Biochemical identification of mutational changes in a nucleotide sequence.
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.
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.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
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.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
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.
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.
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.
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.
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.
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.
Established cell cultures that have the potential to propagate indefinitely.
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.
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.
Deletion of sequences of nucleic acids from the genetic material of an individual.
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.
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.
Proteins found in any species of bacterium.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
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.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
Proteins prepared by recombinant DNA technology.
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
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.
A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed)
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
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.
The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.
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.
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.
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.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
A non-essential amino acid that occurs in high levels in its free state in plasma. It is produced from pyruvate by transamination. It is involved in sugar and acid metabolism, increases IMMUNITY, and provides energy for muscle tissue, BRAIN, and the CENTRAL NERVOUS SYSTEM.
The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.
Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.
Proteins found in any species of virus.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
Proteins obtained from ESCHERICHIA COLI.
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.
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).
The process by which two molecules of the same chemical composition form a condensation product or polymer.
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.
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.
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.
CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)
The facilitation of a chemical reaction by material (catalyst) that is not consumed by the 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.
The rate dynamics in chemical or physical systems.
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.
A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.
Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.
Proteins produced from GENES that have acquired MUTATIONS.
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.
Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.
Transport proteins that carry specific substances in the blood or across cell membranes.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.
Ribonucleic acid that makes up the genetic material of viruses.
Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.
Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.
The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.
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.
The functional hereditary units of BACTERIA.
A species of CERCOPITHECUS containing three subspecies: C. tantalus, C. pygerythrus, and C. sabeus. They are found in the forests and savannah of Africa. The African green monkey (C. pygerythrus) is the natural host of SIMIAN IMMUNODEFICIENCY VIRUS and is used in AIDS research.
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).
A non-essential amino acid occurring in natural form as the L-isomer. It is synthesized from GLYCINE or THREONINE. It is involved in the biosynthesis of PURINES; PYRIMIDINES; and other amino acids.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.
Proteins found in any species of fungus.
Nucleic acid sequences involved in regulating the expression of genes.
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.
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
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.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.
The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.
A type of mutation in which a number of NUCLEOTIDES deleted from or inserted into a protein coding sequence is not divisible by three, thereby causing an alteration in the READING FRAMES of the entire coding sequence downstream of the mutation. These mutations may be induced by certain types of MUTAGENS or may occur spontaneously.
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.
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.
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.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Deoxyribonucleic acid that makes up the genetic material of viruses.
A species of the Chenopodium genus which is the source of edible seed called quinoa. It contains makisterone A and other STEROIDS, some having ECDYSTEROID activity on insects.
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
The part of a cell that contains the CYTOSOL and small structures excluding the CELL NUCLEUS; MITOCHONDRIA; and large VACUOLES. (Glick, Glossary of Biochemistry and Molecular Biology, 1990)
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
Amino acid sequences found in transported proteins that selectively guide the distribution of the proteins to specific cellular compartments.
An essential amino acid occurring naturally in the L-form, which is the active form. It is found in eggs, milk, gelatin, and other proteins.
The process of cleaving a chemical compound by the addition of a molecule of water.
An essential amino acid. It is often added to animal feed.
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.
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
A group of enzymes which catalyze the hydrolysis of ATP. The hydrolysis reaction is usually coupled with another function such as transporting Ca(2+) across a membrane. These enzymes may be dependent on Ca(2+), Mg(2+), anions, H+, or DNA.
Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
The functional hereditary units of VIRUSES.
An enzyme that catalyzes the acetylation of chloramphenicol to yield chloramphenicol 3-acetate. Since chloramphenicol 3-acetate does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase, the enzyme is responsible for the naturally occurring chloramphenicol resistance in bacteria. The enzyme, for which variants are known, is found in both gram-negative and gram-positive bacteria. EC 2.3.1.28.
Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
A non-essential amino acid. In animals it is synthesized from PHENYLALANINE. It is also the precursor of EPINEPHRINE; THYROID HORMONES; and melanin.
Products of proto-oncogenes. Normally they do not have oncogenic or transforming properties, but are involved in the regulation or differentiation of cell growth. They often have protein kinase activity.
A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)
The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN.
The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).
Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.
Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.
A non-essential amino acid that is synthesized from GLUTAMIC ACID. It is an essential component of COLLAGEN and is important for proper functioning of joints and tendons.
A plant genus of the family POACEAE. Folin is the water-soluble extract from Sasa albomarginata. Sasa kurinensis is an ingredient of Sho-ju-sen, a Japanese herbal medicine.
A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.
One of the non-essential amino acids commonly occurring in the L-form. It is found in animals and plants, especially in sugar cane and sugar beets. It may be a neurotransmitter.
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)
Promoter-specific RNA polymerase II transcription factor that binds to the GC box, one of the upstream promoter elements, in mammalian cells. The binding of Sp1 is necessary for the initiation of transcription in the promoters of a variety of cellular and viral GENES.
A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
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).
Actual loss of portion of a chromosome.
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.
The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
An essential amino acid that is required for the production of HISTAMINE.
The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.
Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.
The functional hereditary units of FUNGI.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
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.
An essential amino acid that is physiologically active in the L-form.
A group of enzymes that catalyze the hydrolysis of diphosphate bonds in compounds such as nucleoside di- and tri-phosphates, and sulfonyl-containing anhydrides such as adenylylsulfate. (Enzyme Nomenclature, 1992) EC 3.6.
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.
The process of moving proteins from one cellular compartment (including extracellular) to another by various sorting and transport mechanisms such as gated transport, protein translocation, and vesicular transport.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.
The process by which a DNA molecule is duplicated.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
A species of gram-positive bacteria that is a common soil and water saprophyte.
Protein modules with conserved ligand-binding surfaces which mediate specific interaction functions in SIGNAL TRANSDUCTION PATHWAYS and the specific BINDING SITES of their cognate protein LIGANDS.
An essential branched-chain amino acid important for hemoglobin formation.
Cell lines whose original growing procedure consisted being transferred (T) every 3 days and plated at 300,000 cells per plate (J Cell Biol 17:299-313, 1963). Lines have been developed using several different strains of mice. Tissues are usually fibroblasts derived from mouse embryos but other types and sources have been developed as well. The 3T3 lines are valuable in vitro host systems for oncogenic virus transformation studies, since 3T3 cells possess a high sensitivity to CONTACT INHIBITION.
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)
Single chains of amino acids that are the units of multimeric PROTEINS. Multimeric proteins can be composed of identical or non-identical subunits. One or more monomeric subunits may compose a protomer which itself is a subunit structure of a larger assembly.
Deoxyribonucleic acid that makes up the genetic material of fungi.
Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.
The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.
Short, predominantly basic amino acid sequences identified as nuclear import signals for some proteins. These sequences are believed to interact with specific receptors at the NUCLEAR PORE.
An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition to its crucial roles in metabolism adenosine triphosphate is a neurotransmitter.
A family of anaerobic METHANOCOCCALES whose organisms are motile by means of flagella. These methanogens use carbon dioxide as an electron acceptor.
Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.
A conserved A-T rich sequence which is contained in promoters for RNA polymerase II. The segment is seven base pairs long and the nucleotides most commonly found are TATAAAA.
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.
Products of viral oncogenes, most commonly retroviral oncogenes. They usually have transforming and often protein kinase activities.
A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.
An essential aromatic amino acid that is a precursor of MELANIN; DOPAMINE; noradrenalin (NOREPINEPHRINE), and THYROXINE.
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.
CELL LINE derived from the ovary of the Chinese hamster, Cricetulus griseus (CRICETULUS). The species is a favorite for cytogenetic studies because of its small chromosome number. The cell line has provided model systems for the study of genetic alterations in cultured mammalian cells.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
A broad category of carrier proteins that play a role in SIGNAL TRANSDUCTION. They generally contain several modular domains, each of which having its own binding activity, and act by forming complexes with other intracellular-signaling molecules. Signal-transducing adaptor proteins lack enzyme activity, however their activity can be modulated by other signal-transducing enzymes
Genes that influence the PHENOTYPE both in the homozygous and the heterozygous state.
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).
Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
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.
Proteins encoded by a VIRAL GENOME that are produced in the organisms they infect, but not packaged into the VIRUS PARTICLES. Some of these proteins may play roles within the infected cell during VIRUS REPLICATION or act in regulation of virus replication or VIRUS ASSEMBLY.
A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).
Any method used for determining the location of and relative distances between genes on a chromosome.
Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.
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.
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)
Conversion of an inactive form of an enzyme to one possessing metabolic activity. It includes 1, activation by ions (activators); 2, activation by cofactors (coenzymes); and 3, conversion of an enzyme precursor (proenzyme or zymogen) to an active enzyme.
The first DNA-binding protein motif to be recognized. Helix-turn-helix motifs were originally identified in bacterial proteins but have since been found in hundreds of DNA-BINDING PROTEINS from both eukaryotes and prokaryotes. They are constructed from two alpha helices connected by a short extended chain of amino acids, which constitute the "turn." The two helices are held at a fixed angle, primarily through interactions between the two helices. (From Alberts et al., Molecular Biology of the Cell, 3d ed, p408-9)
Membrane proteins whose primary function is to facilitate the transport of molecules across a biological membrane. Included in this broad category are proteins involved in active transport (BIOLOGICAL TRANSPORT, ACTIVE), facilitated transport and ION CHANNELS.
A plant genus of the family SOLANACEAE. Members contain NICOTINE and other biologically active chemicals; its dried leaves are used for SMOKING.
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.
A metallic element of atomic number 30 and atomic weight 65.38. It is a necessary trace element in the diet, forming an essential part of many enzymes, and playing an important role in protein synthesis and in cell division. Zinc deficiency is associated with ANEMIA, short stature, HYPOGONADISM, impaired WOUND HEALING, and geophagia. It is known by the symbol Zn.
The assembly of VIRAL STRUCTURAL PROTEINS and nucleic acid (VIRAL DNA or VIRAL RNA) to form a VIRUS PARTICLE.
Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.
Virulent bacteriophage and type species of the genus T4-like phages, in the family MYOVIRIDAE. It infects E. coli and is the best known of the T-even phages. Its virion contains linear double-stranded DNA, terminally redundant and circularly permuted.
A non-essential amino acid naturally occurring in the L-form. Glutamic acid is the most common excitatory neurotransmitter in the CENTRAL NERVOUS SYSTEM.
Regions of AMINO ACID SEQUENCE similarity in the SRC-FAMILY TYROSINE KINASES that fold into specific functional tertiary structures. The SH1 domain is a CATALYTIC DOMAIN. SH2 and SH3 domains are protein interaction domains. SH2 usually binds PHOSPHOTYROSINE-containing proteins and SH3 interacts with CYTOSKELETAL PROTEINS.
DNA-binding motifs formed from two alpha-helixes which intertwine for about eight turns into a coiled coil and then bifurcate to form Y shaped structures. Leucines occurring in heptad repeats end up on the same sides of the helixes and are adjacent to each other in the stem of the Y (the "zipper" region). The DNA-binding residues are located in the bifurcated region of the Y.
Proteins which are synthesized as a single polymer and then cleaved into several distinct proteins.
An enzyme that catalyses RNA-template-directed extension of the 3'- end of an RNA strand by one nucleotide at a time, and can initiate a chain de novo. (Enzyme Nomenclature, 1992, p293)
A family of proteins that promote unwinding of RNA during splicing and translation.
Serologic tests in which a positive reaction manifested by visible CHEMICAL PRECIPITATION occurs when a soluble ANTIGEN reacts with its precipitins, i.e., ANTIBODIES that can form a precipitate.
A transferase that catalyzes the addition of aliphatic, aromatic, or heterocyclic FREE RADICALS as well as EPOXIDES and arene oxides to GLUTATHIONE. Addition takes place at the SULFUR. It also catalyzes the reduction of polyol nitrate by glutathione to polyol and nitrite.
The chemical or biochemical addition of carbohydrate or glycosyl groups to other chemicals, especially peptides or proteins. Glycosyl transferases are used in this biochemical reaction.
Amino acids with side chains that are negatively charged at physiological pH.
Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.
A genus of owlet moths of the family Noctuidae. These insects are used in molecular biology studies during all stages of their life cycle.

Correlation between the status of the p53 gene and survival in patients with stage I non-small cell lung carcinoma. (1/15602)

The association of p53 abnormalities with the prognosis of patients with non-small cell lung carcinoma (NSCLC) has been extensively investigated to date, however, this association is still controversial. Therefore, we investigated the prognostic significance of p53 mutations through exons 2 to 11 and p53 protein expression in 103 cases of stage I NSCLC. p53 mutations were detected in 49 of 103 (48%) tumors. Two separate mutations were detected in four tumors giving a total of 53 unique mutations in 49 tumors. Ten (19%) of mutations occurred outside exons 5-8. Positive immunohistochemical staining of p53 protein was detected in 41 of 103 (40%) tumors. The concordance rate between mutations and protein overexpression was only 69%. p53 mutations, but not expression, were significantly associated with a shortened survival of patients (P<0.001). Furthermore, we investigated the correlation between the types of p53 mutations and prognosis. p53 missense mutations rather than null mutations were associated with poor prognosis (P < 0.001 in missense mutations and P=0.243 in null mutations). These results indicated that p53 mutations, in particular missense mutations, rather than p53 expression could be a useful molecular marker for the prognosis of patients with surgically resected stage I NSCLC.  (+info)

Altered trafficking of lysosomal proteins in Hermansky-Pudlak syndrome due to mutations in the beta 3A subunit of the AP-3 adaptor. (2/15602)

Hermansky-Pudlak syndrome (HPS) is a genetic disorder characterized by defective lysosome-related organelles. Here, we report the identification of two HPS patients with mutations in the beta 3A subunit of the heterotetrameric AP-3 complex. The patients' fibroblasts exhibit drastically reduced levels of AP-3 due to enhanced degradation of mutant beta 3A. The AP-3 deficiency results in increased surface expression of the lysosomal membrane proteins CD63, lamp-1, and lamp-2, but not of nonlysosomal proteins. These differential effects are consistent with the preferential interaction of the AP-3 mu 3A subunit with tyrosine-based signals involved in lysosomal targeting. Our results suggest that AP-3 functions in protein sorting to lysosomes and provide an example of a human disease in which altered trafficking of integral membrane proteins is due to mutations in a component of the sorting machinery.  (+info)

p53 status of newly established acute myeloid leukaemia cell lines. (3/15602)

We analysed the status of the p53 gene and protein in eight newly established acute myeloid leukaemia (AML) cell lines representing blast cells of either de novo leukaemia patients in first remission or patients with relapsed and chemotherapy-resistant disease causing their death. There were no mutations in the p53 gene in any of the cell lines as analysed by single-strand conformation polymorphism of amplified exons 5-8. However, the p53 protein was clearly and consistently expressed in all of these cell lines, as shown by immunohistochemistry, Western blotting and flow cytometry. The consistently expressed p53 protein was located in both the nucleus and the cytoplasm of all the cell lines and, as shown by flow cytometry, it was mostly in a conformation typical of the mutated protein. These AML cell lines offer a tool for studying the production and function of the p53 protein and its possible role in cell cycle regulation and chemoresistance as well as in the regulation of apoptosis in AML.  (+info)

Genomic structure and alterations of homeobox gene CDX2 in colorectal carcinomas. (4/15602)

Expression of CDX2, a caudal-related homeobox gene, was found to be decreased in colorectal carcinomas. Heterozygous null mutant mice as to Cdx2 develop multiple intestinal adenomatous polyps. To clarify the role of CDX2 in colorectal carcinogenesis, we determined its genomic structure, and searched for mutations of CDX2 in 49 sporadic colorectal carcinomas and ten hereditary non-polyposis colorectal cancers (HNPCC) without microsatellite instability. None of them exhibited a mutation. We further examined 19 HNPCC carcinomas with microsatellite instability for mutations in a (G)7 repeat site within CDX2. One of them (5.3%) exhibited one G insertion. Loss of heterozygosity was observed in 2 of the 20 (10%) informative sporadic carcinomas, and in one of the three (33.3%) informative HNPCC cancers. These data indicate that CDX2 may play only a minor role in colorectal carcinogenesis.  (+info)

Analysis of TSG101 tumour susceptibility gene transcripts in cervical and endometrial cancers. (5/15602)

Carcinoma of the uterine cervix is a common malignancy among women that has been found to show loss of heterozygosity in the chromosome 11p. Recent studies have localized the TSG101 gene in this region, and also demonstrated a high frequency of abnormalities of this gene in human breast cancer. To determine the role of the TSG101 gene in the carcinogenesis of cervical and uterine carcinoma, 19 cases of cervical carcinoma and five cases of endometrial carcinoma, as well as nearby non-cancerous tissue from the same patients, and 16 blood samples from healthy persons as normal control were analysed by Southern blot analysis of genomic DNA, reverse transcription of the TSG101 mRNA followed by PCR amplification and sequencing of the products. We found that abnormal transcripts of the TSG101 gene were common both in cancerous or non-cancerous tissues of the uterus and cervix and in normal peripheral mononuclear cells. There was no genomic deletion or rearrangement in spite of the presence of abnormal transcripts, and no definite relationship between the abnormal transcripts and HPV infection was found. Although the frequency of abnormal transcripts was higher in cancerous than in non-cancerous tissue, normal peripheral mononuclear cells also had abnormal transcripts. Given these findings, the role of the TSG101 gene as a tumour-suppressor gene should be re-evaluated. Because some aberrant transcripts could be found at the first PCR reaction, we suggest that the aberrant transcripts might be the result of imperfect minor splicesome products.  (+info)

Microsatellite instability, Epstein-Barr virus, mutation of type II transforming growth factor beta receptor and BAX in gastric carcinomas in Hong Kong Chinese. (6/15602)

Microsatellite instability (MI), the phenotypic manifestation of mismatch repair failure, is found in a proportion of gastric carcinomas. Little is known of the links between MI and Epstein-Barr virus (EBV) status and clinicopathological elements. Examination of genes mutated through the MI mechanism could also be expected to reveal important information on the carcinogenic pathway. Seventy-nine gastric carcinomas (61 EBV negative, 18 EBV positive) from local Hong Kong Chinese population, an intermediate-incidence area, were examined. Eight microsatellite loci, inclusive of the A10 tract of type II transforming growth factor beta receptor (TbetaR-II), were used to evaluate the MI status. MI in the BAX and insulin-like growth factor II receptor (IGF-IIR) genes were also examined. High-level MI (>40% unstable loci) was detected in ten cases (12.7%) and low-level MI (1-40% unstable loci) in three (3.8%). High-level MI was detected in two EBV-associated cases (11%) and the incidence was similar for the EBV-negative cases (13%). The high-level MIs were significantly associated with intestinal-type tumours (P = 0.03) and a more prominent lymphoid infiltrate (P = 0.04). Similar associations were noted in the EBV-positive carcinomas. The high-level MIs were more commonly located in the antrum, whereas the EBV-associated carcinomas were mostly located in body. Thirteen cardia cases were negative for both high-level MI and EBV. All patients aged below 55 were MI negative (P = 0.049). Of the high-level MIs, 80% had mutation in TbetaR-II, 40% in BAX and 0% in IGF-IIR. Of low-level MIs, 33% also had TbetaR-II mutation. These mutations were absent in the MI-negative cases. Of three lymphoepithelioma-like carcinomas, two cases were EBV positive and MI negative, one case was EBV negative but with high-level MI. In conclusion, high-level MIs were present regardless of the EBV status, and were found in a particular clinicopathological subset of gastric carcinoma patient. Inactivation of important growth regulatory genes observed in these carcinomas confirms the importance of MI in carcinogenesis.  (+info)

Clinical significance of circulating anti-p53 antibodies in European patients with hepatocellular carcinoma. (7/15602)

p53 alterations are considered to be predictive of poor prognosis in hepatocellular carcinoma (HCC) and may induce a humoral response. Anti-p53 serum antibodies were assessed by enzyme-linked immunosorbent assay (ELISA) using purified recombinant human p53 on 130 European HCC patients before treatment and during the clinical course of the disease. p53 immunohistochemistry was performed on tumours from the 52 patients who underwent surgery, and DNA sequencing analysis was initiated when circulating anti-p53 antibodies were detected. Nine (7%) HCC patients had anti-p53 serum antibodies before treatment. During a mean period of 30 months of follow-up, all the negative patients remained negative, even when recurrence was observed. Of the nine positive patients, eight were still positive 12-30 months after surgery. The presence of anti-p53 serum antibodies was correlated neither with mutation of the p53 gene nor the serum alpha-fetoprotein levels and clinicopathological characteristics of the tumours. However, a greater incidence of vascular invasion and accumulation of p53 protein were observed in the tumours of these patients (P<0.03 and P<0.01 respectively) as well as a better survival rate without recurrence (P = 0.05). In conclusion, as was recently shown in pancreatic cancer, anti-p53 serum antibodies may constitute a marker of relative 'good prognosis' in a subgroup of patients exhibiting one or several markers traditionally thought to be of bad prognosis.  (+info)

Mutations and allelic deletions of the MEN1 gene are associated with a subset of sporadic endocrine pancreatic and neuroendocrine tumors and not restricted to foregut neoplasms. (8/15602)

Endocrine pancreatic tumors (EPT) and neuroendocrine tumors (NET) occur sporadically and rarely in association with multiple endocrine neoplasia type 1 (MEN1). We analyzed the frequency of allelic deletions and mutations of the recently identified MEN1 gene in 53 sporadic tumors including 30 EPT and 23 NET (carcinoids) of different locations and types. Allelic deletion of the MEN1 locus was identified in 18/49 (36.7%) tumors (13/30, 43.3% in EPT and 5/19, 26.3% in NET) and mutations of the MEN1 gene were present in 8/52 (15.3%) tumors (4/30 (13.3%) EPT and 4/22 (18.1%) NET). The somatic mutations were clustered in the 5' region of the coding sequence and most frequently encompassed missense mutations. All tumors with mutations exhibited a loss of the other allele and a wild-type sequence of the MEN1 gene in nontumorous DNA. In one additional patient with a NET of the lung and no clinical signs or history of MEN1, a 5178-9G-->A splice donor site mutation in intron 4 was identified in both the tumor and blood DNA, indicating the presence of a thus far unknown MEN1 syndrome. In most tumor groups the frequency of allelic deletions at 11q13 was 2 to 3 times higher than the frequency of identified MEN1 gene mutations. Some tumor types, including rare forms of EPT and NET of the duodenum and small intestine, exhibited mutations more frequently than other types. Furthermore, somatic mutations were not restricted to foregut tumors but were also detectable in a midgut tumor (15.2% versus 16.6%). Our data indicate that somatic MEN1 gene mutations contribute to a subset of sporadic EPT and NET, including midgut tumors. Because the frequency of mutations varies significantly among the investigated tumor subgroups and allelic deletions are 2 to 3 times more frequently observed, factors other than MEN1 gene inactivation, including other tumor-suppressor genes on 11q13, may also be involved in the tumorigenesis of these neoplasms.  (+info)

Genomic DNA from 97 cases of adult de novo acute myeloid leukaemia (AML) was screened using polymerase chain reaction (PCR) and conformation-sensitive gel electrophoresis (CSGE) for FLT3 exon 20 mutations. Initial sequencing of four cases, representing the spectrum of CSGE abnormalities, revealed ch …
With direct sanger sequencing, FemtoPath PTEN Mutation Screen Kit is able to detect somatic mutation from DNA derived from formalin-fixed paraffin-embedded (FFPET), fine needle biopsy or pleural effusion specimens.. The feature of FemtoPath mutation screen kit ...
DNA Quality Measurement and Somatic Mutation Profiling in PAXgene Tissue Samples with qBiomarker Somatic Mutation PCR Arrays (EN ...
Riken Genesis - SNP genotyping . Riken Genesis has developed a robust technology for gene mutation analysis named F-PHFA, minimizing data inaccuracy .
Here, we describe, in detail, an aggressive GBM that involved the subventricular Inhibitors,Modulators,Libraries zone by which ordinary stem cells reside in. The clinical characterization includes the patients clin ical historical past, diagnosis, brain imaging scientific studies, invasive surgical treatment, and … Continue reading →. ...
TY - JOUR. T1 - Routine multiplex mutational profiling of melanomas enables enrollment in genotype-driven therapeutic trials. AU - Lovly, Christine M.. AU - Dahlman, Kimberly Brown. AU - Fohn, Laurel E.. AU - Su, Zengliu. AU - Dias-Santagata, Dora. AU - Hicks, Donna J.. AU - Hucks, Donald. AU - Berry, Elizabeth. AU - Terry, Charles. AU - Duke, Mar Keesa. AU - Su, Yingjun. AU - Sobolik-Delmaire, Tammy. AU - Richmond, Ann. AU - Kelley, Mark C.. AU - Vnencak-Jones, Cindy L.. AU - Iafrate, A. John. AU - Sosman, Jeffrey. AU - Pao, William. PY - 2012/4/20. Y1 - 2012/4/20. N2 - Purpose: Knowledge of tumor mutation status is becoming increasingly important for the treatment of cancer, as mutation-specific inhibitors are being developed for clinical use that target only sub-populations of patients with particular tumor genotypes. Melanoma provides a recent example of this paradigm. We report here development, validation, and implementation of an assay designed to simultaneously detect 43 common somatic ...
TY - JOUR. T1 - Analysis of pathway mutation profiles highlights collaboration between cancer-associated superpathways. AU - Gu, Yunyan. AU - Zhao, Wenyuan. AU - Xia, Jiguang. AU - Zhang, Yuannv. AU - Wu, Ruihong. AU - Wang, Chenguang. AU - Guo, Zheng. PY - 2011/9/1. Y1 - 2011/9/1. N2 - The biological interpretation of the complexity of cancer somatic mutation profiles is a major challenge in current cancer research. It has been suggested that mutations in multiple genes that participate in different pathways are collaborative in conferring growth advantage to tumor cells. Here, we propose a powerful pathway-based approach to study the functional collaboration of gene mutations in carcinogenesis. We successfully identify many pairs of significantly comutated pathways for a large-scale somatic mutation profile of lung adenocarcinoma. We find that the coordinated pathway pairs detected by comutations are also likely to be coaltered by other molecular changes, such as alterations in multifunctional ...
The Suppression Subtractive Hybridization (SSH) method has previously been used to generate tissue-specific cDNA libraries and to compare gene expression in different types of tissues. We propose that the SSH method can be modified to serve as a mutation detection method. This modified SSH method would scan the entire genome for sequence disruptions in DNA. Two plasmids have been chosen to serve as a model system. One plasmid is a PGL-2 plasmid, and the second plasmid is a PGL-2 plasmid that contains a 935 base pair (bp) segment of the G6PDH gene. The goal of this project is to detect the 935 bp insert in the PGL-2 plasmid. The purpose of the plasmid model system is to demonstrate that the modified SSH method is feasible, and successful as a mutation detection method.
Purpose: : To identify and characterize the gene mutation responsible for photoreceptor degeneration in the rd3 mouse. Methods: : We screened genes in the known rd3 (RBF/DnJ) mapped region by direct sequencing. We additionally screened other rd3 lines (RBJ/Dn, STOCK Rb(11.13)4Bnr/J and STOCK In(5)30Rk) and normal mouse strains to verify the alteration. We carried out a mutation screen of the human RD3 gene in patients with retinopathies and examined 431 patients of Caucasian ethnicity and 103 of Asian-Indian ancestry. Amino acid changes that were identified in patients but not in controls are being examined by immunoblot analysis and immunocytochemisty to determine their effect(s) on protein stability or localization. Results: : The rd3 mutation is a homozygous C to T transition, leading to a stop codon, which is predicted to result in a premature truncation of the rd3 protein. The mutation was present in all rd3 lines tested (RBF/DnJ, RBJ/Dn, 4bnr and IN-30) but not in the control lines ...
|p>p53 is a tumor suppressor protein encoded by the TP53 gene that responds to DNA damage by regulating cell-cycle arrest, apoptosis and senescence. These p53 Hotspot Mutation Cell Panels are composed of select cell lines derived from tumors of various tissue origins. The p53 mutational status of these lines have been sequenced and validated by ATCC.|/p>
|p>p53 is a tumor suppressor protein encoded by the TP53 gene that responds to DNA damage by regulating cell-cycle arrest, apoptosis and senescence. These p53 Hotspot Mutation Cell Panels are composed of select cell lines derived from tumors of various tissue origins. The p53 mutational status of these lines have been sequenced and validated by ATCC.|/p>
Vorkas, P.A.; Poumpouridou, N.; Agelaki, S.; Kroupis, C.; Georgoulias, V.; Lianidou, E.S., 2010: PIK3CA hotspot mutation scanning by a novel and highly sensitive high-resolution small amplicon melting analysis method
Health,...Unknown mutations may account for increased odds researchers say ...MONDAY Nov. 17 (HealthDay News) -- The risk of breast cancer for a wo...And in women younger than age 40 without the BRCA mutations but with ...Over a six-year period the researchers followed up nearly 1500 wome...,Family,History,Ups,Breast,Cancer,Risk,Even,Without,BRCA,Gene,medicine,medical news today,latest medical news,medical newsletters,current medical news,latest medicine news
In this presentation from the 18th European Congress: Perspectives in Lung Cancer, Dr. Céline Mascaux discusses treatment strategies in both the front line and relapse settings of EGFR+ tumors. Earn CME Credit for a related activity: http://elc.imedex.com/ELC/S... © 2017 Imedex, LLC.
truediamond - Patient: Colorectal (Colon) Cancer > Adenocarcinoma Patient Info: Newly diagnosed (has not begun treatment), Diagnosed: about 8 years ago, Female, Age: 54, KRAS mutation positive: Dont Know, BRAF mutation positive: Dont Know, Stage II
/PRNewswire/ -- Collaboration aims to create and commercialize companion diagnostic using genomic data from plasma samples to guide the use of IRESSA for...
The first p53 gene mutation arising in a human tumor was described a decade ago by Baker et al. [S.J. Baker, E.R. Fearon, J.M. Nigro, S.R. Hamilton, A.C. Preisinger, J.M. Jessup, P. van Tuinen, D.H. Ledbetter, D.F. Barker, Y. Nakamura, R. White, B. Vogelstein, Chromosome 17 deletions and p53 gene mu …
Several microarrays have been developed recently to capture various panels of HRD genes.14,15,31-33 Most of these arrays were generated on the Affymetrix resequencing chip platform (Affymetrix, Inc., Cleveland, OH).15,31,32 The nucleotide call rates for the previously reported resequencing chips ranged from 90% to 99%.15 The RDs189-array yielded superior call rates (,99.9%), presumably due to the removal of repetitive elements (see Supplementary Material and Supplementary Table S3). The high call rates of the RDs189-array demonstrate that it is able to capture efficiently nearly all the targeted sequences of the 189 genes. Compared with the aforementioned earlier capture arrays,14,15,31,33 the RDs189-array has a significantly expanded panel of targeted genes including, to our knowledge, all known HRD related genes, and, thus, can be applied to almost all types of HRD patients. Also, simultaneously screening all known HRD genes will theoretically increase the mutation detection rates. Indeed, ...
At least two teams of scientists have been exploring the ability of 454 Life Sciences platform to detect mutations in tumors, testing the potential advantages of massively parallel sequencing over tra
This paper presents a mutation analysis tool based on a reflective macro system. Mutation analysis is a powerful and computationally expensive technique th
No all any recurrent mutations are cancer hotspots, say researchers who have demonstrated that putting recurrent mutations into genomic context can distinguish between passengers and drivers of cancer
The FATE gene maps to Xq28 where one case of a translocation breakpoint has been found in an infertile man. Moreover, the FATE promoter contains a putative SF-1-binding site, and F
The technology could eventually have applications in pathology as well as field-based diagnostic testing for infectious diseases.
TY - JOUR. T1 - Targeted mutational profiling of peripheral T-cell lymphoma not otherwise specified highlights new mechanisms in a heterogeneous pathogenesis. AU - Schatz, J. H.. AU - Horwitz, S. M.. AU - Teruya-Feldstein, J.. AU - Lunning, M. A.. AU - Viale, A.. AU - Huberman, K.. AU - Socci, N. D.. AU - Lailler, N.. AU - Heguy, A.. AU - Dolgalev, I.. AU - Migliacci, J. C.. AU - Pirun, M.. AU - Palomba, M. L.. AU - Weinstock, D. M.. AU - Wendel, H. G.. PY - 2015/1/10. Y1 - 2015/1/10. UR - http://www.scopus.com/inward/record.url?scp=84920670383&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=84920670383&partnerID=8YFLogxK. U2 - 10.1038/leu.2014.261. DO - 10.1038/leu.2014.261. M3 - Letter. C2 - 25257991. AN - SCOPUS:84920670383. VL - 29. SP - 237. EP - 241. JO - Leukemia. JF - Leukemia. SN - 0887-6924. IS - 1. ER - ...
In this second part of our two-part review, we discuss the use of mutation profiling in the diagnosis, prognosis, and treatment of patients with myeloproliferative neoplasms and other myeloid diseases.
van der Klift, H. M., Mensenkamp, A. R., Drost, M., Bik, E. C., Vos, Y. J., Gille, H. J. J. P., Redeker, B. E. J. W., Tiersma, Y., Zonneveld, J. B. M., Garcia, E. G., Letteboer, T. G. W., Olderode-Berends, M. J. W., van Hest, L. P., van Os, T. A., Verhoef, S., Wagner, A., van Asperen, C. J., ten Broeke, S. W., Hes, F. J., ... Tops, C. M. J. (2016). Comprehensive Mutation Analysis of PMS2 in a Large Cohort of Probands Suspected of Lynch Syndrome or Constitutional Mismatch Repair Deficiency Syndrome. Human Mutation, 37(11), 1162-1179. https://doi.org/10.1002/humu.23052 ...
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Background: AML is a clinically and genetically heterogeneous clonal disorder. Approximately 50% are characterized by recurrent clonal chromosome aberrations which have contributed to the classification of disease and are recognized as important prognostic factors. AML patients who lack these recurrent structural abnormalities have been grouped as intermediate cytogenetic risk and are being further subcategorized by the sequence alterations that are being identified. A more complete understanding of the genetic changes that are relevant to the pathogenesis of AML will improve the classification of risk and ultimately better selection of therapy. Our hypothesis is that mutational profiling and analysis of patient outcomes will help better define the risk subgroups of patients and predict prognosis in patients with AML.. Methods: Archived DNA from 37 patients with various AML diagnoses were obtained with IRB approval (IRB#201502763). A panel of 30 commonly mutated genes in AML were designed ...
OncoSpot™ cancer biomarker mutant cell lines carry CRISPR-mediated hotspot mutations in tumor biomarkers, including EGFR, KRAS, BRAF and more.
Mutational profiling can improve risk stratification and inform prognostic and therapeutic decisions regarding patients with AML.
Cancer cells are constantly dying, and their liberated DNA enters the blood stream where it is quickly broken down into minute fragments of DNA with two distinct sizes: ~ 140bp and 35bp. The cancer mutations can be located anywhere along the length of the DNA fragments, and be present at extremely low concentrations.. MutantDx uses its patented PrimaCap technology to detect tumor mutations in DNA fragments of all sizes, irrespective of their location, and at femtogram concentration. This is an unmatched capability. ...
Google Form to fill in, please and thank you! Get any many hands as you can, please. Both of your own, and all available family members. Need something to entertain the kids on a rainy day? Get them to take the measurements ...
Beales PL et al. (2001) Genetic and mutational analyses of a large multiethnic Bardet-Biedl cohort reveal a minor involvement of BBS6 and delineate the critical intervals of other loci.. [^] ...
Beales PL et al. (2001) Genetic and mutational analyses of a large multiethnic Bardet-Biedl cohort reveal a minor involvement of BBS6 and delineate the critical intervals of other loci.. [^] ...
Histone 3.3 (H3.3) hotspot mutations in bone tumors occur in the vast majority of giant cell tumors of bone (GCTBs; 96%), chondroblastomas (95%) and in a few cases of osteosarcomas. However, clinical presentation, histopathological features, and additional molecular characteristics of H3.3 mutant osteosarcomas are largely unknown. In this multicentre, retrospective study, a total of 106 conventional high-grade osteosarcomas, across all age groups were re-examined for hotspot mutations in the H3.3 coding genes H3F3A and H3F3B. H3.3 mutant osteosarcomas were re-evaluated in a multidisciplinary manner and analyzed for genome-wide DNA-methylation patterns and DNA copy number aberrations alongside H3.3 wild-type osteosarcomas and H3F3A G34W/L mutant GCTBs. Six osteosarcomas (6/106) carried H3F3A hotspot mutations. No mutations were found in H3F3B. All patients with H3F3A mutant osteosarcoma were older than 30 years with a median age of 65 years. Copy number aberrations that are commonly encountered in high
TY - JOUR. T1 - Mutational analysis of EGFR and related signaling pathway genes in lung adenocarcinomas identifies a novel somatic kinase domain mutation in FGFR4. AU - Marks, Jenifer L.. AU - McLellan, Michael. AU - Zakowski, Maureen F.. AU - Lash, Alex E.. AU - Kasai, Yumi. AU - Broderick, Stephen. AU - Sarkaria, Inderpal S.. AU - Pham, Duy Khanh. AU - Singh, Bhuvanesh. AU - Miner, Tracie L.. AU - Fewell, Ginger A.. AU - Fulton, Lucinda L.. AU - Mardis, Elaine R.. AU - Wilson, Richard K.. AU - Kris, Mark G.. AU - Rusch, Valerie W.. AU - Varmus, Harold. AU - Pao, William. PY - 2007/5/9. Y1 - 2007/5/9. N2 - Background. Fifty percent of lung adenocarcinomas harbor somatic mutations in six genes that encode proteins in the EGFR signaling pathway, i.e., EGFR, HER2/ERBB2, HER4/ERBB4, PIK3CA, BRAF, and KRAS. We performed mutational profiling of a large cohort of lung adenocarcinomas to uncover other potential somatic mutations in genes of this signaling pathway that could contribute to lung ...
When performing somatic mutation detection by qPCR, your experiments success can be impacted by the method you use. The most sensitive and reliable method for somatic mutation analysis is real-time PCR. Mutation detection with qPCR enables pathway- or disease-focused profiling of somatic mutation status. Our assays and panels for somatic mutation analysis enable you to identify the presence of individual specific sequence mutations present in cell lines or research samples that are critical for toxicological, drug development and cancer studies.
The usefulness of liquid biopsy to detect mutations from cancer patients has been well recognized today. However, because the mutation detection rates from plasma DNA were relatively lower than those of tissue re-biopsy, its clinical utility has not been confirmed yet. As previously we reported, we have developed fully automatic high-sensitive point mutation detecting system named mutation-biased PCR and quenched probe (MBP-QP) system for liquid biopsy. Recently, the importance of pre-analytical procedures for plasma DNA anazysis has been highlighted. In this study, we examined whether the automatic DNA extraction system can improve the mutation detection rate in our MBP-QP system. Sixty-one plasma samples were obtained from advanced non-small cell lung cancer patients, and plasma DNA extraction was performed from 200μl plasma by manually (200-M), and 200μl (200-A), 1000μl (1000-A) plasma by automatically. We used silica membrane spin column system for manual DNA extraction, and magnet beads ...
A fundamental task in precision oncology is to perform mutation profiling of tumors, which traditionally requires invasive tumor biopsy. Liquid biopsy, which requires a simple blood draw, provides a surrogate option for tumor biopsy. Liquid biopsy is noninvasive, repeatable, and especially useful when a tumors location makes tissue biopsy unfeasible.. However, the mutation profiling of cell-free DNA (cfDNA) is challenging, as conventional mutation callers are primarily designed for the mutation calling of genomic DNA. Unlike tumor biopsy, cfDNA is a mixture of DNA derived from tumors and that from normal cells, where tumor-derived cfDNA accounts for a minor fraction. As a result, mutations from tumors have weak signals in blood samples and are therefore hard to identify using conventional methods.. To address this challenge, in our recent work published in Nature Communications [1], we present cfSNV, a cfDNA somatic single nucleotide variant (SNV) caller with five innovative techniques to ...
The allele-specific PCR also called as an ARMS- PCR (amplification refractory mutation system) or PASA (PCR amplification of specific alleles) or AS-PCR used to detect the SNPs. More specifically, it…. ...
Comprehensive mutational profiling data now available on all major cancers have led to proposals of novel molecular tumor classifications that modify or replace the established organ- and tissue-based tumor typing. The rationale behind such molecular reclassifications is that genetic alterations underlying cancer pathology predict response to therapy and may therefore offer a more precise view on cancer than histology. The use of individual actionable mutations to select cancers for treatment across histotypes is already being tested in the so-called basket trials with variable success rates. Here, we present a computational approach that facilitates the systematic analysis of the histological context dependency of mutational effects by integrating genomic and proteomic tumor profiles across cancers. To determine effects of oncogenic mutations on protein profiles, we used the energy distance, which compares the Euclidean distances of protein profiles in tumors with an oncogenic mutation (inner distance)
Comprehensive mutational profiling data now available on all major cancers have led to proposals of novel molecular tumor classifications that modify or replace the established organ- and tissue-based tumor typing. The rationale behind such molecular reclassifications is that genetic alterations underlying cancer pathology predict response to therapy and may therefore offer a more precise view on cancer than histology. The use of individual actionable mutations to select cancers for treatment across histotypes is already being tested in the so-called basket trials with variable success rates. Here, we present a computational approach that facilitates the systematic analysis of the histological context dependency of mutational effects by integrating genomic and proteomic tumor profiles across cancers. To determine effects of oncogenic mutations on protein profiles, we used the energy distance, which compares the Euclidean distances of protein profiles in tumors with an oncogenic mutation (inner distance)
This study presents a comprehensive survey and comparison of oncogene mutation profiles between primary colorectal cancers and metastases from commonly resected distant sites, including the liver, lung, and brain. Consistent with oncogene profiling studies in primary colorectal cancers, BRAF, KRAS, NRAS, and PIK3CA were identified as the main mutation targets in metastases, and somatic changes in the MAPK pathway members BRAF, KRAS, and NRAS were mutually exclusive (30, 31). Overall oncogene mutation status was greater than 88% concordant between primary cancer and distant metastasis from the same patient, suggesting that these activating mutations are generally acquired prior to metastatic spread. Our data are consistent with the high level of concordance between primary colorectal cancers and distant secondary deposits previously reported for KRAS and BRAF mutations (32-35), confirming that mutation testing of primary tumor is a reasonable surrogate for treatment decisions in metastatic ...
Analysis of mutation data.(A) Clustering of whole exome sequencing mutation data based on the mutation status of the genes in P0 and P1 samples of four models.
In this study, the clinical characteristics, laboratory data and genetic features of 65 patients with CHI, the largest CHI cohort from southern China, were reported. Until now, there have been no nationwide data regarding this disorder in China, although several studies have summarized the clinical and genetic characteristics of CHI in northern and eastern China (20,21,22).. In our cohort of patients with CHI, 32.8% were noted to have disease-causing mutations: 16 (25%) patients were positive for ABCC8 mutations; five (7.8%) were positive for GLUD1 mutations; and 44 (67%) were negative for GCK, GLUD1, ABCC8 and KCNJ11 mutations in the gene analysis. No mutations were found in the KCNJ11 gene in this study. As described in previous studies, most of the mutations identified have been detected in the KATP channel. The mutation detection rates of ABCC8 and KCNJ11 genes reported by Kapoor et al (6) and by Snider et al (26) were 36.3% (109/300) and 69% (288/417), respectively. However, in a similar ...
A. There are plausible disease-causing mutations(i) within, affecting or encompassing an interpretable functional region(ii) of this gene identified in multiple (,3) unrelated cases/families with the phenotype(iii).. OR. B. There are plausible disease-causing mutations(i) within, affecting or encompassing cis-regulatory elements convincingly affecting the expression of a single gene identified in multiple (,3) unrelated cases/families with the phenotype(iii).. OR. C. As definitions A or B but in 2 or 3 unrelated cases/families with the phenotype, with the addition of convincing bioinformatic or functional evidence of causation e.g. known inborn error of metabolism with mutation in orthologous gene which is known to have the relevant deficient enzymatic activity in other species; existence of an animal model which recapitulates the human phenotype.. AND. D. Evidence indicates that disease-causing mutations follow a Mendelian pattern of causation appropriate for reporting in a diagnostic ...
SAN DIEGO, July 3, 2012 /PRNewswire/ -- Trovagene to Study Trans-Renal KRAS Mutation Detection in Pancreatic Cancer. Study will compare detection of KRAS...
A. There are plausible disease-causing mutations(i) within, affecting or encompassing an interpretable functional region(ii) of this gene identified in multiple (,3) unrelated cases/families with the phenotype(iii).. OR. B. There are plausible disease-causing mutations(i) within, affecting or encompassing cis-regulatory elements convincingly affecting the expression of a single gene identified in multiple (,3) unrelated cases/families with the phenotype(iii).. OR. C. As definitions A or B but in 2 or 3 unrelated cases/families with the phenotype, with the addition of convincing bioinformatic or functional evidence of causation e.g. known inborn error of metabolism with mutation in orthologous gene which is known to have the relevant deficient enzymatic activity in other species; existence of an animal model which recapitulates the human phenotype.. AND. D. Evidence indicates that disease-causing mutations follow a Mendelian pattern of causation appropriate for reporting in a diagnostic ...
Mutation detection is increasingly undertaken in a wide spectrum of research areas: in medicine it is fundamental in isolating disease genes and diagnosis, and is especially important in cancer research; in biology, commercially important genes can be identified by the mutations they contain. But mutation detection is time-consuming and expensive.
This mutation was identified by sequencing in a CF newborn who was compound heterozygous for p.Gly542X and 2380_2387del. This polymorphism was found on the same allele as 2380_2387del ...
Sequence Variation is sometimes designated as polymorphism, indicating that it is non-disease causing. According to the general definition in human genetics, a polymorphism has to reach an allelic frequency of 1%. In addition, when a sequence variation is found in one single individual, it is not possible to determine if it is non-disease causing ...
This substitution, located in a transmembrane domain and which seems conservative, was found in a CBAVD patient heterozygous for ^ÐF508, but chromosomal assignment was not possible. Eight coding regions remain to be analysed. V920L creates a MaeII restriction site ...
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Dear all,. please could you recommend any packages in R (and BioC) that are specialized on displaying various mutation profiles (eg heatmaps of mutations vs samples, frequency of mutations etc ;) thank you !. -- bogdan. ...
A recent review in Oncogene discusses how fasting may help patients who have been diagnosed with cancer. This is interesting, because at the moment most people are advised to eat extra calories and proteins while undergoing cancer treatments. It turns out that in animals fasting changes the physiology of the body and this can help protect normal cells from the damaging effects of anti-cancer agents. The amazing thing is that cancer cells are abnormal and dont get the same protection, so fasting seems to be a way to help normal cells and not help the targets of the treatment. It More ,. ...
Revision: 7352 http://octave.svn.sourceforge.net/octave/?rev=7352&view=rev Author: schloegl Date: 2010-05-26 19:49:16 +0000 (Wed, 26 May 2010) Log Message: ----------- better sanity checks; more tests; obsolete functions removed; Modified Paths: -------------- trunk/octave-forge/extra/oct2mat/inst/generate_basics.m trunk/octave-forge/extra/oct2mat/inst/oct2mat trunk/octave-forge/extra/oct2mat/inst/test_oct2mat.m Property Changed: ---------------- trunk/octave-forge/extra/oct2mat/inst/freetb4matlab.m trunk/octave-forge/extra/oct2mat/inst/generate_basics.m trunk/octave-forge/extra/oct2mat/inst/test_oct2mat.m Property changes on: trunk/octave-forge/extra/oct2mat/inst/freetb4matlab.m ___________________________________________________________________ Added: svn:keywords + Id Modified: trunk/octave-forge/extra/oct2mat/inst/generate_basics.m =================================================================== --- trunk/octave-forge/extra/oct2mat/inst/generate_basics.m 2010-05-26 18:11:50 UTC (rev 7351) ...
Hi, Im not sure what your question is, but Id not use a 1996 article as statement of the state of the art. Not all viruses can can mix with others; on the other hand many viruses mutation rate...
최근에 병원의 의료 현장에서 NGS 타겟 시퀀싱 패널을 이용하면서 다양한 유전자들을 동시에 검사하는 건수가 폭발적으로 증가하고 있습니다. 다만 안타깝게도 많은 경우에 실제로 그 유전체 정보와 데이터를 충분히 활용하지 못하고 있음을 많이 느낍니다. 즉, 돈을 들여서 구축된 파이프 라인을 통해서 유전체 데이터 생산은 되는데, 이후에 변이들에 대한 적절한 해석을 하고, 환자에 적용하는데 까지는 아직 더 경험이 필요한 것…
A -young -woman -aged 21 was -found to be a new car-rier of Hb-Belfast: β 15 (A 12) Trp-Arg, and the char-ac-ter-is-tics of her hemo-glob-i-nop-athy -were not dif-ferent -from -those of the -four -cases so far -described: -mild hemol-ysis -with molec-ular -instability of the -abnormal Hb, red -cells inclu-sion -bodies, and -slight alter-a-tions of -some func-tional param-e-ters of -whole -blood. On -this occa-sion, -direct DNA anal-ysis indi-cated the -genomic nucle-o-tide replace-ment of the dis-ease: TGG-AGG. This was inherited by the -mother, orig-i-nating -from Bari (Apulia).. ...
A mutational analysis of the FLP binding site". Journal of Molecular Biology. 201 (2): 405-21. doi:10.1016/0022-2836(88)90147-7 ... The nucleophilic properties of the tyrosine attack and bind to the 3'-phosphate at the point of DNA cleavage. The resulting 5'- ... hydroxyl group of the cleaved DNA acts as the nucleophile and attacks the 3'-phosphate on the complementarily cleaved DNA ... It does so by causing recombination between the two inverted repetitions on the 2 µ plasmid during DNA replication. This ...
1999). "Mutational analysis of cysteine-string protein function in insulin exocytosis". J. Cell Sci. 112 (9): 1345-51. PMID ... 2002). "The DNA sequence and comparative analysis of human chromosome 20". Nature. 414 (6866): 865-71. doi:10.1038/414865a. ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... 2001). "Characterization of long cDNA clones from human adult spleen". DNA Res. 7 (6): 357-66. doi:10.1093/dnares/7.6.357. PMID ...
Shen ES, Whitlock JP (April 1992). "Protein-DNA interactions at a dioxin-responsive enhancer. Mutational analysis of the DNA- ... Analysis of six bona fide DNA-binding sites for the liganded Ah receptor". The Journal of Biological Chemistry. 268 (9): 6575- ... "In vitro analysis of Ah receptor domains involved in ligand-activated DNA recognition". Proceedings of the National Academy of ... The first is the basic-region (b), which is involved in the binding of the transcription factor to DNA. The second is the helix ...
Molkentin JD, Black BL, Martin JF, Olson EN (Jun 1996). "Mutational analysis of the DNA binding, dimerization, and ... Molkentin JD, Li L, Olson EN (Jul 1996). "Phosphorylation of the MADS-Box transcription factor MEF2C enhances its DNA binding ...
Miyamoto I, Miura N, Niwa H, Miyazaki J, Tanaka K (Jun 1992). "Mutational analysis of the structure and function of the ... "Analysis of a human DNA excision repair gene involved in group A xeroderma pigmentosum and containing a zinc-finger domain". ... "Enhancement of damage-specific DNA binding of XPA by interaction with the ERCC1 DNA repair protein". Biochemical and ... "Enhancement of damage-specific DNA binding of XPA by interaction with the ERCC1 DNA repair protein". Biochemical and ...
2009 ; 582 : 49-57 Mutational analysis of the preferential binding of human topoisomerase I to supercoiled DNA. Yang Z, Carey ... Effects of DNA and protein size on substrate cleavage by human tyrosyl-DNA phosphodiesterase 1. Interthal H, Champoux JJ The ... DNA Topoisomerases: Structure, Function, and Mechanism, Vol. 70:369-413 (Volume publication date July 2001). Annual review of ... 2009 Nov; 284 47: 32225-38 Assays for the preferential binding of human topoisomerase I to supercoiled DNA. Yang Z, Champoux JJ ...
PMID 11780052.} Soung YH, Lee JW, Kim SY (2006). "Mutational analysis of the kinase domain of MYLK2 gene in common human ... Deloukas P, Matthews LH, Ashurst J (2001). "The DNA sequence and comparative analysis of human chromosome 20". Nature. 414 ( ... Strausberg RL, Feingold EA, Grouse LH (2002). "Generation and initial analysis of more than 15,000 full-length human and mouse ... Jeronimo C, Forget D, Bouchard A (2007). "Systematic analysis of the protein interaction network for the human transcription ...
2001). "Genomic structure and mutational analysis of the human KIF1B gene which is homozygously deleted in neuroblastoma at ... The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro". DNA Res. 5 (1): 31-9. doi ... 2004). "Genomic structure and mutational analysis of the human KIF1Balpha gene located at 1p36.2 in neuroblastoma". Int. J. ... The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Res. 7 (2): 143-50. doi: ...
2006). "DNA sequence and analysis of human chromosome 8". Nature. 439 (7074): 331-5. doi:10.1038/nature04406. PMID 16421571. ... 2007). "Mutational analysis of the HGSNAT gene in Italian patients with mucopolysaccharidosis IIIC (Sanfilippo C syndrome). ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... DNA Res. 12 (2): 117-26. doi:10.1093/dnares/12.2.117. PMID 16303743. Kimura K, Wakamatsu A, Suzuki Y, et al. (2006). " ...
... and Genome Data Analysis Centers. Each cancer type will undergo comprehensive genomic characterization and analysis. The data ... COSMIC also includes mutational data published in scientific literature. The TCGA is a multi-institutional effort to understand ... It is a biochemical laboratory method for the characterization and identification of the DNA or RNA sequences of cancer cell(s ... This analysis can be used to make pharmacological treatment recommendations. As of February 2012, this has only been done for ...
Haber DA, Velculescu VE (June 2014). "Blood-based analyses of cancer: circulating tumor cells and circulating tumor DNA". ... "Mutational analysis of the tyrosine kinome in colorectal cancers". Science. 300 (5621): 949. doi:10.1126/science.1082596. PMID ... Ding L, Wendl MC, Koboldt DC, Mardis ER (October 2010). "Analysis of next-generation genomic data in cancer: accomplishments ... SAGE contributed to the development of next-generation sequencing methods used for genome-wide expression analyses. In the ...
... mutational analysis introduces single/double mutations outside the ribozyme to ensure the observed ribozyme activity is ... Second, a series of DNA oligomer complementary to different regions of AS1/2 were used to rescue the ribozyme activity; the ... Rajagopal P, Feigon J (June 1989). "Triple-strand formation in the homopurine:homopyrimidine DNA oligonucleotides d(G-A)4 and d ... Sklenár V, Feigon J (June 1990). "Formation of a stable triplex from a single DNA strand". Nature. 345 (6278): 836-838. Bibcode ...
NUE's activity depends on 4 relevant sites which have been identified by mutational analysis. The transcriptional factor Pax8 ... There are some mutations in the NIS DNA that cause hypothyroidism and thyroid dyshormonogenesis. Moreover, antibodies anti-NIS ... De La Vieja A, Dohan O, Levy O, Carrasco N (2000). "Molecular analysis of the sodium/iodide symporter: impact on thyroid and ... 1998). "Identification of a structural requirement for thyroid Na+/I- symporter (NIS) function from analysis of a mutation that ...
... that binds to DNA and a C-terminal domain (CTD). Mutational analyses have shown that without a functional RepC protein, the Ti ... affecting its ability to deliver DNA. Conversely, little is known about VirD3, and mutational analyses have not provided any ... priming the process of DNA ligation, where the T-DNA is permanently joint to the plant genome. The T-DNA region is flanked at ... For the T-DNA, a nick will be created at the T-DNA's border sequence, and the nicked T-strand will be transported to the cell ...
DNA mutational analysis revealed that the child was homozygous for a novel E64K mutation and that his mother and father were ... "Real time PCR assays to detect common mutations in the biotinidase gene and application of mutational analysis to newborn ...
Nucleotide sequence context influences mutation probability and analysis of mutational (mutable) DNA motifs can be essential ... If DNA repair is deficient, DNA damage tends to accumulate. Such excess DNA damage can increase mutational errors during DNA ... Mutational analysis of entire gene families revealed that genes of the same family have similar functions, as predicted by ... 2008). "Quantitative analysis of mitochondrial DNA 4977-bp deletion in sporadic breast cancer and benign breast diseases". ...
Phylogenetic analyses and sequence alignment are often considered jointly, as phylogenetic analyses using DNA or RNA require ... Potential benefits include the reduction of mutational biases and a reduced number of characters, which may speed analyses. ... All of which possess their own strengths and weaknesses and may be specialized for distinct sequence types (DNA, RNA or protein ... Using RNA for phylogenetic analysis comes with its own unique set of strengths and weaknesses. large set of characters cost- ...
Mutational analysis for the yeast ARS elements have shown that any mutation in the B1, B2 and B3 regions result in a reduction ... Melting of DNA occurs within domain B2, induced by attachment of ARS binding factor 1 to B3. A1 and B1 domain binds with origin ...
2004). "Proteomics analysis of the centromere complex from HeLa interphase cells: UV-damaged DNA binding protein 1 (DDB-1) is a ... 2002). "Mutational analysis of the central centromere targeting domain of human centromere protein C, (CENP-C)". Exp. Cell Res ... 2006). "Phosphoproteome analysis of the human mitotic spindle". Proc. Natl. Acad. Sci. U.S.A. 103 (14): 5391-6. doi:10.1073/ ... 2006). "Comprehensive analysis of the ICEN (Interphase Centromere Complex) components enriched in the CENP-A chromatin of human ...
Sriskanda V, Schwer B, Ho CK, Shuman S (October 1999). "Mutational analysis of Escherichia coli DNA ligase identifies amino ...
... or they may accumulate so many mutational changes that they are no longer recognizable as former genes. Analysis of these ... Eventually pseudogenes may be deleted from their genomes by chance DNA replication or DNA repair errors, ... Thus, they do not require many genes that are needed by free-living bacteria, such as gene associated with metabolism and DNA ... That is, although every pseudogene has a DNA sequence that is similar to some functional gene, they are usually unable to ...
... transduction and conjugation Recombination and complementation Mutational analysis Genetic mapping and linkage analysis B. ... Genome Maintenance DNA replication DNA damage and repair DNA modification DNA recombination and gene conversion E. Gene ... maps and PCR Nucleic acid blotting and hybridization DNA cloning in prokaryotes and eukaryotes Sequencing and analysis Protein- ... Genomics Genome structure Physical mapping Repeated DNA and gene families Gene identification Transposable elements ...
"Chlorella virus DNA ligase: nick recognition and mutational analysis". Nucleic Acids Research. 26 (2): 525-31. doi:10.1093/nar/ ... DNA ligase 1 is an enzyme that in humans is encoded by the LIG1 gene. DNA ligase I is the only known eukaryotic DNA ligase ... LIG1 encodes DNA ligase I, which functions in DNA replication and the base excision repair process. Eukaryotic DNA ligase 1 ... DNA ligase 1 is responsible for joining Okazaki fragments formed during discontinuous DNA synthesis on the DNA's lagging strand ...
"Mutational analysis of thirty-two double-strand DNA break repair genes in breast and pancreatic cancers". Cancer Res. 68 (4): ... On its own, DNA-PKcs is inactive and relies on Ku to direct it to DNA ends and trigger its kinase activity. DNA-PKcs is ... MicroRNA-101 targets DNA-PKcs via binding to the 3'- UTR of DNA-PKcs mRNA and efficiently reduces protein levels of DNA-PKcs. ... DNA-PK also cooperates with ATR and ATM to phosphorylate proteins involved in the DNA damage checkpoint. DNA damage appears to ...
"Mutational analysis of the damage-recognition and catalytic mechanism of human SMUG1 DNA glycosylase". Nucleic Acids Res. 32 ( ... Uracil-DNA glycosylases are DNA repair enzymes that excise uracil residues from DNA by cleaving the N-glycosydic bond, ... Lindahl, T. (1986). "DNA Glycosylases in DNA Repair". Mechanisms of DNA Damage and Repair. 38: 335-340. doi:10.1007/978-1-4615- ... This was the most frequent DNA repair abnormality found among the 8 DNA repair genes tested. NEIL1 was also one of six DNA ...
Sriskanda V, Shuman S (January 1998). "Chlorella virus DNA ligase: nick recognition and mutational analysis". Nucleic Acids Res ... With human DNA ligase, this forms a crystallized complex. The complex, which has a DNA-adenylate intermediate, allows DNA ... At the end of the segment that DNA polymerase acts on, DNA ligase must repair the final segment of DNA backbone in order to ... The nicks allow the DNA to take on a circular shape. Nicked DNA can be the result of DNA damage or purposeful, regulated ...
"Mutational analysis of the N-terminal DNA-binding domain of sleeping beauty transposase: critical residues for DNA binding and ... DNA transposons translocate from one DNA site to another in a simple, cut-and-paste manner (Fig. 1). Transposition is a precise ... DNA transposons precisely insert defined DNA sequences (Fig. 1) almost randomly into host genomes thereby increasing the ... The insertion site can be elsewhere in the same DNA molecule, or in another DNA molecule (or chromosome). In mammalian genomes ...
"Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis". ... DNA sequences from bacteria in permafrost were amplified using PCR. One series of runs amplified the DNA sequences as-is (to ... One important function of uracil-DNA glycosylases is to prevent mutagenesis by eliminating uracil from DNA molecules by ... no DNA repair), or else through reduction of metabolic activity to a very low rate, just sufficient to carry out ongoing DNA ...
Once regions of DNA methylation are identified, a number of bioinformatics analyses can be applied to answer certain biological ... For example, silencing of tumour-suppressor genes in cancer can be attributed to DNA methylation. By identifying mutational ... Genomic DNA is extracted (DNA extraction) from the cells and purified. The purified DNA is then subjected to sonication to ... as the purified fraction of methylated DNA can be input to high-throughput DNA detection methods such as high-resolution DNA ...
This happens due to the fact that in the absence of recombination, offspring at least bear the same mutational load as their ... However, this fast evolution might also be due to these sequences' inability to repair DNA damage via template-assisted repair ... Freeman S, Herron JC (2007). Evolutionary Analysis, 4th edition. San Francisco: Benjamin Cummings. pp. 308-309. ISBN 978-0-13- ... Andersson DI, Hughes D (January 1996). "Muller's ratchet decreases fitness of a DNA-based microbe". Proceedings of the National ...
"Same DNA deletion paves paths to autism, schizophrenia , Spectrum". Spectrum. 2016-10-18. Retrieved 2016-11-13.. ... Gruneberg, H., 1938 An analysis of the "pleiotropic" effects of a new lethal mutation in the rat (Mus norvegicus). Proc. R. Soc ... evidence from a meta-analysis of twin studies". Archives of General Psychiatry. 60 (12): 1187-1192. doi:10.1001/archpsyc.60.12. ...
Interaction with DNA[edit]. Metabolism of benzo[a]pyrene yielding the carcinogenic benzo[a]pyren-7,8-dihydrodiol-9,10-epoxide. ... Kazerouni, N; Sinha, R; Hsu, CH; Greenberg, A; Rothman, N (2002). "Analysis of 200 food items for benzo[a]pyrene and estimation ... Preferential formation of benzo[a]pyrene adducts at lung cancer mutational hotspots in P53. Science. 1996 October 18;274(5286): ... by confusing the double-helical DNA structure. This disrupts the normal process of copying DNA and causes mutations, which ...
DNA damage[edit]. Marking sites of DNA damage is an important function for histone modifications. It also protects DNA from ... Analysis of histone modifications in embryonic stem cells (and other stem cells) revealed many gene promoters carrying both ... since mutational inactivation of this gene impairs addiction.[112] ... Compacting DNA strands[edit]. Histones act as spools around which DNA winds. This enables the compaction necessary to fit the ...
Further analysis showed that PRK2, a direct target of Rho, is required for the formation of apical junctions. Mutational ... Further DNA testing showed that the transforming sequences in the two cancer cell lines were the same, and the gene was later ... DNA from a rhabdomyosarcoma cell line and a fibrosarcoma cell line transformed a NIH/3T3 mouse fibroblast cell line. After ... After size fractionation of FCS and analysis of the lipids that bound to serum albumin, the lysophosphatidic acid (LPA) was ...
Pereira, S.L. and A.J. Baker (2008), DNA evidence for a Paleocene origin of the Alcidae (Aves: Charadriiformes) in the Pacific ... Livezey, B.C. (2010), Phylogenetics of modern shorebirds (Charadriiformes) based on phenotypic evidence: analysis and ... the Role of Mutational Variance in Gene Trees, Mol. Phylogenet. Evol. 65, 631-641. ... Crochet, P.-A., F. Bonhomme, and J.-D. LeBreton (2002), Systematics of large white-headed gulls: Patterns of mitochondrial DNA ...
DNA sequence differences that would be abundant in a singleton-based study do not interfere with the analysis. Environmental ... Bacteria also use DNA adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA adenine ... DNA damage can also cause epigenetic changes.[27][28][29] DNA damage is very frequent, occurring on average about 60,000 times ... Chromatin is the complex of DNA and the histone proteins with which it associates. If the way that DNA is wrapped around the ...
Feldmann, Kenneth A. (1991-07-01). "T-DNA insertion mutagenesis in Arabidopsis: mutational spectrum". The Plant Journal. 1 (1 ... Koukolíková-Nicola, Z; Raineri, D; Stephens, K; Ramos, C; Tinland, B; Nester, E W; Hohn, B (February 1993). "Genetic analysis ... The transfer DNA (abbreviated T-DNA) is the transferred DNA of the tumor-inducing (Ti) plasmid of some species of bacteria such ... This nick creates a region of single stranded DNA from the left border of the T-DNA gene over to the right border which was cut ...
Separation of B. Subtilis DNA into complementary strands. 3. Direct analysis. . In: Proceedings of the National Academy of ... Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases. . In: Nucleic ... Sie gelten auch für mtDNA und DNA von Plastiden. Für einzelsträngige DNA-Viren oder RNA gelten die Chargaff-Regeln nicht.[3] ... Relative Anteile (%) der Nukleinbasen in DNA verschiedener Arten[12]. Ein Verhältnis, das vom 1:1-Verhältnis abweicht, deutet ...
Mutational and epigenetic signatures in cancer tissue linked to environmental exposures and lifestyle»։ Curr Opin Oncol 30 (1 ... Yang SF, Chang CW, Wei RJ, Shiue YL, Wang SN, Yeh YT (2014)։ «Involvement of DNA damage response pathways in hepatocellular ... a systematic analysis for the Global Burden of Disease Study 2013.»։ Lancet 385: 117-71։ PMC 4340604։ PMID 25530442։ doi: ... 21,0 21,1 «The chemistry and biology of aflatoxin B(1): from mutational spectrometry to carcinogenesis»։ Carcinogenesis 22 (4 ...
DNA damages tend to accumulate. Such excess DNA damage can increase mutational errors during DNA replication due to error-prone ... Hartl DL, Jones EW (2005). Genetics: Analysis of Genes and Genomes (6th ed.). Missisauga: Jones & Bartlett, Canada. p. 477. ... DNA repair genes with hyper/hypo-methylated promoters in cancers[edit]. DNA repair genes are frequently repressed in cancers ... Excess DNA damage can also increase epigenetic alterations due to errors during DNA repair.[41][42] Such mutations and ...
... or by oxidizing DNA or proteins.[53] Damage to DNA can cause mutations and possibly cancer, if not reversed by DNA repair ... "Meta-regression analyses, meta-analyses, and trial sequential analyses of the effects of supplementation with beta-carotene, ... Wu XW, Muzny DM, Lee CC, Caskey CT (January 1992). "Two independent mutational events in the loss of urate oxidase during ... protect DNA from oxidative stress. It has been proposed that polymorphisms in these enzymes are associated with DNA damage and ...
Interaction with DNA[edit]. Metabolism of benzo[a]pyrene yielding the carcinogenic benzo[a]pyren-7,8-dihydrodiol-9,10-epoxide. ... "Environmental Analysis (Volume 3 of Handbook of Analytical Separations). Elsevier. pp. 99-122. ISBN 978-0-08-050576-3. .. ... Preferential formation of benzo[a]pyrene adducts at lung cancer mutational hotspots in P53. Science. 1996 October 18;274(5286): ... by confusing the double-helical DNA structure. This disrupts the normal process of copying DNA and causes mutations, which ...
"Mutational analysis of the conserved basic domain of human immunodeficiency virus tat protein". Journal of Virology. 63 (3): ... injection of a Tat Oyi-based therapeutic HIV vaccine reduces of 1.5 log copies/mL the HIV RNA rebound median and no HIV DNA ... Jeang, K. T. (1996) In: Human Retroviruses and AIDS: "A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences". Los ...
Preferential binding at p53 mutational hotspots and inhibition of DNA repair". Proceedings of the National Academy of Sciences ... Some older analyses have claimed that non-smokers are up to twice as likely as smokers to develop Alzheimer's disease.[116] ... "DNA interaction with Benzopyrene". DNA. Archived from the original on December 23, 2004. Retrieved March 5, 2005.. ... The DNA contains the information on how the cell function; in practice, it contains the recipes for protein synthesis. If the ...
positive regulation of DNA damage response, signal transduction by p53 class mediator. • vasculogenesis involved in coronary ... Blast cells analysis displayed the same abnormality as germline mutation with one mutated allele (no somatic SPRED1 single- ... "Clinical and mutational spectrum of neurofibromatosis type 1-like syndrome". JAMA. 302 (19): 2111-8. doi:10.1001/jama.2009.1663 ...
Nichols JD, Xiang S, Schindelin H, Rajagopalan KV (Jan 2007). "Mutational analysis of Escherichia coli MoeA: two functional ... a DNA methyltransferase is a transferase that catalyzes the transfer of a methyl group to a DNA acceptor. In practice, many ... end of an existing DNA molecule. Terminal transferase is one of the few DNA polymerases that can function without an RNA primer ... Their analysis showed that this reversible reaction could be applied to other tissues. This assertion was validated by Rudolf ...
2000). "Mitochondrial DNA variability in Italian and east European wolves: Detecting the conseguences of small population size ... The phylogenetic tree indicated that the haplotypes represented two haplogroups that were separated by five mutational steps. ... The genetic analysis of Apennine wolves indicates that they went through a population decline of 100-1,000 fold between the ... 1992). "Mitochondrial DNA variability of the gray wolf: genetic consequences of population decline and habitat fragmentation on ...
細胞的癌變與DNA及表觀遺傳等遺傳信息的突變有關,这些变化会影响细胞的正常功能,包括细胞增殖、程序性细胞死亡(细胞凋亡)和DNA修复。损伤累积的越多,癌症发生的风险就越高[23]。 ... Sun Y, Li Z, Li J, Li Z, Han J. A Healthy Dietary Pattern Reduces Lung Cancer Risk: A Systematic Review and Meta-Analysis. ... Nivolumab plus Ipilimumab in Lung Cancer with a High Tumor Mutational
Analysis of the single-stranded DNA bacteriophage phi X174, refined at a resolution of 3.0 A" J Mol Biol 237(5) 517-543 McKenna ... Mutational analysis of the bacteriophage phi X174 replication origin" J Mol Biol 198(1) 51-61 Fluit AC, Baas PD, Jansz HS (1985 ... The host's DNA polymerase converts the single-stranded DNA into double-stranded DNA. 6. Late genes are now transcribed by the ... Protein A* inhibits host DNA replication. Unlike protein A it is capable of cleaving the phi X viral DNA in the presence of ...
"DNA Damage, DNA Repair and Cancer". In Chen C. New Research Directions in DNA Repair. InTech. ISBN 978-953-51-1114-6 ... Yin L, Grandi N, Raum E, Haug U, Arndt V, Brenner H (2011). "Meta-analysis: Serum vitamin D and colorectal adenoma risk". ... Epigenetic alterations are much more frequent in colon cancer than genetic (mutational) alterations. As described by Vogelstein ... Other options include virtual colonoscopy and stool DNA screening testing (FIT-DNA). Virtual colonoscopy via a CT scan appears ...
If DNA repair is deficient, DNA damage tends to accumulate. Such excess DNA damage may increase mutational errors during DNA ... "Mutational analysis of BRCA1 and BRCA2 and clinicopathologic analysis of ovarian cancer in 82 ovarian cancer families: two ... BRCA1 directly binds to DNA, with higher affinity for branched DNA structures. This ability to bind to DNA contributes to its ... DNA damage appears to be the primary underlying cause of cancer,[74][75] and deficiencies in DNA repair appears to underlie ...
For the advantage due to DNA repair, there is an immediate large benefit of removing DNA damage by recombinational DNA repair ... An information theoretic analysis using a simplified but useful model shows that in asexual reproduction, the information gain ... Muller, H.J. (1964). "The Relation of Recombination to Mutational Advance". Mutation Research. 1: 2-9. doi:10.1016/0027-5107(64 ... a b Bernstein H, Bernstein C, Michod RE (2011). "Meiosis as an evolutionary adaptation for DNA repair." In "DNA Repair", Intech ...
Small mutational changes in non-nuclear DNA that become fixed in small populations are likely to be the major driver of ... Analysis of population structure using mitochondrial DNA and microsatellites". Molecular Ecology. 10 (11): 2647-60. doi:10.1046 ... Genetic difference is most often detected in microsatellites in mitochondrial DNA. Animals that spend much of their time at sea ... For example, study of mitochondrial DNA microsatellites found no significant difference between colonies of black-browed ...
All tests and analysis from[76][77] Model organisms have been used in the study of MYH9 function. A conditional knockout mouse ... "The DNA sequence of human chromosome 22". Nature. 402 (6761): 489-95. doi:10.1038/990031. PMID 10591208.. ... an immunofluorescence assay on peripheral blood smears and/or by the detection of the causative mutation through mutational ... Mass spectroscopy analysis of the relative abundance of NMHC IIs in mouse tissues and human cell lines [32] shows that NM IIA ...
... the identification of the two missing Romanov children using DNA analysis". PLoS ONE. 4 (3): e4838. doi:10.1371/journal.pone. ... Although a single mutational event might be rare in its generation, repeated mitotic segregation and clonal expansion can ... Heteroplasmy is the presence of more than one type of organellar genome (mitochondrial DNA or plastid DNA) within a cell or ... In mitochondrial DNA, there is evidence for potent germline purifying selection, as well as purifying selection during ...
... are now known to have complex biochemical processes for repairing DNA damages (see DNA repair). DNA repair processes are also ... led to the finding of a unique linear order of mutational sites within the genes. This result provided strong evidence for the ... Delbruck soon dispelled this initial reaction of disbelief by his own analysis of the phenomenon, and promptly joined in the ... After the discovery of the structure of DNA in 1953, it was still unclear how DNA replicated. The favored model at the time was ...
Kinship analysis (paternity testing)[edit]. Autosomal microsatellites are widely used for DNA profiling in kinship analysis ( ... Amos W, Rubinsztein DC (1996). "Microsatellites show mutational bias and heterozygote instability". Nature Genetics. 13: 390- ... Analysis[edit]. Repetitive DNA is not easily analysed by next generation DNA sequencing methods, which struggle with ... DNA. The name "satellite" DNA refers to the early observation that centrifugation of genomic DNA in a test tube separates a ...
Preferential binding at p53 mutational hotspots and inhibition of DNA repair". Proceedings of the National Academy of Sciences ... Appendix A To Part 136 Methods For Organic Chemical Analysis of Municipal and Industrial Wastewater, Method 603-Acrolein And ...
"Mutational spectrum of the succinate semialdehyde dehydrogenase (ALDH5A1) gene and functional analysis of 27 novel disease- ... "Prenatal diagnosis of succinic semialdehyde dehydrogenase deficiency: increased accuracy employing DNA, enzyme, and metabolite ... "Mutation analysis in a patient with succinic semialdehyde dehydrogenase deficiency: a compound heterozygote with 103-121del and ... analyses". Molecular Genetics and Metabolism 72 (3): 218-22. Mar 2001. doi:10.1006/mgme.2000.3145. PMID 11243727. ...
Reece, Richard J. (2004). Analysis of Genes and Genomes. Chichester: John Wiley & Sons. ISBN 0-470-84379-9.. ... Sanger, F.; Coulson, A.R.; Hong, G.F.; Hill, D.F.; Petersen, G.B. (1982). "Nucleotide sequence of bacteriophage lambda DNA". ... putative functions and mutational mechanisms: a review". Molecular ecology 11 (12): 2453-65. PMID 12453231. doi:10.1046/j.1365- ... GeKnome Technologies Next-Gen Sequencing Data Analysis- secuenciación de seguinte xeración de Illumina e 454 Servizo de GeKnome ...
Mutational analysis of loxP sites for efficient Cre-mediated insertion into genomic DNA.. Thomson JG1, Rucker EB 3rd, ... The Cre/loxP system has been used in transgenic models primarily to excise DNA flanked by loxP sites for gene deletion. However ... coli attB site and the excision-insertion ratios of incoming DNA plasmids carrying a second, complementary mutant loxP site ...
... but none reveal how this enzyme binds to substrate single-stranded DNA. Here, we constructed a panel of APOBEC3G amino acid ... APOBEC3G is the best known of several DNA cytosine deaminases that function to inhibit the replication of parasitic genetic ... A Comparison of Two Single-Stranded DNA Binding Models by Mutational Analysis of APOBEC3G. Keisuke Shindo †. ... "A Comparison of Two Single-Stranded DNA Binding Models by Mutational Analysis of APOBEC3G." Biology 1, no. 2: 260-276. ...
Initiation of polyoma virus DNA synthesis: a mutational analysis. Österlund, Mårten Uppsala University, Disciplinary Domain of ...
Here, we describe the comparative analysis of mutations in tumor tissue DNA and... ... enables the detection and characterization of fragmented DNA that is in low abundance in blood. ... dPCR Mutational Analyses in Cell-Free DNA: A Comparison with Tissues. In: Casadio V., Salvi S. (eds) Cell-free DNA as ... Here, we describe the comparative analysis of mutations in tumor tissue DNA and plasma cell-free DNA (cfDNA) using a dPCR ...
Antithrombin III - analysis Blood Coagulation Factors - analysis - physiology DNA Mutational Analysis English Abstract Enzyme ... DNA Mutational Analysis Exons Family Health Female Finland Genes, APC Genetic Linkage Germ-Line Mutation Haplotypes Humans Loss ... DNA Mutational Analysis Female Founder Effect Genes, BRCA1 Genetic Predisposition to Disease Haplotypes Humans Latvia Male ... DNA Mutational Analysis Denmark Female Humans Likelihood Functions Logistic Models Middle Aged Mutation Neoplasm Recurrence, ...
... exonuclease active site of phi29 DNA polymerase. One of these residues, Phe65, belongs to motif Exo II, previously described to ... Mutational Analysis of phi29 DNA Polymerase Residues Acting as ssDNA Ligands for 3-5 Exonucleolysis J Mol Biol. 1998 Jun 19; ... Site-directed mutagenesis and biochemical analysis of eight phi29 DNA polymerase mutant proteins at residues Phe65, Ser122 and ... proofreading of DNA polymerization errors. Extrapolation to the crystal structures of Klenow and T4 DNA polymerases indicates ...
Analysis of plasma (PL)-derived circulating free tumour DNA (ctDNA) as an adjunct to BM biopsy, for mutational characterisation ... Circulating tumour DNA analysis demonstrates spatial mutational heterogeneity that coincides with disease relapse in myeloma. ... Mutational characterisation in multiple myeloma (MM) currently relies on bone marrow (BM) biopsy, which fails to capture the ... Paired BM MM cell DNA and ctDNA from 33 relapsed/refractory (RR) and 15 newly diagnosed (ND) patients were analysed for KRAS, ...
Separating substrate recognition from base hydrolysis in human thymine DNA glycosylase by mutational analysis ... Download PDF Separating substrate recognition from base hydrolysis in human thymine DNA glycosylase by mutational analysis. ... Separating substrate recognition from base hydrolysis in human thymine DNA glycosylase by mutational analysis. Journal of ... Separating substrate recognition from base hydrolysis in human thymine DNA glycosylase by mutational analysis. Journal of ...
Our broad analysis demonstrates that the qBiomarkers performance is on par with that of other labour-intensive and expensive ... DNA extraction. Genomic DNA was isolated from fresh-frozen samples by the QIAamp DNA Kit (Qiagen) and quantified with the ... Comparative mutational landscape analysis of patient-derived tumour xenografts. *Mariana Brait1. , ... Brait, M., Izumchenko, E., Kagohara, L. et al. Comparative mutational landscape analysis of patient-derived tumour xenografts. ...
Acr-DNA Adduct Analysis.. Acr-DNA adducts formed in cells treated with Acr (0-100 μM) and in purified genomic DNA modified with ... Acr can directly interact with DNA and form DNA adducts (18, 23). Similar to PAH-DNA adducts, Acr-DNA adducts induce mainly G:C ... a) DNA isolated from control cells. (b) Acr-modified genomic DNA. (c) DNA from Acr-treated cells. (d) Acr-modified dGMP. (e) ... Genomic DNA was then isolated, the DNA adduct distribution was mapped by the UvrABC/LMPCR method, and the DNA was separated by ...
"DNA Mutational Analysis" by people in this website by year, and whether "DNA Mutational Analysis" was a major or minor topic of ... "DNA Mutational Analysis" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical ... DNA Mutational Analysis*DNA Mutational Analysis. *Analysis, DNA Mutational. *Analyses, DNA Mutational ... Below are the most recent publications written about "DNA Mutational Analysis" by people in Profiles. ...
Mutational analysis of the catalytic domain of the murine Dnmt3a DNA-(cytosine C5)-methyltransferase. Journal of Molecular ... Mutational analysis of the catalytic domain of the murine Dnmt3a DNA-(cytosine C5)-methyltransferase ... we have performed a mutational analysis of 14 amino acid residues in the catalytic domain of the murine Dnmt3a DNA-(cytosine C5 ... N167A (motif VI) and R202A (motif VIII) have normal AdoMet and DNA binding but reduced catalytic activity. While Asn167 might ...
Mutational Analysis.. PCR amplification using random-primed first-strand cDNAs was performed with the aid of the following ... In addition, Western blot analysis of WRN, ATR, PLK1, BRCA1, and DNA topoisomerase IIα did not show any apparent association ... Assay for Clamp Formation between Topoisomerase II and DNA.. Assay for clamp formation between topoisomerase II and DNA was ... we also observed the rather unexpected occurrence that ICRF-193-induced DNA DSBs and DNA damage checkpoint activation in two ...
55 BIOLOGY AND MEDICINE, BASIC STUDIES; SEROTONIN; RECEPTORS; PATIENTS; NERVOUS SYSTEM DISEASES; MENTAL DISORDERS; GENES; DNA- ... Journal Article: Mutational analysis of the promoter and the coding region of the 5-HT1A gene ... Title: Mutational analysis of the promoter and the coding region of the 5-HT1A gene ...
... p53 mutational analysis was performed on DNA isolated from fresh tumor tissues frozen in liquid nitrogen or, for five of the ... DNA Adduct Analysis.. Methods used for the 32P-postlabeling/ PAGE analysis of AA-derived DNA adducts were described in ref. 29 ... DNA (80 μg) was subjected to enzymatic hydrolysis, followed by solid phase extraction enrichment of AL-DNA adducts (47). DNA ( ... Additionally, AL-DNA adducts are known to be mutagenic (23-28), leading us to determine the p53 mutational spectrum of ...
DNA Mutational Analysis * Female * Genes, Neurofibromatosis 1 * Genetic Association Studies * Genetic Testing ... Clinical and mutational spectrum of neurofibromatosis type 1-like syndrome JAMA. 2009 Nov 18;302(19):2111-8. doi: 10.1001/jama. ... Objective: To determine the frequency, mutational spectrum, and phenotype of neurofibromatosis type 1-like syndrome (NFLS) in a ... but no detectable NF1 germline mutation underwent SPRED1 mutation analysis. ...
Analysis of B-cell leukaemia samples reveals that oncogenic mutations do not cause malignant transformation unless they ... Single-cell mutation and phospho-protein analyses reveal the segregation of oncogenic STAT5 and ERK activation to competing ... Mutational exclusivity analysis. The samples for ALL analysis originate from six different sources, including the St Jude ... scWest chips were then probed for histone H3 and TOTO-1 (DNA stain) to verify cell occupancy. Scout Software (ProteinSimple) ...
DNA sequencing and data analysis.Mutagenized hpaG and xopA DNA fragments in pET14b were sequenced to confirm the presence of ... DNA manipulations.Standard methods were used for DNA cloning, restriction mapping, and gel electrophoresis (23). The vector DNA ... Mutational and deletion analyses narrowed the region essential for elicitor activity to the 23-amino-acid peptide (H2N- ... Mutational Analysis of Xanthomonas Harpin HpaG Identifies a Key Functional Region That Elicits the Hypersensitive Response in ...
The genomic DNA ofP. aeruginosa was extracted by the method of Barcak et al. (2). DNA fragments used in cloning were extracted ... Mutational Analysis of the OprM Outer Membrane Component of the MexA-MexB-OprM Multidrug Efflux System ofPseudomonas aeruginosa ... Mutational Analysis of the OprM Outer Membrane Component of the MexA-MexB-OprM Multidrug Efflux System ofPseudomonas aeruginosa ... Mutational Analysis of the OprM Outer Membrane Component of the MexA-MexB-OprM Multidrug Efflux System ofPseudomonas aeruginosa ...
DNA extraction and mutational analysis. All biopsies were taken using chemotherapy-guided Tru-Cut and were analysed by the ... All variables were dichotomised for survival curve analysis. Cox multivariate analysis was used for adjusting for potential ... they were later embedded in paraffin until processing for DNA extraction. Genomic DNA was extracted from areas of paraffin ... An analysis of Ki-67 in lung tumours showed that high differentiation promotes cell proliferation significantly; tumours with ...
1996 Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc. Natl. Acad. Sci. USA 93: 8449 ... 1997 Genetic analyses of the serrated margin of leaf blades in Arabidopsis: combination of a mutational analysis of leaf ... A Mutational Analysis of Leaf Morphogenesis in Arabidopsis thaliana Message Subject (Your Name) has forwarded a page to you ... A Mutational Analysis of Leaf Morphogenesis in Arabidopsis thaliana. Genoveva Berná, Pedro Robles and José Luis Micol ...
18). The mutational analysis of p53 was done using genomic DNA as template. The primers used were as follows: for EGFR kinase ... DNA Platination. DNA platination was measured as described previously (16). Cells were exposed to cDDP for 1 h. DNA was ... Mutational Analysis of EGFR, PTEN, and p53. Total RNA was isolated with the TRIzol reagent (Invitrogen) according to the ... Indeed, sequence analysis of genomic DNA of IGROV-1/OHP cells indicated the occurrence of a missense mutation affecting exon 6 ...
Mutational analysis by nucleotide sequencing. Primers were designed to PCR amplify all coding exons of PIK3CA and PTEN, and ... DNA extraction and identity testing. Genomic DNA was isolated from macrodissected tumor tissues and normal tissues using the ... Statistical analyses. All comparisons between groups were performed using a 2-tailed Fishers exact test of significance. ... Our study revealed 3 major mutational hotspots at amino acids 88, 93, and 111 within the ABD and its adjacent linker. We ...
Mutational Analyses of the β-Catenin Gene.. Genomic DNA from each tumor sample was amplified for SSCP analysis of exon 3 using ... Sparks A. B., Morin P. J., Vogelstein B., Kinzler K. W. Mutational analysis of the APC/β-catenin/Tcf pathway in colorectal ... DNA and cDNA Preparation.. DNA was extracted from HB samples, peripheral blood, and normal liver tissue by standard proteinase ... DNA sequencing of the excised and reamplified DNA products of tumor D401 uncovers a somatic A→G transition in codon 41, ...
DNA Adducts. DNA Mutational Analysis. DNA, Fungal. Molecular Sequence Data. Mutagenicity Tests. Mutagens / toxicity*. Orotidine ... 0/DNA Adducts; 0/DNA, Fungal; 0/Mutagens; 53-96-3/2-Acetylaminofluorene; EC 4.1.1.23/Orotidine-5-Phosphate Decarboxylase ... Sequence analysis of the URA3 mutants revealed approximately 48% frameshifts, approximately 44% base substitutions and ...
... , Abdulla A Alharthi, Ahmed Gaber, Mohamed ... A summary of results from the mutation analysis of NPHS2 and WT1 genes is given in Table 2. DNA sequence analysis of all 8 ... Genomic DNA Extraction. Genomic DNA was extracted directly from blood according to instructions of genomic DNA extraction kit ( ... Mutational analysis of NPHS2 and WT1 genes in Saudi children with nephrotic syndrome.. Abdulla A Alharthi1,2,3, Ahmed Gaber1,4 ...
This assay is also available as PCR-based pyrosequencing of DNA to examine codons 595 to 600 from exon 15 (the most common ... BRAF Mutational Analysis. Indication. To identify activating point mutations in the kinase domain of BRAF, an oncogene that is ...
Analysis of circulating tumour DNA for mutational characterisation and tracking disease progression in multiple myeloma. * ... Cancer cells shed small amounts of DNA (circulating tumour DNA - ctDNA) into the blood stream and are known to harbour ... subject to sampling bias and does not capture the spatial genomic heterogeneity of MM and thereby inadequate for mutational ... characterisation and disease detection to guide treatment decisions with an ultimate objective to incorporate ctDNA analysis as ...
Direct DNA sequencing and mutational analysis. Purified PCR products were sequenced at the DLMBC sequencing service (Dr. M. ... Mutational analysis of hCDC4 in AML. In this study the common exons 2 to 11 and the three known transcript variants of exon 1 ... Sequence analysis of hCDC4 exon 10 identifies a new intronic SNP. During the analysis of exon 10 and adjacent intronic ... Therefore we carried out a mutational analysis of the hCDC4 gene in 35 samples of AML patients in order to elucidate whether ...
1991 T-DNA insertion mutagenesis in Arabidopsis: mutational spectrum. Plant J. 1: 71-82. ... B52 and ibr4 are mutants from T-DNA lines in the Ws background (Feldmann 1991) and ibr6 is from a Col-0 T-DNA line (Campisiet ... IAA-sensitive mutants were retained for further analysis. Because the 3 mutants from the T-DNA lines are from independent pools ... Luise Rogg for analysis of axr mutants on IBA, Sue Gibson for suggesting GC analysis of eicosenoic acid, Seiichi Matsuda for ...
  • Here, we describe the comparative analysis of mutations in tumor tissue DNA and plasma cell-free DNA (cfDNA) using a dPCR method. (springer.com)
  • Takeshita T, Yamamoto Y, Yamamoto-Ibusuki M et al (2017) Analysis of ESR1 and PIK3CA mutations in plasma cell-free DNA from ER-positive breast cancer patients. (springer.com)
  • Takeshita T, Yamamoto Y, Yamamoto-Ibusuki M et al (2018) Clinical significance of plasma cell-free DNA mutations in PIK3CA, AKT1, and ESR1 gene according to treatment lines in ER-positive breast cancer. (springer.com)
  • Takeshita T, Yamamoto Y, Yamamoto-Ibusuki M et al (2016) Clinical significance of monitoring ESR1 mutations in circulating cell-free DNA in estrogen receptor positive breast cancer patients. (springer.com)
  • Paired BM MM cell DNA and ctDNA from 33 relapsed/refractory (RR) and 15 newly diagnosed (ND) patients were analysed for KRAS, NRAS, BRAF and TP53 mutations using the OnTarget Mutation Detection (OMD) platform. (ovid.com)
  • These findings raise the question of whether Acr-DNA adducts are responsible for p53 mutations in CS-related lung cancer. (pnas.org)
  • It can be taken up reasonably efficiently by human cells and react directly without metabolic activation with guanine residues in DNA to produce exocyclic DNA adducts, 6-hydroxy-1, N 2 -propanodeoxyguanosine and 8-hydroxy-1, N 2 -propanodeoxyguanosine adducts (Acr-dG) ( Fig. 1 ), which are mutagenic and induce predominantly G:C-to-T:A transversion mutations similar to PAHs ( 9 ). (pnas.org)
  • Cancer cells shed small amounts of DNA (circulating tumour DNA - ctDNA) into the blood stream and are known to harbour mutations representative of the tumour genome. (monash.edu)
  • Therefore, we aimed to characterize mutations in the D-loop region of mitochondrial DNA along with the morphological changes and analyzed their impact on survival in retinoblastoma patients. (cdc.gov)
  • mtDNA D-loop region was amplified by Nested-Polymerase Chain Reaction (Nested-PCR) and mutations were analyzed in 60 tumor samples from retinoblastoma patients by DNA sequencing. (cdc.gov)
  • We carried out a mutation analysis of the hCDC4 gene in 35 samples of patients with Acute Myeloid Leukemia (AML) to elucidate a possible role of hCDC4 mutations in this disease. (medsci.org)
  • Therefore we carried out a mutational analysis of the hCDC4 gene in 35 samples of AML patients in order to elucidate whether hCDC4 mutations may be relevant for the genesis of this disease. (medsci.org)
  • We have examined genomic DNA from ALD probands for mutations in the putative ALD gene. (nih.gov)
  • Twenty-five of the ALD probands whose ALD genes appeared normal by Southern blot analysis were surveyed for mutations by Single Strand Conformation Polymorphism (SSCP) procedures and DNA sequence analysis. (nih.gov)
  • From the mutational analysis of mtDNA obtained from blood , 5 confirmed pathogenic mutations were identified in 17 families , and 4 unreported pathogenically suspected mutations were identified in 4 families . (bvsalud.org)
  • Using this strategy, we identified a number of point mutations that altered the function of the Pit-1 DNA binding domain. (elsevier.com)
  • These mutations define a number of amino acid residues that are important for the function of the DNA binding domain of Pit-1. (elsevier.com)
  • In agreement with data for EBNA1, residues in helices 1 and 2 mainly contributed to sequence-specific DNA binding and replication activity, whilst mutations in helix 3 affected replication activity and multimer formation. (bcm.edu)
  • Analysis of somatic mutations provides insight into the mutational processes that have shaped the cancer genome, but such analysis currently requires large cohorts. (biomedcentral.com)
  • The set of somatic mutations observed in a tumor reflects the varied mutational processes that have been active during its life history, providing insights into the routes taken to carcinogenesis. (biomedcentral.com)
  • Additional mutation features such as the presence of indels, dinucleotide mutations, or transcriptional strand bias could also be incorporated into the definition of a mutational signature. (biomedcentral.com)
  • With exome sequencing covering only ~1 % of the human genome, resulting in fewer mutations identified, they estimated that it would take thousands of samples to extract the majority of mutational processes that have been functional during tumor life histories. (biomedcentral.com)
  • About half of these signatures could be attributed to known mutational processes, such as tobacco smoke, exposure to ultraviolet light, activity of the APOBEC family of cytidine deaminases, DNA mismatch repair deficiency, or mutations in POLE . (biomedcentral.com)
  • Mutations are scored only if the variant is present in the PCR families arising from both of the two DNA strands. (nih.gov)
  • DNA samples from all patients were analysed for mutations in COH1 by direct sequencing. (bmj.com)
  • Splice site mutations were characterised using reverse transcriptase PCR analysis from total RNA samples. (bmj.com)
  • Mutations were detected by DNA sequence analysis of the candidate genes. (molvis.org)
  • To investigate whether mutations in TBX22 play a part in the formation of non-syndromic CP in the Thai population, we performed mutation analysis covering all the coding regions of the TBX22 gene in 53 unrelated Thai patients with non-syndromic CP. (biomedsearch.com)
  • Chevillard S, Radicella JP, Levalois C, Lebeau J, Poupon MF, Oudard S, Dutrillaux B, Boiteux S (1998) Mutations in OGG1 , a gene involved in the repair of oxidative DNA damage, are found in human lung and kidney tumours. (springer.com)
  • She has developed a high throughput multiplex microfluidics qPCR platform to detect mutations in fresh frozen, FFPE, TMA and cell free DNA samples from multiple clinical trials routinely. (selectbiosciences.com)
  • Recently, she has been developing ultra-sensitive assays utilizing ddPCR and NGS technologies to detect mutations from circulating tumour DNA, paving the way to develop personalized medicine for cancer patients. (selectbiosciences.com)
  • Double and triple mutants F16W/I24Q, F16W/N27D, and F16W/I24Q/N27D all showed defects in DNA binding, strand transfer, and helix destabilization, suggesting that the I24Q and N27D mutations have a "dominant negative" effect and abolish the positive influence of F16W. (umd.edu)
  • To address how various alterations produce a range of AI phenotypes, we performed a targeted analysis to find MMP20 mutations in French patients diagnosed with non-syndromic AI. (frontiersin.org)
  • This notion has been supported and extended by bioinformatic analysis of the tumor-specific mutation spectra in the TP53 gene which show a highly significant excess of non-synonymous mutations over the neutral expectation, suggesting that p53 evolution in tumors is subject to positive selection [ 13 ] as a result of preferential fixation of missense mutations in p53 [ 14 - 16 ]. (pubmedcentralcanada.ca)
  • Perhaps unsurprisingly in what is a segmental disease, we did not find LEMD3 mutations in peripheral-blood-derived DNA from the two other individuals with sporadic melorheostosis . (curehunter.com)
  • The analysis revealed that about 20% of these patients had treatment-related mutations at relapse, some associated with drug resistance. (newswise.com)
  • We report 21 mutations, including deletions, duplications, and missense, no mutations in 2 samples, and 2 samples with no useful DNA for further analysis. (isciii.es)
  • Mutational analyses of mitochondrial DNA identified the coexistence of heteroplasmic G11778A and homoplasmic T3394C mutations. (aao.org)
  • Over our lifetimes, DNA slowly accumulates mutations due to environmental toxins and radiation, as well as from naturally occurring copying errors. (massgeneral.org)
  • Sequencing the DNA in a tumor reveals not only its driver mutations, but also all the other "passenger mutations" that were present in the tumor-initiating cell. (massgeneral.org)
  • Isolating true somatic mutations is crucial for downstream analyses of mutational signatures and driver events. (massgeneral.org)
  • The mutations were detected using denaturing high-performance liquid chromatography and automated DNA sequencing. (onlinejacc.org)
  • Mutational Analysis of the Mitochondrial DNA Displacement-Loop Region in Human Retinoblastoma with Patient Outcome. (cdc.gov)
  • Alteration in mitochondrial DNA plays an important role in the development and progression of cancer. (cdc.gov)
  • The Displacement Loop (D-loop) region of mitochondrial DNA (mtDNA) is the regulatory region for its replication and transcription. (cdc.gov)
  • Molecular alterations in mitochondrial DNA of hepatocellular carcinomas: is there a correlation with clinicopathological profile? (bmj.com)
  • 3- 12 Extensive analysis of the mitochondrial genome with direct sequencing has shown that about 30-70% of all types of tumours harbour alterations in mtDNA. (bmj.com)
  • 3- 13 The laborious effort involved in sequencing the entire mitochondrial genome means that mutational analyses usually have been performed on small numbers of specimens and were limited to only part of the mitochondrial genome. (bmj.com)
  • 3, 8- 10, 13, 14 The only comprehensive mutational analysis that covered the entire mitochondrial genome with overlapping primers was achieved recently with the use of the effective temperature gradient gel electrophoresis method. (bmj.com)
  • Somatic mitochondrial DNA (mtDNA) alterations were investigated in patients with hepatocellular carcinomas and the molecular changes in mtDNA were correlated with the clinicopathological profile of patients with hepatocellular carcinomas. (bmj.com)
  • We utilize DNA sequence data from the nuclear, chloroplast, and mitochondrial genomes to infer historical processes of biodiversification. (duke.edu)
  • The delimitation of two morphologically similar and not easily separable Vulpicida species, V. juniperinus and V. tubulosus , is analyzed using nuclear ITS and Mcm7, and mitochondrial SSU DNA sequences. (cambridge.org)
  • Mitochondrial ribosomal DNA is commonly used in DNA-based dietary analyses. (cambridge.org)
  • The authors report the case of a 37-year-old man diagnosed with Leber's hereditary optic neuropathy (LHON) with olivocerebellar degeneration due to a heteroplasmic G11778A mutation in mitochondrial (mt) DNA ND4 and a homoplasmic T3394C mutation in the mtDNA NADH dehydrogenase (ND) 1 gene. (aao.org)
  • Our broad analysis demonstrates that the qBiomarker's performance is on par with that of other labour-intensive and expensive methods of cancer mutation detection of frequently altered cancer-associated genes, and provides a foundation for supporting its consideration as an option for molecular diagnostics. (nature.com)
  • Mutational analysis of NPHS2 and WT1 genes in Saudi children with nephrotic syndrome. (alliedacademies.org)
  • Up to date, several causative genes related to NS have been identified by either using direct DNA sequencing approaches or next-generation sequencing technology [ 6 - 12 ]. (alliedacademies.org)
  • We used array comparative genomic hybridization, mutational profiling to assess the status of specific genes, mRNA expression profiling, and immunohistochemical analyses of proteins implicated in thymic tumor pathogenesis. (aacrjournals.org)
  • In this study, molecular genetic analysis was performed on all these 12 genes in 25 Chinese families with congenital cataract. (molvis.org)
  • The establishment of the mutational spectrum for NDMA in endogenous mammalian genes is necessary if exposure to NDMA, based on its mutational specificity, is going to be assessed in human tissues. (epa.gov)
  • However, the systematic analysis of genes implicated in CNS/SRNS with respect to the effectiveness of intensified immunosuppressive therapy is still lacking, especially mutational analysis in patients that responded to CsA. (asnjournals.org)
  • DNA phosphorothioation, conferred by dnd genes, was originally discovered in the soil-dwelling bacterium Streptomyces lividans , and thereafter found to exist in various bacterial genera. (frontiersin.org)
  • RNA-seq experiments revealed that, catalase and organic hydroperoxide resistance gene expression were not up-regulated in the wild type strain, suggesting that the resistance to oxidative stress was not due to the up-regulation of these genes by DNA phosphorothioation. (frontiersin.org)
  • Quantitative RT-PCR analysis was conducted to trace the expression of the catalase and the organic hydroperoxide resistance genes after peroxides treatments. (frontiersin.org)
  • The results of this analysis seem to indicate that positive selection for gain-of-function in tumor suppressor genes is an important aspect of tumorigenesis, blurring the distinction between tumor suppressors and oncogenes. (pubmedcentralcanada.ca)
  • In this retrospective study, we performed polymerase chain reaction (PCR) amplification and deoxyribonucleic acid (DNA) sequencing of KIT (exons 9, 11, 13, and 17) and PDGFRA (exons 12 and 18) genes in 20 FFPE (formalin-fixed, paraffin-embedded) and 5 frozen GIST samples. (isciii.es)
  • The studies seek to identify the signal transduction pathways, specific DNA elements and transcription factors which are required for the tissue-specific, regulated expression of these pituitary hormone genes. (ohsu.edu)
  • The Lawrence Laboratory focuses on using computation as a powerful microscope to study the processes of DNA damage and repair, gene expression and genome replication, and cancer driver genes. (massgeneral.org)
  • The Cre/loxP system has been used in transgenic models primarily to excise DNA flanked by loxP sites for gene deletion. (nih.gov)
  • Reporter gene expression analysis, electrophoretic mobility shift assays and chromatin immunoprecipitation studies were utilized to examine the functional effects of the deletion. (arctichealth.org)
  • DNA methylation is an epigenetic process involved in gene regulation that is key for cell differentiation and viability. (purdue.edu)
  • To determine the role of Acr-DNA adducts in p53 mutagenesis in CS-related lung cancer we mapped the distribution of Acr-DNA adducts at the sequence level in the p53 gene of lung cells using the UvrABC incision method in combination with ligation-mediated PCR. (pnas.org)
  • The tumor suppressor gene p53 is frequently mutated in human cancers ( 1 , 2 ), and its mutational patterns often bear the fingerprints of the etiological carcinogens. (pnas.org)
  • This assay is also available as PCR-based pyrosequencing of DNA to examine codons 595 to 600 from exon 15 (the most common mutation site) and codons 468 to 474 from exon 11 of the BRAF gene. (mdanderson.org)
  • Mutational analysis of the HvDWARF gene with the "reverse genetics" approach allowed for its detailed functional analysis at the level of protein functional domains. (mdpi.com)
  • This assay is available as PCR-based DNA Sanger sequencing for exons 14 and 17 of the CSF3R gene. (mdanderson.org)
  • Genomic DNA was isolated from blood leucocytes, genotyping was performed using more than 100 microsatellite markers for the known cataract candidate gene loci, and LOD scores were calculated using the LINKAGE programs. (molvis.org)
  • In all patients, the HESX1 gene was analyzed by direct sequence analysis and in cases of CPHD the PROP1 gene was also sequenced. (scielo.br)
  • The MT-TL1 gene provides instructions for making a molecule called a transfer RNA (tRNA), which is a chemical cousin of DNA. (medlineplus.gov)
  • Next, the researchers compared these data with clinical data from longitudinal studies and gene expression analyses. (medicalnewstoday.com)
  • Mutational analysis of the PRKAR1A gene may be a useful adjunctive diagnostic test. (medscape.com)
  • Identification of a poxvirus gene encoding a uracil DNA glycosylase. (ebi.ac.uk)
  • A biomarker analysis showed that 26 patients (52%) had deleterious DNA damage response and repair (DDR) and/or RB1 gene alterations. (urotoday.com)
  • Here, three highly conserved amino acid residues have been characterized to function as ssDNA binding ligands at the 3'-5' exonuclease active site of phi29 DNA polymerase. (nih.gov)
  • The other two residues, Ser122 and Leu123, form a newly identified motif "(S/T)Lx2h", and are the homologous counterparts of Pol I residues Asp457 and Met458, and of T4 DNA polymerase residues Ser286 and Leu287, the latter three residues shown to contact ssDNA at their corresponding cocrystal 3D structures. (nih.gov)
  • Extrapolation to the crystal structures of Klenow and T4 DNA polymerases indicates that the invariant aromatic ring contiguous to the catalytic aspartate of the Exo II motif, corresponding to Tyr423 in Klenow, Phe218 in T4, and Phe65 in phi29 DNA polymerase, appears to be critical to orient the ssDNA substrate in a stable conformation to allow 3'-5' exonucleolytic catalysis. (nih.gov)
  • Because conventional DNA polymerase replicates DNA only in the 5′-3′ direction, the so-called DNA end replication problem would occur on lagging strands at the ends of chromosomes. (aacrjournals.org)
  • Results for Reference: Primer-terminus stabilization at the psi 29 DNA polymerase active site. (neb.com)
  • Nick translation is a biological process in which a single-stranded DNA nick serves as the marker for DNA polymerase to excise and replace possibly damaged nucleotides. (wikipedia.org)
  • At the end of the segment that DNA polymerase acts on, DNA ligase must repair the final segment of DNA backbone in order to complete the repair process. (wikipedia.org)
  • In a lab setting, this can be used to introduce fluorescent or other tagged nucleotides by purposefully inducing site-specific, single-stranded nicks in DNA in vitro and then adding the nicked DNA to an environment rich in DNA polymerase and tagged nucleotide. (wikipedia.org)
  • Sequence-independent upstream DNA-alphaCTD interactions strongly stimulate Escherichia coli RNA polymerase-lacUV5 promoter association. (semanticscholar.org)
  • The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase. (semanticscholar.org)
  • Uracil in DNA can arise either through the deamination of cytosine to form mutagenic U:G mispairs, or through the incorporation of dUMP by DNA polymerase to form U:A pairs [ PMID: 17116429 ]. (ebi.ac.uk)
  • Mutational analysis of loxP sites for efficient Cre-mediated insertion into genomic DNA. (nih.gov)
  • Genomic DNA from more than 1200 SALS cases from Ireland, Scotland, Quebec and the USA was genotyped for the 50bp SOD1 promoter deletion. (arctichealth.org)
  • Constitutional genomic DNA was isolated in all cases either from peripheral blood leukocytes or liver tissue adjacent to the tumor. (aacrjournals.org)
  • Contaminating residual genomic DNA was removed by digestion with RNase-free DNase (Boehringer Mannheim) before reverse transcription. (aacrjournals.org)
  • Genomic DNA (gDNA) was extracted from mononuclear cells using TRIZOL reagent (Invitrogen, Life Technologies, Grand Island, NY) according to the manufacturer's protocol. (medsci.org)
  • Genomic DNA was prepared from leukocytes of peripheral venous blood. (molvis.org)
  • Following isolation of NDMA-induced mutants, genomic DNA will be isolated from each for molecular analysis. (epa.gov)
  • Genomic DNA was isolated from saliva and MMP20 exons and exon-intron boundaries sequenced. (frontiersin.org)
  • To gain insights into the biology of thymomas and thymic carcinomas, we did a comprehensive genomic analysis of 45 resected thymic tumors. (aacrjournals.org)
  • deconstructSigs confers the ability to define mutational processes driven by environmental exposures, DNA repair abnormalities, and mutagenic processes in individual tumors with implications for precision cancer medicine. (biomedcentral.com)
  • In this study, the researchers studied the mutational signatures of tumors from 37 people with cSCC using whole-exome analyses. (medicalnewstoday.com)
  • DNA Alterations in Primary and Circulating Tumors, Non-Coding RNAs for Cancer Classification, Detection, and Monitoring, Identifying Pred. (utah.edu)
  • Mutant proteins were purified and tested for their catalytic properties and their abilities to bind DNA and AdoMet. (cf.ac.uk)
  • Mutational analysis of the latency-associated nuclear antigen DNA-binding domain of Kaposi's sarcoma-associated herpesvirus reveals structural conservation among gammaherpesvirus origin-binding proteins. (bcm.edu)
  • Analysis of truncated WT1 proteins demonstrated that three of four zinc fingers were necessary for RNA-protein interaction. (mendeley.com)
  • The N-terminal domain of these proteins has been shown in Escherichia coli PepA to function as a DNA-binding protein in Xer site-specific recombination and in transcriptional control of the carAB operon [ PMID: 10449417 , PMID: 10970742 ]. (ebi.ac.uk)
  • In genetics, Flp-FRT recombination is a site-directed recombination technology, increasingly used to manipulate an organism's DNA under controlled conditions in vivo. (wikipedia.org)
  • Biochemical identification of mutational changes in a nucleotide sequence. (sickkids.ca)
  • We develop deconstructSigs, which allows the identification of mutational signatures within a single tumor sample. (biomedcentral.com)
  • The applicability of in vitro systems for the determination of mutational spectra for a given agent can be validated by comparison to spectra observed using in vivo systems. (epa.gov)
  • This will simplify the comparison of the mutational spectra observed in vitro and in vivo. (epa.gov)
  • Observation of similar mutational spectra for NDMA in human lymphoblastoid cells treated in vitro and in mouse lymphocytes following in vivo exposure will support the application of in vitro results for comparison to humans. (epa.gov)
  • Survey of total mutational burden and mutational spectra across many tumor types. (massgeneral.org)
  • An altered-specificity DNA-binding mutant of Escherichia coli sigma70 facilitates the analysis of sigma70 function in vivo. (semanticscholar.org)
  • Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis. (ebi.ac.uk)
  • We hypothesize that unlike Dnmt3a, Dnmt3b does not oligomerize and to test this hypothesis, we performed mutational analysis of the conserved residues in Dnmt3b that are critical for Dnmt3a tetrameric structure. (purdue.edu)
  • Crystal structure analysis of an Escherichia coli homologue identified conserved amino acid residues that are critical for its substrate recognition/interaction and base hydrolysis functions. (uzh.ch)
  • On the basis of amino acid sequence alignments and structural data of related enzymes, we have performed a mutational analysis of 14 amino acid residues in the catalytic domain of the murine Dnmt3a DNA-(cytosine C5)-methyltransferase. (cf.ac.uk)
  • The target residues are located within the ten conserved amino acid sequence motifs characteristic for cytosine-C5 methyltransferases and in the putative DNA recognition domain of the enzyme (TRD). (cf.ac.uk)
  • Characterization of these mutants, by in vitro/in vivo restriction assays and DNA/AdoMet binding studies, indicated that most of the residues present in the AdoMet-binding pocket were not absolutely essential. (unthsc.edu)
  • Sankpal, UT & Rao, DN 2002, ' Mutational analysis of conserved residues in Hhal DNA methyltransferase ', Nucleic Acids Research , vol. 30, no. 12, pp. 2628-2638. (unthsc.edu)
  • This analysis allowed us to find 324 sensitive positions (out of the 483 MMP20 residues), pinpoint functionally important domains, and build an evolutionary chart of important conserved MMP20 regions. (frontiersin.org)
  • Uracil-DNA glycosylases are DNA repair enzymes that excise uracil residues from DNA by cleaving the N-glycosylic bond, initiating the base excision repair pathway. (ebi.ac.uk)
  • Methods: Mutation analysis was accomplished by direct sequencing of the complete 8 exons of NPHS2 and exons 8 and 9 of WT1 in 20 patients with steroid-resistant nephrotic syndrome, 25 with steroid-dependent nephrotic syndrome, and 13 with frequently-relapse nephrotic syndrome. (alliedacademies.org)
  • In addition to establishing a mutational spectrum for NDMA using human cell lines, in vivo studies will be conducted in mice to determine the mutational spectrum of NDMA at hprt locus. (epa.gov)
  • In vivo analysis of plant 18 S ribosomal RNA structure. (manor.edu)
  • In vivo analysis of plant RNA structure: soybean 18S ribosomal and ribulose-1,5-bisphosphate carboxylase small subunit RNAs. (manor.edu)
  • Using 32 P-postlabeling/PAGE and authentic standards, we identified dA-aristolactam (AL) and dG-AL DNA adducts in the renal cortex of patients with EN but not in patients with other chronic renal diseases. (pnas.org)
  • To determine the frequency, mutational spectrum, and phenotype of neurofibromatosis type 1-like syndrome (NFLS) in a large cohort of patients. (nih.gov)
  • In a second cross-sectional study, 1318 unrelated anonymous samples collected in 2003-2007 from patients with a broad range of signs typically found in neurofibromatosis type 1 (NF1) but no detectable NF1 germline mutation underwent SPRED1 mutation analysis. (nih.gov)
  • This pathology has nuclear heterogeneous genetic origins, and at present, molecular diagnostic tests on nuclear DNA cover only 30% of BrS patients. (cdc.gov)
  • Mutational analysis of patients with X-linked adrenoleukodystrophy. (nih.gov)
  • The accuracy of plasma RAS mutational status determined by OncoBEAM RAS kit was confirmed for Japanese mCRC patients. (oncoletter.ch)
  • The concordance rate between plasma- and tissue-based analyses was 86.4% in overall, rising to 89.2% in patients excluding lung metastasis alone, with 13.6% of discordant cases being potentially attributed to variables of tissue heterogeneity, a longer interval in sample collection from archived tissue to plasma and a lower amount of ctDNA shed into plasma. (oncoletter.ch)
  • this study analyses the impact of using an NGS platform for molecular diagnosis of mCRC patients. (oncoletter.ch)
  • For the case-control analysis of OGG1 R154H, a total of 625 hereditary or sporadic colorectal cancer patients and 527 normal controls were screened. (springer.com)
  • There was "strong positive correlation" between a new mutational signature called signature 32 and the duration of the treatment with azathioprine in immunosuppressed patients. (medicalnewstoday.com)
  • The mutational signatures are specific and therapy-related, as they are only present in the genomes of relapsed ALL patients but not in other pediatric or adult cancer genomes," Zhang said. (newswise.com)
  • The analysis also included targeted deep sequencing of leukemic cells collected regularly during treatment of 16 patients. (newswise.com)
  • These patients also had a higher median tumor mutational burden (TMB). (urotoday.com)
  • Mutational analysis of Escherichia coli PepA, a multifunctional DNA-binding aminopeptidase. (ebi.ac.uk)
  • Figure 5 from Mutational analysis of Escherichia coli heat shock transcription factor sigma 32 reveals similarities with sigma 70 in recognition of the -35 promoter element and differences in promoter DNA melting and -10 recognition. (semanticscholar.org)
  • Mechanistic differences in promoter DNA melting by Thermus aquaticus and Escherichia coli RNA polymerases. (semanticscholar.org)
  • MutS plays a critical role in DNA mismatch repair in Escherichia coli by binding to mismatches and initiating repair in an ATP-dependent manner. (rcsb.org)
  • Mutational spectrum induced in Saccharomyces cerevisiae by the carcinogen N-2-acetylaminofluorene. (biomedsearch.com)
  • The purpose of this project is to establish a mutational spectrum for Nitrosodimethylamine (NDMA) in order to provide evidence that environmental tobacco smoke (ETS) exposure among nonsmokers is involved in the induction of lung cancer, and other tobacco smoke-related cancers. (epa.gov)
  • Initially, two human B lymphoblastoid cell lines AHH-1 and MCL-5 will be used to study the mutational spectrum of NDMA. (epa.gov)
  • Both loci will be used to study the mutational spectrum of NDMA. (epa.gov)
  • Analysis of plasma (PL)-derived circulating free tumour DNA (ctDNA) as an adjunct to BM biopsy, for mutational characterisation and tracking disease progression, was evaluated. (ovid.com)
  • Sensitive tumour detection and classification using plasma cell-free DNA methylomes. (sickkids.ca)
  • This project will evaluate if ctDNA can be utilised for tumour genome characterisation and disease detection to guide treatment decisions with an ultimate objective to incorporate ctDNA analysis as a routine diagnostic modality for MM. (monash.edu)
  • Single-cell mutation and phospho-protein analyses reveal the segregation of oncogenic STAT5 and ERK activation to competing clones. (nature.com)
  • Although a number of studies have characterized the DNA binding properties of the WT1 protein, recent evidence has suggested that WT1 may also have a role in RNA metabolism. (mendeley.com)
  • The p53 protein is called "the guardian of the genome" because this multifunctional transcription factor, which regulates cell cycle progression, repair and programmed cell death in mammals, targets for apoptosis those cells that accumulate unsustainable DNA damage [ 1 - 4 ]. (pubmedcentralcanada.ca)
  • Mutagenesis of region 4 of sigma 28 from Chlamydia trachomatis defines determinants for protein-protein and protein-DNA interactions. (semanticscholar.org)
  • Analysis of the role of the mitogen-activated protein kinase in mediating cyclic-adenosine 3′,5′-Monophosphate effects on prolactin promoter activity. (ohsu.edu)
  • Characterization of DNA regions mediating the ability of Ca2+/calmodulin dependent protein kinase II to stimulate prolactin promoter activity. (ohsu.edu)
  • Senecoff JF, Cox MM. Directionality in FLP protein-promoted site-specific recombination is mediated by DNA-DNA pairing. (manor.edu)
  • HhaI DNA methyltransferase belongs to the C5-cytosine methyltransferase family, which is characterized by the presence of a set of highly conserved amino acids and motifs present in an invariant order. (unthsc.edu)
  • As their family name suggests, a highly conserved tyrosine nucleophile cleaves the DNA strands. (wikipedia.org)
  • Molecular cloning of human uracil-DNA glycosylase, a highly conserved DNA repair enzyme. (ebi.ac.uk)
  • Mutational analysis of a highly conserved glutamate, Glu38, has revealed its role in mismatch recognition by enabling MutS to discriminate between homoduplex and mismatched DNA. (rcsb.org)
  • It does so by causing recombination between the two inverted repetitions on the 2 µ plasmid during DNA replication. (wikipedia.org)
  • The diagram shows the effects of nicks on intersecting DNA in a twisted plasmid. (wikipedia.org)
  • Senecoff JF, Rossmeissl PJ, Cox MM. DNA recognition by the FLP recombinase of the yeast 2 micron plasmid. (manor.edu)
  • Application of deconstructSigs identifies samples with DNA repair deficiencies and reveals distinct and dynamic mutational processes molding the cancer genome in esophageal adenocarcinoma compared to squamous cell carcinomas. (biomedcentral.com)
  • Based on the sequence alignment of promoters recognized by FliA and genome in silico analysis, we propose that P. putida sigma 28 recognizes a TCAAG-t-N-12-GCCGATA consensus sequence located between -34 and -8 and that this sequence is preferentially associated with an AT-rich upstream region. (diva-portal.org)
  • Ligases are versatile and ubiquitous enzymes that join the 3' hydroxyl and 5' phosphate ends to form a phosphodiester bond, making them essential in nicked DNA repair, and ultimately genome fidelity. (wikipedia.org)
  • DNA mismatch repair (MMR) is an important DNA repair system that helps maintain genome plasticity by correcting mismatches, or non Watson-Crick base pairs in the a DNA duplex. (wikipedia.org)
  • They underwent whole genome sequencing of leukemic cells collected at the diagnosis and relapse as well as normal DNA. (newswise.com)
  • A collection of GPU-accelerated edge libraries, reference applications, and open-source applications, the NVIDIA Clara Parabricks Toolkit is created for developers to build AI-assisted workflows for genome analysis. (nvidia.com)
  • There are many challenges in processing the raw DNA sequencing reads from a patient's resected tumor or biopsy material, aligning them accurately to the reference human genome, and then scanning for loci where the tumor DNA differs from the patient's bulk "normal" DNA (e.g. from a blood draw). (massgeneral.org)
  • Furthermore, we found that Acr can greatly reduce the DNA repair capacity for damage induced by benzo[ a ]pyrene diol epoxide. (pnas.org)
  • Together these results suggest that Acr is a major etiological agent for CS-related lung cancer and that it contributes to lung carcinogenesis through two detrimental effects: DNA damage and inhibition of DNA repair. (pnas.org)
  • PAHs have been shown to be strong carcinogens, and thus PAH-induced DNA damage may shape the p53 mutational pattern in lung cancer and may also represent a strong molecular link between lung cancer and cigarette smoking ( 1 , 2 , 5 - 7 ). (pnas.org)
  • In this study, we report for the first time that a proportion of human lung cancer cell lines did not properly arrest before entering mitosis in the presence of a catalytic, circular cramp-forming topoisomerase II inhibitor ICRF-193, whereas the decatenation G 2 checkpoint impairment was present independently of the impaired DNA damage G 2 checkpoint. (aacrjournals.org)
  • (11) previously reported that in contrast to DNA damage checkpoint, decatenation G 2 checkpoint activation relies on ataxia telangiectasia and Rad3-related (ATR) activity and nuclear exclusion of cyclin B1 instead of ataxia-telangiectasia mutated (ATM)-dependent down-regulation of cdc2/cyclin B1 activity. (aacrjournals.org)
  • Independent of replicative age, factors such as oncogenic activation, DNA damage, chromatin remodeling, cellular stress, overexpression of cyclin-dependent kinase (Cdk) inhibitors, and deprotection of chromosome ends can also induce a phenotype resembling senescence ( 11 -16 ). (aacrjournals.org)
  • A nick is a discontinuity in a double stranded DNA molecule where there is no phosphodiester bond between adjacent nucleotides of one strand typically through damage or enzyme action. (wikipedia.org)
  • Nicked DNA can be the result of DNA damage or purposeful, regulated biomolecular reactions carried out in the cell. (wikipedia.org)
  • For instance, some mutational signatures are associated with age, others with DNA damage, and others yet with tobacco smoking or ultraviolet light exposure. (medicalnewstoday.com)
  • The method relies on the ligation of sequencing adapters harboring random yet complementary double-stranded nucleotide sequences to the sample DNA of interest. (nih.gov)
  • Mutational analysis pinpointed ribonucleotide sequences critical for binding. (mendeley.com)
  • In such studies, these sequences are generally assumed to be the only version present in DNA of the organism of interest. (cambridge.org)
  • Immunoprecipitated (ChIP) or whole-cell extract (WCE) DNA was amplified with primers specific to upstream sequences of KAR3 and TEL1 (nonspecific control). (asm.org)
  • Previously we demonstrated that DNA adducts induced by diol epoxides of polycyclic aromatic hydrocarbons (PAHs), a major category of cigarette smoke (CS) carcinogens, preferentially occur at p53 mutational hotspots in CS-related lung cancers and that adducts formed at these locations are poorly repaired ( 5 - 7 ). (pnas.org)
  • Mutational characterisation in multiple myeloma (MM) currently relies on bone marrow (BM) biopsy, which fails to capture the putative spatial and genetic heterogeneity of this multifocal disease. (ovid.com)
  • We conclude that ctDNA analysis as an adjunct to BM biopsy represents a noninvasive and holistic strategy for improved mutational characterisation and therapeutic monitoring of MM. (ovid.com)
  • BM biopsy is invasive, subject to sampling bias and does not capture the spatial genomic heterogeneity of MM and thereby inadequate for mutational characterisation and prognostication. (monash.edu)
  • Cellular resistance to cisplatin (cDDP) is a complex phenomenon involving multiple alterations such as increased defense mechanisms, augmentation of DNA repair, and inhibition of apoptosis ( 2 ). (aacrjournals.org)
  • Circulating cell-free DNA (cfDNA) in plasma offers a non-invasive approach to monitor tumor molecular profiling in real-time at multiple time-points, detection of emerging genomic alterations associated with drug resistance and clarifying cancer prognosis and diagnosis of cancer recurrence or progression. (selectbiosciences.com)
  • Cancer results from alterations to DNA that lead to the activation of oncogenes or the inactivation of tumor suppressors. (massgeneral.org)
  • To examine the contributions of individual amino acids to the function of the DNA binding domain of Pit-1, we developed an approach involving random, in vitro mutagenesis followed by functional screening in Saccharomyces cerevisiae. (elsevier.com)
  • In vitro analyses of apoptosis through flow cytometry and confocal microscopy show that NANOS3 capacity to prevent apoptosis was impaired by this mutation. (hindawi.com)
  • abstract = "Pit-1 is a member of the POU family of transcription factors, which contain a bipartite DNA binding domain. (elsevier.com)
  • APOBEC3G is the best known of several DNA cytosine deaminases that function to inhibit the replication of parasitic genetic elements including the lentivirus HIV. (mdpi.com)
  • Moreover, 100-200 nucleotides of the telomeric DNA are removed from both ends of chromosomes with each round of replication, perhaps due to the action of a 5′-3′ exonuclease ( 9 ). (aacrjournals.org)
  • LANA binds the terminal repeats via the C-terminal DNA-binding domain (DBD) to support latent DNA replication. (bcm.edu)
  • In summary, these data suggest that the secondary and tertiary structures of LANA and EBNA1 DBDs are conserved and are critical for (i) sequence-specific DNA binding, (ii) multimer formation, (iii) LANA-dependent transcriptional repression, and (iv) DNA replication. (bcm.edu)
  • Nicks allow DNA strands to untwist during replication, and are also thought to play a role in the DNA mismatch repair mechanisms that fix errors on both the leading and lagging daughter strands. (wikipedia.org)
  • Some sources of mismatched base pairs include replication errors and deamination of 5-methylcytosine DNA to form thymine. (wikipedia.org)
  • For eukaryotes specifically, the mechanism of DNA replication elongation between the leading and lagging strand differs. (wikipedia.org)
  • Here we apply three independent tests, accounting for non-uniform base compositions in synonymous and non-synonymous sites, to test whether the hotspots emerge via selection or due to mutational bias. (pubmedcentralcanada.ca)
  • The presence of hotspots is compatible with either a mutational or a selectional scenario or a combination thereof [ 14 , 17 ]. (pubmedcentralcanada.ca)
  • DNA Mutational Analysis" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (sickkids.ca)
  • This study implies plasticity in the recognition of cofactor by HhaI DNA methyltransferase. (unthsc.edu)
  • Bruner SD, Norman DP, Verdine GL (2000) Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. (springer.com)
  • The ligase forms a DNA-adenylate complex, assisting recognition. (wikipedia.org)
  • Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions. (ebi.ac.uk)
  • Effects of this combination on downstream markers were analyzed via Western blot analysis. (aacrjournals.org)
  • This allows formation of the stable MutS-ATP-DNA clamp, a key intermediate in triggering downstream repair events. (rcsb.org)
  • Their published Wellcome Trust Sanger Institute (WTSI) Mutational Signature Framework offers an elegant approach to first identify the signatures of mutational processes present in a set of tumor samples and then apply those signatures to the samples to determine the contribution of each mutational process to each individual sample. (biomedcentral.com)
  • Many signatures, corresponding to the activity of both known and unknown mutational processes, were found across multiple tumor types. (biomedcentral.com)
  • In order to address this challenge, we present a method to determine the contributions of each mutational process from a set of published signatures in a single tumor sample. (biomedcentral.com)
  • As Prof. Proby and colleagues explain, different cancer-causing factors have different mutational signatures. (medicalnewstoday.com)
  • The analysis also revealed two novel mutational patterns or signatures. (newswise.com)
  • Researchers showed thiopurines caused one of the new mutational signatures. (newswise.com)
  • Each dot represents a cancer patient whose tumor was subjected to whole-exome DNA sequencing. (massgeneral.org)
  • Analysis of their impact on phenotype of the mutants was performed. (mdpi.com)
  • Here, we constructed a panel of APOBEC3G amino acid substitution mutants and performed a series of biochemical, genetic, and structural assays to distinguish between "Brim" and "Kink" models for single-strand DNA binding. (mdpi.com)
  • As a contribution to a better understanding of the developmental processes that are specific to plants, we have begun a genetic analysis of leaf ontogeny in the model system Arabidopsis thaliana by performing a large-scale screening for mutants with abnormal leaves. (genetics.org)
  • As a contribution to the causal analysis of plant leaf development, we first performed a large-scale screen for EMS-induced mutants with aberrantly shaped or sized leaves. (genetics.org)
  • Sequence analysis of the URA3 mutants revealed approximately 48% frameshifts, approximately 44% base substitutions and approximately 8% complex events. (biomedsearch.com)
  • In the present study, the identification of the HvDWARF genomic sequence, its mutational and functional analysis and characterization of new mutants are reported. (mdpi.com)
  • In this study, we have analyzed the crystal structures, DNA binding and the response to ATP binding of three Glu38 mutants. (rcsb.org)
  • We extracted cfDNA from 500 μL of plasma, which is sufficient for target mutation analysis using dPCR. (springer.com)
  • HhaI DNA methyltransferase has been subjected to a lot of biochemical and crystallographic studies. (unthsc.edu)
  • Mutational and deletion analyses narrowed the region essential for elicitor activity to the 23-amino-acid peptide (H 2 N-NQGISEKQLDQLLTQLIMALLQQ-COOH). (asm.org)
  • The p53 binding pattern of carcinogenic polycyclic aromatic hydrocarbons (PAHs) found in CS coincides with the p53 mutational pattern found in lung cancer, and PAHs have thus been considered to be major culprits for lung cancer. (pnas.org)
  • Human thymine DNA glycosylase (TDG) was discovered as an enzyme that can initiate base excision repair at sites of 5-methylcytosine- or cytosine deamination in DNA by its ability to release thymine or uracil from G.T and G.U mismatches. (uzh.ch)
  • Digital PCR (dPCR) enables the detection and characterization of fragmented DNA that is in low abundance in blood. (springer.com)
  • Several high-resolution structures of the APOBEC3G catalytic domain have been generated, but none reveal how this enzyme binds to substrate single-stranded DNA. (mdpi.com)
  • The overall data set is most consistent with the Brim model for single-stranded DNA binding by APOBEC3G. (mdpi.com)
  • A single-stranded break (nick) in DNA can be formed by the hydrolysis and subsequent removal of a phosphate group within the helical backbone. (wikipedia.org)
  • Thus, a mutational analysis was performed on 35 cases, including all cases with moderate and strong EGFR staining. (pubmedcentralcanada.ca)
  • Mutational EGFR and HER-2 status were assessed by RT-PCR. (clinicaltrials.gov)
  • This family of recombinases performs its function via a type IB topoisomerase mechanism causing the recombination of two separate strands of DNA. (wikipedia.org)
  • Takeshita T., Iwase H. (2019) dPCR Mutational Analyses in Cell-Free DNA: A Comparison with Tissues. (springer.com)
  • Together, the presence of a nick and a ribonucleotide make the leading strand easily recognizable to the DNA mismatch repair machinery. (wikipedia.org)
  • In order to join these fragments, the ligase progresses through three steps: Addition of an adenosine monophosphate (AMP) group to the enzyme, referred to as adenylylation, Adenosine monophosphate transfer to the DNA and Nick sealing, or phosphodiester bond formation. (wikipedia.org)
  • Acr-DNA adducts, similar to PAH-DNA adducts, induce predominantly G-to-T transversions in human cells. (pnas.org)
  • After metabolic activation, AA reacts with DNA to form covalent dA-aristolactam (AL) and dG-AL adducts ( 20 , 21 ). (pnas.org)
  • On the lagging strand, nicks exist between Okazaki fragments and are easily recognizable by the DNA mismatch repair machinery prior to ligation. (wikipedia.org)
  • Hindson BJ, Ness KD, Masquelier DA et al (2011) High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. (springer.com)
  • Current projects in the lab include molecular phylogenetic analyses of familial and ordinal level relationships in the arthrodontous mosses, studies of hybridization using molecular and morphological markers, and investigations of cryptic speciation within geographically widespread species. (duke.edu)
  • Diaz LA Jr, Bardelli A (2014) Liquid biopsies: genotyping circulating tumor DNA. (springer.com)
  • Dawson SJ, Tsui DW, Murtaza M et al (2013) Analysis of circulating tumor DNA to monitor metastatic breast cancer. (springer.com)
  • Garcia-Murillas I, Schiavon G, Weigelt B et al (2015) Mutation tracking in circulating tumor DNA predicts relapse in early breast cancer. (springer.com)
  • Diehl F, Schmidt K, Choti MA et al (2008) Circulating mutant DNA to assess tumor dynamics. (springer.com)
  • In circulating tumor DNA (ctDNA), mutant MEK1 levels declined with treatment, but a previously unrecognized KRAS Q61H mutation was also identified that increased despite therapy. (aacrjournals.org)