Amplified fragment length polymorphism analysis. Medical search

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.Haplotypes: The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.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.Japan Heterozygote Detection: Identification of genetic carriers for a given trait.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.Helicobacter Infections: Infections with organisms of the genus HELICOBACTER, particularly, in humans, HELICOBACTER PYLORI. The clinical manifestations are focused in the stomach, usually the gastric mucosa and antrum, and the upper duodenum. This infection plays a major role in the pathogenesis of type B gastritis and peptic ulcer disease.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.Helicobacter pylori: A spiral bacterium active as a human gastric pathogen. It is a gram-negative, urease-positive, curved or slightly spiral organism initially isolated in 1982 from patients with lesions of gastritis or peptic ulcers in Western Australia. Helicobacter pylori was originally classified in the genus CAMPYLOBACTER, but RNA sequencing, cellular fatty acid profiles, growth patterns, and other taxonomic characteristics indicate that the micro-organism should be included in the genus HELICOBACTER. It has been officially transferred to Helicobacter gen. nov. (see Int J Syst Bacteriol 1989 Oct;39(4):297-405).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.India 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.Belgium Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Turkey Genes, 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.Brazil Interspersed Repetitive Sequences: Copies of transposable elements interspersed throughout the genome, some of which are still active and often referred to as "jumping genes". There are two classes of interspersed repetitive elements. Class I elements (or RETROELEMENTS - such as retrotransposons, retroviruses, LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS) transpose via reverse transcription of an RNA intermediate. Class II elements (or DNA TRANSPOSABLE ELEMENTS - such as transposons, Tn elements, insertion sequence elements and mobile gene cassettes of bacterial integrons) transpose directly from one site in the DNA to another.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.

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

Amplified fragment length polymorphism

... analysis. There are many advantages to AFLP when compared to other marker technologies including randomly amplified polymorphic ... "Amplified fragment length polymorphism", the resulting data are not scored as length polymorphisms, but instead as presence- ... restriction fragment length polymorphism (RFLP), and microsatellites. AFLP not only has higher reproducibility, resolution, and ... A subset of the restriction fragments is then selected to be amplified. This selection is achieved by using primers ...

Terminal restriction fragment length polymorphism

... a tool for optimal resolution of terminal restriction fragment length polymorphism analysis based on user defined primer-enzyme ... The method is based on digesting a mixture of PCR amplified variants of a single gene using one or more restriction enzymes and ... a PCR-Related Bias Affecting Terminal Restriction Fragment Length Polymorphism Analysis of Microbial Community Structure". Appl ... Terminal restriction fragment length polymorphism (TRFLP or sometimes T-RFLP) is a molecular biology technique for profiling of ...

Bacillus subtilis

"Detection of molecular diversity in Bacillus atrophaeus by amplified fragment length polymorphism analysis". Applied and ... Molecular assays (randomly amplified polymorphic DNA PCR assay, denaturing gradient gel electrophoresis analysis, and ... In B. subtilis the length of transferred DNA is greater than 1271kb (more than 1 million bases). The transferred DNA is likely ... Microarray-based comparative genomic analyses have revealed that B. subtilis members show considerable genomic diversity. ...

Sorbaronia mitschurinii

"Investigations into the origin of Aronia mitschurinii using amplified fragment length polymorphism analysis". HortScience. 48 ( ...

Bacillus atrophaeus

"Detection of molecular diversity in Bacillus atrophaeus by amplified fragment length polymorphism analysis". Applied and ... "Detection of Molecular Diversity in Bacillus atrophaeus by Amplified Fragment Length Polymorphism Analysis". Applied and ... Modern phylogenetic analyses using multiple genetic methods have placed B. atrophaeus close to B. subtilis. Its original and ... Subsequent genomic and phenotypic analysis of strains derived from the Camp Detrick isolates revealed that they had been ...

Nepenthes × hookeriana

Study of natural hybridisation in some tropical plants using amplified fragment length polymorphism analysis. M.Sc. thesis, ...

Nepenthes × trichocarpa

Study of natural hybridisation in some tropical plants using amplified fragment length polymorphism analysis. M.Sc. thesis, ... with two fringed wings over the whole length. The colour of the pitchers ranges from green to spotted or striped with red or ...

Xanthomonas

Other tools, including multilocus sequence analysis and amplified fragment-length polymorphism, have been used for ... More recently, genome-wide analysis of multiple Xanthomonas strains mostly supports the previous phylogenies. Individual cell ... "New Zealand strains of plant pathogenic bacteria classified by multi-locus sequence analysis; proposal of Xanthomonas dyei sp. ...

Campylobacter concisus

... yet genomically distinct genomospecies by analysis of amplified fragment length polymorphisms (AFLP), housekeeping genes and a ... "Delineation of Campylobacter concisus Genomospecies by Amplified Fragment Length Polymorphism Analysis and Correlation of ... "Genome analysis of Campylobacter concisus strains from patients with inflammatory bowel disease and gastroenteritis provides ... "Delineation of genetic relatedness and population structure of oral and enteric Campylobacter concisus strains by analysis of ...

Mycobacterium ulcerans

... profile analysis and IS 2404 restriction fragment length polymorphism and amplified fragment length polymorphism fingerprinting ... "Evaluation of amplified fragment length polymorphism analysis for inter- and intraspecific differentiation of Mycobacterium ... and gel analysis of the amplification fragments. Typically 50-100 restriction fragments are amplified and detected on ... Molecular analysis of M. ulcerans has revealed two insertion sequences: IS2404 and IS2606. Southern blot analysis to detect ...

Clostridium novyi

November 2002). "Amplified fragment length polymorphism (AFLP) analysis of Clostridium novyi, C. perfringens and Bacillus ... The toxin is a large 250-kDa protein the active part of which is the NH2-terminal 551 amino acid fragment. Alpha-toxins are ... Hofmann F, Herrmann A, Habermann E, von Eichel-Streiber C (June 1995). "Sequencing and analysis of the gene encoding the alpha- ... have demonstrated by 16S rDNA sequence analysis. Growth in culture proceeds through 3 stages: Initial growth wherein no toxin ...

Yersinia bercovieri

... and Yersinia bercovieri Strains from Switzerland by Amplified Fragment Length Polymorphism Analysis". Applied and Environmental ...

Hispid cotton rat

"Amplified fragment length polymorphism and mitochondrial DNA analyses reveal patterns of divergence and hybridization in the ... Adult size is total length 202-340 mm (7.9-13 in); tail 87-122 mm (3.4-4.8 in), frequently broken or stubbed; hind foot 29-35 ... Smith, Ronald A.; Hanebrink, Earl L. (1982). "Analysis of regurgitated short-eared owl (Asio flammeus) pellets from the Roth ...

Trimeresurus albolabris

The use of amplified fragment length polymorphism in determining species trees at fine taxonomic levels: analysis of a ... Maximum total length males 600 mm (24 in), females 810 mm (32 in); maximum tail length males 120 mm (4.7 in), females 130 mm ( ...

Trimeresurus albolabris septentrionalis

The use of amplified fragment length polymorphism in determining species trees at fine taxonomic levels: analysis of a ... Total length males 610 mm, females 730 mm. The head scalation consists of 10-11(12) upper labials, the first of which are fused ...

Clostridium ramosum

... of Clostridium Species and DNA Fingerprinting of Clostridium perfringens by Amplified Fragment Length Polymorphism Analysis ( ...

Candida auris

Amplified fragment length polymorphism analysis of C. auris isolates from the United Kingdom, India, Japan, South Africa, South ... All isolates were of the same clonal strain and were only identified positively by DNA sequence analysis. As previously, the ... Phenotypic, chemotaxonomic and phylogenetic analyses established C. auris as a new strain of the genus Candida. The first three ... Whole genome sequencing and analyses of isolates from Pakistan, India, South Africa, Venezuela, Japan and previously sequenced ...

Lactobacillus fabifermentans

... pheS sequence analysis, whole-cell protein electrophoresis, fluorescent amplified fragment length polymorphism analysis and ... Analysis of the 16S rRNA gene sequence demonstrated that this species is a member of the Lactobacillus plantarum species group ... "Metagenomic analysis of the microbial community in fermented grape marc reveals that Lactobacillus fabifermentans is one of the ... but further analysis demonstrated that it is possible to differentiate it from the nearest neighbors by means of DNA-DNA ...

Acinetobacter

... random amplified polymorphic DNA, amplified fragment length polymorphism (AFLP), restriction and sequence analysis of tRNA and ... 16S-23S rRNA gene spacers and amplified 16S ribosomal DNA restriction analysis (ARDRA). PFGE, AFLP, and ARDRA are validated ...

Arundinaria

... but upon in depth analysis using modern phylogenetic methods based on morphology and amplified fragment length polymorphisms, ...

Rosa canina

From DNA analysis using amplified fragment length polymorphisms of wild-rose samples from a transect across Europe (900 samples ... De Riek, Jan; De Cock, Katrien; Smulders, Marinus J.M.; Nybom, Hilde (2013). "AFLP-based population structure analysis as a ...

Orbicella annularis

Genetic analysis of the Montastraea annularis complex using amplified fragment length polymorphisms and a microsatellite marker ... "A multi-character analysis of the Caribbean coral Montastraea annularis (Ellis and Solander 1786) and its two sibling species, ...

Academy of Natural Sciences of Drexel University

Recent molecular work mainly employs DNA sequencing, microsatellites, and AFLP (amplified fragment length polymorphism). In ... One such undertaking is the analyses of diatom assemblages in lake sediments (sediment cores) throughout the eastern United ... Substantial increases in annual mean temperatures and growing season length in this semiarid landscape have resulted in ... Studies may range from the analysis of fish tissues for contaminants, monitoring fish populations for environmental assessments ...

European bison

An earlier study, using amplified fragment-length polymorphism fingerprinting, showed a close association of wisent and ... and gayal Y chromosome analysis associated wisent and American bison. ...

Nucleotide diversity

... data and Amplified Fragment Length Polymorphism (AFLP) data. DnaSP - DNA Sequence Polymorphism, is a software package for the ... analysis of nucleotide polymorphism from aligned DNA sequence data. MEGA, Molecular Evolutionary Genetics Analysis, is a ... "Estimating nucleotide diversity from random amplified polymorphic DNA and amplified fragment length polymorphism data". ... Nucleotide diversity is a concept in molecular genetics which is used to measure the degree of polymorphism within a population ...

Multiplex ligation-dependent probe amplification

In a standard multiplex PCR reaction, each fragment needs a unique amplifying primer pair. These primers being present in a ... MLPA has a variety of applications including detection of mutations and single nucleotide polymorphisms, analysis of DNA ... Each complete probe has a unique length, so that its resulting amplicons can be separated and identified by (capillary) ... Dosage quotient analysis is the usual method of interpreting MLPA data. If a and b are the signals from two amplicons in the ...

American bison

Y chromosome analysis associated wisent and American bison. An earlier study using amplified fragment length polymorphism ... "Genetic relationship of wood and plains bison based on restriction fragment length polymorphisms" (PDF). Can J Zool. 69 (1): 43 ... 2006). "Taxonomic placement and origin of yaks: implications from analyses of mtDNA D-loop fragment sequences". Acta ... Head-and-body lengths range from 2 to 3.5 m (6.6 to 11.5 ft) long, the tail adding 30 to 91 cm (12 to 36 in). Shoulder heights ...

Amplified Fragment Length Polymorphism - AFLP Analysis | Thermo Fisher Scientific - US

Following restriction enzyme digestion of DNA, a subset of DNA fragments is selected for PCR amplification and visualization. A ... AFLP is a technique used to detect polymorphisms in DNA when no information about the genome is known. ... Application Note: Amplified Fragment Length Polymorphism (AFLP®) Analysis on Applied Biosystems Capillary Electrophoresis ... Application Note: Amplified Fragment Length Polymorphism (AFLP®) Analysis on Applied Biosystems Capillary Electrophoresis ...

https://www.thermofisher.com/us/en/home/life-science/sequencing/fragment-analysis/amplified-fragment-length-polymorphism-aflp-analysis.html

Genetic Diversity of Actinobacillus pleuropneumoniae Assessed by Amplified Fragment Length Polymorphism Analysis | Journal of...

Genetic Diversity of Actinobacillus pleuropneumoniae Assessed by Amplified Fragment Length Polymorphism Analysis Branko ... Genetic Diversity of Actinobacillus pleuropneumoniae Assessed by Amplified Fragment Length Polymorphism Analysis ... Genetic Diversity of Actinobacillus pleuropneumoniae Assessed by Amplified Fragment Length Polymorphism Analysis ... Genetic Diversity of Actinobacillus pleuropneumoniae Assessed by Amplified Fragment Length Polymorphism Analysis ...

https://jcm.asm.org/content/45/12/3921

Frontiers | Whole Genome-Based Amplified Fragment Length Polymorphism Analysis Reveals Genetic Diversity in Candida africana |...

Amplified fragment length polymorphism (AFLP) fingerprint analysis yielded greater genotypic heterogeneity among the C. ... Amplified fragment length polymorphism (AFLP) fingerprint analysis yielded greater genotypic heterogeneity among the C. ... africana strains lack N-acetylglucosamine assimilation and sequence analysis of the HXK1 gene showed a distinctive polymorphism ... Moreover, all examined C. africana strains lack N-acetylglucosamine assimilation and sequence analysis of the HXK1 gene showed ...

https://www.frontiersin.org/articles/10.3389/fmicb.2017.00556/full

Comparison of Amplified Ribosomal DNA Restriction Analysis, Random Amplified Polymorphic DNA Analysis, and Amplified Fragment...

Random Amplified Polymorphic DNA Analysis, and Amplified Fragment Length Polymorphism Fingerprinting for Identification of ... Comparison of Amplified Ribosomal DNA Restriction Analysis, Random Amplified Polymorphic DNA Analysis, and Amplified Fragment ... Comparison of Amplified Ribosomal DNA Restriction Analysis, Random Amplified Polymorphic DNA Analysis, and Amplified Fragment ... Comparison of Amplified Ribosomal DNA Restriction Analysis, Random Amplified Polymorphic DNA Analysis, and Amplified Fragment ...

https://jcm.asm.org/content/36/9/2522?ijkey=a54d75d7d7a24836aa3969d4c4a942677eb07169&keytype2=tf_ipsecsha

Genetic Analysis and Identification of Amplified Fragment Length Polymorphism Markers Linked to the alm1 Avirulence Gene of...

Amplified fragment length polymorphism (AFLP) markers were used to generate a rudimentary genetic linkage map of the L. ... The analysis of segregating F(1) progenies and 14 test crosses suggested that a single major gene is involved in the ... Genetic Analysis and Identification of Amplified Fragment Length Polymorphism Markers Linked to the alm1 Avirulence Gene of ... article{Pongam1998GeneticAA, title={Genetic Analysis and Identification of Amplified Fragment Length Polymorphism Markers ...

https://www.semanticscholar.org/paper/Genetic-Analysis-and-Identification-of-Amplified-to-Pongam-Osborn/3adb11c444b9caa0bffa95a19c056e2a77c4483f

Analyses of amplified fragment length polymorphisms (AFLP) indicate rapid radiation of Diospyros species (Ebenaceae) endemic to...

... species and evaluate species boundaries we analysed genome-wide DNA variation via amplified fragment length polymorphisms (AFLP ... Correspondingly, analyses of molecular variance showed more variation within species than between them. A Bayesian analysis ... In other cases, our analyses may have revealed evidence for the existence of cryptic species, for which more study of ... highly congruent with those observed in a principal coordinate analysis (PCO). Molecular divergence between the two groups is ...

https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-13-269

Restriction Fragment Length Polymorphism Analysis of PCR-Amplified Fragments (PCR-RFLP) and Gel Electrophoresis - Valuable Tool...

Restriction Fragment Length Polymorphism Analysis of PCR-Amplified Fragments (PCR-RFLP) and Gel Electrophoresis - Valuable Tool ... Henrik Berg Rasmussen (April 4th 2012). Restriction Fragment Length Polymorphism Analysis of PCR-Amplified Fragments (PCR-RFLP ... Henrik Berg Rasmussen (April 4th 2012). Restriction Fragment Length Polymorphism Analysis of PCR-Amplified Fragments (PCR-RFLP ... embed/gel-electrophoresis-principles-and-basics/restriction-fragment-length-polymorphism-analysis-of-pcr-amplified-fragments- ...

https://www.intechopen.com/books/gel-electrophoresis-principles-and-basics/restriction-fragment-length-polymorphism-analysis-of-pcr-amplified-fragments-pcr-rflp-and-related-te/

Sequence Elimination and Cytosine Methylation Are Rapid and Reproducible Responses of the Genome to Wide Hybridization and...

Amplified Fragment Length Polymorphism (AFLP) Analysis. The AFLP procedure was performed according to the protocol of Gibco BRL ... allotetraploids by screening a large number of loci using amplified fragment length polymorphism and DNA gel blot analysis and ... and their derived synthetic allotetraploids using amplified fragment length polymorphism (AFLP) (Vos et al., 1995) and ... Cloning of Fragments Subjected to Genetic or Epigenetic Alterations and Validation by DNA Gel Blot Analysis. Fragments that ...

http://www.plantcell.org/content/13/8/1749?ijkey=73a48ff3d51fd1bfb95f1060a01f6b3a42e29911&keytype2=tf_ipsecsha

Sequence Elimination and Cytosine Methylation Are Rapid and Reproducible Responses of the Genome to Wide Hybridization and...

http://www.plantcell.org/content/13/8/1749?ijkey=59baaec527f00e0cd29eb5930f4e124806cbc72b&keytype2=tf_ipsecsha

Patent US7893325 - Brassica plant resistant to the fungus Leptosphaeria maculans (blackleg) - Google Patents

... wherein this fragment comprises a blackleg resistance locus. Further provided are molecular markers linked to the blackleg ... Provided are Brassica plants and seeds comprising a fragment of chromosome 8 of a wild B. rapa accession in their genome, ... Amplified Fragment Length Polymorphism (AFLP) Analysis. DNA Extraction. DNA was extracted from parental lines, control lines, ... 1990), NAR 18: 6531-6535], AFLP [Amplified Fragment Length Polymorphism; Vos et al. (1995) NAR 23: 4407-4414], SNPs or ...

http://www.google.com/patents/US7893325?dq=7143430

A. Jonathan Shaw, Professor of Biology and Curator of Bryophytes, Duke Herbarium

Adenosine Kinase • Algal Proteins • Alleles • Amplified Fragment Length Polymorphism Analysis • Antarctic Regions • Arabidopsis ... Polymorphism, Single Nucleotide • Polyploidy • Population Dynamics • Population Growth • Principal Component Analysis • ... Current projects in the lab include molecular phylogenetic analyses of familial and ordinal level relationships in the ... Sequence Analysis, DNA • Soil • Species Specificity • Sphagnopsida • Transcriptome • Tropical Climate. Curriculum Vitae. ...

http://fds.duke.edu/db/aas/Herbarium/brophytes/shaw

Genomic Regions Analysis of Seedling Root Traits and Their Regulation in Responses to Phosphorus Deficiency Tolerance in CSSL...

Amplified Fragment Length Polymorphism Analysis. The detection of RESTRICTION FRAGMENT LENGTH POLYMORPHISMS by selective PCR ... of restriction fragments derived from genomic DNA followed by electrophoretic analysis of the amplified restriction fragments. ... Genomic Regions Analysis of Seedling Root Traits and Their Regulation in Responses to Phosphorus Deficiency Tolerance in CSSL ... Genomic Analysis of Peritoneal Mesothelioma by CGH Arrays. Peritoneal mesothelioma is a rare disease representing one third of ...

https://www.bioportfolio.com/resources/pmarticle/2044256/Genomic-Regions-Analysis-of-Seedling-Root-Traits-and-Their-Regulation-in-Responses.html

Rates of evolution of avirulence phenotypes and DNA markers in a northwest European population of Puccinia striiformis f. sp....

Amplified Fragment Length Polymorphism Analysis. Basidiomycota / genetics*, isolation & purification, pathogenicity. Europe. ... and assayed for 14 individual avirulence/virulence alleles and up to 234 amplified fragment length polymorphism (AFLP) primer ... The large number of fragments and a targeted sampling of isolates allowed a reconstruction of phylogenies in great detail, i.e ... per AFLP fragment (locus) per generation, whereas the effective rate by which a mutation from avirulence to virulence was ...

http://www.biomedsearch.com/nih/Rates-evolution-avirulence-phenotypes-DNA/17887968.html

A comprehensive analysis of hydrogen peroxide-induced gene expression in tobacco | PNAS

cDNA-Amplified Fragment Length Polymorphism (AFLP) Analysis and Data Processing. cDNA-AFLP and data were processed essentially ... Abbreviations: AFLP, amplified fragment length polymorphism; CAT1AS, catalase1-deficient tobacco plants; Fv/Fm, measure for ... 14,000 genes were monitored by using transcript profiling technology based on cDNA-amplified fragment length polymorphism. ... Clustering and sequence analysis of 713 differentially expressed transcript fragments revealed a transcriptional response that ...

https://www.pnas.org/content/100/26/16113?ijkey=f2fed2ffe0ff9eaa76fbc702c8b1a9b0456ae223&keytype2=tf_ipsecsha

DNA sequence conservation between the Bacillus anthracis pXO2 plasmid and genomic sequence from closely related bacteria | BMC...

Dot-blot DNA hybridizations between pXO2 ORF fragments and total genomic DNA from AWO6 were consistent with the PCR assay ... analysis, were examined by PCR for the presence of sequences similar to 47 pXO2 ORFs. The two most distantly related isolates ... of pXO2 sequences in the other Bacillus isolates did not correlate with genomic relatedness established by AFLP analysis. The ... as determined by amplified fragment length polymorphism (AFLP) ... Amplified fragment length polymorphism (AFLP) analysis of over ...

https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-3-34

Comparative Genome Analysis of the Mollicutes | SpringerLink

capripneumoniae detected by amplified fragment length polymorphism (AFLP) analysis. FEMS Microbiol. Lett. 184:63-68.PubMed ... Amplify Fragment Length Polymorphism Comparative Genome Analysis Mycoplasma Pneumoniae Mycoplasma Genitalium Genome Phylogeny ... Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24:4420-4449.PubMedCentral ... ComChapautive analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium. Nucleic Acids Res. 25: ...

https://link.springer.com/chapter/10.1007%2F0-306-47606-1_11

A latitudinal cline in flowering time in Arabidopsis thaliana modulated by the flowering time gene FRIGIDA | PNAS

Analysis of amplified fragment length polymorphism loci described by Sharbel et al. (29) by K.M.O. and M.D.P. (unpublished ... we performed the same analyses with 59 of the amplified fragment length polymorphism (AFLP) loci from Sharbel et al.s data set ... based on analysis of the allelic variation at FRI (10). Moreover, an excess of nonsynonymous polymorphisms have been described ... Preliminary analysis indicated that days until bolting was highly correlated with rosette leaf number (r = 0.72, P , 0.0001), a ...

https://www.pnas.org/content/101/13/4712?ijkey=ecf9ad986564dccf98e575606ac70f8e950c07e6&keytype2=tf_ipsecsha

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Survival analysis showed a half-life of 13 months for ESBL-ST131 carriage, vs two to three months for other ESBL-EC (p , 0.001 ... Amplified-fragment length polymorphism analysis: the state of an art. J Clin Microbiol. 1999;37(10):3083-91. PMID: 10488158 ... Survival analysis showed a half-life of 13 months for ESBL-ST131 carriage, vs two to three months for other ESBL-EC (p , 0.001 ... The relationship between antimicrobial resistance and patient outcomes: mortality, length of hospital stay, and health care ...

https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2016.21.42.30376

Study of Blood Samples From High-Risk Postmenopausal Women Who Received Treatment on Breast Cancer Prevention Clinical Trials...

Amplified Fragment Length Polymorphism Analysis. The detection of RESTRICTION FRAGMENT LENGTH POLYMORPHISMS by selective PCR ... of restriction fragments derived from genomic DNA followed by electrophoretic analysis of the amplified restriction fragments. ... A case-control study and meta-analysis reveal the association between COX-2 G-765C polymorphism and primary end-stage hip and ... "NQO1 Gene C609T Polymorphism (dbSNP: rs1800566) and Digestive Tract Cancer Risk: A Meta-Analysis." ...

https://www.bioportfolio.com/resources/trial/73307/Study-of-Blood-Samples-From-High-Risk-Postmenopausal-Women-Who-Received-Treatment.html

Intraspecific Phylogeny and Lineage Group Identification Based on the prfA Virulence Gene Cluster of Listeria monocytogenes† |...

Ripabelli, G., J. McLauchlin, and E. J. Threlfall.2000 . Amplified fragment length polymorphism (AFLP) analysis of Listeria ... and amplified fragment length polymorphism studies (3, 11, 24, 26). However, ribotype and virulence gene polymorphism data were ... AL591824) was included in the phylogenetic analyses. Prior to phylogenetic analyses, ambiguously aligned characters and ... Phylogenetic analyses of the combined pVGC data resolved three distinct L. monocytogenes lineages, with each of the lineages ...

https://jb.asm.org/content/186/15/4994

Frontiers | Floral Volatiles in Parasitic Plants of the Orobanchaceae. Ecological and Taxonomic Implications | Plant Science

Moreover, phylogenetic analysis suggested separation of the broomrapes into two main groups parasitizing annual and perennial ... Moreover, phylogenetic analysis suggested separation of the broomrapes into two main groups parasitizing annual and perennial ... analysis (Román et al., 2003), proteomics (Castillejo et al., 2009), amplified fragment length polymorphism (AFLP) analysis ( ... within and between European populations of Phelipanche ramosa revealed by amplified fragment length polymorphism analysis. Weed ...

https://www.frontiersin.org/articles/10.3389/fpls.2016.00312/full

Remodeling of DNA Methylation and Phenotypic and Transcriptional Changes in Synthetic Arabidopsis Allotetraploids | Plant...

Example of cDNA-amplified fragment length polymorphism (AFLP) analysis. Selections of autoradiographs from cDNA-AFLP ... The c-DNA used for the RT-PCR analysis of all three genes was prepared from the original RNA used for c-DNA-AFLP analysis in ... MSAP Fragment3-a. Len. Rd3-b. Primers3-cEco/M-H. Pattern3-d. GenBank Accession No.. Chromosome (Bacteria Artificial Chromosome ... B, Analysis of replicate blots of four allotetraploid plants either probed with the Arabidopsis or the C. arenosa 180-bp ...

http://www.plantphysiol.org/content/129/2/733/tab-figures-data

Proceedings of the Royal Society of London B: Biological Sciences

Amplified fragment length polymorphism (AFLP) analysis (Vos et al. 1995) was performed for I. punctigera specimens collected at ... 2002 Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship ... amplified fragment length polymorphisms. The unrooted trees were constructed based on Neis genetic distance between ... In addition, a 934-bp fragment of nuclear elongation factor-1α (EF-1α) gene region was PCR-amplified using primers 5′-TGC GGT ...

http://rspb.royalsocietypublishing.org/content/276/1668/2711.short

First Report of Sequence Type 1, Pathotype A Xanthomonas citri pv. citri from Lime and Lemon Fruit Originating from Bangladesh

Amplified fragment length polymorphism (AFLP) analysis of all X. citri pv. citri isolates from Bangladesh and additional ... The expected DNA fragment was only obtained from all of the bacterial isolates using primer pair 4/7 (3). Multilocus sequence ... All five ST1 isolates grouped as a single cluster by AFLP, although not strongly supported by bootstrap analysis. Evolutionary ... Identification of 18 isolates as Xanthomonas was carried out initially by fatty acid methyl ester (FAME) analysis. ...

https://www.apsnet.org/publications/plantdisease/2013/June/Pages/97_6_836.1.aspx

Following restriction enzyme digestion of DNA, a subset of DNA fragments is selected for PCR amplification and visualization. (thermofisher.com)
Cut genomic DNA into fragments with the restriction enzymes Msel and EcoRI and Ligate adaptors. (thermofisher.com)
These include pulsed-field gel electrophoresis ( 14 , 25 ), ribotyping ( 9 , 12 , 25 ), and PCR-based fingerprinting techniques such as random amplified polymorphic DNA analysis (RAPD) ( 15 ), repetitive extragenic palindromic sequence-based PCR ( 26 ), amplified ribosomal DNA restriction analysis (ARDRA) ( 35 ), and RNA spacer fingerprinting ( 11 ). (asm.org)
A restriction fragment length polymorphism (RFLP) analysis of the 16S rDNAs was performed with Smal and MluI. (kribb.re.kr)

This technique detects multiple DNA fragments by means of polymerase chain reaction (PCR) amplification. (thesourcenatural.com)

To identify genes associated with breast events (i.e., the occurrence of invasive breast cancer or ductal carcinoma in situ), in terms of single-nucleotide polymorphisms (SNPs) in a genome-wide association study, in Caucasian women at high risk of developing breast cancer who have received a selective estrogen receptor modulator (SERM) (i.e., tamoxifen or raloxifene) on the NSABP-P-1 OR NSABP-P-2 breast cancer prevention clinical trials. (bioportfolio.com)
DNA samples are used to identify and analyze single nucleotide polymorphisms. (bioportfolio.com)
A single nucleotide polymorphism (SNP, pronounced "snip") is a natural variation in the population. (thesourcenatural.com)

Two primary evolutionary divisions, or lineages, have been identified within L. monocytogenes on the basis of multilocus enzyme electrophoresis, pulsed-field gel electrophoresis, ribotyping, and amplified fragment length polymorphism studies ( 3 , 11 , 24 , 26 ). (asm.org)

Clustering and sequence analysis of 713 differentially expressed transcript fragments revealed a transcriptional response that mimicked that reported during both biotic and abiotic stresses, including the up-regulation of genes involved in the hypersensitive response, vesicular transport, posttranscriptional processes, biosynthesis of ethylene and jasmonic acid, proteolysis, mitochondrial metabolism, and cell death, and was accompanied by a very rapid up-regulation of several signal transduction components. (pnas.org)

Current projects in the lab include molecular phylogenetic analyses of familial and ordinal level relationships in the arthrodontous mosses, studies of hybridization using molecular and morphological markers, and investigations of cryptic speciation within geographically widespread species. (duke.edu)
Ongoing research is grounded in phylogenetic analyses at various levels of biological organization from populations up to genus-wide. (duke.edu)
The results of the multigene phylogenetic analyses confirm that L. monocytogenes comprises at least three evolutionary lineages, demonstrate that lineages most frequently (lineage 1) and least frequently (lineage 3) associated with human listeriosis are sister-groups, and reveal for the first time that the human epidemic associated serotype 4b is prevalent among strains from lineage 1 and lineage 3. (asm.org)
Moreover, phylogenetic analysis suggested separation of the broomrapes into two main groups parasitizing annual and perennial hosts, and for the annual hosts, into weedy and non-weedy broomrapes. (frontiersin.org)

To address these matters, we have surveyed F1 hybrids between diploid species from the wheat ( Aegilops and Triticum ) group and their derived allotetraploids by screening a large number of loci using amplified fragment length polymorphism and DNA gel blot analysis and by assaying the extent of cytosine methylation. (plantcell.org)

Provided are Brassica plants and seeds comprising a fragment of chromosome 8 of a wild B. rapa accession in their genome, wherein this fragment comprises a blackleg resistance. (google.com)

Amplified fragment length polymorphism fingerprint analysis yielded greater genotypic heterogeneity among the C. africana strains. (frontiersin.org)

B, Analysis of replicate blots of four allotetraploid plants either probed with the Arabidopsis or the C. arenosa 180-bp centromeric repeat (one control and three azadC-treated). (plantphysiol.org)

Genetic analysis of roots and shoots in rice seedling by association mapping. (bioportfolio.com)

We found that purification of amplified 16S rDNA products following PCR was necessary for our RFLP analysis. (kribb.re.kr)

Correspondingly, analyses of molecular variance showed more variation within species than between them. (biomedcentral.com)
These QTLs need further analysis, including the fine mapping and cloning, which may use in molecular marker assisted breeding. (bioportfolio.com)

In other cases, our analyses may have revealed evidence for the existence of cryptic species, for which more study of morphology and ecology are now required. (biomedcentral.com)
Finally, analyses of haplotype diversity indicate that lineage 1 has experienced a purge of genetic variation that was not observed in the other lineages, suggesting that the three L. monocytogenes lineages may represent distinct species within the framework of the cohesion species concept. (asm.org)

PCR is used to amplify specific regions of a DNA strand (the DNA target). (thesourcenatural.com)

Forest fragments commonly exhibit suboptimal site conditions, which can result in enhanced clonal reproduction, and a potential reduction in clonal diversity due to increased selfing and inbreeding depression. (cambridge.org)

The overall quality, accuracy and length of the DNA sequence read can be significantly affected by characteristics of the sample itself, and the method chosen for nucleic acid extraction. (thermofisher.com)
Another Bayesian method, this time a clustering method, Structure, demonstrated the presence of two groups, highly congruent with those observed in a principal coordinate analysis (PCO). (biomedcentral.com)

Clonal diversity (Pd) of patches was slightly, yet significantly, lower in forest fragments compared with continuous forest. (cambridge.org)

Many studies have reported that MTHFR C677T (rs 1801133) polymorphism is associated with the risk of alcohol dependence(AD). (bioportfolio.com)

See Figure 4 C for analysis of centromeric repeat methylation in the affected versus unaffected tissue. (plantphysiol.org)

Large-scale genetic [ 10 ] and immunohistochemistry [ 11 ] analyses suggest that DFTD is clonally derived from cells in the neural crest lineage, most probably Schwann cells. (royalsocietypublishing.org)

The recent sequencing of the Tasmanian devil and DFT genomes [ 16 , 17 ] has also demonstrated very low levels of genetic polymorphism in both devils and DFT cells [ 16 , 17 ]. (royalsocietypublishing.org)

RATIONALE: DNA analysis of tumor tissue may help doctors predict how well patients will respond to treatment. (bioportfolio.com)

High voltage is applied so that the fluorescent DNA fragments are separated by size and are detected by a laser/camera system. (thermofisher.com)

A case-control study and meta-analysis reveal the association between COX-2 G-765C polymorphism and primary end-stage hip and knee osteoarthritis. (bioportfolio.com)

A Bayesian analysis with BEAST produced a similar result. (biomedcentral.com)

A STRUCTURE analysis did not show any clear clustering of patches in the continuous forest and forest fragments. (cambridge.org)

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

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

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

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

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

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

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

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

Amplified fragment length polymorphism

Terminal restriction fragment length polymorphism

Bacillus subtilis

Sorbaronia mitschurinii

Bacillus atrophaeus

Nepenthes × hookeriana

Nepenthes × trichocarpa

Xanthomonas

Campylobacter concisus

Mycobacterium ulcerans

Clostridium novyi

Yersinia bercovieri

Hispid cotton rat

Trimeresurus albolabris

Trimeresurus albolabris septentrionalis

Clostridium ramosum

Candida auris

Lactobacillus fabifermentans

Acinetobacter

Arundinaria

Rosa canina

Orbicella annularis

Academy of Natural Sciences of Drexel University

European bison

Nucleotide diversity

Multiplex ligation-dependent probe amplification

American bison

Amplified Fragment Length Polymorphism - AFLP Analysis | Thermo Fisher Scientific - US

Genetic Diversity of Actinobacillus pleuropneumoniae Assessed by Amplified Fragment Length Polymorphism Analysis | Journal of...

Frontiers | Whole Genome-Based Amplified Fragment Length Polymorphism Analysis Reveals Genetic Diversity in Candida africana |...

Comparison of Amplified Ribosomal DNA Restriction Analysis, Random Amplified Polymorphic DNA Analysis, and Amplified Fragment...

Genetic Analysis and Identification of Amplified Fragment Length Polymorphism Markers Linked to the alm1 Avirulence Gene of...

Analyses of amplified fragment length polymorphisms (AFLP) indicate rapid radiation of Diospyros species (Ebenaceae) endemic to...

Restriction Fragment Length Polymorphism Analysis of PCR-Amplified Fragments (PCR-RFLP) and Gel Electrophoresis - Valuable Tool...

Sequence Elimination and Cytosine Methylation Are Rapid and Reproducible Responses of the Genome to Wide Hybridization and...

Sequence Elimination and Cytosine Methylation Are Rapid and Reproducible Responses of the Genome to Wide Hybridization and...

Patent US7893325 - Brassica plant resistant to the fungus Leptosphaeria maculans (blackleg) - Google Patents

A. Jonathan Shaw, Professor of Biology and Curator of Bryophytes, Duke Herbarium

Genomic Regions Analysis of Seedling Root Traits and Their Regulation in Responses to Phosphorus Deficiency Tolerance in CSSL...

Rates of evolution of avirulence phenotypes and DNA markers in a northwest European population of Puccinia striiformis f. sp....

A comprehensive analysis of hydrogen peroxide-induced gene expression in tobacco | PNAS

DNA sequence conservation between the Bacillus anthracis pXO2 plasmid and genomic sequence from closely related bacteria | BMC...

Comparative Genome Analysis of the Mollicutes | SpringerLink

A latitudinal cline in flowering time in Arabidopsis thaliana modulated by the flowering time gene FRIGIDA | PNAS

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Study of Blood Samples From High-Risk Postmenopausal Women Who Received Treatment on Breast Cancer Prevention Clinical Trials...

Intraspecific Phylogeny and Lineage Group Identification Based on the prfA Virulence Gene Cluster of Listeria monocytogenes† |...

Frontiers | Floral Volatiles in Parasitic Plants of the Orobanchaceae. Ecological and Taxonomic Implications | Plant Science

Remodeling of DNA Methylation and Phenotypic and Transcriptional Changes in Synthetic Arabidopsis Allotetraploids | Plant...

Proceedings of the Royal Society of London B: Biological Sciences

First Report of Sequence Type 1, Pathotype A Xanthomonas citri pv. citri from Lime and Lemon Fruit Originating from Bangladesh

Restriction4

Polymerase Chain Re1

Single Nucleotide3

Electrophoresis1

Sequence analysis1

Phylogenetic4

Allotetraploids1

Genome1

Genotypic1

Arabidopsis1

Genetic analysis1

RDNA1

Molecular2

Species2

Regions1

Commonly1

Method2

Significantly1

Studies1

Methylation1

Large1