Terminator Regions, Genetic: DNA sequences recognized as signals to end GENETIC TRANSCRIPTION.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, 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.Rho Factor: A protein which effects termination of RNA synthesis during the genetic transcription process by dissociating the ternary transcription complex RNA;-RNA POLYMERASE DNA at the termination of a gene.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, 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.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.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.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.Transcription Termination, Genetic: The discontinuation of transcription at the end of a transcription unit, including the recognition of termination sites and release of the newly synthesized RNA molecule.Genes, Bacterial: The functional hereditary units of BACTERIA.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.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.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.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.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.Bacillus subtilis: A species of gram-positive bacteria that is a common soil and water saprophyte.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.DNA-Directed RNA Polymerases: Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Bacterial Proteins: Proteins found in any species of bacterium.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.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.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.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).Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Galactokinase: An enzyme that catalyzes reversibly the formation of galactose 1-phosphate and ADP from ATP and D-galactose. Galactosamine can also act as the acceptor. A deficiency of this enzyme results in GALACTOSEMIA. EC 2.7.1.6.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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.RNA, 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.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.Templates, Genetic: Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.Bacteriophage lambda: A temperate inducible phage and type species of the genus lambda-like viruses, in the family SIPHOVIRIDAE. Its natural host is E. coli K12. Its VIRION contains linear double-stranded DNA with single-stranded 12-base 5' sticky ends. The DNA circularizes on infection.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.RNA Polymerase I: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. The enzyme functions in the nucleolar structure and transcribes DNA into RNA. It has different requirements for cations and salts than RNA polymerase II and III and is not inhibited by alpha-amanitin. EC 2.7.7.6.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.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.RNA Folding: The processes of RNA tertiary structure formation.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.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.DNA: 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).Deoxyuracil Nucleotides: Uracil nucleotides which contain deoxyribose as the sugar moiety.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.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.DNA Replication: The process by which a DNA molecule is duplicated.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.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Ribosomes: Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.RNA Polymerase II: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6.AT Rich Sequence: A nucleic acid sequence that contains an above average number of ADENINE and THYMINE bases.Bacteriophage T7: Virulent bacteriophage and type species of the genus T7-like phages, in the family PODOVIRIDAE, that infects E. coli. It consists of linear double-stranded DNA, terminally redundant, and non-permuted.Bacteriophage HK022: A tentative species in the genus lambda-like viruses, family SIPHOVIRIDAE.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.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)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.Peptide Elongation Factors: Protein factors uniquely required during the elongation phase of protein synthesis.Deoxyribonucleotides: A purine or pyrimidine base bonded to a DEOXYRIBOSE containing a bond to a phosphate group.Taq Polymerase: A heat stable DNA-DIRECTED DNA POLYMERASE from the bacteria Thermus aquaticus. It is widely used for the amplification of genes through the process of POLYMERASE CHAIN REACTION. EC 2.7.7.-.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.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)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.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.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.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.DNA-Directed DNA Polymerase: DNA-dependent DNA polymerases found in bacteria, animal and plant cells. During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair.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.Lac Operon: The genetic unit consisting of three structural genes, an operator and a regulatory gene. The regulatory gene controls the synthesis of the three structural genes: BETA-GALACTOSIDASE and beta-galactoside permease (involved with the metabolism of lactose), and beta-thiogalactoside acetyltransferase.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).Genetic Vectors: DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.RNA Phages: Bacteriophages whose genetic material is RNA, which is single-stranded in all except the Pseudomonas phage phi 6 (BACTERIOPHAGE PHI 6). All RNA phages infect their host bacteria via the host's surface pili. Some frequently encountered RNA phages are: BF23, F2, R17, fr, PhiCb5, PhiCb12r, PhiCb8r, PhiCb23r, 7s, PP7, Q beta phage, MS2 phage, and BACTERIOPHAGE PHI 6.Poly U: A group of uridine ribonucleotides in which the phosphate residues of each uridine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.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, Transfer, Leu: A transfer RNA which is specific for carrying leucine to sites on the ribosomes in preparation for protein synthesis.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.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.RNA Polymerase III: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure where it transcribes DNA into RNA. It has specific requirements for cations and salt and has shown an intermediate sensitivity to alpha-amanitin in comparison to RNA polymerase I and II. EC 2.7.7.6.T-Phages: A series of 7 virulent phages which infect E. coli. The T-even phages T2, T4; (BACTERIOPHAGE T4), and T6, and the phage T5 are called "autonomously virulent" because they cause cessation of all bacterial metabolism on infection. Phages T1, T3; (BACTERIOPHAGE T3), and T7; (BACTERIOPHAGE T7) are called "dependent virulent" because they depend on continued bacterial metabolism during the lytic cycle. The T-even phages contain 5-hydroxymethylcytosine in place of ordinary cytosine in their DNA.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.Genes, Viral: The functional hereditary units of VIRUSES.Transformation, Genetic: Change brought about to an organisms genetic composition by unidirectional transfer (TRANSFECTION; TRANSDUCTION, GENETIC; CONJUGATION, GENETIC, etc.) and incorporation of foreign DNA into prokaryotic or eukaryotic cells by recombination of part or all of that DNA into the cell's genome.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.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Deoxycytosine Nucleotides: Cytosine nucleotides which contain deoxyribose as the sugar moiety.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Viral Proteins: Proteins found in any species of virus.DnaB Helicases: A family of DNA helicases that participate in DNA REPLICATION. They assemble into hexameric rings with a central channel and unwind DNA processively in the 5' to 3' direction. DnaB helicases are considered the primary replicative helicases for most prokaryotic organisms.Ribosomal Proteins: Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.Chromosomes, Bacterial: Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.Genes, Fungal: The functional hereditary units of FUNGI.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.Regulatory Sequences, Ribonucleic Acid: Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.Tyrosine-tRNA Ligase: An enzyme that activates tyrosine with its specific transfer RNA. EC 6.1.1.1.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)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.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.RNA Processing, Post-Transcriptional: Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.RNA Cleavage: A reaction that severs one of the sugar-phosphate linkages of the phosphodiester backbone of RNA. It is catalyzed enzymatically, chemically, or by radiation. Cleavage may be exonucleolytic, or endonucleolytic.Polyadenylation: The addition of a tail of polyadenylic acid (POLY A) to the 3' end of mRNA (RNA, MESSENGER). Polyadenylation involves recognizing the processing site signal, (AAUAAA), and cleaving of the mRNA to create a 3' OH terminal end to which poly A polymerase (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) adds 60-200 adenylate residues. The 3' end processing of some messenger RNAs, such as histone mRNA, is carried out by a different process that does not include the addition of poly A as described here.Bacteriophages: Viruses whose hosts are bacterial cells.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.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.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.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.Genes, Synthetic: Biologically functional sequences of DNA chemically synthesized in vitro.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.DNA, Intergenic: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.Genetic Complementation Test: A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.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.Amino Acyl-tRNA Synthetases: A subclass of enzymes that aminoacylate AMINO ACID-SPECIFIC TRANSFER RNA with their corresponding AMINO ACIDS.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)Host Factor 1 Protein: An integration host factor that was originally identified as a bacterial protein required for the integration of bacteriophage Q beta (ALLOLEVIVIRUS). Its cellular function may be to regulate mRNA stability and processing in that it binds tightly to poly(A) RNA and interferes with ribosome binding.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Dideoxynucleosides: Nucleosides that have two hydroxy groups removed from the sugar moiety. The majority of these compounds have broad-spectrum antiretroviral activity due to their action as antimetabolites. The nucleosides are phosphorylated intracellularly to their 5'-triphosphates and act as chain-terminating inhibitors of viral reverse transcription.Kinetics: The rate dynamics in chemical or physical systems.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.Endoribonucleases: A family of enzymes that catalyze the endonucleolytic cleavage of RNA. It includes EC 3.1.26.-, EC 3.1.27.-, EC 3.1.30.-, and EC 3.1.31.-.DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.Gene Order: The sequential location of genes on a chromosome.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Escherichia coli K12: A species of gram-negative, rod-shaped bacteria belonging to the K serogroup of ESCHERICHIA COLI. It lives as a harmless inhabitant of the human LARGE INTESTINE and is widely used in medical and GENETIC RESEARCH.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.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.Chromosome Deletion: Actual loss of portion of a chromosome.Tryptophan: An essential amino acid that is necessary for normal growth in infants and for NITROGEN balance in adults. It is a precursor of INDOLE ALKALOIDS in plants. It is a precursor of SEROTONIN (hence its use as an antidepressant and sleep aid). It can be a precursor to NIACIN, albeit inefficiently, in mammals.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.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.beta-Globins: Members of the beta-globin family. In humans, they are encoded in a gene cluster on CHROMOSOME 11. They include epsilon-globin, gamma-globin, delta-globin and beta-globin. There is also a pseudogene of beta (theta-beta) in the gene cluster. Adult HEMOGLOBIN is comprised of two ALPHA-GLOBIN chains and two beta-globin chains.RNA Stability: The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.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.Polyribonucleotide Nucleotidyltransferase: An enzyme of the transferase class that catalyzes the reaction RNA(n+1) and orthophosphate to yield RNA(n) and a nucleoside diphosphate, or the reverse reaction. ADP, IDP, GDP, UDP, and CDP can act as donors in the latter case. (From Dorland, 27th ed) EC 2.7.7.8.Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating): An NAD-dependent glyceraldehyde-3-phosphate dehydrogenase found in the cytosol of eucaryotes. It catalyses the dehydrogenation and phosphorylation of GLYCERALDEHYDE 3-PHOSPHATE to 3-phospho-D-glyceroyl phosphate, which is an important step in the GLYCOLYSIS pathway.Transformation, Bacterial: The heritable modification of the properties of a competent bacterium by naked DNA from another source. The uptake of naked DNA is a naturally occuring phenomenon in some bacteria. It is often used as a GENE TRANSFER TECHNIQUE.Coliphages: Viruses whose host is Escherichia coli.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Riboswitch: Part of a MESSENGER RNA molecule that undergoes a conformation change upon binding a specific metabolite or other small molecule thereby regulating the messenger RNA's transcription, post-transcriptional processing, transport, translation, or stability in response to varying levels of the metabolite or other small molecule.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Genetic Engineering: Directed modification of the gene complement of a living organism by such techniques as altering the DNA, substituting genetic material by means of a virus, transplanting whole nuclei, transplanting cell hybrids, etc.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.Bacillus: A genus of BACILLACEAE that are spore-forming, rod-shaped cells. Most species are saprophytic soil forms with only a few species being pathogenic.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.DNA Polymerase I: A DNA-dependent DNA polymerase characterized in prokaryotes and may be present in higher organisms. It has both 3'-5' and 5'-3' exonuclease activity, but cannot use native double-stranded DNA as template-primer. It is not inhibited by sulfhydryl reagents and is active in both DNA synthesis and repair. EC 2.7.7.7.Diphosphates: Inorganic salts of phosphoric acid that contain two phosphate groups.RNA Precursors: RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.RNA, Fungal: Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.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.Artificial Gene Fusion: The in vitro fusion of GENES by RECOMBINANT DNA techniques to analyze protein behavior or GENE EXPRESSION REGULATION, or to merge protein functions for specific medical or industrial uses.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.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.HIV Reverse Transcriptase: A reverse transcriptase encoded by the POL GENE of HIV. It is a heterodimer of 66 kDa and 51 kDa subunits that are derived from a common precursor protein. The heterodimer also includes an RNAse H activity (RIBONUCLEASE H, HUMAN IMMUNODEFICIENCY VIRUS) that plays an essential role the viral replication process.3' Untranslated Regions: The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Nucleotide Mapping: Two-dimensional separation and analysis of nucleotides.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Archaea: One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Bacteria: One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.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.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.Endonucleases: Enzymes that catalyze the hydrolysis of the internal bonds and thereby the formation of polynucleotides or oligonucleotides from ribo- or deoxyribonucleotide chains. EC 3.1.-.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.Genetic Variation: Genotypic differences observed among individuals in a population.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.Titrimetry: The determination of the concentration of a given component in solution (the analyte) by addition of a liquid reagent of known strength (the titrant) until an equivalence point is reached (when the reactants are present in stoichiometric proportions). Often an indicator is added to make the equivalence point visible (e.g., a change in color).Plants, Genetically Modified: PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.Dideoxynucleotides: The phosphate esters of DIDEOXYNUCLEOSIDES.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.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.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Recombinant Proteins: Proteins prepared by recombinant DNA technology.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)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.Deoxyadenine Nucleotides: Adenine nucleotides which contain deoxyribose as the sugar moiety.RNA, Antisense: RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.Netropsin: A basic polypeptide isolated from Streptomyces netropsis. It is cytotoxic and its strong, specific binding to A-T areas of DNA is useful to genetics research.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.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Cytidine: A pyrimidine nucleoside that is composed of the base CYTOSINE linked to the five-carbon sugar D-RIBOSE.Pentosyltransferases: Enzymes of the transferase class that catalyze the transfer of a pentose group from one compound to another.RNA-Directed DNA Polymerase: An enzyme that synthesizes DNA on an RNA template. It is encoded by the pol gene of retroviruses and by certain retrovirus-like elements. EC 2.7.7.49.Transcription Initiation Site: The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.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.Exoribonucleases: A family of enzymes that catalyze the exonucleolytic cleavage of RNA. It includes EC 3.1.13.-, EC 3.1.14.-, EC 3.1.15.-, and EC 3.1.16.-. EC 3.1.-Poly A: A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Vision Disparity: The difference between two images on the retina when looking at a visual stimulus. This occurs since the two retinas do not have the same view of the stimulus because of the location of our eyes. Thus the left eye does not get exactly the same view as the right eye.

A premature termination codon interferes with the nuclear function of an exon splicing enhancer in an open reading frame-dependent manner. (1/1018)

Premature translation termination codon (PTC)-mediated effects on nuclear RNA processing have been shown to be associated with a number of human genetic diseases; however, how these PTCs mediate such effects in the nucleus is unclear. A PTC at nucleotide (nt) 2018 that lies adjacent to the 5' element of a bipartite exon splicing enhancer within the NS2-specific exon of minute virus of mice P4 promoter-generated pre-mRNA caused a decrease in the accumulated levels of P4-generated R2 mRNA relative to P4-generated R1 mRNA, although the total accumulated levels of P4 product remained the same. This effect was seen in nuclear RNA and was independent of RNA stability. The 5' and 3' elements of the bipartite NS2-specific exon enhancer are redundant in function, and when the 2018 PTC was combined with a deletion of the 3' enhancer element, the exon was skipped in the majority of the viral P4-generated product. Such exon skipping in response to a PTC, but not a missense mutation at nt 2018, could be suppressed by frame shift mutations in either exon of NS2 which reopened the NS2 open reading frame, as well as by improvement of the upstream intron 3' splice site. These results suggest that a PTC can interfere with the function of an exon splicing enhancer in an open reading frame-dependent manner and that the PTC is recognized in the nucleus.  (+info)

Inhibition of translation and cell growth by minigene expression. (2/1018)

A random five-codon gene library was used to isolate minigenes whose expression causes cell growth arrest. Eight different deleterious minigenes were isolated, five of which had in-frame stop codons; the predicted expressed peptides ranged in size from two to five amino acids. Mutational analysis demonstrated that translation of the inhibitory minigenes is essential for growth arrest. Pulse-labeling experiments showed that expression of at least some of the selected minigenes results in inhibition of cellular protein synthesis. Expression of the deleterious minigenes in cells deficient in peptidyl-tRNA hydrolase causes accumulation of families of peptidyl-tRNAs corresponding to the last minigene codon; the inhibitory action of minigene expression could be suppressed by overexpression of the tRNA corresponding to the last sense codon in the minigene. Experimental data are compatible with the model that the deleterious effect of minigene expression is mediated by depletion of corresponding pools of free tRNAs.  (+info)

Mutations in the nebulin gene associated with autosomal recessive nemaline myopathy. (3/1018)

The congenital nemaline myopathies are rare hereditary muscle disorders characterized by the presence in the muscle fibers of nemaline bodies consisting of proteins derived from the Z disc and thin filament. In a single large Australian family with an autosomal dominant form of nemaline myopathy, the disease is caused by a mutation in the alpha-tropomyosin gene TPM3. The typical form of nemaline myopathy is inherited as an autosomal recessive trait, the locus of which we previously assigned to chromosome 2q21.2-q22. We show here that mutations in the nebulin gene located within this region are associated with the disease. The nebulin protein is a giant protein found in the thin filaments of striated muscle. A variety of nebulin isoforms are thought to contribute to the molecular diversity of Z discs. We have studied the 3' end of the 20. 8-kb cDNA encoding the Z disc part of the 800-kDa protein and describe six disease-associated mutations in patients from five families of different ethnic origins. In two families with consanguineous parents, the patients were homozygous for point mutations. In one family with nonconsanguineous parents, the affected siblings were compound heterozygotes for two different mutations, and in two further families with one detected mutation each, haplotypes are compatible with compound heterozygosity. Immunofluorescence studies with antibodies specific to the C-terminal region of nebulin indicate that the mutations may cause protein truncation possibly associated with loss of fiber-type diversity, which may be relevant to disease pathogenesis.  (+info)

Mutations in the organic cation/carnitine transporter OCTN2 in primary carnitine deficiency. (4/1018)

Primary carnitine deficiency is an autosomal recessive disorder of fatty acid oxidation caused by defective carnitine transport. This disease presents early in life with hypoketotic hypoglycemia or later in life with skeletal myopathy or cardiomyopathy. The gene for this condition maps to 5q31.2-32 and OCTN2, an organic cation/carnitine transporter, also maps to the same chromosomal region. Here we test the causative role of OCTN2 in primary carnitine deficiency by searching for mutations in this gene in affected patients. Fibroblasts from patients with primary carnitine deficiency lacked mediated carnitine transport. Transfection of patient's fibroblasts with the OCTN2 cDNA partially restored carnitine transport. Sequencing of the OCTN2 gene revealed different mutations in two unrelated patients. The first patient was homozygous (and both parents heterozygous) for a single base pair substitution converting the codon for Arg-282 to a STOP codon (R282X). The second patient was a compound heterozygote for a paternal 1-bp insertion producing a STOP codon (Y401X) and a maternal 1-bp deletion that produced a frameshift creating a subsequent STOP codon (458X). These mutations decreased the levels of mature OCTN2 mRNA and resulted in nonfunctional transporters, confirming that defects in the organic cation/carnitine transporter OCTN2 are responsible for primary carnitine deficiency.  (+info)

Infrequent translation of a nonsense codon is sufficient to decrease mRNA level. (5/1018)

In many organisms nonsense mutations decrease the level of mRNA. In the case of mammalian cells, it is still controversial whether translation is required for this nonsense-mediated RNA decrease (NMD). Although previous analyzes have shown that conditions that impede translation termination at nonsense codons also prevent NMD, the residual level of termination was unknown in these experiments. Moreover, the conditions used to impede termination might also have interfered with NMD in other ways. Because of these uncertainties, we have tested the effects of limiting translation of a nonsense codon in a different way, using two mutations in the immunoglobulin mu heavy chain gene. For this purpose we exploited an exceptional nonsense mutation at codon 3, which efficiently terminates translation but nonetheless maintains a high level of mu mRNA. We have shown 1) that translation of Ter462 in the double mutant occurs at only approximately 4% the normal frequency, and 2) that Ter462 in cis with Ter3 can induce NMD. That is, translation of Ter462 at this low (4%) frequency is sufficient to induce NMD.  (+info)

Heterologous sequences greatly affect foreign gene expression in tobacco mosaic virus-based vectors. (6/1018)

A series of tobacco mosaic virus (TMV)-based hybrid vectors for transient gene expression were constructed with similar designs but differing in the source of heterologous tobamovirus sequence: Odontoglossum ringspot virus, tobacco mild green mosaic virus variants U2 and U5, tomato mosaic virus, and sunn-hemp mosaic virus. These vectors contained a heterologous coat protein subgenomic mRNA promoter and coat protein open reading frame (ORF) and either TMV or heterologous 3' nontranslated region. The foreign ORF, from the jellyfish green fluorescent protein (GFP) gene, was transcribed from the native TMV coat protein subgenomic mRNA promoter, which extended into the coat protein ORF. The presence of an in-frame stop codon within the GFP mRNA leader and the choice of sequence of GFP ORFs substantially affected translational efficiency. However, the major regulatory component of gene expression in these vectors appeared to be transcriptional rather than translational. There was an inverse relationship between expression of GFP and the heterologous coat protein genes that was reflected in accumulation of the respective mRNAs and proteins. The most effective vector in this series (30B) contained sequences encoding the coat protein subgenomic mRNA promoter, coat protein ORF, and 3' nontranslated region from tobacco mild green mosaic virus U5. Expressed from 30B, GFP accumulated up to 10% of total soluble protein in leaves.  (+info)

High frequency of germ-line BRCA2 mutations among Hungarian male breast cancer patients without family history. (7/1018)

To determine the contribution of BRCA1 and BRCA2 mutations to the pathogenesis of male breast cancer in Hungary, the country with the highest male breast cancer mortality rates in continental Europe, a series of 18 male breast cancer patients and three patients with gynecomastia was analyzed for germ-line mutations in both BRCA1 and BRCA2. Although no germ-line BRCA1 mutation was observed, 6 of the 18 male breast cancer cases (33%) carried truncating mutations in the BRCA2 gene. Unexpectedly, none of them reported a family history for breast/ovarian cancer. Four of six truncating mutations were novel, and two mutations were recurrent. Four patients (22%) had a family history of breast/ovarian cancer in at least one first- or second-degree relative; however, no BRCA2 mutation was identified among them. No mutation was identified in either of the genes in the gynecomastias. These results provide evidence for a strong genetic component of male breast cancer in Hungary.  (+info)

Analysis of elements involved in pseudoknot-dependent expression and regulation of the repA gene of an IncL/M plasmid. (8/1018)

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)

*Scarlet fever

A transcriptional terminator is located 69 bases downstream from the translational termination codon. The carboxy terminal ...

*Scarlet fever

A transcriptional terminator is located 69 bases downstream from the translational termination codon. The carboxy terminal ...

*Gloria M. Coruzzi

1980) The use of the UGA terminator as a tryptophan codon in yeast mitochondria. Proc. Natl. Acad. Sci. USA 76: 3784-85. ...

*Gene structure

Only the region between the start and stop codons encodes the final protein product. The flanking untranslated regions (UTRs) ... The 3' UTR contains a terminator sequence, which marks the endpoint for transcription and releases the RNA polymerase. The 5' ...

*Release factor

Scolnick, E., R. Tompkins, T. Caskey, and M. Nirenberg (1968). Release factors differing in specificity for terminator codons, ... A release factor is a protein that allows for the termination of translation by recognizing the termination codon or stop codon ... Although these stop codons are triplets just like ordinary codons, they are not decoded by tRNAs. It was discovered by Mario ... RF1 recognizes the termination codons UAA and UAG RF2 recognizes UAA and UGA RF3 is a GTP-binding protein that leads to the ...

*Attenuator (genetics)

First, Yanofsky observed that the ORF contained two tandem Trp codons and the protein had a Trp percent composition which was ... When RNAP reaches the region of the potential terminator, whether it continues or not is dependent on the position of the ... Without domain 4, translation can continue regardless of the level of tryptophan.[6] The attenuator sequence has its codons ... If the ribosome stalls at the tandem Trp codons, waiting for the appropriate tRNA, region 1 is sequestered within the ribosome ...

*Trp operon

This terminator structure forms when no ribosome stalls in the vicinity of the Trp tandem (i.e. Trp or Arg codon): either the ... conservation is observed in these 5 codons whereas mutating the upstream codons do not alter the operon expression. If the ... it will stall at either of the two trp codons. While it is stalled, the ribosome physically shields sequence 1 of the ... role of RNA secondary structure involving the tryptophan codon region". Proceedings of the National Academy of Sciences of the ...

*Gene

... terminator and start and stop codons. In addition, most eukaryotic open reading frames contain untranslated introns which are ... experiment). Additionally, a "start codon", and three "stop codons" indicate the beginning and end of the protein coding region ... There are 64 possible codons (four possible nucleotides at each of three positions, hence 43 possible codons) and only 20 ... The correspondence between codons and amino acids is nearly universal among all known living organisms. Transcription produces ...

*HBAP1

A new type of polymerase-III-dependent terminator and its evolutionary implication". J. Mol. Biol. 184 (1): 7-21. doi:10.1016/ ... A dinucleotide deletion produces a frameshift and a termination codon". J. Biol. Chem. 263 (9): 4328-32. PMID 2831226. Marotta ...

*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 ... terminator regions (genetics) MeSH G14.340.024.340.137.750.840 --- transcription initiation site MeSH G14.340.024.340.137.775 ... terminator regions (genetics) MeSH G14.080.708.330 --- interspersed repetitive sequences MeSH G14.080.708.330.200 --- dna ...

*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. ...

*Index of molecular biology articles

... termination codon - terminator - tertiary structure - tet resistance - thymine - tissue-specific expression - tm - trans - ... start codon - stem-loop - sticky end - stop codon - streptavidin - stringency - structural motif - sub-cloning - substitution ... codon - codon usage bias - competent - complementary - conformational epitope - congenital - consensus sequence - conservative ... nonsense codon - nonsense mutation - nontranslated RNA - Northern blot - NT - nuclear run-on - nuclease - nuclease protection ...

*Attenuator (genetics)

The attenuator sequence has its codons translated into a leader peptide, but is not part of the trp operon gene sequence. The ... When RNAP reaches the region of the potential terminator, whether it continues or not is dependent on the position of the ... First, Yanofsky observed that the ORF contained two tandem Trp codons and the protein had a Trp percent composition which was ... This forces region 4 when it is made to be single stranded, preventing the formation of the region 3/4 terminator structure. ...

*Terminator (genetics)

The Rho-dependent terminator occurs downstream of translational stop codons and consists of an unstructured, cytosine-rich ... Terminator gene Transcription (genetics) Termination codon Termination factor Richardson, J. P. (1996). "Rho-dependent ... Intrinsic transcription terminators or Rho-independent terminators require the formation of a self-annealing hairpin structure ... The terminator sequence in DNA contains a 20 basepair GC-rich region of dyad symmetry followed by a short poly-T tract or "T ...

*Stop codon

Genetic code Start codon Terminator gene Griffiths AJF, Miller JH, Suzuki DT, Lewontin RC, Gelbart WM (2000). "Chapter 10 ( ... Stop codon suppression or translational readthrough occurs when in translation a stop codon is interpreted as a sense codon, ... Because of this terminology, stop codons have also been referred to as nonsense codons. Recognition of stop codons in bacteria ... Codons that can form hidden stops are used in genomes more frequently compared to synonymous codons that would otherwise code ...

*Index of genetics articles

... bank Cloned DNA Cloning Cloning vector Coccus Code Code dictionary Coding strand Codominance Codon Codon usage bias aka Codon ... Telomerase Telomere Telophase Temperate phage Template strand Teratogen Teratogenic Teratogens Terminal redundancy Terminator ... 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 ...

*Nucleic acid sequence

Each group of three bases, called a codon, corresponds to a single amino acid, and there is a specific genetic code by which ... the Kozak consensus sequence and the RNA polymerase III terminator. Peng found the existence of long-range correlations in the ... form also discounts the difference in acceptance rates between silent mutations that do not alter the meaning of a given codon ...

*Stem-loop

The anticodon that recognizes a codon during the translation process is located on one of the unpaired loops in the tRNA. Two ... This process is known as rho-independent or intrinsic termination, and the sequences involved are called terminator sequences. ...

*Northern epilepsy syndrome

A patient's DNA is sequenced from a blood sample with the use of the ABI Big Dye Terminator v.3.0 kit. Since this is a genetic ... This primary mutation can also be paired with a missense at codon 237, where an arginine takes the place of a glycine. When the ... There are at least ten mutations within the chromosome and the most common missense mutation occurs at codon 24, where a ...

*Lamivudine

They inhibit the HIV reverse transcriptase enzyme competitively and act as a chain terminator of DNA synthesis. The lack of a 3 ... The HBV reverse transcriptase gene is 344 amino acids long and occupies codons 349 to 692 on the viral genome. The most ...

*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 ... Dalgarno L, Shine J (1973). "Conserved terminal sequence in 18S rRNA may represent terminator anticodons". Nature. 245: 261-262 ... Since this conserved sequence contained the complement of each of the three eukaryotic termination codons (UAA, UAG and UGA) it ... Kozak consensus sequence, the sequence that targets the ribosome to the initiation codon in eukaryotes. Prokaryotic translation ...

*Golden Gate Cloning

In BioBrick assembly, an eight-nucleotide scar sequence, which codes for a tyrosine and a stop codon, is left between every ... and a terminator. For the purpose of Golden Gate Cloning, the internal sequences of level 0 modules should not contain type IIS ... and terminators. Then, second-tier Golden Gate assembly combine several constructs made in first-tier assembly to make a ...

*Purine riboswitch

Binding of adenine to the pbuE adenine riboswitch disrupts the structure of a terminator stem that had been blocking access to ... The add gene encodes adenosine deaminase, and the adenine riboswitch that is upstream exposes the gene's start codon and the ... Mandal, M; Breaker RR (2004). "Adenine riboswitches and gene activation by disruption of a transcription terminator". Nat ...

*Inverted repeat

However, the replacement also creates a point mutation converting the GCA codon to ACA. If the strand switch event is followed ... The stem-loop on the 3' end is a transcriptional terminator because the sequence immediately following it is a string of ...

*Nucleic acid secondary structure

Importantly, pairing is the mechanism by which codons on messenger RNA molecules are recognized by anticodons on transfer RNA ... some famous examples are the Rho-independent terminator stem-loops and the tRNA cloverleaf. Active research is on-going to ...

*Gene expression

Each triplet of nucleotides of the coding region is called a codon and corresponds to a binding site complementary to an ... which is usually between protein-coding sequence and terminator. The pre-mRNA is first cleaved and then a series of ~200 ... Transcription ends when the polymerase encounters a sequence called the terminator. While transcription of prokaryotic protein- ...

*Epigenetics

... causes ribosomes to have a higher rate of read-through of stop codons, an effect that results in suppression of nonsense ... by giving cells the ability to switch into a PSI+ state and express dormant genetic features normally terminated by stop codon ...

*Synechocystis

Terminators are the DNA signal which halts transcription. No native Synechocystis terminators have been characterized. ... In Escherichia coli, the beta "clamp" first binds loosely and tightens as the RNAP approaches the start codon (AUG). In ...
Ataluren was safe in healthy volunteers. A first trial in Duchenne patients were patients were treated with different daily doses of Ataluren for 4 weeks showed that treatment was well tolerated and that dystrophin expression was increased for treated patients. Trials to test whether this also results in functional improvement after long term treatment have been performed in multiple centers in the USA and Europe.. Unfortunately, treatment did not convincingly lead in to a functional improvement when compared to placebo treated patients using a 6 minute walk test and therefore the trials were put on hold. Patients involved in these trials in the USA and Europe can enrol in an open label trial.. After detailed analysis of the data and further optimization of dosing, a new confirmatory phase 3 trial in 220 DMD patients has been completed in North- and South-America, Asia, Australia and Europe. Translarna treated patients on average walked 15 meters more in 6 minutes compared to placebo treated ...
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Frontotemporal lobar degeneration (FTLD) is a devastating and progressive disorder, and a common cause of early onset dementia. Progranulin (PGRN) haploinsufficiency due to autosomal dominant mutations in the progranulin gene (GRN) is an important cause of FTLD (FTLD-GRN), and nearly a quarter of these genetic cases are due to a nonsense mutation. Premature termination codons (PTC) can be therapeutically targeted by compounds allowing readthrough, and aminoglycoside antibiotics are known to be potent PTC readthrough drugs. Restoring endogenous PGRN through PTC readthrough has not previously been explored as a therapeutic intervention in FTLD. We studied whether the aminoglycoside G418 could increase PGRN expression in HEK293 and human induced pluripotent stem cell (hiPSC)-derived neurons bearing the heterozygous S116X, R418X, and R493X pathogenic GRN nonsense mutations. We further tested a novel substituted phthalimide PTC readthrough enhancer in combination with G418 in our cellular models. We next
The process of decoding is the most crucial determinant of the quality of protein synthesis. Ribosomal protein L9 was first implicated in decoding fidelity when a mutant version of L9 was found to increase the translation of a T4 phage gene. Later studies confirmed that the absence of L9 leads to increased translational bypassing, frameshifting, and stop codon readthrough. L9 is part of the large subunit of the prokaryotic ribosome and is located more than 90 Å from the site of decoding, making it difficult to envision how it might affect decoding and reading frame maintenance. Twenty years after the identification of L9s putative function, there is no mechanism for how a remotely located L9 improves translation fidelity. This mystery makes our picture of translation incomplete. Despite the high conservation of L9 in eubacteria, E.coli lacking L9 does not exhibit any obvious growth defects. Thus, the evolutionary advantage conferred by L9 in bacteria is masked under laboratory conditions. In order to
Toll-like receptors (TLRs) are evolutionarily conserved pattern-recognition molecules resembling the toll proteins that mediate antimicrobial responses in Drosophila. These proteins recognize different microbial products during infection and serve as an important link between the innate and adaptive immune responses. The TLRs act through adaptor molecules such as MyD88 and TIRAP to activate various kinases and transcription factors so the organism can respond to potential infection. TLR5 recognizes flagellin from both Gram-positive and Gram-negative bacteria and will cause the activation of NF-kappaB, leading to the activation of TNF-alpha and other cytokines. A common TLR5 stop codon polymorphism that disrupts TLR5 signaling is associated with susceptibility to Legionnaires disease and demonstrates the importance of TLR5 in the innate immune response ...
There is a long path from a genetic variant to an "organismal" phenotype (i.e. one that is observed at the level of the organism). A variant nucleotide can have many effects: Exonic variants may disrupt proper transcription by generating a premature stop-codon, or alter an amino-acid that is crucial for protein function, while intronic variants may affect splicing. Also variants outside the transcribed region can modify the level of expression by altering regulatory sites for chromatin state, as well as transcriptional and post-transcriptional regulation. It is important to realize that regulatory networks have evolved to function robustly under external and internal perturbations. Any effect of a genetic variant on the organismal phenotype is propagated through these networks. This propagation, in particular if it involves crucial cellular functions, is likely to involve compensatory effects mediated by regulatory circuits like feedback loops. Moreover, robust functions are often achieved by ...
Release Factor 1 (RF1) recognizes the termination codons UAA and UAG, and is responsible for stopping translation at these codons. While obviously important for proper functioning of translation, the presence of RF1 also limits the amount of full-length protein produced if the gene contains an in-frame stop codon by competing with the Amber suppressor tRNA at the ribosome. This problem is compounded with each additional Amber in the gene, leading to a rapid dropoff of full-length protein isolated with greater than one stop codon. Until recently, it was thought that RF1 was essential for cell survival. Several methods have recently been used to make RF1 conditionally inessential, enabling its knockout. Mukai et al. introduced all seven essential genes normally ending in Amber codons on a plasmid, instead ending in UAA. [15] Johnson et al. "fixed" the expression of RF2, the other primary release factor in E. coli.[16] Both these measures enabled the knockout of RF1. The benefit of this knockout ...
Geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, start and stop codons are predicted and scored along the sequence using Position Weight Arrays (PWAs). Next, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the the log-likelihood ratio of a Markov Model for coding DNA. Finally, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons. ...
Geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, start and stop codons are predicted and scored along the sequence using Position Weight Arrays (PWAs). Next, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the the log-likelihood ratio of a Markov Model for coding DNA. Finally, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons. ...
The overall goal of the Karzai lab is to gain new insights into how the fundamental processes of gene expression are integrated inside the cell. We seek to discover novel integrative links, and explore the biological significance and physiological contributions of these links to the fitness, survival, and virulence of pathogenic bacteria. Our current research is aimed at elucidating the mechanistic details of how the essential processes of protein translation, mRNA stability, and protein degradation are linked. We are particularly interested in investigating: 1) Molecular mechanisms that govern translation quality assurance; 2) Molecular basis for mRNA surveillance and selective nonstop mRNA decay; 3) Biochemical mechanisms of targeted proteolysis and the role of AAA+ proteases in bacterial pathogenesis; 5) Discovery of novel antibiotics and the exploration of new vaccine technologies. We use a combination of protein biochemistry, molecular genetics, functional genomics, bioinformatics, and ...
how to stop - MedHelps how to stop Center for Information, Symptoms, Resources, Treatments and Tools for how to stop. Find how to stop information, treatments for how to stop and how to stop symptoms.
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Can you stop drinking? Yes , everyone will stop drinking….Some in this life time, others in the next…… but we are ALL going to stop drinking….. Guaranteed.. ...
Couples counseling is great, but actions always speak louder than words. Here are some things you can do to actually rebuild your relationship.
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Hi, Could anyone help here, my daughter who has been taking dostinex for over a year, was told to stop taking it, that was 2 months ago, since then she has been...
TY - JOUR. T1 - Gentamicin-induced readthrough of stop codons in Duchenne muscular dystrophy. AU - Malik, Vinod. AU - Rodino-Klapac, Louise R.. AU - Viollet, Laurence. AU - Wall, Cheryl. AU - King, Wendy. AU - Al-Dahhak, Roula. AU - Lewis, Sarah. AU - Shilling, Christopher J.. AU - Kota, Janaiah. AU - Serrano-Munuera, Carmen. AU - Hayes, John. AU - Mahan, John D.. AU - Campbell, Katherine J.. AU - Banwell, Brenda. AU - Dasouki, Majed. AU - Watts, Victoria. AU - Sivakumar, Kumaraswamy. AU - Bien-Willner, Ricardo. AU - Flanigan, Kevin M.. AU - Sahenk, Zarife. AU - Barohn, Richard J.. AU - Walker, Christopher M.. AU - Mendell, Jerry R.. PY - 2010/6. Y1 - 2010/6. N2 - Objective: The objective of this study was to establish the feasibility of long-term gentamicin dosing to achieve stop codon readthrough and produce full-length dystrophin. Mutation suppression of stop codons, successfully achieved in the mdx mouse using gentamicin, represents an important evolving treatment strategy in Duchenne ...
Peptide sequence-dependent ribosomal stalling, as occurs after translation of uORF2, has been observed in other eukaryotic and bacterial systems (21, 36, 47). Our results raise the question of whether release factors play a role in other uORF-mediated ribosomal stalling events. The S-adenosylmethionine decarboxylase uORF codes for a sequence-dependent polyamine-responsive peptide that, like uORF2, causes ribosomal stalling specifically at the termination codon and results in accumulation of the uORF peptidyl-tRNA (30, 40). While the critical sequences of this uORF do not include the carboxy-terminal residue, the penultimate and antepenultimate residues have been implicated (35). Thus, it is possible that eRF1 acts in concert with the polyamine effector and the nascent peptide to inhibit the termination reaction. Regulation of the bacterial tryptophanase operon gene tnaC also has intriguing similarities to the uORF2 mechanism (22-24). Toeprinting assays show that ribosomes translating tnaC stall ...
SsrA is a tmRNA involved in tagging polypeptides on stalled ribosomes. The resulting fusion proteins are then degraded. We purified endogenous SsrA-tagged proteins by means of a genetically engineered SsrA and identified some of them. Analysis of the proteins suggested that they are tagged at their C-terminal extremities. One of them, ribokinase, is expressed from a messenger with a poorly efficient stop codon, leading to translational recoding events. A change in the ribokinase coding sequence from a weak to a strong translational stop sequence (UGAc to UAAu) annihilated SsrA tagging. Translational termination by UGA recruits the translational release factor (RF) 2. We observed that SsrA tagging of ribokinase was inversely correlated with RF2 activity, revealing a dynamic competition between translational termination and SsrA tagging.
Termination of protein synthesis in the yeast Saccharomyces cerevisiae occurs when the eukaryotic release factor eRF1 recognises the stop codon. The rate of termination is enhanced by a second release factor, eRF3 (a GTPase). The efficiency of stop codon recognition by eRF1 is influenced by the surrounding nucleotide context of the stop codon, and in yeast, by the structural properties of eRF3, which displays prion-like characteristics. eRF3 in the [PSI+], prion state forms insoluble high molecular weight aggregates that cause inefficient termination (nonsense suppression). This study tested the hypothesis that the [PSI+] state may direct suppression of stop codons, particularly those in weak contexts. This may confer unique phenotypes upon yeast, particularly stress response phenotypes, caused by C-terminal extension of a subset of proteins. Consistent with this hypothesis, the [PSI+] state was found to enhance suppression of all stop codons, with those in weak contexts being most efficiently ...
Database of translational recoding events. RECODE is a database of the utilisation of ribosomal rameshifting, translational bypassing and mRNA specific codon redefinition for gene expression.
N ew versions of the pADL phagemid vectors pADL-20b, pADL-22b, and pADL-23b are now available. The sequence of the Amp(R) gene sequence has been modified, allowing the cloning site to be opened by either SfiI or BglI restriction enzyme. This modification results in lower background during cloning and brings more flexibility for designing libraries. The pADL vector series is a collection of phagemid vectors for controlled display on the minor coat protein III which combines HIS tag for purification, epitope tag for detection and amber stop codon for conditional display. Expression of the fusion protein is tightly controlled, eliminating issues with toxic clones and library misrepresentation.. ...
Pyrrolysine, the 22nd cotranslationally inserted amino acid, was found in the Methanosarcina barkeri monomethylamine methyltransferase protein in a position that is encoded by an in-frame UAG stop codon in the mRNA. M. barkeri encodes a special amber suppressor tRNA (tRNA(Pyl)) that presumably recog …
Für verschiedene Zwecke sind die verschiedenen Markierungen unterschiedlich gut geeignet. Sie werden im Zuge des Proteindesigns bei der Erzeugung rekombinanter Proteine, bzw. deren Reinigung und Nachweis über die Affinitätschromatografie, über Pulldown-Assays, per Western Blot, per Immunhistochemie, per Fluoreszenzmikroskopie oder im Live-Imaging eingesetzt. Zur Erzeugung eines Protein-Tags wird die codierende DNA-Sequenz des Protein-Tags unter Erhalt des Leserasters in die codierende DNA-Sequenz des Fusionsproteins hinter das Start-Codon oder vor das Stop-Codon eingefügt. Dadurch entsteht ein N-terminales bzw. ein C-terminales Protein-Tag am Protein während der Translation. Gelegentlich muss das Protein-Tag vom Protein nach der Reinigung entfernt werden, was z. B. durch eine Protease-Schnittstelle oder ein induzierbares Intein erreicht werden kann. Der Proteolyse-basierte Ansatz verwendet Proteasen mit längerer Erkennungssequenz, die möglichst nur an der Schnittstelle des Protein-Tags ...
Non-stop decay is a cellular mechanism of mRNA surveillance to detect mRNA molecules lacking a stop codon and prevent these mRNAs from translation. The non-stop decay pathway releases ribosomes that have reached the far 3 end of an mRNA and guides the mRNA to the exosome complex, or to RNase R in bacteria for selective degradation. In contrast to NMD, polypeptides do not release from the ribosome, and thus, NSD seems to involve mRNA decay factors distinct from NMD. Non-stop decay is a cellular pathway that identifies and degrades aberrant mRNA transcripts that do not contain a proper stop codons. Stop codons are signals in messenger RNA that signal for synthesis of proteins to end. Aberrant transcripts are identified during translation when the ribosome translates into the poly A tail at the 3 end of mRNA. A non-stop transcript can occur when point mutations damage the normal stop codon. Moreover, some transcriptions are more likely to preserve low scale of gene expression in a particular ...
Freistroffer, D.V., Pavlov, M.Y., MacDougall, J., Buckingham, R.H. and Ehrenberg, M. (1997). „Release factor RF3 in E. coli accelerates the dissociation of release factors RF1 and RF2 from the ribosome in a GTP-dependent manner". EMBO J. 16: 4126-4133. PMID 9233821 ...
Second, if the mistake is done, and wrong amino acid was incorporated after all, bacterial class-1 release factors RF1 and RF2 become prone to peptide-release independent of the stop codon, thus removing the product (the growing protein chain). In mitochondria translational system is bacterial-like, but much more insane, and several (as many as 4 in humans!) class-1 release factors are present, with some of them lacking the ability to recognize the stop codon at all (ICT1, for example), and these resolve stalled ribosomal complexes by cutting off the peptide as well as their bacterial counterparts ...
See also: stop codon The codons UAA, UAG and UGA, which signal the end of a polypeptide chain. From the BioTech Dictionary at http://biotech.icmb.utexas...
Hi guys, I have a list of protein coding DNA sequences to calculate dN/dS but some of these have mutations which introduce a premature stop codon. So, how to calculate the ratio, just use the sequence before the stop codon or just delete the stop codon? And, is this mutation a mark of strong positive selection ...
IS1A, IS1E, IS1H and IS1I are iso-allelic, indicating that the two recent MG1655(Seq)-specific IS1 insertions originated from either IS1A or IS1E. IS1B, IS1C and IS1D are iso-allelic and have nine DNA substitutions relative to the IS1AEHI alleles, causing L81F polymorphism in InsA2-4 as well as T17P, S18P, L19F, S65R, and H128Y polymorphism in InsB2-4. IS1F has accumulated 77 DNA substitutions relative to the IS1AEHI alleles; the insB6 codon for W98 is replaced by an in-frame stop codon and InsB6 has 16 amino acid differences relative to InsB1,5,8,9 ...
Cold Spring Harbor, NY (PRWEB) September 05, 2012 -- Most people understand genes to be specific segments of DNA that determine traits or diseases that are
Abstract Researchers have noted that there are portions of the DNA that look similar to functional genes, but contain lesions or premature stop codons. These genes have been assumed to be largely non-functional, but recent research suggests that many of these pseudogenes are actually functional. This paper is an overview of some of the research done…
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Quitting an addictive habit like smoking is not easy, the longer you have been smoking, the more difficult it is to stop.  However, with the help of a few...
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Abstract. Termination translation in Saccharomyces cerevisiae is controlled by two interacting polypeptide chain release factors, eRF1 and eRF3. Two regions in human eRF1, position at 281-305 and position at 411-415, were proposed to be involved on the interaction to eRF3. In this study we have constructed and characterized yeast eRF1 mutant at position 410 (correspond to 415 human eRF1) from tyrosine to serine residue resulting eRF1(Y410S). The mutations did not affect the viability and temperature sensitivity of the cell. The stop codons suppression of the mutant was analyzed in vivo using PGK-stop codon-LACZ gene fusion and showed that the suppression of the mutant was significantly increased in all of codon terminations. The suppression on UAG codon was the highest increased among the stop codons by comparing the suppression of the wild type respectively. In vitro interaction between eRF1 (mutant and wild type) to eRF3 were carried out using eRF1-(His)6 and eRF1(Y410S)-(His)6 expressed in ...
Duchenne muscular dystrophy (DMD) is a genetic muscle disorder caused by mutations in the Dmd gene resulting in the loss of the protein dystrophin. Patients do not only experience skeletal muscle degeneration, but also develop severe cardiomyopathy by their second decade, one of the main causes of death. The absence of dystrophin in the heart renders cardiomyocytes more sensitive to stretch-induced damage. Moreover, it pathologically alters intracellular calcium (Ca2+) concentration, neuronal nitric oxide synthase (nNOS) localization and mitochondrial function and leads to inflammation and necrosis, all contributing to the development of cardiomyopathy. Current therapies only treat symptoms and therefore the need for targeting the genetic defect is immense. Several preclinical therapies are undergoing development, including utrophin up-regulation, stop codon read-through therapy, viral gene therapy, cell-based therapy and exon skipping. Some of these therapies are undergoing clinical trials, but these
Roodveldt C, Tawfik DS. C. CAS ISI PubMed Article Goddard, J. Error Prone Pcr Mutagenesis It will be impressive if these methodologies can be extended to tune the redox properties of such synthetic cofactors to match the oxidation potential of organic molecules and then to orient For example, aminoacyl tRNA synthetase (aaRS) activity promotes amber stop codon suppression, leading to the expression of full-length Taq polymerase. W. Int. http://parasys.net/error-prone/error-prone-pcr-taq.php Opin. Lutz S, Ostermeier M, Moore GL, Maranas CD, Benkovic SJ. et al. More information Accept Over 10 million scientific documents at your fingertips Browse by Discipline Architecture & Design Astronomy Biomedical Sciences Business & Management Chemistry Computer Science Earth Sciences & Geography Economics Cancer Ther. 12, 2273-2281 (2013). Biocatalytic asymmetric synthesis of chiral amines from ketones applied to sitagliptin manufacture. et al. To provide clearer data to guide improvements, it would also be ...
TY - JOUR. T1 - An orthogonal amber initiator tRNA functions similarly across diverse Escherichia coli laboratory strains. AU - Vincent, Russel. AU - Yiasemides, Pandelitsa. AU - Jaschke, Paul. N1 - Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.. PY - 2019/5/1. Y1 - 2019/5/1. N2 - Translation initiation is a sequential process involving interactions between the 30S small ribosomal subunit, initiation factors and initiator tRNA. The Escherichia coli K-12 strain is unique in the Escherichia because it has two different initiator tRNA sequences, tRNAfMet1 encoded by the metZWV genes and tRNAfMet2 encoded by the metY gene. A mutant of the metY gene was previously made where the anticodon sequence, responsible for specifying the start codon where translation initiation begins, was changed so that it bound to the amber stop codon UAG instead of the usual AUG start codon[1]. ...
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Post-transcriptional and post-translational modifications are very important for the control and optimal efficiency of messenger RNA (mRNA) translation. Among these, methylation is the most widespread modification, as it is found in all domains of life. These methyl groups can be grafted either on nucleic acids (transfer RNA (tRNA), ribosomal RNA (rRNA), mRNA, etc.) or on protein translation factors. This review focuses on Trm112, a small protein interacting with and activating at least four different eukaryotic methyltransferase (MTase) enzymes modifying factors involved in translation. The Trm112-Trm9 and Trm112-Trm11 complexes modify tRNAs, while the Trm112-Mtq2 complex targets translation termination factor eRF1, which is a tRNA mimic. The last complex formed between Trm112 and Bud23 proteins modifies 18S rRNA and participates in the 40S biogenesis pathway. In this review, we present the functions of these eukaryotic Trm112-MTase complexes, the molecular bases responsible for complex formation and
The Drosophila maternal effect mutant, bicaudal (bic), affects the anterior-posterior axis of the embryo. It is incompletely penetrant, producing a variety of lethal embryonic phenotypes, the most severe of which is replacement of the anterior half with a mirror image duplication of the posterior half. Genetic mapping has placed this locus within a region defined by the overlap of two chromosomal deficiencies on the second chromosome. Indirect genetic evidence has suggested that a lethal mutation that maps to the same region, $vr22\sp{P3}$ may represent a more severe allele of the bicaudal locus. A chromosome walk was performed in this region and over 65 kb of overlapping clones isolated. The location of the P-element insertion responsible for the $vr22\sp{P3}$ mutation was localized in the walk, and cDNAs corresponding to two adjacent transcription units isolated. These clones have been analyzed and sequenced, and one shows at least a 65% identity with eukaryotic release factor. Recombination ...
Adverse cellular conditions often lead to nonproductive translational stalling and arrest of ribosomes on mRNAs. Here, we used fast kinetics and cryo-EM to characterize Escherichia coil HflX, a GTPase with unknown function. Our data reveal that HflX is a heat shock-induced ribosome-splitting factor capable of dissociating vacant as well as mRNA-associated ribosomes with deacylated tRNA in the peptidyl site. Structural data demonstrate that the N-terminal effector domain of HflX binds to the peptidyl transferase center in a strikingly similar manner as that of the class I release factors and induces dramatic conformational changes in central intersubunit bridges, thus promoting subunit dissociation. Accordingly, loss of HflX results in an increase in stalled ribosomes upon heat shock, These results suggest a primary role of HflX in rescuing translationally arrested ribosomes under stress conditions.. ...
During translation termination the stop codons UAA and UAG are recognised by release factor one (RF1). RF1 binds to the ribosome and mediates the hydrolysis of the nascent peptide from the peptidyl-tRNA. In this process, RF1 interacts directly or indirectly with several ribosomal proteins (r-proteins). To study this interaction in vivo we have used a mutant allele of RF1, prfA1. The mutation causes a temperature sensitive (Ts) phenotype and increased readthrough of the stop codons. A mutant form of r-protein S4 that suppresses this Ts phenotype was isolated. The S4 mutant also increases the readtrough of UAG caused by prfA1. In the mutated S4 allele, rpsD101, Tyr51 is changed to Asp. That change introduces a negatively charged amino acid in a part of S4 that belongs to the positively charged RNA binding surface. This might affect the binding of S4 to the 16S rRNA, to another r-protein, or to RF1, and in that way influence on the function of RF1.. One of the few things known about the regulation ...
Genes are made up of regions of DNA (known as exons), which include the blueprints or "code" for making protein. The researchers found that one individual had a single-letter change at position 1491 in exon 19 of the PTPRQ gene. This mutation results in a sequence called a "stop codon" appearing in an inappropriate position. Stop codons are usually found at the end of sequences that code for proteins and they tell the protein-making machinery of the cell that the instructions for making the protein are finished. Proteins created using the DNA carrying the PTPRQ mutation would be incomplete.. In another individual, the researchers found a single-letter change at position 1369 of exon 19 of the PTPRQ gene. This change was predicted to result in a change in one of the amino acids (the building blocks of proteins) in the PTPRQ-produced protein. The researchers predicted that this change was likely to affect the function of the protein. The region that contained this change had the same amino acid ...
A viral-encoded polymerase (L gene) transcribes the genomic strand of rabies RNA into leader RNA and five capped and polyadenylated mRNAs, which are translated into proteins. Translation, which involves the synthesis of the N, P, M, G and L proteins, occurs on free ribosomes in the cytoplasm. Although G protein synthesis is initiated on free ribosomes, completion of synthesis and glycosylation (processing of the glycoprotein), occurs in the endoplamsic reticulum (ER) and Golgi apparatus. The intracellular ratio of leader RNA to N protein regulates the switch from transcription to replication. When this switch is activated, replication of the viral genome begins. The first step in viral replication is synthesis of full-length copies (postive strands) of the viral genome. When the switch to replication occurs, RNA transcription becomes "non-stop" and stop codons are ignored. The viral polymerase enters a single site on the 3 end of the genome, and proceeds to synthesize full-length copies of the ...
Nonsense Codon: 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.
Recent studies have revealed that endonucleolytic cleavage is a fundamental aspect of nonsense-mediated mRNA decay in eukaryotes (Stevens et al. 2002; Gatfield and Tzaurralde 2004) and trans-translation in prokaryotes (Sunohara et al. 2004). In these cases, the presence of a stop codon somehow promotes endonucleolytic cleavages of mRNA. Similarly, RNase LS in E. coli was suggested to cleave mRNA, depending on a stop codon to accelerate mRNA degradation (Kai and Yonesaki 2002). In this study, we investigated the stop codon-dependent cleavage of T4 soc mRNA by RNase LS and found several characteristic features of the cleavage. First, any stop codon, amber, ochre, or opal, was effective for inducing cleavage at NE. Second, the initiation of translation was required for cleavage, which did not occur when the Shine-Dalgarno sequence was eliminated. Third, cleavage depending on an amber codon was significantly reduced by the presence of amber-codon-suppressing tRNA. All of these results strongly ...
Budiša je utemeljitelj metode ugradnje aminokiselina u proteine (bjelančevine) pod selekcijskim pritiskom (Selective Pressure Incorporation, SPI[8]) koja omogućuje pojedinačne i višestruke[9] in vivo-ugradnje sintetičkih (ili nekanonskih) analoga prirodnih (kanonskih) aminokiselina, po mogućnosti tripletnom prenamjenom (engleski: codon reassignment) smislenih (sense) kodona genetičkog koda (genske upute).[10] Njegova metodologija omogućuje fine kemijske manipulacije aminokiselinskim pokrajnjim ostacima i to uglavnom prolina, triptofana i metionina; često se ti eksperimenti izvode u sklopu jednostavnog metaboličkog inženjerstva.[11][12] Temeljni cilj njegovih istraživanja i inžinjerskog pristupa biologiji jest prijenos tzv. bio-ortogonalnih fizičko-kemijskih svojstava i reakcija (npr. kemoselektivna ligacija kao što je klik-kemija) te prijenos raznih spektroskopskih svojstva (npr. plava[13] i zlatna[14] fluorescencija) u kemiju živih bića. Na taj način se također ...
SWISS-MODEL Template Library (SMTL) entry for 6ogf.1. 70S termination complex with RF2 bound to the UGA codon. Partially rotated ribosome with RF2 bound (Structure III).
The intricate series of events which produce protein from nucleic acid structural information is called translation. The simplicity of this term largely misrepresents the complexity of the underlying...
The bioscaffold application is quite simple and easy. First of all the bioscaffold must be ligated between the two protein encoding sequences and then treated with the restriction enzymes. Essentially it comprises of two steps: Step 1: The left hand side of the bioscaffold has two BpuEI sites incorporated in inverse orientation. This allows upon cleavage with BpuEI the removal of the stop codons from the upstream part and a small sequence from the Bioscaffold. Complementary overhangs are created between the partly cleaved stop codon and the Bioscaffold sequence, which when ligated together convert the stop codon to a Tyrosine amino acid Step 2: Two BseRI sites are incorporated in the right hand side, again in inverse orientation. On BseRI cleavage both upstream and downstream DNA sequences of the BseRI sites will be removed causing the collapse of the Bioscaffold and creating complementary ends between the Bioscaffold and the downstream coding gene. Upon ligation these ends will give a ...
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...
Now catching the case when the best translation contains stop codons. This is usually due to a wrong genetic code, but for the moment its still very difficult to know the genetic code from encoding organelle+organism taxonomy, so this is the temporary solution ...
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.
.. ۞ Regarding a more accurate assessment. Initiation is suppressed at the false start codon due to either the closeness of the upstream stop codon or the suboptimal[?] context of the codon in the development of acquired drug resistance (DR), complexity and uncertainty is valence neutral, meaning to reevaluate where the left and right ought…
Winterling KW, Chafin D, Hayes JJ, Sun J, Levine AS, Yasbin RE, Woodgate R (1998) The Bacillus subtilis DinR binding site: redefinition of the consensus sequence. J Bacteriol 180:2201-11.[PMID:9555905 ...
View Notes - 10) from BIOL 2107H at UGA. Bio Notes (12/2/10) Obsv RR=18 0.58 RB=0 BB=13 2pq=0.49 = 15.2 q2= 0.18 = 5.6 q=freq(B) = 26/52= 0.42 Exp p2= 0.38 = 10.5 p=freq(R)= 36/52= Number of
View Notes - Test 3 notes from PSYC 1101 at UGA. Test3note 17:19 VariationsinConsciousness Psychoactivedrugs:chemicalsubstancesthataltermental,emotionalor behavioralfunctionings o
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Putting yourself down with negative self-talk damages your self-esteem. Find out how to stop the put downs, negative self-talk and build your self-esteem.
For the love of GOD please tell my the indigestion will stop after I give birth.... I have been dealing with this since week 14 and it is literally driving me CRAZY. BTDT moms, when did it end for you?
Effects when you stop taking zoloft - Fast delivery Worldwide. Over the Counter. We have over 800.000 satisfied customers. Free order processing. Visa&MasterCard payment cards.
Sometimes trying your best isnt enough; when the situation demands it, you need to be perfect. Sometimes trying your best isnt enough; when the situation demands it, you need to be perfect. For
After having my first baby my period never returned till she was about 15 months (we breastfeed) and now that it has it has been very irregular. In the
Mitochondrial peptide chain release factor that directs the termination of translation in response to the peptide chain termination codons UAA and UAG.
Approximately one billion people worldwide are homozygous for a stop codon polymorphism in the ACTN3 gene (R577X) which results in complete deficiency of the fast fibre muscle protein α-actinin-3. ACTN3 genotype is associated with human athletic performance and α-actinin-3 deficient mice [Actn3 knockout (KO) mice] have a shift in the properties of fast muscle fibres towards slower fibre properties, with increased activity of multiple enzymes in the aerobic metabolic pathway and slower contractile properties. α-Actinins have been shown to interact with a number of muscle proteins including the key metabolic regulator glycogen phosphorylase (GPh). In this study, we demonstrated a link between α-actinin-3 and glycogen metabolism which may underlie the metabolic changes seen in the KO mouse. Actn3 KO mice have higher muscle glycogen content and a 50% reduction in the activity of GPh. The reduction in enzyme activity is accompanied by altered post-translational modification of GPh, suggesting ...
This protein is identical to GenBank accession AAD18266 (genome position accession AE001598). The peptide chain release factor 1 (RF-1) directs the termination of translation in response to the peptide chain termination codons UAG and UAA. RF-2 (gene prfB) mediates UAA and UGA-dependent termination ...
In 1968, an ad hoc committee of Harvard faculty publicly redefined death as brain death. What interests and issues compelled the redefinition of death, and formed the spirit of this precedent-setting policy ? This paper reports on an historical study of the files of the Harvard ad hoc committee, the proceedings of an international conference on...
The 274 (active) tRNA genes in strain S288C can be grouped into 42 families of distinct codon specificity. The two methionine-specific tRNAs are counted as separate families, as initiator and elongator tRNAs are clearly distinguished both by primary structure and function. No tRNA(Sec) gene has been identified in yeast. No suppressor tRNA genes are found in this strain; Tables 1 and 1a list suppressors that have been identi fied as particular variants in other yeast strains . Table 4a presents a more detailed version of Table 4 by including cross-references to the tRNAs and tRNA genes the sequences of which had been determined prior to the yeast genome project. Figure 2. Codon usage in highly and lowly expressed yeast genes ...
Sup35p is a subunit of the translation termination complex. Its prionic nature has been proposed to have some effect on the stress response, as a possible mechanism to obtain modified genetic expression products. When the prionic conformation is activated, the termination of translation is less effective and thus new longer proteins form (True and Lindquist, 2000, Nature, 407: 477-483; Tyedmers et al., 2008, PLoS Biology, 6: e294). When the sequence corresponding to the NM domains of Sup35p is fused to other gene, the protein resulting of this construction acquires the prionic behaviour (Li and Lindquist, 2000, Science, 287: 661-664). On the other side, GR (Glucocorticoid Receptor) activates the transcription of genes preceded by GRE (Glucocorticoid Receptor Element) when steroid hormones are present (ARTICLE NEEDED). However, it becomes a constitutive transcription activator when it lacks its C terminal ligand-binding domain (Schena and Yamamoto, 1988, Science, 241: 965-967). Because of the ...
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) ...
Example 2: How to find all stop codon lost variants in grain sorghum Ji_2731?. Stop codons (TAG, TAA, TGA) are terminators of protein translation. If one nucleotide in the triplet changes to another one, then this codon may lost the function as a terminator, and encode an abnormal protein. We may find this type of SNP in Ji_2731 for experimental validation. ...
One codon makes up an amino acid. A codon is defined as a sequence of three nucleotides. Taken together, this sequence of nucleotides forms a single unit of genetic code found within a DNA or RNA...
Small-Molecule Modulation of Read-Through (SMMRT): Discovery of 2-Phenoxyacetanilides as In Vivo Promoters of Dystrophin Synthesis for the Treatment of...
MicrobeTV is an independent podcast network for people who are interested in the sciences. Our shows are about science: viruses, microbes, parasites, evolution, urban agriculture, communication, and engineering.. ...
... I have been seeing quite a few posts regarding the dreaded Blue Screen of Death, and what the STOP codes mean. This is a fairly extensive list of the most common stop errors, their corrasponding codes, and recommended solutions. When Windows XP detects a problem from which it cannot recover, it displays Stop messages. These are text-mode error messages that report information about the condition. Stop messages, sometimes referred to as blue
Artificial genetic code, for the first time replicated in a living organism, opens the door to new biological customizations for vaccines and antibiotics.
The genetic code has been regarded as arbitrary in the sense that the codon-amino acid assignments could be different than they actually are. This general idea has been spelled out differently ...
A codon will be flashed on the screen. Think about the amino acid coded by that codon and then click "Show Answer" button to verify the correct answer. Click "Next Question" button to go to the next question (another codon). Repeat the same. If want to learn before taking the test, click "ordered" and then "reset" to see the codons in sequence. To see questions in shuffled order, select "Random". (Total number of questions and the present question No. are displayed at the right hand top corner ...
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.
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2 Answers - Posted in: bleeding disorder, surgery, pradaxa - Answer: You should stop the Pradaxa at least 7 days prior to any surgery. The coag ...
A week or so ago I got curious about why my period was lasting so long. Id have clots and would go through a "heavy flow" pad every hour or so. Depending on the day. Anyway I went to the doctor and got an exam. Nothing was wrong. Everything was fine. I got put on a pill that was suppose to regulate me. Had to take one for ten days. I took my last one today and Im still bleeding. Its let up a little but not too much. I dont know what to do. The doctor said I was fine but I dont think this is fine. I just want it to stop.. ...
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Nonsense‐mediated mRNA decay (NMD) is a cellular surveillance pathway recognizing and degrading mRNAs that fail to terminate translation properly. However, at which termination codons (TCs) and under which circumstances NMD is triggered, and how normal translation termination differs mechanistically from proper termination is still poorly understood. To study the influence of the evolutionarily conserved NMD factors UPF1, UPF2, and UPF3B on translation termination, Neu‐Yilik et al (2017) adopted a fully reconstituted in vitro translation termination system previously developed in the Pestova laboratory (Alkalaeva et al, 2006). In this system, so‐called pre‐termination complexes (pre‐TCs) are assembled from purified mammalian ribosomal subunits, aminoacylated tRNAs, and initiation and elongation factors. These pre‐TCs contain the peptidyl‐tRNA in the P‐site, and the TC is aligned to the A‐site of the ribosome. Ribosomal occupancy at the termination codon can be visualized at ...
Background: This study was conducted to determine whether intravenous gentamicin can suppress stop codons in cystic fibrosis (CF) patients and, if so, whether it has any clinical benefits.. Methods: We first used a dual gene reporter system to determine the gentamicin-induced readthrough level of the most frequent CFTR stop mutations in the French population. We next investigated readthrough efficiency in response to 10 mg/kg once daily intravenous gentamicin perfusions in patients with stop mutations and in a control group of patients without stop mutations. Respiratory function, sweat chloride concentration, nasal potential difference (NPD) and CFTR expression in nasal epithelial cells were measured at baseline and after 15 days of treatment.. Results: After in vitro gentamicin incubation, the readthrough efficiency for the Y122X mutation was at least five times higher than that for G542X, R1162X, and W1282X. In six of the nine patients with the Y122X mutation, CFTR immunodetection showed ...
Increases the formation of ribosomal termination complexes and stimulates activities of RF-1 and RF-2. It binds guanine nucleotides and has strong preference for UGA stop codons. It may interact directly with the ribosome. The stimulation of RF-1 and RF-2 is significantly reduced by GTP and GDP, but not by GMP.
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 ...
Duchenne/Becker muscular dystrophy (DBMD) is a genetic disorder that develops in boys. It is caused by a mutation in the gene for dystrophin, a protein that is important for maintaining normal muscle structure and function. Loss of dystrophin causes muscle fragility that leads to weakness and loss of walking ability during childhood and teenage years. A specific type of mutation, called a nonsense (premature stop codon) mutation, is the cause of DBMD in approximately 10-15% of boys with the disease. Ataluren is an orally delivered, investigational drug that has the potential to overcome the effects of the nonsense mutation. This study comprises a Phase 3, open-label study of ataluren in patients with nmDBMD who previously received ataluren at an investigator site in a prior PTC-sponsored clinical study. A separate open-label study (PTC124-GD-016-DMD) is being conducted for nmDBMD patients who previously received ataluren at an investigator site in the United States (US ...
Hypovirulent isolates of the fruit tree fungal pathogen Diaporthe ambigua have previously been shown to harbour a double-stranded (ds)RNA genetic element of about 4 kb. In this study, we established the complete cDNA sequence of this dsRNA, which represents a replicative form of a positive-strand RNA virus that we have named D. ambigua RNA virus (DaRV). The nucleotide sequence of the genome is 4113 bp and has a GC content of 53%. Two large ORFs are present in the same reading frame. They are most probably translated by readthrough of a UAG stop codon in the central part of the genome. The longest possible translation product (p125) has a predicted molecular mass of about 125 kDa. A significant homology can be found to the non-structural proteins of carmoviruses of the positive-strand RNA virus family Tombusviridae. These proteins also include the conserved RNA-dependent RNA polymerase (RDRP) domain. In contrast to the genome organization of these plant viruses, no ORF is present at the 3′ end of the

Codon usage influences fitness through RNA toxicity | PNASCodon usage influences fitness through RNA toxicity | PNAS

... and variants containing internal stop codons or transcription terminators. Inset in C shows location of toxic sequence element ... Asterisk-marked codons represent the original codon in GFP_170. (C) Growth estimate (OD) of BL21 cells expressing GFP variants ... Many organisms are subject to selective pressure that gives rise to unequal usage of synonymous codons, known as codon bias. To ... As expected, internal stop codons abrogated GFP protein production (Fig. 2C), but despite the presence of premature stop codons ...
more infohttps://www.pnas.org/content/115/34/8639

IS1675, a Novel Lactococcal Insertion Element, Forms a Transposon-Like Structure Including the Lacticin 481 Lantibiotic Operon ...IS1675, a Novel Lactococcal Insertion Element, Forms a Transposon-Like Structure Including the Lacticin 481 Lantibiotic Operon ...

2A). Whereas no putative terminator was identified downstream of the ORF, a Rho-independent terminator-like sequence was ... stop codon. Dots are placed every 20 bp. (B) Similarities between the IS1675-encoded protein and Tpases encoded by the IS4 ... putative Rho-independent terminator. The IS1675-A terminator is omitted because orf8 is divergent. BamHI, EcoRI, EcoRV,HindIII ... Additional single-strand sequencing showed that this gene contains more than 291 codons (Fig.1A, orf9). The encoded protein ...
more infohttps://jb.asm.org/content/182/19/5600?ijkey=3b158016c30fea470a29d2733528102d5c05586b&keytype2=tf_ipsecsha

The RNA code: Natures Rosetta Stone | PNASThe RNA code: Nature's Rosetta Stone | PNAS

V. The role of release factors in mRNA terminator codon recognition. Proc Natl Acad Sci USA 64(4):1235-1241. ... codon) (5). This radioactive complex bound to nitrocellulose membranes creating a simple and rapid means of codon/amino acid ... cleavage from the tRNA required one of three codons, UAA, UGA, or UAG, thus completing the assignment of 64 codons to either an ... 1966) Codon-anticodon pairing: The wobble hypothesis. J Mol Biol 19(2):548-555. ...
more infohttps://www.pnas.org/content/111/16/5758.full

Scarlet fever - WikipediaScarlet fever - Wikipedia

A transcriptional terminator is located 69 bases downstream from the translational termination codon. The carboxy terminal ...
more infohttps://en.wikipedia.org/wiki/Scarlatiniform_rash

INMT Gene - GeneCards | INMT Protein | INMT AntibodyINMT Gene - GeneCards | INMT Protein | INMT Antibody

stop_lost, terminator_codon_variant. rs1000196075. --. 30,754,432(+). C/T. intron_variant. rs1000432477. --. 30,757,828(+). G/C ...
more infohttp://www.genecards.org/cgi-bin/carddisp.pl?gene=INMT

FKRP Gene - GeneCards | FKRP Protein | FKRP AntibodyFKRP Gene - GeneCards | FKRP Protein | FKRP Antibody

stop_lost, terminator_codon_variant. rs104894683. conflicting-interpretations-of-pathogenicity, likely-benign, benign, Limb- ...
more infohttps://www.genecards.org/cgi-bin/carddisp.pl?gene=FKRP

Glossary of biotechnology and genetic engineeringGlossary of biotechnology and genetic engineering

chain terminator 1. Codons which do not code for an amino acid. They signal ribosomes to terminate protein synthesis. The ... See anticodon; initiation codon; termination codon.. codon optimization An experimental strategy in which codons within a ... Also known as stop codons or termination codons. Often two of these codons are found together at the end of a coding sequence ... codon A set of three nucleotides in mRNA, functioning as a unit of genetic coding by specifying a particular amino acid during ...
more infohttp://www.fao.org/docrep/003/X3910E/X3910E06.htm

Brainstorming - 2008.igem.orgBrainstorming - 2008.igem.org

double STOP codon * transcription terminator Adhesion of Streptococcus mutans to hydroxyapatite (HA) Reference PMID 9062560. ...
more infohttp://2008.igem.org/Brainstorming

Ubuntu Manpage:

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

"Is a terminator\n" if $myCodonTable-,is_ter_codon(tar); print "Is a unknown\n" if $myCodonTable-,is_unknown_codon(JTG); ... 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

Must the terminator be in frame?: post #1Must the terminator be in frame?: post #1

Stop codon is there. The terminator comes immediately thereafter, but unfortunately not in frame. What will happen? The manuals ... My vector is self-made and the promoter and terminator are specific. ... Must the terminator be in frame? - posted in Molecular Cloning: I cloned a gene into a vector. ... for some commercial vectors, such as pET, say that the terminator isnt quite necessary. ...
more infohttp://www.protocol-online.org/forums/topic/28848-must-the-terminator-be-in-frame/

Gene expression - ConservapediaGene expression - Conservapedia

... but note that the promoter is not the same thing as the start codon; nor is the RNA polymerase terminator the stop codon. There ... are needed than the 64 possible codons: 64 codons. 20 amino acids. 30 is the compromise made. ... The A and P sites are so close on the ribosome that tRNAs must fit contiguous codons. tRNAs are brought in by EF-Tu (bacteria) ... Stop codons are bound by cytoplasmic release factors, which add water to tRNApeptidyl, cleaving off the polypeptide. ...
more infohttps://www.conservapedia.com/index.php?title=Gene_expression

Heterocyst Pattern Formation Controlled by a Diffusible Peptide | ScienceHeterocyst Pattern Formation Controlled by a Diffusible Peptide | Science

These precedents, and the fact that the fourpatS missense mutations happened to be in the last five codons (Fig. 2B), led us to ... transcription terminator; P with arrow, external promoter. (B) Nucleotide sequence of the smallest tested DNA fragment that is ... patS potentially encodes a 17-amino acid peptide, starting at the first available ATG codon; however, other in-frame ATG and ... GTG codons are present. PatS has no homologs or sequence motifs in the databases. It contains a stretch of five hydrophobic ...
more infohttps://science.sciencemag.org/content/282/5390/935?ijkey=4b0515c86959c8aaecb0d126b89c4bcab2fa0601&keytype2=tf_ipsecsha

pQE-TriSystem Vector - QIAGEN Online ShoppQE-TriSystem Vector - QIAGEN Online Shop

5. Two strong transcriptional terminators. t0 from phage lambda, and T1 from the rrnB operon of E. coli, to prevent read- ... 4. Translational stop codons In all reading frames for convenient preparation of expression constructs. ...
more infohttps://www.qiagen.com/mx/shop/sample-technologies/protein/pqe-trisystem-vector/

pQE-TriSystem Vector - QIAGEN Online ShoppQE-TriSystem Vector - QIAGEN Online Shop

5. Two strong transcriptional terminators. t0 from phage lambda, and T1 from the rrnB operon of E. coli, to prevent read- ... 4. Translational stop codons In all reading frames for convenient preparation of expression constructs. ...
more infohttps://www.qiagen.com/at/shop/sample-technologies/protein/expression-purification-detection/pqe-trisystem-vector/

Bio::PrimarySeqI - search.cpan.orgBio::PrimarySeqI - search.cpan.org

By default all initiation codons found in the given codon table are used but when start is set to some codon this codon will ... Returns : A Bio::PrimarySeqI implementing object Args : -terminator character for terminator, default * -unknown character ... default false -complete_codons boolean, if true, codons which are incomplete are translated if a suitable amino acid is found. ... For instance, if the incomplete codon is GG, the completed codon is GGN, which is glycine (G). Defaults to false; setting ...
more infohttp://search.cpan.org/~cjfields/BioPerl/Bio/PrimarySeqI.pm

530L notes lecture5 - Lecture 5 IX Protein expression A Strains of bacteria 1 Characteristics of cloning strains Ex DH5alpha...530L notes lecture5 - Lecture 5 IX Protein expression A Strains of bacteria 1 Characteristics of cloning strains Ex DH5alpha...

4. NdeI site : CATATG : this ATG is the initiation codon! • Met- • By placing the Aphos gene right after the NdeI gives a good ... 5. T7 terminator : • T7 polymerase binds to T7 promoter, transcribe mRNA that includes the RBS, and from NdeI to XhoI (which ... Component of mRNA near the 5 end, upstream of the initiation codon, where it is bound by the ribosome for translation. ... proximity to the RBS such that the gene is transcribed right after the ATG codon. • Perfect proximity from the promoter and RBS ...
more infohttps://www.coursehero.com/file/6175864/530L-notes-lecture5/

IGEM:MIT/2008/Brainstorming - OpenWetWareIGEM:MIT/2008/Brainstorming - OpenWetWare

double STOP codon. *transcription terminator. Adhesion of Streptococcus mutans to hydroxyapatite (HA). Reference. PMID 9062560 ...
more infohttps://openwetware.org/wiki/IGEM:MIT/2008/Brainstorming

Plus itPlus it

Using the longer ERECTA terminator (1.9 kb) instead of the 35S terminator (∼200 bp) served the purpose of introducing spacer ... pEPFL2:EPFL2 was generated by amplifying a 4.2-kb fragment including 2.5 kb upstream of the EPFL2 start codon and 1 kb ... All promoter/ERECTA/terminator sequences were cloned into pPZP222 between BamHI and XbaI restriction sites. All created ... The endogenous terminator does not have any regulatory sequences as all regulatory elements are localized in the ERECTA ...
more infohttp://www.plantphysiol.org/content/179/1/265

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 ... transcriptional terminators, a promoter, a ribosome binding 5 site, and the coding sequences with the first codon being an ... 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 ...
more infohttp://www.google.es/patents/WO1999052357A1?cl=en

Plus itPlus it

The LSL sequence contains loxP-stop codons-3x SV40 polyA-loxP as transcriptional terminator. The vector map is shown in Figure ...
more infohttp://www.jneurosci.org/content/36/43/11059

METHODS OF TREATING ALZHEIMERS DISEASE AND OTHER TAUOPATHIES WITH INHIBITORS OF MICROTUBULE AFFINITY REGULATING KINASE - THE...METHODS OF TREATING ALZHEIMER'S DISEASE AND OTHER TAUOPATHIES WITH INHIBITORS OF MICROTUBULE AFFINITY REGULATING KINASE - THE...

Examples of transcription terminator/polyadenylation signals include those derived from SV40, as described in Sambrook et al., ... The nucleotide sequence can be designed with the appropriate codons for the particular amino acid sequence desired. The ... to result in the codon for the desired amino acid. Such a change can include as little as one base pair, effecting a change in ... The boundaries of the coding sequence can be determined by a start codon at the 5′ (amino) terminus and a translation stop ...
more infohttp://www.freepatentsonline.com/y2016/0030510.html

Treatment of a coronary condition by delivery of therapeutics to the pericardial space - Chiron CorporationTreatment of a coronary condition by delivery of therapeutics to the pericardial space - Chiron Corporation

Examples of transcription terminator/polyadenylation signals include those derived from SV40, as described in Sambrook et al. ( ... the use of pVL985 which alters the polyhedrin start codon from ATG to ATT, and which introduces a BamHI cloning site 32 ... 0120] Other control elements which may be included in the yeast expression vectors are terminators, for example, from GAPDH and ... to the translation stop codon. Preferably, a sequence for optimization of initiation of translation, located 5′ to the ...
more infohttp://www.freepatentsonline.com/y2003/0060415.html

An aminoacyl-tRNA Synthetase That Specifically Activates Pyrrolysine - PubMedAn aminoacyl-tRNA Synthetase That Specifically Activates Pyrrolysine - PubMed

Methanosarcina barkeri monomethylamine methyltransferase protein in a position that is encoded by an in-frame UAG stop codon in ... Codon, Terminator Actions. * Search in PubMed * Search in MeSH * Add to Search ... tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus Jannaschii N Yu et al. J Bacteriol 201 (9). 2019 ... Pyrrolysine is the 22nd proteinogenic amino acid encoded into proteins in response to amber (TAG) codons in a small number of ...
more infohttps://pubmed.ncbi.nlm.nih.gov/15314242/
  • By placing the Aphos gene right after the NdeI gives a good proximity to the RBS such that the gene is transcribed right after the ATG codon. (coursehero.com)
  • Different pattern of codon recognition by mammalian mitochondrial tRNAs. (mitomap.org)
  • This radioactive complex bound to nitrocellulose membranes creating a simple and rapid means of codon/amino acid assignments. (pnas.org)
  • Maybe you had to struggle, a little, to come to terms with degeneracy of the genetic code, meaning that it is redundant yet not ambi-guous: there are four codons for proline (P or Pro) but none of them codes for another amino acid. (asmblog.org)
  • Because Mfe1 and EcoR1 restriction sites generate compatible sticky ends that when joined cannot be recleaved by either enzyme, by subcloning the synthetic gene as a HinD3 Mfe1 fragment instead of a HinD3 EcoR1 fragment we were able to destroy the EcoR1 site located at the 3' end of the NOS 3' terminator. (igem.org)