Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
DNA analogs containing neutral amide backbone linkages composed of aminoethyl glycine units instead of the usual phosphodiester linkage of deoxyribose groups. Peptide nucleic acids have high biological stability and higher affinity for complementary DNA or RNA sequences than analogous DNA oligomers.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
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).
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 reformation of all, or part of, the native conformation of a nucleic acid molecule after the molecule has undergone denaturation.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
Copies of transposable elements interspersed throughout the genome, some of which are still active and often referred to as "jumping genes". There are two classes of interspersed repetitive elements. Class I elements (or RETROELEMENTS - such as retrotransposons, retroviruses, LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS) transpose via reverse transcription of an RNA intermediate. Class II elements (or DNA TRANSPOSABLE ELEMENTS - such as transposons, Tn elements, insertion sequence elements and mobile gene cassettes of bacterial integrons) transpose directly from one site in the DNA to another.
Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.
Nucleic acid which complements a specific mRNA or DNA molecule, or fragment thereof; used for hybridization studies in order to identify microorganisms and for genetic studies.
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.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
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.
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)
Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.
Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). Copies of the LINE 1 (L1) family form about 15% of the human genome. The jockey elements of Drosophila are LINEs.
The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). It is derived from the 7SL RNA component of the SIGNAL RECOGNITION PARTICLE and contains an RNA polymerase III promoter. Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases.
The genetic complement of a plant (PLANTS) as represented in its DNA.
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
Deoxyribonucleic acid that makes up the genetic material of plants.
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.
A sequential pattern of amino acids occurring more than once in the same protein sequence.
Highly repetitive DNA sequences found in HETEROCHROMATIN, mainly near centromeres. They are composed of simple sequences (very short) (see MINISATELLITE REPEATS) repeated in tandem many times to form large blocks of sequence. Additionally, following the accumulation of mutations, these blocks of repeats have been repeated in tandem themselves. The degree of repetition is on the order of 1000 to 10 million at each locus. Loci are few, usually one or two per chromosome. They were called satellites since in density gradients, they often sediment as distinct, satellite bands separate from the bulk of genomic DNA owing to a distinct BASE COMPOSITION.
A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
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.
DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.
Any method used for determining the location of and relative distances between genes on a chromosome.
The clear constricted portion of the chromosome at which the chromatids are joined and by which the chromosome is attached to the spindle during cell division.
A plant genus of the family ORCHIDACEAE that contains dihydroayapin (COUMARINS) and phenanthraquinones.
Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).
A technique that labels specific sequences in whole chromosomes by in situ DNA chain elongation or PCR (polymerase chain reaction).
Copies of DNA sequences which lie adjacent to each other in the same orientation (direct tandem repeats) or in the opposite direction to each other (INVERTED TANDEM REPEATS).
A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
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.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE.
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)
One of the Type II site-specific deoxyribonucleases (EC It recognizes and cleaves the sequence G/GATCC at the slash. BamHI is from Bacillus amyloliquefaciens N. Numerous isoschizomers have been identified. EC 3.1.21.-.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.
A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).
A technique with which an unknown region of a chromosome can be explored. It is generally used to isolate a locus of interest for which no probe is available but that is known to be linked to a gene which has been identified and cloned. A fragment containing a known gene is selected and used as a probe to identify other overlapping fragments which contain the same gene. The nucleotide sequences of these fragments can then be characterized. This process continues for the length of the chromosome.
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.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
A genus of achlorophyllic algae in the family Chlorellaceae, and closely related to CHLORELLA. It is found in decayed matter; WATER; SEWAGE; and SOIL; and produces cutaneous and disseminated infections in various VERTEBRATES including humans.
The relationships of groups of organisms as reflected by their genetic makeup.
Plasmids containing at least one cos (cohesive-end site) of PHAGE LAMBDA. They are used as cloning vehicles.
Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.
The region of DNA which borders the 3' end of a transcription unit and where a variety of regulatory sequences are located.
Deoxyribonucleic acid that makes up the genetic material of fungi.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.
Deoxyribonucleic acid that makes up the genetic material of viruses.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
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.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.
A terminal section of a chromosome which has a specialized structure and which is involved in chromosomal replication and stability. Its length is believed to be a few hundred base pairs.
Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
Genotypic differences observed among individuals in a population.
Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions.
Contiguous large-scale (1000-400,000 basepairs) differences in the genomic DNA between individuals, due to SEQUENCE DELETION; SEQUENCE INSERTION; or SEQUENCE INVERSION.
Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.
Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)
Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.
Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).
The most common of the microsatellite tandem repeats (MICROSATELLITE REPEATS) dispersed in the euchromatic arms of chromosomes. They consist of two nucleotides repeated in tandem; guanine and thymine, (GT)n, is the most frequently seen.
Chromosomes in which fragments of exogenous DNA ranging in length up to several hundred kilobase pairs have been cloned into yeast through ligation to vector sequences. These artificial chromosomes are used extensively in molecular biology for the construction of comprehensive genomic libraries of higher organisms.
An isothermal in-vitro nucleotide amplification process. The process involves the concomitant action of a RNA-DIRECTED DNA POLYMERASE, a ribonuclease (RIBONUCLEASES), and DNA-DIRECTED RNA POLYMERASES to synthesize large quantities of sequence-specific RNA and DNA molecules.
A genus of protozoa, formerly also considered a fungus. Characteristics include the presence of violet to brown spores.
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
RNA 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.
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
Sequential operating programs and data which instruct the functioning of a digital computer.
The functional hereditary units of PLANTS.
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.
A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
A pyrimidine base that is a fundamental unit of nucleic acids.
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.
A hepatic carcinogen whose mechanism of activation involves N-hydroxylation to the aryl hydroxamic acid followed by enzymatic sulfonation to sulfoxyfluorenylacetamide. It is used to study the carcinogenicity and mutagenicity of aromatic amines.
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.
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 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.
Deoxyribonucleic acid that makes up the genetic material of protozoa.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
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.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Ribonucleic acid that makes up the genetic material of viruses.
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)
Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.
Established cell cultures that have the potential to propagate indefinitely.
Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.
Structures within the nucleus of fungal cells consisting of or containing DNA, which carry genetic information essential to the cell.
One of the Type II site-specific deoxyribonucleases (EC It recognizes and cleaves the sequence G/AATTC at the slash. EcoRI is from E coliRY13. Several isoschizomers have been identified. EC 3.1.21.-.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Staining of bands, or chromosome segments, allowing the precise identification of individual chromosomes or parts of chromosomes. Applications include the determination of chromosome rearrangements in malformation syndromes and cancer, the chemistry of chromosome segments, chromosome changes during evolution, and, in conjunction with cell hybridization studies, chromosome mapping.
The sum of the weight of all the atoms in a molecule.
The systematic study of the complete DNA sequences (GENOME) of organisms.
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.
Electrophoresis in which agar or agarose gel is used as the diffusion medium.
The rate dynamics in chemical or physical systems.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.
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.
The chromosome region which is active in nucleolus formation and which functions in the synthesis of ribosomal RNA.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)
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.
Chromosome regions that are loosely packaged and more accessible to RNA polymerases than HETEROCHROMATIN. These regions also stain differentially in CHROMOSOME BANDING preparations.
Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)
Fibrous proteins secreted by INSECTS and SPIDERS. Generally, the term refers to silkworm fibroin secreted by the silk gland cells of SILKWORMS, Bombyx mori. Spider fibroins are called spidroins or dragline silk fibroins.
Any cell, other than a ZYGOTE, that contains elements (such as NUCLEI and CYTOPLASM) from two or more different cells, usually produced by artificial CELL FUSION.
A plant genus of the family POACEAE that is the source of EDIBLE GRAIN. A hybrid with rye (SECALE CEREALE) is called TRITICALE. The seed is ground into FLOUR and used to make BREAD, and is the source of WHEAT GERM AGGLUTININS.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Nucleotide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.
The genetic complement of an insect (INSECTS) as represented in its DNA.
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)
The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.
A genus of silkworm MOTHS in the family Bombycidae of the order LEPIDOPTERA. The family contains a single species, Bombyx mori from the Greek for silkworm + mulberry tree (on which it feeds). A native of Asia, it is sometimes reared in this country. It has long been raised for its SILK and after centuries of domestication it probably does not exist in nature. It is used extensively in experimental GENETICS. (From Borror et al., An Introduction to the Study of Insects, 4th ed, p519)
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.
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.
The male sex chromosome, being the differential sex chromosome carried by half the male gametes and none of the female gametes in humans and in some other male-heterogametic species in which the homologue of the X chromosome has been retained.
Microsatellite repeats consisting of three nucleotides dispersed in the euchromatic arms of chromosomes.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
Very long DNA molecules and associated proteins, HISTONES, and non-histone chromosomal proteins (CHROMOSOMAL PROTEINS, NON-HISTONE). Normally 46 chromosomes, including two sex chromosomes are found in the nucleus of human cells. They carry the hereditary information of the individual.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
Deletion of sequences of nucleic acids from the genetic material of an individual.
The process by which a DNA molecule is duplicated.
The sequential location of genes on a chromosome.
Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.
The region of DNA which borders the 5' end of a transcription unit and where a variety of regulatory sequences are located.
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Double-stranded nucleic acid molecules (DNA-DNA or DNA-RNA) which contain regions of nucleotide mismatches (non-complementary). In vivo, these heteroduplexes can result from mutation or genetic recombination; in vitro, they are formed by nucleic acid hybridization. Electron microscopic analysis of the resulting heteroduplexes facilitates the mapping of regions of base sequence homology of nucleic acids.
The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.
The homologous chromosomes that are dissimilar in the heterogametic sex. There are the X CHROMOSOME, the Y CHROMOSOME, and the W, Z chromosomes (in animals in which the female is the heterogametic sex (the silkworm moth Bombyx mori, for example)). In such cases the W chromosome is the female-determining and the male is ZZ. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
A selective increase in the number of copies of a gene coding for a specific protein without a proportional increase in other genes. It occurs naturally via the excision of a copy of the repeating sequence from the chromosome and its extrachromosomal replication in a plasmid, or via the production of an RNA transcript of the entire repeating sequence of ribosomal RNA followed by the reverse transcription of the molecule to produce an additional copy of the original DNA sequence. Laboratory techniques have been introduced for inducing disproportional replication by unequal crossing over, uptake of DNA from lysed cells, or generation of extrachromosomal sequences from rolling circle replication.
The genetic complement of a BACTERIA as represented in its DNA.
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.
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
A type of chromosomal aberration involving DNA BREAKS. Chromosome breakage can result in CHROMOSOMAL TRANSLOCATION; CHROMOSOME INVERSION; or SEQUENCE DELETION.
DNA present in neoplastic tissue.
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).
The genetic complement of MITOCHONDRIA as represented in their DNA.
Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.
A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.
A species of gram-positive, aerobic bacteria that produces TUBERCULOSIS in humans, other primates, CATTLE; DOGS; and some other animals which have contact with humans. Growth tends to be in serpentine, cordlike masses in which the bacilli show a parallel orientation.
The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.
The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.
An aberration in which a chromosomal segment is deleted and reinserted in the same place but turned 180 degrees from its original orientation, so that the gene sequence for the segment is reversed with respect to that of the rest of the chromosome.
Examination of CHROMOSOMES to diagnose, classify, screen for, or manage genetic diseases and abnormalities. Following preparation of the sample, KARYOTYPING is performed and/or the specific chromosomes are analyzed.
Interruption or suppression of the expression of a gene at transcriptional or translational levels.
Somewhat flattened, globular echinoderms, having thin, brittle shells of calcareous plates. They are useful models for studying FERTILIZATION and EMBRYO DEVELOPMENT.
A superfamily of proteins containing the globin fold which is composed of 6-8 alpha helices arranged in a characterstic HEME enclosing structure.
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
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.
A group of 13 or more ribonucleotides in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
The complete gene complement contained in a set of chromosomes in a fungus.
Molecules of DNA that possess enzymatic activity.
Mapping of the KARYOTYPE of a cell.
Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.
Proteins found in any species of bacterium.
Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells.
Higher-order DNA and RNA structures formed from guanine-rich sequences. They are formed around a core of at least 2 stacked tetrads of hydrogen-bonded GUANINE bases. They can be formed from one two or four separate strands of DNA (or RNA) and can display a wide variety of topologies, which are a consequence of various combinations of strand direction, length, and sequence. (From Nucleic Acids Res. 2006;34(19):5402-15)
The female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in human and other male-heterogametic species.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
Agents that are capable of inserting themselves between the successive bases in DNA, thus kinking, uncoiling or otherwise deforming it and therefore preventing its proper functioning. They are used in the study of DNA.
Actual loss of portion of a chromosome.
Tandem arrays of moderately repetitive, short (10-60 bases) DNA sequences which are found dispersed throughout the GENOME, at the ends of chromosomes (TELOMERES), and clustered near telomeres. Their degree of repetition is two to several hundred at each locus. Loci number in the thousands but each locus shows a distinctive repeat unit.
Short fragments of DNA or RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
MOLECULAR BIOLOGY techniques used in the diagnosis of disease.
Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes.
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.
Agents that emit light after excitation by light. The wave length of the emitted light is usually longer than that of the incident light. Fluorochromes are substances that cause fluorescence in other substances, i.e., dyes used to mark or label other compounds with fluorescent tags.
The functional hereditary units of BACTERIA.
Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.
Purine or pyrimidine bases attached to a ribose or deoxyribose. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.
Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.
The functional hereditary units of INSECTS.
Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.
DNA or RNA bound to a substrate thereby having fixed positions.
Studies determining the effectiveness or value of processes, personnel, and equipment, or the material on conducting such studies. For drugs and devices, CLINICAL TRIALS AS TOPIC; DRUG EVALUATION; and DRUG EVALUATION, PRECLINICAL are available.

Analysis of two cosmid clones from chromosome 4 of Drosophila melanogaster reveals two new genes amid an unusual arrangement of repeated sequences. (1/9059)

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

Nonmethylated transposable elements and methylated genes in a chordate genome. (2/9059)

The genome of the invertebrate chordate Ciona intestinalis was found to be a stable mosaic of methylated and nonmethylated domains. Multiple copies of an apparently active long terminal repeat retrotransposon and a long interspersed element are nonmethylated and a large fraction of abundant short interspersed elements are also methylation free. Genes, by contrast, are predominantly methylated. These data are incompatible with the genome defense model, which proposes that DNA methylation in animals is primarily targeted to endogenous transposable elements. Cytosine methylation in this urochordate may be preferentially directed to genes.  (+info)

Telomeric repeats on small polydisperse circular DNA (spcDNA) and genomic instability. (3/9059)

Small polydisperse circular DNA (spcDNA) is a heterogeneous population of extrachromosomal circular molecules present in a large variety of eukaryotic cells. Elevated amounts of total spcDNA are related to endogenous and induced genomic instability in rodent and human cells. We suggested spcDNA as a novel marker for genomic instability, and speculated that spcDNA might serve as a mutator. In this study, we examine the presence of telomeric sequences on spcDNA. We report for the first time the appearance of telomeric repeats in spcDNA molecules (tel-spcDNA) in rodent and human cells. Restriction enzyme analysis indicates that tel-spcDNA molecules harbor mostly, if not exclusively, telomeric repeats. In rodent cells, tel-spcDNA levels are higher in transformed than in normal cells and are enhanced by treatment with carcinogen. Tel-spcDNA is also detected in some human tumors and cell lines, but not in others. We suggest, that its levels in human cells may be primarily related to the amount of the chromosomal telomeric sequences. Tel-spcDNA may serve as a unique mutator, through specific mechanisms related to the telomeric repeats, which distinguish it from the total heterogeneous spcDNA population. It may affect telomere dynamics and genomic instability by clastogenic events, alterations of telomere size and sequestration of telomeric proteins.  (+info)

(CTG)n repeats markedly inhibit differentiation of the C2C12 myoblast cell line: implications for congenital myotonic dystrophy. (4/9059)

Although the mutation for myotonic dystrophy has been identified as a (CTG)n repeat expansion located in the 3'-untranslated region of a gene located on chromosome 19, the mechanism of disease pathogenesis is not understood. The objective of this study was to assess the effect of (CTG)n repeats on the differentiation of myoblasts in cell culture. We report here that C2C12 myoblast cell lines permanently transfected with plasmid expressing 500 bases long CTG repeat sequences, exhibited a drastic reduction in their ability to fuse and differentiate into myotubes. The percentage of cells fused into myotubes in C2 C12 cells (53.4+/-4.4%) was strikingly different from those in the two CTG repeat carrying clones (1.8+/-0.4% and 3.3+/-0. 7%). Control C2C12 cells permanently transfected with vector alone did not show such an effect. This finding may have important implications in understanding the pathogenesis of congenital myotonic dystrophy.  (+info)

Molecular characterization of the nitrite-reducing system of Staphylococcus carnosus. (5/9059)

Characterization of a nitrite reductase-negative Staphylococcus carnosus Tn917 mutant led to the identification of the nir operon, which encodes NirBD, the dissimilatory NADH-dependent nitrite reductase; SirA, the putative oxidase and chelatase, and SirB, the uroporphyrinogen III methylase, both of which are necessary for biosynthesis of the siroheme prosthetic group; and NirR, which revealed no convincing similarity to proteins with known functions. We suggest that NirR is essential for nir promoter activity. In the absence of NirR, a weak promoter upstream of sirA seems to drive transcription of sirA, nirB, nirD, and sirB in the stationary-growth phase. In primer extension experiments one predominant and several weaker transcription start sites were identified in the nir promoter region. Northern blot analyses indicated that anaerobiosis and nitrite are induction factors of the nir operon: cells grown aerobically with nitrite revealed small amounts of full-length transcript whereas cells grown anaerobically with or without nitrite showed large amounts of full-length transcript. Although a transcript is detectable, no nitrite reduction occurs in cells grown aerobically with nitrite, indicating an additional oxygen-controlled step at the level of translation, enzyme folding, assembly, or insertion of prosthetic groups. The nitrite-reducing activity expressed during anaerobiosis is switched off reversibly when the oxygen tension increases, most likely due to competition for electrons with the aerobic respiratory chain. Another gene, nirC, is located upstream of the nir operon. nirC encodes a putative integral membrane-spanning protein of unknown function. A nirC mutant showed no distinct phenotype.  (+info)

Roles of an Ets motif and a novel CACGAC direct repeat in transcription of the murine dihydrolipoamide dehydrogenase (Dld) gene. (6/9059)

The 5'-flanking region of the murine dihydrolipoamide dehydrogenase (Dld) gene was characterized for its promoter activity. DNase I footprinting analysis of the promoter region (-545 bp to +41 bp) revealed six major protein-binding domains (termed P1 to P6) that were protected by NIH3T3 fibroblast nuclear extracts. Transient transfection assays, using a series of nested deletions of the 2.5 kb 5'-flanking region ligated to the chloramphenicol acetyltransferase reporter gene, identified that the -42-bp to +41-bp region, which harbours the P1, P2, and P3 domains, had minimal transcriptional activity. When the 5'-flanking region was extended from -42 bp to -82 bp, there was an approx. 5-fold increase in promoter activity. To identify further the cis elements involved in transcription of the Dld gene (-82 bp to +41 bp), a series of mutations were introduced into this region and evaluated for functional effects using transient transfection and electrophoretic mobility shift assays. Mutation or deletion of the CACGAC direct repeat, located from -61 bp to -46 bp, resulted in minimal promoter activity. Mutation of the Ets motif, located from -37 bp to -32 bp, reduced the minimal promoter activity by approx. 50%, whereas the deletion of this motif almost abolished the promoter activity. These results indicate that: (i) the Ets motif is required for the minimal promoter activity and (ii) the CACGAC direct repeat enhances promoter activity. Database searches failed to identify the direct repeat with the CACGAC motif and hence the CACGAC sequence may represent a novel motif. The requirement of both the Ets motif and the direct repeat element for optimal promoter activity represents a unique combination for gene transcription.  (+info)

Nuclear factor I-mediated repression of the mouse mammary tumor virus promoter is abrogated by the coactivators p300/CBP and SRC-1. (7/9059)

To better understand the function of nuclear factor I (NFI) proteins in transcription, we have used transient transfection assays to assess transcriptional modulation by NFI proteins on the NFI-dependent mouse mammary tumor virus (MMTV) promoter. Expression of NFI-C or NFI-X, but not NFI-A or NFI-B proteins, represses glucocorticoid induction of the MMTV promoter in HeLa cells. Repression is DNA binding-independent as a deletion construct expressing the NH2-terminal 160 residues of NFI-C represses but does not bind DNA. Repression by NFI-C is cell type-dependent and occurs in HeLa and COS-1 cells but not 293 or JEG-3 cells. NFI-C does not repress progesterone induction of the MMTV promoter in HeLa cells, suggesting that progesterone induction of the promoter differs mechanistically from glucocorticoid induction. NFI-C-mediated repression is alleviated by overexpression of glucocorticoid receptor (GR), suggesting that NFI-C represses the MMTV promoter by preventing GR function. However, repression by NFI-C occurs with only a subset of glucocorticoid-responsive promoters, as the chimeric NFIGREbeta-gal promoter that is activated by GR is not repressed by NFI-C. Since the coactivator proteins p300/CBP, SRC-1A, and RAC3 had previously been shown to function at steroid hormone-responsive promoters, we asked whether they could influence NFI-C-mediated repression of MMTV expression. Expression of p300/CBP or SRC-1A alleviates repression by NFI-C, whereas RAC3 has no effect. This abrogation of NFI-C-mediated repression by p300/CBP and SRC-1A suggests that repression by NFI-C may occur by interference with coactivator function at the MMTV promoter.  (+info)

An ankyrin-like protein with transmembrane domains is specifically lost after oncogenic transformation of human fibroblasts. (8/9059)

We have identified a novel transformation-sensitive mRNA, which is present in cultured fibroblasts but is lacking in SV40 transformed cells as well as in many mesenchymal tumor cell lines. The corresponding gene is located on human chromosome 8 in band 8q13. The open reading frame of the mRNA encodes a protein of 1119 amino acids forming two distinct domains. The N-terminal domain consists of 18 repeats that are related to the cytoskeletal protein ankyrin. The C-terminal domain contains six putative transmembrane segments that resemble many ion channels. This overall structure is reminiscent of TRP-like proteins that function as store-operated calcium channels. The novel protein with an Mr of 130 kDa is expressed at a very low level in human fibroblasts and at a moderate level in liposarcoma cells. Overexpression in eukaryotic cells appears to interfere with normal growth, suggesting that it might play a direct or indirect role in signal transduction and growth control.  (+info)

Stern, M.J., Ames, G.F.L., Smith, N.H., Robinson, E.C. and Higgins, C.F. (1984) Repetitive Extragenic Palindromic Sequences A Major Component of the Bacterial Genome. Cell, 37, 1015-1026.
TY - JOUR. T1 - End-to-end transcription of an Alu family repeat. A new type of polymerase-III-dependent terminator and its evolutionary implication. AU - Hess, J.. AU - Perez-Stable, C.. AU - Wu, G. J.. AU - Weir, B.. AU - Tinoco, I.. AU - Shen, C. K.J.. PY - 1985/7/5. Y1 - 1985/7/5. N2 - Four or more consecutive thymidine residues on the non-template strand and G + C-richness of flanking DNA are the two necessary characteristics of efficient RNA polymerase-III-dependent transcriptional terminators. We have identified, from the study of in vitro transcription of a human Alu family repeat, a new type of RNA polymerase-III-dependent transcriptional terminator. A 258 base-pair Alu repeat located on the 3′ side of the human α1 globin gene can be transcribed in a HeLa S-100 extract to generate three RNA species of lengths 404 to 408, 252 to 255 and 173 to 174 nucleotides, respectively. Kinetics, pulse-chase and RNA incubation experiments showed no significant internal processing of the longer ...
One proposed strategy for controlling the transmission of insect-borne pathogens uses a drive mechanism to ensure the rapid spread of transgenes conferring disease refractoriness throughout wild populations. Here, we report the creation of maternal-effect selfish genetic elements in Drosophila that drive population replacement and are resistant to recombination-mediated dissociation of drive and disease refractoriness functions. These selfish elements use microRNA-mediated silencing of a maternally expressed gene essential for embryogenesis, which is coupled with early zygotic expression of a rescuing transgene.. ...
article{221460, abstract = {The distribution of the ribosomal RNA (rRNA) genes and three classes of highly repetitive DNA in the chromatin of interphase nuclei of Arabidopsis thaliana was studied for the first time through non-isotopic in situ hybridization and luminescence digital imaging microscopy. Each of the three classes of highly repetitive DNA exhibited a characteristic hybridization pattern, and one class was seen to be primarily localized on two chromocentres, which would allow it to distinguish a particular chromosome. The rDNA was consistently localized on the two largest chromocentres and on one or two smaller chromocentres. A limited number of nuclei exhibited more than four labelled chromocentres, indicative of either polypoidy or differential amplification of the rDNA. In nuclei where the nucleolus could be clearly observed, the nucleolar associated chromocentres (NACs) were seen to be labelled by the ribosomal DNA (rDNA) probe.}, author = {Bauwens, Serge and Van Oostveldt, ...
Higher eukaryotic genomes are typically large, complex and filled with both genes and multiple classes of repetitive DNA. The repetitive DNAs, primarily transposable elements, are a rapidly evolving genome component that can provide the raw material for novel selected functions and also indicate the mechanisms and history of genome evolution in any ancestral lineage. Despite their abundance, universality and significance, studies of genomic repeat content have been largely limited to analyses of the repeats in fully sequenced genomes. In order to facilitate a broader range of repeat analyses, the Assisted Automated Assembler of Repeat Families algorithm has been developed. This program, written in PERL and with numerous adjustable parameters, identifies sequence overlaps in small shotgun sequence datasets and walks them out to create long pseudomolecules representing the most abundant repeats in any genome. Testing of this program in maize indicated that it found and assembled all of the major repeats
Repetitive sequences are DNA sequences that occur many times in the genome. It has been experimentally shown that repetitive sequences can increase or decrease the expression levels of nearby genes by a variety of mechanisms and that the ability of repetitive sequences to alter gene expression depends on their epigenetic states. The epigenetic states of repetitive sequences depend on random epigenetic drift, stress, the genomic environment of the repetitive sequence, epigenetic inheritance, mutations in the genome, and other factors. Since repetitive sequences constitute approximately one half of the human and mouse genomes, the influence of repetitive sequences on gene expression in the mammalian genome is probably considerable. However, methods to detect and map such effects are lacking. These researchers have developed, and are continuing to develop, methods to associate gene expression changes with repetitive sequences. They use their associations to examine the epigenetic effects of ...
Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). The ini …
Scientists now know why it has been so difficult to sequence a region of the Y-chromosome linked to infertility. The AZFc region contains six massive and virtually identical stretches of repetitive DNA, according to a new study. The repeat elements were too large and too similar to be distinguished by conventional sequencing techniques. David C. Page, of the Whitehead Institute in Boston, and colleagues uncovered the regions details using a modified sequencing-mapping strategy. They identified 27 potential genes in the region, all of which are expressed predominantly or exclusively in the testis. Men with low or no sperm production frequently have deletions in the AZFc region, but the deletions do not seem to cause other health problems. The researchers propose that the repetitive structures in this region cause fertility problems by improperly binding to each other as the Y-chromosome reorganizes over time. DNA is either lost or misplaced. The repetitive elements, or amplicons, can form ...
The two methods of repair for DSBs are homologous recombination (HR) and non-homologous end-joining (NHEJ). In HR the nucleotide sequences of two sets of DNA are exchanged to repair the broken strands. For this to occur one of the sets of DNA must be undamaged. The 3 strand of the DSB invades the undamaged double stranded DNA and partially unwinds it for homologous pairing. The strands form branch migrations and Holiday junctions to restore the DNA with the DSB without any crossing over of the two sets 2. In NHEJ of a DSB, the broken pieces are ligated together (via the KU heterodimer) without the need of an undamaged, homologous set of DNA. However, there can be degradation at the ends of the break that can result in errors and the loss of DNA sequences2. DSBs caused from IR are usually repaired by this method4. DSBs can also be repaired by single-strand annealing (SSA) if the break occurs between two repeated sequences. The repeated sequences are extended on the ends and annealed to repair ...
nearly causes my machine to run out of memory (16G), takes a couple of days to run, and results in a blast output of 5.1G and 84 million rows--thats 84 million blast hits with an e-value below 0.001! By definition, that output is dominated by the repetitive elements. Repetitive elements are interesting, but in the case were we want to look at synteny, we have to wade through that 5.1G of stuff to find the very small chunk of data we need. This adds time to run the sequence comparison, time to parse, time to plot, time to analyze, and data to store, etc ...
The protection of genome integrity of germ cells is essential for animal fertility. Researchers from the Grosshans group characterized a defense mechanism against selfish genetic elements in the C. elegans germline. They identified a protein processing mechanism that controls the activity of small RNAs to achieve specific silencing of transposons while sparing endogenous genes.
Selfish genetic elements that promote their own survival could be used to disrupt mosquito genes essential for malaria transmission.
Repetitive sequences, primarily transposable elements form an indispensable part of eukaryotic genomes. However, little is known about how these sequences originate, evolve and function in context of
Note: Only deletions with sequenced breakpoints are included. Reported deletion junctions may be approximate due to the presence identical repeat sequences at the break points. Alternate junctions may be reported in the cited literature due to the inherent ambiguities of the direct repeats. Other reports of multiple deletions mapped within an individual have been published without specific sequence data for the deletion breakpoints. ...
While the main purpose of DNA is to code for proteins to be built in the cell, we know that a lot of DNA doesnt code for protein after all, such as the repeating region of the C9ORF72 gene. In healthy versions of the gene the repeated region (usually under 30 repeated units) is simply cut out of the RNA copy of the gene before the RNA is exported from the nucleus.. In C9ORF72-MND however, the repeated region is much larger - even up to a thousand repeated units and leads to a build up of the RNA repeats inside the nucleus but also, unexpectedly is made into abnormal toxic constituents in the cell cytoplasm called dipeptide repeat proteins. The discovery of dipeptide repeat proteins was puzzling to scientists as this type of non-protein coding RNA does not normally exit the nucleus to get to where protein can be made.. Dr Hautbergue and colleagues, who have developed expertise in the mechanisms of RNA nuclear export, looked to see how the pathological repeating precursor RNA molecules, that ...
Deutekom, J.C.T. van; Bakker, E.; Lemmers, R.J.L.F.; Wielen, M.J.R. van der; Bik, E.; Hofker, M.H.; Padberg, G.W.A.M. ; Frants, R.R. ...
Persistence of latent, replication-competent provirus in CD4+ T cells of human immunodeficiency virus (HIV)-infected individuals on antiretroviral treatment (ART) is the main obstacle for virus eradication. Methylation of the proviral 5′ long terminal repeat (LTR) promoter region has been proposed as a possible mechanism contributing to HIV latency; however, conflicting observations exist regarding its relevance. We assessed 5′-LTR methylation profiles in total CD4+ T cells from blood of 12 participants on short-term ART (30 months) followed up for 2 years, and a cross-sectional group of participants with long-term ART (6-15 years), using next generation sequencing. We then looked for associations between specific 5′-LTR methylation patterns and baseline and follow-up clinical characteristics. 5′-LTR methylation was observed in all participants and behaved dynamically. The number of 5′-LTR variants found per sample ranged from 1 to 13, with median sequencing depth of 16270× (IQR 4107×-46760
The 72 kDa IE1 protein of human cytomegalovirus (HCMV) is one of a few viral regulatory proteins expressed immediately after infection of a host cell. Although it is now well-established that IE1 is a potent transcriptional activator of the human immunodeficiency virus (HIV) long terminal repeat (LTR), the identity of the nucleotide sequence responsive to IE1 remains elusive and the molecular mechanism of this interaction is not well-understood. We have constructed various LTR mutants and tested them for their ability to be activated by IE1 using transient transfection assays. Mutations in the NF-κB sites, of either a few changes in the nucleotide sequence or a deletion of the entire region, abrogated IE1-driven transactivation. Deletion of the Tat-responsive element (TAR) had no significant effect on reporter expression. Mutations in the Sp1 sites or the TATA box significantly lowered LTR activity, but this is probably due to an effect on the general transcription system, as these elements are also
Molecular karyotypes of H. bogdanii Wilensky, 1918 (2n = 14), and H. brevisubulatum Link, 1844 ssp. brevisubulatum (2n = 28), were characterized by physical mapping of several repetitive sequences. A total of 18 repeats, including all possible di- or trinucleotide SSR (simple sequence repeat) motifs and satellite DNAs, such as pAs1, 5S rDNA, 45S rDNA, and pSc119.2, were used as probes for fluorescence in situ hybridization on root-tip metaphase chromosomes. Except for the SSR motifs AG, AT and GC, all the repeats we examined produced detectable hybridization signals on chromosomes of both species. A detailed molecular karyotype of the I genome of H. bogdanii is described for the first time, and each repetitive sequence is physically mapped. A high degree of chromosome variation, including aneuploidy and structural changes, was observed in H. brevisubulatum. Although the distribution of repeats in the chromosomes of H. brevisubulatum is different from that of H. bogdanii, similar patterns between the two
New enough and long enough for 5X expansion. Main hook seem ok, but the sources have not been quoted for any of the hooks as strongly encouraged to do. In particular, for ALT1, I see no claim in the article that sge can can drive populations extinct, only that a theoretically possible route to do this exists. For ALT2, Im not seeing the claim that sge have been found in virtually all species, and this seems an unlikely claim in any case. How many species have been tested? Certainly not virtually all of them. The copying from PLOS has been done under a compatible license and correctly recorded in edit summaries and on the talk page. However, the question arises of whether an article created and published outside Wikipedia can be considered new. @BlueMoonset: is there any precedent for this? Relevant dates are: creation of the PLOS wiki page, 12:45, 22 June 2018‎; publication of the original paper, 15 November 2018. The image of the book covers is not acceptable. The authors of the ...
Small direct repeats, which are frequent in all genomes, are a potential source of genome instability. To study the occurrence and genetic control of repeat-associated deletions, we developed a system in the yeast Saccharomyces cerevisiae that was based on small direct repeats separated by either random sequences or inverted repeats. Deletions were examined in the LYS2 gene, using a set of 31- to 156-bp inserts that included inserts with no apparent potential for secondary structure as well as two quasipalindromes. All inserts were flanked by 6- to 9-bp direct repeats of LYS2 sequence, providing an opportunity for Lys+ reversion via precise excision. Reversions could arise by extended deletions involving either direct repeats or random sequences and by -1-or +2-bp frameshift mutations. The deletion breakpoints were always associated with short (3- to 9-bp) perfect or imperfect direct repeats. Compared with the POL+ strain, deletions between small direct repeats were increased as much as ...
Davison, A.J., Marsden, H.S. and Wilkie, N.M. (1981) One functional copy of the long terminal repeat gene specifying the immediate-early polypeptide IE 110 suffices for a productive infection of human foetal lung cells by herpes simplex virus. Journal of General Virology, 55(1), pp. 179-191. (doi:10.1099/0022-1317-55-1-179) ...
Listing of all Polbase results with context for Reference: Error-prone replication of repeated DNA sequences by T7 DNA polymerase in the absence of its processivity subunit., Polymerase: T7, Property: Cloned or native
Summary All levels of life entail cooperation and conflict. Genes cooperate to build up a functional genome, which can yet be undermined by selfish genetic elements. Humans and animals cooperate to build up societies, which can yet be subverted by cheats. There is a long-standing interest among biologists to comprehend the tug-of-war between cooperation and conflict. Recently, research on bacteria was successful in identifying key factors that can tip the balance in favour or against cooperation. Bacteria cooperate through the formation of protective biofilms, cell-to-cell communication, and the secretion of shareable public goods. However, the advantage of bacteria being fast replicating units, easily cultivatable in high numbers, is also their disadvantage: they are small and imperceptible, such that measures of cooperation typically rely on averaged responses across millions of cells. Thus, we still know very little about bacterial cooperation at the biological relevant scale: the individual ...
The analysis of species-specific subfamilies of both the LINE and SINE mammalian repetitive DNA families suggests that such subfamilies have arisen by amplification of an extremely small group of master genes. In contrast to the master genes, the vast majority of both SINEs and LINEs appear to beh …
Purpose: Unless clones derived from genomic human DNA are known to be single copy, they can be assumed to contain highly repetitive sequences such as Alu. Hybridizing a probe withrepeats to a human DNA Southern blot will result in a signal in each human lane that looks very much like the ethidium bromide stained pattern: a continuous smear with little or no additional signal from the unique sequences on the probe. To reduce or eliminate the lane background due to the repetitive sequences, we add a large amount of unlabeled human DNA (sonicated to an average size of 400-700 bp for highest efficiency) to the labeled probes immediately before the denaturing and hybridizing steps. The excess number of repeat sequences in the human genomic DNA competes with the probe sequences for those on the blot, effectively reducing the lane background by preventing the probe repeats from hybridizing to the blot. With some probes, this treatment is not sufficient to reduce the lane background. If this is the ...
Repetitive elements are now known to have relevant cellular functions, including self-complementary sequences that form double stranded (ds) RNA. There are numerous pathways that determine the fate of endogenous dsRNA, and misregulation of endogenous dsRNA is a driver of autoimmune disease, particularly in the brain. Unfortunately, the alignment of high-throughput, short-read sequences to repeat elements poses a dilemma: Such sequences may align equally well to multiple genomic locations. In order to differentiate repeat elements, current alignment methods depend on sequence variation in the reference genome. Reads are discarded when no such variations are present. However, RNA hyper-editing, a possible fate for dsRNA, introduces enough variation to distinguish between repeats that are otherwise identical. To take advantage of this variation, we developed a new algorithm, RepProfile, that simultaneously aligns reads and predicts novel variations. RepProfile accurately aligns hyper-edited reads that
Repetitive elements are now known to have relevant cellular functions, including self-complementary sequences that form double stranded (ds) RNA. There are numerous pathways that determine the fate of endogenous dsRNA, and misregulation of endogenous dsRNA is a driver of autoimmune disease, particularly in the brain. Unfortunately, the alignment of high-throughput, short-read sequences to repeat elements poses a dilemma: Such sequences may align equally well to multiple genomic locations. In order to differentiate repeat elements, current alignment methods depend on sequence variation in the reference genome. Reads are discarded when no such variations are present. However, RNA hyper-editing, a possible fate for dsRNA, introduces enough variation to distinguish between repeats that are otherwise identical. To take advantage of this variation, we developed a new algorithm, RepProfile, that simultaneously aligns reads and predicts novel variations. RepProfile accurately aligns hyper-edited reads that
If you have a repeat grid with 5 same images and you drag (1) one image onto it, a popup appears and asks if you want to replace all of the images or only the one you were dragging onto it. OR (2) if you drag one image over the grid, the grid changes in areas (becomes an overlay) where a text appears, like Place here to replace all (same) images OR Place in this area to replace only this image ----, I really like this idea. Let me know if you need a graphic that explains better ...
This invention provides a method, and apparatus for performing the method, for reducing the power consumption of a radiotelephone. The method includes the steps of (a) receiving with a receiver of a radiotelephone at least a Word Synchronization pattern from a frame that is transmitted over a control channel; (b) receiving a first repeat of a control message that follows the Word Synchronization pattern within the frame; and (c) determining if the first repeat was correctly received. If the first repeat was correctly received, the method includes a further step of (d) determining if at least one reception-related criteria is met. If the reception-related criteria is determined to be met, the method includes a further step of (e) selectively removing operating power from one or more portions of the radiotelephone receiver for a predetermined time period during a remainder of the frame. The at least one reception-related criteria is a Message Error Rate (MER) that indicates a number of correctly received
As relatively badly as Greys Anatomy does in repeats, last nights FlashForward repeat had only a preliminary 1.0 rating, and so next weeks FF repeat is off the schedule and replaced by a Greys repeat. At this time still shows the FF repeat on the schedule.
Partially fluorinated ionic compounds are prepared. They are useful in the preparation of partially fluorinated dienes, in which the repeat units are cycloaliphatic.
I am selecting some data from a MySQL database to display in rows on a page using Dreamweavers repeat region function. For some reason that I cannot fathom, the repeat region function is...
One last thought: As I embark on my hiatus from blogging so as to focus on specific tasks at hand and to seek balance in my life, I know I cant achieve anything of lasting value on my own. Im going to need the support of family and friends - support Im already receiving and for which Im incredibly thankful. I also know that in seeking the balance I long for I must make time to feel and respond to the loving and guiding presence of God, my soul-dancing partner. I long to feel myself held, guided and lifted by his touch. This seems particularly important to me - essential, in fact - if I am to do all that I feel called to do. And that includes, at some future time, resuming this blog. ...
When you detail elements that repeat in your project you can choose between several ways of doing it efficiently. Watch this video to learn three alternative ways of handling repetition in your precas
Fantastic news!!! I had my first repeat blood testing after the ones in February that came back positive. My Scl 70 and Ku were negative!!!! My thyroid ...
Join Deke McClelland for an in-depth discussion in this video 097 Creating type that inverts anything behind it, part of Dekes Techniques
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Proc Natl Acad Sci U S A. 1988 Dec;85(23):8850-4. Research Support, Non-U.S. Govt; Research Support, U.S. Govt, Non-P.H.S.; Research Support, U.S. Govt, P.H.S.
TY - JOUR. T1 - Interaction between human tRNA synthetases involves repeated sequence elements. AU - Rho, Seung Bae. AU - Lee, Kyoung Hoa. AU - Kim, Jung Woo. AU - Shiba, Kiyotaka. AU - Jo, Yeong Joon. AU - Kim, Sunghoon. PY - 1996/9/17. Y1 - 1996/9/17. N2 - Aminoacyl-tRNA synthetases (tRNA synthetases) of higher eukaryotes form a multiprotein complex. Sequence elements that are responsible for the protein assembly were searched by using a yeast two-hybrid system. Human cytoplasmic isoleucyl-tRNA synthetase is a component of the multi-tRNA synthetase complex and it contains a unique C-terminal appendix. This part of the protein was used as bait to identify an interacting protein from a HeLa cDNA library. The selected sequence represented the internal 317 amino acids of human bifunctional (glutamyl- and prolyl-) tRNA synthetase, which is also known to be a component of the complex. Both the C-terminal appendix of the isoleucyl-tRNA synthetase and the internal region of bifunctional tRNA ...
TY - JOUR. T1 - A new dinucleotide repeat polymorphism at the telomere of chromosome 21q reveals a significant difference between male and female rates of recombination. AU - Blouin, J. L.. AU - Christie, D. H.. AU - Gos, A.. AU - Lynn, A.. AU - Morris, M. A.. AU - Ledbetter, D. H.. AU - Chakravarti, A.. AU - Antonarakis, S. E.. PY - 1995. Y1 - 1995. N2 - We have used a half-YAC containing the human chromosome 21 long-arm telomere to clone, map, and characterize a new dinucleotide repeat polymorphism (D21S1575) close to 21qter. This marker is AB - We have used a half-YAC containing the human chromosome 21 long-arm telomere to clone, map, and characterize a new dinucleotide repeat polymorphism (D21S1575) close to 21qter. This marker is UR - UR - M3 - Article. C2 - 7668265. AN - SCOPUS:0029013276. VL - 57. SP - 388. EP - 394. JO - American Journal ...
Sex and recombination are ubiquitous across the vast majority of life on earth. In eukaryotes, recombination during meiosis yields new variation that selection acts upon and, thus, facilitates evolution. However, meiosis provides an arena for manipulation and exploitation by selfish genetic elements. Selfish elements can increase in abundance independently of their host organism and frequently at a cost to host fitness. Several types of selfish elements act during meiosis and therefore it is possible for recombination rates and mechanisms to evolve to counteract and ameliorate their negative effects. However, few studies have investigated the interaction between recombination and selfish genetic elements. I conducted three studies on the evolution of recombination mechanisms in light of the impact of selfish elements. I begin my thesis with an introduction on selfish elements, recombination, and their possible interactions in Chapter 1. In Chapter 2, I found evidence that the synaptonemal ...
TY - JOUR. T1 - Crystallization and preliminary investigations on a telomeric repeat sequence C(4)A(2)C(4)A(2). AU - Savitha, G. AU - Leonidas, D. AU - Acharya, K R. AU - Viswamitra, M A. N1 - ID number: ISI:000169533300019. PY - 2001. Y1 - 2001. M3 - Article. VL - 57. SP - 873. EP - 875. JO - Acta Crystallographica Section D-Biological Crystallography. JF - Acta Crystallographica Section D-Biological Crystallography. SN - 0907-4449. ER - ...
Telomerase, a ribonucleoprotein with reverse transcriptase activity, enables human cells to maintain chromosomal stability and to proliferate without limits. Various stud..
|p|Among the goals of RNA structural and functional genomics is determining structures and establishing the functions of a rich repertoire of simple sequence repeats in transcripts. These repeats are present in transcripts from their birth in the nucleus to their death in cytoplasm and have the potential of being involved in many steps of RNA regulation. The knowledge of their structural features and functional roles will also shed more light on the postulated mechanisms of RNA pathogenesis in a growing list of neurological diseases caused by simple sequence repeat expansions. Here, we discuss several different lines of research to support the hypothesis that the mechanism of RNA pathogenesis may be a more common phenomenon triggered or modulated also by abundant long normal repeats. We propose structures of the repeat regions in transcripts of genes involved in Triplet Repeat Expansion Diseases. We have classified the polymorphic repeat alleles of these genes according to their ability to form
This line was derived from an AtT-20ins cell line in which the Rous sarcoma virus long terminal repeat was used for directing insulin cDNA expression.
In this study we demonstrated that Alu repetitive elements can function as inducers of A-to-I editing in adjacent sequences, affecting the expressed proteome. Alu repeats are primate specific and vary also in abundance within primates. Our observation therefore points to a human- or primate-specific phenomenon that cannot be explained by the sequence at the site of editing.. It has previously been speculated by Li and co-workers that non-Alu A/I editing sites are dependent on nearby edited Alu sequences in the human transcriptome [20]. Their theory was based on the fact the two classes of editing are often found within close proximity in the same transcripts. We were able to confirm their hypothesis, and show that editing in non-repetitive elements often depends on nearby repetitive Alu elements. Our previous analysis showed that induction of site-selective editing at the I/M site of Gabra-3 by a long intronic hairpin structure is independent of editing, and instead depends on the ...
Eukaryotic genomes contain a large proportion of repetitive DNA sequences, mostly transposable elements (TEs) and tandem repeats. These repetitive sequences often colonize specific chromosomal (Y or W chromosomes, B chromosomes) or subchromosomal (te
Looking for Repetitive DNA? Find out information about Repetitive DNA. see nucleic acid nucleic acid, any of a group of organic substances found in the chromosomes of living cells and viruses that play a central role in the... Explanation of Repetitive DNA
We isolated Saccharomyces cerevisiae yeast strains that are able to carry out the second fermentation of sparkling wine from spontaneously fermenting musts in El Penedès (Spain) by specifically designed selection protocols. All of them (26 strains) showed one of two very similar mitochondrial DNA (mtDNA) restriction patterns, whereas their karyotypes differed. These strains showed high rates of karyotype instability, which were dependent on both the medium and the strain, during vegetative growth. In all cases, the mtDNA restriction pattern was conserved in strains kept under the same conditions. Analysis of different repetitive sequences in their genomes suggested that ribosomal DNA repeats play an important role in the changes in size observed in chromosome XII, whereas SUC genes or Ty elements did not show amplification or transposition processes that could be related to rearrangements of the chromosomes showing these sequences. Karyotype changes also occurred in monosporidic diploid ...
1PGZ: Structure-based incorporation of 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine into the human telomeric repeat DNA as a probe for UP1 binding and destabilization of G-tetrad structures
To me its always been very confusing why you would break your genome. Its your blueprint, says Hochwagen. Obviously, it helps you make new variations and combinations of genes, but its incredibly dangerous and you really need to make sure that it happens the right way.. In repetitive DNA, this system of breaking and swapping is particularly hazardous, as there are many options that a section of repeat DNA could be swapped with. If the wrong repeat is chosen, a chromosome can gain or lose a large chunk of DNA. In humans, such mistakes have been linked to genetic neurological and developmental disorders, including autism spectrum disorders and schizophrenia.. By studying the highly repetitive DNA that makes up yeasts ribosomal DNA (rDNA), Gerben Vader and Hannah Blitzblau, first authors of the Nature paper and postdoctoral researchers in Hochwagens lab, have determined that yeasts rDNA is protected from inappropriate recombination by two mechanisms. It was previously shown that ...
This institute contributes to the education of students in Graduate School for Environmental and Life Science (Masters and Doctors Degree Course of Okayama University).
This patent search tool allows you not only to search the PCT database of about 2 million International Applications but also the worldwide patent collections. This search facility features: flexible search syntax; automatic word stemming and relevance ranking; as well as graphical results.
Mycobacteriophages--viruses of mycobacterial hosts--are genetically diverse but morphologically are all classified in the Caudovirales with double-stranded DNA and tails. We describe here a group of five closely related mycobacteriophages--Corndog, Catdawg, Dylan, Firecracker, and YungJamal--designated as Cluster O with long flexible tails but with unusual prolate capsids. Proteomic analysis of phage Corndog particles, Catdawg particles, and Corndog-infected cells confirms expression of half of the predicted gene products and indicates a non-canonical mechanism for translation of the Corndog tape measure protein. Bioinformatic analysis identifies 8-9 strongly predicted SigA promoters and all five Cluster O genomes contain more than 30 copies of a 17 bp repeat sequence with dyad symmetry located throughout the genomes. Comparison of the Cluster O phages provides insights into phage genome evolution including the processes of gene flux by horizontal genetic exchange ...
Scientists of the German Cancer Research Center have discovered an alternative mechanism for the extension of the telomere repeat sequence by DNA repair enzymes.
The hallmark of the STAR element is the directly repeated signature sequence T(G/A/T)TGTTG(G/T)GGCCC(C/A), which is present in as many as five copies at one locus. The single exception found was strain 12601, which does not contain a signature sequence and, therefore, has no STAR element in the uvrA-hprKintergenic region.. We defined a beginning (TGGG[A/C]GTGGGACAGAAATGAT) for the STAR element starting at nucleotide 35, which is present in 8 of the 10 sequences, and an end (T[G/A/T]TGTTGGGGCCCCGCC), which is an extended signature sequence and present in all of the sequences, finishing at nucleotide 474. These borders are based on sequence similarity between the two loci and similarity in the flanking sequence only among sequences from the same locus. Signature sequences A/B and C/D in star01 may be part of larger 75-bp imperfect direct repeats. Longer repeats are also found in star02, star03, star05, star07, star08, and star11.. The intergenic region that contains the largest STAR element ...
The extensiveness of cancer-associated genetic instability was first heralded by findings of mutations in repetitive sequences. Peinado et al. (35) used random oligonucleotides as arbitrary primers in PCR reactions and observed additional products of different sizes using DNA obtained from human colon tumors compared with those obtained using DNA from adjacent normal tissues. The tumor-specific PCR products with altered lengths encompassed segments with repetitive nucleotide sequences. These investigators sampled only a small fraction of the genome, and yet within their limited vista they observed large numbers of alterations in DNA sequence. Upon extrapolating these results to the whole genome, they concluded that some tumors contained as many 100,000 mutations. The tumor cells with the greatest numbers of changes in the lengths of repetitive sequences were subsequently shown to possess mutations in mismatch repair genes (36) . Altered repetitive sequences were mainly detected in segments ...
POT1 Antibody is a Rabbit Polyclonal antibody against POT1. Protection of telomeres 1(POT1)is a conserved protein that binds the G-rich stand of its own telomeric repeat sequence, with a role in protecting chromosome ends. Its housekeeping gene that is r
The presence of certain types of repetitive elements in a sequence may sometimes distort the results of GENSCAN. In particular, L1 elements are often predicted as genes. To avoid this potential problem, you may wish to pre-screen for repetitive elements with a program like RepeatMasker or censor which replace sequence segments matching any of a set of elements common to your organism (e.g., Alu, L1, etc.) by the same number of asterisks or `Ns. (To get instructions for the censor email server, send mail to [email protected] with the word help in the body of the message.) Note that GENSCAN does accept sequences containing Ns or asterisks and that long stretches of such symbols are interpreted as probable repetitive elements (i.e. non-coding DNA). For large-scale sequencing efforts, other repeat-screening methods are also available, e.g., masking repeats detected by BLASTN or TBLASTN using the XBLAST procedure (Claverie, J.-M. (1994) In Automated DNA Sequencing and Analysis Techniques, M. ...
The data shown in this track are a subset of the Simple Repeats track, selecting only those repeats of period 2 and 3, with 100% identity and no indels and with at least 15 copies of the repeat. The Simple Repeats track is created using the Tandem Repeats Finder. For more information about this program, see Benson (1999).. ...
ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.. About ASM , Contact Us , Press Room. ASM is a member of. ...
The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance and interactive visualization.. ...
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If you absolutely are convinced that the workouts are too easy, instead of increasing the intensity by going faster, do more repeats. The extra volume will make you stronger while keeping you from getting too fit too soon. Enjoy. Notes About the Workouts. Workouts with a range of numbers (ie, 2-3A) suggest the minimum number of miles or minutes for 800m runners to the maximum for 3,200m runners. They are not fixed, but rely on your judgment based on your current fitness and years of experience. This plan contains a variety of workouts that will require efforts ranging from stride speed to threshold pace. Workouts B, C, E and F are samples of aerobic speedwork. Workouts B and C can be run at stride pace - fast, but well short of a full sprint. The short repeat Interval workouts E and F can be run at the pace of your fastest 5K XC race during the fall. That pace will be fairly easy so shorten the recovery intervals if you find that length of the jogs is too long. At any time, your perceived ...
The entire chromosome consists of DNA. However, less than 3% of the DNA actually consists of genes. There are thought to be about 30,000 genes in humans. Less than 3% of human DNA codes for proteins. Most of the DNA in eukaryotic chromosomes consists of repetitive sequences that never get transcribed.. ...
AncestryDNA and Quest are collaborating to provide in-home DNA testing to users who wish to know about their family heritage and identify possible relatives.
Join Gini von Courter for an in-depth discussion in this video Demonstrating controls that repeat data , part of Word 2010: Forms
When I have trained my best, when this imperfect physical-mental-spiritual machine has reached its racing peak, there are still five ways in which I may improve my racing performance.
Mobile genetic elements, Molecular biology, Repetitive DNA sequences). ... Nucleic Acids Research. 8 (24): 6113-28. doi:10.1093/nar/8.24.6113. PMC 328076. PMID 6258162. Kapitonov VV, Tempel S, Jurka J ( ... Nucleic Acids Research. 42 (1): 396-416. doi:10.1093/nar/gkt898. PMC 3874205. PMID 24101588. Kazazian HH, Wong C, Youssoufian H ... Nucleic Acids Research. 42 (12): 7694-707. doi:10.1093/nar/gku503. PMC 4081101. PMID 24914052. ( ...
... a collective resource for the identification of repetitive sequences in plants". Nucleic Acids Res. England. 32 (Database issue ... The TIGR plant repeat database is a repository of repetitive sequences in plants. repetitive sequences TIGR plant transcript ... Repetitive DNA sequences, All stub articles, Biological database stubs). ...
"Simple sequences are ubiquitous repetitive components of eukaryotic genomes". Nucleic Acids Research. Oxford University Press ( ... Nucleic Acids Research. Oxford University Press (OUP). 17 (16): 6463-6471. doi:10.1093/nar/17.16.6463. ISSN 1362-4962. PMC ... Tribolium Genome Sequencing Consortium; et al. (23 March 2008). "The genome of the model beetle and pest Tribolium castaneum". ... His thesis dealt with the first generic description of simple sequences (now often called microsatellites). This work became ...
v t e (Genetics, Repetitive DNA sequences, All stub articles, Genetics stubs). ... Nucleic Acids Research. 46 (11): 5504-5524. doi:10.1093/nar/gky263. ISSN 0305-1048. PMC 6009586. PMID 29912433. ... "Demethylation of repetitive DNA sequences in neuroblastoma". Genes, Chromosomes and Cancer. 17 (4): 234-244. doi:10.1002/(SICI) ...
Triple-stranded DNA structures have been demonstrated in repetitive polypurine:polypyrimidine Microsatellite sequences and ... DNA supercoil Gene structure Non-helical models of DNA structure Nucleic acid design Nucleic acid double helix Nucleic acid ... Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very ... A nucleic acid sequence is the order of nucleotides within a DNA (GACT) or RNA (GACU) molecule that is determined by a series ...
FISH maps out single copy or repetitive DNA sequences through localization labeling of specific nucleic acids. The technique ... In Situ Hybridization maps out single copy or repetitive DNA sequences through localization labeling of specific nucleic acids ... Some high-throughput sequencing techniques that are used by the CGCI include: whole genome sequencing, transcriptome sequencing ... Introduced in the 1980s, FISH uses probes with complementary base sequences to locate the presence or absence of the specific ...
A transposable element (TE, transposon, or jumping gene) is a nucleic acid sequence in DNA that can change its position within ... "Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences". Tropical Plant Biol. 1: 85-96 ... A consensus sequence is a sequence that is created based on the repeats that comprise a TE family. A base pair in a consensus ... Sequence self-comparison programs use databases such as AB-BLAST to conduct an initial sequence alignment. As these programs ...
"Characterization of repetitive sequence families in mouse heart small polydisperse circular DNAs: age-related studies". Nucleic ... Nucleic Acids and Protein Synthesis. 272 (1): 130-136. doi:10.1016/0005-2787(72)90041-X. PMID 4625469. Wong FY, Wildman SG ( ... Nucleic Acids and Protein Synthesis. 259 (1): 5-12. doi:10.1016/0005-2787(72)90468-6. PMID 5011974. Agsteribbe E, Kroon AM, van ... Nucleic Acids and Protein Synthesis. 269 (2): 299-303. doi:10.1016/0005-2787(72)90439-X. PMID 4260513. Stahl U, Lemke PA, ...
sequence See nucleic acid sequence. sequence-tagged site (STS) Any DNA sequence that occurs exactly once within a particular ... repeat repetitive DNA A region or fragment of DNA consisting largely or entirely of repeated nucleotide sequences. replacement ... nucleic acid sequence The precise order of consecutively linked nucleotides in a nucleic acid molecule such as DNA or RNA. Long ... palindromic sequence A nucleic acid sequence of a double-stranded DNA or RNA molecule in which the unidirectional sequence (e.g ...
Nucleic Acids Research 35(Database issue): 71-75. (Repetitive DNA sequences, Genetics). ...
Nucleic Acids Res. England. 33 (Database issue): D498-500. doi:10.1093/nar/gki044. PMC 539998. PMID 15608246. Penzkofer, T; ... Repetitive DNA sequences, Mobile genetic elements, All stub articles, Biological database stubs). ... Nucleic Acids Research. 45 (D1): D68-D73. doi:10.1093/nar/gkw925. PMC 5210629. PMID 27924012. ...
... a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes". Nucleic Acids Res. England. ... Repetitive DNA sequences, All stub articles, Biological database stubs). ... PSSRdb (Polymorphic Simple Sequence Repeats database) is a database of polymorphic simple sequence repeats sequence repeats ...
... sequences are present within the RNase P RNA gene in heterocyst-forming cyanobacteria". Nucleic Acids Research. 25 (17): 3471-7 ... Vioque A (September 1997). "The RNase P RNA from cyanobacteria: short tandemly repeated repetitive (STRR) ... a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy". Nucleic Acids Research. 41 (Database ... This short sequence is defined as barcode sequence. Requirements for a specific part of the genome to serve as barcode should ...
Nucleic Acids Research. 18 (22): 6531-6535. doi:10.1093/nar/18.22.6531. PMC 332606. PMID 1979162. v t e (CS1: long volume value ... Repetitive DNA sequences, Statistical genetics, All stub articles, Genetics stubs). ... Nucleic Acids Research. 28 (1): 104-107. doi:10.1093/nar/28.1.104. PMC 102397. PMID 10592194. Doyle, J. J.; Doyle, J. L. (1987 ... A sequence related amplified polymorphism (SRAP) is a molecular technique, developed by G. Li and C. F. Quiros in 2001, for ...
Repetitive DNA sequences, All stub articles, Biological database stubs). ... Nucleic Acids Res. England. 35 (Database issue): D71-5. doi:10.1093/nar/gkl806. PMC 1899107. PMID 17202172. http://www.imperial ...
Repetitive DNA sequences, All stub articles, Biological database stubs). ... Nucleic Acids Res. England. 36 (Database issue): D53-6. doi:10.1093/nar/gkm811. PMC 2238862. PMID 17947328. http://veenuash. ...
KSHV has a genome which is approximately 165,000 nucleic acid bases in length. The viral genome consists of a ~145 kilobase- ... Each terminal repeat unit is 801 bp in length, has 85% G+C content and is oriented in a repetitive head-to-tail fashion. KSHV ... Starting from these fragments, this research team was then able to sequence the entire genome of the virus less than two years ... and is a large double-stranded DNA virus with a protein covering that packages its nucleic acids, called the capsid, which is ...
Repetitive DNA sequences, All stub articles, Biological database stubs). ... Nucleic Acids Res. 35 (Database issue): D80-7. doi:10.1093/nar/gkl1013. ISSN 0305-1048. PMC 1781109. PMID 17175540. https:// ...
... a microsatellite database of fully sequenced insect genomes". Nucleic Acids Res. England. 35 (Database issue): D36-9. doi: ... Repetitive DNA sequences, Genome databases, All stub articles, Biological database stubs). ... InSatDb is a database of microsatellites of sequenced insect genomes microsatellite Archak, Sunil; Meduri Eshwar; Kumar P ...
... integrated de novo protein sequence annotation". Nucleic Acids Res. 37 (Web server issue): W435-W440. doi:10.1093/nar/gkp254. ... a graph-based approach for the detection and identification of repetitive elements in low-complexity sequences". Bioinformatics ... Wootton JC, Federhen S (June 2003). "Statistics of local complexity in amino acid sequences and sequence databases". Computers ... Nucleic Acids Research. 48 (W1): W77-W84. doi:10.1093/nar/gkaa339. ISSN 0305-1048. PMC 7319588. PMID 32421769. Ntountoumi, ...
The motif's nucleic acid secondary structure consists of several small hairpins. Although the sizes of the stems and terminal ... suggesting that the hairpins are not repetitive. Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, ... loops of these hairpins are quite consistent, the nucleotide sequences in the hairpins are different, ... Nucleic Acids Res. 45 (18): 10811-10823. doi:10.1093/nar/gkx699. PMC 5737381. PMID 28977401. (Orphaned articles from December ...
Repetitive DNA sequences, Genetic genealogy, DNA profiling techniques, All stub articles, Biological database stubs). ... Nucleic Acids Res. ENGLAND. 29 (1): 320-2. doi:10.1093/nar/29.1.320. PMC 29767. PMID 11125125. ... marker List of biological databases Microsatellite instability Mobile element Satellite DNA Short interspersed repetitive ...
Repeated sequences (also known as repetitive elements, repeating units or repeats) are short or long patterns of nucleic acids ... Repetitive DNA is hard to sequence using next-generation sequencing techniques because sequence assembly from short reads ... other repetitive sequences can be harmful. Many repetitive DNA sequences have been linked to human diseases such as ... Today, the structural and regulatory roles of repetitive DNA sequences remain an active area of research. Many repeat sequences ...
... synthetic DNA mimics called peptide nucleic acid (PNA) oligonucleotides to quantify target sequences in chromosomal DNA using ... Q-FISH is most commonly used to study telomere length, which in vertebrates are repetitive hexameric sequences (TTAGGG) located ... By using conditions that only allow labeled (CCCTAA)3 PNA to hybridize to (TTAGGG)n target sequences, Q-FISH is able to ... The hypotonic solution is then removed by centrifugation and resuspended in a methanol/glacial acetic acid fixative. Place a ...
Short tails of repetitive nucleic acids are often added to the ends of RNA molecules in order to prevent degradation, ... By regulating the transcription in DNA sequences, the stability of RNA, and the capability of messenger RNA to be translated, ... Marguet E, Forterre P (1994). "DNA stability at temperatures typical for hyperthermophiles". Nucleic Acids Res. 22 (9): 1681- ... Nucleic Acids Research. 46 (20): 10535-45. doi:10.1093/nar/gky910. PMC 6237782. PMID 30307534. Bernstein H, Bernstein C, Michod ...
... to stabilize essential compounds like amino acids, nucleic acids and lipids to target age-related diseases. Cantor held ... In post-doctoral work with Thomas Jukes he studied repetitive sequences in polypeptides, but most of his independent research ... has concerned nucleic acids, from his early work with nuclear magnetic resonance (NMR) and repetitive sequences in ... Cantor's reviews include one on the physical chemistry of nucleic acids. Cantor co-authored Biophysical Chemistry with Paul ...
... repetitive sequences, nucleic acid MeSH G06.184.603.080.708.330 - interspersed repetitive sequences MeSH G06.184.603.080. ... amino acid MeSH G06.184.842.200.820 - structural homology, protein MeSH G06.184.842.550 - sequence homology, nucleic acid MeSH ... repetitive sequences, amino acid MeSH G06.184.603.060.720.030 - ankyrin repeat MeSH G06.184.603.080 - base sequence MeSH ... regulatory sequences, nucleic acid MeSH G06.184.603.080.689.330 - enhancer elements (genetics) MeSH G06.184.603.080.689.330.240 ...
Larsen N, Zwieb C (January 1991). "SRP-RNA sequence alignment and secondary structure". Nucleic Acids Research. 19 (2): 209-215 ... "Human 7SL RNA consists of a 140 nucleotide middle-repetitive sequence inserted in an alu sequence". Cell. 29 (1): 195-202. doi: ... "Model for signal sequence recognition from amino-acid sequence of 54K subunit of signal recognition particle". Nature. 340 ( ... Regalia M, Rosenblad MA, Samuelsson T (August 2002). "Prediction of signal recognition particle RNA genes". Nucleic Acids ...
The second hypothesis considered is that MAEB is a repetitive DNA sequence. Although the repetitive nature of MAEB stem-loops ... Nucleic Acids Res. 35 (14): 4809-4819. doi:10.1093/nar/gkm487. PMC 1950547. PMID 17621584. v t e (Articles lacking reliable ... Rather the repetitive nature of MAEB stem-loops probably has a functional role for the cell. The third hypothesis advanced is ... usually with 2-6 consecutive instances of MAEB stem-loops separated by a short and conserved linker sequence. As many as 12 ...
"A human immunoglobulin kappa orphon without sequence defects may be the product of a pericentric inversion". Nucleic Acids ... Guimond, A.; Moss, T. (1999). "A ribosomal orphon sequence from Xenopus laevis flanked by novel low copy number repetitive ... Nucleic Acids Research. 18 (8): 2101-7. doi:10.1093/nar/18.8.2101. PMC 330689. PMID 2159639. Eirín-López, J. M.; González-Tizón ... Childs, G.; Maxson, R.; Cohn, R. H.; Kedes, L. (1981). "Orphons: Dispersed genetic elements derived from tandem repetitive ...
Vassetzky NS, Kramerov DA (January 2013). "SINEBase: a database and tool for SINE analysis". Nucleic Acids Research. 41 ( ... CS1 Russian-language sources (ru), Molecular biology, Repetitive DNA sequences, Mobile genetic elements, Non-coding DNA, ... For example, the 5' of the Alu sine is derived from 7SL RNA, a sequence transcribed by RNA Polymerase III which codes for the ... These dog-specific SINEs may code for a splice acceptor site, altering the sequences that appear as exons or introns in each ...
... that uses fluorescent probes that bind to only particular parts of a nucleic acid sequence with a high degree of sequence ... Repetitive DNA sequences must be blocked by adding short fragments of DNA to the sample. The probe is then applied to the ... In biology, a probe is a single strand of DNA or RNA that is complementary to a nucleotide sequence of interest. RNA probes can ... The size of the human genome is so large, compared to the length that could be sequenced directly, that it was necessary to ...
Due to the amino acid sequence and the periodicity of the helices, the leucine side chains are arranged along one face of the α ... and the usefulness of antisense nucleic acids". Biochemical Pharmacology. 50 (4): 435-42. doi:10.1016/0006-2952(95)00068-B. ... characterized by a periodicity of 3.5 residues per turn and repetitive leucines appearing at every seventh position of the ... 2007). "Retinoic acid inhibits serum-stimulated activator protein-1 via suppression of c-fos and c-jun gene expressions during ...
... nucleic acid - nucleic acid regulatory sequence - nucleic acid repetitive sequence - nucleic acid sequence homology - nucleon ... amino acid - amino acid receptor - amino acid sequence - amino acid sequence homology - aminobutyric acid - ammonia - AMPA ... sequence (biology) - sequence homology - sequence motif - sequencing - serine - serotonin - serotonin receptor - serpin - ... It deals with the structure and function of cellular components such as proteins, carbohydrates, lipids, nucleic acids and ...
A telomere is a region of repetitive sequences at each end of the chromosomes of most eukaryotes. Telomeres protect the end of ... Nucleic Acids Res. 30 (20): 4470-80. doi:10.1093/nar/gkf575. PMC 137139. PMID 12384594. Hayflick L, Moorhead PS (1961). "The ... TERT proteins from many eukaryotes have been sequenced. By using TERC, TERT can add a six-nucleotide repeating sequence, 5'- ... Nucleic Acids Research. 31 (5): 1576-83. doi:10.1093/nar/gkg208. PMC 149817. PMID 12595567. Renault V, Thornell LE, Eriksson PO ...
Essentially this means that the highly repetitive sequences necessary for multiple sgRNA in a single plasmid are constrained by ... The amplification refractory mutation system (ARMS)". Nucleic Acids Res. 17 (7): 2503-2516. doi:10.1093/nar/17.7.2503. PMC ... Of this sequence, at least 15 base pairs should be homologous to the target sequence at both the 5' and 3' ends to provide ... In this system, sequences matching foreign bacteriophage or plasmid DNA are incorporated as "spacer" sequences into the ...
Nucleic Acids Res. 20: 5991-5997. Samadashwily GM, Dayn A, Mirkin SM (1993) Suicidal nucleotide sequences for DNA ... Sergei Mirkin (born September 29, 1956) is a Russian-American biologist who studies genome instability mediated by repetitive ... Nucleic Acids Res 46: 3487-3497. Kononenko AV, Ebersole T, Vasquez KM, Mirkin SM (2018) Mechanisms of genetic instability ... Dayn, A; Malkhosyan, S; Mirkin, S M (1992-11-25). "Transcriptionally driven cruciform formation in vivo". Nucleic Acids ...
A database of plant promoter sequences". Nucleic Acids Research. 31 (1): 114-7. doi:10.1093/nar/gkg041. PMC 165488. PMID ... Enhancer-like structures in middle repetitive DNA elements of eukaryotic genomes. Genetics (USSR/Russia), 22, 357-367 "AMEA-nın ... Shahmuradov IA, Solovyev VV (2003) PromH: promoters identification using orthologous genomic sequences. Nucl. Acids. Res., 31, ... Nucleic Acids Research. 33 (3): 1069-76. doi:10.1093/nar/gki247. PMC 549412. PMID 15722481. Shahmuradov, I. A.; Gammerman, A. J ...
He is known for his discovery of repetitive, functional DNA sequences in bacteria which he named CRISPR (Clustered Regularly ... Molecular Microbiology and Nucleic Acid Research, before finally being accepted by Journal of Molecular Evolution in February, ... Part of the sequence was reported previously by Yoshizumi Ishino in 1987. Mojica described the complete gene sequence repeats ... He continued research on these sequences throughout the 1990s, and in 2000, Mojica recognized that what had been reported as ...
Nucleic acids became the sole and universal means of encoding genetic information, requiring DNA repair mechanisms that in ... SOS boxes are 20-nucleotide long sequences near promoters with palindromic structure and a high degree of sequence conservation ... The telomeres are long regions of repetitive noncoding DNA that cap chromosomes and undergo partial degradation each time a ... Nucleic Acids Res. 29 (10): 2117-26. doi:10.1093/nar/29.10.2117. PMC 55450. PMID 11353081. Ming X, Matter B, Song M, Veliath E ...
These and other studies on repetitive DNA sequences enabled him to suggest how non-coding chromosomal DNA may have evolved. ... Nucleic Acids Research. 20 (7): 1679-1684. doi:10.1093/nar/20.7.1679. PMC 312256. PMID 1579459. Milner, N.; Mir, K. U.; ... had an unexpectedly simple repetitive structure based on a sequence of six nucleotides. In mouse satellite DNA he showed both ... Southern has done pioneering work on the organization of DNA sequences in chromosomes. Apart from studies on crab poly-AT ...
"DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats". Nucleic Acids Research. 43 ... Yang B, Sugio A, White FF (February 2005). "Avoidance of host recognition by alterations in the repetitive and C-terminal ... Bertonati C, Duchateau P, Juillerat A, Silva G, Valton J (24 July 2013). "WO2014018601A2 New modular base-specific nucleic acid ... Nucleic Acids Research. 42 (11): 7436-49. doi:10.1093/nar/gku329. PMC 4066763. PMID 24792163. Juillerat A, Bertonati C, Dubois ...
The human genome has many repetitive regions that can be found within gene sequences or in non-coding regions of the genome. ... Sarkar G, Kapelner S, Sommer SS (December 1990). "Formamide can dramatically improve the specificity of PCR". Nucleic Acids ... for isolation of an unknown sequence flanking a known sequence. Within the known sequence, TAIL-PCR uses a nested pair of ... The amplification refractory mutation system (ARMS)". Nucleic Acids Research. 17 (7): 2503-16. doi:10.1093/nar/17.7.2503. PMC ...
Jaiswal AK, Nebert DW, Gonzalez FJ (Aug 1986). "Human P3(450): cDNA and complete amino acid sequence". Nucleic Acids Research. ... Jaiswal AK, Nebert DW, McBride OW, Gonzalez FJ (1987). "Human P(3)450: cDNA and complete protein sequence, repetitive Alu ... see 20-Hydroxyeicosatetraenoic acid). The EDP (see Epoxydocosapentaenoic acid) and EEQ (see epoxyeicosatetraenoic acid) ... as products of the omega-3 fatty acids, docosahexaenoic acid and eicosapentaenoic acid, the EDP and EEQ metabolites contribute ...
Progress in Nucleic Acid Research and Molecular Biology. Vol. 63. pp. 109-38. doi:10.1016/S0079-6603(08)60721-7. ISBN 978-0-12- ... Zhang L, David G, Esko JD (November 1995). "Repetitive Ser-Gly sequences enhance heparan sulfate assembly in proteoglycans". ... induces adhesion of the same cell types by using integrin receptors recognizing the RGD amino acid sequence". Proceedings of ... Mali M, Jaakkola P, Arvilommi AM, Jalkanen M (April 1990). "Sequence of human syndecan indicates a novel gene family of ...
... and nucleic acids. Small molecule drugs can typically be taken by ingestion, rather than injection. Losmapimod, a selective ... Z indicates it is a repetitive sequence, and 4 is a serial number assigned based on the order of submission. White, J.A.; ... Nucleic Acids Research. 24 (1): 57-63. doi:10.1093/nar/24.1.57. PMC 145602. PMID 8594601. Impossible Things: Through the ... Bisulfite sequencing, if validated, would be valuable due to it being able to use lower quality DNA sources, such as those ...
He also explored the many theoretical possibilities by which short nucleic acid sequences might code for the 20 amino acids. ... Jukes, T. H.; Holmquist, R. (1972). "Evolution of transfer RNA molecules as a repetitive process". Biochemical and Biophysical ... Watson JD, Crick FH (1953). "Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid". Nature. 171 (4356 ... that would hydrogen bond to short sequences of a nucleic acid, and also link to one of the amino acids. ...
Hnedzko D, Cheruiyot SK, Rozners E (September 2014). "Using triple-helix-forming Peptide nucleic acids for sequence-selective ... can form tandem intramolecular triplexes of the H-DNA type and has a repetitive sequence motif (ACCCTCCCC)4. The mutated NSE ... Watson JD, Crick FH (April 1953). "Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid". Nature. 171 ... "High-affinity triplex targeting of double stranded DNA using chemically modified peptide nucleic acid oligomers". Nucleic Acids ...
... derived repetitive sequences. Some of the Mycobacterium leprae pseudogens expression levels will alter upon infection of ... which is an essential component of nucleic acid biosynthesis in M. leprae. Rifampin will interrupt binding of the β-subunit of ... The sequence was obtained by a combined approach, employing automated DNA sequence analysis of selected cosmids and whole- ... The first genome sequence of a strain of Mycobacterium leprae was completed in 2001, which revealed only half of the genome ...
DNA sequencing Duplex sequencing Exome Sequencing Single cell sequencing Horizontal correlation Medical genetics Nucleic acid ... in non-repetitive DNA regions) and their consumables cost of $5000 per 6 billion base pairs is competitive (for some ... Whole genome sequencing (WGS), also known as full genome sequencing, complete genome sequencing, or entire genome sequencing, ... Staden R (June 1979). "A strategy of DNA sequencing employing computer programs". Nucleic Acids Res. 6 (7): 2601-10. doi: ...
September 2009). "Efficient targeting of a SCID gene by an engineered single-chain homing endonuclease". Nucleic Acids Res. 37 ... Repetitive DNA sequences, Zinc proteins). ... Nucleic Acids Res. 34 (Web Server issue): W516-23. doi:10.1093/ ... August 2010). "TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain". Nucleic Acids ... Nucleic Acids Res. 33 (18): 5978-5990. doi:10.1093/nar/gki912. PMC 1270952. PMID 16251401. Lee HJ, Kim E, Kim JS (December 2009 ...
"Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid" (PDF). Nature. 171 (4356): 737-8. Bibcode: ... Telomeres are long stretches of repetitive sequences that cap the ends of the linear chromosomes and prevent degradation of ... The nucleotide sequence of a gene's DNA specifies the amino acid sequence of a protein through the genetic code. Sets of three ... Some mutations do not change the amino acid sequence because multiple codons encode the same amino acid (synonymous mutations ...
Epplen C, Epplen JT (January 1994). "Expression of (cac)n/(gtg)n simple repetitive sequences in mRNA of human lymphocytes". ... Nucleic Acids Research. 37 (8): 2449-60. doi:10.1093/nar/gkp101. PMC 2677868. PMID 19255092. Yates JA, Menon T, Thompson BA, ... The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Research. 7 (4): 273-81. ... Nagase T, Kikuno R, Nakayama M, Hirosawa M, Ohara O (August 2000). "Prediction of the coding sequences of unidentified human ...
Traver, S.; Assou, S.; Scalici, E.; Haouzi, D.; Al-Edani, T.; Belloc, S.; Hamamah, S. (2014). "Cell-free nucleic acids as non- ... When used for women of advanced maternal age and for patients with repetitive IVF failure, PGP is mainly carried out as a ... techniques are in development that can avail for up to full genome sequencing, from which genetic profiling can score the DNA ...
January 2015). "PomBase 2015: updates to the fission yeast database". Nucleic Acids Research. 43 (Database issue): D656-61. doi ... After the initial sequencing of the fission yeast's genome, other previous non-sequenced regions of the genes have been ... On the converse, S. pombe has large, repetitive centromeres (40-100 kb) more similar to mammalian centromeres, and degenerate ... January 2012). "PomBase: a comprehensive online resource for fission yeast". Nucleic Acids Research. 40 (Database issue): D695- ...
Kodama Y, Shumway M, Leinonen R (January 2012). "The Sequence Read Archive: explosive growth of sequencing data". Nucleic Acids ... and background noise is very low for 100 bp reads in non-repetitive regions. RNA-Seq may be used to identify genes within a ... Direct sequencing of RNA using nanopore sequencing represents a current state-of-the-art RNA-Seq technique. Nanopore sequencing ... "Sequence-specific error profile of Illumina sequencers". Nucleic Acids Research. 39 (13): e90. doi:10.1093/nar/gkr344. PMC ...
... synthesis.Shotgun sequencing applications of NGS generate full-length genome sequences by shearing the nucleic acid extracted ... and regions of the genome with long stretches of repetitive sequence can be difficult to reassemble. Whole genome sequencing ( ... and then using a de novo sequence assembler program the genome sequence is reconstituted from the sequence fragments (short ... The distance between sequences is computed by a genetic distance measure (a mathematical formula that maps two sequences to a ...
The distribution of the 2000 copies of the Y-specific repetitive family DYZ2 is controversial since previous reports have ... mapped these sequences to different sites of the Yqh region. In this work, we have performed non-radioactive in situ ... Repetitive Sequences, Nucleic Acid* * Y Chromosome* Substances * Heterochromatin * DNA * Azacitidine ... Distribution of DYZ2 repetitive sequences on the human Y chromosome Hum Genet. 1993 Jan;90(5):572-4. doi: 10.1007/BF00217462. ...
... by binding to response elements in target genes that generally consist of two direct repeat half-sites of consensus sequence ... Retinoic acid receptors (RARs) and retinoid X receptors (RXRs) regulate transcription ... Receptors, Retinoic Acid / metabolism* * Recombinant Fusion Proteins / metabolism * Repetitive Sequences, Nucleic Acid ... Retinoic acid receptors (RARs) and retinoid X receptors (RXRs) regulate transcription by binding to response elements in target ...
Categories: Repetitive Sequences, Nucleic Acid Image Types: Photo, Illustrations, Video, Color, Black&White, PublicDomain, ...
The complete mt genome of O. sinensis, with a size of 157,539 bp, is the fourth largest Ascomycota mt genome sequenced to date ... The complete mt genome of O. sinensis, with a size of 157,539 bp, is the fourth largest Ascomycota mt genome sequenced to date ... A total of 36 sequence sites in rps3 were under positive selection, with dN/dS ,1 in the 20 compared fungi. Among them, 16 ... A total of 36 sequence sites in rps3 were under positive selection, with dN/dS , 1 in the 20 compared fungi. Among them, 16 ...
Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids ... Confirmed E. coli isolates were genotyped by using Rep-PCR, which targets repetitive sequences dispersed throughout bacterial ... Improved repetitive-element PCR fingerprinting for resolving pathogenic and nonpathogenic phylogenetic groups within ... Comparison of ribotyping and repetitive extragenic palindromic-PCR for identification of fecal Escherichia coli from humans and ...
Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids ... BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. ... Multilocus Sequence Typing. To assign the strains to a sequence type (ST), 7 housekeeping genes were subjected to polymerase ... Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Complete genome sequence of a virulent isolate of ...
Nucleic Acid Repetitive Sequences 52% * Gene Expression Profiling 44% * Protein Isoforms 34% ... Nucleic Acids Research.. Research output: Contribution to journal › Article › peer-review ...
... nucleic acid hybridization; repetitive sequences; Solanum lycopersicum var. lycopersicum. Abstract:. ... The molecular and ... amino acid sequences; gene expression; DNA-binding proteins; nucleotide sequences; molecular weight; pollen. Abstract:. ... The ... amino acid sequences; nucleotide sequences; yeast artificial chromosomes; chromosome mapping; gene expression; roots; flowers; ... The deduced amino acid sequences of the proteins are homologous to those from monocotyledonous plants, yeast and mammals. The ...
Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids ... Improved repetitive-element PCR fingerprinting for resolving pathogenic and nonpathogenic phylogenetic groups within ... Comparison of ribotyping and repetitive extragenic palindromic-PCR for identification of fecal Escherichia coli from humans and ... relationships among Escherichia coli isolates from repetitive-element PCR by maximizing correspondence with multilocus sequence ...
Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids ... Nucleic Acids Research, 1990, 18:6503-6508.. *de Bruijn FJ. Use of repetitive (Repetitive Extragenic Palindromic and ... One of such groups of repetitive elements is the enterobacterial repetitive intergenic consensus (ERIC) sequences which are ... assays that utilize primers targeting highly-conserved repetitive sequence elements in the bacterial genome have shown ...
Sequencing coverage analysis reveals that C. gibelio is an amphitriploid (AAABBB) with two triploid sets of chromosomes; each ... Genome sequencing and haplotype assembly of two cyprinid teleosts, a sexual tetraploid and an unisexual hexaploid, reveal ... Here we sequence the genomes of the two species and assemble their haplotypes, which contain two subgenomes (A and B), to the ... Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, ...
Nucleic Acid Repetitive Sequences Medicine & Life Sciences 100% * Plasmodium falciparum Agriculture & Biology 98% ... Different types of repetitive sequences are present in this region, whose copy number is variable in different parasite lines. ... Different types of repetitive sequences are present in this region, whose copy number is variable in different parasite lines. ... Different types of repetitive sequences are present in this region, whose copy number is variable in different parasite lines. ...
Computational analysis of these sequences was carried out by searching for families of repetitive nucleic acid elements sharing ... These sequences have often been claimed to be transcribed and fulfill a functional role. A previous systematic analysis of a ... Sequences selected in this way have a substantially higher aptitude to fold into a stable secondary structure than the initial ... Removal of redundancies and regrouping of the selected sequences resulted in a final set of 92 families, defined by HMM ...
Nucleic Acid Repetitive Sequences 16% * Southern Blotting 15% * Multigene Family 14% * Cytomegalovirus 13% ...
Sun, W., Lorenz, A., Osman, F. & Whitby, M. C., Mar 2011, In: Nucleic Acids Research. 39, 5, p. 1718-1731 14 p.. Research ... DNA sequence differences are determinants of meiotic recombination outcome. Brown, S. D., Mpaulo, S. J., Asogwa, M. N., ... Lorenz, A., West, S. C. & Whitby, M. C., Apr 2010, In: Nucleic Acids Research. 38, 6, p. 1866-1873 8 p.. Research output: ... Lorenz, A., Mehats, A., Osman, F. & Whitby, M. C., 16 Dec 2014, In: Nucleic Acids Research. 42, 22, p. 13723-13735 13 p.. ...
... comparative methods for sequence analysis, phylogenetic analysis, predictive methods for protein and nucleic acid sequence ... The topics to be covered include DNA structure, structure of chromatin, unique and repetitive sequences in genomic DNA, DNA ... CHMI-3217EL - Biochemistry of Nucleic Acids ×. Biochemistry of Nucleic Acids. This course will cover advanced concepts in ... Topics include protein structure and function, nucleic acid chemistry, DNA and its replication, the genetic code and protein ...
Bi, X. & Liu, L-F., 1996, 於: Progress in Nucleic Acid Research and Molecular Biology. 54, p. 253-292 40 p.. 研究成果: 雜誌貢獻 › 文章 › 同 ... recA-independent DNA recombination between repetitive sequences: mechanisms and implications.. ... Preparation of microemulsions using polyglycerol fatty acid esters as surfactant for the delivery of protein drugs. Ho, H. O., ...
Repetitive Sequences, Nucleic Acid. B. He, Caudy, A., Parsons, L., Rosebrock, A., Pane, A., Raj, S., and Wieschaus, E., " ... Sequence Analysis, DNA. B. He, Caudy, A., Parsons, L., Rosebrock, A., Pane, A., Raj, S., and Wieschaus, E., "Mapping the ...
Peptide maps, antibody crossreactivity, peptide sequence analysis, and more recently nucleic acid sequences have defined ... In the recently reported partial sequence of the chicken non-muscle alpha-actinin, a repetitive sequence homologous to the ... 2017) Nucleic Acids Res doi: 10.1093/nar/gkx922. Letunic et al. (2020) Nucleic Acids Res doi: 10.1093/nar/gkaa937 ... Tissue-specific spectrins have the same 106-residue repetitive structure and show sequence homology to erythroid spectrin. ...
Nucleic Acid Repetitive Sequences 12% 54 被引用数 (Scopus) * Within-Subject Correlation Analysis to Detect Functional Areas ... Unsaturated fatty acids and a prenylated tryptophan derivative from a rare actinomycete of the genus Couchioplanes. Saito, S., ... Whole-genome sequencing and comparative genome analysis of bacillus subtilis strains isolated from non-salted fermented soybean ...
... or repetitive sequences (REPETITIVE SEQUENCES, NUCLEIC ACID). Variability in stability of the DNA sequence is seen at ... "DNA Sequence, Unstable" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical ... This graph shows the total number of publications written about "DNA Sequence, Unstable" by people in UAMS Profiles by year, ... Below are the most recent publications written about "DNA Sequence, Unstable" by people in Profiles over the past ten years. ...
Spt5-nucleic acid interactions are directly involved in promoter proximal pausing of RNA polymerase II ... Changes in Icelandic soil microbiomes from the forefield of retreating glaciers revealed by Illumina and MinION sequencing ... Engineering the repetitive 3D genome in human disease. Jennifer Phillips-Cremins, University of Pennsylvania ... Amino acid metabolism controls fatty acid structure in Staphylococcus aureus. Sarah G. Whaley, St. Jude Childrens Research ...
Repetitive Sequences, Nucleic Acid, Risk Factors ...
Repetitive Sequences, Nucleic Acid - Preferred Concept UI. M0018798. Scope note. Sequences of DNA or RNA that occur in multiple ... Repetitive Region. Repetitive Regions. Repetitive Sequence. Repetitive Sequences. Selfish DNA. Selfish DNAs. Selfish Gene. ... Repetitive Regions Repetitive Sequence Repetitive Sequences Selfish Genes - Related but not broader or narrower Concept UI. ... Nucleic Acid Repetitive Sequences. Repeat, Direct. Repeats, Direct. Repetitious Region, DNA. Repetitious Regions, DNA. ...
Repetitive Sequences, Nucleic Acid. en_US. dc.title. Comparative study of repetitive DNA in Phaseolus.. en_US. ... Comparative study of repetitive DNA in Phaseolus. Indian Journal of Biochemistry & Biophysics. 1981 Aug; 18(4): 254-8. en_US. ...
Nucleic Acid Repetitive Sequences Medicine & Life Sciences 14% * Telomere Medicine & Life Sciences 13% ... HPL-2 binding is enriched for repetitive sequences, and on chromosome arms is anticorrelated with centromeres. At the genic ... HPL-2 binding is enriched for repetitive sequences, and on chromosome arms is anticorrelated with centromeres. At the genic ... HPL-2 binding is enriched for repetitive sequences, and on chromosome arms is anticorrelated with centromeres. At the genic ...
Nucleic acid repetitive sequence (finding). Code System Preferred Concept Name. Nucleic acid repetitive sequence (finding). ...
Repetitive Sequences, Nucleic Acid [G02.111.570.080.708] Repetitive Sequences, Nucleic Acid * Tandem Repeat Sequences [G02.111. ... An increase number of repeats of a genomic, tandemly repeated DNA sequence from one generation to the next. ... An increase number of repeats of a genomic, tandemly repeated DNA sequence from one generation to the next.. ... Repetitive Sequences, Nucleic Acid [G05.360.080.708] Repetitive Sequences, Nucleic Acid * Tandem Repeat Sequences [G05.360. ...
Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573-80. ... The Dfam database of repetitive DNA families. Nucleic Acids Res. 2016;44:D81-9. ... The sequencing libraries were loaded on R9.4.1 flow cells and sequenced on a MinION device. Each strain was sequenced until the ... Next-generation sequencing (NGS). Illumina sequencing. For sequencing on an in-house Illumina NextSeq 550 instrument, libraries ...
  • Single molecule, real-time (SMRT) sequencing was used to characterize mitochondrial (mt) genome of Ophiocordyceps sinensis and to analyze the mt genome-wide pattern of epigenetic DNA modification. (
  • The complete mt genome of O. sinensis , with a size of 157,539 bp, is the fourth largest Ascomycota mt genome sequenced to date. (
  • Their predicted structure and genomic location suggest that, even in compact bacterial genomes, a relatively large fraction of the genome consists of non-protein-coding sequences, possibly functioning at the RNA level. (
  • INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements ( DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS ) dispersed throughout the genome. (
  • Noncoding and repetitive sequences make up a large part of the genome of high eukaryotes, but the elucidation of their roles and mechanisms of action are poorly understood. (
  • In this work, we found that interstitial telomeric repeats in the genome of Danio rerio colocalize with repetitive elements, including hAT and EnSpm, which are widely represented in vertebrate genomes. (
  • The presence of long repetitive sequences is demonstrated in the genome of the silkworm, Bombyx mori. (
  • Telomere-related sequences at interstitial sites in the human genome. (
  • Given their repetitive nature, reads associated with these elements are generally discarded or randomly distributed among elements of the same type in genome-wide analyses. (
  • A large portion of a typical mammalian genome is comprised of transposable elements (TEs) however they are typically ignored in high-throughput sequencing-based studies due to their repetitive nature [ 17 , 18 ]. (
  • Here we describe the development of a bacterial artificial chromosome (BAC) resource for lamprey germline DNA and use sequence information from this resource to probe the subchromosomal structure of the lamprey genome. (
  • Analyses of BAC-end sequences reveal that the lamprey genome possesses a high content of repetitive sequences (relative to human), which show strong clustering at the subchromosomal level. (
  • This pattern is not unexpected given that the sea lamprey genome is dispersed across a large number of chromosomes (n approximately 99) and suggests a low-copy DNA targeting strategy for efficiently generating informative paired-BAC-end linkages from highly repetitive genomes. (
  • Nanopore sequencing and assembly of a human genome with ultra-long reads. (
  • Assembly of highly repetitive genomes using short reads: the genome of discrete typing unit III Trypanosoma cruzi strain 231. (
  • Near-Complete Genome Sequences of Several New Norovirus Genogroup II Genotypes. (
  • Whole-Genome Sequence of Human Rhinovirus C47, Isolated from an Adult Respiratory Illness Outbreak in Butte County, California, 2017. (
  • This report presents results from a systematic screen for variation in repetitive DNA in the genome of C. difficile . (
  • This study also indicated a potential beneficial role of repetitive elements in the human genome. (
  • RAR/RXR heterodimers activate transcription in response to all-trans or 9-cis retinoic acid by binding to direct repeats spaced by five base pairs (DR5 elements), such that RAR occupies the downstream half-site. (
  • RXR homodimers activate transcription in response to 9-cis retinoic acid by binding to direct repeats spaced by one base pair (DR1 elements). (
  • Although less prominent than in eukaryotic genomes, sequence repeats are found in most bacterial species. (
  • According to their sizes, sequence repeats may be roughly classified into two main classes. (
  • Large repeats (0.8-2 kb) are mostly insertion sequences (IS), and encode proteins mediating their genomic mobility. (
  • Smaller repeats (50-300 bp) make up a much less defined and more variegate set of genomic sequences. (
  • Sequence alignments and phylogenetic trees of these domains allow us to interpret the evolutionary relationship between these proteins, concluding that spectrin evolved from alpha-actinin by an elongation process that included two duplications of a block of seven repeats. (
  • TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES . (
  • An increase number of repeats of a genomic, tandemly repeated DNA sequence from one generation to the next. (
  • The predicted protein sequence of DcG3 is 163 amino acids and includes two approximately 50 amino acid direct repeats which in turn include additional repetitive elements with an unusual distribution of charged amino acids. (
  • DNA sequencing indicates that this element contains six tandem repeats of 15 bp CpG-rich sequence in the 5′ proximal region. (
  • The polymerase chain reaction (PCR) is the way to go if you want to detect small amounts of nucleic acids like DNA. (
  • Here we sequence the genomes of the two species and assemble their haplotypes, which contain two subgenomes (A and B), to the chromosome level. (
  • In this study, we sequenced the genomes of the Carassius polyploid complex, including C. gibelio and its close relative C. auratus , and assembled their two high-quality subgenomes (A and B) that were created during the allotetraploidy event. (
  • Analysis of non-coding sequences in several bacterial genomes brought to the identification of families of repeated sequences, able to fold as secondary structures. (
  • A previous systematic analysis of a representative set of 40 bacterial genomes produced a large collection of sequences, potentially able to fold as stem-loop structures (SLS). (
  • The initial clustering procedure identified clusters of similar sequences in 29 genomes, corresponding to about 1% of the whole population. (
  • Systematic analysis of 40 bacterial genomes revealed a large number of repeated sequence families, including known and novel ones. (
  • Following these observations, and given the current availability of a large number of sequenced bacterial genomes, a systematic analysis of stem-loop containing repeated sequences appeared of interest. (
  • Using PCR and Capture-based chromosome conformation capture (3C) approaches, collectively called 4Tran, we take advantage of the repetitive nature of transposons to capture interactions from multiple copies of endogenous retrovirus (ERVs) in the human and mouse genomes. (
  • Variability in stability of the DNA sequence is seen at CHROMOSOME FRAGILE SITES. (
  • HPL-2 binding is enriched for repetitive sequences, and on chromosome arms is anticorrelated with centromeres. (
  • Repetitive DNA in and around translocation breakpoints of the Philadelphia chromosome. (
  • Low cost and massively parallel sequencing technologies have revolutionized the area of genomics research in last two decades. (
  • The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). (
  • TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted ( INVERTED REPEAT SEQUENCES ). (
  • Moreover, tandem repeat sequences enabled the reconstruction of the isolates' largely clonal population structure and evolutionary history. (
  • The deduced amino acid sequences of the proteins are homologous to those from monocotyledonous plants, yeast and mammals. (
  • The present status of erythrocyte spectrin structure: the 106-residue repetitive structure is a basic feature of an entire class of proteins. (
  • Other in silico methods that are routinely used in research laboratories include molecular modelling (a technique used to model or mimic the structure of molecules) and protein sequencing and its alignment (methods used to evaluate identities and similarities in the amino acid sequence of proteins) [25-28]. (
  • These interstitial loci share nucleotide sequence similarity outside the repetitive array, suggesting that they are related functionally or have evolved from a common progenitor locus. (
  • We describe two tandem repeat loci, designated 'TR6' and 'TR10', which display extensive sequence variation that may be useful for sequence-based strain typing. (
  • We conclude that sequence analysis of the two repetitive loci introduced here may be highly useful for routine typing of C. difficile . (
  • In addition, there is significant evidence for amino acid sequence homology with reverse transcriptase domains of other L1 families, especially F, Doc and lockey of Drosophila melanogaster. (
  • Analysis of these additional sequences shows considerable homology between human and mouse Epo genes as far as 4 kb (human) or 3 kb (mouse) upstream of the cap sites, as well as far more homology at the 3' end than was previously realized. (
  • 2002. Sequencing of the rat beta-catenin gene (Ctnnb1) and mutational analysis of liver tumors induced by 2-amino-3-methylimidazo[4,5-f]quinoline. . (
  • Gene sequences were amplified in a Perkin/Elmer thermal cycler (model 9600) (PerkinElmer, Waltham, MA, USA). (
  • Considerable insights into important cis regulatory elements in a gene can be gleaned from the identification of sequence homologies among different species. (
  • In addition, we have obtained new sequence information on the mouse Epo gene extending from within the 3' untranslated region (UTR) to 1,001 bp downstream of the polyadenylation site. (
  • 20 and 41) at day 0 or 60 during the clinical treatment trial in the Ancash region of Peru and found that these isolates had citrate synthase ( gltA ) gene sequences that diverged from that of B. bacilliformis reference strain KC583 ( 17 - 19 ). (
  • These regions often harbor palindromic, or repetitive sequences (REPETITIVE SEQUENCES, NUCLEIC ACID). (
  • A thesaurus of genetic variation for interrogation of repetitive genomic regions. (
  • We developed a method that links candidate variant positions within repetitive genomic regions into clusters. (
  • The technique relies on a resource, a thesaurus of genetic variation, that enumerates genomic regions with similar sequence. (
  • The resource is computationally intensive to generate, but once compiled can be applied efficiently to annotate and prioritize variants in repetitive regions. (
  • Spectrin, the major component of the membrane skeleton that provides elasticity to the cell, contains tandemly repeated sequences of 106 amino acid residues. (
  • Retinoic acid receptors (RARs) and retinoid X receptors (RXRs) regulate transcription by binding to response elements in target genes that generally consist of two direct repeat half-sites of consensus sequence AGGTCA (ref. 1). (
  • In contrast to 4Tran-PCR, Capture-4Tran can uniquely identify both ends of an interaction that involve retroviral repeat sequences, providing a powerful tool for uncovering the individual transposable element insertions that interact with and potentially regulate target genes. (
  • To extend and optimize the sequence comparison between human and mouse erythropoietin (Epo) genes, we have obtained new human sequence from 5,547 to 385 bp upstream of the cap site and extended the 3' flank by 489 bp. (
  • electron-accepting light cultures to mathematical Acne Vulgaris: Why sequences hope to ask minerals, ' Department of Physics, Drexel University, February 7, 2002. (
  • Progress in several laboratories over the past few years including substantial partial peptide and nucleotide sequence determination has greatly enhanced our knowledge of the structural properties of this large molecule (heterodimer = 465,000 daltons). (
  • The nucleotide sequence of these telomeric arrays is fundamental to telomere function as a site for protein and ribonucleoprotein binding and varies only slightly in a wide range of organisms. (
  • Although RXR/RAR heterodimers bind to DR1 elements with higher affinity than RXR homodimers, in most contexts they are unable to activate transcription in response to either all-trans or 9-cis retinoic acid. (
  • In addition, both species were found to have a high frequency of short interspersed (SINE) repetitive sequences that interrupt homologies in both the 5' flank and within the transcription unit. (
  • DNA Sequence, Unstable" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (
  • This strategy led to the definition of a large number of sequence families, sharing sequence similarity and, in most cases, a common predicted secondary structure. (
  • These, however, are sometimes difficult to trace because of low sequence similarity between duplicated segments. (
  • The complete sequence of a carrot genomic region, DcG3, encoding a Dc3-like mRNA, was determined. (
  • In the recently reported partial sequence of the chicken non-muscle alpha-actinin, a repetitive sequence homologous to the internal repeat in spectrin occurs several times. (
  • Pneumococcal isolates from sickle cell disease patients from Tennessee were subjected to multilocus sequence typing to characterize antimicrobial drug-resistant strains. (
  • Multilocus sequencing typing and microbiological analyses indicated these 3 isolates are members of a novel Bartonella species, subsequently name B. ancashensis ( 17 ). (
  • Analysis of laboratory lines and field isolates of P. falciparum indicated that polymorphism upstream of pfg27/25 is mainly due to the structure of a repetitive DNA region located at about half a kilobase from the pfg27/25 coding sequence. (
  • A next-generation sequencing and bioinformatics protocol for Malaria drug Resistance marker Surveillance (MaRS). (
  • Detecting genetic variation is one of the main applications of high-throughput sequencing, but is still challenging wherever aligning short reads poses ambiguities. (
  • In addition a GC-rich sequence element contained in this region, which is proposed to be the startpoint of pfg27/25 mRNA, presents either a direct or a reverse orientation in different parasite lines. (
  • The US Neisseria meningitidis urethritis clade (US_NmUC) harbors gonococcal deoxyribonucleic acid alleles and causes gonorrhea-like urogenital tract disease. (
  • We present evidence that arrays of this human telomeric sequence, TTAGGG, are present not only at the ends of human chromosomes but also at numerous interstitial sites. (
  • Inhalation Toxicology Downloaded from by CDC Information Center on 07/06/12 alternative to methyl bromide as a fumigant, there is potential here as a sequence of key events and processes, starting for human exposures to MeI. (
  • High genetic plasticity in multidrug resistant ST3-IncHI2 plasmids revealed by sequence comparison and phylogenetic analysis. (
  • Tandem repeat sequence typing resolves phylogenetic diversity to a level equivalent to PCR ribotypes. (
  • PCR analysis on 64 field isolates of P. falciparum indicated that orf P and orf Gap sequences are present in all tested samples of naturally propagating parasites. (
  • Computational analysis of these sequences was carried out by searching for families of repetitive nucleic acid elements sharing a common secondary structure. (
  • Removal of redundancies and regrouping of the selected sequences resulted in a final set of 92 families, defined by HMM analysis. (
  • Simple repetitive DNA sequences from primates: compilation and analysis. (
  • Sequencing analysis revealed the occurrence of six haplotypes for B. camerunensis and three haplotypes for B. pfeifferi . (
  • Conduct routine DNA characterization and quality control testing including gel electrophoresis and sample preparation for sequencing analysis. (
  • Proficiency in nucleic acid purification and quantitative analysis techniques such as gel electrophoresis, bioanalyzer, endotoxin assessment. (
  • the results suggest a non-uniform distribution of these sequences, which are preferentially located at the proximal and distal parts of Yqh, including the C+/Q- heterochromatin at the boundary with the euchromatic region. (
  • Some of them contain palindromic sequences, demonstrated or proposed to be structured as stem-loops able to function as regulatory elements at DNA or RNA level. (
  • CENSOR--a program for identification and elimination of repetitive elements from DNA sequences. (
  • RNA-dependent structures containing this sequence were identified in D. rerio fibroblast nuclei, which indicates the functional importance of genomic repetitive elements or their transcripts. (
  • Members of this BMC1 family reveal several features typical of the L1 (long interspersed sequence one) family of mammals, except for species specific elements. (
  • The ends (telomeres) of eukaryotic chromosomes are protected from degradation and from loss during DNA replication by buffers of simple tandem repetitive sequence. (
  • 2010. Elevated hepatic fatty acid elongase-5 activity corrects dietary fat-induced hyperglycemia in obese C57BL/6J mice. . (
  • For each bacterial species, sequences obtained from this study and predicted to fold with a free energy lower than -5 Kcal/mol were selected. (
  • In order to avoid obvious structured repeated sequences, they were filtered to eliminate those falling within either mature RNA species (tRNAs, rRNAs) or known ISs. (
  • Free left arms as precursor molecules in the evolution of Alu sequences. (
  • The technique uses gold nanoparticles covered with DNA sequences complementary to the ones they want to detect. (
  • Of the 14 cephalosporin-resistant strains, 9 were sequence types previously described as highly cephalosporin resistant, while resistance was found for the first time in 3 clones: Maryland 6B , ST660, and a novel clone, ST1753. (
  • DNA sequences may be stored in databases accessible over the internet, obviating the need for the exchange of reference strains. (
  • The distribution of the 2000 copies of the Y-specific repetitive family DYZ2 is controversial since previous reports have mapped these sequences to different sites of the Yqh region. (
  • Sequences of DNA or RNA that occur in multiple copies. (
  • Here we extend this study to detect all families of SLS containing sequences in the same bacterial set. (