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.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)Molecular Probes: A group of atoms or molecules attached to other molecules or cellular structures and used in studying the properties of these molecules and structures. Radioactive DNA or RNA sequences are used in MOLECULAR GENETICS to detect the presence of a complementary sequence by NUCLEIC ACID HYBRIDIZATION.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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.DNA Probes, HLA: DNA probes specific for the human leukocyte antigen genes, which represent the major histocompatibility determinants in humans. The four known loci are designated as A, B, C, and D. Specific antigens are identified by a locus notation and number, e.g., HLA-A11. The inheritance of certain HLA alleles is associated with increased risk for certain diseases (e.g., insulin-dependent diabetes mellitus).DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Digoxigenin: 3 beta,12 beta,14-Trihydroxy-5 beta-card-20(22)-enolide. A cardenolide which is the aglycon of digoxin. Can be obtained by hydrolysis of digoxin or from Digitalis orientalis L. and Digitalis lanata Ehrh.In Situ Hybridization, Fluorescence: A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.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.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.Molecular Probe Techniques: The use of devices which use detector molecules to detect, investigate, or analyze other molecules, macromolecules, molecular aggregates, or organisms.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.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Polymorphism, 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: 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).Evaluation Studies as Topic: Studies determining the effectiveness or value of processes, personnel, and equipment, or the material on conducting such studies. For drugs and devices, CLINICAL TRIALS AS TOPIC; DRUG EVALUATION; and DRUG EVALUATION, PRECLINICAL are available.RNA Probes: RNA, usually prepared by transcription from cloned DNA, which complements a specific mRNA or DNA and is generally used for studies of virus genes, distribution of specific RNA in tissues and cells, integration of viral DNA into genomes, transcription, etc. Whereas DNA PROBES are preferred for use at a more macroscopic level for detection of the presence of DNA/RNA from specific species or subspecies, RNA probes are preferred for genetic studies. Conventional labels for the RNA probe include radioisotope labels 32P and 125I and the chemical label biotin. RNA probes may be further divided by category into plus-sense RNA probes, minus-sense RNA probes, and antisense RNA probes.Fluorescent Dyes: Agents that emit light after excitation by light. The wave length of the emitted light is usually longer than that of the incident light. Fluorochromes are substances that cause fluorescence in other substances, i.e., dyes used to mark or label other compounds with fluorescent tags.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 Probes, HPV: DNA probes specific for the identification of human papilloma virus.Biotin: A water-soluble, enzyme co-factor present in minute amounts in every living cell. It occurs mainly bound to proteins or polypeptides and is abundant in liver, kidney, pancreas, yeast, and milk.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)Genes, Bacterial: The functional hereditary units of BACTERIA.Heartwater Disease: A tick-borne septicemic disease of domestic and wild ruminants caused by EHRLICHIA RUMINANTIUM.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Nucleic Acid Probes: Nucleic acid which complements a specific mRNA or DNA molecule, or fragment thereof; used for hybridization studies in order to identify microorganisms and for genetic studies.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Chromosome Banding: Staining of bands, or chromosome segments, allowing the precise identification of individual chromosomes or parts of chromosomes. Applications include the determination of chromosome rearrangements in malformation syndromes and cancer, the chemistry of chromosome segments, chromosome changes during evolution, and, in conjunction with cell hybridization studies, chromosome mapping.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.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.X Chromosome: The female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in human and other male-heterogametic species.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.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.Ehrlichia ruminantium: A species of gram-negative bacteria in the family ANAPLASMATACEAE, that causes HEARTWATER DISEASE in ruminants.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.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.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.In Situ Hybridization: A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.Y Chromosome: The male sex chromosome, being the differential sex chromosome carried by half the male gametes and none of the female gametes in humans and in some other male-heterogametic species in which the homologue of the X chromosome has been retained.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Karyotyping: Mapping of the KARYOTYPE of a cell.Luminescent Measurements: Techniques used for determining the values of photometric parameters of light resulting from LUMINESCENCE.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).Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Shiga Toxin 1: A toxin produced by certain pathogenic strains of ESCHERICHIA COLI such as ESCHERICHIA COLI O157. It is closely related to SHIGA TOXIN produced by SHIGELLA DYSENTERIAE.Electrophoresis, Agar Gel: Electrophoresis in which agar or agarose gel is used as the diffusion medium.DNA, Recombinant: Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.Reagent Kits, Diagnostic: Commercially prepared reagent sets, with accessory devices, containing all of the major components and literature necessary to perform one or more designated diagnostic tests or procedures. They may be for laboratory or personal use.Chromosome Aberrations: Abnormal number or structure of chromosomes. Chromosome aberrations may result in CHROMOSOME DISORDERS.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)Bacteriological Techniques: Techniques used in studying bacteria.Bacterial Toxins: Toxic substances formed in or elaborated by bacteria; they are usually proteins with high molecular weight and antigenicity; some are used as antibiotics and some to skin test for the presence of or susceptibility to certain diseases.Chromosome Deletion: Actual loss of portion of a chromosome.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, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Sex Chromosome Aberrations: Abnormal number or structure of the SEX CHROMOSOMES. Some sex chromosome aberrations are associated with SEX CHROMOSOME DISORDERS and SEX CHROMOSOME DISORDERS OF SEX DEVELOPMENT.Genetic Linkage: The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.ArchivesDNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)Diarrhea: An increased liquidity or decreased consistency of FECES, such as running stool. Fecal consistency is related to the ratio of water-holding capacity of insoluble solids to total water, rather than the amount of water present. Diarrhea is not hyperdefecation or increased fecal weight.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.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.Chromosomes, Human, Pair 1: A specific pair of human chromosomes in group A (CHROMOSOMES, HUMAN, 1-3) of the human chromosome classification.DNA, Satellite: Highly repetitive DNA sequences found in HETEROCHROMATIN, mainly near centromeres. They are composed of simple sequences (very short) (see MINISATELLITE REPEATS) repeated in tandem many times to form large blocks of sequence. Additionally, following the accumulation of mutations, these blocks of repeats have been repeated in tandem themselves. The degree of repetition is on the order of 1000 to 10 million at each locus. Loci are few, usually one or two per chromosome. They were called satellites since in density gradients, they often sediment as distinct, satellite bands separate from the bulk of genomic DNA owing to a distinct BASE COMPOSITION.Cytotoxins: Substances that are toxic to cells; they may be involved in immunity or may be contained in venoms. These are distinguished from CYTOSTATIC AGENTS in degree of effect. Some of them are used as CYTOTOXIC ANTIBIOTICS. The mechanism of action of many of these are as ALKYLATING AGENTS or MITOSIS MODULATORS.Interphase: The interval between two successive CELL DIVISIONS during which the CHROMOSOMES are not individually distinguishable. It is composed of the G phases (G1 PHASE; G0 PHASE; G2 PHASE) and S PHASE (when DNA replication occurs).Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Aneuploidy: The chromosomal constitution of cells which deviate from the normal by the addition or subtraction of CHROMOSOMES, chromosome pairs, or chromosome fragments. In a normally diploid cell (DIPLOIDY) the loss of a chromosome pair is termed nullisomy (symbol: 2N-2), the loss of a single chromosome is MONOSOMY (symbol: 2N-1), the addition of a chromosome pair is tetrasomy (symbol: 2N+2), the addition of a single chromosome is TRISOMY (symbol: 2N+1).Carbocyanines: Compounds that contain three methine groups. They are frequently used as cationic dyes used for differential staining of biological materials.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.Spectrometry, Fluorescence: Measurement of the intensity and quality of fluorescence.Campylobacter: A genus of bacteria found in the reproductive organs, intestinal tract, and oral cavity of animals and man. Some species are pathogenic.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Peptide Nucleic Acids: DNA analogs containing neutral amide backbone linkages composed of aminoethyl glycine units instead of the usual phosphodiester linkage of deoxyribose groups. Peptide nucleic acids have high biological stability and higher affinity for complementary DNA or RNA sequences than analogous DNA oligomers.Feces: Excrement from the INTESTINES, containing unabsorbed solids, waste products, secretions, and BACTERIA of the DIGESTIVE SYSTEM.Mycobacterium avium Complex: A complex that includes several strains of M. avium. M. intracellulare is not easily distinguished from M. avium and therefore is included in the complex. These organisms are most frequently found in pulmonary secretions from persons with a tuberculous-like mycobacteriosis. Strains of this complex have also been associated with childhood lymphadenitis and AIDS; M. avium alone causes tuberculosis in a variety of birds and other animals, including pigs.Hybrid Cells: Any cell, other than a ZYGOTE, that contains elements (such as NUCLEI and CYTOPLASM) from two or more different cells, usually produced by artificial CELL FUSION.Biosensing Techniques: Any of a variety of procedures which use biomolecular probes to measure the presence or concentration of biological molecules, biological structures, microorganisms, etc., by translating a biochemical interaction at the probe surface into a quantifiable physical signal.Colorimetry: Any technique by which an unknown color is evaluated in terms of standard colors. The technique may be visual, photoelectric, or indirect by means of spectrophotometry. It is used in chemistry and physics. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)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.Deoxyribonucleases, Type II Site-Specific: Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 3.1.21.4.Deoxyuracil Nucleotides: Uracil nucleotides which contain deoxyribose as the sugar moiety.Translocation, Genetic: A type of chromosome aberration characterized by CHROMOSOME BREAKAGE and transfer of the broken-off portion to another location, often to a different chromosome.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.Porphyromonas endodontalis: A species of gram-negative bacteria in the genus PORPHYROMONAS, family Porphyromonadaceae. It is a key pathogen in endodontic infections.Nontuberculous Mycobacteria: So-called atypical species of the genus MYCOBACTERIUM that do not cause tuberculosis. They are also called tuberculoid bacilli, i.e.: M. buruli, M. chelonae, M. duvalii, M. flavescens, M. fortuitum, M. gilvum, M. gordonae, M. intracellulare (see MYCOBACTERIUM AVIUM COMPLEX;), M. kansasii, M. marinum, M. obuense, M. scrofulaceum, M. szulgai, M. terrae, M. ulcerans, M. xenopi.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.Bacteroides: A genus of gram-negative, anaerobic, rod-shaped bacteria. Its organisms are normal inhabitants of the oral, respiratory, intestinal, and urogenital cavities of humans, animals, and insects. Some species may be pathogenic.Smegma: A foul-smelling accumulation of SEBUM and desquaminated epidermal cells, especially the cheesy substance found under the foreskin of the penis and at the base of the labia minor near the clitoris.Serotyping: Process of determining and distinguishing species of bacteria or viruses based on antigens they share.Deoxyribonuclease EcoRI: One of the Type II site-specific deoxyribonucleases (EC 3.1.21.4). It recognizes and cleaves the sequence G/AATTC at the slash. EcoRI is from E coliRY13. Several isoschizomers have been identified. EC 3.1.21.-.Fluorescence: The property of emitting radiation while being irradiated. The radiation emitted is usually of longer wavelength than that incident or absorbed, e.g., a substance can be irradiated with invisible radiation and emit visible light. X-ray fluorescence is used in diagnosis.Escherichia coli Infections: Infections with bacteria of the species ESCHERICHIA COLI.Mycobacterium: A genus of gram-positive, aerobic bacteria. Most species are free-living in soil and water, but the major habitat for some is the diseased tissue of warm-blooded hosts.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.Aneugens: Agents which affect CELL DIVISION and the MITOTIC SPINDLE APPARATUS resulting in the loss or gain of whole CHROMOSOMES, thereby inducing an ANEUPLOIDY.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.Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.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, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Bacterial Proteins: Proteins found in any species of bacterium.Chromosomes, Human: Very long DNA molecules and associated proteins, HISTONES, and non-histone chromosomal proteins (CHROMOSOMAL PROTEINS, NON-HISTONE). Normally 46 chromosomes, including two sex chromosomes are found in the nucleus of human cells. They carry the hereditary information of the individual.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.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).Chromosomes, Human, Pair 7: A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.Enterotoxins: Substances that are toxic to the intestinal tract causing vomiting, diarrhea, etc.; most common enterotoxins are produced by bacteria.AcridinesChromosomes: In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Nucleic Acid Amplification Techniques: Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.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.Mycobacterium avium: A bacterium causing tuberculosis in domestic fowl and other birds. In pigs, it may cause localized and sometimes disseminated disease. The organism occurs occasionally in sheep and cattle. It should be distinguished from the M. avium complex, which infects primarily humans.Cosmids: Plasmids containing at least one cos (cohesive-end site) of PHAGE LAMBDA. They are used as cloning vehicles.DNA, Neoplasm: DNA present in neoplastic tissue.Kinetics: The rate dynamics in chemical or physical systems.Streptavidin: A 60-kDa extracellular protein of Streptomyces avidinii with four high-affinity biotin binding sites. Unlike AVIDIN, streptavidin has a near neutral isoelectric point and is free of carbohydrate side chains.Centromere: The clear constricted portion of the chromosome at which the chromatids are joined and by which the chromosome is attached to the spindle during cell division.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.Collodion: A nitrocellulose solution in ether and alcohol. Collodion has a wide range of uses in industry including applications in the manufacture of photographic film, in fibers, in lacquers, and in engraving and lithography. In medicine it is used as a drug solvent and a wound sealant.Avidin: A specific protein in egg albumin that interacts with BIOTIN to render it unavailable to mammals, thereby producing biotin deficiency.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.Gonorrhea: Acute infectious disease characterized by primary invasion of the urogenital tract. The etiologic agent, NEISSERIA GONORRHOEAE, was isolated by Neisser in 1879.Europium: Europium. An element of the rare earth family of metals. It has the atomic symbol Eu, atomic number 63, and atomic weight 152. Europium is used in the form of its salts as coatings for cathode ray tubes and in the form of its organic derivatives as shift reagents in NMR spectroscopy.Cytogenetics: A subdiscipline of genetics which deals with the cytological and molecular analysis of the CHROMOSOMES, and location of the GENES on chromosomes, and the movements of chromosomes during the CELL CYCLE.Deoxyribonuclease BamHI: One of the Type II site-specific deoxyribonucleases (EC 3.1.21.4). It recognizes and cleaves the sequence G/GATCC at the slash. BamHI is from Bacillus amyloliquefaciens N. Numerous isoschizomers have been identified. EC 3.1.21.-.Heterozygote Detection: Identification of genetic carriers for a given trait.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.

Telomeric repeats on small polydisperse circular DNA (spcDNA) and genomic instability. (1/5773)

Small polydisperse circular DNA (spcDNA) is a heterogeneous population of extrachromosomal circular molecules present in a large variety of eukaryotic cells. Elevated amounts of total spcDNA are related to endogenous and induced genomic instability in rodent and human cells. We suggested spcDNA as a novel marker for genomic instability, and speculated that spcDNA might serve as a mutator. In this study, we examine the presence of telomeric sequences on spcDNA. We report for the first time the appearance of telomeric repeats in spcDNA molecules (tel-spcDNA) in rodent and human cells. Restriction enzyme analysis indicates that tel-spcDNA molecules harbor mostly, if not exclusively, telomeric repeats. In rodent cells, tel-spcDNA levels are higher in transformed than in normal cells and are enhanced by treatment with carcinogen. Tel-spcDNA is also detected in some human tumors and cell lines, but not in others. We suggest, that its levels in human cells may be primarily related to the amount of the chromosomal telomeric sequences. Tel-spcDNA may serve as a unique mutator, through specific mechanisms related to the telomeric repeats, which distinguish it from the total heterogeneous spcDNA population. It may affect telomere dynamics and genomic instability by clastogenic events, alterations of telomere size and sequestration of telomeric proteins.  (+info)

Polynucleotide probes that target a hypervariable region of 16S rRNA genes to identify bacterial isolates corresponding to bands of community fingerprints. (2/5773)

Temperature gradient gel electrophoresis (TGGE) is well suited for fingerprinting bacterial communities by separating PCR-amplified fragments of 16S rRNA genes (16S ribosomal DNA [rDNA]). A strategy was developed and was generally applicable for linking 16S rDNA from community fingerprints to pure culture isolates from the same habitat. For this, digoxigenin-labeled polynucleotide probes were generated by PCR, using bands excised from TGGE community fingerprints as a template, and applied in hybridizations with dot blotted 16S rDNA amplified from bacterial isolates. Within 16S rDNA, the hypervariable V6 region, corresponding to positions 984 to 1047 (Escherichia coli 16S rDNA sequence), which is a subset of the region used for TGGE (positions 968 to 1401), best met the criteria of high phylogenetic variability, required for sufficient probe specificity, and closely flanking conserved priming sites for amplification. Removal of flanking conserved bases was necessary to enable the differentiation of closely related species. This was achieved by 5' exonuclease digestion, terminated by phosphorothioate bonds which were synthesized into the primers. The remaining complementary strand was removed by single-strand-specific digestion. Standard hybridization with truncated probes allowed differentiation of bacteria which differed by only two bases within the probe target site and 1.2% within the complete 16S rDNA. However, a truncated probe, derived from an excised TGGE band of a rhizosphere community, hybridized with three phylogenetically related isolates with identical V6 sequences. Only one of the isolates comigrated with the excised band in TGGE, which was shown to be due to identical sequences, demonstrating the utility of a combined TGGE and V6 probe approach.  (+info)

The role of interleukin 12 in the development of atherosclerosis in ApoE-deficient mice. (3/5773)

The cytokine profile of atherosclerotic aortas from apoE-deficient mice was assessed by reverse transcriptase-polymerase chain reaction. The results clearly showed that the expression of mRNA for IL-12p40 was evident in aortas from 3-month-old apoE-deficient mice. The mRNA for IL-10 was detected in aorta from these mice at the age of 6 months, indicating that expression of IL-12 is earlier than that of IL-10 in these animals. Concurrent with IL-12p40, the mRNA for the T-cell cytokine IFN-gamma, but not IL-4, was detected in aortas of mice at young and old ages. Both in situ hybridization and immunostaining further demonstrated the localization of IL-12 in macrophages of atherosclerotic lesions. Immunohistochemistry also demonstrated the expression of costimulatory molecules B7-1 and B7-2 in macrophages, suggesting that activation of T lymphocytes by macrophages may occur via surface antigens in lesions. When the immunoglobulin isotype of the antioxidized LDL antibodies in sera of apoE-deficient mice was determined, it revealed that both IgM and IgG were present. Furthermore, IgG2a is predominant and comprises approximately 50% of the antioxidized LDL IgG in sera from young mice (3 months), but decreased to lower levels (35%) in older mice (6 months). Daily administration of IL-12 led to an increase in serum levels of antioxidized LDL antibodies and accelerated atherosclerosis in young apoE-deficient mice compared with control mice injected with PBS alone. Taken together, these data suggest that IL-12 plays an active role in regulating the immune response during the early phase of atherosclerosis in apoE-deficient mice.  (+info)

Species identification and strain differentiation of dermatophyte fungi by analysis of ribosomal-DNA intergenic spacer regions. (4/5773)

Restriction fragment length polymorphisms (RFLPs) identified in the ribosomal-DNA (rDNA) repeat were used for molecular strain differentiation of the dermatophyte fungus Trichophyton rubrum. The polymorphisms were detected by hybridization of EcoRI-digested T. rubrum genomic DNAs with a probe amplified from the small-subunit (18S) rDNA and adjacent internal transcribed spacer (ITS) regions. The rDNA RFLPs mapped to the nontranscribed spacer (NTS) region of the rDNA repeat and appeared similar to those caused by short repetitive sequences in the intergenic spacers of other fungi. Fourteen individual RFLP patterns (DNA types A to N) were recognized among 50 random clinical isolates of T. rubrum. A majority of strains (19 of 50 [38%]) were characterized by one RFLP pattern (DNA type A), and four types (DNA types A to D) accounted for 78% (39 of 50) of all strains. The remaining types (DNA types E to N) were represented by one or two isolates only. A rapid and simple method was also developed for molecular species identification of dermatophyte fungi. The contiguous ITS and 5.8S rDNA regions were amplified from 17 common dermatophyte species by using the universal primers ITS 1 and ITS 4. Digestion of the amplified ITS products with the restriction endonuclease MvaI produced unique and easily identifiable fragment patterns for a majority of species. However, some closely related taxon pairs, such as T. rubrum-T. soudanense and T. quinkeanum-T. schoenlenii could not be distinguished. We conclude that RFLP analysis of the NTS and ITS intergenic regions of the rDNA repeat is a valuable technique both for molecular strain differentiation of T. rubrum and for species identification of common dermatophyte fungi.  (+info)

Identification of Mycobacterium kansasii by using a DNA probe (AccuProbe) and molecular techniques. (5/5773)

The newly formulated Mycobacterium kansasii AccuProbe was evaluated, and the results obtained with the new version were compared to the results obtained with the old version of this test by using 116 M. kansasii strains, 1 Mycobacterium gastri strain, and 19 strains of several mycobacterial species. The sensitivity of this new formulation was 97.4% and the specificity was 100%. Still, three M. kansasii strains were missed by this probe. To evaluate the variability within the species, genetic analyses of the hsp65 gene, the spacer sequence between the 16S and 23S rRNA genes, and the 16S rRNA gene of several M. kansasii AccuProbe-positive strains as well as all AccuProbe-negative strains were performed. Genetic analyses of the one M. gastri strain from the comparative assay and of two further M. gastri strains were included because of the identity of the 16S rRNA gene in M. gastri to that in M. kansasii. The data confirmed the genetic heterogeneity of M. kansasii. Furthermore, a subspecies with an unpublished hsp65 restriction pattern and spacer sequence was described. The genetic data indicate that all M. kansasii strains missed by the AccuProbe test belong to one subspecies, the newly described subspecies VI, as determined by the hsp65 restriction pattern and the spacer sequence. Since the M. kansasii strains that are missed are rare and all M. gastri strains are correctly negative, the new formulated AccuProbe provides a useful tool for the identification of M. kansasii.  (+info)

Development and characterization of complex DNA fingerprinting probes for the infectious yeast Candida dubliniensis. (6/5773)

Using a strategy to clone large genomic sequences containing repetitive elements from the infectious yeast Candida dubliniensis, the three unrelated sequences Cd1, Cd24, and Cd25, with respective molecular sizes of 15,500, 10,000, and 16,000 bp, were cloned and analyzed for their efficacy as DNA fingerprinting probes. Each generated a complex Southern blot hybridization pattern with endonuclease-digested genomic DNA. Cd1 generated an extremely variable pattern that contained all of the bands of the pattern generated by the repeat element RPS of Candida albicans. We demonstrated that Cd1 does not contain RPS but does contain a repeat element associated with RPS throughout the C. dubliniensis genome. The Cd1 pattern was the least stable over time both in vitro and in vivo and for that reason proved most effective in assessing microevolution. Cd24, which did not exhibit microevolution in vitro, was highly variable in vivo, suggesting in vivo-dependent microevolution. Cd25 was deemed the best probe for broad epidemiological studies, since it was the most stable over time, was the only truly C. dubliniensis-specific probe of the three, generated the most complex pattern, was distributed throughout all C. dubliniensis chromosomes, and separated a worldwide collection of 57 C. dubliniensis isolates into two distinct groups. The presence of a species-specific repetitive element in Cd25 adds weight to the already substantial evidence that C. dubliniensis represents a bona fide species.  (+info)

Molecular evidence for the existence of additional members of the order Chlamydiales. (7/5773)

Respiratory tract infections in man may be caused by several members of the genus Chlamydia and also by two Chlamydia-like strains, 'Simkania negevensis' (Z-agent) and 'Parachlamydia acanthamoebae' (Bng). To facilitate diagnostic procedures a PCR assay able to detect all known Chlamydiaceae sequences in one reaction was developed. For this purpose, primers were selected to amplify a fragment of the 16S rRNA gene. Characterization of the amplified fragments was done by hybridization with specific probes and by sequencing. PCR assays were carried out using DNA isolated from nose/throat specimens or from peripheral blood mononuclear cells of patients with respiratory tract infections, and from vessel wall specimens of abdominal aneurysms. Six of the 42 nose/throat swab specimens analysed yielded strong bands and one yielded a faint band. Three of these bands were identified as Chlamydia pneumoniae and one as Chlamydia trachomatis by sequencing. Analysis of the three other bands yielded two different new sequences. DNA isolated from peripheral blood mononuclear cells of one patient yielded a third new sequence. DNA isolated from peripheral blood mononuclear cells of four healthy controls was negative. One of the abdominal aneurysm specimens also yielded a strong band. Sequencing revealed a fourth new sequence. All negative controls included during specimen processing and PCR analysis remained negative. The typical secondary structure of microbial 16S genes was present in all four new sequences indicating the validity of the sequence data. All four new sequences were distinct from other bacteria and clustered together with known Chlamydiaceae sequences. Phylogenetic analysis suggested a new lineage, separating the four new sequences, 'S. negevensis' and 'P. acanthamoebae' from the genus Chlamydia with the four known chlamydial species. In conclusion, this study provides evidence for the existence of several new members of the order Chlamydiales. Since the source of the Chlamydia-like strains has not been identified and serological and/or molecular cross-reactivities may be expected, results of identification of infecting recognized organisms should be interpreted cautiously.  (+info)

Preimplantation diagnosis by fluorescence in situ hybridization using 13-, 16-, 18-, 21-, 22-, X-, and Y-chromosome probes. (8/5773)

PURPOSE: Our purpose was to select the proper chromosomes for preimplantation diagnosis based on aneuploidy distribution in abortuses and to carry out a feasibility study of preimplantation diagnosis for embryos using multiple-probe fluorescence in situ hybridization (FISH) on the selected chromosomes of biopsied blastomeres. METHODS: After determining the frequency distribution of aneuploidy found in abortuses, seven chromosomes were selected for FISH probes. Blastomeres were obtained from 33 abnormal or excess embryos. The chromosome complements of both the biopsied blastomeres and the remaining sibling blastomeres in each embryo were determined by FISH and compared to evaluate their preimplantation diagnostic potential. RESULTS: Chromosomes (16, 22, X, Y) and (13, 18, 21) were selected on the basis of the high aneuploid prevalence in abortuses for the former group and the presence of trisomy in the newborn for the latter. Thirty-six (72%) of 50 blastomeres gave signals to permit a diagnosis. Diagnoses made from biopsied blastomeres were consistent with the diagnoses made from the remaining sibling blastomeres in 18 embryos. In only 2 of 20 cases did the biopsied blastomere diagnosis and the embryo diagnosis not match. CONCLUSIONS: If FISH of biopsied blastomere was successful, a preimplantation diagnosis could be made with 10% error. When a combination of chromosome-13, -16, -18, -21, -22, -X, and -Y probes was used, up to 65% of the embryos destined to be aborted could be detected.  (+info)

  • Mixtures of fluorophore-encoded probes show integrin mechanical preference for cyclized RGD over linear RGD peptides. (nih.gov)
  • DNA-based digital tension probes(a) Theoretical plot showing the expected increase in fluorescence signal asa function of applied force for the 100% and 22% GC-content hairpin probesand the PEG-based tension probe. (nih.gov)
  • DNA-hairpin tension probe response was obtained byfitting into a two-state Boltzmann distribution. (nih.gov)
  • To this end, we report a new class of molecular tension probes that employs aDNA-hairpin as a "switch" element, thus unfolding at a threshold force andreporting tension in a digital rather than analog fashion (Fig.1a). (nih.gov)
  • Probes weredesigned to be highly adaptable, consisting of three oligonucleotides assembled throughhybridization of 21-mer handles (Fig. 1b): a stem-loopDNA hairpin that is unmodified (black), a peptide-displaying ligand strand conjugated to afluorophore (green), and a surface-anchor strand that is tagged with a quencher (blue). (nih.gov)
  • The one end (5') of the probe contains a fluorophore while the other end (3') contains the quencher molecule which is in close proximity of the fluorophore. (geneticeducation.co.in)
  • To measure these changes in real time, the researchers anchored fluorescent-labeled DNA molecules to electrodes on the gold surface of the TUM platform, and applied an electric field to orient the fluorophores in a well-ordered manner conducive to effective detection of conformational changes. (bu.edu)
  • Pyrene binary probes for unambiguous detection of mRNA using time-resolved fluorescence spectroscopy," Nucleic Acids Research , vol. 34, no. 10, pp. 3161-3168, 2006. (hindawi.com)
  • Detection of nucleic acids in situ: novel oligonucleotide analogues for target-assembled DNA-mounted exciplexes," Organic and Biomolecular Chemistry , vol. 5, no. 7, pp. 1039-1051, 2007. (hindawi.com)
  • 1989. Detection of rotavirus by hybridization with a nonradioactive synthetic DNA probe and comparison with commercial enzyme immunoassays and silver stained Polyacrylamide gels. (springer.com)
  • Detection of enterotoxigenic Escherichia coli by dot blot hybridization with biotinylated DNA probes. (springer.com)
  • These probes, coupled with changes in the chromosome-preparation procedure that improve fluorescent signal detection, allowed the development of a FISH karyotyping method that is effective on all tested maize lines. (pnas.org)
  • With a sandwich immunoassay, one DNA-derived magnetic nanoprobe, simplified as DNA/(ZMPs-HRP-AFP Ab 2 ) n , was employed for the detection of AFP. (hindawi.com)
  • In areas where histoplasmosis is not endemic, including Taiwan, serologic tests, antigen detection reagents, and specific DNA probes for diagnosis of histoplasmosis are not universally available. (thefreedictionary.com)
  • The spectroscopic measurements in the presence of well matched and mismatched DNA support the notion that our systems are interesting probes for mismatch detection and signaling. (caltech.edu)
  • A DNA probe for the specific detection and identification of Streptococcus oralis was isolated from HindII-digested DNA of S. oralis NCTC 11427 and cloned in Escherichia coli. (asm.org)
  • Finally, the probe complexes were reconfigured to act as AND-gates for the detection of co-localized proteins. (rice.edu)
  • A commercial DNA probe kit (Gen-probe) for the detection of rRNA from legionellae was evaluated for its accuracy in diagnosing Legionnaires' disease in 167 patients with pneumonia. (nih.gov)
  • Here, the volume-amplified magnetic nanobead detection assay (VAM-NDA) is for the first time applied for detection of rolling circle amplified (RCA) DNA molecules in a portable, commercial AC susceptometer that operates at ambient temperatures and with an analysis time of about 20 min. (diva-portal.org)
  • The findings show that the VAM-NDA holds promise for future wide-spread implementation in commercial AC susceptometer setups thus opening up for the possibility to perform magnetic bead-based DNA detection in point-of-care and outpatient settings. (diva-portal.org)
  • This thesis describes a new approach to biomolecular analysis, called the volume-amplified magnetic nanobead detection assay (VAM-DNA). (diva-portal.org)
  • Detection of plasmid-mediated beta-lactamases with DNA probes. (asm.org)
  • The limits of detection and quantification were 7 and 100 DNA copies for calibration standards and T. bryosalmonae was reliably detected down to 100 copies in tissue and eDNA samples. (usgs.gov)
  • Gene detection using immobilized DNA probes (PhD thesis). (wikipedia.org)
  • Transcription factor proteins, nucleosomes and other DNA-binding molecules may bend DNA and bring distant segments of DNA into close proximity, thereby causing genes to turn on or off. (bu.edu)
  • Since this intensity increases with height above the gold surface, the researchers could deduce any resulting height changes in segments of the DNA molecules-and thus pinpoint corresponding changes in their shape. (bu.edu)
  • When you introduce a protein in solution, the protein will bind to the DNA and change its shape, resulting in a change in the spectral signature we observe from the fluorescent molecules attached to the DNA," said Ünlü. (bu.edu)
  • In the National Science Foundation study, Spuhler introduced a protein called E. Coli Integration Host Factor (IHF) that can bend DNA molecules by as much as 180 degrees, and observed protein-induced bending upon the binding of IHF to the dsDNA probes. (bu.edu)
  • They aim to eventually use SSFM to analyze different protein-DNA interactions and to identify and characterize specific proteins that induce considerable shape changes in DNA molecules. (bu.edu)
  • Exchange-PAINT, a recently developed DNA-based multiplexing approach, in theory facilitates spectrally-unlimited multiplexing by sequentially imaging target molecules using orthogonal dye-labeled 'imager' strands. (rsc.org)
  • Nanozirconium dioxide (nano-ZrO 2 ), as a kind of Lewis acid, can be directly used to fix the antibody and enzyme through combining the carboxylic acid [ 12 , 13 ] of protein molecules with the phosphoric acid groups [ 14 ] (such as Lewis strong alkali) of DNA. (hindawi.com)
  • Lieb studies chromatin, the protein superstructure that packages DNA and controls which sections of the genome are accessible to regulatory molecules that convert the genetic code into cellular action. (unc.edu)
  • In this thesis, the structural dynamics of water molecules and counterions in the hydration shell of DNA is investigated by two-dimensional infrared (2D IR) spectroscopy and pump-probe transient spectroscopy. (hu-berlin.de)
  • QDFM is based on hybridization of non-isotopically labeled probes onto DNA molecules that were bound to a solid support and stretched homogeneously to ~2.3 kb/µm. (caltech.edu)
  • Dna are the coding molecules found in all living things on earth which contain the instructions on how to build living things. (healthtap.com)
  • The obvious induced circular dichroism signals in circular dichroism spectra reveal that the molecules can specifically interact with DNA. (spie.org)
  • Others mechanically disturb or modify short molecules and therefore do not obtain flexibility properties of unperturbed and pristine DNA. (soton.ac.uk)
  • Double-stranded DNA must disentangle itself into single strands during replication or repair to allow functional molecules to bind and perform their various operations. (nanotech-now.com)
  • The protein molecules alone are smaller in molecular size than the protein-DNA complexes, leading to a less effective steric stabilization of the nanoparticles. (nanotech-now.com)
  • The researchers next plan to combine electrical orientation of fluorescent-tagged DNA with a new optical technique developed by Unlu that uses self-interference fluorescence microscopy (SSFM) to more precisely measure the height of the fluorophores. (bu.edu)
  • 5′-Pyrene modified oligonucleotide provides a highly sensitive fluorescent probe of RNA," Nucleic Acids Research , vol. 27, no. 11, pp. 2387-2392, 1999. (hindawi.com)
  • In addition, the investigators conducted a set of imaging experiments in which they used a short stretch of DNA as a targeting molecule and a fluorescent dye as the imaging agent. (phys.org)
  • Here, dynamic DNA complexes detect a specific DNA-conjugated antibody and undergo strand displacement to liberate a quencher strand and activate a fluorescent reporter. (rice.edu)
  • Zelenin, A. 2004-10-16 00:00:00 To estimate the possibility of plant genome mapping using human genome probes, the probes fluorescent in situ hybridization (FISH) of human 18S-28S rDNA (clon 22F9 from the LA-13NCO1 library) was carried out on chromosomes of the spring barleyHordeum vulgareL. (deepdyve.com)
  • By merging two powerful sequencing-based assays with a machine learning-based tool, a research team led by Xinchen Wang and associate members Melina Claussnitzer and Manolis Kellis in the Broad's Metabolism and Epigenomics programs, respectively, have engineered a powerful new approach for measuring individual noncoding DNA segments' ability to control gene expression, and doing so at both massive scale and high resolution. (broadinstitute.org)
  • On my medical records, it says that a test that was taken was performed using the bd probetec chlamydia trachomatis and neisseria gonorrhoeoae amplified DNA assays, does that indicate that it was a DNA probe test? (healthtap.com)
  • DNA nanotechnology has emerged as a promising technology for applications such as single molecule sensing, super-resolution imaging, and manipulating molecular components. (harvard.edu)
  • however, relative to natural biomolecular machines, the functional scope of DNA nanotechnology is limited by an inability to design dynamic mechanical behavior such as complex motion, conformational dynamics, or force generation. (harvard.edu)
  • The mechanical properties of DNA fundamentally constrain and enable the storage and transmission of genetic information and its use in DNA nanotechnology. (uni-muenchen.de)
  • Research at Western Carolina University on DNA sequencing used in crime labs has gotten a $718,000 grant from the National Institute of Justice. (smokymountainnews.com)
  • Mark Wilson, director of the Forensic Science Program at WCU, has been evaluating new DNA sequencing instrumentation for use in crime laboratories. (smokymountainnews.com)
  • The grant will not only support the research but also provides scholarships for three graduate students working on related projects to help with the work, which builds on previous DNA sequencing done at WCU. (smokymountainnews.com)
  • Here we describe the analysis of sequencing data using the multiple window high-resolution DNA-SIP method (MW-HR-SIP). (springer.com)
  • It suggests principal opportunity for the FISH mapping of plant genomes using probes from human genome libraries, obtained in the course of the total sequencing of the human genomes and corresponding to the coding regions of genes with known functions. (deepdyve.com)
  • V. A. Efimov, A. A. Buryakova, S. V. Reverdatto, and O. G. Chekhmakhcheva, "Use of N-methylimidazolide phosphotriester method for the synthesis of oligonucleotides useful in recombinant DNA studies," Russian Journal of Bioorganic Chemistry , vol. 9, no. 10, pp. 1376-1381, 1983. (hindawi.com)
  • Herein, we present a mechanoselection strategy that uses locking oligonucleotides to preferentially and irreversibly bind DNA probes that are mechanically strained over probes at rest. (pnas.org)
  • Upon addition of unlocking oligonucleotides that drive toehold-mediated strand displacement, the probes reset to the real-time state, thereby erasing stored mechanical information. (pnas.org)
  • DNA aptamers are synthetic, single-stranded DNA oligonucleotides selectedby SELEX methods for their binding with specific ligands. (mdpi.com)
  • The constant oligonucleotides with internal aminated dT were used to capture and immobilize the target oligonucleotides onto the solid surface, and also to provide a primer for later enzymatic extension reactions, while target oligonucleotides took the role of harbouring DNA-binding sites of DNA-binding proteins. (mdpi.com)
  • These cyanine probes show high binding affinity to oligonucleotides but different binding preferences to various secondary structures. (spie.org)
  • Burgeoning Molecular Diagnostics Market Propels the Global DNA Probes-Based Diagnostics Market, According to New Report by Global Industry Analysts, Inc. (prweb.com)
  • GIA announces the release of a comprehensive global report on DNA Probe-Based Diagnostics markets. (prweb.com)
  • The global market for DNA Probe-Based Diagnostics is forecast to reach US$30 billion by the year 2017, driven by the rapidly expanding molecular diagnostics market. (prweb.com)
  • Growth in the marketplace is also expected to stem from affluent population and widening health insurance as well as medical reimbursements, which are making expensive cutting edge diagnostic tools such as DNA-based diagnostics increasingly affordable. (prweb.com)
  • And given the need to rapidly and inexpensively determine the relevant DNA sequence information in a given organism, the potential of DNA probes-based diagnostics is huge. (prweb.com)
  • Also, the boom in the molecular diagnostics market is beginning to echo downstream into the DNA-probe based diagnostics segment. (prweb.com)
  • Further, affluent population and widening health insurance and medical reimbursements are additionally making expensive cutting edge diagnostic tools, such as DNA-based diagnostics, increasingly affordable. (prweb.com)
  • The US represents the largest regional market for DNA Probe-Based Diagnostics market worldwide, as stated by the new market research report on DNA Probes-Based Diagnostics . (prweb.com)
  • In the US, the rapid growth of DNA-based diagnostics is leading to the development of new tests for the treatment of non-contagious diseases, such as diseases related to aging or chronic diseases. (prweb.com)
  • Infectious Diseases represents the key end-use market for DNA probes-based diagnostics worldwide. (prweb.com)
  • The research report titled "DNA Probes-Based Diagnostics: A Global Strategic Business Report" announced by Global Industry Analysts Inc., provides a comprehensive review of the DNA probe-based diagnostics markets, current market trends, key growth drivers, recent product introductions, recent industry activity, and profiles of major/niche global as well as regional market participants. (prweb.com)
  • The report provides annual sales estimates and projections for DNA Probe-Based Diagnostics market for the years 2009 through 2017 for the following geographic markets - US, Canada, Japan, Europe, Asia-Pacific and Latin America. (prweb.com)
  • This econometric study covers the world outlook for DNA probes-based diagnostics across more than 200 countries. (marketresearch.com)
  • This study gives, however, my estimates for the worldwide latent demand, or the P.I.E. for DNA probes-based diagnostics. (marketresearch.com)
  • Reportlinker Adds Molecular Diagnostics Market: DNA Probes and Biochips -- New Product Development Opportunities and Business Expansion Strategies for Instrument and Reagent. (bio-medicine.org)
  • In order to successfully capitalize on the opportunities presented by the molecular diagnostics market, many companies are already exploiting new DNA probe and biochip technologies as corporate strategic assets, managed in support of business and marketing strategies. (bio-medicine.org)
  • Such broadly homologous probes offer advantages over more narrowly specific probes for detecting organisms whose identity is unknown. (nih.gov)
  • Specific probes for H . capsulatum , B . dermatitidis , C . immitis , P . brasiliensis , P . marneffei , S . schenckii , C . neoformans , and P . carinii hybridized with homologous but not heterologous DNA. (asm.org)
  • Using primers that are 9-mer and longer and exonuclease-free enzyme results in higher labeling efficiency and longer probes. (clontech.com)
  • beta-Lactamase identification by colony hybridization with 32P-labeled DNA probes for TEM-1, SHV-1, OXA-1, OXA-2, PSE-1, PSE-2, and PSE-4 was compared with isoelectric focusing in 122 clinical isolates making a variety of enzyme types. (asm.org)
  • All strains producing a probe-type enzyme gave a positive hybridization reaction. (asm.org)
  • The report on "Global DNA Probe-based Diagnostic Market" is a professional report which provides thorough knowledge along with complete information pertaining to the DNA Probe-based Diagnostic industry a propos classifications, definitions, applications , industry chain summary, industry policies in addition to plans, product specifications, manufacturing processes, cost structures, etc. (openpr.com)
  • The Global DNA Probe-based Diagnostic Market Research Report renders deep perception of the key regional market status of the DNA Probe-based Diagnostic Industry on a global level that primarily aims the core regions which comprises of continents like Europe, North America, and Asia and the key countries such as United States, Germany, China and Japan. (openpr.com)
  • It is a methodical research depending on the market and examines the competitive framework of the global DNA Probe-based Diagnostic Market industry. (openpr.com)
  • Players, stakeholders, and other participants in the global DNA Probe-based Diagnostic market will be able to gain the upper hand as they use the report as a powerful resource. (reportsnreports.com)
  • In a bind after a latest forensic report showed the DNA of the child delivered by a minor rape victim did not match with that of the accused, the Chandigarh Police are re-investigating the matter. (ndtv.com)
  • Here we present ethidiumbinding results for three related DNA aptamers (PDB code: 1OLD, 1DB6, and 2ARG)that bind L-argininamide (L-Arm). (mdpi.com)
  • If a laboratory today wants to test for 200 known pathogenic species, they need 200 different tests, each with its own specific DNA probe that was designed specifically to bind with DNA from a particular pathogen," said study co-author Richard Baraniuk, the lead scientist on the new study. (phys.org)
  • With compressive sensing, the disease DNA need not bind with 100 percent of the probes. (phys.org)
  • In this paper, we describe the design of probes that bind specifically to the cloning vector of DNA recombinants to facilitate physical mapping. (caltech.edu)
  • The greatest challenge in this work was to determine the optimum conditions for single-stranded DNA to bind with its binding protein to form complexes that confer the highest stability to gold nanoparticles from salt-induced aggregation," says Tan. (nanotech-now.com)
  • A flow cell which can be used in the synthesis of DNA probes on an active surface of the substrate includes a base having a central window opening and a registration surface against which the substrate may be mounted. (google.com)
  • In the present article, we review the occurrence and synthesis of small DNA circles, and examine their utility in studying the properties of DNA and DNA-protein interactions. (biochemsoctrans.org)
  • Exposure of mammalian cells to a variety of chemical and physical agents depresses the overal rate of DNA synthesis . (springer.com)
  • R. B. Painter, Effect of caffeine on DNA synthesis in irradiated and unirradiated mammalian cells, J. Mol. (springer.com)
  • P. D. Moore, K. K. Bose, S. D. Rabdkin, and B. S. Strauss, Sites of termination of in vitro DNA synthesis on ultraviolet-and N-acetylaminofluorene-treated X174 templates by prokaryotic and eukaryotic DNA polymerases, Proc. (springer.com)
  • J. E. Cleaver, G. H. Thomas, and S. D. Park, Xeroderma pigmentosum variants have a slow recovery of DNA synthesis after irradiation with ultraviolet light, Biochim. (springer.com)
  • D. Dahle, T. D. Griffiths, and J. G. Carpenter, Inhibition and recovery of DNA synthesis in UV-irradiated Chinese hamster V-79 cells, Photochem. (springer.com)
  • S. D. Park and J. E. Cleaver, Recovery of DNA synthesis after ultraviolet irradiation of Xeroderma pigmentosum cells depends on excision repair and is blocked by caffeine, Nucleic Acids Res. (springer.com)
  • Herein, we report a universal approach for the creation of DNA-barcoded labeling probes for highly multiplexed Exchange-PAINT imaging, using a variety of affinity reagents such as primary and secondary antibodies, nanobodies, and small molecule binders. (rsc.org)
  • Now researchers at Boston University's College of Engineering, the Technical University of Munich (TUM) and Nanyang Technological University in Singapore have demonstrated a new strategy to more efficiently measure protein-induced DNA shape, or conformational changes in real-time. (bu.edu)
  • The piece of DNA that the researchers chose recognizes and binds to the BRCA1 tumor suppressor gene, mutations in which increases susceptibility to developing breast cancer. (phys.org)
  • To really understand the functional geography of the noncoding genome, however, researchers need a way to isolate and characterize thousands to millions of regulatory DNA elements within it simultaneously, rapidly, and at high resolution. (broadinstitute.org)
  • By building on these approaches, HiDRA lets researchers create massive libraries of regulatory DNA and study their influence over gene expression at nucleotide-level resolution. (broadinstitute.org)
  • In addition, the team used HiDRA to examine how disease risk DNA variants in regulatory elements affect gene expression compared to variants that do not raise risk - a boon for researchers seeking to study how minute sequence variations in promoters and enhancers can impact human traits and disease states. (broadinstitute.org)
  • Rice University researchers (clockwise from left) Richard Baraniuk, Amirali Aghazadeh and Rebekah Drezek have invented a technology that could potentially identify hundreds of bacterial pathogens simply, quickly and at low cost using a single set of random DNA probes. (phys.org)
  • Writing in the Nov. 18 Proceedings of the National Academy of Sciences (PNAS), Stanford researchers described how newly created circles of synthetic DNA - called "nanocircles" - could help researchers learn more about the aging process in cells. (innovations-report.com)
  • As in many other sensing schemes, the researchers attach DNA probes to the material's surface. (thefreedictionary.com)
  • MIT researchers, led by toxicology graduate student Yelena Margolin of the Biological Engineering Division, have discovered that the DNA damage produced by one of these inflammatory chemicals, nitrosoperoxycarbonate, occurs at unexpected locations along the DNA helix. (wordpress.com)
  • For years researchers have studied how the chemicals associated with the body's response to infection can damage DNA. (wordpress.com)
  • By using comprehensive chemical screening and analysis of the frequency of DNA damage, the researchers found that a chemical produced during inflammation, nitrosoperoxycarbonate, actually caused oxidative damage at guanines that were supposed to be the least easily oxidized. (wordpress.com)
  • The researchers used the optical properties of gold nanoparticles to probe the mechanism of protein-DNA binding. (nanotech-now.com)
  • The researchers attribute binding of the nanoparticles and the DNA-protein complexes to the presence of sulphur-containing groups in the protein, which are known to create strong bonds with gold. (nanotech-now.com)
  • 3. A synthetic DNA hybridization probe as defined by claim which comprises a single sequence at least 12 nucleotides long. (google.com.au)
  • 4. A locus specific synthetic DNA probe which hybridizes at high criteria to form 100% matched duplexes with a nucleotide sequence as described by claim 1. (google.com.au)
  • These three probes, plus centromeric satellite 4 (Cent4), centromeric satellite C (CentC), knob, nucleolus-organizing region (NOR), pMTY9ER telomere-associated sequence, and tandemly repeated DNA sequence 1 (TR-1) were used as a mixture for hybridization to root-tip chromosomes. (pnas.org)
  • a labeled segment of DNA or RNA used to find a specific sequence of nucleotides in a DNA molecule. (thefreedictionary.com)
  • BHQnova is most advantageous in longer probe designs, typically those over 25 bases, to boost the signal-to-noise ratio by overcoming the upper limit on sequence length. (biosearchtech.com)
  • Tan and co-workers showed that there was a minimum length of DNA sequence under which the binding protein-DNA adhesion mechanism could operate. (nanotech-now.com)
  • They found that the binding protein had a preference for binding to specific chemical units (bases) which make up DNA, and were able to spot DNA sequence variations, called single nucleotide polymorphisms (SNPs), even at the extreme ends of the molecule which are difficult to identify. (nanotech-now.com)
  • Dynamic DNA complexes are able to undergo multiple hybridization and dissociation events through a process called strand displacement. (rice.edu)
  • Given the ability to visualize large numbers of cellular markers using dynamic DNA probe complexes, high-content proteomic analyses can be performed on a single sample, enhancing the power of fluorescence imaging techniques. (rice.edu)
  • Furthermore, dynamic DNA complexes offer new avenues to incorporate DNA-based computations and logic for in situ molecular imaging and analyses. (rice.edu)
  • Tan and co-workers discovered that when single-stranded DNA and its binding protein were both present in the solution, coupled with a salt that stimulates nanoparticle aggregation, the DNA remained red in color, indicating that the DNA-protein complexes had bound with the nanoparticles through electrosteric stabilization forces. (nanotech-now.com)
  • The binding protein can thus attach to the dissociated single-stranded DNA to form protein-DNA complexes, offering sites to which gold nanoparticles can adhere. (nanotech-now.com)
  • The license agreement grants Ikonisys a worldwide license under Abbott patents for the manufacture and sale of DNA probes in conjunction with Chromotest(TM), a revolutionary test for the prenatal diagnosis of chromosomal abnormalities using fetal cells from the maternal circulation. (thefreedictionary.com)
  • The results indicate that the examination of respiratory tract secretions by the Gen-probe kit is a suitable screening test for the diagnosis of Legionnaires' disease. (nih.gov)
  • These probes allow us to now drill down to the DNA level and see that the cause of the disease may actually be slightly different between patients with the same diagnosis. (technologynetworks.com)
  • 2017. https://www.tabers.com/tabersonline/view/Tabers-Dictionary/733335/all/DNA_probe. (tabers.com)
  • DNA Probe-based Diagnostic Market 2017-2022, has been prepared based on an in-depth market analysis with inputs from industry experts. (openpr.com)
  • Consequently, almost half of the identifications made so far have been solely on the basis of genetic testing--682 of the 1,411 named--and DNA analysis helped in the identification of 343. (latimes.com)
  • The probes are species-specific and with the use of 32 P labeling sensitive enough so that a squash blot of only a small segment of the mosquito is required for identification. (ajtmh.org)
  • Problems in the Connecticut state police crime lab delayed for at least four years the identification of a woman investigators think was killed by suspected serial killer William Devin Howell and hindered their ability to match several different samples of DNA found in Howell's van, The Courant has learned. (courant.com)
  • Construction of a DNA probe for the specific identification of Streptococcus oralis. (asm.org)
  • Wells, Robert J. 1996-12-01 00:00:00 The random amplified polymorphic DNA (RAPD) method was investigated as a potential fish species identification method. (deepdyve.com)
  • But it is likely to stir up discussions in the DNA damage and mutagenesis fields that could help us better understand the consequences of inflammation. (wordpress.com)
  • Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria. (asm.org)
  • J. D. Hall and D. W. Mount, Mechanism of DNA replication and mutagenesis in ultraviolet-irradiated bacteria and mammalian cells, Prog. (springer.com)
  • Rice University scientists have invented a technology that could potentially identify hundreds of bacterial pathogens simply, quickly and at low cost using a single set of random DNA probes. (phys.org)
  • In a paper online this week in Science Advances, Rice's research team used lab tests to verify that UMD could identify 11 known strains of bacteria using the same five random DNA probes. (phys.org)
  • The new study includes several computer simulations, including one that shows how a random selection of five probes can identify 40 different strains of bacteria, and another that demonstrates how the system can accurately differentiate between 24 different species of Staphylococcus. (phys.org)
  • No P1 lysogens of indigenous soil bacteria were detected with the DNA probe. (asm.org)
  • QY Research Groups has released a most recent report in view of industry research on DNA Probe-based Diagnostic market . (openpr.com)
  • The report cloaks the market analysis and projection of "DNA Probe-based Diagnostic Market" on a regional as well as global level. (openpr.com)
  • Distinguishing the increasing predominance of DNA Probe-based Diagnostic Market, this market research report demonstrates to be a key source of management and thorough data on the market across the globe. (openpr.com)
  • DNA Probe-based Diagnostic Market report helps to increase business/sales activities by understanding competitor's businesses better, company's strategic, business and operational performance, recognize potential partnerships and suppliers. (sbwire.com)
  • New York, NY -- ( SBWIRE ) -- 04/16/2018 -- The latest market intelligence study on DNA Probe-based Diagnostic market relies on statistics derived from the application of both primary and secondary research to present insights pertaining to the operational model, opportunities and competitive landscape of DNA Probe-based Diagnostic market for the forecast period, 2018 - 2025. (sbwire.com)
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  • What are major driving factors impacting the DNA Probe-based Diagnostic market worldwide? (sbwire.com)
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  • DNA Probe-based Diagnostic market is segmented by region (country), players, by Type, and by Application. (reportsnreports.com)
  • The DNA Probe-based Diagnostic market is analysed and market size information is provided by regions (countries). (reportsnreports.com)
  • The key regions covered in the DNA Probe-based Diagnostic market report are North America, Europe, Asia Pacific, Latin America, Middle East and Africa. (reportsnreports.com)
  • DNA Probe-based Diagnostic market competitive landscape provides details and data information by players. (reportsnreports.com)
  • Details included are company description, major business, company total revenue and the sales, revenue generated in DNA Probe-based Diagnostic business, the date to enter into the DNA Probe-based Diagnostic market, DNA Probe-based Diagnostic product introduction, recent developments, etc. (reportsnreports.com)
  • DNA can specifically combine with ZrO 2 [ 10 ], but if DNA was directly used to fix ZrO 2 to make probes, it will be very difficult to separate the probes from the free antibodies which coexist in the suspension. (hindawi.com)
  • We also applied our DNA probes to immunofluorescence imaging using DNA-conjugated antibodies and demonstrated the ability to at least double the number of detectable markers on a single sample. (rice.edu)
  • Is it possible to hav all 3 - P24 antigen, HIV antibodies & HIV DNA undetectable at 4 MONTHS of risky exposure? (healthtap.com)
  • The endorphin probe consistently labelled the rat pituitary pars intermedia which is known to be particularly rich in the corresponding mRNA. (nih.gov)
  • The identity of the major glucose-utilizers was unclear as 13 C-enriched PLFA were common (16:0, 16:1, 18:1ω7, highest incorporation) and there was little difference between 12 C- and 13 C-DNA 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) profiles. (wiley.com)
  • The new test uses DNA probes to pinpoint nucleotide variations that genetically distinguish among head blight species. (thefreedictionary.com)
  • Thermodynamics-guided probe design and empirical optimization of the reaction conditions have been used to enable the discrimination of single-nucleotide variants, but typically these approaches provide only an approximately 25-fold difference in binding affinity. (rice.edu)
  • Instead, the UMD system measures how well the disease DNA binds with each of the random probes and creates a specific binding profile for the test organism. (phys.org)
  • photoisomerization, however, appears to be inhibited for DNA-binding by cyanine, leading to a signal-on emission. (caltech.edu)
  • Both of the cyanine probes possess a symmetric structure and bis-cationic center. (spie.org)
  • In an effort that rivals the Human Genome Project, Shaler has marshaled a national network that includes the New York State Police, the FBI, six biotechnology companies, a score of DNA consultants, computer software developers and an advisory committee of 30 forensic experts that has met every eight weeks to thrash out technical issues. (latimes.com)
  • Approximately 98 percent of the human genome is made up of noncoding DNA, including enhancers, promoters, and other elements that regulate gene activity. (broadinstitute.org)
  • The need is great, as more than 90 percent of variants identified in genome-wide association studies of traits and disease are located in noncoding DNA. (broadinstitute.org)
  • The paper, titled "Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project," was authored by Lieb and other members of the model organism ENCyclopedia Of DNA Elements ( modENCODE ) Consortium, which is funded by the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health. (unc.edu)
  • It turns out that particularly important stretches of DNA in the genome are "conserved," or retained throughout evolutionary history. (unc.edu)
  • That observation overturns the prevailing theory for predicting the location of DNA damage in the genome and complicates our understanding of the basis for diseases arising from chronic inflammation," said Dedon. (wordpress.com)
  • He will discuss their fundamental work to design and characterize nanostructures with controllable dynamic behavior and two applications that focus on implementing dynamic DNA devices to probe the structural dynamics of nucleosomes and to measure depletion forces due to molecular crowding. (harvard.edu)
  • We have studied the stacking thermodynamics of these compounds in short synthetic DNA duplexes, with all four neighboring nucleobases. (docme.ru)
  • We recently developed a procedure termed 'quantitative DNA fiber mapping' (QDFM) to help construct physical maps by measuring the overlap between clones or the physical distance between non-overlapping contigs. (caltech.edu)