Polymorphism, Restriction Fragment Length: Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.Amplified Fragment Length Polymorphism Analysis: The detection of RESTRICTION FRAGMENT LENGTH POLYMORPHISMS by selective PCR amplification of restriction fragments derived from genomic DNA followed by electrophoretic analysis of the amplified restriction fragments.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.DNA Fingerprinting: A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.Polymorphism, Genetic: 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.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Bacterial Typing Techniques: Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.DNA, Ribosomal Spacer: 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).Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Genetic Variation: Genotypic differences observed among individuals in a population.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Polymorphism, Single-Stranded Conformational: Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.Deoxyribonucleases, Type II Site-Specific: Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 3.1.21.4.Gene Frequency: The proportion of one particular in the total of all ALLELES for one genetic locus in a breeding POPULATION.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Molecular Epidemiology: The application of molecular biology to the answering of epidemiological questions. The examination of patterns of changes in DNA to implicate particular carcinogens and the use of molecular markers to predict which individuals are at highest risk for a disease are common examples.DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Serotyping: Process of determining and distinguishing species of bacteria or viruses based on antigens they share.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Genetic Predisposition to Disease: A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.Genes, Bacterial: The functional hereditary units of BACTERIA.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Genes, rRNA: Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.Mycobacterium tuberculosis: A species of gram-positive, aerobic bacteria that produces TUBERCULOSIS in humans, other primates, CATTLE; DOGS; and some other animals which have contact with humans. Growth tends to be in serpentine, cordlike masses in which the bacilli show a parallel orientation.Electrophoresis, Gel, Pulsed-Field: 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.Minisatellite Repeats: Tandem arrays of moderately repetitive, short (10-60 bases) DNA sequences which are found dispersed throughout the GENOME, at the ends of chromosomes (TELOMERES), and clustered near telomeres. Their degree of repetition is two to several hundred at each locus. Loci number in the thousands but each locus shows a distinctive repeat unit.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Random Amplified Polymorphic DNA Technique: 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.DNA Probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.Campylobacter jejuni: A species of bacteria that resemble small tightly coiled spirals. Its organisms are known to cause abortion in sheep and fever and enteritis in man and may be associated with enteric diseases of calves, lambs, and other animals.Campylobacter Infections: Infections with bacteria of the genus CAMPYLOBACTER.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Bacteria: One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Mycobacterium: A genus of gram-positive, aerobic bacteria. Most species are free-living in soil and water, but the major habitat for some is the diseased tissue of warm-blooded hosts.RNA, Ribosomal, 23S: Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.Case-Control Studies: Studies which start with the identification of persons with a disease of interest and a control (comparison, referent) group without the disease. The relationship of an attribute to the disease is examined by comparing diseased and non-diseased persons with regard to the frequency or levels of the attribute in each group.Breast Milk Expression: The act of evacuating BREAST MILK by hand or with a pump.Heterozygote: An individual having different alleles at one or more loci regarding a specific character.Bacterial Proteins: Proteins found in any species of bacterium.DNA, Protozoan: Deoxyribonucleic acid that makes up the genetic material of protozoa.Environmental Microbiology: The study of microorganisms living in a variety of environments (air, soil, water, etc.) and their pathogenic relationship to other organisms including man.Ecosystem: A functional system which includes the organisms of a natural community together with their environment. (McGraw Hill Dictionary of Scientific and Technical Terms, 4th ed)Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Mycological Typing Techniques: Procedures for identifying types and strains of fungi.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Asian Continental Ancestry Group: Individuals whose ancestral origins are in the southeastern and eastern areas of the Asian continent.RNA, Ribosomal, 18S: Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Genetic Linkage: The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Clostridium botulinum type A: Subtype of CLOSTRIDIUM BOTULINUM that produces BOTULINUM TOXINS, TYPE A which is neurotoxic to humans and animals.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Chaperonins: A family of multisubunit protein complexes that form into large cylindrical structures which bind to and encapsulate non-native proteins. Chaperonins utilize the energy of ATP hydrolysis to enhance the efficiency of PROTEIN FOLDING reactions and thereby help proteins reach their functional conformation. The family of chaperonins is split into GROUP I CHAPERONINS, and GROUP II CHAPERONINS, with each group having its own repertoire of protein subunits and subcellular preferences.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Rickettsia: A genus of gram-negative, aerobic, rod-shaped bacteria often surrounded by a protein microcapsular layer and slime layer. The natural cycle of its organisms generally involves a vertebrate and an invertebrate host. Species of the genus are the etiological agents of human diseases, such as typhus.Cryptosporidium: A genus of coccidian parasites of the family CRYPTOSPORIDIIDAE, found in the intestinal epithelium of many vertebrates including humans.Point Mutation: 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.Chaperonin 60: A group I chaperonin protein that forms the barrel-like structure of the chaperonin complex. It is an oligomeric protein with a distinctive structure of fourteen subunits, arranged in two rings of seven subunits each. The protein was originally studied in BACTERIA where it is commonly referred to as GroEL protein.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Pedigree: 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.China: A country spanning from central Asia to the Pacific Ocean.Flagellin: A protein with a molecular weight of 40,000 isolated from bacterial flagella. At appropriate pH and salt concentration, three flagellin monomers can spontaneously reaggregate to form structures which appear identical to intact flagella.Raphanus: A plant genus of the family BRASSICACEAE known for its peppery red root.Dominican Republic: A republic in the Greater Antilles in the West Indies. Its capital is Santo Domingo. With Haiti, it forms the island of Hispaniola - the Dominican Republic occupying the eastern two thirds, and Haiti, the western third. It was created in 1844 after a revolt against the rule of President Boyer over the entire island of Hispaniola, itself visited by Columbus in 1492 and settled the next year. Except for a brief period of annexation to Spain (1861-65), it has been independent, though closely associated with the United States. Its name comes from the Spanish Santo Domingo, Holy Sunday, with reference to its discovery on a Sunday. (From Webster's New Geographical Dictionary, 1988, p338, 506 & Room, Brewer's Dictionary of Names, 1992, p151)Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).Campylobacter: A genus of bacteria found in the reproductive organs, intestinal tract, and oral cavity of animals and man. Some species are pathogenic.Tuberculosis: Any of the infectious diseases of man and other animals caused by species of MYCOBACTERIUM.Ticks: Blood-sucking acarid parasites of the order Ixodida comprising two families: the softbacked ticks (ARGASIDAE) and hardbacked ticks (IXODIDAE). Ticks are larger than their relatives, the MITES. They penetrate the skin of their host by means of highly specialized, hooked mouth parts and feed on its blood. Ticks attack all groups of terrestrial vertebrates. In humans they are responsible for many TICK-BORNE DISEASES, including the transmission of ROCKY MOUNTAIN SPOTTED FEVER; TULAREMIA; BABESIOSIS; AFRICAN SWINE FEVER; and RELAPSING FEVER. (From Barnes, Invertebrate Zoology, 5th ed, pp543-44)Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Chromosomes, Human, Pair 17: A specific pair of GROUP E CHROMOSOMES of the human chromosome classification.Arcobacter: A genus of gram-negative, aerotolerant, spiral-shaped bacteria isolated from water and associated with diarrhea in humans and animals.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Chromosome Deletion: Actual loss of portion of a chromosome.Mycobacterium Infections: Infections with bacteria of the genus MYCOBACTERIUM.Ribotyping: RESTRICTION FRAGMENT LENGTH POLYMORPHISM analysis of rRNA genes that is used for differentiating between species or strains.Disease Outbreaks: Sudden increase in the incidence of a disease. The concept includes EPIDEMICS and PANDEMICS.Electrophoresis, Agar Gel: Electrophoresis in which agar or agarose gel is used as the diffusion medium.Cattle: 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.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Plant Diseases: Diseases of plants.Evaluation Studies as Topic: Studies determining the effectiveness or value of processes, personnel, and equipment, or the material on conducting such studies. For drugs and devices, CLINICAL TRIALS AS TOPIC; DRUG EVALUATION; and DRUG EVALUATION, PRECLINICAL are available.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)Deoxyribonuclease EcoRI: One of the Type II site-specific deoxyribonucleases (EC 3.1.21.4). It recognizes and cleaves the sequence G/AATTC at the slash. EcoRI is from E coliRY13. Several isoschizomers have been identified. EC 3.1.21.-.Genes, p53: Tumor suppressor genes located on the short arm of human chromosome 17 and coding for the phosphoprotein p53.DNA, Neoplasm: DNA present in neoplastic tissue.Symbiosis: The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.Genes, ras: Family of retrovirus-associated DNA sequences (ras) originally isolated from Harvey (H-ras, Ha-ras, rasH) and Kirsten (K-ras, Ki-ras, rasK) murine sarcoma viruses. Ras genes are widely conserved among animal species and sequences corresponding to both H-ras and K-ras genes have been detected in human, avian, murine, and non-vertebrate genomes. The closely related N-ras gene has been detected in human neuroblastoma and sarcoma cell lines. All genes of the family have a similar exon-intron structure and each encodes a p21 protein.Sensitivity and Specificity: Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)Tuberculosis, Pulmonary: MYCOBACTERIUM infections of the lung.DNA, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Poultry Diseases: Diseases of birds which are raised as a source of meat or eggs for human consumption and are usually found in barnyards, hatcheries, etc. The concept is differentiated from BIRD DISEASES which is for diseases of birds not considered poultry and usually found in zoos, parks, and the wild.Microbial Sensitivity Tests: Any tests that demonstrate the relative efficacy of different chemotherapeutic agents against specific microorganisms (i.e., bacteria, fungi, viruses).Cryptosporidiosis: Intestinal infection with organisms of the genus CRYPTOSPORIDIUM. It occurs in both animals and humans. Symptoms include severe DIARRHEA.Food Microbiology: 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.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Seawater: The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.Borrelia burgdorferi Group: Gram-negative helical bacteria, in the genus BORRELIA, that are the etiologic agents of LYME DISEASE. The group comprises many specific species including Borrelia afzelii, Borellia garinii, and BORRELIA BURGDORFERI proper. These spirochetes are generally transmitted by several species of ixodid ticks.Geologic Sediments: A mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)Genetic Association Studies: The analysis of a sequence such as a region of a chromosome, a haplotype, a gene, or an allele for its involvement in controlling the phenotype of a specific trait, metabolic pathway, or disease.Deoxyribonuclease HindIII: One of the Type II site-specific deoxyribonucleases (EC 3.1.21.4). It recognizes and cleaves the sequence A/AGCTT at the slash. HindIII is from Haemophilus influenzae R(d). Numerous isoschizomers have been identified. EC 3.1.21.-.Fresh Water: Water containing no significant amounts of salts, such as water from RIVERS and LAKES.Cattle Diseases: Diseases of domestic cattle of the genus Bos. It includes diseases of cows, yaks, and zebus.Risk Factors: An aspect of personal behavior or lifestyle, environmental exposure, or inborn or inherited characteristic, which, on the basis of epidemiologic evidence, is known to be associated with a health-related condition considered important to prevent.Mycobacterium bovis: The bovine variety of the tubercle bacillus. It is called also Mycobacterium tuberculosis var. bovis.Drug Resistance, Microbial: The ability of microorganisms, especially bacteria, to resist or to become tolerant to chemotherapeutic agents, antimicrobial agents, or antibiotics. This resistance may be acquired through gene mutation or foreign DNA in transmissible plasmids (R FACTORS).Enterococcus faecium: A species of gram-positive, coccoid bacteria whose organisms are normal flora of the intestinal tract. Unlike ENTEROCOCCUS FAECALIS, this species may produce an alpha-hemolytic reaction on blood agar and is unable to utilize pyruvic acid as an energy source.Nucleic Acid Amplification Techniques: Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.Oligonucleotide Probes: Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.Fabaceae: The large family of plants characterized by pods. Some are edible and some cause LATHYRISM or FAVISM and other forms of poisoning. Other species yield useful materials like gums from ACACIA and various LECTINS like PHYTOHEMAGGLUTININS from PHASEOLUS. Many of them harbor NITROGEN FIXATION bacteria on their roots. Many but not all species of "beans" belong to this family.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Feces: Excrement from the INTESTINES, containing unabsorbed solids, waste products, secretions, and BACTERIA of the DIGESTIVE SYSTEM.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Sputum: Material coughed up from the lungs and expectorated via the mouth. It contains MUCUS, cellular debris, and microorganisms. It may also contain blood or pus.Homozygote: An individual in which both alleles at a given locus are identical.Anti-Bacterial Agents: Substances that reduce the growth or reproduction of BACTERIA.Bacteriological Techniques: Techniques used in studying bacteria.Virulence: The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.Deoxyribonuclease HpaII: One of the Type II site-specific deoxyribonucleases (EC 3.1.21.4). It recognizes and cleaves the sequences C/CGG and GGC/C at the slash. HpaII is from Haemophilus parainfluenzae. Several isoschizomers have been identified. EC 3.1.21.-.Drug Resistance, Bacterial: The ability of bacteria to resist or to become tolerant to chemotherapeutic agents, antimicrobial agents, or antibiotics. This resistance may be acquired through gene mutation or foreign DNA in transmissible plasmids (R FACTORS).Swine: 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).Electrophoresis, Capillary: 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)Reproducibility of Results: The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.Bacterial Outer Membrane Proteins: Proteins isolated from the outer membrane of Gram-negative bacteria.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Rhizobium: A genus of gram-negative, aerobic, rod-shaped bacteria that activate PLANT ROOT NODULATION in leguminous plants. Members of this genus are nitrogen-fixing and common soil inhabitants.Linkage Disequilibrium: Nonrandom association of linked genes. This is the tendency of the alleles of two separate but already linked loci to be found together more frequently than would be expected by chance alone.Choline Kinase: An enzyme that is active in the first step of choline phosphoglyceride (lecithin) biosynthesis by catalyzing the phosphorylation of choline to phosphorylcholine in the presence of ATP. Ethanolamine and its methyl and ethyl derivatives can also act as acceptors. EC 2.7.1.32.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Microsatellite Repeats: A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).Molecular Typing: 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.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Antigens, Bacterial: Substances elaborated by bacteria that have antigenic activity.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Chondroitin Sulfates: Derivatives of chondroitin which have a sulfate moiety esterified to the galactosamine moiety of chondroitin. Chondroitin sulfate A, or chondroitin 4-sulfate, and chondroitin sulfate C, or chondroitin 6-sulfate, have the sulfate esterified in the 4- and 6-positions, respectively. Chondroitin sulfate B (beta heparin; DERMATAN SULFATE) is a misnomer and this compound is not a true chondroitin sulfate.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Genetics, Population: The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.Korea: Former kingdom, located on Korea Peninsula between Sea of Japan and Yellow Sea on east coast of Asia. In 1948, the kingdom ceased and two independent countries were formed, divided by the 38th parallel.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Crosses, Genetic: Deliberate breeding of two different individuals that results in offspring that carry part of the genetic material of each parent. The parent organisms must be genetically compatible and may be from different varieties or closely related species.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Culture Media: Any liquid or solid preparation made specifically for the growth, storage, or transport of microorganisms or other types of cells. The variety of media that exist allow for the culturing of specific microorganisms and cell types, such as differential media, selective media, test media, and defined media. Solid media consist of liquid media that have been solidified with an agent such as AGAR or GELATIN.European Continental Ancestry Group: Individuals whose ancestral origins are in the continent of Europe.Methylenetetrahydrofolate Reductase (NADPH2): A flavoprotein amine oxidoreductase that catalyzes the reversible conversion of 5-methyltetrahydrofolate to 5,10-methylenetetrahydrofolate. This enzyme was formerly classified as EC 1.1.1.171.Mice, Inbred Strains: Genetically identical individuals developed from brother and sister matings which have been carried out for twenty or more generations, or by parent x offspring matings carried out with certain restrictions. All animals within an inbred strain trace back to a common ancestor in the twentieth generation.Geography: The science dealing with the earth and its life, especially the description of land, sea, and air and the distribution of plant and animal life, including humanity and human industries with reference to the mutual relations of these elements. (From Webster, 3d ed)Prevalence: The total number of cases of a given disease in a specified population at a designated time. It is differentiated from INCIDENCE, which refers to the number of new cases in the population at a given time.Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.X Chromosome: The female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in human and other male-heterogametic species.BelgiumBase Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.TurkeyGenes, Plant: The functional hereditary units of PLANTS.DNA, Intergenic: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.Gene Amplification: A selective increase in the number of copies of a gene coding for a specific protein without a proportional increase in other genes. It occurs naturally via the excision of a copy of the repeating sequence from the chromosome and its extrachromosomal replication in a plasmid, or via the production of an RNA transcript of the entire repeating sequence of ribosomal RNA followed by the reverse transcription of the molecule to produce an additional copy of the original DNA sequence. Laboratory techniques have been introduced for inducing disproportional replication by unequal crossing over, uptake of DNA from lysed cells, or generation of extrachromosomal sequences from rolling circle replication.Amino Acid Substitution: The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.BrazilPhenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Soil: The unconsolidated mineral or organic matter on the surface of the earth that serves as a natural medium for the growth of land plants.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Ascomycota: A phylum of fungi which have cross-walls or septa in the mycelium. The perfect state is characterized by the formation of a saclike cell (ascus) containing ascospores. Most pathogenic fungi with a known perfect state belong to this phylum.Length of Stay: The period of confinement of a patient to a hospital or other health facility.Staphylococcus aureus: Potentially pathogenic bacteria found in nasal membranes, skin, hair follicles, and perineum of warm-blooded animals. They may cause a wide range of infections and intoxications.

*  Long-distance seed dispersal in a metapopulation of Banksia hookeriana inferred from a population allocation analysis of...

... a metapopulation of Banksia hookeriana inferred from a population allocation analysis of amplified fragment length polymorphism ... a metapopulation of Banksia hookeriana inferred from a population allocation analysis of amplified fragment length polymorphism ...
onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2004.02120.x/references

*  Lack of effect of aerial ammonia on atrophic rhinitis and pneumonia induced by Mycoplasma hyopneumoniae and toxigenic...

Analysis of Mycoplasma hyosynoviae strains by pulsed-field gel electrophoresis (PFGE), amplified fragment length polymorphism ( ... Characterization of Mycoplasma hyosynoviae strains by amplified fragment length polymorphism analysis, pulsed-field gel ... pleuropneumonia in Tanzania based on amplified fragment length polymorphism and pulsed-field gel electrophoresis analysis. ...
orbit.dtu.dk/en/publications/lack-of-effect-of-aerial-ammonia-on-atrophic-rhinitis-and-pneumonia-induced-by-mycoplasma-hyopneumoniae-and-toxigenic-pasteurella-multocida

*  "Population structure, genetic variability, and gene flow of the bean l" by Bamphitlhi Tiroesele, Steven R. Skoda et al.

Results from analysis of molecular variance (AMOVA) indicated that the majority of genetic variation was from within samples; ... Amplified fragment length polymorphism generated 175 markers for analyses. ... Amplified fragment length polymorphism generated 175 markers for analyses. Results from analysis of molecular variance (AMOVA) ...
digitalcommons.unl.edu/entomologyfacpub/389/

*  Gonorrhea - an evolving disease of the new millennium

Palmer HM, Arnold C. Genotyping Neisseria gonorrhoeae Using Fluorescent Amplified Fragment Length Polymorphism Analysis. J Clin ... Cross-linking analysis of the outer membrane proteins of Neisseria gonorrhoeae. Infect Immun. 1980;28(3):785-791. [PMC free ... eBURST analysis determined the total number of QRNG strains that entered a country, the divergence of loci, and the time period ... Analysis of the antigen specificity of the human serum IgG immune response to complicated gonococcal infection. Infect Immun. ...
pubmedcentralcanada.ca/pmcc/articles/PMC5354566/

*  Bacteroides ureolyticus Jackson and Goodman ATCC ® 33387™

... to be reclassified as Campylobacter ureolyticus based on sequencing and genomic amplified fragment length polymorphism analyses ... Chemotaxonomic analyses of Bacteroides gracilis and Bacteroides ureolyticus and reclassification of B. gracilis as ...
https://atcc.org/en/Products/Quality_Control_Strains/By_Instrument/33387.aspx?p=1&rel={0}?p=1&rel={0}

*  0412 Comparison of four molecular approaches to identify Candida parapsilosis complex species

2010), amplified fragment length polymorphism (AFLP) analysis (Tavanti et al. 2007, Hensgens et al. 2009, de Carolis et al. ... 2006), randomly amplified polymorphic DNA (RAPD) analysis (Tay et al. 2009), restriction fragment length polymorphism (RFLP) ... of Candida orthopsilosis strains in Kuwait by ITS region sequencing and amplified fragment length polymorphism analysis. PLoS ... and PCR-restriction fragment length polymorphism patterns in the ITS1-5.8S-ITS2 region of the rDNA gene. There was agreement ...
memorias.ioc.fiocruz.br/issues/current-issue/item/6240-0412_comparison-of-four-molecular-approaches-to-identify-candida-parapsilosis-complex-species

*  Toxins | Free Full-Text | Occurrence of Black Aspergilli and Ochratoxin A on Grapes in Italy | HTML

Ochratoxin A production and amplified fragment length polymorphism analysis of Aspergillus carbonarius, Aspergillus tubigensis ... Mycological Analyses. The mycological analyses of the grape samples were performed using a serial dilution plating method. Two- ... Statistical Analyses. Several analyses were carried out in order to check whether there was any statistically significant ... Mycological Analyses. In general, the species belonging to the Aspergillus genus (mainly Aspergillus section Nigri and, ...
mdpi.com/2072-6651/2/4/840/htm

*  ATCC 11671 Strain Passport - StrainInfo

Amplified fragment length polymorphism and multilocus sequence analysis-based genotypic relatedness among pathogenic variants ... length. GU736599. Xanthomonas axonopodis pv. desmodiigangetici culture-collection LMG:693 PilW-like protein (pilW) gene, ...
straininfo.net/strains/24125

*  ICPB XB9 Strain Passport - StrainInfo

Amplified fragment length polymorphism and multilocus sequence analysis-based genotypic relatedness among pathogenic variants ...
straininfo.net/strains/23211

*  LMG 8652 Strain Passport - StrainInfo

Amplified fragment length polymorphism and multilocus sequence analysis-based genotypic relatedness among pathogenic variants ...
straininfo.net/strains/23856

*  JCI - Natural population dynamics and expansion of pathogenic clones of Staphylococcus aureus

High-throughput amplified fragment length polymorphism (AFLP) analysis revealed 3 major and 2 minor genetic clusters of S. ... Nonstandard abbreviations used: AFLP, amplified fragment length polymorphism; CC, clonal complex; ETA, exfoliative toxin A; ht- ... including amplified fragment length polymorphism (AFLP) (16, 17), document the contribution of accessory genetic elements as ... the average number of fragments (useful for AFLP) generated per genome is 4.373, and the average length of the fragments is 200 ...
https://jci.org/articles/view/23083

*  Construction of an intra-specific sweet cherry (Prunus aviumL.) genetic linkage map and synteny analysis with...

To complete the linkage analysis, 61 amplified fragment length polymorphism and seven sequence-related amplified polymorphism ... Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its ... a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis ... This analysis resulted in the expected eight linkage groups for both parents. The EF and NY maps were 711.1 cM and 565.8 cM, ...
https://link.springer.com/article/10.1007/s11295-008-0161-1

*  Frontiers | Campylobacter concisus - A New Player in Intestinal Disease | Frontiers in Cellular and Infection Microbiology

... using amplified length fragment polymorphism (AFLP) analysis and correlated the results to clinical data. All strains examined ... Delineation of Campylobacter concisus genomospecies by amplified fragment length polymorphism analysis and correlation of ... 1996) who used randomly amplified polymorphic DNA (RAPD) analysis to compare C. concisus strains isolated from fecal samples of ... 1989) used protein analysis, immunotyping, DNA hybridization, and DNA base analysis to determine the species identity of 14 ...
journal.frontiersin.org/article/10.3389/fcimb.2012.00004/full

*  M C Enright

... and fluorescent amplified-fragment length polymorphism analysis. M Ip. Department of Microbiology, The Chinese University of ... To analyse the mutations and epidemiology associated with fluoroquinolone-resistant pneumococci collected as part of the ... Specialized software for automated sequence analysis ensured a common typing nomenclature.... *. Multilocus sequence typing and ... Staphylococcal chromosome cassette evolution in Staphylococcus aureus inferred from ccr gene complex sequence typing analysis. ...
https://labome.org/expert/uk/university/enright/m-c-enright-334759.html

*  IJMS | Free Full-Text | Involvement of Disperse Repetitive Sequences in Wheat/Rye Genome Adjustment | HTML

... analysis with OPH20 10-mer primer we unraveled clear alterations corresponding to the loss of specific bands from both parental ... disappearance of bands observed in progenitor profiles as previously described through Amplified Fragment Length Polymorphism ( ... Sequence-specific amplified polymorphism (SSAP) analysis with distinct anchored primers to pSc20H sequence revealed that not ... In fact, sequence analysis of bands amplified from wheat with OPH20 primer revealed sequence similarity with both repetitive ...
mdpi.com/1422-0067/13/7/8549/htm

*  ASMscience | Molecular Typing of the

Intergenic spacer (IGS) sequence analysis is a powerful tool to delineate the two varieties of C. neoformans and separate the ... The restriction fragment length polymorphism (RFLP) patterns result from the presence of a restriction enzyme cleavage site at ... Amplified-fragment length polymorphism analysis: the state of an art. J. Clin. Microbiol. 37:3083-3091.. ... Currie, B. P.,, L. F. Freundlich, and, A. Casadevall. 1994. Restriction fragment length polymorphism analysis of Cryptococcus ...
asmscience.org/content/book/10.1128/9781555816858.ch24

*  Patent US5733744 - Binary BAC vector - Google Patents

RAPD (random amplified polymorphic DNA) and AFLP (amplified fragment length polymorphism) methods in combination with analysis ... 1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18, 6531-6535. ... 1987). This GUS-NPTII construct is carried on an Eco RI-Hin dIII fragment. The fragment was treated with Klenow and ligated ... When a DNA fragment is inserted into the Bam HI site, the sacB gene is inactivated, and the strain is viable when grown on ...
google.co.uk/patents/US5733744

*  Kudos - helping increase the reach and impact of research

Amplified fragment length polymorphism (AFLP) analysis of closely related wild and captive tsetse fly (Glossina morsitans ... Phylogenomics and Analysis of Shared Genes Suggest a Single Transition to Mutualism in Wolbachia of Nematodes. Published in: ... Genomic Analysis of Highly Virulent Georgia 2007/1 Isolate of African Swine Fever Virus. Published in:Emerging Infectious ... Analysis of gene expression from the Wolbachia genome of a filarial nematode supports both metabolic and defensive roles within ...
https://growkudos.com/profiles/107084

*  Quantitative strain-specific detection of Lactobacillus rhamnosus GG in human faecal samples by real-time PCR - Ahlroos - 2009 ...

... such as random amplified polymorphic DNA analysis (RAPD), pulsed-field gel electrophoresis (PFGE), amplified fragment length ... polymorphism (AFLP) or ribotyping, are used to identify bacteria at the strain level (Zwirglmaier et al. 2001). However, these ... and representational difference analysis (RDA) fragments (Konstantinov et al. 2005) have also been used as the basis for strain ... Kimura, K., McCartney, A.L., McConnel, M.A. and Tannock, G.W. (1997) Analysis of fecal populations of Bifidobacteria and ...
onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2008.04018.x/full

*  Microbiology Society Journals | An investigation into the microflora of heroin

Amplified fragment length polymorphism (AFLP) analysis of Clostridium novyi, C. perfringens and Bacillus cereus isolated from ...
jmm.microbiologyresearch.org/content/journal/jmm/10.1099/0022-1317-51-11-1001

*  Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia | BMC Genomics | Full Text

Amplified fragment-length polymorphism (AFLP) analysis has been used to examine the diversity of Group I [7] and II strains [16 ... and F by amplified fragment length polymorphism analysis. Appl Environ Microb. 2005;71:1148-54.View ArticleGoogle Scholar. ... amplified fragment length polymorphism, variable-number tandem-repeat analysis, and botulinum neurotoxin gene sequencing. Appl ... Whole-genome single-nucleotide-polymorphism analysis for discrimination of Clostridium botulinum Group I strains. Appl Environ ...
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2502-z

*  A reference floral transcriptome of sexual and apomictic Paspalum notatum | BMC Genomics | Full Text

Amplified Fragment Length Polymorphism) [53] analyses. Therefore, they are short (most of them 150-400 nt long) and reveal low ... Identity percentages, score values, alignments length, query coverage (align length/query length), and E-value distributions ... Besides, the analysis of ESTs sequences (average length 215.53 bp) showed that 81.250% and 83.750% of them matched with E-value ... through mapping analysis [26, 27, 29, 42, 64, 65], BAC sequencing [40, 41], differential display [45, 48] or cDNA AFLP [53]. ...
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3700-z

*  Molecular Epidemiology of Rickettsial Diseases | SpringerLink

... among spotted fever group rickettsiae species by analysis of restriction fragment length polymorphism of PCR-amplified DNA. J ... of spotted fever group rickettsiae by sequencing and analysis of restriction fragment length polymorphism of PCR-amplified DNA ... 2010). Genotyping isolates of Rickettsia akari by restriction fragment length polymorphism analysis of intergenic regions. ( ... 2000). Phylogenetic analysis of the rompB genes of Rickettsia felis and Rickettsia prowazekii European-human and North American ...
https://link.springer.com/chapter/10.1007/978-3-319-46859-4_2

*  ORBi: Browsing ORBi

Therefore, the relationship between the genetic structure, revealed by amplified fragment length polymorphism (AFLP), and the ... essential oil chemical composition, determined by GC/MS analysis, of ylang-ylang grown in semi-managed systems in three Indian ... Genetic and morphological variations were assessed using Amplified Fragments Length Polymorphism and morphometrics traits and ...
orbi.ulg.ac.be/browse?type=author&sort_by=1&order=DESC&rpp=20&etal=3&value=Mahy, Grégory p079710&offset=120

Amplified fragment length polymorphismThermal cyclerGene polymorphismColes PhillipsDNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).Amplified Ribosomal DNA Restriction Analysis: Amplified rDNA (Ribosomal DNA) Restriction Analysis is the extension of the technique of RFLP (restriction fragment length polymorphism) to the gene encoding the small (16s) ribosomal subunit of bacteria. The technique involves an enzymatic amplification using primers directed at the conserved regions at the ends of the 16s gene, followed by digestion using tetracutter Restriction enzymes.Symmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.Community Fingerprinting: Community fingerprinting refers to a set of molecular biology techniques that can be used to quickly profile the diversity of a microbial community. Rather than directly identifying or counting individual cells in an environmental sample, these techniques show how many variants of a gene are present.WGAViewer: WGAViewer is a bioinformatics software tool which is designed to visualize, annotate, and help interpret the results generated from a genome wide association study (GWAS). Alongside the P values of association, WGAViewer allows a researcher to visualize and consider other supporting evidence, such as the genomic context of the SNP, linkage disequilibrium (LD) with ungenotyped SNPs, gene expression database, and the evidence from other GWAS projects, when determining the potential importance of an individual SNP.Genetic variation: right|thumbInfinite alleles model: The infinite alleles model is a mathematical model for calculating genetic mutations. The Japanese geneticist Motoo Kimura and American geneticist James F.Single-strand conformation polymorphism: Single-strand conformation polymorphism (SSCP), or single-strand chain polymorphism, is defined as conformational difference of single-stranded nucleotide sequences of identical length as induced by differences in the sequences under certain experimental conditions. This property allows sequences to be distinguished by means of gel electrophoresis, which separates fragments according to their different conformations.Homing endonuclease: The homing endonucleases are a collection of endonucleases encoded either as freestanding genes within introns, as fusions with host proteins, or as self-splicing inteins. They catalyze the hydrolysis of genomic DNA within the cells that synthesize them, but do so at very few, or even singular, locations.Composite transposon: A composite transposon is similar in function to simple transposons and Insertion Sequence (IS) elements in that it has protein coding DNA segments flanked by inverted, repeated sequences that can be recognized by transposase enzymes. A composite transposon, however, is flanked by two separate IS elements which may or may not be exact replicas.Mycobacterium tuberculosis complex: Mycobacterium tuberculosis complex refers to a genetically related group of Mycobacterium species that can cause tuberculosis in humans or other organisms.Pulsenet: PulseNet is a network run by the Centers for Disease Control and Prevention (CDC) which brings together public health and food regulatory agency laboratories around the United States.http://www.Multiple Loci VNTR Analysis: Multiple Loci VNTR Analysis (MLVA ) is a method employed for the genetic analysis of particular microorganisms, such as pathogenic bacteria, that takes advantage of the polymorphism of tandemly repeated DNA sequences. A "VNTR" is a "variable-number tandem repeat".Chromosome regionsRAPD: RAPD (pronounced "rapid") stands for 'Random Amplified Polymorphic DNA'. It is a type of PCR reaction, but the segments of DNA that are amplified are random.Campylobacter jejuni: Campylobacter jejuni is a species of bacterium commonly found in animal feces. It is curved, helical-shaped, non-spore forming, Gram-negative, and microaerophilic.CampylobacteriosisExogenous bacteria: Exogenous bacteria are microorganisms introduced to closed biological systems from the external world. They exist in aquatic and terrestrial environments, as well as the atmosphere.Silent mutation: Silent mutations are mutations in DNA that do not significantly alter the phenotype of the organism in which they occur. Silent mutations can occur in non-coding regions (outside of genes or within introns), or they may occur within exons.Mycobacterium indicus pranii: Mycobacterium indicus pranii (MIP),Mycobacterium indicus pranii earlier known as Mw, is a non-pathogenic mycobacterial species, which, based on its growth characteristics and metabolic properties,Rahman SA, Singh Y, Kohli S, Ahmad J, Ehtesham NZ, Tyagi AK, Hasnain SE. 2014.Gemmatimonadetes: The Gemmatimonadetes are a family of bacteria, given their own phylum (Gemmatimonadetes). This bacterium makes up about 2% of soil bacterial communities and has been identified as one of the top nine phyla found in soils; yet, there are currently only six cultured isolates.Nested case-control study: A nested case control (NCC) study is a variation of a case-control study in which only a subset of controls from the cohort are compared to the incident cases. In a case-cohort study, all incident cases in the cohort are compared to a random subset of participants who do not develop the disease of interest.Breast pumpFerric uptake regulator family: In molecular biology, the ferric uptake regulator (FUR) family of proteins includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria.Gijs Kuenen: Johannes Gijsbrecht Kuenen (born 9 December 1940, Heemstede) is a Dutch microbiologist who is professor emeritus at the Delft University of Technology and a visiting scientist at the University of Southern California. His research is influenced by, and a contribution to, the scientific tradition of the Delft School of Microbiology.EcosystemGenetic linkage: Genetic linkage is the tendency of alleles that are located close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Genes whose loci are nearer to each other are less likely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be genetically linked.Phenotype microarray: The phenotype microarray approach is a technology for high-throughput phenotyping of cells.Transfer-messenger RNA: Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex (tmRNP) together with Small Protein B (SmpB), Elongation Factor Tu (EF-Tu), and ribosomal protein S1.Rickettsia sibirica: Rickettsia sibirica is a species of Rickettsia. This bacterium is the etiologic agent of North Asian tick typhus, which is also known as Siberian tick typhus.Alpha SerpentisPoint mutationRestriction fragment: A restriction fragment is a DNA fragment resulting from the cutting of a DNA strand by a restriction enzyme (restriction endonucleases), a process called restriction. Each restriction enzyme is highly specific, recognising a particular short DNA sequence, or restriction site, and cutting both DNA strands at specific points within this site.Alternative splicing: Alternative splicing is a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene.DNA condensation: DNA condensation refers to the process of compacting DNA molecules in vitro or in vivo. Mechanistic details of DNA packing are essential for its functioning in the process of gene regulation in living systems.Pedigree chart: A pedigree chart is a diagram that shows the occurrence and appearance or phenotypes of a particular gene or organism and its ancestors from one generation to the next,pedigree chart Genealogy Glossary - About.com, a part of The New York Times Company.Layout of the Port of Tianjin: The Port of Tianjin is divided into nine areas: the three core (“Tianjin Xingang”) areas of Beijiang, Nanjiang, and Dongjiang around the Xingang fairway; the Haihe area along the river; the Beitang port area around the Beitangkou estuary; the Dagukou port area in the estuary of the Haihe River; and three areas under construction (Hanggu, Gaoshaling, Nangang).RaphaninArambiletCodon Adaptation Index: The Codon Adaptation Index (CAI) is the most widespread technique for analyzing Codon usage bias. As opposed to other measures of codon usage bias, such as the 'effective number of codons' (Nc), which measure deviation from a uniform bias (null hypothesis), CAI measures the deviation of a given protein coding gene sequence with respect to a reference set of genes.Campylobacter concisus: Campylobacter concisus is a Gram-negative, spiral, and microaerophilic bacteria. Motile, with either unipolar or bipolar flagella, the organisms have a characteristic spiral/corkscrew appearance and are oxidase-positive.Tuberculosis managementTicks of domestic animals: Ticks of domestic animals directly cause poor health and loss of production to their hosts by many parasitic mechanisms. Ticks also transmit numerous kinds of viruses, bacteria, and protozoa between domestic animals.Protein primary structure: The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.Ligation-independent cloning: Ligation-independent cloning (LIC) is a form of molecular cloning that is able to be performed without the use of restriction endonucleases or DNA ligase. This allows genes that have restriction sites to be cloned without worry of chopping up the insert.Mycobacterium genavense: Mycobacterium genavense is a slow-growing species of the phylum actinobacteria (Gram-positive bacteria with high guanine and cytosine content, one of the dominant phyla of all bacteria), belonging to the genus mycobacterium.National Outbreak Reporting System: ==The National Outbreak Reporting System (NORS)==Beef cattle: Beef cattle are cattle raised for meat production (as distinguished from dairy cattle, used for milk production). The meat of adult cattle is known as beef.Direct repeat: Direct repeats are a type of genetic sequence that consists of two or more repeats of a specific sequence.Fungicide use in the United States: A more accurate title for this page would be "Common plant pathogens to food crops in the United States".MT-RNR2: Mitochondrially encoded 16S RNA (often abbreviated as 16S) is a mitochondrial ribosomal RNA (rRNA) that in humans is encoded by the MT-RNR2 gene. The MT-RNR2 gene also encodes the Humanin polypeptide that has been the target of Alzheimer's disease research.Restriction site: Restriction sites, or restriction recognition sites, are locations on a DNA molecule containing specific (4-8 base pairs in length) sequences of nucleotides, which are recognized by restriction enzymes. These are generally palindromic sequences (because restriction enzymes usually bind as homodimers), and a particular restriction enzyme may cut the sequence between two nucleotides within its recognition site, or somewhere nearby.Symbiosis Center of Health Care: Symbiosis Center of Health Care (SCHC) is an organization under Symbiosis Society which takes care of health of symbiosis family be it student or staff.http://www.Fecal coliform: A fecal coliform (British: faecal coliform) is a facultatively anaerobic, rod-shaped, gram-negative, non-sporulating bacterium. Coliform bacteria generally originate in the intestines of warm-blooded animals.

(1/563) The distribution of genetic diversity in a Brassica oleracea gene bank collection related to the effects on diversity of regeneration, as measured with AFLPs.

The ex situ conservation of plant genetic resources in gene banks involves the selection of accessions to be conserved and the maintenance of these accessions for current and future users. Decisions concerning both these issues require knowledge about the distribution of genetic diversity within and between accessions sampled from the gene pool, but also about the changes in variation of these samples as a result of regenerations. These issues were studied in an existing gene bank collection of a cross-pollinating crop using a selection of groups of very similar Dutch white cabbage accessions, and additional groups of reference material representing the Dutch, and the global white cabbage gene pool. Six accessions were sampled both before and after a standard regeneration. 30 plants of each of 50 accessions plus 6 regeneration populations included in the study were characterised with AFLPs, using scores for 103 polymorphic bands. It was shown that the genetic changes as a result of standard gene bank regenerations, as measured by AFLPs, are of a comparable magnitude as the differences between some of the more similar accessions. The observed changes are mainly due to highly significant changes in allele frequencies for a few fragments, whereas for the majority of fragments the alleles occur in similar frequencies before and after regeneration. It is argued that, given the changes of accessions over generations, accessions that display similar levels of differentiation may be combined safely.  (+info)

(2/563) Use of AFLP for differentiation of Metschnikowia pulcherrima strains for postharvest disease biological control.

Metschnikowia pulcherrima occurs naturally on fruits, buds and floral parts of apple trees. Some strains are effective as biocontrol agents against postharvest decay of apples and other fruits. The usefulness of the amplified fragment length polymorphism (AFLP) technique was evaluated for the genetic analysis of 26 strains of M. pulcherrima, isolated from different sources in different geographical regions. With six AFLP primer pairs, 729 polymorphic bands were scored. The technique showed a high discriminatory power. Genetic relationships between strains were also estimated using AFLP. All the isolates from the carposphere of apple, previously tested as biocontrol agents, were grouped in a single cluster with a high bootstrap value (97), indicating robustness and reproducibility. AFLP patterns could clearly distinguish the different strains and research is in progress to use some putative specific bands for single tag sequence (STS) conversion to develop isolate-specific markers.  (+info)

(3/563) Body size evolution simultaneously creates and collapses species boundaries in a clade of scincid lizards.

Speciation is generally viewed as an irreversible process, although habitat alterations can erase reproductive barriers if divergence between ecologically differentiated species is recent. Reversed speciation might also occur if geographical contact is established between species that have evolved the same reproductive isolating barrier in parallel. Here, we demonstrate a loss of intrinsic reproductive isolation in a clade of scincid lizards as a result of parallel body size evolution, which has allowed for gene flow where large-bodied lineages are in secondary contact. An mtDNA phylogeny confirms the monophyly of the Plestiodon skiltonianus species complex, but rejects that of two size-differentiated ecomorphs. Mate compatibility experiments show that the high degree of body size divergence imposes a strong reproductive barrier between the two morphs; however, the strength of the barrier is greatly diminished between parallel-evolved forms. Since two large-bodied lineages are in geographical contact in the Sierra Nevada Mountains of California, we were also able to test for postzygotic isolation under natural conditions. Analyses of amplified fragment length polymorphisms show that extensive gene exchange is occurring across the contact zone, resulting in an overall pattern consistent with isolation by distance. These results provide evidence of reversed speciation between clades that diverged from a common ancestor more than 12Myr ago.  (+info)

(4/563) Genome scan to detect genetic structure and adaptive genes of natural populations of Cryptomeria japonica.

We investigated 29 natural populations of Cryptomeria japonica using 148 cleaved amplified polymorphic sequence markers to elucidate their genetic structure and identify candidate adaptive genes of this species. In accordance with the inferred evolutionary history of the species during and after the last glacial episode, the genetic diversity was higher in western populations than in northern populations. The results of phylogenetic and genetic structure analyses suggest that populations of the two main varieties of the species have clearly diverged from each other and that two of the examined loci are strongly associated with the differentiation between the two varieties. Using a coalescent simulation based on F(ST) and H(e) values, we detected five genes that had higher, and two that had lower, values than the respective 99% confidence intervals (C.I.s) that are theoretically expected intervals under a neutral infinite-island model. We also detected 13 outlier loci using a coalescent simulation based on the assumption that the 2 varieties originated from the splitting of an ancestral population. Four of these loci were detected by both methods, two of which were detected in a genetic structure analysis as loci associated with differentiation between the two varieties of the species, and are strong candidates for genes that have been subject to selection.  (+info)

(5/563) A linkage map reveals a complex basis for segregation distortion in an interpopulation cross in the moss Ceratodon purpureus.

We report the construction of a linkage map for the moss Ceratodon purpureus (n = 13), based on a cross between geographically distant populations, and provide the first experimental confirmation of maternal chloroplast inheritance in bryophytes. From a mapping population of 288 recombinant haploid gametophytes, genotyped at 121 polymorphic AFLP loci, three gene-based nuclear loci, one chloroplast marker, and sex, we resolved 15 linkage groups resulting in a map length of approximately 730 cM. We estimate that the map covers more than three-quarters of the C. purpureus genome. Approximately 35% of the loci were sex linked, not including those in recombining pseudoautosomal regions. Nearly 45% of the loci exhibited significant segregation distortion (alpha = 0.05). Several pairs of unlinked distorted loci showed significant deviations from multiplicative genotypic frequencies, suggesting that distortion arises from genetic interactions among loci. The distorted autosomal loci all exhibited an excess of the maternal allele, suggesting that these interactions may involve nuclear-cytoplasmic factors. The sex ratio of the progeny was significantly male biased, and the pattern of nonrandom associations among loci indicates that this results from interactions between the sex chromosomes. These results suggest that even in interpopulation crosses, multiple mechanisms act to influence segregation ratios.  (+info)

(6/563) Targeted transcript mapping for agronomic traits in potato.

A combination of cDNA-amplified fragment length polymorphism (AFLP) and bulked segregant analysis (BSA) was used to identify genes co-segregating with earliness of tuberization in a diploid potato population. This approach identified 37 transcript-derived fragments with a polymorphic segregation pattern between early and late tuberizing bulks. Most of the identified transcripts mapped to chromosomes 5 (19 markers) and 12 (eight markers) of the paternal map. Quantitative trait locus (QTL) mapping of tuberization time also identified earliness QTLs on these two chromosomes. A potato bacterial artificial chromosome (BAC) library was screened with four of the markers linked to the main QTL. BAC contigs containing the markers showing the highest association with the trait have been identified. One of these contigs has been anchored to chromosome 5 on an ultradense genetic map of potato, which could be used as a starting point for map-based cloning of genes associated with earliness.  (+info)

(7/563) An assessment of the genetic diversity within Ganoderma strains with AFLP and ITS PCR-RFLP.

Ganoderma lucidum is one of the most important medicinal materials and plant pathogens. Because of its specific interhybridization, the genetic background, however, is relatively unclear. It made identification of Ganoderma strains, especially closely related strains difficulty. Amplified fragment length polymorphism (AFLP) using 14 primer combinations and internal transcribed spacer (ITS) PCR-RFLP were used in a comparative study which was designed to investigate the closely related Ganoderma strains genetic relations at molecular level. The analysis of 37 Ganoderma strains showed there were 177 polymorphic AFLP markers and 12 ITS PCR-RFLP markers, and all accessions could be uniquely identified. Among the Ganoderma accessions, similarity coefficients ranged from 0.07692 to 0.99194 in AFLP. The Ganoderma strains formed a tight cluster in nine groups in AFLP whereas seven groups in ITS PCR-RFLP. The cluster analysis revealed that the taxonomical system of subgenus Ganoderma is composed of Sect. Ganoderma and Sect. Phaeonema, and the strain 22 should be a variant form of strain 21. All methods delineated the Ganoderma strains from the different regions seeming to show a greater level of genetic diversity. It indicated that the genotype study at molecular level is a useful complement method to the current classification system of Ganoderma strains based on morphological traits. The congruency of the experiments was analyzed using the biostatistical software DPS V3.01.  (+info)

(8/563) A large Legionnaires' disease outbreak in Pamplona, Spain: early detection, rapid control and no case fatality.

An outbreak of Legionnaire's disease was detected in Pamplona, Spain, on 1 June 2006. Patients with pneumonia were tested to detect Legionella pneumophila antigen in urine (Binax Now; Binax Inc., Scarborough, ME, USA), and all 146 confirmed cases were interviewed. The outbreak was related to district 2 (22 012 inhabitants), where 45% of the cases lived and 50% had visited; 5% lived in neighbouring districts. The highest incidence was found in the resident population of district 2 (3/1000 inhabitants), section 2 (14/1000). All 31 cooling towers of district 2 were analysed. L. pneumophila antigen (Binax Now) was detected in four towers, which were closed on 2 June. Only the strain isolated in a tower situated in section 2 of district 2 matched all five clinical isolates, as assessed by mAb and two genotyping methods, AFLP and PFGE. Eight days after closing the towers, new cases ceased appearing. Early detection and rapid coordinated medical and environmental actions permitted immediate control of the outbreak and probably contributed to the null case fatality.  (+info)



RAPD


  • 2006), randomly amplified polymorphic DNA (RAPD) analysis (Tay et al. (fiocruz.br)
  • Chaparro JX, Werner DJ, O'Malley D, Sederoff RR (1994) Targeted mapping and linkage analysis of morphological, isozyme, and RAPD markers in peach. (springer.com)
  • Through Random Amplified Polymorphic DNA (RAPD) analysis with OPH20 10-mer primer we unraveled clear alterations corresponding to the loss of specific bands from both parental genomes. (mdpi.com)
  • A unique random amplified polymorphic DNA (RAPD) band of the L. rhamnosus GG strain was isolated and sequenced. (wiley.com)

polymorphic


  • To increase marker density, we developed four cleaved amplified polymorphic sequence markers (CAPS), 19 derived CAPS markers, and four insertion-deletion markers for cherry based on 101 Prunus expressed sequence tags. (springer.com)

AFLP


  • Analysis of Mycoplasma hyosynoviae strains by pulsed-field gel electrophoresis (PFGE), amplified fragment length polymorphism (AFLP), and 16S rDNA sequencing. (dtu.dk)
  • 2010), amplified fragment length polymorphism (AFLP) analysis (Tavanti et al. (fiocruz.br)

restriction


  • Species-specific uniplex polymerase chain reaction (PCR) was performed and compared with sequencing of the D1/D2 region of the LSU 28S rDNA gene, microsatellite typing of C. parapsilosis sensu stricto, and PCR-restriction fragment length polymorphism patterns in the ITS1-5.8S-ITS2 region of the rDNA gene. (fiocruz.br)
  • 2009), restriction fragment length polymorphism (RFLP) pattern analysis (Lockhart et al. (fiocruz.br)
  • The restriction fragment length polymorphism (RFLP) patterns result from the presence of a restriction enzyme cleavage site at one place in the genome in one individual and the absence of that specific site in another individual. (asmscience.org)

markers


  • Amplified fragment length polymorphism generated 175 markers for analyses. (unl.edu)
  • The success rate for identifying SSR markers that could be placed on either the EF or NY maps was only 26% due to two factors: a reduced transferability of other Prunus -species-derived markers and a low level of polymorphism in the mapping parents. (springer.com)
  • To complete the linkage analysis, 61 amplified fragment length polymorphism and seven sequence-related amplified polymorphism markers were also used for map construction. (springer.com)
  • Supplemental Table 1 Markers that did not amplify EF or NY DNA arranged by linkage group a . (springer.com)
  • Aranzana MJ, Garcia-Mas J, Carbo J, Arús P (2002) Development and variability analysis of microsatellite markers in peach. (springer.com)

sequence analysis


  • 2012), intein sequence analysis (Prandini et al. (fiocruz.br)
  • Amplified fragment length polymorphism and multilocus sequence analysis-based genotypic relatedness among pathogenic variants of Xanthomonas citri pv. (straininfo.net)