Citric Acid: A key intermediate in metabolism. It is an acid compound found in citrus fruits. The salts of citric acid (citrates) can be used as anticoagulants due to their calcium chelating ability.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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.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.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.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.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.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.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.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.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.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.Genes, Bacterial: The functional hereditary units of BACTERIA.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.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Bacterial Proteins: Proteins found in any species of bacterium.Myristates: Salts and esters of the 14-carbon saturated monocarboxylic acid--myristic acid.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.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)Sequence Analysis, Protein: A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.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).Maximal Expiratory Flow Rate: The airflow rate measured during the first liter expired after the first 200 ml have been exhausted during a FORCED VITAL CAPACITY determination. Common abbreviations are MEFR, FEF 200-1200, and FEF 0.2-1.2.Counterpulsation: A technique for assisting the circulation by decreasing the afterload of the left ventricle and augmenting the diastolic pressure. It may be achieved by intra-aortic balloon, or by implanting a special pumping device in the chest, or externally by applying a negative pressure to the lower extremities during cardiac systole.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.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.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.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 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.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)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.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).RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Genetic Variation: Genotypic differences observed among individuals in a population.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.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.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.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.Sigmoidoscopes: Endoscopes for examining the interior of the sigmoid colon.Aesculus: A plant genus of the family HIPPOCASTANACEAE (or SAPINDACEAE by some) that contains antimicrobial protein 1 and escin. A. hippocastanum is used in folk medicine for treating chronic venous insufficiency.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.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).Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Molecular Weight: The sum of the weight of all the atoms in a molecule.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.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.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.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.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Genes, Viral: The functional hereditary units of VIRUSES.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Genetic Complementation Test: A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.Fatty Acids: Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)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.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.Mutagenesis, Insertional: Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.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).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.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).RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Chromatography, High Pressure Liquid: Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.HMGB2 Protein: A 23-kDa HMG-box protein that binds to and distorts the minor grove of DNA.Recombinant Proteins: Proteins prepared by recombinant DNA technology.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.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.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.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Viral Proteins: Proteins found in any species of virus.Palaquium: A plant genus of the family SAPOTACEAE. Latex from bark incisions is processed into GUTTA-PERCHA.Seawater: The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.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.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Actinomycetales: An order of gram-positive, primarily aerobic BACTERIA that tend to form branching filaments.Multilocus Sequence Typing: Direct nucleotide sequencing of gene fragments from multiple housekeeping genes for the purpose of phylogenetic analysis, organism identification, and typing of species, strain, serovar, or other distinguishable phylogenetic level.Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.Amino Acids: Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Genes, Fungal: The functional hereditary units of FUNGI.Environmental Remediation: Removal of ENVIRONMENTAL POLLUTANTS or contaminants for the general protection of the environment. This is accomplished by various chemical, biological, and bulk movement methods, in conjunction with ENVIRONMENTAL MONITORING.Cisplatin: An inorganic and water-soluble platinum complex. After undergoing hydrolysis, it reacts with DNA to produce both intra and interstrand crosslinks. These crosslinks appear to impair replication and transcription of DNA. The cytotoxicity of cisplatin correlates with cellular arrest in the G2 phase of the cell cycle.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.Cyanogen Bromide: Cyanogen bromide (CNBr). A compound used in molecular biology to digest some proteins and as a coupling reagent for phosphoroamidate or pyrophosphate internucleotide bonds in DNA duplexes.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)Alphaproteobacteria: A class in the phylum PROTEOBACTERIA comprised mostly of two major phenotypes: purple non-sulfur bacteria and aerobic bacteriochlorophyll-containing bacteria.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.Autonomic Nervous System Diseases: Diseases of the parasympathetic or sympathetic divisions of the AUTONOMIC NERVOUS SYSTEM; which has components located in the CENTRAL NERVOUS SYSTEM and PERIPHERAL NERVOUS SYSTEM. Autonomic dysfunction may be associated with HYPOTHALAMIC DISEASES; BRAIN STEM disorders; SPINAL CORD DISEASES; and PERIPHERAL NERVOUS SYSTEM DISEASES. Manifestations include impairments of vegetative functions including the maintenance of BLOOD PRESSURE; HEART RATE; pupil function; SWEATING; REPRODUCTIVE AND URINARY PHYSIOLOGY; and DIGESTION.Geologic Sediments: A mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)Virulence: The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.Protein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.RNA, Ribosomal, 23S: Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.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.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Chickens: Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.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.Lead Radioisotopes: Unstable isotopes of lead that decay or disintegrate emitting radiation. Pb atoms with atomic weights 194-203, 205, and 209-214 are radioactive lead isotopes.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.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Protein PrecursorsPolymorphism, 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.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Dacarbazine: An antineoplastic agent. It has significant activity against melanomas. (from Martindale, The Extra Pharmacopoeia, 31st ed, p564)Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Central Nervous System Venous Angioma: A vascular anomaly characterized by a radial or wedge-shaped arrangement of dilated VEINS draining into a larger vein in the brain, spinal cord, or the meninges. Veins in a venous angioma are surrounded by normal nervous tissue, unlike a CENTRAL NERVOUS SYSTEM CAVERNOUS HEMANGIOMA that lacks intervening nervous tissue. Drainage of venous angioma is fully integrated with the body's venous system, therefore, in most cases there is no clinical signs and rare bleeding.Plants: Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.Korea: Former kingdom, located on Korea Peninsula between Sea of Japan and Yellow Sea on east coast of Asia. In 1948, the kingdom ceased and two independent countries were formed, divided by the 38th parallel.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Genes, Regulator: Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.Gammaproteobacteria: A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.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.Dermatitis, Perioral: A papular eruption of unknown etiology that progresses to residual papular erythema and scaling usually confined to the area of the mouth, and almost exclusively occurring in young women. It may also be localized or extend to involve the eyelids and adjacent glabella area of the forehead (periocular dermatitis). (Dorland, 28th ed)Oxidoreductases: The class of all enzymes catalyzing oxidoreduction reactions. The substrate that is oxidized is regarded as a hydrogen donor. The systematic name is based on donor:acceptor oxidoreductase. The recommended name will be dehydrogenase, wherever this is possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the acceptor. (Enzyme Nomenclature, 1992, p9)Pigments, Biological: Any normal or abnormal coloring matter in PLANTS; ANIMALS or micro-organisms.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.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.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)Bacterial Outer Membrane Proteins: Proteins isolated from the outer membrane of Gram-negative bacteria.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Poly A: A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Outliers, DRG: In health care reimbursement, especially in the prospective payment system, those patients who require an unusually long hospital stay or whose stay generates unusually high costs.Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Gene Order: The sequential location of genes on a chromosome.Peptide Mapping: Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Pseudomonas: A genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in nature. Some species are pathogenic for humans, animals, and plants.RNA, Ribosomal, 18S: Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Kinetics: The rate dynamics in chemical or physical systems.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.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.Peptides: Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.Mycological Typing Techniques: Procedures for identifying types and strains of fungi.China: A country spanning from central Asia to the Pacific Ocean.Capsid Proteins: Proteins that form the CAPSID of VIRUSES.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.RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.Cosmids: Plasmids containing at least one cos (cohesive-end site) of PHAGE LAMBDA. They are used as cloning vehicles.Quinones: Hydrocarbon rings which contain two ketone moieties in any position. They can be substituted in any position except at the ketone groups.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)Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Fungal Proteins: Proteins found in any species of fungus.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.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Fresh Water: Water containing no significant amounts of salts, such as water from RIVERS and LAKES.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Fiber Optic Technology: The technology of transmitting light over long distances through strands of glass or other transparent material.Prevotella: A genus of gram-negative, anaerobic, nonsporeforming, nonmotile rods. Organisms of this genus had originally been classified as members of the BACTEROIDES genus but overwhelming biochemical and chemical findings in 1990 indicated the need to separate them from other Bacteroides species, and hence, this new genus was established.Protein Structure, Secondary: The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.Reading Frames: The three possible sequences of CODONS by which GENETIC TRANSLATION may occur from one nucleotide sequence. A segment of mRNA 5'AUCCGA3' could be translated as 5'AUC.. or 5'UCC.. or 5'CCG.., depending on the location of the START CODON.Bacillus: A genus of BACILLACEAE that are spore-forming, rod-shaped cells. Most species are saprophytic soil forms with only a few species being pathogenic.Frameshift Mutation: A type of mutation in which a number of NUCLEOTIDES deleted from or inserted into a protein coding sequence is not divisible by three, thereby causing an alteration in the READING FRAMES of the entire coding sequence downstream of the mutation. These mutations may be induced by certain types of MUTAGENS or may occur spontaneously.Endopeptidases: A subclass of PEPTIDE HYDROLASES that catalyze the internal cleavage of PEPTIDES or PROTEINS.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.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.Cephacetrile: A derivative of 7-aminocephalosporanic acid.Capsid: The outer protein protective shell of a virus, which protects the viral nucleic acid.Molecular Epidemiology: The application of molecular biology to the answering of epidemiological questions. The examination of patterns of changes in DNA to implicate particular carcinogens and the use of molecular markers to predict which individuals are at highest risk for a disease are common examples.Aerobiosis: Life or metabolic reactions occurring in an environment containing oxygen.Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.Pseudogenes: Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.Cocaine-Related Disorders: Disorders related or resulting from use of cocaine.Genes, Plant: The functional hereditary units of PLANTS.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.Serine Endopeptidases: Any member of the group of ENDOPEPTIDASES containing at the active site a serine residue involved in catalysis.Chromosomes, Artificial, Bacterial: DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.DNA, Intergenic: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.Amino Acid Motifs: Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.Macromolecular Substances: Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.Hot Springs: Habitat of hot water naturally heated by underlying geologic processes. Surface hot springs have been used for BALNEOLOGY. Underwater hot springs are called HYDROTHERMAL VENTS.Chromosomes, Bacterial: Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.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.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Sodium Chloride: A ubiquitous sodium salt that is commonly used to season food.Hydrogen-Ion Concentration: The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Chromosome Deletion: Actual loss of portion of a chromosome.Sewage: Refuse liquid or waste matter carried off by sewers.DNA, Archaeal: Deoxyribonucleic acid that makes up the genetic material of archaea.Rabbits: The species Oryctolagus cuniculus, in the family Leporidae, order LAGOMORPHA. Rabbits are born in burrows, furless, and with eyes and ears closed. In contrast with HARES, rabbits have 22 chromosome pairs.Structure-Activity Relationship: The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.Protein Sorting Signals: Amino acid sequences found in transported proteins that selectively guide the distribution of the proteins to specific cellular compartments.Lactobacillus: A genus of gram-positive, microaerophilic, rod-shaped bacteria occurring widely in nature. Its species are also part of the many normal flora of the mouth, intestinal tract, and vagina of many mammals, including humans. Pathogenicity from this genus is rare.

Novel regulation of the homeotic gene Scr associated with a crustacean leg-to-maxilliped appendage transformation. (1/46886)

Homeotic genes are known to be involved in patterning morphological structures along the antero-posterior axis of insects and vertebrates. Because of their important roles in development, changes in the function and expression patterns of homeotic genes may have played a major role in the evolution of different body plans. For example, it has been proposed that during the evolution of several crustacean lineages, changes in the expression patterns of the homeotic genes Ultrabithorax and abdominal-A have played a role in transformation of the anterior thoracic appendages into mouthparts termed maxillipeds. This homeotic-like transformation is recapitulated at the late stages of the direct embryonic development of the crustacean Porcellio scaber (Oniscidea, Isopoda). Interestingly, this morphological change is associated with apparent novelties both in the transcriptional and post-transcriptional regulation of the Porcellio scaber ortholog of the Drosophila homeotic gene, Sex combs reduced (Scr). Specifically, we find that Scr mRNA is present in the second maxillary segment and the first pair of thoracic legs (T1) in early embryos, whereas protein accumulates only in the second maxillae. In later stages, however, high levels of SCR appear in the T1 legs, which correlates temporally with the transformation of these appendages into maxillipeds. Our observations provide further insight into the process of the homeotic leg-to-maxilliped transformation in the evolution of crustaceans and suggest a novel regulatory mechanism for this process in this group of arthropods.  (+info)

Mrj encodes a DnaJ-related co-chaperone that is essential for murine placental development. (2/46886)

We have identified a novel gene in a gene trap screen that encodes a protein related to the DnaJ co-chaperone in E. coli. The gene, named Mrj (mammalian relative of DnaJ) was expressed throughout development in both the embryo and placenta. Within the placenta, expression was particularly high in trophoblast giant cells but moderate levels were also observed in trophoblast cells of the chorion at embryonic day 8.5, and later in the labyrinth which arises from the attachment of the chorion to the allantois (a process called chorioallantoic fusion). Insertion of the ROSAbetageo gene trap vector into the Mrj gene created a null allele. Homozygous Mrj mutants died at mid-gestation due to a failure of chorioallantoic fusion at embryonic day 8.5, which precluded formation of the mature placenta. At embryonic day 8.5, the chorion in mutants was morphologically normal and expressed the cell adhesion molecule beta4 integrin that is known to be required for chorioallantoic fusion. However, expression of the chorionic trophoblast-specific transcription factor genes Err2 and Gcm1 was significantly reduced. The mutants showed no abnormal phenotypes in other trophoblast cell types or in the embryo proper. This study indicates a previously unsuspected role for chaperone proteins in placental development and represents the first genetic analysis of DnaJ-related protein function in higher eukaryotes. Based on a survey of EST databases representing different mouse tissues and embryonic stages, there are 40 or more DnaJ-related genes in mammals. In addition to Mrj, at least two of these genes are also expressed in the developing mouse placenta. The specificity of the developmental defect in Mrj mutants suggests that each of these genes may have unique tissue and cellular activities.  (+info)

Requirement of a novel gene, Xin, in cardiac morphogenesis. (3/46886)

A novel gene, Xin, from chick (cXin) and mouse (mXin) embryonic hearts, may be required for cardiac morphogenesis and looping. Both cloned cDNAs have a single open reading frame, encoding proteins with 2,562 and 1,677 amino acids for cXin and mXin, respectively. The derived amino acid sequences share 46% similarity. The overall domain structures of the predicted cXin and mXin proteins, including proline-rich regions, 16 amino acid repeats, DNA-binding domains, SH3-binding motifs and nuclear localization signals, are highly conserved. Northern blot analyses detect a single message of 8.9 and 5.8 kilo base (kb) from both cardiac and skeletal muscle of chick and mouse, respectively. In situ hybridization reveals that the cXin gene is specifically expressed in cardiac progenitor cells of chick embryos as early as stage 8, prior to heart tube formation. cXin continues to be expressed in the myocardium of developing hearts. By stage 15, cXin expression is also detected in the myotomes of developing somites. Immunofluorescence microscopy reveals that the mXin protein is colocalized with N-cadherin and connexin-43 in the intercalated discs of adult mouse hearts. Incubation of stage 6 chick embryos with cXin antisense oligonucleotides results in abnormal cardiac morphogenesis and an alteration of cardiac looping. The myocardium of the affected hearts becomes thickened and tends to form multiple invaginations into the heart cavity. This abnormal cellular process may account in part for the abnormal looping. cXin expression can be induced by bone morphogenetic protein (BMP) in explants of anterior medial mesoendoderm from stage 6 chick embryos, a tissue that is normally non-cardiogenic. This induction occurs following the BMP-mediated induction of two cardiac-restricted transcription factors, Nkx2.5 and MEF2C. Furthermore, either MEF2C or Nkx2.5 can transactivate a luciferase reporter driven by the mXin promoter in mouse fibroblasts. These results suggest that Xin may participate in a BMP-Nkx2.5-MEF2C pathway to control cardiac morphogenesis and looping.  (+info)

Characterization of an amphioxus paired box gene, AmphiPax2/5/8: developmental expression patterns in optic support cells, nephridium, thyroid-like structures and pharyngeal gill slits, but not in the midbrain-hindbrain boundary region. (4/46886)

On the basis of developmental gene expression, the vertebrate central nervous system comprises: a forebrain plus anterior midbrain, a midbrain-hindbrain boundary region (MHB) having organizer properties, and a rhombospinal domain. The vertebrate MHB is characterized by position, by organizer properties and by being the early site of action of Wnt1 and engrailed genes, and of genes of the Pax2/5/8 subfamily. Wada and others (Wada, H., Saiga, H., Satoh, N. and Holland, P. W. H. (1998) Development 125, 1113-1122) suggested that ascidian tunicates have a vertebrate-like MHB on the basis of ascidian Pax258 expression there. In another invertebrate chordate, amphioxus, comparable gene expression evidence for a vertebrate-like MHB is lacking. We, therefore, isolated and characterized AmphiPax2/5/8, the sole member of this subfamily in amphioxus. AmphiPax2/5/8 is initially expressed well back in the rhombospinal domain and not where a MHB would be expected. In contrast, most of the other expression domains of AmphiPax2/5/8 correspond to expression domains of vertebrate Pax2, Pax5 and Pax8 in structures that are probably homologous - support cells of the eye, nephridium, thyroid-like structures and pharyngeal gill slits; although AmphiPax2/5/8 is not transcribed in any structures that could be interpreted as homologues of vertebrate otic placodes or otic vesicles. In sum, the developmental expression of AmphiPax2/5/8 indicates that the amphioxus central nervous system lacks a MHB resembling the vertebrate isthmic region. Additional gene expression data for the developing ascidian and amphioxus nervous systems would help determine whether a MHB is a basal chordate character secondarily lost in amphioxus. The alternative is that the MHB is a vertebrate innovation.  (+info)

Regulation of body length and male tail ray pattern formation of Caenorhabditis elegans by a member of TGF-beta family. (5/46886)

We have identified a new member of the TGF-beta superfamily, CET-1, from Caenorhabditis elegans, which is expressed in the ventral nerve cord and other neurons. cet-1 null mutants have shortened bodies and male tail abnormal phenotype resembling sma mutants, suggesting cet-1, sma-2, sma-3 and sma-4 share a common pathway. Overexpression experiments demonstrated that cet-1 function requires wild-type sma genes. Interestingly, CET-1 appears to affect body length in a dose-dependent manner. Heterozygotes for cet-1 displayed body lengths ranging between null mutant and wild type, and overexpression of CET-1 in wild-type worms elongated body length close to lon mutants. In male sensory ray patterning, lack of cet-1 function results in ray fusions. Epistasis analysis revealed that mab-21 lies downstream and is negatively regulated by the cet-1/sma pathway in the male tail. Our results show that cet-1 controls diverse biological processes during C. elegans development probably through different target genes.  (+info)

Molecular cloning and epitope analysis of the peanut allergen Ara h 3. (6/46886)

Peanut allergy is a significant IgE-mediated health problem because of the increased prevalence, potential severity, and chronicity of the reaction. Following our characterization of the two peanut allergens Ara h 1 and Ara h 2, we have isolated a cDNA clone encoding a third peanut allergen, Ara h 3. The deduced amino acid sequence of Ara h 3 shows homology to 11S seed-storage proteins. The recombinant form of this protein was expressed in a bacterial system and was recognized by serum IgE from approximately 45% of our peanut-allergic patient population. Serum IgE from these patients and overlapping, synthetic peptides were used to map the linear, IgE-binding epitopes of Ara h 3. Four epitopes, between 10 and 15 amino acids in length, were found within the primary sequence, with no obvious sequence motif shared by the peptides. One epitope is recognized by all Ara h 3-allergic patients. Mutational analysis of the epitopes revealed that single amino acid changes within these peptides could lead to a reduction or loss of IgE binding. By determining which amino acids are critical for IgE binding, it might be possible to alter the Ara h 3 cDNA to encode a protein with a reduced IgE-binding capacity. These results will enable the design of improved diagnostic and therapeutic approaches for food-hypersensitivity reactions.  (+info)

TIF1gamma, a novel member of the transcriptional intermediary factor 1 family. (7/46886)

We report the cloning and characterization of a novel member of the Transcriptional Intermediary Factor 1 (TIF1) gene family, human TIF1gamma. Similar to TIF1alpha and TIF1beta, the structure of TIF1beta is characterized by multiple domains: RING finger, B boxes, Coiled coil, PHD/TTC, and bromodomain. Although structurally related to TIF1alpha and TIF1beta, TIF1gamma presents several functional differences. In contrast to TIF1alpha, but like TIF1beta, TIF1 does not interact with nuclear receptors in yeast two-hybrid or GST pull-down assays and does not interfere with retinoic acid response in transfected mammalian cells. Whereas TIF1alpha and TIF1beta were previously found to interact with the KRAB silencing domain of KOX1 and with the HP1alpha, MODI (HP1beta) and MOD2 (HP1gamma) heterochromatinic proteins, suggesting that they may participate in a complex involved in heterochromatin-induced gene repression, TIF1gamma does not interact with either the KRAB domain of KOX1 or the HP1 proteins. Nevertheless, TIF1gamma, like TIF1alpha and TIF1beta, exhibits a strong silencing activity when tethered to a promoter. Since deletion of a novel motif unique to the three TIF1 proteins, called TIF1 signature sequence (TSS), abrogates transcriptional repression by TIF1gamma, this motif likely participates in TIF1 dependent repression.  (+info)

Detailed methylation analysis of the glutathione S-transferase pi (GSTP1) gene in prostate cancer. (8/46886)

Glutathione-S-Transferases (GSTs) comprise a family of isoenzymes that provide protection to mammalian cells against electrophilic metabolites of carcinogens and reactive oxygen species. Previous studies have shown that the CpG-rich promoter region of the pi-class gene GSTP1 is methylated at single restriction sites in the majority of prostate cancers. In order to understand the nature of abnormal methylation of the GSTP1 gene in prostate cancer we undertook a detailed analysis of methylation at 131 CpG sites spanning the promoter and body of the gene. Our results show that DNA methylation is not confined to specific CpG sites in the promoter region of the GSTP1 gene but is extensive throughout the CpG island in prostate cancer cells. Furthermore we found that both alleles are abnormally methylated in this region. In normal prostate tissue, the entire CpG island was unmethylated, but extensive methylation was found outside the island in the body of the gene. Loss of GSTP1 expression correlated with DNA methylation of the CpG island in both prostate cancer cell lines and cancer tissues whereas methylation outside the CpG island in normal prostate tissue appeared to have no effect on gene expression.  (+info)

Massively parallel high throughput sequencing technologies allow us to interrogate the microbial composition of biological samples at unprecedented resolution. The typical approach is to perform high-throughout sequencing of 16S rRNA genes, which are then taxonomically classified based on similarity to known sequences in existing databases. Current technologies cause a predicament though, because although they enable deep coverage of samples, they are limited in the length of sequence they can produce. As a result, high-throughout studies of microbial communities often do not sequence the entire 16S rRNA gene. The challenge is to obtain reliable representation of bacterial communities through taxonomic classification of short 16S rRNA gene sequences. In this study we explored properties of different study designs and developed specific recommendations for effective use of short-read sequencing technologies for the purpose of interrogating bacterial communities, with a focus on classification using
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. Numerous factors, including DNA extraction method, primer sequences and sequencing platform employed, can affect the accuracy of the results achieved. 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. 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. The V4-V5 primers gave the most comparable results across platforms. The three Ion PGM primer sets detected more of the 20 mock community species than the equivalent MiSeq primer sets. Data generated from DNA extracted using the 2 extraction methods were very similar. Conclusions Microbiota compositional data ...
Next generation sequencing technologies open exciting new possibilities for genome and transcriptome sequencing. While reads produced by these technologies are relatively short and error-prone compared to the Sanger method, their throughput is several magnitudes higher. We present a novel approach, called QPALMA, for computing accurate spliced alignments of short sequence reads that take advantage of the reads quality information as well as computational splice site predictions. In computational experiments we illustrate that the quality information as well as the splice site predictions [1] help to considerably improve the alignment quality. Our algorithms were optimized and tested using artificially spliced genomic reads produced with the Illumina Genome Analyzer for the model plant Arabidopsis thaliana. ...
First Roche GS-FLX Genome Sequencing System Installed At VBI - read this article along with other careers information, tips and advice on BioSpace
454 Life Sciences, a Roche Company, announced today the launch and immediate availability of the new GS GType HLA Primer Sets for high- and medium-resolution genotyping of class I and class II loci of the Human Leukocyte Antigen (HLA) genes. The primer sets are designed for use with the companys benchtop GS Junior and GS FLX next-generation sequencing systems.
The SK-BR-3 cell line is one of the most important models for HER2+ breast cancers, which affect one in five breast cancer patients. SK-BR-3 is known to be highly rearranged although much of the variation is in complex and repetitive regions that may be underreported. Addressing this, we sequenced SK-BR-3 using long-read single molecule sequencing from Pacific Biosciences, and develop one of the most detailed maps of structural variations (SVs) in a cancer genome available with nearly 20,000 variants present, most of which were missed by short read sequencing. Surrounding the important ERBB2 oncogene (also known as HER2), we discover a complex sequence of nested duplications and translocations, suggesting a punctuated progression. Full-length transcriptome sequencing further revealed several novel gene fusions within the nested genomic variants. Combining long-read genome and transcriptome sequencing enables an in-depth analysis of how SVs disrupt the genome and sheds new light on the complex ...
As one of the most studied genome rearrangements, tandem repeats have a considerable impact on genetic backgrounds of inherited diseases. Many methods designed for tandem repeat detection on reference sequences obtain high quality results. However, in the case of a de novo context, where no reference sequence is available, tandem repeat detection remains a difficult problem. The short reads obtained with the second-generation sequencing methods are not long enough to span regions that contain long repeats. This length limitation was tackled by the long reads obtained with the third-generation sequencing platforms such as Pacific Biosciences technologies. Nevertheless, the gain on the read length came with a significant increase of the error rate. The main objective of nowadays studies on long reads is to handle the high error rate up to 16%. In this paper we present MixTaR, the first de novo method for tandem repeat detection that combines the high-quality of short reads and the large length of long
SEOUL, South Korea and SAN DIEGO, Jan. 11, 2016 - Macrogen, a global leader in genome sequencing services, and Edico Genome today announced Macrogen has chosen multiple DRAGEN™ Bio-IT Processors to reinforce its big data processing and analysis capacity for large-scale genome analysis and clinical sequencing services. Macrogen has world-class next-generation sequencing (NGS) facilities, which are equipped with Illuminas HiSeq™ X Ten, HiSeq 2000, HiSeq 2500, HiSeq 4000 and MiSeq® sequencing systems; Thermo Fishers Ion PGM™ and Ion Proton™ systems; Roches GS-FLX system; and PacBio instruments. Macrogens IT infrastructure capacity exceeds 11 petabytes of storage and more than 3,000 core clusters. Using DRAGEN, Macrogen was able to analyze each genome (30x coverage) produced by their HiSeq X Ten sequencing system in only 26 minutes, while maintaining high sensitivity and specificity. This analysis included conversion from BCL, the file that is delivered by the sequencing instrument, to ...
Progress in genetics and breeding in pea still suffers from the limited availability of molecular resources. SNP markers that can be identified through affordable sequencing processes, without the need for prior genome reduction or a reference genome to assemble sequencing data would allow the discovery and genetic mapping of thousands of molecular markers. Such an approach could significantly speed up genetic studies and marker assisted breeding for non-model species. A total of 419,024 SNPs were discovered using HiSeq whole genome sequencing of four pea lines, followed by direct identification of SNP markers without assembly using the discoSnp tool. Subsequent filtering led to the identification of 131,850 highly designable SNPs, polymorphic between at least two of the four pea lines. A subset of 64,754 SNPs was called and genotyped by short read sequencing on a subpopulation of 48 RILs from the cross Baccara x PI180693. This data was used to construct a WGGBS-derived pea genetic map comprising 64
Recent DNA sequencing technology, the so-called next-generation sequencing (NGS) technology, enables researchers to read a number of DNA sequences that is several orders of magnitudes bigger and at a cost that is several orders of magnitude smaller than the previous generation DNA sequencing technologies. The cost of determining the human genome was estimated at $2.7 billion for the IHGSC genome and at $300 million for the Celera genome. Recently several human genomes were sequenced in about 1.5 months at a cost that is around $1.5 million [1, 2].. Large-scale parallel pyrosequencing from 454/Roche generates hundreds of thousands sequenced DNA reads within a matter of hours [3]. The latest version of the sequencing technology (Titanium) enables a throughput of 0.4-0.6 gigabases per 10 h run [4]. The amount of data to be analyzed keeps growing at an increasing speed. Other NGS platforms such as Illuminas Genome Analyzer (San Diego, CA, USA), Applied Biosystems SOLiD (Foster City, CA, USA) and ...
Author Summary Human individual genome sequencing has recently become affordable, enabling highly detailed genetic sequence comparisons. While the identification and genotyping of single-nucleotide polymorphisms has already been successfully established for different sequencing platforms, the detection, quantification and genotyping of large-scale copy-number variants (CNVs), i.e., losses or gains of long genomic segments, has remained challenging. We present a computational approach that enables detecting CNVs in sequencing data and accurately identifies the actual copy-number at which DNA segments of interest occur in an individual genome. This approach enabled us to obtain novel insights into the largest human gene family - the olfactory receptors (ORs) - involved in smell perception. While previous studies reported an abundance of CNVs in ORs, our approach enabled us to globally identify absolute differences in OR gene counts that exist between humans. While several OR genes have very high gene
Recent advances in high-throughput sequencing (HTS) technologies have led to orders of magnitude higher throughput compared to classic Sanger sequencing (see [3] for a review). Coupled with continuous
Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly1. The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE)2. Here we report the whole-genome sequencing and assembly of the desiccation-tolerant grass Oropetium thomaeum. Using only single-molecule real-time sequencing, which generates long (,16 kilobases) reads with random errors, we assembled 99% (244 megabases) of the Oropetium genome into 625 contigs with an N50 length of 2.4 megabases. Oropetium is an example of a near-complete draft genome which includes gapless coverage over gene space as well as intergenic sequences such as centromeres, telomeres, transposable elements and ...
The goal of this demonstration project is to develop the capability to express complete biosynthetic pathways for natural products that are usually silent in their native microbial host (i.e. orphan biosynthetic gene clusters). Such a technology will increase our access to new chemical entities for potential use in drug development. By tailoring synthetic genomics techniques to the expression of biosynthetic gene clusters, we believe we will create the capacity to produce small molecules directly using synthetic expression constructs in platform production microorganisms. Publicly available high-throughput DNA sequencing data has already cataloged up to 20,000 orphan clusters; as a result, our approach has the potential to bring about the biological synthesis of a large number of natural products that are currently unavailable for evaluation as potential drugs. The proposed clones and expression constructs can be used as a starting point for evaluating the bioactivities of metabolites whose ...
The multikilobase reads that can be produced by single-molecule sequencing technologies may span complex, repetitive genomic regions but have high error rates. Bashir et al. use these reads to organize contigs assembled from accurate, short-read data, facilitating the analysis of clinically important regions of an outbreak strain of cholera. Advances in DNA sequencing technology have improved our ability to characterize most genomic diversity. However, accurate resolution of large structural events is challenging because of the short read lengths of second-generation technologies. Third-generation sequencing technologies, which can yield longer multikilobase reads, have the potential to address limitations associated with genome assembly. Here we combine sequencing data from second- and third-generation DNA sequencing technologies to assemble the two-chromosome genome of a recent Haitian cholera outbreak strain into two nearly finished contigs at |99.9% accuracy. Complex regions with clinically relevant
SCOTTSDALE, Ariz. - Whole genome sequencing - spelling out a persons entire DNA genetic code - has moved one step closer to being a medical option for direct patient care.. Physicians and researchers at Mayo Clinic in Arizona and the Translational Genomics Research Institute (TGen) successfully completed sequencing both a single patients normal and cancer cells - a tour de force of more than 6 billion DNA chemical bases.. While the whole genomes of several individuals or their cancers have been sequenced in recent years, this is believed to be among the first successful application of whole genome sequencing performed in support of the medical care of a specific cancer patient.. A male patient with pancreatic cancer was the first patient at Mayo Clinic to have whole genome sequencing performed on both his tumor and non-cancerous cells as part of a clinical research project. By comparing the tumor DNA to the patients normal DNA, researchers found genetic changes (mutations) that were important ...
Reference quality genomes provide a resource for studying gene structure, function, and evolution. However, often genes of interest are not completely or accurately assembled, leading to unknown errors in analyses or additional cloning efforts for the correct sequences. A promising solution is long-read sequencing. Here we tested PacBio-based long-read sequencing and diploid assembly for potential improvements to the Sanger-based intermediate-read zebra finch reference and Illumina-based short-read Annas hummingbird reference, two vocal learning avian species widely studied in neuroscience and genomics. With DNA of the same individuals used to generate the reference genomes, we generated diploid assemblies with the FALCON-Unzip assembler, resulting in contigs with no gaps in the megabase range, representing 150-fold and 200-fold improvements over the current zebra finch and hummingbird references, respectively. These long-read and phased assemblies corrected and resolved what we discovered to be
AUSTRALIAS capacity to detect, respond to and control infectious threats, and to improve regional health security is hampered by the lack of a national approach to whole genome sequencing resources, and data sharing, according to the authors of a Perspective published in the Medical Journal of Australia.. Whole genome sequencing involves parsing out the entire genome of a pathogen, the data from which can be used to determine the pathogens identity, predict its resistance to antimicrobials and its virulence traits and understand the relationships between pathogens.. University of Melbourne Associate Professor Deborah Williamson, Deputy Director of the Microbiological Diagnostic Unit Public Health Laboratory at the Doherty Institute, and colleagues wrote that the use of whole genome sequencing "has the potential to transform the investigation and surveillance of communicable diseases by providing the highest possible characterisation of pathogens, enabling earlier and accurate detection of ...
The advent of next-generation sequencing (NGS)4 technologies, which grew exponentially in the decade after publication of the first iteration of the human genome sequence (4), has provided substantial insights into new genes and the biological processes that underlie cancer pathogenesis. These insights are outlined below. NGS technologies "parallelize" sequencing processes via high-throughput means to produce millions of short sequencing "reads" from amplified DNA clones (5). NGS is also referred to as "massively parallel sequencing," because the reaction steps occur in parallel with the detection steps and millions of reactions occur simultaneously (6). This parallelism makes it possible to read the same segment of a DNA sequence repeatedly to increase confidence in the sequence obtained for the targeted genomic segment. This multiple sampling of a genomic segment is referred to as the "coverage" of the sequencing run.. Before the NGS era, much progress had been made toward identifying mutated ...
We have developed and validated a low-coverage whole genome sequencing assay for genome-wide and high-resolution detection of copy number aberrations (CNAs) from inherited disorders. The analytical sensitivity was 0.765 for detecting CNVs of 25-50kb in size and 0.990 for detecting CNVs of over 50kb in size. The smallest detected deletion was 10kb.
The transcriptional architecture is a complex and dynamic aspect of a cells function. Next generation sequencing of steady state RNA (RNA-seq) gives unprecedented detail about the RNA landscape within a cell. Not only can expression levels of genes be interrogated without specific prior knowledge, but comparisons of expression levels between genes within a sample can be made. It has also been demonstrated that splicing variants [1, 2] and single nucleotide polymorphisms [3] can be detected through sequencing the transcriptome, opening up the opportunity to interrogate allele-specific expression and RNA editing.. An important aspect of dealing with the vast amounts of data generated from short read sequencing is the processing methods used to extract and interpret the information. Experience with microarray data has repeatedly shown that normalization is a critical component of the processing pipeline, allowing accurate estimation and detection of differential expression (DE) [4]. The aim of ...
Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes. However, false positive variant predictions due to sequencing errors and mapping artifacts of short reads need to be prevented. We therefore created VarCap, a workflow for the reliable prediction of different types of variants even at low frequencies. In order to predict SNPs, InDels and structural variations, we evaluated the sensitivity and accuracy of different software tools using synthetic read data. The results suggested that the best ...
This dataset contains the digitized treatments in Plazi based on the original journal article Straube, Nicolas, White, William T., Ho, Hsuan-Ching, Rochel, Elisabeth, Corrigan, Shannon, Li, Chenhong, Naylor, Gavin J. P. (2013): A DNA sequence-based identification checklist for Taiwanese chondrichthyans. Zootaxa 3752 (1): 256-278, DOI: http://dx.doi.org/10.11646/zootaxa.3752.1.16 ...
Genome sequencing technologies are improving at a rapid pace. The current challenge is to find ways to extract all of the genetic information from the data. One of the biggest challenges has been the detection of CNVs. Sebat, in collaboration with Seungtai Yoon of CSHL and Kenny Ye, Ph.D., at the Albert Einstein College of Medicine, developed a statistical method to estimate DNA copy number of a genomic region based on the number of sequences that map to that location (or "read depth"). When the genomes of multiple individuals are compared, regions that differ in copy number between individuals can be identified.. The new method allows the detection of small structural variants that could not be detected using earlier microarray-based methods. This is significant because most of the CNVs the genome are less than 5000 nucleotides in length. The new method is also able to detect certain classes of CNVs that other sequencing-based approaches struggle with, particularly those located in complex ...
Strategies for assembling large, complex genomes have evolved to include a combination of whole-genome shotgun sequencing and hierarchal map-assisted sequencing. Whole-genome maps of all types can aid genome assemblies, generally starting with low-resolution cytogenetic maps and ending with the highest resolution of sequence. Fingerprint clone maps are based upon complete restriction enzyme digests of clones representative of the target genome, and ultimately comprise a near-contiguous path of clones across the genome. Such clone-based maps are used to validate sequence assembly order, supply long-range linking information for assembled sequences, anchor sequences to the genetic map and provide templates for closing gaps. Fingerprint maps are also a critical resource for subsequent functional genomic studies, because they provide a redundant and ordered sampling of the genome with clones. In an accompanying paper we describe the draft genome sequence of the chicken, Gallus gallus, the first ...
A framework technology comprising file format and toolkit in which we combine highly efficient and tunable reference-based compression of sequence data with a data format that is directly available for computational use. This compression method is tunable: The storage of quality scores and unaligned sequences may be adjusted for different experiments to conserve information or to minimize storage costs, and provides one opportunity to address the threat that increasing DNA sequence volumes will overcome our ability to store the sequences.
Whole genome sequencing (WGS), which is the process of determining an organisms complete DNA sequence, can be used to identify DNA anomalies that cause disease. Identifying disease-causing DNA abnormalities allows clinicians to better predict an effective course of treatment for the patient.
Capillary sequencing PCR tubes and caps are for use with the ABI Prism 310 sequencerThese PCR tubes are made of high-quality virgin polypropylene and feature uniform thin walls for efficient heat transfer. Tubes and caps are compatible with most leading thermal cyclers, and are autoclavable. Caps, available as either flat or domed, fit perfectly and create a uniform, tight seal that prevents sample evaporation in the thermal cycler. Tubes are nonpyrogenic and RNase- and DNase-free. Certain models feature assorted packs of color-coded tubes for easy identification of samples.
Over the last few years, several initiatives have described efforts to combine previously invented techniques in molecular biology with parallel detection principles to sequence or genotype DNA signatures. The Infinium (R) system from Illumina and the Affymetrix GeneChips (R) are two systems suitable for whole-genome scoring of variable positions. However, directed candidate-gene approaches are more cost effective and several academic groups and the private sector provide techniques with moderate typing throughput combined with large sample capacity suiting these needs. Recently, whole-genome sequencing platforms based on the sequencing-by-synthesis principle were presented by 454 Life Sciences and Solexa, showing great potential as alternatives to conventional genotyping approaches. In addition to these sequencing initiatives, many efforts are pursuing novel ideas to facilitate fast and cost-effective whole genome sequencing, such as ligation-based sequencing. Reliable methods for routine ...
Illumina, Inc. (NASDAQ:ILMN) today broke the sound barrier of human genomics by enabling the $1,000 genome. This achievement is made possible by the
Upon the establishment of the genome project at Celera in 1998, the company purchased and connected 700 CPUs and 70 terabites of hard drive space. This computing system was established to run the initial test of their algorithm code, which was used to sequence the genome of the Drosophilla fruit fly with a 13-fold coverage of the genome successfully in 1999. The most surprising thing about this approach was that it succeeded in coding the algorithm and sequencing the 120 Megabase pair genome of the fruit fly to that extent of completeness in just 11 months. Myers (Gene Myers, a professor of Computer Science at Berkeley) then modified the process so that the Whole Genome Shotgun Sequencing process would make a 5-fold coverage of the human genome, as he believed it would be adequate to provide a complete sequence of the human genome. In addition, Venter purchased 4 supercomputers referred to as the GeneMatcher from a company called Parcel Inc. Parcel Inc, a company that typically produces ...
Patient-derived tumor xenografts in mice are widely used in cancer research and have become important in developing personalized therapies. When these xenografts are subject to DNA sequencing, the samples could contain various amounts of mouse DNA. It has been unclear how the mouse reads would affect data analyses. We conducted comprehensive simulations to compare three alignment strategies at different mutation rates, read lengths, sequencing error rates, human-mouse mixing ratios and sequenced regions. We also sequenced a nasopharyngeal carcinoma xenograft and a cell line to test how the strategies work on real data. We found the filtering and combined reference strategies performed better than aligning reads directly to human reference in terms of alignment and variant calling accuracies. The combined reference strategy was particularly good at reducing false negative variants calls without significantly increasing the false positive rate. In some scenarios the performance gain of these two
2015. The Oxford Nanopore Technologies (ONT) MinION is a new sequencing technology that potentially offers read lengths of tens of kilobases (kb) limited only by the length of DNA molecules presented to it. The device has a low capital cost, is by far the most portable DNA sequencer available, and can produce data in real-time. It has numerous prospective applications including improving genome sequence assemblies and resolution of repeat-rich regions. Before such a technology is widely adopted, it is important to assess its performance and limitations in respect of throughput and accuracy. In this study we assessed the performance of the MinION by re-sequencing three bacterial genomes, with very different nucleotide compositions ranging from 28.6% to 70.7%; the high G. +. C strain was underrepresented in the sequencing reads. We estimate the error rate of the MinION (after base calling) to be 38.2%. Mean and median read lengths were 2. kb and 1. kb respectively, while the longest single read ...
Track 9: Gene Sequencing. DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. It includes any method or technology that is used to determine the order of the four bases is: adenine, guanine, cytosine, and thymine, in a strand of DNA. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery. Knowledge of DNA sequences has become indispensable for basic biological research, and in numerous applied fields such as medical diagnosis, biotechnology, forensic biology, virology and biological systematics. The rapid speed of sequencing attained with modern DNA sequencing technology has been instrumental in the sequencing of complete DNA sequences, or genomes of numerous types and species of life, including the human genome and other complete DNA sequences of many animal, plants, and microbial species.. ...
In article ,4q6b5m$i9u at net.bio.net, jea at ukrv.de writes: ,From: jea at ukrv.de ,Subject: sequencing strategy 2 ,Date: 18 Jun 1996 06:32:38 -0700 ,I want to know if someone can help me to decide which sequencing strategy ,is the best one. I want to start sequencing on a ABI377. I want to ,sequence PCR-Products after cloning them in pUC18 (sureClone Kit, ,Pharmacia). Do you really need them cloned, or do you just want the sequence? If you just need the sequence its best not clone them (the possibility of PCR errors, you see), but rather cycle sequence the PCR fragments straight. , My question is: is it better to sequence plasmid DNA with the , cycle sequencing Kit or is it better to do solid phase sequencing , (Dynabeads) and use Sequenase? Cycle sequencing is easier and faster. In my experience using T7 is only really worth it if you are searching for heterozygotes or something in that vein. Ari-Matti -- *********************** Ari-Matti Saren ************************** * WORK: Institute of ...
Hi guys, I need to PCR amplify a gene from Sea Urchin cDNA for protein expression. This gene is ~1.9kb, GC%~41%. I sequenced the PCR products directly several weeks ago, and sent another tube of PCR products (from the same cDNA library from the same tube, but different enzyme, Ex Taq vs Phusion) for sequencing this week, but the results are quite different: though their size are the same, only 94% bases are identical. I think these two sequencing result might come from polymorphism, I searched the net and one paper said: The sea-urchin genome is highly polymorphic, meaning that the two copies of the genome in the diploid organism vary from each other by about 4 percent, or one difference in spelling every 25 letters ...
Research in genetics has developed rapidly recently due to the aid of next generation sequencing (NGS). However, massively-parallel NGS produces enormous amounts of data, which leads to storage, compatibility, scalability, and performance issues. The Cloud Computing and MapReduce framework, which utilizes hundreds or thousands of shared computers to map sequencing reads quickly and efficiently to reference genome sequences, appears to be a very promising solution for these issues. Consequently, it has been adopted by many organizations recently, and the initial results are very promising. However, since these are only initial steps toward this trend, the developed software does not provide adequate primary functions like bisulfite, pair-end mapping, etc., in on-site software such as RMAP or BS Seeker. In addition, existing MapReduce-based applications were not designed to process the long reads produced by the most recent second-generation and third-generation NGS instruments and, therefore, are
Usually the sequencing primer is used at 0.3µM in annealing buffer but some assays might require additional optimization of the sequencing primer concentration.. For PyroMark Q24 and PyroMark Q96 MD the final concentration of the sequencing primer is 0.3µM and for PyroMark Q96 ID 0.4µM ...
The Genome Sciences Centre sequencing platform is a high-throughput large-scale DNA analysis facility that has been designed to maximize capacity while maintaining efficiency, scalability and flexibility. The platform is one of the largest platforms of its type in Canada and is well recognized internationally.. Current production scale capabilities of the capillary based platform include fosmid end sequencing, PCR amplicon sequencing, plasmid, and BAC end sequencing. We have two Applied Biosytems 3730xls yielding a capacity of 7680 lanes per week, or approx 6 million Q20 bases per week. The GSC sequencing platform prides itself on its flexibility and molecular biology enabling PCR, BAC, fosmid and plasmid DNA preps and several optimized reaction chemistries, allowing us to provide high-quality, high-yield, consistent data generation.. More information on the Illumina Platform.. Through our sequencing validation team we offer several high quality, high throughput targeted sequencing services. We ...
The UMD 3.1 assembly (NCBI assembly accesion GCA_000003055.3), released in December 2009, is the third release of the cow (Bos taurus) assembly from the Center for Bioinformatics and Computational Biology (CBCB) at University of Maryland. The genome sequences were generated using a combination of BAC-by-BAC hierarchical (~11 million reads) and whole-genome shotgun (~24 million reads) sequencing methods, assembled using the Celera Assembler version 5.2. The total length of the UMD3.1 assembly is 2.65Gb. The N50 size is the median sequence length, i.e. 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 size for contigs in the UMD3.1 assembly is 103785. The genome assembly represented here corresponds to GenBank Assembly ID GCA_000003055.3. ...
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The Genotyping laboratory, is a core facility of the Center for Integrated BioSystems at Utah State University. It is equipped with a Fluidigm BioMark™ system, a Fluidigm Access Array™ system, and an Illumina MiSeq next-generation sequencing system.. Two units comprising the CIB Genotyping core are the Fluidigm BioMark™ application service and the Cattle MHC Typing service. The first application provides custom services available to run real-time PCR, SNP genotyping, and digital PCR assays in a high-throughput, low volume fluidics chip. The MHC Typing service provides Major Histocompatibility Complex (MHC) Typing of cattle. Services offer high-throughput genomic DNA sequencing to determine MHC class I and class II haplotypes of cattle.. The CIB Genotyping facility provides consultation and guidance to researchers in designing and performing genetic studies, and genotyping data for their research projects. Services are offered as fee for service. For more information, please contact Dr. ...
The scale of genomic sequencing data and the complexity of bioinformatic algorithms make it difficult for students to develop a concrete understanding of assembling complete genomes from millions of short DNA sequences. We present a hands-on activity where students explore the genome assembly process using short DNA sequences printed on paper. Topics highlighted during the lesson include overlap identification, reference sequences, and the challenges arising from sequencing errors, low-frequency mutations, and repetitive regions. Sample materials provide reads and solutions for assembling clinically relevant regions of the S. gordonii penicillin binding protein and the human HTT gene. An online tool allows instructors to generate custom read sets from other DNA sequences.
Next Generation Sequencing (NGS) has recently revolutionized the approach to genomic studies enabling the sequencing of billions of bases in massively parallel reactions. These new sequencing technologies collectively referred to as ”ultra-deep” sequencing or “massively parallel” sequencing are currently used for SNP discovery, detection of structural variants, genome-wide measurement of transcript levels, analysis of epigenetic modifications and a number of other applications, and are revolutionizing biological research. IGA courses are addressed to researchers interested in understanding how to generate sequences and interpret information obtained. 
Features of the HiSeq platforms HiSeq 2000 The HiSeq 2000, installed in July 2011, is the flagship of the Illumina fleet of next-generation sequencers. The instrument is capable of producing more than 40-60Gbp per run. Each flow cell lane produces about 200-300 million clusters. The HiSeq 2000 utilizes Illuminas proven and widely-adopted, reversible terminator-based sequencing by synthesis chemistry. The ultra-high output of the HiSeq 2000 now makes it possible to sequence more than six human genomes at ~30× coverage simultaneously.
Vol 9: Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing.. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Yu W, Andersson B, Worley KC, Muzny DM, Ding Y, Liu W, Ricafrente JY,Wentland MA, Lennon G, Gibbs RA. Large-scale concatenation cDNA sequencing.Genome Res. 1997 Apr;7(4):353-8. PMID: 9110174 [PubMed - indexed for MEDLINE]. A total of 100 kb of DNA derived from 69 individual human brain cDNA clones of 0.7-2.0 kb were sequenced by concatenated cDNA sequencing (CCS), whereby multiple individual DNA fragments are sequenced simultaneously in a single shotgun library. The method yielded accurate sequences and a similar efficiency compared with other shotgun libraries constructed from single DNA fragments (, 20 kb). Computer analyses were carried out on 65 cDNA clone sequences and their corresponding end sequences to examine both nucleic acid and amino acid sequence similarities in the databases. Thirty-seven clones revealed no DNA database matches, 12 clones generated exact matches (, or = 98% identity), and 16 clones generated nonexact matches (57%-97% identity) to either known human or other species ...
Preparing ultra HMW DNA libraries for long-range genomic applications With Pippin Prep, BluePippin, or PippinHT, users can select their desired fragment length and the instrument will automatically select and collect those fragments, eliminating all others. With SageELF, users get 12 contiguous fractions from each sample, allowing them to construct libraries with multiple insert sizes for improved genome assembly accuracy while making the most of every sample. The SageHLS instrument can extract DNA fragments up to 2 Mb in size or purify large genes directly from cells.. For short-read sequencing, a cleanly-sized library improves sequence efficiency by providing fragments that are more ideal for the flow cell or substrate used, and the reagent chemistries that have been optimized for a given read length or performance. This often boosts data quality and efficiency by making structural variation and indel discovery more straightforward.. For long-read sequencing, it is usually beneficial to remove ...
p, ,strong,,em,Note: ,/em,The following text comes from phytozome.org:,/strong,,/p, ,p, ,u,Genome Size / Loci,/u,,br /, This version (v.1) of the assembly is 319 Mb spread over 12,574 scaffolds. Half the genome is accounted for by 236 scaffolds 251 kb or longer. The current gene set (orange1.1) integrates 3.8 million ESTs with homology and ab initio-based gene predictions (see below). 25,376 protein-coding loci have been predicted, each with a primary transcript. An additional 20,771 alternative transcripts have been predicted, generating a total of 46,147 transcripts. 16,318 primary transcripts have EST support over at least 50% of their length. Two-fifths of the primary transcripts (10,813) have EST support over 100% of their length.,/p, ,p, ,u,Sequencing Method,/u,,br /, Genomic sequence was generated using a whole genome shotgun approach with 2Gb sequence coming from GS FLX Titanium; 2.4 Gb from FLX Standard; 440 Mb from Sanger paired-end libraries; 2.0 Gb from 454 paired-end libraries,/p, ...
The coverage of SNP indel matched reads was set as not smaller than two. If a SNP indel was identified only from just one read through, it had been regarded as for being very likely from a sequen cing error and as a result not thought to be a authentic SNP indel within this research. To test the accuracy of SNP calling, we created a statistical system to model the sequencing error distribution. The model is described briefly under. According on the Illumina Solexa sequencing technology report, the sequencing error charge should be reduce than 2%, and accordingly, a somewhat stringent sequencing error price, 0. 02, was selected. Provided the complete read coverage of the nu cleotide web page and the substitution coverage, the probability of the nucleotide in a specified internet site currently being brought about by sequencing errors, p, might be simulated like a Poisson distribution, using the single parameter, A nucleotide which has a probability lower compared to the pre defined sizeable level ...
The vast majority of DNA sequencers now generate short sequence reads. Although they are very efficient, many biological problems can not be solved by short fragments. A few days ago, Illumina research team found a simple solution. They used a transposon to temporarily combine short fragments, preserving sequence order or proximity.. On genomic DNA, the single base difference of different individuals is called single nucleotide polymorphism(SNP). Neighboring SNPs tend to be inherited to a progeny in the form of a whole, and this associated SNP in a chromosomal specific region is called haplotype. Haplotype can help people find genetic variations that affect gene function, performing grafting and receptor pairing, understanding structural variations in the cancer genome editing cell, and so on. Proximity is very important for haplotype.. When preparing for sequencing, Tn5 transposase are often used for DNA cleavage and sequences adding. This robust Tn5 transposase can link the sequence fragments ...
The study of how microbes affect human disease is an area I am very much interested in. In this research paper we developed a method that uses frequentist probabilities to detect bacterial strains in metagenomic samples - samples that are collected from anywhere: rivers, soil, humans, etc - using DNA sequencing data. Our approach introduces artificial point mutations at the nucleotide level in each DNA sequencing read to define a test statistic for each genome in our reference database of bacterial genomes. Most of the methods out there have a detection resolution that goes as far as the Species-level, but our method achieved a Strain-level resolution.. ...
In the last decade we have seen a tremendous development in the omics area (genomics, transcriptomics, proteomics etc.), making high throughput methods increasingly costeffective and available. The development in RNA-sequencing technology now enables us to sequence whole transcriptomes of hundreds or even thousands of samples or single cells simultaneously in only a few days. With the ability to quickly create millions of reads for thousands of genes in thousands of samples comes a computational challenge of how to make sense of the data. Due to the use of short sequencing reads, duplicate genes, biased base composition and repetitive regions in the genome, reads might not be uniquely assignable to a single gene. This problem can be solved either by computationally assigning multi-mapping reads to the most likely position, or excluding these reads and normalizing gene expression for the uniquely mappable positions in a gene. In paper I, we describe a software application for efficiently finding ...
In future studies of adult stem cell potential, it will be crucial to rule out the possibility that stem cells are merely fusing to local cells rather than generating new ones. Still, tissue-specific cells have already produced encouraging results. In the German TOPCARE-AMI study of patients with severe heart damage following myocardial infarction, the patients 35 own heart progenitor cells were infused directly into the infarcted artery. Four months later the size of the damaged tissue swath had decreased by nearly 36 percent, and the patients heart function had increased by 10 percent. Amplification followed by base-extension sequencing with py- 43 runs per base - of the target genome, 454 achieved accurophosphate detection in an array of wells. Both groups read racy of one error per 2,500 base pairs. The Harvard group had about the same amount of sequence, 30 million base pairs, in less than one error per three million base pairs with 7× covereach sequencing run. Our system read about 400 ...
We describe a sensitive technique for mutation detection using clonal sequencing. We analyzed DNA extracted from 13 cancer cell lines and 35 tumor samples and applied a novel approach to identify disease-associated somatic mutations. By matching reads against an index of known variants, noise can be dramatically reduced, enabling the detection and quantification of those variants, even when they are present at less than 1% of the total sequenced population; this is comparable to, or better than, current diagnostic methods. Following the identification or exclusion of known variants, unmatched reads are grouped for BLAST searching to identify novel variants or contaminants. Known variants, novel variants, and contaminants were readily identified in tumor tissue using this approach. Our approach also enables an estimation of the per-base sequencing error rate, providing a confidence threshold for interpretation of the results in the clinic. This novel approach has immediate applicability to ...
The molecular interactions that occur during Sanger cycle sequencing are complex. The animation explains the chemistry behind the dye terminator sequencing reactions used at genome sequencing centers. It will give you a better understanding of the details involved in the synthesis of fluorescently labeled DNA fragments that provide the data for genomic sequencing projects. ...
Next Generation Sequencing (NGS) enables rapid sequencing of large stretches of DNA base pairs spanning entire genomes, with some instruments capable of producing hundreds of gigabases of data in a single sequencing run.. The NGS data management and analysis are complex and include:. ...
Our research projects focus on a combination of field ecology with bioinformatics and new sequencing technologies. Conceptually, we are interested in patterns and structuring forces of communities, where organisms are not easily identifiable or distinguishable from each other. This interest applies to various levels, starting with abundance and diversity of taxa, over phylogenetic reconstructions, towards environmental and spatial influences and lastly regarding organisms molecular interactions with each other on a genomic level. Methodologically, the workgroup is developing computational workflows and databases as well as laboratory protocols to analyse ecological samples with next-generation sequencing technologies. Biologically, the focus of current projects is the dynamics of bacteria-host associations in changing environments. Regarding this, we currently consider changes in microbiota induced by ...
Gene Interval Updater Go to page. Gene Interval Updater is a tool that can be used to convert U00096.2 gene (and feature) genomic addresses to U00096.3 coordinates. The MG1655(Seq) [ATCC 700926] represented in Genbank U00096.2 [4,639,675 bp] has several sequence errors, including two missed IS element insertions, that were reported in 2012 by Freddolino et al. [pmid: 22081388]. We have confirmed these DNA sequence errors and corrected them, creating U00096.3 [4,641,652 bp]. MG1655(Seq) has three previously unknown gene mutations, in crl, gatC and glpR; two sequencing errors in ylbE were corrected, including a frameshift error that restored this ORF previously thought to be a pseudogene. EcoGene Database Table Go to page. Download a customized table from the current EcoGene database. The table will be a tab delimited ascii text file. You can specify the fields you want to download and each field will be separated by a tab. Please be aware that the database contents are being altered daily and ...
Gene Interval Updater Go to page. Gene Interval Updater is a tool that can be used to convert U00096.2 gene (and feature) genomic addresses to U00096.3 coordinates. The MG1655(Seq) [ATCC 700926] represented in Genbank U00096.2 [4,639,675 bp] has several sequence errors, including two missed IS element insertions, that were reported in 2012 by Freddolino et al. [pmid: 22081388]. We have confirmed these DNA sequence errors and corrected them, creating U00096.3 [4,641,652 bp]. MG1655(Seq) has three previously unknown gene mutations, in crl, gatC and glpR; two sequencing errors in ylbE were corrected, including a frameshift error that restored this ORF previously thought to be a pseudogene. EcoGene Database Table Go to page. Download a customized table from the current EcoGene database. The table will be a tab delimited ascii text file. You can specify the fields you want to download and each field will be separated by a tab. Please be aware that the database contents are being altered daily and ...
Gene Interval Updater Go to page. Gene Interval Updater is a tool that can be used to convert U00096.2 gene (and feature) genomic addresses to U00096.3 coordinates. The MG1655(Seq) [ATCC 700926] represented in Genbank U00096.2 [4,639,675 bp] has several sequence errors, including two missed IS element insertions, that were reported in 2012 by Freddolino et al. [pmid: 22081388]. We have confirmed these DNA sequence errors and corrected them, creating U00096.3 [4,641,652 bp]. MG1655(Seq) has three previously unknown gene mutations, in crl, gatC and glpR; two sequencing errors in ylbE were corrected, including a frameshift error that restored this ORF previously thought to be a pseudogene. EcoGene Database Table Go to page. Download a customized table from the current EcoGene database. The table will be a tab delimited ascii text file. You can specify the fields you want to download and each field will be separated by a tab. Please be aware that the database contents are being altered daily and ...
Gene Interval Updater Go to page. Gene Interval Updater is a tool that can be used to convert U00096.2 gene (and feature) genomic addresses to U00096.3 coordinates. The MG1655(Seq) [ATCC 700926] represented in Genbank U00096.2 [4,639,675 bp] has several sequence errors, including two missed IS element insertions, that were reported in 2012 by Freddolino et al. [pmid: 22081388]. We have confirmed these DNA sequence errors and corrected them, creating U00096.3 [4,641,652 bp]. MG1655(Seq) has three previously unknown gene mutations, in crl, gatC and glpR; two sequencing errors in ylbE were corrected, including a frameshift error that restored this ORF previously thought to be a pseudogene. EcoGene Database Table Go to page. Download a customized table from the current EcoGene database. The table will be a tab delimited ascii text file. You can specify the fields you want to download and each field will be separated by a tab. Please be aware that the database contents are being altered daily and ...
I realize that there are people who will cheer this or support this approach in the U.K., but I think I’m feeling sick reading this news report that Joe...
Immune-profiling analyses of tumors showed that response to PD-1 inhibition was associated with higher concentrations of immune filtrates in tumors at baseline, including several T-cell markers (CD3, CD8, and PD-1). In particular, higher concentrations of CD8-positive cells in tumors correlated with a higher abundance of Faecalibacteria in the gut, which is part of the -Ruminococcaceae family.. Whole-genome shotgun sequencing of tumor samples from the "best" and "worst" responders revealed differences in the metabolic pathways that were activated. The initial data suggest that the gut bacteria in responders tend to "turn on" pathways that tip the balance toward biosynthesis, whereas those in nonresponders tend to be more degradative. Dr. Wargo said her "hunch" is this: "An unfavorable gut microbiome is essentially creating chronic inflammation and an immunosuppressive phenotype, which is translating into a weak antitumor immune response.". Moving Forward. These study findings could have ...
As such, it presents a detailed comparative analysis of commercially available platforms as well as insights into alternative, emerging sequencing techniques. In addition, the book not only covers the principles of DNA sequencing techniques but also social, ethical and commercial aspects, the concept of personalized medicine and a five-year perspective of DNA sequencing.. ...
The clonally amplified fragments are enriched and loaded onto a PicoTiterPlate device for sequencing. The diameter of the PicoTiterPlate wells allows for only one bead per well. After addition of sequencing enzymes and reagents, the fluidics subsystem of the Genome Sequencer System serially flows nucleotides in a fixed order (i.e. first T, then A, and so on) across the hundreds of thousands of wells containing one bead each. Addition of one (or more) nucleotide(s) complementary to the template strand results in a chemiluminescent signal recorded by the CCD camera of the Genome Sequencer System. The intensity of the resulting signal is proportional to the number of bases incorporated.. 6. Data Analysis ...
NucleoSEQ columns are prefilled single spin columns for efficient removal of unincorporated dye terminators (e.g., BigDye Terminators) from sequencing reactions, resulting in high-quality sequence with a long reading length and minimized background.
NucleoSEQ columns are prefilled single spin columns for efficient removal of unincorporated dye terminators (e.g., BigDye Terminators) from sequencing reactions, resulting in high-quality sequence with a long reading length and minimized background.
As an additional check, the number of reads in EBV-negative tumors were counted with the expectation of finding virtually nothing if human reads are not contaminating. Out of 35 EBV-negative genomes, 25 (71%) had exactly zero reads. The remaining genomes, with one exception (which had 90), had at most 19 (range: 1-19) reads. When a few randomly selected reads were attempted to align to the human genome, only short matches (20-30 bp) were found that were expected to be spurious. Therefore, it is believed that these are real EBV reads.. Given that EBV is ubiquitous (e.g. over 90% of adults globally and most African children are infected), it is possible that EBV-infected normal B cells were included at very low levels in otherwise EBV-negative tumor biopsies. This would explain the presence of a few EBV reads found in EBV-negative BL samples. In general, EBV reads are often found in DNA sequencing data. For more information, see http://www.cureffi.org/2013/02/01/the-decoy-genome/ .Therefore, we ...
Integrative analysis of environmental sequences using MEGAN 4, Genome Res., 21, 2011, 1552-1560. CHEBEŇOVÁ-TURCOVSKÁ, V., ŽENIŠOVÁ, K., KUCHTA, T., PANGALLO, D., BREŽNÁ, B.: Culture-independent detection of microorganisms in traditional Slovakian bryndza cheese. Int. J. Food Microbiol., 150, 2011, 73-78. CHEN, C., KHALEEL, SS., HUANG, H., WU, CH.: Software for pre-processing Illumina next-generation sequencing short read sequences. Source Code Biol. Med., 9, 2014, 1-11. ERCOLINI, D. : High-Throughput Sequencing and. ...
We developed a novel approach for targeted resequencing, Oligonucleotide-Selective Sequencing (OS-Seq), in which we modify the immobilized oligonucleotide primer lawn of a next generation DNA sequencer to function as both a capture and sequencing substrate. We designed two targeting assays in which .. [more] we flanked the exons of 10 or 344 cancer genes. In our assessment of capture performance, 87% or higher of the captured sequence originated from the target region and the target sequencing fold coverage generally fell within a 10 fold range. To determine OS-Seqs performance for single nucleotide variant (SNV) calling, we analyzed an individual who had undergone complete genome analysis and compared the published variants with our data with generally excellent concordance. We also showed a similar high performance for SNV calling from the OS-Seq analysis of a matched normal colorectal cancer pair in comparison to SNP array genotyping. [less] ...
Personalized medicine and genetic testing: Whole genome sequencing can identify oncogenes, lower treatment cost, and improve cancer diagnosis and treatment
Fred Sanger developed the first technique for sequencing DNA. DNA is replicated in the presence of chemically altered versions of the A, C, G, and T bases. These bases stop the replication process when they are incorporated into the growing strand of DNA, resulting in varying lengths of short DNA. These short DNA strands are ordered by size, and by reading the end letters from the shortest to the longest piece, the whole sequence of the original DNA is revealed.
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A group of my scientific colleagues who are working on novel next-generation sequencing approaches, recently approached me about developing some computational simulations of the processes underlying these new methods with a view to demonstrating their feasibility, but also to optimize them for use with large genomes - specifically our own human genome. This article is not about these new sequencing approaches per se, which are still under development and about which I am not in any case, at liberty to talk - but rather it is more a story about how a challenging genome sequencing project demonstrated once again, what an awesome tool Python can be, and inspired me to pen another "Python-for-the-biologist" mini tutorial.. The human genome is about 3 gigabases (3.0 x 109 bases) in length, and for sequences of such a size, there can be significant technical challenges both in the laboratory, to accurately and reliably capture the sequence data from the relatively delicate, nanoscale biopolymers that ...
Eventbrite - Melbourne Bioinformatics presents Introduction to long-read genome assembly - 22 Mar - Thursday, March 22, 2018 at Melbourne Bioinformatics Boardroom, Carlton, VIC. Find event and registration information.
D27 Advanced Strategies for Direct Sequencing of BACs and Repeated Regions of Mammalian Genomes. A. Slesarev, A. Malykh, O. Malykh N. Pavlov, N. Polushin, S. Kozyavkin. Fidelity Systems, Inc., 7961 Cessna Avenue, Gaithersburg, MD 20879. We have been developing the ThermoFidelase series of thermostable proteins and advanced sequencing protocols aiming to solve problems associated with sequencing of difficult DNA templates and to reduce the cost of genome projects.. Our first application was the use of unlinking activity ThermoFidelase I (TF I) to prepare DNA templates for robust primer annealing and extension during sequencing reactions. Enzymatic unlinking of circular BAC, long bacterial genomic templates and eucaryotic DNA samples with GC- and CT-rich islands with newly developed TF II allows to reduce the duration of the denaturation step during cycle sequencing and results in high yield and quality of Sanger fragments. Furthermore, topological selection of DNA template treated by TF II, which ...
The invention provides methods for correcting misincorporation of a nucleotide in a primer during a sequencing-by-synthesis reaction by using both a polymerase substantially lacking in exonuclease activity and an enzyme, preferably a polymerase, having exonuclease activity.
Researchers at Stanford have used a next-generation technology called long-read sequencing to diagnose a patients rare genetic condition that current technology failed to diagnose.
Pyrosequencing is a sequencing‐by‐synthesis method for DNA analysis that has emerged as a platform not only for de novo sequencing applications, but also for quantitative analysis of genomic methylation, single‐nucleotide polymorphisms, and allele quantification
DNA sequencing technology, a key tool in characterizing microbes in the environment, just keeps getting cheaper and easier. Right now there are some really nice technologies out there in machines from Illumina/Solexa, Roche/454 and ABI. And coming on the horizon are some new systems that possibly will be either "better" in some way or allow …. ...
Genotype by sequencing is a type of genetic recombination that utilizes next generation sequencing techniques to construct reduced representation libraries for the Ilumina platform. The genotype by...
It is very important to have a reliable measurement of the amount of starting material so that the sample can be prepared for hybridization and amplification on the flow cell. The ideal sample is a library with 10nM of successfully ligated DNA. A 1.3ng/ul, 200bp sample is approximately 10nM. As of July 2012 the optimum cluster range is from about 250,000 to 350,000 per tile on the GAIIx and 700,000-900,000 on the HiSeq. It is crucial that we have accurate concentrations on hand to prevent under- and over-clustering. If a sample is loaded at too high of a concentration or the fragment size is highly variable the sequencers will not be able to distinguish between clusters properly, resulting in the loss of reads. If the sample is too dilute the optimum number of reads per lane will not be achieved. Having reliable concentration measurements allows us to optimize the number of reads per lane and maximize the quality of data produced. ...
WZhao68 wrote: , , Hello there, , Does anybody have a good, robust dsDNA cycle seqencing protocol other , than the Perkin Elmer one. Somebody , use DMSO in the reaction, what does it do? Do you have to increase the , amount of DNA when the plasmid is big? , Does high salt concentratin in DNA sample inhibit the cycle sequencing , reaction? , Thanks in advance! , David Hi David, we use (successfully) the following protocoll in our lab: · Master-Mix for every sequence: 4 × 50 ng/kb plasmid 4 × 2 pmol primer 4 × ad 6 µl H2O · Make aliquots of 6 µl each · add 2 µl Reactionsmix (e. g. Amersham) · Cycle-Sequencing: 2 98 °C \ 15 95 °C , 20 55 °C , 25 × 30 70 °C / 15 95 °C , 20 70 °C , 10 × · Shortly bevor loading the gel: heat samples 2 95 °C add 8 µl formamide marker-solution As you can see the amount of dna used depends on the size of the plasmid (5 ng for each kb plasmid). We add DMSO usually to PCR samples. It helps denaturating the dna, especially if there is extensive ...
Resequencing of specific regions with ultra deep amplicon sequencing or use an sequence capture approach is an cost-efficient alternative to whole genome sequencing
The increasing demand for DNA sequences can be met by replacement of each DNA sample in a device with a mixture of N samples so that the normal throughput is increased by a factor of N. Such a method is described. In order to separate the sequence information at the end of the processing, the DNA molecules of interest are ligated to a set of oligonucleotide "tags" at the beginning. The tagged DNA molecules are pooled, amplified, and chemically fragmented in 96-well plates. The resulting reaction products are fractionated by size on sequencing gels and transferred to nylon membranes. These membranes are then probed as many times as there are types of tags in the original pools, producing, in each cycle of probing, autoradiographs similar to those from standard DNA sequencing methods. Thus, each reaction and gel yields a quantity of data equivalent to that obtained from conventional reactions and gels multiplied by the number of probes used. To date, even after 50 successive probings, the original ...
All children with cancer in England will be offered whole genome sequencing from this year in a move that will enable more comprehensive and precise diagnosis and access to more personalised treatments.. NHS Englands long term plan says that this will reduce the use of harmful drugs and interventions, support increased access to clinical trials, and reduce the number of young patients who have health problems caused by chemotherapy and radiotherapy.12. The smaller numbers-there are around 1800 paediatric cancers diagnosed a year-means it is more feasible to offer whole genome sequencing to all children rather than all adults with cancer. However, adults with certain rare conditions or specific cancers will also be offered full genome screening. NHS England says by 2029 over 100 000 people a year can access these tests.. Aine McCarthy, from Cancer Research UKs childrens cancers team, said that the announcement was very exciting. "It will give us a load of new … ...
WGS offers a comprehensive approach to identifying genetic variation across the genome. We now show that rare variants can be detected in cardiomyopathy genes using WGS and targeted analysis. Although the comprehensive nature of WGS or even WES is attractive, analytic tools must be refined to identify pathogenic variants. The pipeline applied herein relied on (1) restricting the number of genes for analysis to a super gene set, (2) filtering based on frequency with the assumption that a rare disease is caused by rare genetic variation, and (3) protein prediction algorithms that largely rely on disrupting conserved regions. The method successfully identified 3 known mutations (DES c.735+3 A,G in patient MDC-01, TNNT2 K210del in patient DCM-Bl01, TPM1 D230N in patient DCM-AAB03) providing proof of principle that WGS at 30 to 40× coverage is sensitive to detect these rare variants. Likely pathogenic variants were identified in 6 of the remaining patients. Each proband had 1 to 14 variants that ...
Shotgun sequencing is the dominant method for genome sequencing in the post-genomic world. The approach, in a nutshell, involves sequencing random fragments of the genome, then assembling those fragments based on sequence overlaps and mate-pair information. You can learn much more about the method here. The shotgun method has benefits in that you do not need to know much about the genetics of the organism whose genome you plan to sequence (of course, the more you know, the easier the process). The main drawback of the method, however, is that it is extremely labor intensive (involving many intermediate steps) and costs an arm and a leg to sequence a eukaryotic genome with good coverage. The quality of a genome sequencing project is defined by how much "coverage" we have of the entire genome. The modern standard is 6-10x coverage. This means that, on average, each nucleotide is sequenced 6-10 times. The higher the coverage, the more confident we are in our nucleotide calls and the higher the ...
Advances in technology have made it much easier, faster and less expensive to do whole genome sequencing - to spell out all three billion letters in a
In one case (#1251), SNV observed in the tumor DNA were not detected in plasma DNA. In another case (#1559), SNV were barely detectable (VAF of 0.5% for two variants). Of note, both cases displayed limited disease (stage I or II) and normal lactate dehydrogenase levels, indicating that the amount of tumor-specific circulating cfDNA is at least partially related to tumor burden. Despite a low amount of circulating DNA extracted from plasma for cases #1251 and #1559, we obtained adequate sequencing quality and depth (the overall number of reads sequenced with mutated targets was 4,685 and 51,195 respectively; Table 1), indicating that in some rare cases, tumor-specific cfDNA is absent or beneath the level of sensitivity of the NGS method used. Of note, in case #1631 characterized by limited stage I disease, SNV were detected with a mean VAF of 5.2% in plasma DNA, as compared to a mean VAF of 34.6% in the tumor DNA (Table 1). In contrast, cases #1639 and #1768 (both with stage IV disease and ...
Although recent studies highlighted the importance of T cell repertoire composition for immune recognition of specific pathogens (3, 36-38) and the maintenance of immune efficacy with age (39), our current understanding of these processes is derived predominantly from analyses of small samples of epitope-specific repertoires. Next-generation sequencing technologies provide an opportunity to study complete memory and naive T cell repertoires in depth. In this study, we rigorously sorted the memory and naive CD8+ T cell populations from four donors and pyrosequenced the portions of the corresponding TCRβ repertoires with TRBV12-4/TRBJ1-2 gene rearrangements. We found that there is a high degree of overlap between the memory and naive repertoires within individuals; TCRβ clonotypes common to the memory and naive pools tend to be more frequent in both pools; a substantial proportion of the memory and naive repertoires consist of TCRβ clonotypes that are shared between individuals; shared TCRβ ...
Even though Next Gen sequencing gives us the technical capabilities to ask detailed and quantitative questions about gene structure and expression, successful experiments demand that we pay close attention to the details. Obtaining data that are free of confounding artifacts and accurately represent the molecules in a sample, demands good technique and a focus on detail. DNA libraries no longer involve cloning, but their preparation does require multiple steps performed over multiple days. During this process, different kinds of data ranging from gel images to discrete data values, may be collected and used later for trouble shooting. Tracking the experimental details requires that a system be in place that can be configured to collect information from any number and kind of process. The system also needs to be able to link data to the samples, and convert the information from millions of sequence data points to tables, graphics and other representations that match the context of the experiment ...
Cercis chinensis is a species of redbud that is becoming increasingly popular in the landscape. An understanding of its genome and the identification of molecular markers will assist in breeding new cultivars. This project has two objectives: 1) Assemble the partial genome of Cercis chinensis using data from a 454 DNA sequencer; and 2) Identify molecular markers from this partial preliminary genome, ie, single-nucleotide polymorphisms (SNPs). DNA sequence reads from the Cercis chinensis genome (454 DNA sequencer) were obtained, and assembled using the Abyss assembler as well as a second sequence assembler, CAP3, independently. An Entrez search of the results on the NCBI website for the Cercis chinensis revealed no records for the genome, three hits on the Protein database records, and 15 hits on the Nucleotide database records. The database search also revealed no SNPS for Cercis chinensis. A BLAST analysis of the assembled contigs from CAP3 for the dissimilar database provides results with ...
Velculescu and his team acknowledge there may be challenges in implementing tumor-normal analyses in a clinical setting. These include the additional work and costs of sequencing and analyzing a patients normal tissue along with his or her tumor tissue but Velculescu says some efficiencies could be realized by using the patients saliva, blood or normal tissue recovered during a biopsy or tumor removal. Costs for tumor gene sequencing begin at several thousand dollars, which would increase if sequencing was done on DNA from normal tissue as well ...
However, the Next Gen methods come out far ahead if you multiplex a group of individuals together in the same sequencing reaction. This is not possible with Sanger methods since the sequence is read from the average of a large number of molecules. Then the question becomes how deep can you multiplex while still producing enough reads from each individual research subject to achieve the depth of coverage needed? Our Illumina GAII currently produces about 2 million (usable) 35 bp reads per lane, but we are ramping up toward 5 million 50 bp reads with the latest upgrades ...
...Next-generation DNA sequencing (NGS) technology has revolutionized bio......,Essential,informatics,methods,and,tools,for,analyzing,the,explosion,of,NGS,data,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
Publisher: University of Delaware. Date Issued: 2015. Abstract: Viral infection and lysis are important processes contributing to the diversification and evolution of microbial communities. In marine ecosystems that cover 70% of the earths surface, there are ~10 million viruses per milliliter of seawater, indicating an incredible diversity of viruses waiting to be explored. An important breakthrough in viral ecology was the application of high-throughput DNA sequencing to entire viral communities. Known as shotgun viral metagenomics, this approach allows access to the majority of viruses that cannot be maintained in culture. Viral metagenomics has revealed surprising insight into ancient associations between viruses and hosts. However, making quantitative inferences from next generation sequencing data requires careful evaluation of viral isolation and DNA library preparation techniques. Many library preparation strategies employ some form of amplification to obtain sufficient DNA for ...
The effect of EMS mutagenesis initially can be observed through phenotypic changes of mutagenized plants, and numerous reports have been published on the effects. The abnormal phenotypic variance due to EMS exposure also has been reported previously in L. japonicus (Perry et al. 2003) and other plants such as Glycine max (soybean; Carroll et al. 1986), Hordeum vulgare L. (barley; Caldwell et al. 2004), Sorghum bicolor (L.) Moench Xin et al. 2008), Solanum lycopersicum (tomato; Minoia et al. 2010), and Capsicum annuum L. (chilli pepper; Sri Devi and Mullainathan 2012). The percentage of the abnormal phenotypes varied in different plants depending on the concentration of EMS used (Xin et al. 2008). Phenotypic changes are not restricted to plant growth but also affect their physiological characteristics. For examples, reduced sensitivity to ABA was reported by Biswas et al. (2009) in L. japonicus mutagenized by EMS. Response to high temperature also was affected in EMS-induced Arabidopsis mutants ...
TY - JOUR. T1 - OTOF mutation analysis with massively parallel DNA sequencing in 2,265 Japanese sensorineural hearing loss patients. AU - Iwasa, Yoh ichiro. AU - Nishio, Shin ya. AU - Sugaya, Akiko. AU - Kataoka, Yuko. AU - Kanda, Yukihiko. AU - Taniguchi, Mirei. AU - Nagai, Kyoko. AU - Naito, Yasushi. AU - Ikezono, Tetsuo. AU - Horie, Rie. AU - Sakurai, Yuika. AU - Matsuoka, Rina. AU - Takeda, Hidehiko. AU - Abe, Satoko. AU - Kihara, Chiharu. AU - Ishino, Takashi. AU - Morita, Shin ya. AU - Iwasaki, Satoshi. AU - Takahashi, Masahiro. AU - Ito, Tsukasa. AU - Arai, Yasuhiro. AU - Usami, Shin ichi. PY - 2019/5/1. Y1 - 2019/5/1. N2 - The OTOF gene (Locus: DFNB9), encoding otoferlin, is reported to be one of the major causes of non-syndromic recessive sensorineural hearing loss, and is also reported to be the most common cause of non-syndromic recessive auditory neuropathy spectrum disorder (ANSD). In the present study, we performed OTOF mutation analysis using massively parallel DNA sequencing ...
Obtaining full-length 16S rRNA gene sequences is important for generating accurate taxonomy assignments of bacteria, which normally is realized via clone library construction. However, the application of clone library has been hindered due to its limitations in sample throughput and in capturing minor populations (<1 % of total microorganisms). To overcome these limitations, a new strategy, two-step denaturing gradient gel electrophoresis (2S-DGGE), is developed to obtain full-length 16S rRNA gene sequences. 2S-DGGE can compare microbial communities based on its first-round DGGE profiles and generate partial 16S rRNA gene sequences (8-534 bp, Escherichia coli numbering). Then, strain-specific primers can be designed based on sequence information of bacteria of interest to PCR amplify their remaining 16S rRNA gene sequences (515-1541 bps, E. coli numbering). The second-round DGGE can confirm DNA sequence purity of these PCR products. Finally, the full-length 16S rRNA gene sequences can be ...
The increasing speed and decreasing cost of high-throughput DNA sequencing technologies are enabling its application to the practice of medicine (35). Here, we tested whether genome sequencing could help to unravel a nosocomial outbreak and affect hospital infection control decisions. We sequenced patient and environmental isolates within a clinically relevant turnaround time during a hospital KPC-K. pneumoniae outbreak. Among the key insights provided by sequencing were that (i) the outbreak was monoclonal, despite a 3-week interval between the index case and the identification of subsequent cases, (ii) transmission likely occurred from at least two different sites of the index patient, (iii) at least three independent transmission events from the index patient led to two major clusters of colonized patients, (iv) one patient could be linked to a contaminated ventilator, and (v) a small number of putative resistance mutations could be identified in newly colistin-resistant isolates. Moreover, ...
TY - JOUR. T1 - Cryptosporidium parvum mixed genotypes detected by PCR-restriction fragment length polymorphism analysis. AU - Reed, C.. AU - Sturbaum, G. D.. AU - Hoover, P. J.. AU - Sterling, Charles R. PY - 2002. Y1 - 2002. N2 - Combinations of 10 Cryptosporidium parvum oocysts, with various ratios of genotype I to genotype II, were isolated and subjected to PCR-restriction fragment length polymorphism analysis. Amplification of both genotypes in these samples ranged from 31 to 74% and yielded no information about the genotype proportions. In addition, since both genotypes were not always detected, amplification of a single genotype is not conclusive evidence that the sample contains only a single genotype.. AB - Combinations of 10 Cryptosporidium parvum oocysts, with various ratios of genotype I to genotype II, were isolated and subjected to PCR-restriction fragment length polymorphism analysis. Amplification of both genotypes in these samples ranged from 31 to 74% and yielded no information ...
article{7225551, abstract = {A Gram-stain-positive, ovoid, lactic acid bacterium, strain LMG 27676(T), was isolated from a spoiled sous-vide-cooked rutabaga. 16S rRNA gene sequence analysis indicated that the novel strain belongs to the genus Leuconostoc, with Leuconostoc kimchii and Leuconostoc miyukkimchii as the nearest neighbours (99.1 and 98.8\% 16S rRNA gene sequence similarity towards the type strain, respectively). Phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of the pheS, rpoA and atpA genes, and biochemical and genotypic characteristics allowed differentiation of strain LMG 27676(T) from all established species of the genus Leuconostoc. Strain LMG 27676(T) (=R-50029(T)=MHB 277(T)=DSM 27776(T)) therefore represents the type strain of a novel species, for which the name Leuconostoc rapi sp. nov. is proposed.}, author = {Lyhs, Ulrike and Snauwaert, Isabel and Pihlajaviita, Seija and De Vuyst, Luc and Vandamme, Peter}, issn = {1466-5026}, journal = {INTERNATIONAL ...
A novel Ferrimonas species is described on the basis of phenotypic, chemotaxonomic and phylogenetic studies. Four halophilic organisms were isolated from marine sand and marine macroalgae samples by using high-pH marine agar 2216. An analysis of the nearly complete 16S rRNA gene sequences of these new isolates indicated that they were phylogenetically close (16S rRNA gene sequence similarity |99·5 %, gyrB gene sequence similarity |97·8 %), and were most closely related to Ferrimonas balearica (16S rRNA gene sequence similarity 97·1-97·3 %, gyrB gene sequence similarity 84·4-85·0 %). Chemotaxonomic data (major menaquinone MK7; major fatty acids C16 : 0 and C18 : 1 ω9c) supported the affiliation of the new isolates to the genus Ferrimonas. The results of physiological and biochemical tests allowed phenotypic differentiation of the isolates from F. balearica. It is therefore proposed that the new isolates represent a novel species with the name Ferrimonas marina sp. nov. and type strain A4D-4T (
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... and the position of their DNA cleavage site relative to the target sequence.[31][32][33] DNA sequence analyses of restriction ... Freeware DNA cloning, sequence analysis and plasmid/DNA plotting software. *. Čermák V. "Restriction Analyzer". Retrieved 2016- ... Recognition sequences in DNA differ for each restriction enzyme, producing differences in the length, sequence and strand ... but the forward and backward sequences are found in complementary DNA strands (i.e., of double-stranded DNA), as in GTATAC ( ...
Sequencing and analysis of Neanderthal genomic DNA. Science. 2006 Nov 17;314(5802):1113-8. Tringe SG et al. Comparative ... during which time the DOE JGI completed the sequencing and analyses of chromosomes 5, 16 and 19. After that project, he ... harnessing sequence comparisons between species for the discovery of genes and non-coding sequences of pivotal evolutionary and ... his DOE JGI collaborators have played a leading role in the emerging field of metagenomics-sequencing and characterizing DNA ...
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Taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data". Proceedings of the Royal Society of ... DNA analysis has shown the family Maluridae to be related to the Meliphagidae (honeyeaters), and the Pardalotidae (pardalotes, ... A 2017 genetic study using both mitochondrial and nuclear DNA found the ancestors of the superb and splendid fairywrens ...
"Theoretical analysis of mutation hotspots and their DNA sequence context specificity" (PDF). Mutation Research. 544 (1): 65-85 ... Hotspots can arise at certain nucleotide sequences because of interactions between the DNA and DNA repair, replication, and ... At the genotype level recurrent evolution can only be detected using DNA sequencing data. The same or similar changes in the ... An example of this would include some types of phase variation that involve highly directed changes at the DNA sequence level. ...
Schmutz J, Martin J, Terry A, et al. (2004). «The DNA sequence and comparative analysis of human chromosome 5.». Nature 431 ( ... Chen Q, Baird SD, Mahadevan M, et al. (1998). «Sequence of a 131-kb region of 5q13.1 containing the spinal muscular atrophy ...
Structure and sequence analysis of influenza A virus nucleoprotein. Science in China Series C: Life Sciences. 2009-05-27, 52 (5 ... 最普遍的脱氧核糖核蛋白是核小体,其中组分是核DNA。 与DNA结合的蛋白质是组蛋白和精蛋白; 所得到的核蛋白位于染色体中。 因此,整个染色体,即真核生物中的染色质由这种核蛋白组成[13][14]。 ... Forces during Bacteriophage DNA Packaging and Ejection. Biophysical Journal: 851-866
DNA sequence analysis further confirmed the identity.[16]. Another case found N. sphaerica isolated from a corneal ulcer. A ... rRNA sequence comparison of the ITS region confirmed N. sphaerica identity.[14] Cases of leaf spot disease of kiwi fruit ( ... Analysis of corneal scrapings showed presence of hyphae elements suggesting cause of ulcer from a fungal pathogen. Isolated ...
Analysis of the nucleotide sequence of these remaining strands revealed 'correct' solutions to the original problem.[1] ... DNA computing#History *^ "Adleman, Leonard - USC Viterbi Department of Computer Science". www.cs.usc.edu. Archived from the ... DNA computing has been shown to have potential as a means to solve several other large-scale combinatorial search problems.[8] ... In 1994, his paper Molecular Computation of Solutions To Combinatorial Problems described the experimental use of DNA as a ...
"Regulatory DNA sequences: predictability of their function". Genome Analysis - from Sequence to Function; BioTechForum - ... matrix-based sequence analysis with a number of different algorithms ConTra - matrix-based sequence analysis in conserved ... matrix-based sequence analysis in conserved promoter regions Comparison of matrices with the matrix library of TRANSFAC and ... Visualisation and analysis of transcription factor binding sites in nucleotide sequences". Nucleic Acids Res. 31 (13): 3572-5. ...
Complete sequence and analysis of the plastid genome of the unicellular red alga Cyanidioschyzon merolae. DNA Res. 2003 ... Complete sequence of the mitochondrial DNA of the red alga Porphyra purpurea: cyanobacterial introns and shared ancestry of red ... Complete sequence and analysis of the mitochondrial genome of Hemiselmis andersenii CCMP644 (Cryptophyceae). BMC Genomics. 2008 ... Gupta RS, Singh B. Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic ...
"DNA sequence and analysis of human chromosome 9.". Nature. 429 (6990): 369-74. Bibcode:2004Natur.429..369H. PMC 2734081. . PMID ... regulation of transcription, DNA-templated. • transcription from RNA polymerase II promoter. • transcription, DNA-templated. • ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.". Proc. Natl. Acad. Sci. U.S.A ... 2003). "The small nuclear RNA-activating protein 190 Myb DNA binding domain stimulates TATA box-binding protein-TATA box ...
"DNA sequence and analysis of human chromosome 9". Nature. 429 (6990): 369-74. doi:10.1038/nature02465. PMC 2734081. PMID ... The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro". DNA Res. 5 (1): 31-9. doi ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ...
The paternal DNA in the mother's plasma had to have come from the fetus. Then, they could reliably identify fetal DNA, which ... And each case seems to present a new low in terms of the depth and quality of analysis." She sees a common thread in these ... So they wanted to focus on genetic fragments containing paternally inherited sequences the mother did not share, but had ... The inventors realized that the fetus had DNA derived from the father as well as the mother, and that paternal DNA was not ...
1999b). Further DNA sequence analyses (Madsen et al. 2001, Murphy et al., 2001 Waddell et al. 2001) supported the Euarchonta ... Early history of mammals is elucidated with the ENCODE multiple species sequencing data. PLoS Genet. 3:e2, doi:10.1371/journal. ... 2001) showing near total congruence of mtDNA-based and nuclear-based trees when such sequences were excluded, some authors ... Kumar, Vikas; Hallström, Björn M.; Janke, Axel (2013-04-01). "Coalescent-Based Genome Analyses Resolve the Early Branches of ...
... Stephen A. Karl karl at CHUMA.CAS.USF.EDU Mon Dec 4 14:34:28 EST 1995 *Previous message: DNA ... People working with ribosomal DNA sequence are probably not in this group and have legitimate concerns. For others where in/ ... If many gaps are needed to align a sequence then it would seem that the degree of divergence between the sequences are such ... If the sequences are easily aligned and there are clear gaps necessary for the alignment then including them in the data set ...
These probe arrays, or DNA chips, can then be applied to parallel DNA hybridization analysis, directly yielding sequence ... Light-generated oligonucleotide arrays for rapid DNA sequence analysis. A C Pease, D Solas, E J Sullivan, M T Cronin, C P ... Light-generated oligonucleotide arrays for rapid DNA sequence analysis. A C Pease, D Solas, E J Sullivan, M T Cronin, C P ... Light-generated oligonucleotide arrays for rapid DNA sequence analysis. A C Pease, D Solas, E J Sullivan, M T Cronin, C P ...
Recent advances in DNA sequencing methodologies have caused an exponential growth of publicly available genomic sequence data. ... web-based software toolkit DNA sequence analysis DNA compression This is a preview of subscription content, log in to check ... Pratas D., Pinho A.J., Garcia S.P. (2012) Exon: A Web-Based Software Toolkit for DNA Sequence Analysis. In: Rocha M., Luscombe ... Dix, T.I., Powell, D.R., Allison, L., Bernal, J., Jaeger, S., Stern, L.: Comparative analysis of long DNA sequences by per ...
We have developed a method for the partial automation of DNA sequence analysis. Fluorescence detection of the DNA fragments is ... Fluorescence detection in automated DNA sequence analysis.. Smith LM, Sanders JZ, Kaiser RJ, Hughes P, Dodd C, Connell CR, ... by means of a fluorophore covalently attached to the oligonucleotide primer used in enzymatic DNA sequence analysis. A ... the separated fluorescent bands of DNA are detected near the bottom of the tube, and the sequence information is acquired ...
... Gigi Murphy MCBKANGI at nusvm.bitnet Fri May 4 16:29:30 EST 1990 * ... I am trying to set up a DNA/Protein sequence analysis software on our University IBM 3081 or IBM 3090 running VM/CMS since our ...
Sampling properties of DNA sequence data in phylogenetic analysis. Title. Sampling properties of DNA sequence data in ...
A case of onychomycosis due to Aspergillus sydowii diagnosed using DNA sequence analysis.. Takahata Y, Hiruma M, Sugita T, Muto ... The causative agent was identified as Aspergillus sydowii based on DNA sequencing and the macroscopic and microscopic ...
DNA sequence analysis of artificially evolved ebg enzyme and ebg repressor genes.. B G Hall, P W Betts and J C Wootton ... DNA sequence analysis of artificially evolved ebg enzyme and ebg repressor genes.. B G Hall, P W Betts and J C Wootton ... DNA sequence analysis of artificially evolved ebg enzyme and ebg repressor genes.. B G Hall, P W Betts and J C Wootton ... DNA sequence analysis of artificially evolved ebg enzyme and ebg repressor genes. ...
DNA methylation is the paradigm epigenetic modification that is associated with transcriptional repression.... ... Epigenetic modifications of chromatin and DNA are relevant for eukaryotic gene expression. ... Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res 67 ... Baubec T., Akalin A. (2016) Genome-Wide Analysis of DNA Methylation Patterns by High-Throughput Sequencing. In: Aransay A., ...
Also discussed are important recent diagnostic applications of DNA sequencing in cancer, including analysis of tumor derived ... Also discussed are important recent diagnostic applications of DNA sequencing in cancer, including analysis of tumor derived ... Pharmogenetic variants detected by DNA sequence analysis are gaining in importance and are particularly relevant to ... Applications involving analysis of cell free DNA in maternal DNA for prenatal diagnosis of specific autosomal trisomies are ...
Sequencing and Analysis of Neanderthal Genomic DNA. By James P. Noonan, Graham Coop, Sridhar Kudaravalli, Doug Smith, Johannes ... Sequencing and Analysis of Neanderthal Genomic DNA. By James P. Noonan, Graham Coop, Sridhar Kudaravalli, Doug Smith, Johannes ... Our analyses suggest that on average the Neanderthal genomic sequence we obtained and the reference human genome sequence share ... The sequences of DNA fragments from Neanderthal bones date the divergence of humans and Neanderthals to about 370,000 years ago ...
Cytogenetic Analysis of Populus trichocarpa - Ribosomal DNA, Telomere Repeat Sequence, and Marker-selected BACs. Cytogenet ... Cytogenetic Analysis of Populus trichocarpa - Ribosomal DNA, Telomere Repeat Sequence, and Marker-selected BACs ... Six BAC clones selected from 2 linkage groups based on genome sequence assembly (LG-I and LG-VI) were localized on 2 ... All BAC positions were found to be concordant with sequence assembly positions. BAC-FISH will be useful for delineating each of ...
BACKGROUND: A computational system for analysis of the repetitive structure of genomic sequences is described. The method uses ... This method has been incorporated into a system that can find repeats in individual genome sequences or sets of sequences, and ... should prove helpful in the analysis of repeat structure for both complete and partial genome sequences. ... CONCLUSIONS: We propose a new clustering method for analysis of the repeat data captured in suffix trees. ...
DNA SEQUENCE ANALYSIS - SANGER OR NGS. Sequencher DNA Sequence Analysis Software is an indispensable tool for the benchtop ... With powerful analyses and rich visualizations, it has a unique paradigm where every analysis is an experiment that make your ... Next-Gen Sequencing (NGS), and RNA-Seq sequence data. Come see what Sequencher can do for you, Power with Simplicity. ... RNA-SEQ OR MICROARRAY DATA ANALYSIS CodeLinker is a user-friendly and powerful desktop software program for analyzing your RNA- ...
Sanger DNA Analysis. Sequenchers extensive Sanger analysis features are the foundation it was built upon. Customizable from ... Easily use consensus sequences from the Project Window as a reference sequence for NGS alignments for hybrid sequencing ... NEXT-GENERATION DNA SEQUENCING (NGS). Sequencher empowers the benchtop scientist by bringing the latest peer-reviewed NGS ... Send primer pair sequences from Primer-BLAST runs in Sequencher Connections to your Sequencher project. ...
BI101 Introduction to DNA and Protein Sequence Analysis; Jul. 9-13, 2012. (ACTG). This course teaches the individual how to ... analyze DNA and protein sequences using computer software. Topics to be covered include description of sequence alignments, ...
... algorithms are the traditional ways to compare and analyze DNA sequences. However, for large DNA sequences, these algorithms ... Results: We perform similarity/dissimilarity analyses among two real DNA data sets, the coding sequences of the first exon of ... Objective: Here we will propose a new numerical method to characterize and compare DNA sequences quickly. Method: Based on a ... graphical representation of DNA sequences, we can obtain an 8-dimensional vector using two basic concepts of probability, the ...
Phylogenetic Analysis of DNA Sequences has 1 available editions to buy at Alibris ... Phylogenetic Analysis of DNA Sequences by Miyamoto, Cracraft starting at $13.07. ... Phylogenetic Analysis of DNA Sequences. by Miyamoto, Cracraft Write The First Customer Review ... In this volume, international contributors address crucial questions about DNA systematics, including DNA sequence data ...
HUMAN MITOCHONDRIAL DNA VARIATION AND EVOLUTION: ANALYSIS OF NUCLEOTIDE SEQUENCES FROM SEVEN INDIVIDUALS. Charles F. Aquadro ... HUMAN MITOCHONDRIAL DNA VARIATION AND EVOLUTION: ANALYSIS OF NUCLEOTIDE SEQUENCES FROM SEVEN INDIVIDUALS. Charles F. Aquadro ... HUMAN MITOCHONDRIAL DNA VARIATION AND EVOLUTION: ANALYSIS OF NUCLEOTIDE SEQUENCES FROM SEVEN INDIVIDUALS. Charles F. Aquadro ... HUMAN MITOCHONDRIAL DNA VARIATION AND EVOLUTION: ANALYSIS OF NUCLEOTIDE SEQUENCES FROM SEVEN INDIVIDUALS ...
Before any analysis of a DNA sequence can take place it is first necessary to determine the actual sequence itself, at least as ... Before any analysis of a DNA sequence can take place it is first necessary to determine the actual sequence itself, at least as ... Ewens W.J., Grant G.R. (2001) The Analysis of One DNA Sequence. In: Statistical Methods in Bioinformatics. Statistics for ... Unfortunately, technical considerations make it impossible to sequence very long pieces of DNA all at once. Instead, many ...
The new system is ideal for applications requiring analysis of longer sequences, such as DNA methylation analysis in epigenetic ... The new system is ideal for applications requiring analysis of longer sequences, such as DNA methylation analysis in epigenetic ... Single Base Resolution DNA Methylation and Mutation Analysis in Long Sequence Runs. ... DNA methylation analysis at single base resolution at CpG and CpN sites ...
His other research focus is using computers for DNA analysis to prevent disease.. More than 99 percent of the DNA in every ... Computer science graduate develops models for DNA sequence analysis ... Computer science graduate develops models for DNA sequence analysis ... Two broad areas that Hustons research focuses are developing computer models for cellular networks and performing DNA analysis ...
download bioinformatics for dna of Heterocyclic Compounds An golden tam of single quae and causes. ... Each download bioinformatics for dna runs a many understanding, with hands being 3,4-dimethyl-3-penten-2-one and certain ... download bioinformatics for dna sequence analysis of similar divisions thermodynamic esse of single ideas and parts. ... 2019; d objects of download bioinformatics for dna and resemblance. This download bioinformatics for dna sequence analysis of ...
... a guide to mapping and sequencing DNA from different organisms. [S B Primrose] -- The aim of this successful text is to provide ... Principles of genome analysis : a guide to mapping and sequencing DNA from different organisms. Author:. S B Primrose. ... Add tags for "Principles of genome analysis : a guide to mapping and sequencing DNA from different organisms". Be the first. ... schema:name "Principles of genome analysis : a guide to mapping and sequencing DNA from different organisms"@en ;. schema: ...
Both distance and parsimony methods were used to infer the evolutionary relationships of the rrs gene sequence of this genomic ... We determined the complete sequence of the rrs gene from five strains of genomic species PotiB2. ... species in comparison with the rrs gene sequence of Borrelia valaisiana and … ... By 16S Ribosomal DNA Sequence Analysis Int J Syst Bacteriol. 1997 Oct;47(4):921-5. doi: 10.1099/00207713-47-4-921. ...
  • Average nucleotide diversity among the sequences is 1.7%, several-fold higher than estimates from restriction endonuclease site variation in mtDNA from these individuals and previously reported for other humans. (genetics.org)
  • In addition, other results suggest that restriction site (as well as pairwise sequence) comparisons may underestimate the total number of substitutions that have occurred since the divergence of two mtDNA sequences from a common ancestral sequence, even at low levels of divergence. (genetics.org)
  • Alternatively, fingerprinting of total PCR products may be carried out by using, for example, amplified ribosomal DNA (rDNA) restriction analysis ( 28 , 34 ), length heterogeneity PCR ( 30 ), single-strand conformation polymorphism ( 19 , 31 ), and terminal restriction fragment length polymorphism ( 20 , 37 ). (asm.org)
  • The cloning approach has provided lists of sequence percentages or restriction fragment length polymorphism classes, along with their relative amounts in libraries. (asm.org)
  • We have developed a method for discriminating between alleles that uses a synthetic nanopore to measure the binding of a restriction enzyme to DNA. (ed.gov)
  • By digestion with HindIII restriction enzyme, a human hepatocellular carcinoma was shown to contain only 2 hepatitis B virus (HBV) DNA inserts. (eurekamag.com)
  • Strain typing and plasmid restriction analysis were performed to identify common lineages. (cdc.gov)
  • Phylogeny of R. fascians isolates obtained from Plant Clinic submissions was determined with 16S ribosomal DNA (16S rDNA) sequence analysis with sequence primers designed to amplify specific regions of R. fascians 16S rDNA. (oregonstate.edu)
  • A preliminary set of 21 Plant Clinic isolates was sequenced at the USDA/ARS Floral and Nursery Plants Research Unit in Beltsville, MD. Partial 16S rDNA sequences from the preliminary analysis were used to identify related database sequences of R. fascians isolated from non-plant environments with a nucleotide blast algorithm through the National Center for Biotechnology Information (NCBI). (oregonstate.edu)
  • Bacterial diversity in unimproved and improved grassland soils was assessed by PCR amplification of bacterial 16S ribosomal DNA (rDNA) from directly extracted soil DNA, followed by sequencing of ∼45 16S rDNA clones from each of three unimproved and three improved grassland samples (A. E. McCaig, L. A. Glover, and J. I. Prosser, Appl. (asm.org)
  • Two variable regions, comprising 390 to 450 nucleotides of the 16S rDNA molecules of 17 additional Francisella strains, including members of the species F. tularensis and F. philomiragia , were also sequenced. (microbiologyresearch.org)
  • Screening the millions of reads that next-generation sequencing produces presents a major challenge when searching for candidate SNPs. (genecodes.com)
  • With GSNAP(2) the SNP analysis takes a different approach looking at both previously reported SNPs as well as new candidates. (genecodes.com)
  • The user must supply a list of known SNPs as well as the reads and a reference sequence. (genecodes.com)
  • Most meQTLs involve CpG-SNPs, while sequence-dependent effects on chromatin binding are also important in regions of active chromatin. (harvard.edu)
  • After quality control, a total of 185,117 autosomal SNPs were kept for further analysis. (g3journal.org)
  • A genotyping technique that interrogates SNPs by hybridizing complementary DNA probes to the SNP site. (ohsu.edu)
  • Chromocenters DNA have been isolated by a biochemical approach from mouse liver cells nuclei and sequenced on the Illumina MiSeq resulting in ChrmC dataset. (biomedcentral.com)
  • Regions of DNA that can be interpreted as 'barcodes' were amplified from each sample and sequenced using Illumina Miseq technology. (kombuchabrewers.org)
  • If many gaps are needed to align a sequence then it would seem that the degree of divergence between the sequences are such that little 'true' phylogenetic information may be available. (bio.net)
  • Because of the generally low sequence divergence among P. jirovecii isolates at these loci, they are not highly discriminative for P. jirovecii typing. (cdc.gov)
  • The pair wise distance between two sequences is then calculated Jensen-Shannon (JS) divergence between their respective FFPs. (wikipedia.org)
  • DGGE banding profiles obtained from triplicate samples pooled prior to analysis indicated that there was less evenness in improved soils, suggesting that selection for specific bacterial groups occurred. (asm.org)
  • Sequence Analysis of Bacterial DNA in the Colon and Stomach of the Tyr" by Raul J. Cano, Friedrich Tiefenbrunner et al. (calpoly.edu)
  • Genomic sequencing of clinical microbiological specimens expands our capacity to study cultivable, fastidious and uncultivable members of the bacterial community. (semanticscholar.org)
  • The sequence variation indicates both known and novel mechanisms for the elaboration and variation of surface structures, and suggests that immune evasion and host interaction play an important part in the lifestyle of this persistent bacterial pathogen. (sanger.ac.uk)
  • Our new technology, software, and chemistry overcome this bottleneck and give sequence reads that are typically twice as long as those from previous PyroMark systems. (qiagen.com)
  • Maq(1) has a two level screening process which searches initially for differences between the reads and the reference sequence. (genecodes.com)
  • The approach adopts an optimized DNA extraction followed by modified library preparations to generate hundreds of kilobase reads with moderate coverage from human cells. (jove.com)
  • The sequencer then reads each individual DNA strand and gives a combination of letters that can be millions of characters long. (wateronline.com)
  • Partek and READSCAN detected 69.66% and 60.54% of the input number of reads as HCMV sequences. (aacrjournals.org)
  • More precisely, the recovery of the target pair of haplotype sequences using short reads is rephrased as the joint source-channel coding problem. (utexas.edu)
  • Two binary messages, representing haplotypes and chromosome memberships of reads, are encoded and transmitted over a channel with erasures and errors, where the channel model reflects salient features of highthroughput sequencing. (utexas.edu)
  • In this study, we determined the DNA sequences of the putative substrate-binding subunits from human endothelial cells and compared them with the sequences from leukocytes. (ahajournals.org)
  • RESULTS: The resulting software tool collects all repeat classes and outputs summary statistics as well as a file containing multiple sequences (multi fasta), that can be used as the target of searches. (jcvi.org)
  • My question here is, because I direct sequenced the PCR product which is heterogenous, I had multiple sequences in some position, I heard that there are some ways that we measure the peak of the eletrogram to measure the percentage of methylation at that particular position, any idea how to do it? (protocol-online.org)
  • Applications involving analysis of cell free DNA in maternal blood for prenatal diagnosis of specific autosomal trisomies are reviewed. (frontiersin.org)
  • 7. The method of claim 1, wherein said determining the methylation status of said defined set of CpG loci comprises digital analysis of each of a plurality of CpG loci in a plurality of individual copies of a marker nucleic acid. (patentsencyclopedia.com)
  • Predicts R-loop Forming Sequences (RLFSs) in nucleic acid sequences based on experimentally supported structural models of RLFSs. (omictools.com)
  • Here we discuss commonly used wet-lab methodologies and computational approaches to identify DNA methylation patterns and measure their dynamics during biological processes in a quantitative and unbiased manner. (springer.com)
  • Therefore, a number of reduced representation sequencing approaches exist that make re-sequencing cost effective. (biomedcentral.com)
  • By analyzing ancient DNA from more than 5,000 nondiagnostic and fragmented bones from 38 subfossil assemblages, we describe species and patterns that have been missed by morphological approaches. (pnas.org)
  • The pioneering approaches for sequence analysis were based on sequence alignment either global or local, pairwise or multiple sequence alignment. (wikipedia.org)
  • Alignment-based approaches generally give excellent results when the sequences under study are closely related and can be reliably aligned, but when the sequences are divergent, a reliable alignment cannot be obtained and hence the applications of sequence alignment are limited. (wikipedia.org)
  • There is no convincing evidence that recombination has contributed to the mtDNA sequence diversity we have observed. (genetics.org)
  • The PCR products were cloned in plasmid vectors, and the recombinant clones (amplicons) were sequenced. (calpoly.edu)
  • Send primer pair sequences from Primer-BLAST runs in Sequencher Connections to your Sequencher project. (genecodes.com)
  • Evidence suggests that massively parallel sequencing analysis of ctDNA from patients with advanced disease allows for the identification of the entire constellation of somatic mutations found in cancer cells, either from the primary tumor or from metastatic lesions. (ascopost.com)
  • Adeno-associated virus type 2 DNA replication in vivo: mutation analyses of the D sequence in viral inverted terminal repeats. (asm.org)
  • Analysis of potentially pathogenic genera showed presence of Staphylococcus and Streptococcus . (peerj.com)
  • Sequence editor features include editing of chromatogram files, contig assembly, sequence alignment, translation and other utilities. (ox.ac.uk)
  • The wild type ebg operon has been sequenced, and the sequence differences of the mutant enzymes and repressors have been determined. (genetics.org)
  • 2017). This study identified differences in the DNA extraction method as the biggest influence on the downstream gut microbiota analysis results. (bio-protocol.org)
  • We report here how modern photolithographic techniques can be used to facilitate sequence analysis by generating miniaturized arrays of densely packed oligonucleotide probes. (pnas.org)
  • DNA microarrays or biochips are formed by grafting multiple capture probes onto a surface. (bats.ch)
  • Although silicon surfaces bearing printed circuits can be used for DNA binding, the term biochip is now broadly used to describe all surfaces bearing microscopic spots, each one being formed by specific capture probes. (bats.ch)
  • The capture probes are chosen to complement the target sequence to be detected. (bats.ch)
  • The capture probes are covalently linked by their 5' end in order to control both the amount fixed and the length of the sequence available for hybridisation. (bats.ch)
  • The genome has an overall G+C content of 58.7%, consists of 230,278 bp, and is arranged as a single unique sequence with short (31-bp) terminal direct repeats and several short internal repeats. (asm.org)