DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.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.Templates, Genetic: Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.RNA-Directed DNA Polymerase: An enzyme that synthesizes DNA on an RNA template. It is encoded by the pol gene of retroviruses and by certain retrovirus-like elements. EC 188.8.131.52.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.HIV Reverse Transcriptase: A reverse transcriptase encoded by the POL GENE of HIV. It is a heterodimer of 66 kDa and 51 kDa subunits that are derived from a common precursor protein. The heterodimer also includes an RNAse H activity (RIBONUCLEASE H, HUMAN IMMUNODEFICIENCY VIRUS) that plays an essential role the viral replication process.Ribonuclease H: A ribonuclease that specifically cleaves the RNA moiety of RNA:DNA hybrids. It has been isolated from a wide variety of prokaryotic and eukaryotic organisms as well as RETROVIRUSES.Euplotes: A genus of ciliate protozoa having a dorsoventrally flattened body with widely spaced rows of short bristle-like cilia on the dorsal surface.Deoxyguanine Nucleotides: Guanine nucleotides which contain deoxyribose as the sugar moiety.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).DNA-Directed DNA Polymerase: DNA-dependent DNA polymerases found in bacteria, animal and plant cells. During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)DNA Replication: The process by which a DNA molecule is duplicated.Dideoxynucleotides: The phosphate esters of DIDEOXYNUCLEOSIDES.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Telomerase: An essential ribonucleoprotein reverse transcriptase that adds telomeric DNA to the ends of eukaryotic CHROMOSOMES.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.DNA, Single-Stranded: A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.Aphidicolin: An antiviral antibiotic produced by Cephalosporium aphidicola and other fungi. It inhibits the growth of eukaryotic cells and certain animal viruses by selectively inhibiting the cellular replication of DNA polymerase II or the viral-induced DNA polymerases. The drug may be useful for controlling excessive cell proliferation in patients with cancer, psoriasis or other dermatitis with little or no adverse effect upon non-multiplying cells.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.DNA Polymerase I: A DNA-dependent DNA polymerase characterized in prokaryotes and may be present in higher organisms. It has both 3'-5' and 5'-3' exonuclease activity, but cannot use native double-stranded DNA as template-primer. It is not inhibited by sulfhydryl reagents and is active in both DNA synthesis and repair. EC 184.108.40.206.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Nucleotides: The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Kinetics: The rate dynamics in chemical or physical systems.Reverse Transcriptase Inhibitors: Inhibitors of reverse transcriptase (RNA-DIRECTED DNA POLYMERASE), an enzyme that synthesizes DNA on an RNA template.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Exome: That part of the genome that corresponds to the complete complement of EXONS of an organism or cell.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Sensitivity and Specificity: Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.HIV-1: The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Genetic Variation: Genotypic differences observed among individuals in a population.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.Genes, Bacterial: The functional hereditary units of BACTERIA.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.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.RNA, Transfer, Lys: A transfer RNA which is specific for carrying lysine to sites on the ribosomes in preparation for protein synthesis.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Software: Sequential operating programs and data which instruct the functioning of a digital computer.RNA, Messenger: 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.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Bacterial Proteins: Proteins found in any species of bacterium.Nucleic Acid Amplification Techniques: Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.Polymorphism, Restriction Fragment Length: Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Microsatellite Repeats: A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).Oligonucleotide Probes: Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.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, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Polymorphism, Genetic: The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.DNA Fingerprinting: A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Sequence Analysis: A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Taq Polymerase: A heat stable DNA-DIRECTED DNA POLYMERASE from the bacteria Thermus aquaticus. It is widely used for the amplification of genes through the process of POLYMERASE CHAIN REACTION. EC 2.7.7.-.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.DNA Probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Bacteria: One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.Electrophoresis, Agar Gel: Electrophoresis in which agar or agarose gel is used as the diffusion medium.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.DNA, Ribosomal Spacer: The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.DNA Primase: A single-stranded DNA-dependent RNA polymerase that functions to initiate, or prime, DNA synthesis by synthesizing oligoribonucleotide primers. EC 2.7.7.-.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Methacrylates: Acrylic acids or acrylates which are substituted in the C-2 position with a methyl group.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.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.Dental Bonding: An adhesion procedure for orthodontic attachments, such as plastic DENTAL CROWNS. This process usually includes the application of an adhesive material (DENTAL CEMENTS) and letting it harden in-place by light or chemical curing.Genomic Library: A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).Pedigree: The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Resin Cements: Dental cements composed either of polymethyl methacrylate or dimethacrylate, produced by mixing an acrylic monomer liquid with acrylic polymers and mineral fillers. The cement is insoluble in water and is thus resistant to fluids in the mouth, but is also irritating to the dental pulp. It is used chiefly as a luting agent for fabricated and temporary restorations. (Jablonski's Dictionary of Dentistry, 1992, p159)Genes, rRNA: Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.Bacterial Typing Techniques: Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.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).Contig Mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.RNA, Ribosomal, 18S: Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Metagenomics: The genomic analysis of assemblages of organisms.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Sulfites: Inorganic salts of sulfurous acid.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Multiplex Polymerase Chain Reaction: Methods for using more than one primer set in a polymerase chain reaction to amplify more than one segment of the target DNA sequence in a single reaction.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.DNA, Protozoan: Deoxyribonucleic acid that makes up the genetic material of protozoa.Point Mutation: A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.Shear Strength: The internal resistance of a material to moving some parts of it parallel to a fixed plane, in contrast to stretching (TENSILE STRENGTH) or compression (COMPRESSIVE STRENGTH). Ionic crystals are brittle because, when subjected to shear, ions of the same charge are brought next to each other, which causes repulsion.Sequence Homology: The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.Gene Amplification: A selective increase in the number of copies of a gene coding for a specific protein without a proportional increase in other genes. It occurs naturally via the excision of a copy of the repeating sequence from the chromosome and its extrachromosomal replication in a plasmid, or via the production of an RNA transcript of the entire repeating sequence of ribosomal RNA followed by the reverse transcription of the molecule to produce an additional copy of the original DNA sequence. Laboratory techniques have been introduced for inducing disproportional replication by unequal crossing over, uptake of DNA from lysed cells, or generation of extrachromosomal sequences from rolling circle replication.Genetic Loci: Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Mutation, Missense: A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed)Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Environmental Microbiology: The study of microorganisms living in a variety of environments (air, soil, water, etc.) and their pathogenic relationship to other organisms including man.Molecular Diagnostic Techniques: MOLECULAR BIOLOGY techniques used in the diagnosis of disease.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Genotyping Techniques: Methods used to determine individuals' specific ALLELES or SNPS (single nucleotide polymorphisms).Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.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.Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.DNA, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.Genetic Techniques: Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.Sequence Tagged Sites: Short tracts of DNA sequence that are used as landmarks in GENOME mapping. In most instances, 200 to 500 base pairs of sequence define a Sequence Tagged Site (STS) that is operationally unique in the human genome (i.e., can be specifically detected by the polymerase chain reaction in the presence of all other genomic sequences). The overwhelming advantage of STSs over mapping landmarks defined in other ways is that the means of testing for the presence of a particular STS can be completely described as information in a database.Reverse Transcription: The biosynthesis of DNA carried out on a template of RNA.Metagenome: A collective genome representative of the many organisms, primarily microorganisms, existing in a community.Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).DNA Barcoding, Taxonomic: Techniques for standardizing and expediting taxonomic identification or classification of organisms that are based on deciphering the sequence of one or a few regions of DNA known as the "DNA barcode".Operon: In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.INDEL Mutation: A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.Blotting, Northern: Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
The marker could be a short DNA sequence, such as a sequence surrounding a single base-pair change, known as a single ... the development and use of evolutionarily conserved sets of PCR primers. the use of microsatellite loci that vary among ... A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or ... the development of advanced DNA sequencing techniques. Many things utilized for studying larger organisms has not been possible ...
With this strategy, PCR primers specific to a variant region of DNA are used (called SSP-PCR). If a product of the right size ... The sequence of the antigens determines the antibody reactivities, and so having a good sequencing capability (or sequence- ... To interpret this table, it is necessary to consider that an allele is a variant of the nucleotide (DNA) sequence at a locus, ... These sequence features can be overlapping and continuous or discontinuous in the linear sequence. Variant types for each ...
As in most PCR reactions, two primers-one for each end-are used per sequence. To splice two DNA molecules, special primers are ... To insert a mutation into a DNA sequence, a specific primer is designed. The primer may contain a single substitution or ... The duplex is denatured and the second primer anneals to the newly formed DNA strand, containing sequence from the first primer ... The overlapping complementary sequences introduced will serve as primers and the two sequences will be fused. This method has ...
Primosomes gives RNA primers for DNA synthesis to strands. Notes. Phi X is regularly used as a positive control in DNA ... and the first DNA-based genome to be sequenced. This work was completed by Fred Sanger and his team in 1977. In 1962, Walter ... DNA pilot protein (or minor spike protein) J. 60 in virion. Binds to new single-stranded phage DNA; accompanies phage DNA into ... Nicks RF DNA to initiate rolling circle replication; ligates ends of linear phage DNA to form single-stranded circular DNA ...
... therefore making the sequence of the DNA in between them available upon search (if full-genome sequence data is available) or ... Before sequencing, these PETs are ligated to adaptors to which PCR primers anneal for amplification. The advantage of cloning ... linker sequence, a short 5' sequence tag, a short 3' sequence tag, and a short 3' linker sequence. It was shown conceptually ... The sequences unique to the clone are now paired together. Depending on the next-generation sequencing technique, PET sequences ...
This structure becomes a stem-loop when the FIP or BIP primer once again initiates DNA synthesis at one of the target sequence ... The outer primers (F3 and B3) anneal to the template strand and also generate new DNA. These primers are accompanied by DNA ... The primers bind only to these sequences which allows for high specificity. Out of the 4 primers involved, two of them are " ... The F3 primer, with DNA polymerase, binds to this end and generates a new double stranded DNA molecule while displacing the ...
By using two opposing primers, much like PCR, if the target sequence is indeed present, an exponential DNA amplification ... Recombinases are capable of pairing oligonucleotide primers with homologous sequence in duplex DNA. SSB bind to displaced ... Finally, the strand displacing polymerase begins DNA synthesis where the primer has bound to the target DNA. ... for rapid detection of viral genomic DNA or RNA, pathogenic bacterial genomic DNA, as well as short length aptamer DNA. The ...
... and then purified for DNA sequencing. Results are determined by a sequence analysis ... Uses gene specific degenerate primers to amplify pieces of DNA, these fragments are resolved using electrophoresis, ... DNA gyrase (topoisomerase II) subunit A (point mutation C7313T). SH1553. parC (grlA). Topoisomerase IV subunit A (point ... However, S. haemolyticus does have unique chromosome regions distributed near oriC (the origin of chromosomal DNA replication ...
DNA-based tests. These are based on detecting a leukaemic specific DNA sequence. Generally this is achieved through the ... From this sequence, PCR primers are designed that will only amplify the specific leukemic clone from the patient. ... The DNA sequence chosen may contribute to the genesis of the leukaemia, or may simply be linked to it. ... Some new techniques use Next-Generation Sequencing to detect MRD. RNA-based tests. These are based on detecting a ...
From a known sequence, a primer is designed to sequence across the circularised junction. This primer is used to jump 100 kb- ... Chromosome jumping enables two ends of a DNA sequence to be cloned without the middle section. Genomic DNA may be partially ... a sequence 100 kb away would have come near the known sequence on circularisation. Thus, sequences not reachable by chromosome ... Chromosome walking can be used from the new jump position (in either direction) to look for gene-like sequences, or additional ...
The primer pair, HSF19-HSR447, has been generated to be specific for amplifying only a section of Helminthosporium Solani DNA. ... Another way that silver scurf can be diagnosed is through molecular techniques, such as PCR and sequencing to identify the ... "Detection of Helminthosporium solani from soil and plant tissue with species-specific PCR primers". FEMS Microbiology Letters. ...
At each end of the DNA molecule there are palindromic sequences which form "hairpin" loops. The hairpin at the 3' end serves as ... a primer for the DNA polymerase. It is classified as erythrovirus because of its capability to invade red blood cell precursors ... This rate is similar to that of other single stranded DNA viruses. VP2 codons were found to be under purifying selection. In ... The name is derived from Latin, parvum meaning small, reflecting the fact that B19 ranks among the smallest DNA viruses. B19 ...
"Blocking primers to enhance PCR amplification of rare sequences in mixed samples - a case study on prey DNA in Antarctic krill ... it was estimated that the total global environmental DNA sequencing effort had produced less than 1 percent of the total DNA ... A common marker for human microbiome studies is the gene for bacterial 16S rRNA (i.e. "16S rDNA", the sequence of DNA which ... Metagenomics is also used extensively for studying microbial communities. In metagenomic sequencing, DNA is ...
These tools are used to optimize the design of primers for target DNA or cDNA sequences. Primer optimization has two goals: ... results using a given set of primers (probes) to amplify DNA sequences from a sequenced genome or transcriptome. ... A primer may bind to many predicted sequences, but only sequences with no or few mismatches (1 or 2, depending on location and ... allows simultaneous testing of a single primer or a set of primers designed for multiplex target sequences. It performs a fast ...
Certain polymerase chain reaction (PCR) primers have been designed and tested to consistently identify S. perseae with DNA ... sequencing techniques. An isolate of the pathogen in pure culture can also be identified by its morphological characteristics ...
The cDNA produced from the mRNA is labeled using primers homologous to the spliced leader sequences of the organism. In a nine ... RNA-seq DNA microarray Riddle, Donald L. (1997). C. elegans II. Plainview, N.Y: Cold Spring Harbor Laboratory Press. ISBN 0- ... end of the messenger RNA require the presence of a trans-spliced leader sequence. Spliced leader sequences are short sequences ... which have adapter sequences ligated on the 5' end. 5' SAGE utilizes oligo-capping technology. Both use their adapter sequence ...
DNA replication enzymes use the primers as docking points and start doubling the target sequences. The process is repeated over ... DNA based detection looks for a part of the foreign DNA inserted in a GMO. For technical reasons, certain DNA sequences are ... The method works by pairing the targeted genetic sequence with custom designed complementary bits of DNA called primers. In the ... Detection methods based on DNA rely on the complementarity of two strands of DNA double helix that hybridize in a sequence- ...
DNA motifs are specific short DNA sequences, often 8-20 nucleotides in length , which are statistically overrepresented in a ... This is done by ligating universal primers to all fragments. However, 5C has relatively low coverage. The 5C technique ... Ka-Chun Wong; MotifHyades: expectation maximization for de novo DNA motif pair discovery on paired sequences, Bioinformatics, ... Inverse PCR allows the known sequence to be used to amplify the unknown sequence ligated to it. In contrast to 3C and 5C, the ...
June 1991). "Complementary DNA sequencing: expressed sequence tags and human genome project". Science. 252 (5013): 1651-6. ... within the original cDNA/mRNA sequence); 3) A short primer sequence unique to either adaptor A or B, which will later be used ... The cDNA concatemers can then be isolated and sequenced using modern high-throughput DNA sequencers, and these sequences can be ... Comparison to DNA microarrays. The general goal of the technique is similar to the DNA microarray. However, SAGE sampling ...
List of Y-DNA single-nucleotide polymorphisms Non-canonical base pairing "Sequence-Dependent Variability of B-DNA". DNA ... GC content and melting temperature must also be taken into account when designing primers for PCR reactions. The following DNA ... A base-paired DNA sequence: ATCGATTGAGCTCTAGCG TAGCTAACTCGAGATCGC The corresponding RNA sequence, in which uracil is ... DNA sequences have been described which use newly created nucleobases to form a third base pair, in addition to the two base ...
This method involves the use of hexamer primers that bind randomly to the template, followed by DNA elongation using phi29 DNA ... By simultaneously capturing and sequencing both DNA and RNA through a method called G&T sequencing, researchers are able to ... DNA and RNA sequencing). The primary difference between the two techniques is the amplification step, where DNA and polyA-RNA ... containing the ad2 primer on the 5' end. The 3' end contains the ad1 primer, which is the original poly-dT primer used for ...
T5 exonuclease attacks the 5' ends of sequences, creating single-stranded DNA in the ends of all sequences where the different ... sequence=1" (PDF). MIT. Retrieved 27 March 2014. Baldwin, Geoff (2012). Synthetic Biology A Primer. London: Imperial College Pr ... ends of the DNA part respectively. These standard sequences encode specific restriction enzyme sites. The prefix sequence ... which now forms a 6 bp scar sequence. The 6 bp sequence allows the reading frame to be maintained.The scar sequence codes for ...
This new location does not have to be in a homologous sequence or in close proximity to the donor DNA sequence. The donor DNA ... This process is initiated by a replication protein which helps generate a primer for DNA synthesis. While one DNA strand is ... Additional information has led to the belief that trans-mobilization of the DNA sequence is another mechanism of L1 to shuffle ... Upon transposition, L1 associates with 3' flanking DNA and carries the non-L1 sequence to a new genomic location. ...
DNA sequencing technologies such as next-generation sequencing have made it possible to study amplicons in genome biology and ... The primers bind adjacent to one another, forming a segment of double stranded DNA that once separated, can serve as a target ... and increasingly by cheaper and more high-throughput technologies for DNA sequencing or next-generation sequencing, such as ion ... An amplicon sequence template that has been prepared for amplification. The target sequence to be amplified is colored green. ...
First, restriction enzymes are used to cleave near the target sequence on DNA contained in a suitable vector. This step removes ... Unlike many site directed mutagenesis methods, cassette mutagenesis also does not involve primer extension by DNA polymerase. ... To use this method, the sequence of the target sequence and nearby restriction sites must be known. Since restriction enzymes ... Finally, the resultant construct is sequenced to check that the target sequence contains the intended mutation. The use of ...
A primer binding site is a region of a nucleotide sequence where an RNA or DNA single-stranded primer binds to start replication. The primer binding site is on one of the two complementary strands of a double-stranded nucleotide polymer, in the strand which is to be copied, or is within a single-stranded nucleotide polymer sequence. A PCR primer binding site is a site where a polymerase chain reaction (PCR) primer binds, to prime duplication of a complement to an existing DNA or RNA sequence. The HIV primer binding site is a structured RNA element in the genomes of retroviruses to which tRNA binds to initiate reverse transcription. In HIV, the tRNA is tRNA(3)(Lys) although it can use other tRNAs. It consists of 18 nucleotides and follows the U5 region of the 5'-long terminal repeat (LTR) of the retrovirus. Berg, Jeremy M.; Tymoczko, John L. & Stryer, Lubert. (c. 2002). "DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites". ...
... (Inverse PCR) is a variant of the polymerase chain reaction that is used to amplify DNA with only one known sequence. One limitation of conventional PCR is that it requires primers complementary to both termini of the target DNA, but this method allows PCR to be carried out even if only one sequence is available from which primers may be designed. Inverse PCR is especially useful for the determination of insert locations. For example, various retroviruses and transposons randomly integrate into genomic DNA. To identify the sites where they have entered, the known, "internal" viral or transposon sequences can be used to design primers that will amplify a small portion of the flanking, "external" genomic DNA. The amplified product can then be sequenced and compared with DNA databases to locate the sequence which has been ...
... (Nested PCR) is a modification of polymerase chain reaction intended to reduce non-specific binding in products due to the amplification of unexpected primer binding sites. Polymerase chain reaction itself is the process used to amplify DNA samples, via a temperature-mediated DNA polymerase. The products can be used for sequencing or analysis, and this process is a key part of many genetics research laboratories, along with uses in DNA fingerprinting for forensics and other human genetic cases. Conventional PCR requires primers complementary to the termini of the target DNA. The amount of product from the PCR increases with the number of temperature cycles that the reaction is subjected to. A commonly occurring problem is primers binding to incorrect regions of the DNA, giving unexpected products. This problem becomes more likely with ...
... is a way to rapidly propagate beneficial mutations in a directed evolution experiment. It is used to rapidly increase DNA library size. First, DNase is used to fragment a set of parent genes into pieces of 50-100 bp in length. This is then followed by a polymerase chain reaction (PCR) without primers- DNA fragments with sufficient overlapping homologous sequence will anneal to each other and are then extended by DNA polymerase. Several rounds of this PCR extension are allowed to occur, after some of the DNA molecules reach the size of the parental genes. These genes can then be amplified with another PCR, this time with the addition of primers that are designed to complement the ends of the strands. The primers may have additional sequences added to their 5' ends, such as sequences for restriction enzyme recognition ...
Hensikten med en primer er binding til bestemte sekvenser i DNA og muligheter for amplifisering (produksjon) av bestemte områder i større DNA-molekyler. Bindingen oppstår fordi primerne er designet slik at de er komplementære til de to trådene i DNA. Til hver PCR trengs det to primere (figur 1). En som er komplementær til starten av genet (forward) og en til slutten (revers). På denne måten er det mulig å isolere ønskede områder av DNA som ellers ville vært utilgjengelig, for eksempel gener eller deler av gener (jf. PCR). ...
Kisik in žveplo sta nekovini, selen, telur in polonij pa so polprevodne polkovine. To pomeni, da so njihove električne lastnosti nekje med lastnostmi kovin in izolatorjev. Telur, pa tudi selen, se kljub temu pogosto razvrščata med kovine. Kovinski halkogenidi se v naravi pojavljajo kot minerali. Nekateri so zelo pogosti, na primer pirit (FeS), ki je železova ruda, nekateri pa so zelo redki, na primer zlatov ditelurid kalaverit (AuTe2). Najboolj pogosto formalno oksidacijsko stanje halkogenih spojin je 2-. Pogosta so tudi druga oksidacijska stanja, na primer 1- v piritu. Najvišje formalno oksidacijsko stanje je 6+ v sulfatih (žveplova kislina H2SO4), selenatih (natrijev selenat Na2SeO4) in teluratih. ...
Kisík je kemijski element s simbolom O in atomskim številom 8. V periodnem sistemu elementov spada med halkogene elemente. Je zelo reaktivna nekovina in oksidant, ki se zlahka spaja z večino elementov in z njimi tvori okside. V Vesolju je za vodikom in helijem po masi tretji najpogostejši element. Pri standardni temperaturi in tlaku (STP) sta dva atoma kisika vezana v dikisik O2, ki je brezbarven plin brez vonja in okusa. Veliko glavnih razredov organskih spojin v živih organizmih, na primer proteini, nukleinske kisline, ogljikovi hidrati in maščobe, vsebujejo tudi kisik. Prisoten je tudi v anorganskih delih organizmov, na primer v lupinah školjk in polžev ter v kosteh in zobeh. Večino mase živih organizmov sestavlja voda, v kateri sta vezana kisik in vodik (voda tvori približno dve tretjini človekove telesne mase). Kisik iz ozračja in vode je potreben za dihanje in ohranitev skoraj vsega življenja na Zemlji. Porabljeni kisik se stalno obnavlja s fotosintezo v živih ...
V primeru zvišanega CSF tlaka je moten pretok krvi v možganih. Ko pride do problemov v pretoku likvorja to zmoti ne samo likvor sam, temveč tudi stistljivost kraniospinalnega prostora in pretok krvi znotraj lobanje, s posledično ranljivostjo nevronov in glie. Kot je bilo že omenjeno sta cerebrospinalna tekočina in limfni sistem povezana. Primer patologije ki prikazuje odnose med motnjami cerebrospinalne tekočine je primer hidrocefalusa ter motenega CSF limfatičnega transporta. Likvor se lahko testira za diagnozo mnogih nevroloških bolezni, nujno ob sumu na meningitis in subarahnoidalno krvavitev ter je dobra dodatna preiskava ob sumu na multiplo sklerozo ter razne inflamatorne (vnetne) bolezni. To se dela z lumbalno funkcijo. Lumbalna punkcija je postopek, ko zdravnik z injekcijo vbode med dvema vretencema hrbtenice (tretjim in četrtim ledvenim vretencem) in s punkcijo odvzame vzorec cerebrospinalne tekočine-likvorja za nadaljnjo diagnostiko). Pacient ob tem leži na boku, skrčen s ...
V primeru zvišanega CSF tlaka je moten pretok krvi v možganih. Ko pride do problemov v pretoku likvorja to zmoti ne samo likvor sam, temveč tudi stistljivost kraniospinalnega prostora in pretok krvi znotraj lobanje, s posledično ranljivostjo nevronov in glie.. Kot je bilo že omenjeno sta cerebrospinalna tekočina in limfni sistem povezana. Primer patologije ki prikazuje odnose med motnjami cerebrospinalne tekočine je primer hidrocefalusa ter motenega CSF limfatičnega transporta. Likvor se lahko testira za diagnozo mnogih nevroloških bolezni, nujno ob sumu na meningitis in subarahnoidalno krvavitev ter je dobra dodatna preiskava ob sumu na multiplo sklerozo ter razne inflamatorne (vnetne) bolezni. To se dela z lumbalno funkcijo.. Lumbalna punkcija je postopek, ko zdravnik z injekcijo vbode med dvema vretencema hrbtenice (tretjim in četrtim ledvenim vretencem) in s punkcijo odvzame vzorec cerebrospinalne tekočine-likvorja za nadaljnjo diagnostiko). Pacient ob tem leži na boku, skrčen s ...
V primeru zvišanega CSF tlaka je moten pretok krvi v možganih. Ko pride do problemov v pretoku likvorja to zmoti ne samo likvor sam, temveč tudi stistljivost kraniospinalnega prostora in pretok krvi znotraj lobanje, s posledično ranljivostjo nevronov in glie. Kot je bilo že omenjeno sta cerebrospinalna tekočina in limfni sistem povezana. Primer patologije ki prikazuje odnose med motnjami cerebrospinalne tekočine je primer hidrocefalusa ter motenega CSF limfatičnega transporta. Likvor se lahko testira za diagnozo mnogih nevroloških bolezni, nujno ob sumu na meningitis in subarahnoidalno krvavitev ter je dobra dodatna preiskava ob sumu na multiplo sklerozo ter razne inflamatorne (vnetne) bolezni. To se dela z lumbalno funkcijo. Lumbalna punkcija je postopek, ko zdravnik z injekcijo vbode med dvema vretencema hrbtenice (tretjim in četrtim ledvenim vretencem) in s punkcijo odvzame vzorec cerebrospinalne tekočine-likvorja za nadaljnjo diagnostiko). Pacient ob tem leži na boku, skrčen s ...
Veliko glavnih razredov organskih spojin v živih organizmih, na primer proteini, nukleinske kisline, ogljikovi hidrati in maščobe, vsebujejo tudi kisik. Prisoten je tudi v anorganskih delih organizmov, na primer v lupinah školjk in polžev ter v kosteh in zobeh. Večino mase živih organizmov sestavlja voda, v kateri sta vezana kisik in vodik (voda tvori približno dve tretjini človekove telesne mase). Kisik iz ozračja in vode je potreben za dihanje in ohranitev skoraj vsega življenja na Zemlji. Porabljeni kisik se stalno obnavlja s fotosintezo v živih organizmih, v kateri nastaja kisik iz vode s pomočjo sončne svetlobe. Elementarni kisik proizvajajo cianobakterije, alge in zelene rastline, vsa živa bitja pa ga porabljajo za celično dihanje. Za anaerobne organizme, ki so prevladovali na Zemlji preden se je v ozračju začel kopičiti kisik, je strupen. Kopičenje kisika se je začelo med tako imenovano kisikovo katastrofo pred približno 2,3 milijarde let. Dvoatomni kisik tvori ...
Filogenija je v biologiji shematska predstavitev evolucijske zgodovine in sorodnosti skupin organizmov (taksonov). Temelji na osnovni predpostavki, da novi taksoni (na primer vrste) nastajajo z razcepom skupnega prednika na dve evolucijski liniji, zato ima obliko drevesa, kjer od najstarejšega skupnega prednika nastajajo nove in nove razvejitve. Filogenetsko drevo je torej sestavljeno iz dveh osnovnih enot: vozlišča predstavljajo skupne prednike, veje pa njihove potomce, pri čemer število vozlišč med vejami ponazarja, kako blizu ali daljno sorodna sta si taksona. Filogenetika je panoga biologije, ki se ukvarja s konstruiranjem teh dreves (filogenij) na podlagi znanih podatkov o lastnostih organizmov (znakov). Neposredni materialni dokazi o poteku evolucije pogosto niso na voljo, zato biologi uporabljajo še eno temeljno predpostavko: če si dva taksona delita mnogo znakov, to pomeni, da sta si bolj sorodna, in obratno. Obstaja več teoretskih pristopov k interpretaciji ...
Prehranski vir citidina predstavlja hrana, ki je bogata z RNK, na primer meso, pivski kvas, ter hrana, bogata s pirimidini (npr. pivo). Pri prebavljanju se RNK razcepi na ribozilpirimidine (citidin in uridin), le-ti pa se absorbirajo skozi prebavila. Pri ljudeh se citidin iz prehranskih virov pretvori v uridin.  ...
Primers were purchased from Operon Technologies, Alameda CA. Primers discussed in the text have the following sequences (5-3 ... primer; 0.2-4.0 ng/ul template DNA; and 0.02-0.06 U/ul (0.5-1.5 units) Taq DNA polymerase. PCR conditions. A Perkin-Elmer Cetus ... primers A01, B16, (2 markers); Sp B, primers C07, B02, C15 (4 markers); Sp C, primers A01, C16, C19, D01 (7 markers); and Sp D ... DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nuc Acids Res 18: 6531-6535.. Williams JGK, ...
... coli strain that carries the Taq DNA polymerase gene. Taq DNA Polymerase is the most common polymerase used for PCR reactions. ... Taq DNA Polymerase is a thermostable DNA Polymerase isolated from an E. ... Primer extension *DNA sequencing. Formulation: Genscript Taq DNA Polymerase has been formulated using a proprietary technology ... Description: Taq DNA Polymerase is a thermostable DNA Polymerase isolated from an E. coli strain that carries the Taq DNA ...
... was used for optimization of LAMP using six primers that target the HVT070 gene sequence of the virus. These primers can ... HVT was detected in the feathers, liver, skin, and spleen with average DNA purity of 3.05-4.52 μg DNA/mg (A260/A280) using LAMP ... Wozniakowski, G. and Niczyporuk, J.S. (2015) Detection of specific UL49 sequences of Mareks diseasevirus CVI988/rispens strain ... Loop-mediated isothermal amplification of DNA. Nucleic Acids Res., 28: 63-68. [Crossref] ...
Plasmid DNA Sequencing with Universal Primers - (Mar/08/2007 ). Hi all, Ive been having some trouble with sequencing. The gene ... Big peaks for a short time, then nothing - too much DNA.. Nothing - bad primer, loss of DNA, bad cycling conditions.. If your ... Also use of sequencing buffer is a must for reliable results. The next important thing the amount of DNA and Big Dye terminator ... Low peaks, sequence gets scrambly quite quickly, peaks have smaller peaks underneath them - not enough DNA.. Peaks are an OK ...
In this study we designed a set of PCR primers for the mitochondrial 12S ribosomal DNA sequence based on 64 complete ... Alignment of sequences was performed for the excised mitochondrial 12S ribosomal DNA sequences, and conserved regions were ... Unlike microbial studies, where analysis of the 16S ribosomal DNA sequence is standard, the best gene for metazoan metagenetics ... DNA primers have considerable potential for metazoan metagenetic analysis because of their ability to amplify sequences from ...
Primer-BLAST. You are here. Home » Products » Sequencher » Sequencher Features » Connections » Primer-BLAST ... Use Primer-BLAST to analyze sequences and check specificity.. Parallelize your analyses - use several different sets of ... Your new primers are automatically tagged with a GenBank style feature key that makes them easier to see in an alignment. The ... If you want to learn more about Primer-BLAST, check out the Sequencher Connections tutorial. ...
... enable amplification of mtDNA for downstream mtDNA sequencing in evolutionary studies, SNP identification, and forensics. Learn ... Mitochondrial DNA Sequencing Primers mtDNA sequencing is useful in evolutionary studies, single nucleotide polymorphism (SNP) ... within the D-loop region of human mitochondrial DNA (mtDNA). ...
Identification of the DNA bases of a DNase I footprint by the use of dye primer sequencing on an automated capillary DNA ... Identification of the DNA Bases of a DNase I Footprint by the Use of Dye Primer Sequencing on an Automated Capillary DNA ... Identification of the DNA Bases of a DNase I Footprint by the Use of Dye Primer Sequencing on an Automated Capillary DNA ... Identification of the DNA Bases of a DNase I Footprint by the Use of Dye Primer Sequencing on an Automated Capillary DNA ...
How should I store my targeted DNA sequencing library prep assay primers?. Primer pools are stable for up to one year at -20 °C ...
This technique involves a one-step PCR reaction utilizing genomic DNA and sequence-specific primers to determine the ... specificity of each allele and to produce a larger primer data base ideal for serological analysis. The application of this ... Chiu, Angela Chen-Yen. DNA Typing of HLA-B by PCR with Primer Mixes Utilizing Sequence-Specific Primers, thesis, August 1997; ... DNA Typing of HLA-B by PCR with Primer Mixes Utilizing Sequence-Specific Primers ...
... pyrene-dG adduct positioned opposite dC at a DNA template-primer junction. ... STRUCTURAL ALIGNMENT OF THE (+)-TRANS-ANTI-[BP]DG ADDUCT POSITIONED OPPOSITE DC AT A DNA TEMPLATE-PRIMER JUNCTION, NMR, 6 ... Sequence Similarity Cutoff. Rank. Chains in Cluster. Cluster ID / Name. Legend Entity #2 , Chains: B DNA DUPLEX D(AAC-[BP]G- ... Sequence Similarity Clusters for the Entities in PDB 1AXO Legend Entity #1 , Chains: A DNA DUPLEX D(AAC-[BP]G-CTACCATCC)D( ...
What species and targets do you design Targeted DNA Sequencing Library Prep assay primers to?. Targeted DNA Seq Library assays ... are designed to human species for targets with an associated RefSeq ID, gene name, target sequence or genome coordinate. (See ...
Blocking primers to enhance PCR amplification of rare sequences in mixed samples - a case study on prey DNA in Antarctic krill ... Dietary item DNA was PCR amplified from a range of species in krill stomachs for which we had no prior sequence knowledge. ... and a third elongation arrest primer located between the two universal primers. All blocking primers were modified with a C3 ... The diversity of sequences within a sample that can be detected by universal primers is often compromised by high ...
Results: The developed primers successfully amplified DNA of their target organism from various soil DNA extracts. This was ... The DNA sequences obtained from methods that do not require culturing can be identified post-hoc and placed phylogenetically as ... Environmental sequencing as shown here differs from other molecular survey methods in that there is no need to pre-isolate the ... Our noncultured environmental sequence based approach will be able to provide a rapid and large-scale screening of the presence ...
The method is compatible with automated DNA sequencing procedures. ... A simplified method for isolating primer extension products and generating them in a form appropriate for electrophoresis is ... DNA sequences by mass spectrometry US6194144B1 (en) 1993-01-07. 2001-02-27. Sequenom, Inc.. DNA sequencing by mass spectrometry ... However, sequencing reactions of more complex DNA such as cosmid, lambda clone, or genomic DNA generate primer extension ...
The developed primers successfully amplified DNA of their target organism from various soil DNA extracts. This was confirmed by ... The DNA sequences obtained from methods that do not require culturing can be identified post-hoc and placed phylogenetically as ... Environmental sequencing as shown here differs from other molecular survey methods in that there is no need to pre-isolate the ... Our PCR primers, specific to the 18s small-subunit rRNA gene, were developed for both eutardigrades and bdelloid rotifers. ...
Boron Compounds, DNA Primers, DNA, Viral, DNA-Directed DNA Polymerase, Genes, env, Genes, pol, Genetic Heterogeneity, Genetic ... Quantitation of mixed-base populations of HIV-1 variants by automated DNA sequencing with BODIPY dye-labeled primers.. Title. ... Quantitation of mixed-base populations of HIV-1 variants by automated DNA sequencing with BODIPY dye-labeled primers.. ... Quantitation of mixed-base populations of HIV-1 variants by automated DNA sequencing with BODIPY dye-labeled primers. ...
DNA segments to genomic DNA samples, for instance through incorporation of barcode sequences in PCR primers. Although several ... The program bartab can be used to deconvolute DNA sequence datasets produced by the use of multiple barcoded primers. This ... Barcrawl is a software program that facilitates the design of barcoded primers, for multiplexed high-throughput sequencing. ... of-concept case study of both programs in which barcoded rRNA primers were designed and validated by high-throughput sequencing ...
primers. Consult the Table of Concentrations when you are ready to submit the primer for sequencing. If there are other primers ... What Primers Does the Core Provide?. Here are the five primers we provide free of charge, along with their sequences:. T7. 5- ... commonly-needed primers, and there must be a readily available source of template DNA to use as positive. control (preferably a ... We supply the above primers free of charge. If you want to use one of these to sequence your template,. just check the ...
Primer design and DNA sequencing:. Primer pairs were designed using the Primer3 program (Rozen and Skaletsky 2000) to amplify ... Sequence data analysis:. All DNA sequences from Pi-ta and 12 flanking genes were aligned using Vector NTI 10 (Invitrogen) and ... All primers were verified by BLAST against both 93-11 (indica) and Nipponbare (japonica) genome sequences. Primers were also ... Patterns of DNA sequence variation at and around the Pi-ta locus in the AA genome of Oryza species. (A) Sliding-window analysis ...
Custom primer synthesis is provided as an adjunct service to sequencing within the MRC PPU DNA Sequencing and Services facility ... Services , DNA Sequencing , Custom Primer Synthesis. We have found that many customers appreciate the benefits of not having to ... We ask that customers identify optimal primer sequences for their template and supply the primer sequence to us. We encourage ... We are happy to store those primers that customers have requested generation of by MRC PPU DNA Sequencing and Services. ...
To mine the gene information relevant to GlcNAc metabolism, the DNA sequences of dasR-dasA-dasBCD-nagB and nagKA in S. ... For the production of 6 × His-tagged DasR, the DNA sequence of DasR without stop codon was amplified using primers PdasR/F and ... The dre sequence was proposed by Rigali et al. . Based on MAST analysis, the DNA sequences of the dre motif in the promoter ... d WebLogo of the dre element, and nucleotide sequence of dre motifs in S. verticillus. The DNA binding sequences of DasR were ...
Subsequently, targeted bidirectional DNA re-sequencing of polymerase chain reaction (PCR)-amplified high-risk regions of MYO5B ... Subsequently, targeted bidirectional DNA re-sequencing of polymerase chain reaction (PCR)-amplified high-risk regions of MYO5B ... we performed exome sequencing on 12 familial genomes (6 affected individuals, 2 obligate carriers, and 4 seemingly unaffected ... we performed exome sequencing on 12 familial genomes (6 affected individuals, 2 obligate carriers, and 4 seemingly unaffected ...
We provide standard sequencing primers (see below) at no charge. If using your own custom primers, please see Primer ... Molecular Biology: DNA Sequencing Services. The DNA sequencing facility at CFG offers DNA sequencing services for a wide range ... 2. Bacterial Genomic (BG) Sequencing. DNA sequence can be obtained directly from bacterial chromosomal DNA by Sanger sequencing ... or BAC DNA template sequenced with one primer to produce one chromatogram (A single template sequenced with both forward and ...
A DNA-based detection and screening system for identifying HLA class I expression variants by sequence-specific primers ... 1999) A DNA-based detection and screening system for identifying HLA class I expression variants by sequence-specific primers. ... repeat mutations may occur frequently at points where unusual nucleotide sequences make accurate DNA replication by DNA ... We describe here a polymerase chain reaction using sequence-specific primers (PCR-SSP) system that can not only detect all ...
GenePolymeraseUniversal PrimersPlasmidMiSeqAbstractProbesNucleic acidsDegenerate primersPlasmidsMoleculeMitochondrial DNAOligonucleotideStandard sequencReactionNucleotidesNext Generation SequencingHybridizationAmpliconFluorescently labeledSimilarityRRNA primersMethodsMicrobiologyRandom primersCharacterizeGenome SequencingReverseSpeciesCustom primersChromosomesSamplesEvolutionaryOligosAmplify DNA fragmentsForward primerBidirectionalFragmentsHigh-throughputMultiple sequenceBlastMismatchesMutationElectrophoresisVectorsNCBIGenomic libraries
- The gene I want is about 1.8kbp, but I've got nothing reliable after 2 trials with the primers I designed. (protocol-online.org)
- Targeted DNA Seq Library assays are designed to human species for targets with an associated RefSeq ID, gene name, target sequence or genome coordinate. (fluidigm.com)
- Our PCR primers, specific to the 18s small-subunit rRNA gene, were developed for both eutardigrades and bdelloid rotifers. (byu.edu)
- Instead of isolating and culturing individuals, communities are characterized by extracting all of the DNA in a particular sample (soil, water, air), amplifying a specific gene using PCR, cloning individual PCR products, and then sequencing individual clones. (biomedcentral.com)
- Our survey focuses on the 18S rRNA gene, commonly used for phylogenetic inference of eukaryotes due to its highly conserved sequence and ability to resolve relatively deep nodes. (biomedcentral.com)
- Direct DNA sequencing of human immunodeficiency virus type 1 (HIV-1) pol and env gene regions was characterized for accuracy and precision. (bcm.edu)
- To mine the gene information relevant to GlcNAc metabolism, the DNA sequences of dasR - dasA - dasBCD - nagB and nagKA in S. verticillus were determined by chromosome walking. (springer.com)
- Subsequently, targeted bidirectional DNA re-sequencing of polymerase chain reaction (PCR)-amplified high-risk regions of MYO5B gene and sequenom iPLEX genotpying of 29 candidate SNPs were performed on a larger set of 33 members of this NSCL/P family (10 affected + 4 obligate carriers + 19 unaffected relatives) to find SNPs significantly associated with NSCL/P trait. (frontiersin.org)
- All the DNA sequences were complete coding regions, except for the 4-Cl gene. (biomedcentral.com)
- Finally, the DNA sequences of each PAs biosynthetic gene were grouped according to their taxon and then used to design universal primers using alignment PCR analysis in the VectorNTI software. (biomedcentral.com)
- The presence of pXO2 ORF sequences in other Bacillus species suggests the possibility that certain pXO2 plasmid gene functions may also be present in other closely related bacteria. (biomedcentral.com)
- Conservation of plasmid sequences can provide clues about the origin of the pXO2 plasmid and about potentially conserved gene functions. (biomedcentral.com)
- In addition, four primer mixes were designed for determining codon 57 of the HLA-DQB1 gene. (nih.gov)
- These products include random primers , Oligo (dT) primers , gene specific primers for sequencing, forward and reverse sequencing primers and kits, and the MegaPlex RT Primers and Megaplex Primer Pools developed for assessing expression profiles. (thermofisher.com)
- An E. coli strain that carries the Q5 High-Fidelity DNA Polymerase gene. (neb.com)
- We analyzed the TGFB2 gene by sequencing in a cohort of 88 individuals with a Marfan-like phenotype and/or TAAD, who did not have mutations in known genes causing thoracic aortic disease. (nature.com)
- Background: Next-generation sequencing platforms have revolutionised our ability to investigate the microbiota composition of complex environments, frequently through 16S rRNA gene sequencing of the bacterial component of the community. (ucc.ie)
- The aim of this study was to determine the impact of these three factors on 16S rRNA gene sequencing results, using mock communities and mock community DNA. (ucc.ie)
- S inha and G oodman 1983 ), these studies reported small mutator effects from mutations in genes 32 , 44 , 45 , and 62 , whereas mutations in gene 43 (which encodes gp43, the DNA polymerase/proofreading exonuclease itself) could produce huge mutator factors. (genetics.org)
- These qualities make Scorpions primers valuable tools for rapid, real-time PCR, endpoint PCR, SNP detection, and gene quantification. (biosearchtech.com)
- An E. coli strain that carries the Vent (D141A / E143A) DNA Polymerase gene, a genetically engineered form of the native DNA polymerase from Thermococcus litoralis (4). (neb.com)
- Sequence analysis of the CCG polymorphic region adjacent to the CAG triplet repeat of the HD gene in normal and HD chromosomes. (biomedsearch.com)
- The microbiome was characterized on the basis of the V3 and V4 hypervariable region of the 16S rRNA gene by using paired-end sequencing on Illumina MiSeq device. (hindawi.com)
- Since the development of methods of high-throughput production of gene and protein sequences, the rate of addition of new sequences to the databases increased exponentially. (wikipedia.org)
- These sequences fall into many groups of related sequences known as protein families or gene families. (wikipedia.org)
- We established a nationwide DNA repository of samples from deaf probands to pursue a sequential screening strategy to identify gene mutations for deafness and to inform etiological diagnoses in China. (biomedcentral.com)
- ABgene® supplies a 94kDa ultra-pure recombinant thermostable DNA polymerase obtained by high level expression of the Taq DNA polymerase gene in E. coli. (bio-medicine.org)
- They exert their regulatory role on protein-coding gene (PCG) expression by binding to either full or partial complementary sequences primarily in the 3′ untranslated region (UTR), but also inside the coding sequence (CDS) and the 5′ UTR, of the corresponding mRNAs. (aacrjournals.org)
- Identification of the most likely sites of recombination with the Bayesian multiple change point model, an approach which has not previously been applied to prokaryotic gene sequence analysis, serves as a model for future studies of recombination in molecular evolution of genes. (asm.org)
- Species assignments are consistent with phylogenetic analysis based on 16S gene sequences ( 19 , 36 ). (asm.org)
- The term "chromosome walking" is used instead when the sequence is known but there is no clone of a gene. (wikipedia.org)
- For example, the gene for a disease may be located near a specific marker such as an RFLP on the sequence. (wikipedia.org)
- Polymerase chain reaction (PCR) was performed with a 6FAM-labeled primer to amplify a typical target promoter region. (nih.gov)
- We describe here a polymerase chain reaction using sequence-specific primers (PCR-SSP) system that can not only detect all previously-sequenced HLA class I expression variants but can also screen for mutations between positions 621-627 in HLA-A, B or C alleles which may give rise to potentially null alleles. (edu.au)
- Q5 ® High-Fidelity DNA Polymerase sets a new standard for both fidelity and robust performance. (neb.com)
- With the highest fidelity amplification available (~280 times higher than Taq ), Q5 DNA Polymerase results in ultra-low error rates. (neb.com)
- Q5 DNA Polymerase is composed of a novel polymerase that is fused to the processivity-enhancing Sso7d DNA binding domain, improving speed, fidelity and reliability of performance. (neb.com)
- Q5 ® High-Fidelity DNA Polymerase is a high-fidelity, thermostable DNA polymerase with 3´→ 5´ exonuclease activity, fused to a processivity-enhancing Sso7d domain to support robust DNA amplification. (neb.com)
- With an error rate ~280-fold lower than that of Taq DNA Polymerase, Q5 High-Fidelity DNA Polymerase is ideal for cloning and can be used for long or difficult amplicons. (neb.com)
- Q5 High-Fidelity DNA Polymerase is supplied with an optimized buffer system that allows robust amplification regardless of GC content. (neb.com)
- Q5 High-Fidelity DNA Polymerase is unlike typical, lower fidelity PCR enzymes. (neb.com)
- Amplification of a variety of human genomic amplicons from low to high GC content using Q5 High-Fidelity DNA Polymerase. (neb.com)
- Here we present 10 high resolution crystal structures and enzyme kinetic analyses of Bacillus DNA polymerase I large fragment variants complexed with deoxy-, ribo-, and dideoxynucleotides and a DNA substrate. (rcsb.org)
- The contributions of polymerase accessory proteins to the accuracy of DNA synthesis have also been explored, both in vivo and in vitro . (genetics.org)
- Vent (exo-) DNA Polymerase has been genetically engineered to eliminate the 3´→ 5´ proofreading exonuclease activity associated with Vent DNA Polymerase (1). (neb.com)
- The fidelity of polymerization by this form is reduced to a level about 2-fold higher than that of Taq DNA Polymerase (2,3). (neb.com)
- A nucleic acid molecule to be sequenced is exposed to a polymerase in the presence of nucleotides which are to be incorporated into a complementary nucleic acid strand. (freepatentsonline.com)
- Previously, bacterial diversity of the infected root canal system was determined by broad-range polymerase chain reaction followed by cloning and Sanger sequencing as well as molecular fingerprinting techniques such as denaturing gradient gel and terminal restriction fragment length polymorphism analysis [ 5 , 11 ]. (hindawi.com)
- The most common molecular strategies for estimating taxonomic composition depend upon PCR with universal primers that amplify an orthologous DNA region from a range of species. (uio.no)
- The diversity of sequences within a sample that can be detected by universal primers is often compromised by high concentrations of some DNA templates. (uio.no)
- one annealing inhibiting primer overlapping with the 3' end of one of the universal primers, another annealing inhibiting primer also having an internal modification of five dI molecules making it a dual priming oligo, and a third elongation arrest primer located between the two universal primers. (uio.no)
- Sequencing is performed from each end using either universal primers or specifically designed ones. (wikipedia.org)
- How did you isolate your plasmid DNA? (protocol-online.org)
- I use 1ul for plasmid DNA eg read lenghts of 900bp+. (protocol-online.org)
- A standard single reaction consists of one plasmid, PCR fragment, or BAC DNA template sequenced with one primer to produce one chromatogram (A single template sequenced with both forward and reverse primers would comprise two reactions, for example). (albany.edu)
- For common plasmid vectors we provide a number of standard sequencing primers free-of-charge (see list below) or customers can provide custom-designed primers. (albany.edu)
- Complete sequencing and annotation of the 96.2 kb Bacillus anthracis plasmid, pXO2, predicted 85 open reading frames (ORFs). (biomedcentral.com)
- Kits are available for total RNA purification, plasmid miniprep, gel extraction, and DNA & RNA cleanup. (neb.com)
- Because we had not worked with LPV prior to this investigation, and because the archetypal LPV sequence was different from that of the control plasmid, we were able to rule out laboratory contamination of the PCR. (asm.org)
- Although bacteriocin (antibacterial-peptide) production constitutes a clear advantage and although the genetic sequences responsible for it are frequently plasmid borne, only nisin was shown to be transposon encoded ( 10 ). (asm.org)
- Plasmid sequence and annotations. (addgene.org)
- Use text editor or plasmid mapping software to view sequence. (addgene.org)
- The DNA of interest may be a plasmid insert, a PCR product or a fragment representing a gap when sequencing a genome. (wikipedia.org)
- The three Ion PGM primer sets detected more of the 20 mock community species than the equivalent MiSeq primer sets. (ucc.ie)
- The specific aim of this study was to investigate the microbial diversity of primary endodontic infections using Illumina MiSeq sequencing platform in Egyptian patients. (hindawi.com)
- Illumina MiSeq platform sequencing can be used to investigate oral microbiome composition of endodontic infections. (hindawi.com)
- A consequence of reliance on molecular methods using primers or probes based on existing sequence information is that unsequenced or partially-sequenced null, or low expressed variants are not discriminated from expressed alleles. (edu.au)
- The Prime-It Fluor fluorescence labeling kit generates directly fluoresceinated DNA probes using random 9-mer primers and Exo-Klenow to incorporate fluor-12-dUTP into the probe fragments. (selectscience.net)
- BHQ® (Black Hole Quencher®)-labeled Scorpions primers for PCR analysis are unlike dual-labeled probes and Molecular Beacons because they combine primer and probe in one molecule, with the primer at the 3' end and the probe contained within a hairpin-loop structure at the 5' end. (biosearchtech.com)
- We designed the S. sanguinis-, S. parasanguinis-, and S. gordonii-specific primers, Ssa21-F3/Ssa21-R2, Spa17-F/Spa17-R, and Sgo41-F1/Sgo41-R1 respectively, based on the nucleotide sequences of the Ssa21, Spa17, and Sgo41 DNA probes that were screened using inverted dot blot hybridization (IDBH). (bvsalud.org)
- o To play a central role in assembly of comparative physical maps of maize, sorghum, rice, and other grasses, by hybridization of mapped DNA probes to BAC grids. (bio.net)
- 4. The kit of claim 1 , wherein said first and second nucleic acid probes are PCR primers. (google.es)
- We are stil trying to decide which primer to choose since degenerate primers tend to have different efficiencies in different annealing temperatures. (protocol-online.org)
- Results: The use of different primer sequences (V4-V5, V1-V2 and V1-V2 degenerate primers) resulted in differences in the genera and species detected. (ucc.ie)
- If you are using degenerate primers, please discuss their use with the technician beforehand. (uoguelph.ca)
- A DNA molecule of known length is sequenced from both ends. (cdc.gov)
- DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. (wikipedia.org)
- thymine (T), adenine (A), cytosine (C), and guanine (G). DNA sequencing is the determination of the physical order of these bases in a molecule of DNA. (wikipedia.org)
- Robert Holley and his team in Cornell University was believed to be the first to sequence RNA molecule. (wikipedia.org)
- To construct the peptide fusion molecule, the myc epitope peptide (NH2 -EQKLISEEDLC-COOH, 20 nmol) was incubated with the SMCC-conjugated DNA (10 nmol) in 1 mL of 0.1 M KHPO4 buffer (pH 7.8) for 3 h at room temperature. (psu.edu)
- The correct detection of mitochondrial DNA (mtDNA) heteroplasmy by automated sequencing presents methodological constraints. (scicombinator.com)
- Since the prior disposable human reference sequence - hg18 - was previously used for the mitochondrial DNA primer BLAST validation, a revision of those previously published primer pairs is required. (uab.cat)
- However, if you have your primer designed with us, should there ever be a concern regarding the quality of the oligonucleotide, we will take that up with our supplier. (dnaseq.co.uk)
- A 5'-amine modified DNA oligonucleotide (5'-ACC AGC TGT GCA GGC CTC GC-3') purchased from Integrative DNA Technologies (Coralville, IA) was conjugated to the bifunctional linker 4-(maleimidomethyl)-1-cyclohexane carboxylic acid N-hydroxysuccinimide ester (SMCC, Sigma Aldrich) by combining 1 mL of SMCC (1 mg/mL) in acetonitrile with 2 mL of DNA (195 nmol) in 0.1 M KHPO4 buffer (pH 7.8). (psu.edu)
- How much DNA is in each reaction? (protocol-online.org)
- If you clean up your own sequencing reactions, this is another point that could ruin your reaction. (protocol-online.org)
- I percipitate my 10ul reaction sample by first diluting it with 90ul of sterile distiled water and 1ul Pellet paint (basically coloured dextran that helps pulls down the DNA into a nice colour pellet). (protocol-online.org)
- At these concentrations we use 1 µl template and 1 µl primer per reaction. (albany.edu)
- If you cannot achieve the stated template concentration, we can compensate by adding more template volume (up to 6 µl) per reaction, but note that we have observed a decline in sequencing quality with DNAs less than 1/4 the recommended concentration, regardless of this adjustment. (albany.edu)
- All accession numbers from the specimens, primers sequences and reaction protocols are within the paper and its Supporting Information files. (plos.org)
- This method was chosen to detect sequences with potential similarity to pXO2 because it is rapid and the reaction products can be readily sequenced. (biomedcentral.com)
- This pre-designed probe and primer set enables you to normalize the amount of sample RNA or DNA in a reaction when used with a control sample. (thermofisher.com)
- 1X ThermoPol Reaction Buffer, 200 µM each dNTP including [ 3 H]-dTTP, 15 nM primed M13 DNA. (neb.com)
- The use of fluorescently labeled primers eliminates the need for radioactively labeled nucleotides, as well as slab gel electrophoresis, and takes advantage of commonly available automated fluorescent capillary electrophoresis instruments. (nih.gov)
- Through the use of Genemapper software, the Thermo sequenase and DNasei digestion products were accurately aligned, providing a ready means to assign correct nucleotides to each peak from the DNA footprint. (nih.gov)
- 5. The method of claim 2 in which the enzymatic extension is carried out in the presence of four different terminating nucleotides, each of which terminates primer extension at a different template nucleotide and is labeled with a different, spectrally resolvable fluorescent dye, at least one of which is the energy transfer dye. (google.com)
- The series of emission signals from the acceptor fluorophores is detected, and correlated with a sequence of nucleotides that correspond to the sequence of emission signals. (freepatentsonline.com)
- Review our pre-designed, pre-synthesized offerings that are commonly used in a variety of molecular biology and genomic applications ranging from expression analyses, RNAi-based studies, epigenetic research, and next generation sequencing. (thermofisher.com)
- Next-generation sequencing (NGS) of amplicons is used in a wide variety of contexts. (cdc.gov)
- The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. (psu.edu)
- Hybridization of myc peptide fusion to the DNA capture probe was verified by 10 % native PAGE. (psu.edu)
- The genus Leptospira consists of a diverse group of pathogenic and saprophytic spirochetes, currently classified into 17 genomospecies based on DNA-DNA hybridization studies ( 25 ). (asm.org)
- Yet another thing to worry about in the insanely complicated craziness that is 16S amplicon sequencing. (microbe.net)
- Adapterama II: universal amplicon sequencing on illumina platforms (TaggiMatrix). (cdc.gov)
- In many cases, NGS amplicon sequencing remains overly expensive and inflexible, with library preparation strategies relying upon the fusion of locus-specific primers to full-length adapter sequences with a single identifying sequence or ligating adapters onto PCR products. (cdc.gov)
- Here, we describe multiple ways to use the Adapterama system and other approaches for amplicon sequencing on Illumina instruments. (cdc.gov)
- The number of sequencing reads from the amplicon pools can be adjusted, facilitating deep sequencing when required or reducing sequencing costs per sample to an economically trivial amount when deep coverage is not needed. (cdc.gov)
- This paper describes the functions implemented by barcrawl and bartab and presents a proof-of-concept case study of both programs in which barcoded rRNA primers were designed and validated by high-throughput sequencing. (biomedcentral.com)
- However, it's important to note that the primers used here were for mitochondrial 16S DNA from metazoans exclusively and not the standard 16S rRNA primers used to characterize bacteria. (microbe.net)
- Environmental sequencing as shown here differs from other molecular survey methods in that there is no need to pre-isolate the organisms of interest from soil in order to amplify their DNA. (byu.edu)
- The DNA sequences obtained from methods that do not require culturing can be identified post-hoc and placed phylogenetically as additional closely related sequences are obtained from morphologically identified conspecifics. (byu.edu)
- The DNA Sequencing Core Laboratory, with the help of outside contractors, uses biochemical methods to determine the order of nucleotide bases in a DNA sample. (nih.gov)
- 2005), Supplementary Methods for the article Genome Sequencing in Microfabricated High-Density Picolitre Reactors, Nature, vol. 437:1-34. (freepatentsonline.com)
- We detail the methods used to computationally process and interpret sequence data to inform medical or preventative action. (cdc.gov)
- Data generated from DNA extracted using the 2 extraction methods were very similar. (ucc.ie)
- The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery. (wikipedia.org)
- The first DNA sequences were obtained in the early 1970s by academic researchers using laborious methods based on two-dimensional chromatography . (wikipedia.org)
- Following the development of fluorescence -based sequencing methods with a DNA sequencer , DNA sequencing has become easier and orders of magnitude faster. (wikipedia.org)
- DNA sequencing may be used along with DNA profiling methods for forensic identification and paternity testing . (wikipedia.org)
- In sociology, sequence methods are increasingly used to study life-course and career trajectories, patterns of organizational and national development, conversation and interaction structure, and the problem of work/family synchrony. (wikipedia.org)
- Rather than using a single sequence, profile methods use a multiple sequence alignment to encode a profile which contains information about the conservation level of each residue. (wikipedia.org)
- In particular, the present invention relates to methods for the identification of species-specific DNA in a population of a different species or following contact. (google.es)
- These are short oligodeoxyribonucleotides with random base sequences (usually [d(N) and are commonly referred to as random primers or hexamers. (thermofisher.com)
- Primer walking was also the basis for the development of shotgun sequencing, which uses random primers instead of specifically chosen ones. (wikipedia.org)
- Taken together, these results show that BODIPY and BET direct DNA sequencing can accurately and precisely characterize complex mixed-base populations. (bcm.edu)
- The polyomavirus regulatory regions contain enhancer, promoter, and origin of DNA replication ( ori ) sequences that are distinct and represent unambiguous genetic markers that characterize each member. (asm.org)
- Suitability of whole-genome sequencing, whole-exome sequencing, and targeted sequencing for various applications. (cdc.gov)
- Described here is a method for the extraction, purification, and quality control of genomic DNA from the obligate biotrophic fungal pathogen, powdery mildew, for use in long-read genome sequencing. (jove.com)
- Barcodes are evaluated within the context of other sequences contained in the forward and reverse PCR primers in order to cull potentially problematic sequences (e.g., due to inhibitory homopolymers, potential hairpins or heteroduplex formation between primers). (biomedcentral.com)
- Our data provide evidence that there is a significant difference between the use of forward and reverse primers. (scicombinator.com)
- For the nested primers, I could not excluded CGs (one CG) in forward but reverse is ok but again the problem is forward primer 17bp, reverse primer 16bp long. (protocol-online.org)
- So in the 1st round of PCR I used this new forward primer and previously designed reverse primer. (protocol-online.org)
- I performed the 2nd round of PCR with previous primers, so I have used the same reverse primers for both PCRs. (protocol-online.org)
- Forward primer (contains two CGs) have both methylated and unmethylated CGs in the clones however reverse primer (containing 1 CG) has always methylated CG in the clones. (protocol-online.org)
- R, reverse primer. (cdc.gov)
- It consists of a VIC dye-labeled QSY probe plus sequence-specific forward and reverse primers. (thermofisher.com)
- The SMCC conjugated DNA was purified by reverse phase HPLC, the sample was collected, and the conjugation was verified by MALDI-MS (calculated- 6477.3 Da, observed-6465.87 Da). (psu.edu)
- These fusion primers can be used combinatorially to amplify samples within a 96-well plate (8 forward primers + 12 reverse primers yield 8 x 12 = 96 combinations), and the resulting amplicons can be pooled. (cdc.gov)
- What species and targets do you design Targeted DNA Sequencing Library Prep assay primers to? (fluidigm.com)
- Identification of DNA sequence diversity is a powerful means for assessing the species present in environmental samples. (uio.no)
- Dietary item DNA was PCR amplified from a range of species in krill stomachs for which we had no prior sequence knowledge. (uio.no)
- Environmental sequencing is valuable for performing large-scale surveys of the diversity of organisms that cannot be cultured or grown in the laboratory or when species are difficult to distinguish using phenotypic characters. (biomedcentral.com)
- Detects mature miRNA Detects human, mouse, rat, worm and other species Highly-specific sequences assure single n. (selectscience.net)
- These results suggest that the Ssa21-F3/Ssa21-R2, Spa17-F/Spa17-R, and Sgo41-F1/Sgo41-R1 primers may be useful in detecting S. sanguinis, S. parasanguinis, and S. gordonii at the species level, respectively. (bvsalud.org)
- We encourage you to review the information below prior to requesting custom primers. (dnaseq.co.uk)
- Information pertaining to these custom primers will be retained in your file and in our freezers for 1 year. (dnaseq.co.uk)
- If using your own custom primers, please see Primer Concentrations below and include with template shipment. (albany.edu)
- Custom primers should be provided at a concentration of 5 pmol/ul. (uoguelph.ca)
- Background: The time it takes to isolate individuals from environmental samples and then extract DNA from each individual is one of the problems with generating molecular data from meiofauna such as eutardigrades and bdelloid rotifers. (byu.edu)
- An increasingly popular means of increasing project throughput is by multiplexing samples during the sequencing phase. (biomedcentral.com)
- This can be achieved by covalently linking short, unique "barcode" DNA segments to genomic DNA samples, for instance through incorporation of barcode sequences in PCR primers. (biomedcentral.com)
- Two strategies are in general use for barcoding samples in preparation for high-throughput sequencing. (biomedcentral.com)
- If you have large numbers of samples to be sequenced, we offer discounted pricing for submission of samples in full 96-well plates for sequencing. (albany.edu)
- A minimum of 80 samples (template + primer) are required. (albany.edu)
- Submission of primers that are not at the requested concentration may result in a delay in the processing of your samples. (albany.edu)
- Basically the authors are concerned about template bias in a sequence-specific manner, meaning that samples with some indices will amplify better or worse than others. (microbe.net)
- However, the number of reads produced per sequencing run far exceeds the number required per sample for many applications, compelling researchers to sequence multiple samples per run in order to maximize efficiency. (microbe.net)
- The assay can be used for multiplex or singleplex PCR reactions and it is primer limited, so it can be used with samples that overexpress RNase P. For a primer-limited assay with ABY™ dye-labeled probe rather than VIC dye-labeled probe, see Cat. (thermofisher.com)
- Multiplexing with barcoded libraries leads to more cost-effective runs by permitting up to 24 samples per run (or more if combined with Tag Sequencing BC Set 25-48, Cat. (thermofisher.com)
- The performance of the panel was verified using orthogonal testing, robustness testing, and field testing with diverse canine oral swab DNA samples. (thermofisher.com)
- This service provides cycle sequencing and electrophoresis of DNA samples. (umaine.edu)
- Total DNA was extracted from the collected samples. (usda.gov)
- The primers were developed based on influenza A/H3N2 sequence worldwide from Global Initiative on Sharing All Influenza Data (GISAID) and further tested using Indonesian influenza A/H3N2 archived samples of influenza-like illness (ILI) surveillance from 2008 to 2009. (biomedcentral.com)
- mtDNA sequencing is useful in evolutionary studies, single nucleotide polymorphism (SNP) identification, and forensics. (trilinkbiotech.com)
- Since DNA is an informative macromolecule in terms of transmission from one generation to another, DNA sequencing is used in evolutionary biology to study how different organisms are related and how they evolved. (wikipedia.org)
- The forward primer is the primer that seems to give a better approximation to the real proportion of the variants. (scicombinator.com)
- I have designed BSP primers containing degenerate bases but the PCR did not work, then I decided to design one forward primer(new) outside of my region to perform a semi-nested PCR. (protocol-online.org)
- Dot-blot DNA hybridizations between pXO2 ORF fragments and total genomic DNA from AWO6 were consistent with the PCR assay results for this isolate and also revealed nine additional ORFs shared between these two bacteria. (biomedcentral.com)
- This basically extracts DNA and runs whatever natural fragments form across a gel - definitely not sequencing, but certainly cute. (slashdot.org)
- DNA sequencers and genetic analyzers are based on capillary electrophoresis, where labeled DNA fragments are electrophoretically separated by size as they migrate through a polymer. (selectscience.net)
- Primer walking is a sequencing method of choice for sequencing DNA fragments between 1.3 and 7 kilobases. (wikipedia.org)
- Such fragments are too long to be sequenced in a single sequence read using the chain termination method. (wikipedia.org)
- Barcrawl is a software program that facilitates the design of barcoded primers, for multiplexed high-throughput sequencing. (biomedcentral.com)
- High-throughput sequencing platforms now have the capacity to analyze multiple specimens in a single run. (biomedcentral.com)
- In this review, we describe several massively parallel high-throughput DNA sequencing technologies and their associated strengths, limitations, and error modes, with a focus on applications in epidemiologic research and precision medicine. (cdc.gov)
- If you want to learn more about Primer-BLAST, check out the Sequencher Connections tutorial. (genecodes.com)
- Blast this sequence against all of PDB Archive. (rcsb.org)
- BLAST searching with the selected DNA sequences retrieved related DNA sequences from different plant, including DNA sequences encoding PAs biosynthetic enzymes from the Spiraeoideae , Rosaceae , Rosales and Fabids taxa (data not shown). (biomedcentral.com)
- Design and test primers for this sequence using Primer-BLAST. (nih.gov)
- I also tried to blast my primers but methblast is under maintenance, so I found a web site http://bisearch.enzim.hu/ for blast. (protocol-online.org)
- Thus, the aim of this Short Communication is to perform an in silico BLAST test of the published disposable nine primer pairs using the new human reference sequence and to report the pertinent modifications. (uab.cat)
- Popular tools for sequence alignment include: Pair-wise alignment - BLAST Multiple alignment - ClustalW, PROBCONS, MUSCLE, MAFFT, and T-Coffee. (wikipedia.org)
- Citation Query Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: sequence dependence and pH effects. (psu.edu)
- Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: sequence dependence and pH effects. (psu.edu)
- The primers may bind with mismatches, and the amplified PCR product will have the priimer sequence, not the template sequence. (protocol-online.org)
- In addition to discriminating against base pair mismatches, DNA polymerases exhibit a high degree of selectivity for deoxyribonucleotides over ribo- or dideoxynucleotides. (rcsb.org)
- DNA sequence of the hrpS promoter as determined by automated fluorescent capillary electrophoresis. (nih.gov)
- Then again, the discovery website lists a DNA stain fabricated to look like real DNA in its brief description - so if that is added to the well prior to electrophoresis you could get a pattern of bands - though this would not be from the DNA in your sample. (slashdot.org)