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).Codon, Initiator: A codon that directs initiation of protein translation (TRANSLATION, GENETIC) by stimulating the binding of initiator tRNA (RNA, TRANSFER, MET). In prokaryotes, the codons AUG or GUG can act as initiators while in eukaryotes, AUG is the only initiator codon.Codon, Terminator: Any codon that signals the termination of genetic translation (TRANSLATION, GENETIC). PEPTIDE TERMINATION FACTORS bind to the stop codon and trigger the hydrolysis of the aminoacyl bond connecting the completed polypeptide to the tRNA. Terminator codons do not specify amino acids.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.RNA, Transfer, Met: A transfer RNA which is specific for carrying methionine to sites on the ribosomes. During initiation of protein synthesis, tRNA(f)Met in prokaryotic cells and tRNA(i)Met in eukaryotic cells binds to the start codon (CODON, INITIATOR).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.Codon, Nonsense: An amino acid-specifying codon that has been converted to a stop codon (CODON, TERMINATOR) by mutation. Its occurance is abnormal causing premature termination of protein translation and results in production of truncated and non-functional proteins. A nonsense mutation is one that converts an amino acid-specific codon to a stop codon.Peptide Chain Initiation, Translational: A process of GENETIC TRANSLATION whereby the formation of a peptide chain is started. It includes assembly of the RIBOSOME components, the MESSENGER RNA coding for the polypeptide to be made, INITIATOR TRNA, and PEPTIDE INITIATION FACTORS; and placement of the first amino acid in the peptide chain. The details and components of this process are unique for prokaryotic protein biosynthesis and eukaryotic protein biosynthesis.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.RNA, Transfer: The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.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.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.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.Anticodon: The sequential set of three nucleotides in TRANSFER RNA that interacts with its complement in MESSENGER RNA, the CODON, during translation in the ribosome.Caspases, Initiator: A subtype of caspases that contain long pro-domain regions that regulate the activation of the enzyme. The pro-domain regions contain protein-protein interaction motifs that can interact with specific signaling adaptor proteins such as DEATH DOMAIN RECEPTORS; DED SIGNALING ADAPTOR PROTEINS; and CARD SIGNALING ADAPTOR PROTEINS. Once activated, the initiator caspases can activate other caspases such as the EFFECTOR CASPASES.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.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.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)Ribosomes: Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.Genetic Code: The meaning ascribed to the BASE SEQUENCE with respect to how it is translated into AMINO ACID SEQUENCE. The start, stop, and order of amino acids of a protein is specified by consecutive triplets of nucleotides called codons (CODON).DNA Replication: The process by which a DNA molecule is duplicated.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.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.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.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.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.RNA, Transfer, Amino Acyl: Intermediates in protein biosynthesis. The compounds are formed from amino acids, ATP and transfer RNA, a reaction catalyzed by aminoacyl tRNA synthetase. They are key compounds in the genetic translation process.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.Hydroxymethyl and Formyl Transferases: Enzymes that catalyze the transfer of hydroxymethyl or formyl groups. EC 2.1.2.Bacterial Proteins: Proteins found in any species of bacterium.Prokaryotic Initiation Factor-2: The largest of the three prokaryotic initiation factors with a molecular size of approximately 80 kD. It functions in the transcription initiation process by promoting the binding of formylmethionine-tRNA to the P-site of the 30S ribosome and by preventing the incorrect binding of elongator tRNA to the translation initiation site.Peptide Initiation Factors: Protein factors uniquely required during the initiation phase of protein synthesis in GENETIC TRANSLATION.DNA Helicases: Proteins that catalyze the unwinding of duplex DNA during replication by binding cooperatively to single-stranded regions of DNA or to short regions of duplex DNA that are undergoing transient opening. In addition DNA helicases are DNA-dependent ATPases that harness the free energy of ATP hydrolysis to translocate DNA strands.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.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).Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.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.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.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Genes, Bacterial: The functional hereditary units of BACTERIA.Prokaryotic Initiation Factor-3: A prokaryotic initiation factor that plays a role in recycling of ribosomal subunits for a new round of translational initiation. It binds to 16S RIBOSOMAL RNA and stimulates the dissociation of vacant 70S ribosomes. It may also be involved in the preferential binding of initiator tRNA to the 30S initiation complex.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.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.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.Methionine-tRNA Ligase: An enzyme that activates methionine with its specific transfer RNA. EC 6.1.1.10.Eukaryotic Initiation Factor-1: A eukaryotic initiation factor that binds to 40S ribosomal subunits. Although initially considered a "non-essential" factor for eukaryotic transcription initiation, eukaryotic initiation factor-1 is now thought to play an important role in localizing RIBOSOMES at the initiation codon of MRNA.Peptide Chain Termination, Translational: A process of GENETIC TRANSLATION whereby the terminal amino acid is added to a lengthening polypeptide. This termination process is signaled from the MESSENGER RNA, by one of three termination codons (CODON, TERMINATOR) that immediately follows the last amino acid-specifying CODON.Viral Proteins: Proteins found in any species of virus.Methionine: A sulfur-containing essential L-amino acid that is important in many body functions.Caspases: A family of intracellular CYSTEINE ENDOPEPTIDASES that play a role in regulating INFLAMMATION and APOPTOSIS. They specifically cleave peptides at a CYSTEINE amino acid that follows an ASPARTIC ACID residue. Caspases are activated by proteolytic cleavage of a precursor form to yield large and small subunits that form the enzyme. Since the cleavage site within precursors matches the specificity of caspases, sequential activation of precursors by activated caspases can occur.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.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.Caspase 2: A long pro-domain caspase that contains a caspase recruitment domain in its pro-domain region. Activation of this enzyme can occur via the interaction of its caspase recruitment domain with CARD SIGNALING ADAPTOR PROTEINS. Caspase 2 plays a role in APOPTOSIS by cleaving and activating effector pro-caspases. Several isoforms of this protein exist due to multiple alternative splicing of its MESSENGER RNA.N-Formylmethionine: Effective in the initiation of protein synthesis. The initiating methionine residue enters the ribosome as N-formylmethionyl tRNA. This process occurs in Escherichia coli and other bacteria as well as in the mitochondria of eucaryotic cells.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.RNA, Transfer, Amino Acid-Specific: A group of transfer RNAs which are specific for carrying each one of the 20 amino acids to the ribosome in preparation for protein synthesis.Oligoribonucleotides: A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.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.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.Benzoyl Peroxide: A peroxide derivative that has been used topically for BURNS and as a dermatologic agent in the treatment of ACNE and POISON IVY DERMATITIS. It is used also as a bleach in the food industry.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Peptide Chain Elongation, Translational: A process of GENETIC TRANSLATION, when an amino acid is transferred from its cognate TRANSFER RNA to the lengthening chain of PEPTIDES.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Caspase 9: A long pro-domain caspase that contains a caspase recruitment domain in its pro-domain region. Caspase 9 is activated during cell stress by mitochondria-derived proapoptotic factors and by CARD SIGNALING ADAPTOR PROTEINS such as APOPTOTIC PROTEASE-ACTIVATING FACTOR 1. It activates APOPTOSIS by cleaving and activating EFFECTOR CASPASES.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.Thromboplastin: Constituent composed of protein and phospholipid that is widely distributed in many tissues. It serves as a cofactor with factor VIIa to activate factor X in the extrinsic pathway of blood coagulation.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Genes, ras: Family of retrovirus-associated DNA sequences (ras) originally isolated from Harvey (H-ras, Ha-ras, rasH) and Kirsten (K-ras, Ki-ras, rasK) murine sarcoma viruses. Ras genes are widely conserved among animal species and sequences corresponding to both H-ras and K-ras genes have been detected in human, avian, murine, and non-vertebrate genomes. The closely related N-ras gene has been detected in human neuroblastoma and sarcoma cell lines. All genes of the family have a similar exon-intron structure and each encodes a p21 protein.Caspase 8: A long pro-domain caspase that contains a death effector domain in its pro-domain region. Caspase 8 plays a role in APOPTOSIS by cleaving and activating EFFECTOR CASPASES. Activation of this enzyme can occur via the interaction of its N-terminal death effector domain with DEATH DOMAIN RECEPTOR SIGNALING ADAPTOR PROTEINS.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.Eukaryotic Initiation Factor-2: Eukaryotic initiation factor of protein synthesis. In higher eukaryotes the factor consists of three subunits: alpha, beta, and gamma. As initiation proceeds, eIF-2 forms a ternary complex with Met-tRNAi and GTP.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Suppression, Genetic: Mutation process that restores the wild-type PHENOTYPE in an organism possessing a mutationally altered GENOTYPE. The second "suppressor" mutation may be on a different gene, on the same gene but located at a distance from the site of the primary mutation, or in extrachromosomal genes (EXTRACHROMOSOMAL INHERITANCE).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.Caspase 10: A long pro-domain caspase that contains a death effector domain in its pro-domain region. Activation of this enzyme can occur via the interaction of its N-terminal death effector domain with DEATH DOMAIN RECEPTOR SIGNALING ADAPTOR PROTEINS. Caspase 10 plays a role in APOPTOSIS by cleaving and activating EFFECTOR CASPASES. Several isoforms of this protein exist due to multiple alternative splicing of its MESSENGER RNA.Genes, Viral: The functional hereditary units of VIRUSES.Peptide Termination Factors: Proteins that are involved in the peptide chain termination reaction (PEPTIDE CHAIN TERMINATION, TRANSLATIONAL) on RIBOSOMES. They include codon-specific class-I release factors, which recognize stop signals (TERMINATOR CODON) in the MESSENGER RNA; and codon-nonspecific class-II release factors.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.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Cocarcinogenesis: The combination of two or more different factors in the production of cancer.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.Transcription Factor TFIID: The major sequence-specific DNA-binding component involved in the activation of transcription of RNA POLYMERASE II. It was originally described as a complex of TATA-BOX BINDING PROTEIN and TATA-BINDING PROTEIN ASSOCIATED FACTORS. It is now know that TATA BOX BINDING PROTEIN-LIKE PROTEINS may take the place of TATA-box binding protein in the complex.Kinetics: The rate dynamics in chemical or physical systems.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.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)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.Origin Recognition Complex: The origin recognition complex is a multi-subunit DNA-binding protein that initiates DNA REPLICATION in eukaryotes.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.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.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Amino Acyl-tRNA Synthetases: A subclass of enzymes that aminoacylate AMINO ACID-SPECIFIC TRANSFER RNA with their corresponding AMINO ACIDS.Alanine-tRNA Ligase: An enzyme that activates alanine with its specific transfer RNA. EC 6.1.1.7.Apoptosis: One of the mechanisms by which CELL DEATH occurs (compare with NECROSIS and AUTOPHAGOCYTOSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA; (DNA FRAGMENTATION); at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Replicon: Any DNA sequence capable of independent replication or a molecule that possesses a REPLICATION ORIGIN and which is therefore potentially capable of being replicated in a suitable cell. (Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)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.Reading Frames: The three possible sequences of CODONS by which GENETIC TRANSLATION may occur from one nucleotide sequence. A segment of mRNA 5'AUCCGA3' could be translated as 5'AUC.. or 5'UCC.. or 5'CCG.., depending on the location of the START CODON.Carcinogens: Substances that increase the risk of NEOPLASMS in humans or animals. Both genotoxic chemicals, which affect DNA directly, and nongenotoxic chemicals, which induce neoplasms by other mechanism, are included.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Caspase Inhibitors: Endogenous and exogenous compounds and that either inhibit CASPASES or prevent their activation.Papilloma: A circumscribed benign epithelial tumor projecting from the surrounding surface; more precisely, a benign epithelial neoplasm consisting of villous or arborescent outgrowths of fibrovascular stroma covered by neoplastic cells. (Stedman, 25th ed)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.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Transcription Initiation Site: The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.Polymorphism, Genetic: The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.DNA, 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.Reticulocytes: Immature ERYTHROCYTES. In humans, these are ERYTHROID CELLS that have just undergone extrusion of their CELL NUCLEUS. They still contain some organelles that gradually decrease in number as the cells mature. RIBOSOMES are last to disappear. Certain staining techniques cause components of the ribosomes to precipitate into characteristic "reticulum" (not the same as the ENDOPLASMIC RETICULUM), hence the name reticulocytes.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.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)ToluidinesPhenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.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.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.RNA, Fungal: Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.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.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.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.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.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.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.CRADD Signaling Adaptor Protein: A death domain receptor signaling adaptor protein that plays a role in signaling the activation of INITIATOR CASPASES such as CASPASE 2. It contains a death domain that is specific for RIP SERINE-THEONINE KINASES and a caspase-binding domain that binds to and activates CASPASES such as CASPASE 2.Edeine: Basic peptide antibiotic from Bacillus brevis. It exhibits broad-spectrum antibacterial activity and inhibits bacterial DNA synthesis.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.Cell-Free System: A fractionated cell extract that maintains a biological function. A subcellular fraction isolated by ultracentrifugation or other separation techniques must first be isolated so that a process can be studied free from all of the complex side reactions that occur in a cell. The cell-free system is therefore widely used in cell biology. (From Alberts et al., Molecular Biology of the Cell, 2d ed, p166)Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Apoptosomes: Multimeric protein complexes formed in the CYTOSOL that play a role in the activation of APOPTOSIS. They can occur when MITOCHONDRIA become damaged due to cell stress and release CYTOCHROME C. Cytosolic cytochrome C associates with APOPTOTIC PROTEASE-ACTIVATING FACTOR 1 to form the apoptosomal protein complex. The apoptosome signals apoptosis by binding to and activating specific INITIATOR CASPASES such as CASPASE 9.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.Ribonuclease T1: An enzyme catalyzing the endonucleolytic cleavage of RNA at the 3'-position of a guanylate residue. EC 3.1.27.3.Eukaryotic Initiation Factor-3: A multisubunit eukaryotic initiation factor that contains at least 8 distinct polypeptides. It plays a role in recycling of ribosomal subunits to the site of transcription initiation by promoting the dissociation of non-translating ribosomal subunits. It also is involved in promoting the binding of a ternary complex of EUKARYOTIC INITIATION FACTOR-2; GTP; and INITIATOR TRNA to the 40S ribosomal subunit.Eukaryotic Cells: Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.Polymerization: Chemical reaction in which monomeric components are combined to form POLYMERS (e.g., POLYMETHYLMETHACRYLATE).Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Amino Acids: Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.Guanosine Triphosphate: Guanosine 5'-(tetrahydrogen triphosphate). A guanine nucleotide containing three phosphate groups esterified to the sugar moiety.Amino 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.Chromosomes, Bacterial: Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Photoinitiators, Dental: Chemical compound used to initiate polymerization of dental resins by the use of DENTAL CURING LIGHTS. It absorbs UV light and undergoes decomposition into free radicals that initiate polymerization process of the resins in the mix. Each photoinitiator has optimum emission spectrum and intensity for proper curing of dental materials.Methylmethacrylate: The methyl ester of methacrylic acid. It polymerizes easily to form POLYMETHYL METHACRYLATE. It is used as a bone cement.Methylmethacrylates: The methyl esters of methacrylic acid that polymerize easily and are used as tissue cements, dental materials, and absorbent for biological substances.Ribosomal Proteins: Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.Bovine papillomavirus 1: A species of DELTAPAPILLOMAVIRUS infecting cattle.AmidinesGenes, Fungal: The functional hereditary units of FUNGI.tRNA Methyltransferases: Enzymes that catalyze the S-adenosyl-L-methionine-dependent methylation of ribonucleotide bases within a transfer RNA molecule. EC 2.1.1.9,10-Dimethyl-1,2-benzanthracene: 7,12-Dimethylbenzanthracene. Polycyclic aromatic hydrocarbon found in tobacco smoke that is a potent carcinogen.Nucleotides: The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)Mitochondria: Semiautonomous, self-reproducing organelles that occur in the cytoplasm of all cells of most, but not all, eukaryotes. Each mitochondrion is surrounded by a double limiting membrane. The inner membrane is highly invaginated, and its projections are called cristae. Mitochondria are the sites of the reactions of oxidative phosphorylation, which result in the formation of ATP. They contain distinctive RIBOSOMES, transfer RNAs (RNA, TRANSFER); AMINO ACYL T RNA SYNTHETASES; and elongation and termination factors. Mitochondria depend upon genes within the nucleus of the cells in which they reside for many essential messenger RNAs (RNA, MESSENGER). Mitochondria are believed to have arisen from aerobic bacteria that established a symbiotic relationship with primitive protoeukaryotes. (King & Stansfield, A Dictionary of Genetics, 4th ed)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.Transfer RNA Aminoacylation: The conversion of uncharged TRANSFER RNA to AMINO ACYL TRNA.Polymorphism, Single-Stranded Conformational: Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.Frameshifting, Ribosomal: A directed change in translational READING FRAMES that allows the production of a single protein from two or more OVERLAPPING GENES. The process is programmed by the nucleotide sequence of the MRNA and is sometimes also affected by the secondary or tertiary mRNA structure. It has been described mainly in VIRUSES (especially RETROVIRUSES); RETROTRANSPOSONS; and bacterial insertion elements but also in some cellular genes.Polymethyl Methacrylate: Polymerized methyl methacrylate monomers which are used as sheets, moulding, extrusion powders, surface coating resins, emulsion polymers, fibers, inks, and films (From International Labor Organization, 1983). This material is also used in tooth implants, bone cements, and hard corneal contact lenses.Virus Replication: The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.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.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.RNA, Transfer, Gln: A transfer RNA which is specific for carrying glutamine to sites on the ribosomes in preparation for protein synthesis.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.Pedigree: The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.Potassium Permanganate: Permanganic acid (HMnO4), potassium salt. A highly oxidative, water-soluble compound with purple crystals, and a sweet taste. (From McGraw-Hill Dictionary of Scientific and Technical Information, 4th ed)DNA, Recombinant: Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.Ribonucleases: Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.Methacrylates: Acrylic acids or acrylates which are substituted in the C-2 position with a methyl group.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.Genes, p53: Tumor suppressor genes located on the short arm of human chromosome 17 and coding for the phosphoprotein p53.Nanovirus: A genus in the family NANOVIRIDAE containing multiple circular single-stranded DNA molecules. The type species is Subterranean clover stunt virus.DNA, Single-Stranded: A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.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.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 Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.Enzyme Activation: Conversion of an inactive form of an enzyme to one possessing metabolic activity. It includes 1, activation by ions (activators); 2, activation by cofactors (coenzymes); and 3, conversion of an enzyme precursor (proenzyme or zymogen) to an active enzyme.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)Genetic Variation: Genotypic differences observed among individuals in a population.RNA, Transfer, Ser: A transfer RNA which is specific for carrying serine to sites on the ribosomes in preparation for protein synthesis.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.Prokaryotic Cells: Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.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.RNA, Transfer, Arg: A transfer RNA which is specific for carrying arginine to sites on the ribosomes in preparation for protein synthesis.Skin Neoplasms: Tumors or cancer of the SKIN.Genes, Suppressor: Genes that have a suppressor allele or suppressor mutation (SUPPRESSION, GENETIC) which cancels the effect of a previous mutation, enabling the wild-type phenotype to be maintained or partially restored. For example, amber suppressors cancel the effect of an AMBER NONSENSE MUTATION.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Phosphines: Inorganic or organic compounds derived from phosphine (PH3) by the replacement of H atoms. (From Grant & Hackh's Chemical Dictionary, 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).Caspase 6: A short pro-domain caspase that plays an effector role in APOPTOSIS. It is activated by INITIATOR CASPASES such as CASPASE 7; CASPASE 8; and CASPASE 10. Isoforms of this protein exist due to multiple alternative splicing of its MESSENGER RNA.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.Peptide Elongation Factor Tu: A protein found in bacteria and eukaryotic mitochondria which delivers aminoacyl-tRNA's to the A site of the ribosome. The aminoacyl-tRNA is first bound to a complex of elongation factor Tu containing a molecule of bound GTP. The resulting complex is then bound to the 70S initiation complex. Simultaneously the GTP is hydrolyzed and a Tu-GDP complex is released from the 70S ribosome. The Tu-GTP complex is regenerated from the Tu-GDP complex by the Ts elongation factor and GTP.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.Methionyl Aminopeptidases: Aminopeptidases that remove METHIONINE from the amino-terminus of a peptide chain, such as the initiator METHIONINE found on nascent peptide chains.Rabbits: The species Oryctolagus cuniculus, in the family Leporidae, order LAGOMORPHA. Rabbits are born in burrows, furless, and with eyes and ears closed. In contrast with HARES, rabbits have 22 chromosome pairs.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.

Machine learning approaches for the prediction of signal peptides and other protein sorting signals. (1/852)

Prediction of protein sorting signals from the sequence of amino acids has great importance in the field of proteomics today. Recently, the growth of protein databases, combined with machine learning approaches, such as neural networks and hidden Markov models, have made it possible to achieve a level of reliability where practical use in, for example automatic database annotation is feasible. In this review, we concentrate on the present status and future perspectives of SignalP, our neural network-based method for prediction of the most well-known sorting signal: the secretory signal peptide. We discuss the problems associated with the use of SignalP on genomic sequences, showing that signal peptide prediction will improve further if integrated with predictions of start codons and transmembrane helices. As a step towards this goal, a hidden Markov model version of SignalP has been developed, making it possible to discriminate between cleaved signal peptides and uncleaved signal anchors. Furthermore, we show how SignalP can be used to characterize putative signal peptides from an archaeon, Methanococcus jannaschii. Finally, we briefly review a few methods for predicting other protein sorting signals and discuss the future of protein sorting prediction in general.  (+info)

Exon shuffling by L1 retrotransposition. (2/852)

Long interspersed nuclear elements (LINE-1s or L1s) are the most abundant retrotransposons in the human genome, and they serve as major sources of reverse transcriptase activity. Engineered L1s retrotranspose at high frequency in cultured human cells. Here it is shown that L1s insert into transcribed genes and retrotranspose sequences derived from their 3' flanks to new genomic locations. Thus, retrotransposition-competent L1s provide a vehicle to mobilize non-L1 sequences, such as exons or promoters, into existing genes and may represent a general mechanism for the evolution of new genes.  (+info)

The chloroplast infA gene with a functional UUG initiation codon. (3/852)

All chloroplast genes reported so far possess ATG start codons and sometimes GTGs as an exception. Sequence alignments suggested that the chloroplast infA gene encoding initiation factor 1 in the green alga Chlorella vulgaris has TTG as a putative initiation codon. This gene was shown to be transcribed by RT-PCR analysis. The infA mRNA was translated accurately from the UUG codon in a tobacco chloroplast in vitro translation system. Mutation of the UUG codon to AUG increased translation efficiency approximately 300-fold. These results indicate that the UUG is functional for accurate translation initiation of Chlorella infA mRNA but it is an inefficient initiation codon.  (+info)

Involvement of the aphthovirus RNA region located between the two functional AUGs in start codon selection. (4/852)

Initiation of translation in picornavirus RNAs occurs internally, mediated by an element termed internal ribosome entry site (IRES). In the aphthovirus RNA, the IRES element directs translation initiation at two in-frame AUGs separated by 84 nucleotides. We have found that bicistronic constructs that contained the IRES element followed by the fragment including the aphthovirus start codons in front of the second gene mimicked the translation initiation pattern of viral RNA observed in infected cells. In those constructs, the frequency of initiation at the first AUG was increased by a sequence context that resembled the favorable consensus for cap-dependent translation, although initiation at the second site was always preferred. In addition, we have found that initiation at the second start codon was not diminished under conditions in which the first initiation codon was blocked by antisense oligonucleotide interference. Interestingly, mutations that positioned the second AUG out-of-frame with the first AUG did not interfere with the frequency of initiation at the second one. On the contrary, IRES-dependent translation initiation in bicistronic constructs lacking the sequences present between functional AUGs in the viral RNA was sensitive to the presence of out-of-frame initiator codons and hairpins in the spacer region. This remarkable difference in start codon recognition was due to the nucleotide composition of the RNA that separated the IRES from the initiator codon. Thus our results indicate that the region located in the aphthovirus RNA between functional AUGs is involved in start codon recognition, strongly favoring selection of the second start AUG as the main initiator codon.  (+info)

Analysis of elements involved in pseudoknot-dependent expression and regulation of the repA gene of an IncL/M plasmid. (5/852)

Replication of the IncL/M plasmid pMU604 is controlled by a small antisense RNA molecule (RNAI), which, by inhibiting the formation of an RNA pseudoknot, regulates translation of the replication initiator protein, RepA. Efficient translation of the repA mRNA was shown to require the translation and correct termination of the leader peptide, RepB, and the formation of the pseudoknot. Although the pseudoknot was essential for the expression of repA, its presence was shown to interfere with the translation of repB. The requirement for pseudoknot formation could in large part be obviated by improving the ribosome binding region of repA, either by replacing the GUG start codon by AUG or by increasing the spacing between the start codon and the Shine-Dalgarno sequence (SD). The spacing between the distal pseudoknot sequence and the repA SD was shown to be suboptimal for maximal expression of repA.  (+info)

Multiple murine double minute gene 2 (MDM2) proteins are induced by ultraviolet light. (6/852)

The mdm2 (murine double minute 2) oncogene encodes several proteins, the largest of which (p90) binds to and inactivates the p53 tumor suppressor protein. Multiple MDM2 proteins have been detected in tumors and in cell lines expressing high levels of mdm2 mRNAs. Here we show that one of these proteins (p76) is expressed, along with p90, in wild-type and p53-null mouse embryo fibroblasts, indicating that it may have an important physiological role in normal cells. Expression of this protein is induced, as is that of p90, by UV light in a p53-dependent manner. The p76 protein is synthesized via translational initiation at AUG codon 50 and thus lacks the N terminus of p90 and does not bind p53. In cells, p90 and p76 can be synthesized from mdm2 mRNAs transcribed from both the P1 (constitutive) and P2 (p53-responsive) promoters. Site-directed mutagenesis reveals that these RNAs give rise to p76 via internal initiation of translation. In addition, mdm2 mRNAs lacking exon 3 give rise to p76 exclusively, and such mRNAs are induced by p53 in response to UV light. These data indicate that p76 may be an important product of the mdm2 gene and a downstream effector of p53.  (+info)

Postsynaptic alpha-neurotoxin gene of the spitting cobra, Naja naja sputatrix: structure, organization, and phylogenetic analysis. (7/852)

The venom of the spitting cobra, Naja naja sputatrix contains highly potent alpha-neurotoxins (NTXs) in addition to phospholipase A2 (PLA2) and cardiotoxin (CTX). In this study, we report the complete characterization of three genes that are responsible for the synthesis of three isoforms of alpha-NTX in the venom of a single spitting cobra. DNA amplification by long-distance polymerase chain reaction (LD-PCR) and genome walking have provided information on the gene structure including their promoter and 5' and 3' UTRs. Each NTX isoform is approximately 4 kb in size and contains three exons and two introns. The sequence homology among these isoforms was found to be 99%. Two possible transcription sites were identified by primer extension analysis and they corresponded to the adenine (A) nucleotide at positions +1 and -45. The promoter also contains two TATA boxes and a CCAAT box. Putative binding sites for transcriptional factors AP-2 and GATA are also present. The high percentage of similarity observed among the NTX gene isoforms of N. n. sputatrix as well as with the alpha-NTX and kappa-NTX genes from other land snakes suggests that the NTX gene has probably evolved from a common ancestral gene.  (+info)

The cis acting sequences responsible for the differential decay of the unstable MFA2 and stable PGK1 transcripts in yeast include the context of the translational start codon. (8/852)

A general pathway of mRNA turnover has been described for yeast in which the 3' poly(A) tail is first deadenylated to an oligo(A) length, leading to decapping and subsequent 5'-3' exonucleolytic decay. The unstable MFA2 mRNA and the stable PGK1 mRNAs both decay through this pathway, albeit at different rates of deadenylation and decapping. To determine the regions of the mRNAs that are responsible for these differences, we examined the decay of chimeric mRNAs derived from the 5' untranslated, coding, and 3' untranslated regions of these two mRNAs. These experiments have led to the identification of the features of these mRNAs that lead to their different stabilities. The MFA2 mRNA is unstable solely because its 3' UTR promotes the rates of deadenylation and decapping; all other features of this mRNA are neutral with respect to mRNA decay rates. The PGK1 mRNA is stable because the sequence context of the PGK1 translation start codon and the coding region function together to stabilize the transcript, whereas the PGK13' UTR is neutral with respect to decay. Importantly, changes in the PGK1 start codon context that destabilized the transcript also reduced its translational efficiency. This observation suggests that the nature of the translation initiation complex modulates the rates of mRNA decapping and decay.  (+info)

*Marilyn Kozak

Kozak, M (31 January 1986). "Point mutations define a sequence flanking the AUG initiator codon that modulates translation by ... Kozak, Marilyn (4 October 1993). "Identifying AUG Initiator Codons" (PDF). Citation Classic Commentaries. 36 (40). Retrieved 4 ...

*Kozak consensus sequence

Kozak M (1984). "Point mutations close to the AUG initiator codon affect the efficiency of translation of rat preproinsulin in ... Kozak M (1986). "Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ... "Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes". Proc. Natl. Acad. Sci. U.S ... Rarely, GUG is used as an initiation codon, but methionine is still the first amino acid as it is the met-tRNA in the ...

*Inferring horizontal gene transfer

Wuitschick, J. D.; Karrer, K. M. (1999). "Analysis of genomic G + C content, codon usage, initiator codon context and ... Codon usage bias, a measure related to codon frequencies, was one of the first detection methods used in methodical assessments ... This approach requires a host genome which contains a bias towards certain synonymous codons (different codons which code for ... for example the third nucleotide in a codon and the first nucleotide in the following codon represent the dinucleotide least ...

*GC-content

Wuitschick JD, Karrer KM (1999). "Analysis of genomic G + C content, codon usage, initiator codon context and translation ... This has been pointed to the fact that the stop codon has a bias towards A and T nucleotides, and, thus, the shorter the ... Codon usage bias Definition of GC - content on CancerWeb of Newcastle University,UK Yakovchuk P, Protozanova E, Frank- ...

*Shine-Dalgarno sequence

The degree of base pairing also plays a role in determining the rate of initiation at different AUG initiator codons. In 1973 ... Since this conserved sequence contained the complement of each of the three eukaryotic termination codons (UAA, UAG and UGA) it ... doi:10.1016/0092-8674(89)90122-0. Steitz J A, Jakes K (1975). "How ribosomes select initiator regions in mRNA: base pair ... Kozak consensus sequence, the sequence that targets the ribosome to the initiation codon in eukaryotes. Prokaryotic translation ...

*Internal ribosome entry site

HCV-like IRESs directly bind the 40S ribosomal subunit to position their initiator codons are located in ribosomal P-site ...

*Start codon

Presence of an AUU initiator codon". The EMBO Journal. 1 (3): 311-315. PMC 553041 . PMID 6325158. Missiakas, D.; Georgopoulos, ... The start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon always codes ... Alternate start codons are still translated as Met when they are at the start of a protein (even if the codon encodes a ... Alternative start codons are different from the standard AUG codon and are found in both prokaryotes (bacteria) and eukaryotes ...

*Hepatitis C virus internal ribosome entry site

Moreover, it binds 40S in such a manner that AUG initiator codon is positioned in the ribosomal P-site, thus no ribosomal ... Initiator tRNA is delivered either by eIF2 or, in stress conditions when eIF2 is inactivated, by eIF2A, eIF2D, or possibly ... UTR to reach to start codon. In contrast, translation of hepatitis C virus (HCV) mRNA is initiated by a different mechanism ...

*TUBA4A

... exons either provide or deny an initiator methionine codon to the same alpha-tubulin coding region". Nucleic Acids Research. 15 ...

*List of MeSH codes (G14)

... codon MeSH G14.340.024.340.137.190.225 --- codon, initiator MeSH G14.340.024.340.137.190.250 --- codon, terminator MeSH G14.340 ... codon, initiator MeSH G14.335.355.250 --- codon, terminator MeSH G14.335.355.250.235 --- codon, nonsense MeSH G14.335.760.640 ...

*Reelin

ATG initiator codon of the RELN gene in an Italian population. Longer triplet repeats in the 5' region were associated with an ...

*List of MeSH codes (D13)

... codon MeSH D13.444.735.544.355.225 --- codon, initiator MeSH D13.444.735.544.355.250 --- codon, terminator MeSH D13.444.735.544 ... 235 --- codon, nonsense MeSH D13.444.735.544.500 --- rna caps MeSH D13.444.735.544.500.710 --- rna cap analogs MeSH D13.444. ...

*TPSB2

These genes have an intron immediately upstream of the initiator Met codon, which separates the site of transcription ...

*Glycine dehydrogenase (decarboxylating)

2005). "A single nucleotide substitution that abolishes the initiator methionine codon of the GLDC gene is prevalent among ...

*Central dogma of molecular biology

The ribosome reads the mRNA triplet codons, usually beginning with an AUG (adenine−uracil−guanine), or initiator methionine ... matching the codon in the mRNA to the anti-codon on the tRNA. Each tRNA bears the appropriate amino acid residue to add to the ... Translation ends with a stop codon which may be a UAA, UGA, or UAG triplet. The mRNA does not contain all the information for ... codon downstream of the ribosome binding site. Complexes of initiation factors and elongation factors bring aminoacylated ...

*Prokaryotic initiation factor-3

It also allows for rapid codon-anticodon pairing for the initiator tRNA to bind quickly to. IF3 is required by the small ...

*Prokaryotic initiation factor

It also allows for rapid codon-anticodon pairing for the initiator tRNA to bind quickly to. IF3 is required by the small ... Prokaryotic initiation factor-2 binds to an initiator tRNA and controls the entry of that tRNA into the ribosome. IF2, bound to ...

*TPSD1

... most of the tryptase genes have an intron immediately upstream of the initiator Met codon, which separates the site of ...

*Parathyroid hormone-related protein

... in-frame and downstream of the initiator AUG codon, to give rise to nuclear forms of this hormone. The protein was first ...

*Index of genetics articles

Industrial melanism Infectious transfer Informed consent Inherit Inherited Initiation codon Initiation Initiation Initiator ... bank Cloned DNA Cloning Cloning vector Coccus Code Code dictionary Coding strand Codominance Codon Codon usage bias aka Codon ... Ochre codon Okazaki fragment Oligo Oligogenic Oligonucleotide Oncogene Oncogenes Oncovirus Oocyte Oogenesis Oogonia Opal codon ... Non-disjunction Non-histone protein Non-linear tetrad Non-Mendelian ratio Non-parental Non-recombinant Nonsense codon Nonsense ...

*P-site

Initiation involves recognition of the start codon (AUG) by initiator tRNA in the P-site, elongation phase involves passage of ... The A-site binds to incoming to aminoacyl-tRNA which has the anti-codon for the corresponding codon in the mRNA presented in ... When a stop codon is reached, the peptidyl-tRNA bond of the tRNA located in the P-site is cleaved releasing the newly ... Translation moves the tRNA from the A-site through the P- and E-sites, with the exception of the initiator tRNA, which binds ...

*Eukaryotic initiation factor

Following placement of the initiator tRNA on the AUG start codon in the P-site, eIF1 dissociates and eIF2 switches to the GDP- ... along the mRNA to reach an AUG start codon. Recognition of the start codon by the Met-tRNAiMet promotes gated phosphate and ... In particular, eIF1 dissociation from the 40S subunit is considered to be a key step in start codon recognition. eIF1 and eIF1A ... eIF2 is the main protein complex responsible for delivering the initiator tRNA to the P-site of the preinitiation complex, as a ...

*Eukaryotic translation

... the amino acid encoded by the start codon is methionine. The Met-charged initiator tRNA (Met-tRNAiMet) is brought to the P-site ... The initiator tRNA occupies the P site in the ribosome, and the A site is ready to receive an aminoacyl-tRNA. During chain ... At the end of the initiation step, the mRNA is positioned so that the next codon can be translated during the elongation stage ... Leaky termination in these genes leads to translational readthrough of up to 10% of the stop codons of these genes. Some of ...

*SUI1 protein domain

... helped by eIF2 and the initiator Met-tRNAiMet. SUI1 ensures that translation initiation commences from the correct start codon ... SUI1 promotes a high initiation fidelity for the AUG codon, discriminating against non-AUG codons. . The primary structure of ... and 2β discriminate against poor AUG context and non-AUG start codons". Molecular and Cellular Biology. 31 (23): 4814-31. doi: ... recognition of the start codon". Molecular and Cellular Biology. 12 (1): 248-60. PMC 364089 . PMID 1729602. Martin-Marcos P, ...

*Biosynthesis

In all, there are 64 codons, 61 of each code for one of the 20 amino acids, while the remaining codons specify chain ... The binding of a charged initiator tRNA into the P site of the ribosome 3. The proper alignment of the ribosome with mRNA's ... The last stage of translation occurs when a stop codon enters the A site. Then, the following steps occur: 1. The recognition ... start codon Following initiation, the polypeptide chain is extended via anticodon:codon interactions, with the ribosome adding ...

*Stringent response

W Haseltine; R Block (1973). "Synthesis of guanosine tetra- and pentaphosphate requires the presence of a codon-specific, ... "Thermodynamic characterization of ppGpp binding to EF-G or IF2 and of initiator tRNA binding to free IF2 in the presence of GDP ...
Medicina di varicosity che sta a uomini; Il massager per gambe da varicosity. merlicam. on at Aug 30, · Video embedded 10/10(22). Medicina di varicosity che sta a uomini; Il massager per gambe da varicosity. merlicam. on at Aug 30, · Video embedded 10/10(22). Medicina di varicosity che sta a uomini; Il massager per gambe da varicosity. merlicam. on at Aug 30, · Video embedded 10/10(22). Medicina di varicosity che sta a uomini; Il massager per gambe da varicosity. merlicam. on at Aug 30, · Video embedded 10/10(22). Medicina di varicosity che sta a uomini; Il massager per gambe da varicosity. merlicam. on at Aug 30, · Video embedded 10/10(22). ...
The PLRV gene coding for the pr17 protein was modified by the addition of a 5 terminal extension by fusion to the multiple cloning site (polylinker) of the vector pBluescript. By targeted mutagenesis, the first two AUG translation start codons of the pr17 gene were changed into ACG codons and an AUG codon was inserted into the polylinker sequence ...
SYSTEM AND METHOD FOR VIRTUAL PARTITION MONITORING | PROCESS TESTING APPARATUS, PROCESS TESTING PROGRAM, AND PROCESS TESTING METHOD | Automated Code Lockdown To Reduce Attack Surface For Software | SYSTEM AND METHOD FOR HYPERVISOR-BASED SECURITY | FILE INTEGRITY PRESERVATION |
METHOD FOR CONSTRUCTING CYLINDRICAL TANK | MULTIFUNCTIONAL ENCLOSURE | AUTONOMOUS BEAM ASSEMBLY SYSTEM FOR STEEL STRUCTURE | ARCHITECTURAL BUILDING BLOCK | FILTRATION APPARATUS FOR USE WITH DRAINAGE STRUCTURES AND METHOD FOR INSTALLING THE SAME |
This gene product is a member of a family of proteins characterized by a specific cysteine-rich C-terminal domain, which is involved in transcriptional regulation of viral genome expression. Alternative translation initiation from an upstream non-AUG (GUG), and an in-frame, downstream AUG codon, results in the production of two isoforms, which in human have been shown to have different subcellular localization. [provided by RefSeq, Jul 2008 ...
c-myc_Antibody- by Western blot 1:2,000 dilution will yield a strong band in WB.There is evidence to show that alternative translation initiations from an upstream
In prokaryotes, several mRNA sequences surrounding the initiation codon have been found to influence the translation process; these include the downstream region and its codon context, the Shine-Dalgarno sequence and the S1 ribosomal protein-binding site. In this thesis, the purpose has been to study the role of the downstream region and Shine-Dalgarno-like sequences on early translation elongation and gene expression in Escherichia coli.. The downstream region (DR) after the initiation codon (around five to seven codons), has an important role in the initiation of translation. We find that most of the codons which give very low gene expression at +2 (considering AUG as +1), reach 5 to 10 fold higher expression when those codons are positioned posteriori to +2, with the exception of the NGG codons. The NGG codons abort the translation process if located within the first five codons of the DR, due to peptidyl-tRNA drop-off. However, when the NGG codons are situated further down from the DR, the ...
From UniProtKB/Swiss-Prot: Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis. The eIF-3 complex associates with the 40S ribosome and facilitates the recruitment of eIF-1, eIF-1A, eIF-2:GTP:methionyl-tRNAi and eIF-5 to form the 43S preinitiation complex (43S PIC). The eIF-3 complex stimulates mRNA recruitment to the 43S PIC and scanning of the mRNA for AUG recognition. The eIF-3 complex is also required for disassembly and recycling of post-termination ribosomal complexes and subsequently prevents premature joining of the 40S and 60S ribosomal subunits prior to initiation. Required for nonsense-mediated mRNA decay (NMD); may act in conjunction with UPF2 to divert mRNAs from translation to the NMD pathway. May interact with MCM7 and EPAS1 and regulate the proteasome-mediated degradation of these proteins.
This gene encodes a transcription factor that contains four zinc-finger motifs at the C-terminus and a proline/glutamine-rich DNA-binding domain at the N-terminus. It plays an essential role in the normal development of the urogenital system, and the orthologous human gene is mutated in a small subset of patients with Wilm's tumors. Alternative splicing has been noted for this gene, however, the full-length nature of these variants is not known. The mRNA for this gene has been shown to initiate translation from non-AUG (CUG) and AUG translation start sites, resulting in different isoforms. [provided by RefSeq, Apr 2013 ...
Prodigal: prokaryotic gene recognition and translation initiation site identification. Background: The quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. Increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals. Results: With our years of experience in manually curating genomes for the Joint Genome Institute, we developed a new gene prediction algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm). With Prodigal, we focused specifically on the three goals of improved gene structure prediction, improved translation initiation site recognition, and reduced false positives. We compared the results of Prodigal to existing gene-finding methods to demonstrate that it met each of these objectives. Conclusion: We built a fast, lightweight, open source gene
A typical fully processed mRNA includes one reference-protein coding ORF (RefORF) or coding sequence. This overly simplistic view is however challenged by recent evidence of translation of alternative ORFs (AltORFs). AltORFs are defined as ORFs occurring either in untranslated regions, or overlapping the RefORF in the non-canonical +2 and +3 reading frames. The use of alternative translation initiation is well-described for viruses and provide small viral genomes with an increased coding capacity, but has been overlooked in eukaryotes. To address this issue, we generated a database of predicted AltORFs in the human transcriptome. We identified 83,886 AltORFs with a minimum size of 40 codons. This threshold was established to increase the chances of detecting the predicted alternative proteins by proteomic techniques, including tryptic digestion and mass spectrometry, and SDS-PAGE. For the majority of mRNAs (87.58 %) we found at least one predicted AltORF and, on average, 3.88 predicted AltORFs ...
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(KudoZ) English to Portuguese translation of environmental initiators : desencadeadores ambientais [Diabetes - Medical: Pharmaceuticals (Medical)].
Everlasting Blort - a compendium of the webs weird underbelly, updated daily with links to the strange, absurd, bizarre, humorous, surreal and satiric.
Whatever happens with Floyd, I cant help but think this could have been handled better. No one at the Chatenay-Malabry lab should be discussing the results of the A test, and it does cycling no good for information to be leaked in dribs and drabs like this.. I suppose well know the truth soon, but whether the B sample exonerates Landis or shows that he did have synthetic testosterone in his system, Ill always have doubts. Posted by: Jason at Aug 1, 2006 1:14:42 AM. As discussed in the I need testosterone comments, what other lab governing body leaks details and isnt that suspect?. Posted by: DL Byron at Aug 1, 2006 9:08:56 AM. Is Red Bull a permitted drink for cyclists? Does Floyd partake? I imagine the rumors about it containing testosterone are silly urban legend, but one cant help but wonder.. Posted by: Julie at Aug 1, 2006 9:52:53 AM. The leaks are a little irritating, no doubt, but the bottom line is this: it aint looking good for Landis. We cant cut him any slack because we like ...
Codons are three-letter codes that make up the genetic code. Both RNA and DNA have triplets known as codons. Each codon codes one of 20 amino acids that the body uses to synthesize amino acids....
MRNA codons are molecules that act as a template for protein synthesis when a cell passes on its genetic code. Each mRNA codon...
Amino acids and codons: arithmetical patterns in assignment of amino acids to codons. Variants of a 5-dimensional chain applied from a suggested model in theoretical physics.
Time to say goodbye - In January 2012, I decided it was time to plan ahead. I knew which way I wanted my life to go and had a pretty good idea of the time frame. I made a decisi... ...
In this article we will go through important interview questions around JQuery, JSON and Angular.js.; Author: |b|Shivprasad koirala|/b|; Updated: 11 Aug 2014; Section: ASP.NET; Chapter: Web Development; Updated: 11 Aug 2014
The hepatitis B virus X gene encodes a transcription activator which stimulates the synthesis of RNAs from a variety of class II and III promoter elements. In this report, we present a mutational analysis which genetically demonstrates that the X gene actually encodes two, and possibly three, related polypeptides from a single mRNA using alternate translation initiation from any of three in-frame AUG codons. Genetic analysis shows that translation initiates at the 5 proximal AUG of X mRNA and produces a full-length 17-kDa X protein but in addition also likely initiates at either of two conserved, in-frame AUG codons, producing two amino-terminally truncated X proteins presumably of 8 and 6.6 kDa. Expression of mRNAs capable of encoding only one of each X protein all individually transactivate class III (RNA polymerase III)-transcribed promoters. However, class II (RNA polymerase II)-transcribed promoters displayed various requirements for the different X proteins. Expression of two X proteins, ...
Mitochondria are essential organelles of eukaryotic cells and are responsible for their energy metabolism. The citric acid cycle, a chain of redox reactions in the mitochondrial matrix, is a central metabolic hub. The energy of these redox reactions is preserved in reducing equivalents, which are fed into the electron transport chain of the inner mitochondrial membrane. This process ultimately produces ATP.. Mitochondrial ribosomes are responsible for the synthesis of the hydrophobic core components of the respiratory chain complexes. Using the bakers yeast Saccharomyces cerevisiae as a eukaryotic model organism, the composition of the polypeptide tunnel exit of mitochondrial ribosomes was defined. We identified novel mitochondria-specific ribosomal proteins and generated insights into how they contribute to the specialization of mitochondrial ribosomes.. In a second approach, Kgd4 was identified as a novel structural component of the a-ketoglutarate dehydrogenase complex (KGDH), which is part ...
Well in terms of my own career it was the first time you discover something is always probably-in some ways the most memorable and certainly the work that Mario Cappechi and I did in discovering the initiation mechanism for polypeptides was quite extraordinary. I had done part of the experiment by learning how to label the formal methionine transfer in a way that it sort of could be studied. And Mario had a protein synthetic system working. So the idea was to see if in fact this formal methionine would actually be incorporated into protein, and indeed it was. And so I can remember standing beside Mario as he was taking the radioactive tape off the machine and it was immediately clear that formal methionine had been incorporated in the polypeptides and by its nature that meant that it had to be going in at the amino-terminus. That it had to be the initiator of polypeptide synthesis. So it was a very exciting time trying to quickly round off that story and get it ready for publication. It helped a ...
2. A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes [LINK]. 3. Translation efficiency is determined by both codon bias and folding energy [LINK]. Optional Listen to Yoshimi Battles The Pink Robots as you read the papers.... ...
Initiator polymers having an initiator group and a ligand group are provided. The initiator polymers are capable of specifically binding to a receptor on a surface. Using a macromer system, the initiator polymers are useful for the formation of a polymeric matrix on the surface of a material. In particular, initiator polymers are provided that have specificity to pancreatic β cells and can be used to encapsulate cells for transplantation and the treatment of diabetes.
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Clipping found in The Ogden Standard in Ogden, Utah on Fri, Aug 1, 1913. Kaysville Pioneer Honored by Many_ Standard 01Aug1913 weeks pit) hed excellent ball and won his initial virion of the season, holding the visitors to four hits. The only run scored by Chicago resulted resulted from an error by Hartzell in the fifth Innin
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State Fair exhibits. 4-H exhibits that are eligible to advance to the state fair must be brought to the Extension Service office by 8:30 a.m. Aug. 17. Exhibits will be transported to the State Fair for entry that morning. Items will be returned to the Extension office Aug. 31. Exhibits and ribbons can be picked up after 3 p.m. State Fair Shows. The Kentucky State Fair 4-H Rabbit Show will be Aug. 21; the 4-H and FFA youth Beef shows will be Aug. 27.. ...
The orientation session, which is a prerequisite for the course, will be held from 9 a.m. to noon on Aug. 4-8 at 1025 Main St. in Great Bend. Those interested can call ahead or arrive on the first day of orientation ...
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What is the most efficient translation initiation signal? Does the small subunit ribosome do the scanning for the start codon or can a fully formed ribosome scan for start codon, too? When to scan from the 5 end and when to scan from the middle of 5UTR (internal ribosomal entry)? If secondary structure embedding start codon (or Shine-Dalgarno sequence or Kozak consensus) can obscure the translation initiation signal, how would highly expressed genes avoid this? What is the best way of measuring gene expression experimentally or bioinformatically? Do translation initiation efficiency affect elongation efficiency/accuracy? How to measure translation elongation efficiency/accuracy? Will a few closely spaced minor codons severely affect translation elongation? What is the optimal translation stop signal? How do release factors decode the stop signal? How the relative concentration and decoding capacity of different release factors affect stop codon usage? How frequent do tRNAs misread stop codons ...
kulmburg at aug.ukl.uni-freiburg.de (Peter.Kulmburg at AUG.UKL.UNI-FREIBURG.DE) wrote: : Dear collegues, : I do not adhere to your list, however, Iwould like to get some infos. : Please reply to my private address and not to the list. Thank you in : advance. : 8 of 20 amino acids are known to be essential for human beings, any book of : biology tells us. But none told me yet, which (key) enzymes lack in humans : or mice for the production of the respective amino acid. : I have been asked by my students today and could not answer. Can anybody : help me? I am especially interested in the biosynthesis of methionine. : Thank you very much for your help Peter Kulmburg I dont know the answer, but there are some nice metabolism databases available on the net. With them and SwissProt (or another protein database), your students should be able to figure things out for themselves (it would make a nice assignment for a university student or even a team of high schoolers). I had an assignment like this in ...
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4Dipartimento di Biochimica e Biologia Molecolare, Università di Bari, Italy. The AUG start codon context features have been investigated by analyzing eukaryotic mRNAs belonging to various taxonomic groups. The functional relevance of each specific position surrounding the AUG start codon has been established as a function of the measured shift between base composition observed at that particular position, and base composition averaged over all the 5 untranslated regions. A more detailed analysis carried out on human genes belonging to different isochores showed significant isochore-specific features that cannot be explained only by a mutational bias effect.. The most represented heptamers spanning from position -3 to +4 with respect to the initiator AUG have been determined for mRNAs belonging to different taxonomic groups and a web page utility has been set up (http://bigarea.area.ba.cnr.it:8000/BioWWW/ATG.html) to determine the relative abundance of a user submitted oligonucleotide context ...
Destin City Hall All City Council meetings, workshops, executive sessions and CRA Board meetings are held at the City Hall Annex, 4100 Indian Bayou Trail. All other board and committee meetings are held at City Hall, 4200 Indian Bayou Trail. • Budget Workshop, 5:30 p.m. Aug. 14 • Town Center CRA-AC, 5:30 p.m. Aug. 16 • City Council, 6 p.m. Aug. 21 • Business Tax Receipt Study Commission, 1 p.m. Aug. 22 • Environmental/Parks & Recreation Committee/Tree Board, 4 p.m.
A codon is a sequence of three nucleotides in DNA or RNA that either codes for a particular amino acid or tells the cellular machinery to start or stop using the code. A group of codons starts with the initiation codon. ... More » ...
once it was found out that codons consisted of three-nucleotide sequences the specificity of each and every codon could, Hire Biology Expert, Ask Academics Expert, Assignment Help, Homework Help, Textbooks Solutions
Can you name the 8b GUG? Test your knowledge on this science quiz to see how you do and compare your score to others. Quiz by jenjen001
Plasmid pAAV-CAG-tdTomato (codon diversified) from Dr. Edward Boydens lab contains the insert tdTomato and is published in Unpublished This plasmid is available through Addgene.
Prison officials have recommended that Oscar Pistorius, who killed his girlfriend, be released from prison Aug. 21 for good behavior after serving just 10 months and be moved to house arrest, the head of correctional services said on Monday.
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Plasmid pGWB505 from Dr. Tsuyoshi Nakagawas lab is published in Biosci Biotechnol Biochem. 2007 Aug;71(8):2095-100. Epub 2007 Aug 7. This plasmid is available through Addgene.
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My facebook status today is "Only a small percentage of people understand how conflicted my soul is on any given day." I chose not to post this part of what I typed as my status... This does not mean I am not joyful, happy, thankful, blessed, living and doing. This also does not make me the strongest person you know, brave, or amazing...I am merely carrying the cross I was given to carry and sometimes it gets heavy...though Id never lay it down, abandon it, or begrudge it ...
Aug. 9 - Now that the S&P has broken a key technical level, the bears could find they have nowhere to go, according to Reuters Correspondent Ed Krudy.
Avian encephalomyelitis virus (AEV) is a picornavirus that affects young chickens, quails, pheasants and turkeys. Translation initiation on picornavirus mRNA is cap independent and occurs through a mechanism known as internal initiation, which depends on Internal Ribosome Entry Site (IRES) element within the 5 untranslated region (UTR) of the viral RNA. AEV has been assigned within the Hepatovirus genus and shares protein sequence similarity with hepatitis A virus (HAV). I have demonstrated that the 494 nucleotide 5 UTR of the AEV genome contains an internal ribosome entry site (IRES) element. However, in contrast to the HAV IRES, the AEV IRES functions efficiently in the presence of cleaved eEF4G, suggesting functional differences exist. Characterization of the AEV IRES element revealed that there are remarkable structural and functional similarities between the AEV, flavivirus [especially hepatitis C virus (HCV)] and newly discovered type 4 picornaviras IRES elements, including porcine ...
The IRESite database presents information about the experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5-terminal 7mG cap structure. It is not yet clear whether the activity could be attributed to a common sequence or to a common secondary structure present in them. Such IRES regions were found in a broad range of +RNA viruses and in some eukaryotic cellular mRNAs. Certain IRESs have been predicted based on the fact that closely related viruses should share its features and indeed, their sequences are in some regions conserved enough to allow identification of a new IRES. In contrast, cellular IRESs do not have almost anything in common in terms of their sequence or secondary structure. Therefore, cellular IRESs cannot be predicted. Either way, IRESite is focused only on IRESs which have been at ...
IL-1R antagonist (IL-1Ra) exists as three well-characterized isoforms. The 17-kDa secretory IL-1Ra (sIL-1Ra) and 18-kDa intracellular IL-1Ra (icIL-1RaI) arise by alternative transcription of the same IL-1Ra gene. The recently described 16-kDa intracellular IL-1Ra (icIL-1RaII) is formed by alternative translation initiation of sIL-1Ra mRNA. Transcription and translation of IL-1Ra isoforms were examined in LPS-stimulated human neutrophils and PBMC using RT-PCR, ELISA, and Western blot analysis. LPS stimulation of neutrophils resulted in elevated sIL-1Ra mRNA levels by 1 h, whereas icIL-1RaI mRNA remained undetectable through 22 h of culture. Extracellular glycosylated sIL-1Ra protein and intracellular icIL-1RaII were observed in LPS-stimulated neutrophils by 3 h of culture; no icIL-1RaI protein was detected by immunoblot. LPS stimulation of PBMC resulted in elevated sIL-1Ra mRNA levels by 1 h and detectable icIL-1RaI mRNA at 8 h of culture. LPS-stimulated PBMC demonstrated extracellular glycosylated sIL
Start site selection. Ribosome profiling revealed an unexpected degree of variability in translation initiation in mammalian cells, including substantial use of non-AUG codons. These diverse start sites led to the translation of alternate protein isoforms as well as short reading frames that likely served principally as decoys repressing translation of a protein-coding gene. Alternate initiation has been recognized as a mechanism for controlling protein expression level and isoform choice for a few specific genes. Our finding that alternate initiation was pervasive posed questions about the ways in which start site selection is controlled and its impact on expression genome-wide. We are using ribosome profiling to study the effects of modulating the factors that control start site usage. We are also pursuing one specific, interesting mode of alternate protein production: the regulated expression of truncated dominant negative isoforms from the same transcript that encodes a full-length protein. ...
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 ...
use strict; use warnings; my @processed; while (my $a_line = ,DATA,) { chomp $a_line; if ($a_line =~ /^,/) { #this is a header, keep as is push @processed, $a_line; } else { # This is a dna seq, process # Translate each three-base codon into amino acid, # and append to a protein my $protein = ; my $len = length($a_line) -2; for(my $i=0; $i , $len ; $i += 3) { my $codon = substr($a_line, $i,3); $protein .= codon2aa($codon); } push @processed, $protein; } } #now display what we have processed print $_, \n for @processed; # codon2aa # # A subroutine to translate a DNA 3-character codon to an amino acid sub codon2aa { my($codon) = @_; if ( $codon =~ /GC./i) { return A } # Alanine elsif ( $codon =~ /TG[TC]/i) { return C } # Cysteine elsif ( $codon =~ /GA[TC]/i) { return D } # Aspartic Acid elsif ( $codon =~ /GA[AG]/i) { return E } # Glutamic Acid elsif ( $codon =~ /TT[TC]/i) { return F } # Phenylalanine elsif ( $codon =~ /GG./i) { return G } # Glycine elsif ( $codon =~ /CA[TC]/i) ...
Research in our group focuses on the investigation of the signals involved in gene specification in genomic sequences (promoter elements, splice sites, translation initiation sites, etc…). We are interested both in the mechanism of their recognition and processing, and in their evolution. In addition, but related to this basic component of our research, our group is also involved in the development of software for gene prediction and annotation in genomic sequences.. ...
Dr Nikolay Shirokikh is a biochemist and molecular biologist interested in mechanisms underlying the decoding of genetic information. Instructions on how, when and where to make proteins to fulfil the ever-changing requirements of the living cells are encoded in the ribonucleic acid messages (messenger(m)RNA). Translation of mRNA into protein is central to all life. Mechanisms regulating translation are important for cell survival and wellbeing. In eukaryotic cells, where production of each type or variant of protein can be individually regulated, translational control is especially complex. Control of protein synthesis is directly involved in the processes critical for multicellular eukaryotes, such as cell differentiation, synaptic plasticity, adaptation and pro- and counter-survival decision making of the somatic and germline cells. Malignant cells utilise alternative translation pathways to survive and escape treatment through drug resistance. The primary interest of Dr Shirokikh is to ...
Xia, X. , MacKay, V., Yao, X., Wu, J., Miura, F. Ito, T. Morris, D. R. 2011. Translation initiation: a regulatory role for poly(A) tracts in front of the AUG codon in Saccharomyces cerevisiae. Genetics 189:469-478 ...
How efficient, relative to CAP-proximal cistron translation, is translation initiation from the ECMV IRES? Qualitative estimates are okay also. Thanks in advance -- Its only in uncertainty that youre naked and alive --Peter Gabriel ...
same as mdfenko. as the positionning of ribosome is driven by more that ATG, the first codon is the starting met and the other one is an extra methionine. Moreover i dont think 2 met in begining will be a severe problem, as its only 1 repetition.. ...
Hi couldnt find a thread for July/Aug so thought I would start one for anyone who might want to join me. Just had my review appointment with FS after my last failed transfer and 3 month break he wasnt very interested in any questions I - page 151
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Unlike many gamers, I game for the fluff. The outfits! The cool things I can find! There is a lot to see around World of Warcraft but Im looking for the best of the best outfits and screenshots! Not just Wow, all games! This week: Have a screenshot or outfit you like? Send it to…
A blog containing writings of ioanes rakhmat composed to liberate and enlighten the human mind so as to make the world a better place for all to live
A blog containing writings of ioanes rakhmat composed to liberate and enlighten the human mind so as to make the world a better place for all to live
Sorry I have not been on much. I made it through my move to ground floor. It was rough as I got sick in the middle of it but mostly finished now. I am tired a...
The Federal Reserve decided not to raise interest rates earlier this month. And after the minutes from that meeting were released Tuesday, investors quickly decided that the Feds more than two-year interest rate hiking campaign may be over for the foreseeable future.
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The invention is directed to a high-throughput screening system for identifying new antibacterial agents specifically targeted against an essential component of the bacterial translation apparatus, IF3. The assay uses a reporter gene system in whole cells, and is based on the ability of IF3 to discriminate against translation initiation at the atypical start codon of the reporter gene. The figure is a schematic diagram of the pAUU-CAT reporter gene construct in which the CAT gene has its ATG initiator codon replaced with ATT. Inhibitors of IF3 are expected to result in increased growth of specially-designed test cells due to higher levels of expression from the reporter gene. The invention further provides secondary assays which are used to further study the test compounds which produced positive results in the screening assays of the invention. The invention also encompasses reporter gene constructs, test cells, and compounds identified by the methods of the invention.
The reports of dual-targeted proteins in plants have steadily increased over the past years. The vast majority of these proteins are soluble proteins distributed between compartments of the non-secretory pathway, predominantly chloroplasts and mitochondria. In contrast, dual-targeted transmembrane proteins, especially of the secretory pathway, are rare and the mechanisms leading to their differential targeting remain largely unknown. Here, we report dual-targeting of the Arabidopsis DUF679 Membrane Protein 1 (DMP1) to the tonoplast (TP) and the plasma membrane (PM). In Arabidopsis and tobacco two equally abundant DMP1 isoforms are synthesized by alternative translation initiation: a full length protein, DMP1.1, and a truncated one, DMP1.2, which lacks the N-terminal 19 amino acids including a TP-targeting dileucine motif. Accumulation of DMP1.1 and DMP1.2 in the TP and the PM, respectively, is Brefeldin A-sensitive, indicating transit via the Golgi. However, DMP1.2 interacts with DMP1.1, leading to
Mammalian cells employ numerous innate cellular mechanisms to inhibit viral replication and spread. Tetherin, also known as Bst2 or CD317, is an interferon-induced, cellular response factor that was initially found to block release of HIV-1 and other retroviruses from infected cells. Our lab demonstrated that Tetherin functions as a broadly acting antiviral factor by showing that both human and murine Tetherin potently inhibit the release of the filovirus, ebolavirus, from the surface of cells. Moreover we found that the ebolavirus glycoprotein (GP) antagonized the antiviral effect of human and murine Tetherin and facilitated viral budding. However, the mechanism by which ebolavirus impedes Tetherin function is unknown and is one of the areas under active investigation in our lab. Additionally, we recently identified two species of the Tetherin protein generated by alternative translation initiation that display dramatically different biologic activities. Although both protein isoforms act as ...
Inhibition of translation initiation by antisense oligonucleotides via an RNase-H independent mechanism.: We have used alpha-oligomers as antisense oligonucleot
Previous in vivo studies showing a lack of correlation between CRH binding and CRHR-1 mRNA levels have suggested that receptor levels in the pituitary may be regulated at the translational level (Rabadan-Diehl et al., 1996, 1997). Modulation of translation rate is determined not only by the stability of the mRNA, but also by structural features of the mRNA, such as a secondary structure or initiation codons in the 5′-UTR (Kozak, 1991; Geballe and Morris, 1994). Because it has been shown that the presence of ORFs in the 5′-UTR of the mRNA can influence the translation efficiency of the main ORF, this study was conducted to determine whether the 5′-UTR could be involved in the regulation of the CRHR-1 receptor translation. The present experiments provide evidence that an upstream ORF, potentially encoding 10 amino acids, in the 5′-UTR of the CRHR1, decreases translation of the CRHR or a reporter gene. Mutation of the upstream ATG in constructs with the main ORF of CRHR1 or luciferase ...
Biology translations - Best Text - Your Professional TRANSLATION AGENCY. Swift Delivery and Affordable Prices! Medical Translations, Pharmaceutical Translations, Chemical Translations, Biology Translations, Biotech Translations, Veterinary Translations and more
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Im now stuck on basic terminology, but your suggestion has already been helpful. I will try to use "word" in the code comments (where instructions and how it works are first explained) to see how well it fits in with all else that the program has to include for terminology. There is still something peculiar about the word "Codon" though. It is short and still infers that it is a code unit, which makes and an excellent word to use, as though it was originally intended for any codon size but since biology (at least mostly) uses triplets it has lost its meaning. For example it has been speculatively theorized that two letter coding led to the current three in which case it still seems to be a codon, but there is again the problem of what to call a two letter code element. Since its my program I can call it anything I want. But I do cant go off on my own naming things. I need to find the most appropriate and would rather use a word that is precise but somehow losing its meaning, than one that ...
Im now stuck on basic terminology, but your suggestion has already been helpful. I will try to use "word" in the code comments (where instructions and how it works are first explained) to see how well it fits in with all else that the program has to include for terminology. There is still something peculiar about the word "Codon" though. It is short and still infers that it is a code unit, which makes and an excellent word to use, as though it was originally intended for any codon size but since biology (at least mostly) uses triplets it has lost its meaning. For example it has been speculatively theorized that two letter coding led to the current three in which case it still seems to be a codon, but there is again the problem of what to call a two letter code element. Since its my program I can call it anything I want. But I do cant go off on my own naming things. I need to find the most appropriate and would rather use a word that is precise but somehow losing its meaning, than one that ...
No ones gonna tell me/Whats wrong or whats right/Or tell me who to eat with, sleep with/Or that Ive won the big fight, big fight, Adam Ant, Goody Two ShoesROCKKendrews Lounge, Aliquippa, 9 p.m. Aug. 24, Glitz (80s rock), $5. Luannes Route 68, Industry, 9:30 p.m. Aug. 24, The Zoo, no cover.Rooks East End Saloon, Ambridge, 9 p.m. Aug. 23, House Band, (classic) no cover.Uncl Chucks, Rochester, 9:30 p.m. Aug. 24, Hy Winz, no cover. The Venue at Harmony Ridge, Harmony
Codon tables describe how the triplet codon of RNA (or DNA) is read by specific tRNAs to map to a particular amino acid. Many organisms use the Standard Codon Table, shown below. ...
PARIS, Aug 28 (Reuters) - Below are company-related news and stories from French and Benelux media which could have an impact on the regions markets or individual stocks.
You are not logged in. Please log in to work on translations. Templates which are more important to translate are listed first. ...
EGFP - inserted GTG as second codon, F64L, S65T + optimized for human codons with 35-fold increase in fluorescence over GFP [3] ...
Question posted in: pain, nausea/vomiting, side effect, cramp, nexplanon - Additional details: ... bad cramps mostly on left side and was throwing up ...
The next big private equity buyout will likely involve an offshore affiliate, a flurry of money exchanges, a lower tax bill, and higher returns. But the IRS is knocking. ...
HOBART, Tuesday.-A meeting of the Fauna Board was hold to-day. The chairman (Colonel J. E. C. Lord) presided, and there were also present ...
Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis (PubMed:17581632, PubMed:25849773, PubMed:27462815). The eIF-3 complex associates with the 40S ribosome and facilitates the recruitment of eIF-1, eIF-1A, eIF-2:GTP:methionyl-tRNAi and eIF-5 to form the 43S pre-initiation complex (43S PIC). The eIF-3 complex stimulates mRNA recruitment to the 43S PIC and scanning of the mRNA for AUG recognition. The eIF-3 complex is also required for disassembly and recycling of post-termination ribosomal complexes and subsequently prevents premature joining of the 40S and 60S ribosomal subunits prior to initiation (PubMed:17581632). The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation, including cell cycling, differentiation and apoptosis, and uses different modes of RNA stem-loop binding to exert either translational activation or repression (PubMed
An increase in the cellular levels of dihydrofolate reductase (DHFR) is one of the most common mechanisms of tumor resistance to methotrexate (MTX), an antimetabolite that is widely used in the treatment of a variety of human malignancies. The MTX-resistant phenotype generally occurs as a consequence of DHFR gene amplification which in turn is responsible for DHFR gene overexpression. We have designed antisense oligodeoxynucleotides (aODNs) against the DHFR mRNA and tested their in vitro effect on human leukemia CCRF-CEM/E cells, overexpressing the DHFR gene about 20-fold in comparison with the CCRF-CEM/S parental cell line. An aODN complementary to a region encompassing the AUG translation start (DHFR1) of DHFR mRNA and a mixture of two aODNs complementary to the 5 untranslated region (DHFR2+DHFR3) have been used. A DHFR1 scrambled-sequence ODN and a fully degenerated ODN were the controls. All ODNs had a phosphodiester backbone. DHFR1 and the relevant scrambled ODN were also capped with two

Patente WO1999052357A1 - Assays for inhibitors of bacterial translation initiation factor 3 - Google PatentesPatente WO1999052357A1 - Assays for inhibitors of bacterial translation initiation factor 3 - Google Patentes

The figure is a schematic diagram of the pAUU-CAT reporter gene construct in which the CAT gene has its ATG initiator codon ... and is based on the ability of IF3 to discriminate against translation initiation at the atypical start codon of the reporter ... 15 the first codon of the reporter gene is an atypical start codon. To make a test strain, the native ATG start codon of a ... The figure is a schematic diagram of the pAUU-CAT reporter gene construct in which the CAT gene has its ATG initiator codon ...
more infohttp://www.google.es/patents/WO1999052357A1?cl=en

Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes.  -...Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. -...

By analyzing the effects of single base substitutions around the ATG initiator codon in a cloned preproinsulin gene, I have ... Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes.. Kozak M ... A purine in position -3 (i.e., 3 nucleotides upstream from the ATG codon) has a dominant effect; when a pyrimidine replaces the ... The mechanism by which nucleotides flanking the ATG codon might exert their effect is discussed. ...
more infohttps://www.ncbi.nlm.nih.gov/pubmed/3943125?dopt=Abstract

A single sequence context cannot satisfy all non-AUG initiator codons in yeast† | BMC Microbiology | Full TextA single sequence context cannot satisfy all non-AUG initiator codons in yeast† | BMC Microbiology | Full Text

We next tested whether the non-AUG initiator codons identified above can also act as initiator codons in GRS1. To this end, the ... it was interesting to point out that the non-AUG initiator codons of ALA1 and GRS1 and the cryptic initiator codon of ALA1 ... a less-efficient non-AUG initiator codon in the context of ALA1, was one of the strongest non-AUG initiator codons in the ... Codon PositionInitiator CodonFusion ConstructSequence ContextAlternative Translation Initiation. Background. Aminoacyl-tRNA ...
more infohttps://0-bmcmicrobiol-biomedcentral-com.brum.beds.ac.uk/articles/10.1186/1471-2180-10-188

Analysis of Genomic G + C Content, Codon Usage, Initiator Codon Contex by Jeffrey D. Wuitschick and Kathleen M. Karrer"Analysis of Genomic G + C Content, Codon Usage, Initiator Codon Contex" by Jeffrey D. Wuitschick and Kathleen M. Karrer

We analyzed G + C content, codon usage, initiator codon context and stop codon sites in the extremely A + T rich genome of this ... Regions immediately preceding Tetrahymena translation initiator codons were generally A-rich. For the 60 stop codons examined, ... the 75 available T. thermophila protein coding sequences favored codons ending in T and, where possible, avoided those with G ... Highly expressed genes were relatively G + C-rich and exhibited an extremely biased pattern of codon usage while ...
more infohttps://epublications.marquette.edu/bio_fac/241/

Marilyn Kozak - WikipediaMarilyn Kozak - Wikipedia

Kozak, M (31 January 1986). "Point mutations define a sequence flanking the AUG initiator codon that modulates translation by ... Kozak, Marilyn (4 October 1993). "Identifying AUG Initiator Codons" (PDF). Citation Classic Commentaries. 36 (40). Retrieved 4 ...
more infohttps://en.wikipedia.org/wiki/Marilyn_Kozak

Kozak consensus sequence - WikipediaKozak consensus sequence - Wikipedia

Kozak M (1984). "Point mutations close to the AUG initiator codon affect the efficiency of translation of rat preproinsulin in ... Kozak M (1986). "Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ... "Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes". Proc. Natl. Acad. Sci. U.S ... Rarely, GUG is used as an initiation codon, but methionine is still the first amino acid as it is the met-tRNA in the ...
more infohttps://en.wikipedia.org/wiki/Kozak_consensus_sequence

NADP Transhydrogenase
      - Transhydrogenase
     Summary Report | CureHunterNADP Transhydrogenase - Transhydrogenase Summary Report | CureHunter

10/01/2011 - "The insertion of the transposon, which occurred 16 bp upstream from the start codon of an ORF encoding a soluble ...
more infohttp://www.curehunter.com/public/keywordSummaryD009250-NADP-Transhydrogenase-Transhydrogenase.do

Weblogo representation of the region surrounding the kn | Open-iWeblogo representation of the region surrounding the kn | Open-i

However, in certain cases, initiation can occur at codons differing from AUG by a single nucleotide, especially the codons CUG ... However, in certain cases, initiation can occur at codons differing from AUG by a single nucleotide, especially the codons CUG ... Mentions: Of the 9 possible codons that differ from AUG in a single position, 5 are used to initiate the extensions of the 17 ... Mentions: Of the 9 possible codons that differ from AUG in a single position, 5 are used to initiate the extensions of the 17 ...
more infohttps://openi.nlm.nih.gov/detailedresult.php?img=PMC3105428_gkr007f6&req=4

Variant Annotation Integrator	Variant Annotation Integrator

initiator_codon_variant. A codon variant that changes at least one base of the first codon of a transcript. ... initiator_codon_variant, incomplete_terminal_codon_variant, stop_lost, stop_retained_variant, stop_gained, NMD_transcript_ ... incomplete_terminal_codon_variant. A sequence variant where at least one base of the final codon of an incompletely annotated ... A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened ...
more infohttp://genome.ucsc.edu/cgi-bin/hgVai?hgsid=793633659_J9faMgImABK9dUiw24u4yCUWPA6x

Variant Annotation Integrator	Variant Annotation Integrator

initiator_codon_variant. A codon variant that changes at least one base of the first codon of a transcript. ... initiator_codon_variant, incomplete_terminal_codon_variant, stop_lost, stop_retained_variant, stop_gained, NMD_transcript_ ... incomplete_terminal_codon_variant. A sequence variant where at least one base of the final codon of an incompletely annotated ... A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened ...
more infohttp://genome.ucsc.edu/cgi-bin/hgVai?hgsid=790643313_EkpBc5unyF1kuXyN19owYdIqhFgA

Beta alpha)8-barrel proteins of tryptophan biosynthesis in the hyperthermophile Thermotoga maritima.  - University of...Beta alpha)8-barrel proteins of tryptophan biosynthesis in the hyperthermophile Thermotoga maritima. - University of...

Codon, Initiator. MESH. Enzyme Stability/genetics. MESH. Escherichia coli/genetics. MESH. Genetic Complementation Test. MESH. ... and N-terminal sequencing of their polypeptide products showed that their translation is initiated at the rate start codons TTG ...
more infohttps://epub.uni-regensburg.de/13715/

Nucleotide sequence of tobacco mosaic virus RNA | PNASNucleotide sequence of tobacco mosaic virus RNA | PNAS

This gene terminates two nucleotides before the initiator codon of the coat protein gene. Potential signal sequences ... Overlapping the terminal five codons of this readthrough reading frame is a second reading frame coding for a protein of Mr ...
more infohttps://www.pnas.org/content/79/19/5818?ijkey=55fbee10d9e6d511914b010bf789e94c7e55378b&keytype2=tf_ipsecsha

Fritz S[au] - PubMed - NCBIFritz S[au] - PubMed - NCBI

An initiator codon mutation in SDE2 causes recessive embryonic lethality in Holstein cattle. ...
more infohttps://www.ncbi.nlm.nih.gov/pubmed?cmd=search&term=Fritz+S%5Bau%5D&dispmax=50

Comparative chloroplast genomes of Paris Sect. Marmorata: insights into repeat regions and evolutionary implications |...Comparative chloroplast genomes of Paris Sect. Marmorata: insights into repeat regions and evolutionary implications |...

Codon usage pattern. Most protein-coding genes employed the standard initiator codon AUG; however, six unusual start codons ... the codon usage patterns were determined for 71 distinct protein-coding genes in Sect. Marmorata chloroplast genomes. Codons of ... Wright F. The effective number of codons used in a gene. Gene. 1990;87(1):23-9.PubMedGoogle Scholar ... Codon usage and substitution rate calculation. RSCU, GC3s, and ENc for 71 protein-coding genes were calculated using CodonW ...
more infohttps://link.springer.com/article/10.1186%2Fs12864-018-5281-x

DHCR7 Gene - GeneCards | DHCR7 Protein | DHCR7 AntibodyDHCR7 Gene - GeneCards | DHCR7 Protein | DHCR7 Antibody

initiator_codon_variant, missense_variant. rs104886035. pathogenic, not provided, Smith-Lemli-Opitz syndrome, Smith-Lemli-Opitz ...
more infohttp://www.genecards.org/cgi-bin/carddisp.pl?gene=DHCR7&origene_3utr_trans=2

RPS26 Gene - GeneCards | RS26 Protein | RS26 AntibodyRPS26 Gene - GeneCards | RS26 Protein | RS26 Antibody

initiator_codon_variant, missense_variant. rs148622862. pathogenic, Diamond-Blackfan anemia 10. 56,042,170(+). G/A. splice_ ...
more infohttps://www.genecards.org/cgi-bin/carddisp.pl?gene=RPS26

Recombinant Measles Viruses with Mutations in the C, V, or F Gene Have Altered Growth Phenotypes In Vivo | Journal of VirologyRecombinant Measles Viruses with Mutations in the C, V, or F Gene Have Altered Growth Phenotypes In Vivo | Journal of Virology

... two nucleotide substitutions altering the initiator methionine codon and creating a new stop codon six amino acids into the C ... 1988) ACG, the initiator codon for a Sendai virus protein. J. Biol. Chem. 263:8553-8556. ... The first mutation was predicted to inactivate the initiator methionine. The second mutation created a stop codon after the ... 1988) Ribosomal initiation from an ACG codon in the Sendai virus P/C mRNA. EMBO J. 7:245-251. ...
more infohttps://jvi.asm.org/content/72/10/7754?ijkey=9fb5d869bd079f5a36aed8e1b4eaa56e897efb7b&keytype2=tf_ipsecsha

Variant Annotation Integrator	Variant Annotation Integrator

initiator_codon_variant. A codon variant that changes at least one base of the first codon of a transcript. ... initiator_codon_variant, incomplete_terminal_codon_variant, stop_lost, stop_retained_variant, stop_gained, NMD_transcript_ ... incomplete_terminal_codon_variant. A sequence variant where at least one base of the final codon of an incompletely annotated ... A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened ...
more infohttp://genome.cse.ucsc.edu/cgi-bin/hgVai?hgsid=817482233_n7w21cKqKtn5e1NGUPAHNOYx20Vn

Ubuntu Manpage:

       Bio::Tools::CodonTable - Codon table objectUbuntu Manpage: Bio::Tools::CodonTable - Codon table object

The only differences are in available initiator codons. NCBI Genetic Codes home page: (Last update of the Genetic Codes: April ... codon is_ter_codon Title : is_ter_codon Usage : $obj-,is_ter_codon(GAA) Function: returns true (1) for all codons that can be ... codon unambiguous_codons Title : unambiguous_codons Usage : @codons = $self-,unambiguous_codons(ACN) Returns : array of ... Example : $myCodonTable-,is_ter_codon(ATG) Returns : boolean Args : codon is_unknown_codon Title : is_unknown_codon Usage : $ ...
more infohttp://manpages.ubuntu.com/manpages/eoan/man3/Bio::Tools::CodonTable.3pm.html

Magnitude and breadth of CTL responses to frameshift-de | Open-iMagnitude and breadth of CTL responses to frameshift-de | Open-i

Codon, Initiator/genetics/immunology. *Female. *Frameshift Mutation/immunology. *HLA-A3 Antigen. *Humans ...
more infohttps://openi.nlm.nih.gov/detailedresult.php?img=PMC2812535_JEM_20091808_RGB_Fig1&req=4

A Test of the Cytosolic Apolipoprotein E Hypothesis Fails to Detect the Escape of Apolipoprotein E from the Endocytic Pathway...A Test of the Cytosolic Apolipoprotein E Hypothesis Fails to Detect the Escape of Apolipoprotein E from the Endocytic Pathway...

1986) Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. ... This primer also incorporated a start codon that conforms to the Kozak consensus sequence (Kozak, 1986). A nuclear localization ...
more infohttps://www.jneurosci.org/content/19/7/2464?ijkey=a258035a9845d9380c9430159fa7dbba97f3073c&keytype2=tf_ipsecsha

Plus itPlus it

Kozak M. At least six nucleotides preceding the AUG initiator codon enhance translation in mammalian cells. J. Mol. Biol., 196: ... The sequences (CCAGAGAUGG) around the predicted initiator methionine codon of the XPA gene agree with the Kozaks consensus ... Kozak M. Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes ... C for codon 228; and primer extension, 20 s at 72°C for A23G and 30 s at 72°C for codon 228. The cycles were followed by a ...
more infohttp://cebp.aacrjournals.org/content/11/10/993

K Sreekumaran Nair, PhD, MD - Research Output
     - Mayo ClinicK Sreekumaran Nair, PhD, MD - Research Output - Mayo Clinic

Langer, H. T., Mossakowski, A. A., Baar, K., Alcazar, J., Martin-Rincon, M., Alegre, L. M., Ara, I., Calbet, J. A. L., Hinkley, J. M., Coen, P. M., Irving, B. A., Allerton, T. D., Nair, S., Lima, R. M., Rey-López, J. P., Scott, D., Daly, R. M., Ebeling, P. R., Hayes, A., Tessier, A. J. & 10 others, Chevalier, S., Yates, B. A., Brown, L. A. R., Storer, T. W., Westcott, W. L., Nifli, A. P., Musci, R. V., Konopka, A. R., Hamilton, K. L. & Hepple less, R. T., Jan 1 2019, In : Journal of applied physiology. 126, 1, p. 257-262 6 p.. Research output: Contribution to journal › Comment/debate ...
more infohttps://mayoclinic.pure.elsevier.com/en/persons/k-sreekumaran-nair/publications/
  • Of the 9 possible codons that differ from AUG in a single position, 5 are used to initiate the extensions of the 17 known cases that passed our qualitative analysis for conservation of the extension. (nih.gov)
  • For the 60 stop codons examined, the frequency of G in the end + 1 site was much higher than expected whereas C never occupied this position. (marquette.edu)
  • A bit more complete picture of the full complexity of codon usage in various taxonomic groups is presented at the NCBI Genetic Codes Home page. (ubuntu.com)
  • Among these initiator codons, TTG, CTG, ACG, and ATT had ~50% initiating activities relative to that of ATG, while GTG, ATA, and ATC had ~20% initiating activities relative to that of ATG. (beds.ac.uk)