Polymorphism, Restriction Fragment Length
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.
Polymerase Chain Reaction
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Polymorphism, Single Nucleotide
DNA Restriction Enzymes
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
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.
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Amplified Fragment Length Polymorphism Analysis
Deoxyribonucleases, Type II Site-Specific
Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 184.108.40.206.
Bacterial Typing Techniques
Sequence Analysis, DNA
Nucleic Acid Hybridization
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
RNA, Ribosomal, 16S
Genetic Predisposition to Disease
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).
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.
DNA Transposable Elements
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
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.
DNA, Ribosomal Spacer
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.
Amino Acid Sequence
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.
Electrophoresis, Gel, Pulsed-Field
Gel electrophoresis in which the direction of the electric field is changed periodically. This technique is similar to other electrophoretic methods normally used to separate double-stranded DNA molecules ranging in size up to tens of thousands of base-pairs. However, by alternating the electric field direction one is able to separate DNA molecules up to several million base-pairs in length.
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.
Asian Continental Ancestry Group
Electrophoresis, Agar Gel
Repetitive Sequences, Nucleic Acid
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
Sequence Homology, Nucleic Acid
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.
Polymorphism, Single-Stranded Conformational
Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.
Genetic Association Studies
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)
Random Amplified Polymorphic DNA Technique
Technique that utilizes low-stringency polymerase chain reaction (PCR) amplification with single primers of arbitrary sequence to generate strain-specific arrays of anonymous DNA fragments. RAPD technique may be used to determine taxonomic identity, assess kinship relationships, analyze mixed genome samples, and create specific probes.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
RNA, Ribosomal, 23S
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).
Interspersed Repetitive Sequences
Copies of transposable elements interspersed throughout the genome, some of which are still active and often referred to as "jumping genes". There are two classes of interspersed repetitive elements. Class I elements (or RETROELEMENTS - such as retrotransposons, retroviruses, LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS) transpose via reverse transcription of an RNA intermediate. Class II elements (or DNA TRANSPOSABLE ELEMENTS - such as transposons, Tn elements, insertion sequence elements and mobile gene cassettes of bacterial integrons) transpose directly from one site in the DNA to another.
Promoter Regions, Genetic
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)
Methylenetetrahydrofolate Reductase (NADPH2)
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.
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.
RNA, Ribosomal, 18S
European Continental Ancestry Group
Sensitivity and Specificity
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Electrophoresis, Polyacrylamide Gel
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.
Immunoglobulin Fab Fragments
Univalent antigen-binding fragments composed of one entire IMMUNOGLOBULIN LIGHT CHAIN and the amino terminal end of one of the IMMUNOGLOBULIN HEAVY CHAINS from the hinge region, linked to each other by disulfide bonds. Fab contains the IMMUNOGLOBULIN VARIABLE REGIONS, which are part of the antigen-binding site, and the first IMMUNOGLOBULIN CONSTANT REGIONS. This fragment can be obtained by digestion of immunoglobulins with the proteolytic enzyme PAPAIN.
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)
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).
Evaluation Studies as Topic
Drug Resistance, Microbial
Sequence Homology, Amino Acid
One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.
Chromosomes, Human, 13-15
Tandem Repeat Sequences
Staining of bands, or chromosome segments, allowing the precise identification of individual chromosomes or parts of chromosomes. Applications include the determination of chromosome rearrangements in malformation syndromes and cancer, the chemistry of chromosome segments, chromosome changes during evolution, and, in conjunction with cell hybridization studies, chromosome mapping.
Chromosomes, Human, Pair 17
The ratio of two odds. The exposure-odds ratio for case control data is the ratio of the odds in favor of exposure among cases to the odds in favor of exposure among noncases. The disease-odds ratio for a cohort or cross section is the ratio of the odds in favor of disease among the exposed to the odds in favor of disease among the unexposed. The prevalence-odds ratio refers to an odds ratio derived cross-sectionally from studies of prevalent cases.
Mycobacterium avium subsp. paratuberculosis
Reproducibility of Results
The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.
Nucleic Acid Conformation
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.
Amino Acid Substitution
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
Mycobacterium avium Complex
A complex that includes several strains of M. avium. M. intracellulare is not easily distinguished from M. avium and therefore is included in the complex. These organisms are most frequently found in pulmonary secretions from persons with a tuberculous-like mycobacteriosis. Strains of this complex have also been associated with childhood lymphadenitis and AIDS; M. avium alone causes tuberculosis in a variety of birds and other animals, including pigs.
Bacterial Outer Membrane Proteins
Borrelia burgdorferi Group
Gram-negative helical bacteria, in the genus BORRELIA, that are the etiologic agents of LYME DISEASE. The group comprises many specific species including Borrelia afzelii, Borellia garinii, and BORRELIA BURGDORFERI proper. These spirochetes are generally transmitted by several species of ixodid ticks.
A family of the order Rodentia containing 250 genera including the two genera Mus (MICE) and Rattus (RATS), from which the laboratory inbred strains are developed. The fifteen subfamilies are SIGMODONTINAE (New World mice and rats), CRICETINAE, Spalacinae, Myospalacinae, Lophiomyinae, ARVICOLINAE, Platacanthomyinae, Nesomyinae, Otomyinae, Rhizomyinae, GERBILLINAE, Dendromurinae, Cricetomyinae, MURINAE (Old World mice and rats), and Hydromyinae.
Reverse Transcriptase Polymerase Chain Reaction
Microbial Sensitivity Tests
Glutathione S-Transferase pi
RNA, usually prepared by transcription from cloned DNA, which complements a specific mRNA or DNA and is generally used for studies of virus genes, distribution of specific RNA in tissues and cells, integration of viral DNA into genomes, transcription, etc. Whereas DNA PROBES are preferred for use at a more macroscopic level for detection of the presence of DNA/RNA from specific species or subspecies, RNA probes are preferred for genetic studies. Conventional labels for the RNA probe include radioisotope labels 32P and 125I and the chemical label biotin. RNA probes may be further divided by category into plus-sense RNA probes, minus-sense RNA probes, and antisense RNA probes.
Proteins, usually found in the cytoplasm, that specifically bind calcitriol, migrate to the nucleus, and regulate transcription of specific segments of DNA with the participation of D receptor interacting proteins (called DRIP). Vitamin D is converted in the liver and kidney to calcitriol and ultimately acts through these receptors.
Identification of DNA polymorphisms associated with the V type alpha1-antitrypsin gene. (1/8395)alpha1-Antitrypsin (alpha1-AT) is a highly polymorphic protein. The V allele of alpha1-AT has been shown to be associated with focal glomerulosclerosis (FGS) in Negroid and mixed race South African patients. To identify mutations and polymorphisms in the gene for the V allele of alpha1-AT in five South African patients with FGS nephrotic syndrome DNA sequence analysis and restriction fragment length polymorphisms of the coding exons were carried out. Four of the patients were heterozygous for the BstEII RFLP in exon III [M1(Val213)(Ala213)] and one patient was a M1(Ala213) homozygote. The mutation for the V allele was identified in exon II as Gly-148 (GGG)-->Arg (AGG) and in all patients was associated with a silent mutation at position 158 (AAC-->AAT). The patient who was homozygous for (Ala213) also had a silent mutation at position 256 in exon III (GAT-->GAC) which was not present in any of the other four patients. Although the V allele of alpha1-AT is not associated with severe plasma deficiency, it may be in linkage disequilibrium with other genes on chromosome 14 that predispose to FGS. Furthermore, the associated silent mutation at position 158 and the Ala213 polymorphism are of interest, as these could represent an evolutionary intermediate between the M1(Ala213) and M1(Val213) subtypes. (+info)
Identification of a cytolethal distending toxin gene locus and features of a virulence-associated region in Actinobacillus actinomycetemcomitans. (2/8395)A genetic locus for a cytolethal distending toxin (CDT) was identified in a polymorphic region of the chromosome of Actinobacillus actinomycetemcomitans, a predominant oral pathogen. The locus was comprised of three open reading frames (ORFs) that had significant amino acid sequence similarity and more than 90% sequence identity to the cdtABC genes of some pathogenic Escherichia coli strains and Haemophilus ducreyi, respectively. Sonic extracts from recombinant E. coli, containing the A. actinomycetemcomitans ORFs, caused the distension and killing of Chinese hamster ovary cells characteristic of a CDT. Monoclonal antibodies made reactive with the CdtA, CdtB, and CdtC proteins of H. ducreyi recognized the corresponding gene products from the recombinant strain. CDT-like activities were no longer expressed by the recombinant strain when an OmegaKan-2 interposon was inserted into the cdtA and cdtB genes. Expression of the CDT-like activities in A. actinomycetemcomitans was strain specific. Naturally occurring expression-negative strains had large deletions within the region of the cdt locus. The cdtABC genes were flanked by an ORF (virulence plasmid protein), a partial ORF (integrase), and DNA sequences (bacteriophage integration site) characteristic of virulence-associated regions. These results provide evidence for a functional CDT in a human oral pathogen. (+info)
Role of the angiotensin type 2 receptor gene in congenital anomalies of the kidney and urinary tract, CAKUT, of mice and men. (3/8395)Angiotensin type 2 receptor gene null mutant mice display congenital anomalies of the kidney and urinary tract (CAKUT). Various features of mouse CAKUT impressively mimic human CAKUT. Studies of the human type 2 receptor (AGTR2) gene in two independent cohorts found that a significant association exists between CAKUT and a nucleotide transition within the lariat branchpoint motif of intron 1, which perturbs AGTR2 mRNA splicing efficiency. AGTR2, therefore, has a significant ontogenic role for the kidney and urinary tract system. Studies revealed that the establishment of CAKUT is preceded by delayed apoptosis of undifferentiated mesenchymal cells surrounding the urinary tract during key ontogenic events, from the ureteral budding to the expansive growth of the kidney and ureter. (+info)
Diversity of rhizobia associated with Amorpha fruticosa isolated from Chinese soils and description of Mesorhizobium amorphae sp. nov. (4/8395)Fifty-five Chinese isolates from nodules of Amorpha fruticosa were characterized and compared with the type strains of the species and genera of bacteria which form nitrogen-fixing symbioses with leguminous host plants. A polyphasic approach, which included RFLP of PCR-amplified 16S rRNA genes, multilocus enzyme electrophoresis (MLEE), DNA-DNA hybridization, 16S rRNA gene sequencing, electrophoretic plasmid profiles, cross-nodulation and a phenotypic study, was used in the comparative analysis. The isolates originated from several different sites in China and they varied in their phenotypic and genetic characteristics. The majority of the isolates had moderate to slow growth rates, produced acid on YMA and harboured a 930 kb symbiotic plasmid (pSym). Five different RFLP patterns were identified among the 16S rRNA genes of all the isolates. Isolates grouped by PCR-RFLP of the 16S rRNA genes were also separated into groups by variation in MLEE profiles and by DNA-DNA hybridization. A representative isolate from each of these DNA homology groups had a separate position in a phylogenetic tree as determined from sequencing analysis of the 16S rRNA genes. A new species, Mesorhizobium amorphae, is proposed for the majority of the isolates, which belonged to a moderately slow- to slow-growing, acid-producing group based upon their distinct phylogenetic position, their unique electrophoretic type, their low DNA homology with reference strains representing the species within the genus Mesorhizobium and their distinct phenotypic features. Strain ACCC 19665 was chosen as the type strain for M. amorphae sp. nov. (+info)
RFLP of rRNA genes and sequencing of the 16S-23S rDNA intergenic spacer region of ammonia-oxidizing bacteria: a phylogenetic approach. (5/8395)It has been established that 16S rRNA gene-based phylogeny gives a low resolution between members of the chemoautotrophic ammonia-oxidizing bacteria (AOB) belonging to the beta-subclass of the Proteobacteria. In this study, 12 isolates of AOB were ribotyped, and the sequences of the 16S-23S rDNA intergenic spacer region (ISR) were determined and used in a phylogenetic study. 16S and 23S rDNA ribotyping revealed that the AOB studied contain only one rrn operon per genome, in contrast to most bacteria, which have 5-10 copies of the rRNA genes per genome. It is likely that the presence of only one set of rRNA genes is related to the slow growth of the AOB. The 16S and 23S rRNA genes of the AOB were shown to be arranged in the classical way: a 16S rRNA gene, an ISR and a 23S rRNA gene. Despite the close phylogenetic relationship among the AOB, the relative location of the rRNA genes in the genome appears to vary considerably. The size of the ISR was approximately 400 bp in the Nitrosomonas isolates and 645-694 bp in the Nitrosospira isolates, suggesting a species-specific size difference in the ISR. The ISR contained two potential tRNA genes in the 5' end in all isolates studied. The similarity values between the ISR sequences of the AOB are low (42.9-96.2%) compared with the 16S rDNA sequence similarity values, and therefore the ISR sequences are valuable as a complementary phylogenetic tool in combination with 16S rRNA gene sequences. The phylogenetic analysis of the AOB based on ISR sequences confirms the 16S rRNA gene-based phylogeny but has the benefit of giving a higher resolution. (+info)
Identification of yeasts by RFLP analysis of the 5.8S rRNA gene and the two ribosomal internal transcribed spacers. (6/8395)The identification and classification of yeasts have traditionally been based on morphological, physiological and biochemical traits. Various kits have been developed as rapid systems for yeast identification, but mostly for clinical diagnosis. In recent years, different molecular biology techniques have been developed for yeast identification, but there is no available database to identify a large number of species. In the present study, the restriction patterns generated from the region spanning the internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene were used to identify a total of 132 yeast species belonging to 25 different genera, including teleomorphic and anamorphic ascomycetous and basidiomycetous yeasts. In many cases, the size of the PCR products and the restriction patterns obtained with endonucleases CfoI, HaeIII and HinfI yielded a unique profile for each species. Accordingly, the use of this molecular approach is proposed as a new rapid and easy method of routine yeast identification. (+info)
Epidemiological characterization of methicillin-resistant Staphylococcus aureus isolated in the North West of England by protein A (spa) and coagulase (coa) gene polymorphisms. (7/8395)In a comparative study, isolates of methicillin-resistant Staphylococcus aureus (MRSA) with known pulsed-field gel electrophoresis (PFGE) and bacteriophage type were analysed by polymerase chain reaction (PCR) and restriction fragment length polymorphisms (RFLP) for additional discriminatory subtyping information. PFGE was previously performed using standardized, commercially available kits and pre-programmed software. Isolates were examined for coagulase (coa) and protein A (spa) gene polymorphisms following PCR amplification of the coa hypervariable and spa repeat regions. Coa gene RFLPs produced a total of 38 distinct combined patterns after digestion with HaeIII and AluI and identified the predominant epidemic (EMRSA) types 15 and 16. A unique HaeIII restriction site was identified by RFLP and sequence analysis in the coa gene for EMRSA 15 but not EMRSA 16. The spa gene PCR yielded a total of 14 different profiles ranging from 3-18 repeats with the 2 predominant EMRSA types falling into 2 distinct groups. PCR detection of coa and spa polymorphisms offer a rapid preliminary strain identification and discriminatory subtyping information for surveillance of MRSA. (+info)
Molecular cloning and characterization of three cDNAs encoding putative mitogen-activated protein kinase kinases (MAPKKs) in Arabidopsis thaliana. (8/8395)We isolated three Arabidopsis thaliana cDNA clones (ATMKK3, ATMKK4 and ATMKK5) encoding protein kinases with extensive homology to the mitogen-activated protein kinase kinases (MAPKKs) of various organisms in the catalytic domain. ATMKK3 shows high homology (85% identity) to NPK2, a tobacco MAPKK homologue. ATMKK4 and 5 are closely related to each other (84% identity). Phylogenetic analysis showed that the plant MAPKKs constitute at least three subgroups. The recombinant ATMKK3 and ATMKK4 were expressed as a fusion protein with glutathione S-transferase (GST) in Escherichia coli. Affinity purified GST-ATMKK3 and GST-ATMKK4 proteins contained phosphorylation activity, which shows that both the ATMKK3 and ATMKK4 genes encode functional protein kinases. Northern blot analysis revealed that the ATMKK3 gene expressed in all the organs. The levels of ATMKK4 and 5 mRNAs were relatively higher in steins and leaves than in flowers and roots. We determined the map positions of the ATMKK3, 4 and 5 genes on Arabidopsis chromosomes by RFLP mapping using P1 genomic clones. (+info)
Cryptosporidium parvum mixed genotypes detected by PCR-restriction fragment length polymorphism analysis<...
TY - JOUR. T1 - Cryptosporidium parvum mixed genotypes detected by PCR-restriction fragment length polymorphism analysis. AU - Reed, C.. AU - Sturbaum, G. D.. AU - Hoover, P. J.. AU - Sterling, Charles R. PY - 2002. Y1 - 2002. N2 - Combinations of 10 Cryptosporidium parvum oocysts, with various ratios of genotype I to genotype II, were isolated and subjected to PCR-restriction fragment length polymorphism analysis. Amplification of both genotypes in these samples ranged from 31 to 74% and yielded no information about the genotype proportions. In addition, since both genotypes were not always detected, amplification of a single genotype is not conclusive evidence that the sample contains only a single genotype.. AB - Combinations of 10 Cryptosporidium parvum oocysts, with various ratios of genotype I to genotype II, were isolated and subjected to PCR-restriction fragment length polymorphism analysis. Amplification of both genotypes in these samples ranged from 31 to 74% and yielded no information ...
Uji Diagnostik Polymerase Chain Reaction -Restriction Fragment Length Polymorphism Dalam Menegakkan Diagnosis Onikomikosis.
Background: Onychomycosis is a fungal infection of one or more units of the nail caused by dermatophytes, or mold and nondermatophytes yeast. Investigations are needed to establish the diagnosis of onychomycosis before starting treatment. Several investigations methods for diagnosing onychomycosis such as microscopic examination with 20% KOH, fungal culture, histopathology examination with PAS staining (Periodic acid Schiff) and PCR (Polymerase Chain Reaction), for culture methods require a long time about 4 weeks to identify fungal that cause onychomycosis. A molecular technology such as PCR is a sensitive and specific test for the diagnosis of a variety of microorganisms including fungal pathogens. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) is a method with the addition of the enzyme after PCR amplification allowing more specific results. Objective: To determine the diagnostic value of Polymerase Chain Reaction-Restriction Fragment Length Polymorphism ...
Characterization of MHC DRB3.2 Alleles of Crossbred Cattle by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism
The present investigation was undertaken to study the genetic polymorphism of the DRB3 exon 2 in 75 crossbred cattle by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. Five genotypes i.e. HaeIII-a, HaeIII-b, HaeIII-e, HaeIII-ab and HaeIII-ae were observed when the 284 bp PCR products were digested with HaeIII restriction enzyme. The corresponding frequencies of these patterns were 0.53, 0.04, 0.01, 0.38 and 0.04, respectively. Digestion with RsaI restriction enzyme resolved 24 different restriction patterns. The frequencies of these patterns ranged from 0.013 (RsaI-f, RsaI-k and RsaI-c/n) to 0.120 (RsaI-n). The results revealed that the crossbred cows belonged to the RsaI patterns namely b, k, l, a/l, d/s, l/n, l/o and m/n, whose corresponding frequencies were 0.027, 0.013, 0.040, 0.027, 0.040, 0.067, 0.027 and 0.067, respectively. Digestion of the 284 bp PCR product of DRB3.2 gene with PstI in the crossbred cattle did not reveal any restriction site. ...
Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) Analysis of Three Lipooligosaccharide-Associated...
Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) Analysis of Three Lipooligosaccharide-Associated Genes of Campylobacter jejuni and Campylobacter coli Isolated From Animal Samples ...
Two DNA restriction fragment length polymorphisms associated with Ag(t/z) and Ag(g/c) antigenic sites of human apolipoprotein B...
Several high frequency restriction fragment length polymorphisms (RFLPs) associated with the human gene for apolipoprotein B have been previously reported by Priestly et al. The EcoRI RFLP here was shown to be very strongly associated with the Ag(t/z) immunochemical polymorphism of human low density lipoproteins, allowing correct Ag(t/z) phenotyping of 17 (out of 17 tested) unrelated individuals. The Xbal RFLP was associated with the Ag(g/c) immunochemical polymorphism, permitting correct phenotyping of 14 (out of 17 tested) unrelated individuals. Its close association with an RFLP permitted localization of the Ag(t/z) polymorphism to the C-terminal end of the apolipoprotein B peptide, and allowed detailed discussion of its probable molecular basis. ...
Terminal restriction fragment length polymorphism - Wikipedia
Terminal restriction fragment length polymorphism (TRFLP or sometimes T-RFLP) is a molecular biology technique for profiling of microbial communities based on the position of a restriction site closest to a labelled end of an amplified gene. The method is based on digesting a mixture of PCR amplified variants of a single gene using one or more restriction enzymes and detecting the size of each of the individual resulting terminal fragments using a DNA sequencer. The result is a graph image where the x-axis represents the sizes of the fragment and the y-axis represents their fluorescence intensity. TRFLP is one of several molecular methods aimed to generate a fingerprint of an unknown microbial community. Other similar methods include DGGE, TGGE, ARISA, ARDRA, PLFA, etc. These relatively high throughput methods were developed in order to reduce the cost and effort in analyzing microbial communities using a clone library. The method was first described by Liu and colleagues in 1997 which employed ...
Quantitative real-time polymerase chain reaction (qRT-PCR) restriction fragment length polymorphism (RFLP) method for...
TY - JOUR. T1 - Quantitative real-time polymerase chain reaction (qRT-PCR) restriction fragment length polymorphism (RFLP) method for monitoring highly conserved transgene expression during gene therapy. AU - Bruzzone, Carol M.. AU - Belcher, John D.. AU - Schuld, Nathan J.. AU - Newman, Kristal A.. AU - Vineyard, Julie. AU - Nguyen, Julia. AU - Chen, Chunsheng. AU - Beckman, Joan D.. AU - Steer, Clifford J.. AU - Vercellotti, Gregory M.. PY - 2008/12. Y1 - 2008/12. N2 - Evaluation of the transfer efficiency of a rat heme oxygenase-1 (HO-1) transgene into mice requires differentiation of rat and mouse HO-1. However, rat and mouse HO-1 have 94% homology; antibodies and enzyme activity cannot adequately distinguish HO-1. We designed a quantitative real-time polymerase chain reaction (qRT-PCR) method to monitor HO-1 transcription relative to a housekeeping gene, GAPDH. The ratio of rat and mouse HO-1 mRNA could be estimated through restriction fragment length polymorphism (RFLP) analysis of the PCR ...
Restriction fragment length polymorphism Synonyms, Restriction fragment length polymorphism Antonyms | Thesaurus.com
Synonyms for restriction fragment length polymorphism at Thesaurus.com with free online thesaurus, antonyms, and definitions. Dictionary and Word of the Day.
Typing Neisseria meningitidis by analysis of restriction fragment length polymorphisms in the gene encoding the class 1 outer...
A typing method was developed for Neisseria meningitidis serogroup A by analysis of restriction fragment length polymorphisms (RFLP) of the class 1 outer membrane protein gene (porA). By using appropriate primers, an approximately 1,116-bp fragment of the porA gene was amplified by PCR and then was digested with the restriction endonuclease MspI. The digestion products were separated on 10% polyacrylamide gels and were stained with silver. One hundred three clinical isolates of group A N. meningitidis from 17 provinces of China collected over a 26-year period were analyzed. Results of MspI-generated RFLP profiles of PCR-amplified porA genes were compared with those obtained by conventional serosubtyping. There was a band of about 400 bp common to all strains examined, and the 103 strains of serogroup A resulted in 22 unique RFLP patterns. The differences in bands could be observed mainly in the range of 120 to 280 bp. The smaller fragments were useful in distinguishing meningococci with the same ...
PPT - RFLP (Restriction Fragment Length Polymorphism) PowerPoint presentation | free to download - id: 425ce8-OTc2N
RFLP (Restriction Fragment Length Polymorphism) RFLP RFLP was developed at the late 70 s due to the discovery of restriction enzymes (REs; or called as restriction ... – A free PowerPoint PPT presentation (displayed as a Flash slide show) on PowerShow.com - id: 425ce8-OTc2N
Restriction maps and restriction fragment length polymorphisms of the human 21-hydroxylase genes<...
TY - JOUR. T1 - Restriction maps and restriction fragment length polymorphisms of the human 21-hydroxylase genes. AU - Donohoue, Patricia A.. AU - Jospe, Nicholas. AU - Migeon, Claude J.. AU - McLean, Robert H.. AU - Bias, Wilma B.. AU - White, Perrin C.. AU - Van Dop, Cornelis. N1 - Funding Information: ACKNOWLEDGEMENTS: We thank Dr. M. C. Carroll of Harvard pK4 clone, Ms. S. F. Klupt for assistance in preparation Ms. C. Schaefer for C4 phenotyping, Drs. E. Fleischnick, Crigler, Jr., for aid in obtaining blood samples from Bw47-linked CAH, and Ms. D. Qgorzalek for preparation work was supported in part by NIH grants AM-00180 AM-31920 (R.H.M.), AM-36085 (C.V.D.) and CA-22507 University for the of restriction blots, L. Key, and J. F. two patients with HLA-of this manuscript. This (C.J.M.), AM-07116 (C.J.M.), (P.C.W.).. PY - 1986/4/29. Y1 - 1986/4/29. N2 - Restriction maps were constructed for the two human 21-hydroxylase genes (21-OHA and 21-OHB) by using DNA from subjects homozygous for a ...
Adelaide Research & Scholarship: Restriction fragment length polymorphism of the apolipoprotein B gene and response to dietary...
OBJECTIVE: The relationship between response to dietary fat and cholesterol, and the EcoRI restriction fragment length polymorphism (RFLP) of the apolipoprotein B(apoB) gene was examined. DESIGN: Forty-nine free-living subjects took part in a prospective double-blind crossover dietary intervention study. The apoB EcoRI cutting site was present in five women and 18 men (E+) and absent in 15 women and 11 men (E-). INTERVENTION: Subjects consumed a low fat (25% energy), low cholesterol (less than 200 mg/day) diet. After two weeks on this background diet (baseline) subjects were randomly assigned to consume a liquid supplement for three weeks which was either fat and cholesterol free or which contained fat (30 to 36 g) and cholesterol (650 to 780 mg). After the first three-week period subjects switched to the other supplement. Blood samples were collected for plasma lipid analysis after an overnight fast on two consecutive days at the end of baseline and on three consecutive days after each ...
Interpretation of restriction fragment length polymorphism analysis of Mycobacterium tuberculosis isolates from a state with a...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Community terminal restriction fragment length polymorphisms reveal insights into the diversity and dynamics of leaf endophytic...
The Hallman et al.  definition of endophytic bacteria requires surface-disinfested plant tissue or extraction from the plant. Disinfestation by killing all the epiphytic bacteria may be effective when culture-dependent protocols are used, but is not appropriate in culture-independent protocols, such as the present one, since the DNA or RNA of dead epiphytes, if not removed, would still be amplified by bacteria-specific PCR. For those organs, like tubers, whose outer layers can be easily peeled off, endophytic bacteria can be isolated from inside of the plants unambiguously. However, peeling the epidermis off leaves, while possible, is not practical for a study like the present one. Therefore, to study leaf endophytic bacterial communities, it is critical to dislodge epiphytic bacteria from the leaf surfaces as far as possible. We have dislodged epiphytes using methods similar to those reported by others [13, 26-28]. Since we did not test the rinse water for rDNA amplicons, we cannot be ...
Genetic analysis and FISH mapping of the Colourless non-ripening locus by M Tor, K Manning et al.
Cnr (Colourless non-ripening) is a dominant pleiotropic ripening mutation of tomato (Lycopersicon esculentum) which has previously been mapped to the proximal region of tomato chromosome 2. We describe the fine mapping of the Cnr locus using both linkage analysis and fluorescence in situ hybridisation (FISH). Restriction fragment length polymorphism (RFLP)-, amplified restriction fragment polymorphism (AFLP)-, and cleaved amplified polymorphic sequence (CAPS)- based markers, linked to the Cnr locus were mapped onto the long arm of chromosome 2. Detailed linkage analysis indicated that the Cnr locus was likely to lie further away from the top of the long arm than previously thought. This was confirmed by FISH, which was applied to tomato pachytene chromosomes in order to gain an insight into the organisation of hetero- and euchromatin and its relationship to the physical and genetic distances in the Cnr region. Three molecular markers linked to Cnr were unambiguously located by FISH to the long arm of
The association between IL-17 gene variants and risk of colorectal cancer in a Chinese population: A case-control study |...
Peripheral blood (2 ml) was taken from all subjects and genomic DNA was extracted from peripheral blood using the TIANamp Blood DNA kit (Tiangen Biotech, Beijing, China) according to manufacturers instructions. The quality and concentration of extracted DNA was measured in two OD wavelength 260 and 280 nm using NanoDrop (Thermo Scientific, U.S.A.). SNP genotyping was performed using polymerase chain reaction-restriction fragment length polymorphism method. The primers used for the nucleotide extension reaction were AACAAGTAAGAATGAAAAGAGGACATGGT (forward) and CCCCCAATGAGGTCATAGAAGAATC (reverse) for rs2275913 and ACCAAGGCTGCTCTGTTTCT (forward) and GGTAAGGAGTGGCATTTCTA (reverse) for rs763780 polymorphism. For PCR, 25 μl reaction mixture contained as follows: 2.5 μl of 10× reaction buffer (with 1.5 mM MgCl2), 2 μl of deoxynucleotide triphosphate (dNTP; 2.5 mM), 2 μl of each pair primer, 50 ng DNA template, 1 μl of 0.4U Taq polymerase (Applied Biosystems, Evry, France) and 14.5 μl ddH2O. The ...
Single-strand restriction fragment length polymorphism analysis of the second internal transcribed spacer (ribosomal DNA) for...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Association of MDR1 C3435T and C1236T single nucleotide polymorphisms with male factor infertility. - Infectoforum
Infertility affects 1 in 6 couples and approximately 1 in 25 men. Male factor infertility is a major cause of spermatogenic anomalies, the causes of which are largely unknown. Impaired repro-ductive functions in men might result from physiological, genetic, and/or environmental factors such as xenobiotics. The multi-drug re-sistance1 (MDR1) gene encodes a P-glycoprotein which has a role in the active transport of various substrates providing protection of somatic cells from potentially toxic substances, including xenobi-otics. MDR1 is highly expressed at the luminal surface of capillary endothelial cells, and is expressed in Leydig cells, testicular mac-rophages, and Sertoli cells. We performed genotype and haplotype analyses of MDR1 in 192 infertile and 102 fertile Turkish men for the genetic markers C1236T and C3435T, using polymerase chain reaction-restriction fragment length polymorphism analysis. In the overall population, correlations were analyzed in all genotype mod-els. We found that ...
Molecular characterization of Sardinian Mycobacterium tuberculosis isolates by IS6110 restriction fragment length polymorphism,...
An evaluation of the utility of rep PCR typing compared to the 15 loci discriminatory set of MIRU-VNTR was undertaken. Twenty-nine isolates of Mycobacterium tuberculosis from patients were examined. Genomic DNA was extracted from the isolates by standard method. The number of copies of tandem repeats of the 15 MIRU-VNTR loci was determined by PCR amplification and agarose gel electrophoresis of the amplicons. M. tuberculosis outbreak-related strains were distinguished from other isolates. MIRU-VNTR typing identified 4 major clusters of strains. The same isolates clustered together after RFLP typing, but rep-PCR identified only 3 of them. The concordance between RFLP and MIRU-VNTR typing was complete, with the exception of two isolates with identical RFLP patterns that differed in the number of tandem repeat copies at two MIRU-VNTR alleles. A further isolate, even sharing the same RFLP pattern, differed by one repeat from the rest of its cluster. We also tested the use of an automated rep-PCR for ...
Abstract 17123: CYP2C19 Phenotype, Stent Thrombosisin, Myocardial Infarction, and Mortality in Patients with Coronary Stent...
Aims: Several studies indicated that CYP2C19 loss-of-function polymorphisms have a higher risk of stent thrombosis (ST) after percutaneous coronary interventions (PCIs). However, this association has not been investigated thoroughly in Chinese population. In this study, we aimed to determine the effect of CYP2C19 loss-of-function polymorphisms on the occurrence of ST and other adverse clinical events in Chinese population.. Methods: The study population included 1 068 consecutive patients undergoing intracoronary stent implantation after pre-loading with 600mg of clopidogrel. CYP2C19*2 and CYP2C19*3 were genotyped by use of polymerase chain reaction-restriction fragment length polymorphism analysis. The adverse clinical events recorded were ST, death, myocardial infarction, and bleeding events. The primary end point of the study was the incidence of cumulative ST within 1 year following PCI. The secondary end point was other adverse clinical outcomes 1 year after the procedure.. Results: The ...
Proliferative diabetic retinopathy is an important cause of visual impairment. We investigated whether the polymorphism of the β3-adrenoreceptor (β3-AR) gene, which is associated with insulin resistance and an earlier onset of NIDDM, was associated with proliferative diabetic retinopathy (PDR) in 215 Japanese NIDDM patients with a duration of diabetes of ,10 years. The polymorphism of the β3-AR gene was determined by polymerase chain reaction-restriction fragment length polymorphism analysis. The Trp64Arg allele of the β3-AR gene was significantly more frequent in the NIDDM patients with PDR (P = 0.002), but not in those with non-PDR (P = 0.151), than in NIDDM patients without diabetic retinopathy. Those with the mutation had an earlier onset of diabetes, a longer duration of diabetes, and higher current and maximal BMI values, compared with those without the mutation. Moreover, this mutation was also associated with higher serum triglyceride and decreased HDL-cholesterol levels. When ...
Annette Reineke - Pestinfo-Wiki
Molecular identification of larval stages of Otiorhynchus (Coleoptera: Curculionidae) species based on polymerase chain reaction-restriction fragment length polymorphism analysis Journal of Applied Entomology (2008) 132, 230-238 ...
Identification of Isolated Salmonella enterica Serotype gallinarum Biotype Pullorum and Gallinarum by PCR-RFLP | Jundishapur...
Salmonella spp. is the major bacterial pathogen in poultry and is responsible for significant economic losses of the poultry industry in many parts of the world. Among Salmonella spp., Salmonellagallinarum and S.pullorum are the most common causative agents of chicken salmonellosis resulting in high mortality and morbidity.The aim of this study was to identify S. gallinarum and S. pullorum by using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method.In this study, 13 samples of Salmonella, isolated from local poultry, were obtained from Razi Type Culture Collection (RTCC). For the PCR-RFLP method based on the fliC gene, extracted DNA was used as a template for amplifying of the fliC gene (197bp) using specific primers. PCR products were subjected to digestion using Hinp1I restriction endonuclease.For the PCR, 197 bp fliC fragment was amplified from all 13 isolates. Ten out of 13 were S.gallinarum and the other three were S. pullorum. As part of the PCR-RFLP, two
probeBase 2016 | An online resource for rRNA-targeted oligonucleotides
A quantitative molecular technique was developed for rapid analysis of microbial community diversity in various environments. The technique employed PCR in which one of the two primers used was fluorescently labeled at the 5 end and was used to amplify a selected region of bacterial genes encoding 16S rRNA from total community DNA. The PCR product was digested with restriction enzymes, and the fluorescently labeled terminal restriction fragment was precisely measured by using an automated DNA sequencer. Computer-simulated analysis of terminal restriction fragment length polymorphisms (T-RFLP) for 1,002 eubacterial sequences showed that with proper selection of PCR primers and restriction enzymes, 686 sequences could be PCR amplified and classified into 233 unique terminal restriction fragment lengths or ribotypes. Using T-RFLP, we were able to distinguish all bacterial strains in a model bacterial community, and the pattern was consistent with the predicted outcome. Analysis of complex ...
Restriction fragment length polymorphism - Wikipedia
The technique for RFLP analysis is, however, slow and cumbersome. It requires a large amount of sample DNA, and the combined process of probe labeling, DNA fragmentation, electrophoresis, blotting, hybridization, washing, and autoradiography can take up to a month to complete. A limited version of the RFLP method that used oligonucleotide probes was reported in 1985. 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). The analysis of VNTR alleles continues, but is now usually performed by polymerase chain reaction (PCR) methods. For example, the standard protocols for DNA fingerprinting involve PCR analysis of panels of more than a dozen VNTRs. RFLP is still used in marker-assisted selection. Terminal restriction fragment ...
An Association between Single Nucleotide Polymorphisms of Lys751Gln ERCC2 Gene and Ovarian Cancer in Polish Women
|i |Aim.|/i| The aim of this study was to evaluate the role of the Lys751Gln (rs13181) |i |ERCC2|/i| gene polymorphism in clinical parameters and the risk for development of ovarian cancer. |i |Material and Methods.|/i| The study consisted of 430 patients with ovarian cancer (mean age: 53.2 ± 10.11) and 430 healthy subjects (mean age: 50.31 ± 18.21). Analysis of the gene polymorphisms was performed using the PCR-based restriction fragment length polymorphism (PCR-RFLP). The odds ratios (ORs) and 95% confidence intervals (CIs) for each genotype and allele were calculated. |i |Results.|/i| The results obtained indicate that the genotype Gln/Gln is associated with an increased risk of ovarian cancer (OR 5.01; 95% CI 3.37–7.43; |svg xmlns:xlink=http://www.w3.org/1999/xlink xmlns=http://www.w3.org/2000/svg style=vertical-align:-3.42938pt id=M1 height=11.7782pt version=1.1 viewBox=-0.0498162 -8.34882 57.0529 11.7782 width=57.0529pt||g transform=matrix(.013,0
Lack of association between polymorphisms in the testis-specific angiotension converting enzyme gene and male infertility in an...
Angiotensin converting enzyme (ACE) is a membrane-bound dipeptidyl carboxy-peptidase that generates vasoconstricting angiotensin II and inactivates vasodilating bradykinin. The ACE gene encodes two isozymes: the somatic isozyme (sACE) is found in many tissues including vascular endothelial cells, whereas the testis-specific isozyme (tACE) is expressed exclusively in developing spermatids and mature sperm. Thus, ACE might have physiological functions in addition to blood pressure regulation. Male mice lacking tACE activity show reduced fertility, indicating its importance in male fertility. In this study, we screened five recently defined tACE gene polymorphisms in 90 Singapore Chinese men with infertility and 84 fertile controls using PCR-based restriction fragment length polymorphism and DNA sequencing. However, only one of these polymorphisms was identified in both patient and control groups, the frequency of which was not significantly different in patients and controls. Thus, these ACE gene ...
Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. | Journal of...
Widespread use of DNA restriction fragment length polymorphism (RFLP) to differentiate strains of Mycobacterium tuberculosis to monitor the transmission of tuberculosis has been hampered by the need to culture this slow-growing organism and by the level of technical sophistication needed for RFLP typing. We have developed a simple method which allows simultaneous detection and typing of M. tuberculosis in clinical specimens and reduces the time between suspicion of the disease and typing from 1 or several months to 1 or 3 days. The method is based on polymorphism of the chromosomal DR locus, which contains a variable number of short direct repeats interspersed with nonrepetitive spacers. The method is referred to as spacer oligotyping or spoligotyping because it is based on strain-dependent hybridization patterns of in vitro-amplified DNA with multiple spacer oligonucleotides. Most of the clinical isolates tested showed unique hybridization patterns, whereas outbreak strains shared the same ...
Loss of Heterozygosity for Loci on the Long Arm of Chromosome 6 in Human Malignant Melanoma<...
TY - JOUR. T1 - Loss of Heterozygosity for Loci on the Long Arm of Chromosome 6 in Human Malignant Melanoma. AU - Millikin, D.. AU - Trent, J.. PY - 1991/10/15. Y1 - 1991/10/15. N2 - Malignant melanoma has been documented to display recurring abnormalities of chromosome 6, particularly the long arm (6q). Restriction fragment length polymorphism analysis was used as a molecular genetic approach to examine loci on chromosome 6q for loss of constitutional heterozygosity (LOH). Five DNA markers that recognize restriction fragment length polymorphisms along 6q and one polymorphic DNA marker for 6p were used to screen 20 autologous pairs of tumor DNA and normal DNA to determine the tumor and constitutional genotypes of each patient. LOH on chromosome 6q was identified at 21 of S3 inform ative loci (40%). Five patients with more than one informative locus had allele losses consistent with the loss of the entire long arm (or of an entire copy) of chromosome 6, while four other patients demonstrated ...
PPAR-Gamma Pro12Ala Polymorphism and Gastric Cancer Risk in a Turkish Population | AVESİS
Background: Peroxisome proliferator-activated receptor gamma (PPAR gamma) is a ligand dependent transcription factor involved in various processes, including carcinogenesis. We aimed to investigate any possible association of the PPAR gamma Pro12Ala (rs1801282) polymorphism with risk of developing gastric cancer (GC). Patients and Methods: A hospital based case control study was designed covering 50 patients with GC and 120 healthy controls. The frequencies of PPAR gamma Pro12Ala (rs1801282) were determined using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. Results: The Ala12 allele of the PPAR gamma Pro12Ala G gene was associated with a 1.95 fold increased risk of GC development (p: 0.022; 95% CI: 1.58-2.40). Subgroup analyses showed that the same allele was also associated with metastasis (p: 0.000; OR: 4.09; 95% CI: 2.273-7.368) and differentiation (p: 0.004; OR: 1.95; 95% CI: 1.335-2.875) in patients with GC. Conclusion: This study suggests that the ...
Influences of IL-1b-3953 C | T and MMP-9-1562C | T Gene Variants on Myocardial Infarction Susceptibility in a Subset of the...
Aims: IL-1b-3953 C,T and MMP-9-1562C,T variants have been shown to be linked to the development of myocardial infarction (MI), although previous studies have reported inconsistent results. The aim of the present study was to determine whether these genetic variations are associated with MI susceptibility in an Iranian population. Methods: In the current study, 117 patients with MI and 120 control group members were selected as participants. Peripheral blood samples were taken from all the subjects for genomic DNA extraction. Single nucleotide polymorphism (SNP) genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assays. Results: Multiple logistic regression analysis revealed that the TT genotype of the IL-1b-3953 C,T polymorphism is associated with a significant MI protective effect in: the homozygote model after adjustment for MI risk factors (odds ratio OR]: 0.18, confidence interval 95% CI] = 0.04-0.72; p = 0.01); and also in the recessive ...
Loughborough University Institutional Repository: Genetic analysis of CYP2D6 polymorphism in Indian populations and its...
Despite the rapid development of pharmacogenetic testing and the frequencies of medication related emergencies increasing, pharmacogentic testing is not yet implemented extensively in clinical practice. Several studies document that polymorphic Cytochrome P450 isoenzymes CYP2C9, CYP2C19 and CYP2D6 are responsible for the metabolism of many clinically important drugs and xenobiotics. These polymorphisms contribute to inter-individual and interethnic variation in drug metabolism which may lead to differences in drug response, suggesting that common dose regimen will not always equivocate to efficacious dosing. The CYP2D6*2, CYP2D6*4 and CYP2D6*10 variants were studied in four Indian populations (Gujarati, Punjabi, Bengali and Koya tribe). Genotypes at individual alleles were identified using Polymerase Chain Reaction Restriction Fragment Length Polymorphism (PCR-RFLP) method. Differences in frequencies of CYP2D6 genotypes/ alleles were compared at regional and global level. CYP2D6*2 variant ...
Effects of Tobacco Habits on the Polymorphism of NFKB1 and NFKB1A Gene of Head and Neck Squamous Cell Carcinoma in Indian...
Background: Polymorphism of NFKB1 and NFKB1A are highly associated with cancer. We have assessed polymorphism in the promoter region of NFKB1 -94 del/ins ATTG (rs28362491) and NFKB1A -826 C/T (rs2233406) with the risk of HNSCC in Indian population. Methods: Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used for the genotyping NFKB1 -94 del/ins ATTG and NFKB1A -826 C/T. Sequencing was done to validate the results of PCR-RFLP. Statistical analysis of data was done by Stata/SE-14.0 software. Results: ins/ins genotype was observed to be a risk factor of HNSCC as compared del/del genotype of NFKB1 -94 ATTG. Interactive effects of smoking and chewing on ins/ins genotype showed 13.96 and 10.92 fold increased risk of HNSCC. NFKB1A -826 C/T polymorphism, TT genotype showed no association with the risk of HNSCC as compared to wild type CC genotype. Conclusion: Our results showed NFKB1 -94 del/ins ATTG with smoking and tobacco chewing may increase the risk of HNSCC
Rare Genetic Disorder: Diagnosis (2/3)
After immunoflurescent microscopy DNA mutational analysis is the final step in elucidating the underlying molecular defect, and in most cases, it reduces the number of genes to be screened. DNA is extracted from blood of the patient and family members. Initial mutation screening is performed by restriction fragment-length polymorphism analysis, hotspot analysis, and finally, direct DNA sequencing ...
Gene Variants, mRNA and NOD1/2 Protein Levels in Tunisian Childhood Asthma | Read by QxMD
INTRODUCTION: Asthma is a common respiratory childhood disease that results from an interaction between genetic, environmental and immunologic factors. The implication of nucleotide-binding and oligomerization domain 1 and 2 (NOD1/CARD4, NOD2/CARD15) was highlighted in many inflammatory diseases.. METHODS: In this case-control study, we analyzed the association of three NOD2 polymorphisms and one NOD1 variant, in 338 Tunisian asthmatic children and 425 healthy Controls, using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. We also assessed NOD1 and NOD2 mRNA and protein levels by qRT-PCR and ELISA techniques.. RESULTS: The homozygous AA genotype of rs2075820 was a risk factor for asthma (OR 2.39). The influence of the E266K variant in the presence of the heterozygous AG genotype was higher in male than female groups. The homozygous AA genotype was a risk factor associated with asthma, for patients aged between 6 and 18 years OR 2.39, IC95% (1.04-5.49) p , ...
Evidence of association of Vitamin D receptor Apa I gene polymorphism with bone mineral density in postmenopausal women with...
The vitamin D receptor (VDR) was the first candidate gene to be studied in relation to osteoporosis, and most attention has focused on polymorphisms situated near the 3 flank of VDR. The aim of this study was to investigate the association about VDR gene Apa I polymorphism with bone mineral density (BMD) in postmenopausal women with osteoporosis. We studied a total of 136 postmenopausal women with a mean age of 56.36 +/- 10.29 years. Among them, a total of 75 had osteoporosis, 37 had osteopenia, and 24 had normal BMD. Venous blood samples were obtained for evaluation of bone metabolism and genotyping. The VDR Apa I genotype was determined by polymerase chain reaction-restriction fragment length polymorphism. BMDs at the lumbar spine and hip were measured by dual-energy X-ray absorptiometry. Postmenopausal women with aa genotype had significantly lower BMD values (grams per centimeter square) at lumbar spines compared to persons with AA genotype. Also, postmenopausal women with AA genotype had ...
Search Results | De Gruyter
Molecular analysis of the CYP21A2 gene was performed for the detection of the six most common point mutations (p.P30L, p.I172N, p.V281L, p.Q318X, the splice site mutation Int2 [IVS2-13A/C,G], and the cluster of three mutations [p.I236N, p.V237E, and p.M239K] designed as CL6). Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was performed on 47 unrelated Egyptian 21α-OH deficiency patients and their available parents to detect the presence of the six most common point mutations. ...
IKZF1 | Cancer Genetics Web
Genome-wide association studies (GWAS) have proved the association of IKZF1 polymorphisms with childhood acute lymphoblastic leukemia (ALL). In the present study, we aimed to inspect the impact of IKZF1 gene polymorphisms and childhood ALL in a sample of Iranian population who live in south east of Iran. This case-control study was done on 110 children diagnosed with ALL and 120 healthy children. The IKZF1 (rs4132601 T > G, rs11978267 A > G, rs11980379 T > C, and rs10272724 T > C) polymorphisms were determined using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP). The results showed that rs4132601 T > G polymorphism increased the risk of ALL in the codominant (OR = 2.96, 95 % CI = 1.58-5.54, p = 0.0008, TG vs TT; and OR = 2.75, 95 % CI = 1.31-5.76, p = 0.0094, GG vs TT) and dominant (OR = 2.89, 95 % CI = 1.61-5.19, p = 0.0004, TG + GG vs TT) inheritance models. On the other hand, the rs4132601 G allele increased the risk of ALL (OR = 1.86, 95 % CI = 1.28-2.96; p = ...
Isolasi DNA dari Sampel Daging dan Sirip Delapan Spesies Ikan Laut untuk PCR-RFLP
Penelitian ini bertujuan untuk membandingkan konsentrasi, tingkat kemurnian, visualisasi elektroforesis, dan penggunaan DNA hasil isolasi untuk polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) dari delapan spesies ikan laut. Sampel DNA yang diperoleh dari daging dan sirip ikan baronang (Siganus javus), kerapu (Epinephelus sp), ekor kuning (Caesionidae sp), kakap merah (Lutjanus campechanus), kurisi (Nemipterus nematophorus), kue (Caranx melampygus), bawal hitam (Parastromateus niger), dan selar (Selaroides leptolepis) diisolasi menggunakan metode presipitasi amonium asetat. Primer universal sitokrom b digunakan untuk mengamplifikasi mtDNA menggunakan PCR. Amplikon dipotong menggunakan enzim restriksi Hinf I. Hasil menunjukkan bahwa konsentrasi dan kemurnian DNA sampel daging dan sirip tidak berbeda nyata (P,0.05) yaitu berturut-turut 22.01±20.29 dan 1.44±0.27 untuk konsentrasi dan kemurnian DNA sampel daging, serta 52.86±41.37 dan 1.54±0.23 untuk konsentrasi dan ...
Background Assess the relation between the presence of PVUII and XBAI polymorphisms in the estrogen receptor alpha gene and mammographic density in postmenopausal women.. Methods For the present analysis, 189 postmenopausal women who had never used hormonal therapy and who did not have clinical or mammographic features were selected. Based on the ACR-BIRADSâ 2003 classification, the mammographic density was determined by three independent readers (two subjective ratings and one computerized - Adobe Photoshop â 7.0 software). Blood samples were available to extract DNA according to KIT GFX â protocol. PCR-RFLP (Polymerase Chain Reaction - Restriction Fragment Length Polymorphism) was then used to identify the polymorphisms.. Results There was a high degree of agreement among the three readers to determine the mammographic density (Kappa,0.75). Sixty women (32%) had dense breasts and 129 (68%) had non-dense breasts. The PVUII polymorphism was found in 132 (69.8%) of 189 women, while the XBAI ...
OBJECTIVE: To determine whether transforming growth factor beta1 (TGFbeta1) gene DNA polymorphism is associated with pathogenesis in the fibrosis of patients with systemic sclerosis (SSc). METHODS: Eighty-seven Japanese patients with SSc including 30 with diffuse type and 57 with limited type together with 110 unrelated controls were investigated. Pulmonary fibrosis was determined in 34 SSc patients using high-resolution chest computed tomography. TGFbeta1 genetic polymorphisms were analyzed in 2 loci; T869C (Leu10Pro) in codon 10 at exon 1, and C-509T in the promoter region using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). RESULTS: Neither the genotype of T/C polymorphism in T869C nor C/T polymorphism in C-509T revealed any difference in distribution between SSc and controls. In the group of SSc patients with pulmonary fibrosis, a weak but significantly high frequency (p = 0.05) of TC+CC (the presence of C allele) in T869C, and CT+TT (the presence of T allele) ...
Gly1057Asp polymorphism of insulin receptor substrate-2 is associated with coronary artery disease in the Taiwanese population ...
Gly1057Asp polymorphism in insulin receptor substrate (IRS)-2 is related to insulin resistance and diabetes mellitus (DM), which both contribute to the pathogenesis of coronary artery disease (CAD). Hence, we hypothesize that Gly1057Asp polymorphism in IRS-2 is associated with CAD. Patients receiving elective coronary angiography were enrolled. Significant stenosis is defined as a luminal diameter stenosis greater than 50%. Patients without significant stenosis were defined as group A, and those with significant stenosis in at least one major coronary artery were defined as group B. Genotypes were determined by polymerase chain reaction/restriction fragment length polymorphism. Chi-square test and multivariate logistic regression were used to evaluate the relationship between Gly1057Asp polymorphism in IRS-2 and CAD. The homeostasis model assessment of insulin resistance (HOMA-IR) index was calculated as a representative of insulin resistance. Multiple linear regression was used to analyze the
A Promoter Polymorphism of Pri-miR-34b/c Is Associated With an Increased Risk of Breast Cancer | Current Science
P53 can bind to the promoter of miR-34a/b/c, inducing their expression at the transcriptional level. Previous reports have shown that TP-53 and miR-34b/c may play crucial roles in carcinogenesis. We conducted a case-control study to investigate the association between miR-34b/c rs4938723 and TP-53 Arg72Pro polymorphisms and the risk of breast cancer (BC) in Chinese women. We genotyped the two polymorphisms in 228 BC patients and 307 healthy controls using polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing assay. We found that the miR-34b/c rs4938723 CT genotype and C allele were associated with significantly increased risks of BC compared with the TT genotype and T allele (CT vs. TT: OR = 1.81, 95 % CI, 1.24 - 2.65, P = 0.002; C vs. T: OR = 1.36, 95 % CI, 1.06 - 1.74, P = 0.016, respectively). Moreover, a significant association between the cases and controls was also observed in a dominant model (OR = 1.75; 95 % CI, 1.22 - 2.51, P = 0.002). Stratified analysis ...
Interleukin-23 Receptor Gene Variants in Acute Lymphoblastic Leukemia and Their Relation to Prognostic Factors
Background: Interleukin (IL)-23 has an important role in tumor immune regulation. Objective: To investigate the possible association of interleukin-23 receptor (IL23R) gene variants rs1884444, rs10889677 and rs11209026 with development of acute lymphoblastic leukemia (ALL). Methods: The IL23R variants were studied in 164 ALL patients and compared to 175 healthy controls by polymerase chain reaction-restriction fragment length polymorphism. The relationship between these variants and clinical and laboratory features of the patients and response to therapy were evaluated. Results: No significant differences in genotype and allele frequencies existed between patients and controls. The rs1884444TG genotype was significantly lower in patients who relapsed (24.2%) compared to those without relapse (55.9%, p=0.006). Fewer patients who relapsed had evidence of the G allele (P=0.034). The TG genotype was associated with a longer complete remission at1804±116 days compared to other genotypes (|1217 days, p=0.028
Polimorfismo genético de la apolipoproteína E en un grupo de escolares del centro-oriente colombiano: comparación con las...
CALLAS, Ney et al. Genetic polymorphism of the E apolipoprotein in school age children: comparison with levels of plasma lipids and apolipoproteins. Biomédica [online]. 2007, vol.27, n.4, pp.526-536. ISSN 0120-4157.. Introduction. Research in laboratories around the world has documented the contribution of the E apolipoprotein alleles to structural variations of lipids and apolipoproteins. Objective. The gene frequencies of the E apolipoprotein alleles were compared with the lipid and apolipoprotein levels in school age children. Materials and methods. Six hundred and ninety one 5 to 15 years old school age children from the Colombian departments of Cundinamarca, Boyacá, Meta, Santander and Norte de Santander, were evaluated.The genotypes of the E apolipoprotein were identified by polymerase chain reaction-restriction fragment length polymorphism. Plasma levels for the following 5 lipids and lipoproteins were assayed: total cholesterol, HDL (high density lipoprotein) cholesterol, LDL (low ...
In a group of 50 randomly selected case-matched patients from 1999, the positive blood cultures were concomitant with fever in 98%, intravenous phlebitis in 44%, and recurrent bacteremia in 20%. Fever disappeared approximately 6 hours after intravenous catheter removal. Polymerase chain reaction-restriction fragment length polymorphism revealed strain homogeneity in patient, water, and alcohol isolates. Contaminated tap water had been used to dilute alcohol for skin antisepsis and for decontamination of the caps of heparin vials. Only sporadic cases directly attributable to breach of protocol were reported after single-use alcohol swabs were substituted ...
IJMS | Free Full-Text | The Influence of Ecological and Conventional Plant Production Systems on Soil Microbial Quality under ...
The knowledge about microorganisms-activity and diversity under hop production is still limited. We assumed that, different systems of hop production (within the same soil and climatic conditions) significantly influence on the composition of soil microbial populations and its functional activity (metabolic potential). Therefore, we compared a set of soil microbial properties in the field experiment of two hop production systems (a) ecological based on the use of probiotic preparations and organic fertilization (b) conventional-with the use of chemical pesticides and mineral fertilizers. Soil analyses included following microbial properties: The total number microorganisms, a bunch of soil enzyme activities, the catabolic potential was also assessed following Biolog EcoPlates®. Moreover, the abundance of ammonia-oxidizing archaea (AOA) was characterized by terminal restriction fragment length polymorphism analysis (T-RFLP) of PCR ammonia monooxygenase α-subunit (amoA) gene products. Conventional and
Frontiers | Whole Genome-Based Amplified Fragment Length Polymorphism Analysis Reveals Genetic Diversity in Candida africana |...
This study aimed at investigating the genetic diversity of a panel of Candida africana strains recovered from vaginal samples in different countries. All fungal strains were heterozygous at the mating type-like locus and belonged to the genotype A of Candida albicans. 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 aminosugar in this yeast.Multilocus sequencing of seven housekeeping genes revealed a substantial genetic homogeneity among the strains, except for the CaMPIb and VPS13 loci which contributed significantly to the classification of our set of C. africana strains into 6 existing diploid sequence types. Amplified fragment length polymorphism (AFLP) fingerprint analysis yielded greater genotypic heterogeneity among the C. africana strains. Overall the data reported here show that in C. africana genetic diversity occurs and the existence of this intriguing
Dataset: SPOT Microbial Observatory Myovirus g23 5 TRFLP relative peak abundance data from 2014 (Bacterial, Archaeal, and...
This dataset contains the 5 TRFLP fragment data.. T4-like myovirus communities were analyzed by terminal restriction fragment length polymorphism (TRFLP) of g23, which encodes the major capsid protein (Chow and Fuhrman, 2012). Viral fingerprints were obtained from both terminal fragments (5 and 3). g23-TRFLP products were run in duplicate on non-adjacent lanes on an ABI377 by slab gel electrophoresis with internal size standards (Bioventures, Murfreesboro, TN, USA) every 25 bp (50-900 bp) or 50 bp (900-1400 bp). Peaks were identified in DAx (van Mierlo, Inc, Eindhoven, The Netherlands). Fragments (50-500 bp) were rounded to the nearest 0.1 bp and dynamically binned (Ruan, et al., 2006b; Chow and Fuhrman, 2012). The resulting bins were manually curated to merge bins ,0.1 bp wide with the nearest neighbor. Terminal fragments from in silico analysis of publicly available T4-like viral genomes were used to assign identities to environmental g23-TRFLP OTUs. Unique fragment lengths were considered ...
RFLP analysis RFLP= Restriction fragment length polymorphism - ppt video online download
RFLP Lets generate a restriction map for a region of human X-chromosome 5kb 3kb The restriction map in the same region of the X chromosome of a second individual may appear as 8kb Normal GAATTC Mutant GAGTTC
Restriction fragment length polymorphism
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 ... a DNA sample is digested into fragments by one or more restriction enzymes, and the resulting restriction fragments are then ...
Terminal restriction fragment length polymorphism
... (TRFLP or sometimes T-RFLP) is a molecular biology technique for profiling of ... "Formation of Pseudo-Terminal Restriction Fragments, a PCR-Related Bias Affecting Terminal Restriction Fragment Length ... a tool for optimal resolution of terminal restriction fragment length polymorphism analysis based on user defined primer-enzyme ... THE FIRST DECADE OF TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISM (T-RFLP) IN MICROBIAL ECOLOGY (Articles with J9U ...
Restriction fragment mass polymorphism
Restriction Fragment Length Polymorphism RFMP platform technology Hong, Sun Pyo; Ji, Seung Il; Rhee, Hwanseok; Shin, Soo Kyeong ... Restriction Fragment Mass Polymorphism (RFMP) is a technology which digests DNA into oligonucleotide fragments, and detects ... RFMP was developed as a successor to the similar restriction fragment length polymorphism (RFLP) with the intent to allow for ... Restriction fragment mass polymorphism (RFMP) is an application of matrix-assisted laser desorption ionization time-of-flight ( ...
... restriction fragment length polymorphism; and hybridization analysis. An important group of SNPs are those that corresponds to ... and a possible reduction of required fragment length to less than 100bp. Pharmacogenetics focuses on identifying genetic ... a web tool for analysis of genetic association studies Restriction HomePage - a set of tools for DNA restriction and SNP ... Cao R, Shi Y, Chen S, Ma Y, Chen J, Yang J, Chen G, Shi T (January 2017). "dbSAP: single amino-acid polymorphism database for ...
Intra-individual tissue-specific restriction fragment length polymorphism". FEBS Lett. 221 (1): 129-33. doi:10.1016/0014-5793( ... Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, Suyama A, Sugano S (1997). "Construction and characterization of a full length- ...
Intra-individual tissue-specific restriction fragment length polymorphism". FEBS Lett. 221 (1): 129-33. doi:10.1016/0014-5793( ... Ruiz A, Bhat SP, Bok D (1995). "Characterization and quantification of full-length and truncated Na,K-ATPase alpha 1 and beta 1 ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... 2004). "The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)". Genome ...
Intra-individual tissue-specific restriction fragment length polymorphism". FEBS Lett. 221 (1): 129-33. doi:10.1016/0014-5793( ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... 2004). "The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)". Genome ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ...
The latter example is called restriction fragment length polymorphism (RFLP). Artificial restriction enzymes created by linking ... A restriction enzyme, restriction endonuclease, REase, ENase or restrictase is an enzyme that cleaves DNA into fragments at or ... The sample is first digested with the restriction enzyme to generate DNA fragments, and then the different sized fragments ... a restriction enzyme EcoRI - a restriction enzyme HindIII - a restriction enzyme Homing endonuclease List of homing ...
The markers were mostly PCR-based restriction fragment length polymorphisms. Zygospores are the sexual structures of P. ...
Colony stimulating factor 1 receptor
Xu DQ, Guilhot S, Galibert F (May 1985). "Restriction fragment length polymorphism of the human c-fms gene". Proc. Natl. Acad. ... It is 60.002 kilobases in length. The encoded protein has 972 amino acids and a predicted molecular weight of 107.984 ...
David C. Page
The work relied on locating restriction fragment length polymorphisms (RFLP). The first RFLP that Page found was from a site of ...
Terminal restriction fragment length polymorphism (T-RFLP) is a method that uses fluorescently-labeled DNA fragments to produce ... Marsh, T.L. (2005). "Culture-independent microbial community analysis with terminal restriction fragment length polymorphism". ... terminal restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis, for determination of ... "An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community ...
Amplified fragment length polymorphism
... restriction fragment length polymorphism (RFLP), and microsatellites. AFLP not only has higher reproducibility, resolution, and ... "Amplified fragment length polymorphism". However, the resulting data are not scored as length polymorphisms, but instead as ... followed by ligation of adaptors to the sticky ends of the restriction fragments. A subset of the restriction fragments is then ... DNA with one or more restriction enzymes and ligation of restriction half-site specific adaptors to all restriction fragments. ...
Peter M. Schneider
"Polymorphism of the human complement C4 and steroid 21-hydroxylase genes. Restriction fragment length polymorphisms revealing ... Schneider, Peter M; Würzner, Reinhard (1999). "Complement genetics: biological implications of polymorphisms and deficiencies ... such as the FP5 project High Throughput Analysis of Single Nucleotide Polymorphisms for the Identification of Persons - ...
Restriction fragment length polymorphism analysis demonstrated this classification scheme needed revision. As of 2018, this ... "Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA". Fungal Genet Biol ...
Palsdottir A, Cross SJ, Edwards JH, Carroll MC (1984). "Correlation between a DNA restriction fragment length polymorphism and ... Hessing M, van 't Veer C, Hackeng TM, Bouma BN, Iwanaga S (Oct 1990). "Importance of the alpha 3-fragment of complement C4 for ... DNA sequences, polymorphism, and linkage to the 21-hydroxylase gene". Journal of Immunology. 146 (3): 1057-66. PMID 1988494. ... Jenhani F, Bardi R, Gorgi Y, Ayed K, Jeddi M (Apr 1992). "C4 polymorphism in multiplex families with insulin dependent diabetes ...
Molecular-weight size marker
RFLP Restriction fragment length polymorphism is a technique used to detect variations in homologous DNA. Specific restriction ... AFLP Amplified fragment length polymorphism is a PCR-based DNA fingerprinting technique. DNA is first digested with ... The restriction fragments are then ligated together. A molecular marker is then generated when specific fragments are selected ... The DNA marker allows for the size of the restriction fragments to be estimated. Minisatellites Similar to RFLP, this technique ...
... chromosomal localization and associated restriction fragment length polymorphisms". Proc Natl Acad Sci U S A. 83 (15): 5592-6. ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...
"Genetic relationship of wood and plains bison based on restriction fragment length polymorphisms". Canadian Journal of Zoology ...
Santillano, D.; Boetius, A.; Ramette, A. (2010). "Improved dsrA-based Terminal Restriction Fragment Length Polymorphism ...
"Lactobacillus hilgardii and Lactobacillus brevis DNA analysis by restriction fragment length polymorphism (RFLP)". Food ...
HLA-B associated transcript 3
Cross SJ, Tonks S, Trowsdale J, Campbell RD (1992). "Novel detection of restriction fragment length polymorphisms in the human ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... 2004). "The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)". Genome ...
Forensic DNA analysis
The first true method of DNA profiling was restriction fragment length polymorphism analysis. The first use of RFLP analysis in ... By 1995, scientists attempted to return to a VNTR based analysis combined with PCR technology called amplified fragment length ... Smaller fragments would travel farther through the gel than larger fragments separating them out. These differences were used ... The process of RFLP analysis was extremely time consuming and due to the length of the repeats used, between 9 and 100 base ...
Ronald W. Davis
... and Ray White developed the method for constructing a genetic linkage map using restriction fragment length polymorphisms that ... "Construction of a genetic linkage map in man using restriction fragment length polymorphisms". American Journal of Human ... With Janet E. Mertz, Davis was the first to demonstrate the use of restriction endonucleases for joining DNA fragments. Davis ... "Cleavage of DNA by RI restriction endonuclease generates cohesive ends". Proceedings of the National Academy of Sciences. 69 ( ...
"Genetic relationship of wood and plains bison based on restriction fragment length polymorphisms" (PDF). Can J Zool. 69 (1): 43 ... Head-rump lengths at maximum up to 3.5 m (11 ft 6 in) for males and 2.85 m (9 ft 4 in) for females long and the tail adding 30 ... The length of a predation episode varies, ranging from a few minutes to over nine hours. Bison display five apparent defense ...
Vogelstein B, Fearon ER, Hamilton SR, Feinberg AP (1985). "Use of restriction fragment length polymorphisms to determine the ...
as identified by 16S rDNA restriction fragment length polymorphism analysis in a trout farm". Journal of Applied Microbiology. ...
Suzuki H, Yamashiro K (2002). "L-myc restriction fragment length polymorphism and histological pattern of invasion in lung ... "Ethnic differences in frequencies of gene polymorphisms in the MYCL1 region and modulation of lung cancer patients' survival" ( ...
DNA can be analyzed through restriction fragment length polymorphism (RFLP) and Polymerase chain reactions (PCR). The RFLP ... There are multiple methods for testing and analyzing genetic information including restriction fragment length polymorphism ( ... These fragments are sorted through gel electrophoresis. The gel demonstrates the length of the fragments allowing specialists ... Restriction enzymes digest portions of the DNA, leaving short fragments. ...
Strains were characterized by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. ... and short tandemly repeating sequences of varying number and length. The ITRs of poxviridae vary in length across strains and ... The genome of variola major virus is about 186,000 base pairs in length. It is made from linear double stranded DNA and ... and purchases of smallpox genome fragments are monitored and regulated, a group with malicious intentions could compile, from ...
Multiplex ligation-dependent probe amplification
... a DNA treatment with restriction enzymes that cut on both sides of the region of interest is necessary. The fragments obtained ... Each complete probe pair must have a unique length, so that its resulting amplicons can be uniquely identified during ... MLPA has a variety of applications including detection of mutations and single nucleotide polymorphisms, analysis of DNA ... In a standard multiplex PCR reaction, each fragment needs a unique amplifying primer pair. These primers being present in a ...
... or assumed noncoding DNA sequences such as microsatellites or those generating restriction fragment length polymorphisms (RFLPs ... This result provided evidence for the key idea that the gene has a linear structure equivalent to a length of DNA with many ...
... menggunakan teknik terminal restriction fragment length polymorphism (T-RFLP) dan amplified ribosomul DNA restriction analysis ... Study of natural hybridisation in some tropical plants using amplified fragment length polymorphism analysis. MSc thesis, ... of its total cross-sectional surface length. Upper pitchers are very rarely produced and are considerably smaller than those ...
The technique they used was restriction fragment length polymorphism (RFLP), which was more affordable at the time compared to ... Brown WM (June 1980). "Polymorphism in mitochondrial DNA of humans as revealed by restriction endonuclease analysis". Proc. ... Using this he can estimate (24/(14*2, the "2" is for the length of the branch to human (14my) and the branch to orangutan (14 ... Mutation rates are given, however, as rate per nucleotide(nt)-site, so if the sequence were say 100 nt in length that rate ...
Current methods of genotyping include restriction fragment length polymorphism identification (RFLPI) of genomic DNA, random ... amplified fragment length polymorphism detection (AFLPD), polymerase chain reaction (PCR), DNA sequencing, allele specific ... For this purpose, single nucleotide polymorphisms (SNPs) are used as markers and RNA sequencing is used to look at gene ... like single-nucleotide polymorphism (SNPs)), which represent a tiny fraction of the human genome. When genotyping transgenic ...
Restriction Fragment Length Polymorphism (RFLP) is a technique for analyzing the variable lengths of DNA fragments that result ... About 90% of fragment lengths fall within a two-fold range. Needle shearing creates shearing forces by passing DNA libraries ... It is an enzyme-based treatment used in biotechnology to cut DNA into smaller strands in order to study fragment length ... The presence or absence of certain recognition sites in a DNA sample generates variable lengths of DNA fragments, which are ...
... restriction fragment length polymorphism patterns, and discontinuous 23S rRNA in Lyme disease spirochetes: phylogenetic ...
... marginata based on ribosomal DNA sequences and restriction fragment length polymorphism analyses. Because of differences in ...
... an activity that is especially promoted under conditions of caloric restriction. Caloric restriction has been closely linked to ... Partially overlapping fragments are then used for synthesis of homologous regions through a moving D-loop that can continue ... In other classes and phyla, the sequence of SOS boxes varies considerably, with different length and composition, but it is ... Mechanism of allele methylation polymorphism". Sci Rep. 6: 33222. doi:10.1038/srep33222. PMC 5024116. PMID 27629060. Farris MH ...
... menggunakan teknik terminal restriction fragment length polymorphism (T-RFLP) dan amplified ribosomul DNA restriction analysis ...
Through restriction fragment length polymorphism analysis, the two strains have been shown to differ only slightly. In all ... Connie J. Wolfe and Margo G. Haygood (August 1991). "Restriction Fragment Length Polymorphism Analysis Reveals High Levels of ... The javelin spookfish (Bathylychnops exilis) is by far the largest species at 50 centimetres (20 in) standard length; most ... Dolichopteryx has several along the length of its belly, and Opisthoproctus has a single organ in the form of a rectal pouch. ...
"Genetic Relationship of Wood and Plains Bison Based on Restriction Fragment Length Polymorphisms" (PDF). Canadian Journal of ... Despite a limited number of samples, large males have been recorded to reach 3.35 m (11.0 ft) in body length with 95 cm (3.12 ...
... enzymes cut DNA at a specific site and the DNA fragments that are left are called restriction fragment length polymorphisms, or ... Prenatal ultrasound may reveal several common characteristics including: growth restriction, ventriculomegaly, cleft lip or ...
When the exact species need be determined (e.g. in epidemiological studies), restriction fragment length polymorphisms can be ... D. latum tapeworms are the longest and typically reach a length of 4-15m, but may grow up to 25m in length within the human ... Adult tapeworms may grow to over 10m in length and may constitute of over 3,000 proglottids which contain sets of male and ...
Agriculture in Thailand
A2 was unknown here until a restriction fragment length polymorphism (TH-1) was found in a 1994 sample by Gotoh et al 2005. ... They lifted the ban on glyphosate with restrictions on usage: glyphosate will be used only on six major crops: corn, cassava, ... farms in the north and northeast and is partly to blame for an oversupply of rubber as it was implemented with few restrictions ...
Davis proposed a method for constructing a genetic linkage map using restriction fragment length polymorphisms that was used in ... "Construction of a genetic linkage map in man using restriction fragment length polymorphisms". American Journal of Human ...
A recent molecular study using restriction fragment length polymorphism analysis suggests that the three subspecies are ... The adults are relatively large flies, with lengths of 0.5-1.5 centimetres (1⁄4-5⁄8 in), and have a recognizable shape, or ... Feasibility studies indicated that the fly population was confined to very fragmented habitats and a population genetics study ...
For a full-length treatment of the language, see "Programming ALGOL 68 Made Easy" by Dr. Sian Mountbatten, or "Learning ALGOL ... This restriction can be circumvented by using different comment delimiters (e.g. use hash only for temporary code deletions). ... so this next fragment is legal: INT a real int = 3 ; The programmer who writes executable code does not always have an option ... for implementation of limited parametrical polymorphism (most operations on data structures like lists, trees or other data ...
... fucosyltransferase gene and two H locus-related DNA restriction fragments. Isolation of a candidate for the human Secretor ... 1998). "Extensive polymorphism of the FUT2 gene in an African (Xhosa) population of South Africa". Hum. Genet. 103 (2): 204-10 ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... 2002). "The cytoplasmic tail of alpha 1,3-galactosyltransferase inhibits Golgi localization of the full-length enzyme". J. Biol ...
Polymerase chain reaction
... in length, although some techniques allow for amplification of fragments up to 40 kbp. The amount of amplified product is ... Mullis's 1985 paper with R. K. Saiki and H. A. Erlich, "Enzymatic Amplification of β-globin Genomic Sequences and Restriction ... improved specificity and single nucleotide polymorphism detection using blocked cleavable primers". BMC Biotechnology. 11: 80. ... The precise time required for elongation depends both on the DNA polymerase used and on the length of the DNA target region to ...
... research groups have reported identification of male-associated markers using RAPD and amplified fragment length polymorphism. ... Recent phylogenetic studies based on cpDNA restriction site analysis and gene sequencing strongly suggest that the Cannabaceae ... A polymerase chain reaction-based method for the detection of female-associated DNA polymorphisms by genotyping has been ... Shao H, Song SJ, Clarke RC (2003). "Female-Associated DNA Polymorphisms of Hemp (Cannabis sativaL.)". Journal of Industrial ...
DNA paternity testing
... and restriction fragment length polymorphism (RFLP). Paternity testing can now also be performed while the woman is still ... In the United Kingdom, there were no restrictions on paternity tests until the Human Tissue Act 2004 came into force in ... cite book}}: Check ,isbn= value: length (help) Butler, John (2005). Forensic DNA Typing Biology, Technology, and Genetics of ... Genetic parental testing technology advanced further with the isolation of the first restriction enzyme in 1970. Highly ...
Facioscapulohumeral muscular dystrophy
Restriction fragment length polymorphism (RFLP) analysis was the first genetic test developed and is still used as of 2020, ... It involves dicing the DNA with restriction enzymes and sorting the resulting restriction fragments by size using southern blot ... The EcoRI restriction fragment is composed of three parts: 1) 5.7 kb proximal part, 2) the central, variable size D4Z4 repeat ... For example, NGS is not useful for assessing D4Z4 length, because it breaks DNA into fragments before reading them, and it is ...
Chung, WK; Chua, SC; Lee, GH; Leibel, RL (1997). "Polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP ... polymorphisms with body mass index and waist circumference". Int J Obes Relat Metab Disord. 26 (5): 640-6. doi:10.1038/sj.ijo. ... polymorphisms with variables related to human adiposity". Genetics. 159 (3): 1163-78. doi:10.1093/genetics/159.3.1163. PMC ... "A radioisotopic method for the measurement of free fatty acid turnover and adrenoceptor response in small fragments of human ...
... variants in the Cx29 gene of nonsyndromic hearing loss patients using buccal cells and restriction fragment length polymorphism ...
... interspecific backcross panel along with genomic southern blot analysis to identify restriction fragment length polymorphisms ( ... Restriction landmark genomic scanning (RLGS) along a region of recurrent loss of heterozygosity (LOH) at chromosome 6q23-q24 to ... Also TCF21 rs12190287 polymorphism can regulate TCF21 expression and may serve as a potential marker for genetic susceptibility ... Gao X, Yang J, Wang M, Zhang J (June 2016). "TCF21 genetic polymorphisms and breast cancer risk in Chinese women". Oncotarget. ...
Restriction Fragment Length Polymorphisms (RFLP) are also useful in the differentiation of fusaria, as differences in base-pair ... sequence cause the sample DNA sequences to be fragmented at different sites by restriction enzymes, resulting in DNA fragments ... Today, species of Fusarium can be identified through the cloning and sequencing of RAPD fragments to produce primers for use in ... of different lengths. This identification method is particularly useful for screening large numbers of samples. As conidial ...
Browsing by Subject "Polymorphism, Restriction Fragment Length"
The Gunnera symbiosis: DNA restriction fragment length polymorphism and protein comparisons of Nostoc symbionts
Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communites - LTER
DNA profiling of banana and plantain cultivars using random amplified polymorphic DNA (RAPD) and restriction fragment length...
... comparisons of amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers. ... Organellar DNA restriction fragment length polymorphism (RFLP) and nuclear random amplified polymorphic DNA (RAPD) analyses of ... Organellar DNA restriction fragment length polymorphism (RFLP) and nuclear random amplified polymorphic DNA (RAPD) analyses of ... Identification of restriction fragment length polymorphism and random amplified polymorphic DNA markers linked to downy mildew ...
Genotyping of flavin-containing mono-oxygenase 3 (FMO3) gene by polymerase chain reaction-restriction fragment length...
Restriction maps and restriction fragment length polymorphisms of the human 21-hydroxylase genes<...
Restriction maps and restriction fragment length polymorphisms of the human 21-hydroxylase genes. Biochemical and Biophysical ... Restriction maps and restriction fragment length polymorphisms of the human 21-hydroxylase genes. In: Biochemical and ... Restriction maps and restriction fragment length polymorphisms of the human 21-hydroxylase genes. / Donohoue, Patricia A.; ... title = "Restriction maps and restriction fragment length polymorphisms of the human 21-hydroxylase genes", ...
Genotyping Guide | Description of Genotyping Methods | Laboratory Procedures | TB | CDC
IS6110-based Restriction Fragment Length Polymorphism (RFLP). IS6110-based RFLP genotyping detects variations generated by the ... A restriction enzyme is added that cuts the DNA at specific sequences into hundreds of different fragments. The fragments are ... A probe is used to detect fragments containing IS6110, and the image is captured on film. Each copy of IS6110 produces one band ...
Variability for restriction fragment-length polymorphisms (RFLPs) and relationships among elite commercial inbred and virtual...
Variability for restriction fragment-length polymorphisms (RFLPs) and relationships among elite commercial inbred and virtual ... Variability for restriction fragment-length polymorphisms (RFLPs) and relationships among elite commercial inbred and virtual ... Variability for restriction fragment-length polymorphisms (RFLPs) and relationships among elite commercial inbred and virtual ... title = "Variability for restriction fragment-length polymorphisms (RFLPs) and relationships among elite commercial inbred and ...
HindIII-based restriction fragment length polymorphism in hemophilic and nonhemophilic patients - Journal of Natural Science,...
Keywords: Gene, hemophilia, polymerase chain reaction, restriction enzyme, restriction fragment length polymorphism. ... restriction fragment length polymorphism (RFLP). This marker of polymorphism could only be detected by amplifying the ... HindIII-based restriction fragment length polymorphism in hemophilic and nonhemophilic patients. Posted on : October 23, 2010 ... The polymorphic region of HindIII is 608 bp in length and after the restriction digestion, different sizes of fragments, i.e., ...
Modifications to improve the effectiveness of restriction fragment length polymorphism typing. - Fingerprint - HSC
Chapter 9 Flashcards
IMSEAR at SEARO: Rapid identification of Campylobacter jejuni strains by polymerase chain reaction & their restriction fragment...
Restriction fragment length polymorphism analysis (RFLP) of fla A amplified product by using Bgl II enzyme classified 15 ... their restriction fragment length polymorphism analysis. Indian Journal of Medical Research. 1997 Jan; 105(): 9-14. ... Rapid identification of Campylobacter jejuni strains by polymerase chain reaction & their restriction fragment length ...
TGFbeta1 polymorphisms and late clinical radiosensitivity in patients treated for gynecologic tumors
Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), single base extension and genotyping assays were ... TGFbeta1 polymorphisms and late clinical radiosensitivity in patients treated for gynecologic tumors Int J Radiat Oncol Biol ... There was perfect linkage disequilibrium (LD) between the -1.552delAGG and the -509C,T polymorphisms, and tight LD between the ... Purpose: To investigate the association between six transforming growth factor beta1 gene (TGFbeta1) polymorphisms (-1.552 ...
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The history of Biotechnology (Valentina Modolo) timeline | Timetoast
Visible Proofs: Forensic Views of the Body: Galleries: Technologies: Key accomplishments: DNA
Restriction-Fragment-Length Polymorphism (RFLP) proposed. American geneticist David Botstein, biochemist Ronald W. Davis, ... and biologist Ray White publish a paper on their theory that restriction fragment-length-polymorphisms (RFLPs) can be used to ... Role of Restriction Enzymes. Swiss molecular biologist Werner Arber shows how specialized enzymes can cut DNA into short ... These enzymes are subsequently dubbed restriction enzymes. In 1970, American molecular biologist Hamilton Smith and ...
Molecular genetic testing and the future of clinical genomics | Nature Reviews Genetics
Restriction fragment length polymorphisms. (RFLP). Variations between individuals in the lengths of DNA regions that are cut by ... Complement factor H polymorphism, complement activators, and risk of age-related macular degeneration. JAMA 296, 301-309 (2006 ... Single-nucleotide polymorphisms. (SNPs). Differences in the nucleotide composition at single positions in the DNA sequence. ... A method used to determine the nucleotides present in a fragment of DNA. It is based on the chain terminator method developed ...
Brage IMR: Rapid polymerase chain reaction-restriction fragment length polymorphism method for discrimination of the two...
Rapid polymerase chain reaction-restriction fragment length polymorphism method for discrimination of the two Atlantic cryptic ... provides an efficient diagnostic method based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) ... Two DNA fragments from the mtDNA, including control region and partial cytochrome oxidase subunit I genes of about 1100 bp and ... of the amplicon including the control region with HaeII and the amplicon including the COI gene with Sau3AI restriction enzymes ...
Restriction fragment-length polymorphism analysis of 16S ribosomal RNA genes amplified by polymerase chain reaction for rapid...
Restriction fragment-length polymorphism analysis of 16S ribosomal RNA genes amplified by polymerase chain reaction for rapid ... Restriction fragment-length polymorphism analysis of 16S ribosomal RNA genes amplified by polymerase chain reaction for rapid ... Restriction fragment-length polymorphism analysis of 16S ribosomal RNA genes amplified by polymerase chain reaction for rapid ... T1 - Restriction fragment-length polymorphism analysis of 16S ribosomal RNA genes amplified by polymerase chain reaction for ...
A precaution in the detection of heterozygotes by sequencing: Comparison of automated DNA sequencing and PCR-restriction...
T2 - Comparison of automated DNA sequencing and PCR-restriction fragment length polymorphism methods ... Comparison of automated DNA sequencing and PCR-restriction fragment length polymorphism methods. / Simsek, M.; Tanira, M. O.M. ... Comparison of automated DNA sequencing and PCR-restriction fragment length polymorphism methods. Clinical Chemistry, 47(1), 134 ... Comparison of automated DNA sequencing and PCR-restriction fragment length polymorphism methods, Clinical Chemistry, vol. 47, ...
Intestinal Flukes Workup: Laboratory Studies, Other Tests
Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)  and simple sequence repeat anchored PCR [52 ... These methodologies are based on differences in restriction fragment length polymorphisms and simple sequence repeats among the ... Dzikowski R, Levy MG, Poore MF, Flowers JR, Paperna I. Use of rDNA polymorphism for identification of Heterophyidae infecting ... the genus Heterophyidae were reported to be distinguished with PCR assays developed based on variations in rDNA polymorphisms ...
SciELO - Brazil - ASSOCIATION OF TNF- α-308G>A POLYMORPHISM WITH SUSCEPTIBILITY TO CELIAC DISEASE: A SYSTEMATIC REVIEW AND...
SOC: source of control; HB: Hospital Based; RFLP: Restriction Fragment Length Polymorphism; PCR-SSP: Single Specific Primer- ... Polymorphism. Genetic model. Type of model. Heterogeneity Odds Ratio Publication Bias I2 (%). P H OR. 95% CI. Z-test. P OR P ... Celiac disease and TNF promoter polymorphisms. Hum Immunol. 2000;61:513-7.. There are several polymorphisms in the upstream ... Funnel plot for publication bias in the meta-analysis of TNF-α -308G,A polymorphism and CD risk. A. Allele model (A vs G). B. ...
Let A Pro Analyze Your Gels: Media Cybernetics upgrades Gel-Pro Analyzer | The Scientist Magazine®
This software quantitatively analyzes PCR, Northern, Southern, and Western Blots, as well as Restriction Fragment Length ... Polymorphism. The original Gel-Pro Analyzer was designed to automate gel reading functions to improve throughput, minimize ... as well as Restriction Fragment Length Polymorphism. The original Gel-Pro Analyzer was designed to automate gel reading ... as well as Restriction Fragment Length Polymorphism. The original Gel-Pro Analyzer was designed to automate gel reading ...
Pure B-Cell Disorders Workup: Laboratory Studies, Imaging Studies, Other Tests
Management of Persons Exposed to Multidrug-Resistant Tuberculosis
Araçatuba Virus: A Vaccinialike Virus Associated with Infection in Humans and Cattle - Volume 9, Number 2-February 2003 -...
Amplification and Restriction Fragment Length Polymorphism (RFLP) of ATI Gene. A PCR-based method for rapid screening and ... Detection and restriction fragment length polymorphism taxonomic analysis of the Araçatuba virus ATI gene. Primers based on the ... Detection and restriction fragment length polymorphism taxonomic analysis of the Araçatuba virus ATI gene. Primers based on the ... We also analyzed the A-type gene (ATI) based on restriction length polymorphism, which is a phylogenetic tool used to ...
WHO EMRO | Molecular typing of Mycobacterium spp. isolates from Yemeni tuberculosis patients | Volume 19, issue 11 | EMHJ...
Figure 2A Polymerase chain reaction-restriction fragment length polymorphism assay using restriction enzymes of confirmed ... Figure 2B Polymerase chain reaction-restriction fragment length polymorphism assay using restriction enzymes of confirmed ... Restriction fragment length polymorphism (RFLP). Following amplification of the rpoB gene the product was subjected to ... following restriction of the PCR product by HindIII restriction enzyme that produced 2 DNA fragments in the amplicons of M. ...
- Polymerase chain reactionrestriction fragment length polymorphism (PCR-RFLP) method was based on general primers, whereas another employed method was the mismatch amplification mutation assay (MAMA) primers. (ajol.info)
- Variability for known alleles at 75 RFLP loci and 194 polymorphic fragments revealed by 69 anonymous cDNA probes and a clone of alliinase were scored to yield genetically characterized and uncharacterized data sets, respectively. (umn.edu)
- This limitation has been overcome by the use of polymorphic DNA marker, i.e., restriction fragment length polymorphism (RFLP). (jnsbm.org)
- This marker of polymorphism could only be detected by amplifying the polymorphic region and digestion the polymerase chain reaction (PCR) product with the restriction enzyme (PCR−RFLP), i.e. (jnsbm.org)
- Therefore, in this study, we have analyzed the factor VIII gene in the 17 different families using restriction enzyme Hin dIII-based RFLP molecular marker technique. (jnsbm.org)
- Restriction fragment length polymorphism analysis (RFLP) of fla A amplified product by using Bgl II enzyme classified 15 strains into 5 types. (who.int)
- Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), single base extension and genotyping assays were performed to examine the polymorphic sites in TGFbeta1. (nih.gov)
- This DNA fingerprint was called a Restriction Fragment Length Polymorphism (RFLP). (timetoast.com)
- The present investigation provides an efficient diagnostic method based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis to discriminate between two cryptic species of scabbardfish, Aphanopus carbo and A. intermedius, with commercial relevance in several European fish markets. (unit.no)
- In this study, restriction fragment-length polymorphism (RFLP) analysis of polymerase chain reaction (PCR)-amplified 16S ribosomal RNA genes (16S rRNA gene PCR-RFLP) was used to generate restriction profiles of reference strains of oral treponemes including Treponema denticola, Treponema socranskii, Treponema vincentii, Treponema pectinovorum and Treponema medium as well as for Treponema phagedenis and Treponema pallidum and five treponeme strains isolated from human periodontal pockets. (elsevier.com)
- Homozygous and heterozygous CD4.A and CD4.B alleles in the Microminipigs herd were characterised by using the RFLP technique with the restriction endonuclease, Bse RI. (biomedcentral.com)
- We analyzed the internal transcribed spacer 2 (ITS2) region of Biomphalaria ribosomal DNA (rDNA) using polymerase chain reaction amplification (PCR) and restriction fragment length polymorphism (RFLP). (biomedcentral.com)
- Cases with similar restriction fragment length polymorphism (IS 6110 -RFLP) patterns of their Mycobacterium tuberculosis complex isolates were grouped in clusters (recent transmission). (biomedcentral.com)
- Additional restriction fragment length polymorphism (RFLP) assays may provide a simple strategy to identify the virus subtype. (medscape.com)
- The turnaround time of RFLP (restriction fragment length polymorphism) analysis has recently been reduced. (ncjrs.gov)
- CYBA polymorphisms were determined by restriction fragment length polymorphism (RFLP) or allelic discrimination. (cun.es)
- Polymerase chain reaction-Restriction fragment length polymorphism (PCR-RFLP) was performed for genotyping Xmn1 γ G globin polymorphism. (medrxiv.org)
- In this study, the polymorphisms of β 2 -AR gene on cattle were detected by methods of Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) and DNA sequencing in two cattle breeds in China, Xinjiang Brown cattle and Chinese Holstein cows. (scialert.net)
- PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism) and DNA sequencing methods were used to scan single nucleotide polymorphisms (SNPs) in the parts of the encoding region of β 2 -AR gene, in order to identify potential genetic markers for lactation performance. (scialert.net)
- Examples of full digital T-RFLP profiles obtained with the restriction enzymes HaeIII and MspI for the samples GRW01 (A) and AGS01 (B). (PDF 102 KB) Additional file 5: Comparison of mirror plots obtained on raw (left) and on denoised (right) pyrosequencing datasets. (mdm2signaling.com)
- length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. (mdm2signaling.com)
- Marsh TL: Terminal restriction fragment length polymorphism BCKDHA (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products. (mdm2signaling.com)
Polymerase chain re6
- IMSEAR at SEARO: Rapid identification of Campylobacter jejuni strains by polymerase chain reaction & their restriction fragment length polymorphism analysis. (who.int)
- Sato, T & Kuramitsu, HK 1999, ' Restriction fragment-length polymorphism analysis of 16S ribosomal RNA genes amplified by polymerase chain reaction for rapid identification of cultivable oral treponemes ', Oral Microbiology and Immunology , vol. 14, no. 2, pp. 117-121. (elsevier.com)
- In the present study, we screened for previously described polymorphisms in the coding region of this gene using polymerase chain reaction (PCR)-restriction fragment length polymorphism or allele specific-PCR analyses. (aspetjournals.org)
- Genotyping was carried out by polymerase chain reaction-restriction fragment length polymorphism technique. (cdc.gov)
- Polymerase chain reaction (PCR) was conducted using groEL PCR-restriction fragment length polymorphism and sequence analysis. (who.int)
- One thousand thirty-eight normal glucose-tolerant and 1031 type 2 diabetic subjects selected from the Chennai Urban Rural Epidemiology Study were genotyped using polymerase chain reaction-restriction fragment length polymorphism assay to investigate the association of rs12255372(G/T) and rs7903146(C/T) polymorphisms of the transcription factor 7-like 2 (TCF7L2) gene with type 2 diabetes mellitus in Asian Indians. (qxmd.com)
- The restriction fragment length polymorphisms (RFLPs) prevalent among the cultivars were studied by hybridization of 19 random genomic clones to blots of HindIII, EcoRI and MspI digests. (eurekamag.com)
- Allelic and genetically uncharacterized RFLPs confidently distinguished among these hybrids, even though heterozygosity for many markers produced a majority of monomorphic fragments. (umn.edu)
- King, JJ, Bradeen, JM & Havey, MJ 1998, ' Variability for restriction fragment-length polymorphisms (RFLPs) and relationships among elite commercial inbred and virtual hybrid onion populations ', Journal of the American Society for Horticultural Science , vol. 123, no. 6, pp. 1034-1037. (umn.edu)
- American geneticist David Botstein, biochemist Ronald W. Davis, population geneticist Mark Skolnick, and biologist Ray White publish a paper on their theory that restriction fragment-length-polymorphisms (RFLPs) can be used to produce a linkage map of the human genome and to map the genes that cause disease in humans. (nih.gov)
- Different fragment lengths of base pairs that result from cutting a DNA molecule with restriction enzymes. (flashcardmachine.com)
- Arber, Nathans, and Smith discovered bacterial restriction enzymes that cut DNA. (timetoast.com)
- These enzymes are subsequently dubbed 'restriction enzymes. (nih.gov)
- In 1970, American molecular biologist Hamilton Smith and colleagues determine that restriction enzymes can cut DNA molecules at precise and predictable locations. (nih.gov)
- Digestion of the amplicon including the control region with HaeII and the amplicon including the COI gene with Sau3AI restriction enzymes allowed an unequivocal discrimination between the two scabbardfish species. (unit.no)
- The mtDNA of each species was analyzed using 17 restriction enzymes and restriction maps were built. (apidologie.org)
- Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment. (bvsalud.org)
- The search for new and unusual restriction enzymes continued apace so that, by 1982, a list of 357 identified restriction enzymes recognizing 90 different dna sequences was published 7. (web.app)
- Restriction enzymes recognize and cut at specific places along the dna molecule called restriction sites. (web.app)
- Restriction enzymes are part of a bacterial immune system, and have been very useful as a tool to cut and paste dna sequences in laboratory applications. (web.app)
- Who ate the cheese use restriction enzymes to cut dna and place on a chart to simulate movement of fragments during eletrophoresis. (web.app)
- Other types of restriction enzymes cleave dna at positions somewhat distant from their. (web.app)
- Restriction enzymes are not only sequence specific but also structure sensitive and may exhibit either enhanced or inhibited cleavage activity. (web.app)
- Enzymes, which are produced naturally by bacteria, cut dna molecules at specific sites denoted by base sequences when a restriction enzyme is used to cut different dna molecules, the size of the fragments generated will be unique to each molecule. (web.app)
- Introduction to restriction enzymes objectives at the end of this activity, students should be able to 1. (web.app)
- Cut smarter with restriction enzymes from neb with over 40 years of offering restriction enzymes to the research community, neb has earned the reputation of being a leader in enzyme technologies. (web.app)
- However, most of naturally occurring restriction enzymes recognize only 48 basepair sequences so that their scission sites statistically appear at every 4 4 256, 4 6 4096, and 4 8 65,536 basepair sequences, respectively. (web.app)
- Inside a prokaryote, the restriction enzymes selectively cut up foreign dna in a process called. (web.app)
- Restriction enzymes are special proteins produced by bacteria to prevent or restrict invasion by foreign dna such as from viruses. (web.app)
- As part of bacterial defense system, restriction enzymes cut digest any foreign dna. (web.app)
- These enzymes are called sitespecific restriction endonucleases, or more simply restriction enzymes, and they naturally function as part of bacterial defenses against viruses and other sources of foreign dna. (web.app)
- Restriction maps were constructed for the two human 21-hydroxylase genes (21-OHA and 21-OHB) by using DNA from subjects homozygous for a deletion of each gene. (elsevier.com)
- Comparing the patterns of these two genes, a KpnI restriction site occurred in the 21-OHA gene in place of a TaqI site in the 21-OHB gene about 1-kb from the 5′ end of the gene, and an extra EcoRI site was located 500 bp 5′ to the common EcoRI site. (elsevier.com)
- Immunohistochemistry and genotyping was performed to test ERCC1, III β-tubulin, COX-2, CD4, CD8 and ERCC1 (C8092A and N118 N) and MDR1 (C3435T and G2677 T) gene polymorphisms, as possible predictive and prognostic markers. (biomedcentral.com)
- Polymorphisms of the IL-1 gene complex in coal miners with silicosis. (cdc.gov)
- The C242T polymorphism of CYBA, the human gene that encodes p22phox, has been found to be functionally associated with vascular NADPH oxidase activity in atherosclerotic patients. (cun.es)
- DNA alignment results showed that three single nucleotide polymorphisms (SNPs), C11A, G53A and C129T were found in 5-coding region of β 2 -AR gene. (scialert.net)
- However, there is little information about polymorphisms of β-AR gene in cattle at present. (scialert.net)
- Heterogeneity of Porphyromonas gingivalis strains on fimbrillin gene locus by restriction fragment length polymorphism analysis. (bvsalud.org)
- Expression in Escherichia coli of cDNA fragments encoding the gene for the host-protective antigen of infectious bursal disease virus. (nchu.edu.tw)
- The rs12255372(G/T) and rs7903146(C/T) polymorphisms of the TCF7L2 gene are associated with type 2 diabetes mellitus in Asian Indians. (qxmd.com)
- In conclusion, the T allele of the rs12255372(G/T) and rs7903146(C/T) polymorphisms of TCF7L2 gene confer susceptibility to type 2 diabetes mellitus in Asian Indians. (qxmd.com)
- If you dont see any interesting for you, use our search form on bottom v. In order to facilitate the topics of restriction enzyme digestion and the generation of compatible ends in the process of gene cloning, an inclass activity was designed. (web.app)
- The other single nucleotide polymorphisms (SNPs) were not found in the Japanese subjects in the present study. (aspetjournals.org)
- In addition, concerning the SNPs of T130N, E154D, N193K, K249R, and H411L, it remains clear that these alleles exist as polymorphisms or represent sequence errors or cloning artifacts. (aspetjournals.org)
- To study whether functional single nucleotide polymorphisms (SNPs) located in the regulatory elements of genes coding for the IL-1alpha, IL-1beta, and IL-1 receptor antagonist (RA) cytokines are associated with silicosis, we examined 318 Caucasian cases confirmed histopathologically with pulmonary silicosis and 163 controls without any apparent inflammation or other pulmonary disease. (cdc.gov)
- Although genetic polymorphisms of CYP2C8 were reported, there is little information on CYP2C8 polymorphisms in the Japanese population. (aspetjournals.org)
- Genetic material was obtained from blood samples, amplified by PCR and analyzed by restriction fragment length polymorphism. (scielo.cl)
- Restriction fragment length polymorphisms were found with EcoRI, HindIII and AccI that resulted from polymorphic endonuclease sites outside the genes. (elsevier.com)
- The polymorphic region of Hin dIII is 608 bp in length and after the restriction digestion, different sizes of fragments, i.e., 427 and 181 bp were, respectively, obtained. (jnsbm.org)
- The PCR products were then purified and characterized by single digestion with restriction endonuclease HpaII, and this allowed discrimination between the respective reference strains. (elsevier.com)
- 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. (bvsalud.org)
- Two DNA fragments from the mtDNA, including control region and partial cytochrome oxidase subunit I genes of about 1100 bp and 700 bp, respectively, were isolated by PCR amplification. (unit.no)
- Through a combination of PCR and examination of restriction fragment length polymorphism, the locations of 14 of the main mitochondrial genes were located on restriction maps. (apidologie.org)
- The amplification of the ITS2 region of Biomphalaria snails resulted in a 490 bp fragment and produced two profiles for each species after digestion with the restriction enzyme Hpa II. (biomedcentral.com)
- The activity of a restriction enzyme in each of the four standard. (web.app)
- Here is an example of a restriction enzyme called ecori that cuts dna at a particular sequence, creating sticky ends. (web.app)
- Restriction enzyme are used to cut desired double stranded dna at specific base sequences called recognition sites to create sticky ends the plasmid is then cut by the same restriction enzyme, creating the same sticky ends as the desired donor dna. (web.app)
- Restriction enzyme lab report essay example graduateway. (web.app)
- Militsopoulou M, Lamari FN, Hjerpe A, Karamanos NK: Adaption of a fragment analysis technique to an automated high-throughput multicapillary electrophoresis device for the precise qualitative and quantitative characterization of microbial communities. (mdm2signaling.com)
- 7. Thies JE: Soil microbial community analysis using terminal restriction fragment length polymorphisms. (mdm2signaling.com)
- Five clinical isolates, four T. denticola and one T. socranskii, were assigned on the basis of their restriction profiles by digestion with HpaII. (elsevier.com)
- Furthermore, hypertensives carrying the CC genotype of this polymorphism exhibit features of NADPH oxidase-mediated oxidative stress and endothelial damage. (cun.es)
- Normal glucose-tolerant subjects with the TT genotype of rs7903146(C/T) polymorphism had significantly higher 2-hour plasma glucose levels (mean +/- SD, 6.0 +/- 1.3 mmol/L) than those with the CC genotype (5.6 +/- 1.0 mmol/L, P = .004). (qxmd.com)
- Spoligotyping, a new method for simultaneous detec- ment length polymorphism typing, spoligotyping overesti- tion and typing of M. tuberculosis complex bacteria, has mated the number of isolates with identical DNA been recently developed (9-11). (cdc.gov)
- micro electropheresis based methods have already reached their limit while sequencing by hybridization has severe restrictions when it comes to de novo (or re-) sequencing of whole genomes. (wjst.de)
- because each molecule is amplified in isolation from other molecules it also precludes template competition, which frequently occurs when large numbers of different DNA fragments are amplified together. (wjst.de)
- The C242T polymorphism was not in linkage disequilibrium with the -930A/G CYBA promoter variation, which also associates with hypertension. (cun.es)
- Delta F508 has linkage disequilibrium with two Single Nucleotide Polymorphisms (SNP), often used to define the haplotypic frameworks of CF mutations. (scielo.cl)
- Patients with TT in the site of ERCC1 N118 N and GT in the site of MDR1 G2677 T polymorphisms had significantly longer PFS ( p = 0.006 and p = 0.027 respectively). (biomedcentral.com)
- Here, we aimed to assess clinical HU response among patients with HbE/β-thalassemia with respect to Xmn1 γ G globin polymorphism and elucidate the association between this polymorphism and HU response efficacy. (medrxiv.org)
- Patients with Xmn1 polymorphism were found to be good responders for HU therapy and showed increased hemoglobin levels. (medrxiv.org)
- This is the first report showing an association between the IL-1RA (+ 2018) polymorphism and silicosis, and suggests that this polymorphism may confer increased risk for the development of the disease. (cdc.gov)
- We also analysed the interaction of C242T polymorphism with the -930A/G CYBA variant. (cun.es)
- A polymorphism may be a risk factor for celiac disease, but the results are inconsistent. (scielo.br)
- We investigated the association of the C242T polymorphism with hypertension and its potential impact on NADPH oxidase activity. (cun.es)
- A polymorphism plays an important role in celiac disease susceptibility. (scielo.br)
- There are no available reports related to the role of Keap1 polymorphism and MEG3 methylation in the pathogenesis of preeclampsia. (researchsquare.com)
- A polymorphism and celiac disease risk in Italy, Spain and PCR-FRLP group studies. (scielo.br)
- It is also notable that the eDOS within the bandgap are nearly identical regardless of the cell length (in z). (mdm2signaling.com)