Amplified fragment length polymorphism analysis. Medical search

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.

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.

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.

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.

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.

Deoxyribonucleic acid that makes up the genetic material of bacteria.

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.

The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.

Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.

A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.

DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.

Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.

The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.

The relationships of groups of organisms as reflected by their genetic makeup.

The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).

A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.

Genotypic differences observed among individuals in a population.

Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.

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.

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.

The proportion of one particular in the total of all ALLELES for one genetic locus in a breeding POPULATION.

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.

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.

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.

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.

Process of determining and distinguishing species of bacteria or viruses based on antigens they share.

A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.

A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.

The functional hereditary units of BACTERIA.

A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.

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.

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.

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.

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.

Any method used for determining the location of and relative distances between genes on a chromosome.

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.

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.

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.

Infections with bacteria of the genus CAMPYLOBACTER.

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.

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.

Deoxyribonucleic acid that makes up the genetic material of fungi.

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.

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.

Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.

The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.

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.

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.

An individual having different alleles at one or more loci regarding a specific character.

Proteins found in any species of bacterium.

Deoxyribonucleic acid that makes up the genetic material of protozoa.

The study of microorganisms living in a variety of environments (air, soil, water, etc.) and their pathogenic relationship to other organisms including man.

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)

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)

Procedures for identifying types and strains of fungi.

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.

Individuals whose ancestral origins are in the southeastern and eastern areas of the Asian continent.

Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.

The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.

The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.

Subtype of CLOSTRIDIUM BOTULINUM that produces BOTULINUM TOXINS, TYPE A which is neurotoxic to humans and animals.

Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.

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.

Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.

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.

A genus of coccidian parasites of the family CRYPTOSPORIDIIDAE, found in the intestinal epithelium of many vertebrates including humans.

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.

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.

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.

The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.

A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).

The 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.

A country spanning from central Asia to the Pacific Ocean.

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.

Identification of genetic carriers for a given trait.

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).

A genus of bacteria found in the reproductive organs, intestinal tract, and oral cavity of animals and man. Some species are pathogenic.

Any of the infectious diseases of man and other animals caused by species of MYCOBACTERIUM.

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)

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.

A specific pair of GROUP E CHROMOSOMES of the human chromosome classification.

A genus of gram-negative, aerotolerant, spiral-shaped bacteria isolated from water and associated with diarrhea in humans and animals.

Biochemical identification of mutational changes in a nucleotide sequence.

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.

Actual loss of portion of a chromosome.

Infections with bacteria of the genus MYCOBACTERIUM.

RESTRICTION FRAGMENT LENGTH POLYMORPHISM analysis of rRNA genes that is used for differentiating between species or strains.

Sudden increase in the incidence of a disease. The concept includes EPIDEMICS and PANDEMICS.

Electrophoresis in which agar or agarose gel is used as the diffusion medium.

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.

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).

Diseases of plants.

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.

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)

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.-.

Tumor suppressor genes located on the short arm of human chromosome 17 and coding for the phosphoprotein p53.

DNA present in neoplastic tissue.

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.

The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.

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.

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)

MYCOBACTERIUM infections of the lung.

Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.

Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.

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.

Any tests that demonstrate the relative efficacy of different chemotherapeutic agents against specific microorganisms (i.e., bacteria, fungi, viruses).

Intestinal infection with organisms of the genus CRYPTOSPORIDIUM. It occurs in both animals and humans. Symptoms include severe DIARRHEA.

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.

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.

The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.

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.

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)

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.

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.-.

Water containing no significant amounts of salts, such as water from RIVERS and LAKES.

Diseases of domestic cattle of the genus Bos. It includes diseases of cows, yaks, and zebus.

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.

The bovine variety of the tubercle bacillus. It is called also Mycobacterium tuberculosis var. bovis.

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).

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.

Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.

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.

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.

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.

Deoxyribonucleic acid that makes up the genetic material of viruses.

Excrement from the INTESTINES, containing unabsorbed solids, waste products, secretions, and BACTERIA of the DIGESTIVE SYSTEM.

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)

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.

An individual in which both alleles at a given locus are identical.

Substances that reduce the growth or reproduction of BACTERIA.

Techniques used in studying bacteria.

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.

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.-.

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).

Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).

A highly-sensitive (in the picomolar range, which is 10,000-fold more sensitive than conventional electrophoresis) and efficient technique that allows separation of PROTEINS; NUCLEIC ACIDS; and CARBOHYDRATES. (Segen, Dictionary of Modern Medicine, 1992)

The 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.

Proteins isolated from the outer membrane of Gram-negative bacteria.

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.

The genetic complement of a BACTERIA as represented in its DNA.

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.

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.

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.

Deoxyribonucleic acid that makes up the genetic material of plants.

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).

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.

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.

Substances elaborated by bacteria that have antigenic activity.

The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.

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).

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.

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.

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.

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.

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.

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.

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.

Individuals whose ancestral origins are in the continent of Europe.

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.

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)

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.

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.

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.

The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.

The functional hereditary units of PLANTS.

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.

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.

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.

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.

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.

The unconsolidated mineral or organic matter on the surface of the earth that serves as a natural medium for the growth of land plants.

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.

The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.

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.

The period of confinement of a patient to a hospital or other health facility.

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)

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

https://en.wikipedia.org/wiki/×_Sorbaronia_mitschurinii

"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 ...

https://en.wikipedia.org/wiki/Bacillus_atrophaeus

Study of natural hybridisation in some tropical plants using amplified fragment length polymorphism analysis. MSc thesis, ... menggunakan teknik terminal restriction fragment length polymorphism (T-RFLP) dan amplified ribosomul DNA restriction analysis ... Comparative analysis of a translocated copy of the trnK intron in carnivorous family Nepenthaceae. Molecular Phylogenetics and ... Molecular phylogeny of Nepenthaceae based on cladistic analysis of plastid trnK intron sequence data. Plant Biology 3(2): 164- ...

https://en.wikipedia.org/wiki/Nepenthes_ampullaria

... menggunakan teknik terminal restriction fragment length polymorphism (T-RFLP) dan amplified ribosomul DNA restriction analysis ... Comparative analysis of a translocated copy of the trnK intron in carnivorous family Nepenthaceae. Molecular Phylogenetics and ... Molecular phylogeny of Nepenthaceae based on cladistic analysis of plastid trnK intron sequence data. Plant Biology 3(2): 164- ... Introduction of a nuclear marker for phylogenetic analysis of Nepenthaceae. Plant Biology 8(6): 831-840. doi:10.1055/s-2006- ...

https://en.wikipedia.org/wiki/Nepenthes_gymnamphora

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 ...

https://en.wikipedia.org/wiki/Clostridium_novyi

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

https://en.wikipedia.org/wiki/Yersinia_bercovieri

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 ...

https://en.wikipedia.org/wiki/Trimeresurus_septentrionalis

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 ( ...

https://en.wikipedia.org/wiki/Trimeresurus_albolabris

"Ochratoxin A production and amplified fragment length polymorphism analysis of Aspergillus carbonarius, Aspergillus tubingensis ...

https://en.wikipedia.org/wiki/Aspergillus_tubingensis

... terminal restriction fragment length polymorphism (t-RFLP), amplified fragment length polymorphism (AFLP), and multiplex ... Software for Terminal-Restriction Fragment Length Polymorphism (T-RFLP) Data Analysis" (PDF). SoftGenetics. Archived from the ... Several common genotyping techniques include restriction fragment length polymorphism (RFLP), ... Also known as a genotypic assay, techniques include PCR, DNA fragment analysis, allele specific oligonucleotide (ASO) probes, ...

https://en.wikipedia.org/wiki/Genotype

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, ...

https://en.wikipedia.org/wiki/Orbicella_annularis

Phylogenetic analysis of North American Armillaria species based on analysis of amplified fragment length polymorphism data ... The analysis used restriction fragment length polymorphism (RFLP) and random amplification of polymorphic DNA (RAPD) to examine ... The results suggest that based on the restriction fragment length polymorphism patterns observed, there are four global A. ... A Chinese study published in 2001 used the molecular biological technique restriction fragment length polymorphism to analyze ...

https://en.wikipedia.org/wiki/Armillaria_gallica

... 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 ...

https://en.wikipedia.org/wiki/Nucleotide_diversity

... like RFLP or amplified fragment length polymorphism (AFLP), which use fragment length polymorphism caused by different ... This procedure was used initially to isolate RAD tags for microarray analysis. More recently, the RAD tag isolation procedure ... and using PCR to specifically amplify fragments that contain both adapters. Importantly, the first adapter contains a short DNA ... they can be used to identify and genotype DNA sequence polymorphisms mainly in form of single nucleotide polymorphisms (SNPs). ...

https://en.wikipedia.org/wiki/Restriction_site_associated_DNA_markers

... attempted to return to a VNTR based analysis combined with PCR technology called amplified fragment length polymorphisms ( ... The first true method of DNA profiling was restriction fragment length polymorphism analysis. The first use of RFLP analysis in ... analysis is the primary type of forensic DNA analysis performed in modern DNA laboratories. STR analysis builds upon RFLP and ... The process of RFLP analysis was extremely time consuming and due to the length of the repeats used, between 9 and 100 base ...

https://en.wikipedia.org/wiki/Forensic_DNA_analysis

It is an extension to the restriction fragment length polymorphism (RFLP) method, using polymerase chain reaction (PCR) to more ... The cleaved amplified polymorphic sequence (CAPS) method is a technique in molecular biology for the analysis of genetic ... and that these differences can be detected in the resulting DNA fragment length after digestion. In the CAPS method, PCR ... Alternatively, the amplified segment can be analyzed by allele-specific oligonucleotide (ASO) probes, a process that can often ...

https://en.wikipedia.org/wiki/Cleaved_amplified_polymorphic_sequence

For example, using the amplified fragment length polymorphism (AFLP) technique, researchers have been able to infer the ... For example, through allozyme analysis, researchers have been able to confirm the continuous distribution of Zygaena exulans in ...

https://en.wikipedia.org/wiki/Glacial_refugium

... with the seagrass Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA ... "Identification of species by multiplex analysis of variable-length sequences". Nucleic Acids Research 38 (22): e203. PMC ... "Phylogenetic analysis of Aquaspirillum magnetotacticum using polymerase chain reaction-amplified 16S rRNA-specific DNA". ... "A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria". Journal of Microbiological ...

https://gl.wikipedia.org/wiki/ARNr_16S

Citrus as Inferred from Internal Transcribed Spacer and Chloroplast DNA Sequence and Amplified Fragment Length Polymorphism ... analysis of chromosome 2". BMC Genetics. 15. doi:10.1186/s12863-014-0152-1.. ...

https://en.wikipedia.org/wiki/Lime_(fruit)

Amplified fragment length polymorphism (AFLP). *RAPD. *STR analysis. References[edit]. *^ Saiki, R.; Scharf, S; Faloona, F; ... A restriction fragment length polymorphism is said to occur when the length of a detected fragment varies between individuals, ... In molecular biology, restriction fragment length polymorphism (RFLP) is a technique that exploits variations in homologous DNA ... Terminal restriction fragment length polymorphism (TRFLP or sometimes T-RFLP) is a technique initially developed for ...

https://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism

"Molecular Characterization of Iranian Almond Cultivars and Related Wild Species Using Amplified Fragment-Length Polymorphisms ( ... and a full genetic and morphological analysis shows that its closest relative is Prunus bucharica. Fl. Afghan. 2:179. 1960 Bull ...

https://en.wikipedia.org/wiki/Prunus_kuramica

Kumar, Awanish; Anuradha Dube (February 2013). "Amplified fragment length polymorphism: an adept technique for genome mapping, ... A comprehensive systematic review and meta analysis". American Journal of Rhinology & Allergy. 30 (5): 157-175. doi:10.2500/ ... and amplified fragment length polymorphism (AFLP). MLST is a technique used for classifying microbes by the use of DNA ... AFLP is a Polymerase Chain Reaction (PCR) tool used in DNA profiling to amplify a desired DNA fragment with the use of ...

https://en.wikipedia.org/wiki/Lactobacillus_paracasei

Restriction fragment length polymorphism AFLP - Amplified fragment length polymorphism STRP - Short tandem repeat polymorphism ... Analysis of Genes and Genomes, Fifth Edition. ISBN 0-7637-0913-1 "Cleavage Close to the End of DNA Fragments". New England ... Agarose gel electrophoresis DNA sequencing Genetic fingerprinting PCR Restriction fragment length polymorphism Hartl, Daniel L ... each fragment that contains the desired sequence has the sequence located at exactly the same position within the fragment. The ...

https://en.wikipedia.org/wiki/Restriction_digest

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

https://en.wikipedia.org/wiki/Arundinaria

Genetics and Molecular Phylogeny Based On Amplified Fragment Length Polymorphisms". Malacologia 49(2): 367-382. doi:10.4002/ ... Analysis of morphological variation within Oncomelania hupensis population. Chinese Journal of Zoology 40:90-97. Media related ... hupensis guangxiensis out from Oncomelania hupensis tangi based on allozymes and amplified fragment length polymorphism (AFLP ... with internal transcribed spacer (ITS) and 16S fragments. It may also be possible that continuous control efforts, such as ...

https://en.wikipedia.org/wiki/Oncomelania_hupensis

... analyses are used in assignment tests based on an individual's microsatellites or Amplified Fragment Length Polymorphisms ( ... STR is common in forensic analysis because they are easily amplified using polymerase chain reaction (PCR) and they have unique ... from the video recording of their walk by gait analysis, from an audio recording by voice analysis, from their handwriting by ... Forensic DNA analysis can be a useful tool in aiding forensic identification because DNA is found in almost all cells of our ...

https://en.m.wikipedia.org/wiki/Forensic_identification

An earlier method, Restriction Fragment Length Polymorphism (RFLP) didn't need to know the sequence change beforehand, but ... 278-282 (1983). Saiki RK, Bugawan TL, Horn GT, Mullis KB, and Erlich HE "Analysis of enzymatically amplified beta-globin and ... ASO analysis is only one of the methods used to detect genetic polymorphisms. Direct DNA sequencing is used to initially ... amplified DNA. The PCR technique itself has been adapted to detect polymorphisms, as allele-specific PCR. However, the ...

https://en.wikipedia.org/wiki/Allele-specific_oligonucleotide

... restriction fragment length polymorphism (RFLP), random amplification of polymorphic DNA (RAPD), amplified fragment length ... Those markers have been used in diversity analysis, parentage detection, DNA fingerprinting, and prediction of hybrid ... The term 'perfect marker' is sometimes used when tests are performed to detect a SNP or other DNA polymorphism in the gene of ... polymorphism (AFLP), and single nucleotide polymorphisms (SNPs). The following terms are generally less relevant to discussions ...

https://en.wikipedia.org/wiki/Marker-assisted_selection

According to Amplified Fragment Length Polymorphisms". Journal of Forensic Sciences. 51 (2): 371-375. doi:10.1111/j.1556- ... "Conde Nast, Custom Analysis. 2014. Retrieved 19 February 2015.. *^ a b Callaway, J. C. (1 January 2004). "Hempseed as a ... Robinson, Matthew B; Scherlen, Renee G (2007). Lies, damned lies, and drug war statistics: a critical analysis of claims made ... Crime, United Nations Office on Drugs and (2009). Recommended Methods for the Identification and Analysis of Cannabis and ...

https://en.wikipedia.org/wiki/Hemp

Instead, the adapters are added after the DNA is treated and fragmented with bisulfite, allowing all fragments to be amplified ... MDA products result in a length of about 12 kb and ranges up to around 100 kb, enabling its use in DNA sequencing.[10] In 2017 ... Single-nucleotide polymorphisms (SNPs), which are a big part of genetic variation in the human genome, and copy number ... May 2009). "mRNA-Seq whole-transcriptome analysis of a single cell". Nature Methods. 6 (5): 377-82. doi:10.1038/NMETH.1315. ...

https://en.wikipedia.org/wiki/Single_cell_sequencing?source=post_page---------------------------

Amplified fragment length polymorphism fingerprinting of the pandemic isolates of V. cholerae has revealed variation in the ... Treatment is usually started without or before confirmation by laboratory analysis. Stool and swab samples collected in the ... and Relationships within the Seventh Pandemic Clone of Vibrio cholerae Determined by Amplified Fragment Length Polymorphism". J ... It reduced the length of disease by eight hours and the amount of diarrhea stool by 10%.[62] Supplementation appears to be also ...

https://en.wikipedia.org/wiki/Cholera

According to Amplified Fragment Length Polymorphisms". Journal of Forensic Sciences. 51 (2): 371-375. doi:10.1111/j.1556- ... "Conde Nast, Custom Analysis. 2014. Retrieved 19 February 2015.. *^ a b Callaway, J. C. (2004-01-01). "Hempseed as a nutritional ... Robinson, Matthew B & Scherlen, Renee G (2007). Lies, damned lies, and drug war statistics: a critical analysis of claims made ... Crime, United Nations Office on Drugs and (2009). Recommended Methods for the Identification and Analysis of Cannabis and ...

https://en.m.wikipedia.org/wiki/Hemp

2005): «A single domestication for potato based on multilocus amplified fragment length polymorphism genotyping» i: PNAS 102 ( ... a b Griffiths, Anthony J. F. (1999): An Introduction to genetic analysis. New York: W.H. Freeman. ISBN 0-7167-3771-X ... i: Boldykova, Zhamilya; Berdigulova, Assel: Ornament as a Universal Language of Peace (Based on Comparative Analysis of ... 2005): «Reconstructing the population history of Puerto Rico by means of mtDNA phylogeographic analysis» i: Am J Phys Anthropol ...

https://no.wikipedia.org/wiki/Indianer

... large DNA fragments into shorter DNA fragments. The fragmented DNA may then be cloned into a DNA vector and amplified in a ... Read length. Accuracy (single read not consensus). Reads per run. Time per run. Cost per 1 million bases (in US$). Advantages. ... Wu R, Tu CD, Padmanabhan R (1973). "Nucleotide sequence analysis of DNA. XII. The chemical synthesis and sequence analysis of a ... Even so, a recent study did use the short sequence reads and mass spectroscopy to compare single-nucleotide polymorphisms in ...

https://en.wikipedia.org/wiki/Sequencing_technology

... amplified fragment length polymorphisms, DNA sequences and microsatellites) on a worldwide sample of specimens suggested the ... White NA; Dehal-Prabhjyot K; Duncan JM (2001). "Molecular analysis of intraspecific variation between building and 'wild' ...

https://en.wikipedia.org/wiki/Serpula_lacrymans

Left: A full-length argonaute protein from the archaea species Pyrococcus furiosus. Right: The PIWI domain of an argonaute ... Zhang XHD (2011). Optimal High-Throughput Screening: Practical Experimental Design and Data Analysis for Genome-scale RNAi ... Amplified silencing". Science. 315 (5809): 199-200. doi:10.1126/science.1138030. PMID 17218517. S2CID 46285020.. ... As the fragments produced by dicer are double-stranded, they could each in theory produce a functional siRNA. However, only one ...

https://en.m.wikipedia.org/wiki/RNA_interference

"A single domestication for potato based on multilocus amplified fragment length polymorphism genotyping". Proc. Natl. Acad. Sci ... 2002). "Analysis of acrylamide, a carcinogen formed in heated foodstuffs". J. Agric. Food Chem. 50 (17): 4998-5006. doi:10.1021 ... "A single domestication for potato based on multilocus amplified fragment length polymorphism genotyping". PNAS. 102 (41): 14694 ... Tubers form in response to decreasing day length, although this tendency has been minimized in commercial varieties.[21] ...

https://en.wikipedia.org/wiki/Solanum_tuberosum_tuberosum

In 1995, the idea of reducing the tag length from 100 to 800 bp down to tag length of 10 to 22 bp helped reduce the cost of ... In addition, the longer contigs can be screened for polymorphisms. As UTRs show a large number of polymorphisms between ... These cDNA tag fragments (with adaptor primers and AE and TE recognition sites attached) are ligated, sandwiching the two tag ... In 1979 teams at Harvard and Caltech extended the basic idea of making DNA copies of mRNAs in vitro to amplifying a library of ...

https://en.wikipedia.org/wiki/Serial_analysis_of_gene_expression

All tests and analysis from[76][77] Model organisms have been used in the study of MYH9 function. A conditional knockout mouse ... Cheng W, Zhou X, Zhu L, Shi S, Lv J, Liu L, Zhang H (August 2011). "Polymorphisms in the nonmuscle myosin heavy chain 9 gene ( ... The neck acts as a lever arm that amplifies the movement produced by conformational changes of the motor domain, and is the ... It encodes a protein of the same length, with 97.1% amino acid identity with the human MYH9 protein.[15] ...

https://en.wikipedia.org/wiki/MYH9

The use of PCR means that microsatellite length analysis is prone to PCR limitations like any other PCR-amplified DNA locus. A ... "Functional analysis of a novel DNA polymorphism of a tandem repeated sequence in the asparagine synthetase gene in acute ... Instruments built to resolve microsatellite fragments by capillary electrophoresis also use fluorescent dyes.[61] Forensic ... In forensics, the analysis is performed by extracting nuclear DNA from the cells of a sample of interest, then amplifying ...

https://en.wikipedia.org/wiki/Short_tandem_repeats

A comparative genomic analysis showed that E. coli and S. enterica evolve much more slowly than S. thermophilus. The latter's ... Where many reference genomes are available, polymerase chain reaction (PCR) can be used to amplify CRISPR arrays and analyse ... Groenen PM, Bunschoten AE, van Soolingen D, van Embden JD (December 1993). "Nature of DNA polymorphism in the direct repeat ... the spacers are fragments of DNA gathered from viruses that previously tried to attack the cell. The source of the spacers was ...

https://en.m.wikipedia.org/wiki/CRISPR

Citrus as Inferred from Internal Transcribed Spacer and Chloroplast DNA Sequence and Amplified Fragment Length Polymorphism ... Genetic analysis has shown the parents of the Dancy to have been two mandarin orange hybrids each with a small pomelo ...

https://en.wikipedia.org/wiki/Tangerines

... that amplifies regions between simple sequence repeats to produce a unique fingerprint of amplified fragment lengths.[51] ... or functional analysis of genes; diagnosis and monitoring of hereditary diseases; amplification of ancient DNA;[7] analysis of ... "RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable ... PCR amplifies a specific region of a DNA strand (the DNA target). Most PCR methods amplify DNA fragments of between 0.1 and 10 ...

https://en.m.wikipedia.org/wiki/Polymerase_chain_reaction

Microsatellite DNA, single nucleotide polymorphisms (SNPs), and insertion/deletion polymorphisms (INDELS) have shown that Nilo- ... Analysis of mtDNA shows that Eurasia was occupied in a single migratory event between 60 and 70 kya. Genetic evidence shows ... Polymerase chain reaction is a process that can amplify segments of DNA and is often used on extracted ancient DNA. It has ... This results in samples having strands of DNA measuring around 100 base pairs in length. Contamination is another significant ...

https://en.wikipedia.org/wiki/Archaeogenetics

"A single domestication for potato based on multilocus amplified fragment length polymorphism genotyping". PNAS. 102 (41): 14694 ... "Analysis of farming systems". Food and Agriculture Organization. Archived from the original on 6 August 2013. Retrieved 22 May ... Neither included subsidies in their analysis, but they noted that subsidies also influence the cost of agriculture to society.[ ... A 2005 analysis of these costs in the US concluded that cropland imposes approximately $5 to $16 billion ($30 to $96 per ...

https://en.m.wikipedia.org/wiki/Agriculture

Gene-set analysis (a.k.a. pathway analysis; usually performed tools such as DAVID, GoSeq or GSEA) has been shown to be severely ... DNA methylation polymorphisms may be used as an early biomarker of atherosclerosis since they are present before lesions are ... PCR amplification is then carried out with primers designed to amplify both methylated and unmethylated templates. After this ... a length greater than 200bp, 2) a G+C content greater than 50%, 3) a ratio of observed to expected CpG greater than 0.6, ...

https://en.wikipedia.org/wiki/DNA_methylation?wprov=sfti1

Left: A full-length argonaute protein from the archaea species Pyrococcus furiosus. Right: The PIWI domain of an argonaute ... Zhang XHD (2011). Optimal High-Throughput Screening: Practical Experimental Design and Data Analysis for Genome-scale RNAi ... In C. elegans this initiation response is amplified through the synthesis of a population of 'secondary' siRNAs during which ... As the fragments produced by dicer are double-stranded, they could each in theory produce a functional siRNA. However, only one ...

https://en.m.wikipedia.org/wiki/RNAi

... restriction fragment length polymorphism (RFLP), random amplification of polymorphic DNA (RAPD), amplified fragment length ... 26 October 2013), More than meets the eye: A multi-year expressivity analyses of tomato sterility in ps and ps-2 lines (PDF), ... polymorphism (AFLP), and single nucleotide polymorphisms (SNPs).[6]. Positive and negative selectable markers[edit]. The ... The term 'perfect marker' is sometimes used when tests are performed to detect a SNP or other DNA polymorphism in the gene of ...

https://en.wikipedia.org/wiki/Marker_assisted_selection

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 ...

https://en.wikipedia.org/wiki/Multiplex_ligation-dependent_probe_amplification

2005). "A single domestication for potato based on multilocus amplified fragment length polymorphism genotyping". Proceedings ... the time of this millennium and all dates mentioned here are estimates mostly based on geological and anthropological analysis ...

https://en.wikipedia.org/wiki/8th_millennium_BC

Restriction Fragment Length Polymorphism (RFLP) is a technique for analyzing the variable lengths of DNA fragments that result ... It used to amplify a specific region of a DNA strand (the DNA target). Most PCR methods typically amplify DNA fragments of ... In polymerase chain reaction (PCR) analysis, millions of exact copies of DNA from a biological sample are made. ... About 90% of fragment lengths fall within a two-fold range. Needle shearing creates shearing forces by passing DNA libraries ...

https://en.wikipedia.org/wiki/DNA_fragmentation

We used AFLP (amplified fragment length polymorphism) markers to analyse changes in population genetic differentiation ( ... AFLP analysis of changes in population genetic diversity and structure in forage legume germplasm grown in contrasting ... Collins R.P., Frankow-Lindberg B.E., Helgadottir, A., Skot, L., Jones, C., Skot, K.P. (2010). AFLP analysis of changes in ... AFLP analysis of changes in population genetic diversity and structure in forage legume germplasm grown in contrasting ...

http://cadair.aber.ac.uk/dspace/handle/2160/6841

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

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

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

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

Therefore, in this study we developed a simple method using restriction fragment length polymorphism analysis of PCR-amplified ... of mutans streptococci by restriction fragment length polymorphism analysis of polymerase chain reaction-amplified 16S ... We amplified 16S rRNA gene sequences from genomic DNA samples by PCR using universal primers and digested the PCR products with ...

https://pubmed.ncbi.nlm.nih.gov/12930526/?dopt=Abstract

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/

... the intercentre reproducibility and epidemiological concordance of amplified fragment length polymorphism analysis for ... the intercentre reproducibility and epidemiological concordance of amplified fragment length polymorphism analysis for ... epidemiological concordance of Legionella pneumophila serogroup 1 genotyping by amplified fragment length polymorphism analysis ... Analysis of three data-sets by the coordinating centre using gel analysis software yielded R=1.00 and E=1.00, with 12, 13 or 14 ...

https://pubmed.ncbi.nlm.nih.gov/11117642/?dopt=Abstract

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

... 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

... analysis. There are many advantages to AFLP when compared to other marker technologies including randomly amplified polymorphic ... "Amplified fragment length polymorphism". However, the resulting data are not scored as length polymorphisms, but instead as ... 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 ...

https://en.wikipedia.org/wiki/Amplified_fragment_length_polymorphism

Amplified fragment length polymorphism (AFLP) RAPD STR analysis Saiki, R.; Scharf, S; Faloona, F; Mullis, K.; Horn, G.; Erlich ... A restriction fragment length polymorphism is said to occur when the length of a detected fragment varies between individuals, ... Terminal restriction fragment length polymorphism (TRFLP or sometimes T-RFLP) is a technique initially developed for ... In molecular biology, restriction fragment length polymorphism (RFLP) is a technique that exploits variations in homologous DNA ...

https://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism

We used amplified fragment length polymorphism (AFLP) and multilocus sequence analysis (MLSA) based on four partial ... We used amplified fragment length polymorphism (AFLP) and multilocus sequence analysis (MLSA) based on four partial ... Amplified fragment length polymorphism and multilocus sequence analysis-based genotypic relatedness among pathogenic variants ... Amplified fragment length polymorphism and multilocus sequence analysis-based genotypic relatedness among pathogenic variants ...

https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.009514-0

... for Asian persimmon cultivar relationships and pollination status was conducted with 496 amplified fragment length polymorphism ... Amplified fragment length polymorphism analysis. AFLP analysis was performed using the AFLP Analysis System I Kit (Life ... Amplified fragment length polymorphism analysis. Four hundred ninety-six AFLP markers were obtained for each of the initial 153 ... studied the relationships among 19 Japanese PCNA and 14 non-PCNA cultivars with 138 amplified fragment length polymorphisms ( ...

https://link.springer.com/article/10.1007/s11295-015-0848-z?error=cookies_not_supported&code=89f73abf-6977-4107-9400-385f562c6370

Amplified Fragment Length Polymorphism. Analysis: Computer Network. Analysis: Neutron Activation. Anthropology. Anthropology: ... Mr John Lentini, Scientific Fire Analysis, USA. Behavioral Sciences. Dr Carl N Edwards, Attorney, Clinical and Forensic ... Toxicology and Drug Analysis. Prof. Olaf H Drummer, Head (Forensic & Scientific Services), Victorian Institute of Forensic ... DNA and the Analysis of Biological Fluids. Allan Jamieson, Director, The Forensic Institute, UK ...

https://www.wiley.com/en-ca/Wiley+Encyclopedia+of+Forensic+Science%2C+5+Volume+Set-p-9780470018262

Restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA for rapid identification of ... A restriction fragment length polymorphism (RFLP) analysis of the 16S rDNAs was performed with Smal and MluI. The four validly ... bacterial DNA; ribosome DNA; DNA sequence; restriction fragment length polymorphism; strain difference; Saccharomonospora; ... We found that purification of amplified 16S rDNA products following PCR was necessary for our RFLP analysis. ...

https://repository.kribb.re.kr/handle/201005/4130

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

... 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

title = "Genotyping by amplified fragment length polymorphism analysis reveals persistence and recurrence of infection with ... abstract = "Genotyping by amplified fragment length polymorphism analysis reveals persistence and recurrence of infection with ... T1 - Genotyping by amplified fragment length polymorphism analysis reveals persistence and recurrence of infection with ... N2 - Genotyping by amplified fragment length polymorphism analysis reveals persistence and recurrence of infection with ...

https://cris.maastrichtuniversity.nl/en/publications/genotyping-by-amplified-fragment-length-polymorphism-analysis-rev

Amplified (Restriction) Fragment Length Polymorphism (AFLP) Analysis Daniel K. Masiga, C. Michael R. Turner ... Analysis of Gene Function in Trypanosoma brucei Using RNA Interference Appolinaire Djikeng, Shuiyuan Shen, Christian Tschudi, ... Typing Single-Nucleotide Polymorphisms in Toxoplasma gondii by Allele-Specific Primer Extension and Microarray Detection ... Analysis of Differentially Expressed Parasite Genes and Proteins Using Transcriptomics and Proteomics ...

https://link.springer.com/book/10.1385/1592597939

The results of the AFLP analysis and sequencing were in complete agreement with each other. Seven species-specific padlock ... Identification and Typing of Isolates of Cyphellophora and Relatives by Use of Amplified Fragment Length Polymorphism and ... were studied using amplified fragment length polymorphism (AFLP). A total of 76 Cyphellophora and Phialophora isolates were ...

http://dare.uva.nl/search?metis.record.id=446262

DNA extraction and amplified fragment-length polymorphism (AFLP) analysis. DNA extraction from 7-d-old seedlings followed a ... Principal coordinates analysis of the diploid wheat accessions considered in this study, based on 257 amplified fragment-length ... Double arrows indicate the borders of chromosome segments to which groups of amplified fragment-length polymorphisms were ... urartu fragments of 57.1 cM (10 fragments; 44.6%), 96.6 cM (16 fragments; 46.4%), 131.9 cM (13 fragments; 87.1%), 36.7 cM (4 ...

https://www.g3journal.org/content/4/10/1931

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

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

Analysis of molecular variance in both grouping and without grouping revealed larger genetic diversity within the populations ( ... Six ISSR primers amplified a total of 45 clear and reproducible bands. The total genetic diversity (H) and Shannons diversity ... AFLP, Amplified fragment length polymorphism; AMOVA, analysis of molecular variance; CTAB, cetyl trimethyl ammonium bromide; 2D ... random amplified polymorphic DNA; RFLP, restriction fragment length polymorphism; SSR, simple sequence repeat; TBE, trisborate ...

https://academicjournals.org/journal/AJB/article-abstract/29730E464477

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

AFLP = amplified fragment length polymorphism *ANOVA = analysis of variance *A-PAGE = acid polyacrylamide gel electrophoresis * ... RAPD = random amplified polymorphic DNA *RCB = randomized-complete block *RFLP = restriction fragment length polymorphism *RILs ... SCAR = sequence-characterized amplified region *SDS-PAGE = sodium dodecyl sulphate polyacrylamide gel electrophoresis *SH = ...

https://wheat.pw.usda.gov/ggpages/awn/51/Textfiles/ABBREVIATIONS.html

... restriction fragment length polymorphism analysis of the PLB1 and URA5 loci, amplified fragment length polymorphism (AFLP) ... Keywords: Keywords: Cryptococcus gattii, multilocus sequence typing, amplified fragment length polymorphism analysis, ... AFLP, amplified fragment length polymorphism; ST, sequence type. Scale bar indicates number of substitutions per site. See ... AFLP, amplified fragment length polymorphism; human, human clinical patient. †Total number of isolates per geographic area. ‡ ...

http://www.biomedsearch.com/nih/Autochthonous-Dormant-Cryptococcus-gattii-Infections/23017442.html

... and the PCR analysis of the markers was done as described (14). The amplified fragment length polymorphism (AFLP) analysis was ... simple sequence length polymorphisms;. AFLP,. amplified fragment length polymorphisms;. BAC,. bacterial artificial chromosome; ... DNA was isolated from these progeny as described (13). The simple sequence length polymorphisms (SSLP) markers used are ... Analysis of the PKL ORF revealed PKL codes for a predicted CHD3 homolog that is 1,384 amino acids in length. A search of the ...

https://www.pnas.org/content/96/24/13839?ijkey=2ff7930d52cefc40f405aa6738d93f97b7eccb23&keytype2=tf_ipsecsha

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

Amplified-fragment length polymorphism analysis: The state of the art. J. Clin. Microbiol. 37: 3083-3091. ... Specific or randomly distributed regions are amplified by PCR, and sequence polymorphism of the fragments generated will ... In an AFLP reaction, subsets of genomic DNA fragments are amplified. The key is the use of selective nucleotides, enabling a ... In the third method, DNA sequence analysis is used for identification. Several defined regions are amplified by PCR and ...

https://www.ift.org/news-and-publications/food-technology-magazine/issues/2003/february/features/fingerprinting-microorganisms

Cut genomic DNA into fragments with the restriction enzymes Msel and EcoRI and Ligate adaptors. (thermofisher.com)
Thirty-one strains of Acinetobacter species, including type strains of the 18 genomic species and 13 clinical isolates, were compared by amplified ribosomal DNA restriction analysis (ARDRA), random amplified polymorphic DNA analysis (RAPD), and amplified fragment length polymorphism (AFLP) fingerprinting. (asm.org)
The standardized commercially available RAPD kit clearly enabled the discrimination of all Acinetobacter genomic species but showed great polymorphism between isolates of Acinetobacter baumannii . (asm.org)
A novel high-resolution genomic fingerprinting method, the amplified fragment length polymorphism (AFLP), has been shown to be applicable to a wide range of bacterial species including those of the genus Acinetobacter ( 10 , 18 , 19 , 36 ). (asm.org)
We amplified 16S rRNA gene sequences from genomic DNA samples by PCR using universal primers and digested the PCR products with the restriction endonucleases, HpaII and HaeIII. (nih.gov)
Developed in the early 1990s by Keygene, AFLP uses restriction enzymes to digest genomic DNA, followed by ligation of adaptors to the sticky ends of the restriction fragments. (wikipedia.org)
The AFLP technology has the capability to detect various polymorphisms in different genomic regions simultaneously. (wikipedia.org)
These readily reproducible techniques can be used in genomic, functional genomic, and postgenomic studies and include transfection methods and vectors for several protozoan parasites, global analysis using microarrays, gene ablation using RNA interference, gene knockout, mutagenesis, and chromosome manipulation. (springer.com)
Genomic Regions Analysis of Seedling Root Traits and Their Regulation in Responses to Phosphorus Deficiency Tolerance in CSSL Population of Elite Super Hybrid Rice. (bioportfolio.com)
In 2015, the comparative genomic analysis of 21 clinical isolates, which had been previously assigned to existing MLST clades, recapitulated relationships between isolates, and the authors reported the discovery of extensive variation between these 21 isolates, including single nucleotide polymorphisms (SNPs) and frequent whole or partial chromosomal aneuploidies 17 . (nature.com)
New methods for gene identification based on genomic analysis and their application for molecular breeding in plants. (nii.ac.jp)
Bacillus cereus and Bacillus thuringiensis isolates that ranged in genomic similarity to B. anthracis , as determined by amplified fragment length polymorphism (AFLP) analysis, were examined by PCR for the presence of sequences similar to 47 pXO2 ORFs. (biomedcentral.com)
Dot-blot DNA hybridizations between pXO2 ORF fragments and total genomic DNA from AWO6 were consistent with the PCR assay results for this isolate and also revealed nine additional ORFs shared between these two bacteria. (biomedcentral.com)
The presence of pXO2 sequences in the other Bacillus isolates did not correlate with genomic relatedness established by AFLP analysis. (biomedcentral.com)
Based on 12 genomes of corresponding serovar reference strains including three publicly available complete genomes (serovars 3, 5b, and 7) of this bacterium, we performed a comprehensive analysis of comparative genomics and first reported a global genomic characterization for this pathogen. (asm.org)
A list of the 242 primer pairs that amplify mapped SSRs from total barley genomic DNA is presented. (genetics.org)
analysis allows detection of genomic polymorphisms using nanogram amounts of DNA. (bioreliance.com)
Other methods involve using PCR, such as amplified fragment length polymorphisms (AFLPs) uses restriction enzymes to digestc genomic DNA [ 3 ]. (omicsonline.org)
Amplified fragment length polymorphism (AFLP™) is a PCR based DNA fingerprinting technique that generates band profiles via the selective amplification of restriction fragments of whole genomic DNA. (belspo.be)

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)
There are many advantages to AFLP when compared to other marker technologies including randomly amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), and microsatellites. (wikipedia.org)
Out of the 813 polymerase chain reaction fragments that were scored, 781 (96.23%) were polymorphic. (csic.es)
This method uses highly polymorphic regions that have short repeated sequences of DNA (the most common is 4 bases repeated, but there are other lengths in use, including 3 and 5 bases). (wikidoc.org)
There are different kinds of molecular markers, such as restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), amplified fragment length polymorphisms (AFLPs), microsatellites and single nucleotide polymorphisms (SNPs). (omicsonline.org)
We have used random amplified polymorphic DNA (RAPD) analysis to characterize eleven cultivars of the five economically most important yam species grown in Jamaica (Dioscorea alata, D. cayenensis, D. rotundata, D. trifida and D. esculenta). (semanticscholar.org)
Concentration of primer and template qualitatively affects products in random-amplified polymorphic DNA PCR. (semanticscholar.org)
AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). (scielo.br)
Though restriction fragments length polymorphism (RFLP) markers have been the basis for most of the work in crop plants, valuable markers have been generated from random amplification polymorphic DNA (RAPD) and amplified fragments length polymorphism (AFLP). (science20.com)

Therefore, in this study we developed a simple method using restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal RNA genes (16S rRNA genes PCR-RFLP) for the identification of seven different species included in the group of mutans streptococci. (nih.gov)
In molecular biology, restriction fragment length polymorphism (RFLP) is a technique that exploits variations in homologous DNA sequences, known as polymorphisms, in order to distinguish individuals, populations, or species or to pinpoint the locations of genes within a sequence.The term may refer to a polymorphism itself, as detected through the differing locations of restriction enzyme sites, or to a related laboratory technique by which such differences can be illustrated. (wikipedia.org)
In RFLP analysis, a DNA sample is digested into fragments by one or more restriction enzymes, and the resulting restriction fragments are then separated by gel electrophoresis according to their size. (wikipedia.org)
Although now largely obsolete due to the emergence of inexpensive DNA sequencing technologies, RFLP analysis was the first DNA profiling technique inexpensive enough to see widespread application. (wikipedia.org)
RFLP analysis was an important early tool in genome mapping, localization of genes for genetic disorders, determination of risk for disease, and paternity testing. (wikipedia.org)
Analysis of RFLP variation in genomes was formerly a vital tool in genome mapping and genetic disease analysis. (wikipedia.org)
Once a disease gene was localized, RFLP analysis of other families could reveal who was at risk for the disease, or who was likely to be a carrier of the mutant genes. (wikipedia.org)
RFLP analysis was also the basis for early methods of genetic fingerprinting, useful in the identification of samples retrieved from crime scenes, in the determination of paternity, and in the characterization of genetic diversity or breeding patterns in animal populations. (wikipedia.org)
The technique for RFLP analysis is, however, slow and cumbersome. (wikipedia.org)
The results of the Human Genome Project have largely replaced the need for RFLP mapping, and the identification of many single-nucleotide polymorphisms (SNPs) in that project (as well as the direct identification of many disease genes and mutations) has replaced the need for RFLP disease linkage analysis (see SNP genotyping). (wikipedia.org)
A restriction fragment length polymorphism (RFLP) analysis of the 16S rDNAs was performed with Smal and MluI. (kribb.re.kr)
We found that purification of amplified 16S rDNA products following PCR was necessary for our RFLP analysis. (kribb.re.kr)
The first method for creating a DNA profile was RFLP , or restriction fragment length polymorphism. (howstuffworks.com)
Some of the steps for RFLP analysis are also used in other types of DNA profiling. (howstuffworks.com)
In molecular biology, the term restriction fragment length polymorphism, or RFLP, (commonly pronounced "rif-lip") refers to a difference between two or more samples of homologous DNA molecules arising from differing locations of restriction sites, and to a related laboratory technique by which these segments can be distinguished. (science20.com)
In RFLP analysis the DNA sample is broken into pieces (digested) by restriction enzymes and the resulting restriction fragments are separated according to their lengths by gel electrophoresis. (science20.com)

The amplified fragments are separated and visualized on denaturing on agarose gel electrophoresis , either through autoradiography or fluorescence methodologies, or via automated capillary sequencing instruments. (wikipedia.org)
The DNA fragments produced by the digest are then separated by length through a process known as agarose gel electrophoresis and transferred to a membrane via the Southern blot procedure. (wikipedia.org)
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)
The DNA fragments that result are then separated and detected using electrophoresis. (wikidoc.org)
Then, the fragments are amplified using PCR and sorted using gel electrophoresis. (howstuffworks.com)
Genotypic characterization of Salmonella typhi by amplified fragment length polymorphism fingerprinting provides increased discrimination as compared to pulsed-field gel electrophoresis and ribotyping. (nih.gov)

Moreover, all examined C. africana strains lack N -acetylglucosamine assimilation and sequence analysis of the HXK1 gene showed a distinctive polymorphism that impair the utilization of this amino sugar in this yeast. (frontiersin.org)
Genetic Analysis and Identification of Amplified Fragment Length Polymorphism Markers Linked to the alm1 Avirulence Gene of Leptosphaeria maculans. (semanticscholar.org)
We used amplified fragment length polymorphism (AFLP) and multilocus sequence analysis (MLSA) based on four partial housekeeping gene sequences ( atpD , dnaK , efp and gyrB ) for the genotypic classification of Xanthomonas citri pv. (microbiologyresearch.org)
The differences between epidemic and nonepidemic isolates were based on genetic relatedness, as determined by amplified fragment length polymorphism analysis (AFLP), and the presence of an identical sequence of the purK housekeeping gene in epidemic strains ( 12 ). (cdc.gov)
However, ribotype and virulence gene polymorphism data were used to describe the existence of a third lineage ( 25 , 33 ), with some researchers suggesting that this lineage may represent a distinct taxonomic unit requiring recognition as a new species or subspecies ( 33 , 34 ). (asm.org)
Fragmented populations are usually exposed to the negative effects of reduced gene flow, genetic drift and population differentiation. (cambridge.org)
Lack of association between MTHFR C677T Gene polymorphism with alcohol dependence: a meta-analysis of case-control studies. (bioportfolio.com)
NQO1 Gene C609T Polymorphism (dbSNP: rs1800566) and Digestive Tract Cancer Risk: A Meta-Analysis. (bioportfolio.com)
Several studies reported that polymorphism C609T (rs1800566) in (NAD(P)H): quinoneoxidoreductase 1 (NQO1) gene is associated with risk to digestive tract (DT) cancers, like esophageal cancer (EC), gas. (bioportfolio.com)
Actin was used as a control gene and either amplified in the same PCR reaction (multiplex, no. 19, and no. 139) or, if competition between bands did not allow multiplexing, amplified in separate reaction tubes (no. 109). (plantphysiol.org)
Comparison of MVLST with housekeeping-gene-based MLST analysis showed that MVLST provided higher discriminatory power for serotype 1/2a and 4b strains than MLST. (asm.org)
Analysis of global gene expression patterns provides valuable insight into the role of differential expression in normal biological and disease processes. (thermofisher.com)
The Ion PGM™ and Ion Proton™ systems put gene expression analysis within reach for any lab, enabling scientists to get more accurate and comprehensive data than microarrays can provide for a comparable price. (thermofisher.com)
High-throughput digital gene expression analysis with the ability to multiplex up to 96 samples in a single lane. (thermofisher.com)
HiCep (High Coverage Gene Expression Profiling) - An amplified fragment length polymorphism (AFLP)-based method. (thermofisher.com)
Serial Analysis of Gene Expression (SAGE™) Sequencing - A library of short sequence tags, each of which is then used to uniquely identify a transcript. (thermofisher.com)
Recent DNA-DNA hybridization and 16S rRNA gene sequence experiments proved that the classification based on SC-minimization forms separate clusters that contain the fAFLP patterns for all representatives of the species Enterovibrio norvegicus, Vibrio fortis, Vibrio diazotrophicus or Vibrio campbellii, while previous hierarchical cluster analysis had suggested more heterogeneity within the fAFLP patterns by splitting the representatives of the above-mentioned species into multiple distant clusters. (stir.ac.uk)
The combination of PCR direct amplification and AFLP provides a 2-step procedure, where P. damselae is rapidly identified at genus level on the basis of its 16S rRNA gene sequence and then grouped into distinct clusters on the basis of AFLP polymorphisms. (int-res.com)
Compared to sequence analysis of housekeeping gene(s), AFLP™ is sometimes more suitable for identification at the subspecies level, e.g. (belspo.be)
Using this novel technology, we did comparative analyses of gene expression for ∼23,000 transcripts in normal human fibroblasts and found that low-dose X-rays up-regulated a distinct set of chemokines that have not been shown to be associated with radiation. (aacrjournals.org)

A molecular marker analysis for Asian persimmon cultivar relationships and pollination status was conducted with 496 amplified fragment length polymorphism (AFLP) markers and 146 cultivars of Asian origin. (springer.com)
Microsatellite markers were tested on A u and A m genomes, ordered in a T. monococcum molecular map, and used to characterize the exotic DNA fragments present in each introgression line. (g3journal.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)
Inheritance of amplified fragment length polymorphism markers and their utility in population genetic analysis of Plecoglossus altivelis. (thefreedictionary.com)
Amplified fragment length polymorphism (AFLP) and Targeted Region Amplified Polymorphism (TRAP) markers were used to measure genetic diversity. (usda.gov)
Dense genetic maps were constructed for the maternal and paternal genomes of a hexaploid (2n = 6x = 36) B. humidicola F 1 mapping population ( n = 102) using genotyping-by-sequencing, simple sequence repeat, amplified fragment length polymorphism, and transcriptome derived single nucleotide polymorphism markers. (biomedcentral.com)
Qualitative and quantitative analyses of the resistance with restriction fragment length polymorphism markers spanning the genome showed that this resistance was controlled by a single, incompletely dominant allele, Ph-2, present on the distal part of the long arm of chromosome 10 in an interval of 8.4 cM flanked by markers CP105 and TG233. (apsnet.org)
Amplified fragment length polymorphism markers closely linked to Ph-2 were screened by bulked segregant analysis. (apsnet.org)
Therefore, five populations of J. curcas were studied in the state of Chiapas, Mexico, using amplified fragment length polymorphism (AFLP) markers. (mdpi.com)
One hundred and fifty-two useful markers were obtained: overall polymorphism = 81.18% and overall Nei's genetic diversity ( He ) = 0.192. (mdpi.com)
Identification of the markers linked to useful traits has been based on complete linkage maps and bulked segregant analysis. (science20.com)
Amplified Fragment Length Polymorphism markers (AFLP) were used to test the genetic variation among the forms. (unl.edu)

AFLP analysis provided a clear separation of A. lignieresii and A. pleuropneumoniae and divided the isolates of A. pleuropneumoniae into 20 clusters. (asm.org)
Amplified fragment length polymorphism (AFLP) analysis of the SAG isolates produced discriminatory and reproducible patterns. (maastrichtuniversity.nl)
The large number of fragments and a targeted sampling of isolates allowed a reconstruction of phylogenies in great detail, i.e. no homoplasy and a representation of sequential, evolutionary steps by pathogen samples. (biomedsearch.com)
PCR was performed using template DNA from 11 Bacillus isolates that vary in relatedness to B. anthracis with primer sets designed to amplify DNA fragments from 47 different pXO2 ORFs. (biomedcentral.com)
Six S. typhi isolates from diverse geographic areas (Malaysia, Indonesia, India, Chile, Papua New Guinea and Switzerland) gave unique, heterogeneous profiles when typed by AFLP, a result which was consistent with ribotyping and PFGE analysis. (nih.gov)
Identification of 18 isolates as Xanthomonas was carried out initially by fatty acid methyl ester (FAME) analysis. (apsnet.org)
The expected DNA fragment was only obtained from all of the bacterial isolates using primer pair 4/7 (3). (apsnet.org)
Multilocus sequence analysis (MLSA) of four housekeeping genes ( atpD, dnaK, efp , and gyrB ) identified isolates from Bangladesh as two sequence types of X. citri pv. (apsnet.org)
All five ST1 isolates grouped as a single cluster by AFLP, although not strongly supported by bootstrap analysis. (apsnet.org)
Amplified fragment length polymorphism analysis of a subset of isolates showed that they clustered closely, supporting the PFGE results. (nih.gov)

Also, commercial kits are available that analyze Single Nucleotide Polymorphisms (SNPs). (wikidoc.org)
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)
Amplified fragment length polymorphism-polymerase chain reaction (AFLP-PCR), commonly called "DNA fingerprinting," is a highly sensitive and reproducible method for detecting SNPs in DNA. (thesourcenatural.com)

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)
Although polymorphisms can exist in the restriction enzyme cleavage sites, more commonly the enzymes and DNA probes were used to analyze VNTR loci. (wikidoc.org)
These STR loci (locations) are targeted with sequence-specific primers and are amplified using PCR. (wikidoc.org)
When looking at multiple loci, it is the unique combination of these polymorphisms to an individual that makes this method discriminating as an identification tool. (wikidoc.org)
A total of 27 SSRs amplified multiple loci. (genetics.org)
After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. (scielo.br)
A primer amplifying a dominant marker could amplify at many loci in one sample of DNA with one PCR reaction. (science20.com)

AFLP technology can detect various polymorphisms in different areas of the genome simultaneously. (thesourcenatural.com)

Following restriction enzyme digestion of DNA, a subset of DNA fragments is selected for PCR amplification and visualization. (thermofisher.com)
Selective amplification of some of these fragments with two PCR primers that have corresponding adaptor and restriction site specific sequences. (wikipedia.org)
1993. Selective restriction fragment amplification: a general method for DNA fingerprinting. (wikipedia.org)
and (iii) some other combined amplification-restriction methods, e.g., amplified fragment length polymorphism ( 14 ) and PCR-restriction fragment length polymorphism ( 17 ). (asm.org)
This technique detects multiple DNA fragments by means of polymerase chain reaction (PCR) amplification. (thesourcenatural.com)

Correspondingly, analyses of molecular variance showed more variation within species than between them. (biomedcentral.com)
Significant differences for cultivar origin and pollination status were found for analysis of molecular variance (AMOVA), but most of the variation was among cultivars, not classification groups. (springer.com)
Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. (scielo.br)

PCR greatly amplifies the amounts of a specific region of DNA, using oligonucleotide primers and a thermostable DNA polymerase . (wikidoc.org)
PCR (polymerase chain reaction) analysis is usually the first step in the creation of a DNA profile today. (howstuffworks.com)

The basic technique for the detection of RFLPs involves fragmenting a sample of DNA with the application of a restriction enzyme, which can selectively cleave a DNA molecule wherever a short, specific sequence is recognized in a process known as a restriction digest. (wikipedia.org)
Several different kinds of molecular marker could be applied on plant selection: such as restriction fragment length polymorphisms (RFLPs), is detected by southern hybridization. (omicsonline.org)

Amplified fragment length polymorphism fingerprint analysis yielded greater genotypic heterogeneity among the C. africana strains. (frontiersin.org)
Amplified fragment length polymorphism (AFLP) was evaluated as a method for genotypic characterization and subtyping within the bacterial species Actinobacillus pleuropneumoniae . (asm.org)
Amplified fragment length polymorphism and multilocus sequence analysis-based genotypic relatedness among pathogenic variants of Xanthomonas citri pv. (microbiologyresearch.org)
Genotypic characterization of Salmonella typhi by amplified fragment length polymorphism fingerprinting provides increased discrimination as compar. (nih.gov)

The species diversity and identification of black fungi belonging to Cyphellophora and Phialophora, which colonize and infect human skin and nails, were studied using amplified fragment length polymorphism (AFLP). (uva.nl)

The 16S rDNAs were amplified by PCR by using oligonucleotide primers complementary to 16S rRNA genes. (kribb.re.kr)
An interpretation of phenotypic changes within lineages as independent mutation events resulted in mutation frequencies from 1.4x10(-6) to 4.1x10(-6) per AFLP fragment (locus) per generation, whereas the effective rate by which a mutation from avirulence to virulence was established in the pathogen population, when subject to selection by host resistance genes, was approximately three orders of magnitude faster. (biomedsearch.com)
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 Figure 5 . (plantphysiol.org)
Internal fragments (ca. 418 to 469 bp) of three virulence genes ( prfA , inlB , and inlC ) and three virulence-associated genes ( dal , lisR , and clpP ) were sequenced and analyzed. (asm.org)
Cluster analysis based on the intragenic sequences of the selected virulence genes indicated a strain phylogeny closely related to serotypes and genetic lineages. (asm.org)

Pathogen samples were collected between 1975 and 2002 in the UK and Denmark, and assayed for 14 individual avirulence/virulence alleles and up to 234 amplified fragment length polymorphism (AFLP) primer pairs producing approximately 17,000 AFLP fragments. (biomedsearch.com)

The power of AFLP® analysis is the speed with which the technique can quickly generate large numbers of marker fragments for any organism, without the need for any sequence data. (thermofisher.com)
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)
This selection is achieved by using primers complementary to the adaptor sequence, the restriction site sequence and a few nucleotides inside the restriction site fragments (as described in detail below). (wikipedia.org)
A restriction fragment length polymorphism is said to occur when the length of a detected fragment varies between individuals, indicating non-identical sequence homologies. (wikipedia.org)
State-of-the-art and highly practical, Parasite Genomics Protocols offers bench investigators in parasitology a wide-ranging collection of diverse methods for elucidating the content of the genomes of parasitic organisms, utilizing the genome sequence for genetic analysis, and ascribing function to the available genome sequences. (springer.com)
These kits use PCR to amplify specific regions with known variations and hybridize them to probes anchored on cards, which results in a colored spot corresponding to the particular sequence variation. (wikidoc.org)
To overcome the ambiguities of fragment-based typing methods, multilocus sequence typing (MLST), a DNA sequence-based method, was recently developed by Chan et al. (asm.org)
A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like minisatellites. (science20.com)

The methods listed above target nucleotide variations at endonuclease restriction or primer annealing sites, utilize the electrophoretic mobility of digested or amplified DNA fragments in agarose gels, and define L. monocytogenes strains by their unique banding patterns. (asm.org)
A primer amplifying a co-dominant marker would yield one targeted product. (science20.com)

To resolve relationships within a clade of 21 closely related New Caledonian Diospyros species and evaluate species boundaries we analysed genome-wide DNA variation via amplified fragment length polymorphisms (AFLP). (biomedcentral.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)
In this study, Amplified Fragment Length Polymorphism (AFLP) analysis of 56 Hypericum accessions, representing 11 species, was conducted to gain a better understanding of diversity within Hypericum species, especially within cultivated accessions of H. perforatum, and to establish a molecular method that will provide breeders and regulators with a simple, affordable, and accurate tool with which to identify H. perforatum material in commercial products. (usda.gov)
Cluster analysis based on AFLP data clearly differentiated the genotypes and wild species according to their origin and pedigree, whereas, cluster analysis based on agronomic data differentiated according the pomological characterization. (csic.es)
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)
Population genetic analyses of the data revealed high levels of genetic diversity in H. erato relative to H. melpomene , widespread genetic differentiation among populations of both species, and no evidence for isolation-by-distance. (biomedcentral.com)
Cladophialophora bantiana, C. emmonsii, C. arxii, C. devriesii, and C. modesta, previously identified on the basis of sequencing and phenotypic and physiological criteria, were confirmed by cluster analysis, demonstrating the clear separation of C. bantiana as a rather homogeneous group from the other species. (uva.nl)
However, it is intraspecific diversity (genetic polymorphism) that represents the evolutionary and adaptive potential of each species in changing environments. (wsl.ch)

The AFLP technology has been used in criminal and paternity tests, also to determine slight differences within populations, and in linkage studies to generate maps for quantitative trait locus (QTL) analysis. (wikipedia.org)
Analysis of the marker populations demonstrated chromosome pairing and recombination in F 1 hybrid plants. (g3journal.org)
Ongoing research is grounded in phylogenetic analyses at various levels of biological organization from populations up to genus-wide. (duke.edu)
AFLP analysis is a whole-genome approach that has broad applicability in determining genetic variability within and among plant populations, crop origins, and relationships among cultivars. (usda.gov)
5) high-resolution melting analysis (HRM) for tracking genetic diversity in plant populations. (cuny.edu)
STRUCTURE analysis of the Snake River populations showed a large, panmictic population, while Salmon River populations were more distinct from one another, as well as from the Snake River populations. (usda.gov)
Natural populations of forest trees show remarkably fine-scale adaptation to the length of the frost-free growing season characteristic of their local environment. (genetics.org)
The number of genetic populations (K) was five, with mixed ancestry in most individuals (genetic migrants), except in the Soconusco, where there was a tiny fraction of fragments from other populations. (mdpi.com)

Additional chapters survey the available genome sequences, helping novice researchers overcome the difficulties of accessing the databases and applying bioinformatics analysis to biological function. (springer.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)
Compared to radioactive AFLP, fluorescent AFLP was technically fast and simple to perform, and it permitted analysis with an automated DNA sequencer. (asm.org)
The method was applied to fluorescent amplified fragment length polymorphism (fAFLP) fingerprint patterns of 507 Vibrionaceae representatives. (stir.ac.uk)

AFLP-PCR is a highly sensitive method for detecting polymorphisms in DNA. (wikipedia.org)
Amplified Fragment Length Polymorphism PCR (or AFLP-PCR or just AFLP) is a PCR-based tool used in genetics research, DNA fingerprinting, and in the practice of genetic engineering. (science20.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)
Amplified fragment length polymorphism (AFLP), also known as DNA fingerprinting, is a highly sensitive and reproducible method for detecting single nucleotide changes, or polymorphisms, in DNA. (thesourcenatural.com)

Participating workers were randomly allocated by length of employment, age, department, and job to receive either vaccine or placebo. (nap.edu)
Out of 64 random primers being used, 55 pairs gave an increase in DNA bands but only 12 pairs of random primers were randomly chosen for the final analysis of the experiment. (scialert.net)

Analysis of the SSRs on 16 barley cultivars revealed variable levels of informativeness but no obvious correlation was found with SSR repeat length, motif type, or map position. (genetics.org)
The experiment was carried out at the Department of Horticulture, Ubon Ratchathani University, Ubon Ratchathani province, Northeast Thailand during June 2002 to May 2003 aims to identify DNA fingerprints of thirty papaya cultivars with the use of Amplified Fragment Length Polymorphisms (AFLP) technique. (scialert.net)
The results on dendrogram cluster analysis revealed that the thirty papaya cultivars were classified into six groups i.e., (1) Kaeg Dum and Malador (2) Kaeg Nuan (3) Pakchong and Solo (4) Taiwan (5) Co Coa Hai Nan and (6) Sitong. (scialert.net)
À 25°C, P. ultimum détenait le plus grand pouvoir pathogène, provoquant 97,0 % de PR et 46,4 % de FS, en moyenne, chez les deux cultivars utilisés. (erudit.org)

AFLP®, first developed for plant studies, is now used for a wide variety of genetic analysis applications. (thermofisher.com)
Each fragment length is considered an allele, whether it actually contains a coding region or not, and can be used in subsequent genetic analysis. (wikipedia.org)
Genetic analysis of roots and shoots in rice seedling by association mapping. (bioportfolio.com)
Genetic analysis of the resistance to this pathogen was performed on an F 2 progeny of 322 plants derived from a cross between the tomato line L. esculentum var. (apsnet.org)
Genetic analysis of F 2 progeny from a second cross between an L. esculentum introgression line IL10-3 carrying a homozygous L. pennellii segment spanning the distal part of the long arm of chromosome 10 and WVa700 confirmed the map location, but high suppression of recombination was observed in this cross in the introgressed fragment. (apsnet.org)
The development of molecular techniques for genetic analysis has led to a great augmentation in our knowledge of crop genetics and our understanding of the structure and behavior of various crop genomes. (science20.com)
The results of this study indicate that host plants can influence phenotype and suggest the need for further genetic analysis of subspecies recognized based on morphology. (unl.edu)

Dawyndt P, Thompson FL, Austin B, Swings J, Koski T & Gyllenberg M (2005) Application of sliding-window discretization and minimization of stochastic complexity for the analysis of fAFLP genotyping fingerprint patterns of Vibrionaceae, International Journal of Systematic and Evolutionary Microbiology, 55 (1), pp. 57-66. (stir.ac.uk)

AFLP® is a technique used to detect polymorphisms in DNA when no information about the genome is known. (thermofisher.com)
In detail, the procedure of this technique is divided into three steps: Digestion of total cellular DNA with one or more restriction enzymes and ligation of restriction half-site specific adaptors to all restriction fragments. (wikipedia.org)
Which technique to use depends on a couple of factors, including cost, time available for analysis and the quality and amount of the DNA sample available. (howstuffworks.com)
AmpFLP , amplified fragment length polymorphism, is another technique that uses PCR to replicate DNA. (howstuffworks.com)
Usually this technique has three steps: first, digestion of total plant DNA with one or more restriction enzymes and ligation of restriction half-site specific adaptors to all restriction fragments. (omicsonline.org)
The amplified fragment length polymorphism technique has been applied to identify neurotropic chaetothyrialean black yeasts and relatives from clinical sources. (uva.nl)

Six ISSR primers amplified a total of 45 clear and reproducible bands. (academicjournals.org)

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)

Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. (scielo.br)

abstract = "Genotyping by amplified fragment length polymorphism analysis reveals persistence and recurrence of infection with Streptococcus anginosus group organisms.Jacobs JA, Tjhie JH, Smeets MG, Schot CS, Schouls LM.Department of Medical Microbiology, University Hospital Maastricht, 6202 AZ Maastricht, The Netherlands. (maastrichtuniversity.nl)

The second diagram shows how this fragment size variation would look on a Southern blot, and how each allele (two per individual) might be inherited in members of a family. (wikipedia.org)
The first methods used for DNA fingerprinting involved restriction enzyme digestion, followed by Southern blot analysis. (wikidoc.org)

Hybridization of the membrane to a labeled DNA probe then determines the length of the fragments which are complementary to the probe. (wikipedia.org)
A subset of the restriction fragments are then amplified using primers complementary to the adaptor and part of the restriction site fragments (as described in detail below). (science20.com)

A subset of the restriction fragments is then selected to be amplified. (wikipedia.org)

Methods: To investigate whether low-dose BPA exposure in the fetal stage can alter CpG methylation levels in the central nervous system, the hippocampus of the inbred C57BL/6 J mouse as the target tissue was collected to detect alterations in CpG methylation levels using a highly sensitive method of genome-wide DNA methylation analysis, methylated site display-amplified fragment length polymorphism (MSD-AFLP). (deepdyve.com)
Various fragment-based typing methods have been used to differentiate L. monocytogenes strains at the subspecies or strain level ( 30 ). (asm.org)

In allele c, there are five repeats in the VNTR, and the probe detects a longer fragment between the two restriction sites. (wikipedia.org)
In allele d, there are only two repeats in the VNTR, so the probe detects a shorter fragment between the same two restriction sites. (wikipedia.org)
Variations of VNTR allele lengths in 6 individuals. (wikidoc.org)

In genetics, a molecular marker is a fragment of DNA that associated with a certain location within the genome. (omicsonline.org)

In a test based on 28 interspecific introgression lines, the existence of genetic variation associated with T. urartu chromosome fragments was proven for the seed content of carotenoids, lutein, β-cryptoxanthin, and zinc. (g3journal.org)
A variation on STR analysis is Y-STR. (howstuffworks.com)

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)

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)

Amplified fragment length polymorphism (AFLP) analysis is a rapid and efficient method for producing DNA fingerprints and molecular characterization. (csic.es)

The aims of this work were to assess (i) the intercentre reproducibility and epidemiological concordance of amplified fragment length polymorphism analysis for epidemiological typing of Legionella pneumophila serogroup 1, and (ii) the suitability of the method for standardisation and implementation by members of the European Working Group on Legionella Infections. (nih.gov)
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)
Amplified fragment length polymorphism (AFLP) is a recently developed, PCR-based high resolution fingerprinting method that is able to generate complex banding patterns which can be used to delineate intraspecific genetic relationships among bacteria. (nih.gov)
23,000 transcripts in normal human fibroblasts, HFLIII, using a novel comprehensive expression analysis method. (aacrjournals.org)