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.Peptide Nucleic Acids: DNA analogs containing neutral amide backbone linkages composed of aminoethyl glycine units instead of the usual phosphodiester linkage of deoxyribose groups. Peptide nucleic acids have high biological stability and higher affinity for complementary DNA or RNA sequences than analogous DNA oligomers.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.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.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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.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.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)Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.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).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.Nucleic Acid Probes: Nucleic acid which complements a specific mRNA or DNA molecule, or fragment thereof; used for hybridization studies in order to identify microorganisms and for genetic studies.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.Nucleic Acid Amplification Techniques: Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.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)Nucleic Acid Denaturation: Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.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.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.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.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another 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.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.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.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Genes, Bacterial: The functional hereditary units of BACTERIA.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.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.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.Structural Homology, Protein: The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN.Bacterial Proteins: Proteins found in any species of bacterium.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.src Homology Domains: Regions of AMINO ACID SEQUENCE similarity in the SRC-FAMILY TYROSINE KINASES that fold into specific functional tertiary structures. The SH1 domain is a CATALYTIC DOMAIN. SH2 and SH3 domains are protein interaction domains. SH2 usually binds PHOSPHOTYROSINE-containing proteins and SH3 interacts with CYTOSKELETAL PROTEINS.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).Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Molecular Weight: The sum of the weight of all the atoms in a molecule.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Recombinant Proteins: Proteins prepared by recombinant DNA technology.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.DNA 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.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.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.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.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).Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Kinetics: The rate dynamics in chemical or physical systems.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)Viral Proteins: Proteins found in any species of virus.Genes, Viral: The functional hereditary units of VIRUSES.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.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.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.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.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.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.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.DNA, Single-Stranded: A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.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.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.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.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.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.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.Self-Sustained Sequence Replication: An isothermal in-vitro nucleotide amplification process. The process involves the concomitant action of a RNA-DIRECTED DNA POLYMERASE, a ribonuclease (RIBONUCLEASES), and DNA-DIRECTED RNA POLYMERASES to synthesize large quantities of sequence-specific RNA and DNA molecules.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.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.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.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)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.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.Nucleic Acid Heteroduplexes: Double-stranded nucleic acid molecules (DNA-DNA or DNA-RNA) which contain regions of nucleotide mismatches (non-complementary). In vivo, these heteroduplexes can result from mutation or genetic recombination; in vitro, they are formed by nucleic acid hybridization. Electron microscopic analysis of the resulting heteroduplexes facilitates the mapping of regions of base sequence homology of nucleic acids.Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Nucleic Acid Renaturation: The reformation of all, or part of, the native conformation of a nucleic acid molecule after the molecule has undergone denaturation.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.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.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.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)Ribonucleases: Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.Sensitivity and Specificity: Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)DNA, 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.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.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.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.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.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.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.Nucleotides: The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)Software: Sequential operating programs and data which instruct the functioning of a digital computer.Fungal Proteins: Proteins found in any species of fungus.Retroviridae: Family of RNA viruses that infects birds and mammals and encodes the enzyme reverse transcriptase. The family contains seven genera: DELTARETROVIRUS; LENTIVIRUS; RETROVIRUSES TYPE B, MAMMALIAN; ALPHARETROVIRUS; GAMMARETROVIRUS; RETROVIRUSES TYPE D; and SPUMAVIRUS. A key feature of retrovirus biology is the synthesis of a DNA copy of the genome which is integrated into cellular DNA. After integration it is sometimes not expressed but maintained in a latent state (PROVIRUSES).HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.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.Genes, Fungal: The functional hereditary units of FUNGI.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.Circular Dichroism: A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)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.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.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.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.Cross Reactions: Serological reactions in which an antiserum against one antigen reacts with a non-identical but closely related antigen.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.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.Aptamers, Nucleotide: Nucleotide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.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.Trypsin: A serine endopeptidase that is formed from TRYPSINOGEN in the pancreas. It is converted into its active form by ENTEROPEPTIDASE in the small intestine. It catalyzes hydrolysis of the carboxyl group of either arginine or lysine. EC 3.4.21.4.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.GuanineConsensus Sequence: A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.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.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.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.ComputersChromatography, High Pressure Liquid: Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.Plant Viruses: Viruses parasitic on plants higher than bacteria.Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.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.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).Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.COS Cells: CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.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.Thermodynamics: A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.Nucleotide Mapping: Two-dimensional separation and analysis of nucleotides.Cricetinae: A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.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.Ligands: A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Oligoribonucleotides: A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.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.Hot Temperature: Presence of warmth or heat or a temperature notably higher than an accustomed norm.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Viruses: Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells.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.Hydrolysis: The process of cleaving a chemical compound by the addition of a molecule of water.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.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)Molecular Structure: The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.PhosphoproteinsRNA Probes: RNA, usually prepared by transcription from cloned DNA, which complements a specific mRNA or DNA and is generally used for studies of virus genes, distribution of specific RNA in tissues and cells, integration of viral DNA into genomes, transcription, etc. Whereas DNA PROBES are preferred for use at a more macroscopic level for detection of the presence of DNA/RNA from specific species or subspecies, RNA probes are preferred for genetic studies. Conventional labels for the RNA probe include radioisotope labels 32P and 125I and the chemical label biotin. RNA probes may be further divided by category into plus-sense RNA probes, minus-sense RNA probes, and antisense RNA probes.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.Oligonucleotides, Antisense: Short fragments of DNA or RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.Polyribonucleotides: A group of 13 or more ribonucleotides in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.RNA, Transfer: The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.PolynucleotidesDNA, Catalytic: Molecules of DNA that possess enzymatic activity.Tissue Distribution: Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios.In Situ Hybridization: A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.Chemistry: A basic science concerned with the composition, structure, and properties of matter; and the reactions that occur between substances and the associated energy exchange.Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Bacteriophages: Viruses whose hosts are bacterial cells.G-Quadruplexes: Higher-order DNA and RNA structures formed from guanine-rich sequences. They are formed around a core of at least 2 stacked tetrads of hydrogen-bonded GUANINE bases. They can be formed from one two or four separate strands of DNA (or RNA) and can display a wide variety of topologies, which are a consequence of various combinations of strand direction, length, and sequence. (From Nucleic Acids Res. 2006;34(19):5402-15)Hydrogen Bonding: A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.Magnetic Resonance Spectroscopy: Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).Models, Chemical: Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.Electrophoresis, Agar Gel: Electrophoresis in which agar or agarose gel is used as the diffusion medium.Microscopy, Electron: Microscopy using an electron beam, instead of light, to visualize the sample, thereby allowing much greater magnification. The interactions of ELECTRONS with specimens are used to provide information about the fine structure of that specimen. In TRANSMISSION ELECTRON MICROSCOPY the reactions of the electrons that are transmitted through the specimen are imaged. In SCANNING ELECTRON MICROSCOPY an electron beam falls at a non-normal angle on the specimen and the image is derived from the reactions occurring above the plane of the specimen.Fluorescent Dyes: Agents that emit light after excitation by light. The wave length of the emitted light is usually longer than that of the incident light. Fluorochromes are substances that cause fluorescence in other substances, i.e., dyes used to mark or label other compounds with fluorescent tags.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Chemical Phenomena: The composition, conformation, and properties of atoms and molecules, and their reaction and interaction processes.RNA, Double-Stranded: RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. Most of the double-stranded segments are formed from transcription of DNA by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. Some double-stranded segments of RNA are normal in all organisms.RNA-Directed DNA Polymerase: An enzyme that synthesizes DNA on an RNA template. It is encoded by the pol gene of retroviruses and by certain retrovirus-like elements. EC 2.7.7.49.Intercalating Agents: Agents that are capable of inserting themselves between the successive bases in DNA, thus kinking, uncoiling or otherwise deforming it and therefore preventing its proper functioning. They are used in the study of DNA.Signal Transduction: The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.Endopeptidases: A subclass of PEPTIDE HYDROLASES that catalyze the internal cleavage of PEPTIDES or PROTEINS.Spectrophotometry, Ultraviolet: Determination of the spectra of ultraviolet absorption by specific molecules in gases or liquids, for example Cl2, SO2, NO2, CS2, ozone, mercury vapor, and various unsaturated compounds. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)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).Molecular Diagnostic Techniques: MOLECULAR BIOLOGY techniques used in the diagnosis of disease.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Nucleosides: Purine or pyrimidine bases attached to a ribose or deoxyribose. (From King & Stansfield, A Dictionary of Genetics, 4th ed)RNA Viruses: Viruses whose genetic material is RNA.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.Bacillus subtilis: A species of gram-positive bacteria that is a common soil and water saprophyte.Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.Glycoproteins: Conjugated protein-carbohydrate compounds including mucins, mucoid, and amyloid glycoproteins.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.Serine Endopeptidases: Any member of the group of ENDOPEPTIDASES containing at the active site a serine residue involved in catalysis.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.Swine: Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).Immobilized Nucleic Acids: DNA or RNA bound to a substrate thereby having fixed positions.Blood Proteins: Proteins that are present in blood serum, including SERUM ALBUMIN; BLOOD COAGULATION FACTORS; and many other types of proteins.Epitopes: Sites on an antigen that interact with specific antibodies.

Ultrabithorax function in butterfly wings and the evolution of insect wing patterns. (1/18435)

BACKGROUND: . The morphological and functional evolution of appendages has played a critical role in animal evolution, but the developmental genetic mechanisms underlying appendage diversity are not understood. Given that homologous appendage development is controlled by the same Hox gene in different organisms, and that Hox genes are transcription factors, diversity may evolve from changes in the regulation of Hox target genes. Two impediments to understanding the role of Hox genes in morphological evolution have been the limited number of organisms in which Hox gene function can be studied and the paucity of known Hox-regulated target genes. We have therefore analyzed a butterfly homeotic mutant 'Hindsight', in which portions of the ventral hindwing pattern are transformed to ventral forewing identity, and we have compared the regulation of target genes by the Ultrabithorax (Ubx) gene product in Lepidopteran and Dipteran hindwings. RESULTS: . We show that Ubx gene expression is lost from patches of cells in developing Hindsight hindwings, correlating with changes in wing pigmentation, color pattern elements, and scale morphology. We use this mutant to study how regulation of target genes by Ubx protein differs between species. We find that several Ubx-regulated genes in the Drosophila haltere are not repressed by Ubx in butterfly hindwings, but that Distal-less (Dll) expression is regulated by Ubx in a unique manner in butterflies. CONCLUSIONS: . The morphological diversification of insect hindwings has involved the acquisition of different sets of target genes by Ubx in different lineages. Changes in Hox-regulated target gene sets are, in general, likely to underlie the morphological divergence of homologous structures between animals.  (+info)

Telomerase reverse transcriptase gene is a direct target of c-Myc but is not functionally equivalent in cellular transformation. (2/18435)

The telomerase reverse transcriptase component (TERT) is not expressed in most primary somatic human cells and tissues, but is upregulated in the majority of immortalized cell lines and tumors. Here, we identify the c-Myc transcription factor as a direct mediator of telomerase activation in primary human fibroblasts through its ability to specifically induce TERT gene expression. Through the use of a hormone inducible form of c-Myc (c-Myc-ER), we demonstrate that Myc-induced activation of the hTERT promoter requires an evolutionarily conserved E-box and that c-Myc-ER-induced accumulation of hTERT mRNA takes place in the absence of de novo protein synthesis. These findings demonstrate that the TERT gene is a direct transcriptional target of c-Myc. Since telomerase activation frequently correlates with immortalization and telomerase functions to stabilize telomers in cycling cells, we tested whether Myc-induced activation of TERT gene expression represents an important mechanism through which c-Myc acts to immortalize cells. Employing the rat embryo fibroblast cooperation assay, we show that TERT is unable to substitute for c-Myc in the transformation of primary rodent fibroblasts, suggesting that the transforming activities of Myc extend beyond its ability to activate TERT gene expression and hence telomerase activity.  (+info)

Analysis of two cosmid clones from chromosome 4 of Drosophila melanogaster reveals two new genes amid an unusual arrangement of repeated sequences. (3/18435)

Chromosome 4 from Drosophila melanogaster has several unusual features that distinguish it from the other chromosomes. These include a diffuse appearance in salivary gland polytene chromosomes, an absence of recombination, and the variegated expression of P-element transgenes. As part of a larger project to understand these properties, we are assembling a physical map of this chromosome. Here we report the sequence of two cosmids representing approximately 5% of the polytenized region. Both cosmid clones contain numerous repeated DNA sequences, as identified by cross hybridization with labeled genomic DNA, BLAST searches, and dot matrix analysis, which are positioned between and within the transcribed sequences. The repetitive sequences include three copies of the mobile element Hoppel, one copy of the mobile element HB, and 18 DINE repeats. DINE is a novel, short repeated sequence dispersed throughout both cosmid sequences. One cosmid includes the previously described cubitus interruptus (ci) gene and two new genes: that a gene with a predicted amino acid sequence similar to ribosomal protein S3a which is consistent with the Minute(4)101 locus thought to be in the region, and a novel member of the protein family that includes plexin and met-hepatocyte growth factor receptor. The other cosmid contains only the two short 5'-most exons from the zinc-finger-homolog-2 (zfh-2) gene. This is the first extensive sequence analysis of noncoding DNA from chromosome 4. The distribution of the various repeats suggests its organization is similar to the beta-heterochromatic regions near the base of the major chromosome arms. Such a pattern may account for the diffuse banding of the polytene chromosome 4 and the variegation of many P-element transgenes on the chromosome.  (+info)

The mouse Aire gene: comparative genomic sequencing, gene organization, and expression. (4/18435)

Mutations in the human AIRE gene (hAIRE) result in the development of an autoimmune disease named APECED (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy; OMIM 240300). Previously, we have cloned hAIRE and shown that it codes for a putative transcription-associated factor. Here we report the cloning and characterization of Aire, the murine ortholog of hAIRE. Comparative genomic sequencing revealed that the structure of the AIRE gene is highly conserved between human and mouse. The conceptual proteins share 73% homology and feature the same typical functional domains in both species. RT-PCR analysis detected three splice variant isoforms in various mouse tissues, and interestingly one isoform was conserved in human, suggesting potential biological relevance of this product. In situ hybridization on mouse and human histological sections showed that AIRE expression pattern was mainly restricted to a few cells in the thymus, calling for a tissue-specific function of the gene product.  (+info)

ATF-2-binding regulatory element is responsible for the Ly49A expression in murine T lymphoid line, EL-4. (5/18435)

To understand the mechanism of Ly49A-expression and its significance in T-cell differentiation, we analyzed the 5'-flanking region of the Ly49A gene in a search for the Ly49A-regulatory element. Since very few known regulatory elements have been found in this region, presumably a novel regulatory sequence(s) could exist. Accordingly, we defined the 13-bp regulatory element, 5'-ATGACGAGGAGGA-3', restricted to Ly49A-expression in EL-4 cells in comparison with two other representative cell lines tested. This element, designated as EL13, proved to be previously undiscovered by homology search and is highly homologous with several virus DNAs. Using EL13 as a probe we have cloned a cDNA encoding a binding protein to EL13. Its deduced nucleotide sequence revealed that EL13-binding protein is almost identical with rat ATF-2. Although ATF-2 is known to bind to cyclic AMP responsive element (CRE), EL13 shares five out of eight nucleotides with this consensus sequence. Our results suggested that ATF-2 may play an important role via binding to EL13 for the expression of Ly49A. These data will provide useful information for understanding T-cell and NK-cell differentiation in murine immune system.  (+info)

Cloning and functional characterization of the 5'-flanking region of the human bone morphogenetic protein-2 gene. (6/18435)

Bone morphogenetic protein-2 (BMP-2) is involved in bone formation, organogenesis or pattern formation during development. The expression of BMP-2 is regulated accurately and coordinately with that of other transforming growth factor-beta (TGF-beta) superfamily members. To elucidate the mechanism underlying the regulation of BMP-2 expression, a 6.7 kb SpeI-SalI fragment, from the P1 phage library, encompassing the 5'-flanking region of the human BMP-2 gene, was isolated and sequenced. Transcription start sites were mapped by the 5'-rapid amplification of cDNA ends (RACE) method. It has been found that the human BMP-2 gene contains, largely, two promoter regions surrounded by GC-rich sequences with several Sp1 consensus motifs. The proximal promoter possesses a single start site, whereas several start sites are clustered in the distal promoter region. Neither TATA nor CAAT consensus sequences are found in the proximity of the start sites for either promoter. Interestingly, in no case is the transcription-initiation site common between the human and mouse BMP-2 genes, although the sequence of the BMP-2 gene is well conserved in the promoter region between two species. Transient transfection experiments with the reporter fused with various lengths of the BMP-2 promoter sequence demonstrated that there exist enhancer elements in an 1.1 kb GC-rich fragment covering both promoter regions. It is noteworthy that the enhancer elements are 5'-flanked by a 790 bp strong repressor element that is characterized by numerous AT stretches. This intriguing organization may be amenable to the tight control of the expression of BMP-2 that is essential for development or bone morphogenesis.  (+info)

Use of RhD fusion protein expressed on K562 cell surface in the study of molecular basis for D antigenic epitopes. (7/18435)

The human D antigens, one of the most clinically important blood groups, are presented by RhD protein with a putative 12 transmembrane topology. To understand the molecular basis for the complex antigenic profile of RhD protein, we expressed a series of RhD fusion proteins using different portions of Duffy protein as a tag in erythroleukemic K562 cells. Because the reactivity of monoclonal anti-RhD antibody, LOR15C9, depends mainly on the sequence coded by exon 7 of RhD, we altered DNA sequence corresponding to the amino acid residues 323-331(A) and 350-354(B) in the exon 7. The mutation in region B resulted in a severe reduction in LOR15C9 binding by flow cytometry analysis, suggesting that region B may play an important role in constituting antigen epitopes recognized by LOR15C9. On the other hand, a slight decrease in the antibody binding was observed for the region A mutant, suggesting that the intracellularly located region A may elicit a long distance effect on the formation of exofacial antigen epitopes. In addition, using various monoclonal antibodies against RhD, we compared the antigenic profile of expressed RhD fusion protein with that of endogenous RhD in K562 cells as well as in erythrocytes.  (+info)

Suppression subtractive hybridization identifies high glucose levels as a stimulus for expression of connective tissue growth factor and other genes in human mesangial cells. (8/18435)

Accumulation of mesangial matrix is a pivotal event in the pathophysiology of diabetic nephropathy. The molecular triggers for matrix production are still being defined. Here, suppression subtractive hybridization identified 15 genes differentially induced when primary human mesangial cells are exposed to high glucose (30 mM versus 5 mM) in vitro. These genes included (a) known regulators of mesangial cell activation in diabetic nephropathy (fibronectin, caldesmon, thrombospondin, and plasminogen activator inhibitor-1), (b) novel genes, and (c) known genes whose induction by high glucose has not been reported. Prominent among the latter were genes encoding cytoskeleton-associated proteins and connective tissue growth factor (CTGF), a modulator of fibroblast matrix production. In parallel experiments, elevated CTGF mRNA levels were demonstrated in glomeruli of rats with streptozotocin-induced diabetic nephropathy. Mannitol provoked less mesangial cell CTGF expression in vitro than high glucose, excluding hyperosmolality as the key stimulus. The addition of recombinant CTGF to cultured mesangial cells enhanced expression of extracellular matrix proteins. High glucose stimulated expression of transforming growth factor beta1 (TGF-beta1), and addition of TGF-beta1 to mesangial cells triggered CTGF expression. CTGF expression induced by high glucose was partially suppressed by anti-TGF-beta1 antibody and by the protein kinase C inhibitor GF 109203X. Together, these data suggest that 1) high glucose stimulates mesangial CTGF expression by TGFbeta1-dependent and protein kinase C dependent pathways, and 2) CTGF may be a mediator of TGFbeta1-driven matrix production within a diabetic milieu.  (+info)

How closely related two or more separate strands of DNA are to each other, based on their base sequences. For more information, see homology. From the B...
I will describe a spectral sequence that starts at reduced odd Khovanov homology and converges to a version of instanton homology for double branched covers.. ...
A review of the literature on homology indicates that the theory does not provide evidence for evolutionary naturalism, and that the common examples of homology can be better explained by Creation.
Please call it sequence SIMILARITY In a search you may find many sequence similarities but only few of the matches may represent homologies. See Reeck et al. (1987) Homology in proteins and nucleic acids: A terminology muddle and a way out of it. Cell 60, 667 ...
Page 1 of 4 - Vestigial Organs - posted in Best all time threads.: Most of the obvious anatomical homologies are between anatomical structures which are in active use by the species in question, but some anatomical homologies involve structures which are no longer needed but which also havent disappeared entirely. A vestigial organ or structure is any organ or structure found in a species which is not being used as it is in other species. Contrary to popular belief, vestigial organs a...
Considerable insights into important cis regulatory elements in a gene can be gleaned from the identification of sequence homologies among different species. To extend and optimize the sequence comparison between human and mouse erythropoietin (Epo) genes, we have obtained new human sequence from 5,547 to 385 bp upstream of the cap site and extended the 3 flank by 489 bp. In addition, we have obtained new sequence information on the mouse Epo gene extending from within the 3 untranslated region (UTR) to 1,001 bp downstream of the polyadenylation site. Analysis of these additional sequences shows considerable homology between human and mouse Epo genes as far as 4 kb (human) or 3 kb (mouse) upstream of the cap sites, as well as far more homology at the 3 end than was previously realized. In addition, both species were found to have a high frequency of short interspersed (SINE) repetitive sequences that interrupt homologies in both the 5 flank and within the transcription unit.
Knowledge of the sequence of a DNA segment has many uses, and some examples follow. First, it can be used to find genes, segments of DNA that code for a specific protein or phenotype. If a region of DNA has been sequenced, it can be screened for characteristic features of genes. For example, open reading frames (ORFs)-long sequences that begin with a start codon (three adjacent nucleotides; the sequence of a codon dictates amino acid production) and are uninterrupted by stop codons (except for one at their termination)-suggest a protein-coding region. Also, human genes are generally adjacent to so-called CpG islands-clusters of cytosine and guanine, two of the nucleotides that make up DNA. If a gene with a known phenotype (such as a disease gene in humans) is known to be in the chromosomal region sequenced, then unassigned genes in the region will become candidates for that function. Second, homologous DNA sequences of different organisms can be compared in order to plot evolutionary ...
NPC1s amino acid sequence homology to PATCHED, human HMG-CoA reductase and SCAP. Credit: Reprinted with permission from AAAS / Carstea et al., Science 277:228, 1997." />NPC1s amino acid sequence homology to PATCHED, human HMG-CoA reductase and SCAP. Credit: Reprinted with permission from AAAS / Carstea et al., Science 277:228, 1997. In the 1990s, the Ara Parseghian Foundation donated money to the National I. 0 Comments. ...
package transeq import ( "bufio" "bytes" "context" "encoding/binary" "fmt" "io" "runtime" "sync" ) var ( letterCode = map[byte]uint8{ A: aCode, C: cCode, T: tCode, G: gCode, N: nCode, U: uCode, } standard = map[string]byte{ "TTT": F, "TCT": S, "TAT": Y, "TGT": C, "TTC": F, "TCC": S, "TAC": Y, "TGC": C, "TTA": L, "TCA": S, "TAA": *, "TGA": *, "TTG": L, "TCG": S, "TAG": *, "TGG": W, "CTT": L, "CCT": P, "CAT": H, "CGT": R, "CTC": L, "CCC": P, "CAC": H, "CGC": R, "CTA": L, "CCA": P, "CAA": Q, "CGA": R, "CTG": L, "CCG": P, "CAG": Q, "CGG": R, "ATT": I, "ACT": T, "AAT": N, "AGT": S, "ATC": I, "ACC": T, "AAC": N, "AGC": S, "ATA": I, "ACA": T, "AAA": K, "AGA": R, "ATG": M, "ACG": T, "AAG": K, "AGG": R, "GTT": V, "GCT": A, "GAT": D, "GGT": G, "GTC": V, "GCC": A, "GAC": D, "GGC": G, "GTA": V, "GCA": A, "GAA": E, "GGA": G, "GTG": V, "GCG": A, "GAG": E, "GGG": G, } ) ...
Definition of homologies in the Legal Dictionary - by Free online English dictionary and encyclopedia. What is homologies? Meaning of homologies as a legal term. What does homologies mean in law?
Sequencing: is the process of determining the nucleic acid sequence - the order of nucleotides in DNA. It includes any method or technology that is used
The degree of similarity between sequences of Amino Acids. This information is useful for the analyzing genetic relatedness of Proteins and species ...
The observed gene overlays in the viruses ФX174 and SV40 show a surprising economy of information storage; two different amino acid sequences are read in different frames from the same stretch of DNA.
LOC FOR DETECTION OF HYBRIDIZATION OF NUCLEIC ACID SEQUENCES WITH PRIMER-LINKED STEM-AND-LOOP PROBES - diagram, schematic, and image 20 ...
In article ,36nmhcINN2ng at bigbird.cc.williams.edu, writes: , Hello, , Does anyone have any experience producing a very crude , structural hypothesis from sequence data? We have Sybyl, but Ive , been unable to get the Homology modeler to produce adequate results. , The situation is this: I have a sequence-structure coordinate file of , a protein with , 85 % homology to the protein I want to make a , structure for, but Sybyl complains about not having enough short , regions of homology! Are there any free programs that can do this? , Ive tried Sybyls built in structure-seq database, and constructed my , own database with many similar proteins and just the resolved protein , with homology. Any suggestions or references would be appreciated, , , Max Nanao , 95mhn at cc.williams.edu , nanao at ochre.mgh.harvard.edu Depends on what exactly is meant by , 85% homology (% sequence identity?), but, by most definitions of homology in most situations like this, you should not have a problem to calculate ...
M.P.E.P. Section 1823.02: Nucleotide and/or Amino Acid Sequence Listings, and Tables Related to Sequence Listings. Taken from the 9th Edition of the MPEP, Revision 08.2017, (Last Revised Jan. 2018). Updated in BitLaw in February 2018
No matter what the length of A and B are, A and B (the aligned sequences) will be of the same length. This simply comes from the definition of an alignment. The characters (representing base pairs) from the two sequences are arranged as to minimize the differences between them, and then the empty spaces (if any) are filled in with gaps (dash characters). These gaps are typically interpreted as evolutionary events between two homologous sequences, i.e. an insertion of nucleotides to one sequence or a deletion of nucleotides from the other (indels).. ...
Amino acid sequences of SsCOMT, SbCOMT, OsCOMT, TaCOMT, AtCOMT, and ZmCOMT were initially aligned by DNAMAN6.0 using default parameters, and followed by manual
The FASTA programs provide a comprehensive set of rapid similarity searching tools (fasta36, fastx36, tfastx36, fasty36, tfasty36), similar to those provided by the BLAST package, as well as programs for slower, optimal, local, and global similarity searches (ssearch36, ggsearch36), and for searching with short peptides and oligonucleotides (fasts36, fastm36)
CACCTAAATT GTAAGCGTTA ATATTTTGTT AAAATTCGCG TTAAATTTTT GTTAAATCAG CTCATTTTTT AACCAATAGG CCGAAATCGG CAAAATCCCT TATAAATCAA AAGAATAGAC CGAGATAGGG TTGAGTGTTG TTCCAGTTTG GAACAAGAGT CCACTATTAA AGAACGTGGA CTCCAACGTC AAAGGGCGAA AAACCGTCTA TCAGGGCGAT GGCCCACTAC GTGAACCATC ACCCTAATCA AGTTTTTTGG GGTCGAGGTG CCGTAAAGCA CTAAATCGGA ACCCTAAAGG GAGCCCCCGA TTTAGAGCTT GACGGGGAAA GCCGGCGAAC GTGGCGAGAA AGGAAGGGAA GAAAGCGAAA GGAGCGGGCG CTAGGGCGCT GGCAAGTGTA GCGGTCACGC TGCGCGTAAC CACCACACCC GCCGCGCTTA ATGCGCCGCT ACAGGGCGCG TCCCATTCGC CATTCAGGCT GCGCAACTGT TGGGAAGGGC GATCGGTGCG GGCCTCTTCG CTATTACGCC AGCTGGCGAA AGGGGGATGT GCTGCAAGGC GATTAAGTTG GGTAACGCCA GGGTTTTCCC AGTCACGACG TTGTAAAACG ACGGCCAGTG AATTGTAATA CGACTCACTA TAGGGCGAAT TGGAGCTCCA CCGCGGTGGC GGCCGCTCTA GAACTAGTGG ATCCCCCGGG CTGCAGGAAT TCGGCACGAG AAAACCTTCA CTACTCTTGA CCCTGCGTCC CTAGCTTGGC TGACAGAGGA GCCAGGGCCA ACAGAGGTCA CACGCACATC CCAAAGCCCT CGCTCTCCAG ATTCCAGTCA GAGTTCTATG GCCCAGGAGG AAGAGGAGGA AGAGCAAGGA AGAACTAGGA AACGGAAACA GAGTGGTCAG TGCCCAGCCC ...
7800gccttctctg ccctgagggt cgaaggtcga gcaggccggg ggtgtccggg aggtctttgg 7860gcatcgcggt ctggggttgg gacgtgtaag cgcctgggag agcctagacc aggctccggg 7920ctgccaataa agaagtgaaa tgcgtatctg gtctcctgtc gtgggagagt gtgaggtgta 7980acggattcaa gtctgaaccc agagcctgga aaaggctgac cgcccagatt gacgttgcta 8040ggcaactccg gaggcgggcc cagcgccaaa agaacagggc gaggcgtcgt ccccgcatcc 8100cattggccgt tctctgcggg gccccgccct cgggggccgg agctagaagc tctacgcttc 8160cgaggcgcac ctcctggcct gcacgctttg acgt 8194162526DNAHomo sapiens 16atgctgctct gcacggctcg cctggtcggc ctgcagcttc tcatttcctg ctgctgggcc 60tttgcctgcc atagcacgga gtcttctcct gacttcaccc tccccggaga ttacctcctg 120gcaggcctgt tccctctcca ttctggctgt ctgcaggtga ggcacagacc cgaggtgacc 180ctgtgtgaca ggtcttgtag cttcaatgag catggctacc acctcttcca ggctatgcgg 240cttggggttg aggagataaa caactccacg gccctgctgc ccaacatcac cctggggtac 300cagctgtatg atgtgtgttc tgactctgcc aatgtgtatg ccacgctgag agtgctctcc 360ctgccagggc aacaccacat agagctccaa ggagaccttc tccactattc ccctacggtg 420ctggcagtga ttgggcctga cagcaccaac ...
Anyway, if you get some proteins, you identify them with mass spec (either MALDI or digest on LC-MS) and this information you use for the identification ...
human CSDE1 protein: amino acid sequence in first source; unr gene located close to N-ras locus and may interact with it; RefSeq NM_007158
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We have conducted a human cDNA project to predict protein-coding sequences (CDSs) in large cDNAs (, 4 kb) since 1994, and the number of newly identified genes, known as KIAA genes, already exceeds 2000. The ultimate goal of this project is to clarify the physiological functions of the proteins encoded by KIAA genes. To this end, the project has recently been expanded to include isolation and characterization of mouse KIAA-counterpart genes. We herein present the entire sequences and the chromosome loci of 500 mKIAA cDNA clones and 13 novel cDNA clones that were incidentally identified during this project. The average size of the 513 cDNA sequences reached 4.3 kb and that of the deduced amino acid sequences from these cDNAs was 816 amino acid residues. By comparison of the predicted CDSs between mouse and human KIAAs, 12 mKIAA cDNA clones were assumed to be differently spliced isoforms of the human cDNA clones. The comparison of mouse and human sequences also revealed that four pairs of human ...
cloning of non-coding region for protein expression - posted in Protein Expression and Purification: Hi! I am trying to see the function of my non-coding region in protein expression. I have clone my gene and its non-coding region upstream of 5UTR to find if non-coding region plays any role in expression of cloned protein. I have other clones with no non-coding region just 5UTR and coding region. Has anybody cloned these type construct in mammalian expression vector and does...
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Genomic organization, chromosomal mapping, nucleotide sequence, and predicted amino acid sequence of the murine MCP-5 gene. (A) Partial restriction map and ge
develop a new model summarizing the entire process of transcription and translation with your lab group you will be asked to communicate share amino acid sequence chart dna.. ...
This MATLAB function cuts SeqAA, an amino acid sequence, into parts at the cleavage sites specific for Enzyme, a character vector specifying a name or abbreviation code for an enzyme or compound for which the literature specifies a cleavage rule.
This MATLAB function cuts SeqAA, an amino acid sequence, into parts at the cleavage sites specific for Enzyme, a character vector specifying a name or abbreviation code for an enzyme or compound for which the literature specifies a cleavage rule.
I was wondering if I did something wrong with the deletion, it seems pretty self explanatory but I just want to make sure I did this right. The filled in answers are in bold And Im completely lost with the Amino Acid sequence, my TA did this in class and I still dont get it ...
The next few posts are presented to help you prepare for the AP exam. This first post addresses the homologies between humans and chimps. Recall that homologies are traits that are derived from the same ancestral form - they have a shared ancestry ...
lets assume that i fould a valuable gene fragment ex. dna sequence homology with one of the human myosin ii genes1., Hire Biology Expert, Ask Academics Expert, Assignment Help, Homework Help, Textbooks Solutions
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Tsou, C.H., Li, L. & Vijayan, K. 2016. The Intra-familial Relationships of Pentaphylacaceae sl as Revealed by DNA Sequence Analysis. Biochemical Genetics pp.1-13. doi: 10.1007/s10528-016-9717-1 ...
Mc kean, D J.; Potter, M; and Hood, L, "Amino acid sequence comparison of three new balb/c mouse kappa chains. Abstr." (1972). Subject Strain Bibliography 1972. 679 ...
The full-length ORF clone contains only the coding sequence of the full-length protein, while the other full-length cDNA clones contain some untranslated sequences, such as the 5side or 3′ side non translation. It is well known that these untranslated sequences may have a negative effect on the transcription and translation processes of the encoded proteins in the host.. If it is the ORF expressed clone, it can be transfected into cells and expressed in cells.. In the general situation, the carrier of cDNA clone is not the expression vector, so it can not be directly used for transfection of cells.. The difference between ORF, cDNA and CDS:. 1.what is a full-length ORF clone?. A full-length ORF clone is a plasmid inserted into a DNA fragment encoding a full-length protein. The inserted DNA fragment only contains sequence incoding a full-length protein, and does not contain the untranslated region of 5 or 3 end (UTRs) or intron.. 2.why should the full length ORF cDNA clones are used instead ...
Read "Hop mosaic virus: complete nucleotide sequence and relationship to other carlaviruses, Archives of Virology" on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Chang, E., et al. N-Terminal Amino Acid Sequence Determination of Proteins by N-Terminal Dimethyl Labeling: Pitfalls and Advantages When Compared with Edman Degradation Sequence Analysis. Journal of Biomolecular Technology. 27(2). 07/03/2016.. ...
I) instructions for representing the set of sequence elements on a display, each sequence element representing an amino acid sequence segment or a nucleic acid sequence segment, wherein the set of sequence elements collectively encode the design nucleic acid sequence, wherein said instructions for representing said set of sequence elements comprise instructions for displaying a plurality of icons in a linear or a near linear arrangement on a display, each respective icon in said plurality of icons uniquely representing a corresponding sequence element in said set of sequence elements such that neighboring icons in said plurality of icons represent neighboring sequence elements in said plurality of sequence elements in said design nucleic acid sequence, and each said respective icon in said plurality of icons depicts a directional property for the corresponding sequence element in said set of sequence elements; and ...
Stanniocalcins (STCs) represent small glycoprotein hormones, found in all vertebrates, which have been functionally implicated in Calcium homeostasis. However, recent data from mammalian systems indicated that they may be also involved in embryogenesis, tumorigenesis and in the context of the latter especially in angiogenesis. Human STC1 is a 247 amino acids protein with a predicted molecular mass of 27 kDa, but preliminary data suggested its di- or multimerization. The latter in conjunction with alternative splicing and/or post-translational modification gives rise to forms described as STC50 and big STC, which molecular weights range from 56 to 135 kDa. In this study we performed a biochemical and structural analysis of STC1 with the aim of obtaining low resolution structural information about the human STC1, since structural information in this protein family is scarce. We expressed STC1 in both E. coli and insect cells using the baculo virus system with a C-terminal 6 × His fusion tag. From the
Maloy W.L.; Nathenson S.G.; Coligan J.E., 1981: Primary structure of murine major histo compatibility complex allo antigens amino acid sequence of the amino terminal 98 residues of the h 2d b glyco protein
The distinct subcellular redistribution of p53 and p73 in MDM2-expressing cells suggests the existence of structural differences between the proteins. Whereas the oligermerization domain of p53 and p73 share 33% identity, the extreme CT (outside of the oligermerization domain) of the two proteins is much less conserved. Inspection of the primary amino acid sequence reveals that the p53 CT contains five lysine residues that are not conserved in p73. In addition, we showed recently that under conditions where p53 is highly ubiquitinated, p73 exhibits a much lower tendency for ubiquitination (10) . According to the current model of p53 nuclear export, the p53 NES is inactive when p53 is in tetramer. Ubiquitination of the p53 CT lysine residues by MDM2 results in the revealing of the NES that then permits p53 to be nuclear-exported (5, 6, 7) . It is therefore possible that the NES of p73 is unable to be activated because of its lack of the corresponding lysine residues available for ubiquitination. ...
Patenting around nuisance prior art. Patenting gene sequences. Patenting nucleotide and amino acid sequences in view of electronic sequence database searches
A RecA-single-stranded DNA (RecA-ssDNA) filament searches a genome for sequence homology by rapidly binding and unbinding double-stranded DNA (dsDNA) until homology is found. We demonstrate that pulling on the opposite termini (3′ and 5′) of one of the two DNA strands in a dsDNA molecule stabilizes the normally unstable binding of that dsDNA to non-homologous RecA-ssDNA filaments, whereas pulling on the two 3′, the two 5′, or all four termini does not. We propose that the outgoing strand in the dsDNA is extended by strong DNA-protein contacts, whereas the complementary strand is extended by the tension on the base pairs that connect the complementary strand to the outgoing strand. The stress resulting from different levels of tension on its constitutive strands causes rapid dsDNA unbinding unless sufficient homology is present ...
Ben Hanelt, D. Van Schyndel, C. M. Adema, L. A. Lewis, E. S. Loker. The Phylogenetic Position of Rhopaluva ophiocomae (Orthonectida) Based on 18s Ribosomal DNA Sequence Analysis. -Molecular Biology and Evolution, 1996,. 13 (9), lk 1187-1191. Veebiversioon. ...
Every protein in a cell is created through the transcription of a specific sequence, that is part of the DNA. This transcription provides the sequence in which amino acids are to be linked, to form a protein.
LBHD1 - C11orf48 (untagged)-Human chromosome 11 open reading frame 48 (C11orf48) available for purchase from OriGene - Your Gene Company.
Definition of primary structure - the characteristic sequence of amino acids forming a protein or polypeptide chain, considered as the most basic element of its str
Hloch P, Schiedner G, Stahl H (1990). "Complete cDNA sequence of the human p68 protein". Nucleic Acids Res. 18 (10): 3045. doi: ... Ford MJ, Anton IA, Lane DP (1988). "Nuclear protein with sequence homology to translation initiation factor eIF-4A". Nature. ... 2000). "Structure and expression of the human p68 RNA helicase gene". Nucleic Acids Res. 28 (4): 932-9. doi:10.1093/nar/28.4. ... Nucleic Acids Res. 31 (5): 1470-80. doi:10.1093/nar/gkg236. PMC 149829 . PMID 12595555. Wilson BJ, Giguère V (2007). " ...
"The MPI Bioinformatics Toolkit as an Integrative Platform for Advanced Protein Sequence and Structure Analysis." Nucleic Acids ... Homology is the relationship between biological structures or sequences derived from a common ancestor. Homologous proteins ( ... Nucleic Acids Research 25.17 (1997): 3389-402. Oxford University Press. Print [4] Bigert, A., and J. Söding. "Sequence Context- ... The figure illustrates the sequence to sequence and profile to sequence equivalence with the alignment matrix. The query ...
"Nucleic Acids Research. 38 (Database issue): D190-5. doi:10.1093/nar/gkp951. PMC 2808932. PMID 19900971.. ... Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the ... Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. Significant ... A sequence alignment of mammalian histone proteins. Sequences are the middle 120-180 amino acid residues of the proteins. ...
Venta PJ, Tashian RE (1990). "PCR detection of the TAQ1 polymorphism at the CA2 locus". Nucleic Acids Res. 18 (18): 5585. doi: ... 1988). "Cloning, expression, and sequence homologies of cDNA for human carbonic anhydrase II". Genomics. 1 (2): 159-66. doi: ... Nucleic Acids Res. 15 (11): 4687. doi:10.1093/nar/15.11.4687. PMC 340889 . PMID 3108857. Murakami H, Marelich GP, Grubb JH, et ... Montgomery JC, Venta PJ, Tashian RE, Hewett-Emmett D (1987). "Nucleotide sequence of human liver carbonic anhydrase II cDNA". ...
"The primary structure of human hemopexin deduced from cDNA sequence: evidence for internal, repeating homology". Nucleic Acids ... "The primary structure of human hemopexin deduced from cDNA sequence: evidence for internal, repeating homology". Nucleic Acids ... As the introns were not placed randomly; they fell in the center of the region of amino acid sequence homology in strikingly ... Computer-assisted analysis of the internal homology in amino acid sequence suggested duplication of an ancestral gene thus ...
"Nucleotide sequence of transforming human c-sis cDNA clones with homology to platelet-derived growth factor". Nucleic Acids Res ...
The problem arises often in homology modeling, where the tertiary structure of an amino acid sequence is predicted based on a ... The FALC-Loop web server for protein loop modeling" Nucleic Acids Research 39, W210-W214 (2011). Lee J, Lee D, Park H, Coutsias ... Chung SY, Subbiah S. (1996.) A structural explanation for the twilight zone of protein sequence homology" Structure 4: 1123-27 ... The extent of the inaccuracy increases with the number of amino acids in the loop. The loop amino acids' side chains dihedral ...
"Identification of two large subdomains in TFIIE-alpha on the basis of homology between Xenopus and human sequences". Nucleic ... Acids Res. 20 (21): 5838. doi:10.1093/nar/20.21.5838. PMC 334425 . PMID 1454543. Heng HH, Xiao H, Shi XM, Greenblatt J, Tsui LC ... Sumimoto H, Ohkuma Y, Sinn E, Kato H, Shimasaki S, Horikoshi M, Roeder RG (1991). "Conserved sequence motifs in the small ... "Structural motifs and potential sigma homologies in the large subunit of human general transcription factor TFIIE". Nature. 354 ...
... sequence homology with other human acute phase protein genes". Nucleic Acids Res. 13 (11): 3941-52. doi:10.1093/nar/13.11.3941 ... 1973). "Structure of 1 -acid glycoprotein. The complete amino acid sequence, multiple amino acid substitutions, and homology ... acid glycoprotein and the elucidation of the amino acid sequence of the carboxyl-terminal cyanogen bromide fragment". ... Board PG, Jones IM, Bentley AK (1986). "Molecular cloning and nucleotide sequence of human alpha 1 acid glycoprotein cDNA". ...
... "cDNA sequence of a new ras-related gene (rap2b) isolated from human platelets with sequence homology to rap2". Nucleic Acids ... The most striking difference between the RAP and RAS proteins resides in their 61st amino acid: glutamine in RAS is replaced by ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... The proteins encoded by these genes share approximately 50% amino acid identity with the classical RAS proteins and have ...
Krogh A, Mian IS, Haussler D (1994). "A hidden Markov model that finds genes in E. coli DNA". Nucleic Acids Res. 22 (22): 4768- ... 1996). "Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology". Comput. Appl. ... Nucleic Acids Res. 36 (Database issue): D102-6. doi:10.1093/nar/gkm955. PMC 2238834 . PMID 18006571. Lindow M, Jacobsen A, ... Probabilistic Models of Proteins and Nucleic Acids (1st ed.), Cambridge, New York: Cambridge University Press, doi:10.2277/ ...
... a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology ... Nucleic Acids Res. 39 (Web Server issue): W13-7. doi:10.1093/nar/gkr245. PMC 3125728 . PMID 21558174. Kemena C, Notredame C ( ... In its latest version, T-Coffee can be used to combine protein sequences and structures, RNA sequences and structures. It can ... It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences ...
... which recognizes the novel hexanucleotide sequence 5'-G(G/T)GC(A/C)C-3'". Nucleic Acids Res. 27 (13): 2644-5. doi:10.1093/nar/ ... Rina M, Markaki M, Bouriotis V (December 1994). "Sequence of the cloned bseCIM gene: M.BseCI reveals high homology to M.BanIII ... and the discovery of a wrongly sequenced site in pACYC177". Nucleic Acids Res. 19 (9): 2321-3. doi:10.1093/nar/19.9.2321. PMC ... which recognizes the pentanucleotide sequence 5'-CTCAG(N)(10/8)". Nucleic Acids Res. 29 (4): 895-903. doi:10.1093/nar/29.4.895 ...
E6 is a 151 amino-acid peptide that incorporates a type 1 motif with a consensus sequence -(T/S)-(X)-(V/I)-COOH. It also has ... Coggins LW, Ma JQ, Slater AA, Campo MS (1985). "Sequence homologies between bovine papillomavirus genomes mapped by a novel low ... Nucleic Acids Res. 20 (11): 2889. doi:10.1093/nar/20.11.2889. PMC 336941 . PMID 1319576. Varsani A1, Kraberger S, Jennings S, ... Compared to other papillomavirus genes, the amino acid sequences of most portions of L1 are well-conserved between types. ...
... complete coding sequence and homology with other type II topoisomerases". Biochimica et Biophysica Acta. 1172 (3): 283-91. doi: ... Nucleic Acids Research. 21 (16): 3719-23. doi:10.1093/nar/21.16.3719. PMC 309874 . PMID 8396237. Nakano H, Yamazaki T, Miyatake ... Nucleic Acids Research. 20 (21): 5587-92. doi:10.1093/nar/20.21.5587. PMC 334390 . PMID 1333583. "Entrez Gene: TOP2B ... Ng SW, Liu Y, Schnipper LE (Dec 1997). "Cloning and characterization of the 5'-flanking sequence for the human DNA ...
Information may come from nucleic acid sequence homology, gene expression profiles, protein domain structures, text mining of ... coli protein sequences for homology in other genomes and find over 6000 pairs of sequences with shared homology to single ... 1987). ""Homology" in proteins and nucleic acids: a terminology muddle and a way out of it". Nature. 50 (5): 667. doi:10.1016/ ... Because the two sequences in each protein pair are non-homologous, these interactions could not be predicted using homology- ...
Beintema JJ, Wietzes P, Weickmann JL, Glitz DG (Jan 1984). "The amino acid sequence of human pancreatic ribonuclease". ... Nucleic Acids Research. 20 (3): 612. doi:10.1093/nar/20.3.612. PMC 310435 . PMID 1741299. Sakakibara R, Hashida K, Tominaga N, ... N-terminal sequence homology with human nonsecretory ribonuclease". Chemical & Pharmaceutical Bulletin. 39 (1): 146-9. doi: ... Haugg M, Schein CH (Feb 1992). "The DNA sequences of the human and hamster secretory ribonucleases determined with the ...
... probabilistic models of proteins and nucleic acids, Cambridge University Press, 1998. *^ Söding J (2005). "Protein homology ... sequences of S. {\displaystyle S}. until the modified sequences, S. i. ′. {\displaystyle S_{i}^{'}}. , all conform to length L ... A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or ... From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' ...
Nucleic Acids Research. 22 (4): 625-31. doi:10.1093/nar/22.4.625. PMC 307853 . PMID 7510398. Turnbough CL, Switzer RL (2008). " ... "The activity of Escherichia coli dihydroorotate dehydrogenase is dependent on a conserved loop identified by sequence homology ... Translation initiation can occur at more than one different site within this leader sequence, under high CTP or GTP conditions ... This hairpin blocks ribosome-binding at the Shine-Dalgarno sequence, and therefore blocks expression of PyrD. Under low CTP/GTP ...
Homology (biology) KEGG Multiple Sequence Alignment MicrobesOnline home page IMG home page reference: Nucleic Acids Research, ... A curated non-redundant sequence database of genomes, transcripts and proteins". Nucleic Acids Research. 35 (Database issue): ... Bates, J. T.; Chivian, D.; Arkin, A. P. (2011). "GLAMM: Genome-Linked Application for Metabolic Maps". Nucleic Acids Research. ... Letunic, I.; Doerks, T.; Bork, P. (2009). "SMART 6: Recent updates and new developments". Nucleic Acids Research. 37 (Database ...
WU virus was discovered by shotgun sequencing of the nucleic acids found in the respiratory secretions of a young patient ... Sequence homology was detected among the sequences found in the clinical sample and the known genomes of other human ... The complete genome of the WU virus has been sequenced and found to be a circular double-stranded DNA genome of 5229 base pairs ...
... sequence homology, amino acid MeSH G13.810.550 --- sequence homology, nucleic acid MeSH G13.810.550.830 --- synteny MeSH ... sequence deletion MeSH G13.920.590.762.180 --- chromosome deletion MeSH G13.920.590.762.320 --- gene deletion MeSH G13.920. ...
1998). Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge, UK: Cambridge University ... Girdea, M; Noe, L; Kucherov, G (January 2010). "Back-translation for discovering distant protein homologies in the presence of ... Sequence type: protein or nucleotide *Sequence type: protein or nucleotide **Alignment type: local or global *Sequence type: ... September 1997). "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs". Nucleic Acids Research. 25 ...
Li J, Xia Z, Ding J (Sep 2005). "Thioredoxin-like domain of human kappa class glutathione transferase reveals sequence homology ... Nucleic Acids Research. 34 (Database issue): D415-8. doi:10.1093/nar/gkj139. PMC 1347501 . PMID 16381901. Ewing RM, Chu P, ... Li J, Xia Z, Ding J (Sep 2005). "Thioredoxin-like domain of human kappa class glutathione transferase reveals sequence homology ... 13-eicosatetraenoic acid. The amount of expression of adiponectin has been observed to be related to diseases such as insulin ...
The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The phosphate group and the sugar of ... Methods like sequence alignments and structural alignments are powerful tools that help scientists identify homologies between ... of a nucleic acid will form hydrogen bonds with certain other nitrogenous bases in a complementary strand of nucleic acid ( ... making it an α-keto acid) to another α-keto acid (making it an amino acid). This is important in the biosynthesis of amino ...
"Nucleic Acids Research. 25 (19): 3868-74. doi:10.1093/nar/25.19.3868. PMC 146972 . PMID 9380510.. ... They each share about 25% amino acid sequence identity with RAD51 and with each other.[28] ... RAD51 is involved in the search for homology and strand pairing stages of the process. ... "Nucleic Acids Res. 32 (1): 169-78. doi:10.1093/nar/gkg925. PMC 373258 . PMID 14704354.. ...
A system for quickly identifying segments of a nucleic acid sequence that may be of vector origin. VecScreen searches a query ... Homology*BLAST (Basic Local Alignment Search Tool). *BLAST (Stand-alone). *BLAST Link (BLink) ... Sequence Read Archive (SRA) The Sequence Read Archive (SRA) stores sequencing data from the next generation of sequencing ... A database that contains sequences built from the existing primary sequence data in GenBank. The sequences and corresponding ...
I. Conserved genetic and nucleic acid base sequence homologies. D Dubnau, I Smith, P Morell, and J Marmur ... I. Conserved genetic and nucleic acid base sequence homologies. D Dubnau, I Smith, P Morell, J Marmur ... I. Conserved genetic and nucleic acid base sequence homologies. D Dubnau, I Smith, P Morell, J Marmur ... I. Conserved genetic and nucleic acid base sequence homologies Message Subject (Your Name) has sent you a message from PNAS ...
Fri, 21 Oct 2011 , Nucleic Acids There is a high level of sequence homology (98-100%) between D4Z4 repeats from the 4q35 and ... Sequence Homology And Genetic Recombination Between 4q35 And 10q26. ... DNA sequencing was successful in identifying a unique BluI restriction site present only in each copy of the 10q26-derived ... The high degree of homology between the 4q35 and the 10q26 D4F104S1 region is thought to have been responsible for ...
"Nucleic Acids Research. 38 (Database issue): D190-5. doi:10.1093/nar/gkp951. PMC 2808932. PMID 19900971.. ... Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the ... Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. Significant ... A sequence alignment of mammalian histone proteins. Sequences are the middle 120-180 amino acid residues of the proteins. ...
... capsid protein major-homology-region peptide analogs by NMR spectroscopy. ... Nucleic Acid Database. *wwPDB Partners. *RCSB PDB. *PDBe. *PDBj. *BMRB. RCSB PDB (citation) is managed by two members of the ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ... Sequence Similarity Clusters for the Entities in PDB 1BMX Legend Entity #1 , Chains: A HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 ...
Structural basis for relief of autoinhibition of the Dbl homology domain of proto-oncogene Vav by tyrosine phosphorylation. ... Nucleic Acid Database. *wwPDB Partners. *RCSB PDB. *PDBe. *PDBj. *BMRB. RCSB PDB (citation) is managed by two members of the ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ... Sequence Similarity Clusters for the Entities in PDB 1F5X Legend Entity #1 , Chains: A RHO-GEF VAV protein, length: 208 (BLAST ...
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W13-7. doi: 10.1093/nar/gkr245. Epub 2011 May 9. Research Support, Non-U.S. ... These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the ... a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology ... a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology ...
... we have cloned and sequenced novel junctions produced by six spontaneous deletion mutations at the aprt locus of Chinese ... To examine the factors governing the generation of DNA sequence rearrangements in mammalian somatic cells, ... Sequence Homology, Nucleic Acid Substances * Pentosyltransferases * Adenine Phosphoribosyltransferase * DNA Restriction Enzymes ... Spontaneous deletion formation at the aprt locus of hamster cells: the presence of short sequence homologies and dyad ...
The primary amino acid sequence of the toxin was deduced from the nucleotide sequence data. entC3 contains 801 bp and encodes a ... which encodes staphylococcal enterotoxin C3 was cloned from the genome of Staphylococcus aureus FRI-913 and sequenced. ... Molecular Sequence Data * Molecular Weight * Protein Precursors / genetics * Sequence Homology, Nucleic Acid ... The primary amino acid sequence of the toxin was deduced from the nucleotide sequence data. entC3 contains 801 bp and encodes a ...
We have shown, by molecular cloning and DNA sequencing, that a 2058 bp Sau3A right-junction fragment of transposon Tn1545 ... Molecular Sequence Data * Plasmids * Protein Biosynthesis * Restriction Mapping * Sequence Homology, Nucleic Acid ... The DNA sequence of these genes, designated orf1 and orf2, has been determined and the corresponding proteins, ORF1 and ORF2, ... We also found that ORF1 and ORF2 display local homology with, respectively, proteins Xis and Int from lamboid phages, which ...
Sequence Homology, Nucleic Acid • Serine • Serotonin • Serotonin Plasma Membrane Transport Proteins • Serotonin Receptor ... Folic Acid • Folic Acid Deficiency • Food • Food Deprivation • Formate-Tetrahydrofolate Ligase • Gene Expression • Gene ... Abdomen • Abscisic Acid • Acetaminophen • Acetylcholinesterase • Actins • Action Potentials • Adaptation, Biological • ... Pyrrolidonecarboxylic Acid • Quantitative Trait Loci • Quantitative Trait, Heritable • Raphe Nuclei • Rats • Receptor, Insulin ...
Modelling of proteins and nucleic acids. • Sequence alignments and sequence homology. • Homology modelling. • De novo modelling ... Key elements of biochemistry: proteins, peptides, nucleic acids, lipids, and small molecules. • Important metabolic pathways. ... This will include structure prediction using homology and ab initio protein modelling, building protein-ligand and protein- ...
Sequence Homology, Nucleic Acid. *DUX4. *p53 Protein. *MDM2. *Cancer Gene Expression Regulation ... Using a luciferase reporting system and sequence analysis, the potential target of miR-411-5p was identified as sprouty homolog ... Here we studied 60 RMSs using whole-exome/-transcriptome sequencing, copy number (CN) and DNA methylome analyses to unravel the ... Given that the Pax3-Foxo1 fusion gene will contain all the regulatory sequences necessary for precise regulation of its ...
... was isolated and its DNA sequence determined. The cDNA is assumed to encode alpha-1-antitrypsin on the basis of its sequence ... A cDNA clone encoding the complete coding sequence for porcine alpha-1-antitrypsin (or alpha 1-protease inhibitor, PI) ... Sequence Analysis, DNA. Sequence Homology, Amino Acid. Sequence Homology, Nucleic Acid. Swine / genetics*. alpha 1-Antitrypsin ... was isolated and its DNA sequence determined. The cDNA is assumed to encode alpha-1-antitrypsin on the basis of its sequence ...
Molecular Sequence Data. *RNA. *Sequence Homology, Nucleic Acid. *Peptide Fragments. *Biomarkers, Tumor ... Multiplexed amplicon sequencing of PCR products from bisulfite-treated DNA of matched CRC and non-neoplastic tissue as well as ... Because there is no data available about the transcription factors which bind to ING1 promoter, the promoter sequence was ... qMSP assays were developed for 32 genes, including 15 of the sequenced genes, and used to quantify methylation in tumor, ...
Nucleic Acid Hybridization. Oncogenes*. RNA. Sequence Homology, Nucleic Acid. Transcription, Genetic. Trophoblasts / physiology ... 18639569 - Gene expression profiles modulated by the human carcinogen aristolochic acid i in human.... 7903339 - Molecular ...
Computer Analysis of Protein and Nucleic Acid Sequences, Volume 183 - 1st Edition. Print Book & E-Book. ISBN 9780121820848, ... C.B. Lawrence, Use of Homology Domains in Sequence Similarity Detection.. M. Gribskov, R. L~aduthy, and D. Eisenberg, Profile ... J.C.W. Shepherd, Ancient Patterns in Nucleic Acid Sequences.. R. Staden, Searching for Patterns in Protein and Nucleic Acid ... Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences, Volume 183 1st Edition. 0.0 star rating Write a ...
Sequence Homology; Nucleic Acid, Transcription Factors/genetics, Variation (Genetics) National Category Genetics Identifiers. ...
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W526-31. doi: 10.1093/nar/gkp316. Epub 2009 May 6. ... HorA web server to infer homology between proteins using sequence and structural similarity. ... Nucleic Acids Res. 2009 Jul;37(Web Server issue):W532-8. doi: 10.1093/nar/gkp328. Epub 2009 May 5. ... Nucleic Acids Res. 2012 Jul;40(12):5189-200. doi: 10.1093/nar/gks226. Epub 2012 Mar 9. Review. ...
Repetitive Sequences, Nucleic Acid. *Retrotransposons*. *Sequence Homology, Amino Acid. *Support, Non-U.S. Govt ... A polymerase chain reaction assay was developed based on conserved amino acid sequences shared between the Ta11-1 reverse ... these sequences over most of their evolutionary history. One sequence, Ta17, is located in the mitochondrial genome. The ... DNA sequence analysis near the Arabidopsis thaliana ABI3 gene revealed the presence of a non-LTR retrotransposon insertion that ...
The invention relates to the protein and nucleic acids encoding the protein. The invention further relates to an assay system ... The nucleic acid sequence of EER-7 shows homology to known lysyl oxidase genes. All previously identified lysyl oxidase ... The present invention provides a novel LO protein termed EER-7. Nucleic acid sequences, protein sequence, nucleic acid and ... the isolated nucleic acid lacks one or more introns. Isolated nucleic acid molecules include sequences inserted into plasmids, ...
Regulatory Sequences, Nucleic Acid Response Elements Sequence Homology, Nucleic Acid Transcription Factors Transcription, ... Base Sequence Binding Sites Circadian Clocks Circadian Rhythm Conserved Sequence DNA-Binding Proteins Evolution, Molecular Gene ... Molecular Sequence Data Mutation Nucleotide Motifs Plants, Genetically Modified Promoter Regions, Genetic Protein Binding ...
For example, the amino acid sequence of the E. coli RpoD is very well preserved among a very large number of Gram− bacteria ( ... 1992). "Stable Propagation of Cosmid Sized Human DNA Inserts in an F-Factor Based Vector." Nucleic Acids Research 20(5): 1083- ... KEGG database Eco RpoD (2010). "Protein sequence homology search for E. coli k12 R p o D protein." http://ssdb.genome.jp/ssdb- ... 1991). Amplified 16S RNA genes will be cloned (in pCR®8/GW/TOPO) for sequencing to compare them with the nonredundant sequence ...
... impeding searches for nucleic acid sequence homology between angiosperms and loblolly pine. However, we expect a subset of ... 1999 Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27: 573-580. ... A total of 4397 full-length PtAppalachian sequences and 2835 PtRLG_13 sequences were ,80% similar to their reference sequences ... sequence identity. Sequencing technology did not affect the percentage of sequence sets aligning to the genome as much as the ...
CPHmodels-3.0-Remote homology modeling using structure-guided sequence profiles. Nucleic Acids Res. 2010, 38, W576-W581. [ ... Sequence Analysis. The amino acid sequence of BmR1 antigen was retrieved from GenBank (accession number AF225296). ProtParam ... Sequence. M I K M N E K Y V K. E L I L L L L F A M. I Y T S L E S N C E. F W I E D D F H P F. ... Sequence. V P K S E E A R E E. Y C G F F K E M N L. S R N E L M D T I R. K W A S K Y G V L E. ...
  • For example, a population set provides information on genetic variation within an organism, while a phylogenetic set may contain sequences, and their alignment, of a single gene obtained from several related organisms. (unt.edu)
  • A collection of human gene-specific reference genomic sequences. (unt.edu)
  • A public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities. (unt.edu)
  • Endoproteinase-cleaved peptides of the APO-1 protein were subjected to amino acid sequencing, and corresponding oligonucleotides were used to identify a full-length APO-1 cDNA clone from an SKW6.4 cDNA library. (uni-regensburg.de)
  • A high number of specific clones was obtained after immunization with a pool of nine mimotopes, and the resulting mAbs were shown to recognize several 16- and 27-mer peptides derived from natural HVR1 sequences isolated from patients with acute and chronic HCV infection, suggesting that HVR1 mimotopes were efficient antigenic and immunogenic mimics of naturally occurring HCV variants. (jimmunol.org)
  • Prospective studies of serological responses to synthetic oligopeptides derived from HVR1 sequences of patients with acute and chronic HCV infection showed apparently extensive serological cross-reactivity for unrelated HVR1 peptides in the majority of the patients ( 3 , 4 , 5 , 6 , 7 , 8 , 9 ). (jimmunol.org)
  • With the advent of the post genome era and the development of sequencing technology, how to find all forms of miRNAs from millions of reads has become one of the challenging topics in bioinformatics. (springer.com)
  • Computer analysis of the uvrD coding sequence has indicated that it contains seven conserved motifs that are shared by a superfamily of proteins involved in DNA metabolism ( 16 ). (asm.org)
  • Motifs IA, IB, and II, previously identified as Walker A and Walker B sequences, respectively, are conserved segments found in many nucleoside triphosphate-binding proteins and all helicases characterized to date ( 14 , 15 , 46 ). (asm.org)
  • Combining expression and sequence data: searching for motifs in expression clusters (Tavazoie), linear contribution of motifs to expression levels (Bussemaker), combinations of motifs (Pilpel). (indiana.edu)
  • There is a high level of sequence homology (98-100%) between D4Z4 repeats from the 4q35 and the 10q26 D4F104S1 loci. (barnardhealth.us)
  • DNA sequencing was successful in identifying a unique BluI restriction site present only in each copy of the 10q26-derived repeat units and a XapI site in all 4q35-derived repeats. (barnardhealth.us)
  • Our analyses indicate that these rearrangements were produced by non-homologous recombinational events occurring between short (2-7 bp) sequence repeats at the two termini of the deletion which leave one copy of the repeat in the mutant gene. (nih.gov)
  • Typically, vector systems package versions of the cognate viral genome, where the majority of viral RNA sequences have been removed. (asm.org)
  • We propose the name NUPAVs (nuclear sequences of plasmid and viral origin) for these objects, by analogy to NUMTs (nuclear copies of mitochondrial DNA) and NUPTs (nuclear copies of plastid DNA, in plants) of organellar origin. (asm.org)
  • We propose that this region was formed by the capture of plasmid and viral sequences by the same mechanism that captures mitochondrial DNA to form NUMTs ( 43 , 65 ). (asm.org)
  • Based on the functional properties of the integrase of bacteriophage lambda, on the analysis of the nucleotide sequence of the junction fragments and of the target before insertion and after excision, a model is proposed for ORF2-catalysed excision of Tn1545 and related conjugative transposons. (nih.gov)
  • In this report, we provide an analysis of the nucleotide sequence for a 57,988-bp region. (asm.org)
  • Kluyveromyces polysporus ) ( 49 ), we were therefore surprised to find the genomic region we describe here, which contains integrated fragments of several plasmid- and virus-like sequences. (asm.org)
  • Conversely, an organism that is further removed evolutionarily from another organism is likely to display a greater divergence in the sequence of the orthologs being studied. (wikipedia.org)