomal rna and s ribosomal rna references external links http pathmicro med sc edu mayer antibiot htm category ribosomal rna category protein biosynthesis...
https://en.wikipedia.org/wiki/30S
*  MT-RNR2
mt rnr mt rnr mitochondrially encoded s rna often abbreviated as s is a mitochondrial ribosomal rna rrna that in humans is encoded by the mt rnr gene the mt rnr gene also encodes the humanin polypeptide that has been the target of alzheimer s disease research see also mitochondrial dna humanin references category ribosomal rna...
https://en.wikipedia.org/wiki/MT-RNR2
*  PRNA
... may refer to norc associated rna a non coding rna element which regulates ribosomal rna transcription tryptophan halogenase an enzyme...
https://en.wikipedia.org/wiki/PRNA
*  CH391L/S12/CH391L/S12/Ancestral Sequence Reconstruction - OpenWetWare
... CH391L/S12/CH391L/S12/Ancestral Sequence Reconstruction From OpenWetWare CH391L/S12 Revision as of 15:45, 13 February 2012 by Jared Ellefson Talk. 1 What is Ancestral Sequence Reconstruction. 1.1 Pipeline for Generating Ancestral Genes 1.1.1 Methods of Inferring Ancient Sequences 1.1.2 Gene Synthesis 1.1.3 Testing Ancestral Variants. 1.2 Examples of Ancestral Sequence Reconstructions 1.2.1 Evolution of Coral Pigments 1.2.2 Inferring the Paleoenvironment of ancient Earth. What is Ancestral Sequence Reconstruction. Sequence information Nucleic Acid and Protein from extant species can be used to infer the sequences of common ancestor species which can be synthesized and tested in the lab. Sequence Reconstruction Example. Sequences from extant species of the desired common ancestral gene and outgroup genes are aligned. The ancestral gene is inferred based on evolutionary models typically maximum parsimony or maximum likelihood. Ancestral genes are cloned and tested for function. Methods of Inferring Ancient ...
http://openwetware.org/index.php?title=CH391L/S12/CH391L/S12/Ancestral_Sequence_Reconstruction&oldid=583945
*  CH391L/S13/Ancestral Sequence Reconstruction - OpenWetWare
... Ancestral Sequence Reconstruction refers to the construction of hypothesized protein or DNA sequences belonging to a common ancestor of extant proteins or DNA. Sequence information Nucleic Acid and Protein from extant species can be used to infer the sequences of common ancestor species which can be synthesized and tested in the lab. The method was originally discussed by Pauling and Zuckerkandl in 1963 cite Pauling /cite, almost 30 years before the theory was experimentally tested. Ancestral Sequence Reconstruction refers to the construction of hypothesized protein or DNA sequences belonging to a common ancestor of extant proteins or DNA. Sequence information Nucleic Acid and Protein from extant species can be used to infer the sequences of common ancestor species which can be synthesized and tested in the lab. The method was originally discussed by Pauling and Zuckerkandl in 1963 cite Pauling /cite, almost 30 years before the theory was experimentally tested. ==Pipeline for Generating Ancestral Genes==...
http://openwetware.org/index.php?title=CH391L/S13/Ancestral_Sequence_Reconstruction&diff=677463&oldid=677462
*  CH391L/S13/Ancestral Sequence Reconstruction - OpenWetWare
... CH391L/S13/Ancestral Sequence Reconstruction From OpenWetWare Difference between revisions Jump to: navigation, search Revision as of 19:53, 24 February 2013 view source Aurko Dasgupta Talk. contribs → Evolution of Coral Pigments ← Previous diff. Revision as of 19:55, 24 February 2013 view source Aurko Dasgupta Talk. contribs → Evolution of Coral Pigments Next diff →. Line 30:. Line 30:. One example of ancestral sequence reconstruction was done by the Matz group currently residing at the University of Texas at Austin. Fluorescent proteins from related coral species had wavelengths corresponding to Cyan, Green, and Red cite #Ugalde /cite. The details of the evolution of fluorescent color in the GFP superfamily was not fully understand. That is, what fluorescent spectra did the common ancestors of the modern corals have. One example of ancestral sequence reconstruction was done by the Matz group currently residing at the University of Texas at Austin. Fluorescent proteins from related coral species had wav...
http://openwetware.org/index.php?title=CH391L/S13/Ancestral_Sequence_Reconstruction&diff=678933&oldid=678932
*  Branching order of bacterial phyla (Gupta, 2001)
branching order of bacterial phyla gupta branching order of bacterial phyla gupta bacterial phyla there are several models of the branching order of bacterial phyla one of these was proposed in 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 one feature of the cladogram obtained with this method is the clustering of cell wall morphology with some exceptions from monoderms to transitional diderms to traditional diderms in the cladogram below yellow pseudopeptidoglycan monoderms gram variable red thick peptidoglycan monoderms gram positive blue thin peptidoglycan diderms gram negative green atypical see note in parethesis cladex style width auto bar gold archaea cladex bar crimson firmicutes cladex bar crimson actinobacteria see also branching order of bacterial phyla woese branching order ...
https://en.wikipedia.org/wiki/Branching_order_of_bacterial_phyla_(Gupta,_2001)
*  CH391L/S13/Ancestral Sequence Reconstruction - OpenWetWare
Fluorescent proteins from related coral species had wavelengths corresponding to Cyan, Green, and Red. That is, what fluorescent spectra did the common ancestors of the modern corals have. Sequences for the common ancestor nodes were synthesized and tested for their activity. The common ancestor to all the superfamily had a green emission peak. The more recent common ancestor of Green/Red had two emission peaks; a strong green peak and a smaller red peak. Fluorescent proteins from related coral species had wavelengths corresponding to Cyan, Green, and Red. That is, what fluorescent spectra did the common ancestors of the modern corals have. Sequences for the common ancestor nodes were synthesized and tested for their activity. The common ancestor to all the superfamily had a green emission peak. The more recent common ancestor of Green/Red had two emission peaks; a strong green peak and a smaller red peak. 1.2 Examples of Ancestral Sequence Reconstructions 1.2.1 Evolution of Coral Pigments 1.2.2 Inferring the...
http://openwetware.org/index.php?title=CH391L/S13/Ancestral_Sequence_Reconstruction&diff=678913&oldid=678912
*  The FASTML Server - Server for computing Maximum Likelihood ancestral sequence reconstruction
the fastml server server for computing maximum likelihood ancestral sequence reconstruction home overview gallery source code citing credits old version the fastml server server for computing maximum likelihood ancestral sequence reconstruction type your multiple sequence alignment msa fasta format only or upload your multiple sequence alignment msa file sequences type amino acids nucleotides codons type your phylogenetic tree optional newick format only or upload phylogenetic tree file newick format only model of substitution jtt default lg mtrev for mitochondrial proteins cprev for chloroplasts proteins wag dayhoff jc model jukes and cantor t model tamura hky model hasegawa kishino and yano gtr generalised time reversible yang for codon sequences empiricodon for codon sequences please enter your email address optional your email address will be used to update you the moment the results are ready load an example advanced options phylogenetic tree method maximum likelihood ml neighbor joining optimize branch ...
http://fastml.tau.ac.il/
*  Comparison of Protein Sequences: BLAST searching and Phylogenetic Tree Construction
... Inquiry-based Integrated Instructional Units Comparison of Protein Sequences: BLAST searching and Phylogenetic Tree Construction. It accompanies several weeks of wet lab work in which students clone cDNAs encoding Cytochrome P450 1A CYP1A from animals primarily fish collected locally and exposed to pollution compounds that induce expression of the enzyme. In this exercise, students perform BLAST searches of reported CYP1A sequences and construct phylogenetic trees using CYP1A amino acid sequences from various vertebrate species, especially those with multiple CYP1A paralogs. Thus, evolutionary analysis of CYP1A sequences from many species provides an opportunity to explore the number and timing of gene duplications during vertebrate evolution. Three short readings about gene duplication in evolution and phylogenetic analysis are provided at least one week prior to class. These readings complement earlier readings that specifically concern the cloning and evolutionary analysis of CYP1A genes in fish. Mate...
http://serc.carleton.edu/genomics/units/19100.html
*  Talk:CH391L/S13/Ancestral Sequence Reconstruction - OpenWetWare
... Talk:CH391L/S13/Ancestral Sequence Reconstruction. From OpenWetWare. Talk:CH391L/S13 Revision as of 00:02, 24 February 2013 by Aurko Dasgupta Talk. contribs. diff ←Older revision. Current revision diff. Newer revision→ diff. Jump to: navigation, search. Gabriel Wu 16:59, 18 February 2013 EST : Remove the cost and methods of gene synthesis or just reference the dna assembly section we've already gone over. Expand the codon optimization section unless this fits better in somewhere else. Gabriel Wu 16:59, 18 February 2013 EST : How does Pauling's proposal for ancestral gene construction relate to the actual discovery of DNA structure. Benjamin Gilman 13:21, 21 February 2013 EST : The Pauling and Zuckerkandl paper came out when the only protein sequence information we had came from limited peptide sequencing methods like Edman degradation N-terminal sequencing. You might add something about the shift to using DNA or RNA sequences to infer protein sequence once techniques like Maxam-Gilbert and Sanger sequenc...
http://openwetware.org/index.php?title=Talk:CH391L/S13/Ancestral_Sequence_Reconstruction&direction=prev&oldid=678776
*  Ancestral reconstruction
'Ancestral Reconstruction' also known as 'Character Mapping' or 'Character Optimization' is a method in evolutionary biology by which one can attempt to understand the phenotypic and genetic states of organisms that lived millions of years ago. Maximum Parsimony. Maximum likelihood. They are: maximum parsimony, maximum likelihood, and the Bayesian Inference. Maximum parsimony is the method that came about first. Maximum likelihood accounts for what we know about the likelihood of various events, which is that they are not all equal. Maximum Parsimony. Maximum Parsimony. Maximum likelihood. The main difference between this and maximum parsimony is that the maximum likelihood test accounts for the fact that not all events are equally likely to happen. When this is the case, maximum parsimony may actually be more accurate because it is more willing to make large, unlikely leaps than maximum likelihood is. Maximum likelihood has been shown to be quite reliable in reconstructing character states however it does no...
https://en.wikipedia.org/wiki/Ancestral_reconstruction
*  Viral phylodynamics
... Due to the impact that transmission dynamics and selection can have on viral genetic variation, viral phylogenies can therefore be used to investigate important epidemiological, immunological, and evolutionary processes, such as epidemic spread,. Methods Coalescent theory and phylodynamics. Examples Phylodynamics of Influenza. Phylodynamics of HIV. The clustering of taxa on a viral phylogeny will be affected by host population structure see figure 2 Viruses within similar hosts, such as hosts that reside in the same geographic region, are expected to be more closely related genetically if transmission occurs more commonly between them. For example, an application to HIV sequences within infected hosts showed that viral substitution rates dropped to effectively zero following the initiation of antiretroviral drug therapy. If the population size N t changes over time, the coalescent rate \lambda n t will also be a function of time. derived this rate for a time-varying population size under the assumption o...
https://en.wikipedia.org/wiki/Viral_phylodynamics
*  Diagnostic characters from Consortium of mx users. - Encyclopedia of Life
... Diagnostic characters. 2011, by Lewis L. Deitz and Matthew S. Wallace. Add to a collection. Diagnostic characters. Distance from eye to base of forewing usually greater than half eye width exceptions: Deiroderes and many Nicomiinae. Pronotum usually produced posteriorly over scutellum exceptions: Endoiastinae, Nicomiinae, Deiroderes, Abelus, and Hemicentrus, often also with anterior, lateral, or dorsal projections. Forewings with vein M fused with Cu basally share common stem; exceptions: some Nicomia and some Smiliinae. Prothoracic trochanter and femur not fused. Male abdominal segment IX usually with lateral plates discrete from pygofer exceptions: fused to pygofer in few members of various tribes; lateral plates absent in Anchistrotus and some Stegaspidini. Female pygofer not strongly produced posteroventrally. Nymph with abdominal tergum IX forming sheath around segment X, anal opening dorsal or posterior. Latest updates. No one has provided updates yet. Learn how to contribute. Add a new comment. Yo...
http://eol.org/data_objects/12685167
*  Browse By Person: Phillips, Matthew | QUT ePrints
Browse By Person: Phillips, Matthew. Browse By Person: Phillips, Matthew Statistics dashboard. Review. Book Chapter Phillips, Matthew J. Penny, David 2010 Mammalian phylogeny., Phillips, Matthew J. PLoS ONE, 10 5, e0125723., Carrano, Matthew T. Systematic Biology. Phillips, Matthew J., Gibb, Gillian C. 2014 Molecular phylogeny, biogeography, and habitat preference evolution of marsupials. Molecular Biology and Evolution, 31 9, pp., Phillips, Matthew J. Phillips, Matthew J., Gibb, Gillian,. Bunce, Michael 2013 Inferring kangaroo phylogeny from incongruent nuclear and mitochondrial genes. PLoS ONE, 8 2, pp. Phillips, Matthew J. Current Biology, 23 14, R603-R605., Phillips, Matthew J. Molecular Phylogenetics and Evolution, 59 3, pp., Phillips, Matthew J. 2010 Evolutionary relationships and divergence times among the native rats of Australia. 2009 The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography. 2009 Accounting for calibration uncertainty in phylogenetic estimation of evo...
http://eprints.qut.edu.au/view/person/Phillips,_Matthew.html
*  Wiegmann Lab: Current Research
Insect Molecular Systematics at NCSU. phylogenetic relationships and testing hypotheses about the evolution and diversification of insects. A major component of these studies is uncovering patterns and processes of DNA sequence evolution and using these to improve interpretation of morphological and developmental evolutionary pathways. Molecular Phylogenetics of Diptera: FLYTREE - NSF - Assembling the Tree of Life project on Diptera a Collaborative Research Effort in Dipteran Phylogenetics. The need for new, large, comprehensive datasets for Diptera phylogeny motivates our collaborative, National Science Foundation funded, Assembling the Tree of Life ATOL project-- FLYTREE. Within this study, we are assembling multiple phylogenetic data sets to simultaneously assess dipteran phylogenetic relationships and the information content of specific character systems. For example, we will compare large by character data sets 1st tier; 45 taxa; 15-20 genes and mt genomes to those with increased numbers of taxa by taxa ...
http://www4.ncsu.edu/unity/users/b/bwiegman/public_html/labweb/currentresearch.html
*  Talk:CH391L/S13/DirectedProteinEvolution - OpenWetWare
Gabriel Wu Talk. *' ] 21:45, 21 February 2013 EST ':It would be nice if you added literature examples of Directed Evolution of Proteins for each approach as done in the Ancestral Sequence Reconstruction or take a similar approach. *' ] 21:45, 21 February 2013 EST ':It would be nice if you added literature examples of Directed Evolution of Proteins for each approach as done in the Ancestral Sequence Reconstruction or take a similar approach. + *' ] 15:33, 2 March 2013 EST ':It would be nice to put some numbers on the typical plasmid screening in 'E. + ****' ] 14:03, 4 March 2013 EST ': This is an interesting point. *' ] 04:13, 27 February 2013 EST ':I thought it'd be nice to have a section explaining fitness landscapes and moving through sequence space. *' ] 04:13, 27 February 2013 EST ':I thought it'd be nice to have a section explaining fitness landscapes and moving through sequence space. It's true that many times the selection will result in being trapped in a local optima, but other times the selection wi...
http://openwetware.org/index.php?title=Talk:CH391L/S13/DirectedProteinEvolution&diff=680636&oldid=680003
*  Systematics
thumb|400px|A comparison of phylogenetic and phenetic concepts Biological '''systematics''' is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Phylogenetic trees of species and higher taxa are used to study the evolution of traits e.g., anatomical or molecular characteristics and the distribution of organisms biogeography. Systematics, in other words, is used to understand the evolutionary history of life on Earth. Definition and relation with taxonomy Taxonomic characters See also References Notes. Definition and relation with taxonomy. Europeans tend to use the terms "systematics" and "biosystematics" for the field of the study of biodiversity as a whole, whereas North Americans tend to use "taxonomy" more frequently. Taxonomic characters. Molecular characters. Immunological distance Electrophoretic differences Amino acid sequences of proteins DNA hybridization DNA and RNA sequences Restriction endonuclease analyses Other molec...
https://en.wikipedia.org/wiki/Systematics
*  Difference between revisions of "Molecular Systematics Spring 2014" - EEBedia
Difference between revisions of "Molecular Systematics Spring 2014" From EEBedia. Chris Simon. Chris Simon. :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lab%208.%20Kasey%20Pregler%20MiniPresentation%2012April12.pdf}}EEB 5350 Lab 8. Kasey Pregler MiniPresentation 12April12.pdf. :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lab%208.%20Kasey%20Pregler%20MiniPresentation%2012April12.pdf}}EEB 5350 Lab 8. Kasey Pregler MiniPresentation 12April12.pdf. Instructor: Chris Simon, Biopharm 305D, 6-4640, chris.simon@uconn.edu Graduate Assistant: Chris Owen, Biopharm 325A, christopher.l.owen@uconn.edu ; 6-3947. Readings: will be posted as PDF’s. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. Syllabus Molecular Systematics rev 28 Mar 12.pdf Assignment 1. How molecules evo...
http://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2012&diff=21831&oldid=21782
*  Molecular phylogenetics
'Molecular phylogenetics ' is the branch of phylogeny that analyses hereditary molecular differences, mainly in DNA sequences, to gain information on an organism's evolutionary relationships. History of molecular phylogenetics Techniques and applications Theoretical background Limitations of molecular systematics See also Notes and references Further reading External links. A comprehensive step-by-step protocol on constructing phylogenetic tree, including DNA/Amino Acid contiguous sequence assembly, multiple sequence alignment, model-test testing best-fitting substitution models and phylogeny reconstruction using Maximum Likelihood and Bayesian Inference, is available at Nature Protocol Bast, F. These have been replaced in recent times largely by DNA sequencing, which produces the exact sequences of nucleotides or 'bases' in either DNA or RNA segments extracted using different techniques. In a molecular systematic analysis, the haplotypes are determined for a defined area of genetic material ; a substantial s...
https://en.wikipedia.org/wiki/Molecular_phylogenetics
*  CH391L/S13/DNA Computing - OpenWetWare
... CH391L/S13/DNA Computing From OpenWetWare Difference between revisions Jump to: navigation, search Revision as of 11:55, 1 April 2013 view source Dwight Tyler Fields Talk. contribs m New page: Hello world. ← Previous diff. Revision as of 12:03, 1 April 2013 view source Dwight Tyler Fields Talk. contribs m Next diff →. Line 1:. Line 1:. - Hello world. + ] ]. + =Introduction=. + Ancestral Sequence Reconstruction refers to the construction of hypothesized protein or DNA sequences belonging to a common ancestor of extant proteins or DNA. It enables scientists to synthesize biomolecules from extinct organisms. Sequence information Nucleic Acid and Protein from extant species can be used to infer the sequences of common ancestor species which can be synthesized and tested in the lab. The method was originally discussed by Pauling and Zuckerkandl in 1963 cite Pauling /cite, almost 30 years before the theory was experimentally tested. + ]. + + ==Pipeline for Generating Ancestral Genes==. + # Sequences from extan...
http://openwetware.org/index.php?title=CH391L/S13/DNA_Computing&diff=687401&oldid=687389
*  Phylogenetic Classification ( Real World ) | Biology | CK-12 Foundation
Phylogenetic Classification Real World. Help. Help. You are viewing an older version of this Concept. Go to the latest version. Phylogenetic Classification. Practice Phylogenetic Classification Practice. 0% Practice Now. Evolution. Resources. Published. Cows Gone Wild. The "cows" you see are Aurochs Bos primigenius. They are the species of bovine that humans domesticated to form our modern day cows. Looking at the cave paintings of aurochs, you may get the sense that they were a bit different than our domesticated cattle. The characteristics which made aurochs successful in the wild were not the characteristics that humans thought were most useful. For example, packing on lots of meat may be a great trait in a cow for a cattle rancher, but if that meat hampers mobility, then it can make a cow an easy target to predators. This is one of the differences between artificial selection and natural selection. However, it does not take 600 years for noticeable changes to appear in bred species once the artificial sel...
http://ck12.org/biology/Phylogenetic-Classification/rwa/21st-Century-Auroch/r8/
*  Filosofía, especie y sistemática
Host structure of the Phylogeny of West Nile Virus WNV: Does it shape the spatiotemporal structure. Methods Sequence Data: All the available sequences of complete genome of WNV, with collection times, and geographic locations 453 sequences, from 25 countries, and 79 hosts species were retrieved from GenBank. Phylogeny inferred using a Maximum likelihood analysis of 53 sequences. Phylogeny with Host structure for WNV. Just Testudines present a different resutl, where the non-nuclear and nuclear partitions had the lowest values Fig. Estimating Evolutionary Rates and Times to the last Common Ancestor DEV-2, using partitions vs complete coding region. Several studies have been aimed at understanding the epidemiology of DENV, rates and dates of evolution, and selection pressure in its different genes and genotypes Rico-hesse Rico-hesse, 1990; Rico-Hesse et al., 1997; S. The objectives of this study were to infer the time to the Most recent common ancestor MRCA of the DENV2 genotypes, and estimate the evolutionary ...
http://elecsist.blogspot.com/
*  PCA and clustering reveal alternate mtDNA phylogeny of N and M clades. | Broad Institute of MIT and
PCA and clustering reveal alternate mtDNA phylogeny of N and M clades. Broad Institute of MIT and Harvard. Partnerships Philanthropy Careers Contact Us. What is Broad. Our Approach Areas of Focus History Leadership Who is Broad Partner Institutions Artist-in-Residence Media Center. Press Room News from the Broad Photos for Journalists Spotlight: Ebola Spotlight: CRISPR BroadMinded Blog Video Library For the Scientific Community. Scientific Publications Science Data Software. Scientific Publications Science Data Software. Home. News & Publications:Scientific Publications PCA and clustering reveal alternate mtDNA phylogeny of N and M clades. Recent Broad Publications Inherited CHST11/MIR3922 deletion is associated with a novel recessive syndrome presenting with skeletal malformation and malignant lymphoproliferative disease. Read More / View Supplemental Materials Ferritinophagy via NCOA4 is required for erythropoiesis and is regulated by iron dependent HERC2-mediated proteolysis. Read More / View Supplemental ...
https://broadinstitute.org/publications/broad3822
*  Phylogenomics
It is a group of techniques within the larger fields of phylogenetics and genomics. Phylogenomics draws information by comparing entire genomes, or at least large portions of genomes. 1 Phylogenetics compares and analyzes the sequences of single genes, or a small number of genes, as well as many other types of data. Prediction of gene function Establishment and clarification of evolutionary relationships Gene family evolution Prediction and retracing lateral gene transfer. Prediction of Gene Function Prediction and Retracing Lateral Gene Transfer Gene family evolution Establishment of Evolutionary Relationships Databases See also References. Before the use of phylogenomic techniques, predicting gene function was done primarily by comparing the gene sequence with the sequences of genes with known functions. 3 This prediction was based on the fact that this organism has a gene for which the sequence is highly similar to genes from other species in the "MutS" gene family which included many known to be involved ...
https://en.wikipedia.org/wiki/Phylogenomics
*  Wikiomics:RNA phylogenetics - OpenWetWare
... Wikiomics:RNA phylogenetics From OpenWetWare Difference between revisions Jump to: navigation, search Revision as of 17:04, 3 March 2008 view source Torsten Waldminghaus Talk. contribs added tags ← Previous diff. Current revision 05:34, 20 October 2009 view source Albert Vilella Talk. contribs adding rnasalsa. One intermediate revision not shown. Line 16:. Line 16:. * Bayesian Inference of Phylogeny. Allows secondary structure models. * Bayesian Inference of Phylogeny. Allows secondary structure models. * Designed specifically for use with RNA sequences that have a conserved secondary structure, e.g., rRNA and tRNA. Substitution models of sequence evolution that consider pairs of sites rather than single sites are implemented in this package along with standard nucleotides substitution models used nowadays. When a RNA molecule with a secondary structure is used in conjunction with a RNA substitution model, PHASE requires a structure-based alignment of the sequences with the consensus secondary structure ...
http://openwetware.org/index.php?title=Wikiomics:RNA_phylogenetics&diff=360520&oldid=189099
*  Polyphyly
Image:Monophyly, paraphyly, polyphyly.png File:Phylogenetic-Groups.svg|thumbnail|300px|Phylogenetic groups: A monophyletic taxon in yellow, the group of "reptiles and birds" contains a common ancestor and all of its descendants. A paraphyletic taxon in cyan, the reptiles contains its most recent common ancestor, but does not contain all the descendants of that ancestor. A polyphyletic in red, the group of all warm-blooded animals taxon does not contain the most recent common ancestor of all its members. A 'polyphyletic' Greek for "of many races" group is characterized by one or more homoplasies : phenotype s which have converged or reverted so as to appear to be the same but which have not been inherited from common ancestors. For example, warm-bloodedness evolved separately in the ancestors of mammals and the ancestors of birds 1. Researchers concerned more with ecology than with systematics may take polyphyletic groups as legitimate subject matter; the similarities in activity within the fungus group ' Alte...
https://en.wikipedia.org/wiki/Polyphyly
*  Difference between revisions of "Molecular Systematics Spring 2014" - EEBedia
Chris Simon. Chris Simon. :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20Lab%209.%20Minipresentation%20RT-PCR%20Brigette.pdf}}EEB 5350 Lab 9. Minipresentation RT-PCR Brigette.pdf. :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20Lab%209.%20Minipresentation%20RT-PCR%20Brigette.pdf}}EEB 5350 Lab 9. Minipresentation RT-PCR Brigette.pdf. Combining Data/Comparing Trees. + + :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Comparing%20Trees%20Combining%20Data%20Readings%202012.pdf}}Comparing Trees Combining Data Readings 2012.pdf. + + Reading for next week: :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Simon%2C%20Buckley%2C%20Frati%2C%20Stewart%2C%20Beckenbach%202006%20AREES%20%26%20supplement.pdf}}Simon, Buckley, Frati, Stewart, Beckenbach 2006 AREES supplement.pdf. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, ...
http://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2012&diff=21847&oldid=21846
*  Darwin's Evolutionary Tree 'Annihilated' | The Institute for Creation Research
Darwin s Evolutionary Tree Annihilated. Timely news related to creation and evolution. Life Sciences. Problems with Evolution. Evidence for Creation. Evidence for Truth. Evidence from Science. Apologetics Articles. ICR Store. Darwin's Evolutionary Tree 'Annihilated' by Brian Thomas, M.S. * Resources. Life Sciences Resources. Problems with Evolution. In 1837, Charles Darwin drew his first evolutionary tree in his B notebook, with the words I think scrawled above it, to illustrate his idea that all of today s species arose from a single common ancestor. But the poor fit of gene sequence data is forcing scientists to abandon the tree. A non-Darwinian evolutionary view has been offered, but this proposition is actually just the old Hopeful Monster with a twist. 3 Darwin s tree illustrated a long macroevolutionary past that never happened. 4 Finally, evolutionary biologists seem to be catching up with creation biologists. 5 Michael Syvanen, co-editor of Horizontal Gene Transfer 1998 and a medical biochemist at the...
http://icr.org/articles/view/4404/295/
*  Phylogenetic profiling
... 'Phylogenetic profiling' is a bioinformatics technique in which the joint presence or joint absence of two traits across large numbers of species is used to infer a meaningful biological connection, such as involvement of two different proteins in the same biological pathway. Along with examination of conserved synteny, conserved operon structure, or "Rosetta Stone" domain fusions, comparing phylogenetic profiles is a designated a "post-homology" technique, in that the computation essential to this method begins after it is determined which proteins are homologous to which. A number of these techniques were developed by David Eisenberg and colleagues; phylogenetic profile comparison was introduced in 1999 by Pellegrini, 'et al.' Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Method Theory Advances and Challenges Notes. For a given protein family, its presence or absence in each genome in the original formulation is represented by 1 present and 0 absent. The large number of complete genom...
https://en.wikipedia.org/wiki/Phylogenetic_profiling
*  Structural Biochemistry/Analyzing protein structure and function using ancestral gene reconstruction
... - Wikibooks, open books for an open world. Structural Biochemistry/Analyzing protein structure and function using ancestral gene reconstruction. 1 Analyzing protein structure and function using ancestral gene reconstruction. Analyzing protein structure and function using ancestral gene reconstruction. Learning how protein sequence determines structure and function as well as learning the processes that generated the diverse structures and functions of extant proteins requires knowledge of the distribution of structures and functions through the multidimensional space of possible protein sequences. The outcomes of that massive experiment are preserved in the sequences, structures, and functions of modern-day protein families. Evolutionary analysis of these families can provide key insights into the nature of protein sequence space and the determinants of protein structure and function. Horizontal and Vertical Analysis. One way to study protein families is to identify candidate amino acid differences betwe...
https://en.wikibooks.org/wiki/Structural_Biochemistry/Analyzing_protein_structure_and_function_using_ancestral_gene_reconstruction
*  Patrocladogram
2 " and is used exclusively to determine the amount of divergence of a characteristic from a common ancestor. This means that cladistic and patristic distances are combined to construct a new tree using various phenetic algorithms. 3 The purpose of the patrocladogram in biological classification is to form a hypothesis about which evolutionary processes are actually involved before making a taxonomic decision. 4 Patrocladograms are based on biostatistics that include but are not limited to: parsimony, distance matrix, likelihood method s, and Bayesian probability. Some examples of genomically related data that can be used as inputs for these methods are: molecular sequences, whole genome sequences, gene frequencies, restriction site s, distance matrices, unique characters, mutations such as SNPs, and mitochondrial genome data. Cautions with patrocladogram usage Programs for patrocladogram analysis PATRISTIC. RAMI. Further reading References External links. Cautions with patrocladogram usage. Patrocladograms a...
https://en.wikipedia.org/wiki/Patrocladogram
*  SMART: DUF1866 domain taxonomic distribution
smart duf domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with duf domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing duf domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DUF1866
*  SMART: DUF3700 domain taxonomic distribution
smart duf domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with duf domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing duf domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DUF3700
*  SMART: PTPc motif domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with PTPc motif domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing PTPc motif domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=PTPc_motif
*  SMART: HOX domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with HOX domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing HOX domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=HOX
*  SMART: Citrate ly lig domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with Citrate ly lig domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing Citrate ly lig domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Citrate_ly_lig
*  SMART: Catalase domain taxonomic distribution
smart catalase domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with catalase domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing catalase domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Catalase
*  SMART: LRR RI domain taxonomic distribution
smart lrr ri domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with lrr ri domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing lrr ri domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=LRR_RI
*  SMART: Fib alpha domain taxonomic distribution
smart fib alpha domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with fib alpha domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing fib alpha domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Fib_alpha
*  SMART: Frataxin Cyay domain taxonomic distribution
smart frataxin cyay domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with frataxin cyay domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing frataxin cyay domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Frataxin_Cyay
*  SMART: Integrin B tail domain taxonomic distribution
smart integrin b tail domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with integrin b tail domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing integrin b tail domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Integrin_B_tail
*  SMART: BMC domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with BMC domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing BMC domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=BMC
*  SMART: GA domain taxonomic distribution
smart ga domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with ga domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing ga domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=GA
*  SMART: ELK domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with ELK domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing ELK domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=ELK
*  SMART: SEC14 domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with SEC14 domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing SEC14 domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=SEC14
*  SMART: CP12 domain taxonomic distribution
smart cp domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with cp domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing cp domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=CP12
*  SMART: NH domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with NH domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing NH domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=NH
*  SMART: DM13 domain taxonomic distribution
smart dm domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with dm domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing dm domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DM13
*  SMART: LY domain taxonomic distribution
smart ly domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with ly domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing ly domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=LY
*  SMART: zf-AD domain taxonomic distribution
smart zf ad domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with zf ad domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing zf ad domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=zf-AD
*  SMART: AWS domain taxonomic distribution
smart aws domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with aws domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing aws domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=AWS
*  SMART: Amelin domain taxonomic distribution
smart amelin domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with amelin domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing amelin domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Amelin
*  SMART: Ami 3 domain taxonomic distribution
smart ami domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with ami domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing ami domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Ami_3
*  SMART: CVNH domain taxonomic distribution
smart cvnh domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with cvnh domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing cvnh domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=CVNH
*  SMART: Cache 2 domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with Cache 2 domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing Cache 2 domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Cache_2
*  SMART: ChSh domain taxonomic distribution
smart chsh domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with chsh domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing chsh domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=ChSh
*  SMART: DAX domain taxonomic distribution
smart dax domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with dax domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing dax domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DAX
*  SMART: DEFSN domain taxonomic distribution
smart defsn domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with defsn domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing defsn domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DEFSN
*  SMART: DSHCT domain taxonomic distribution
smart dshct domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with dshct domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing dshct domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DSHCT
*  SMART: DSPc domain taxonomic distribution
smart dspc domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with dspc domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing dspc domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DSPc
*  SMART: EPEND domain taxonomic distribution
smart epend domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with epend domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing epend domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=EPEND
*  SMART: GPS domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with GPS domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing GPS domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=GPS
*  SMART: GYR domain taxonomic distribution
smart gyr domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with gyr domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing gyr domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=GYR
*  SMART: HALZ domain taxonomic distribution
smart halz domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with halz domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing halz domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=HALZ
*  SMART: MltA domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with MltA domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing MltA domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=MltA
*  SMART: MutL C domain taxonomic distribution
smart mutl c domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with mutl c domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing mutl c domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=MutL_C
*  SMART: NRF domain taxonomic distribution
smart nrf domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with nrf domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing nrf domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=NRF
*  SMART: NurA domain taxonomic distribution
smart nura domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with nura domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing nura domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=NurA
*  SMART: PA14 domain taxonomic distribution
smart pa domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with pa domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing pa domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=PA14
*  SMART: PMEI domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with PMEI domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing PMEI domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=PMEI
*  SMART: ParB domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with ParB domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing ParB domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=ParB
*  SMART: RPEL domain taxonomic distribution
smart rpel domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with rpel domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing rpel domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=RPEL
*  SMART: RasGAP domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with RasGAP domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing RasGAP domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=RasGAP
*  SMART: VRR NUC domain taxonomic distribution
smart vrr nuc domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with vrr nuc domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing vrr nuc domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=VRR_NUC

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)


How do the genes on chromosome 17 relate to cancer?


How do the genes on chromosome 17 (Death Chromosome)  relate to cancer?
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Changes in chromosome 17 have been identified in several types of human cancer. These genetic changes are somatic, which means they are acquired during a person's lifetime and are present only in certain cells. A particular chromosomal abnormality called an isochromosome 17q occurs frequently in some cancers. This abnormal version of chromosome 17 has two long (q) arms instead of one long arm and one short (p) arm. As a result, the chromosome has an extra copy of some genes and is missing copies of other genes.

An isochromosome 17q is commonly found in a cancer of blood-forming tissue called chronic myeloid leukemia (CML). It also has been identified in certain solid tumors, including a type of brain tumor called a medulloblastoma and tumors of the brain and spinal cord known as primitive neuroectodermal tumors. Although an isochromosome 17q probably plays a role in both the development and progression of these cancers, the specific genetic changes related to cancer growth are unknown.


What ethnic groups tend to have dominant genes when determining physical features of your children?


I have heard that asian genes tend to be dominant when there are bi-racial parents and was just wondering if there were any other ethnic groups or races that tend to have dominant genes when determining the physical features of kids of bi-racial parents?
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I don't think it has to do with the ethnicity...
But dark hair is a dominant gene, and light hair is recessive. Brown and green eyes are dominant, the others are recessive -although you see combinations of eye colors. Curly hair is dominant, straight is recessive. If a caucasian person marries a person of ethnicity, that child will have darker skin than their caucasian parent, but lighter skin than their "ethnic" parent.

If a full-blooded latino with curly hair were to marry a blond haired, blue eyed girl, for example, ALL of their kids would have dark, curly hair, and brown eyes. But they would all be lighter than their dad.


How do you know if you have good genes for bodybuilding?


Or what im trying to say is that, how do you know if you got good genes for muscle if that makes sense. BEcause me and my brother use to workout in the gym for maybe 4 times a week for like 3 months without really a schedule just lifting some weights here and there without any knowledge of bodybuilding. And right now we are in pretty good shape.
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A couple of factors can tip you off if you have good "muscle" genetics or not.  

Before you began any kind of training, what were your builds like?  Short and stocky?  Medium height with narrow waist and broad shoulders?  Tall and lean?  Somewhere in between?  I'm refering to what are called somatotypes.  Usually those who center near the middle--or mesomorphs--tend to have the best genes for bodybuilding.  They probably have naturally low body fat, plus have the ability to add quality muscle mass. Short and stocky put on muscle mass easily but have extra trouble shedding excess weight (endomorphs).  Tall and skinny have low fat levels but find it difficult to add muscle mass (ectomorphs).  The best bodybuilders in the world are mostly, or more likely have characteristics like, mesomorphs.

To check yourself, there are a couple of way to determine your build.  

Muscle bellies--works most of the time:  flex your bicep and place fingers in between your elbow joint and biceps muscle belly.  More than two fingers means you have high origin/insertions and probably have to work a little harder for mass.  Two fingers tightly probably means a medium muscle.  One finger or less and you are pretty blessed with big, full muscle bellies--enjoy.

Joints--In bodybuliding, it's always impressive when someone puts on a lot of mass with small joints.  The bellies look huge.  Unfortunatly, those with small joints tend to have a little more trouble building size.  To test joint size, measure you wrist circumference.  Grasp your wrist with your opposing thumb and middle finger.  If your fingers overlap easily--small frame.  If they barely touch--medium frame.  If they don't touch at all--large frame.  Usually larger frames have the capasity to hold more mass.

Measure your "V" taper.  Take a tape measure around your shoulders, then around your waist.  The bigger the difference in numbers (shoulders should be bigger) the bigger the "V" taper and better genetics you probably have.

These are just a couple of tests.  Are they difinitive...no.  But they seem to be pretty close.  Hope this answered your question!


How does gene therapy help a cystic fibrosis sufferer?


How does gene therapy help a cystic fibrosis sufferer?

Also :

what 2 reasons may genetic testing be carried out when a couple are undergoing IVF treatment?
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Gene therapy aims to effectively replace a faulty gene. So in Cystic Fibrosis it would replace the gene (or genes) which causes the problem and hopefully make the patient much better. As for IVF some tests are done to check for chromosomal abnormalities like Down's Syndrome and other genetic problems.


What are the genes you need to have to be considered identical?


im going a research paper and i dont know how to put the types of genes part in it...i cant find a page that tells me how are identical twins different?
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Babies are made when a sperm and an egg combine. The embryo then starts multiplying and eventually becomes a baby. Identical twins happens the same as a single baby, but the egg splits into two separate embryos and then begins to multiply. Fraternal twins happen when two eggs are fertilized with two different sperm. Semi-Identical twins (this is a recent discovery because of fertility drugs and such) happens when two sperm get into one egg. It then begins to split into two and then multiply.


what kind of genes does it take to create a child who is forever natural blonde?


I am learning about genes in my classes, and i have noticed that the percentage of natural blondes is low.  A person who is a natural light blonde must have his/her eyebrows blonde, people who have dark eye brows and light hair will turn darker haired when older,   What kind of genes or how many does it take to create a blonde person with natural hair?  (I know recessive genes but what kind)
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probably both sets of grandparents, great grandparents, and possibly great great grandparents, and of course parents that are all blondes. There of course would have to be more light blondes then dark blondes though.

I hope that helps. It's been a while since I've had biology though so yea. 

Good Luck


why do genes regulating the amount of glucose and fat in the body start to shut down when you dont exercise?


helppp!
why do genes regulating the amount of glucose and fat in the body start to shut down when you dont exercise
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I believe you are referring to insulin. Your body breaks down the food you eat into glucose (blood sugar), then the pancreas releases insulin to open a door to your cells to be used as energy. The constant eating of high glycemic carbs (bread,pasta,cereal) create an imbalance overtime. The body won't be able to create enough insulin in relation to the amount of glucose. This causes weight gain. I don't believe weight gain happens when you stop working out. Too many carbs is the largest problem on the planet, which is why type 2 diabetes is so abundant. Many people have pre type 2 and don't even know it. The highly processed carbs in all the bread, pasta and cereals we consume as Americans are causing the overweight and obesity epidemic!


What genes allow you to grow a third set of teeth?


Alright now, don't be too fancy, please, or I won't get any of it. I ask this because my grandpa grew a third set of teeth. He got and loss his baby teeth. Than he grew his adult and wisdom teeth. Than when he was about 30, he lost all his adult teeth (including his wisdom teeth), and regrew a whole, healthy, third set of teeth. But neither my mom nor my uncle got this, and I'm pretty sure neither me nor my brother are going to get that either. So I was just wondering, what genes and such would cause this?
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That gene is not yet identified.

Hyperdontia, or "supernumerary teeth" is believed to be hereditary as its more in the relatives of affected children, but it does not follow a simple Mendelian pattern. Studies have also shown that even though it's hard to tell what causes this, a portion of the developing tissue from early on may get pushed off and a tooth bud might split. It could also be caused by hyperactivity of the dental lamina since this is the precursor to a tooth.