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.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
An electrochemical process in which macromolecules or colloidal particles with a net electric charge migrate in a solution under the influence of an electric current.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
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.
Electrophoresis in which agar or agarose gel is used as the diffusion medium.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
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.
Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.
Gel electrophoresis in which the direction of the electric field is changed periodically. This technique is similar to other electrophoretic methods normally used to separate double-stranded DNA molecules ranging in size up to tens of thousands of base-pairs. However, by alternating the electric field direction one is able to separate DNA molecules up to several million base-pairs in length.
Electrophoresis in which a second perpendicular electrophoretic transport is performed on the separate components resulting from the first electrophoresis. This technique is usually performed on polyacrylamide gels.
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.
Colloids with a solid continuous phase and liquid as the dispersed phase; gels may be unstable when, due to temperature or other cause, the solid phase liquefies; the resulting colloid is called a sol.
The variety of all native living organisms and their various forms and interrelationships.
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)
The relationships of groups of organisms as reflected by their genetic makeup.
The sum of the weight of all the atoms in a molecule.
Water containing no significant amounts of salts, such as water from RIVERS and LAKES.
A highly-sensitive (in the picomolar range, which is 10,000-fold more sensitive than conventional electrophoresis) and efficient technique that allows separation of PROTEINS; NUCLEIC ACIDS; and CARBOHYDRATES. (Segen, Dictionary of Modern Medicine, 1992)
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A class in the phylum PROTEOBACTERIA comprised of chemoheterotrophs and chemoautotrophs which derive nutrients from decomposition of organic material.
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.
The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.
The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.
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.
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.
Elimination of ENVIRONMENTAL POLLUTANTS; PESTICIDES and other waste using living organisms, usually involving intervention of environmental or sanitation engineers.
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.
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.
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.
Separation of particles according to density by employing a gradient of varying densities. At equilibrium each particle settles in the gradient at a point equal to its density. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
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.
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.
Relating to the size of solids.
Electrophoresis applied to BLOOD PROTEINS.
A group of different species of microorganisms that act together as a community.
A selective pre- and post-emergence herbicide. (From Merck Index, 11th ed)
The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.
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)
A collective genome representative of the many organisms, primarily microorganisms, existing in a community.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
Low-density subclass of the high-density lipoproteins, with particle sizes between 8 to 13 nm.
A genus of gram-negative, ellipsoidal or rod-shaped bacteria whose major source of energy and reducing power is from the oxidation of ammonia to nitrite. Its species occur in soils, oceans, lakes, rivers, and sewage disposal systems.
One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.
Excrement from the INTESTINES, containing unabsorbed solids, waste products, secretions, and BACTERIA of the DIGESTIVE SYSTEM.
A nutritious food consisting primarily of the curd or the semisolid substance formed when milk coagulates.
Intermediate-density subclass of the high-density lipoproteins, with particle sizes between 7 to 8 nm. As the larger lighter HDL2 lipoprotein, HDL3 lipoprotein is lipid-rich.
Naturally occurring complex liquid hydrocarbons which, after distillation, yield combustible fuels, petrochemicals, and lubricants.
A group of gram-negative, anaerobic bacteria that is able to oxidize acetate completely to carbon dioxide using elemental sulfur as the electron acceptor.
A plant family of the order Rhizophorales, subclass Rosidae, class Magnoliopsida, that includes mangrove trees.
A class of lipoproteins of small size (4-13 nm) and dense (greater than 1.063 g/ml) particles. HDL lipoproteins, synthesized in the liver without a lipid core, accumulate cholesterol esters from peripheral tissues and transport them to the liver for re-utilization or elimination from the body (the reverse cholesterol transport). Their major protein component is APOLIPOPROTEIN A-I. HDL also shuttle APOLIPOPROTEINS C and APOLIPOPROTEINS E to and from triglyceride-rich lipoproteins during their catabolism. HDL plasma level has been inversely correlated with the risk of cardiovascular diseases.
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
The unconsolidated mineral or organic matter on the surface of the earth that serves as a natural medium for the growth of land plants.
The discarding or destroying of liquid waste products or their transformation into something useful or innocuous.
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.
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.
Substances which pollute the soil. Use for soil pollutants in general or for which there is no specific heading.
Genotypic differences observed among individuals in a population.
Biochemical identification of mutational changes in a nucleotide sequence.
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.
A rod-shaped, gram-positive, non-acid-fast, non-spore-forming, non-motile bacterium that is a genus of the family Bifidobacteriaceae, order Bifidobacteriales, class ACTINOBACTERIA. It inhabits the intestines and feces of humans as well as the human vagina.
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.
The immediate physical zone surrounding plant roots that include the plant roots. It is an area of intense and complex biological activity involving plants, microorganisms, other soil organisms, and the soil.
The study of microorganisms living in a variety of environments (air, soil, water, etc.) and their pathogenic relationship to other organisms including man.
A plant family of the order Myrtales, subclass Rosidae, class Magnoliopsida. They are mostly trees and shrubs growing in warm areas.
Chromatography on non-ionic gels without regard to the mechanism of solute discrimination.
Electrophoresis in which a pH gradient is established in a gel medium and proteins migrate until they reach the site (or focus) at which the pH is equal to their isoelectric point.
The rate dynamics in chemical or physical systems.
Refuse liquid or waste matter carried off by sewers.
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)
A family of gram-positive non-sporing bacteria including many parasitic, pathogenic, and saprophytic forms.
Centrifugation with a centrifuge that develops centrifugal fields of more than 100,000 times gravity. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
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)
Any of several processes in which undesirable impurities in water are removed or neutralized; for example, chlorination, filtration, primary treatment, ion exchange, and distillation. It includes treatment of WASTE WATER to provide potable and hygienic water in a controlled or closed environment as well as provision of public drinking water supplies.
A colorless alkaline gas. It is formed in the body during decomposition of organic materials during a large number of metabolically important reactions. Note that the aqueous form of ammonia is referred to as AMMONIUM HYDROXIDE.
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.
Large natural streams of FRESH WATER formed by converging tributaries and which empty into a body of water (lake or ocean).
Areas of the earth where hydrocarbon deposits of PETROLEUM and/or NATURAL GAS are located.
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.
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.
A class of lipoproteins of small size (18-25 nm) and light (1.019-1.063 g/ml) particles with a core composed mainly of CHOLESTEROL ESTERS and smaller amounts of TRIGLYCERIDES. The surface monolayer consists mostly of PHOSPHOLIPIDS, a single copy of APOLIPOPROTEIN B-100, and free cholesterol molecules. The main LDL function is to transport cholesterol and cholesterol esters to extrahepatic tissues.
An order of anaerobic methanogens in the kingdom EURYARCHAEOTA. There are two families: METHANOSARCINACEAE and Methanosaetaceae.
Anaerobic degradation of GLUCOSE or other organic nutrients to gain energy in the form of ATP. End products vary depending on organisms, substrates, and enzymatic pathways. Common fermentation products include ETHANOL and LACTIC ACID.
Electrophoresis in which discontinuities in both the voltage and pH gradients are introduced by using buffers of different composition and pH in the different parts of the gel column. The term 'disc' was originally used as an abbreviation for 'discontinuous' referring to the buffers employed, and does not have anything to do with the shape of the separated zones.
Adverse effect upon bodies of water (LAKES; RIVERS; seas; groundwater etc.) caused by CHEMICAL WATER POLLUTANTS.
Proteins found in any species of bacterium.
A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.
Electrophoresis in which a starch gel (a mixture of amylose and amylopectin) is used as the diffusion medium.
Deoxyribonucleic acid that makes up the genetic material of archaea.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
A chromatographic technique that utilizes the ability of biological molecules to bind to certain ligands specifically and reversibly. It is used in protein biochemistry. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Protein components on the surface of LIPOPROTEINS. They form a layer surrounding the hydrophobic lipid core. There are several classes of apolipoproteins with each playing a different role in lipid transport and LIPID METABOLISM. These proteins are synthesized mainly in the LIVER and the INTESTINES.
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)
Generally refers to the digestive structures stretching from the MOUTH to ANUS, but does not include the accessory glandular organs (LIVER; BILIARY TRACT; PANCREAS).
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.
A family of gram-positive bacteria found regularly in the mouth and intestinal tract of man and other animals, in food and dairy products, and in fermenting vegetable juices. A few species are highly pathogenic.
A highly miniaturized version of ELECTROPHORESIS performed in a microfluidic device.
Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.
Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.
Technique that utilizes low-stringency polymerase chain reaction (PCR) amplification with single primers of arbitrary sequence to generate strain-specific arrays of anonymous DNA fragments. RAPD technique may be used to determine taxonomic identity, assess kinship relationships, analyze mixed genome samples, and create specific probes.
The most abundant protein component of HIGH DENSITY LIPOPROTEINS or HDL. This protein serves as an acceptor for CHOLESTEROL released from cells thus promoting efflux of cholesterol to HDL then to the LIVER for excretion from the body (reverse cholesterol transport). It also acts as a cofactor for LECITHIN CHOLESTEROL ACYLTRANSFERASE that forms CHOLESTEROL ESTERS on the HDL particles. Mutations of this gene APOA1 cause HDL deficiency, such as in FAMILIAL ALPHA LIPOPROTEIN DEFICIENCY DISEASE and in some patients with TANGIER DISEASE.
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.
A phylum of bacteria comprised of three classes: Bacteroides, Flavobacteria, and Sphingobacteria.
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.
Deoxyribonucleic acid that makes up the genetic material of fungi.
Using MOLECULAR BIOLOGY techniques, such as DNA SEQUENCE ANALYSIS; PULSED-FIELD GEL ELECTROPHORESIS; and DNA FINGERPRINTING, to identify, classify, and compare organisms and their subtypes.
The measurement of the density of a material by measuring the amount of light or radiation passing through (or absorbed by) the material.
Presence of warmth or heat or a temperature notably higher than an accustomed norm.
The presence of bacteria, viruses, and fungi in food and food products. This term is not restricted to pathogenic organisms: the presence of various non-pathogenic bacteria and fungi in cheeses and wines, for example, is included in this concept.
A plant species of the genus CHRYSANTHEMUM, family ASTERACEAE. The flowers contain PYRETHRINS, cinerolones, and chrysanthemines which are powerful contact insecticides. Most in the old Pyrethrum genus are reclassified to TANACETUM; some to other ASTERACEAE genera.
A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).
A large group of bacteria including those which oxidize ammonia or nitrite, metabolize sulfur and sulfur compounds, or deposit iron and/or manganese oxides.
A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
Infections with BACTERIA of the order Bifidobacteriales. This includes infections in the genera BIFIDOBACTERIUM and GARDNERELLA, in the family Bifidobacteriaceae.
The pH in solutions of proteins and related compounds at which the dipolar ions are at a maximum.
Structural proteins of the alpha-lipoproteins (HIGH DENSITY LIPOPROTEINS), including APOLIPOPROTEIN A-I and APOLIPOPROTEIN A-II. They can modulate the activity of LECITHIN CHOLESTEROL ACYLTRANSFERASE. These apolipoproteins are low in atherosclerotic patients. They are either absent or present in extremely low plasma concentration in TANGIER DISEASE.
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.
A genus of motile or nonmotile gram-positive bacteria of the family Clostridiaceae. Many species have been identified with some being pathogenic. They occur in water, soil, and in the intestinal tract of humans and lower animals.
A thin-walled distention of the alimentary tract protruding just outside the body cavity in the distal end of the neck (esophagus), used for the temporary storage of food and water.
Lipid-protein complexes involved in the transportation and metabolism of lipids in the body. They are spherical particles consisting of a hydrophobic core of TRIGLYCERIDES and CHOLESTEROL ESTERS surrounded by a layer of hydrophilic free CHOLESTEROL; PHOSPHOLIPIDS; and APOLIPOPROTEINS. Lipoproteins are classified by their varying buoyant density and sizes.
Progressive, autosomal recessive, diffuse atrophy of the choroid, pigment epithelium, and sensory retina that begins in childhood.
A process facilitated by specialized bacteria involving the oxidation of ammonium to nitrite and nitrate.
Phylum of green nonsulfur bacteria including the family Chloroflexaceae, among others.
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.
Cultivation of natural faunal resources of water. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
A class in the phylum PROTEOBACTERIA comprised mostly of two major phenotypes: purple non-sulfur bacteria and aerobic bacteriochlorophyll-containing bacteria.
The usually underground portions of a plant that serve as support, store food, and through which water and mineral nutrients enter the plant. (From American Heritage Dictionary, 1982; Concise Dictionary of Biology, 1990)
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
RESTRICTION FRAGMENT LENGTH POLYMORPHISM analysis of rRNA genes that is used for differentiating between species or strains.
Microscopy using an electron beam, instead of light, to visualize the sample, thereby allowing much greater magnification. The interactions of ELECTRONS with specimens are used to provide information about the fine structure of that specimen. In TRANSMISSION ELECTRON MICROSCOPY the reactions of the electrons that are transmitted through the specimen are imaged. In SCANNING ELECTRON MICROSCOPY an electron beam falls at a non-normal angle on the specimen and the image is derived from the reactions occurring above the plane of the specimen.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).
A phylum of oxygenic photosynthetic bacteria comprised of unicellular to multicellular bacteria possessing CHLOROPHYLL a and carrying out oxygenic PHOTOSYNTHESIS. Cyanobacteria are the only known organisms capable of fixing both CARBON DIOXIDE (in the presence of light) and NITROGEN. Cell morphology can include nitrogen-fixing heterocysts and/or resting cells called akinetes. Formerly called blue-green algae, cyanobacteria were traditionally treated as ALGAE.
Chemical groups containing the covalent sulfur bonds -S-. The sulfur atom can be bound to inorganic or organic moieties.
Separation technique in which the stationary phase consists of ion exchange resins. The resins contain loosely held small ions that easily exchange places with other small ions of like charge present in solutions washed over the resins.
Conjugated protein-carbohydrate compounds including mucins, mucoid, and amyloid glycoproteins.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
Inorganic salts of sulfuric acid.
Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.
An anionic surfactant, usually a mixture of sodium alkyl sulfates, mainly the lauryl; lowers surface tension of aqueous solutions; used as fat emulsifier, wetting agent, detergent in cosmetics, pharmaceuticals and toothpastes; also as research tool in protein biochemistry.
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.
Encrustations, formed from microbes (bacteria, algae, fungi, plankton, or protozoa) embedding in extracellular polymers, that adhere to surfaces such as teeth (DENTAL DEPOSITS); PROSTHESES AND IMPLANTS; and catheters. Biofilms are prevented from forming by treating surfaces with DENTIFRICES; DISINFECTANTS; ANTI-INFECTIVE AGENTS; and antifouling agents.
The functional hereditary units of BACTERIA.
The class of all enzymes catalyzing oxidoreduction reactions. The substrate that is oxidized is regarded as a hydrogen donor. The systematic name is based on donor:acceptor oxidoreductase. The recommended name will be dehydrogenase, wherever this is possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the acceptor. (Enzyme Nomenclature, 1992, p9)
Technique involving the diffusion of antigen or antibody through a semisolid medium, usually agar or agarose gel, with the result being a precipitin reaction.
Articles of food which are derived by a process of manufacture from any portion of carcasses of any animal used for food (e.g., head cheese, sausage, scrapple).
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.
A family of gram-negative aerobic bacteria in the class BETA PROTEOBACTERIA, encompassing the acidovorans rRNA complex. Some species are pathogenic for PLANTS.
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.
Total mass of all the organisms of a given type and/or in a given area. (From Concise Dictionary of Biology, 1990) It includes the yield of vegetative mass produced from any given crop.
The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.
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)
Double-stranded nucleic acid molecules (DNA-DNA or DNA-RNA) which contain regions of nucleotide mismatches (non-complementary). In vivo, these heteroduplexes can result from mutation or genetic recombination; in vitro, they are formed by nucleic acid hybridization. Electron microscopic analysis of the resulting heteroduplexes facilitates the mapping of regions of base sequence homology of nucleic acids.
Transport proteins that carry specific substances in the blood or across cell membranes.
The section of the alimentary canal from the STOMACH to the ANAL CANAL. It includes the LARGE INTESTINE and SMALL INTESTINE.
Major structural proteins of triacylglycerol-rich LIPOPROTEINS. There are two forms, apolipoprotein B-100 and apolipoprotein B-48, both derived from a single gene. ApoB-100 expressed in the liver is found in low-density lipoproteins (LIPOPROTEINS, LDL; LIPOPROTEINS, VLDL). ApoB-48 expressed in the intestine is found in CHYLOMICRONS. They are important in the biosynthesis, transport, and metabolism of triacylglycerol-rich lipoproteins. Plasma Apo-B levels are high in atherosclerotic patients but non-detectable in ABETALIPOPROTEINEMIA.
Electrophoresis in which cellulose acetate is the diffusion medium.
Baked food product made of flour or meal that is moistened, kneaded, and sometimes fermented. A major food since prehistoric times, it has been made in various forms using a variety of ingredients and methods.
A genus of gram-positive bacteria in the family Lachnospiraceae that inhabits the RUMEN; LARGE INTESTINE; and CECUM of MAMMALS.
Live microbial DIETARY SUPPLEMENTS which beneficially affect the host animal by improving its intestinal microbial balance. Antibiotics and other related compounds are not included in this definition. In humans, lactobacilli are commonly used as probiotics, either as single species or in mixed culture with other bacteria. Other genera that have been used are bifidobacteria and streptococci. (J. Nutr. 1995;125:1401-12)
The blind sac or outpouching area of the LARGE INTESTINE that is below the entrance of the SMALL INTESTINE. It has a worm-like extension, the vermiform APPENDIX.
The systematic study of the complete complement of proteins (PROTEOME) of organisms.
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)
Substances or mixtures that are added to the soil to supply nutrients or to make available nutrients already present in the soil, in order to increase plant growth and productivity.
The study of the origin, structure, development, growth, function, genetics, and reproduction of organisms which inhabit the OCEANS AND SEAS.
Contaminated water generated as a waste product of human activity.
A genus of gram-negative, anaerobic, rod-shaped bacteria. Its organisms are normal inhabitants of the oral, respiratory, intestinal, and urogenital cavities of humans, animals, and insects. Some species may be pathogenic.
Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
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.
A plant genus of the family POACEAE that is the source of EDIBLE GRAIN. A hybrid with rye (SECALE CEREALE) is called TRITICALE. The seed is ground into FLOUR and used to make BREAD, and is the source of WHEAT GERM AGGLUTININS.
A genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in nature. Some species are pathogenic for humans, animals, and plants.
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.
A genus of gram-negative, aerobic, rod-shaped bacteria characterized by an outer membrane that contains glycosphingolipids but lacks lipopolysaccharide. They have the ability to degrade a broad range of substituted aromatic compounds.
The protein complement of an organism coded for by its genome.
Accumulations of solid or liquid animal excreta usually from stables and barnyards with or without litter material. Its chief application is as a fertilizer. (From Webster's 3d ed)
A large family of narrow-leaved herbaceous grasses of the order Cyperales, subclass Commelinidae, class Liliopsida (monocotyledons). Food grains (EDIBLE GRAIN) come from members of this family. RHINITIS, ALLERGIC, SEASONAL can be induced by POLLEN of many of the grasses.
Elements of limited time intervals, contributing to particular results or situations.
The species Oryctolagus cuniculus, in the family Leporidae, order LAGOMORPHA. Rabbits are born in burrows, furless, and with eyes and ears closed. In contrast with HARES, rabbits have 22 chromosome pairs.
The first stomach of ruminants. It lies on the left side of the body, occupying the whole of the left side of the abdomen and even stretching across the median plane of the body to the right side. It is capacious, divided into an upper and a lower sac, each of which has a blind sac at its posterior extremity. The rumen is lined by mucous membrane containing no digestive glands, but mucus-secreting glands are present in large numbers. Coarse, partially chewed food is stored and churned in the rumen until the animal finds circumstances convenient for rumination. When this occurs, little balls of food are regurgitated through the esophagus into the mouth, and are subjected to a second more thorough mastication, swallowed, and passed on into other parts of the compound stomach. (From Black's Veterinary Dictionary, 17th ed)
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
A type of ion exchange chromatography using diethylaminoethyl cellulose (DEAE-CELLULOSE) as a positively charged resin. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
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)
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.
Techniques used to separate mixtures of substances based on differences in the relative affinities of the substances for mobile and stationary phases. A mobile phase (fluid or gas) passes through a column containing a stationary phase of porous solid or liquid coated on a solid support. Usage is both analytical for small amounts and preparative for bulk amounts.
A species of gram-positive, rod-shaped bacteria isolated from the intestinal tract of humans and animals, the human mouth, and vagina. This organism produces the fermented product, acidophilus milk.
Methods of comparing two or more samples on the same two-dimensional gel electrophoresis gel.
The contents included in all or any segment of the GASTROINTESTINAL TRACT.
A technique that combines protein electrophoresis and double immunodiffusion. In this procedure proteins are first separated by gel electrophoresis (usually agarose), then made visible by immunodiffusion of specific antibodies. A distinct elliptical precipitin arc results for each protein detectable by the antisera.
A 513-kDa protein synthesized in the LIVER. It serves as the major structural protein of low-density lipoproteins (LIPOPROTEINS, LDL; LIPOPROTEINS, VLDL). It is the ligand for the LDL receptor (RECEPTORS, LDL) that promotes cellular binding and internalization of LDL particles.
Established cell cultures that have the potential to propagate indefinitely.
Bacteria which retain the crystal violet stain when treated by Gram's method.
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.
Cholesterol which is contained in or bound to high-density lipoproteins (HDL), including CHOLESTEROL ESTERS and free cholesterol.
Techniques to partition various components of the cell into SUBCELLULAR FRACTIONS.

In vitro communities derived from oral and gut microbial floras inhibit the growth of bacteria of foreign origins. (1/242)

 (+info)

Interplay between wheat cultivars, biocontrol pseudomonads, and soil. (2/242)

 (+info)

SDHB loss predicts malignancy in pheochromocytomas/sympathethic paragangliomas, but not through hypoxia signalling. (3/242)

 (+info)

Correlation of particular bacterial PCR-denaturing gradient gel electrophoresis patterns with bovine ruminal fermentation parameters and feed efficiency traits. (4/242)

 (+info)

Genotyping of fluconazole-resistant Candida albicans isolated from Uighurian people in Xinjing (China) using ALTS/RFLP and micro-TGGE method. (5/242)

Antifungal susceptibility tests were performed for 38 Candida albicans strains isolated from oral cavities of 43 Uighurian AIDS patients. Results showed that six isolates were resistant to fluconazole; one showed low susceptibility. We attempted to examine these strains molecular-epidemiologically, but 25S rDNA genotyping was insufficient for their discrimination. To estimate whether the origins of resistant strains were identical, we developed a new combination method of C. albicans tandem repeating units (ALTS)/RFLP and micro-temperature gradient gel electrophoresis (micro-TGGE). This new method was able to distinguish all seven strains. A suspected nosocomial infection was ruled out.  (+info)

Diversity of caecal bacteria is altered in interleukin-10 gene-deficient mice before and after colitis onset and when fed polyunsaturated fatty acids. (6/242)

 (+info)

Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis. (7/242)

 (+info)

Longitudinal investigation of the faecal microbiota of healthy full-term infants using fluorescence in situ hybridization and denaturing gradient gel electrophoresis. (8/242)

 (+info)

We hypothesize that sweet potato genotypes can influence the bacterial communities related to phosphate mineralization and nitrogen fixation in the rhizosphere. Tuberous roots of field-grown sweet potato from genotypes IPB-149, IPB-052, and IPB-137 were sampled three and six months after planting. The total community DNA was extracted from the rhizosphere and analyzed by Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) and quantitative real-time PCR (qPCR), based on the alkaline phosphatase coding gene (alp gene) and on the nitrogenase coding gene (nifH gene). The cluster analysis based on DGGE showed that plant age slightly influenced the bacterial community related to phosphate mineralization in the rhizosphere of IPB-137, although it did not affect the bacterial community related to nitrogen fixation. The statistical analysis of DGGE fingerprints (Permutation test, p ≤ 0.05) showed that nitrogen-fixing bacterial community of IPB-052 statistically differed from genotypes
There is increasing interest in good agriculture practices that address the issues of sustainability, reduction in inputs such as fertilizers and pesticides while maintaining crop yield and soil fertility. It is important that soil microbial diversity and function are not impaired by altered agricultural practice. In this study, as indicators of soil quality, the bacterial community structure was evaluated from a long-term field trial managed with conventional and low-input fertilization/pesticide regimes. The low-input plots under study received approximately one fifth less N fertilizer than the conventional-input plots, a maximum of half the recommended application rates of fungicides and pesticides and no externally added P source. A non-culturable approach was taken using polymerase chain reaction-denaturing gradient gel electrophoresis analysis of 16S rRNA and alkaline phosphomonoesterase [phosphatase] (ALP) genes in an attempt to relate bacterial community structure to respective field ...
Seagrass meadows represent one of the highest productive marine ecosystems and are of great ecological and economic values. Recently, they have been confronted with worldwide decline. Fungi play important roles in sustaining the ecosystem health as degraders of polycyclic aromatic hydrocarbons (PAHs), but fewer studies have been conducted in seagrass ecosystems. Hence, we investigated the dynamic variations of the fungal community succession under PAH stress in rhizosphere sediment of seagrasses Enhalus acoroides in this study. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), quantitative PCR (qPCR) and a clone library have been employed to analyze the fungal communitys shifts. Sequencing results of DGGE and the clone library showed that the predominant species belong to phyla Ascomycota and Basidiomycota. The abundance of three groups decreased sharply over the incubation period, whereas they demonstrated different fungal diversity patterns. Both the exposure time and the
Abstract. Constipation, a common and complex clinical symptom, is a predisposing factor for many serious diseases, such as gastrointestinal diseases, cardiovascular diseases and cancers. Some reports suggest that constipation is associated with gut microbiota, but the specific mechanism is unknown. To clarify how constipation interferes with the normal physiological function of organisms, 1H NMR profiles combined with polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16s rRNA gene sequencing were used to investigate the relationship among constipation, metabolism of gut microbiota and host. 27 urinary metabolites and 22 faecal metabolites were found to be associated with constipation, which affect the metabolism of energy, butyric acid, choline, amino acid and the functions of liver and kidney. 5 biomarkers were screened to diagnose the constipation based on the receiver operating characteristic (ROC) analysis. Meanwhile, the levels of Lactobacillus, ...
The first goal of the thesis is to summarize current knowledge on some of the most popular molecular biology methods used in wastewater treatment, fluorescent in situ hybridization (FISH) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Problems and solutions relating to these methods are also mentioned and are included in theoretical part of the presented work together with nitrogen cycle processes where particular attention is paid to nitrification because of its key role in efficient nitrogen removal process.. The experimental part of this thesis is divided into two chapters. The first part is focused on microbial analysis of nitrifying bacteria in activated sludge samples from five Czech sewage wastewater treatment plants (WWTPs). FISH analysis is used for identification and quantification of bacteria. Samples were collected twice a year for subsequent evaluation of the effect of season and temperature. The present study also investigated nitrification ...
The genus Pseudomonas is one of the best-studied bacterial groups in soil, and includes numerous species of environmental interest. Pseudomonas species play key roles in soil, for instance in biological control of soil-borne plant pathogens and in bioremediation of pollutants. A polymerase chain reaction-denaturing gradient gel electrophoresis system that specifically describes the diversity of Pseudomonas spp. in soil was developed. On the basis of this molecular method as well as cultivation-based approaches, the diversity of Pseudomonas species in soil under different agricultural regimes (permanent grassland, arable land either under rotation or under monoculture of maize) was studied. Both types of approaches revealed differences in the composition of Pseudomonas populations between the treatments. Differences between the treatments were also found based on the frequency of isolation of Pseudomonas strains with antagonistic properties against the soil-borne pathogen Rhizoctonia solani AG3. ...
Denaturing gradient gel electrophoresis analyses of the vertical distribution and diversity of Vibrio spp. populations in the Cariaco Basin ...
article{157352, author = {Boon, Nico and De Windt, Wim and Verstraete, Willy and Top, Eva}, issn = {0168-6496}, journal = {FEMS MICROBIOLOGY ECOLOGY}, language = {eng}, number = {2}, pages = {101--112}, title = {Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants.}, volume = {39}, year = {2002 ...
Shock loads of pollutants represent a significant hazard in wastewater treatment systems because they disturb the microbial community, resulting in loss of mineralization activity. To restore activity, time-consuming and costly measures must be taken. Therefore, as far as possible, shock loads are prevented from entering the plants by buffering tanks (1). Alternately, specialized inocula could be kept ready to protect the activated sludge microbial community from pollutant shock loads and thus allow continued functioning of the plant. However, to select strains which are appropriate for the pollutants in question and to ensure their effectiveness in bioprotection, an in-depth analysis of the community response to the shock, with and without inoculation with specialist inocula, is required.. Analysis of cloned ribosomal gene sequences directly retrieved from nature is the state-of-the-art technique for determining microbial community structure without bias introduced by cultivation (10). However, ...
Digital X Ray Film for sale, Quality Denaturing gradient gel electrophoresis on sale of Nanjing Chishun Science & Technology Co.,Ltd from China.
Author summary Dynamic changes in microbial communities play an important role in human health and disease. Specifically, deciphering how microbial species in a community interact with each other and their environment can elucidate mechanisms of disease, a problem typically investigated using tools from community ecology. Yet, such methods require measurements of absolute densities, whereas typical only provide estimates of relative abundances. We investigate methods for describing microbial dynamics in terms of relative abundances using approaches from machine learning and dynamical systems. Across three real datasets, we show that relative abundances are sufficient to describe compositional dynamics. Additionally, we show that models trained on relative abundances alone predict future compositions as well models trained on absolute abundances. Finally, we provide criteria for when direct effects, which typically can only be learned from absolute abundances, are recoverable for relative data. As a
...Bernd Eschweiler and Beate Kilb Institute for Water Research Schwert... Introduction Bacterial diversit... Materials and Methods DNA from s...,Microbial,Diversity,in,Ground,and,Surface,Water,Analyzed,by,Denaturing,Gradient,Gel,Electrophoresis,Using,the,DCode,System,biological,advanced biology technology,biology laboratory technology,biology device technology,latest biology technology
...Akira Ichikawa and Seiji Igarashi Tochigi Cancer Center... Introduction Denaturing gradien... The principle of DGGE is based on the fact that DNA duplexes melt at ... A PCR* product begins to melt from the region which has the lowest me...,Detection,of,p53,Gene,in,Breast,Cancer,by,Denaturing,Gradient,Gel,Electrophoresis,and,the,DCode,System,biological,advanced biology technology,biology laboratory technology,biology device technology,latest biology technology
Looking for online definition of denaturing gradient gel electrophoresis in the Medical Dictionary? denaturing gradient gel electrophoresis explanation free. What is denaturing gradient gel electrophoresis? Meaning of denaturing gradient gel electrophoresis medical term. What does denaturing gradient gel electrophoresis mean?
Abstract: A group-specific PCR-based denaturing gradient gel electrophoresis (DGGE) method was developed and combined with group-specific clone library analysis to investigate the diversity of the Clostridium leptum subgroup in human feces. PCR products (length, 239 bp) were amplified using C. leptum cluster-specific primers and were well separated by DGGE. The DGGE patterns of fecal amplicons from 11 human individuals revealed host-specific profiles; the patterns for fecal samples collected from a child for 3 years demonstrated the structural succession of the population in the first 2 years and its stability in the third year. A clone library was constructed with 100 clones consisting of 1,143-bp inserts of 16S rRNA gene fragments that were amplified from one adult fecal DNA with one forward universal bacterial primer and one reverse group-specific primer. Eighty-six of the clones produced the 239-bp C. leptum cluster-specific amplicons, and the remaining 14 clones did not produce these ...
This review focuses on the culture-independent methods available for the description of both bacterial and fungal communities in cheese. Important steps of the culture-independent strategy, which relies on bulk DNA extraction from cheese and polymerase chain reaction (PCR) amplification of selected sequences, are discussed. We critically evaluate the identification techniques already used for monitoring microbial communities in cheese, including PCR-denaturing gradient gel electrophoresis (PCR-DGGE), PCR-temporal temperature gradient gel electrophoresis (PCR-TTGE) or single-strand conformation polymorphism-PCR (SSCP-PCR) as well as some other techniques that remain to be adapted to the study of cheese communities. Further, our analysis draws attention to the lack of data available on suitable DNA sequences for identifying fungal communities in cheese and proposes some potential DNA targets.
Culture-dependent denaturing gradient gel electrophoresis (CD DGGE) fingerprinting of the 16S rRNA gene was developed to characterize mixed soil bacterial communities recovered on agar plates. CD DGGE analyses resulted in clear banding patterns of sufficient complexity (16-32 major bands) and reproducibility to investigate differences in bacterial communities in silt loam soils. Replicate CD DGGE profiles from plates inoculated with less-dilute samples (10 -3) had a higher band count and were more similar (72-77%) than profiles from more-dilute samples (51-61%). When CD DGGE fingerprints were compared to profiles constructed from 16S rRNA genes obtained from culture-independent clone libraries (CB DGGE profiles) 34% of the bands were unique to the culture-dependent profiles, 32% were unique to the culture-independent profiles and 34% were found in both communities. CD DGGE fingerprints of the 16S rRNA gene were used to compare culturable microbial communities in soils from an organic farm and ...
TY - JOUR. T1 - Microbial dynamics in RAS water: Effects of adding acetate as a biodegradable carbon-source. AU - Rojas-Tirado, Paula Andrea. AU - Pedersen, Per Bovbjerg. AU - Vadstein, Olav. AU - Pedersen, Lars-Flemming. PY - 2019. Y1 - 2019. N2 - This study evaluated the effect of an abrupt increase in easily biodegradable carbon (acetate) on bacterial activity and abundance in the water of recirculating aquaculture systems (RAS). The study included a batch experiment with RAS water only, and an experiment at system level where twelve pilot scale RAS were used. The batch experiment was made to test how acetate concentration would influence the microbial state in RAS water. Further, we wanted to observe if the selected microbial analysis tools would be able to detect these changes. The second experiment was carried out in twelve identical and independent RAS that had been operated under constant loading conditions (1.6 kg/m3 make-up water) for five months prior to the trial. The twelve RAS were ...
Drinking water utilities currently rely on a range of microbiological detection techniques to evaluate the quality of their drinking water (DW). However, microbiota profiling using culture-free 16S rRNA gene next-generation sequencing (NGS) provides an opportunity for improved monitoring of the microbial ecology and quality of DW. Here, we evaluated the utility of a previously validated microbiota profiling platform (MYcrobiota) to investigate the microbial dynamics of a full-scale, non-chlorinated DW distribution system (DWDS). In contrast to conventional methods, we observed spatial and temporal bacterial genus changes (expressed as operational taxonomic units - OTUs) within the DWDS. Further, a small subset of bacterial OTUs dominated with abundances that shifted across the length of the DWDS, and were particularly affected by a post-disinfection step. We also found seasonal variation in OTUs within the DWDS and that many OTUs could not be identified, even though MYcrobiota is specifically ...
Biofilms may be both beneficial - for example, when they form on plant roots to protect them from the contamination in the soil - and harmful. They are responsible for several chronic diseases that are difficult to treat, such as cystic fibrosis, endocarditis and cystitis ...
Sequence-dependent electrophoresis (SDE) fingerprinting techniques such as denaturing gradient gel electrophoresis (DGGE) have become commonplace in the field of molecular microbial ecology. The success of the SDE technology lays in the fact that it allows visualization of the predominant members of …
Prohibitin, an evolutionarily conserved gene situated on chromosome 17q21, was originally identified as a gene with antiproliferative properties. Studies of a Japanese population have shown prohibitin to be somatically mutated in a proportion of breast tumours. The gene has not heretofore been shown to have an association with inherited forms of breast or other cancers. In this thesis the technique of denaturing gradient gel electrophoresis (DGGE) was developed to analyse the complete coding sequence of the prohibitin gene from fragments generated by the polymerase chain reaction (PCR). This was achieved by examining the melting profiles of different regions of the prohibitin sequence with the melt map program MELT87. Four overlapping fragments were designed and subsequently amplified by reverse transcription PCR thus enabling analysis of the prohibitin cDNA sequence by DGGE. A further five fragments were developed for analysis of prohibitin from genomic DNA. These five fragments were generated ...
Gradient Makers, C.B.S. Scientific - Each (10 ML) : Designed for use in sucrose density gradient centrifugation, gradient gel electrophoresis, and li
Abstract: This study monitored structural shifts of gut microbiota of rats developing precancerous mucosal lesions induced by carcinogen 1,2-dimethyl hydrazine (DMH) treatment using PCR-denaturing gradient gel electrophoresis (DGGE) and 454 pyrosequencing on the 16S rRNA gene V3 region. Partial least square discriminant analysis of DGGE fingerprints showed that the gut microbiota structure of treated animals was similar to that of the controls 1 and 3 weeks after DMH treatments, but significantly different 7 weeks after DMH treatments, when a large number of aberrant crypt foci (ACF) developed in their colons. Martens uncertainty test, followed by anova test ( ...
Denaturing gradient gel electrophoresis (DGGE) of PCR amplicons of the ammonia monooxygenase gene (amoA) was developed and employed to investigate the diversity of ammonia-oxidizing bacteria (AOB) in four different habitats. The results were compared to DGGE of PCR-amplified partial 16S rDNA sequenc …
BIOACCUMULATION AND RISK ASSESSMENT OF BUTACHLOR IN THE SOIL ECOSYSTEM. ABSTRACT. Bioaccumulation of butachlor in plants following its application in the farm against weeds was evaluated using Phaseolus vulgaris (bean plant). Also, the risk of the consumption of such plants with some amount of bioaccumulated butachlor by non-target humans was studied using rabbits as animal model. The field experiments were carried out by crop cultivation with the application of 4.0 liters per hectare (2.6 kg a.i/ha), 4.4 liters per hectare (2.9 kga.i/ha) and 5.0 liters per hectare (3.2 kg a.i/ha) concentrations of butachlor at pre-emergence of the bean plant and the leaves of the plant were analyzed for the presence of butachlor residues using GC-MS , the result gave 0.10, 0.13 and 0.20 ppm bioaccumulated butachlor respectively for the concentrations of the butachlor applied to the plots of land. For 28 days three replicate groups of rabbits (4 per group) were fed the leaves containing these different ...
The ability of butachlor to induce cytotoxicity, clastogenicity and DNA damage was assessed using Chinese hamster ovary cells (CHO), Swiss mouse embryo fibroblasts (MEF) and human peripheral blood lymphocytes. A dose and time dependent loss of viability was evident upon treatment of CHO cells with butachlor. Cell killing to an extent of 50 % was observed when cells were treated with 16.2 μg/ml of butachlor for 24 hr or with 11.5 μg/ml for 48 hr. The herbicide induced micronuclei significantly in cultured lymphocytes at 24 and 48 hr of treatment suggesting that it is clastogenic. To understand the mechanism of cell death caused by butachlor, its effect on DNA strand breaks was studied in MEF. A concomitant decrease in cell viability was observed with increase in DNA strand breaks. Agarose gel electrophoresis of DNA from herbicide treated CHO cells and cytochemical staining indicate the induction of apoptosis by butachlor ...
Early Methanogenic Colonisation in the Faeces of Meishan and Yorkshire Piglets as Determined by Pyrosequencing Analysis. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Mentor: Jen Blank. Researched the microbial diversity in ophiolite-hosted coldsprings as an analog to martian environments. Microbe-bearing water samples were collected in Del Puerto Canyon, California. DNA was extracted from the samples followed by PCR, denaturing gradient gel electrophoresis, and DNA sequencing. Rock and water samples were evaluated for mineral/chemical content.. ...
emscope:(USP_PRODUCAO),scope:(USP_EBOOKS),scope:(PRIMO),scope:(USP),scope:(USP_EREVISTAS),scope:(USP_FISICO),primo_central_multiple_fe ...
Yamaha (XG Standard), Yamaha Tyros 1, Yamaha Tyros 2, Yamaha Tyros 3, Yamaha Tyros 4, Yamaha Tyros 5, Yamaha Genos, Yamaha PSR-S600, Yamaha PSR-S700, Yamaha PSR-S900, Yamaha PSR-S650, Yamaha PSR-S750, Yamaha PSR-S950, Yamaha PSR-S670, Yamaha PSR-S770, Yamaha PSR-S970, Yamaha PSR-S775, Yamaha PSR-S975, Yamaha PSR-A1000, Yamaha PSR-A2000, Yamaha PSR-A3000, Yamaha PSR-8000, Yamaha PSR-9000… ...
Yamaha (XG Standard), Yamaha Tyros 1, Yamaha Tyros 2, Yamaha Tyros 3, Yamaha Tyros 4, Yamaha Tyros 5, Yamaha Genos, Yamaha PSR-S600, Yamaha PSR-S700, Yamaha PSR-S900, Yamaha PSR-S650, Yamaha PSR-S750, Yamaha PSR-S950, Yamaha PSR-S670, Yamaha PSR-S770, Yamaha PSR-S970, Yamaha PSR-S775, Yamaha PSR-S975, Yamaha PSR-A1000, Yamaha PSR-A2000, Yamaha PSR-A3000, Yamaha PSR-8000, Yamaha PSR-9000… ...
This study constitutes the largest and deepest sampling of the composition of the elderly gut microbiota reported to date. The fecal microbiota of younger adults was previously shown by temperature gradient gel electrophoresis (TGGE) and phylochip (HitChip) analysis to be stable and individual-specific (7, 42). In the present study, all 161 of the time-0 microbiota samples could be clearly separated by UniFrac analysis (Fig. S5), and fine-detail analysis of genus confirmed individual-specific microbiota configurations. The HitChip study also found that temporally paired samples from elderly subjects were more similar than randomly compared samples from different subjects. However, the similarity of paired samples decreased from time 1 mo to time 2 mo. In the five elderly subjects that they investigated, the decrease in microbiota similarity was more pronounced in the Actinobacteria (42), whereas in younger adults, greatest divergence was recorded for Clostridium cluster IV. We observed a similar ...
TY - JOUR. T1 - Effects of vegetation and seasonality on bacterial communities in Amazonian dark earth and adjacent soils. AU - Lima, Amanda Barbosa. AU - Cannavan, Fabiana de Souza. AU - Germano, Marina Gomes. AU - Dini-Andreote, F.. AU - Paula, Alessandra Monteiro de. AU - Franchini, Julio Cezar. AU - Teixeira, Wenceslau Geraldes. AU - Tsai, Siu Mui. PY - 2015. Y1 - 2015. M3 - Article. JO - African Journal of Microbiology Research. JF - African Journal of Microbiology Research. SN - 1996-0808. ER - ...
We evaluated and optimized three rapid methods for extraction of high-quality DNA from carbonate-encrusted microbial communities using modern calcifying oncolites built by cyanobacteria and diatoms in a high-calcium freshwater river. Pulverization, acid (HCl) dissolution, and chelator-mediated (EDTA) dissolution of the carbonate matrix were used and optimized to liberate microbial cells from their mineral encasing. This was followed by cell lysis and DNA extraction and isolation. HCl dissolution yielded no measurable DNA, probably due to hydrolysis, whereas pulverization and EDTA dissolution yielded averages of 3.5 and 7.8 μg per gram of sample, respectively, of high molecular weight DNA. These DNA isolates could be used successfully for PCR-amplification of 16S rRNA gene segments (alleles) and subsequent fingerprinting of the cyanobacterial (including diatoms) and total bacterial communities through denaturing gradient gel electrophoresis (DGGE) separation. Fingerprints showed no differences
Résumé: Background Bacterial communities that are associated with tropical reef-forming corals are being increasingly recognized for their role in host physiology and health. However, little is known about the microbial diversity of the communities associated with temperate gorgonian corals, even though these communities are key structural components of the ecosystem. In the Northwestern Mediterranean Sea, gorgonians undergo recurrent mass mortalities, but the potential relationship between these events and the structure of the associated bacterial communities remains unexplored. Because microbial assemblages may contribute to the overall health and disease resistance of their host, a detailed baseline of the associated bacterial diversity is required to better understand the functioning of the gorgonian holobiont. Methodology/Principal Findings The bacterial diversity associated with the gorgonian Paramuricea clavata was determined using denaturing gradient gel electrophoresis, ...
In human microbiome analysis, sequencing of bacterial 16S rRNA genes has revealed a role for the gut microbiota in maintaining health and contributing to various pathologies. Novel community analysis techniques must be evaluated in terms of bias, sensitivity, and reproducibility and compared to existing techniques to be effectively implemented. Next- generation sequencing technologies offer many advantages over traditional fingerprinting methods, but this extensive evaluation required for the most efficacious use of data has not been performed previously. Illumina libraries were generated from the V3 region of the 16S rRNA gene of samples taken from 12 unique sites within the gastrointestinal tract for each of 4 individuals. Fingerprint data were generated from these samples and prominent bands were sequenced. Sequenced bands were matched with OTUs within their respective libraries. The results demonstrate that denaturing gradient gel electrophoresis (DGGE) represents relatively abundant ...
Diatoms associated with foraminifers of the genus Amphistegina were assessed using a combination of morphological and molecular techniques. These included: 1) microscopic identification of diatoms cultured from the host, 2) sequencing of portions of the small subunit of the ribosomal RNA gene (18S) and the large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase [i.e., RubisCO] gene (rbcL) from DNA extracted directly from the Amphistegina hosts and also from diatoms cultured from these hosts, and 3) denaturing gradient gel electrophoresis (DGGE) profiles of rbcL and internal transcribed spacer 1 (ITS1) PCR amplicons from DNA extracted directly from hosts and from cultures. Consistent with previous culture studies, multiple species of pennate diatoms of the genera Nitzschia, Fragilaria (including Nanofrustulum), Amphora, and Navicula, were cultured from |900 host specimens collected from |20 sites in the western Atlantic and four sites in the Pacific. Diatoms of the genus Nitzschia grew in
The federal Centers for Disease Control has announced it no longer will conduct inspections of sanitary conditions on cruise ships. The industry will become self-regulating. The only explanation is
Travelling is an exciting way to meet people and learn about different cultures. But you have to be careful. Travelling can expose you to disease and poor sanitary conditions. In this document, you will find practical information for safe and healthy travel. In a foreign country, just like at home, a little prevention goes a long way. - Uniprix
Interestingly, there was a significant drop in interindividual beta-diversity in a short period of time after birth (3-10 days), as assessed by mixed sequencing. Due to practical reasons, many temporal research studies of faecal microbiota face a trade-off between sampling frequency and number of individuals included in the study. To our knowledge, all temporal faecal microbiota studies to date that have extensive sampling during first weeks of life (Favier et al., 2003; Palmer et al., 2007; Koenig et al., 2011) have few individuals analysed, whereas studies with high sample numbers often have fewer or more infrequent time points (Yatsunenko et al., 2012). However, our results illustrate that significant differences in average bacterial composition and beta-diversity occur between 3 and 10 days of age. These data therefore suggest that to better understand the development of gut microbiota, gaps between sampling periods should be reduced, particularly for those studies that compare different ...
A method is presented to directly characterize the yeast diversity in wine fermentations using denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR) amplified ribosomal RNA genes. PCR-DGGE analysis of a commercial sweet wine fermentation clearly profiled the shifts in microbial diversity that occurred throughout the fermentation. Botrytis populations identified in press pan samples were absent from the settling tank and ensuing fermentation samples. Indigenous yeasts including Candida, Metschnikowia, and Pichia species were distinguished in the early stages of the fermentation prior to emergence of a Saccharomyces population. Surprisingly, the PCR-DGGE signature of Candida species persisted well into the fermentation long after the development of a dominant Saccharomyces population. By direct identification of yeast populations, PCR-DGGE can provide a rapid and comprehensive view of the microbial diversity present in wine fermentations without the necessity for ...
Bacterial vaginosis (BV) is one of the most common infections in women of reproductive age. Clinical studies have shown an association among BV and abnormal pregnancy, pelvic inflammatory disease and an increased risk of sexually transmitted infections, including HIV.1 This disorder was first described in 1914 by Curtis as a white discharge syndrome2 and despite the decades of research we have only limited, and clearly not conclusive, evidence of microbial cause of BV, mechanism of disease and effective treatment.. The development of molecular techniques such as Denaturing Gradient Gel Electrophoresis (DGGE) and DNA sequencing produced a clearer picture of the ...
The gut microbiota (GM) may influence disease expression in several animal models for inflammatory diseases. It may therefore seem reasonable to pursue reduction in the number of animals used for individual studies by reducing the variation in the GM. Previous studies have shown that the composition of the GM is related to genetics to a certain extent. We hypothesized that the GM similarity in a group of mice born by mothers not being sisters would be lower than that in a group born by mothers being sisters. The lower similarity could lead to clustering of the GM of mice born by non-sisters according to their mothers, while such clustering would not be visible if the mothers were sisters. We used 16S rRNA gene (V3 region) polymerase chain reaction-derived amplicon profiling by denaturing gradient gel electrophoresis (DGGE) to study the GM composition in caecum samples of 33 eight-week-old C57BL/6Sca mice from a breeding set-up with dam breeders that were sisters, as well as caecum samples of 35 ...
Microbial diversity associated with odor modification for production of fertilizers from chicken litter. Distribution of bacterioplankton in meromictic lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA
The bacterial microflora of maple sap and biofilms in collection system tubing were studied through the use of bacterial counts, scanning electron microscopy (SEM) of surfaces and the analysis of 16S rRNA gene by denaturing gradient gel electrophoresis (DGGE). Samples were taken at five times during the 2002 and 2003 seasons in order to follow the changes in the microflora of this complex ecosystem. Bacterial counts showed the growth of bacterial populations as the season advanced. These populations were mainly composed of psychrotrophic bacteria and Pseudomonas spp. SEM results confirmed the suspected presence of biofilms on the inner surfaces of tubing samples. Bacterial colonization and biofilm formation progressively increased during the season for both lateral and main line surfaces, and biofilms were mainly composed of rod shape bacteria. The bacterial microflora profiles obtained for sap and corresponding biofilm by DGGE showed up to 12 major bands. The Shannon-Weaver index of diversity ...
Disease, Ixodes, Tick, Bacteria, Gene, Microbiota, rRNA Gene, Bite, Lyme Disease, Report, Risk, River, Ticks, Acetic Acid, Aedes, Animal, Anopheles, Anopheles Gambiae, Cell, Denaturing Gradient Gel Electrophoresis
The IW Series Bench Scales is a water-proof digital platform scale, constructed of stainless steel, conforms to IP-67 requirements, even allowing washdown for highest sanitary conditions.
Unless you have family in India, or have spent a lot of time there before retiring, the chaos, lack of sanitary conditions and gross disparities between rich and poor could send you into culture shock. On the other hand, living there is a chance to cut your living costs significantly and enjoy exotic sights like Hawa Mahal in Jaipur (shown here). 15 Top Foreign Retirement Havens - pg.9
Hi Stephanie! You could use a simple PAGE with just a modified acrylamid solution (T: 49.5%, C:3%). The final acrylamide concentration should be about 6 to 8 %. To determine the best concentration, I would simply run a gradient gel from 10 to 4%. Hope it helps! Anne , , -- , , -- ...
"Analysis of yeast and archaeal population dynamics in kimchi using denaturing gradient gel electrophoresis". International ... "Analysis of yeast and archaeal population dynamics in kimchi using denaturing gradient gel electrophoresis". International ... "Analysis of kimchi microflora using denaturing gradient gel electrophoresis". International Journal of Food Microbiology. 102 ( ... Bacterial Community Changes in Fermenting Kimchi at Two Different Temperatures Using a Denaturing Gradient Gel Electrophoresis ...
Detection and Localization of Single Base Changes by Denaturing Gradient Gel Electrophoresis. Methods in Enzymology. 155. pp. ... In the context of a single isolated region of DNA, denaturing gradient gels and temperature gradient gels can be used to detect ... a process known as temperature gradient gel electrophoresis. Methods of DNA analysis based on melting temperature have the ... experimental analysis of necrogenic and non-necrogenic variants by temperature-gradient gel electrophoresis". Nucleic Acids ...
1999). "Screening for mutations in the uroporphyrinogen decarboxylase gene using denaturing gradient gel electrophoresis. ...
1995). "Seven new mutations in hMSH2, an HNPCC gene, identified by denaturing gradient-gel electrophoresis". Am. J. Hum. Genet ...
"Molecular analysis of 16 Turkish families with DHPR deficiency using denaturing gradient gel electrophoresis (DGGE)". Hum Genet ...
... of novel rhodopsin mutations associated with retinitis pigmentosa by GC-clamped denaturing gradient gel electrophoresis". ...
"Investigating the fermentation of cocoa by correlating Denaturing Gradient Gel Electrophoresis profiles and Near Infrared ...
Denaturing gradient gel electrophoresis (DGGE) is a microbial fingerprinting technique that separates amplicons of roughly the ... affecting denaturing gradient gel electrophoresis profiles". FEMS Microbiology Letters. 312 (1): 55-62. doi:10.1111/j.1574- ... "Analysis of β-subgroup Proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis ... "Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction- ...
Its use in denaturing gradient gel electrophoresis methods for broad-range mutation analysis has also been described. TAE has ... in gel composition and electrophoretic conditions for broad-range mutation analysis by denaturing gradient gel electrophoresis ... TBE buffer LB buffer Ogden, R.C., and Adams, D.A., (1987) Electrophoresis in agarose and acrylamide gels. Methods Enzymol., 152 ... In molecular biology it is used in agarose electrophoresis typically for the separation of nucleic acids such as DNA and RNA. ...
"Denaturing Gradient Gel Electrophoresis as a Tool To Determine Batch Similarity of Probiotic Cultures of Porcine Cecal Bacteria ...
The technique is similar in some aspects to temperature gradient or denaturing gradient gel electrophoresis (TGGE and DGGE). ... The DNA fragments produced by the digest are then separated by length through a process known as agarose gel electrophoresis ... and the resulting restriction fragments are then separated by gel electrophoresis according to their size. Although now largely ... It requires a large amount of sample DNA, and the combined process of probe labeling, DNA fragmentation, electrophoresis, ...
Qualitative analysis by denaturing gradient gel electrophoresis". Applied and Environmental Microbiology. 65 (6): 2478-84. doi: ...
... of Spoilage-Related Bacteria in Pasteurized Milk during Refrigeration by PCR and Denaturing Gradient Gel Electrophoresis". ... that those few enzymes that are present in raw milk and denatured in pasteurized milk are ultimately degraded in the low pH ...
Smalla, K., Berg, G. et al.: Bulk and rhizosphere soil bacterial communities studied by Denaturing Gradient Gel Electrophoresis ...
... of the microbial communities involved in the soy sauce manufacturing process by PCR-denaturing gradient gel electrophoresis". ...
"Single-strand conformational polymorphism and denaturing gradient gel electrophoresis in screening for variegate porphyria: ...
Finkelstein JE, Francomano CA, Brusilow SW, Traystman MD (June 1990). "Use of denaturing gradient gel electrophoresis for ...
"Analysis of fungal communities on historical church window glass by denaturing gradient gel electrophoresis and phylogenetic ... pannorum is unique in its ability to grow on silica gel in the absence of organic material. It produces a range of ...
April 2004). "Polymerase chain reaction denaturing gradient gel electrophoresis analysis of the N2-fixing bacterial diversity ...
"Analysis of fungal communities on historical church window glass by denaturing gradient gel electrophoresis and phylogenetic ...
... gap junction gene mutations in patients with hypoplastic left heart syndrome by denaturing gradient gel electrophoresis (DGGE ...
Levan-type Exopolysaccharides from Lactobacilli and Non-digestible Carbohydrates Using Denaturing Gradient Gel Electrophoresis ... In hair care products, levan acts to form a film which creates a hair holding effect utilized in various gels and mousses. ...
"Molecular Profiling of the Clostridium leptum Subgroup in Human Fecal Microflora by PCR-Denaturing Gradient Gel Electrophoresis ...
1992). "Rapid identification by denaturing gradient gel electrophoresis of mutations in the gamma-globin gene promoters in non- ...
... bifidobacteria from breast milk and assessment of the bifidobacterial population by PCR-denaturing gradient gel electrophoresis ... Almost all medicines pass into breastmilk in small amounts by a concentration gradient. The amount of drug bound by maternal ...
... bifidobacteria from breast milk and assessment of the bifidobacterial population by PCR-denaturing gradient gel electrophoresis ...
Denaturing Gradient Gel Electrophoresis, and Seed Germination Assay". Environmental Toxicology and Chemistry. 19 (8): 2154-160 ... One example is the use of a known concentration gradient of Tri-n-butylin to assess PICT in periphyton. Tolerance patterns ... The aquariums were dosed with different concentrations of herbicide to get a gradient of long-term (14-day) contaminant ... The samples thus represent a gradient in contaminant concentration, assuming that the contaminant becomes more dilute with ...
PCR denaturing gradient gel electrophoresis is used to identify the 16S rRNA, and then the sequences are run through 16S rDNA ...
Detection and Localization of Single Base Changes by Denaturing Gradient Gel Electrophoresis. Methods in Enzymology. Methods in ... experimental analysis of necrogenic and non-necrogenic variants by temperature-gradient gel electrophoresis. Nucleic Acids ...
... bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis ... under different land management regimens by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis ...
Investigating the fermentation of cocoa by correlating Denaturing Gradient Gel Electrophoresis profiles and Near Infrared ...
These denaturants have been employed to make Denaturing Gradient Gel Electrophoresis gel (DGGE), which promotes denaturation of ... "Denaturing Polyacrylamide Gel Electrophoresis of DNA & RNA". Electrophoresis. National Diagnostics. Retrieved 13 October 2016. ... of formamide denatured nucleic acids are similar to those of heat-denatured nucleic acids.[22][24][25] Therefore, depending on ... chemically denaturing DNA can provide a gentler procedure for denaturing nucleic acids than denaturation induced by heat. ...
During electrophoresis in a discontinuous gel system, an ion gradient is formed in the early stage of electrophoresis that ... Native gels, also known as non-denaturing gels, analyze proteins that are still in their folded state. Thus, the ... SDS polyacrylamide gel electrophoresis (in short: gel electrophoresis, PAGE, or SDS-electrophoresis), free-flow electrophoresis ... Affinity electrophoresis Electroblotting Electrofocusing Polyacrylamide gel electrophoresis, PAGE, or gel electrophoresis ...
For electrophoresis, for example, proteins are classically treated with SDS to denature the native tertiary and quaternary ... shower gel, hair conditioners (after shampoo), toothpastes. Surfactants are used in firefighting and pipelines (liquid drag ... Reduced gradient bubble model. *Thalmann algorithm. *Thermodynamic model of decompression. *Varying Permeability Model ... octyl glucoside or dodecyl maltoside are used to solubilize membrane proteins such as enzymes and receptors without denaturing ...
Once these sequences have been amplified, they are resolved either through gel electrophoresis or capillary electrophoresis, ... DNA is repeatedly denatured at a high temperature to separate the double strand, then cooled to allow annealing of primers and ... Kit, S. (1961). "Equilibrium sedimentation in density gradients of DNA preparations from animal tissues". J. Mol. Biol. 3 (6): ... If the DNA was resolved by gel electrophoresis, the DNA can be visualized either by silver staining (low sensitivity, safe, ...
... of novel rhodopsin mutations associated with retinitis pigmentosa by GC-clamped denaturing gradient gel electrophoresis". Am. J ...
Ethidium bromide-stained PCR products after gel electrophoresis. Two sets of primers were used to amplify a target sequence ... If the polymerase used was heat-susceptible, it would denature under the high temperatures of the denaturation step. Before the ... Instead of repeatedly heating and cooling the PCR mixture, the solution is subjected to a thermal gradient. The resulting ... That is, their base pair length should be different enough to form distinct bands when visualized by gel electrophoresis. ...
... of novel rhodopsin mutations associated with retinitis pigmentosa by GC-clamped denaturing gradient gel electrophoresis.". Am. ...
... is a powerful tool used to analyze RNA samples. When polyacrylamide gel is denatured after ... The gel mobility is defined as the rate of migration traveled with a voltage gradient of 1V/cm and has units of cm2/sec/V.[7] ... Polyacrylamide gels are composed of a stacking gel and separating gel. Stacking gels have a higher porosity relative to the ... After the gel is polymerized the comb can be removed and the gel is ready for electrophoresis. ...
It is essentially a combination of denaturing RNA gel electrophoresis, and a blot. In this process RNA is separated based on ... prior to sucrose gradients, viscometry was used. Aside from their historical interest, it is often worth knowing about older ... In agarose gel electrophoresis, DNA and RNA can be separated on the basis of size by running the DNA through an electrically ... Gel electrophoresis is one of the principal tools of molecular biology. The basic principle is that DNA, RNA, and proteins can ...
Various techniques including DGGE (Denaturing Gradient Gel Electrophoresis), DHPLC (Denaturing High Performance Liquid ... electrophoresis. This avoids the resolution limitations of multiplex PCR. Because the forward primer used for probe ...
These denaturants have been employed to make Denaturing Gradient Gel Electrophoresis gel (DGGE), which promotes denaturation of ... "Denaturing Polyacrylamide Gel Electrophoresis of DNA & RNA". Electrophoresis. National Diagnostics. Retrieved 13 October 2016. ... Therefore, depending on the desired effect, chemically denaturing DNA can provide a gentler procedure for denaturing nucleic ... of formamide denatured nucleic acids are similar to those of heat-denatured nucleic acids. ...
That is, their base pair length should be different enough to form distinct bands when visualized by gel electrophoresis. ... If the polymerase used was heat-susceptible, it would denature under the high temperatures of the denaturation step. Before the ... Instead of repeatedly heating and cooling the PCR mixture, the solution is subjected to a thermal gradient. The resulting ... agarose gel electrophoresis may be employed for size separation of the PCR products. The size of the PCR products is determined ...
Lerman's last major effort, begun with Stuart Fischer at SUNY, was the invention of denaturing gradient gel electrophoresis ( ... "DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: Correspondence with ... "Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis" Cell 1979, Jan;16(1), 191- ...
Molecular assays (randomly amplified polymorphic DNA PCR assay, denaturing gradient gel electrophoresis analysis, and ...
Silver staining is also used in temperature gradient gel electrophoresis. Argentaffin cells reduce silver solution to metallic ... direct way to stain denatured collagens of any type (Type I, II, IV, etc.) regardless if they were damaged or degraded via ... Biological staining is also used to mark cells in flow cytometry, and to flag proteins or nucleic acids in gel electrophoresis ... It is often used in gel electrophoresis. Cresyl violet stains the acidic components of the neuronal cytoplasm a violet colour, ...
Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis ... Her research has shown how microbes respond to different environmental gradients and how they contribute and control ... ecosystems where microbes are significantly more diverse than originally surmised and exhibit strong seasonal gradients in ...
... detection by denaturing gradient gel electrophoresis of a PCR product". American Journal of Human Genetics. 50 (6): 1291-300. ...
... (TGGE) and denaturing gradient gel electrophoresis (DGGE) are forms of electrophoresis ... Denaturing gradient gel electrophoresis (DGGE) works by applying a small sample of DNA (or RNA) to an electrophoresis gel that ... 1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain ... By comparing the melting behavior of the polymorphic DNA fragments side-by side on denaturing gradient gels, it is possible to ...
A new, improved protocol for denaturing gradient gel electrophoresis (DGGE), to screen for point mutations in genomic DNA, is ... Detection of p53 point mutations by double-gradient, denaturing gradient gel electrophoresis Electrophoresis. 1997 Dec;18(15): ... A new, improved protocol for denaturing gradient gel electrophoresis (DGGE), to screen for point mutations in genomic DNA, is ... In this technique, to the primary, denaturing gradient (typically 30-80% or 40-80% urea/formamide) a secondary gradient, ...
Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ... Denaturing Gradient Gel Electrophoresis (DGGE) is such a technique that attempts to do this. This molecular biology approach is ... 16S rDNA PCR and denaturing gradient gel electrophoresis; a single generic test for detecting and differentiating Mycoplasma ... 16S rDNA PCR and denaturing gradient gel electrophoresis; a single generic test for detecting and differentiating Mycoplasma ...
Denaturing gradient gel electrophoresis as a tool for the identification of commercially important Crassostrea oysters in China ...
Denaturing gradient gel electrophoresis (DGGE) of PCR amplicons of the ammonia monooxygenase gene (amoA) was developed and ... Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria J Microbiol ... Denaturing gradient gel electrophoresis (DGGE) of PCR amplicons of the ammonia monooxygenase gene (amoA) was developed and ... Some phylogenetic information could be deduced from the position of amoA bands in DGGE gels. The Nitrosomonas-like sequences ...
Detection of eleven mutations causing acute intermittent porphyria using denaturing gradient gel electrophoresis. ... Denaturing gradient gel electrophoresis for rapid detection of latent carriers of a subtype of acute intermittent porphyria ... Detection and localisation of single base changes by denaturing gradient gel electrophoresis. Methods Enzymol 155:501-527Google ... Computational simulation of DNA melting and its application to denaturing gradient gel electrophoresis. Methods Enzymol 155:482 ...
Community structure was analyzed by denaturing gradient gel electrophoresis (DGGE) of the PCR and RT-PCR amplified V3 region of ... Analyses of microbial activity in biomass-recycle reactors using denaturing gradient gel electrophoresis of 16S rDNA and 16S ...
Quality Denaturing gradient gel electrophoresis on sale of Nanjing Chishun Science & Technology Co.,Ltd from China. ... Denaturing Gradient Gel Electrophoresis, Time Temperature Gradient Gel Electrophoresis, Gel electrophoresis and Image Analysis ... Denaturing gradient gel electrophoresis DGGE denaturing gradient gel electrophoresis system which is our latest patent product ... among which Denaturing Gradient Gel Electrophoresis and Time Temperature Gradient Gel Electrophoresis are domestically original ...
What is denaturing gradient gel electrophoresis? Meaning of denaturing gradient gel electrophoresis medical term. What does ... Looking for online definition of denaturing gradient gel electrophoresis in the Medical Dictionary? denaturing gradient gel ... denaturing gradient gel electrophoresis. Also found in: Acronyms. denaturing gradient gel electrophoresis (DGGE). ... Denaturing gradient gel electrophoresis , definition of denaturing gradient gel electrophoresis by Medical dictionary https:// ...
Denaturing,Gradient,Gel,Electrophoresis,and,the,DCode,System,biological,advanced biology technology,biology laboratory ... Akira Ichikawa and Seiji Igarashi Tochigi Cancer Center... Introduction Denaturing gradien... The principle of DGGE is based on ... and parallel gradient gels. PERPENDICULAR GRADIENT GEL ANALYSIS A 7.5 x 10 cm, 1 mm thick, 25% to 65% denatured gradient gel ... PARALLEL GRADIENT GEL ANALYSIS A 16 x 16 cm, 1 mm thick, 45% to 60% denatured gradient gel was made using 6% aclylamide/bis ( ...
Denaturing,Gradient,Gel,Electrophoresis,Using,the,DCode,System,biological,advanced biology technology,biology laboratory ... A Multiple Mutation Model System as a Test Development and Training Tool for Denaturing Gradient Gel Electrophoresis. 10. ... Detection of Mutations in the Fas Antigen of Lymphoma Tumors by RT-PCR and Denaturing Gradient Gel Electrophoresis. ... Microbial Diversity in Ground and Surface Water Analyzed by Denaturing Gradient Gel Electrophoresis Using the DCode System ...
Screening for human mitochondrial DNA polymorphisms with denaturing gradient gel electrophoresis. Hum Genet. 1996 Aug; 98(2): ... Screening for human mitochondrial DNA polymorphisms with denaturing gradient gel electrophoresis.. *See All Pages ...
16S rRNA gene-based identification of bacteria in postoperative endophthalmitis by PCR- Denaturing Gradient Gel Electrophoresis ... Denaturing gradient gel electrophoresis of PCR-amplified gki genes: a new technique for tracking streptococci. J. Clin. ... PCR Denaturing Gradient Gel Electrophoresis (PCR DGGE) is a sensitive technique based on differential melting and separation of ... Investigation of an anaerobic microbial community associated with a corneal ulcer by denaturing gradient gel electrophoresis ...
Palabras clave : Agaricus bisporus; bacteria; casing; denaturing gradient gel electrophoresis. · texto en Inglés · Inglés ( pdf ... using denaturing gradient gel electrophoresis. S. Afr. j. sci. [online]. 2010, vol.106, n.9-10, pp.1-6. ISSN 1996-7489. ... were examined using denaturing gradient gel electrophoresis (DGGE) at three phases of mushroom growth: (1) casing, (2) pinning ...
Denaturing gradient gel electrophoresis The DGGE was performed using a D-Code (Bio-Rad, Johannesburg, South Africa) universal ... Fingerprinting molecular techniques such as denaturing gradient gel electrophoresis (DGGE) provide more accurate and detailed ... Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction- ... were examined using denaturing gradient gel electrophoresis (DGGE) at three phases of mushroom growth: (1) casing, (2) pinning ...
A fungi-specific PCR-denaturing gradient gel electrophoresis (DGGE) system was established to monitor the development of the ... and Weissella species in human feces by using group-specific PCR primers and denaturing gradient gel electrophoresis. Appl. ... and Population Dynamics of Yeasts in Sourdough Fermentation Processes by PCR-Denaturing Gradient Gel Electrophoresis. ... fermentation process in four continuously propagated sourdoughs by a LAB-specific PCR-denaturing gradient gel electrophoresis ( ...
1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in ... Bifidobacterial Diversity in Human Feces Detected by Genus-Specific PCR and Denaturing Gradient Gel Electrophoresis. Reetta M. ... 1987) Detection and localization of single base changes by denaturing gradient gel electrophoresis. Methods Enzymol. 155:501- ... 1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain ...
PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative real-time PCR (qRTi-PCR) analyses of breast milk ... Immediately after the denaturing gel was poured (28-ml gradient volume), a 7.5-ml stacking gel without denaturing chemicals was ... Bifidobacterial communities in breast milk were assessed by PCR-denaturing gradient gel electrophoresis (PCR-DGGE), and their ... Isolation of Bifidobacteria from Breast Milk and Assessment of the Bifidobacterial Population by PCR-Denaturing Gradient Gel ...
PCR amplified DNA was separated by Denaturing Gradient Gel Electrophoresis (DGGE) analysis. Comparative evaluation of primers ... Keywords: Petrochemical industrial effluent, polymerase chain reaction, Denaturing gradient gel electrophoresis (DGGE), ... for Decontaminating Eleme Petrochemical Industrial Effluent Using 16s RDNA PCR Denaturing Gradient Gel Electrophoresis * CU ... Denaturing gradient gel ratio of 20% : 80% was most suitable for differentiation of bacterial profiles. Sequencing and ...
Spatial variation of bacterial community composition near the Luzon strait assessed by polymerase chain reaction-denaturing ... denaturing gradient gel electrophoresis (DGGE), redundancy analysis (RDA). ... community composition near the Luzon strait assessed by polymerase chain reaction-denaturing gradient gel electrophoresis ( ... estimate the spatial variation of surface water bacterial community composition using denaturing gradient gel electrophoresis ( ...
Abstract: A group-specific PCR-based denaturing gradient gel electrophoresis (DGGE) method was developed and combined with ... Molecular Profiling of the Clostridium leptum Subgroup in Human Fecal Microflora by PCR-Denaturing Gradient Gel Electrophoresis ... Molecular Profiling of the Clostridium leptum Subgroup in Human Fecal Microflora by PCR-Denaturing Gradient Gel Electrophoresis ...
Denaturing gradient gel electrophoresis (DGGE) is one of the most commonly used molecular tools to study complex microbial ... article{1203969, abstract = {Denaturing gradient gel electrophoresis (DGGE) is one of the most commonly used molecular tools to ... HEALTH, COMMUNITIES, MICROBIOTA, INFLAMMATORY-BOWEL-DISEASE, 16S RIBOSOMAL-RNA, denaturing gradient gel electrophoresis, ... High-throughput method for comparative analysis of denaturing gradient gel electrophoresis profiles from human fecal samples ...
Denaturing gradient gel electrophoresis analyses of the vertical distribution and diversity of Vibrio spp. populations in the ... Denaturing gradient gel electrophoresis analyses of the vertical distribution and diversity of Vibrio spp. populations in the ...
Boon N, De Windt W, Verstraete W, Top E. Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group- ... Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis ... "Evaluation of Nested PCR-DGGE (denaturing Gradient Gel Electrophoresis) with Group-specific 16S rRNA Primers for the Analysis ... "Evaluation of Nested PCR-DGGE (denaturing Gradient Gel Electrophoresis) with Group-specific 16S rRNA Primers for the Analysis ...
Two-step denaturing gradient gel electrophoresis (2S-DGGE), a gel-based strategy to capture full-length 16S rRNA gene sequences ... Wang, S., He, J. (2012-09). Two-step denaturing gradient gel electrophoresis (2S-DGGE), a gel-based strategy to capture full- ... two-step denaturing gradient gel electrophoresis (2S-DGGE), is developed to obtain full-length 16S rRNA gene sequences. 2S-DGGE ...
University of Toledo Denaturing Gradient Gel Electrophoresis (DGGE) Background Information Denaturing gradient gel ... University of Toledo Denaturing Gradient Gel Electrophoresis (DGGE) Background Information Denaturing gradient gel ... Introduction to Gel Electrophoresis Experiment 1 Introduction to Gel Electrophoresis Gel Electrophoresis is a method used by ... RAINBOW ELECTROPHORESIS 1 An Introduction to Gel Electrophoresis RAINBOW ELECTROPHORESIS 1 An Introduction to Gel ...
... armandi at different developmental stages using a culture-independent method involving PCR-denaturing gradient gel ... electrophoresis (DGGE). Analysis of PCR-amplified 16S rRNA gene fragments of bacteria from the guts of larvae, pupae, and male ... Figure 1. Denaturing gradient gel electrophoresis (DGGE) profiles of nested PCR-amplified 16Sr RNA gene fragments of bacteria ... Figure 1. Denaturing gradient gel electrophoresis (DGGE) profiles of nested PCR-amplified 16Sr RNA gene fragments of bacteria ...
... and denaturing gradient gel electrophoresis (DGGE). CARD-FISH cell counts and qPCR measurements showed the presence of Bacteria ... and denaturing gradient gel electrophoresis (DGGE). CARD-FISH cell counts and qPCR measurements showed the presence of Bacteria ... Denaturing Gradient Gel Electrophoresis. For DGGE, 16S rRNA genes of Bacteria were amplified using the primer set 533F (5′- ... Figure 5. Denaturing gradient gel electrophoresis photographs showing the 16S rRNA gene sequence diversity of Bacteria (left) ...
Methylation-specific PCR (MSP) and bisulfite denaturing gradient gel electrophoresis (DGGE). Methylation of the CpG island in ... Abrams ES, Stanton VP . Use of denaturing gradient gel electrophoresis to study conformational transitions in nucleic acids ... Detection of mutations in GC-rich DNA by bisulphite denaturing gradient gel electrophoresis Nucleic Acids Res 1998 26: 1548- ... denaturing gradient gel (100% denaturant = 7 mol/l urea and 40% formamide).61 The gel was run at 160 V for 4 h in 1 × TAE ...
Literature Review for Denaturing Gradient Gel Electrophoresis. Denaturing Gradient Gel Electrophoresis (DGGE) is a robust ... 2002) Denaturing gradient gel electrophoresis analysis of the tissue nonspecific alkaline phosphatase isoenzyme gene in ... Blaiotta G, Pennacchia C, Ercolini D, Moschetti G, Villani F. (Sep 2003) Combining denaturing gradient gel electrophoresis of ... Jeroen H. Roelfsema and Dorien J. M. Peters (2005), Denaturing Gradient Gel Electrophoresis (DGGE), Medical Biomethods Handbook ...
  • A new, improved protocol for denaturing gradient gel electrophoresis (DGGE), to screen for point mutations in genomic DNA, is reported: double gradient (DG) DGGE. (nih.gov)
  • It is therefore important to find ways to solve these problems that are found in extensive culture methods, and PCR-DGGE (Polymerase Chain Reaction Denaturing Gradient Gel Electrophoresis) is one such way. (ubc.ca)
  • In essence, PCR-DGGE involves amplification of DNA by genus-specific primers that target 16S rDNA sequences and the subsequent differentiation of this DNA on DGGE gel (1-5). (ubc.ca)
  • Denaturing Gradient Gel Electrophoresis (DGGE) is such a technique that attempts to do this. (ubc.ca)
  • Denaturing gradient gel electrophoresis (DGGE) of PCR amplicons of the ammonia monooxygenase gene (amoA) was developed and employed to investigate the diversity of ammonia-oxidizing bacteria (AOB) in four different habitats. (nih.gov)
  • Some phylogenetic information could be deduced from the position of amoA bands in DGGE gels. (nih.gov)
  • Community structure was analyzed by denaturing gradient gel electrophoresis (DGGE) of the PCR and RT-PCR amplified V3 region of 16S rDNA and 16S rRNA templates, respectively. (nih.gov)
  • DGGE denaturing gradient gel electrophoresis system which is our latest patent product (3 patents), consists of a built-in temperature control system, a Chinese programmable power supply, gradient gel generator, built-in buffer circulating pump mixing paddle, electrophoresis tank, gradient generator system, glass plates, multimedia DVD etc. (brakesband.com)
  • DGGE (denaturing gradient gel electrophoresis) analyzes PCR product. (brakesband.com)
  • Then DGGE (denaturing gradient gel electrophoresis system) is used to separate the mixture. (brakesband.com)
  • DGGE gel is made from a 6% polyacrylamide gel in which denaturing agent of linear gradient is added and the concentration of denaturant is regularly becoming higher from top to bottom. (brakesband.com)
  • DGGE gel has concentration gradient of denaturant, can distinguish different DNA fragments according to the annealing temperature of them, and the resolution is up to a base. (brakesband.com)
  • Caption: Figure 1: (a) Denaturing gradient gel electrophoresis (DGGE) fingerprints of 16S rRNA gene fragments amplified from endophytic DNA templates isolated from sweet sorghum plants grown under high (+) and low (-) N fertilization levels (100 and 0 kg N [ha.sup. (thefreedictionary.com)
  • Table 5: Values of R of the analysis of similarity of the culture/ independent total diazotrophic bacterial community determined through Denaturing Gradient Gel Electrophoresis (DGGE) of the nif H gene in different regions of the plant/bacteria association in B. (thefreedictionary.com)
  • Denaturing gradient gel electrophoresis (DGGE), one such method, provides a technique that allows relatively small DNA fragments to be separated by single base pair differences (Miller et al. (thefreedictionary.com)
  • Details of partial amoA sequences (150 amino acid) of denaturing gradient gel electrophoresis (DGGE) bands and their closest relatives DNA sequences can be accessed through DNA Data Base of Japan (DDBJ: www.ddbj.nig.ac jp) and National Centre for Biotechnology Information (NCBI: www.ncbi.ncbi.nih.gov) Closest relative (closest DGGE band amoA protein sequence) Band Accession Microorganism Accession no. (thefreedictionary.com)
  • Denaturing gradient gel electrophoresis (DGGE) is one of the most consistently used mutation scanning methods. (bio-medicine.org)
  • The principle of DGGE is based on the fact that DNA duplexes melt at high temperature in the presence of a gradient of chemical denaturant. (bio-medicine.org)
  • The optimum denaturant gradient was determined by performing perpendicular DGGE according to the instruction manual (Bio-Rad). (bio-medicine.org)
  • The complex DGGE patterns are further analyzed and compared by digitized gel imaging using the model GS-700 Imaging Densitometer and Multi Analyst software (Bio-Rad). (bio-medicine.org)
  • PCR Denaturing Gradient Gel Electrophoresis (PCR DGGE) is a sensitive technique based on differential melting and separation of similar-sized PCR-amplicons in a linear urea-formamide gradient (15). (scielo.br)
  • DGGE gels were fixed and DNA bands were visualized by silver staining. (scielo.br)
  • Bacterial species richness and diversity within peat and peat-based casing mixtures made from industrial waste materials (i.e. those containing coir, wattle bark, bagasse and filter cake) were examined using denaturing gradient gel electrophoresis (DGGE) at three phases of mushroom growth: (1) casing, (2) pinning and (3) harvesting. (scielo.org.za)
  • A fungi-specific PCR-denaturing gradient gel electrophoresis (DGGE) system was established to monitor the development of the yeast biota. (pubmedcentralcanada.ca)
  • In a previous study, we reported the monitoring of lactic acid bacterium (LAB) population dynamics during the fermentation process in four continuously propagated sourdoughs by a LAB-specific PCR-denaturing gradient gel electrophoresis (DGGE) system ( 25 ). (pubmedcentralcanada.ca)
  • We describe the development and validation of a method for the qualitative analysis of complex bifidobacterial communities based on PCR and denaturing gradient gel electrophoresis (DGGE). (asm.org)
  • Bifidobacterial communities in breast milk were assessed by PCR-denaturing gradient gel electrophoresis (PCR-DGGE), and their levels were estimated by quantitative real-time PCR (qRTi-PCR). (asm.org)
  • Identification of bacteria community responsible for decontaminating Eleme petrochemical industrial effluent using 16S PCR denaturing gradient gel electrophoresis (DGGE) was determined. (ajol.info)
  • PCR amplified DNA was separated by Denaturing Gradient Gel Electrophoresis (DGGE) analysis. (ajol.info)
  • Kuroshio Current, denaturing gradient gel electrophoresis (DGGE), redundancy analysis (RDA). (ajol.info)
  • A group-specific PCR-based denaturing gradient gel electrophoresis (DGGE) method was developed and combined with group-specific clone library analysis to investigate the diversity of the Clostridium leptum subgroup in human feces. (uncg.edu)
  • Denaturing gradient gel electrophoresis (DGGE) is one of the most commonly used molecular tools to study complex microbial communities. (ugent.be)
  • Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants. (ugent.be)
  • 1 Craig Tepper 9/10 Modified from Laboratory of Microbial Ecology, University of Toledo Denaturing Gradient Gel Electrophoresis (DGGE) Background Information Denaturing gradient gel electrophoresis (DGGE) is a molecular fingerprinting method that separates polymerase chain reaction (PCR) generated DNA products. (docplayer.net)
  • DGGE can overcome this limitation by separating PCR products based on sequence differences that results in differential denaturing characteristics of the DNA. (docplayer.net)
  • During DGGE, PCR products encounter increasingly higher concentrations of chemical denaturant as they migrate through a polyacrylamide gel. (docplayer.net)
  • Protocol DGGE gels will be poured and run to separate similarly sized PCR products. (docplayer.net)
  • The aim of this study was to investigate the composition of the bacterial communities present in the guts of D . armandi at different developmental stages using a culture-independent method involving PCR-denaturing gradient gel electrophoresis (DGGE). (mdpi.com)
  • The microbial community was analyzed by total cell counting, catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH), quantitative real-time PCR (qPCR), and denaturing gradient gel electrophoresis (DGGE). (frontiersin.org)
  • Denaturing Gradient Gel Electrophoresis (DGGE) is a robust process by which point mutation can be detected. (studyproessay.com)
  • The DGGE process has many complicated steps that entail trial and error starting with designing the proper Gradient Gel so that the PCR product will enter one end as a double strand, quickly denature and then stop progressing and stick in place. (studyproessay.com)
  • In this study, we analyzed stool samples using polymerase chain reaction - denaturing gradient gel electrophoresis ( PCR -DGGE) to differentiate between Entamoeba histolytica (pathogenic) and E. dispar (non-pathogenic). (bvsalud.org)
  • Aims: Three previously published fungal specific PCR primer sets, referred to as the NS, EF and NL primer sets, were evaluated for use in compost microbial community analysis by PCR and denaturing gradient gel electrophoresis (DGGE). (elsevier.com)
  • In this study we used denaturing gradient gel electrophoresis (DGGE), and direct sequencing, for BoLA-DRB3-typing. (elsevier.com)
  • The denaturing gradient needed to produce separation of alleles was determined using perpendicular DGGE, and this gradient was then applied to parallel denaturing gels. (elsevier.com)
  • Fingerprinting analysis of the bacterial 16S rRNA gene fragment was done by denaturing gradient gel electrophoresis (DGGE). (pubmedcentralcanada.ca)
  • Denaturing gradient gel electrophoresis (DGGE) with 16S rDNA primers generally indicated that microbial community structures were similar on different individuals of the same plant species, but unique on different plant species. (pnas.org)
  • Design The predominant microbiota from 127 UC patients and 87 age and sex-matched controls was analysed using denaturing gradient gel electrophoresis (DGGE) analysis. (bmj.com)
  • A method based on denaturing gradient gel electrophoresis (DGGE) banding polymorphism was developed for rapid small-subunit (SSU) rDNA clone screening and microbial diversity estimation. (ttu.edu)
  • An average of five to 10 individual DGGE-PCR products could be mixed together and loaded into a DGGE well, and at least 125 to 250 clones could be screened and compared within one DGGE gel. (ttu.edu)
  • The aim of the study was to investigate the association between early intestinal colonisation and the development of asthma in the first 3 years of life using DGGE (denaturing gradient gel electrophoresis). (beds.ac.uk)
  • Denaturing gradient gel electrophoresis (DGGE) is a molecular sequence dependent fingerprinting technique that allows to characterize the intestinal microbiota without pre-existing knowledge of its composition. (beds.ac.uk)
  • The assays for analysis of the most frequent mutations of PAH gene in Ukraine (R158Q, R408W, Y414C, P281L, R252W, R261Q) for RKU patients and healthy people using denaturing gradient gel-electrophoresis (DGGE) were developed. (cdc.gov)
  • Here we report the identification of connexin43 gene mutations that represent a minor population of connexin43 alleles, which could be reliably detected by using denaturing gradient gel electrophoresis (DGGE) to visualize normal and mutant DNAs that were separately sequenced. (cdc.gov)
  • The denaturing gradient gel electrophoresis (DGGE) profiles and Illumina-based metagenomic sequencing on colon contents of 15 semi-domestic yaks were investigated. (ajas.info)
  • the products were then subjected to denaturing gradient gel electrophoresis (DGGE) and sequence analysis. (microbiologyresearch.org)
  • In the present study, we investigated the bacterial diversity of aMasi, a traditional South African fermented milk product, by 16S rRNA clone library and Denaturing Gradient Gel Electrophoresis (DGGE) analysis. (uit.no)
  • Denaturing gradient gel electrophoresis (DGGE) of 350-bp fragments of phlD, a key gene involved in DAPG biosynthesis, allowed discrimination between genotypically different phlD+ reference strains and indigenous isolates. (wur.nl)
  • In this report we have compared mutation and polymorphism detection by denaturing gradient gel electrophoresis (DGGE) with denaturing high performance liquid chromatography (DHPLC) in a set of 130 families. (biomedcentral.com)
  • There are two mutation detection strategies that are most commonly used for genes involved in HNPCC, these being denaturing gradient gel electrophoresis (DGGE) and single strand conformation polymorphism analysis (SSCP). (biomedcentral.com)
  • In this study, we examined bacterial populations associated with the intestines of wild-caught and domesticated adult black tiger shrimp using high-throughput next-generation pyrosequencing analysis in parallel with denaturing gradient gel electrophoresis (DGGE). (thefishsite.com)
  • Hence, in the present study, we employed culture-independent methods (polymerase chain reaction-denaturing gradient gel electrophoresis - PCR-DGGE) that are more reliable to detect various bacteria present in the human body fluids [8]. (termedia.pl)
  • Besides, scanning electron microscope (SEM), polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE), Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy-energy spectrum (SEM-EDX) were used to analysis the effect of Cu 2+ on the morphological structure of biofilm. (iwaponline.com)
  • Assignment denaturing gradient gel electrophoresis (DGGE) method of sequences to a taxon was based on the E (expect) values shown to detect and identify Epsilonproteobacteria ( 8 ). (cdc.gov)
  • In addition, modern molecular biological techniques, such as fluorescence in situ hybridization (FISH), reverse transcriptase polymerase chain reaction (RT-PCR), denaturing gradient gel electrophoresis (DGGE), and terminal restriction fragment length polymorphism (T-RFLP), have facilitated the analysis of microbial biodiversity and activity, whereas the application of modern analytical techniques, such as nuclear magnetic resonance (NMR) and pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS), have provided data on soil chemistry. (isciii.es)
  • In this study, we used a culture-independent method, PCR-denaturing gradient gel electrophoresis (PCR-DGGE), to investigate the composition of the Streptomyces community in house dust. (cdc.gov)
  • Application of denaturing gradient gel electrophoresis (DGGE) to the analysis of microbial communities of subgingival plaque. (thefreedictionary.com)
  • Muyzer G, Brinkhoff T, Nubel U, Santegoeds C, Schafer H, Wawer C (2004) Denaturing gradient gel electrophoresis (DGGE) in microbial ecology. (thefreedictionary.com)
  • Three frequently used fingerprinting techniques that generate these multivariate datasets are phospholipid fatty acid analysis (PLFA), denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism analysis (TRFLP). (thefreedictionary.com)
  • fingerprinting technique, called denaturing gradient gel electrophoresis (DGGE), which is used to evaluate microbial ecology. (thefreedictionary.com)
  • 1999) and DGGE/ TGGE (denaturing/temperature gradient gel electrophoresis) method (Millar et al. (scribd.com)
  • All DGGE analyses were run using a D-Gene system (Bio-Rad Laboratories, Hercules, California, USA) at a constant temperature of 60 °C. Electrophoresis was for 10 min at 200 V, after which the voltage was lowered to 80 V for an additional 16 h. (esapubs.org)
  • 1998. Denaturing gradient gel electrophoresis (DGGE) in microbial ecology. (esapubs.org)
  • Here, we have examined seven of the fifteen exons of the gene from 43 unrelated Dutch and French AIP patients using denaturing gradient gel electrophoresis after polymerase chain reaction amplification. (springer.com)
  • It depends upon polymerase chain reaction (PCR) products which denature at different temperatures depending upon if they contain homoduplex or different products from both wild type and mutated genes or heteroduplex or combined strains of wild type and mutated DNA strains. (studyproessay.com)
  • We have now used polymerase chain reaction and denaturing gradient gel electrophoresis to characterize single nucleotide substitutions in the factor VIII gene. (elsevier.com)
  • Denaturing gradient gel electrophoresis of 26S rRNA gene fragments, obtained through polymerase chain reaction with universal eukaryotic primers, was carried out with two different commercial apparatus (the DCode and CBS systems). (nih.gov)
  • Fidelity of Thermococcus Litoralis DNA Polymerase (Vent) in PCR determined by denaturing gradient gel electrophoresis. (bio.net)
  • Han, H, Takase, S & Nishino, N 2012, ' Survival of silage lactic acid bacteria in the goat gastrointestinal tract as determined by denaturing gradient gel electrophoresis ', Letters in Applied Microbiology , vol. 55, no. 5, pp. 384-389. (elsevier.com)
  • Separation of PCR products amplified with bacteria specific 16S rRNA primers in 6% polyacrylamide gels with 0-100% denaturing gradient. (biomedcentral.com)
  • The polyacrylamide gels (7.5%) contained a denaturing gradient from 40 to 70% (100% denaturant: 7 M urea and 40% formamide) and were run in 0.5x TAE buffer (40 mM Tris base, pH 7.4, 20 mM sodium acetate, 1 mM EDTA). (bio-medicine.org)
  • 15). The PCR products were analyzed using a DCode mutation detection system, following the procedure described by the manufacturer (Bio-Rad Laboratories, Hercules, CA). Twenty µL of PCR samples were applied to 8% (w/v) polyacrylamide gels prepared in 1 x TAE buffer. (scielo.br)
  • In such cases we used SYBR Green I instead of ethidium bromide to stain the gels. (bio-medicine.org)
  • The gel will be stained with ethidium bromide and visualized to reveal band patterns that can be used to determine the similarity of samples. (docplayer.net)
  • Gels were stained in MilliQ (Millipore B. V., Etten-Leur, the Netherlands) water containing 0.5 mg L -1 ethidium bromide and de-stained twice in MilliQ water prior to UV transillumination. (esapubs.org)
  • A gradient of increasingly denaturing conditions, using a chemical denaturant such as formamide or urea, is applied across a gel and as double-stranded DNA molecules migrate through the gel, they denature into partially and then fully single-stranded DNA , with a consequent change in electrophoretic mobility, which dictates their final position in the gel. (thefreedictionary.com)
  • Thus DNA molecules of similar size, but different %G+C will denature and separate at different denaturant concentrations. (thefreedictionary.com)
  • The optimum concentration of denaturant to be used for parallel gradient gels was determined from the perpendicular gradient gel analysis. (bio-medicine.org)
  • Gels were poured with a stacker on top (7.5% polyacrylamide, no denaturant). (bio-medicine.org)
  • The denaturing gradients contained 40-60% denaturant [100% denaturant corresponds to 7 M urea and 40% (w/v) formamide]. (scielo.br)
  • Upon reaching a threshold denaturant concentration, the weaker melting domains of the doublestranded PCR product will begin to denature at which time migration slows dramatically. (docplayer.net)
  • Differing sequences of DNA will denature at different denaturant concentrations resulting in a unique pattern of bands. (docplayer.net)
  • You will create gels by combining two solutions containing acrylamide (structural material) and differing amounts of denaturants (urea and formamide) to form a gradient of denaturant in which double stranded DNA fragments that differ in sequence will be denatured during electrophoresis. (docplayer.net)
  • 20 × 20 cm) The linear gradient used was from 25% - 35% denaturant, where 100% denaturing acrylamide is defined as containing 7 M urea and 40% formamide (Muyzer et al. (esapubs.org)
  • PCR products from a given reaction may be of similar size (bp) and conventional separation by agarose gel electrophoresis results only in a single DNA band that is largely non-descriptive. (docplayer.net)
  • Analyses of microbial activity in biomass-recycle reactors using denaturing gradient gel electrophoresis of 16S rDNA and 16S rRNA PCR products. (nih.gov)
  • Liu, WT, Huang, CL & Song, L 2002, ' Denaturing gradient gel electrophoresis polymorphism for rapid 16S rDNA clone screening and microbial diversity study ', Journal of Bioscience and Bioengineering , vol. 93, no. 1, pp. 101-103. (ttu.edu)
  • In the context of a single isolated region of DNA, denaturing gradient gels and temperature gradient gels can be used to detect the presence of small mismatches between two sequences, a process known as temperature gradient gel electrophoresis. (wikipedia.org)
  • Because sequencing of these PCR fragments from the gel failed, cloning experiments with 28S rRNA amplicons obtained from rye flour were performed, which revealed Cladosporium sp. (pubmedcentralcanada.ca)
  • Denaturing high performance liquid chromatography is a relatively new method by which heteroduplex structures formed during the PCR amplification of heterozygote samples can be rapidly identified. (biomedcentral.com)
  • VanderGheynst, J. S. / Evaluation of PCR primers for denaturing gradient gel electrophoresis analysis of fungal communities in compost . (elsevier.com)
  • If there are point mutations in the PCR product, the melting point will change, and thus its mobility on a polyacrylamide gel will be different from the mobility of the wild type DNA. (bio-medicine.org)
  • Moreover, these mutations can be detected when the GC-clamped PCR products from all five regions are run in the same denaturing gel. (elsevier.com)
  • Our results indicate that denaturing gradient gel electrophoresis can be successfully applied to the analysis of point mutations in large genes whose transcripts are not readily available. (elsevier.com)
  • in particular, point mutations in codon 61 of exon 2 of the N -ras gene occur frequently in malignant melanoma (MM). We searched for point mutations in the N -ras gene in a large series of primary and metastatic MM from 81 different retrospectively selected patients using the very sensitive denaturing gradient gel electrophoresis technique, followed by sequencing. (aacrjournals.org)
  • Other methods that have been developed to study mutations include denaturing HPLC (DHPLC) (1-6), single-strand conformation polymorphism (7-9), denaturing gradient gel electrophoresis (10-12), temperature gradient gel electrophoresis (13), temporal temperature gradient gel electrophoresis (14-16), and pyrosequencing (2,17). (thefreedictionary.com)
  • In this technique, to the primary, denaturing gradient (typically 30-80% or 40-80% urea/formamide) a secondary gradient, colinear with the first, is superimposed: a porosity gradient (typically 6.5-12% polyacrylamide). (nih.gov)
  • B. Pouring the gel 1 Run a 6% polyacrylamide denaturing gel containing a 40-80% gradient (2.8 M urea/16% formamide to 5.6 M urea/32% formamide). (docplayer.net)
  • Effects of fasting on rumen microbiota based on the banding profile of denaturing gradient gel electrophoresis (A, B, and C indicate specific animals). (thefreedictionary.com)
  • Gut microbiota profiling by denaturing gradient gel electrophoresis and 454/FLX-based 16S rRNA gene amplicon sequencing revealed that mice born by C-section had a distinct bacterial profile at weaning characterized by higher abundance of Bacteroides and Lachnospiraceae, and less Rikenellaceae and Ruminococcus . (jimmunol.org)
  • The bands representing individual BoLA-DRB3 alleles were excised from the gels, reamplified, and the nucleotide sequence determined using fluorescent-based automated cycle sequencing. (elsevier.com)
  • A variation of this technique, temperature/ thermal gradient gel electrophoresis ( TGGE ), employs a temperature gradient, rather than chemical denaturants. (thefreedictionary.com)
  • Denaturing gradient gel electrophoresis in combination with PCR has found a wide application for analysis of genetic variants in many disciplines of bioscience, especially evaluation of microbial diversity in environmental samples. (thefreedictionary.com)
  • Bourgeois F, Gu XF, Deybach JC, Te Velde MP, Rooij FWM de, Nordmann Y, Grandchamp B (1992) Denaturing gradient gel electrophoresis for rapid detection of latent carriers of a subtype of acute intermittent porphyria with normal erythrocyte porphobilinogen deaminase activity. (springer.com)
  • Since denaturing gradient gel electrophoresis make use of temperature and gradient gel migration rate for detection, a dedicated electrophoresis device is needed. (brakesband.com)
  • Detection of p53 Gene in Breast Cancer by Denaturing Gradient Gel Electrophoresis and the DCode System ( Akira Ichikawa and Seiji. (bio-medicine.org)
  • Under similar and optimal denaturing gradient gel electrophoresis conditions, the CBS system allowed a better separated band pattern than the DCode system and an unambiguous detection of the prevailing species present in the fermentation samples. (nih.gov)
  • Therefore, denaturing gradient gel electrophoresis can be used to study microbial community structure, microbial population dynamics analysis of enrichment cultures and isolates the analysis of ribosomal RNA homology analysis. (brakesband.com)
  • Denaturing gradient gel electrophoresis analysis to study bacterial community structure in pockets of periodontitis patients. (thefreedictionary.com)
  • Five ml of PCR products (approximately 200300 ng) was mixed with 5 l 2x gel loading dye and electrophoresed on the DCode system at 150 V for 3.5 hours at 60 C. The post-run analysis was the same as perpendicular gradient gel analysis. (bio-medicine.org)
  • Therefore a gradient of 45 to 60% was used for parallel gel analysis. (bio-medicine.org)
  • We chose to use parallel gradient method because it provides high throughput analysis. (bio-medicine.org)
  • A spatio-temporal comparison of picoeukaryotes in the Alborán Sea (SW Mediterranean) by denaturing gradient gel electrophoresis and HPLC pigment analysis. (slideplayer.com)
  • Presentation on theme: "A spatio-temporal comparison of picoeukaryotes in the Alborán Sea (SW Mediterranean) by denaturing gradient gel electrophoresis and HPLC pigment analysis. (slideplayer.com)
  • Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. (microbiologyresearch.org)
  • No clustering according to delivery method as determined by principal component analysis of denaturing gradient gel electrophoresis profiles was evident in adult mice. (jimmunol.org)
  • We added 100 ml 2x gel loading dye (70% glycerol, 0.05% bromophenol blue, 0.05% xylene cyanol, 2 mM EDTA) to these samples, and electrophoresed them on the DCode system at 130 V for 2.5 hours at 56 C. After electrophoresis, the gels were stained in a 1:10,000 dilution of SYBR Green I (Molecular Probes) in 1x TAE buffer for 45 minutes and destained in 1x TAE buffer for 45 minutes. (bio-medicine.org)
  • Denaturing gradient gel ratio of 20% : 80% was most suitable for differentiation of bacterial profiles. (ajol.info)
  • 2 All products were analyzed both in perpendicular gradient gels and parallel gradient gels. (bio-medicine.org)
  • DNA from 34 cases was found to have a mutation on perpendicular gels and in 33 cases on parallel gels. (bio-medicine.org)
  • The sample missed showed a mutation of exon 7 on perpendicular gels but not on parallel gels. (bio-medicine.org)
  • When the double-stranded DNA in the denaturing gradient gel reaches the denaturation temperature of DNA, DNA will partially melt, and electrophoretic mobility rate will drop. (brakesband.com)
  • 8. The method of claim 1, wherein the chemically modified heteroduplex is treated by gel electrophoresis and transferred to a solid support before being detected by the immunochemical reagent. (google.com)
  • DNA is heated and denatured into single-stranded state, and the mixture is cooled to allow strands to rehybridize. (wikipedia.org)
  • A possible explanation for this could be that the parallel gel gradient of 45 to 60% was too wide for that particular sample. (bio-medicine.org)
  • A narrow gradient may be required to identify the mutation of exon 7 on parallel gels. (bio-medicine.org)
  • DNA, when in a state where its two strands are dissociated (i.e., the dsDNA molecule exists as two independent strands), is referred to as having been denatured by the high temperature. (wikipedia.org)
  • Screening for human mitochondrial DNA polymorphisms with denaturing gradient gel electrophoresis. (harvard.edu)
  • 1998). To ensure well-polymerized slots, a 10 mL top gel containing no denaturants was added before polymerization was complete. (esapubs.org)
  • Denaturing gradient gel electrophoresis analyses of the vertical distribution and diversity of Vibrio spp. (usf.edu)
  • Microbial Diversity in Ground and Surface Water Analyzed by Denaturing Gradient Gel Electrophoresis Using the DCode System ( Bernd Eschweiler and Bea. (bio-medicine.org)
  • Screening for mutation variants in exons 5, 7, 12 of phenylalanine hydroxylase gene using denaturing gradient gel-electrophoresis]. (cdc.gov)
  • gel electrophoresis performed in a concentration gradient gel with progressively decreasing pore size. (thefreedictionary.com)
  • van den Berg, F. Investigating the fermentation of cocoa by correlating Denaturing Gradient Gel Electrophoresis profiles and Near Infrared spectra. (worldcocoafoundation.org)
  • A 7.5 x 10 cm, 1 mm thick, 25% to 65% denatured gradient gel was made using 6% aclylamide/bis (37.5:1) in 1x TAE buffer (50 mM Tris, 25 mM acetic acid, 1.25 mM EDTA). (bio-medicine.org)
  • A 16 x 16 cm, 1 mm thick, 45% to 60% denatured gradient gel was made using 6% aclylamide/bis (37.5:1) in 1xTAE buffer. (bio-medicine.org)