Consensus 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.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Consensus: General agreement or collective opinion; the judgment arrived at by most of those concerned.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.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.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.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.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.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Sequence 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.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, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.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.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Consensus Development Conferences as Topic: Presentations of summary statements representing the majority agreement of physicians, scientists, and other professionals convening for the purpose of reaching a consensus--often with findings and recommendations--on a subject of interest. The Conference, consisting of participants representing the scientific and lay viewpoints, is a significant means of evaluating current medical thought and reflects the latest advances in research for the respective field being addressed.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.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.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.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.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.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.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.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).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.Interferon Regulatory Factors: A family of transcription factors that share an N-terminal HELIX-TURN-HELIX MOTIF and bind INTERFERON-inducible promoters to control GENE expression. IRF proteins bind specific DNA sequences such as interferon-stimulated response elements, interferon regulatory elements, and the interferon consensus sequence.Cell Line: Established cell cultures that have the potential to propagate indefinitely.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.Genes, Bacterial: The functional hereditary units of BACTERIA.Bacterial Proteins: Proteins found in any species of bacterium.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.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.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.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.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.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.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.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.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.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.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.RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.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.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.Electrophoretic Mobility Shift Assay: An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.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.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.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.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.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.Chloramphenicol O-Acetyltransferase: An enzyme that catalyzes the acetylation of chloramphenicol to yield chloramphenicol 3-acetate. Since chloramphenicol 3-acetate does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase, the enzyme is responsible for the naturally occurring chloramphenicol resistance in bacteria. The enzyme, for which variants are known, is found in both gram-negative and gram-positive bacteria. EC 2.3.1.28.Delphi Technique: An iterative questionnaire designed to measure consensus among individual responses. In the classic Delphi approach, there is no interaction between responder and interviewer.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.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.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 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.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Response Elements: Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.DNA Footprinting: A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)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 Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Deoxyribonuclease I: An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.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).Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Zinc Fingers: Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites.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.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Glycosylation: The chemical or biochemical addition of carbohydrate or glycosyl groups to other chemicals, especially peptides or proteins. Glycosyl transferases are used in this biochemical reaction.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.Nucleotide Mapping: Two-dimensional separation and analysis of nucleotides.Kinetics: The rate dynamics in chemical or physical systems.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Genes, Reporter: Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.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.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)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).Sp1 Transcription Factor: Promoter-specific RNA polymerase II transcription factor that binds to the GC box, one of the upstream promoter elements, in mammalian cells. The binding of Sp1 is necessary for the initiation of transcription in the promoters of a variety of cellular and viral GENES.Point Mutation: A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.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.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.Furin: A proprotein convertase with specificity for the proproteins of PROALBUMIN; COMPLEMENT 3C; and VON WILLEBRAND FACTOR. It has specificity for cleavage near paired ARGININE residues that are separated by two amino acids.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.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).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)Genes, Fungal: The functional hereditary units of FUNGI.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.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)RNA Precursors: RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.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.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.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)Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Peptide Library: A collection of cloned peptides, or chemically synthesized peptides, frequently consisting of all possible combinations of amino acids making up an n-amino acid peptide.Genetic Variation: Genotypic differences observed among individuals in a population.RNA Splice Sites: Nucleotide sequences located at the ends of EXONS and recognized in pre-messenger RNA by SPLICEOSOMES. They are joined during the RNA SPLICING reaction, forming the junctions between exons.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.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.Single-Strand Specific DNA and RNA Endonucleases: Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.Interferon Regulatory Factor-2: An interferon regulatory factor that represses transcription of TYPE I INTERFERONS and activates transcription of HISTONE H4.TATA Box: A conserved A-T rich sequence which is contained in promoters for RNA polymerase II. The segment is seven base pairs long and the nucleotides most commonly found are TATAAAA.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)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.Gene Expression Regulation, Enzymologic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Binding, Competitive: The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Viral Proteins: Proteins found in any species of virus.Tumor Cells, Cultured: Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.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.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Cricetinae: A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.DNA-Directed RNA Polymerases: Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.Consensus Development Conferences, NIH as Topic: Articles on conferences sponsored by NIH presenting summary statements representing the majority agreement of physicians, scientists, and other professionals convening for the purpose of reaching a consensus on a subject of interest. This heading is used for NIH consensus conferences as a means of scientific communication. In indexing it is viewed as a type of review article and as a tag for any article appearing in any publication of the NIH Office of Medical Applications of Research (OMAR).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.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.Sigma Factor: A protein which is a subunit of RNA polymerase. It effects initiation of specific RNA chains from DNA.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.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.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.Genes, Viral: The functional hereditary units of VIRUSES.Protein Processing, Post-Translational: Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.Molecular Weight: The sum of the weight of all the atoms in a molecule.Fungal Proteins: Proteins found in any species of fungus.beta-Galactosidase: A group of enzymes that catalyzes the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-galactosides. Deficiency of beta-Galactosidase A1 may cause GANGLIOSIDOSIS, GM1.Ribonucleoproteins: Complexes of RNA-binding proteins with ribonucleic acids (RNA).Chromosome Deletion: Actual loss of portion of a chromosome.5' Untranslated Regions: The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating 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.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.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).Serine: A non-essential amino acid occurring in natural form as the L-isomer. It is synthesized from GLYCINE or THREONINE. It is involved in the biosynthesis of PURINES; PYRIMIDINES; and other amino acids.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.DNA Replication: The process by which a DNA molecule is duplicated.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.Regulon: In eukaryotes, a genetic unit consisting of a noncontiguous group of genes under the control of a single regulator gene. In bacteria, regulons are global regulatory systems involved in the interplay of pleiotropic regulatory domains and consist of several OPERONS.Transcription Initiation Site: The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Interferon Regulatory Factor-1: An interferon regulatory factor that binds upstream TRANSCRIPTIONAL REGULATORY ELEMENTS in the GENES for INTERFERON-ALPHA and INTERFERON-BETA. It functions as a transcriptional activator for the INTERFERON TYPE I genes.Lorisidae: A family of Primates of the suborder Strepsirhini containing six genera. The family is distributed in parts of Africa, India, Asia, and the Philippines. The six genera are: Arctocebus (golden potto), GALAGO (bush babies), Loris (slender loris), Nycticebus (slow loris), and Perodicticus (potto). Lorises and pottos are relatively common except for Arctocebus, the golden potto. All are arboreal and nocturnal.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.Protein PrecursorsAmino Acid Substitution: The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.Subtilisins: A family of SERINE ENDOPEPTIDASES isolated from Bacillus subtilis. EC 3.4.21.-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.RNA, Small Nuclear: Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.Luciferases: Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.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.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.PhosphoproteinsSequence 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.5' Flanking Region: The region of DNA which borders the 5' end of a transcription unit and where a variety of regulatory sequences are located.Peptide Mapping: Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.Mutagenesis, Insertional: Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.DNA, Satellite: Highly repetitive DNA sequences found in HETEROCHROMATIN, mainly near centromeres. They are composed of simple sequences (very short) (see MINISATELLITE REPEATS) repeated in tandem many times to form large blocks of sequence. Additionally, following the accumulation of mutations, these blocks of repeats have been repeated in tandem themselves. The degree of repetition is on the order of 1000 to 10 million at each locus. Loci are few, usually one or two per chromosome. They were called satellites since in density gradients, they often sediment as distinct, satellite bands separate from the bulk of genomic DNA owing to a distinct BASE COMPOSITION.Heat-Shock Proteins: Proteins which are synthesized in eukaryotic organisms and bacteria in response to hyperthermia and other environmental stresses. They increase thermal tolerance and perform functions essential to cell survival under these conditions.Contig Mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.Bacillus subtilis: A species of gram-positive bacteria that is a common soil and water saprophyte.Replication Origin: A unique DNA sequence of a replicon at which DNA REPLICATION is initiated and proceeds bidirectionally or unidirectionally. It contains the sites where the first separation of the complementary strands occurs, a primer RNA is synthesized, and the switch from primer RNA to DNA synthesis takes place. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)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.3T3 Cells: Cell lines whose original growing procedure consisted being transferred (T) every 3 days and plated at 300,000 cells per plate (J Cell Biol 17:299-313, 1963). Lines have been developed using several different strains of mice. Tissues are usually fibroblasts derived from mouse embryos but other types and sources have been developed as well. The 3T3 lines are valuable in vitro host systems for oncogenic virus transformation studies, since 3T3 cells possess a high sensitivity to CONTACT INHIBITION.Integration Host Factors: Bacterial proteins that are used by BACTERIOPHAGES to incorporate their DNA into the DNA of the "host" bacteria. They are DNA-binding proteins that function in genetic recombination as well as in transcriptional and translational regulation.Genetic Vectors: DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.Proto-Oncogene Proteins: Products of proto-oncogenes. Normally they do not have oncogenic or transforming properties, but are involved in the regulation or differentiation of cell growth. They often have protein kinase activity.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.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.Short Interspersed Nucleotide Elements: Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).CHO Cells: CELL LINE derived from the ovary of the Chinese hamster, Cricetulus griseus (CRICETULUS). The species is a favorite for cytogenetic studies because of its small chromosome number. The cell line has provided model systems for the study of genetic alterations in cultured mammalian cells.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.Protein Kinases: A family of enzymes that catalyze the conversion of ATP and a protein to ADP and a phosphoprotein.Operator Regions, Genetic: The regulatory elements of an OPERON to which activators or repressors bind thereby effecting the transcription of GENES in the operon.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.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.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Precipitin Tests: Serologic tests in which a positive reaction manifested by visible CHEMICAL PRECIPITATION occurs when a soluble ANTIGEN reacts with its precipitins, i.e., ANTIBODIES that can form a precipitate.Chromatin Immunoprecipitation: A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.Societies, Medical: Societies whose membership is limited to physicians.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Protein Sorting Signals: Amino acid sequences found in transported proteins that selectively guide the distribution of the proteins to specific cellular compartments.Transcription Factor AP-1: A multiprotein complex composed of the products of c-jun and c-fos proto-oncogenes. These proteins must dimerize in order to bind to the AP-1 recognition site, also known as the TPA-responsive element (TRE). AP-1 controls both basal and inducible transcription of several genes.Lac Operon: The genetic unit consisting of three structural genes, an operator and a regulatory gene. The regulatory gene controls the synthesis of the three structural genes: BETA-GALACTOSIDASE and beta-galactoside permease (involved with the metabolism of lactose), and beta-thiogalactoside acetyltransferase.Proline: A non-essential amino acid that is synthesized from GLUTAMIC ACID. It is an essential component of COLLAGEN and is important for proper functioning of joints and tendons.Bacteriophages: Viruses whose hosts are bacterial cells.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.PhosphopeptidesCOS 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).)

Concomitant activation of pathways downstream of Grb2 and PI 3-kinase is required for MET-mediated metastasis. (1/4818)

The Met tyrosine kinase - the HGF receptor - induces cell transformation and metastasis when constitutively activated. Met signaling is mediated by phosphorylation of two carboxy-terminal tyrosines which act as docking sites for a number of SH2-containing molecules. These include Grb2 and p85 which couple the receptor, respectively, with Ras and PI 3-kinase. We previously showed that a Met mutant designed to obtain preferential coupling with Grb2 (Met2xGrb2) is permissive for motility, increases transformation, but - surprisingly - is impaired in causing invasion and metastasis. In this work we used Met mutants optimized for binding either p85 alone (Met2xPI3K) or p85 and Grb2 (MetPI3K/Grb2) to evaluate the relative importance of Ras and PI 3-kinase as downstream effectors of Met. Met2xPI3K was competent in eliciting motility, but not transformation, invasion, or metastasis. Conversely, MetP13K/Grb2 induced motility, transformation, invasion and metastasis as efficiently as wild type Met. Furthermore, the expression of constitutively active PI 3-kinase in cells transformed by the Met2xGrb2 mutant, fully rescued their ability to invade and metastasize. These data point to a central role for PI 3-kinase in Met-mediated invasiveness, and indicate that simultaneous activation of Ras and PI 3-kinase is required to unleash the Met metastatic potential.  (+info)

ATF-2-binding regulatory element is responsible for the Ly49A expression in murine T lymphoid line, EL-4. (2/4818)

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)

Identification of a cAMP response element within the glucose- 6-phosphatase hydrolytic subunit gene promoter which is involved in the transcriptional regulation by cAMP and glucocorticoids in H4IIE hepatoma cells. (3/4818)

The expression of a luciferase reporter gene under the control of the human glucose 6-phosphatase gene promoter was stimulated by both dexamethasone and dibutyryl cAMP in H4IIE hepatoma cells. A cis-active element located between nucleotides -161 and -152 in the glucose 6-phosphatase gene promoter was identified and found to be necessary for both basal reporter-gene expression and induction of expression by both dibutyryl cAMP and dexamethasone. Nucleotides -161 to -152 were functionally replaced by the consensus sequence for a cAMP response element. An antibody against the cAMP response element-binding protein caused a supershift in gel-electrophoretic-mobility-shift assays using an oligonucleotide probe representing the glucose 6-phosphatase gene promoter from nucleotides -161 to -152. These results strongly indicate that in H4IIE cells the glucose 6-phosphatase gene-promoter sequence from -161 to -152 is a cAMP response element which is important for the regulation of transcription of the glucose 6-phosphatase gene by both cAMP and glucocorticoids.  (+info)

Analysis of 4-phosphopantetheinylation of polyhydroxybutyrate synthase from Ralstonia eutropha: generation of beta-alanine auxotrophic Tn5 mutants and cloning of the panD gene region. (4/4818)

The postulated posttranslational modification of the polyhydroxybutyrate (PHA) synthase from Ralstonia eutropha by 4-phosphopantetheine was investigated. Four beta-alanine auxotrophic Tn5-induced mutants of R. eutropha HF39 were isolated, and two insertions were mapped in an open reading frame with strong similarity to the panD gene from Escherichia coli, encoding L-aspartate-1-decarboxylase (EC 4.1.1.15), whereas two other insertions were mapped in an open reading frame (ORF) with strong similarity to the NAD(P)+ transhydrogenase (EC 1.6.1.1) alpha 1 subunit, encoded by the pntAA gene from Escherichia coli. The panD gene was cloned by complementation of the panD mutant of R. eutropha Q20. DNA sequencing of the panD gene region (3,312 bp) revealed an ORF of 365 bp, encoding a protein with 63 and 67% amino acid sequence similarity to PanD from E. coli and Bacillus subtilis, respectively. Subcloning of only this ORF into vectors pBBR1MCS-3 and pBluescript KS- led to complementation of the panD mutants of R. eutropha and E. coli SJ16, respectively. panD-encoded L-aspartate-1-decarboxylase was further confirmed by an enzymatic assay. Upstream of panD, an ORF with strong similarity to pntAA from E. coli, encoding NAD(P)+ transhydrogenase subunit alpha 1 was found; downstream of panD, two ORFs with strong similarity to pntAB and pntB, encoding subunits alpha 2 and beta of the NAD(P)+ transhydrogenase, respectively, were identified. Thus, a hitherto undetermined organization of pan and pnt genes was found in R. eutropha. Labeling experiments using one of the R. eutropha panD mutants and [2-14C]beta-alanine provided no evidence that R. eutropha PHA synthase is covalently modified by posttranslational attachment of 4-phosphopantetheine, nor did the E. coli panD mutant exhibit detectable labeling of functional PHA synthase from R. eutropha.  (+info)

An Lrp-like protein of the hyperthermophilic archaeon Sulfolobus solfataricus which binds to its own promoter. (5/4818)

Regulation of gene expression in the domain Archaea, and specifically hyperthermophiles, has been poorly investigated so far. Biochemical experiments and genome sequencing have shown that, despite the prokaryotic cell and genome organization, basal transcriptional elements of members of the domain Archaea (i.e., TATA box-like sequences, RNA polymerase, and transcription factors TBP, TFIIB, and TFIIS) are of the eukaryotic type. However, open reading frames potentially coding for bacterium-type transcription regulation factors have been recognized in different archaeal strains. This finding raises the question of how bacterial and eukaryotic elements interact in regulating gene expression in Archaea. We have identified a gene coding for a bacterium-type transcription factor in the hyperthermophilic archaeon Sulfolobus solfataricus. The protein, named Lrs14, contains a potential helix-turn-helix motif and is related to the Lrp-AsnC family of regulators of gene expression in the class Bacteria. We show that Lrs14, expressed in Escherichia coli, is a highly thermostable DNA-binding protein. Bandshift and DNase I footprint analyses show that Lrs14 specifically binds to multiple sequences in its own promoter and that the region of binding overlaps the TATA box, suggesting that, like the E. coli Lrp, Lrs14 is autoregulated. We also show that the lrs14 transcript is accumulated in the late growth stages of S. solfataricus.  (+info)

Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. (6/4818)

The complete 184,457-bp sequence of the aromatic catabolic plasmid, pNL1, from Sphingomonas aromaticivorans F199 has been determined. A total of 186 open reading frames (ORFs) are predicted to encode proteins, of which 79 are likely directly associated with catabolism or transport of aromatic compounds. Genes that encode enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-cresol are predicted to be distributed among 15 gene clusters. The unusual coclustering of genes associated with different pathways appears to have evolved in response to similarities in biochemical mechanisms required for the degradation of intermediates in different pathways. A putative efflux pump and several hypothetical membrane-associated proteins were identified and predicted to be involved in the transport of aromatic compounds and/or intermediates in catabolism across the cell wall. Several genes associated with integration and recombination, including two group II intron-associated maturases, were identified in the replication region, suggesting that pNL1 is able to undergo integration and excision events with the chromosome and/or other portions of the plasmid. Conjugative transfer of pNL1 to another Sphingomonas sp. was demonstrated, and genes associated with this function were found in two large clusters. Approximately one-third of the ORFs (59 of them) have no obvious homology to known genes.  (+info)

A binding site for homeodomain and Pax proteins is necessary for L1 cell adhesion molecule gene expression by Pax-6 and bone morphogenetic proteins. (7/4818)

The cell adhesion molecule L1 regulates axonal guidance and fasciculation during development. We previously identified the regulatory region of the L1 gene and showed that it was sufficient for establishing the neural pattern of L1 expression in transgenic mice. In the present study, we characterize a DNA element within this region called the HPD that contains binding motifs for both homeodomain and Pax proteins and responds to signals from bone morphogenetic proteins (BMPs). An ATTA sequence within the core of the HPD was required for binding to the homeodomain protein Barx2 while a separate paired domain recognition motif was necessary for binding to Pax-6. In cellular transfection experiments, L1-luciferase reporter constructs containing the HPD were activated an average of 4-fold by Pax-6 in N2A cells and 5-fold by BMP-2 and BMP-4 in Ng108 cells. Both of these responses were eliminated on deletion of the HPD from L1 constructs. In transgenic mice, deletion of the HPD from an L1-lacZ reporter resulted in a loss of beta-galactosidase expression in the telencephalon and mesencephalon. Collectively, our experiments indicate that the HPD regulates L1 expression in neural tissues via homeodomain and Pax proteins and is likely to be a target of BMP signaling during development.  (+info)

Functional analysis of the promoter of the yeast SNQ2 gene encoding a multidrug resistance transporter that confers the resistance to 4-nitroquinoline N-oxide. (8/4818)

The yeast gene SNQ2, which encodes a multidrug resistance ABC superfamily protein, is required for resistance to the mutagen 4-nitroquinoline N-oxide (4-NQO). The expression of the SNQ2 gene is under the control of a regulatory network that involves the transcription factor Yrr1p, as well as Pdr1p/Pdr3p (Cui et al., Mol. Microbiol., 29, 1307-1315 (1998)). By 5'-deletion analysis of the promoter by using SNQ2-lacZ fusion constructs, four regions: -745 to -639 (region I), -639 to -578 (region II), -548 to -533 (region III) and -533 to -485 (region IV) were found to be important for SNQ2 expression. Genetic analysis suggested that the site in region IV was responsible for the Yrr1p-mediated SNQ2 expression. A consensus motif known for the binding of Pdr1p/Pdr3p (PDRE) was not found in region IV.  (+info)

*Consensus sequence

... can also be considered as consensus sequences. Thus a consensus sequence is a model for a putative DNA binding site: it is ... The conserved sequence motifs are called consensus sequences and they show which residues are conserved and which residues are ... Any mutation allowing a mutated nucleotide in the core promoter sequence to look more like the consensus sequence is known as ... A protein binding site, represented by a consensus sequence, may be a short sequence of nucleotides which is found several ...

*Kozak consensus sequence

The Kozak consensus sequence, Kozak consensus or Kozak sequence is a sequence which occurs on eukaryotic mRNA and has the ... The Kozak consensus sequence plays a major role in the initiation of the translation process. The sequence was named after the ... consensus, the nucleotides at positions +4 (i.e. G in the consensus) and -3 (i.e. either A or G in the consensus) relative to ... Lmx1b is an example of a gene with a weak Kozak consensus sequence. For initiation of translation from such a site, other ...

*DNA binding site

... restriction sites can be generally represented by consensus sequences. This is because they target mostly identical sequences ... This makes it difficult to accurately represent transcription factor binding sites using consensus sequences, and they are ... Schneider T.D (2002). "Consensus sequence Zen". Applied Bioinformatics. 1 (3): 111-119. PMC 1852464 . PMID 15130839. Bulyk M.L ... can be represented by a consensus sequence. This representation has the advantage of being compact, but at the expense of ...

*GLIS1

It has the consensus sequence GACCACCCAC. The individual zinc finger motifs are separated from one another by the amino acid ... to interact with target DNA sequences to regulate gene transcription. The domain interacts sequence specifically with the DNA, ... The protein's termini are fairly unusual, and have no strong sequence similarity other proteins. Glis1 can be used as one of ... a change in a single nucleotide of the DNA sequence of the gene, has been implicated as a risk factor in the neurodegenerative ...

*Short Oligonucleotide Analysis Package

SOAPsnp is a consensus sequence builder. This tool uses the output from SOAPaligner to generate a consensus sequence which ... The first release of SOAP consisted only of the sequence alignment tool SOAPaligner. SOAP v2 extended and improved on SOAP v1 ... SOAPindel is a tool to find insertions and deletions from next generation paired-end sequencing data. ... "The sequence and de novo assembly of the giant panda genome". Nature. 463 (7279): 311-317. doi:10.1038/nature08696. ISSN 0028- ...

*Initiator element

The consensus sequence of Inr in humans was inferred to be YYANWYY. The census sequence in Drosophila is TCAKTY. Studies have ... It has the consensus sequence YYANWYY. Similarly to the TATA box, the Inr element facilitates the binding of transcription ... Out of those sequences with the TATA box, 62% contained the Inr element as well. Though the Inr element is not fully understood ... This sequence encompasses where the RNA polymerase will begin transcribing. The Inr element is located about ~20 bp downstream ...

*Alternative splicing

... the consensus around this sequence varies somewhat. In humans the branch site consensus sequence is yUnAy. The branch site is ... The intron upstream from exon 4 has a polypyrimidine tract that doesn't match the consensus sequence well, so that U2AF ... The typical eukaryotic nuclear intron has consensus sequences defining important regions. Each intron has GU at its 5' end. ... Gao, K.; Masuda, A.; Matsuura, T.; Ohno, K. (2008). "Human branch point consensus sequence is yUnAy". Nucleic Acids Research. ...

*Ras subfamily

The G5 motif contains a SAK consensus sequence. The A is alanine146, which provides specificity for guanine rather than adenine ... Dynamic electrostatic interactions between its positively charged basic sequence with negative charges at the inner leaflet of ... or the combination of prenylation and a polybasic sequence adjacent to the prenylation site (KRAS). The C-terminal CaaX box of ...

*Lipid-anchored protein

No consensus sequence for protein palmitoylation has been identified. Palmitoylated proteins are mainly found on the ... In the CAAX box sequence, the C represents the cysteine that is prenylated, the A's represent any aliphatic amino acid and the ... This reaction is facilitated by N-myristoyltransferase . These proteins usually begin with a Met-Gly sequence and with either a ...

*Scaffold/matrix attachment region

S/MARs do not have an obvious consensus sequence. Although prototype elements consist of AT-rich regions several hundred base ... are sequences in the DNA of eukaryotic chromosomes where the nuclear matrix attaches. As architectural DNA components that ...

*E-box

The consensus sequence of the E-box is usually CANNTG; however, there exist other E-boxes of similar sequences called ... Furthermore, HES1, which can bind to a different consensus sequence (CACNAG, known as the N-box), shows suppression effect in ... Its specific DNA sequence, CANNTG (where N can be any nucleotide), with a palindromic canonical sequence of CACGTG, is ... gene and regulates its expression CAGCTT sequence found within the MyoD core enhancer CACCTCGTGAC sequence in the proximal ...

*ADAM10

The consensus sequence for catalytically active ADAM proteins is HEXGHNLGXXHD. Structural analysis of ADAM17, which has the ... 2000). "Shotgun sequencing of the human transcriptome with ORF expressed sequence tags". Proceedings of the National Academy of ... The proposed active site of ADAM10 has been identified by sequence analysis, and is identical to enzymes in the Snake Venom ... same active site sequence as ADAM10, suggests that the three histidines in this sequence bind a Zn2+ atom, and that the ...

*CTCF

... binds to the consensus sequence CCGCGNGGNGGCAG (in IUPAC notation). This sequence is defined by 11 zinc finger motifs in ... This protein was found to be binding to three regularly spaced repeats of the core sequence CCCTC and thus was named CCCTC ... Binding of targeting sequence elements by CTCF can block the interaction between enhancers and promoters, therefore limiting ... CTCF is thought to be a primary part of the activity of insulators, sequences that block the interaction between enhancers and ...

*FAM231B

... contains a Kozak consensus sequence surrounding the start codon nucleotides. The primary promoter region for the human ... Its mRNA sequence is 1312 base pairs long, with the coding sequence in region 343 through 852, and there is only one exon. The ... FAM231B, or family with sequence similarity 231B, is a protein found in humans and is encoded by FAM231B gene. Orthologs of ... "Homo sapiens family with sequence similarity 231 member B (FAM231B), mRNA". National Center for Biotechnology Information, U.S ...

*Calcium-binding protein 1

CAbP1 and CAbP2 contain a consensus sequence for N-terminal myristoylation. Transcription factor binding sites identified by ...

*HIST1H1A

Absence of a consensus sequence for the p34cdc2/cyclin B kinase". J. Biol. Chem. 270 (46): 27653-60. doi:10.1074/jbc.270.46. ... Meergans T, Albig W, Doenecke D (1998). "Conserved sequence elements in human main type-H1 histone gene promoters: their role ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... conserved and varied sequence elements in two H1 subtype genes". Eur J Cell Biol. 49 (1): 110-5. PMID 2759094. Marzluff WF, ...

*SOS box

15 April 1998). "The Bacillus subtilis DinR Binding Site: Redefinition of the Consensus Sequence". J. Bacteriol. 180 (8): 2201- ... Mazón G, Lucena JM, Campoy S, Fernández de Henestrosa AR, Candau P, Barbé J (February 2004). "LexA-binding sequences in Gram- ... SOS boxes differ in DNA sequences and binding affinity towards LexA from organism to organism. Furthermore, SOS boxes may be ...

*Glycan

Unlike N-linked glycans, there is no known consensus sequence yet. However, the placement of a proline residue at either -1 or ... The sequon is an Asn-X-Ser or Asn-X-Thr sequence, where X is any amino acid except proline and the glycan may be composed of N- ...

*Peroxisome proliferator-activated receptor

These DNA sequences are termed PPREs (peroxisome proliferator hormone response elements). The DNA consensus sequence is ... In general, this sequence occurs in the promoter region of a gene, and, when the PPAR binds its ligand, transcription of target ... which bind to specific sequences of DNA known as hormone response elements when the receptor is activated. The LBD has an ...

*CAAT box

... and is typically accompanied by a conserved consensus sequence. It is an invariant DNA sequence at about minus 70 base pairs ... Some sequences lack the CAAT-box completely. Secondly, the surrounding nucleotides in plants do not match the consensus ... Both of these consensus sequences belong to the regulatory promoter. Full gene expression occurs when transcription activator ... In the direction of transcription of the template strand, the consensus sequence, or the calculated order of the most frequent ...

*Mothers against decapentaplegic homolog 4

These additional sites contain the CAGCC motif and the GGC(GC),(CG) consensus sequences, the latter also known as 5GC sites. ... The sequence of intracellular reactions involving SMADS is called the SMAD pathway or the transforming growth factor beta (TGF- ... Zawel L, Dai JL, Buckhaults P, Zhou S, Kinzler KW, Vogelstein B, Kern SE (Mar 1998). "Human Smad3 and Smad4 are sequence- ... SMAD3/SMAD4 complex also binds to the TPA-responsive gene promoter elements, which have the sequence motif TGAGTCAG. The first ...

*Thyroglobulin

Lamas L, Anderson PC, Fox JW, Dunn JT (1989). "Consensus sequences for early iodination and hormonogenesis in human ... Malthiéry Y, Lissitzky S (1985). "Sequence of the 5'-end quarter of the human-thyroglobulin messenger ribonucleic acid and of ... Malthiéry Y, Lissitzky S (1987). "Primary structure of human thyroglobulin deduced from the sequence of its 8448-base ... "A consensus report of the role of serum thyroglobulin as a monitoring method for low-risk patients with papillary thyroid ...

*Mothers against decapentaplegic homolog 3

... consensus sequences, the latter also known as 5GC sites. The 5GC-motifs are highly represented as clusters of sites, in SMAD- ... The c-myc TIE is a composite element, composed of an overlapping RSBE and a consensus E2F site, which is capable of binding at ... SMAD3/SMAD4 complex also binds to the TPA-responsive gene promoter elements, which have the sequence motif TGAGTCAG. The X-ray ...

*Pre-replication complex

DnaA binds tightly to a 9-base pair consensus sequence in oriC; 5' - TTATCCACA - 3'. There are 5 such 9-bp sequences (R1-R5) ... Initiation sequences in S. pombe and higher eukaryotes are not well defined. However, the initiation sequences are generally ... and 4 non-consensus sequences (I1-I4) within oriC that DnaA binds with differential affinity. DnaA binds R4, R1, and R2 with ... Saccharomyces cerevisiae (S. cerevisiae) is the only known eukaryote with a defined initiation sequence TTTTTATG/ATTTA/T. This ...

*RpoN

The RpoN-regulated promoter elements have the consensus sequence as follows: TTGGCACGGTTTTTGCT. Dong, T; Yu, R; Schellhorn, H ( ...

*Antonius Suwanto

Isolated from Tempe based on Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction (ERIC-PCR)". HAYATI ... DNA sequence and mechanism of transfer". Journal of Bacteriology. 182 (1): 81-90. doi:10.1128/jb.182.1.81-90.2000. PMC 94243 . ...
Transcription factor p53 regulates its target genes through binding to DNA consensus sequence and activating the promoters of its downstream genes. The conventional p53 consensus binding sequence was defined as two copies of the 10-bp motif 5-PuPuPuC(A/T)(T/A)GPyPyPy-3 with a spacer of 0 to 13 bp, which exists in the regulatory regions of some p53 target genes. However, there is no such p53 cons
Molecular Cloning, also known as Maniatis, has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential.
Thus, terms like natural "laws" or "phenomena" in complex, probabilistic fields should have significantly less force: they are less "laws" or "phenomena" of nature than they are "laws" or "phenomena" of a statistical, "simulacrum account" of observations of nature.. Similarly, defining a "product" of nature is also often an exercise in probabilism, complicated by natural complexity. What scientists refer to as a "typical" human gene, for example, actually encompasses a wide variety of genetic sequences within the human population.184 Determining the archetypal sequence of that gene, the "consensus sequence," is therefore very much a product of statistics, rather than the specific identification of a gene with the consensus sequence as it actually exists in nature.185 Characterizing a particular genetic sequence as a "natural product" is consequently a two-step act of probabilism: using statistical methodology to determine a consensus sequence, and then using statistical methodology to ...
Molecular Cloning, also known as Maniatis, has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential.
CLUSTAL W (1.82) multiple sequence alignment consensus_2681#0 ---ATTTCCATTTTCATCGGCCTCGTATCTTGAAAGATATACAAAGTAAGAAAAAAATTT 57 consensus_2681#1 GGGATCACTGACTT-ACTTTAAAAGCATCTAGGTTATTGCGTTGACCGATAAATTATGTA 59 ** * ** * * **** * * * * *** * * consensus_2681#0 TATTAAAAAAAAGATAAGGACAAAGAA-ATTGTTGCTCACTTAACAGAAATGGGAAGACC 116 consensus_2681#1 AAATAATTAAGAAGTGTGAATATGAAATATCGATAAAATTTTTGTTAAAA-GAGATCATG 118 * *** ** * * * * * ** ** * * ** *** * ** * consensus_2681#0 TTCGGGGCTTTTATAAGAGAAGCTTCCTTTTACAGTTCGCACT----AGTTCACCGTCCA 172 consensus_2681#1 ATGTTGAATTGTGAGAAAAAATTTATAATTCAAAATTTACTTTTTGAAATATAAGATCAA 178 * * ** * * * ** * ** * * ** * * * * * ** * consensus_2681#0 CTAATTTCAGCATTTCCGTTTCCTCTTTTTGCACGTTATTCACCGGTGCATTTACATTTG 232 consensus_2681#1 CAAA---AAATATTTTTATCCAAAATATTAAAGCATTGAAAGCTG----AATTAGAAGTA 231 * ** * **** * * ** * ** * * * *** * * consensus_2681#0 AAATCGGACGATTCCTGGCTTTATTGTCCTCGAAGGGCGTATTCAAGATCAATCCACCAG 292 consensus_2681#1 ...
No abstract is available; but the full text article can be downloaded by clciking on the link on the right side. This article can be cited as: R. Egel, On the Misgivings of Anthropomorphic Consensus Polling in Defining the Complexity of LifeJ. Biomo
Alnylams third quarter 2013 loss of 48 cents per share was wider than the Zacks Consensus Estimate of a loss of 38 cents per share.
The Kozak consensus sequence, Kozak consensus or Kozak sequence is a sequence which occurs on eukaryotic mRNA and has the consensus (gcc)gccRccAUGG. The Kozak consensus sequence plays a major role in the initiation of the translation process. The sequence was named after the person who brought it to prominence, Marilyn Kozak. The sequence is identified by the notation (gcc)gccRccAUGG, which summarizes data analysed by Kozak from a wide variety of sources (about 699 in all) as follows: a lower-case letter denotes the most common base at a position where the base can nevertheless vary; upper-case letters indicate highly conserved bases, i.e. the AUGG sequence is constant or rarely, if ever, changes, with the exception being the IUPAC ambiguity code R which indicates that a purine (adenine or guanine) is always observed at this position (with adenine being claimed by Kozak to be more frequent); and the sequence in parentheses (gcc) is of uncertain significance. Kozaks paper was limited to a ...
Abstract:. Previous works from our laboratory demonstrated that the monoclonal antibody (MAb) called R7B4 is directed to an epitope shared by various receptors corresponding to the type I cytokine receptor family, containing the common motif WSXWS or the homologous F(Y)GEFS. Later a consensus peptide significantly recognized by the MAb was identified and synthesized (sequence HGYWSEWSPE). In the present work, an homologous of the consensus sequence (HHGYWSEWSPE) was conjugated to PADRE adjuvant to produce Ab that could simulate the MAb activity, that is, acting as hormone and/or cytokine antagonists. The covalently conjugated peptide-PADRE was a better immunogen than the consensus peptide alone according to the reactivity of sera from C57BL/6 immunized mice and, besides, no Ab to PADRE were detected. Furthermore, Ab to consensus peptide elicited after peptide-PADRE inoculation into mice behaved as immunomodulatory agents, since they improved the humoral response to a foreign antigen (in this ...
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation , 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution ...
The CCDS database identifies a core set of human protein coding regions that are consistently annotated by multiple public resources and pass quality tests.
The CCDS database identifies a core set of human protein coding regions that are consistently annotated by multiple public resources and pass quality tests.
Bitcoin Blasts Through $15,000 - Its A Consensus Hallucination by Tyler Durden Dec 7, 2017 5:13 AM In the last 36 hours, Bitcoin has blasted through $12,000, $13,000, $14,000, and now $15,000 levels in an unprecedented 28% surge...
Bitcoin Blasts Through $15,000 - Its A Consensus Hallucination by Tyler Durden Dec 7, 2017 5:13 AM In the last 36 hours, Bitcoin has blasted through $12,000, $13,000, $14,000, and now $15,000 levels in an unprecedented 28% surge...
'Appallingly unmusical,' 'hirsute' and 'destined to fade away' - that pretty much sums up the general consensus.
Secondary structure prediction and consensus sequence of PelD and PleD. A. Secondary structure predication was made using the web-based ProteinPredict program h
The large number of protein consensus sequences that may be recognized without computer analysis are reviewed. These include the extensive range of known phosphorylation site motifs for protein kinase
Read "Whole-genome consensus sequence analysis of a South African rotavirus SA11 sample reveals a mixed infection with two close derivatives of the SA11-H96 strain, Archives of Virology" on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Transcriptional repressor with bimodal DNA-binding specificity. Represses transcription in a methyl-CpG-dependent manner. Binds with a higher affinity to methylated CpG dinucleotides in the consensus sequence 5-CGCG-3 but can also bind to the non-methylated consensus sequence 5-CTGCNA-3 also known as the consensus kaiso binding site (KBS). Can also bind specifically to a single methyl-CpG pair and can bind hemimethylated DNA but with a lower affinity compared to methylated DNA (PubMed:16354688 ...
I want to pause here and talk about this notion of consensus, and the rise of what has been called consensus science. I regard consensus science as an extremely pernicious development that ought to be stopped cold in its tracks. Historically, the claim of consensus has been the first refuge of scoundrels; it is a way to avoid debate by claiming that the matter is already settled. Whenever you hear the consensus of scientists agrees on something or other, reach for your wallet, because youre being had ...
Something elese comes into my mind: Do you have ribosome biding site , (Kozak consensus element, reads gccaccaccATGg or similar) in your , construct? Not sure if applicable: Do you get expression, when you , transfect the construct in cells? Yes, there is a ribosome binding site (luciferase ATG translation start site). Although the flanking sequence surrounding the ATG may not be the optimal Kozak consensus sequence. I have not tried in-vivo transformation yet, but considering my in-vitro results I would expect the same results ...
We investigate to what extent the market uses information that is predictive of whether earnings will meet or beat the analyst consensus forecast of earnings (M
Italian lawmakers will begin voting on Thursday to elect a new president, in the hope that they can end the countrys political impasse, over which concerns are growing.
Start End Score Size Count Identity Consensus 109775 110239 158 93 5 77.0 gactccatctcggactccaactcgggtccatctcgggtcctacttgggctccatttcggactccatctcgg actccatctcgggtccatctcg 116809 117552 142 186 4 72.0 gtcaaagtgggaatttgtacaaagccatgaagatgttcgattggatgccagacaagaatttgatctcatgg aactcaattctaagagcctttgctcatcatgggcaacttgacgaagcaaagatattatttgataaaatgcc cgagtgggacctaatgtcgttgaattcaatgcttgcggcatata 117603 118253 106 93 7 65.3 cctgagcgaaatcttgtttcttggaacgctatgcttgcagcatatgctcaacatgggcatattgaagatgc aaaggtgctgtttgataacatg 34251 34462 104 106 2 99.5 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnna 32398 32553 71 39 4 85.3 actctccaacttactttgattcatcgcagtagctccatc 19938 20059 47 61 2 94.3 accgaaacacatcaagaaaaggaagacctcgaaactaggattgatagaacaagagctcacc 5405 5500 42 32 3 88.5 cgcaagaacaacaccatgaatcgcaaagaaaa 109582 109773 38 96 2 84.9 ggcctcggtctcggtctcggtcccgatctcggtctcggtctcggtctcggtcccggtctcggtctcgactt cggactccatctcggactccatctc 113787 114065 34 93 3 72.8 ...
Rabbit anti IRF8 antibody recognizes Interferon regulatory factor 8, (IRF8) also known as Interferon consensus sequence-binding protein (I
Winterling KW, Chafin D, Hayes JJ, Sun J, Levine AS, Yasbin RE, Woodgate R (1998) The Bacillus subtilis DinR binding site: redefinition of the consensus sequence. J Bacteriol 180:2201-11.[PMID:9555905 ...
Probab=100.00 E-value=0 Score=636.12 Aligned_cols=238 Identities=42% Similarity=0.741 Sum_probs=223.6 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCH Q ss_conf 99999999831231023222212468888751248999999999999999999999748999999999995302022433 Q gi,254780372,r 4 YCFFALFLVTPELVFAKSSLHDVMNIPADLSISTWIVRTFGIFTILSIAPILLIMVTCFPRFIIVFSILRTGMGMGSVPP 83 (246) Q Consensus 4 ~~~~~~~~~~~~~a~aq~~~~~~~~~~~~~~~~~~~iqll~llt~LsL~P~ilim~TsFtrIvIVLsilRnALG~QQ~PP 83 (246) T Consensus 140 ~~~~~~~~~~~p~~~~~~p~~~~~~~~~g~q~~S~~iQ~Li~lT~LsllPaiLiM~TSFtRIvIVLslLRnALG~QQ~PP 219 (379) T PRK12430 140 IIPLCFLLLFCPSAYADIPGVTSHILSDGSQTWSIPVQTLVFLTSLTFLPAFLLMMTSFTRIVIVFGLLRNALGTPYAPP 219 (379) T ss_pred HHHHHHHHHHCHHHHHCCCCCCCCCCCCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCH T ss_conf 79799999967497853885215305899801230899999999999999999998520899999999987307688986 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCC Q ss_conf ...
This strategy guide introduces Consensus Decision Making, a method for facilitating and engaging students in a critical discussion of the central ideas of a text.
An organization headed by a senior IPCC official (Working Group 3 Vice-Chair, Carlo Carraro) has ranked TERI, an organization headed by the IPCCs chairman, first in the world ...
Uffe Ravnskov, MD, PhD is a Danish independent researcher and author.Famous for questioning the scientific consensus regarding the Lipid Hypothesis.
Curis reported fourth quarter 2013 net loss per share of 5 cents, narrower than the Zacks Consensus Estimate of a loss of 7 cents.
TSNAX Full-Length MS Protein Standard (NP_005990), Labeled with [U- 13C6, 15N4]-L-Arginine and [U- 13C6, 15N2]-L-Lysine, was produced in human 293 cells (HEK293) with fully chemically defined cell culture medium to obtain incorporation efficiency at Creative-Proteomics. This gene encodes a protein which specifically interacts with translin, a DNA-binding protein that binds consensus sequences at breakpoint junctions of chromosomal translocations. The encoded protein contains bipartite nuclear targeting sequences that may provide nuclear transport for translin, which lacks any nuclear targeting motifs.
Downloadable (with restrictions)! In this paper we consider the dynamic process of race track betting. We show that there is a close connection between the dynamic race track betting process and the pari-mutuel method for constructing consensus of subjective probabilities considered in Eisenberg and Gale. This enables us to show that there exists a unique equilibrium point for the betting process. We further show that the dynamic betting process converges to this equilibrium point almost surely. Therefore the sequential race track betting gives a natural approach to inducing the consensus probabilities in Eisenberg and Gale. These consensus probabilities are different from the average of the subjective probabilities which is used in the conventional way of combining individually held opinions into a collective group statement. We compare these probabilities and this leads to a potential explanation of the favorite-longshot bias consistently observed in the studies of race track betting.
Diabetes has reached serious proportions and accounts for around 5% of the population of India. Its complications are the cause of tremendous socioeconomic problems.It is the single largest cause leading to atherosclerosis and its attendant complications such as heart attacks, strokes, paralysis, and non-healing ulcers of the foot
Diabetes has reached serious proportions and accounts for around 5% of the population of India. Its complications are the cause of tremendous socioeconomic problems.It is the single largest cause leading to atherosclerosis and its attendant complications such as heart attacks, strokes, paralysis, and non-healing ulcers of the foot
mouse Gbp3 protein: 71-kDa guanylate-binding protein; mGBP3 lacks CAAX consensus sequence for isoprenylation and methylation and thus is cytosolic, unlike other GBP3 proteins; RefSeq NM_018734
By using a consensus spot pattern in Delta2D (a), complete expression profiles (b) are generated. Profiles can be imported into DNA array analysis software (her
Is British Columbias carbon offset scheme really just a green slush fund - one in which the well-connected receive money that should have been spent on sick people ...
Synergy Pharma reported a loss of 17 cents per share in the fourth quarter, wider than the year-ago loss and the Zacks Consensus Estimate of a loss of 15 cents
This paper considers the consensus problem of nonlinear multi-agent systems under switching directed topologies. Specifically, the dynamics of each agent incorporates an intrinsic nonlinear term and the interaction topology may not contain a spanning tree at any time. By designing a state-controlled switching law, we show that the multi-agent system with the neighbor-based protocol can achieve consensus if the switching topologies jointly contain a spanning tree. Moreover, an easily manageable algebraic criterion is deduced to unravel the underlying mechanisms in reaching consensus. Finally, a numerical example is exploited to illustrate the effectiveness of the developed theoretical results.
Botswana Democratic Party (BDP) has resolved to promote a safe-mode of settling for consensus candidates in next years by-elections in 2017. BDP secretary general Botsalo Ntuane told local media on Tuesday that the decision was made because it has been realised that the party tends to do better when fielding a consensus candidate. BDP will contend in four by-elections in 2017 - three council seats and one parliamentary seat. Council by-elections will be held at Boikaelo Madiba in Palapye, Tsabong North an
Text of H.R. 979 (110th): Bipartisan Consensus Managed Care Improvement ... as of Feb 12, 2007 (Introduced version). H.R. 979 (110th): Bipartisan Consensus Managed Care Improvement Act of 2007
Guidelines, released by Prostate Cancer Foundation of Australia and Cancer Council Australia have established consensus on the use of PSA blood tests.
In business and procurement, there has been a greater focus over the last 20 years or so on consensus decision making, which is seen as a positive approach that motivates staff and helps to get buy-in from our teams and stakeholders in a business context. But is this truly the right approach?. ...
The Lok Satta Party will be organizing public meetings in all the three regions of the State shortly to educate and enlighten people on issues arising out of the Centers decision to form Telangana State and strive for a consensus on practical solutions.
non-consensus, without understanding that their policy might fail. Wie gings weiter?. Section 2.2: Concepts Applied to British Airways and Marks & Spencer. The method of authority described by Gravetter and Forzano (2008) can ...
The HIV and Aging Consensus Project The HIV and Aging Consensus Project Recommended Treatment Strategies for Clinicians Managing Older Patients with HIV Recommended Treatment Strategies for Clinicians
Avaliação Prática dos Detectores de Defeitos e sua Influência no Desempenho das Operações de Consenso (Practical Evaluation of Failure Detectors and their Influence on the Consensus Operations Performance) ...
Abf1 has been defined as a general regulatory factor involved in determining chromatin structure in the yeast Saccharomyces cerevisiae. As such, it plays a major role in a range of functions including DNA replication, transcriptional activation and gene silencing, as well as DNA repair. Previous studies have identified an Abf1 DNA consensus binding sequence and Abf1 binding at up to several hundred locations throughout the genome. Depletion of Abf1 in the cell, however, results in altered nucleosome structure at many thousands of sites throughout the yeast genome, suggesting a far greater role for Abf1 in chromatin structure and dynamics. Here, we examine genome-wide Abf1 binding using ChIP-Chip to measure its chromatin occupancy. Using a novel software package, Sandcastle, we detect 3,821 genomic positions at which Abf1 binds. We conducted a detailed bioinformatic analysis of these novel Abf1 binding sites, defining variations in the current consensus sequence and identifying many more genomic ...
Transcriptional repressor with bimodal DNA-binding specificity. Represses transcription in a methyl-CpG-dependent manner. Binds with a higher affinity to methylated CpG dinucleotides in the consensus sequence 5-CGCG-3 but can also bind to the non-methylated consensus sequence 5-CTGCNA-3 also known as the consensus kaiso binding site (KBS). Can also bind specifically to a single methyl-CpG pair and can bind hemimethylated DNA but with a lower affinity compared to methylated DNA. Plays a role in postnatal myogenesis, may be involved in the regulation of satellite cells self-renewal (By similarity).
Sorry about my previous reply. The question was for DNA sequence motifs and my answer was for protein sequence motifs. The TFD database has several DNA sequence motifs found in yeast, however it is a Transcription Factor Database and would lack some of the types of sequence motifs that the original message was requesting. TFD is available as flat files, in a variety of formats, via anonymous ftp from ncbi.nlm.nih.gov look in the repository/TFD directory. TFD is the creation of D. Ghosh, NCBI. Mike ...
... accepts one or more sequences along with a search pattern and returns the number and positions of sites that match the pattern. Use Protein Pattern Find to locate sequence regions that match a consensus sequence of interest ...
Probab=96.63 E-value=0.029 Score=34.56 Aligned_cols=76 Identities=21% Similarity=0.404 Sum_probs=49.1 Q ss_pred HHHHHHHHHHCCCCH-----HHHHHHHHHHHHHHHHHHHHHHHHHCCCCC--CCCH------------------------ Q ss_conf 379999999508867-----889999999999999999999986047899--8545------------------------ Q gi,254780338,r 2 IGIGFLFNLISGIKQ-----RHYSIMILGAITTCIIATRQVLIHILPGDL--GYSI------------------------ 50 (129) Q Consensus 2 vg~g~llNlr~G~r~-----~hyg~~il~A~~G~~~s~RQi~lHi~pg~~--GyG~------------------------ 50 (129) T Consensus 51 igl~~li~~l~~p~~~~~r~~~~~l~~l~a~~G~~~A~rhv~LQ~~p~~~~~~Cg~~l~~~~~~~p~~e~l~~~f~g~g~ 130 (172) T PRK04388 51 LALLFLIGALHGPRNAGGRKAYGVLAFIAAGVGMGIAARHVWVQIRPKDMMSSCGPPLSFLSETMGPFEVFRTVLTGTGD 130 (172) T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHCCCHHHHHHHHHCCCCC T ss_conf 99999999995732025999999999999999999999999999388534787887166776213799999998568998 Q ss_pred ------HHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf ------6752257999999999999999999960 Q gi,254780338,r 51 ...
New class PhiPsiAverager to get consensus of phi/psi angles from a TemplateList and an Alignment. Tested with a few examples and seems to work. The wrapping of angles at 180/-180 is not yet taking into account, i.e. if an interval falls in the region just below 180 and just above -180, no consensus will be found. Pdb: added some checks to methods getPhi/Psi so that it doesnt fail when theres no coordinates. Changed yet again the design of TemplateList/Template. Now loading of PDB data happens upon call of the loadPDBdata method. Changed dependencies accordingly ...
This summary encapsulates the initiatives of the developing Galveston Bay Plan, the Plan consists of fifteen action plans, eleven of which directly address estuarine problems identified by consensus. Areas of concern are ...
Simon Michael wrote: Chris Withers wrote: Is it going to move to the great new style thats been used for the Zope 3 wiki? I took some time to get used to the new skin. I like it a lot - great work Kevin (and Tom). Yes indeed :-) I have been guessing the consensus will be to use the new ...
Di dalam hati manusia ada kekusutan dan tidak akan terurai kecuali menerima kehendak Allah s.w.t. - Ibn al-Qayyim al-Jauziyyah ...
CiteSeerX - Scientific documents that cite the following paper: Cyclic amplification and selection of targets (CASTing) for the myogenin consensus binding site
The pyrrolo[2,1-c][1,4]benzodiazepines (PBDs) are sequence-selective DNA minor-groove interacting agents. The PBD dimer SJG-136 has currently been investigated in Phase II clinical trials in ovarian cancer and leukaemia in the UK and the USA. More recently, PBD dimer analogues are being attached to tumour-targeting antibodies to create Antibody-Drug Conjugates (ADCs), some which are now in Phase 3 clinical trials with many others in pre-clinical and clinical development. Transcription factors (TFs) are sequence-specific DNA-interacting proteins that bind to consensus DNA sequences, thereby controlling transcription. TFs regulate processes such as cell differentiation, proliferation and apoptosis. The interaction of a small-molecule with the consensus DNA recognition sequences of TFs can prevent a TF from interacting with its cognate sequence, thereby inhibiting the expression of genes critical for the survival and proliferation of cancer cells. There is growing evidence that PBDs may exert, at ...
Sequences matching input query are shown below. Original reference, patient identifier, isolate name, partial treatment histories and accession number are indicated. Complete treatment histories, when available, can be accessed by clicking the isolate name. Sequences may additionally be downloaded in the fasta format, or viewed as individual or composite alignments using the options above. If the user wishes to view individual alignments of isolates for which there are multiple clones, the user can choose to view either an alignment of consensus sequences derived from the clones or an alignment of each clone as well as a consensus sequence ...
Sequences matching input query are shown below. Original reference, patient identifier, isolate name, partial treatment histories and accession number are indicated. Complete treatment histories, when available, can be accessed by clicking the isolate name. Sequences may additionally be downloaded in the fasta format, or viewed as individual or composite alignments using the options above. If the user wishes to view individual alignments of isolates for which there are multiple clones, the user can choose to view either an alignment of consensus sequences derived from the clones or an alignment of each clone as well as a consensus sequence ...
Pileup method for calling consensus bases. Majority : Deciding the base by the majority of the number of basecall. Example 1 , Total depth at a site = 30 ("A":28, "G":2) → Consensus base : "A". Example 2 , Total depth at a site = 30 ("A":15, "G":15) → Consensus base : "N". BestScore : Deciding the base with the highest basecall quality at each site Example 1 , Total depth at a site = 10 ("A":8, "G":2), Best phred score at each bases : "A"(Q=35), "G"(Q=40) → Consensus base : "G" Example 2 , Total depth at a site = 10 ("A":8, "G":2), Best phred score at each bases : "A"(Q=40), "G"(Q=40) → Consensus base : "N" Majority + BestScore : Incorporating the best quality method with the majority decision method at each site. Example 1 , Total depth at a site = 10 ("A":5, "G":5), Best phred score at each bases : "A"(Q=35), "G"(Q=40) → Consensus base : "G" Example 2 , Total depth at a site = 10 ("A":5, "G":4), Best phred score at each bases : "A"(Q=40), "G"(Q=40) → Consensus base : "A" ...
I am trying to clone a 1.1 kb gene into pEGFP N1 vector (in MCS). The same promoter works for both the MCS and EGFP protein enabling a fusion protein unless a stop codon intervenes. MCS is a few Bases upstream of EGFP. My gene of interest does not have Eco RI and Bam H1 site, which needs to be incorporated. I am also incorporating a Kozak consensus sequence in my forward primer for amplification of gene of interest ...
The problem is that she works in an metatherian mammal species that hasnt got much published sequence. The gene she works on is NBC and she has fully cloned it but the full clone was made using a primer derived from a consensus sequence, so may not be the actual sequence from this species. The lab now wants to express this gene in a cell culture system and if the sequence is wrong, may get erroneous results, so they need to check the first 20 bases or so at the 5 end of the gene. Rather than perform another RACE and go through the cloning again if they dont need to, why not sequence directly from the cDNA using a single primer pointing in the 5 direction ...
Hi,. I am trying to call SNPs with at least 1X depth (My estimation is that most of the SNPs I want to see have indeed 1X / 2X depth). I have mapped consensus sequences to the Tomato reference genome (generating in theory 1X/2X depth on specific target positions) with Bowtie2 and perform SNP/INDEL calling with samtools mpileup and bcftools. However, I cant retrieve SNPs with 1X depth although I do mention it on the command line. Can anyone help me?. Commands:. ...
The general consensus is that we should all reduce Salt in our Diet. Certainly that is the advice of my Doctor. (Apart from some that believe Sugar
CONSORF is a fully automatic high-accuracy identification system that provides consensus prokaryotic CDS information. It first predicts the CDSs supported by consensus alignments. The alignments are derived from multiple genome-to-proteome comparisons with other prokaryotes using the FASTX program. Then, it fills the empty genomic regions with the CDSs supported by consensus ab initio predictions. From those consensus results, CONSORF provides prediction reliability scores, predicted frame-shifts, alternative start sites and best pair-wise match information against other prokaryotes. These results are easily accessed from a website.
From the excellent book Wisdom of Crowds by James Suroweicki: Collective decision making is often confused with a quest for consensus. But they are different. Heres how they contrast: Consensus Collective Decision Making Encourages lowest-common-denominator solutions which offend no one. Encourages the free exchange of conflicting views, which excites everyone. Tends to stick with the…
House Speaker Michael Busch said a meeting with Gov. Martin OMalley and the Senate president resulted in no conclusion on a consensus on whether to call lawmakers back to Annapolis to expand gambling in Maryland.
DI-fusion, le Dépôt institutionnel numérique de lULB, est loutil de référencementde la production scientifique de lULB.Linterface de recherche DI-fusion permet de consulter les publications des chercheurs de lULB et les thèses qui y ont été défendues.
Calculation of consensus values for atomic weights, isotope amount ratios, and isotopic abundances with the associated uncertainties using multivariate meta-regression approach for consensus building.. ...
Its been in the works for over three years now. Thats right, the first we heard of Bulldozer as a processor architecture under development was shortly...
Simple question really. Im by no means a veteran of competitive battling, so sorry if a consensus has been reached by now. What ability do you prefer on Jellicent, or which one is more widely used?
Simple question really. Im by no means a veteran of competitive battling, so sorry if a consensus has been reached by now. What ability do you prefer on Jellicent, or which one is more widely used?
OpenWetWare:Reviews is an experiment in providing always up-to-date scientific reviews. When a new publication comes out it can be easily incorporated into the review by OWW editors. This should be a win-win for both the review-writer (less work) and the readers (who get a more up-to-date resource). Well be trying reviews with a curator (as discussed for consensus protocols) as well as ones without. ...

Protein consensus sequence motifs | SpringerLinkProtein consensus sequence motifs | SpringerLink

The large number of protein consensus sequences that may be recognized without computer analysis are reviewed. These include ... and consensus sequences that may be carried out on the internet.. Index Entries. Protein consensus sequences motifs protein- ... The large number of protein consensus sequences that may be recognized without computer analysis are reviewed. These include ... Aitken, A. (1995) Protein chemistry methods, posttranslational modification, consensus sequences, in Proteins Labfax (Price, N ...
more infohttps://link.springer.com/article/10.1385%2FMB%3A12%3A3%3A241

Consensus sequence - Biology-Online DictionaryConsensus sequence - Biology-Online Dictionary

Consensus sequence Of a series of related dna, rna or protein sequences, the sequence that reflects the most common choice of ... The generation of consensus sequences has been subjected to intensive mathematical analysis. ... Retrieved from "https://www.biology-online.org/dictionary/index.php?title=Consensus_sequence&oldid=10105" ...
more infohttps://www.biology-online.org/dictionary/Consensus_sequence

GTP-binding domain: three consensus sequence elements with distinct spacing | PNASGTP-binding domain: three consensus sequence elements with distinct spacing | PNAS

... including a consensus sequence composed of three consensus elements GXXXXGK, DXXG, and NKXD with consensus spacings of either ... GTP-binding domain: three consensus sequence elements with distinct spacing. T E Dever, M J Glynias, and W C Merrick ... GTP-binding domain: three consensus sequence elements with distinct spacing Message Subject (Your Name) has sent you a message ... the sequence NKXW in place of NKXD in the sequence element responsible for base specificity allows the use of ITP as well as ...
more infohttps://www.pnas.org/content/84/7/1814?ijkey=c96fc20effa24544b9455f04c5a156aa404ba11d&keytype2=tf_ipsecsha

CiteSeerX - Sequence Logos: A New Way to Display Consensus SequencesCiteSeerX - Sequence Logos: A New Way to Display Consensus Sequences

Sequence logos concentrate the following information into a single graphic [2]: 1. The general consensus of the sequences. ... 4. The amount of information present at every position in the sequence, measured in bits. 5. An initiation point, cut point, or ... we use logos to display aligned sets of sequences. ... RNA or protein sequences can be represented using this ... sequence logo display consensus sequence new way aligned set general consensus development center separate element following ...
more infohttp://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.5863&rank=2

Consensus sequences - Biology-Online DictionaryConsensus sequences - Biology-Online Dictionary

Consensus sequence Of a series of related dna, rna or protein sequences, the sequence that reflects the most common choice of ... The generation of consensus sequences has been subjected to intensive mathematical analysis. ... Retrieved from "https://www.biology-online.org/dictionary/index.php?title=Consensus_sequences&oldid=75543" ...
more infohttps://www.biology-online.org/dictionary/Consensus_sequences

Consensus sequence - WikipediaConsensus sequence - Wikipedia

... can also be considered as consensus sequences. Thus a consensus sequence is a model for a putative DNA binding site: it is ... The conserved sequence motifs are called consensus sequences and they show which residues are conserved and which residues are ... Any mutation allowing a mutated nucleotide in the core promoter sequence to look more like the consensus sequence is known as ... A protein binding site, represented by a consensus sequence, may be a short sequence of nucleotides which is found several ...
more infohttps://en.wikipedia.org/wiki/Consensus_sequence

Kozak consensus sequence - WikipediaKozak consensus sequence - Wikipedia

The Kozak consensus sequence, Kozak consensus or Kozak sequence is a sequence which occurs on eukaryotic mRNA and has the ... The Kozak consensus sequence plays a major role in the initiation of the translation process. The sequence was named after the ... consensus, the nucleotides at positions +4 (i.e. G in the consensus) and -3 (i.e. either A or G in the consensus) relative to ... Lmx1b is an example of a gene with a weak Kozak consensus sequence. For initiation of translation from such a site, other ...
more infohttps://en.wikipedia.org/wiki/Kozak_consensus_sequence

Consensus sequence | Article about consensus sequence by The Free DictionaryConsensus sequence | Article about consensus sequence by The Free Dictionary

An average nucleotide sequence; each nucleotide is the most frequent at its position in the sequence Explanation of consensus ... Looking for consensus sequence? Find out information about consensus sequence. ... consensus sequence. Also found in: Dictionary, Thesaurus, Medical, Legal, Wikipedia. consensus sequence. [kən′sen·səs ‚sē·kwəns ... Then comparisons were made between the consensus sequence and the entries in the MicroSeq database.. DNA sequencing by Microseq ...
more infohttp://encyclopedia2.thefreedictionary.com/consensus+sequence

Anti Protein Kinase Consensus Sequence | Oxford Biomedical ResearchAnti Protein Kinase Consensus Sequence | Oxford Biomedical Research

This polyclonal antibody is excellent for Western blot detection of protein kinases containing this sequence.. References:. 1. ...
more infohttps://www.oxfordbiomed.com/anti-protein-kinase-consensus-sequence

Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments. | ROSTLAB.ORGConsensus sequences improve PSI-BLAST through mimicking profile-profile alignments. | ROSTLAB.ORG

Amino Acid Sequence, Amino Acid Substitution, Base Sequence, Consensus Sequence, Sequence Alignment, Sequence Analysis, Protein ... Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments. Title. Consensus sequences improve PSI- ... sequence relatedness through profile-profile comparisons are much slower and more complex than sequence-sequence and sequence- ... can be represented by consensus sequences that list the nucleic/amino acid most frequent at each sequence position in that ...
more infohttps://www.rostlab.org/node/778

FOXM1 binds directly to non-consensus sequences in the human genome | Genome Biology | Full TextFOXM1 binds directly to non-consensus sequences in the human genome | Genome Biology | Full Text

... assay identified point mutations in the DNA binding domain of FOXM1 that inhibit binding to a FKH consensus sequence. Cell ... FOXM1 is specifically recruited to chromatin through co-factor interactions by binding directly to non-canonical DNA sequences. ... As expected the FOXM1B DBD associates with a positive control FKH consensus sequence in a dose dependent manner (K d of 224 ± ... The first (1) shows FOXM1 binding to FKH consensus sequences in concert with recruitment of the MuvB complex present at cell ...
more infohttps://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0696-z

How to get the consensus sequence from a BAM alignmentHow to get the consensus sequence from a BAM alignment

Ngs Question ~ Consensus Could anybody point towards the direction in how to generate a "consensus" fasta sequence file in... ... Extract consensus dna sequence of multiple genes from multiple bam files in fasta format Hi, I have multiple bam files (aligned ... In the most general case the SNPs may not resolve into a single consensus sequence because that is not how the SNP callers work ... What the original poster needs is creating a consensus sequence out of BAM alignments. It is easy to misread that into the ...
more infohttps://www.biostars.org/p/186536/

Effects of lysine-to-glycine mutations in the ATP-binding consensus sequences in the AddA and AddB subunits on the Bacillus...Effects of lysine-to-glycine mutations in the ATP-binding consensus sequences in the AddA and AddB subunits on the Bacillus...

Effects of lysine-to-glycine mutations in the ATP-binding consensus sequences in the AddA and AddB subunits on the Bacillus ... Effects of lysine-to-glycine mutations in the ATP-binding consensus sequences in the AddA and AddB subunits on the Bacillus ... Effects of lysine-to-glycine mutations in the ATP-binding consensus sequences in the AddA and AddB subunits on the Bacillus ... Effects of lysine-to-glycine mutations in the ATP-binding consensus sequences in the AddA and AddB subunits on the Bacillus ...
more infohttps://jb.asm.org/content/178/17/5130

A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target | Science...A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target | Science...

1 Graphical representations of G-rich sequences consensus in the HCV genome.. (A and B) A total of 1056 partial cds of the C ... Sequences of oligomers used in our studies.. * Table S5. Calculated Tm of synthetic HCV G-rich sequences in the presence of ... Sequence of the C gene for HCV JFH1 virus.. * Fig. S31. Premade sequence alignment in the central part of the HCV C gene ( ... Sequence of the C gene for HCV JFH1 virus.. Fig. S31. Premade sequence alignment in the central part of the HCV C gene (subtype ...
more infohttps://advances.sciencemag.org/content/2/4/e1501535/tab-figures-data

A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target | Science...A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target | Science...

A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target ... A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target ... A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target ... A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target ...
more infohttp://advances.sciencemag.org/content/2/4/e1501535

Whole-genome consensus sequence analysis of a South African rotavirus SA11 sample reveals a mixed infection with two close...Whole-genome consensus sequence analysis of a South African rotavirus SA11 sample reveals a mixed infection with two close...

"Whole-genome consensus sequence analysis of a South African rotavirus SA11 sample reveals a mixed infection with two close ... Determination of the whole-genome consensus sequence of the prototype DS-1 rotavirus using sequence-independent genome ... Whole-genome consensus sequence analysis of a South African rotavirus SA11 sample reveals a mixed... Mlera, Luwanika; ONeill, ... Whole-genome consensus sequence analysis of a South African rotavirus SA11 sample reveals a mixed infection with two close ...
more infohttps://www.deepdyve.com/lp/springer_journal/whole-genome-consensus-sequence-analysis-of-a-south-african-rotavirus-l2Ykhqwm3c

Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in...Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in...

In S. cerevisiae, Autonomously Replicating Sequences (ARSs) contain a consensus sequence (ACS) that binds the Origin ... To identify essential origin sequences genome-wide, we utilized a tiled oligonucleotide array (NimbleGen) to map the ORC and ... These binding sites define a set of potential Autonomously Replicating Sequences (ARSs), which we term nimARSs. The nimARS set ... exact features of chromatin that impinge on replication origin function is to define the precise locations of the DNA sequences ...
more infohttps://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-7-276

Microsatellite detection and consensus sequence verification by virtual PCR and machine learningMicrosatellite detection and consensus sequence verification by virtual PCR and machine learning

... ... Microsatellites, or simple sequence repeats, are genetic loci where several nucleotide bases are repeated in tandem. Since they ... or a shotgun-sequencing database without the overhead required to perform PCR chemically with human intervention. Moreover, a ... a program that detects and then verifies microsatellites by modeling PCR digitally from an Expressed Sequence Tag (EST) ...
more infohttps://athenaeum.libs.uga.edu/handle/10724/21091

GenomeCons 1.0 - Manipulate Multiple Genome Sequence Alignments and their Consensus SequencesGenomeCons 1.0 - Manipulate Multiple Genome Sequence Alignments and their Consensus Sequences

... web server to manipulate multiple genome sequence alignments and their consensus sequences for high-throughput genome sequence ... Posted by admin at 4:46 pm Tagged with: Consensus Sequence, Genome, GenomeCons, Sequence Alignments 50 views. Sorry, the ... GenomeCons: a web server for manipulating multiple genome sequence alignments and their consensus sequences.. Sato T, Suyama M. ... GenomeCons 1.0 - Manipulate Multiple Genome Sequence Alignments and their Consensus Sequences. Alignment / BLAST ...
more infohttp://www.mybiosoftware.com/genomecons-1-0-manipulate-multiple-genome-sequence-alignments-and-their-consensus-sequences.html

Nuclear targeting sequences--a consensus?  - PubMed - NCBINuclear targeting sequences--a consensus? - PubMed - NCBI

Nuclear targeting sequences--a consensus?. Dingwall C1, Laskey RA.. Author information. 1. Wellcome Trust/Cancer Research ... many nuclear targeting sequences appear to be more complex. We suggest in this review that, despite this diversity, a consensus ... Nuclear targeting sequences. [Trends Biochem Sci. 1992]. *A bipartite nuclear targeting motif in protein kinase C? [Trends ... Nuclear targeting sequences are essential for the transport of proteins into the nucleus. The seven-amino-acid nuclear ...
more infohttps://www.ncbi.nlm.nih.gov/pubmed/1664152?dopt=Abstract

Secondary structure prediction and consensus sequence o | Open-iSecondary structure prediction and consensus sequence o | Open-i

Secondary structure prediction and consensus sequence of PelD and PleD. A. Secondary structure predication was made using the ... B. Consensus sequence of PelD and PleD was based on Phyre alignment of 20 and 100 homologues respectively. Residues required ... B. Consensus sequence of PelD and PleD was based on Phyre alignment of 20 and 100 homologues respectively. Residues required ... fig05: Secondary structure prediction and consensus sequence of PelD and PleD. A. Secondary structure predication was made ...
more infohttps://openi.nlm.nih.gov/detailedresult.php?img=PMC2170427_mmi0065-1474-f5&req=4

A base-specific recognition signal in the 5 consensus sequence of rotavirus plus-strand RNAs promotes replication of the...A base-specific recognition signal in the 5' consensus sequence of rotavirus plus-strand RNAs promotes replication of the...

The 5 recognition signal is associated with the G2 residue of the 5-consensus sequence, a residue that shows absolute ... Complementary sequences proximal to the 5 and 3 termini are predicted to direct cyclization of the (+)RNAs by forming ... strand initiation sequence. In contrast to the 3-end, the role of the 5-end has been less well defined. In this study, we ... panhandle structures from which short highly conserved terminal sequences protrude as single-stranded tails. Cell-free ...
more infohttps://research.pasteur.fr/en/publication/a-base-specific-recognition-signal-in-the-5-consensus-sequence-of-rotavirus-plus-strand-rnas-promotes-replication-of-the-double-stranded-rna-genome-segments/

The Consensus Coding Sequences of Human Breast and Colorectal Cancers | ScienceThe Consensus Coding Sequences of Human Breast and Colorectal Cancers | Science

The Consensus Coding Sequences of Human Breast and Colorectal Cancers. By Tobias Sjöblom, Siân Jones, Laura D. Wood, D. ... The Consensus Coding Sequences of Human Breast and Colorectal Cancers. By Tobias Sjöblom, Siân Jones, Laura D. Wood, D. ... The Consensus Coding Sequences of Human Breast and Colorectal Cancers Message Subject. (Your Name) has forwarded a page to you ... These sequences were used to design primers for PCR amplification and sequencing of exons and adjacent splice sites. Primers ...
more infohttps://science.sciencemag.org/content/314/5797/268?ijkey=a0191b98c5d58528dbaf7acceaf2f2e1c9db6da2&keytype2=tf_ipsecsha

Gentaur Molecular :GenWay \ Interferon Consensus Sequence Binding Protein 1 (IRF8 ICSBP1) Rabbit anti-Human Polyclonal (C...Gentaur Molecular :GenWay \ Interferon Consensus Sequence Binding Protein 1 (IRF8 ICSBP1) Rabbit anti-Human Polyclonal (C...

Interferon Consensus Sequence Binding Protein 1 (IRF8_ICSBP1) Rabbit anti-Human Polyclonal (C-Terminus) Antibody \ GWB-60223C ... Interferon Consensus Sequence Binding Protein 1 (IRF8_ICSBP1) Rabbit anti-Human Polyclonal (C-Terminus) Antibody Human samples ... Interferon Consensus Sequence Binding Protein 1 (IRF8_ICSBP1) Rabbit anti-Human Polyclonal (C-Terminus) Antibody antibody ... Interferon Consensus Sequence Binding Protein 1 (IRF8_ICSBP1) Rabbit anti-Human Polyclonal (C-Terminus) Antibody storing ...
more infohttp://www.antibody-antibodies.com/product4275524-search-Interferon_Consensus_Sequence_Binding_Protein_1_

FOXM1 binds directly to non-consensus sequences in the human genome - omicXFOXM1 binds directly to non-consensus sequences in the human genome - omicX

... of FOXM1 that inhibit binding to a FKH consensus sequence. Stable cell lines expressing either WT or DBD mutant green ... recruited to chromatin through co-factor interactions by binding directly to both canonical and non-canonical DNA sequences. ... FOXM1 binds directly to non-consensus sequences in the human genome. The Forkhead transcription factor, FOXM1, is a key ... of FOXM1 that inhibit binding to a FKH consensus sequence. Stable cell lines expressing either WT or DBD mutant green ...
more infohttps://omictools.com/80b0750f1573f7c3538fae0107b3c6b0-dataset
  • CSIRO Entomology 120 Meiers Road Indooroopilly, Qld 4068, Australia) for providing the consensus sequences in the genetic divergence analysis. (thefreedictionary.com)
  • We established a genetic linkage map employing 518 simple sequence repeat (SSR, or microsatellite) markers for Bombyx mori (silkworm), the economically and culturally important lepidopteran insect, as part of an international genomics program. (semanticscholar.org)
  • Finally splice sites (sequences immediately surrounding the exon-intron boundaries) can also be considered as consensus sequences. (wikipedia.org)
  • A possible explanation of the in-frame skipping of exon 2 and of the neighboring exon 3 is the complete removal of the consensus sequence of the 5' splice site of exon 2/intron 2 (13) and splicing alterations circumventing the nonsense codon in exon 3 of the cDNA so that translation terminates normally (14). (thefreedictionary.com)
  • Conclusions: Recent upgrades to the Pacific Biosciences RS instrument have improved the CCS technology and offer an alternative to traditional sequencing approaches. (duhnnae.com)
  • These types of mutations down-regulate transcription since RNA polymerase can no longer bind as tightly to the core promoter sequence. (wikipedia.org)
  • Hii people, I have paired-end sequence read of my target species which I have mapped to the refe. (biostars.org)
  • Hi, I have bisulfite converted sequencing reads and, from my bam file, would like to select reads. (biostars.org)
  • 4. The amount of information present at every position in the sequence, measured in bits. (psu.edu)